openai-cookbook/examples/data/scifact_corpus.jsonl

{"doc_id": 4983, "title": "Microstructural development of human newborn cerebral white matter assessed in vivo by diffusion tensor magnetic resonance imaging.", "abstract": ["Alterations of the architecture of cerebral white matter in the developing human brain can affect cortical development and result in functional disabilities.", "A line scan diffusion-weighted magnetic resonance imaging (MRI) sequence with diffusion tensor analysis was applied to measure the apparent diffusion coefficient, to calculate relative anisotropy, and to delineate three-dimensional fiber architecture in cerebral white matter in preterm (n = 17) and full-term infants (n = 7).", "To assess effects of prematurity on cerebral white matter development, early gestation preterm infants (n = 10) were studied a second time at term.", "In the central white matter the mean apparent diffusion coefficient at 28 wk was high, 1.8 microm2/ms, and decreased toward term to 1.2 microm2/ms.", "In the posterior limb of the internal capsule, the mean apparent diffusion coefficients at both times were similar (1.2 versus 1.1 microm2/ms).", "Relative anisotropy was higher the closer birth was to term with greater absolute values in the internal capsule than in the central white matter.", "Preterm infants at term showed higher mean diffusion coefficients in the central white matter (1.4 +/-", "0.24 versus 1.15 +/-", "0.09 microm2/ms, p = 0.016) and lower relative anisotropy in both areas compared with full-term infants (white matter, 10.9 +/- 0.6 versus 22.9 +/-", "3.0%, p = 0.001; internal capsule, 24.0 +/-", "4.44 versus 33.1 +/-", "0.6% p = 0.006).", "Nonmyelinated fibers in the corpus callosum were visible by diffusion tensor MRI as early as 28 wk; full-term and preterm infants at term showed marked differences in white matter fiber organization.", "The data indicate that quantitative assessment of water diffusion by diffusion tensor MRI provides insight into microstructural development in cerebral white matter in living infants."], "structured": false}
{"doc_id": 5836, "title": "Induction of myelodysplasia by myeloid-derived suppressor cells.", "abstract": ["Myelodysplastic syndromes (MDS) are age-dependent stem cell malignancies that share biological features of activated adaptive immune response and ineffective hematopoiesis.", "Here we report that myeloid-derived suppressor cells (MDSC), which are classically linked to immunosuppression, inflammation, and cancer, were markedly expanded in the bone marrow of MDS patients and played a pathogenetic role in the development of ineffective hematopoiesis.", "These clonally distinct MDSC overproduce hematopoietic suppressive cytokines and function as potent apoptotic effectors targeting autologous hematopoietic progenitors.", "Using multiple transfected cell models, we found that MDSC expansion is driven by the interaction of the proinflammatory molecule S100A9 with CD33.", "These 2 proteins formed a functional ligand/receptor pair that recruited components to CD33\u2019s immunoreceptor tyrosine-based inhibition motif (ITIM), inducing secretion of the suppressive cytokines IL-10 and TGF-\u03b2 by immature myeloid cells.", "S100A9 transgenic mice displayed bone marrow accumulation of MDSC accompanied by development of progressive multilineage cytopenias and cytological dysplasia.", "Importantly, early forced maturation of MDSC by either all-trans-retinoic acid treatment or active immunoreceptor tyrosine-based activation motif\u2013bearing (ITAM-bearing) adapter protein (DAP12) interruption of CD33 signaling rescued the hematologic phenotype.", "These findings indicate that primary bone marrow expansion of MDSC driven by the S100A9/CD33 pathway perturbs hematopoiesis and contributes to the development of MDS."], "structured": false}
{"doc_id": 7912, "title": "BC1 RNA, the transcript from a master gene for ID element amplification, is able to prime its own reverse transcription.", "abstract": ["ID elements are short interspersed elements (SINEs) found in high copy number in many rodent genomes.", "BC1 RNA, an ID-related transcript, is derived from the single copy BC1 RNA gene.", "The BC1 RNA gene has been shown to be a master gene for ID element amplification in rodent genomes.", "ID elements are dispersed through a process termed retroposition.", "The retroposition process involves a number of potential regulatory steps.", "These regulatory steps may include transcription in the appropriate tissue, transcript stability, priming of the RNA transcript for reverse transcription and integration.", "This study focuses on priming of the RNA transcript for reverse transcription.", "BC1 RNA gene transcripts are shown to be able to prime their own reverse transcription in an efficient intramolecular and site-specific fashion.", "This self-priming ability is a consequence of the secondary structure of the 3'-unique region.", "The observation that a gene actively amplified throughout rodent evolution makes a RNA capable of efficient self-primed reverse transcription strongly suggests that self-priming is at least one feature establishing the BC1 RNA gene as a master gene for amplification of ID elements."], "structured": false}
{"doc_id": 18670, "title": "The DNA Methylome of Human Peripheral Blood Mononuclear Cells", "abstract": ["DNA methylation plays an important role in biological processes in human health and disease.", "Recent technological advances allow unbiased whole-genome DNA methylation (methylome) analysis to be carried out on human cells.", "Using whole-genome bisulfite sequencing at 24.7-fold coverage (12.3-fold per strand), we report a comprehensive (92.62%) methylome and analysis of the unique sequences in human peripheral blood mononuclear cells (PBMC) from the same Asian individual whose genome was deciphered in the YH project.", "PBMC constitute an important source for clinical blood tests world-wide.", "We found that 68.4% of CpG sites and <0.2% of non-CpG sites were methylated, demonstrating that non-CpG cytosine methylation is minor in human PBMC.", "Analysis of the PBMC methylome revealed a rich epigenomic landscape for 20 distinct genomic features, including regulatory, protein-coding, non-coding, RNA-coding, and repeat sequences.", "Integration of our methylome data with the YH genome sequence enabled a first comprehensive assessment of allele-specific methylation (ASM) between the two haploid methylomes of any individual and allowed the identification of 599 haploid differentially methylated regions (hDMRs) covering 287 genes.", "Of these, 76 genes had hDMRs within 2 kb of their transcriptional start sites of which >80% displayed allele-specific expression (ASE).", "These data demonstrate that ASM is a recurrent phenomenon and is highly correlated with ASE in human PBMCs.", "Together with recently reported similar studies, our study provides a comprehensive resource for future epigenomic research and confirms new sequencing technology as a paradigm for large-scale epigenomics studies."], "structured": false}
{"doc_id": 19238, "title": "The human myelin basic protein gene is included within a 179-kilobase transcription unit: expression in the immune and central nervous systems.", "abstract": ["Two human Golli (for gene expressed in the oligodendrocyte lineage)-MBP (for myelin basic protein) cDNAs have been isolated from a human oligodendroglioma cell line.", "Analysis of these cDNAs has enabled us to determine the entire structure of the human Golli-MBP gene.", "The Golli-MBP gene, which encompasses the MBP transcription unit, is approximately 179 kb in length and consists of 10 exons, seven of which constitute the MBP gene.", "The human Golli-MBP gene contains two transcription start sites, each of which gives rise to a family of alternatively spliced transcripts.", "At least two Golli-MBP transcripts, containing the first three exons of the gene and one or more MBP exons, are produced from the first transcription start site.", "The second family of transcripts contains only MBP exons and produces the well-known MBPs.", "In humans, RNA blot analysis revealed that Golli-MBP transcripts were expressed in fetal thymus, spleen, and human B-cell and macrophage cell lines, as well as in fetal spinal cord.", "These findings clearly link the expression of exons encoding the autoimmunogen/encephalitogen MBP in the central nervous system to cells and tissues of the immune system through normal expression of the Golli-MBP gene.", "They also establish that this genetic locus, which includes the MBP gene, is conserved among species, providing further evidence that the MBP transcription unit is an integral part of the Golli transcription unit and suggest that this structural arrangement is important for the genetic function and/or regulation of these genes."], "structured": false}
{"doc_id": 33370, "title": "Targeting A20 Decreases Glioma Stem Cell Survival and Tumor Growth", "abstract": ["Glioblastomas are deadly cancers that display a functional cellular hierarchy maintained by self-renewing glioblastoma stem cells (GSCs).", "GSCs are regulated by molecular pathways distinct from the bulk tumor that may be useful therapeutic targets.", "We determined that A20 (TNFAIP3), a regulator of cell survival and the NF-kappaB pathway, is overexpressed in GSCs relative to non-stem glioblastoma cells at both the mRNA and protein levels.", "To determine the functional significance of A20 in GSCs, we targeted A20 expression with lentiviral-mediated delivery of short hairpin RNA (shRNA).", "Inhibiting A20 expression decreased GSC growth and survival through mechanisms associated with decreased cell-cycle progression and decreased phosphorylation of p65/RelA. Elevated levels of A20 in GSCs contributed to apoptotic resistance: GSCs were less susceptible to TNFalpha-induced cell death than matched non-stem glioma cells, but A20 knockdown sensitized GSCs to TNFalpha-mediated apoptosis.", "The decreased survival of GSCs upon A20 knockdown contributed to the reduced ability of these cells to self-renew in primary and secondary neurosphere formation assays.", "The tumorigenic potential of GSCs was decreased with A20 targeting, resulting in increased survival of mice bearing human glioma xenografts.", "In silico analysis of a glioma patient genomic database indicates that A20 overexpression and amplification is inversely correlated with survival.", "Together these data indicate that A20 contributes to glioma maintenance through effects on the glioma stem cell subpopulation.", "Although inactivating mutations in A20 in lymphoma suggest A20 can act as a tumor suppressor, similar point mutations have not been identified through glioma genomic sequencing: in fact, our data suggest A20 may function as a tumor enhancer in glioma through promotion of GSC survival.", "A20 anticancer therapies should therefore be viewed with caution as effects will likely differ depending on the tumor type."], "structured": false}
{"doc_id": 36474, "title": "Efficient targeting of expressed and silent genes in human ESCs and iPSCs using zinc-finger nucleases", "abstract": ["Realizing the full potential of human embryonic stem cells (hESCs) and induced pluripotent stem cells (hiPSCs) requires efficient methods for genetic modification.", "However, techniques to generate cell type\u2013specific lineage reporters, as well as reliable tools to disrupt, repair or overexpress genes by gene targeting, are inefficient at best and thus are not routinely used.", "Here we report the highly efficient targeting of three genes in human pluripotent cells using zinc-finger nuclease (ZFN)\u2013mediated genome editing.", "First, using ZFNs specific for the OCT4 (POU5F1) locus, we generated OCT4-eGFP reporter cells to monitor the pluripotent state of hESCs.", "Second, we inserted a transgene into the AAVS1 locus to generate a robust drug-inducible overexpression system in hESCs.", "Finally, we targeted the PITX3 gene, demonstrating that ZFNs can be used to generate reporter cells by targeting non-expressed genes in hESCs and hiPSCs."], "structured": false}
{"doc_id": 54440, "title": "Empirical Bayesian models for analysing molecular serotyping microarrays", "abstract": ["BACKGROUND Microarrays offer great potential as a platform for molecular diagnostics, testing clinical samples for the presence of numerous biomarkers in highly multiplexed assays.", "In this study applied to infectious diseases, data from a microarray designed for molecular serotyping of Streptococcus pneumoniae was used, identifying the presence of any one of 91 known pneumococcal serotypes from DNA extracts.", "This microarray incorporated oligonucleotide probes for all known capsular polysaccharide synthesis genes and required a statistical analysis of the microarray intensity data to determine which serotype, or combination of serotypes, were present within a sample based on the combination of genes detected.   \n", "RESULTS We propose an empirical Bayesian model for calculating the probabilities of combinations of serotypes from the microarray data.", "The model takes into consideration the dependencies between serotypes, induced by genes they have in common, and by homologous genes which, although not identical, are similar to each other in sequence.", "For serotypes which are very similar in capsular gene composition, extra probes are included on the microarray, providing additional information which is integrated into the Bayesian model.", "For each serotype combination with high probability, a second model, a Bayesian random effects model is applied to determine the relative abundance of each serotype.   \n", "CONCLUSIONS To assess the accuracy of the proposed analysis we applied our methods to experimental data from samples containing individual serotypes and samples containing combinations of serotypes with known levels of abundance.", "All but two of the known serotypes of S. pneumoniae that were tested as individual samples could be uniquely determined by the Bayesian model.", "The model also enabled the presence of combinations of serotypes within samples to be determined.", "Serotypes with very low abundance within a combination of serotypes can be detected (down to 2% abundance in this study).", "As well as detecting the presence of serotype combinations, an approximate measure of the percentage abundance of the serotypes within the combination can be obtained."], "structured": true}
{"doc_id": 70115, "title": "Bayesian measures of model complexity and fit", "abstract": ["Summary.", "We consider the problem of comparing complex hierarchical models in which the number of parameters is not clearly defined.", "Using an information theoretic argument we derive a measure pD for the effective number of parameters in a model as the difference between the posterior mean of the deviance and the deviance at the posterior means of the parameters of interest.", "In general pD approximately corresponds to the trace of the product of Fisher's information and the posterior covariance, which in normal models is the trace of the \u2018hat\u2019 matrix projecting observations onto fitted values.", "Its properties in exponential families are explored.", "The posterior mean deviance is suggested as a Bayesian measure of fit or adequacy, and the contributions of individual observations to the fit and complexity can give rise to a diagnostic plot of deviance residuals against leverages.", "Adding pD to the posterior mean deviance gives a deviance information criterion for comparing models, which is related to other information criteria and has an approximate decision theoretic justification.", "The procedure is illustrated in some examples, and comparisons are drawn with alternative Bayesian and classical proposals.", "Throughout it is emphasized that the quantities required are trivial to compute in a Markov chain Monte Carlo analysis."], "structured": false}
{"doc_id": 70490, "title": "Simplifying likelihood ratios", "abstract": ["Likelihood ratios are one of the best measures of diagnostic accuracy, although they are seldom used, because interpreting them requires a calculator to convert back and forth between \u201cprobability\u201d and \u201codds\u201d of disease.", "This article describes a simpler method of interpreting likelihood ratios, one that avoids calculators, nomograms, and conversions to \u201codds\u201d of disease.", "Several examples illustrate how the clinician can use this method to refine diagnostic decisions at the bedside."], "structured": false}
{"doc_id": 72159, "title": "induction of early IFN-inducible genes in the absence of type", "abstract": ["On recognition of influenza virus (Flu) by TLR7, plasmacytoid dendritic cells (pDCs) produce type I IFN in significant amounts.", "Synthetic TLR7 ligands induce the maturation of pDCs, as evidenced by the expression of costimulatory molecules and the production of proinflammatory cytokines; however, they induce only low-level production of IFN-alpha.", "To dissect the TLR7 signaling in pDCs and how these different profiles are induced, we studied the effects of 2 TLR7 ligands (Flu and CL097) on the activation of blood-isolated pDCs and the human GEN2.2 pDC cell line.", "Type I IFN production by pDCs correlates with differential interferon regulatory factor 7 (IRF7) translocation into the nucleus induced by the 2 TLR7 ligands.", "Surprisingly, with both activators we nevertheless observed the rapid expression of the IFN-inducible genes mxa, cxcl10, and trail within 4 hours of stimulation.", "This expression, controlled by STAT1 phosphorylation, was independent of type I IFN.", "STAT1 activation was found to be strictly dependent on the PI3K-p38MAPK pathway, showing a new signaling pathway leading to rapid expression of IFN-inducible genes after TLR7 triggering.", "Thus, pDCs, through this unusual TLR7 signaling, have the capacity to promptly respond to viral infection during the early phases of the innate immune response."], "structured": false}
{"doc_id": 79447, "title": "Arteriolar function in visceral adipose tissue is impaired in human obesity.", "abstract": ["OBJECTIVE The purpose of this study was to characterize the relationship between adipose tissue phenotype and depot-specific microvascular function in fat.   \n", "METHODS AND RESULTS In 30 obese subjects (age 42\u00b111 years, body mass index 46\u00b111 kg/m(2)) undergoing bariatric surgery, we intraoperatively collected visceral and subcutaneous adipose tissue and characterized depot-specific adipose phenotypes.", "We assessed vasomotor function of the adipose microvasculature using videomicroscopy of small arterioles (75-250 \u03bcm) isolated from different fat compartments.", "Endothelium-dependent, acetylcholine-mediated vasodilation was severely impaired in visceral arterioles, compared to the subcutaneous depot (P<0.001 by ANOVA).", "Nonendothelium dependent responses to papaverine and nitroprusside were similar.", "Endothelial nitric oxide synthase inhibition with N(\u03c9)-nitro-l-arginine methyl ester reduced subcutaneous vasodilation but had no effect on severely blunted visceral arteriolar responses.", "Visceral fat exhibited greater expression of proinflammatory, oxidative stress-related, hypoxia-induced, and proangiogenic genes; increased activated macrophage populations; and had a higher capacity for cytokine production ex vivo.   \n", "CONCLUSIONS Our findings provide clinical evidence that the visceral microenvironment may be intrinsically toxic to arterial health providing a potential mechanism by which visceral adiposity burden is linked to atherosclerotic vascular disease.", "Our findings also support the evolving concept that both adipose tissue quality and quantity may play significant roles in shaping cardiovascular phenotypes in human obesity."], "structured": true}
{"doc_id": 87758, "title": "Common Carotid Intima Media Thickness and Ankle-Brachial Pressure Index Correlate with Local but Not Global Atheroma Burden: A Cross Sectional Study Using Whole Body Magnetic Resonance Angiography", "abstract": ["BACKGROUND Common carotid intima media thickness (CIMT) and ankle brachial pressure index (ABPI) are used as surrogate marker of atherosclerosis, and have been shown to correlate with arterial stiffness, however their correlation with global atherosclerotic burden has not been previously assessed.", "We compare CIMT and ABPI with atheroma burden as measured by whole body magnetic resonance angiography (WB-MRA).   \n", "METHODS 50 patients with symptomatic peripheral arterial disease were recruited.", "CIMT was measured using ultrasound while rest and exercise ABPI were performed.", "WB-MRA was performed in a 1.5T MRI scanner using 4 volume acquisitions with a divided dose of intravenous gadolinium gadoterate meglumine (Dotarem, Guerbet, FR).", "The WB-MRA data was divided into 31 anatomical arterial segments with each scored according to degree of luminal narrowing: 0 = normal, 1 = <50%, 2 = 50-70%, 3 = 70-99%, 4 = vessel occlusion.", "The segment scores were summed and from this a standardized atheroma score was calculated.   \n", "RESULTS The atherosclerotic burden was high with a standardised atheroma score of 39.5\u00b111.", "Common CIMT showed a positive correlation with the whole body atheroma score (\u03b2 0.32, p = 0.045), however this was due to its strong correlation with the neck and thoracic segments (\u03b2 0.42 p = 0.01) with no correlation with the rest of the body.", "ABPI correlated with the whole body atheroma score (\u03b2 -0.39, p = 0.012), which was due to a strong correlation with the ilio-femoral vessels with no correlation with the thoracic or neck vessels.", "On multiple linear regression, no correlation between CIMT and global atheroma burden was present (\u03b2 0.13 p = 0.45), while the correlation between ABPI and atheroma burden persisted (\u03b2 -0.45 p = 0.005).   \n", "CONCLUSION ABPI but not CIMT correlates with global atheroma burden as measured by whole body contrast enhanced magnetic resonance angiography in a population with symptomatic peripheral arterial disease.", "However this is primarily due to a strong correlation with ilio-femoral atheroma burden."], "structured": true}
{"doc_id": 92308, "title": "Loss of immune escape mutations during persistent HCV infection in pregnancy enhances replication of vertically transmitted viruses", "abstract": ["Globally, about 1% of pregnant women are persistently infected with the hepatitis C virus (HCV).", "Mother-to-child transmission of HCV occurs in 3-5% of pregnancies and accounts for most new childhood infections.", "HCV-specific CD8(+) cytotoxic T lymphocytes (CTLs) are vital in the clearance of acute HCV infections, but in the 60-80% of infections that persist, these cells become functionally exhausted or select for mutant viruses that escape T cell recognition.", "Increased HCV replication during pregnancy suggests that maternofetal immune tolerance mechanisms may further impair HCV-specific CTLs, limiting their selective pressure on persistent viruses.", "To assess this possibility, we characterized circulating viral quasispecies during and after consecutive pregnancies in two women.", "This revealed a loss of some escape mutations in HLA class I epitopes during pregnancy that was associated with emergence of more fit viruses.", "CTL selective pressure was reimposed after childbirth, at which point escape mutations in these epitopes again predominated in the quasispecies and viral load dropped sharply.", "Importantly, the viruses transmitted perinatally were those with enhanced fitness due to reversion of escape mutations.", "Our findings indicate that the immunoregulatory changes of pregnancy reduce CTL selective pressure on HCV class I epitopes, thereby facilitating vertical transmission of viruses with optimized replicative fitness."], "structured": false}
{"doc_id": 92499, "title": "The journey of developing hematopoietic stem cells.", "abstract": ["Hematopoietic stem cells (HSCs) develop during embryogenesis in a complex process that involves multiple anatomical sites.", "Once HSC precursors have been specified from mesoderm, they have to mature into functional HSCs and undergo self-renewing divisions to generate a pool of HSCs.", "During this process, developing HSCs migrate through various embryonic niches, which provide signals for their establishment and the conservation of their self-renewal ability.", "These processes have to be recapitulated to generate HSCs from embryonic stem cells.", "Elucidating the interactions between developing HSCs and their niches should facilitate the generation and expansion of HSCs in vitro to exploit their clinical potential."], "structured": false}
{"doc_id": 97884, "title": "The sacroiliac joint in the spondyloarthropathies.", "abstract": ["The term spondyloarthropathy (SpA) describes and defines a group of related inflammatory joint disease that share characteristic clinical features and a unique association with the major histocompatibility complex class I molecule HLA-B27.", "Five subgroups can be differentiated: ankylosing spondylitis, reactive arthritis, psoriatic arthritis, arthritis associated with inflammatory bowel disease, and undifferentiated SpA. The sacroiliac joints are centrally involved in the SpA, most clearly and pathognomonic in ankylosing spondylitis, in which most patients are affected early in the disease.", "Overcoming some of the diagnostic difficulties of early sacroiliitis, dynamic magnetic resonance imaging was shown to visualize both acute and chronic changes in the sacroiliac joints.", "The inflammation in the sacroiliac joints in patients with SpA was recently examined in more detail; using immunohistology and in situ hybridrization, T cells, macrophages, and various cytokines were found in infiltrates.", "Biopsy specimens were obtained under guided computed tomography, and in the same study, intra-articular corticosteroid treatment was successfully undertaken.", "Further investigation of such biopsy specimens showed the absence of DNA of reactive arthritis-associated bacteria.", "The pathogenesis of the SpA and the reason for the tropism for the sacroiliac joints is still obscure.", "The nature of the relation of the genetic background of SpA to initially triggering bacterial infections remains to be established.", "In chronic disease, autoimmune mechanisms might be more important."], "structured": false}
{"doc_id": 102662, "title": "A rapid method for extraction of cotton (Gossypium spp.) genomic DNA suitable for RFLP or PCR analysis", "abstract": ["Extraction of high-quality genomic DNA fromGossypium (cotton) species is difficult due to high levels of polysaccharide, oxidizable quinones, and other interfering substances.", "We describe a procedure that consistently permits isolation of cotton genomic DNA of satisfactory size and quality for RFLP and PCR analysis, as well as for most routine cloning applications.", "Several antioxidants, phenol-binding reagents, and phenol oxidase inhibitors are used throughout the procedure, and most polysaccharides are eliminated early in the procedure by isolation of nuclei."], "structured": false}
{"doc_id": 103007, "title": "Cross sectional stature and weight reference curves for the UK, 1990.", "abstract": ["The current reference curves of stature and weight for the UK were first published in 1966 and have been used ever since despite increasing concern that they may not adequately describe the growth of present day British children.", "Using current data from seven sources new reference curves have been estimated from birth to 20 years for children in 1990.", "The great majority of the data are nationally representative.", "The analysis used Cole's LMS method and has produced efficient estimates of the conventional centiles and gives a good fit to the data.", "These curves differ from the currently used curves at key ages for both stature and weight.", "In view of the concerns expressed about the current curves and the differences between them and the new curves, it is proposed that the curves presented here should be adopted as the new UK reference curves."], "structured": false}
{"doc_id": 104130, "title": "The suture provides a niche for mesenchymal stem cells of craniofacial bones", "abstract": ["Bone tissue undergoes constant turnover supported by stem cells.", "Recent studies showed that perivascular mesenchymal stem cells (MSCs) contribute to the turnover of long bones.", "Craniofacial bones are flat bones derived from a different embryonic origin than the long bones.", "The identity and regulating niche for craniofacial-bone MSCs remain unknown.", "Here, we identify Gli1+ cells within the suture mesenchyme as the main MSC population for craniofacial bones.", "They are not associated with vasculature, give rise to all craniofacial bones in the adult and are activated during injury repair.", "Gli1+ cells are typical MSCs in vitro.", "Ablation of Gli1+ cells leads to craniosynostosis and arrest of skull growth, indicating that these cells are an indispensable stem cell population.", "Twist1(+/-) mice with craniosynostosis show reduced Gli1+ MSCs in sutures, suggesting that craniosynostosis may result from diminished suture stem cells.", "Our study indicates that craniofacial sutures provide a unique niche for MSCs for craniofacial bone homeostasis and repair."], "structured": false}
{"doc_id": 106301, "title": "Cardiac neural crest cells contribute to the dormant multipotent stem cell in the mammalian heart", "abstract": ["Arodent cardiac side population cell fraction formed clonal spheroids in serum-free medium, which expressed nestin, Musashi-1, and multi-drug resistance transporter gene 1, markers of undifferentiated neural precursor cells.", "These markers were lost following differentiation, and were replaced by the expression of neuron-, glial-, smooth muscle cell\u2013, or cardiomyocyte-specific proteins.", "Cardiosphere-derived cells transplanted into chick embryos migrated to the truncus arteriosus and cardiac outflow tract and contributed to dorsal root ganglia, spinal nerves, and aortic smooth muscle cells.", "Lineage studies using double transgenic mice encoding protein 0\u2013Cre/Floxed-EGFP revealed undifferentiated and differentiated neural crest-derived cells in the fetal myocardium.", "Undifferentiated cells expressed GATA-binding protein 4 and nestin, but not actinin, whereas the differentiated cells were identified as cardiomyocytes.", "These results suggest that cardiac neural crest-derived cells migrate into the heart, remain there as dormant multipotent stem cells\u2014and under the right conditions\u2014differentiate into cardiomyocytes and typical neural crest-derived cells, including neurons, glia, and smooth muscle."], "structured": false}
{"doc_id": 116792, "title": "The mammalian target of rapamycin signaling pathway mediates epileptogenesis in a model of temporal lobe epilepsy.", "abstract": ["Understanding molecular mechanisms mediating epileptogenesis is critical for developing more effective therapies for epilepsy.", "We recently found that the mammalian target of rapamycin (mTOR) signaling pathway is involved in epileptogenesis, and mTOR inhibitors prevent epilepsy in a mouse model of tuberous sclerosis complex.", "Here, we investigated the potential role of mTOR in a rat model of temporal lobe epilepsy initiated by status epilepticus.", "Acute kainate-induced seizures resulted in biphasic activation of the mTOR pathway, as evident by an increase in phospho-S6 (P-S6) expression.", "An initial rise in P-S6 expression started approximately 1 h after seizure onset, peaked at 3-6 h, and returned to baseline by 24 h in both hippocampus and neocortex, reflecting widespread stimulation of mTOR signaling by acute seizure activity.", "After resolution of status epilepticus, a second increase in P-S6 was observed in hippocampus only, which started at 3 d, peaked 5-10 d, and persisted for several weeks after kainate injection, correlating with the development of chronic epileptogenesis within hippocampus.", "The mTOR inhibitor rapamycin, administered before kainate, blocked both the acute and chronic phases of seizure-induced mTOR activation and decreased kainate-induced neuronal cell death, neurogenesis, mossy fiber sprouting, and the development of spontaneous epilepsy.", "Late rapamycin treatment, after termination of status epilepticus, blocked the chronic phase of mTOR activation and reduced mossy fiber sprouting and epilepsy but not neurogenesis or neuronal death.", "These findings indicate that mTOR signaling mediates mechanisms of epileptogenesis in the kainate rat model and that mTOR inhibitors have potential antiepileptogenic effects in this model."], "structured": false}
{"doc_id": 118568, "title": "Acute administration of recombinant Angiopoietin-1 ameliorates multiple-organ dysfunction syndrome and improves survival in murine sepsis.", "abstract": ["INTRODUCTION Endothelial activation leading to vascular barrier breakdown plays an essential role in the pathophysiology of multiple-organ dysfunction syndrome (MODS) in sepsis.", "Increasing evidence suggests that the function of the vessel-protective factor Angiopoietin-1 (Ang-1), a ligand of the endothelial-specific Tie2 receptor, is inhibited by its antagonist Angiopoietin-2 (Ang-2) during sepsis.", "In order to reverse the effects of the sepsis-induced suppression of Ang-1 and elevation of Ang-2 we aimed to investigate whether an intravenous injection of recombinant human (rh) Ang-1 protects against MODS in murine sepsis.   \n", "METHODS Polymicrobiological abdominal sepsis was induced by cecal ligation and puncture (CLP).", "Mice were treated with either 1 \u03bcg of intravenous rhAng-1 or control buffer immediately after CLP induction and every 8h thereafter.", "Sham-operated animals served as time-matched controls.   \n", "RESULTS Compared to buffer-treated controls, rhAng-1 treated septic mice showed significant improvements in several hematologic and biochemical indicators of MODS.", "Moreover, rhAng-1 stabilized endothelial barrier function, as evidenced by inhibition of protein leakage from lung capillaries into the alveolar compartment.", "Histological analysis revealed that rhAng-1 treatment attenuated leukocyte infiltration in lungs and kidneys of septic mice, probably due to reduced endothelial adhesion molecule expression in rhAng-1 treated mice.", "Finally, the protective effects of rhAng-1 treatment were reflected by an improved survival time in a lethal CLP model.   \n", "CONCLUSIONS In a clinically relevant murine sepsis model, intravenous rhAng-1 treatment alone is sufficient to significantly improve a variety of sepsis-associated organ dysfunctions and survival time, most likely by preserving endothelial barrier function.", "Further studies are needed to pave the road for clinical application of this therapy concept."], "structured": true}
{"doc_id": 120626, "title": "Mechanisms linking obesity to insulin resistance and type 2 diabetes", "abstract": ["Obesity is associated with an increased risk of developing insulin resistance and type 2 diabetes.", "In obese individuals, adipose tissue releases increased amounts of non-esterified fatty acids, glycerol, hormones, pro-inflammatory cytokines and other factors that are involved in the development of insulin resistance.", "When insulin resistance is accompanied by dysfunction of pancreatic islet \u03b2-cells \u2014 the cells that release insulin \u2014 failure to control blood glucose levels results.", "Abnormalities in \u03b2-cell function are therefore critical in defining the risk and development of type 2 diabetes.", "This knowledge is fostering exploration of the molecular and genetic basis of the disease and new approaches to its treatment and prevention."], "structured": false}
{"doc_id": 123859, "title": "Tracking the fate of glomerular epithelial cells in vivo using serial multiphoton imaging in novel mouse models with fluorescent lineage tags", "abstract": ["Podocytes are critical in the maintenance of a healthy glomerular filter; however, they have been difficult to study in the intact kidney because of technical limitations.", "Here we report the development of serial multiphoton microscopy (MPM) of the same glomeruli over several days to visualize the motility of podocytes and parietal epithelial cells (PECs) in vivo.", "In podocin-GFP mice, podocytes formed sporadic multicellular clusters after unilateral ureteral ligation and migrated into the parietal Bowman's capsule.", "The tracking of single cells in podocin-confetti mice featuring cell-specific expression of CFP, GFP, YFP or RFP revealed the simultaneous migration of multiple podocytes.", "In phosphoenolpyruvate carboxykinase (PEPCK)-GFP mice, serial MPM found PEC-to-podocyte migration and nanotubule connections.", "Our data support a highly dynamic rather than a static nature of the glomerular environment and cellular composition.", "Future application of this new approach should advance our understanding of the mechanisms of glomerular injury and regeneration."], "structured": false}
{"doc_id": 140874, "title": "CTCF binding at the H19 imprinting control region mediates maternally inherited higher-order chromatin conformation to restrict enhancer access to Igf2.", "abstract": ["It is thought that the H19 imprinting control region (ICR) directs the silencing of the maternally inherited Igf2 allele through a CTCF-dependent chromatin insulator.", "The ICR has been shown to interact physically with a silencer region in Igf2, differentially methylated region (DMR)1, but the role of CTCF in this chromatin loop and whether it restricts the physical access of distal enhancers to Igf2 is not known.", "We performed systematic chromosome conformation capture analyses in the Igf2/H19 region over >160 kb, identifying sequences that interact physically with the distal enhancers and the ICR.", "We found that, on the paternal chromosome, enhancers interact with the Igf2 promoters but that, on the maternal allele, this is prevented by CTCF binding within the H19 ICR.", "CTCF binding in the maternal ICR regulates its interaction with matrix attachment region (MAR)3 and DMR1 at Igf2, thus forming a tight loop around the maternal Igf2 locus, which may contribute to its silencing.", "Mutation of CTCF binding sites in the H19 ICR leads to loss of CTCF binding and de novo methylation of a CTCF target site within Igf2 DMR1, showing that CTCF can coordinate regional epigenetic marks.", "This systematic chromosome conformation capture analysis of an imprinting cluster reveals that CTCF has a critical role in the epigenetic regulation of higher-order chromatin structure and gene silencing over considerable distances in the genome."], "structured": false}
{"doc_id": 143251, "title": "De novo assembly of a PML nuclear subcompartment occurs through multiple pathways and induces telomere elongation.", "abstract": ["Telomerase-negative tumor cells use an alternative lengthening of telomeres (ALT) pathway that involves DNA recombination and repair to maintain their proliferative potential.", "The cytological hallmark of this process is the accumulation of promyelocytic leukemia (PML) nuclear protein at telomeric DNA to form ALT-associated PML bodies (APBs).", "Here, the de novo formation of a telomeric PML nuclear subcompartment was investigated by recruiting APB protein components.", "We show that functionally distinct proteins were able to initiate the formation of bona fide APBs with high efficiency in a self-organizing and self-propagating manner.", "These included: (1) PML and Sp100 as the constituting components of PML nuclear bodies, (2) telomere repeat binding factors 1 and 2 (TRF1 and TRF2, respectively), (3) the DNA repair protein NBS1 and (4) the SUMO E3 ligase MMS21, as well as the isolated SUMO1 domain, through an interacting domain of another protein factor.", "By contrast, the repair factors Rad9, Rad17 and Rad51 were less efficient in APB nucleation but were recruited to preassembled APBs.", "The artificially created APBs induced telomeric extension through a DNA repair mechanism, as inferred from their colocalization with sites of non-replicative DNA synthesis and histone H2A.X phosphorylation, and an increase of the telomere repeat length.", "These activities were absent after recruitment of the APB factors to a pericentric locus and establish APBs as functional intermediates of the ALT pathway."], "structured": false}
{"doc_id": 152245, "title": "Effects of an opal termination codon preceding the nsP4 gene sequence in the O'Nyong-Nyong virus genome on Anopheles gambiae infectivity.", "abstract": ["The genomic RNA of an alphavirus encodes four different nonstructural proteins, nsP1, nsP2, nsP3, and nsP4.", "The polyprotein P123 is produced when translation terminates at an opal termination codon between nsP3 and nsP4.", "The polyprotein P1234 is produced when translational readthrough occurs or when the opal termination codon has been replaced by a sense codon in the alphavirus genome.", "Evolutionary pressures appear to have maintained genomic sequences encoding both a stop codon (opal) and an open reading frame (arginine) as a general feature of the O'nyong-nyong virus (ONNV) genome, indicating that both are required at some point.", "Alternate replication of ONNVs in both vertebrate and invertebrate hosts may determine predominance of a particular codon at this locus in the viral quasispecies.", "However, no systematic study has previously tested this hypothesis in whole animals.", "We report here the results of the first study to investigate in a natural mosquito host the functional significance of the opal stop codon in an alphavirus genome.", "We used a full-length cDNA clone of ONNV to construct a series of mutants in which the arginine between nsP3 and nsP4 was replaced with an opal, ochre, or amber stop codon.", "The presence of an opal stop codon upstream of nsP4 nearly doubled (75.5%) the infectivity of ONNV over that of virus possessing a codon for the amino acid arginine at the corresponding position (39.8%).", "Although the frequency with which the opal virus disseminated from the mosquito midgut did not differ significantly from that of the arginine virus on days 8 and 10, dissemination did began earlier in mosquitoes infected with the opal virus.", "Although a clear fitness advantage is provided to ONNV by the presence of an opal codon between nsP3 and nsP4 in Anopheles gambiae, sequence analysis of ONNV RNA extracted from mosquito bodies and heads indicated codon usage at this position corresponded with that of the virus administered in the blood meal.", "These results suggest that while selection of ONNV variants is occurring, de novo mutation at the position between nsP3 and nsP4 does not readily occur in the mosquito.", "Taken together, these results suggest that the primary fitness advantage provided to ONNV by the presence of an opal codon between nsP3 and nsP4 is related to mosquito infectivity."], "structured": false}
{"doc_id": 153744, "title": "Down-regulation of a host microRNA by a Herpesvirus saimiri noncoding RNA.", "abstract": ["T cells transformed by Herpesvirus saimiri express seven viral U-rich noncoding RNAs of unknown function called HSURs.", "We noted that conserved sequences in HSURs 1 and 2 constitute potential binding sites for three host-cell microRNAs (miRNAs).", "Coimmunoprecipitation experiments confirmed that HSURs 1 and 2 interact with the predicted miRNAs in virally transformed T cells.", "The abundance of one of these miRNAs, miR-27, is dramatically lowered in transformed cells, with consequent effects on the expression of miR-27 target genes.", "Transient knockdown and ectopic expression of HSUR 1 demonstrate that it directs degradation of mature miR-27 in a sequence-specific and binding-dependent manner.", "This viral strategy illustrates use of a ncRNA to manipulate host-cell gene expression via the miRNA pathway."], "structured": false}
{"doc_id": 159469, "title": "HTRF: A Technology Tailored for Drug Discovery \u2013A Review of Theoretical Aspects and Recent Applications", "abstract": ["HTRF (Homogeneous Time Resolved Fluorescence) is the most frequently used generic assay technology to measure analytes in a homogenous format, which is the ideal platform used for drug target studies in high-throughput screening (HTS).", "This technology combines fluorescence resonance energy transfer technology (FRET) with time-resolved measurement (TR).", "In TR-FRET assays, a signal is generated through fluorescent resonance energy transfer between a donor and an acceptor molecule when in close proximity to each other.", "Buffer and media interference is dramatically reduced by dual-wavelength detection, and the final signal is proportional to the extent of product formation.", "The HTRF assay is usually sensitive and robust that can be miniaturized into the 384 and 1536-well plate formats.", "This assay technology has been applied to many antibody-based assays including GPCR signaling (cAMP and IP-One), kinases, cytokines and biomarkers, bioprocess (antibody and protein production), as well as the assays for protein-protein, proteinpeptide, and protein-DNA/RNA interactions.", "Since its introduction to the drug-screening world over ten years ago, researchers have used HTRF to expedite the study of GPCRs, kinases, new biomarkers, protein-protein interactions, and other targets of interest.", "HTRF has also been utilized as an alternative method for bioprocess monitoring.", "The first-generation HTRF technology, which uses Europium cryptate as a fluorescence donor to monitor reactions between biomolecules, was extended in 2008 through the introduction of a second-generation donor, Terbium cryptate (Tb), enhancing screening performance.", "Terbium cryptate possesses different photophysical properties compared to Europium, including increased quantum yield and a higher molar extinction coefficient.", "In addition to being compatible with the same acceptor fluorophors used with Europium, it can serve as a donor fluorophore to green-emitting fluors because it has multiple emission peaks including one at 490 nm.", "Moreover, all Terbium HTRF assays can be read on the same HTRF-compatible instruments as Europium HTRF assays.", "Overall, HTRF is a highly sensitive, robust technology for the detection of molecular interactions in vitro and is widely used for primary and secondary screening phases of drug development.", "This review addresses the general principles of HTRF and its current applications in drug discovery."], "structured": false}
{"doc_id": 164189, "title": "Chk1 inhibits replication factory activation but allows dormant origin firing in existing factories", "abstract": ["Replication origins are licensed by loading MCM2-7 hexamers before entry into S phase.", "However, only \u223c10% of licensed origins are normally used in S phase, with the others remaining dormant.", "When fork progression is inhibited, dormant origins initiate nearby to ensure that all of the DNA is eventually replicated.", "In apparent contrast, replicative stress activates ataxia telangiectasia and rad-3-related (ATR) and Chk1 checkpoint kinases that inhibit origin firing.", "In this study, we show that at low levels of replication stress, ATR/Chk1 predominantly suppresses origin initiation by inhibiting the activation of new replication factories, thereby reducing the number of active factories.", "At the same time, inhibition of replication fork progression allows dormant origins to initiate within existing replication factories.", "The inhibition of new factory activation by ATR/Chk1 therefore redirects replication toward active factories where forks are inhibited and away from regions that have yet to start replication.", "This minimizes the deleterious consequences of fork stalling and prevents similar problems from arising in unreplicated regions of the genome."], "structured": false}
{"doc_id": 164985, "title": "Fra-1 protooncogene regulates IL-6 expression in macrophages and promotes the generation of M2d macrophages", "abstract": ["The tumor microenvironment (TME) plays a prominent role in the growth of tumor cells.", "As the major inflammatory component of the TME, M2d macrophages are educated by the TME such that they adopt an immunosuppressive role that promotes tumor metastasis and progression.", "Fra-1 forms activator protein-1 heterodimers with Jun partners and drives gene transcription.", "Fra-1 is thought to drastically induce tumorigenesis and progression.", "However, the functional role of Fra-1 in the generation of M2d macrophages is poorly understood to date.", "Here, we demonstrate that 4T1 mammary carcinoma cells, when co-cultured with RAW264.7 macrophage cells, skew the RAW264.7 macrophage cell differentiation into M2d macrophages.", "The 4T1 cells stimulate de novo overexpression of Fra-1 in RAW264.7 cells, and then Fra-1 binds to the interleukin 6 (IL-6) promoter to increase the production of the cytokine IL-6 in RAW264.7 cells.", "IL-6 acts in an autocrine fashion to skew RAW264.7 macrophage cell differentiation into M2d macrophages.", "These findings open new insights into how to reverse M2d macrophage-induced immune tolerance to improve the efficacy of immunotherapeutic approaches."], "structured": false}
{"doc_id": 169264, "title": "Analysis of SiO2 nanoparticles binding proteins in rat blood and brain homogenate", "abstract": ["A multitude of nanoparticles, such as titanium oxide (TiO2), zinc oxide, aluminum oxide, gold oxide, silver oxide, iron oxide, and silica oxide, are found in many chemical, cosmetic, pharmaceutical, and electronic products.", "Recently, SiO2 nanoparticles were shown to have an inert toxicity profile and no association with an irreversible toxicological change in animal models.", "Hence, exposure to SiO2 nanoparticles is on the increase.", "SiO2 nanoparticles are routinely used in numerous materials, from strengthening filler for concrete and other construction composites, to nontoxic platforms for biomedical application, such as drug delivery and theragnostics.", "On the other hand, recent in vitro experiments indicated that SiO2 nanoparticles were cytotoxic.", "Therefore, we investigated these nanoparticles to identify potentially toxic pathways by analyzing the adsorbed protein corona on the surface of SiO2 nanoparticles in the blood and brain of the rat.", "Four types of SiO2 nanoparticles were chosen for investigation, and the protein corona of each type was analyzed using liquid chromatography-tandem mass spectrometry technology.", "In total, 115 and 48 plasma proteins from the rat were identified as being bound to negatively charged 20 nm and 100 nm SiO2 nanoparticles, respectively, and 50 and 36 proteins were found for 20 nm and 100 nm arginine-coated SiO2 nanoparticles, respectively.", "Higher numbers of proteins were adsorbed onto the 20 nm sized SiO2 nanoparticles than onto the 100 nm sized nanoparticles regardless of charge.", "When proteins were compared between the two charges, higher numbers of proteins were found for arginine-coated positively charged SiO2 nanoparticles than for the negatively charged nanoparticles.", "The proteins identified as bound in the corona from SiO2 nanoparticles were further analyzed with ClueGO, a Cytoscape plugin used in protein ontology and for identifying biological interaction pathways.", "Proteins bound on the surface of nanoparticles may affect functional and conformational properties and distributions in complicated biological processes."], "structured": false}
{"doc_id": 175735, "title": "Inferring nucleosome positions with their histone mark annotation from ChIP data", "abstract": ["MOTIVATION The nucleosome is the basic repeating unit of chromatin.", "It contains two copies each of the four core histones H2A, H2B, H3 and H4 and about 147 bp of DNA.", "The residues of the histone proteins are subject to numerous post-translational modifications, such as methylation or acetylation.", "Chromatin immunoprecipitiation followed by sequencing (ChIP-seq) is a technique that provides genome-wide occupancy data of these modified histone proteins, and it requires appropriate computational methods.   \n", "RESULTS We present NucHunter, an algorithm that uses the data from ChIP-seq experiments directed against many histone modifications to infer positioned nucleosomes.", "NucHunter annotates each of these nucleosomes with the intensities of the histone modifications.", "We demonstrate that these annotations can be used to infer nucleosomal states with distinct correlations to underlying genomic features and chromatin-related processes, such as transcriptional start sites, enhancers, elongation by RNA polymerase II and chromatin-mediated repression.", "Thus, NucHunter is a versatile tool that can be used to predict positioned nucleosomes from a panel of histone modification ChIP-seq experiments and infer distinct histone modification patterns associated to different chromatin states.   ", "AVAILABILITY The software is available at http://epigen.molgen.mpg.de/nuchunter/."], "structured": true}
{"doc_id": 188911, "title": "Generation of large numbers of dendritic cells from mouse bone marrow cultures supplemented with granulocyte/macrophage colony-stimulating factor", "abstract": ["Antigen-presenting, major histocompatibility complex (MHC) class II-rich dendritic cells are known to arise from bone marrow.", "However, marrow lacks mature dendritic cells, and substantial numbers of proliferating less-mature cells have yet to be identified.", "The methodology for inducing dendritic cell growth that was recently described for mouse blood now has been modified to MHC class II-negative precursors in marrow.", "A key step is to remove the majority of nonadherent, newly formed granulocytes by gentle washes during the first 2-4 d of culture.", "This leaves behind proliferating clusters that are loosely attached to a more firmly adherent \"stroma.", "\"", "At days 4-6 the clusters can be dislodged, isolated by 1-g sedimentation, and upon reculture, large numbers of dendritic cells are released.", "The latter are readily identified on the basis of their distinct cell shape, ultrastructure, and repertoire of antigens, as detected with a panel of monoclonal antibodies.", "The dendritic cells express high levels of MHC class II products and act as powerful accessory cells for initiating the mixed leukocyte reaction.", "Neither the clusters nor mature dendritic cells are generated if macrophage colony-stimulating factor rather than granulocyte/macrophage colony-stimulating factor (GM-CSF) is applied.", "Therefore, GM-CSF generates all three lineages of myeloid cells (granulocytes, macrophages, and dendritic cells).", "Since > 5 x 10(6) dendritic cells develop in 1 wk from precursors within the large hind limb bones of a single animal, marrow progenitors can act as a major source of dendritic cells.", "This feature should prove useful for future molecular and clinical studies of this otherwise trace cell type."], "structured": false}
{"doc_id": 195352, "title": "Insulin action and resistance in obesity and type 2 diabetes", "abstract": ["Nutritional excess is a major forerunner of type 2 diabetes.", "It enhances the secretion of insulin, but attenuates insulin's metabolic actions in the liver, skeletal muscle and adipose tissue.", "However, conflicting evidence indicates a lack of knowledge of the timing of these events during the development of obesity and diabetes, pointing to a key gap in our understanding of metabolic disease.", "This Perspective reviews alternate viewpoints and recent results on the temporal and mechanistic connections between hyperinsulinemia, obesity and insulin resistance.", "Although much attention has addressed early steps in the insulin signaling cascade, insulin resistance in obesity seems to be largely elicited downstream of these steps.", "New findings also connect insulin resistance to extensive metabolic cross-talk between the liver, adipose tissue, pancreas and skeletal muscle.", "These and other advances over the past 5 years offer exciting opportunities and daunting challenges for the development of new therapeutic strategies for the treatment of type 2 diabetes."], "structured": false}
{"doc_id": 202259, "title": "Effect of lowering blood pressure on cardiovascular events and mortality in patients on dialysis: a systematic review and meta-analysis of randomised controlled trials", "abstract": ["BACKGROUND Patients undergoing dialysis have a substantially increased risk of cardiovascular mortality and morbidity.", "Although several trials have shown the cardiovascular benefits of lowering blood pressure in the general population, there is uncertainty about the efficacy and tolerability of reducing blood pressure in patients on dialysis.", "We did a systematic review and meta-analysis to assess the effect of blood pressure lowering in patients on dialysis.   \n", "METHODS We systematically searched Medline, Embase, and the Cochrane Library database for trials reported between 1950 and November, 2008, without language restriction.", "We extracted a standardised dataset from randomised controlled trials of blood pressure lowering in patients on dialysis that reported cardiovascular outcomes.", "Meta-analysis was done with a random effects model.   \n", "FINDINGS We identified eight relevant trials, which provided data for 1679 patients and 495 cardiovascular events.", "Weighted mean systolic blood pressure was 4.5 mm Hg lower and diastolic blood pressure 2.3 mm Hg lower in actively treated patients than in controls.", "Blood pressure lowering treatment was associated with lower risks of cardiovascular events (RR 0.71, 95% CI 0.55-0.92; p=0.009), all-cause mortality (RR 0.80, 0.66-0.96; p=0.014), and cardiovascular mortality (RR 0.71, 0.50-0.99; p=0.044) than control regimens.", "The effects seem to be consistent across a range of patient groups included in the studies.   \n", "INTERPRETATION Treatment with agents that lower blood pressure should routinely be considered for individuals undergoing dialysis to reduce the very high cardiovascular morbidity and mortality rate in this population."], "structured": true}
{"doc_id": 207972, "title": "Interaction of an adenovirus E3 14.7-kilodalton protein with a novel tumor necrosis factor alpha-inducible cellular protein containing leucine zipper domains.", "abstract": ["Early region 3 (E3) of group C human adenoviruses (Ad) encodes several inhibitors of tumor necrosis factor alpha (TNF-alpha) cytolysis, including an E3 14.7-kDa protein (E3-14.7K) and a heterodimer containing two polypeptides of 10.4 and 14.5 kDa.", "To understand the mechanism by which the viral proteins inhibit TNF-alpha functions, the E3-14.7K protein was used to screen a HeLa cell cDNA library to search for interacting proteins in the yeast two-hybrid system.", "A novel protein containing multiple leucine zipper domains without any significant homology with any known protein was identified and has been named FIP-2 (for 14.7K-interacting protein).", "FIP-2 interacted with E3-14.7K both in vitro and in vivo.", "It colocalized with Ad E3-14.7K in the cytoplasm, especially near the nuclear membrane, and caused redistribution of the viral protein.", "FIP-2 by itself does not cause cell death; however, it can reverse the protective effect of E3-14.7K on cell killing induced by overexpression of the intracellular domain of the 55-kDa TNF receptor or by RIP, a death protein involved in the TNF-alpha and Fas apoptosis pathways.", "Deletion analysis indicates that the reversal effect of FIP-2 depends on its interaction with E3-14.7K.", "Three major mRNA forms of FIP-2 have been detected in multiple human tissues, and expression of the transcripts was induced by TNF-alpha treatment in a time-dependent manner in two different cell lines.", "FIP-2 has consensus sequences for several potential posttranslational modifications.", "These data suggest that FIP-2 is one of the cellular targets for Ad E3-14.7K and that its mechanism of affecting cell death involves the TNF receptor, RIP, or a downstream molecule affected by either of these two molecules."], "structured": false}
{"doc_id": 213017, "title": "PML induces compaction, TRF2 depletion and DNA damage signaling at telomeres and promotes their alternative lengthening.", "abstract": ["The alternative lengthening of telomeres (ALT) mechanism allows cancer cells to escape senescence and apoptosis in the absence of active telomerase.", "A characteristic feature of this pathway is the assembly of ALT-associated promyelocytic leukemia (PML) nuclear bodies (APBs) at telomeres.", "Here, we dissected the role of APBs in a human ALT cell line by performing an RNA interference screen using an automated 3D fluorescence microscopy platform and advanced 3D image analysis.", "We identified 29 proteins that affected APB formation, which included proteins involved in telomere and chromatin organization, protein sumoylation and DNA repair.", "By integrating and extending these findings, we found that APB formation induced clustering of telomere repeats, telomere compaction and concomitant depletion of the shelterin protein TRF2 (also known as TERF2).", "These APB-dependent changes correlated with the induction of a DNA damage response at telomeres in APBs as evident by a strong enrichment of the phosphorylated form of the ataxia telangiectasia mutated (ATM) kinase.", "Accordingly, we propose that APBs promote telomere maintenance by inducing a DNA damage response in ALT-positive tumor cells through changing the telomeric chromatin state to trigger ATM phosphorylation."], "structured": false}
{"doc_id": 219475, "title": "Gr-1+CD11b+ myeloid cells tip the balance of immune protection to tumor promotion in the premetastatic lung.", "abstract": ["The mechanisms by which a primary tumor affects a selected distant organ before tumor cell arrival remain to be elucidated.", "This report shows that Gr-1+CD11b+ cells are significantly increased in lungs of mice bearing mammary adenocarcinomas before tumor cell arrival.", "In the premetastatic lungs, these immature myeloid cells significantly decrease IFN-gamma production and increase proinflammatory cytokines.", "In addition, they produce large quantities of matrix metalloproteinase 9 (MMP9) and promote vascular remodeling.", "Deletion of MMP9 normalizes aberrant vasculature in the premetastatic lung and diminishes lung metastasis.", "The production and activity of MMP9 is selectively restricted to lungs and organs with a large number of Gr-1+CD11b+ cells.", "Our work reveals a novel protumor mechanism for Gr-1+CD11b+ cells that changes the premetastatic lung into an inflammatory and proliferative environment, diminishes immune protection, and promotes metastasis through aberrant vasculature formation.", "Thus, inhibition of Gr-1+CD11b+ cells could normalize the premetastatic lung environment, improve host immunosurveillance, and inhibit tumor metastasis."], "structured": false}
{"doc_id": 226488, "title": "Activin/Nodal signalling in stem cells.", "abstract": ["Activin/Nodal growth factors control a broad range of biological processes, including early cell fate decisions, organogenesis and adult tissue homeostasis.", "Here, we provide an overview of the mechanisms by which the Activin/Nodal signalling pathway governs stem cell function in these different stages of development.", "We describe recent findings that associate Activin/Nodal signalling to pathological conditions, focusing on cancer stem cells in tumorigenesis and its potential as a target for therapies.", "Moreover, we will discuss future directions and questions that currently remain unanswered on the role of Activin/Nodal signalling in stem cell self-renewal, differentiation and proliferation."], "structured": false}
{"doc_id": 236204, "title": "Distinct RNA-dependent RNA polymerases are required for RNAi triggered by double-stranded RNA versus truncated transgenes in Paramecium tetraurelia", "abstract": ["In many eukaryotes, RNA-dependent RNA polymerases (RdRPs) play key roles in the RNAi pathway.", "They have been implicated in the recognition and processing of aberrant transcripts triggering the process, and in amplification of the silencing response.", "We have tested the functions of RdRP genes from the ciliate Paramecium tetraurelia in experimentally induced and endogenous mechanisms of gene silencing.", "In this organism, RNAi can be triggered either by high-copy, truncated transgenes or by directly feeding cells with double-stranded RNA (dsRNA).", "Surprisingly, dsRNA-induced silencing depends on the putatively functional RDR1 and RDR2 genes, which are required for the accumulation of both primary siRNAs and a distinct class of small RNAs suggestive of secondary siRNAs.", "In contrast, a third gene with a highly divergent catalytic domain, RDR3, is required for siRNA accumulation when RNAi is triggered by truncated transgenes.", "Our data further implicate RDR3 in the accumulation of previously described endogenous siRNAs and in the regulation of the surface antigen gene family.", "While only one of these genes is normally expressed in any clonal cell line, the knockdown of RDR3 leads to co-expression of multiple antigens.", "These results provide evidence for a functional specialization of Paramecium RdRP genes in distinct RNAi pathways operating during vegetative growth."], "structured": false}
{"doc_id": 238409, "title": "Mechanisms of Renal Cell Apoptosis Induced by Cyclosporine A: A Systematic Review of in vitro Studies", "abstract": ["Background:Chronic cyclosporine A (CsA) nephrotoxicity (CCN) is a major cause of chronic renal dysfunction and has no effective clinical interventions yet.", "Objective: To reveal the mechanisms of renal cell apoptosis in CCN, we analyzed all in vitro studies of such mechanisms.", "Methods: We collected all in vitro studies about the mechanisms of renal cell apoptosis induced by CsA in Medline (1966 to July 2010), Embase (1980 to July 2010) and ISI (1986 to July 2010), evaluated their quality according to in vitro standards and extracted data following the PICOS principles and synthesized the data.", "Results: First,CsA could upregulate Fas and Fas-L expression, increase FADD and apoptosis enzymes (caspase-2, -3, -4, -7, -8, -9 and -10) and downregulate the Bcl-2 and Bcl-xL. Second, CsA could induce oxidative stress and damage the antioxidant defense system.", "Third, CsA could increase the expression of HERP, GRP78 and CHOP.", "Fourth, CsA could induce renal cell apoptosis and increase their iNOS and p53 expression in cultured cells.", "Conclusions: At least four pathways are involved in renal cell apoptosis induced by CsA in different cell species.", "Caspases might be their final common pathway in vitro.", "They might all provide potential points for interventions, but these need to be confirmed in vivo."], "structured": false}
{"doc_id": 243694, "title": "Blood stem cells emerge from aortic endothelium by a novel type of cell transition", "abstract": ["The ontogeny of haematopoietic stem cells (HSCs) during embryonic development is still highly debated, especially their possible lineage relationship to vascular endothelial cells.", "The first anatomical site from which cells with long-term HSC potential have been isolated is the aorta-gonad-mesonephros (AGM), more specifically the vicinity of the dorsal aortic floor.", "But although some authors have presented evidence that HSCs may arise directly from the aortic floor into the dorsal aortic lumen, others support the notion that HSCs first emerge within the underlying mesenchyme.", "Here we show by non-invasive, high-resolution imaging of live zebrafish embryos, that HSCs emerge directly from the aortic floor, through a stereotyped process that does not involve cell division but a strong bending then egress of single endothelial cells from the aortic ventral wall into the sub-aortic space, and their concomitant transformation into haematopoietic cells.", "The process is polarized not only in the dorso-ventral but also in the rostro-caudal versus medio-lateral direction, and depends on Runx1 expression: in Runx1-deficient embryos, the exit events are initially similar, but much rarer, and abort into violent death of the exiting cell.", "These results demonstrate that the aortic floor is haemogenic and that HSCs emerge from it into the sub-aortic space, not by asymmetric cell division but through a new type of cell behaviour, which we call an endothelial haematopoietic transition."], "structured": false}
{"doc_id": 253672, "title": "Probable person to person transmission of novel avian influenza A (H7N9) virus in Eastern China, 2013: epidemiological investigation", "abstract": ["OBJECTIVE To determine whether the novel avian influenza H7N9 virus can transmit from person to person and its efficiency.   \n", "DESIGN Epidemiological investigations conducted after a family cluster of two patients with avian H7N9 in March 2013.   \n", "SETTING Wuxi, Eastern China.   \n", "PARTICIPANTS Two patients, their close contacts, and relevant environments.", "Samples from the patients and environments were collected and tested by real time reverse transcriptase-polymerase chain reaction (rRT-PCR), viral culture, and haemagglutination inhibition assay.", "Any contacts who became ill had samples tested for avian H7N9 by rRT-PCR.", "Paired serum samples were obtained from contacts for serological testing by haemagglutination inhibition assays.   \n", "MAIN OUTCOMES MEASURES Clinical data, history of exposure before the onset of illnesses, and results of laboratory testing of pathogens and further analysis of sequences and phylogenetic tree to isolated strains.   \n", "RESULTS The index patient became ill five to six days after his last exposure to poultry.", "The second patient, his daughter aged 32, who provided unprotected bedside care in the hospital, had no known exposure to poultry.", "She developed symptoms six days after her last contact with her father.", "Two strains were isolated successfully from the two patients.", "Genome sequence and analyses of phylogenetic trees showed that both viruses were almost genetically identical.", "Forty three close contacts of both patients were identified.", "One had mild illness but had negative results for avian H7N9 by rRT-PCR.", "All 43 close contacts tested negative for haemagglutination inhibition antibodies specific for avian H7N9.   \n", "CONCLUSIONS The infection of the daughter probably resulted from contact with her father (the index patient) during unprotected exposure, suggesting that in this cluster the virus was able to transmit from person to person.", "The transmissibility was limited and non-sustainable."], "structured": true}
{"doc_id": 263364, "title": "Genetic Variation in the Interleukin-28B Gene Is Associated with Spontaneous Clearance and Progression of Hepatitis C Virus in Moroccan Patients", "abstract": ["BACKGROUND Genetic variation in the IL28B gene has been strongly associated with treatment outcomes, spontaneous clearance and progression of the hepatitis C virus infection (HCV).", "The aim of the present study was to investigate the role of polymorphisms at this locus with progression and outcome of HCV infection in a Moroccan population.   \n", "METHODS We analyzed a cohort of 438 individuals among them 232 patients with persistent HCV infection, of whom 115 patients had mild chronic hepatitis and 117 had advanced liver disease (cirrhosis and hepatocellular carcinoma), 68 individuals who had naturally cleared HCV and 138 healthy subjects.", "The IL28B SNPs rs12979860 and rs8099917 were genotyped using a TaqMan 5' allelic discrimination assay.   \n", "RESULTS The protective rs12979860-C and rs8099917-T alleles were more common in subjects with spontaneous clearance (77.9% vs 55.2%; p = 0.00001 and 95.6% vs 83.2%; p = 0.0025, respectively).", "Individuals with clearance were 4.69 (95% CI, 1.99-11.07) times more likely to have the C/C genotype for rs12979860 polymorphism (p = 0.0017) and 3.55 (95% CI, 0.19-66.89) times more likely to have the T/T genotype at rs8099917.", "Patients with advanced liver disease carried the rs12979860-T/T genotype more frequently than patients with mild chronic hepatitis C (OR = 1.89; 95% CI, 0.99-3.61; p = 0.0532) and this risk was even more pronounced when we compared them with healthy controls (OR = 4.27; 95% CI, 2.08-8.76; p = 0.0005).", "The rs8099917-G allele was also associated with advanced liver disease (OR = 2.34; 95% CI, 1.40-3.93; p = 0.0100).   \n", "CONCLUSIONS In the Moroccan population, polymorphisms near the IL28B gene play a role both in spontaneous clearance and progression of HCV infection."], "structured": true}
{"doc_id": 266641, "title": "CD127 expression inversely correlates with FoxP3 and suppressive function of human CD4+ T reg cells", "abstract": ["Regulatory T (T reg) cells are critical regulators of immune tolerance.", "Most T reg cells are defined based on expression of CD4, CD25, and the transcription factor, FoxP3.", "However, these markers have proven problematic for uniquely defining this specialized T cell subset in humans.", "We found that the IL-7 receptor (CD127) is down-regulated on a subset of CD4+ T cells in peripheral blood.", "We demonstrate that the majority of these cells are FoxP3+, including those that express low levels or no CD25.", "A combination of CD4, CD25, and CD127 resulted in a highly purified population of T reg cells accounting for significantly more cells that previously identified based on other cell surface markers.", "These cells were highly suppressive in functional suppressor assays.", "In fact, cells separated based solely on CD4 and CD127 expression were anergic and, although representing at least three times the number of cells (including both CD25+CD4+ and CD25\u2212CD4+ T cell subsets), were as suppressive as the \u201cclassic\u201d CD4+CD25hi T reg cell subset.", "Finally, we show that CD127 can be used to quantitate T reg cell subsets in individuals with type 1 diabetes supporting the use of CD127 as a biomarker for human T reg cells."], "structured": false}
{"doc_id": 275294, "title": "Environmental factors that influence the cutaneous production of vitamin D", "abstract": ["All vertebrates, including humans, obtain most of their daily vitamin D requirement from casual exposure to sunlight.", "During exposure to sunlight, the solar ultraviolet B photons (290-315 nm) penetrate into the skin where they cause the photolysis of 7-dehydrocholesterol to precholecalciferol.", "Once formed, precholecalciferol undergoes a thermally induced rearrangement of its double bonds to form cholecalciferol.", "An increase in skin pigmentation, aging, and the topical application of a sunscreen diminishes the cutaneous production of cholecalciferol.", "Latitude, season, and time of day as well as ozone pollution in the atmosphere influence the number of solar ultraviolet B photons that reach the earth's surface, and thereby, alter the cutaneous production of cholecalciferol.", "In Boston, exposure to sunlight during the months of November through February will not produce any significant amounts of cholecalciferol in the skin.", "Because windowpane glass absorbs ultraviolet B radiation, exposure of sunlight through glass windows will not result in any production of cholecalciferol.", "It is now recognized that vitamin D insufficiency and vitamin D deficiency are common in elderly people, especially in those who are infirm and not exposed to sunlight or who live at latitudes that do not provide them with sunlight-mediated cholecalciferol during the winter months.", "Vitamin D insufficiency and deficiency exacerbate osteoporosis, cause osteomalacia, and increase the risk of skeletal fractures.", "Vitamin D insufficiency and deficiency can be prevented by encouraging responsible exposure to sunlight and/or consumption of a multivitamin tablet that contains 10 micrograms (400 IU) vitamin D."], "structured": false}
{"doc_id": 279052, "title": "Genomic imprinting in development, growth, behavior and stem cells.", "abstract": ["Genes that are subject to genomic imprinting in mammals are preferentially expressed from a single parental allele.", "This imprinted expression of a small number of genes is crucial for normal development, as these genes often directly regulate fetal growth.", "Recent work has also demonstrated intricate roles for imprinted genes in the brain, with important consequences on behavior and neuronal function.", "Finally, new studies have revealed the importance of proper expression of specific imprinted genes in induced pluripotent stem cells and in adult stem cells.", "As we review here, these findings highlight the complex nature and developmental importance of imprinted genes."], "structured": false}
{"doc_id": 285794, "title": "Quantitative Detection of Hepatitis C Virus RNA by Light Cycler PCR and Comparison with Two Different PCR Assays", "abstract": ["The new Light Cycler technology was adapted to the detection of hepatitis C virus (HCV) RNA in clinical samples.", "Sera from 81 patients were tested by Light Cycler PCR, AMPLICOR HCV Monitor assay, and in-house PCR.", "Our data demonstrate that Light Cycler is a fast and reliable method for the detection and quantitation of HCV RNA."], "structured": false}
{"doc_id": 293661, "title": "Targeting arginine metabolism pathway to treat arginine-dependent cancers.", "abstract": ["The significant disparities in metabolism between tumor and normal cells have inspired the development of metabolism-based anti-tumor therapeutics.", "Arginine is a semi-essential amino acid because normal cells can not only synthesize arginine de novo but also take up extracellular arginine.", "Several types of tumors have abnormalities in arginine metabolism enzymes and completely rely on extracellular arginine to support necessary biological processes.", "This property is referred to as arginine auxotrophy.", "Taking advantage of characteristic arginine auxotrophy in tumors, arginine deprivation, which is generally induced by the use of arginine deiminase (ADI) and arginase I, has been investigated as a novel strategy for cancer therapy.", "Arginine deprivation demonstrated promising efficacy against arginine-auxotrophic tumors.", "By integrating perspectives from both clinical oncologists and laboratory scientists, this article reviews the important aspects of arginine deprivation as a promising anticancer therapy."], "structured": false}
{"doc_id": 301838, "title": "Rank Signaling Links the Development of Invariant \u03b3\u03b4 T Cell Progenitors and Aire+ Medullary Epithelium", "abstract": ["The thymic medulla provides a specialized microenvironment for the negative selection of T cells, with the presence of autoimmune regulator (Aire)-expressing medullary thymic epithelial cells (mTECs) during the embryonic-neonatal period being both necessary and sufficient to establish long-lasting tolerance.", "Here we showed that emergence of the first cohorts of Aire(+) mTECs at this key developmental stage, prior to \u03b1\u03b2 T cell repertoire selection, was jointly directed by Rankl(+) lymphoid tissue inducer cells and invariant V\u03b35(+) dendritic epidermal T cell (DETC) progenitors that are the first thymocytes to express the products of gene rearrangement.", "In turn, generation of Aire(+) mTECs then fostered Skint-1-dependent, but Aire-independent, DETC progenitor maturation and the emergence of an invariant DETC repertoire.", "Hence, our data attributed a functional importance to the temporal development of V\u03b35(+) \u03b3\u03b4 T cells during thymus medulla formation for \u03b1\u03b2 T cell tolerance induction and demonstrated a Rank-mediated reciprocal link between DETC and Aire(+) mTEC maturation."], "structured": false}
{"doc_id": 301866, "title": "Long-term immune deficiency after allogeneic stem cell transplantation: B-cell deficiency is associated with late infections.", "abstract": ["Immune reconstitution was analyzed in 140 consecutive patients who were 2-year disease-free and who underwent myeloablative allogeneic transplantation.", "A CD4 and CD8 defect was observed involving naive, terminally differentiated, memory and competent cells and above limits values for activated subsets.", "Natural killer cells normalize at six months while we observed expansion of CD19(+)/CD5(+) B cells after three months and a persisting defect of memory B cells.", "Chronic graft-versus-host disease did not influence significantly those parameters for CD8 subsets while the na\u00efve and competent CD4 subsets were strongly affected.", "But the most profound impact of chronic graft-versus-host disease was on B-cell subsets, especially on the memory B population.", "The cumulative incidence of late severe infections was low (14% at four years).", "Using Cox's models, only low B-cell counts at 12 (P=0.02) and 24 (P=0.001) months were associated with the hazard of developing late infection, in particular if patients did not develop chronic graft-versus-host disease."], "structured": false}
{"doc_id": 306006, "title": "The stimulatory potency of T cell antigens is influenced by the formation of the immunological synapse.", "abstract": ["T cell activation is predicated on the interaction between the T cell receptor and peptide-major histocompatibility (pMHC) ligands.", "The factors that determine the stimulatory potency of a pMHC molecule remain unclear.", "We describe results showing that a peptide exhibiting many hallmarks of a weak agonist stimulates T cells to proliferate more than the wild-type agonist ligand.", "An in silico approach suggested that the inability to form the central supramolecular activation cluster (cSMAC) could underlie the increased proliferation.", "This conclusion was supported by experiments that showed that enhancing cSMAC formation reduced stimulatory capacity of the weak peptide.", "Our studies highlight the fact that a complex interplay of factors determines the quality of a T cell antigen."], "structured": false}
{"doc_id": 306311, "title": "Control of glutamate clearance and synaptic efficacy by glial coverage of neurons.", "abstract": ["Analysis of excitatory synaptic transmission in the rat hypothalamic supraoptic nucleus revealed that glutamate clearance and, as a consequence, glutamate concentration and diffusion in the extracellular space, is associated with the degree of astrocytic coverage of its neurons.", "Reduction in glutamate clearance, whether induced pharmacologically or associated with a relative decrease of glial coverage in the vicinity of synapses, affected transmitter release through modulation of presynaptic metabotropic glutamate receptors.", "Astrocytic wrapping of neurons, therefore, contributes to the regulation of synaptic efficacy in the central nervous system."], "structured": false}
{"doc_id": 308862, "title": "Duration of androgen suppression in the treatment of prostate cancer.", "abstract": ["BACKGROUND The combination of radiotherapy plus long-term medical suppression of androgens (> or = 2 years) improves overall survival in patients with locally advanced prostate cancer.", "We compared the use of radiotherapy plus short-term androgen suppression with the use of radiotherapy plus long-term androgen suppression in the treatment of locally advanced prostate cancer.   \n", "METHODS We randomly assigned patients with locally advanced prostate cancer who had received external-beam radiotherapy plus 6 months of androgen suppression to two groups, one to receive no further treatment (short-term suppression) and the other to receive 2.5 years of further treatment with a luteinizing hormone-releasing hormone agonist (long-term suppression).", "An outcome of noninferiority of short-term androgen suppression as compared with long-term suppression required a hazard ratio of more than 1.35 for overall survival, with a one-sided alpha level of 0.05.", "An interim analysis showed futility, and the results are presented with an adjusted one-sided alpha level of 0.0429.   \n", "RESULTS A total of 1113 men were registered, of whom 970 were randomly assigned, 483 to short-term suppression and 487 to long-term suppression.", "After a median follow-up of 6.4 years, 132 patients in the short-term group and 98 in the long-term group had died; the number of deaths due to prostate cancer was 47 in the short-term group and 29 in the long-term group.", "The 5-year overall mortality for short-term and long-term suppression was 19.0% and 15.2%, respectively; the observed hazard ratio was 1.42 (upper 95.71% confidence limit, 1.79; P=0.65 for noninferiority).", "Adverse events in both groups included fatigue, diminished sexual function, and hot flushes.   \n", "CONCLUSIONS The combination of radiotherapy plus 6 months of androgen suppression provides inferior survival as compared with radiotherapy plus 3 years of androgen suppression in the treatment of locally advanced prostate cancer.", "(ClinicalTrials.gov number, NCT00003026.)"], "structured": true}
{"doc_id": 313394, "title": "A Functional Neuroimaging Study of Sound Localization: Visual Cortex Activity Predicts Performance in Early-Blind Individuals", "abstract": ["Blind individuals often demonstrate enhanced nonvisual perceptual abilities.", "However, the neural substrate that underlies this improved performance remains to be fully understood.", "An earlier behavioral study demonstrated that some early-blind people localize sounds more accurately than sighted controls using monaural cues.", "In order to investigate the neural basis of these behavioral differences in humans, we carried out functional imaging studies using positron emission tomography and a speaker array that permitted pseudo-free-field presentations within the scanner.", "During binaural sound localization, a sighted control group showed decreased cerebral blood flow in the occipital lobe, which was not seen in early-blind individuals.", "During monaural sound localization (one ear plugged), the subgroup of early-blind subjects who were behaviorally superior at sound localization displayed two activation foci in the occipital cortex.", "This effect was not seen in blind persons who did not have superior monaural sound localization abilities, nor in sighted individuals.", "The degree of activation of one of these foci was strongly correlated with sound localization accuracy across the entire group of blind subjects.", "The results show that those blind persons who perform better than sighted persons recruit occipital areas to carry out auditory localization under monaural conditions.", "We therefore conclude that computations carried out in the occipital cortex specifically underlie the enhanced capacity to use monaural cues.", "Our findings shed light not only on intermodal compensatory mechanisms, but also on individual differences in these mechanisms and on inhibitory patterns that differ between sighted individuals and those deprived of vision early in life."], "structured": false}
{"doc_id": 313403, "title": "High-Infiltration of Tumor-Associated Macrophages Predicts Unfavorable Clinical Outcome for Node-Negative Breast Cancer", "abstract": ["The tumor microenvironment is composed of tumor cells, fibroblasts, endothelial cells and infiltrating immune cells, which may inhibit or promote tumor growth and progression.", "The objectives of this retrospective study were to characterize the density of tumor-associated macrophages (TAMs) in breast cancer, and to correlate the density of TAMs with clinicopathological parameters.", "Paraffin-embedded specimens and clinicopathological data, including up to 5 years follow-up information, were obtained from 172 breast cancer patients.", "Immunohistochemical staining for CD68 (marker for macrophages) was performed and evaluated in a blinded fashion.", "We found that TAMs were significantly frequent in high histopathological grade breast cancer patients.", "Breast cancer patients with a high density of TAMs had significantly lower rates of disease-free survival and 5-year overall survival than patients with low density of TAMs.", "Furthermore, high-infiltration of TAMs indicated worse survival rate for patients with node-negative breast cancer.", "In conclusion, the number of TAMs in the tumor stroma is an independent predictor of survival time for breast cancer patients.", "High-infiltration of TAMs is a significant unfavorable prognostic factor for patients with invasive breast cancer and, as such, is a potentially useful prognostic marker for breast cancer."], "structured": false}
{"doc_id": 317204, "title": "Murine Dishevelled 3 Functions in Redundant Pathways with Dishevelled 1 and 2 in Normal Cardiac Outflow Tract, Cochlea, and Neural Tube Development", "abstract": ["Dishevelled (Dvl) proteins are important signaling components of both the canonical beta-catenin/Wnt pathway, which controls cell proliferation and patterning, and the planar cell polarity (PCP) pathway, which coordinates cell polarity within a sheet of cells and also directs convergent extension cell (CE) movements that produce narrowing and elongation of the tissue.", "Three mammalian Dvl genes have been identified and the developmental roles of Dvl1 and Dvl2 were previously determined.", "Here, we identify the functions of Dvl3 in development and provide evidence of functional redundancy among the three murine Dvls.", "Dvl3(-/-) mice died perinatally with cardiac outflow tract abnormalities, including double outlet right ventricle and persistent truncus arteriosis.", "These mutants also displayed a misorientated stereocilia in the organ of Corti, a phenotype that was enhanced with the additional loss of a single allele of the PCP component Vangl2/Ltap (LtapLp/+).", "Although neurulation appeared normal in both Dvl3(-/-) and LtapLp/+ mutants, Dvl3(+/-);LtapLp/+ combined mutants displayed incomplete neural tube closure.", "Importantly, we show that many of the roles of Dvl3 are also shared by Dvl1 and Dvl2.", "More severe phenotypes were observed in Dvl3 mutants with the deficiency of another Dvl, and increasing Dvl dosage genetically with Dvl transgenes demonstrated the ability of Dvls to compensate for each other to enable normal development.", "Interestingly, global canonical Wnt signaling appeared largely unaffected in the double Dvl mutants, suggesting that low Dvl levels are sufficient for functional canonical Wnt signals.", "In summary, we demonstrate that Dvl3 is required for cardiac outflow tract development and describe its importance in the PCP pathway during neurulation and cochlea development.", "Finally, we establish several developmental processes in which the three Dvls are functionally redundant."], "structured": false}
{"doc_id": 323030, "title": "Dynamics of adherens junctions in epithelial establishment, maintenance, and remodeling", "abstract": ["The epithelial cadherin (E-cadherin)-catenin complex binds to cytoskeletal components and regulatory and signaling molecules to form a mature adherens junction (AJ).", "This dynamic structure physically connects neighboring epithelial cells, couples intercellular adhesive contacts to the cytoskeleton, and helps define each cell's apical-basal axis.", "Together these activities coordinate the form, polarity, and function of all cells in an epithelium.", "Several molecules regulate AJ formation and integrity, including Rho family GTPases and Par polarity proteins.", "However, only recently, with the development of live-cell imaging, has the extent to which E-cadherin is actively turned over at junctions begun to be appreciated.", "This turnover contributes to junction formation and to the maintenance of epithelial integrity during tissue homeostasis and remodeling."], "structured": false}
{"doc_id": 323335, "title": "Long-term outcome of patients with asystole induced by head-up tilt test.", "abstract": ["AIMS To analyse the long-term outcome of the largest reported cohort of patients presenting asystole during head-up tilt test.   \n", "METHODS AND RESULTS Since 1990, 1322 patients with syncope of unknown origin have undergone tilt-table testing.", "Of those, 330 patients (24 X 9%) presented an abnormal response (syncope or pre-syncope).", "Furthermore, 58 of those patients (17 X 5%) suffered a period of asystole (> or = 3000 ms) during the test.", "Asystole (median (interquartile range)) lasted 10 (4, 19 X 2) s (range 3-90).", "Two different protocols (angles) of tilting (Westminster (60 degrees) n=1124; isoproterenol (80 degrees) n=198)) influenced the time to the syncopal episode (13 (6 X 5, 20 X 5) vs 2 (1, 6 X 5) min, P=0,0005) but not the duration of the asystole.", "During this period, therapy for asystole featured three different stages: first patients were treated with pacemakers; later drug therapy (metoprolol and/or etilefrine) was recommended; lastly (from 1995), no specific treatment was given.", "In a cohort age- and gender-matched study, those patients without were compared to those with asystole in a 2:1 basis.", "During 40 X 7 months of follow-up (17 X 7, 66 X 8), 12 patients (20 X 6%) with asystole had syncopal recurrences.", "Furthermore, 34 patients (28 X 8%) without asystole presented syncopal episodes during a follow-up of 51 X 6 months (29 X 3, 73 X 1) (P=ns).", "The Kaplan-Meier analysis in patients with and without asystole showed a mean time free of recurrence of 92 X 6 +/-", "6 months vs 82 X 6 +/-", "4 X 7 months (P=ns).", "The previous number of syncopes had a significant relationship with recurrences (P=0 X 002), but not therapy.", "There were no cardiac related deaths.   \n", "CONCLUSIONS (1) Asystole during head-up tilt test does not imply a malignant outcome and syncope recurrence is low; (2) pacemaker or drug therapy do not significantly influence outcome which correlates to the previous number of syncopal episodes but not to gender, age, asystole occurrence, asystole duration and timing to asystole during head-up tilt test; (3) tilting protocol (angle) might influence time to and incidence of asystole during head-up tilt test."], "structured": true}
{"doc_id": 327319, "title": "ZINC 15 \u2013 Ligand Discovery for Everyone", "abstract": ["Many questions about the biological activity and availability of small molecules remain inaccessible to investigators who could most benefit from their answers.", "To narrow the gap between chemoinformatics and biology, we have developed a suite of ligand annotation, purchasability, target, and biology association tools, incorporated into ZINC and meant for investigators who are not computer specialists.", "The new version contains over 120 million purchasable \"drug-like\" compounds--effectively all organic molecules that are for sale--a quarter of which are available for immediate delivery.", "ZINC connects purchasable compounds to high-value ones such as metabolites, drugs, natural products, and annotated compounds from the literature.", "Compounds may be accessed by the genes for which they are annotated as well as the major and minor target classes to which those genes belong.", "It offers new analysis tools that are easy for nonspecialists yet with few limitations for experts.", "ZINC retains its original 3D roots--all molecules are available in biologically relevant, ready-to-dock formats.", "ZINC is freely available at http://zinc15.docking.org."], "structured": false}
{"doc_id": 335029, "title": "Condensin-mediated remodeling of the mitotic chromatin landscape in fission yeast", "abstract": ["The eukaryotic genome consists of DNA molecules far longer than the cells that contain them.", "They reach their greatest compaction during chromosome condensation in mitosis.", "This process is aided by condensin, a structural maintenance of chromosomes (SMC) family member.", "The spatial organization of mitotic chromosomes and how condensin shapes chromatin architecture are not yet fully understood.", "Here we use chromosome conformation capture (Hi-C) to study mitotic chromosome condensation in the fission yeast Schizosaccharomyces pombe.", "This showed that the interphase landscape characterized by small chromatin domains is replaced by fewer but larger domains in mitosis.", "Condensin achieves this by setting up longer-range, intrachromosomal DNA interactions, which compact and individualize chromosomes.", "At the same time, local chromatin contacts are constrained by condensin, with profound implications for local chromatin function during mitosis.", "Our results highlight condensin as a major determinant that changes the chromatin landscape as cells prepare their genomes for cell division."], "structured": false}
{"doc_id": 341324, "title": "Efficacy of the 6-month thrice-weekly regimen in the treatment of new sputum smear-positive pulmonary tuberculosis under clinical trial conditions.", "abstract": ["BACKGROUND Under the Revised National Tuberculosis Control Programme of India, patients with new smear-positive pulmonary tuberculosis are treated with a thrice-weekly regimen of antitubercular drugs (2H(3)R(3)Z(3)E(3)/4H(3)R(3) [H isoniazid, R rifampicin, Z pyrazinamide and E ethambutol]) for 6 months.", "We conducted a retrospective analysis of the efficacy andtolerability of this regimen under clinical trial conditions in HIV-negative patients with newly diagnosed smear-positive pulmonary tuberculosis.   \n", "METHODS We retrospectively analysed the data on patients assigned to the control regimen (2H (3)R(3)Z(3)E(3)/4H(3)R(3)) in two clinical trials during 2001-06 at the National Institute for Research in Tuberculosis, Chennai, India.   \n", "RESULTS Of the 268 patients treated with this regimen, data for efficacy analysis were available for 249.", "At the end of treatment, of 249 patients, 238 (96%) had a favourable status.", "Treatment failure occurred in the remaining 11: 7 in whom the organisms were initially drug-susceptible and 4 with initial drug resistance.", "Of the 238 patients who had a favourable status at the end of treatment, 14 (6%) had recurrence of tuberculosis during the following 24 months.", "In the intention-to-treat analysis, 245 (94%) of 262 patients had a favourable status at the end of treatment.", "Of the 28 patients with initial drug resistance, 24 (86%) had a favourable outcome.", "Only 4 of these 24 patients were found to have recurrence of tuberculosis in 2 years of follow-up.", "Among the 221 patients initially infected with drug-susceptible organisms, drug resistance did not develop in any of the 7 patients in whom the treatment failed or the 10 who had recurrence of tuberculosis.", "Further, 5 of the 7 patients in whom the treatment failed continued to excrete drug-susceptible bacilli at 6 months.", "Adverse drug reactions were observed in 38 (14%) of the 262 patients.", "Only 3 (1.1%) needed a modification in the treatment.   \n", "CONCLUSION This thrice-weekly 6-month regimen of antitubercular drugs, when administered under full supervision, is associated with a high rate of favourable treatment outcomes in HIV-negative patients with newly diagnosed sputum smearpositive pulmonary tuberculosis.", "There are few adverse drug reactions in these patients."], "structured": true}
{"doc_id": 343052, "title": "Curcumin attenuates inflammatory response in IL-1beta-induced human synovial fibroblasts and collagen-induced arthritis in mouse model.", "abstract": ["Curcumin, a major component of turmeric, has been shown to exhibit anti-oxidant and anti-inflammatory activities.", "The present study was performed to determine whether curcumin is efficacious against both collagen-induced arthritis (CIA) in mice and IL-1beta-induced activation in fibroblast-like synoviocytes (FLSs).", "DBA/1 mice were immunized with bovine type II collagen (CII) and treated with curcumin every other day for 2weeks after the initial immunization.", "For arthritis, we evaluated the incidence of disease and used an arthritis index based on paw thickness.", "In vitro proliferation of CII- or concanavalin A-induced splenic T cells was examined using IFN-gamma production.", "Pro-inflammatory cytokines TNF-alpha and IL-1beta were examined in the mouse ankle joint and serum IgG1 and IgG2a isotypes were analyzed.", "The expression levels of prostaglandin E(2) (PGE(2)), cyclooxygenase-2 (COX-2), and matrix metalloproteinases (MMPs) in human FLSs were also determined.", "The results showed that compared with untreated CIA mice, curcumin-treated mice downregulated clinical arthritis score, the proliferation of splenic T cells, expression levels of TNF-alpha and IL-1beta in the ankle joint, and expression levels of IgG2a in serum.", "Additionally, by altering nuclear factor (NF)-kappaB transcription activity in FLSs, curcumin inhibited PGE(2) production, COX-2 expression, and MMP secretion.", "These results suggest that curcumin can effectively suppress inflammatory response by inhibiting pro-inflammatory mediators and regulating humoral and cellular immune responses."], "structured": false}
{"doc_id": 344240, "title": "Loss of IGF-IEa or IGF-IEb impairs myogenic differentiation.", "abstract": ["Actions of protein products resulting from alternative splicing of the Igf1 gene have received increasing attention in recent years.", "However, the significance and functional relevance of these observations remain poorly defined.", "To address functions of IGF-I splice variants, we examined the impact of loss of IGF-IEa and IGF-IEb on the proliferation and differentiation of cultured mouse myoblasts.", "RNA interference-mediated reductions in total IGF-I, IGF-IEa alone, or IGF-IEb alone had no effect on cell viability in growth medium.", "However, cells deficient in total IGF-I or IGF-IEa alone proliferated significantly slower than control cells or cells deficient in IGF-IEb in serum-free media.", "Simultaneous loss of both or specific loss of either splice variant significantly inhibited myosin heavy chain (MyHC) immunoreactivity by 70-80% (P < 0.01) under differentiation conditions (48 h in 2% horse serum) as determined by Western immunoblotting.", "This loss in protein was associated with reduced MyHC isoform mRNAs, because reductions in total IGF-I or IGF-IEa mRNA significantly reduced MyHC mRNAs by approximately 50-75% (P < 0.05).", "Loss of IGF-IEb also reduced MyHC isoform mRNA significantly, with the exception of Myh7, but to a lesser degree (\u223c20-40%, P < 0.05).", "Provision of mature IGF-I, but not synthetic E peptides, restored Myh3 expression to control levels in cells deficient in IGF-IEa or IGF-IEb.", "Collectively, these data suggest that IGF-I splice variants may regulate myoblast differentiation through the actions of mature IGF-I and not the E peptides."], "structured": false}
{"doc_id": 350542, "title": "Antimicrobial peptide pleurocidin synergizes with antibiotics through hydroxyl radical formation and membrane damage, and exerts antibiofilm activity.", "abstract": ["BACKGROUND Pleurocidin, a 25-mer antimicrobial peptide (AMP), is known to exert bactericidal activity.", "However, the synergistic activity and mechanism(s) of pleurocidin in combination with conventional antibiotics, and the antibiofilm effect of the peptide are poorly understood.   \n", "METHODS The interaction between pleurocidin and antibiotics was evaluated using checkerboard assay.", "To study the mechanism(s) involved in their synergism, we detected hydroxyl radical formation using 3'-(p-hydroxyphenyl) fluorescein, measured the NAD(+)/NADH ratio by NAD(+) cycling assay, observed change in bacterial viability with the hydroxyl radical scavenger thiourea, and investigated cytoplasmic membrane damage using propidium iodide.", "Also, the antibiofilm effect of pleurocidin was examined with the tissue culture plate method.   \n", "RESULTS All combinations of pleurocidin and antibiotics showed synergistic interaction against bacterial strains (fractional inhibitory concentration index (FICI)\u22640.5) except for Enterococcus faecium treated with a combination of the peptide and ampicillin (FICI=0.75).", "We identified that pleurocidin alone and in combinations with antibiotics induced formation of hydroxyl radicals.", "The oxidative stress was caused by a transient NADH depletion and the addition of thiourea prevented bacterial death, especially in the case of the combined treatment of pleurocidin and ampicillin showing synergisms.", "The combination of pleurocidin and erythromycin increased permeability of bacterial cytoplasmic membrane.", "Additionally, pleurocidin exhibited a potent inhibitory effect on preformed biofilm of bacterial organisms.", "In conclusion, pleurocidin synergized with antibiotics through hydroxyl radical formation and membrane-active mechanism, and exerted antibiofilm activity.   ", "GENERAL SIGNIFICANCE The synergistic effect between pleurocidin and antibiotics suggests the AMP is a potential therapeutic agent and adjuvant for antimicrobial chemotherapy."], "structured": true}
{"doc_id": 356218, "title": "Outcome of pregnancy in women with moderate or severe renal insufficiency.", "abstract": ["BACKGROUND Pregnant women with mild preexisting renal disease have relatively few complications of pregnancy, but the risks of maternal and obstetrical complications in women with moderate or severe renal insufficiency remain uncertain.   \n", "METHODS We determined the frequency and types of maternal and obstetrical complications and the outcomes of pregnancy in 67 women with primary renal disease (82 pregnancies).", "All the women had initial serum creatinine concentrations of at least 1.4 mg per deciliter (124 mumol per liter) and gestations that continued beyond the first trimester.   \n", "RESULTS The mean (+/-", "SD) serum creatinine concentration increased from 1.9 +/-", "0.8 mg per deciliter (168 +/-", "71 mumol per liter) in early pregnancy to 2.5 +/-", "1.3 mg per deciliter (221 +/-", "115 mumol per liter) in the third trimester.", "The frequency of hypertension rose from 28 percent at base line to 48 percent in the third trimester, and that of high-grade proteinuria (urinary protein excretion, > 3000 mg per liter) from 23 percent to 41 percent.", "For the 70 pregnancies (57 women) for which data were available during pregnancy and immediately post partum, pregnancy-related loss of maternal renal function occurred in 43 percent.", "Eight of these pregnancies (10 percent of the total) were associated with rapid acceleration of maternal renal insufficiency.", "Obstetrical complications included a high rate of preterm delivery (59 percent) and growth retardation (37 percent).", "The infant survival rate was 93 percent.   \n", "CONCLUSIONS Among pregnant women with moderate or severe renal insufficiency, the rates of complications due to worsening renal function, hypertension, and obstetrical complications are increased, but fetal survival is high."], "structured": true}
{"doc_id": 364522, "title": "High-mobility group box-1 protein induces osteogenic phenotype changes in aortic valve interstitial cells.", "abstract": ["OBJECTIVES Calcific aortic valve (AV) disease is known to be an inflammation-related process.", "High-mobility group box-1 (HMGB1) protein and Toll-like receptor 4 (TLR4) have been reported to participate in several inflammatory diseases.", "The purpose of the present study was to determine whether the HMGB1-TLR4 axis is involved in calcific AV disease, and to evaluate the effect of HMGB1, and its potential mechanisms, on the pro-osteogenic phenotype change of valvular interstitial cells (VICs).   \n", "METHODS Expression of HMGB1 and TLR4 in human calcific AVs was evaluated using immunohistochemical staining and immunoblotting.", "Cultured VICs were used as an in vitro model.", "The VICs were stimulated with HMGB1 for analysis, with versus without TLR4 small interfering ribonucleic acid (siRNA), c-Jun N-terminal kinase mitogen-activated protein kinase (JNK MAPK), and nuclear factor kappa-B (NF-\u03baB) inhibitors.   \n", "RESULTS Enhanced accumulation of HMGB1 and TLR4 was observed in calcific valves.", "Moreover, we found that HMGB1 induced high levels of pro-inflammatory cytokine production and promoted the osteoblastic differentiation and calcification of VICs.", "In addition, HMGB1 induced phosphorylation of JNK MAPK and NF-\u03baB. However, these effects were markedly suppressed by siRNA silencing of TLR4.", "In addition, blockade of JNK MAPK and NF-\u03baB phosphorylation prohibited HMGB1-induced production of pro-osteogenic factors, and mineralization of VICs.   \n", "CONCLUSIONS The HMGB1 protein may promote osteoblastic differentiation and calcification of VICs, through the TLR4-JNK-NF-\u03baB signaling pathway."], "structured": true}
{"doc_id": 365896, "title": "RiboSys, a high-resolution, quantitative approach to measure the in vivo kinetics of pre-mRNA splicing and 3'-end processing in Saccharomyces cerevisiae.", "abstract": ["We describe methods for obtaining a quantitative description of RNA processing at high resolution in budding yeast.", "As a model gene expression system, we constructed tetON (for induction studies) and tetOFF (for repression, derepression, and RNA degradation studies) yeast strains with a series of reporter genes integrated in the genome under the control of a tetO7 promoter.", "Reverse transcription and quantitative real-time-PCR (RT-qPCR) methods were adapted to allow the determination of mRNA abundance as the average number of copies per cell in a population.", "Fluorescence in situ hybridization (FISH) measurements of transcript numbers in individual cells validated the RT-qPCR approach for the average copy-number determination despite the broad distribution of transcript levels within a population of cells.", "In addition, RT-qPCR was used to distinguish the products of the different steps in splicing of the reporter transcripts, and methods were developed to map and quantify 3'-end cleavage and polyadenylation.", "This system permits pre-mRNA production, splicing, 3'-end maturation and degradation to be quantitatively monitored with unprecedented kinetic detail, suitable for mathematical modeling.", "Using this approach, we demonstrate that reporter transcripts are spliced prior to their 3'-end cleavage and polyadenylation, that is, cotranscriptionally."], "structured": false}
{"doc_id": 368506, "title": "Generation of mice with a conditional allele for the p75(NTR) neurotrophin receptor gene.", "abstract": ["The p75(NTR) neurotrophin receptor has been implicated in multiple biological and pathological processes.", "While significant advances have recently been made in understanding the physiologic role of p75(NTR) , many details and aspects remain to be determined.", "This is in part because the two existing knockout mouse models (Exons 3 or 4 deleted, respectively), both display features that defy definitive conclusions.", "Here we describe the generation of mice that carry a conditional p75(NTR) (p75(NTR-FX) ) allele made by flanking Exons 4-6, which encode the transmembrane and all cytoplasmic domains, by loxP sites.", "To validate this novel conditional allele, both neural crest-specific p75(NTR) /Wnt1-Cre mutants and conventional p75(NTR) null mutants were generated.", "Both mutants displayed abnormal hind limb reflexes, implying that loss of p75(NTR) in neural crest-derived cells causes a peripheral neuropathy similar to that seen in conventional p75(NTR) mutants.", "This novel conditional p75(NTR) allele will offer new opportunities to investigate the role of p75(NTR) in specific tissues and cells."], "structured": false}
{"doc_id": 371289, "title": "A Triple-Stain Flow Cytometric Method to Assess Plasma- and Acrosome-Membrane Integrity of Cryopreserved Bovine Sperm Immediately after Thawing in Presence of Egg-Yolk Particles1", "abstract": ["Abstract Simultaneously evaluating postthaw viability and acrosome integrity of spermatozoa by flow cytometry would provide a valuable testing tool in both research and routine work.", "In the present study, a new triple-stain combination was developed for the simultaneous evaluation of viability and acrosome integrity of bovine sperm processed in egg yolk-based extender by flow cytometer.", "SYBR-14 and propidium iodide (PI) enabled the discrimination of sperm cells from egg yolk and debris particles, which was instrumental for the flow cytometric analyses of frozen-thawed bovine sperm, because it implied that washing steps to remove egg yolk were no longer required.", "In addition, phycoerythrin-conjugated peanut agglutinin (PE-PNA) was used to discriminate acrosome-damaged/reacted sperm cells from acrosome-intact cells.", "Repeatability was calculated using two processed ejaculates of 10 bulls.", "Three straws per batch were analyzed in duplicate measurements.", "Method-agreement analysis between the SYBR-14/PE-PNA/PI and fluorescein isothiocyanate (FITC)-conjugated PNA was performed, with FITC-PNA/PI staining being carried out on 14 frozen-thawed semen samples immediately after thawing and after a 3-h incubation at 37\u00b0C.", "The British Standards Institution repeatability index of the SYBR-14/PE-PNA/PI combination was 2.6%.", "On average, the FITC-PNA/PI method showed a 6.3% overestimation of the live and acrosome-intact sperm cell subpopulation.", "In conclusion, the new triple-stain combination is highly repeatable and easy to use in routine application, and it provides a more precise estimate for the rate of sperm cells with intact head membrane and acrosome compared to the generally used and validated FITC-PNA/PI staining."], "structured": false}
{"doc_id": 374902, "title": "Universal voluntary HIV testing with immediate antiretroviral therapy as a strategy for elimination of HIV transmission: a mathematical model.", "abstract": ["BACKGROUND Roughly 3 million people worldwide were receiving antiretroviral therapy (ART) at the end of 2007, but an estimated 6.7 million were still in need of treatment and a further 2.7 million became infected with HIV in 2007.", "Prevention efforts might reduce HIV incidence but are unlikely to eliminate this disease.", "We investigated a theoretical strategy of universal voluntary HIV testing and immediate treatment with ART, and examined the conditions under which the HIV epidemic could be driven towards elimination.   \n", "METHODS We used mathematical models to explore the effect on the case reproduction number (stochastic model) and long-term dynamics of the HIV epidemic (deterministic transmission model) of testing all people in our test-case community (aged 15 years and older) for HIV every year and starting people on ART immediately after they are diagnosed HIV positive.", "We used data from South Africa as the test case for a generalised epidemic, and assumed that all HIV transmission was heterosexual.   \n", "FINDINGS The studied strategy could greatly accelerate the transition from the present endemic phase, in which most adults living with HIV are not receiving ART, to an elimination phase, in which most are on ART, within 5 years.", "It could reduce HIV incidence and mortality to less than one case per 1000 people per year by 2016, or within 10 years of full implementation of the strategy, and reduce the prevalence of HIV to less than 1% within 50 years.", "We estimate that in 2032, the yearly cost of the present strategy and the theoretical strategy would both be US$1.7 billion; however, after this time, the cost of the present strategy would continue to increase whereas that of the theoretical strategy would decrease.   \n", "INTERPRETATION Universal voluntary HIV testing and immediate ART, combined with present prevention approaches, could have a major effect on severe generalised HIV/AIDS epidemics.", "This approach merits further mathematical modelling, research, and broad consultation."], "structured": true}
{"doc_id": 380526, "title": "Common variants in DGKK are strongly associated with risk of hypospadias", "abstract": ["Hypospadias is a common congenital malformation of the male external genitalia.", "We performed a genome-wide association study using pooled DNA from 436 individuals with hypospadias (cases) and 494 controls of European descent and selected the highest ranked SNPs for individual genotyping in the discovery sample, an additional Dutch sample of 133 cases and their parents, and a Swedish series of 266 cases and 402 controls.", "Individual genotyping of two SNPs (rs1934179 and rs7063116) in DGKK, encoding diacylglycerol kinase \u03ba, produced compelling evidence for association with hypospadias in the discovery sample (allele-specific odds ratio (OR) = 2.5, P = 2.5 \u00d7 10\u221211 and OR = 2.3, P = 2.9 \u00d7 10\u22129, respectively) and in the Dutch (OR = 3.9, P = 2.4 \u00d7 10\u22125 and OR = 3.8, P = 3.4 \u00d7 10\u22125) and Swedish (OR = 2.5, P = 2.6 \u00d7 10\u22128 and OR = 2.2, P = 2.7 \u00d7 10\u22126) replication samples.", "Expression studies showed expression of DGKK in preputial tissue of cases and controls, which was lower in carriers of the risk allele of rs1934179 (P = 0.047).", "We propose DGKK as a major risk gene for hypospadias."], "structured": false}
{"doc_id": 381602, "title": "Neutrophils Suppress Intraluminal NK Cell-Mediated Tumor Cell Clearance and Enhance Extravasation of Disseminated Carcinoma Cells.", "abstract": ["UNLABELLED Immune cells promote the initial metastatic dissemination of carcinoma cells from primary tumors.", "In contrast to their well-studied functions in the initial stages of metastasis, the specific roles of immunocytes in facilitating progression through the critical later steps of the invasion-metastasis cascade remain poorly understood.", "Here, we define novel functions of neutrophils in promoting intraluminal survival and extravasation at sites of metastatic dissemination.", "We show that CD11b(+)/Ly6G(+) neutrophils enhance metastasis formation via two distinct mechanisms.", "First, neutrophils inhibit natural killer cell function, which leads to a significant increase in the intraluminal survival time of tumor cells.", "Thereafter, neutrophils operate to facilitate extravasation of tumor cells through the secretion of IL1\u03b2 and matrix metalloproteinases.", "These results identify neutrophils as key regulators of intraluminal survival and extravasation through their cross-talk with host cells and disseminating carcinoma cells.   ", "SIGNIFICANCE This study provides important insights into the systemic contributions of neutrophils to cancer metastasis by identifying how neutrophils facilitate intermediate steps of the invasion-metastasis cascade.", "We demonstrate that neutrophils suppress natural killer cell activity and increase extravasation of tumor cells.", "Cancer Discov; 6(6); 630-49.", "\u00a92016 AACR.This article is highlighted in the In This Issue feature, p. 561."], "structured": false}
{"doc_id": 393001, "title": "High Km soluble 5'-nucleotidase from human placenta. Properties and allosteric regulation by IMP and ATP.", "abstract": ["A human placental soluble \"high Km\" 5'-nucleotidase has been separated from \"low Km\" 5'-nucleotidase and nonspecific phosphatase by AMP-Sepharose affinity chromatography.", "The enzyme was purified 8000-fold to a specific activity of 25.6 mumol/min/mg.", "The subunit molecular mass is 53 kDa, and the native molecular mass is 210 kDa, suggesting a tetrameric structure.", "Soluble high Km 5'-nucleotidase is most active with IMP and GMP and their deoxy derivatives.", "IMP is hydrolyzed 15 times faster than AMP.", "The enzyme has a virtually absolute requirement for magnesium ions and is regulated by them.", "Purine nucleoside 5'-triphosphates strongly activate the enzyme with the potency order dATP greater than ATP greater than GTP.", "2,3-Diphosphoglycerate activates the enzyme as potently as ATP.", "Three millimolar ATP decreased the Km for IMP from 0.33 to 0.09 mM and increased the Vmax 12-fold.", "ATP activation was modified by the IMP concentration.", "At 20 microM IMP the ATP-dependent activation curve was sigmoidal, while at 2 mM IMP it was hyperbolic.", "The A0.5 values for ATP were 2.26 and 0.70 mM, and the relative maximal velocities were 32.9 and 126.0 nmol/min, respectively.", "Inorganic phosphate shifts the hyperbolic substrate velocity relationship for IMP to a sigmoidal one.", "With physiological concentrations of cofactors (3 mM ATP, 1-4 mM Pi, 150 mM KCl) at pH 7.4, the enzyme is 25-35 times more active toward 100 microM IMP than 100 microM AMP.", "These data show that: (a) soluble human placental high Km 5'-nucleotidase coexists in human placenta with the low Km enzyme; (b) under physiological conditions the enzyme favors the hydrolysis of IMP and is critically regulated by IMP, ATP, and Pi levels; and (c) kinetic properties of ATP and IMP are each modified by the other compound suggesting complex interaction of the associated binding sites."], "structured": false}
{"doc_id": 406733, "title": "Histones are incorporated in trans during reassembly of the yeast PHO5 promoter.", "abstract": ["In yeast, remodeling of PHO5 promoter chromatin upon activation is accompanied by transient hyperacetylation and subsequent eviction of histones from the promoter in trans.", "In the course of rerepression, nucleosomes have to be reassembled on the promoter.", "We have analyzed where the histones for reassembly of the inactive promoter chromatin come from.", "The use of a strain with two differently tagged and differently regulated versions of histone H3 allowed us to discriminate between histones originating from the chromatin fraction and histones arising from the soluble histone pool.", "In this way, we show that the incorporated histones originate from a source in trans.", "Promoter closure occurs very rapidly, and the histone chaperones Asf1 and Hir1 as well as the SWI/SNF nucleosome remodeling complex appear to be important for rapid reassembly of nucleosomes at the PHO5 promoter."], "structured": false}
{"doc_id": 409280, "title": "National study of physician awareness and adherence to cardiovascular disease prevention guidelines.", "abstract": ["BACKGROUND Few data have evaluated physician adherence to cardiovascular disease (CVD) prevention guidelines according to physician specialty or patient characteristics, particularly gender.   \n", "METHODS AND RESULTS An online study of 500 randomly selected physicians (300 primary care physicians, 100 obstetricians/gynecologists, and 100 cardiologists) used a standardized questionnaire to assess awareness of, adoption of, and barriers to national CVD prevention guidelines by specialty.", "An experimental case study design tested physician accuracy and determinants of CVD risk level assignment and application of guidelines among high-, intermediate-, or low-risk patients.", "Intermediate-risk women, as assessed by the Framingham risk score, were significantly more likely to be assigned to a lower-risk category by primary care physicians than men with identical risk profiles (P<0.0001), and trends were similar for obstetricians/gynecologists and cardiologists.", "Assignment of risk level significantly predicted recommendations for lifestyle and preventive pharmacotherapy.", "After adjustment for risk assignment, the impact of patient gender on preventive care was not significant except for less aspirin (P<0.01) and more weight management recommended (P<0.04) for intermediate-risk women.", "Physicians did not rate themselves as very effective in their ability to help patients prevent CVD.", "Fewer than 1 in 5 physicians knew that more women than men die each year from CVD.   \n", "CONCLUSIONS Perception of risk was the primary factor associated with CVD preventive recommendations.", "Gender disparities in recommendations for preventive therapy were explained largely by the lower perceived risk despite similar calculated risk for women versus men.", "Educational interventions for physicians are needed to improve the quality of CVD preventive care and lower morbidity and mortality from CVD for men and women."], "structured": true}
{"doc_id": 410286, "title": "TECHNICAL ADVANCE Floral dip: a simplified method for Agrobacterium-mediated", "abstract": ["The Agrobacterium vacuum infiltration method has made it possible to transform Arabidopsis thaliana without plant tissue culture or regeneration.", "In the present study, this method was evaluated and a substantially modified transformation method was developed.", "The labor-intensive vacuum infiltration process was eliminated in favor of simple dipping of developing floral tissues into a solution containing Agrobacterium tumefaciens, 5% sucrose and 500 microliters per litre of surfactant Silwet L-77.", "Sucrose and surfactant were critical to the success of the floral dip method.", "Plants inoculated when numerous immature floral buds and few siliques were present produced transformed progeny at the highest rate.", "Plant tissue culture media, the hormone benzylamino purine and pH adjustment were unnecessary, and Agrobacterium could be applied to plants at a range of cell densities.", "Repeated application of Agrobacterium improved transformation rates and overall yield of transformants approximately twofold.", "Covering plants for 1 day to retain humidity after inoculation also raised transformation rates twofold.", "Multiple ecotypes were transformable by this method.", "The modified method should facilitate high-throughput transformation of Arabidopsis for efforts such as T-DNA gene tagging, positional cloning, or attempts at targeted gene replacement."], "structured": false}
{"doc_id": 418246, "title": "Pathway connectivity and signaling coordination in the yeast stress-activated signaling network", "abstract": ["Stressed cells coordinate a multi-faceted response spanning many levels of physiology.", "Yet knowledge of the complete stress-activated regulatory network as well as design principles for signal integration remains incomplete.", "We developed an experimental and computational approach to integrate available protein interaction data with gene fitness contributions, mutant transcriptome profiles, and phospho-proteome changes in cells responding to salt stress, to infer the salt-responsive signaling network in yeast.", "The inferred subnetwork presented many novel predictions by implicating new regulators, uncovering unrecognized crosstalk between known pathways, and pointing to previously unknown 'hubs' of signal integration.", "We exploited these predictions to show that Cdc14 phosphatase is a central hub in the network and that modification of RNA polymerase II coordinates induction of stress-defense genes with reduction of growth-related transcripts.", "We find that the orthologous human network is enriched for cancer-causing genes, underscoring the importance of the subnetwork's predictions in understanding stress biology."], "structured": false}
{"doc_id": 427082, "title": "Premigratory and migratory neural crest cells are multipotent in vivo.", "abstract": ["The neural crest (NC) is an embryonic stem/progenitor cell population that generates a diverse array of cell lineages, including peripheral neurons, myelinating Schwann cells, and melanocytes, among others.", "However, there is a long-standing controversy as to whether this broad developmental perspective reflects in vivo multipotency of individual NC cells or whether the NC is comprised of a heterogeneous mixture of lineage-restricted progenitors.", "Here, we resolve this controversy by performing in vivo fate mapping of single trunk NC cells both at premigratory and migratory stages using the R26R-Confetti mouse model.", "By combining quantitative clonal analyses with definitive markers of differentiation, we demonstrate that the vast majority of individual NC cells are multipotent, with only few clones contributing to single derivatives.", "Intriguingly, multipotency is maintained in migratory NC cells.", "Thus, our findings provide definitive evidence for the in vivo multipotency of both premigratory and migrating NC cells in the mouse."], "structured": false}
{"doc_id": 427865, "title": "Implementing the ESHRE 'poor responder' criteria in research studies: methodological implications.", "abstract": ["The Bologna criteria for defining poor ovarian response (POR) during IVF provide a useful template for new research in this field of assisted conception.", "However, designing studies around the European Society for Human Reproduction and Embryology POR criteria can be methodologically challenging, as the new definition includes various POR subpopulations with diverse baseline characteristics and unknown clinical prognosis.", "When designing RCTs, potential result bias may be introduced if women from each subpopulation are not evenly allocated between intervention groups.", "In the case of small or moderate-size RCTs, a single-sequence randomization method may not ensure balanced allocation between groups.", "Stratified randomization methods provide an alternative methodological approach.", "Depending on the chosen methodology, patient characteristics and outcomes within each intervention group may be better reported according to relevant subpopulations."], "structured": false}
{"doc_id": 432261, "title": "Generation of gene-edited rats by delivery of CRISPR/Cas9 protein and donor DNA into intact zygotes using electroporation", "abstract": ["The generation of gene-edited animals using the CRISPRs/Cas9 system is based on microinjection into zygotes which is inefficient, time consuming and demands high technical skills.", "We report the optimization of an electroporation method for intact rat zygotes using sgRNAs and Cas9 protein in combination or not with ssODNs (~100 nt).", "This resulted in high frequency of knockouts, between 15 and 50% of analyzed animals.", "Importantly, using ssODNs as donor template resulted in precise knock-in mutations in 25-100% of analyzed animals, comparable to microinjection.", "Electroporation of long ssDNA or dsDNA donors successfully used in microinjection in the past did not allow generation of genome-edited animals despite dsDNA visualization within zygotes.", "Thus, simultaneous electroporation of a large number of intact rat zygotes is a rapid, simple, and efficient method for the generation of a variety of genome-edited rats."], "structured": false}
{"doc_id": 435529, "title": "Uridylation of miRNAs by HEN1 SUPPRESSOR1 in Arabidopsis", "abstract": ["HEN1-mediated 2'-O-methylation has been shown to be a key mechanism to protect plant microRNAs (miRNAs) and small interfering RNAs (siRNAs) as well as animal piwi-interacting RNAs (piRNAs) from degradation and 3' terminal uridylation [1-8].", "However, enzymes uridylating unmethylated miRNAs, siRNAs, or piRNAs in hen1 are unknown.", "In this study, a genetic screen identified a second-site mutation hen1 suppressor1-2 (heso1-2) that partially suppresses the morphological phenotypes of the hypomorphic hen1-2 allele and the null hen1-1 allele in Arabidopsis.", "HESO1 encodes a terminal nucleotidyl transferase that prefers to add untemplated uridine to the 3' end of RNA, which is completely abolished by 2'-O-methylation.", "heso1-2 affects the profile of u-tailed miRNAs and siRNAs and increases the abundance of truncated and/or normal sized ones in hen1, which often results in increased total amount of miRNAs and siRNAs in hen1.", "In contrast, overexpressing HESO1 in hen1-2 causes more severe morphological defects and less accumulation of miRNAs.", "These results demonstrate that HESO1 is an enzyme uridylating unmethylated miRNAs and siRNAs in hen1.", "These observations also suggest that uridylation may destabilize unmethylated miRNAs through an unknown mechanism and compete with 3'-to-5' exoribonuclease activities in hen1.", "This study shall have implications on piRNA uridylation in hen1 in animals."], "structured": false}
{"doc_id": 437924, "title": "Pre-Exposure Prophylaxis to Prevent HIV Infection: Current Status, Future Opportunities and Challenges", "abstract": ["As the global incidence of HIV exceeds 2 million new infections annually, effective interventions to decrease HIV transmission are needed.", "Randomized, placebo-controlled studies have demonstrated that daily oral antiretroviral pre-exposure prophylaxis (PrEP) with a fixed-dose combination tablet containing tenofovir disoproxil fumarate and emtricitabine can significantly reduce HIV incidence among diverse at-risk populations.", "In these studies, the efficacy of PrEP was correlated with levels of adherence.", "Official guidelines recommend provision of PrEP to people at greatest risk of HIV acquisition, and demonstration projects suggest that high levels of uptake and adherence are possible outside of controlled studies.", "However, several potential barriers to implementing PrEP remain.", "These challenges include low awareness and utilization of PrEP by at-risk individuals, uncertainty about adherence in \u2018real-world\u2019 settings, the majority of healthcare providers being untrained in PrEP provision, limited data about potential adverse effects from long-term use of tenofovir\u2013emtricitabine, high costs of PrEP medications, and stigma associated with PrEP use and the behaviors that would warrant PrEP.", "Innovative pharmacologic chemoprophylactic approaches could provide solutions to some of these challenges.", "Less-than-daily oral dosing regimens and long-acting injectable medications could reduce pill burdens and facilitate adherence, and local delivery of PrEP medications to genital compartments via gels, rings and films may limit systemic drug exposure and potential toxicities.", "As the portfolio of chemoprophylactic agents and delivery systems expands to meet the diverse sexual health needs and product preferences of individuals who may benefit from PrEP, it is hoped that antiretroviral chemoprophylaxis could become an acceptable, feasible, and highly effective addition to existing HIV prevention strategies."], "structured": false}
{"doc_id": 439670, "title": "Prepregnancy BMI and the risk of gestational diabetes: a systematic review of the literature with meta-analysis.", "abstract": ["The objective of this study is to assess and quantify the risk for gestational diabetes mellitus (GDM) according to prepregnancy maternal body mass index (BMI).", "The design is a systematic review of observational studies published in the last 30 years.", "Four electronic databases were searched for publications (1977-2007).", "BMI was elected as the only measure of obesity, and all diagnostic criteria for GDM were accepted.", "Studies with selective screening for GDM were excluded.", "There were no language restrictions.", "The methodological quality of primary studies was assessed.", "Some 1745 citations were screened, and 70 studies (two unpublished) involving 671 945 women were included (59 cohorts and 11 case-controls).", "Most studies were of high or medium quality.", "Compared with women with a normal BMI, the unadjusted pooled odds ratio (OR) of an underweight woman developing GDM was 0.75 (95% confidence interval [CI] 0.69 to 0.82).", "The OR for overweight, moderately obese and morbidly obese women were 1.97 (95% CI 1.77 to 2.19), 3.01 (95% CI 2.34 to 3.87) and 5.55 (95% CI 4.27 to 7.21) respectively.", "For every 1 kg m(-2) increase in BMI, the prevalence of GDM increased by 0.92% (95% CI 0.73 to 1.10).", "The risk of GDM is positively associated with prepregnancy BMI.", "This information is important when counselling women planning a pregnancy."], "structured": false}
{"doc_id": 456304, "title": "Multiple risk behaviour: increasing socio-economic gap over time?", "abstract": ["BACKGROUND Unhealthy behaviours often occur in combination.", "In this study the relationship between education and lifestyle, defined as a cluster of risk behaviours, has been analysed with the purpose to assess socio-economic changes in multiple risk behaviour over time.   \n", "METHODS Cross-sectional data from the Belgian Health Interview Surveys 1997, 2001 and 2004 were analysed.", "This study is restricted to persons aged \u2265 15 years with information on those health behaviours and education (n = 7431, n = 8142 and n = 7459, respectively).", "A lifestyle index was created based on the sum of the four unhealthy behaviours: smokers vs. non-smokers, risky versus non-risky alcohol use, sedentaryness vs. physically active and poor vs. healthy diet.", "The lifestyle index was dichotomized as low (0-2) vs. high (3-4).", "For the assessment of socio-economic inequalities in multiple risk behaviour, summary measures as Odds Ratio (OR) and Relative Index of Inequality (RII) were calculated using logistic regression, stratified by sex.   \n", "RESULTS Of the adult population, 7.5% combined three to four unhealthy behaviours.", "Lower educated men are the most at risk.", "Besides, the OR among men significantly increased from 1.6 in 2001 to 3.4 in 2004 (P = 0.029).", "The increase of the OR among women was less pronounced.", "The RII, on the other hand, did not show any gradient, neither for men nor for women.   \n", "CONCLUSION Multiple risk behaviour is more common among lower educated people.", "An increasing polarization in socio-economic inequalities is assessed from 2001 to 2004 among men.", "Therefore, health promotion programmes should focus on the lower socio-economic classes and target risk behaviours simultaneously."], "structured": true}
{"doc_id": 457630, "title": "Variations and Trends in Health Burden of Visual Impairment Due to Cataract: A Global Analysis.", "abstract": ["Purpose To evaluate the global trends in health burden of people visually impaired from cataract in terms of disability-adjusted life years (DALY) and its correlations with national levels of socioeconomic development.   ", "Methods Global, regional, and national DALY numbers, crude rate, and age-standardized rate of cataract vision loss by age and sex were obtained from the database of the Global Burden of Disease Study 2015.", "The human development index, per capita gross domestic product, and other country-level data were derived from international open databases.", "Regression analysis was used to assess the correlations between age-standardized DALY rate and socioeconomic variables.   ", "Results The global DALY numbers of cataract vision loss increased by 89.42%, from 2048.18 (95%CI [confidence interval]: 1457.60-2761.80) thousands in 1990 to 3879.74 (95% CI: 2766.07-5232.43) thousands in 2015 (P < 0.001).", "Females had higher DALY number 315.83 (95%CI: 237.17-394.4) and crude rate 38.29 (95%CI: 35.35-41.23) after adjusting for age and country (all P < 0.001).", "The age-standardized DALY rate was higher in countries with low human development index (HDI), with 91.03 (95%CI: 73.04-108.75) for low HDI, 81.67 (95%CI: 53.24-108.82) for medium HDI, 55.89 (95%CI: 36.87-69.63) for high HDI, and 17.10 (95%CI: 13.91-26.84) for very high HDI countries (P < 0.01), respectively.", "The national age-standardized DALY rates in 2015 were negatively associated with both HDI (R2 = 0.489, P < 0.001) and per capita gross domestic product (R2 = 0.331, P < 0.001).", "Stepwise multiple regression showed that HDI was significantly correlated with national age-standardized DALY rates in 2015 after adjusting for other confounding factors (P < 0.001).   ", "Conclusions The global health burden of vision loss due to cataract increased between 1990 and 2015 despite considerable efforts from the World Health Organization and VISION 2020 initiatives."], "structured": false}
{"doc_id": 461550, "title": "Multiplex genome engineering using CRISPR/Cas systems.", "abstract": ["Functional elucidation of causal genetic variants and elements requires precise genome editing technologies.", "The type II prokaryotic CRISPR (clustered regularly interspaced short palindromic repeats)/Cas adaptive immune system has been shown to facilitate RNA-guided site-specific DNA cleavage.", "We engineered two different type II CRISPR/Cas systems and demonstrate that Cas9 nucleases can be directed by short RNAs to induce precise cleavage at endogenous genomic loci in human and mouse cells.", "Cas9 can also be converted into a nicking enzyme to facilitate homology-directed repair with minimal mutagenic activity.", "Lastly, multiple guide sequences can be encoded into a single CRISPR array to enable simultaneous editing of several sites within the mammalian genome, demonstrating easy programmability and wide applicability of the RNA-guided nuclease technology."], "structured": false}
{"doc_id": 463309, "title": "Transformation of intact yeast cells treated with alkali cations.", "abstract": ["Intact yeast cells treated with alkali cations took up plasmid DNA.", "Li+, Cs+, Rb+, K+, and Na+ were effective in inducing competence.", "Conditions for the transformation of Saccharomyces cerevisiae D13-1A with plasmid YRp7 were studied in detail with CsCl.", "The optimum incubation time was 1 h, and the optimum cell concentration was 5 x 10(7) cells per ml.", "The optimum concentration of Cs+ was 1.0 M. Transformation efficiency increased with increasing concentrations of plasmid DNA.", "Polyethylene glycol was absolutely required.", "Heat pulse and various polyamines or basic proteins stimulated the uptake of plasmid DNA.", "Besides circular DNA, linear plasmid DNA was also taken up by Cs+-treated yeast cells, although the uptake efficiency was considerably reduced.", "The transformation efficiency with Cs+ or Li+ was comparable with that of conventional protoplast methods for a plasmid containing ars1, although not for plasmids containing a 2 microns origin replication."], "structured": false}
{"doc_id": 463533, "title": "Health-Related Quality of Life as Measured with EQ-5D among Populations with and without Specific Chronic Conditions: A Population-Based Survey in Shaanxi Province, China", "abstract": ["INTRODUCTION The aim of this study was to examine health-related quality of life (HRQoL) as measured by EQ-5D and to investigate the influence of chronic conditions and other risk factors on HRQoL based on a distributed sample located in Shaanxi Province, China.   \n", "METHODS A multi-stage stratified cluster sampling method was performed to select subjects.", "EQ-5D was employed to measure the HRQoL. The likelihood that individuals with selected chronic diseases would report any problem in the EQ-5D dimensions was calculated and tested relative to that of each of the two reference groups.", "Multivariable linear regression models were used to investigate factors associated with EQ VAS.   \n", "RESULTS The most frequently reported problems involved pain/discomfort (8.8%) and anxiety/depression (7.6%).", "Nearly half of the respondents who reported problems in any of the five dimensions were chronic patients.", "Higher EQ VAS scores were associated with the male gender, higher level of education, employment, younger age, an urban area of residence, access to free medical service and higher levels of physical activity.", "Except for anemia, all the selected chronic diseases were indicative of a negative EQ VAS score.", "The three leading risk factors were cerebrovascular disease, cancer and mental disease.", "Increases in age, number of chronic conditions and frequency of physical activity were found to have a gradient effect.   \n", "CONCLUSION The results of the present work add to the volume of knowledge regarding population health status in this area, apart from the known health status using mortality and morbidity data.", "Medical, policy, social and individual attention should be given to the management of chronic diseases and improvement of HRQoL. Longitudinal studies must be performed to monitor changes in HRQoL and to permit evaluation of the outcomes of chronic disease intervention programs."], "structured": true}
{"doc_id": 464511, "title": "Memory and Modularity in Cell-Fate Decision Making", "abstract": ["Genetically identical cells sharing an environment can display markedly different phenotypes.", "It is often unclear how much of this variation derives from chance, external signals, or attempts by individual cells to exert autonomous phenotypic programs.", "By observing thousands of cells for hundreds of consecutive generations under constant conditions, we dissect the stochastic decision between a solitary, motile state and a chained, sessile state in Bacillus subtilis.", "We show that the motile state is 'memoryless', exhibiting no autonomous control over the time spent in the state.", "In contrast, the time spent as connected chains of cells is tightly controlled, enforcing coordination among related cells in the multicellular state.", "We show that the three-protein regulatory circuit governing the decision is modular, as initiation and maintenance of chaining are genetically separable functions.", "As stimulation of the same initiating pathway triggers biofilm formation, we argue that autonomous timing allows a trial commitment to multicellularity that external signals could extend."], "structured": false}
{"doc_id": 469066, "title": "Lpd depletion reveals that SRF specifies radial versus tangential migration of pyramidal neurons", "abstract": ["During corticogenesis, pyramidal neurons (\u223c80% of cortical neurons) arise from the ventricular zone, pass through a multipolar stage to become bipolar and attach to radial glia, and then migrate to their proper position within the cortex.", "As pyramidal neurons migrate radially, they remain attached to their glial substrate as they pass through the subventricular and intermediate zones, regions rich in tangentially migrating interneurons and axon fibre tracts.", "We examined the role of lamellipodin (Lpd), a homologue of a key regulator of neuronal migration and polarization in Caenorhabditis elegans, in corticogenesis.", "Lpd depletion caused bipolar pyramidal neurons to adopt a tangential, rather than radial-glial, migration mode without affecting cell fate.", "Mechanistically, Lpd depletion reduced the activity of SRF, a transcription factor regulated by changes in the ratio of polymerized to unpolymerized actin.", "Therefore, Lpd depletion exposes a role for SRF in directing pyramidal neurons to select a radial migration pathway along glia rather than a tangential migration mode."], "structured": false}
{"doc_id": 470625, "title": "Identification of p18 INK4c as a tumor suppressor gene in glioblastoma multiforme.", "abstract": ["Genomic alterations leading to aberrant activation of cyclin/cyclin-dependent kinase (cdk) complexes drive the pathogenesis of many common human tumor types.", "In the case of glioblastoma multiforme (GBM), these alterations are most commonly due to homozygous deletion of p16(INK4a) and less commonly due to genomic amplifications of individual genes encoding cyclins or cdks.", "Here, we describe deletion of the p18(INK4c) cdk inhibitor as a novel genetic alteration driving the pathogenesis of GBM.", "Deletions of p18(INK4c) often occurred in tumors also harboring homozygous deletions of p16(INK4a).", "Expression of p18(INK4c) was completely absent in 43% of GBM primary tumors studied by immunohistochemistry.", "Lentiviral reconstitution of p18(INK4c) expression at physiologic levels in p18(INK4c)-deficient but not p18(INK4c)-proficient GBM cells led to senescence-like G(1) cell cycle arrest.", "These studies identify p18(INK4c) as a GBM tumor suppressor gene, revealing an additional mechanism leading to aberrant activation of cyclin/cdk complexes in this terrible malignancy."], "structured": false}
{"doc_id": 471735, "title": "Two-stage control of an oxidative stress regulon: the Escherichia coli SoxR protein triggers redox-inducible expression of the soxS regulatory gene.", "abstract": ["Escherichia coli responds to the redox stress imposed by superoxide-generating agents such as paraquat by activating the synthesis of as many as 80 polypeptides.", "Expression of a key group of these inducible proteins is controlled at the transcriptional level by the soxRS locus (the soxRS regulon).", "A two-stage control system was hypothesized for soxRS, in which an intracellular redox signal would trigger the SoxR protein as a transcriptional activator of the soxS gene and the resulting increased levels of SoxS protein would activate transcription of the various soxRS regulon genes (B. Demple and C.F. Am\u00e1bile Cuevas, Cell 67:837-839, 1990).", "We have constructed operon fusions of the E. coli lac genes to the soxS promoter to monitor soxS transcription.", "Expression from the soxS promoter is strongly inducible by paraquat in a manner strictly dependent on a functional soxR gene.", "Several other superoxide-generating agents also trigger soxR(+)-dependent soxS expression, and the inductions by paraquat and phenazine methosulfate were dependent on the presence of oxygen.", "Numerous other oxidative stress agents (H2O2, gamma rays, heat shock, etc.) failed to induce soxS, while aerobic growth of superoxide dismutase-deficient bacteria triggered soxR-dependent soxS expression.", "These results indicate a specific redox signal for soxS induction.", "A direct role for SoxR protein in the activation of the soxS gene is indicated by band-shift and DNase I footprinting experiments that demonstrate specific binding of the SoxR protein in cell extracts to the soxS promoter.", "The mode of SoxR binding to DNA appears to be similar to that of its homolog MerR in that the SoxR footprint spans the -10 to -35 region of the soxS promoter."], "structured": false}
{"doc_id": 471921, "title": "Air pollution and cardiovascular disease: a statement for healthcare professionals from the Expert Panel on Population and Prevention Science of the American Heart Association.", "abstract": ["Air pollution is a heterogeneous, complex mixture of gases, liquids, and particulate matter.", "Epidemiological studies have demonstrated a consistent increased risk for cardiovascular events in relation to both short- and long-term exposure to present-day concentrations of ambient particulate matter.", "Several plausible mechanistic pathways have been described, including enhanced coagulation/thrombosis, a propensity for arrhythmias, acute arterial vasoconstriction, systemic inflammatory responses, and the chronic promotion of atherosclerosis.", "The purpose of this statement is to provide healthcare professionals and regulatory agencies with a comprehensive review of the literature on air pollution and cardiovascular disease.", "In addition, the implications of these findings in relation to public health and regulatory policies are addressed.", "Practical recommendations for healthcare providers and their patients are outlined.", "In the final section, suggestions for future research are made to address a number of remaining scientific questions."], "structured": false}
{"doc_id": 474325, "title": "Non-invasive ventilation in chronic obstructive pulmonary disease patients: helmet versus facial mask", "abstract": ["The helmet is a new interface with the potential of increasing the success rate of non-invasive ventilation by improving tolerance.", "To perform a physiological comparison between the helmet and the conventional facial mask in delivering non-invasive ventilation in hypercapnic patients with chronic obstructive pulmonary disease.", "Prospective, controlled, randomized study with cross-over design.", "In 10 patients we evaluated gas exchange, inspiratory effort, patient\u2013ventilator synchrony and patient tolerance after 30 min of non-invasive ventilation delivered either by helmet or facial mask; both trials were preceded by periods of spontaneous unassisted breathing.", "Arterial blood gases, inspiratory effort, duration of diaphragm contraction and ventilator assistance, effort-to-support delays (at the beginning and at the end of inspiration), number of ineffective efforts, and patient comfort.", "Non-invasive ventilation improved gas exchange (p< 0.05) and inspiratory effort (p< 0.01) with both interfaces.", "The helmet, however, was less efficient than the mask in reducing inspiratory effort (p< 0.05) and worsened the patient\u2013ventilator synchrony, as indicated by the longer delays to trigger on (p< 0.05) and cycle off (p< 0.05) the mechanical assistance and by the number of ineffective efforts (p< 0.005).", "Patient comfort was no different with the two interfaces.", "Helmet and facial mask were equally tolerated and both were effective in ameliorating gas exchange and decreasing inspiratory effort.", "The helmet, however, was less efficient in decreasing inspiratory effort and worsened the patient\u2013ventilator interaction."], "structured": false}
{"doc_id": 485020, "title": "Case Management and Client Access to Health and Social Services in Outpatient Substance Abuse Treatment", "abstract": ["A primary goal of case management is to coordinate services across treatment settings and to integrate substance abuse services with other types of services offered in the community, including housing, mental health, medical, and social services.", "However, case management is a global construct that consists of several key dimensions, which include extent of case management coverage, the degree of management of the referral process, and the location of case management activity (on-site, off-site, or both).", "This study examines the relationship between specific dimensions of case management and the utilization of health and ancillary social services in outpatient substance abuse treatment.", "In general, results suggest that more active case management during the referral process and providing case management both on-site and off-site are most consistent with our predictions of greater use of health and ancillary social services by substance abuse clients.", "However, these effects are specific to general health care and mental health services.", "Case management appears to have little effect on use of social services or aftercare plans."], "structured": false}
{"doc_id": 493346, "title": "Evidence that the Ipl1-Sli15 (Aurora Kinase-INCENP) Complex Promotes Chromosome Bi-orientation by Altering Kinetochore-Spindle Pole Connections", "abstract": ["How sister kinetochores attach to microtubules from opposite spindle poles during mitosis (bi-orientation) remains poorly understood.", "In yeast, the ortholog of the Aurora B-INCENP protein kinase complex (Ipl1-Sli15) may have a role in this crucial process, because it is necessary to prevent attachment of sister kinetochores to microtubules from the same spindle pole.", "We investigated IPL1 function in cells that cannot replicate their chromosomes but nevertheless duplicate their spindle pole bodies (SPBs).", "Kinetochores detach from old SPBs and reattach to old and new SPBs with equal frequency in IPL1+ cells, but remain attached to old SPBs in ipl1 mutants.", "This raises the possibility that Ipl1-Sli15 facilitates bi-orientation by promoting turnover of kinetochore-SPB connections until traction of sister kinetochores toward opposite spindle poles creates tension in the surrounding chromatin."], "structured": false}
{"doc_id": 496873, "title": "CRITICAL REVIEW Cutaneous Vasculitis Update: Diagnostic Criteria,", "abstract": ["Vasculitis, inflammation of the vessel wall, can result in mural destruction with hemorrhage, aneurysm formation, and infarction, or intimal-medial hyperplasia and subsequent stenosis leading to tissue ischemia.", "The skin, in part due to its large vascular bed, exposure to cold temperatures, and frequent presence of stasis, is involved in many distinct as well as un-named vasculitic syndromes that vary from localized and self-limited to generalized and life-threatening with multi-organ disease.", "To exclude mimics of vasculitis, diagnosis of cutaneous vasculitis requires biopsy confirmation where its acute signs (fibrinoid necrosis), chronic signs (endarteritis obliterans), or past signs (acellular scar of healed arteritis) must be recognized and presence of extravascular findings such as patterned fibrosis or collagenolytic granulomas noted.", "Although vasculitis can be classified by etiology, many cases have no identifiable cause, and a single etiologic agent can elicit several distinct clinicopathologic expressions of vasculitis.", "Therefore, the classification of cutaneous vasculitis is best approached morphologically by determining vessel size and principal inflammatory response.", "These histologic patterns roughly correlate with pathogenic mechanisms that, when coupled with direct immunofluorescent examination, anti-neutrophil cytoplasmic antibody (ANCA) status, and findings from work-up for systemic disease, allow for specific diagnosis, and ultimately, more effective therapy.", "Herein, we review cutaneous vasculitis focusing on diagnostic criteria, classification, epidemiology, etiology, pathogenesis, and evaluation of the cutaneous vasculitis patient."], "structured": false}
{"doc_id": 502591, "title": "E2F-dependent histone acetylation and recruitment of the Tip60 acetyltransferase complex to chromatin in late G1.", "abstract": ["E2F proteins can either activate or repress transcription.", "Following mitogenic stimulation, repressive E2F4-p130-histone deacetylase complexes dissociate from, while activating species (E2F1, -2, and -3) associate with, target promoters.", "Histones H3 and H4 simultaneously become hyperacetylated, but it remains unclear whether this is a prerequisite or a consequence of E2F binding.", "Here, we show that activating E2F species are required for hyperacetylation of target chromatin in human cells.", "Overexpression of a dominant-negative (DN) E2F1 mutant in serum-stimulated T98G cells blocked all E2F binding, H4 acetylation, and, albeit partially, H3 acetylation.", "Target gene activation and S-phase entry were also blocked by DN E2F1.", "Conversely, ectopic activation of E2F1 rapidly induced H3 and H4 acetylation, demonstrating a direct role for E2F in these events.", "E2F1 was previously shown to bind the histone acetyltransferases (HATs) p300/CBP and PCAF/GCN5.", "In our hands, ectopically expressed E2F1 also bound the unrelated HAT Tip60 and induced recruitment of five subunits of the Tip60 complex (Tip60, TRRAP, p400, Tip48, and Tip49) to target promoters in vivo.", "Moreover, E2F-dependent recruitment of Tip60 to chromatin occurred in late G(1) following serum stimulation.", "We speculate that the activities of multiple HAT complexes account for E2F-dependent acetylation, transcription, and S-phase entry."], "structured": false}
{"doc_id": 502797, "title": "Chemical approaches to stem cell biology and therapeutics.", "abstract": ["Small molecules that modulate stem cell fate and function offer significant opportunities that will allow the full realization of the therapeutic potential of stem cells.", "Rational design and screening for small molecules have identified useful compounds to probe fundamental mechanisms of stem cell self-renewal, differentiation, and reprogramming and have facilitated the development of cell-based therapies and therapeutic drugs targeting endogenous stem and progenitor cells for repair and regeneration.", "Here, we will discuss recent scientific and therapeutic progress, as well as new perspectives and future challenges for using chemical approaches in stem cell biology and regenerative medicine."], "structured": false}
{"doc_id": 503050, "title": "Genome-wide maps of chromatin state in pluripotent and lineage-committed cells", "abstract": ["We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in mammalian cells.", "By obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of mouse embryonic stem cells, neural progenitor cells and embryonic fibroblasts.", "We find that lysine 4 and lysine 27 trimethylation effectively discriminates genes that are expressed, poised for expression, or stably repressed, and therefore reflect cell state and lineage potential.", "Lysine 36 trimethylation marks primary coding and non-coding transcripts, facilitating gene annotation.", "Trimethylation of lysine 9 and lysine 20 is detected at satellite, telomeric and active long-terminal repeats, and can spread into proximal unique sequences.", "Lysine 4 and lysine 9 trimethylation marks imprinting control regions.", "Finally, we show that chromatin state can be read in an allele-specific manner by using single nucleotide polymorphisms.", "This study provides a framework for the application of comprehensive chromatin profiling towards characterization of diverse mammalian cell populations."], "structured": false}
{"doc_id": 515489, "title": "Oncofetal long noncoding RNA PVT1 promotes proliferation and stem cell-like property of hepatocellular carcinoma cells by stabilizing NOP2.", "abstract": ["UNLABELLED Many protein-coding oncofetal genes are highly expressed in murine and human fetal liver and silenced in adult liver.", "The protein products of these hepatic oncofetal genes have been used as clinical markers for the recurrence of hepatocellular carcinoma (HCC) and as therapeutic targets for HCC.", "Herein we examined the expression profiles of long noncoding RNAs (lncRNAs) found in fetal and adult liver in mice.", "Many fetal hepatic lncRNAs were identified; one of these, lncRNA-mPvt1, is an oncofetal RNA that was found to promote cell proliferation, cell cycling, and the expression of stem cell-like properties of murine cells.", "Interestingly, we found that human lncRNA-hPVT1 was up-regulated in HCC tissues and that patients with higher lncRNA-hPVT1 expression had a poor clinical prognosis.", "The protumorigenic effects of lncRNA-hPVT1 on cell proliferation, cell cycling, and stem cell-like properties of HCC cells were confirmed both in vitro and in vivo by gain-of-function and loss-of-function experiments.", "Moreover, mRNA expression profile data showed that lncRNA-hPVT1 up-regulated a series of cell cycle genes in SMMC-7721 cells.", "By RNA pulldown and mass spectrum experiments, we identified NOP2 as an RNA-binding protein that binds to lncRNA-hPVT1.", "We confirmed that lncRNA-hPVT1 up-regulated NOP2 by enhancing the stability of NOP2 proteins and that lncRNA-hPVT1 function depends on the presence of NOP2.   \n", "CONCLUSION Our study demonstrates that the expression of many lncRNAs is up-regulated in early liver development and that the fetal liver can be used to search for new diagnostic markers for HCC.", "LncRNA-hPVT1 promotes cell proliferation, cell cycling, and the acquisition of stem cell-like properties in HCC cells by stabilizing NOP2 protein.", "Regulation of the lncRNA-hPVT1/NOP2 pathway may have beneficial effects on the treatment of HCC."], "structured": true}
{"doc_id": 516867, "title": "Candida albicans, a distinctive fungal model for cellular aging study", "abstract": ["The unicellular eukaryotic organisms represent the popular model systems to understand aging in eukaryotes.", "Candida albicans, a polymorphic fungus, appears to be another distinctive unicellular aging model in addition to the budding yeast Saccharomyces cerevisiae and fission yeast Schizosaccharomyces pombe.", "The two types of Candida cells, yeast (blastospore) form and hyphal (filamentous) form, have similar replicative lifespan.", "Taking the advantage of morphologic changes, we are able to obtain cells of different ages.", "Old Candida cells tend to accumulate glycogen and oxidatively damaged proteins.", "Deletion of the SIR2 gene causes a decrease of lifespan, while insertion of an extra copy of SIR2 extends lifespan, indicating that like in S. cerevisiae, Sir2 regulates cellular aging in C. albicans.", "Interestingly, Sir2 deletion does not result in the accumulation of extra-chromosomal rDNA molecules, but influences the retention of oxidized proteins in mother cells, suggesting that the extra-chromosomal rDNA molecules may not be associated with cellular aging in C. albicans.", "This novel aging model, which allows efficient large-scale isolation of old cells, may facilitate biochemical characterizations and genomics/proteomics studies of cellular aging, and help to verify the aging pathways observed in other organisms including S. cerevisiae."], "structured": false}
{"doc_id": 519974, "title": "ANKTM1, a TRP-like Channel Expressed in Nociceptive Neurons, Is Activated by Cold Temperatures", "abstract": ["Mammals detect temperature with specialized neurons in the peripheral nervous system.", "Four TRPV-class channels have been implicated in sensing heat, and one TRPM-class channel in sensing cold.", "The combined range of temperatures that activate these channels covers a majority of the relevant physiological spectrum sensed by most mammals, with a significant gap in the noxious cold range.", "Here, we describe the characterization of ANKTM1, a cold-activated channel with a lower activation temperature compared to the cold and menthol receptor, TRPM8.", "ANKTM1 is a distant family member of TRP channels with very little amino acid similarity to TRPM8.", "It is found in a subset of nociceptive sensory neurons where it is coexpressed with TRPV1/VR1 (the capsaicin/heat receptor) but not TRPM8.", "Consistent with the expression of ANKTM1, we identify noxious cold-sensitive sensory neurons that also respond to capsaicin but not to menthol."], "structured": false}
{"doc_id": 520579, "title": "Plasma vitamin D metabolites and risk of colorectal cancer in women.", "abstract": ["OBJECTIVE Experimental evidence suggests that 1,25-dihydroxyvitamin D and its precursor, 25-hydroxyvitamin D [25(OH)D], may aid in the prevention of colorectal cancer.", "We therefore examined risk in relation to plasma concentrations of these vitamin D metabolites.   \n", "METHODS In a nested case-control study among women in the Nurses' Health Study, we identified 193 colorectal cancer cases, ages 46 to 78 years, diagnosed up to 11 years after blood collection.", "Two controls were matched per case on year of birth and month of blood draw.", "Odds ratios (OR) for risk of colorectal cancer were calculated using conditional logistic regression adjusted for body mass index, physical activity, smoking, family history, use of hormone replacement therapy, aspirin use, and dietary intakes.   \n", "RESULTS We found a significant inverse linear association between plasma 25(OH)D and risk of colorectal cancer (P = 0.02).", "Among women in the highest quintile, the OR (95% confidence interval) was 0.53 (0.27-1.04).", "This inverse association remained strong when limited to women > or =60 years at blood collection (P = 0.006) but was not apparent among the younger women (P = 0.70).", "Benefit from higher 25(OH)D concentrations was observed for cancers at the distal colon and rectum (P = 0.02) but was not evident for those at the proximal colon (P = 0.81).", "In contrast to 25(OH)D, we did not observe an association between 1,25-dihydroxyvitamin D and colorectal cancer, although risk was elevated among the women in the highest quintile if they were also in the lower half of the 25(OH)D distribution (OR, 2.52; 95% confidence interval, 1.04-6.11).   \n", "CONCLUSION From these results and supporting evidence from previous studies, we conclude that higher plasma levels of 25(OH)D are associated with a lower risk of colorectal cancer in older women, particularly for cancers at the distal colon and rectum."], "structured": true}
{"doc_id": 544971, "title": "DNA Deamination Mediates Innate Immunity to Retroviral Infection", "abstract": ["CEM15/APOBEC3G is a cellular protein required for resistance to infection by virion infectivity factor (Vif)-deficient human immunodeficiency virus (HIV).", "Here, using a murine leukemia virus (MLV)-based system, we provide evidence that CEM15/APOBEC3G is a DNA deaminase that is incorporated into virions during viral production and subsequently triggers massive deamination of deoxycytidine to deoxyuridine within the retroviral minus (first)-strand cDNA, thus providing a probable trigger for viral destruction.", "Furthermore, HIV Vif can protect MLV from this CEM15/APOBEC3G-dependent restriction.", "These findings imply that targeted DNA deamination is a major strategy of innate immunity to retroviruses and likely also contributes to the sequence variation observed in many viruses (including HIV)."], "structured": false}
{"doc_id": 581832, "title": "Global, regional, and national disability-adjusted life-years (DALYs) for 315 diseases and injuries and healthy life expectancy (HALE), 1990\u20132015: a systematic analysis for the Global Burden of Disease Study 2015", "abstract": ["BACKGROUND Healthy life expectancy (HALE) and disability-adjusted life-years (DALYs) provide summary measures of health across geographies and time that can inform assessments of epidemiological patterns and health system performance, help to prioritise investments in research and development, and monitor progress toward the Sustainable Development Goals (SDGs).", "We aimed to provide updated HALE and DALYs for geographies worldwide and evaluate how disease burden changes with development.   \n", "METHODS We used results from the Global Burden of Diseases, Injuries, and Risk Factors Study 2015 (GBD 2015) for all-cause mortality, cause-specific mortality, and non-fatal disease burden to derive HALE and DALYs by sex for 195 countries and territories from 1990 to 2015.", "We calculated DALYs by summing years of life lost (YLLs) and years of life lived with disability (YLDs) for each geography, age group, sex, and year.", "We estimated HALE using the Sullivan method, which draws from age-specific death rates and YLDs per capita.", "We then assessed how observed levels of DALYs and HALE differed from expected trends calculated with the Socio-demographic Index (SDI), a composite indicator constructed from measures of income per capita, average years of schooling, and total fertility rate.   \n", "FINDINGS Total global DALYs remained largely unchanged from 1990 to 2015, with decreases in communicable, neonatal, maternal, and nutritional (Group 1) disease DALYs offset by increased DALYs due to non-communicable diseases (NCDs).", "Much of this epidemiological transition was caused by changes in population growth and ageing, but it was accelerated by widespread improvements in SDI that also correlated strongly with the increasing importance of NCDs.", "Both total DALYs and age-standardised DALY rates due to most Group 1 causes significantly decreased by 2015, and although total burden climbed for the majority of NCDs, age-standardised DALY rates due to NCDs declined.", "Nonetheless, age-standardised DALY rates due to several high-burden NCDs (including osteoarthritis, drug use disorders, depression, diabetes, congenital birth defects, and skin, oral, and sense organ diseases) either increased or remained unchanged, leading to increases in their relative ranking in many geographies.", "From 2005 to 2015, HALE at birth increased by an average of 2\u00b79 years (95% uncertainty interval 2\u00b79-3\u00b70) for men and 3\u00b75 years (3\u00b74-3\u00b77) for women, while HALE at age 65 years improved by 0\u00b785 years (0\u00b778-0\u00b792) and 1\u00b72 years (1\u00b71-1\u00b73), respectively.", "Rising SDI was associated with consistently higher HALE and a somewhat smaller proportion of life spent with functional health loss; however, rising SDI was related to increases in total disability.", "Many countries and territories in central America and eastern sub-Saharan Africa had increasingly lower rates of disease burden than expected given their SDI.", "At the same time, a subset of geographies recorded a growing gap between observed and expected levels of DALYs, a trend driven mainly by rising burden due to war, interpersonal violence, and various NCDs.   \n", "INTERPRETATION Health is improving globally, but this means more populations are spending more time with functional health loss, an absolute expansion of morbidity.", "The proportion of life spent in ill health decreases somewhat with increasing SDI, a relative compression of morbidity, which supports continued efforts to elevate personal income, improve education, and limit fertility.", "Our analysis of DALYs and HALE and their relationship to SDI represents a robust framework on which to benchmark geography-specific health performance and SDG progress.", "Country-specific drivers of disease burden, particularly for causes with higher-than-expected DALYs, should inform financial and research investments, prevention efforts, health policies, and health system improvement initiatives for all countries along the development continuum.   \n", "FUNDING Bill & Melinda Gates Foundation."], "structured": true}
{"doc_id": 583260, "title": "Adverse drug events: database construction and in silico prediction.", "abstract": ["Adverse drug events (ADEs) are the harms associated with uses of given medications at normal dosages, which are crucial for a drug to be approved in clinical use or continue to stay on the market.", "Many ADEs are not identified in trials until the drug is approved for clinical use, which results in adverse morbidity and mortality.", "To date, millions of ADEs have been reported around the world.", "Methods to avoid or reduce ADEs are an important issue for drug discovery and development.", "Here, we reported a comprehensive database of adverse drug events (namely MetaADEDB), which included more than 520,000 drug-ADE associations among 3059 unique compounds (including 1330 drugs) and 13,200 ADE items by data integration and text mining.", "All compounds and ADEs were annotated with the most commonly used concepts defined in Medical Subject Headings (MeSH).", "Meanwhile, a computational method, namely the phenotypic network inference model (PNIM), was developed for prediction of potential ADEs based on the database.", "The area under the receive operating characteristic curve (AUC) is more than 0.9 by 10-fold cross validation, while the AUC value was 0.912 for an external validation set extracted from the US-FDA Adverse Events Reporting System, which indicated that the prediction capability of the method was reliable.", "MetaADEDB is accessible free of charge at http://www.lmmd.org/online_services/metaadedb/. The database and the method provide us a useful tool to search for known side effects or predict potential side effects for a given drug or compound."], "structured": false}
{"doc_id": 596817, "title": "Genetic Tests for Ecological and Allopatric Speciation in Anoles on an Island Archipelago", "abstract": ["From Darwin's study of the Galapagos and Wallace's study of Indonesia, islands have played an important role in evolutionary investigations, and radiations within archipelagos are readily interpreted as supporting the conventional view of allopatric speciation.", "Even during the ongoing paradigm shift towards other modes of speciation, island radiations, such as the Lesser Antillean anoles, are thought to exemplify this process.", "Geological and molecular phylogenetic evidence show that, in this archipelago, Martinique anoles provide several examples of secondary contact of island species.", "Four precursor island species, with up to 8 mybp divergence, met when their islands coalesced to form the current island of Martinique.", "Moreover, adjacent anole populations also show marked adaptation to distinct habitat zonation, allowing both allopatric and ecological speciation to be tested in this system.", "We take advantage of this opportunity of replicated island coalescence and independent ecological adaptation to carry out an extensive population genetic study of hypervariable neutral nuclear markers to show that even after these very substantial periods of spatial isolation these putative allospecies show less reproductive isolation than conspecific populations in adjacent habitats in all three cases of subsequent island coalescence.", "The degree of genetic interchange shows that while there is always a significant genetic signature of past allopatry, and this may be quite strong if the selection regime allows, there is no case of complete allopatric speciation, in spite of the strong primae facie case for it.", "Importantly there is greater genetic isolation across the xeric/rainforest ecotone than is associated with any secondary contact.", "This rejects the development of reproductive isolation in allopatric divergence, but supports the potential for ecological speciation, even though full speciation has not been achieved in this case.", "It also explains the paucity of anole species in the Lesser Antilles compared to the Greater Antilles."], "structured": false}
{"doc_id": 597790, "title": "Deficiency and pharmacological stabilization of mast cells reduce diet-induced obesity and diabetes in mice", "abstract": ["Although mast cell functions have classically been related to allergic responses, recent studies indicate that these cells contribute to other common diseases such as multiple sclerosis, rheumatoid arthritis, atherosclerosis, aortic aneurysm and cancer.", "This study presents evidence that mast cells also contribute to diet-induced obesity and diabetes.", "For example, white adipose tissue (WAT) from obese humans and mice contain more mast cells than WAT from their lean counterparts.", "Furthermore, in the context of mice on a Western diet, genetically induced deficiency of mast cells, or their pharmacological stabilization, reduces body weight gain and levels of inflammatory cytokines, chemokines and proteases in serum and WAT, in concert with improved glucose homeostasis and energy expenditure.", "Mechanistic studies reveal that mast cells contribute to WAT and muscle angiogenesis and associated cell apoptosis and cathepsin activity.", "Adoptive transfer experiments of cytokine-deficient mast cells show that these cells, by producing interleukin-6 (IL-6) and interferon-gamma (IFN-gamma), contribute to mouse adipose tissue cysteine protease cathepsin expression, apoptosis and angiogenesis, thereby promoting diet-induced obesity and glucose intolerance.", "Our results showing reduced obesity and diabetes in mice treated with clinically available mast cell-stabilizing agents suggest the potential of developing new therapies for these common human metabolic disorders."], "structured": false}
{"doc_id": 599582, "title": "Familial aphasic episodes: another variant of partial epilepsy with simple inheritance?", "abstract": ["We report on a family having partial epilepsy with simple inheritance.", "The affected members commonly have aphasic episodes with secondary generalization; onset occurred either in adolescence or adulthood.", "Patients' response to medication has varied greatly.", "No neurological defects or decline in intelligence were found.", "The case represents another variety of rare familial partial epilepsy with neocortical epilepsy features."], "structured": false}
{"doc_id": 600437, "title": "Endosome-ER Contacts Control Actin Nucleation and Retromer Function through VAP-Dependent Regulation of PI4P", "abstract": ["VAP (VAPA and VAPB) is an evolutionarily conserved endoplasmic reticulum (ER)-anchored protein that helps generate tethers between the ER and other membranes through which lipids are exchanged across adjacent bilayers.", "Here, we report that by regulating PI4P levels on endosomes, VAP affects WASH-dependent actin nucleation on these organelles and the function of the retromer, a protein coat responsible for endosome-to-Golgi traffic.", "VAP is recruited to retromer budding sites on endosomes via an interaction with the retromer SNX2 subunit.", "Cells lacking VAP accumulate high levels of PI4P, actin comets, and trans-Golgi proteins on endosomes.", "Such defects are mimicked by downregulation of OSBP, a VAP interactor and PI4P transporter that participates in VAP-dependent ER-endosomes tethers.", "These results reveal a role of PI4P in retromer-/WASH-dependent budding from endosomes.", "Collectively, our data show how the ER can control budding dynamics and association with the cytoskeleton of another membrane by direct contacts leading to bilayer lipid modifications."], "structured": false}
{"doc_id": 600808, "title": "Anaphase-Promoting Complex/Cyclosome\u2013Dependent Proteolysis of Human Cyclin a Starts at the Beginning of Mitosis and Is Not Subject to the Spindle Assembly Checkpoint", "abstract": ["Cyclin A is a stable protein in S and G2 phases, but is destabilized when cells enter mitosis and is almost completely degraded before the metaphase to anaphase transition.", "Microinjection of antibodies against subunits of the anaphase-promoting complex/cyclosome (APC/C) or against human Cdc20 (fizzy) arrested cells at metaphase and stabilized both cyclins A and B1.", "Cyclin A was efficiently polyubiquitylated by Cdc20 or Cdh1-activated APC/C in vitro, but in contrast to cyclin B1, the proteolysis of cyclin A was not delayed by the spindle assembly checkpoint.", "The degradation of cyclin B1 was accelerated by inhibition of the spindle assembly checkpoint.", "These data suggest that the APC/C is activated as cells enter mitosis and immediately targets cyclin A for degradation, whereas the spindle assembly checkpoint delays the degradation of cyclin B1 until the metaphase to anaphase transition.", "The \u201cdestruction box\u201d (D-box) of cyclin A is 10\u201320 residues longer than that of cyclin B. Overexpression of wild-type cyclin A delayed the metaphase to anaphase transition, whereas expression of cyclin A mutants lacking a D-box arrested cells in anaphase."], "structured": false}
{"doc_id": 601033, "title": "Human T Cell Leukemia Virus Reactivation with Progression of Adult T-Cell Leukemia-Lymphoma", "abstract": ["BACKGROUND Human T-cell leukemia virus-associated adult T-cell leukemia-lymphoma (ATLL) has a very poor prognosis, despite trials of a variety of different treatment regimens.", "Virus expression has been reported to be limited or absent when ATLL is diagnosed, and this has suggested that secondary genetic or epigenetic changes are important in disease pathogenesis.   \n", "METHODS AND FINDINGS We prospectively investigated combination chemotherapy followed by antiretroviral therapy for this disorder.", "Nineteen patients were prospectively enrolled between 2002 and 2006 at five medical centers in a phase II clinical trial of infusional chemotherapy with etoposide, doxorubicin, and vincristine, daily prednisone, and bolus cyclophosphamide (EPOCH) given for two to six cycles until maximal clinical response, and followed by antiviral therapy with daily zidovudine, lamivudine, and alpha interferon-2a for up to one year.", "Seven patients were on study for less than one month due to progressive disease or chemotherapy toxicity.", "Eleven patients achieved an objective response with median duration of response of thirteen months, and two complete remissions.", "During chemotherapy induction, viral RNA expression increased (median 190-fold), and virus replication occurred, coincident with development of disease progression.   \n", "CONCLUSIONS EPOCH chemotherapy followed by antiretroviral therapy is an active therapeutic regimen for adult T-cell leukemia-lymphoma, but viral reactivation during induction chemotherapy may contribute to treatment failure.", "Alternative therapies are sorely needed in this disease that simultaneously prevent virus expression, and are cytocidal for malignant cells."], "structured": true}
{"doc_id": 602760, "title": "Montelukast and fluticasone compared with salmeterol and fluticasone in protecting against asthma exacerbation in adults: one year, double blind, randomised, comparative trial.", "abstract": ["OBJECTIVES To assess the effect of montelukast versus salmeterol added to inhaled fluticasone propionate on asthma exacerbation in patients whose symptoms are inadequately controlled with fluticasone alone.", "Design and setting A 52 week, two period, double blind, multicentre trial during which patients whose symptoms remained uncontrolled by inhaled corticosteroids were randomised to add montelukast or salmeterol.   \n", "PARTICIPANTS Patients (15-72 years; n = 1490) had a clinical history of chronic asthma for > or = 1 year, a baseline forced expiratory volume in one second (FEV1) value 50-90% predicted, and a beta agonist improvement of > or = 12% in FEV1.   \n", "MAIN OUTCOME MEASURES The primary end point was the percentage of patients with at least one asthma exacerbation.   \n", "RESULTS 20.1% of the patients in the group receiving montelukast and fluticasone had an asthma exacerbation compared with 19.1% in the group receiving salmeterol and fluticasone; the difference was 1% (95% confidence interval -3.1% to 5.0%).", "With a risk ratio (montelukast-fluticasone/salmeterol-fluticasone) of 1.05 (0.86 to 1.29), treatment with montelukast and fluticasone was shown to be non-inferior to treatment with salmeterol and fluticasone.", "Salmeterol and fluticasone significantly increased FEV1 before a beta agonist was used and morning peak expiratory flow compared with montelukast and fluticasone (P < or = 0.001), whereas FEV1 after a beta agonist was used and improvements in asthma specific quality of life and nocturnal awakenings were similar between the groups.", "Montelukast and fluticasone significantly (P = 0.011) reduced peripheral blood eosinophil counts compared with salmeterol and fluticasone.", "Both treatments were generally well tolerated.   \n", "CONCLUSION The addition of montelukast in patients whose symptoms remain uncontrolled by inhaled fluticasone could provide equivalent clinical control to salmeterol."], "structured": true}
{"doc_id": 612002, "title": "Control of assembly and function of glutamate receptors by the amino-terminal domain.", "abstract": ["The extracellular amino-terminal domains (ATDs) of the ionotropic glutamate receptor subunits form a semiautonomous component of all glutamate receptors that resides distal to the membrane and controls a surprisingly diverse set of receptor functions.", "These functions include subunit assembly, receptor trafficking, channel gating, agonist potency, and allosteric modulation.", "The many divergent features of the different ionotropic glutamate receptor classes and different subunits within a class may stem from differential regulation by the amino-terminal domains.", "The emerging knowledge of the structure and function of the amino-terminal domains reviewed here may enable targeting of this region for the therapeutic modulation of glutamatergic signaling.", "Toward this end, NMDA receptor antagonists that interact with the GluN2B ATD show promise in animal models of ischemia, neuropathic pain, and Parkinson's disease."], "structured": false}
{"doc_id": 615047, "title": "Fission yeast and other yeasts as emergent models to unravel cellular aging in eukaryotes.", "abstract": ["In the past years, simple organisms such as yeasts and worms have contributed a great deal to aging research.", "Studies pioneered in Saccharomyces cerevisiae were useful to elucidate a significant number of molecular mechanisms underlying cellular aging and to discover novel longevity genes.", "Importantly, these genes proved many times to be conserved in multicellular eukaryotes.", "Consequently, such discovery approaches are being extended to other yeast models, such as Schizosaccharomyces pombe, Candida albicans, Kluyveromyces lactis, and Cryptococcus neoformans.", "In fission yeast, researchers have found links between asymmetrical cell division and nutrient signaling pathways with aging.", "In this review, we discuss the state of knowledge on the mechanisms controlling both replicative and chronological aging in S pombe and the other emergent yeast models."], "structured": false}
{"doc_id": 623486, "title": "Centrifugal elutriation as a method for isolation of large numbers of functionally intact human peripheral blood monocytes.", "abstract": ["Centrifugal elutriation was used further to isolate human peripheral blood monocytes (HPBM) from mononuclear-enriched cells harvested as a secondary component following platelet concentration collection samples.", "HPBM were recovered in either one or two populations consisting of either total HPBM or small (SM) and large monocytes (LM).", "The elutriation was carried out at 3,500 +/-", "5 rpm for the separation of lymphocytes and HPBM in Ca++- and Mg++-free PBS without EDTA.", "An average of 5.05 +/-", "1.50 X 10(8) HPBM were recovered in the total HPBM with a purity of 95% +/-", "3%.", "The SM and LM were obtained by splitting the total HPBM into two equal populations with an HPBM purity of 92% +/-", "3% and 93% +/-", "3, respectively, by nonspecific esterase staining.", "The elutriation media were shown to have no effect on viability by trypan blue exclusion.", "All three HPBM populations were shown to be histochemically (lack of reactivity to leu-1 and leu-7) and functionally (depletion of NK cell activity) purified from the lymphocyte population.", "The HPBM populations were enriched in HLA-Dr, OKM-1, OKM-5, MY-8, and leu M-3 monoclonal antibody marker staining.", "There were no differences in percent positive cells between SM and LM populations for any of the monocyte-specific monoclonal antibodies.", "All three monocyte populations mediated antibody-dependent cell-mediated cytotoxicity to human red blood cells, with LM mediating more lysis (27.0% +/-", "5%) than SM (7% +/-", "3%).(ABSTRACT TRUNCATED AT 250 WORDS)"], "structured": false}
{"doc_id": 641459, "title": "Asthma in United States Olympic athletes who participated in the 1996 Summer Games.", "abstract": ["BACKGROUND Asthma prevalence appears to be increasing in the general population.", "We sought to determine whether asthma prevalence has also increased in highly competitive athletes.   \n", "OBJECTIVE Our aim was to determine how many United States Olympic athletes who were chosen to participate in the 1996 Summer Olympic Games had a past history of asthma or symptoms that suggested asthma or took asthma medications.   \n", "METHODS We analyzed responses to questions that asked about allergic and respiratory diseases on the United States Olympic Committee (USOC) Medical History Questionnaire that was completed by all athletes who were chosen to represent the US at the 1996 Summer Olympic Games in Atlanta.   \n", "RESULTS Of the 699 athletes who completed the questionnaire, 107 (15.3%) had a previous diagnosis of asthma, and 97 (13.9%) recorded use of an asthma medication at some time in the past.", "One hundred seventeen (16.7%) reported use of an asthma medication, a diagnosis of asthma, or both (which was our basis for the diagnosis of asthma).", "Seventy-three (10. 4%) of the athletes were currently taking an asthma medication at the time that they were processed in Atlanta or noted that they took asthma medications on a permanent or semipermanent basis and were considered to have active asthma.", "Athletes who participated in cycling and mountain biking had the highest prevalence of having been told that they had asthma or had taken an asthma medication in the past (50%).", "Frequency of active asthma varied from 45% of cyclists and emountain bikers to none of the divers and weight lifters.", "Only about 11% of the athletes who participated in the 1984 Summer Olympic Games were reported to have had exercise-induced asthma on the basis of other criteria that may have been less restrictive.", "On the basis of these less restrictive criteria, more than 20% of the athletes who participated in the 1996 Olympic Games might have been considered to have had asthma.   \n", "CONCLUSIONS Asthma appeared to have been more prevalent in athletes who participated in the 1996 Summer Games than in the general population or in those who participated in the 1984 Summer Games.", "This study also suggests that asthma may influence the sport that an athlete chooses."], "structured": true}
{"doc_id": 641786, "title": "Relapse specific mutations in NT5C2 in childhood acute lymphoblastic leukemia", "abstract": ["Relapsed childhood acute lymphoblastic leukemia (ALL) carries a poor prognosis, despite intensive retreatment, owing to intrinsic drug resistance.", "The biological pathways that mediate resistance are unknown.", "Here, we report the transcriptome profiles of matched diagnosis and relapse bone marrow specimens from ten individuals with pediatric B-lymphoblastic leukemia using RNA sequencing.", "Transcriptome sequencing identified 20 newly acquired, novel nonsynonymous mutations not present at initial diagnosis, with 2 individuals harboring relapse-specific mutations in the same gene, NT5C2, encoding a 5'-nucleotidase.", "Full-exon sequencing of NT5C2 was completed in 61 further relapse specimens, identifying additional mutations in 5 cases.", "Enzymatic analysis of mutant proteins showed that base substitutions conferred increased enzymatic activity and resistance to treatment with nucleoside analog therapies.", "Clinically, all individuals who harbored NT5C2 mutations relapsed early, within 36 months of initial diagnosis (P = 0.03).", "These results suggest that mutations in NT5C2 are associated with the outgrowth of drug-resistant clones in ALL."], "structured": false}
{"doc_id": 643765, "title": "Relationship between Sloan-Kettering virus expression and mouse follicular development", "abstract": ["Sloan-Kettering virus gene product (Ski) is an unique nuclear pro-oncoprotein and belongs to the ski/sno proto-oncogene family.", "Ski plays multiple roles in a variety of cell types, it can induce both oncogenic transformation and terminal muscle differentiation when expressed at high levels.", "Ski/SnoN are important transcription regulators of the transforming growth factor-\u03b2 (TGF-\u03b2) superfamily and function mainly through heterodimers.", "Since TGF-\u03b2 superfamily are key regulators of follicle development and it has been previously shown that SnoN is also vital to follicle development, this research was conducted to clarify the relationship between Ski expression and mouse follicular development, in ovaries of neonatal and gonadotropin-induced immature mice by immunohistochemical and real-time PCR techniques.", "In postnatal mice, positive staining for Ski was highly detected in oocyte nuclei at postnatal day 1.", "With follicular development, the localization moved gradually from oocyte nuclei to perinuclear space and the total levels decreased.", "During the estrous cycle, Ski expression was apparent at proestrus and estrus, faint at metestrus, highest at diestrus.", "After injection of gonadotropin, Ski was found in perinuclear space and weak in oocyte nuclei.", "Following the initiation of luteinization, the expression of Ski was found in corpus luteum.", "Real-time PCR results also showed that Ski mRNA expression was opposite to ovulation-related genes during the cumulus expansion, with the development of the follicles, its expression level decreased.", "Ski is expressed in a specific manner during follicle development, ovulation and luteinization.", "So Ski might play essential roles in these processes especially during early follicular development."], "structured": false}
{"doc_id": 649951, "title": "Involvement of CB1 cannabinoid receptors in emotional behaviour", "abstract": ["Rationale: Endogenous and exogenous cannabinoids acting through the CB1 cannabinoid receptors are implicated in the control of a variety of behavioural and neuroendocrine functions, including emotional responses, and learning and memory processes.", "Recently, knockout mice deficient in the CB1 cannabinoid receptor have been generated, and these animals result in an excellent tool to evaluate the neurophysiology of the endogenous cannabinoid system.", "Objectives: To establish the role of the CB1 cannabinoid receptor in several emotional-related behavioural responses, including aggressiveness, anxiety, depression and learning models, using CB1 knockout mice.", "Methods: We evaluated the spontaneous responses of CB1 knockout mice and wild-type controls under different behavioural paradigms, including the light/dark box, the chronic unpredictable mild stress, the resident\u2013intruder test and the active avoidance paradigm.", "Results: Our findings showed that CB1 knockout mice presented an increase in the aggressive response measured in the resident\u2013intruder test and an anxiogenic-like response in the light/dark box.", "Furthermore, a higher sensitivity to exhibit depressive-like responses in the chronic unpredictable mild stress procedure was observed in CB1 knockout mice, suggesting an increased susceptibility to develop an anhedonic state in these animals.", "Finally, CB1 knockout mice showed a significant increase in the conditioned responses produced in the active avoidance model, suggesting an improvement of learning and memory processes.", "Conclusions: Taken together these findings demonstrate that endogenous cannabinoids through the activation of CB1 receptors are implicated in the control of emotional behaviour and participate in the physiological processes of learning and memory."], "structured": false}
{"doc_id": 654735, "title": "Exosomal levels of miRNA-21 from cerebrospinal fluids associated with poor prognosis and tumor recurrence of glioma patients", "abstract": ["Glioma is a most common type of primary brain tumors.", "Extracellular vesicles, in the form of exosomes, are known to mediate cell-cell communication by transporting cell-derived proteins and nucleic acids, including various microRNAs (miRNAs).", "Here we examined the cerebrospinal fluid (CSF) from patients with recurrent glioma for the levels of cancer-related miRNAs, and evaluated the values for prognosis by comparing the measures of CSF-, serum-, and exosome-contained miR-21 levels.", "Samples from seventy glioma patients following surgery were compared with those from brain trauma patients as a non-tumor control group.", "Exosomal miR-21 levels in the CSF of glioma patients were found significantly higher than in the controls; whereas no difference was detected in serum-derived exosomal miR-21 expression.", "The CSF-derived exosomal miR-21 levels correlated with tumor spinal/ventricle metastasis and the recurrence with anatomical site preference.", "From additional 198 glioma tissue samples, we verified that miR-21 levels associated with tumor grade of diagnosis and negatively correlated with the median values of patient overall survival time.", "We further used a lentiviral inhibitor to suppress miR-21 expression in U251 cells.", "The results showed that the levels of miR-21 target genes of PTEN, RECK and PDCD4 were up-regulated at protein levels.", "Therefore, we concluded that the exosomal miR-21 levels could be demonstrated as a promising indicator for glioma diagnosis and prognosis, particularly with values to predict tumor recurrence or metastasis."], "structured": false}
{"doc_id": 663464, "title": "Age\u2010associated microRNA expression in human peripheral blood is associated with all\u2010cause mortality and age\u2010related traits", "abstract": ["Recent studies provide evidence of correlations of DNA methylation and expression of protein-coding genes with human aging.", "The relations of microRNA expression with age and age-related clinical outcomes have not been characterized thoroughly.", "We explored associations of age with whole-blood microRNA expression in 5221 adults and identified 127 microRNAs that were differentially expressed by age at P < 3.3 \u00d7 10-4 (Bonferroni-corrected).", "Most microRNAs were underexpressed in older individuals.", "Integrative analysis of microRNA and mRNA expression revealed changes in age-associated mRNA expression possibly driven by age-associated microRNAs in pathways that involve RNA processing, translation, and immune function.", "We fitted a linear model to predict 'microRNA age' that incorporated expression levels of 80 microRNAs.", "MicroRNA age correlated modestly with predicted age from DNA methylation (r = 0.3) and mRNA expression (r = 0.2), suggesting that microRNA age may complement mRNA and epigenetic age prediction models.", "We used the difference between microRNA age and chronological age as a biomarker of accelerated aging (\u0394age) and found that \u0394age was associated with all-cause mortality (hazards ratio 1.1 per year difference, P = 4.2 \u00d7 10-5 adjusted for sex and chronological age).", "Additionally, \u0394age was associated with coronary heart disease, hypertension, blood pressure, and glucose levels.", "In conclusion, we constructed a microRNA age prediction model based on whole-blood microRNA expression profiling.", "Age-associated microRNAs and their targets have potential utility to detect accelerated aging and to predict risks for age-related diseases."], "structured": false}
{"doc_id": 665817, "title": "Histone deacetylases (HDACs) in frontotemporal lobar degeneration.", "abstract": ["AIMS Frontotemporal lobar degeneration (FTLD) is clinically and pathologically heterogeneous.", "Although associated with variations in MAPT, GRN and C9ORF72, the pathogenesis of these, and of other nongenetic, forms of FTLD, remains unknown.", "Epigenetic factors such as histone regulation by histone deacetylases (HDAC) may play a role in the dysregulation of transcriptional activity, thought to underpin the neurodegenerative process.   \n", "METHODS The distribution and intensity of HDACs 4, 5 and 6 was assessed semi-quantitatively in immunostained sections of temporal cortex with hippocampus, and cerebellum, from 33 pathologically confirmed cases of FTLD and 27 controls.   \n", "RESULTS We found a significantly greater intensity of cytoplasmic immunostaining for HDAC4 and HDAC6 in granule cells of the dentate gyrus in cases of FTLD overall compared with controls, and specifically in cases of FTLD tau-Picks compared with FTLD tau-MAPT and controls.", "No differences were noted between FTLD-TDP subtypes, or between the different genetic and nongenetic forms of FTLD.", "No changes were seen in HDAC5 in any FTLD or control cases.   \n", "CONCLUSIONS Dysregulation of HDAC4 and/or HDAC6 could play a role in the pathogenesis of FTLD-tau associated with Pick bodies, although their lack of immunostaining implies that such changes do not contribute directly to the formation of Pick bodies."], "structured": true}
{"doc_id": 667451, "title": "Evolution and Impact of Subclonal Mutations in Chronic Lymphocytic Leukemia", "abstract": ["Clonal evolution is a key feature of cancer progression and relapse.", "We studied intratumoral heterogeneity in 149 chronic lymphocytic leukemia (CLL) cases by integrating whole-exome sequence and copy number to measure the fraction of cancer cells harboring each somatic mutation.", "We identified driver mutations as predominantly clonal (e.g., MYD88, trisomy 12, and del(13q)) or subclonal (e.g., SF3B1 and TP53), corresponding to earlier and later events in CLL evolution.", "We sampled leukemia cells from 18 patients at two time points.", "Ten of twelve CLL cases treated with chemotherapy (but only one of six without treatment) underwent clonal evolution, predominantly involving subclones with driver mutations (e.g., SF3B1 and TP53) that expanded over time.", "Furthermore, presence of a subclonal driver mutation was an independent risk factor for rapid disease progression.", "Our study thus uncovers patterns of clonal evolution in CLL, providing insights into its stepwise transformation, and links the presence of subclones with adverse clinical outcomes."], "structured": false}
{"doc_id": 680949, "title": "The transcriptional program of sporulation in budding yeast", "abstract": ["Diploid cells of budding yeast produce haploid cells through the developmental program of sporulation, which consists of meiosis and spore morphogenesis.", "DNA microarrays containing nearly every yeast gene were used to assay changes in gene expression during sporulation.", "At least seven distinct temporal patterns of induction were observed.", "The transcription factor Ndt80 appeared to be important for induction of a large group of genes at the end of meiotic prophase.", "Consensus sequences known or proposed to be responsible for temporal regulation could be identified solely from analysis of sequences of coordinately expressed genes.", "The temporal expression pattern provided clues to potential functions of hundreds of previously uncharacterized genes, some of which have vertebrate homologs that may function during gametogenesis."], "structured": false}
{"doc_id": 695938, "title": "Grass plants bind, retain, uptake, and transport infectious prions.", "abstract": ["Prions are the protein-based infectious agents responsible for prion diseases.", "Environmental prion contamination has been implicated in disease transmission.", "Here, we analyzed the binding and retention of infectious prion protein (PrP(Sc)) to plants.", "Small quantities of PrP(Sc) contained in diluted brain homogenate or in excretory materials (urine and feces) can bind to wheat grass roots and leaves.", "Wild-type hamsters were efficiently infected by ingestion of prion-contaminated plants.", "The prion-plant interaction occurs with prions from diverse origins, including chronic wasting disease.", "Furthermore, leaves contaminated by spraying with a prion-containing preparation retained PrP(Sc) for several weeks in the living plant.", "Finally, plants can uptake prions from contaminated soil and transport them to aerial parts of the plant (stem and leaves).", "These findings demonstrate that plants can efficiently bind infectious prions and act as carriers of infectivity, suggesting a possible role of environmental prion contamination in the horizontal transmission of the disease."], "structured": false}
{"doc_id": 696006, "title": "Innate lymphoid cells mediate influenza-induced airway hyper-reactivity independently of adaptive immunity", "abstract": ["Patients with asthma, a major public health problem, are at high risk for serious disease from influenza virus infection, but the pathogenic mechanisms by which influenza A causes airway disease and asthma are not fully known.", "We show here in a mouse model that influenza infection acutely induced airway hyper-reactivity (AHR), a cardinal feature of asthma, independently of T helper type 2 (TH2) cells and adaptive immunity.", "Instead, influenza infection induced AHR through a previously unknown pathway that required the interleukin 13 (IL-13)\u2013IL-33 axis and cells of the non-T cell, non-B cell innate lymphoid type called 'natural helper cells'.", "Infection with influenza A virus, which activates the NLRP3 inflammasome, resulted in much more production of IL-33 by alveolar macrophages, which in turn activated natural helper cells producing substantial IL-13."], "structured": false}
{"doc_id": 704526, "title": "The behaviour change wheel: A new method for characterising and designing behaviour change interventions", "abstract": ["BACKGROUND Improving the design and implementation of evidence-based practice depends on successful behaviour change interventions.", "This requires an appropriate method for characterising interventions and linking them to an analysis of the targeted behaviour.", "There exists a plethora of frameworks of behaviour change interventions, but it is not clear how well they serve this purpose.", "This paper evaluates these frameworks, and develops and evaluates a new framework aimed at overcoming their limitations.   \n", "METHODS A systematic search of electronic databases and consultation with behaviour change experts were used to identify frameworks of behaviour change interventions.", "These were evaluated according to three criteria: comprehensiveness, coherence, and a clear link to an overarching model of behaviour.", "A new framework was developed to meet these criteria.", "The reliability with which it could be applied was examined in two domains of behaviour change: tobacco control and obesity.   \n", "RESULTS Nineteen frameworks were identified covering nine intervention functions and seven policy categories that could enable those interventions.", "None of the frameworks reviewed covered the full range of intervention functions or policies, and only a minority met the criteria of coherence or linkage to a model of behaviour.", "At the centre of a proposed new framework is a 'behaviour system' involving three essential conditions: capability, opportunity, and motivation (what we term the 'COM-B system').", "This forms the hub of a 'behaviour change wheel' (BCW) around which are positioned the nine intervention functions aimed at addressing deficits in one or more of these conditions; around this are placed seven categories of policy that could enable those interventions to occur.", "The BCW was used reliably to characterise interventions within the English Department of Health's 2010 tobacco control strategy and the National Institute of Health and Clinical Excellence's guidance on reducing obesity.   \n", "CONCLUSIONS Interventions and policies to change behaviour can be usefully characterised by means of a BCW comprising: a 'behaviour system' at the hub, encircled by intervention functions and then by policy categories.", "Research is needed to establish how far the BCW can lead to more efficient design of effective interventions."], "structured": true}
{"doc_id": 708425, "title": "Intermittent prophylaxis with oral truvada protects macaques from rectal SHIV infection.", "abstract": ["HIV continues to spread globally, mainly through sexual contact.", "Despite advances in treatment and care, preventing transmission with vaccines or microbicides has proven difficult.", "A promising strategy to avoid transmission is prophylactic treatment with antiretroviral drugs before exposure to HIV.", "Clinical trials evaluating the efficacy of daily treatment with the reverse transcriptase inhibitors tenofovir disoproxil fumarate (TDF) or Truvada (TDF plus emtricitabine) are under way.", "We hypothesized that intermittent prophylactic treatment with long-acting antiviral drugs would be as effective as daily dosing in blocking the earliest stages of viral replication and preventing mucosal transmission.", "We tested this hypothesis by intermittently giving prophylactic Truvada to macaque monkeys and then exposing them rectally to simian-human immunodeficiency virus (SHIV) once a week for 14 weeks.", "A simple regimen with an oral dose of Truvada given 1, 3, or 7 days before exposure followed by a second dose 2 hours after exposure was as protective as daily drug administration, possibly because of the long intracellular persistence of the drugs.", "In addition, a two-dose regimen initiated 2 hours before or after virus exposure was effective, and full protection was obtained by doubling the Truvada concentration in both doses.", "We saw no protection if the first dose was delayed until 24 hours after exposure, underscoring the importance of blocking initial replication in the mucosa.", "Our results show that intermittent prophylactic treatment with an antiviral drug can be highly effective in preventing SHIV infection, with a wide window of protection.", "They strengthen the possibility of developing feasible, cost-effective strategies to prevent HIV transmission in humans."], "structured": false}
{"doc_id": 711256, "title": "RNA is favourable for analysing EGFR mutations in malignant pleural effusion of lung cancer.", "abstract": ["Malignant pleural effusion (MPE) is a useful specimen allowing for the evaluation of EGFR status in nonsmall cell lung cancer (NSCLC).", "However, direct sequencing of genomic DNA from MPE samples was found not to be sensitive for EGFR mutation detection.", "To test whether EGFR analysis from RNA is less prone to interference from nontumour cells that have no or lower EGFR expression, we compared three methods (sequencing from cell-derived RNA versus sequencing and mass-spectrometric analysis from genomic DNA), in parallel, for EGFR mutation detection from MPE samples in 150 lung adenocarcinoma patients receiving first-line tyrosine kinase inhibitors (TKIs).", "Among these MPE samples, EGFR mutations were much more frequently identified by sequencing using RNA than by sequencing and mass-spectrometric analysis from genomic DNA (for all mutations, 67.3 versus 44.7 and 46.7%; for L858R or exon 19 deletions, 61.3 versus 41.3 and 46.7%, respectively).", "The better mutation detection yield of sequencing from RNA was coupled with the superior prediction of clinical efficacy of first-line TKIs.", "In patients with acquired resistance, EGFR sequencing from RNA provided satisfactory detection of T790M (54.2%).", "These results demonstrated that EGFR sequencing using RNA as template greatly improves sensitivity for EGFR mutation detection from samples of MPE, highlighting RNA as the favourable source for analysing EGFR mutations from heterogeneous MPE specimens in NSCLC."], "structured": false}
{"doc_id": 712078, "title": "Pharmacological correction of a defect in PPAR\u03b3 signaling ameliorates disease severity in Cftr-deficient mice", "abstract": ["Cystic fibrosis is caused by mutations in the cystic fibrosis transmembrane conductance regulator (encoded by Cftr) that impair its role as an apical chloride channel that supports bicarbonate transport.", "Individuals with cystic fibrosis show retained, thickened mucus that plugs airways and obstructs luminal organs as well as numerous other abnormalities that include inflammation of affected organs, alterations in lipid metabolism and insulin resistance.", "Here we show that colonic epithelial cells and whole lung tissue from Cftr-deficient mice show a defect in peroxisome proliferator-activated receptor-gamma (PPAR-gamma, encoded by Pparg) function that contributes to a pathological program of gene expression.", "Lipidomic analysis of colonic epithelial cells suggests that this defect results in part from reduced amounts of the endogenous PPAR-gamma ligand 15-keto-prostaglandin E(2) (15-keto-PGE(2)).", "Treatment of Cftr-deficient mice with the synthetic PPAR-gamma ligand rosiglitazone partially normalizes the altered gene expression pattern associated with Cftr deficiency and reduces disease severity.", "Rosiglitazone has no effect on chloride secretion in the colon, but it increases expression of the genes encoding carbonic anhydrases 4 and 2 (Car4 and Car2), increases bicarbonate secretion and reduces mucus retention.", "These studies reveal a reversible defect in PPAR-gamma signaling in Cftr-deficient cells that can be pharmacologically corrected to ameliorate the severity of the cystic fibrosis phenotype in mice."], "structured": false}
{"doc_id": 712320, "title": "Visualization of volatile substances in different organelles with an atmospheric-pressure mass microscope.", "abstract": ["We have developed a mass microscope (mass spectrometry imager with spatial resolution higher than the naked eye) equipped with an atmospheric pressure ion-source chamber for laser desorption/ionization (AP-LDI) and a quadrupole ion trap time-of-flight (QIT-TOF) analyzer.", "The optical microscope combined with the mass spectrometer permitted us to precisely determine the relevant tissue region prior to performing imaging mass spectrometry (IMS).", "An ultraviolet laser tightly focused with a triplet lens was used to achieve high spatial resolution.", "An atmospheric pressure ion-source chamber enables us to analyze fresh samples with minimal loss of intrinsic water or volatile compounds.", "Mass-microscopic AP-LDI imaging of freshly cut ginger rhizome sections revealed that 6-gingerol ([M + K](+)at m/z 333.15, positive mode; [M - H](-) at m/z 293.17, negative mode) and the monoterpene ([M + K](+) at m/z 191.09), which are the compounds related to pungency and flavor, respectively, were localized in oil drop-containing organelles.", "AP-LDI-tandem MS/MS analyses were applied to compare authentic signals from freshly cut ginger directly with the standard reagent.", "Thus, our atmosphere-imaging mass spectrometer enabled us to monitor a quality of plants at the organelle level."], "structured": false}
{"doc_id": 718601, "title": "Coding of Sweet, Bitter, and Umami Tastes Different Receptor Cells Sharing Similar Signaling Pathways", "abstract": ["Mammals can taste a wide repertoire of chemosensory stimuli.", "Two unrelated families of receptors (T1Rs and T2Rs) mediate responses to sweet, amino acids, and bitter compounds.", "Here, we demonstrate that knockouts of TRPM5, a taste TRP ion channel, or PLCbeta2, a phospholipase C selectively expressed in taste tissue, abolish sweet, amino acid, and bitter taste reception, but do not impact sour or salty tastes.", "Therefore, despite relying on different receptors, sweet, amino acid, and bitter transduction converge on common signaling molecules.", "Using PLCbeta2 taste-blind animals, we then examined a fundamental question in taste perception: how taste modalities are encoded at the cellular level.", "Mice engineered to rescue PLCbeta2 function exclusively in bitter-receptor expressing cells respond normally to bitter tastants but do not taste sweet or amino acid stimuli.", "Thus, bitter is encoded independently of sweet and amino acids, and taste receptor cells are not broadly tuned across these modalities."], "structured": false}
{"doc_id": 719812, "title": "Green synthesis of silver nanoparticles and characterization of their inhibitory effects on AGEs formation using biophysical techniques", "abstract": ["Advanced glycation end-products (AGEs) resulting from non-enzymatic glycation are one of the major factors implicated in secondary complications of diabetes.", "Scientists are focusing on discovering new compounds that may be used as potential AGEs inhibitors without affecting the normal structure and function of biomolecules.", "A number of natural and synthetic compounds have been proposed as AGE inhibitors.", "In this study, we investigated the inhibitory effects of AgNPs (silver nanoparticles) in AGEs formation.", "AgNPs (~30.5 nm) synthesized from Aloe Vera leaf extract were characterized using UV-Vis spectroscopy, energy-dispersive X-ray spectroscopy (EDX), high resolution-transmission electron microscopy, X-ray diffraction and dynamic light scattering (DLS) techniques.", "The inhibitory effects of AgNPs on AGEs formation were evaluated by investigating the degree of reactivity of free amino groups (lysine and arginine residues), protein-bound carbonyl and carboxymethyl lysine (CML) content, and the effects on protein structure using various physicochemical techniques.", "The results showed that AgNPs significantly inhibit AGEs formation in a concentration dependent manner and that AgNPs have a positive effect on protein structure.", "These findings strongly suggest that AgNPs may play a therapeutic role in diabetes-related complications."], "structured": false}
{"doc_id": 735130, "title": "Myosin Light Chain\u2013activating Phosphorylation Sites Are Required for Oogenesis in Drosophila ", "abstract": ["The Drosophila spaghetti squash ( sqh ) gene encodes the regulatory myosin light chain (RMLC) of nonmuscle myosin II.", "Biochemical analysis of vertebrate nonmuscle and smooth muscle myosin II has established that phosphorylation of certain amino acids of the RMLC greatly increases the actin-dependent myosin ATPase and motor activity of myosin in vitro.", "We have assessed the in vivo importance of these sites, which in Drosophila correspond to serine-21 and threonine-20, by creating a series of transgenes in which these specific amino acids were altered.", "The phenotypes of the transgenes were examined in an otherwise null mutant background during oocyte development in Drosophila females.", "Germ line cystoblasts entirely lacking a functional sqh gene show severe defects in proliferation and cytokinesis.", "The ring canals, cytoplasmic bridges linking the oocyte to the nurse cells in the egg chamber, are abnormal, suggesting a role of myosin II in their establishment or maintenance.", "In addition, numerous aggregates of myosin heavy chain accumulate in the sqh null cells.", "Mutant sqh transgene sqh -A20, A21 in which both serine-21 and threonine-20 have been replaced by alanines behaves in most respects identically to the null allele in this system, with the exception that no heavy chain aggregates are found.", "In contrast, expression of sqh -A21, in which only the primary phosphorylation target serine-21 site is altered, partially restores functionality to germ line myosin II, allowing cystoblast division and oocyte development, albeit with some cytokinesis failure, defects in the rapid cytoplasmic transport from nurse cells to cytoplasm characteristic of late stage oogenesis, and some damaged ring canals.", "Substituting a glutamate for the serine-21 (mutant sqh -E21) allows oogenesis to be completed with minimal defects, producing eggs that can develop normally to produce fertile adults.", "Flies expressing sqh -A20, in which only the secondary phosphorylation site is absent, appear to be entirely wild type.", "Taken together, this genetic evidence argues that phosphorylation at serine-21 is critical to RMLC function in activating myosin II in vivo, but that the function can be partially provided by phosphorylation at threonine-20."], "structured": false}
{"doc_id": 739734, "title": "Stages of the pathologic process in Alzheimer disease: age categories from 1 to 100 years.", "abstract": ["Two thousand three hundred and thirty two nonselected brains from 1- to 100-year-old individuals were examined using immunocytochemistry (AT8) and Gallyas silver staining for abnormal tau; immunocytochemistry (4G8) and Campbell-Switzer staining were used for the detection of\u03b2-amyloid.", "A total of 342 cases was negative in the Gallyas stain but when restaged for AT8 only 10 were immunonegative.", "Fifty-eight cases had subcortical tau predominantly in the locus coeruleus, but there was no abnormal cortical tau (subcortical Stages a-c).", "Cortical involvement (abnormal tau in neurites) was identified first in the transentorhinal region (Stage 1a, 38 cases).", "Transentorhinal pyramidal cells displayed pretangle material (Stage 1b, 236 cases).", "Pretangles gradually became argyrophilic neurofibrillary tangles (NFTs) that progressed in parallel with NFT Stages I to VI.", "Pretangles restricted to subcortical sites were seen chiefly at younger ages.", "Of the total cases, 1,031 (44.2%) had \u03b2-amyloid plaques.", "The first plaques occurred in the neocortex after the onset of tauopathy in the brainstem.", "Plaques generally developed in the 40s in 4% of all cases, culminating in their tenth decade (75%).", "\u03b2-amyloid plaques and NFTs were significantly correlated (p < 0.0001).", "These data suggest that tauopathy associated with sporadic Alzheimer disease may begin earlier than previously thought and possibly in the lower brainstem rather than in the transentorhinal region."], "structured": false}
{"doc_id": 750781, "title": "Coronary bypass graft patency in patients with diabetes in the Bypass Angioplasty Revascularization Investigation (BARI).", "abstract": ["BACKGROUND Few studies have compared long-term status of bypass grafts between patients with and without diabetes, and uncertainty exists as to whether diabetes independently predicts poor clinical outcome after CABG.   \n", "METHODS AND RESULTS Among 1526 patients in BARI who underwent CABG as initial revascularization, 99 of 292 (34%) with treated diabetes mellitus (TDM) (those on insulin or oral hypoglycemic agents) and 469 of 1234 (38%) without TDM had follow-up angiography.", "Angiograms with the longest interval from initial surgery and before any percutaneous graft intervention (mean 3.9 years) were reviewed.", "An average of 3.0 grafts were placed at initial CABG for patients with TDM (n=297; internal mammary artery [IMA], 33%) and 2.9 grafts for patients without TDM (n=1347; IMA, 34%).", "Patients with TDM were more likely than those without to have small (<1.5 mm) grafted distal vessels (29% versus 22%) and vessels of poor quality (9% versus 6%).", "On follow-up angiography, 89% of IMA grafts were free of stenoses > or =50% among patients with TDM versus 85% among patients without TDM (P=0.23).", "For vein grafts, the corresponding percentages were 71% versus 75% (P=0.40).", "After statistical adjustment, TDM was unrelated to having a graft stenosis > or =50% (adjusted odds ratio, 0.87; 95% CI, 0.58 to 1.32).   \n", "CONCLUSIONS Despite diabetic patients' having smaller distal vessels and vessels judged to be of poorer quality, diabetes does not appear to adversely affect patency of IMA or vein grafts over an average of 4-year follow-up.", "Previously observed differences in survival between CABG-treated patients with and without diabetes may be largely a result of differential risk of mortality from noncardiac causes."], "structured": true}
{"doc_id": 751192, "title": "A novel ATAC-seq approach reveals lineage-specific reinforcement of the open chromatin landscape via cooperation between BAF and p63", "abstract": ["BACKGROUND Open chromatin regions are correlated with active regulatory elements in development and are dysregulated in diseases.", "The BAF (SWI/SNF) complex is essential for development, and has been demonstrated to remodel reconstituted chromatin in vitro and to control the accessibility of a few individual regions in vivo.", "However, it remains unclear where and how BAF controls the open chromatin landscape to regulate developmental processes, such as human epidermal differentiation.   \n", "RESULTS Using a novel \"on-plate\" ATAC-sequencing approach for profiling open chromatin landscapes with a low number of adherent cells, we demonstrate that the BAF complex is essential for maintaining 11.6 % of open chromatin regions in epidermal differentiation.", "These BAF-dependent open chromatin regions are highly cell-type-specific and are strongly enriched for binding sites for p63, a master epidermal transcription factor.", "The DNA sequences of p63 binding sites intrinsically favor nucleosome formation and are inaccessible in other cell types without p63 to prevent ectopic activation.", "In epidermal cells, BAF and p63 mutually recruit each other to maintain 14,853 open chromatin regions.", "We further demonstrate that BAF and p63 cooperatively position nucleosomes away from p63 binding sites and recruit transcriptional machinery to control tissue differentiation.   \n", "CONCLUSIONS BAF displays high specificity in controlling the open chromatin landscape during epidermal differentiation by cooperating with the master transcription factor p63 to maintain lineage-specific open chromatin regions."], "structured": true}
{"doc_id": 752423, "title": "Aging, habitual exercise, and dynamic arterial compliance.", "abstract": ["BACKGROUND A reduction in compliance of the large-sized cardiothoracic (central) arteries is an independent risk factor for the development of cardiovascular disease with advancing age.   \n", "METHODS AND RESULTS We determined the role of habitual exercise on the age-related decrease in central arterial compliance by using both cross-sectional and interventional approaches.", "First, we studied 151 healthy men aged 18 to 77 years: 54 were sedentary, 45 were recreationally active, and 53 were endurance exercise-trained.", "Central arterial compliance (simultaneous B-mode ultrasound and arterial applanation tonometry on the common carotid artery) was lower (P:<0.05) in middle-aged and older men than in young men in all 3 groups.", "There were no significant differences between sedentary and recreationally active men at any age.", "However, arterial compliance in the endurance-trained middle-aged and older men was 20% to 35% higher than in the 2 less active groups (P:<0.01).", "As such, age-related differences in central arterial compliance were smaller in the endurance-trained men than in the sedentary and recreationally active men.", "Second, we studied 20 middle-aged and older (53+/-2 years) sedentary healthy men before and after a 3-month aerobic exercise intervention (primarily walking).", "Regular exercise increased central arterial compliance (P:<0.01) to levels similar to those of the middle-aged and older endurance-trained men.", "These effects were independent of changes in body mass, adiposity, arterial blood pressure, or maximal oxygen consumption.   \n", "CONCLUSIONS Regular aerobic-endurance exercise attenuates age-related reductions in central arterial compliance and restores levels in previously sedentary healthy middle-aged and older men.", "This may be one mechanism by which habitual exercise lowers the risk of cardiovascular disease in this population."], "structured": true}
{"doc_id": 756887, "title": "A comparison of cancer screening practices in cancer survivors and in the general population: the Korean national health and nutrition examination survey (KNHANES) 2001\u20132007", "abstract": ["This study aimed to describe cancer screening rates for second primary cancer among cancer survivors in Korea, and to compare these rates with those of two control groups: individuals without a history of cancer but with other chronic diseases, and individuals without a history of cancer and without other chronic diseases.", "The study is a cross-sectional analysis of 15,556 adults \u226530 years old who participated in the 2001, 2005, and 2007 Korean National Health and Nutrition Examination Surveys (KNHANES).", "The prevalence of breast, cervical, gastric, and colorectal cancer screening examinations according to national guidelines was assessed and compared to two control groups.", "Screening rates among cancer survivors were 48.5, 54.7, 34.7, and 28.6% for breast, cervical, gastric, and colorectal cancer screening, respectively.", "Cancer survivors showed higher screening rates for all four cancer sites compared with both control groups, but breast cancer screening was only statistically significant after adjusting gender, age, marital status, education, income, working status, health insurance, smoking and drinking status, and self-reported health status.", "Cancer survivors were more likely than individuals without a cancer history to obtain screening examinations according to recommended guidelines.", "Still, screening rates even among survivors were suboptimal, emphasizing the need for a more systematic approach to second primary cancer screening and prevention."], "structured": false}
{"doc_id": 778436, "title": "Negative effect of the transcriptional activator GAL4", "abstract": ["The yeast transcriptional activator GAL4 binds specific sites on DNA to activate transcription of adjacent genes1\u20135.", "The distinct activating regions of GAL4 are rich in acidic residues and it has been suggested that these regions interact with another protein component of the transcriptional machinery (such as the TATA-binding protein or RNA polymerase II) while the DNA-binding region serves to position the activating region near the gene6,7,8.", "Here we show that various GAL4 derivatives, when expressed at high levels in yeast, inhibit transcription of certain genes lacking GAL4 binding sites, that more efficient activators inhibit more strongly and that inhibition does not depend on the DNA-binding domain.", "We suggest that this inhibition, which we call squelching, reflects titration of a transcription factor by the activating region of GAL4."], "structured": false}
{"doc_id": 790598, "title": "The Bayh\u2013Dole Act and university research and development", "abstract": ["This paper examines the relationship between university research and development (R&D) activities and the Bayh-Dole Act.", "This act made it much easier for universities to obtain patents from research funded by the federal government and may have provided universities with an incentive to alter their R&D activities.", "The Act may provide an incentive to reduce basic research (which does not generate licensing fees) and increase applied research (which does generate patents and licensing fees).", "In addition, industry might be more willing to fund university R&D projects since the results would now be easier to patent.", "This paper differs from the existing literature which uses patent data (a measure of research output) by using research and development data (a measure of inventive input) to examine the effect of the Act."], "structured": false}
{"doc_id": 791050, "title": "The relation between past exposure to fine particulate air pollution and prevalent anxiety: observational cohort study", "abstract": ["OBJECTIVE To determine whether higher past exposure to particulate air pollution is associated with prevalent high symptoms of anxiety.   \n", "DESIGN Observational cohort study.   \n", "SETTING Nurses' Health Study.   \n", "PARTICIPANTS 71,271 women enrolled in the Nurses' Health Study residing throughout the contiguous United States who had valid estimates on exposure to particulate matter for at least one exposure period of interest and data on anxiety symptoms.   \n", "MAIN OUTCOME MEASURES Meaningfully high symptoms of anxiety, defined as a score of 6 points or greater on the phobic anxiety subscale of the Crown-Crisp index, administered in 2004.   \n", "RESULTS The 71,271 eligible women were aged between 57 and 85 years (mean 70 years) at the time of assessment of anxiety symptoms, with a prevalence of high anxiety symptoms of 15%.", "Exposure to particulate matter was characterized using estimated average exposure to particulate matter <2.5 \u03bcm in diameter (PM2.5) and 2.5 to 10 \u03bcm in diameter (PM2.5-10) in the one month, three months, six months, one year, and 15 years prior to assessment of anxiety symptoms, and residential distance to the nearest major road two years prior to assessment.", "Significantly increased odds of high anxiety symptoms were observed with higher exposure to PM2.5 for multiple averaging periods (for example, odds ratio per 10 \u00b5g/m(3) increase in prior one month average PM2.5: 1.12, 95% confidence interval 1.06 to 1.19; in prior 12 month average PM2.5: 1.15, 1.06 to 1.26).", "Models including multiple exposure windows suggested short term averaging periods were more relevant than long term averaging periods.", "There was no association between anxiety and exposure to PM2.5-10.", "Residential proximity to major roads was not related to anxiety symptoms in a dose dependent manner.   \n", "CONCLUSIONS Exposure to fine particulate matter (PM2.5) was associated with high symptoms of anxiety, with more recent exposures potentially more relevant than more distant exposures.", "Research evaluating whether reductions in exposure to ambient PM2.5 would reduce the population level burden of clinically relevant symptoms of anxiety is warranted."], "structured": true}
{"doc_id": 797114, "title": "A mitochondrially targeted compound delays aging in yeast through a mechanism linking mitochondrial membrane lipid metabolism to mitochondrial redox biology\u2606", "abstract": ["A recent study revealed a mechanism of delaying aging in yeast by a natural compound which specifically impacts mitochondrial redox processes.", "In this mechanism, exogenously added lithocholic bile acid enters yeast cells, accumulates mainly in the inner mitochondrial membrane, and elicits an age-related remodeling of phospholipid synthesis and movement within both mitochondrial membranes.", "Such remodeling of mitochondrial phospholipid dynamics progresses with the chronological age of a yeast cell and ultimately causes significant changes in mitochondrial membrane lipidome.", "These changes in the composition of membrane phospholipids alter mitochondrial abundance and morphology, thereby triggering changes in the age-related chronology of such longevity-defining redox processes as mitochondrial respiration, the maintenance of mitochondrial membrane potential, the preservation of cellular homeostasis of mitochondrially produced reactive oxygen species, and the coupling of electron transport to ATP synthesis."], "structured": false}
{"doc_id": 798152, "title": "Isolation from African Sykes' monkeys (Cercopithecus mitis) of a lentivirus related to human and simian immunodeficiency viruses.", "abstract": ["Analysis of serum samples from 100 wild-caught or colony-born Sykes' monkeys (Cercopithecus mitis) in Kenya revealed that 59 animals had antibodies cross-reactive to human immunodeficiency virus type 2 (HIV-2) and to simian immunodeficiency viruses (SIVs).", "A lentivirus, designated SIVsyk, was isolated from five of six seropositive asymptomatic Sykes' monkeys, but in four cases isolation was possible only after depletion of CD8+ lymphocytes and cocultivation of the CD4(+)-enriched cell population with peripheral blood mononuclear cells from seronegative Sykes' monkeys.", "SIVsyk resembled other SIVs and HIVs morphologically, had an Mg2(+)-dependent reverse transcriptase enzyme, and replicated in and was cytopathic for CEMx174 and Sup-T1 cells.", "SIVsyk differred substantially from other SIVs, however, in that it failed to replicate in normal human, mangabey, and macaque peripheral blood mononuclear cells and serum from seropositive Sykes' monkeys immunoprecipitated env antigens from HIV-1 as well as from HIV-2, SIVsmm, and SIVagm.", "These data demonstrate a high prevalence of natural infection in Sykes' monkeys in Kenya with a lentivirus that appears to be unique with respect to its host range and antigenic cross-reactivity."], "structured": false}
{"doc_id": 799586, "title": "Role of the Single-Stranded DNA\u2013Binding Protein SsbB in Pneumococcal Transformation: Maintenance of a Reservoir for Genetic Plasticity", "abstract": ["Bacteria encode a single-stranded DNA (ssDNA) binding protein (SSB) crucial for genome maintenance.", "In Bacillus subtilis and Streptococcus pneumoniae, an alternative SSB, SsbB, is expressed uniquely during competence for genetic transformation, but its precise role has been disappointingly obscure.", "Here, we report our investigations involving comparison of a null mutant (ssbB(-)) and a C-ter truncation (ssbB\u03947) of SsbB of S. pneumoniae, the latter constructed because SSBs' acidic tail has emerged as a key site for interactions with partner proteins.", "We provide evidence that SsbB directly protects internalized ssDNA.", "We show that SsbB is highly abundant, potentially allowing the binding of ~1.15 Mb ssDNA (half a genome equivalent); that it participates in the processing of ssDNA into recombinants; and that, at high DNA concentration, it is of crucial importance for chromosomal transformation whilst antagonizing plasmid transformation.", "While the latter observation explains a long-standing observation that plasmid transformation is very inefficient in S. pneumoniae (compared to chromosomal transformation), the former supports our previous suggestion that SsbB creates a reservoir of ssDNA, allowing successive recombination cycles.", "SsbB\u03947 fulfils the reservoir function, suggesting that SsbB C-ter is not necessary for processing protein(s) to access stored ssDNA.", "We propose that the evolutionary raison d'\u00eatre of SsbB and its abundance is maintenance of this reservoir, which contributes to the genetic plasticity of S. pneumoniae by increasing the likelihood of multiple transformation events in the same cell."], "structured": false}
{"doc_id": 803312, "title": "Cerebral organoids model human brain development and microcephaly", "abstract": ["The complexity of the human brain has made it difficult to study many brain disorders in model organisms, highlighting the need for an in vitro model of human brain development.", "Here we have developed a human pluripotent stem cell-derived three-dimensional organoid culture system, termed cerebral organoids, that develop various discrete, although interdependent, brain regions.", "These include a cerebral cortex containing progenitor populations that organize and produce mature cortical neuron subtypes.", "Furthermore, cerebral organoids are shown to recapitulate features of human cortical development, namely characteristic progenitor zone organization with abundant outer radial glial stem cells.", "Finally, we use RNA interference and patient-specific induced pluripotent stem cells to model microcephaly, a disorder that has been difficult to recapitulate in mice.", "We demonstrate premature neuronal differentiation in patient organoids, a defect that could help to explain the disease phenotype.", "Together, these data show that three-dimensional organoids can recapitulate development and disease even in this most complex human tissue."], "structured": false}
{"doc_id": 810480, "title": "Localization of a gene for partial epilepsy to chromosome 10q", "abstract": ["There is strong evidence for a genetic contribution to epilepsy, but it is commonly assumed that this genetic contribution is limited to \u2018generalized\u2019 epilepsies, and that most forms of \u2018partial\u2019 epilepsy are nongenetic.", "In a linkage analysis of a single family containing 11 affected individuals, we obtained strong evidence for localization of a gene for partial epilepsy.", "This susceptibility gene maps to chromosome 10q, with a maximum two\u2013point lod score for D10S192 of 3.99 at \u03b8=0.0.", "All affected individuals share a single haplotype for seven tightly linked contiguous markers; the maximum lod score for this haplotype is 4.83 at \u03b8=0.0.", "Key recombinants place the susceptibility locus within a 10 centimorgan interval."], "structured": false}
{"doc_id": 825728, "title": "Metastatic colonization requires the repression of the epithelial-mesenchymal transition inducer Prrx1.", "abstract": ["The epithelial-mesenchymal transition (EMT) is required in the embryo for the formation of tissues for which cells originate far from their final destination.", "Carcinoma cells hijack this program for tumor dissemination.", "The relevance of the EMT in cancer is still debated because it is unclear how these migratory cells colonize distant tissues to form macrometastases.", "We show that the homeobox factor Prrx1 is an EMT inducer conferring migratory and invasive properties.", "The loss of Prrx1 is required for cancer cells to metastasize in vivo, which revert to the epithelial phenotype concomitant with the acquisition of stem cell properties.", "Thus, unlike the classical EMT transcription factors, Prrx1 uncouples EMT and stemness, and is a biomarker associated with patient survival and lack of metastasis."], "structured": false}
{"doc_id": 829646, "title": "A cohort study of the risk of cervical intraepithelial neoplasia grade 2 or 3 in relation to papillomavirus infection.", "abstract": ["BACKGROUND Human papillomavirus (HPV) has been associated with cervical intraepithelial neoplasia, but the temporal relation between the infection and the neoplasia remains unclear, as does the relative importance of the specific type of HPV, other sexually transmitted diseases, and other risk factors.   \n", "METHODS We studied prospectively a cohort of 241 women who presented for evaluation of sexually transmitted disease and had negative cervical cytologic tests.", "The women were followed every four months with cytologic and colposcopic examinations of the uterine cervix and tests for HPV DNA and other sexually transmitted diseases.   \n", "RESULTS Cervical intraepithelial neoplasia grade 2 or 3 was confirmed by biopsy in 28 women.", "On the basis of survival analysis, the cumulative incidence of cervical intraepithelial neoplasia at two years was 28 percent among women with a positive test for HPV and 3 percent among those without detectable HPV DNA: The risk was highest among those with HPV type 16 or 18 infection (adjusted relative risk as compared with that in women without HPV infection, 11; 95 percent confidence interval, 4.6 to 26; attributable risk, 52 percent).", "All 24 cases of cervical intraepithelial neoplasia grade 2 or 3 among HPV-positive women were detected within 24 months after the first positive test for HPV.", "After adjustment for the presence of HPV infection, the development of cervical intraepithelial neoplasia was also associated with younger age at first intercourse, the presence of serum antibodies to Chlamydia trachomatis, the presence of serum antibodies to cytomegalovirus, and cervical infection with Neisseria gonorrhoeae.   \n", "CONCLUSIONS Cervical intraepithelial neoplasia is a common and apparently early manifestation of cervical infection by HPV, particularly types 16 and 18."], "structured": true}
{"doc_id": 831167, "title": "Investigating survival prognosis of glioblastoma using evolutional properties of gene networks", "abstract": ["In recent years, there has been widespread interest and a large number of publications on the application of graph theory techniques into constructing and analyzing biologically-informed gene networks from cancer cell line data sets.", "Current research efforts have predominantly looked at an overall static, topological, representation of the network, and have not investigated the application of graph theoretical techniques to evolutionary investigations of cancer.", "A number of these studies have used graph theory metrics, such as degree, betweenness, and closeness centrality, to identify important hub genes in these networks.", "However, these have not fully investigated the importance of genes across the different stages of the disease.", "Previous human glioblastoma publications have identified four subtypes of glioblastoma in adults, based on signature genes.", "In one such publication, Verhaak et al. found that the subtypes correspond to a narrow median survival range, from 11.3 months for the most aggressive subtype, to 13.1 months for the least aggressive one.", "In this work, we present an evolutionary graph theory study of glioblastoma based on survival data categorization, confirming genes associated with different survival times identified using established graph theory metrics.", "The work is extending the application of graph theory approaches to evolutionary studies of cancer cell line data."], "structured": false}
{"doc_id": 834336, "title": "Compound heterozygous ZMPSTE24 mutations reduce prelamin A processing and result in a severe progeroid phenotype.", "abstract": ["Hutchinson\u2013Gilford progeria syndrome (HGPS; OMIM 176670) is an extremely rare but devastating disorder that mimics premature aging.1\u20133 Affected children appear normal at birth but typically develop failure to thrive in the first two years.", "Other features include alopecia, micrognathia, loss of subcutaneous fat with prominent veins, abnormal dentition, sclerodermatous skin changes, and osteolysis of the clavicles and distal phalanges.", "The mean age of death is at age 13 years, most commonly due to atherosclerosis.", "HGPS is mainly sporadic in occurrence, but a genetic cause has now been implicated following the identification of de novo heterozygous mutations in the LMNA gene in the majority of HGPS patients.4,5 A single family showing autosomal recessive inheritance of homozygous LMNA mutations has also been reported.6  LMNA encodes lamins A and C, components of the nuclear lamina, a meshwork underlying the nuclear envelope that serves as a structural support and is also thought to contribute to chromatin organisation and the regulation of gene expression.7,8 Interestingly, mutations in LMNA have recently been associated with at least eight inherited disorders, known as laminopathies, with differential dystrophic effects on a variety of tissues including muscle, neurones, skin, bone, and adipose tissue (reviewed in Mounkes et al 9).", "However, the realisation that these disorders share common genetic defects has led to clinical re-evaluation, with emerging evidence of significant phenotypic overlap.10 Hence the laminopathies might reasonably be considered as a spectrum of related diseases.  ", "HGPS has phenotypic similarities to several other laminopathies, in particular the atypical Werner\u2019s syndrome11 and mandibuloacral dysplasia (MAD; OMIM 248370 and 608612).12 These diseases are associated with lipodystrophy,3,13 which is the most prominent feature of another laminopathy, familial partial lipodystrophy of the Dunnigan variety (OMIM 151660).14 MAD has been further classified as two \u2026"], "structured": false}
{"doc_id": 841371, "title": "Reliability of patient responses in pay for performance schemes: analysis of national General Practitioner Patient Survey data in England", "abstract": ["OBJECTIVE To assess the robustness of patient responses to a new national survey of patient experience as a basis for providing financial incentives to doctors.   \n", "DESIGN Analysis of the representativeness of the respondents to the GP Patient Survey compared with those who were sampled (5.5 million patients registered with 8273 general practices in England in January 2009) and with the general population.", "Analysis of non-response bias looked at the relation between practice response rates and scores on the survey.", "Analysis of the reliability of the survey estimated the proportion of the variance of practice scores attributable to true differences between practices.   \n", "RESULTS The overall response rate was 38.2% (2.2 million responses), which is comparable to that in surveys using similar methodology in the UK.", "Men, young adults, and people living in deprived areas were under-represented among respondents.", "However, for questions related to pay for performance, there was no systematic association between response rates and questionnaire scores.", "Two questions which triggered payments to general practitioners were reliable measures of practice performance, with average practice-level reliability coefficients of 93.2% and 95.0%.", "Less than 3% and 0.5% of practices had fewer than the number of responses required to achieve conventional reliability levels of 90% and 70%.", "A change to the payment formula in 2009 resulted in an increase in the average impact of random variation in patient scores on payments to general practitioners compared with payments made in 2007 and 2008.   \n", "CONCLUSIONS There is little evidence to support the concern of some general practitioners that low response rates and selective non-response bias have led to systematic unfairness in payments attached to questionnaire scores.", "The study raises issues relating to the validity and reliability of payments based on patient surveys and provides lessons for the UK and for other countries considering the use of patient experience as part of pay for performance schemes."], "structured": true}
{"doc_id": 849771, "title": "Impact of low alcohol verbal descriptors on perceived strength: An experimental study", "abstract": ["OBJECTIVES Low alcohol labels are a set of labels that carry descriptors such as 'low' or 'lighter' to denote alcohol content in beverages.", "There is growing interest from policymakers and producers in lower strength alcohol products.", "However, there is a lack of evidence on how the general population perceives verbal descriptors of strength.", "The present research examines consumers' perceptions of strength (% ABV) and appeal of alcohol products using low or high alcohol verbal descriptors.   \n", "DESIGN A within-subjects experimental study in which participants rated the strength and appeal of 18 terms denoting low (nine terms), high (eight terms) and regular (one term) strengths for either (1) wine or (2) beer according to drinking preference.   \n", "METHODS Thousand six hundred adults (796 wine and 804 beer drinkers) sampled from a nationally representative UK panel.   \n", "RESULTS Low, Lower, Light, Lighter, and Reduced formed a cluster and were rated as denoting lower strength products than Regular, but higher strength than the cluster with intensifiers consisting of Extra Low, Super Low, Extra Light, and Super Light.", "Similar clustering in perceived strength was observed amongst the high verbal descriptors.", "Regular was the most appealing strength descriptor, with the low and high verbal descriptors using intensifiers rated least appealing.   \n", "CONCLUSIONS The perceived strength and appeal of alcohol products diminished the more the verbal descriptors implied a deviation from Regular.", "The implications of these findings are discussed in terms of policy implications for lower strength alcohol labelling and associated public health outcomes.", "Statement of contribution What is already known about this subject?", "Current UK and EU legislation limits the number of low strength verbal descriptors and the associated alcohol by volume (ABV) to 1.2% ABV and lower.", "There is growing interest from policymakers and producers to extend the range of lower strength alcohol products above the current cap of 1.2% ABV set out in national legislation.", "There is a lack of evidence on how the general population perceives verbal descriptors of alcohol product strength (both low and high).", "What does this study add?", "Verbal descriptors of lower strength wine and beer form two clusters and effectively communicate reduced alcohol content.", "Low, Lower, Light, Lighter, and Reduced were considered lower in strength than Regular (average % ABV).", "Descriptors using intensifiers (Extra Low, Super Low, Extra Light, and Super Light) were considered lowest in strength.", "Similar clustering in perceived strength was observed amongst the high verbal descriptors.", "The appeal of alcohol products reduced the more the verbal descriptors implied a deviation from Regular."], "structured": true}
{"doc_id": 854417, "title": "Transgenic Interleukin 10 Prevents Induction of Experimental Autoimmune Encephalomyelitis ", "abstract": ["The effectiveness of interleukin 10 (IL-10) in the treatment of autoimmune-mediated central nervous system inflammation is controversial.", "Studies of the model system, experimental autoimmune encephalomyelitis (EAE), using various routes, regimens, and delivery methods of IL-10 suggest that these variables may affect its immunoregulatory function.", "To study the influence of these factors on IL-10 regulation of EAE pathogenesis, we have analyzed transgenic mice expressing human IL-10 (hIL-10) transgene under the control of a class II major histocompatibility complex (MHC) promoter.", "The hIL-10 transgenic mice are highly resistant to EAE induced by active immunization, and this resistance appears to be mediated by suppression of autoreactive T cell function.", "Myelin-reactive T helper 1 cells are induced but nonpathogenic in the IL-10 transgenic mice.", "Antibody depletion confirmed that EAE resistance is dependent on the presence of the transgenic IL-10.", "Mice expressing the hIL-10 transgene but not the endogenous murine IL-10 gene demonstrated that transgenic IL-10 from MHC class II\u2013expressing cells is sufficient to block induction of EAE.", "This study demonstrates that IL-10 can prevent EAE completely if present at appropriate levels and times during disease induction."], "structured": false}
{"doc_id": 857189, "title": "Autosomal dominant immune dysregulation syndrome in humans with CTLA4 mutations", "abstract": ["The protein cytotoxic T lymphocyte antigen-4 (CTLA-4) is an essential negative regulator of immune responses, and its loss causes fatal autoimmunity in mice.", "We studied a large family in which five individuals presented with a complex, autosomal dominant immune dysregulation syndrome characterized by hypogammaglobulinemia, recurrent infections and multiple autoimmune clinical features.", "We identified a heterozygous nonsense mutation in exon 1 of CTLA4.", "Screening of 71 unrelated patients with comparable clinical phenotypes identified five additional families (nine individuals) with previously undescribed splice site and missense mutations in CTLA4.", "Clinical penetrance was incomplete (eight adults of a total of 19 genetically proven CTLA4 mutation carriers were considered unaffected).", "However, CTLA-4 protein expression was decreased in regulatory T cells (Treg cells) in both patients and carriers with CTLA4 mutations.", "Whereas Treg cells were generally present at elevated numbers in these individuals, their suppressive function, CTLA-4 ligand binding and transendocytosis of CD80 were impaired.", "Mutations in CTLA4 were also associated with decreased circulating B cell numbers.", "Taken together, mutations in CTLA4 resulting in CTLA-4 haploinsufficiency or impaired ligand binding result in disrupted T and B cell homeostasis and a complex immune dysregulation syndrome."], "structured": false}
{"doc_id": 864491, "title": "Specific inhibition of cyclin-dependent kinase 4/6 by PD 0332991 and associated antitumor activity in human tumor xenografts.", "abstract": ["PD 0332991 is a highly specific inhibitor of cyclin-dependent kinase 4 (Cdk4) (IC50, 0.011 micromol/L) and Cdk6 (IC50, 0.016 micromol/L), having no activity against a panel of 36 additional protein kinases.", "It is a potent antiproliferative agent against retinoblastoma (Rb)-positive tumor cells in vitro, inducing an exclusive G1 arrest, with a concomitant reduction of phospho-Ser780/Ser795 on the Rb protein.", "Oral administration of PD 0332991 to mice bearing the Colo-205 human colon carcinoma produces marked tumor regression.", "Therapeutic doses of PD 0332991 cause elimination of phospho-Rb and the proliferative marker Ki-67 in tumor tissue and down-regulation of genes under the transcriptional control of E2F.", "The results indicate that inhibition of Cdk4/6 alone is sufficient to cause tumor regression and a net reduction in tumor burden in some tumors."], "structured": false}
{"doc_id": 878526, "title": "Neutrophils support lung colonization of metastasis-initiating breast cancer cells", "abstract": ["Despite progress in the development of drugs that efficiently target cancer cells, treatments for metastatic tumours are often ineffective.", "The now well-established dependency of cancer cells on their microenvironment suggests that targeting the non-cancer-cell component of the tumour might form a basis for the development of novel therapeutic approaches.", "However, the as-yet poorly characterized contribution of host responses during tumour growth and metastatic progression represents a limitation to exploiting this approach.", "Here we identify neutrophils as the main component and driver of metastatic establishment within the (pre-)metastatic lung microenvironment in mouse breast cancer models.", "Neutrophils have a fundamental role in inflammatory responses and their contribution to tumorigenesis is still controversial.", "Using various strategies to block neutrophil recruitment to the pre-metastatic site, we demonstrate that neutrophils specifically support metastatic initiation.", "Importantly, we find that neutrophil-derived leukotrienes aid the colonization of distant tissues by selectively expanding the sub-pool of cancer cells that retain high tumorigenic potential.", "Genetic or pharmacological inhibition of the leukotriene-generating enzyme arachidonate 5-lipoxygenase (Alox5) abrogates neutrophil pro-metastatic activity and consequently reduces metastasis.", "Our results reveal the efficacy of using targeted therapy against a specific tumour microenvironment component and indicate that neutrophil Alox5 inhibition may limit metastatic progression."], "structured": false}
{"doc_id": 881332, "title": "Effect of Previous Miscarriage on Depressive Symptoms During Subsequent Pregnancy and Postpartum in the First Baby Study", "abstract": ["Our objective was to test the hypothesis that nulliparous women with a history of miscarriage have an increased risk of depression during late pregnancy, and at 1, 6, and 12 months postpartum compared to women without a history of miscarriage.", "We conducted secondary analysis of a longitudinal cohort study, the First Baby Study, and compared 448 pregnant women with a history of miscarriage to 2,343 pregnant women without a history of miscarriage on risk of probable depression (score >12 on the Edinburgh Postnatal Depression Scale).", "Logistic regression models were used to estimate odds ratios at each time point and generalized estimating equations were used to obtain estimates in longitudinal analysis.", "Women with a history of miscarriage were not more likely than woman without a history of miscarriage to score in the probable depression range during the third trimester or at 6 or 12 months postpartum but were more likely at 1 month postpartum, after adjustment for sociodemographic factors (OR 1.66, 95 % CI 1.03\u20132.69).", "Women with a history of miscarriage may be more vulnerable to depression during the first month postpartum than women without prior miscarriage, but this effect does not appear to persist beyond this time period.", "We support the promotion of awareness surrounding this issue and recommend that research is planned to identify risk factors that may position a woman with a history of miscarriage to be at higher risk for depression."], "structured": false}
{"doc_id": 883747, "title": "IL-1\u03b2, IL-4 and IL-12 control the fate of group 2 innate lymphoid cells in human airway inflammation in the lungs", "abstract": ["Group 2 innate lymphoid cells (ILC2s) secrete type 2 cytokines, which protect against parasites but can also contribute to a variety of inflammatory airway diseases.", "We report here that interleukin 1\u03b2 (IL-1\u03b2) directly activated human ILC2s and that IL-12 induced the conversion of these activated ILC2s into interferon-\u03b3 (IFN-\u03b3)-producing ILC1s, which was reversed by IL-4.", "The plasticity of ILCs was manifested in diseased tissues of patients with severe chronic obstructive pulmonary disease (COPD) or chronic rhinosinusitis with nasal polyps (CRSwNP), which displayed IL-12 or IL-4 signatures and the accumulation of ILC1s or ILC2s, respectively.", "Eosinophils were a major cellular source of IL-4, which revealed cross-talk between IL-5-producing ILC2s and IL-4-producing eosinophils.", "We propose that IL-12 and IL-4 govern ILC2 functional identity and that their imbalance results in the perpetuation of type 1 or type 2 inflammation."], "structured": false}
{"doc_id": 885056, "title": "Summary", "abstract": ["Steroid receptor RNA activator (SRA), the only known RNA coactivator, augments transactivation by nuclear receptors (NRs).", "We identified SLIRP (SRA stem-loop interacting RNA binding protein) binding to a functional substructure of SRA, STR7.", "SLIRP is expressed in normal and tumor tissues, contains an RNA recognition motif (RRM), represses NR transactivation in a SRA- and RRM-dependent manner, augments the effect of Tamoxifen, and modulates association of SRC-1 with SRA.", "SHARP, a RRM-containing corepressor, also binds STR7, augmenting repression with SLIRP.", "SLIRP colocalizes with SKIP (Chr14q24.3), another NR coregulator, and reduces SKIP-potentiated NR signaling.", "SLIRP is recruited to endogenous promoters (pS2 and metallothionein), the latter in a SRA-dependent manner, while NCoR promoter recruitment is dependent on SLIRP.", "The majority of the endogenous SLIRP resides in the mitochondria.", "Our data demonstrate that SLIRP modulates NR transactivation, suggest it may regulate mitochondrial function, and provide mechanistic insight into interactions between SRA, SLIRP, SRC-1, and NCoR."], "structured": false}
{"doc_id": 888896, "title": "Naringenin inhibits allergen-induced airway inflammation and airway responsiveness and inhibits NF-kappaB activity in a murine model of asthma.", "abstract": ["Naringenin, a flavonoid, has antiinflammatory and immunomodulatory properties.", "We investigated whether naringenin could attenuate allergen-induced airway inflammation and its possible mechanism in a murine model of asthma.", "Mice were sensitized and challenged with ovalbumin.", "Some mice were administered with naringenin before ovalbumin challenge.", "We evaluated the development of airway inflammation and airway reactivity.", "Interleukin (IL)4, IL13, chemokine (C-C motif) ligand (CCL)5, and CCL11 in bronchoalveolar lavage fluid and serum total IgE were detected by ELISA.", "IkappaBalpha degradation and inducible nitric oxide synthase (iNOS) in lungs were measured by Western blot.", "We also tested NF-kappaB binding activity by electrophoretic mobility shift assay.", "The mRNA levels of iNOS, CCL5, and CCL11 were detected by real-time PCR.", "Naringenin attenuated ovalbumin-induced airway inflammation and airway reactivity in experimental mice.", "The naringenin-treated mice had lower levels of IL4 and IL13 in the bronchoalveolar lavage fluid and lower serum total IgE. Furthermore, naringenin inhibited pulmonary IkappaBalpha degradation and NF-kappaB DNA-binding activity.", "The levels of CCL5, CCL11, and iNOS were also significantly reduced.", "The results indicated that naringenin may play protective roles in the asthma process.", "The inhibition of NF-kappaB and the decreased expression of its target genes may account for this phenomenon."], "structured": false}
{"doc_id": 919007, "title": "The evolution of Fox genes and their role in development and disease", "abstract": ["The forkhead box (Fox) family of transcription factors, which originated in unicellular eukaryotes, has expanded over time through multiple duplication events, and sometimes through gene loss, to over 40 members in mammals.", "Fox genes have evolved to acquire a specialized function in many key biological processes.", "Mutations in Fox genes have a profound effect on human disease, causing phenotypes as varied as cancer, glaucoma and language disorders.", "We summarize the salient features of the evolution of the Fox gene family and highlight the diverse contribution of various Fox subfamilies to developmental processes, from organogenesis to speech acquisition."], "structured": false}
{"doc_id": 927561, "title": "Emergent structures and dynamics of cell colonies by contact inhibition of locomotion", "abstract": ["Cells in tissues can organize into a broad spectrum of structures according to their function.", "Drastic changes of organization, such as epithelial-mesenchymal transitions or the formation of spheroidal aggregates, are often associated either to tissue morphogenesis or to cancer progression.", "Here, we study the organization of cell colonies by means of simulations of self-propelled particles with generic cell-like interactions.", "The interplay between cell softness, cell-cell adhesion, and contact inhibition of locomotion (CIL) yields structures and collective dynamics observed in several existing tissue phenotypes.", "These include regular distributions of cells, dynamic cell clusters, gel-like networks, collectively migrating monolayers, and 3D aggregates.", "We give analytical predictions for transitions between noncohesive, cohesive, and 3D cell arrangements.", "We explicitly show how CIL yields an effective repulsion that promotes cell dispersal, thereby hindering the formation of cohesive tissues.", "Yet, in continuous monolayers, CIL leads to collective cell motion, ensures tensile intercellular stresses, and opposes cell extrusion.", "Thus, our work highlights the prominent role of CIL in determining the emergent structures and dynamics of cell colonies."], "structured": false}
{"doc_id": 928281, "title": "Failure of cell cleavage induces senescence in tetraploid primary cells", "abstract": ["Tetraploidy can arise from various mitotic or cleavage defects in mammalian cells, and inheritance of multiple centrosomes induces aneuploidy when tetraploid cells continue to cycle.", "Arrest of the tetraploid cell cycle is therefore potentially a critical cellular control.", "We report here that primary rat embryo fibroblasts (REF52) and human foreskin fibroblasts become senescent in tetraploid G1 after drug- or small interfering RNA (siRNA)-induced failure of cell cleavage.", "In contrast, T-antigen-transformed REF52 and p53+/+ HCT116 tumor cells rapidly become aneuploid by continuing to cycle after cleavage failure.", "Tetraploid primary cells quickly become quiescent, as determined by loss of the Ki-67 proliferation marker and of the fluorescent ubiquitination-based cell cycle indicator/late cell cycle marker geminin.", "Arrest is not due to DNA damage, as the \u03b3-H2AX DNA damage marker remains at control levels after tetraploidy induction.", "Arrested tetraploid cells finally become senescent, as determined by SA-\u03b2-galactosidase activity.", "Tetraploid arrest is dependent on p16INK4a expression, as siRNA suppression of p16INK4a bypasses tetraploid arrest, permitting primary cells to become aneuploid.", "We conclude that tetraploid primary cells can become senescent without DNA damage and that induction of senescence is critical to tetraploidy arrest."], "structured": false}
{"doc_id": 935034, "title": "Cell death: the significance of apoptosis.", "abstract": ["Publisher Summary The classification of cell death can be based on morphological or biochemical criteria or on the circumstances of its occurrence.", "Currently, irreversible structural alteration provides the only unequivocal evidence of death; biochemical indicators of cell death that are universally applicable have to be precisely defined and studies of cell function or of reproductive capacity do not necessarily differentiate between death and dormant states from which recovery may be possible.", "It has also proved feasible to categorize most if not all dying cells into one or the other of two discrete and distinctive patterns of morphological change, which have, generally, been found to occur under disparate but individually characteristic circumstances.", "One of these patterns is the swelling proceeding to rupture of plasma and organelle membranes and dissolution of organized structure\u2014termed \u201ccoagulative necrosis.", "\u201d It results from injury by agents, such as toxins and ischemia, affects cells in groups rather than singly, and evokes exudative inflammation when it develops in vivo.", "The other morphological pattern is characterized by condensation of the cell with maintenance of organelle integrity and the formation of surface protuberances that separate as membrane-bounded globules; in tissues, these are phagocytosed and digested by resident cells, there being no associated inflammation."], "structured": false}
{"doc_id": 935538, "title": "The mitochondrial RNA-binding protein GRSF1 localizes to RNA granules and is required for posttranscriptional mitochondrial gene expression.", "abstract": ["RNA-binding proteins are at the heart of posttranscriptional gene regulation, coordinating the processing, storage, and handling of cellular RNAs.", "We show here that GRSF1, previously implicated in the binding and selective translation of influenza mRNAs, is targeted to mitochondria where it forms granules that colocalize with foci of newly synthesized mtRNA next to mitochondrial nucleoids.", "GRSF1 preferentially binds RNAs transcribed from three contiguous genes on the light strand of mtDNA, the ND6 mRNA, and the long noncoding RNAs for cytb and ND5, each of which contains multiple consensus binding sequences.", "RNAi-mediated knockdown of GRSF1 leads to alterations in mitochondrial RNA stability, abnormal loading of mRNAs and lncRNAs on the mitochondrial ribosome, and impaired ribosome assembly.", "This results in a specific protein synthesis defect and a failure to assemble normal amounts of the oxidative phosphorylation complexes.", "These data implicate GRSF1 as a key regulator of posttranscriptional mitochondrial gene expression."], "structured": false}
{"doc_id": 946756, "title": "Identification and purification of a 62,000-dalton protein that binds specifically to the polypyrimidine tract of introns.", "abstract": ["A protein of molecular size 62,000 daltons (p62) was detected in HeLa cell nuclear extracts by UV cross-linking to mRNA precursors.", "p62 binds specifically to the polypyrimidine tract of the 3' splice site region of introns.", "p62 purified to homogeneity binds the polypyrimidine tract of pre-mRNAs.", "This binding does not require the AG dinucleotide at the 3' splice site.", "Alterations in the polypyrimidine tract that reduce the binding of p62 yield a corresponding reduction in the efficiency of formation of a U2 snRNP/pre-mRNA complex and splicing.", "The p62 protein is retained in the spliceosome, where it remains bound to the pre-mRNA.", "This polypyrimidine tract binding protein (pPTB) is proposed to be a critical component in recognition of the 3' splice site during splicing."], "structured": false}
{"doc_id": 947631, "title": "Capsule endoscopy in acute upper gastrointestinal hemorrhage: a prospective cohort study.", "abstract": ["BACKGROUND AND STUDY AIMS Capsule endoscopy may play a role in the evaluation of patients presenting with acute upper gastrointestinal hemorrhage in the emergency department.   \n", "PATIENTS AND METHODS We evaluated adults with acute upper gastrointestinal hemorrhage presenting to the emergency departments of two academic centers.", "Patients ingested a wireless video capsule, which was followed immediately by a nasogastric tube aspiration and later by esophagogastroduodenoscopy (EGD).", "We compared capsule endoscopy with nasogastric tube aspiration for determination of the presence of blood, and with EGD for discrimination of the source of bleeding, identification of peptic/inflammatory lesions, safety, and patient satisfaction.   \n", "RESULTS The study enrolled 49 patients (32 men, 17 women; mean age 58.3 \u00b1 19 years), but three patients did not complete the capsule endoscopy and five were intolerant of the nasogastric tube.", "Blood was detected in the upper gastrointestinal tract significantly more often by capsule endoscopy (15 /18 [83.3 %]) than by nasogastric tube aspiration (6 /18 [33.3 %]; P = 0.035).", "There was no significant difference in the identification of peptic/inflammatory lesions between capsule endoscopy (27 /40 [67.5 %]) and EGD (35 /40 [87.5 %]; P = 0.10, OR 0.39 95 %CI 0.11 - 1.15).", "Capsule endoscopy reached the duodenum in 45 /46 patients (98 %).", "One patient (2.2 %) had self-limited shortness of breath and one (2.2 %) had coughing on capsule ingestion.   \n", "CONCLUSIONS In an emergency department setting, capsule endoscopy appears feasible and safe in people presenting with acute upper gastrointestinal hemorrhage.", "Capsule endoscopy identifies gross blood in the upper gastrointestinal tract, including the duodenum, significantly more often than nasogastric tube aspiration and identifies inflammatory lesions, as well as EGD.", "Capsule endoscopy may facilitate patient triage and earlier endoscopy, but should not be considered a substitute for EGD."], "structured": true}
{"doc_id": 949309, "title": "Electroporation of Cas9 protein/sgRNA into early pronuclear zygotes generates non-mosaic mutants in the mouse.", "abstract": ["The CRISPR/Cas9 system is a powerful tool for elucidating the roles of genes in a wide variety of organisms including mice.", "To obtain genetically modified embryos or mice by this method, Cas9 mRNA and sgRNA are usually introduced into zygotes by microinjection or electroporation.", "However, most mutants generated with this method are genetically mosaic, composed of several types of cells carrying different mutations, which complicates phenotype analysis in founder embryos or mice.", "To simplify the analysis and to elucidate the roles of genes involved in developmental processes, a method for producing non-mosaic mutants is needed.", "Here, we established a method for generating non-mosaic mouse mutant embryos.", "We introduced Cas9 protein and sgRNA into in vitro fertilized (IVF) zygotes by electroporation, which enabled the genome editing to occur before the first replication of the mouse genome.", "As a result, all of the cells in the mutant carried the same set of mutations.", "This method solves the problem of mosaicism/allele complexity in founder mutant embryos or mice generated by the CRIPSR/Cas9 system."], "structured": false}
{"doc_id": 950306, "title": "Molecular Basis for Target RNA Recognition and Cleavage by Human RISC", "abstract": ["The RNA-Induced Silencing Complex (RISC) is a ribonucleoprotein particle composed of a single-stranded short interfering RNA (siRNA) and an endonucleolytically active Argonaute protein, capable of cleaving mRNAs complementary to the siRNA.", "The mechanism by which RISC cleaves a target RNA is well understood, however it remains enigmatic how RISC finds its target RNA.", "Here, we show, both in vitro and in vivo, that the accessibility of the target site correlates directly with the efficiency of cleavage, demonstrating that RISC is unable to unfold structured RNA.", "In the course of target recognition, RISC transiently contacts single-stranded RNA nonspecifically and promotes siRNA-target RNA annealing.", "Furthermore, the 5' part of the siRNA within RISC creates a thermodynamic threshold that determines the stable association of RISC and the target RNA.", "We therefore provide mechanistic insights by revealing features of RISC and target RNAs that are crucial to achieve efficiency and specificity in RNA interference."], "structured": false}
{"doc_id": 952111, "title": "Cancer associated fibroblasts (CAFs) in tumor microenvironment.", "abstract": ["Cancer associated fibroblasts (CAFs) is one of the most crucial components of the tumor microenvironment which promotes the growth and invasion of cancer cells by various mechanisms.", "CAFs demonstrate a high degree of heterogeneity due to their various origins; however, many distinct morphological features and physiological functions of CAFs have been identified.", "It is becoming clear that the crosstalk between the cancer cells and the CAFs plays a key role in the progression of cancer, and understanding this mutual relationship would eventually enable us to treat cancer patients by targeting CAFs.", "In this review, we will discuss the latest findings on the role of CAFs in tumorigenesis and metastasis as well as potential therapeutic implication of CAFs."], "structured": false}
{"doc_id": 970012, "title": "Cold Exposure Promotes Atherosclerotic Plaque Growth and Instability via UCP1-Dependent Lipolysis", "abstract": ["Molecular mechanisms underlying the cold-associated high cardiovascular risk remain unknown.", "Here, we show that the cold-triggered food-intake-independent lipolysis significantly increased plasma levels of small low-density lipoprotein (LDL) remnants, leading to accelerated development of atherosclerotic lesions in mice.", "In two genetic mouse knockout models (apolipoprotein E(-/-) [ApoE(-/-)] and LDL receptor(-/-) [Ldlr(-/-)] mice), persistent cold exposure stimulated atherosclerotic plaque growth by increasing lipid deposition.", "Furthermore, marked increase of inflammatory cells and plaque-associated microvessels were detected in the cold-acclimated ApoE(-/-) and Ldlr(-/-) mice, leading to plaque instability.", "Deletion of uncoupling protein 1 (UCP1), a key mitochondrial protein involved in thermogenesis in brown adipose tissue (BAT), in the ApoE(-/-) strain completely protected mice from the cold-induced atherosclerotic lesions.", "Cold acclimation markedly reduced plasma levels of adiponectin, and systemic delivery of adiponectin protected ApoE(-/-) mice from plaque development.", "These findings provide mechanistic insights on low-temperature-associated cardiovascular risks."], "structured": false}
{"doc_id": 980008, "title": "Mild overexpression of MeCP2 causes a progressive neurological disorder in mice.", "abstract": ["Mutations in the X-linked methyl-CpG-binding protein 2 (MECP2), encoding a transcriptional repressor, cause Rett syndrome and a variety of related neurodevelopmental disorders.", "The vast majority of mutations associated with human disease are loss-of-function mutations, but precisely what aspect of MeCP2 function is responsible for these phenotypes remains unknown.", "We overexpressed wild-type human protein in transgenic mice using a large genomic clone containing the entire human MECP2 locus.", "Detailed neurobehavioral and electrophysiological studies in transgenic line MeCP2(Tg1), which expresses MeCP2 at approximately 2-fold wild-type levels, demonstrated onset of phenotypes around 10 weeks of age.", "Surprisingly, these mice displayed enhanced motor and contextual learning and enhanced synaptic plasticity in the hippocampus.", "After 20 weeks of age, however, these mice developed seizures, became hypoactive and approximately 30% of them died by 1 year of age.", "These data demonstrate that MeCP2 levels must be tightly regulated in vivo, and that even mild overexpression of this protein is detrimental.", "Furthermore, these results support the possibility that duplications or gain-of-function mutations in MECP2 might underlie some cases of X-linked delayed-onset neurobehavioral disorders."], "structured": false}
{"doc_id": 980196, "title": "Alcohol Sales and Risk of Serious Assault", "abstract": ["BACKGROUND Alcohol is a contributing cause of unintentional injuries, such as motor vehicle crashes.", "Prior research on the association between alcohol use and violent injury was limited to survey-based data, and the inclusion of cases from a single trauma centre, without adequate controls.", "Beyond these limitations was the inability of prior researchers to comprehensively capture most alcohol sales.", "In Ontario, most alcohol is sold through retail outlets run by the provincial government, and hospitals are financed under a provincial health care system.", "We assessed the risk of being hospitalized due to assault in association with retail alcohol sales across Ontario.   \n", "METHODS AND FINDINGS We performed a population-based case-crossover analysis of all persons aged 13 years and older hospitalized for assault in Ontario from 1 April 2002 to 1 December 2004.", "On the day prior to each assault case's hospitalization, the volume of alcohol sold at the store in closest proximity to the victim's home was compared to the volume of alcohol sold at the same store 7 d earlier.", "Conditional logistic regression analysis was used to determine the associated relative risk (RR) of assault per 1,000 l higher daily sales of alcohol.", "Of the 3,212 persons admitted to hospital for assault, nearly 25% were between the ages of 13 and 20 y, and 83% were male.", "A total of 1,150 assaults (36%) involved the use of a sharp or blunt weapon, and 1,532 (48%) arose during an unarmed brawl or fight.", "For every 1,000 l more of alcohol sold per store per day, the relative risk of being hospitalized for assault was 1.13 (95% confidence interval [CI] 1.02-1.26).", "The risk was accentuated for males (1.18, 95% CI 1.05-1.33), youth aged 13 to 20 y (1.21, 95% CI 0.99-1.46), and those in urban areas (1.19, 95% CI 1.06-1.35).   \n", "CONCLUSIONS The risk of being a victim of serious assault increases with alcohol sales, especially among young urban men.", "Akin to reducing the risk of driving while impaired, consideration should be given to novel methods of preventing alcohol-related violence."], "structured": true}
{"doc_id": 982650, "title": "miR-375 inhibits autophagy and reduces viability of hepatocellular carcinoma cells under hypoxic conditions.", "abstract": ["BACKGROUND & AIMS Tumor cells survive hypoxic conditions by inducing autophagy.", "We investigated the roles of microRNAs (miRNAs) in regulating autophagy of hepatocellular carcinoma (HCC) cells under hypoxic conditions.   \n", "METHODS We used gain- and loss-of-function methods to evaluate the effect of miRNAs on autophagy in human HCC cell lines (Huh7 and Hep3B) under hypoxic conditions.", "Autophagy was quantified by immunoblot, immunofluoresence, and transmission electron microscopy analyses, and after incubation of cells with bafilomycin A1.", "We used a luciferase reporter assay to confirm associations between miRNAs and their targets.", "We analyzed growth of HCC xenograft tumors in nude mice.   \n", "RESULTS miR-375 was down-regulated in HCC cells and tissues; it inhibited autophagy under hypoxic conditions by suppressing the conversion of LC3I to LC3II and thereby autophagic flux.", "The ability of miR-375 to inhibit autophagy was independent of its ability to regulate 3'-phosphoinositide-dependent protein kinase-1-AKT-mammalian target of rapamycin signaling, but instead involved suppression of ATG7, an autophagy-associated gene.", "miR-375 bound directly to a predicted site in the 3' untranslated region of ATG7.", "Up-regulating miR-375 or down-regulating ATG7 inhibited mitochondrial autophagy of HCC cells, reduced the elimination of damaged mitochondria under hypoxia, increased release of mitochondrial apoptotic proteins, and reduced viability of HCC cells.", "In mice, xenograft tumors that expressed miR-375 had fewer autophagic cells, larger areas of necrosis, and grew more slowly than tumors from HCC cells that expressed lower levels of miR-375.   \n", "CONCLUSIONS miR-375 inhibits autophagy by reducing expression of ATG7 and impairs viability of HCC cells under hypoxic conditions in culture and in mice.", "miRNAs that inhibit autophagy of cancer cells might be developed as therapeutics."], "structured": true}
{"doc_id": 984825, "title": "Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells", "abstract": ["Post-transcriptional modification of RNA nucleosides occurs in all living organisms.", "Pseudouridine, the most abundant modified nucleoside in non-coding RNAs, enhances the function of transfer RNA and ribosomal RNA by stabilizing the RNA structure.", "Messenger RNAs were not known to contain pseudouridine, but artificial pseudouridylation dramatically affects mRNA function--it changes the genetic code by facilitating non-canonical base pairing in the ribosome decoding centre.", "However, without evidence of naturally occurring mRNA pseudouridylation, its physiological relevance was unclear.", "Here we present a comprehensive analysis of pseudouridylation in Saccharomyces cerevisiae and human RNAs using Pseudo-seq, a genome-wide, single-nucleotide-resolution method for pseudouridine identification.", "Pseudo-seq accurately identifies known modification sites as well as many novel sites in non-coding RNAs, and reveals hundreds of pseudouridylated sites in mRNAs.", "Genetic analysis allowed us to assign most of the new modification sites to one of seven conserved pseudouridine synthases, Pus1-4, 6, 7 and 9.", "Notably, the majority of pseudouridines in mRNA are regulated in response to environmental signals, such as nutrient deprivation in yeast and serum starvation in human cells.", "These results suggest a mechanism for the rapid and regulated rewiring of the genetic code through inducible mRNA modifications.", "Our findings reveal unanticipated roles for pseudouridylation and provide a resource for identifying the targets of pseudouridine synthases implicated in human disease."], "structured": false}
{"doc_id": 991137, "title": "The descent of memory T-cell subsets", "abstract": ["The immune system has evolved by continuously increasing its complexity to provide the host with an advantage over infectious agents.", "The development of immunological memory engenders long-lasting protection and lengthens the lifespan of the host.", "The generation of subsets of memory T cells with distinct homing and functional properties increases our defensive capabilities.", "However, the developmental relationship of memory T-cell subsets is a matter of debate.", "In this Opinion article, in light of recent developments, we suggest that it is probable that two distinct lineages comprise the memory CD8+ T-cell population generated in response to infection."], "structured": false}
{"doc_id": 991139, "title": "Differential distribution of IL28B.rs12979860 single-nucleotide polymorphism among Egyptian healthcare workers with and without a hepatitis C virus-specific cellular immune response", "abstract": ["The CC genotype of the interleukin (IL)-28B.rs12979860 gene has been associated with spontaneous hepatitis C virus (HCV) clearance and treatment response.", "The distribution and correlation of an IL28B.rs12979860 single-nucleotide polymorphism (SNP) with HCV-specific cell-mediated immune (CMI) responses among Egyptian healthcare workers (HCWs) is not known.", "We determined this relationship in 402 HCWs who serve a patient cohort with ~85 % HCV prevalence.", "We enrolled 402 HCWs in four groups: group 1 (n = 258), seronegative aviremic subjects; group 2 (n = 25), seronegative viremic subjects; group 3 (n = 41), subjects with spontaneously resolved HCV infection; and group 4 (n = 78), chronic HCV patients.", "All subjects were tested for an HCV-specific CMI response using an ex-vivo interferon-gamma (IFN\u03b3) ELISpot assay with nine HCV genotype-4a overlapping 15-mer peptide pools corresponding to all of the HCV proteins.", "All subjects were tested for IL28B.rs12979860 SNP by real-time PCR.", "An HCV-specific CMI was demonstrated in ~27 % of the seronegative aviremic HCWs (group 1), suggesting clearance of infection after low-level exposure to HCV.", "The frequency of IL28B.rs12979860 C allele homozygosity in the four groups was 49 %, 48 %, 49 %, and 23 %, while that of the T allele was 14 %, 16 %, 12 and 19 %, respectively, suggesting differential distributions among subjects with different HCV status.", "As reported, IL28B.rs12979860 predicted the outcome of HCV infection (p < 0.05), but we did not find any relationship between the IL28B genotypes and the outcome of HCV-specific CMI responses in the four groups (p > 0.05).", "The data show differential IL28B.rs12979860 genotype distribution among Egyptian HCWs with different HCV status and could not predict the outcome of HCV-specific CMI responses."], "structured": false}
{"doc_id": 994800, "title": "TCR ligand density and affinity determine peripheral induction of Foxp3 in vivo", "abstract": ["T cell receptor (TCR) ligation is required for the extrathymic differentiation of forkhead box p3(+) (Foxp3(+)) regulatory T cells.", "Several lines of evidence indicate that weak TCR stimulation favors induction of Foxp3 in the periphery; however, it remains to be determined how TCR ligand potency influences this process.", "We characterized the density and affinity of TCR ligand favorable for Foxp3 induction and found that a low dose of a strong agonist resulted in maximal induction of Foxp3 in vivo.", "Initial Foxp3 induction by weak agonist peptide could be enhanced by disruption of TCR-peptide major histocompatibility complex (pMHC) interactions or alteration of peptide dose.", "However, time course experiments revealed that Foxp3-positive cells induced by weak agonist stimulation are deleted, along with their Foxp3-negative counterparts, whereas Foxp3-positive cells induced by low doses of the strong agonist persist.", "Our results suggest that, together, pMHC ligand potency, density, and duration of TCR interactions define a cumulative quantity of TCR stimulation that determines initial peripheral Foxp3 induction.", "However, in the persistence of induced Foxp3(+) T cells, TCR ligand potency and density are noninterchangeable factors that influence the route to peripheral tolerance."], "structured": false}
{"doc_id": 997143, "title": "Electromagnetic interference from radio frequency identification inducing potentially hazardous incidents in critical care medical equipment.", "abstract": ["CONTEXT Health care applications of autoidentification technologies, such as radio frequency identification (RFID), have been proposed to improve patient safety and also the tracking and tracing of medical equipment.", "However, electromagnetic interference (EMI) by RFID on medical devices has never been reported.   \n", "OBJECTIVE To assess and classify incidents of EMI by RFID on critical care equipment.   \n", "DESIGN AND SETTING Without a patient being connected, EMI by 2 RFID systems (active 125 kHz and passive 868 MHz) was assessed under controlled conditions during May 2006, in the proximity of 41 medical devices (in 17 categories, 22 different manufacturers) at the Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands.", "Assessment took place according to an international test protocol.", "Incidents of EMI were classified according to a critical care adverse events scale as hazardous, significant, or light.   \n", "RESULTS In 123 EMI tests (3 per medical device), RFID induced 34 EMI incidents: 22 were classified as hazardous, 2 as significant, and 10 as light.", "The passive 868-MHz RFID signal induced a higher number of incidents (26 incidents in 41 EMI tests; 63%) compared with the active 125-kHz RFID signal (8 incidents in 41 EMI tests; 20%); difference 44% (95% confidence interval, 27%-53%; P < .001).", "The passive 868-MHz RFID signal induced EMI in 26 medical devices, including 8 that were also affected by the active 125-kHz RFID signal (26 in 41 devices; 63%).", "The median distance between the RFID reader and the medical device in all EMI incidents was 30 cm (range, 0.1-600 cm).   \n", "CONCLUSIONS In a controlled nonclinical setting, RFID induced potentially hazardous incidents in medical devices.", "Implementation of RFID in the critical care environment should require on-site EMI tests and updates of international standards."], "structured": true}
{"doc_id": 1006165, "title": "Potent RNAi by short RNA triggers.", "abstract": ["RNA interference (RNAi) is a gene-silencing mechanism by which a ribonucleoprotein complex, the RNA-induced silencing complex (RISC) and a double-stranded (ds) short-interfering RNA (siRNA), targets a complementary mRNA for site-specific cleavage and subsequent degradation.", "While longer dsRNA are endogenously processed into 21- to 24-nucleotide (nt) siRNAs or miRNAs to induce gene silencing, RNAi studies in human cells typically use synthetic 19- to 20-nt siRNA duplexes with 2-nt overhangs at the 3'-end of both strands.", "Here, we report that systematic synthesis and analysis of siRNAs with deletions at the passenger and/or guide strand revealed a short RNAi trigger, 16-nt siRNA, which induces potent RNAi in human cells.", "Our results indicate that the minimal requirement for dsRNA to trigger RNAi is an approximately 42 A A-form helix with approximately 1.5 helical turns.", "The 16-nt siRNA more effectively knocked down mRNA and protein levels than 19-nt siRNA when targeting the endogenous CDK9 gene, suggesting that 16-nt siRNA is a more potent RNAi trigger.", "In vitro kinetic analysis of RNA-induced silencing complex (RISC) programmed in HeLa cells indicates that 16-nt siRNA has a higher RISC-loading capacity than 19-nt siRNA.", "These results suggest that RISC assembly and activation during RNAi does not necessarily require a 19-nt duplex siRNA and that 16-nt duplexes can be designed as more potent triggers to induce RNAi."], "structured": false}
{"doc_id": 1022115, "title": "IL-23\u2013responsive innate lymphoid cells are increased in inflammatory bowel disease", "abstract": ["Results of experimental and genetic studies have highlighted the role of the IL-23/IL-17 axis in the pathogenesis of inflammatory bowel disease (IBD).", "IL-23-driven inflammation has been primarily linked to Th17 cells; however, we have recently identified a novel population of innate lymphoid cells (ILCs) in mice that produces IL-17, IL-22, and IFN-\u03b3 in response to IL-23 and mediates innate colitis.", "The relevance of ILC populations in human health and disease is currently poorly understood.", "In this study, we have analyzed the role of IL-23-responsive ILCs in the human intestine in control and IBD patients.", "Our results show increased expression of the Th17-associated cytokine genes IL17A and IL17F among intestinal CD3\u207b cells in IBD.", "IL17A and IL17F expression is restricted to CD56\u207b ILCs, whereas IL-23 induces IL22 and IL26 in the CD56\u207a ILC compartment.", "Furthermore, we observed a significant and selective increase in CD127\u207aCD56\u207b ILCs in the inflamed intestine in Crohn's disease (CD) patients but not in ulcerative colitis patients.", "These results indicate that IL-23-responsive ILCs are present in the human intestine and that intestinal inflammation in CD is associated with the selective accumulation of a phenotypically distinct ILC population characterized by inflammatory cytokine expression.", "ILCs may contribute to intestinal inflammation through cytokine production, lymphocyte recruitment, and organization of the inflammatory tissue and may represent a novel tissue-specific target for subtypes of IBD."], "structured": false}
{"doc_id": 1031534, "title": "Scaling of Dorsal-Ventral Patterning by Embryo Size-Dependent Degradation of Spemann\u2019s Organizer Signals", "abstract": ["Spemann's organizer plays a key role in dorsal-ventral (DV) patterning in the amphibian embryo by secreting diffusible proteins such as Chordin, an antagonist to ventralizing bone morphogenetic proteins (BMPs).", "The DV patterning is so robust that an amphibian embryo with its ventral half surgically removed can develop into a smaller but proportionally patterned larva.", "Here, we show that this robust patterning depends on facilitated Chordin degradation and requires the expression of the Chordin-proteinase inhibitor Sizzled on the opposite side.", "Sizzled, which is stable and diffuses widely along the DV axis, stabilizes Chordin and expands its distribution in the ventral direction.", "This expanded Chordin distribution, in turn, limits BMP-dependent Sizzled production, forming an axis-wide feedback loop for shaping Chordin's activity.", "Using bisection assays, we demonstrate that Chordin degradation is dynamically controlled by embryo-size-coupled Sizzled accumulation.", "We propose a scaling model that enables the DV pattern to adjust proportionally to embryonic axis size."], "structured": false}
{"doc_id": 1032372, "title": "Augmenting Antitumor Immune Responses with Epigenetic Modifying Agents", "abstract": ["Epigenetic silencing of immune-related genes is a striking feature of the cancer genome that occurs in the process of tumorigenesis.", "This phenomena impacts antigen processing and antigen presentation by tumor cells and facilitates evasion of immunosurveillance.", "Further modulation of the tumor microenvironment by altered expression of immunosuppressive cytokines impairs antigen-presenting cells and cytolytic T-cell function.", "The potential reversal of immunosuppression by epigenetic modulation is therefore a promising and versatile therapeutic approach to reinstate endogenous immune recognition and tumor lysis.", "Pre-clinical studies have identified multiple elements of the immune system that can be modulated by epigenetic mechanisms and result in improved antigen presentation, effector T-cell function, and breakdown of suppressor mechanisms.", "Recent clinical studies are utilizing epigenetic therapies prior to, or in combination with, immune therapies to improve clinical outcomes."], "structured": false}
{"doc_id": 1044552, "title": "Activation of proteinase-activated receptor 2 in human osteoarthritic cartilage upregulates catabolic and proinflammatory pathways capable of inducing cartilage degradation: a basic science study", "abstract": ["Proteinase-activated receptors (PARs) belong to a family of G protein-coupled receptors.", "PARs are activated by a serine-dependent cleavage generating a tethered activating ligand.", "PAR-2 was shown to be involved in inflammatory pathways.", "We investigated the in situ levels and modulation of PAR-2 in human normal and osteoarthritis (OA) cartilage/chondrocytes.", "Furthermore, we evaluated the role of PAR-2 on the synthesis of the major catabolic factors in OA cartilage, including metalloproteinase (MMP)-1 and MMP-13 and the inflammatory mediator cyclooxygenase 2 (COX-2), as well as the PAR-2-activated signalling pathways in OA chondrocytes.", "PAR-2 expression was determined using real-time reverse transcription-polymerase chain reaction and protein levels by immunohistochemistry in normal and OA cartilage.", "Protein modulation was investigated in OA cartilage explants treated with a specific PAR-2-activating peptide (PAR-2-AP), SLIGKV-NH2 (1 to 400 \u03bcM), interleukin 1 beta (IL-1\u03b2) (100 pg/mL), tumor necrosis factor-alpha (TNF-\u03b1) (5 ng/mL), transforming growth factor-beta-1 (TGF-\u03b21) (10 ng/mL), or the signalling pathway inhibitors of p38 (SB202190), MEK1/2 (mitogen-activated protein kinase kinase) (PD98059), and nuclear factor-kappa B (NF-\u03baB) (SN50), and PAR-2 levels were determined by immunohistochemistry.", "Signalling pathways were analyzed on OA chondrocytes by Western blot using specific phospho-antibodies against extracellular signal-regulated kinase 1/2 (Erk1/2), p38, JNK (c-jun N-terminal kinase), and NF-\u03baB in the presence or absence of the PAR-2-AP and/or IL-1\u03b2.", "PAR-2-induced MMP and COX-2 levels in cartilage were determined by immunohistochemistry.", "PAR-2 is produced by human chondrocytes and is significantly upregulated in OA compared with normal chondrocytes (p < 0.04 and p < 0.03, respectively).", "The receptor levels were significantly upregulated by IL-1\u03b2 (p < 0.006) and TNF-\u03b1 (p < 0.002) as well as by the PAR-2-AP at 10, 100, and 400 \u03bcM (p < 0.02) and were downregulated by the inhibition of p38.", "After 48 hours of incubation, PAR-2 activation significantly induced MMP-1 and COX-2 starting at 10 \u03bcM (both p < 0.005) and MMP-13 at 100 \u03bcM (p < 0.02) as well as the phosphorylation of Erk1/2 and p38 within 5 minutes of incubation (p < 0.03).", "Though not statistically significant, IL-1\u03b2 produced an additional effect on the activation of Erk1/2 and p38.", "This study documents, for the first time, functional consequences of PAR-2 activation in human OA cartilage, identifies p38 as the major signalling pathway regulating its synthesis, and demonstrates that specific PAR-2 activation induces Erk1/2 and p38 in OA chondrocytes.", "These results suggest PAR-2 as a potential new therapeutic target for the treatment of OA."], "structured": false}
{"doc_id": 1049501, "title": "Neutrophil extracellular traps enriched in oxidized mitochondrial DNA are interferogenic and contribute to lupus-like disease", "abstract": ["Neutrophil extracellular traps (NETs) are implicated in autoimmunity, but how they are generated and their roles in sterile inflammation remain unclear.", "Ribonucleoprotein immune complexes (RNP ICs), inducers of NETosis, require mitochondrial reactive oxygen species (ROS) for maximal NET stimulation.", "After RNP IC stimulation of neutrophils, mitochondria become hypopolarized and translocate to the cell surface.", "Extracellular release of oxidized mitochondrial DNA is proinflammatory in vitro, and when this DNA is injected into mice, it stimulates type I interferon (IFN) signaling through a pathway dependent on the DNA sensor STING.", "Mitochondrial ROS are also necessary for spontaneous NETosis of low-density granulocytes from individuals with systemic lupus erythematosus.", "This was also observed in individuals with chronic granulomatous disease, who lack NADPH oxidase activity but still develop autoimmunity and type I IFN signatures.", "Mitochondrial ROS inhibition in vivo reduces disease severity and type I IFN responses in a mouse model of lupus.", "Together, these findings highlight a role for mitochondria in the generation not only of NETs but also of pro-inflammatory oxidized mitochondrial DNA in autoimmune diseases."], "structured": false}
{"doc_id": 1065627, "title": "Microenvironment rigidity modulates responses to the HER2 receptor tyrosine kinase inhibitor lapatinib via YAP and TAZ transcription factors.", "abstract": ["Stiffness is a biophysical property of the extracellular matrix that modulates cellular functions, including proliferation, invasion, and differentiation, and it also may affect therapeutic responses.", "Therapeutic durability in cancer treatments remains a problem for both chemotherapies and pathway-targeted drugs, but the reasons for this are not well understood.", "Tumor progression is accompanied by changes in the biophysical properties of the tissue, and we asked whether matrix rigidity modulated the sensitive versus resistant states in HER2-amplified breast cancer cell responses to the HER2-targeted kinase inhibitor lapatinib.", "The antiproliferative effect of lapatinib was inversely proportional to the elastic modulus of the adhesive substrata.", "Down-regulation of the mechanosensitive transcription coactivators YAP and TAZ, either by siRNA or with the small-molecule YAP/TEAD inhibitor verteporfin, eliminated modulus-dependent lapatinib resistance.", "Reduction of YAP in vivo in mice also slowed the growth of implanted HER2-amplified tumors, showing a trend of increasing sensitivity to lapatinib as YAP decreased.", "Thus we address the role of stiffness in resistance to and efficacy of a HER2 pathway-targeted therapeutic via the mechanotransduction arm of the Hippo pathway."], "structured": false}
{"doc_id": 1067605, "title": "Effective population size and patterns of molecular evolution and variation", "abstract": ["The effective size of a population, Ne, determines the rate of change in the composition of a population caused by genetic drift, which is the random sampling of genetic variants in a finite population.", "Ne is crucial in determining the level of variability in a population, and the effectiveness of selection relative to drift.", "This article reviews the properties of Ne in a variety of different situations of biological interest, and the factors that influence it.", "In particular, the action of selection means that Ne varies across the genome, and advances in genomic techniques are giving new insights into how selection shapes Ne."], "structured": false}
{"doc_id": 1068106, "title": "Is emotional dysregulation part of the psychopathology of ADHD in adults?", "abstract": ["Attention-deficit hyperactivity disorder is a common condition in adulthood.", "The disorder is characterized by symptoms of inattention, hyperactivity, and impulsivity.", "Alongside these symptoms, it is discussed whether symptoms of emotional dysregulation could add additional and better description of the psychopathology of ADHD.", "Neither the current ICD-10 and DSM-IV nor the upcoming DSM-5 includes symptoms of emotional dysregulation as a core aspect of ADHD.", "Several authors (e.g., Wender 1995) describe adult ADHD in a more differentiated way and propose concepts of the disorder that consider the subjective experiences of the adult patient by introducing the symptomatology of emotional symptoms.", "Empirical studies attest this dimension sufficient reliability and validity.", "Symptoms of emotional dysregulation are definable and seem to be distinct factors of the psychopathology of adult ADHD.", "Pharmacological and psychotherapeutic interventions help to alleviate this type of symptoms.", "This review attests a decisive role to the emotional symptoms in the ADHD symptomatology, which should be taken in serious consideration by future research."], "structured": false}
{"doc_id": 1070920, "title": "A neural basis for melanocortin-4 receptor regulated appetite", "abstract": ["Pro-opiomelanocortin (POMC)- and agouti-related peptide (AgRP)-expressing neurons of the arcuate nucleus of the hypothalamus (ARC) are oppositely regulated by caloric depletion and coordinately stimulate and inhibit homeostatic satiety, respectively.", "This bimodality is principally underscored by the antagonistic actions of these ligands at downstream melanocortin-4 receptors (MC4R) in the paraventricular nucleus of the hypothalamus (PVH).", "Although this population is critical to energy balance, the underlying neural circuitry remains unknown.", "Using mice expressing Cre recombinase in MC4R neurons, we demonstrate bidirectional control of feeding following real-time activation and inhibition of PVH(MC4R) neurons and further identify these cells as a functional exponent of ARC(AgRP) neuron-driven hunger.", "Moreover, we reveal this function to be mediated by a PVH(MC4R)\u2192lateral parabrachial nucleus (LPBN) pathway.", "Activation of this circuit encodes positive valence, but only in calorically depleted mice.", "Thus, the satiating and appetitive nature of PVH(MC4R)\u2192LPBN neurons supports the principles of drive reduction and highlights this circuit as a promising target for antiobesity drug development."], "structured": false}
{"doc_id": 1071991, "title": "Lymph node T cell responses predict the efficacy of live attenuated SIV vaccines", "abstract": ["Live attenuated simian immunodeficiency virus (SIV) vaccines (LAVs) remain the most efficacious of all vaccines in nonhuman primate models of HIV and AIDS, yet the basis of their robust protection remains poorly understood.", "Here we show that the degree of LAV-mediated protection against intravenous wild-type SIVmac239 challenge strongly correlates with the magnitude and function of SIV-specific, effector-differentiated T cells in the lymph node but not with the responses of such T cells in the blood or with other cellular, humoral and innate immune parameters.", "We found that maintenance of protective T cell responses is associated with persistent LAV replication in the lymph node, which occurs almost exclusively in follicular helper T cells.", "Thus, effective LAVs maintain lymphoid tissue-based, effector-differentiated, SIV-specific T cells that intercept and suppress early wild-type SIV amplification and, if present in sufficient frequencies, can completely control and perhaps clear infection, an observation that provides a rationale for the development of safe, persistent vectors that can elicit and maintain such responses."], "structured": false}
{"doc_id": 1084062, "title": "Activation of Serotonin 2C Receptors in Dopamine Neurons Inhibits Binge-like Eating in Mice", "abstract": ["BACKGROUND Neural networks that regulate binge eating remain to be identified, and effective treatments for binge eating are limited.   \n", "METHODS We combined neuroanatomic, pharmacologic, electrophysiological, Cre-lox, and chemogenetic approaches to investigate the functions of 5-hydroxytryptamine (5-HT) 2C receptor (5-HT2CR) expressed by dopamine (DA) neurons in the regulation of binge-like eating behavior in mice.   \n", "RESULTS We showed that 5-HT stimulates DA neural activity through a 5-HT2CR-mediated mechanism, and activation of this midbrain 5-HT\u2192DA neural circuit effectively inhibits binge-like eating behavior in mice.", "Notably, 5-HT medications, including fluoxetine, d-fenfluramine, and lorcaserin (a selective 5-HT2CR agonist), act on 5-HT2CRs expressed by DA neurons to inhibit binge-like eating in mice.   \n", "CONCLUSIONS We identified the 5-HT2CR population in DA neurons as one potential target for antibinge therapies, and provided preclinical evidence that 5-HT2CR agonists could be used to treat binge eating."], "structured": true}
{"doc_id": 1084345, "title": "Restoration of chaperone-mediated autophagy in aging liver improves cellular maintenance and hepatic function", "abstract": ["Chaperone-mediated autophagy (CMA), a selective mechanism for degradation of cytosolic proteins in lysosomes, contributes to the removal of altered proteins as part of the cellular quality-control systems.", "We have previously found that CMA activity declines in aged organisms and have proposed that this failure in cellular clearance could contribute to the accumulation of altered proteins, the abnormal cellular homeostasis and, eventually, the functional loss characteristic of aged organisms.", "To determine whether these negative features of aging can be prevented by maintaining efficient autophagic activity until late in life, in this work we have corrected the CMA defect in aged rodents.", "We have generated a double transgenic mouse model in which the amount of the lysosomal receptor for CMA, previously shown to decrease in abundance with age, can be modulated.", "We have analyzed in this model the consequences of preventing the age-dependent decrease in receptor abundance in aged rodents at the cellular and organ levels.", "We show here that CMA activity is maintained until advanced ages if the decrease in the receptor abundance is prevented and that preservation of autophagic activity is associated with lower intracellular accumulation of damaged proteins, better ability to handle protein damage and improved organ function."], "structured": false}
{"doc_id": 1102268, "title": "The Incidence and Repetition of Hospital-Treated Deliberate Self Harm: Findings from the World's First National Registry", "abstract": ["BACKGROUND Suicide is a significant public health issue with almost one million people dying by suicide each year worldwide.", "Deliberate self harm (DSH) is the single most important risk factor for suicide yet few countries have reliable data on DSH.", "We developed a national DSH registry in the Republic of Ireland to establish the incidence of hospital-treated DSH at national level and the spectrum and pattern of presentations with DSH and repetition.   \n", "METHODS AND FINDINGS Between 2003 and 2009, the Irish National Registry of Deliberate Self Harm collected data on DSH presentations to all 40 hospital emergency departments in the country.", "Data were collected by trained data registration officers using standard methods of case ascertainment and definition.", "The Registry recorded 75,119 DSH presentations involving 48,206 individuals.", "The total incidence rate fell from 209 (95% CI: 205-213) per 100,000 in 2003 to 184 (95% CI: 180-189) per 100,000 in 2006 and increased again to 209 (95% CI: 204-213) per 100,000 in 2009.", "The most notable annual changes were successive 10% increases in the male rate in 2008 and 2009.", "There was significant variation by age with peak rates in women in the 15-19 year age group (620 (95% CI: 605-636) per 100,000), and in men in the 20-24 age group (427 (95% CI: 416-439) per 100,000).", "Repetition rates varied significantly by age, method of self harm and number of previous episodes.   \n", "CONCLUSIONS Population-based data on hospital-treated DSH represent an important index of the burden of mental illness and suicide risk in the community.", "The increased DSH rate in Irish men in 2008 and 2009 coincided with the advent of the economic recession in Ireland.", "The findings underline the need for developing effective interventions to reduce DSH repetition rates as a key priority for health systems."], "structured": true}
{"doc_id": 1103795, "title": "A Common Mechanism of Cellular Death Induced by Bactericidal Antibiotics", "abstract": ["Antibiotic mode-of-action classification is based upon drug-target interaction and whether the resultant inhibition of cellular function is lethal to bacteria.", "Here we show that the three major classes of bactericidal antibiotics, regardless of drug-target interaction, stimulate the production of highly deleterious hydroxyl radicals in Gram-negative and Gram-positive bacteria, which ultimately contribute to cell death.", "We also show, in contrast, that bacteriostatic drugs do not produce hydroxyl radicals.", "We demonstrate that the mechanism of hydroxyl radical formation induced by bactericidal antibiotics is the end product of an oxidative damage cellular death pathway involving the tricarboxylic acid cycle, a transient depletion of NADH, destabilization of iron-sulfur clusters, and stimulation of the Fenton reaction.", "Our results suggest that all three major classes of bactericidal drugs can be potentiated by targeting bacterial systems that remediate hydroxyl radical damage, including proteins involved in triggering the DNA damage response, e.g., RecA."], "structured": false}
{"doc_id": 1122198, "title": "Increased atherosclerosis in mice reconstituted with apolipoprotein E null macrophages.", "abstract": ["Macrophage-derived foam cells express apolipoprotein E (apoE) abundantly in atherosclerotic lesions.", "To examine the physiologic role of apoE secretion by the macrophage in atherogenesis, bone marrow transplantation was used to reconstitute C57BL/6 mice with macrophages that were either null or wild type for the apoE gene.", "After 13 weeks on an atherogenic diet, C57BL/6 mice reconstituted with apoE null marrow developed 10-fold more atherosclerosis than controls in the absence of significant differences in serum cholesterol levels or lipoprotein profiles.", "ApoE expression was absent in the macrophage-derived foam cells of C57BL/6 mice reconstituted with apoE null marrow.", "Thus, lack of apoE expression by the macrophage promotes foam cell formation.", "These data support a protective role for apoE expression by the macrophage in early atherogenesis."], "structured": false}
{"doc_id": 1122279, "title": "Endothelium-mediated relaxation of porcine collateral-dependent arterioles is improved by exercise training.", "abstract": ["BACKGROUND Endothelium-dependent modulation of coronary tone is impaired in the collateral-dependent coronary microcirculation.", "We used a porcine model of chronic coronary occlusion and collateral development to evaluate the hypothesis that exercise training enhances endothelium-mediated relaxation and increases endothelial nitric oxide synthase (ecNOS) mRNA levels of collateral-dependent microvasculature.   \n", "METHODS AND RESULTS Adult female miniature swine were subjected to chronic, progressive ameroid occlusion of the proximal left circumflex coronary artery (LCx); after 2 months, animals were randomly exposed to 16-week exercise-training (EX group; treadmill running) or sedentary (SED group; cage confinement) protocols.", "After completion of EX or SED programs, coronary arterioles ( approximately 100 microm in diameter) were isolated from collateral-dependent LCx (distal to occlusion) and nonoccluded left anterior descending coronary artery (LAD) regions of each heart.", "Arterioles were studied by in vitro videomicroscopy or frozen for ecNOS mRNA analysis (RT-PCR techniques).", "Relaxation to the endothelium-dependent vasodilator bradykinin was decreased (P<0.05) in arterioles isolated from collateral-dependent LCx versus nonoccluded LAD regions of SED animals.", "Bradykinin-mediated relaxation, however, was not different in LCx versus LAD arterioles isolated from EX animals.", "Nitroprusside-induced relaxation was unaffected by either chronic occlusion or exercise.", "Importantly, ecNOS mRNA expression was significantly decreased in arterioles isolated from LCx versus LAD regions of SED animals.", "After training, ecNOS mRNA expression was not different between LAD and LCx arterioles.   \n", "CONCLUSIONS These data indicate that exercise training enhances bradykinin-mediated relaxation of collateral-dependent LCx arterioles isolated after chronic coronary occlusion, most likely because of effects on ecNOS mRNA expression and increased production of NO."], "structured": true}
{"doc_id": 1127562, "title": "Loss of the RhoGAP SRGP-1 promotes the clearance of dead and injured cells in Caenorhabditis elegans", "abstract": ["Multicellular animals rapidly clear dying cells from their bodies.", "Many of the pathways that mediate this cell removal are conserved through evolution.", "Here, we identify srgp-1 as a negative regulator of cell clearance in both Caenorhabditis elegans and mammalian cells.", "Loss of srgp-1 function results in improved engulfment of apoptotic cells, whereas srgp-1 overexpression inhibits apoptotic cell corpse removal.", "We show that SRGP-1 functions in engulfing cells and functions as a GTPase activating protein (GAP) for CED-10 (Rac1).", "Interestingly, loss of srgp-1 function promotes not only the clearance of already dead cells, but also the removal of cells that have been brought to the verge of death through sublethal apoptotic, necrotic or cytotoxic insults.", "In contrast, impaired engulfment allows damaged cells to escape clearance, which results in increased long-term survival.", "We propose that C. elegans uses the engulfment machinery as part of a primitive, but evolutionarily conserved, survey mechanism that identifies and removes unfit cells within a tissue."], "structured": false}
{"doc_id": 1145473, "title": "Abnormalities in the myeloid progenitor compartment in Down syndrome fetal liver precede acquisition of GATA1 mutations.", "abstract": ["Down syndrome (DS) children have a high frequency of acute megakaryoblastic leukemia (AMKL) in early childhood.", "At least 2 in utero genetic events are required, although not sufficient, for DS-AMKL: trisomy 21 (T21) and N-terminal-truncating GATA1 mutations.", "To investigate the role of T21 in DS-AMKL, we compared second trimester hemopoiesis in DS without GATA1 mutations to gestation-matched normal controls.", "In all DS fetal livers (FLs), but not marrows, megakaryocyte-erythroid progenitor frequency was increased (55.9% +/-", "4% vs 17.1% +/-", "3%, CD34(+)CD38(+) cells; P < .001) with common myeloid progenitors (19.6% +/-", "2% vs 44.0% +/-", "7%) and granulocyte-monocyte (GM) progenitors (15.8% +/-", "4% vs 34.5% +/-", "9%) commensurately reduced.", "Clonogenicity of DS-FL versus normal FL CD34(+) cells was markedly increased (78% +/-", "7% vs 15% +/-", "3%) affecting megakaryocyte-erythroid ( approximately 7-fold higher) and GM and colony-forming unit-granulocyte, erythrocyte macrophage, megakaryocyte (CFU-GEMM) progenitors.", "Replating efficiency of CFU-GEMM was also markedly increased.", "These data indicate that T21 itself profoundly disturbs FL hemopoiesis and they provide a testable hypothesis to explain the increased susceptibility to GATA1 mutations in DS-AMKL and DS-associated transient myeloproliferative disorder."], "structured": false}
{"doc_id": 1148122, "title": "Regulatory and metabolic rewiring during laboratory evolution of ethanol tolerance in E. coli", "abstract": ["Understanding the genetic basis of adaptation is a central problem in biology.", "However, revealing the underlying molecular mechanisms has been challenging as changes in fitness may result from perturbations to many pathways, any of which may contribute relatively little.", "We have developed a combined experimental/computational framework to address this problem and used it to understand the genetic basis of ethanol tolerance in Escherichia coli.", "We used fitness profiling to measure the consequences of single-locus perturbations in the context of ethanol exposure.", "A module-level computational analysis was then used to reveal the organization of the contributing loci into cellular processes and regulatory pathways (e.g. osmoregulation and cell-wall biogenesis) whose modifications significantly affect ethanol tolerance.", "Strikingly, we discovered that a dominant component of adaptation involves metabolic rewiring that boosts intracellular ethanol degradation and assimilation.", "Through phenotypic and metabolomic analysis of laboratory-evolved ethanol-tolerant strains, we investigated naturally accessible pathways of ethanol tolerance.", "Remarkably, these laboratory-evolved strains, by and large, follow the same adaptive paths as inferred from our coarse-grained search of the fitness landscape."], "structured": false}
{"doc_id": 1153655, "title": "Familial risk of lymphoproliferative tumors in families of patients with chronic lymphocytic leukemia: results from the Swedish Family-Cancer Database.", "abstract": ["The importance of genetic factors in etiology of chronic lymphocytic leukemia (CLL) is suggested by family and population studies.", "However, the spectrum of malignancies sharing common genetic factors with CLL and the effects of sex and age on familial risk are unknown.", "We used the Swedish Family-Cancer Database to test for increased familial risks of CLL and other lymphoproliferative tumors.", "Cancer diagnoses from 1958 to 1998 were assessed in 14 336 first-degree relatives of 5918 CLL cases and in 28 876 first-degree relatives of 11 778 controls.", "Cancer risks in relatives of cases were compared with those in relatives of controls using marginal survival models.", "Relatives of cases were at significantly increased risk for CLL (relative risk [RR] = 7.52; 95% confidence interval [CI], 3.63-15.56), for non-Hodgkin lymphoma (RR = 1.45; 95% CI, 0.98-2.16), and for Hodgkin lymphoma (RR = 2.35; 95% CI, 1.08-5.08).", "CLL risks were similar in parents, siblings, and offspring of cases, in male and female relatives, and were not affected by the case's age at diagnosis.", "Anticipation was not significant when analyzed using life table methods.", "We conclude that the familial component of CLL is shared with other lymphoproliferative malignances, suggesting common genetic pathways.", "However, because clinically diagnosed CLL is uncommon, absolute excess risk to relatives is small."], "structured": false}
{"doc_id": 1156322, "title": "Collagen/Polypropylene composite mesh biocompatibility in abdominal wall reconstruction.", "abstract": ["BACKGROUND Intraperitoneal placement of polypropylene mesh leads to extensive visceral adhesions and is contraindicated.", "Different coatings are used to improve polypropylene mesh properties.", "Collagen is a protein with unique biocompatibility and cell ingrowth enhancement potential.", "A novel acetic acid extracted collagen coating was developed to allow placement of polypropylene mesh in direct contact with viscera.", "The authors' aim was to evaluate the long-term influence of acetic acid extracted collagen coating on surgical aspects and biomechanical properties of polypropylene mesh implanted in direct contact with viscera, including complications, adhesions with viscera, strength of incorporation, and microscopic inflammatory reaction.   \n", "METHODS Forty adult Wistar rats were divided into two groups: experimental (polypropylene mesh/acetic acid extracted collagen coating) and control (polypropylene mesh only).", "Astandardized procedure of mesh implantation was performed.", "Animals were killed 3 months after surgery and analyzed for complications, mesh area covered by adhesions, type of adhesions, strength of incorporation, and intensity of inflammatory response.   \n", "RESULTS The mean adhesion area was lower for polypropylene mesh/acetic acid extracted collagen coating (14.5 percent versus 69.9 percent, p < 0.001).", "Adhesion severity was decreased in the experimental group: grades 0 and 1 were more frequent (p < 0.04 and p < 0.002, respectively) and grade 3 was less frequent (p < 0.0001).", "An association between adhesion area and severity was found (p < 0.0001).", "Complications, strength of incorporation, and intensity of inflammatory response to the mesh were similar.   \n", "CONCLUSIONS Visceral adhesions to polypropylene mesh are significantly reduced because of acetic acid extracted collagen coating.", "The collagen coating does not increase complications or induce alterations of polypropylene mesh incorporation."], "structured": true}
{"doc_id": 1171121, "title": "Microvessel Density and Status of p53 Protein as Potential Prognostic Factors for Adjuvant Anthracycline Chemotherapy in Retrospective Analysis of Early Breast Cancer Patients Group", "abstract": ["A considerable subgroup of patients with early breast cancer does not address benefits of anthracycline based chemotherapy.", "The aim of this retrospective study was to investigate the effect of microvessel density (MVD) and status of p53 protein on 5-year disease free survival (DFS) in the group of breast cancer patients treated with anthracyclines in adjuvant setting.", "Correlations between MVD, p53 status and other clinicopathological parameters were also assessed.", "MVD and p53 status were analyzed immunohistochemically in the group of 172 women with breast cancer in clinical stage T1-2, N1-N2, M0.", "There were 123 tumors (71.5 %) with lower MVD (\u2264 214.8 microvesells/mm(2)) and 49 (28.5 %) with higher MVD (>214.8 microvesells/mm(2)).", "The proportion of higher MVD tumors significantly increased in N2 (P = 0.000) and in estrogen (P = 0.046) or progesterone receptors (P = 0.029) negative tumors.", "p53 positivity was indicated in 50 cancers (29.1 %) and was significantly associated with higher grade (P = 0.000), steroid receptors negativity (P = 0.000), cytokeratin5/6 positivity (P = 0.026), topoisomerase II\u03b1 overexpression (P = 0.005) and higher proliferation rate (P = 0.001).", "In univariate analysis, higher MVD (P = 0.016) and p53 negativity (P = 0.023) were significantly related with longer DFS (median follow-up 36 months).", "In multivariate Cox regression analysis MVD was independently associated with DFS.", "These data suggest that higher MVD is favourable prognostic factors for early advanced breast cancer patients after adjuvant anthracycline based chemotherapy."], "structured": false}
{"doc_id": 1173667, "title": "Ranking of elimination feasibility between malaria-endemic countries", "abstract": ["Experience gained from the Global Malaria Eradication Program (1955-72) identified a set of shared technical and operational factors that enabled some countries to successfully eliminate malaria.", "Spatial data for these factors were assembled for all malaria-endemic countries and combined to provide an objective, relative ranking of countries by technical, operational, and combined elimination feasibility.", "The analysis was done separately for Plasmodium falciparum and Plasmodium vivax, and the limitations of the approach were discussed.", "The relative rankings suggested that malaria elimination would be most feasible in countries in the Americas and Asia, and least feasible in countries in central and west Africa.", "The results differed when feasibility was measured by technical or operational factors, highlighting the different types of challenge faced by each country.", "The results are not intended to be prescriptive, predictive, or to provide absolute assessments of feasibility, but they do show that spatial information is available to facilitate evidence-based assessments of the relative feasibility of malaria elimination by country that can be rapidly updated."], "structured": false}
{"doc_id": 1180972, "title": "Genetics of obesity in adult adoptees and their biological siblings.", "abstract": ["An adoption study of genetic effects on obesity in adulthood was carried out in which adoptees separated from their natural parents very early in life were compared with their biological full and half siblings reared by their natural parents.", "The adoptees represented four groups who by sampling from a larger population were categorised as either thin, medium weight, overweight, or obese.", "Weight and height were obtained for 115 full siblings of 57 adoptees and for 850 half siblings of 341 adoptees.", "In full siblings body mass index (kg/m2) significantly increased with weight of the adoptees.", "Body mass index of the half siblings showed a steady but weaker increase across the four weight groups of adoptees.", "There were no significant interactions with sex of the adoptees, sex of the siblings, or (for the half siblings) sex of the common parent.", "In contrast with the findings in half siblings and (previously) the natural parents there was a striking, significant increase in body mass index between full siblings of overweight and obese adoptees.", "The degree of fatness in adults living in the same environment appears to be influenced by genetic factors independent of sex, which may include polygenic as well as major gene effects on obesity."], "structured": false}
{"doc_id": 1191830, "title": "2010 rheumatoid arthritis classification criteria: an American College of Rheumatology/European League Against Rheumatism collaborative initiative.", "abstract": ["OBJECTIVE The 1987 American College of Rheumatology (ACR; formerly the American Rheumatism Association) classification criteria for rheumatoid arthritis (RA) have been criticised for their lack of sensitivity in early disease.", "This work was undertaken to develop new classification criteria for RA.   \n", "METHODS A joint working group from the ACR and the European League Against Rheumatism developed, in three phases, a new approach to classifying RA.", "The work focused on identifying, among patients newly presenting with undifferentiated inflammatory synovitis, factors that best discriminated between those who were and those who were not at high risk for persistent and/or erosive disease--this being the appropriate current paradigm underlying the disease construct 'RA'.   \n", "RESULTS In the new criteria set, classification as 'definite RA' is based on the confirmed presence of synovitis in at least one joint, absence of an alternative diagnosis better explaining the synovitis, and achievement of a total score of 6 or greater (of a possible 10) from the individual scores in four domains: number and site of involved joints (range 0-5), serological abnormality (range 0-3), elevated acute-phase response (range 0-1) and symptom duration (two levels; range 0-1).   \n", "CONCLUSION This new classification system redefines the current paradigm of RA by focusing on features at earlier stages of disease that are associated with persistent and/or erosive disease, rather than defining the disease by its late-stage features.", "This will refocus attention on the important need for earlier diagnosis and institution of effective disease-suppressing therapy to prevent or minimise the occurrence of the undesirable sequelae that currently comprise the paradigm underlying the disease construct 'RA'."], "structured": true}
{"doc_id": 1192458, "title": "A role for fibroblasts in mediating the effects of tobacco-induced epithelial cell growth and invasion.", "abstract": ["Cigarette smoke and smokeless tobacco extracts contain multiple carcinogenic compounds, but little is known about the mechanisms by which tumors develop and progress upon chronic exposure to carcinogens such as those present in tobacco products.", "Here, we examine the effects of smokeless tobacco extracts on human oral fibroblasts.", "We show that smokeless tobacco extracts elevated the levels of intracellular reactive oxygen, oxidative DNA damage, and DNA double-strand breaks in a dose-dependent manner.", "Extended exposure to extracts induced fibroblasts to undergo a senescence-like growth arrest, with striking accompanying changes in the secretory phenotype.", "Using cocultures of smokeless tobacco extracts-exposed fibroblasts and immortalized but nontumorigenic keratinocytes, we further show that factors secreted by extracts-modified fibroblasts increase the proliferation and invasiveness of partially transformed epithelial cells, but not their normal counterparts.", "In addition, smokeless tobacco extracts-exposed fibroblasts caused partially transformed keratinocytes to lose the expression of E-cadherin and ZO-1, as well as involucrin, changes that are indicative of compromised epithelial function and commonly associated with malignant progression.", "Together, our results suggest that fibroblasts may contribute to tumorigenesis indirectly by increasing epithelial cell aggressiveness.", "Thus, tobacco may not only initiate mutagenic changes in epithelial cells but also promote the growth and invasion of mutant cells by creating a procarcinogenic stromal environment."], "structured": false}
{"doc_id": 1196631, "title": "ImmTAC-redirected tumour cell killing induces and potentiates antigen cross-presentation by dendritic cells", "abstract": ["Antigen cross-presentation by dendritic cells (DCs) is thought to play a critical role in driving a polyclonal and durable T cell response against cancer.", "It follows, therefore, that the capacity of emerging immunotherapeutic agents to orchestrate tumour eradication may depend on their ability to induce antigen cross-presentation.", "ImmTACs [immune-mobilising monoclonal TCRs (T cell receptors) against cancer] are a new class of soluble bi-specific anti-cancer agents that combine pico-molar affinity TCR-based antigen recognition with T cell activation via a CD3-specific antibody fragment.", "ImmTACs specifically recognise human leucocyte antigen (HLA)-restricted tumour-associated antigens, presented by cancer cells, leading to T cell redirection and a potent anti-tumour response.", "Using an ImmTAC specific for a HLA-A*02-restricted peptide derived from the melanoma antigen gp100 (termed IMCgp100), we here observe that ImmTAC-driven melanoma-cell death leads to cross-presentation of melanoma antigens by DCs.", "These, in turn, can activate both melanoma-specific T cells and polyclonal T cells redirected by IMCgp100.", "Moreover, activation of melanoma-specific T cells by cross-presenting DCs is enhanced in the presence of IMCgp100; a feature that serves to increase the prospect of breaking tolerance in the tumour microenvironment.", "The mechanism of DC cross-presentation occurs via \u2018cross-dressing\u2019 which involves the rapid and direct capture by DCs of membrane fragments from dying tumour cells.", "DC cross-presentation of gp100-peptide-HLA complexes was visualised and quantified using a fluorescently labelled soluble TCR.", "These data demonstrate how ImmTACs engage with the innate and adaptive components of the immune system enhancing the prospect of mediating an effective and durable anti-tumour response in patients."], "structured": false}
{"doc_id": 1203035, "title": "Basal keratinocyte tetrasomy in low-grade squamous intra-epithelial lesions of the cervix is restricted to high and intermediate risk HPV infection but is not type-specific", "abstract": ["Human papillomavirus (HPV) infection appears to be an early event in cervical carcinogenesis with additional abnormalities being required for biological transformation.", "We have analysed 179 low-grade cervical squamous intra-epithelial lesions (SILs) and 15 normal cervices for the presence of HPV using both in situ hybridization and polymerase chain reaction (PCR).", "PCR was performed with GP5+/GP6+ primers followed by hybridization using probes for low (HPV 6, 11, 40, 42, 43, 44), intermediate (HPV 31, 33, 35, 39, 51, 52, 58, 59, 66 and 68) and high-risk HPVs (HPV 16, 18, 45 and 56).", "Interphase cytogenetic analysis using pericentromeric probes for chromosomes 1, 3, 4, 6, 10, 11, 17, 18 and X was also performed to identify numerical chromosomal abnormalities.", "Tetrasomy of all nine chromosomes was identified within basal keratinocytes, was restricted to epithelia infected with high risk (17 of 46) or intermediate risk (23 of 83) HPVs but was not HPV type-specific.", "Tetrasomy was not identified in any of the epithelia infected with low risk HPVs (n = 62).", "These numbers include multiple infection.", "These findings indicate that the induction of tetrasomy is a property restricted to high and intermediate-risk HPV types but that it is not type-specific.", "The factors governing which lesions will develop this abnormality are as yet unclear.", "\u00a9 2000 Cancer Research Campaign"], "structured": false}
{"doc_id": 1215116, "title": "\u201cRapid-Impact Interventions\u201d: How a Policy of Integrated Control for Africa's Neglected Tropical Diseases Could Benefit the Poor", "abstract": ["Over the past two decades there have been significant achievements in the control of a handful of important human tropical infections [1].", "These achievements include the substantive reductions in the prevalence and incidence of the so-called neglected diseases such as lymphatic filariasis, onchocerciasis, guinea worm, leprosy, and trachoma (Box 1) [2].                ", "Each of these neglected diseases is a poverty-promoting and often stigmatizing condition occurring primarily in rural areas of low-income countries (Box 2) [3].", "They are ancient afflictions, described in the Bible and other ancient texts, which have burdened humanity for millennia [3].", "But now, as a result of aggressive regional vertical interventions, there is a possibility that some neglected tropical infections could be eventually controlled to the point of elimination in some areas of endemicity [2\u20138].", "In the case of guinea worm infection, disease eradication might also soon be possible [9].      ", "Box 2.", "Common Features of the Neglected Tropical Diseases          Ancient afflictions that have burdened humanity for centuries      Poverty-promoting conditions      Associated with stigma      Rural areas of low-income countries and fragile states      No commercial markets for products that target these diseases      Interventions, when applied, have a history of success"], "structured": false}
{"doc_id": 1220287, "title": "FTY720 (fingolimod) is a neuroprotective and disease-modifying agent in cellular and mouse models of Huntington disease.", "abstract": ["Huntington disease (HD) is a genetic neurodegenerative disorder for which there is currently no cure and no way to stop or even slow the brain changes it causes.", "In the present study, we aimed to investigate whether FTY720, the first approved oral therapy for multiple sclerosis, may be effective in HD models and eventually constitute an alternative therapeutic approach for the treatment of the disease.", "Here, we utilized preclinical target validation paradigms and examined the in vivo efficacy of chronic administration of FTY720 in R6/2 HD mouse model.", "Our findings indicate that FTY720 improved motor function, prolonged survival and reduced brain atrophy in R6/2 mice.", "The beneficial effect of FTY720 administration was associated with a significant strengthening of neuronal activity and connectivity and, with reduction of mutant huntingtin aggregates, and it was also paralleled by increased phosphorylation of mutant huntingtin at serine 13/16 residues that are predicted to attenuate protein toxicity."], "structured": false}
{"doc_id": 1225513, "title": "Specificity Residues Determine Binding Affinity for Two-Component Signal Transduction Systems", "abstract": ["UNLABELLED Two-component systems (TCS) comprise histidine kinases and their cognate response regulators and allow bacteria to sense and respond to a wide variety of signals.", "Histidine kinases (HKs) phosphorylate and dephosphorylate their cognate response regulators (RRs) in response to stimuli.", "In general, these reactions appear to be highly specific and require an appropriate association between the HK and RR proteins.", "The Myxococcus xanthus genome encodes one of the largest repertoires of signaling proteins in bacteria (685 open reading frames [ORFs]), including at least 127 HKs and at least 143 RRs.", "Of these, 27 are bona fide NtrC-family response regulators, 21 of which are encoded adjacent to their predicted cognate kinases.", "Using system-wide profiling methods, we determined that the HK-NtrC RR pairs display a kinetic preference during both phosphotransfer and phosphatase functions, thereby defining cognate signaling systems in M. xanthus.", "Isothermal titration calorimetry measurements indicated that cognate HK-RR pairs interact with dissociation constants (Kd) of approximately 1 \u00b5M, while noncognate pairs had no measurable binding.", "Lastly, a chimera generated between the histidine kinase, CrdS, and HK1190 revealed that residues conferring phosphotransfer and phosphatase specificity dictate binding affinity, thereby establishing discrete protein-protein interactions which prevent cross talk.", "The data indicate that binding affinity is a critical parameter governing system-wide signaling fidelity for bacterial signal transduction proteins.   ", "IMPORTANCE Using in vitro phosphotransfer and phosphatase profiling assays and isothermal titration calorimetry, we have taken a system-wide approach to demonstrate specificity for a family of two-component signaling proteins in Myxococcus xanthus.", "Our results demonstrate that previously identified specificity residues dictate binding affinity and that phosphatase specificity follows phosphotransfer specificity for cognate HK-RR pairs.", "The data indicate that preferential binding affinity is the basis for signaling fidelity in bacterial two-component systems."], "structured": false}
{"doc_id": 1226452, "title": "hnRNP A1 associates with telomere ends and stimulates telomerase activity.", "abstract": ["Telomerase is a ribonucleoprotein enzyme complex that reverse-transcribes an integral RNA template to add short DNA repeats to the 3'-ends of telomeres.", "G-quadruplex structure in a DNA substrate can block its extension by telomerase.", "We have found that hnRNP A1--which was previously implicated in telomere length regulation--binds to both single-stranded and structured human telomeric repeats, and in the latter case, it disrupts their higher-order structure.", "Using an in vitro telomerase assay, we observed that depletion of hnRNP A/B proteins from 293 human embryonic kidney cell extracts dramatically reduced telomerase activity, which was fully recovered upon addition of purified recombinant hnRNP A1.", "This finding suggests that hnRNP A1 functions as an auxiliary, if not essential, factor of telomerase holoenzyme.", "We further show, using chromatin immunoprecipitation, that hnRNP A1 associates with human telomeres in vivo.", "We propose that hnRNP A1 stimulates telomere elongation through unwinding of a G-quadruplex or G-G hairpin structure formed at each translocation step."], "structured": false}
{"doc_id": 1227277, "title": "Rapamycin passes the torch: a new generation of mTOR inhibitors", "abstract": ["Mammalian target of rapamycin (mTOR) is an atypical protein kinase that controls growth and metabolism in response to nutrients, growth factors and cellular energy levels, and it is frequently dysregulated in cancer and metabolic disorders.", "Rapamycin is an allosteric inhibitor of mTOR, and was approved as an immuno-suppressant in 1999.", "In recent years, interest has focused on its potential as an anticancer drug.", "However, the performance of rapamycin and its analogues (rapalogues) has been undistinguished despite isolated successes in subsets of cancer, suggesting that the full therapeutic potential of targeting mTOR has yet to be exploited.", "A new generation of ATP-competitive inhibitors that directly target the mTOR catalytic site display potent and comprehensive mTOR inhibition and are in early clinical trials."], "structured": false}
{"doc_id": 1234098, "title": "Dynamic capsule restructuring by the main pneumococcal autolysin LytA in response to the epithelium", "abstract": ["Bacterial pathogens produce complex carbohydrate capsules to protect against bactericidal immune molecules.", "Paradoxically, the pneumococcal capsule sensitizes the bacterium to antimicrobial peptides found on epithelial surfaces.", "Here we show that upon interaction with antimicrobial peptides, encapsulated pneumococci survive by removing capsule from the cell surface within minutes in a process dependent on the suicidal amidase autolysin LytA. In contrast to classical bacterial autolysis, during capsule shedding, LytA promotes bacterial survival and is dispersed circumferentially around the cell.", "However, both autolysis and capsule shedding depend on the cell wall hydrolytic activity of LytA. Capsule shedding drastically increases invasion of epithelial cells and is the main pathway by which pneumococci reduce surface bound capsule during early acute lung infection of mice.", "The previously unrecognized role of LytA in removing capsule to combat antimicrobial peptides may explain why nearly all clinical isolates of pneumococci conserve this enzyme despite the lethal selective pressure of antibiotics."], "structured": false}
{"doc_id": 1241113, "title": "The mammalian Scribble polarity protein regulates epithelial cell adhesion and migration through E-cadherin", "abstract": ["Scribble (Scrib) is a conserved polarity protein required in Drosophila melanogaster for synaptic function, neuroblast differentiation, and epithelial polarization.", "It is also a tumor suppressor.", "In rodents, Scrib has been implicated in receptor recycling and planar polarity but not in apical/basal polarity.", "We now show that knockdown of Scrib disrupts adhesion between Madin\u2013Darby canine kidney epithelial cells.", "As a consequence, the cells acquire a mesenchymal appearance, migrate more rapidly, and lose directionality.", "Although tight junction assembly is delayed, confluent monolayers remain polarized.", "These effects are independent of Rac activation or Scrib binding to \u03b2PIX.", "Rather, Scrib depletion disrupts E-cadherin\u2013mediated cell\u2013cell adhesion.", "The changes in morphology and migration are phenocopied by E-cadherin knockdown.", "Adhesion is partially rescued by expression of an E-cadherin\u2013\u03b1-catenin fusion protein but not by E-cadherin\u2013green fluorescent protein.", "These results suggest that Scrib stabilizes the coupling between E-cadherin and the catenins and are consistent with the idea that mammalian Scrib could behave as a tumor suppressor by regulating epithelial cell adhesion and migration."], "structured": false}
{"doc_id": 1243475, "title": "Histone acetylation and DNA demethylation of T cells result in an anaplastic large cell lymphoma-like phenotype.", "abstract": ["A characteristic feature of anaplastic large cell lymphoma is the significant repression of the T-cell expression program despite its T-cell origin.", "The reasons for this down-regulation of T-cell phenotype are still unknown.", "To elucidate whether epigenetic mechanisms are responsible for the loss of the T-cell phenotype, we treated anaplastic large cell lymphoma and T-cell lymphoma/leukemia cell lines (n=4, each) with epigenetic modifiers to evoke DNA demethylation and histone acetylation.", "Global gene expression data from treated and untreated cell lines were generated and selected, and differentially expressed genes were evaluated by real-time reverse transcriptase polymerase chain reaction and western blot analysis.", "Additionally, histone H3 lysine 27 trimethylation was analyzed by chromatin immunoprecipitation.", "Combined DNA demethylation and histone acetylation of anaplastic large cell lymphoma cells was not able to reconstitute their T-cell phenotype.", "Instead, the same treatment induced in T cells: (i) an up-regulation of anaplastic large cell lymphoma-characteristic genes (e.g. ID2, LGALS1, c-JUN), and (ii) an almost complete extinction of their T-cell phenotype including CD3, LCK and ZAP70.", "In addition, suppressive trimethylation of histone H3 lysine 27 of important T-cell transcription factor genes (GATA3, LEF1, TCF1) was present in anaplastic large cell lymphoma cells, which is in line with their absence in primary tumor specimens as demonstrated by immunohistochemistry.", "Our data suggest that epigenetically activated suppressors (e.g. ID2) contribute to the down-regulation of the T-cell expression program in anaplastic large cell lymphoma, which is maintained by trimethylation of histone H3 lysine 27."], "structured": false}
{"doc_id": 1256116, "title": "YEASTRACT: providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interface", "abstract": ["The YEAst Search for Transcriptional Regulators And Consensus Tracking (YEASTRACT) information system (http://www.yeastract.com) was developed to support the analysis of transcription regulatory associations in Saccharomyces cerevisiae.", "Last updated in June 2010, this database contains over 48,200 regulatory associations between transcription factors (TFs) and target genes, including 298 specific DNA-binding sites for 110 characterized TFs.", "All regulatory associations stored in the database were revisited and detailed information on the experimental evidences that sustain those associations was added and classified as direct or indirect evidences.", "The inclusion of this new data, gathered in response to the requests of YEASTRACT users, allows the user to restrict its queries to subsets of the data based on the existence or not of experimental evidences for the direct action of the TFs in the promoter region of their target genes.", "Another new feature of this release is the availability of all data through a machine readable web-service interface.", "Users are no longer restricted to the set of available queries made available through the existing web interface, and can use the web service interface to query, retrieve and exploit the YEASTRACT data using their own implementation of additional functionalities.", "The YEASTRACT information system is further complemented with several computational tools that facilitate the use of the curated data when answering a number of important biological questions.", "Since its first release in 2006, YEASTRACT has been extensively used by hundreds of researchers from all over the world.", "We expect that by making the new data and services available, the system will continue to be instrumental for yeast biologists and systems biology researchers."], "structured": false}
{"doc_id": 1259280, "title": "Mechanisms that Specify Promoter Nucleosome Location and Identity", "abstract": ["The chromatin architecture of eukaryotic gene promoters is generally characterized by a nucleosome-free region (NFR) flanked by at least one H2A.Z variant nucleosome.", "Computational predictions of nucleosome positions based on thermodynamic properties of DNA-histone interactions have met with limited success.", "Here we show that the action of the essential RSC remodeling complex in S. cerevisiae helps explain the discrepancy between theory and experiment.", "In RSC-depleted cells, NFRs shrink such that the average positions of flanking nucleosomes move toward predicted sites.", "Nucleosome positioning at distinct subsets of promoters additionally requires the essential Myb family proteins Abf1 and Reb1, whose binding sites are enriched in NFRs.", "In contrast, H2A.Z deposition is dispensable for nucleosome positioning.", "By regulating H2A.Z deposition using a steroid-inducible protein splicing strategy, we show that NFR establishment is necessary for H2A.Z deposition.", "These studies suggest an ordered pathway for the assembly of promoter chromatin architecture."], "structured": false}
{"doc_id": 1259359, "title": "HIV seropositivity and tuberculosis in a large general hospital in Malawi.", "abstract": ["The incidence of the acquired immunodeficiency syndrome (AIDS) in Malawi is one of the highest in Central Africa.", "Since tuberculosis is an important initial manifestations of the disease, consecutive patients admitted to the tuberculosis (TB) wards of Zomba General Hospital, Malawi, were asked for permission to undergo a human immunodeficiency virus (HIV)-antibodies test.", "In addition, two other studies were done: from September 1986 all medical in-patients, clinically suspected for immune deficiency and from April 1988 all blood donors were tested for HIV seropositivity.", "Seventy-five percent of the TB patients volunteered; 32 out of 125 (26%) were seropositive.", "In the high-risk age groups (20-40 years)", "this percentage rose to 32.", "Among the medical in-patients suspected of immune deficiency the seropositivity rose sharply from April 1987 to October 1988.", "Among the blood donors tested, 20% were seropositive."], "structured": false}
{"doc_id": 1263446, "title": "Determinants of neonatal mortality in Indonesia", "abstract": ["BACKGROUND Neonatal mortality accounts for almost 40 per cent of under-five child mortality, globally.", "An understanding of the factors related to neonatal mortality is important to guide the development of focused and evidence-based health interventions to prevent neonatal deaths.", "This study aimed to identify the determinants of neonatal mortality in Indonesia, for a nationally representative sample of births from 1997 to 2002.   \n", "METHODS The data source for the analysis was the 2002-2003 Indonesia Demographic and Health Survey from which survival information of 15,952 singleton live-born infants born between 1997 and 2002 was examined.", "Multilevel logistic regression using a hierarchical approach was performed to analyze the factors associated with neonatal deaths, using community, socio-economic status and proximate determinants.   \n", "RESULTS At the community level, the odds of neonatal death was significantly higher for infants from East Java (OR = 5.01, p = 0.00), and for North, Central and Southeast Sulawesi and Gorontalo combined (OR = 3.17, p = 0.03) compared to the lowest neonatal mortality regions of Bali, South Sulawesi and Jambi provinces.", "A progressive reduction in the odds was found as the percentage of deliveries assisted by trained delivery attendants in the cluster increased.", "The odds of neonatal death were higher for infants born to both mother and father who were employed (OR = 1.84, p = 0.00) and for infants born to father who were unemployed (OR = 2.99, p = 0.02).", "The odds were also higher for higher rank infants with a short birth interval (OR = 2.82, p = 0.00), male infants (OR = 1.49, p = 0.01), smaller than average-sized infants (OR = 2.80, p = 0.00), and infant's whose mother had a history of delivery complications (OR = 1.81, p = 0.00).", "Infants receiving any postnatal care were significantly protected from neonatal death (OR = 0.63, p = 0.03).   \n", "CONCLUSION Public health interventions directed at reducing neonatal death should address community, household and individual level factors which significantly influence neonatal mortality in Indonesia.", "Low birth weight and short birth interval infants as well as perinatal health services factors, such as the availability of skilled birth attendance and postnatal care utilization should be taken into account when planning the interventions to reduce neonatal mortality in Indonesia."], "structured": true}
{"doc_id": 1265945, "title": "High density mapping of the MHC identifies a shared role for HLA-DRB1*01:03 in inflammatory bowel diseases and heterozygous advantage in ulcerative colitis", "abstract": ["Genome-wide association studies of the related chronic inflammatory bowel diseases (IBD) known as Crohn's disease and ulcerative colitis have shown strong evidence of association to the major histocompatibility complex (MHC).", "This region encodes a large number of immunological candidates, including the antigen-presenting classical human leukocyte antigen (HLA) molecules.", "Studies in IBD have indicated that multiple independent associations exist at HLA and non-HLA genes, but they have lacked the statistical power to define the architecture of association and causal alleles.", "To address this, we performed high-density SNP typing of the MHC in >32,000 individuals with IBD, implicating multiple HLA alleles, with a primary role for HLA-DRB1*01:03 in both Crohn's disease and ulcerative colitis.", "Noteworthy differences were observed between these diseases, including a predominant role for class II HLA variants and heterozygous advantage observed in ulcerative colitis, suggesting an important role of the adaptive immune response in the colonic environment in the pathogenesis of IBD."], "structured": false}
{"doc_id": 1275505, "title": "High-Threshold Mechanosensitive Ion Channels Blocked by a Novel Conopeptide Mediate Pressure-Evoked Pain", "abstract": ["Little is known about the molecular basis of somatosensory mechanotransduction in mammals.", "We screened a library of peptide toxins for effects on mechanically activated currents in cultured dorsal root ganglion neurons.", "One conopeptide analogue, termed NMB-1 for noxious mechanosensation blocker 1, selectively inhibits (IC50 1 \u00b5M) sustained mechanically activated currents in a subset of sensory neurons.", "Biotinylated NMB-1 retains activity and binds selectively to peripherin-positive nociceptive sensory neurons.", "The selectivity of NMB-1 was confirmed by the fact that it has no inhibitory effects on voltage-gated sodium and calcium channels, or ligand-gated channels such as acid-sensing ion channels or TRPA1 channels.", "Conversely, the tarantula toxin, GsMTx-4, which inhibits stretch-activated ion channels, had no effects on mechanically activated currents in sensory neurons.", "In behavioral assays, NMB-1 inhibits responses only to high intensity, painful mechanical stimulation and has no effects on low intensity mechanical stimulation or thermosensation.", "Unexpectedly, NMB-1 was found to also be an inhibitor of rapid FM1-43 loading (a measure of mechanotransduction) in cochlear hair cells.", "These data demonstrate that pharmacologically distinct channels respond to distinct types of mechanical stimuli and suggest that mechanically activated sustained currents underlie noxious mechanosensation.", "NMB-1 thus provides a novel diagnostic tool for the molecular definition of channels involved in hearing and pressure-evoked pain."], "structured": false}
{"doc_id": 1281769, "title": "Hyperactive Neuroendocrine Secretion Causes Size, Feeding, and Metabolic Defects of C. elegans Bardet-Biedl Syndrome Mutants", "abstract": ["Bardet-Biedl syndrome, BBS, is a rare autosomal recessive disorder with clinical presentations including polydactyly, retinopathy, hyperphagia, obesity, short stature, cognitive impairment, and developmental delays.", "Disruptions of BBS proteins in a variety of organisms impair cilia formation and function and the multi-organ defects of BBS have been attributed to deficiencies in various cilia-associated signaling pathways.", "In C. elegans, bbs genes are expressed exclusively in the sixty ciliated sensory neurons of these animals and bbs mutants exhibit sensory defects as well as body size, feeding, and metabolic abnormalities.", "Here we show that in contrast to many other cilia-defective mutants, C. elegans bbs mutants exhibit increased release of dense-core vesicles and organism-wide phenotypes associated with enhanced activities of insulin, neuropeptide, and biogenic amine signaling pathways.", "We show that the altered body size, feeding, and metabolic abnormalities of bbs mutants can be corrected to wild-type levels by abrogating the enhanced secretion of dense-core vesicles without concomitant correction of ciliary defects.", "These findings expand the role of BBS proteins to the regulation of dense-core-vesicle exocytosis and suggest that some features of Bardet-Biedl Syndrome may be caused by excessive neuroendocrine secretion."], "structured": false}
{"doc_id": 1283401, "title": "Fiji: an open-source platform for biological-image analysis", "abstract": ["Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis.", "Fiji uses modern software engineering practices to combine powerful software libraries with a broad range of scripting languages to enable rapid prototyping of image-processing algorithms.", "Fiji facilitates the transformation of new algorithms into ImageJ plugins that can be shared with end users through an integrated update system.", "We propose Fiji as a platform for productive collaboration between computer science and biology research communities."], "structured": false}
{"doc_id": 1285713, "title": "Pharmacologic characterization of a potent inhibitor of class I phosphatidylinositide 3-kinases.", "abstract": ["Extensive evidence implicates activation of the lipid phosphatidylinositide 3-kinase (PI3K) pathway in the genesis and progression of various human cancers.", "PI3K inhibitors thus have considerable potential as molecular cancer therapeutics.", "Here, we detail the pharmacologic properties of a prototype of a new series of inhibitors of class I PI3K.", "PI103 is a potent inhibitor with low IC50 values against recombinant PI3K isoforms p110alpha (2 nmol/L), p110beta (3 nmol/L), p110delta (3 nmol/L), and p110gamma (15 nmol/L).", "PI103 also inhibited TORC1 by 83.9% at 0.5 micromol/L and exhibited an IC50 of 14 nmol/L against DNA-PK.", "A high degree of selectivity for the PI3K family was shown by the lack of activity of PI103 in a panel of 70 protein kinases.", "PI103 potently inhibited proliferation and invasion of a wide variety of human cancer cells in vitro and showed biomarker modulation consistent with inhibition of PI3K signaling.", "PI103 was extensively metabolized, but distributed rapidly to tissues and tumors.", "This resulted in tumor growth delay in eight different human cancer xenograft models with various PI3K pathway abnormalities.", "Decreased phosphorylation of AKT was observed in U87MG gliomas, consistent with drug levels achieved.", "We also showed inhibition of invasion in orthotopic breast and ovarian cancer xenograft models and obtained evidence that PI103 has antiangiogenic potential.", "Despite its rapid in vivo metabolism, PI103 is a valuable tool compound for exploring the biological function of class I PI3K and importantly represents a lead for further optimization of this novel class of targeted molecular cancer therapeutic."], "structured": false}
{"doc_id": 1286352, "title": "Optimized CRISPR/Cas tools for efficient germline and somatic genome engineering in Drosophila.", "abstract": ["The type II clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) system has emerged recently as a powerful method to manipulate the genomes of various organisms.", "Here, we report a toolbox for high-efficiency genome engineering of Drosophila melanogaster consisting of transgenic Cas9 lines and versatile guide RNA (gRNA) expression plasmids.", "Systematic evaluation reveals Cas9 lines with ubiquitous or germ-line-restricted patterns of activity.", "We also demonstrate differential activity of the same gRNA expressed from different U6 snRNA promoters, with the previously untested U6:3 promoter giving the most potent effect.", "An appropriate combination of Cas9 and gRNA allows targeting of essential and nonessential genes with transmission rates ranging from 25-100%.", "We also demonstrate that our optimized CRISPR/Cas tools can be used for offset nicking-based mutagenesis.", "Furthermore, in combination with oligonucleotide or long double-stranded donor templates, our reagents allow precise genome editing by homology-directed repair with rates that make selection markers unnecessary.", "Last, we demonstrate a novel application of CRISPR/Cas-mediated technology in revealing loss-of-function phenotypes in somatic cells following efficient biallelic targeting by Cas9 expressed in a ubiquitous or tissue-restricted manner.", "Our CRISPR/Cas tools will facilitate the rapid evaluation of mutant phenotypes of specific genes and the precise modification of the genome with single-nucleotide precision.", "Our results also pave the way for high-throughput genetic screening with CRISPR/Cas."], "structured": false}
{"doc_id": 1287809, "title": "Cost-effectiveness of 10-Year Risk Thresholds for Initiation of Statin Therapy for Primary Prevention of Cardiovascular Disease.", "abstract": ["IMPORTANCE The American College of Cardiology and the American Heart Association (ACC/AHA) cholesterol treatment guidelines have wide-scale implications for treating adults without history of atherosclerotic cardiovascular disease (ASCVD) with statins.   \n", "OBJECTIVE To estimate the cost-effectiveness of various 10-year ASCVD risk thresholds that could be used in the ACC/AHA cholesterol treatment guidelines.   \n", "DESIGN, SETTING, AND PARTICIPANTS Microsimulation model, including lifetime time horizon, US societal perspective, 3% discount rate for costs, and health outcomes.", "In the model, hypothetical individuals from a representative US population aged 40 to 75 years received statin treatment, experienced ASCVD events, and died from ASCVD-related or non-ASCVD-related causes based on ASCVD natural history and statin treatment parameters.", "Data sources for model parameters included National Health and Nutrition Examination Surveys, large clinical trials and meta-analyses for statin benefits and treatment, and other published sources.   \n", "MAIN OUTCOMES AND MEASURES Estimated ASCVD events prevented and incremental costs per quality-adjusted life-year (QALY) gained.   \n", "RESULTS In the base-case scenario, the current ASCVD threshold of 7.5% or higher, which was estimated to be associated with 48% of adults treated with statins, had an incremental cost-effectiveness ratio (ICER) of $37,000/QALY compared with a 10% or higher threshold.", "More lenient ASCVD thresholds of 4.0% or higher (61% of adults treated) and 3.0% or higher (67% of adults treated) had ICERs of $81,000/QALY and $140,000/QALY, respectively.", "Shifting from a 7.5% or higher ASCVD risk threshold to a 3.0% or higher ASCVD risk threshold was estimated to be associated with an additional 161,560 cardiovascular disease events averted.", "Cost-effectiveness results were sensitive to changes in the disutility associated with taking a pill daily, statin price, and the risk of statin-induced diabetes.", "In probabilistic sensitivity analysis, there was a higher than 93% chance that the optimal ASCVD threshold was 5.0% or lower using a cost-effectiveness threshold of $100,000/QALY.   \n", "CONCLUSIONS AND RELEVANCE In this microsimulation model of US adults aged 45 to 75 years [corrected], the current 10-year ASCVD risk threshold (\u22657.5% risk threshold) used in the ACC/AHA cholesterol treatment guidelines has an acceptable cost-effectiveness profile (ICER, $37,000/QALY), but more lenient ASCVD thresholds would be optimal using cost-effectiveness thresholds of $100,000/QALY (\u22654.0% risk threshold) or $150,000/QALY (\u22653.0% risk threshold).", "The optimal ASCVD threshold was sensitive to patient preferences for taking a pill daily, changes to statin price, and the risk of statin-induced diabetes."], "structured": true}
{"doc_id": 1292369, "title": "Biochemical Properties of Highly Neuroinvasive Prion Strains", "abstract": ["Infectious prions propagate from peripheral entry sites into the central nervous system (CNS), where they cause progressive neurodegeneration that ultimately leads to death.", "Yet the pathogenesis of prion disease can vary dramatically depending on the strain, or conformational variant of the aberrantly folded and aggregated protein, PrP(Sc).", "Although most prion strains invade the CNS, some prion strains cannot gain entry and do not cause clinical signs of disease.", "The conformational basis for this remarkable variation in the pathogenesis among strains is unclear.", "Using mouse-adapted prion strains, here we show that highly neuroinvasive prion strains primarily form diffuse aggregates in brain and are noncongophilic, conformationally unstable in denaturing conditions, and lead to rapidly lethal disease.", "These neuroinvasive strains efficiently generate PrP(Sc) over short incubation periods.", "In contrast, the weakly neuroinvasive prion strains form large fibrillary plaques and are stable, congophilic, and inefficiently generate PrP(Sc) over long incubation periods.", "Overall, these results indicate that the most neuroinvasive prion strains are also the least stable, and support the concept that the efficient replication and unstable nature of the most rapidly converting prions may be a feature linked to their efficient spread into the CNS."], "structured": false}
{"doc_id": 1320137, "title": "The twin-arginine translocation (Tat) protein export pathway", "abstract": ["The twin-arginine translocation (Tat) protein export system is present in the cytoplasmic membranes of most bacteria and archaea and has the highly unusual property of transporting fully folded proteins.", "The system must therefore provide a transmembrane pathway that is large enough to allow the passage of structured macromolecular substrates of different sizes but that maintains the impermeability of the membrane to ions.", "In the Gram-negative bacterium Escherichia coli, this complex task can be achieved by using only three small membrane proteins: TatA, TatB and TatC. In this Review, we summarize recent advances in our understanding of how this remarkable machine operates."], "structured": false}
{"doc_id": 1322614, "title": "New developments in the ATSAS program package for small-angle scattering data analysis", "abstract": ["New developments in the program package ATSAS (version 2.4) for the processing and analysis of isotropic small-angle X-ray and neutron scattering data are described.", "They include (i) multiplatform data manipulation and display tools, (ii) programs for automated data processing and calculation of overall parameters, (iii) improved usage of high- and low-resolution models from other structural methods, (iv) new algorithms to build three-dimensional models from weakly interacting oligomeric systems and complexes, and (v) enhanced tools to analyse data from mixtures and flexible systems.", "The new ATSAS release includes installers for current major platforms (Windows, Linux and Mac OSX) and provides improved indexed user documentation.", "The web-related developments, including a user discussion forum and a widened online access to run ATSAS programs, are also presented."], "structured": false}
{"doc_id": 1332250, "title": "The First Myriapod Genome Sequence Reveals Conservative Arthropod Gene Content and Genome Organisation in the Centipede Strigamia maritima ", "abstract": ["Myriapods (e.g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods.", "All members of the class are terrestrial, but they attained terrestriality independently of insects.", "Myriapoda is the only arthropod class not represented by a sequenced genome.", "We present an analysis of the genome of the centipede Strigamia maritima.", "It retains a compact genome that has undergone less gene loss and shuffling than previously sequenced arthropods, and many orthologues of genes conserved from the bilaterian ancestor that have been lost in insects.", "Our analysis locates many genes in conserved macro-synteny contexts, and many small-scale examples of gene clustering.", "We describe several examples where S. maritima shows different solutions from insects to similar problems.", "The insect olfactory receptor gene family is absent from S. maritima, and olfaction in air is likely effected by expansion of other receptor gene families.", "For some genes S. maritima has evolved paralogues to generate coding sequence diversity, where insects use alternate splicing.", "This is most striking for the Dscam gene, which in Drosophila generates more than 100,000 alternate splice forms, but in S. maritima is encoded by over 100 paralogues.", "We see an intriguing linkage between the absence of any known photosensory proteins in a blind organism and the additional absence of canonical circadian clock genes.", "The phylogenetic position of myriapods allows us to identify where in arthropod phylogeny several particular molecular mechanisms and traits emerged.", "For example, we conclude that juvenile hormone signalling evolved with the emergence of the exoskeleton in the arthropods and that RR-1 containing cuticle proteins evolved in the lineage leading to Mandibulata.", "We also identify when various gene expansions and losses occurred.", "The genome of S. maritima offers us a unique glimpse into the ancestral arthropod genome, while also displaying many adaptations to its specific life history."], "structured": false}
{"doc_id": 1333643, "title": "Genetic and Functional Diversification of Small RNA Pathways in Plants", "abstract": ["Multicellular eukaryotes produce small RNA molecules (approximately 21\u201324 nucleotides) of two general types, microRNA (miRNA) and short interfering RNA (siRNA).", "They collectively function as sequence-specific guides to silence or regulate genes, transposons, and viruses and to modify chromatin and genome structure.", "Formation or activity of small RNAs requires factors belonging to gene families that encode DICER (or DICER-LIKE [DCL]) and ARGONAUTE proteins and, in the case of some siRNAs, RNA-dependent RNA polymerase (RDR) proteins.", "Unlike many animals, plants encode multiple DCL and RDR proteins.", "Using a series of insertion mutants of Arabidopsis thaliana, unique functions for three DCL proteins in miRNA (DCL1), endogenous siRNA (DCL3), and viral siRNA (DCL2) biogenesis were identified.", "One RDR protein (RDR2) was required for all endogenous siRNAs analyzed.", "The loss of endogenous siRNA in dcl3 and rdr2 mutants was associated with loss of heterochromatic marks and increased transcript accumulation at some loci.", "Defects in siRNA-generation activity in response to turnip crinkle virus in dcl2 mutant plants correlated with increased virus susceptibility.", "We conclude that proliferation and diversification of DCL and RDR genes during evolution of plants contributed to specialization of small RNA-directed pathways for development, chromatin structure, and defense."], "structured": false}
{"doc_id": 1336292, "title": "Immunosuppressant FTY720 inhibits thymocyte emigration.", "abstract": ["One major role of the thymus is to provide the peripheral immune system with mature T cells, but the mechanisms involving the cellular export are not fully understood.", "In this study, we examined the ability of a novel immunosuppressive reagent, FTY720, to inhibit T cell export from the thymus.", "Daily administration of FTY720 at a dose of 1 mg / kg resulted in a marked decrease in the number of peripheral blood T lymphocytes.", "In the thymus, long-term daily administration of FTY720 caused a three- to fourfold increase in the proportion of mature medullary thymocytes (CD4(+)CD8(-) and CD4(-)CD8(+)) as well as a slight decrease in the double-positive cell (CD4(+)CD8(+)) ratio.", "Phenotypic analysis (TCRalpha beta, H-2K(d), CD44, CD69 and CD24) revealed that these increased subsets represent possible peripheral recent thymic emigrants.", "High level expression of L-selectin by these subsets further suggests that they were prevented from leaving the thymus.", "By intrathymic labeling with fluorescein isothiocyanate, only one fourth of labeled cells could be detected in the lymph nodes and in the spleen of FTY720-treated mice compared to saline-treated control mice.", "Taken together, these results suggest that the immunosuppressive action of FTY720, at least in part, could be due to its inhibitory effect on T cell emigration from the thymus to the periphery."], "structured": false}
{"doc_id": 1338283, "title": "Validating a conceptual model for an inter-professional approach to shared decision making: a mixed methods study", "abstract": ["RATIONALE, AIMS AND OBJECTIVES Following increased interest in having inter-professional (IP) health care teams engage patients in decision making, we developed a conceptual model for an IP approach to shared decision making (SDM) in primary care.", "We assessed the validity of the model with stakeholders in Canada.   \n", "METHODS In 15 individual interviews and 7 group interviews with 79 stakeholders, we asked them to: (1) propose changes to the IP-SDM model; (2) identify barriers and facilitators to the model's implementation in clinical practice; and (3) assess the model using a theory appraisal questionnaire.", "We performed a thematic analysis of the transcripts and a descriptive analysis of the questionnaires.   \n", "RESULTS Stakeholders suggested placing the patient at its centre; extending the concept of family to include significant others; clarifying outcomes; highlighting the concept of time; merging the micro, meso and macro levels in one figure; and recognizing the influence of the environment and emotions.", "The most common barriers identified were time constraints, insufficient resources and an imbalance of power among health professionals.", "The most common facilitators were education and training in inter-professionalism and SDM, motivation to achieve an IP approach to SDM, and mutual knowledge and understanding of disciplinary roles.", "Most stakeholders considered that the concepts and relationships between the concepts were clear and rated the model as logical, testable, having clear schematic representation, and being relevant to inter-professional collaboration, SDM and primary care.   \n", "CONCLUSIONS Stakeholders validated the new IP-SDM model for primary care settings and proposed few modifications.", "Future research should assess if the model helps implement SDM in IP clinical practice."], "structured": true}
{"doc_id": 1344498, "title": "Glutaminolysis activates Rag-mTORC1 signaling.", "abstract": ["Amino acids control cell growth via activation of the highly conserved kinase TORC1.", "Glutamine is a particularly important amino acid in cell growth control and metabolism.", "However, the role of glutamine in TORC1 activation remains poorly defined.", "Glutamine is metabolized through glutaminolysis to produce \u03b1-ketoglutarate.", "We demonstrate that glutamine in combination with leucine activates mammalian TORC1 (mTORC1) by enhancing glutaminolysis and \u03b1-ketoglutarate production.", "Inhibition of glutaminolysis prevented GTP loading of RagB and lysosomal translocation and subsequent activation of mTORC1.", "Constitutively active Rag heterodimer activated mTORC1 in the absence of glutaminolysis.", "Conversely, enhanced glutaminolysis or a cell-permeable \u03b1-ketoglutarate analog stimulated lysosomal translocation and activation of mTORC1.", "Finally, cell growth and autophagy, two processes controlled by mTORC1, were regulated by glutaminolysis.", "Thus, mTORC1 senses and is activated by glutamine and leucine via glutaminolysis and \u03b1-ketoglutarate production upstream of Rag.", "This may provide an explanation for glutamine addiction in cancer cells."], "structured": false}
{"doc_id": 1346695, "title": "microRNA-31/factor-inhibiting hypoxia-inducible factor 1 nexus regulates keratinocyte differentiation.", "abstract": ["Notch plays a critical role in the transition from proliferation to differentiation in the epidermis and corneal epithelium.", "Furthermore, aberrant Notch signaling is a feature of diseases like psoriasis, eczema, nonmelanoma skin cancer, and melanoma where differentiation and proliferation are impaired.", "Whereas much is known about the downstream events following Notch signaling, factors responsible for negatively regulating Notch receptor signaling after ligand activation are incompletely understood.", "Notch can undergo hydroxylation by factor-inhibiting hypoxia-inducible factor 1 (FIH-1); however, the biological significance of this phenomenon is unclear.", "Here we show that FIH-1 expression is up-regulated in diseased epidermis and corneal epithelium.", "Elevating FIH-1 levels in primary human epidermal keratinocytes (HEKs) and human corneal epithelial keratinocytes (HCEKs) impairs differentiation in submerged cultures and in a \"three-dimensional\" organotypic raft model of human epidermis, in part, via a coordinate decrease in Notch signaling.", "Knockdown of FIH-1 enhances keratinocyte differentiation.", "Loss of FIH-1 in vivo increased Notch activity in the limbal epithelium, resulting in a more differentiated phenotype.", "microRNA-31 (miR-31) is an endogenous negative regulator of FIH-1 expression that results in keratinocyte differentiation, mediated by Notch activation.", "Ectopically expressing miR-31 in an undifferentiated corneal epithelial cell line promotes differentiation and recapitulates a corneal epithelium in a three-dimensional raft culture model.", "Our results define a previously unknown mechanism for keratinocyte fate decisions where Notch signaling potential is, in part, controlled through a miR-31/FIH-1 nexus."], "structured": false}
{"doc_id": 1349033, "title": "Advantages of larval control for African malaria vectors: Low mobility and behavioural responsiveness of immature mosquito stages allow high effective coverage", "abstract": ["Based on sensitivity analysis of the MacDonald-Ross model, it has long been argued that the best way to reduce malaria transmission is to target adult female mosquitoes with insecticides that can reduce the longevity and human-feeding frequency of vectors.", "However, these analyses have ignored a fundamental biological difference between mosquito adults and the immature stages that precede them: adults are highly mobile flying insects that can readily detect and avoid many intervention measures whereas mosquito eggs, larvae and pupae are confined within relatively small aquatic habitats and cannot readily escape control measures.", "We hypothesize that the control of adult but not immature mosquitoes is compromised by their ability to avoid interventions such as excito-repellant insecticides.", "We apply a simple model of intervention avoidance by mosquitoes and demonstrate that this can substantially reduce effective coverage, in terms of the proportion of the vector population that is covered, and overall impact on malaria transmission.", "We review historical evidence that larval control of African malaria vectors can be effective and conclude that the only limitations to the effective coverage of larval control are practical rather than fundamental.", "Larval control strategies against the vectors of malaria in sub-Saharan Africa could be highly effective, complementary to adult control interventions, and should be prioritized for further development, evaluation and implementation as an integral part of Rolling Back Malaria."], "structured": false}
{"doc_id": 1354567, "title": "The Arabidopsis Chromatin-Modifying Nuclear siRNA Pathway Involves a Nucleolar RNA Processing Center", "abstract": ["In Arabidopsis thaliana, small interfering RNAs (siRNAs) direct cytosine methylation at endogenous DNA repeats in a pathway involving two forms of nuclear RNA polymerase IV (Pol IVa and Pol IVb), RNA-DEPENDENT RNA POLYMERASE 2 (RDR2), DICER-LIKE 3 (DCL3), ARGONAUTE4 (AGO4), the chromatin remodeler DRD1, and the de novo cytosine methyltransferase DRM2.", "We show that RDR2, DCL3, AGO4, and NRPD1b (the largest subunit of Pol IVb) colocalize with siRNAs within the nucleolus.", "By contrast, Pol IVa and DRD1 are external to the nucleolus and colocalize with endogenous repeat loci.", "Mutation-induced loss of pathway proteins causes downstream proteins to mislocalize, revealing their order of action.", "Pol IVa acts first, and its localization is RNA dependent, suggesting an RNA template.", "We hypothesize that maintenance of the heterochromatic state involves locus-specific Pol IVa transcription followed by siRNA production and assembly of AGO4- and NRPD1b-containing silencing complexes within nucleolar processing centers."], "structured": false}
{"doc_id": 1358909, "title": "Peripheral arterial disease in the elderly: The Rotterdam Study.", "abstract": ["To assess the age- and sex-specific prevalence of peripheral arterial disease (PAD) and intermittent claudication (IC) in an elderly population, we performed a population-based study in 7715 subjects (40% men, 60% women) aged 55 years and over.", "The presence of PAD and IC was determined by measuring the ankle-arm systolic blood pressure index (AAI) and by means of the World Health Organization/Rose questionnaire, respectively.", "PAD was considered present when the AAI was <0.90 in either leg.", "The prevalence of PAD was 19.1% (95% confidence interval, 18.1% to 20.0%): 16.9% in men and 20.5% in women.", "Symptoms of IC were reported by 1.6% (95% confidence interval, 1.3% to 1.9%) of the study population (2.2% in men, 1.2% in women).", "Of those with PAD, 6.3% reported symptoms of IC (8.7% in men, 4.9% in women), whereas in 68.9% of those with IC an AAI below 0.90 was found.", "Subjects with an AAI <0.90 were more likely to be smokers, to have hypertension, and to have symptomatic or asymptomatic cardiovascular disease compared with subjects with an AAI of 0.90 or higher.", "The authors conclude that the prevalence of PAD in the elderly is high whereas the prevalence of IC is rather low, although both prevalences clearly increase with advancing age.", "The vast majority of PAD patients reports no symptoms of IC."], "structured": false}
{"doc_id": 1360607, "title": "Antioxidants attenuate the plasma cytokine response to exercise in humans.", "abstract": ["Exercise increases plasma TNF-alpha, IL-1beta, and IL-6, yet the stimuli and sources of TNF-alpha and IL-1beta remain largely unknown.", "We tested the role of oxidative stress and the potential contribution of monocytes in this cytokine (especially IL-1beta) response in previously untrained individuals.", "Six healthy nonathletes performed two 45-min bicycle exercise sessions at 70% of Vo(2 max) before and after a combination of antioxidants (vitamins E, A, and C for 60 days; allopurinol for 15 days; and N-acetylcysteine for 3 days).", "Blood was drawn at baseline, end-exercise, and 30 and 120 min postexercise.", "Plasma cytokines were determined by ELISA and monocyte intracellular cytokine level by flow cytometry.", "Before antioxidants, TNF-alpha increased by 60%, IL-1beta by threefold, and IL-6 by sixfold secondary to exercise (P < 0.05).", "After antioxidants, plasma IL-1beta became undetectable, the TNF-alpha response to exercise was abolished, and the IL-6 response was significantly blunted (P < 0.05).", "Exercise did not increase the percentage of monocytes producing the cytokines or their mean fluorescence intensity.", "We conclude that in untrained humans oxidative stress is a major stimulus for exercise-induced cytokine production and that monocytes play no role in this process."], "structured": false}
{"doc_id": 1365188, "title": "Relation between colonic proglucagon expression and metabolic response to oligofructose in high fat diet-fed mice.", "abstract": ["Several data suggest that fermentable dietary fiber could play a role in the control of obesity and associated metabolic disorders.", "The aim of this study was to investigate the putative role of short chain fructo-oligosaccharide (OFS) - a non-digestible oligosaccharide - in mice fed a standard diet and in mice fed two distinct high fat diets inducing metabolic disorders associated to obesity.", "We confirmed, in mice, several effects previously shown in rats fed a standard diet enriched with OFS, namely an increase in total and empty caecum weight, a significant decrease in epididymal fat mass, and an increase in colonic and portal plasma glucagon-like peptide-1 (GLP-1), a phenomenon positively correlated with a higher colonic proglucagon mRNA level.", "Curiously, 4-week treatment with OFS added at the same dose induced different effects when added in the two different high fat diets.", "OFS decreased energy intake, body weight gain, glycemia, and epididymal fat mass only when added together with the high fat-carbohydrate free diet, in which OFS promoted colonic proglucagon expression and insulin secretion.", "Our results support an association between the increase in proglucagon expression in the proximal colon and OFS effects on glycemia, fat mass development, and/or body weight gain.", "In conclusion, dietary oligosaccharides would constitute an interesting class of dietary fibers promoting, in certain conditions, endogenous GLP-1 production, with beneficial physiological consequences.", "This remains to be proven in human studies."], "structured": false}
{"doc_id": 1371440, "title": "Aurora B phosphorylates spatially distinct targets to differentially regulate the kinetochore-microtubule interface.", "abstract": ["Accurate chromosome segregation requires carefully regulated interactions between kinetochores and microtubules, but how plasticity is achieved to correct diverse attachment defects remains unclear.", "Here we demonstrate that Aurora B kinase phosphorylates three spatially distinct targets within the conserved outer kinetochore KNL1/Mis12 complex/Ndc80 complex (KMN) network, the key player in kinetochore-microtubule attachments.", "The combinatorial phosphorylation of the KMN network generates graded levels of microtubule-binding activity, with full phosphorylation severely compromising microtubule binding.", "Altering the phosphorylation state of each protein causes corresponding chromosome segregation defects.", "Importantly, the spatial distribution of these targets along the kinetochore axis leads to their differential phosphorylation in response to changes in tension and attachment state.", "In total, rather than generating exclusively binary changes in microtubule binding, our results suggest a mechanism for the tension-dependent fine-tuning of kinetochore-microtubule interactions."], "structured": false}
{"doc_id": 1373287, "title": "Prognostic importance of 6-mercaptopurine dose intensity in acute lymphoblastic leukemia.", "abstract": ["6-Mercaptopurine (6MP) and methotrexate are the backbone of continuation therapy for childhood acute lymphoblastic leukemia (ALL).", "In studies of oral 6MP and methotrexate, indices of chronic systemic exposure to active metabolites of these agents, namely, red blood cell (RBC) concentrations of methotrexate polyglutamates (MTXPGs) and thioguanine nucleotides (TGNs) have positively correlated with event-free survival (EFS).", "Our objective was to evaluate whether MTXPGs, TGNs, and the dose intensity of administered methotrexate and 6MP were prognostic in the setting of a treatment protocol in which all treatment was coordinated through a single center, and the weekly doses of methotrexate were given parenterally.", "On protocol Total XII, 182 children achieved remission and received weekly methotrexate 40 mg/m2 parenterally and daily oral 6MP, interrupted every 6 weeks during the first year by pulse chemotherapy.", "A total of 709 TGN, 418 MTX-PG, and 267 thiopurine methyltransferase (TPMT) measurements, along with complete dose intensity information (dose received divided by protocol dose per week) for 19,046 weeks of 6MP and methotrexate, were analyzed.", "In univariate analyses, only higher dose intensity of 6MP and of weekly methotrexate were significant predictors of overall EFS (P =.006 and.", "039, respectively).", "The occurrence of neutropenia was associated with worse outcome (P =.040).", "In a multivariate analysis, only higher dose intensity of 6MP (P =.020) was a significant predictor of EFS, with lower TPMT activity (P =.096) tending to associate with better outcome.", "6MP dose intensity was also associated (P =.007) with EFS among patients with homozygous wild-type TPMT phenotype.", "Lower 6MP dose intensity was primarily due to missed weeks of therapy and not to reductions in daily dose.", "We conclude that increased dose-intensity of oral 6MP is an important determinant of EFS in ALL, particularly among those children with a homozygous wild-type TPMT phenotype.", "However, increasing intensity of therapy such that neutropenia precludes chemotherapy administration may be counterproductive."], "structured": false}
{"doc_id": 1379127, "title": "Orai1 and STIM1 are critical for breast tumor cell migration and metastasis.", "abstract": ["Tumor metastasis is the primary cause of death of cancer patients.", "Understanding the molecular mechanisms underlying tumor metastasis will provide potential drug targets.", "We report here that Orai1 and STIM1, both of which are involved in store-operated calcium entry, are essential for breast tumor cell migration in vitro and tumor metastasis in mice.", "Reduction of Orai1 or STIM1 by RNA interference in highly metastatic human breast cancer cells or treatment with a pharmacological inhibitor of store-operated calcium channels decreased tumor metastasis in animal models.", "Our data demonstrate a role for Orai1 and STIM1 in tumor metastasis and suggest store-operated calcium entry channels as potential cancer therapeutic targets."], "structured": false}
{"doc_id": 1381673, "title": "Mouse Spermatogenic Stem Cells Continually Interconvert between Equipotent Singly Isolated and Syncytial States", "abstract": ["The identity and behavior of mouse spermatogenic stem cells have been a long-standing focus of interest.", "In the prevailing \"As model,\" stem cell function is restricted to singly isolated (As) spermatogonia.", "By examining single-cell dynamics of GFR\u03b11+ stem cells in vivo, we evaluate an alternative hypothesis that, through fragmentation, syncytial spermatogonia also contribute to stem cell function in homeostasis.", "We use live imaging and pulse labeling to quantitatively determine the fates of individual GFR\u03b11+ cells and find that, during steady-state spermatogenesis, the entire GFR\u03b11+ population comprises a single stem cell pool, in which cells continually interconvert between As and syncytial states.", "A minimal biophysical model, relying only on the rates of incomplete cell division and syncytial fragmentation, precisely predicts the stochastic fates of GFR\u03b11+ cells during steady state and postinsult regeneration.", "Thus, our results define an alternative and dynamic model for spermatogenic stem cell function in the mouse testis."], "structured": false}
{"doc_id": 1383826, "title": "Pseudoknots: RNA Structures with Diverse Functions", "abstract": ["RNA molecules fulfill a diverse set of biological functions within cells, from the transfer of genetic information from DNA to protein, to enzymatic catalysis.", "Reflecting this range of roles, simple linear strings of RNA\u2014made up of uracil, guanine, cytosine, and adenine\u2014form a variety of complex three-dimensional structures.", "Just as proteins form distinct structural motifs such as zinc fingers and beta barrels, certain structures are also commonly adopted by RNA molecules.", "Among the most prevalent RNA structures is a motif known as the pseudoknot.", "First recognized in the turnip yellow mosaic virus [1], a pseudoknot is an RNA structure that is minimally composed of two helical segments connected by single-stranded regions or loops (Figure 1).", "Although several distinct folding topologies of pseudoknots exist, the best characterized is the H type.", "In the H-type fold, the bases in the loop of a hairpin form intramolecular pairs with bases outside of the stem (Figure 1A and \u200band1B).1B).", "This causes the formation of a second stem and loop, resulting in a pseudoknot with two stems and two loops (Figure 1C).", "The two stems are able to stack on top of each other to form a quasi-continuous helix with one continuous and one discontinuous strand.", "The single-stranded loop regions often interact with the adjacent stems (loop 1\u2013stem 2 or loop 2\u2013stem 1) to form hydrogen bonds and to participate in the overall structure of the molecule.", "Hence, this relatively simple fold can yield very complex and stable RNA structures.", "Due to variation of the lengths of the loops and stems, as well as the types of interactions between them, pseudoknots represent a structurally diverse group.", "It is fitting that they play a variety of diverse roles in biology.", "These roles include forming the catalytic core of various ribozymes [2,3], self-splicing introns [4], and telomerase [5].", "Additionally, pseudoknots play critical roles in altering gene expression by inducing ribosomal frameshifting in many viruses [6\u20139]."], "structured": false}
{"doc_id": 1386103, "title": "An essential role for interferon gamma in resistance to Mycobacterium tuberculosis infection", "abstract": ["Tuberculosis, a major health problem in developing countries, has reemerged in recent years in many industrialized countries.", "The increased susceptibility of immunocompromised individuals to tuberculosis, and many experimental studies indicate that T cell-mediated immunity plays an important role in resistance.", "The lymphokine interferon gamma (IFN-gamma) is thought to be a principal mediator of macrophage activation and resistance to intracellular pathogens.", "Mice have been developed which fail to produce IFN-gamma (gko), because of a targeted disruption of the gene for IFN-gamma.", "Upon infection with Mycobacterium tuberculosis, although they develop granulomas, gko mice fail to produce reactive nitrogen intermediates and are unable to restrict the growth of the bacilli.", "In contrast to control mice, gko mice exhibit heightened tissue necrosis and succumb to a rapid and fatal course of tuberculosis that could be delayed, but not prevented, by treatment with exogenous recombinant IFN-gamma."], "structured": false}
{"doc_id": 1387104, "title": "Malignancies, prothrombotic mutations, and the risk of venous thrombosis.", "abstract": ["CONTEXT Venous thrombosis is a common complication in patients with cancer, leading to additional morbidity and compromising quality of life.   \n", "OBJECTIVE To identify individuals with cancer with an increased thrombotic risk, evaluating different tumor sites, the presence of distant metastases, and carrier status of prothrombotic mutations.   \n", "DESIGN, SETTING, AND PATIENTS A large population-based, case-control (Multiple Environmental and Genetic Assessment [MEGA] of risk factors for venous thrombosis) study of 3220 consecutive patients aged 18 to 70 years, with a first deep venous thrombosis of the leg or pulmonary embolism, between March 1, 1999, and May 31, 2002, at 6 anticoagulation clinics in the Netherlands, and separate 2131 control participants (partners of the patients) reported via a questionnaire on acquired risk factors for venous thrombosis.", "Three months after discontinuation of the anticoagulant therapy, all patients and controls were interviewed, a blood sample was taken, and DNA was isolated to ascertain the factor V Leiden and prothrombin 20210A mutations.   \n", "MAIN OUTCOME MEASURE Risk of venous thrombosis.   \n", "RESULTS The overall risk of venous thrombosis was increased 7-fold in patients with a malignancy (odds ratio [OR], 6.7; 95% confidence interval [CI], 5.2-8.6) vs persons without malignancy.", "Patients with hematological malignancies had the highest risk of venous thrombosis, adjusted for age and sex (adjusted OR, 28.0; 95% CI, 4.0-199.7), followed by lung cancer and gastrointestinal cancer.", "The risk of venous thrombosis was highest in the first few months after the diagnosis of malignancy (adjusted OR, 53.5; 95% CI, 8.6-334.3).", "Patients with cancer with distant metastases had a higher risk vs patients without distant metastases (adjusted OR, 19.8; 95% CI, 2.6-149.1).", "Carriers of the factor V Leiden mutation who also had cancer had a 12-fold increased risk vs individuals without cancer and factor V Leiden (adjusted OR, 12.1; 95% CI, 1.6-88.1).", "Similar results were indirectly calculated for the prothrombin 20210A mutation in patients with cancer.   \n", "CONCLUSIONS Patients with cancer have a highly increased risk of venous thrombosis especially in the first few months after diagnosis and in the presence of distant metastases.", "Carriers of the factor V Leiden and prothrombin 20210A mutations appear to have an even higher risk."], "structured": true}
{"doc_id": 1387654, "title": "The Hippo signaling pathway restricts the oncogenic potential of an intestinal regeneration program.", "abstract": ["Although a developmental role for Hippo signaling in organ size control is well appreciated, how this pathway functions in tissue regeneration is largely unknown.", "Here we address this issue using a dextran sodium sulfate (DSS)-induced colonic regeneration model.", "We find that regenerating crypts express elevated Yes-associated protein (YAP) levels.", "Inactivation of YAP causes no obvious intestinal defects under normal homeostasis, but severely impairs DSS-induced intestinal regeneration.", "Conversely, hyperactivation of YAP results in widespread early-onset polyp formation following DSS treatment.", "Thus, the YAP oncoprotein must be exquisitely controlled in tissue regeneration to allow compensatory proliferation and prevent the intrinsic oncogenic potential of a tissue regeneration program."], "structured": false}
{"doc_id": 1388704, "title": "The essence of SNPs.", "abstract": ["Single nucleotide polymorphisms (SNPs) are an abundant form of genome variation, distinguished from rare variations by a requirement for the least abundant allele to have a frequency of 1% or more.", "A wide range of genetics disciplines stand to benefit greatly from the study and use of SNPs.", "The recent surge of interest in SNPs stems from, and continues to depend upon, the merging and coincident maturation of several research areas, i.e. (i) large-scale genome analysis and related technologies, (ii) bio-informatics and computing, (iii) genetic analysis of simple and complex disease states, and (iv) global human population genetics.", "These fields will now be propelled forward, often into uncharted territories, by ongoing discovery efforts that promise to yield hundreds of thousands of human SNPs in the next few years.", "Major questions are now being asked, experimentally, theoretically and ethically, about the most effective ways to unlock the full potential of the upcoming SNP revolution."], "structured": false}
{"doc_id": 1389264, "title": "Combination inhibition of PI3K and mTORC1 yields durable remissions in orthotopic patient-derived xenografts of HER2-positive breast cancer brain metastases", "abstract": ["Brain metastases represent the greatest clinical challenge in treating HER2-positive breast cancer.", "We report the development of orthotopic patient-derived xenografts (PDXs) of HER2-expressing breast cancer brain metastases (BCBM), and their use for the identification of targeted combination therapies.", "Combined inhibition of PI3K and mTOR resulted in durable tumor regressions in three of five PDXs, and therapeutic response was correlated with a reduction in the phosphorylation of 4EBP1, an mTORC1 effector.", "The two nonresponding PDXs showed hypermutated genomes with enrichment of mutations in DNA-repair genes, which suggests an association of genomic instability with therapeutic resistance.", "These findings suggest that a biomarker-driven clinical trial of PI3K inhibitor in combination with an mTOR inhibitor should be conducted for patients with HER2-positive BCBM."], "structured": false}
{"doc_id": 1391126, "title": "Activation of Frontal Neocortical Areas by Vocal Production in Marmosets", "abstract": ["Primates often rely on vocal communication to mediate social interactions.", "Although much is known about the acoustic structure of primate vocalizations and the social context in which they are usually uttered, our knowledge about the neocortical control of audio-vocal interactions in primates is still incipient, being mostly derived from lesion studies in squirrel monkeys and macaques.", "To map the neocortical areas related to vocal control in a New World primate species, the common marmoset, we employed a method previously used with success in other vertebrate species: Analysis of the expression of the immediate early gene Egr-1 in freely behaving animals.", "The neocortical distribution of Egr-1 immunoreactive cells in three marmosets that were exposed to the playback of conspecific vocalizations and vocalized spontaneously (H/V group) was compared to data from three other marmosets that also heard the playback but did not vocalize (H/n group).", "The anterior cingulate cortex, the dorsomedial prefrontal cortex and the ventrolateral prefrontal cortex presented a higher number of Egr-1 immunoreactive cells in the H/V group than in H/n animals.", "Our results provide direct evidence that the ventrolateral prefrontal cortex, the region that comprises Broca's area in humans and has been associated with auditory processing of species-specific vocalizations and orofacial control in macaques, is engaged during vocal output in marmosets.", "Altogether, our results support the notion that the network of neocortical areas related to vocal communication in marmosets is quite similar to that of Old world primates.", "The vocal production role played by these areas and their importance for the evolution of speech in primates are discussed."], "structured": false}
{"doc_id": 1398021, "title": "Familial hiatal hernia in a large five generation family confirming true autosomal dominant inheritance.", "abstract": ["BACKGROUND Familial hiatal hernia has only rarely been documented.   ", "AIMS To describe the pattern of inheritance of familial hiatal hernia within an affected family.   ", "SUBJECTS Thirty eight members of a family pedigree across five generations.   \n", "METHODS All family members were interviewed and investigated by barium meal for evidence of a hiatal hernia.   \n", "RESULTS Twenty three of 38 family members had radiological evidence of a hiatal hernia.", "No individual with a hiatal hernia was born to unaffected parents.", "In one case direct male to male transmission was shown.   \n", "CONCLUSIONS Familial inheritance of hiatal hernia does occur.", "Evidence of direct male to male transmission points to an autosomal dominant mode of inheritance."], "structured": true}
{"doc_id": 1410197, "title": "An Excitatory Loop with Astrocytes Contributes to Drive Neurons to Seizure Threshold", "abstract": ["Seizures in focal epilepsies are sustained by a highly synchronous neuronal discharge that arises at restricted brain sites and subsequently spreads to large portions of the brain.", "Despite intense experimental research in this field, the earlier cellular events that initiate and sustain a focal seizure are still not well defined.", "Their identification is central to understand the pathophysiology of focal epilepsies and to develop new pharmacological therapies for drug-resistant forms of epilepsy.", "The prominent involvement of astrocytes in ictogenesis was recently proposed.", "We test here whether a cooperation between astrocytes and neurons is a prerequisite to support ictal (seizure-like) and interictal epileptiform events.", "Simultaneous patch-clamp recording and Ca2+ imaging techniques were performed in a new in vitro model of focal seizures induced by local applications of N-methyl-D-aspartic acid (NMDA) in rat entorhinal cortex slices.", "We found that a Ca2+ elevation in astrocytes correlates with both the initial development and the maintenance of a focal, seizure-like discharge.", "A delayed astrocyte activation during ictal discharges was also observed in other models (including the whole in vitro isolated guinea pig brain) in which the site of generation of seizure activity cannot be precisely monitored.", "In contrast, interictal discharges were not associated with Ca2+ changes in astrocytes.", "Selective inhibition or stimulation of astrocyte Ca2+ signalling blocked or enhanced, respectively, ictal discharges, but did not affect interictal discharge generation.", "Our data reveal that neurons engage astrocytes in a recurrent excitatory loop (possibly involving gliotransmission) that promotes seizure ignition and sustains the ictal discharge.", "This neuron-astrocyte interaction may represent a novel target to develop effective therapeutic strategies to control seizures."], "structured": false}
{"doc_id": 1412089, "title": "Diminished performance on neuropsychological testing in late life depression is correlated with microstructural white matter abnormalities.", "abstract": ["BACKGROUND Traditional T2 weighted MR imaging results are non-specific for the extent of underlying white matter structural abnormalities present in late life depression (LLD).", "Diffusion tensor imaging provides a unique opportunity to investigate the extent and nature of structural injury, but has been limited by examining only a subset of regions of interest (ROI) and by confounds common to the study of an elderly population, including comorbid vascular pathology.", "Furthermore, comprehensive correlation of diffusion tensor imaging (DTI) measurements, including axial and radial diffusivity measurements, has not been demonstrated in the late life depression population.   \n", "METHODS 51 depressed and 16 non-depressed, age- and cerebrovascular risk factor-matched elderly subjects underwent traditional anatomic T1 and T2 weight imaging, as well as DTI.", "The DTI data were skeletonized using tract based spatial statistics (TBSS), and both regional and global analyses were performed.   \n", "RESULTS Widespread structural abnormalities within white matter were detected in the LLD group, accounting for age, gender and education and matched for cerebrovascular risk factors and global T2 white matter hyperintensities (T2WMH).", "Regional differences were most prominent in uncinate and cingulate white matter and were generally characterized by an increase in radial diffusivity.", "Age-related changes particularly in the cingulate bundle were more advanced in individuals with LLD relative to controls.", "Regression analysis demonstrated significant correlations of regional fractional anisotropy and radial diffusivity with five different neuropsychological factor scores.", "TBSS analysis demonstrated a greater extent of white matter abnormalities in LLD not responsive to treatment, as compared to controls.   \n", "CONCLUSIONS White matter integrity is compromised in late life depression, largely manifested by increased radial diffusivity in specific regions, suggesting underlying myelin injury.", "A possible mechanism for underlying myelin injury is chronic white matter ischemia related to intrinsic cerebrovascular disease.", "In some regions such as the cingulate bundle, the white matter injury related to late life depression appears to be independent of and compounded by age-related changes.", "The correlations with neuropsychological testing indicate the essential effects of white matter injury on functional status.", "Lastly, response to treatment may depend on the extent of white matter injury, suggesting a need for intact functional networks."], "structured": true}
{"doc_id": 1428830, "title": "The atypical antipsychotic olanzapine causes weight gain by targeting serotonin receptor 2C.", "abstract": ["Atypical antipsychotics such as olanzapine often induce excessive weight gain and type 2 diabetes.", "However, the mechanisms underlying these drug-induced metabolic perturbations remain poorly understood.", "Here, we used an experimental model that reproduces olanzapine-induced hyperphagia and obesity in female C57BL/6 mice.", "We found that olanzapine treatment acutely increased food intake, impaired glucose tolerance, and altered physical activity and energy expenditure in mice.", "Furthermore, olanzapine-induced hyperphagia and weight gain were blunted in mice lacking the serotonin 2C receptor (HTR2C).", "Finally, we showed that treatment with the HTR2C-specific agonist lorcaserin suppressed olanzapine-induced hyperphagia and weight gain.", "Lorcaserin treatment also improved glucose tolerance in olanzapine-fed mice.", "Collectively, our studies suggest that olanzapine exerts some of its untoward metabolic effects via antagonism of HTR2C."], "structured": false}
{"doc_id": 1428840, "title": "Case-control study of endogenous steroid hormones and endometrial cancer.", "abstract": ["BACKGROUND It has been suggested that identified risk factors for endometrial cancer operate through a single etiologic pathway, i.e., exposure to relatively high levels of unopposed estrogen (estrogen in the absence of progestins).", "Only a few studies, however, have addressed this issue directly.   ", "PURPOSE We assessed the risk of developing endometrial cancer among both premenopausal and postmenopausal women in relation to the circulating levels of steroid hormones and sex hormone-binding globulin (SHBG).", "The independent effect of hormones was assessed after adjustment for other known risk factors.   \n", "METHODS The data used in the analysis are from a case-control study conducted in five geographic regions in the United States.", "Incident cases were newly diagnosed during the period from June 1, 1987, through May 15, 1990.", "The case patients, aged 20-74 years, were matched to control subjects by age, race, and geographic region.", "The community control subjects were obtained by random-digit-dialing procedures (for subjects 20-64 years old) and from files of the Health Care Financing Administration (for subjects > or = 65 years old).", "Additional control subjects who were having a hysterectomy performed for benign conditions were obtained from the participating centers.", "Women reporting use of exogenous estrogens or oral contraceptives within 6 months of interview were excluded, resulting in 68 case patients and 107 control subjects among premenopausal women and 208 case patients and 209 control subjects among postmenopausal women.", "The hormone analyses were performed on blood samples obtained from case patients or from hysterectomy control subjects before surgery.", "The odds ratios (ORs) and 95% confidence intervals (CIs) were estimated by use of an unconditional logistic regression analysis after we controlled for matching variables and potential confounders.", "All P values were two-sided.   \n", "RESULTS High circulating levels of androstenedione were associated with 3.6-fold and 2.8-fold increased risks among premenopausal and postmenopausal women, respectively, after adjustment for other factors (P for trend = .01 and < .001, respectively).", "Risks related to other hormone fractions varied by menopausal status.", "Among postmenopausal women, a reduced risk was associated with high SHBG levels and persisted after adjustment was made for obesity and other factors (OR = 0.51; 95% CI = 0.27-0.95).", "High estrone levels were associated with increased risk (OR = 3.8; 95% CI = 2.2-6.6), although adjustment for other risk factors (particularly body mass index) diminished the effect (OR = 2.2; 95% CI = 1.2-4.4).", "Albumin-bound estradiol (E2), a marker of the bioavailable fraction, also remained an important risk factor after adjustment was made for other factors (OR = 2.0; 95% CI = 1.0-3.9).", "In contrast, high concentrations of total, free, and albumin-bound E2 were unrelated to increased risk in premenopausal women.", "In both premenopausal and postmenopausal groups, risks associated with obesity and fat distribution were not affected by adjustment for hormones.   \n", "CONCLUSION High endogenous levels of unopposed estrogen are related to increased risk of endometrial cancer, but their independence from other risk factors is inconsistent with being a common underlying biologic pathway through which all risk factors for endometrial cancer operate.   ", "IMPLICATIONS Further research should focus on alternative endocrinologic mechanisms for risk associated with obesity and body fat distribution and for the biologic relevance of the increased risk associated with androstenedione in both premenopausal and postmenopausal disease."], "structured": true}
{"doc_id": 1447990, "title": "FOXO4 is necessary for neural differentiation of human embryonic stem cells.", "abstract": ["Proteostasis is critical for maintaining cell function and proteome stability may play an important role in human embryonic stem cell (hESC) immortality.", "Notably, hESC populations exhibit a high assembly of active proteasomes, a key node of the proteostasis network.", "FOXO4, an insulin/IGF-1 responsive transcription factor, regulates proteasome activity in hESCs.", "We find that loss of FOXO4 reduces the potential of hESCs to differentiate into neural lineages.", "Therefore, FOXO4 crosses evolutionary boundaries and links hESC function to invertebrate longevity modulation."], "structured": false}
{"doc_id": 1449692, "title": "Gestational protein restriction affects trophoblast differentiation.", "abstract": ["Whether and how gestational protein restriction (PR) affects placental development and function remain unknown.", "To test the hypothesis that PR can affect trophoblast differentiation in mid-and late pregnancy, rats were fed a 20% or an isocaloric 6% protein diet from Day 1 to 14 or 18 of pregnancy and effects of PR on trophoblast differentiation were determined by changes in expressions of marker gene(s) for trophoblast lineages.", "At Day 18 of pregnancy, PR increased expressions of Esrrb, Id1 andId2 (trophoblast stem cell markers), decreased expressions of Ascl2 (spongiotrophblast cell marker) and Prl2c1 (trophoblast giant cell marker), but did not alter expressions of Gjb3 and Pcdh12(glycogen cell markers) in the junctional zone (JZ).", "In the labyrinth zone (LZ), PR did not change expressions of Prl2b1 (trophoblast giant cell marker), Gcm1 and Syna (syncytiotrophoblast cell markers), but decrease expression of Ctsq (sinusoidal trophoblast giant cell marker).", "These results indicate that PR impairs the differentiation of trophoblast stem cell into spongiotrophoblast and trophoblast giant cells in JZ, and formation of sinusoidal trophoblast giant cells in LZ."], "structured": false}
{"doc_id": 1454773, "title": "In vitro characterization of the anti-PD-1 antibody nivolumab, BMS-936558, and in vivo toxicology in non-human primates.", "abstract": ["The programmed death-1 (PD-1) receptor serves as an immunologic checkpoint, limiting bystander tissue damage and preventing the development of autoimmunity during inflammatory responses.", "PD-1 is expressed by activated T cells and downmodulates T-cell effector functions upon binding to its ligands, PD-L1 and PD-L2, on antigen-presenting cells.", "In patients with cancer, the expression of PD-1 on tumor-infiltrating lymphocytes and its interaction with the ligands on tumor and immune cells in the tumor microenvironment undermine antitumor immunity and support its rationale for PD-1 blockade in cancer immunotherapy.", "This report details the development and characterization of nivolumab, a fully human IgG4 (S228P) anti-PD-1 receptor-blocking monoclonal antibody.", "Nivolumab binds to PD-1 with high affinity and specificity, and effectively inhibits the interaction between PD-1 and its ligands.", "In vitro assays demonstrated the ability of nivolumab to potently enhance T-cell responses and cytokine production in the mixed lymphocyte reaction and superantigen or cytomegalovirus stimulation assays.", "No in vitro antibody-dependent cell-mediated or complement-dependent cytotoxicity was observed with the use of nivolumab and activated T cells as targets.", "Nivolumab treatment did not induce adverse immune-related events when given to cynomolgus macaques at high concentrations, independent of circulating anti-nivolumab antibodies where observed.", "These data provide a comprehensive preclinical characterization of nivolumab, for which antitumor activity and safety have been demonstrated in human clinical trials in various solid tumors."], "structured": false}
{"doc_id": 1456068, "title": "Combined Impact of Lifestyle-Related Factors on Total and Cause-Specific Mortality among Chinese Women: Prospective Cohort Study", "abstract": ["BACKGROUND Although cigarette smoking, excessive alcohol drinking, obesity, and several other well-studied unhealthy lifestyle-related factors each have been linked to the risk of multiple chronic diseases and premature death, little is known about the combined impact on mortality outcomes, in particular among Chinese and other non-Western populations.", "The objective of this study was to quantify the overall impact of lifestyle-related factors beyond that of active cigarette smoking and alcohol consumption on all-cause and cause-specific mortality in Chinese women.   \n", "METHODS AND FINDINGS We used data from the Shanghai Women's Health Study, an ongoing population-based prospective cohort study in China.", "Participants included 71,243 women aged 40 to 70 years enrolled during 1996-2000 who never smoked or drank alcohol regularly.", "A healthy lifestyle score was created on the basis of five lifestyle-related factors shown to be independently associated with mortality outcomes (normal weight, lower waist-hip ratio, daily exercise, never exposed to spouse's smoking, higher daily fruit and vegetable intake).", "The score ranged from zero (least healthy) to five (most healthy) points.", "During an average follow-up of 9 years, 2,860 deaths occurred, including 775 from cardiovascular disease (CVD) and 1,351 from cancer.", "Adjusted hazard ratios for mortality decreased progressively with an increasing number of healthy lifestyle factors.", "Compared to women with a score of zero, hazard ratios (95% confidence intervals) for women with four to five factors were 0.57 (0.44-0.74) for total mortality, 0.29 (0.16-0.54) for CVD mortality, and 0.76 (0.54-1.06) for cancer mortality.", "The inverse association between the healthy lifestyle score and mortality was seen consistently regardless of chronic disease status at baseline.", "The population attributable risks for not having 4-5 healthy lifestyle factors were 33% for total deaths, 59% for CVD deaths, and 19% for cancer deaths.   \n", "CONCLUSIONS In this first study, to our knowledge, to quantify the combined impact of lifestyle-related factors on mortality outcomes in Chinese women, a healthier lifestyle pattern-including being of normal weight, lower central adiposity, participation in physical activity, nonexposure to spousal smoking, and higher fruit and vegetable intake-was associated with reductions in total and cause-specific mortality among lifetime nonsmoking and nondrinking women, supporting the importance of overall lifestyle modification in disease prevention.", "Please see later in the article for the Editors' Summary."], "structured": true}
{"doc_id": 1469751, "title": "Aptamer-functionalized lipid nanoparticles targeting osteoblasts as a novel RNA interference\u2013based bone anabolic strategy", "abstract": ["Currently, major concerns about the safety and efficacy of RNA interference (RNAi)-based bone anabolic strategies still exist because of the lack of direct osteoblast-specific delivery systems for osteogenic siRNAs.", "Here we screened the aptamer CH6 by cell-SELEX, specifically targeting both rat and human osteoblasts, and then we developed CH6 aptamer\u2013functionalized lipid nanoparticles (LNPs) encapsulating osteogenic pleckstrin homology domain-containing family O member 1 (Plekho1) siRNA (CH6-LNPs-siRNA).", "Our results showed that CH6 facilitated in vitro osteoblast-selective uptake of Plekho1 siRNA, mainly via macropinocytosis, and boosted in vivo osteoblast-specific Plekho1 gene silencing, which promoted bone formation, improved bone microarchitecture, increased bone mass and enhanced mechanical properties in both osteopenic and healthy rodents.", "These results indicate that osteoblast-specific aptamer-functionalized LNPs could act as a new RNAi-based bone anabolic strategy, advancing the targeted delivery selectivity of osteogenic siRNAs from the tissue level to the cellular level."], "structured": false}
{"doc_id": 1471041, "title": "High abundance of plasma cells secreting transglutaminase 2\u2013specific IgA autoantibodies with limited somatic hypermutation in celiac disease intestinal lesions", "abstract": ["Celiac disease is an immune-mediated disorder in which mucosal autoantibodies to the enzyme transglutaminase 2 (TG2) are generated in response to the exogenous antigen gluten in individuals who express human leukocyte antigen HLA-DQ2 or HLA-DQ8 (ref.", "3).", "We assessed in a comprehensive and nonbiased manner the IgA anti-TG2 response by expression cloning of the antibody repertoire of ex vivo\u2013isolated intestinal antibody-secreting cells (ASCs).", "We found that TG2-specific plasma cells are markedly expanded within the duodenal mucosa in individuals with active celiac disease.", "TG2-specific antibodies were of high affinity yet showed little adaptation by somatic mutations.", "Unlike infection-induced peripheral blood plasmablasts, the TG2-specific ASCs had not recently proliferated and were not short-lived ex vivo.", "Altogether, these observations demonstrate that there is a germline repertoire with high affinity for TG2 that may favor massive generation of autoreactive B cells.", "TG2-specific antibodies did not block enzymatic activity and served as substrates for TG2-mediated crosslinking when expressed as IgD or IgM but not as IgA1 or IgG1.", "This could result in preferential recruitment of plasma cells from naive IgD- and IgM-expressing B cells, thus possibly explaining why the antibody response to TG2 bears signs of a primary immune response despite the disease chronicity."], "structured": false}
{"doc_id": 1472815, "title": "Alterations of white matter integrity in adults with major depressive disorder: a magnetic resonance imaging study.", "abstract": ["OBJECTIVE The purpose of our study was to investigate alterations of white matter integrity in adults with major depressive disorder (MDD) using magnetic resonance imaging (MRI).   \n", "METHODS We performed diffusion tensor imaging with a 3T MRI scanner on 45 patients with major depression and 45 healthy controls matched for age, sex and education.", "Using a voxel-based analysis, we measured the fractional anisotropy (FA), and we investigated the differences between the patient and control groups.", "We examined the correlations between the microstructure abnormalities of white matter and symptom severity, age of illness onset and cumulative illness duration, respectively.   \n", "RESULTS We found a significant decrease in FA in the left hemisphere, including the anterior limb of the internal capsule and the inferior parietal portion of the superior longitudinal fasciculus, in patients with MDD compared with healthy controls.", "Diffusion tensor imaging measures in the left anterior limb of the internal capsule were negatively related to the severity of depressive symptoms, even after we controlled for age and sex.   \n", "CONCLUSION Our findings provide new evidence of microstructural changes of white matter in non-late-onset adult depression.", "Our results complement those observed in late-life depression and support the hypothesis that the disruption of cortical- subcortical circuit integrity may be involved in the etiology of major depressive disorder."], "structured": true}
{"doc_id": 1495563, "title": "[Clinical study on the therapeutic effect of acupuncture in the treatment of post-stroke depression].", "abstract": ["OBJECTIVE To observe the therapeutic effect of \"Xingnao Kaiqiao Zhenfa\" (Acupuncture Technique for Restoring Consciousness) in the treatment of post-stroke depression.   \n", "METHODS A total of 256 stroke patients were divided into acupuncture group (n = 180, male 138, female 42) and medication group (n = 76, male 57 and female 19) according to their visiting sequence to our hospital.", "Acupoints used were Neiguan (PC 6), Renzhong (GV 26), Baihui (GV 20), Yintang (EX-HN 3) and Sanyinjiao (SP 6,the affected side) and the needles were retained for 20 min every time.", "Patients of medication group were asked to take Amitriptyline (50 mg/d at first, 200 mg/d).", "Acupuncture treatment was conducted twice daily, and after one month's treatment the therapeutic effect was evaluated.", "Self-Rating Depression Scale (SDS) and Hamilton Rating Scale for Depression (HRSD) were used to assess the patient's state of depression.   \n", "RESULTS After the treatment, of the 180 and 76 cases in acupuncture and medication groups, 31 (17.2%) and 13 (17.1%) were cured, 73 (40.6%) and 18 (23.7%) had a marked improvement in their depression state, 27 (15.0%) and 12 (15.8%) had an improvement, 49 (27.2%) and 33 (43.4%) failed, with the effective rates being 72.8% and 56.6% respectively.", "The markedly effective rate and the total effective rate of acupuncture group were significantly higher than those of medication group (P < 0.05).", "After the treatment, the total scores of SDS and HRSD and the severity index of two groups decreased pronouncedly in comparison with those of their individual pre-treatment; and the therapeutic effects of acupuncture group were significantly better than those of medication group in reducing SDS, HRSD and severity index (P < 0 .05).", "In addition, the decreased values of depression, pessimistic mood and irritability of acupuncture group were all bigger than those of medication group (P < 0.05).", "No significant difference was found between two groups in the decreased value of insomnia (P > 0.05).   \n", "CONCLUSION \"Acupuncture Technique for Restoring Consciousness\" can effectively improve depression patients' symptoms and the therapeutic effect of acupuncture is markedly superior to that of medication for post-stroke patients."], "structured": true}
{"doc_id": 1499964, "title": "30 Years of NF-\u03baB: A Blossoming of Relevance to Human Pathobiology", "abstract": ["NF-\u03baB was discovered 30 years ago as a rapidly inducible transcription factor.", "Since that time, it has been found to have a broad role in gene induction in diverse cellular responses, particularly throughout the immune system.", "Here, we summarize elaborate regulatory pathways involving this transcription factor and use recent discoveries in human genetic diseases to place specific proteins within their relevant medical and biological contexts."], "structured": false}
{"doc_id": 1507222, "title": "Increased gene expression of brown fat uncoupling protein (UCP)1 and skeletal muscle UCP2 and UCP3 in MAC16-induced cancer cachexia.", "abstract": ["Weight loss in cancer cachexia is attributable to decreased food intake and/or enhanced energy expenditure.", "We investigated the roles of the uncoupling proteins (UCPs) UCPI, -2, and -3 in a murine model of cachexia, the MAC16 adenocarcinoma.", "Weight fell to 24% below that of non-tumor-bearing controls (P < 0.01) 18 days after MAC16 inoculation, with significant reductions in fat-pad mass (-67%; P < 0.01) and muscle mass (-20%; P < 0.01).", "Food intake was 26-60% lower (P < 0.01) than in controls on days 17-18.", "Non-tumor-bearing mice, pair-fed to match MAC16-induced hypophagia, showed less weight loss (10% below controls, P < 0.01; 16% above MAC-16, P < 0.01) and smaller decreases in fat-pad mass (21% below controls, P < 0.01).", "Core temperature in MAC16 mice was significantly lower (-2.4 degrees C, P < 0.01) than in controls, and pair-feeding had no effect.", "MAC16 mice showed significantly higher UCP1 mRNA levels in brown adipose tissue (BAT) than in controls (+63%, P < 0.01), and pair-feeding had no effect.", "UCP2 and -3 expression in BAT did not differ significantly between groups.", "By contrast, UCP2 mRNA levels in skeletal muscle were comparably increased in both MAC16 and pair-fed groups (respectively, 183 and 163% above controls; both, P < 0.05), with no significant difference between these two groups.", "Similarly, UCP3 mRNA was significantly higher than controls in both MAC16 (+163%, P < 0.05) and pair-fed (+253%, P < 0.01) groups, with no significant difference between the two experimental groups.", "Overexpression of UCP1 in BAT in MAC16-bearing mice may be an adaptive response to hypothermia, which is apparently induced by tumor products; increased thermogenesis in BAT could increase total energy expenditure and, thus, contribute to tissue wasting.", "Increased UCP2 and -3 expression in muscle are both attributable to reduced food intake and may be involved in lipid utilization during lipolysis in MAC16-induced cachexia."], "structured": false}
{"doc_id": 1522336, "title": "In vitro Anti-Tumor Effects of Statins on Head and Neck Squamous Cell Carcinoma: A Systematic Review", "abstract": ["BACKGROUND Statins are commonly used against arteriosclerotic disease, but recent retrospective analyses have suggested that statins also prevent cancer.", "The aim of this systematic review is to verify the vitro anti-tumor effects of statins on head and neck squamous cell carcinoma.   \n", "METHODS Studies were gathered by searching Cochrane, MEDLINE, EMBASE, LILACS, and PubMed, up until May 9, 2015, with no time or language restrictions.", "Only in vitro studies that discuss the effect of statins on head and neck carcinoma were selected.   \n", "RESULTS Of 153 identified papers, 14 studies met the inclusion criteria.", "These studies demonstrated that statins had a significant effect on head and neck squamous cell carcinoma cell lines and influenced cell viability, cell cycle, cell death, and protein expression levels involved in pathways of carcinogenesis, which corroborates with the potential in vitro anti-tumor effects.", "It provides highlights about the biological mechanisms of statins used alone or associated with traditional therapy for cancer.   \n", "CONCLUSIONS Though there are few studies on the topic, currently available evidence suggests that statins shows that preclinical experiments supports the potentiality of statin as an adjuvant agent in chemotherapy and/or radiotherapy approaches routinely used in the management of HNSCC and should undergo further clinical assessment."], "structured": true}
{"doc_id": 1522647, "title": "Circulating Mitochondrial DNA in Patients in the ICU as a Marker of Mortality: Derivation and Validation", "abstract": ["BACKGROUND Mitochondrial DNA (mtDNA) is a critical activator of inflammation and the innate immune system.", "However, mtDNA level has not been tested for its role as a biomarker in the intensive care unit (ICU).", "We hypothesized that circulating cell-free mtDNA levels would be associated with mortality and improve risk prediction in ICU patients.   \n", "METHODS AND FINDINGS Analyses of mtDNA levels were performed on blood samples obtained from two prospective observational cohort studies of ICU patients (the Brigham and Women's Hospital Registry of Critical Illness [BWH RoCI, n = 200] and Molecular Epidemiology of Acute Respiratory Distress Syndrome [ME ARDS, n = 243]).", "mtDNA levels in plasma were assessed by measuring the copy number of the NADH dehydrogenase 1 gene using quantitative real-time PCR.", "Medical ICU patients with an elevated mtDNA level (\u22653,200 copies/\u00b5l plasma) had increased odds of dying within 28 d of ICU admission in both the BWH RoCI (odds ratio [OR] 7.5, 95% CI 3.6-15.8, p = 1\u00d710(-7)) and ME ARDS (OR 8.4, 95% CI 2.9-24.2, p = 9\u00d710(-5)) cohorts, while no evidence for association was noted in non-medical ICU patients.", "The addition of an elevated mtDNA level improved the net reclassification index (NRI) of 28-d mortality among medical ICU patients when added to clinical models in both the BWH RoCI (NRI 79%, standard error 14%, p<1\u00d710(-4)) and ME ARDS (NRI 55%, standard error 20%, p = 0.007) cohorts.", "In the BWH RoCI cohort, those with an elevated mtDNA level had an increased risk of death, even in analyses limited to patients with sepsis or acute respiratory distress syndrome.", "Study limitations include the lack of data elucidating the concise pathological roles of mtDNA in the patients, and the limited numbers of measurements for some of biomarkers.   \n", "CONCLUSIONS Increased mtDNA levels are associated with ICU mortality, and inclusion of mtDNA level improves risk prediction in medical ICU patients.", "Our data suggest that mtDNA could serve as a viable plasma biomarker in medical ICU patients."], "structured": true}
{"doc_id": 1538080, "title": "Fructosamine Is a Useful Indicator of Hyperglycaemia and Glucose Control in Clinical and Epidemiological Studies \u2013 Cross-Sectional and Longitudinal Experience from the AMORIS Cohort", "abstract": ["CONTEXT Fructosamine is a glycemic biomarker which may be useful for indication and control of diabetes respectively.   \n", "OBJECTIVE The objective of the study was to evaluate fructosamine as an indicator of hyperglycaemia and glucose control in subjects with diabetes.   \n", "DESIGN, SETTING & PATIENTS From the AMORIS cohort, subjects with serum glucose, fructosamine and HbA1c from the same examination were studied cross-sectionally and longitudinally (n = 10,987; 5,590 overnight-fasting).", "The guidelines of the American Diabetes Association were followed for classification of prediabetes and diabetes.", "Separate analyses were performed in patients with a newly detected or a known diagnosis of type 1 or type 2 diabetes respectively.   \n", "RESULTS All three biomarkers were strongly correlated.", "With regard to the association between fructosamine and HbA1c Pearson linear correlation coefficients in the range of 0.67-0.75 were observed in fasting and non-fasting subjects with type 1 or type 2 diabetes.", "Analyses of glucose control in fasting patients with type 2 diabetes having all three biomarkers measured at three separate occasions within on average 290 days of the index examination showed similar trends over time for glucose, fructosamine and HbA1c.", "Discrimination of subjects with and without diabetes across the range of fructosamine levels was good (area under curve (AUC) 0.91-0.95) and a fructosamine level of 2.5 mmol/L classified subjects to diabetes with a sensitivity of 61% and a specificity of 97%.   \n", "CONCLUSIONS Fructosamine is closely associated with HbA1c and glucose respectively and may be a useful biomarker of hyperglycaemia and glucose control in clinical and epidemiological studies."], "structured": true}
{"doc_id": 1539159, "title": "Lifeact: a versatile marker to visualize F-actin", "abstract": ["Live imaging of the actin cytoskeleton is crucial for the study of many fundamental biological processes, but current approaches to visualize actin have several limitations.", "Here we describe Lifeact, a 17-amino-acid peptide, which stained filamentous actin (F-actin) structures in eukaryotic cells and tissues.", "Lifeact did not interfere with actin dynamics in vitro and in vivo and in its chemically modified peptide form allowed visualization of actin dynamics in nontransfectable cells."], "structured": false}
{"doc_id": 1542437, "title": "Robustness of Random Forest-based gene selection methods", "abstract": ["Gene selection is an important part of microarray data analysis because it provides information that can lead to a better mechanistic understanding of an investigated phenomenon.", "At the same time, gene selection is very difficult because of the noisy nature of microarray data.", "As a consequence, gene selection is often performed with machine learning methods.", "The Random Forest method is particularly well suited for this purpose.", "In this work, four state-of-the-art Random Forest-based feature selection methods were compared in a gene selection context.", "The analysis focused on the stability of selection because, although it is necessary for determining the significance of results, it is often ignored in similar studies.", "The comparison of post-selection accuracy in the validation of Random Forest classifiers revealed that all investigated methods were equivalent in this context.", "However, the methods substantially differed with respect to the number of selected genes and the stability of selection.", "Of the analysed methods, the Boruta algorithm predicted the most genes as potentially important.", "The post-selection classifier error rate, which is a frequently used measure, was found to be a potentially deceptive measure of gene selection quality.", "When the number of consistently selected genes was considered, the Boruta algorithm was clearly the best.", "Although it was also the most computationally intensive method, the Boruta algorithm's computational demands could be reduced to levels comparable to those of other algorithms by replacing the Random Forest importance with a comparable measure from Random Ferns (a similar but simplified classifier).", "Despite their design assumptions, the minimal optimal selection methods, were found to select a high fraction of false positives."], "structured": false}
{"doc_id": 1544804, "title": "Improved variant discovery through local re-alignment of short-read next-generation sequencing data using SRMA", "abstract": ["A primary component of next-generation sequencing analysis is to align short reads to a reference genome, with each read aligned independently.", "However, reads that observe the same non-reference DNA sequence are highly correlated and can be used to better model the true variation in the target genome.", "A novel short-read micro realigner, SRMA, that leverages this correlation to better resolve a consensus of the underlying DNA sequence of the targeted genome is described here."], "structured": false}
{"doc_id": 1546650, "title": "Functional elements within the dynein microtubule-binding domain", "abstract": ["Dynein interacts with microtubules through an ATP-sensitive linkage mapped to a structurally complex region of the heavy chain following the fourth P-loop motif.", "Virtually nothing is known regarding how binding affinity is achieved and modulated during ATP hydrolysis.", "We have performed a detailed dissection of the microtubule contact site, using fragment expression, alanine substitution, and peptide competition.", "Our work identifies three clusters of amino acids important for the physical contact with microtubules; two of these fall within a region sharing sequence homology with MAP1B, the third in a region just downstream.", "Amino acid substitutions within any one of these regions can eliminate or weaken microtubule binding (KK3379, 80, E3385, K3387, K3397, KK3410,11, W3414, RKK3418-20, F3426, R3464, S3466, and K3467), suggesting that their activities are highly coordinated.", "A peptide that actively displaces MAP1B from microtubules perturbs dynein binding, supporting previous evidence for similar sites of interaction.", "We have also identified four amino acids whose substitutions affect release of the motor from the microtubule (E3413, R3444, E3460, and C3469).", "These suggest that nucleotide-sensitive affinity may be locally controlled at the site of contact.", "Our work is the first detailed description of dynein-tubulin interactions and provides a framework for understanding how affinity is achieved and modulated."], "structured": false}
{"doc_id": 1550937, "title": "The Transcription Factors Egr2 and Egr3 Are Essential for the Control of Inflammation and Antigen-Induced Proliferation of B and T Cells", "abstract": ["Lymphocytes provide optimal responses against pathogens with minimal inflammatory pathology.", "However, the intrinsic mechanisms regulating these responses are unknown.", "Here, we report that deletion of both transcription factors Egr2 and Egr3 in lymphocytes resulted in a lethal autoimmune syndrome with excessive serum proinflammatory cytokines but also impaired antigen receptor-induced proliferation of B and T cells.", "Egr2- and Egr3-defective B and T cells had hyperactive signal transducer and activator of transcription-1 (STAT1) and STAT3 while antigen receptor-induced activation of transcription factor AP-1 was severely impaired.", "We discovered that Egr2 and/or Egr3 directly induced expression of suppressor of cytokine signaling-1 (SOCS1) and SOCS3, inhibitors of STAT1 and STAT3, and also blocked the function of Batf, an AP-1 inhibitor, in B and T cells.", "Thus, Egr2 and Egr3 regulate B and T cell function in adaptive immune responses and homeostasis by promoting antigen receptor signaling and controlling inflammation."], "structured": false}
{"doc_id": 1554348, "title": "Effect of hyperosmolality on alkaline phosphatase and stress-response protein 27 of MCF-7 breast cancer cells", "abstract": ["MCF-7, a continuous cell line derived from a human breast carcinoma, exhibits very low alkaline phosphatase (ALP) activity.", "The enzyme is heat-stable and is inhibited by L-phenylalanine and L-phenylalanylgly-cylglycine, but not by L-homoarginine, 1-bromotetramisole, or levamisole.", "These data indicate that MCF-7 produces term-placental ALP, the oncodevelopmental enzyme form inappropriately expressed by a variety of human tumors.", "In contrast to human cancer cells that produce this enzyme monophenotypically, ALP activity of MCF-7 cells is not significantly increased by glucocorticoids or sodium butyrate.", "By comparison, exposure to hyperosmolality causes a striking increase in enzyme activity.", "Cycloheximide blocks this effect.", "The results obtained with cell-free assays were confirmed by cytochemical and immunocytochemical assays on whole cells.", "Because some of the agents tested in the enzyme modulation experiments affect cell proliferation, their possible effect on two stress-response proteins (srp 27 and srp 72) was also examined; specific immunocytochemical assays were used.", "These tests revealed that neither protein is affected by glucocorticoids; that sodium butyrate has no effect on srp 27, but alters the intracellular distribution of srp 72; and that hyperosmolality, while not significantly affecting srp 72, causes an increase in srp 27."], "structured": false}
{"doc_id": 1568684, "title": "The Bile Acid Chenodeoxycholic Acid Increases Human Brown Adipose Tissue Activity.", "abstract": ["The interest in brown adipose tissue (BAT) as a target to combat metabolic disease has recently been renewed with the discovery of functional BAT in humans.", "In rodents, BAT can be activated by bile acids, which activate type 2 iodothyronine deiodinase (D2) in BAT via the G-coupled protein receptor TGR5, resulting in increased oxygen consumption and energy expenditure.", "Here we examined the effects of oral supplementation of the bile acid chenodeoxycholic acid (CDCA) on human BAT activity.", "Treatment of 12 healthy female subjects with CDCA for 2 days resulted in increased BAT activity.", "Whole-body energy expenditure was also increased upon CDCA treatment.", "In vitro treatment of primary human brown adipocytes derived with CDCA or specific TGR5 agonists increased mitochondrial uncoupling and D2 expression, an effect that was absent in human primary white adipocytes.", "These findings identify bile acids as a target to activate BAT in humans."], "structured": false}
{"doc_id": 1569031, "title": "RNase H and Postreplication Repair Protect Cells from Ribonucleotides Incorporated in DNA", "abstract": ["The chemical identity and integrity of the genome is challenged by the incorporation of ribonucleoside triphosphates (rNTPs) in place of deoxyribonucleoside triphosphates (dNTPs) during replication.", "Misincorporation is limited by the selectivity of DNA replicases.", "We show that accumulation of ribonucleoside monophosphates (rNMPs) in the genome causes replication stress and has toxic consequences, particularly in the absence of RNase H1 and RNase H2, which remove rNMPs.", "We demonstrate that postreplication repair (PRR) pathways-MMS2-dependent template switch and Pol \u03b6-dependent bypass-are crucial for tolerating the presence of rNMPs in the chromosomes; indeed, we show that Pol \u03b6 efficiently replicates over 1-4 rNMPs.", "Moreover, cells lacking RNase H accumulate mono- and polyubiquitylated PCNA and have a constitutively activated PRR.", "Our findings describe a crucial function for RNase H1, RNase H2, template switch, and translesion DNA synthesis in overcoming rNTPs misincorporated during DNA replication, and may be relevant for the pathogenesis of Aicardi-Gouti\u00e8res syndrome."], "structured": false}
{"doc_id": 1574014, "title": "Selective elimination of high constitutive activity or chemokine binding in the human herpesvirus 8 encoded seven transmembrane oncogene ORF74.", "abstract": ["Open reading frame 74 (ORF74) encoded by human herpesvirus 8 is a highly constitutively active seven transmembrane (7TM) receptor stimulated by angiogenic chemokines, e.g. growth-related oncogene-alpha, and inhibited by angiostatic chemokines e.g. interferon-gamma-inducible protein.", "Transgenic mice expressing ORF74 under control of the CD2 promoter develop highly vascularized Kaposi's sarcoma-like tumors.", "Through targeted mutagenesis we here create three distinct phenotypes of ORF74: a receptor with normal, high constitutive signaling through the phospholipase C pathway but deprived of binding and action of chemokines obtained through deletion of 22 amino acids from the N-terminal extension; an ORF74 with high constitutive activity but with selective elimination of stimulatory regulation by angiogenic chemokines obtained through substitution of basic residues at the extracellular ends of TM-V or TM-VI; and an ORF74 lacking constitutive activity but with preserved ability to be stimulated by agonist chemokines obtained through introduction of an Asp residue on the hydrophobic, presumed membrane-exposed face of TM-II.", "It is concluded that careful molecular dissection can selectively eliminate either agonist or inverse agonist modulation as well as high constitutive activity of the virally encoded oncogene ORF74 and that these mutant forms presumably can be used in transgenic animals to identify the molecular mechanism of its transforming activity."], "structured": false}
{"doc_id": 1576955, "title": "An insulin-like signaling pathway affects both longevity and reproduction in Caenorhabditis elegans.", "abstract": ["Mutations in daf-2 and age-1 cause a dramatic increase in longevity as well as developmental arrest at the dauer diapause stage in Caenorhabditis elegans.", "daf-2 and age-1 encode components of an insulin-like signaling pathway.", "Both daf-2 and age-1 act at a similar point in the genetic epistasis pathway for dauer arrest and longevity and regulate the activity of the daf-16 gene.", "Mutations in daf-16 cause a dauer-defective phenotype and are epistatic to the diapause arrest and life span extension phenotypes of daf-2 and age-1 mutants.", "Here we show that mutations in this pathway also affect fertility and embryonic development.", "Weak daf-2 alleles, and maternally rescued age-1 alleles that cause life span extension but do not arrest at the dauer stage, also reduce fertility and viability.", "We find that age-1(hx546) has reduced both maternal and zygotic age-1 activity.", "daf-16 mutations suppress all of the daf-2 and age-1 phenotypes, including dauer arrest, life span extension, reduced fertility, and viability defects.", "These data show that insulin signaling, mediated by DAF-2 through the AGE-1 phosphatidylinositol-3-OH kinase, regulates reproduction and embryonic development, as well as dauer diapause and life span, and that DAF-16 transduces these signals.", "The regulation of fertility, life span, and metabolism by an insulin-like signaling pathway is similar to the endocrine regulation of metabolism and fertility by mammalian insulin signaling."], "structured": false}
{"doc_id": 1583041, "title": "Estimating prion concentration in fluids and tissues by quantitative PMCA", "abstract": ["Prions, the proteinaceous infectious agent responsible for prion diseases, can be detected with high sensitivity by protein misfolding cyclic amplification (PMCA) technology.", "Here we describe a quantitative PMCA procedure to calculate the concentration of very low levels of prions in biological samples.", "Using this procedure, we determined the quantities of misfolded prion protein (PrPSc) in brain, spleen, blood and urine of scrapie-affected hamsters."], "structured": false}
{"doc_id": 1583134, "title": "Positional cloning of the APECED gene", "abstract": ["Autoimmune polyglandular syndrome type I (APS 1, also called APECED) is an autosomal-recessive disorder that maps to human chromosome 21q22.3 between markers D21S49 and D21S171 by linkage studies.", "We have isolated a novel gene from this region, AIRE (autoimmune regulator), which encodes a protein containing motifs suggestive of a transcription factor including two zinc-finger (PHD-finger) motifs, a proline-rich region and three LXXLL motifs.", "Two mutations, a C\u2192T substitution that changes the Arg 257 (CGA) to a stop codon (TGA) and an A\u2192G substitution that changes the Lys 83 (AAG) to a Glu codon (GAG), were found in this novel gene in Swiss and Finnish APECED patients.", "The Arg257stop (R257X) is the predominant mutation in Finnish APECED patients, accounting for 10/12 alleles studied.", "These results indicate that this gene is responsible for the pathogenesis of APECED.", "The identification of the gene defective in APECED should facilitate the genetic diagnosis and potential treatment of the disease and further enhance our general understanding of the mechanisms underlying autoimmune diseases."], "structured": false}
{"doc_id": 1590744, "title": "AMP-Activated Protein Kinase: An Ubiquitous Signaling Pathway With Key Roles in the Cardiovascular System", "abstract": ["The AMP-activated protein kinase (AMPK) is a key regulator of cellular and whole-body energy homeostasis, which acts to restore energy homoeostasis whenever cellular energy charge is depleted.", "Over the last 2 decades, it has become apparent that AMPK regulates several other cellular functions and has specific roles in cardiovascular tissues, acting to regulate cardiac metabolism and contractile function, as well as promoting anticontractile, anti-inflammatory, and antiatherogenic actions in blood vessels.", "In this review, we discuss the role of AMPK in the cardiovascular system, including the molecular basis of mutations in AMPK that alter cardiac physiology and the proposed mechanisms by which AMPK regulates vascular function under physiological and pathophysiological conditions."], "structured": false}
{"doc_id": 1595617, "title": "Differentiation of trophoblast stem cells into giant cells is triggered by p57/Kip2 inhibition of CDK1 activity.", "abstract": ["Genome endoreduplication during mammalian development is a rare event for which the mechanism is unknown.", "It first appears when fibroblast growth factor 4 (FGF4) deprivation induces differentiation of trophoblast stem (TS) cells into the nonproliferating trophoblast giant (TG) cells required for embryo implantation.", "Here we show that RO3306 inhibition of cyclin-dependent protein kinase 1 (CDK1), the enzyme required to enter mitosis, induced differentiation of TS cells into TG cells.", "In contrast, RO3306 induced abortive endoreduplication and apoptosis in embryonic stem cells, revealing that inactivation of CDK1 triggers endoreduplication only in cells programmed to differentiate into polyploid cells.", "Similarly, FGF4 deprivation resulted in CDK1 inhibition by overexpressing two CDK-specific inhibitors, p57/KIP2 and p21/CIP1.", "TS cell mutants revealed that p57 was required to trigger endoreduplication by inhibiting CDK1, while p21 suppressed expression of the checkpoint protein kinase CHK1, thereby preventing induction of apoptosis.", "Furthermore, Cdk2(-/-) TS cells revealed that CDK2 is required for endoreduplication when CDK1 is inhibited.", "Expression of p57 in TG cells was restricted to G-phase nuclei to allow CDK activation of S phase.", "Thus, endoreduplication in TS cells is triggered by p57 inhibition of CDK1 with concomitant suppression of the DNA damage response by p21."], "structured": false}
{"doc_id": 1605196, "title": "Atg5-independent autophagy regulates mitochondrial clearance and is essential for iPSC reprogramming", "abstract": ["Successful generation of induced pluripotent stem cells entails a major metabolic switch from mitochondrial oxidative phosphorylation to glycolysis during the reprogramming process.", "The mechanism of this metabolic reprogramming, however, remains elusive.", "Here, our results suggest that an Atg5-independent autophagic process mediates mitochondrial clearance, a characteristic event involved in the metabolic switch.", "We found that blocking such autophagy, but not canonical autophagy, inhibits mitochondrial clearance, in turn, preventing iPSC induction.", "Furthermore, AMPK seems to be upstream of this autophagic pathway and can be targeted by small molecules to modulate mitochondrial clearance during metabolic reprogramming.", "Our work not only reveals that the Atg5-independent autophagy is crucial for establishing pluripotency, but it also suggests that iPSC generation and tumorigenesis share a similar metabolic switch."], "structured": false}
{"doc_id": 1605392, "title": "A mutation in Orai1 causes immune deficiency by abrogating CRAC channel function", "abstract": ["Antigen stimulation of immune cells triggers Ca2+ entry through Ca2+ release-activated Ca2+ (CRAC) channels, promoting the immune response to pathogens by activating the transcription factor NFAT.", "We have previously shown that cells from patients with one form of hereditary severe combined immune deficiency (SCID) syndrome are defective in store-operated Ca2+ entry and CRAC channel function.", "Here we identify the genetic defect in these patients, using a combination of two unbiased genome-wide approaches: a modified linkage analysis with single-nucleotide polymorphism arrays, and a Drosophila RNA interference screen designed to identify regulators of store-operated Ca2+ entry and NFAT nuclear import.", "Both approaches converged on a novel protein that we call Orai1, which contains four putative transmembrane segments.", "The SCID patients are homozygous for a single missense mutation in ORAI1, and expression of wild-type Orai1 in SCID T cells restores store-operated Ca2+ influx and the CRAC current (ICRAC).", "We propose that Orai1 is an essential component or regulator of the CRAC channel complex."], "structured": false}
{"doc_id": 1606628, "title": "Estimates of global prevalence of childhood underweight in 1990 and 2015.", "abstract": ["CONTEXT One key target of the United Nations Millennium Development goals is to reduce the prevalence of underweight among children younger than 5 years by half between 1990 and 2015.   \n", "OBJECTIVE To estimate trends in childhood underweight by geographic regions of the world.   \n", "DESIGN, SETTING, AND PARTICIPANTS Time series study of prevalence of underweight, defined as weight 2 SDs below the mean weight for age of the National Center for Health Statistics and World Health Organization (WHO) reference population.", "National prevalence rates derived from the WHO Global Database on Child Growth and Malnutrition, which includes data on approximately 31 million children younger than 5 years who participated in 419 national nutritional surveys in 139 countries from 1965 through 2002.   \n", "MAIN OUTCOME MEASURES Linear mixed-effects modeling was used to estimate prevalence rates and numbers of underweight children by region in 1990 and 2015 and to calculate the changes (ie, increase or decrease) to these values between 1990 and 2015.   \n", "RESULTS Worldwide, underweight prevalence was projected to decline from 26.5% in 1990 to 17.6% in 2015, a change of -34% (95% confidence interval [CI], -43% to -23%).", "In developed countries, the prevalence was estimated to decrease from 1.6% to 0.9%, a change of -41% (95% CI, -92% to 343%).", "In developing regions, the prevalence was forecasted to decline from 30.2% to 19.3%, a change of -36% (95% CI, -45% to -26%).", "In Africa, the prevalence of underweight was forecasted to increase from 24.0% to 26.8%, a change of 12% (95% CI, 8%-16%).", "In Asia, the prevalence was estimated to decrease from 35.1% to 18.5%, a change of -47% (95% CI, -58% to -34%).", "Worldwide, the number of underweight children was projected to decline from 163.8 million in 1990 to 113.4 million in 2015, a change of -31% (95% CI, -40% to -20%).", "Numbers are projected to decrease in all subregions except the subregions of sub-Saharan, Eastern, Middle, and Western Africa, which are expected to experience substantial increases in the number of underweight children.   \n", "CONCLUSIONS An overall improvement in the global situation is anticipated; however, neither the world as a whole, nor the developing regions, are expected to achieve the Millennium Development goals.", "This is largely due to the deteriorating situation in Africa where all subregions, except Northern Africa, are expected to fail to meet the goal."], "structured": true}
{"doc_id": 1616661, "title": "Canonical Wnt signaling regulates organ-specific assembly and differentiation of CNS vasculature.", "abstract": ["Every organ depends on blood vessels for oxygen and nutrients, but the vasculature associated with individual organs can be structurally and molecularly diverse.", "The central nervous system (CNS) vasculature consists of a tightly sealed endothelium that forms the blood-brain barrier, whereas blood vessels of other organs are more porous.", "Wnt7a and Wnt7b encode two Wnt ligands produced by the neuroepithelium of the developing CNS coincident with vascular invasion.", "Using genetic mouse models, we found that these ligands directly target the vascular endothelium and that the CNS uses the canonical Wnt signaling pathway to promote formation and CNS-specific differentiation of the organ's vasculature."], "structured": false}
{"doc_id": 1617327, "title": "Bone progenitor dysfunction induces myelodysplasia and secondary leukemia", "abstract": ["Mesenchymal cells contribute to the 'stroma' of most normal and malignant tissues, with specific mesenchymal cells participating in the regulatory niches of stem cells.", "By examining how mesenchymal osteolineage cells modulate haematopoiesis, here we show that deletion of Dicer1 specifically in mouse osteoprogenitors, but not in mature osteoblasts, disrupts the integrity of haematopoiesis.", "Myelodysplasia resulted and acute myelogenous leukaemia emerged that had acquired several genetic abnormalities while having intact Dicer1.", "Examining gene expression altered in osteoprogenitors as a result of Dicer1 deletion showed reduced expression of Sbds, the gene mutated in Schwachman-Bodian-Diamond syndrome-a human bone marrow failure and leukaemia pre-disposition condition.", "Deletion of Sbds in mouse osteoprogenitors induced bone marrow dysfunction with myelodysplasia.", "Therefore, perturbation of specific mesenchymal subsets of stromal cells can disorder differentiation, proliferation and apoptosis of heterologous cells, and disrupt tissue homeostasis.", "Furthermore, primary stromal dysfunction can result in secondary neoplastic disease, supporting the concept of niche-induced oncogenesis."], "structured": false}
{"doc_id": 1624106, "title": "Generating diploid embryos from Xenopus tropicalis.", "abstract": ["A spectacular advantage of Xenopus tropicalis is the ease with which diploid embryos can be generated year round.", "By the simple administration of human chorionic gonadotropin, an investigator can generate many hundreds of synchronized embryos by in vitro fertilization or thousands of embryos from a mating pair.", "The ability to induce ovulations when desired facilitates many different experiments such as experimental embryology, molecular manipulation of gene products, and genetics."], "structured": false}
{"doc_id": 1630949, "title": "Oct4-Induced Pluripotency in Adult Neural Stem Cells", "abstract": ["The four transcription factors Oct4, Sox2, Klf4, and c-Myc can induce pluripotency in mouse and human fibroblasts.", "We previously described direct reprogramming of adult mouse neural stem cells (NSCs) by Oct4 and either Klf4 or c-Myc.", "NSCs endogenously express Sox2, c-Myc, and Klf4 as well as several intermediate reprogramming markers.", "Here we report that exogenous expression of the germline-specific transcription factor Oct4 is sufficient to generate pluripotent stem cells from adult mouse NSCs.", "These one-factor induced pluripotent stem cells (1F iPS) are similar to embryonic stem cells in vitro and in vivo.", "Not only can these cells can be efficiently differentiated into NSCs, cardiomyocytes, and germ cells in vitro, but they are also capable of teratoma formation and germline transmission in vivo.", "Our results demonstrate that Oct4 is required and sufficient to directly reprogram NSCs to pluripotency."], "structured": false}
{"doc_id": 1631583, "title": "Getting started with yeast.", "abstract": ["Publisher Summary The yeast Saccharomyces cerevisiae is now recognized as a model system representing a simple eukaryote whose genome can be easily manipulated.", "Yeast has only a slightly greater genetic complexity than bacteria and shares many of the technical advantages that permitted rapid progress in the molecular genetics of prokaryotes and their viruses.", "Some of the properties that make yeast particularly suitable for biological studies include rapid growth, dispersed cells, the ease of replica plating and mutant isolation, a well-defined genetic system, and most important, a highly versatile DNA transformation system.", "Being nonpathogenic, yeast can be handled with little precautions.", "Large quantities of normal baker's yeast are commercially available and can provide a cheap source for biochemical studies.", "The development of DNA transformation has made yeast particularly accessible to gene cloning and genetic engineering techniques.", "Structural genes corresponding to virtually any genetic trait can be identified by complementation from plasmid libraries.", "Plasmids can be introduced into yeast cells either as replicating molecules or by integration into the genome.", "In contrast to most other organisms, integrative recombination of transforming DNA in yeast proceeds exclusively via homologous recombination.", "Cloned yeast sequences, accompanied by foreign sequences on plasmids, can therefore be directed at will to specific locations in the genome."], "structured": false}
{"doc_id": 1635872, "title": "PCNA functions as a molecular platform to trigger Cdt1 destruction and prevent re-replication", "abstract": ["Ubiquitin-mediated proteolysis of the replication licensing factor Cdt1 (Cdc10-dependent transcript 1) in S phase is a key mechanism that limits DNA replication to a single round per cell cycle in metazoans.", "In Xenopus egg extracts, Cdt1 is destroyed on chromatin during DNA replication.", "Here, we report that replication-dependent proteolysis of Cdt1 requires its interaction with proliferating cell nuclear antigen (PCNA), a homotrimeric processivity factor for DNA polymerases.", "Cdt1 binds to PCNA through a consensus PCNA-interaction motif that is conserved in Cdt1 of all metazoans, and removal of PCNA from egg extracts inhibits replication-dependent Cdt1 destruction.", "Mutation of the PCNA-interaction motif yields a stabilized Cdt1 protein that induces re-replication.", "DDB1, a component of the Cul4 E3 ubiquitin ligase that mediates human Cdt1 proteolysis in response to DNA damage, is also required for replication-dependent Cdt1 destruction.", "Cdt1 and DDB1 interact in extracts, and DDB1 chromatin loading is dependent on the binding of Cdt1 to PCNA, which indicates that PCNA docking activates the pre-formed Cdt1\u2013Cul4DDB1 ligase complex.", "Thus, PCNA functions as a platform for Cdt1 destruction, ensuring efficient and temporally restricted inactivation of a key cell-cycle regulator."], "structured": false}
{"doc_id": 1641873, "title": "Meiosis in Drosophila: seeing is believing.", "abstract": ["Recently many exciting advances have been achieved in our understanding of Drosophila meiosis due to combined cytological and genetic approaches.", "New techniques have permitted the characterization of chromosome position and spindle formation in female meiosis I. The proteins encoded by the nod and ncd genes, two genes known to be needed for the proper partitioning of chromosomes lacking exchange events, have been identified and found to be kinesin-like motors.", "The effects of mutations in these genes on the spindle and chromosomes, together with the localization of the proteins, have yielded a model for the mechanism of female meiosis I. In male meiosis I, the chromosomal regions responsible for homolog pairing have been resolved to the level of specific DNA sequences.", "This provides a foundation for elucidating the molecular basis of meiotic pairing.", "The cytological techniques available in Drosophila also have permitted inroads into the regulation of sister-chromatid segregation.", "The products of two genes (mei-S332 and ord) essential for sister-chromatid cohesion have been identified recently.", "Additional advances in understanding Drosophila meiosis are the delineation of a functional centromere by using minichromosome derivatives and the identification of several regulatory genes for the meiotic cell cycle."], "structured": false}
{"doc_id": 1642727, "title": "Effect of physical activity on cognitive function in older adults at risk for Alzheimer disease: a randomized trial.", "abstract": ["CONTEXT Many observational studies have shown that physical activity reduces the risk of cognitive decline; however, evidence from randomized trials is lacking.   \n", "OBJECTIVE To determine whether physical activity reduces the rate of cognitive decline among older adults at risk.   \n", "DESIGN AND SETTING Randomized controlled trial of a 24-week physical activity intervention conducted between 2004 and 2007 in metropolitan Perth, Western Australia.", "Assessors of cognitive function were blinded to group membership.   \n", "PARTICIPANTS We recruited volunteers who reported memory problems but did not meet criteria for dementia.", "Three hundred eleven individuals aged 50 years or older were screened for eligibility, 89 were not eligible, and 52 refused to participate.", "A total of 170 participants were randomized and 138 participants completed the 18-month assessment.   \n", "INTERVENTION Participants were randomly allocated to an education and usual care group or to a 24-week home-based program of physical activity.   \n", "MAIN OUTCOME MEASURE Change in Alzheimer Disease Assessment Scale-Cognitive Subscale (ADAS-Cog) scores (possible range, 0-70) over 18 months.   \n", "RESULTS In an intent-to-treat analysis, participants in the intervention group improved 0.26 points (95% confidence interval, -0.89 to 0.54) and those in the usual care group deteriorated 1.04 points (95% confidence interval, 0.32 to 1.82) on the ADAS-Cog at the end of the intervention.", "The absolute difference of the outcome measure between the intervention and control groups was -1.3 points (95% confidence interval,-2.38 to -0.22) at the end of the intervention.", "At 18 months, participants in the intervention group improved 0.73 points (95% confidence interval, -1.27 to 0.03) on the ADAS-Cog, and those in the usual care group improved 0.04 points (95% confidence interval, -0.46 to 0.88).", "Word list delayed recall and Clinical Dementia Rating sum of boxes improved modestly as well, whereas word list total immediate recall, digit symbol coding, verbal fluency, Beck depression score, and Medical Outcomes 36-Item Short-Form physical and mental component summaries did not change significantly.   \n", "CONCLUSIONS In this study of adults with subjective memory impairment, a 6-month program of physical activity provided a modest improvement in cognition over an 18-month follow-up period.   \n", "TRIAL REGISTRATION anzctr.org.au Identifier: ACTRN12605000136606."], "structured": true}
{"doc_id": 1649738, "title": "Variants at 6q21 implicate PRDM1 in the etiology of therapy-induced second malignancies after Hodgkin's lymphoma", "abstract": ["Survivors of pediatric Hodgkin's lymphoma are at risk for radiation therapy\u2013induced second malignant neoplasms (SMNs).", "We identified two variants at chromosome 6q21 associated with SMNs in survivors of Hodgkin's lymphoma treated with radiation therapy as children but not as adults.", "The variants comprise a risk locus associated with decreased basal expression of PRDM1 (encoding PR domain containing 1, with ZNF domain) and impaired induction of the PRDM1 protein after radiation exposure.", "These data suggest a new gene-exposure interaction that may implicate PRDM1 in the etiology of radiation therapy-induced SMNs."], "structured": false}
{"doc_id": 1667063, "title": "Long non-coding RNA profiling of human lymphoid progenitor cells reveals transcriptional divergence of B cell and T cell lineages", "abstract": ["To elucidate the transcriptional 'landscape' that regulates human lymphoid commitment during postnatal life, we used RNA sequencing to assemble the long non-coding transcriptome across human bone marrow and thymic progenitor cells spanning the earliest stages of B lymphoid and T lymphoid specification.", "Over 3,000 genes encoding previously unknown long non-coding RNAs (lncRNAs) were revealed through the analysis of these rare populations.", "Lymphoid commitment was characterized by lncRNA expression patterns that were highly stage specific and were more lineage specific than those of protein-coding genes.", "Protein-coding genes co-expressed with neighboring lncRNA genes showed enrichment for ontologies related to lymphoid differentiation.", "The exquisite cell-type specificity of global lncRNA expression patterns independently revealed new developmental relationships among the earliest progenitor cells in the human bone marrow and thymus."], "structured": false}
{"doc_id": 1669173, "title": "The VTI family of SNARE proteins is necessary for plant viability and mediates different protein transport pathways.", "abstract": ["The Arabidopsis genome contains a family of v-SNAREs: VTI11, VTI12, and VTI13.", "Only VTI11 and VTI12 are expressed at appreciable levels.", "Although these two proteins are 60% identical, they complement different transport pathways when expressed in the yeast vti1 mutant.", "VTI11 was identified recently as the mutated gene in the shoot gravitropic mutant zig.", "Here, we show that the vti11 zig mutant has defects in vascular patterning and auxin transport.", "An Arabidopsis T-DNA insertion mutant, vti12, had a normal phenotype under nutrient-rich growth conditions.", "However, under nutrient-poor conditions, vti12 showed an accelerated senescence phenotype, suggesting that VTI12 may play a role in the plant autophagy pathway.", "VTI11 and VTI12 also were able to substitute for each other in their respective SNARE complexes, and a double-mutant cross between zig and vti12 was embryo lethal.", "These results suggest that some VTI1 protein was necessary for plant viability and that the two proteins were partially functionally redundant."], "structured": false}
{"doc_id": 1676568, "title": "CLASPs link focal adhesion-associated microtubule capture to localized exocytosis and adhesion site turnover", "abstract": ["Turnover of integrin-based focal adhesions (FAs) with the extracellular matrix (ECM) is essential for coordinated cell movement.", "In collectively migrating human keratinocytes, FAs assemble near the leading edge, grow and mature as a result of contractile forces and disassemble underneath the advancing cell body.", "We report that clustering of microtubule-associated CLASP1 and CLASP2 proteins around FAs temporally correlates with FA turnover.", "CLASPs and LL5\u03b2 (also known as PHLDB2), which recruits CLASPs to FAs, facilitate FA disassembly.", "CLASPs are further required for FA-associated ECM degradation, and matrix metalloprotease inhibition slows FA disassembly similarly to CLASP or PHLDB2 (LL5\u03b2) depletion.", "Finally, CLASP-mediated microtubule tethering at FAs establishes an FA-directed transport pathway for delivery, docking and localized fusion of exocytic vesicles near FAs.", "We propose that CLASPs couple microtubule organization, vesicle transport and cell interactions with the ECM, establishing a local secretion pathway that facilitates FA turnover by severing cell-matrix connections."], "structured": false}
{"doc_id": 1684489, "title": "CHD4 Is a RanGTP-Dependent MAP that Stabilizes Microtubules and Regulates Bipolar Spindle Formation", "abstract": ["BACKGROUND Production of the GTP-bound form of the Ran GTPase (RanGTP) around chromosomes induces spindle assembly by activating nuclear localization signal (NLS)-containing proteins.", "Several NLS proteins have been identified as spindle assembly factors, but the complexity of the process led us to search for additional proteins with distinct roles in spindle assembly.   \n", "RESULTS We identify a chromatin-remodeling ATPase, CHD4, as a RanGTP-dependent microtubule (MT)-associated protein (MAP).", "MT binding occurs via the region containing an NLS and chromatin-binding domains.", "In Xenopus egg extracts and cultured cells, CHD4 largely dissociates from mitotic chromosomes and partially localizes to the spindle.", "Immunodepletion of CHD4 from egg extracts significantly reduces the quantity of MTs produced around chromatin and prevents spindle assembly.", "CHD4 RNAi in both HeLa and Drosophila S2 cells induces defects in spindle assembly and chromosome alignment in early mitosis, leading to chromosome missegregation.", "Further analysis in egg extracts and in HeLa cells reveals that CHD4 is a RanGTP-dependent MT stabilizer.", "Moreover, the CHD4-containing NuRD complex promotes organization of MTs into bipolar spindles in egg extracts.", "Importantly, this function of CHD4 is independent of chromatin remodeling.   \n", "CONCLUSIONS Our results uncover a new role for CHD4 as a MAP required for MT stabilization and involved in generating spindle bipolarity."], "structured": true}
{"doc_id": 1686881, "title": "Myocardial muscarinic receptor upregulation and normal response to isoproterenol in denervated hearts by familial amyloid polyneuropathy.", "abstract": ["BACKGROUND Patients with familial amyloid polyneuropathy, a rare hereditary form of amyloidosis, have progressive autonomic neuropathy.", "The disease usually does not induce heart failure but is associated with sudden death, conduction disturbances, and an increased risk of complications during anesthesia.", "Although cardiac sympathetic denervation has been clearly demonstrated, the postsynaptic status of the cardiac autonomic nervous system remains unelucidated.   \n", "METHODS AND RESULTS Twenty-one patients were studied (age, 39+/-11 years; normal coronary arteries; left ventricular ejection fraction 68+/-9%).", "To evaluate the density and affinity constants of myocardial muscarinic receptors, PET with (11)C-MQNB (methylquinuclidinyl benzilate), a specific hydrophilic antagonist, was used.", "Cardiac beta-receptor functional efficiency was studied by the heart rate (HR) response to intravenous infusion of isoproterenol (5 minutes after 2 mg of atropine, 5, 10, and 15 ng/kg per minute during 5 minutes per step).", "The mean muscarinic receptor density was higher in patients than in control subjects (B'(max), 35.5+/-8.9 versus 26.1+/-6.7 pmol/mL, P=0.003), without change in receptor affinity.", "The increase in HR after injection of atropine as well as of MQNB was lower in patients compared with control subjects despite a similar basal HR (DeltaHR after atropine, 11+/-21% versus 62+/-17%; P<0.001), consistent with parasympathetic denervation.", "Incremental infusion of isoproterenol induced a similar increase in HR in patients and control subjects.   \n", "CONCLUSIONS Cardiac autonomic denervation in familial amyloid polyneuropathy results in an upregulation of myocardial muscarinic receptors but without change in cardiac beta-receptor responsiveness to catecholamines."], "structured": true}
{"doc_id": 1686997, "title": "6-phosphogluconate dehydrogenase links oxidative PPP, lipogenesis and tumor growth by inhibiting LKB1-AMPK signaling", "abstract": ["The oxidative pentose phosphate pathway (PPP) contributes to tumour growth, but the precise contribution of 6-phosphogluconate dehydrogenase (6PGD), the third enzyme in this pathway, to tumorigenesis remains unclear.", "We found that suppression of 6PGD decreased lipogenesis and RNA biosynthesis and elevated ROS levels in cancer cells, attenuating cell proliferation and tumour growth.", "6PGD-mediated production of ribulose-5-phosphate (Ru-5-P) inhibits AMPK activation by disrupting the active LKB1 complex, thereby activating acetyl-CoA carboxylase 1 and lipogenesis.", "Ru-5-P and NADPH are thought to be precursors in RNA biosynthesis and lipogenesis, respectively; thus, our findings provide an additional link between the oxidative PPP and lipogenesis through Ru-5-P-dependent inhibition of LKB1-AMPK signalling.", "Moreover, we identified and developed 6PGD inhibitors, physcion and its derivative S3, that effectively inhibited 6PGD, cancer cell proliferation and tumour growth in nude mice xenografts without obvious toxicity, suggesting that 6PGD could be an anticancer target."], "structured": false}
{"doc_id": 1695604, "title": "Plant Nuclear RNA Polymerase IV Mediates siRNA and DNA Methylation-Dependent Heterochromatin Formation", "abstract": ["All eukaryotes have three nuclear DNA-dependent RNA polymerases, namely, Pol I, II, and III.", "Interestingly, plants have catalytic subunits for a fourth nuclear polymerase, Pol IV.", "Genetic and biochemical evidence indicates that Pol IV does not functionally overlap with Pol I, II, or III and is nonessential for viability.", "However, disruption of the Pol IV catalytic subunit genes NRPD1 or NRPD2 inhibits heterochromatin association into chromocenters, coincident with losses in cytosine methylation at pericentromeric 5S gene clusters and AtSN1 retroelements.", "Loss of CG, CNG, and CNN methylation in Pol IV mutants implicates a partnership between Pol IV and the methyltransferase responsible for RNA-directed de novo methylation.", "Consistent with this hypothesis, 5S gene and AtSN1 siRNAs are essentially eliminated in Pol IV mutants.", "The data suggest that Pol IV helps produce siRNAs that target de novo cytosine methylation events required for facultative heterochromatin formation and higher-order heterochromatin associations."], "structured": false}
{"doc_id": 1701063, "title": "Sema3A regulates bone-mass accrual through sensory innervations", "abstract": ["Semaphorin 3A (Sema3A) is a diffusible axonal chemorepellent that has an important role in axon guidance.", "Previous studies have demonstrated that Sema3a\u2212/\u2212 mice have multiple developmental defects due to abnormal neuronal innervations.", "Here we show in mice that Sema3A is abundantly expressed in bone, and cell-based assays showed that Sema3A affected osteoblast differentiation in a cell-autonomous fashion.", "Accordingly, Sema3a\u2212/\u2212 mice had a low bone mass due to decreased bone formation.", "However, osteoblast-specific Sema3A-deficient mice (Sema3acol1\u2212/\u2212 and Sema3aosx\u2212/\u2212 mice) had normal bone mass, even though the expression of Sema3A in bone was substantially decreased.", "In contrast, mice lacking Sema3A in neurons (Sema3asynapsin\u2212/\u2212 and Sema3anestin\u2212/\u2212 mice) had low bone mass, similar to Sema3a\u2212/\u2212 mice, indicating that neuron-derived Sema3A is responsible for the observed bone abnormalities independent of the local effect of Sema3A in bone.", "Indeed, the number of sensory innervations of trabecular bone was significantly decreased in Sema3asynapsin\u2212/\u2212 mice, whereas sympathetic innervations of trabecular bone were unchanged.", "Moreover, ablating sensory nerves decreased bone mass in wild-type mice, whereas it did not reduce the low bone mass in Sema3anestin\u2212/\u2212 mice further, supporting the essential role of the sensory nervous system in normal bone homeostasis.", "Finally, neuronal abnormalities in Sema3a\u2212/\u2212 mice, such as olfactory development, were identified in Sema3asynasin\u2212/\u2212 mice, demonstrating that neuron-derived Sema3A contributes to the abnormal neural development seen in Sema3a\u2212/\u2212 mice, and indicating that Sema3A produced in neurons regulates neural development in an autocrine manner.", "This study demonstrates that Sema3A regulates bone remodelling indirectly by modulating sensory nerve development, but not directly by acting on osteoblasts."], "structured": false}
{"doc_id": 1709625, "title": "Direct lineage reprogramming: strategies, mechanisms, and applications.", "abstract": ["The direct lineage reprogramming of one specialized cell type into another using defined factors has fundamentally re-shaped traditional concepts regarding the epigenetic stability of differentiated cells.", "With the rapid increase in cell types generated through direct conversion in recent years, this strategy has become a promising approach for producing functional cells.", "Here, we review recent advances in lineage reprogramming, including the identification of novel reprogramming factors, underlying molecular mechanisms, strategies for generating functionally mature cells, and assays for characterizing induced cells.", "We also discuss progress toward the application of lineage reprogramming and the major future challenges for this strategy."], "structured": false}
{"doc_id": 1710116, "title": "Converging Intracranial Markers of Conscious Access", "abstract": ["We compared conscious and nonconscious processing of briefly flashed words using a visual masking procedure while recording intracranial electroencephalogram (iEEG) in ten patients.", "Nonconscious processing of masked words was observed in multiple cortical areas, mostly within an early time window (<300 ms), accompanied by induced gamma-band activity, but without coherent long-distance neural activity, suggesting a quickly dissipating feedforward wave.", "In contrast, conscious processing of unmasked words was characterized by the convergence of four distinct neurophysiological markers: sustained voltage changes, particularly in prefrontal cortex, large increases in spectral power in the gamma band, increases in long-distance phase synchrony in the beta range, and increases in long-range Granger causality.", "We argue that all of those measures provide distinct windows into the same distributed state of conscious processing.", "These results have a direct impact on current theoretical discussions concerning the neural correlates of conscious access."], "structured": false}
{"doc_id": 1711571, "title": "Hyperglycemia is associated with increased bone mineral density and decreased trabecular bone score in elderly Japanese men: The Fujiwara-kyo osteoporosis risk in men (FORMEN) study.", "abstract": ["PURPOSE Patients with type 2 diabetes mellitus (T2DM) have an increased fracture risk despite having higher areal bone mineral density (aBMD).", "This study aimed to clarify the association between glycemic and insulin resistance status and bone microarchitecture, and whether pentosidine and bone turnover markers play any roles in the association.   \n", "METHODS A total of 2012 community-dwelling men aged \u226565years completed baseline measurements of spine aBMD, fasting plasma glucose (FPG) and serum insulin, hemoglobin A1c (HbA1c), osteocalcin, type I procollagen N-terminal propeptide, type I collagen C-terminal crosslinking telopeptide, tartrate-resistant acid phosphatase isoenzyme 5b, pentosidine, height and weight and an interview regarding past disease history.", "Homeostasis model assessment-insulin resistance (HOMA-IR) was also calculated.", "T2DM was defined as physician-diagnosed middle age or elderly-onset diabetes mellitus, or according to biochemical test results.", "To evaluate bone microarchitecture, trabecular bone score (TBS) was calculated at the same vertebrae as those used for aBMD measurement.   \n", "RESULTS After excluding participants who had a disease history and/or were taking medications affecting bone metabolism, 1683 men (age, 72.9\u00b15.2years) were analyzed.", "Men with T2DM had significantly higher aBMD compared to those without T2DM.", "There was no significant difference in TBS.", "However, FPG, HbA1c and HOMA-IR levels were significantly inversely correlated with TBS after adjusting for age, BMI and aBMD.", "Multivariate linear regression analyses revealed that glycemic indices (FPG and HbA1c) were significantly associated with increased aBMD and decreased TBS, and that HOMA-IR was associated only with TBS.", "These associations did not change after further adjusting for bone turnover makers and pentosidine levels.   \n", "CONCLUSIONS Hyperglycemia and elevated insulin-resistance were associated with low TBS independently of bone turnover and pentosidine levels."], "structured": true}
{"doc_id": 1727042, "title": "Matrix Remodeling Promotes Pulmonary Hypertension through Feedback Mechanoactivation of the YAP/TAZ-miR-130/301 Circuit.", "abstract": ["Pulmonary hypertension (PH) is a deadly vascular disease with enigmatic molecular origins.", "We found that vascular extracellular matrix (ECM) remodeling and stiffening are early and pervasive processes that promote PH.", "In multiple pulmonary vascular cell types, such ECM stiffening induced the microRNA-130/301 family via activation of the co-transcription factors YAP and TAZ.", "MicroRNA-130/301 controlled a PPAR?-APOE-LRP8 axis, promoting collagen deposition and LOX-dependent remodeling and further upregulating YAP/TAZ via a mechanoactive feedback loop.", "In turn, ECM remodeling controlled pulmonary vascular cell crosstalk via such mechanotransduction, modulation of secreted vasoactive effectors, and regulation of associated microRNA pathways.", "In vivo, pharmacologic inhibition of microRNA-130/301, APOE, or LOX activity ameliorated ECM remodeling and PH.", "Thus, ECM remodeling, as controlled by the YAP/TAZ-miR-130/301 feedback circuit, is an early PH trigger and offers combinatorial therapeutic targets for this devastating disease."], "structured": false}
{"doc_id": 1727493, "title": "Exosomal transfer of stroma-derived miR21 confers paclitaxel resistance in ovarian cancer cells through targeting APAF1", "abstract": ["Advanced ovarian cancer usually spreads to the visceral adipose tissue of the omentum.", "However, the omental stromal cell-derived molecular determinants that modulate ovarian cancer growth have not been characterized.", "Here, using next-generation sequencing technology, we identify significantly higher levels of microRNA-21 (miR21) isomiRNAs in exosomes and tissue lysates isolated from cancer-associated adipocytes (CAAs) and fibroblasts (CAFs) than in those from ovarian cancer cells.", "Functional studies reveal that miR21 is transferred from CAAs or CAFs to the cancer cells, where it suppresses ovarian cancer apoptosis and confers chemoresistance by binding to its direct novel target, APAF1.", "These data suggest that the malignant phenotype of metastatic ovarian cancer cells can be altered by miR21 delivered by exosomes derived from neighbouring stromal cells in the omental tumour microenvironment, and that inhibiting the transfer of stromal-derived miR21 is an alternative modality in the treatment of metastatic and recurrent ovarian cancer."], "structured": false}
{"doc_id": 1733337, "title": "Age-related changes in kynurenic acid production in rat brain.", "abstract": ["Two separate in vitro assays were used to examine the biosynthesis of the broad spectrum excitatory amino acid receptor antagonist kynurenic acid (KYNA) during the life span of the adult rat.", "Assessment of KYNA's anabolic enzyme kynurenine aminotransferase revealed steady increases between 3 and 24 months of age in all five brain regions examined.", "No changes were observed in the liver.", "The changes were particularly pronounced in the cortex and in the striatum where enzyme activity increased three-fold during the period studied.", "KYNA production from its bioprecursor L-kynurenine was also investigated in tissue slices and was found to be significantly enhanced in the cortex and hippocampus of old animals.", "The effect of depolarizing agents or sodium replacement was virtually identical in tissues from young and old rats.", "These data, which are in excellent agreement with reports on an age-dependent increase of KYNA concentration in brain tissue, suggest an enhanced KYNA tone in the aged brain.", "Together with the reported decline in cerebral excitatory amino acid receptor densities with age, increased production of KYNA may play a role in cognitive and memory dysfunction in old animals."], "structured": false}
{"doc_id": 1744097, "title": "The polycomb group protein Suz12 is required for embryonic stem cell differentiation.", "abstract": ["Polycomb group (PcG) proteins form multiprotein complexes, called Polycomb repressive complexes (PRCs).", "PRC2 contains the PcG proteins EZH2, SUZ12, and EED and represses transcription through methylation of lysine (K) 27 of histone H3 (H3).", "Suz12 is essential for PRC2 activity and its inactivation results in early lethality of mouse embryos.", "Here, we demonstrate that Suz12(-/-) mouse embryonic stem (ES) cells can be established and expanded in tissue culture.", "The Suz12(-/-) ES cells are characterized by global loss of H3K27 trimethylation (H3K27me3) and higher expression levels of differentiation-specific genes.", "Moreover, Suz12(-/-) ES cells are impaired in proper differentiation, resulting in a lack of repression of ES cell markers as well as activation of differentiation-specific genes.", "Finally, we demonstrate that the PcGs are actively recruited to several genes during ES cell differentiation, which despite an increase in H3K27me3 levels is not always sufficient to prevent transcriptional activation.", "In summary, we demonstrate that Suz12 is required for the establishment of specific expression programs required for ES cell differentiation.", "Furthermore, we provide evidence that PcGs have different mechanisms to regulate transcription during cellular differentiation."], "structured": false}
{"doc_id": 1744752, "title": "The 1.9 A structure of a proteasome-11S activator complex and implications for proteasome-PAN/PA700 interactions.", "abstract": ["Proteasomes are cylindrical structures that function in multiple cellular processes by degrading a wide variety of cytosolic and nuclear proteins.", "Substrate access and product release from the enclosed catalytic chamber occurs through axial pores that are opened by activator complexes.", "Here, we report high-resolution structures of wild-type and mutant archaeal proteasomes bound to the activator PA26.", "These structures support the proposal that an ordered open conformation is required for proteolysis and that its formation can be triggered by outward displacement of surrounding residues.", "The structures and associated biochemical assays reveal the mechanism of binding, which involves an interaction between the PA26 C terminus and a conserved lysine.", "Surprisingly, biochemical observations implicate an equivalent interaction for the unrelated ATP-dependent activators PAN and PA700."], "structured": false}
{"doc_id": 1748921, "title": "Innate Immune and Chemically Triggered Oxidative Stress Modifies Translational Fidelity", "abstract": ["Translational fidelity, essential for protein and cell function, requires accurate transfer RNA (tRNA) aminoacylation.", "Purified aminoacyl-tRNA synthetases exhibit a fidelity of one error per 10,000 to 100,000 couplings.", "The accuracy of tRNA aminoacylation in vivo is uncertain, however, and might be considerably lower.", "Here we show that in mammalian cells, approximately 1% of methionine (Met) residues used in protein synthesis are aminoacylated to non-methionyl-tRNAs.", "Remarkably, Met-misacylation increases up to tenfold upon exposing cells to live or non-infectious viruses, toll-like receptor ligands or chemically induced oxidative stress.", "Met is misacylated to specific non-methionyl-tRNA families, and these Met-misacylated tRNAs are used in translation.", "Met-misacylation is blocked by an inhibitor of cellular oxidases, implicating reactive oxygen species (ROS) as the misacylation trigger.", "Among six amino acids tested, tRNA misacylation occurs exclusively with Met.", "As Met residues are known to protect proteins against ROS-mediated damage, we propose that Met-misacylation functions adaptively to increase Met incorporation into proteins to protect cells against oxidative stress.", "In demonstrating an unexpected conditional aspect of decoding mRNA, our findings illustrate the importance of considering alternative iterations of the genetic code."], "structured": false}
{"doc_id": 1754001, "title": "Yeast sirtuins and the regulation of aging.", "abstract": ["The sirtuins are a phylogenetically conserved family of NAD(+) -dependent protein deacetylases that consume one molecule of NAD(+) for every deacetylated lysine side chain.", "Their requirement for NAD(+) potentially makes them prone to regulation by fluctuations in NAD(+) or biosynthesis intermediates, thus linking them to cellular metabolism.", "The Sir2 protein from Saccharomyces cerevisiae is the founding sirtuin family member and has been well characterized as a histone deacetylase that functions in transcriptional silencing of heterochromatin domains and as a pro-longevity factor for replicative life span (RLS), defined as the number of times a mother cell divides (buds) before senescing.", "Deleting SIR2 shortens RLS, while increased gene dosage causes extension.", "Furthermore, Sir2 has been implicated in mediating the beneficial effects of caloric restriction (CR) on life span, not only in yeast, but also in higher eukaryotes.", "While this paradigm has had its share of disagreements and debate, it has also helped rapidly drive the aging research field forward.", "S. cerevisiae has four additional sirtuins, Hst1, Hst2, Hst3, and Hst4.", "This review discusses the function of Sir2 and the Hst homologs in replicative aging and chronological aging, and also addresses how the sirtuins are regulated in response to environmental stresses such as CR."], "structured": false}
{"doc_id": 1759213, "title": "The effect of combination treatment with aliskiren and blockers of the renin-angiotensin system on hyperkalaemia and acute kidney injury: systematic review and meta-analysis", "abstract": ["OBJECTIVE To examine the safety of using aliskiren combined with agents used to block the renin-angiotensin system.   \n", "DESIGN Systematic review and meta-analysis of randomised controlled trials.   \n", "DATA SOURCES Medline, Embase, the Cochrane Library, and two trial registries, published up to 7 May 2011.   ", "STUDY SELECTION Published and unpublished randomised controlled trials that compared combined treatment using aliskiren and angiotensin converting enzyme inhibitors or angiotensin receptor blockers with monotherapy using these agents for at least four weeks and that provided numerical data on the adverse event outcomes of hyperkalaemia and acute kidney injury.", "A random effects model was used to calculate pooled risk ratios and 95% confidence intervals for these outcomes.   \n", "RESULTS 10 randomised controlled studies (4814 participants) were included in the analysis.", "Combination therapy with aliskiren and angiotensin converting enzyme inhibitors or angiotensin receptor blockers significantly increased the risk of hyperkalaemia compared with monotherapy using angiotensin converting enzymes or angiotensin receptor blockers (relative risk 1.58, 95% confidence interval 1.24 to 2.02) or aliskiren alone (1.67, 1.01 to 2.79).", "The risk of acute kidney injury did not differ significantly between the combined therapy and monotherapy groups (1.14, 0.68 to 1.89).   \n", "CONCLUSION Use of aliskerin in combination with angiotensin converting enzyme inhibitors or angiotensin receptor blockers is associated with an increased risk for hyperkalaemia.", "The combined use of these agents warrants careful monitoring of serum potassium levels."], "structured": true}
{"doc_id": 1769799, "title": "The ins and outs of DNA transfer in bacteria.", "abstract": ["Transformation and conjugation permit the passage of DNA through the bacterial membranes and represent dominant modes for the transfer of genetic information between bacterial cells or between bacterial and eukaryotic cells.", "As such, they are responsible for the spread of fitness-enhancing traits, including antibiotic resistance.", "Both processes usually involve the recognition of double-stranded DNA, followed by the transfer of single strands.", "Elaborate molecular machines are responsible for negotiating the passage of macromolecular DNA through the layers of the cell surface.", "All or nearly all the machine components involved in transformation and conjugation have been identified, and here we present models for their roles in DNA transport."], "structured": false}
{"doc_id": 1771079, "title": "Synaptic islands defined by the territory of a single astrocyte.", "abstract": ["In the mammalian brain, astrocytes modulate neuronal function, in part, by synchronizing neuronal firing and coordinating synaptic networks.", "Little, however, is known about how this is accomplished from a structural standpoint.", "To investigate the structural basis of astrocyte-mediated neuronal synchrony and synaptic coordination, the three-dimensional relationships between cortical astrocytes and neurons was investigated.", "Using a transgenic and viral approach to label astrocytes with enhanced green fluorescent protein, we performed a three-dimensional reconstruction of astrocytes from tissue sections or live animals in vivo.", "We found that cortical astrocytes occupy nonoverlapping territories similar to those described in the hippocampus.", "Using immunofluorescence labeling of neuronal somata, a single astrocyte enwraps on average four neuronal somata with an upper limit of eight.", "Single-neuron dye-fills allowed us to estimate that one astrocyte contacts 300-600 neuronal dendrites.", "Together with the recent findings showing that glial Ca2+ signaling is restricted to individual astrocytes in vivo, and that Ca2+ signaling leads to gliotransmission, we propose the concept of functional islands of synapses in which groups of synapses confined within the boundaries of an individual astrocyte are modulated by the gliotransmitter environment controlled by that astrocyte.", "Our description offers a new structurally based conceptual framework to evaluate functional data involving interactions between neurons and astrocytes in the mammalian brain."], "structured": false}
{"doc_id": 1780819, "title": "Role of DNA Methylation and Epigenetic Silencing of HAND2 in Endometrial Cancer Development", "abstract": ["BACKGROUND Endometrial cancer incidence is continuing to rise in the wake of the current ageing and obesity epidemics.", "Much of the risk for endometrial cancer development is influenced by the environment and lifestyle.", "Accumulating evidence suggests that the epigenome serves as the interface between the genome and the environment and that hypermethylation of stem cell polycomb group target genes is an epigenetic hallmark of cancer.", "The objective of this study was to determine the functional role of epigenetic factors in endometrial cancer development.   \n", "METHODS AND FINDINGS Epigenome-wide methylation analysis of >27,000 CpG sites in endometrial cancer tissue samples (n = 64) and control samples (n = 23) revealed that HAND2 (a gene encoding a transcription factor expressed in the endometrial stroma) is one of the most commonly hypermethylated and silenced genes in endometrial cancer.", "A novel integrative epigenome-transcriptome-interactome analysis further revealed that HAND2 is the hub of the most highly ranked differential methylation hotspot in endometrial cancer.", "These findings were validated using candidate gene methylation analysis in multiple clinical sample sets of tissue samples from a total of 272 additional women.", "Increased HAND2 methylation was a feature of premalignant endometrial lesions and was seen to parallel a decrease in RNA and protein levels.", "Furthermore, women with high endometrial HAND2 methylation in their premalignant lesions were less likely to respond to progesterone treatment.", "HAND2 methylation analysis of endometrial secretions collected using high vaginal swabs taken from women with postmenopausal bleeding specifically identified those patients with early stage endometrial cancer with both high sensitivity and high specificity (receiver operating characteristics area under the curve = 0.91 for stage 1A and 0.97 for higher than stage 1A).", "Finally, mice harbouring a Hand2 knock-out specifically in their endometrium were shown to develop precancerous endometrial lesions with increasing age, and these lesions also demonstrated a lack of PTEN expression.   \n", "CONCLUSIONS HAND2 methylation is a common and crucial molecular alteration in endometrial cancer that could potentially be employed as a biomarker for early detection of endometrial cancer and as a predictor of treatment response.", "The true clinical utility of HAND2 DNA methylation, however, requires further validation in prospective studies.", "Please see later in the article for the Editors' Summary."], "structured": true}
{"doc_id": 1781626, "title": "Socioeconomic factors, material inequalities, and perceived control in self-rated health: cross-sectional data from seven post-communist countries.", "abstract": ["This study examined the association between perceived control and several socioeconomic variables and self-rated health in seven post-communist countries (Russia, Estonia, Lithuania, Latvia, Hungary, Poland, Czech Republic).", "Questionnaire interviews were used to collect data on self-rated health in the last 12 months, education, marital status, perceived control based on nine questions, and material deprivation based on availability of food, clothing and heating.", "For each population, two ecological measures of material inequalities were available: an inequality score estimated from the survey data as the distance between the 90th and 10th percentiles of material deprivation, and Gini coefficient from published sources.", "Data on 5330 men and women aged 20-60 were analysed.", "Prevalence of poor health (worse than average) varied between 8% in Czechs and 19% in Hungarians.", "The age-sex-adjusted odds ratio for university vs primary education was 0.36 (0.26-0.49); odds ratios per 1 standard deviation increase in perceived control and in material deprivation were 0.58 (95% CI 0.48-0.69) and 1.51 (1.40-1.63), respectively.", "The odds ratio for an increase in inequality equivalent to the difference between the most and the least unequal populations was 1.49 (0.88-2.52) using the material inequality score and 1.41 (0.91-2.20) using the Gini coefficient.", "No indication of an effect of either inequality measure was seen after adjustment for individuals' deprivation or perceived control.", "The results suggest that, as in western populations, education and material deprivation are strongly related to self-rated health.", "Perceived control appeared statistically to mediate some of the effects of material deprivation.", "The non-significant effects of both ecological measures of inequality were eliminated by controlling for individuals' characteristics."], "structured": false}
{"doc_id": 1782201, "title": "Integrin \u03b1v\u03b23/c-src \u201cOncogenic Unit\u201d Promotes Anchorage-independence and Tumor Progression", "abstract": ["Integrins regulate adhesion-dependent growth, survival and invasion of tumor cells.", "In particular, expression of integrin alpha(v)beta(3) is associated with progression of a variety of human tumors.", "Here we reveal a previously undescribed adhesion-independent role for integrin alpha(v)beta(3) in pancreatic cancer and other carcinomas.", "Specifically, alpha(v)beta(3) expressed in carcinoma cells enhanced anchorage-independent tumor growth in vitro and increased lymph node metastases in vivo.", "These effects required recruitment of c-Src to the beta(3) integrin cytoplasmic tail, leading to c-Src activation, Crk-associated substrate (CAS) phosphorylation and tumor cell survival that, unexpectedly, was independent of cell adhesion or focal adhesion kinase (FAK) activation.", "Pharmacological blockade of c-Src kinase activity or decreased expression of endogenous alpha(v)beta(3) integrin or c-Src not only inhibited anchorage-independent growth but also suppressed metastasis in vivo, yet these manipulations did not affect tumor cell migration or invasion.", "These data define an unexpected role for an integrin as a mediator of anchorage independence, suggesting that an alpha(v)beta(3)-c-Src signaling module may account for the aggressive behavior of integrin alpha(v)beta(3)-expressing tumors in humans."], "structured": false}
{"doc_id": 1791637, "title": "Genomewide Analysis of PRC1 and PRC2 Occupancy Identifies Two Classes of Bivalent Domains", "abstract": ["In embryonic stem (ES) cells, bivalent chromatin domains with overlapping repressive (H3 lysine 27 tri-methylation) and activating (H3 lysine 4 tri-methylation) histone modifications mark the promoters of more than 2,000 genes.", "To gain insight into the structure and function of bivalent domains, we mapped key histone modifications and subunits of Polycomb-repressive complexes 1 and 2 (PRC1 and PRC2) genomewide in human and mouse ES cells by chromatin immunoprecipitation, followed by ultra high-throughput sequencing.", "We find that bivalent domains can be segregated into two classes -- the first occupied by both PRC2 and PRC1 (PRC1-positive) and the second specifically bound by PRC2 (PRC2-only).", "PRC1-positive bivalent domains appear functionally distinct as they more efficiently retain lysine 27 tri-methylation upon differentiation, show stringent conservation of chromatin state, and associate with an overwhelming number of developmental regulator gene promoters.", "We also used computational genomics to search for sequence determinants of Polycomb binding.", "This analysis revealed that the genomewide locations of PRC2 and PRC1 can be largely predicted from the locations, sizes, and underlying motif contents of CpG islands.", "We propose that large CpG islands depleted of activating motifs confer epigenetic memory by recruiting the full repertoire of Polycomb complexes in pluripotent cells."], "structured": false}
{"doc_id": 1791714, "title": "Spatiotemporal regulation of epithelial-mesenchymal transition is essential for squamous cell carcinoma metastasis.", "abstract": ["Epithelial-mesenchymal transition (EMT) is implicated in converting stationary epithelial tumor cells into motile mesenchymal cells during metastasis.", "However, the involvement of EMT in metastasis is still controversial, due to the lack of a mesenchymal phenotype in human carcinoma metastases.", "Using a spontaneous squamous cell carcinoma mouse model, we show that activation of the EMT-inducing transcription factor Twist1 is sufficient to promote carcinoma cells to undergo EMT and disseminate into blood circulation.", "Importantly, in distant sites, turning off Twist1 to allow reversion of EMT is essential for disseminated tumor cells to proliferate and form metastases.", "Our study demonstrates in vivo the requirement of \"reversible EMT\" in tumor metastasis and may resolve the controversy on the importance of EMT in carcinoma metastasis."], "structured": false}
{"doc_id": 1797622, "title": "Control of Apoptosis by Asymmetric Cell Division", "abstract": ["Asymmetric cell division and apoptosis (programmed cell death) are two fundamental processes that are important for the development and function of multicellular organisms.", "We have found that the processes of asymmetric cell division and apoptosis can be functionally linked.", "Specifically, we show that asymmetric cell division in the nematode Caenorhabditis elegans is mediated by a pathway involving three genes, dnj-11 MIDA1, ces-2 HLF, and ces-1 Snail, that directly control the enzymatic machinery responsible for apoptosis.", "Interestingly, the MIDA1-like protein GlsA of the alga Volvox carteri, as well as the Snail-related proteins Snail, Escargot, and Worniu of Drosophila melanogaster, have previously been implicated in asymmetric cell division.", "Therefore, C. elegans dnj-11 MIDA1, ces-2 HLF, and ces-1 Snail may be components of a pathway involved in asymmetric cell division that is conserved throughout the plant and animal kingdoms.", "Furthermore, based on our results, we propose that this pathway directly controls the apoptotic fate in C. elegans, and possibly other animals as well."], "structured": false}
{"doc_id": 1800734, "title": "CXCR2 mediates NADPH oxidase\u2013independent neutrophil extracellular trap formation in cystic fibrosis airway inflammation", "abstract": ["Upon activation, neutrophils release DNA fibers decorated with antimicrobial proteins, forming neutrophil extracellular traps (NETs).", "Although NETs are bactericidal and contribute to innate host defense, excessive NET formation has been linked to the pathogenesis of autoinflammatory diseases.", "However, the mechanisms regulating NET formation, particularly during chronic inflammation, are poorly understood.", "Here we show that the G protein\u2013coupled receptor (GPCR) CXCR2 mediates NET formation.", "Downstream analyses showed that CXCR2-mediated NET formation was independent of NADPH oxidase and involved Src family kinases.", "We show the pathophysiological relevance of this mechanism in cystic fibrosis lung disease, characterized by chronic neutrophilic inflammation.", "We found abundant NETs in airway fluids of individuals with cystic fibrosis and mouse cystic fibrosis lung disease, and NET amounts correlated with impaired obstructive lung function.", "Pulmonary blockade of CXCR2 by intra-airway delivery of small-molecule antagonists inhibited NET formation and improved lung function in vivo without affecting neutrophil recruitment, proteolytic activity or antibacterial host defense.", "These studies establish CXCR2 as a receptor mediating NADPH oxidase\u2013independent NET formation and provide evidence that this GPCR pathway is operative and druggable in cystic fibrosis lung disease."], "structured": false}
{"doc_id": 1805641, "title": "Modelling the Impact of Artemisinin Combination Therapy and Long-Acting Treatments on Malaria Transmission Intensity", "abstract": ["BACKGROUND Artemisinin derivatives used in recently introduced combination therapies (ACTs) for Plasmodium falciparum malaria significantly lower patient infectiousness and have the potential to reduce population-level transmission of the parasite.", "With the increased interest in malaria elimination, understanding the impact on transmission of ACT and other antimalarial drugs with different pharmacodynamics becomes a key issue.", "This study estimates the reduction in transmission that may be achieved by introducing different types of treatment for symptomatic P. falciparum malaria in endemic areas.   \n", "METHODS AND FINDINGS We developed a mathematical model to predict the potential impact on transmission outcomes of introducing ACT as first-line treatment for uncomplicated malaria in six areas of varying transmission intensity in Tanzania.", "We also estimated the impact that could be achieved by antimalarials with different efficacy, prophylactic time, and gametocytocidal effects.", "Rates of treatment, asymptomatic infection, and symptomatic infection in the six study areas were estimated using the model together with data from a cross-sectional survey of 5,667 individuals conducted prior to policy change from sulfadoxine-pyrimethamine to ACT.", "The effects of ACT and other drug types on gametocytaemia and infectiousness to mosquitoes were independently estimated from clinical trial data.", "Predicted percentage reductions in prevalence of infection and incidence of clinical episodes achieved by ACT were highest in the areas with low initial transmission.", "A 53% reduction in prevalence of infection was seen if 100% of current treatment was switched to ACT in the area where baseline slide-prevalence of parasitaemia was lowest (3.7%), compared to an 11% reduction in the highest-transmission setting (baseline slide prevalence = 57.1%).", "Estimated percentage reductions in incidence of clinical episodes were similar.", "The absolute size of the public health impact, however, was greater in the highest-transmission area, with 54 clinical episodes per 100 persons per year averted compared to five per 100 persons per year in the lowest-transmission area.", "High coverage was important.", "Reducing presumptive treatment through improved diagnosis substantially reduced the number of treatment courses required per clinical episode averted in the lower-transmission settings although there was some loss of overall impact on transmission.", "An efficacious antimalarial regimen with no specific gametocytocidal properties but a long prophylactic time was estimated to be more effective at reducing transmission than a short-acting ACT in the highest-transmission setting.   \n", "CONCLUSIONS Our results suggest that ACTs have the potential for transmission reductions approaching those achieved by insecticide-treated nets in lower-transmission settings.", "ACT partner drugs and nonartemisinin regimens with longer prophylactic times could result in a larger impact in higher-transmission settings, although their long term benefit must be evaluated in relation to the risk of development of parasite resistance."], "structured": true}
{"doc_id": 1818578, "title": "Systems metabolic engineering of Escherichia coli for L-threonine production", "abstract": ["Amino-acid producers have traditionally been developed by repeated random mutagenesis owing to the difficulty in rationally engineering the complex and highly regulated metabolic network.", "Here, we report the development of the genetically defined L-threonine overproducing Escherichia coli strain by systems metabolic engineering.", "Feedback inhibitions of aspartokinase I and III (encoded by thrA and lysC, respectively) and transcriptional attenuation regulations (located in thrL) were removed.", "Pathways for Thr degradation were removed by deleting tdh and mutating ilvA. The metA and lysA genes were deleted to make more precursors available for Thr biosynthesis.", "Further target genes to be engineered were identified by transcriptome profiling combined with in silico flux response analysis, and their expression levels were manipulated accordingly.", "The final engineered E. coli strain was able to produce Thr with a high yield of 0.393 g per gram of glucose, and 82.4 g/l Thr by fed-batch culture.", "The systems metabolic engineering strategy reported here may be broadly employed for developing genetically defined organisms for the efficient production of various bioproducts."], "structured": false}
{"doc_id": 1831916, "title": "Association Between ADHD and Obesity: A Systematic Review and Meta-Analysis.", "abstract": ["OBJECTIVE Impulsivity and inattention related to attention deficit hyperactivity disorder (ADHD) may increase food intake and, consequently, weight gain.", "However, findings on the association between obesity/overweight and ADHD are mixed.", "The authors conducted a meta-analysis to estimate this association.   \n", "METHOD A broad range of databases was searched through Aug. 31, 2014.", "Unpublished studies were also obtained.", "Study quality was rated with the Newcastle-Ottawa Scale.", "Random-effects models were used.   \n", "RESULTS Forty-two studies that included a total of 728,136 individuals (48,161 ADHD subjects; 679,975 comparison subjects) were retained.", "A significant association between obesity and ADHD was found for both children (odds ratio=1.20, 95% CI=1.05-1.37) and adults (odds ratio=1.55, 95% CI=1.32-1.81).", "The pooled prevalence of obesity was increased by about 70% in adults with ADHD (28.2%, 95% CI=22.8-34.4) compared with those without ADHD (16.4%, 95% CI=13.4-19.9), and by about 40% in children with ADHD (10.3%, 95% CI=7.9-13.3) compared with those without ADHD (7.4%, 95% CI=5.4-10.1).", "The significant association between ADHD and obesity remained when limited to studies 1) reporting odds ratios adjusted for possible confounding factors; 2) diagnosing ADHD by direct interview; and 3) using directly measured height and weight.", "Gender, study setting, study country, and study quality did not moderate the association between obesity and ADHD.", "ADHD was also significantly associated with overweight.", "Individuals medicated for ADHD were not at higher risk of obesity.   \n", "CONCLUSIONS This study provides meta-analytic evidence for a significant association between ADHD and obesity/overweight.", "Further research should address possible underlying mechanisms and the long-term effects of ADHD treatments on weight in individuals with both ADHD and obesity."], "structured": true}
{"doc_id": 1834762, "title": "Amyloid-DNA Composites of Bacterial Biofilms Stimulate Autoimmunity.", "abstract": ["Research on the human microbiome has established that commensal and pathogenic bacteria can influence obesity, cancer, and autoimmunity through mechanisms mostly unknown.", "We found that a component of bacterial biofilms, the amyloid protein curli, irreversibly formed fibers with bacterial DNA during biofilm formation.", "This interaction accelerated amyloid polymerization and created potent immunogenic complexes that activated immune cells, including dendritic cells, to produce cytokines such as type I interferons, which are pathogenic in systemic lupus erythematosus (SLE).", "When given systemically, curli-DNA composites triggered immune activation and production of autoantibodies in lupus-prone and wild-type mice.", "We also found that the infection of lupus-prone mice with curli-producing bacteria triggered higher autoantibody titers compared to curli-deficient bacteria.", "These data provide a mechanism by which the microbiome and biofilm-producing enteric infections may contribute to the progression of SLE and point to a potential molecular target for treatment of autoimmunity."], "structured": false}
{"doc_id": 1836154, "title": "Comprehensive genomic characterization defines human glioblastoma genes and core pathways", "abstract": ["Human cancer cells typically harbour multiple chromosomal aberrations, nucleotide substitutions and epigenetic modifications that drive malignant transformation.", "The Cancer Genome Atlas ( TCGA) pilot project aims to assess the value of large- scale multi- dimensional analysis of these molecular characteristics in human cancer and to provide the data rapidly to the research community.", "Here we report the interim integrative analysis of DNA copy number, gene expression and DNA methylation aberrations in 206 glioblastomas - the most common type of primary adult brain cancer - and nucleotide sequence aberrations in 91 of the 206 glioblastomas.", "This analysis provides new insights into the roles of ERBB2, NF1 and TP53, uncovers frequent mutations of the phosphatidylinositol- 3- OH kinase regulatory subunit gene PIK3R1, and provides a network view of the pathways altered in the development of glioblastoma.", "Furthermore, integration of mutation, DNA methylation and clinical treatment data reveals a link between MGMT promoter methylation and a hypermutator phenotype consequent to mismatch repair deficiency in treated glioblastomas, an observation with potential clinical implications.", "Together, these findings establish the feasibility and power of TCGA, demonstrating that it can rapidly expand knowledge of the molecular basis of cancer."], "structured": false}
{"doc_id": 1840993, "title": "LY2405319, an Engineered FGF21 Variant, Improves the Metabolic Status of Diabetic Monkeys", "abstract": ["Fibroblast growth factor 21 (FGF21) is a novel metabolic regulator that represents a promising target for the treatment of several metabolic diseases.", "Administration of recombinant wild type FGF21 to diabetic animals leads to a dramatic improvement in glycaemia and ameliorates other systemic measures of metabolic health.", "Here we report the pharmacologic outcomes observed in non-human primates upon administration of a recently described FGF21 analogue, LY2405319 (LY).", "Diabetic rhesus monkeys were treated subcutaneously with LY once daily for a period of seven weeks.", "The doses of LY used were 3, 9 and 50 mg/kg each delivered in an escalating fashion with washout measurements taken at 2, 4, 6 and 8 weeks following the final LY dose.", "LY therapy led to a dramatic and rapid lowering of several important metabolic parameters including glucose, body weight, insulin, cholesterol and triglyceride levels at all doses tested.", "In addition, we observed favorable changes in circulating profiles of adipokines, with increased adiponectin and reduced leptin indicative of direct FGF21 action on adipose tissue.", "Importantly, and for the first time we show that FGF21 based therapy has metabolic efficacy in an animal with late stage diabetes.", "While the glycemic efficacy of LY in this animal was partially attenuated its lipid lowering effect was fully preserved suggesting that FGF21 may be a viable treatment option even in patients with advanced disease progression.", "These findings support continued exploration of the FGF21 pathway for the treatment of metabolic disease."], "structured": false}
{"doc_id": 1848452, "title": "Epigenetic Control of Stem Cell Potential during Homeostasis, Aging, and Disease.", "abstract": ["Stem cell decline is an important cellular driver of aging-associated pathophysiology in multiple tissues.", "Epigenetic regulation is central to establishing and maintaining stem cell function, and emerging evidence indicates that epigenetic dysregulation contributes to the altered potential of stem cells during aging.", "Unlike terminally differentiated cells, the impact of epigenetic dysregulation in stem cells is propagated beyond self; alterations can be heritably transmitted to differentiated progeny, in addition to being perpetuated and amplified within the stem cell pool through self-renewal divisions.", "This Review focuses on recent studies examining epigenetic regulation of tissue-specific stem cells in homeostasis, aging, and aging-related disease."], "structured": false}
{"doc_id": 1852826, "title": "Host\u2013Parasite Interactions and the Evolution of Gene Expression", "abstract": ["Interactions between hosts and parasites provide an ongoing source of selection that promotes the evolution of a variety of features in the interacting species.", "Here, we use a genetically explicit mathematical model to explore how patterns of gene expression evolve at genetic loci responsible for host resistance and parasite infection.", "Our results reveal the striking yet intuitive conclusion that gene expression should evolve along very different trajectories in the two interacting species.", "Specifically, host resistance loci should frequently evolve to co-express alleles, whereas parasite infection loci should evolve to express only a single allele.", "This result arises because hosts that co-express resistance alleles are able to recognize and clear a greater diversity of parasite genotypes.", "By the same token, parasites that co-express antigen or elicitor alleles are more likely to be recognized and cleared by the host, and this favours the expression of only a single allele.", "Our model provides testable predictions that can help interpret accumulating data on expression levels for genes relevant to host\u2212parasite interactions."], "structured": false}
{"doc_id": 1855679, "title": "A crucial role for interleukin (IL)-1 in the induction of IL-17\u2013producing T cells that mediate autoimmune encephalomyelitis", "abstract": ["It was recently demonstrated that interleukin (IL)-23\u2013driven IL-17\u2013producing (ThIL-17) T cells mediate inflammatory pathology in certain autoimmune diseases.", "We show that the induction of antigen-specific ThIL-17 cells, but not T helper (Th)1 or Th2 cells, by immunization with antigens and adjuvants is abrogated in IL-1 receptor type I\u2013deficient (IL-1RI\u2212/\u2212) mice.", "Furthermore, the incidence of experimental autoimmune encephalomyelitis (EAE) was significantly lower in IL-1RI\u2212/\u2212 compared with wild-type mice, and this correlated with a failure to induce autoantigen-specific ThIL-17 cells, whereas induction of Th1 and Th2 responses was not substantially different.", "However, EAE was induced in IL-1RI\u2212/\u2212 mice by adoptive transfer of autoantigen-specific cells from wild-type mice with EAE.", "IL-23 alone did not induce IL-17 production by T cells from IL-1RI\u2212/\u2212 mice, and IL-23\u2013induced IL-17 production was substantially enhanced by IL-1\u03b1 or IL-1\u03b2, even in the absence of T cell receptor stimulation.", "We demonstrate essential roles for phosphatidylinositol 3-kinase, nuclear factor \u03baB, and novel protein kinase C isoforms in IL-1\u2013 and IL-23\u2013mediated IL-17 production.", "Tumor necrosis factor \u03b1 also synergized with IL-23 to enhance IL-17 production, and this was IL-1 dependent.", "Our findings demonstrate that IL-1 functions upstream of IL-17 to promote pathogenic ThIL-17 cells in EAE."], "structured": false}
{"doc_id": 1866911, "title": "Aberrant luminal progenitors as the candidate target population for basal tumor development in BRCA1 mutation carriers", "abstract": ["Basal-like breast cancers arising in women carrying mutations in the BRCA1 gene, encoding the tumor suppressor protein BRCA1, are thought to develop from the mammary stem cell.", "To explore early cellular changes that occur in BRCA1 mutation carriers, we have prospectively isolated distinct epithelial subpopulations from normal mammary tissue and preneoplastic specimens from individuals heterozygous for a BRCA1 mutation.", "We describe three epithelial subsets including basal stem/progenitor, luminal progenitor and mature luminal cells.", "Unexpectedly, we found that breast tissue from BRCA1 mutation carriers harbors an expanded luminal progenitor population that shows factor-independent growth in vitro.", "Moreover, gene expression profiling revealed that breast tissue heterozygous for a BRCA1 mutation and basal breast tumors were more similar to normal luminal progenitor cells than any other subset, including the stem cell\u2013enriched population.", "The c-KIT tyrosine kinase receptor (encoded by KIT) emerged as a key marker of luminal progenitor cells and was more highly expressed in BRCA1-associated preneoplastic tissue and tumors.", "Our findings suggest that an aberrant luminal progenitor population is a target for transformation in BRCA1-associated basal tumors ."], "structured": false}
{"doc_id": 1871230, "title": "Getting to the site of inflammation: the leukocyte adhesion cascade updated", "abstract": ["Neutrophil recruitment, lymphocyte recirculation and monocyte trafficking all require adhesion and transmigration through blood-vessel walls.", "The traditional three steps of rolling, activation and firm adhesion have recently been augmented and refined.", "Slow rolling, adhesion strengthening, intraluminal crawling and paracellular and transcellular migration are now recognized as separate, additional steps.", "In neutrophils, a second activation pathway has been discovered that does not require signalling through G-protein-coupled receptors and the signalling steps leading to integrin activation are beginning to emerge.", "This Review focuses on new aspects of one of the central paradigms of inflammation and immunity \u2014 the leukocyte adhesion cascade."], "structured": false}
{"doc_id": 1871499, "title": "Genome-wide loss of 5-hmC is a novel epigenetic feature of Huntington's disease.", "abstract": ["5-Hydroxymethylcytosine (5-hmC) may represent a new epigenetic modification of cytosine.", "While the dynamics of 5-hmC during neurodevelopment have recently been reported, little is known about its genomic distribution and function(s) in neurodegenerative diseases such as Huntington's disease (HD).", "We here observed a marked reduction of the 5-hmC signal in YAC128 (yeast artificial chromosome transgene with 128 CAG repeats) HD mouse brain tissues when compared with age-matched wild-type (WT) mice, suggesting a deficiency of 5-hmC reconstruction in HD brains during postnatal development.", "Genome-wide distribution analysis of 5-hmC further confirmed the diminishment of the 5-hmC signal in striatum and cortex in YAC128 HD mice.", "General genomic features of 5-hmC are highly conserved, not being affected by either disease or brain regions.", "Intriguingly, we have identi\ufb01ed disease-specific (YAC128 versus WT) differentially hydroxymethylated regions (DhMRs), and found that acquisition of DhmRs in gene body is a positive epigenetic regulator for gene expression.", "Ingenuity pathway analysis (IPA) of genotype-specific DhMR-annotated genes revealed that alternation of a number of canonical pathways involving neuronal development/differentiation (Wnt/\u03b2-catenin/Sox pathway, axonal guidance signaling pathway) and neuronal function/survival (glutamate receptor/calcium/CREB, GABA receptor signaling, dopamine-DARPP32 feedback pathway, etc.) could be important for the onset of HD.", "Our results indicate that loss of the 5-hmC marker is a novel epigenetic feature in HD, and that this aberrant epigenetic regulation may impair the neurogenesis, neuronal function and survival in HD brain.", "Our study also opens a new avenue for HD treatment; re-establishing the native 5-hmC landscape may have the potential to slow/halt the progression of HD."], "structured": false}
{"doc_id": 1886551, "title": "Planning for Postdisaster Resiliency", "abstract": ["The focus of this article is planning for resiliency in the aftermath of a catastrophe.", "First, the authors offer their conception of planning for resiliency as a goal for recovering communities, and the benefits of planning in efforts to create more resilient places.", "Next, they discuss major issues associated with planning for postdisaster recovery, including barriers posed by federal and state governments to planning for resiliency, the promise and risks of compact urban form models for guiding rebuilding, and the failure to involve citizens in planning for disasters.", "Finally, they discuss lessons from prior research that address these issues and policy recommendations that foster predisaster recovery planning for resilient communities."], "structured": false}
{"doc_id": 1887056, "title": "Increased stress-induced inflammatory responses in male patients with major depression and increased early life stress.", "abstract": ["OBJECTIVE The authors sought to determine innate immune system activation following psychosocial stress in patients with major depression and increased early life stress.   \n", "METHOD Plasma interleukin (IL)-6, lymphocyte subsets, and DNA binding of nuclear factor (NF)-kB in peripheral blood mononuclear cells were compared in medically healthy male subjects with current major depression and increased early life stress (N=14) versus nondepressed male comparison subjects (N=14) before and after completion of the Trier Social Stress Test.   \n", "RESULTS Trier Social Stress Test-induced increases in IL-6 and NF-kappaB DNA-binding were greater in major depression patients with increased early life stress and independently correlated with depression severity, but not early life stress.", "Natural killer (NK) cell percentages also increased following stress.", "However, there were no differences between groups and no correlation between NK cell percentage and stress-induced NF-kappaB DNA-binding or IL-6.   \n", "CONCLUSIONS Male major depression patients with increased early life stress exhibit enhanced inflammatory responsiveness to psychosocial stress, providing preliminary indication of a link between major depression, early life stress and adverse health outcomes in diseases associated with inflammation."], "structured": true}
{"doc_id": 1889358, "title": "KIF3A/B: a heterodimeric kinesin superfamily protein that works as a microtubule plus end-directed motor for membrane organelle transport", "abstract": ["We cloned a new member of the murine brain kinesin superfamily, KIF3B, and found that its amino acid sequence is highly homologous but not identical to KIF3A, which we previously cloned and named KIF3 (47% identical).", "KIF3B is localized in various organ tissues and developing neurons of mice and accumulates with anterogradely moving membranous organelles after ligation of nerve axons.", "Immunoprecipitation assay of the brain revealed that KIF3B forms a complex with KIF3A and three other high molecular weight (approximately 100 kD)-associated polypeptides, called the kinesin superfamily-associated protein 3 (KAP3).", "In vitro reconstruction using baculovirus expression systems showed that KIF3A and KIF3B directly bind with each other in the absence of KAP3.", "The recombinant KIF3A/B complex (approximately 50-nm rod with two globular heads and a single globular tail) demonstrated plus end-directed microtubule sliding activity in vitro.", "In addition, we showed that KIF3B itself has motor activity in vitro, by making a complex of wild-type KIF3B and a chimeric motor protein (KIF3B head and KIF3A rod tail).", "Subcellular fractionation of mouse brain homogenates showed a considerable amount of the native KIF3 complex to be associated with membrane fractions other than synaptic vesicles.", "Immunoprecipitation by anti-KIF3B antibody-conjugated beads and its electron microscopic study also revealed that KIF3 is associated with membranous organelles.", "Moreover, we found that the composition of KAP3 is different in the brain and testis.", "Our findings suggest that KIF3B forms a heterodimer with KIF3A and functions as a new microtubule-based anterograde translocator for membranous organelles, and that KAP3 may determine functional diversity of the KIF3 complex in various kinds of cells in vivo."], "structured": false}
{"doc_id": 1897324, "title": "A genetic screen identifies an LKB1\u2013MARK signalling axis controlling the Hippo\u2013YAP pathway", "abstract": ["The Hippo\u2013YAP pathway is an emerging signalling cascade involved in the regulation of stem cell activity and organ size.", "To identify components of this pathway, we performed an RNAi-based kinome screen in human cells.", "Our screen identified several kinases not previously associated with Hippo signalling that control multiple cellular processes.", "One of the hits, LKB1, is a common tumour suppressor whose mechanism of action is only partially understood.", "We demonstrate that LKB1 acts through its substrates of the microtubule affinity-regulating kinase family to regulate the localization of the polarity determinant Scribble and the activity of the core Hippo kinases.", "Our data also indicate that YAP is functionally important for the tumour suppressive effects of LKB1.", "Our results identify a signalling axis that links YAP activation with LKB1 mutations, and have implications for the treatment of LKB1-mutant human malignancies.", "In addition, our findings provide insight into upstream signals of the Hippo\u2013YAP signalling cascade."], "structured": false}
{"doc_id": 1900152, "title": "Beyond melanoma: inhibiting the PD-1/PD-L1 pathway in solid tumors.", "abstract": ["Immune checkpoint inhibitors have been identified as breakthrough treatment in melanoma given its dramatic response to PD-1/PD-L1 blockade.", "This is likely to extend to many other cancers as hundreds of clinical trials are being conducted or proposed using this exciting modality of therapy in a variety of malignancies.", "While immune checkpoint inhibitors have been extensively studied in melanoma and more recently in lung cancer, little is known regarding immune checkpoint blockade in other cancers.", "This review will focus on the tumor immune microenvironment, the expression of PD-1/PD-L1 and the effect of immune modulation using PD-1 or PD-L1 inhibitors in patients with head and neck, prostate, urothelial, renal, breast, gastrointestinal and lung cancers."], "structured": false}
{"doc_id": 1904291, "title": "Partitioning the symptoms of hypoglycaemia using multi-sample confirmatory factor analysis", "abstract": ["The allocation of hypoglycaemic symptoms to autonomie or neuroglycopenic groups tends to occur on an a priori basis.", "In view of the practical need for clear symptom markers of hypoglycaemia more scientific approaches must be pursued.", "Substantial evidence is presented from two large scale studies we performed which support a three factor model of hypoglycaemic symptomatology, based on the statistical associations discovered among symptoms reported by diabetic patients.", "Study 1 involved 295 insulin-treated outpatients and found that 11 key hypoglycaemic symptoms segregated into three clear factors: autonomie (sweating, palpitation, shaking and hunger) neuroglycopenic (confusion, drowsiness, odd behaviour, speech difficulty and incoordination), and malaise (nausea and headache).", "The three factors were validated on a separate group of 303 insulin-treated diabetic out-patients.", "Confirmatory factor analyses showed that the three factor model was the optimal model for explaining symptom covariance in each group.", "A multi-sample confirmatory factor analysis tested the rigorous assumptions that the relative loadings of symptoms on factors across groups were equal, and that the residual variance for each symptom was identical across groups.", "These assumptions were successful, indicating that the three factor model was replicated in detail across these two large samples.", "It is suggested that the results indicate valid groupings of symptoms that may be used in future research and in clinical practice."], "structured": false}
{"doc_id": 1905095, "title": "Extracellular vesicles from human cardiac progenitor cells inhibit cardiomyocyte apoptosis and improve cardiac function after myocardial infarction.", "abstract": ["AIMS Recent evidence suggests that cardiac progenitor cells (CPCs) may improve cardiac function after injury.", "The underlying mechanisms are indirect, but their mediators remain unidentified.", "Exosomes and other secreted membrane vesicles, hereafter collectively referred to as extracellular vesicles (EVs), act as paracrine signalling mediators.", "Here, we report that EVs secreted by human CPCs are crucial cardioprotective agents.   \n", "METHODS AND RESULTS CPCs were derived from atrial appendage explants from patients who underwent heart valve surgery.", "CPC-conditioned medium (CM) inhibited apoptosis in mouse HL-1 cardiomyocytic cells, while enhancing tube formation in human umbilical vein endothelial cells.", "These effects were abrogated by depleting CM of EVs.", "They were reproduced by EVs secreted by CPCs, but not by those secreted by human dermal fibroblasts.", "Transmission electron microscopy and nanoparticle tracking analysis showed most EVs to be 30-90 nm in diameter, the size of exosomes, although smaller and larger vesicles were also present.", "MicroRNAs most highly enriched in EVs secreted by CPCs compared with fibroblasts included miR-210, miR-132, and miR-146a-3p.", "miR-210 down-regulated its known targets, ephrin A3 and PTP1b, inhibiting apoptosis in cardiomyocytic cells.", "miR-132 down-regulated its target, RasGAP-p120, enhancing tube formation in endothelial cells.", "Infarcted hearts injected with EVs from CPCs, but not from fibroblasts, exhibited less cardiomyocyte apoptosis, enhanced angiogenesis, and improved LV ejection fraction (0.8 \u00b1 6.8 vs. -21.3 \u00b1 4.5%; P < 0.05) compared with those injected with control medium.   \n", "CONCLUSION EVs are the active component of the paracrine secretion by human CPCs.", "As a cell-free approach, EVs could circumvent many of the limitations of cell transplantation."], "structured": true}
{"doc_id": 1907601, "title": "Increased Adipocyte O2 Consumption Triggers HIF-1\u03b1, Causing Inflammation and Insulin Resistance in Obesity", "abstract": ["Adipose tissue hypoxia and inflammation have been causally implicated in obesity-induced insulin resistance.", "Here, we report that, early in the course of high-fat diet (HFD) feeding and obesity, adipocyte respiration becomes uncoupled, leading to increased oxygen consumption and a state of relative adipocyte hypoxia.", "These events are sufficient to trigger HIF-1\u03b1 induction, setting off the chronic adipose tissue inflammatory response characteristic of obesity.", "At the molecular level, these events involve saturated fatty acid stimulation of the adenine nucleotide translocase 2 (ANT2), an inner mitochondrial membrane protein, which leads to the uncoupled respiratory state.", "Genetic or pharmacologic inhibition of either ANT2 or HIF-1\u03b1 can prevent or reverse these pathophysiologic events, restoring a state of insulin sensitivity and glucose tolerance.", "These results reveal the sequential series of events in obesity-induced inflammation and insulin resistance."], "structured": false}
{"doc_id": 1910120, "title": "Lpcat3-dependent production of arachidonoyl phospholipids is a key determinant of triglyceride secretion", "abstract": ["The role of specific phospholipids (PLs) in lipid transport has been difficult to assess due to an inability to selectively manipulate membrane composition in vivo.", "Here we show that the phospholipid remodeling enzyme lysophosphatidylcholine acyltransferase 3 (Lpcat3) is a critical determinant of triglyceride (TG) secretion due to its unique ability to catalyze the incorporation of arachidonate into membranes.", "Mice lacking Lpcat3 in the intestine fail to thrive during weaning and exhibit enterocyte lipid accumulation and reduced plasma TGs.", "Mice lacking Lpcat3 in the liver show reduced plasma TGs, hepatosteatosis, and secrete lipid-poor very low-density lipoprotein (VLDL) lacking arachidonoyl PLs.", "Mechanistic studies indicate that Lpcat3 activity impacts membrane lipid mobility in living cells, suggesting a biophysical basis for the requirement of arachidonoyl PLs in lipidating lipoprotein particles.", "These data identify Lpcat3 as a key factor in lipoprotein production and illustrate how manipulation of membrane composition can be used as a regulatory mechanism to control metabolic pathways."], "structured": false}
{"doc_id": 1914588, "title": "Characterization of a single-stranded DNA-binding protein from Pseudomonas aeruginosa PAO1.", "abstract": ["Single-stranded DNA-binding protein (SSB) plays an important role in DNA metabolism, such as in DNA replication, repair, and recombination, and is essential for cell survival.", "We characterized the single-stranded DNA (ssDNA)-binding properties of Pseudomonas aeruginosa PAO1 SSB (PaSSB) by using fluorescence quenching measurements and electrophoretic mobility shift analysis (EMSA).", "Analysis of purified PaSSB by gel filtration chromatography revealed a stable tetramer in solution.", "In fluorescence titrations, PaSSB bound 22-32 nucleotides (nt) per tetramer depending on salt concentration.", "Using EMSA, we characterized the stoichiometry of PaSSB complexed with a series of ssDNA homopolymers, and the size of the binding site was determined to be 29 \u00b1 1 nt.", "Furthermore, EMSA results indicated that the dissociation constants of PaSSB for the first tetramer were less than those for the second tetramer.", "On the basis of these biophysical analyses, the ssDNA binding mode of PaSSB is expected to be noncooperative."], "structured": false}
{"doc_id": 1917068, "title": "Primary cilia and coordination of receptor tyrosine kinase (RTK) signalling.", "abstract": ["Primary cilia are microtubule-based sensory organelles that coordinate signalling pathways in cell-cycle control, migration, differentiation and other cellular processes critical during development and for tissue homeostasis.", "Accordingly, defects in assembly or function of primary cilia lead to a plethora of developmental disorders and pathological conditions now known as ciliopathies.", "In this review, we summarize the current status of the role of primary cilia in coordinating receptor tyrosine kinase (RTK) signalling pathways.", "Further, we present potential mechanisms of signalling crosstalk and networking in the primary cilium and discuss how defects in ciliary RTK signalling are linked to human diseases and disorders."], "structured": false}
{"doc_id": 1921218, "title": "Detecting and targeting tumor relapse by its resistance to innate effectors at early recurrence", "abstract": ["Tumor recurrence represents a major clinical challenge.", "Our data show that emergent recurrent tumors acquire a phenotype radically different from that of their originating primary tumors.", "This phenotype allows them to evade a host-derived innate immune response elicited by the progression from minimal residual disease (MRD) to actively growing recurrence.", "Screening for this innate response predicted accurately in which mice recurrence would occur.", "Premature induction of recurrence resensitized MRD to the primary therapy, suggesting a possible paradigm shift for clinical treatment of dormant disease in which the current expectant approach is replaced with active attempts to uncover MRD before evolution of the escape phenotype is complete.", "By combining screening with second-line treatments targeting innate insensitivity, up to 100% of mice that would have otherwise relapsed were cured.", "These data may open new avenues for early detection and appropriately timed, highly targeted treatment of tumor recurrence irrespective of tumor type or frontline treatment."], "structured": false}
{"doc_id": 1922901, "title": "Forces in Tissue Morphogenesis and Patterning", "abstract": ["During development, mechanical forces cause changes in size, shape, number, position, and gene expression of cells.", "They are therefore integral to any morphogenetic processes.", "Force generation by actin-myosin networks and force transmission through adhesive complexes are two self-organizing phenomena driving tissue morphogenesis.", "Coordination and integration of forces by long-range force transmission and mechanosensing of cells within tissues produce large-scale tissue shape changes.", "Extrinsic mechanical forces also control tissue patterning by modulating cell fate specification and differentiation.", "Thus, the interplay between tissue mechanics and biochemical signaling orchestrates tissue morphogenesis and patterning in development."], "structured": false}
{"doc_id": 1933281, "title": "CD169+ MACROPHAGES PRESENT LIPID ANTIGENS TO MEDIATE EARLY ACTIVATION OF INVARIANT NKT CELLS IN LYMPH NODES", "abstract": ["Invariant natural killer T cells (iNKT cells) are involved in the host defense against microbial infection.", "Although it is known that iNKT cells recognize glycolipids presented by CD1d, how and where they encounter antigen in vivo remains unclear.", "Here we used multiphoton microscopy to visualize the dynamics and activation of iNKT cells in lymph nodes.", "After antigen administration, iNKT cells became confined in a CD1d-dependent manner in close proximity to subcapsular sinus CD169(+) macrophages.", "These macrophages retained, internalized and presented lipid antigen and were required for iNKT cell activation, cytokine production and population expansion.", "Thus, CD169(+) macrophages can act as true antigen-presenting cells controlling early iNKT cell activation and favoring the fast initiation of immune responses."], "structured": false}
{"doc_id": 1941721, "title": "Oxygen Metabolism Causes Chromosome Breaks and Is Associated with the Neuronal Apoptosis Observed in DNA Double-Strand Break Repair Mutants", "abstract": ["Cells deficient in a major DNA double-strand break repair pathway (nonhomologous DNA end joining [NHEJ]) have increased spontaneous chromosome breaks; however, the source of these chromosome breaks has remained undefined.", "Here, we show that the observed spontaneous chromosome breaks are partially suppressed by reducing the cellular oxygen tension.", "Conversely, elevating the level of reactive oxygen species by overexpressing the antioxidant enzyme superoxide dismutase 1 (SOD1), in a transgenic mouse, increases chromosome breakage.", "The effect of SOD1 can also be modulated by cellular oxygen tension.", "The elevated chromosome breakage correlates histologically with a significant increase in the amount of neuronal cell death in Ku86(-/-) SOD1 transgenic embryos over that seen in Ku86(-/-) embryos.", "Therefore, oxygen metabolism is a major source of the genomic instability observed in NHEJ-deficient cells and, presumably, in all cells."], "structured": false}
{"doc_id": 1944452, "title": "Insertional mutagenesis in gene therapy and stem cell biology.", "abstract": ["PURPOSE OF REVIEW Recent preclinical and clinical studies revealed that the semirandom insertion of transgenes into chromosomal DNA of hematopoietic cells may induce clonal competition, which potentially may even trigger leukemia or sarcoma.", "Insertional mutagenesis caused by gene vectors has thus led to major uncertainty among those developing advanced hematopoietic cell therapies.", "This review summarizes novel studies of underlying mechanisms; these studies have demonstrated the possibility of improved gene vector biosafety and generated new insights into stem cell biology.   ", "RECENT FINDINGS The characteristic insertion pattern of various retroviral gene vector systems may be explained by properties of the viral integrase and associated cellular cofactors.", "Cell culture assays and animal models, including disease-specific and cancer-prone mouse models, are emerging that reveal the contributions of vector features and systemic factors to induction of clonal imbalance.", "Databases summarizing vector insertion sites in dominant hematopoietic clones are evolving as new tools to identify genes that regulate clonal homeostasis.   ", "SUMMARY Mechanistic studies of insertional mutagenesis by random gene vector insertion will lead to improved tools for advanced hematopoietic cell therapy.", "Simultaneously, fascinating insights into gene networks that regulate cell fitness will be generated, with important consequences for the fields of hematology, oncology and regenerative medicine."], "structured": true}
{"doc_id": 1946610, "title": "Markets, voucher subsidies and free nets combine to achieve high bed net coverage in rural Tanzania", "abstract": ["BACKGROUND Tanzania has a well-developed network of commercial ITN retailers.", "In 2004, the government introduced a voucher subsidy for pregnant women and, in mid 2005, helped distribute free nets to under-fives in small number of districts, including Rufiji on the southern coast, during a child health campaign.", "Contributions of these multiple insecticide-treated net delivery strategies existing at the same time and place to coverage in a poor rural community were assessed.   \n", "METHODS Cross-sectional household survey in 6,331 members of randomly selected 1,752 households of 31 rural villages of Demographic Surveillance System in Rufiji district, Southern Tanzania was conducted in 2006.", "A questionnaire was administered to every consenting respondent about net use, treatment status and delivery mechanism.   \n", "FINDINGS Net use was 62.7% overall, 87.2% amongst infants (0 to 1 year), 81.8% amongst young children (>1 to 5 years), 54.5% amongst older children (6 to 15 years) and 59.6% amongst adults (>15 years).", "30.2% of all nets had been treated six months prior to interview.", "The biggest source of nets used by infants was purchase from the private sector with a voucher subsidy (41.8%).", "Half of nets used by young children (50.0%) and over a third of those used by older children (37.2%) were obtained free of charge through the vaccination campaign.", "The largest source of nets amongst the population overall was commercial purchase (45.1% use) and was the primary means for protecting adults (60.2% use).", "All delivery mechanisms, especially sale of nets at full market price, under-served the poorest but no difference in equity was observed between voucher-subsidized and freely distributed nets.   \n", "CONCLUSION All three delivery strategies enabled a poor rural community to achieve net coverage high enough to yield both personal and community level protection for the entire population.", "Each of them reached their relevant target group and free nets only temporarily suppressed the net market, illustrating that in this setting that these are complementary rather than mutually exclusive approaches."], "structured": true}
{"doc_id": 1958440, "title": "Human chorionic gonadotropin levels in maternal blood in late pregnancy: relation to birthweight, sex and condition of the infant at birth.", "abstract": ["A total of 527 blood samples was obtained from an unselected population of women between 36 and 40 weeks gestation.", "Serum human chorionic gonadotropin (hCG) levels were measured using a specific radioimmunoassay for the beta 1-subunit of hCG.", "Serum hCG levels were higher in primigravidae and in women carrying female fetuses.", "They were also related to the birthweight of the child and to the occurrence of fetal distress."], "structured": false}
{"doc_id": 1964163, "title": "Brain-Specific Phosphorylation of MeCP2 Regulates Activity-Dependent Bdnf Transcription, Dendritic Growth, and Spine Maturation", "abstract": ["Mutations or duplications in MECP2 cause Rett and Rett-like syndromes, neurodevelopmental disorders characterized by mental retardation, motor dysfunction, and autistic behaviors.", "MeCP2 is expressed in many mammalian tissues and functions as a global repressor of transcription; however, the molecular mechanisms by which MeCP2 dysfunction leads to the neural-specific phenotypes of RTT remain poorly understood.", "Here, we show that neuronal activity and subsequent calcium influx trigger the de novo phosphorylation of MeCP2 at serine 421 (S421) by a CaMKII-dependent mechanism.", "MeCP2 S421 phosphorylation is induced selectively in the brain in response to physiological stimuli.", "Significantly, we find that S421 phosphorylation controls the ability of MeCP2 to regulate dendritic patterning, spine morphogenesis, and the activity-dependent induction of Bdnf transcription.", "These findings suggest that, by triggering MeCP2 phosphorylation, neuronal activity regulates a program of gene expression that mediates nervous system maturation and that disruption of this process in individuals with mutations in MeCP2 may underlie the neural-specific pathology of RTT."], "structured": false}
{"doc_id": 1967017, "title": "A Candidate Gene Approach Identifies the TRAF1/C5 Region as a Risk Factor for Rheumatoid Arthritis", "abstract": ["Correction for:    Kurreeman FAS, Padyukov L, Marques RB, Schrodi SJ, Seddighzadeh M, et al. (2007)", "A Candidate Gene Approach Identifies the TRAF1/C5 Region as a Risk Factor for Rheumatoid Arthritis.", "PLoS Med 4(9): e278.", "doi:10.1371/journal.pmed.0040278    In Table 1, the allele ratio in column eight (Allele Ratiosb: Cases, Controls) refers to allele A: allele B and not allele1:allele2 as described in footnote b, with Allele A being the Susceptibility Allele as denoted in column seven.    ", "The footnote should read:    bNumber of alleles were compared in cases versus controls: allele A: allele B cases, allele A: allele B controls.", "Allele A refers to the susceptibility alleles as given in column seven."], "structured": false}
{"doc_id": 1967410, "title": "Potential use of \u03b3-secretase modulators in the treatment of Alzheimer disease.", "abstract": ["Although significant progress has occurred in the past 20 years regarding our understanding of Alzheimer disease pathogenesis, we have yet to identify disease-modifying therapeutics capable of substantially altering the clinical course of this prevalent neurodegenerative disease.", "In this short review, we discuss 2 approaches that are currently being tested clinically (\u03b3-secretase inhibition and \u03b3-secretase modulation) and emphasize the significant differences between these 2 therapeutic approaches.", "We also discuss certain genetic- and biomarker-based translational and clinical trial paradigms that may assist in developing a useful therapeutic agent."], "structured": false}
{"doc_id": 1970884, "title": "Rational design of a flavivirus vaccine by abolishing viral RNA 2'-O methylation.", "abstract": ["Viruses that replicate in the cytoplasm cannot access the host nuclear capping machinery.", "These viruses have evolved viral methyltransferase(s) to methylate N-7 and 2'-O cap of their RNA; alternatively, they \"snatch\" host mRNA cap to form the 5' end of viral RNA.", "The function of 2'-O methylation of viral RNA cap is to mimic cellular mRNA and to evade host innate immune restriction.", "A cytoplasmic virus defective in 2'-O methylation is replicative, but its viral RNA lacks 2'-O methylation and is recognized and eliminated by the host immune response.", "Such a mutant virus could be rationally designed as a live attenuated vaccine.", "Here, we use Japanese encephalitis virus (JEV), an important mosquito-borne flavivirus, to prove this novel vaccine concept.", "We show that JEV methyltransferase is responsible for both N-7 and 2'-O cap methylations as well as evasion of host innate immune response.", "Recombinant virus completely defective in 2'-O methylation was stable in cell culture after being passaged for >30 days.", "The mutant virus was attenuated in mice, elicited robust humoral and cellular immune responses, and retained the engineered mutation in vivo.", "A single dose of immunization induced full protection against lethal challenge with JEV strains in mice.", "Mechanistically, the attenuation phenotype was attributed to the enhanced sensitivity of the mutant virus to the antiviral effects of interferon and IFIT proteins.", "Collectively, the results demonstrate the feasibility of using 2'-O methylation-defective virus as a vaccine approach; this vaccine approach should be applicable to other flaviviruses and nonflaviviruses that encode their own viral 2'-O methyltransferases."], "structured": false}
{"doc_id": 1974176, "title": "Fruit consumption and risk of type 2 diabetes: results from three prospective longitudinal cohort studies", "abstract": ["OBJECTIVE To determine whether individual fruits are differentially associated with risk of type 2 diabetes.   \n", "DESIGN Prospective longitudinal cohort study.   \n", "SETTING Health professionals in the United States.   \n", "PARTICIPANTS 66,105 women from the Nurses' Health Study (1984-2008), 85,104 women from the Nurses' Health Study II (1991-2009), and 36,173 men from the Health Professionals Follow-up Study (1986-2008) who were free of major chronic diseases at baseline in these studies.   \n", "MAIN OUTCOME MEASURE Incident cases of type 2 diabetes, identified through self report and confirmed by supplementary questionnaires.   \n", "RESULTS During 3,464,641 person years of follow-up, 12,198 participants developed type 2 diabetes.", "After adjustment for personal, lifestyle, and dietary risk factors of diabetes, the pooled hazard ratio of type 2 diabetes for every three servings/week of total whole fruit consumption was 0.98 (95% confidence interval 0.97 [corrected] to 0.99).", "With mutual adjustment of individual fruits, the pooled hazard ratios of type 2 diabetes for every three servings/week were 0.74 (0.66 to 0.83) for blueberries, 0.88 (0.83 to 0.93) for grapes and raisins, 0.89 (0.79 to 1.01) for prunes, 0.93 (0.90 to 0.96) for apples and pears, 0.95 (0.91 to 0.98) for bananas, 0.95 (0.91 to 0.99) for grapefruit, 0.97 (0.92 to 1.02) for peaches, plums, and apricots, 0.99 (0.95 to 1.03) for oranges, 1.03 (0.96 to 1.10) for strawberries, and 1.10 (1.02 to 1.18) for cantaloupe.", "The pooled hazard ratio for the same increment in fruit juice consumption was 1.08 (1.05 to 1.11).", "The associations with risk of type 2 diabetes differed significantly among individual fruits (P<0.001 in all cohorts).   \n", "CONCLUSION Our findings suggest the presence of heterogeneity in the associations between individual fruit consumption and risk of type 2 diabetes.", "Greater consumption of specific whole fruits, particularly blueberries, grapes, and apples, is significantly associated with a lower risk of type 2 diabetes, whereas greater consumption of fruit juice is associated with a higher risk."], "structured": true}
{"doc_id": 1976183, "title": "OncomiR-196 promotes an invasive phenotype in oral cancer through the NME4-JNK-TIMP1-MMP signaling pathway", "abstract": ["BACKGROUND MicroRNA-196 (miR-196), which is highly up-regulated in oral cancer cells, has been reported to be aberrantly expressed in several cancers; however, the significance of miR-196 in oral cancer has not yet been addressed.   \n", "METHODS Cellular functions in response to miR-196 modulation were examined, including cell growth, migration, invasion and radio/chemosensitivity.", "Algorithm-based studies were used to identify the regulatory target of miR-196.", "The miR-196 target gene and downstream molecular mechanisms were confirmed by RT-qPCR, western blot, luciferase reporter and confocal microscopy analyses.", "miR-196 expression was determined in paired cancer and adjacent normal tissues from oral cancer patients.   \n", "RESULTS Both miR-196a and miR-196b were highly over-expressed in the cancer tissue and correlated with lymph node metastasis (P = 0.001 and P = 0.006, respectively).", "Functionally, miR-196 actively promoted cell migration and invasion without affecting cell growth.", "Mechanistically, miR-196 performed it's their function by inhibiting NME4 expression and further activating p-JNK, suppressing TIMP1, and augmenting MMP1/9.   \n", "CONCLUSION miR-196 contributes to oral cancer by promoting cell migration and invasion.", "Clinically, miR-196a/b was significantly over-expressed in the cancer tissues and correlated with lymph node metastasis.", "Thus, our findings provide new knowledge of the underlying mechanism of cancer metastasis.", "miR-196 may serve as a promising marker for better oral cancer management."], "structured": true}
{"doc_id": 1982286, "title": "Reverse engineering of TLX oncogenic transcriptional networks identifies RUNX1 as tumor suppressor in T-ALL", "abstract": ["The TLX1 and TLX3 transcription factor oncogenes have a key role in the pathogenesis of T cell acute lymphoblastic leukemia (T-ALL).", "Here we used reverse engineering of global transcriptional networks to decipher the oncogenic regulatory circuit controlled by TLX1 and TLX3.", "This systems biology analysis defined T cell leukemia homeobox 1 (TLX1) and TLX3 as master regulators of an oncogenic transcriptional circuit governing T-ALL.", "Notably, a network structure analysis of this hierarchical network identified RUNX1 as a key mediator of the T-ALL induced by TLX1 and TLX3 and predicted a tumor-suppressor role for RUNX1 in T cell transformation.", "Consistent with these results, we identified recurrent somatic loss-of-function mutations in RUNX1 in human T-ALL.", "Overall, these results place TLX1 and TLX3 at the top of an oncogenic transcriptional network controlling leukemia development, show the power of network analyses to identify key elements in the regulatory circuits governing human cancer and identify RUNX1 as a tumor-suppressor gene in T-ALL."], "structured": false}
{"doc_id": 1986482, "title": "The Impact of the New WHO Antiretroviral Treatment Guidelines on HIV Epidemic Dynamics and Cost in South Africa", "abstract": ["BACKGROUND Since November 2009, WHO recommends that adults infected with HIV should initiate antiretroviral therapy (ART) at CD4+ cell counts of \u2264350 cells/\u00b5l rather than \u2264200 cells/\u00b5l.", "South Africa decided to adopt this strategy for pregnant and TB co-infected patients only.", "We estimated the impact of fully adopting the new WHO guidelines on HIV epidemic dynamics and associated costs.   \n", "METHODS AND FINDING We used an established model of the transmission and control of HIV in specified sexual networks and healthcare settings.", "We quantified the model to represent Hlabisa subdistrict, KwaZulu-Natal, South Africa.", "We predicted the HIV epidemic dynamics, number on ART and program costs under the new guidelines relative to treating patients at \u2264200 cells/\u00b5l for the next 30 years.", "During the first five years, the new WHO treatment guidelines require about 7% extra annual investments, whereas 28% more patients receive treatment.", "Furthermore, there will be a more profound impact on HIV incidence, leading to relatively less annual costs after seven years.", "The resulting cumulative net costs reach a break-even point after on average 16 years.   \n", "CONCLUSIONS Our study strengthens the WHO recommendation of starting ART at \u2264350 cells/\u00b5l for all HIV-infected patients.", "Apart from the benefits associated with many life-years saved, a modest frontloading appears to lead to net savings within a limited time-horizon.", "This finding is robust to alternative assumptions and foreseeable changes in ART prices and effectiveness.", "Therefore, South Africa should aim at rapidly expanding its healthcare infrastructure to fully embrace the new WHO guidelines."], "structured": true}
{"doc_id": 1991105, "title": "ER-associated mitochondrial division links the distribution of mitochondria and mitochondrial DNA in yeast", "abstract": ["Mitochondrial division is important for mitochondrial distribution and function.", "Recent data have demonstrated that ER-mitochondria contacts mark mitochondrial division sites, but the molecular basis and functions of these contacts are not understood.", "Here we show that in yeast, the ER-mitochondria tethering complex, ERMES, and the highly conserved Miro GTPase, Gem1, are spatially and functionally linked to ER-associated mitochondrial division.", "Gem1 acts as a negative regulator of ER-mitochondria contacts, an activity required for the spatial resolution and distribution of newly generated mitochondrial tips following division.", "Previous data have demonstrated that ERMES localizes with a subset of actively replicating mitochondrial nucleoids.", "We show that mitochondrial division is spatially linked to nucleoids and that a majority of these nucleoids segregate prior to division, resulting in their distribution into newly generated tips in the mitochondrial network.", "Thus, we postulate that ER-associated division serves to link the distribution of mitochondria and mitochondrial nucleoids in cells.", "DOI:http://dx.doi.org/10.7554/eLife.00422.001."], "structured": false}
{"doc_id": 1996292, "title": "BMI-1 Autoantibody as a New Potential Biomarker for Cervical Carcinoma", "abstract": ["BMI-1 is overexpressed in a variety of cancers, which can elicit an immune response leading to the induction of autoantibodies.", "However, BMI-1 autoantibody as a biomarker has seldom been studied with the exception of nasopharyngeal carcinoma.", "Whether BMI-1 autoantibodies can be used as a biomarker for cervical carcinoma is unclear.", "In this study,BMI-1 proteins were isolated by screening of a T7 phage cDNA library from mixed cervical carcinoma tissues.", "We analyzed BMI-1 autoantibody levels in serum samples from 67 patients with cervical carcinoma and 65 controls using ELISA and immunoblot.", "BMI-1 mRNA or protein levels were over-expressed in cervical carcinoma cell lines.", "Immunoblot results exhibited increased BMI-1 autoantibody levels in patient sera compared to normal sera.", "Additionally, the results for antibody affinity assay showed that there was no difference between cervical polyps and normal sera of BMI-1 autoantibody levels, but it was significantly greater in patient sera than that in normal controls (patient 0.827\u00b10.043 and normal 0.445\u00b10.023; P<0.001).", "What's more, the levels of BMI-1 autoantibody increased significantly at stage I (0.672\u00b10.019) compared to normal sera (P<0.001), and levels of BMI-1 autoantibodies were increased gradually during the tumor progression (stage I 0.672\u00b10.019; stage II 0.775 \u00b10.019; stage III 0.890 \u00b10.027; stage IV 1.043\u00b10.041), which were significantly correlated with disease progression of cervical cancer (P<0.001).", "Statistical analyses using logistic regression and receiver operating characteristics (ROC) curves indicated that the BMI-1 autoantibody level can be used as a biomarker for cervical carcinoma (sensitivity 0.78 and specificity 0.76; AUC = 0.922).", "In conclusion, measuring BMI-1 autoantibody levels of patients with cervical cancer could have clinical prognostic value as well as a non-tissue specific biomarker for neoplasms expressing BMI-1."], "structured": false}
{"doc_id": 2000038, "title": "MicroRNAs can generate thresholds in target gene expression", "abstract": ["MicroRNAs (miRNAs) are short, highly conserved noncoding RNA molecules that repress gene expression in a sequence-dependent manner.", "We performed single-cell measurements using quantitative fluorescence microscopy and flow cytometry to monitor a target gene's protein expression in the presence and absence of regulation by miRNA.", "We find that although the average level of repression is modest, in agreement with previous population-based measurements, the repression among individual cells varies dramatically.", "In particular, we show that regulation by miRNAs establishes a threshold level of target mRNA below which protein production is highly repressed.", "Near this threshold, protein expression responds sensitively to target mRNA input, consistent with a mathematical model of molecular titration.", "These results show that miRNAs can act both as a switch and as a fine-tuner of gene expression."], "structured": false}
{"doc_id": 2014909, "title": "Oncogenic mTOR signaling recruits myeloid-derived suppressor cells to promote tumor initiation", "abstract": ["Myeloid-derived suppressor cells (MDSCs) play critical roles in primary and metastatic cancer progression.", "MDSC regulation is widely variable even among patients harbouring the same type of malignancy, and the mechanisms governing such heterogeneity are largely unknown.", "Here, integrating human tumour genomics and syngeneic mammary tumour models, we demonstrate that mTOR signalling in cancer cells dictates a mammary tumour's ability to stimulate MDSC accumulation through regulating G-CSF.", "Inhibiting this pathway or its activators (for example, FGFR) impairs tumour progression, which is partially rescued by restoring MDSCs or G-CSF.", "Tumour-initiating cells (TICs) exhibit elevated G-CSF.", "MDSCs reciprocally increase TIC frequency through activating Notch in tumour cells, forming a feedforward loop.", "Analyses of primary breast cancers and patient-derived xenografts corroborate these mechanisms in patients.", "These findings establish a non-canonical oncogenic role of mTOR signalling in recruiting pro-tumorigenic MDSCs and show how defined cancer subsets may evolve to promote and depend on a distinct immune microenvironment."], "structured": false}
{"doc_id": 2015126, "title": "Management of women who have a genetic predisposition for breast cancer.", "abstract": ["The management of women who have a genetic predisposition for breast cancer requires careful planning.", "Women who have BRCA 1 and BRCA 2 mutations are at increased risk for breast cancer and for other cancers as well, particularly ovarian cancer.", "Screening, prophlyactic surgery, and chemoprevention are commonly utilized strategies in the management of these patients, and women may choose more than one of these strategies.", "No randomized prospective trials have assessed the impact of these strategies specifically in mutation carriers.", "All patients should be informed that screening, prophylactic surgery, and chemoprevention have the potential for harm as well as benefit."], "structured": false}
{"doc_id": 2015929, "title": "Astrocytes from Familial and Sporadic ALS Patients are Toxic to Motor Neurons", "abstract": ["Amyotrophic lateral sclerosis (ALS) is a fatal motor neuron disease, with astrocytes implicated as contributing substantially to motor neuron death in familial (F)ALS.", "However, the proposed role of astrocytes in the pathology of ALS derives in part from rodent models of FALS based upon dominant mutations within the superoxide dismutase 1 (SOD1) gene, which account for <2% of all ALS cases.", "Their role in sporadic (S)ALS, which affects >90% of ALS patients, remains to be established.", "Using astrocytes generated from postmortem tissue from both FALS and SALS patients, we show that astrocytes derived from both patient groups are similarly toxic to motor neurons.", "We also demonstrate that SOD1 is a viable target for SALS, as its knockdown significantly attenuates astrocyte-mediated toxicity toward motor neurons.", "Our data highlight astrocytes as a non-cell autonomous component in SALS and provide an in vitro model system to investigate common disease mechanisms and evaluate potential therapies for SALS and FALS."], "structured": false}
{"doc_id": 2028532, "title": "High-intensity functional exercise program and protein-enriched energy supplement for older persons dependent in activities of daily living: a randomised controlled trial.", "abstract": ["The aims of this randomised controlled trial were to determine if a high-intensity functional exercise program improves balance, gait ability, and lower-limb strength in older persons dependent in activities of daily living and if an intake of protein-enriched energy supplement immediately after the exercises increases the effects of the training.", "One hundred and ninety-one older persons dependent in activities of daily living, living in residential care facilities, and with a Mini-Mental State Examination (MMSE) score of ?", "10 participated.", "They were randomised to a high-intensity functional exercise program or a control activity, which included 29 sessions over 3 months, as well as to protein-enriched energy supplement or placebo.", "Berg Balance Scale, self-paced and maximum gait speed, and one-repetition maximum in lower-limb strength were followed-up at three and six months and analysed by 2 x 2 factorial ANCOVA, using the intention-to-treat principle.", "At three months, the exercise group had improved significantly in self-paced gait speed compared with the control group (mean difference 0.04 m/s, p = 0.02).", "At six months, there were significant improvements favouring the exercise group for Berg Balance Scale (1.9 points, p = 0.05), self-paced gait speed (0.05 m/s, p = 0.009), and lower-limb strength (10.8 kg, p = 0.03).", "No interaction effects were seen between the exercise and nutrition interventions.", "In conclusion, a high-intensity functional exercise program has positive long-term effects in balance, gait ability, and lower-limb strength for older persons dependent in activities of daily living.", "An intake of protein-enriched energy supplement immediately after the exercises does not appear to increase the effects of the training."], "structured": false}
{"doc_id": 2030623, "title": "Inhibition of fatty acid oxidation modulates immunosuppressive functions of myeloid-derived suppressor cells and enhances cancer therapies", "abstract": ["Myeloid-derived suppressor cells (MDSC) promote tumor growth by inhibiting T-cell immunity and promoting malignant cell proliferation and migration.", "The therapeutic potential of blocking MDSC in tumors has been limited by their heterogeneity, plasticity, and resistance to various chemotherapy agents.", "Recent studies have highlighted the role of energy metabolic pathways in the differentiation and function of immune cells; however, the metabolic characteristics regulating MDSC remain unclear.", "We aimed to determine the energy metabolic pathway(s) used by MDSC, establish its impact on their immunosuppressive function, and test whether its inhibition blocks MDSC and enhances antitumor therapies.", "Using several murine tumor models, we found that tumor-infiltrating MDSC (T-MDSC) increased fatty acid uptake and activated fatty acid oxidation (FAO).", "This was accompanied by an increased mitochondrial mass, upregulation of key FAO enzymes, and increased oxygen consumption rate.", "Pharmacologic inhibition of FAO blocked immune inhibitory pathways and functions in T-MDSC and decreased their production of inhibitory cytokines.", "FAO inhibition alone significantly delayed tumor growth in a T-cell-dependent manner and enhanced the antitumor effect of adoptive T-cell therapy.", "Furthermore, FAO inhibition combined with low-dose chemotherapy completely inhibited T-MDSC immunosuppressive effects and induced a significant antitumor effect.", "Interestingly, a similar increase in fatty acid uptake and expression of FAO-related enzymes was found in human MDSC in peripheral blood and tumors.", "These results support the possibility of testing FAO inhibition as a novel approach to block MDSC and enhance various cancer therapies."], "structured": false}
{"doc_id": 2032877, "title": "Predicting mortality of patients hospitalized for acutely exacerbated chronic obstructive pulmonary disease.", "abstract": ["PURPOSE To identify factors affecting the short-term prognosis of patients with acutely exacerbated chronic obstructive pulmonary disease (COPD).   \n", "PATIENTS AND METHODS The 590 patients having COPD as primary disease who were hospitalized in the pneumology unit of a university hospital from 1981 to 1990 were studied.", "A standardized protocol for the treatment of acutely exacerbated COPD was adopted for all the patients.", "The patient records were retrospectively analyzed by two observers, and 23 clinical and laboratory variables defining the patient status on admission were collected.", "Age and arterial gas data were also taken into account, and the outcome mortality was recorded.", "Interobserver reproducibility was tested by computing the kappa coefficient and Spearman's rho for dichotomous and continuous variables, respectively.", "The relationship of clinical and laboratory factors to the outcome was assessed first by univariate analysis and then by a logistic regression analysis assessing the independent predictive role of variables previously shown to be univariately correlated with mortality.   \n", "RESULTS The mortality rate was 14.4%.", "The logistic regression analysis identified four independent predictors of death: age (odds ratio [OR] 1.07; 95% confidence interval [CI] 1.04 to 1.11), alveolar-arterial oxygen gradient greater than 41 mm Hg (OR 2.33; 95% CI 1.39 to 3.90), ventricular arrhythmias (OR 1.91; 95% CI 1.10 to 3.31), and atrial fibrillation (OR 2.27; 95% CI 1.14 to 4.51).   \n", "CONCLUSIONS Patients with acutely exacerbated COPD having a high risk of death can be identified at the time of admission.", "Variables reflecting heart dysfunction are important determinants of this risk.", "Among pulmonary function data, only alveolar-arterial oxygen gradient contributes to the predictive model."], "structured": true}
{"doc_id": 2033917, "title": "Clathrin is required for the function of the mitotic spindle", "abstract": ["Clathrin has an established function in the generation of vesicles that transfer membrane and proteins around the cell.", "The formation of clathrin-coated vesicles occurs continuously in non-dividing cells, but is shut down during mitosis, when clathrin concentrates at the spindle apparatus.", "Here, we show that clathrin stabilizes fibres of the mitotic spindle to aid congression of chromosomes.", "Clathrin bound to the spindle directly by the amino-terminal domain of clathrin heavy chain.", "Depletion of clathrin heavy chain using RNA interference prolonged mitosis; kinetochore fibres were destabilized, leading to defective congression of chromosomes to the metaphase plate and persistent activation of the spindle checkpoint.", "Normal mitosis was rescued by clathrin triskelia but not the N-terminal domain of clathrin heavy chain, indicating that stabilization of kinetochore fibres was dependent on the unique structure of clathrin.", "The importance of clathrin for normal mitosis may be relevant to understanding human cancers that involve gene fusions of clathrin heavy chain."], "structured": false}
{"doc_id": 2039912, "title": "The origin and neuronal function of in vivo nonsynaptic glutamate.", "abstract": ["Basal extracellular glutamate sampled in vivo is present in micromolar concentrations in the extracellular space outside the synaptic cleft, and neither the origin nor the function of this glutamate is known.", "This report reveals that blockade of glutamate release from the cystine-glutamate antiporter produced a significant decrease (60%) in extrasynaptic glutamate levels in the rat striatum, whereas blockade of voltage-dependent Na+ and Ca2+ channels produced relatively minimal changes (0-30%).", "This indicates that the primary origin of in vivo extrasynaptic glutamate in the striatum arises from nonvesicular glutamate release by the cystine-glutamate antiporter.", "By measuring [35S]cystine uptake, it was shown that similar to vesicular release, the activity of the cystine-glutamate antiporter is negatively regulated by group II metabotropic glutamate receptors (mGluR2/3) via a cAMP-dependent protein kinase mechanism.", "Extracellular glutamate derived from the antiporter was shown to regulate extracellular levels of glutamate and dopamine.", "Infusion of the mGluR2/3 antagonist (RS)-1-amino-5-phosphonoindan-1-carboxylic acid (APICA) increased extracellular glutamate levels, and previous blockade of the antiporter prevented the APICA-induced rise in extracellular glutamate.", "This suggests that glutamate released from the antiporter is a source of endogenous tone on mGluR2/3.", "Blockade of the antiporter also produced an increase in extracellular dopamine that was reversed by infusing the mGluR2/3 agonist (2R,4R)-4-aminopyrrolidine-2,4-dicarboxlylate, indicating that antiporter-derived glutamate can modulate dopamine transmission via mGluR2/3 heteroreceptors.", "These results suggest that nonvesicular release from the cystine-glutamate antiporter is the primary source of in vivo extracellular glutamate and that this glutamate can modulate both glutamate and dopamine transmission."], "structured": false}
{"doc_id": 2042250, "title": "Disease-associated functions of IL-33: the new kid in the IL-1 family", "abstract": ["Interleukin-33 (IL-33), a newly described member of the IL-1 family, is expressed by many cell types following pro-inflammatory stimulation and is thought to be released on cell lysis.", "The IL-33 receptor, consisting of ST2 and IL-1 receptor accessory protein, is also widely expressed, particularly by T helper 2 (TH2) cells and mast cells.", "IL-33 is host-protective against helminth infection and reduces atherosclerosis by promoting TH2-type immune responses.", "However, IL-33 can also promote the pathogenesis of asthma by expanding TH2 cells and mediate joint inflammation, atopic dermatitis and anaphylaxis by mast cell activation.", "Thus IL-33 could be a new target for therapeutic intervention across a range of diseases."], "structured": false}
{"doc_id": 2048139, "title": "Interferon alpha therapy for hepatitis C: treatment completion and response rates among patients with substance use disorders", "abstract": ["BackgroundIndividuals with substance use disorders (SUDs) are at increased risk for hepatitis C viral infection (HCV), and few studies have explored their treatment responses empirically.", "The objective of this study was to assess interferon alpha therapy (IFN) completion and response rates among patients with HCV who had a history of comorbid SUDs.", "More data is needed to inform treatment strategies and guidelines for these patients.", "Using a medical record database, information was retrospectively collected on 307,437 veterans seen in the Veterans Integrated Service Network 20 (VISN 20) of the Veterans Healthcare Administration (VHA) between 1998 and 2003.", "For patients treated with any type of IFN (including regular or pegylated IFN) or combination therapy (IFN and ribavirin) who had a known HCV genotype, IFN completion and response rates were compared among patients with a history of SUD (SUD+ Group) and patients without a history of SUD (SUD- Group).ResultsOdds ratio analyses revealed that compared with the SUD- Group, the SUD+ Group was equally likely to complete IFN therapy if they had genotypes 2 and 3 (73.1% vs. 68.0%), and if they had genotypes 1 and 4 (39.5% vs. 39.9%).", "Within the sample of all patients who began IFN therapy, the SUD- and SUD+ groups were similarly likely to achieve an end of treatment response (genotypes 2 and 3, 52.8% vs. 54.3%; genotypes 1 and 4, 24.5% vs. 24.8%) and a sustained viral response (genotypes 2 and 3, 42.6% vs. 41.1%; genotypes 1 and 4: 16.0% vs. 22.3%).ConclusionIndividuals with and without a history of SUD responded to antiviral therapy for HCV at similar rates.", "Collectively, these findings suggest that patients who have co-morbid SUD and HCV diagnoses can successfully complete a course of antiviral therapy."], "structured": false}
{"doc_id": 2052720, "title": "Association between infection with Helicobacter pylori and risk of gastric cancer: evidence from a prospective investigation.", "abstract": ["OBJECTIVE To investigate the association between gastric cancer and prior infection with Helicobacter pylori.   \n", "DESIGN Case-control comparison of prevalence of IgG antibodies to H pylori in blood samples collected prospectively, before diagnosis of gastric cancer in the cases.", "Presence of H pylori antibody (greater than 10 micrograms IgG/ml) determined by enzyme linked immunosorbent assay (ELISA).   ", "SUBJECTS 29 men with a subsequent diagnosis of gastric cancer and 116 aged matched controls selected from over 22,000 middle aged men participating in two ongoing cohort studies (the British United Provident Association study and the Caerphilly collaborative heart disease study), who had provided blood samples during 1975-1982.   \n", "RESULTS 20 of the 29 cases (69%) and 54 of the 116 controls (47%) were positive for H pylori specific antibody.", "The median specific IgG concentration was significantly higher in the cases than controls (90 micrograms/ml v 3.6 micrograms/ml, p less than 0.01).", "The estimated odds ratio for the risk of gastric cancer in those with a history of infection with H pylori was 2.77 (95% confidence interval 1.04 to 7.97, 2p = 0.039).   \n", "CONCLUSIONS H pylori infection may be an important cause of gastric cancer; between 35% and 55% of all cases may be associated with such an infection."], "structured": true}
{"doc_id": 2053540, "title": "Oncostatin M and leukemia inhibitory factor do not use the same functional receptor in mice.", "abstract": ["Oncostatin M (OSM) and leukemia inhibitory factor (LIF) are members of the interleukin-6 (IL-6) subfamily of cytokines that use a common signal transducer gp130.", "Human OSM (hOSM) and LIF share a functional high-affinity receptor that is composed of gp130 and LIF receptor beta subunit (LIFRbeta).", "A second high-affinity receptor for hOSM was recently found to be formed by gp130 and the hOSM receptor beta subunit.", "However, the nature of murine OSM (mOSM) and its receptors has remained unknown.", "Using the recently cloned mOSM cDNA, we produced recombinant mOSM and studied its biological activity and receptor structure.", "Murine hematopoietic cell lines M1 and DA1.a, an embryonic stem cell line CCE, and Ba/F3 transfectants expressing gp130 and LIFRbeta responded to murine LIF (mLIF) and hOSM equally well, while these cells responded to mOSM only at a 30-fold to 100-fold higher concentration than those of mLIF and hOSM.", "In contrast, NIH3T3 cells responded to mOSM, but not to mLIF and hOSM.", "Scatchard plot analyses showed that mOSM bound to gp130 with low-affinity (kd = 2.8 to 4.2 nmol/L) and that the binding affinity did not increase in the presence of LIFRbeta.", "However, mOSM bound to NIH3T3 cells with high-affinity (kd = 660 pmol/L), whereas mLIF did not bind to NIH3T3 cells at all.", "These results indicate that unlike hOSM, mOSM and mLIF do not share the same functional receptor, and mOSM delivers signals only through its specific receptor complex.", "Further studies in mice will define the physiological roles of OSM."], "structured": false}
{"doc_id": 2056197, "title": "Multifunctional in vivo vascular imaging using near-infrared II fluorescence", "abstract": ["In vivo real-time epifluorescence imaging of mouse hind limb vasculatures in the second near-infrared region (NIR-II) is performed using single-walled carbon nanotubes as fluorophores.", "Both high spatial (\u223c30 \u03bcm) and temporal (<200 ms per frame) resolution for small-vessel imaging are achieved at 1\u20133 mm deep in the hind limb owing to the beneficial NIR-II optical window that affords deep anatomical penetration and low scattering.", "This spatial resolution is unattainable by traditional NIR imaging (NIR-I) or microscopic computed tomography, and the temporal resolution far exceeds scanning microscopic imaging techniques.", "Arterial and venous vessels are unambiguously differentiated using a dynamic contrast-enhanced NIR-II imaging technique on the basis of their distinct hemodynamics.", "Further, the deep tissue penetration and high spatial and temporal resolution of NIR-II imaging allow for precise quantifications of blood velocity in both normal and ischemic femoral arteries, which are beyond the capabilities of ultrasonography at lower blood velocities."], "structured": false}
{"doc_id": 2058909, "title": "Colorectal cancer survival in socioeconomic groups in England: variation is mainly in the short term after diagnosis.", "abstract": ["UNLABELLED The objective of this study was to examine differences in cancer survival between socioeconomic groups in England, with particular attention to survival in the short term of follow-up.   \n", "PATIENTS AND METHODS Individuals diagnosed with colorectal cancer between 1996 and 2004 in England were identified from cancer registry records.", "Five-year cumulative relative survival and excess death rates were computed.   \n", "RESULTS For colon cancer there was a very high excess death rate in the first month of follow-up, and the excess death rate was highest in the socioeconomically deprived groups.", "In subsequent periods, excess mortality rates were much lower and there was less socioeconomic variation.", "The pattern of variation in excess death rates was generally similar in rectal cancer but the socioeconomic difference in death rates persisted several years longer.", "If the excess death rates in the entire colorectal cancer patient population were the same as those observed in the most affluent socioeconomic quintile, the annual reduction would be 360 deaths in colon cancer and 336 deaths in rectal cancer patients.", "These deaths occurred almost entirely in the first month and the first year after diagnosis.   \n", "CONCLUSION Recent developments in the national cancer control agenda have included an increasing emphasis on outcome measures, with short-term cancer survival an operational measure of variation and progress in cancer control.", "In providing clues to the nature of the survival differences between socioeconomic groups, the results presented here give strong support for this strategy."], "structured": true}
{"doc_id": 2060137, "title": "Cardiac myocyte remodeling mediated by N-cadherin-dependent mechanosensing.", "abstract": ["Cell-to-cell adhesions are crucial in maintaining the structural and functional integrity of cardiac cells.", "Little is known about the mechanosensitivity and mechanotransduction of cell-to-cell interactions.", "Most studies of cardiac mechanotransduction and myofibrillogenesis have focused on cell-extracellular matrix (ECM)-specific interactions.", "This study assesses the direct role of intercellular adhesion, specifically that of N-cadherin-mediated mechanotransduction, on the morphology and internal organization of neonatal ventricular cardiac myocytes.", "The results show that cadherin-mediated cell attachments are capable of eliciting a cytoskeletal network response similar to that of integrin-mediated force response and transmission, affecting myofibrillar organization, myocyte shape, and cortical stiffness.", "Traction forces mediated by N-cadherin were shown to be comparable to those sustained by ECM.", "The directional changes in predicted traction forces as a function of imposed loads (gel stiffness) provide the added evidence that N-cadherin is a mechanoresponsive adhesion receptor.", "Strikingly, the mechanical sensitivity response (gain) in terms of the measured cell-spread area as a function of imposed load (adhesive substrate rigidity) was consistently higher for N-cadherin-coated surfaces compared with ECM protein-coated surfaces.", "In addition, the cytoskeletal architecture of myocytes on an N-cadherin adhesive microenvironment was characteristically different from that on an ECM environment, suggesting that the two mechanotransductive cell adhesion systems may play both independent and complementary roles in myocyte cytoskeletal spatial organization.", "These results indicate that cell-to-cell-mediated force perception and transmission are involved in the organization and development of cardiac structure and function."], "structured": false}
{"doc_id": 2061878, "title": "NEAT1: A novel cancer\u2010related long non\u2010coding RNA", "abstract": ["Aberrant overexpression of the long non-coding RNA NEAT1 (nuclear paraspeckle assembly transcript 1) has been documented in different types of solid tumours, such as lung cancer, oesophageal cancer, colorectal cancer and hepatocellular carcinoma, in which its high levels are associated with poor prognosis.", "In contrast, NEAT1 is downregulated in acute promyelocytic leukaemia where it promotes leucocyte differentiation.", "In this review, we provide an overview of current evidence concerning the oncogenic role and potential clinical utilities of NEAT1.", "Further investigations are warranted to elucidate the upstream and downstream mechanisms of NEAT1 overexpression."], "structured": false}
{"doc_id": 2062382, "title": "The Function and Therapeutic Potential of Long Non-coding RNAs in Cardiovascular Development and Disease", "abstract": ["The popularization of genome-wide analyses and RNA sequencing led to the discovery that a large part of the human genome, while effectively transcribed, does not encode proteins.", "Long non-coding RNAs have emerged as critical regulators of gene expression in both normal and disease states.", "Studies of long non-coding RNAs expressed in the heart, in combination with gene association studies, revealed that these molecules are regulated during cardiovascular development and disease.", "Some long non-coding RNAs have been functionally implicated in cardiac pathophysiology and constitute potential therapeutic targets.", "Here, we review the current knowledge of the function of long non-coding RNAs in the cardiovascular system, with an emphasis on cardiovascular development and biology, focusing on hypertension, coronary artery disease, myocardial infarction, ischemia, and heart failure.", "We discuss potential therapeutic implications and the challenges of long non-coding RNA research, with directions for future research and translational focus."], "structured": false}
{"doc_id": 2078658, "title": "Oct4 links multiple epigenetic pathways to the pluripotency network", "abstract": ["Oct4 is a well-known transcription factor that plays fundamental roles in stem cell self-renewal, pluripotency, and somatic cell reprogramming.", "However, limited information is available on Oct4-associated protein complexes and their intrinsic protein-protein interactions that dictate Oct4's critical regulatory activities.", "Here we employed an improved affinity purification approach combined with mass spectrometry to purify Oct4 protein complexes in mouse embryonic stem cells (mESCs), and discovered many novel Oct4 partners important for self-renewal and pluripotency of mESCs.", "Notably, we found that Oct4 is associated with multiple chromatin-modifying complexes with documented as well as newly proved functional significance in stem cell maintenance and somatic cell reprogramming.", "Our study establishes a solid biochemical basis for genetic and epigenetic regulation of stem cell pluripotency and provides a framework for exploring alternative factor-based reprogramming strategies."], "structured": false}
{"doc_id": 2086909, "title": "Tet1 is dispensable for maintaining pluripotency and its loss is compatible with embryonic and postnatal development.", "abstract": ["The Tet family of enzymes (Tet1/2/3) converts 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC).", "Mouse embryonic stem cells (mESCs) highly express Tet1 and have an elevated level of 5hmC. Tet1 has been implicated in ESC maintenance and lineage specification in vitro but its precise function in development is not well defined.", "To establish the role of Tet1 in pluripotency and development, we have generated Tet1 mutant mESCs and mice.", "Tet1(-/-) ESCs have reduced levels of 5hmC and subtle changes in global gene expression, and are pluripotent and support development of live-born mice in tetraploid complementation assay, but display skewed differentiation toward trophectoderm in vitro.", "Tet1 mutant mice are viable, fertile, and grossly normal, though some mutant mice have a slightly smaller body size at birth.", "Our data suggest that Tet1 loss leading to a partial reduction in 5hmC levels does not affect pluripotency in ESCs and is compatible with embryonic and postnatal development."], "structured": false}
{"doc_id": 2095573, "title": "LDL-cholesterol concentrations: a genome-wide association study", "abstract": ["BACKGROUND LDL cholesterol has a causal role in the development of cardiovascular disease.", "Improved understanding of the biological mechanisms that underlie the metabolism and regulation of LDL cholesterol might help to identify novel therapeutic targets.", "We therefore did a genome-wide association study of LDL-cholesterol concentrations.   \n", "METHODS We used genome-wide association data from up to 11,685 participants with measures of circulating LDL-cholesterol concentrations across five studies, including data for 293 461 autosomal single nucleotide polymorphisms (SNPs) with a minor allele frequency of 5% or more that passed our quality control criteria.", "We also used data from a second genome-wide array in up to 4337 participants from three of these five studies, with data for 290,140 SNPs.", "We did replication studies in two independent populations consisting of up to 4979 participants.", "Statistical approaches, including meta-analysis and linkage disequilibrium plots, were used to refine association signals; we analysed pooled data from all seven populations to determine the effect of each SNP on variations in circulating LDL-cholesterol concentrations.   \n", "FINDINGS In our initial scan, we found two SNPs (rs599839 [p=1.7x10(-15)] and rs4970834 [p=3.0x10(-11)]) that showed genome-wide statistical association with LDL cholesterol at chromosomal locus 1p13.3.", "The second genome screen found a third statistically associated SNP at the same locus (rs646776 [p=4.3x10(-9)]).", "Meta-analysis of data from all studies showed an association of SNPs rs599839 (combined p=1.2x10(-33)) and rs646776 (p=4.8x10(-20)) with LDL-cholesterol concentrations.", "SNPs rs599839 and rs646776 both explained around 1% of the variation in circulating LDL-cholesterol concentrations and were associated with about 15% of an SD change in LDL cholesterol per allele, assuming an SD of 1 mmol/L.   INTERPRETATION We found evidence for a novel locus for LDL cholesterol on chromosome 1p13.3.", "These results potentially provide insight into the biological mechanisms that underlie the regulation of LDL cholesterol and might help in the discovery of novel therapeutic targets for cardiovascular disease."], "structured": true}
{"doc_id": 2097256, "title": "Population Density, Water Supply, and the Risk of Dengue Fever in Vietnam: Cohort Study and Spatial Analysis", "abstract": ["BACKGROUND Aedes aegypti, the major vector of dengue viruses, often breeds in water storage containers used by households without tap water supply, and occurs in high numbers even in dense urban areas.", "We analysed the interaction between human population density and lack of tap water as a cause of dengue fever outbreaks with the aim of identifying geographic areas at highest risk.   \n", "METHODS AND FINDINGS We conducted an individual-level cohort study in a population of 75,000 geo-referenced households in Vietnam over the course of two epidemics, on the basis of dengue hospital admissions (n = 3,013).", "We applied space-time scan statistics and mathematical models to confirm the findings.", "We identified a surprisingly narrow range of critical human population densities between around 3,000 to 7,000 people/km\u00b2 prone to dengue outbreaks.", "In the study area, this population density was typical of villages and some peri-urban areas.", "Scan statistics showed that areas with a high population density or adequate water supply did not experience severe outbreaks.", "The risk of dengue was higher in rural than in urban areas, largely explained by lack of piped water supply, and in human population densities more often falling within the critical range.", "Mathematical modeling suggests that simple assumptions regarding area-level vector/host ratios may explain the occurrence of outbreaks.   \n", "CONCLUSIONS Rural areas may contribute at least as much to the dissemination of dengue fever as cities.", "Improving water supply and vector control in areas with a human population density critical for dengue transmission could increase the efficiency of control efforts.", "Please see later in the article for the Editors' Summary."], "structured": true}
{"doc_id": 2099400, "title": "Helicobacter pylori induces AGS cell motility and elongation via independent signaling pathways.", "abstract": ["Helicobacter pylori induces motogenic and cytoskeletal responses in gastric epithelial cells.", "We demonstrate that these responses can be induced via independent signaling pathways that often occur in parallel.", "The cag pathogenicity island appears to be nonessential for induction of motility, whereas the elongation phenotype depends on translocation and phosphorylation of CagA."], "structured": false}
{"doc_id": 2107238, "title": "The Sequence Alignment/Map format and SAMtools", "abstract": ["SUMMARY The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms.", "It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released.", "SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments.   ", "AVAILABILITY http://samtools.sourceforge.net."], "structured": false}
{"doc_id": 2119889, "title": "Characterization of two classes of small molecule inhibitors of Arp2/3 complex", "abstract": ["Polymerization of actin filaments directed by the actin-related protein (Arp)2/3 complex supports many types of cellular movements.", "However, questions remain regarding the relative contributions of Arp2/3 complex versus other mechanisms of actin filament nucleation to processes such as path finding by neuronal growth cones; this is because of the lack of simple methods to inhibit Arp2/3 complex reversibly in living cells.", "Here we describe two classes of small molecules that bind to different sites on the Arp2/3 complex and inhibit its ability to nucleate actin filaments.", "CK-0944636 binds between Arp2 and Arp3, where it appears to block movement of Arp2 and Arp3 into their active conformation.", "CK-0993548 inserts into the hydrophobic core of Arp3 and alters its conformation.", "Both classes of compounds inhibit formation of actin filament comet tails by Listeria and podosomes by monocytes.", "Two inhibitors with different mechanisms of action provide a powerful approach for studying the Arp2/3 complex in living cells."], "structured": false}
{"doc_id": 2121272, "title": "Stresses at the cell-to-substrate interface during locomotion of fibroblasts", "abstract": ["Recent technological improvements in the elastic substrate method make it possible to produce spatially resolved measurements of the tractions exerted by single motile cells.", "In this study we have applied these developments to produce maps of the tractions exerted by 3T3 fibroblasts during steady locomotion.", "The resulting images have a spatial resolution of approximately 5 micrometers and a maximum intensity of approximately 10(2) kdyn/cm2 (10(4) pN/micrometers2).", "We find that the propulsive thrust for fibroblast locomotion, approximately 0.2 dyn, is imparted to the substratum within 15 micrometers of the leading edge.", "These observations demonstrate that the lamellipodium of the fibroblast is able to generate intense traction stress.", "The cell body and posterior seem to be mechanically passive structures pulled forward entirely by this action."], "structured": false}
{"doc_id": 2130391, "title": "Cancer-associated adipocytes exhibit an activated phenotype and contribute to breast cancer invasion.", "abstract": ["Early local tumor invasion in breast cancer results in a likely encounter between cancer cells and mature adipocytes, but the role of these fat cells in tumor progression remains unclear.", "We show that murine and human tumor cells cocultivated with mature adipocytes exhibit increased invasive capacities in vitro and in vivo, using an original two-dimensional coculture system.", "Likewise, adipocytes cultivated with cancer cells also exhibit an altered phenotype in terms of delipidation and decreased adipocyte markers associated with the occurrence of an activated state characterized by overexpression of proteases, including matrix metalloproteinase-11, and proinflammatory cytokines [interleukin (IL)-6, IL-1\u03b2].", "In the case of IL-6, we show that it plays a key role in the acquired proinvasive effect by tumor cells.", "Equally important, we confirm the presence of these modified adipocytes in human breast tumors by immunohistochemistry and quantitative PCR.", "Interestingly, the tumors of larger size and/or with lymph nodes involvement exhibit the higher levels of IL-6 in tumor surrounding adipocytes.", "Collectively, all our data provide in vitro and in vivo evidence that (i) invasive cancer cells dramatically impact surrounding adipocytes; (ii) peritumoral adipocytes exhibit a modified phenotype and specific biological features sufficient to be named cancer-associated adipocytes (CAA); and (iii) CAAs modify the cancer cell characteristics/phenotype leading to a more aggressive behavior.", "Our results strongly support the innovative concept that adipocytes participate in a highly complex vicious cycle orchestrated by cancer cells to promote tumor progression that might be amplified in obese patients."], "structured": false}
{"doc_id": 2138767, "title": "Prevalence of cardiovascular disease risk factor in the Chinese population: the 2007-2008 China National Diabetes and Metabolic Disorders Study.", "abstract": ["AIMS Cardiovascular disease (CVD) is now the most prevalent and debilitating disease affecting the Chinese population.", "The goal of the present manuscript was to analyse cardiovascular risk factors and the prevalence of non-fatal CVDs from data gathered from the 2007-2008 China National Diabetes and Metabolic Disorders Study.   \n", "METHODS AND RESULTS A nationally representative sample of 46 239 adults, 20 years of age or older, was randomly recruited using a multistage stratified design method.", "Lifestyle factors, diagnosis of CVD, stroke, diabetes, and family history of each subject were collected, and an oral glucose tolerance test or a standard meal test was performed.", "Various non-fatal CVDs were reported by the subjects.", "SUDAAN software was used to perform all weighted statistical analyses, with P < 0.05 considered statistically significant.", "The prevalence of coronary heart disease, stroke, and CVDs was 0.74, 1.07, and 1.78% in males; and 0.51, 0.60, and 1.10% in females, respectively.", "The presence of CVDs increased with age in both males and females.", "The prevalence of being overweight or obese, hypertension, dyslipidaemia, or hyperglycaemia was 36.67, 30.09, 67.43, and 26.69% in males; and 29.77, 24.79, 63.98, and 23.62% in females, respectively.", "In the total sample of 46 239 patients, the prevalence of one subject having 1, 2, 3, or \u22654 of the 5 defined risk factors (i.e. smoking, overweight or obese, hypertension, dyslipidaemia, or hyperglycaemia) was 31.17, 27.38, 17.76, and 10.19%, respectively.", "Following adjustment for gender and age, the odds ratio of CVDs for those who had 1, 2, 3, or \u22654 risk factors was 2.36, 4.24, 4.88, and 7.22, respectively, when compared with patients with no risk factors.   \n", "CONCLUSION Morbidity attributed to the five defined cardiovascular risk factors was high in the Chinese population, with multiple risk factors present in the same individual.", "Therefore, reasonable prevention strategies should be designed to attenuate the rapid rise in cardiovascular morbidity."], "structured": true}
{"doc_id": 2138843, "title": "Microvascular and Macrovascular Complications of Diabetes", "abstract": ["Diabetes is a group of chronic diseases characterized by hyperglycemia.", "Modern medical care uses a vast array of lifestyle and pharmaceutical interventions aimed at preventing and controlling hyperglycemia.", "In addition to ensuring the adequate delivery of glucose to the tissues of the body, treatment of diabetes attempts to decrease the likelihood that the tissues of the body are harmed by hyperglycemia.  ", "The importance of protecting the body from hyperglycemia cannot be overstated; the direct and indirect effects on the human vascular tree are the major source of morbidity and mortality in both type 1 and type 2 diabetes.", "Generally, the injurious effects of hyperglycemia are separated into macrovascular complications (coronary artery disease, peripheral arterial disease, and stroke) and microvascular complications (diabetic nephropathy, neuropathy, and retinopathy).", "It is important for physicians to understand the relationship between diabetes and vascular disease because the prevalence of diabetes continues to increase in the United States, and the clinical armamentarium for primary and secondary prevention of these complications is also expanding.  ", "### Diabetic retinopathy  Diabetic retinopathy may be the most common microvascular complication of diabetes.", "It is responsible for \u223c 10,000 new cases of blindness every year in the United States alone.1 The risk of developing diabetic retinopathy or other microvascular complications of diabetes depends on both the duration and the severity of hyperglycemia.", "Development of diabetic retinopathy in patients with type 2 diabetes was found to be related to both severity of hyperglycemia and presence of hypertension in the U.K. Prospective Diabetes Study (UKPDS), and most patients with type 1 diabetes develop evidence of retinopathy within 20 years of diagnosis.2,3 Retinopathy may begin to develop as early as 7 years before the diagnosis of diabetes in patients with type 2 diabetes.1 There are several proposed pathological mechanisms by which diabetes may lead \u2026"], "structured": false}
{"doc_id": 2139357, "title": "Involvement of S-nitrosylation of actin in inhibition of neurotransmitter release by nitric oxide", "abstract": ["BACKGROUND The role of the diffusible messenger nitric oxide (NO) in the regulation of pain transmission is still a debate of matter, pro-nociceptive and/or anti-nociceptive.", "S-Nitrosylation, the reversible post-translational modification of selective cysteine residues in proteins, has emerged as an important mechanism by which NO acts as a signaling molecule.", "The occurrence of S-nitrosylation in the spinal cord and its targets that may modulate pain transmission remain unclarified.", "The \"biotin-switch\" method and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry were employed for identifying S-nitrosylated proteins.   \n", "RESULTS Here we show that actin was a major protein S-nitrosylated in the spinal cord by the NO donor, S-nitroso-N-acetyl-DL-penicillamine (SNAP).", "Interestingly, actin was S-nitrosylated, more in the S2 fraction than in the P2 fraction of the spinal homogenate.", "Treatment of PC12 cells with SNAP caused rapid S-nitrosylation of actin and inhibited dopamine release from the cells.", "Just like cytochalasin B, which depolymerizes actin, SNAP decreased the amount of filamentous actin cytoskeleton just beneath the membrane.", "The inhibition of dopamine release was not attenuated by inhibitors of soluble guanylyl cyclase and cGMP-dependent protein kinase.   \n", "CONCLUSION The present study demonstrates that actin is a major S-nitrosylated protein in the spinal cord and suggests that NO directly regulates neurotransmitter release by S-nitrosylation in addition to the well-known phosphorylation by cGMP-dependent protein kinase."], "structured": true}
{"doc_id": 2140497, "title": "Independent Association of Lobular Involution and Mammographic Breast Density With Breast Cancer Risk", "abstract": ["BACKGROUND Lobular involution, or age-related atrophy of breast lobules, is inversely associated with breast cancer risk, and mammographic breast density (MBD) is positively associated with breast cancer risk.   \n", "METHODS To evaluate whether lobular involution and MBD are independently associated with breast cancer risk in women with benign breast disease, we performed a nested cohort study among women (n = 2666) with benign breast disease diagnosed at Mayo Clinic between January 1, 1985, and December 31, 1991 and a mammogram available within 6 months of the diagnosis.", "Women were followed up for an average of 13.3 years to document any breast cancer incidence.", "Lobular involution was categorized as none, partial, or complete; parenchymal pattern was classified using the Wolfe classification as N1 (nondense), P1, P2 (ductal prominence occupying <25%, or >25% of the breast, respectively), or DY (extremely dense).", "Hazard ratios (HRs) and 95% confidence intervals (CIs) to assess associations of lobular involution and MBD with breast cancer risk were estimated using adjusted Cox proportional hazards model.", "All tests of statistical significance were two-sided.   \n", "RESULTS After adjustment for MBD, having no or partial lobular involution was associated with a higher risk of breast cancer than having complete involution (none: HR of breast cancer incidence = 2.62, 95% CI = 1.39 to 4.94; partial: HR of breast cancer incidence = 1.61, 95% CI = 1.03 to 2.53; P(trend) = .002).", "Similarly, after adjustment for involution, having dense breasts was associated with higher risk of breast cancer than having nondense breasts (for DY: HR of breast cancer incidence = 1.67, 95% CI = 1.03 to 2.73; for P2: HR of breast cancer incidence = 1.96, 95% CI = 1.20 to 3.21; for P1: HR of breast cancer incidence = 1.23, 95% CI = 0.67 to 2.26; P(trend) = .02).", "Having a combination of no involution and dense breasts was associated with higher risk of breast cancer than having complete involution and nondense breasts (HR of breast cancer incidence = 4.08, 95% CI = 1.72 to 9.68; P = .006).   \n", "CONCLUSION Lobular involution and MBD are independently associated with breast cancer incidence; combined, they are associated with an even greater risk for breast cancer."], "structured": true}
{"doc_id": 2140513, "title": "Pleiotropy as a mechanism to stabilize cooperation", "abstract": ["Most genes affect many traits.", "This phenomenon, known as pleiotropy, is a major constraint on evolution because adaptive change in one trait may be prevented because it would compromise other traits affected by the same genes.", "Here we show that pleiotropy can have an unexpected effect and benefit one of the most enigmatic of adaptations\u2014cooperation.", "A spectacular act of cooperation occurs in the social amoeba Dictyostelium discoideum, in which some cells die to form a stalk that holds the other cells aloft as reproductive spores.", "We have identified a gene, dimA, in D. discoideum that has two contrasting effects.", "It is required to receive the signalling molecule DIF-1 that causes differentiation into prestalk cells.", "Ignoring DIF-1 and not becoming prestalk should allow cells to cheat by avoiding the stalk.", "However, we find that in aggregations containing the wild-type cells, lack of the dimA gene results in exclusion from spores.", "This pleiotropic linkage of stalk and spore formation limits the potential for cheating in D. discoideum because defecting on prestalk cell production results in an even greater reduction in spores.", "We propose that the evolution of pleiotropic links between cheating and personal costs can stabilize cooperative adaptations."], "structured": false}
{"doc_id": 2147704, "title": "The homeobox gene goosecoid controls cell migration in Xenopus embryos.", "abstract": ["Goosecoid (gsc), a homeobox gene expressed specifically in the dorsal blastopore lip of the Xenopus gastrula, is considered to play an important role in Spemann's organizer phenomenon.", "Lineage tracing and time-lapse microscopy were used to follow the fate of embryonic cells microinjected with gsc mRNA.", "Microinjected gsc has non-cell autonomous effects, recruiting neighboring uninjected cells into a twinned dorsal axis.", "Ectopic expression of gsc mRNA in ventral blastomeres as well as overexpression of gsc in dorsal blastomeres leads to cell movement toward the anterior of the embryo.", "The results suggest a function for gsc in the control of gastrulation movements in groups of cells, but not in dissociated cells, and demonstrate that a vertebrate homeobox gene can regulate region-specific cell migration."], "structured": false}
{"doc_id": 2151983, "title": "Epigenetic switch involved in activation of pioneer factor FOXA1-dependent enhancers.", "abstract": ["Transcription factors (TFs) bind specifically to discrete regions of mammalian genomes called cis-regulatory elements.", "Among those are enhancers, which play key roles in regulation of gene expression during development and differentiation.", "Despite the recognized central regulatory role exerted by chromatin in control of TF functions, much remains to be learned regarding the chromatin structure of enhancers and how it is established.", "Here, we have analyzed on a genomic-scale enhancers that recruit FOXA1, a pioneer transcription factor that triggers transcriptional competency of these cis-regulatory sites.", "Importantly, we found that FOXA1 binds to genomic regions showing local DNA hypomethylation and that its cell-type-specific recruitment to chromatin is linked to differential DNA methylation levels of its binding sites.", "Using neural differentiation as a model, we showed that induction of FOXA1 expression and its subsequent recruitment to enhancers is associated with DNA demethylation.", "Concomitantly, histone H3 lysine 4 methylation is induced at these enhancers.", "These epigenetic changes may both stabilize FOXA1 binding and allow for subsequent recruitment of transcriptional regulatory effectors.", "Interestingly, when cloned into reporter constructs, FOXA1-dependent enhancers were able to recapitulate their cell type specificity.", "However, their activities were inhibited by DNA methylation.", "Hence, these enhancers are intrinsic cell-type-specific regulatory regions of which activities have to be potentiated by FOXA1 through induction of an epigenetic switch that includes notably DNA demethylation."], "structured": false}
{"doc_id": 2158500, "title": "Leptin treatment ameliorates anxiety in ob/ob obese mice.", "abstract": ["We investigated whether or not administered leptin influences anxiety-like behavior in ob/ob mice.", "Repeated intraperitoneal administrations of leptin were continued for 5 days.", "Anxiety was assessed in the standard elevated plus maze.", "Body weight was measured daily.", "Repeated administrations of leptin significantly increased the percentage of the total number of entries in the open arms and the number of total entries.", "The body weight was significantly reduced by 13.2% after treatment.", "Leptin treatment ameliorated not only obesity but also anxiety in ob/ob mice.", "Our results indicate that the treatment of obesity may lead to the solution of psychological problems."], "structured": false}
{"doc_id": 2158516, "title": "Predicting new molecular targets for known drugs", "abstract": ["Although drugs are intended to be selective, at least some bind to several physiological targets, explaining side effects and efficacy.", "Because many drug-target combinations exist, it would be useful to explore possible interactions computationally.", "Here we compared 3,665 US Food and Drug Administration (FDA)-approved and investigational drugs against hundreds of targets, defining each target by its ligands.", "Chemical similarities between drugs and ligand sets predicted thousands of unanticipated associations.", "Thirty were tested experimentally, including the antagonism of the beta(1) receptor by the transporter inhibitor Prozac, the inhibition of the 5-hydroxytryptamine (5-HT) transporter by the ion channel drug Vadilex, and antagonism of the histamine H(4) receptor by the enzyme inhibitor Rescriptor.", "Overall, 23 new drug-target associations were confirmed, five of which were potent (<100 nM).", "The physiological relevance of one, the drug N,N-dimethyltryptamine (DMT) on serotonergic receptors, was confirmed in a knockout mouse.", "The chemical similarity approach is systematic and comprehensive, and may suggest side-effects and new indications for many drugs."], "structured": false}
{"doc_id": 2159648, "title": "Bone loss and vascular calcification: A bi-directional interplay?", "abstract": ["Vascular calcification (VC) represents a recognized adverse predictor for cardiovascular morbidity and mortality.", "Previously considered passive and degenerative, VC is now recognized as an active process that resembles bone formation, and shares a number of histopathological features, mineral composition, and initiation mechanisms with bone development and metabolism.", "Oxidative stress and inflammation are key factors in both VC and osteoporosis (OP).", "Biochemical factors known to be primarily involved in the healthy bone metabolism also regulate VC.", "These biomarkers include vitamin D, osteoprotegerin, osteopontin, matrix Gla protein, cathepsin K, fibroblast growth factor-23, and fetuin-A. A better understanding of this highly controlled regulatory network, with multiple, nested feedback loops and cross talk between organs, may help to decrease the growing prevalence of calcific vasculopathy as well as OP in the aging population, and to advance in common preventive and therapeutic interventions targeted at both conditions."], "structured": false}
{"doc_id": 2177022, "title": "Immobilized chemokine fields and soluble chemokine gradients cooperatively shape migration patterns of dendritic cells.", "abstract": ["Chemokines orchestrate immune cell trafficking by eliciting either directed or random migration and by activating integrins in order to induce cell adhesion.", "Analyzing dendritic cell (DC) migration, we showed that these distinct cellular responses depended on the mode of chemokine presentation within tissues.", "The surface-immobilized form of the chemokine CCL21, the heparan sulfate-anchoring ligand of the CC-chemokine receptor 7 (CCR7), caused random movement of DCs that was confined to the chemokine-presenting surface because it triggered integrin-mediated adhesion.", "Upon direct contact with CCL21, DCs truncated the anchoring residues of CCL21, thereby releasing it from the solid phase.", "Soluble CCL21 functionally resembles the second CCR7 ligand, CCL19, which lacks anchoring residues and forms soluble gradients.", "Both soluble CCR7 ligands triggered chemotactic movement, but not surface adhesion.", "Adhesive random migration and directional steering cooperate to produce dynamic but spatially restricted locomotion patterns closely resembling the cellular dynamics observed in secondary lymphoid organs."], "structured": false}
{"doc_id": 2192419, "title": "Local proliferation dominates lesional macrophage accumulation in atherosclerosis", "abstract": ["During the inflammatory response that drives atherogenesis, macrophages accumulate progressively in the expanding arterial wall.", "The observation that circulating monocytes give rise to lesional macrophages has reinforced the concept that monocyte infiltration dictates macrophage buildup.", "Recent work has indicated, however, that macrophage accumulation does not depend on monocyte recruitment in some inflammatory contexts.", "We therefore revisited the mechanism underlying macrophage accumulation in atherosclerosis.", "In murine atherosclerotic lesions, we found that macrophages turn over rapidly, after 4 weeks.", "Replenishment of macrophages in these experimental atheromata depends predominantly on local macrophage proliferation rather than monocyte influx.", "The microenvironment orchestrates macrophage proliferation through the involvement of scavenger receptor A (SR-A).", "Our study reveals macrophage proliferation as a key event in atherosclerosis and identifies macrophage self-renewal as a therapeutic target for cardiovascular disease."], "structured": false}
{"doc_id": 2194320, "title": "Enzymatically active lysosomal proteases are associated with amyloid deposits in Alzheimer brain.", "abstract": ["The formation of beta-amyloid in the brains of individuals with Alzheimer disease requires the proteolytic cleavage of a membrane-associated precursor protein.", "The proteases that may be involved in this process have not yet been identified.", "Cathepsins are normally intracellular proteolytic enzymes associated with lysosomes; however, when sections from Alzheimer brains were stained by antisera to cathepsin D and cathepsin B, high levels of immunoreactivity were also detected in senile plaques.", "Extracellular sites of cathepsin immunoreactivity were not seen in control brains from age-matched individuals without neurologic disease or from patients with Huntington disease or Parkinson disease.", "In situ enzyme histochemistry of cathepsin D and cathepsin B on sections of neocortex using synthetic peptides and protein substrates showed that senile plaques contained the highest levels of enzymatically active cathepsin.", "At the ultrastructural level, cathepsin immunoreactivity in senile plaques was localized principally to lysosomal dense bodies and lipofuscin granules, which were extracellular.", "Similar structures were abundant in degenerating neurons of Alzheimer neocortex, and cathepsin-laden neuronal perikarya in various stages of disintegration could be seen within some senile plaques.", "The high levels of enzymatically competent lysosomal proteases abnormally localized in senile plaques represent evidence for candidate enzymes that may mediate the proteolytic formation of amyloid.", "We propose that amyloid precursor protein within senile plaques is processed by lysosomal proteases principally derived from degenerating neurons.", "Escape of cathepsins from the stringently regulated intracellular milieu provides a basis for an abnormal sequence of proteolytic cleavages of accumulating amyloid precursor protein."], "structured": false}
{"doc_id": 2205779, "title": "Gastric juice miR-129 as a potential biomarker for screening gastric cancer", "abstract": ["MicroRNAs (miRNAs) play crucial roles during the occurrence and development of gastric cancer.", "Conventional serological tests for screening gastric cancer have limits on sensitivity and specificity.", "Several miRNAs in peripheral blood have been used as biomarkers of gastric cancer.", "However, most of these miRNAs are shared by several types of cancer.", "Thanks to the tissue specificity of gastric juice, here we examined the feasibility of using gastric juice miR-129-1/2, which are aberrantly expressed in gastric cancer, to screen gastric cancer.", "Total of 141 gastric juices samples from gastric cancer, gastric ulcer, atrophic gastritis, and minimal gastritis patients or subjects with normal mucosa were collected by gastroscopy.", "The gastric juice miR-129-1/2 levels were detected by quantitative reverse transcription-polymerase chain reaction.", "A receiver operating characteristic (ROC) curve was constructed for differentiating patients with gastric cancer from patients with benign gastric diseases.", "We showed that, compared with patients with benign gastric diseases, patients with gastric cancer had significantly lower levels of gastric juice miR-129-1-3p and miR-129-2-3p.", "The areas under ROC curve (AUC) were 0.639 and 0.651 for miR-129-1-3p and miR-129-2-3p, respectively.", "Using the parallel combination test, the AUC was up to 0.656.", "In summary, our results suggest that gastric juice miR-129-1-3p and miR-129-2-3p are potential biomarkers for the screening gastric cancer, and the detection of gastric juice miRNAs is a convenient non-invasion method for the diagnosis of gastric cancer."], "structured": false}
{"doc_id": 2211868, "title": "Epidemiological expansion, structural studies, and clinical challenges of new \u03b2-lactamases from gram-negative bacteria.", "abstract": ["\u03b2-Lactamase evolution presents to the infectious disease community a major challenge in the treatment of infections caused by multidrug-resistant gram-negative bacteria.", "Because over 1,000 of these naturally occurring \u03b2-lactamases exist, attempts to correlate structure and function have become daunting.", "Although new enzymes in the extended-spectrum \u03b2-lactamase (ESBL) families are frequently identified, the older CTX-M-14 and CTX-M-15 enzymes have become the most prevalent ESBLs in global surveillance.", "Carbapenemases with either serine-based or zinc-facilitated hydrolysis mechanisms are posing some of the most critical problems.", "Most geographical regions now report KPC serine carbapenemases and the metallo-\u03b2-lactamases VIM, IMP, and NDM-1, even though NDM-1 was only recently identified.", "The rapid emergence of these newer enzymes, with multiple \u03b2-lactamases appearing in a single organism, makes the design of new \u03b2-lactamase inactivators or \u03b2-lactamase-stable \u03b2-lactams all the more difficult.", "Combination therapy will likely be required to counteract the continuing evolution of these insidious enzymes in multidrug-resistant pathogens."], "structured": false}
{"doc_id": 2212067, "title": "Robust synchronization of coupled circadian and cell cycle oscillators in single mammalian cells", "abstract": ["Circadian cycles and cell cycles are two fundamental periodic processes with a period in the range of 1 day.", "Consequently, coupling between such cycles can lead to synchronization.", "Here, we estimated the mutual interactions between the two oscillators by time-lapse imaging of single mammalian NIH3T3 fibroblasts during several days.", "The analysis of thousands of circadian cycles in dividing cells clearly indicated that both oscillators tick in a 1:1 mode-locked state, with cell divisions occurring tightly 5 h before the peak in circadian Rev-Erb\u03b1-YFP reporter expression.", "In principle, such synchrony may be caused by either unidirectional or bidirectional coupling.", "While gating of cell division by the circadian cycle has been most studied, our data combined with stochastic modeling unambiguously show that the reverse coupling is predominant in NIH3T3 cells.", "Moreover, temperature, genetic, and pharmacological perturbations showed that the two interacting cellular oscillators adopt a synchronized state that is highly robust over a wide range of parameters.", "These findings have implications for circadian function in proliferative tissues, including epidermis, immune cells, and cancer."], "structured": false}
{"doc_id": 2225918, "title": "Identification of a Brainstem Circuit Controlling Feeding", "abstract": ["Hunger, driven by negative energy balance, elicits the search for and consumption of food.", "While this response is in part mediated by neurons in the hypothalamus, the role of specific cell types in other brain regions is less well defined.", "Here, we show that neurons in the dorsal raphe nucleus, expressing vesicular transporters for GABA or glutamate (hereafter, DRNVgat and DRNVGLUT3 neurons), are reciprocally activated by changes in energy balance and that modulating their activity has opposite effects on feeding-DRNVgat neurons increase, whereas DRNVGLUT3 neurons suppress, food intake.", "Furthermore, modulation of these neurons in obese (ob/ob) mice suppresses food intake and body weight and normalizes locomotor activity.", "Finally, using molecular profiling, we identify druggable targets in these neurons and show that local infusion of agonists for specific receptors on these neurons has potent effects on feeding.", "These data establish the DRN as an important node controlling energy balance.", "PAPERCLIP."], "structured": false}
{"doc_id": 2236768, "title": "Infection-induced NETosis is a dynamic process involving neutrophil multitasking in vivo", "abstract": ["Neutrophil extracellular traps (NETs) are released as neutrophils die in vitro in a process requiring hours, leaving a temporal gap that invasive microbes may exploit.", "Neutrophils capable of migration and phagocytosis while undergoing NETosis have not been documented.", "During Gram-positive skin infections, we directly visualized live polymorphonuclear cells (PMNs) in vivo rapidly releasing NETs, which prevented systemic bacterial dissemination.", "NETosis occurred during crawling, thereby casting large areas of NETs.", "NET-releasing PMNs developed diffuse decondensed nuclei, ultimately becoming devoid of DNA.", "Cells with abnormal nuclei showed unusual crawling behavior highlighted by erratic pseudopods and hyperpolarization consistent with the nucleus being a fulcrum for crawling.", "A requirement for both Toll-like receptor 2 and complement-mediated opsonization tightly regulated NET release.", "Additionally, live human PMNs injected into mouse skin developed decondensed nuclei and formed NETS in vivo, and intact anuclear neutrophils were abundant in Gram-positive human abscesses.", "Therefore early in infection NETosis involves neutrophils that do not undergo lysis and retain the ability to multitask."], "structured": false}
{"doc_id": 2242416, "title": "Swim training suppresses tumor growth in mice.", "abstract": ["The present study was designed to determine the effects of physical training on the development of cancer induced by the injection of Ehrlich tumor cells in mice.", "Male Swiss mice were subjected to a swim training protocol (5 days/wk for 6 wk, 1 h at 50% of maximal capacity-trained groups) or remained sedentary in their cages (sedentary groups).", "The inoculation of Ehrlich tumor cells was performed at the end of the fourth week, and animals were killed after 6 wk of training.", "Heart and solid tumor weights were recorded, and tumor volumes were calculated.", "Portions of the tumors were used for the evaluation of macrophages and neutrophil accumulation or fixed in neutral 10% buffered formalin for histological analysis.", "The tumor volume and weight were, respectively, approximately 270% and 280% greater in sedentary mice than in trained mice.", "Macrophage infiltration in the tumor tissue was significantly lower in trained mice (0.65 +/- 0.16 vs. 1.78 +/-", "0.43 macrophages x 10(3) in the sedentary group).", "Moreover, neutrophil accumulation in tumors was slightly reduced after exercise training, and the amount of tumor cells was reduced in trained mice.", "Exercise capacity was substantially increased in trained mice, as determined by a 440% increase in the exercise time at 50% of maximal capacity.", "In summary, swim training retarded the development of Ehrlich tumors in mice, accompanied by a reduction in macrophage infiltration and neutrophil accumulation.", "These findings provide conceptual support for clinical observations that controlled physical activities may be a therapeutically important approach to preventing cancer progression and may improve the outcome of cancer treatment."], "structured": false}
{"doc_id": 2248870, "title": "Lung dendritic cells imprint T cell lung homing and promote lung immunity through the chemokine receptor CCR4", "abstract": ["T cell trafficking into the lung is critical for lung immunity, but the mechanisms that mediate T cell lung homing are not well understood.", "Here, we show that lung dendritic cells (DCs) imprint T cell lung homing, as lung DC-activated T cells traffic more efficiently into the lung in response to inhaled antigen and at homeostasis compared with T cells activated by DCs from other tissues.", "Consequently, lung DC-imprinted T cells protect against influenza more effectively than do gut and skin DC-imprinted T cells.", "Lung DCs imprint the expression of CCR4 on T cells, and CCR4 contributes to T cell lung imprinting.", "Lung DC-activated, CCR4-deficient T cells fail to traffic into the lung as efficiently and to protect against influenza as effectively as lung DC-activated, CCR4-sufficient T cells.", "Thus, lung DCs imprint T cell lung homing and promote lung immunity in part through CCR4."], "structured": false}
{"doc_id": 2251426, "title": "microRNAs: A Safeguard against Turmoil?", "abstract": ["Emerging data suggest that microRNAs (miRNAs) are instrumental in a variety of stress responses in addition to their more recognized role in development.", "Surprisingly, miRNAs, which normally suppress expression of target transcripts, may become activators of expression during stress.", "This might be partially explained by new interactions of miRNA/Argonaute complexes with RNA-binding proteins that relocate from different subcellular compartments during stress."], "structured": false}
{"doc_id": 2260571, "title": "Vascular smooth muscle cell calcification is mediated by regulated exosome secretion.", "abstract": ["RATIONALE Matrix vesicles (MVs), secreted by vascular smooth muscle cells (VSMCs), form the first nidus for mineralization and fetuin-A, a potent circulating inhibitor of calcification, is specifically loaded into MVs.", "However, the processes of fetuin-A intracellular trafficking and MV biogenesis are poorly understood.   \n", "OBJECTIVE The objective of this study is to investigate the regulation, and role, of MV biogenesis in VSMC calcification.   \n", "METHODS AND RESULTS Alexa488-labeled fetuin-A was internalized by human VSMCs, trafficked via the endosomal system, and exocytosed from multivesicular bodies via exosome release.", "VSMC-derived exosomes were enriched with the tetraspanins CD9, CD63, and CD81, and their release was regulated by sphingomyelin phosphodiesterase 3.", "Comparative proteomics showed that VSMC-derived exosomes were compositionally similar to exosomes from other cell sources but also shared components with osteoblast-derived MVs including calcium-binding and extracellular matrix proteins.", "Elevated extracellular calcium was found to induce sphingomyelin phosphodiesterase 3 expression and the secretion of calcifying exosomes from VSMCs in vitro, and chemical inhibition of sphingomyelin phosphodiesterase 3 prevented VSMC calcification.", "In vivo, multivesicular bodies containing exosomes were observed in vessels from chronic kidney disease patients on dialysis, and CD63 was found to colocalize with calcification.", "Importantly, factors such as tumor necrosis factor-\u03b1 and platelet derived growth factor-BB were also found to increase exosome production, leading to increased calcification of VSMCs in response to calcifying conditions.   \n", "CONCLUSIONS This study identifies MVs as exosomes and shows that factors that can increase exosome release can promote vascular calcification in response to environmental calcium stress.", "Modulation of the exosome release pathway may be as a novel therapeutic target for prevention."], "structured": true}
{"doc_id": 2264455, "title": "Vaccines against malaria", "abstract": ["There is no licenced vaccine against any human parasitic disease and Plasmodium falciparum malaria, a major cause of infectious mortality, presents a great challenge to vaccine developers.", "This has led to the assessment of a wide variety of approaches to malaria vaccine design and development, assisted by the availability of a safe challenge model for small-scale efficacy testing of vaccine candidates.", "Malaria vaccine development has been at the forefront of assessing many new vaccine technologies including novel adjuvants, vectored prime-boost regimes and the concept of community vaccination to block malaria transmission.", "Most current vaccine candidates target a single stage of the parasite's life cycle and vaccines against the early pre-erythrocytic stages have shown most success.", "A protein in adjuvant vaccine, working through antibodies against sporozoites, and viral vector vaccines targeting the intracellular liver-stage parasite with cellular immunity show partial efficacy in humans, and the anti-sporozoite vaccine is currently in phase III trials.", "However, a more effective malaria vaccine suitable for widespread cost-effective deployment is likely to require a multi-component vaccine targeting more than one life cycle stage.", "The most attractive near-term approach to develop such a product is to combine existing partially effective pre-erythrocytic vaccine candidates."], "structured": false}
{"doc_id": 2266471, "title": "MicroRNA-21 is Induced by Rapamycin in a Model of Tuberous Sclerosis (TSC) and Lymphangioleiomyomatosis (LAM)", "abstract": ["Lymphangioleiomyomatosis (LAM), a multisystem disease of women, is manifest by the proliferation of smooth muscle-like cells in the lung resulting in cystic lung destruction.", "Women with LAM can also develop renal angiomyolipomas.", "LAM is caused by mutations in the tuberous sclerosis complex genes (TSC1 or TSC2), resulting in hyperactive mammalian Target of Rapamycin (mTOR) signaling.", "The mTOR inhibitor, Rapamycin, stabilizes lung function in LAM and decreases the volume of renal angiomyolipomas, but lung function declines and angiomyolipomas regrow when treatment is discontinued, suggesting that factors induced by mTORC1 inhibition may promote the survival of TSC2-deficient cells.", "Whether microRNA (miRNA, miR) signaling is involved in the response of LAM to mTORC1 inhibition is unknown.", "We identified Rapamycin-dependent miRNA in LAM patient angiomyolipoma-derived cells using two separate screens.", "First, we assayed 132 miRNA of known significance to tumor biology.", "Using a cut-off of >1.5-fold change, 48 microRNA were Rapamycin-induced, while 4 miRs were downregulated.", "In a second screen encompassing 946 miRNA, 18 miRs were upregulated by Rapamycin, while eight were downregulated.", "Dysregulation of miRs 29b, 21, 24, 221, 106a and 199a were common to both platforms and were classified as candidate \"RapamiRs.", "\" Validation by qRT-PCR confirmed that these microRNA were increased.", "miR-21, a pro-survival miR, was the most significantly increased by mTOR-inhibition (p<0.01).", "The regulation of miR-21 by Rapamycin is cell type independent.", "mTOR inhibition promotes the processing of the miR-21 transcript (pri-miR-21) to a premature form (pre-miR-21).", "In conclusion, our findings demonstrate that Rapamycin upregulates multiple miRs, including pro-survival miRs, in TSC2-deficient patient-derived cells.", "The induction of miRs may contribute to the response of LAM and TSC patients to Rapamycin therapy."], "structured": false}
{"doc_id": 2272614, "title": "Reduced NF1 expression confers resistance to EGFR inhibition in lung cancer.", "abstract": ["Activating mutations in the EGF receptor (EGFR) are associated with clinical responsiveness to EGFR tyrosine kinase inhibitors (TKI), such as erlotinib and gefitinib.", "However, resistance eventually arises, often due to a second EGFR mutation, most commonly T790M.", "Through a genome-wide siRNA screen in a human lung cancer cell line and analyses of murine mutant EGFR-driven lung adenocarcinomas, we found that erlotinib resistance was associated with reduced expression of neurofibromin, the RAS GTPase-activating protein encoded by the NF1 gene.", "Erlotinib failed to fully inhibit RAS-ERK signaling when neurofibromin levels were reduced.", "Treatment of neurofibromin-deficient lung cancers with a MAP-ERK kinase (MEK) inhibitor restored sensitivity to erlotinib.", "Low levels of NF1 expression were associated with primary and acquired resistance of lung adenocarcinomas to EGFR TKIs in patients.", "These findings identify a subgroup of patients with EGFR-mutant lung adenocarcinoma who might benefit from combination therapy with EGFR and MEK inhibitors."], "structured": false}
{"doc_id": 2274272, "title": "Human IRGM induces autophagy to eliminate intracellular mycobacteria.", "abstract": ["Immunity-related p47 guanosine triphosphatases (IRG) play a role in defense against intracellular pathogens.", "We found that the murine Irgm1 (LRG-47) guanosine triphosphatase induced autophagy and generated large autolysosomal organelles as a mechanism for the elimination of intracellular Mycobacterium tuberculosis.", "We also identified a function for a human IRG protein in the control of intracellular pathogens and report that the human Irgm1 ortholog, IRGM, plays a role in autophagy and in the reduction of intracellular bacillary load."], "structured": false}
{"doc_id": 2276126, "title": "Implementation of a Clinical Pharmacy Education Program in a Teaching Hospital: Resident Oriented Documentation and Intervention", "abstract": ["The aim of this study was to provide a clinical pharmacy education program at Masih Daneshvari hospital, a University affiliated hospital, located in Tehran, Iran.", "For this purpose, the most common pharmacist involved interventions and aspects of potential fields for pharmacy students and residents education was firstly identified.", "Clinical pharmacy interventions and drug information forms were filled during the study period, from January 2006 till January 2007.", "Based on the results of this study, a total number of 772 interventions were conducted during the study year.", "Drug information had the highest rate of 22.30% among all interventions, followed by dose adjustment, and therapeutic reduction or addition.", "The mean number of medications per patient was 8.62 \u00b1 7.54.", "In conclusion, it could be said that although in our country the challenge for the pharmacy as a profession is in its initial stages compared to the developed countries, the result of this study revealed a high demand for this service among health care providers."], "structured": false}
{"doc_id": 2291922, "title": "The surgical anatomy of the conduction tissues.", "abstract": ["On the basis of our collective experience we have reviewed the disposition of the cardiac conduction tissues as they might be observed by the surgeon in both normal and abnormal hearts.", "The sinus node lies subepicardially in the terminal sulcus; because of its variable blood supply the entire superior cavoatrial junction is a potential danger area.", "There are no morphologically discrete tracts extending through the atrial tissues between sinus and atrioventricular nodes.", "The atrioventricular node, the atrial extent of the atrioventricular conduction axis, is contained exclusively within the triangle of Koch.", "The axis penetrates through the central fibrous body and branches on the muscular ventricular septum immediately beneath the interventricular component of the membranous septum.", "The landmarks to these structures are described as they might be seen through the right atrium, left atrium, and aorta.", "Consideration is then given to the surgical anatomy of the abnormal muscular atrioventricular connections that underscore the ventricular pre-excitation syndromes.", "Finally, rules are developed whereby the disposition of the conduction tissues can be predicted with accuracy in congenitally malformed hearts, in the settings of both normal and abnormal chamber connections.", "The most important variables in this respect are alignment between the atrial and ventricular septal structures and the pattern of ventricular architecture present."], "structured": false}
{"doc_id": 2295434, "title": "Agreement between an online dietary assessment tool (myfood24) and an interviewer-administered 24-h dietary recall in British adolescents aged 11-18 years.", "abstract": ["myfood24 Is an online 24-h dietary assessment tool developed for use among British adolescents and adults.", "Limited information is available regarding the validity of using new technology in assessing nutritional intake among adolescents.", "Thus, a relative validation of myfood24 against a face-to-face interviewer-administered 24-h multiple-pass recall (MPR) was conducted among seventy-five British adolescents aged 11-18 years.", "Participants were asked to complete myfood24 and an interviewer-administered MPR on the same day for 2 non-consecutive days at school.", "Total energy intake (EI) and nutrients recorded by the two methods were compared using intraclass correlation coefficients (ICC), Bland-Altman plots (using between and within-individual information) and weighted \u03ba to assess the agreement.", "Energy, macronutrients and other reported nutrients from myfood24 demonstrated strong agreement with the interview MPR data, and ICC ranged from 0\u00b746 for Na to 0\u00b788 for EI.", "There was no significant bias between the two methods for EI, macronutrients and most reported nutrients.", "The mean difference between myfood24 and the interviewer-administered MPR for EI was -230 kJ (-55 kcal) (95 % CI -490, 30 kJ (-117, 7 kcal); P=0\u00b74) with limits of agreement ranging between 39 % (3336 kJ (-797 kcal)) lower and 34 % (2874 kJ (687 kcal)) higher than the interviewer-administered MPR.", "There was good agreement in terms of classifying adolescents into tertiles of EI (\u03ba w =0\u00b764).", "The agreement between day 1 and day 2 was as good for myfood24 as for the interviewer-administered MPR, reflecting the reliability of myfood24.", "myfood24 Has the potential to collect dietary data of comparable quality with that of an interviewer-administered MPR."], "structured": false}
{"doc_id": 2296264, "title": "Modulation of cancer chemotherapy by green tea.", "abstract": ["Biochemical modulation has played an important role in the development of cancer chemotherapy.", "We have directed our attention to the intake of common beverages and investigated the effects of green tea and tea components on the antitumor activity of doxorubicin.", "We carried out the combined treatment of toxorubicin and green tea on Ehrlich ascites carcinoma tumor-bearing mice.", "The oral administration of green tea enhanced 2.5-fold the inhibitory effects of doxorubicin on tumor growth.", "The Doxorubicin concentration in the tumor was increased by the combination of green tea with doxorubicin.", "In contrast, the increase in doxorubicin concentration was not observed in normal tissues after green tea combination.", "Furthermore, the enhancement of antitumor activity of doxorubicin induced by green tea was observed in M5076 ovarian sarcoma, which has low sensitivity to doxorubicin.", "These results suggest that drinking green tea can encourage cancer chemotherapy and may improve the quality of life of clinical patients."], "structured": false}
{"doc_id": 2316374, "title": "Histone deacetylase 5 interacts with Kr\u00fcppel-like factor 2 and inhibits its transcriptional activity in endothelium.", "abstract": ["AIMS Vascular endothelial dysfunction and inflammation are hallmarks of atherosclerosis.", "Kr\u00fcppel-like factor 2 (KLF2) is a key mediator of anti-inflammatory and anti-atherosclerotic properties of the endothelium.", "However, little is known of the molecular mechanisms for regulating KLF2 transcriptional activation.   \n", "METHODS AND RESULTS Here, we found that histone deacetylase 5 (HDAC5) associates with KLF2 and represses KLF2 transcriptional activation.", "HDAC5 resided with KLF2 in the nuclei of human umbilical cord vein endothelial cells (HUVECs).", "Steady laminar flow attenuated the association of HDAC5 with KLF2 via stimulating HDAC5 phosphorylation-dependent nuclear export in HUVEC.", "We also mapped the KLF2-HDAC5-interacting domains and found that the N-terminal region of HDAC5 interacts with the C-terminal domain of KLF2.", "Chromatin immunoprecipitation and luciferase reporter assays showed that HDAC5 through a direct association with KLF2 suppressed KLF2 transcriptional activation.", "HDAC5 overexpression inhibited KLF2-dependent endothelial nitric oxide synthesis (eNOS) promoter activity in COS7 cell and gene expression in both HUVECs and bovine aortic endothelial cells (BAECs).", "Conversely, HDAC5 silencing enhanced KLF2 transcription and hence eNOS expression in HUVEC.", "Moreover, we observed that the level of eNOS protein in the thoracic aorta isolated from HDAC5 knockout mice was higher, whereas expression of pro-inflammatory vascular cell adhesion molecule 1 was lower, compared with those of HDAC5 wild-type mice.   \n", "CONCLUSIONS We reveal a novel role of HDAC5 in modulating the KLF2 transcriptional activation and eNOS expression.", "These findings suggest that HDAC5, a binding partner and modulator of KLF2, could be a new therapeutic target to prevent vascular endothelial dysfunction associated with cardiovascular diseases."], "structured": true}
{"doc_id": 2319305, "title": "N348I in HIV-1 reverse transcriptase can counteract the nevirapine-mediated bias toward RNase H cleavage during plus-strand initiation.", "abstract": ["Drug resistance-associated mutations in HIV-1 reverse transcriptase (RT) can affect the balance between polymerase and ribonuclease H (RNase H) activities of the enzyme.", "We have recently demonstrated that the N348I mutation in the connection domain causes selective dissociation from RNase H-competent complexes, whereas the functional integrity of the polymerase-competent complex remains largely unaffected.", "N348I has been associated with resistance to the non-nucleoside RT inhibitor (NNRTI), nevirapine; however, a possible mechanism that links changes in RNase H activity to changes in NNRTI susceptibility remains to be established.", "To address this problem, we consider recent findings suggesting that NNRTIs may affect the orientation of RT on its nucleic acid substrate and increase RNase H activity.", "Here we demonstrate that RNase H-mediated primer removal is indeed more efficient in the presence of NNRTIs; however, the N348I mutant enzyme is able to counteract this effect.", "Efavirenz, a tight binding inhibitor, restricts the influence of the mutation.", "These findings provide strong evidence to suggest that N348I can thwart the inhibitory effects of nevirapine during initiation of (+)-strand DNA synthesis, which provides a novel mechanism for resistance.", "The data are in agreement with clinical data, which demonstrate a stronger effect of N348I on susceptibility to nevirapine as compared with efavirenz."], "structured": false}
{"doc_id": 2328272, "title": "Cancer survivorship research: the challenge of recruiting adult long term cancer survivors from a cooperative clinical trials group", "abstract": ["INTRODUCTION With the growing number of adult cancer survivors, there is increasing need for information that links potential late and long term effects with specific treatment regimens.", "Few adult cancer patients are treated on clinical trials; however, patients previously enrolled in these trials are an important source of information about treatment-related late effects.   \n", "METHODS Focusing on colorectal cancer survivors, we used the database from five phase III randomized clinical trials from the National Surgical Adjuvant Breast & Bowel Project (NSABP) to recruit and enroll long term survivors in a study of late health outcomes and quality of life.", "We describe the challenges to recruitment of patients more than 5 -20 years after treatment.   \n", "RESULTS Sixty-five NSABP treatment sites were invited to enroll patients in the study.", "Sixty participated with the potential to recruit 2,408 patients.", "We received registration forms on only 976 patients (41%) of whom 744 (76%) expressed interest in participating and 708 completed interviews (95% of those expressing interest; 29% of total potential sample).", "There were multiple barriers to recruitment (difficulty locating patients, lack of institutional commitment, lack of patient interest).   \n", "CONCLUSIONS Patients treated on clinical trials are an important potential source for examining the late effects of cancer treatments.", "Retrospective recruitment has substantial limitations.", "In the future, mechanisms should be established for prospective long-term follow-up to identify and understand the frequency and type of late effects associated with cancer treatments.   ", "IMPLICATIONS FOR CANCER SURVIVORS As cancer patients are living longer, it will be important to learn from participants in clinical trials whether or not specific treatment regimens are associated with any serious late effects."], "structured": true}
{"doc_id": 2335873, "title": "Arylsulfatase B Improves Locomotor Function after Mouse Spinal Cord Injury", "abstract": ["Bacterial chondroitinase ABC (ChaseABC) has been used to remove the inhibitory chondroitin sulfate chains from chondroitin sulfate proteoglycans to improve regeneration after rodent spinal cord injury.", "We hypothesized that the mammalian enzyme arylsulfatase B (ARSB) would also enhance recovery after mouse spinal cord injury.", "Application of the mammalian enzyme would be an attractive alternative to ChaseABC because of its more robust chemical stability and reduced immunogenicity.", "A one-time injection of human ARSB into injured mouse spinal cord eliminated immunoreactivity for chondroitin sulfates within five days, and up to 9 weeks after injury.", "After a moderate spinal cord injury, we observed improvements of locomotor recovery assessed by the Basso Mouse Scale (BMS) in ARSB treated mice, compared to the buffer-treated control group, at 6 weeks after injection.", "After a severe spinal cord injury, mice injected with equivalent units of ARSB or ChaseABC improved similarly and both groups achieved significantly more locomotor recovery than the buffer-treated control mice.", "Serotonin and tyrosine hydroxylase immunoreactive axons were more extensively present in mouse spinal cords treated with ARSB and ChaseABC, and the immunoreactive axons penetrated further beyond the injury site in ARSB or ChaseABC treated mice than in control mice.", "These results indicate that mammalian ARSB improves functional recovery after CNS injury.", "The structural/molecular mechanisms underlying the observed functional improvement remain to be elucidated."], "structured": false}
{"doc_id": 2338488, "title": "The World Health Organization Adult ADHD Self-Report Scale (ASRS): a short screening scale for use in the general population.", "abstract": ["BACKGROUND A self-report screening scale of adult attention-deficit/hyperactivity disorder (ADHD), the World Health Organization (WHO) Adult ADHD Self-Report Scale (ASRS) was developed in conjunction with revision of the WHO Composite International Diagnostic Interview (CIDI).", "The current report presents data on concordance of the ASRS and of a short-form ASRS screener with blind clinical diagnoses in a community sample.   \n", "METHOD The ASRS includes 18 questions about frequency of recent DSM-IV Criterion A symptoms of adult ADHD.", "The ASRS screener consists of six out of these 18 questions that were selected based on stepwise logistic regression to optimize concordance with the clinical classification.", "ASRS responses were compared to blind clinical ratings of DSM-IV adult ADHD in a sample of 154 respondents who previously participated in the US National Comorbidity Survey Replication (NCS-R), oversampling those who reported childhood ADHD and adult persistence.   \n", "RESULTS Each ASRS symptom measure was significantly related to the comparable clinical symptom rating, but varied substantially in concordance (Cohen's kappa in the range 0.16-0.81).", "Optimal scoring to predict clinical syndrome classifications was to sum unweighted dichotomous responses across all 18 ASRS questions.", "However, because of the wide variation in symptom-level concordance, the unweighted six-question ASRS screener outperformed the unweighted 18-question ASRS in sensitivity (68.7% v. 56.3%), specificity (99.5% v. 98.3%), total classification accuracy (97.9% v. 96.2%), and kappa (0.76 v. 0.58).   \n", "CONCLUSIONS Clinical calibration in larger samples might show that a weighted version of the 18-question ASRS outperforms the six-question ASRS screener.", "Until that time, however, the unweighted screener should be preferred to the full ASRS, both in community surveys and in clinical outreach and case-finding initiatives."], "structured": true}
{"doc_id": 2344892, "title": "Human milk proresolving mediators stimulate resolution of acute inflammation", "abstract": ["Human milk contains nutrients and bioactive products relevant to infant development and immunological protection.", "Here, we investigated the proresolving properties of milk using human milk lipid mediator isolates (HLMIs) and determined their impact on resolution programs in vivo and with human macrophages.", "HLMIs reduced the maximum neutrophil numbers (14.6\u00b11.2 \u00d7 106\u201311.0\u00b11.0 \u00d7 106 cells per exudate) and shortened the resolution interval (Ri; 50% neutrophil reduction) by 54% compared with peritonitis.", "Using rigorous liquid-chromatography tandem-mass spectrometry (LC-MS-MS)-based lipid mediator (LM) metabololipidomics, we demonstrated that human milk possesses a proresolving LM-specialized proresolving mediator (LM-SPM) signature profile, containing SPMs (e.g. resolvins (Rv), protectins (PDs), maresins (MaRs), and lipoxins (LXs)) at bioactive levels (pico-nanomolar concentrations) that enhanced human macrophage efferocytosis and bacterial containment.", "SPMs identified in human milk included D-series Rvs (e.g., RvD1, RvD2, RvD3, AT-RvD3, and RvD4), PD1, MaR1, E-series Rvs (e.g. RvE1, RvE2, and RvE3), and LXs (LXA4 and LXB4).", "Of the SPMs identified in human milk, RvD2 and MaR1 (50 ng per mouse) individually shortened Ri by \u223c75%.", "Milk from mastitis gave higher leukotriene B4 and prostanoids and lower SPM levels.", "Taken together, these findings provide evidence that human milk has proresolving actions via comprehensive LM-SPM profiling, describing a potentially novel mechanism in maternal\u2013infant biochemical imprinting."], "structured": false}
{"doc_id": 2352142, "title": "Cerebral perfusion and stroke.", "abstract": ["Stroke is a heterogeneous syndrome caused by multiple disease mechanisms, but all result in a disruption of cerebral blood flow with subsequent tissue damage.", "This review covers the mechanisms responsible for regulation of the normal cerebral circulation, and how they are disrupted in disease states.", "A central concept in treating patients with acute ischaemic stroke is the existence of an ischaemic penumbra of potentially salvageable tissue, and the evidence for its existence in humans is reviewed."], "structured": false}
{"doc_id": 2356950, "title": "Epigenetic regulation of miR-184 by MBD1 governs neural stem cell proliferation and differentiation.", "abstract": ["Methyl-CpG binding protein 1 (MBD1) regulates gene expression via a DNA methylation-mediated epigenetic mechanism.", "We have previously demonstrated that MBD1 deficiency impairs adult neural stem/progenitor cell (aNSC) differentiation and neurogenesis, but the underlying mechanism was unclear.", "Here, we show that MBD1 regulates the expression of several microRNAs in aNSCs and, specifically, that miR-184 is directly repressed by MBD1.", "High levels of miR-184 promoted proliferation but inhibited differentiation of aNSCs, whereas inhibition of miR-184 rescued the phenotypes associated with MBD1 deficiency.", "We further found that miR-184 regulates the expression of Numblike (Numbl), a known regulator of brain development, by binding to the 3'-UTR of Numbl mRNA and affecting its translation.", "Expression of exogenous Numbl could rescue the aNSC defects that result from either miR-184 overexpression or MBD1 deficiency.", "Therefore, MBD1, miR-184, and Numbl form a regulatory network that helps control the balance between proliferation and differentiation of aNSCs."], "structured": false}
{"doc_id": 2359152, "title": "Landscape of genetic lesions in 944 patients with myelodysplastic syndromes", "abstract": ["High-throughput DNA sequencing significantly contributed to diagnosis and prognostication in patients with myelodysplastic syndromes (MDS).", "We determined the biological and prognostic significance of genetic aberrations in MDS.", "In total, 944 patients with various MDS subtypes were screened for known/putative mutations/deletions in 104 genes using targeted deep sequencing and array-based genomic hybridization.", "In total, 845/944 patients (89.5%) harbored at least one mutation (median, 3 per patient; range, 0-12).", "Forty-seven genes were significantly mutated with TET2, SF3B1, ASXL1, SRSF2, DNMT3A, and RUNX1 mutated in >10% of cases.", "Many mutations were associated with higher risk groups and/or blast elevation.", "Survival was investigated in 875 patients.", "By univariate analysis, 25/48 genes (resulting from 47 genes tested significantly plus PRPF8) affected survival (P<0.05).", "The status of 14 genes combined with conventional factors revealed a novel prognostic model ('Model-1') separating patients into four risk groups ('low', 'intermediate', 'high', 'very high risk') with 3-year survival of 95.2, 69.3, 32.8, and 5.3% (P<0.001).", "Subsequently, a 'gene-only model' ('Model-2') was constructed based on 14 genes also yielding four significant risk groups (P<0.001).", "Both models were reproducible in the validation cohort (n=175 patients; P<0.001 each).", "Thus, large-scale genetic and molecular profiling of multiple target genes is invaluable for subclassification and prognostication in MDS patients."], "structured": false}
{"doc_id": 2360905, "title": "Integrated molecular genetic profiling of pediatric high-grade gliomas reveals key differences with the adult disease.", "abstract": ["PURPOSE To define copy number alterations and gene expression signatures underlying pediatric high-grade glioma (HGG).   \n", "PATIENTS AND METHODS We conducted a high-resolution analysis of genomic imbalances in 78 de novo pediatric HGGs, including seven diffuse intrinsic pontine gliomas, and 10 HGGs arising in children who received cranial irradiation for a previous cancer using single nucleotide polymorphism microarray analysis.", "Gene expression was analyzed with gene expression microarrays for 53 tumors.", "Results were compared with publicly available data from adult tumors.   \n", "RESULTS Significant differences in copy number alterations distinguish childhood and adult glioblastoma.", "PDGFRA was the predominant target of focal amplification in childhood HGG, including diffuse intrinsic pontine gliomas, and gene expression analyses supported an important role for deregulated PDGFRalpha signaling in pediatric HGG.", "No IDH1 hotspot mutations were found in pediatric tumors, highlighting molecular differences with adult secondary glioblastoma.", "Pediatric and adult glioblastomas were clearly distinguished by frequent gain of chromosome 1q (30% v 9%, respectively) and lower frequency of chromosome 7 gain (13% v 74%, respectively) and 10q loss (35% v 80%, respectively).", "PDGFRA amplification and 1q gain occurred at significantly higher frequency in irradiation-induced tumors, suggesting that these are initiating events in childhood gliomagenesis.", "A subset of pediatric HGGs showed minimal copy number changes.   \n", "CONCLUSION Integrated molecular profiling showed substantial differences in the molecular features underlying pediatric and adult HGG, indicating that findings in adult tumors cannot be simply extrapolated to younger patients.", "PDGFRalpha may be a useful target for pediatric HGG, including diffuse pontine gliomas."], "structured": true}
{"doc_id": 2374637, "title": "Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.", "abstract": ["Although genomewide RNA expression analysis has become a routine tool in biomedical research, extracting biological insight from such information remains a major challenge.", "Here, we describe a powerful analytical method called Gene Set Enrichment Analysis (GSEA) for interpreting gene expression data.", "The method derives its power by focusing on gene sets, that is, groups of genes that share common biological function, chromosomal location, or regulation.", "We demonstrate how GSEA yields insights into several cancer-related data sets, including leukemia and lung cancer.", "Notably, where single-gene analysis finds little similarity between two independent studies of patient survival in lung cancer, GSEA reveals many biological pathways in common.", "The GSEA method is embodied in a freely available software package, together with an initial database of 1,325 biologically defined gene sets."], "structured": false}
{"doc_id": 2380002, "title": "The evolution of RNAs with multiple functions.", "abstract": ["Increasing numbers of transcripts have been reported to transmit both protein-coding and regulatory information.", "Apart from challenging our conception of the gene, this observation raises the question as to what extent this phenomenon occurs across the genome and how and why such dual encoding of function has evolved in the eukaryotic genome.", "To address this question, we consider the evolutionary path of genes in the earliest forms of life on Earth, where it is generally regarded that proteins evolved from a cellular machinery based entirely within RNA.", "This led to the domination of protein-coding genes in the genomes of microorganisms, although it is likely that RNA never lost its other capacities and functionalities, as evidenced by cis-acting riboswitches and UTRs.", "On the basis that the subsequent evolution of a more sophisticated regulatory architecture to provide higher levels of epigenetic control and accurate spatiotemporal expression in developmentally complex organisms is a complicated task, we hypothesize: (i) that mRNAs have been and remain subject to secondary selection to provide trans-acting regulatory capability in parallel with protein-coding functions; (ii) that some and perhaps many protein-coding loci, possibly as a consequence of gene duplication, have lost protein-coding functions en route to acquiring more sophisticated trans-regulatory functions; (iii) that many transcripts have become subject to secondary processing to release different products; and (iv) that novel proteins have emerged within loci that previously evolved functionality as regulatory RNAs.", "In support of the idea that there is a dynamic flux between different types of informational RNAs in both evolutionary and real time, we review recent observations that have arisen from transcriptomic surveys of complex eukaryotes and reconsider how these observations impact on the notion that apparently discrete loci may express transcripts with more than one function.", "In conclusion, we posit that many eukaryotic loci have evolved the capacity to transact a multitude of overlapping and potentially independent functions as both regulatory and protein-coding RNAs."], "structured": false}
{"doc_id": 2388819, "title": "In Vitro\u2013expanded Antigen-specific Regulatory T Cells Suppress Autoimmune Diabetes", "abstract": ["The low number of CD4+ CD25+ regulatory T cells (Tregs), their anergic phenotype, and diverse antigen specificity present major challenges to harnessing this potent tolerogenic population to treat autoimmunity and transplant rejection.", "In this study, we describe a robust method to expand antigen-specific Tregs from autoimmune-prone nonobese diabetic mice.", "Purified CD4+ CD25+ Tregs were expanded up to 200-fold in less than 2 wk in vitro using a combination of anti-CD3, anti-CD28, and interleukin 2.", "The expanded Tregs express a classical cell surface phenotype and function both in vitro and in vivo to suppress effector T cell functions.", "Most significantly, small numbers of antigen-specific Tregs can reverse diabetes after disease onset, suggesting a novel approach to cellular immunotherapy for autoimmunity."], "structured": false}
{"doc_id": 2389574, "title": "Stathmin overexpression identifies high-risk patients and lymph node metastasis in endometrial cancer.", "abstract": ["PURPOSE Overexpression of the oncogen Stathmin has been linked to aggressive endometrial carcinoma and a potential for PI3Kinase inhibitors in this disease.", "We wanted to validate the prognostic value of Stathmin expression in a large prospective multicenter setting.", "As lymph node sampling is part of current surgical staging, we also aimed to test if Stathmin expression in endometrial curettage specimens could predict lymph node metastasis.   ", "EXPERIMENTAL DESIGN A total of 1,076 endometrial cancer patients have been recruited from 10 centers to investigate the biological tumor marker Stathmin in relation to clinicopathologic variables, including lymph node status and survival.", "Stathmin immunohistochemical staining was carried out in 477 hysterectomy and 818 curettage specimens.   \n", "RESULTS Seventy-one percent of the patients (n = 763) were subjected to lymph node sampling, of which 12% had metastatic nodes (n = 94).", "Overexpression of Stathmin was detected in 37% (302 of 818) of the curettage and in 18% (84 of 477) of the hysterectomy specimens investigated.", "Stathmin overexpression in curettage and hysterectomy specimens were highly correlated and significantly associated with nonendometrioid histology, high grade, and aneuploidy.", "Stathmin analysis in preoperative curettage samples significantly correlated with, and was an independent predictor of, lymph node metastases.", "High Stathmin expression was associated with poor disease-specific survival (P \u2264 0.002) both in curettage and hysterectomy specimens.   \n", "CONCLUSIONS Stathmin immunohistochemical staining identifies endometrial carcinomas with lymph node metastases and poor survival.", "The value, as a predictive marker for response to PI3Kinase inhibition and as a tool to stratify patients for lymph node sampling in endometrial carcinomas, remains to be determined."], "structured": true}
{"doc_id": 2391552, "title": "Statin prophylaxis and inflammatory mediators following cardiopulmonary bypass: a systematic review", "abstract": ["INTRODUCTION Induction of an inflammatory response is thought to have a significant role in the complications that follow cardiopulmonary bypass (CPB).", "The statin drugs are increasingly being recognized as having potent anti-inflammatory effects and hence have potential to influence an important mechanism of injury in CPB, although there is no current confirmation that this is indeed the case.", "Our objective was to systematically review if pre-operative prophylactic statin therapy, compared with placebo or standard of care, can decrease the inflammatory response in people undergoing heart surgery with CPB.   \n", "METHODS We performed a systematic and comprehensive literature search for all randomized controlled trials (RCTs) of open heart surgery with CPB in adults or children who received prophylactic statin treatment prior to CPB, with reported outcomes which included markers of inflammation.", "Two authors independently identified eligible studies, extracted data, and assessed study quality using standardized instruments.", "Weighted mean difference (WMD) was the primary summary statistic with data pooled using a random effects model.", "Descriptive analysis was used when data could not be pooled.   \n", "RESULTS Eight RCTs were included in the review, with the number of trials for each inflammatory outcome being even more limited.", "Pooled data demonstrated benefit with the use of statin to attenuate the post-CPB increase in interleukins 6 and 8 (IL-6, IL-8), peak high sensitivity C-reactive protein (hsCRP), and tumor necrosis factor-alpha (TNF-alpha) post-CPB (WMD [95% confidence interval (CI)] -23.5 pg/ml [-36.6 to -10.5]; -23.4 pg/ml [-35.8 to -11.0]; -15.3 mg/L [CI -26.9 to -3.7]; -2.10 pg/ml [-3.83 to -0.37] respectively).", "Very limited RCT evidence suggests that prophylactic statin therapy may also decrease adhesion molecules following CPB including neutrophil CD11b and soluble P (sP)-selectin.   \n", "CONCLUSIONS Although the RCT evidence may suggest a reduction in post-CPB inflammation by statin therapy, the evidence is not definitive due to significant limitations.", "Several of the trials were not methodologically rigorous and statin intervention was highly variable in this small number of studies.", "This systematic review demonstrates that there is a significant gap that exists in the current literature in regards to the potential anti-inflammatory effect of statin therapy prior to CPB."], "structured": true}
{"doc_id": 2402323, "title": "Array-based Comparative Genomic Hybridization for Genome-Wide Screening of DNA Copy Number in Bladder Tumors", "abstract": ["Genome-wide copy number profiles were characterized in 41 primary bladder tumors using array-based comparative genomic hybridization (array CGH).", "In addition to previously identified alterations in large chromosomal regions, alterations were identified in many small genomic regions, some with high-level amplifications or homozygous deletions.", "High-level amplifications were detected for 192 genomic clones, most frequently at 6p22.3 (E2F3), 8p12 (FGFR1), 8q22.2 (CMYC), 11q13 (CCND1, EMS1, INT2), and 19q13.1 (CCNE).", "Homozygous deletions were detected in 51 genomic clones, with four showing deletions in more than one case: two clones mapping to 9p21.3 (CDKN2A/p16, in nine cases), one at 8p23.1 (three cases), and one at 11p13 (two cases).", "Significant correlations were observed between copy number gain of clones containing CCNE1 and gain of ERBB2, and between gain of CCND1 and deletion of TP53.", "In addition, there was a significant complementary association between gain of CCND1 and gain of E2F3.", "Although there was no significant relationship between copy number changes and tumor stage or grade, the linked behavior among genomic loci suggests that array CGH will be increasingly important in understanding pathways critical to bladder tumor biology."], "structured": false}
{"doc_id": 2405259, "title": "Tet2 is required to resolve inflammation by recruiting Hdac2 to specifically repress IL-6", "abstract": ["Epigenetic modifiers have fundamental roles in defining unique cellular identity through the establishment and maintenance of lineage-specific chromatin and methylation status.", "Several DNA modifications such as 5-hydroxymethylcytosine (5hmC) are catalysed by the ten eleven translocation (Tet) methylcytosine dioxygenase family members, and the roles of Tet proteins in regulating chromatin architecture and gene transcription independently of DNA methylation have been gradually uncovered.", "However, the regulation of immunity and inflammation by Tet proteins independent of their role in modulating DNA methylation remains largely unknown.", "Here we show that Tet2 selectively mediates active repression of interleukin-6 (IL-6) transcription during inflammation resolution in innate myeloid cells, including dendritic cells and macrophages.", "Loss of Tet2 resulted in the upregulation of several inflammatory mediators, including IL-6, at late phase during the response to lipopolysaccharide challenge.", "Tet2-deficient mice were more susceptible to endotoxin shock and dextran-sulfate-sodium-induced colitis, displaying a more severe inflammatory phenotype and increased IL-6 production compared to wild-type mice.", "I\u03baB\u03b6, an IL-6-specific transcription factor, mediated specific targeting of Tet2 to the Il6 promoter, further indicating opposite regulatory roles of I\u03baB\u03b6 at initial and resolution phases of inflammation.", "For the repression mechanism, independent of DNA methylation and hydroxymethylation, Tet2 recruited Hdac2 and repressed transcription of Il6 via histone deacetylation.", "We provide mechanistic evidence for the gene-specific transcription repression activity of Tet2 via histone deacetylation and for the prevention of constant transcription activation at the chromatin level for resolving inflammation."], "structured": false}
{"doc_id": 2417551, "title": "Control of immunity by the TNFR-related molecule OX40 (CD134).", "abstract": ["TNFR/TNF superfamily members can control diverse aspects of immune function.", "Research over the past 10 years has shown that one of the most important and prominent interactions in this family is that between OX40 (CD134) and its partner OX40L (CD252).", "These molecules strongly regulate conventional CD4 and CD8 T cells, and more recent data are highlighting their ability to modulate NKT cell and NK cell function as well as to mediate cross-talk with professional antigen-presenting cells and diverse cell types such as mast cells, smooth muscle cells, and endothelial cells.", "Additionally, OX40-OX40L interactions alter the differentiation and activity of regulatory T cells.", "Blocking OX40L has produced strong therapeutic effects in multiple animal models of autoimmune and inflammatory disease, and, in line with a prospective clinical future, reagents that stimulate OX40 signaling are showing promise as adjuvants for vaccination as well as for treatment of cancer."], "structured": false}
{"doc_id": 2423940, "title": "The Drosophila DHR96 nuclear receptor binds cholesterol and regulates cholesterol homeostasis.", "abstract": ["Cholesterol homeostasis is required to maintain normal cellular function and avoid the deleterious effects of hypercholesterolemia.", "Here we show that the Drosophila DHR96 nuclear receptor binds cholesterol and is required for the coordinate transcriptional response of genes that are regulated by cholesterol and involved in cholesterol uptake, trafficking, and storage.", "DHR96 mutants die when grown on low levels of cholesterol and accumulate excess cholesterol when maintained on a high-cholesterol diet.", "The cholesterol accumulation phenotype can be attributed to misregulation of npc1b, an ortholog of the mammalian Niemann-Pick C1-like 1 gene NPC1L1, which is essential for dietary cholesterol uptake.", "These studies define DHR96 as a central regulator of cholesterol homeostasis."], "structured": false}
{"doc_id": 2424794, "title": "A neuroimaging investigation of the association between aerobic fitness, hippocampal volume, and memory performance in preadolescent children.", "abstract": ["Because children are becoming overweight, unhealthy, and unfit, understanding the neurocognitive benefits of an active lifestyle in childhood has important public health and educational implications.", "Animal research has indicated that aerobic exercise is related to increased cell proliferation and survival in the hippocampus as well as enhanced hippocampal-dependent learning and memory.", "Recent evidence extends this relationship to elderly humans by suggesting that high aerobic fitness levels in older adults are associated with increased hippocampal volume and superior memory performance.", "The present study aimed to further extend the link between fitness, hippocampal volume, and memory to a sample of preadolescent children.", "To this end, magnetic resonance imaging was employed to investigate whether higher- and lower-fit 9- and 10-year-old children showed differences in hippocampal volume and if the differences were related to performance on an item and relational memory task.", "Relational but not item memory is primarily supported by the hippocampus.", "Consistent with predictions, higher-fit children showed greater bilateral hippocampal volumes and superior relational memory task performance compared to lower-fit children.", "Hippocampal volume was also positively associated with performance on the relational but not the item memory task.", "Furthermore, bilateral hippocampal volume was found to mediate the relationship between fitness level (VO(2) max) and relational memory.", "No relationship between aerobic fitness, nucleus accumbens volume, and memory was reported, which strengthens the hypothesized specific effect of fitness on the hippocampus.", "The findings are the first to indicate that aerobic fitness may relate to the structure and function of the preadolescent human brain."], "structured": false}
{"doc_id": 2425364, "title": "Association between maternal serum 25-hydroxyvitamin D level and pregnancy and neonatal outcomes: systematic review and meta-analysis of observational studies.", "abstract": ["OBJECTIVE To assess the effect of 25-hydroxyvitamin D (25-OHD) levels on pregnancy outcomes and birth variables.   \n", "DESIGN Systematic review and meta-analysis.   \n", "DATA SOURCES Medline (1966 to August 2012), PubMed (2008 to August 2012), Embase (1980 to August 2012), CINAHL (1981 to August 2012), the Cochrane database of systematic reviews, and the Cochrane database of registered clinical trials.   ", "STUDY SELECTION Studies reporting on the association between serum 25-OHD levels during pregnancy and the outcomes of interest (pre-eclampsia, gestational diabetes, bacterial vaginosis, caesarean section, small for gestational age infants, birth weight, birth length, and head circumference).   \n", "DATA EXTRACTION Two authors independently extracted data from original research articles, including key indicators of study quality.", "We pooled the most adjusted odds ratios and weighted mean differences.", "Associations were tested in subgroups representing different patient characteristics and study quality.   \n", "RESULTS 3357 studies were identified and reviewed for eligibility.", "31 eligible studies were included in the final analysis.", "Insufficient serum levels of 25-OHD were associated with gestational diabetes (pooled odds ratio 1.49, 95% confidence interval 1.18 to 1.89), pre-eclampsia (1.79, 1.25 to 2.58), and small for gestational age infants (1.85, 1.52 to 2.26).", "Pregnant women with low serum 25-OHD levels had an increased risk of bacterial vaginosis and low birthweight infants but not delivery by caesarean section.   \n", "CONCLUSION Vitamin D insufficiency is associated with an increased risk of gestational diabetes, pre-eclampsia, and small for gestational age infants.", "Pregnant women with low 25-OHD levels had an increased risk of bacterial vaginosis and lower birth weight infants, but not delivery by caesarean section."], "structured": true}
{"doc_id": 2436602, "title": "\u03b2-Adrenergic receptor antagonism prevents anxiety-like behavior and microglial reactivity induced by repeated social defeat.", "abstract": ["Psychosocial stress is associated with altered immune function and development of psychological disorders including anxiety and depression.", "Here we show that repeated social defeat in mice increased c-Fos staining in brain regions associated with fear and threat appraisal and promoted anxiety-like behavior in a \u03b2-adrenergic receptor-dependent manner.", "Repeated social defeat also significantly increased the number of CD11b(+)/CD45(high)/Ly6C(high) macrophages that trafficked to the brain.", "In addition, several inflammatory markers were increased on the surface of microglia (CD14, CD86, and TLR4) and macrophages (CD14 and CD86) after social defeat.", "Repeated social defeat also increased the presence of deramified microglia in the medial amygdala, prefrontal cortex, and hippocampus.", "Moreover, mRNA analysis of microglia indicated that repeated social defeat increased levels of interleukin (IL)-1\u03b2 and reduced levels of glucocorticoid responsive genes [glucocorticoid-induced leucine zipper (GILZ) and FK506 binding protein-51 (FKBP51)].", "The stress-dependent changes in microglia and macrophages were prevented by propranolol, a \u03b2-adrenergic receptor antagonist.", "Microglia isolated from socially defeated mice and cultured ex vivo produced markedly higher levels of IL-6, tumor necrosis factor-\u03b1, and monocyte chemoattractant protein-1 after stimulation with lipopolysaccharide compared with microglia from control mice.", "Last, repeated social defeat increased c-Fos activation in IL-1 receptor type-1-deficient mice, but did not promote anxiety-like behavior or microglia activation in the absence of functional IL-1 receptor type-1.", "These findings indicate that repeated social defeat-induced anxiety-like behavior and enhanced reactivity of microglia was dependent on activation of \u03b2-adrenergic and IL-1 receptors."], "structured": false}
{"doc_id": 2437807, "title": "In vitro differentiation of transplantable neural precursors from human embryonic stem cells", "abstract": ["The remarkable developmental potential and replicative capacity of human embryonic stem (ES) cells promise an almost unlimited supply of specific cell types for transplantation therapies.", "Here we describe the in vitro differentiation, enrichment, and transplantation of neural precursor cells from human ES cells.", "Upon aggregation to embryoid bodies, differentiating ES cells formed large numbers of neural tube\u2013like structures in the presence of fibroblast growth factor 2 (FGF-2).", "Neural precursors within these formations were isolated by selective enzymatic digestion and further purified on the basis of differential adhesion.", "Following withdrawal of FGF-2, they differentiated into neurons, astrocytes, and oligodendrocytes.", "After transplantation into the neonatal mouse brain, human ES cell\u2013derived neural precursors were incorporated into a variety of brain regions, where they differentiated into both neurons and astrocytes.", "No teratoma formation was observed in the transplant recipients.", "These results depict human ES cells as a source of transplantable neural precursors for possible nervous system repair."], "structured": false}
{"doc_id": 2443495, "title": "Characterization of prostaglandin E2 production by Candida albicans.", "abstract": ["Candida albicans produces lipid metabolites that are functionally similar to host prostaglandins.", "These studies, using mass spectrometry, demonstrate that C. albicans produces authentic prostaglandin E(2) (PGE(2)) from arachidonic acid.", "Maximal PGE(2) production was achieved at 37 degrees C in stationary-phase culture supernatants and in cell-free lysates generated from stationary-phase cells.", "Interestingly, PGE(2) production is inhibited by both nonspecific cyclooxygenase and lipoxygenase inhibitors but not by inhibitors specific for the cyclooxygenase 2 isoenzyme.", "The C. albicans genome does not possess a cyclooxygenase homolog; however, several genes that may play a role in prostaglandin production from C. albicans were investigated.", "It was found that a C. albicans fatty acid desaturase homolog (Ole2) and a multicopper oxidase homolog (Fet3) play roles in prostaglandin production, with ole2/ole2 and fet3/fet3 mutant strains exhibiting reduced PGE(2) levels compared with parent strains.", "This work demonstrates that the synthesis of PGE(2) in C. albicans proceeds via novel pathways."], "structured": false}
{"doc_id": 2452989, "title": "A global role for KLF1 in erythropoiesis revealed by ChIP-seq in primary erythroid cells.", "abstract": ["KLF1 regulates a diverse suite of genes to direct erythroid cell differentiation from bipotent progenitors.", "To determine the local cis-regulatory contexts and transcription factor networks in which KLF1 operates, we performed KLF1 ChIP-seq in the mouse.", "We found at least 945 sites in the genome of E14.5 fetal liver erythroid cells which are occupied by endogenous KLF1.", "Many of these recovered sites reside in erythroid gene promoters such as Hbb-b1, but the majority are distant to any known gene.", "Our data suggests KLF1 directly regulates most aspects of terminal erythroid differentiation including production of alpha- and beta-globin protein chains, heme biosynthesis, coordination of proliferation and anti-apoptotic pathways, and construction of the red cell membrane and cytoskeleton by functioning primarily as a transcriptional activator.", "Additionally, we suggest new mechanisms for KLF1 cooperation with other transcription factors, in particular the erythroid transcription factor GATA1, to maintain homeostasis in the erythroid compartment."], "structured": false}
{"doc_id": 2454002, "title": "KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases", "abstract": ["High-throughput experimental technologies often identify dozens to hundreds of genes related to, or changed in, a biological or pathological process.", "From these genes one wants to identify biological pathways that may be involved and diseases that may be implicated.", "Here, we report a web server, KOBAS 2.0, which annotates an input set of genes with putative pathways and disease relationships based on mapping to genes with known annotations.", "It allows for both ID mapping and cross-species sequence similarity mapping.", "It then performs statistical tests to identify statistically significantly enriched pathways and diseases.", "KOBAS 2.0 incorporates knowledge across 1327 species from 5 pathway databases (KEGG PATHWAY, PID, BioCyc, Reactome and Panther) and 5 human disease databases (OMIM, KEGG DISEASE, FunDO, GAD and NHGRI GWAS Catalog).", "KOBAS 2.0 can be accessed at http://kobas.cbi.pku.edu.cn."], "structured": false}
{"doc_id": 2460304, "title": "Translocation of sickle cell erythrocyte microRNAs into Plasmodium falciparum inhibits parasite translation and contributes to malaria resistance.", "abstract": ["Erythrocytes carrying a variant hemoglobin allele (HbS), which causes sickle cell disease and resists infection by the malaria parasite Plasmodium falciparum.", "The molecular basis of this resistance, which has long been recognized as multifactorial, remains incompletely understood.", "Here we show that the dysregulated microRNA (miRNA) composition, of either heterozygous HbAS or homozygous HbSS erythrocytes, contributes to resistance against P. falciparum.", "During the intraerythrocytic life cycle of P. falciparum, a subset of erythrocyte miRNAs translocate into the parasite.", "Two miRNAs, miR-451 and let-7i, were highly enriched in HbAS and HbSS erythrocytes, and these miRNAs, along with miR-223, negatively regulated parasite growth.", "Surprisingly, we found that miR-451 and let-7i integrated into essential parasite messenger RNAs and, via impaired ribosomal loading, resulted in translational inhibition.", "Hence, sickle cell erythrocytes exhibit cell-intrinsic resistance to malaria in part through an atypical miRNA activity, which may represent a unique host defense strategy against complex eukaryotic pathogens."], "structured": false}
{"doc_id": 2462673, "title": "CD28 and ITK signals regulate autoreactive T cell trafficking", "abstract": ["Activation of self-reactive T cells and their trafficking to target tissues leads to autoimmune organ destruction.", "Mice lacking the co-inhibitory receptor cytotoxic T lymphocyte antigen-4 (CTLA-4) develop fatal autoimmunity characterized by lymphocytic infiltration into nonlymphoid tissues.", "Here, we demonstrate that the CD28 co-stimulatory pathway regulates the trafficking of self-reactive Ctla4(-/-) T cells to tissues.", "Concurrent ablation of the CD28-activated Tec family kinase ITK does not block spontaneous T cell activation but instead causes self-reactive Ctla4(-/-) T cells to accumulate in secondary lymphoid organs.", "Despite excessive spontaneous T cell activation and proliferation in lymphoid organs, Itk(-/-); Ctla4(-/-) mice are otherwise healthy, mount antiviral immune responses and exhibit a long lifespan.", "We propose that ITK specifically licenses autoreactive T cells to enter tissues to mount destructive immune responses.", "Notably, ITK inhibitors mimic the null mutant phenotype and also prevent pancreatic islet infiltration by diabetogenic T cells in mouse models of type 1 diabetes, highlighting their potential utility for the treatment of human autoimmune disorders."], "structured": false}
{"doc_id": 2466614, "title": "Delayed and Accelerated Aging Share Common Longevity Assurance Mechanisms", "abstract": ["Mutant dwarf and calorie-restricted mice benefit from healthy aging and unusually long lifespan.", "In contrast, mouse models for DNA repair-deficient progeroid syndromes age and die prematurely.", "To identify mechanisms that regulate mammalian longevity, we quantified the parallels between the genome-wide liver expression profiles of mice with those two extremes of lifespan.", "Contrary to expectation, we find significant, genome-wide expression associations between the progeroid and long-lived mice.", "Subsequent analysis of significantly over-represented biological processes revealed suppression of the endocrine and energy pathways with increased stress responses in both delayed and premature aging.", "To test the relevance of these processes in natural aging, we compared the transcriptomes of liver, lung, kidney, and spleen over the entire murine adult lifespan and subsequently confirmed these findings on an independent aging cohort.", "The majority of genes showed similar expression changes in all four organs, indicating a systemic transcriptional response with aging.", "This systemic response included the same biological processes that are triggered in progeroid and long-lived mice.", "However, on a genome-wide scale, transcriptomes of naturally aged mice showed a strong association to progeroid but not to long-lived mice.", "Thus, endocrine and metabolic changes are indicative of \"survival\" responses to genotoxic stress or starvation, whereas genome-wide associations in gene expression with natural aging are indicative of biological age, which may thus delineate pro- and anti-aging effects of treatments aimed at health-span extension."], "structured": false}
{"doc_id": 2474731, "title": "Arginine depletion as a mechanism for the immune privilege of corneal allografts", "abstract": ["The cornea is an immune privileged tissue.", "Since arginase has been found to modulate T-cell function by depleting arginine, we investigated the expression of arginase in the cornea and its possible role in immune privilege using a murine transplant model.", "We found that both the endothelium and epithelium of murine corneas express functional arginase I, capable of down-regulating T-cell proliferation in an in vitro culture system.", "The administration of the specific arginase inhibitor N-hydroxy-nor-L-Arg to recipient mice resulted in an accelerated rejection of allogeneic C57BL/6 (B6) corneal grafts.", "In contrast, in vivo blockade of arginase activity had no effect in altering the course of rejection of primary skin grafts that express little, if any, arginase.", "In addition, the inhibition of arginase did not alter systemic T-cell proliferation.", "These data show that arginase is functional in the cornea and contributes to the immune privilege of the eye, and that modulation of arginase contributes to graft survival."], "structured": false}
{"doc_id": 2475059, "title": "Once-a-day Concerta methylphenidate versus three-times-daily methylphenidate in laboratory and natural settings.", "abstract": ["OBJECTIVE Methylphenidate (MPH), the most commonly prescribed drug for attention-deficit/hyperactivity disorder (ADHD), has a short half-life, which necessitates multiple daily doses.", "The need for multiple doses produces problems with medication administration during school and after-school hours, and therefore with compliance.", "Previous long-acting stimulants and preparations have shown effects equivalent to twice-daily dosing of MPH.", "This study tests the efficacy and duration of action, in natural and laboratory settings, of an extended-release MPH preparation designed to last 12 hours and therefore be equivalent to 3-times-daily dosing.   \n", "METHODS Sixty-eight children with ADHD, 6 to 12 years old, participated in a within-subject, double-blind comparison of placebo, immediate-release (IR) MPH 3 times a day (tid), and Concerta, a once-daily MPH formulation.", "Three dosing levels of medication were used: 5 mg IR MPH tid/18 mg Concerta once a day (qd);", "10 mg IR MPH tid/36 mg Concerta qd;", "and 15 mg IR MPH tid/54 mg Concerta qd.", "All children were currently medicated with MPH at enrollment, and each child's dose level was based on that child's MPH dosing before the study.", "The doses of Concerta were selected to be comparable to the daily doses of MPH that each child received.", "To achieve the ascending rate of MPH delivery determined by initial investigations to provide the necessary continuous coverage, Concerta doses were 20% higher on a daily basis than a comparable tid regimen of IR MPH.", "Children received each medication condition for 7 days.", "The investigation was conducted in the context of a background clinical behavioral intervention in both the natural environment and the laboratory setting.", "Parents received behavioral parent training and teachers were taught to establish a school-home daily report card (DRC).", "A DRC is a list of individual target behaviors that represent a child's most salient areas of impairment.", "Teachers set daily goals for each child's impairment targets, and parents provided rewards at home for goal attainment.", "Each weekday, teachers completed the DRC, and it was used as a dependent measure of individualized medication response.", "Teachers and parents also completed weekly standardized ratings of behavior and treatment effectiveness.", "To evaluate the time course of medication effects, children spent 12 hours in a laboratory setting on Saturdays and medication effects were measured using procedures and methods adapted from our summer treatment program.", "Measures of classroom behavior and academic productivity/accuracy were taken in a laboratory classroom setting during which children completed independent math and reading worksheets.", "Measures of social behavior were taken in structured, small-group board game settings and unstructured recess settings.", "Measures included behavior frequency counts, academic problems completed and accuracy, independent observations, teacher and counselor ratings, and individualized behavioral target goals.", "Reports of adverse events, sleep quality, and appetite were collected.   \n", "RESULTS On virtually all measures in all settings, both drug conditions were significantly different from placebo, and the 2 drugs were not different from each other.", "In children's regular school settings, both medications improved behavior as measured by teacher ratings and individualized target behaviors (the DRC); these effects were seen into the evening as measured by parent ratings.", "In the laboratory setting, effects of Concerta were equivalent to tid MPH and lasted at least through 12 hours after dosing.", "Concerta was significantly superior to tid MPH on 2 parent rating scores, and when asked, more parents preferred Concerta than preferred tid IR MPH or placebo.", "Side effects on children's sleep and appetite were similar for the 2 preparations.", "In the lab setting, both medications improved productivity and accuracy on arithmetic seatwork assignments, disruptive and on-task behavior, and classroom rule following.", "Both medications improved children's rule following and negative behavior in small group board games, as well as in unstructured recess settings.", "Individual target behaviors also showed significant improvement with medication across domains in the laboratory setting.", "Children's behavior across settings deteriorated across the laboratory day, and the primary effect of medication was to prevent this deterioration as the day wore on.", "Results support the use of background behavioral treatment in clinical trials of stimulant medication, and illustrate the utility of a measure of individualized daily target goals (ie, the DRC) as an objective measure of medication response in both the laboratory and natural school settings.   \n", "CONCLUSION This investigation clearly supports the efficacy of the Concerta long-acting formulation of MPH for parents who desire to have medication benefits for their child throughout the day and early evening.", "(ABSTRACT TRUNCATED)"], "structured": true}
{"doc_id": 2479538, "title": "Leaderless genes in bacteria: clue to the evolution of translation initiation mechanisms in prokaryotes", "abstract": ["BACKGROUND Shine-Dalgarno (SD) signal has long been viewed as the dominant translation initiation signal in prokaryotes.", "Recently, leaderless genes, which lack 5'-untranslated regions (5'-UTR) on their mRNAs, have been shown abundant in archaea.", "However, current large-scale in silico analyses on initiation mechanisms in bacteria are mainly based on the SD-led initiation way, other than the leaderless one.", "The study of leaderless genes in bacteria remains open, which causes uncertain understanding of translation initiation mechanisms for prokaryotes.   \n", "RESULTS Here, we study signals in translation initiation regions of all genes over 953 bacterial and 72 archaeal genomes, then make an effort to construct an evolutionary scenario in view of leaderless genes in bacteria.", "With an algorithm designed to identify multi-signal in upstream regions of genes for a genome, we classify all genes into SD-led, TA-led and atypical genes according to the category of the most probable signal in their upstream sequences.", "Particularly, occurrence of TA-like signals about 10 bp upstream to translation initiation site (TIS) in bacteria most probably means leaderless genes.   \n", "CONCLUSIONS Our analysis reveals that leaderless genes are totally widespread, although not dominant, in a variety of bacteria.", "Especially for Actinobacteria and Deinococcus-Thermus, more than twenty percent of genes are leaderless.", "Analyzed in closely related bacterial genomes, our results imply that the change of translation initiation mechanisms, which happens between the genes deriving from a common ancestor, is linearly dependent on the phylogenetic relationship.", "Analysis on the macroevolution of leaderless genes further shows that the proportion of leaderless genes in bacteria has a decreasing trend in evolution."], "structured": true}
{"doc_id": 2481032, "title": "Neuronal Sirt1 deficiency increases insulin sensitivity in both brain and peripheral tissues.", "abstract": ["Sirt1 is a NAD(+)-dependent class III deacetylase that functions as a cellular energy sensor.", "In addition to its well-characterized effects in peripheral tissues, emerging evidence suggests that neuronal Sirt1 activity plays a role in the central regulation of energy balance and glucose metabolism.", "To assess this idea, we generated Sirt1 neuron-specific knockout (SINKO) mice.", "On both standard chow and HFD, SINKO mice were more insulin sensitive than Sirt1(f/f) mice.", "Thus, SINKO mice had lower fasting insulin levels, improved glucose tolerance and insulin tolerance, and enhanced systemic insulin sensitivity during hyperinsulinemic euglycemic clamp studies.", "Hypothalamic insulin sensitivity of SINKO mice was also increased over controls, as assessed by hypothalamic activation of PI3K, phosphorylation of Akt and FoxO1 following systemic insulin injection.", "Intracerebroventricular injection of insulin led to a greater systemic effect to improve glucose tolerance and insulin sensitivity in SINKO mice compared with controls.", "In line with the in vivo results, insulin-induced AKT and FoxO1 phosphorylation were potentiated by inhibition of Sirt1 in a cultured hypothalamic cell line.", "Mechanistically, this effect was traced to a reduced effect of Sirt1 to directly deacetylate and repress IRS-1 function.", "The enhanced central insulin signaling in SINKO mice was accompanied by increased insulin receptor signal transduction in liver, muscle, and adipose tissue.", "In summary, we conclude that neuronal Sirt1 negatively regulates hypothalamic insulin signaling, leading to systemic insulin resistance.", "Interventions that reduce neuronal Sirt1 activity have the potential to improve systemic insulin action and limit weight gain on an obesigenic diet."], "structured": false}
{"doc_id": 2485101, "title": "Candidate Causal Regulatory Effects by Integration of Expression QTLs with Complex Trait Genetic Associations", "abstract": ["The recent success of genome-wide association studies (GWAS) is now followed by the challenge to determine how the reported susceptibility variants mediate complex traits and diseases.", "Expression quantitative trait loci (eQTLs) have been implicated in disease associations through overlaps between eQTLs and GWAS signals.", "However, the abundance of eQTLs and the strong correlation structure (LD) in the genome make it likely that some of these overlaps are coincidental and not driven by the same functional variants.", "In the present study, we propose an empirical methodology, which we call Regulatory Trait Concordance (RTC) that accounts for local LD structure and integrates eQTLs and GWAS results in order to reveal the subset of association signals that are due to cis eQTLs.", "We simulate genomic regions of various LD patterns with both a single or two causal variants and show that our score outperforms SNP correlation metrics, be they statistical (r(2)) or historical (D').", "Following the observation of a significant abundance of regulatory signals among currently published GWAS loci, we apply our method with the goal to prioritize relevant genes for each of the respective complex traits.", "We detect several potential disease-causing regulatory effects, with a strong enrichment for immunity-related conditions, consistent with the nature of the cell line tested (LCLs).", "Furthermore, we present an extension of the method in trans, where interrogating the whole genome for downstream effects of the disease variant can be informative regarding its unknown primary biological effect.", "We conclude that integrating cellular phenotype associations with organismal complex traits will facilitate the biological interpretation of the genetic effects on these traits."], "structured": false}
{"doc_id": 2488880, "title": "Gender-dependent differences in outcome after the treatment of infection in hospitalized patients.", "abstract": ["CONTEXT While it is established that management strategies and outcomes differ by gender for many diseases, its effect on infection has not been adequately studied.   \n", "OBJECTIVE To investigate the role of gender among hospitalized patients treated for infection.   \n", "DESIGN Observational cohort study conducted during a 26-month period from December 1996 through January 1999.   \n", "SETTING University-affiliated hospital.   \n", "PARTICIPANTS A total of 892 patients in the surgical units of the hospital with 1470 consecutive infectious episodes (782 in men and 688 in women).   \n", "MAIN OUTCOME MEASURES Mortality during hospitalization by gender for infection episodes overall and for specific infectious sites, including lung, peritoneum, bloodstream, catheter, urine, surgical site, and skin/soft tissue.   \n", "RESULTS Among all infections, there was no significant difference in mortality based on gender (men, 11.1% vs women, 14.2%; P = .07).", "After logistic regression analysis, factors independently associated with mortality included higher APACHE (Acute Physiology and Chronic Health Evaluation) II score, older age, malignancy, blood transfusion, and diagnosis of infection more than 7 days after admission, but not gender (female odds ratio [OR] for death, 1.32; 95% confidence interval [CI], 0.90-1.94; P = .16).", "Mortality was higher in women for lung (men, 18% vs women, 34%; P = .002) and soft tissue (men, 2% vs women, 10%; P < or = .05) infection; for other infectious sites, mortality did not differ by gender.", "Factors associated with mortality due to pneumonia by logistic regression included higher APACHE II score, malignancy, diabetes mellitus, diagnosis of infection more than 7 days after admission, older age, transplantation, and female gender (OR for death, 2.25; 95% CI, 1.17-4.32; P = .02).   \n", "CONCLUSIONS Although gender may not be predictive of mortality among all infections, women appear to be at increased risk for death from hospital-acquired pneumonia, even after controlling for other comorbidities."], "structured": true}
{"doc_id": 2492146, "title": "Comparative Safety of Targeted Therapies for Metastatic Colorectal Cancer between Elderly and Younger Patients: a Study Using the International Pharmacovigilance Database", "abstract": ["Metastatic colorectal cancer (mCRC) is increasingly treated using targeted therapies.", "Post-marketing safety of these agents is understudied, especially in the elderly.", "This study aimed to compare, according to age, the adverse drug reactions (ADRs) of targeted therapies used for mCRC in real life.", "An extraction of VigiBase, which contains World Health Organization individual case safety reports (ICSRs), was performed.", "All ADR reports with aflibercept, bevacizumab, cetuximab, panitumumab, or regorafenib used in CRC were considered.", "For all drugs, chi-square tests were used to compare frequencies of serious ADRs between patients aged \u226575 and <75 years.", "For selected ADRs and each drug, the drug-ADR association compared to other anticancer drugs was estimated through the proportional reporting ratio (PRR) in both age groups.", "There were 21,565 ICSRs included, among which 74% were serious and 11% were fatal.", "Median age was 64 years (Inter Quartile Range = 56\u201371) and 15% of patients were aged \u226575; 57% were male.", "Serious ICSRs accounted for 47,292 ADRs.", "Neutropenia was not more reported in elderly for all drugs while diarrhea was more reported in elderly for panitumumab.", "Cardiac disorders were more reported in elderly patients, in particular heart failure, especially for bevacizumab, cetuximab, and regorafenib, as were respiratory, thoracic, and mediastinal disorders.", "Most of PRR were not different between the two groups, except encephalopathies, which were significantly associated with bevacizumab in the elderly only.", "ADRs related to targeted therapies used for mCRC treatment were different across age groups; yet, not systematically more reported or worse in elderly patients.", "Selected elderly patients could, therefore, be treated with these targeted therapies."], "structured": false}
{"doc_id": 2494748, "title": "CpG island methylation in premalignant stages of gastric carcinoma.", "abstract": ["There are limited reports on methylation analysis of the premalignant lesions of gastric carcinoma thus far.", "This is despite the fact that gastric carcinoma is one of the tumors with a high frequency of CpG island hypermethylation.", "To determine the frequency and timing of hypermethylation during multistep gastric carcinogenesis, non-neoplastic gastric mucosa (n = 118), adenomas (n = 61), and carcinomas (n = 64) were analyzed for their p16, human Mut L homologue 1 (hMLH1), death-associated protein (DAP)-kinase, thromobospondin-1 (THBS1), and tissue inhibitor of metalloproteinase 3 (TIMP-3) methylation status using methylation-specific PCR.", "Three different classes of methylation behaviors were found in the five tested genes.", "DAP-kinase was methylated at a similar frequency in all four stages, whereas hMLH1 and p16 were methylated in cancer samples (20.3% and 42.2%, respectively) more frequently than in intestinal metaplasia (6.3% and 2.1%, respectively) or adenomas (9.8% and 11.5%, respectively).", "However, hMLH1 and p16 were not methylated in chronic gastritis.", "THBS-1 and TIMP-3 were methylated in all stages but showed a marked increase in hypermethylation frequency from chronic gastritis (10.1% and 14.5%, respectively) to intestinal metaplasia (34.7% and 36.7%, respectively; P < 0.05) and from adenomas (28.3% and 26.7%, respectively) to carcinomas (48.4% and 57.4%, respectively: P < 0.05).", "The hMLH1, THBS1, and TIMP-3 hypermethylation frequencies were similar in both intestinal metaplasia and adenomas, but the p16 hypermethylation frequency tended to be higher in adenomas (11.5%) than in intestinal metaplasia (2.1%; P = 0.073).", "The average number of methylated genes was 0.6, 1.1, 1.1, and 2.0 per five genes per sample in chronic gastritis, intestinal metaplasia, adenomas, and carcinomas, respectively.", "This shows a marked increase in methylated genes from non-metaplastic mucosa to intestinal metaplasia (P = 0.001) as well as from premalignant lesions to carcinomas (P = 0.002).", "These results suggest that CpG island hypermethylation occur early in multistep gastric carcinogenesis and tend to accumulate along the multistep carcinogenesis."], "structured": false}
{"doc_id": 2496002, "title": "Familial amyloidotic polyneuropathy: current and emerging treatment options for transthyretin-mediated amyloidosis", "abstract": ["Transthyretin familial amyloid polyneuropathy (TTR-FAP) is a fatal clinical disorder characterized by extracellular deposition of abnormal fibrils derived from misfolded, normally soluble transthyretin (TTR) molecules.", "The disease is most commonly caused by a point mutation within the TTR gene inherited in an autosomal dominant fashion.", "Over 100 of such mutations have been identified, leading to destabilization of the physiological TTR tetramer.", "As a result, many monomers originate with a tendency for spontaneous conformational changes and self-aggregation.", "The main clinical feature of TTR-FAP is progressive sensorimotor and autonomic neuropathy.", "In the beginning, this polyneuropathy predominantly involves small unmyelinated nerve fibers with the result of dissociated sensory loss disproportionately affecting sensation of pain and temperature.", "Autonomic neuropathy typically accompanies sensory deficits early in the disease course.", "The symptoms include orthostatic hypotension, constipation alternating with diarrhea, erectile dysfunction, anhydrosis, and urinary retention or incontinence.", "Later, involvement of motor fibers causes rapidly progressive weakness and gait disturbances.", "In addition to the peripheral nervous system, the heart and the gut are frequently affected.", "Onset of symptoms is bimodal, with one peak at age 33 years (early onset) and another distinct peak in the sixth decade of life (late onset).", "The course of TTR-FAP is uniformly progressive and fatal.", "Death occurs an average of 10.8 years after the onset of symptoms in Portuguese patients, and 7.3 years in late-onset Japanese patients.", "Common causes include cachexia, cardiac failure, arrhythmia, and secondary infections.", "Liver transplantation is the standard therapy for patients who are in a clinical condition good enough to tolerate this intervention because it stops progression of neuropathy by removing the main source of mutant TTR.", "Recently, orally administered tafamidis meglumine has been approved by European authorities for treatment of FAP.", "The substance has been shown to stabilize the TTR tetramer, thereby improving the outcome of patients with TTR-FAP.", "Various other strategies have been studied in vitro to prevent TTR amyloidosis, including gene therapy, immunization, dissolution of TTR aggregates, and free radical scavengers, but none of them is ready for clinical use so far."], "structured": false}
{"doc_id": 2506153, "title": "Invariant natural killer T cells: bridging innate and adaptive immunity", "abstract": ["Cells of the innate immune system interact with pathogens via conserved pattern-recognition receptors, whereas cells of the adaptive immune system recognize pathogens through diverse, antigen-specific receptors that are generated by somatic DNA rearrangement.", "Invariant natural killer T (iNKT) cells are a subset of lymphocytes that bridge the innate and adaptive immune systems.", "Although iNKT cells express T cell receptors that are generated by somatic DNA rearrangement, these receptors are semi-invariant and interact with a limited set of lipid and glycolipid antigens, thus resembling the pattern-recognition receptors of the innate immune system.", "Functionally, iNKT cells most closely resemble cells of the innate immune system, as they rapidly elicit their effector functions following activation, and fail to develop immunological memory.", "iNKT cells can become activated in response to a variety of stimuli and participate in the regulation of various immune responses.", "Activated iNKT cells produce several cytokines with the capacity to jump-start and modulate an adaptive immune response.", "A variety of glycolipid antigens that can differentially elicit distinct effector functions in iNKT cells have been identified.", "These reagents have been employed to test the hypothesis that iNKT cells can be harnessed for therapeutic purposes in human diseases.", "Here, we review the innate-like properties and functions of iNKT cells and discuss their interactions with other cell types of the immune system."], "structured": false}
{"doc_id": 2522977, "title": "Olmesartan-based therapies: an effective way to improve blood pressure control and cardiovascular protection.", "abstract": ["The main purpose in hypertension treatment is the reduction of cardiovascular disease burden.", "Among different first-line antihypertensive drug classes, angiotensin-receptor blockers are characterized by their both good effectiveness and tolerability.", "Furthermore, the interruption of the renin-angiotensin cascade is related with several benefits in target organ protection and cardiovascular prevention.", "Among different angiotensin-receptor blockers, olmesartan has been examined in several trial of organ protection, showing improvements in several disease markers, such as microinflammation, regression of both plaque volume and vascular hypertrophy, as well as microalbuminuria prevention.", "Olmesartan has been also widely examined in combination of either hydrochlorothiazide or amlodipine, as well as with both drugs in a single-pill triple combination, showing improvements in antihypertensive efficacy without significant effects on tolerability.", "This treatment strategy based on a drug with such characteristics and the availability of different types of combinations with other first-line drug classes may represent an effective way for achieving blood pressure control in a majority of hypertensive patients and this could also be related with a better cardiovascular disease prevention."], "structured": false}
{"doc_id": 2526777, "title": "Manslaughter by Fake Artesunate in Asia\u2014Will Africa Be Next?", "abstract": ["Falciparum malaria kills, and it particularly kills the rural poor.", "Artemisinin derivatives, such as artesunate, are a vital component of Plasmodium falciparum malaria treatment and control in the face of globally increasing antimalarial drug resistance.", "Since 1998 a worsening epidemic of sophisticated counterfeit \u201cartesunate\u201d tablets (containing no artesunate) has plagued mainland Southeast Asia (see Figure S1).", "In some countries, most of the available artesunate is fake [ 1\u20135].    ", "Artemisinin derivatives are remarkably rapid in their antimalarial effects, and they are very well tolerated.", "So where these medicines are available, they are sought after.", "But as they are relatively expensive, a demand is created for cheaper versions amongst the poorest and most vulnerable people, upon whom the counterfeiters have preyed\u2013with fatal results."], "structured": false}
{"doc_id": 2533768, "title": "Workshop: endothelial cell dysfunction leading to diabetic nephropathy : focus on nitric oxide.", "abstract": ["Clinical manifestations of diabetic nephropathy are an expression of diabetic microangiopathy.", "This review revisits the previously proposed Steno hypothesis and advances our hypothesis that development of endothelial cell dysfunction represents a common pathophysiological pathway of diabetic complications.", "Specifically, the ability of glucose to scavenge nitric oxide is proposed as the initiation phase of endothelial dysfunction.", "Gradual accumulation of advanced glycated end products and induction of plasminogen activator inhibitor-1, resulting in the decreased expression of endothelial nitric oxide synthase and reduced generation of nitric oxide, are proposed to be pathophysiologically critical for the maintenance phase of endothelial dysfunction.", "The proposed conceptual shift toward the role of endothelial dysfunction in diabetic complications may provide new strategies for their prevention."], "structured": false}
{"doc_id": 2541699, "title": "A nuclear Argonaute promotes multi-generational epigenetic inheritance and germline immortality", "abstract": ["Epigenetic information is frequently erased near the start of each new generation.", "In some cases, however, epigenetic information can be transmitted from parent to progeny (multigenerational epigenetic inheritance).", "A particularly notable example of this type of epigenetic inheritance is double-stranded RNA-mediated gene silencing in Caenorhabditis elegans.", "This RNA-mediated interference (RNAi) can be inherited for more than five generations.", "To understand this process, here we conduct a genetic screen for nematodes defective in transmitting RNAi silencing signals to future generations.", "This screen identified the heritable RNAi defective 1 (hrde-1) gene.", "hrde-1 encodes an Argonaute protein that associates with small interfering RNAs in the germ cells of progeny of animals exposed to double-stranded RNA.", "In the nuclei of these germ cells, HRDE-1 engages the nuclear RNAi defective pathway to direct the trimethylation of histone H3 at Lys 9 (H3K9me3) at RNAi-targeted genomic loci and promote RNAi inheritance.", "Under normal growth conditions, HRDE-1 associates with endogenously expressed short interfering RNAs, which direct nuclear gene silencing in germ cells.", "In hrde-1- or nuclear RNAi-deficient animals, germline silencing is lost over generational time.", "Concurrently, these animals exhibit steadily worsening defects in gamete formation and function that ultimately lead to sterility.", "These results establish that the Argonaute protein HRDE-1 directs gene-silencing events in germ-cell nuclei that drive multigenerational RNAi inheritance and promote immortality of the germ-cell lineage.", "We propose that C. elegans use the RNAi inheritance machinery to transmit epigenetic information, accrued by past generations, into future generations to regulate important biological processes."], "structured": false}
{"doc_id": 2543135, "title": "Autophagic programmed cell death by selective catalase degradation.", "abstract": ["Autophagy plays a central role in regulating important cellular functions such as cell survival during starvation and control of infectious pathogens.", "Recently, it has been shown that autophagy can induce cells to die; however, the mechanism of the autophagic cell death program is unclear.", "We now show that caspase inhibition leading to cell death by means of autophagy involves reactive oxygen species (ROS) accumulation, membrane lipid oxidation, and loss of plasma membrane integrity.", "Inhibition of autophagy by chemical compounds or knocking down the expression of key autophagy proteins such as ATG7, ATG8, and receptor interacting protein (RIP) blocks ROS accumulation and cell death.", "The cause of abnormal ROS accumulation is the selective autophagic degradation of the major enzymatic ROS scavenger, catalase.", "Caspase inhibition directly induces catalase degradation and ROS accumulation, which can be blocked by autophagy inhibitors.", "These findings unveil a molecular mechanism for the role of autophagy in cell death and provide insight into the complex relationship between ROS and nonapoptotic programmed cell death."], "structured": false}
{"doc_id": 2547636, "title": "Human epidermal stem cell function is regulated by circadian oscillations.", "abstract": ["Human skin copes with harmful environmental factors that are circadian in nature, yet how circadian rhythms modulate the function of human epidermal stem cells is mostly unknown.", "Here we show that in human epidermal stem cells and their differentiated counterparts, core clock genes peak in a successive and phased manner, establishing distinct temporal intervals during the 24 hr day period.", "Each of these successive clock waves is associated with a peak in the expression of subsets of transcripts that temporally segregate the predisposition of epidermal stem cells to respond to cues that regulate their proliferation or differentiation, such as TGF\u03b2 and calcium.", "Accordingly, circadian arrhythmia profoundly affects stem cell function in culture and in vivo.", "We hypothesize that this intricate mechanism ensures homeostasis by providing epidermal stem cells with environmentally relevant temporal functional cues during the course of the day and that its perturbation may contribute to aging and carcinogenesis."], "structured": false}
{"doc_id": 2559303, "title": "Engraftment of engineered ES cell\u2013derived cardiomyocytes but not BM cells restores contractile function to the infarcted myocardium", "abstract": ["Cellular cardiomyoplasty is an attractive option for the treatment of severe heart failure.", "It is, however, still unclear and controversial which is the most promising cell source.", "Therefore, we investigated and examined the fate and functional impact of bone marrow (BM) cells and embryonic stem cell (ES cell)\u2013derived cardiomyocytes after transplantation into the infarcted mouse heart.", "This proved particularly challenging for the ES cells, as their enrichment into cardiomyocytes and their long-term engraftment and tumorigenicity are still poorly understood.", "We generated transgenic ES cells expressing puromycin resistance and enhanced green fluorescent protein cassettes under control of a cardiac-specific promoter.", "Puromycin selection resulted in a highly purified (>99%) cardiomyocyte population, and the yield of cardiomyocytes increased 6\u201310-fold because of induction of proliferation on purification.", "Long-term engraftment (4\u20135 months) was observed when co-transplanting selected ES cell\u2013derived cardiomyocytes and fibroblasts into the injured heart of syngeneic mice, and no teratoma formation was found (n = 60).", "Although transplantation of ES cell\u2013derived cardiomyocytes improved heart function, BM cells had no positive effects.", "Furthermore, no contribution of BM cells to cardiac, endothelial, or smooth muscle neogenesis was detected.", "Hence, our results demonstrate that ES-based cell therapy is a promising approach for the treatment of impaired myocardial function and provides better results than BM-derived cells."], "structured": false}
{"doc_id": 2565138, "title": "Hyaluronan impairs vascular function and drug delivery in a mouse model of pancreatic cancer", "abstract": ["OBJECTIVE Pancreatic ductal adenocarcinoma (PDA) is characterised by stromal desmoplasia and vascular dysfunction, which critically impair drug delivery.", "This study examines the role of an abundant extracellular matrix component, the megadalton glycosaminoglycan hyaluronan (HA), as a novel therapeutic target in PDA.   \n", "METHODS Using a genetically engineered mouse model of PDA, the authors enzymatically depleted HA by a clinically formulated PEGylated human recombinant PH20 hyaluronidase (PEGPH20) and examined tumour perfusion, vascular permeability and drug delivery.", "The preclinical utility of PEGPH20 in combination with gemcitabine was assessed by short-term and survival studies.   \n", "RESULTS PEGPH20 rapidly and sustainably depleted HA, inducing the re-expansion of PDA blood vessels and increasing the intratumoral delivery of two chemotherapeutic agents, doxorubicin and gemcitabine.", "Moreover, PEGPH20 triggered fenestrations and interendothelial junctional gaps in PDA tumour endothelia and promoted a tumour-specific increase in macromolecular permeability.", "Finally, combination therapy with PEGPH20 and gemcitabine led to inhibition of PDA tumour growth and prolonged survival over gemcitabine monotherapy, suggesting immediate clinical utility.   \n", "CONCLUSIONS The authors demonstrate that HA impedes the intratumoral vasculature in PDA and propose that its enzymatic depletion be explored as a means to improve drug delivery and response in patients with pancreatic cancer."], "structured": true}
{"doc_id": 2566674, "title": "Ribose 2\u2032-O-methylation provides a molecular signature for the distinction of self and non-self mRNA dependent on the RNA sensor Mda5", "abstract": ["The 5\u2032 cap structures of higher eukaryote mRNAs have ribose 2\u2032-O-methylation.", "Likewise, many viruses that replicate in the cytoplasm of eukaryotes have evolved 2\u2032-O-methyltransferases to autonomously modify their mRNAs.", "However, a defined biological role for 2\u2032-O-methylation of mRNA remains elusive.", "Here we show that 2\u2032-O-methylation of viral mRNA was critically involved in subverting the induction of type I interferon.", "We demonstrate that human and mouse coronavirus mutants lacking 2\u2032-O-methyltransferase activity induced higher expression of type I interferon and were highly sensitive to type I interferon.", "Notably, the induction of type I interferon by viruses deficient in 2\u2032-O-methyltransferase was dependent on the cytoplasmic RNA sensor Mda5.", "This link between Mda5-mediated sensing of viral RNA and 2\u2032-O-methylation of mRNA suggests that RNA modifications such as 2\u2032-O-methylation provide a molecular signature for the discrimination of self and non-self mRNA."], "structured": false}
{"doc_id": 2575938, "title": "Relationship between activity levels, aerobic fitness, and body fat in 8- to 10-yr-old children.", "abstract": ["The relationships between children's activity, aerobic fitness, and fatness are unclear.", "Indirect estimates of activity, e.g., heart rate (HR) and recall, may mask any associations.", "The purpose of this study was to assess these relationships by using the Tritrac-R3D, a pedometer, and heart rate.", "Thirty-four children, ages 8-10 yr, participated in the study.", "The Tritrac and pedometer were worn for up to 6 days.", "HR was measured for 1 day.", "Activity measured by Tritrac or pedometer correlated positively to fitness in the whole group (Tritrac, r = 0.66; pedometer, r = 0.59; P < 0.01) and in boys and girls separately (P < 0.05) and correlated negatively to fatness in the whole group (r = -0.42, P < 0.05).", "In contrast, HR did not correlate significantly to fitness, and HR of >139 beats/min correlated positively to fatness in girls (r = 0.64, P < 0.05).", "This suggests that HR is misleading as a measure of activity.", "This study supports a positive relationship between activity and fitness and suggests a negative relationship between fatness and activity."], "structured": false}
{"doc_id": 2576811, "title": "Junctional actin assembly is mediated by Formin-like 2 downstream of Rac1", "abstract": ["Epithelial integrity is vitally important, and its deregulation causes early stage cancer.", "De novo formation of an adherens junction (AJ) between single epithelial cells requires coordinated, spatial actin dynamics, but the mechanisms steering nascent actin polymerization for cell-cell adhesion initiation are not well understood.", "Here we investigated real-time actin assembly during daughter cell-cell adhesion formation in human breast epithelial cells in 3D environments.", "We identify formin-like 2 (FMNL2) as being specifically required for actin assembly and turnover at newly formed cell-cell contacts as well as for human epithelial lumen formation.", "FMNL2 associates with components of the AJ complex involving Rac1 activity and the FMNL2 C terminus.", "Optogenetic control of Rac1 in living cells rapidly drove FMNL2 to epithelial cell-cell contact zones.", "Furthermore, Rac1-induced actin assembly and subsequent AJ formation critically depends on FMNL2.", "These data uncover FMNL2 as a driver for human epithelial AJ formation downstream of Rac1."], "structured": false}
{"doc_id": 2582169, "title": "Inhibition of HDM2 and activation of p53 by ribosomal protein L23.", "abstract": ["The importance of coordinating cell growth with proliferation has been recognized for a long time.", "The molecular basis of this relationship, however, is poorly understood.", "Here we show that the ribosomal protein L23 interacts with HDM2.", "The interaction involves the central acidic domain of HDM2 and an N-terminal domain of L23.", "L23 and L11, another HDM2-interacting ribosomal protein, can simultaneously yet distinctly interact with HDM2 together to form a ternary complex.", "We show that, when overexpressed, L23 inhibits HDM2-induced p53 polyubiquitination and degradation and causes a p53-dependent cell cycle arrest.", "On the other hand, knocking down L23 causes nucleolar stress and triggers translocation of B23 from the nucleolus to the nucleoplasm, leading to stabilization and activation of p53.", "Our data suggest that cells may maintain a steady-state level of L23 during normal growth; alternating the levels of L23 in response to changing growth conditions could impinge on the HDM2-p53 pathway by interrupting the integrity of the nucleolus."], "structured": false}
{"doc_id": 2587396, "title": "Association of Blood Monocyte and Platelet Markers with Carotid Artery Characteristics: The Atherosclerosis Risk in Communities Carotid MRI Study", "abstract": ["Background: Atherosclerosis is characterized by infiltration of inflammatory cells from circulating blood.", "Blood cell activation could play an important role in plaque formation.", "Methods: We analyzed the relationship between blood cellular markers and quantitative measures of carotid wall components in 1,546 participants from the ARIC (Atherosclerosis Risk in Communities)", "Carotid MRI Study.", "Carotid imaging was performed using a gadolinium contrast-enhanced MRI and cellular phenotyping by flow cytometry.", "Results: Monocyte Toll-like receptor (TLR)-2 is associated with larger plaques, while CD14, myeloperoxidase, and TLR-4 associate with smaller.", "Platelet CD40L is associated with smaller plaques and thinner caps, while P-selectin is associated with smaller core size.", "Conclusions: Blood cell activation is significantly associated with atherosclerotic changes of the carotid wall."], "structured": false}
{"doc_id": 2593298, "title": "Vascular endothelial cadherin controls VEGFR-2 internalization and signaling from intracellular compartments", "abstract": ["Receptor endocytosis is a fundamental step in controlling the magnitude, duration, and nature of cell signaling events.", "Confluent endothelial cells are contact inhibited in their growth and respond poorly to the proliferative signals of vascular endothelial growth factor (VEGF).", "In a previous study, we found that the association of vascular endothelial cadherin (VEC) with VEGF receptor (VEGFR) type 2 contributes to density-dependent growth inhibition (Lampugnani, G.M., A. Zanetti, M. Corada, T. Takahashi, G. Balconi, F. Breviario, F. Orsenigo, A. Cattelino, R. Kemler, T.O. Daniel, and E. Dejana.", "2003.", "J. Cell Biol.", "161:793\u2013804).", "In the present study, we describe the mechanism through which VEC reduces VEGFR-2 signaling.", "We found that VEGF induces the clathrin-dependent internalization of VEGFR-2.", "When VEC is absent or not engaged at junctions, VEGFR-2 is internalized more rapidly and remains in endosomal compartments for a longer time.", "Internalization does not terminate its signaling; instead, the internalized receptor is phosphorylated, codistributes with active phospholipase C\u2013\u03b3, and activates p44/42 mitogen-activated protein kinase phosphorylation and cell proliferation.", "Inhibition of VEGFR-2 internalization reestablishes the contact inhibition of cell growth, whereas silencing the junction-associated density-enhanced phosphatase-1/CD148 phosphatase restores VEGFR-2 internalization and signaling.", "Thus, VEC limits cell proliferation by retaining VEGFR-2 at the membrane and preventing its internalization into signaling compartments."], "structured": false}
{"doc_id": 2601135, "title": "Diversification in the HIV-1 Envelope Hyper-variable Domains V2, V4, and V5 and Higher Probability of Transmitted/Founder Envelope Glycosylation Favor the Development of Heterologous Neutralization Breadth", "abstract": ["A recent study of plasma neutralization breadth in HIV-1 infected individuals at nine International AIDS Vaccine Initiative (IAVI) sites reported that viral load, HLA-A*03 genotype, and subtype C infection were strongly associated with the development of neutralization breadth.", "Here, we refine the findings of that study by analyzing the impact of the transmitted/founder (T/F) envelope (Env), early Env diversification, and autologous neutralization on the development of plasma neutralization breadth in 21 participants identified during recent infection at two of those sites: Kigali, Rwanda (n = 9) and Lusaka, Zambia (n = 12).", "Single-genome analysis of full-length T/F Env sequences revealed that all 21 individuals were infected with a highly homogeneous population of viral variants, which were categorized as subtype C (n = 12), A1 (n = 7), or recombinant AC (n = 2).", "An extensive amino acid sequence-based analysis of variable loop lengths and glycosylation patterns in the T/F Envs revealed that a lower ratio of NXS to NXT-encoded glycan motifs correlated with neutralization breadth.", "Further analysis comparing amino acid sequence changes, insertions/deletions, and glycan motif alterations between the T/F Env and autologous early Env variants revealed that extensive diversification focused in the V2, V4, and V5 regions of gp120, accompanied by contemporaneous viral escape, significantly favored the development of breadth.", "These results suggest that more efficient glycosylation of subtype A and C T/F Envs through fewer NXS-encoded glycan sites is more likely to elicit antibodies that can transition from autologous to heterologous neutralizing activity following exposure to gp120 diversification.", "This initiates an Env-antibody co-evolution cycle that increases neutralization breadth, and is further augmented over time by additional viral and host factors.", "These findings suggest that understanding how variation in the efficiency of site-specific glycosylation influences neutralizing antibody elicitation and targeting could advance the design of immunogens aimed at inducing antibodies that can transition from autologous to heterologous neutralizing activity."], "structured": false}
{"doc_id": 2601324, "title": "Glycolytic oligodendrocytes maintain myelin and long-term axonal integrity", "abstract": ["Oligodendrocytes, the myelin-forming glial cells of the central nervous system, maintain long-term axonal integrity.", "However, the underlying support mechanisms are not understood.", "Here we identify a metabolic component of axon\u2013glia interactions by generating conditional Cox10 (protoheme IX farnesyltransferase) mutant mice, in which oligodendrocytes and Schwann cells fail to assemble stable mitochondrial cytochrome c oxidase (COX, also known as mitochondrial complex IV).", "In the peripheral nervous system, Cox10 conditional mutants exhibit severe neuropathy with dysmyelination, abnormal Remak bundles, muscle atrophy and paralysis.", "Notably, perturbing mitochondrial respiration did not cause glial cell death.", "In the adult central nervous system, we found no signs of demyelination, axonal degeneration or secondary inflammation.", "Unlike cultured oligodendrocytes, which are sensitive to COX inhibitors, post-myelination oligodendrocytes survive well in the absence of COX activity.", "More importantly, by in vivo magnetic resonance spectroscopy, brain lactate concentrations in mutants were increased compared with controls, but were detectable only in mice exposed to volatile anaesthetics.", "This indicates that aerobic glycolysis products derived from oligodendrocytes are rapidly metabolized within white matter tracts.", "Because myelinated axons can use lactate when energy-deprived, our findings suggest a model in which axon\u2013glia metabolic coupling serves a physiological function."], "structured": false}
{"doc_id": 2603304, "title": "Siglec-1 Is a Novel Dendritic Cell Receptor That Mediates HIV-1 Trans-Infection Through Recognition of Viral Membrane Gangliosides", "abstract": ["Dendritic cells (DCs) are essential antigen-presenting cells for the induction of immunity against pathogens.", "However, HIV-1 spread is strongly enhanced in clusters of DCs and CD4(+) T cells.", "Uninfected DCs capture HIV-1 and mediate viral transfer to bystander CD4(+) T cells through a process termed trans-infection.", "Initial studies identified the C-type lectin DC-SIGN as the HIV-1 binding factor on DCs, which interacts with the viral envelope glycoproteins.", "Upon DC maturation, however, DC-SIGN is down-regulated, while HIV-1 capture and trans-infection is strongly enhanced via a glycoprotein-independent capture pathway that recognizes sialyllactose-containing membrane gangliosides.", "Here we show that the sialic acid-binding Ig-like lectin 1 (Siglec-1, CD169), which is highly expressed on mature DCs, specifically binds HIV-1 and vesicles carrying sialyllactose.", "Furthermore, Siglec-1 is essential for trans-infection by mature DCs.", "These findings identify Siglec-1 as a key factor for HIV-1 spread via infectious DC/T-cell synapses, highlighting a novel mechanism that mediates HIV-1 dissemination in activated tissues."], "structured": false}
{"doc_id": 2604063, "title": "The composition of the gut microbiota throughout life, with an emphasis on early life", "abstract": ["The intestinal microbiota has become a relevant aspect of human health.", "Microbial colonization runs in parallel with immune system maturation and plays a role in intestinal physiology and regulation.", "Increasing evidence on early microbial contact suggest that human intestinal microbiota is seeded before birth.", "Maternal microbiota forms the first microbial inoculum, and from birth, the microbial diversity increases and converges toward an adult-like microbiota by the end of the first 3-5 years of life.", "Perinatal factors such as mode of delivery, diet, genetics, and intestinal mucin glycosylation all contribute to influence microbial colonization.", "Once established, the composition of the gut microbiota is relatively stable throughout adult life, but can be altered as a result of bacterial infections, antibiotic treatment, lifestyle, surgical, and a long-term change in diet.", "Shifts in this complex microbial system have been reported to increase the risk of disease.", "Therefore, an adequate establishment of microbiota and its maintenance throughout life would reduce the risk of disease in early and late life.", "This review discusses recent studies on the early colonization and factors influencing this process which impact on health."], "structured": false}
{"doc_id": 2605032, "title": "Intrauterine protein restriction combined with early postnatal overfeeding was not associated with adult-onset obesity but produced glucose intolerance by pancreatic dysfunction", "abstract": ["We investigated if whether intrauterine protein restriction in combination with overfeeding during lactation would cause adult-onset obesity and metabolic disorders.", "After birth, litters from dams fed with control (17% protein) and low protein (6% protein) diets were adjusted to a size of four (CO and LO groups, respectively) or eight (CC and LC groups, respectively) pups.", "All of the offspring were fed a diet containing 12% protein from the time of weaning until they were 90 d old.", "Compared to the CC and LC groups, the CO and LO groups had higher relative and absolute food intakes, oxygen consumption and carbon dioxide production; lower brown adipose tissue weight and lipid content and greater weight gain and absolute and relative white adipose tissue weight and absolute lipid content.", "Compared with the CO and CC rats, the LC and LO rats exhibited higher relative food intake, brown adipose tissue weight and lipid content, reduced oxygen consumption, carbon dioxide production and spontaneous activity, increased relative retroperitoneal adipose tissue weight and unaltered absolute white adipose tissue weight and lipid content.", "The fasting serum glucose was similar among the groups.", "The area under the glucose curve was higher in the LO and CO rats than in the LC and CC rats.", "The basal insulinemia and homeostasis model assessment of insulin resistance (HOMA-IR) were lower in the LO group than in the other groups.", "The total area under the insulin curve for the LO rats was similar to the CC rats, and both were lower than the CO and LC rats.", "Kitt was higher in the LO, LC and CO groups than in the CC group.", "Thus, intrauterine protein restriction followed by overfeeding during lactation did not induce obesity, but produced glucose intolerance by impairing pancreatic function in adulthood."], "structured": false}
{"doc_id": 2608447, "title": "Somatic coding mutations in human induced pluripotent stem cells", "abstract": ["Defined transcription factors can induce epigenetic reprogramming of adult mammalian cells into induced pluripotent stem cells.", "Although DNA factors are integrated during some reprogramming methods, it is unknown whether the genome remains unchanged at the single nucleotide level.", "Here we show that 22 human induced pluripotent stem (hiPS) cell lines reprogrammed using five different methods each contained an average of five protein-coding point mutations in the regions sampled (an estimated six protein-coding point mutations per exome).", "The majority of these mutations were non-synonymous, nonsense or splice variants, and were enriched in genes mutated or having causative effects in cancers.", "At least half of these reprogramming-associated mutations pre-existed in fibroblast progenitors at low frequencies, whereas the rest occurred during or after reprogramming.", "Thus, hiPS cells acquire genetic modifications in addition to epigenetic modifications.", "Extensive genetic screening should become a standard procedure to ensure hiPS cell safety before clinical use."], "structured": false}
{"doc_id": 2613411, "title": "Cell cycle, CDKs and cancer: a changing paradigm", "abstract": ["Tumour-associated cell cycle defects are often mediated by alterations in cyclin-dependent kinase (CDK) activity.", "Misregulated CDKs induce unscheduled proliferation as well as genomic and chromosomal instability.", "According to current models, mammalian CDKs are essential for driving each cell cycle phase, so therapeutic strategies that block CDK activity are unlikely to selectively target tumour cells.", "However, recent genetic evidence has revealed that, whereas CDK1 is required for the cell cycle, interphase CDKs are only essential for proliferation of specialized cells.", "Emerging evidence suggests that tumour cells may also require specific interphase CDKs for proliferation.", "Thus, selective CDK inhibition may provide therapeutic benefit against certain human neoplasias."], "structured": false}
{"doc_id": 2613775, "title": "Sudden infant death syndrome.", "abstract": ["Despite declines in prevalence during the past two decades, sudden infant death syndrome (SIDS) continues to be the leading cause of death for infants aged between 1 month and 1 year in developed countries.", "Behavioural risk factors identified in epidemiological studies include prone and side positions for infant sleep, smoke exposure, soft bedding and sleep surfaces, and overheating.", "Evidence also suggests that pacifier use at sleep time and room sharing without bed sharing are associated with decreased risk of SIDS.", "Although the cause of SIDS is unknown, immature cardiorespiratory autonomic control and failure of arousal responsiveness from sleep are important factors.", "Gene polymorphisms relating to serotonin transport and autonomic nervous system development might make affected infants more vulnerable to SIDS.", "Campaigns for risk reduction have helped to reduce SIDS incidence by 50-90%.", "However, to reduce the incidence even further, greater strides must be made in reducing prenatal smoke exposure and implementing other recommended infant care practices.", "Continued research is needed to identify the pathophysiological basis of SIDS."], "structured": false}
{"doc_id": 2613813, "title": "Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi.", "abstract": ["Eukaryotic heterochromatin is characterized by a high density of repeats and transposons, as well as by modified histones, and influences both gene expression and chromosome segregation.", "In the fission yeast Schizosaccharomyces pombe, we deleted the argonaute, dicer, and RNA-dependent RNA polymerase gene homologs, which encode part of the machinery responsible for RNA interference (RNAi).", "Deletion results in the aberrant accumulation of complementary transcripts from centromeric heterochromatic repeats.", "This is accompanied by transcriptional de-repression of transgenes integrated at the centromere, loss of histone H3 lysine-9 methylation, and impairment of centromere function.", "We propose that double-stranded RNA arising from centromeric repeats targets formation and maintenance of heterochromatin through RNAi."], "structured": false}
{"doc_id": 2617858, "title": "Conformational Changes during Pore Formation by the Perforin-Related Protein Pleurotolysin", "abstract": ["Membrane attack complex/perforin-like (MACPF) proteins comprise the largest superfamily of pore-forming proteins, playing crucial roles in immunity and pathogenesis.", "Soluble monomers assemble into large transmembrane pores via conformational transitions that remain to be structurally and mechanistically characterised.", "Here we present an 11 \u00c5 resolution cryo-electron microscopy (cryo-EM) structure of the two-part, fungal toxin Pleurotolysin (Ply), together with crystal structures of both components (the lipid binding PlyA protein and the pore-forming MACPF component PlyB).", "These data reveal a 13-fold pore 80 \u00c5 in diameter and 100 \u00c5 in height, with each subunit comprised of a PlyB molecule atop a membrane bound dimer of PlyA. The resolution of the EM map, together with biophysical and computational experiments, allowed confident assignment of subdomains in a MACPF pore assembly.", "The major conformational changes in PlyB are a \u223c70\u00b0 opening of the bent and distorted central \u03b2-sheet of the MACPF domain, accompanied by extrusion and refolding of two \u03b1-helical regions into transmembrane \u03b2-hairpins (TMH1 and TMH2).", "We determined the structures of three different disulphide bond-trapped prepore intermediates.", "Analysis of these data by molecular modelling and flexible fitting allows us to generate a potential trajectory of \u03b2-sheet unbending.", "The results suggest that MACPF conformational change is triggered through disruption of the interface between a conserved helix-turn-helix motif and the top of TMH2.", "Following their release we propose that the transmembrane regions assemble into \u03b2-hairpins via top down zippering of backbone hydrogen bonds to form the membrane-inserted \u03b2-barrel.", "The intermediate structures of the MACPF domain during refolding into the \u03b2-barrel pore establish a structural paradigm for the transition from soluble monomer to pore, which may be conserved across the whole superfamily.", "The TMH2 region is critical for the release of both TMH clusters, suggesting why this region is targeted by endogenous inhibitors of MACPF function."], "structured": false}
{"doc_id": 2619579, "title": "The widespread regulation of microRNA biogenesis, function and decay", "abstract": ["MicroRNAs (miRNAs) are a large family of post-transcriptional regulators of gene expression that are \u223c21 nucleotides in length and control many developmental and cellular processes in eukaryotic organisms.", "Research during the past decade has identified major factors participating in miRNA biogenesis and has established basic principles of miRNA function.", "More recently, it has become apparent that miRNA regulators themselves are subject to sophisticated control.", "Many reports over the past few years have reported the regulation of miRNA metabolism and function by a range of mechanisms involving numerous protein\u2013protein and protein\u2013RNA interactions.", "Such regulation has an important role in the context-specific functions of miRNAs."], "structured": false}
{"doc_id": 2638387, "title": "The cytidine deaminase CEM15 induces hypermutation in newly synthesized HIV-1 DNA", "abstract": ["High mutation frequency during reverse transcription has a principal role in the genetic variation of primate lentiviral populations.", "It is the main driving force for the generation of drug resistance and the escape from immune surveillance.", "G to A hypermutation is one of the characteristics of primate lentiviruses, as well as other retroviruses, during replication in vivo and in cell culture.", "The molecular mechanisms of this process, however, remain to be clarified.", "Here, we demonstrate that CEM15 (also known as apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3G; APOBEC3G), an endogenous inhibitor of human immunodeficiency virus type 1 (HIV-1) replication, is a cytidine deaminase and is able to induce G to A hypermutation in newly synthesized viral DNA.", "This effect can be counteracted by the HIV-1 virion infectivity factor (Vif).", "It seems that this viral DNA mutator is a viral defence mechanism in host cells that may induce either lethal hypermutation or instability of the incoming nascent viral reverse transcripts, which could account for the Vif-defective phenotype.", "Importantly, the accumulation of CEM15-mediated non-lethal hypermutation in the replicating viral genome could potently contribute to the genetic variation of primate lentiviral populations."], "structured": false}
{"doc_id": 2647374, "title": "Variants in the Toll-interacting protein gene are associated with susceptibility to sepsis in the Chinese Han population", "abstract": ["INTRODUCTION Deregulated or excessive host immune responses contribute to the pathogenesis of sepsis.", "Toll-like receptor (TLR) signaling pathways and their negative regulators play a pivotal role in the modulation of host immune responses and the development of sepsis.", "The objective of this study was to investigate the association of variants in the TLR signaling pathway genes and their negative regulator genes with susceptibility to sepsis in the Chinese Han population.   \n", "METHODS Patients with severe sepsis (n = 378) and healthy control subjects (n = 390) were enrolled.", "Five genes, namely TLR2, TLR4, TLR9, MyD88 and TOLLIP, were investigated for their association with sepsis susceptibility by a tag single nucleotide polymorphism (SNP) strategy.", "Twelve tag SNPs were selected based on the data of Chinese Han in Beijing from the HapMap project and genotyped by direct sequencing.", "The mRNA expression levels of TOLLIP were determined using real-time quantitative Polymerase Chain Reaction (PCR) assays, and concentrations of tumor necrosis factor alpha (TNF-\u03b1) and interleukin-6 (IL-6) were measured by enzyme-linked immunosorbent assay (ELISA).   \n", "RESULTS Our results showed that the minor C-allele of rs5743867 in TOLLIP was significantly associated with the decreased risk of sepsis (Padj = 0.00062, odds ratio (OR)adj = 0.71, 95% confidence interval (CI) 0.59 to 0.86) after adjustment for covariates in multiple logistic regression analysis.", "A 3-SNP haplotype block harboring the associated SNP rs5743867 also displayed strong association with omnibus test P value of 0.00049.", "Haplotype GTC showed a protective role against sepsis (Padj = 0.0012), while haplotype GCT showed an increased risk for sepsis (Padj = 0.00092).", "After exposure to lipopolysaccharide (LPS), TOLLIP mRNA expression levels in peripheral blood mononuclear cells (PBMCs) from homozygotes for the rs5743867C allele were significantly higher than in heterozygotes and homozygotes for the rs5743867T allele (P = 0.013 and P = 0.01, respectively).", "Moreover, the concentrations of TNF-\u03b1 and IL-6 in culture supernatants were significantly lower in the subjects of rs5743867CC genotype than in CT and TT genotype subjects (P = 0.016 and P = 0.003 for TNF-\u03b1; P = 0.01 and P = 0.002 for IL-6, respectively).   \n", "CONCLUSIONS Our findings indicated that the variants in TOLLIP were significantly associated with sepsis susceptibility in the Chinese Han population."], "structured": true}
{"doc_id": 2659805, "title": "Children's estimates of food portion size: the development and evaluation of three portion size assessment tools for use with children.", "abstract": ["A number of methods have been developed to assist subjects in providing an estimate of portion size but their application in improving portion size estimation by children has not been investigated systematically.", "The aim was to develop portion size assessment tools for use with children and to assess the accuracy of children's estimates of portion size using the tools.", "The tools were food photographs, food models and an interactive portion size assessment system (IPSAS).", "Children (n 201), aged 4-16 years, were supplied with known quantities of food to eat, in school.", "Food leftovers were weighed.", "Children estimated the amount of each food using each tool, 24 h after consuming the food.", "The age-specific portion sizes represented were based on portion sizes consumed by children in a national survey.", "Significant differences were found between the accuracy of estimates using the three tools.", "Children of all ages performed well using the IPSAS and food photographs.", "The accuracy and precision of estimates made using the food models were poor.", "For all tools, estimates of the amount of food served were more accurate than estimates of the amount consumed.", "Issues relating to reporting of foods left over which impact on estimates of the amounts of foods actually consumed require further study.", "The IPSAS has shown potential for assessment of dietary intake with children.", "Before practical application in assessment of dietary intake of children the tool would need to be expanded to cover a wider range of foods and to be validated in a 'real-life' situation."], "structured": false}
{"doc_id": 2665425, "title": "A 3D Map of the Yeast Kinetochore Reveals the Presence of Core and Accessory Centromere-Specific Histone", "abstract": ["The budding yeast kinetochore is ~68 nm in length with a diameter slightly larger than a 25 nm microtubule.", "The kinetochores from the 16 chromosomes are organized in a stereotypic cluster encircling central spindle microtubules.", "Quantitative analysis of the inner kinetochore cluster (Cse4, COMA) reveals structural features not apparent in singly attached kinetochores.", "The cluster of Cse4-containing kinetochores is physically larger perpendicular to the spindle axis relative to the cluster of Ndc80 molecules.", "If there was a single Cse4 (molecule or nucleosome) at the kinetochore attached to each microtubule plus end, the cluster of Cse4 would appear geometrically identical to Ndc80.", "Thus, the structure of the inner kinetochore at the surface of the chromosomes remains unsolved.", "We have used point fluorescence microscopy and statistical probability maps to deduce the two-dimensional mean position of representative components of the yeast kinetochore relative to the mitotic spindle in metaphase.", "Comparison of the experimental images to three-dimensional architectures from convolution of mathematical models reveals a pool of Cse4 radially displaced from Cse4 at the kinetochore and kinetochore microtubule plus ends.", "The pool of displaced Cse4 can be experimentally depleted in mRNA processing pat1\u0394 or xrn1\u0394 mutants.", "The peripheral Cse4 molecules do not template outer kinetochore components.", "This study suggests an inner kinetochore plate at the centromere-microtubule interface in budding yeast and yields information on the number of Ndc80 molecules at the microtubule attachment site."], "structured": false}
{"doc_id": 2665675, "title": "American Society of Clinical Oncology policy statement: the role of the oncologist in cancer prevention and risk assessment.", "abstract": ["Oncologists have a critical opportunity to utilize risk assessment and cancer prevention strategies to interrupt the initiation or progression of cancer in cancer survivors and individuals at high risk of developing cancer.", "Expanding knowledge about the natural history and prognosis of cancers positions oncologists to advise patients regarding the risk of second malignancies and treatment-related cancers.", "In addition, as recognized experts in the full spectrum of cancer care, oncologists are afforded opportunities for involvement in community-based cancer prevention activities.", "Although oncologists are currently providing many cancer prevention and risk assessment services to their patients, economic barriers exist, including inadequate or lack of insurance, that may compromise uniform patient access to these services.", "Additionally, insufficient reimbursement for existing and developing interventions may discourage patient access to these services.", "The American Society of Clinical Oncology (ASCO), the medical society representing cancer specialists involved in patient care and clinical research, is committed to supporting oncologists in their wide-ranging involvement in cancer prevention.", "This statement on risk assessment and prevention counseling, although not intended to be a comprehensive overview of cancer prevention describes the current role of oncologists in risk assessment and prevention; provides examples of risk assessment and prevention activities that should be offered by oncologists; identifies potential opportunities for coordination between oncologists and primary care physicians in prevention education and coordination of care for cancer survivors; describes ASCO's involvement in education and training of oncologists regarding prevention; and proposes improvement in the payment environment to encourage patient access to these services."], "structured": false}
{"doc_id": 2679511, "title": "The BLM helicase contributes to telomere maintenance through processing of late-replicating intermediate structures", "abstract": ["Werner's syndrome (WS) and Bloom's syndrome (BS) are cancer predisposition disorders caused by loss of function of the RecQ helicases WRN or BLM, respectively.", "BS and WS are characterized by replication defects, hyperrecombination events and chromosomal aberrations, which are hallmarks of cancer.", "Inefficient replication of the G-rich telomeric strand contributes to chromosome aberrations in WS cells, demonstrating a link between WRN, telomeres and genomic stability.", "Herein, we provide evidence that BLM also contributes to chromosome-end maintenance.", "Telomere defects (TDs) are observed in BLM-deficient cells at an elevated frequency, which is similar to cells lacking a functional WRN helicase.", "Loss of both helicases exacerbates TDs and chromosome aberrations, indicating that BLM and WRN function independently in telomere maintenance.", "BLM localization, particularly its recruitment to telomeres, changes in response to replication dysfunction, such as in WRN-deficient cells or after aphidicolin treatment.", "Exposure to replication challenge causes an increase in decatenated deoxyribonucleic acid (DNA) structures and late-replicating intermediates (LRIs), which are visible as BLM-covered ultra-fine bridges (UFBs) in anaphase.", "A subset of UFBs originates from telomeric DNA and their frequency correlates with telomere replication defects.", "We propose that the BLM complex contributes to telomere maintenance through its activity in resolving LRIs."], "structured": false}
{"doc_id": 2682251, "title": "Formation of a thymus from rat ES cells in xenogeneic nude mouse\u2194rat ES chimeras.", "abstract": ["Various conditions for differentiating embryonic stem (ES) cells or induced pluripotent stem (iPS) cells into specific kinds of cell lines are under intensive investigation.", "However, the production of a functional organ with a three-dimensional structure from ES or iPS cells is difficult to achieve in vitro.", "In the present paper, we describe the establishment of a green fluorescent protein-expressing rat ES cell line and production of mouse\u2194rat ES chimera by injecting rat ES cells into mouse blastocysts.", "The rat ES cells contributed to various organs in the chimera, including germ cells.", "When we injected ES cells into blastocysts of nu/nu mice lacking a thymus, the resultant chimeras produced thymus derived from rat ES cells in their bodies.", "The chimeric animals may provide a method for the derivation of various organs from ES or iPS cells."], "structured": false}
{"doc_id": 2682997, "title": "Wnt/beta-catenin signaling is required for CNS, but not non-CNS, angiogenesis.", "abstract": ["Despite the importance of CNS blood vessels, the molecular mechanisms that regulate CNS angiogenesis and blood-brain barrier (BBB) formation are largely unknown.", "Here we analyze the role of Wnt/beta-catenin signaling in regulating the formation of CNS blood vessels.", "First, through the analysis of TOP-Gal Wnt reporter mice, we identify that canonical Wnt/beta-catenin signaling is specifically activated in CNS, but not non-CNS, blood vessels during development.", "This activation correlates with the expression of different Wnt ligands by neural progenitor cells in distinct locations throughout the CNS, including Wnt7a and Wnt7b in ventral regions and Wnt1, Wnt3, Wnt3a, and Wnt4 in dorsal regions.", "Blockade of Wnt/beta-catenin signaling in vivo specifically disrupts CNS, but not non-CNS, angiogenesis.", "These defects include reduction in vessel number, loss of capillary beds, and the formation of hemorrhagic vascular malformations that remain adherent to the meninges.", "Furthermore, we demonstrate that Wnt/beta-catenin signaling regulates the expression of the BBB-specific glucose transporter glut-1.", "Taken together these experiments reveal an essential role for Wnt/beta-catenin signaling in driving CNS-specific angiogenesis and provide molecular evidence that angiogenesis and BBB formation are in part linked."], "structured": false}
{"doc_id": 2686003, "title": "Cyanidin-3-rutinoside, a natural polyphenol antioxidant, selectively kills leukemic cells by induction of oxidative stress.", "abstract": ["Anthocyanins are a group of naturally occurring phenolic compounds widely available in fruits and vegetables in human diets.", "They have broad biological activities including anti-mutagenesis and anticarcinogenesis, which are generally attributed to their antioxidant activities.", "We studied the effects and the mechanisms of the most common type of anthocyanins, cyanidin-3-rutinoside, in several leukemia and lymphoma cell lines.", "We found that cyanidin-3-rutinoside extracted and purified from the black raspberry cultivar Jewel induced apoptosis in HL-60 cells in a dose- and time-dependent manner.", "Paradoxically, this compound induced the accumulation of peroxides, which are involved in the induction of apoptosis in HL-60 cells.", "In addition, cyanidin-3-rutinoside treatment resulted in reactive oxygen species (ROS)-dependent activation of p38 MAPK and JNK, which contributed to cell death by activating the mitochondrial pathway mediated by Bim.", "Down-regulation of Bim or overexpression of Bcl-2 or Bcl-x(L) considerably blocked apoptosis.", "Notably, cyanidin-3-rutinoside treatment did not lead to increased ROS accumulation in normal human peripheral blood mononuclear cells and had no cytotoxic effects on these cells.", "These results indicate that cyanidin-3-rutinoside has the potential to be used in leukemia therapy with the advantages of being widely available and selective against tumors."], "structured": false}
{"doc_id": 2692522, "title": "Gout-associated uric acid crystals activate the NALP3 inflammasome", "abstract": ["Development of the acute and chronic inflammatory responses known as gout and pseudogout are associated with the deposition of monosodium urate (MSU) or calcium pyrophosphate dihydrate (CPPD) crystals, respectively, in joints and periarticular tissues.", "Although MSU crystals were first identified as the aetiological agent of gout in the eighteenth century and more recently as a \u2018danger signal\u2019 released from dying cells, little is known about the molecular mechanisms underlying MSU- or CPPD-induced inflammation.", "Here we show that MSU and CPPD engage the caspase-1-activating NALP3 (also called cryopyrin) inflammasome, resulting in the production of active interleukin (IL)-1\u03b2 and IL-18.", "Macrophages from mice deficient in various components of the inflammasome such as caspase-1, ASC and NALP3 are defective in crystal-induced IL-1\u03b2 activation.", "Moreover, an impaired neutrophil influx is found in an in vivo model of crystal-induced peritonitis in inflammasome-deficient mice or mice deficient in the IL-1\u03b2 receptor (IL-1R).", "These findings provide insight into the molecular processes underlying the inflammatory conditions of gout and pseudogout, and further support a pivotal role of the inflammasome in several autoinflammatory diseases."], "structured": false}
{"doc_id": 2701077, "title": "Hematopoietic stem cell quiescence promotes error-prone DNA repair and mutagenesis.", "abstract": ["Most adult stem cells, including hematopoietic stem cells (HSCs), are maintained in a quiescent or resting state in vivo.", "Quiescence is widely considered to be an essential protective mechanism for stem cells that minimizes endogenous stress caused by cellular respiration and DNA replication.", "We demonstrate that HSC quiescence can also have detrimental effects.", "We found that HSCs have unique cell-intrinsic mechanisms ensuring their survival in response to ionizing irradiation (IR), which include enhanced prosurvival gene expression and strong activation of p53-mediated DNA damage response.", "We show that quiescent and proliferating HSCs are equally radioprotected but use different types of DNA repair mechanisms.", "We describe how nonhomologous end joining (NHEJ)-mediated DNA repair in quiescent HSCs is associated with acquisition of genomic rearrangements, which can persist in vivo and contribute to hematopoietic abnormalities.", "Our results demonstrate that quiescence is a double-edged sword that renders HSCs intrinsically vulnerable to mutagenesis following DNA damage."], "structured": false}
{"doc_id": 2714623, "title": "Recruitment of Nck by CD3\u03f5 Reveals a Ligand-Induced Conformational Change Essential for T Cell Receptor Signaling and Synapse Formation", "abstract": ["How membrane receptors initiate signal transduction upon ligand binding is a matter of intense scrutiny.", "The T cell receptor complex (TCR-CD3) is composed of TCR alpha/beta ligand binding subunits bound to the CD3 subunits responsible for signal transduction.", "Although it has long been speculated that TCR-CD3 may undergo a conformational change, confirmation is still lacking.", "We present strong evidence that ligand engagement of TCR-CD3 induces a conformational change that exposes a proline-rich sequence in CD3 epsilon and results in recruitment of the adaptor protein Nck.", "This occurs earlier than and independently of tyrosine kinase activation.", "Finally, by interfering with Nck-CD3 epsilon association in vivo, we demonstrate that TCR-CD3 recruitment of Nck is critical for maturation of the immune synapse and for T cell activation."], "structured": false}
{"doc_id": 2721426, "title": "Pseudo-Seq: Genome-Wide Detection of Pseudouridine Modifications in RNA.", "abstract": ["RNA molecules contain a variety of chemically diverse, posttranscriptionally modified bases.", "The most abundant modified base found in cellular RNAs, pseudouridine (\u03a8), has recently been mapped to hundreds of sites in mRNAs, many of which are dynamically regulated.", "Though the pseudouridine landscape has been determined in only a few cell types and growth conditions, the enzymes responsible for mRNA pseudouridylation are universally conserved, suggesting many novel pseudouridylated sites remain to be discovered.", "Here, we present Pseudo-seq, a technique that allows the identification of sites of pseudouridylation genome-wide with single-nucleotide resolution.", "In this chapter, we provide a detailed description of Pseudo-seq.", "We include protocols for RNA isolation from Saccharomyces cerevisiae, Pseudo-seq library preparation, and data analysis, including descriptions of processing and mapping of sequencing reads, computational identification of sites of pseudouridylation, and assignment of sites to specific pseudouridine synthases.", "The approach presented here is readily adaptable to any cell or tissue type from which high-quality mRNA can be isolated.", "Identification of novel pseudouridylation sites is an important first step in elucidating the regulation and functions of these modifications."], "structured": false}
{"doc_id": 2722988, "title": "The Mammalian Epigenome", "abstract": ["Chemical modifications to DNA and histone proteins form a complex regulatory network that modulates chromatin structure and genome function.", "The epigenome refers to the complete description of these potentially heritable changes across the genome.", "The composition of the epigenome within a given cell is a function of genetic determinants, lineage, and environment.", "With the sequencing of the human genome completed, investigators now seek a comprehensive view of the epigenetic changes that determine how genetic information is made manifest across an incredibly varied background of developmental stages, tissue types, and disease states.", "Here we review current research efforts, with an emphasis on large-scale studies, emerging technologies, and challenges ahead."], "structured": false}
{"doc_id": 2727303, "title": "Microtubule-associated histone deacetylase 6 supports the calcium store sensor STIM1 in mediating malignant cell behaviors.", "abstract": ["Stromal-interaction molecule 1 (STIM1) is an endoplasmic reticulum Ca(2+) storage sensor that promotes cell growth, migration, and angiogenesis in breast and cervical cancers.", "Here, we report that the microtubule-associated histone deacetylase 6 (HDAC6) differentially regulates activation of STIM1-mediated store-operated Ca(2+) entry (SOCE) between cervical cancer cells and normal cervical epithelial cells.", "Confocal microscopy of living cells indicated that microtubule integrity was necessary for STIM1 trafficking to the plasma membrane and interaction with Orai1, an essential pore subunit of SOCE.", "Cancer cells overexpressed both STIM1 and Orai1 compared with normal cervical epithelial cells.", "HDAC6 upregulation in cancer cells was accompanied by hypoacetylated \u03b1-tubulin.", "Tubastatin-A, a specific HDAC6 inhibitor, inhibited STIM1 translocation to plasma membrane and blocked SOCE activation in cancer cells but not normal epithelial cells.", "Genetic or pharmacologic inhibition of HDAC6 blocked STIM1 membrane trafficking and downstream Ca(2+) influx, as evidenced by total internal reflection fluorescent images and intracellular Ca(2+) determination.", "In contrast, HDAC6 inhibition did not affect interactions between STIM1 and the microtubule plus end-binding protein EB1.", "Analysis of surgical specimens confirmed that most cervical cancer tissues overexpressed STIM1 and Orai1, accompanied by hypoacetylated \u03b1-tubulin.", "Together, our results identify HDAC6 as a candidate target to disrupt STIM1-mediated SOCE as a general strategy to block malignant cell behavior."], "structured": false}
{"doc_id": 2734421, "title": "The tumor necrosis factor family receptors RANK and CD40 cooperatively establish the thymic medullary microenvironment and self-tolerance.", "abstract": ["Medullary thymic epithelial cells (mTECs) establish T cell self-tolerance through the expression of autoimmune regulator (Aire) and peripheral tissue-specific self-antigens.", "However, signals underlying mTEC development remain largely unclear.", "Here, we demonstrate crucial regulation of mTEC development by receptor activator of NF-kappaB (RANK) and CD40 signals.", "Whereas only RANK signaling was essential for mTEC development during embryogenesis, in postnatal mice, cooperation between CD40 and RANK signals was required for mTEC development to successfully establish the medullary microenvironment.", "Ligation of RANK or CD40 on fetal thymic stroma in vitro induced mTEC development in a tumor necrosis factor-associated factor 6 (TRAF6)-, NF-kappaB inducing kinase (NIK)-, and IkappaB kinase beta (IKKbeta)-dependent manner.", "These results show that developmental-stage-dependent cooperation between RANK and CD40 promotes mTEC development, thereby establishing self-tolerance."], "structured": false}
{"doc_id": 2739854, "title": "Rare and common variants: twenty arguments", "abstract": ["Genome-wide association studies have greatly improved our understanding of the genetic basis of disease risk.", "The fact that they tend not to identify more than a fraction of the specific causal loci has led to divergence of opinion over whether most of the variance is hidden as numerous rare variants of large effect or as common variants of very small effect.", "Here I review 20 arguments for and against each of these models of the genetic basis of complex traits and conclude that both classes of effect can be readily reconciled."], "structured": false}
{"doc_id": 2754534, "title": "DNA methylation status predicts cell type-specific enhancer activity.", "abstract": ["Cell-selective glucocorticoid receptor (GR) binding to distal regulatory elements is associated with cell type-specific regions of locally accessible chromatin.", "These regions can either pre-exist in chromatin (pre-programmed) or be induced by the receptor (de novo).", "Mechanisms that create and maintain these sites are not well understood.", "We observe a global enrichment of CpG density for pre-programmed elements, and implicate their demethylated state in the maintenance of open chromatin in a tissue-specific manner.", "In contrast, sites that are actively opened by GR (de novo) are characterized by low CpG density, and form a unique class of enhancers devoid of suppressive effect of agglomerated methyl-cytosines.", "Furthermore, treatment with glucocorticoids induces rapid changes in methylation levels at selected CpGs within de novo sites.", "Finally, we identify GR-binding elements with CpGs at critical positions, and show that methylation can affect GR-DNA interactions in vitro.", "The findings present a unique link between tissue-specific chromatin accessibility, DNA methylation and transcription factor binding and show that DNA methylation can be an integral component of gene regulation by nuclear receptors."], "structured": false}
{"doc_id": 2758012, "title": "BLM helicase facilitates telomere replication during leading strand synthesis of telomeres", "abstract": ["Based on its in vitro unwinding activity on G-quadruplex (G4) DNA, the Bloom syndrome-associated helicase BLM is proposed to participate in telomere replication by aiding fork progression through G-rich telomeric DNA.", "Single molecule analysis of replicated DNA (SMARD) was used to determine the contribution of BLM helicase to telomere replication.", "In BLM-deficient cells, replication forks initiating from origins within the telomere, which copy the G-rich strand by leading strand synthesis, moved slower through the telomere compared with the adjacent subtelomere.", "Fork progression through the telomere was further slowed in the presence of a G4 stabilizer.", "Using a G4-specific antibody, we found that deficiency of BLM, or another G4-unwinding helicase, the Werner syndrome-associated helicase WRN, resulted in increased G4 structures in cells.", "Importantly, deficiency of either helicase led to greater increases in G4 DNA detected in the telomere compared with G4 seen genome-wide.", "Collectively, our findings are consistent with BLM helicase facilitating telomere replication by resolving G4 structures formed during copying of the G-rich strand by leading strand synthesis."], "structured": false}
{"doc_id": 2762601, "title": "Reflecting on 25 years with MYC", "abstract": ["Just over 25 years ago, MYC, the human homologue of a retroviral oncogene, was identified.", "Since that time, MYC research has been intense and the advances impressive.", "On reflection, it is astonishing how each incremental insight into MYC regulation and function has also had an impact on numerous biological disciplines, including our understanding of molecular oncogenesis in general.", "Here we chronicle the major advances in our understanding of MYC biology, and peer into the future of MYC research."], "structured": false}
{"doc_id": 2774906, "title": "Protective effects of exercise and phosphoinositide 3-kinase(p110alpha) signaling in dilated and hypertrophic cardiomyopathy.", "abstract": ["Physical activity protects against cardiovascular disease, and physiological cardiac hypertrophy associated with regular exercise is usually beneficial, in marked contrast to pathological hypertrophy associated with disease.", "The p110alpha isoform of phosphoinositide 3-kinase (PI3K) plays a critical role in the induction of exercise-induced hypertrophy.", "Whether it or other genes activated in the athlete's heart might have an impact on cardiac function and survival in a setting of heart failure is unknown.", "To examine whether progressive exercise training and PI3K(p110alpha) activity affect survival and/or cardiac function in two models of heart disease, we subjected a transgenic mouse model of dilated cardiomyopathy (DCM) to swim training, genetically crossed cardiac-specific transgenic mice with increased or decreased PI3K(p110alpha) activity to the DCM model, and subjected PI3K(p110alpha) transgenics to acute pressure overload (ascending aortic constriction).", "Life-span, cardiac function, and molecular markers of pathological hypertrophy were examined.", "Exercise training and increased cardiac PI3K(p110alpha) activity prolonged survival in the DCM model by 15-20%.", "In contrast, reduced PI3K(p110alpha) activity drastically shortened lifespan by approximately 50%.", "Increased PI3K(p110alpha) activity had a favorable effect on cardiac function and fibrosis in the pressure-overload model and attenuated pathological growth.", "PI3K(p110alpha) signaling negatively regulated G protein-coupled receptor stimulated extracellular responsive kinase and Akt (via PI3K, p110gamma) activation in isolated cardiomyocytes.", "These findings suggest that exercise and enhanced PI3K(p110alpha) activity delay or prevent progression of heart disease, and that supraphysiologic activity can be beneficial.", "Identification of genes important for hypertrophy in the athlete's heart could offer new strategies for treating heart failure."], "structured": false}
{"doc_id": 2787558, "title": "The effect of cigarette smoking, alcohol consumption and fruit and vegetable consumption on IVF outcomes: a review and presentation of original data", "abstract": ["BACKGROUND Lifestyle factors including cigarette smoking, alcohol consumption and nutritional habits impact on health, wellness, and the risk of chronic diseases.", "In the areas of in-vitro fertilization (IVF) and pregnancy, lifestyle factors influence oocyte production, fertilization rates, pregnancy and pregnancy loss, while chronic, low-grade oxidative stress may underlie poor outcomes for some IVF cases.   \n", "METHODS Here, we review the current literature and present some original, previously unpublished data, obtained from couples attending the PIVET Medical Centre in Western Australia.   \n", "RESULTS During the study, 80 % of females and 70 % of male partners completed a 1-week diary documenting their smoking, alcohol and fruit and vegetable intake.", "The subsequent clinical outcomes of their IVF treatment such as quantity of oocytes collected, fertilization rates, pregnancy and pregnancy loss were submitted to multiple regression analysis, in order to investigate the relationship between patients, treatment and the recorded lifestyle factors.", "Of significance, it was found that male smoking caused an increased risk of pregnancy loss (p = 0.029), while female smoking caused an adverse effect on ovarian reserve.", "Both alcohol consumption (\u03b2 = 0.074, p < 0.001) and fruit and vegetable consumption (\u03b2 = 0.034, p < 0.001) had positive effects on fertilization.   \n", "CONCLUSION Based on our results and the current literature, there is an important impact of lifestyle factors on IVF clinical outcomes.", "Currently, there are conflicting results regarding other lifestyle factors such as nutritional habits and alcohol consumption, but it is apparent that chronic oxidative stress induced by lifestyle factors and poor nutritional habits associate with a lower rate of IVF success."], "structured": true}
{"doc_id": 2810997, "title": "Efficient Mitochondrial Genome Editing by CRISPR/Cas9", "abstract": ["The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 system has been widely used for nuclear DNA editing to generate mutations or correct specific disease alleles.", "Despite its flexible application, it has not been determined if CRISPR/Cas9, originally identified as a bacterial defense system against virus, can be targeted to mitochondria for mtDNA editing.", "Here, we show that regular FLAG-Cas9 can localize to mitochondria to edit mitochondrial DNA with sgRNAs targeting specific loci of the mitochondrial genome.", "Expression of FLAG-Cas9 together with gRNA targeting Cox1 and Cox3 leads to cleavage of the specific mtDNA loci.", "In addition, we observed disruption of mitochondrial protein homeostasis following mtDNA truncation or cleavage by CRISPR/Cas9.", "To overcome nonspecific distribution of FLAG-Cas9, we also created a mitochondria-targeted Cas9 (mitoCas9).", "This new version of Cas9 localizes only to mitochondria; together with expression of gRNA targeting mtDNA, there is specific cleavage of mtDNA.", "MitoCas9-induced reduction of mtDNA and its transcription leads to mitochondrial membrane potential disruption and cell growth inhibition.", "This mitoCas9 could be applied to edit mtDNA together with gRNA expression vectors without affecting genomic DNA.", "In this brief study, we demonstrate that mtDNA editing is possible using CRISPR/Cas9.", "Moreover, our development of mitoCas9 with specific localization to the mitochondria should facilitate its application for mitochondrial genome editing."], "structured": false}
{"doc_id": 2817000, "title": "Histone Variant H2A.Z Marks the 5\u2032 Ends of Both Active and Inactive Genes in Euchromatin", "abstract": ["In S. cerevisiae, histone variant H2A.Z is deposited in euchromatin at the flanks of silent heterochromatin to prevent its ectopic spread.", "We show that H2A.Z nucleosomes are found at promoter regions of nearly all genes in euchromatin.", "They generally occur as two positioned nucleosomes that flank a nucleosome-free region (NFR) that contains the transcription start site.", "Astonishingly, enrichment at 5' ends is observed not only at actively transcribed genes but also at inactive loci.", "Mutagenesis of a typical promoter revealed a 22 bp segment of DNA sufficient to program formation of a NFR flanked by two H2A.Z nucleosomes.", "This segment contains a binding site of the Myb-related protein Reb1 and an adjacent dT:dA tract.", "Efficient deposition of H2A.Z is further promoted by a specific pattern of histone H3 and H4 tail acetylation and the bromodomain protein Bdf1, a component of the Swr1 remodeling complex that deposits H2A.Z."], "structured": false}
{"doc_id": 2820454, "title": "Exercise and respiratory training improve exercise capacity and quality of life in patients with severe chronic pulmonary hypertension.", "abstract": ["BACKGROUND Pulmonary hypertension (PH) is associated with restricted physical capacity, limited quality of life, and a poor prognosis because of right heart failure.", "The present study is the first prospective randomized study to evaluate the effects of exercise and respiratory training in patients with severe symptomatic PH.   \n", "METHODS AND RESULTS Thirty patients with PH (21 women; mean age, 50+/-13 years; mean pulmonary artery pressure, 50+/-15 mm Hg; mean World Health Organization [WHO] class, 2.9+/-0.5; pulmonary arterial hypertension, n=23; chronic thromboembolic PH, n=7) on stable disease-targeted medication were randomly assigned to a control (n=15) and a primary training (n=15) group.", "Medication remained unchanged during the study period.", "Primary end points were the changes from baseline to week 15 in the distance walked in 6 minutes and in scores of the Short Form Health Survey quality-of-life questionnaire.", "Changes in WHO functional class, Borg scale, and parameters of echocardiography and gas exchange also were assessed.", "At week 15, patients in the primary and secondary training groups had an improved 6-minute walking distance; the mean difference between the control and the primary training group was 111 m (95% confidence interval, 65 to 139 m; P<0.001).", "Exercise training was well tolerated and improved scores of quality of life, WHO functional class, peak oxygen consumption, oxygen consumption at the anaerobic threshold, and achieved workload.", "Systolic pulmonary artery pressure values at rest did not change significantly after 15 weeks of exercise and respiratory training (from 61+/-18 to 54+/-18 mm Hg) within the training group.   \n", "CONCLUSIONS This study indicates that respiratory and physical training could be a promising adjunct to medical treatment in severe PH.", "The effects add to the beneficial results of modern medical treatment."], "structured": true}
{"doc_id": 2824347, "title": "HIV-1 regulation of latency in the monocyte-macrophage lineage and in CD4+ T lymphocytes.", "abstract": ["The introduction in 1996 of the HAART raised hopes for the eradication of HIV-1.", "Unfortunately, the discovery of latent HIV-1 reservoirs in CD4+ T cells and in the monocyte-macrophage lineage proved the optimism to be premature.", "The long-lived HIV-1 reservoirs constitute a major obstacle to the eradication of HIV-1.", "In this review, we focus on the establishment and maintenance of HIV-1 latency in the two major targets for HIV-1: the CD4+ T cells and the monocyte-macrophage lineage.", "Understanding the cell-type molecular mechanisms of establishment, maintenance, and reactivation of HIV-1 latency in these reservoirs is crucial for efficient therapeutic intervention.", "A complete viral eradication, the holy graal for clinicians, might be achieved by strategic interventions targeting latently and productively infected cells.", "We suggest that new approaches, such as the combination of different kinds of proviral activators, may help to reduce dramatically the size of latent HIV-1 reservoirs in patients on HAART."], "structured": false}
{"doc_id": 2825340, "title": "Effects of Electro-Acupuncture Therapy on Post-Stroke Depression in Patients with Different Degrees of Motor Function Impairments: a Pilot Study", "abstract": ["[Purpose] The present study examined whether electro-acupuncture therapy reduces post-stroke depression (PSD) and whether motor function impairments interact with the effects of the therapy.", "[Subjects] Twenty-eight PSD patients were assessed and assigned to either a good or poor motor function group depending on their motor grade.", "[Methods] The Beck Depression Inventory (BDI), Hamilton Depression Rating Scale (HDRS) and Manual Muscle Test (MMT) were administered at the screening and initial phases of the study, and at the 4th, 8th, 12th and 16th week of the daily electro-acupuncture treatment.", "[Results] The electro-acupuncture treatment reduced PSD (as assessed by BDI and HDRS) of the patients.", "In particular, the depression of the good motor function group was significantly more reduced than that of the poor motor function group.", "The degree of motor function impairment did not change throughout the study in either group.", "[Conclusion] The results of the present study demonstrate that electro-acupuncture therapy can improve PSD, and that the treatment effect varies depending on the degree of motor function impairment."], "structured": false}
{"doc_id": 2825380, "title": "T cell receptor ligation induces the formation of dynamically regulated signaling assemblies", "abstract": ["Tcell antigen receptor (TCR) ligation initiates tyrosine kinase activation, signaling complex assembly, and immune synapse formation.", "Here, we studied the kinetics and mechanics of signaling complex formation in live Jurkat leukemic T cells using signaling proteins fluorescently tagged with variants of enhanced GFP (EGFP).", "Within seconds of contacting coverslips coated with stimulatory antibodies, T cells developed small, dynamically regulated clusters which were enriched in the TCR, phosphotyrosine, ZAP-70, LAT, Grb2, Gads, and SLP-76, excluded the lipid raft marker enhanced yellow fluorescent protein\u2013GPI, and were competent to induce calcium elevations.", "LAT, Grb2, and Gads were transiently associated with the TCR.", "Although ZAP-70\u2013containing clusters persisted for more than 20 min, photobleaching studies revealed that ZAP-70 continuously dissociated from and returned to these complexes.", "Strikingly, SLP-76 translocated to a perinuclear structure after clustering with the TCR.", "Our results emphasize the dynamically changing composition of signaling complexes and indicate that these complexes can form within seconds of TCR engagement, in the absence of either lipid raft aggregation or the formation of a central TCR-rich cluster."], "structured": false}
{"doc_id": 2828460, "title": "Developmental heterogeneity of cardiac fibroblasts does not predict pathological proliferation and activation.", "abstract": ["RATIONALE Fibrosis is mediated partly by extracellular matrix-depositing fibroblasts in the heart.", "Although these mesenchymal cells are reported to have multiple embryonic origins, the functional consequence of this heterogeneity is unknown.   \n", "OBJECTIVE We sought to validate a panel of surface markers to prospectively identify cardiac fibroblasts.", "We elucidated the developmental origins of cardiac fibroblasts and characterized their corresponding phenotypes.", "We also determined proliferation rates of each developmental subset of fibroblasts after pressure overload injury.   \n", "METHODS AND RESULTS We showed that Thy1(+)CD45(-)CD31(-)CD11b(-)Ter119(-) cells constitute the majority of cardiac fibroblasts.", "We characterized these cells using flow cytometry, epifluorescence and confocal microscopy, and transcriptional profiling (using reverse transcription polymerase chain reaction and RNA-seq).", "We used lineage tracing, transplantation studies, and parabiosis to show that most adult cardiac fibroblasts derive from the epicardium, a minority arises from endothelial cells, and a small fraction from Pax3-expressing cells.", "We did not detect generation of cardiac fibroblasts by bone marrow or circulating cells.", "Interestingly, proliferation rates of fibroblast subsets on injury were identical, and the relative abundance of each lineage remained the same after injury.", "The anatomic distribution of fibroblast lineages also remained unchanged after pressure overload.", "Furthermore, RNA-seq analysis demonstrated that Tie2-derived and Tbx18-derived fibroblasts within each operation group exhibit similar gene expression profiles.   \n", "CONCLUSIONS The cellular expansion of cardiac fibroblasts after transaortic constriction surgery was not restricted to any single developmental subset.", "The parallel proliferation and activation of a heterogeneous population of fibroblasts on pressure overload could suggest that common signaling mechanisms stimulate their pathological response."], "structured": true}
{"doc_id": 2829179, "title": "Pre-eclampsia: connecting angiogenic and metabolic pathways.", "abstract": ["Pre-eclampsia is a hypertensive disease of pregnancy with a worldwide incidence of 5-8%.", "This review focuses on recent developments in pre-eclampsia research related to angiogenesis and metabolism.", "We first address the 'angiogenic imbalance' theory, which hypothesizes that pre-eclampsia results from an imbalance of factors that promote or antagonize angiogenesis, such as soluble fms-like tyrosine kinase (sFlt1), 2-methoxyestradiol (2-ME) and catechol-O-methyltransferase (COMT).", "Next, we analyze the association between pre-eclampsia and dysfunctional metabolism of both homocysteine and placental glycogen.", "We hope that illuminating some of the various connections existing between angiogenesis and metabolism in pre-eclampsia will facilitate the update or reconsideration of old models of pathogenesis."], "structured": false}
{"doc_id": 2831620, "title": "Protein Lysine Acetylated/Deacetylated Enzymes and the Metabolism-Related Diseases", "abstract": ["Lysine acetylation is a reversible posttranslational modifcation, an epigenetic phenomenon, referred to as transfer of an acetyl group from acetyl CoA to lysine e- amino group of targeted protein, which is modulated by acetyltransferases (histone/ lysine (K) acetyltransferases, HATs/KATs) and deacetylases (histone/lysine (K) deacetylases, HDACs/KDACs).", "Lysine acetylation regulates various metabolic processes, such as fatty acid oxidation, Krebs cycle, oxidative phosphorylation, angiogenesis and so on.", "Thus disorders of lysine acetylation may be correlated with obesity, diabetes and cardiovascular disease, which are termed as the metabolic complication.", "With accumulating studies on proteomic acetylation, lysine acetylation also involves in cell immune status and degenerative diseases, for example, Alzheimer\u2019s disease and Huntington\u2019s disease.", "This review primarily summarizes the current studies of lysine acetylation in metabolism modulation and in metabolism-related diseases, such as cardiovascular disease and fat metabolism disorder."], "structured": false}
{"doc_id": 2832403, "title": "Differential Specificity of Endocrine FGF19 and FGF21 to FGFR1 and FGFR4 in Complex with KLB", "abstract": ["BACKGROUND Recent studies suggest that betaKlotho (KLB) and endocrine FGF19 and FGF21 redirect FGFR signaling to regulation of metabolic homeostasis and suppression of obesity and diabetes.", "However, the identity of the predominant metabolic tissue in which a major FGFR-KLB resides that critically mediates the differential actions and metabolism effects of FGF19 and FGF21 remain unclear.   \n", "METHODOLOGY/PRINCIPAL FINDINGS We determined the receptor and tissue specificity of FGF21 in comparison to FGF19 by using direct, sensitive and quantitative binding kinetics, and downstream signal transduction and expression of early response gene upon administration of FGF19 and FGF21 in mice.", "We found that FGF21 binds FGFR1 with much higher affinity than FGFR4 in presence of KLB; while FGF19 binds both FGFR1 and FGFR4 in presence of KLB with comparable affinity.", "The interaction of FGF21 with FGFR4-KLB is very weak even at high concentration and could be negligible at physiological concentration.", "Both FGF19 and FGF21 but not FGF1 exhibit binding affinity to KLB.", "The binding of FGF1 is dependent on where FGFRs are present.", "Both FGF19 and FGF21 are unable to displace the FGF1 binding, and conversely FGF1 cannot displace FGF19 and FGF21 binding.", "These results indicate that KLB is an indispensable mediator for the binding of FGF19 and FGF21 to FGFRs that is not required for FGF1.", "Although FGF19 can predominantly activate the responses of the liver and to a less extent the adipose tissue, FGF21 can do so significantly only in the adipose tissue and adipocytes.", "Among several metabolic and endocrine tissues, the response of adipose tissue to FGF21 is predominant, and can be blunted by the ablation of KLB or FGFR1.   \n", "CONCLUSIONS Our results indicate that unlike FGF19, FGF21 is unable to bind FGFR4-KLB complex with affinity comparable to FGFR1-KLB, and therefore, at physiological concentration less likely to directly and significantly target the liver where FGFR4-KLB predominantly resides.", "However, both FGF21 and FGF19 have the potential to activate responses of primarily the adipose tissue where FGFR1-KLB resides."], "structured": true}
{"doc_id": 2837758, "title": "Therapeutic efficacy of a multi-epitope vaccine against Helicobacter pylori infection in BALB/c mice model.", "abstract": ["Epitope vaccine is a promising option for therapeutic vaccination against Helicobacter pylori (H. pylori) infection.", "In this study, we constructed a multi-epitope vaccine with five epitopes and mucosal adjuvant E. coli heat-labile enterotoxin B subunit (LTB) named HUepi-LTB and evaluated its therapeutic effect against H. pylori infection in BALB/c mice model.", "HUepi-LTB containing three Th epitopes from UreB and two B cell epitopes from UreB and HpaA was constructed and expressed in E. coli.", "Oral therapeutic immunization with HUepi-LTB significantly decreased H. pylori colonization compared with oral immunization with PBS, and the protection was correlated with antigen-specific CD4+ T cells and IgG and mucosal IgA antibody responses.", "This multi-epitope vaccine may be a promising vaccine candidate that may help to control H. pylori infection."], "structured": false}
{"doc_id": 2841164, "title": "DNA fragments in the blood plasma of cancer patients: quantitations and evidence for their origin from apoptotic and necrotic cells.", "abstract": ["Increased levels of DNA fragments have frequently been found in the blood plasma of cancer patients.", "Published data suggest that only a fraction of the DNA in blood plasma is derived from cancer cells.", "However, it is not known how much of the circulating DNA is from cancer or from noncancer cells.", "By quantitative methylation-specific PCR of the promoter region of the CDKN2A tumor suppressor gene, we were able to quantify the fraction of plasma DNA derived from tumor cells.", "In the plasma samples of 30 unselected cancer patients, we detected quantities of tumor DNA from only 3% to as much as 93% of total circulating DNA.", "We investigated possible origins of nontumor DNA in the plasma and demonstrate here a contribution of T-cell DNA in a few cases only.", "To investigate the possibility that plasma DNA originates from apoptotic or necrotic cells, we performed studies with apoptotic (staurosporine) and necrotic (staurosporine plus oligomycin) cells in vitro and with mice after induction of apoptotic (anti-CD95) or necrotic (acetaminophen) liver injury.", "Increasing amounts of DNA were found to be released in the supernatants of cells and in the blood plasma samples of treated animals.", "A clear discrimination of apoptotic and necrotic plasma DNA was possible by gel electrophoresis.", "The same characteristic patterns of DNA fragments could be identified in plasma derived from different cancer patients.", "The data are consistent with the possibility that apoptotic and necrotic cells are a major source for plasma DNA in cancer patients."], "structured": false}
{"doc_id": 2842550, "title": "Pharmacodynamics and pharmacokinetics of eptifibatide in patients with acute coronary syndromes: prospective analysis from PURSUIT.", "abstract": ["BACKGROUND Platelet deposition and aggregation are central to the pathogenesis of ischemic complications of acute coronary syndromes (ACS).", "Pharmacodynamic effects of the platelet glycoprotein IIb/IIIa antagonist eptifibatide have been delineated in healthy subjects but not in patients with ACS.", "We assessed effects of eptifibatide on ex vivo platelet aggregation in patients enrolled in the Platelet glycoprotein IIb/IIIa in Unstable angina: Receptor Suppression Using Integrilin (eptifibatide) Therapy (PURSUIT) trial of ACS.   \n", "METHODS AND RESULTS Patients were randomly assigned to an intravenous bolus (180 microgram/kg) and 72-hour infusion of eptifibatide (2.0 microgram/kg per minute, n=48) or placebo (n=50).", "We assessed correlations of plasma eptifibatide levels with receptor occupancy and inhibition of ex vivo platelet aggregation at 5 minutes and 1, 4, 24, 48, and 72 hours during treatment and 4 and 8 hours after termination of infusion.", "Blood was collected in buffered citrate and D-phenylalanyl-L-prolyl-L-arginine chloromethylketone anticoagulants.", "Although eptifibatide produced profound, prolonged inhibition of platelet aggregation during therapy, aggregation appeared to recover partially by 4 hours after the bolus.", "The aggregation response was greater with thrombin receptor agonist peptide versus ADP stimulation; inhibition of platelet aggregation was greater in blood samples anticoagulated with citrate versus D-phenylalanyl-L-prolyl-L-arginine chloromethylketone (PPACK).", "Plasma eptifibatide levels correlated significantly with receptor occupancy but not with inhibition of platelet aggregation.   \n", "CONCLUSIONS A bolus and infusion of eptifibatide inhibits platelet aggregation profoundly in patients with ACS and is followed by brief, partial recovery.", "These results enhance our understanding of the relation between pharmacodynamic and clinical effects of eptifibatide in such patients and may have important implications for its use in percutaneous interventions."], "structured": true}
{"doc_id": 2844490, "title": "Proinflammatory cytokines underlying the inflammation of Crohn's disease.", "abstract": ["PURPOSE OF REVIEW To encapsulate our current understanding of the proinflammatory cytokines responsible for the inflammation underlying Crohn's disease and the prospect of using this information to devise therapy for this condition based on inhibition of these cytokines.   ", "RECENT FINDINGS Current research is shedding new light on the role of both T helper cell (Th)1 and Th17 responses in the pathogenesis of Crohn's disease.", "Initial studies conducted a decade ago highlighted the view that Crohn's disease inflammation is caused by an interleukin-12-driven Th1 response, which resulted in the generation of interferon-gamma, which then served as the main inflammatory mediator.", "In recent years, however, this view has been largely eclipsed by studies, conducted mainly in murine models, showing that a Th17 response is the main cause of Crohn's disease inflammation through the production of interleukin-17.", "Now, a somewhat more balanced view is emerging, which holds that interferon-gamma is still a major proinflammatory cytokine in Crohn's disease, although it may arise from both the Th1 and Th17-mediated responses at different phases of the inflammatory process.   ", "SUMMARY The new findings continue to support the idea that anti-interleukin-12p40, an antibody that inhibits both the Th1 and Th17 response, is logically the most potent anticytokine for the treatment of Crohn's disease."], "structured": true}
{"doc_id": 2844897, "title": "STATISTICAL METHODS FOR ASSESSING AGREEMENT BETWEEN TWO METHODS OF CLINICAL MEASUREMENT", "abstract": ["In clinical measurement comparison of a new measurement technique with an established one is often needed to see whether they agree sufficiently for the new to replace the old.", "Such investigations are often analysed inappropriately, notably by using correlation coefficients.", "The use of correlation is misleading.", "An alternative approach, based on graphical techniques and simple calculations, is described, together with the relation between this analysis and the assessment of repeatability."], "structured": false}
{"doc_id": 2851611, "title": "The multidrug ABC transporter BmrC/BmrD of Bacillus subtilis is regulated via a ribosome-mediated transcriptional attenuation mechanism", "abstract": ["Expression of particular drug transporters in response to antibiotic pressure is a critical element in the development of bacterial multidrug resistance, and represents a serious concern for human health.", "To obtain a better understanding of underlying regulatory mechanisms, we have dissected the transcriptional activation of the ATP-binding cassette (ABC) transporter BmrC/BmrD of the Gram-positive model bacterium Bacillus subtilis.", "By using promoter-GFP fusions and live cell array technology, we demonstrate a temporally controlled transcriptional activation of the bmrCD genes in response to antibiotics that target protein synthesis.", "Intriguingly, bmrCD expression only occurs during the late-exponential and stationary growth stages, irrespective of the timing of the antibiotic challenge.", "We show that this is due to tight transcriptional control by the transition state regulator AbrB. Moreover, our results show that the bmrCD genes are co-transcribed with bmrB (yheJ), a small open reading frame immediately upstream of bmrC that harbors three alternative stem-loop structures.", "These stem-loops are apparently crucial for antibiotic-induced bmrCD transcription.", "Importantly, the antibiotic-induced bmrCD expression requires translation of bmrB, which implies that BmrB serves as a regulatory leader peptide.", "Altogether, we demonstrate for the first time that a ribosome-mediated transcriptional attenuation mechanism can control the expression of a multidrug ABC transporter."], "structured": false}
{"doc_id": 2853291, "title": "The neural crest is a source of mesenchymal stem cells with specialized hematopoietic stem cell niche function", "abstract": ["Mesenchymal stem cells (MSCs) and osteolineage cells contribute to the hematopoietic stem cell (HSC) niche in the bone marrow of long bones.", "However, their developmental relationships remain unclear.", "In this study, we demonstrate that different MSC populations in the developing marrow of long bones have distinct functions.", "Proliferative mesoderm-derived nestin(-) MSCs participate in fetal skeletogenesis and lose MSC activity soon after birth.", "In contrast, quiescent neural crest-derived nestin(+) cells preserve MSC activity, but do not generate fetal chondrocytes.", "Instead, they differentiate into HSC niche-forming MSCs, helping to establish the HSC niche by secreting Cxcl12.", "Perineural migration of these cells to the bone marrow requires the ErbB3 receptor.", "The neonatal Nestin-GFP(+) Pdgfr\u03b1(-) cell population also contains Schwann cell precursors, but does not comprise mature Schwann cells.", "Thus, in the developing bone marrow HSC niche-forming MSCs share a common origin with sympathetic peripheral neurons and glial cells, and ontogenically distinct MSCs have non-overlapping functions in endochondrogenesis and HSC niche formation."], "structured": false}
{"doc_id": 2853685, "title": "Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells", "abstract": ["Induced pluripotent stem cells (iPSCs) offer immense potential for regenerative medicine and studies of disease and development.", "Somatic cell reprogramming involves epigenomic reconfiguration, conferring iPSCs with characteristics similar to embryonic stem (ES) cells.", "However, it remains unknown how complete the reestablishment of ES-cell-like DNA methylation patterns is throughout the genome.", "Here we report the first whole-genome profiles of DNA methylation at single-base resolution in five human iPSC lines, along with methylomes of ES cells, somatic cells, and differentiated iPSCs and ES cells.", "iPSCs show significant reprogramming variability, including somatic memory and aberrant reprogramming of DNA methylation.", "iPSCs share megabase-scale differentially methylated regions proximal to centromeres and telomeres that display incomplete reprogramming of non-CG methylation, and differences in CG methylation and histone modifications.", "Lastly, differentiation of iPSCs into trophoblast cells revealed that errors in reprogramming CG methylation are transmitted at a high frequency, providing an iPSC reprogramming signature that is maintained after differentiation."], "structured": false}
{"doc_id": 2867345, "title": "Inheritance of coronary artery disease in men: an analysis of the role of the Y chromosome", "abstract": ["BACKGROUND A sexual dimorphism exists in the incidence and prevalence of coronary artery disease--men are more commonly affected than are age-matched women.", "We explored the role of the Y chromosome in coronary artery disease in the context of this sexual inequity.   \n", "METHODS We genotyped 11 markers of the male-specific region of the Y chromosome in 3233 biologically unrelated British men from three cohorts: the British Heart Foundation Family Heart Study (BHF-FHS), West of Scotland Coronary Prevention Study (WOSCOPS), and Cardiogenics Study.", "On the basis of this information, each Y chromosome was tracked back into one of 13 ancient lineages defined as haplogroups.", "We then examined associations between common Y chromosome haplogroups and the risk of coronary artery disease in cross-sectional BHF-FHS and prospective WOSCOPS.", "Finally, we undertook functional analysis of Y chromosome effects on monocyte and macrophage transcriptome in British men from the Cardiogenics Study.   \n", "FINDINGS Of nine haplogroups identified, two (R1b1b2 and I) accounted for roughly 90% of the Y chromosome variants among British men.", "Carriers of haplogroup I had about a 50% higher age-adjusted risk of coronary artery disease than did men with other Y chromosome lineages in BHF-FHS (odds ratio 1\u00b775, 95% CI 1\u00b720-2\u00b754, p=0\u00b7004), WOSCOPS (1\u00b745, 1\u00b708-1\u00b795, p=0\u00b7012), and joint analysis of both populations (1\u00b756, 1\u00b724-1\u00b797, p=0\u00b70002).", "The association between haplogroup I and increased risk of coronary artery disease was independent of traditional cardiovascular and socioeconomic risk factors.", "Analysis of macrophage transcriptome in the Cardiogenics Study revealed that 19 molecular pathways showing strong differential expression between men with haplogroup I and other lineages of the Y chromosome were interconnected by common genes related to inflammation and immunity, and that some of them have a strong relevance to atherosclerosis.   \n", "INTERPRETATION The human Y chromosome is associated with risk of coronary artery disease in men of European ancestry, possibly through interactions of immunity and inflammation.   \n", "FUNDING British Heart Foundation; UK National Institute for Health Research; LEW Carty Charitable Fund; National Health and Medical Research Council of Australia; European Union 6th Framework Programme; Wellcome Trust."], "structured": true}
{"doc_id": 2883827, "title": "Cytoscape 2.8: new features for data integration and network visualization", "abstract": ["UNLABELLED Cytoscape is a popular bioinformatics package for biological network visualization and data integration.", "Version 2.8 introduces two powerful new features--Custom Node Graphics and Attribute Equations--which can be used jointly to greatly enhance Cytoscape's data integration and visualization capabilities.", "Custom Node Graphics allow an image to be projected onto a node, including images generated dynamically or at remote locations.", "Attribute Equations provide Cytoscape with spreadsheet-like functionality in which the value of an attribute is computed dynamically as a function of other attributes and network properties.   ", "AVAILABILITY AND IMPLEMENTATION Cytoscape is a desktop Java application released under the Library Gnu Public License (LGPL).", "Binary install bundles and source code for Cytoscape 2.8 are available for download from http://cytoscape.org."], "structured": false}
{"doc_id": 2888272, "title": "Detection of Histone Modifications at Specific Gene Loci in Single Cells in Histological Sections", "abstract": ["Chromatin immunoprecipitation assays have contributed greatly to our understanding of the role of histone modifications in gene regulation.", "However, they do not permit analysis with single-cell resolution, thus confounding analyses of heterogeneous cell populations.", "Here we present a method that permits visualization of histone modifications of single genomic loci with single-cell resolution in formaldehyde-fixed paraffin-embedded tissue sections based on combined use of in situ hybridization and proximity ligation assays.", "We show that dimethylation of lysine 4 of histone H3 (H3K4me2) at the MYH11 locus is restricted to the smooth muscle cell (SMC) lineage in human and mouse tissue sections and that the mark persists even in phenotypically modulated SMC in atherosclerotic lesions that show no detectable expression of SMC marker genes.", "This methodology has promise for broad applications in the study of epigenetic mechanisms in complex multicellular tissues in development and disease."], "structured": false}
{"doc_id": 2890952, "title": "Mechanistic characterization of the sulfur-relay system for eukaryotic 2-thiouridine biogenesis at tRNA wobble positions", "abstract": ["The wobble modification in tRNAs, 5-methoxycarbonylmethyl-2-thiouridine (mcm(5)s(2)U), is required for the proper decoding of NNR codons in eukaryotes.", "The 2-thio group confers conformational rigidity of mcm(5)s(2)U by largely fixing the C3'-endo ribose puckering, ensuring stable and accurate codon-anticodon pairing.", "We have identified five genes in Saccharomyces cerevisiae, YIL008w (URM1), YHR111w (UBA4), YOR251c (TUM1), YNL119w (NCS2) and YGL211w (NCS6), that are required for 2-thiolation of mcm(5)s(2)U. An in vitro sulfur transfer experiment revealed that Tum1p stimulated the cysteine desulfurase of Nfs1p, and accepted persulfide sulfurs from Nfs1p.", "URM1 is a ubiquitin-related modifier, and UBA4 is an E1-like enzyme involved in protein urmylation.", "The carboxy-terminus of Urm1p was activated as an acyl-adenylate (-COAMP), then thiocarboxylated (-COSH) by Uba4p.", "The activated thiocarboxylate can be utilized in the subsequent reactions for 2-thiouridine formation, mediated by Ncs2p/Ncs6p.", "We could successfully reconstitute the 2-thiouridine formation in vitro using recombinant proteins.", "This study revealed that 2-thiouridine formation shares a pathway and chemical reactions with protein urmylation.", "The sulfur-flow of eukaryotic 2-thiouridine formation is distinct mechanism from the bacterial sulfur-relay system which is based on the persulfide chemistry."], "structured": false}
{"doc_id": 2891825, "title": "High prevalence of asthma in cross country skiers.", "abstract": ["OBJECTIVES To study the prevalence of asthma (asthma symptoms and bronchial hyperresponsiveness) in Swedish cross country skiers compared with non-skiers and monitor changes in symptoms and bronchial hyperresponsiveness during the year.   \n", "DESIGN Cross sectional study during the winter ski season and in the summer.   \n", "SETTING Six ski clubs for \u00e9lite skiers (total 47) in two different areas of Sweden.   ", "SUBJECTS 42 \u00e9lite cross country skiers and 29 non-skiing referents.   \n", "MAIN OUTCOME MEASURES Bronchial responsiveness, asthma symptoms, and lung function.   \n", "RESULTS Bronchial responsiveness was significantly greater and asthma symptoms more prevalent in the skiers than in the referents.", "There was no difference in bronchial responsiveness within either group between winter and summer.", "15 of the 42 skiers used antiasthmatic drugs regularly and 23 had a combination of asthma symptoms and hyperresponsive airways or physician diagnosed asthma, or both.", "Altogether 33 skiers had symptoms of asthma or bronchial hyperresponsiveness.", "One of the referents had symptoms of asthma and bronchial hyperresponsiveness, and none used antiasthmatic drugs regularly.   \n", "CONCLUSIONS Asthma, asthma-like symptoms, and bronchial hyperresponsiveness are much more common in cross country skiers than in the general population and non-skiers.", "Strenuous exercise at low temperatures entailing breathing large volumes of cold air is the most probable explanation of persistent asthma in skiers."], "structured": true}
{"doc_id": 2904102, "title": "Characterization of biochemical properties of Bacillus subtilis RecQ helicase.", "abstract": ["RecQ family helicases function as safeguards of the genome.", "Unlike Escherichia coli, the Gram-positive Bacillus subtilis bacterium possesses two RecQ-like homologues, RecQ[Bs] and RecS, which are required for the repair of DNA double-strand breaks.", "RecQ[Bs] also binds to the forked DNA to ensure a smooth progression of the cell cycle.", "Here we present the first biochemical analysis of recombinant RecQ[Bs].", "RecQ[Bs] binds weakly to single-stranded DNA (ssDNA) and blunt-ended double-stranded DNA (dsDNA) but strongly to forked dsDNA.", "The protein exhibits a DNA-stimulated ATPase activity and ATP- and Mg(2+)-dependent DNA helicase activity with a 3' \u2192 5' polarity.", "Molecular modeling shows that RecQ[Bs] shares high sequence and structure similarity with E. coli RecQ. Surprisingly, RecQ[Bs] resembles the truncated Saccharomyces cerevisiae Sgs1 and human RecQ helicases more than RecQ[Ec] with regard to its enzymatic activities.", "Specifically, RecQ[Bs] unwinds forked dsDNA and DNA duplexes with a 3'-overhang but is inactive on blunt-ended dsDNA and 5'-overhung duplexes.", "Interestingly, RecQ[Bs] unwinds blunt-ended DNA with structural features, including nicks, gaps, 5'-flaps, Kappa joints, synthetic replication forks, and Holliday junctions.", "We discuss these findings in the context of RecQ[Bs]'s possible functions in preserving genomic stability."], "structured": false}
{"doc_id": 2919030, "title": "SOD1 Integrates Signals from Oxygen and Glucose to Repress Respiration", "abstract": ["Cu/Zn superoxide dismutase (SOD1) is an abundant enzyme that has been best studied as a regulator of antioxidant defense.", "Using the yeast Saccharomyces cerevisiae, we report that SOD1 transmits signals from oxygen and glucose to repress respiration.", "The mechanism involves SOD1-mediated stabilization of two casein kinase 1-gamma (CK1\u03b3) homologs, Yck1p and Yck2p, required for respiratory repression.", "SOD1 binds a C-terminal degron we identified in Yck1p/Yck2p and promotes kinase stability by catalyzing superoxide conversion to peroxide.", "The effects of SOD1 on CK1\u03b3 stability are also observed with mammalian SOD1 and CK1\u03b3 and in a human cell line.", "Therefore, in a single circuit, oxygen, glucose, and reactive oxygen can repress respiration through SOD1/CK1\u03b3 signaling.", "Our data therefore may provide mechanistic insight into how rapidly proliferating cells and many cancers accomplish glucose-mediated repression of respiration in favor of aerobic glycolysis."], "structured": false}
{"doc_id": 2931832, "title": "The prognostic impact of the platelet distribution width-to-platelet count ratio in patients with breast cancer", "abstract": ["Activated platelets promote tumor cell growth, angiogenesis, and invasion.", "Platelet activity can be inferred by platelet volume indices (PVIs), which include platelet distribution width (PDW), mean platelet volume (MPV), platelet distribution width-to-platelet count ratio (PDW/P), and mean platelet volume-to-platelet count ratio.", "Platelets and platelet-related markers, such as the platelet-to-lymphocyte ratio, have been found to be significant prognostic factors in patients with breast cancer.", "However, the role of PVIs for predicting survival in breast cancer remains unknown; hence, we performed this retrospective analysis of 275 patients with breast cancer.", "PVIs were compared with clinicopathological variables, and were assessed to identify independent indicators associated with disease-free survival (DFS) using the Cox proportional hazards model.", "An elevated PDW/P significantly correlated with age and HER2 status.", "Univariate analysis revealed that elevated PDW, MPV, and PDW/P as well as tumor size, nuclear grade, and lymph node involvement were significantly associated with inferior DFS rates (tumor size: p<0.01; nuclear grade, lymph node involvement, PDW, MPV, and PDW/P: p<0.05).", "On multivariate analysis, a large tumor size and elevated PDW/P were significant prognostic factors for DFS, with hazard ratios of 3.24 (95% confidence interval [CI]: 1.24-8.47) and 2.99 (95% CI: 1.18-7.57), respectively (p<0.05).", "Our study is the first to reveal that an elevated PDW/P significantly reduces DFS in patients with breast carcinoma.", "Measuring the PDW/P is simple, relatively inexpensive, and almost universally available using routine blood counts; this makes it an attractive biomarker for improved risk assessment."], "structured": false}
{"doc_id": 2947124, "title": "Persistent LCMV infection is controlled by blockade of type I interferon signaling.", "abstract": ["During persistent viral infections, chronic immune activation, negative immune regulator expression, an elevated interferon signature, and lymphoid tissue destruction correlate with disease progression.", "We demonstrated that blockade of type I interferon (IFN-I) signaling using an IFN-I receptor neutralizing antibody reduced immune system activation, decreased expression of negative immune regulatory molecules, and restored lymphoid architecture in mice persistently infected with lymphocytic choriomeningitis virus.", "IFN-I blockade before and after establishment of persistent virus infection resulted in enhanced virus clearance and was CD4 T cell-dependent.", "Hence, we demonstrate a direct causal link between IFN-I signaling, immune activation, negative immune regulator expression, lymphoid tissue disorganization, and virus persistence.", "Our results suggest that therapies targeting IFN-I may help control persistent virus infections."], "structured": false}
{"doc_id": 2947540, "title": "Lam6 Regulates the Extent of Contacts between Organelles", "abstract": ["Communication between organelles is crucial for eukaryotic cells to function as one coherent unit.", "An important means of communication is through membrane contact sites, where two organelles come into close proximity allowing the transport of lipids and small solutes between them.", "Contact sites are dynamic in size and can change in response to environmental or cellular stimuli; however, how this is regulated has been unclear.", "Here, we show that Saccharomyces cerevisiae Lam6 resides in several central contact sites: ERMES (ER/mitochondria encounter structure), vCLAMP (vacuole and mitochondria patch), and NVJ (nuclear vacuolar junction).", "We show that Lam6 is sufficient for expansion of contact sites under physiological conditions and necessary for coordination of contact site size.", "Given that Lam6 is part of a large protein family and is conserved in vertebrates, our work opens avenues for investigating the underlying principles of organelle communication."], "structured": false}
{"doc_id": 2958458, "title": "Endocrine regulation of human fetal growth: the role of the mother, placenta, and fetus.", "abstract": ["The environment in which the fetus develops is critical for its survival and long-term health.", "The regulation of normal human fetal growth involves many multidirectional interactions between the mother, placenta, and fetus.", "The mother supplies nutrients and oxygen to the fetus via the placenta.", "The fetus influences the provision of maternal nutrients via the placental production of hormones that regulate maternal metabolism.", "The placenta is the site of exchange between mother and fetus and regulates fetal growth via the production and metabolism of growth-regulating hormones such as IGFs and glucocorticoids.", "Adequate trophoblast invasion in early pregnancy and increased uteroplacental blood flow ensure sufficient growth of the uterus, placenta, and fetus.", "The placenta may respond to fetal endocrine signals to increase transport of maternal nutrients by growth of the placenta, by activation of transport systems, and by production of placental hormones to influence maternal physiology and even behavior.", "There are consequences of poor fetal growth both in the short term and long term, in the form of increased mortality and morbidity.", "Endocrine regulation of fetal growth involves interactions between the mother, placenta, and fetus, and these effects may program long-term physiology."], "structured": false}
{"doc_id": 2973910, "title": "Endothelial-to-mesenchymal transition contributes to cardiac fibrosis", "abstract": ["Cardiac fibrosis, associated with a decreased extent of microvasculature and with disruption of normal myocardial structures, results from excessive deposition of extracellular matrix, which is mediated by the recruitment of fibroblasts.", "The source of these fibroblasts is unclear and specific anti-fibrotic therapies are not currently available.", "Here we show that cardiac fibrosis is associated with the emergence of fibroblasts originating from endothelial cells, suggesting an endothelial-mesenchymal transition (EndMT) similar to events that occur during formation of the atrioventricular cushion in the embryonic heart.", "Transforming growth factor-\u03b21 (TGF-\u03b21) induced endothelial cells to undergo EndMT, whereas bone morphogenic protein 7 (BMP-7) preserved the endothelial phenotype.", "The systemic administration of recombinant human BMP-7 (rhBMP-7) significantly inhibited EndMT and the progression of cardiac fibrosis in mouse models of pressure overload and chronic allograft rejection.", "Our findings show that EndMT contributes to the progression of cardiac fibrosis and that rhBMP-7 can be used to inhibit EndMT and to intervene in the progression of chronic heart disease associated with fibrosis."], "structured": false}
{"doc_id": 2988714, "title": "Coupled local translation and degradation regulate growth cone collapse", "abstract": ["Local translation mediates axonal responses to Semaphorin3A (Sema3A) and other guidance cues.", "However, only a subset of the axonal proteome is locally synthesized, whereas most proteins are trafficked from the soma.", "The reason why only specific proteins are locally synthesized is unknown.", "Here we show that local protein synthesis and degradation are linked events in growth cones.", "We find that growth cones exhibit high levels of ubiquitination and that local signalling pathways trigger the ubiquitination and degradation of RhoA, a mediator of Sema3A-induced growth cone collapse.", "Inhibition of RhoA degradation is sufficient to remove the protein-synthesis requirement for Sema3A-induced growth cone collapse.", "In addition to RhoA, we find that locally translated proteins are the main targets of the ubiquitin-proteasome system in growth cones.", "Thus, local protein degradation is a major feature of growth cones and creates a requirement for local translation to replenish proteins needed to maintain growth cone responses."], "structured": false}
{"doc_id": 2991954, "title": "Cdk11 is a RanGTP-dependent microtubule stabilization factor that regulates spindle assembly rate", "abstract": ["Production of Ran-guanosine triphosphate (GTP) around chromosomes induces local nucleation and plus end stabilization of microtubules (MTs).", "The nuclear protein TPX2 is required for RanGTP-dependent MT nucleation.", "To find the MT stabilizer, we affinity purify nuclear localization signal (NLS)-containing proteins from Xenopus laevis egg extracts.", "This NLS protein fraction contains the MT stabilization activity.", "After further purification, we used mass spectrometry to identify proteins in active fractions, including cyclin-dependent kinase 11 (Cdk11).", "Cdk11 localizes on spindle poles and MTs in Xenopus culture cells and egg extracts.", "Recombinant Cdk11 demonstrates RanGTP-dependent MT stabilization activity, whereas a kinase-dead mutant does not.", "Inactivation of Cdk11 in egg extracts blocks RanGTP-dependent MT stabilization and dramatically decreases the spindle assembly rate.", "Simultaneous depletion of TPX2 completely inhibits centrosome-dependent spindle assembly.", "Our results indicate that Cdk11 is responsible for RanGTP-dependent MT stabilization around chromosomes and that this local stabilization is essential for normal rates of spindle assembly and spindle function."], "structured": false}
{"doc_id": 3001685, "title": "Population dynamics of a pathogen: the conundrum of vivax malaria", "abstract": ["Building a mathematical model of population dynamics of pathogens within their host involves considerations of factors similar to those in ecology, as pathogens can prey on cells in the host.", "But within the multicellular host, attacked cell types are integrated with other cellular systems, which in turn intervene in the infection.", "For example, immune responses attempt to sense and then eliminate or contain pathogens, and homeostatic mechanisms try to compensate for cell loss.", "This review focuses on modeling applied to malarias, diseases caused by single-cell eukaryote parasites that infect red blood cells, with special concern given to vivax malaria, a disease often thought to be benign (if sometimes incapacitating) because the parasite only attacks a small proportion of red blood cells, the very youngest ones.", "However, I will use mathematical modeling to argue that depletion of this pool of red blood cells can be disastrous to the host if growth of the parasite is not vigorously check by host immune responses.", "Also, modeling can elucidate aspects of new field observations that indicate that vivax malaria is more dangerous than previously thought.", "ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s12551-010-0034-3) contains supplementary material, which is available to authorized users."], "structured": false}
{"doc_id": 3033830, "title": "Identification and analysis of ribonuclease P and MRP RNA in a broad range of eukaryotes", "abstract": ["RNases P and MRP are ribonucleoprotein complexes involved in tRNA and rRNA processing, respectively.", "The RNA subunits of these two enzymes are structurally related to each other and play an essential role in the enzymatic reaction.", "Both of the RNAs have a highly conserved helical region, P4, which is important in the catalytic reaction.", "We have used a bioinformatics approach based on conserved elements to computationally analyze available genomic sequences of eukaryotic organisms and have identified a large number of novel nuclear RNase P and MRP RNA genes.", "For MRP RNA for instance, this investigation increases the number of known sequences by a factor of three.", "We present secondary structure models of many of the predicted RNAs.", "Although all sequences are able to fold into the consensus secondary structure of P and MRP RNAs, a striking variation in size is observed, ranging from a Nosema locustae MRP RNA of 160 nt to much larger RNAs, e.g. a Plasmodium knowlesi P RNA of 696 nt.", "The P and MRP RNA genes appear in tandem in some protists, further emphasizing the close evolutionary relationship of these RNAs."], "structured": false}
{"doc_id": 3034412, "title": "Calcium absorption varies within the reference range for serum 25-hydroxyvitamin D.", "abstract": ["BACKGROUND Calcium absorption is generally considered to be impaired under conditions of vitamin D deficiency, but the vitamin D status that fully normalizes absorption is not known for humans.   \n", "OBJECTIVE To quantify calcium absorption at two levels of vitamin D repletion, using pharmacokinetic methods and commercially marketed calcium supplements.   \n", "DESIGN Two experiments performed in the spring of the year, one year apart.", "In the first, in which participants were pretreated with 25-hydroxyvitamin D (25OHD), mean serum 25OHD concentration was 86.5 nmol/L; and in the other, with no pretreatment, mean serum concentration was 50.2 nmol/L. Participants received 500 mg oral calcium loads as a part of a standard low calcium breakfast.", "A low calcium lunch was provided at mid-day.", "Blood was obtained fasting and at frequent intervals for 10 to 12 hours thereafter.   \n", "METHODS Relative calcium absorption at the two 25OHD concentrations was estimated from the area under the curve (AUC) for the load-induced increment in serum total calcium.   \n", "RESULTS AUC(9) (+/-", "SEM), was 3.63 mg hr/dL +/-", "0.234 in participants pretreated with 25OHD and 2.20 +/-", "0.240 in those not pretreated (P < 0.001).", "In brief, absorption was 65% higher at serum 25OHD levels averaging 86.5 nmol/L than at levels averaging 50 nmol/L (both values within the nominal reference range for this analyte).   \n", "CONCLUSIONS Despite the fact that the mean serum 25OHD level in the experiment without supplementation was within the current reference ranges, calcium absorptive performance at 50 nmol/L was significantly reduced relative to that at a mean 25OHD level of 86 nmol/L. Thus, individuals with serum 25-hydroxyvitamin D levels at the low end of the current reference ranges may not be getting the full benefit from their calcium intake.", "We conclude that the lower end of the current reference range is set too low."], "structured": true}
{"doc_id": 3038933, "title": "Evolution of virulence in opportunistic pathogens: generalism, plasticity, and control", "abstract": ["Standard virulence evolution theory assumes that virulence factors are maintained because they aid parasitic exploitation, increasing growth within and/or transmission between hosts.", "An increasing number of studies now demonstrate that many opportunistic pathogens (OPs) do not conform to these assumptions, with virulence factors maintained instead because of advantages in non-parasitic contexts.", "Here we review virulence evolution theory in the context of OPs and highlight the importance of incorporating environments outside a focal virulence site.", "We illustrate that virulence selection is constrained by correlations between these external and focal settings and pinpoint drivers of key environmental correlations, with a focus on generalist strategies and phenotypic plasticity.", "We end with a summary of key theoretical and empirical challenges to be met for a fuller understanding of OPs."], "structured": false}
{"doc_id": 3052213, "title": "Genome-Wide Profiling of H3K56 Acetylation and Transcription Factor Binding Sites in Human Adipocytes", "abstract": ["The growing epidemic of obesity and metabolic diseases calls for a better understanding of adipocyte biology.", "The regulation of transcription in adipocytes is particularly important, as it is a target for several therapeutic approaches.", "Transcriptional outcomes are influenced by both histone modifications and transcription factor binding.", "Although the epigenetic states and binding sites of several important transcription factors have been profiled in the mouse 3T3-L1 cell line, such data are lacking in human adipocytes.", "In this study, we identified H3K56 acetylation sites in human adipocytes derived from mesenchymal stem cells.", "H3K56 is acetylated by CBP and p300, and deacetylated by SIRT1, all are proteins with important roles in diabetes and insulin signaling.", "We found that while almost half of the genome shows signs of H3K56 acetylation, the highest level of H3K56 acetylation is associated with transcription factors and proteins in the adipokine signaling and Type II Diabetes pathways.", "In order to discover the transcription factors that recruit acetyltransferases and deacetylases to sites of H3K56 acetylation, we analyzed DNA sequences near H3K56 acetylated regions and found that the E2F recognition sequence was enriched.", "Using chromatin immunoprecipitation followed by high-throughput sequencing, we confirmed that genes bound by E2F4, as well as those by HSF-1 and C/EBP\u03b1, have higher than expected levels of H3K56 acetylation, and that the transcription factor binding sites and acetylation sites are often adjacent but rarely overlap.", "We also discovered a significant difference between bound targets of C/EBP\u03b1 in 3T3-L1 and human adipocytes, highlighting the need to construct species-specific epigenetic and transcription factor binding site maps.", "This is the first genome-wide profile of H3K56 acetylation, E2F4, C/EBP\u03b1 and HSF-1 binding in human adipocytes, and will serve as an important resource for better understanding adipocyte transcriptional regulation."], "structured": false}
{"doc_id": 3052642, "title": "Detecting and characterizing circular RNAs", "abstract": ["Circular RNA transcripts were first identified in the early 1990s but knowledge of these species has remained limited, as their study through traditional methods of RNA analysis has been difficult.", "Now, novel bioinformatic approaches coupled with biochemical enrichment strategies and deep sequencing have allowed comprehensive studies of circular RNA species.", "Recent studies have revealed thousands of endogenous circular RNAs in mammalian cells, some of which are highly abundant and evolutionarily conserved.", "Evidence is emerging that some circRNAs might regulate microRNA (miRNA) function, and roles in transcriptional control have also been suggested.", "Therefore, study of this class of noncoding RNAs has potential implications for therapeutic and research applications.", "We believe the key future challenge for the field will be to understand the regulation and function of these unusual molecules."], "structured": false}
{"doc_id": 3056682, "title": "A classification of unstable angina revisited.", "abstract": ["Unstable angina is a critical phase of coronary heart disease with widely variable symptoms and prognosis.", "A decade ago, a classification of unstable angina based on clinical symptoms was introduced.", "This system was then validated by prospective clinical studies to correlate with the prognosis and was linked to angiographic and histological findings.", "It has been used to categorize patients in many large clinical trials.", "In recent years, the pathophysiological roles of platelet activation and inflammation in unstable angina have been elucidated.", "Subsequently, improved markers of myocardial injury, acute-phase proteins, and hemostatic markers that may be associated with clinical outcomes have been identified.", "Particularly, cardiac-specific troponin T and troponin I have been shown to represent the best predictors of early risk in patients with angina at rest.", "Accordingly, it is suggested that the original classification be extended by subclassifying one large group of unstable angina patients, ie, those with angina at rest within the past 48 hours (class IIIB), into troponin-positive (T(pos)) and troponin-negative (T(neg)) patients.", "The 30-days risk for death and myocardial infarction is considered to be up to 20% in class IIIB-T(pos) but <2% in class IIIB-T(neg) patients.", "Initial results suggest that troponins may function as surrogate markers for thrombus formation and can effectively guide therapy with glycoprotein IIb/IIIa antagonists or low-molecular-weight heparins.", "These observations provide additional impetus for adding the measurement of these markers to the clinical classification and represent a novel concept of treating these high-risk patients."], "structured": false}
{"doc_id": 3067015, "title": "Alcohol Intake and Blood Pressure: A Systematic Review Implementing a Mendelian Randomization Approach", "abstract": ["BACKGROUND Alcohol has been reported to be a common and modifiable risk factor for hypertension.", "However, observational studies are subject to confounding by other behavioural and sociodemographic factors, while clinical trials are difficult to implement and have limited follow-up time.", "Mendelian randomization can provide robust evidence on the nature of this association by use of a common polymorphism in aldehyde dehydrogenase 2 (ALDH2) as a surrogate for measuring alcohol consumption.", "ALDH2 encodes a major enzyme involved in alcohol metabolism.", "Individuals homozygous for the null variant (*2*2) experience adverse symptoms when drinking alcohol and consequently drink considerably less alcohol than wild-type homozygotes (*1*1) or heterozygotes.", "We hypothesise that this polymorphism may influence the risk of hypertension by affecting alcohol drinking behaviour.   \n", "METHODS AND FINDINGS We carried out fixed effect meta-analyses of the ALDH2 genotype with blood pressure (five studies, n = 7,658) and hypertension (three studies, n = 4,219) using studies identified via systematic review.", "In males, we obtained an overall odds ratio of 2.42 (95% confidence interval [CI] 1.66-3.55, p = 4.8 x 10(-6)) for hypertension comparing *1*1 with *2*2 homozygotes and an odds ratio of 1.72 (95% CI 1.17-2.52, p = 0.006) comparing heterozygotes (surrogate for moderate drinkers) with *2*2 homozygotes.", "Systolic blood pressure was 7.44 mmHg (95% CI 5.39-9.49, p = 1.1 x 10(-12)) greater among *1*1 than among *2*2 homozygotes, and 4.24 mmHg (95% CI 2.18-6.31, p = 0.00005) greater among heterozygotes than among *2*2 homozygotes.   \n", "CONCLUSIONS These findings support the hypothesis that alcohol intake has a marked effect on blood pressure and the risk of hypertension."], "structured": true}
{"doc_id": 3078080, "title": "Rapid and Sensitive RT-QuIC Detection of Human Creutzfeldt-Jakob Disease Using Cerebrospinal Fluid", "abstract": ["UNLABELLED Fast, definitive diagnosis of Creutzfeldt-Jakob disease (CJD) is important in assessing patient care options and transmission risks.", "Real-time quaking-induced conversion (RT-QuIC) assays of cerebrospinal fluid (CSF) and nasal-brushing specimens are valuable in distinguishing CJD from non-CJD conditions but have required 2.5 to 5 days.", "Here, an improved RT-QuIC assay is described which identified positive CSF samples within 4 to 14 h with better analytical sensitivity.", "Moreover, analysis of 11 CJD patients demonstrated that while 7 were RT-QuIC positive using the previous conditions, 10 were positive using the new assay.", "In these and further analyses, a total of 46 of 48 CSF samples from sporadic CJD patients were positive, while all 39 non-CJD patients were negative, giving 95.8% diagnostic sensitivity and 100% specificity.", "This second-generation RT-QuIC assay markedly improved the speed and sensitivity of detecting prion seeds in CSF specimens from CJD patients.", "This should enhance prospects for rapid and accurate ante mortem CJD diagnosis.   ", "IMPORTANCE A long-standing problem in dealing with various neurodegenerative protein misfolding diseases is early and accurate diagnosis.", "This issue is particularly important with human prion diseases, such as CJD, because prions are deadly, transmissible, and unusually resistant to decontamination.", "The recently developed RT-QuIC test allows for highly sensitive and specific detection of CJD in human cerebrospinal fluid and is being broadly implemented as a key diagnostic tool.", "However, as currently applied, RT-QuIC takes 2.5 to 5 days and misses 11 to 23% of CJD cases.", "Now, we have markedly improved RT-QuIC analysis of human CSF such that CJD and non-CJD patients can be discriminated in a matter of hours rather than days with enhanced sensitivity.", "These improvements should allow for much faster, more accurate, and practical testing for CJD.", "In broader terms, our study provides a prototype for tests for misfolded protein aggregates that cause many important amyloid diseases, such as Alzheimer's, Parkinson's, and tauopathies."], "structured": false}
{"doc_id": 3078550, "title": "Wortmannin, a phosphoinositide 3-kinase inhibitor, selectively enhances cytotoxicity of receptor-directed-toxin chimeras in vitro and in vivo.", "abstract": ["BACKGROUND Generalized resistance of some neoplastic cell lines to treatment with ligand-toxin chimeras has been attributed to an increased rate of lysosomal uptake and degradation following endocytosis of the chimera-receptor complex.", "Because phosphoinositide 3-kinase (Pl 3-kinase) activity is known to play a role in intracellular trafficking, particularly from endosomes to lysosomes, we hypothesized that co-exposing cells to the Pl 3-kinase inhibitor, wortmannin, might enhance cytotoxicity of ligand-toxin chimeras.   \n", "METHODS In vitro, cytotoxicity of five receptor directed-toxin chimeras (bFGF-SAP, bFGF-PE, aFGF-PE, HBEGF-SAP, bFGF-gelonin) and an immunotoxin (11A8-SAP) was examined in the presence or absence of this Pl 3-kinase inhibitor against a panel of human neoplastic cell lines: SK-MEL-5 (melanoma), PA-1 (ovarian teratocarcinoma), DU145 (prostatic carcinoma) and MCF-7 (breast carcinoma).", "In vivo, antitumor activity of a treatment regimen combining wortmannin (1 or 2 mg/kg i.p.) and bFGF-SAP (10 micrograms/kg i.v.) once a week for 4 weeks was evaluated compared to administration of each agent alone in C3H/HeN mice implanted with the FSallC murine fibrosarcoma.   \n", "RESULTS At concentrations greater than the reported Ki for Pl 3-kinase inhibition (1-10 microM), wortmannin enhanced cytotoxicity when combined with saporin or gelonin chimeras, but produced subadditive cytotoxicity when combined with Pseudomonas exotoxin chimeras.", "When low nanomolar concentrations selective for Pl 3-kinase inhibition (5-100 nM) were examined for effects on one receptor directed-toxin chimera, wortmannin dramatically enhanced bFGF-SAP cytotoxicity in three of the four cell lines.", "A different Pl 3-kinase inhibitor, LY294002 (Ki approximately 1 microM), however, failed to potentiate bFGF-SAP.", "When administered to mice, wortmannin combined with bFGF-SAP resulted in a significant decrease in tumor volumes compared to vehicle-treated controls that was not observed in mice treated with either agent alone.   \n", "CONCLUSIONS Taken together, these results suggest that although wortmannin increases the cytotoxic efficacy of some receptor-directed chimeras, potentiation may occur through an alternative pathway not involving Pl 3-kinase inhibition."], "structured": true}
{"doc_id": 3083927, "title": "Chronic stress, glucocorticoid receptor resistance, inflammation, and disease risk.", "abstract": ["We propose a model wherein chronic stress results in glucocorticoid receptor resistance (GCR) that, in turn, results in failure to down-regulate inflammatory response.", "Here we test the model in two viral-challenge studies.", "In study 1, we assessed stressful life events, GCR, and control variables including baseline antibody to the challenge virus, age, body mass index (BMI), season, race, sex, education, and virus type in 276 healthy adult volunteers.", "The volunteers were subsequently quarantined, exposed to one of two rhinoviruses, and followed for 5 d with nasal washes for viral isolation and assessment of signs/symptoms of a common cold.", "In study 2, we assessed the same control variables and GCR in 79 subjects who were subsequently exposed to a rhinovirus and monitored at baseline and for 5 d after viral challenge for the production of local (in nasal secretions) proinflammatory cytokines (IL-1\u03b2, TNF-\u03b1, and IL-6).", "Study 1: After covarying the control variables, those with recent exposure to a long-term threatening stressful experience demonstrated GCR; and those with GCR were at higher risk of subsequently developing a cold.", "Study 2: With the same controls used in study 1, greater GCR predicted the production of more local proinflammatory cytokines among infected subjects.", "These data provide support for a model suggesting that prolonged stressors result in GCR, which, in turn, interferes with appropriate regulation of inflammation.", "Because inflammation plays an important role in the onset and progression of a wide range of diseases, this model may have broad implications for understanding the role of stress in health."], "structured": false}
{"doc_id": 3085264, "title": "Pituitary Adenylate Cyclase-Activating Polypeptide (PACAP), a Neuron-Derived Peptide Regulating Glial Glutamate Transport and Metabolism", "abstract": ["In the brain, glutamatergic neurotransmission is terminated predominantly by the rapid uptake of synaptically released glutamate into astrocytes through the Na(+)-dependent glutamate transporters GLT-1 and GLAST and its subsequent conversion into glutamine by the enzyme glutamine synthetase (GS).", "To date, several factors have been identified that rapidly alter glial glutamate uptake by post-translational modification of glutamate transporters.", "The only condition known to affect the expression of glial glutamate transporters and GS is the coculturing of glia with neurons.", "We now demonstrate that neurons regulate glial glutamate turnover via pituitary adenylate cyclase-activating polypeptide (PACAP).", "In the cerebral cortex PACAP is synthesized by neurons and acts on the subpopulation of astroglia involved in glutamate turnover.", "Exposure of astroglia to PACAP increased the maximal velocity of [(3)H]glutamate uptake by promoting the expression of GLT-1, GLAST, and GS.", "Moreover, the stimulatory effects of neuron-conditioned medium on glial glutamate transporter expression were attenuated in the presence of PACAP-inactivating antibodies or the PACAP receptor antagonist PACAP 6-38.", "In contrast to PACAP, vasoactive intestinal peptide promoted glutamate transporter expression only at distinctly higher concentrations, suggesting that PACAP exerts its effects on glial glutamate turnover via PAC1 receptors.", "Although PAC1 receptor-dependent activation of protein kinase A (PKA) was sufficient to promote the expression of GLAST, the activation of both PKA and protein kinase C (PKC) was required to promote GLT-1 expression optimally.", "Given the existence of various PAC1 receptor isoforms that activate PKA and PKC to different levels, these findings point to a complex mechanism by which PACAP regulates glial glutamate transport and metabolism.", "Disturbances of these regulatory mechanisms could represent a major cause for glutamate-associated neurological and psychiatric disorders."], "structured": false}
{"doc_id": 3090454, "title": "Factors influencing B lymphopoiesis after allogeneic hematopoietic cell transplantation.", "abstract": ["In 93 allograft recipients, the numbers of marrow B-cell precursors on days 80 and 365 correlated with the counts of circulating B cells, suggesting that the posttransplantation B-cell deficiency is at least in part due to insufficient B lymphopoiesis.", "Factors that could affect B lymphopoiesis were evaluated.", "The number of marrow B-cell precursors on days 30 and 80 was at least 4-fold lower in patients with grade 2 to 4 acute graft-versus-host disease (GVHD) compared with patients with grade 0 to 1 acute GVHD.", "The number of B-cell precursors on day 365 was 18-fold lower in patients with extensive chronic GVHD compared with patients with no or limited chronic GVHD.", "The number of B-cell precursors was not related to CD34 cell dose, type of transplant (marrow versus blood stem cells), donor age, or patient age.", "It was concluded that posttransplantation B-cell deficiency results in part from inhibition of B lymphopoiesis by GVHD and/or its treatment."], "structured": false}
{"doc_id": 3093512, "title": "Genetic variants rs1994016 and rs3825807 in ADAMTS7 affect its mRNA expression in atherosclerotic occlusive peripheral arterial disease", "abstract": ["AIM Peripheral artery disease (PAD) is a vascular disease affecting peripheral circulation.", "Recently, genome-wide association studies revealed a relationship between single nucleotide polymorphisms (SNPs) in ADAMTS7 (a disintegrin and metalloprotease with thrombospondin motif 7) and atherosclerosis.", "In this study, we aimed to determine ADAMTS7 expression in peripheral blood mononuclear cells (PBMCs) and the frequency of ADAMTS7 rs1994016 and rs3825807 polymorphisms in a sample of Turkish patients with PAD, and to evaluate the association of matrix metalloproteinase (MMP) levels with PAD development.   \n", "METHODS In this case-control study, ADAMTS7mRNA and protein expression was determined using reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) and western blot, respectively, and rs1994016 and rs3825807 variants in ADAMTS7 were determined by real-time PCR in 115 PAD patients and 116 healthy controls.", "Plasma levels of nine MMPs were determined using a multiplex immunoassay system.   \n", "RESULTS ADAMTS7mRNA levels were significantly higher in PAD patients than in controls (t=-2.75, P=.007).", "There was no significant difference in the frequencies of rs1994016 and rs3825807 between PAD patients and controls (P>.05).", "In PAD patients, ADAMTS7mRNA levels were significantly increased for the CC genotype of rs1994016 (t=-2.31, P=.026) and TT genotype of rs3825807 (t=-2.23, P=.032).", "Furthermore, plasma levels of MMP-1, MMP-3, MMP-7, MMP-10, MMP-12, and MMP-13 were significantly higher in PAD patients than in controls (P<.05).   \n", "CONCLUSION This is the first report of the relationship between PAD and ADAMTS7 expression and the effects of the rs1994016 and rs3825807 variants on PAD development.", "ADAMTS7 may be associated with PAD development."], "structured": true}
{"doc_id": 3095620, "title": "Distinct Parietal and Temporal Pathways to the Homologues of Broca's Area in the Monkey", "abstract": ["The homologues of the two distinct architectonic areas 44 and 45 that constitute the anterior language zone (Broca's region) in the human ventrolateral frontal lobe were recently established in the macaque monkey.", "Although we know that the inferior parietal lobule and the lateral temporal cortical region project to the ventrolateral frontal cortex, we do not know which of the several cortical areas found in those regions project to the homologues of Broca's region in the macaque monkey and by means of which white matter pathways.", "We have used the autoradiographic method, which permits the establishment of the cortical area from which axons originate (i.e., the site of injection), the precise course of the axons in the white matter, and their termination within particular cortical areas, to examine the parietal and temporal connections to area 44 and the two subdivisions of area 45 (i.e., areas 45A and 45B).", "The results demonstrated a ventral temporo-frontal stream of fibers that originate from various auditory, multisensory, and visual association cortical areas in the intermediate superolateral temporal region.", "These axons course via the extreme capsule and target most strongly area 45 with a more modest termination in area 44.", "By contrast, a dorsal stream of axons that originate from various cortical areas in the inferior parietal lobule and the adjacent caudal superior temporal sulcus was found to target both areas 44 and 45.", "These axons course in the superior longitudinal fasciculus, with some axons originating from the ventral inferior parietal lobule and the adjacent superior temporal sulcus arching and forming a simple arcuate fasciculus.", "The cortex of the most rostral part of the inferior parietal lobule is preferentially linked with the ventral premotor cortex (ventral area 6) that controls the orofacial musculature.", "The cortex of the intermediate part of the inferior parietal lobule is linked with both areas 44 and 45.", "These findings demonstrate the posterior parietal and temporal connections of the ventrolateral frontal areas, which, in the left hemisphere of the human brain, were adapted for various aspects of language production.", "These precursor circuits that are found in the nonlinguistic, nonhuman, primate brain also exist in the human brain.", "The possible reasons why these areas were adapted for language use in the human brain are discussed.", "The results throw new light on the prelinguistic precursor circuitry of Broca's region and help understand functional interactions between Broca's ventrolateral frontal region and posterior parietal and temporal association areas."], "structured": false}
{"doc_id": 3098821, "title": "MIRA-seq for DNA methylation analysis of CpG islands", "abstract": ["AIM To develop a reliable method for whole genome analysis of DNA methylation.   ", "MATERIALS & METHODS Genome-scale analysis of DNA methylation includes affinity-based approaches such as enrichment using methyl-CpG-binding proteins.", "One of these methods, the methylated-CpG island recovery assay (MIRA), is based on the high affinity of the MBD2b-MBD3L1 complex for CpG-methylated DNA.", "Here we provide a detailed description of MIRA and combine it with next generation sequencing platforms (MIRA-seq).   \n", "RESULTS We assessed the performance of MIRA-seq and compared the data with whole genome bisulfite sequencing.   \n", "CONCLUSION MIRA-seq is a reliable, genome-scale DNA methylation analysis platform for scoring DNA methylation differences at CpG-rich genomic regions.", "The method is not limited by primer or probe design and is cost effective."], "structured": true}
{"doc_id": 3099497, "title": "How many images are in an auditory scene?", "abstract": ["If an auditory scene consists of many spatially separated sound sources, how many sound sources can be processed by the auditory system?", "Experiment I determined how many speech sources could be localized simultaneously on the azimuth plane.", "Different words were played from multiple loudspeakers, and listeners reported the total number of sound sources and their individual locations.", "In experiment II the accuracy of localizing one speech source in a mixture of multiple speech sources was determined.", "An extra sound source was added to an existing set of sound sources, and the task was to localize that extra source.", "In experiment III the setup and task were the same as in experiment I, except that the sounds were tones.", "The results showed that the maximum number of sound sources that listeners could perceive was limited to approximately four spatially separated speech signals and three for tonal signals.", "The localization errors increased along with the increase of total number of sound sources.", "When four or more speech sources already existed, the accuracy in localizing an additional source was near chance."], "structured": false}
{"doc_id": 3105781, "title": "Mobilization of intracellular copper stores by the ctr2 vacuolar copper transporter.", "abstract": ["Copper plays an essential role in processes including signaling to the transcription and protein trafficking machinery, oxidative phosphorylation, iron mobilization, neuropeptide maturation, and normal development.", "Whereas much is known about intracellular mobilization of ions such as calcium, little information is available on how eukaryotic cells mobilize intracellular copper stores.", "We describe a mechanism by which the Saccharomyces cerevisiae Ctr2 protein provides bioavailable copper via mobilization of intracellular copper stores.", "Whereas Ctr2 exhibits structural similarity to the Ctr1 plasma membrane copper importer, microscopic and biochemical fractionation studies localize Ctr2 to the vacuole membrane.", "We demonstrate that Ctr2 mobilizes vacuolar copper stores in a manner dependent on amino acid residues conserved between the Ctr1 and Ctr2 copper transport family and that ctr2 Delta mutants hyper-accumulate vacuolar copper.", "Furthermore, a Ctr2 mutant that is mislocalized to the plasma membrane stimulates extracellular copper uptake, supporting a direct role for Ctr2 in copper transport across membranes.", "These studies identify a novel mechanism for copper mobilization and suggest that organisms cope with copper deprivation via the use of intracellular vesicular stores."], "structured": false}
{"doc_id": 3107733, "title": "Peroxisomes Are Signaling Platforms for Antiviral Innate Immunity", "abstract": ["Peroxisomes have long been established to play a central role in regulating various metabolic activities in mammalian cells.", "These organelles act in concert with mitochondria to control the metabolism of lipids and reactive oxygen species.", "However, while mitochondria have emerged as an important site of antiviral signal transduction, a role for peroxisomes in immune defense is unknown.", "Here, we report that the RIG-I-like receptor (RLR) adaptor protein MAVS is located on peroxisomes and mitochondria.", "We find that peroxisomal and mitochondrial MAVS act sequentially to create an antiviral cellular state.", "Upon viral infection, peroxisomal MAVS induces the rapid interferon-independent expression of defense factors that provide short-term protection, whereas mitochondrial MAVS activates an interferon-dependent signaling pathway with delayed kinetics, which amplifies and stabilizes the antiviral response.", "The interferon regulatory factor IRF1 plays a crucial role in regulating MAVS-dependent signaling from peroxisomes.", "These results establish that peroxisomes are an important site of antiviral signal transduction."], "structured": false}
{"doc_id": 3112885, "title": "Two-sided confidence intervals for the single proportion: comparison of seven methods. Stat. Med", "abstract": ["Simple interval estimate methods for proportions exhibit poor coverage and can produce evidently inappropriate intervals.", "Criteria appropriate to the evaluation of various proposed methods include: closeness of the achieved coverage probability to its nominal value; whether intervals are located too close to or too distant from the middle of the scale; expected interval width; avoidance of aberrations such as limits outside [0,1] or zero width intervals; and ease of use, whether by tables, software or formulae.", "Seven methods for the single proportion are evaluated on 96,000 parameter space points.", "Intervals based on tail areas and the simpler score methods are recommended for use.", "In each case, methods are available that aim to align either the minimum or the mean coverage with the nominal 1 -alpha."], "structured": false}
{"doc_id": 3113630, "title": "Nuclear accumulation of HDAC4 in ATM deficiency promotes neurodegeneration in ataxia-telangiectasia", "abstract": ["Ataxia telangiectasia is a neurodegenerative disease caused by mutation of the Atm gene.", "Here we report that ataxia telangiectasia mutated (ATM) deficiency causes nuclear accumulation of histone deacetylase 4 (HDAC4) in neurons and promotes neurodegeneration.", "Nuclear HDAC4 binds to chromatin, as well as to myocyte enhancer factor 2A (MEF2A) and cAMP-responsive element binding protein (CREB), leading to histone deacetylation and altered neuronal gene expression.", "Blocking either HDAC4 activity or its nuclear accumulation blunts these neurodegenerative changes and rescues several behavioral abnormalities of ATM-deficient mice.", "Full rescue of the neurodegeneration, however, also requires the presence of HDAC4 in the cytoplasm, suggesting that the ataxia telangiectasia phenotype results both from a loss of cytoplasmic HDAC4 as well as its nuclear accumulation.", "To remain cytoplasmic, HDAC4 must be phosphorylated.", "The activity of the HDAC4 phosphatase, protein phosphatase 2A (PP2A), is downregulated by ATM-mediated phosphorylation.", "In ATM deficiency, enhanced PP2A activity leads to HDAC4 dephosphorylation and the nuclear accumulation of HDAC4.", "Our results define a crucial role of the cellular localization of HDAC4 in the events leading to ataxia telangiectasia neurodegeneration."], "structured": false}
{"doc_id": 3118719, "title": "Regulation and function of the E-cadherin/catenin complex in cells of the monocyte-macrophage lineage and DCs.", "abstract": ["E-cadherin is best characterized as adherens junction protein, which through homotypic interactions contributes to the maintenance of the epithelial barrier function.", "In epithelial cells, the cytoplasmic tail of E-cadherin forms a dynamic complex with catenins and regulates several intracellular signal transduction pathways, including Wnt/\u03b2-catenin, PI3K/Akt, Rho GTPase, and NF-\u03baB signaling.", "Recent progress uncovered a novel and critical role for this adhesion molecule in mononuclear phagocyte functions.", "E-cadherin regulates the maturation and migration of Langerhans cells, and its ligation prevents the induction of a tolerogenic state in bone marrow-derived dendritic cells (DCs).", "In this respect, the functionality of \u03b2-catenin could be instrumental in determining the balance between immunogenicity and tolerogenicity of DCs in vitro and in vivo.", "Fusion of alternatively activated macrophages and osteoclasts is also E-cadherin-dependent.", "In addition, the E-cadherin ligands CD103 and KLRG1 are expressed on DC-, T-, and NK-cell subsets and contribute to their interaction with E-cadherin-expressing DCs and macrophages.", "Here we discuss the regulation, function, and implications of E-cadherin expression in these central orchestrators of the immune system."], "structured": false}
{"doc_id": 3127341, "title": "Polymorphism and ligand dependent changes in human glucagon-like peptide-1 receptor (GLP-1R) function: allosteric rescue of loss of function mutation.", "abstract": ["The glucagon-like peptide-1 receptor (GLP-1R) is a key physiological regulator of insulin secretion and a major therapeutic target for the treatment of type II diabetes.", "However, regulation of GLP-1R function is complex with multiple endogenous peptides that interact with the receptor, including full-length (1-37) and truncated (7-37) forms of GLP-1 that can exist in an amidated form (GLP-1(1-36)NH\u2082 and GLP-1(7-36)NH\u2082) and the related peptide oxyntomodulin.", "In addition, the GLP-1R possesses exogenous agonists, including exendin-4, and the allosteric modulator, compound 2 (6,7-dichloro-2-methylsulfonyl-3-tert-butylaminoquinoxaline).", "The complexity of this ligand-receptor system is further increased by the presence of several single nucleotide polymorphisms (SNPs) that are distributed across the receptor.", "We have investigated 10 GLP-1R SNPs, which were characterized in three physiologically relevant signaling pathways (cAMP accumulation, extracellular signal-regulated kinase 1/2 phosphorylation, and intracellular Ca\u00b2\u207a mobilization); ligand binding and cell surface receptor expression were also determined.", "We demonstrate both ligand- and pathway-specific effects for multiple SNPs, with the most dramatic effect observed for the Met\u00b9\u2074\u2079 receptor variant.", "At the Met\u00b9\u2074\u2079 variant, there was selective loss of peptide-induced responses across all pathways examined, but preservation of response to the small molecule compound 2.", "In contrast, at the Cys\u00b3\u00b3\u00b3 variant, peptide responses were preserved but there was attenuated response to compound 2.", "Strikingly, the loss of peptide function at the Met\u00b9\u2074\u2079 receptor variant could be allosterically rescued by compound 2, providing proof-of-principle evidence that allosteric drugs could be used to treat patients with this loss of function variant."], "structured": false}
{"doc_id": 3140772, "title": "Neuronal circuitry mechanism regulating adult quiescent neural stem cell fate decision", "abstract": ["Adult neurogenesis arises from neural stem cells within specialized niches.", "Neuronal activity and experience, presumably acting on this local niche, regulate multiple stages of adult neurogenesis, from neural progenitor proliferation to new neuron maturation, synaptic integration and survival.", "It is unknown whether local neuronal circuitry has a direct impact on adult neural stem cells.", "Here we show that, in the adult mouse hippocampus, nestin-expressing radial glia-like quiescent neural stem cells (RGLs) respond tonically to the neurotransmitter \u03b3-aminobutyric acid (GABA) by means of \u03b32-subunit-containing GABAA receptors.", "Clonal analysis of individual RGLs revealed a rapid exit from quiescence and enhanced symmetrical self-renewal after conditional deletion of \u03b32.", "RGLs are in close proximity to terminals expressing 67-kDa glutamic acid decarboxylase (GAD67) of parvalbumin-expressing (PV+) interneurons and respond tonically to GABA released from these neurons.", "Functionally, optogenetic control of the activity of dentate PV+ interneurons, but not that of somatostatin-expressing or vasoactive intestinal polypeptide (VIP)-expressing interneurons, can dictate the RGL choice between quiescence and activation.", "Furthermore, PV+ interneuron activation restores RGL quiescence after social isolation, an experience that induces RGL activation and symmetrical division.", "Our study identifies a niche cell\u2013signal\u2013receptor trio and a local circuitry mechanism that control the activation and self-renewal mode of quiescent adult neural stem cells in response to neuronal activity and experience."], "structured": false}
{"doc_id": 3150030, "title": "Global vitamin D levels in relation to age, gender, skin pigmentation and latitude: an ecologic meta-regression analysis", "abstract": ["We performed a meta-analysis of cross-sectional studies on serum 25(OH)D status globally.", "Serum 25(OH)D levels on average were 54 nmol/l, were higher in women than men, and higher in Caucasians than in non-Caucasians.", "There was no trend in serum 25(OH)D level with latitude.", "Vitamin D deficiency was widespread.", "We studied vitamin D status (expressed as serum 25-hydroxy-vitamin D [25(OH)D]) in native subjects worldwide.", "Meta-analysis and meta-regression of studies reporting on 25(OH)D in healthy subjects retrieved from Pubmed, Embase and Web of Science using the terms \u201cserum\u201d, \u201c25-hydroxy-vitamin D\u201d, \u201ccholecalciferol\u201d, and \u201chuman\u201d.", "A total of 394 studies were included.", "The mean 25(OH)D level was 54 nmol/l (95% CI: 52\u201357 nmol/l).", "Women had borderline significantly higher 25(OH)D levels than men, and Caucasians had higher levels than non-Caucasians.", "25(OH)D levels were higher in subjects aged >15 years than in younger subjects.", "Unadjusted there was no significant decrease in 25(OH)D with latitude (slope of curve \u22120.03 \u00b1 0.12 nmol/l per degree latitude north or south of equator, p = 0.8).", "There was a significant decline with latitude for Caucasians (\u22120.69 \u00b1 0.30 nmol/l per degree, p = 0.02), but not for non-Caucasians (0.03 \u00b1 0.39 nmol/l per degree, p = 0.14).", "After adjustment for age, gender, and ethnicity, no overall correlation was present between 25(OH)D and latitude (\u22120.29 \u00b1 0.24 nmol/l per degree, p = 0.23).", "There was no overall influence of latitude on 25(OH)D. However, in separate analyses 25(OH)D decreased with latitude in Caucasians but not in non-Caucasians.", "A widespread global vitamin D insufficiency was present compared with proposed threshold levels."], "structured": false}
{"doc_id": 3152612, "title": "Identification and characterization of a novel monocyte/macrophage differentiation-dependent gene that is responsive to lipopolysaccharide, ceramide, and lysophosphatidylcholine.", "abstract": ["A novel differentiation-dependent cDNA (DIF-2) has been isolated from human mononuclear phagocytes by differential display.", "The full-length cDNA was cloned and sequenced.", "DIF-2 consists of 156 amino acids and has a predicted isoelectric point of 8.84.", "The mRNA is expressed in freshly isolated monocytes and is downregulated significantly when monocytes are subjected to differentiation.", "A similar differentiation-dependent downregulation is observed in normal hepatocytes compared to undifferentiated HepG2 cells.", "The mRNA expression in monocytes is sensitive to lipopolysaccharide and ceramide which both strongly increase DIF-2 transcription, while lysophosphatidylcholine results in a weaker upregulation of DIF-2 expression.", "A DIF-2 homologous gene has been previously isolated from mouse fibroblasts and was shown to be a serum growth factor-inducible immediate early gene.", "Our results indicate that DIF-2 represents a gene which is regulated in differentiation processes and strongly responsive to lipopolysaccharide, ceramide and lysophosphatidylcholine."], "structured": false}
{"doc_id": 3153673, "title": "A Novel 3-Hydroxysteroid Dehydrogenase That Regulates Reproductive Development and Longevity", "abstract": ["Endogenous small molecule metabolites that regulate animal longevity are emerging as a novel means to influence health and life span.", "In C. elegans, bile acid-like steroids called the dafachronic acids (DAs) regulate developmental timing and longevity through the conserved nuclear hormone receptor DAF-12, a homolog of mammalian sterol-regulated receptors LXR and FXR.", "Using metabolic genetics, mass spectrometry, and biochemical approaches, we identify new activities in DA biosynthesis and characterize an evolutionarily conserved short chain dehydrogenase, DHS-16, as a novel 3-hydroxysteroid dehydrogenase.", "Through regulation of DA production, DHS-16 controls DAF-12 activity governing longevity in response to signals from the gonad.", "Our elucidation of C. elegans bile acid biosynthetic pathways reveals the possibility of novel ligands as well as striking biochemical conservation to other animals, which could illuminate new targets for manipulating longevity in metazoans."], "structured": false}
{"doc_id": 3154880, "title": "An Argonaute transports siRNAs from the cytoplasm to the nucleus.", "abstract": ["Ribonucleoprotein complexes consisting of Argonaute-like proteins and small regulatory RNAs function in a wide range of biological processes.", "Many of these small regulatory RNAs are predicted to act, at least in part, within the nucleus.", "We conducted a genetic screen to identify factors essential for RNA interference (RNAi) in nuclei of Caenorhabditis elegans and identified the Argonaute protein NRDE-3.", "In the absence of small interfering RNAs (siRNAs), NRDE-3 resides in the cytoplasm.", "NRDE-3 binds siRNAs generated by RNA-dependent RNA polymerases acting on messenger RNA templates in the cytoplasm and redistributes to the nucleus.", "Nuclear redistribution of NRDE-3 requires a functional nuclear localization signal, is required for nuclear RNAi, and results in NRDE-3 association with nuclear-localized nascent transcripts.", "Thus, specific Argonaute proteins can transport specific classes of small regulatory RNAs to distinct cellular compartments to regulate gene expression."], "structured": false}
{"doc_id": 3155374, "title": "Phosphatidylinositol 4,5-Bisphosphate Functions as a Second Messenger that Regulates Cytoskeleton\u2013Plasma Membrane Adhesion", "abstract": ["Binding interactions between the plasma membrane and the cytoskeleton define cell functions such as cell shape, formation of cell processes, cell movement, and endocytosis.", "Here we use optical tweezers tether force measurements and show that plasma membrane phosphatidylinositol 4,5-bisphosphate (PIP2) acts as a second messenger that regulates the adhesion energy between the cytoskeleton and the plasma membrane.", "Receptor stimuli that hydrolyze PIP2 lowered adhesion energy, a process that could be mimicked by expressing PH domains that sequester PIP2 or by targeting a 5'-PIP2-phosphatase to the plasma membrane to selectively lower plasma membrane PIP2 concentration.", "Our study suggests that plasma membrane PIP2 controls dynamic membrane functions and cell shape by locally increasing and decreasing the adhesion between the actin-based cortical cytoskeleton and the plasma membrane."], "structured": false}
{"doc_id": 3155731, "title": "Tissue-resident memory T cells: local specialists in immune defence", "abstract": ["T cells have crucial roles in protection against infection and cancer.", "Although the trafficking of memory T cells around the body is integral to their capacity to provide immune protection, studies have shown that specialization of some memory T cells into unique tissue-resident subsets gives the host enhanced regional immunity.", "In recent years, there has been considerable progress in our understanding of tissue-resident T cell development and function, revealing mechanisms for enhanced protective immunity that have the potential to influence rational vaccine design.", "This Review discusses the major advances and the emerging concepts in this field, summarizes what is known about the differentiation and the protective functions of tissue-resident memory T cells in different tissues in the body and highlights key unanswered questions."], "structured": false}
{"doc_id": 3173489, "title": "Defective replication stress response inhibits lymphomagenesis and impairs lymphocyte reconstitution", "abstract": ["DNA replication stress promotes genome instability in cancer.", "However, the contribution of the replication stress response to the development of malignancies remains unresolved.", "The DNA replication stress response protein SMARCAL1 stabilizes DNA replication forks and prevents replication fork collapse, a cause of DNA breaks and apoptosis.", "While the fork regression/remodeling functions of SMARCAL1 have been investigated, its in vivo functions in replication stress and cancer are unclear.", "Using a gamma radiation (IR)-induced replication stress T-cell lymphoma mouse model, we observed a significant inhibition of lymphomagenesis in mice lacking one or both alleles of Smarcal1.", "Notably, a quarter of the Smarcal1-deficient mice did not develop tumors.", "Moreover, hematopoietic stem/progenitor cells (HSPCs) and developing thymocytes in Smarcal1-deficient mice showed increased DNA damage and apoptosis during the proliferation burst following IR and an impaired ability to repopulate the thymus after IR.", "Additionally, mice lacking Smarcal1 showed significant HSPC defects when challenged to respond to other replication stress stimuli.", "Thus, our data reveal the critical function of the DNA replication stress response and, specifically, Smarcal1 in hematopoietic cell survival and tumor development.", "Our results also provide important insight into the immunodeficiency observed in individuals with mutations in SMARCAL1 by suggesting that it is an HSPC defect."], "structured": false}
{"doc_id": 3174305, "title": "Human DNA methylomes at base resolution show widespread epigenomic differences", "abstract": ["DNA cytosine methylation is a central epigenetic modification that has essential roles in cellular processes including genome regulation, development and disease.", "Here we present the first genome-wide, single-base-resolution maps of methylated cytosines in a mammalian genome, from both human embryonic stem cells and fetal fibroblasts, along with comparative analysis of messenger RNA and small RNA components of the transcriptome, several histone modifications, and sites of DNA\u2013protein interaction for several key regulatory factors.", "Widespread differences were identified in the composition and patterning of cytosine methylation between the two genomes.", "Nearly one-quarter of all methylation identified in embryonic stem cells was in a non-CG context, suggesting that embryonic stem cells may use different methylation mechanisms to affect gene regulation.", "Methylation in non-CG contexts showed enrichment in gene bodies and depletion in protein binding sites and enhancers.", "Non-CG methylation disappeared upon induced differentiation of the embryonic stem cells, and was restored in induced pluripotent stem cells.", "We identified hundreds of differentially methylated regions proximal to genes involved in pluripotency and differentiation, and widespread reduced methylation levels in fibroblasts associated with lower transcriptional activity.", "These reference epigenomes provide a foundation for future studies exploring this key epigenetic modification in human disease and development."], "structured": false}
{"doc_id": 3190689, "title": "Laparoscopic adhesiolysis in patients with chronic abdominal pain: a blinded randomised controlled multi-centre trial.", "abstract": ["BACKGROUND Laparoscopic adhesiolysis for chronic abdominal pain is controversial and is not evidence based.", "We aimed to test our hypothesis that laparoscopic adhesiolysis leads to substantial pain relief and improvement in quality of life in patients with adhesions and chronic abdominal pain.   \n", "METHODS Patients had diagnostic laparoscopy for chronic abdominal pain attributed to adhesions; other causes for their pain had been excluded.", "If adhesions were confirmed during diagnostic laparoscopy, patients were randomly assigned either to laparoscopic adhesiolysis or no treatment.", "Treatment allocation was concealed from patients, and assessors were unaware of patients' treatment and outcome.", "Pain was assessed for 1 year by visual analogue score (VAS) score (scale 0-100), pain change score, use of analgesics, and quality of life score.", "Analysis was by intention to treat.   \n", "FINDINGS Of 116 patients enrolled for diagnostic laparoscopy, 100 were randomly allocated either laparoscopic adhesiolysis (52) or no treatment (48).", "Both groups reported substantial pain relief and a significantly improved quality of life, but there was no difference between the groups (mean change from baseline of VAS score at 12 months: difference 3 points, p=0.53; 95% CI -7 to 13).   \n", "INTERPRETATION Although laparoscopic adhesiolysis relieves chronic abdominal pain, it is not more beneficial than diagnostic laparoscopy alone.", "Therefore, laparoscopic adhesiolysis cannot be recommended as a treatment for adhesions in patients with chronic abdominal pain."], "structured": true}
{"doc_id": 3202143, "title": "Insulin Signaling and Dietary Restriction Differentially Influence the Decline of Learning and Memory with Age", "abstract": ["Of all the age-related declines, memory loss is one of the most devastating.", "While conditions that increase longevity have been identified, the effects of these longevity-promoting factors on learning and memory are unknown.", "Here we show that the C. elegans Insulin/IGF-1 receptor mutant daf-2 improves memory performance early in adulthood and maintains learning ability better with age but, surprisingly, demonstrates no extension in long-term memory with age.", "By contrast, eat-2 mutants, a model of Dietary Restriction (DR), exhibit impaired long-term memory in young adulthood but maintain this level of memory longer with age.", "We find that crh-1, the C. elegans homolog of the CREB transcription factor, is required for long-term associative memory, but not for learning or short-term memory.", "The expression of crh-1 declines with age and differs in the longevity mutants, and CREB expression and activity correlate with memory performance.", "Our results suggest that specific longevity treatments have acute and long-term effects on cognitive functions that decline with age through their regulation of rate-limiting genes required for learning and memory."], "structured": false}
{"doc_id": 3203590, "title": "Unique response pathways are established by allosteric interactions among nuclear hormone receptors", "abstract": ["Heterodimerization is a common paradigm among eukaryotic transcription factors.", "The 9-cis retinoic acid receptor (RXR) serves as a common heterodimerization partner for several nuclear receptors, including the thyroid hormone receptor (T3R) and retinoic acid receptor (RAR).", "This raises the question as to whether these complexes possess dual hormonal responsiveness.", "We devised a strategy to examine the transcriptional properties of each receptor individually or when tethered to a heterodimeric partner.", "We find that the intrinsic binding properties of RXR are masked in T3R-RXR and RAR-RXR heterodimers.", "In contrast, RXR is active as a non-DNA-binding cofactor with the NGFI-B/Nurr1 orphan receptors.", "Heterodimerization of RXR with constitutively active NGFI-B/Nurr1 creates a novel hormone-dependent complex.", "These findings suggest that allosteric interactions among heterodimers create complexes with unique properties.", "We suggest that allostery is a critical feature underlying the generation of diversity in hormone response networks."], "structured": false}
{"doc_id": 3205945, "title": "Midlife and Late\u2010Life Vascular Risk Factors and White Matter Microstructural Integrity: The Atherosclerosis Risk in Communities Neurocognitive Study", "abstract": ["BACKGROUND Diffusion tensor imaging measures of white matter (WM) microstructural integrity appear to provide earlier indication of WM injury than WM hyperintensities; however, risk factors for poor WM microstructural integrity have not been established.", "Our study quantifies the association between vascular risk factors in midlife and late life with measures of late-life WM microstructural integrity.   \n", "METHODS AND RESULTS We used data from 1851 participants in ARIC (Atherosclerosis Risk in Communities Study) who completed 3-T magnetic resonance imaging, including diffusion tensor imaging, as part of the ARIC Neurocognitive Study (ARIC-NCS).", "We quantified the association among lipids, glucose, and blood pressure from the baseline ARIC visit (1987-1989, ages 44-65, midlife) and visit 5 of ARIC (2011-2013, ages 67-90, late life, concurrent with ARIC-NCS) with regional and overall WM mean diffusivity and fractional anisotropy obtained at ARIC visit 5 for ARIC participants.", "We also considered whether these associations were independent of or modified by WM hyperintensity volumes.", "We found that elevated blood pressure in midlife and late life and elevated glucose in midlife, but not late life, were associated with worse late-life WM microstructural integrity.", "These associations were independent of the degree of WM hyperintensity, and the association between glucose and WM microstructural integrity appeared stronger for those with the least WM hyperintensity.", "There was little support for an adverse association between lipids and WM microstructural integrity.   \n", "CONCLUSIONS Hypertension in both midlife and late life and elevated glucose in midlife are related to worse WM microstructural integrity in late life."], "structured": true}
{"doc_id": 3210545, "title": "KRAS gene amplification and overexpression but not mutation associates with aggressive and metastatic endometrial cancer", "abstract": ["BACKGROUND Three quarter of endometrial carcinomas are treated at early stage.", "Still, 15 to 20% of these patients experience recurrence, with little effect from systemic therapies.", "Homo sapiens v-Ki-ras2 Kirsten rat sarcoma viral oncogenes homologue (KRAS) mutations have been reported to have an important role in tumorigenesis for human cancers, but there is limited knowledge regarding clinical relevance of KRAS status in endometrial carcinomas.   \n", "METHODS We have performed a comprehensive and integrated characterisation of genome-wide expression related to KRAS mutations and copy-number alterations in primary- and metastatic endometrial carcinoma lesions in relation to clinical and histopathological data.", "A primary investigation set and clinical validation set was applied, consisting of 414 primary tumours and 61 metastatic lesions totally.   \n", "RESULTS Amplification and gain of KRAS present in 3% of the primary lesions and 18% of metastatic lesions correlated significantly with poor outcome, high International Federation of Gynaecology and Obstetrics stage, non-endometrioid subtype, high grade, aneuploidy, receptor loss and high KRAS mRNA levels, also found to be associated with aggressive phenotype.", "In contrast, KRAS mutations were present in 14.7% of primary lesions with no increase in metastatic lesions, and did not influence outcome, but was significantly associated with endometrioid subtype, low grade and obesity.   \n", "CONCLUSION These results support that KRAS amplification and KRAS mRNA expression, both increasing from primary to metastatic lesions, are relevant for endometrial carcinoma disease progression."], "structured": true}
{"doc_id": 3215494, "title": "Hyperhomocysteinemia and atherosclerotic vascular disease: pathophysiology, screening, and treatment. off.", "abstract": ["Hyperhomocysteinemia has recently been identified as an important risk factor for atherosclerotic vascular disease.", "This article reviews homocysteine metabolism, causes of hyperhomocysteinemia, the pathophysiological findings of this disorder, and epidemiological studies of homocysteine and vascular disease.", "Screening for hyperhomocysteinemia should be considered for patients at high risk for vascular disease or abnormalities of homocysteine metabolism.", "For primary prevention of vascular disease, treatment of patients with homocysteine levels of 14 micromol/L or higher should be considered.", "For secondary prevention, treatment of patients with homocysteine levels of 11 micromol/L or higher should be considered.", "Treatment is most conveniently administered as a folic acid supplement (400-1000 microg) and a high-potency multivitamin that contains at least 400 microg of folate.", "Higher doses of folic acid and cyanocobalamin supplements may be required in some patients.", "Until prospective clinical trial data become available, these conservative recommendations provide a safe, effective, and evidence-based approach to the diagnosis, evaluation, and management of patients with hyperhomocysteinemia."], "structured": false}
{"doc_id": 3222122, "title": "Best--worst scaling: What it can do for health care research and how to do it.", "abstract": ["Statements like \"quality of care is more highly valued than waiting time\" can neither be supported nor refuted by comparisons of utility parameters from a traditional discrete choice experiment (DCE).", "Best--worst scaling can overcome this problem because it asks respondents to perform a different choice task.", "However, whilst the nature of the best--worst task is generally understood, there are a number of issues relating to the design and analysis of a best--worst choice experiment that require further exposition.", "This paper illustrates how to aggregate and analyse such data and using a quality of life pilot study demonstrates how richer insights can be drawn by the use of best--worst tasks."], "structured": false}
{"doc_id": 3222187, "title": "Genetic variants and non-genetic factors predict circulating vitamin D levels in Hispanic and non-Hispanic White women: the Breast Cancer Health Disparities Study.", "abstract": ["Genome-wide association studies (GWAS) have identified common polymorphisms in or near GC, CYP2R1, CYP24A1, and NADSYN1/DHCR7 genes to be associated with circulating levels of 25-hydroxyvitamin D [25(OH)D] in European populations.", "To replicate these GWAS findings, we examined six selected polymorphisms from these regions and their relation with circulating 25(OH)D levels in 1,605 Hispanic women (629 U.S. Hispanics and 976 Mexicans) and 354 non-Hispanic White (NHW) women.", "We also assessed the potential interactions between these variants and known non-genetic predictors of 25(OH)D levels, including body mass index (BMI), sunlight exposure and vitamin D intake from diet and supplements.", "The minor alleles of the two GC polymorphisms (rs7041 and rs2282679) were significantly associated with lower 25(OH)D levels in both Hispanic and NHW women.", "The CYP2R1 polymorphism, rs2060793, also was significantly associated with 25(OH)D levels in both groups.", "We found no significant associations for the polymorphisms in the CYP24A1.", "In Hispanic controls, 25(OH)D levels were significantly associated with the rs12785878T and rs1790349G haplotype in the NADSYN1/DHCR7 region.", "Significant interactions between GC rs2282679 and BMI and between rs12785878 and time spent in outdoor activities were observed.", "These results provide further support for the contribution of common genetic variants to individual variability in circulating 25(OH)D levels.", "The observed interactions between SNPs and non-genetic factors warrant confirmation."], "structured": false}
{"doc_id": 3230361, "title": "Generation and characterization of methyl-lysine histone antibodies.", "abstract": ["Publisher Summary This chapter summarizes the development and characterization of rabbit polyclonal antibodies named histone that are directed against the methylated H3-K9 position.", "It provides protocols for peptide design, rabbit immunizations, and quality controls of methyl-lysine histone antibodies, followed by their in vivo characterization using indirect IF of inter-and metaphase chromatin in wild-type (wt) and mutant mouse cells that are deficient for the Suv39h histone methyltransferases (HMTases).", "Histone amino-termini (tails) protrude from the nucleosome core and are subject to a variety of post-translational modifications, including acetylation (on lysine residues), phosphorylation (on serine and threonine residues), methylation (on lysine and arginine residues), ubiquitination (on lysine residues), and ADP-ribosylation (on glutamic acid residues).", "In addition to their structural roles, histones play important functions in the control of gene expression by regulating access to the underlying nucleosomal template.", "It is without doubt that the development of high-quality, position-specific methyl-lysine histone antibodies can provide important tools for the further decoding of the epigenetic information, which is in part, indexed by distinct methylation states of selective lysine residues in the histone amino-termini.", "A comparative analysis indicates significant discrepancies in the specificity and avidity of the available methyl-lysine histone antibodies and highlights the need for extensive quality controls, such that experimental data can be correctly interpreted despite the exquisite complexity of histone lysine methylation."], "structured": false}
{"doc_id": 3230557, "title": "The Hallmarks of Aging", "abstract": ["Aging is characterized by a progressive loss of physiological integrity, leading to impaired function and increased vulnerability to death.", "This deterioration is the primary risk factor for major human pathologies, including cancer, diabetes, cardiovascular disorders, and neurodegenerative diseases.", "Aging research has experienced an unprecedented advance over recent years, particularly with the discovery that the rate of aging is controlled, at least to some extent, by genetic pathways and biochemical processes conserved in evolution.", "This Review enumerates nine tentative hallmarks that represent common denominators of aging in different organisms, with special emphasis on mammalian aging.", "These hallmarks are: genomic instability, telomere attrition, epigenetic alterations, loss of proteostasis, deregulated nutrient sensing, mitochondrial dysfunction, cellular senescence, stem cell exhaustion, and altered intercellular communication.", "A major challenge is to dissect the interconnectedness between the candidate hallmarks and their relative contributions to aging, with the final goal of identifying pharmaceutical targets to improve human health during aging, with minimal side effects."], "structured": false}
{"doc_id": 3270834, "title": "A sensitive mass spectrometry platform identifies metabolic changes of life history traits in C. elegans", "abstract": ["Abnormal nutrient metabolism is a hallmark of aging, and the underlying genetic and nutritional framework is rapidly being uncovered, particularly using C. elegans as a model.", "However, the direct metabolic consequences of perturbations in life history of C. elegans remain to be clarified.", "Based on recent advances in the metabolomics field, we optimized and validated a sensitive mass spectrometry (MS) platform for identification of major metabolite classes in worms and applied it to study age and diet related changes.", "Using this platform that allowed detection of over 600 metabolites in a sample of 2500 worms, we observed marked changes in fatty acids, amino acids and phospholipids during worm life history, which were independent from the germ-line.", "Worms underwent a striking shift in lipid metabolism after early adulthood that was at least partly controlled by the metabolic regulator AAK-2/AMPK.", "Most amino acids peaked during development, except aspartic acid and glycine, which accumulated in aged worms.", "Dietary intervention also influenced worm metabolite profiles and the regulation was highly specific depending on the metabolite class.", "Altogether, these MS-based methods are powerful tools to perform worm metabolomics for aging and metabolism-oriented studies."], "structured": false}
{"doc_id": 3272084, "title": "Characterisation of antibiotic prescriptions for acute respiratory tract infections in Danish general practice: a retrospective registry based cohort study", "abstract": ["Inappropriate use of antibiotics is contributing to the increasing rates of antimicrobial resistance.", "Several Danish guidelines on antibiotic prescribing for acute respiratory tract infections in general practice have been issued to promote rational prescribing of antibiotics, however it is unclear if these recommendations are followed.", "We aimed to characterise the pattern of antibiotic prescriptions for patients diagnosed with acute respiratory tract infections, by means of electronic prescriptions, labeled with clinical indications, from Danish general practice.", "Acute respiratory tract infections accounted for 456,532 antibiotic prescriptions issued between July 2012 and June 2013.", "Pneumonia was the most common indication with 178,354 prescriptions (39%), followed by acute tonsillitis (21%) and acute otitis media (19%).", "In total, penicillin V accounted for 58% of all prescriptions, followed by macrolides (18%) and amoxicillin (15%).", "The use of second-line agents increased with age for all indications, and comprised more than 40% of the prescriptions in patients aged >75 years.", "Women were more often prescribed antibiotics regardless of clinical indication.", "This is the first Danish study to characterise antibiotic prescription patterns for acute respiratory tract infections by data linkage of clinical indications.", "The findings confirm that penicillin V is the most commonly prescribed antibiotic agent for treatment of patients with an acute respiratory tract infection in Danish general practice.", "However, second-line agents like macrolides and amoxicillin with or without clavulanic acid are overused.", "Strategies to improve the quality of antibiotic prescribing especially for pneumonia, acute otitis media and acute rhinosinusitis are warranted.   ", "RESPIRATORY TRACT INFECTIONS TRACKING THE OVERUSE OF ANTIBIOTICS: Better adherence to guidelines for prescribing antibiotics for different respiratory tract infections are warranted in Danish general practice.", "The over-use of antibiotics, particularly so-called 'second-line' agents such as amoxicillin, increases resistance and may lead to a potentially catastrophic scenario where antibiotics are no longer effective.", "Exactly how widespread the over-use of antibiotics is for different infections, however, is not clear.", "Rune Aabenhus at the University of Copenhagen and co-workers analyzed primary care data regarding antibiotic prescriptions for acute respiratory tract infections including pneumonia and ear infections in Denmark.", "They found that penicillin V-the current recommended first-line drug in Scandinavian countries-accounted for 58 per cent of prescriptions, a figure which should be improved.", "Amoxicillin and macrolides were over-prescribed, particularly in elderly patients.", "The team also call for further analysis of prescriptions given by out-of-hours clinics."], "structured": false}
{"doc_id": 3285059, "title": "Lack of Skeletal Muscle IL-6 Affects Pyruvate Dehydrogenase Activity at Rest and during Prolonged Exercise", "abstract": ["Pyruvate dehydrogenase (PDH) plays a key role in the regulation of skeletal muscle substrate utilization.", "IL-6 is produced in skeletal muscle during exercise in a duration dependent manner and has been reported to increase whole body fatty acid oxidation, muscle glucose uptake and decrease PDHa activity in skeletal muscle of fed mice.", "The aim of the present study was to examine whether muscle IL-6 contributes to exercise-induced PDH regulation in skeletal muscle.", "Skeletal muscle-specific IL-6 knockout (IL-6 MKO) mice and floxed littermate controls (control) completed a single bout of treadmill exercise for 10, 60 or 120 min, with rested mice of each genotype serving as basal controls.", "The respiratory exchange ratio (RER) was overall higher (P<0.05) in IL-6 MKO than control mice during the 120 min of treadmill exercise, while RER decreased during exercise independent of genotype.", "AMPK and ACC phosphorylation also increased with exercise independent of genotype.", "PDHa activity was in control mice higher (P<0.05) at 10 and 60 min of exercise than at rest but remained unchanged in IL-6 MKO mice.", "In addition, PDHa activity was higher (P<0.05) in IL-6 MKO than control mice at rest and 60 min of exercise.", "Neither PDH phosphorylation nor acetylation could explain the genotype differences in PDHa activity.", "Together, this provides evidence that skeletal muscle IL-6 contributes to the regulation of PDH at rest and during prolonged exercise and suggests that muscle IL-6 normally dampens carbohydrate utilization during prolonged exercise via effects on PDH."], "structured": false}
{"doc_id": 3285322, "title": "Clinical and pathologic characteristics of patients with BRCA-positive and BRCA-negative breast cancer.", "abstract": ["PURPOSE Mutations in the BRCA1 and BRCA2 genes confer greater risk of developing breast cancer.", "We determined whether tumor pathologic features and clinical features differ in patients with and without BRCA mutations.   \n", "PATIENTS AND METHODS Tumor pathologic features and clinical characteristics were examined in 491 women with breast cancer who underwent genetic testing for BRCA mutations between 1997 and 2006.", "A retrospective review of medical records was conducted to determine clinical characteristics including ethnicity, age and clinical stage at diagnosis, age at parity, number of full-term pregnancies, use of oral contraceptives and hormone replacement therapy, and BRCA mutation status.", "Tumor pathology was reviewed to determine histologic type, tumor grade, and estrogen receptor, progesterone receptor, and HER-2/neu status.   \n", "RESULTS Of the 491 patients with identified breast cancers, 391 patients were BRCA negative, and 86 patients were BRCA positive.", "Triple-negative breast cancer (ie, those with negative estrogen receptor, progesterone receptor, and HER-2/neu status) was diagnosed in 57.1% of the BRCA1-positive patients, 23.3% of the BRCA2-positive patients, and 13.8% of the BRCA-negative patients.", "BRCA1 mutation carriers had higher nuclear grade tumors than the other two groups (P < .001).", "Of the triple-negative cancer patients, BRCA2 mutation carriers were older when diagnosed than BRCA1 mutation carriers and noncarriers (P < .01).   \n", "CONCLUSION These results suggest that tumors associated with BRCA1 mutations may be divided into two distinct groups, triple-negative and non-triple-negative groups.", "Future studies should seek to determine whether patients with BRCA1 mutations and triple-negative breast cancer respond to treatment better than BRCA-negative patients with similar tumor pathology."], "structured": true}
{"doc_id": 3308636, "title": "Interferons: Success in anti-viral immunotherapy.", "abstract": ["The interferons (IFNs) are glycoproteins with strong antiviral activities that represent one of the first lines of host defense against invading pathogens.", "These proteins are classified into three groups, Type I, II and III IFNs, based on the structure of their receptors on the cell surface.", "Due to their ability to modulate immune responses, they have become attractive therapeutic options to control chronic virus infections.", "In combination with other drugs, Type I IFNs are considered as \"standard of care\" in suppressing Hepatitis C (HCV) and Hepatitis B (HBV) infections, while Type III IFN has generated encouraging results as a treatment for HCV infection in phase III clinical trials.", "However, though effective, using IFNs as a treatment is not without the need for caution.", "IFNs are such powerful cytokines that affect a wide array of cell types; as a result, patients usually experience unpleasant symptoms, with a percentage of patients suffering system wide effects.", "Thus, constant monitoring is required for patients treated with IFN in order to reach the treatment goals of suppressing virus infection and maintaining quality of life."], "structured": false}
{"doc_id": 3315558, "title": "Genetic analysis of human obesity in an Italian sample.", "abstract": ["An analysis of the genetic factors in obesity has been carried out on a sample of nuclear families from Aosta (N. Italy).", "The families consisted of the parents and sibs of all elementary school children considered to be obese during a preliminary screening and a similar sample of non-obese children and their nuclear families.", "The numbers of such families were 67 and 112, respectively.", "Several tests were applied in order to examine the genetic contribution to obesity, and in particular to investigate the presence of a dominant major gene.", "Our conclusions are that genetic factors are certainly present.", "Several analyses suggest the presence of a dominant major gene with weak effect."], "structured": false}
{"doc_id": 3321943, "title": "The non-coding RNA landscape of human hematopoiesis and leukemia", "abstract": ["Non-coding RNAs have emerged as crucial regulators of gene expression and cell fate decisions.", "However, their expression patterns and regulatory functions during normal and malignant human hematopoiesis are incompletely understood.", "Here we present a comprehensive resource defining the non-coding RNA landscape of the human hematopoietic system.", "Based on highly specific non-coding RNA expression portraits per blood cell population, we identify unique fingerprint non-coding RNAs-such as LINC00173 in granulocytes-and assign these to critical regulatory circuits involved in blood homeostasis.", "Following the incorporation of acute myeloid leukemia samples into the landscape, we further uncover prognostically relevant non-coding RNA stem cell signatures shared between acute myeloid leukemia blasts and healthy hematopoietic stem cells.", "Our findings highlight the importance of the non-coding transcriptome in the formation and maintenance of the human blood hierarchy.", "While micro-RNAs are known regulators of haematopoiesis and leukemogenesis, the role of long non-coding RNAs is less clear.", "Here the authors provide a non-coding RNA expression landscape of the human hematopoietic system, highlighting their role in the formation and maintenance of the human blood hierarchy."], "structured": false}
{"doc_id": 3329824, "title": "Incidence and risk of central nervous system metastases as site of first recurrence in patients with HER2-positive breast cancer treated with adjuvant trastuzumab.", "abstract": ["BACKGROUND Central nervous system (CNS) disease as the site of first relapse after exposure to adjuvant trastuzumab has been reported.", "We carried out comprehensive meta-analysis to determine the risk of CNS metastases as the first site of recurrence in patients with HER2-positive breast cancer who received adjuvant trastuzumab.   \n", "METHODS Eligible studies include randomized trials of adjuvant trastuzumab administered for 1 year to patients with HER2-positive breast cancer who reported CNS metastases as first site of disease recurrence.", "Statistical analyses were conducted to calculate the incidence, relative risk (RR), and 95% confidence intervals (CIs) using fixed-effects inverse variance and random-effects models.   \n", "RESULTS A total of 9020 patients were included.", "The incidence of CNS metastases as first site of disease recurrence in HER2-positive patients receiving adjuvant trastuzumab was 2.56% (95% CI 2.07% to 3.01%) compared with 1.94% (95% CI 1.54% to 2.38%) in HER2-positive patients who did not receive adjuvant trastuzumab.", "The RR of the CNS as first site of relapse in trastuzumab-treated patients was 1.35 (95% CI 1.02-1.78, P = 0.038) compared with control arms without trastuzumab therapy.", "The ratio of CNS metastases to total number of recurrence events was 16.94% (95% CI 10.85% to 24.07%) and 8.33% (95% CI 6.49% to 10.86%) for the trastuzumab-treated and control groups, respectively.", "No statistically significant differences were found based on trastuzumab schedule or median follow-up time.", "No evidence of publication bias was observed.   \n", "CONCLUSIONS Adjuvant trastuzumab is associated with a significant increased risk of CNS metastases as the site of first recurrence in HER2-positive breast cancer patients."], "structured": true}
{"doc_id": 3330111, "title": "Neutrophils in the activation and regulation of innate and adaptive immunity", "abstract": ["Neutrophils have long been viewed as the final effector cells of an acute inflammatory response, with a primary role in the clearance of extracellular pathogens.", "However, more recent evidence has extended the functions of these cells.", "The newly discovered repertoire of effector molecules in the neutrophil armamentarium includes a broad array of cytokines, extracellular traps and effector molecules of the humoral arm of the innate immune system.", "In addition, neutrophils are involved in the activation, regulation and effector functions of innate and adaptive immune cells.", "Accordingly, neutrophils have a crucial role in the pathogenesis of a broad range of diseases, including infections caused by intracellular pathogens, autoimmunity, chronic inflammation and cancer."], "structured": false}
{"doc_id": 3346812, "title": "Functions of DNA methylation: islands, start sites, gene bodies and beyond", "abstract": ["DNA methylation is frequently described as a 'silencing' epigenetic mark, and indeed this function of 5-methylcytosine was originally proposed in the 1970s.", "Now, thanks to improved genome-scale mapping of methylation, we can evaluate DNA methylation in different genomic contexts: transcriptional start sites with or without CpG islands, in gene bodies, at regulatory elements and at repeat sequences.", "The emerging picture is that the function of DNA methylation seems to vary with context, and the relationship between DNA methylation and transcription is more nuanced than we realized at first.", "Improving our understanding of the functions of DNA methylation is necessary for interpreting changes in this mark that are observed in diseases such as cancer."], "structured": false}
{"doc_id": 3353748, "title": "Metaplasia and transdifferentiation: from pure biology to the clinic", "abstract": ["Transformations from one tissue type to another make up a well established set of phenomena that can be explained by the principles of developmental biology.", "Although these phenomena might be rare in nature, we can now imagine the possibility of deliberately reprogramming cells from one tissue type to another by manipulating the expression of transcription factors.", "This approach could generate new therapies for many human diseases."], "structured": false}
{"doc_id": 3355397, "title": "Pioglitazone Use and Risk of Bladder Cancer and Other Common Cancers in Persons With Diabetes.", "abstract": ["IMPORTANCE Studies suggest pioglitazone use may increase risk of cancers.   \n", "OBJECTIVE To examine whether pioglitazone use for diabetes is associated with risk of bladder and 10 additional cancers.   \n", "DESIGN, SETTING, AND PARTICIPANTS Cohort and nested case-control analyses among persons with diabetes.", "A bladder cancer cohort followed 193,099 persons aged 40 years or older in 1997-2002 until December 2012; 464 case patients and 464 matched controls were surveyed about additional confounders.", "A cohort analysis of 10 additional cancers included 236,507 persons aged 40 years or older in 1997-2005 and followed until June 2012.", "Cohorts were from Kaiser Permanente Northern California.   ", "EXPOSURES Ever use, duration, cumulative dose, and time since initiation of pioglitazone as time dependent.   \n", "MAIN OUTCOMES AND MEASURES Incident cancer, including bladder, prostate, female breast, lung/bronchus, endometrial, colon, non-Hodgkin lymphoma, pancreas, kidney/renal pelvis, rectum, and melanoma.   \n", "RESULTS Among 193,099 persons in the bladder cancer cohort, 34,181 (18%) received pioglitazone (median duration, 2.8 years; range, 0.2-13.2 years) and 1261 had incident bladder cancer.", "Crude incidences of bladder cancer in pioglitazone users and nonusers were 89.8 and 75.9 per 100,000 person-years, respectively.", "Ever use of pioglitazone was not associated with bladder cancer risk (adjusted hazard ratio [HR], 1.06; 95% CI, 0.89-1.26).", "Results were similar in case-control analyses (pioglitazone use: 19.6% among case patients and 17.5% among controls; adjusted odds ratio, 1.18; 95% CI, 0.78-1.80).", "In adjusted analyses, there was no association with 8 of the 10 additional cancers; ever use of pioglitazone was associated with increased risk of prostate cancer (HR, 1.13; 95% CI, 1.02-1.26) and pancreatic cancer (HR, 1.41; 95% CI, 1.16-1.71).", "Crude incidences of prostate and pancreatic cancer in pioglitazone users vs nonusers were 453.3 vs 449.3 and 81.1 vs 48.4 per 100,000 person-years, respectively.", "No clear patterns of risk for any cancer were observed for time since initiation, duration, or dose.   \n", "CONCLUSIONS AND RELEVANCE Pioglitazone use was not associated with a statistically significant increased risk of bladder cancer, although an increased risk, as previously observed, could not be excluded.", "The increased prostate and pancreatic cancer risks associated with ever use of pioglitazone merit further investigation to assess whether they are causal or are due to chance, residual confounding, or reverse causality."], "structured": true}
{"doc_id": 3360421, "title": "Embryonic stem cell lines from human blastocysts: somatic differentiation in vitro", "abstract": ["We describe the derivation of pluripotent embryonic stem (ES) cells from human blastocysts.", "Two diploid ES cell lines have been cultivated in vitro for extended periods while maintaining expression of markers characteristic of pluripotent primate cells.", "Human ES cells express the transcription factor Oct-4, essential for development of pluripotential cells in the mouse.", "When grafted into SCID mice, both lines give rise to teratomas containing derivatives of all three embryonic germ layers.", "Both cell lines differentiate in vitro into extraembryonic and somatic cell lineages.", "Neural progenitor cells may be isolated from differentiating ES cell cultures and induced to form mature neurons.", "Embryonic stem cells provide a model to study early human embryology, an investigational tool for discovery of novel growth factors and medicines, and a potential source of cells for use in transplantation therapy."], "structured": false}
{"doc_id": 3360428, "title": "Multipoint Kras oncogene mutations potentially indicate mucinous carcinoma on the entire spectrum of mucinous ovarian neoplasms", "abstract": ["Kras mutation is a common phenomenon in many human neoplasms.", "We aimed to assess the Kras mutational status along the histological continuum from normal ovaries to the development of benign, borderline and malignant ovarian mucinous neoplasms.", "We analyzed 41 cases of malignant, 10 cases of borderline, 7 cases of benign mucinous ovarian tumors and 7 cases of normal ovarian tissue.", "The prevalence of Kras mutations in the normal ovary was 0.00% (n=0/7), while the prevalence in benign, borderline and malignant mucinous neoplasms was 57.14% (n=4/7), 90.00% (n=9/10) and 75.61% (n=31/41), respectively.", "Multiple Kras mutations were detected in 6 cases of mucinous carcinoma, including 5 double mutations with G13D/V14I (n=1), G12V/G13S (n=1), G12D/G13S (n=3) and one triple mutation with A11V/G13N/V14I (n=1).", "We identified six cases with 3 novel Kras mutations not previously described in the COSMIC database, which included A11V (n=3) and V14I (n=2) in mucinous carcinomas, and A11T (n=1) in a mucinous borderline tumor.", "In conclusion, Kras mutation appears to be one of the imperative events in the ovarian mucinous adenoma-borderline tumor-carcinoma sequence, as increased numbers of Kras mutations have been shown to be the strongest predictor of unequivocal malignancy in ovarian mucinous neoplasms."], "structured": false}
{"doc_id": 3367829, "title": "Identification and distinct regulation of yeast TATA box-containing genes.", "abstract": ["Despite being one of the first eukaryotic transcriptional regulatory elements identified, the sequence of a native TATA box and its significance remain elusive.", "Applying criteria associated with TATA boxes we queried several Saccharomyces genomes and arrived at the consensus TATA(A/T)A(A/T)(A/G).", "Approximately 20% of yeast genes contain a TATA box.", "Strikingly, TATA box-containing genes are associated with responses to stress, are highly regulated, and preferentially utilize SAGA rather than TFIID when compared to TATA-less promoters.", "Transcriptional regulation in yeast appears to be mechanistically bipolar, possibly reflecting a need to balance inducible stress-related responses with constitutive housekeeping functions."], "structured": false}
{"doc_id": 3376731, "title": "IL6 derived from cancer-associated fibroblasts promotes chemoresistance via CXCR7 in esophageal squamous cell carcinoma", "abstract": ["Various factors and cellular components in the tumor microenvironment are key drivers associated with drug resistance in many cancers.", "Here, we analyzed the factors and molecular mechanisms involved in chemoresistance in patients with esophageal squamous cell carcinoma (ESCC).", "We found that interleukin 6 (IL6) derived mainly from cancer-associated fibroblasts played the most important role in chemoresistance by upregulating C-X-C motif chemokine receptor 7 (CXCR7) expression through signal transducer and activator of transcription 3/nuclear factor-\u03baB pathway.", "CXCR7 knockdown resulted in the inhibition of IL6-induced proliferation and chemoresistance.", "In addition, CXCR7 silencing significantly decreased gene expression associated with stemness, chemoresistance and epithelial\u2013mesenchymal transition and suppressed the proliferation ability of ESCC cells in three-dimensional culture systems and angiogenesis assay.", "In clinical samples, ESCC patients with high expression of CXCR7 and IL6 presented a significantly worse overall survival and progression-free survival upon receiving cisplatin after operation.", "These results suggest that the IL6\u2013CXCR7 axis may provide a promising target for the treatment of ESCC."], "structured": false}
{"doc_id": 3391547, "title": "Myelodysplastic syndromes: revisiting the role of the bone marrow microenvironment in disease pathogenesis", "abstract": ["Myelodysplastic syndromes are a heterogeneous group of diseases characterized by ineffective hematopoiesis and the propensity to leukemic transformation.", "Their pathogenesis is complex and likely depends on interplay between aberrant hematopoietic cells and their microenvironment.", "How niche cells play a role in disease evolution is poorly defined, but the delineation of the hematopoietic stem cell niche and the ability to interrogate its role in hematopoietic disease in animal models have furthered our insights in recent years.", "The data support a view in which the microenvironment can play an active role in the evolution of myelodysplasia and myeloproliferative disorders, thus providing further rationale to explore therapeutic targeting of mesenchymal\u2013hematopoietic interactions in these diseases."], "structured": false}
{"doc_id": 3400973, "title": "SMC complexes differentially compact mitotic chromosomes according to genomic context", "abstract": ["Structural maintenance of chromosomes (SMC) protein complexes are key determinants of chromosome conformation.", "Using Hi-C and polymer modelling, we study how cohesin and condensin, two deeply conserved SMC complexes, organize chromosomes in the budding yeast Saccharomyces cerevisiae.", "The canonical role of cohesin is to co-align sister chromatids, while condensin generally compacts mitotic chromosomes.", "We find strikingly different roles for the two complexes in budding yeast mitosis.", "First, cohesin is responsible for compacting mitotic chromosome arms, independently of sister chromatid cohesion.", "Polymer simulations demonstrate that this role can be fully accounted for through cis-looping of chromatin.", "Second, condensin is generally dispensable for compaction along chromosome arms.", "Instead, it plays a targeted role compacting the rDNA proximal regions and promoting resolution of peri-centromeric regions.", "Our results argue that the conserved mechanism of SMC complexes is to form chromatin loops and that distinct SMC-dependent looping activities are selectively deployed to appropriately compact chromosomes."], "structured": false}
{"doc_id": 3413083, "title": "Patterns of chlamydia testing in different settings and implications for wider STI diagnosis and care: a probability sample survey of the British population", "abstract": ["BACKGROUND Following widespread rollout of chlamydia testing to non-specialist and community settings in the UK, many individuals receive a chlamydia test without being offered comprehensive STI and HIV testing.", "We assess sexual behaviour among testers in different settings with a view to understanding their need for other STI diagnostic services.   \n", "METHODS A probability sample survey of the British population undertaken 2010-2012 (the third National Survey of Sexual Attitudes and Lifestyles).", "We analysed weighted data on chlamydia testing (past year), including location of most recent test, and diagnoses (past 5 years) from individuals aged 16-44 years reporting at least one sexual partner in the past year (4992 women, 3406 men).   \n", "RESULTS Of the 26.8% (95% CI 25.4% to 28.2%) of women and 16.7% (15.5% to 18.1%) of men reporting a chlamydia test in the past year, 28.4% of women and 41.2% of men had tested in genitourinary medicine (GUM), 41.1% and 20.7% of women and men respectively tested in general practice (GP) and the remainder tested in other non-GUM settings.", "Women tested outside GUM were more likely to be older, in a relationship and to live in rural areas.", "Individuals tested outside GUM reported fewer risk behaviours; nevertheless, 11.0% (8.6% to 14.1%) of women and 6.8% (3.9% to 11.6%) of men tested in GP and 13.2% (10.2% to 16.8%) and 9.6% (6.5% to 13.8%) of women and men tested in other non-GUM settings reported 'unsafe sex', defined as two or more partners and no condom use with any partner in the past year.", "Individuals treated for chlamydia outside GUM in the past 5 years were less likely to report an HIV test in that time frame (women: 54.5% (42.7% to 65.7%) vs 74.1% (65.9% to 80.9%) in GUM; men: 23.9% (12.7% to 40.5%) vs 65.8% (56.2% to 74.3%)).   \n", "CONCLUSIONS Most chlamydia testing occurred in non-GUM settings, among populations reporting fewer risk behaviours.", "However, there is a need to provide pathways to comprehensive STI care to the sizeable minority at higher risk."], "structured": true}
{"doc_id": 3419709, "title": "Treatment of nonalcoholic fatty liver disease: role of AMPK.", "abstract": ["Nonalcoholic fatty liver disease (NAFLD) is a growing worldwide epidemic and an important risk factor for the development of insulin resistance, type 2 diabetes, nonalcoholic steatohepatitis (NASH), and hepatic cellular carcinoma (HCC).", "Despite the prevalence of NAFLD, lifestyle interventions involving exercise and weight loss are the only accepted treatments for this disease.", "Over the last decade, numerous experimental compounds have been shown to improve NAFLD in preclinical animal models, and many of these therapeutics have been shown to increase the activity of the cellular energy sensor AMP-activated protein kinase (AMPK).", "Because AMPK activity is reduced by inflammation, obesity, and diabetes, increasing AMPK activity has been viewed as a viable therapeutic strategy to improve NAFLD.", "In this review, we propose three primary mechanisms by which AMPK activation may improve NAFLD.", "In addition, we examine the mechanisms by which AMPK is activated.", "Finally, we identify 27 studies that have used AMPK activators to reduce NAFLD.", "Future considerations for studies examining the relationship between AMPK and NAFLD are highlighted."], "structured": false}
{"doc_id": 3419802, "title": "Microenvironment-dependent growth of pre-neoplastic and malignant plasma cells in humanized mice", "abstract": ["Most human cancers, including myeloma, are preceded by a precursor state.", "There is an unmet need for in vivo models to study the interaction of human preneoplastic cells in the bone marrow microenvironment with non-malignant cells.", "Here, we genetically humanized mice to permit the growth of primary human preneoplastic and malignant plasma cells together with non-malignant cells in vivo.", "Growth was largely restricted to the bone marrow, mirroring the pattern in patients with myeloma.", "Xenografts captured the genomic complexity of parental tumors and revealed additional somatic changes.", "Moreover, xenografts from patients with preneoplastic gammopathy showed progressive growth, suggesting that the clinical stability of these lesions may in part be due to growth controls extrinsic to tumor cells.", "These data demonstrate a new approach to investigate the entire spectrum of human plasma cell neoplasia and illustrate the utility of humanized models for understanding the functional diversity of human tumors."], "structured": false}
{"doc_id": 3430789, "title": "Effect of activated charcoal hemoperfusion on renal function in patients with paraquat poisoning.", "abstract": ["The present study retrospectively analyzed 19 patients diagnosed with paraquat (PQ) poisoning with the aim to investigate the effect of activated charcoal hemoperfusion on renal function and PQ elimination.", "The results indicated that 7 patients died and 12 survived.", "Non-oliguric renal failure occurred in all of the 7 patients who died.", "Among the 12 surviving patients, 10 had normal renal function and 2 developed non-oliguric renal failure.", "There was a linear correlation between plasma and urine paraquat concentration prior to and during activated charcoal hemoperfusion.", "The equation parameters together with the correlation coefficient on admission were as follows: Y=0.5820+1.7348X (R2=0.678; F=35.768; P<0.0001).", "The equation parameters together with the correlation coefficient were as follows during activated charcoal hemoperfusion: Y=0.6827+1.2649X (R2=0.626; F=50.308; P<0.0001).", "Therefore, it was concluded that in patients with normal renal function, the elimination kinetics of PQ by the kidneys were only associated with the plasma PQ concentration.", "Activated charcoal hemoperfusion had little effect on avoiding acute kidney injury in patients with severe PQ poisoning."], "structured": false}
{"doc_id": 3435889, "title": "Diabetes-induced effects on cardiomyocytes in chick embryonic heart micromass and mouse embryonic D3 differentiated stem cells.", "abstract": ["Diabetes mellitus during pregnancy is a considerable medical challenge, since it is related to \u200eaugmented morbidity and mortality concerns for both the fetus \u200eand the pregnant woman.", "Records show that the etiology of diabetic \u200eembryopathy is complicated, as many teratological factors might be involved \u200ein the mechanisms of diabetes mellitus-induced congenital malformation.", "\u200eIn this study, the potential cardiotoxic effect of hyperglycemia with hyperketonemia was investigated by using two in vitro models; primary chick embryonic cardiomyocytes and stem cell derived cardiomyocytes, where adverse effects were recorded in both systems.", "The cells were evaluated by changes in beating activity, cell activity, protein content, ROS production, DNA damage and differentiating stem cell migration.", "The diabetic formulae used produced an increase in DNA damage and a decline in cell migration in mouse embryonic stem cells.", "These results provide an additional insight into adverse effects during gestational diabetes mellitus and a recommendation for expectant mothers and maternity staff to monitor glycaemic levels months ahead of conception.", "This study also supports the recommendation of using antioxidants during pregnancy to prevent DNA damage by the production of ROS, which might result in heart defects as well as other developmental anomalies."], "structured": false}
{"doc_id": 3437084, "title": "Motion magnification", "abstract": ["We present motion magnification, a technique that acts like a microscope for visual motion.", "It can amplify subtle motions in a video sequence, allowing for visualization of deformations that would otherwise be invisible.", "To achieve motion magnification, we need to accurately measure visual motions, and group the pixels to be modified.", "After an initial image registration step, we measure motion by a robust analysis of feature point trajectories, and segment pixels based on similarity of position, color, and motion.", "A novel measure of motion similarity groups even very small motions according to correlation over time, which often relates to physical cause.", "An outlier mask marks observations not explained by our layered motion model, and those pixels are simply reproduced on the output from the original registered observations.", "The motion of any selected layer may be magnified by a user-specified amount; texture synthesis fills-in unseen \"holes\" revealed by the amplified motions.", "The resulting motion-magnified images can reveal or emphasize small motions in the original sequence, as we demonstrate with deformations in load-bearing structures, subtle motions or balancing corrections of people, and \"rigid\" structures bending under hand pressure."], "structured": false}
{"doc_id": 3441524, "title": "Human TRPML1 channel structures in open and closed conformations", "abstract": ["Transient receptor potential mucolipin 1 (TRPML1) is a Ca2+-releasing cation channel that mediates the calcium signalling and homeostasis of lysosomes.", "Mutations in TRPML1 lead to mucolipidosis type IV, a severe lysosomal storage disorder.", "Here we report two electron cryo-microscopy structures of full-length human TRPML1: a 3.72-\u00c5 apo structure at pH 7.0 in the closed state, and a 3.49-\u00c5 agonist-bound structure at pH 6.0 in an open state.", "Several aromatic and hydrophobic residues in pore helix 1, helices S5 and S6, and helix S6 of a neighbouring subunit, form a hydrophobic cavity to house the agonist, suggesting a distinct agonist-binding site from that found in TRPV1, a TRP channel from a different subfamily.", "The opening of TRPML1 is associated with distinct dilations of its lower gate together with a slight structural movement of pore helix 1.", "Our work reveals the regulatory mechanism of TRPML channels, facilitates better understanding of TRP channel activation, and provides insights into the molecular basis of mucolipidosis type IV pathogenesis."], "structured": false}
{"doc_id": 3444507, "title": "Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration", "abstract": ["Data visualization is an essential component of genomic data analysis.", "However, the size and diversity of the data sets produced by today's sequencing and array-based profiling methods present major challenges to visualization tools.", "The Integrative Genomics Viewer (IGV) is a high-performance viewer that efficiently handles large heterogeneous data sets, while providing a smooth and intuitive user experience at all levels of genome resolution.", "A key characteristic of IGV is its focus on the integrative nature of genomic studies, with support for both array-based and next-generation sequencing data, and the integration of clinical and phenotypic data.", "Although IGV is often used to view genomic data from public sources, its primary emphasis is to support researchers who wish to visualize and explore their own data sets or those from colleagues.", "To that end, IGV supports flexible loading of local and remote data sets, and is optimized to provide high-performance data visualization and exploration on standard desktop systems.", "IGV is freely available for download from http://www.broadinstitute.org/igv, under a GNU LGPL open-source license."], "structured": false}
{"doc_id": 3446400, "title": "Can genome engineering be used to target cancer-associated enhancers?", "abstract": ["Transcriptional misregulation is involved in the development of many diseases, especially neoplastic transformation.", "Distal regulatory elements, such as enhancers, play a major role in specifying cell-specific transcription patterns in both normal and diseased tissues, suggesting that enhancers may be prime targets for therapeutic intervention.", "By focusing on modulating gene regulation mediated by cell type-specific enhancers, there is hope that normal epigenetic patterning in an affected tissue could be restored with fewer side effects than observed with treatments employing relatively nonspecific inhibitors such as epigenetic drugs.", "New methods employing genomic nucleases and site-specific epigenetic regulators targeted to specific genomic regions, using either artificial DNA-binding proteins or RNA-DNA interactions, may allow precise genome engineering at enhancers.", "However, this field is still in its infancy and further refinements that increase specificity and efficiency are clearly required."], "structured": false}
{"doc_id": 3462075, "title": "Long\u2010Term Follow\u2010up of CD19 CAR Therapy in Acute Lymphoblastic Leukemia", "abstract": ["Background CD19\u2010specific chimeric antigen receptor (CAR) T cells induce high rates of initial response among patients with relapsed B\u2010cell acute lymphoblastic leukemia (ALL) and long\u2010term remissions in a subgroup of patients.", "Methods We conducted a phase 1 trial involving adults with relapsed B\u2010cell ALL who received an infusion of autologous T cells expressing the 19\u201028z CAR at the Memorial Sloan Kettering Cancer Center (MSKCC).", "Safety and long\u2010term outcomes were assessed, as were their associations with demographic, clinical, and disease characteristics.", "Results A total of 53 adults received 19\u201028z CAR T cells that were manufactured at MSKCC.", "After infusion, severe cytokine release syndrome occurred in 14 of 53 patients (26%; 95% confidence interval [CI], 15 to 40); 1 patient died.", "Complete remission was observed in 83% of the patients.", "At a median follow\u2010up of 29 months (range, 1 to 65), the median event\u2010free survival was 6.1 months (95% CI, 5.0 to 11.5), and the median overall survival was 12.9 months (95% CI, 8.7 to 23.4).", "Patients with a low disease burden (<5% bone marrow blasts) before treatment had markedly enhanced remission duration and survival, with a median event\u2010free survival of 10.6 months (95% CI, 5.9 to not reached) and a median overall survival of 20.1 months (95% CI, 8.7 to not reached).", "Patients with a higher burden of disease (\u22655% bone marrow blasts or extramedullary disease) had a greater incidence of the cytokine release syndrome and neurotoxic events and shorter long\u2010term survival than did patients with a low disease burden.", "Conclusions In the entire cohort, the median overall survival was 12.9 months.", "Among patients with a low disease burden, the median overall survival was 20.1 months and was accompanied by a markedly lower incidence of the cytokine release syndrome and neurotoxic events after 19\u201028z CAR T\u2010cell infusion than was observed among patients with a higher disease burden.", "(Funded by the Commonwealth Foundation for Cancer Research and others; ClinicalTrials.gov number, NCT01044069.)"], "structured": false}
{"doc_id": 3464191, "title": "Periosteum contains skeletal stem cells with high bone regenerative potential controlled by Periostin", "abstract": ["Bone regeneration relies on the activation of skeletal stem cells (SSCs) that still remain poorly characterized.", "Here, we show that periosteum contains SSCs with high bone regenerative potential compared to bone marrow stromal cells/skeletal stem cells (BMSCs) in mice.", "Although periosteal cells (PCs) and BMSCs are derived from a common embryonic mesenchymal lineage, postnatally PCs exhibit greater clonogenicity, growth and differentiation capacity than BMSCs.", "During bone repair, PCs can efficiently contribute to cartilage and bone, and integrate long-term after transplantation.", "Molecular profiling uncovers genes encoding Periostin and other extracellular matrix molecules associated with the enhanced response to injury of PCs.", "Periostin gene deletion impairs PC functions and fracture consolidation.", "Periostin-deficient periosteum cannot reconstitute a pool of PCs after injury demonstrating the presence of SSCs within periosteum and the requirement of Periostin in maintaining this pool.", "Overall our results highlight the importance of analyzing periosteum and PCs to understand bone phenotypes."], "structured": false}
{"doc_id": 3468459, "title": "Metabolism strikes back: metabolic flux regulates cell signaling.", "abstract": ["Mammalian cells depend on growth factor signaling to take up nutrients; however, coordination of glucose and glutamine uptake has been a mystery.", "In this issue of Genes & Development, Wellen and colleagues (pp.", "2784-2799) show that glucose flux through the hexosamine biosynthesis pathway regulates growth factor receptor glycosylation and enables glutamine consumption.", "This mechanism ensures that cells do not engage in anabolic metabolism when nutrients are limiting, and highlights how substrate availability for protein modifications can modulate cell signaling."], "structured": false}
{"doc_id": 3471191, "title": "Association of Pembrolizumab With Tumor Response and Survival Among Patients With Advanced Melanoma.", "abstract": ["IMPORTANCE The programmed death 1 (PD-1) pathway limits immune responses to melanoma and can be blocked with the humanized anti-PD-1 monoclonal antibody pembrolizumab.   \n", "OBJECTIVE To characterize the association of pembrolizumab with tumor response and overall survival among patients with advanced melanoma.   \n", "DESIGN, SETTINGS, AND PARTICIPANTS Open-label, multicohort, phase 1b clinical trials (enrollment, December 2011-September 2013).", "Median duration of follow-up was 21 months.", "The study was performed in academic medical centers in Australia, Canada, France, and the United States.", "Eligible patients were aged 18 years and older and had advanced or metastatic melanoma.", "Data were pooled from 655 enrolled patients (135 from a nonrandomized cohort [n = 87 ipilimumab naive; n = 48 ipilimumab treated] and 520 from randomized cohorts [n = 226 ipilimumab naive; n = 294 ipilimumab treated]).", "Cutoff dates were April 18, 2014, for safety analyses and October 18, 2014, for efficacy analyses.   ", "EXPOSURES Pembrolizumab 10 mg/kg every 2 weeks, 10 mg/kg every 3 weeks, or 2 mg/kg every 3 weeks continued until disease progression, intolerable toxicity, or investigator decision.   \n", "MAIN OUTCOMES AND MEASURES The primary end point was confirmed objective response rate (best overall response of complete response or partial response) in patients with measurable disease at baseline per independent central review.", "Secondary end points included toxicity, duration of response, progression-free survival, and overall survival.   \n", "RESULTS Among the 655 patients (median [range] age, 61 [18-94] years; 405 [62%] men), 581 had measurable disease at baseline.", "An objective response was reported in 194 of 581 patients (33% [95% CI, 30%-37%]) and in 60 of 133 treatment-naive patients (45% [95% CI, 36% to 54%]).", "Overall, 74% (152/205) of responses were ongoing at the time of data cutoff; 44% (90/205) of patients had response duration for at least 1 year and 79% (162/205) had response duration for at least 6 months.", "Twelve-month progression-free survival rates were 35% (95% CI, 31%-39%) in the total population and 52% (95% CI, 43%-60%) among treatment-naive patients.", "Median overall survival in the total population was 23 months (95% CI, 20-29) with a 12-month survival rate of 66% (95% CI, 62%-69%) and a 24-month survival rate of 49% (95% CI, 44%-53%).", "In treatment-naive patients, median overall survival was 31 months (95% CI, 24 to not reached) with a 12-month survival rate of 73% (95% CI, 65%-79%) and a 24-month survival rate of 60% (95% CI, 51%-68%).", "Ninety-two of 655 patients (14%) experienced at least 1 treatment-related grade 3 or 4 adverse event (AE) and 27 of 655 (4%) patients discontinued treatment because of a treatment-related AE.", "Treatment-related serious AEs were reported in 59 patients (9%).", "There were no drug-related deaths.   \n", "CONCLUSIONS AND RELEVANCE Among patients with advanced melanoma, pembrolizumab administration was associated with an overall objective response rate of 33%, 12-month progression-free survival rate of 35%, and median overall survival of 23 months; grade 3 or 4 treatment-related AEs occurred in 14%.   \n", "TRIAL REGISTRATION clinicaltrials.gov Identifier: NCT01295827."], "structured": true}
{"doc_id": 3475317, "title": "Inflammatory signaling in human Tuberculosis granulomas is spatially organized", "abstract": ["Granulomas are the pathological hallmark of tuberculosis (TB).", "However, their function and mechanisms of formation remain poorly understood.", "To understand the role of granulomas in TB, we analyzed the proteomes of granulomas from subjects with tuberculosis in an unbiased manner.", "Using laser-capture microdissection, mass spectrometry and confocal microscopy, we generated detailed molecular maps of human granulomas.", "We found that the centers of granulomas have a pro-inflammatory environment that is characterized by the presence of antimicrobial peptides, reactive oxygen species and pro-inflammatory eicosanoids.", "Conversely, the tissue surrounding the caseum has a comparatively anti-inflammatory signature.", "These findings are consistent across a set of six human subjects and in rabbits.", "Although the balance between systemic pro- and anti-inflammatory signals is crucial to TB disease outcome, here we find that these signals are physically segregated within each granuloma.", "From the protein and lipid snapshots of human and rabbit lesions analyzed here, we hypothesize that the pathologic response to TB is shaped by the precise anatomical localization of these inflammatory pathways during the development of the granuloma."], "structured": false}
{"doc_id": 3493623, "title": "Suppression of interferon-mediated anti-HBV response by single CpG methylation in the 5\u2032-UTR of TRIM22", "abstract": ["Objective Interferons (IFNs) mediate direct antiviral activity.", "They play a crucial role in the early host immune response against viral infections.", "However, IFN therapy for HBV infection is less effective than for other viral infections.", "Design We explored the cellular targets of HBV in response to IFNs using proteome-wide screening.", "Results Using LC-MS/MS, we identified proteins downregulated and upregulated by IFN treatment in HBV X protein (HBx)-stable and control cells.", "We found several IFN-stimulated genes downregulated by HBx, including TRIM22, which is known as an antiretroviral protein.", "We demonstrated that HBx suppresses the transcription of TRIM22 through a single CpG methylation in its 5\u2032-UTR, which further reduces the IFN regulatory factor-1 binding affinity, thereby suppressing the IFN-stimulated induction of TRIM22.", "Conclusions We verified our findings using a mouse model, primary human hepatocytes and human liver tissues.", "Our data elucidate a mechanism by which HBV evades the host innate immune system."], "structured": false}
{"doc_id": 3495456, "title": "Developmental Analysis of Bone Marrow Neutrophils Reveals Populations Specialized in Expansion, Trafficking, and Effector Functions", "abstract": ["Summary Neutrophils are specialized innate cells that require constant replenishment from proliferative bone marrow (BM) precursors as a result of their short half\u2010life.", "Although it is established that neutrophils are derived from the granulocyte\u2010macrophage progenitor (GMP), the differentiation pathways from GMP to functional mature neutrophils are poorly defined.", "Using mass cytometry (CyTOF) and cell\u2010cycle\u2010based analysis, we identified three neutrophil subsets within the BM: a committed proliferative neutrophil precursor (preNeu) which differentiates into non\u2010proliferating immature neutrophils and mature neutrophils.", "Transcriptomic profiling and functional analysis revealed that preNeu require the C/EBP&egr; transcription factor for their generation from the GMP, and their proliferative program is substituted by a gain of migratory and effector function as they mature.", "preNeus expand under microbial and tumoral stress, and immature neutrophils are recruited to the periphery of tumor\u2010bearing mice.", "In summary, our study identifies specialized BM granulocytic populations that ensure supply under homeostasis and stress responses.", "Graphical Abstract Figure.", "No Caption available.", "HighlightsProliferation activity identifies committed neutrophil precursor in mice and humansNeutrophil subsets possess distinct transcriptomic and functional signaturesDefect in neutrophil development leads to impaired neutrophil\u2010mediated responsesIncreased circulating immature neutrophils are associated with cancer progression &NA; The neutrophil differentiation pathway is poorly defined.", "Evrard et.", "al. demonstrate a workflow of characterizing bone marrow neutrophil subsets on the basis of their proliferative capacity and molecular signatures and thereby define the developmental trajectory and functional properties of neutrophils."], "structured": false}
{"doc_id": 3504761, "title": "TAK1-mediated autophagy and fatty acid oxidation prevent hepatosteatosis and tumorigenesis.", "abstract": ["The MAP kinase kinase kinase TGF\u03b2-activated kinase 1 (TAK1) is activated by TLRs, IL-1, TNF, and TGF\u03b2 and in turn activates IKK-NF-\u03baB and JNK, which regulate cell survival, growth, tumorigenesis, and metabolism.", "TAK1 signaling also upregulates AMPK activity and autophagy.", "Here, we investigated TAK1-dependent regulation of autophagy, lipid metabolism, and tumorigenesis in the liver.", "Fasted mice with hepatocyte-specific deletion of Tak1 exhibited severe hepatosteatosis with increased mTORC1 activity and suppression of autophagy compared with their WT counterparts.", "TAK1-deficient hepatocytes exhibited suppressed AMPK activity and autophagy in response to starvation or metformin treatment; however, ectopic activation of AMPK restored autophagy in these cells.", "Peroxisome proliferator-activated receptor \u03b1 (PPAR\u03b1) target genes and \u03b2-oxidation, which regulate hepatic lipid degradation, were also suppressed in hepatocytes lacking TAK1.", "Due to suppression of autophagy and \u03b2-oxidation, a high-fat diet challenge aggravated steatohepatitis in mice with hepatocyte-specific deletion of Tak1.", "Notably, inhibition of mTORC1 restored autophagy and PPAR\u03b1 target gene expression in TAK1-deficient livers, indicating that TAK1 acts upstream of mTORC1.", "mTORC1 inhibition also suppressed spontaneous liver fibrosis and hepatocarcinogenesis in animals with hepatocyte-specific deletion of Tak1.", "These data indicate that TAK1 regulates hepatic lipid metabolism and tumorigenesis via the AMPK/mTORC1 axis, affecting both autophagy and PPAR\u03b1 activity."], "structured": false}
{"doc_id": 3506723, "title": "Formins at the Junction.", "abstract": ["The actin cytoskeleton and adhesion junctions are physically and functionally coupled at the cell-cell interface between epithelial cells.", "The actin regulatory complex Arp2/3 has an established role in the turnover of junctional actin; however, the role of formins, the largest group of actin regulators, is less clear.", "Formins dynamically shape the actin cytoskeleton and have various functions within cells.", "In this review we describe recent progress on how formins regulate actin dynamics at cell-cell contacts and highlight formin functions during polarized protein traffic necessary for epithelialization."], "structured": false}
{"doc_id": 3512154, "title": "CRISPR adaptation biases explain preference for acquisition of foreign DNA", "abstract": ["CRISPR-Cas (clustered, regularly interspaced short palindromic repeats coupled with CRISPR-associated proteins) is a bacterial immunity system that protects against invading phages or plasmids.", "In the process of CRISPR adaptation, short pieces of DNA ('spacers') are acquired from foreign elements and integrated into the CRISPR array.", "So far, it has remained a mystery how spacers are preferentially acquired from the foreign DNA while the self chromosome is avoided.", "Here we show that spacer acquisition is replication-dependent, and that DNA breaks formed at stalled replication forks promote spacer acquisition.", "Chromosomal hotspots of spacer acquisition were confined by Chi sites, which are sequence octamers highly enriched on the bacterial chromosome, suggesting that these sites limit spacer acquisition from self DNA.", "We further show that the avoidance of self is mediated by the RecBCD double-stranded DNA break repair complex.", "Our results suggest that, in Escherichia coli, acquisition of new spacers largely depends on RecBCD-mediated processing of double-stranded DNA breaks occurring primarily at replication forks, and that the preference for foreign DNA is achieved through the higher density of Chi sites on the self chromosome, in combination with the higher number of forks on the foreign DNA.", "This model explains the strong preference to acquire spacers both from high copy plasmids and from phages."], "structured": false}
{"doc_id": 3514072, "title": "High-resolution mapping of open chromatin in the rice genome.", "abstract": ["Gene expression is controlled by the complex interaction of transcription factors binding to promoters and other regulatory DNA elements.", "One common characteristic of the genomic regions associated with regulatory proteins is a pronounced sensitivity to DNase I digestion.", "We generated genome-wide high-resolution maps of DNase I hypersensitive (DH) sites from both seedling and callus tissues of rice (Oryza sativa).", "Approximately 25% of the DH sites from both tissues were found in putative promoters, indicating that the vast majority of the gene regulatory elements in rice are not located in promoter regions.", "We found 58% more DH sites in the callus than in the seedling.", "For DH sites detected in both the seedling and callus, 31% displayed significantly different levels of DNase I sensitivity within the two tissues.", "Genes that are differentially expressed in the seedling and callus were frequently associated with DH sites in both tissues.", "The DNA sequences contained within the DH sites were hypomethylated, consistent with what is known about active gene regulatory elements.", "Interestingly, tissue-specific DH sites located in the promoters showed a higher level of DNA methylation than the average DNA methylation level of all the DH sites located in the promoters.", "A distinct elevation of H3K27me3 was associated with intergenic DH sites.", "These results suggest that epigenetic modifications play a role in the dynamic changes of the numbers and DNase I sensitivity of DH sites during development."], "structured": false}
{"doc_id": 3514540, "title": "Prospective study of body fat distribution and the risk of endometrial cancer.", "abstract": ["BACKGROUND Epidemiologic studies have found that overall obesity is positively related to endometrial cancer (EC) risk.", "However, data assessing the association between body fat distribution and risk of EC are still limited.   \n", "METHODS We followed 51,948 women who first reported waist circumference (WC) and hip circumference in 1986 in the Nurses' Health Study.", "Waist-to-hip ratio (WHR) was calculated.   \n", "RESULTS During 24 years of follow-up, 449 incident invasive EC cases were diagnosed.", "In a multivariate analysis without adjusting for body mass index (BMI), the relative risks (RRs) for EC comparing extreme categories were 2.44 (95% confidence interval [CI] 1.72-3.45) for WC and 1.69 (95% CI=1.20-2.40) for WHR.", "However, after adjustment of BMI, those positive associations were substantially attenuated and no longer significant; RR=1.08 (95% CI=0.69-1.67) for WC and 1.15 (95% CI=0.81-1.64) for WHR, respectively.   \n", "CONCLUSION In our prospective cohort study, we found no independent association between body fat distribution and the risk of EC after adjustment for BMI."], "structured": true}
{"doc_id": 3524352, "title": "Breast cancer clusters in the northeast United States: a geographic analysis.", "abstract": ["High breast cancer mortality rates have been reported in the northeastern part of the United States, with recent attention focused on Long Island, New York.", "In this study, the authors investigate whether the high breast cancer mortality is evenly spread over the Northeast, in the sense that any observed clusters of deaths can be explained by chance alone, or whether there are clusters of statistical significance.", "Demographic data and age-specific breast cancer mortality rates for women were obtained for all 244 counties in 11 northeastern states and for the District of Columbia for 1988-1992.", "A recently developed spatial scan statistic is used, which searches for clusters of cases without specifying their size or location ahead of time, and which tests for their statistical significance while adjusting for the multiple testing inherent in such a procedure.", "The basic analysis is adjusted for age, with further analyses examining how the results are affected by incorporating race, urbanicity, and parity as confounding variables.", "There is a statistically significant and geographically broad cluster of breast cancer deaths in the New York City-Philadelphia, Pennsylvania, metropolitan area (p = 0.0001), which has a 7.4% higher mortality rate than the rest of the Northeast.", "The cluster remains significant when race, urbanicity, and/or parity are included as confounding variables.", "Four smaller subclusters within this area are also significant on their own strength: Philadelphia with suburbs (p = 0.0001), Long Island (p = 0.0001), central New Jersey (p = 0.0001), and northeastern New Jersey (p = 0.0001).", "The elevated breast cancer mortality on Long Island might be viewed less as a unique local phenomenon and more as part of a more general situation involving large parts of the New York City-Philadelphia metropolitan area.", "The several known and hypothesized risk factors for which we could not adjust and that may explain the detected cluster are most notably age at first birth, age at menarche, age at menopause, breastfeeding, genetic mutations, and environmental factors."], "structured": false}
{"doc_id": 3531388, "title": "CD200R/CD200 Inhibits Osteoclastogenesis: New Mechanism of Osteoclast Control by Mesenchymal Stem Cells in Human", "abstract": ["Bone homeostasis is maintained by the balance between bone-forming osteoblasts and bone-degrading osteoclasts.", "Osteoblasts have a mesenchymal origin whereas osteoclasts belong to the myeloid lineage.", "Osteoclast and osteoblast communication occurs through soluble factors secretion, cell-bone interaction and cell-cell contact, which modulate their activities.", "CD200 is an immunoglobulin superfamilly member expressed on various types of cells including mesenchymal stem cells (MSCs).", "CD200 receptor (CD200R) is expressed on myeloid cells such as monocytes/macrophages.", "We assume that CD200 could be a new molecule involved in the control of osteoclastogenesis and could play a role in MSC-osteoclast communication in humans.", "In this study, we demonstrated that soluble CD200 inhibited the differentiation of osteoclast precursors as well as their maturation in bone-resorbing cells in vitro.", "Soluble CD200 did not modify the monocyte phenotype but inhibited the receptor activator of nuclear factor kappa-B ligand (RANKL) signaling pathway as well as the gene expression of osteoclast markers such as osteoclast-associated receptor (OSCAR) and nuclear factor of activated T cells cytoplasmic 1 (NFATc1).", "Moreover, MSCs inhibited osteoclast formation, which depended on cell-cell contact and was associated with CD200 expression on the MSC surface.", "Our results clearly demonstrate that MSCs, through the expression of CD200, play a major role in the regulation of bone resorption and bone physiology and that the CD200-CD200R couple could be a new target to control bone diseases."], "structured": false}
{"doc_id": 3545805, "title": "Tumor-specific Th17-polarized cells eradicate large established melanoma.", "abstract": ["CD4+ T cells can differentiate into multiple effector subsets, but the potential roles of these subsets in anti-tumor immunity have not been fully explored.", "Seeking to study the impact of CD4+ T cell polarization on tumor rejection in a model mimicking human disease, we generated a new MHC class II-restricted, T-cell receptor (TCR) transgenic mouse model in which CD4+ T cells recognize a novel epitope in tyrosinase-related protein 1 (TRP-1), an antigen expressed by normal melanocytes and B16 murine melanoma.", "Cells could be robustly polarized into Th0, Th1, and Th17 subtypes in vitro, as evidenced by cytokine, chemokine, and adhesion molecule profiles and by surface markers, suggesting the potential for differential effector function in vivo.", "Contrary to the current view that Th1 cells are most important in tumor rejection, we found that Th17-polarized cells better mediated destruction of advanced B16 melanoma.", "Their therapeutic effect was critically dependent on interferon-gamma (IFN-gamma) production, whereas depletion of interleukin (IL)-17A and IL-23 had little impact.", "Taken together, these data indicate that the appropriate in vitro polarization of effector CD4+ T cells is decisive for successful tumor eradication.", "This principle should be considered in designing clinical trials involving adoptive transfer-based immunotherapy of human malignancies."], "structured": false}
{"doc_id": 3552753, "title": "Defining community acquired pneumonia severity on presentation to hospital: an international derivation and validation study.", "abstract": ["BACKGROUND In the assessment of severity in community acquired pneumonia (CAP), the modified British Thoracic Society (mBTS) rule identifies patients with severe pneumonia but not patients who might be suitable for home management.", "A multicentre study was conducted to derive and validate a practical severity assessment model for stratifying adults hospitalised with CAP into different management groups.   \n", "METHODS Data from three prospective studies of CAP conducted in the UK, New Zealand, and the Netherlands were combined.", "A derivation cohort comprising 80% of the data was used to develop the model.", "Prognostic variables were identified using multiple logistic regression with 30 day mortality as the outcome measure.", "The final model was tested against the validation cohort.   \n", "RESULTS 1068 patients were studied (mean age 64 years, 51.5% male, 30 day mortality 9%).", "Age >/=65 years (OR 3.5, 95% CI 1.6 to 8.0) and albumin <30 g/dl (OR 4.7, 95% CI 2.5 to 8.7) were independently associated with mortality over and above the mBTS rule (OR 5.2, 95% CI 2.7 to 10).", "A six point score, one point for each of Confusion, Urea >7 mmol/l, Respiratory rate >/=30/min, low systolic(<90 mm Hg) or diastolic (</=60 mm Hg) Blood pressure), age >/=65 years (CURB-65 score) based on information available at initial hospital assessment, enabled patients to be stratified according to increasing risk of mortality: score 0, 0.7%; score 1, 3.2%; score 2, 3%; score 3, 17%; score 4, 41.5% and score 5, 57%.", "The validation cohort confirmed a similar pattern.   \n", "CONCLUSIONS A simple six point score based on confusion, urea, respiratory rate, blood pressure, and age can be used to stratify patients with CAP into different management groups."], "structured": true}
{"doc_id": 3553087, "title": "Mitochondrial iron chelation ameliorates cigarette-smoke induced bronchitis and emphysema in mice", "abstract": ["Chronic obstructive pulmonary disease (COPD) is linked to both cigarette smoking and genetic determinants.", "We have previously identified iron-responsive element-binding protein 2 (IRP2) as an important COPD susceptibility gene and have shown that IRP2 protein is increased in the lungs of individuals with COPD.", "Here we demonstrate that mice deficient in Irp2 were protected from cigarette smoke (CS)-induced experimental COPD.", "By integrating RNA immunoprecipitation followed by sequencing (RIP-seq), RNA sequencing (RNA-seq), and gene expression and functional enrichment clustering analysis, we identified Irp2 as a regulator of mitochondrial function in the lungs of mice.", "Irp2 increased mitochondrial iron loading and levels of cytochrome c oxidase (COX), which led to mitochondrial dysfunction and subsequent experimental COPD.", "Frataxin-deficient mice, which had higher mitochondrial iron loading, showed impaired airway mucociliary clearance (MCC) and higher pulmonary inflammation at baseline, whereas mice deficient in the synthesis of cytochrome c oxidase, which have reduced COX, were protected from CS-induced pulmonary inflammation and impairment of MCC.", "Mice treated with a mitochondrial iron chelator or mice fed a low-iron diet were protected from CS-induced COPD.", "Mitochondrial iron chelation also alleviated CS-induced impairment of MCC, CS-induced pulmonary inflammation and CS-associated lung injury in mice with established COPD, suggesting a critical functional role and potential therapeutic intervention for the mitochondrial-iron axis in COPD."], "structured": false}
{"doc_id": 3559136, "title": "Cancer-Associated Fibroblasts Neutralize the Anti-tumor Effect of CSF1 Receptor Blockade by Inducing PMN-MDSC Infiltration of Tumors.", "abstract": ["Tumor-associated macrophages (TAM) contribute to all aspects of tumor progression.", "Use of CSF1R inhibitors to target TAM is therapeutically appealing, but has had very limited anti-tumor effects.", "Here, we have identified the mechanism that limited the effect of CSF1R targeted therapy.", "We demonstrated that carcinoma-associated fibroblasts (CAF) are major sources of chemokines that recruit granulocytes to tumors.", "CSF1 produced by tumor cells caused HDAC2-mediated downregulation of granulocyte-specific chemokine expression in CAF, which limited migration of these cells to tumors.", "Treatment with CSF1R inhibitors disrupted this crosstalk and triggered a profound increase in granulocyte recruitment to tumors.", "Combining CSF1R inhibitor with a CXCR2 antagonist blocked granulocyte infiltration of tumors and showed strong anti-tumor effects."], "structured": false}
{"doc_id": 3566945, "title": "Phenotypic deficits in the HIV-1 envelope are associated with the maturation of a V2-directed broadly neutralizing antibody lineage", "abstract": ["Broadly neutralizing antibodies (bnAbs) to HIV-1 can evolve after years of an iterative process of virus escape and antibody adaptation that HIV-1 vaccine design seeks to mimic.", "To enable this, properties that render HIV-1 envelopes (Env) capable of eliciting bnAb responses need to be defined.", "Here, we followed the evolution of the V2 apex directed bnAb lineage VRC26 in the HIV-1 subtype C superinfected donor CAP256 to investigate the phenotypic changes of the virus populations circulating before and during the early phases of bnAb induction.", "Longitudinal viruses that evolved from the VRC26-resistant primary infecting (PI) virus, the VRC26-sensitive superinfecting (SU) virus and ensuing PI-SU recombinants revealed substantial phenotypic changes in Env, with a switch in Env properties coinciding with early resistance to VRC26.", "Decreased sensitivity of SU-like viruses to VRC26 was linked with reduced infectivity, altered entry kinetics and lower sensitivity to neutralization after CD4 attachment.", "VRC26 maintained neutralization activity against cell-associated CAP256 virus, indicating that escape through the cell-cell transmission route is not a dominant escape pathway.", "Reduced fitness of the early escape variants and sustained sensitivity in cell-cell transmission are both features that limit virus replication, thereby impeding rapid escape.", "This supports a scenario where VRC26 allowed only partial viral escape for a prolonged period, possibly increasing the time window for bnAb maturation.", "Collectively, our data highlight the phenotypic plasticity of the HIV-1 Env in evading bnAb pressure and the need to consider phenotypic traits when selecting and designing Env immunogens.", "Combinations of Env variants with differential phenotypic patterns and bnAb sensitivity, as we describe here for CAP256, may maximize the potential for inducing bnAb responses by vaccination."], "structured": false}
{"doc_id": 3572885, "title": "High somatic mutation and neoantigen burden are correlated with decreased progression-free survival in multiple myeloma", "abstract": ["Tumor-specific mutations can result in immunogenic neoantigens, both of which have been correlated with responsiveness to immune checkpoint inhibitors in highly mutagenic cancers.", "However, early results of single-agent checkpoint inhibitors in multiple myeloma (MM) have been underwhelming.", "Therefore, we sought to understand the relationship between mutation and neoantigen landscape of MM patients and responsiveness to therapies.", "Somatic mutation burden, neoantigen load, and response to therapy were determined using interim data from the MMRF CoMMpass study (NCT01454297) on 664 MM patients.", "In this population, the mean somatic and missense mutation loads were 405.84(s=608.55) and 63.90(s=95.88) mutations per patient, respectively.", "There was a positive linear relationship between mutation and neoantigen burdens (R2=0.862).", "The average predicted neoantigen load was 23.52(s=52.14) neoantigens with an average of 9.40(s=26.97) expressed neoantigens.", "Survival analysis revealed significantly shorter progression-free survival (PFS) in patients with greater than average somatic missense mutation load (N=163, 0.493 vs 0.726 2-year PFS, P=0.0023) and predicted expressed neoantigen load (N=214, 0.555 vs 0.729 2-year PFS, P=0.0028).", "This pattern is maintained when stratified by disease stage and cytogenetic abnormalities.", "Therefore, high mutation and neoantigen load are clinically relevant risk factors that negatively impact survival of MM patients under current standards of care."], "structured": false}
{"doc_id": 3578380, "title": "Postmarket Safety Events Among Novel Therapeutics Approved by the US Food and Drug Administration Between 2001 and 2010", "abstract": ["Importance Postmarket safety events of novel pharmaceuticals and biologics occur when new safety risks are identified after initial regulatory approval of these therapeutics.", "These safety events can change how novel therapeutics are used in clinical practice and inform patient and clinician decision making.", "Objectives To characterize the frequency of postmarket safety events among novel therapeutics approved by the US Food and Drug Administration (FDA), and to examine whether any novel therapeutic characteristics known at the time of FDA approval were associated with increased risk.", "Design and Setting Cohort study of all novel therapeutics approved by the FDA between January 1, 2001, and December 31, 2010, followed up through February 28, 2017.", "Exposures Novel therapeutic characteristics known at the time of FDA approval, including drug class, therapeutic area, priority review, accelerated approval, orphan status, near\u2013regulatory deadline approval, and regulatory review time.", "Main Outcomes and Measures A composite of (1) withdrawals due to safety concerns, (2) FDA issuance of incremental boxed warnings added in the postmarket period, and (3) FDA issuance of safety communications.", "Results From 2001 through 2010, the FDA approved 222 novel therapeutics (183 pharmaceuticals and 39 biologics).", "There were 123 new postmarket safety events (3 withdrawals, 61 boxed warnings, and 59 safety communications) during a median follow-up period of 11.7 years (interquartile range [IQR], 8.7-13.8 years), affecting 71 (32.0%) of the novel therapeutics.", "The median time from approval to first postmarket safety event was 4.2 years (IQR, 2.5-6.0 years), and the proportion of novel therapeutics affected by a postmarket safety event at 10 years was 30.8% (95% CI, 25.1%-37.5%).", "In multivariable analysis, postmarket safety events were statistically significantly more frequent among biologics (incidence rate ratio [IRR] = 1.93; 95% CI, 1.06-3.52; P = .03), therapeutics indicated for the treatment of psychiatric disease (IRR = 3.78; 95% CI, 1.77-8.06; P < .001), those receiving accelerated approval (IRR = 2.20; 95% CI, 1.15-4.21; P = .02), and those with near\u2013regulatory deadline approval (IRR = 1.90; 95% CI, 1.19-3.05; P = .008); events were statistically significantly less frequent among those with regulatory review times less than 200 days (IRR = 0.46; 95% CI, 0.24-0.87; P = .02).", "Conclusions and Relevance Among 222 novel therapeutics approved by the FDA from 2001 through 2010, 32% were affected by a postmarket safety event.", "Biologics, psychiatric therapeutics, and accelerated and near\u2013regulatory deadline approval were statistically significantly associated with higher rates of events, highlighting the need for continuous monitoring of the safety of novel therapeutics throughout their life cycle."], "structured": false}
{"doc_id": 3580005, "title": "Who is where at risk for Chronic Obstructive Pulmonary Disease? A spatial epidemiological analysis of health insurance claims for COPD in Northeastern Germany", "abstract": ["BACKGROUND Chronic obstructive pulmonary disease (COPD) has a high prevalence rate in Germany and a further increase is expected within the next years.", "Although risk factors on an individual level are widely understood, only little is known about the spatial heterogeneity and population-based risk factors of COPD.", "Background knowledge about broader, population-based processes could help to plan the future provision of healthcare and prevention strategies more aligned to the expected demand.", "The aim of this study is to analyze how the prevalence of COPD varies across northeastern Germany on the smallest spatial-scale possible and to identify the location-specific population-based risk factors using health insurance claims of the AOK Nordost.   \n", "METHODS To visualize the spatial distribution of COPD prevalence at the level of municipalities and urban districts, we used the conditional autoregressive Besag-York-Molli\u00e9 (BYM) model.", "Geographically weighted regression modelling (GWR) was applied to analyze the location-specific ecological risk factors for COPD.   \n", "RESULTS The sex- and age-adjusted prevalence of COPD was 6.5% in 2012 and varied widely across northeastern Germany.", "Population-based risk factors consist of the proportions of insurants aged 65 and older, insurants with migration background, household size and area deprivation.", "The results of the GWR model revealed that the population at risk for COPD varies considerably across northeastern Germany.   \n", "CONCLUSION Area deprivation has a direct and an indirect influence on the prevalence of COPD.", "Persons ageing in socially disadvantaged areas have a higher chance of developing COPD, even when they are not necessarily directly affected by deprivation on an individual level.", "This underlines the importance of considering the impact of area deprivation on health for planning of healthcare.", "Additionally, our results reveal that in some parts of the study area, insurants with migration background and persons living in multi-persons households are at elevated risk of COPD."], "structured": true}
{"doc_id": 3583084, "title": "Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells", "abstract": ["The conversion of lineage-committed cells to induced pluripotent stem cells (iPSCs) by reprogramming is accompanied by a global remodeling of the epigenome, resulting in altered patterns of gene expression.", "Here we characterize the transcriptional reorganization of large intergenic non-coding RNAs (lincRNAs) that occurs upon derivation of human iPSCs and identify numerous lincRNAs whose expression is linked to pluripotency.", "Among these, we defined ten lincRNAs whose expression was elevated in iPSCs compared with embryonic stem cells, suggesting that their activation may promote the emergence of iPSCs.", "Supporting this, our results indicate that these lincRNAs are direct targets of key pluripotency transcription factors.", "Using loss-of-function and gain-of-function approaches, we found that one such lincRNA (lincRNA-RoR) modulates reprogramming, thus providing a first demonstration for critical functions of lincRNAs in the derivation of pluripotent stem cells."], "structured": false}
{"doc_id": 3588621, "title": "Extracellular vesicle isolation and characterization: toward clinical application.", "abstract": ["Two broad categories of extracellular vesicles (EVs), exosomes and shed microvesicles (sMVs), which differ in size distribution as well as protein and RNA profiles, have been described.", "EVs are known to play key roles in cell-cell communication, acting proximally as well as systemically.", "This Review discusses the nature of EV subtypes, strategies for isolating EVs from both cell-culture media and body fluids, and procedures for quantifying EVs.", "We also discuss proteins selectively enriched in exosomes and sMVs that have the potential for use as markers to discriminate between EV subtypes, as well as various applications of EVs in clinical diagnosis."], "structured": false}
{"doc_id": 3590806, "title": "Up-regulated NRIP2 in colorectal cancer initiating cells modulates the Wnt pathway by targeting ROR\u03b2", "abstract": ["BACKGROUND Colorectal cancer remains one of the most common malignant tumors worldwide.", "Colorectal cancer initiating cells (CCICs) are a small subpopulation responsible for malignant behaviors of colorectal cancer.", "Aberrant activation of the Wnt pathways regulates the self-renewal of CCIC.", "However, the underlying mechanism(s) remain poorly understood.   \n", "METHODS Via retroviral library screening, we identified Nuclear Receptor-Interacting Protein 2 (NRIP2) as a novel interactor of the Wnt pathway from enriched colorectal cancer colosphere cells.", "The expression levels of NRIP2 and retinoic acid-related orphan receptor \u03b2 (ROR\u03b2) were further examined by FISH, qRT-PCR, IHC and Western blot.", "NRIP2 overexpressed and knockdown colorectal cancer cells were produced to study the role of NRIP2 in Wnt pathway.", "We also verified the binding between NRIP2 and ROR\u03b2 and investigated the effect of ROR\u03b2 on CCICs both in vitro and in vivo.", "Genechip-scanning speculated downstream target HBP1.", "Western blot, ChIP and luciferase reporter were carried to investigate the interaction between NRIP2, ROR\u03b2, and HBP1.   \n", "RESULTS NRIP2 was significantly up-regulated in CCICs from both cell lines and primary colorectal cancer tissues.", "Reinforced expression of NRIP2 increased Wnt activity, while silencing of NRIP2 attenuated Wnt activity.", "The transcription factor ROR\u03b2 was a key target through which NRIP2 regulated Wnt pathway activity.", "ROR\u03b2 was a transcriptional enhancer of inhibitor HBP1 of the Wnt pathway.", "NRIP2 prevented ROR\u03b2 to bind with downstream HBP1 promoter regions and reduced the transcription of HBP1.", "This, in turn, attenuated the HBP1-dependent inhibition of TCF4-mediated transcription.   \n", "CONCLUSIONS NRIP2 is a novel interactor of the Wnt pathway in colorectal cancer initiating cells.", "interactions between NRIP2, ROR\u03b2, and HBP1 mediate a new mechanism for CCIC self-renewal via the Wnt activity."], "structured": true}
{"doc_id": 3591070, "title": "Speed Limits for Nonvesicular Intracellular Sterol Transport.", "abstract": ["Sterol transport between the endoplasmic reticulum (ER) and plasma membrane (PM) occurs by nonvesicular mechanisms requiring sterol transport proteins (STPs).", "Here we examine the idea that transport is enhanced at membrane contact sites where the ER is closely apposed to the PM.", "We conclude that sterol desorption from the membrane, rather than STP-mediated diffusion, is rate limiting in the cellular context, so there is no apparent kinetic benefit to having STP-mediated sterol transfer occur at contact sites.", "Contact sites may instead compartmentalize lipid synthesis or transport machinery, providing opportunities for regulation."], "structured": false}
{"doc_id": 3610080, "title": "Misunderstandings in prescribing decisions in general practice: qualitative study.", "abstract": ["OBJECTIVES To identify and describe misunderstandings between patients and doctors associated with prescribing decisions in general practice.   \n", "DESIGN Qualitative study.   \n", "SETTING 20 general practices in the West Midlands and south east England.   \n", "PARTICIPANTS 20 general practitioners and 35 consulting patients.   \n", "MAIN OUTCOME MEASURES Misunderstandings between patients and doctors that have potential or actual adverse consequences for taking medicine.   \n", "RESULTS 14 categories of misunderstanding were identified relating to patient information unknown to the doctor, doctor information unknown to the patient, conflicting information, disagreement about attribution of side effects, failure of communication about doctor's decision, and relationship factors.", "All the misunderstandings were associated with lack of patients' participation in the consultation in terms of the voicing of expectations and preferences or the voicing of responses to doctors' decisions and actions.", "They were all associated with potential or actual adverse outcomes such as non-adherence to treatment.", "Many were based on inaccurate guesses and assumptions.", "In particular doctors seemed unaware of the relevance of patients' ideas about medicines for successful prescribing.   \n", "CONCLUSIONS Patients' participation in the consultation and the adverse consequences of lack of participation are important.", "The authors are developing an educational intervention that builds on these findings."], "structured": true}
{"doc_id": 3610282, "title": "Phase-plate cryo-EM structure of a biased agonist-bound human GLP-1 receptor\u2013Gs complex", "abstract": ["The class B glucagon-like peptide-1 (GLP-1) G protein-coupled receptor is a major target for the treatment of type 2 diabetes and obesity.", "Endogenous and mimetic GLP-1 peptides exhibit biased agonism\u2014a difference in functional selectivity\u2014that may provide improved therapeutic outcomes.", "Here we describe the structure of the human GLP-1 receptor in complex with the G protein-biased peptide exendin-P5 and a G\u03b1s heterotrimer, determined at a global resolution of 3.3 \u00c5. At the extracellular surface, the organization of extracellular loop 3 and proximal transmembrane segments differs between our exendin-P5-bound structure and previous GLP-1-bound GLP-1 receptor structure.", "At the intracellular face, there was a six-degree difference in the angle of the G\u03b1s\u2013\u03b15 helix engagement between structures, which was propagated across the G protein heterotrimer.", "In addition, the structures differed in the rate and extent of conformational reorganization of the G\u03b1s protein.", "Our structure provides insights into the molecular basis of biased agonism."], "structured": false}
{"doc_id": 3613041, "title": "Therapeutic equivalence of alendronate 70 mg once-weekly and alendronate 10 mg daily in the treatment of osteoporosis. Alendronate Once-Weekly Study Group.", "abstract": ["Dosing convenience is a key element in the effective management of any chronic disease, and is particularly important in the long-term management of osteoporosis.", "Less frequent dosing with any medication may enhance compliance, thereby maximizing the effectiveness of therapy.", "Animal data support the rationale that once-weekly dosing with alendronate 70 mg (7 times the daily oral treatment dose) could provide similar efficacy to daily dosing with alendronate 10 mg due to its long duration of effect in bone.", "In addition, dog studies suggest that the potential for esophageal irritation, observed with daily oral bisphosphonates, may be substantially reduced with once-weekly dosing.", "This dosing regimen would provide patients with increased convenience and would be likely to enhance patient compliance.", "We compared the efficacy and safety of treatment with oral once-weekly alendronate 70 mg (N=519), twice-weekly alendronate 35 mg (N=369), and daily alendronate 10 mg (N=370) in a one-year, double-blind, multicenter study of postmenopausal women (ages 42 to 95) with osteoporosis (bone mineral density [BMD] of either lumbar spine or femoral neck at least 2.5 SDs below peak premenopausal mean, or prior vertebral or hip fracture).", "The primary efficacy endpoint was the comparability of increases in lumbar spine BMD, using strict pre-defined equivalence criteria.", "Secondary endpoints included changes in BMD at the hip and total body and rate of bone turnover, as assessed by biochemical markers.", "Both of the new regimens fully satisfied the equivalence criteria relative to daily therapy.", "Mean increases in lumbar spine BMD at 12 months were: 5.1% (95% CI 4.8, 5.4) in the 70 mg once-weekly group, 5.2% (4.9, 5.6) in the 35 mg twice-weekly group, and 5.4% (5.0, 5.8) in the 10 mg daily treatment group.", "Increases in BMD at the total hip, femoral neck, trochanter, and total body were similar for the three dosing regimens.", "All three treatment groups similarly reduced biochemical markers of bone resorption (urinary N-telopeptides of type I collagen) and bone formation (serum bone-specific alkaline phosphatase) into the middle of the premenopausal reference range.", "All treatment regimens were well tolerated with a similar incidence of upper GI adverse experiences.", "There were fewer serious upper GI adverse experiences and a trend toward a lower incidence of esophageal events in the once-weekly dosing group compared to the daily dosing group.", "These data are consistent with preclinical animal models, and suggest that once-weekly dosing has the potential for improved upper GI tolerability.", "Clinical fractures, captured as adverse experiences, were similar among the groups.", "We conclude that the alendronate 70 mg once-weekly dosing regimen will provide patients with a more convenient, therapeutically equivalent alternative to daily dosing, and may enhance compliance and long-term persistence with therapy."], "structured": false}
{"doc_id": 3616843, "title": "Association of Toll-Like Receptor 4 on Human Monocyte Subsets and Vulnerability Characteristics of Coronary Plaque as Assessed by 64-Slice Multidetector Computed Tomography.", "abstract": ["BACKGROUND Although Toll-like receptor 4 (TLR-4) is involved in monocyte activation in patients with accelerated forms of atherosclerosis, the relationship between the expression of TLR-4 on circulating monocytes and coronary plaque vulnerability has not previously been evaluated.", "We investigated this relationship using 64-slice multidetector computed tomography (MDCT) in patients with stable angina pectoris (SAP).Methods and Results:We enrolled 65 patients with SAP who underwent MDCT.", "Three monocyte subsets (CD14++CD16-, CD14++CD16+, and CD14+CD16+) and expression of TLR-4 were measured by flow cytometry.", "Intracoronary plaques were assessed by 64-slice MDCT.", "We defined vulnerability of intracoronary plaques according to the presence of positive remodeling (remodeling index >1.05) and/or low CT attenuation (<35 HU).", "The circulating CD14++CD16+monocytes more frequently expressed TLR-4 than CD14++CD16-and CD14+CD16+monocytes (P<0.001).", "The relative proportion of the expression of TLR-4 on CD14++CD16+monocytes was significantly greater in patients with vulnerable plaque compared with those without (10.4 [4.1-14.5] % vs. 4.5 [2.8-7.8] %, P=0.012).", "In addition, the relative proportion of TLR-4 expression on CD14++CD16+monocytes positively correlated with the remodeling index (r=0.28, P=0.025) and negatively correlated with CT attenuation value (r=-0.31, P=0.013).   \n", "CONCLUSIONS Upregulation of TLR-4 on CD14++CD16+monocytes might be associated with coronary plaque vulnerability in patients with SAP."], "structured": true}
{"doc_id": 3619372, "title": "Expandable Cardiovascular Progenitor Cells Reprogrammed from Fibroblasts.", "abstract": ["Stem cell-based approaches to cardiac regeneration are increasingly viable strategies for treating heart failure.", "Generating abundant and functional autologous cells for transplantation in such a setting, however, remains a significant challenge.", "Here, we isolated a cell population with extensive proliferation capacity and restricted cardiovascular differentiation potentials during cardiac transdifferentiation of mouse fibroblasts.", "These induced expandable cardiovascular progenitor cells (ieCPCs) proliferated extensively for more than 18 passages in chemically defined conditions, with 10(5) starting fibroblasts robustly producing 10(16) ieCPCs.", "ieCPCs expressed cardiac signature genes and readily differentiated into functional cardiomyocytes (CMs), endothelial cells (ECs), and smooth muscle cells (SMCs) in vitro, even after long-term expansion.", "When transplanted into mouse hearts following myocardial infarction, ieCPCs spontaneously differentiated into CMs, ECs, and SMCs and improved cardiac function for up to 12 weeks after transplantation.", "Thus, ieCPCs are a powerful system to study cardiovascular specification and provide strategies for regenerative medicine in the heart."], "structured": false}
{"doc_id": 3619931, "title": "Thyroid hormone inhibits lung fibrosis in mice by improving epithelial mitochondrial function", "abstract": ["Thyroid hormone (TH) is critical for the maintenance of cellular homeostasis during stress responses, but its role in lung fibrosis is unknown.", "Here we found that the activity and expression of iodothyronine deiodinase 2 (DIO2), an enzyme that activates TH, were higher in lungs from patients with idiopathic pulmonary fibrosis than in control individuals and were correlated with disease severity.", "We also found that Dio2-knockout mice exhibited enhanced bleomycin-induced lung fibrosis.", "Aerosolized TH delivery increased survival and resolved fibrosis in two models of pulmonary fibrosis in mice (intratracheal bleomycin and inducible TGF-\u03b21).", "Sobetirome, a TH mimetic, also blunted bleomycin-induced lung fibrosis.", "After bleomycin-induced injury, TH promoted mitochondrial biogenesis, improved mitochondrial bioenergetics and attenuated mitochondria-regulated apoptosis in alveolar epithelial cells both in vivo and in vitro.", "TH did not blunt fibrosis in Ppargc1a- or Pink1-knockout mice, suggesting dependence on these pathways.", "We conclude that the antifibrotic properties of TH are associated with protection of alveolar epithelial cells and restoration of mitochondrial function and that TH may thus represent a potential therapy for pulmonary fibrosis."], "structured": false}
{"doc_id": 3621011, "title": "Tenomodulin promotes human adipocyte differentiation and beneficial visceral adipose tissue expansion.", "abstract": ["Proper regulation of energy storage in adipose tissue is crucial for maintaining insulin sensitivity and molecules contributing to this process have not been fully revealed.", "Here we show that type II transmembrane protein tenomodulin (TNMD) is upregulated in adipose tissue of insulin-resistant versus insulin-sensitive individuals, who were matched for body mass index (BMI).", "TNMD expression increases in human preadipocytes during differentiation, whereas silencing TNMD blocks adipogenesis.", "Upon high-fat diet feeding, transgenic mice overexpressing Tnmd develop increased epididymal white adipose tissue (eWAT) mass, and preadipocytes derived from Tnmd transgenic mice display greater proliferation, consistent with elevated adipogenesis.", "In Tnmd transgenic mice, lipogenic genes are upregulated in eWAT, as is Ucp1 in brown fat, while liver triglyceride accumulation is attenuated.", "Despite expanded eWAT, transgenic animals display improved systemic insulin sensitivity, decreased collagen deposition and inflammation in eWAT, and increased insulin stimulation of Akt phosphorylation.", "Our data suggest that TNMD acts as a protective factor in visceral adipose tissue to alleviate insulin resistance in obesity."], "structured": false}
{"doc_id": 3623127, "title": "Evidence for a limit to human lifespan", "abstract": ["Driven by technological progress, human life expectancy has increased greatly since the nineteenth century.", "Demographic evidence has revealed an ongoing reduction in old-age mortality and a rise of the maximum age at death, which may gradually extend human longevity.", "Together with observations that lifespan in various animal species is flexible and can be increased by genetic or pharmaceutical intervention, these results have led to suggestions that longevity may not be subject to strict, species-specific genetic constraints.", "Here, by analysing global demographic data, we show that improvements in survival with age tend to decline after age 100, and that the age at death of the world\u2019s oldest person has not increased since the 1990s.", "Our results strongly suggest that the maximum lifespan of humans is fixed and subject to natural constraints."], "structured": false}
{"doc_id": 3654468, "title": "Effect of Oral Semaglutide Compared With Placebo and Subcutaneous Semaglutide on Glycemic Control in Patients With Type 2 Diabetes: A Randomized Clinical Trial", "abstract": ["Importance Glucagon-like peptide-1 (GLP-1) receptor agonists are effective therapies for the treatment of type 2 diabetes and are all currently available as an injection.", "Objectives To compare the effects of oral semaglutide with placebo (primary) and open-label subcutaneous semaglutide (secondary) on glycemic control in patients with type 2 diabetes.", "Design, Setting, and Patients Phase 2, randomized, parallel-group, dosage-finding, 26-week trial with 5-week follow-up at 100 sites (hospital clinics, general practices, and clinical research centers) in 14 countries conducted between December 2013 and December 2014.", "Of 1106 participants assessed, 632 with type 2 diabetes and insufficient glycemic control using diet and exercise alone or a stable dose of metformin were randomized.", "Randomization was stratified by metformin use.", "Interventions Once-daily oral semaglutide of 2.5 mg (n = 70), 5 mg (n = 70), 10 mg (n = 70), 20 mg (n = 70), 40-mg 4-week dose escalation (standard escalation; n = 71), 40-mg 8-week dose escalation (slow escalation; n = 70), 40-mg 2-week dose escalation (fast escalation, n = 70), oral placebo (n = 71; double-blind) or once-weekly subcutaneous semaglutide of 1.0 mg (n = 70) for 26 weeks.", "Main Outcomes and Measures The primary end point was change in hemoglobing A1c (HbA1c) from baseline to week 26.", "Secondary end points included change from baseline in body weight and adverse events.", "Results Baseline characteristics were comparable across treatment groups.", "Of the 632 randomized patients (mean age, 57.1 years [SD, 10.6]; men, 395 (62.7%); diabetes duration, 6.3 years [SD, 5.2]; body weight, 92.3 kg [SD, 16.8]; BMI, 31.7 [SD, 4.3]), 583 (92%) completed the trial.", "Mean change in HbA1c level from baseline to week 26 decreased with oral semaglutide (dosage-dependent range, \u22120.7% to \u22121.9%) and subcutaneous semaglutide (\u22121.9%) and placebo (\u22120.3%); oral semaglutide reductions were significant vs placebo (dosage-dependent estimated treatment difference [ETD] range for oral semaglutide vs placebo, \u20130.4% to \u20131.6%; P = .01 for 2.5 mg, <.001 for all other dosages).", "Reductions in body weight were greater with oral semaglutide (dosage-dependent range, \u22122.1 kg to \u22126.9 kg) and subcutaneous semaglutide (\u22126.4 kg) vs placebo (\u22121.2 kg), and significant for oral semaglutide dosages of 10 mg or more vs placebo (dosage-dependent ETD range, \u20130.9 to \u20135.7 kg; P < .001).", "Adverse events were reported by 63% to 86% (371 of 490 patients) in the oral semaglutide groups, 81% (56 of 69 patients) in the subcutaneous semaglutide group, and 68% (48 of 71 patients) in the placebo group; mild to moderate gastrointestinal events were most common.", "Conclusions and Relevance Among patients with type 2 diabetes, oral semaglutide resulted in better glycemic control than placebo over 26 weeks.", "These findings support phase 3 studies to assess longer-term and clinical outcomes, as well as safety.", "Trial Registration clinicaltrials.gov Identifier: NCT01923181"], "structured": false}
{"doc_id": 3662132, "title": "Fast and accurate short read alignment with Burrows\u2013Wheeler transform", "abstract": ["MOTIVATION The enormous amount of short reads generated by the new DNA sequencing technologies call for the development of fast and accurate read alignment programs.", "A first generation of hash table-based methods has been developed, including MAQ, which is accurate, feature rich and fast enough to align short reads from a single individual.", "However, MAQ does not support gapped alignment for single-end reads, which makes it unsuitable for alignment of longer reads where indels may occur frequently.", "The speed of MAQ is also a concern when the alignment is scaled up to the resequencing of hundreds of individuals.   \n", "RESULTS We implemented Burrows-Wheeler Alignment tool (BWA), a new read alignment package that is based on backward search with Burrows-Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps.", "BWA supports both base space reads, e.g. from Illumina sequencing machines, and color space reads from AB SOLiD machines.", "Evaluations on both simulated and real data suggest that BWA is approximately 10-20x faster than MAQ, while achieving similar accuracy.", "In addition, BWA outputs alignment in the new standard SAM (Sequence Alignment/Map) format.", "Variant calling and other downstream analyses after the alignment can be achieved with the open source SAMtools software package.   ", "AVAILABILITY http://maq.sourceforge.net."], "structured": true}
{"doc_id": 3662510, "title": "The financial cost of doctors emigrating from sub-Saharan Africa: human capital analysis", "abstract": ["OBJECTIVE To estimate the lost investment of domestically educated doctors migrating from sub-Saharan African countries to Australia, Canada, the United Kingdom, and the United States.   \n", "DESIGN Human capital cost analysis using publicly accessible data.   \n", "SETTINGS Sub-Saharan African countries.   \n", "PARTICIPANTS Nine sub-Saharan African countries with an HIV prevalence of 5% or greater or with more than one million people with HIV/AIDS and with at least one medical school (Ethiopia, Kenya, Malawi, Nigeria, South Africa, Tanzania, Uganda, Zambia, and Zimbabwe), and data available on the number of doctors practising in destination countries.   \n", "MAIN OUTCOME MEASURES The financial cost of educating a doctor (through primary, secondary, and medical school), assuming that migration occurred after graduation, using current country specific interest rates for savings converted to US dollars; cost according to the number of source country doctors currently working in the destination countries; and savings to destination countries of receiving trained doctors.   \n", "RESULTS In the nine source countries the estimated government subsidised cost of a doctor's education ranged from $21,000 (\u00a313,000; \u20ac15,000) in Uganda to $58,700 in South Africa.", "The overall estimated loss of returns from investment for all doctors currently working in the destination countries was $2.17bn (95% confidence interval 2.13bn to 2.21bn), with costs for each country ranging from $2.16m (1.55m to 2.78m) for Malawi to $1.41bn (1.38bn to 1.44bn) for South Africa.", "The ratio of the estimated compounded lost investment over gross domestic product showed that Zimbabwe and South Africa had the largest losses.", "The benefit to destination countries of recruiting trained doctors was largest for the United Kingdom ($2.7bn) and United States ($846m).   \n", "CONCLUSIONS Among sub-Saharan African countries most affected by HIV/AIDS, lost investment from the emigration of doctors is considerable.", "Destination countries should consider investing in measurable training for source countries and strengthening of their health systems."], "structured": true}
{"doc_id": 3669694, "title": "Chromatin modifying enzymes as modulators of reprogramming", "abstract": ["Generation of induced pluripotent stem cells (iPSCs) by somatic cell reprogramming involves global epigenetic remodelling.", "Whereas several proteins are known to regulate chromatin marks associated with the distinct epigenetic states of cells before and after reprogramming, the role of specific chromatin-modifying enzymes in reprogramming remains to be determined.", "To address how chromatin-modifying proteins influence reprogramming, we used short hairpin RNAs (shRNAs) to target genes in DNA and histone methylation pathways, and identified positive and negative modulators of iPSC generation.", "Whereas inhibition of the core components of the polycomb repressive complex 1 and 2, including the histone 3 lysine 27 methyltransferase EZH2, reduced reprogramming efficiency, suppression of SUV39H1, YY1 and DOT1L enhanced reprogramming.", "Specifically, inhibition of the H3K79 histone methyltransferase DOT1L by shRNA or a small molecule accelerated reprogramming, significantly increased the yield of iPSC colonies, and substituted for KLF4 and c-Myc (also known as MYC).", "Inhibition of DOT1L early in the reprogramming process is associated with a marked increase in two alternative factors, NANOG and LIN28, which play essential functional roles in the enhancement of reprogramming.", "Genome-wide analysis of H3K79me2 distribution revealed that fibroblast-specific genes associated with the epithelial to mesenchymal transition lose H3K79me2 in the initial phases of reprogramming.", "DOT1L inhibition facilitates the loss of this mark from genes that are fated to be repressed in the pluripotent state.", "These findings implicate specific chromatin-modifying enzymes as barriers to or facilitators of reprogramming, and demonstrate how modulation of chromatin-modifying enzymes can be exploited to more efficiently generate iPSCs with fewer exogenous transcription factors."], "structured": false}
{"doc_id": 3672261, "title": "Natural variation in the parameters of innate immune cells is preferentially driven by genetic factors", "abstract": ["The quantification and characterization of circulating immune cells provide key indicators of human health and disease.", "To identify the relative effects of environmental and genetic factors on variation in the parameters of innate and adaptive immune cells in homeostatic conditions, we combined standardized flow cytometry of blood leukocytes and genome-wide DNA genotyping of 1,000 healthy, unrelated people of Western European ancestry.", "We found that smoking, together with age, sex and latent infection with cytomegalovirus, were the main non-genetic factors that affected variation in parameters of human immune cells.", "Genome-wide association studies of 166 immunophenotypes identified 15 loci that showed enrichment for disease-associated variants.", "Finally, we demonstrated that the parameters of innate cells were more strongly controlled by genetic variation than were those of adaptive cells, which were driven by mainly environmental exposure.", "Our data establish a resource that will generate new hypotheses in immunology and highlight the role of innate immunity in susceptibility to common autoimmune diseases.", "Both environmental factors and genetic factors influence human immunity.", "Albert and colleagues leverage data from the Milieu Int\u00e9rieur Consortium to comprehensively describe the effects of lifestyle, environment and genetics on human innate and adaptive immunity."], "structured": false}
{"doc_id": 3680979, "title": "The transcriptional program, functional heterogeneity, and clinical targeting of mast cells", "abstract": ["Mast cells are unique tissue-resident immune cells that express an array of receptors that can be activated by several extracellular cues, including antigen-immunoglobulin E (IgE) complexes, bacteria, viruses, cytokines, hormones, peptides, and drugs.", "Mast cells constitute a small population in tissues, but their extraordinary ability to respond rapidly by releasing granule-stored and newly made mediators underpins their importance in health and disease.", "In this review, we document the biology of mast cells and introduce new concepts and opinions regarding their role in human diseases beyond IgE-mediated allergic responses and antiparasitic functions.", "We bring to light recent discoveries and developments in mast cell research, including regulation of mast cell functions, differentiation, survival, and novel mouse models.", "Finally, we highlight the current and future opportunities for therapeutic intervention of mast cell functions in inflammatory diseases."], "structured": false}
{"doc_id": 3684342, "title": "LIN28B enhanced tumorigenesis in an autochthonous KRASG12V-driven lung carcinoma mouse model", "abstract": ["LIN28B is a RNA-binding protein regulating predominantly let-7 microRNAs with essential functions in inflammation, wound healing, embryonic stem cells, and cancer.", "LIN28B expression is associated with tumor initiation, progression, resistance, and poor outcome in several solid cancers, including lung cancer.", "However, the functional role of LIN28B, especially in non-small cell lung adenocarcinomas, remains elusive.", "Here, we investigated the effects of LIN28B expression on lung tumorigenesis using LIN28B transgenic overexpression in an autochthonous KRASG12V-driven mouse model.", "We found that LIN28B overexpression significantly increased the number of CD44+/CD326+ tumor cells, upregulated VEGF-A and miR-21 and promoted tumor angiogenesis and epithelial-to-mesenchymal transition (EMT) accompanied by enhanced AKT phosphorylation and nuclear translocation of c-MYC.", "Moreover, LIN28B accelerated tumor initiation and enhanced proliferation which led to a shortened overall survival.", "In addition, we analyzed lung adenocarcinomas of the Cancer Genome Atlas (TCGA) and found LIN28B expression in 24% of KRAS-mutated cases, which underscore the relevance of our model."], "structured": false}
{"doc_id": 3690068, "title": "Cost-effectiveness comparison between topical silver sulfadiazine and enclosed silver dressing for partial-thickness burn treatment.", "abstract": ["The standard treatment of partial-thickness burns includes topical silver products such as silver sulfadiazine (SSD) cream and enclosed dressings including silver-impregnated foam (Mepilex Ag; Molnlycke Health Care, Gothenburg, Sweden) and silver-laden sheets (Aquacel Ag; ConvaTec, Skillman, NJ).", "The current state of health care is limited by resources, with an emphasis on evidence-based outcomes and cost-effective treatments.", "This study includes a decision analysis with an incremental cost-utility ratio comparing enclosed silver dressings with SSD in partial-thickness burn patients with TBSA less than 20%.", "A comprehensive literature review was conducted to identify clinically relevant health states in partial-thickness burn patients.", "These health states include successful healing, infection, and noninfected delayed healing requiring either surgery or conservative management.", "The probabilities of these health states were combined with Medicare CPT reimbursement codes (cost) and patient-derived utilities to fit into the decision model.", "Utilities were obtained using a visual analog scale during patient interviews.", "Expected cost and quality-adjusted life years (QALYs) were calculated using the roll-back method.", "The incremental cost-utility ratio for enclosed silver dressing relative to SSD was $40,167.99/QALY.", "One-way sensitivity analysis of complication rates confirmed robustness of the model.", "Assuming a maximum willingness to pay $50,000/QALY, the complication rate for SSD must be 22% or higher for enclosed silver dressing to be cost effective.", "By varying complication rates for SSD and enclosed silver dressings, the two-way sensitivity analysis demonstrated the cost effectiveness of using enclosed silver dressing at the majority of complication rates for both treatment modalities.", "Enclosed silver dressings are a cost-effective means of treating partial thickness burns."], "structured": false}
{"doc_id": 3692112, "title": "Randomized clinical study of Hydrofiber dressing with silver or silver sulfadiazine in the management of partial-thickness burns.", "abstract": ["This prospective, randomized study compared protocols of care using either AQUACEL Ag Hydrofiber (ConvaTec, a Bristol-Myers Squibb company, Skillman, NJ) dressing with silver (n = 42) or silver sulfadiazine (n = 42) for up to 21 days in the management of partial-thickness burns covering 5% to 40% body surface area (BSA).", "AQUACEL Ag dressing was associated with less pain and anxiety during dressing changes, less burning and stinging during wear, fewer dressing changes, less nursing time, and fewer procedural medications.", "Silver sulfadiazine was associated with greater flexibility and ease of movement.", "Adverse events, including infection, were comparable between treatment groups.", "The AQUACEL Ag dressing protocol tended to have lower total treatment costs (Dollars 1040 vs. Dollars 1180) and a greater rate of re-epithelialization (73.8% vs 60.0%), resulting in cost-effectiveness per burn healed of Dollars 1,409.06 for AQUACEL Ag dressing and Dollars 1,967.95 for silver sulfadiazine.", "A protocol of care with AQUACEL(R) Ag provided clinical and economic benefits compared with silver sulfadiazine in patients with partial-thickness burns."], "structured": false}
{"doc_id": 3698758, "title": "Hepatitis C virus and blood transfusion: past and present risks.", "abstract": ["The risk of HCV transmission by blood and blood products has been greatly reduced since the early 1980's.", "Selection of non-remunerated donors, donor selection to prevent HIV transmission, initial surrogate testing in some regions, and introduction of anti-HCV testing have all contributed to this.", "ALT surrogate testing has become obsolete since the introduction of anti-HCV testing.", "The residual risk of HCV transmission due to donations in the anti-HCV window period at present is about 1 in 100 000 transfusions of cellular products, and transmission of HCV by plasma products treated with modern inactivation methods such as solvent-detergent treatment, has not been reported.", "Hemovigilance programmes, which are presently being installed, will provide more data on the safety of blood transfusion.", "Introduction of HCV nucleic amplification technology (NAT) as a quality control of manufacturing pools for plasma products or as a form of blood donor screening by minipools is anticipated in many European countries for the coming year.", "Given industrial developments, NAT testing of individual blood donations may become available within the next 2 years.", "HCV NAT testing will further annihilate the residual risk, and the cost-effectiveness will become relatively low in comparison with other public health measures."], "structured": false}
{"doc_id": 3701541, "title": "p62/SQSTM1 by Binding to Vitamin D Receptor Inhibits Hepatic Stellate Cell Activity, Fibrosis, and Liver Cancer.", "abstract": ["Hepatic stellate cells (HSCs) play critical roles in liver fibrosis and hepatocellular carcinoma (HCC).", "Vitamin D receptor (VDR) activation in HSCs inhibits liver inflammation and fibrosis.", "We found that p62/SQSTM1, a protein upregulated in liver parenchymal cells but downregulated in HCC-associated HSCs, negatively controls HSC activation.", "Total body or HSC-specific p62 ablation potentiates HSCs and enhances inflammation, fibrosis, and HCC progression.", "p62 directly interacts with VDR and RXR promoting their heterodimerization, which is critical for VDR:RXR target gene recruitment.", "Loss of p62 in HSCs impairs the repression of fibrosis and inflammation by VDR agonists.", "This demonstrates that p62 is a negative regulator of liver inflammation and fibrosis through its ability to promote VDR signaling in HSCs, whose activation supports HCC."], "structured": false}
{"doc_id": 3707035, "title": "Developing criteria for evaluation of geroprotectors as a key stage toward translation to the clinic", "abstract": ["In the coming decades, a massive shift in the aging segment of the population will have major social and economic consequences around the world.", "One way to offset this increase is to expedite the development of geroprotectors, substances that slow aging, repair age-associated damage and extend healthy lifespan, or healthspan.", "While over 200 geroprotectors are now reported in model organisms and some are in human use for specific disease indications, the path toward determining whether they affect aging in humans remains obscure.", "Translation to the clinic is hampered by multiple issues including absence of a common set of criteria to define, select, and classify these substances, given the complexity of the aging process and their enormous diversity in mechanism of action.", "Translational research efforts would benefit from the formation of a scientific consensus on the following: the definition of 'geroprotector', the selection criteria for geroprotectors, a comprehensive classification system, and an analytical model.", "Here, we review current approaches to selection and put forth our own suggested selection criteria.", "Standardizing selection of geroprotectors will streamline discovery and analysis of new candidates, saving time and cost involved in translation to clinic."], "structured": false}
{"doc_id": 3710557, "title": "\u03b2-Catenin Signaling and Roles in Liver Homeostasis, Injury, and Tumorigenesis.", "abstract": ["\u03b2-catenin (encoded by CTNNB1) is a subunit of the cell surface cadherin protein complex that acts as an intracellular signal transducer in the WNT signaling pathway; alterations in its activity have been associated with the development of hepatocellular carcinoma and other liver diseases.", "Other than WNT, additional signaling pathways also can converge at \u03b2-catenin.", "\u03b2-catenin also interacts with transcription factors such as T-cell factor, forkhead box protein O, and hypoxia inducible factor 1\u03b1 to regulate the expression of target genes.", "We discuss the role of \u03b2-catenin in metabolic zonation of the adult liver.", "\u03b2-catenin also regulates the expression of genes that control metabolism of glucose, nutrients, and xenobiotics; alterations in its activity may contribute to the pathogenesis of nonalcoholic steatohepatitis.", "Alterations in \u03b2-catenin signaling may lead to activation of hepatic stellate cells, which is required for fibrosis.", "Many hepatic tumors such as hepatocellular adenomas, hepatocellular cancers, and hepatoblastomas have mutations in CTNNB1 that result in constitutive activation of \u03b2-catenin, so this molecule could be a therapeutic target.", "We discuss how alterations in \u03b2-catenin activity contribute to liver disease and how these might be used in diagnosis and prognosis, as well as in the development of therapeutics."], "structured": false}
{"doc_id": 3716075, "title": "The global burden of dengue: an analysis from the Global Burden of Disease Study 2013.", "abstract": ["BACKGROUND Dengue is the most common arbovirus infection globally, but its burden is poorly quantified.", "We estimated dengue mortality, incidence, and burden for the Global Burden of Disease Study 2013.   \n", "METHODS We modelled mortality from vital registration, verbal autopsy, and surveillance data using the Cause of Death Ensemble Modelling tool.", "We modelled incidence from officially reported cases, and adjusted our raw estimates for under-reporting based on published estimates of expansion factors.", "In total, we had 1780 country-years of mortality data from 130 countries, 1636 country-years of dengue case reports from 76 countries, and expansion factor estimates for 14 countries.   \n", "FINDINGS We estimated an average of 9221 dengue deaths per year between 1990 and 2013, increasing from a low of 8277 (95% uncertainty estimate 5353-10 649) in 1992, to a peak of 11 302 (6790-13 722) in 2010.", "This yielded a total of 576 900 (330 000-701 200) years of life lost to premature mortality attributable to dengue in 2013.", "The incidence of dengue increased greatly between 1990 and 2013, with the number of cases more than doubling every decade, from 8\u00b73 million (3\u00b73 million-17\u00b72 million) apparent cases in 1990, to 58\u00b74 million (23\u00b76 million-121\u00b79 million) apparent cases in 2013.", "When accounting for disability from moderate and severe acute dengue, and post-dengue chronic fatigue, 566 000 (186 000-1 415 000) years lived with disability were attributable to dengue in 2013.", "Considering fatal and non-fatal outcomes together, dengue was responsible for 1\u00b714 million (0\u00b773 million-1\u00b798 million) disability-adjusted life-years in 2013.   \n", "INTERPRETATION Although lower than other estimates, our results offer more evidence that the true symptomatic incidence of dengue probably falls within the commonly cited range of 50 million to 100 million cases per year.", "Our mortality estimates are lower than those presented elsewhere and should be considered in light of the totality of evidence suggesting that dengue mortality might, in fact, be substantially higher.   \n", "FUNDING Bill & Melinda Gates Foundation."], "structured": true}
{"doc_id": 3720107, "title": "Formin-mediated actin polymerization at cell\u2013cell junctions stabilizes E-cadherin and maintains monolayer integrity during wound repair", "abstract": ["Cadherin-mediated cell-cell adhesion is required for epithelial tissue integrity in homeostasis, during development, and in tissue repair.", "E-cadherin stability depends on F-actin, but the mechanisms regulating actin polymerization at cell-cell junctions remain poorly understood.", "Here we investigated a role for formin-mediated actin polymerization at cell-cell junctions.", "We identify mDia1 and Fmnl3 as major factors enhancing actin polymerization and stabilizing E-cadherin at epithelial junctions.", "Fmnl3 localizes to adherens junctions downstream of Src and Cdc42 and its depletion leads to a reduction in F-actin and E-cadherin at junctions and a weakening of cell-cell adhesion.", "Of importance, Fmnl3 expression is up-regulated and junctional localization increases during collective cell migration.", "Depletion of Fmnl3 or mDia1 in migrating monolayers results in dissociation of leader cells and impaired wound repair.", "In summary, our results show that formin activity at epithelial cell-cell junctions is important for adhesion and the maintenance of epithelial cohesion during dynamic processes, such as wound repair."], "structured": false}
{"doc_id": 3727986, "title": "A mechanically active heterotypic E-cadherin/N-cadherin adhesion enables fibroblasts to drive cancer cell invasion", "abstract": ["Cancer-associated fibroblasts (CAFs) promote tumour invasion and metastasis.", "We show that CAFs exert a physical force on cancer cells that enables their collective invasion.", "Force transmission is mediated by a heterophilic adhesion involving N-cadherin at the CAF membrane and E-cadherin at the cancer cell membrane.", "This adhesion is mechanically active; when subjected to force it triggers \u03b2-catenin recruitment and adhesion reinforcement dependent on \u03b1-catenin/vinculin interaction.", "Impairment of E-cadherin/N-cadherin adhesion abrogates the ability of CAFs to guide collective cell migration and blocks cancer cell invasion.", "N-cadherin also mediates repolarization of the CAFs away from the cancer cells.", "In parallel, nectins and afadin are recruited to the cancer cell/CAF interface and CAF repolarization is afadin dependent.", "Heterotypic junctions between CAFs and cancer cells are observed in patient-derived material.", "Together, our findings show that a mechanically active heterophilic adhesion between CAFs and cancer cells enables cooperative tumour invasion."], "structured": false}
{"doc_id": 3730196, "title": "Long non-coding RNA HOTTIP promotes BCL-2 expression and induces chemoresistance in small cell lung cancer by sponging miR-216a", "abstract": ["Despite progress in treatment of small cell lung cancer (SCLC), its multidrug chemoresistance and poor prognosis still remain.", "Recently, we globally assessed long non-coding RNAs (lncRNAs) for contributions to SCLC chemoresistance using microarray data, in vitro and in vivo assays.", "Here we reported that HOTTIP, encoding a lncRNA that is frequently amplified in SCLC, was associated with SCLC cell chemosensitivity, proliferation, and poor prognosis of SCLC patients.", "Moreover, mechanistic investigations showed that HOTTIP functioned as an oncogene in SCLC progression by binding miR-216a and abrogating its tumor-suppressive function in this setting.", "On the other hand, HOTTIP increased the expression of anti-apoptotic factor BCL-2, another important target gene of miR-216a, and jointly enhanced chemoresistance of SCLC by regulating BCL-2.", "Taken together, our study established a role for HOTTIP in SCLC progression and chemoresistance suggest its candidacy as a new diagnostic and prognostic biomarker for clinical management of SCLC."], "structured": false}
{"doc_id": 3743071, "title": "GSDS 2.0: an upgraded gene feature visualization server", "abstract": ["UNLABELLED : Visualizing genes' structure and annotated features helps biologists to investigate their function and evolution intuitively.", "The Gene Structure Display Server (GSDS) has been widely used by more than 60 000 users since its first publication in 2007.", "Here, we reported the upgraded GSDS 2.0 with a newly designed interface, supports for more types of annotation features and formats, as well as an integrated visual editor for editing the generated figure.", "Moreover, a user-specified phylogenetic tree can be added to facilitate further evolutionary analysis.", "The full source code is also available for downloading.   ", "AVAILABILITY AND IMPLEMENTATION Web server and source code are freely available at http://gsds.cbi.pku.edu.cn.   ", "CONTACT gaog@mail.cbi.pku.edu.cn or gsds@mail.cbi.pku.edu.cn   SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online."], "structured": false}
{"doc_id": 3748310, "title": "SLP-65 regulates immunoglobulin light chain gene recombination through the PI(3)K-PKB-Foxo pathway", "abstract": ["Although the essential role of the adaptor protein SLP-65 in pre-B cell differentiation is established, the molecular mechanism underlying its function is poorly understood.", "In this study, we uncover a link between SLP-65\u2013dependent signaling and the phosphoinositide-3-OH kinase (PI(3)K)\u2013protein kinase B (PKB)\u2013Foxo pathway.", "We show that the forkhead box transcription factor Foxo3a promotes light chain rearrangement in pre-B cells.", "Our data suggest that PKB suppresses light chain recombination by phosphorylating Foxo proteins, whereas reconstitution of SLP-65 function counteracts PKB activation and promotes Foxo3a and Foxo1 activity in pre-B cells.", "Together, these data illuminate a molecular function of SLP-65 and identify a key role for Foxo proteins in the regulation of light chain recombination, receptor editing and B cell selection."], "structured": false}
{"doc_id": 3752408, "title": "A case-mix classification system for explaining healthcare costs using administrative data in Italy.", "abstract": ["BACKGROUND The Italian National Health Service (NHS) provides universal coverage to all citizens, granting primary and hospital care with a copayment system for outpatient and drug services.", "Financing of Local Health Trusts (LHTs) is based on a capitation system adjusted only for age, gender and area of residence.", "We applied a risk-adjustment system (Johns Hopkins Adjusted Clinical Groups System, ACG\u00ae System) in order to explain health care costs using routinely collected administrative data in the Veneto Region (North-eastern Italy).   \n", "METHODS All residents in the Veneto Region were included in the study.", "The ACG system was applied to classify the regional population based on the following information sources for the year 2015: Hospital Discharges, Emergency Room visits, Chronic disease registry for copayment exemptions, ambulatory visits, medications, the Home care database, and drug prescriptions.", "Simple linear regressions were used to contrast an age-gender model to models incorporating more comprehensive risk measures aimed at predicting health care costs.   \n", "RESULTS A simple age-gender model explained only 8% of the variance of 2015 total costs.", "Adding diagnoses-related variables provided a 23% increase, while pharmacy based variables provided an additional 17% increase in explained variance.", "The adjusted R-squared of the comprehensive model was 6 times that of the simple age-gender model.   \n", "CONCLUSIONS ACG System provides substantial improvement in predicting health care costs when compared to simple age-gender adjustments.", "Aging itself is not the main determinant of the increase of health care costs, which is better explained by the accumulation of chronic conditions and the resulting multimorbidity."], "structured": true}
{"doc_id": 3756384, "title": "EpCAM-regulated intramembrane proteolysis induces a cancer stem cell-like gene signature in hepatitis B virus-infected hepatocytes.", "abstract": ["BACKGROUND & AIMS Hepatocytes in which the hepatitis B virus (HBV) is replicating exhibit loss of the chromatin modifying polycomb repressive complex 2 (PRC2), resulting in re-expression of specific, cellular PRC2-repressed genes.", "Epithelial cell adhesion molecule (EpCAM) is a PRC2-repressed gene, normally expressed in hepatic progenitors, but re-expressed in hepatic cancer stem cells (hCSCs).", "Herein, we investigated the functional significance of EpCAM re-expression in HBV-mediated hepatocarcinogenesis.   \n", "METHODS Employing molecular approaches (transfections, fluorescence-activated cell sorting, immunoblotting, qRT-PCR), we investigated the role of EpCAM-regulated intramembrane proteolysis (RIP) in HBV replicating cells in vitro, and in liver tumors from HBV X/c-myc mice and chronically HBV infected patients.   \n", "RESULTS EpCAM undergoes RIP in HBV replicating cells, activating canonical Wnt signaling.", "Transfection of Wnt-responsive plasmid expressing green fluorescent protein (GFP) identified a GFP + population of HBV replicating cells.", "These GFP+/Wnt+ cells exhibited cisplatin- and sorafenib-resistant growth resembling hCSCs, and increased expression of pluripotency genes NANOG, OCT4, SOX2, and hCSC markers BAMBI, CD44 and CD133.", "These genes are referred as EpCAM RIP and Wnt-induced hCSC-like gene signature.", "Interestingly, this gene signature is also overexpressed in liver tumors of X/c-myc bitransgenic mice.", "Clinically, a group of HBV-associated hepatocellular carcinomas was identified, exhibiting elevated expression of the hCSC-like gene signature and associated with reduced overall survival post-surgical resection.   \n", "CONCLUSIONS The hCSC-like gene signature offers promise as prognostic tool for classifying subtypes of HBV-induced HCCs.", "Since EpCAM RIP and Wnt signaling drive expression of this hCSC-like signature, inhibition of these pathways can be explored as therapeutic strategy for this subtype of HBV-associated HCCs.   ", "LAY SUMMARY In this study, we provide evidence for a molecular mechanism by which chronic infection by the hepatitis B virus results in the development of poor prognosis liver cancer.", "Based on this mechanism our results suggest possible therapeutic interventions."], "structured": true}
{"doc_id": 3758260, "title": "Parathyroid Hormone Directs Bone Marrow Mesenchymal Cell Fate.", "abstract": ["Intermittent PTH administration builds bone mass and prevents fractures, but its mechanism of action is unclear.", "We genetically deleted the PTH/PTHrP receptor (PTH1R) in mesenchymal stem cells using Prx1Cre and found low bone formation, increased bone resorption, and high bone marrow adipose tissue (BMAT).", "Bone marrow adipocytes traced to Prx1 and expressed classic adipogenic markers and high receptor activator of nuclear factor kappa B ligand (Rankl) expression.", "RANKL levels were also elevated in bone marrow supernatant and serum, but undetectable in other adipose depots.", "By cell sorting, Pref1+RANKL+ marrow progenitors were twice as great in mutant versus control marrow.", "Intermittent PTH administration to control mice reduced BMAT significantly.", "A similar finding was noted in male osteoporotic patients.", "Thus, marrow adipocytes exhibit osteogenic and adipogenic characteristics, are uniquely responsive to PTH, and secrete RANKL.", "These studies reveal an important mechanism for PTH's therapeutic action through its ability to direct mesenchymal cell fate."], "structured": false}
{"doc_id": 3761017, "title": "Metformin attenuates blood-brain barrier disruption in mice following middle cerebral artery occlusion", "abstract": ["BACKGROUND Metformin, a widely used hypoglycemic drug, reduces stroke incidence and alleviates chronic inflammation in clinical trials.", "However, the effect of metformin in ischemic stroke is unclear.", "Here, we investigated the effect of metformin on ischemic stroke in mice and further explored the possible underlying mechanisms.   \n", "METHODS Ninety-eight adult male CD-1 mice underwent 90-minute transient middle cerebral artery occlusion (tMCAO).", "Metformin (200 mg/kg) was administrated for up to 14 days.", "Neurobehavioral outcomes, brain infarct volume, inflammatory factors, blood-brain barrier (BBB) permeability and AMPK signaling pathways were evaluated following tMCAO.", "Oxygen glucose deprivation was performed on bEND.3 cells to explore the mechanisms of metformin in inhibiting inflammatory signaling pathways.   \n", "RESULTS Infarct volume was reduced in metformin-treated mice compared to the control group following tMCAO (P < 0.05).", "Neurobehavioral outcomes were greatly improved in metformin-treated mice (P < 0.05).", "MPO+ cells, Gr1+ cells, MPO activity and BBB permeability were decreased after metformin administration (P < 0.05).", "In addition, metformin activated AMPK phosphorylation, inhibited NF-\u03baB activation, down-regulated cytokine (IL-1\u03b2, IL-6, TNF-\u03b1) and ICAM-1 expression following tMCAO (P < 0.05).", "Furthermore, metformin activated AMPK signaling pathway and alleviated oxygen-glucose deprivation-induced ICAM-1 expression in bEND.3 cells (P < 0.05).", "Compound C, a selective AMPK inhibitor, eliminated this promotional effect.   \n", "CONCLUSIONS Metformin down-regulated ICAM-1 in an AMPK-dependent manner, which could effectively prevent ischemia-induced brain injury by alleviating neutrophil infiltration, suggesting that metformin is a promising therapeutic agent in stroke therapy."], "structured": true}
{"doc_id": 3765739, "title": "Epstein-Barr Virus nuclear antigen 1 (EBNA1) confers resistance to apoptosis in EBV-positive B-lymphoma cells through up-regulation of survivin.", "abstract": ["Resistance to apoptosis is an important component of the overall mechanism which drives the tumorigenic process.", "EBV is a ubiquitous human gamma-herpesvirus which preferentially establishes latent infection in viral infected B-lymphocytes.", "EBNA1 is typically expressed in most forms of EBV-positive malignancies and is important for replication of the latent episome in concert with replication of the host cells.", "Here, we investigate the effects of EBNA1 on survivin up-regulation in EBV-infected human B-lymphoma cells.", "We present evidence which demonstrates that EBNA1 forms a complex with Sp1 or Sp1-like proteins bound to their cis-element at the survivin promoter.", "This enhances the activity of the complex and up-regulates survivin.", "Knockdown of survivin and EBNA1 showed enhanced apoptosis in infected cells and thus supports a role for EBNA1 in suppressing apoptosis in EBV-infected cells.", "Here, we suggest that EBV encoded EBNA1 can contribute to the oncogenic process by up-regulating the apoptosis suppressor protein, survivin in EBV-associated B-lymphoma cells."], "structured": false}
{"doc_id": 3770726, "title": "Microfluidic platform to evaluate migration of cells from patients with DYT1 dystonia.", "abstract": ["BACKGROUND Microfluidic platforms for quantitative evaluation of cell biologic processes allow low cost and time efficient research studies of biological and pathological events, such as monitoring cell migration by real-time imaging.", "In healthy and disease states, cell migration is crucial in development and wound healing, as well as to maintain the body's homeostasis.   ", "NEW METHOD The microfluidic chambers allow precise measurements to investigate whether fibroblasts carrying a mutation in the TOR1A gene, underlying the hereditary neurologic disease--DYT1 dystonia, have decreased migration properties when compared to control cells.   \n", "RESULTS We observed that fibroblasts from DYT1 patients showed abnormalities in basic features of cell migration, such as reduced velocity and persistence of movement.   ", "COMPARISON WITH EXISTING METHOD The microfluidic method enabled us to demonstrate reduced polarization of the nucleus and abnormal orientation of nuclei and Golgi inside the moving DYT1 patient cells compared to control cells, as well as vectorial movement of single cells.   \n", "CONCLUSION We report here different assays useful in determining various parameters of cell migration in DYT1 patient cells as a consequence of the TOR1A gene mutation, including a microfluidic platform, which provides a means to evaluate real-time vectorial movement with single cell resolution in a three-dimensional environment."], "structured": true}
{"doc_id": 3770750, "title": "Sugar-sweetened beverages and weight gain in children and adults: a systematic review and meta-analysis.", "abstract": ["BACKGROUND The relation between sugar-sweetened beverages (SSBs) and body weight remains controversial.   \n", "OBJECTIVE We conducted a systematic review and meta-analysis to summarize the evidence in children and adults.   \n", "DESIGN We searched PubMed, EMBASE, and Cochrane databases through March 2013 for prospective cohort studies and randomized controlled trials (RCTs) that evaluated the SSB-weight relation.", "Separate meta-analyses were conducted in children and adults and for cohorts and RCTs by using random- and fixed-effects models.   \n", "RESULTS Thirty-two original articles were included in our meta-analyses: 20 in children (15 cohort studies, n = 25,745; 5 trials, n = 2772) and 12 in adults (7 cohort studies, n = 174,252; 5 trials, n = 292).", "In cohort studies, one daily serving increment of SSBs was associated with a 0.06 (95% CI: 0.02, 0.10) and 0.05 (95% CI: 0.03, 0.07)-unit increase in BMI in children and 0.22 kg (95% CI: 0.09, 0.34 kg) and 0.12 kg (95% CI: 0.10, 0.14 kg) weight gain in adults over 1 y in random- and fixed-effects models, respectively.", "RCTs in children showed reductions in BMI gain when SSBs were reduced [random and fixed effects: -0.17 (95% CI: -0.39, 0.05) and -0.12 (95% CI: -0.22, -0.2)], whereas RCTs in adults showed increases in body weight when SSBs were added (random and fixed effects: 0.85 kg; 95% CI: 0.50, 1.20 kg).", "Sensitivity analyses of RCTs in children showed more pronounced benefits in preventing weight gain in SSB substitution trials (compared with school-based educational programs) and among overweight children (compared with normal-weight children).   \n", "CONCLUSION Our systematic review and meta-analysis of prospective cohort studies and RCTs provides evidence that SSB consumption promotes weight gain in children and adults."], "structured": true}
{"doc_id": 3773719, "title": "The tumorigenic potential of pluripotent stem cells: What can we do to minimize it?", "abstract": ["Human pluripotent stem cells (hPSCs) have the potential to fundamentally change the way that we go about treating and understanding human disease.", "Despite this extraordinary potential, these cells also have an innate capability to form tumors in immunocompromised individuals when they are introduced in their pluripotent state.", "Although current therapeutic strategies involve transplantation of only differentiated hPSC derivatives, there is still a concern that transplanted cell populations could contain a small percentage of cells that are not fully differentiated.", "In addition, these cells have been frequently reported to acquire genetic alterations that, in some cases, are associated with certain types of human cancers.", "Here, we try to separate the panic from reality and rationally evaluate the true tumorigenic potential of these cells.", "We also discuss a recent study examining the effect of culture conditions on the genetic integrity of hPSCs.", "Finally, we present a set of sensible guidelines for minimizing the tumorigenic potential of hPSC-derived cells.", "\u00a9 2016 The Authors.", "Inside the Cell published by Wiley Periodicals, Inc."], "structured": false}
{"doc_id": 3776162, "title": "Epidemiology of sepsis and septic shock in critical care units: comparison between sepsis-2 and sepsis-3 populations using a national critical care database", "abstract": ["Background New sepsis and septic shock definitions could change the epidemiology of sepsis because of differences in criteria.", "We therefore compared the sepsis populations identified by the old and new definitions.   ", "Methods We used a high-quality, national, intensive care unit (ICU) database of 654 918 consecutive admissions to 189 adult ICUs in England, from January 2011 to December 2015.", "Primary outcome was acute hospital mortality.", "We compared old (Sepsis-2) and new (Sepsis-3) incidence, outcomes, trends in outcomes, and predictive validity of sepsis and septic shock populations.   ", "Results From among 197 724 Sepsis-2 severe sepsis and 197 142 Sepsis-3 sepsis cases, we identified 153 257 Sepsis-2 septic shock and 39 262 Sepsis-3 septic shock cases.", "The extrapolated population incidence of Sepsis-3 sepsis and Sepsis-3 septic shock was 101.8 and 19.3 per 100 000 person-years, respectively, in 2015.", "Sepsis-2 severe sepsis and Sepsis-3 sepsis had similar incidence, similar mortality and showed significant risk-adjusted improvements in mortality over time.", "Sepsis-3 septic shock had a much higher Acute Physiology And Chronic Health Evaluation II (APACHE II) score, greater mortality and no risk-adjusted trends in mortality improvement compared with Sepsis-2 septic shock.", "ICU admissions identified either as Sepsis-3 sepsis or septic shock and as Sepsis-2 severe sepsis or septic shock had significantly greater risk-adjusted odds of death compared with non-sepsis admissions (P<0.001).", "The predictive validity was greatest for Sepsis-3 septic shock.   ", "Conclusions In an ICU database, compared with Sepsis-2, Sepsis-3 identifies a similar sepsis population with 92% overlap and much smaller septic shock population with improved predictive validity."], "structured": false}
{"doc_id": 3788528, "title": "Thymic expression of the golli-myelin basic protein gene in the SJL/J mouse", "abstract": ["The T cell antigen-specific repertoire is thought to be shaped by thymic expression of self molecules.", "Since a myelin basic protein (MBP)-like gene (golli-MBP) has been reported to be expressed by cells of the immune system, the present study was undertaken to determine whether the golli-MBP gene was expressed in the mouse thymus and, if so, to characterize transcripts of this gene in this organ.", "Using exon-specific primers for MBP and golli-MBP, cDNA from thymus and other tissues was amplified, and the amplified products analyzed by Southern blotting with exon-specific oligonucleotide probes.", "The amplified products were subcloned, and the inserts characterized by DNA sequencing.", "The thymic transcripts were found to contain golli-MBP exons 1, 2, 3, 5A, 5B, 5C, 6, 7, 8, and 11."], "structured": false}
{"doc_id": 3790895, "title": "Urine microRNAs as biomarkers for bladder cancer: a diagnostic meta-analysis", "abstract": ["BACKGROUND The diagnostic value of microRNA (miRNA) detection in patients with bladder cancer (BCa) is controversial.", "We performed a diagnostic meta-analysis to evaluate current evidence on the use of miRNA assays to diagnose BCa.   \n", "METHODS We systematically searched PubMed, Embase, and Web of Science for studies published before March 31, 2015.", "The pooled sensitivity, specificity, positive and negative likelihood ratios, diagnostic odds ratio, and area under the curve (AUC) were calculated to evaluate the overall test performance.", "Subgroup analyses were used to explore the between-study heterogeneity.", "Deeks' funnel plot asymmetry test was used to test publication bias.", "We applied the software of RevMan 5.2 and Stata 11.0 to the meta-analysis.   \n", "RESULTS A total of 23 studies from nine articles were included in the meta-analysis, with a total of 719 patients and 494 controls.", "The pooled sensitivity and specificity were 0.75 (95% confidence interval [CI], 0.68-0.80) and 0.75 (95% CI, 0.70-0.80), respectively.", "The pooled positive likelihood ratio was 3.03 (95% CI, 2.50-3.67); negative likelihood ratio was 0.33 (95% CI, 0.27-0.42); and diagnostic odds ratio was 9.07 (95% CI, 6.35-12.95).", "The pooled AUC was 0.81 (95% CI, 0.78-0.85).", "Subgroup analyses indicated that the multiple miRNAs assays and urine supernatant assays showed high accuracies in diagnosing BCa.   \n", "CONCLUSION The miRNA assays may serve as potential noninvasive diagnostic tool for the detection of BCa.", "However, the clinical application of miRNA assays for BCa diagnosis still needs further validation by large prospective studies."], "structured": true}
{"doc_id": 3801693, "title": "Elevated Plasma Transforming Growth Factor &bgr;1 Levels Predict the Development of Hypertension in Normotensives: The 14-Year Follow-Up Study", "abstract": ["BACKGROUND Transforming growth factor \u03b21 (TGF-\u03b21) is a multifunctional cytokine.", "There is growing evidence that TGF-\u03b21 is involved in the pathogenesis of hypertension and the development of target organ damage in hypertensives.", "Although several studies have shown that TGF-\u03b21 induced vascular hypertrophy and remodelling in various vascular diseases, there are no longitudinal data on hypertension in the epidemiological studies.", "The present study tested the hypothesis whether elevated TGF-\u03b21 levels can predict the development of hypertension.   \n", "METHODS In 2002-2004, 528 subjects received health examinations in Uku town, southwestern Japan.", "We examined blood pressure (BP), body mass index, and blood test.", "Data on fasting plasma TGF-\u03b21 were obtained from 528 individuals.", "Of these, 149 normotensives (BP <140/90 mm Hg without antihypertensive medications) at baseline were followed-up for 14 years.   \n", "RESULTS The receiver-operating characteristic curve was used and the calculated cutoff value was 8.9 ng/ml.", "Of 149 normotensives at baseline, 59 subjects developed hypertension.", "Plasma TGF-\u03b21 levels were significantly associated with the development of hypertension after adjustment for confounding factors.", "To further examine the association between them, we performed logistic regression analysis.", "We divided the baseline plasma TGF-\u03b21 levels into 2 groups using a cutoff value.", "The significant high odds ratio [3.582 (95% confidence interval, 1.025-12.525)] for the development of hypertension was found in the highest group of TGF-\u03b21 level vs. the lowest group after adjustment for confounders.   \n", "CONCLUSIONS This is the first report demonstrating the causal relationship between them.", "Elevated plasma TGF-\u03b21 levels predicted the development of hypertension in normotensives in a population of community-dwelling Japanese."], "structured": true}
{"doc_id": 3805841, "title": "MYC Disrupts the Circadian Clock and Metabolism in Cancer Cells.", "abstract": ["The MYC oncogene encodes MYC, a transcription factor that binds the genome through sites termed E-boxes (5'-CACGTG-3'), which are identical to the binding sites of the heterodimeric CLOCK-BMAL1 master circadian transcription factor.", "Hence, we hypothesized that ectopic MYC expression perturbs the clock by deregulating E-box-driven components of the circadian network in cancer cells.", "We report here that deregulated expression of MYC or N-MYC disrupts the molecular clock in vitro by directly inducing REV-ERB\u03b1 to dampen expression and oscillation of BMAL1, and this could be rescued by knockdown of REV-ERB.", "REV-ERB\u03b1 expression predicts poor clinical outcome for N-MYC-driven human neuroblastomas that have diminished BMAL1 expression, and re-expression of ectopic BMAL1 in neuroblastoma cell lines suppresses their clonogenicity.", "Further, ectopic MYC profoundly alters oscillation of glucose metabolism and perturbs glutaminolysis.", "Our results demonstrate an unsuspected link between oncogenic transformation and circadian and metabolic dysrhythmia, which we surmise to be advantageous for cancer."], "structured": false}
{"doc_id": 3823862, "title": "Integrated maps in quail (Coturnix japonica) confirm the high degree of synteny conservation with chicken (Gallus gallus) despite 35 million years of divergence", "abstract": ["BackgroundBy comparing the quail genome with that of chicken, chromosome rearrangements that have occurred in these two galliform species over 35 million years of evolution can be detected.", "From a more practical point of view, the definition of conserved syntenies helps to predict the position of genes in quail, based on information taken from the chicken sequence, thus enhancing the utility of this species in biological studies through a better knowledge of its genome structure.", "A microsatellite and an Amplified Fragment Length Polymorphism (AFLP) genetic map were previously published for quail, as well as comparative cytogenetic data with chicken for macrochromosomes.", "Quail genomics will benefit from the extension and the integration of these maps.", "ResultsThe integrated linkage map presented here is based on segregation analysis of both anonymous markers and functional gene loci in 1,050 quail from three independent F2 populations.", "Ninety-two loci are resolved into 14 autosomal linkage groups and a Z chromosome-specific linkage group, aligned with the quail AFLP map.", "The size of linkage groups ranges from 7.8 cM to 274.8 cM. The total map distance covers 904.3 cM with an average spacing of 9.7 cM between loci.", "The coverage is not complete, as macrochromosome CJA08, the gonosome CJAW and 23 microchromosomes have no marker assigned yet.", "Significant sequence identities of quail markers with chicken enabled the alignment of the quail linkage groups on the chicken genome sequence assembly.", "This, together with interspecific Fluorescence In Situ Hybridization (FISH), revealed very high similarities in marker order between the two species for the eight macrochromosomes and the 14 microchromosomes studied.", "ConclusionIntegrating the two microsatellite and the AFLP quail genetic maps greatly enhances the quality of the resulting information and will thus facilitate the identification of Quantitative Trait Loci (QTL).", "The alignment with the chicken chromosomes confirms the high conservation of gene order that was expected between the two species for macrochromosomes.", "By extending the comparative study to the microchromosomes, we suggest that a wealth of information can be mined in chicken, to be used for genome analyses in quail."], "structured": false}
{"doc_id": 3825472, "title": "Cadherin activity is required for activity-induced spine remodeling", "abstract": ["Neural activity induces the remodeling of pre- and postsynaptic membranes, which maintain their apposition through cell adhesion molecules.", "Among them, N-cadherin is redistributed, undergoes activity-dependent conformational changes, and is required for synaptic plasticity.", "Here, we show that depolarization induces the enlargement of the width of spine head, and that cadherin activity is essential for this synaptic rearrangement.", "Dendritic spines visualized with green fluorescent protein in hippocampal neurons showed an expansion by the activation of AMPA receptor, so that the synaptic apposition zone may be expanded.", "N-cadherin-venus fusion protein laterally dispersed along the expanding spine head.", "Overexpression of dominant-negative forms of N-cadherin resulted in the abrogation of the spine expansion.", "Inhibition of actin polymerization with cytochalasin D abolished the spine expansion.", "Together, our data suggest that cadherin-based adhesion machinery coupled with the actin-cytoskeleton is critical for the remodeling of synaptic apposition zone."], "structured": false}
{"doc_id": 3825750, "title": "Aliskiren combined with losartan in type 2 diabetes and nephropathy.", "abstract": ["BACKGROUND Diabetic nephropathy is the leading cause of end-stage renal disease in developed countries.", "We evaluated the renoprotective effects of dual blockade of the renin-angiotensin-aldosterone system by adding treatment with aliskiren, an oral direct renin inhibitor, to treatment with the maximal recommended dose of losartan (100 mg daily) and optimal antihypertensive therapy in patients who had hypertension and type 2 diabetes with nephropathy.   \n", "METHODS We enrolled 599 patients in this multinational, randomized, double-blind study.", "After a 3-month, open-label, run-in period during which patients received 100 mg of losartan daily, patients were randomly assigned to receive 6 months of treatment with aliskiren (150 mg daily for 3 months, followed by an increase in dosage to 300 mg daily for another 3 months) or placebo, in addition to losartan.", "The primary outcome was a reduction in the ratio of albumin to creatinine, as measured in an early-morning urine sample, at 6 months.   \n", "RESULTS The baseline characteristics of the two groups were similar.", "Treatment with 300 mg of aliskiren daily, as compared with placebo, reduced the mean urinary albumin-to-creatinine ratio by 20% (95% confidence interval, 9 to 30; P<0.001), with a reduction of 50% or more in 24.7% of the patients who received aliskiren as compared with 12.5% of those who received placebo (P<0.001).", "A small difference in blood pressure was seen between the treatment groups by the end of the study period (systolic, 2 mm Hg lower [P=0.07] and diastolic, 1 mm Hg lower [P=0.08] in the aliskiren group).", "The total numbers of adverse and serious adverse events were similar in the groups.   \n", "CONCLUSIONS Aliskiren may have renoprotective effects that are independent of its blood-pressure-lowering effect in patients with hypertension, type 2 diabetes, and nephropathy who are receiving the recommended renoprotective treatment.", "(ClinicalTrials.gov number, NCT00097955 [ClinicalTrials.gov].)."], "structured": true}
{"doc_id": 3828508, "title": "Overweight in Celiac Disease: Prevalence, Clinical Characteristics, and Effect of a Gluten-Free Diet", "abstract": ["BACKGROUND:It is well established that a minority of celiac patients present with \u201cclassic\u201d symptoms due to malabsorption.", "However, few studies have focussed on the distribution of body mass index (BMI) in celiac populations and its relationship to clinical characteristics, or on its response to treatment.\n", "METHODS:We reviewed BMI measurements and other clinical and pathological characteristics from a database of 371 celiac patients diagnosed over a 10-yr period and seen by a single gastroenterologist.", "To assess response to gluten exclusion, we compared BMI at diagnosis and after 2 yr treatment in patients with serological support for dietary compliance.\n", "RESULTS:Mean BMI was 24.6 kg/m2 (range 16.3\u201343.5).", "Seventeen patients (5%) were underweight (BMI <18.5), 211 (57%) were normal, and 143 (39%) were overweight (BMI \u226525), including 48 (13% of all patients) in the obese range (BMI \u226530.0).", "There was a significant association between low BMI and female gender, history of diarrhea, reduced hemoglobin concentration, reduced bone mineral density (BMD), osteoporosis, and higher grades (subtotal/total) of villous atrophy.", "Of patients compliant with a gluten-free diet, 81% had gained weight after 2 yr, including 82% of initially overweight patients.\n", "CONCLUSIONS:Few celiac patients are underweight at diagnosis and a large minority is overweight; these are less likely to present with classical features of diarrhea and reduced hemoglobin.", "Failed or delayed diagnosis of celiac disease may reflect lack of awareness of this large subgroup.", "The increase in weight of already overweight patients after dietary gluten exclusion is a potential cause of morbidity, and the gluten-free diet as conventionally prescribed needs to be modified accordingly."], "structured": true}
{"doc_id": 3829232, "title": "Structural Studies of a Four-MBT Repeat Protein MBTD1", "abstract": ["BACKGROUND The Polycomb group (PcG) of proteins is a family of important developmental regulators.", "The respective members function as large protein complexes involved in establishment and maintenance of transcriptional repression of developmental control genes.", "MBTD1, Malignant Brain Tumor domain-containing protein 1, is one such PcG protein.", "MBTD1 contains four MBT repeats.   \n", "METHODOLOGY/PRINCIPAL FINDINGS We have determined the crystal structure of MBTD1 (residues 130-566aa covering the 4 MBT repeats) at 2.5 A resolution by X-ray crystallography.", "The crystal structure of MBTD1 reveals its similarity to another four-MBT-repeat protein L3MBTL2, which binds lower methylated lysine histones.", "Fluorescence polarization experiments confirmed that MBTD1 preferentially binds mono- and di-methyllysine histone peptides, like L3MBTL1 and L3MBTL2.", "All known MBT-peptide complex structures characterized to date do not exhibit strong histone peptide sequence selectivity, and use a \"cavity insertion recognition mode\" to recognize the methylated lysine with the deeply buried methyl-lysine forming extensive interactions with the protein while the peptide residues flanking methyl-lysine forming very few contacts [1].", "Nevertheless, our mutagenesis data based on L3MBTL1 suggested that the histone peptides could not bind to MBT repeats in any orientation.   \n", "CONCLUSIONS The four MBT repeats in MBTD1 exhibits an asymmetric rhomboid architecture.", "Like other MBT repeat proteins characterized so far, MBTD1 binds mono- or dimethylated lysine histones through one of its four MBT repeats utilizing a semi-aromatic cage.   ", "ENHANCED VERSION This article can also be viewed as an enhanced version in which the text of the article is integrated with interactive 3D representations and animated transitions.", "Please note that a web plugin is required to access this enhanced functionality.", "Instructions for the installation and use of the web plugin are available in Text S1."], "structured": true}
{"doc_id": 3831884, "title": "Glutamine supports pancreatic cancer growth through a Kras-regulated metabolic pathway", "abstract": ["Cancer cells have metabolic dependencies that distinguish them from their normal counterparts.", "Among these dependencies is an increased use of the amino acid glutamine to fuel anabolic processes.", "Indeed, the spectrum of glutamine-dependent tumours and the mechanisms whereby glutamine supports cancer metabolism remain areas of active investigation.", "Here we report the identification of a non-canonical pathway of glutamine use in human pancreatic ductal adenocarcinoma (PDAC) cells that is required for tumour growth.", "Whereas most cells use glutamate dehydrogenase (GLUD1) to convert glutamine-derived glutamate into \u03b1-ketoglutarate in the mitochondria to fuel the tricarboxylic acid cycle, PDAC relies on a distinct pathway in which glutamine-derived aspartate is transported into the cytoplasm where it can be converted into oxaloacetate by aspartate transaminase (GOT1).", "Subsequently, this oxaloacetate is converted into malate and then pyruvate, ostensibly increasing the NADPH/NADP(+) ratio which can potentially maintain the cellular redox state.", "Importantly, PDAC cells are strongly dependent on this series of reactions, as glutamine deprivation or genetic inhibition of any enzyme in this pathway leads to an increase in reactive oxygen species and a reduction in reduced glutathione.", "Moreover, knockdown of any component enzyme in this series of reactions also results in a pronounced suppression of PDAC growth in vitro and in vivo.", "Furthermore, we establish that the reprogramming of glutamine metabolism is mediated by oncogenic KRAS, the signature genetic alteration in PDAC, through the transcriptional upregulation and repression of key metabolic enzymes in this pathway.", "The essentiality of this pathway in PDAC and the fact that it is dispensable in normal cells may provide novel therapeutic approaches to treat these refractory tumours."], "structured": false}
{"doc_id": 3835423, "title": "CD4+ T cell help guides formation of CD103+ lung-resident memory CD8+ T cells during influenza viral infection.", "abstract": ["Tissue-resident memory T (Trm) cells provide enhanced protection against infection at mucosal sites.", "Here we found that CD4(+) T cells are important for the formation of functional lung-resident CD8(+) T cells after influenza virus infection.", "In the absence of CD4(+) T cells, CD8(+) T cells displayed reduced expression of CD103 (Itgae), were mislocalized away from airway epithelia, and demonstrated an impaired ability to recruit CD8(+) T cells to the lung airways upon heterosubtypic challenge.", "CD4(+) T cell-derived interferon-\u03b3 was necessary for generating lung-resident CD103(+) CD8(+) Trm cells.", "Furthermore, expression of the transcription factor T-bet was increased in \"unhelped\" lung Trm cells, and a reduction in T-bet rescued CD103 expression in the absence of CD4(+) T cell help.", "Thus, CD4(+) T cell-dependent signals are important to limit expression of T-bet and allow for the development of CD103(+) CD8(+) Trm cells in the lung airways following respiratory infection."], "structured": false}
{"doc_id": 3840043, "title": "Inhibition of Apoptosis Overcomes Stage-Related Compatibility Barriers to Chimera Formation in Mouse Embryos.", "abstract": ["Cell types more advanced in development than embryonic stem cells, such as EpiSCs, fail to contribute to chimeras when injected into pre-implantation-stage blastocysts, apparently because the injected cells undergo apoptosis.", "Here we show that transient promotion of cell survival through expression of the anti-apoptotic gene BCL2 enables EpiSCs and Sox17+ endoderm progenitors to integrate into blastocysts and contribute to chimeric embryos.", "Upon injection into blastocyst, BCL2-expressing EpiSCs contributed to all bodily tissues in chimeric animals while Sox17+ endoderm progenitors specifically contributed in a region-specific fashion to endodermal tissues.", "In addition, BCL2 expression enabled rat EpiSCs to contribute to mouse embryonic chimeras, thereby forming interspecies chimeras that could survive to adulthood.", "Our system therefore provides a method to overcome cellular compatibility issues that typically restrict chimera formation.", "Application of this type of approach could broaden the use of embryonic chimeras, including region-specific chimeras, for basic developmental biology research and regenerative medicine."], "structured": false}
{"doc_id": 3845894, "title": "Computational and Statistical Analyses of Amino Acid Usage and Physico-Chemical Properties of the Twelve Late Embryogenesis Abundant Protein Classes", "abstract": ["Late Embryogenesis Abundant Proteins (LEAPs) are ubiquitous proteins expected to play major roles in desiccation tolerance.", "Little is known about their structure - function relationships because of the scarcity of 3-D structures for LEAPs.", "The previous building of LEAPdb, a database dedicated to LEAPs from plants and other organisms, led to the classification of 710 LEAPs into 12 non-overlapping classes with distinct properties.", "Using this resource, numerous physico-chemical properties of LEAPs and amino acid usage by LEAPs have been computed and statistically analyzed, revealing distinctive features for each class.", "This unprecedented analysis allowed a rigorous characterization of the 12 LEAP classes, which differed also in multiple structural and physico-chemical features.", "Although most LEAPs can be predicted as intrinsically disordered proteins, the analysis indicates that LEAP class 7 (PF03168) and probably LEAP class 11 (PF04927) are natively folded proteins.", "This study thus provides a detailed description of the structural properties of this protein family opening the path toward further LEAP structure - function analysis.", "Finally, since each LEAP class can be clearly characterized by a unique set of physico-chemical properties, this will allow development of software to predict proteins as LEAPs."], "structured": false}
{"doc_id": 3847200, "title": "Direct Reprogramming of Hepatic Myofibroblasts into Hepatocytes In Vivo Attenuates Liver Fibrosis.", "abstract": ["Direct induction of induced hepatocytes (iHeps) from fibroblasts holds potential as a strategy for regenerative medicine but until now has only been shown in culture settings.", "Here, we describe in vivo iHep formation using transcription factor induction and genetic fate tracing in mouse models of chronic liver disease.", "We show that ectopic expression of the transcription factors FOXA3, GATA4, HNF1A, and HNF4A from a polycistronic lentiviral vector converts mouse myofibroblasts into cells with a hepatocyte phenotype.", "In vivo expression of the same set of transcription factors from a p75 neurotrophin receptor peptide (p75NTRp)-tagged adenovirus enabled the generation of hepatocyte-like cells from myofibroblasts in fibrotic mouse livers and reduced liver fibrosis.", "We have therefore been able to convert pro-fibrogenic myofibroblasts in the liver into hepatocyte-like cells with positive functional benefits.", "This direct in vivo reprogramming approach may open new avenues for the treatment of chronic liver disease."], "structured": false}
{"doc_id": 3848469, "title": "Epithelial to Mesenchymal Transition by TGF\u03b2-1 Induction Increases Stemness Characteristics in Primary Non Small Cell Lung Cancer Cell Line", "abstract": ["BACKGROUND Cancer Stem Cells (CSCs) hypothesis asserts that only a small subset of cells within a tumour is capable of both tumour initiation and sustainment.", "The Epithelial-Mesenchymal Transition (EMT) is an embryonic developmental program that is often activated during cancer invasion and metastasis.", "The aim of this study is to shed light on the relationship between EMT and CSCs by using LC31 lung cancer primary cell line.   ", "MATERIALS AND METHODS A549 and LC31 cell lines were treated with 2 ng/ml TGF\u03b2-1 for 30 days, and 80 days, respectively.", "To evaluate EMT, morphological changes were assessed by light microscopy, immunofluorescence and cytometry for following markers: cytokeratins, e-cadherin, CD326 (epithelial markers) and CD90, and vimentin (mesenchymal markers).", "Moreover, RT-PCR for Slug, Twist and \u03b2-catenin genes were performed.", "On TGF\u03b2-1 treated and untreated LC31 cell lines, we performed stemness tests such as pneumospheres growth and stem markers expression such as Oct4, Nanog, Sox2, c-kit and CD133.", "Western Blot for CD133 and tumorigenicity assays using NOD/SCID mice were performed.   \n", "RESULTS TGF\u03b2-1 treated LC31 cell line lost its epithelial morphology assuming a fibroblast-like appearance.", "The same results were obtained for the A549 cell line (as control).", "Immunofluorescence and cytometry showed up-regulation of vimentin and CD90 and down-regulation of cytocheratin, e-cadherin and CD326 in TGF\u03b2-1 treated LC31 and A549 cell lines.", "Slug, Twist and \u03b2-catenin m-RNA transcripts were up-regulated in TGF\u03b2-1 treated LC31 cell line confirming EMT.", "This cell line showed also over-expression of Oct4, Nanog, Sox2 and CD133, all genes of stemness.", "In addition, in TGF\u03b2-1 treated LC31 cell line, an increased pneumosphere-forming capacity and tumours-forming ability in NOD/SCID mice were detectable.   \n", "CONCLUSIONS The induction of EMT by TGF\u03b2-1 exposure, in primary lung cancer cell line results in the acquisition of mesenchymal profile and in the expression of stem cell markers."], "structured": true}
{"doc_id": 3849194, "title": "Dnmt3a and Dnmt3b Associate with Enhancers to Regulate Human Epidermal Stem Cell Homeostasis.", "abstract": ["The genome-wide localization and function of endogenous Dnmt3a and Dnmt3b in adult stem cells are unknown.", "Here, we show that in human epidermal stem cells, the two proteins bind in a histone H3K36me3-dependent manner to the most active enhancers and are required to produce their associated enhancer RNAs.", "Both proteins prefer super-enhancers associated to genes that either define the ectodermal lineage or establish the stem cell and differentiated states.", "However, Dnmt3a and Dnmt3b differ in their mechanisms of enhancer regulation: Dnmt3a associates with p63 to maintain high levels of DNA hydroxymethylation at the center of enhancers in a Tet2-dependent manner, whereas Dnmt3b promotes DNA methylation along the body of the enhancer.", "Depletion of either protein inactivates their target enhancers and profoundly affects epidermal stem cell function.", "Altogether, we reveal novel functions for Dnmt3a and Dnmt3b at enhancers that could contribute to their roles in disease and tumorigenesis."], "structured": false}
{"doc_id": 3851329, "title": "CDK inhibitors in cancer therapy: what is next?", "abstract": ["The pursuit for drugs that inhibit cyclin-dependent kinases (CDKs) has been an intense area of research for more than 15 years.", "The first-generation inhibitors, Flavopiridol and CY-202, are in late-stage clinical trials, but so far have demonstrated only modest activity.", "Several second-generation inhibitors are now in clinical trials.", "Future approaches to determine clinical benefit need to incorporate both the lessons learned from these early compounds and information recently obtained from the genetic analysis of CDKs in preclinical models.", "Here we discuss key concepts that should be considered when validating the clinical utility of CDK inhibitors in cancer therapy."], "structured": false}
{"doc_id": 3858268, "title": "Lipid Desaturation Is a Metabolic Marker and Therapeutic Target of Ovarian Cancer Stem Cells.", "abstract": ["Lack of sensitive single-cell analysis tools has limited the characterization of metabolic activity in cancer stem cells.", "By hyperspectral-stimulated Raman scattering imaging of single living cells and mass spectrometry analysis of extracted lipids, we report here significantly increased levels of unsaturated lipids in ovarian cancer stem cells (CSCs) as compared to non-CSCs.", "Higher lipid unsaturation levels were also detected in CSC-enriched spheroids compared to monolayer cultures of ovarian cancer cell lines or primary cells.", "Inhibition of lipid desaturases effectively eliminated CSCs, suppressed sphere formation in vitro, and blocked tumor initiation capacity in vivo.", "Mechanistically, we demonstrate that nuclear factor \u03baB (NF-\u03baB) directly regulates the expression levels of lipid desaturases, and inhibition of desaturases blocks NF-\u03baB signaling.", "Collectively, our findings reveal that increased lipid unsaturation is a metabolic marker for ovarian CSCs and a target for CSC-specific therapy."], "structured": false}
{"doc_id": 3863543, "title": "Mesenchymal Inflammation Drives Genotoxic Stress in Hematopoietic Stem Cells and Predicts Disease Evolution in Human Pre-leukemia.", "abstract": ["Mesenchymal niche cells may drive tissue failure and malignant transformation in the hematopoietic system, but the underlying molecular mechanisms and relevance to human disease remain poorly defined.", "Here, we show that perturbation of mesenchymal cells in a mouse model of the pre-leukemic disorder Shwachman-Diamond syndrome (SDS) induces mitochondrial dysfunction, oxidative stress, and activation of DNA damage responses in hematopoietic stem and progenitor cells.", "Massive parallel RNA sequencing of highly purified mesenchymal cells in the SDS mouse model and a range of human pre-leukemic syndromes identified p53-S100A8/9-TLR inflammatory signaling as a common driving mechanism of genotoxic stress.", "Transcriptional activation of this signaling axis in the mesenchymal niche predicted leukemic evolution and progression-free survival in myelodysplastic syndrome (MDS), the principal leukemia predisposition syndrome.", "Collectively, our findings identify mesenchymal niche-induced genotoxic stress in heterotypic stem and progenitor cells through inflammatory signaling as a targetable determinant of disease outcome in human pre-leukemia."], "structured": false}
{"doc_id": 3866315, "title": "Novel Functional Sets of Lipid-Derived Mediators with Antiinflammatory Actions Generated from Omega-3 Fatty Acids via Cyclooxygenase 2\u2013Nonsteroidal Antiinflammatory Drugs and Transcellular Processing", "abstract": ["Aspirin therapy inhibits prostaglandin biosynthesis without directly acting on lipoxygenases, yet via acetylation of cyclooxygenase 2 (COX-2) it leads to bioactive lipoxins (LXs) epimeric at carbon 15 (15-epi-LX, also termed aspirin-triggered LX [ATL]).", "Here, we report that inflammatory exudates from mice treated with \u03c9-3 polyunsaturated fatty acid and aspirin (ASA) generate a novel array of bioactive lipid signals.", "Human endothelial cells with upregulated COX-2 treated with ASA converted C20:5 \u03c9-3 to 18R-hydroxyeicosapentaenoic acid (HEPE) and 15R-HEPE.", "Each was used by polymorphonuclear leukocytes to generate separate classes of novel trihydroxy-containing mediators, including 5-series 15R-LX5 and 5,12,18R-triHEPE.", "These new compounds proved to be potent inhibitors of human polymorphonuclear leukocyte transendothelial migration and infiltration in vivo (ATL analogue > 5,12,18R-triHEPE > 18R-HEPE).", "Acetaminophen and indomethacin also permitted 18R-HEPE and 15R-HEPE generation with recombinant COX-2 as well as \u03c9-5 and \u03c9-9 oxygenations of other fatty acids that act on hematologic cells.", "These findings establish new transcellular routes for producing arrays of bioactive lipid mediators via COX-2\u2013nonsteroidal antiinflammatory drug\u2013dependent oxygenations and cell\u2013cell interactions that impact microinflammation.", "The generation of these and related compounds provides a novel mechanism(s) for the therapeutic benefits of \u03c9-3 dietary supplementation, which may be important in inflammation, neoplasia, and vascular diseases."], "structured": false}
{"doc_id": 3868322, "title": "Cholesteryl Ester Transfer Protein (CETP) Polymorphisms Affect mRNA Splicing, HDL Levels, and Sex-Dependent Cardiovascular Risk", "abstract": ["Polymorphisms in and around the Cholesteryl Ester Transfer Protein (CETP) gene have been associated with HDL levels, risk for coronary artery disease (CAD), and response to therapy.", "The mechanism of action of these polymorphisms has yet to be defined.", "We used mRNA allelic expression and splice isoform measurements in human liver tissues to identify the genetic variants affecting CETP levels.", "Allelic CETP mRNA expression ratios in 56 human livers were strongly associated with several variants 2.5-7 kb upstream of the transcription start site (e.g., rs247616 p = 6.4 \u00d7 10(-5), allele frequency 33%).", "In addition, a common alternatively spliced CETP isoform lacking exon 9 (\u03949), has been shown to prevent CETP secretion in a dominant-negative manner.", "The \u0394 9 expression ranged from 10 to 48% of total CETP mRNA in 94 livers.", "Increased formation of this isoform was exclusively associated with an exon 9 polymorphism rs5883-C>T (p = 6.8 \u00d7 10(-10)) and intron 8 polymorphism rs9930761-T>C (5.6 \u00d7 10(-8)) (in high linkage disequilibrium with allele frequencies 6-7%).", "rs9930761 changes a key splicing branch point nucleotide in intron 8, while rs5883 alters an exonic splicing enhancer sequence in exon 9.The effect of these polymorphisms was evaluated in two clinical studies.", "In the Whitehall II study of 4745 subjects, both rs247616 and rs5883T/rs9930761C were independently associated with increased HDL-C levels in males with similar effect size (rs247616 p = 9.6 \u00d7 10(-28) and rs5883 p = 8.6 \u00d7 10(-10), adjusted for rs247616).", "In an independent multiethnic US cohort of hypertensive subjects with CAD (INVEST-GENE), rs5883T/rs9930761C alone were significantly associated with increased incidence of MI, stroke, and all-cause mortality in males (rs5883: OR 2.36 (CI 1.29-4.30), p = 0.005, n = 866).", "These variants did not reach significance in females in either study.", "Similar to earlier results linking low CETP activity with poor outcomes in males, our results suggest genetic, sex-dependent CETP splicing effects on cardiovascular risk by a mechanism independent of circulating HDL-C levels."], "structured": false}
{"doc_id": 3870062, "title": "6-Sulphated Chondroitins Have a Positive Influence on Axonal Regeneration", "abstract": ["Chondroitin sulphate proteoglycans (CSPGs) upregulated in the glial scar inhibit axon regeneration via their sulphated glycosaminoglycans (GAGs).", "Chondroitin 6-sulphotransferase-1 (C6ST-1) is upregulated after injury leading to an increase in 6-sulphated GAG.", "In this study, we ask if this increase in 6-sulphated GAG is responsible for the increased inhibition within the glial scar, or whether it represents a partial reversion to the permissive embryonic state dominated by 6-sulphated glycosaminoglycans (GAGs).", "Using C6ST-1 knockout mice (KO), we studied post-injury changes in chondroitin sulphotransferase (CSST) expression and the effect of chondroitin 6-sulphates on both central and peripheral axon regeneration.", "After CNS injury, wild-type animals (WT) showed an increase in mRNA for C6ST-1, C6ST-2 and C4ST-1, but KO did not upregulate any CSSTs.", "After PNS injury, while WT upregulated C6ST-1, KO showed an upregulation of C6ST-2.", "We examined regeneration of nigrostriatal axons, which demonstrate mild spontaneous axon regeneration in the WT.", "KO showed many fewer regenerating axons and more axonal retraction than WT.", "However, in the PNS, repair of the median and ulnar nerves led to similar and normal levels of axon regeneration in both WT and KO.", "Functional tests on plasticity after the repair also showed no evidence of enhanced plasticity in the KO.", "Our results suggest that the upregulation of 6-sulphated GAG after injury makes the extracellular matrix more permissive for axon regeneration, and that the balance of different CSs in the microenvironment around the lesion site is an important factor in determining the outcome of nervous system injury."], "structured": false}
{"doc_id": 3874000, "title": "Tissue Mechanics Orchestrate Wnt-Dependent Human Embryonic Stem Cell Differentiation.", "abstract": ["Regenerative medicine is predicated on understanding the mechanisms regulating development and applying these conditions to direct stem cell fate.", "Embryogenesis is guided by cell-cell and cell-matrix interactions, but it is unclear how these physical cues influence stem cells in culture.", "We used human embryonic stem cells (hESCs) to examine whether mechanical features of the extracellular microenvironment could differentially modulate mesoderm specification.", "We found that, on a hydrogel-based compliant matrix, hESCs accumulate \u03b2-catenin at cell-cell adhesions and show enhanced Wnt-dependent mesoderm differentiation.", "Mechanistically, Src-driven ubiquitination of E-cadherin by Cbl-like ubiquitin ligase releases P120-catenin to facilitate transcriptional activity of \u03b2-catenin, which initiates and reinforces mesoderm differentiation.", "By contrast, on a stiff hydrogel matrix, hESCs show elevated integrin-dependent GSK3 and Src activity that promotes \u03b2-catenin degradation and inhibits differentiation.", "Thus, we found that mechanical features of the microenvironmental matrix influence tissue-specific differentiation of hESCs by altering the cellular response to morphogens."], "structured": false}
{"doc_id": 3878434, "title": "Predictive performance of the quick Sequential Organ Failure Assessment score as a screening tool for sepsis, mortality, and intensive care unit admission in patients with febrile neutropenia", "abstract": ["In Sepsis-3, the quick Sequential Organ Failure Assessment (qSOFA) score was developed as criteria to use for recognizing patients who may have poor outcomes.", "This study was performed to evaluate the predictive performance of the qSOFA score as a screening tool for sepsis, mortality, and intensive care unit (ICU) admission in patients with febrile neutropenia (FN).", "We also tried to compare its performance with that of the systemic inflammatory response syndrome (SIRS) criteria and Multinational Association of Supportive Care in Cancer (MASCC) score for FN.", "We used a prospectively collected adult FN data registry.", "The qSOFA and SIRS scores were calculated retrospectively using the preexisting data.", "The primary outcome was the development of sepsis.", "The secondary outcomes were ICU admission and 28-day mortality.", "Of the 615 patients, 100 developed sepsis, 20 died, and 38 were admitted to ICUs.", "In multivariate analysis, qSOFA was an independent factor predicting sepsis and ICU admission.", "However, compared to the MASCC score, the area under the receiver operating curve of qSOFA was lower.", "qSOFA showed a low sensitivity (0.14, 0.2, and 0.23) but high specificity (0.98, 0.97, and 0.97) in predicting sepsis, 28-day mortality, and ICU admission.", "Performance of the qSOFA score was inferior to that of the MASCC score.", "The preexisting risk stratification tool is more useful for predicting outcomes in patients with FN."], "structured": false}
{"doc_id": 3882374, "title": "LIN28 Regulates Stem Cell Metabolism and Conversion to Primed Pluripotency.", "abstract": ["The RNA-binding proteins LIN28A and LIN28B play critical roles in embryonic development, tumorigenesis, and pluripotency, but their exact functions are poorly understood.", "Here, we show that, like LIN28A, LIN28B can function effectively with NANOG, OCT4, and SOX2 in reprogramming to pluripotency and that reactivation of both endogenous LIN28A and LIN28B loci are required for maximal reprogramming efficiency.", "In human fibroblasts, LIN28B is activated early during reprogramming, while LIN28A is activated later during the transition to bona fide induced pluripotent stem cells (iPSCs).", "In murine cells, LIN28A and LIN28B facilitate conversion from naive to primed pluripotency.", "Proteomic and metabolomic analysis highlighted roles for LIN28 in maintaining the low mitochondrial function associated with primed pluripotency and in regulating one-carbon metabolism, nucleotide metabolism, and histone methylation.", "LIN28 binds to mRNAs of proteins important for oxidative phosphorylation and modulates protein abundance.", "Thus, LIN28A and LIN28B play cooperative roles in regulating reprogramming, naive/primed pluripotency, and stem cell metabolism."], "structured": false}
{"doc_id": 3883485, "title": "Genetic Drift Can Compromise Mitochondrial Replacement by Nuclear Transfer in Human Oocytes.", "abstract": ["Replacement of mitochondria through nuclear transfer between oocytes of two different women has emerged recently as a strategy for preventing inheritance of mtDNA diseases.", "Although experiments in human oocytes have shown effective replacement, the consequences of small amounts of mtDNA carryover have not been studied sufficiently.", "Using human mitochondrial replacement stem cell lines, we show that, even though the low levels of heteroplasmy introduced into human oocytes by mitochondrial carryover during nuclear transfer often vanish, they can sometimes instead result in mtDNA genotypic drift and reversion to the original genotype.", "Comparison of cells with identical oocyte-derived nuclear DNA but different mtDNA shows that either mtDNA genotype is compatible with the nucleus and that drift is independent of mitochondrial function.", "Thus, although functional replacement of the mitochondrial genome is possible, even low levels of heteroplasmy can affect the stability of the mtDNA genotype and compromise the efficacy of mitochondrial replacement."], "structured": false}
{"doc_id": 3893473, "title": "TAL effectors are remote controls for gene activation.", "abstract": ["TAL (transcription activator-like) effectors constitute a novel class of DNA-binding proteins with predictable specificity.", "They are employed by Gram-negative plant-pathogenic bacteria of the genus Xanthomonas which translocate a cocktail of different effector proteins via a type III secretion system (T3SS) into plant cells where they serve as virulence determinants.", "Inside the plant cell, TALs localize to the nucleus, bind to target promoters, and induce expression of plant genes.", "DNA-binding specificity of TALs is determined by a central domain of tandem repeats.", "Each repeat confers recognition of one base pair (bp) in the DNA.", "Rearrangement of repeat modules allows design of proteins with desired DNA-binding specificities.", "Here, we summarize how TAL specificity is encoded, first structural data and first data on site-specific TAL nucleases."], "structured": false}
{"doc_id": 3896759, "title": "Vascular heterogeneity and specialization in development and disease", "abstract": ["Blood and lymphatic vessels pervade almost all body tissues and have numerous essential roles in physiology and disease.", "The inner lining of these networks is formed by a single layer of endothelial cells, which is specialized according to the needs of the tissue that it supplies.", "Whereas the general mechanisms of blood and lymphatic vessel development are being defined with increasing molecular precision, studies of the processes of endothelial specialization remain mostly descriptive.", "Recent insights from genetic animal models illuminate how endothelial cells interact with each other and with their tissue environment, providing paradigms for vessel type- and organ-specific endothelial differentiation.", "Delineating these governing principles will be crucial for understanding how tissues develop and maintain, and how their function becomes abnormal in disease."], "structured": false}
{"doc_id": 3898784, "title": "Association of Intracerebral Hemorrhage Among Patients Taking Non\u2013Vitamin K Antagonist vs Vitamin K Antagonist Oral Anticoagulants With In-Hospital Mortality", "abstract": ["Importance Although non\u2013vitamin K antagonist oral anticoagulants (NOACs) are increasingly used to prevent thromboembolic disease, there are limited data on NOAC-related intracerebral hemorrhage (ICH).", "Objective To assess the association between preceding oral anticoagulant use (warfarin, NOACs, and no oral anticoagulants [OACs]) and in-hospital mortality among patients with ICH.", "Design, Setting, and Participants Retrospective cohort study of 141 311 patients with ICH admitted from October 2013 to December 2016 to 1662 Get With The Guidelines\u2013Stroke hospitals.", "Exposures Anticoagulation therapy before ICH, defined as any use of OACs within 7 days prior to hospital arrival.", "Main Outcomes and Measures In-hospital mortality.", "Results Among 141 311 patients with ICH (mean [SD] age, 68.3 [15.3] years; 48.1% women), 15 036 (10.6%) were taking warfarin and 4918 (3.5%) were taking NOACs preceding ICH, and 39 585 (28.0%) and 5783 (4.1%) were taking concomitant single and dual antiplatelet agents, respectively.", "Patients with prior use of warfarin or NOACs were older and had higher prevalence of atrial fibrillation and prior stroke.", "Acute ICH stroke severity (measured by the National Institutes of Health Stroke Scale) was not significantly different across the 3 groups (median, 9 [interquartile range, 2-21] for warfarin, 8 [2-20] for NOACs, and 8 [2-19] for no OACs).", "The unadjusted in-hospital mortality rates were 32.6% for warfarin, 26.5% for NOACs, and 22.5% for no OACs.", "Compared with patients without prior use of OACs, the risk of in-hospital mortality was higher among patients with prior use of warfarin (adjusted risk difference [ARD], 9.0% [97.5% CI, 7.9% to 10.1%]; adjusted odds ratio [AOR], 1.62 [97.5% CI, 1.53 to 1.71]) and higher among patients with prior use of NOACs (ARD, 3.3% [97.5% CI, 1.7% to 4.8%]; AOR, 1.21 [97.5% CI, 1.11-1.32]).", "Compared with patients with prior use of warfarin, patients with prior use of NOACs had a lower risk of in-hospital mortality (ARD, \u22125.7% [97.5% CI, \u22127.3% to \u22124.2%]; AOR, 0.75 [97.5% CI, 0.69 to 0.81]).", "The difference in mortality between NOAC-treated patients and warfarin-treated patients was numerically greater among patients with prior use of dual antiplatelet agents (32.7% vs 47.1%; ARD, \u221215.0% [95.5% CI, \u221226.3% to \u22123.8%]; AOR, 0.50 [97.5% CI, 0.29 to 0.86]) than among those taking these agents without prior antiplatelet therapy (26.4% vs 31.7%; ARD, \u22125.0% [97.5% CI, \u22126.8% to \u22123.2%]; AOR, 0.77 [97.5% CI, 0.70 to 0.85]), although the interaction P value (.07) was not statistically significant.", "Conclusions and Relevance Among patients with ICH, prior use of NOACs or warfarin was associated with higher in-hospital mortality compared with no OACs.", "Prior use of NOACs, compared with prior use of warfarin, was associated with lower risk of in-hospital mortality."], "structured": false}
{"doc_id": 3899896, "title": "Elevated red blood cell distribution width contributes to poor prognosis in patients undergoing resection for nonmetastatic rectal cancer", "abstract": ["Several studies have reported that elevated red blood cell distribution width (RDW) was associated with the poor prognosis of different kinds of cancers.", "The aim of this study was to investigate the prognostic role of RDW in patients undergoing resection for nonmetastatic rectal cancer.", "We retrospectively reviewed a database of 625 consecutive patients who underwent curative resection for nonmetastatic rectal cancer at our institution from January 2009 to December 2014.", "The cutoff value of RDW was calculated by receiver-operating characteristic curve.", "The results demonstrated that patients in high RDW-cv group had a lower overall survival (OS) (P = .018) and disease-free survival (P = .004).", "We also observed that patients in high RDW-sd group were associated with significantly lower OS (P = .033), whereas the disease-free survival (DFS) was not significantly different (P = .179).In multivariate analysis, we found elevated RDW-cv was associated poor DFS (hazard ratio [HR] = 1.56, P = .010) and RDW-sd can predict a worse OS (HR = 1.70, P = .009).We confirmed that elevated RDW can be an independently prognostic factor in patients undergoing resection for nonmetastatic rectal cancer.", "So more intervention or surveillance might be paid to the patients with nonmetastatic rectal cancer and elevated RDW values in the future."], "structured": false}
{"doc_id": 3903084, "title": "Health workers cohort study: methods and study design.", "abstract": ["Objective: To examine different health outcomes that are associated with specific lifestyle and genetic factors.   ", "Materials and methods: From March 2004 to April 2006, a sample of employees from three different health and academic institutions, as well as their family members, were enrolled in the study after providing informed consent.", "At baseline and follow-up (2010-2013), participants completed a self-administered questionnaire, a physical examination, and provided blood samples.   ", "Results: A total of 10 729 participants aged 6 to 94 years were recruited at baseline.", "Of these, 70% were females, and 50% were from the Mexican Social Security Institute.", "Nearly 42% of the adults in the sample were overweight, while 20% were obese.   ", "Conclusion: Our study can offer new insights into disease mechanisms and prevention through the analysis of risk factor information in a large sample of Mexicans."], "structured": false}
{"doc_id": 3912660, "title": "Aberrant pro-atrial natriuretic peptide/corin/natriuretic peptide receptor signaling is present in maternal vascular endothelium in preeclampsia.", "abstract": ["OBJECTIVE Corin is a serine protease that converts pro-atrial natriuretic peptide (pro-ANP) to atrial natriuretic peptide (ANP), a cardiac hormone that regulates salt-water balance and blood pressure.", "ANP is degraded by natriuretic peptide receptor (NPR).", "This study was to determine if aberrant pro-ANP/corin/NPR signaling is present in maternal vascular system in preeclampsia.   ", "STUDY DESIGN Maternal venous blood was obtained from 197 pregnant women (84 normotensive, 16 complicated with chronic hypertension (CHT), 11 mild and 86 severe preeclampsia).", "Plasma corin and pro-ANP concentrations were measured by enzyme-linked immunosorbent assay.", "Maternal subcutaneous fat tissue was obtained from 12 pregnant women with cesarean section delivery (6 normotensive and 6 preeclampsia).", "Vascular ANP and its receptors NPR-A, NPR-B, and NPR-C expression were examined by immunostaining of paraffin embedded subcutaneous fat tissue sections.   \n", "RESULTS Corin concentrations were significantly higher in mild (2.78 \u00b1 0.67 ng/ml, p < .05) and severe (2.53 \u00b1 0.18 ng/ml, p < .01) preeclampsia than in normotensive (1.58 \u00b1 0.08 ng/ml) and CHT (1.55 \u00b1 0.20 ng/ml) groups.", "Pro-ANP concentrations were significantly higher in CHT (1.59 \u00b1 0.53 ng/ml, p < .05) and severe preeclampsia (1.42 \u00b1 0.24 ng/ml, p < .01) than in normotensive (0.48 \u00b1 0.06 ng/ml) and mild preeclampsia (0.52 \u00b1 0.09 ng/ml) groups.", "ANP and NPR-B expression was undetectable in maternal vessels from normotensive and preeclamptic pregnancies, but reduced NPR-A expression and increased NPR-C expression was found in maternal vessel endothelium in preeclampsia.   \n", "CONCLUSIONS ANP is a vasodilator and NPR-C is a clearance receptor for ANP.", "The finding of upregulation of NPR-C expression suggests that circulating ANP clearance or degradation is increased in preeclampsia.", "These results also suggest that pro-ANP/corin/NPR signaling is dominant in the vascular system in preeclampsia."], "structured": true}
{"doc_id": 3929361, "title": "Optimising Strategies for Plasmodium falciparum Malaria Elimination in Cambodia: Primaquine, Mass Drug Administration and Artemisinin Resistance", "abstract": ["BACKGROUND Malaria elimination requires a variety of approaches individually optimized for different transmission settings.", "A recent field study in an area of low seasonal transmission in South West Cambodia demonstrated dramatic reductions in malaria parasite prevalence following both mass drug administration (MDA) and high treatment coverage of symptomatic patients with artemisinin-piperaquine plus primaquine.", "This study employed multiple combined strategies and it was unclear what contribution each made to the reductions in malaria.   \n", "METHOD AND FINDINGS A mathematical model fitted to the trial results was used to assess the effects of the various components of these interventions, design optimal elimination strategies, and explore their interactions with artemisinin resistance, which has recently been discovered in Western Cambodia.", "The modelling indicated that most of the initial reduction of P. falciparum malaria resulted from MDA with artemisinin-piperaquine.", "The subsequent continued decline and near elimination resulted mainly from high coverage with artemisinin-piperaquine treatment.", "Both these strategies were more effective with the addition of primaquine.", "MDA with artemisinin combination therapy (ACT) increased the proportion of artemisinin resistant infections, although much less than treatment of symptomatic cases with ACT, and this increase was slowed by adding primaquine.", "Artemisinin resistance reduced the effectiveness of interventions using ACT when the prevalence of resistance was very high.", "The main results were robust to assumptions about primaquine action, and immunity.   \n", "CONCLUSIONS The key messages of these modelling results for policy makers were: high coverage with ACT treatment can produce a long-term reduction in malaria whereas the impact of MDA is generally only short-term; primaquine enhances the effect of ACT in eliminating malaria and reduces the increase in proportion of artemisinin resistant infections; parasite prevalence is a better surveillance measure for elimination programmes than numbers of symptomatic cases; combinations of interventions are most effective and sustained efforts are crucial for successful elimination."], "structured": true}
{"doc_id": 3930020, "title": "Role of the Parasite-Derived Prostaglandin D2 in the Inhibition of Epidermal Langerhans Cell Migration during Schistosomiasis Infection", "abstract": ["Epidermal Langerhans cells (LCs) play a key role in immune defense mechanisms and in numerous immunological disorders.", "In this report, we show that percutaneous infection of C57BL/6 mice with the helminth parasite Schistosoma mansoni leads to the activation of LCs but, surprisingly, to their retention in the epidermis.", "Moreover, using an experimental model of LC migration induced by tumor necrosis factor (TNF)-\u03b1, we show that parasites transiently impair the departure of LCs from the epidermis and their subsequent accumulation as dendritic cells in the draining lymph nodes.", "The inhibitory effect is mediated by soluble lipophilic factors released by the parasites and not by host-derived antiinflammatory cytokines, such as interleukin-10.", "We find that prostaglandin (PG)D2, but not the other major eicosanoids produced by the parasites, specifically impedes the TNF-\u03b1\u2013triggered migration of LCs through the adenylate cyclase\u2013coupled PGD2 receptor (DP receptor).", "Moreover, the potent DP receptor antagonist BW A868C restores LC migration in infected mice.", "Finally, in a model of contact allergen-induced LC migration, we show that activation of the DP receptor not only inhibits LC emigration but also dramatically reduces the contact hypersensitivity responses after challenge.", "Taken together, we propose that the inhibition of LC migration could represent an additional stratagem for the schistosomes to escape the host immune system and that PGD2 may play a key role in the control of cutaneous immune responses."], "structured": false}
{"doc_id": 3935126, "title": "Axicabtagene Ciloleucel CAR T\u2010Cell Therapy in Refractory Large B\u2010Cell Lymphoma", "abstract": ["Background In a phase 1 trial, axicabtagene ciloleucel (axi\u2010cel), an autologous anti\u2010CD19 chimeric antigen receptor (CAR) T\u2010cell therapy, showed efficacy in patients with refractory large B\u2010cell lymphoma after the failure of conventional therapy.", "Methods In this multicenter, phase 2 trial, we enrolled 111 patients with diffuse large B\u2010cell lymphoma, primary mediastinal B\u2010cell lymphoma, or transformed follicular lymphoma who had refractory disease despite undergoing recommended prior therapy.", "Patients received a target dose of 2\u00d7106 anti\u2010CD19 CAR T cells per kilogram of body weight after receiving a conditioning regimen of low\u2010dose cyclophosphamide and fludarabine.", "The primary end point was the rate of objective response (calculated as the combined rates of complete response and partial response).", "Secondary end points included overall survival, safety, and biomarker assessments.", "Results Among the 111 patients who were enrolled, axi\u2010cel was successfully manufactured for 110 (99%) and administered to 101 (91%).", "The objective response rate was 82%, and the complete response rate was 54%.With a median follow\u2010up of 15.4 months, 42% of the patients continued to have a response, with 40% continuing to have a complete response.", "The overall rate of survival at 18 months was 52%.", "The most common adverse events of grade 3 or higher during treatment were neutropenia (in 78% of the patients), anemia (in 43%), and thrombocytopenia (in 38%).", "Grade 3 or higher cytokine release syndrome and neurologic events occurred in 13% and 28% of the patients, respectively.", "Three of the patients died during treatment.", "Higher CAR T\u2010cell levels in blood were associated with response.", "Conclusions In this multicenter study, patients with refractory large B\u2010cell lymphoma who received CAR T\u2010cell therapy with axi\u2010cel had high levels of durable response, with a safety profile that included myelosuppression, the cytokine release syndrome, and neurologic events.", "(Funded by Kite Pharma and the Leukemia and Lymphoma Society Therapy Acceleration Program; ZUMA\u20101 ClinicalTrials.gov number, NCT02348216.)"], "structured": false}
{"doc_id": 3943235, "title": "Beta adrenergic blockade decreases the immunomodulatory effects of social disruption stress", "abstract": ["During physiological or psychological stress, catecholamines produced by the sympathetic nervous system (SNS) regulate the immune system.", "Previous studies report that the activation of \u03b2-adrenergic receptors (\u03b2ARs) mediates the actions of catecholamines and increases pro-inflammatory cytokine production in a number of different cell types.", "The impact of the SNS on the immune modulation of social defeat has not been examined.", "The following studies were designed to determine whether SNS activation during social disruption stress (SDR) influences anxiety-like behavior as well as the activation, priming, and glucocorticoid resistance of splenocytes after social stress.", "CD-1 mice were exposed to one, three, or six cycles of SDR and HPLC analysis of the plasma and spleen revealed an increase in catecholamines.", "After six cycles of SDR the open field test was used to measure behaviors characteristic of anxiety and indicated that the social defeat induced increase in anxiety-like behavior was blocked by pre-treatment with the \u03b2-adrenergic antagonist propranolol.", "Pre-treatment with the \u03b2-adrenergic antagonist propranolol did not significantly alter corticosterone levels indicating no difference in activation of the hypothalamic-pituitary-adrenal axis.", "In addition to anxiety-like behavior the SDR induced splenomegaly and increase in plasma IL-6, TNF\u03b1, and MCP-1 were each reversed by pre-treatment with propranolol.", "Furthermore, flow cytometric analysis of cells from propranolol pretreated mice reduced the SDR-induced increase in the percentage of CD11b(+) splenic macrophages and significantly decreased the expression of TLR2, TLR4, and CD86 on the surface of these cells.", "In addition, supernatants from 18h LPS-stimulated ex vivo cultures of splenocytes from propranolol-treated SDR mice contained less IL-6.", "Likewise propranolol pre-treatment abrogated the glucocorticoid insensitivity of CD11b(+) cells ex vivo when compared to splenocytes from SDR vehicle-treated mice.", "Together, this study demonstrates that the immune activation and priming effects of SDR result, in part, as a consequence of SNS activation."], "structured": false}
{"doc_id": 3944632, "title": "Stereotactic radiosurgery plus whole-brain radiation therapy vs stereotactic radiosurgery alone for treatment of brain metastases: a randomized controlled trial.", "abstract": ["CONTEXT In patients with brain metastases, it is unclear whether adding up-front whole-brain radiation therapy (WBRT) to stereotactic radiosurgery (SRS) has beneficial effects on mortality or neurologic function compared with SRS alone.   \n", "OBJECTIVE To determine if WBRT combined with SRS results in improvements in survival, brain tumor control, functional preservation rate, and frequency of neurologic death.   \n", "DESIGN, SETTING, AND PATIENTS Randomized controlled trial of 132 patients with 1 to 4 brain metastases, each less than 3 cm in diameter, enrolled at 11 hospitals in Japan between October 1999 and December 2003.   \n", "INTERVENTIONS Patients were randomly assigned to receive WBRT plus SRS (65 patients) or SRS alone (67 patients).   \n", "MAIN OUTCOME MEASURES The primary end point was overall survival; secondary end points were brain tumor recurrence, salvage brain treatment, functional preservation, toxic effects of radiation, and cause of death.   \n", "RESULTS The median survival time and the 1-year actuarial survival rate were 7.5 months and 38.5% (95% confidence interval, 26.7%-50.3%) in the WBRT + SRS group and 8.0 months and 28.4% (95% confidence interval, 17.6%-39.2%) for SRS alone (P = .42).", "The 12-month brain tumor recurrence rate was 46.8% in the WBRT + SRS group and 76.4% for SRS alone group (P<.001).", "Salvage brain treatment was less frequently required in the WBRT + SRS group (n = 10) than with SRS alone (n = 29) (P<.001).", "Death was attributed to neurologic causes in 22.8% of patients in the WBRT + SRS group and in 19.3% of those treated with SRS alone (P = .64).", "There were no significant differences in systemic and neurologic functional preservation and toxic effects of radiation.   \n", "CONCLUSIONS Compared with SRS alone, the use of WBRT plus SRS did not improve survival for patients with 1 to 4 brain metastases, but intracranial relapse occurred considerably more frequently in those who did not receive WBRT.", "Consequently, salvage treatment is frequently required when up-front WBRT is not used.   \n", "TRIAL REGISTRATION umin.ac.jp/ctr Identifier: C000000412."], "structured": true}
{"doc_id": 3952288, "title": "RANK signals from CD4+3\u2212 inducer cells regulate development of Aire-expressing epithelial cells in the thymic medulla", "abstract": ["Aire-expressing medullary thymic epithelial cells (mTECs) play a key role in preventing autoimmunity by expressing tissue-restricted antigens to help purge the emerging T cell receptor repertoire of self-reactive specificities.", "Here we demonstrate a novel role for a CD4+3\u2212 inducer cell population, previously linked to development of organized secondary lymphoid structures and maintenance of T cell memory in the functional regulation of Aire-mediated promiscuous gene expression in the thymus.", "CD4+3\u2212 cells are closely associated with mTECs in adult thymus, and in fetal thymus their appearance is temporally linked with the appearance of Aire+ mTECs.", "We show that RANKL signals from this cell promote the maturation of RANK-expressing CD80\u2212Aire\u2212 mTEC progenitors into CD80+Aire+ mTECs, and that transplantation of RANK-deficient thymic stroma into immunodeficient hosts induces autoimmunity.", "Collectively, our data reveal cellular and molecular mechanisms leading to the generation of Aire+ mTECs and highlight a previously unrecognized role for CD4+3\u2212RANKL+ inducer cells in intrathymic self-tolerance."], "structured": false}
{"doc_id": 3960385, "title": "Proteomic approach to characterize biochemistry of meat quality defects.", "abstract": ["Proteomics can be used to characterize quality defects including pale, soft, and exudative (PSE) meat (pork and poultry), woody broiler breast meat, reddish catfish fillets, meat toughness, and beef myoglobin oxidation.", "PSE broiler meat was characterized by 15 proteins that differed in abundance in comparison to normal broiler breast meat, and eight proteins were differentially expressed in woody breast meat in comparison to normal breast meat.", "Hemoglobin was the only protein that was differentially expressed between red and normal catfish fillets.", "However, inducing low oxygen and/or heat stress conditions to catfish fillets did not lead to the production of red fillets.", "Proteomic data provided information pertaining to the protein differences that exist in meat quality defects.", "However, these data need to be evaluated in conjunction with information pertaining to genetics, nutrition, environment of the live animal, muscle to meat conversion, meat quality analyses and sensory attributes to understand causality, protein biomarkers, and ultimately how to prevent quality defects."], "structured": false}
{"doc_id": 3973445, "title": "Phosphorylation of Janus kinase 1 (JAK1) by AMP-activated protein kinase (AMPK) links energy sensing to anti-inflammatory signaling", "abstract": ["Adenosine 5\u2032-monophosphate\u2013activated protein kinase (AMPK) is a pivotal regulator of metabolism at cellular and organismal levels.", "AMPK also suppresses inflammation.", "We found that pharmacological activation of AMPK rapidly inhibited the Janus kinase (JAK)\u2013signal transducer and activator of transcription (STAT) pathway in various cells.", "In vitro kinase assays revealed that AMPK directly phosphorylated two residues (Ser515 and Ser518) within the Src homology 2 domain of JAK1.", "Activation of AMPK enhanced the interaction between JAK1 and 14-3-3 proteins in cultured vascular endothelial cells and fibroblasts, an effect that required the presence of Ser515 and Ser518 and was abolished in cells lacking AMPK catalytic subunits.", "Mutation of Ser515 and Ser518 abolished AMPK-mediated inhibition of JAK-STAT signaling stimulated by either the sIL-6R\u03b1/IL-6 complex or the expression of a constitutively active V658F-mutant JAK1 in human fibrosarcoma cells.", "Clinically used AMPK activators metformin and salicylate enhanced the inhibitory phosphorylation of endogenous JAK1 and inhibited STAT3 phosphorylation in primary vascular endothelial cells.", "Therefore, our findings reveal a mechanism by which JAK1 function and inflammatory signaling may be suppressed in response to metabolic stress and provide a mechanistic rationale for the investigation of AMPK activators in a range of diseases associated with enhanced activation of the JAK-STAT pathway."], "structured": false}
{"doc_id": 3981033, "title": "IAP antagonists induce anti-tumor immunity in multiple myeloma", "abstract": ["The cellular inhibitors of apoptosis (cIAP) 1 and 2 are amplified in about 3% of cancers and have been identified in multiple malignancies as being potential therapeutic targets as a result of their role in the evasion of apoptosis.", "Consequently, small-molecule IAP antagonists, such as LCL161, have entered clinical trials for their ability to induce tumor necrosis factor (TNF)-mediated apoptosis of cancer cells.", "However, cIAP1 and cIAP2 are recurrently homozygously deleted in multiple myeloma (MM), resulting in constitutive activation of the noncanonical nuclear factor (NF)-\u03baB pathway.", "To our surprise, we observed robust in vivo anti-myeloma activity of LCL161 in a transgenic myeloma mouse model and in patients with relapsed-refractory MM, where the addition of cyclophosphamide resulted in a median progression-free-survival of 10 months.", "This effect was not a result of direct induction of tumor cell death, but rather of upregulation of tumor-cell-autonomous type I interferon (IFN) signaling and a strong inflammatory response that resulted in the activation of macrophages and dendritic cells, leading to phagocytosis of tumor cells.", "Treatment of a MM mouse model with LCL161 established long-term anti-tumor protection and induced regression in a fraction of the mice.", "Notably, combination of LCL161 with the immune-checkpoint inhibitor anti-PD1 was curative in all of the treated mice."], "structured": false}
{"doc_id": 3981244, "title": "Psychobiological Protective Factors Modifying the Association Between Age and Sexual Health in Men: Findings From the Men\u2019s Health 40+ Study", "abstract": ["Sexual health severely decreases with age.", "For males older than 40 years, erectile dysfunction (ED) is the most common sexual disorder.", "Although physical and psychological risk factors for ED have been identified, protective factors are yet to be determined.", "To date, no study has examined endocrine and psychosocial factors in parallel with regard to their modifying effect on the age-related increase in ED.", "Two hundred and seventy-one self-reporting healthy men aged between 40 and 75 years provided both psychometric data on sexual function and a set of potential psychosocial protective factors, and saliva samples for the analysis of steroid hormones and proinflammatory cytokines.", "Around 35% of the participants reported at least a mild form of ED.", "Direct associations with ED were identified for perceived general health, emotional support, relationship quality, intimacy motivation but not for steroid hormones or proinflammatory markers.", "Moderation analyses for the association between age and ED revealed positive effects for testosterone (T), dehydroepiandrosterone (DHEA), perceived general health, emotional support, intimacy motivation, and a negative effect for interleukin-6 (all p < .05; f2 > .17).", "Group differences between older men with and without ED emerged for T, DHEA, and psychometric measures such as perceived general health, emotional support, satisfaction with life, and intimacy motivation (all p < .05; d > .3).", "Both psychosocial and endocrine parameters moderated the association between age and sexual health.", "Perceived general health, emotional support, intimacy motivation, and relationship quality emerged as psychosocial protective factors against ED.", "Higher T and DHEA and lower interleukin-6 levels also buffered against an age-related increase in ED."], "structured": false}
{"doc_id": 3981613, "title": "Patient-derived induced pluripotent stem cells in cancer research and precision oncology", "abstract": ["Together with recent advances in the processing and culture of human tissue, bioengineering, xenotransplantation and genome editing, Induced pluripotent stem cells (iPSCs) present a range of new opportunities for the study of human cancer.", "Here we discuss the main advantages and limitations of iPSC modeling, and how the method intersects with other patient-derived models of cancer, such as organoids, organs-on-chips and patient-derived xenografts (PDXs).", "We highlight the opportunities that iPSC models can provide beyond those offered by existing systems and animal models and present current challenges and crucial areas for future improvements toward wider adoption of this technology."], "structured": false}
{"doc_id": 3981729, "title": "Structural basis for sequence-specific recognition of DNA by TAL effectors.", "abstract": ["TAL (transcription activator-like) effectors, secreted by phytopathogenic bacteria, recognize host DNA sequences through a central domain of tandem repeats.", "Each repeat comprises 33 to 35 conserved amino acids and targets a specific base pair by using two hypervariable residues [known as repeat variable diresidues (RVDs)] at positions 12 and 13.", "Here, we report the crystal structures of an 11.5-repeat TAL effector in both DNA-free and DNA-bound states.", "Each TAL repeat comprises two helices connected by a short RVD-containing loop.", "The 11.5 repeats form a right-handed, superhelical structure that tracks along the sense strand of DNA duplex, with RVDs contacting the major groove.", "The 12th residue stabilizes the RVD loop, whereas the 13th residue makes a base-specific contact.", "Understanding DNA recognition by TAL effectors may facilitate rational design of DNA-binding proteins with biotechnological applications."], "structured": false}
{"doc_id": 3984231, "title": "Caveolin-1 deletion exacerbates cardiac interstitial fibrosis by promoting M2 macrophage activation in mice after myocardial infarction.", "abstract": ["Adverse remodeling following myocardial infarction (MI) leading to heart failure is driven by an imbalanced resolution of inflammation.", "The macrophage cell is an important control of post-MI inflammation, as macrophage subtypes secrete mediators to either promote inflammation and extend injury (M1 phenotype) or suppress inflammation and promote scar formation (M2 phenotype).", "We have previously shown that the absence of caveolin-1 (Cav1), a membrane scaffolding protein, is associated with adverse cardiac remodeling in mice, but the mechanisms responsible remain to be elucidated.", "We explore here the role of Cav1 in the activation of macrophages using wild type C57BL6/J (WT) and Cav1(tm1Mls/J) (Cav1(-/-)) mice.", "By echocardiography, cardiac function was comparable between WT and Cav1(-/-) mice at 3days post-MI.", "In the absence of Cav1, there were a surprisingly higher percentage of M2 macrophages (arginase-1 positive) detected in the infarcted zone.", "Conversely, restoring Cav1 function after MI in WT mice by adding back the Cav1 scaffolding domain reduced the M2 activation profile.", "Further, adoptive transfer of Cav1 null macrophages into WT mice on d3 post-MI exacerbated adverse cardiac remodeling at d14 post-MI.", "In vitro studies revealed that Cav1 null macrophages had a more pronounced M2 profile activation in response to IL-4 stimulation.", "In conclusion, Cav1 deletion promotes an array of maladaptive repair processes after MI, including increased TGF-\u03b2 signaling, increased M2 macrophage infiltration and dysregulation of the M1/M2 balance.", "Our data also suggest that cardiac remodeling can be improved by therapeutic intervention regulating Cav1 function during the inflammatory response phase."], "structured": false}
{"doc_id": 3986403, "title": "Lipid hydroperoxide measurement by oxidation of Fe2+ in the presence of xylenol orange. Comparison with the TBA assay and an iodometric method", "abstract": ["Study of the role of hydroperoxides and lipid peroxidation in disease requires simple and sensitive methods for direct hydroperoxide measurement.", "We report on a technique for measuring hydroperoxide which relies upon the rapid hydroperoxide-mediated oxidation of Fe2+ under acidic conditions.", "Fe3+ forms a chromophore with xylenol orange which absorbs strongly at 560 nm, yielding an apparent E560 (for H2O2, butyl hydroperoxide and cumene hydroperoxide) of 4.3\u00d7104 M\u22121 cm\u22121.", "The assay was validated in a study of liposomal lipid peroxidation and shown to give results comparable with those obtained by an iodometric method or by measuring conjugated dienes.", "The assay involving thiobarbituric acid, by comparison, underestimates lipid peroxidation and does not measure hydroperoxideper se."], "structured": false}
{"doc_id": 4020950, "title": "Roles of exosomes in cardioprotection.", "abstract": ["Exosomes are extracellular vesicles of endosomal origin which have emerged as key mediators of intercellular communication.", "All major cardiac cell types-including cardiomyocytes, endothelial cells, and fibroblasts-release exosomes that modulate cellular functions.", "Exosomes released from human cardiac progenitor cells (CPCs) are cardioprotective and improve cardiac function after myocardial infarction to an extent comparable with that achieved by their parent cells.", "Cardiac progenitor cell-derived exosomes are enriched in cardioprotective microRNAs, particularly miR-146a-3p.", "Circulating exosomes mediate remote ischaemic preconditioning.", "Moreover, they currently are being investigated as diagnostic markers.", "The discovery that cell-derived extracellular signalling organelles mediate the paracrine effects of stem cells suggests that cell-free strategies could supplant cell transplantation.", "This review discusses emerging roles of exosomes in cardiovascular physiology, with a focus on cardioprotective activities of CPC-derived exosomes."], "structured": false}
{"doc_id": 4036038, "title": "The rate of change in declining steroid hormones: a new parameter of healthy aging in men?", "abstract": ["Research on healthy aging in men has increasingly focused on age-related hormonal changes.", "Testosterone (T) decline is primarily investigated, while age-related changes in other sex steroids (dehydroepiandrosterone [DHEA], estradiol [E2], progesterone [P]) are mostly neglected.", "An integrated hormone parameter reflecting aging processes in men has yet to be identified.", "271 self-reporting healthy men between 40 and 75 provided both psychometric data and saliva samples for hormone analysis.", "Correlation analysis between age and sex steroids revealed negative associations for the four sex steroids (T, DHEA, E2, and P).", "Principal component analysis including ten salivary analytes identified a principal component mainly unifying the variance of the four sex steroid hormones.", "Subsequent principal component analysis including the four sex steroids extracted the principal component of declining steroid hormones (DSH).", "Moderation analysis of the association between age and DSH revealed significant moderation effects for psychosocial factors such as depression, chronic stress and perceived general health.", "In conclusion, these results provide further evidence that sex steroids decline in aging men and that the integrated hormone parameter DSH and its rate of change can be used as biomarkers for healthy aging in men.", "Furthermore, the negative association of age and DSH is moderated by psychosocial factors."], "structured": false}
{"doc_id": 4037034, "title": "Development of a novel helper-dependent adenovirus-Epstein-Barr virus hybrid system for the stable transformation of mammalian cells.", "abstract": ["Epstein-Barr virus (EBV) episomes are stably maintained in permissive proliferating cell lines due to EBV nuclear antigen 1 (EBNA-1) protein-mediated replication and segregation.", "Previous studies showed the ability of EBV episomes to confer long-term transgene expression and correct genetic defects in deficient cells.", "To achieve quantitative delivery of EBV episomes in vitro and in vivo, we developed a binary helper-dependent adenovirus (HDA)-EBV hybrid system that consists of one HDA vector for the expression of Cre recombinase and a second HDA vector that contains all of the sequences for the EBV episome flanked by loxP sites.", "Upon coinfection of cells, Cre expressed from the first vector recombined loxP sites on the second vector.", "The resulting circular EBV episomes expressed a transgene and contained the EBV-derived family of repeats, an EBNA-1 expression cassette, and 19 kb of human DNA that functions as a replication origin in mammalian cells.", "This HDA-EBV hybrid system transformed 40% of cultured cells.", "Transgene expression in proliferating cells was observed for over 20 weeks under conditions that selected for the expression of the transgene.", "In the absence of selection, EBV episomes were lost at a rate of 8 to 10% per cell division.", "Successful delivery of EBV episomes in vivo was demonstrated in the liver of transgenic mice expressing Cre from the albumin promoter.", "This novel gene transfer system has the potential to confer long-term episomal transgene expression and therefore to correct genetic defects with reduced vector-related toxicity and without insertional mutagenesis."], "structured": false}
{"doc_id": 4067274, "title": "Spliceosome assembly pathways for different types of alternative splicing converge during commitment to splice site pairing in the A complex.", "abstract": ["Differential splice site pairing establishes alternative splicing patterns resulting in the generation of multiple mRNA isoforms.", "This process is carried out by the spliceosome, which is activated by a series of sequential structural rearrangements of its five core snRNPs.", "To determine when splice sites become functionally paired, we carried out a series of kinetic trap experiments using pre-mRNAs that undergo alternative 5' splice site selection or alternative exon inclusion.", "We show that commitment to splice site pairing in both cases occurs in the A complex, which is characterized by the ATP-dependent association of the U2 snRNP with the branch point.", "Interestingly, the timing of splice site pairing is independent of the intron or exon definition modes of splice site recognition.", "Using the ATP analog ATPgammaS, we showed that ATP hydrolysis is required for splice site pairing independent from U2 snRNP binding to the pre-mRNA.", "These results identify the A complex as the spliceosomal assembly step dedicated to splice site pairing and suggest that ATP hydrolysis locks splice sites into a splicing pattern after stable U2 snRNP association to the branch point."], "structured": false}
{"doc_id": 4085204, "title": "Transcripts of the MHM region on the chicken Z chromosome accumulate as non-coding RNA in the nucleus of female cells adjacent to the DMRT1 locus", "abstract": ["The male hypermethylated (MHM) region, located near the middle of the short arm of the Z chromosome of chickens, consists of approximately 210 tandem repeats of a BamHI 2.2-kb sequence unit.", "Cytosines of the CpG dinucleotides of this region are extensively methylated on the two Z chromosomes in the male but much less methylated on the single Z chromosome in the female.", "The state of methylation of the MHM region is established after fertilization by about the 1-day embryonic stage.", "The MHM region is transcribed only in the female from the particular strand into heterogeneous, high molecular-mass, non-coding RNA, which is accumulated at the site of transcription, adjacent to the DMRT1 locus, in the nucleus.", "The transcriptional silence of the MHM region in the male is most likely caused by the CpG methylation, since treatment of the male embryonic fibroblasts with 5-azacytidine results in hypo-methylation and active transcription of this region.", "In ZZW triploid chickens, MHM regions are hypomethylated and transcribed on the two Z chromosomes, whereas MHM regions are hypermethylated and transcriptionally inactive on the three Z chromosomes in ZZZ triploid chickens, suggesting a possible role of the W chromosome on the state of the MHM region."], "structured": false}
{"doc_id": 4138659, "title": "Macropinocytosis of protein is an amino acid supply route in Ras-transformed cells", "abstract": ["Macropinocytosis is a highly conserved endocytic process by which extracellular fluid and its contents are internalized into cells through large, heterogeneous vesicles known as macropinosomes.", "Oncogenic Ras proteins have been shown to stimulate macropinocytosis but the functional contribution of this uptake mechanism to the transformed phenotype remains unknown.", "Here we show that Ras-transformed cells use macropinocytosis to transport extracellular protein into the cell.", "The internalized protein undergoes proteolytic degradation, yielding amino acids including glutamine that can enter central carbon metabolism.", "Accordingly, the dependence of Ras-transformed cells on free extracellular glutamine for growth can be suppressed by the macropinocytic uptake of protein.", "Consistent with macropinocytosis representing an important route of nutrient uptake in tumours, its pharmacological inhibition compromises the growth of Ras-transformed pancreatic tumour xenografts.", "These results identify macropinocytosis as a mechanism by which cancer cells support their unique metabolic needs and point to the possible exploitation of this process in the design of anticancer therapies."], "structured": false}
{"doc_id": 4162857, "title": "Linking Splicing to Pol II Transcription Stabilizes Pre-mRNAs and Influences Splicing Patterns", "abstract": ["RNA processing is carried out in close proximity to the site of transcription, suggesting a regulatory link between transcription and pre-mRNA splicing.", "Using an in vitro transcription/splicing assay, we demonstrate that an association of RNA polymerase II (Pol II) transcription and pre-mRNA splicing is required for efficient gene expression.", "Pol II-synthesized RNAs containing functional splice sites are protected from nuclear degradation, presumably because the local concentration of the splicing machinery is sufficiently high to ensure its association over interactions with nucleases.", "Furthermore, the process of transcription influences alternative splicing of newly synthesized pre-mRNAs.", "Because other RNA polymerases do not provide similar protection from nucleases, and their RNA products display altered splicing patterns, the link between transcription and RNA processing is RNA Pol II-specific.", "We propose that the connection between transcription by Pol II and pre-mRNA splicing guarantees an extended half-life and proper processing of nascent pre-mRNAs."], "structured": false}
{"doc_id": 4164929, "title": "The emerging role of skeletal muscle extracellular matrix remodelling in obesity and exercise.", "abstract": ["Skeletal muscle extracellular matrix remodelling has been proposed as a new feature associated with obesity and metabolic dysfunction.", "Exercise training improves muscle function in obesity, which may be mediated by regulatory effects on the muscle extracellular matrix.", "This review examined available literature on skeletal muscle extracellular matrix remodelling during obesity and the effects of exercise.", "A non-systematic literature review was performed on PubMed of publications from 1970 to 2015.", "A total of 37 studies from humans and animals were retained.", "Studies reported overall increases in gene and protein expression of different types of collagen, growth factors and enzymatic regulators of the skeletal muscle extracellular matrix in obesity.", "Only two studies investigated the effects of exercise on skeletal muscle extracellular matrix during obesity, with both suggesting a regulatory effect of exercise.", "The effects of exercise on muscle extracellular matrix seem to be influenced by the duration and type of exercise training with variable effects from a single session compared with a longer duration of exercise.", "More studies are needed to elucidate the mechanisms behind skeletal muscle extracellular matrix remodelling during obesity and the effects of exercise."], "structured": false}
{"doc_id": 4200695, "title": "Effect of specific exercise strategy on need for surgery in patients with subacromial impingement syndrome: randomised controlled study", "abstract": ["OBJECTIVE To evaluate if a specific exercise strategy, targeting the rotator cuff and scapula stabilisers, improves shoulder function and pain more than unspecific exercises in patients with subacromial impingement syndrome, thereby decreasing the need for arthroscopic subacromial decompression.   \n", "DESIGN Randomised, participant and single assessor blinded, controlled study.   \n", "SETTING Department of orthopaedics in a Swedish university hospital.   \n", "PARTICIPANTS 102 patients with long standing (over six months) persistent subacromial impingement syndrome in whom earlier conservative treatment had failed, recruited through orthopaedic specialists.   \n", "INTERVENTIONS The specific exercise strategy consisted of strengthening eccentric exercises for the rotator cuff and concentric/eccentric exercises for the scapula stabilisers in combination with manual mobilisation.", "The control exercise programme consisted of unspecific movement exercises for the neck and shoulder.", "Patients in both groups received five to six individual guided treatment sessions during 12 weeks.", "In between these supervised sessions the participants performed home exercises once or twice a day for 12 weeks.   \n", "MAIN OUTCOME MEASURES The primary outcome was the Constant-Murley shoulder assessment score evaluating shoulder function and pain.", "Secondary outcomes were patients' global impression of change because of treatment and decision regarding surgery.   \n", "RESULTS Most (97, 95%) participants completed the 12 week study.", "There was a significantly greater improvement in the Constant-Murley score in the specific exercise group than in the control exercise group (24 points (95% confidence interval 19 to 28.0) v 9 points (5 to 13); mean difference between group: 15 points (8.5 to 20.6)).", "Significantly more patients in the specific exercise group reported successful outcome (defined as large improvement or recovered) in the patients' global assessment of change because of treatment: 69% (35/51) v 24% (11/46); odds ratio 7.6, 3.1 to 18.9; P<0.001.", "A significantly lower proportion of patients in the specific exercise group subsequently chose to undergo surgery: 20% (10/51) v 63% (29/46); odds ratio 7.7, 3.1 to 19.4; P<0.001).   \n", "CONCLUSION A specific exercise strategy, focusing on strengthening eccentric exercises for the rotator cuff and concentric/eccentric exercises for the scapula stabilisers, is effective in reducing pain and improving shoulder function in patients with persistent subacromial impingement syndrome.", "By extension, this exercise strategy reduces the need for arthroscopic subacromial decompression within the three month timeframe used in the study.   \n", "TRIAL REGISTRATION Clinical trials NCT01037673."], "structured": true}
{"doc_id": 4231060, "title": "Nucleotide sequence of an avian sarcoma virus oncogene (src) and proposed amino acid sequence for gene product", "abstract": ["The transforming gene (src) of avian sarcoma virus (ASV) and adjacent regions of the viral genome have been isolated by molecular cloning of viral DNA.", "Their nucleotide sequence encompasses the whole of src and the portion of the gene env that encodes gp 37, one of two glycoproteins found in the viral envelope.", "Src encodes a single, hydrophobic protein with structural features that conform to previous descriptions of the gene product (pp60src).", "It appears that a single viral protein is responsible for both the initiation and maintenance of neoplastic transformation by avian sarcoma virus.", "Neither src nor its product bear any obvious structural relationship to several other viral oncogenes and their encoded proteins.", "Src is flanked by a repeated nucleotide sequence that may facilitate frequent deletion of the gene from the viral genome."], "structured": false}
{"doc_id": 4246523, "title": "Issues in design and interpretation of MDR-TB clinical trials: report of the first Global MDR-TB Clinical Trials Landscape Meeting", "abstract": ["Recognizing that the current MDR-TB regimen is suboptimal and based on low-quality evidence, the Global MDR-TB Clinical Trials Landscape Meeting was held in December, 2014 to strategize about coordination of research and development of new treatment regimens for this disease that affects millions of people worldwide every year.", "Sixty international experts on multidrug-resistant tuberculosis (MDR-TB) met in Washington D.C. and Cape Town, South Africa to consider key MDR-TB trial-related issues, including: standardization of definitions; clinical trial capacity building and; regimens optimized to foster compliance, avoid the emergence of resistance and have clinical relevance for special populations, including children and those co-infected with HIV.", "Underpinning all of this is the generation of a sufficient evidence base to facilitate regulatory approval and improved normative guidance.", "Participants discussed treatment combinations currently being studied in Phase 2B and Phase 3 trials as well as other promising new regimens and combinations that may be evaluated in the near future.", "These include regimens designed specifically to enable shorter duration and all-oral treatment as a means of maximizing treatment completion.", "It is hoped that clear definition of these challenges will facilitate the process of identifying solutions that accelerate progress towards effective, non-toxic treatments that can be programmatically implemented."], "structured": false}
{"doc_id": 4254064, "title": "Para-aortic splanchnopleura from early mouse embryos contains B1a cell progenitors", "abstract": ["DEFINITIVE erythropoiesis in birds originates from stem cells that emerge in the splanchnopleural mesoderm near the embryonic aorta1\u20134.", "The yolk sac is still generally held to be the unique provider of haematopoietic stem cells during mammalian ontogeny5, although there may be an alternative intraembryonic source of stem cells in the mouse fetus6,7.", "Here we search for a possible non-yolk-sac source of stem cells by grafting intraembryonic splanchnopleura from 10- to 18-somite mouse embryos into adult immunodeficient SCID mice.", "We find significant amounts of donor-derived serum IgM, normal numbers of IgM-secreting plasma cells, and the Bla (IgMa brightB220dullCD5+) cell subset to be fully reconstituted by donor progenitors 3 to 6 months after engraftment.", "The haematogenic capacity revealed in our experiments is present in a previously unrecognized site, the earliest described in the embryo, 12 hours before fetal liver colonization."], "structured": false}
{"doc_id": 4256553, "title": "Establishment in culture of pluripotential cells from mouse embryos", "abstract": ["Pluripotential cells are present in a mouse embryo until at least an early post-implantation stage, as shown by their ability to take part hi the formation of chimaeric animals1 and to form teratocarcinomas2.", "Until now it has not been possible to establish progressively growing cultures of these cells in vitro, and cell lines have only been obtained after teratocarcinoma formation in vivo.", "We report here the establishment in tissue culture of pluripotent cell lines which have been isolated directly from in vitro cultures of mouse blastocysts.", "These cells are able to differentiate either in vitro or after innoculation into a mouse as a tumour in vivo.", "They have a normal karyotype."], "structured": false}
{"doc_id": 4270992, "title": "MHC class II interaction with CD4 mediated by a region analogous to the MHC class I binding site for CD8", "abstract": ["INTERACTIONS between major histocompatibility complex (MHC) molecules and the CD4 or CDS coreceptors have a major role in intrathymic T-cell selection1.", "On mature T cells, each of these two glycoproteins is associated with a class-specific bias in MHC molecule recognition by the T-cell receptor.", "CD4+ T cells respond to antigen in association with MHC class II molecules and CD8+ T cells respond to antigen in association with MHC class I molecules.", "Physical interaction between the CD4/MHC class II molecules and CD8/MHC class I molecules has been demonstrated by cell adhesion assay2\u20135, and a binding site for CDS on class I has been identified6,7.", "Here we demonstrate that a region of the MHC class II\u03b2-chain \u03b22 domain, structurally analogous to the CDS-binding loop in the MHC class I \u03b13 domain, is critical for function with both mouse and human CD4."], "structured": false}
{"doc_id": 4283694, "title": "Instability and decay of the primary structure of DNA", "abstract": ["Although DNA is the carrier of genetic information, it has limited chemical stability.", "Hydrolysis, oxidation and nonenzymatic methylation of DNA occur at significant ratesin vivo, and are counteracted by specific DNA repair processes.", "The spontaneous decay of DNA is likely to be a major factor in mutagenesis, carcinogenesis and ageing, and also sets limits for the recovery of DNA fragments from fossils."], "structured": false}
{"doc_id": 4300851, "title": "Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise", "abstract": ["A major goal of biology is to provide a quantitative description of cellular behaviour.", "This task, however, has been hampered by the difficulty in measuring protein abundances and their variation.", "Here we present a strategy that pairs high-throughput flow cytometry and a library of GFP-tagged yeast strains to monitor rapidly and precisely protein levels at single-cell resolution.", "Bulk protein abundance measurements of >2,500 proteins in rich and minimal media provide a detailed view of the cellular response to these conditions, and capture many changes not observed by DNA microarray analyses.", "Our single-cell data argue that noise in protein expression is dominated by the stochastic production/destruction of messenger RNAs.", "Beyond this global trend, there are dramatic protein-specific differences in noise that are strongly correlated with a protein's mode of transcription and its function.", "For example, proteins that respond to environmental changes are noisy whereas those involved in protein synthesis are quiet.", "Thus, these studies reveal a remarkable structure to biological noise and suggest that protein noise levels have been selected to reflect the costs and potential benefits of this variation."], "structured": false}
{"doc_id": 4303075, "title": "Direct conversion of fibroblasts to functional neurons by defined factors", "abstract": ["Cellular differentiation and lineage commitment are considered to be robust and irreversible processes during development.", "Recent work has shown that mouse and human fibroblasts can be reprogrammed to a pluripotent state with a combination of four transcription factors.", "This raised the question of whether transcription factors could directly induce other defined somatic cell fates, and not only an undifferentiated state.", "We hypothesized that combinatorial expression of neural-lineage-specific transcription factors could directly convert fibroblasts into neurons.", "Starting from a pool of nineteen candidate genes, we identified a combination of only three factors, Ascl1, Brn2 (also called Pou3f2) and Myt1l, that suffice to rapidly and efficiently convert mouse embryonic and postnatal fibroblasts into functional neurons in vitro.", "These induced neuronal (iN) cells express multiple neuron-specific proteins, generate action potentials and form functional synapses.", "Generation of iN cells from non-neural lineages could have important implications for studies of neural development, neurological disease modelling and regenerative medicine."], "structured": false}
{"doc_id": 4303939, "title": "Inflammasome-mediated dysbiosis regulates progression of NAFLD and obesity", "abstract": ["Non-alcoholic fatty liver disease (NAFLD) is the hepatic manifestation of metabolic syndrome and the leading cause of chronic liver disease in the Western world.", "Twenty per cent of NAFLD individuals develop chronic hepatic inflammation (non-alcoholic steatohepatitis, NASH) associated with cirrhosis, portal hypertension and hepatocellular carcinoma, yet the causes of progression from NAFLD to NASH remain obscure.", "Here, we show that the NLRP6 and NLRP3 inflammasomes and the effector protein IL-18 negatively regulate NAFLD/NASH progression, as well as multiple aspects of metabolic syndrome via modulation of the gut microbiota.", "Different mouse models reveal that inflammasome-deficiency-associated changes in the configuration of the gut microbiota are associated with exacerbated hepatic steatosis and inflammation through influx of TLR4 and TLR9 agonists into the portal circulation, leading to enhanced hepatic tumour-necrosis factor (TNF)-\u03b1 expression that drives NASH progression.", "Furthermore, co-housing of inflammasome-deficient mice with wild-type mice results in exacerbation of hepatic steatosis and obesity.", "Thus, altered interactions between the gut microbiota and the host, produced by defective NLRP3 and NLRP6 inflammasome sensing, may govern the rate of progression of multiple metabolic syndrome-associated abnormalities, highlighting the central role of the microbiota in the pathogenesis of heretofore seemingly unrelated systemic auto-inflammatory and metabolic disorders."], "structured": false}
{"doc_id": 4305576, "title": "Chromatin remodelling at promoters suppresses antisense transcription", "abstract": ["Chromatin allows the eukaryotic cell to package its DNA efficiently.", "To understand how chromatin structure is controlled across the Saccharomyces cerevisiae genome, we have investigated the role of the ATP-dependent chromatin remodelling complex Isw2 in positioning nucleosomes.", "We find that Isw2 functions adjacent to promoter regions where it repositions nucleosomes at the interface between genic and intergenic sequences.", "Nucleosome repositioning by Isw2 is directional and results in increased nucleosome occupancy of the intergenic region.", "Loss of Isw2 activity leads to inappropriate transcription, resulting in the generation of both coding and noncoding transcripts.", "Here we show that Isw2 repositions nucleosomes to enforce directionality on transcription by preventing transcription initiation from cryptic sites.", "Our analyses reveal how chromatin is organized on a global scale and advance our understanding of how transcription is regulated."], "structured": false}
{"doc_id": 4306711, "title": "The Human Mitochondrial DEAD-Box Protein DDX28 Resides in RNA Granules and Functions in Mitoribosome Assembly.", "abstract": ["Human mitochondrial ribosomes are specialized in the synthesis of 13 proteins, which are fundamental components of the oxidative phosphorylation system.", "The pathway of mitoribosome biogenesis, the compartmentalization of the process, and factors involved remain largely unknown.", "Here, we have identified the DEAD-box protein DDX28 as an RNA granule component essential for the biogenesis of the mitoribosome large subunit (mt-LSU).", "DDX28 interacts with the 16S rRNA and the mt-LSU.", "RNAi-mediated DDX28 silencing in HEK293T cells does not affect mitochondrial mRNA stability or 16S rRNA processing or modification.", "However, it leads to reduced levels of 16S rRNA and mt-LSU proteins, impaired mt-LSU assembly, deeply attenuated mitochondrial protein synthesis, and consequent failure to assemble oxidative phosphorylation complexes.", "Our findings identify DDX28 as essential during the early stages of mitoribosome mt-LSU biogenesis, a process that takes place mainly near the mitochondrial nucleoids, in the compartment defined by the RNA granules."], "structured": false}
{"doc_id": 4311206, "title": "Conversion of Adult Pancreatic \u03b1-cells to \u03b2-cells After Extreme \u03b2-cell Loss", "abstract": ["Pancreatic insulin-producing beta-cells have a long lifespan, such that in healthy conditions they replicate little during a lifetime.", "Nevertheless, they show increased self-duplication after increased metabolic demand or after injury (that is, beta-cell loss).", "It is not known whether adult mammals can differentiate (regenerate) new beta-cells after extreme, total beta-cell loss, as in diabetes.", "This would indicate differentiation from precursors or another heterologous (non-beta-cell) source.", "Here we show beta-cell regeneration in a transgenic model of diphtheria-toxin-induced acute selective near-total beta-cell ablation.", "If given insulin, the mice survived and showed beta-cell mass augmentation with time.", "Lineage-tracing to label the glucagon-producing alpha-cells before beta-cell ablation tracked large fractions of regenerated beta-cells as deriving from alpha-cells, revealing a previously disregarded degree of pancreatic cell plasticity.", "Such inter-endocrine spontaneous adult cell conversion could be harnessed towards methods of producing beta-cells for diabetes therapies, either in differentiation settings in vitro or in induced regeneration."], "structured": false}
{"doc_id": 4312169, "title": "Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma", "abstract": ["Glioblastoma multiforme (GBM) is a lethal brain tumour in adults and children.", "However, DNA copy number and gene expression signatures indicate differences between adult and paediatric cases.", "To explore the genetic events underlying this distinction, we sequenced the exomes of 48 paediatric GBM samples.", "Somatic mutations in the H3.3-ATRX-DAXX chromatin remodelling pathway were identified in 44% of tumours (21/48).", "Recurrent mutations in H3F3A, which encodes the replication-independent histone 3 variant H3.3, were observed in 31% of tumours, and led to amino acid substitutions at two critical positions within the histone tail (K27M, G34R/G34V) involved in key regulatory post-translational modifications.", "Mutations in ATRX (\u03b1-thalassaemia/mental retardation syndrome X-linked) and DAXX (death-domain associated protein), encoding two subunits of a chromatin remodelling complex required for H3.3 incorporation at pericentric heterochromatin and telomeres, were identified in 31% of samples overall, and in 100% of tumours harbouring a G34R or G34V H3.3 mutation.", "Somatic TP53 mutations were identified in 54% of all cases, and in 86% of samples with H3F3A and/or ATRX mutations.", "Screening of a large cohort of gliomas of various grades and histologies (n = 784) showed H3F3A mutations to be specific to GBM and highly prevalent in children and young adults.", "Furthermore, the presence of H3F3A/ATRX-DAXX/TP53 mutations was strongly associated with alternative lengthening of telomeres and specific gene expression profiles.", "This is, to our knowledge, the first report to highlight recurrent mutations in a regulatory histone in humans, and our data suggest that defects of the chromatin architecture underlie paediatric and young adult GBM pathogenesis."], "structured": false}
{"doc_id": 4313478, "title": "Translational control of intron splicing in eukaryotes", "abstract": ["Most eukaryotic genes are interrupted by non-coding introns that must be accurately removed from pre-messenger RNAs to produce translatable mRNAs.", "Splicing is guided locally by short conserved sequences, but genes typically contain many potential splice sites, and the mechanisms specifying the correct sites remain poorly understood.", "In most organisms, short introns recognized by the intron definition mechanism cannot be efficiently predicted solely on the basis of sequence motifs.", "In multicellular eukaryotes, long introns are recognized through exon definition and most genes produce multiple mRNA variants through alternative splicing.", "The nonsense-mediated mRNA decay (NMD) pathway may further shape the observed sets of variants by selectively degrading those containing premature termination codons, which are frequently produced in mammals.", "Here we show that the tiny introns of the ciliate Paramecium tetraurelia are under strong selective pressure to cause premature termination of mRNA translation in the event of intron retention, and that the same bias is observed among the short introns of plants, fungi and animals.", "By knocking down the two P. tetraurelia genes encoding UPF1, a protein that is crucial in NMD, we show that the intrinsic efficiency of splicing varies widely among introns and that NMD activity can significantly reduce the fraction of unspliced mRNAs.", "The results suggest that, independently of alternative splicing, species with large intron numbers universally rely on NMD to compensate for suboptimal splicing efficiency and accuracy."], "structured": false}
{"doc_id": 4319174, "title": "Alternatively activated macrophages produce catecholamines to sustain adaptive thermogenesis", "abstract": ["All homeotherms use thermogenesis to maintain their core body temperature, ensuring that cellular functions and physiological processes can continue in cold environments.", "In the prevailing model of thermogenesis, when the hypothalamus senses cold temperatures it triggers sympathetic discharge, resulting in the release of noradrenaline in brown adipose tissue and white adipose tissue.", "Acting via the \u03b2(3)-adrenergic receptors, noradrenaline induces lipolysis in white adipocytes, whereas it stimulates the expression of thermogenic genes, such as PPAR-\u03b3 coactivator 1a (Ppargc1a), uncoupling protein 1 (Ucp1) and acyl-CoA synthetase long-chain family member 1 (Acsl1), in brown adipocytes.", "However, the precise nature of all the cell types involved in this efferent loop is not well established.", "Here we report in mice an unexpected requirement for the interleukin-4 (IL-4)-stimulated program of alternative macrophage activation in adaptive thermogenesis.", "Exposure to cold temperature rapidly promoted alternative activation of adipose tissue macrophages, which secrete catecholamines to induce thermogenic gene expression in brown adipose tissue and lipolysis in white adipose tissue.", "Absence of alternatively activated macrophages impaired metabolic adaptations to cold, whereas administration of IL-4 increased thermogenic gene expression, fatty acid mobilization and energy expenditure, all in a macrophage-dependent manner.", "Thus, we have discovered a role for alternatively activated macrophages in the orchestration of an important mammalian stress response, the response to cold."], "structured": false}
{"doc_id": 4319844, "title": "Alternative Lengthening of Telomeres Mediated by Mitotic DNA Synthesis Engages Break-Induced Replication Processes.", "abstract": ["Alternative lengthening of telomeres (ALT) is a telomerase-independent telomere maintenance mechanism that occurs in a subset of cancers.", "By analyzing telomerase-positive cells and their human TERC knockout-derived ALT human cell lines, we show that ALT cells harbor more fragile telomeres representing telomere replication problems.", "ALT-associated replication defects trigger mitotic DNA synthesis (MiDAS) at telomeres in a RAD52-dependent, but RAD51-independent, manner.", "Telomeric MiDAS is a conservative DNA synthesis process, potentially mediated by break-induced replication, similar to type II ALT survivors in Saccharomyces cerevisiae Replication stresses induced by ectopic oncogenic expression of cyclin E, G-quadruplexes, or R-loop formation facilitate the ALT pathway and lead to telomere clustering, a hallmark of ALT cancers.", "The TIMELESS/TIPIN complex suppresses telomere clustering and telomeric MiDAS, whereas the SMC5/6 complex promotes them.", "In summary, ALT cells exhibit more telomere replication defects that result in persistent DNA damage responses at telomeres, leading to the engagement of telomeric MiDAS (spontaneous mitotic telomere synthesis) that is triggered by DNA replication stress, a potential driver of genomic duplications in cancer."], "structured": false}
{"doc_id": 4320111, "title": "Light acts directly on organs and cells in culture to set the vertebrate circadian clock.", "abstract": ["The expression of clock genes in vertebrates is widespread and not restricted to classical clock structures.", "The expression of the Clock gene in zebrafish shows a strong circadian oscillation in many tissues in vivo and in culture, showing that endogenous oscillators exist in peripheral organs.", "A defining feature of circadian clocks is that they can be set or entrained to local time, usually by the environmental light-dark cycle.", "An important question is whether peripheral oscillators are entrained to local time by signals from central pacemakers such as the eyes or are themselves directly light-responsive.", "Here we show that the peripheral organ clocks of zebrafish are set by light-dark cycles in culture.", "We also show that a zebrafish-derived cell line contains a circadian oscillator, which is also directly light entrained."], "structured": false}
{"doc_id": 4320424, "title": "Small molecule inhibition of the KRAS\u2013PDE\u03b4 interaction impairs oncogenic KRAS signalling", "abstract": ["The KRAS oncogene product is considered a major target in anticancer drug discovery.", "However, direct interference with KRAS signalling has not yet led to clinically useful drugs.", "Correct localization and signalling by farnesylated KRAS is regulated by the prenyl-binding protein PDE\u03b4, which sustains the spatial organization of KRAS by facilitating its diffusion in the cytoplasm.", "Here we report that interfering with binding of mammalian PDE\u03b4 to KRAS by means of small molecules provides a novel opportunity to suppress oncogenic RAS signalling by altering its localization to endomembranes.", "Biochemical screening and subsequent structure-based hit optimization yielded inhibitors of the KRAS\u2013PDE\u03b4 interaction that selectively bind to the prenyl-binding pocket of PDE\u03b4 with nanomolar affinity, inhibit oncogenic RAS signalling and suppress in vitro and in vivo proliferation of human pancreatic ductal adenocarcinoma cells that are dependent on oncogenic KRAS.", "Our findings may inspire novel drug discovery efforts aimed at the development of drugs targeting oncogenic RAS."], "structured": false}
{"doc_id": 4321295, "title": "Evolution of novel cooperative swarming in the bacterium Myxococcus xanthus", "abstract": ["Cooperation among individuals is necessary for evolutionary transitions to higher levels of biological organization.", "In such transitions, groups of individuals at one level (such as single cells) cooperate to form selective units at a higher level (such as multicellular organisms).", "Though the evolution of cooperation is difficult to observe directly in higher eukaryotes, microorganisms do offer such an opportunity.", "Here we report the evolution of novel cooperative behaviour in experimental lineages of the bacterium Myxococcus xanthus.", "Wild-type strains of M. xanthus exhibit socially dependent swarming across soft surfaces by a mechanism known as \u2018S-motility\u2019 that requires the presence of extracellular type IV pili.", "In lineages of M. xanthus unable to make pili, a new mechanistic basis for cooperative swarming evolved.", "Evolved swarming is mediated, at least in part, by enhanced production of an extracellular fibril matrix that binds cells\u2014and their evolutionary interests\u2014together.", "Though costly to individuals, fibril production greatly enhanced population expansion in groups of interconnected cells.", "These results show that fundamental transitions to primitive cooperation can readily occur in bacteria."], "structured": false}
{"doc_id": 4321947, "title": "Exon duplication and divergence in the human preproglucagon gene", "abstract": ["Glucagon is a 29-amino acid pancreatic hormone which counteracts the blood glucose-lowering action of insulin by stimulating hepatic glycogenolysis and gluconeogenesis1.", "The structure of the hamster pancreatic glucagon precursor has recently been determined from the sequence of a cloned cDNA2.", "Hamster preproglucagon is a 180-amino acid protein which contains five functional regions; a signal or pre-peptide, an NH2-terminal peptide (also called glicentin-related pancreatic peptide, GRPP), glucagon, and two carboxy-terminal glucagon-like peptides (GLP-1 and GLP-2).", "The sequences of two non-allelic anglerfish pancreatic glucagon precursors3\u20135 have also been determined and their organization is similar but not identical to the hamster protein; they lack the polypeptide segment corresponding to hamster GLP-2.", "The presence of three regions possessing internal homology, that is, glucagon, GLP-1 and GLP-2, within proglucagon, and the absence of GLP-2 in the anglerfish precursors suggests that the structure of the preproglucagon gene might provide insight into the evolution of this polyprotein.", "We have isolated and sequenced the human preproglucagon gene and report here that the organization of the human precursor deduced from this sequence is identical to the hamster protein.", "The gene contains at least three intervening sequences which divide the protein-coding portion of the gene into four regions corresponding to the signal peptide and part of the NH2-terminal peptide, the remainder of the NH2-terminal peptide and glucagon, GLP-1, and GLP-2.", "The data suggest that triplication and subsequent sequence divergence of an exon encoding glucagon or a glucagon-like peptide produced this polyprotein precursor."], "structured": false}
{"doc_id": 4323425, "title": "BH1 and BH2 domains of Bcl-2 are required for inhibition of apoptosis and heterodimerization with Bax", "abstract": ["BCL-2 was isolated from the t(14;18) chromosomal breakpoint in follicular B-cell lymphoma1\u20133.", "Bcl-2 has the unique oncogenic role of extending cell survival by inhibiting a variety of apoptotic deaths4\u201313.", "An emerging family of Bcl-2 -related proteins share two highly conserved regions14\u201320 referred to here as Bcl-2 homology 1 and 2 (BH1 and BH2) domains (Fig. 1).", "This includes Bax which heterodimerizes with Bcl-2 and when overexpressed counteracts Bcl-214.", "We report here that site-specific mutagenesis of Bcl-2 establishes the two domains as novel dimerization motifs.", "Substitu-tion of Gly 145 in BHl domain or Trp 188 in BH2 domain completely abrogated Bcl-2's death-repressor activity in inter-leukin-3 deprivation, \u03b3-irradiation and glucocorticoid-induced apoptosis.", "Mutations that affected Bcl-2's function also disrupted its heterodimerization with Bax, yet still permitted Bcl-2 homo-dimerization.", "These results establish a functional role for the BH1 and BH2 domains and suggest Bcl-2 exerts its action through heterodimerization with Bax."], "structured": false}
{"doc_id": 4323449, "title": "KAP1 controls endogenous retroviruses in embryonic stem cells", "abstract": ["More than forty per cent of the mammalian genome is derived from retroelements, of which about one-quarter are endogenous retroviruses (ERVs).", "Some are still active, notably in mice the highly polymorphic early transposon (ETn)/MusD and intracisternal A-type particles (IAP).", "ERVs are transcriptionally silenced during early embryogenesis by histone and DNA methylation (and reviewed in ref.", "7), although the initiators of this process, which is essential to protect genome integrity, remain largely unknown.", "KAP1 (KRAB-associated protein 1, also known as tripartite motif-containing protein 28, TRIM28) represses genes by recruiting the histone methyltransferase SETDB1, heterochromatin protein 1 (HP1) and the NuRD histone deacetylase complex, but few of its physiological targets are known.", "Two lines of evidence suggest that KAP1-mediated repression could contribute to the control of ERVs: first, KAP1 can trigger permanent gene silencing during early embryogenesis, and second, a KAP1 complex silences the retrovirus murine leukaemia virus in embryonic cells.", "Consistent with this hypothesis, here we show that KAP1 deletion leads to a marked upregulation of a range of ERVs, in particular IAP elements, in mouse embryonic stem (ES) cells and in early embryos.", "We further demonstrate that KAP1 acts synergistically with DNA methylation to silence IAP elements, and that it is enriched at the 5\u2032 untranslated region (5\u2032UTR) of IAP genomes, where KAP1 deletion leads to the loss of histone 3 lysine 9 trimethylation (H3K9me3), a hallmark of KAP1-mediated repression.", "Correspondingly, IAP 5\u2032UTR sequences can impose in cis KAP1-dependent repression on a heterologous promoter in ES cells.", "Our results establish that KAP1 controls endogenous retroelements during early embryonic development."], "structured": false}
{"doc_id": 4324278, "title": "The TOR signalling pathway controls nuclear localization of nutrient-regulated transcription factors.", "abstract": ["The rapamycin-sensitive TOR signalling pathway in Saccharomyces cerevisiae activates a cell-growth program in response to nutrients such as nitrogen and carbon.", "The TOR1 and TOR2 kinases (TOR) control cytoplasmic protein synthesis and degradation through the conserved TAP42 protein.", "Upon phosphorylation by TOR, TAP42 binds and possibly inhibits type 2A and type-2A-related phosphatases; however, the mechanism by which TOR controls nuclear events such as global repression of starvation-specific transcription is unknown.", "Here we show that TOR prevents transcription of genes expressed upon nitrogen limitation by promoting the association of the GATA transcription factor GLN3 with the cytoplasmic protein URE2.", "The binding of GLN3 to URE2 requires TOR-dependent phosphorylation of GLN3.", "Phosphorylation and cytoplasmic retention of GLN3 are also dependent on the TOR effector TAP42, and are antagonized by the type-2A-related phosphatase SIT4.", "TOR inhibits expression of carbon-source-regulated genes by stimulating the binding of the transcriptional activators MSN2 and MSN4 to the cytoplasmic 14-3-3 protein BMH2.", "Thus, the TOR signalling pathway broadly controls nutrient metabolism by sequestering several transcription factors in the cytoplasm."], "structured": false}
{"doc_id": 4325137, "title": "Inhibition of pluripotential embryonic stem cell differentiation by purified polypeptides", "abstract": ["Murine embryonic stem (ES) cells are pluripotent cell lines established directly from the early embryo1,2 which can contribute differentiated progeny to all adult tissues, including the germ-cell lineage3, after re-incorporation into the normal embryo.", "They provide both a cellular vector for the generation of transgenic animals4 and a useful system for the identification of polypeptide factors controlling differentiation processes in early development5.", "In particular, medium conditioned by Buffalo rat liver cells contains a polypeptide factor, ES cell differentiation inhibitory activity (DIA), which specifically suppresses the spontaneous differentiation of ES cells in vitro, thereby permitting their growth as homogeneous stem cell populations in the absence of heterologous feeder cells6.", "ES cell pluripotentiality, including the ability to give rise to functional gametes, is preserved after prolonged culture in Buffalo rat liver media as a source of DIA7.", "Here, we report that purified DIA is related in structure and function to the recently identified haemopoetic regulatory factors human interleukin for DA cells8,9 and leukaemia inhibitory factor10.", "DIA and human interleukin DA/leukaemia inhibitory factor have thus been identified as related multifunctional regulatory factors with distinct biological activities in both early embryonic and haemopoetic stem cell systems."], "structured": false}
{"doc_id": 4325398, "title": "Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes", "abstract": ["Pancreatic cancer is a highly lethal malignancy with few effective therapies.", "We performed exome sequencing and copy number analysis to define genomic aberrations in a prospectively accrued clinical cohort (n = 142) of early (stage I and II) sporadic pancreatic ductal adenocarcinoma.", "Detailed analysis of 99 informative tumours identified substantial heterogeneity with 2,016 non-silent mutations and 1,628 copy-number variations.", "We define 16 significantly mutated genes, reaffirming known mutations (KRAS, TP53, CDKN2A, SMAD4, MLL3, TGFBR2, ARID1A and SF3B1), and uncover novel mutated genes including additional genes involved in chromatin modification (EPC1 and ARID2), DNA damage repair (ATM) and other mechanisms (ZIM2, MAP2K4, NALCN, SLC16A4 and MAGEA6).", "Integrative analysis with in vitro functional data and animal models provided supportive evidence for potential roles for these genetic aberrations in carcinogenesis.", "Pathway-based analysis of recurrently mutated genes recapitulated clustering in core signalling pathways in pancreatic ductal adenocarcinoma, and identified new mutated genes in each pathway.", "We also identified frequent and diverse somatic aberrations in genes described traditionally as embryonic regulators of axon guidance, particularly SLIT/ROBO signalling, which was also evident in murine Sleeping Beauty transposon-mediated somatic mutagenesis models of pancreatic cancer, providing further supportive evidence for the potential involvement of axon guidance genes in pancreatic carcinogenesis."], "structured": false}
{"doc_id": 4326318, "title": "Rejuvenation of aged progenitor cells by exposure to a young systemic environment", "abstract": ["The decline of tissue regenerative potential is a hallmark of ageing and may be due to age-related changes in tissue-specific stem cells.", "A decline in skeletal muscle stem cell (satellite cell) activity due to a loss of Notch signalling results in impaired regeneration of aged muscle.", "The decline in hepatic progenitor cell proliferation owing to the formation of a complex involving cEBP-\u03b1 and the chromatin remodelling factor brahma (Brm) inhibits the regenerative capacity of aged liver.", "To examine the influence of systemic factors on aged progenitor cells from these tissues, we established parabiotic pairings (that is, a shared circulatory system) between young and old mice (heterochronic parabioses), exposing old mice to factors present in young serum.", "Notably, heterochronic parabiosis restored the activation of Notch signalling as well as the proliferation and regenerative capacity of aged satellite cells.", "The exposure of satellite cells from old mice to young serum enhanced the expression of the Notch ligand (Delta), increased Notch activation, and enhanced proliferation in vitro.", "Furthermore, heterochronic parabiosis increased aged hepatocyte proliferation and restored the cEBP-\u03b1 complex to levels seen in young animals.", "These results suggest that the age-related decline of progenitor cell activity can be modulated by systemic factors that change with age."], "structured": false}
{"doc_id": 4335423, "title": "Continuous single-cell imaging of blood generation from haemogenic endothelium", "abstract": ["Despite decades of research, the identity of the cells generating the first haematopoietic cells in mammalian embryos is unknown.", "Indeed, whether blood cells arise from mesodermal cells, mesenchymal progenitors, bipotent endothelial\u2013haematopoietic precursors or haemogenic endothelial cells remains controversial.", "Proximity of endothelial and blood cells at sites of embryonic haematopoiesis, as well as their similar gene expression, led to the hypothesis of the endothelium generating blood.", "However, owing to lacking technology it has been impossible to observe blood cell emergence continuously at the single-cell level, and the postulated existence of haemogenic endothelial cells remains disputed.", "Here, using new imaging and cell-tracking methods, we show that embryonic endothelial cells can be haemogenic.", "By continuous long-term single-cell observation of mouse mesodermal cells generating endothelial cell and blood colonies, it was possible to detect haemogenic endothelial cells giving rise to blood cells.", "Living endothelial and haematopoietic cells were identified by simultaneous detection of morphology and multiple molecular and functional markers.", "Detachment of nascent blood cells from endothelium is not directly linked to asymmetric cell division, and haemogenic endothelial cells are specified from cells already expressing endothelial markers.", "These results improve our understanding of the developmental origin of mammalian blood and the potential generation of haematopoietic stem cells from embryonic stem cells."], "structured": false}
{"doc_id": 4335599, "title": "Formation of germ-line chimaeras from embryo-derived teratocarcinoma cell lines", "abstract": ["The recent availability in culture of embryo-derived pluripotential cells which exhibit both a normal karyotype and a high differentiative ability1\u20133 has encouraged us to assess the potential of these cells to form functional germ cells following their incorporation into chimaeric mice.", "We report here the results of blastocyst injection studies using three independently isolated XY embryo-derived cell lines (EK.CP1, EK.CC1.1 and EKCC1.2) which produce a very high proportion (>50%) of live-born animals that are overtly chimaeric.", "Seven chimaeric male mice, derived from these three lines, have, so far, proved to be functional germ-line chimaeras."], "structured": false}
{"doc_id": 4336849, "title": "Chloroquine resistance not linked to mdr-like genes in a Plasmodium falciparum cross", "abstract": ["CHLOROQUINE is thought to act against falciparum malaria by accumulating in the acid vesicles of the parasite and interfering with their function1\u00964.", "Parasites resistant to chloroquine expel the drug rapidly in an unaltered form, thereby reducing levels of accumulation in the vesicles5.", "The discovery that verapamil partially reverses chloroquine resistance in vitro 6 led to the proposal that efflux may involve an ATP-driven P-glycoprotein pump similar to that in mammalian multidrug-resistant (mdr) tumor cell lines.", "Indeed, Plasmodium falciparum contains at least two mdr-like genes7,8, one of which has been suggested to confer the chloroquine resistant (CQR) phenotype7,9,10.", "To determine if either of these genes is linked to chloroquine resistance, we performed a genetic cross between CQR and chloroquine-susceptible (CQS) clones of P. falciparum.", "Examination of 16 independent recombinant progeny indicated that the rapid efflux phenotype is controlled by a single gene or a closely linked group of genes.", "But, there was no linkage between the rapid efflux, CQR phenotype and either of the mdr-like P. falciparum genes or amplification of those genes.", "These data indicate that the genetic locus governing chloroquine efflux and resistance is independent of the known mdr-like genes."], "structured": false}
{"doc_id": 4340358, "title": "Identification of a cold receptor reveals a general role for TRP channels in thermosensation", "abstract": ["The cellular and molecular mechanisms that enable us to sense cold are not well understood.", "Insights into this process have come from the use of pharmacological agents, such as menthol, that elicit a cooling sensation.", "Here we have characterized and cloned a menthol receptor from trigeminal sensory neurons that is also activated by thermal stimuli in the cool to cold range.", "This cold- and menthol-sensitive receptor, CMR1, is a member of the TRP family of excitatory ion channels, and we propose that it functions as a transducer of cold stimuli in the somatosensory system.", "These findings, together with our previous identification of the heat-sensitive channels VR1 and VRL-1, demonstrate that TRP channels detect temperatures over a wide range and are the principal sensors of thermal stimuli in the mammalian peripheral nervous system."], "structured": false}
{"doc_id": 4340509, "title": "Surface mechanics mediate pattern formation in the developing retina", "abstract": ["Pattern formation of biological structures involves organizing different types of cells into a spatial configuration.", "In this study, we investigate the physical basis of biological patterning of the Drosophila retina in vivo.", "We demonstrate that E- and N-cadherins mediate apical adhesion between retina epithelial cells.", "Differential expression of N-cadherin within a sub-group of retinal cells (cone cells) causes them to form an overall shape that minimizes their surface contact with surrounding cells.", "The cells within this group, in both normal and experimentally manipulated conditions, pack together in the same way as soap bubbles do.", "The shaping of the cone cell group and packing of its components precisely imitate the physical tendency for surfaces to be minimized.", "Thus, simple patterned expression of N-cadherin results in a complex spatial pattern of cells owing to cellular surface mechanics."], "structured": false}
{"doc_id": 4343437, "title": "Role of inscuteable in orienting asymmetric cell divisions in Drosophila", "abstract": ["Drosophila neuroblasts and epithelial cells in the procephalic neurogenic region divide perpendicular to the surface, and segregate the proteins Numb and Prospero into the basal daughter cell.", "We demonstrate here that orientation of the mitotic spindle and correct localization of Numb and Prospero in these cells require the inscuteable gene.", "Moreover, ectopic expression of inscuteable in other epithelial cells leads to spindle reorientation.", "The Inscuteable protein localizes to the apical cell cortex before mitosis, suggesting that Inscuteable functions in establishing polarity for asymmetric cell division."], "structured": false}
{"doc_id": 4343811, "title": "Specific interference by ingested dsRNA.", "abstract": ["A genetic interference phenomenon in the nematode Caenorhabditis elegans has been described in which expression of an individual gene can be specifically reduced by microinjecting a corresponding fragment of double-stranded (ds) RNA.", "One striking feature of this process is a spreading effect: interference in a broad region of the animal is observed following the injection of dsRNA into the extracellular body cavity.", "Here we show that C. elegans can respond in a gene-specific manner to dsRNA encountered in the environment.", "C. elegans normally feed on bacteria, ingesting and grinding them in the pharynx and subsequently absorbing bacterial contents in the gut.", "We find that Escherichia coli bacteria expressing dsRNAs can confer specific interference effects on the nematode larvae that feed on them."], "structured": false}
{"doc_id": 4345315, "title": "Bacterial RNA and small antiviral compounds activate caspase-1 through cryopyrin/Nalp3", "abstract": ["Missense mutations in the CIAS1 gene cause three autoinflammatory disorders: familial cold autoinflammatory syndrome, Muckle\u2013Wells syndrome and neonatal-onset multiple-system inflammatory disease.", "Cryopyrin (also called Nalp3), the product of CIAS1, is a member of the NOD-LRR protein family that has been linked to the activation of intracellular host defence signalling pathways.", "Cryopyrin forms a multi-protein complex termed \u2018the inflammasome\u2019, which contains the apoptosis-associated speck-like protein (ASC) and caspase-1, and promotes caspase-1 activation and processing of pro-interleukin (IL)-1\u03b2 (ref.", "4).", "Here we show the effect of cryopyrin deficiency on inflammasome function and immune responses.", "Cryopyrin and ASC are essential for caspase-1 activation and IL-1\u03b2 and IL-18 production in response to bacterial RNA and the imidazoquinoline compounds R837 and R848.", "In contrast, secretion of tumour-necrosis factor-\u03b1 and IL-6, as well as activation of NF-\u03baB and mitogen-activated protein kinases (MAPKs) were unaffected by cryopyrin deficiency.", "Furthermore, we show that Toll-like receptors and cryopyrin control the secretion of IL-1\u03b2 and IL-18 through different intracellular pathways.", "These results reveal a critical role for cryopyrin in host defence through bacterial RNA-mediated activation of caspase-1, and provide insights regarding the pathogenesis of autoinflammatory syndromes."], "structured": false}
{"doc_id": 4345605, "title": "Control of cortical GABA circuitry development by Nrg1 and ErbB4 signalling", "abstract": ["Schizophrenia is a complex disorder that interferes with the function of several brain systems required for cognition and normal social behaviour.", "Although the most notable clinical aspects of the disease only become apparent during late adolescence or early adulthood, many lines of evidence suggest that schizophrenia is a neurodevelopmental disorder with a strong genetic component.", "Several independent studies have identified neuregulin 1 (NRG1) and its receptor ERBB4 as important risk genes for schizophrenia, although their precise role in the disease process remains unknown.", "Here we show that Nrg1 and ErbB4 signalling controls the development of inhibitory circuitries in the mammalian cerebral cortex by cell-autonomously regulating the connectivity of specific GABA (\u03b3-aminobutyric acid)-containing interneurons.", "In contrast to the prevalent view, which supports a role for these genes in the formation and function of excitatory synapses between pyramidal cells, we found that ErbB4 expression in the mouse neocortex and hippocampus is largely confined to certain classes of interneurons.", "In particular, ErbB4 is expressed by many parvalbumin-expressing chandelier and basket cells, where it localizes to axon terminals and postsynaptic densities receiving glutamatergic input.", "Gain- and loss-of-function experiments, both in vitro and in vivo, demonstrate that ErbB4 cell-autonomously promotes the formation of axo-axonic inhibitory synapses over pyramidal cells, and that this function is probably mediated by Nrg1.", "In addition, ErbB4 expression in GABA-containing interneurons regulates the formation of excitatory synapses onto the dendrites of these cells.", "By contrast, ErbB4 is dispensable for excitatory transmission between pyramidal neurons.", "Altogether, our results indicate that Nrg1 and ErbB4 signalling is required for the wiring of GABA-mediated circuits in the postnatal cortex, providing a new perspective to the involvement of these genes in the aetiology of schizophrenia."], "structured": false}
{"doc_id": 4345757, "title": "Obesity as a medical problem.", "abstract": ["Obesity is now so common within the world's population that it is beginning to replace undernutrition and infectious diseases as the most significant contributor to ill health.", "In particular, obesity is associated with diabetes mellitus, coronary heart disease, certain forms of cancer, and sleep-breathing disorders.", "Obesity is defined by a body-mass index (weight divided by square of the height) of 30 kg m(-2) or greater, but this does not take into account the morbidity and mortality associated with more modest degrees of overweight, nor the detrimental effect of intra-abdominal fat.", "The global epidemic of obesity results from a combination of genetic susceptibility, increased availability of high-energy foods and decreased requirement for physical activity in modern society.", "Obesity should no longer be regarded simply as a cosmetic problem affecting certain individuals, but an epidemic that threatens global well being."], "structured": false}
{"doc_id": 4346436, "title": "Nonlinear Elasticity in Biological Gels", "abstract": ["Unlike most synthetic materials, biological materials often stiffen as they are deformed.", "This nonlinear elastic response, critical for the physiological function of some tissues, has been documented since at least the 19th century, but the molecular structure and the design principles responsible for it are unknown.", "Current models for this response require geometrically complex ordered structures unique to each material.", "In this Article we show that a much simpler molecular theory accounts for strain stiffening in a wide range of molecularly distinct biopolymer gels formed from purified cytoskeletal and extracellular proteins.", "This theory shows that systems of semi-flexible chains such as filamentous proteins arranged in an open crosslinked meshwork invariably stiffen at low strains without the need for a specific architecture or multiple elements with different intrinsic stiffnesses."], "structured": false}
{"doc_id": 4346731, "title": "Live-cell delamination counterbalances epithelial growth to limit tissue overcrowding", "abstract": ["The development and maintenance of an epithelium requires finely balanced rates of growth and cell death.", "However, the mechanical and biochemical mechanisms that ensure proper feedback control of tissue growth, which when deregulated contribute to tumorigenesis, are poorly understood.", "Here we use the fly notum as a model system to identify a novel process of crowding-induced cell delamination that balances growth to ensure the development of well-ordered cell packing.", "In crowded regions of the tissue, a proportion of cells undergo a serial loss of cell\u2013cell junctions and a progressive loss of apical area, before being squeezed out by their neighbours.", "This path of delamination is recapitulated by a simple computational model of epithelial mechanics, in which stochastic cell loss relieves overcrowding as the system tends towards equilibrium.", "We show that this process of delamination is mechanistically distinct from apoptosis-mediated cell extrusion and precedes the first signs of cell death.", "Overall, this analysis reveals a simple mechanism that buffers epithelia against variations in growth.", "Because live-cell delamination constitutes a mechanistic link between epithelial hyperplasia and cell invasion, this is likely to have important implications for our understanding of the early stages of cancer development."], "structured": false}
{"doc_id": 4347374, "title": "Broad antiretroviral defence by human APOBEC3G through lethal editing of nascent reverse transcripts", "abstract": ["Viral replication usually requires that innate intracellular lines of defence be overcome, a task usually accomplished by specialized viral gene products.", "The virion infectivity factor (Vif) protein of human immunodeficiency virus (HIV) is required during the late stages of viral production to counter the antiviral activity of APOBEC3G (apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like 3G; also known as CEM15), a protein expressed notably in human T lymphocytes.", "When produced in the presence of APOBEC3G, vif-defective virus is non-infectious.", "APOBEC3G is closely related to APOBEC1, the central component of an RNA-editing complex that deaminates a cytosine residue in apoB messenger RNA.", "APOBEC family members also have potent DNA mutator activity through dC deamination; however, whether the editing potential of APOBEC3G has any relevance to HIV inhibition is unknown.", "Here, we demonstrate that it does, as APOBEC3G exerts its antiviral effect during reverse transcription to trigger G-to-A hypermutation in the nascent retroviral DNA.", "We also find that APOBEC3G can act on a broad range of retroviruses in addition to HIV, suggesting that hypermutation by editing is a general innate defence mechanism against this important group of pathogens."], "structured": false}
{"doc_id": 4350400, "title": "Generation of cell polarity in plants links endocytosis, auxin distribution and cell fate decisions", "abstract": ["Dynamically polarized membrane proteins define different cell boundaries and have an important role in intercellular communication\u2014a vital feature of multicellular development.", "Efflux carriers for the signalling molecule auxin from the PIN family are landmarks of cell polarity in plants and have a crucial involvement in auxin distribution-dependent development including embryo patterning, organogenesis and tropisms.", "Polar PIN localization determines the direction of intercellular auxin flow, yet the mechanisms generating PIN polarity remain unclear.", "Here we identify an endocytosis-dependent mechanism of PIN polarity generation and analyse its developmental implications.", "Real-time PIN tracking showed that after synthesis, PINs are initially delivered to the plasma membrane in a non-polar manner and their polarity is established by subsequent endocytic recycling.", "Interference with PIN endocytosis either by auxin or by manipulation of the Arabidopsis Rab5 GTPase pathway prevents PIN polarization.", "Failure of PIN polarization transiently alters asymmetric auxin distribution during embryogenesis and increases the local auxin response in apical embryo regions.", "This results in ectopic expression of auxin pathway-associated root-forming master regulators in embryonic leaves and promotes homeotic transformation of leaves to roots.", "Our results indicate a two-step mechanism for the generation of PIN polar localization and the essential role of endocytosis in this process.", "It also highlights the link between endocytosis-dependent polarity of individual cells and auxin distribution-dependent cell fate establishment for multicellular patterning."], "structured": false}
{"doc_id": 4353857, "title": "Congenital leptin deficiency is associated with severe early-onset obesity in humans.", "abstract": ["The extreme obesity of the obese (ob/ob) mouse is attributable to mutations in the gene encoding leptin, an adipocyte-specific secreted protein which has profound effects on appetite and energy expenditure.", "We know of no equivalent evidence regarding leptin's role in the control of fat mass in humans.", "We have examined two severely obese children who are members of the same highly consanguineous pedigree.", "Their serum leptin levels were very low despite their markedly elevated fat mass and, in both, a homozygous frame-shift mutation involving the deletion of a single guanine nucleotide in codon 133 of the gene for leptin was found.", "The severe obesity found in these congenitally leptin-deficient subjects provides the first genetic evidence that leptin is an important regulator of energy balance in humans."], "structured": false}
{"doc_id": 4361990, "title": "Targeting of cell-surface \u03b2-amyloid precursor protein to lysosomes: alternative processing into amyloid-bearing fragments", "abstract": ["PROGRESSIVE cerebral deposition of the amyloid \u03b2-peptide is an early and invariant feature of Alzheimer's disease.", "The \u03b2-peptide is released by proteolytic cleavages from the \u03b2-amyloid precursor protein (\u03b2APP)1, a membrane-spanning glycoprotein expressed in most mammalian cells.", "Normal secretion of \u03b2APP involves a cleavage in the \u03b2-peptide region2-3, releasing the soluble extramembranous portion4,5 and retaining a 10K C-terminal fragment in the membrane6.", "Because this secretory pathway precludes \u03b2-amyloid formation, we searched for an alternative proteolytic processing pathway that can generate \u03b2-peptide-bearing fragments from full-length \u03b2 APP.", "Incubation of living human endothelial cells with a \u03b2APP antibody revealed reinternalization of mature \u03b2APP from the cell surface and its targeting to endosomes/lysosomes.", "After cell-surface biotinylation, full-length biotinylated \u03b2APP was recovered inside the cells.", "Purification of lysosomes directly demonstrated the presence of mature \u03b2APP and an extensive array of \u03b2-peptide-containing proteolytic products.", "Our results define a second processing pathway for \u03b2APP and suggest that it may be responsible for generating amyloid-bearing fragments in Alzheimer's disease."], "structured": false}
{"doc_id": 4362729, "title": "A keratin cytoskeletal protein regulates protein synthesis and epithelial cell growth", "abstract": ["Cell growth, an increase in mass and size, is a highly regulated cellular event.", "The Akt/mTOR (mammalian target of rapamycin) signalling pathway has a central role in the control of protein synthesis and thus the growth of cells, tissues and organisms.", "A striking example of a physiological context requiring rapid cell growth is tissue repair in response to injury.", "Here we show that keratin 17, an intermediate filament protein rapidly induced in wounded stratified epithelia, regulates cell growth through binding to the adaptor protein 14-3-3\u03c3.", "Mouse skin keratinocytes lacking keratin 17 (ref.", "4) show depressed protein translation and are of smaller size, correlating with decreased Akt/mTOR signalling activity.", "Other signalling kinases have normal activity, pointing to the specificity of this defect.", "Two amino acid residues located in the amino-terminal head domain of keratin 17 are required for the serum-dependent relocalization of 14-3-3\u03c3 from the nucleus to the cytoplasm, and for the concomitant stimulation of mTOR activity and cell growth.", "These findings reveal a new and unexpected role for the intermediate filament cytoskeleton in influencing cell growth and size by regulating protein synthesis."], "structured": false}
{"doc_id": 4363526, "title": "Co-crystal structure of the HNF-3/fork head DNA-recognition motif resembles histone H5", "abstract": ["The three-dimensional structure of an HNF-3/fork head DNA-recognition motif complexed with DNA has been determined by X-ray crystallography at 2.5 \u212b resolution.", "This \u03b1/\u03b2 protein binds B-DNA as a monomer, through interactions with the DNA backbone and through both direct and water-mediated major and minor groove base contacts, inducing a 13\u00b0 bend.", "The transcription factor fold is very similar to the structure of histone H5.", "In its amino-terminal half, three \u03b1-helices adopt a compact structure that presents the third helix to the major groove.", "The remainder of the protein includes a twisted, antiparallel \u03b2-structure and random coil that interacts with the minor groove."], "structured": false}
{"doc_id": 4364884, "title": "A Mechanism Linking Extra Centrosomes to Chromosomal Instability", "abstract": ["Chromosomal instability (CIN) is a hallmark of many tumours and correlates with the presence of extra centrosomes.", "However, a direct mechanistic link between extra centrosomes and CIN has not been established.", "It has been proposed that extra centrosomes generate CIN by promoting multipolar anaphase, a highly abnormal division that produces three or more aneuploid daughter cells.", "Here we use long-term live-cell imaging to demonstrate that cells with multiple centrosomes rarely undergo multipolar cell divisions, and the progeny of these divisions are typically inviable.", "Thus, multipolar divisions cannot explain observed rates of CIN.", "In contrast, we observe that CIN cells with extra centrosomes routinely undergo bipolar cell divisions, but display a significantly increased frequency of lagging chromosomes during anaphase.", "To define the mechanism underlying this mitotic defect, we generated cells that differ only in their centrosome number.", "We demonstrate that extra centrosomes alone are sufficient to promote chromosome missegregation during bipolar cell division.", "These segregation errors are a consequence of cells passing through a transient 'multipolar spindle intermediate' in which merotelic kinetochore-microtubule attachment errors accumulate before centrosome clustering and anaphase.", "These findings provide a direct mechanistic link between extra centrosomes and CIN, two common characteristics of solid tumours.", "We propose that this mechanism may be a common underlying cause of CIN in human cancer."], "structured": false}
{"doc_id": 4366738, "title": "Haematopoietic stem cells and early lymphoid progenitors occupy distinct bone marrow niches", "abstract": ["Although haematopoietic stem cells (HSCs) are commonly assumed to reside within a specialized microenvironment, or niche, most published experimental manipulations of the HSC niche have affected the function of diverse restricted progenitors.", "This raises the fundamental question of whether HSCs and restricted progenitors reside within distinct, specialized niches or whether they share a common niche.", "Here we assess the physiological sources of the chemokine CXCL12 for HSC and restricted progenitor maintenance.", "Cxcl12(DsRed) knock-in mice (DsRed-Express2 recombined into the Cxcl12 locus) showed that Cxcl12 was primarily expressed by perivascular stromal cells and, at lower levels, by endothelial cells, osteoblasts and some haematopoietic cells.", "Conditional deletion of Cxcl12 from haematopoietic cells or nestin-cre-expressing cells had little or no effect on HSCs or restricted progenitors.", "Deletion of Cxcl12 from endothelial cells depleted HSCs but not myeloerythroid or lymphoid progenitors.", "Deletion of Cxcl12 from perivascular stromal cells depleted HSCs and certain restricted progenitors and mobilized these cells into circulation.", "Deletion of Cxcl12 from osteoblasts depleted certain early lymphoid progenitors but not HSCs or myeloerythroid progenitors, and did not mobilize these cells into circulation.", "Different stem and progenitor cells thus reside in distinct cellular niches in bone marrow: HSCs occupy a perivascular niche and early lymphoid progenitors occupy an endosteal niche."], "structured": false}
{"doc_id": 4373433, "title": "Broad neutralization coverage of HIV by multiple highly potent antibodies", "abstract": ["Broadly neutralizing antibodies against highly variable viral pathogens are much sought after to treat or protect against global circulating viruses.", "Here we probed the neutralizing antibody repertoires of four human immunodeficiency virus (HIV)-infected donors with remarkably broad and potent neutralizing responses and rescued 17 new monoclonal antibodies that neutralize broadly across clades.", "Many of the new monoclonal antibodies are almost tenfold more potent than the recently described PG9, PG16 and VRC01 broadly neutralizing monoclonal antibodies and 100-fold more potent than the original prototype HIV broadly neutralizing monoclonal antibodies.", "The monoclonal antibodies largely recapitulate the neutralization breadth found in the corresponding donor serum and many recognize novel epitopes on envelope (Env) glycoprotein gp120, illuminating new targets for vaccine design.", "Analysis of neutralization by the full complement of anti-HIV broadly neutralizing monoclonal antibodies now available reveals that certain combinations of antibodies should offer markedly more favourable coverage of the enormous diversity of global circulating viruses than others and these combinations might be sought in active or passive immunization regimes.", "Overall, the isolation of multiple HIV broadly neutralizing monoclonal antibodies from several donors that, in aggregate, provide broad coverage at low concentrations is a highly positive indicator for the eventual design of an effective antibody-based HIV vaccine."], "structured": false}
{"doc_id": 4373445, "title": "Coordination of Rho GTPase activities during cell protrusion", "abstract": ["The GTPases Rac1, RhoA and Cdc42 act together to control cytoskeleton dynamics.", "Recent biosensor studies have shown that all three GTPases are activated at the front of migrating cells, and biochemical evidence suggests that they may regulate one another: Cdc42 can activate Rac1 (ref. 8), and Rac1 and RhoA are mutually inhibitory.", "However, their spatiotemporal coordination, at the seconds and single-micrometre dimensions typical of individual protrusion events, remains unknown.", "Here we examine GTPase coordination in mouse embryonic fibroblasts both through simultaneous visualization of two GTPase biosensors and using a 'computational multiplexing' approach capable of defining the relationships between multiple protein activities visualized in separate experiments.", "We found that RhoA is activated at the cell edge synchronous with edge advancement, whereas Cdc42 and Rac1 are activated 2 micro-m behind the edge with a delay of 40 s. This indicates that Rac1 and RhoA operate antagonistically through spatial separation and precise timing, and that RhoA has a role in the initial events of protrusion, whereas Rac1 and Cdc42 activate pathways implicated in reinforcement and stabilization of newly expanded protrusions."], "structured": false}
{"doc_id": 4378885, "title": "Understanding mechanisms underlying human gene expression variation with RNA sequencing", "abstract": ["Understanding the genetic mechanisms underlying natural variation in gene expression is a central goal of both medical and evolutionary genetics, and studies of expression quantitative trait loci (eQTLs) have become an important tool for achieving this goal.", "Although all eQTL studies so far have assayed messenger RNA levels using expression microarrays, recent advances in RNA sequencing enable the analysis of transcript variation at unprecedented resolution.", "We sequenced RNA from 69 lymphoblastoid cell lines derived from unrelated Nigerian individuals that have been extensively genotyped by the International HapMap Project.", "By pooling data from all individuals, we generated a map of the transcriptional landscape of these cells, identifying extensive use of unannotated untranslated regions and more than 100 new putative protein-coding exons.", "Using the genotypes from the HapMap project, we identified more than a thousand genes at which genetic variation influences overall expression levels or splicing.", "We demonstrate that eQTLs near genes generally act by a mechanism involving allele-specific expression, and that variation that influences the inclusion of an exon is enriched within and near the consensus splice sites.", "Our results illustrate the power of high-throughput sequencing for the joint analysis of variation in transcription, splicing and allele-specific expression across individuals."], "structured": false}
{"doc_id": 4380004, "title": "Mesenchymal and haematopoietic stem cells form a unique bone marrow niche", "abstract": ["The cellular constituents forming the haematopoietic stem cell (HSC) niche in the bone marrow are unclear, with studies implicating osteoblasts, endothelial and perivascular cells.", "Here we demonstrate that mesenchymal stem cells (MSCs), identified using nestin expression, constitute an essential HSC niche component.", "Nestin+ MSCs contain all the bone-marrow colony-forming-unit fibroblastic activity and can be propagated as non-adherent \u2018mesenspheres\u2019 that can self-renew and expand in serial transplantations.", "Nestin+ MSCs are spatially associated with HSCs and adrenergic nerve fibres, and highly express HSC maintenance genes.", "These genes, and others triggering osteoblastic differentiation, are selectively downregulated during enforced HSC mobilization or \u03b23 adrenoreceptor activation.", "Whereas parathormone administration doubles the number of bone marrow nestin+ cells and favours their osteoblastic differentiation, in vivo nestin+ cell depletion rapidly reduces HSC content in the bone marrow.", "Purified HSCs home near nestin+ MSCs in the bone marrow of lethally irradiated mice, whereas in vivo nestin+ cell depletion significantly reduces bone marrow homing of haematopoietic progenitors.", "These results uncover an unprecedented partnership between two distinct somatic stem-cell types and are indicative of a unique niche in the bone marrow made of heterotypic stem-cell pairs."], "structured": false}
{"doc_id": 4380287, "title": "Response to self antigen imprints regulatory memory in tissues", "abstract": ["Immune homeostasis in tissues is achieved through a delicate balance between pathogenic T-cell responses directed at tissue-specific antigens and the ability of the tissue to inhibit these responses.", "The mechanisms by which tissues and the immune system communicate to establish and maintain immune homeostasis are currently unknown.", "Clinical evidence suggests that chronic or repeated exposure to self antigen within tissues leads to an attenuation of pathological autoimmune responses, possibly as a means to mitigate inflammatory damage and preserve function.", "Many human organ-specific autoimmune diseases are characterized by the initial presentation of the disease being the most severe, with subsequent flares being of lesser severity and duration.", "In fact, these diseases often spontaneously resolve, despite persistent tissue autoantigen expression.", "In the practice of antigen-specific immunotherapy, allergens or self antigens are repeatedly injected in the skin, with a diminution of the inflammatory response occurring after each successive exposure.", "Although these findings indicate that tissues acquire the ability to attenuate autoimmune reactions upon repeated responses to antigens, the mechanism by which this occurs is unknown.", "Here we show that upon expression of self antigen in a peripheral tissue, thymus-derived regulatory T cells (Treg cells) become activated, proliferate and differentiate into more potent suppressors, which mediate resolution of organ-specific autoimmunity in mice.", "After resolution of the inflammatory response, activated Treg cells are maintained in the target tissue and are primed to attenuate subsequent autoimmune reactions when antigen is re-expressed.", "Thus, Treg cells function to confer \u2018regulatory memory\u2019 to the target tissue.", "These findings provide a framework for understanding how Treg cells respond when exposed to self antigen in peripheral tissues and offer mechanistic insight into how tissues regulate autoimmunity."], "structured": false}
{"doc_id": 4380451, "title": "Reprogramming of human somatic cells to pluripotency with defined factors", "abstract": ["Pluripotency pertains to the cells of early embryos that can generate all of the tissues in the organism.", "Embryonic stem cells are embryo-derived cell lines that retain pluripotency and represent invaluable tools for research into the mechanisms of tissue formation.", "Recently, murine fibroblasts have been reprogrammed directly to pluripotency by ectopic expression of four transcription factors (Oct4, Sox2, Klf4 and Myc) to yield induced pluripotent stem (iPS) cells.", "Using these same factors, we have derived iPS cells from fetal, neonatal and adult human primary cells, including dermal fibroblasts isolated from a skin biopsy of a healthy research subject.", "Human iPS cells resemble embryonic stem cells in morphology and gene expression and in the capacity to form teratomas in immune-deficient mice.", "These data demonstrate that defined factors can reprogramme human cells to pluripotency, and establish a method whereby patient-specific cells might be established in culture."], "structured": false}
{"doc_id": 4381486, "title": "Haematopoietic stem cells do not asymmetrically segregate chromosomes or retain BrdU", "abstract": ["Stem cells are proposed to segregate chromosomes asymmetrically during self-renewing divisions so that older (\u2018immortal\u2019) DNA strands are retained in daughter stem cells whereas newly synthesized strands segregate to differentiating cells.", "Stem cells are also proposed to retain DNA labels, such as 5-bromo-2-deoxyuridine (BrdU), either because they segregate chromosomes asymmetrically or because they divide slowly.", "However, the purity of stem cells among BrdU-label-retaining cells has not been documented in any tissue, and the \u2018immortal strand hypothesis\u2019 has not been tested in a system with definitive stem cell markers.", "Here we tested these hypotheses in haematopoietic stem cells (HSCs), which can be highly purified using well characterized markers.", "We administered BrdU to newborn mice, mice treated with cyclophosphamide and granulocyte colony-stimulating factor, and normal adult mice for 4 to 10 days, followed by 70 days without BrdU. In each case, less than 6% of HSCs retained BrdU and less than 0.5% of all BrdU-retaining haematopoietic cells were HSCs, revealing that BrdU has poor specificity and poor sensitivity as an HSC marker.", "Sequential administration of 5-chloro-2-deoxyuridine and 5-iodo-2-deoxyuridine indicated that all HSCs segregate their chromosomes randomly.", "Division of individual HSCs in culture revealed no asymmetric segregation of the label.", "Thus, HSCs cannot be identified on the basis of BrdU-label retention and do not retain older DNA strands during division, indicating that these are not general properties of stem cells."], "structured": false}
{"doc_id": 4385779, "title": "Circadian Clocks in Human Red Blood Cells", "abstract": ["Circadian (\u223c24 hour)", "clocks are fundamentally important for coordinated physiology in organisms as diverse as cyanobacteria and humans.", "All current models of the molecular circadian clockwork in eukaryotic cells are based on transcription-translation feedback loops.", "Non-transcriptional mechanisms in the clockwork have been difficult to study in mammalian systems.", "We circumvented these problems by developing novel assays using human red blood cells, which have no nucleus (or DNA) and therefore cannot perform transcription.", "Our results show that transcription is not required for circadian oscillations in humans, and that non-transcriptional events seem to be sufficient to sustain cellular circadian rhythms.", "Using red blood cells, we found that peroxiredoxins, highly conserved antioxidant proteins, undergo \u223c24-hour redox cycles, which persist for many days under constant conditions (that is, in the absence of external cues).", "Moreover, these rhythms are entrainable (that is, tunable by environmental stimuli) and temperature-compensated, both key features of circadian rhythms.", "We anticipate that our findings will facilitate more sophisticated cellular clock models, highlighting the interdependency of transcriptional and non-transcriptional oscillations in potentially all eukaryotic cells."], "structured": false}
{"doc_id": 4387484, "title": "G-protein-coupled receptor of Kaposi's sarcoma-associated herpesvirus is a viral oncogene and angiogenesis activator.", "abstract": ["The Kaposi's sarcoma-associated herpesvirus (KSHV/HHV8) is a gamma-2 herpesvirus that is implicated in the pathogenesis of Kaposi's sarcoma and of primary effusion B-cell lymphomas (PELs).", "KSHV infects malignant and progenitor cells of Kaposi's sarcoma and PEL, it encodes putative oncogenes and genes that may cause Kaposi's sarcoma pathogenesis by stimulating angiogenesis.", "The G-protein-coupled receptor encoded by an open reading frame (ORF 74) of KSHV is expressed in Kaposi's sarcoma lesions and in PEL and stimulates signalling pathways linked to cell proliferation in a constitutive (agonist-independent) way.", "Here we show that signalling by this KSHV G-protein-coupled receptor leads to cell transformation and tumorigenicity, and induces a switch to an angiogenic phenotype mediated by vascular endothelial growth factor, an angiogenesis and Kaposi's-spindle-cell growth factor.", "We find that this receptor can activate two protein kinases, JNK/SAPK and p38MAPK, by triggering signalling cascades like those induced by inflammatory cytokines that are angiogenesis activators and mitogens for Kaposi's sarcoma cells and B cells.", "We conclude that the KSHV G-protein-coupled receptor is a viral oncogene that can exploit cell signalling pathways to induce transformation and angiogenesis in KSHV-mediated oncogenesis."], "structured": false}
{"doc_id": 4387494, "title": "Therapeutic potential of GSK-J4, a histone demethylase KDM6B/JMJD3 inhibitor, for acute myeloid leukemia", "abstract": ["PURPOSE Acute myeloid leukemia (AML) is a heterogeneous disease with poor outcomes.", "Despite increased evidence shows that dysregulation of histone modification contributes to AML, specific drugs targeting key histone modulators are not applied in the clinical treatment of AML.", "Here, we investigated whether targeting KDM6B, the demethylase of tri-methylated histone H3 lysine 27 (H3K27me3), has a therapeutic potential for AML.   \n", "METHODS A KDM6B-specific inhibitor, GSK-J4, was applied to treat the primary cells from AML patients and AML cell lines in vitro and in vivo.", "RNA-sequencing was performed to reveal the underlying mechanisms of inhibiting KDM6B for the treatment of AML.   \n", "RESULTS Here we observed that the mRNA expression of KDM6B was up-regulated in AML and positively correlated with poor survival.", "Treatment with GSK-J4 increased the global level of H3K27me3 and reduced the proliferation and colony-forming ability of primary AML cells and AML cell lines.", "GSK-J4 treatment significantly induced cell apoptosis and cell-cycle arrest in Kasumi-1 cells, and displayed a synergistic effect with cytosine arabinoside.", "Notably, injection of GSK-J4 attenuated the disease progression in a human AML xenograft mouse model in vivo.", "Treatment with GSK-J4 predominantly resulted in down-regulation of DNA replication and cell-cycle-related pathways, as well as abrogated the expression of critical cancer-promoting HOX genes.", "ChIP-qPCR validated an increased enrichment of H3K27me3 in the transcription start sites of these HOX genes.   \n", "CONCLUSIONS In summary, our findings suggest that targeting KDM6B with GSK-J4 has a therapeutic potential for the treatment of AML."], "structured": true}
{"doc_id": 4387784, "title": "Structure of the proton-gated urea channel from the gastric pathogen Helicobacter pylori", "abstract": ["Half the world's population is chronically infected with Helicobacter pylori, causing gastritis, gastric ulcers and an increased incidence of gastric adenocarcinoma.", "Its proton-gated inner-membrane urea channel, HpUreI, is essential for survival in the acidic environment of the stomach.", "The channel is closed at neutral pH and opens at acidic pH to allow the rapid access of urea to cytoplasmic urease.", "Urease produces NH(3) and CO(2), neutralizing entering protons and thus buffering the periplasm to a pH of roughly 6.1 even in gastric juice at a pH below 2.0.", "Here we report the structure of HpUreI, revealing six protomers assembled in a hexameric ring surrounding a central bilayer plug of ordered lipids.", "Each protomer encloses a channel formed by a twisted bundle of six transmembrane helices.", "The bundle defines a previously unobserved fold comprising a two-helix hairpin motif repeated three times around the central axis of the channel, without the inverted repeat of mammalian-type urea transporters.", "Both the channel and the protomer interface contain residues conserved in the AmiS/UreI superfamily, suggesting the preservation of channel architecture and oligomeric state in this superfamily.", "Predominantly aromatic or aliphatic side chains line the entire channel and define two consecutive constriction sites in the middle of the channel.", "Mutation of Trp 153 in the cytoplasmic constriction site to Ala or Phe decreases the selectivity for urea in comparison with thiourea, suggesting that solute interaction with Trp 153 contributes specificity.", "The previously unobserved hexameric channel structure described here provides a new model for the permeation of urea and other small amide solutes in prokaryotes and archaea."], "structured": false}
{"doc_id": 4388082, "title": "Drosophila oocyte localization is mediated by differential cadherin-based adhesion.", "abstract": ["In a Drosophila follicle the oocyte always occupies a posterior position among a group of sixteen germline cells.", "Although the importance of this cell arrangement for the subsequent formation of the anterior-posterior axis of the embryo is well documented, the molecular mechanism responsible for the posterior localization of the oocyte was unknown.", "Here we show that the homophilic adhesion molecule DE-cadherin mediates oocyte positioning.", "During follicle biogenesis, DE-cadherin is expressed in germline (including oocyte) and surrounding follicle cells, with the highest concentration of DE-cadherin being found at the interface between oocyte and posterior follicle cells.", "Mosaic analysis shows that DE-cadherin is required in both germline and follicle cells for correct oocyte localization, indicating that germline-soma interactions may be involved in this process.", "By analysing the behaviour of the oocyte in follicles with a chimaeric follicular epithelium, we find that the position of the oocyte is determined by the position of DE-cadherin-expressing follicle cells, to which the oocyte attaches itself selectively.", "Among the DE-cadherin positive follicle cells, the oocyte preferentially contacts those cells that express higher levels of DE-cadherin.", "On the basis of these data, we propose that in wild-type follicles the oocyte competes successfully with its sister germline cells for contact to the posterior follicle cells, a sorting process driven by different concentrations of DE-cadherin.", "This is, to our knowledge, the first in vivo example of a cell-sorting process that depends on differential adhesion mediated by a cadherin."], "structured": false}
{"doc_id": 4388470, "title": "Somatic sex identity is cell-autonomous in the chicken", "abstract": ["In the mammalian model of sex determination, embryos are considered to be sexually indifferent until the transient action of a sex-determining gene initiates gonadal differentiation.", "Although this model is thought to apply to all vertebrates, this has yet to be established.", "Here we have examined three lateral gynandromorph chickens (a rare, naturally occurring phenomenon in which one side of the animal appears male and the other female) to investigate the sex-determining mechanism in birds.", "These studies demonstrated that gynandromorph birds are genuine male:female chimaeras, and indicated that male and female avian somatic cells may have an inherent sex identity.", "To test this hypothesis, we transplanted presumptive mesoderm between embryos of reciprocal sexes to generate embryos containing male:female chimaeric gonads.", "In contrast to the outcome for mammalian mixed-sex chimaeras, in chicken mixed-sex chimaeras the donor cells were excluded from the functional structures of the host gonad.", "In an example where female tissue was transplanted into a male host, donor cells contributing to the developing testis retained a female identity and expressed a marker of female function.", "Our study demonstrates that avian somatic cells possess an inherent sex identity and that, in birds, sexual differentiation is substantively cell autonomous."], "structured": false}
{"doc_id": 4389252, "title": "Centrosome polarization delivers secretory granules to the immunological synapse", "abstract": ["Cytotoxic T lymphocytes (CTLs) destroy virally infected and tumorigenic cells by releasing the contents of specialized secretory lysosomes\u2014termed \u2018lytic granules\u2019\u2014at the immunological synapse formed between the CTL and the target.", "On contact with the target cell, the microtubule organizing centre of the CTL polarizes towards the target and granules move along microtubules in a minus-end direction towards the polarized microtubule organizing centre.", "However, the final steps of secretion have remained unclear.", "Here we show that CTLs do not require actin or plus-end microtubule motors for secretion, but instead the centrosome moves to and contacts the plasma membrane at the central supramolecular activation cluster of the immunological synapse.", "Actin and IQGAP1 are cleared away from the synapse, and granules are delivered directly to the plasma membrane.", "These data show that CTLs use a previously unreported mechanism for delivering secretory granules to the immunological synapse, with granule secretion controlled by centrosome delivery to the plasma membrane."], "structured": false}
{"doc_id": 4389394, "title": "Deubiquitination of p53 by HAUSP is an important pathway for p53 stabilization", "abstract": ["The p53 tumour suppressor is a short-lived protein that is maintained at low levels in normal cells by Mdm2-mediated ubiquitination and subsequent proteolysis.", "Stabilization of p53 is crucial for its tumour suppressor function.", "However, the precise mechanism by which ubiquitinated p53 levels are regulated in vivo is not completely understood.", "By mass spectrometry of affinity-purified p53-associated factors, we have identified herpesvirus-associated ubiquitin-specific protease (HAUSP) as a novel p53-interacting protein.", "HAUSP strongly stabilizes p53 even in the presence of excess Mdm2, and also induces p53-dependent cell growth repression and apoptosis.", "Significantly, HAUSP has an intrinsic enzymatic activity that specifically deubiquitinates p53 both in vitro and in vivo.", "In contrast, expression of a catalytically inactive point mutant of HAUSP in cells increases the levels of p53 ubiquitination and destabilizes p53.", "These findings reveal an important mechanism by which p53 can be stabilized by direct deubiquitination and also imply that HAUSP might function as a tumour suppressor in vivo through the stabilization of p53."], "structured": false}
{"doc_id": 4391121, "title": "Defective tryptophan catabolism underlies inflammation in mouse chronic granulomatous disease", "abstract": ["Half a century ago, chronic granulomatous disease (CGD) was first described as a disease fatally affecting the ability of children to survive infections.", "Various milestone discoveries have since been made, from an insufficient ability of patients\u2019 leucocytes to kill microbes to the underlying genetic abnormalities.", "In this inherited disorder, phagocytes lack NADPH oxidase activity and do not generate reactive oxygen species, most notably superoxide anion, causing recurrent bacterial and fungal infections.", "Patients with CGD also suffer from chronic inflammatory conditions, most prominently granuloma formation in hollow viscera.", "The precise mechanisms of the increased microbial pathogenicity have been unclear, and more so the reasons for the exaggerated inflammatory response.", "Here we show that a superoxide-dependent step in tryptophan metabolism along the kynurenine pathway is blocked in CGD mice with lethal pulmonary aspergillosis, leading to unrestrained V\u03b31+ \u03b3\u03b4 T-cell reactivity, dominant production of interleukin (IL)-17, defective regulatory T-cell activity and acute inflammatory lung injury.", "Although beneficial effects are induced by IL-17 neutralization or \u03b3\u03b4 T-cell contraction, complete cure and reversal of the hyperinflammatory phenotype are achieved by replacement therapy with a natural kynurenine distal to the blockade in the pathway.", "Effective therapy, which includes co-administration of recombinant interferon-\u03b3 (IFN-\u03b3), restores production of downstream immunoactive metabolites and enables the emergence of regulatory V\u03b34+ \u03b3\u03b4 and Foxp3+ \u03b1\u03b2 T cells.", "Therefore, paradoxically, the lack of reactive oxygen species contributes to the hyperinflammatory phenotype associated with NADPH oxidase deficiencies, through a dysfunctional kynurenine pathway of tryptophan catabolism.", "Yet, this condition can be reverted by reactivating the pathway downstream of the superoxide-dependent step."], "structured": false}
{"doc_id": 4391685, "title": "Experimental and theoretical study of mitotic spindle orientation", "abstract": ["The architecture and adhesiveness of a cell microenvironment is a critical factor for the regulation of spindle orientation in vivo.", "Using a combination of theory and experiments, we have investigated spindle orientation in HeLa (human) cells.", "Here we show that spindle orientation can be understood as the result of the action of cortical force generators, which interact with spindle microtubules and are activated by cortical cues.", "We develop a simple physical description of this spindle mechanics, which allows us to calculate angular profiles of the torque acting on the spindle, as well as the angular distribution of spindle orientations.", "Our model accounts for the preferred spindle orientation and the shape of the full angular distribution of spindle orientations observed in a large variety of different cellular microenvironment geometries.", "It also correctly describes asymmetric spindle orientations, which are observed for certain distributions of cortical cues.", "We conclude that, on the basis of a few simple assumptions, we can provide a quantitative description of the spindle orientation of adherent cells."], "structured": false}
{"doc_id": 4391817, "title": "CHROMOTHRIPSIS FROM DNA DAMAGE IN MICRONUCLEI", "abstract": ["Genome sequencing has uncovered a new mutational phenomenon in cancer and congenital disorders called chromothripsis.", "Chromothripsis is characterized by extensive genomic rearrangements and an oscillating pattern of DNA copy number levels, all curiously restricted to one or a few chromosomes.", "The mechanism for chromothripsis is unknown, but we previously proposed that it could occur through the physical isolation of chromosomes in aberrant nuclear structures called micronuclei.", "Here, using a combination of live cell imaging and single-cell genome sequencing, we demonstrate that micronucleus formation can indeed generate a spectrum of genomic rearrangements, some of which recapitulate all known features of chromothripsis.", "These events are restricted to the mis-segregated chromosome and occur within one cell division.", "We demonstrate that the mechanism for chromothripsis can involve the fragmentation and subsequent reassembly of a single chromatid from a micronucleus.", "Collectively, these experiments establish a new mutational process of which chromothripsis is one extreme outcome."], "structured": false}
{"doc_id": 4392608, "title": "DNA-binding factors shape the mouse methylome at distal regulatory regions", "abstract": ["Methylation of cytosines is an essential epigenetic modification in mammalian genomes, yet the rules that govern methylation patterns remain largely elusive.", "To gain insights into this process, we generated base-pair-resolution mouse methylomes in stem cells and neuronal progenitors.", "Advanced quantitative analysis identified low-methylated regions (LMRs) with an average methylation of 30%.", "These represent CpG-poor distal regulatory regions as evidenced by location, DNase I hypersensitivity, presence of enhancer chromatin marks and enhancer activity in reporter assays.", "LMRs are occupied by DNA-binding factors and their binding is necessary and sufficient to create LMRs.", "A comparison of neuronal and stem-cell methylomes confirms this dependency, as cell-type-specific LMRs are occupied by cell-type-specific transcription factors.", "This study provides methylome references for the mouse and shows that DNA-binding factors locally influence DNA methylation, enabling the identification of active regulatory regions."], "structured": false}
{"doc_id": 4393153, "title": "Molecular basis of RNA-dependent RNA polymerase II activity", "abstract": ["RNA polymerase (Pol) II catalyses DNA-dependent RNA synthesis during gene transcription.", "There is, however, evidence that Pol II also possesses RNA-dependent RNA polymerase (RdRP) activity.", "Pol II can use a homopolymeric RNA template, can extend RNA by several nucleotides in the absence of DNA, and has been implicated in the replication of the RNA genomes of hepatitis delta virus (HDV) and plant viroids.", "Here we show the intrinsic RdRP activity of Pol II with only pure polymerase, an RNA template\u2013product scaffold and nucleoside triphosphates (NTPs).", "Crystallography reveals the template\u2013product duplex in the site occupied by the DNA\u2013RNA hybrid during transcription.", "RdRP activity resides at the active site used during transcription, but it is slower and less processive than DNA-dependent activity.", "RdRP activity is also obtained with part of the HDV antigenome.", "The complex of transcription factor IIS (TFIIS) with Pol II can cleave one HDV strand, create a reactive stem-loop in the hybrid site, and extend the new RNA 3\u2032 end.", "Short RNA stem-loops with a 5\u2032 extension suffice for activity, but their growth to a critical length apparently impairs processivity.", "The RdRP activity of Pol II provides a missing link in molecular evolution, because it suggests that Pol II evolved from an ancient replicase that duplicated RNA genomes."], "structured": false}
{"doc_id": 4394525, "title": "Bacteria activate sensory neurons that modulate pain and inflammation", "abstract": ["Nociceptor sensory neurons are specialized to detect potentially damaging stimuli, protecting the organism by initiating the sensation of pain and eliciting defensive behaviours.", "Bacterial infections produce pain by unknown molecular mechanisms, although they are presumed to be secondary to immune activation.", "Here we demonstrate that bacteria directly activate nociceptors, and that the immune response mediated through TLR2, MyD88, T cells, B cells, and neutrophils and monocytes is not necessary for Staphylococcus aureus-induced pain in mice.", "Mechanical and thermal hyperalgesia in mice is correlated with live bacterial load rather than tissue swelling or immune activation.", "Bacteria induce calcium flux and action potentials in nociceptor neurons, in part via bacterial N-formylated peptides and the pore-forming toxin \u03b1-haemolysin, through distinct mechanisms.", "Specific ablation of Nav1.8-lineage neurons, which include nociceptors, abrogated pain during bacterial infection, but concurrently increased local immune infiltration and lymphadenopathy of the draining lymph node.", "Thus, bacterial pathogens produce pain by directly activating sensory neurons that modulate inflammation, an unsuspected role for the nervous system in host-pathogen interactions."], "structured": false}
{"doc_id": 4394817, "title": "E2F1-3 Switch from Activators in Progenitor Cells to Repressors in Differentiating Cells", "abstract": ["In the established model of mammalian cell cycle control, the retinoblastoma protein (Rb) functions to restrict cells from entering S phase by binding and sequestering E2f activators (E2f1, E2f2 and E2f3), which are invariably portrayed as the ultimate effectors of a transcriptional program that commit cells to enter and progress through S phase.", "Using a panel of tissue-specific cre-transgenic mice and conditional E2f alleles we examined the effects of E2f1, E2f2 and E2f3 triple deficiency in murine embryonic stem cells, embryos and small intestines.", "We show that in normal dividing progenitor cells E2f1-3 function as transcriptional activators, but contrary to the current view, are dispensable for cell division and instead are necessary for cell survival.", "In differentiating cells E2f1-3 function in a complex with Rb as repressors to silence E2f targets and facilitate exit from the cell cycle.", "The inactivation of Rb in differentiating cells resulted in a switch of E2f1-3 from repressors to activators, leading to the superactivation of E2f responsive targets and ectopic cell divisions.", "Loss of E2f1-3 completely suppressed these phenotypes caused by Rb deficiency.", "This work contextualizes the activator versus repressor functions of E2f1-3 in vivo, revealing distinct roles in dividing versus differentiating cells and in normal versus cancer-like cell cycles."], "structured": false}
{"doc_id": 4396105, "title": "K-Ras(G12C) inhibitors allosterically control GTP affinity and effector interactions", "abstract": ["Somatic mutations in the small GTPase K-Ras are the most common activating lesions found in human cancer, and are generally associated with poor response to standard therapies.", "Efforts to target this oncogene directly have faced difficulties owing to its picomolar affinity for GTP/GDP and the absence of known allosteric regulatory sites.", "Oncogenic mutations result in functional activation of Ras family proteins by impairing GTP hydrolysis.", "With diminished regulation by GTPase activity, the nucleotide state of Ras becomes more dependent on relative nucleotide affinity and concentration.", "This gives GTP an advantage over GDP and increases the proportion of active GTP-bound Ras.", "Here we report the development of small molecules that irreversibly bind to a common oncogenic mutant, K-Ras(G12C).", "These compounds rely on the mutant cysteine for binding and therefore do not affect the wild-type protein.", "Crystallographic studies reveal the formation of a new pocket that is not apparent in previous structures of Ras, beneath the effector binding switch-II region.", "Binding of these inhibitors to K-Ras(G12C) disrupts both switch-I and switch-II, subverting the native nucleotide preference to favour GDP over GTP and impairing binding to Raf.", "Our data provide structure-based validation of a new allosteric regulatory site on Ras that is targetable in a mutant-specific manner."], "structured": false}
{"doc_id": 4398832, "title": "Cyclin A Regulates Kinetochore-Microtubules to Promote Faithful Chromosome Segregation", "abstract": ["The most conspicuous event in the cell cycle is the alignment of chromosomes in metaphase.", "Chromosome alignment fosters faithful segregation through the formation of bi-oriented attachments of kinetochores to spindle microtubules.", "Notably, numerous kinetochore-microtubule (k-MT) attachment errors are present in early mitosis (prometaphase), and the persistence of those errors is the leading cause of chromosome mis-segregation in aneuploid human tumour cells that continually mis-segregate whole chromosomes and display chromosomal instability.", "How robust error correction is achieved in prometaphase to ensure error-free mitosis remains unknown.", "Here we show that k-MT attachments in prometaphase cells are considerably less stable than in metaphase cells.", "The switch to more stable k-MT attachments in metaphase requires the proteasome-dependent destruction of cyclin A in prometaphase.", "Persistent cyclin A expression prevents k-MT stabilization even in cells with aligned chromosomes.", "By contrast, k-MTs are prematurely stabilized in cyclin-A-deficient cells.", "Consequently, cells lacking cyclin A display higher rates of chromosome mis-segregation.", "Thus, the stability of k-MT attachments increases decisively in a coordinated fashion among all chromosomes as cells transit from prometaphase to metaphase.", "Cyclin A creates a cellular environment that promotes microtubule detachment from kinetochores in prometaphase to ensure efficient error correction and faithful chromosome segregation."], "structured": false}
{"doc_id": 4399268, "title": "Induced pluripotent stem cells from a spinal muscular atrophy patient", "abstract": ["Spinal muscular atrophy is one of the most common inherited forms of neurological disease leading to infant mortality.", "Patients have selective loss of lower motor neurons resulting in muscle weakness, paralysis and often death.", "Although patient fibroblasts have been used extensively to study spinal muscular atrophy, motor neurons have a unique anatomy and physiology which may underlie their vulnerability to the disease process.", "Here we report the generation of induced pluripotent stem cells from skin fibroblast samples taken from a child with spinal muscular atrophy.", "These cells expanded robustly in culture, maintained the disease genotype and generated motor neurons that showed selective deficits compared to those derived from the child\u2019s unaffected mother.", "This is the first study to show that human induced pluripotent stem cells can be used to model the specific pathology seen in a genetically inherited disease.", "As such, it represents a promising resource to study disease mechanisms, screen new drug compounds and develop new therapies."], "structured": false}
{"doc_id": 4399311, "title": "A role for mitochondria in NLRP3 inflammasome activation", "abstract": ["An inflammatory response initiated by the NLRP3 inflammasome is triggered by a variety of situations of host \u2018danger\u2019, including infection and metabolic dysregulation.", "Previous studies suggested that NLRP3 inflammasome activity is negatively regulated by autophagy and positively regulated by reactive oxygen species (ROS) derived from an uncharacterized organelle.", "Here we show that mitophagy/autophagy blockade leads to the accumulation of damaged, ROS-generating mitochondria, and this in turn activates the NLRP3 inflammasome.", "Resting NLRP3 localizes to endoplasmic reticulum structures, whereas on inflammasome activation both NLRP3 and its adaptor ASC redistribute to the perinuclear space where they co-localize with endoplasmic reticulum and mitochondria organelle clusters.", "Notably, both ROS generation and inflammasome activation are suppressed when mitochondrial activity is dysregulated by inhibition of the voltage-dependent anion channel.", "This indicates that NLRP3 inflammasome senses mitochondrial dysfunction and may explain the frequent association of mitochondrial damage with inflammatory diseases."], "structured": false}
{"doc_id": 4401289, "title": "Break-induced telomere synthesis underlies alternative telomere maintenance", "abstract": ["Homology-directed DNA repair is essential for genome maintenance through templated DNA synthesis.", "Alternative lengthening of telomeres (ALT) necessitates homology-directed DNA repair to maintain telomeres in about 10\u201315% of human cancers.", "How DNA damage induces assembly and execution of a DNA replication complex (break-induced replisome) at telomeres or elsewhere in the mammalian genome is poorly understood.", "Here we define break-induced telomere synthesis and demonstrate that it utilizes a specialized replisome, which underlies ALT telomere maintenance.", "DNA double-strand breaks enact nascent telomere synthesis by long-tract unidirectional replication.", "Proliferating cell nuclear antigen (PCNA) loading by replication factor C (RFC) acts as the initial sensor of telomere damage to establish predominance of DNA polymerase \u03b4 (Pol \u03b4) through its POLD3 subunit.", "Break-induced telomere synthesis requires the RFC\u2013PCNA\u2013Pol \u03b4 axis, but is independent of other canonical replisome components, ATM and ATR, or the homologous recombination protein Rad51.", "Thus, the inception of telomere damage recognition by the break-induced replisome orchestrates homology-directed telomere maintenance."], "structured": false}
{"doc_id": 4402497, "title": "Innate immunity induced by composition-dependent RIG-I recognition of hepatitis C virus RNA", "abstract": ["Innate immune defences are essential for the control of virus infection and are triggered through host recognition of viral macromolecular motifs known as pathogen-associated molecular patterns (PAMPs).", "Hepatitis C virus (HCV) is an RNA virus that replicates in the liver, and infects 200 million people worldwide.", "Infection is regulated by hepatic immune defences triggered by the cellular RIG-I helicase.", "RIG-I binds PAMP RNA and signals interferon regulatory factor 3 activation to induce the expression of interferon-\u03b1/\u03b2 and antiviral/interferon-stimulated genes (ISGs) that limit infection.", "Here we identify the polyuridine motif of the HCV genome 3\u2032 non-translated region and its replication intermediate as the PAMP substrate of RIG-I, and show that this and similar homopolyuridine or homopolyriboadenine motifs present in the genomes of RNA viruses are the chief feature of RIG-I recognition and immune triggering in human and murine cells.", "5\u2032 terminal triphosphate on the PAMP RNA was necessary but not sufficient for RIG-I binding, which was primarily dependent on homopolymeric ribonucleotide composition, linear structure and length.", "The HCV PAMP RNA stimulated RIG-I-dependent signalling to induce a hepatic innate immune response in vivo, and triggered interferon and ISG expression to suppress HCV infection in vitro.", "These results provide a conceptual advance by defining specific homopolymeric RNA motifs within the genome of HCV and other RNA viruses as the PAMP substrate of RIG-I, and demonstrate immunogenic features of the PAMP\u2013RIG-I interaction that could be used as an immune adjuvant for vaccine and immunotherapy approaches."], "structured": false}
{"doc_id": 4404433, "title": "Generation of transgenic non-human primates with germline transmission", "abstract": ["The common marmoset (Callithrix jacchus) is increasingly attractive for use as a non-human primate animal model in biomedical research.", "It has a relatively high reproduction rate for a primate, making it potentially suitable for transgenic modification.", "Although several attempts have been made to produce non-human transgenic primates, transgene expression in the somatic tissues of live infants has not been demonstrated by objective analyses such as polymerase chain reaction with reverse transcription or western blots.", "Here we show that the injection of a self-inactivating lentiviral vector in sucrose solution into marmoset embryos results in transgenic common marmosets that expressed the transgene in several organs.", "Notably, we achieved germline transmission of the transgene, and the transgenic offspring developed normally.", "The successful creation of transgenic marmosets provides a new animal model for human disease that has the great advantage of a close genetic relationship with humans.", "This model will be valuable to many fields of biomedical research."], "structured": false}
{"doc_id": 4405194, "title": "Induction of human neuronal cells by defined transcription factors", "abstract": ["Somatic cell nuclear transfer, cell fusion, or expression of lineage-specific factors have been shown to induce cell-fate changes in diverse somatic cell types.", "We recently observed that forced expression of a combination of three transcription factors, Brn2 (also known as Pou3f2), Ascl1 and Myt1l, can efficiently convert mouse fibroblasts into functional induced neuronal (iN) cells.", "Here we show that the same three factors can generate functional neurons from human pluripotent stem cells as early as 6 days after transgene activation.", "When combined with the basic helix-loop-helix transcription factor NeuroD1, these factors could also convert fetal and postnatal human fibroblasts into iN cells showing typical neuronal morphologies and expressing multiple neuronal markers, even after downregulation of the exogenous transcription factors.", "Importantly, the vast majority of human iN cells were able to generate action potentials and many matured to receive synaptic contacts when co-cultured with primary mouse cortical neurons.", "Our data demonstrate that non-neural human somatic cells, as well as pluripotent stem cells, can be converted directly into neurons by lineage-determining transcription factors.", "These methods may facilitate robust generation of patient-specific human neurons for in vitro disease modelling or future applications in regenerative medicine."], "structured": false}
{"doc_id": 4406819, "title": "PAAR-repeat proteins sharpen and diversify the Type VI secretion system spike", "abstract": ["The bacterial type VI secretion system (T6SS) is a large multicomponent, dynamic macromolecular machine that has an important role in the ecology of many Gram-negative bacteria.", "T6SS is responsible for translocation of a wide range of toxic effector molecules, allowing predatory cells to kill both prokaryotic as well as eukaryotic prey cells.", "The T6SS organelle is functionally analogous to contractile tails of bacteriophages and is thought to attack cells by initially penetrating them with a trimeric protein complex called the VgrG spike.", "Neither the exact protein composition of the T6SS organelle nor the mechanisms of effector selection and delivery are known.", "Here we report that proteins from the PAAR (proline-alanine-alanine-arginine) repeat superfamily form a sharp conical extension on the VgrG spike, which is further involved in attaching effector domains to the spike.", "The crystal structures of two PAAR-repeat proteins bound to VgrG-like partners show that these proteins sharpen the tip of the T6SS spike complex.", "We demonstrate that PAAR proteins are essential for T6SS-mediated secretion and target cell killing by Vibrio cholerae and Acinetobacter baylyi.", "Our results indicate a new model of the T6SS organelle in which the VgrG-PAAR spike complex is decorated with multiple effectors that are delivered simultaneously into target cells in a single contraction-driven translocation event."], "structured": false}
{"doc_id": 4407318, "title": "Replication stress activates DNA repair synthesis in mitosis", "abstract": ["Oncogene-induced DNA replication stress has been implicated as a driver of tumorigenesis.", "Many chromosomal rearrangements characteristic of human cancers originate from specific regions of the genome called common fragile sites (CFSs).", "CFSs are difficult-to-replicate loci that manifest as gaps or breaks on metaphase chromosomes (termed CFS \u2018expression\u2019), particularly when cells have been exposed to replicative stress.", "The MUS81\u2013EME1 structure-specific endonuclease promotes the appearance of chromosome gaps or breaks at CFSs following replicative stress.", "Here we show that entry of cells into mitotic prophase triggers the recruitment of MUS81 to CFSs.", "The nuclease activity of MUS81 then promotes POLD3-dependent DNA synthesis at CFSs, which serves to minimize chromosome mis-segregation and non-disjunction.", "We propose that the attempted condensation of incompletely duplicated loci in early mitosis serves as the trigger for completion of DNA replication at CFS loci in human cells.", "Given that this POLD3-dependent mitotic DNA synthesis is enhanced in aneuploid cancer cells that exhibit intrinsically high levels of chromosomal instability (CIN+) and replicative stress, we suggest that targeting this pathway could represent a new therapeutic approach."], "structured": false}
{"doc_id": 4407385, "title": "A specific amyloid-\u03b2 protein assembly in the brain impairs memory", "abstract": ["Memory function often declines with age, and is believed to deteriorate initially because of changes in synaptic function rather than loss of neurons.", "Some individuals then go on to develop Alzheimer's disease with neurodegeneration.", "Here we use Tg2576 mice, which express a human amyloid-\u03b2 precursor protein (APP) variant linked to Alzheimer's disease, to investigate the cause of memory decline in the absence of neurodegeneration or amyloid-\u03b2 protein amyloidosis.", "Young Tg2576 mice (< 6 months old) have normal memory and lack neuropathology, middle-aged mice (6\u201314 months old) develop memory deficits without neuronal loss, and old mice (> 14 months old) form abundant neuritic plaques containing amyloid-\u03b2 (refs 3\u20136).", "We found that memory deficits in middle-aged Tg2576 mice are caused by the extracellular accumulation of a 56-kDa soluble amyloid-\u03b2 assembly, which we term A\u03b2*56 (A\u03b2 star 56).", "A\u03b2*56 purified from the brains of impaired Tg2576 mice disrupts memory when administered to young rats.", "We propose that A\u03b2*56 impairs memory independently of plaques or neuronal loss, and may contribute to cognitive deficits associated with Alzheimer's disease."], "structured": false}
{"doc_id": 4407455, "title": "Cleavage of GSDMD by inflammatory caspases determines pyroptotic cell death", "abstract": ["Inflammatory caspases (caspase-1, -4, -5 and -11) are critical for innate defences.", "Caspase-1 is activated by ligands of various canonical inflammasomes, and caspase-4, -5 and -11 directly recognize bacterial lipopolysaccharide, both of which trigger pyroptosis.", "Despite the crucial role in immunity and endotoxic shock, the mechanism for pyroptosis induction by inflammatory caspases is unknown.", "Here we identify gasdermin D (Gsdmd) by genome-wide clustered regularly interspaced palindromic repeat (CRISPR)-Cas9 nuclease screens of caspase-11- and caspase-1-mediated pyroptosis in mouse bone marrow macrophages.", "GSDMD-deficient cells resisted the induction of pyroptosis by cytosolic lipopolysaccharide and known canonical inflammasome ligands.", "Interleukin-1\u03b2 release was also diminished in Gsdmd\u2212/\u2212 cells, despite intact processing by caspase-1.", "Caspase-1 and caspase-4/5/11 specifically cleaved the linker between the amino-terminal gasdermin-N and carboxy-terminal gasdermin-C domains in GSDMD, which was required and sufficient for pyroptosis.", "The cleavage released the intramolecular inhibition on the gasdermin-N domain that showed intrinsic pyroptosis-inducing activity.", "Other gasdermin family members were not cleaved by inflammatory caspases but shared the autoinhibition; gain-of-function mutations in Gsdma3 that cause alopecia and skin defects disrupted the autoinhibition, allowing its gasdermin-N domain to trigger pyroptosis.", "These findings offer insight into inflammasome-mediated immunity/diseases and also change our understanding of pyroptosis and programmed necrosis."], "structured": false}
{"doc_id": 4409524, "title": "Role of corin in trophoblast invasion and uterine spiral artery remodelling in pregnancy", "abstract": ["In pregnancy, trophoblast invasion and uterine spiral artery remodelling are important for lowering maternal vascular resistance and increasing uteroplacental blood flow.", "Impaired spiral artery remodelling has been implicated in pre-eclampsia, a major complication of pregnancy, for a long time but the underlying mechanisms remain unclear.", "Corin (also known as atrial natriuretic peptide-converting enzyme) is a cardiac protease that activates atrial natriuretic peptide (ANP), a cardiac hormone that is important in regulating blood pressure.", "Unexpectedly, corin expression was detected in the pregnant uterus.", "Here we identify a new function of corin and ANP in promoting trophoblast invasion and spiral artery remodelling.", "We show that pregnant corin- or ANP-deficient mice developed high blood pressure and proteinuria, characteristics of pre-eclampsia.", "In these mice, trophoblast invasion and uterine spiral artery remodelling were markedly impaired.", "Consistent with this, the ANP potently stimulated human trophoblasts in invading Matrigels.", "In patients with pre-eclampsia, uterine Corin messenger RNA and protein levels were significantly lower than that in normal pregnancies.", "Moreover, we have identified Corin gene mutations in pre-eclamptic patients, which decreased corin activity in processing pro-ANP.", "These results indicate that corin and ANP are essential for physiological changes at the maternal\u2013fetal interface, suggesting that defects in corin and ANP function may contribute to pre-eclampsia."], "structured": false}
{"doc_id": 4410181, "title": "Metabolic rescue in pluripotent cells from patients with mtDNA disease", "abstract": ["Mitochondria have a major role in energy production via oxidative phosphorylation, which is dependent on the expression of critical genes encoded by mitochondrial (mt)DNA.", "Mutations in mtDNA can cause fatal or severely debilitating disorders with limited treatment options.", "Clinical manifestations vary based on mutation type and heteroplasmy (that is, the relative levels of mutant and wild-type mtDNA within each cell).", "Here we generated genetically corrected pluripotent stem cells (PSCs) from patients with mtDNA disease.", "Multiple induced pluripotent stem (iPS) cell lines were derived from patients with common heteroplasmic mutations including 3243A>G, causing mitochondrial encephalomyopathy and stroke-like episodes (MELAS), and 8993T>G and 13513G>A, implicated in Leigh syndrome.", "Isogenic MELAS and Leigh syndrome iPS cell lines were generated containing exclusively wild-type or mutant mtDNA through spontaneous segregation of heteroplasmic mtDNA in proliferating fibroblasts.", "Furthermore, somatic cell nuclear transfer (SCNT) enabled replacement of mutant mtDNA from homoplasmic 8993T>G fibroblasts to generate corrected Leigh-NT1 PSCs.", "Although Leigh-NT1 PSCs contained donor oocyte wild-type mtDNA (human haplotype D4a) that differed from Leigh syndrome patient haplotype (F1a) at a total of 47 nucleotide sites, Leigh-NT1 cells displayed transcriptomic profiles similar to those in embryo-derived PSCs carrying wild-type mtDNA, indicative of normal nuclear-to-mitochondrial interactions.", "Moreover, genetically rescued patient PSCs displayed normal metabolic function compared to impaired oxygen consumption and ATP production observed in mutant cells.", "We conclude that both reprogramming approaches offer complementary strategies for derivation of PSCs containing exclusively wild-type mtDNA, through spontaneous segregation of heteroplasmic mtDNA in individual iPS cell lines or mitochondrial replacement by SCNT in homoplasmic mtDNA-based disease."], "structured": false}
{"doc_id": 4411655, "title": "The yeast Pif1p helicase removes telomerase from telomeric DNA", "abstract": ["Telomeres are the physical ends of eukaryotic chromosomes.", "Genetic studies have established that the baker's yeast Pif1p DNA helicase is a negative regulator of telomerase, the specialized reverse transcriptase that maintains telomeric DNA, but the biochemical basis for this inhibition was unknown.", "Here we show that in vitro, Pif1p reduces the processivity of telomerase and releases telomerase from telomeric oligonucleotides.", "The released telomerase is enzymatically active because it is able to lengthen a challenger oligonucleotide.", "In vivo, overexpression of Pif1p reduces telomerase association with telomeres, whereas depleting cells of Pif1p increases the levels of telomere-bound Est1p, a telomerase subunit that is present on the telomere when telomerase is active.", "We propose that Pif1p helicase activity limits telomerase action both in vivo and in vitro by displacing active telomerase from DNA ends."], "structured": false}
{"doc_id": 4411760, "title": "Small regulatory RNAs inhibit RNA Polymerase II during the elongation phase of transcription", "abstract": ["Eukaryotic cells express a wide variety of endogenous small regulatory RNAs that regulate heterochromatin formation, developmental timing, defence against parasitic nucleic acids and genome rearrangement.", "Many small regulatory RNAs are thought to function in nuclei.", "For instance, in plants and fungi, short interfering RNA (siRNAs) associate with nascent transcripts and direct chromatin and/or DNA modifications.", "To understand further the biological roles of small regulatory RNAs, we conducted a genetic screen to identify factors required for RNA interference (RNAi) in Caenorhabditis elegans nuclei.", "Here we show that the gene nuclear RNAi defective-2 (nrde-2) encodes an evolutionarily conserved protein that is required for siRNA-mediated silencing in nuclei.", "NRDE-2 associates with the Argonaute protein NRDE-3 within nuclei and is recruited by NRDE-3/siRNA complexes to nascent transcripts that have been targeted by RNAi.", "We find that nuclear-localized siRNAs direct an NRDE-2-dependent silencing of pre-messenger RNAs (pre-mRNAs) 3' to sites of RNAi, an NRDE-2-dependent accumulation of RNA polymerase (RNAP) II at genomic loci targeted by RNAi, and NRDE-2-dependent decreases in RNAP II occupancy and RNAP II transcriptional activity 3' to sites of RNAi.", "These results define NRDE-2 as a component of the nuclear RNAi machinery and demonstrate that metazoan siRNAs can silence nuclear-localized RNAs co-transcriptionally.", "In addition, these results establish a novel mode of RNAP II regulation: siRNA-directed recruitment of NRDE factors that inhibit RNAP II during the elongation phase of transcription."], "structured": false}
{"doc_id": 4412772, "title": "Cdk1 is sufficient to drive the mammalian cell cycle", "abstract": ["Unicellular organisms such as yeasts require a single cyclin-dependent kinase, Cdk1, to drive cell division.", "In contrast, mammalian cells are thought to require the sequential activation of at least four different cyclin-dependent kinases, Cdk2, Cdk3, Cdk4 and Cdk6, to drive cells through interphase, as well as Cdk1 to proceed through mitosis.", "This model has been challenged by recent genetic evidence that mice survive in the absence of individual interphase Cdks.", "Moreover, most mouse cell types proliferate in the absence of two or even three interphase Cdks.", "Similar results have been obtained on ablation of some of the activating subunits of Cdks, such as the D-type and E-type cyclins.", "Here we show that mouse embryos lacking all interphase Cdks (Cdk2, Cdk3, Cdk4 and Cdk6) undergo organogenesis and develop to midgestation.", "In these embryos, Cdk1 binds to all cyclins, resulting in the phosphorylation of the retinoblastoma protein pRb and the expression of genes that are regulated by E2F transcription factors.", "Mouse embryonic fibroblasts derived from these embryos proliferate in vitro, albeit with an extended cell cycle due to inefficient inactivation of Rb proteins.", "However, they become immortal on continuous passage.", "We also report that embryos fail to develop to the morula and blastocyst stages in the absence of Cdk1.", "These results indicate that Cdk1 is the only essential cell cycle Cdk.", "Moreover, they show that in the absence of interphase Cdks, Cdk1 can execute all the events that are required to drive cell division."], "structured": false}
{"doc_id": 4414481, "title": "Calorie restriction extends Saccharomyces cerevisiae lifespan by increasing respiration", "abstract": ["Calorie restriction (CR) extends lifespan in a wide spectrum of organisms and is the only regimen known to lengthen the lifespan of mammals.", "We established a model of CR in budding yeast Saccharomyces cerevisiae.", "In this system, lifespan can be extended by limiting glucose or by reducing the activity of the glucose-sensing cyclic-AMP-dependent kinase (PKA).", "Lifespan extension in a mutant with reduced PKA activity requires Sir2 and NAD (nicotinamide adenine dinucleotide).", "In this study we explore how CR activates Sir2 to extend lifespan.", "Here we show that the shunting of carbon metabolism toward the mitochondrial tricarboxylic acid cycle and the concomitant increase in respiration play a central part in this process.", "We discuss how this metabolic strategy may apply to CR in animals."], "structured": false}
{"doc_id": 4414547, "title": "Mosaic PPM1D mutations are associated with predisposition to breast and ovarian cancer", "abstract": ["Improved sequencing technologies offer unprecedented opportunities for investigating the role of rare genetic variation in common disease.", "However, there are considerable challenges with respect to study design, data analysis and replication.", "Using pooled next-generation sequencing of 507 genes implicated in the repair of DNA in 1,150 samples, an analytical strategy focused on protein-truncating variants (PTVs) and a large-scale sequencing case\u2013control replication experiment in 13,642 individuals, here we show that rare PTVs in the p53-inducible protein phosphatase PPM1D are associated with predisposition to breast cancer and ovarian cancer.", "PPM1D PTV mutations were present in 25 out of 7,781 cases versus 1 out of 5,861 controls (P = 1.12 \u00d7 10\u22125), including 18 mutations in 6,912 individuals with breast cancer (P = 2.42 \u00d7 10\u22124) and 12 mutations in 1,121 individuals with ovarian cancer (P = 3.10 \u00d7 10\u22129).", "Notably, all of the identified PPM1D PTVs were mosaic in lymphocyte DNA and clustered within a 370-base-pair region in the final exon of the gene, carboxy-terminal to the phosphatase catalytic domain.", "Functional studies demonstrate that the mutations result in enhanced suppression of p53 in response to ionizing radiation exposure, suggesting that the mutant alleles encode hyperactive PPM1D isoforms.", "Thus, although the mutations cause premature protein truncation, they do not result in the simple loss-of-function effect typically associated with this class of variant, but instead probably have a gain-of-function effect.", "Our results have implications for the detection and management of breast and ovarian cancer risk.", "More generally, these data provide new insights into the role of rare and of mosaic genetic variants in common conditions, and the use of sequencing in their identification."], "structured": false}
{"doc_id": 4416964, "title": "Immunogenicity of induced pluripotent stem cells", "abstract": ["Induced pluripotent stem cells (iPSCs), reprogrammed from somatic cells with defined factors, hold great promise for regenerative medicine as the renewable source of autologous cells.", "Whereas it has been generally assumed that these autologous cells should be immune-tolerated by the recipient from whom the iPSCs are derived, their immunogenicity has not been vigorously examined.", "We show here that, whereas embryonic stem cells (ESCs) derived from inbred C57BL/6 (B6) mice can efficiently form teratomas in B6 mice without any evident immune rejection, the allogeneic ESCs from 129/SvJ mice fail to form teratomas in B6 mice due to rapid rejection by recipients.", "B6 mouse embryonic fibroblasts (MEFs) were reprogrammed into iPSCs by either retroviral approach (ViPSCs) or a novel episomal approach (EiPSCs) that causes no genomic integration.", "In contrast to B6 ESCs, teratomas formed by B6 ViPSCs were mostly immune-rejected by B6 recipients.", "In addition, the majority of teratomas formed by B6 EiPSCs were immunogenic in B6 mice with T cell infiltration, and apparent tissue damage and regression were observed in a small fraction of teratomas.", "Global gene expression analysis of teratomas formed by B6 ESCs and EiPSCs revealed a number of genes frequently overexpressed in teratomas derived from EiPSCs, and several such gene products were shown to contribute directly to the immunogenicity of the B6 EiPSC-derived cells in B6 mice.", "These findings indicate that, in contrast to derivatives of ESCs, abnormal gene expression in some cells differentiated from iPSCs can induce T-cell-dependent immune response in syngeneic recipients.", "Therefore, the immunogenicity of therapeutically valuable cells derived from patient-specific iPSCs should be evaluated before any clinic application of these autologous cells into the patients."], "structured": false}
{"doc_id": 4417177, "title": "Direct conversion of human fibroblasts to multilineage blood progenitors", "abstract": ["As is the case for embryo-derived stem cells, application of reprogrammed human induced pluripotent stem cells is limited by our understanding of lineage specification.", "Here we demonstrate the ability to generate progenitors and mature cells of the haematopoietic fate directly from human dermal fibroblasts without establishing pluripotency.", "Ectopic expression of OCT4 (also called POU5F1)-activated haematopoietic transcription factors, together with specific cytokine treatment, allowed generation of cells expressing the pan-leukocyte marker CD45.", "These unique fibroblast-derived cells gave rise to granulocytic, monocytic, megakaryocytic and erythroid lineages, and demonstrated in vivo engraftment capacity.", "We note that adult haematopoietic programs are activated, consistent with bypassing the pluripotent state to generate blood fate: this is distinct from haematopoiesis involving pluripotent stem cells, where embryonic programs are activated.", "These findings demonstrate restoration of multipotency from human fibroblasts, and suggest an alternative approach to cellular reprogramming for autologous cell-replacement therapies that avoids complications associated with the use of human pluripotent stem cells."], "structured": false}
{"doc_id": 4417558, "title": "Mical links semaphorins to F-actin disassembly", "abstract": ["How instructive cues present on the cell surface have their precise effects on the actin cytoskeleton is poorly understood.", "Semaphorins are one of the largest families of these instructive cues and are widely studied for their effects on cell movement, navigation, angiogenesis, immunology and cancer.", "Semaphorins/collapsins were characterized in part on the basis of their ability to drastically alter actin cytoskeletal dynamics in neuronal processes, but despite considerable progress in the identification of semaphorin receptors and their signalling pathways, the molecules linking them to the precise control of cytoskeletal elements remain unknown.", "Recently, highly unusual proteins of the Mical family of enzymes have been found to associate with the cytoplasmic portion of plexins, which are large cell-surface semaphorin receptors, and to mediate axon guidance, synaptogenesis, dendritic pruning and other cell morphological changes.", "Mical enzymes perform reduction\u2013oxidation (redox) enzymatic reactions and also contain domains found in proteins that regulate cell morphology.", "However, nothing is known of the role of Mical or its redox activity in mediating morphological changes.", "Here we report that Mical directly links semaphorins and their plexin receptors to the precise control of actin filament (F-actin) dynamics.", "We found that Mical is both necessary and sufficient for semaphorin\u2013plexin-mediated F-actin reorganization in vivo.", "Likewise, we purified Mical protein and found that it directly binds F-actin and disassembles both individual and bundled actin filaments.", "We also found that Mical utilizes its redox activity to alter F-actin dynamics in vivo and in vitro, indicating a previously unknown role for specific redox signalling events in actin cytoskeletal regulation.", "Mical therefore is a novel F-actin-disassembly factor that provides a molecular conduit through which actin reorganization\u2014a hallmark of cell morphological changes including axon navigation\u2014can be precisely achieved spatiotemporally in response to semaphorins."], "structured": false}
{"doc_id": 4418070, "title": "Novel Foxo1-dependent transcriptional programs control Treg cell function", "abstract": ["Regulatory T (Treg) cells, characterized by expression of the transcription factor forkhead box P3 (Foxp3), maintain immune homeostasis by suppressing self-destructive immune responses.", "Foxp3 operates as a late-acting differentiation factor controlling Treg cell homeostasis and function, whereas the early Treg-cell-lineage commitment is regulated by the Akt kinase and the forkhead box O (Foxo) family of transcription factors.", "However, whether Foxo proteins act beyond the Treg-cell-commitment stage to control Treg cell homeostasis and function remains largely unexplored.", "Here we show that Foxo1 is a pivotal regulator of Treg cell function.", "Treg cells express high amounts of Foxo1 and display reduced T-cell-receptor-induced Akt activation, Foxo1 phosphorylation and Foxo1 nuclear exclusion.", "Mice with Treg-cell-specific deletion of Foxo1 develop a fatal inflammatory disorder similar in severity to that seen in Foxp3-deficient mice, but without the loss of Treg cells.", "Genome-wide analysis of Foxo1 binding sites reveals \u223c300 Foxo1-bound target genes, including the pro-inflammatory cytokine Ifng, that do not seem to be directly regulated by Foxp3.", "These findings show that the evolutionarily ancient Akt\u2013Foxo1 signalling module controls a novel genetic program indispensable for Treg cell function."], "structured": false}
{"doc_id": 4418112, "title": "Functional screening identifies miRNAs inducing cardiac regeneration", "abstract": ["In mammals, enlargement of the heart during embryonic development is primarily dependent on the increase in cardiomyocyte numbers.", "Shortly after birth, however, cardiomyocytes stop proliferating and further growth of the myocardium occurs through hypertrophic enlargement of the existing myocytes.", "As a consequence of the minimal renewal of cardiomyocytes during adult life, repair of cardiac damage through myocardial regeneration is very limited.", "Here we show that the exogenous administration of selected microRNAs (miRNAs) markedly stimulates cardiomyocyte proliferation and promotes cardiac repair.", "We performed a high-content microscopy, high-throughput functional screening for human miRNAs that promoted neonatal cardiomyocyte proliferation using a whole-genome miRNA library.", "Forty miRNAs strongly increased both DNA synthesis and cytokinesis in neonatal mouse and rat cardiomyocytes.", "Two of these miRNAs (hsa-miR-590 and hsa-miR-199a) were further selected for testing and were shown to promote cell cycle re-entry of adult cardiomyocytes ex vivo and to promote cardiomyocyte proliferation in both neonatal and adult animals.", "After myocardial infarction in mice, these miRNAs stimulated marked cardiac regeneration and almost complete recovery of cardiac functional parameters.", "The miRNAs identified hold great promise for the treatment of cardiac pathologies consequent to cardiomyocyte loss."], "structured": false}
{"doc_id": 4418269, "title": "Specificity of sensory\u2013motor connections encoded by Sema3e\u2013Plxnd1 recognition", "abstract": ["Spinal reflexes are mediated by synaptic connections between sensory afferents and motor neurons.", "The organization of these circuits shows several levels of specificity.", "Only certain classes of proprioceptive sensory neurons make direct, monosynaptic connections with motor neurons.", "Those that do are bound by rules of motor pool specificity: they form strong connections with motor neurons supplying the same muscle, but avoid motor pools supplying antagonistic muscles.", "This pattern of connectivity is initially accurate and is maintained in the absence of activity, implying that wiring specificity relies on the matching of recognition molecules on the surface of sensory and motor neurons.", "However, determinants of fine synaptic specificity here, as in most regions of the central nervous system, have yet to be defined.", "To address the origins of synaptic specificity in these reflex circuits we have used molecular genetic methods to manipulate recognition proteins expressed by subsets of sensory and motor neurons.", "We show here that a recognition system involving expression of the class 3 semaphorin Sema3e by selected motor neuron pools, and its high-affinity receptor plexin D1 (Plxnd1) by proprioceptive sensory neurons, is a critical determinant of synaptic specificity in sensory\u2013motor circuits in mice.", "Changing the profile of Sema3e\u2013Plxnd1 signalling in sensory or motor neurons results in functional and anatomical rewiring of monosynaptic connections, but does not alter motor pool specificity.", "Our findings indicate that patterns of monosynaptic connectivity in this prototypic central nervous system circuit are constructed through a recognition program based on repellent signalling."], "structured": false}
{"doc_id": 4418582, "title": "A chromatin remodelling complex involved in transcription and DNA processing.", "abstract": ["The packaging of the eukaryotic genome in chromatin presents barriers that restrict the access of enzymes that process DNA.", "To overcome these barriers, cells possess a number of multi-protein, ATP-dependent chromatin remodelling complexes, each containing an ATPase subunit from the SNF2/SWI2 superfamily.", "Chromatin remodelling complexes function by increasing nucleosome mobility and are clearly implicated in transcription.", "Here we have analysed SNF2/SWI2- and ISWI-related proteins to identify remodelling complexes that potentially assist other DNA transactions.", "We purified a complex from Saccharomyces cerevisiae that contains the Ino80 ATPase.", "The INO80 complex contains about 12 polypeptides including two proteins related to the bacterial RuvB DNA helicase, which catalyses branch migration of Holliday junctions.", "The purified complex remodels chromatin, facilitates transcription in vitro and displays 3' to 5' DNA helicase activity.", "Mutants of ino80 show hypersensitivity to agents that cause DNA damage, in addition to defects in transcription.", "These results indicate that chromatin remodelling driven by the Ino80 ATPase may be connected to transcription as well as DNA damage repair."], "structured": false}
{"doc_id": 4418878, "title": "Oncogenic pathway signatures in human cancers as a guide to targeted therapies", "abstract": ["The development of an oncogenic state is a complex process involving the accumulation of multiple independent mutations that lead to deregulation of cell signalling pathways central to the control of cell growth and cell fate.", "The ability to define cancer subtypes, recurrence of disease and response to specific therapies using DNA microarray-based gene expression signatures has been demonstrated in multiple studies.", "Various studies have also demonstrated the potential for using gene expression profiles for the analysis of oncogenic pathways.", "Here we show that gene expression signatures can be identified that reflect the activation status of several oncogenic pathways.", "When evaluated in several large collections of human cancers, these gene expression signatures identify patterns of pathway deregulation in tumours and clinically relevant associations with disease outcomes.", "Combining signature-based predictions across several pathways identifies coordinated patterns of pathway deregulation that distinguish between specific cancers and tumour subtypes.", "Clustering tumours based on pathway signatures further defines prognosis in respective patient subsets, demonstrating that patterns of oncogenic pathway deregulation underlie the development of the oncogenic phenotype and reflect the biology and outcome of specific cancers.", "Predictions of pathway deregulation in cancer cell lines are also shown to predict the sensitivity to therapeutic agents that target components of the pathway.", "Linking pathway deregulation with sensitivity to therapeutics that target components of the pathway provides an opportunity to make use of these oncogenic pathway signatures to guide the use of targeted therapeutics."], "structured": false}
{"doc_id": 4421547, "title": "CTCF mediates methylation-sensitive enhancer-blocking activity at the H19/Igf2 locus.", "abstract": ["The Insulin-like growth factor 2 (Igf2) and H19 genes are imprinted, resulting in silencing of the maternal and paternal alleles, respectively.", "This event is dependent upon an imprinted-control region two kilobases upstream of H19 (refs 1, 2).", "On the paternal chromosome this element is methylated and required for the silencing of H19 (refs 2-4).", "On the maternal chromosome the region is unmethylated and required for silencing of the Igf2 gene 90 kilobases upstream.", "We have proposed that the unmethylated imprinted-control region acts as a chromatin boundary that blocks the interaction of Igf2 with enhancers that lie 3' of H19 (refs 5, 6).", "This enhancer-blocking activity would then be lost when the region was methylated, thereby allowing expression of Igf2 paternally.", "Here we show, using transgenic mice and tissue culture, that the unmethylated imprinted-control regions from mouse and human H19 exhibit enhancer-blocking activity.", "Furthermore, we show that CTCF, a zinc finger protein implicated in vertebrate boundary function, binds to several sites in the unmethylated imprinted-control region that are essential for enhancer blocking.", "Consistent with our model, CTCF binding is abolished by DNA methylation.", "This is the first example, to our knowledge, of a regulated chromatin boundary in vertebrates."], "structured": false}
{"doc_id": 4421578, "title": "Broad and potent neutralization of HIV-1 by a gp41-specific human antibody", "abstract": ["Characterization of human monoclonal antibodies is providing considerable insight into mechanisms of broad HIV-1 neutralization.", "Here we report an HIV-1 gp41 membrane-proximal external region (MPER)-specific antibody, named 10E8, which neutralizes \u223c98% of tested viruses.", "An analysis of sera from 78 healthy HIV-1-infected donors demonstrated that 27% contained MPER-specific antibodies and 8% contained 10E8-like specificities.", "In contrast to other neutralizing MPER antibodies, 10E8 did not bind phospholipids, was not autoreactive, and bound cell-surface envelope.", "The structure of 10E8 in complex with the complete MPER revealed a site of vulnerability comprising a narrow stretch of highly conserved gp41-hydrophobic residues and a critical arginine or lysine just before the transmembrane region.", "Analysis of resistant HIV-1 variants confirmed the importance of these residues for neutralization.", "The highly conserved MPER is a target of potent, non-self-reactive neutralizing antibodies, suggesting that HIV-1 vaccines should aim to induce antibodies to this region of HIV-1 envelope glycoprotein."], "structured": false}
{"doc_id": 4421742, "title": "Disruption of the Hepcidin/Ferroportin Regulatory System Causes Pulmonary Iron Overload and Restrictive Lung Disease", "abstract": ["Emerging evidence suggests that pulmonary iron accumulation is implicated in a spectrum of chronic lung diseases.", "However, the mechanism(s) involved in pulmonary iron deposition and its role in the in vivo pathogenesis of lung diseases remains unknown.", "Here we show that a point mutation in the murine ferroportin gene, which causes hereditary hemochromatosis type 4 (Slc40a1C326S), increases iron levels in alveolar macrophages, epithelial cells lining the conducting airways and lung parenchyma, and in vascular smooth muscle cells.", "Pulmonary iron overload is associated with oxidative stress, restrictive lung disease with decreased total lung capacity and reduced blood oxygen saturation in homozygous Slc40a1C326S/C326S mice compared to wild-type controls.", "These findings implicate iron in lung pathology, which is so far not considered a classical iron-related disorder."], "structured": false}
{"doc_id": 4421746, "title": "Genome-wide genetic analysis of polyploidy in yeast", "abstract": ["Polyploidy, increased sets of chromosomes, occurs during development, cellular stress, disease and evolution.", "Despite its prevalence, little is known about the physiological alterations that accompany polyploidy.", "We previously described \u2018ploidy-specific lethality\u2019, where a gene deletion that is not lethal in haploid or diploid budding yeast causes lethality in triploids or tetraploids.", "Here we report a genome-wide screen to identify ploidy-specific lethal functions.", "Only 39 out of 3,740 mutations screened exhibited ploidy-specific lethality.", "Almost all of these mutations affect genomic stability by impairing homologous recombination, sister chromatid cohesion, or mitotic spindle function.", "We uncovered defects in wild-type tetraploids predicted by the screen, and identified mechanisms by which tetraploidization affects genomic stability.", "We show that tetraploids have a high incidence of syntelic/monopolar kinetochore attachments to the spindle pole.", "We suggest that this defect can be explained by mismatches in the ability to scale the size of the spindle pole body, spindle and kinetochores.", "Thus, geometric constraints may have profound effects on genome stability; the phenomenon described here may be relevant in a variety of biological contexts, including disease states such as cancer."], "structured": false}
{"doc_id": 4421787, "title": "Diverse and heritable lineage imprinting of early haematopoietic progenitors", "abstract": ["Haematopoietic stem cells (HSCs) and their subsequent progenitors produce blood cells, but the precise nature and kinetics of this production is a contentious issue.", "In one model, lymphoid and myeloid production branch after the lymphoid-primed multipotent progenitor (LMPP), with both branches subsequently producing dendritic cells.", "However, this model is based mainly on in vitro clonal assays and population-based tracking in vivo, which could miss in vivo single-cell complexity.", "Here we avoid these issues by using a new quantitative version of \u2018cellular barcoding\u2019 to trace the in vivo fate of hundreds of LMPPs and HSCs at the single-cell level.", "These data demonstrate that LMPPs are highly heterogeneous in the cell types that they produce, separating into combinations of lymphoid-, myeloid- and dendritic-cell-biased producers.", "Conversely, although we observe a known lineage bias of some HSCs, most cellular output is derived from a small number of HSCs that each generates all cell types.", "Crucially, in vivo analysis of the output of sibling cells derived from single LMPPs shows that they often share a similar fate, suggesting that the fate of these progenitors was imprinted.", "Furthermore, as this imprinting is also observed for dendritic-cell-biased LMPPs, dendritic cells may be considered a distinct lineage on the basis of separate ancestry.", "These data suggest a \u2018graded commitment\u2019 model of haematopoiesis, in which heritable and diverse lineage imprinting occurs earlier than previously thought."], "structured": false}
{"doc_id": 4422723, "title": "Crowding induces live cell extrusion to maintain homeostatic cell numbers in epithelia", "abstract": ["For an epithelium to provide a protective barrier, it must maintain homeostatic cell numbers by matching the number of dividing cells with the number of dying cells.", "Although compensatory cell division can be triggered by dying cells, it is unknown how cell death might relieve overcrowding due to proliferation.", "When we trigger apoptosis in epithelia, dying cells are extruded to preserve a functional barrier.", "Extrusion occurs by cells destined to die signalling to surrounding epithelial cells to contract an actomyosin ring that squeezes the dying cell out.", "However, it is not clear what drives cell death during normal homeostasis.", "Here we show in human, canine and zebrafish cells that overcrowding due to proliferation and migration induces extrusion of live cells to control epithelial cell numbers.", "Extrusion of live cells occurs at sites where the highest crowding occurs in vivo and can be induced by experimentally overcrowding monolayers in vitro.", "Like apoptotic cell extrusion, live cell extrusion resulting from overcrowding also requires sphingosine 1-phosphate signalling and Rho-kinase-dependent myosin contraction, but is distinguished by signalling through stretch-activated channels.", "Moreover, disruption of a stretch-activated channel, Piezo1, in zebrafish prevents extrusion and leads to the formation of epithelial cell masses.", "Our findings reveal that during homeostatic turnover, growth and division of epithelial cells on a confined substratum cause overcrowding that leads to their extrusion and consequent death owing to the loss of survival factors.", "These results suggest that live cell extrusion could be a tumour-suppressive mechanism that prevents the accumulation of excess epithelial cells."], "structured": false}
{"doc_id": 4422734, "title": "Direct observation of ligand recognition by T cells", "abstract": ["The activation of T cells through interaction of their T-cell receptors with antigenic peptide bound to major histocompatibility complex (MHC) on the surface of antigen presenting cells (APCs) is a crucial step in adaptive immunity.", "Here we use three-dimensional fluorescence microscopy to visualize individual peptide\u2013I-Ek class II MHC complexes labelled with the phycobiliprotein phycoerythrin in an effort to characterize T-cell sensitivity and the requirements for forming an immunological synapse in single cells.", "We show that T cells expressing the CD4 antigen respond with transient calcium signalling to even a single agonist peptide\u2013MHC ligand, and that the organization of molecules in the contact zone of the T cell and APC takes on the characteristics of an immunological synapse when only about ten agonists are present.", "This sensitivity is highly dependant on CD4, because blocking this molecule with antibodies renders T cells unable to detect less than about 30 ligands."], "structured": false}
{"doc_id": 4422868, "title": "Crypt stem cells as the cells-of-origin of intestinal cancer", "abstract": ["Intestinal cancer is initiated by Wnt-pathway-activating mutations in genes such as adenomatous polyposis coli (APC).", "As in most cancers, the cell of origin has remained elusive.", "In a previously established Lgr5 (leucine-rich-repeat containing G-protein-coupled receptor 5) knockin mouse model, a tamoxifen-inducible Cre recombinase is expressed in long-lived intestinal stem cells.", "Here we show that deletion of Apc in these stem cells leads to their transformation within days.", "Transformed stem cells remain located at crypt bottoms, while fuelling a growing microadenoma.", "These microadenomas show unimpeded growth and develop into macroscopic adenomas within 3-5weeks.", "The distribution of Lgr5+ cells within stem-cell-derived adenomas indicates that a stem cell/progenitor cell hierarchy is maintained in early neoplastic lesions.", "When Apc is deleted in short-lived transit-amplifying cells using a different cre mouse, the growth of the induced microadenomas rapidly stalls.", "Even after 30weeks, large adenomas are very rare in these mice.", "We conclude that stem-cell-specific loss of Apc results in progressively growing neoplasia."], "structured": false}
{"doc_id": 4423203, "title": "Microbial engineering for the production of advanced biofuels", "abstract": ["Advanced biofuels produced by microorganisms have similar properties to petroleum-based fuels, and can 'drop in' to the existing transportation infrastructure.", "However, producing these biofuels in yields high enough to be useful requires the engineering of the microorganism's metabolism.", "Such engineering is not based on just one specific feedstock or host organism.", "Data-driven and synthetic-biology approaches can be used to optimize both the host and pathways to maximize fuel production.", "Despite some success, challenges still need to be met to move advanced biofuels towards commercialization, and to compete with more conventional fuels."], "structured": false}
{"doc_id": 4423220, "title": "Sperm chromatin proteomics identifies evolutionarily conserved fertility factors", "abstract": ["Male infertility is a long-standing enigma of significant medical concern.", "The integrity of sperm chromatin is a clinical indicator of male fertility and in vitro fertilization potential: chromosome aneuploidy and DNA decondensation or damage are correlated with reproductive failure.", "Identifying conserved proteins important for sperm chromatin structure and packaging can reveal universal causes of infertility.", "Here we combine proteomics, cytology and functional analysis in Caenorhabditis elegans to identify spermatogenic chromatin-associated proteins that are important for fertility.", "Our strategy employed multiple steps: purification of chromatin from comparable meiotic cell types, namely those undergoing spermatogenesis or oogenesis; proteomic analysis by multidimensional protein identification technology (MudPIT) of factors that co-purify with chromatin; prioritization of sperm proteins based on abundance; and subtraction of common proteins to eliminate general chromatin and meiotic factors.", "Our approach reduced 1,099 proteins co-purified with spermatogenic chromatin, currently the most extensive catalogue, to 132 proteins for functional analysis.", "Reduction of gene function through RNA interference coupled with protein localization studies revealed conserved spermatogenesis-specific proteins vital for DNA compaction, chromosome segregation, and fertility.", "Unexpected roles in spermatogenesis were also detected for factors involved in other processes.", "Our strategy to find fertility factors conserved from C. elegans to mammals achieved its goal: of mouse gene knockouts corresponding to nematode proteins, 37% (7/19) cause male sterility.", "Our list therefore provides significant opportunity to identify causes of male infertility and targets for male contraceptives."], "structured": false}
{"doc_id": 4423327, "title": "Nanog safeguards pluripotency and mediates germline development", "abstract": ["Nanog is a divergent homeodomain protein found in mammalian pluripotent cells and developing germ cells.", "Deletion of Nanog causes early embryonic lethality, whereas constitutive expression enables autonomous self-renewal of embryonic stem cells.", "Nanog is accordingly considered a core element of the pluripotent transcriptional network.", "However, here we report that Nanog fluctuates in mouse embryonic stem cells.", "Transient downregulation of Nanog appears to predispose cells towards differentiation but does not mark commitment.", "By genetic deletion we show that, although they are prone to differentiate, embryonic stem cells can self-renew indefinitely in the permanent absence of Nanog.", "Expanded Nanog null cells colonize embryonic germ layers and exhibit multilineage differentiation both in fetal and adult chimaeras.", "Although they are also recruited to the germ line, primordial germ cells lacking Nanog fail to mature on reaching the genital ridge.", "This defect is rescued by repair of the mutant allele.", "Thus Nanog is dispensible for expression of somatic pluripotency but is specifically required for formation of germ cells.", "Nanog therefore acts primarily in construction of inner cell mass and germ cell states rather than in the housekeeping machinery of pluripotency.", "We surmise that Nanog stabilizes embryonic stem cells in culture by resisting or reversing alternative gene expression states."], "structured": false}
{"doc_id": 4423401, "title": "Succinate is an inflammatory signal that induces IL-1\u03b2 through HIF-1\u03b1", "abstract": ["Macrophages activated by the Gram-negative bacterial product lipopolysaccharide switch their core metabolism from oxidative phosphorylation to glycolysis.", "Here we show that inhibition of glycolysis with 2-deoxyglucose suppresses lipopolysaccharide-induced interleukin-1\u03b2 but not tumour-necrosis factor-\u03b1 in mouse macrophages.", "A comprehensive metabolic map of lipopolysaccharide-activated macrophages shows upregulation of glycolytic and downregulation of mitochondrial genes, which correlates directly with the expression profiles of altered metabolites.", "Lipopolysaccharide strongly increases the levels of the tricarboxylic-acid cycle intermediate succinate.", "Glutamine-dependent anerplerosis is the principal source of succinate, although the \u2018GABA (\u03b3-aminobutyric acid) shunt\u2019 pathway also has a role.", "Lipopolysaccharide-induced succinate stabilizes hypoxia-inducible factor-1\u03b1, an effect that is inhibited by 2-deoxyglucose, with interleukin-1\u03b2 as an important target.", "Lipopolysaccharide also increases succinylation of several proteins.", "We therefore identify succinate as a metabolite in innate immune signalling, which enhances interleukin-1\u03b2 production during inflammation."], "structured": false}
{"doc_id": 4423559, "title": "Planar cell polarity signalling couples cell division and morphogenesis during neurulation", "abstract": ["Environmental and genetic aberrations lead to neural tube closure defects (NTDs) in 1 out of every 1,000 births.", "Mouse and frog models for these birth defects have indicated that Van Gogh-like 2 (Vangl2, also known as Strabismus) and other components of planar cell polarity (PCP) signalling might control neurulation by promoting the convergence of neural progenitors to the midline.", "Here we show a novel role for PCP signalling during neurulation in zebrafish.", "We demonstrate that non-canonical Wnt/PCP signalling polarizes neural progenitors along the anteroposterior axis.", "This polarity is transiently lost during cell division in the neural keel but is re-established as daughter cells reintegrate into the neuroepithelium.", "Loss of zebrafish Vangl2 (in trilobite mutants) abolishes the polarization of neural keel cells, disrupts re-intercalation of daughter cells into the neuroepithelium, and results in ectopic neural progenitor accumulations and NTDs.", "Remarkably, blocking cell division leads to rescue of trilobite neural tube morphogenesis despite persistent defects in convergence and extension.", "These results reveal a function for PCP signalling in coupling cell division and morphogenesis at neurulation and indicate a previously unrecognized mechanism that might underlie NTDs."], "structured": false}
{"doc_id": 4424888, "title": "The challenge of new drug discovery for tuberculosis", "abstract": ["Tuberculosis (TB) is more prevalent in the world today than at any other time in human history.", "Mycobacterium tuberculosis, the pathogen responsible for TB, uses diverse strategies to survive in a variety of host lesions and to evade immune surveillance.", "A key question is how robust are our approaches to discovering new TB drugs, and what measures could be taken to reduce the long and protracted clinical development of new drugs.", "The emergence of multi-drug-resistant strains of M. tuberculosis makes the discovery of new molecular scaffolds a priority, and the current situation even necessitates the re-engineering and repositioning of some old drug families to achieve effective control.", "Whatever the strategy used, success will depend largely on our proper understanding of the complex interactions between the pathogen and its human host.", "In this review, we discuss innovations in TB drug discovery and evolving strategies to bring newer agents more quickly to patients."], "structured": false}
{"doc_id": 4425507, "title": "Subunit Arrangement and Phenylethanolamine Binding in GluN1/GluN2B NMDA Receptors", "abstract": ["Since it was discovered that the anti-hypertensive agent ifenprodil has neuroprotective activity through its effects on NMDA (N-methyl-D-aspartate) receptors, a determined effort has been made to understand the mechanism of action and to develop improved therapeutic compounds on the basis of this knowledge.", "Neurotransmission mediated by NMDA receptors is essential for basic brain development and function.", "These receptors form heteromeric ion channels and become activated after concurrent binding of glycine and glutamate to the GluN1 and GluN2 subunits, respectively.", "A functional hallmark of NMDA receptors is that their ion-channel activity is allosterically regulated by binding of small compounds to the amino-terminal domain (ATD) in a subtype-specific manner.", "Ifenprodil and related phenylethanolamine compounds, which specifically inhibit GluN1 and GluN2B NMDA receptors, have been intensely studied for their potential use in the treatment of various neurological disorders and diseases, including depression, Alzheimer's disease and Parkinson's disease.", "Despite considerable enthusiasm, mechanisms underlying the recognition of phenylethanolamines and ATD-mediated allosteric inhibition remain limited owing to a lack of structural information.", "Here we report that the GluN1 and GluN2B ATDs form a heterodimer and that phenylethanolamine binds at the interface between GluN1 and GluN2B, rather than within the GluN2B cleft.", "The crystal structure of the heterodimer formed between the GluN1b ATD from Xenopus laevis and the GluN2B ATD from Rattus norvegicus shows a highly distinct pattern of subunit arrangement that is different from the arrangements observed in homodimeric non-NMDA receptors and reveals the molecular determinants for phenylethanolamine binding.", "Restriction of domain movement in the bi-lobed structure of the GluN2B ATD, by engineering of an inter-subunit disulphide bond, markedly decreases sensitivity to ifenprodil, indicating that conformational freedom in the GluN2B ATD is essential for ifenprodil-mediated allosteric inhibition of NMDA receptors.", "These findings pave the way for improving the design of subtype-specific compounds with therapeutic value for neurological disorders and diseases."], "structured": false}
{"doc_id": 4427060, "title": "Association of NOD2 leucine-rich repeat variants with susceptibility to Crohn's disease.", "abstract": ["Crohn's disease and ulcerative colitis, the two main types of chronic inflammatory bowel disease, are multifactorial conditions of unknown aetiology.", "A susceptibility locus for Crohn's disease has been mapped to chromosome 16.", "Here we have used a positional-cloning strategy, based on linkage analysis followed by linkage disequilibrium mapping, to identify three independent associations for Crohn's disease: a frameshift variant and two missense variants of NOD2, encoding a member of the Apaf-1/Ced-4 superfamily of apoptosis regulators that is expressed in monocytes.", "These NOD2 variants alter the structure of either the leucine-rich repeat domain of the protein or the adjacent region.", "NOD2 activates nuclear factor NF-kB; this activating function is regulated by the carboxy-terminal leucine-rich repeat domain, which has an inhibitory role and also acts as an intracellular receptor for components of microbial pathogens.", "These observations suggest that the NOD2 gene product confers susceptibility to Crohn's disease by altering the recognition of these components and/or by over-activating NF-kB in monocytes, thus documenting a molecular model for the pathogenic mechanism of Crohn's disease that can now be further investigated."], "structured": false}
{"doc_id": 4427392, "title": "Human cardiovascular progenitor cells develop from a KDR+ embryonic-stem-cell-derived population", "abstract": ["The functional heart is comprised of distinct mesoderm-derived lineages including cardiomyocytes, endothelial cells and vascular smooth muscle cells.", "Studies in the mouse embryo and the mouse embryonic stem cell differentiation model have provided evidence indicating that these three lineages develop from a common Flk-1+ (kinase insert domain protein receptor, also known as Kdr) cardiovascular progenitor that represents one of the earliest stages in mesoderm specification to the cardiovascular lineages.", "To determine whether a comparable progenitor is present during human cardiogenesis, we analysed the development of the cardiovascular lineages in human embryonic stem cell differentiation cultures.", "Here we show that after induction with combinations of activin A, bone morphogenetic protein 4 (BMP4), basic fibroblast growth factor (bFGF, also known as FGF2), vascular endothelial growth factor (VEGF, also known as VEGFA) and dickkopf homolog 1 (DKK1) in serum-free media, human embryonic-stem-cell-derived embryoid bodies generate a KDRlow/C-KIT(CD117)neg population that displays cardiac, endothelial and vascular smooth muscle potential in vitro and, after transplantation, in vivo.", "When plated in monolayer cultures, these KDRlow/C-KITneg cells differentiate to generate populations consisting of greater than 50% contracting cardiomyocytes.", "Populations derived from the KDRlow/C-KITneg fraction give rise to colonies that contain all three lineages when plated in methylcellulose cultures.", "Results from limiting dilution studies and cell-mixing experiments support the interpretation that these colonies are clones, indicating that they develop from a cardiovascular colony-forming cell.", "Together, these findings identify a human cardiovascular progenitor that defines one of the earliest stages of human cardiac development."], "structured": false}
{"doc_id": 4429118, "title": "Cancer-related inflammation", "abstract": ["The mediators and cellular effectors of inflammation are important constituents of the local environment of tumours.", "In some types of cancer, inflammatory conditions are present before a malignant change occurs.", "Conversely, in other types of cancer, an oncogenic change induces an inflammatory microenvironment that promotes the development of tumours.", "Regardless of its origin, 'smouldering' inflammation in the tumour microenvironment has many tumour-promoting effects.", "It aids in the proliferation and survival of malignant cells, promotes angiogenesis and metastasis, subverts adaptive immune responses, and alters responses to hormones and chemotherapeutic agents.", "The molecular pathways of this cancer-related inflammation are now being unravelled, resulting in the identification of new target molecules that could lead to improved diagnosis and treatment."], "structured": false}
{"doc_id": 4429388, "title": "ESCRT-III recognition by VPS4 ATPases", "abstract": ["The ESCRT (endosomal sorting complex required for transport) pathway is required for terminal membrane fission events in several important biological processes, including endosomal intraluminal vesicle formation, HIV budding and cytokinesis.", "VPS4 ATPases perform a key function in this pathway by recognizing membrane-associated ESCRT-III assemblies and catalysing their disassembly, possibly in conjunction with membrane fission.", "Here we show that the microtubule interacting and transport (MIT) domains of human VPS4A and VPS4B bind conserved sequence motifs located at the carboxy termini of the CHMP1\u20133 class of ESCRT-III proteins.", "Structures of VPS4A MIT\u2013CHMP1A and VPS4B MIT\u2013CHMP2B complexes reveal that the C-terminal CHMP motif forms an amphipathic helix that binds in a groove between the last two helices of the tetratricopeptide-like repeat (TPR) of the VPS4 MIT domain, but in the opposite orientation to that of a canonical TPR interaction.", "Distinct pockets in the MIT domain bind three conserved leucine residues of the CHMP motif, and mutations that inhibit these interactions block VPS4 recruitment, impair endosomal protein sorting and relieve dominant-negative VPS4 inhibition of HIV budding.", "Thus, our studies reveal how the VPS4 ATPases recognize their CHMP substrates to facilitate the membrane fission events required for the release of viruses, endosomal vesicles and daughter cells."], "structured": false}
{"doc_id": 4429668, "title": "Pif1 family helicases suppress genome instability at G-quadruplex motifs", "abstract": ["The Saccharomyces cerevisiae Pif1 helicase is the prototypical member of the Pif1 DNA helicase family, which is conserved from bacteria to humans.", "Here we show that exceptionally potent G-quadruplex unwinding is conserved among Pif1 helicases.", "Moreover, Pif1 helicases from organisms separated by more than 3 billion years of evolution suppressed DNA damage at G-quadruplex motifs in yeast.", "The G-quadruplex-induced damage generated in the absence of Pif1 helicases led to new genetic and epigenetic changes.", "Furthermore, when expressed in yeast, human PIF1 suppressed both G-quadruplex-associated DNA damage and telomere lengthening."], "structured": false}
{"doc_id": 4429932, "title": "Lysyl oxidase is essential for hypoxia-induced metastasis", "abstract": ["Metastasis is a multistep process responsible for most cancer deaths, and it can be influenced by both the immediate microenvironment (cell\u2013cell or cell\u2013matrix interactions) and the extended tumour microenvironment (for example vascularization).", "Hypoxia (low oxygen) is clinically associated with metastasis and poor patient outcome, although the underlying processes remain unclear.", "Microarray studies have shown the expression of lysyl oxidase (LOX) to be elevated in hypoxic human tumour cells.", "Paradoxically, LOX expression is associated with both tumour suppression and tumour progression, and its role in tumorigenesis seems dependent on cellular location, cell type and transformation status.", "Here we show that LOX expression is regulated by hypoxia-inducible factor (HIF) and is associated with hypoxia in human breast and head and neck tumours.", "Patients with high LOX-expressing tumours have poor distant metastasis-free and overall survivals.", "Inhibition of LOX eliminates metastasis in mice with orthotopically grown breast cancer tumours.", "Mechanistically, secreted LOX is responsible for the invasive properties of hypoxic human cancer cells through focal adhesion kinase activity and cell to matrix adhesion.", "Furthermore, LOX may be required to create a niche permissive for metastatic growth.", "Our findings indicate that LOX is essential for hypoxia-induced metastasis and is a good therapeutic target for preventing and treating metastases."], "structured": false}
{"doc_id": 4430962, "title": "Identification of human brain tumour initiating cells", "abstract": ["The cancer stem cell (CSC) hypothesis suggests that neoplastic clones are maintained exclusively by a rare fraction of cells with stem cell properties.", "Although the existence of CSCs in human leukaemia is established, little evidence exists for CSCs in solid tumours, except for breast cancer.", "Recently, we prospectively isolated a CD133+ cell subpopulation from human brain tumours that exhibited stem cell properties in vitro.", "However, the true measures of CSCs are their capacity for self renewal and exact recapitulation of the original tumour.", "Here we report the development of a xenograft assay that identified human brain tumour initiating cells that initiate tumours in vivo.", "Only the CD133+ brain tumour fraction contains cells that are capable of tumour initiation in NOD-SCID (non-obese diabetic, severe combined immunodeficient) mouse brains.", "Injection of as few as 100 CD133+ cells produced a tumour that could be serially transplanted and was a phenocopy of the patient's original tumour, whereas injection of 105 CD133- cells engrafted but did not cause a tumour.", "Thus, the identification of brain tumour initiating cells provides insights into human brain tumour pathogenesis, giving strong support for the CSC hypothesis as the basis for many solid tumours, and establishes a previously unidentified cellular target for more effective cancer therapies."], "structured": false}
{"doc_id": 4432763, "title": "Anthropometric reference data for international use: recommendations from a World Health Organization Expert Committee.", "abstract": ["The World Health Organization (WHO) convened an Expert Committee to reevaluate the use of anthropometry at different ages for assessing health, nutrition, and social wellbeing.", "The Committee's task included identifying reference data for anthropometric indexes when appropriate, and providing guidelines on how the data should be used.", "For fetal growth, the Committee recommended an existing sex-specific multiracial reference.", "In view of the significant technical drawbacks of the current National Center for Health Statistics (NCHS)/WHO reference and its inadequacy for assessing the growth of breast-fed infants, the Committee recommended the development of a new reference concerning weight and length/height for infants and children, which will be a complex and costly undertaking.", "Proper interpretation of midupper arm circumference for preschoolers requires age-specific reference data.", "To evaluate adolescent height-for-age, the Committee recommended the current NCHS/WHO reference.", "Use of the NCHS body mass index (BMI) data, with their upper percentile elevations and skewness, is undesirable for setting health goals; however, these data were provisionally recommended for defining obesity based on a combination of elevated BMI and high subcutaneous fat.", "The NCHS values were provisionally recommended as reference data for subscapular and triceps skinfold thicknesses.", "Guidelines were also provided for adjusting adolescent anthropometric comparisons for maturational status.", "Currently, there is no need for adult reference data for BMI; interpretation should be based on pragmatic BMI cutoffs.", "Finally, the Committee noted that few normative anthropometric data exist for the elderly, especially for those > 80 y of age.", "Proper definitions of health status, function, and biologic age remain to be developed for this group."], "structured": false}
{"doc_id": 4434951, "title": "Diverse interventions that extend mouse lifespan suppress shared age-associated epigenetic changes at critical gene regulatory regions", "abstract": ["BACKGROUND Age-associated epigenetic changes are implicated in aging.", "Notably, age-associated DNA methylation changes comprise a so-called aging \"clock\", a robust biomarker of aging.", "However, while genetic, dietary and drug interventions can extend lifespan, their impact on the epigenome is uncharacterised.", "To fill this knowledge gap, we defined age-associated DNA methylation changes at the whole-genome, single-nucleotide level in mouse liver and tested the impact of longevity-promoting interventions, specifically the Ames dwarf Prop1 df/df mutation, calorie restriction and rapamycin.   \n", "RESULTS In wild-type mice fed an unsupplemented ad libitum diet, age-associated hypomethylation was enriched at super-enhancers in highly expressed genes critical for liver function.", "Genes harbouring hypomethylated enhancers were enriched for genes that change expression with age.", "Hypermethylation was enriched at CpG islands marked with bivalent activating and repressing histone modifications and resembled hypermethylation in liver cancer.", "Age-associated methylation changes are suppressed in Ames dwarf and calorie restricted mice and more selectively and less specifically in rapamycin treated mice.   \n", "CONCLUSIONS Age-associated hypo- and hypermethylation events occur at distinct regulatory features of the genome.", "Distinct longevity-promoting interventions, specifically genetic, dietary and drug interventions, suppress some age-associated methylation changes, consistent with the idea that these interventions exert their beneficial effects, in part, by modulation of the epigenome.", "This study is a foundation to understand the epigenetic contribution to healthy aging and longevity and the molecular basis of the DNA methylation clock."], "structured": true}
{"doc_id": 4435369, "title": "Extracellular vesicles for drug delivery.", "abstract": ["Extracellular vesicles (EVs) are cell-derived membrane vesicles, and represent an endogenous mechanism for intercellular communication.", "Since the discovery that EVs are capable of functionally transferring biological information, the potential use of EVs as drug delivery vehicles has gained considerable scientific interest.", "EVs may have multiple advantages over currently available drug delivery vehicles, such as their ability to overcome natural barriers, their intrinsic cell targeting properties, and stability in the circulation.", "However, therapeutic applications of EVs as drug delivery systems have been limited due to a lack of methods for scalable EV isolation and efficient drug loading.", "Furthermore, in order to achieve targeted drug delivery, their intrinsic cell targeting properties should be tuned through EV engineering.", "Here, we review and discuss recent progress and remaining challenges in the development of EVs as drug delivery vehicles."], "structured": false}
{"doc_id": 4442799, "title": "Effects of soy isoflavones and phytate on homocysteine, C-reactive protein, and iron status in postmenopausal women.", "abstract": ["BACKGROUND Soy protein or its components may protect against the atherosclerotic cardiovascular disease (CVD) risk factors total homocysteine (tHcy), C-reactive protein (CRP), and excess body iron, which generally increase with menopause.   \n", "OBJECTIVE The primary objective of this study was to determine the independent effect of the soy protein components isoflavones and phytate on CVD risk factors in postmenopausal women.", "The secondary objective was to identify factors [blood lipids, oxidative stress indexes, serum ferritin, plasma folate, plasma vitamin B-12, and body mass index (BMI)] contributing to tHcy and CRP concentrations.   \n", "DESIGN In a double-blind, 6-wk study, 55 postmenopausal women aged 47-72 y were randomly assigned to 1 of 4 soy protein (40 g/d) isolate treatments: native phytate and native isoflavone (n = 14), native phytate and low isoflavone (n = 13), low phytate and native isoflavone (n = 14), or low phytate and low isoflavone (n = 14).", "We measured iron indexes, tHcy, CRP, and BMI.   \n", "RESULTS Soy protein with native phytate significantly reduced tHcy (P = 0.017), transferrin saturation (P = 0.027), and ferritin (P = 0.029), whereas soy protein with native isoflavones had no effect on any variables.", "At baseline, BMI was highly correlated with tHcy (r = 0.39, P = 0.003) and CRP (r = 0.55, P < 0.0001), whereas HDL cholesterol was correlated with CRP (r = -0.30, P = 0.02).", "Multiple regression analysis showed that LDL cholesterol and BMI contributed significantly (R2= 19.9%, P = 0.003) to the overall variance in tHcy.   \n", "CONCLUSION Consuming phytate-rich foods and maintaining a healthy weight may reduce atherosclerotic CVD risk factors in postmenopausal women."], "structured": true}
{"doc_id": 4444861, "title": "Replication Fork Stability Confers Chemoresistance in BRCA-deficient Cells", "abstract": ["Cells deficient in the Brca1 and Brca2 genes have reduced capacity to repair DNA double-strand breaks by homologous recombination and consequently are hypersensitive to DNA-damaging agents, including cisplatin and poly(ADP-ribose) polymerase (PARP) inhibitors.", "Here we show that loss of the MLL3/4 complex protein, PTIP, protects Brca1/2-deficient cells from DNA damage and rescues the lethality of Brca2-deficient embryonic stem cells.", "However, PTIP deficiency does not restore homologous recombination activity at double-strand breaks.", "Instead, its absence inhibits the recruitment of the MRE11 nuclease to stalled replication forks, which in turn protects nascent DNA strands from extensive degradation.", "More generally, acquisition of PARP inhibitors and cisplatin resistance is associated with replication fork protection in Brca2-deficient tumour cells that do not develop Brca2 reversion mutations.", "Disruption of multiple proteins, including PARP1 and CHD4, leads to the same end point of replication fork protection, highlighting the complexities by which tumour cells evade chemotherapeutic interventions and acquire drug resistance."], "structured": false}
{"doc_id": 4445629, "title": "Plasma Corin as a Predictor of Cardiovascular Events in Patients With Chronic Heart Failure.", "abstract": ["OBJECTIVES The aim of this study was to determine the prognostic value of plasma corin in patients with chronic heart failure (CHF).   \n", "BACKGROUND In recent years, accumulating evidence has indicated that corin plays a critical role in regulating blood pressure and cardiac function.   \n", "METHODS We enrolled 1,148 consecutive CHF patients in a prospective cohort study and explored the association between plasma corin levels and clinical prognosis using multivariate Cox regression analysis.   \n", "RESULTS Patients with low corin levels (<458 pg/ml) were more likely to be women and to be hypertensive.", "Low corin was found to be associated with an increase in New York Heart Association (NYHA) functional class and N-terminal pro-B-type natriuretic peptide (NT-proBNP) levels, and a decrease in left ventricular ejection fraction (LVEF) and the estimated glomerular filtration rate (eGFR).", "Multivariate Cox regression analysis suggested that log corin was an independent predictor of major adverse cardiac event(s) (MACE) (hazard ratio: 0.62; 95% confidence interval: 0.39 to 0.95), together with age, diabetes, NYHA functional class, LVEF, eGFR, and log NT-proBNP.", "In addition, log corin was also a significant predictor for cardiovascular death (p = 0.041) and heart failure rehospitalization (p = 0.015) after adjustment for clinical variables and established biomarkers of adverse prognosis.", "The Kaplan-Meier survival curves showed that low corin was a significant predictor of MACE in patients with NT-proBNP levels above and below the median.   \n", "CONCLUSIONS Our study demonstrates that plasma corin is a valuable prognostic marker of MACE in patients with CHF, independent of established conventional risk factors."], "structured": true}
{"doc_id": 4446814, "title": "Cryo-EM structures of Tau filaments from Alzheimer\u2019s disease brain", "abstract": ["Alzheimer's disease is the most common neurodegenerative disease, and there are no mechanism-based therapies.", "The disease is defined by the presence of abundant neurofibrillary lesions and neuritic plaques in the cerebral cortex.", "Neurofibrillary lesions comprise paired helical and straight tau filaments, whereas tau filaments with different morphologies characterize other neurodegenerative diseases.", "No high-resolution structures of tau filaments are available.", "Here we present cryo-electron microscopy (cryo-EM) maps at 3.4-3.5 \u00c5 resolution and corresponding atomic models of paired helical and straight filaments from the brain of an individual with Alzheimer's disease.", "Filament cores are made of two identical protofilaments comprising residues 306-378 of tau protein, which adopt a combined cross-\u03b2/\u03b2-helix structure and define the seed for tau aggregation.", "Paired helical and straight filaments differ in their inter-protofilament packing, showing that they are ultrastructural polymorphs.", "These findings demonstrate that cryo-EM allows atomic characterization of amyloid filaments from patient-derived material, and pave the way for investigation of a range of neurodegenerative diseases."], "structured": false}
{"doc_id": 4447055, "title": "Modulation of the proteoglycan receptor PTP\u03c3 promotes recovery after spinal cord injury", "abstract": ["Contusive spinal cord injury leads to a variety of disabilities owing to limited neuronal regeneration and functional plasticity.", "It is well established that an upregulation of glial-derived chondroitin sulphate proteoglycans (CSPGs) within the glial scar and perineuronal net creates a barrier to axonal regrowth and sprouting.", "Protein tyrosine phosphatase \u03c3 (PTP\u03c3), along with its sister phosphatase leukocyte common antigen-related (LAR) and the nogo receptors 1 and 3 (NgR), have recently been identified as receptors for the inhibitory glycosylated side chains of CSPGs.", "Here we find in rats that PTP\u03c3 has a critical role in converting growth cones into a dystrophic state by tightly stabilizing them within CSPG-rich substrates.", "We generated a membrane-permeable peptide mimetic of the PTP\u03c3 wedge domain that binds to PTP\u03c3 and relieves CSPG-mediated inhibition.", "Systemic delivery of this peptide over weeks restored substantial serotonergic innervation to the spinal cord below the level of injury and facilitated functional recovery of both locomotor and urinary systems.", "Our results add a new layer of understanding to the critical role of PTP\u03c3 in mediating the growth-inhibited state of neurons due to CSPGs within the injured adult spinal cord."], "structured": false}
{"doc_id": 4447785, "title": "A gp130\u2013Src\u2013YAP module links inflammation to epithelial regeneration", "abstract": ["Inflammation promotes regeneration of injured tissues through poorly understood mechanisms, some of which involve interleukin (IL)-6 family members, the expression of which is elevated in many diseases including inflammatory bowel diseases and colorectal cancer.", "Here we show in mice and human cells that gp130, a co-receptor for IL-6 cytokines, triggers activation of YAP and Notch, transcriptional regulators that control tissue growth and regeneration, independently of the gp130 effector STAT3.", "Through YAP and Notch, intestinal gp130 signalling stimulates epithelial cell proliferation, causes aberrant differentiation and confers resistance to mucosal erosion.", "gp130 associates with the related tyrosine kinases Src and Yes, which are activated on receptor engagement to phosphorylate YAP and induce its stabilization and nuclear translocation.", "This signalling module is strongly activated upon mucosal injury to promote healing and maintain barrier function."], "structured": false}
{"doc_id": 4449524, "title": "Hemoglobin concentration in white, black, and Oriental children: is there a need for separate criteria in screening for anemia?", "abstract": ["The concentration of hemoglobin in blacks was found to be 0.5 to 1.0 g/dl lower than that of income-matched whites in several large surveys.", "This difference could be a racial characteristic of blacks, or it might be due to a higher frequency of genetic traits such as thalassemia minor and hemoglobinopathies, or to environmental factors such as iron deficiency.", "To help in making this distinction, we analyzed the data from multiphasic examinations (1973 to 1975) on 1718 white, 741 black, and 315 Oriental healthy, nonindigent children between 5 and 14 years of age.", "In the entire population, the median hemoglobin concentration averaged 0.5 g/dl lower in blacks than in whites of both sexes (t test, P less than 0.001).", "The differences still averaged 0.5 g/dl (P less than 0.001) after exclusion of all those with abnormal hemoglobin by electrophoresis (Hgb S and C) and those whose mean corpuscular volume was more than 5% below the normal mean for age (to exclude iron deficiency or thalassemia minor).", "The data strengthen the impression that blacks normally have a concentration of hemoglobin averaging about 0.5 g/dl less than in whites.", "If this is the case, about 10% of normal blacks will be mistakenly designated anemic, if the same norms are applied."], "structured": false}
{"doc_id": 4452318, "title": "Divergent reprogramming routes lead to alternative stem-cell states", "abstract": ["Pluripotency is defined by the ability of a cell to differentiate to the derivatives of all the three embryonic germ layers: ectoderm, mesoderm and endoderm.", "Pluripotent cells can be captured via the archetypal derivation of embryonic stem cells or via somatic cell reprogramming.", "Somatic cells are induced to acquire a pluripotent stem cell (iPSC) state through the forced expression of key transcription factors, and in the mouse these cells can fulfil the strictest of all developmental assays for pluripotent cells by generating completely iPSC-derived embryos and mice.", "However, it is not known whether there are additional classes of pluripotent cells, or what the spectrum of reprogrammed phenotypes encompasses.", "Here we explore alternative outcomes of somatic reprogramming by fully characterizing reprogrammed cells independent of preconceived definitions of iPSC states.", "We demonstrate that by maintaining elevated reprogramming factor expression levels, mouse embryonic fibroblasts go through unique epigenetic modifications to arrive at a stable, Nanog-positive, alternative pluripotent state.", "In doing so, we prove that the pluripotent spectrum can encompass multiple, unique cell states."], "structured": false}
{"doc_id": 4452659, "title": "Autophagy mediates degradation of nuclear lamina", "abstract": ["Macroautophagy (hereafter referred to as autophagy) is a catabolic membrane trafficking process that degrades a variety of cellular constituents and is associated with human diseases.", "Although extensive studies have focused on autophagic turnover of cytoplasmic materials, little is known about the role of autophagy in degrading nuclear components.", "Here we report that the autophagy machinery mediates degradation of nuclear lamina components in mammals.", "The autophagy protein LC3/Atg8, which is involved in autophagy membrane trafficking and substrate delivery, is present in the nucleus and directly interacts with the nuclear lamina protein lamin B1, and binds to lamin-associated domains on chromatin.", "This LC3-lamin B1 interaction does not downregulate lamin B1 during starvation, but mediates its degradation upon oncogenic insults, such as by activated RAS.", "Lamin B1 degradation is achieved by nucleus-to-cytoplasm transport that delivers lamin B1 to the lysosome.", "Inhibiting autophagy or the LC3-lamin B1 interaction prevents activated RAS-induced lamin B1 loss and attenuates oncogene-induced senescence in primary human cells.", "Our study suggests that this new function of autophagy acts as a guarding mechanism protecting cells from tumorigenesis."], "structured": false}
{"doc_id": 4454788, "title": "Pro-resolving lipid mediators are leads for resolution physiology", "abstract": ["Advances in our understanding of the mechanisms that bring about the resolution of acute inflammation have uncovered a new genus of pro-resolving lipid mediators that include the lipoxin, resolvin, protectin and maresin families, collectively called specialized pro-resolving mediators.", "Synthetic versions of these mediators have potent bioactions when administered in vivo.", "In animal experiments, the mediators evoke anti-inflammatory and novel pro-resolving mechanisms, and enhance microbial clearance.", "Although they have been identified in inflammation resolution, specialized pro-resolving mediators are conserved structures that also function in host defence, pain, organ protection and tissue remodelling.", "This Review covers the mechanisms of specialized pro-resolving mediators and omega-3 essential fatty acid pathways that could help us to understand their physiological functions."], "structured": false}
{"doc_id": 4455466, "title": "ZMYND11 links histone H3.3K36me3 to transcription elongation and tumour suppression", "abstract": ["Recognition of modified histones by \u2018reader\u2019 proteins plays a critical role in the regulation of chromatin.", "H3K36 trimethylation (H3K36me3) is deposited onto the nucleosomes in the transcribed regions after RNA polymerase II elongation.", "In yeast, this mark in turn recruits epigenetic regulators to reset the chromatin to a relatively repressive state, thus suppressing cryptic transcription.", "However, much less is known about the role of H3K36me3 in transcription regulation in mammals.", "This is further complicated by the transcription-coupled incorporation of the histone variant H3.3 in gene bodies.", "Here we show that the candidate tumour suppressor ZMYND11 specifically recognizes H3K36me3 on H3.3 (H3.3K36me3) and regulates RNA polymerase II elongation.", "Structural studies show that in addition to the trimethyl-lysine binding by an aromatic cage within the PWWP domain, the H3.3-dependent recognition is mediated by the encapsulation of the H3.3-specific \u2018Ser 31\u2019 residue in a composite pocket formed by the tandem bromo\u2013PWWP domains of ZMYND11.", "Chromatin immunoprecipitation followed by sequencing shows a genome-wide co-localization of ZMYND11 with H3K36me3 and H3.3 in gene bodies, and its occupancy requires the pre-deposition of H3.3K36me3.", "Although ZMYND11 is associated with highly expressed genes, it functions as an unconventional transcription co-repressor by modulating RNA polymerase II at the elongation stage.", "ZMYND11 is critical for the repression of a transcriptional program that is essential for tumour cell growth; low expression levels of ZMYND11 in breast cancer patients correlate with worse prognosis.", "Consistently, overexpression of ZMYND11 suppresses cancer cell growth in vitro and tumour formation in mice.", "Together, this study identifies ZMYND11 as an H3.3-specific reader of H3K36me3 that links the histone-variant-mediated transcription elongation control to tumour suppression."], "structured": false}
{"doc_id": 4456756, "title": "Autocrine BDNF\u2013TrkB signalling within a single dendritic spine", "abstract": ["Brain-derived neurotrophic factor (BDNF) and its receptor TrkB are crucial for many forms of neuronal plasticity, including structural long-term potentiation (sLTP), which is a correlate of an animal\u2019s learning.", "However, it is unknown whether BDNF release and TrkB activation occur during sLTP, and if so, when and where.", "Here, using a fluorescence resonance energy transfer-based sensor for TrkB and two-photon fluorescence lifetime imaging microscopy, we monitor TrkB activity in single dendritic spines of CA1 pyramidal neurons in cultured murine hippocampal slices.", "In response to sLTP induction, we find fast (onset < 1 min) and sustained (>20 min) activation of TrkB in the stimulated spine that depends on NMDAR (N-methyl-d-aspartate receptor) and CaMKII signalling and on postsynaptically synthesized BDNF.", "We confirm the presence of postsynaptic BDNF using electron microscopy to localize endogenous BDNF to dendrites and spines of hippocampal CA1 pyramidal neurons.", "Consistent with these findings, we also show rapid, glutamate-uncaging-evoked, time-locked BDNF release from single dendritic spines using BDNF fused to superecliptic pHluorin.", "We demonstrate that this postsynaptic BDNF\u2013TrkB signalling pathway is necessary for both structural and functional LTP.", "Together, these findings reveal a spine-autonomous, autocrine signalling mechanism involving NMDAR\u2013CaMKII-dependent BDNF release from stimulated dendritic spines and subsequent TrkB activation on these same spines that is crucial for structural and functional plasticity."], "structured": false}
{"doc_id": 4457160, "title": "Whole genomes redefine the mutational landscape of pancreatic cancer", "abstract": ["Pancreatic cancer remains one of the most lethal of malignancies and a major health burden.", "We performed whole-genome sequencing and copy number variation (CNV) analysis of 100 pancreatic ductal adenocarcinomas (PDACs).", "Chromosomal rearrangements leading to gene disruption were prevalent, affecting genes known to be important in pancreatic cancer (TP53, SMAD4, CDKN2A, ARID1A and ROBO2) and new candidate drivers of pancreatic carcinogenesis (KDM6A and PREX2).", "Patterns of structural variation (variation in chromosomal structure) classified PDACs into 4 subtypes with potential clinical utility: the subtypes were termed stable, locally rearranged, scattered and unstable.", "A significant proportion harboured focal amplifications, many of which contained druggable oncogenes (ERBB2, MET, FGFR1, CDK6, PIK3R3 and PIK3CA), but at low individual patient prevalence.", "Genomic instability co-segregated with inactivation of DNA maintenance genes (BRCA1, BRCA2 or PALB2) and a mutational signature of DNA damage repair deficiency.", "Of 8 patients who received platinum therapy, 4 of 5 individuals with these measures of defective DNA maintenance responded."], "structured": false}
{"doc_id": 4457834, "title": "Human oocytes reprogram adult somatic nuclei of a type 1 diabetic to diploid pluripotent stem cells", "abstract": ["The transfer of somatic cell nuclei into oocytes can give rise to pluripotent stem cells that are consistently equivalent to embryonic stem cells, holding promise for autologous cell replacement therapy.", "Although methods to induce pluripotent stem cells from somatic cells by transcription factors are widely used in basic research, numerous differences between induced pluripotent stem cells and embryonic stem cells have been reported, potentially affecting their clinical use.", "Because of the therapeutic potential of diploid embryonic stem-cell lines derived from adult cells of diseased human subjects, we have systematically investigated the parameters affecting efficiency of blastocyst development and stem-cell derivation.", "Here we show that improvements to the oocyte activation protocol, including the use of both kinase and translation inhibitors, and cell culture in the presence of histone deacetylase inhibitors, promote development to the blastocyst stage.", "Developmental efficiency varied between oocyte donors, and was inversely related to the number of days of hormonal stimulation required for oocyte maturation, whereas the daily dose of gonadotropin or the total number of metaphase II oocytes retrieved did not affect developmental outcome.", "Because the use of concentrated Sendai virus for cell fusion induced an increase in intracellular calcium concentration, causing premature oocyte activation, we used diluted Sendai virus in calcium-free medium.", "Using this modified nuclear transfer protocol, we derived diploid pluripotent stem-cell lines from somatic cells of a newborn and, for the first time, an adult, a female with type 1 diabetes."], "structured": false}
{"doc_id": 4459491, "title": "A three-dimensional human neural cell culture model of Alzheimer\u2019s disease", "abstract": ["Alzheimer\u2019s disease is the most common form of dementia, characterized by two pathological hallmarks: amyloid-\u03b2 plaques and neurofibrillary tangles.", "The amyloid hypothesis of Alzheimer\u2019s disease posits that the excessive accumulation of amyloid-\u03b2 peptide leads to neurofibrillary tangles composed of aggregated hyperphosphorylated tau.", "However, to date, no single disease model has serially linked these two pathological events using human neuronal cells.", "Mouse models with familial Alzheimer\u2019s disease (FAD) mutations exhibit amyloid-\u03b2-induced synaptic and memory deficits but they do not fully recapitulate other key pathological events of Alzheimer\u2019s disease, including distinct neurofibrillary tangle pathology.", "Human neurons derived from Alzheimer\u2019s disease patients have shown elevated levels of toxic amyloid-\u03b2 species and phosphorylated tau but did not demonstrate amyloid-\u03b2 plaques or neurofibrillary tangles.", "Here we report that FAD mutations in \u03b2-amyloid precursor protein and presenilin 1 are able to induce robust extracellular deposition of amyloid-\u03b2, including amyloid-\u03b2 plaques, in a human neural stem-cell-derived three-dimensional (3D) culture system.", "More importantly, the 3D-differentiated neuronal cells expressing FAD mutations exhibited high levels of detergent-resistant, silver-positive aggregates of phosphorylated tau in the soma and neurites, as well as filamentous tau, as detected by immunoelectron microscopy.", "Inhibition of amyloid-\u03b2 generation with \u03b2- or \u03b3-secretase inhibitors not only decreased amyloid-\u03b2 pathology, but also attenuated tauopathy.", "We also found that glycogen synthase kinase 3 (GSK3) regulated amyloid-\u03b2-mediated tau phosphorylation.", "We have successfully recapitulated amyloid-\u03b2 and tau pathology in a single 3D human neural cell culture system.", "Our unique strategy for recapitulating Alzheimer\u2019s disease pathology in a 3D neural cell culture model should also serve to facilitate the development of more precise human neural cell models of other neurodegenerative disorders."], "structured": false}
{"doc_id": 4460880, "title": "Mesenchymal-endothelial-transition contributes to cardiac neovascularization", "abstract": ["Endothelial cells contribute to a subset of cardiac fibroblasts by undergoing endothelial-to-mesenchymal transition, but whether cardiac fibroblasts can adopt an endothelial cell fate and directly contribute to neovascularization after cardiac injury is not known.", "Here, using genetic fate map techniques, we demonstrate that cardiac fibroblasts rapidly adopt an endothelial-cell-like phenotype after acute ischaemic cardiac injury.", "Fibroblast-derived endothelial cells exhibit anatomical and functional characteristics of native endothelial cells.", "We show that the transcription factor p53 regulates such a switch in cardiac fibroblast fate.", "Loss of p53 in cardiac fibroblasts severely decreases the formation of fibroblast-derived endothelial cells, reduces post-infarct vascular density and worsens cardiac function.", "Conversely, stimulation of the p53 pathway in cardiac fibroblasts augments mesenchymal-to-endothelial transition, enhances vascularity and improves cardiac function.", "These observations demonstrate that mesenchymal-to-endothelial transition contributes to neovascularization of the injured heart and represents a potential therapeutic target for enhancing cardiac repair."], "structured": false}
{"doc_id": 4462079, "title": "Estimation of optimal serum concentrations of 25-hydroxyvitamin D for multiple health outcomes.", "abstract": ["Recent evidence suggests that vitamin D intakes above current recommendations may be associated with better health outcomes.", "However, optimal serum concentrations of 25-hydroxyvitamin D [25(OH)D] have not been defined.", "This review summarizes evidence from studies that evaluated thresholds for serum 25(OH)D concentrations in relation to bone mineral density (BMD), lower-extremity function, dental health, and risk of falls, fractures, and colorectal cancer.", "For all endpoints, the most advantageous serum concentrations of 25(OH)D begin at 75 nmol/L (30 ng/mL), and the best are between 90 and 100 nmol/L (36-40 ng/mL).", "In most persons, these concentrations could not be reached with the currently recommended intakes of 200 and 600 IU vitamin D/d for younger and older adults, respectively.", "A comparison of vitamin D intakes with achieved serum concentrations of 25(OH)D for the purpose of estimating optimal intakes led us to suggest that, for bone health in younger adults and all studied outcomes in older adults, an increase in the currently recommended intake of vitamin D is warranted.", "An intake for all adults of > or =1000 IU (25 microg) [DOSAGE ERROR CORRECTED] vitamin D (cholecalciferol)/d is needed to bring vitamin D concentrations in no less than 50% of the population up to 75 nmol/L. The implications of higher doses for the entire adult population should be addressed in future studies."], "structured": false}
{"doc_id": 4462139, "title": "Cohesin-dependent globules and heterochromatin shape 3D genome architecture in S. pombe", "abstract": ["Eukaryotic genomes are folded into three-dimensional structures, such as self-associating topological domains, the borders of which are enriched in cohesin and CCCTC-binding factor (CTCF) required for long-range interactions.", "How local chromatin interactions govern higher-order folding of chromatin fibres and the function of cohesin in this process remain poorly understood.", "Here we perform genome-wide chromatin conformation capture (Hi-C) analysis to explore the high-resolution organization of the Schizosaccharomyces pombe genome, which despite its small size exhibits fundamental features found in other eukaryotes.", "Our analyses of wild-type and mutant strains reveal key elements of chromosome architecture and genome organization.", "On chromosome arms, small regions of chromatin locally interact to form 'globules'.", "This feature requires a function of cohesin distinct from its role in sister chromatid cohesion.", "Cohesin is enriched at globule boundaries and its loss causes disruption of local globule structures and global chromosome territories.", "By contrast, heterochromatin, which loads cohesin at specific sites including pericentromeric and subtelomeric domains, is dispensable for globule formation but nevertheless affects genome organization.", "We show that heterochromatin mediates chromatin fibre compaction at centromeres and promotes prominent inter-arm interactions within centromere-proximal regions, providing structural constraints crucial for proper genome organization.", "Loss of heterochromatin relaxes constraints on chromosomes, causing an increase in intra- and inter-chromosomal interactions.", "Together, our analyses uncover fundamental genome folding principles that drive higher-order chromosome organization crucial for coordinating nuclear functions."], "structured": false}
{"doc_id": 4462155, "title": "A temporal shift in the circuits mediating retrieval of fear memory", "abstract": ["Fear memories allow animals to avoid danger, thereby increasing their chances of survival.", "Fear memories can be retrieved long after learning, but little is known about how retrieval circuits change with time.", "Here we show that the dorsal midline thalamus of rats is required for the retrieval of auditory conditioned fear at late (24 hours, 7 days, 28 days), but not early (0.5 hours, 6 hours) time points after learning.", "Consistent with this, the paraventricular nucleus of the thalamus (PVT), a subregion of the dorsal midline thalamus, showed increased c-Fos expression only at late time points, indicating that the PVT is gradually recruited for fear retrieval.", "Accordingly, the conditioned tone responses of PVT neurons increased with time after training.", "The prelimbic (PL) prefrontal cortex, which is necessary for fear retrieval, sends dense projections to the PVT.", "Retrieval at late time points activated PL neurons projecting to the PVT, and optogenetic silencing of these projections impaired retrieval at late, but not early, time points.", "In contrast, silencing of PL inputs to the basolateral amygdala impaired retrieval at early, but not late, time points, indicating a time-dependent shift in retrieval circuits.", "Retrieval at late time points also activated PVT neurons projecting to the central nucleus of the amygdala, and silencing these projections at late, but not early, time points induced a persistent attenuation of fear.", "Thus, the PVT may act as a crucial thalamic node recruited into cortico-amygdalar networks for retrieval and maintenance of long-term fear memories."], "structured": false}
{"doc_id": 4462419, "title": "Derivation of novel human ground state naive pluripotent stem cells", "abstract": ["Mouse embryonic stem (ES) cells are isolated from the inner cell mass of blastocysts, and can be preserved in vitro in a naive inner-cell-mass-like configuration by providing exogenous stimulation with leukaemia inhibitory factor (LIF) and small molecule inhibition of ERK1/ERK2 and GSK3\u03b2 signalling (termed 2i/LIF conditions).", "Hallmarks of naive pluripotency include driving Oct4 (also known as Pou5f1) transcription by its distal enhancer, retaining a pre-inactivation X chromosome state, and global reduction in DNA methylation and in H3K27me3 repressive chromatin mark deposition on developmental regulatory gene promoters.", "Upon withdrawal of 2i/LIF, naive mouse ES cells can drift towards a primed pluripotent state resembling that of the post-implantation epiblast.", "Although human ES cells share several molecular features with naive mouse ES cells, they also share a variety of epigenetic properties with primed murine epiblast stem cells (EpiSCs).", "These include predominant use of the proximal enhancer element to maintain OCT4 expression, pronounced tendency for X chromosome inactivation in most female human ES cells, increase in DNA methylation and prominent deposition of H3K27me3 and bivalent domain acquisition on lineage regulatory genes.", "The feasibility of establishing human ground state naive pluripotency in vitro with equivalent molecular and functional features to those characterized in mouse ES cells remains to be defined.", "Here we establish defined conditions that facilitate the derivation of genetically unmodified human naive pluripotent stem cells from already established primed human ES cells, from somatic cells through induced pluripotent stem (iPS) cell reprogramming or directly from blastocysts.", "The novel naive pluripotent cells validated herein retain molecular characteristics and functional properties that are highly similar to mouse naive ES cells, and distinct from conventional primed human pluripotent cells.", "This includes competence in the generation of cross-species chimaeric mouse embryos that underwent organogenesis following microinjection of human naive iPS cells into mouse morulas.", "Collectively, our findings establish new avenues for regenerative medicine, patient-specific iPS cell disease modelling and the study of early human development in vitro and in vivo."], "structured": false}
{"doc_id": 4462777, "title": "Predicting immunogenic tumour mutations by combining mass spectrometry and exome sequencing", "abstract": ["Human tumours typically harbour a remarkable number of somatic mutations.", "If presented on major histocompatibility complex class I molecules (MHCI), peptides containing these mutations could potentially be immunogenic as they should be recognized as \u2018non-self\u2019 neo-antigens by the adaptive immune system.", "Recent work has confirmed that mutant peptides can serve as T-cell epitopes.", "However, few mutant epitopes have been described because their discovery required the laborious screening of patient tumour-infiltrating lymphocytes for their ability to recognize antigen libraries constructed following tumour exome sequencing.", "We sought to simplify the discovery of immunogenic mutant peptides by characterizing their general properties.", "We developed an approach that combines whole-exome and transcriptome sequencing analysis with mass spectrometry to identify neo-epitopes in two widely used murine tumour models.", "Of the >1,300 amino acid changes identified, \u223c13% were predicted to bind MHCI, a small fraction of which were confirmed by mass spectrometry.", "The peptides were then structurally modelled bound to MHCI.", "Mutations that were solvent-exposed and therefore accessible to T-cell antigen receptors were predicted to be immunogenic.", "Vaccination of mice confirmed the approach, with each predicted immunogenic peptide yielding therapeutically active T-cell responses.", "The predictions also enabled the generation of peptide\u2013MHCI dextramers that could be used to monitor the kinetics and distribution of the anti-tumour T-cell response before and after vaccination.", "These findings indicate that a suitable prediction algorithm may provide an approach for the pharmacodynamic monitoring of T-cell responses as well as for the development of personalized vaccines in cancer patients."], "structured": false}
{"doc_id": 4462919, "title": "In vivo genome editing using Staphylococcus aureus Cas9", "abstract": ["The RNA-guided endonuclease Cas9 has emerged as a versatile genome-editing platform.", "However, the size of the commonly used Cas9 from Streptococcus pyogenes (SpCas9) limits its utility for basic research and therapeutic applications that use the highly versatile adeno-associated virus (AAV) delivery vehicle.", "Here, we characterize six smaller Cas9 orthologues and show that Cas9 from Staphylococcus aureus (SaCas9) can edit the genome with efficiencies similar to those of SpCas9, while being more than 1 kilobase shorter.", "We packaged SaCas9 and its single guide RNA expression cassette into a single AAV vector and targeted the cholesterol regulatory gene Pcsk9 in the mouse liver.", "Within one week of injection, we observed >40% gene modification, accompanied by significant reductions in serum Pcsk9 and total cholesterol levels.", "We further assess the genome-wide targeting specificity of SaCas9 and SpCas9 using BLESS, and demonstrate that SaCas9-mediated in vivo genome editing has the potential to be efficient and specific."], "structured": false}
{"doc_id": 4463588, "title": "Effects of exercise intensity on cardiovascular fitness, total body composition, and visceral adiposity of obese adolescents.", "abstract": ["BACKGROUND Little is known about how the intensity of exercise influences cardiovascular fitness and body composition, especially in obese adolescents.   \n", "OBJECTIVE Our goal was to determine the effects of physical training intensity on the cardiovascular fitness, percentage of body fat (%BF), and visceral adipose tissue (VAT) of obese adolescents.   \n", "DESIGN Obese 13-16-y-olds (n = 80) were assigned to 1) biweekly lifestyle education (LSE), 2) LSE + moderate-intensity physical training, or 3) LSE + high-intensity physical training.", "The intervention lasted 8 mo.", "Physical training was offered 5 d/wk, and the target energy expenditure for all subjects in physical training groups was 1047 kJ (250 kcal)/session.", "Cardiovascular fitness was measured with a multistage treadmill test, %BF with dual-energy X-ray absorptiometry, and VAT with magnetic resonance imaging.   \n", "RESULTS The increase in cardiovascular fitness in the high-intensity physical training group, but not in the moderate-intensity group, was significantly greater than that in the LSE alone group (P = 0.009); no other comparisons of the 3 groups were significant.", "Compared with the LSE alone group, a group composed of subjects in both physical training groups combined who attended training sessions >or=2 d/wk showed favorable changes in cardiovascular fitness (P < 0.001), %BF (P = 0.001), and VAT (P = 0.029).", "We found no evidence that the high-intensity physical training was more effective than the moderate-intensity physical training in enhancing body composition.   \n", "CONCLUSIONS The cardiovascular fitness of obese adolescents was significantly improved by physical training, especially high-intensity physical training.", "The physical training also reduced both visceral and total-body adiposity, but there was no clear effect of the intensity of physical training."], "structured": true}
{"doc_id": 4463811, "title": "Low methionine ingestion by rats extends life span.", "abstract": ["Dietary energy restriction has been a widely used means of experimentally extending mammalian life span.", "We report here that lifelong reduction in the concentration of a single dietary component, the essential amino acid L-methionine, from 0.86 to 0.17% of the diet results in a 30% longer life span of male Fischer 344 rats.", "Methionine restriction completely abolished growth, although food intake was actually greater on a body weight basis.", "Studies of energy consumption in early life indicated that the energy intake of 0.17% methionine-fed animals was near normal for animals of their size, although consumption per animal was below that of the much larger 0.86% methionine-fed rats.", "Increasing the energy intake of rats fed 0.17% methionine failed to increase their rate of growth, whereas restricting 0.85% methionine-fed rats to the food intake of 0.17% methionine-fed animals did not materially reduce growth, indicating that food restriction was not a factor in life span extension in these experiments.", "The biochemically well-defined pathways of methionine metabolism and utilization offer the potential for uncovering the precise mechanism(s) underlying this specific dietary restriction-related extension of life span."], "structured": false}
{"doc_id": 4464565, "title": "Epicatechin and a cocoa polyphenolic extract modulate gene expression in human Caco-2 cells.", "abstract": ["We performed a functional genomic analysis to study the effect of epicatechin and polyphenolic cocoa extract in the human colon adenocarcinoma cell line Caco-2.", "The specific Human Hematology/Immunology cDNA arrays by Clontech, containing 406 genes in duplicate, were used.", "The differentially expressed genes were classified according to their level of expression, calculated as the ratio of the value obtained after each treatment relative to control cells, with a statistical significance of P < 0.05 (upregulated: ratio > 1.5; downregulated: ratio < 0.6).", "Treatment with epicatechin decreased the expression of 21 genes and upregulated 24 genes.", "Upon incubation with the cocoa polyphenolic extract, 24 genes were underexpressed and 28 were overexpressed.", "The changes in expression for ferritin heavy polypeptide 1 (FTH1), mitogen-activated protein kinase kinase 1 (MAPKK1), signal transducer and activator of transcription 1 (STAT1), and topoisomerase 1 upon incubation with epicatechin, and for myeloid leukemia factor 2 (MLF2), CCAAT/enhancer binding protein gamma (C/EBPG), MAPKK1, ATP-binding cassette, subfamily c member 1 (MRP1), STAT1, topoisomerase 1, and x-ray repair complementing defective repair 1 (XRCC1) upon incubation with the cocoa polyphenolic extract were validated by RT-PCR.", "Changes in the messenger RNA levels for MAPKK1, STAT1, MRP1, and topoisomerase 1 upon incubation with either epicatechin or cocoa extract were further confirmed at the protein level by Western blotting.", "The changes in the expression of STAT1, MAPKK1, MRP1, and FTH1 genes, which are involved in the cellular response to oxidative stress, are in agreement with the antioxidant properties of cocoa flavonoids.", "In addition, the changes in the expression of C/EBPG, topoisomerase 1, MLF2, and XRCC1 suggest novel mechanisms of action of flavonoids at the molecular level."], "structured": false}
{"doc_id": 4465608, "title": "An atlas of active enhancers across human cell types and tissues", "abstract": ["Enhancers control the correct temporal and cell-type-specific activation of gene expression in multicellular eukaryotes.", "Knowing their properties, regulatory activity and targets is crucial to understand the regulation of differentiation and homeostasis.", "Here we use the FANTOM5 panel of samples, covering the majority of human tissues and cell types, to produce an atlas of active, in vivo-transcribed enhancers.", "We show that enhancers share properties with CpG-poor messenger RNA promoters but produce bidirectional, exosome-sensitive, relatively short unspliced RNAs, the generation of which is strongly related to enhancer activity.", "The atlas is used to compare regulatory programs between different cells at unprecedented depth, to identify disease-associated regulatory single nucleotide polymorphisms, and to classify cell-type-specific and ubiquitous enhancers.", "We further explore the utility of enhancer redundancy, which explains gene expression strength rather than expression patterns.", "The online FANTOM5 enhancer atlas represents a unique resource for studies on cell-type-specific enhancers and gene regulation."], "structured": false}
{"doc_id": 4465735, "title": "Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile", "abstract": ["The gastrointestinal tracts of mammals are colonized by hundreds of microbial species that contribute to health, including colonization resistance against intestinal pathogens.", "Many antibiotics destroy intestinal microbial communities and increase susceptibility to intestinal pathogens.", "Among these, Clostridium difficile, a major cause of antibiotic-induced diarrhoea, greatly increases morbidity and mortality in hospitalized patients.", "Which intestinal bacteria provide resistance to C. difficile infection and their in vivo inhibitory mechanisms remain unclear.", "Here we correlate loss of specific bacterial taxa with development of infection, by treating mice with different antibiotics that result in distinct microbiota changes and lead to varied susceptibility to C. difficile.", "Mathematical modelling augmented by analyses of the microbiota of hospitalized patients identifies resistance-associated bacteria common to mice and humans.", "Using these platforms, we determine that Clostridium scindens, a bile acid 7\u03b1-dehydroxylating intestinal bacterium, is associated with resistance to C. difficile infection and, upon administration, enhances resistance to infection in a secondary bile acid dependent fashion.", "Using a workflow involving mouse models, clinical studies, metagenomic analyses, and mathematical modelling, we identify a probiotic candidate that corrects a clinically relevant microbiome deficiency.", "These findings have implications for the rational design of targeted antimicrobials as well as microbiome-based diagnostics and therapeutics for individuals at risk of C. difficile infection."], "structured": false}
{"doc_id": 4465762, "title": "Transcription initiation complex structures elucidate DNA opening", "abstract": ["Transcription of eukaryotic protein-coding genes begins with assembly of the RNA polymerase (Pol) II initiation complex and promoter DNA opening.", "Here we report cryo-electron microscopy (cryo-EM) structures of yeast initiation complexes containing closed and open DNA at resolutions of 8.8 \u00c5 and 3.6 \u00c5, respectively.", "DNA is positioned and retained over the Pol II cleft by a network of interactions between the TATA-box-binding protein TBP and transcription factors TFIIA, TFIIB, TFIIE, and TFIIF.", "DNA opening occurs around the tip of the Pol II clamp and the TFIIE \u2018extended winged helix\u2019 domain, and can occur in the absence of TFIIH.", "Loading of the DNA template strand into the active centre may be facilitated by movements of obstructing protein elements triggered by allosteric binding of the TFIIE \u2018E-ribbon\u2019 domain.", "The results suggest a unified model for transcription initiation with a key event, the trapping of open promoter DNA by extended protein\u2013protein and protein\u2013DNA contacts."], "structured": false}
{"doc_id": 4467129, "title": "Multiple mechanisms disrupt the let-7 microRNA family in neuroblastoma", "abstract": ["Poor prognosis in neuroblastoma is associated with genetic amplification of MYCN.", "MYCN is itself a target of let-7, a tumour suppressor family of microRNAs implicated in numerous cancers.", "LIN28B, an inhibitor of let-7 biogenesis, is overexpressed in neuroblastoma and has been reported to regulate MYCN.", "Here we show, however, that LIN28B is dispensable in MYCN-amplified neuroblastoma cell lines, despite de-repression of let-7.", "We further demonstrate that MYCN messenger RNA levels in amplified disease are exceptionally high and sufficient to sponge let-7, which reconciles the dispensability of LIN28B.", "We found that genetic loss of let-7 is common in neuroblastoma, inversely associated with MYCN amplification, and independently associated with poor outcomes, providing a rationale for chromosomal loss patterns in neuroblastoma.", "We propose that let-7 disruption by LIN28B, MYCN sponging, or genetic loss is a unifying mechanism of neuroblastoma development with broad implications for cancer pathogenesis."], "structured": false}
{"doc_id": 4468861, "title": "Radiation and Dual Checkpoint Blockade Activates Non-Redundant Immune Mechanisms in Cancer", "abstract": ["Immune checkpoint inhibitors result in impressive clinical responses, but optimal results will require combination with each other and other therapies.", "This raises fundamental questions about mechanisms of non-redundancy and resistance.", "Here we report major tumour regressions in a subset of patients with metastatic melanoma treated with an anti-CTLA4 antibody (anti-CTLA4) and radiation, and reproduced this effect in mouse models.", "Although combined treatment improved responses in irradiated and unirradiated tumours, resistance was common.", "Unbiased analyses of mice revealed that resistance was due to upregulation of PD-L1 on melanoma cells and associated with T-cell exhaustion.", "Accordingly, optimal response in melanoma and other cancer types requires radiation, anti-CTLA4 and anti-PD-L1/PD-1.", "Anti-CTLA4 predominantly inhibits T-regulatory cells (Treg cells), thereby increasing the CD8 T-cell to Treg (CD8/Treg) ratio.", "Radiation enhances the diversity of the T-cell receptor (TCR) repertoire of intratumoral T cells.", "Together, anti-CTLA4 promotes expansion of T cells, while radiation shapes the TCR repertoire of the expanded peripheral clones.", "Addition of PD-L1 blockade reverses T-cell exhaustion to mitigate depression in the CD8/Treg ratio and further encourages oligoclonal T-cell expansion.", "Similarly to results from mice, patients on our clinical trial with melanoma showing high PD-L1 did not respond to radiation plus anti-CTLA4, demonstrated persistent T-cell exhaustion, and rapidly progressed.", "Thus, PD-L1 on melanoma cells allows tumours to escape anti-CTLA4-based therapy, and the combination of radiation, anti-CTLA4 and anti-PD-L1 promotes response and immunity through distinct mechanisms."], "structured": false}
{"doc_id": 4469125, "title": "G-protein-independent coupling of MC4R to Kir7.1 in hypothalamic neurons", "abstract": ["The regulated release of anorexigenic \u03b1-melanocyte stimulating hormone (\u03b1-MSH) and orexigenic Agouti-related protein (AgRP) from discrete hypothalamic arcuate neurons onto common target sites in the central nervous system has a fundamental role in the regulation of energy homeostasis.", "Both peptides bind with high affinity to the melanocortin-4 receptor (MC4R); existing data show that \u03b1-MSH is an agonist that couples the receptor to the G\u03b1s signalling pathway, while AgRP binds competitively to block \u03b1-MSH binding and blocks the constitutive activity mediated by the ligand-mimetic amino-terminal domain of the receptor.", "Here we show that, in mice, regulation of firing activity of neurons from the paraventricular nucleus of the hypothalamus (PVN) by \u03b1-MSH and AgRP can be mediated independently of G\u03b1s signalling by ligand-induced coupling of MC4R to closure of inwardly rectifying potassium channel, Kir7.1.", "Furthermore, AgRP is a biased agonist that hyperpolarizes neurons by binding to MC4R and opening Kir7.1, independently of its inhibition of \u03b1-MSH binding.", "Consequently, Kir7.1 signalling appears to be central to melanocortin-mediated regulation of energy homeostasis within the PVN.", "Coupling of MC4R to Kir7.1 may explain unusual aspects of the control of energy homeostasis by melanocortin signalling, including the gene dosage effect of MC4R and the sustained effects of AgRP on food intake."], "structured": false}
{"doc_id": 4474874, "title": "Role of ghrelin in the relationship between hyperphagia and accelerated gastric emptying in diabetic mice.", "abstract": ["BACKGROUND & AIMS Ghrelin is an orexigenic peptide with gastroprokinetic effects.", "Mice with streptozotocin (STZ)-induced diabetes exhibit hyperphagia, altered gastric emptying, and increased plasma ghrelin levels.", "We investigated the causative role of ghrelin herein by comparing changes in ghrelin receptor knockout (growth hormone secretagogue receptor [GHS-R](-/-)) and wild-type (GHS-R(+/+)) mice with STZ-induced diabetes.   \n", "METHODS Gastric emptying was measured with the [(13)C]octanoic acid breath test.", "The messenger RNA (mRNA) expression of neuropeptide Y (NPY), agouti-related peptide (AgRP), and proopiomelanocortin was quantified by real-time reverse-transcription polymerase chain reaction.", "Neural contractions were elicited by electrical field stimulation in fundic smooth muscle strips.   \n", "RESULTS Diabetes increased plasma ghrelin levels to a similar extent in both genotypes.", "Hyperphagia was more pronounced in GHS-R(+/+) than in GHS-R(-/-) mice between days 12 and 21.", "Increases in NPY and AgRP mRNA expression were less pronounced in diabetic GHS-R(-/-) than in GHS-R(+/+) mice from day 15 on, whereas decreases in proopiomelanocortin mRNA levels were similar in both genotypes.", "Gastric emptying was accelerated to a similar extent in both genotypes, starting on day 16.", "In fundic smooth muscle strips of diabetic GHS-R(+/+) and GHS-R(-/-) mice, neuronal relaxations were reduced, whereas contractions were increased; this increase was related to an increased affinity of muscarinic and tachykinergic receptors.   \n", "CONCLUSIONS Diabetic hyperphagia is regulated by central mechanisms in which the ghrelin-signaling pathway affects the expression of NPY and AgRP in the hypothalamus.", "The acceleration of gastric emptying, which is not affected by ghrelin signaling, is not the cause of diabetic hyperphagia and probably involves local contractility changes in the fundus."], "structured": true}
{"doc_id": 4483571, "title": "Human serum 25-hydroxycholecalciferol response to extended oral dosing with cholecalciferol.", "abstract": ["BACKGROUND The cholecalciferol inputs required to achieve or maintain any given serum 25-hydroxycholecalciferol concentration are not known, particularly within ranges comparable to the probable physiologic supply of the vitamin.   \n", "OBJECTIVES The objectives were to establish the quantitative relation between steady state cholecalciferol input and the resulting serum 25-hydroxycholecalciferol concentration and to estimate the proportion of the daily requirement during winter that is met by cholecalciferol reserves in body tissue stores.   \n", "DESIGN Cholecalciferol was administered daily in controlled oral doses labeled at 0, 25, 125, and 250 micro g cholecalciferol for approximately 20 wk during the winter to 67 men living in Omaha (41.2 degrees N latitude).", "The time course of serum 25-hydroxycholecalciferol concentration was measured at intervals over the course of treatment.   \n", "RESULTS From a mean baseline value of 70.3 nmol/L, equilibrium concentrations of serum 25-hydroxycholecalciferol changed during the winter months in direct proportion to the dose, with a slope of approximately 0.70 nmol/L for each additional 1 micro g cholecalciferol input.", "The calculated oral input required to sustain the serum 25-hydroxycholecalciferol concentration present before the study (ie, in the autumn) was 12.5 micro g (500 IU)/d, whereas the total amount from all sources (supplement, food, tissue stores) needed to sustain the starting 25-hydroxycholecalciferol concentration was estimated at approximately 96 micro g (approximately 3800 IU)/d.", "By difference, the tissue stores provided approximately 78-82 micro g/d.   \n", "CONCLUSIONS Healthy men seem to use 3000-5000 IU cholecalciferol/d, apparently meeting > 80% of their winter cholecalciferol need with cutaneously synthesized accumulations from solar sources during the preceding summer months.", "Current recommended vitamin D inputs are inadequate to maintain serum 25-hydroxycholecalciferol concentration in the absence of substantial cutaneous production of vitamin D."], "structured": true}
{"doc_id": 4489217, "title": "Intratumor heterogeneity and branched evolution revealed by multiregion sequencing.", "abstract": ["BACKGROUND Intratumor heterogeneity may foster tumor evolution and adaptation and hinder personalized-medicine strategies that depend on results from single tumor-biopsy samples.   \n", "METHODS To examine intratumor heterogeneity, we performed exome sequencing, chromosome aberration analysis, and ploidy profiling on multiple spatially separated samples obtained from primary renal carcinomas and associated metastatic sites.", "We characterized the consequences of intratumor heterogeneity using immunohistochemical analysis, mutation functional analysis, and profiling of messenger RNA expression.   \n", "RESULTS Phylogenetic reconstruction revealed branched evolutionary tumor growth, with 63 to 69% of all somatic mutations not detectable across every tumor region.", "Intratumor heterogeneity was observed for a mutation within an autoinhibitory domain of the mammalian target of rapamycin (mTOR) kinase, correlating with S6 and 4EBP phosphorylation in vivo and constitutive activation of mTOR kinase activity in vitro.", "Mutational intratumor heterogeneity was seen for multiple tumor-suppressor genes converging on loss of function; SETD2, PTEN, and KDM5C underwent multiple distinct and spatially separated inactivating mutations within a single tumor, suggesting convergent phenotypic evolution.", "Gene-expression signatures of good and poor prognosis were detected in different regions of the same tumor.", "Allelic composition and ploidy profiling analysis revealed extensive intratumor heterogeneity, with 26 of 30 tumor samples from four tumors harboring divergent allelic-imbalance profiles and with ploidy heterogeneity in two of four tumors.   \n", "CONCLUSIONS Intratumor heterogeneity can lead to underestimation of the tumor genomics landscape portrayed from single tumor-biopsy samples and may present major challenges to personalized-medicine and biomarker development.", "Intratumor heterogeneity, associated with heterogeneous protein function, may foster tumor adaptation and therapeutic failure through Darwinian selection.", "(Funded by the Medical Research Council and others.)."], "structured": true}
{"doc_id": 4492358, "title": "Succession of microbial consortia in the developing infant gut microbiome.", "abstract": ["The colonization process of the infant gut microbiome has been called chaotic, but this view could reflect insufficient documentation of the factors affecting the microbiome.", "We performed a 2.5-y case study of the assembly of the human infant gut microbiome, to relate life events to microbiome composition and function.", "Sixty fecal samples were collected from a healthy infant along with a diary of diet and health status.", "Analysis of >300,000 16S rRNA genes indicated that the phylogenetic diversity of the microbiome increased gradually over time and that changes in community composition conformed to a smooth temporal gradient.", "In contrast, major taxonomic groups showed abrupt shifts in abundance corresponding to changes in diet or health.", "Community assembly was nonrandom: we observed discrete steps of bacterial succession punctuated by life events.", "Furthermore, analysis of \u2248 500,000 DNA metagenomic reads from 12 fecal samples revealed that the earliest microbiome was enriched in genes facilitating lactate utilization, and that functional genes involved in plant polysaccharide metabolism were present before the introduction of solid food, priming the infant gut for an adult diet.", "However, ingestion of table foods caused a sustained increase in the abundance of Bacteroidetes, elevated fecal short chain fatty acid levels, enrichment of genes associated with carbohydrate utilization, vitamin biosynthesis, and xenobiotic degradation, and a more stable community composition, all of which are characteristic of the adult microbiome.", "This study revealed that seemingly chaotic shifts in the microbiome are associated with life events; however, additional experiments ought to be conducted to assess how different infants respond to similar life events."], "structured": false}
{"doc_id": 4500832, "title": "gamma-tocopherol, the major form of vitamin E in the US diet, deserves more attention.", "abstract": ["gamma-tocopherol is the major form of vitamin E in many plant seeds and in the US diet, but has drawn little attention compared with alpha-tocopherol, the predominant form of vitamin E in tissues and the primary form in supplements.", "However, recent studies indicate that gamma-tocopherol may be important to human health and that it possesses unique features that distinguish it from alpha-tocopherol.", "gamma-Tocopherol appears to be a more effective trap for lipophilic electrophiles than is alpha-tocopherol.", "gamma-Tocopherol is well absorbed and accumulates to a significant degree in some human tissues; it is metabolized, however, largely to 2,7,8-trimethyl-2-(beta-carboxyethyl)-6-hydroxychroman (gamma-CEHC), which is mainly excreted in the urine.", "gamma-CEHC, but not the corresponding metabolite derived from alpha-tocopherol, has natriuretic activity that may be of physiologic importance.", "Both gamma-tocopherol and gamma-CEHC, but not alpha-tocopherol, inhibit cyclooxygenase activity and, thus, possess antiinflammatory properties.", "Some human and animal studies indicate that plasma concentrations of gamma-tocopherol are inversely associated with the incidence of cardiovascular disease and prostate cancer.", "These distinguishing features of gamma-tocopherol and its metabolite suggest that gamma-tocopherol may contribute significantly to human health in ways not recognized previously.", "This possibility should be further evaluated, especially considering that high doses of alpha-tocopherol deplete plasma and tissue gamma-tocopherol, in contrast with supplementation with gamma-tocopherol, which increases both.", "We review current information on the bioavailability, metabolism, chemistry, and nonantioxidant activities of gamma-tocopherol and epidemiologic data concerning the relation between gamma-tocopherol and cardiovascular disease and cancer."], "structured": false}
{"doc_id": 4505748, "title": "Disclosure of APOE genotype for risk of Alzheimer's disease.", "abstract": ["BACKGROUND The apolipoprotein E (APOE) genotype provides information on the risk of Alzheimer's disease, but the genotyping of patients and their family members has been discouraged.", "We examined the effect of genotype disclosure in a prospective, randomized, controlled trial.   \n", "METHODS We randomly assigned 162 asymptomatic adults who had a parent with Alzheimer's disease to receive the results of their own APOE genotyping (disclosure group) or not to receive such results (nondisclosure group).", "We measured symptoms of anxiety, depression, and test-related distress 6 weeks, 6 months, and 1 year after disclosure or nondisclosure.   \n", "RESULTS", "There were no significant differences between the two groups in changes in time-averaged measures of anxiety (4.5 in the disclosure group and 4.4 in the nondisclosure group, P=0.84), depression (8.8 and 8.7, respectively; P=0.98), or test-related distress (6.9 and 7.5, respectively; P=0.61).", "Secondary comparisons between the nondisclosure group and a disclosure subgroup of subjects carrying the APOE epsilon4 allele (which is associated with increased risk) also revealed no significant differences.", "However, the epsilon4-negative subgroup had a significantly lower level of test-related distress than did the epsilon4-positive subgroup (P=0.01).", "Subjects with clinically meaningful changes in psychological outcomes were distributed evenly among the nondisclosure group and the epsilon4-positive and epsilon4-negative subgroups.", "Baseline scores for anxiety and depression were strongly associated with post-disclosure scores of these measures (P<0.001 for both comparisons).   \n", "CONCLUSIONS The disclosure of APOE genotyping results to adult children of patients with Alzheimer's disease did not result in significant short-term psychological risks.", "Test-related distress was reduced among those who learned that they were APOE epsilon4-negative.", "Persons with high levels of emotional distress before undergoing genetic testing were more likely to have emotional difficulties after disclosure.", "(ClinicalTrials.gov number, NCT00571025.)"], "structured": true}
{"doc_id": 4506414, "title": "Blood pressure and incidence of twelve cardiovascular diseases: lifetime risks, healthy life-years lost, and age-specific associations in 1\u00b725 million people", "abstract": ["BACKGROUND The associations of blood pressure with the different manifestations of incident cardiovascular disease in a contemporary population have not been compared.", "In this study, we aimed to analyse the associations of blood pressure with 12 different presentations of cardiovascular disease.   \n", "METHODS We used linked electronic health records from 1997 to 2010 in the CALIBER (CArdiovascular research using LInked Bespoke studies and Electronic health Records) programme to assemble a cohort of 1\u00b725 million patients, 30 years of age or older and initially free from cardiovascular disease, a fifth of whom received blood pressure-lowering treatments.", "We studied the heterogeneity in the age-specific associations of clinically measured blood pressure with 12 acute and chronic cardiovascular diseases, and estimated the lifetime risks (up to 95 years of age) and cardiovascular disease-free life-years lost adjusted for other risk factors at index ages 30, 60, and 80 years.", "This study is registered at ClinicalTrials.gov, number NCT01164371.   \n", "FINDINGS During 5\u00b72 years median follow-up, we recorded 83,098 initial cardiovascular disease presentations.", "In each age group, the lowest risk for cardiovascular disease was in people with systolic blood pressure of 90-114 mm Hg and diastolic blood pressure of 60-74 mm Hg, with no evidence of a J-shaped increased risk at lower blood pressures.", "The effect of high blood pressure varied by cardiovascular disease endpoint, from strongly positive to no effect.", "Associations with high systolic blood pressure were strongest for intracerebral haemorrhage (hazard ratio 1\u00b744 [95% CI 1\u00b732-1\u00b758]), subarachnoid haemorrhage (1\u00b743 [1\u00b725-1\u00b763]), and stable angina (1\u00b741 [1\u00b736-1\u00b746]), and weakest for abdominal aortic aneurysm (1\u00b708 [1\u00b700-1\u00b717]).", "Compared with diastolic blood pressure, raised systolic blood pressure had a greater effect on angina, myocardial infarction, and peripheral arterial disease, whereas raised diastolic blood pressure had a greater effect on abdominal aortic aneurysm than did raised systolic pressure.", "Pulse pressure associations were inverse for abdominal aortic aneurysm (HR per 10 mm Hg 0\u00b791 [95% CI 0\u00b786-0\u00b798]) and strongest for peripheral arterial disease (1\u00b723 [1\u00b720-1\u00b727]).", "People with hypertension (blood pressure \u2265140/90 mm Hg or those receiving blood pressure-lowering drugs) had a lifetime risk of overall cardiovascular disease at 30 years of age of 63\u00b73% (95% CI 62\u00b79-63\u00b78) compared with 46\u00b71% (45\u00b75-46\u00b78) for those with normal blood pressure, and developed cardiovascular disease 5\u00b70 years earlier (95% CI 4\u00b78-5\u00b72).", "Stable and unstable angina accounted for most (43%) of the cardiovascular disease-free years of life lost associated with hypertension from index age 30 years, whereas heart failure and stable angina accounted for the largest proportion (19% each) of years of life lost from index age 80 years.   \n", "INTERPRETATION The widely held assumptions that blood pressure has strong associations with the occurrence of all cardiovascular diseases across a wide age range, and that diastolic and systolic associations are concordant, are not supported by the findings of this high-resolution study.", "Despite modern treatments, the lifetime burden of hypertension is substantial.", "These findings emphasise the need for new blood pressure-lowering strategies, and will help to inform the design of randomised trials to assess them.   \n", "FUNDING Medical Research Council, National Institute for Health Research, and Wellcome Trust."], "structured": true}
{"doc_id": 4506702, "title": "Can Online Consumers Contribute to Drug Knowledge? A Mixed-Methods Comparison of Consumer-Generated and Professionally Controlled Psychotropic Medication Information on the Internet", "abstract": ["BACKGROUND Ongoing initiatives to filter online health searches exclude consumer-generated content from search returns, though its inferiority compared with professionally controlled content is not demonstrated.", "The antidepressant escitalopram and the antipsychotic quetiapine have ranked over the last 5 years as top-selling agents in their respective drug classes.", "Both drugs have various off-label mental health and non-mental health uses, ranging from the relief of insomnia and migraines to the treatment of severe developmental disorders.   \n", "OBJECTIVE Our objective was to describe the most frequently reported effects of escitalopram and quetiapine in online consumer reviews, to compare them with effects described in professionally controlled commercial health websites, and to gauge the usability of online consumer medication reviews.   \n", "METHODS A stratified simple random sample of 960 consumer reviews was selected from all 6998 consumer reviews of the two drugs in 2 consumer-generated (www.askapatient.com and www.crazymeds.us) and 2 professionally controlled (www.webmd.com and www.revolutionhealth.com) health websites.", "Professional medication descriptions included all standard information on the medications from the latter 2 websites.", "All textual data were inductively coded for medication effects, and intercoder agreement was assessed.", "Chi-square was used to test for associations between consumer-reported effects and website origination.   \n", "RESULTS Consumers taking either escitalopram (n = 480) or quetiapine (n = 480) most frequently reported symptom improvement (30.4% or 146/480, 24.8% or 119/480) or symptom worsening (15.8% or 76/480, 10.2% or 49/480), changes in sleep (36% or 173/480, 60.6% or 291/480) and changes in weight and appetite (22.5% or 108/480, 30.8% or 148/480).", "More consumers posting reviews on consumer-generated rather than professionally controlled websites reported symptom worsening on quetiapine (17.3% or 38/220 versus 5% or 11/220, P < .001), while more consumers posting on professionally controlled websites reported symptom improvement (32.7% or 72/220 versus 21.4% or 47/220, P = .008).", "Professional descriptions more frequently listed physical adverse effects and warnings about suicidal ideation while consumer reviews emphasized effects disrupting daily routines and provided richer descriptions of effects in context.", "The most recent 20 consumer reviews on each drug from each website (n = 80) were comparable to the full sample of reviews in the frequency of commonly reported effects.   \n", "CONCLUSION Consumer reviews and professional medication descriptions generally reported similar effects of two psychotropic medications but differed in their descriptions and in frequency of reporting.", "Professional medication descriptions offer the advantage of a concise yet comprehensive listing of drug effects, while consumer reviews offer greater context and situational examples of how effects may manifest in various combinations and to varying degrees.", "The dispersion of consumer reviews across websites limits their integration, but a brief browsing strategy on the two target medications nonetheless retrieved representative consumer content.", "Current strategies for filtering online health searches to return only trusted or approved websites may inappropriately address the challenge to identify quality health sources on the Internet because such strategies unduly limit access to an entire complementary source for health information."], "structured": true}
{"doc_id": 4515975, "title": "Effect of supplemental zinc on the growth and serum zinc concentrations of prepubertal children: a meta-analysis of randomized controlled trials.", "abstract": ["BACKGROUND Multiple studies have been carried out to assess the effect of zinc supplementation on children's growth.", "The results of these studies are inconsistent, and the factors responsible for these varied outcomes are unknown.   \n", "OBJECTIVE Meta-analyses of randomized controlled intervention trials were therefore completed to assess the effect of zinc supplementation on the physical growth and serum zinc concentrations of prepubertal children.   \n", "DESIGN A total of 33 acceptable studies with appropriate data were identified by MEDLINE (National Library of Medicine, Bethesda, MD) searches and other methods.", "Weighted mean effect sizes (expressed in SD units) were calculated for changes in height, weight, weight-for-height, and serum zinc concentration by using random-effects models; factors associated with effect sizes were explored by meta-regression techniques.   \n", "RESULTS Zinc supplementation produced highly significant, positive responses in height and weight increments, with effect sizes of 0.350 (95% CI: 0.189, 0.511) and 0.309 (0.178, 0.439), respectively.", "There was no significant effect of zinc on weight-for-height indexes [weighted mean effect size: -0.018 (-0.132, 0.097)].", "Zinc supplementation caused a large increase in the children's serum zinc concentrations, with an effect size of 0.820 (0.499, 1.14).", "Growth responses were greater in children with low initial weight-for-age z scores and in those aged >6 mo with low initial height-for-age z scores.   \n", "CONCLUSIONS Interventions to improve children's zinc nutriture should be considered in populations at risk of zinc deficiency, especially where there are elevated rates of underweight or stunting.", "The population mean serum zinc concentration is a useful indicator of the successful delivery and absorption of zinc supplements in children."], "structured": true}
{"doc_id": 4530659, "title": "Mechanisms of Age-Related Macular Degeneration", "abstract": ["Age-related macular degeneration (AMD), a progressive condition that is untreatable in up to 90% of patients, is a leading cause of blindness in the elderly worldwide.", "The two forms of AMD, wet and dry, are classified based on the presence or absence of blood vessels that have disruptively invaded the retina, respectively.", "A detailed understanding of the molecular mechanisms underlying wet AMD has led to several robust FDA-approved therapies.", "In contrast, there are no approved treatments for dry AMD.", "In this review, we provide insight into the critical effector pathways mediating each form of the disease.", "A recurring theme that spans most aspects of AMD pathogenesis is defective immune modulation in the classically immune-privileged ocular haven.", "Interestingly, the latest advances in AMD research also highlight common molecular disease pathways with other neurodegenerative disorders.", "Finally, the therapeutic potential of intervening at known mechanistic steps of AMD pathogenesis is discussed."], "structured": false}
{"doc_id": 4544916, "title": "The N-end rule pathway regulates pathogen responses in plants.", "abstract": ["To efficiently counteract pathogens, plants rely on a complex set of immune responses that are tightly regulated to allow the timely activation, appropriate duration and adequate amplitude of defense programs.", "The coordination of the plant immune response is known to require the activity of the ubiquitin/proteasome system, which controls the stability of proteins in eukaryotes.", "Here, we demonstrate that the N-end rule pathway, a subset of the ubiquitin/proteasome system, regulates the defense against a wide range of bacterial and fungal pathogens in the model plant Arabidopsis thaliana.", "We show that this pathway positively regulates the biosynthesis of plant-defense metabolites such as glucosinolates, as well as the biosynthesis and response to the phytohormone jasmonic acid, which plays a key role in plant immunity.", "Our results also suggest that the arginylation branch of the N-end rule pathway regulates the timing and amplitude of the defense program against the model pathogen Pseudomonas syringae AvrRpm1."], "structured": false}
{"doc_id": 4547102, "title": "H3K9 demethylase KDM4E is an epigenetic regulator for bovine embryonic development and a defective factor for nuclear reprogramming.", "abstract": ["Aberrant epigenetic reprogramming often results in developmental defects in somatic cell nuclear transfer (SCNT) embryos during embryonic genome activation (EGA).", "Bovine eight-cell SCNT embryos exhibit global hypermethylation of histone H3 lysine 9 tri- and di-methylation (H3K9me3/2), but the intrinsic reason for this remains elusive.", "Here, we provide evidence that two H3K9 demethylase genes, lysine-specific demethylase 4D (KDM4D) and 4E (KDM4E), are related to active H3K9me3/2 demethylation in in vitro fertilized (IVF) embryos and are deficiently expressed in cloned embryos at the time of EGA.", "Moreover, KDM4E plays a more crucial role in IVF and SCNT embryonic development, and overexpression of KDM4E can restore the global transcriptome, improve blastocyst formation and increase the cloning efficiency of SCNT embryos.", "Our results thereby indicate that KDM4E can function as a crucial epigenetic regulator of EGA and as an internal defective factor responsible for persistent H3K9me3/2 barriers to SCNT-mediated reprogramming.", "Furthermore, we show that interactions between RNA and KDM4E are essential for H3K9 demethylation during EGA.", "These observations advance the understanding of incomplete nuclear reprogramming and are of great importance for transgenic cattle procreation."], "structured": false}
{"doc_id": 4550036, "title": "Risk of gestational hypertension in relation to folic acid supplementation during pregnancy.", "abstract": ["The authors investigated the association between folic acid supplementation and gestational hypertension.", "The study population included women with nonmalformed infants in the United States and Canada who were participating in the Slone Epidemiology Center Birth Defects Study between 1993 and 2000.", "Women were interviewed within 6 months after delivery about sociodemographic and medical factors, the occurrence of hypertension with or without preeclampsia, and multivitamin use in pregnancy.", "Relative risks, adjusted for weight, parity, twin pregnancy, diabetes, smoking, education, and family income, were estimated using Cox regression models.", "Of 2,100 women, 204 (9.7%) reported gestational hypertension (onset after the 20th week of gestation).", "The multivariate-adjusted relative risk of developing gestational hypertension during the month after folic acid supplementation, compared with not using folic acid during that same month, was 0.55 (95% confidence interval: 0.39, 0.79).", "This finding suggests that folic acid-containing multivitamins may reduce the risk of gestational hypertension."], "structured": false}
{"doc_id": 4561402, "title": "Aire regulates negative selection of organ-specific T cells", "abstract": ["Autoimmune polyendocrinopathy syndrome type 1 is a recessive Mendelian disorder resulting from mutations in a novel gene, AIRE, and is characterized by a spectrum of organ-specific autoimmune diseases.", "It is not known what tolerance mechanisms are defective as a result of AIRE mutation.", "By tracing the fate of autoreactive CD4+ T cells with high affinity for a pancreatic antigen in transgenic mice with an Aire mutation, we show here that Aire deficiency causes almost complete failure to delete the organ-specific cells in the thymus.", "These results indicate that autoimmune polyendocrinopathy syndrome 1 is caused by failure of a specialized mechanism for deleting forbidden T cell clones, establishing a central role for this tolerance mechanism."], "structured": false}
{"doc_id": 4583180, "title": "Extracellular Acidic pH Activates the Sterol Regulatory Element-Binding Protein 2 to Promote Tumor Progression.", "abstract": ["Conditions of the tumor microenvironment, such as hypoxia and nutrient starvation, play critical roles in cancer progression.", "However, the role of acidic extracellular pH in cancer progression is not studied as extensively as that of hypoxia.", "Here, we show that extracellular acidic pH (pH 6.8) triggered activation of sterol regulatory element-binding protein 2 (SREBP2) by stimulating nuclear translocation and promoter binding to its targets, along with intracellular acidification.", "Interestingly, inhibition of SREBP2, but not SREBP1, suppressed the upregulation of low pH-induced cholesterol biosynthesis-related genes.", "Moreover, acyl-CoA synthetase short-chain family member 2 (ACSS2), a direct SREBP2 target, provided a growth advantage to cancer cells under acidic pH. Furthermore, acidic pH-responsive SREBP2 target genes were associated with reduced overall survival of cancer patients.", "Thus, our findings show that SREBP2 is a key transcriptional regulator of metabolic genes and progression of cancer cells, partly in response to extracellular acidification."], "structured": false}
{"doc_id": 4587978, "title": "Mutation of the Human Circadian Clock Gene CRY1 in Familial Delayed Sleep Phase Disorder", "abstract": ["Patterns of daily human activity are controlled by an intrinsic circadian clock that promotes \u223c24 hr rhythms in many behavioral and physiological processes.", "This system is altered in delayed sleep phase disorder (DSPD), a common form of insomnia in which sleep episodes are shifted to later times misaligned with the societal norm.", "Here, we report a hereditary form of DSPD associated with a dominant coding variation in the core circadian clock gene CRY1, which creates a transcriptional inhibitor with enhanced affinity for circadian activator proteins Clock and Bmal1.", "This gain-of-function CRY1 variant causes reduced expression of key transcriptional targets and lengthens the period of circadian molecular rhythms, providing a mechanistic link to DSPD symptoms.", "The allele has a frequency of up to 0.6%, and reverse phenotyping of unrelated families corroborates late and/or fragmented sleep patterns in carriers, suggesting that it affects sleep behavior in a sizeable portion of the human population."], "structured": false}
{"doc_id": 4611267, "title": "Lateral Hypothalamic Signaling Mechanisms Underlying Feeding Stimulation: Differential Contributions of Src Family Tyrosine Kinases to Feeding Triggered Either by NMDA Injection or by Food Deprivation", "abstract": ["In rats, feeding can be triggered experimentally using many approaches.", "Included among these are (1) food deprivation and (2) acute microinjection of the neurotransmitter l-glutamate (Glu) or its receptor agonist NMDA into the lateral hypothalamic area (LHA).", "Under both paradigms, the NMDA receptor (NMDA-R) within the LHA appears critically involved in transferring signals encoded by Glu to stimulate feeding.", "However, the intracellular mechanisms underlying this signal transfer are unknown.", "Because protein-tyrosine kinases (PTKs) participate in NMDA-R signaling mechanisms, we determined PTK involvement in LHA mechanisms underlying both types of feeding stimulation through food intake and biochemical measurements.", "LHA injections of PTK inhibitors significantly suppressed feeding elicited by LHA NMDA injection (up to 69%) but only mildly suppressed deprivation feeding (24%), suggesting that PTKs may be less critical for signals underlying this feeding behavior.", "Conversely, food deprivation but not NMDA injection produced marked increases in apparent activity for Src PTKs and in the expression of Pyk2, an Src-activating PTK.", "When considered together, the behavioral and biochemical results demonstrate that, although it is easier to suppress NMDA-elicited feeding by PTK inhibitors, food deprivation readily drives PTK activity in vivo.", "The latter result may reflect greater PTK recruitment by neurotransmitter receptors, distinct from the NMDA-R, that are activated during deprivation-elicited but not NMDA-elicited feeding.", "These results also demonstrate how the use of only one feeding stimulation paradigm may fail to reveal the true contributions of signaling molecules to pathways underlying feeding behavior in vivo."], "structured": false}
{"doc_id": 4627816, "title": "Relationship between advanced glycation end\u2010product accumulation and low skeletal muscle mass in Japanese men and women", "abstract": ["AIM The present study aimed to investigate the relationship between advanced glycation end-product accumulation and skeletal muscle mass among middle-aged and older Japanese men and women.   \n", "METHODS A total of 132 participants enrolled in this cross-sectional study.", "Skin autofluorescence was assessed as a measure of advanced glycation-end products.", "Appendicular skeletal muscle mass was measured using dual-energy X-ray absorptiometry, and skeletal muscle index was calculated by dividing appendicular skeletal muscle mass by height squared.", "Participants were divided into two groups (low skeletal muscle index and normal skeletal muscle index) using the Asian Working Group for Sarcopenia's skeletal muscle index criteria for diagnosing sarcopenia.", "Multivariate logistic regression analysis and the area under the receiver operating characteristic curve were used to determine significant factors associated with low skeletal muscle index.   \n", "RESULTS Participants consisted of 70 men (mean age 57 \u00b1 10 years) and 62 women (mean age 60 \u00b1 11 years).", "There were 31 and 101 participants in the low and normal skeletal muscle index groups, respectively.", "Skin autofluorescence was significantly higher in the low skeletal muscle index group compared with the normal skeletal muscle index group (P < 0.01).", "Skin autofluorescence was a significant independent factor associated with low skeletal muscle index based on multivariate logistic regression analysis (odds ratio 15.7, 95% confidence interval 1.85-133.01; P = 0.012).", "The cut-off for skin autofluorescence was 2.45 arbitrary units, with a sensitivity of 0.75 and specificity of 0.91.   \n", "CONCLUSIONS Skin autofluorescence was an independent factor associated with low skeletal muscle index among middle-aged and older Japanese men and women.", "Geriatr Gerontol Int 2017; 17: 785-790."], "structured": true}
{"doc_id": 4632921, "title": "Large-Scale Profiling Reveals the Influence of Genetic Variation on Gene Expression in Human Induced Pluripotent Stem Cells.", "abstract": ["In this study, we used whole-genome sequencing and gene expression profiling of 215 human induced pluripotent stem cell (iPSC) lines from different donors to identify genetic variants associated with RNA expression for 5,746 genes.", "We were able to predict causal variants for these expression quantitative trait loci (eQTLs) that disrupt transcription factor binding and validated a subset of them experimentally.", "We also identified copy-number variant (CNV) eQTLs, including some that appear to affect gene expression by altering the copy number of intergenic regulatory regions.", "In addition, we were able to identify effects on gene expression of rare genic CNVs and regulatory single-nucleotide variants and found that reactivation of gene expression on the X chromosome depends on gene chromosomal position.", "Our work highlights the value of iPSCs for genetic association analyses and provides a unique resource for investigating the genetic regulation of gene expression in pluripotent cells."], "structured": false}
{"doc_id": 4641348, "title": "Ethanol extract of Allium fistulosum inhibits development of non-alcoholic fatty liver disease", "abstract": ["BACKGROUND/OBJECTIVES Non-alcoholic fatty liver disease (NAFLD) is a leading cause of chronic liver disease and is closely associated with metabolic syndrome.", "In the present study, we observed the effect of ethanol extract of Allium fistulosum (EAF) on NAFLD and have suggested the possibility of using EAF as a natural product for application in the development of a treatment for NAFLD.   \n", "MATERIALS/METHODS The preventive effect on hepatic lipid accumulation was estimated by using an oleic acid (OA)-induced NAFLD model in vitro and a Western diet (high-fat high-sucrose; WD)-induced obese mouse model.", "Animals were divided into three groups (n = 7): normal diet group (ND), WD group, and WD plus 1% EAF group.   \n", "RESULTS EAF reduced OA-stimulated lipid accumulation in HepG2 cells in the absence of cellular cytotoxicity and significantly blocked transcriptional activation of sterol regulatory element-binding protein 1 and fatty acid synthase genes.", "Subsequently, we investigated these effects in vivo in mice fed either ND or WD in the presence or absence of EAF supplementation.", "In comparison to the ND controls, the WD-fed mice exhibited increases in body weight, liver weight, epididymal fat weight, and accumulation of fat in hepatocytes, and these effects were significantly attenuated by EAF supplementation.   \n", "CONCLUSIONS Allium fistulosum attenuates the development of NAFLD, and EAF elicits anti-lipogenic activity in liver.", "Therefore, EAF represents a promising candidate for use in the development of novel therapeutic drugs or drug combinations for the prevention and treatment of NAFLD."], "structured": true}
{"doc_id": 4647303, "title": "Cardiovascular risk factors in childhood and carotid artery intima-media thickness in adulthood: the Cardiovascular Risk in Young Finns Study.", "abstract": ["CONTEXT Exposure to cardiovascular risk factors during childhood and adolescence may be associated with the development of atherosclerosis later in life.   \n", "OBJECTIVE To study the relationship between cardiovascular risk factors measured in childhood and adolescence and common carotid artery intima-media thickness (IMT), a marker of preclinical atherosclerosis, measured in adulthood.   \n", "DESIGN, SETTING, AND PARTICIPANTS Population-based, prospective cohort study conducted at 5 centers in Finland among 2229 white adults aged 24 to 39 years who were examined in childhood and adolescence at ages 3 to 18 years in 1980 and reexamined 21 years later, between September 2001 and January 2002.   \n", "MAIN OUTCOME MEASURES Association between cardiovascular risk variables (levels of low-density lipoprotein cholesterol [LDL-C], high-density lipoprotein cholesterol [HDL-C], and triglycerides; LDL-C/HDL-C ratio; systolic and diastolic blood pressure; body mass index; smoking) measured in childhood and adulthood and common carotid artery IMT measured in adulthood.   \n", "RESULTS In multivariable models adjusted for age and sex, IMT in adulthood was significantly associated with childhood LDL-C levels (P =.001), systolic blood pressure (P<.001), body mass index (P =.007), and smoking (P =.02), and with adult systolic blood pressure (P<.001), body mass index (P<.001), and smoking (P =.004).", "The number of risk factors measured in 12- to 18-year-old adolescents, including high levels (ie, extreme age- and sex-specific 80th percentile) of LDL-C, systolic blood pressure, body mass index, and cigarette smoking, were directly related to carotid IMT measured in young adults at ages 33 through 39 years (P<.001 for both men and women), and remained significant after adjustment for contemporaneous risk variables.", "The number of risk factors measured at ages 3 to 9 years demonstrated a weak direct relationship with carotid IMT at ages 24 to 30 years in men (P =.02) but not in women (P =.63).   \n", "CONCLUSIONS Risk factor profile assessed in 12- to 18-year-old adolescents predicts adult common carotid artery IMT independently of contemporaneous risk factors.", "These findings suggest that exposure to cardiovascular risk factors early in life may induce changes in arteries that contribute to the development of atherosclerosis."], "structured": true}
{"doc_id": 4653837, "title": "MicroRNA-29 induces cellular senescence in aging muscle through multiple signaling pathways", "abstract": ["The mechanisms underlying the development of aging-induced muscle atrophy are unclear.", "By microRNA array and individual qPCR analyses, we found significant up-regulation of miR-29 in muscles of aged rodents vs. results in young.", "With aging, p85\u03b1, IGF-1 and B-myb muscle levels were lower while the expression of certain cell arrest proteins (p53, p16 and pRB) increased.", "When miR-29 was expressed in muscle progenitor cells (MPC), their proliferation was impaired while SA-\u03b2gal expression increased signifying the development of senescence.", "Impaired MPC proliferation resulted from interactions between miR-29 and the 3'-UTR of p85a, IGF-1 and B-myb, suppressing the translation of these mediators of myoblast proliferation.", "In vivo, electroporation of miR-29 into muscles of young mice suppressed the proliferation and increased levels of cellular arrest proteins, recapitulating aging-induced responses in muscle.", "A potential stimulus of miR-29 expression is Wnt-3a since we found that exogenous Wnt-3a stimulated miR-29 expression 2.7-fold in primary cultures of MPCs.", "Thus, aging-induced muscle senescence results from activation of miR-29 by Wnt-3a leading to suppressed expression of several signaling proteins (p85\u03b1, IGF-1 and B-myb) that act coordinately to impair the proliferation of MPCs contributing to muscle atrophy.", "The increase in miR-29 provides a potential mechanism for aging-induced sarcopenia."], "structured": false}
{"doc_id": 4658268, "title": "Rictor, a Novel Binding Partner of mTOR, Defines a Rapamycin-Insensitive and Raptor-Independent Pathway that Regulates the Cytoskeleton", "abstract": ["The mammalian TOR (mTOR) pathway integrates nutrient- and growth factor-derived signals to regulate growth, the process whereby cells accumulate mass and increase in size.", "mTOR is a large protein kinase and the target of rapamycin, an immunosuppressant that also blocks vessel restenosis and has potential anticancer applications.", "mTOR interacts with the raptor and GbetaL proteins to form a complex that is the target of rapamycin.", "Here, we demonstrate that mTOR is also part of a distinct complex defined by the novel protein rictor (rapamycin-insensitive companion of mTOR).", "Rictor shares homology with the previously described pianissimo from D. discoidieum, STE20p from S. pombe, and AVO3p from S. cerevisiae.", "Interestingly, AVO3p is part of a rapamycin-insensitive TOR complex that does not contain the yeast homolog of raptor and signals to the actin cytoskeleton through PKC1.", "Consistent with this finding, the rictor-containing mTOR complex contains GbetaL but not raptor and it neither regulates the mTOR effector S6K1 nor is it bound by FKBP12-rapamycin.", "We find that the rictor-mTOR complex modulates the phosphorylation of Protein Kinase C alpha (PKCalpha) and the actin cytoskeleton, suggesting that this aspect of TOR signaling is conserved between yeast and mammals."], "structured": false}
{"doc_id": 4662264, "title": "Activation of the estrogen receptor through phosphorylation by mitogen-activated protein kinase.", "abstract": ["The phosphorylation of the human estrogen receptor (ER) serine residue at position 118 is required for full activity of the ER activation function 1 (AF-1).", "This Ser118 is phosphorylated by mitogen-activated protein kinase (MAPK) in vitro and in cells treated with epidermal growth factor (EGF) and insulin-like growth factor (IGF) in vivo.", "Overexpression of MAPK kinase (MAPKK) or of the guanine nucleotide binding protein Ras, both of which activate MAPK, enhanced estrogen-induced and antiestrogen (tamoxifen)-induced transcriptional activity of wild-type ER, but not that of a mutant ER with an alanine in place of Ser118.", "Thus, the activity of the amino-terminal AF-1 of the ER is modulated by the phosphorylation of Ser118 through the Ras-MAPK cascade of the growth factor signaling pathways."], "structured": false}
{"doc_id": 4664540, "title": "Regulation of the antimicrobial response by NLR proteins.", "abstract": ["Nucleotide-binding, oligomerization domain (NOD)-like receptor (NLR) proteins are a family of innate immune receptors that play a pivotal role in microbial sensing, leading to the initiation of antimicrobial immune responses.", "Dysregulation of the function of multiple NLR family members has been linked, both in mice and humans, to a propensity for infection and autoinflammatory disease.", "Despite our increased understanding of NLR function and interactions, many aspects related to mechanisms of sensing, downstream signaling, and in vivo functions remain elusive.", "In this review, we focus on key members of the NLR family, describing their activation by diverse microbes, downstream effector functions, and interactions with each other and with other innate sensor protein families.", "Also discussed is the role of microbial sensing by NLR receptors leading to activation of the adaptive immune arm that collaborates in the antimicrobial defense."], "structured": false}
{"doc_id": 4678846, "title": "Acetylcysteine for prevention of acute deterioration of renal function following elective coronary angiography and intervention: a randomized controlled trial.", "abstract": ["CONTEXT The antioxidant acetylcysteine prevents acute contrast nephrotoxicity in patients with impaired renal function who undergo computed tomography scanning.", "However, its role in coronary angiography is unclear.   \n", "OBJECTIVE To determine whether oral acetylcysteine prevents acute deterioration in renal function in patients with moderate renal insufficiency who undergo elective coronary angiography.   \n", "DESIGN AND SETTING Prospective, randomized, double-blind, placebo-controlled trial conducted from May 2000 to December 2001 at the Grantham Hospital at the University of Hong Kong.   \n", "PARTICIPANTS Two hundred Chinese patients aged mean (SD) 68 (6.5) years with stable moderate renal insufficiency (creatinine clearance <60 mL/min [1.00 mL/s]) who were undergoing elective coronary angiography with or without intervention.   \n", "INTERVENTION Participants were randomly assigned to receive oral acetylcysteine(600 mg twice per day; n = 102) or matching placebo tablets (n = 98) on the day before and the day of angiography.", "All patients received low-osmolality contrast agent.   \n", "MAIN OUTCOME MEASURES Occurrence of more than a 25% increase in serum creatinine level within 48 hours after contrast administration; change in creatinine clearance and serum creatinine level.   \n", "RESULTS Twelve control patients (12%) and 4 acetylcysteine patients (4%) developed a more than 25% increase in serum creatinine level within 48 hours after contrast administration (relative risk, 0.32; 95% confidence interval [CI], 0.10-0.96; P =.03).", "Serum creatinine was lower in the acetylcysteine group (1.22 mg/dL [107.8 micromol/L]; 95% CI, 1.11-1.33 mg/dL vs 1.38 mg/dL [122.9 micromol/L]; 95% CI, 1.27-1.49 mg/dL; P =.006) during the first 48 hours after angiography.", "Acetylcysteine treatment significantly increased creatinine clearance from 44.8 mL/min (0.75 mL/s) (95% CI, 42.7-47.6 mL/min) to 58.9 mL/min (0.98 mL/s) (95% CI, 55.6-62.3 mL/min) 2 days after the contrast administration (P<.001).", "The increase was not significant in the control group (from 42.1 to 44.1 mL/min [0.70 to 0.74 mL/s]; P =.15).", "The benefit of acetylcysteine was consistent among various patient subgroups and persistent for at least 7 days.", "There were no major treatment-related adverse events.   \n", "CONCLUSION Acetylcysteine protects patients with moderate chronic renal insufficiency from contrast-induced deterioration in renal function after coronary angiographic procedures, with minimal adverse effects and at a low cost."], "structured": true}
{"doc_id": 4679264, "title": "DNA Methylation in the Human Cerebral Cortex Is Dynamically Regulated throughout the Life Span and Involves Differentiated Neurons", "abstract": ["The role of DNA cytosine methylation, an epigenetic regulator of chromatin structure and function, during normal and pathological brain development and aging remains unclear.", "Here, we examined by MethyLight PCR the DNA methylation status at 50 loci, encompassing primarily 5\u2032 CpG islands of genes related to CNS growth and development, in temporal neocortex of 125 subjects ranging in age from 17 weeks of gestation to 104 years old.", "Two psychiatric disease cohorts\u2014defined by chronic neurodegeneration (Alzheimer's) or lack thereof (schizophrenia)\u2014were included.", "A robust and progressive rise in DNA methylation levels across the lifespan was observed for 8/50 loci (GABRA2, GAD1, HOXA1, NEUROD1, NEUROD2, PGR, STK11, SYK) typically in conjunction with declining levels of the corresponding mRNAs.", "Another 16 loci were defined by a sharp rise in DNA methylation levels within the first few months or years after birth.", "Disease-associated changes were limited to 2/50 loci in the Alzheimer's cohort, which appeared to reflect an acceleration of the age-related change in normal brain.", "Additionally, methylation studies on sorted nuclei provided evidence for bidirectional methylation events in cortical neurons during the transition from childhood to advanced age, as reflected by significant increases at 3, and a decrease at 1 of 10 loci.", "Furthermore, the DNMT3a de novo DNA methyl-transferase was expressed across all ages, including a subset of neurons residing in layers III and V of the mature cortex.", "Therefore, DNA methylation is dynamically regulated in the human cerebral cortex throughout the lifespan, involves differentiated neurons, and affects a substantial portion of genes predominantly by an age-related increase."], "structured": false}
{"doc_id": 4680262, "title": "Mulberry leaves (Morus alba L.) ameliorate obesity-induced hepatic lipogenesis, fibrosis, and oxidative stress in high-fat diet-fed mice", "abstract": ["Obesity is associated with chronic diseases such as fatty liver, type 2 diabetes, cardiovascular disease, and severe metabolic syndrome.", "Obesity causes metabolic impairment including excessive lipid accumulation and fibrosis in the hepatic tissue as well as the increase in oxidative stress.", "In order to investigate the effect of mulberry leaf (Morus alba L.) extract (MLE) on obesity-induced oxidative stress, lipogenesis, and fibrosis in liver, MLE has been gavaged for 12 weeks in high-fat diet (HFD)-induced obese mice.", "MLE treatment significantly ameliorated LXR\u03b1-mediated lipogenesis and hepatic fibrosis markers such as \u03b1-smooth muscle actin, while MLE up-regulated lipolysis-associated markers such as lipoprotein lipase in the HFD-fed mice.", "Moreover, MLE normalized the activities of antioxidant enzymes including heme oxygenase-1 and glutathione peroxidase in accordance with protein levels of 4-hydroxynonenal in the HFD-fed mice.", "MLE has beneficial effects on obesity-related fatty liver disease by regulation of hepatic lipid metabolism, fibrosis, and antioxidant defense system.", "MLE supplementation might be a potential therapeutic approach for obesity-related disease including non-alcoholic fatty liver disease."], "structured": false}
{"doc_id": 4687948, "title": "HMG-CoA reductase inhibitors and the risk of hip fractures in elderly patients.", "abstract": ["CONTEXT Recent animal studies have found that 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) lipid-lowering drugs (statins) substantially increase bone formation, but whether statin use in humans results in clinically meaningful bone formation or a reduction in the risk of osteoporotic fractures is not known.   \n", "OBJECTIVE To determine whether the use of statins is associated with reduced hip fracture risk.   \n", "DESIGN Case-control study.   \n", "SETTING AND PATIENTS A total of 6110 New Jersey residents aged 65 years or older and enrolled in Medicare and either Medicaid or the Pharmacy Assistance for the Aged and Disabled program.", "Case patients (n=1222) underwent surgical repair of a hip fracture in 1994.", "Control patients (n=4888) were identified at a ratio of 4:1 and frequency-matched to case patients for age and sex.   \n", "MAIN OUTCOME MEASURE Adjusted odds ratio (OR) of hip fracture by statin use in the 180 days and 3 years prior to the index date (the earliest date of admission for surgery), adjusted for demographic and clinical characteristics and health care utilization.   \n", "RESULTS Use of statins in either the prior 180 days (adjusted OR, 0.50; 95% confidence interval [CI], 0.33-0.76) or prior 3 years (adjusted OR, 0.57; 95% CI, 0.40-0.82) was associated with a significant reduction in the risk of hip fracture, even after controlling for variables such as race, insurance status, psychoactive medications, estrogen and thiazide use, ischemic heart disease, cancer, and diabetes mellitus.", "No significant relationship was observed between use of nonstatin lipid-lowering agents and hip fracture risk.", "Clear relationships were observed between the degree of reduction in hip fracture risk and the extent of statin use; there was no evidence of such relationships with nonstatin lipid-lowering agents.", "After adjusting for extent of statin use in the prior 3 years, current use (on the index date) was associated with a 71% reduction in risk (adjusted OR, 0.29; 95% CI, 0.10-0.81).", "The relationship between statin use and hip fracture risk persisted after controlling for variables such as the number of medications, the Charlson comorbidity index score, and hospitalization or nursing home stay in the last 180 days, as well as after excluding patients who were in a nursing home prior to their index date or who died in the year after their index date.", "Use of nonstatin lipid-lowering agents was not observed to be associated with reduction in hip fracture risk in any of these alternative models or analyses.   \n", "CONCLUSIONS These findings support an association between statin use by elderly patients and reduction in the risk of hip fracture.", "Controlled trials are needed to exclude the possibility of unmeasured confounders.", "JAMA.", "2000;283:3211-3216"], "structured": true}
{"doc_id": 4688277, "title": "The quality of modern cross-sectional ecologic studies: a bibliometric review.", "abstract": ["The ecologic study design is routinely used by epidemiologists in spite of its limitations.", "It is presently unknown how well the challenges of the design are dealt with in epidemiologic research.", "The purpose of this bibliometric review was to critically evaluate the characteristics, statistical methods, and reporting of results of modern cross-sectional ecologic papers.", "A search through 6 major epidemiology journals identified all cross-sectional ecologic studies published since January 1, 2000.", "A total of 125 articles met the inclusion requirements and were assessed via common evaluative criteria.", "It was found that a considerable number of cross-sectional ecologic studies use unreliable methods or contain statistical oversights; most investigators who adjusted their outcomes for age or sex did so improperly (64%), statistical validity was a potential issue for 20% of regression models, and simple linear regression was the most common analytic approach (31%).", "Many authors omitted important information when discussing the ecologic nature of their study (31%), the choice of study design (58%), and the susceptibility of their research to the ecological fallacy (49%).", "These results suggest that there is a need for an international set of guidelines that standardizes reporting on ecologic studies.", "Additionally, greater attention should be given to the relevant biostatistical literature."], "structured": false}
{"doc_id": 4688340, "title": "Efficacy of Beta1 Integrin and EGFR Targeting in Sphere-Forming Human Head and Neck Cancer Cells", "abstract": ["BACKGROUND Resistance to radiotherapy continues to be a limiting factor in the treatment of cancer including head and neck squamous cell carcinoma (HNSCC).", "Simultaneous targeting of \u03b21 integrin and EGFR was shown to have a higher radiosensitizing potential than mono-targeting in the majority of tested HNSCC cancer models.", "As tumor-initiating cells (TIC) are thought to play a key role for therapy resistance and recurrence and can be enriched in sphere forming conditions, this study investigated the efficacy of \u03b21 integrin/EGFR targeting without and in combination with X-ray irradiation on the behavior of sphere-forming cells (SFC).   \n", "METHODS HNSCC cell lines (UTSCC15, UTSCC5, Cal33, SAS) were injected subcutaneously into nude mice for tumor up-take and plated for primary and secondary sphere formation under non-adhesive conditions which is thought to reflect the enrichment of SFC and their self-renewal capacity, respectively.", "Treatment was accomplished by inhibitory antibodies for \u03b21 integrin (AIIB2) and EGFR (Cetuximab) as well as X-ray irradiation (2 - 6 Gy single doses).", "Further, flow cytometry for TIC marker expression and cell cycling as well as Western blotting for DNA repair protein expression and phosphorylation were employed.   \n", "RESULTS We found higher primary and secondary sphere forming capacity of SAS cells relative to other HNSCC cell lines, which was in line with the tumor up-take rates of SAS versus UTSCC15 cells.", "AIIB2 and Cetuximab administration had minor cytotoxic and no radiosensitizing effects on SFC.", "Intriguingly, secondary SAS spheres, representing the fraction of surviving SFC upon passaging, showed greatly enhanced radiosensitivity compared to primary spheres.", "Intriguingly, neither AIIB2 nor Cetuximab significantly altered basal sphere forming capacity and radiosensitivity.", "While an increased accumulation of G0/G1 phase cells was observable in secondary SAS spheres, DNA double strand break repair indicated no difference on the basis of significantly enhanced ATM and Chk2 dephosphorylation upon irradiation.   \n", "CONCLUSIONS In the HNSCC model, sphere-forming conditions select for cells, which are unsusceptible to both anti-\u03b21 integrin and anti-EGFR inhibitory antibodies.", "With regard to primary and secondary sphere formation, our data suggest that both of these SFC fractions express distinct survival strategies independent from \u03b21 integrin and EGFR and that future work is warranted to better understand SFC survival and enrichment before and after treatment to untangle the underlying mechanisms for identifying novel, druggable cancer targets in SFC."], "structured": true}
{"doc_id": 4695046, "title": "Anxiety", "abstract": ["OBJECTIVES To examine the effect of routinely administered psychiatric questionnaires on the recognition, management, and outcome of psychiatric disorders in non-psychiatric settings.   \n", "DATA SOURCES Embase, Medline, PsycLIT, Cinahl, Cochrane Controlled Trials Register, and hand searches of key journals.   \n", "METHODS A systematic review of randomised controlled trials of the administration and routine feedback of psychiatric screening and outcome questionnaires to clinicians in non-psychiatric settings.", "Narrative overview of key design features and end points, together with a random effects quantitative synthesis of comparable studies.   \n", "MAIN OUTCOME MEASURES Recognition of psychiatric disorders after feedback of questionnaire results; interventions for psychiatric disorders; and outcome of psychiatric disorders.   \n", "RESULTS Nine randomised studies were identified that examined the use of common psychiatric instruments in primary care and general hospital settings.", "Studies compared the effect of the administration of these instruments followed by the feedback of the results to clinicians, with administration with no feedback.", "Meta-analytic pooling was possible for four of these studies (2457 participants), which measured the effect of feedback on the recognition of depressive disorders.", "Routine administration and feedback of scores for all patients (irrespective of score) did not increase the overall rate of recognition of mental disorders such as anxiety and depression (relative risk of detection of depression by clinician after feedback 0.95, 95% confidence interval 0.83 to 1.09).", "Two studies showed that routine administration followed by selective feedback for only high scorers increased the rate of recognition of depression (relative risk of detection of depression after feedback 2.64, 1.62 to 4.31).", "This increased recognition, however, did not translate into an increased rate of intervention.", "Overall, studies of routine administration of psychiatric measures did not show an effect on patient outcome.   \n", "CONCLUSIONS The routine measurement of outcome is a costly exercise.", "Little evidence shows that it is of benefit in improving psychosocial outcomes of those with psychiatric disorder managed in non-psychiatric settings."], "structured": true}
{"doc_id": 4695107, "title": "The challenges of overcoming antibiotic resistance: Plant extracts as potential sources of antimicrobial and resistance modifying agents", "abstract": ["The problem of antibiotic resistance, which has limited the use of cheap and old antibiotics, has necessitated the need for a continued search for new antimicrobial compounds.", "Understanding the mechanisms of resistance is important in the development of strategies to solving the problem.", "Active efflux of drugs, alteration of target sites and enzymatic degradations are the strategies by which pathogenic bacteria acquire or develop intrinsic resistance to antibiotics.", "Multi-drug resistance (MDR) pumps, capable of recognizing and expelling a variety of structurally unrelated compounds from the bacterial cell and conferring resistance to a wide range of antibiotics have since been characterized in many gram positive and gram negative pathogens like Staphylococcus aureus, Pseudomonas aeruginosa, Escherichia coli and, more recently, in mycobacteria.", "The ability of some chemical compounds (called MDR inhibitors or resistance modifying agents) to modify the resistance phenotype in bacteria by working synergistically with antibiotics in vitro has since been observed.", "The search for such compounds which can be combined with antibiotics in the treatment of drug resistant infections may be an alternative to overcoming the problem of resistance in bacteria.", "Crude extracts of medicinal plants stand out as veritable sources of potential resistance modifying agents and the African biosphere promises to be a potential source of such compounds owing to its rich plant species diversity."], "structured": false}
{"doc_id": 4700428, "title": "The effect of N-acetylcysteine in the nucleus accumbens on neurotransmission and relapse to cocaine.", "abstract": ["BACKGROUND Relapse to cocaine seeking has been linked with low glutamate in the nucleus accumbens core (NAcore) causing potentiation of synaptic glutamate transmission from prefrontal cortex (PFC) afferents.", "Systemic N-acetylcysteine (NAC) has been shown to restore glutamate homeostasis, reduce relapse to cocaine seeking, and depotentiate PFC-NAcore synapses.", "Here, we examine the effects of NAC applied directly to the NAcore on relapse and neurotransmission in PFC-NAcore synapses, as well as the involvement of the metabotropic glutamate receptors 2/3 (mGluR2/3) and 5 (mGluR5).   \n", "METHODS Rats were trained to self-administer cocaine for 2 weeks and following extinction received either intra-accumbens NAC or systemic NAC 30 or 120 minutes, respectively, before inducing reinstatement with a conditioned cue or a combined cue and cocaine injection.", "We also recorded postsynaptic currents using in vitro whole cell recordings in acute slices and measured cystine and glutamate uptake in primary glial cultures.   \n", "RESULTS NAC microinjection into the NAcore inhibited the reinstatement of cocaine seeking.", "In slices, a low concentration of NAC reduced the amplitude of evoked glutamatergic synaptic currents in the NAcore in an mGluR2/3-dependent manner, while high doses of NAC increased amplitude in an mGluR5-dependent manner.", "Both effects depended on NAC uptake through cysteine transporters and activity of the cysteine/glutamate exchanger.", "Finally, we showed that by blocking mGluR5 the inhibition of cocaine seeking by NAC was potentiated.   \n", "CONCLUSIONS The effect of NAC on relapse to cocaine seeking depends on the balance between stimulating mGluR2/3 and mGluR5 in the NAcore, and the efficacy of NAC can be improved by simultaneously inhibiting mGluR5."], "structured": true}
{"doc_id": 4701662, "title": "A phospholipid transfer function of ER-mitochondria encounter structure revealed in vitro", "abstract": ["As phospholipids are synthesized mainly in the endoplasmic reticulum (ER) and mitochondrial inner membranes, how cells properly distribute specific phospholipids to diverse cellular membranes is a crucial problem for maintenance of organelle-specific phospholipid compositions.", "Although the ER-mitochondria encounter structure (ERMES) was proposed to facilitate phospholipid transfer between the ER and mitochondria, such a role of ERMES is still controversial and awaits experimental demonstration.", "Here we developed a novel in vitro assay system with isolated yeast membrane fractions to monitor phospholipid exchange between the ER and mitochondria.", "With this system, we found that phospholipid transport between the ER and mitochondria relies on membrane intactness, but not energy sources such as ATP, GTP or the membrane potential across the mitochondrial inner membrane.", "We further found that lack of the ERMES component impairs the phosphatidylserine transport from the ER to mitochondria, but not the phosphatidylethanolamine transport from mitochondria to the ER.", "This in vitro assay system thus offers a powerful tool to analyze the non-vesicular phospholipid transport between the ER and mitochondria."], "structured": false}
{"doc_id": 4702639, "title": "An integrin \u03b23\u2013KRAS\u2013RalB complex drives tumour stemness and resistance to EGFR inhibition", "abstract": ["Tumour cells, with stem-like properties, are highly aggressive and often show drug resistance.", "Here, we reveal that integrin \u03b1v\u03b23 serves as a marker of breast, lung and pancreatic carcinomas with stem-like properties that are highly resistant to receptor tyrosine kinase inhibitors such as erlotinib.", "This was observed in vitro and in mice bearing patient-derived tumour xenografts or in clinical specimens from lung cancer patients who had progressed on erlotinib.", "Mechanistically, \u03b1v\u03b23, in the unliganded state, recruits KRAS and RalB to the tumour cell plasma membrane, leading to the activation of TBK1 and NF-\u03baB. In fact, \u03b1v\u03b23 expression and the resulting KRAS\u2013RalB\u2013NF-\u03baB pathway were both necessary and sufficient for tumour initiation, anchorage independence, self-renewal and erlotinib resistance.", "Pharmacological targeting of this pathway with bortezomib reversed both tumour stemness and erlotinib resistance.", "These findings not only identify \u03b1v\u03b23 as a marker/driver of carcinoma stemness but also reveal a therapeutic strategy to sensitize such tumours to RTK inhibition."], "structured": false}
{"doc_id": 4709641, "title": "Gain of toxic Apolipoprotein E4 effects in Human iPSC-Derived Neurons Is Ameliorated by a Small-Molecule Structure Corrector", "abstract": ["Efforts to develop drugs for Alzheimer's disease (AD) have shown promise in animal studies, only to fail in human trials, suggesting a pressing need to study AD in human model systems.", "Using human neurons derived from induced pluripotent stem cells that expressed apolipoprotein E4 (ApoE4), a variant of the APOE gene product and the major genetic risk factor for AD, we demonstrated that ApoE4-expressing neurons had higher levels of tau phosphorylation, unrelated to their increased production of amyloid-\u03b2 (A\u03b2) peptides, and that they displayed GABAergic neuron degeneration.", "ApoE4 increased A\u03b2 production in human, but not in mouse, neurons.", "Converting ApoE4 to ApoE3 by gene editing rescued these phenotypes, indicating the specific effects of ApoE4.", "Neurons that lacked APOE behaved similarly to those expressing ApoE3, and the introduction of ApoE4 expression recapitulated the pathological phenotypes, suggesting a gain of toxic effects from ApoE4.", "Treatment of ApoE4-expressing neurons with a small-molecule structure corrector ameliorated the detrimental effects, thus showing that correcting the pathogenic conformation of ApoE4 is a viable therapeutic approach for ApoE4-related AD."], "structured": false}
{"doc_id": 4729644, "title": "LncRNA NEAT1/let-7a-5p axis regulates the cisplatin resistance in nasopharyngeal carcinoma by targeting Rsf-1 and modulating the Ras-MAPK pathway.", "abstract": ["The long non-coding RNA nuclear paraspeckle assembly transcript 1 (NEAT1) was reported to be upregulated and be involved in oncogenic growth and drug resistance in nasopharyngeal carcinoma (NPC).", "However, the exact roles of NEAT1 and its underlying mechanisms in the drug resistance of NPC remain largely unclear.", "In this study, the expressions of NEAT1, let-72-5p and Rsf-1 mRNA were detected by reverse transcription-quantitative polymerase chain reaction (RT-qPCR).", "The effects of NEAT1 and let-72-5p on cell proliferation and cisplatin resistance of NPC cells were investigated by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) assay and 5-ethynyl-20-deoxyuridine (EdU) assay.", "Western blot analysis was performed to detect the protein levels of Rsf-1, Ras, p-Raf1, Raf1, p-MEK1, MEK1, p-ERK1/2 and ERK1/2.", "Xenograft tumor assay was done to elucidate the role of NEAT1 involved in NPC tumor growth in vivo.", "We found that NEAT1 was upregulated and let-7a-5p was downregulated in NPC tissues, as well as NPC cell lines.", "Inhibition of NEAT1 markedly repressed the cisplatin resistance of NPC cells.", "NEAT1 was demonstrated to interact with let-7a-5p.", "Besides, a negative correlation between NEAT1 and let-7a-5p expression was observed in NPC tissues.", "Rsf-1 was confirmed as a target of let-7a-5p.", "NEAT1 remarkably reversed the inhibitory effect of let-7q-5p on the cisplatin resistance of NPC cells in vitro.", "Additionally, NEAT1 knockdown inhibited the Ras-MAPK pathway in NPC cells.", "NEAT1 knockdown suppressed tumor growth in the presence of cisplatin in vivo.", "Overall, these findings suggest that NEAT1/let-7a-5p axis regulates the cisplatin resistance in NPC by targeting Rsf-1 and modulating the Ras-MAPK signaling pathway."], "structured": false}
{"doc_id": 4740447, "title": "Antibacterial peptide microcin J25 inhibits transcription by binding within and obstructing the RNA polymerase secondary channel.", "abstract": ["The antibacterial peptide microcin J25 (MccJ25) inhibits transcription by bacterial RNA polymerase (RNAP).", "Biochemical results indicate that inhibition of transcription occurs at the level of NTP uptake or NTP binding by RNAP.", "Genetic results indicate that inhibition of transcription requires an extensive determinant, comprising more than 50 amino acid residues, within the RNAP secondary channel (also known as the \"NTP-uptake channel\" or \"pore\").", "Biophysical results indicate that inhibition of transcription involves binding of MccJ25 within the RNAP secondary channel.", "Molecular modeling indicates that binding of MccJ25 within the RNAP secondary channel obstructs the RNAP secondary channel.", "We conclude that MccJ25 inhibits transcription by binding within and obstructing the RNAP secondary channel--acting essentially as a \"cork in a bottle.", "\"", "Obstruction of the RNAP secondary channel represents an attractive target for drug discovery."], "structured": false}
{"doc_id": 4767806, "title": "Exploring and exploiting the systemic effects of deregulated replication licensing.", "abstract": ["Maintenance and accurate propagation of the genetic material are key features for physiological development and wellbeing.", "The replication licensing machinery is crucial for replication precision as it ensures that replication takes place once per cell cycle.", "Thus, the expression status of the components comprising the replication licensing apparatus is tightly regulated to avoid re-replication; a form of replication stress that leads to genomic instability, a hallmark of cancer.", "In the present review we discuss the mechanistic basis of replication licensing deregulation, which leads to systemic effects, exemplified by its role in carcinogenesis and a variety of genetic syndromes.", "In addition, new insights demonstrate that above a particular threshold, the replication licensing factor Cdc6 acts as global transcriptional regulator, outlining new lines of exploration.", "The role of the putative replication licensing factor ChlR1/DDX11, mutated in the Warsaw Breakage Syndrome, in cancer is also considered.", "Finally, future perspectives focused on the potential therapeutic advantage by targeting replication licensing factors, and particularly Cdc6, are discussed."], "structured": false}
{"doc_id": 4784069, "title": "Regulatory principles of pluripotency: from the ground state up.", "abstract": ["Pluripotency is the remarkable capacity of a single cell to engender all the specialized cell types of an adult organism.", "This property can be captured indefinitely through derivation of self-renewing embryonic stem cells (ESCs), which represent an invaluable platform to investigate cell fate decisions and disease.", "Recent advances have revealed that manipulation of distinct signaling cues can render ESCs in a uniform \"ground state\" of pluripotency, which more closely recapitulates the pluripotent naive epiblast.", "Here we discuss the extrinsic and intrinsic regulatory principles that underpin the nature of pluripotency and consider the emerging spectrum of pluripotent states."], "structured": false}
{"doc_id": 4791384, "title": "Neonatal Mortality Levels for 193 Countries in 2009 with Trends since 1990: A Systematic Analysis of Progress, Projections, and Priorities", "abstract": ["BACKGROUND Historically, the main focus of studies of childhood mortality has been the infant and under-five mortality rates.", "Neonatal mortality (deaths <28 days of age) has received limited attention, although such deaths account for about 41% of all child deaths.", "To better assess progress, we developed annual estimates for neonatal mortality rates (NMRs) and neonatal deaths for 193 countries for the period 1990-2009 with forecasts into the future.   \n", "METHODS AND FINDINGS We compiled a database of mortality in neonates and children (<5 years) comprising 3,551 country-years of information.", "Reliable civil registration data from 1990 to 2009 were available for 38 countries.", "A statistical model was developed to estimate NMRs for the remaining 155 countries, 17 of which had no national data.", "Country consultation was undertaken to identify data inputs and review estimates.", "In 2009, an estimated 3.3 million babies died in the first month of life-compared with 4.6 million neonatal deaths in 1990-and more than half of all neonatal deaths occurred in five countries of the world (44% of global livebirths): India 27.8% (19.6% of global livebirths), Nigeria 7.2% (4.5%), Pakistan 6.9% (4.0%), China 6.4% (13.4%), and Democratic Republic of the Congo 4.6% (2.1%).", "Between 1990 and 2009, the global NMR declined by 28% from 33.2 deaths per 1,000 livebirths to 23.9.", "The proportion of child deaths that are in the neonatal period increased in all regions of the world, and globally is now 41%.", "While NMRs were halved in some regions of the world, Africa's NMR only dropped 17.6% (43.6 to 35.9).   \n", "CONCLUSIONS Neonatal mortality has declined in all world regions.", "Progress has been slowest in the regions with high NMRs.", "Global health programs need to address neonatal deaths more effectively if Millennium Development Goal 4 (two-thirds reduction in child mortality) is to be achieved."], "structured": true}
{"doc_id": 4795303, "title": "Neuroprotective Effects of Four Phenylethanoid Glycosides on H2O2-Induced Apoptosis on PC12 Cells via the Nrf2/ARE Pathway", "abstract": ["Nuclear factor erythroid 2-related factor 2 (Nrf2) is a key transcription factor against oxidative stress and neurodegenerative disorders.", "Phenylethanoid glycosides (PhGs; salidroside, acteoside, isoacteoside, and echinacoside) exhibit antioxidant and neuroprotective bioactivities.", "This study was performed to investigate the neuroprotective effect and molecular mechanism of PhGs.", "PhGs pretreatment significantly suppressed H\u2082O\u2082-induced cytotoxicity in PC12 cells by triggering the nuclear translocation of Nrf2 and reversing the downregulated protein expression of heme oxygenase 1 (HO-1), NAD(P)H quinone oxidoreductase 1 (NQO1), glutamate cysteine ligase-catalytic subunit (GCLC), and glutamate-cysteine ligase modifier subunit (GCLM).", "Nrf2 siRNA or HO-1 inhibitor zinc protoporphyrin (ZnPP) reduced the neuroprotective effect.", "PhGs showed potential interaction with the Nrf2 binding site in Kelch-like ECH-association protein 1 (Keap1).", "This result may support the hypothesis that PhGs are activators of Nrf2.", "We demonstrated the potential binding between PhGs and the Keap1-activated Nrf2/ARE pathway, and that PhGs with more glycosides had enhanced effects."], "structured": false}
{"doc_id": 4810810, "title": "Mortality risk attributable to high and low ambient temperature: a multicountry observational study", "abstract": ["BACKGROUND Although studies have provided estimates of premature deaths attributable to either heat or cold in selected countries, none has so far offered a systematic assessment across the whole temperature range in populations exposed to different climates.", "We aimed to quantify the total mortality burden attributable to non-optimum ambient temperature, and the relative contributions from heat and cold and from moderate and extreme temperatures.   \n", "METHODS We collected data for 384 locations in Australia, Brazil, Canada, China, Italy, Japan, South Korea, Spain, Sweden, Taiwan, Thailand, UK, and USA.", "We fitted a standard time-series Poisson model for each location, controlling for trends and day of the week.", "We estimated temperature-mortality associations with a distributed lag non-linear model with 21 days of lag, and then pooled them in a multivariate metaregression that included country indicators and temperature average and range.", "We calculated attributable deaths for heat and cold, defined as temperatures above and below the optimum temperature, which corresponded to the point of minimum mortality, and for moderate and extreme temperatures, defined using cutoffs at the 2\u00b75th and 97\u00b75th temperature percentiles.   \n", "FINDINGS We analysed 74,225,200 deaths in various periods between 1985 and 2012.", "In total, 7\u00b771% (95% empirical CI 7\u00b743-7\u00b791) of mortality was attributable to non-optimum temperature in the selected countries within the study period, with substantial differences between countries, ranging from 3\u00b737% (3\u00b706 to 3\u00b763) in Thailand to 11\u00b700% (9\u00b729 to 12\u00b747) in China.", "The temperature percentile of minimum mortality varied from roughly the 60th percentile in tropical areas to about the 80-90th percentile in temperate regions.", "More temperature-attributable deaths were caused by cold (7\u00b729%, 7\u00b702-7\u00b749) than by heat (0\u00b742%, 0\u00b739-0\u00b744).", "Extreme cold and hot temperatures were responsible for 0\u00b786% (0\u00b784-0\u00b787) of total mortality.   \n", "INTERPRETATION Most of the temperature-related mortality burden was attributable to the contribution of cold.", "The effect of days of extreme temperature was substantially less than that attributable to milder but non-optimum weather.", "This evidence has important implications for the planning of public-health interventions to minimise the health consequences of adverse temperatures, and for predictions of future effect in climate-change scenarios.   \n", "FUNDING UK Medical Research Council."], "structured": true}
{"doc_id": 4816339, "title": "Survivin is not required for the endomitotic cell cycle of megakaryocytes.", "abstract": ["Survivin is a member of the chromosome passenger complex, which plays an important role in chromosome alignment, separation, and cytokinesis.", "Although survivin is required for the proliferation and survival of hematopoietic stem and progenitor cells, the extent to which it is necessary for endomitosis of megakaryocytes remains controversial.", "To determine whether survivin is required for polyploidization, we analyzed mice with a megakaryocyte-specific deletion.", "PF4-Cre/survivin(fl/fl) mice harbored normal platelet counts with megakaryocytes that reached ploidy states comparable with those of control littermates.", "The CD41(+) cells within these animals showed little excision but increased annexin V staining, implying that survivin is required for survival of megakaryocyte progenitors in vivo.", "In contrast, megakaryocytes in which survivin was excised ex vivo showed robust excision and an increased degree of polyploidization.", "These results demonstrate that survivin is necessary for survival of megakaryocyte progenitors, but is not required for polyploidization of committed megakaryocytes."], "structured": false}
{"doc_id": 4820792, "title": "\u03b21 integrin mediates an alternative survival pathway in breast cancer cells resistant to lapatinib", "abstract": ["INTRODUCTION The overexpression of human epidermal growth factor receptor (HER)-2 in 20% of human breast cancers and its association with aggressive growth has led to widespread use of HER2-targeted therapies, such as trastuzumab (T) and lapatinib (L).", "Despite the success of these drugs, their efficacy is limited in patients whose tumors demonstrate de novo or acquired resistance to treatment.", "The \u03b21 integrin resides on the membrane of the breast cancer cell, activating several elements of breast tumor progression including proliferation and survival.   \n", "METHODS We developed a panel of HER2-overexpressing cell lines resistant to L, T, and the potent LT combination through long-term exposure and validated these models in 3D culture.", "Parental and L/T/LT-resistant cells were subject to HER2 and \u03b21 integrin inhibitors in 3D and monitored for 12 days, followed by quantification of colony number.", "Parallel experiments were conducted where cells were either stained for Ki-67 and Terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) or harvested for protein and analyzed by immunoblot.", "Results were subjected to statistical testing using analysis of variance and linear contrasts, followed by adjustment with the Sidak method.   \n", "RESULTS Using multiple cell lines including BT474 and HCC1954, we reveal that in L and LT resistance, where phosphorylation of EGFR/HER1, HER2, and HER3 are strongly inhibited, kinases downstream of \u03b21 integrin--including focal adhesion kinase (FAK) and Src--are up-regulated.", "Blockade of \u03b21 by the antibody AIIB2 abrogates this up-regulation and functionally achieves significant growth inhibition of L and LT resistant cells in 3D, without dramatically affecting the parental cells.", "SiRNA against \u03b21 as well as pharmacologic inhibition of FAK achieve the same growth inhibitory effect.", "In contrast, trastuzumab-resistant cells, which retain high levels of phosphorylated EGFR/HER1, HER2, and HER3, are only modestly growth-inhibited by AIIB2.   \n", "CONCLUSIONS Our data suggest that HER2 activity, which is suppressed in resistance involving L but not T alone, dictates whether \u03b21 mediates an alternative pathway driving resistance.", "Our findings justify clinical studies investigating the inhibition of \u03b21 or its downstream signaling moieties as strategies to overcome acquired L and LT resistance."], "structured": true}
{"doc_id": 4824840, "title": "Incidence and Trends of Sepsis in US Hospitals Using Clinical vs Claims Data, 2009-2014", "abstract": ["Importance Estimates from claims-based analyses suggest that the incidence of sepsis is increasing and mortality rates from sepsis are decreasing.", "However, estimates from claims data may lack clinical fidelity and can be affected by changing diagnosis and coding practices over time.", "Objective To estimate the US national incidence of sepsis and trends using detailed clinical data from the electronic health record (EHR) systems of diverse hospitals.", "Design, Setting, and Population Retrospective cohort study of adult patients admitted to 409 academic, community, and federal hospitals from 2009-2014.", "Exposures Sepsis was identified using clinical indicators of presumed infection and concurrent acute organ dysfunction, adapting Third International Consensus Definitions for Sepsis and Septic Shock (Sepsis-3) criteria for objective and consistent EHR-based surveillance.", "Main Outcomes and Measures Sepsis incidence, outcomes, and trends from 2009-2014 were calculated using regression models and compared with claims-based estimates using International Classification of Diseases, Ninth Revision, Clinical Modification codes for severe sepsis or septic shock.", "Case-finding criteria were validated against Sepsis-3 criteria using medical record reviews.", "Results A total of 173 690 sepsis cases (mean age, 66.5 [SD, 15.5] y; 77 660 [42.4%] women) were identified using clinical criteria among 2 901 019 adults admitted to study hospitals in 2014 (6.0% incidence).", "Of these, 26 061 (15.0%) died in the hospital and 10 731 (6.2%) were discharged to hospice.", "From 2009-2014, sepsis incidence using clinical criteria was stable (+0.6% relative change/y [95% CI, \u22122.3% to 3.5%], P = .67) whereas incidence per claims increased (+10.3%/y [95% CI, 7.2% to 13.3%], P < .001).", "In-hospital mortality using clinical criteria declined (\u22123.3%/y [95% CI, \u22125.6% to \u22121.0%], P = .004), but there was no significant change in the combined outcome of death or discharge to hospice (\u22121.3%/y [95% CI, \u22123.2% to 0.6%], P = .19).", "In contrast, mortality using claims declined significantly (\u22127.0%/y [95% CI, \u22128.8% to \u22125.2%], P < .001), as did death or discharge to hospice (\u22124.5%/y [95% CI, \u22126.1% to \u22122.8%], P < .001).", "Clinical criteria were more sensitive in identifying sepsis than claims (69.7% [95% CI, 52.9% to 92.0%] vs 32.3% [95% CI, 24.4% to 43.0%], P < .001), with comparable positive predictive value (70.4% [95% CI, 64.0% to 76.8%] vs 75.2% [95% CI, 69.8% to 80.6%], P = .23).", "Conclusions and Relevance In clinical data from 409 hospitals, sepsis was present in 6% of adult hospitalizations, and in contrast to claims-based analyses, neither the incidence of sepsis nor the combined outcome of death or discharge to hospice changed significantly between 2009-2014.", "The findings also suggest that EHR-based clinical data provide more objective estimates than claims-based data for sepsis surveillance."], "structured": false}
{"doc_id": 4828631, "title": "Body-mass index and risk of 22 specific cancers: a population-based cohort study of 5\u00b724 million UK adults", "abstract": ["BACKGROUND High body-mass index (BMI) predisposes to several site-specific cancers, but a large-scale systematic and detailed characterisation of patterns of risk across all common cancers adjusted for potential confounders has not previously been undertaken.", "We aimed to investigate the links between BMI and the most common site-specific cancers.   \n", "METHODS With primary care data from individuals in the Clinical Practice Research Datalink with BMI data, we fitted Cox models to investigate associations between BMI and 22 of the most common cancers, adjusting for potential confounders.", "We fitted linear then non-linear (spline) models; investigated effect modification by sex, menopausal status, smoking, and age; and calculated population effects.   \n", "FINDINGS 5\u00b724 million individuals were included; 166,955 developed cancers of interest.", "BMI was associated with 17 of 22 cancers, but effects varied substantially by site.", "Each 5 kg/m(2) increase in BMI was roughly linearly associated with cancers of the uterus (hazard ratio [HR] 1\u00b762, 99% CI 1\u00b756-1\u00b769; p<0\u00b70001), gallbladder (1\u00b731, 1\u00b712-1\u00b752; p<0\u00b70001), kidney (1\u00b725, 1\u00b717-1\u00b733; p<0\u00b70001), cervix (1\u00b710, 1\u00b703-1\u00b717; p=0\u00b700035), thyroid (1\u00b709, 1\u00b700-1\u00b719; p=0\u00b70088), and leukaemia (1\u00b709, 1\u00b705-1\u00b713; p\u22640\u00b70001).", "BMI was positively associated with liver (1\u00b719, 1\u00b712-1\u00b727), colon (1\u00b710, 1\u00b707-1\u00b713), ovarian (1\u00b709, 1.04-1.14), and postmenopausal breast cancers (1\u00b705, 1\u00b703-1\u00b707) overall (all p<0\u00b70001), but these effects varied by underlying BMI or individual-level characteristics.", "We estimated inverse associations with prostate and premenopausal breast cancer risk, both overall (prostate 0\u00b798, 0\u00b795-1\u00b700; premenopausal breast cancer 0\u00b789, 0\u00b786-0\u00b792) and in never-smokers (prostate 0\u00b796, 0\u00b793-0\u00b799; premenopausal breast cancer 0\u00b789, 0\u00b785-0\u00b794).", "By contrast, for lung and oral cavity cancer, we observed no association in never smokers (lung 0\u00b799, 0\u00b793-1\u00b705; oral cavity 1\u00b707, 0\u00b791-1\u00b726): inverse associations overall were driven by current smokers and ex-smokers, probably because of residual confounding by smoking amount.", "Assuming causality, 41% of uterine and 10% or more of gallbladder, kidney, liver, and colon cancers could be attributable to excess weight.", "We estimated that a 1 kg/m(2) population-wide increase in BMI would result in 3790 additional annual UK patients developing one of the ten cancers positively associated with BMI.   \n", "INTERPRETATION BMI is associated with cancer risk, with substantial population-level effects.", "The heterogeneity in the effects suggests that different mechanisms are associated with different cancer sites and different patient subgroups.   \n", "FUNDING National Institute for Health Research, Wellcome Trust, and Medical Research Council."], "structured": true}
{"doc_id": 4828984, "title": "Cryo-EM structure of a herpesvirus capsid at 3.1 \u00c5", "abstract": ["Structurally and genetically, human herpesviruses are among the largest and most complex of viruses.", "Using cryo\u2013electron microscopy (cryo-EM) with an optimized image reconstruction strategy, we report the herpes simplex virus type 2 (HSV-2) capsid structure at 3.1 angstroms, which is built up of about 3000 proteins organized into three types of hexons (central, peripentonal, and edge), pentons, and triplexes.", "Both hexons and pentons contain the major capsid protein, VP5; hexons also contain a small capsid protein, VP26; and triplexes comprise VP23 and VP19C.", "Acting as core organizers, VP5 proteins form extensive intermolecular networks, involving multiple disulfide bonds (about 1500 in total) and noncovalent interactions, with VP26 proteins and triplexes that underpin capsid stability and assembly.", "Conformational adaptations of these proteins induced by their microenvironments lead to 46 different conformers that assemble into a massive quasisymmetric shell, exemplifying the structural and functional complexity of HSV."], "structured": false}
{"doc_id": 4833016, "title": "Asymptotic and resampling strategies for assessing and comparing indirect effects in multiple mediator models.", "abstract": ["Hypotheses involving mediation are common in the behavioral sciences.", "Mediation exists when a predictor affects a dependent variable indirectly through at least one intervening variable, or mediator.", "Methods to assess mediation involving multiple simultaneous mediators have received little attention in the methodological literature despite a clear need.", "We provide an overview of simple and multiple mediation and explore three approaches that can be used to investigate indirect processes, as well as methods for contrasting two or more mediators within a single model.", "We present an illustrative example, assessing and contrasting potential mediators of the relationship between the helpfulness of socialization agents and job satisfaction.", "We also provide SAS and SPSS macros, as well as Mplus and LISREL syntax, to facilitate the use of these methods in applications."], "structured": false}
{"doc_id": 4841908, "title": "Distinct Metabolomic Signatures Are Associated with Longevity in Humans", "abstract": ["Alterations in metabolism influence lifespan in experimental models, but data in humans are lacking.", "Here we use liquid chromatography/mass spectrometry to quantify 217 plasma metabolites and examine their relation to longevity in a large cohort of men and women followed for up to 20 years.", "We find that, higher concentrations of the citric acid cycle intermediate, isocitrate, and the bile acid, taurocholate, are associated with lower odds of longevity, defined as attaining 80 years of age.", "Higher concentrations of isocitrate, but not taurocholate, are also associated with worse cardiovascular health at baseline, as well as risk of future cardiovascular disease and death.", "None of the metabolites identified are associated with cancer risk.", "Our findings suggest that some, but not all, metabolic pathways related to human longevity are linked to the risk of common causes of death."], "structured": false}
{"doc_id": 4854076, "title": "The expanding problem of adipose depot remodeling and postnatal adipocyte progenitor recruitment.", "abstract": ["The rising incidence of obesity and associated metabolic diseases has increased the urgency in understanding all aspects of adipose tissue biology.", "This includes the function of adipocytes, how adipose tissue expands in obesity, and how expanded adipose tissues in adults can impact physiology.", "Here, we highlight the growing appreciation for the importance of de novo adipocyte differentiation to adipose tissue expansion in adult humans and animals.", "We detail recent efforts to identify adipose precursor populations that contribute to the physiological postnatal recruitment of white, brown, and beige adipocytes in mice, and summarize new data that reveal the complexity of adipose tissue development in vivo."], "structured": false}
{"doc_id": 4856149, "title": "Clonal competition in BcrAbl-driven leukemia: how transplantations can accelerate clonal conversion", "abstract": ["BACKGROUND Clonal competition in cancer describes the process in which the progeny of a cell clone supersedes or succumbs to other competing clones due to differences in their functional characteristics, mostly based on subsequently acquired mutations.", "Even though the patterns of those mutations are well explored in many tumors, the dynamical process of clonal selection is underexposed.   \n", "METHODS We studied the dynamics of clonal competition in a BcrAbl-induced leukemia using a \u03b3-retroviral vector library encoding the oncogene in conjunction with genetic barcodes.", "To this end, we studied the growth dynamics of transduced cells on the clonal level both in vitro and in vivo in transplanted mice.   \n", "RESULTS While we detected moderate changes in clonal abundancies in vitro, we observed monoclonal leukemias in 6/30 mice after transplantation, which intriguingly were caused by only two different BcrAbl clones.", "To analyze the success of these clones, we applied a mathematical model of hematopoietic tissue maintenance, which indicated that a differential engraftment capacity of these two dominant clones provides a possible explanation of our observations.", "These findings were further supported by additional transplantation experiments and increased BcrAbl transcript levels in both clones.   \n", "CONCLUSION Our findings show that clonal competition is not an absolute process based on mutations, but highly dependent on selection mechanisms in a given environmental context."], "structured": true}
{"doc_id": 4857085, "title": "Open Babel: An open chemical toolbox", "abstract": ["BACKGROUND A frequent problem in computational modeling is the interconversion of chemical structures between different formats.", "While standard interchange formats exist (for example, Chemical Markup Language) and de facto standards have arisen (for example, SMILES format)", ", the need to interconvert formats is a continuing problem due to the multitude of different application areas for chemistry data, differences in the data stored by different formats (0D versus 3D, for example), and competition between software along with a lack of vendor-neutral formats.   \n", "RESULTS We discuss, for the first time, Open Babel, an open-source chemical toolbox that speaks the many languages of chemical data.", "Open Babel version 2.3 interconverts over 110 formats.", "The need to represent such a wide variety of chemical and molecular data requires a library that implements a wide range of cheminformatics algorithms, from partial charge assignment and aromaticity detection, to bond order perception and canonicalization.", "We detail the implementation of Open Babel, describe key advances in the 2.3 release, and outline a variety of uses both in terms of software products and scientific research, including applications far beyond simple format interconversion.   \n", "CONCLUSIONS Open Babel presents a solution to the proliferation of multiple chemical file formats.", "In addition, it provides a variety of useful utilities from conformer searching and 2D depiction, to filtering, batch conversion, and substructure and similarity searching.", "For developers, it can be used as a programming library to handle chemical data in areas such as organic chemistry, drug design, materials science, and computational chemistry.", "It is freely available under an open-source license from http://openbabel.org."], "structured": true}
{"doc_id": 4857093, "title": "Young adolescents' nutrition assessment on computer (YANA-C)", "abstract": ["Objective:To assess the relative validity and acceptability of the computerised 24-h recall \u2018Young Adolescent's Nutrition Assessment on Computer (YANA-C)\u2019.Design:Food and nutrient intakes assessed with YANA-C were compared with food records (study 1) and 24-h dietary recall interviews (study 2).Main outcome measures:Intakes of food groups (fruit, fruit juice, vegetables, potatoes, bread, cereals, milk, cheese, other milk products, soft drinks, diet soft drinks, sugar/sweets, pastry/cookies, savoury snacks, butter/sauces, eggs, fish, meat) and nutrients (energy, carbohydrates, protein, fat, fiber, calcium, vitamin C and iron).Subjects and setting:A total of 237 pupils (11\u201314 y) from two primary and four secondary schools (study 1: n=136; study 2: n=101) in Belgium-Flanders.", "Results:YANA-C proved to agree well with both standard methods in categorizing subjects in consumers and nonconsumers (\u03bastudy 1=0.48\u20130.92; \u03bastudy 2=0.38\u20130.90).", "Spearman's correlations for energy and nutrient intakes ranged between 0.44 and 0.79 for study 1 and between 0.44 and 0.86 for study 2.", "Nutrient and energy intakes were in general (excluding calcium) significantly higher in YANA-C in comparison with the food record, but not in comparison with the interview (only fiber).", "Statistics used to investigate whether YANA-C agreed with the other methods in ranking portions/amounts in consumers only were fair to moderate for most of the food groups (weighted \u03ba study 1=0.11\u20130.55; study 2=0.04\u20130.73); amounts in consumers only, were significantly lower in YANA-C against both standards for cereals; amounts were significantly higher in YANA-C against the food record for milk, soft drinks, sugar/sweets and savoury snacks and against the interview for potatoes.", "Only a few pupils evaluated the program negatively.", "Conclusion:YANA-C is a promising method to collect detailed dietary information from young adolescents with relatively low staff resources, useful in many nutrition research applications."], "structured": false}
{"doc_id": 4883040, "title": "Antiretroviral Therapy for Prevention of Tuberculosis in Adults with HIV: A Systematic Review and Meta-Analysis", "abstract": ["BACKGROUND Human immunodeficiency virus (HIV) infection is the strongest risk factor for developing tuberculosis and has fuelled its resurgence, especially in sub-Saharan Africa.", "In 2010, there were an estimated 1.1 million incident cases of tuberculosis among the 34 million people living with HIV worldwide.", "Antiretroviral therapy has substantial potential to prevent HIV-associated tuberculosis.", "We conducted a systematic review of studies that analysed the impact of antiretroviral therapy on the incidence of tuberculosis in adults with HIV infection.   \n", "METHODS AND FINDINGS PubMed, Embase, African Index Medicus, LILACS, and clinical trial registries were systematically searched.", "Randomised controlled trials, prospective cohort studies, and retrospective cohort studies were included if they compared tuberculosis incidence by antiretroviral therapy status in HIV-infected adults for a median of over 6 mo in developing countries.", "For the meta-analyses there were four categories based on CD4 counts at antiretroviral therapy initiation: (1) less than 200 cells/\u00b5l, (2) 200 to 350 cells/\u00b5l, (3) greater than 350 cells/\u00b5l, and (4) any CD4 count.", "Eleven studies met the inclusion criteria.", "Antiretroviral therapy is strongly associated with a reduction in the incidence of tuberculosis in all baseline CD4 count categories: (1) less than 200 cells/\u00b5l (hazard ratio [HR] 0.16, 95% confidence interval [CI] 0.07 to 0.36), (2) 200 to 350 cells/\u00b5l (HR 0.34, 95% CI 0.19 to 0.60), (3) greater than 350 cells/\u00b5l (HR 0.43, 95% CI 0.30 to 0.63), and (4) any CD4 count (HR 0.35, 95% CI 0.28 to 0.44).", "There was no evidence of hazard ratio modification with respect to baseline CD4 count category (p = 0.20).   \n", "CONCLUSIONS Antiretroviral therapy is strongly associated with a reduction in the incidence of tuberculosis across all CD4 count strata.", "Earlier initiation of antiretroviral therapy may be a key component of global and national strategies to control the HIV-associated tuberculosis syndemic.   ", "REVIEW REGISTRATION International Prospective Register of Systematic Reviews CRD42011001209 Please see later in the article for the Editors' Summary."], "structured": true}
{"doc_id": 4886637, "title": "Diabetes, metabolic syndrome, and breast cancer: a review of the current evidence.", "abstract": ["Incidences of breast cancer, type 2 diabetes, and metabolic syndrome have increased over the past decades with the obesity epidemic, especially in industrialized countries.", "Insulin resistance, hyperinsulinemia, and changes in the signaling of growth hormones and steroid hormones associated with diabetes may affect the risk of breast cancer.", "We reviewed epidemiologic studies of the association between type 2 diabetes and risk of breast cancer and the available evidence on the role of hormonal mediators of an association between diabetes and breast cancer.", "The combined evidence supports a modest association between type 2 diabetes and the risk of breast cancer, which appears to be more consistent among postmenopausal than among premenopausal women.", "Despite many proposed potential pathways, the mechanisms underlying an association between diabetes and breast cancer risk remain unclear, particularly because the 2 diseases share several risk factors, including obesity, a sedentary lifestyle, and possibly intake of saturated fat and refined carbohydrates, that may confound this association.", "Although the metabolic syndrome is closely related to diabetes and embraces additional components that might influence breast cancer risk, the role of the metabolic syndrome in breast carcinogenesis has not been studied and thus remains unknown."], "structured": false}
{"doc_id": 4889228, "title": "Loss of TDP43 inhibits progression of triple-negative breast cancer in coordination with SRSF3", "abstract": ["Aberrant alternative splicing has been highlighted as a potential hallmark of cancer.", "Here, we identify TDP43 (TAR DNA-binding protein 43) as an important splicing regulator responsible for the unique splicing profile in triple-negative breast cancer (TNBC).", "Clinical data demonstrate that TDP43 is highly expressed in TNBC with poor prognosis.", "Knockdown of TDP43 inhibits tumor progression, including proliferation and metastasis, and overexpression of TDP43 promotes proliferation and malignancy of mammary epithelial cells.", "Deep sequencing analysis and functional experiments indicate that TDP43 alters most splicing events with splicing factor SRSF3 (serine/arginine-rich splicing factor 3), in the regulation of TNBC progression.", "The TDP43/SRSF3 complex controls specific splicing events, including downstream genes PAR3 and NUMB The effect of reduced metastasis and proliferation upon the knockdown of TDP43 or SRSF3 is mediated by the splicing regulation of PAR3 and NUMB exon 12, respectively.", "The TDP43/SRSF3 complex and downstream PAR3 isoform are potential therapeutic targets for TNBC."], "structured": false}
{"doc_id": 4890578, "title": "Atherosclerotic plaque rupture--pathologic basis of plaque stability and instability.", "abstract": ["Time for primary reveiw 27 days   Atherosclerosis continues to be one of the main subjects in pathology research.", "The intriguing complexity of its pathogenesis as well as the importance of its clinical sequelae provide a rationale for this [1].", "A large number of diseases with totally different clinical presentations are basically atherosclerosis related, and among these, myocardial infarction, stroke, abdominal aneurysms and lower limb ischemia determine to a large extent the morbidity and mortality in Western style populations.", "But, despite this broad spectrum of clinical disease, most of the acute manifestations of atherosclerosis share a common pathogenetic feature: rupture of an atherosclerotic plaque [2\u20134].", "Plaque disruptions may vary greatly in extent from tiny fissures or erosions of the plaque surface to deep intimal tears which extend into the soft lipid core of lesions; in all these instances, at least some degree of thrombus formation occurs [5, 6].", "The abdominal aorta is the arterial site most prominently involved in the process of plaque formation, and also of plaque complications.", "In this large diameter vessel the process of plaque disruption and thrombosis is not ended by luminal occlusion, and may lead to extensive surface ulcerations comprising large areas of the aortic wall, as can be observed in many autopsy cases at older age.", "Apart from the undisputable role of atherosclerosis in abdominal aneurysm formation [7], mural thrombosis leads to a surprisingly low rate of clinically significant complications in these patients, although cholesterol emboli can be regularly found in their kidneys and skin at autopsy.", "Still, it is presently unclear what impact the various biologically active mediators released from eroded aortic surfaces may have on the human body.  ", "In contrast, in small diameter vessels such as coronary arteries, occlusive thrombosis is a frequent and often fatal complication of plaque \u2026   * Corresponding author.", "Tel.: +31-20-5665-633; fax: +31-20-914-738; e-mail a.c.vanderwal@amc.uva.nl"], "structured": false}
{"doc_id": 4896726, "title": "Pioneer factor Pax7 deploys a stable enhancer repertoire for specification of cell fate", "abstract": ["Pioneer transcription factors establish new cell-fate competence by triggering chromatin remodeling.", "However, many features of pioneer action, such as their kinetics and stability, remain poorly defined.", "Here, we show that Pax7, by opening a unique repertoire of enhancers, is necessary and sufficient for specification of one pituitary lineage.", "Pax7 binds its targeted enhancers rapidly, but chromatin remodeling and gene activation are slower.", "Enhancers opened by Pax7 show a loss of DNA methylation and acquire stable epigenetic memory, as evidenced by binding of nonpioneer factors after Pax7 withdrawal.", "This work shows that transient Pax7 expression is sufficient for stable specification of cell identity.", "Analysis of Pax7 dynamics during pituitary lineage specification shows that Pax7 binds rapidly at uniquely marked heterochromatin pioneer sites and initiates chromatin opening that remains stable after Pax7 withdrawal, with loss of DNA hypermethylation at pioneered enhancers."], "structured": false}
{"doc_id": 4899981, "title": "Human cancer cells utilize mitotic DNA synthesis to resist replication stress at telomeres regardless of their telomere maintenance mechanism", "abstract": ["Telomeres resemble common fragile sites (CFSs) in that they are difficult-to-replicate and exhibit fragility in mitosis in response to DNA replication stress.", "At CFSs, this fragility is associated with a delay in the completion of DNA replication until early mitosis, whereupon cells are proposed to switch to a RAD52-dependent form of break-induced replication.", "Here, we show that this mitotic DNA synthesis (MiDAS) is also a feature of human telomeres.", "Telomeric MiDAS is not restricted to those telomeres displaying overt fragility, and is a feature of a wide range of cell lines irrespective of whether their telomeres are maintained by telomerase or by the alternative lengthening of telomeres (ALT) mechanism.", "MiDAS at telomeres requires RAD52, and is mechanistically similar to CFS-associated MiDAS, with the notable exception that telomeric MiDAS does not require the MUS81-EME1 endonuclease.", "We propose a model whereby replication stress initiates a RAD52-dependent form of break-induced replication that bypasses a requirement for MUS81-EME1 to complete DNA synthesis in mitosis."], "structured": false}
{"doc_id": 4910408, "title": "Low drug levels and thrombotic complications in high\u2010risk atrial fibrillation patients treated with direct oral anticoagulants", "abstract": ["Essentials Direct oral anticoagulants (DOACs) do not require laboratory monitoring currently.", "DOAC specific measurements were performed at trough in patients with atrial fibrillation.", "Patients who developed thromboembolic events showed lower DOAC plasma levels.", "This study supports the concept of measuring DOAC levels at steady state.   ", "SUMMARY Background Direct oral anticoagulants (DOACs) are administered at fixed doses without the need for dose adjustment according to laboratory testing.", "High interindividual variability in drug blood levels has been shown with all DOACs.", "To evaluate a possible relationship between DOAC C-trough anticoagulant levels and thromboembolic events, 565 consecutive naive patients with atrial fibrillation (AF) were enrolled in this study performed within the START Laboratory Registry.", "Methods DOAC-specific measurements (diluted thrombin time or anti-activated factor II calibrated for dabigatran; anti-activated FX calibrated for rivaroxaban or apixaban) at C-trough were performed locally at steady state within 15-25 days after the start of treatment.", "For each DOAC, the interval of C-trough levels, from the limit of quantification to the highest value, was subdivided into four equal classes, and results were attributed to these classes; the median values of results were also calculated.", "Thromboembolic complications occurring during 1 year of follow-up were recorded.", "Results Thromboembolic events (1.8%) occurred in 10 patients who had baseline C-trough levels in the lowest class of drug levels.", "The incidence of thromboembolic events among patients with DOAC C-trough levels in the lowest level class was 2.4%, and that in the remaining groups was 0%.", "The patients with thrombotic complications also had a higher mean CHA2 DS2 -VASc score than that of the total patient population: 5.3 (95% confidence interval [CI] 4.3-6.3 versus 3.0 (95% CI 2.9-3.1).", "Conclusion In this study cohort, thrombotic complications occurred only in DOAC-treated AF patients who had very low C-trough levels, with a relatively high CHA2 DS2 -VASc score.", "Larger studies are warranted to confirm these preliminary observations."], "structured": false}
{"doc_id": 4911006, "title": "Consensus guidelines for the detection of immunogenic cell death.", "abstract": ["Apoptotic cells have long been considered as intrinsically tolerogenic or unable to elicit immune responses specific for dead cell-associated antigens.", "However, multiple stimuli can trigger a functionally peculiar type of apoptotic demise that does not go unnoticed by the adaptive arm of the immune system, which we named \"immunogenic cell death\" (ICD).", "ICD is preceded or accompanied by the emission of a series of immunostimulatory damage-associated molecular patterns (DAMPs) in a precise spatiotemporal configuration.", "Several anticancer agents that have been successfully employed in the clinic for decades, including various chemotherapeutics and radiotherapy, can elicit ICD.", "Moreover, defects in the components that underlie the capacity of the immune system to perceive cell death as immunogenic negatively influence disease outcome among cancer patients treated with ICD inducers.", "Thus, ICD has profound clinical and therapeutic implications.", "Unfortunately, the gold-standard approach to detect ICD relies on vaccination experiments involving immunocompetent murine models and syngeneic cancer cells, an approach that is incompatible with large screening campaigns.", "Here, we outline strategies conceived to detect surrogate markers of ICD in vitro and to screen large chemical libraries for putative ICD inducers, based on a high-content, high-throughput platform that we recently developed.", "Such a platform allows for the detection of multiple DAMPs, like cell surface-exposed calreticulin, extracellular ATP and high mobility group box 1 (HMGB1), and/or the processes that underlie their emission, such as endoplasmic reticulum stress, autophagy and necrotic plasma membrane permeabilization.", "We surmise that this technology will facilitate the development of next-generation anticancer regimens, which kill malignant cells and simultaneously convert them into a cancer-specific therapeutic vaccine."], "structured": false}
{"doc_id": 4920376, "title": "Long-Term ERK Inhibition in KRAS-Mutant Pancreatic Cancer Is Associated with MYC Degradation and Senescence-like Growth Suppression.", "abstract": ["Induction of compensatory mechanisms and ERK reactivation has limited the effectiveness of Raf and MEK inhibitors in RAS-mutant cancers.", "We determined that direct pharmacologic inhibition of ERK suppressed the growth of a subset of KRAS-mutant pancreatic cancer cell lines and that concurrent phosphatidylinositol 3-kinase (PI3K) inhibition caused synergistic cell death.", "Additional combinations that enhanced ERK inhibitor action were also identified.", "Unexpectedly, long-term treatment of sensitive cell lines caused senescence, mediated in part by MYC degradation and p16 reactivation.", "Enhanced basal PI3K-AKT-mTOR signaling was associated with de novo resistance to ERK inhibitor, as were other protein kinases identified by kinome-wide siRNA screening and a genetic gain-of-function screen.", "Our findings reveal distinct consequences of inhibiting this kinase cascade at the level of ERK."], "structured": false}
{"doc_id": 4926049, "title": "TRF2 Recruits RTEL1 to Telomeres in S Phase to Promote T-Loop Unwinding", "abstract": ["The helicase RTEL1 promotes t-loop unwinding and suppresses telomere fragility to maintain the integrity of vertebrate telomeres.", "An interaction between RTEL1 and PCNA is important to prevent telomere fragility, but how RTEL1 engages with the telomere to promote t-loop unwinding is unclear.", "Here, we establish that the shelterin protein TRF2 recruits RTEL1 to telomeres in S phase, which is required to prevent catastrophic t-loop processing by structure-specific nucleases.", "We show that the TRF2-RTEL1 interaction is mediated by a metal-coordinating C4C4 motif in RTEL1, which is compromised by the Hoyeraal-Hreidarsson syndrome (HHS) mutation, RTEL1(R1264H).", "Conversely, we define a TRF2(I124D) substitution mutation within the TRFH domain of TRF2, which eliminates RTEL1 binding and phenocopies the RTEL1(R1264H) mutation, giving rise to aberrant t-loop excision, telomere length heterogeneity, and loss of the telomere as a circle.", "These results implicate TRF2 in the recruitment of RTEL1 to facilitate t-loop disassembly at telomeres in S phase."], "structured": false}
{"doc_id": 4928057, "title": "Macrophages Facilitate Electrical Conduction in the Heart", "abstract": ["Organ-specific functions of tissue-resident macrophages in the steady-state heart are unknown.", "Here, we show that cardiac macrophages facilitate electrical conduction through the distal atrioventricular node, where conducting cells densely intersperse with elongated macrophages expressing connexin 43.", "When coupled to spontaneously beating cardiomyocytes via connexin-43-containing gap junctions, cardiac macrophages have a negative resting membrane potential and depolarize in synchrony with cardiomyocytes.", "Conversely, macrophages render the resting membrane potential of cardiomyocytes more positive and, according to computational modeling, accelerate their repolarization.", "Photostimulation of channelrhodopsin-2-expressing macrophages improves atrioventricular conduction, whereas conditional deletion of connexin 43 in macrophages and congenital lack of macrophages delay atrioventricular conduction.", "In the Cd11bDTR mouse, macrophage ablation induces progressive atrioventricular block.", "These observations implicate macrophages in normal and aberrant cardiac conduction."], "structured": false}
{"doc_id": 4928282, "title": "A Tunable Diffusion\u2010Consumption Mechanism of Cytokine Propagation Enables Plasticity in Cell\u2010to\u2010Cell Communication in the Immune System", "abstract": ["&NA; Immune cells communicate by exchanging cytokines to achieve a context\u2010appropriate response, but the distances over which such communication happens are not known.", "Here, we used theoretical considerations and experimental models of immune responses in vitro and in vivo to quantify the spatial extent of cytokine communications in dense tissues.", "We established that competition between cytokine diffusion and consumption generated spatial niches of high cytokine concentrations with sharp boundaries.", "The size of these self\u2010assembled niches scaled with the density of cytokine\u2010consuming cells, a parameter that gets tuned during immune responses.", "In vivo, we measured interactions on length scales of 80\u2013120 &mgr;m, which resulted in a high degree of cell\u2010to\u2010cell variance in cytokine exposure.", "Such heterogeneous distributions of cytokines were a source of non\u2010genetic cell\u2010to\u2010cell variability that is often overlooked in single\u2010cell studies.", "Our findings thus provide a basis for understanding variability in the patterning of immune responses by diffusible factors.", "Graphical Abstract Figure.", "No caption available.", "HighlightsCytokine penetration in tissues is governed by a diffusion\u2010consumption mechanismSpherical cytokine niches are generated around cytokine\u2010producing cellsThe characteristic niche size depends on the density of cytokine consumersCytokine niches are a source of variability in otherwise identical cells &NA; Cytokine\u2010mediated communication allows immune cells to achieve a context\u2010appropriate response, but the distance over which this communication happens is unclear.", "Oyler\u2010Yaniv et al. (2017) show that a simple diffusion\u2010consumption mechanism quantitatively describes the spatial spread of cytokines in vivo and results in localized niches of high cytokine concentrations that contribute to cell\u2010to\u2010cell variability."], "structured": false}
{"doc_id": 4932668, "title": "Cardiac neural crest contributes to cardiomyogenesis in zebrafish.", "abstract": ["In birds and mammals, cardiac neural crest is essential for heart development and contributes to conotruncal cushion formation and outflow tract septation.", "The zebrafish prototypical heart lacks outflow tract septation, raising the question of whether cardiac neural crest exists in zebrafish.", "Here, results from three distinct lineage-labeling approaches identify zebrafish cardiac neural crest cells and indicate that these cells have the ability to generate MF20-positive muscle cells in the myocardium of the major chambers during development.", "Fate-mapping demonstrates that cardiac neural crest cells originate both from neural tube regions analogous to those found in birds, as well as from a novel region rostral to the otic vesicle.", "In contrast to other vertebrates, cardiac neural crest invades the myocardium in all segments of the heart, including outflow tract, atrium, atrioventricular junction, and ventricle in zebrafish.", "Three distinct groups of premigratory neural crest along the rostrocaudal axis have different propensities to contribute to different segments in the heart and are correspondingly marked by unique combinations of gene expression patterns.", "Zebrafish will serve as a model for understanding interactions between cardiac neural crest and cardiovascular development."], "structured": false}
{"doc_id": 4939312, "title": "Sodium Hydroxide Production from Seawater Desalination Brine: Process Design and Energy Efficiency.", "abstract": ["The ability to increase pH is a crucial need for desalination pretreatment (especially in reverse osmosis) and for other industries, but processes used to raise pH often incur significant emissions and nonrenewable resource use.", "Alternatively, waste brine from desalination can be used to create sodium hydroxide, via appropriate concentration and purification pretreatment steps, for input into the chlor-alkali process.", "In this work, an efficient process train (with variations) is developed and modeled for sodium hydroxide production from seawater desalination brine using membrane chlor-alkali electrolysis.", "The integrated system includes nanofiltration, concentration via evaporation or mechanical vapor compression, chemical softening, further ion-exchange softening, dechlorination, and membrane electrolysis.", "System productivity, component performance, and energy consumption of the NaOH production process are highlighted, and their dependencies on electrolyzer outlet conditions and brine recirculation are investigated.", "The analysis of the process also includes assessment of the energy efficiency of major components, estimation of system operating expense and comparison with similar processes.", "The brine-to-caustic process is shown to be technically feasible while offering several advantages, that is, the reduced environmental impact of desalination through lessened brine discharge, and the increase in the overall water recovery ratio of the reverse osmosis facility.", "Additionally, best-use conditions are given for producing caustic not only for use within the plant, but also in excess amounts for potential revenue."], "structured": false}
{"doc_id": 4942718, "title": "High-Throughput Genetic Screens Identify a Large and Diverse Collection of New Sporulation Genes in Bacillus subtilis", "abstract": ["The differentiation of the bacterium Bacillus subtilis into a dormant spore is among the most well-characterized developmental pathways in biology.", "Classical genetic screens performed over the past half century identified scores of factors involved in every step of this morphological process.", "More recently, transcriptional profiling uncovered additional sporulation-induced genes required for successful spore development.", "Here, we used transposon-sequencing (Tn-seq) to assess whether there were any sporulation genes left to be discovered.", "Our screen identified 133 out of the 148 genes with known sporulation defects.", "Surprisingly, we discovered 24 additional genes that had not been previously implicated in spore formation.", "To investigate their functions, we used fluorescence microscopy to survey early, middle, and late stages of differentiation of null mutants from the B. subtilis ordered knockout collection.", "This analysis identified mutants that are delayed in the initiation of sporulation, defective in membrane remodeling, and impaired in spore maturation.", "Several mutants had novel sporulation phenotypes.", "We performed in-depth characterization of two new factors that participate in cell-cell signaling pathways during sporulation.", "One (SpoIIT) functions in the activation of \u03c3E in the mother cell; the other (SpoIIIL) is required for \u03c3G activity in the forespore.", "Our analysis also revealed that as many as 36 sporulation-induced genes with no previously reported mutant phenotypes are required for timely spore maturation.", "Finally, we discovered a large set of transposon insertions that trigger premature initiation of sporulation.", "Our results highlight the power of Tn-seq for the discovery of new genes and novel pathways in sporulation and, combined with the recently completed null mutant collection, open the door for similar screens in other, less well-characterized processes."], "structured": false}
{"doc_id": 4951831, "title": "Psychobiological mechanisms underlying the social buffering of the hypothalamic-pituitary-adrenocortical axis: a review of animal models and human studies across development.", "abstract": ["Discovering the stress-buffering effects of social relationships has been one of the major findings in psychobiology in the last century.", "However, an understanding of the underlying neurobiological and psychological mechanisms of this buffering is only beginning to emerge.", "An important avenue of this research concerns the neurocircuitry that can regulate the activity of the hypothalamic-pituitary-adrenocortical (HPA) axis.", "The present review is a translational effort aimed at integrating animal models and human studies of the social regulation of the HPA axis from infancy to adulthood, specifically focusing on the process that has been named social buffering.", "This process has been noted across species and consists of a dampened HPA axis stress response to threat or challenge that occurs with the presence or assistance of a conspecific.", "We describe aspects of the relevant underlying neurobiology when enough information exists and expose major gaps in our understanding across all domains of the literatures we aimed to integrate.", "We provide a working conceptual model focused on the role of oxytocinergic systems and prefrontal neural networks as 2 of the putative biological mediators of this process, and propose that the role of early experiences is critical in shaping later social buffering effects.", "This synthesis points to both general future directions and specific experiments that need to be conducted to build a more comprehensive model of the HPA social buffering effect across the life span that incorporates multiple levels of analysis: neuroendocrine, behavioral, and social."], "structured": false}
{"doc_id": 4959368, "title": "Elevation of circulating branched-chain amino acids is an early event in human pancreatic adenocarcinoma development", "abstract": ["Most patients with pancreatic ductal adenocarcinoma (PDAC) are diagnosed with advanced disease and survive less than 12 months.", "PDAC has been linked with obesity and glucose intolerance, but whether changes in circulating metabolites are associated with early cancer progression is unknown.", "To better understand metabolic derangements associated with early disease, we profiled metabolites in prediagnostic plasma from individuals with pancreatic cancer (cases) and matched controls from four prospective cohort studies.", "We find that elevated plasma levels of branched-chain amino acids (BCAAs) are associated with a greater than twofold increased risk of future pancreatic cancer diagnosis.", "This elevated risk was independent of known predisposing factors, with the strongest association observed among subjects with samples collected 2 to 5 years before diagnosis, when occult disease is probably present.", "We show that plasma BCAAs are also elevated in mice with early-stage pancreatic cancers driven by mutant Kras expression but not in mice with Kras-driven tumors in other tissues, and that breakdown of tissue protein accounts for the increase in plasma BCAAs that accompanies early-stage disease.", "Together, these findings suggest that increased whole-body protein breakdown is an early event in development of PDAC."], "structured": false}
{"doc_id": 4961038, "title": "Effective Use of PI3K and MEK Inhibitors to Treat Mutant K-Ras G12D and PIK3CA H1047R Murine Lung Cancers", "abstract": ["Somatic mutations that activate phosphoinositide 3-kinase (PI3K) have been identified in the p110-alpha catalytic subunit (encoded by PIK3CA).", "They are most frequently observed in two hotspots: the helical domain (E545K and E542K) and the kinase domain (H1047R).", "Although the p110-alpha mutants are transforming in vitro, their oncogenic potential has not been assessed in genetically engineered mouse models.", "Furthermore, clinical trials with PI3K inhibitors have recently been initiated, and it is unknown if their efficacy will be restricted to specific, genetically defined malignancies.", "In this study, we engineered a mouse model of lung adenocarcinomas initiated and maintained by expression of p110-alpha H1047R.", "Treatment of these tumors with NVP-BEZ235, a dual pan-PI3K and mammalian target of rapamycin (mTOR) inhibitor in clinical development, led to marked tumor regression as shown by positron emission tomography-computed tomography, magnetic resonance imaging and microscopic examination.", "In contrast, mouse lung cancers driven by mutant Kras did not substantially respond to single-agent NVP-BEZ235.", "However, when NVP-BEZ235 was combined with a mitogen-activated protein kinase kinase (MEK) inhibitor, ARRY-142886, there was marked synergy in shrinking these Kras-mutant cancers.", "These in vivo studies suggest that inhibitors of the PI3K-mTOR pathway may be active in cancers with PIK3CA mutations and, when combined with MEK inhibitors, may effectively treat KRAS mutated lung cancers."], "structured": false}
{"doc_id": 4979184, "title": "Transdifferentiation of glioblastoma cells into vascular endothelial cells.", "abstract": ["Glioblastoma (GBM) is the most malignant brain tumor and is highly resistant to intensive combination therapies and anti-VEGF therapies.", "To assess the resistance mechanism to anti-VEGF therapy, we examined the vessels of GBMs in tumors that were induced by the transduction of p53(+/-) heterozygous mice with lentiviral vectors containing oncogenes and the marker GFP in the hippocampus of GFAP-Cre recombinase (Cre) mice.", "We were surprised to observe GFP(+) vascular endothelial cells (ECs).", "Transplantation of mouse GBM cells revealed that the tumor-derived endothelial cells (TDECs) originated from tumor-initiating cells and did not result from cell fusion of ECs and tumor cells.", "An in vitro differentiation assay suggested that hypoxia is an important factor in the differentiation of tumor cells to ECs and is independent of VEGF.", "TDEC formation was not only resistant to an anti-VEGF receptor inhibitor in mouse GBMs but it led to an increase in their frequency.", "A xenograft model of human GBM spheres from clinical specimens and direct clinical samples from patients with GBM also showed the presence of TDECs.", "We suggest that the TDEC is an important player in the resistance to anti-VEGF therapy, and hence a potential target for GBM therapy."], "structured": false}
{"doc_id": 4993011, "title": "Ribosomal DNA copy loss and repeat instability in ATRX-mutated cancers", "abstract": ["ATRX (alpha thalassemia/mental retardation X-linked) complexes with DAXX to deposit histone variant H3.3 into repetitive heterochromatin.", "Recent genome sequencing studies in cancers have revealed mutations in ATRX and their association with ALT (alternative lengthening of telomeres) activation.", "Here we report depletion of ATRX in mouse ES cells leads to selective loss in ribosomal RNA gene (rDNA) copy number.", "Supporting this, ATRX-mutated human ALT-positive tumors also show a substantially lower rDNA copy than ALT-negative tumors.", "Further investigation shows that the rDNA copy loss and repeat instability are caused by a disruption in H3.3 deposition and thus a failure in heterochromatin formation at rDNA repeats in the absence of ATRX.", "We also find that ATRX-depleted cells are reduced in ribosomal RNA transcription output and show increased sensitivity to RNA polymerase I (Pol I) transcription inhibitor CX5461.", "In addition, human ALT-positive cancer cell lines are also more sensitive to CX5461 treatment.", "Our study provides insights into the contribution of ATRX loss of function to tumorigenesis through the loss of rDNA stability and suggests the therapeutic potential of targeting Pol I transcription in ALT cancers."], "structured": false}
{"doc_id": 4999387, "title": "Combining indoor residual spraying and insecticide-treated nets for malaria control in Africa: a review of possible outcomes and an outline of suggestions for the future", "abstract": ["Insecticide-treated nets (ITNs) and indoor residual spraying (IRS) are currently the preferred methods of malaria vector control.", "In many cases, these methods are used together in the same households, especially to suppress transmission in holoendemic and hyperendemic scenarios.", "Though widespread, there has been limited evidence suggesting that such co-application confers greater protective benefits than either ITNs or IRS when used alone.", "Since both methods are insecticide-based and intradomicilliary, this article hypothesises that outcomes of their combination would depend on effects of the candidate active ingredients on mosquitoes that enter or those that attempt to enter houses.", "It is suggested here that enhanced household level protection can be achieved if the ITNs and IRS have divergent yet complementary properties, e.g. highly deterrent IRS compounds coupled with highly toxic ITNs.", "To ensure that the problem of insecticide resistance is avoided, the ITNs and IRS products should preferably be of different insecticide classes, e.g. pyrethroid-based nets combined with organophosphate or carbamate based IRS.", "The overall community benefits would however depend also on other factors such as proportion of people covered by the interventions and the behaviour of vector species.", "This article concludes by emphasizing the need for basic and operational research, including mathematical modelling to evaluate IRS/ITN combinations in comparison to IRS alone or ITNs alone."], "structured": false}
{"doc_id": 4999633, "title": "Membrane estrogen receptor-\u03b1 levels in MCF-7 breast cancer cells predict cAMP and proliferation responses", "abstract": ["17\u03b2-estradiol (E2) can rapidly induce cAMP production, but the conditions under which these cAMP levels are best measured and the signaling pathways responsible for the consequent proliferative effects on breast cancer cells are not fully understood.", "To help resolve these issues, we compared cAMP mechanistic responses in MCF-7 cell lines selected for low (mERlow) and high (mERhigh) expression of the membrane form of estrogen receptor (mER)-\u03b1, and thus addressed the receptor subform involved in cAMP signaling.", "MCF-7 cells were immunopanned and subsequently separated by fluorescence activated cell sorting into mERhigh (mER-\u03b1-enriched) and mERlow (mER-\u03b1-depleted) populations.", "Unique (compared with previously reported) incubation conditions at 4\u00b0C were found to be optimal for demonstrating E2-induced cAMP production.", "Time-dependent and dose-dependent effects of E2 on cAMP production were determined for both cell subpopulations.", "The effects of forskolin, 8-CPT cAMP, protein kinase A inhibitor (H-89), and adenylyl cyclase inhibitor (SQ 22,536) on E2-induced cell proliferation were assessed using the crystal violet assay.", "We demonstrated a rapid and transient cAMP increase after 1 pmol/l E2 stimulation in mERhigh cells; at 4\u00b0C these responses were much more reliable and robust than at 37\u00b0C (the condition most often used).", "The loss of cAMP at 37\u00b0C was not due to export.", "3-Isobutyl-1-methylxanthine (IBMX; 1 mmol/l) only partially preserved cAMP, suggesting that multiple phosphodiesterases modulate its level.", "The accumulated cAMP was consistently much higher in mERhigh cells than in mERlow cells, implicating mER-\u03b1 levels in the process.", "ICI172,780 blocked the E2-induced response and 17\u03b1-estradiol did not elicit the response, also suggesting activity through an estrogen receptor.", "E2 dose-dependent cAMP production, although biphasic in both cell types, was responsive to 50-fold higher E2 concentrations in mERhigh cells.", "Proliferation of mERlow cells was stimulated over the whole range of E2concentrations, whereas the number of mERhigh cells was greatly decreased at concentrations above 1 nmol/l, suggesting that estrogen over-stimulation can lead to cell death, as has previously been reported, and that mER-\u03b1 participates.", "E2-mediated activation of adenylyl cyclase and downstream participation of protein kinase A were shown to be involved in these responses.", "Rapid mER-\u03b1-mediated nongenomic signaling cascades generate cAMP and downstream signaling events, which contribute to the regulation of breast cancer cell number."], "structured": false}
{"doc_id": 5002665, "title": "The embryonic cell lineage of the nematode Caenorhabditis elegans.", "abstract": ["The embryonic cell lineage of Caenorhabditis elegans has been traced from zygote to newly hatched larva, with the result that the entire cell lineage of this organism is now known.", "During embryogenesis 671 cells are generated; in the hermaphrodite 113 of these (in the male 111) undergo programmed death and the remainder either differentiate terminally or become postembryonic blast cells.", "The embryonic lineage is highly invariant, as are the fates of the cells to which it gives rise.", "In spite of the fixed relationship between cell ancestry and cell fate, the correlation between them lacks much obvious pattern.", "Thus, although most neurons arise from the embryonic ectoderm, some are produced by the mesoderm and a few are sisters to muscles; again, lineal boundaries do not necessarily coincide with functional boundaries.", "Nevertheless, cell ablation experiments (as well as previous cell isolation experiments) demonstrate substantial cell autonomy in at least some sections of embryogenesis.", "We conclude that the cell lineage itself, complex as it is, plays an important role in determining cell fate.", "We discuss the origin of the repeat units (partial segments) in the body wall, the generation of the various orders of symmetry, the analysis of the lineage in terms of sublineages, and evolutionary implications."], "structured": false}
{"doc_id": 5003144, "title": "Self-Reactive B Cells in the Germinal Center Reaction.", "abstract": ["Maintenance of immunological self-tolerance requires lymphocytes carrying self-reactive antigen receptors to be selectively prevented from mounting destructive or inflammatory effector responses.", "Classically, self-tolerance is viewed in terms of the removal, editing, or silencing of B and T cells that have formed self-reactive antigen receptors during their early development.", "However, B cells activated by foreign antigen can enter germinal centers (GCs), where they further modify their antigen receptor by somatic hypermutation (SHM) of their immunoglobulin genes.", "The inevitable emergence of activated, self-reactive GC B cells presents a unique challenge to the maintenance of self-tolerance that must be rapidly countered to avoid autoantibody production.", "Here we discuss current knowledge of the mechanisms that enforce B cell self-tolerance, with particular focus on the control of self-reactive GC B cells.", "We also consider how self-reactive GC B cells can escape self-tolerance to initiate autoantibody production or instead be redeemed via SHM and used in productive antibody responses."], "structured": false}
{"doc_id": 5035827, "title": "Chronic inflammation (inflammaging) and its potential contribution to age-associated diseases.", "abstract": ["Human aging is characterized by a chronic, low-grade inflammation, and this phenomenon has been termed as \"inflammaging.", "\"", "Inflammaging is a highly significant risk factor for both morbidity and mortality in the elderly people, as most if not all age-related diseases share an inflammatory pathogenesis.", "Nevertheless, the precise etiology of inflammaging and its potential causal role in contributing to adverse health outcomes remain largely unknown.", "The identification of pathways that control age-related inflammation across multiple systems is therefore important in order to understand whether treatments that modulate inflammaging may be beneficial in old people.", "The session on inflammation of the Advances in Gerosciences meeting held at the National Institutes of Health/National Institute on Aging in Bethesda on October 30 and 31, 2013 was aimed at defining these important unanswered questions about inflammaging.", "This article reports the main outcomes of this session."], "structured": false}
{"doc_id": 5035851, "title": "Cryptochromes Enabling Plants and Animals to Determine Circadian Time", "abstract": ["Cryptochromes are flavin-containing blue light photoreceptors related to photolyases-they are found in both plants and animals and have recently been described for bacteria.", "In plants, cryptochromes perform a variety of functions including the entrainment of circadian rhythms.", "They serve a similar role in Drosophila and mammals, where the cryptochromes also perform an additional function as an essential component of the circadian clock."], "structured": false}
{"doc_id": 5085118, "title": "Neural crest-derived stem cells migrate and differentiate into cardiomyocytes after myocardial infarction.", "abstract": ["OBJECTIVE We recently demonstrated that primitive neural crest-derived (NC) cells migrate from the cardiac neural crest during embryonic development and remain in the heart as dormant stem cells, with the capacity to differentiate into various cell types, including cardiomyocytes.", "Here, we examined the migration and differentiation potential of these cells on myocardial infarction (MI).   \n", "METHODS AND RESULTS We obtained double-transgenic mice by crossing protein-0 promoter-Cre mice with Floxed-enhanced green fluorescent protein mice, in which the NC cells express enhanced green fluorescent protein.", "In the neonatal heart, NC stem cells (NCSCs) were localized predominantly in the outflow tract, but they were also distributed in a gradient from base to apex throughout the ventricular myocardium.", "Time-lapse video analysis revealed that the NCSCs were migratory.", "Some NCSCs persisted in the adult heart.", "On MI, NCSCs accumulated at the ischemic border zone area (BZA), which expresses monocyte chemoattractant protein-1 (MCP-1).", "Ex vivo cell migration assays demonstrated that MCP-1 induced NCSC migration and that this chemotactic effect was significantly depressed by an anti-MCP-1 antibody.", "Small NC cardiomyocytes first appeared in the BZA 2 weeks post-MI and gradually increased in number thereafter.   \n", "CONCLUSIONS These results suggested that NCSCs migrate into the BZA via MCP-1/CCR2 signaling and contribute to the provision of cardiomyocytes for cardiac regeneration after MI."], "structured": true}
{"doc_id": 5094468, "title": "Mitochondria as sensors and regulators of calcium signalling", "abstract": ["During the past two decades calcium (Ca2+) accumulation in energized mitochondria has emerged as a biological process of utmost physiological relevance.", "Mitochondrial Ca2+ uptake was shown to control intracellular Ca2+ signalling, cell metabolism, cell survival and other cell-type specific functions by buffering cytosolic Ca2+ levels and regulating mitochondrial effectors.", "Recently, the identity of mitochondrial Ca2+ transporters has been revealed, opening new perspectives for investigation and molecular intervention."], "structured": false}
{"doc_id": 5099266, "title": "Caspase-11 promotes the fusion of phagosomes harboring pathogenic bacteria with lysosomes by modulating actin polymerization.", "abstract": ["Inflammasomes are multiprotein complexes that include members of the NLR (nucleotide-binding domain leucine-rich repeat containing) family and caspase-1.", "Once bacterial molecules are sensed within the macrophage, the inflammasome is assembled, mediating the activation of caspase-1.", "Caspase-11 mediates caspase-1 activation in response to lipopolysaccharide and bacterial toxins, and yet its role during bacterial infection is unknown.", "Here, we demonstrated that caspase-11 was dispensable for caspase-1 activation in response to Legionella, Salmonella, Francisella, and Listeria.", "We also determined that active mouse caspase-11 was required for restriction of L. pneumophila infection.", "Similarly, human caspase-4 and caspase-5, homologs of mouse caspase-11, cooperated to restrict L. pneumophila infection in human macrophages.", "Caspase-11 promoted the fusion of the L. pneumophila vacuole with lysosomes by modulating actin polymerization through cofilin.", "However, caspase-11 was dispensable for the fusion of lysosomes with phagosomes containing nonpathogenic bacteria, uncovering a fundamental difference in the trafficking of phagosomes according to their cargo."], "structured": false}
{"doc_id": 5106691, "title": "Adipocyte inflammation is essential for healthy adipose tissue expansion and remodeling.", "abstract": ["Chronic inflammation constitutes an important link between obesity and its pathophysiological sequelae.", "In contrast to the belief that inflammatory signals exert a fundamentally negative impact on metabolism, we show that proinflammatory signaling in the adipocyte is in fact required for proper adipose tissue remodeling and expansion.", "Three mouse models with an adipose tissue-specific reduction in proinflammatory potential were generated that display a reduced capacity for adipogenesis in vivo, while the differentiation potential is unaltered in vitro.", "Upon high-fat-diet exposure, the expansion of visceral adipose tissue is prominently affected.", "This is associated with decreased intestinal barrier function, increased hepatic steatosis, and metabolic dysfunction.", "An impaired local proinflammatory response in the adipocyte leads to increased ectopic lipid accumulation, glucose intolerance, and systemic inflammation.", "Adipose tissue inflammation is therefore an adaptive response that enables safe storage of excess nutrients and contributes to a visceral depot barrier that effectively filters gut-derived endotoxin."], "structured": false}
{"doc_id": 5107861, "title": "Chronic variable stress activates hematopoietic stem cells", "abstract": ["Exposure to psychosocial stress is a risk factor for many diseases, including atherosclerosis.", "Although incompletely understood, interaction between the psyche and the immune system provides one potential mechanism linking stress and disease inception and progression.", "Known cross-talk between the brain and immune system includes the hypothalamic-pituitary-adrenal axis, which centrally drives glucocorticoid production in the adrenal cortex, and the sympathetic-adrenal-medullary axis, which controls stress-induced catecholamine release in support of the fight-or-flight reflex.", "It remains unknown, however, whether chronic stress changes hematopoietic stem cell activity.", "Here we show that stress increases proliferation of these most primitive hematopoietic progenitors, giving rise to higher levels of disease-promoting inflammatory leukocytes.", "We found that chronic stress induced monocytosis and neutrophilia in humans.", "While investigating the source of leukocytosis in mice, we discovered that stress activates upstream hematopoietic stem cells.", "Under conditions of chronic variable stress in mice, sympathetic nerve fibers released surplus noradrenaline, which signaled bone marrow niche cells to decrease CXCL12 levels through the \u03b23-adrenergic receptor.", "Consequently, hematopoietic stem cell proliferation was elevated, leading to an increased output of neutrophils and inflammatory monocytes.", "When atherosclerosis-prone Apoe(-/-) mice were subjected to chronic stress, accelerated hematopoiesis promoted plaque features associated with vulnerable lesions that cause myocardial infarction and stroke in humans."], "structured": false}
{"doc_id": 5108807, "title": "CNTF reverses obesity-induced insulin resistance by activating skeletal muscle AMPK", "abstract": ["Ciliary neurotrophic factor (CNTF) induces weight loss and improves glucose tolerance in humans and rodents.", "CNTF is thought to act centrally by inducing hypothalamic neurogenesis to modulate food intake and peripherally by altering hepatic gene expression, in a manner similar to that of leptin.", "Here, we show that CNTF signals through the CNTFR\u03b1\u2013IL-6R\u2013gp130\u03b2 receptor complex to increase fatty-acid oxidation and reduce insulin resistance in skeletal muscle by activating AMP-activated protein kinase (AMPK), independent of signaling through the brain.", "Thus, our findings further show that the antiobesogenic effects of CNTF in the periphery result from direct effects on skeletal muscle, and that these peripheral effects are not suppressed by diet-induced or genetic models of obesity, an essential requirement for the therapeutic treatment of obesity-related diseases."], "structured": false}
{"doc_id": 5114282, "title": "The Global Spread of Hepatitis C Virus 1a and 1b: A Phylodynamic and Phylogeographic Analysis", "abstract": ["BACKGROUND Hepatitis C virus (HCV) is estimated to affect 130-180 million people worldwide.", "Although its origin is unknown, patterns of viral diversity suggest that HCV genotype 1 probably originated from West Africa.", "Previous attempts to estimate the spatiotemporal parameters of the virus, both globally and regionally, have suggested that epidemic HCV transmission began in 1900 and grew steadily until the late 1980s.", "However, epidemiological data suggest that the expansion of HCV may have occurred after the Second World War.", "The aim of our study was to elucidate the timescale and route of the global spread of HCV.   \n", "METHODS AND FINDINGS We show that the rarely sequenced HCV region (E2P7NS2) is more informative for molecular epidemiology studies than the more commonly used NS5B region.", "We applied phylodynamic methods to a substantial set of new E2P7NS2 and NS5B sequences, together with all available global HCV sequences with information in both of these genomic regions, in order to estimate the timescale and nature of the global expansion of the most prevalent HCV subtypes, 1a and 1b.", "We showed that transmission of subtypes 1a and 1b \"exploded\" between 1940 and 1980, with the spread of 1b preceding that of 1a by at least 16 y (95% confidence interval 15-17).", "Phylogeographic analysis of all available NS5B sequences suggests that HCV subtypes 1a and 1b disseminated from the developed world to the developing countries.   \n", "CONCLUSIONS The evolutionary rate of HCV appears faster than previously suggested.", "The global spread of HCV coincided with the widespread use of transfused blood and blood products and with the expansion of intravenous drug use but slowed prior to the wide implementation of anti-HCV screening.", "Differences in the transmission routes associated with subtypes 1a and 1b provide an explanation of the relatively earlier expansion of 1b.", "Our data show that the most plausible route of the HCV dispersal was from developed countries to the developing world.", "Please see later in the article for the Editors' Summary."], "structured": true}
{"doc_id": 5114940, "title": "Pharmacological interventions for smoking cessation: an overview and network meta-analysis.", "abstract": ["BACKGROUND Smoking is the leading preventable cause of illness and premature death worldwide.", "Some medications have been proven to help people to quit, with three licensed for this purpose in Europe and the USA: nicotine replacement therapy (NRT), bupropion, and varenicline.", "Cytisine (a treatment pharmacologically similar to varenicline) is also licensed for use in Russia and some of the former socialist economy countries.", "Other therapies, including nortriptyline, have also been tested for effectiveness.   \n", "OBJECTIVES How do NRT, bupropion and varenicline compare with placebo and with each other in achieving long-term abstinence (six months or longer)?", "How do the remaining treatments compare with placebo in achieving long-term abstinence?", "How do the risks of adverse and serious adverse events (SAEs) compare between the treatments, and are there instances where the harms may outweigh the benefits?   \n", "METHODS The overview is restricted to Cochrane reviews, all of which include randomised trials.", "Participants are usually adult smokers, but we exclude reviews of smoking cessation for pregnant women and in particular disease groups or specific settings.", "We cover nicotine replacement therapy (NRT), antidepressants (bupropion and nortriptyline), nicotine receptor partial agonists (varenicline and cytisine), anxiolytics, selective type 1 cannabinoid receptor antagonists (rimonabant), clonidine, lobeline, dianicline, mecamylamine, Nicobrevin, opioid antagonists, nicotine vaccines, and silver acetate.", "Our outcome for benefit is continuous or prolonged abstinence at least six months from the start of treatment.", "Our outcome for harms is the incidence of serious adverse events associated with each of the treatments.", "We searched the Cochrane Database of Systematic Reviews (CDSR) in The Cochrane Library, for any reviews with 'smoking' in the title, abstract or keyword fields.", "The last search was conducted in November 2012.", "We assessed methodological quality using a revised version of the AMSTAR scale.", "For NRT, bupropion and varenicline we conducted network meta-analyses, comparing each with the others and with placebo for benefit, and varenicline and bupropion for risks of serious adverse events.   \n", "MAIN RESULTS We identified 12 treatment-specific reviews.", "The analyses covered 267 studies, involving 101,804 participants.", "Both NRT and bupropion were superior to placebo (odds ratios (OR) 1.84; 95% credible interval (CredI) 1.71 to 1.99, and 1.82; 95% CredI 1.60 to 2.06 respectively).", "Varenicline increased the odds of quitting compared with placebo (OR 2.88; 95% CredI 2.40 to 3.47).", "Head-to-head comparisons between bupropion and NRT showed equal efficacy (OR 0.99; 95% CredI 0.86 to 1.13).", "Varenicline was superior to single forms of NRT (OR 1.57; 95% CredI 1.29 to 1.91), and to bupropion (OR 1.59; 95% CredI 1.29 to 1.96).", "Varenicline was more effective than nicotine patch (OR 1.51; 95% CredI 1.22 to 1.87), than nicotine gum (OR 1.72; 95% CredI 1.38 to 2.13), and than 'other' NRT (inhaler, spray, tablets, lozenges; OR 1.42; 95% CredI 1.12 to 1.79), but was not more effective than combination NRT (OR 1.06; 95% CredI 0.75 to 1.48).", "Combination NRT also outperformed single formulations.", "The four categories of NRT performed similarly against each other, apart from 'other' NRT, which was marginally more effective than NRT gum (OR 1.21; 95% CredI 1.01 to 1.46).", "Cytisine (a nicotine receptor partial agonist) returned positive findings (risk ratio (RR) 3.98; 95% CI 2.01 to 7.87), without significant adverse events or SAEs.", "Across the 82 included and excluded bupropion trials, our estimate of six seizures in the bupropion arms versus none in the placebo arms was lower than the expected rate (1:1000), at about 1:1500.", "SAE meta-analysis of the bupropion studies demonstrated no excess of neuropsychiatric (RR 0.88; 95% CI 0.31 to 2.50) or cardiovascular events (RR 0.77; 95% CI 0.37 to 1.59).", "SAE meta-analysis of 14 varenicline trials found no difference between the varenicline and placebo arms (RR 1.06; 95% CI 0.72 to 1.55), and subgroup analyses detected no significant excess of neuropsychiatric events (RR 0.53; 95% CI 0.17 to 1.67), or of cardiac events (RR 1.26; 95% CI 0.62 to 2.56).", "Nortriptyline increased the chances of quitting (RR 2.03; 95% CI 1.48 to 2.78).", "Neither nortriptyline nor bupropion were shown to enhance the effect of NRT compared with NRT alone.", "Clonidine increased the chances of quitting (RR 1.63; 95% CI 1.22 to 2.18), but this was offset by a dose-dependent rise in adverse events.", "Mecamylamine in combination with NRT may increase the chances of quitting, but the current evidence is inconclusive.", "Other treatments failed to demonstrate a benefit compared with placebo.", "Nicotine vaccines are not yet licensed for use as an aid to smoking cessation or relapse prevention.", "Nicobrevin's UK license is now revoked, and the manufacturers of rimonabant, taranabant and dianicline are no longer supporting the development or testing of these treatments.   ", "AUTHORS' CONCLUSIONS NRT, bupropion, varenicline and cytisine have been shown to improve the chances of quitting.", "Combination NRT and varenicline are equally effective as quitting aids.", "Nortriptyline also improves the chances of quitting.", "On current evidence, none of the treatments appear to have an incidence of adverse events that would mitigate their use.", "Further research is warranted into the safety of varenicline and into cytisine's potential as an effective and affordable treatment, but not into the efficacy and safety of NRT."], "structured": true}
{"doc_id": 5116145, "title": "A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters.", "abstract": ["The sequence specificity of DNA-binding proteins is the primary mechanism by which the cell recognizes genomic features.", "Here, we describe systematic determination of yeast transcription factor DNA-binding specificities.", "We obtained binding specificities for 112 DNA-binding proteins representing 19 distinct structural classes.", "One-third of the binding specificities have not been previously reported.", "Several binding sequences have striking genomic distributions relative to transcription start sites, supporting their biological relevance and suggesting a role in promoter architecture.", "Among these are Rsc3 binding sequences, containing the core CGCG, which are found preferentially approximately 100 bp upstream of transcription start sites.", "Mutation of RSC3 results in a dramatic increase in nucleosome occupancy in hundreds of proximal promoters containing a Rsc3 binding element, but has little impact on promoters lacking Rsc3 binding sequences, indicating that Rsc3 plays a broad role in targeting nucleosome exclusion at yeast promoters."], "structured": false}
{"doc_id": 5123516, "title": "EphA3 maintains tumorigenicity and is a therapeutic target in glioblastoma multiforme.", "abstract": ["Significant endeavor has been applied to identify functional therapeutic targets in glioblastoma (GBM) to halt the growth of this aggressive cancer.", "We show that the receptor tyrosine kinase EphA3 is frequently overexpressed in GBM and, in particular, in the most aggressive mesenchymal subtype.", "Importantly, EphA3 is highly expressed on the tumor-initiating cell population in glioma and appears critically involved in maintaining tumor cells in a less differentiated state by modulating mitogen-activated protein kinase signaling.", "EphA3 knockdown or depletion of EphA3-positive tumor cells reduced tumorigenic potential to a degree comparable to treatment with a therapeutic radiolabelled EphA3-specific monoclonal antibody.", "These results identify EphA3 as a functional, targetable receptor in GBM."], "structured": false}
{"doc_id": 5132358, "title": "Chimeric antigen receptor-modified T cells for acute lymphoid leukemia.", "abstract": ["Chimeric antigen receptor-modified T cells with specificity for CD19 have shown promise in the treatment of chronic lymphocytic leukemia (CLL).", "It remains to be established whether chimeric antigen receptor T cells have clinical activity in acute lymphoblastic leukemia (ALL).", "Two children with relapsed and refractory pre-B-cell ALL received infusions of T cells transduced with anti-CD19 antibody and a T-cell signaling molecule (CTL019 chimeric antigen receptor T cells), at a dose of 1.4\u00d710(6) to 1.2\u00d710(7) CTL019 cells per kilogram of body weight.", "In both patients, CTL019 T cells expanded to a level that was more than 1000 times as high as the initial engraftment level, and the cells were identified in bone marrow.", "In addition, the chimeric antigen receptor T cells were observed in the cerebrospinal fluid (CSF), where they persisted at high levels for at least 6 months.", "Eight grade 3 or 4 adverse events were noted.", "The cytokine-release syndrome and B-cell aplasia developed in both patients.", "In one child, the cytokine-release syndrome was severe; cytokine blockade with etanercept and tocilizumab was effective in reversing the syndrome and did not prevent expansion of chimeric antigen receptor T cells or reduce antileukemic efficacy.", "Complete remission was observed in both patients and is ongoing in one patient at 11 months after treatment.", "The other patient had a relapse, with blast cells that no longer expressed CD19, approximately 2 months after treatment.", "Chimeric antigen receptor-modified T cells are capable of killing even aggressive, treatment-refractory acute leukemia cells in vivo.", "The emergence of tumor cells that no longer express the target indicates a need to target other molecules in addition to CD19 in some patients with ALL."], "structured": false}
{"doc_id": 5132461, "title": "Extended-connectivity fingerprints.", "abstract": ["Extended-connectivity fingerprints (ECFPs) are a novel class of topological fingerprints for molecular characterization.", "Historically, topological fingerprints were developed for substructure and similarity searching.", "ECFPs were developed specifically for structure-activity modeling.", "ECFPs are circular fingerprints with a number of useful qualities: they can be very rapidly calculated; they are not predefined and can represent an essentially infinite number of different molecular features (including stereochemical information); their features represent the presence of particular substructures, allowing easier interpretation of analysis results; and the ECFP algorithm can be tailored to generate different types of circular fingerprints, optimized for different uses.", "While the use of ECFPs has been widely adopted and validated, a description of their implementation has not previously been presented in the literature."], "structured": false}
{"doc_id": 5137019, "title": "Suppressor of cytokine signaling 3 inhibits antiviral IFN-beta signaling to enhance HIV-1 replication in macrophages.", "abstract": ["HIV-1 replication within macrophages of the CNS often results in cognitive and motor impairment, which is known as HIV-associated dementia (HAD) in its most severe form.", "IFN-beta suppresses viral replication within these cells during early CNS infection, but the effect is transient.", "HIV-1 eventually overcomes this protective innate immune response to resume replication through an unknown mechanism, initiating the progression toward HAD.", "In this article, we show that Suppressor of Cytokine Signaling (SOCS)3, a molecular inhibitor of IFN signaling, may allow HIV-1 to evade innate immunity within the CNS.", "We found that SOCS3 is elevated in an in vivo SIV/macaque model of HAD and that the pattern of expression correlates with recurrence of viral replication and onset of CNS disease.", "In vitro, the HIV-1 regulatory protein transactivator of transcription induces SOCS3 in human and murine macrophages in a NF-kappaB-dependent manner.", "SOCS3 expression attenuates the response of macrophages to IFN-beta at proximal levels of pathway activation and downstream antiviral gene expression and consequently overcomes the inhibitory effect of IFN-beta on HIV-1 replication.", "These studies indicate that SOCS3 expression, induced by stimuli present in the HIV-1-infected brain, such as transactivator of transcription, inhibits antiviral IFN-beta signaling to enhance HIV-1 replication in macrophages.", "This consequence of SOCS3 expression in vitro, supported by a correlation with increased viral load and onset of CNS disease in vivo, suggests that SOCS3 may allow HIV-1 to evade the protective innate immune response within the CNS, allowing the recurrence of viral replication and, ultimately, promoting progression toward HAD."], "structured": false}
{"doc_id": 5144381, "title": "Molecular model of the human 26S proteasome.", "abstract": ["The 26S proteasome plays a fundamental role in eukaryotic homeostasis by undertaking the highly controlled degradation of a wide range of proteins, including key cellular regulators such as those controlling cell-cycle progression and apoptosis.", "Here we report the structure of the human 26S proteasome determined by cryo-electron microscopy and single-particle analysis, with secondary structure elements identified both in the 20S proteolytic core region and in the 19S regulatory particle.", "We have used this information together with crystal structures, homology models, and other biochemical information to construct a molecular model of the complete 26S proteasome.", "This model allows for a detailed description of the 20S core within the 26S proteasome and redefines the overall assignment of subunits within the 19S regulatory particle.", "The information presented here provides a strong basis for a mechanistic understanding of the 26S proteasome."], "structured": false}
{"doc_id": 5145974, "title": "Urinary bisphenol A concentrations and early reproductive health outcomes among women undergoing IVF.", "abstract": ["STUDY QUESTION In women undergoing IVF, are urinary bisphenol A (BPA) concentrations associated with ovarian response and early reproductive outcomes, including oocyte maturation and fertilization, Day 3 embryo quality and blastocyst formation?   ", "SUMMARY ANSWER Higher urinary BPA concentrations were found to be associated with decreased ovarian response, number of fertilized oocytes and decreased blastocyst formation.   ", "WHAT IS KNOWN ALREADY Experimental animal and in vitro studies have reported associations between BPA exposure and adverse reproductive outcomes.", "We previously reported an association between urinary BPA and decreased ovarian response [peak serum estradiol (E(2)) and oocyte count at the time of retrieval] in women undergoing IVF; however, there are limited human data on reproductive health outcomes, such as fertilization and embryo development.   ", "STUDY DESIGN, SIZE AND DURATION Prospective preconception cohort study.", "One hundred and seventy-four women aged 18-45 years and undergoing 237 IVF cycles were recruited at the Massachusetts General Hospital Fertility Center, Boston, MA, USA, between November 2004 and August 2010.", "These women were followed until they either had a live birth or discontinued treatment.", "Cryothaw and donor egg cycles were not included in the analysis.   \n", "PARTICIPANTS/MATERIALS, SETTING AND METHODS Urinary BPA concentrations were measured by online solid-phase extraction-high-performance liquid chromatography-isotope dilution-tandem mass spectrometry.", "Mixed effect models, poisson regression and multivariate logistic regression models were used wherever appropriate to evaluate the association between cycle-specific urinary BPA concentrations and measures of ovarian response, oocyte maturation (metaphase II), fertilization, embryo quality and cleavage rate.", "We accounted for correlation among multiple IVF cycles in the same woman using generalized estimating equations.   \n", "MAIN RESULTS AND THE ROLE OF CHANCE The geometric mean (SD) for urinary BPA concentrations was 1.50 (2.22) \u00b5g/l.", "After adjustment for age and other potential confounders (Day 3 serum FSH, smoking, BMI), there was a significant linear dose-response association between increased urinary BPA concentrations and decreased number of oocytes (overall and mature), decreased number of normally fertilized oocytes and decreased E(2) levels (mean decreases of 40, 253 and 471 pg/ml for urinary BPA quartiles 2, 3 and 4, when compared with the lowest quartile, respectively; P-value for trend = 0.001).", "The mean number of oocytes and normally fertilized oocytes decreased by 24 and 27%, respectively, for the highest versus the lowest quartile of urinary BPA (trend test P < 0.001 and 0.002, respectively).", "Women with urinary BPA above the lowest quartile had decreased blastocyst formation (trend test P-value = 0.08).   ", "LIMITATIONS AND REASONS FOR CAUTION Potential limitations include exposure misclassification due to the very short half-life of BPA and its high variability over time; uncertainty about the generalizability of the results to the general population of women conceiving naturally and limited sample.   ", "WIDER IMPLICATIONS OF THE FINDINGS The results from this extended study, using IVF as a model to study early reproductive health outcomes in humans, indicate a negative dose-response association between urinary BPA concentrations and serum peak E(2) and oocyte yield, confirming our previous findings.", "In addition, we found significantly decreased metaphase II oocyte count and number of normally fertilizing oocytes and a suggestive association between BPA urinary concentrations and decreased blastocyst formation, thus indicating that BPA may alter reproductive function in susceptible women undergoing IVF.   ", "STUDY FUNDING/COMPETING INTEREST(S) This work was supported by grants ES009718 and ES000002 from the National Institute of Environmental Health Sciences and grant OH008578 from the National Institute for Occupational Safety and Health.", "None of the authors has actual or potential competing financial interests.   ", "DISCLAIMER The findings and conclusions in this report are those of the authors and do not necessarily represent the views of the Centers for Disease Control and Prevention."], "structured": true}
{"doc_id": 5151024, "title": "Cost-effectiveness of options for the diagnosis of high blood pressure in primary care: a modelling study.", "abstract": ["BACKGROUND The diagnosis of hypertension has traditionally been based on blood-pressure measurements in the clinic, but home and ambulatory measurements better correlate with cardiovascular outcome, and ambulatory monitoring is more accurate than both clinic and home monitoring in diagnosing hypertension.", "We aimed to compare the cost-effectiveness of different diagnostic strategies for hypertension.   \n", "METHODS We did a Markov model-based probabilistic cost-effectiveness analysis.", "We used a hypothetical primary-care population aged 40 years or older with a screening blood-pressure measurement greater than 140/90 mm Hg and risk-factor prevalence equivalent to the general population.", "We compared three diagnostic strategies-further blood pressure measurement in the clinic, at home, and with an ambulatory monitor-in terms of lifetime costs, quality-adjusted life years, and cost-effectiveness.   \n", "FINDINGS Ambulatory monitoring was the most cost-effective strategy for the diagnosis of hypertension for men and women of all ages.", "It was cost-saving for all groups (from -\u00a356 [95% CI -105 to -10] in men aged 75 years to -\u00a3323 [-389 to -222] in women aged 40 years) and resulted in more quality-adjusted life years for men and women older than 50 years (from 0\u00b7006 [0\u00b7000 to 0\u00b7015] for women aged 60 years to 0\u00b7022 [0\u00b7012 to 0\u00b7035] for men aged 70 years).", "This finding was robust when assessed with a wide range of deterministic sensitivity analyses around the base case, but was sensitive if home monitoring was judged to have equal test performance to ambulatory monitoring or if treatment was judged effective irrespective of whether an individual was hypertensive.   \n", "INTERPRETATION Ambulatory monitoring as a diagnostic strategy for hypertension after an initial raised reading in the clinic would reduce misdiagnosis and save costs.", "Additional costs from ambulatory monitoring are counterbalanced by cost savings from better targeted treatment.", "Ambulatory monitoring is recommended for most patients before the start of antihypertensive drugs.   \n", "FUNDING National Institute for Health Research and the National Institute for Health and Clinical Excellence."], "structured": true}
{"doc_id": 5152028, "title": "Folic acid improves endothelial function in coronary artery disease via mechanisms largely independent of homocysteine lowering.", "abstract": ["BACKGROUND Homocysteine is a risk factor for coronary artery disease (CAD), although a causal relation remains to be proven.", "The importance of determining direct causality rests in the fact that plasma homocysteine can be safely and inexpensively reduced by 25% with folic acid.", "This reduction is maximally achieved by doses of 0.4 mg/d.", "High-dose folic acid (5 mg/d) improves endothelial function in CAD, although the mechanism is controversial.", "It has been proposed that improvement occurs through reduction in total (tHcy) or free (non-protein bound) homocysteine (fHcy).", "We investigated the effects of folic acid on endothelial function before a change in homocysteine in patients with CAD.   \n", "METHODS AND RESULTS A randomized, placebo-controlled study of folic acid (5 mg/d) for 6 weeks was undertaken in 33 patients.", "Endothelial function, assessed by flow-mediated dilatation (FMD), was measured before, at 2 and 4 hours after the first dose of folic acid, and after 6 weeks of treatment.", "Plasma folate increased markedly by 1 hour (200 compared with 25.8 nmol/L; P<0.001).", "FMD improved at 2 hours (83 compared with 47 microm; P<0.001) and was largely complete by 4 hours (101 compared with 51 microm; P<0.001).", "tHcy did not significantly differ acutely (4-hour tHcy, 9.56 compared with 9.79 micromol/L; P=NS).", "fHcy did not differ at 3 hours but was slightly reduced at 4 hours (1.55 compared with 1.78 micromol/L; P=0.02).", "FMD improvement did not correlate with reductions in either fHcy or tHcy at any time.   \n", "CONCLUSIONS These data suggest that folic acid improves endothelial function in CAD acutely by a mechanism largely independent of homocysteine."], "structured": true}
{"doc_id": 5172048, "title": "Focal adhesion kinase links mechanical force to skin fibrosis via inflammatory signaling", "abstract": ["Exuberant fibroproliferation is a common complication after injury for reasons that are not well understood.", "One key component of wound repair that is often overlooked is mechanical force, which regulates cell-matrix interactions through intracellular focal adhesion components, including focal adhesion kinase (FAK).", "Here we report that FAK is activated after cutaneous injury and that this process is potentiated by mechanical loading.", "Fibroblast-specific FAK knockout mice have substantially less inflammation and fibrosis than control mice in a model of hypertrophic scar formation.", "We show that FAK acts through extracellular-related kinase (ERK) to mechanically trigger the secretion of monocyte chemoattractant protein-1 (MCP-1, also known as CCL2), a potent chemokine that is linked to human fibrotic disorders.", "Similarly, MCP-1 knockout mice form minimal scars, indicating that inflammatory chemokine pathways are a major mechanism by which FAK mechanotransduction induces fibrosis.", "Small-molecule inhibition of FAK blocks these effects in human cells and reduces scar formation in vivo through attenuated MCP-1 signaling and inflammatory cell recruitment.", "These findings collectively indicate that physical force regulates fibrosis through inflammatory FAK\u2013ERK\u2013MCP-1 pathways and that molecular strategies targeting FAK can effectively uncouple mechanical force from pathologic scar formation."], "structured": false}
{"doc_id": 5185871, "title": "Prognostic Accuracy of the SOFA Score, SIRS Criteria, and qSOFA Score for In-Hospital Mortality Among Adults With Suspected Infection Admitted to the Intensive Care Unit", "abstract": ["Importance The Sepsis-3 Criteria emphasized the value of a change of 2 or more points in the Sequential [Sepsis-related] Organ Failure Assessment (SOFA) score, introduced quick SOFA (qSOFA), and removed the systemic inflammatory response syndrome (SIRS) criteria from the sepsis definition.", "Objective Externally validate and assess the discriminatory capacities of an increase in SOFA score by 2 or more points, 2 or more SIRS criteria, or a qSOFA score of 2 or more points for outcomes among patients who are critically ill with suspected infection.", "Design, Setting, and Participants Retrospective cohort analysis of 184 875 patients with an infection-related primary admission diagnosis in 182 Australian and New Zealand intensive care units (ICUs) from 2000 through 2015.", "Exposures SOFA, qSOFA, and SIRS criteria applied to data collected within 24 hours of ICU admission.", "Main Outcomes and Measures The primary outcome was in-hospital mortality.", "In-hospital mortality or ICU length of stay (LOS) of 3 days or more was a composite secondary outcome.", "Discrimination was assessed using the area under the receiver operating characteristic curve (AUROC).", "Adjusted analyses were performed using a model of baseline risk determined using variables independent of the scoring systems.", "Results Among 184 875 patients (mean age, 62.9 years [SD, 17.4]; women, 82 540 [44.6%]; most common diagnosis bacterial pneumonia, 32 634 [17.7%]), a total of 34 578 patients (18.7%) died in the hospital, and 102 976 patients (55.7%) died or experienced an ICU LOS of 3 days or more.", "SOFA score increased by 2 or more points in 90.1%; 86.7% manifested 2 or more SIRS criteria, and 54.4% had a qSOFA score of 2 or more points.", "SOFA demonstrated significantly greater discrimination for in-hospital mortality (crude AUROC, 0.753 [99% CI, 0.750-0.757]) than SIRS criteria (crude AUROC, 0.589 [99% CI, 0.585-0.593]) or qSOFA (crude AUROC, 0.607 [99% CI, 0.603-0.611]).", "Incremental improvements were 0.164 (99% CI, 0.159-0.169) for SOFA vs SIRS criteria and 0.146 (99% CI, 0.142-0.151) for SOFA vs qSOFA (P <.001).", "SOFA (AUROC, 0.736 [99% CI, 0.733-0.739]) outperformed the other scores for the secondary end point (SIRS criteria: AUROC, 0.609 [99% CI, 0.606-0.612]; qSOFA: AUROC, 0.606 [99% CI, 0.602-0.609]).", "Incremental improvements were 0.127 (99% CI, 0.123-0.131) for SOFA vs SIRS criteria and 0.131 (99% CI, 0.127-0.134) for SOFA vs qSOFA (P <.001).", "Findings were consistent for both outcomes in multiple sensitivity analyses.", "Conclusions and Relevance Among adults with suspected infection admitted to an ICU, an increase in SOFA score of 2 or more had greater prognostic accuracy for in-hospital mortality than SIRS criteria or the qSOFA score.", "These findings suggest that SIRS criteria and qSOFA may have limited utility for predicting mortality in an ICU setting."], "structured": false}
{"doc_id": 5222182, "title": "Predictors of mammographic density: insights gained from a novel regression analysis of a twin study.", "abstract": ["Understanding which factors influence mammographically dense and nondense areas is important because percent mammographic density adjusted for age is a strong, continuously distributed risk factor for breast cancer, especially when adjusted for weight or body mass index.", "Using computer-assisted methods, we measured mammographically dense areas for 571 monozygotic and 380 dizygotic Australian and North American twin pairs ages 40 to 70 years.", "We used a novel regression modeling approach in which each twin's measure of dense and nondense area was regressed against one or both of the twin's and co-twin's covariates.", "The nature of changes to regression estimates with the inclusion of the twin and/or co-twin's covariates can be evaluated for consistency with causal and/or other models.", "By causal, we mean that if it were possible to vary a covariate experimentally then the expected value of the outcome measure would change.", "After adjusting for the individual's weight, the co-twin associations with weight were attenuated, consistent with a causal effect of weight on mammographic measures, which in absolute log cm(2)/kg was thrice stronger for nondense than dense area.", "After adjusting for weight, later age at menarche, and greater height were associated with greater dense and lesser nondense areas in a manner inconsistent with causality.", "The associations of dense and nondense areas with parity are consistent with a causal effect and/or within-person confounding.", "The associations between mammographic density measures and height are consistent with shared early life environmental factors that predispose to both height and percent mammographic density and possibly breast cancer risk."], "structured": false}
{"doc_id": 5223817, "title": "Shaping the landscape of the Escherichia coli chromosome: replication-transcription encounters in cells with an ectopic replication origin", "abstract": ["Each cell division requires the unwinding of millions of DNA base pairs to allow chromosome duplication and gene transcription.", "As DNA replication and transcription share the same template, conflicts between both processes are unavoidable and head-on collisions are thought to be particularly problematic.", "Surprisingly, a recent study reported unperturbed cell cycle progression in Escherichia coli cells with an ectopic replication origin in which highly transcribed rrn operons were forced to be replicated opposite to normal.", "In this study we have re-generated a similar strain and found the doubling time to be twice that of normal cells.", "Replication profiles of this background revealed significant deviations in comparison to wild-type profiles, particularly in highly transcribed regions and the termination area.", "These deviations were alleviated by mutations that either inactivate the termination area or destabilise RNA polymerase complexes and allow their easier displacement by replication forks.", "Our data demonstrate that head-on replication-transcription conflicts are highly problematic.", "Indeed, analysis of the replication profile of the previously published E. coli construct revealed a chromosomal rearrangement that alleviates replication-transcription conflicts in an intriguingly simple way.", "Our data support the idea that avoiding head-on collisions has significantly contributed to shaping the distinct architecture of bacterial chromosomes."], "structured": false}
{"doc_id": 5236443, "title": "Epithelial\u2013mesenchymal transitions in tumour progression", "abstract": ["Without epithelial\u2013mesenchymal transitions, in which polarized epithelial cells are converted into motile cells, multicellular organisms would be incapable of getting past the blastula stage of embryonic development.", "However, this important developmental programme has a more sinister role in tumour progression.", "Epithelial\u2013mesenchymal transition provides a new basis for understanding the progression of carcinoma towards dedifferentiated and more malignant states."], "structured": false}
{"doc_id": 5238341, "title": "Platelets at the interface of thrombosis, inflammation, and cancer.", "abstract": ["Although once primarily recognized for its roles in hemostasis and thrombosis, the platelet has been increasingly recognized as a multipurpose cell.", "Indeed, circulating platelets have the ability to influence a wide range of seemingly unrelated pathophysiologic events.", "Here, we highlight some of the notable observations that link platelets to inflammation, reinforcing the platelet's origin from a lower vertebrate cell type with both hemostatic and immunologic roles.", "In addition, we consider the relevance of platelets in cancer biology by focusing on the hallmarks of cancer and the ways platelets can influence multistep development of tumors.", "Beyond its traditional role in hemostasis and thrombosis, the platelet's involvement in the interplay between hemostasis, thrombosis, inflammation, and cancer is likely complex, yet extremely important in each disease process.", "The existence of animal models of platelet dysfunction and currently used antiplatelet therapies provide a framework for understanding mechanistic insights into a wide range of pathophysiologic events.", "Thus, the basic scientist studying platelet function can think beyond the traditional hemostasis and thrombosis paradigms, while the practicing hematologist must appreciate platelet relevance in a wide range of disease processes."], "structured": false}
{"doc_id": 5252837, "title": "Cellular roles of DNA topoisomerases: a molecular perspective", "abstract": ["DNA topoisomerases are the magicians of the DNA world \u2014 by allowing DNA strands or double helices to pass through each other, they can solve all of the topological problems of DNA in replication, transcription and other cellular transactions.", "Extensive biochemical and structural studies over the past three decades have provided molecular models of how the various subfamilies of DNA topoisomerase manipulate DNA.", "In this review, the cellular roles of these enzymes are examined from a molecular point of view."], "structured": false}
{"doc_id": 5253987, "title": "MicroRNA sponges: progress and possibilities.", "abstract": ["The microRNA (miRNA) \"sponge\" method was introduced three years ago as a means to create continuous miRNA loss of function in cell lines and transgenic organisms.", "Sponge RNAs contain complementary binding sites to a miRNA of interest, and are produced from transgenes within cells.", "As with most miRNA target genes, a sponge's binding sites are specific to the miRNA seed region, which allows them to block a whole family of related miRNAs.", "This transgenic approach has proven to be a useful tool to probe miRNA functions in a variety of experimental systems.", "Here we will discuss the ways sponge and related constructs can be optimized and review recent applications of this method with particular emphasis on stable expression in cancer studies and in transgenic animals."], "structured": false}
{"doc_id": 5254463, "title": "Wip1 phosphatase regulates p53-dependent apoptosis of stem cells and tumorigenesis in the mouse intestine.", "abstract": ["Colorectal cancer is one of the major causes of cancer-related deaths.", "To gain further insights into the mechanisms underlying its development, we investigated the role of Wip1 phosphatase, which is highly expressed in intestinal stem cells, in the mouse model of APC(Min)-driven polyposis.", "We found that Wip1 removal increased the life span of APC(Min) mice through a significant suppression of polyp formation.", "This protection was dependent on the p53 tumor suppressor, which plays a putative role in the regulation of apoptosis of intestinal stem cells.", "Activation of apoptosis in stem cells of Wip1-deficient mice, but not wild-type APC(Min) mice, increased when the Wnt pathway was constitutively activated.", "We propose, therefore, that the Wip1 phosphatase regulates homeostasis of intestinal stem cells.", "In turn, Wip1 loss suppresses APC(Min)-driven polyposis by lowering the threshold for p53-dependent apoptosis of stem cells, thus preventing their conversion into tumor-initiating stem cells."], "structured": false}
{"doc_id": 5254741, "title": "The shunt problem: control of functional shunting in normal and tumour vasculature", "abstract": ["Networks of blood vessels in normal and tumour tissues have heterogeneous structures, with widely varying blood flow pathway lengths.", "To achieve efficient blood flow distribution, mechanisms for the structural adaptation of vessel diameters must be able to inhibit the formation of functional shunts (whereby short pathways become enlarged and flow bypasses long pathways).", "Such adaptation requires information about tissue metabolic status to be communicated upstream to feeding vessels, through conducted responses.", "We propose that impaired vascular communication in tumour microvascular networks, leading to functional shunting, is a primary cause of dysfunctional microcirculation and local hypoxia in cancer.", "We suggest that anti-angiogenic treatment of tumours may restore vascular communication and thereby improve or normalize flow distribution in tumour vasculature."], "structured": false}
{"doc_id": 5256564, "title": "Pharmacological Blockade of ASCT2-dependent Glutamine Transport Leads To Anti-tumor Efficacy in Preclinical Models", "abstract": ["The unique metabolic demands of cancer cells underscore potentially fruitful opportunities for drug discovery in the era of precision medicine.", "However, therapeutic targeting of cancer metabolism has led to surprisingly few new drugs to date.", "The neutral amino acid glutamine serves as a key intermediate in numerous metabolic processes leveraged by cancer cells, including biosynthesis, cell signaling, and oxidative protection.", "Herein we report the preclinical development of V-9302, a competitive small molecule antagonist of transmembrane glutamine flux that selectively and potently targets the amino acid transporter ASCT2.", "Pharmacological blockade of ASCT2 with V-9302 resulted in attenuated cancer cell growth and proliferation, increased cell death, and increased oxidative stress, which collectively contributed to antitumor responses in vitro and in vivo.", "This is the first study, to our knowledge, to demonstrate the utility of a pharmacological inhibitor of glutamine transport in oncology, representing a new class of targeted therapy and laying a framework for paradigm-shifting therapies targeting cancer cell metabolism."], "structured": false}
{"doc_id": 5260382, "title": "An Antidepressant Decreases CSF A\u03b2 Production in Healthy Individuals and in Transgenic AD Mice", "abstract": ["Serotonin signaling suppresses generation of amyloid-\u03b2 (A\u03b2) in vitro and in animal models of Alzheimer\u2019s disease (AD).", "We show that in an aged transgenic AD mouse model (APP/PS1 plaque-bearing mice), the antidepressant citalopram, a selective serotonin reuptake inhibitor, decreased A\u03b2 in brain interstitial fluid in a dose-dependent manner.", "Growth of individual amyloid plaques was assessed in plaque-bearing mice that were chronically administered citalopram.", "Citalopram arrested the growth of preexisting plaques and reduced the appearance of new plaques by 78%.", "In healthy human volunteers, citalopram\u2019s effects on A\u03b2 production and A\u03b2 concentrations in cerebrospinal fluid (CSF) were measured prospectively using stable isotope labeling kinetics, with CSF sampling during acute dosing of citalopram.", "A\u03b2 production in CSF was slowed by 37% in the citalopram group compared to placebo.", "This change was associated with a 38% decrease in total CSF A\u03b2 concentrations in the drug-treated group.", "The ability to safely decrease A\u03b2 concentrations is potentially important as a preventive strategy for AD.", "This study demonstrates key target engagement for future AD prevention trials."], "structured": false}
{"doc_id": 5262240, "title": "Variations in the quality and sustainability of long-term glycaemic control with continuous subcutaneous insulin infusion.", "abstract": ["AIMS To investigate the pattern of changes in HbA1c in people with Type 1 diabetes managed by long-term Continuous subcutaneous insulin infusion.   \n", "METHODS We studied HbA1c changes using computerized clinic records in 35 adult people with Type 1 diabetes and an elevated HbA1c (\u2265 64 mmol/mol, 8.0%) on multiple daily insulin injections, who were then switched to continuous subcutaneous insulin infusion for at least 5 years.   \n", "RESULTS We identified three subgroups with similar baseline HbA1c but different long-term responses to pump therapy: group A--those with improvement followed by deterioration (57%); group B--those with improvement that was sustained throughout the 5 years (31%); and group C-those where HbA1c did not change significantly from baseline (12%).", "The patients in group C had a higher BMI: 31.0 \u00b1 5.2 vs. 25.9 \u00b1 3.3 vs. 25.2 \u00b1 3.1 kg/m\u00b2 (group C vs. group A and group B; P = 0.02).   \n", "CONCLUSIONS Improved glycaemic control with continuous subcutaneous insulin infusion was maintained over 5 years by 88% of people with Type 1 diabetes in this study, but there were variations in the long-term efficacy, with some people improving and worsening, others maintaining strict control and a few subcutaneous insulin infusion 'non-responders'."], "structured": true}
{"doc_id": 5266423, "title": "Historical review: megakaryopoiesis and thrombopoiesis.", "abstract": ["The study of thrombopoiesis has evolved greatly since an era when platelets were termed \"the dust of the blood,\" only about 100 years ago.", "During this time megakaryocytes were identified as the origin of blood platelets; marrow-derived megakaryocytic progenitor cells were functionally defined and then purified; and the primary regulator of the process, thrombopoietin, was cloned and characterized and therapeutic thrombopoietic agents developed.", "During this journey we continue to learn that the physiologic mechanisms that drive proplatelet formation can be recapitulated in cell-free systems and their biochemistry evaluated; the molecular underpinnings of endomitosis are being increasingly understood; the intracellular signals sent by engagement of a large number of megakaryocyte surface receptors have been defined; and many of the transcription factors that drive megakaryocytic fate determination have been identified and experimentally manipulated.", "While some of these biologic processes mimic those seen in other cell types, megakaryocytes and platelets possess enough unique developmental features that we are virtually assured that continued study of thrombopoiesis will yield innumerable clinical and scientific insights for many decades to come."], "structured": false}
{"doc_id": 5268462, "title": "Obesity and Its Metabolic Complications: The Role of Adipokines and the Relationship between Obesity, Inflammation, Insulin Resistance, Dyslipidemia and Nonalcoholic Fatty Liver Disease", "abstract": ["Accumulating evidence indicates that obesity is closely associated with an increased risk of metabolic diseases such as insulin resistance, type 2 diabetes, dyslipidemia and nonalcoholic fatty liver disease.", "Obesity results from an imbalance between food intake and energy expenditure, which leads to an excessive accumulation of adipose tissue.", "Adipose tissue is now recognized not only as a main site of storage of excess energy derived from food intake but also as an endocrine organ.", "The expansion of adipose tissue produces a number of bioactive substances, known as adipocytokines or adipokines, which trigger chronic low-grade inflammation and interact with a range of processes in many different organs.", "Although the precise mechanisms are still unclear, dysregulated production or secretion of these adipokines caused by excess adipose tissue and adipose tissue dysfunction can contribute to the development of obesity-related metabolic diseases.", "In this review, we focus on the role of several adipokines associated with obesity and the potential impact on obesity-related metabolic diseases.", "Multiple lines evidence provides valuable insights into the roles of adipokines in the development of obesity and its metabolic complications.", "Further research is still required to fully understand the mechanisms underlying the metabolic actions of a few newly identified adipokines."], "structured": false}
{"doc_id": 5270265, "title": "Combating trastuzumab resistance by targeting SRC, a common node downstream of multiple resistance pathways", "abstract": ["Trastuzumab is a successful rationally designed ERBB2-targeted therapy.", "However, about half of individuals with ERBB2-overexpressing breast cancer do not respond to trastuzumab-based therapies, owing to various resistance mechanisms.", "Clinically applicable regimens for overcoming trastuzumab resistance of different mechanisms are not yet available.", "We show that the nonreceptor tyrosine kinase c-SRC (SRC) is a key modulator of trastuzumab response and a common node downstream of multiple trastuzumab resistance pathways.", "We find that SRC is activated in both acquired and de novo trastuzumab-resistant cells and uncover a novel mechanism of SRC regulation involving dephosphorylation by PTEN.", "Increased SRC activation conferred considerable trastuzumab resistance in breast cancer cells and correlated with trastuzumab resistance in patients.", "Targeting SRC in combination with trastuzumab sensitized multiple lines of trastuzumab-resistant cells to trastuzumab and eliminated trastuzumab-resistant tumors in vivo, suggesting the potential clinical application of this strategy to overcome trastuzumab resistance."], "structured": false}
{"doc_id": 5271210, "title": "MicroRNAs: new tools for diagnosis, prognosis, and therapy in hepatocellular carcinoma?", "abstract": ["MicroRNAs (miRNAs) are evolutionarily conserved small noncoding RNAs involved in the regulation of gene expression and protein translation.", "Many studies have shown that they play a crucial role in driving organ and tissue differentiation during embryogenesis and in the fine-tuning of fundamental biological processes, such as proliferation and apoptosis.", "Growing evidence indicates that their deregulation plays an important role in cancer onset and progression as well, where they act as oncogenes or oncosuppressors.", "In this review, we highlight the most recent findings regarding the role of miRNAs in hepatocellular carcinoma (HCC) by analyzing the possible mechanisms by which they contribute to this neoplasm.", "Moreover, we discuss the possible role of circulating miRNAs as biomarkers, a field that needs urgent improvement in the clinical surveillance of HCC, and the fascinating possibility of using them as therapeutic targets or drugs themselves."], "structured": false}
{"doc_id": 5273056, "title": "A vertebrate gene, ticrr, is an essential checkpoint and replication regulator.", "abstract": ["Eukaryotes have numerous checkpoint pathways to protect genome fidelity during normal cell division and in response to DNA damage.", "Through a screen for G2/M checkpoint regulators in zebrafish, we identified ticrr (for TopBP1-interacting, checkpoint, and replication regulator), a previously uncharacterized gene that is required to prevent mitotic entry after treatment with ionizing radiation.", "Ticrr deficiency is embryonic-lethal in the absence of exogenous DNA damage because it is essential for normal cell cycle progression.", "Specifically, the loss of ticrr impairs DNA replication and disrupts the S/M checkpoint, leading to premature mitotic entry and mitotic catastrophe.", "We show that the human TICRR ortholog associates with TopBP1, a known checkpoint protein and a core component of the DNA replication preinitiation complex (pre-IC), and that the TICRR-TopBP1 interaction is stable without chromatin and requires BRCT motifs essential for TopBP1's replication and checkpoint functions.", "Most importantly, we find that ticrr deficiency disrupts chromatin binding of pre-IC, but not prereplication complex, components.", "Taken together, our data show that TICRR acts in association with TopBP1 and plays an essential role in pre-IC formation.", "It remains to be determined whether Ticrr represents the vertebrate ortholog of the yeast pre-IC component Sld3, or a hitherto unknown metazoan replication and checkpoint regulator."], "structured": false}
{"doc_id": 5278233, "title": "A maternally methylated CpG island in KvLQT1 is associated with an antisense paternal transcript and loss of imprinting in Beckwith-Wiedemann syndrome.", "abstract": ["Loss of imprinting at IGF2, generally through an H19-independent mechanism, is associated with a large percentage of patients with the overgrowth and cancer predisposition condition Beckwith-Wiedemann syndrome (BWS).", "Imprinting control elements are proposed to exist within the KvLQT1 locus, because multiple BWS-associated chromosome rearrangements disrupt this gene.", "We have identified an evolutionarily conserved, maternally methylated CpG island (KvDMR1) in an intron of the KvLQT1 gene.", "Among 12 cases of BWS with normal H19 methylation, 5 showed demethylation of KvDMR1 in fibroblast or lymphocyte DNA; whereas, in 4 cases of BWS with H19 hypermethylation, methylation at KvDMRl was normal.", "Thus, inactivation of H19 and hypomethylation at KvDMR1 (or an associated phenomenon) represent distinct epigenetic anomalies associated with biallelic expression of IGF2.", "Reverse transcription-PCR analysis of the human and syntenic mouse loci identified the presence of a KvDMR1-associated RNA transcribed exclusively from the paternal allele and in the opposite orientation with respect to the maternally expressed KvLQT1 gene.", "We propose that KvDMR1 and/or its associated antisense RNA (KvLQT1-AS) represents an additional imprinting control element or center in the human 11p15.5 and mouse distal 7 imprinted domains."], "structured": false}
{"doc_id": 5284188, "title": "Alarming levels of drug-resistant tuberculosis in Belarus: results of a survey in Minsk", "abstract": ["Resistance to anti-tuberculosis (TB) medicines is a major public health threat in most countries of the former Soviet Union.", "As no representative and quality-assured information on the magnitude of this problem existed in Belarus, a survey was conducted in the capital city of Minsk.", "Between November 2009 and December 2010, 156 consecutively diagnosed new and 68 previously treated culture-positive TB patients residing in Minsk were enrolled in the survey.", "Mycobacterium tuberculosis isolates were obtained from each patient and tested for susceptibility to first- and second-line anti-TB drugs.", "Multidrug-resistant (MDR)-TB was found in 35.3% (95% CI 27.7-42.8) of new patients and 76.5% (95% CI 66.1-86.8) of those previously treated.", "Overall, nearly one in two patients enrolled had MDR-TB.", "Extensively drug-resistant TB was reported in 15 of the 107 MDR-TB patients (14.0%, 95% CI 7.3-20.7).", "Patients <35 yrs of age have shown a two times higher odds ratio of multidrug-resistant TB than those aged >35 yrs.", "The findings of this survey in Minsk city are alarming and represent the highest proportions of MDR-TB ever recorded in the world.", "This study greatly contributes to the understanding of the burden of drug-resistant TB in urban areas of Belarus."], "structured": false}
{"doc_id": 5289038, "title": "Partitioning regulatory mechanisms of within-host malaria dynamics using the effective propagation number.", "abstract": ["Immune clearance and resource limitation (via red blood cell depletion) shape the peaks and troughs of malaria parasitemia, which in turn affect disease severity and transmission.", "Quantitatively partitioning the relative roles of these effects through time is challenging.", "Using data from rodent malaria, we estimated the effective propagation number, which reflects the relative importance of contrasting within-host control mechanisms through time and is sensitive to the inoculating parasite dose.", "Our analysis showed that the capacity of innate responses to restrict initial parasite growth saturates with parasite dose and that experimentally enhanced innate immunity can affect parasite density indirectly via resource depletion.", "Such a statistical approach offers a tool to improve targeting of drugs or vaccines for human therapy by revealing the dynamics and interactions of within-host regulatory mechanisms."], "structured": false}
{"doc_id": 5293024, "title": "Life is sweet: candy consumption and longevity.", "abstract": ["Our attitude towards candy\u2014\u201cif it tastes that good, it can't be healthy\u201d\u2014betrays society's puritanical stance towards pleasure.", "Candy has been blamed for various ills, including hyperactivity in children; however, clinical trials have not supported this.1  Candy\u2014sugar confectionery and chocolate\u2014is not a recent invention: the ancient Arabs, Chinese, and Egyptians candied fruits and nuts in honey, and the Aztecs made a chocolate drink from the bean of the cacao tree.", "Today, Americans gratify themselves with, on average, 5.4 kg of sugar candy and 6.5 kg of chocolate per person annually.2  Since candy has existed for centuries, we surmised that it cannot be totally unhealthy.", "We decided to investigate whether candy consumption was associated with longevity.  ", "Subjects were from the Harvard alumni health study, an ongoing study of men entering Harvard University as undergraduates between 1916 and 1950.", "We included 7841 men, free of cardiovascular disease and cancer, who responded to a health survey \u2026"], "structured": false}
{"doc_id": 5304891, "title": "Inter-individual variability and genetic influences on cytokine responses to bacteria and fungi", "abstract": ["Little is known about the inter-individual variation of cytokine responses to different pathogens in healthy individuals.", "To systematically describe cytokine responses elicited by distinct pathogens and to determine the effect of genetic variation on cytokine production, we profiled cytokines produced by peripheral blood mononuclear cells from 197 individuals of European origin from the 200 Functional Genomics (200FG) cohort in the Human Functional Genomics Project (http://www.humanfunctionalgenomics.org), obtained over three different years.", "We compared bacteria- and fungi-induced cytokine profiles and found that most cytokine responses were organized around a physiological response to specific pathogens, rather than around a particular immune pathway or cytokine.", "We then correlated genome-wide single-nucleotide polymorphism (SNP) genotypes with cytokine abundance and identified six cytokine quantitative trait loci (QTLs).", "Among them, a cytokine QTL at the NAA35-GOLM1 locus markedly modulated interleukin (IL)-6 production in response to multiple pathogens and was associated with susceptibility to candidemia.", "Furthermore, the cytokine QTLs that we identified were enriched among SNPs previously associated with infectious diseases and heart diseases.", "These data reveal and begin to explain the variability in cytokine production by human immune cells in response to pathogens."], "structured": false}
{"doc_id": 5321708, "title": "Integrins promote cytokinesis through the RSK signaling axis.", "abstract": ["Cytokinesis is the final stage in cell division.", "Although integrins can regulate cytokinesis, the mechanisms involved are not fully understood.", "In this study, we demonstrate that integrin-regulated ERK (extracellular signal-related kinase) and RSK (p90 ribosomal S6 kinase) signaling promotes successful cytokinesis.", "Inhibiting the activation of ERK and RSK in CHO cells by a mutation in the integrin \u03b21 cytoplasmic tail or with pharmacological inhibitors results in the accumulation of cells with midbodies and the formation of binucleated cells.", "Activation of ERK and RSK signaling by the expression of constitutively active RAF1 suppresses the mutant phenotype in a RSK-dependent manner.", "Constitutively active RSK2 also restores cytokinesis inhibited by the mutant integrin.", "Importantly, the regulatory role of the RSK pathway is not specific to CHO cells.", "MCF-10A human mammary epithelial cells and HPNE human pancreatic ductal epithelial cells exhibit a similar dependence on RSK for successful cytokinesis.", "In addition, depriving mitotic MCF10A cells of integrin-mediated adhesion by incubating them in suspension suppressed ERK and RSK activation and resulted in a failure of cytokinesis.", "Furthermore, inhibition of RSK or integrins within the 3D context of a developing salivary gland organ explant also leads to an accumulation of epithelial cells with midbodies, suggesting a similar defect in cytokinesis.", "Interestingly, neither ERK nor RSK regulates cytokinesis in human fibroblasts, suggesting cell-type specificity.", "Taken together, our results identify the integrin-RSK signaling axis as an important regulator of cytokinesis in epithelial cells.", "We propose that the proper interaction of cells with their microenvironment through integrins contributes to the maintenance of genomic stability by promoting the successful completion of cytokinesis."], "structured": false}
{"doc_id": 5323845, "title": "Sympathetic neural mechanisms in normal and hypertensive pregnancy in humans.", "abstract": ["BACKGROUND Direct recordings from peripheral sympathetic nerves have shown an increased sympathetic drive in pregnancy-induced hypertension (PIH) and preeclampsia (PE).", "It is unknown whether sympathetic drive is altered in normal pregnancy, when arterial blood pressure can be normal or relatively low.", "The aim of this study was to measure and compare peripheral sympathetic discharge, its vasoconstrictor effect and its baroreceptor control, during pregnancy and postpartum in women with normal pregnancy (NP) and PIH and in normotensive nonpregnant (NN) women.   \n", "METHODS AND RESULTS Twenty-one women with NP, 18 women with PIH, and 21 NN women had muscle sympathetic nerve activity assessed from multiunit discharges (MSNA) and from single units with defined vasoconstrictor properties (s-MSNA).", "The s-MSNA in NP (38+/-6.6 impulses/100 beats) was greater (P<0.05) than in NN women (19+/-1.8 impulses/100 beats) despite similar age and body weight but less than in PIH women (P<0.001) (146+/-23.5 impulses/100 beats).", "MSNA followed a similar trend.", "Cardiac baroreceptor reflex sensitivity (BRS) was impaired in NP and PIH women relative to NN.", "After delivery, sympathetic activity decreased to values similar to those obtained in NN, and there was an increase in BRS.", "In women with NP, the decrease in sympathetic output occurred despite an insignificant change in blood pressure.   \n", "CONCLUSIONS Central sympathetic output was increased in women with normal pregnancy and was even greater in the hypertensive pregnant group.", "The findings suggest that the moderate sympathetic hyperactivity during the latter months of normal pregnancy may help to return the arterial pressure to nonpregnant levels, although when the increase in activity is excessive, hypertension may ensue."], "structured": true}
{"doc_id": 5339554, "title": "Barriers to recruiting urban African American women into research studies in community settings.", "abstract": ["This qualitative study identified barriers to African American women's participation in a community-based behavioral intervention trial to increase mammography screening.", "Four themes emerged from focus group discussions with community agency providers and research team members.", "These themes were (1) going to the gatekeepers; (2) knowing the culture; (3) location is everything; and (4) protocols, policies, and possibilities.", "A checklist of actions that nurse researchers could consider to increase African American women's participation in community trials is provided."], "structured": false}
{"doc_id": 5372432, "title": "Geographical access to healthcare in Northern England and post-mortem diagnosis of cancer.", "abstract": ["BACKGROUND There is some previous evidence that diagnosis of cancer at death, recorded as registry death certificate only records, is associated with problems of access to care.   \n", "METHODS Records from the Northern and Yorkshire Cancer Registry for patients registered with breast, colorectal, lung, ovarian or prostate cancer between 1994 and 2002 were supplemented with measures of travel time to general practitioner and hospital services, and social deprivation.", "Logistic regression was used to identify predictors of records where diagnosis was at death.   \n", "RESULTS There was no association between the odds diagnosis at death and access to primary care.", "For all sites except breast, the highest odds of being a cancer diagnosed at death fell among those living in the highest quartile of hospital travel time, although it was only statistically significant for colorectal and ovary tumours.", "Those in the most deprived and furthest travel time to hospital quartile were 2.6 times more likely to be a diagnosis at death case compared with those in the most affluent and proximal areas.   \n", "CONCLUSIONS There is some evidence that poorer geographical access to tertiary care, in particular when coupled with social disadvantages, may be associated with increased odds of diagnosis at death."], "structured": true}
{"doc_id": 5372773, "title": "Enhanced monocyte Fc phagocytosis by a homologue of interleukin-10 encoded by human cytomegalovirus.", "abstract": ["Human cytomegalovirus (HCMV) expresses several homologues of human interleukin 10 (hIL-10) possessing immunomodulatory properties which may promote viral infection by modulating the function of myeloid cells.", "We examined the phenotype and phagocytic capability of human monocytes exposed to hIL-10, an HCMV-encoded hIL-10 homologue expressed during the productive phase of infection (cmvIL-10), and a differentially spliced form of cmvIL-10 expressed during latent and productive phases of infection, (LAcmvIL-10).", "hIL-10 and cmvIL-10 upregulated expression of Fcgamma receptors, stimulated phagocytosis of IgG-opsonised erythrocytes and decreased MHC class II (HLA-DR) expression on purified monocytes within 24 h. In contrast, LAcmvIL-10 decreased HLA-DR expression at later times (48 h and 72 h) but did not increase Fcgamma receptor expression.", "We conclude that cmvIL-10 promotes differentiation of monocytes towards a pro-phagocytic phenotype and that LAcmvIL-10 does not affect monocytes by the same mechanism as cmvIL-10.", "The significance of these properties to cytomegalovirus pathogenesis is discussed."], "structured": false}
{"doc_id": 5373138, "title": "3D Chromosome Regulatory Landscape of Human Pluripotent Cells.", "abstract": ["In this study, we describe the 3D chromosome regulatory landscape of human naive and primed embryonic stem cells.", "To devise this map, we identified transcriptional enhancers and insulators in these cells and placed them within the context of cohesin-associated CTCF-CTCF loops using cohesin ChIA-PET data.", "The CTCF-CTCF loops we identified form a chromosomal framework of insulated neighborhoods, which in turn form topologically associating domains (TADs) that are largely preserved during the transition between the naive and primed states.", "Regulatory changes in enhancer-promoter interactions occur within insulated neighborhoods during cell state transition.", "The CTCF anchor regions we identified are conserved across species, influence gene expression, and are a frequent site of mutations in cancer cells, underscoring their functional importance in cellular regulation.", "These 3D regulatory maps of human pluripotent cells therefore provide a foundation for future interrogation of the relationships between chromosome structure and gene control in development and disease."], "structured": false}
{"doc_id": 5377059, "title": "Functional analysis via standardized whole-blood stimulation systems defines the boundaries of a healthy immune response to complex stimuli.", "abstract": ["Standardization of immunophenotyping procedures has become a high priority.", "We have developed a suite of whole-blood, syringe-based assay systems that can be used to reproducibly assess induced innate or adaptive immune responses.", "By eliminating preanalytical errors associated with immune monitoring, we have defined the protein signatures induced by (1) medically relevant bacteria, fungi, and viruses; (2) agonists specific for defined host sensors; (3) clinically employed cytokines; and (4) activators of T cell immunity.", "Our results provide an initial assessment of healthy donor reference values for induced cytokines and chemokines and we report the failure to release interleukin-1\u03b1 as a common immunological phenotype.", "The observed naturally occurring variation of the immune response may help to explain differential susceptibility to disease or response to therapeutic intervention.", "The implementation of a general solution for assessment of functional immune responses will help support harmonization of clinical studies and data sharing."], "structured": false}
{"doc_id": 5377642, "title": "SATB1 Expression Governs Epigenetic Repression of PD\u20101 in Tumor\u2010Reactive T Cells", "abstract": ["&NA; Despite the importance of programmed cell death\u20101 (PD\u20101) in inhibiting T cell effector activity, the mechanisms regulating its expression remain poorly defined.", "We found that the chromatin organizer special AT\u2010rich sequence\u2010binding protein\u20101 (Satb1) restrains PD\u20101 expression induced upon T cell activation by recruiting a nucleosome remodeling deacetylase (NuRD) complex to Pdcd1 regulatory regions.", "Satb1 deficienct T cells exhibited a 40\u2010fold increase in PD\u20101 expression.", "Tumor\u2010derived transforming growth factor &bgr; (Tgf\u2010&bgr;) decreased Satb1 expression through binding of Smad proteins to the Satb1 promoter.", "Smad proteins also competed with the Satb1\u2010NuRD complex for binding to Pdcd1 enhancers, releasing Pdcd1 expression from Satb1\u2010mediated repression, Satb1\u2010deficient tumor\u2010reactive T cells lost effector activity more rapidly than wild\u2010type lymphocytes at tumor beds expressing PD\u20101 ligand (CD274), and these differences were abrogated by sustained CD274 blockade.", "Our findings suggest that Satb1 functions to prevent premature T cell exhaustion by regulating Pdcd1 expression upon T cell activation.", "Dysregulation of this pathway in tumor\u2010infiltrating T cells results in diminished anti\u2010tumor immunity.", "Graphical Abstract Figure.", "No caption available.", "HighlightsT cell activation increased the expression of Satb1 in mature CD8+ and CD4+ T cellsRecruitment of the NuRD repression complex by Satb1 inhibits expression of Pdcd1In tumors, TGF\u2010&bgr; inhibits Satb1 expression in T cells, increasing Pdcd1 expressionSatb1\u2212/\u2212 T cells express high amounts of PD\u20101 and have decreased anti\u2010tumor activity &NA; Stephen et al. show that the chromatin organizer Satb1 controls expression levels of PD\u20101 upon T cell activation through the recruitment of a de\u2010acetylase complex to regulatory regions of the Pdcd1 gene.", "Tumor\u2010derived TGF\u2010&bgr; dysregulates this pathway, unleashing PD\u20101 expression in tumor\u2010infiltrating T cells and decreasing anti\u2010tumor immunity."], "structured": false}
{"doc_id": 5386514, "title": "Activation of the NLRP3 inflammasome in dendritic cells induces IL-1\u03b2\u2013dependent adaptive immunity against tumors", "abstract": ["The therapeutic efficacy of anticancer chemotherapies may depend on dendritic cells (DCs), which present antigens from dying cancer cells to prime tumor-specific interferon-\u03b3 (IFN-\u03b3)\u2013producing T lymphocytes.", "Here we show that dying tumor cells release ATP, which then acts on P2X7 purinergic receptors from DCs and triggers the NOD-like receptor family, pyrin domain containing-3 protein (NLRP3)-dependent caspase-1 activation complex ('inflammasome'), allowing for the secretion of interleukin-1\u03b2 (IL-1\u03b2).", "The priming of IFN-\u03b3\u2013producing CD8+ T cells by dying tumor cells fails in the absence of a functional IL-1 receptor 1 and in Nlpr3-deficient (Nlrp3\u2212/\u2212) or caspase-1\u2013deficient (Casp-1\u2212/\u2212) mice unless exogenous IL-1\u03b2 is provided.", "Accordingly, anticancer chemotherapy turned out to be inefficient against tumors established in purinergic receptor P2rx7\u2212/\u2212 or Nlrp3\u2212/\u2212 or Casp1\u2212/\u2212 hosts.", "Anthracycline-treated individuals with breast cancer carrying a loss-of-function allele of P2RX7 developed metastatic disease more rapidly than individuals bearing the normal allele.", "These results indicate that the NLRP3 inflammasome links the innate and adaptive immune responses against dying tumor cells."], "structured": false}
{"doc_id": 5389095, "title": "Mfge8 promotes obesity by mediating the uptake of dietary fats and serum fatty acids", "abstract": ["Fatty acids are integral mediators of energy storage, membrane formation and cell signaling.", "The pathways that orchestrate uptake of fatty acids remain incompletely understood.", "Expression of the integrin ligand Mfge8 is increased in human obesity and in mice on a high-fat diet, but its role in obesity is unknown.", "We show here that Mfge8 promotes the absorption of dietary triglycerides and the cellular uptake of fatty acid and that Mfge8-deficient (Mfge8\u2212/\u2212) mice are protected from diet-induced obesity, steatohepatitis and insulin resistance.", "Mechanistically, we found that Mfge8 coordinates fatty acid uptake through \u03b1v\u03b23 integrin\u2013 and \u03b1v\u03b25 integrin\u2013dependent phosphorylation of Akt by phosphatidylinositide-3 kinase and mTOR complex 2, leading to translocation of Cd36 and Fatp1 from cytoplasmic vesicles to the cell surface.", "Collectively, our results imply a role for Mfge8 in regulating the absorption and storage of dietary fats, as well as in the development of obesity and its complications."], "structured": false}
{"doc_id": 5389523, "title": "RAD52 Facilitates Mitotic DNA Synthesis Following Replication Stress.", "abstract": ["Homologous recombination (HR) is necessary to counteract DNA replication stress.", "Common fragile site (CFS) loci are particularly sensitive to replication stress and undergo pathological rearrangements in tumors.", "At these loci, replication stress frequently activates DNA repair synthesis in mitosis.", "This mitotic DNA synthesis, termed MiDAS, requires the MUS81-EME1 endonuclease and a non-catalytic subunit of the Pol-delta complex, POLD3.", "Here, we examine the contribution of HR factors in promoting MiDAS in human cells.", "We report that RAD51 and BRCA2 are dispensable for MiDAS but are required to counteract replication stress at CFS loci during S-phase.", "In contrast, MiDAS is RAD52 dependent, and RAD52 is required for the timely recruitment of MUS81 and POLD3 to CFSs in early mitosis.", "Our results provide further mechanistic insight into MiDAS and define a specific function for human RAD52.", "Furthermore, selective inhibition of MiDAS may comprise a potential therapeutic strategy to sensitize cancer cells undergoing replicative stress."], "structured": false}
{"doc_id": 5395426, "title": "Excitotoxic brain injury in adult zebrafish stimulates neurogenesis and long-distance neuronal integration.", "abstract": ["Zebrafish maintain a greater capacity than mammals for central nervous system repair after injury.", "Understanding differences in regenerative responses between different vertebrate species may shed light on mechanisms to improve repair in humans.", "Quinolinic acid is an excitotoxin that has been used to induce brain injury in rodents for modeling Huntington's disease and stroke.", "When injected into the adult rodent striatum, this toxin stimulates subventricular zone neurogenesis and neuroblast migration to injury.", "However, most new neurons fail to survive and lesion repair is minimal.", "We used quinolinic acid to lesion the adult zebrafish telencephalon to study reparative processes.", "We also used conditional transgenic lineage mapping of adult radial glial stem cells to explore survival and integration of neurons generated after injury.", "Telencephalic lesioning with quinolinic acid, and to a lesser extent vehicle injection, produced cell death, microglial infiltration, increased cell proliferation, and enhanced neurogenesis in the injured hemisphere.", "Lesion repair was more complete with quinolinic acid injection than after vehicle injection.", "Fate mapping of her4-expressing radial glia showed injury-induced expansion of radial glial stem cells that gave rise to neurons which migrated to injury, survived at least 8 weeks and formed long-distance projections that crossed the anterior commissure and synapsed in the contralateral hemisphere.", "These findings suggest that quinolinic acid lesioning of the zebrafish brain stimulates adult neural stem cells to produce robust regeneration with long-distance integration of new neurons.", "This model should prove useful for elucidating reparative mechanisms that can be applied to restorative therapies for mammalian brain injury."], "structured": false}
{"doc_id": 5398179, "title": "Germinal Center T Follicular Helper Cells Are Highly Permissive to HIV-1 and Alter Their Phenotype during Virus Replication.", "abstract": ["HIV-1 replication is concentrated within CD4(+) T cells in B cell follicles of secondary lymphoid tissues during asymptomatic disease.", "Limited data suggest that a subset of T follicular helper cells (TFH) within germinal centers (GC) is highly permissive to HIV-1.", "Whether GC TFH are the major HIV-1 virus-producing cells in vivo has not been established.", "In this study, we investigated TFH permissivity to HIV-1 ex vivo by spinoculating and culturing tonsil cells with HIV-1 GFP reporter viruses.", "Using flow cytometry, higher percentages of GC TFH (CXCR5(high)PD-1(high)) and CXCR5(+)programmed cell death-1 (PD-1)(low) cells were GFP(+) than non-GC TFH (CXCR5(+)PD-1(intermediate)) or extrafollicular (EF) (CXCR5(-)) cells.", "When sorted prior to spinoculation, however, GC TFH were substantially more permissive than CXCR5(+)PD-1(low) or EF cells, suggesting that many GC TFH transition to a CXCR5(+)PD-1(low) phenotype during productive infection.", "In situ hybridization on inguinal lymph node sections from untreated HIV-1-infected individuals without AIDS revealed higher frequencies of HIV-1 RNA(+) cells in GC than non-GC regions of follicle or EF regions.", "Superinfection of HIV-1-infected individuals' lymph node cells with GFP reporter virus confirmed the permissivity of follicular cells ex vivo.", "Lymph node immunostaining revealed 96% of CXCR5(+)CD4(+) cells were located in follicles.", "Within sorted lymph node cells from four HIV-infected individuals, CXCR5(+) subsets harbored 11-66-fold more HIV-1 RNA than CXCR5(-) subsets, as determined by RT PCR.", "Thus, GC TFH are highly permissive to HIV-1, but downregulate PD-1 and, to a lesser extent, CXCR5 during HIV-1 replication.", "These data further implicate GC TFH as the major HIV-1-producing cells in chronic asymptomatic HIV-1 infection."], "structured": false}
{"doc_id": 5402581, "title": "Risk of death with atypical antipsychotic drug treatment for dementia: meta-analysis of randomized placebo-controlled trials.", "abstract": ["CONTEXT Atypical antipsychotic medications are widely used to treat delusions, aggression, and agitation in people with Alzheimer disease and other dementia; however, concerns have arisen about the increased risk for cerebrovascular adverse events, rapid cognitive decline, and mortality with their use.   \n", "OBJECTIVE To assess the evidence for increased mortality from atypical antipsychotic drug treatment for people with dementia.   \n", "DATA SOURCES MEDLINE (1966 to April 2005), the Cochrane Controlled Trials Register (2005, Issue 1), meetings presentations (1997-2004), and information from the sponsors were searched using the terms for atypical antipsychotic drugs (aripiprazole, clozapine, olanzapine, quetiapine, risperidone, and ziprasidone), dementia, Alzheimer disease, and clinical trial.   ", "STUDY SELECTION Published and unpublished randomized placebo-controlled, parallel-group clinical trials of atypical antipsychotic drugs marketed in the United States to treat patients with Alzheimer disease or dementia were selected by consensus of the authors.   \n", "DATA EXTRACTION Trials, baseline characteristics, outcomes, all-cause dropouts, and deaths were extracted by one reviewer; treatment exposure was obtained or estimated.", "Data were checked by a second reviewer.   \n", "DATA SYNTHESIS Fifteen trials (9 unpublished), generally 10 to 12 weeks in duration, including 16 contrasts of atypical antipsychotic drugs with placebo met criteria (aripiprazole [n = 3], olanzapine [n = 5], quetiapine [n = 3], risperidone [n = 5]).", "A total of 3353 patients were randomized to study drug and 1757 were randomized to placebo.", "Outcomes were assessed using standard methods (with random- or fixed-effects models) to calculate odds ratios (ORs) and risk differences based on patients randomized and relative risks based on total exposure to treatment.", "There were no differences in dropouts.", "Death occurred more often among patients randomized to drugs (118 [3.5%] vs 40 [2.3%].", "The OR by meta-analysis was 1.54; 95% confidence interval [CI], 1.06-2.23; P = .02; and risk difference was 0.01; 95% CI, 0.004-0.02; P = .01).", "Sensitivity analyses did not show evidence for differential risks for individual drugs, severity, sample selection, or diagnosis.   \n", "CONCLUSIONS Atypical antipsychotic drugs may be associated with a small increased risk for death compared with placebo.", "This risk should be considered within the context of medical need for the drugs, efficacy evidence, medical comorbidity, and the efficacy and safety of alternatives.", "Individual patient analyses modeling survival and causes of death are needed."], "structured": true}
{"doc_id": 5403286, "title": "PI3K in cancer: divergent roles of isoforms, modes of activation and therapeutic targeting", "abstract": ["Phosphatidylinositol 3-kinases (PI3Ks) are crucial coordinators of intracellular signalling in response to extracellular stimuli.", "Hyperactivation of PI3K signalling cascades is one of the most common events in human cancers.", "In this Review, we discuss recent advances in our knowledge of the roles of specific PI3K isoforms in normal and oncogenic signalling, the different ways in which PI3K can be upregulated, and the current state and future potential of targeting this pathway in the clinic."], "structured": false}
{"doc_id": 5406411, "title": "Amphiregulin enhances regulatory T cell-suppressive function via the epidermal growth factor receptor.", "abstract": ["Epidermal growth factor receptor (EGFR) is known to be critically involved in tissue development and homeostasis as well as in the pathogenesis of cancer.", "Here we showed that Foxp3(+) regulatory T (Treg) cells express EGFR under inflammatory conditions.", "Stimulation with the EGF-like growth factor Amphiregulin (AREG) markedly enhanced Treg cell function in vitro, and in a colitis and tumor vaccination model we showed that AREG was critical for efficient Treg cell function in vivo.", "In addition, mast cell-derived AREG fully restored optimal Treg cell function.", "These findings reveal EGFR as a component in the regulation of local immune responses and establish a link between mast cells and Treg cells.", "Targeting of this immune regulatory mechanism may contribute to the therapeutic successes of EGFR-targeting treatments in cancer patients."], "structured": false}
{"doc_id": 5409325, "title": "Gonadotrope-specific deletion of Dicer results in severely suppressed gonadotropins and fertility defects.", "abstract": ["Pituitary gonadotropins follicle-stimulating hormone and luteinizing hormone are heterodimeric glycoproteins expressed in gonadotropes.", "They act on gonads and promote their development and functions including steroidogenesis and gametogenesis.", "Although transcriptional regulation of gonadotropin subunits has been well studied, the post-transcriptional regulation of gonadotropin subunits is not well understood.", "To test if microRNAs regulate the hormone-specific gonadotropin \u03b2 subunits in vivo, we deleted Dicer in gonadotropes by a Cre-lox genetic approach.", "We found that many of the DICER-dependent microRNAs, predicted in silico to bind gonadotropin \u03b2 subunit mRNAs, were suppressed in purified gonadotropes of mutant mice.", "Loss of DICER-dependent microRNAs in gonadotropes resulted in profound suppression of gonadotropin-\u03b2 subunit proteins and, consequently, the heterodimeric hormone secretion.", "In addition to suppression of basal levels, interestingly, the post-gonadectomy-induced rise in pituitary gonadotropin synthesis and secretion were both abolished in mutants, indicating a defective gonadal negative feedback control.", "Furthermore, mutants lacking Dicer in gonadotropes displayed severely reduced fertility and were rescued with exogenous hormones confirming that the fertility defects were secondary to suppressed gonadotropins.", "Our studies reveal that DICER-dependent microRNAs are essential for gonadotropin homeostasis and fertility in mice.", "Our studies also implicate microRNAs in gonadal feedback control of gonadotropin synthesis and secretion.", "Thus, DICER-dependent microRNAs confer a new layer of transcriptional and post-transcriptional regulation in gonadotropes to orchestrate the hypothalamus-pituitary-gonadal axis physiology."], "structured": false}
{"doc_id": 5409905, "title": "Sequential histone-modifying activities determine the robustness of transdifferentiation", "abstract": ["Natural interconversions between distinct somatic cell types have been reported in species as diverse as jellyfish and mice.", "The efficiency and reproducibility of some reprogramming events represent unexploited avenues in which to probe mechanisms that ensure robust cell conversion.", "We report that a conserved H3K27me3/me2 demethylase, JMJD-3.1, and the H3K4 methyltransferase Set1 complex cooperate to ensure invariant transdifferentiation (Td) of postmitotic Caenorhabditis elegans hindgut cells into motor neurons.", "At single-cell resolution, robust conversion requires stepwise histone-modifying activities, functionally partitioned into discrete phases of Td through nuclear degradation of JMJD-3.1 and phase-specific interactions with transcription factors that have conserved roles in cell plasticity and terminal fate selection.", "Our results draw parallels between epigenetic mechanisms underlying robust Td in nature and efficient cell reprogramming in vitro."], "structured": false}
{"doc_id": 5415832, "title": "Normal and leukemic stem cell niches: insights and therapeutic opportunities.", "abstract": ["Hematopoietic stem cells (HSCs) rely on instructive cues from the bone marrow (BM) niche to maintain their quiescence and adapt blood production to the organism's needs.", "Alterations in the BM niche are commonly observed in blood malignancies and directly contribute to the aberrant function of disease-initiating leukemic stem cells (LSCs).", "Here, we review recent insights into the cellular and molecular determinants of the normal HSC niche and describe how genetic changes in stromal cells and leukemia-induced BM niche remodeling contribute to blood malignancies.", "Moreover, we discuss how these findings can be applied to non-cell-autonomous therapies targeting the LSC niche."], "structured": false}
{"doc_id": 5431268, "title": "Role of common hypnotics on the phenotypic causes of obstructive sleep apnoea: paradoxical effects of zolpidem.", "abstract": ["Hypnotics are contraindicated in obstructive sleep apnoea (OSA) because of concerns of pharyngeal muscle relaxation and delayed arousal worsening hypoxaemia.", "However, human data are lacking.", "This study aimed to determine the effects of three common hypnotics on the respiratory arousal threshold, genioglossus muscle responsiveness and upper airway collapsibility during sleep.21 individuals with and without OSA (18-65 years) completed 84 detailed sleep studies after receiving temazepam (10 mg), zolpidem (10 mg), zopiclone (7.5 mg) and placebo on four occasions in a randomised, double-blind, placebo-controlled, crossover trial (ACTRN12612001004853).The arousal threshold increased with zolpidem and zopiclone versus placebo (mean\u00b1sd -18.3\u00b110 and -19.1\u00b19 versus -14.6\u00b17 cmH2O; p=0.02 and p<0.001) but not with temazepam (-16.8\u00b19 cmH2O; p=0.17).", "Genioglossus muscle activity during stable non-REM sleep and responsiveness during airway narrowing was not different with temazepam and zopiclone versus placebo but, paradoxically, zolpidem increased median muscle responsiveness three-fold during airway narrowing (median -0.15 (interquartile range -1.01 to -0.04) versus -0.05 (-0.29 to -0.03)% maximum EMG per cmH2O epiglottic pressure; p=0.03).", "The upper airway critical closing pressure did not change with any of the hypnotics.", "These doses of common hypnotics have differential effects on the respiratory arousal threshold but do not reduce upper airway muscle activity or alter airway collapsibility during sleep.", "Rather, muscle activity increases during airway narrowing with zolpidem."], "structured": false}
{"doc_id": 5433667, "title": "Clinical human papillomavirus detection forecasts cervical cancer risk in women over 18 years of follow-up.", "abstract": ["PURPOSE To describe the long-term (\u2265 10 years) benefits of clinical human papillomavirus (HPV) DNA testing for cervical precancer and cancer risk prediction.   \n", "METHODS Cervicovaginal lavages collected from 19,512 women attending a health maintenance program were retrospectively tested for HPV using a clinical test.", "HPV positives were tested for HPV16 and HPV18 individually using a research test.", "A Papanicolaou (Pap) result classified as atypical squamous cells of undetermined significance (ASC-US) or more severe was considered abnormal.", "Women underwent follow-up prospectively with routine annual Pap testing up to 18 years.", "Cumulative incidence rates (CIRs) of \u2265 grade 3 cervical intraepithelial neoplasia (CIN3+) or cancer for enrollment test results were calculated.   \n", "RESULTS A baseline negative HPV test provided greater reassurance against CIN3+ over the 18-year follow-up than a normal Pap (CIR, 0.90% v 1.27%).", "Although both baseline Pap and HPV tests predicted who would develop CIN3+ within the first 2 years of follow-up, only HPV testing predicted who would develop CIN3+ 10 to 18 years later (P = .004).", "HPV16- and HPV18-positive women with normal Pap were at elevated risk of CIN3+ compared with other HPV-positive women with normal Pap and were at similar risk of CIN3+ compared with women with a low-grade squamous intraepithelial Pap.   \n", "CONCLUSION HPV testing to rule out cervical disease followed by Pap testing and possibly combined with the detection of HPV16 and HPV18 among HPV positives to identify those at immediate risk of CIN3+ would be an efficient algorithm for cervical cancer screening, especially in women age 30 years or older."], "structured": true}
{"doc_id": 5436081, "title": "MG53 nucleates assembly of cell membrane repair machinery", "abstract": ["Dynamic membrane repair and remodelling is an elemental process that maintains cell integrity and mediates efficient cellular function.", "Here we report that MG53, a muscle-specific tripartite motif family protein (TRIM72), is a component of the sarcolemmal membrane-repair machinery.", "MG53 interacts with phosphatidylserine to associate with intracellular vesicles that traffic to and fuse with sarcolemmal membranes.", "Mice null for MG53 show progressive myopathy and reduced exercise capability, associated with defective membrane-repair capacity.", "Injury of the sarcolemmal membrane leads to entry of the extracellular oxidative environment and MG53 oligomerization, resulting in recruitment of MG53-containing vesicles to the injury site.", "After vesicle translocation, entry of extracellular Ca2+ facilitates vesicle fusion to reseal the membrane.", "Our data indicate that intracellular vesicle translocation and Ca2+-dependent membrane fusion are distinct steps involved in the repair of membrane damage and that MG53 may initiate the assembly of the membrane repair machinery in an oxidation-dependent manner."], "structured": false}
{"doc_id": 5448119, "title": "A large-scale replication study identifies TNIP1, PRDM1, JAZF1, UHRF1BP1 and IL10 as risk loci for systemic lupus erythematosus", "abstract": ["Genome-wide association studies have recently identified at least 15 susceptibility loci for systemic lupus erythematosus (SLE).", "To confirm additional risk loci, we selected SNPs from 2,466 regions that showed nominal evidence of association to SLE (P < 0.05) in a genome-wide study and genotyped them in an independent sample of 1,963 cases and 4,329 controls.", "This replication effort identified five new SLE susceptibility loci (P < 5 \u00d7 10\u22128): TNIP1 (odds ratio (OR) = 1.27), PRDM1 (OR = 1.20), JAZF1 (OR = 1.20), UHRF1BP1 (OR = 1.17) and IL10 (OR = 1.19).", "We identified 21 additional candidate loci with P\u2264 1 \u00d7 10\u22125.", "A candidate screen of alleles previously associated with other autoimmune diseases suggested five loci (P < 1 \u00d7 10\u22123) that may contribute to SLE: IFIH1, CFB, CLEC16A, IL12B and SH2B3.", "These results expand the number of confirmed and candidate SLE susceptibility loci and implicate several key immunologic pathways in SLE pathogenesis."], "structured": false}
{"doc_id": 5468807, "title": "ARID1A-mutated ovarian cancers depend on HDAC6 activity", "abstract": ["ARID1A, encoding a subunit of the SWI/SNF chromatin-remodelling complex, is the most frequently mutated epigenetic regulator across all human cancers.", "ARID1A and TP53 mutations are typically mutually exclusive.", "Therapeutic approaches that correlate with this genetic characteristic remain to be explored.", "Here, we show that HDAC6 activity is essential in ARID1A-mutated ovarian cancers.", "Inhibition of HDAC6 activity using a clinically applicable small-molecule inhibitor significantly improved the survival of mice bearing ARID1A-mutated tumours.", "This correlated with the suppression of growth and dissemination of ARID1A-mutated, but not wild-type, tumours.", "The dependence on HDAC6 activity in ARID1A-mutated cells correlated with a direct transcriptional repression of HDAC6 by ARID1A.", "HDAC6 inhibition selectively promoted apoptosis of ARID1A-mutated cells.", "HDAC6 directly deacetylates Lys120 of p53, a pro-apoptotic post-translational modification.", "Thus, ARID1A mutation inactivates the apoptosis-promoting function of p53 by upregulating HDAC6.", "Together, these results indicate that pharmacological inhibition of HDAC6 is a therapeutic strategy for ARID1A-mutated cancers."], "structured": false}
{"doc_id": 5473074, "title": "Solution NMR structure of the TatA component of the twin-arginine protein transport system from gram-positive bacterium Bacillus subtilis.", "abstract": ["The twin-arginine transport (Tat) system translocates folded proteins across the bacterial cytoplasmic or chloroplast thylakoid membrane of plants.", "The Tat system in most Gram-positive bacteria consists of two essential components, the TatA and TatC proteins.", "TatA is considered to be a bifunctional subunit, which can form a protein-conducting channel by self-oligomerization and can also participate in substrate recognition.", "However, the molecular mechanism underlying protein translocation remains elusive.", "Herein, we report the solution structure of the TatA(d) protein from Bacillus subtilis by NMR spectroscopy, the first structure of the Tat system at atomic resolution.", "TatA(d) shows an L-shaped structure formed by a transmembrane helix and an amphipathic helix, while the C-terminal tail is largely unstructured.", "Our results strongly support the postulated topology of TatA(d) in which the transmembrane helix is inserted into the lipid bilayer while the amphipathic helix lies at the membrane-water interface.", "Moreover, the structure of TatA(d) revealed the structural importance of several conserved residues at the hinge region, thus shedding new light on further elucidation of the protein transport mechanism of the Tat system."], "structured": false}
{"doc_id": 5476778, "title": "Autoimmunity due to molecular mimicry as a cause of neurological disease", "abstract": ["One hypothesis that couples infection with autoimmune disease is molecular mimicry.", "Molecular mimicry is characterized by an immune response to an environmental agent that cross-reacts with a host antigen, resulting in disease.", "This hypothesis has been implicated in the pathogenesis of diabetes, lupus and multiple sclerosis (MS).", "There is limited direct evidence linking causative agents with pathogenic immune reactions in these diseases.", "Our study establishes a clear link between viral infection, autoimmunity and neurological disease in humans.", "As a model for molecular mimicry, we studied patients with human T-lymphotropic virus type 1 (HTLV-1)-associated myelopathy/tropical spastic paraparesis (HAM/TSP), a disease that can be indistinguishable from MS (refs.", "5,6,7).", "HAM/TSP patients develop antibodies to neurons.", "We hypothesized these antibodies would identify a central nervous system (CNS) autoantigen.", "Immunoglobulin G isolated from HAM/TSP patients identified heterogeneous nuclear ribonuclear protein-A1 (hnRNP-A1) as the autoantigen.", "Antibodies to hnRNP-A1 cross-reacted with HTLV-1-tax, the immune response to which is associated with HAM/TSP (refs.", "5,9).", "Immunoglobulin G specifically stained human Betz cells, whose axons are preferentially damaged.", "Infusion of autoantibodies in brain sections inhibited neuronal firing, indicative of their pathogenic nature.", "These data demonstrate the importance of molecular mimicry between an infecting agent and hnRNP-A1 in autoimmune disease of the CNS."], "structured": false}
{"doc_id": 5483793, "title": "Altered recognition of antigen is a mechanism of CD8+ T cell tolerance in cancer", "abstract": ["Antigen-specific CD8+ T-cell tolerance, induced by myeloid-derived suppressor cells (MDSCs), is one of the main mechanisms of tumor escape.", "Using in vivo models, we show here that MDSCs directly disrupt the binding of specific peptide\u2013major histocompatibility complex (pMHC) dimers to CD8-expressing T cells through nitration of tyrosines in a T-cell receptor (TCR)-CD8 complex.", "This process makes CD8-expressing T cells unable to bind pMHC and to respond to the specific peptide, although they retain their ability to respond to nonspecific stimulation.", "Nitration of TCR-CD8 is induced by MDSCs through hyperproduction of reactive oxygen species and peroxynitrite during direct cell-cell contact.", "Molecular modeling suggests specific sites of nitration that might affect the conformational flexibility of TCR-CD8 and its interaction with pMHC.", "These data identify a previously unknown mechanism of T-cell tolerance in cancer that is also pertinent to many pathological conditions associated with accumulation of MDSCs."], "structured": false}
{"doc_id": 5484763, "title": "A new genetic subgroup of chronic granulomatous disease with autosomal recessive mutations in p40 phox and selective defects in neutrophil NADPH oxidase activity.", "abstract": ["Chronic granulomatous disease (CGD), an immunodeficiency with recurrent pyogenic infections and granulomatous inflammation, results from loss of phagocyte superoxide production by recessive mutations in any 1 of 4 genes encoding subunits of the phagocyte NADPH oxidase.", "These include gp91(phox) and p22(phox), which form the membrane-integrated flavocytochrome b, and cytosolic subunits p47(phox) and p67(phox).", "A fifth subunit, p40(phox), plays an important role in phagocytosis-induced superoxide production via a phox homology (PX) domain that binds to phosphatidylinositol 3-phosphate (PtdIns(3)P).", "We report the first case of autosomal recessive mutations in NCF4, the gene encoding p40(phox), in a boy who presented with granulomatous colitis.", "His neutrophils showed a substantial defect in intracellular superoxide production during phagocytosis, whereas extracellular release of superoxide elicited by phorbol ester or formyl-methionyl-leucyl-phenylalanine (fMLF) was unaffected.", "Genetic analysis of NCF4 showed compound heterozygosity for a frameshift mutation with premature stop codon and a missense mutation predicting a R105Q substitution in the PX domain.", "Parents and a sibling were healthy heterozygous carriers.", "p40(phox)R105Q lacked binding to PtdIns(3)P and failed to reconstitute phagocytosis-induced oxidase activity in p40(phox)-deficient granulocytes, with premature loss of p40(phox)R105Q from phagosomes.", "Thus, p40(phox) binding to PtdIns(3)P is essential for phagocytosis-induced oxidant production in human neutrophils and its absence can be associated with disease."], "structured": false}
{"doc_id": 5487448, "title": "Birth weight and mammographic density among postmenopausal women in Sweden.", "abstract": ["Birth weight is a significant predictor of breast cancer risk in adult life and mammary gland mass could be an intermediate stage in this long process.", "We have studied the association of birth size measurements with mammographic density, a marker of mammary gland mass.", "For a population-based sample of 893 postmenopausal women without previous cancer in Sweden, we retrieved information on birth size from birth records and their most recent mammography.", "Film mammograms of the medio-lateral oblique view were digitized and the Cumulus software was used for computer-assisted semi-automated thresholding of mammographic density.", "Results were analyzed using generalized linear models controlling for possible confounders.", "Mean percent mammographic density increased when comparing the extreme categories of birth weight (from 15.6% to 18.6%) and head circumference (from 15.5% to 20.4%), and the corresponding linear trends were statistically significant (p values 0.02 and 0.007, respectively).", "The associations were particularly strong when the cutoff for high versus low mammographic density was set at the relatively high value of 50%.", "Compared to women weighing 3001-3500 grams at birth, women with birth weights >4000g were at almost 3-fold risk of developing high mammographic density (odds ratio: 2.9, 95% confidence interval 1.1 to 7.9).", "No association with mammographic density was evident with respect to birth length which, however, is known to be less accurately measured.", "These results indicate that adult breast density, a powerful predictor of breast cancer risk, has intrauterine roots, as reflected in birth size."], "structured": false}
{"doc_id": 5492542, "title": "Oral ciclopirox olamine displays biological activity in a phase I study in patients with advanced hematologic malignancies.", "abstract": ["The antimycotic ciclopirox olamine is an intracellular iron chelator that has anticancer activity in vitro and in vivo.", "We developed an oral formulation of ciclopirox olamine and conducted the first-in-human phase I study of this drug in patients with relapsed or refractory hematologic malignancies (Trial registration ID: NCT00990587).", "Patients were treated with 5-80 mg/m\u00b2 oral ciclopirox olamine once daily for five days in 21-day treatment cycles.", "Pharmacokinetic and pharmacodynamic companion studies were performed in a subset of patients.", "Following definition of the half-life of ciclopirox olamine, an additional cohort was enrolled and treated with 80 mg/m\u00b2 ciclopirox olamine four times daily.", "Adverse events and clinical response were monitored throughout the trial.", "Twenty-three patients received study treatment.", "Ciclopirox was rapidly absorbed and cleared with a short half-life.", "Plasma concentrations of an inactive ciclopirox glucuronide metabolite were greater than those of ciclopirox.", "Repression of survivin expression was observed in peripheral blood cells isolated from patients treated once daily with ciclopirox olamine at doses greater than 10 mg/m\u00b2, demonstrating biological activity of the drug.", "Dose-limiting gastrointestinal toxicities were observed in patients receiving 80 mg/m\u00b2 four times daily, and no dose limiting toxicity was observed at 40 mg/m\u00b2 once daily.", "Hematologic improvement was observed in two patients.", "Once-daily dosing of oral ciclopirox olamine was well tolerated in patients with relapsed or refractory hematologic malignancies, and further optimization of dosing regimens is warranted in this patient population."], "structured": false}
{"doc_id": 5500086, "title": "Cancer cell\u2013autonomous contribution of type I interferon signaling to the efficacy of chemotherapy", "abstract": ["Some of the anti-neoplastic effects of anthracyclines in mice originate from the induction of innate and T cell\u2013mediated anticancer immune responses.", "Here we demonstrate that anthracyclines stimulate the rapid production of type I interferons (IFNs) by malignant cells after activation of the endosomal pattern recognition receptor Toll-like receptor 3 (TLR3).", "By binding to IFN-\u03b1 and IFN-\u03b2 receptors (IFNARs) on neoplastic cells, type I IFNs trigger autocrine and paracrine circuitries that result in the release of chemokine (C-X-C motif) ligand 10 (CXCL10).", "Tumors lacking Tlr3 or Ifnar failed to respond to chemotherapy unless type I IFN or Cxcl10, respectively, was artificially supplied.", "Moreover, a type I IFN\u2013related signature predicted clinical responses to anthracycline-based chemotherapy in several independent cohorts of patients with breast carcinoma characterized by poor prognosis.", "Our data suggest that anthracycline-mediated immune responses mimic those induced by viral pathogens.", "We surmise that such 'viral mimicry' constitutes a hallmark of successful chemotherapy."], "structured": false}
{"doc_id": 5503194, "title": "alphaE-catenin controls cerebral cortical size by regulating the hedgehog signaling pathway.", "abstract": ["During development, cells monitor and adjust their rates of accumulation to produce organs of predetermined size.", "We show here that central nervous system-specific deletion of the essential adherens junction gene, alphaE-catenin, causes abnormal activation of the hedgehog pathway, resulting in shortening of the cell cycle, decreased apoptosis, and cortical hyperplasia.", "We propose that alphaE-catenin connects cell-density-dependent adherens junctions with the developmental hedgehog pathway and that this connection may provide a negative feedback loop controlling the size of developing cerebral cortex."], "structured": false}
{"doc_id": 5508750, "title": "Molecular regulation of effector and memory T cell differentiation", "abstract": ["Immunological memory is a cardinal feature of adaptive immunity and an important goal of vaccination strategies.", "Here we highlight advances in the understanding of the diverse T lymphocyte subsets that provide acute and long-term protection from infection.", "These include new insights into the transcription factors, and the upstream 'pioneering' factors that regulate their accessibility to key sites of gene regulation, as well as metabolic regulators that contribute to the differentiation of effector and memory subsets; ontogeny and defining characteristics of tissue-resident memory lymphocytes; and origins of the remarkable heterogeneity exhibited by activated T cells.", "Collectively, these findings underscore progress in delineating the underlying pathways that control diversification in T cell responses but also reveal gaps in the knowledge, as well as the challenges that arise in the application of this knowledge to rationally elicit desired T cell responses through vaccination and immunotherapy."], "structured": false}
{"doc_id": 5511240, "title": "Liver-resident macrophage necroptosis orchestrates type 1 microbicidal inflammation and type-2-mediated tissue repair during bacterial infection.", "abstract": ["Kupffer cells, the phagocytes of fetal origin that line the liver sinusoids, are key contributors of host defense against enteroinvasive bacteria.", "Here, we found that infection by Listeria monocytogenes induced the early necroptotic death of Kupffer cells, which was followed by monocyte recruitment and an anti-bacterial type 1 inflammatory response.", "Kupffer cell death also triggered a type 2 response that involved the hepatocyte-derived alarmin interleukin-33 (IL-33) and basophil-derived interleukin-4 (IL-4).", "This led to the alternative activation of the monocyte-derived macrophages recruited to the liver, which thereby replaced ablated Kupffer cells and restored liver homeostasis.", "Kupffer cell death is therefore a key signal orchestrating type 1 microbicidal inflammation and type-2-mediated liver repair upon infection.", "This indicates that beyond the classical dichotomy of type 1 and type 2 responses, these responses can develop sequentially in the context of a bacterial infection and act interdependently, orchestrating liver immune responses and return to homeostasis, respectively."], "structured": false}
{"doc_id": 5519177, "title": "Gene regulation in the immune system by long noncoding RNAs", "abstract": ["Long noncoding RNAs (lncRNAs) are emerging as critical regulators of gene expression in the immune system.", "Studies have shown that lncRNAs are expressed in a highly lineage-specific manner and control the differentiation and function of innate and adaptive cell types.", "In this Review, we focus on mechanisms used by lncRNAs to regulate genes encoding products involved in the immune response, including direct interactions with chromatin, RNA and proteins.", "In addition, we address new areas of lncRNA biology, such as the functions of enhancer RNAs, circular RNAs and chemical modifications to RNA in cellular processes.", "We emphasize critical gaps in knowledge and future prospects for the roles of lncRNAs in the immune system and autoimmune disease."], "structured": false}
{"doc_id": 5531479, "title": "The Ly49Q receptor plays a crucial role in neutrophil polarization and migration by regulating raft trafficking.", "abstract": ["Neutrophils rapidly undergo polarization and directional movement to infiltrate the sites of infection and inflammation.", "Here, we show that an inhibitory MHC I receptor, Ly49Q, was crucial for the swift polarization of and tissue infiltration by neutrophils.", "During the steady state, Ly49Q inhibited neutrophil adhesion by preventing focal-complex formation, likely by inhibiting Src and PI3 kinases.", "However, in the presence of inflammatory stimuli, Ly49Q mediated rapid neutrophil polarization and tissue infiltration in an ITIM-domain-dependent manner.", "These opposite functions appeared to be mediated by distinct use of effector phosphatase SHP-1 and SHP-2.", "Ly49Q-dependent polarization and migration were affected by Ly49Q regulation of membrane raft functions.", "We propose that Ly49Q is pivotal in switching neutrophils to their polarized morphology and rapid migration upon inflammation, through its spatiotemporal regulation of membrane rafts and raft-associated signaling molecules."], "structured": false}
{"doc_id": 5548081, "title": "Prevalence of Kaposi sarcoma-associated herpesvirus infection in homosexual men at beginning of and during the HIV epidemic.", "abstract": ["CONTEXT Some studies have inferred that an epidemic of Kaposi sarcoma-associated herpesvirus (KSHV) infection in homosexual men in the United States occurred concurrently with that of human immunodeficiency virus (HIV), but there have been no direct measurements of KSHV prevalence at the beginning of the HIV epidemic.   \n", "OBJECTIVES To determine the prevalence of KSHV infection in homosexual men in San Francisco, Calif, at the beginning of the HIV epidemic in 1978 and 1979 and to examine changes in prevalence of KSHV at time points from 1978 through 1996 in light of changes in sexual behavior.   \n", "DESIGN, SETTING, AND PARTICIPANTS Analysis of a clinic-based sample (n = 398) derived from the San Francisco City Clinic Cohort (ages 18-66 years) (n = 2666 for analyses herein) and from population-based samples from the San Francisco Men's Health Study (MHS) (ages 25-54 years) (n = 825 and 252) and the San Francisco Young Men's Health Study (YMHS) (ages 18-29 years) (n = 428-976, and 557); behavioral studies were longitudinal and KSHV prevalence studies were cross-sectional.   \n", "MAIN OUTCOME MEASURES Antibodies against KSHV and HIV; sexual behaviors.   \n", "RESULTS The prevalence of KSHV infection in 1978 and 1979 was 26.5% of 235 (a random sample) overall (weighted for HIV infection) vs 6.9% (128/1842) for HIV in the San Francisco City Clinic Cohort sample.", "The prevalence of KSHV infection remained essentially unchanged between an MHS sample of 252 in 1984 and 1985 (29.6%) and a YMHS sample of 557 in 1995 and 1996 (26.4%), while HIV prevalence dropped from 49.5% of 825 in 1984 and 1985 (MHS) to 17.6% of 428 in 1992 and 1993 (YMHS).", "The proportion of men practicing unprotected receptive anal intercourse with 1 or more partners declined from 54% to 11% during the 1984 through 1993 period (MHS) with similar though slightly higher values in the YMHS in 1992 and 1993; whereas for unprotected oral intercourse it ranged between 60% and 90% in the 1984 through 1996 period (MHS and YMHS).   \n", "CONCLUSIONS Infection with KSHV was already highly prevalent in homosexual men when the HIV epidemic began in San Francisco, and its prevalence has been maintained at a nearly constant level.", "Any declines in the incidence of Kaposi sarcoma do not appear to be caused by a decline in KSHV transmission."], "structured": true}
{"doc_id": 5551138, "title": "Nortriptyline for smoking cessation: a review.", "abstract": ["This article reviews the efficacy of nortriptyline for smoking cessation based on a meta-analysis of the Cochrane Library.", "Six placebo-controlled trials have shown nortriptyline (75-100 mg) doubles quit rates (OR = 2.1).", "Between 4% and 12% of smokers dropped out because of adverse events, but no serious adverse events occurred.", "The efficacy of nortriptyline did not appear to be related to its antidepressant actions.", "Nortriptyline is an efficacious aid to smoking cessation with a magnitude of effect similar to that for bupropion and nicotine replacement therapies.", "Whether nortriptyline produces serious side effects at these doses in healthy, nondepressed smokers remains unclear because it has been tested in only 500 smokers.", "The finding that nortriptyline and bupropion are effective for smoking cessation but that selective serotonin-reuptake inhibitors are not suggests that dopaminergic or adrenergic, but not serotonergic, activity is important for cessation efficacy.", "Until further studies can verify a low incidence of significant adverse events, nortriptyline should be a second-line treatment for smoking cessation."], "structured": false}
{"doc_id": 5556809, "title": "Emotion dysregulation in attention deficit hyperactivity disorder.", "abstract": ["Although it has long been recognized that many individuals with attention deficit hyperactivity disorder (ADHD) also have difficulties with emotion regulation, no consensus has been reached on how to conceptualize this clinically challenging domain.", "The authors examine the current literature using both quantitative and qualitative methods.", "Three key findings emerge.", "First, emotion dysregulation is prevalent in ADHD throughout the lifespan and is a major contributor to impairment.", "Second, emotion dysregulation in ADHD may arise from deficits in orienting toward, recognizing, and/or allocating attention to emotional stimuli; these deficits implicate dysfunction within a striato-amygdalo-medial prefrontal cortical network.", "Third, while current treatments for ADHD often also ameliorate emotion dysregulation, a focus on this combination of symptoms reframes clinical questions and could stimulate novel therapeutic approaches.", "The authors then consider three models to explain the overlap between emotion dysregulation and ADHD: emotion dysregulation and ADHD are correlated but distinct dimensions; emotion dysregulation is a core diagnostic feature of ADHD; and the combination constitutes a nosological entity distinct from both ADHD and emotion dysregulation alone.", "The differing predictions from each model can guide research on the much-neglected population of patients with ADHD and emotion dysregulation."], "structured": false}
{"doc_id": 5558754, "title": "Use of serum C reactive protein and procalcitonin concentrations in addition to symptoms and signs to predict pneumonia in patients presenting to primary care with acute cough: diagnostic study", "abstract": ["OBJECTIVES To quantify the diagnostic accuracy of selected inflammatory markers in addition to symptoms and signs for predicting pneumonia and to derive a diagnostic tool.   \n", "DESIGN Diagnostic study performed between 2007 and 2010.", "Participants had their history taken, underwent physical examination and measurement of C reactive protein (CRP) and procalcitonin in venous blood on the day they first consulted, and underwent chest radiography within seven days.   \n", "SETTING Primary care centres in 12 European countries.   \n", "PARTICIPANTS Adults presenting with acute cough.   \n", "MAIN OUTCOME MEASURES Pneumonia as determined by radiologists, who were blind to all other information when they judged chest radiographs.   \n", "RESULTS Of 3106 eligible patients, 286 were excluded because of missing or inadequate chest radiographs, leaving 2820 patients (mean age 50, 40% men) of whom 140 (5%) had pneumonia.", "Re-assessment of a subset of 1675 chest radiographs showed agreement in 94% (\u03ba 0.45, 95% confidence interval 0.36 to 0.54).", "Six published \"symptoms and signs models\" varied in their discrimination (area under receiver operating characteristics curve (ROC) ranged from 0.55 (95% confidence interval 0.50 to 0.61) to 0.71 (0.66 to 0.76)).", "The optimal combination of clinical prediction items derived from our patients included absence of runny nose and presence of breathlessness, crackles and diminished breath sounds on auscultation, tachycardia, and fever, with an ROC area of 0.70 (0.65 to 0.75).", "Addition of CRP at the optimal cut off of >30 mg/L increased the ROC area to 0.77 (0.73 to 0.81) and improved the diagnostic classification (net reclassification improvement 28%).", "In the 1556 patients classified according to symptoms, signs, and CRP >30 mg/L as \"low risk\" (<2.5%) for pneumonia, the prevalence of pneumonia was 2%.", "In the 132 patients classified as \"high risk\" (>20%), the prevalence of pneumonia was 31%.", "The positive likelihood ratio of low, intermediate, and high risk for pneumonia was 0.4, 1.2, and 8.6 respectively.", "Measurement of procalcitonin added no relevant additional diagnostic information.", "A simplified diagnostic score based on symptoms, signs, and CRP >30 mg/L resulted in proportions of pneumonia of 0.7%, 3.8%, and 18.2% in the low, intermediate, and high risk group respectively.   \n", "CONCLUSIONS A clinical rule based on symptoms and signs to predict pneumonia in patients presenting to primary care with acute cough performed best in patients with mild or severe clinical presentation.", "Addition of CRP concentration at the optimal cut off of >30 mg/L improved diagnostic information, but measurement of procalcitonin concentration did not add clinically relevant information in this group."], "structured": true}
{"doc_id": 5560962, "title": "Somatic Mutations of the Immunoglobulin Framework Are Generally Required for Broad and Potent HIV-1 Neutralization", "abstract": ["Broadly neutralizing antibodies (bNAbs) to HIV-1 can prevent infection and are therefore of great importance for HIV-1 vaccine design.", "Notably, bNAbs are highly somatically mutated and generated by a fraction of HIV-1-infected individuals several years after infection.", "Antibodies typically accumulate mutations in the complementarity determining region (CDR) loops, which usually contact the antigen.", "The CDR loops are scaffolded by canonical framework regions (FWRs) that are both resistant to and less tolerant of mutations.", "Here, we report that in contrast to most antibodies, including those with limited HIV-1 neutralizing activity, most bNAbs require somatic mutations in their FWRs.", "Structural and functional analyses reveal that somatic mutations in FWR residues enhance breadth and potency by providing increased flexibility and/or direct antigen contact.", "Thus, in bNAbs, FWRs play an essential role beyond scaffolding the CDR loops and their unusual contribution to potency and breadth should be considered in HIV-1 vaccine design."], "structured": false}
{"doc_id": 5567005, "title": "Etiology of type 1 diabetes.", "abstract": ["Recent genetic mapping and gene-phenotype studies have revealed the genetic architecture of type 1 diabetes.", "At least ten genes so far can be singled out as strong causal candidates.", "The known functions of these genes indicate the primary etiological pathways of this disease, including HLA class II and I molecules binding to preproinsulin peptides and T cell receptors, T and B cell activation, innate pathogen-viral responses, chemokine and cytokine signaling, and T regulatory and antigen-presenting cell functions.", "This review considers research in the field of type 1 diabetes toward identifying disease mechanisms using genetic approaches.", "The expression and functions of these pathways, and, therefore, disease susceptibility, will be influenced by epigenetic and environmental factors.", "Certain inherited immune phenotypes will be early precursors of type 1 diabetes and could be useful in future clinical trials."], "structured": false}
{"doc_id": 5567223, "title": "Plasticity of epithelial stem cells in tissue regeneration", "abstract": ["Tissues rely upon stem cells for homeostasis and repair.", "Recent studies show that the fate and multilineage potential of epithelial stem cells can change depending on whether a stem cell exists within its resident niche and responds to normal tissue homeostasis, whether it is mobilized to repair a wound, or whether it is taken from its niche and challenged to de novo tissue morphogenesis after transplantation.", "In this Review, we discuss how different populations of naturally lineage-restricted stem cells and committed progenitors can display remarkable plasticity and reversibility and reacquire long-term self-renewing capacities and multilineage differentiation potential during physiological and regenerative conditions.", "We also discuss the implications of cellular plasticity for regenerative medicine and for cancer."], "structured": false}
{"doc_id": 5572127, "title": "Atm-deficient mice exhibit increased sensitivity to dextran sulfate sodium-induced colitis characterized by elevated DNA damage and persistent immune activation.", "abstract": ["The role of ataxia telangiectasia mutated (ATM), a DNA double-strand break recognition and response protein, in inflammation and inflammatory diseases is unclear.", "We have previously shown that high levels of systemic DNA damage are induced by intestinal inflammation in wild-type mice.", "To determine the effect of Atm deficiency in inflammation, we induced experimental colitis in Atm(-/-), Atm(+/-), and wild-type mice via dextran sulfate sodium (DSS) administration.", "Atm(-/-) mice had higher disease activity indices and rates of mortality compared with heterozygous and wild-type mice.", "Systemic DNA damage and immune response were characterized in peripheral blood throughout and after three cycles of treatment.", "Atm(-/-) mice showed increased sensitivity to levels of DNA strand breaks in peripheral leukocytes, as well as micronucleus formation in erythroblasts, compared with heterozygous and wild-type mice, especially during remission periods and after the end of treatment.", "Markers of reactive oxygen and nitrogen species-mediated damage, including 8-oxoguanine and nitrotyrosine, were present both in the distal colon and in peripheral leukocytes, with Atm(-/-) mice manifesting more 8-oxoguanine formation than wild-type mice.", "Atm(-/-) mice showed greater upregulation of inflammatory cytokines and significantly higher percentages of activated CD69+ and CD44+ T cells in the peripheral blood throughout treatment.", "ATM, therefore, may be a critical immunoregulatory factor dampening the deleterious effects of chronic DSS-induced inflammation, necessary for systemic genomic stability and homeostasis of the gut epithelial barrier."], "structured": false}
{"doc_id": 5573975, "title": "Activin\u2013like kinase\u20133 activity is important for kidney regeneration and reversal of fibrosis", "abstract": ["Molecules associated with the transforming growth factor \u03b2 (TGF-\u03b2) superfamily, such as bone morphogenic proteins (BMPs) and TGF-\u03b2, are key regulators of inflammation, apoptosis and cellular transitions.", "Here we show that the BMP receptor activin-like kinase 3 (Alk3) is elevated early in diseased kidneys after injury.", "We also found that its deletion in the tubular epithelium leads to enhanced TGF-\u03b21-Smad family member 3 (Smad3) signaling, epithelial damage and fibrosis, suggesting a protective role for Alk3-mediated signaling in the kidney.", "A structure-function analysis of the BMP-Alk3-BMP receptor, type 2 (BMPR2) ligand-receptor complex, along with synthetic organic chemistry, led us to construct a library of small peptide agonists of BMP signaling that function through the Alk3 receptor.", "One such peptide agonist, THR-123, suppressed inflammation, apoptosis and the epithelial-to-mesenchymal transition program and reversed established fibrosis in five mouse models of acute and chronic renal injury.", "THR-123 acts specifically through Alk3 signaling, as mice with a targeted deletion for Alk3 in their tubular epithelium did not respond to therapy with THR-123.", "Combining THR-123 and the angiotensin-converting enzyme inhibitor captopril had an additive therapeutic benefit in controlling renal fibrosis.", "Our studies show that BMP signaling agonists constitute a new line of therapeutic agents with potential utility in the clinic to induce regeneration, repair and reverse established fibrosis."], "structured": false}
{"doc_id": 5579368, "title": "COHCAP: an integrative genomic pipeline for single-nucleotide resolution DNA methylation analysis", "abstract": ["COHCAP (City of Hope CpG Island Analysis Pipeline) is an algorithm to analyze single-nucleotide resolution DNA methylation data produced by either an Illumina methylation array or targeted bisulfite sequencing.", "The goal of the COHCAP algorithm is to identify CpG islands that show a consistent pattern of methylation among CpG sites.", "COHCAP is currently the only DNA methylation package that provides integration with gene expression data to identify a subset of CpG islands that are most likely to regulate downstream gene expression, and it can generate lists of differentially methylated CpG islands with \u223c50% concordance with gene expression from both cell line data and heterogeneous patient data.", "For example, this article describes known breast cancer biomarkers (such as estrogen receptor) with a negative correlation between DNA methylation and gene expression.", "COHCAP also provides visualization for quality control metrics, regions of differential methylation and correlation between methylation and gene expression.", "This software is freely available at https://sourceforge.net/projects/cohcap/."], "structured": false}
{"doc_id": 5586392, "title": "Subgrouping of patients with neuropathic pain according to pain-related sensory abnormalities: a first step to a stratified treatment approach.", "abstract": ["BACKGROUND Patients with neuropathic pain present with various pain-related sensory abnormalities.", "These sensory features form different patterns or mosaics-the sensory profile-in individual patients.", "One hypothesis for the development of sensory profiles is that distinct pathophysiological mechanisms of pain generation produce specific sensory abnormalities.", "Several controlled trials of promising new drugs have produced negative results, but these findings could have been a result of heterogeneity in the patient population.", "Subgrouping patients on the basis of individual sensory profiles could reduce this heterogeneity and improve trial design.   ", "RECENT DEVELOPMENTS A statistical categorisation of patients with neuropathic pain showed that subgroups of patients with distinct sensory profiles who perceive their pain differently do exist across a range of neuropathic disorders, although some distinct disorder-specific profiles were also detected.", "Results of the first clinical trials to use the subgroup approach at baseline could show a superior effect of the study drugs in specific subgroups, rather than in the entire cohort of patients.", "WHERE NEXT?: A new classification of neuropathic pain should take into account subgroups of patients with different sensory profiles.", "Sensory phenotyping has the potential to improve clinical trial design by enriching the study population with potential treatment responders, and might lead to a stratified treatment approach and ultimately to personalised treatment."], "structured": false}
{"doc_id": 5596332, "title": "The Third International Consensus Definitions for Sepsis and Septic Shock (Sepsis-3).", "abstract": ["IMPORTANCE Definitions of sepsis and septic shock were last revised in 2001.", "Considerable advances have since been made into the pathobiology (changes in organ function, morphology, cell biology, biochemistry, immunology, and circulation), management, and epidemiology of sepsis, suggesting the need for reexamination.   \n", "OBJECTIVE To evaluate and, as needed, update definitions for sepsis and septic shock.   ", "PROCESS A task force (n = 19) with expertise in sepsis pathobiology, clinical trials, and epidemiology was convened by the Society of Critical Care Medicine and the European Society of Intensive Care Medicine.", "Definitions and clinical criteria were generated through meetings, Delphi processes, analysis of electronic health record databases, and voting, followed by circulation to international professional societies, requesting peer review and endorsement (by 31 societies listed in the Acknowledgment).   ", "KEY FINDINGS FROM EVIDENCE SYNTHESIS Limitations of previous definitions included an excessive focus on inflammation, the misleading model that sepsis follows a continuum through severe sepsis to shock, and inadequate specificity and sensitivity of the systemic inflammatory response syndrome (SIRS) criteria.", "Multiple definitions and terminologies are currently in use for sepsis, septic shock, and organ dysfunction, leading to discrepancies in reported incidence and observed mortality.", "The task force concluded the term severe sepsis was redundant.   ", "RECOMMENDATIONS Sepsis should be defined as life-threatening organ dysfunction caused by a dysregulated host response to infection.", "For clinical operationalization, organ dysfunction can be represented by an increase in the Sequential [Sepsis-related] Organ Failure Assessment (SOFA) score of 2 points or more, which is associated with an in-hospital mortality greater than 10%.", "Septic shock should be defined as a subset of sepsis in which particularly profound circulatory, cellular, and metabolic abnormalities are associated with a greater risk of mortality than with sepsis alone.", "Patients with septic shock can be clinically identified by a vasopressor requirement to maintain a mean arterial pressure of 65 mm Hg or greater and serum lactate level greater than 2 mmol/L (>18 mg/dL) in the absence of hypovolemia.", "This combination is associated with hospital mortality rates greater than 40%.", "In out-of-hospital, emergency department, or general hospital ward settings, adult patients with suspected infection can be rapidly identified as being more likely to have poor outcomes typical of sepsis if they have at least 2 of the following clinical criteria that together constitute a new bedside clinical score termed quickSOFA (qSOFA): respiratory rate of 22/min or greater, altered mentation, or systolic blood pressure of 100 mm Hg or less.   \n", "CONCLUSIONS AND RELEVANCE These updated definitions and clinical criteria should replace previous definitions, offer greater consistency for epidemiologic studies and clinical trials, and facilitate earlier recognition and more timely management of patients with sepsis or at risk of developing sepsis."], "structured": true}
{"doc_id": 5597586, "title": "Stem cell transplantation in patients with autonomic neuropathy due to primary (AL) amyloidosis.", "abstract": ["OBJECTIVES Patients with AL amyloidosis can benefit from high-dose chemotherapy and autologous stem cell transplantation (ASCT).", "Transplantation can be challenging due to fluid shifts, sepsis, and cardiac dysrhythmias.", "Amyloidosis may present with autonomic neuropathy (AN) that renders peritransplant care problematic.", "The purpose of this study was to determine the outcome of patients with AN during and after ASCT.   \n", "METHODS We performed a case-control study of patients with AL amyloidosis with associated AN and compared them to a large matched cohort without AN who also underwent ASCT.   \n", "RESULTS We identified 13 patients with AN who underwent ASCT and a matched control group of 95 patients without AN.", "Patients with AN had more organs involved (median 2.5 vs 1, p < 0.001) and the conditioning dose of melphalan was often reduced by 30% compared to controls without AN (p = 0.0015).", "Median duration of hospitalization was similar for both cohorts, as were engraftment kinetics.", "Atrial fibrillation occurred in all patients with AN but in only 1 control patient (p < 0.0001).", "Median overall survival (OS) for patients with AN was 29 months but >60 months for controls (p < 0.0001).", "On univariate analysis, cardiac involvement (p = 0.0132), AN (p = 0.0011), glomerular filtration rate (p = 0.038), number of organs involved (p = 0.0064), and NT-pro-BNP (p = 0.039) all had an impact on OS.", "On multivariate analysis, AN retained an independent adverse impact on OS.   \n", "CONCLUSIONS Patients with autonomic neuropathy secondary to AL amyloidosis can undergo autologous stem cell transplantation with relative safety.", "Autonomic neuropathy is an independent, adverse determinant of survival in these patients."], "structured": true}
{"doc_id": 5612738, "title": "MicroRNA-148a regulates LDL receptor and ABCA1 expression to control circulating lipoprotein levels", "abstract": ["The hepatic low-density lipoprotein receptor (LDLR) pathway is essential for clearing circulating LDL cholesterol (LDL-C).", "Whereas the transcriptional regulation of LDLR is well characterized, the post-transcriptional mechanisms that govern LDLR expression are just beginning to emerge.", "Here we develop a high-throughput genome-wide screening assay to systematically identify microRNAs (miRNAs) that regulate LDLR activity in human hepatic cells.", "From this screen we identified and characterized miR-148a as a negative regulator of LDLR expression and activity and defined a sterol regulatory element\u2013binding protein 1 (SREBP1)-mediated pathway through which miR-148a regulates LDL-C uptake.", "In mice, inhibition of miR-148a increased hepatic LDLR expression and decreased plasma LDL-C. Moreover, we found that miR-148a regulates hepatic expression of ATP-binding cassette, subfamily A, member 1 (ABCA1) and circulating high-density lipoprotein cholesterol (HDL-C) levels in vivo.", "These studies uncover a role for miR-148a as a key regulator of hepatic LDL-C clearance through direct modulation of LDLR expression and demonstrate the therapeutic potential of inhibiting miR-148a to ameliorate an elevated LDL-C/HDL-C ratio, a prominent risk factor for cardiovascular disease."], "structured": false}
{"doc_id": 5633876, "title": "BRACHYURY and CDX2 Mediate BMP-Induced Differentiation of Human and Mouse Pluripotent Stem Cells into Embryonic and Extraembryonic Lineages", "abstract": ["BMP is thought to induce hESC differentiation toward multiple lineages including mesoderm and trophoblast.", "The BMP-induced trophoblast phenotype is a long-standing paradox in stem cell biology.", "Here we readdressed BMP function in hESCs and mouse epiblast-derived cells.", "We found that BMP4 cooperates with FGF2 (via ERK) to induce mesoderm and to inhibit endoderm differentiation.", "These conditions induced cells with high levels of BRACHYURY (BRA) that coexpressed CDX2.", "BRA was necessary for and preceded CDX2 expression; both genes were essential for expression not only of mesodermal genes but also of trophoblast-associated genes.", "Maximal expression of the latter was seen in the absence of FGF but these cells coexpressed mesodermal genes and moreover they differed in cell surface and epigenetic properties from placental trophoblast.", "We conclude that BMP induces human and mouse pluripotent stem cells primarily to form mesoderm, rather than trophoblast, acting through BRA and CDX2."], "structured": false}
{"doc_id": 5633957, "title": "Degradation of Cellular miR-27 by a Novel, Highly Abundant Viral Transcript Is Important for Efficient Virus Replication In Vivo", "abstract": ["Cytomegaloviruses express large amounts of viral miRNAs during lytic infection, yet, they only modestly alter the cellular miRNA profile.", "The most prominent alteration upon lytic murine cytomegalovirus (MCMV) infection is the rapid degradation of the cellular miR-27a and miR-27b.", "Here, we report that this regulation is mediated by the \u223c1.7 kb spliced and highly abundant MCMV m169 transcript.", "Specificity to miR-27a/b is mediated by a single, apparently optimized, miRNA binding site located in its 3'-UTR.", "This site is easily and efficiently retargeted to other cellular and viral miRNAs by target site replacement.", "Expression of the 3'-UTR of m169 by an adenoviral vector was sufficient to mediate its function, indicating that no other viral factors are essential in this process.", "Degradation of miR-27a/b was found to be accompanied by 3'-tailing and -trimming.", "Despite its dramatic effect on miRNA stability, we found this interaction to be mutual, indicating potential regulation of m169 by miR-27a/b.", "Most interestingly, three mutant viruses no longer able to target miR-27a/b, either due to miRNA target site disruption or target site replacement, showed significant attenuation in multiple organs as early as 4 days post infection, indicating that degradation of miR-27a/b is important for efficient MCMV replication in vivo."], "structured": false}
{"doc_id": 5641851, "title": "Social and geographical factors affecting access to treatment of colorectal cancer: a cancer registry study", "abstract": ["OBJECTIVE Cancer outcomes vary between and within countries with patients from deprived backgrounds known to have inferior survival.", "The authors set out to explore the effect of deprivation in relation to the accessibility of hospitals offering diagnostic and therapeutic services on stage at presentation and receipt of treatment.   \n", "DESIGN Analysis of a Cancer Registry Database.", "Data included stage and treatment details from the first 6 months.", "The socioeconomic status of the immediate area of residence and the travel time from home to hospital was derived from the postcode.   \n", "SETTING Population-based study of patients resident in a large area in the north of England.   \n", "PARTICIPANTS 39 619 patients with colorectal cancer diagnosed between 1994 and 2002.   \n", "OUTCOMES MEASURED Stage of diagnosis and receipt of treatment in relation to deprivation and distance from hospital.   \n", "RESULTS Patients in the most deprived quartile were significantly more likely to be diagnosed at stage 4 for rectal cancer (OR 1.516, p<0.05) but less so for colonic cancer.", "There was a trend for both sites for patients in the most deprived quartile to be less likely to receive chemotherapy for stage 4 disease.", "Patients with colonic cancer were very significantly less likely to receive any treatment if they came from any but the most affluent area (ORs 0.639, 0.603 and 0.544 in increasingly deprived quartiles), this may have been exacerbated if the hospital was distant from their residence (OR for forth quartile for both travel and deprivation 0.731, not significant).", "The effect was less for rectal cancer and no effect of distance was seen.   \n", "CONCLUSIONS Residing in a deprived area is associated with tendencies to higher stage at diagnosis and especially in the case of colonic cancer to reduced receipt of treatment.", "These observations are consistent with other findings and indicate that access to diagnosis requires further investigation."], "structured": true}
{"doc_id": 5649538, "title": "Development of candidate genomic markers to select breast cancer patients for dasatinib therapy.", "abstract": ["Patient selection is important for targeted therapies, yet phase I/II trials are often underpowered for developing predictors of drug response.", "The goal of this research was to define genomic predictors for dasatinib that could be prospectively tested in early-phase clinical trials.", "Gene expression profiles of dasatinib-sensitive and dasatinib-resistant cell lines (n = 23) were compared to develop a dasatinib-sensitivity index (modified DS index).", "A Src pathway activity index (revised Src index) was defined using genes induced by the Src transfection of mammary epithelial cells and was optimized to be reproducible across cell lines and human specimens.", "A dasatinib target index was devised using the weighted sum of 19 kinases that bind to dasatinib with variable affinity.", "The performance of these prediction models was assessed in independent cell lines with known dasatinib sensitivity.", "The feasibility of applying these genomic tests to human samples was evaluated on 133 biopsies of primary breast cancers.", "The modified DS index showed 90% accuracy in independent breast cancer cell lines (n = 12) and the target index, but not the revised Src index signature, also distinguished dasatinib-sensitive and dasatinib-resistant cells (P = 0.0024).", "The genomic predictors showed acceptable reproducibility in replicate cell line and human gene expression data.", "When all three predictors were applied to the same 133 patient samples, the predictors identified different patient subsets as potentially sensitive.", "We defined three conceptually different potential predictors of dasatinib response that were reproducible across cell lines and human data.", "These candidate markers are being tested in a clinical trial to determine their utility."], "structured": false}
{"doc_id": 5650232, "title": "BEDTools: a flexible suite of utilities for comparing genomic features", "abstract": ["MOTIVATION Testing for correlations between different sets of genomic features is a fundamental task in genomics research.", "However, searching for overlaps between features with existing web-based methods is complicated by the massive datasets that are routinely produced with current sequencing technologies.", "Fast and flexible tools are therefore required to ask complex questions of these data in an efficient manner.   \n", "RESULTS This article introduces a new software suite for the comparison, manipulation and annotation of genomic features in Browser Extensible Data (BED) and General Feature Format (GFF) format.", "BEDTools also supports the comparison of sequence alignments in BAM format to both BED and GFF features.", "The tools are extremely efficient and allow the user to compare large datasets (e.g. next-generation sequencing data) with both public and custom genome annotation tracks.", "BEDTools can be combined with one another as well as with standard UNIX commands, thus facilitating routine genomics tasks as well as pipelines that can quickly answer intricate questions of large genomic datasets.   ", "AVAILABILITY AND IMPLEMENTATION BEDTools was written in C++.", "Source code and a comprehensive user manual are freely available at http://code.google.com/p/bedtools   CONTACT aaronquinlan@gmail.com; imh4y@virginia.edu   SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online."], "structured": true}
{"doc_id": 5687200, "title": "Vegetarian diet improves insulin resistance and oxidative stress markers more than conventional diet in subjects with Type 2 diabetes", "abstract": ["AIMS The aim of this study was to compare the effects of calorie-restricted vegetarian and conventional diabetic diets alone and in combination with exercise on insulin resistance, visceral fat and oxidative stress markers in subjects with Type 2 diabetes.   \n", "METHODS A 24-week, randomized, open, parallel design was used.", "Seventy-four patients with Type 2 diabetes were randomly assigned to either the experimental group (n = 37), which received a vegetarian diet, or the control group (n = 37), which received a conventional diabetic diet.", "Both diets were isocaloric, calorie restricted (-500 kcal/day).", "All meals during the study were provided.", "The second 12 weeks of the diet were combined with aerobic exercise.", "Participants were examined at baseline, 12 weeks and 24 weeks.", "Primary outcomes were: insulin sensitivity measured by hyperinsulinaemic isoglycaemic clamp; volume of visceral and subcutaneous fat measured by magnetic resonance imaging; and oxidative stress measured by thiobarbituric acid reactive substances.", "Analyses were by intention to treat.   \n", "RESULTS Forty-three per cent of participants in the experimental group and 5% of participants in the control group reduced diabetes medication (P < 0.001).", "Body weight decreased more in the experimental group than in the control group [-6.2 kg (95% CI -6.6 to -5.3) vs. -3.2 kg (95% CI -3.7 to -2.5); interaction group \u00d7 time P = 0.001].", "An increase in insulin sensitivity was significantly greater in the experimental group than in the control group [30% (95% CI 24.5-39) vs. 20% (95% CI 14-25), P = 0.04].", "A reduction in both visceral and subcutaneous fat was greater in the experimental group than in the control group (P = 0.007 and P = 0.02, respectively).", "Plasma adiponectin increased (P = 0.02) and leptin decreased (P = 0.02) in the experimental group, with no change in the control group.", "Vitamin C, superoxide dismutase and reduced glutathione increased in the experimental group (P = 0.002, P < 0.001 and P = 0.02, respectively).", "Differences between groups were greater after the addition of exercise training.", "Changes in insulin sensitivity and enzymatic oxidative stress markers correlated with changes in visceral fat.   \n", "CONCLUSIONS A calorie-restricted vegetarian diet had greater capacity to improve insulin sensitivity compared with a conventional diabetic diet over 24 weeks.", "The greater loss of visceral fat and improvements in plasma concentrations of adipokines and oxidative stress markers with this diet may be responsible for the reduction of insulin resistance.", "The addition of exercise training further augmented the improved outcomes with the vegetarian diet."], "structured": true}
{"doc_id": 5691302, "title": "Antidepressant use and risk of adverse outcomes in older people: population based cohort study", "abstract": ["OBJECTIVES To investigate the association between antidepressant treatment and risk of several potential adverse outcomes in older people with depression and to examine risks by class of antidepressant, duration of use, and dose.   \n", "DESIGN Cohort study of people aged 65 and over diagnosed as having depression.   \n", "SETTING 570 general practices in the United Kingdom supplying data to the QResearch primary care database.   \n", "PARTICIPANTS 60,746 patients diagnosed as having a new episode of depression between the ages of 65 and 100 years from 1 January 1996 to 31 December 2007 and followed up until 31 December 2008.   \n", "MAIN OUTCOME MEASURES Hazard ratios associated with antidepressant use for all cause mortality, attempted suicide/self harm, myocardial infarction, stroke/transient ischaemic attack, falls, fractures, upper gastrointestinal bleeding, epilepsy/seizures, road traffic accidents, adverse drug reactions, and hyponatraemia, adjusted for a range of potential confounding variables.", "Hazard ratios were calculated for antidepressant class (tricyclic and related antidepressants, selective serotonin reuptake inhibitors, other antidepressants), dose, and duration of use and for commonly prescribed individual drugs.   \n", "RESULTS 54,038 (89.0%) patients received at least one prescription for an antidepressant during follow-up.", "A total of 1,398,359 antidepressant prescriptions were issued: 764,659 (54.7%) for selective serotonin reuptake inhibitors, 442,192 (31.6%) for tricyclic antidepressants, 2203 (0.2%) for monoamine oxidase inhibitors, and 189,305 (13.5%) for the group of other antidepressants.", "The associations with the adverse outcomes differed significantly between the antidepressant classes for seven outcomes.", "Selective serotonin reuptake inhibitors were associated with the highest adjusted hazard ratios for falls (1.66, 95% confidence interval 1.58 to 1.73) and hyponatraemia (1.52, 1.33 to 1.75) compared with when antidepressants were not being used.", "The group of other antidepressants was associated with the highest adjusted hazard ratios for all cause mortality (1.66, 1.56 to 1.77), attempted suicide/self harm (5.16, 3.90 to 6.83), stroke/transient ischaemic attack (1.37, 1.22 to 1.55), fracture (1.64, 1.46 to 1.84), and epilepsy/seizures (2.24, 1.60 to 3.15), compared with when antidepressants were not being used.", "Tricyclic antidepressants did not have the highest hazard ratio for any of the outcomes.", "Significantly different associations also existed between the individual drugs for the same seven outcomes; trazodone (tricyclic antidepressant), mirtazapine, and venlafaxine (both in the group of other antidepressants) were associated with the highest rates for some of these outcomes.", "Absolute risks over 1 year for all cause mortality were 7.04% for patients while not taking antidepressants, 8.12% for those taking tricyclic antidepressants, 10.61% for selective serotonin reuptake inhibitors, and 11.43% for other antidepressants.   \n", "CONCLUSIONS Selective serotonin reuptake inhibitors and drugs in the group of other antidepressants were associated with an increased risk of several adverse outcomes compared with tricyclic antidepressants.", "Among individual drugs, trazodone, mirtazapine, and venlafaxine were associated with the highest risks for some outcomes.", "As this is an observational study, it is susceptible to confounding by indication, channelling bias, and residual confounding, so differences in characteristics between patients prescribed different antidepressant drugs that could account for some of the associations between the drugs and the adverse outcomes may remain.", "Further research is needed to confirm these findings, but the risks and benefits of different antidepressants should be carefully evaluated when these drugs are prescribed to older people."], "structured": true}
{"doc_id": 5698494, "title": "The benefits of statins in people without established cardiovascular disease but with cardiovascular risk factors: meta-analysis of randomised controlled trials", "abstract": ["OBJECTIVES To investigate whether statins reduce all cause mortality and major coronary and cerebrovascular events in people without established cardiovascular disease but with cardiovascular risk factors, and whether these effects are similar in men and women, in young and older (>65 years) people, and in people with diabetes mellitus.   \n", "DESIGN Meta-analysis of randomised trials.   \n", "DATA SOURCES Cochrane controlled trials register, Embase, and Medline.", "Data abstraction Two independent investigators identified studies on the clinical effects of statins compared with a placebo or control group and with follow-up of at least one year, at least 80% or more participants without established cardiovascular disease, and outcome data on mortality and major cardiovascular disease events.", "Heterogeneity was assessed using the Q and I(2) statistics.", "Publication bias was assessed by visual examination of funnel plots and the Egger regression test.   \n", "RESULTS 10 trials enrolled a total of 70 388 people, of whom 23 681 (34%) were women and 16 078 (23%) had diabetes mellitus.", "Mean follow-up was 4.1 years.", "Treatment with statins significantly reduced the risk of all cause mortality (odds ratio 0.88, 95% confidence interval 0.81 to 0.96), major coronary events (0.70, 0.61 to 0.81), and major cerebrovascular events (0.81, 0.71 to 0.93).", "No evidence of an increased risk of cancer was observed.", "There was no significant heterogeneity of the treatment effect in clinical subgroups.   \n", "CONCLUSION In patients without established cardiovascular disease but with cardiovascular risk factors, statin use was associated with significantly improved survival and large reductions in the risk of major cardiovascular events."], "structured": true}
{"doc_id": 5700349, "title": "Mechanical coupling between transsynaptic N-cadherin adhesions and actin flow stabilizes dendritic spines", "abstract": ["The morphology of neuronal dendritic spines is a critical indicator of synaptic function.", "It is regulated by several factors, including the intracellular actin/myosin cytoskeleton and transcellular N-cadherin adhesions.", "To examine the mechanical relationship between these molecular components, we performed quantitative live-imaging experiments in primary hippocampal neurons.", "We found that actin turnover and structural motility were lower in dendritic spines than in immature filopodia and increased upon expression of a nonadhesive N-cadherin mutant, resulting in an inverse relationship between spine motility and actin enrichment.", "Furthermore, the pharmacological stimulation of myosin II induced the rearward motion of actin structures in spines, showing that myosin II exerts tension on the actin network.", "Strikingly, the formation of stable, spine-like structures enriched in actin was induced at contacts between dendritic filopodia and N-cadherin-coated beads or micropatterns.", "Finally, computer simulations of actin dynamics mimicked various experimental conditions, pointing to the actin flow rate as an important parameter controlling actin enrichment in dendritic spines.", "Together these data demonstrate that a clutch-like mechanism between N-cadherin adhesions and the actin flow underlies the stabilization of dendritic filopodia into mature spines, a mechanism that may have important implications in synapse initiation, maturation, and plasticity in the developing brain."], "structured": false}
{"doc_id": 5702790, "title": "Phosphate and R2D2 restrict the substrate specificity of Dicer-2, an ATP-driven ribonuclease.", "abstract": ["Drosophila Dicer-2 generates small interfering RNAs (siRNAs) from long double-stranded RNA (dsRNA), whereas Dicer-1 produces microRNAs (miRNAs) from pre-miRNA.", "What makes the two Dicers specific for their biological substrates?", "We find that purified Dicer-2 can efficiently cleave pre-miRNA, but that inorganic phosphate and the Dicer-2 partner protein R2D2 inhibit pre-miRNA cleavage.", "Dicer-2 contains C-terminal RNase III domains that mediate RNA cleavage and an N-terminal helicase motif, whose function is unclear.", "We show that Dicer-2 is a dsRNA-stimulated ATPase that hydrolyzes ATP to ADP; ATP hydrolysis is required for Dicer-2 to process long dsRNA, but not pre-miRNA.", "Wild-type Dicer-2, but not a mutant defective in ATP hydrolysis, can generate siRNAs faster than it can dissociate from a long dsRNA substrate.", "We propose that the Dicer-2 helicase domain uses ATP to generate many siRNAs from a single molecule of dsRNA before dissociating from its substrate."], "structured": false}
{"doc_id": 5704562, "title": "Therapeutic potential of mood stabilizers lithium and valproic acid: beyond bipolar disorder.", "abstract": ["The mood stabilizers lithium and valproic acid (VPA) are traditionally used to treat bipolar disorder (BD), a severe mental illness arising from complex interactions between genes and environment that drive deficits in cellular plasticity and resiliency.", "The therapeutic potential of these drugs in other central nervous system diseases is also gaining support.", "This article reviews the various mechanisms of action of lithium and VPA gleaned from cellular and animal models of neurologic, neurodegenerative, and neuropsychiatric disorders.", "Clinical evidence is included when available to provide a comprehensive perspective of the field and to acknowledge some of the limitations of these treatments.", "First, the review describes how action at these drugs' primary targets--glycogen synthase kinase-3 for lithium and histone deacetylases for VPA--induces the transcription and expression of neurotrophic, angiogenic, and neuroprotective proteins.", "Cell survival signaling cascades, oxidative stress pathways, and protein quality control mechanisms may further underlie lithium and VPA's beneficial actions.", "The ability of cotreatment to augment neuroprotection and enhance stem cell homing and migration is also discussed, as are microRNAs as new therapeutic targets.", "Finally, preclinical findings have shown that the neuroprotective benefits of these agents facilitate anti-inflammation, angiogenesis, neurogenesis, blood-brain barrier integrity, and disease-specific neuroprotection.", "These mechanisms can be compared with dysregulated disease mechanisms to suggest core cellular and molecular disturbances identifiable by specific risk biomarkers.", "Future clinical endeavors are warranted to determine the therapeutic potential of lithium and VPA across the spectrum of central nervous system diseases, with particular emphasis on a personalized medicine approach toward treating these disorders."], "structured": false}
{"doc_id": 5710820, "title": "The feasibility of malaria elimination in South Africa", "abstract": ["BACKGROUND Following the last major malaria epidemic in 2000, malaria incidence in South Africa has declined markedly.", "The decrease has been so emphatic that South Africa now meets the World Health Organization (WHO) threshold for malaria elimination.", "Given the Millennium Development Goal of reversing the spread of malaria by 2015, South Africa is being urged to adopt an elimination agenda.", "This study aimed to determine the appropriateness of implementing a malaria elimination programme in present day South Africa.   \n", "METHODS An assessment of the progress made by South Africa in terms of implementing an integrated malaria control programme across the three malaria-endemic provinces was undertaken.", "Vector control and case management data were analysed from the period of 2000 until 2011.   \n", "RESULTS Both malaria-related morbidity and mortality have decreased significantly across all three malaria-endemic provinces since 2000.", "The greatest decline was seen in KwaZulu-Natal where cases decreased from 42,276 in 2000 to 380 in 2010 and deaths dropped from 122 in 2000 to six in 2010.", "Although there has been a 49.2 % (8,553 vs 4,214) decrease in the malaria cases reported in Limpopo Province, currently it is the largest contributor to the malaria incidence in South Africa.", "Despite all three provinces reporting average insecticide spray coverage of over 80%, malaria incidence in both Mpumalanga and Limpopo remains above the elimination threshold.", "Locally transmitted case numbers have declined in all three malaria provinces but imported case numbers have been increasing.", "Knowledge gaps in vector distribution, insecticide resistance status and drug usage were also identified.   \n", "CONCLUSIONS Malaria elimination in South Africa is a realistic possibility if certain criteria are met.", "Firstly, there must be continued support for the existing malaria control programmes to ensure the gains made are sustained.", "Secondly, cross border malaria control initiatives with neighbouring countries must be strongly encouraged and supported to reduce malaria in the region and the importation of malaria into South Africa.", "Thirdly, operational research, particularly on vector distribution and insecticide resistance status must be conducted as a matter of urgency, and finally, the surveillance systems must be refined to ensure the information required to inform an elimination agenda are routinely collected."], "structured": true}
{"doc_id": 5735492, "title": "The epidemiology of sexually transmitted co-infections in HIV-positive and HIV-negative African-Caribbean women in Toronto", "abstract": ["BACKGROUND HIV disproportionately affects African-Caribbean women in Canada but the frequency and distribution of sexually transmitted infections in this community have not been previously studied.   \n", "METHODS We recruited women based on HIV status through a Toronto community health centre.", "Participants completed a socio-behavioural questionnaire using Audio Computer Assisted Self-Interview (ACASI) and provided blood for syphilis, HIV, hepatitis B and C, herpes simplex virus type 1 (HSV-1), herpes simplex virus type 2 (HSV-2), and human cytomegalovirus (CMV) serology, urine for chlamydia and gonorrhea molecular testing and vaginal secretions for bacterial vaginosis (BV) and human papillomavirus (HPV).", "Differences in prevalence were assessed for statistical significance using chi-square.   \n", "RESULTS We recruited 126 HIV-positive and 291 HIV-negative women, with a median age of 40 and 31 years, respectively (p < 0.001).", "Active HBV infection and lifetime exposure to HBV infection were more common in HIV-positive women (4.8% vs. 0.34%, p = 0.004; and 47.6% vs. 21.2%, p < 0.0001), as was a self-reported history of HBV vaccination (66.1% vs. 44.0%, p = 0.0001).", "Classical STIs were rare in both groups; BV prevalence was low and did not vary by HIV status.", "HSV-2 infection was markedly more frequent in HIV-positive (86.3%) than HIV-negative (46.6%) women (p < 0.0001).", "Vaginal HPV infection was also more common in HIV-positive than in HIV-negative women (50.8% vs. 22.6%, p < 0.0001) as was infection with high-risk oncogenic HPV types (48.4% vs. 17.3%, p < 0.0001).   \n", "CONCLUSIONS Classical STIs were infrequent in this clinic-based population of African-Caribbean women in Toronto.", "However, HSV-2 prevalence was higher than that reported in previous studies in the general Canadian population and was strongly associated with HIV infection, as was infection with hepatitis B and HPV."], "structured": true}
{"doc_id": 5752492, "title": "Characterization of Programmed Death-1 Homologue-1 (PD-1H) Expression and Function in Normal and HIV Infected Individuals", "abstract": ["Chronic immune activation that persists despite anti-retroviral therapy (ART) is the strongest predictor of disease progression in HIV infection.", "Monocyte/macrophages in HIV-infected individuals are known to spontaneously secrete cytokines, although neither the mechanism nor the molecules involved are known.", "Here we show that overexpression of the newly described co-stimulatory molecule, PD1 homologue (PD-1H) in human monocyte/macrophages is sufficient to induce spontaneous secretion of multiple cytokines.", "The process requires signaling via PD-1H as cytokine secretion could be abrogated by deletion of the cytoplasmic domain.", "Such overexpression of PD-1H, associated with spontaneous cytokine expression is seen in monocytes from chronically HIV-infected individuals and this correlates with immune activation and CD4 depletion, but not viral load.", "Moreover, antigen presentation by PD-1H-overexpressing monocytes results in enhanced cytokine secretion by HIV-specific T cells.", "These results suggest that PD-1H might play a crucial role in modulating immune activation and immune response in HIV infection."], "structured": false}
{"doc_id": 5760247, "title": "A conserved mechanism for centromeric nucleosome recognition by centromere protein CENP-C.", "abstract": ["Chromosome segregation during mitosis requires assembly of the kinetochore complex at the centromere.", "Kinetochore assembly depends on specific recognition of the histone variant CENP-A in the centromeric nucleosome by centromere protein C (CENP-C).", "We have defined the determinants of this recognition mechanism and discovered that CENP-C binds a hydrophobic region in the CENP-A tail and docks onto the acidic patch of histone H2A and H2B.", "We further found that the more broadly conserved CENP-C motif uses the same mechanism for CENP-A nucleosome recognition.", "Our findings reveal a conserved mechanism for protein recruitment to centromeres and a histone recognition mode whereby a disordered peptide binds the histone tail through hydrophobic interactions facilitated by nucleosome docking."], "structured": false}
{"doc_id": 5764562, "title": "Chemical tools for biomolecular imaging.", "abstract": ["The visualization of biologically relevant molecules and activities inside living cells continues to transform cell biology into a truly quantitative science.", "However, despite the spectacular achievements in some areas of cell biology, the majority of cellular processes still operate invisibly, not illuminated by even our brightest laser beams.", "Further progress therefore will depend not only on improvements in instrumentation but also increasingly on the development of new fluorophores and fluorescent sensors to target these activities.", "In the following, we review some of the recent approaches to generating such sensors, the methods to attach them to selected biomolecules, and their applications to various biological problems."], "structured": false}
{"doc_id": 5765455, "title": "Reactive oxygen species, DNA damage, and error-prone repair: a model for genomic instability with progression in myeloid leukemia?", "abstract": ["Myelodysplastic syndromes (MDS) comprise a heterogeneous group of disorders characterized by ineffective hematopoiesis, with an increased propensity to develop acute myelogenous leukemia (AML).", "The molecular basis for MDS progression is unknown, but a key element in MDS disease progression is loss of chromosomal material (genomic instability).", "Using our two-step mouse model for myeloid leukemic disease progression involving overexpression of human mutant NRAS and BCL2 genes, we show that there is a stepwise increase in the frequency of DNA damage leading to an increased frequency of error-prone repair of double-strand breaks (DSB) by nonhomologous end-joining.", "There is a concomitant increase in reactive oxygen species (ROS) in these transgenic mice with disease progression.", "Importantly, RAC1, an essential component of the ROS-producing NADPH oxidase, is downstream of RAS, and we show that ROS production in NRAS/BCL2 mice is in part dependent on RAC1 activity.", "DNA damage and error-prone repair can be decreased or reversed in vivo by N-acetyl cysteine antioxidant treatment.", "Our data link gene abnormalities to constitutive DNA damage and increased DSB repair errors in vivo and provide a mechanism for an increase in the error rate of DNA repair with MDS disease progression.", "These data suggest treatment strategies that target RAS/RAC pathways and ROS production in human MDS/AML."], "structured": false}
{"doc_id": 5774746, "title": "A link between inflammation and metastasis: serum amyloid A1 and A3 induce metastasis, and are targets of metastasis-inducing S100A4", "abstract": ["S100A4 is implicated in metastasis and chronic inflammation, but its function remains uncertain.", "Here we establish an S100A4-dependent link between inflammation and metastatic tumor progression.", "We found that the acute-phase response proteins serum amyloid A (SAA) 1 and SAA3 are transcriptional targets of S100A4 via Toll-like receptor 4 (TLR4)/nuclear factor-\u03baB signaling.", "SAA proteins stimulated the transcription of RANTES (regulated upon activation normal T-cell expressed and presumably secreted), G-CSF (granulocyte-colony-stimulating factor) and MMP2 (matrix metalloproteinase 2), MMP3, MMP9 and MMP13.", "We have also shown for the first time that SAA stimulate their own transcription as well as that of proinflammatory S100A8 and S100A9 proteins.", "Moreover, they strongly enhanced tumor cell adhesion to fibronectin, and stimulated migration and invasion of human and mouse tumor cells.", "Intravenously injected S100A4 protein induced expression of SAA proteins and cytokines in an organ-specific manner.", "In a breast cancer animal model, ectopic expression of SAA1 or SAA3 in tumor cells potently promoted widespread metastasis formation accompanied by a massive infiltration of immune cells.", "Furthermore, coordinate expression of S100A4 and SAA in tumor samples from colorectal carcinoma patients significantly correlated with reduced overall survival.", "These data show that SAA proteins are effectors for the metastasis-promoting functions of S100A4, and serve as a link between inflammation and tumor progression."], "structured": false}
{"doc_id": 5775033, "title": "Pyruvate dehydrogenase activity and acetyl group accumulation during exercise after different diets.", "abstract": ["Pyruvate dehydrogenase activity (PDHa) and acetyl group accumulation were examined in human skeletal muscle at rest and during exercise after different diets.", "Five males cycled at 75% of maximal O2 uptake (VO2 max) to exhaustion after consuming a low-carbohydrate diet (LCD) for 3 days and again 1-2 wk later for the same duration after consuming a high-carbohydrate diet (HCD) for 3 days.", "Resting PDHa was lower after a LCD (0.20 +/- 0.04 vs. 0.69 +/-", "0.05 mmol.min-1.kg wet wt-1; P < 0.05) and coincided with a greater intramuscular acetyl-CoA-to-CoASH ratio, acetyl-CoA content, and acetylcarnitine content.", "PDHa increased during exercise in both conditions but at a lower rate in the LCD condition compared with the HCD condition (1.46 +/- 0.25 vs. 2.65 +/-", "0.23 mmol.min-1.kg wet wt-1 at 16 min and 1.88 +/-", "0.20 vs. 3.11 +/-", "0.14 at the end of exercise; P < 0.05).", "During exercise muscle acetyl-CoA and acetylcarnitine content and the acetyl-CoA-to-CoASH ratio decreased in the LCD condition but increased in the HCD condition.", "Under resting conditions PDHa was influenced by the availability of fat or carbohydrate fuels acting through changes in the acetyl-CoA-to-CoASH ratio.", "However, during exercise the activation of PDHa occurred independent of changes in the acetyl-CoA-to-CoASH ratio, suggesting that other factors are more important."], "structured": false}
{"doc_id": 5782614, "title": "Clonal hematopoiesis of indeterminate potential and its distinction from myelodysplastic syndromes.", "abstract": ["Recent genetic analyses of large populations have revealed that somatic mutations in hematopoietic cells leading to clonal expansion are commonly acquired during human aging.", "Clonally restricted hematopoiesis is associated with an increased risk of subsequent diagnosis of myeloid or lymphoid neoplasia and increased all-cause mortality.", "Although myelodysplastic syndromes (MDS) are defined by cytopenias, dysplastic morphology of blood and marrow cells, and clonal hematopoiesis, most individuals who acquire clonal hematopoiesis during aging will never develop MDS.", "Therefore, acquisition of somatic mutations that drive clonal expansion in the absence of cytopenias and dysplastic hematopoiesis can be considered clonal hematopoiesis of indeterminate potential (CHIP), analogous to monoclonal gammopathy of undetermined significance and monoclonal B-cell lymphocytosis, which are precursor states for hematologic neoplasms but are usually benign and do not progress.", "Because mutations are frequently observed in healthy older persons, detection of an MDS-associated somatic mutation in a cytopenic patient without other evidence of MDS may cause diagnostic uncertainty.", "Here we discuss the nature and prevalence of CHIP, distinction of this state from MDS, and current areas of uncertainty regarding diagnostic criteria for myeloid malignancies."], "structured": false}
{"doc_id": 5783785, "title": "DNA Methylation mediated down-regulating of MicroRNA-33b and its role in gastric cancer", "abstract": ["The discovery of microRNAs (miRNAs) provides a new and powerful tool for studying the mechanism, diagnosis and treatment of human cancers.", "Currently, down-regulation of tumor suppressive miRNAs by CpG island hypermethylation is emerging as a common hallmark of cancer.", "Here, we reported that the down-regulation of miR-33b was associated with pM stage of gastric cancer (GC) patients.", "Ectopic expression of miR-33b in HGC-27 and MGC-803 cells inhibited cell proliferation, migration and invasion, which might be due to miR-33b targeting oncogene c-Myc.", "Moreover, enhanced methylation level of the CpG island upstream of miR-33b in GC patients with down-regulated miR-33b was confirmed by methylation-specific PCR (MSP) amplification.", "Furthermore, re-introduction of miR-33b significantly suppressed tumorigenesis of GC cells in the nude mice.", "In conclusion, miR-33b acts as a tumor suppressor and hypermethylation of the CpG island upstream of miR-33b is responsible for its down-regulation in gastric cancer."], "structured": false}
{"doc_id": 5785219, "title": "Modulation of glucose metabolism in macrophages by products of nitric oxide synthase.", "abstract": ["Nitric oxide (NO) is a product of L-arginine metabolism that suppresses cellular oxidative metabolism through the inhibition of tricarboxylic acid cycle and electron transport chain enzymes.", "The impact of NO synthase (NOS) activity on specific pathways of glucose metabolism in freshly harvested and overnight-cultured rat resident peritoneal macrophages, at rest and after stimulation with zymosan, was investigated using radiolabeled glucose.", "NOS activity was modulated through the L-arginine concentration in culture media and the use of its specific inhibitor, NG-monomethyl-L-arginine, and quantitated using radiolabeled L-arginine.", "Results demonstrated that NOS activity was associated with increased glucose disappearance, glycolysis, and hexose monophosphate shunt activity and, in line with the known inhibition of oxidative metabolism associated with the production of NO, with a decrease in the flux of glucose and butyrate carbon through the tricarboxylic acid cycle.", "In addition, the relative increase in glucose utilization that follows zymosan stimulation was enhanced by treatments that suppressed NOS activity.", "These results demonstrate that the characteristics of glucose metabolism by macrophages are, to a significant extent, determined by products of NOS."], "structured": false}
{"doc_id": 5798227, "title": "SOCS1/JAB is a negative regulator of LPS-induced macrophage activation.", "abstract": ["Bacterial lipopolysaccharide (LPS) triggers innate immune responses through Toll-like receptor (TLR) 4.", "We show here that the suppressor of cytokine-signaling-1 (SOCS1/JAB) is rapidly induced by LPS and negatively regulates LPS signaling.", "SOCS1(+/-) mice or SOCS1(-/-) mice with interferon-gamma (IFNgamma)-deficient background were more sensitive to LPS-induced lethal effects than were wild-type littermates.", "LPS-induced NO(2)(-) synthesis and TNFalpha production were augmented in SOCS1(-/-) macrophages.", "Furthermore, LPS tolerance, a protection mechanism against endotoxin shock, was also strikingly reduced in SOCS1(-/-) cells.", "LPS-induced I-kappaB and p38 phosphorylation was upregulated in SOCS1(-/-) macrophages, and forced expression of SOCS1 suppressed LPS-induced NF-kappaB activation.", "Thus, SOCS1 directly suppresses TLR4 signaling and modulates innate immunity."], "structured": false}
{"doc_id": 5800138, "title": "Bacteria-triggered CD4+ T Regulatory Cells Suppress Helicobacter hepaticus\u2013induced Colitis", "abstract": ["We have previously demonstrated that interleukin (IL)-10\u2013deficient (IL-10 knockout [KO]) but not wild-type (WT) mice develop colitis after infection with Helicobacter hepaticus .", "Here, we show that infected recombination activating gene (RAG) KO mice develop intestinal inflammation after reconstitution with CD4+ T cells from IL-10 KO animals and that the cotransfer of CD4+ T cells from H. hepaticus \u2013infected but not uninfected WT mice prevents this colitis.", "The disease-protective WT CD4+ cells are contained within the CD45RBlow fraction and unexpectedly were found in both the CD25+ and the CD25\u2212 subpopulations of these cells, their frequency being higher in the latter.", "The mechanism by which CD25+ and CD25\u2212 CD45RBlow CD4+ cells block colitis involves IL-10 and not transforming growth factor (TGF)-\u03b2, as treatment with anti\u2013IL-10R but not anti\u2013TGF-\u03b2 monoclonal antibody abrogated their protective effect.", "In vitro, CD45RBlow CD4+ cells from infected WT mice were shown to produce IL-10 and suppress interferon-\u03b3 production by IL-10 KO CD4+ cells in an H. hepaticus antigen\u2013specific manner.", "Together, our data support the concept that H. hepaticus infection results in the induction in WT mice of regulatory T cells that prevent bacteria-induced colitis.", "The induction of such cells in response to gut flora may be a mechanism protecting normal individuals against inflammatory bowel disease."], "structured": false}
{"doc_id": 5811042, "title": "The NLRP12 Sensor Negatively Regulates Autoinflammatory Disease by Modulating Interleukin-4 Production in T Cells.", "abstract": ["Missense mutations in the nucleotide-binding oligomerization domain (NOD)-like receptor pyrin domain containing family of gene 12 (Nlrp12) are associated with periodic fever syndromes and atopic dermatitis in humans.", "Here, we have demonstrated a crucial role for NLRP12 in negatively regulating pathogenic T cell responses.", "Nlrp12(-/-) mice responded to antigen immunization with hyperinflammatory T cell responses.", "Furthermore, transfer of CD4(+)CD45RB(hi)Nlrp12(-/-) T cells into immunodeficient mice led to more severe colitis and atopic dermatitis.", "NLRP12 deficiency did not, however, cause exacerbated ascending paralysis during experimental autoimmune encephalomyelitis (EAE); instead, Nlrp12(-/-) mice developed atypical neuroinflammatory symptoms that were characterized by ataxia and loss of balance.", "Enhanced T-cell-mediated interleukin-4 (IL-4) production promotes the development of atypical EAE disease in Nlrp12(-/-) mice.", "These results define an unexpected role for NLRP12 as an intrinsic negative regulator of T-cell-mediated immunity and identify altered NF-\u03baB regulation and IL-4 production as key mediators of NLRP12-associated disease."], "structured": false}
{"doc_id": 5821617, "title": "Shc coordinates signals from intercellular junctions and integrins to regulate flow-induced inflammation", "abstract": ["Atherosclerotic plaques develop in regions of the vasculature associated with chronic inflammation due to disturbed flow patterns.", "Endothelial phenotype modulation by flow requires the integration of numerous mechanotransduction pathways, but how this is achieved is not well understood.", "We show here that, in response to flow, the adaptor protein Shc is activated and associates with cell-cell and cell-matrix adhesions.", "Shc activation requires the tyrosine kinases vascular endothelial growth factor receptor 2 and Src.", "Shc activation and its vascular endothelial cadherin (VE-cadherin) association are matrix independent.", "In contrast, Shc binding to integrins requires VE-cadherin but occurs only on specific matrices.", "Silencing Shc results in reduction in both matrix-independent and matrix-dependent signals.", "Furthermore, Shc regulates flow-induced inflammatory signaling by activating nuclear factor kappaB-dependent signals that lead to atherogenesis.", "In vivo, Shc is activated in atherosclerosis-prone regions of arteries, and its activation correlates with areas of atherosclerosis.", "Our results support a model in which Shc orchestrates signals from cell-cell and cell-matrix adhesions to elicit flow-induced inflammatory signaling."], "structured": false}
{"doc_id": 5824955, "title": "SIRT1 Redistribution on Chromatin Promotes Genomic Stability but Alters Gene Expression during Aging", "abstract": ["Genomic instability and alterations in gene expression are hallmarks of eukaryotic aging.", "The yeast histone deacetylase Sir2 silences transcription and stabilizes repetitive DNA, but during aging or in response to a DNA break, the Sir complex relocalizes to sites of genomic instability, resulting in the desilencing of genes that cause sterility, a characteristic of yeast aging.", "Using embryonic stem cells, we show that mammalian Sir2, SIRT1, represses repetitive DNA and a functionally diverse set of genes across the mouse genome.", "In response to DNA damage, SIRT1 dissociates from these loci and relocalizes to DNA breaks to promote repair, resulting in transcriptional changes that parallel those in the aging mouse brain.", "Increased SIRT1 expression promotes survival in a mouse model of genomic instability and suppresses age-dependent transcriptional changes.", "Thus, DNA damage-induced redistribution of SIRT1 and other chromatin-modifying proteins may be a conserved mechanism of aging in eukaryotes."], "structured": false}
{"doc_id": 5824985, "title": "Bariatric Surgery in the United Kingdom: A Cohort Study of Weight Loss and Clinical Outcomes in Routine Clinical Care.", "abstract": ["BACKGROUND Bariatric surgery is becoming a more widespread treatment for obesity.", "Comprehensive evidence of the long-term effects of contemporary surgery on a broad range of clinical outcomes in large populations treated in routine clinical practice is lacking.", "The objective of this study was to measure the association between bariatric surgery, weight, body mass index, and obesity-related co-morbidities.   \n", "METHODS AND FINDINGS This was an observational retrospective cohort study using data from the United Kingdom Clinical Practice Research Datalink.", "All 3,882 patients registered in the database and with bariatric surgery on or before 31 December 2014 were included and matched by propensity score to 3,882 obese patients without surgery.", "The main outcome measures were change in weight and body mass index over 4 y; incident diagnoses of type 2 diabetes mellitus (T2DM), hypertension, angina, myocardial infarction (MI), stroke, fractures, obstructive sleep apnoea, and cancer; mortality; and resolution of hypertension and T2DM.", "Weight measures were available for 3,847 patients between 1 and 4 mo, 2,884 patients between 5 and 12 mo, and 2,258 patients between 13 and 48 mo post-procedure.", "Bariatric surgery patients exhibited rapid weight loss for the first four postoperative months, at a rate of 4.98 kg/mo (95% CI 4.88-5.08).", "Slower weight loss was sustained to the end of 4 y. Gastric bypass (6.56 kg/mo) and sleeve gastrectomy (6.29 kg/mo) were associated with greater initial weight reduction than gastric banding (2.77 kg/mo).", "Protective hazard ratios (HRs) were detected for bariatric surgery for incident T2DM, 0.68 (95% CI 0.55-0.83); hypertension, 0.35 (95% CI 0.27-0.45); angina, 0.59 (95% CI 0.40-0.87);MI, 0.28 (95% CI 0.10-0.74); and obstructive sleep apnoea, 0.55 (95% CI 0.40-0.87).", "Strong associations were found between bariatric surgery and the resolution of T2DM, with a HR of 9.29 (95% CI 6.84-12.62), and between bariatric surgery and the resolution of hypertension, with a HR of 5.64 (95% CI 2.65-11.99).", "No association was detected between bariatric surgery and fractures, cancer, or stroke.", "Effect estimates for mortality found no protective association with bariatric surgery overall, with a HR of 0.97 (95% CI 0.66-1.43).", "The data used were recorded for the management of patients in primary care and may be subject to inaccuracy, which would tend to lead to underestimates of true relative effect sizes.   \n", "CONCLUSIONS Bariatric surgery as delivered in the UK healthcare system is associated with dramatic weight loss, sustained at least 4 y after surgery.", "This weight loss is accompanied by substantial improvements in pre-existing T2DM and hypertension, as well as a reduced risk of incident T2DM, hypertension, angina, MI, and obstructive sleep apnoea.", "Widening the availability of bariatric surgery could lead to substantial health benefits for many people who are morbidly obese."], "structured": true}
{"doc_id": 5828251, "title": "Notch signalling acts in postmitotic avian myogenic cells to control MyoD activation.", "abstract": ["During Drosophila myogenesis, Notch signalling acts at multiple steps of the muscle differentiation process.", "In vertebrates, Notch activation has been shown to block MyoD activation and muscle differentiation in vitro, suggesting that this pathway may act to maintain the cells in an undifferentiated proliferative state.", "In this paper, we address the role of Notch signalling in vivo during chick myogenesis.", "We first demonstrate that the Notch1 receptor is expressed in postmitotic cells of the myotome and that the Notch ligands Delta1 and Serrate2 are detected in subsets of differentiating myogenic cells and are thus in position to signal to Notch1 during myogenic differentiation.", "We also reinvestigate the expression of MyoD and Myf5 during avian myogenesis, and observe that Myf5 is expressed earlier than MyoD, consistent with previous results in the mouse.", "We then show that forced expression of the Notch ligand, Delta1, during early myogenesis, using a retroviral system, has no effect on the expression of the early myogenic markers Pax3 and Myf5, but causes strong down-regulation of MyoD in infected somites.", "Although Delta1 overexpression results in the complete lack of differentiated muscles, detailed examination of the infected embryos shows that initial formation of a myotome is not prevented, indicating that exit from the cell cycle has not been blocked.", "These results suggest that Notch signalling acts in postmitotic myogenic cells to control a critical step of muscle differentiation."], "structured": false}
{"doc_id": 5835149, "title": "Hepatitis C virus infection in a large cohort of homosexually active men: independent associations with HIV-1 infection and injecting drug use but not sexual behaviour.", "abstract": ["OBJECTIVE To determine the prevalence and risk factors for hepatitis C virus (HCV) infection in a cohort of homosexually active men, with particular reference to assessing sexual transmission.   \n", "DESIGN Prevalence based on cross-sectional testing for HCV (c100 protein) antibody in a cohort using sera stored between 1984 and 1989, and assessment of risk factors using a case-control analysis based on questionnaire data from HCV positive and negative subjects.   \n", "SUBJECTS/SETTING 1038 homosexually active men who were participating in a prospective study established to identify risk factors for AIDS.", "They had been recruited through private and public primary care and sexually transmissible disease (STD) services in central Sydney.   \n", "MAIN OUTCOME MEASURES Prevalence of HCV antibody and its association with human immunodeficiency virus type 1 (HIV-1) infection and other STDs, number of sexual partners, sexual practices and recreational drug use.   \n", "RESULTS Overall, 7.6% of subjects tested were seropositive for HCV antibody.", "In univariate analysis, HCV infection was significantly associated with injecting drug use (IDU) (OR = 8.18, p < 0.0001) and HIV infection (OR = 3.14, p < 0.0001) and with self reported history of syphilis (OR = 1.88, p = 0.016), anogenital herpes (OR = 1.93, p = 0.017), gonorrhoea (OR = 2.43, p = 0.009) and hepatitis B (OR = 1.92, p = 0.010).", "In case control analysis, similar sexual behaviours (partner numbers and practices) were reported by HCV positive and HCV negative subjects except that HCV negative subjects more frequently reported engaging than HCV positive subject in unprotected receptive anal intercourse without ejaculation (OR = 0.61, p = 0.034), unprotected insertive (OR = 0.59, p = 0.039) and receptive (OR = 0.56, p = 0.016) oro-anal intercourse (rimming) and insertive fisting (OR = 0.48, p = 0.034).", "In multiple logistic regression analyses, only HIV-1 infection (OR = 3.18, p < 0.0001) and IDU in the previous six months (OR = 7.24, p < 0.0001) remained significantly associated with the presence of HCV antibody.   \n", "CONCLUSIONS IDU was the major behavioural risk factor for HCV infection.", "If sexual or another from of transmission did occur, it may have been facilitated by concurrent HIV-1 infection."], "structured": true}
{"doc_id": 5838067, "title": "Analysis of human cytomegalovirus-encoded microRNA activity during infection.", "abstract": ["MicroRNAs (miRNAs) are expressed in a wide variety of organisms, ranging from plants to animals, and are key posttranscriptional regulators of gene expression.", "Virally encoded miRNAs are unique in that they could potentially target both viral and host genes.", "Indeed, we have previously demonstrated that a human cytomegalovirus (HCMV)-encoded miRNA, miR-UL112, downregulates the expression of a host immune gene, MICB.", "Remarkably, it was shown that the same miRNA also downregulates immediate-early viral genes and that its ectopic expression resulted in reduced viral replication and viral titers.", "The targets for most of the viral miRNAs, and hence their functions, are still unknown.", "Here we demonstrate that miR-UL112 also targets the UL114 gene, and we present evidence that the reduction of UL114 by miR-UL112 reduces its activity as uracil DNA glycosylase but only minimally affects virus growth.", "In addition, we show that two additional HCMV-encoded miRNAs, miR-US25-1 and miR-US25-2, reduce the viral replication and DNA synthesis not only of HCMV but also of other viruses, suggesting that these two miRNAs target cellular genes that are essential for virus growth.", "Thus, we suggest that in addition to miR-UL112, two additional HCMV miRNAs control the life cycle of the virus."], "structured": false}
{"doc_id": 5839365, "title": "Anti-obesity drugs: past, present and future", "abstract": ["The ideal anti-obesity drug would produce sustained weight loss with minimal side effects.", "The mechanisms that regulate energy balance have substantial built-in redundancy, overlap considerably with other physiological functions, and are influenced by social, hedonic and psychological factors that limit the effectiveness of pharmacological interventions.", "It is therefore unsurprising that anti-obesity drug discovery programmes have been littered with false starts, failures in clinical development, and withdrawals due to adverse effects that were not fully appreciated at the time of launch.", "Drugs that target pathways in metabolic tissues, such as adipocytes, liver and skeletal muscle, have shown potential in preclinical studies but none has yet reached clinical development.", "Recent improvements in the understanding of peptidergic signalling of hunger and satiety from the gastrointestinal tract mediated by ghrelin, cholecystokinin (CCK), peptide YY (PYY) and glucagon-like peptide-1 (GLP-1), and of homeostatic mechanisms related to leptin and its upstream pathways in the hypothalamus, have opened up new possibilities.", "Although some have now reached clinical development, it is uncertain whether they will meet the strict regulatory hurdles required for licensing of an anti-obesity drug.", "However, GLP-1 receptor agonists have already succeeded in diabetes treatment and, owing to their attractive body-weight-lowering effects in humans, will perhaps also pave the way for other anti-obesity agents.", "To succeed in developing drugs that control body weight to the extent seen following surgical intervention, it seems obvious that a new paradigm is needed.", "In other therapeutic arenas, such as diabetes and hypertension, lower doses of multiple agents targeting different pathways often yield better results than strategies that modify one pathway alone.", "Some combination approaches using peptides and small molecules have now reached clinical trials, although recent regulatory experience suggests that large challenges lie ahead.", "In future, this polytherapeutic strategy could possibly rival surgery in terms of efficacy, safety and sustainability of weight loss."], "structured": false}
{"doc_id": 5849439, "title": "Cytochemical Analysis of Pollen Development in Wild-Type Arabidopsis and a Male-Sterile Mutant.", "abstract": ["Microsporogenesis has been examined in wild-type Arabidopsis thaliana and the nuclear male-sterile mutant BM3 by cytochemical staining.", "The mutant lacks adenine phosphoribosyltransferase, an enzyme of the purine salvage pathway that converts adenine to AMP.", "Pollen development in the mutant began to diverge from wild type just after meiosis, as the tetrads of microspores were released from their callose walls.", "The first indication of abnormal pollen development in the mutant was a darker staining of the microspore wall due to an incomplete synthesis of the intine.", "Vacuole formation was delayed and irregular in the mutant, and the majority of the mutant microspores failed to undergo mitotic divisions.", "Enzyme activities of alcohol dehydrogenase and esterases decreased in the mutant soon after meiosis and were undetectable in mature pollen grains of the mutant.", "RNA accumulation was also diminished.", "These results are discussed in relation to the possible role(s) of adenine salvage in pollen development."], "structured": false}
{"doc_id": 5850219, "title": "Prevalence, risk factors, and uptake of interventions for sexually transmitted infections in Britain: findings from the National Surveys of Sexual Attitudes and Lifestyles (Natsal)", "abstract": ["BACKGROUND Population-based estimates of prevalence, risk distribution, and intervention uptake inform delivery of control programmes for sexually transmitted infections (STIs).", "We undertook the third National Survey of Sexual Attitudes and Lifestyles (Natsal-3) after implementation of national sexual health strategies, and describe the epidemiology of four STIs in Britain (England, Scotland, and Wales) and the uptake of interventions.   \n", "METHODS Between Sept 6, 2010 and Aug 31, 2012", ", we did a probability sample survey of 15,162 women and men aged 16-74 years in Britain.", "Participants were interviewed with computer-assisted face-to-face and self-completion questionnaires.", "Urine from a sample of participants aged 16-44 years who reported at least one sexual partner over the lifetime was tested for the presence of Chlamydia trachomatis, type-specific human papillomavirus (HPV), Neisseria gonorrhoeae, and HIV antibody.", "We describe age-specific and sex-specific prevalences of infection and intervention uptake, in relation to demographic and behavioural factors, and explore changes since Natsal-1 (1990-91) and Natsal-2 (1999-2001).   \n", "FINDINGS Of 8047 eligible participants invited to provide a urine sample, 4828 (60%) agreed.", "We excluded 278 samples, leaving 4550 (94%) participants with STI test results.", "Chlamydia prevalence was 1\u00b75% (95% CI 1\u00b71-2\u00b70) in women and 1\u00b71% (0\u00b77-1\u00b76) in men.", "Prevalences in individuals aged 16-24 years were 3\u00b71% (2\u00b72-4\u00b73) in women and 2\u00b73% (1\u00b75-3\u00b74) in men.", "Area-level deprivation and higher numbers of partners, especially without use of condoms, were risk factors.", "However, 60\u00b74% (45\u00b75-73\u00b77) of chlamydia in women and 43\u00b73% (25\u00b79-62\u00b75) in men was in individuals who had had one partner in the past year.", "Among sexually active 16-24-year-olds, 54\u00b72% (51\u00b74-56\u00b79) of women and 34\u00b76% (31\u00b78-37\u00b74) of men reported testing for chlamydia in the past year, with testing higher in those with more partners.", "High-risk HPV was detected in 15\u00b79% (14\u00b74-17\u00b75) of women, similar to in Natsal-2.", "Coverage of HPV catch-up vaccination was 61\u00b75% (58\u00b72-64\u00b77).", "Prevalence of HPV types 16 and 18 in women aged 18-20 years was lower in Natsal-3 than Natsal-2 (5\u00b78% [3\u00b79-8\u00b76] vs 11\u00b73% [6\u00b78-18\u00b72]; age-adjusted odds ratio 0\u00b744 [0\u00b721-0\u00b794]).", "Gonorrhoea (<0\u00b71% prevalence in women and men) and HIV (0\u00b71% prevalence in women and 0\u00b72% in men) were uncommon and restricted to participants with recognised high-risk factors.", "Since Natsal-2, substantial increases were noted in attendance at sexual health clinics (from 6\u00b77% to 21\u00b74% in women and from 7\u00b77% to 19\u00b76% in men) and HIV testing (from 8\u00b77% to 27\u00b76% in women and from 9\u00b72% to 16\u00b79% in men) in the past 5 years.   \n", "INTERPRETATION STIs were distributed heterogeneously, requiring general and infection-specific interventions.", "Increases in testing and attendance at sexual health clinics, especially in people at highest risk, are encouraging.", "However, STIs persist both in individuals accessing and those not accessing services.", "Our findings provide empirical evidence to inform future sexual health interventions and services.   \n", "FUNDING Grants from the UK Medical Research Council and the Wellcome Trust, with support from the Economic and Social Research Council and the Department of Health."], "structured": true}
{"doc_id": 5855168, "title": "Cancer Pharmacogenomics and Pharmacoepidemiology: Setting a Research Agenda to Accelerate Translation", "abstract": ["Recent advances in genomic research have demonstrated a substantial role for genomic factors in predicting response to cancer therapies.", "Researchers in the fields of cancer pharmacogenomics and pharmacoepidemiology seek to understand why individuals respond differently to drug therapy, in terms of both adverse effects and treatment efficacy.", "To identify research priorities as well as the resources and infrastructure needed to advance these fields, the National Cancer Institute (NCI) sponsored a workshop titled \"Cancer Pharmacogenomics: Setting a Research Agenda to Accelerate Translation\" on July 21, 2009, in Bethesda, MD.", "In this commentary, we summarize and discuss five science-based recommendations and four infrastructure-based recommendations that were identified as a result of discussions held during this workshop.", "Key recommendations include 1) supporting the routine collection of germline and tumor biospecimens in NCI-sponsored clinical trials and in some observational and population-based studies; 2) incorporating pharmacogenomic markers into clinical trials; 3) addressing the ethical, legal, social, and biospecimen- and data-sharing implications of pharmacogenomic and pharmacoepidemiologic research; and 4) establishing partnerships across NCI, with other federal agencies, and with industry.", "Together, these recommendations will facilitate the discovery and validation of clinical, sociodemographic, lifestyle, and genomic markers related to cancer treatment response and adverse events, and they will improve both the speed and efficiency by which new pharmacogenomic and pharmacoepidemiologic information is translated into clinical practice."], "structured": false}
{"doc_id": 5860364, "title": "Differential transcription of the orphan receptor RORbeta in nuclear extracts derived from Neuro2A and HeLa cells.", "abstract": ["An important model system for studying the process leading to productive transcription is provided by the superfamily of nuclear receptors, which are for the most part ligand-controlled transcription factors.", "Over the past years several 'orphan' nuclear receptors have been isolated for which no ligand has yet been identified.", "Very little is known about how these 'orphan' receptors regulate transcription.", "In this study we have analysed the biochemical and transcriptional properties of the neuronally expressed orphan nuclear receptor RORbeta (NR1F2) and compared them with the retinoic acid receptor heterodimer RXRalpha-RARalpha (NR2B1-NR1B1) and Gal-VP16 in vitro.", "Although RORbeta binds to its DNA-binding sites with comparatively low affinity, it efficiently directs transcription in nuclear extracts derived from a neuronal cell line, Neuro2A, but not in nuclear extracts from non-neuronal HeLa cells.", "In contrast, RXRalpha-RARalpha and the acidic transcription factor Gal-VP16 support transcription in Neuro2A and HeLa nuclear extracts equally efficiently.", "These observations point to a different (co)factor requirement for transactivation by members of the NR1 subfamily of nuclear receptors."], "structured": false}
{"doc_id": 5864770, "title": "Estrogens, progestogens, normal breast cell proliferation, and breast cancer risk.", "abstract": ["Epidemiologic studies suggest that ovarian hormones contribute to the development of breast cancer at all stages.", "Early menopause and premenopausal obesity reduces the risk while postmenopausal obesity and menopausal estrogen replacement therapy increases the risk.", "Combined oral contraceptives and Depo-Provera do not reduce the risk.", "It appears that estrogens and progestogens act through and with proto-oncogenes and growth factors to affect breast cell proliferation and breast cancer etiology.", "Animal studies suggest that estrogen causes interlobular ductal cell division and progesterone causes increased terminal duct lobular unit cell division in the luteal phase.", "Most breast carcinomas originate from terminal duct lobular unit cells.", "During pregnancy, these cells fully multiply.", "Their reproduction is also increased during the luteal phase.", "Yet, there is considerable interpersonal variation.", "No studies examining breast cell division have compared cell division rates with serum hormone concentrations, however.", "The peak of mitosis occurs about 3 days before breast cell death in the late luteal and very early follicular phases.", "Other research suggests that breast stem cell proliferation is linked to breast cancer development.", "Endocrine therapy reduces mitotic activity, indicating the estrogen and progesterone receptor content of breast cancers.", "Hormone-dependent breast cancer cell lines are all estrogen-dependent.", "Progesterone can block the estrogen-dependent cell lines which act like endometrial cells.", "The results of the various breast cell proliferation studies in relation to breast cancer are unclear and research identifying a molecular explanation would help in understanding the different findings."], "structured": false}
{"doc_id": 5867846, "title": "Analysis of the interaction of primate retroviruses with the human RNA interference machinery.", "abstract": ["The question of whether retroviruses, including human immunodeficiency virus type 1 (HIV-1), interact with the cellular RNA interference machinery has been controversial.", "Here, we present data showing that neither HIV-1 nor human T-cell leukemia virus type 1 (HTLV-1) expresses significant levels of either small interfering RNAs or microRNAs in persistently infected T cells.", "We also demonstrate that the retroviral nuclear transcription factors HIV-1 Tat and HTLV-1 Tax, as well as the Tas transactivator encoded by primate foamy virus, fail to inhibit RNA interference in human cells.", "Moreover, the stable expression of physiological levels of HIV-1 Tat did not globally inhibit microRNA production or expression in infected human cells.", "Together, these data argue that HIV-1 and HTLV-1 neither induce the production of viral small interfering RNAs or microRNAs nor repress the cellular RNA interference machinery in infected cells."], "structured": false}
{"doc_id": 5884524, "title": "Impact of diabetes on long-term prognosis in patients with unstable angina and non-Q-wave myocardial infarction: results of the OASIS (Organization to Assess Strategies for Ischemic Syndromes) Registry.", "abstract": ["BACKGROUND Although unstable coronary artery disease is the most common reason for admission to a coronary care unit, the long-term prognosis of patients with this diagnosis is unknown.", "This is particularly true for patients with diabetes mellitus, who are known to have a high morbidity and mortality after an acute myocardial infarction.   \n", "METHODS AND RESULTS Prospectively collected data from 6 different countries in the Organization to Assess Strategies for Ischemic Syndromes (OASIS) registry were analyzed to determine the 2-year prognosis of diabetic and nondiabetic patients who were hospitalized with unstable angina or non-Q-wave myocardial infarction.", "Overall, 1718 of 8013 registry patients (21%) had diabetes.", "Diabetic patients had a higher rate of coronary bypass surgery than nondiabetic patients (23% versus 20%, P:<0.001) but had similar rates of catheterization and angioplasty.", "Diabetes independently predicted mortality (relative risk [RR], 1.57; 95% CI, 1.38 to 1.81; P:<0.001), as well as cardiovascular death, new myocardial infarction, stroke, and new congestive heart failure.", "Moreover, compared with their nondiabetic counterparts, women had a significantly higher risk than men (RR, 1.98; 95% CI, 1.60 to 2.44; and RR, 1.28; 95% CI, 1.06 to 1.56, respectively).", "Interestingly, diabetic patients without prior cardiovascular disease had the same event rates for all outcomes as nondiabetic patients with previous vascular disease.   \n", "CONCLUSIONS Hospitalization for unstable angina or non-Q-wave myocardial infarction predicts a high 2-year morbidity and mortality; this is especially evident for patients with diabetes.", "Diabetic patients with no previous cardiovascular disease have the same long-term morbidity and mortality as nondiabetic patients with established cardiovascular disease after hospitalization for unstable coronary artery disease."], "structured": true}
{"doc_id": 5885376, "title": "Strain improvement by metabolic engineering: lysine production as a case study for systems biology.", "abstract": ["A central goal of systems biology is the elucidation of cell function and physiology through the integrated use of broad based genomic and physiological data.", "Such systemic approaches have been employed extensively in the past, as they are a central element of metabolic flux analysis, the distribution of kinetic control in pathways, and the key differentiating characteristic of metabolic engineering.", "In one case study, these tools have been applied to the improvement of lysine-producing strains of Corynebacterium glutamicum.", "The systematic study of the physiology of this organism allowed the identification of specific metabolic targets and subsequently led to significant improvements in product yield and productivity.", "This case study can serve as a guide for the development of systems biology tools for the utilization of large volumes of cell- and genome-wide transcriptional and physiological data."], "structured": false}
{"doc_id": 5912283, "title": "Cognitive behavioral therapy vs zopiclone for treatment of chronic primary insomnia in older adults: a randomized controlled trial.", "abstract": ["CONTEXT Insomnia is a common condition in older adults and is associated with a number of adverse medical, social, and psychological consequences.", "Previous research has suggested beneficial outcomes of both psychological and pharmacological treatments, but blinded placebo-controlled trials comparing the effects of these treatments are lacking.   \n", "OBJECTIVE To examine short- and long-term clinical efficacy of cognitive behavioral therapy (CBT) and pharmacological treatment in older adults experiencing chronic primary insomnia.   \n", "DESIGN, SETTING, AND PARTICIPANTS A randomized, double-blinded, placebo-controlled trial of 46 adults (mean age, 60.8 y; 22 women) with chronic primary insomnia conducted between January 2004 and December 2005 in a single Norwegian university-based outpatient clinic for adults and elderly patients.   \n", "INTERVENTION CBT (sleep hygiene, sleep restriction, stimulus control, cognitive therapy, and relaxation; n = 18), sleep medication (7.5-mg zopiclone each night; n = 16), or placebo medication (n = 12).", "All treatment duration was 6 weeks, and the 2 active treatments were followed up at 6 months.   \n", "MAIN OUTCOME MEASURES Ambulant clinical polysomnographic data and sleep diaries were used to determine total wake time, total sleep time, sleep efficiency, and slow-wave sleep (only assessed using polysomnography) on all 3 assessment points.   \n", "RESULTS CBT resulted in improved short- and long-term outcomes compared with zopiclone on 3 out of 4 outcome measures.", "For most outcomes, zopiclone did not differ from placebo.", "Participants receiving CBT improved their sleep efficiency from 81.4% at pretreatment to 90.1% at 6-month follow-up compared with a decrease from 82.3% to 81.9% in the zopiclone group.", "Participants in the CBT group spent much more time in slow-wave sleep (stages 3 and 4) compared with those in other groups, and spent less time awake during the night.", "Total sleep time was similar in all 3 groups; at 6 months, patients receiving CBT had better sleep efficiency using polysomnography than those taking zopiclone.   \n", "CONCLUSION These results suggest that interventions based on CBT are superior to zopiclone treatment both in short- and long-term management of insomnia in older adults.   \n", "TRIAL REGISTRATION clinicaltrials.gov Identifier: NCT00295386."], "structured": true}
{"doc_id": 5914739, "title": "Local changes in lipid environment of TCR microclusters regulate membrane binding by the CD3\u03b5 cytoplasmic domain", "abstract": ["The CD3\u03b5 and \u03b6 cytoplasmic domains of the T cell receptor bind to the inner leaflet of the plasma membrane (PM), and a previous nuclear magnetic resonance structure showed that both tyrosines of the CD3\u03b5 immunoreceptor tyrosine-based activation motif partition into the bilayer.", "Electrostatic interactions between acidic phospholipids and clusters of basic CD3\u03b5 residues were previously shown to be essential for CD3\u03b5 and \u03b6 membrane binding.", "Phosphatidylserine (PS) is the most abundant negatively charged lipid on the inner leaflet of the PM and makes a major contribution to membrane binding by the CD3\u03b5 cytoplasmic domain.", "Here, we show that TCR triggering by peptide--MHC complexes induces dissociation of the CD3\u03b5 cytoplasmic domain from the plasma membrane.", "Release of the CD3\u03b5 cytoplasmic domain from the membrane is accompanied by a substantial focal reduction in negative charge and available PS in TCR microclusters.", "These changes in the lipid composition of TCR microclusters even occur when TCR signaling is blocked with a Src kinase inhibitor.", "Local changes in the lipid composition of TCR microclusters thus render the CD3\u03b5 cytoplasmic domain accessible during early stages of T cell activation."], "structured": false}
{"doc_id": 5921065, "title": "Humans and great apes share a large frontal cortex", "abstract": ["Some of the outstanding cognitive capabilities of humans are commonly attributed to a disproportionate enlargement of the human frontal lobe during evolution.", "This claim is based primarily on comparisons between the brains of humans and of other primates, to the exclusion of most great apes.", "We compared the relative size of the frontal cortices in living specimens of several primate species, including all extant hominoids, using magnetic resonance imaging.", "Human frontal cortices were not disproportionately large in comparison to those of the great apes.", "We suggest that the special cognitive abilities attributed to a frontal advantage may be due to differences in individual cortical areas and to a richer interconnectivity, none of which required an increase in the overall relative size of the frontal lobe during hominid evolution."], "structured": false}
{"doc_id": 5922085, "title": "Virus-Plus-Susceptibility Gene Interaction Determines Crohn's Disease Gene Atg16L1 Phenotypes in Intestine", "abstract": ["It is unclear why disease occurs in only a small proportion of persons carrying common risk alleles of disease susceptibility genes.", "Here we demonstrate that an interaction between a specific virus infection and a mutation in the Crohn's disease susceptibility gene Atg16L1 induces intestinal pathologies in mice.", "This virus-plus-susceptibility gene interaction generated abnormalities in granule packaging and unique patterns of gene expression in Paneth cells.", "Further, the response to injury induced by the toxic substance dextran sodium sulfate was fundamentally altered to include pathologies resembling aspects of Crohn's disease.", "These pathologies triggered by virus-plus-susceptibility gene interaction were dependent on TNFalpha and IFNgamma and were prevented by treatment with broad spectrum antibiotics.", "Thus, we provide a specific example of how a virus-plus-susceptibility gene interaction can, in combination with additional environmental factors and commensal bacteria, determine the phenotype of hosts carrying common risk alleles for inflammatory disease."], "structured": false}
{"doc_id": 5927534, "title": "CaMKII Triggers the Diffusional Trapping of Surface AMPARs through Phosphorylation of Stargazin", "abstract": ["The Ca(2+)/calmodulin-dependent protein kinase II (CaMKII) is critically required for the synaptic recruitment of AMPA-type glutamate receptors (AMPARs) during both development and plasticity.", "However, the underlying mechanism is unknown.", "Using single-particle tracking of AMPARs, we show that CaMKII activation and postsynaptic translocation induce the synaptic trapping of AMPARs diffusing in the membrane.", "AMPAR immobilization requires both phosphorylation of the auxiliary subunit Stargazin and its binding to PDZ domain scaffolds.", "It does not depend on the PDZ binding domain of GluA1 AMPAR subunit nor its phosphorylation at Ser831.", "Finally, CaMKII-dependent AMPAR immobilization regulates short-term plasticity.", "Thus, NMDA-dependent Ca(2+) influx in the post-synapse triggers a CaMKII- and Stargazin-dependent decrease in AMPAR diffusional exchange at synapses that controls synaptic function."], "structured": false}
{"doc_id": 5935987, "title": "Epigenetics in diabetic nephropathy, immunity and metabolism", "abstract": ["When it comes to the epigenome, there is a fine line between clarity and confusion-walk that line and you will discover another fascinating level of transcription control.", "With the genetic code representing the cornerstone of rules for information that is encoded to proteins somewhere above the genome level there is a set of rules by which chemical information is also read.", "These epigenetic modifications show a different side of the genetic code that is diverse and regulated, hence modifying genetic transcription transiently, ranging from short- to long-term alterations.", "While this complexity brings exquisite control it also poses a formidable challenge to efforts to decode mechanisms underlying complex disease.", "Recent technological and computational advances have improved unbiased acquisition of epigenomic patterns to improve our understanding of the complex chromatin landscape.", "Key to resolving distinct chromatin signatures of diabetic complications is the identification of the true physiological targets of regulatory proteins, such as reader proteins that recognise, writer proteins that deposit and eraser proteins that remove specific chemical moieties.", "But how might a diverse group of proteins regulate the diabetic landscape from an epigenomic perspective?", "Drawing from an ever-expanding compendium of experimental and clinical studies, this review details the current state-of-play and provides a perspective of chromatin-dependent mechanisms implicated in diabetic complications, with a special focus on diabetic nephropathy.", "We hypothesise a codified signature of the diabetic epigenome and provide examples of prime candidates for chemical modification.", "As for the pharmacological control of epigenetic marks, we explore future strategies to expedite and refine the search for clinically relevant discoveries.", "We also consider the challenges associated with therapeutic strategies targeting epigenetic pathways."], "structured": false}
{"doc_id": 5939172, "title": "Drinking pattern and mortality: the Italian Risk Factor and Life Expectancy pooling project.", "abstract": ["PURPOSE To analyze the relationship between an aspect of drinking pattern (i.e., drinking with or without meals) and risk of all-cause and specific-cause mortality.   \n", "METHODS The Risk Factors and Life Expectancy Study, is a pooling of a series of epidemiological studies conducted in Italy.", "Eight-thousand six-hundred and forty-seven men and 6521 women, age 30-59 at baseline, and free of cardiovascular disease, were followed for mortality from all causes, cardiovascular and noncardiovascular, during an average follow-up of 7 years.   \n", "RESULTS Drinkers of wine outside meals exhibited higher death rates from all causes, noncardiovascular diseases, and cancer, as compared to drinkers of wine with meals.", "This association was independent from the cardiovascular disease (CVD) risk factors measured at baseline and the amount of alcohol consumed and seemed to be stronger in women as compared to men.   \n", "CONCLUSIONS The present results indicate that drinking patterns may have important health implications, and attention should be given to this aspect of alcohol use and its relationship to health outcomes.", "The relationship between alcohol consumption and disease has been the focus of intensive scientific investigation (1-9).", "Most studies to date, however, have limitations.", "A major drawback is that limited information has been collected regarding the complex issue of alcohol consumption.", "In many studies, ascertainment of alcohol consumption frequently focused only on quantity of alcohol consumed without considering the many different components of alcohol consumption, particularly drinking pattern (10-12).", "It has been hypothesized, and preliminary data support the notion, that drinking pattern could have important influences on determining the health effects of alcohol (13,14).", "The present study examines the relationship between one aspect of drinking pattern (drinking wine outside meals) and mortality in a large cohort of men and women."], "structured": true}
{"doc_id": 5944514, "title": "Pointing in the right direction: new developments in the field of planar cell polarity", "abstract": ["Planar cell polarity (PCP) is observed in an array of developmental processes that involve collective cell movement and tissue organization, and its disruption can lead to severe developmental defects.", "Recent studies in flies and vertebrates have identified new functions for PCP as well as new signalling components, and have proposed new mechanistic models.", "However, despite this progress, the search to simplify principles of understanding continues and important mechanistic uncertainties still pose formidable challenges."], "structured": false}
{"doc_id": 5953485, "title": "ADAR1 Forms a Complex with Dicer to Promote MicroRNA Processing and RNA-Induced Gene Silencing", "abstract": ["Adenosine deaminases acting on RNA (ADARs) are involved in RNA editing that converts adenosine residues to inosine specifically in double-stranded RNAs.", "In this study, we investigated the interaction of the RNA editing mechanism with the RNA interference (RNAi) machinery and found that ADAR1 forms a complex with Dicer through direct protein-protein interaction.", "Most importantly, ADAR1 increases the maximum rate (Vmax) of pre-microRNA (miRNA) cleavage by Dicer and facilitates loading of miRNA onto RNA-induced silencing complexes, identifying a new role of ADAR1 in miRNA processing and RNAi mechanisms.", "ADAR1 differentiates its functions in RNA editing and RNAi by the formation of either ADAR1/ADAR1 homodimer or Dicer/ADAR1 heterodimer complexes, respectively.", "As expected, the expression of miRNAs is globally inhibited in ADAR1(-/-) mouse embryos, which, in turn, alters the expression of their target genes and might contribute to their embryonic lethal phenotype."], "structured": false}
{"doc_id": 5956016, "title": "Interchangeability of Biosimilars: A European Perspective", "abstract": ["Many of the best-selling \u2018blockbuster\u2019 biological medicinal products are, or will soon be, facing competition from similar biological medicinal products (biosimilars) in the EU.", "Biosimilarity is based on the comparability concept, which has been used successfully for several decades to ensure close similarity of a biological product before and after a manufacturing change.", "Over the last 10 years, experience with biosimilars has shown that even complex biotechnology-derived proteins can be copied successfully.", "Most best-selling biologicals are used for chronic treatment.", "This has triggered intensive discussion on the interchangeability of a biosimilar with its reference product, with the main concern being immunogenicity.", "We explore the theoretical basis of the presumed risks of switching between a biosimilar and its reference product and the available data on switches.", "Our conclusion is that a switch between comparable versions of the same active substance approved in accordance with EU legislation is not expected to trigger or enhance immunogenicity.", "On the basis of current knowledge, it is unlikely and very difficult to substantiate that two products, comparable on a population level, would have different safety or efficacy in individual patients upon a switch.", "Our conclusion is that biosimilars licensed in the EU are interchangeable."], "structured": false}
{"doc_id": 5956380, "title": "Exome sequencing identifies somatic gain-of-function PPM1D mutations in brainstem gliomas", "abstract": ["Gliomas arising in the brainstem and thalamus are devastating tumors that are difficult to surgically resect.", "To determine the genetic and epigenetic landscape of these tumors, we performed exomic sequencing of 14 brainstem gliomas (BSGs) and 12 thalamic gliomas.", "We also performed targeted mutational analysis of an additional 24 such tumors and genome-wide methylation profiling of 45 gliomas.", "This study led to the discovery of tumor-specific mutations in PPM1D, encoding wild-type p53-induced protein phosphatase 1D (WIP1), in 37.5% of the BSGs that harbored hallmark H3F3A mutations encoding p.", "Lys27Met substitutions.", "PPM1D mutations were mutually exclusive with TP53 mutations in BSG and attenuated p53 activation in vitro.", "PPM1D mutations were truncating alterations in exon 6 that enhanced the ability of PPM1D to suppress the activation of the DNA damage response checkpoint protein CHK2.", "These results define PPM1D as a frequent target of somatic mutation and as a potential therapeutic target in brainstem gliomas."], "structured": false}
{"doc_id": 5966635, "title": "Crystal structure of a nucleosome core particle containing the variant histone H2A.Z", "abstract": ["Activation of transcription within chromatin has been correlated with the incorporation of the essential histone variant H2A.Z into nucleosomes.", "H2A.Z and other histone variants may establish structurally distinct chromosomal domains; however, the molecular mechanism by which they function is largely unknown.", "Here we report the 2.6 \u00c5 crystal structure of a nucleosome core particle containing the histone variant H2A.Z. The overall structure is similar to that of the previously reported 2.8 \u00c5 nucleosome structure containing major histone proteins.", "However, distinct localized changes result in the subtle destabilization of the interaction between the (H2A.Z\u2013H2B) dimer and the (H3\u2013H4)2 tetramer.", "Moreover, H2A.Z nucleosomes have an altered surface that includes a metal ion.", "This altered surface may lead to changes in higher order structure, and/or could result in the association of specific nuclear proteins with H2A.Z. Finally, incorporation of H2A.Z and H2A within the same nucleosome is unlikely, due to significant changes in the interface between the two H2A.Z\u2013H2B dimers."], "structured": false}
{"doc_id": 5979056, "title": "Dendritic Cell KLF2 Expression Regulates T Cell Activation and Proatherogenic Immune Responses.", "abstract": ["Dendritic cells (DCs) have been implicated as important regulators of innate and adaptive inflammation in many diseases, including atherosclerosis.", "However, the molecular mechanisms by which DCs mitigate or promote inflammatory pathogenesis are only partially understood.", "Previous studies have shown an important anti-inflammatory role for the transcription factor Kr\u00fcppel-like factor 2 (KLF2) in regulating activation of various cell types that participate in atherosclerotic lesion development, including endothelial cells, macrophages, and T cells.", "We used a pan-DC, CD11c-specific cre-lox gene knockout mouse model to assess the role of KLF2 in DC activation, function, and control of inflammation in the context of hypercholesterolemia and atherosclerosis.", "We found that KLF2 deficiency enhanced surface expression of costimulatory molecules CD40 and CD86 in DCs and promoted increased T cell proliferation and apoptosis.", "Transplant of bone marrow from mice with KLF2-deficient DCs into Ldlr-/- mice aggravated atherosclerosis compared with control mice, most likely due to heightened vascular inflammation evidenced by increased DC presence within lesions, enhanced T cell activation and cytokine production, and increased cell death in atherosclerotic lesions.", "Taken together, these data indicate that KLF2 governs the degree of DC activation and hence the intensity of proatherogenic T cell responses."], "structured": false}
{"doc_id": 5991309, "title": "Targeting tumor-necrosis factor receptor pathways for tumor immunotherapy", "abstract": ["With the success of ipilimumab and promise of programmed death-1 pathway-targeted agents, the field of tumor immunotherapy is expanding rapidly.", "Newer targets for clinical development include select members of the tumor necrosis factor receptor (TNFR) family.", "Agonist antibodies to these co-stimulatory molecules target both T and B cells, modulating T-cell activation and enhancing immune responses.", "In vitro and in vivo preclinical data have provided the basis for continued development of 4-1BB, OX40, glucocorticoid-induced TNFR-related gene, herpes virus entry mediator, and CD27 as potential therapies for patients with cancer.", "In this review, we summarize the immune response to tumors, consider preclinical and early clinical data on select TNFR family members, discuss potential translational challenges and suggest possible combination therapies with the aim of inducing durable antitumor responses."], "structured": false}
{"doc_id": 5993745, "title": "Plasma soluble corin in patients with heart failure.", "abstract": ["BACKGROUND Corin is a transmembrane protease that processes natriuretic peptides in the heart.", "Like many membrane proteins, corin is shed from the cell surface.   \n", "METHODS AND RESULTS In this study, we obtained plasma samples from healthy controls and patients with heart failure (HF) and acute myocardial infarction.", "Soluble corin levels in plasma were measured by an ELISA method.", "In healthy adults (n=198), plasma corin levels were 690 pg/mL (SD, 260 pg/mL).", "The corin levels did not differ significantly among different age groups.", "In patients with HF (n=291), plasma corin levels were significantly lower compared with that of healthy controls (365 pg/mL [SD, 259]; P<0.001).", "The reduction in plasma corin levels seemed to correlate with the severity of HF.", "In patients of New York Heart Association classes II, III, and IV, plasma corin levels were 450 pg/mL (SD, 281 pg/mL; n=69), 377 pg/mL (SD, 270 pg/mL; n=132), and 282 pg/mL (SD, 194 pg/mL; n=90), respectively (P<0.001 class II vs class IV; P<0.05 class III vs class IV).", "In contrast, plasma corin levels in patients with acute myocardial infarction (n=73) were similar to that of healthy controls (678 pg/mL [SD, 285 pg/mL]; P>0.05).   \n", "CONCLUSIONS Soluble corin was detected in human plasma.", "Plasma corin levels were reduced significantly in patients with HF but not in those with acute myocardial infarction.", "Our results indicate that corin deficiency may contribute to the pathogenesis of HF and that plasma corin may be used as a biomarker in the diagnosis of HF."], "structured": true}
{"doc_id": 6000423, "title": "The NLRP3 inflammasome functions as a driver of the myelodysplastic syndrome phenotype.", "abstract": ["Despite genetic heterogeneity, myelodysplastic syndromes (MDSs) share features of cytological dysplasia and ineffective hematopoiesis.", "We report that a hallmark of MDSs is activation of the NLRP3 inflammasome, which drives clonal expansion and pyroptotic cell death.", "Independent of genotype, MDS hematopoietic stem and progenitor cells (HSPCs) overexpress inflammasome proteins and manifest activated NLRP3 complexes that direct activation of caspase-1, generation of interleukin-1\u03b2 (IL-1\u03b2) and IL-18, and pyroptotic cell death.", "Mechanistically, pyroptosis is triggered by the alarmin S100A9 that is found in excess in MDS HSPCs and bone marrow plasma.", "Further, like somatic gene mutations, S100A9-induced signaling activates NADPH oxidase (NOX), increasing levels of reactive oxygen species (ROS) that initiate cation influx, cell swelling, and \u03b2-catenin activation.", "Notably, knockdown of NLRP3 or caspase-1, neutralization of S100A9, and pharmacologic inhibition of NLRP3 or NOX suppress pyroptosis, ROS generation, and nuclear \u03b2-catenin in MDSs and are sufficient to restore effective hematopoiesis.", "Thus, alarmins and founder gene mutations in MDSs license a common redox-sensitive inflammasome circuit, which suggests new avenues for therapeutic intervention."], "structured": false}
{"doc_id": 6036535, "title": "Structural Brain Correlates Associated with Professional Handball Playing", "abstract": ["BACKGROUND There is no doubt that good bimanual performance is very important for skilled handball playing.", "The control of the non-dominant hand is especially demanding since efficient catching and throwing needs both hands.   \n", "METHODOLOGY/HYPOTHESES We investigated training-induced structural neuroplasticity in professional handball players using several structural neuroimaging techniques and analytic approaches and also provide a review of the literature about sport-induced structural neuroplastic alterations.", "Structural brain adaptations were expected in regions relevant for motor and somatosensory processing such as the grey matter (GM) of the primary/secondary motor (MI/supplementary motor area, SMA) and somatosensory cortex (SI/SII), basal ganglia, thalamus, and cerebellum and in the white matter (WM) of the corticospinal tract (CST) and corpus callosum, stronger in brain regions controlling the non-dominant left hand.   \n", "RESULTS Increased GM volume in handball players compared with control subjects were found in the right MI/SI, bilateral SMA/cingulate motor area, and left intraparietal sulcus.", "Fractional anisotropy (FA) and axial diffusivity were increased within the right CST in handball players compared with control women.", "Age of handball training commencement correlated inversely with GM volume in the right and left MI/SI and years of handball training experience correlated inversely with radial diffusivity in the right CST.", "Subcortical structures tended to be larger in handball players.", "The anatomical measures of the brain regions associated with handball playing were positively correlated in handball players, but not interrelated in control women.   \n", "DISCUSSION/CONCLUSION Training-induced structural alterations were found in the somatosensory-motor network of handball players, more pronounced in the right hemisphere controlling the non-dominant left hand.", "Correlations between handball training-related measures and anatomical differences suggest neuroplastic adaptations rather than a genetic predisposition for a ball playing affinity.", "Investigations of neuroplasticity specifically in sportsmen might help to understand the neural mechanisms of expertise in general."], "structured": true}
{"doc_id": 6040392, "title": "The role of epigenetics in aging and age-related diseases", "abstract": ["The role of epigenetics in aging and age-related diseases is a key issue in molecular physiology and medicine because certain epigenetic factors are thought to mediate, at least in part, the relationship between the genome and the environment.", "An active role for epigenetics in aging must meet two prior conditions: there must be specific epigenetic changes during aging and they must be functionally associated with the aged phenotype.", "Assuming that specific epigenetic modifications can have a direct functional outcome in aging, it is also essential to establish whether they depend on genetic, environmental or stochastic factors, and if they can be transmitted from one generation to the next.", "Here we discuss current knowledge about these matters and future directions in the field."], "structured": false}
{"doc_id": 6042706, "title": "Effects of a high-fat diet exposure in utero on the metabolic syndrome-like phenomenon in mouse offspring through epigenetic changes in adipocytokine gene expression.", "abstract": ["The links between obesity in parents and their offspring and the role of genes and a shared environment are not completely understood.", "Adipocytokines such as leptin and adiponectin play important roles in glucose and lipid metabolism.", "Therefore, we examined whether the offspring from dams exposed to a high-fat diet during pregnancy (OH mice) exhibited hypertension, insulin resistance, and hyperlipidemia along with epigenetic changes in the expression of adipocytokine genes.", "OH mice were significantly heavier than the offspring of dams exposed to a control diet during pregnancy (OC mice) from 14 wk of age after an increased caloric intake from 8 wk.", "OH mice exhibited higher blood pressure and worse glucose tolerance than the OC mice at 24 wk.", "Total triglyceride and leptin levels were significantly higher and the adiponectin level was significantly lower in OH compared with OC mice at 12 wk of age.", "This was associated with changes in leptin and adiponectin expression in white adipose tissue.", "There were lower acetylation and higher methylation levels of histone H3 at lysine 9 of the promoter of adiponectin in adipose tissues of OH mice at 2 wk of age as well as at 12 and 24 wk of age compared with OC mice.", "In contrast, methylation of histone 4 at lysine 20 in the leptin promoter was significantly higher in OH compared with OC mice.", "Thus, exposure to a high-fat diet in utero might cause a metabolic syndrome-like phenomenon through epigenetic modifications of adipocytokine, adiponectin, and leptin gene expression."], "structured": false}
{"doc_id": 6054657, "title": "Highly efficient miRNA-mediated reprogramming of mouse and human somatic cells to pluripotency.", "abstract": ["Transcription factor-based cellular reprogramming has opened the way to converting somatic cells to a pluripotent state, but has faced limitations resulting from the requirement for transcription factors and the relative inefficiency of the process.", "We show here that expression of the miR302/367 cluster rapidly and efficiently reprograms mouse and human somatic cells to an iPSC state without a requirement for exogenous transcription factors.", "This miRNA-based reprogramming approach is two orders of magnitude more efficient than standard Oct4/Sox2/Klf4/Myc-mediated methods.", "Mouse and human miR302/367 iPSCs display similar characteristics to Oct4/Sox2/Klf4/Myc-iPSCs, including pluripotency marker expression, teratoma formation, and, for mouse cells, chimera contribution and germline contribution.", "We found that miR367 expression is required for miR302/367-mediated reprogramming and activates Oct4 gene expression, and that suppression of Hdac2 is also required.", "Thus, our data show that miRNA and Hdac-mediated pathways can cooperate in a powerful way to reprogram somatic cells to pluripotency."], "structured": false}
{"doc_id": 6057195, "title": "Unmet needs and depression among carers of people newly diagnosed with cancer.", "abstract": ["AIMS", "The aims of this analysis were to examine levels of unmet needs and depression among carers of people newly diagnosed with cancer and to identify groups who may be at higher risk, by examining relationships with demographic characteristics.   \n", "METHODS One hundred and fifty dyads of people newly diagnosed with cancer and their carers, aged 18 years and older, were recruited from four Australian hospitals.", "People with cancer receiving adjuvant cancer treatment with curative intent, were eligible to participate.", "Carers completed the Supportive Care Needs Survey-Partners & Caregivers (SCNS-P&C45), and both carers and patients completed the Centre of Epidemiologic-Depression Scale (CES-D).   \n", "RESULTS Overall, 57% of carers reported at least one, 37% at least three, 31% at least five, and 15% at least 10 unmet needs; the most commonly endorsed unmet needs were in the domains of information and health care service needs.", "Thirty percent of carers and 36% of patients were at risk of clinical depression.", "A weak to moderate positive relationship was observed between unmet needs and carer depression (r=0.30, p<0.001).", "Carer levels of unmet needs were significantly associated with carer age, hospital type, treatment type, cancer type, living situation, relationship status (in both uni- and multi-factor analysis); person with cancer age and carer level of education (in unifactor analysis only); but not with carer gender or patient gender (in both uni- and multi-factor analyses).   \n", "CONCLUSION Findings highlight the importance of developing tailored programmes to systematically assist carers who are supporting patients through the early stages of cancer treatment."], "structured": true}
{"doc_id": 6061927, "title": "Glucose Sensing in L Cells: A Primary Cell Study", "abstract": ["Glucagon-like peptide-1 (GLP-1) is an enteric hormone that stimulates insulin secretion and improves glycaemia in type 2 diabetes.", "Although GLP-1-based treatments are clinically available, alternative strategies to increase endogenous GLP-1 release from L cells are hampered by our limited physiological understanding of this cell type.", "By generating transgenic mice with L cell-specific expression of a fluorescent protein, we studied the characteristics of primary L cells by electrophysiology, fluorescence calcium imaging, and expression analysis and show that single L cells are electrically excitable and glucose responsive.", "Sensitivity to tolbutamide and low-millimolar concentrations of glucose and alpha-methylglucopyranoside, assessed in single L cells and by hormone secretion from primary cultures, suggested that GLP-1 release is regulated by the activity of sodium glucose cotransporter 1 and ATP-sensitive K(+) channels, consistent with their high expression levels in purified L cells by quantitative RT-PCR.", "These and other pathways identified using this approach will provide exciting opportunities for future physiological and therapeutic exploration."], "structured": false}
{"doc_id": 6070278, "title": "Total atherosclerotic burden by whole body magnetic resonance angiography predicts major adverse cardiovascular events.", "abstract": ["OBJECTIVE The purpose of the present study was to investigate the relationship between the Total Atherosclerotic Score (TAS), a measurement of the overall atherosclerotic burden of the arterial tree by whole body magnetic resonance angiography (WBMRA), and the risk of major adverse cardiovascular events (MACE), defined as cardiac death, myocardial infarction, stroke and/or coronary revascularization, assuming that TAS predicts MACE.   \n", "METHODS AND RESULTS 305 randomly selected 70 year-old subjects (47% women) underwent WBMRA.", "Their atherosclerotic burden was evaluated and TAS > 0, that is atherosclerotic changes, were found in 68% of subjects.", "During follow-up (mean 4.8 years), MACE occurred in 25 subjects (8.2%).", "Adjusting for multiple risk factors, TAS was associated with MACE (OR 8.86 for any degree of vessel lumen abnormality, 95%CI 1.14-69.11, p = 0.037).", "In addition, TAS improved discrimination and reclassification when added to the Framingham risk score (FRS), and ROC (Receiver Operator Curve) increased from 0.681 to 0.750 (p = 0.0421).   \n", "CONCLUSION In a population-based sample of 70 year old men and women WBMRA, with TAS, predicted MACE independently of major cardiovascular risk factors."], "structured": true}
{"doc_id": 6076903, "title": "Regulation of ADMP and BMP2/4/7 at Opposite Embryonic Poles Generates a Self-Regulating Morphogenetic Field", "abstract": ["Embryos have the ability to self-regulate and regenerate normal structures after being sectioned in half.", "How is such a morphogenetic field established?", "We discovered that quadruple knockdown of ADMP and BMP2/4/7 in Xenopus embryos eliminates self-regulation, causing ubiquitous neural induction throughout the ectoderm.", "ADMP transcription in the Spemann organizer is activated at low BMP levels.", "When ventral BMP2/4/7 signals are depleted, Admp expression increases, allowing for self-regulation.", "ADMP has BMP-like activity and signals via the ALK-2 receptor.", "It is unable to signal dorsally because of inhibition by Chordin.", "The ventral BMP antagonists Sizzled and Bambi further refine the pattern.", "By transplanting dorsal or ventral wild-type grafts into ADMP/BMP2/4/7-depleted hosts, we demonstrate that both poles serve as signaling centers that can induce histotypic differentiation over considerable distances.", "We conclude that dorsal and ventral BMP signals and their extracellular antagonists expressed under opposing transcriptional regulation provide a molecular mechanism for embryonic self-regulation."], "structured": false}
{"doc_id": 6077214, "title": "Genetic control of mosquitoes.", "abstract": ["Genetics can potentially provide new, species-specific, environmentally friendly methods for mosquito control.", "Genetic control strategies aim either to suppress target populations or to introduce a harm-reducing novel trait.", "Different approaches differ considerably in their properties, especially between self-limiting strategies, where the modification has limited persistence, and self-sustaining strategies, which are intended to persist indefinitely in the target population and may invade other populations.", "Several methods with different molecular biology are under development and the first field trials have been completed successfully."], "structured": false}
{"doc_id": 6078882, "title": "Colorectal Cancers from Distinct Ancestral Populations Show Variations in BRAF Mutation Frequency", "abstract": ["It has been demonstrated for some cancers that the frequency of somatic oncogenic mutations may vary in ancestral populations.", "To determine whether key driver alterations might occur at different frequencies in colorectal cancer, we applied a high-throughput genotyping platform (OncoMap) to query 385 mutations across 33 known cancer genes in colorectal cancer DNA from 83 Asian, 149 Black and 195 White patients.", "We found that Asian patients had fewer canonical oncogenic mutations in the genes tested (60% vs Black 79% (P = 0.011) and White 77% (P = 0.015)), and that BRAF mutations occurred at a higher frequency in White patients (17% vs Asian 4% (P = 0.004) and Black 7% (P = 0.014)).", "These results suggest that the use of genomic approaches to elucidate the different ancestral determinants harbored by patient populations may help to more precisely and effectively treat colorectal cancer."], "structured": false}
{"doc_id": 6079486, "title": "Direct neuronal reprogramming: learning from and for development.", "abstract": ["The key signalling pathways and transcriptional programmes that instruct neuronal diversity during development have largely been identified.", "In this Review, we discuss how this knowledge has been used to successfully reprogramme various cell types into an amazing array of distinct types of functional neurons.", "We further discuss the extent to which direct neuronal reprogramming recapitulates embryonic development, and examine the particular barriers to reprogramming that may exist given a cell's unique developmental history.", "We conclude with a recently proposed model for cell specification called the 'Cook Islands' model, and consider whether it is a fitting model for cell specification based on recent results from the direct reprogramming field."], "structured": false}
{"doc_id": 6082738, "title": "Cell fusion hypothesis of the cancer stem cell.", "abstract": ["A major advance in recent cancer research is the identification of tumor cells with stem cell-like properties.", "Cancer stem cells (CSCs) often represent a rare population in the tumor mass and possess the exclusive ability to initiate the growth of a heterogeneous tumor.", "The origin of CSCs remains elusive and is likely to be cancer type specific.", "One possible but under-appreciated potential mechanism for the generation of CSCs is through fusion between stem cells and differentiated cells.", "The cell fusion hypothesis of CSCs adds an important functional underpinning to the potential multifaceted roles of cell fusion in the initiation and progression of cancer."], "structured": false}
{"doc_id": 6083952, "title": "Antidepressant fluoxetine enhances glucocorticoid receptor function in vitro by modulating membrane steroid transporters.", "abstract": ["1.", "Incubation of LMCAT fibroblast cells with antidepressants potentiates glucocorticoid receptor (GR)-mediated gene transcription in the presence of dexamethasone and cortisol, but not of corticosterone.", "We have shown that antidepressants do so by inhibiting the LMCAT cell membrane steroid transporter (which is virtually identical to the multidrug resistance P-glycoprotein) and thus by increasing dexamethasone or cortisol intracellular concentrations.", "However, previous experiments with the antidepressant fluoxetine in the presence of dexamethasone have produced negative results (Pariante et al. (2001).", "Br.", "J. Pharmacol., 134, 1335-1343).", "2.", "We have since re-examined the effects of fluoxetine on GR-mediated gene transcription in the presence of dexamethasone.", "Moreover, we have examined the effects of fluoxetine on GR-mediated gene transcription in the presence of cortisol and corticosterone, and on the intracellular accumulation of radioactive cortisol and corticosterone.", "Finally, we have examined the effects of fluoxetine on inhibition of P-glycoprotein activity in Caco-2 cells.", "3.", "We now find that fluoxetine (1-10 micro M) enhances GR-mediated gene transcription in the presence of dexamethasone and cortisol (+140-170%), but not of corticosterone, and increases the intracellular accumulation of (3)H-cortisol (+5-15%), but not of (3)H-corticosterone.", "Moreover, fluoxetine (10 micro M) induces approximately 30% inhibition of PGP activity in Caco-2 cells.", "4.", "Our results show that fluoxetine, like other antidepressants, inhibits membrane steroid transporters."], "structured": false}
{"doc_id": 6085365, "title": "Physician knowledge levels and barriers to coronary risk prevention in women: survey results from the Women and Heart Disease Physician Education Initiative.", "abstract": ["BACKGROUND Few studies have examined whether physician knowledge, attitudes, or practice patterns might contribute to gender disparities in the primary prevention of coronary heart disease (CHD), including among physicians caring for the largest number of reproductive-age women, obstetricians and gynecologists (OB/GYNs).", "We sought to identify barriers affecting the provision of recommended coronary risk factor therapies in women.   \n", "METHODS We surveyed internists and OB/GYNs who attended Grand Rounds presentations developed for the New York State Women and Heart Disease Physician Education Initiative.", "This program was designed to improve screening and management of coronary risk factors in women.", "Attendees were asked to complete a 7-minute questionnaire.   \n", "RESULTS The mean age of the 529 respondents was 40.3 years (standard deviation = 12.3), 75.1% were internists (n=378), and 42.7% (n=226) were women.", "Physicians correctly responded to 71.5% of the 13 questions assessing knowledge of coronary risk prevention (range, 4-13).", "Almost one third of internists and half of the OB/GYNs did not know that tobacco use was the leading cause of myocardial infarction in young women.", "For patients who smoked tobacco, only two thirds of internists and 55.4% of OB/GYNs reported suggesting a quit date (p=.007).", "After controlling for covariates, physicians who did not perceive time as a barrier were more likely to discuss smoking cessation (odds ratio=1.7 [1.1-2.7]).   \n", "CONCLUSIONS Among the internists and OB/GYNs surveyed, time was perceived as a barrier to implementing risk prevention.", "These physicians also underestimated the impact of tobacco use as a risk factor for CHD in young women.", "To lessen gender disparities in CHD prevention, both specialties need time-efficient educational programs that reflect specialty differences."], "structured": true}
{"doc_id": 6106004, "title": "Separation of mother and daughter cells.", "abstract": ["Publisher Summary The budding yeast Saccharomyces cerevisiae ( S. cerevisiae ) divides asymmetrically.", "In vegetative growth, yeast cells reproduce by budding, and the position where the bud forms ultimately determines the plane of cell division.", "This chapter describes the detailed procedures for the separation and isolation of mothers and daughters.", "These protocols have been used by investigators studying aging, bud site selection, and other aspects of asymmetric cell division.", "The chapter describes the procedures for performing life span analysis by micromanipulation and the steps for the large-scale collection of old cells.", "At the beginning and the end of a life span, it can be difficult to distinguish mothers from daughters.", "At most points in the life span, daughter cells are smaller than the mothers that produced them.", "In addition, mother cells will generally bud a second time before their daughter cells form their first bud.", "One method for effective isolation of virgin daughter cells from mother cells, but not for recovery of old mothers, is called a \u201cbaby machine.", "\u201d Mother cells are attached to a membrane and allowed to divide.", "Daughter cells from these attached cells are eluted continuously by washing the membrane."], "structured": false}
{"doc_id": 6108481, "title": "Postnatal development of adipocyte cellularity in the normal rat.", "abstract": ["It has been shown by several investigators that adipocyte number is stable in mature human beings and several species of rodents.", "Although the number of new cells appearing in the adipose depot can be measured histometrically and by Coulter counting of osmium-fixed cells, such methods do not distinguish between \"lipid filling\" of preexistent adipocytes and synthesis of new adipocytes.", "The experiments reported here using in vivo injection of [(3)H]thymidine show that synthesis of new adipocytes in the Sprague-Dawley rat continues after birth and ceases before sexual maturity.", "Furthermore, during the second and third postnatal weeks, a \"bed\" of preadipocytes is synthesized.", "Preadipocytes may take as long as 30 days to appear as mature adipocytes."], "structured": false}
{"doc_id": 6112053, "title": "Withdrawal Symptoms after Selective Serotonin Reuptake Inhibitor Discontinuation: A Systematic Review", "abstract": ["Background: Selective serotonin reuptake inhibitors (SSRI) are widely used in medical practice.", "They have been associated with a broad range of symptoms, whose clinical meaning has not been fully appreciated.", "Methods: The PRISMA guidelines were followed to conduct a systematic review of the literature.", "Titles, abstracts, and topics were searched using the following terms: \u2018withdrawal symptoms' OR \u2018withdrawal syndrome' OR \u2018discontinuation syndrome' OR \u2018discontinuation symptoms', AND \u2018SSRI' OR \u2018serotonin' OR \u2018antidepressant' OR \u2018paroxetine' OR \u2018fluoxetine' OR \u2018sertraline' OR \u2018fluvoxamine' OR \u2018citalopram' OR \u2018escitalopram'.", "The electronic research literature databases included CINAHL, the Cochrane Library, PubMed and Web-of-Science from inception of each database to July 2014.", "Results:", "There were 15 randomized controlled studies, 4 open trials, 4 retrospective investigations, and 38 case reports.", "The prevalence of the syndrome was variable, and its estimation was hindered by a lack of case identification in many studies.", "Symptoms typically occur within a few days from drug discontinuation and last a few weeks, also with gradual tapering.", "However, many variations are possible, including late onset and/or longer persistence of disturbances.", "Symptoms may be easily misidentified as signs of impending relapse.", "Conclusions: Clinicians need to add SSRI to the list of drugs potentially inducing withdrawal symptoms upon discontinuation, together with benzodiazepines, barbiturates, and other psychotropic drugs.", "The term \u2018discontinuation syndrome' that is currently used minimizes the potential vulnerabilities induced by SSRI and should be replaced by \u2018withdrawal syndrome'."], "structured": false}
{"doc_id": 6121555, "title": "Sphingosine Kinase 1 Regulates the Akt/FOXO3a/Bim Pathway and Contributes to Apoptosis Resistance in Glioma Cells", "abstract": ["The aim of this study was to investigate the mechanism through which Sphingosine kinase-1 (SPHK1) exerts its anti-apoptosis activity in glioma cancer cells.", "We here report that dysregulation of SPHK1 alters the sensitivity of glioma to apoptosis both in vitro and in vivo.", "Further mechanistic study examined the expression of Bcl-2 family members, including Bcl-2, Mcl-1, Bax and Bim, in SPHK1-overexpressing glioma cells and revealed that only pro-apoptotic Bim was downregulated by SPHK1.", "Moreover, the transcriptional level of Bim was also altered by SPHK1 in glioma cells.", "We next confirmed the correlation between SPHK1 and Bim expression in primary glioma specimens.", "Importantly, increasing SPHK1 expression in glioma cells markedly elevated Akt activity and phosphorylated inactivation of FOXO3a, which led to downregulation of Bim.", "A pharmacological approach showed that these effects of SPHK1 were dependent on phosphatidylinositol 3-kinase (PI3K).", "Furthermore, effects of SPHK1 on Akt/FOXO3a/Bim pathway could be reversed by SPHK1 specific RNA interference or SPHK1 inhibitor.", "Collectively, our results indicate that regulation of the Akt/FOXO3a/Bim pathway may be a novel mechanism by which SPHK1 protects glioma cells from apoptosis, thereby involved in glioma tumorigenesis."], "structured": false}
{"doc_id": 6121668, "title": "COX-2 and survivin are overexpressed and positively correlated in endometrial carcinoma.", "abstract": ["OBJECTIVES To investigate the expressions of survivin and Cyclooxygenase-2 (COX-2), and their possible correlations in the development of endometrial adenocarcinoma (EC).", "We also looked at their association with classical prognostic factors in EC.", "To our knowledge, this is the first time survivin expression is investigated in terms of its relation to COX-2 in the developmental pathway of EC.   \n", "METHODS Archived tissue samples of 50 EC, 30 endometrial hyperplasia and 20 proliferative endometrium were selected and immunohistochemically analyzed for survivin and COX-2 expression.   \n", "RESULTS Both survivin and COX-2 were overexpressed in hyperplasia and endometrial adenocarcinoma cases compared to proliferative endometrium, which was statistically significant (p=0.01, p=0.02, respectively).", "Among EC cases, survivin and COX-2 were strongly positive in 38 (76%) and 30 (60%) patients, respectively.", "Furthermore, we found survivin and COX-2 to be positively correlated, which was also statistically significant (p=0.0001, r=0.46).", "Neither survivin nor COX-2 expression was correlated with classical prognostic factors of endometrial carcinoma such as myometrial invasion, grade or lymph node metastasis (p>0.05).", "Neither COX-2 nor survivin had an impact on overall survival (p>0.05).   \n", "CONCLUSIONS Both survivin and COX-2 are overexpressed, and they seem to be early events in the occurrence of EC.", "Moreover, protein products of these two genes are positively correlated.", "COX-2 and survivin might share a common molecular pathway or enhance each other's actions in the developmental pathway of EC.", "Molecular basis of such a relationship should be further investigated in endometrial carcinogenesis."], "structured": true}
{"doc_id": 6123521, "title": "Structural plasticity of the adult brain: how animal models help us understand brain changes in depression and systemic disorders related to depression", "abstract": ["The brain interprets experiences and translates them into behavioral and physiological responses.", "Stressful events are those which are threatening or, at the very least, unexpected and surprising, and the physiological and behavioral responses are intended to promote adaptation via a process called \"allostasis.", "\"", "Chemical mediators of allostasis include cortisol and adrenalin from the adrenal glands, other hormones, and neurotransmitters, the parasympathetic and sympathetic nervous systems, and cytokines and chemokines from the immune system.", "Two brain structures, the amygdala and hippocampus, play key roles in interpreting what is stressful and determining appropriate responses.", "The hippocampus, a key structure for memories of events and contexts, expresses receptors that enable it to respond to glucocorticoid hormones in the blood, it undergoes atrophy in a number of psychiatric disorders; it also responds to stressors with changes in excitability, decreased dendritic branching, and reduction in number of neurons in the dentate gyrus.", "The amygdala, which is important for \"emotional memories, \" becomes hyperactive in posttraumatic stress disorder and depressive illness, in animal models of stress, there is evidence for growth and hypertrophy of nerve cells in the amygdala.", "Changes in the brain after acute and chronic stressors mirror the pattern seen in the metabolic, cardiovascular, and immune systems, that is, short-term adaptation (allostasis) followed by long-term damage (allostatic load), eg, atherosclerosis, fat deposition obesity, bone demineralization, and impaired immune function.", "Allostatic load of this kind is seen in major depressive illness and may also be expressed in other chronic anxiety and mood disorders."], "structured": false}
{"doc_id": 6123924, "title": "CCR7 provides localized access to IL-2 and defines homeostatically distinct regulatory T cell subsets", "abstract": ["Immune tolerance and activation depend on precise control over the number and function of immunosuppressive Foxp3(+) regulatory T (T reg) cells, and the importance of IL-2 in maintaining tolerance and preventing autoimmunity is clear.", "However, the homeostatic requirement for IL-2 among specific populations of peripheral T reg cells remains poorly understood.", "We show that IL-2 selectively maintains a population of quiescent CD44(lo)CD62L(hi) T reg cells that gain access to paracrine IL-2 produced in the T cell zones of secondary lymphoid tissues due to their expression of the chemokine receptor CCR7.", "In contrast, CD44(hi)CD62L(lo)CCR7(lo) T reg cells that populate nonlymphoid tissues do not access IL-2-prevalent regions in vivo and are insensitive to IL-2 blockade; instead, their maintenance depends on continued signaling through the co-stimulatory receptor ICOS (inducible co-stimulator).", "Thus, we define a fundamental homeostatic subdivision in T reg cell populations based on their localization and provide an integrated framework for understanding how T reg cell abundance and function are controlled by unique signals in different tissue environments."], "structured": false}
{"doc_id": 6128334, "title": "Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships.", "abstract": ["Pairwise sequence comparison methods have been assessed using proteins whose relationships are known reliably from their structures and functions, as described in the SCOP database [Murzin, A. G., Brenner, S. E., Hubbard, T. & Chothia C. (1995) J. Mol.", "Biol.", "247, 536-540].", "The evaluation tested the programs BLAST [Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. (1990).", "J. Mol.", "Biol.", "215, 403-410], WU-BLAST2 [Altschul, S. F. & Gish, W. (1996) Methods Enzymol.", "266, 460-480], FASTA [Pearson, W. R. & Lipman, D. J. (1988) Proc.", "Natl.", "Acad.", "Sci.", "USA 85, 2444-2448], and SSEARCH [Smith, T. F. & Waterman, M. S. (1981) J. Mol.", "Biol.", "147, 195-197] and their scoring schemes.", "The error rate of all algorithms is greatly reduced by using statistical scores to evaluate matches rather than percentage identity or raw scores.", "The E-value statistical scores of SSEARCH and FASTA are reliable: the number of false positives found in our tests agrees well with the scores reported.", "However, the P-values reported by BLAST and WU-BLAST2 exaggerate significance by orders of magnitude.", "SSEARCH, FASTA ktup = 1, and WU-BLAST2 perform best, and they are capable of detecting almost all relationships between proteins whose sequence identities are >30%.", "For more distantly related proteins, they do much less well; only one-half of the relationships between proteins with 20-30% identity are found.", "Because many homologs have low sequence similarity, most distant relationships cannot be detected by any pairwise comparison method; however, those which are identified may be used with confidence."], "structured": false}
{"doc_id": 6129301, "title": "Evaluation of a mental health outreach service for homeless families.", "abstract": ["AIMS To describe the characteristics of homeless children and families seen by the mental health outreach service (MHOS), to evaluate the impact of this service on the short term psychosocial functioning of children and parents, and to establish perceptions of, and satisfaction with, the service.   \n", "METHODS Twenty seven children from 23 families who were in receipt of the MHOS and 27 children from 23 families residing in other hostels where no such service was available were studied.", "The MHOS was delivered by a clinical nurse specialist with expertise in child mental health, who offered the following interventions: assessment and brief treatment of mental health disorders in children; liaison with agencies; and training of homeless centre staff.   \n", "RESULTS Children in the experimental group had a significantly higher decrease in Strengths and Difficulties Questionnaire (SDQ) total scores.", "Having received the intervention was the strongest predictor of improvement in SDQ total scores.", "There was no significant impact on parental mental health (General Health Questionnaire) scores.", "Homeless families and staff expressed high satisfaction with the MHOS.   \n", "CONCLUSION This MHOS for homeless families is an innovative intervention which meets the complex and multiple needs of a vulnerable population unable to access mainstream mental health services.", "The primary objective of the service was to improve child mental health problems; however, the service developed in a responsive way by meeting social and practical needs of families in addition to its clinical role."], "structured": true}
{"doc_id": 6137330, "title": "Evaluation of individuals with pulmonary nodules: when is it lung cancer? Diagnosis and management of lung cancer, 3rd ed: American College of Chest Physicians evidence-based clinical practice guidelines.", "abstract": ["OBJECTIVES The objective of this article is to update previous evidence-based recommendations for evaluation and management of individuals with solid pulmonary nodules and to generate new recommendations for those with nonsolid nodules.   \n", "METHODS We updated prior literature reviews, synthesized evidence, and formulated recommendations by using the methods described in the \"Methodology for Development of Guidelines for Lung Cancer\" in the American College of Chest Physicians Lung Cancer Guidelines, 3rd ed.   \n", "RESULTS We formulated recommendations for evaluating solid pulmonary nodules that measure > 8 mm in diameter, solid nodules that measure \u2264 8 mm in diameter, and subsolid nodules.", "The recommendations stress the value of assessing the probability of malignancy, the utility of imaging tests, the need to weigh the benefits and harms of different management strategies (nonsurgical biopsy, surgical resection, and surveillance with chest CT imaging), and the importance of eliciting patient preferences.   \n", "CONCLUSIONS Individuals with pulmonary nodules should be evaluated and managed by estimating the probability of malignancy, performing imaging tests to better characterize the lesions, evaluating the risks associated with various management alternatives, and eliciting their preferences for management."], "structured": true}
{"doc_id": 6144337, "title": "AgDscam, a Hypervariable Immunoglobulin Domain-Containing Receptor of the       Anopheles gambiae Innate Immune System     ", "abstract": ["Activation of the insect innate immune system is dependent on a limited number of pattern recognition receptors (PRRs) capable of interacting with pathogen-associated molecular pattern.", "Here we report a novel role of an alternatively spliced hypervariable immunoglobulin domain-encoding gene, Dscam, in generating a broad range of PRRs implicated in immune defense in the malaria vector Anopheles gambiae.", "The mosquito Down syndrome cell adhesion molecule gene, AgDscam, has a complex genome organization with 101 exons that can produce over 31,000 potential alternative splice forms with different combinations of adhesive domains and interaction specificities.", "AgDscam responds to infection by producing pathogen challenge-specific splice form repertoires.", "Transient silencing of AgDscam compromises the mosquito's resistance to infections with bacteria and the malaria parasite Plasmodium.", "AgDscam is mediating phagocytosis of bacteria with which it can associate and defend against in a splice form\u2013specific manner.", "AgDscam is a hypervariable PRR of the A. gambiae innate immune system."], "structured": false}
{"doc_id": 6144969, "title": "Enterovirus-induced gene expression profile is critical for human pancreatic islet destruction", "abstract": ["Virally induced inflammatory responses, beta cell destruction and release of beta cell autoantigens may lead to autoimmune reactions culminating in type 1 diabetes.", "Therefore, viral capability to induce beta cell death and the nature of virus-induced immune responses are among key determinants of diabetogenic viruses.", "We hypothesised that enterovirus infection induces a specific gene expression pattern that results in islet destruction and that such a host response pattern is not shared among all enterovirus infections but varies between virus strains.", "The changes in global gene expression and secreted cytokine profiles induced by lytic or benign enterovirus infections were studied in primary human pancreatic islet using DNA microarrays and viral strains either isolated at the clinical onset of type 1 diabetes or capable of causing a diabetes-like condition in mice.", "The expression of pro-inflammatory cytokine genes (IL-1-\u03b1, IL-1-\u03b2 and TNF-\u03b1) that also mediate cytokine-induced beta cell dysfunction correlated with the lytic potential of a virus.", "Temporally increasing gene expression levels of double-stranded RNA recognition receptors, antiviral molecules, cytokines and chemokines were detected for all studied virus strains.", "Lytic coxsackievirus B5 (CBV-5)-DS infection also downregulated genes involved in glycolysis and insulin secretion.", "The results suggest a distinct, virus-strain-specific, gene expression pattern leading to pancreatic islet destruction and pro-inflammatory effects after enterovirus infection.", "However, neither viral replication nor cytotoxic cytokine production alone are sufficient to induce necrotic cell death.", "More likely the combined effect of these and possibly cellular energy depletion lie behind the enterovirus-induced necrosis of islets."], "structured": false}
{"doc_id": 6148876, "title": "Islet1 derivatives in the heart are of both neural crest and second heart field origin.", "abstract": ["RATIONALE Islet1 (Isl1) has been proposed as a marker of cardiac progenitor cells derived from the second heart field and is utilized to identify and purify cardiac progenitors from murine and human specimens for ex vivo expansion.", "The use of Isl1 as a specific second heart field marker is dependent on its exclusion from other cardiac lineages such as neural crest.   \n", "OBJECTIVE Determine whether Isl1 is expressed by cardiac neural crest.   \n", "METHODS AND RESULTS We used an intersectional fate-mapping system using the RC::FrePe allele, which reports dual Flpe and Cre recombination.", "Combining Isl1(Cre/+), a SHF driver, and Wnt1::Flpe, a neural crest driver, with Rc::FrePe reveals that some Isl1 derivatives in the cardiac outflow tract derive from Wnt1-expressing neural crest progenitors.", "In contrast, no overlap was observed between Wnt1-derived neural crest and an alternative second heart field driver, Mef2c-AHF-Cre.   \n", "CONCLUSIONS Isl1 is not restricted to second heart field progenitors in the developing heart but also labels cardiac neural crest.", "The intersection of Isl1 and Wnt1 lineages within the heart provides a caveat to using Isl1 as an exclusive second heart field cardiac progenitor marker and suggests that some Isl1-expressing progenitor cells derived from embryos, embryonic stem cultures, or induced pluripotent stem cultures may be of neural crest lineage."], "structured": true}
{"doc_id": 6153754, "title": "Review of the secondary injury theory of acute spinal cord trauma with emphasis on vascular mechanisms.", "abstract": ["In patients with spinal cord injury, the primary or mechanical trauma seldom causes total transection, even though the functional loss may be complete.", "In addition, biochemical and pathological changes in the cord may worsen after injury.", "To explain these phenomena, the concept of the secondary injury has evolved for which numerous pathophysiological mechanisms have been postulated.", "This paper reviews the concept of secondary injury with special emphasis on vascular mechanisms.", "Evidence is presented to support the theory of secondary injury and the hypothesis that a key mechanism is posttraumatic ischemia with resultant infarction of the spinal cord.", "Evidence for the role of vascular mechanisms has been obtained from a variety of models of acute spinal cord injury in several species.", "Many different angiographic methods have been used for assessing microcirculation of the cord and for measuring spinal cord blood flow after trauma.", "With these techniques, the major systemic and local vascular effects of acute spinal cord injury have been identified and implicated in the etiology of secondary injury.", "The systemic effects of acute spinal cord injury include hypotension and reduced cardiac output.", "The local effects include loss of autoregulation in the injured segment of the spinal cord and a marked reduction of the microcirculation in both gray and white matter, especially in hemorrhagic regions and in adjacent zones.", "The microcirculatory loss extends for a considerable distance proximal and distal to the site of injury.", "Many studies have shown a dose-dependent reduction of spinal cord blood flow varying with the severity of injury, and a reduction of spinal cord blood flow which worsens with time after injury.", "The functional deficits due to acute spinal cord injury have been measured electrophysiologically with techniques such as motor and somatosensory evoked potentials and have been found proportional to the degree of posttraumatic ischemia.", "The histological effects include early hemorrhagic necrosis leading to major infarction at the injury site.", "These posttraumatic vascular effects can be treated.", "Systemic normotension can be restored with volume expansion or vasopressors, and spinal cord blood flow can be improved with dopamine, steroids, nimodipine, or volume expansion.", "The combination of nimodipine and volume expansion improves posttraumatic spinal cord blood flow and spinal cord function measured by evoked potentials.", "These results provide strong evidence that posttraumatic ischemia is an important secondary mechanism of injury, and that it can be counteracted."], "structured": false}
{"doc_id": 6157371, "title": "Chronophin mediates an ATP-sensing mechanism for cofilin dephosphorylation and neuronal cofilin-actin rod formation.", "abstract": ["Actin and its key regulatory component, cofilin, are found together in large rod-shaped assemblies in neurons subjected to energy stress.", "Such inclusions are also enriched in Alzheimer's disease brain, and appear in transgenic models of neurodegeneration.", "Neuronal insults, such as energy loss and/or oxidative stress, result in rapid dephosphorylation of the cellular cofilin pool prior to its assembly into rod-shaped inclusions.", "Although these events implicate a role for phosphatases in cofilin rod formation, a mechanism linking energy stress, phosphocofilin turnover, and subsequent rod assembly has been elusive.", "We demonstrate the ATP-sensitive interaction of the cofilin phosphatase chronophin (CIN) with the chaperone hsp90 to form a biosensor that mediates cofilin/actin rod formation.", "Our results suggest a model whereby attenuated interactions between CIN and hsp90 during ATP depletion enhance CIN-dependent cofilin dephosphorylation and consequent rod assembly, thereby providing a mechanism for the formation of pathological actin/cofilin aggregates during neurodegenerative energy flux."], "structured": false}
{"doc_id": 6157837, "title": "Renal considerations in angiotensin converting enzyme inhibitor therapy: a statement for healthcare professionals from the Council on the Kidney in Cardiovascular Disease and the Council for High Blood Pressure Research of the American Heart Association.", "abstract": ["Angiotensin converting enzyme (ACE) inhibitors are now one of the most frequently used classes of antihypertensive drugs.", "Beyond their utility in the management of hypertension, their use has been extended to the long-term management of patients with congestive heart failure (CHF), as well as diabetic and nondiabetic nephropathies.", "Although ACE inhibitor therapy usually improves renal blood flow (RBF) and sodium excretion rates in CHF and reduces the rate of progressive renal injury in chronic renal disease, its use can also be associated with a syndrome of \u201cfunctional renal insufficiency\u201d and/or hyperkalemia.", "This form of acute renal failure (ARF) most commonly develops shortly after initiation of ACE inhibitor therapy but can be observed after months or years of therapy, even in the absence of prior ill effects.", "ARF is most likely to occur when renal perfusion pressure cannot be sustained because of substantial decreases in mean arterial pressure (MAP) or when glomerular filtration rate (GFR) is highly angiotensin II (Ang II) dependent.", "Conditions that predict an adverse hemodynamic effect of ACE inhibitors in patients with CHF are preexisting hypotension and low cardiac filling pressures.", "The GFR is especially dependent on Ang II during extracellular fluid (ECF) volume depletion, high-grade bilateral renal artery stenosis, or stenosis of a dominant or single kidney, as in a renal transplant recipient.", "Understanding the pathophysiological mechanisms and the common risk factors for ACE inhibitor\u2013induced functional ARF is critical, because preventive strategies for ARF exist, and if effectively used, they may permit use of these compounds in a less restricted fashion.  ", "Under normal physiological conditions, renal autoregulation adjusts renal vascular resistance, so that RBF and GFR remain constant over a wide range of MAPs.1 The intrinsic renal autoregulation mechanism is adjusted by Ang II and the sympathetic nervous system.", "When renal perfusion pressure falls (as in \u2026"], "structured": false}
{"doc_id": 6158879, "title": "Greater clinical benefit of more intensive oral antiplatelet therapy with prasugrel in patients with diabetes mellitus in the trial to assess improvement in therapeutic outcomes by optimizing platelet inhibition with prasugrel-Thrombolysis in Myocardial Infarction 38.", "abstract": ["BACKGROUND Patients with diabetes mellitus (DM) are at high risk for recurrent cardiovascular events after acute coronary syndromes, in part because of increased platelet reactivity.", "The Trial to Assess Improvement in Therapeutic Outcomes by Optimizing Platelet Inhibition With Prasugrel-Thrombolysis in Myocardial Infarction 38 (TRITON-TIMI 38) showed an overall reduction in ischemic events with more intensive antiplatelet therapy with prasugrel than with clopidogrel but with more bleeding.", "We compared prasugrel with clopidogrel among subjects with DM in TRITON-TIMI 38.   \n", "METHODS AND RESULTS We classified 13 608 subjects on the basis of preexisting history of DM and further according to insulin use.", "Prespecified analyses of the primary (cardiovascular death, nonfatal myocardial infarction, or nonfatal stroke) and key secondary end points, including net clinical benefit (death, nonfatal myocardial infarction, nonfatal stroke, and nonfatal TIMI major bleeding) were compared by use of the log-rank test.", "We found that 3146 subjects had a preexisting history of DM, including 776 receiving insulin.", "The primary end point was reduced significantly with prasugrel among subjects without DM (9.2% versus 10.6%; hazard ratio [HR], 0.86; P=0.02) and with DM (12.2% versus 17.0%; HR, 0.70; P<0.001, P(interaction)=0.09).", "A benefit for prasugrel was observed among DM subjects on insulin (14.3% versus 22.2%; HR, 0.63; P=0.009) and those not on insulin (11.5% versus 15.3%; HR, 0.74; P=0.009).", "Myocardial infarction was reduced with prasugrel by 18% among subjects without DM (7.2% versus 8.7%; HR, 0.82; P=0.006) and by 40% among subjects with DM (8.2% versus 13.2%; HR, 0.60; P<0.001, P(interaction)=0.02).", "Although TIMI major hemorrhage was increased among subjects without DM on prasugrel (1.6% versus 2.4%; HR, 1.43; P=0.02), the rates were similar among subjects with DM for clopidogrel and prasugrel (2.6% versus 2.5%; HR, 1.06; P=0.81, P(interaction)=0.29).", "Net clinical benefit with prasugrel was greater for subjects with DM (14.6% versus 19.2%; HR, 0.74; P=0.001) than for subjects without DM (11.5% versus 12.3%; HR, 0.92; P=0.16, P(interaction)=0.05).   \n", "CONCLUSIONS Subjects with DM tended to have a greater reduction in ischemic events without an observed increase in TIMI major bleeding and therefore a greater net treatment benefit with prasugrel compared with clopidogrel.", "These data demonstrate that the more intensive oral antiplatelet therapy provided with prasugrel is of particular benefit to patients with DM."], "structured": true}
{"doc_id": 6163801, "title": "Kinetics of early T cell receptor signaling regulate the pathway of lytic granule delivery to the secretory domain.", "abstract": ["Cytolytic granules mediate killing of virus-infected cells by cytotoxic T lymphocytes.", "We show here that the granules can take long or short paths to the secretory domain.", "Both paths utilized the same intracellular molecular events, which have different spatial and temporal arrangements and are regulated by the kinetics of Ca(2+)-mediated signaling.", "Rapid signaling caused swift granule concentration near the microtubule-organizing center (MTOC) and subsequent delivery by the polarized MTOC directly to the secretory domain-the shortest path.", "Indolent signaling led to late recruitment of granules that moved along microtubules to the periphery of the synapse and then moved tangentially to fuse at the outer edge of the secretory domain-a longer path.", "The short pathway is associated with faster granule release and more efficient killing than the long pathway.", "Thus, the kinetics of early signaling regulates the quality of the T cell cytolytic response."], "structured": false}
{"doc_id": 6171953, "title": "Sirtuin-1 is a nutrient-dependent modulator of inflammation", "abstract": ["Inflammation accompanies obesity and its comorbidities-type 2 diabetes, non-alcoholic fatty liver disease and atherosclerosis, among others-and may contribute to their pathogenesis.", "Yet the cellular machinery that links nutrient sensing to inflammation remains incompletely characterized.", "The protein deacetylase sirtuin-1 (SirT1) is activated by energy depletion and plays a critical role in the mammalian response to fasting.", "More recently it has been implicated in the repression of inflammation.", "SirT1 mRNA and protein expression are suppressed in obese rodent and human white adipose tissue, while experimental reduction of SirT1 in adipocytes and macrophages causes low-grade inflammation that mimics that observed in obesity.", "Thus suppression of SirT1 during overnutrition may be critical to the development of obesity-associated inflammation.", "This effect is attributable to multiple actions of SirT1, including direct deacetylation of NF\u03baB and chromatin remodeling at inflammatory gene promoters.", "In this work, we report that SirT1 is also suppressed by diet-induced obesity in macrophages, which are key contributors to the ontogeny of metabolic inflammation.", "Thus, SirT1 may be a common mechanism by which cells sense nutrient status and modulate inflammatory signaling networks in accordance with organismal energy availability."], "structured": false}
{"doc_id": 6173523, "title": "A culture-independent sequence-based metagenomics approach to the investigation of an outbreak of Shiga-toxigenic Escherichia coli O104:H4.", "abstract": ["IMPORTANCE Identification of the bacterium responsible for an outbreak can aid in disease management.", "However, traditional culture-based diagnosis can be difficult, particularly if no specific diagnostic test is available for an outbreak strain.   \n", "OBJECTIVE To explore the potential of metagenomics, which is the direct sequencing of DNA extracted from microbiologically complex samples, as an open-ended clinical discovery platform capable of identifying and characterizing bacterial strains from an outbreak without laboratory culture.   \n", "DESIGN, SETTING, AND PATIENTS In a retrospective investigation, 45 samples were selected from fecal specimens obtained from patients with diarrhea during the 2011 outbreak of Shiga-toxigenic Escherichia coli (STEC) O104:H4 in Germany.", "Samples were subjected to high-throughput sequencing (August-September 2012), followed by a 3-phase analysis (November 2012-February 2013).", "In phase 1, a de novo assembly approach was developed to obtain a draft genome of the outbreak strain.", "In phase 2, the depth of coverage of the outbreak strain genome was determined in each sample.", "In phase 3, sequences from each sample were compared with sequences from known bacteria to identify pathogens other than the outbreak strain.   \n", "MAIN OUTCOMES AND MEASURES The recovery of genome sequence data for the purposes of identification and characterization of the outbreak strain and other pathogens from fecal samples.   \n", "RESULTS During phase 1, a draft genome of the STEC outbreak strain was obtained.", "During phase 2, the outbreak strain genome was recovered from 10 samples at greater than 10-fold coverage and from 26 samples at greater than 1-fold coverage.", "Sequences from the Shiga-toxin genes were detected in 27 of 40 STEC-positive samples (67%).", "In phase 3, sequences from Clostridium difficile, Campylobacter jejuni, Campylobacter concisus, and Salmonella enterica were recovered.   \n", "CONCLUSIONS AND RELEVANCE These results suggest the potential of metagenomics as a culture-independent approach for the identification of bacterial pathogens during an outbreak of diarrheal disease.", "Challenges include improving diagnostic sensitivity, speeding up and simplifying workflows, and reducing costs."], "structured": true}
{"doc_id": 6176498, "title": "Biomarkers of endothelial dysfunction and risk of type 2 diabetes mellitus.", "abstract": ["CONTEXT Endothelial dysfunction occurs in diagnosed type 2 diabetes mellitus but may also precede development of diabetes.   \n", "OBJECTIVE To determine whether elevated plasma levels of biomarkers reflecting endothelial dysfunction (E-selectin; intercellular adhesion molecule 1 [ICAM-1]; and vascular cell adhesion molecule 1 [VCAM-1]) predict development of type 2 diabetes in initially nondiabetic women.   \n", "DESIGN AND SETTING Prospective, nested case-control study within the Nurses' Health Study, an ongoing US study initiated in 1976.   \n", "PARTICIPANTS Of 121 700 women initially enrolled, 32 826 provided blood samples in 1989-1990; of those free of diabetes, cardiovascular disease, or cancer at baseline, 737 developed incident diabetes by 2000.", "Controls (n = 785) were selected according to matched age, fasting status, and race.   \n", "MAIN OUTCOME MEASURE Risk of confirmed clinically diagnosed type 2 diabetes by baseline levels of E-selectin, ICAM-1, and VCAM-1.   \n", "RESULTS Baseline median levels of the biomarkers were significantly higher among cases than among controls (E-selectin, 61.2 vs 45.4 ng/mL; ICAM-1, 264.9 vs 247.0 ng/mL; VCAM-1, 545.4 vs 526.0 ng/mL [all P values < or =.004]).", "Elevated E-selectin and ICAM-1 levels predicted incident diabetes in logistic regression models conditioned on matching criteria and adjusted for body mass index (BMI), family history of diabetes, smoking, diet score, alcohol intake, activity index, and postmenopausal hormone use.", "The adjusted relative risks for incident diabetes in the top quintile vs the bottom quintiles were 5.43 for E-selectin (95% confidence interval [CI], 3.47-8.50), 3.56 for ICAM-1 (95% CI, 2.28-5.58), and 1.12 for VCAM-1 (95% CI, 0.76-1.66).", "Adjustment for waist circumference instead of BMI or further adjustment for baseline levels of C-reactive protein, fasting insulin, and hemoglobin A(1c) or exclusion of cases diagnosed during the first 4 years of follow-up did not alter these associations.   \n", "CONCLUSION Endothelial dysfunction predicts type 2 diabetes in women independent of other known risk factors, including obesity and subclinical inflammation."], "structured": true}
{"doc_id": 6182947, "title": "Nrf2 protects human alveolar epithelial cells against injury induced by influenza A virus", "abstract": ["BACKGROUND Influenza A virus (IAV) infection primarily targets respiratory epithelial cells and produces clinical outcomes ranging from mild upper respiratory infection to severe pneumonia.", "Recent studies have shown the importance of lung antioxidant defense systems against injury by IAV.", "Nuclear factor-erythroid 2 related factor 2 (Nrf2) activates the majority of antioxidant genes.   \n", "METHODS Alveolar type II (ATII) cells and alveolar macrophages (AM) were isolated from human lungs not suitable for transplantation and donated for medical research.", "In some studies ATII cells were transdifferentiated to alveolar type I-like (ATI-like) cells.", "Alveolar epithelial cells were infected with A/PR/8/34 (PR8) virus.", "We analyzed PR8 virus production, influenza A nucleoprotein levels, ROS generation and expression of antiviral genes.", "Immunocytofluorescence was used to determine Nrf2 translocation and western blotting to detect Nrf2, HO-1 and caspase 1 and 3 cleavage.", "We also analyzed ingestion of PR8 virus infected apoptotic ATII cells by AM, cytokine levels by ELISA, glutathione levels, necrosis and apoptosis by TUNEL assay.", "Moreover, we determined the critical importance of Nrf2 using adenovirus Nrf2 (AdNrf2) or Nrf2 siRNA to overexpress or knockdown Nrf2, respectively.   \n", "RESULTS We found that IAV induced oxidative stress, cytotoxicity and apoptosis in ATI-like and ATII cells.", "We also found that AM can ingest PR8 virus-induced apoptotic ATII cells (efferocytosis) but not viable cells, whereas ATII cells did not ingest these apoptotic cells.", "PR8 virus increased ROS production, Nrf2, HO-1, Mx1 and OAS1 expression and Nrf2 translocation to the nucleus.", "Nrf2 knockdown with siRNA sensitized ATI-like cells and ATII cells to injury induced by IAV and overexpression of Nrf2 with AdNrf2 protected these cells.", "Furthermore, Nrf2 overexpression followed by infection with PR8 virus decreased virus replication, influenza A nucleoprotein expression, antiviral response and oxidative stress.", "However, AdNrf2 did not increase IFN-\u03bb1 (IL-29) levels.   \n", "CONCLUSIONS Our results indicate that IAV induces alveolar epithelial injury and that Nrf2 protects these cells from the cytopathic effects of IAV likely by increasing the expression of antioxidant genes.", "Identifying the pathways involved in protecting cells from injury during influenza infection may be particularly important for developing new therapeutic strategies."], "structured": true}
{"doc_id": 6190603, "title": "Dynamics in the plasma membrane: how to combine fluidity and order.", "abstract": ["Cell membranes are fascinating supramolecular aggregates that not only form a barrier between compartments but also harbor many chemical reactions essential to the existence and functioning of a cell.", "Here, it is proposed to review the molecular dynamics and mosaic organization of the plasma membrane, which are thought to have important functional implications.", "We will first summarize the basic concepts of Brownian diffusion and lipid domain formation in model membranes and then track the development of ideas and tools in this field, outlining key results obtained on the dynamic processes at work in membrane structure and assembly.", "We will focus in particular on findings made using fluorescent labeling and imaging procedures to record these dynamic processes.", "We will also discuss a few examples showing the impact of lateral diffusion on cell signal transduction, and outline some future methodological challenges which must be met before we can answer some of the questions arising in this field of research."], "structured": false}
{"doc_id": 6191684, "title": "Management of chronic tension-type headache with tricyclic antidepressant medication, stress management therapy, and their combination: a randomized controlled trial.", "abstract": ["CONTEXT Chronic tension-type headaches are characterized by near-daily headaches and often are difficult to manage in primary practice.", "Behavioral and pharmacological therapies each appear modestly effective, but data are lacking on their separate and combined effects.   \n", "OBJECTIVE To evaluate the clinical efficacy of behavioral and pharmacological therapies, singly and combined, for chronic tension-type headaches.   \n", "DESIGN AND SETTING Randomized placebo-controlled trial conducted from August 1995 to January 1998 at 2 outpatient sites in Ohio.   \n", "PARTICIPANTS Two hundred three adults (mean age, 37 years; 76% women) with diagnosis of chronic tension-type headaches (mean, 26 headache d/mo).   \n", "INTERVENTIONS Participants were randomly assigned to receive tricyclic antidepressant (amitriptyline hydrochloride, up to 100 mg/d, or nortriptyline hydrochloride, up to 75 mg/d) medication (n = 53), placebo (n = 48), stress management (eg, relaxation, cognitive coping) therapy (3 sessions and 2 telephone contacts) plus placebo (n = 49), or stress management therapy plus antidepressant medication (n = 53).   \n", "MAIN OUTCOME MEASURES Monthly headache index scores calculated as the mean of pain ratings (0-10 scale) recorded by participants in a daily diary 4 times per day; number of days per month with at least moderate pain (pain rating >/=5), analgesic medication use, and Headache Disability Inventory scores, compared by intervention group.   \n", "RESULTS Tricyclic antidepressant medication and stress management therapy each produced larger reductions in headache activity, analgesic medication use, and headache-related disability than placebo, but antidepressant medication yielded more rapid improvements in headache activity.", "Combined therapy was more likely to produce clinically significant (>/=50%) reductions in headache index scores (64% of participants) than antidepressant medication (38% of participants; P =.006), stress management therapy (35%; P =.003), or placebo (29%; P =.001).", "On other measures the combined therapy and its 2 component therapies produced similar outcomes.   \n", "CONCLUSIONS Our results indicate that antidepressant medication and stress management therapy are each modestly effective in treating chronic tension-type headaches.", "Combined therapy may improve outcome relative to monotherapy."], "structured": true}
{"doc_id": 6202834, "title": "Maximum likelihood estimates of species trees: how accuracy of phylogenetic inference depends upon the divergence history and sampling design.", "abstract": ["The understanding that gene trees are often in discord with each other and with the species trees that contain them has led researchers to methods that incorporate the inherent stochasticity of genetic processes in the phylogenetic estimation procedure.", "Recently developed methods for species-tree estimation that not only consider the retention and sorting of ancestral polymorphism but also quantify the actual probabilities of incomplete lineage sorting are expected to provide an improvement over earlier summary-statistic based approaches that discard much of the information content of gene trees.", "However, these new methods have yet to be tested on truly challenging evolutionary histories such as those marked by recent rapid speciation where high levels of incomplete lineage sorting and discord among gene trees predominate.", "Here, we test a new maximum-likelihood method that incorporates stochastic models of both nucleotide substitution and lineage sorting for species-tree estimation.", "Using a simulation approach, we consider a broad range of species-tree topologies under 2 scenarios representing moderate and severe incomplete lineage sorting.", "We show that the maximum-likelihood method results in more accurate species trees than a summary-statistic based approach, demonstrating that information contained in discordant gene trees can be effectively extracted using a full probabilistic model.", "Moreover, we demonstrate that the shape of the original species tree (i.e., the relative lengths of internal branches) has a significant impact on whether the species tree is estimated accurately.", "In the speciation histories explored here, it is not just the recent origin of species that affects the accuracy of the estimates but the variance in relative species divergence times as well.", "Additionally, we show that sampling effort (number of individuals and/or loci) and sampling design (ratio of individuals to loci) are both important factors affecting the accuracy of species-tree estimates, which is again affected by the relative timing of divergence among species.", "The inherent difficulties of estimating relationships when species have undergone a recent radiation are discussed, and in particular, the limitations with maximum-likelihood estimates of species trees that do not consider uncertainty in the estimated gene trees of individual loci.", "Thus, despite substantial improvements over current summary-statistic based approaches, and the increased sophistication of procedures that incorporate the process of gene lineage coalescence, recent radiations still appear to pose daunting challenges for phylogenetics."], "structured": false}
{"doc_id": 6207111, "title": "Relationship of soft drink consumption to global overweight, obesity, and diabetes: a cross-national analysis of 75 countries.", "abstract": ["OBJECTIVES We estimated the relationship between soft drink consumption and obesity and diabetes worldwide.   \n", "METHODS We used multivariate linear regression to estimate the association between soft drink consumption and overweight, obesity, and diabetes prevalence in 75 countries, controlling for other foods (cereals, meats, fruits and vegetables, oils, and total calories), income, urbanization, and aging.", "Data were obtained from the Euromonitor Global Market Information Database, the World Health Organization, and the International Diabetes Federation.", "Bottled water consumption, which increased with per-capita income in parallel to soft drink consumption, served as a natural control group.   \n", "RESULTS Soft drink consumption increased globally from 9.5 gallons per person per year in 1997 to 11.4 gallons in 2010.", "A 1% rise in soft drink consumption was associated with an additional 4.8 overweight adults per 100 (adjusted B; 95% confidence interval [CI] = 3.1, 6.5), 2.3 obese adults per 100 (95% CI = 1.1, 3.5), and 0.3 adults with diabetes per 100 (95% CI = 0.1, 0.8).", "These findings remained robust in low- and middle-income countries.   \n", "CONCLUSIONS Soft drink consumption is significantly linked to overweight, obesity, and diabetes worldwide, including in low- and middle-income countries."], "structured": true}
{"doc_id": 6209599, "title": "Extensive translation of circular RNAs driven by N6-methyladenosine", "abstract": ["Extensive pre-mRNA back-splicing generates numerous circular RNAs (circRNAs) in human transcriptome.", "However, the biological functions of these circRNAs remain largely unclear.", "Here we report that N6-methyladenosine (m6A), the most abundant base modification of RNA, promotes efficient initiation of protein translation from circRNAs in human cells.", "We discover that consensus m6A motifs are enriched in circRNAs and a single m6A site is sufficient to drive translation initiation.", "This m6A-driven translation requires initiation factor eIF4G2 and m6A reader YTHDF3, and is enhanced by methyltransferase METTL3/14, inhibited by demethylase FTO, and upregulated upon heat shock.", "Further analyses through polysome profiling, computational prediction and mass spectrometry reveal that m6A-driven translation of circRNAs is widespread, with hundreds of endogenous circRNAs having translation potential.", "Our study expands the coding landscape of human transcriptome, and suggests a role of circRNA-derived proteins in cellular responses to environmental stress."], "structured": false}
{"doc_id": 6212802, "title": "Simvastatin reduces CD40 expression in an experimental model of early arterialization of saphenous vein graft.", "abstract": ["BACKGROUND Saphenous vein graft (VG) failure occurs more frequently compared with arterial grafts, and graft thrombosis represents the main cause of early occlusion.", "Because CD40-CD40L pathway CD40 represents a culprit link between local inflammation and coagulation cascade, we investigate the role of CD40 and its soluble ligand (sCD40L) in the immediate in vitro response of VG to arterial pressures, and the potential effects of Simvastatin (Merck Sharp&Dohme, White-house Station, NJ) supplementation.   \n", "METHODS Samples of saphenous vein and of internal mammary artery (IMA) were obtained from sixteen patients without history of statin therapy.", "Segments underwent pulsatile pressure distension and culture with or without supplementation of Simvastatin.", "CD40 and sCD40L were assessed in tissue lysate and in culture supernatant, respectively.", "sCD40L serum concentrations were also measured.   \n", "RESULTS During the course of the experiment, the CD40 expression was significantly lower in IMA samples compared with both distended and not distended VG.", "Pressure distension up-regulated the production of CD40 in VG segments after 24 and 48 h. Statin supplementation significantly reduced the expression of CD40 in both venous (P < 0.001) and arterial samples (P < 0.001).", "This effect of Simvastatin was not affected by the treatment with L-NAME, but it was reversed by the addition of mevalonic acid.", "Mean sCD40L content in culture supernatants increased over time, suggesting that not only platelets but also the vessel wall is a source of CD40 and sCD40L.   \n", "CONCLUSIONS Simvastatin treatment modulates endothelial CD40-sCD40L in both venous and arterial grafts, and therefore may represent a useful tool in the pharmacological prevention of graft failure."], "structured": true}
{"doc_id": 6219790, "title": "Cancer Cell Membrane-Coated Nanoparticles for Anticancer Vaccination and Drug Delivery", "abstract": ["Cell-derived nanoparticles have been garnering increased attention due to their ability to mimic many of the natural properties displayed by their source cells.", "This top-down engineering approach can be applied toward the development of novel therapeutic strategies owing to the unique interactions enabled through the retention of complex antigenic information.", "Herein, we report on the biological functionalization of polymeric nanoparticles with a layer of membrane coating derived from cancer cells.", "The resulting core-shell nanostructures, which carry the full array of cancer cell membrane antigens, offer a robust platform with applicability toward multiple modes of anticancer therapy.", "We demonstrate that by coupling the particles with an immunological adjuvant, the resulting formulation can be used to promote a tumor-specific immune response for use in vaccine applications.", "Moreover, we show that by taking advantage of the inherent homotypic binding phenomenon frequently observed among tumor cells the membrane functionalization allows for a unique cancer targeting strategy that can be utilized for drug delivery applications."], "structured": false}
{"doc_id": 6227220, "title": "Autophagy deficiency leads to protection from obesity and insulin resistance by inducing Fgf21 as a mitokine", "abstract": ["Despite growing interest and a recent surge in papers, the role of autophagy in glucose and lipid metabolism is unclear.", "We produced mice with skeletal muscle\u2013specific deletion of Atg7 (encoding autophagy-related 7).", "Unexpectedly, these mice showed decreased fat mass and were protected from diet-induced obesity and insulin resistance; this phenotype was accompanied by increased fatty acid oxidation and browning of white adipose tissue (WAT) owing to induction of fibroblast growth factor 21 (Fgf21).", "Mitochondrial dysfunction induced by autophagy deficiency increased Fgf21 expression through induction of Atf4, a master regulator of the integrated stress response.", "Mitochondrial respiratory chain inhibitors also induced Fgf21 in an Atf4-dependent manner.", "We also observed induction of Fgf21, resistance to diet-induced obesity and amelioration of insulin resistance in mice with autophagy deficiency in the liver, another insulin target tissue.", "These findings suggest that autophagy deficiency and subsequent mitochondrial dysfunction promote Fgf21 expression, a hormone we consequently term a 'mitokine', and together these processes promote protection from diet-induced obesity and insulin resistance."], "structured": false}
{"doc_id": 6250701, "title": "Laboratory prediction of the requirement for renal replacement in acute falciparum malaria", "abstract": ["BACKGROUND Acute renal failure is a common complication of severe malaria in adults, and without renal replacement therapy (RRT), it carries a poor prognosis.", "Even when RRT is available, delaying its initiation may increase mortality.", "Earlier identification of patients who will need RRT may improve outcomes.   \n", "METHOD Prospectively collected data from two intervention studies in adults with severe malaria were analysed focusing on laboratory features on presentation and their association with a later requirement for RRT.", "In particular, laboratory indices of acute tubular necrosis (ATN) and acute kidney injury (AKI) that are used in other settings were examined.   \n", "RESULTS Data from 163 patients were available for analysis.", "Whether or not the patients should have received RRT (a retrospective assessment determined by three independent reviewers) was used as the reference.", "Forty-three (26.4%) patients met criteria for dialysis, but only 19 (44.2%) were able to receive this intervention due to the limited availability of RRT.", "Patients with impaired renal function on admission (creatinine clearance < 60 ml/min) (n = 84) had their laboratory indices of ATN/AKI analysed.", "The plasma creatinine level had the greatest area under the ROC curve (AUC): 0.83 (95% confidence interval 0.74-0.92), significantly better than the AUCs for, urinary sodium level, the urea to creatinine ratio (UCR), the fractional excretion of urea (FeUN) and the urinary neutrophil gelatinase-associated lipocalcin (NGAL) level.", "The AUC for plasma creatinine was also greater than the AUC for blood urea nitrogen level, the fractional excretion of sodium (FeNa), the renal failure index (RFI), the urinary osmolality, the urine to plasma creatinine ratio (UPCR) and the creatinine clearance, although the difference for these variables did not reach statistical significance.   \n", "CONCLUSIONS In adult patients with severe malaria and impaired renal function on admission, none of the evaluated laboratory indices was superior to the plasma creatinine level when used to predict a later requirement for renal replacement therapy."], "structured": true}
{"doc_id": 6251620, "title": "Antineutrophil cytoplasmic antibodies (ANCA).", "abstract": ["Antineutrophil cytoplasmic antibodies (ANCA) are a sensitive and specific marker for ANCA-associated systemic vasculitis.", "Using indirect immunofluorescence on ethanol-fixed neutrophils, two major fluoroscopic patterns can be recognised: a diffuse cytoplasmic staining (C-ANCA), and a perinuclear/nuclear staining (P-ANCA).", "In patients with vasculitis, more of 90% of C-ANCA are directed against proteinase 3 (PR3-ANCA) whereas approximately 80-90% of P-ANCA recognise myelperoxidase (MPO-ANCA).", "Although C-ANCA (PR3-ANCA) is preferentially associated with Wegener's granulomatosis (WG), and P-ANCA (MPO-ANCA) with microscopic polyangiitis (MPA), idiopathic necrotising crescentic glomerulonephritis (iNCGN) and Churg-Strauss syndrome (CSS), there is not absolute specificity.", "Between 10-20% of patients with classical WG show P-ANCA (MPO-ANCA), and even a larger percentage of patients with MPA or CSS have C-ANCA (PR3-ANCA).", "Furthermore, it should be stressed that approximately 10-20% of patients with WG or MPA (and 40-50% of cases of CSS) have negative assay for ANCA.", "The best diagnostic performance is obtained when indirect immunofluorescence is combined with PR3 and MPO-specific ELISAs.", "ANCA with different and unknown antigen specificity are found in a variety of conditions other than AASV, including inflammatory bowel diseases, other autoimmune diseases, and infections where their clinical significance is unclear.", "ANCA levels are useful to monitor disease activity but should not be used by themselves to guide treatment.", "A significant increase in ANCA titres, or the reappearance of ANCA, should alert the clinicians and lead to a stricter patient control."], "structured": false}
{"doc_id": 6259170, "title": "Emerging functional cross-talk between the Keap1-Nrf2 system and mitochondria", "abstract": ["Nuclear factor erythroid-derived 2-related factor 2 (Nrf2) was originally identified as a positive regulator of drug detoxifying enzyme gene expression during exposure to environmental electrophiles.", "Currently, Nrf2 is known to regulate the expression of hundreds of cytoprotective genes to counteract endogenously or exogenously generated oxidative stress.", "Furthermore, when activated in human tumors by somatic mutations, Nrf2 confers growth advantages and chemoresistance by regulating genes involved in various processes such as the pentose phosphate pathway and nucleotide synthesis in addition to antioxidant proteins.", "Interestingly, increasing evidence shows that Nrf2 is associated with mitochondrial biogenesis during environmental stresses in certain tissues such as the heart.", "Furthermore, SKN-1, a functional homolog of Nrf2 in C. elegans, is activated by mitochondrial reactive oxygen species and extends life span by promoting mitochondrial homeostasis (i.e., mitohormesis).", "Similarly, Nrf2 activation was recently observed in the heart of surfeit locus protein 1 (Surf1) -/- mice in which cellular respiration was decreased due to cytochrome c oxidase defects.", "In this review, we critically examine the relationship between Nrf2 and mitochondria and argue that the Nrf2 stress pathway intimately communicates with mitochondria to maintain cellular homeostasis during oxidative stress."], "structured": false}
{"doc_id": 6264468, "title": "Regulation of pluripotency by RNA binding proteins.", "abstract": ["Establishment, maintenance, and exit from pluripotency require precise coordination of a cell's molecular machinery.", "Substantial headway has been made in deciphering many aspects of this elaborate system, particularly with respect to epigenetics, transcription, and noncoding RNAs.", "Less attention has been paid to posttranscriptional regulatory processes such as alternative splicing, RNA processing and modification, nuclear export, regulation of transcript stability, and translation.", "Here, we introduce the RNA binding proteins that enable the posttranscriptional regulation of gene expression, summarizing current and ongoing research on their roles at different regulatory points and discussing how they help script the fate of pluripotent stem cells."], "structured": false}
{"doc_id": 6268106, "title": "The ubiquitin ligase Drosophila Mind bomb promotes Notch signaling by regulating the localization and activity of Serrate and Delta.", "abstract": ["The receptor Notch and its ligands of the Delta/Serrate/LAG2 (DSL) family are the central components in the Notch pathway, a fundamental cell signaling system that regulates pattern formation during animal development.", "Delta is directly ubiquitinated by Drosophila and Xenopus Neuralized, and by zebrafish Mind bomb, two unrelated RING-type E3 ubiquitin ligases with common abilities to promote Delta endocytosis and signaling activity.", "Although orthologs of both Neuralized and Mind bomb are found in most metazoan organisms, their relative contributions to Notch signaling in any single organism have not yet been assessed.", "We show here that a Drosophila ortholog of Mind bomb (D-mib) is a positive component of Notch signaling that is required for multiple Neuralized-independent, Notch-dependent developmental processes.", "Furthermore, we show that D-mib associates physically and functionally with both Serrate and Delta.", "We find that D-mib uses its ubiquitin ligase activity to promote DSL ligand activity, an activity that is correlated with its ability to induce the endocytosis and degradation of both Delta and Serrate (see also Le Borgne et al., 2005).", "We further demonstrate that D-mib can functionally replace Neuralized in multiple cell fate decisions that absolutely require endogenous Neuralized, a testament to the highly similar activities of these two unrelated ubiquitin ligases in regulating Notch signaling.", "We conclude that ubiquitination of Delta and Serrate by Neuralized and D-mib is an obligate feature of DSL ligand activation throughout Drosophila development."], "structured": false}
{"doc_id": 6270720, "title": "Myeloid differentiation factor-88/interleukin-1 signaling controls cardiac fibrosis and heart failure progression in inflammatory dilated cardiomyopathy.", "abstract": ["RATIONALE The myeloid differentiation factor (MyD)88/interleukin (IL)-1 axis activates self-antigen-presenting cells and promotes autoreactive CD4(+) T-cell expansion in experimental autoimmune myocarditis, a mouse model of inflammatory heart disease.   \n", "OBJECTIVE The aim of this study was to determine the role of MyD88 and IL-1 in the progression of acute myocarditis to an end-stage heart failure.   \n", "METHODS AND RESULTS Using alpha-myosin heavy chain peptide (MyHC-alpha)-loaded, activated dendritic cells, we induced myocarditis in wild-type and MyD88(-/-) mice with similar distributions of heart-infiltrating cell subsets and comparable CD4(+) T-cell responses.", "Injection of complete Freund's adjuvant (CFA) or MyHC-alpha/CFA into diseased mice promoted cardiac fibrosis, induced ventricular dilation, and impaired heart function in wild-type but not in MyD88(-/-) mice.", "Experiments with chimeric mice confirmed the bone marrow origin of the fibroblasts replacing inflammatory infiltrates and showed that MyD88 and IL-1 receptor type I signaling on bone marrow-derived cells was critical for development of cardiac fibrosis during progression to heart failure.   \n", "CONCLUSIONS Our findings indicate a critical role of MyD88/IL-1 signaling in the bone marrow compartment in postinflammatory cardiac fibrosis and heart failure and point to novel therapeutic strategies against inflammatory cardiomyopathy."], "structured": true}
{"doc_id": 6277638, "title": "Mechanisms of Life Span Extension by Rapamycin in the Fruit Fly Drosophila melanogaster", "abstract": ["The target of rapamycin (TOR) pathway is a major nutrient-sensing pathway that, when genetically downregulated, increases life span in evolutionarily diverse organisms including mammals.", "The central component of this pathway, TOR kinase, is the target of the inhibitory drug rapamycin, a highly specific and well-described drug approved for human use.", "We show here that feeding rapamycin to adult Drosophila produces the life span extension seen in some TOR mutants.", "Increase in life span by rapamycin was associated with increased resistance to both starvation and paraquat.", "Analysis of the underlying mechanisms revealed that rapamycin increased longevity specifically through the TORC1 branch of the TOR pathway, through alterations to both autophagy and translation.", "Rapamycin could increase life span of weak insulin/Igf signaling (IIS) pathway mutants and of flies with life span maximized by dietary restriction, indicating additional mechanisms."], "structured": false}
{"doc_id": 6280907, "title": "Conversion of vascular endothelial cells into multipotent stem-like cells", "abstract": ["Mesenchymal stem cells can give rise to several cell types, but varying results depending on isolation methods and tissue source have led to controversies about their usefulness in clinical medicine.", "Here we show that vascular endothelial cells can transform into multipotent stem-like cells by an activin-like kinase-2 (ALK2) receptor\u2013dependent mechanism.", "In lesions from individuals with fibrodysplasia ossificans progressiva (FOP), a disease in which heterotopic ossification occurs as a result of activating ALK2 mutations, or from transgenic mice expressing constitutively active ALK2, chondrocytes and osteoblasts expressed endothelial markers.", "Lineage tracing of heterotopic ossification in mice using a Tie2-Cre construct also suggested an endothelial origin of these cell types.", "Expression of constitutively active ALK2 in endothelial cells caused endothelial-to-mesenchymal transition and acquisition of a stem cell\u2013like phenotype.", "Similar results were obtained by treatment of untransfected endothelial cells with the ligands transforming growth factor-\u03b22 (TGF-\u03b22) or bone morphogenetic protein-4 (BMP4) in an ALK2-dependent manner.", "These stem-like cells could be triggered to differentiate into osteoblasts, chondrocytes or adipocytes.", "We suggest that conversion of endothelial cells to stem-like cells may provide a new approach to tissue engineering."], "structured": false}
{"doc_id": 6285534, "title": "miR-302 Is Required for Timing of Neural Differentiation, Neural Tube Closure, and Embryonic Viability", "abstract": ["The evolutionarily conserved miR-302 family of microRNAs is expressed during early mammalian embryonic development.", "Here, we report that deletion of miR-302a-d in mice results in a fully penetrant late embryonic lethal phenotype.", "Knockout embryos have an anterior neural tube closure defect associated with a thickened neuroepithelium.", "The neuroepithelium shows increased progenitor proliferation, decreased cell death, and precocious neuronal differentiation.", "mRNA profiling at multiple time points during neurulation uncovers a complex pattern of changing targets over time.", "Overexpression of one of these targets, Fgf15, in the neuroepithelium of the chick embryo induces precocious neuronal differentiation.", "Compound mutants between mir-302 and the related mir-290 locus have a synthetic lethal phenotype prior to neurulation.", "Our results show that mir-302 helps regulate neurulation by suppressing neural progenitor expansion and precocious differentiation.", "Furthermore, these results uncover redundant roles for mir-290 and mir-302 early in development."], "structured": false}
{"doc_id": 6290112, "title": "Low copy number of the salivary amylase gene predisposes to obesity", "abstract": ["Common multi-allelic copy number variants (CNVs) appear enriched for phenotypic associations compared to their biallelic counterparts.", "Here we investigated the influence of gene dosage effects on adiposity through a CNV association study of gene expression levels in adipose tissue.", "We identified significant association of a multi-allelic CNV encompassing the salivary amylase gene (AMY1) with body mass index (BMI) and obesity, and we replicated this finding in 6,200 subjects.", "Increased AMY1 copy number was positively associated with both amylase gene expression (P = 2.31 \u00d7 10(-14)) and serum enzyme levels (P < 2.20 \u00d7 10(-16)), whereas reduced AMY1 copy number was associated with increased BMI (change in BMI per estimated copy = -0.15 (0.02) kg/m(2); P = 6.93 \u00d7 10(-10)) and obesity risk (odds ratio (OR) per estimated copy = 1.19, 95% confidence interval (CI) = 1.13-1.26; P = 1.46 \u00d7 10(-10)).", "The OR value of 1.19 per copy of AMY1 translates into about an eightfold difference in risk of obesity between subjects in the top (copy number > 9) and bottom (copy number < 4) 10% of the copy number distribution.", "Our study provides a first genetic link between carbohydrate metabolism and BMI and demonstrates the power of integrated genomic approaches beyond genome-wide association studies."], "structured": false}
{"doc_id": 6296189, "title": "Loss, trauma, and human resilience: have we underestimated the human capacity to thrive after extremely aversive events?", "abstract": ["Many people are exposed to loss or potentially traumatic events at some point in their lives, and yet they continue to have positive emotional experiences and show only minor and transient disruptions in their ability to function.", "Unfortunately, because much of psychology's knowledge about how adults cope with loss or trauma has come from individuals who sought treatment or exhibited great distress, loss and trauma theorists have often viewed this type of resilience as either rare or pathological.", "The author challenges these assumptions by reviewing evidence that resilience represents a distinct trajectory from the process of recovery, that resilience in the face of loss or potential trauma is more common than is often believed, and that there are multiple and sometimes unexpected pathways to resilience."], "structured": false}
{"doc_id": 6308416, "title": "Role of boundary conditions in an experimental model of epithelial wound healing.", "abstract": ["Coordinated cell movements in epithelial layers are essential for proper tissue morphogenesis and homeostasis, but our understanding of the mechanisms that coordinate the behavior of multiple cells in these processes is far from complete.", "Recent experiments with Madin-Darby canine kidney epithelial monolayers revealed a wave-like pattern of injury-induced MAPK activation and showed that it is essential for collective cell migration after wounding.", "To investigate the effects of the different aspects of wounding on cell sheet migration, we engineered a system that allowed us to dissect the classic wound healing assay.", "We studied Madin-Darby canine kidney sheet migration under three different conditions: 1) the classic wound healing assay, 2) empty space induction, where a confluent monolayer is grown adjacent to a slab of polydimethylsiloxane and the monolayer is not injured but allowed to migrate upon removal of the slab, and 3) injury via polydimethylsiloxane membrane peel-off, where an injured monolayer migrates onto plain tissue culture surface, as in the case of empty space induction allowing for direct comparison.", "By tracking the motion of individual cells within the sheet under these three conditions, we show how the dynamics of the individual cells' motion is responsible for the coordinated migration of the sheet and is coordinated with the activation of ERK1/2 MAPK.", "In addition, we demonstrate that the propagation of the waves of MAPK activation depends on the generation of reactive oxygen species at the wound edge."], "structured": false}
{"doc_id": 6309659, "title": "Reproductive period and risk of dementia in postmenopausal women.", "abstract": ["CONTEXT Exogenous estrogen use may lower risk of dementia in postmenopausal women.", "A relationship between long-term exposure to endogenous estrogens and incident dementia has been hypothesized but not studied.   \n", "OBJECTIVE To determine whether a longer reproductive period, as an indicator of longer exposure to endogenous estrogens, is associated with lower risk of dementia and Alzheimer disease (AD) in women who have natural menopause.   \n", "DESIGN AND SETTING The Rotterdam Study, a population-based prospective cohort study conducted in the Netherlands.   \n", "PARTICIPANTS A total of 3601 women aged 55 years or older who did not have dementia at baseline (1990-1993) and had information on age at menarche, age at menopause, and type of menopause.", "Participants were reexamined in 1993-1994 and 1997-1999 and were continuously monitored for development of dementia.   \n", "MAIN OUTCOME MEASURES Incidence of dementia, based on Diagnostic and Statistical Manual of Mental Disorders, Revised Third Edition criteria, and AD, based on National Institute of Neurological Disorders and Stroke/Alzheimer's Disease and Related Disorders Association criteria, compared by quartiles of reproductive period among women with natural menopause.   \n", "RESULTS During 21 046 person-years of follow-up (median follow-up, 6.3 years), 199 women developed dementia, including 159 who developed AD.", "After adjusting for age, dementia was not clearly associated with length of reproductive period.", "However, after adjusting for multiple covariates, women with natural menopause and more reproductive years had an increased risk of dementia (adjusted rate ratio [RR] for women with >39 reproductive years [highest quartile] compared with <34 reproductive years [lowest quartile], 1.78; 95% confidence interval [CI], 1.12-2.84).", "The adjusted RR per year of increase was 1.04 (95% CI, 1.01-1.08).", "For risk of AD, the adjusted RRs were 1.51 (95% CI, 0.91-2.50) and 1.03 (95% CI, 1.00-1.07), respectively.", "Risk of dementia associated with a longer reproductive period was most pronounced in APOE epsilon4 carriers (adjusted RR for >39 reproductive years compared with <34 reproductive years, 4.20 [95% CI, 1.97-8.92] for dementia and 3.42 [95% CI, 1.51-7.75] for AD), whereas in noncarriers, no clear association with dementia or AD was observed.   \n", "CONCLUSION Our findings do not support the hypothesis that a longer reproductive period reduces risk of dementia in women who have natural menopause."], "structured": true}
{"doc_id": 6313547, "title": "Effects of growth hormone and insulin-like growth factor 1 deficiency on ageing and longevity.", "abstract": ["Present knowledge on the effects of growth hormone (GH)/insulin-like growth hormone (IGF)1 deficiency on ageing and lifespan are reviewed.", "Evidence is presented that isolated GH deficiency (IGHD), multiple pituitary hormone deficiencies (MPHD) including GH, as well as primary IGE1 deficiency (GH resistance, Laron syndrome) present signs of early ageing such as thin and wrinkled skin, obesity, hyperglycemia and osteoporosis.", "These changes do not seem to affect the lifespan, as patients reach old age.", "Animal models of genetic MPHD (Ames and Snell mice) and GH receptor knockout mice (primary IGF1 deficiency) also have a statistically significant higher longevity compared to normal controls.", "On the contrary, mice transgenic for GH and acromegalic patients secreting large amounts of GH have premature death.", "In conclusion longstanding GH/IGF1 deficiency affects several parameters of the ageing process without impairing lifespan, and as shown in animal models prolongs longevity.", "In contrast high GH/IGF1 levels accelerate death."], "structured": false}
{"doc_id": 6315132, "title": "KLF1-null neonates display hydrops fetalis and a deranged erythroid transcriptome.", "abstract": ["We describe a case of severe neonatal anemia with kernicterus caused by compound heterozygosity for null mutations in KLF1, each inherited from asymptomatic parents.", "One of the mutations is novel.", "This is the first described case of a KLF1-null human.", "The phenotype of severe nonspherocytic hemolytic anemia, jaundice, hepatosplenomegaly, and marked erythroblastosis is more severe than that present in congenital dyserythropoietic anemia type IV as a result of dominant mutations in the second zinc-finger of KLF1.", "There was a very high level of HbF expression into childhood (>70%), consistent with a key role for KLF1 in human hemoglobin switching.", "We performed RNA-seq on circulating erythroblasts and found that human KLF1 acts like mouse Klf1 to coordinate expression of many genes required to build a red cell including those encoding globins, cytoskeletal components, AHSP, heme synthesis enzymes, cell-cycle regulators, and blood group antigens.", "We identify novel KLF1 target genes including KIF23 and KIF11 which are required for proper cytokinesis.", "We also identify new roles for KLF1 in autophagy, global transcriptional control, and RNA splicing.", "We suggest loss of KLF1 should be considered in otherwise unexplained cases of severe neonatal NSHA or hydrops fetalis."], "structured": false}
{"doc_id": 6319826, "title": "Quantifying heterogeneity in a meta-analysis.", "abstract": ["The extent of heterogeneity in a meta-analysis partly determines the difficulty in drawing overall conclusions.", "This extent may be measured by estimating a between-study variance, but interpretation is then specific to a particular treatment effect metric.", "A test for the existence of heterogeneity exists, but depends on the number of studies in the meta-analysis.", "We develop measures of the impact of heterogeneity on a meta-analysis, from mathematical criteria, that are independent of the number of studies and the treatment effect metric.", "We derive and propose three suitable statistics: H is the square root of the chi2 heterogeneity statistic divided by its degrees of freedom; R is the ratio of the standard error of the underlying mean from a random effects meta-analysis to the standard error of a fixed effect meta-analytic estimate, and I2 is a transformation of (H) that describes the proportion of total variation in study estimates that is due to heterogeneity.", "We discuss interpretation, interval estimates and other properties of these measures and examine them in five example data sets showing different amounts of heterogeneity.", "We conclude that H and I2, which can usually be calculated for published meta-analyses, are particularly useful summaries of the impact of heterogeneity.", "One or both should be presented in published meta-analyses in preference to the test for heterogeneity."], "structured": false}
{"doc_id": 6323196, "title": "Neurocognitive Development in Children Experiencing Intrauterine Growth Retardation and Born Small for Gestational Age: Pathological, Constitutional and Therapeutic Pathways", "abstract": ["Interest in the neurocognitive and psychosocial outcomes in children who are born small for gestational age (SGA) has increased since the recent approval of growth hormone (GH) therapy in this indication.", "The objective of GH treatment in SGA children is to provide a symptomatic treatment for growth retardation.", "From a patient perspective, the ultimate goals of GH therapy are the reduction in the present or future risk of neurocognitive, psychological, social or occupational impairment, not the accompanying improvements in growth velocity and final height per se.", "Therefore, from a scientific perspective, neurocognitive and psychosocial endpoints become relevant domains of assessment to determine the final treatment benefit experienced by the patient born SGA.", "This article reviews recent available studies on developmental risks in SGA, and then transforms the empirical findings into an integrated conceptual framework on the sources and mediators of neurocognitive and psychosocial outcomes in intrauterine growth retardation and SGA.", "This framework depicts two distinct therapeutic pathways by which GH therapy may improve neurocognitive and behavioural outcomes.", "The first (\u2018traditional\u2019) pathway is the prevention of exposure to short-stature-related stressors via an improvement in growth velocity and final height.", "The second pathway refers to potential metabolic, and thus neurotropic and psychotropic, effects of GH binding at receptors in the central nervous system, thus changing neuronal activity.", "To date, the existence and potential mechanisms of such physiologically and not psychologically mediated effects of GH on neurocognitive functioning in SGA patients remain hypothetical."], "structured": false}
{"doc_id": 6325527, "title": "Gpr124 is essential for blood\u2013brain barrier integrity in central nervous system disease", "abstract": ["Although blood\u2013brain barrier (BBB) compromise is central to the etiology of diverse central nervous system (CNS) disorders, endothelial receptor proteins that control BBB function are poorly defined.", "The endothelial G-protein-coupled receptor (GPCR) Gpr124 has been reported to be required for normal forebrain angiogenesis and BBB function in mouse embryos, but the role of this receptor in adult animals is unknown.", "Here Gpr124 conditional knockout (CKO) in the endothelia of adult mice did not affect homeostatic BBB integrity, but resulted in BBB disruption and microvascular hemorrhage in mouse models of both ischemic stroke and glioblastoma, accompanied by reduced cerebrovascular canonical Wnt\u2013\u03b2-catenin signaling.", "Constitutive activation of Wnt\u2013\u03b2-catenin signaling fully corrected the BBB disruption and hemorrhage defects of Gpr124-CKO mice, with rescue of the endothelial gene tight junction, pericyte coverage and extracellular-matrix deficits.", "We thus identify Gpr124 as an endothelial GPCR specifically required for endothelial Wnt signaling and BBB integrity under pathological conditions in adult mice.", "This finding implicates Gpr124 as a potential therapeutic target for human CNS disorders characterized by BBB disruption."], "structured": false}
{"doc_id": 6327940, "title": "Vegan proteins may reduce risk of cancer, obesity, and cardiovascular disease by promoting increased glucagon activity.", "abstract": ["Amino acids modulate the secretion of both insulin and glucagon; the composition of dietary protein therefore has the potential to influence the balance of glucagon and insulin activity.", "Soy protein, as well as many other vegan proteins, are higher in non-essential amino acids than most animal-derived food proteins, and as a result should preferentially favor glucagon production.", "Acting on hepatocytes, glucagon promotes (and insulin inhibits) cAMP-dependent mechanisms that down-regulate lipogenic enzymes and cholesterol synthesis, while up-regulating hepatic LDL receptors and production of the IGF-I antagonist IGFBP-1.", "The insulin-sensitizing properties of many vegan diets--high in fiber, low in saturated fat--should amplify these effects by down-regulating insulin secretion.", "Additionally, the relatively low essential amino acid content of some vegan diets may decrease hepatic IGF-I synthesis.", "Thus, diets featuring vegan proteins can be expected to lower elevated serum lipid levels, promote weight loss, and decrease circulating IGF-I activity.", "The latter effect should impede cancer induction (as is seen in animal studies with soy protein), lessen neutrophil-mediated inflammatory damage, and slow growth and maturation in children.", "In fact, vegans tend to have low serum lipids, lean physiques, shorter stature, later puberty, and decreased risk for certain prominent 'Western' cancers; a vegan diet has documented clinical efficacy in rheumatoid arthritis.", "Low-fat vegan diets may be especially protective in regard to cancers linked to insulin resistance--namely, breast and colon cancer--as well as prostate cancer; conversely, the high IGF-I activity associated with heavy ingestion of animal products may be largely responsible for the epidemic of 'Western' cancers in wealthy societies.", "Increased phytochemical intake is also likely to contribute to the reduction of cancer risk in vegans.", "Regression of coronary stenoses has been documented during low-fat vegan diets coupled with exercise training; such regimens also tend to markedly improve diabetic control and lower elevated blood pressure.", "Risk of many other degenerative disorders may be decreased in vegans, although reduced growth factor activity may be responsible for an increased risk of hemorrhagic stroke.", "By altering the glucagon/insulin balance, it is conceivable that supplemental intakes of key non-essential amino acids could enable omnivores to enjoy some of the health advantages of a vegan diet.", "An unnecessarily high intake of essential amino acids--either in the absolute sense or relative to total dietary protein--may prove to be as grave a risk factor for 'Western' degenerative diseases as is excessive fat intake."], "structured": false}
{"doc_id": 6333347, "title": "AIR-2: An Aurora/Ipl1-related Protein Kinase Associated with Chromosomes and Midbody Microtubules Is  Required for Polar Body Extrusion and Cytokinesis  in Caenorhabditis elegans Embryos ", "abstract": ["An emerging family of kinases related to the Drosophila Aurora and budding yeast Ipl1 proteins has been implicated in chromosome segregation and mitotic spindle formation in a number of organisms.", "Unlike other Aurora/Ipl1-related kinases, the Caenorhabditis elegans orthologue, AIR-2, is associated with meiotic and mitotic chromosomes.", "AIR-2 is initially localized to the chromosomes of the most mature prophase I\u2013arrested oocyte residing next to the spermatheca.", "This localization is dependent on the presence of sperm in the spermatheca.", "After fertilization, AIR-2 remains associated with chromosomes during each meiotic division.", "However, during both meiotic anaphases, AIR-2 is present between the separating chromosomes.", "AIR-2 also remains associated with both extruded polar bodies.", "In the embryo, AIR-2 is found on metaphase chromosomes, moves to midbody microtubules at anaphase, and then persists at the cytokinesis remnant.", "Disruption of AIR-2 expression by RNA- mediated interference produces entire broods of one-cell embryos that have executed multiple cell cycles in the complete absence of cytokinesis.", "The embryos accumulate large amounts of DNA and microtubule asters.", "Polar bodies are not extruded, but remain in the embryo where they continue to replicate.", "The cytokinesis defect appears to be late in the cell cycle because transient cleavage furrows initiate at the proper location, but regress before the division is complete.", "Additionally, staining with a marker of midbody microtubules revealed that at least some of the components of the midbody are not well localized in the absence of AIR-2 activity.", "Our results suggest that during each meiotic and mitotic division, AIR-2 may coordinate the congression of metaphase chromosomes with the subsequent events of polar body extrusion and cytokinesis."], "structured": false}
{"doc_id": 6334188, "title": "History of chronic comorbidity and risk of chemotherapy-induced febrile neutropenia in cancer patients not receiving G-CSF prophylaxis.", "abstract": ["BACKGROUND Chemotherapy-induced febrile neutropenia (FN) is a clinically important complication that affects patient outcome by delaying chemotherapy doses or reducing dose intensity.", "Risk of FN depends on chemotherapy- and patient-level factors.", "We sought to determine the effects of chronic comorbidities on risk of FN.   \n", "DESIGN We conducted a cohort study to examine the association between a variety of chronic comorbidities and risk of FN in patients diagnosed with six types of cancer (non-Hodgkin lymphoma and breast, colorectal, lung, ovary, and gastric cancer) from 2000 to 2009 who were treated with chemotherapy at Kaiser Permanente Southern California, a large managed care organization.", "We excluded those patients who received primary prophylactic granulocyte colony-stimulating factor.", "History of comorbidities and FN events were identified using electronic medical records.", "Cox models adjusting for propensity score, stratified by cancer type, were used to determine the association between comorbid conditions and FN.", "Models that additionally adjusted for cancer stage, baseline neutrophil count, chemotherapy regimen, and dose reduction were also evaluated.   \n", "RESULTS A total of 19 160 patients with mean age of 60 years were included; 963 (5.0%) developed FN in the first chemotherapy cycle.", "Chronic obstructive pulmonary disease [hazard ratio (HR) = 1.30 (1.07-1.57)], congestive heart failure [HR = 1.43 (1.00-1.98)], HIV infection [HR = 3.40 (1.90-5.63)], autoimmune disease [HR = 2.01 (1.10-3.33)], peptic ulcer disease [HR = 1.57 (1.05-2.26)], renal disease [HR = 1.60 (1.21-2.09)], and thyroid disorder [HR = 1.32 (1.06-1.64)] were all associated with a significantly increased FN risk.   \n", "CONCLUSIONS These results provide evidence that history of several chronic comorbidities increases risk of FN, which should be considered when managing patients during chemotherapy."], "structured": true}
{"doc_id": 6363093, "title": "Glioblastoma Subclasses Can Be Defined by Activity among Signal Transduction Pathways and Associated Genomic Alterations", "abstract": ["BACKGROUND Glioblastoma multiforme (GBM) is an umbrella designation that includes a heterogeneous group of primary brain tumors.", "Several classification strategies of GBM have been reported, some by clinical course and others by resemblance to cell types either in the adult or during development.", "From a practical and therapeutic standpoint, classifying GBMs by signal transduction pathway activation and by mutation in pathway member genes may be particularly valuable for the development of targeted therapies.   \n", "METHODOLOGY/PRINCIPAL FINDINGS We performed targeted proteomic analysis of 27 surgical glioma samples to identify patterns of coordinate activation among glioma-relevant signal transduction pathways, then compared these results with integrated analysis of genomic and expression data of 243 GBM samples from The Cancer Genome Atlas (TCGA).", "In the pattern of signaling, three subclasses of GBM emerge which appear to be associated with predominance of EGFR activation, PDGFR activation, or loss of the RAS regulator NF1.", "The EGFR signaling class has prominent Notch pathway activation measured by elevated expression of Notch ligands, cleaved Notch receptor, and downstream target Hes1.", "The PDGF class showed high levels of PDGFB ligand and phosphorylation of PDGFRbeta and NFKB.", "NF1-loss was associated with lower overall MAPK and PI3K activation and relative overexpression of the mesenchymal marker YKL40.", "These three signaling classes appear to correspond with distinct transcriptomal subclasses of primary GBM samples from TCGA for which copy number aberration and mutation of EGFR, PDGFRA, and NF1 are signature events.   \n", "CONCLUSIONS/SIGNIFICANCE Proteomic analysis of GBM samples revealed three patterns of expression and activation of proteins in glioma-relevant signaling pathways.", "These three classes are comprised of roughly equal numbers showing either EGFR activation associated with amplification and mutation of the receptor, PDGF-pathway activation that is primarily ligand-driven, or loss of NF1 expression.", "The associated signaling activities correlating with these sentinel alterations provide insight into glioma biology and therapeutic strategies."], "structured": true}
{"doc_id": 6368017, "title": "Loss of sex discrimination and male-male aggression in mice deficient for TRP2.", "abstract": ["The mouse vomeronasal organ (VNO) is thought to mediate social behaviors and neuroendocrine changes elicited by pheromonal cues.", "The molecular mechanisms underlying the sensory response to pheromones and the behavioral repertoire induced through the VNO are not fully characterized.", "Using the tools of mouse genetics and multielectrode recording, we demonstrate that the sensory activation of VNO neurons requires TRP2, a putative ion channel of the transient receptor potential family that is expressed exclusively in these neurons.", "Moreover, we show that male mice deficient in TRP2 expression fail to display male-male aggression, and they initiate sexual and courtship behaviors toward both males and females.", "Our study suggests that, in the mouse, sensory activation of the VNO is essential for sex discrimination of conspecifics and thus ensures gender-specific behavior."], "structured": false}
{"doc_id": 6372244, "title": "Antibiotic-induced shifts in the mouse gut microbiome and metabolome increase susceptibility to Clostridium difficile infection", "abstract": ["Antibiotics can have significant and long-lasting effects on the gastrointestinal tract microbiota, reducing colonization resistance against pathogens including Clostridium difficile.", "Here we show that antibiotic treatment induces substantial changes in the gut microbial community and in the metabolome of mice susceptible to C. difficile infection.", "Levels of secondary bile acids, glucose, free fatty acids and dipeptides decrease, whereas those of primary bile acids and sugar alcohols increase, reflecting the modified metabolic activity of the altered gut microbiome.", "In vitro and ex vivo analyses demonstrate that C. difficile can exploit specific metabolites that become more abundant in the mouse gut after antibiotics, including the primary bile acid taurocholate for germination, and carbon sources such as mannitol, fructose, sorbitol, raffinose and stachyose for growth.", "Our results indicate that antibiotic-mediated alteration of the gut microbiome converts the global metabolic profile to one that favours C. difficile germination and growth."], "structured": false}
{"doc_id": 6374918, "title": "Chemosensitization of acute myeloid leukemia (AML) following mobilization by the CXCR4 antagonist AMD3100.", "abstract": ["The CXCR4-SDF-1 axis plays a central role in the trafficking and retention of normal and malignant stem cells in the bone marrow (BM) microenvironment.", "Here, we used a mouse model of acute promyelocytic leukemia (APL) and a small molecule competitive antagonist of CXCR4, AMD3100, to examine the interaction of mouse APL cells with the BM microenvironment.", "APL cells from a murine cathepsin G-PML-RARalpha knockin mouse were genetically modified with firefly luciferase (APL(luc)) to allow tracking by bioluminescence imaging.", "Coculture of APL(luc) cells with M2-10B4 stromal cells protected the leukemia cells from chemotherapy-induced apoptosis in vitro.", "Upon injection into syngeneic recipients, APL(luc) cells rapidly migrated to the BM followed by egress to the spleen then to the peripheral blood with death due to leukostasis by day 15.", "Administration of AMD3100 to leukemic mice induced a 1.6-fold increase in total leukocytes and a 9-fold increase of circulating APL blast counts, which peak at 3 hours and return to baseline by 12 hours.", "Treatment of leukemic mice with chemotherapy plus AMD3100 resulted in decreased tumor burden and improved overall survival compared with mice treated with chemotherapy alone.", "These studies provide a proof-of-principle for directing therapy to the critical tethers that promote AML-niche interactions."], "structured": false}
{"doc_id": 6386930, "title": "Insights into G-quadruplex specific recognition by the DEAH-box helicase RHAU: Solution structure of a peptide-quadruplex complex.", "abstract": ["Four-stranded nucleic acid structures called G-quadruplexes have been associated with important cellular processes, which should require G-quadruplex-protein interaction.", "However, the structural basis for specific G-quadruplex recognition by proteins has not been understood.", "The DEAH (Asp-Glu-Ala-His) box RNA helicase associated with AU-rich element (RHAU) (also named DHX36 or G4R1) specifically binds to and resolves parallel-stranded G-quadruplexes.", "Here we identified an 18-amino acid G-quadruplex-binding domain of RHAU and determined the structure of this peptide bound to a parallel DNA G-quadruplex.", "Our structure explains how RHAU specifically recognizes parallel G-quadruplexes.", "The peptide covers a terminal guanine base tetrad (G-tetrad), and clamps the G-quadruplex using three-anchor-point electrostatic interactions between three positively charged amino acids and negatively charged phosphate groups.", "This binding mode is strikingly similar to that of most ligands selected for specific G-quadruplex targeting.", "Binding to an exposed G-tetrad represents a simple and efficient way to specifically target G-quadruplex structures."], "structured": false}
{"doc_id": 6387956, "title": "IQ and non-clinical psychotic symptoms in 12-year-olds: results  from the ALSPAC birth cohort", "abstract": ["BACKGROUND Non-clinical psychotic symptoms appear common in children, but it is possible that a proportion of reported symptoms result from misinterpretation.", "There is a well-established association between pre-morbid low IQ score and schizophrenia.", "Psychosis-like symptoms in children may also be a risk factor for psychotic disorder but their relationship with IQ is unclear.   ", "AIMS To investigate the prevalence, nature and frequency of psychosis-like symptoms in 12-year-old children and study their relationship with IQ.   \n", "METHOD Longitudinal study using the Avon Longitudinal Study of Parents and Children (ALSPAC) birth cohort.", "A total of 6455 children completed screening questions for 12 psychotic symptoms followed by a semi-structured clinical assessment.", "IQ was assessed at 8 years of age using the Wechsler Intelligence Scale for Children (3rd UK edition).   \n", "RESULTS The 6-month period prevalence for one or more symptoms was 13.7% (95% CI 12.8-14.5).", "After adjustment for confounding variables, there was a non-linear association between IQ score and psychosis-like symptoms, such that only those with below average IQ score had an increased risk of reporting such symptoms.   \n", "CONCLUSIONS Non-clinical psychotic symptoms occur in a significant proportion of 12-year-olds.", "Symptoms are associated with low IQ and also less strongly with a high IQ score.", "The pattern of association with IQ differs from that observed in schizophrenia."], "structured": true}
{"doc_id": 6397191, "title": "Endothelin-1 is induced by cytokines in human vascular smooth muscle cells: evidence for intracellular endothelin-converting enzyme.", "abstract": ["Endothelin-1 (ET-1) is the predominant endothelin isopeptide generated by the vascular wall and therefore appears to be the most important peptide involved in regulation of cardiovascular events.", "Many pathologic conditions are associated with elevations of ET-1 in the blood vessel wall.", "Because these conditions are often cytokine driven, we examined the effects of a mixture of cytokines on ET-1 production in human vascular smooth muscle cells (VSMCs) derived from internal mammary artery and saphenous vein (SV).", "Incubation of IMA and SV VSMCs with tumor necrosis factor-alpha (10 ng/ml) and interferon-gamma (1000 U/ml) in combination for up to 48 h markedly elevated the expression of mRNA for prepro-ET-1 and the release of ET-1 into the culture medium.", "This cytokine-stimulated release of ET-1 was inhibited by a series of dual endothelin-converting enzyme (ECE)/neutral endopeptidase inhibitors, phosphoramidon, CGS 26303, and CGS 26393, with an accompanying increase in big ET-1 release but with no effect on expression of mRNA for prepro-ET-1.", "These same compounds were 10 times more potent at inhibiting the conversion of exogenously applied big ET-1 to ET-1.", "ECE-1b/c mRNA is present in SV VSMCs, however no ECE-1a is present in these cells.", "Thus VSMCs most probably contain, like endothelial cells, an intracellular ECE responsible for the endogenous synthesis of ET-1.", "Under the influence of pro-inflammatory mediators the vascular smooth muscle can therefore become an important site of ET-1 production, as has already been established for the dilator mediators nitric oxide, prostaglandin I2, and prostaglandin E2."], "structured": false}
{"doc_id": 6401675, "title": "Transposable elements have rewired the core regulatory network of human embryonic stem cells", "abstract": ["Detection of new genomic control elements is critical in understanding transcriptional regulatory networks in their entirety.", "We studied the genome-wide binding locations of three key regulatory proteins (POU5F1, also known as OCT4; NANOG; and CTCF) in human and mouse embryonic stem cells.", "In contrast to CTCF, we found that the binding profiles of OCT4 and NANOG are markedly different, with only \u223c5% of the regions being homologously occupied.", "We show that transposable elements contributed up to 25% of the bound sites in humans and mice and have wired new genes into the core regulatory network of embryonic stem cells.", "These data indicate that species-specific transposable elements have substantially altered the transcriptional circuitry of pluripotent stem cells."], "structured": false}
{"doc_id": 6404801, "title": "Cytomegalovirus microRNAs Facilitate Persistent Virus Infection in Salivary Glands", "abstract": ["Micro (mi)RNAs are small non-coding RNAs that regulate the expression of their targets' messenger RNAs through both translational inhibition and regulation of target RNA stability.", "Recently, a number of viruses, particularly of the herpesvirus family, have been shown to express their own miRNAs to control both viral and cellular transcripts.", "Although some targets of viral miRNAs are known, their function in a physiologically relevant infection remains to be elucidated.", "As such, no in vivo phenotype of a viral miRNA knock-out mutant has been described so far.", "Here, we report on the first functional phenotype of a miRNA knock-out virus in vivo.", "During subacute infection of a mutant mouse cytomegalovirus lacking two viral miRNAs, virus production is selectively reduced in salivary glands, an organ essential for virus persistence and horizontal transmission.", "This phenotype depends on several parameters including viral load and mouse genetic background, and is abolished by combined but not single depletion of natural killer (NK) and CD4+ T cells.", "Together, our results point towards a miRNA-based immunoevasion mechanism important for long-term virus persistence."], "structured": false}
{"doc_id": 6407356, "title": "Coxibs and other nonsteroidal anti-inflammatory drugs in animal models of cancer chemoprevention.", "abstract": ["Coxibs, including celecoxib, and other nonsteroidal anti-inflammatory drugs (NSAID), including aspirin, are among the most promising cancer chemopreventive agents in development today.", "This article examines the data on the efficacy of these agents in animal model studies of cancer prevention carried out by the authors.", "The studies evaluated here are restricted to our rodent models of colon/intestinal, bladder, and nonmelanoma skin cancer, in which celecoxib and other NSAIDs were administered as either cancer preventive or therapeutic agents.", "These studies may shed light on several questions.", "Is celecoxib unique compared with other NSAIDs, and if so, what implications would this have for human use?", "Are standard NSAIDs (which inhibit both COX-1 and COX-2) as effective as celecoxib in animal studies?", "Is the efficacy of celecoxib in particular or NSAIDs in general due to their off-target effects or to their effects on COX-1 and COX-2?", "What is the likely efficacy of low-dose aspirin?", "Some questions raised by human trials and epidemiology are discussed and related to our observations in animal model studies.", "We also discuss the problem of cardiovascular (CV) events associated with coxibs and certain other NSAIDs and whether results in animal models are predictive of efficacy in humans.", "On the basis of epidemiologic studies and its CV profile, aspirin seems to be the most promising NSAID for preventing human colorectal, bladder, and skin cancer, although the animal data for aspirin are less clear.", "A comprehensive understanding of the results of coxibs and other NSAIDs in animal studies may help inform and shape human trials of these commonly employed, relatively inexpensive, and highly effective compounds."], "structured": false}
{"doc_id": 6415816, "title": "The porphyrias: advances in diagnosis and treatment.", "abstract": ["The inborn errors of heme biosynthesis, the porphyrias, are 8 genetically distinct metabolic disorders that can be classified as \"acute hepatic,\" \"hepatic cutaneous,\" and \"erythropoietic cutaneous\" diseases.", "Recent advances in understanding their pathogenesis and molecular genetic heterogeneity have led to improved diagnosis and treatment.", "These advances include DNA-based diagnoses for all the porphyrias, new understanding of the pathogenesis of the acute hepatic porphyrias, identification of the iron overload-induced inhibitor of hepatic uroporphyrin decarboxylase activity that causes the most common porphyria, porphyria cutanea tarda, the identification of an X-linked form of erythropoietic protoporphyria due to gain-of-function mutations in erythroid-specific 5-aminolevulinate synthase (ALAS2), and new and experimental treatments for the erythropoietic porphyrias.", "Knowledge of these advances is relevant for hematologists because they administer the hematin infusions to treat the acute attacks in patients with the acute hepatic porphyrias, perform the chronic phlebotomies to reduce the iron overload and clear the dermatologic lesions in porphyria cutanea tarda, and diagnose and treat the erythropoietic porphyrias, including chronic erythrocyte transfusions, bone marrow or hematopoietic stem cell transplants, and experimental pharmacologic chaperone and stem cell gene therapies for congenital erythropoietic protoporphyria.", "These developments are reviewed to update hematologists on the latest advances in these diverse disorders."], "structured": false}
{"doc_id": 6417632, "title": "Neutrophilic infiltration within the airway smooth muscle in patients with COPD.", "abstract": ["BACKGROUND COPD is an inflammatory disorder characterised by chronic airflow limitation, but the extent to which airway inflammation is related to functional abnormalities is still uncertain.", "The interaction between inflammatory cells and airway smooth muscle may have a crucial role.   \n", "METHODS To investigate the microlocalisation of inflammatory cells within the airway smooth muscle in COPD, surgical specimens obtained from 26 subjects undergoing thoracotomy (eight smokers with COPD, 10 smokers with normal lung function, and eight non-smoking controls) were examined.", "Immunohistochemical analysis was used to quantify the number of neutrophils, macrophages, mast cells, CD4+ and CD8+ cells localised within the smooth muscle of peripheral airways.   \n", "RESULTS Smokers with COPD had an increased number of neutrophils and CD8+ cells in the airway smooth muscle compared with non-smokers.", "Smokers with normal lung function also had a neutrophilic infiltration in the airway smooth muscle, but to a lesser extent.", "When all the subjects were analysed as one group, neutrophilic infiltration was inversely related to forced expiratory volume in 1 second (% predicted).   \n", "CONCLUSIONS Microlocalisation of neutrophils and CD8+ cells in the airway smooth muscle in smokers with COPD suggests a possible role for these cells in the pathogenesis of smoking induced airflow limitation."], "structured": true}
{"doc_id": 6421734, "title": "Characteristics of service users and provider organisations associated with experience of out of hours general practitioner care in England: population based cross sectional postal questionnaire survey.", "abstract": ["OBJECTIVE To investigate the experience of users of out of hours general practitioner services in England, UK.   \n", "DESIGN Population based cross sectional postal questionnaire survey.   \n", "SETTING General Practice Patient Survey 2012-13.   \n", "MAIN OUTCOME MEASURES Potential associations between sociodemographic factors (including ethnicity and ability to take time away from work during working hours to attend a healthcare consultation) and provider organisation type (not for profit, NHS, or commercial) and service users' experience of out of hours care (timeliness, confidence and trust in the out of hours clinician, and overall experience of the service), rated on a scale of 0-100.", "Which sociodemographic/provider characteristics were associated with service users' experience, the extent to which any observed differences could be because of clustering of service users of a particular sociodemographic group within poorer scoring providers, and the extent to which observed differences in experience varied across types of provider.   \n", "RESULTS The overall response rate was 35%; 971,232/2,750,000 patients returned surveys.", "Data from 902,170 individual service users were mapped through their registered practice to one of 86 providers of out of hours GP care with known organisation type.", "Commercial providers of out of hours GP care were associated with poorer reports of overall experience of care, with a mean difference of -3.13 (95% confidence interval -4.96 to -1.30) compared with not for profit providers.", "Asian service users reported lower scores for all three experience outcomes than white service users (mean difference for overall experience of care -3.62, -4.36 to -2.89), as did service users who were unable to take time away from work compared with service users who did not work (mean difference for overall experience of care -4.73, -5.29 to -4.17).   \n", "CONCLUSIONS Commercial providers of out of hours GP care were associated with poorer experience of care.", "Targeted interventions aimed at improving experience for patients from ethnic minorities and patients who are unable to take time away from work might be warranted."], "structured": true}
{"doc_id": 6421792, "title": "Activating mutations in the NT5C2 nucleotidase gene drive chemotherapy resistance in relapsed ALL", "abstract": ["Acute lymphoblastic leukemia (ALL) is an aggressive hematological tumor resulting from the malignant transformation of lymphoid progenitors.", "Despite intensive chemotherapy, 20% of pediatric patients and over 50% of adult patients with ALL do not achieve a complete remission or relapse after intensified chemotherapy, making disease relapse and resistance to therapy the most substantial challenge in the treatment of this disease.", "Using whole-exome sequencing, we identify mutations in the cytosolic 5'-nucleotidase II gene (NT5C2), which encodes a 5'-nucleotidase enzyme that is responsible for the inactivation of nucleoside-analog chemotherapy drugs, in 20/103 (19%) relapse T cell ALLs and 1/35 (3%) relapse B-precursor ALLs.", "NT5C2 mutant proteins show increased nucleotidase activity in vitro and conferred resistance to chemotherapy with 6-mercaptopurine and 6-thioguanine when expressed in ALL lymphoblasts.", "These results support a prominent role for activating mutations in NT5C2 and increased nucleoside-analog metabolism in disease progression and chemotherapy resistance in ALL."], "structured": false}
{"doc_id": 6422576, "title": "Ubiquitin-dependent protein degradation.", "abstract": ["A growing number of cellular regulatory mechanisms are being linked to protein modification by the polypeptide ubiquitin.", "These include key transitions in the cell cycle, class I antigen processing, signal transduction pathways, and receptor-mediated endocytosis.", "In most, but not all, of these examples, ubiquitination of a protein leads to its degradation by the 26S proteasome.", "Following attachment of ubiquitin to a substrate and binding of the ubiquitinated protein to the proteasome, the bound substrate must be unfolded (and eventually deubiquitinated) and translocated through a narrow set of channels that leads to the proteasome interior, where the polypeptide is cleaved into short peptides.", "Protein ubiquitination and deubiquitination are both mediated by large enzyme families, and the proteasome itself comprises a family of related but functionally distinct particles.", "This diversity underlies both the high substrate specificity of the ubiquitin system and the variety of regulatory mechanisms that it serves."], "structured": false}
{"doc_id": 6426919, "title": "A novel molecular mechanism of dual resistance to nucleoside and nonnucleoside reverse transcriptase inhibitors.", "abstract": ["Recently, mutations in the connection subdomain (CN) and RNase H domain of HIV-1 reverse transcriptase (RT) were observed to exhibit dual resistance to nucleoside and nonnucleoside reverse transcriptase inhibitors (NRTIs and NNRTIs).", "To elucidate the mechanism by which CN and RH mutations confer resistance to NNRTIs, we hypothesized that these mutations reduce RNase H cleavage and provide more time for the NNRTI to dissociate from the RT, resulting in the resumption of DNA synthesis and enhanced NNRTI resistance.", "We observed that the effect of the reduction in RNase H cleavage on NNRTI resistance is dependent upon the affinity of each NNRTI to the RT and further influenced by the presence of NNRTI-binding pocket (BP) mutants.", "D549N, Q475A, and Y501A mutants, which reduce RNase H cleavage, enhance resistance to nevirapine (NVP) and delavirdine (DLV), but not to efavirenz (EFV) and etravirine (ETR), consistent with their increase in affinity for RT.", "Combining the D549N mutant with NNRTI BP mutants further increases NNRTI resistance from 3- to 30-fold, supporting the role of NNRTI-RT affinity in our NNRTI resistance model.", "We also demonstrated that CNs from treatment-experienced patients, previously reported to enhance NRTI resistance, also reduce RNase H cleavage and enhance NNRTI resistance in the context of the patient RT pol domain or a wild-type pol domain.", "Together, these results confirm key predictions of our NNRTI resistance model and provide support for a unifying mechanism by which CN and RH mutations can exhibit dual NRTI and NNRTI resistance."], "structured": false}
{"doc_id": 6431384, "title": "Location Coding by Opponent Neural Populations in the Auditory Cortex", "abstract": ["Although the auditory cortex plays a necessary role in sound localization, physiological investigations in the cortex reveal inhomogeneous sampling of auditory space that is difficult to reconcile with localization behavior under the assumption of local spatial coding.", "Most neurons respond maximally to sounds located far to the left or right side, with few neurons tuned to the frontal midline.", "Paradoxically, psychophysical studies show optimal spatial acuity across the frontal midline.", "In this paper, we revisit the problem of inhomogeneous spatial sampling in three fields of cat auditory cortex.", "In each field, we confirm that neural responses tend to be greatest for lateral positions, but show the greatest modulation for near-midline source locations.", "Moreover, identification of source locations based on cortical responses shows sharp discrimination of left from right but relatively inaccurate discrimination of locations within each half of space.", "Motivated by these findings, we explore an opponent-process theory in which sound-source locations are represented by differences in the activity of two broadly tuned channels formed by contra- and ipsilaterally preferring neurons.", "Finally, we demonstrate a simple model, based on spike-count differences across cortical populations, that provides bias-free, level-invariant localization\u2014and thus also a solution to the \u201cbinding problem\u201d of associating spatial information with other nonspatial attributes of sounds."], "structured": false}
{"doc_id": 6441369, "title": "MLL1 Inhibition Reprograms Epiblast Stem Cells to Naive Pluripotency.", "abstract": ["The interconversion between naive and primed pluripotent states is accompanied by drastic epigenetic rearrangements.", "However, it is unclear whether intrinsic epigenetic events can drive reprogramming to naive pluripotency or if distinct chromatin states are instead simply a reflection of discrete pluripotent states.", "Here, we show that blocking histone H3K4 methyltransferase MLL1 activity with the small-molecule inhibitor MM-401 reprograms mouse epiblast stem cells (EpiSCs) to naive pluripotency.", "This reversion is highly efficient and synchronized, with more than 50% of treated EpiSCs exhibiting features of naive embryonic stem cells (ESCs) within 3 days.", "Reverted ESCs reactivate the silenced X chromosome and contribute to embryos following blastocyst injection, generating germline-competent chimeras.", "Importantly, blocking MLL1 leads to global redistribution of H3K4me1 at enhancers and represses lineage determinant factors and EpiSC markers, which indirectly regulate ESC transcription circuitry.", "These findings show that discrete perturbation of H3K4 methylation is sufficient to drive reprogramming to naive pluripotency."], "structured": false}
{"doc_id": 6446747, "title": "MafB/c-Maf deficiency enables self-renewal of differentiated functional macrophages.", "abstract": ["In metazoan organisms, terminal differentiation is generally tightly linked to cell cycle exit, whereas the undifferentiated state of pluripotent stem cells is associated with unlimited self-renewal.", "Here, we report that combined deficiency for the transcription factors MafB and c-Maf enables extended expansion of mature monocytes and macrophages in culture without loss of differentiated phenotype and function.", "Upon transplantation, the expanded cells are nontumorigenic and contribute to functional macrophage populations in vivo.", "Small hairpin RNA inactivation shows that continuous proliferation of MafB/c-Maf deficient macrophages requires concomitant up-regulation of two pluripotent stem cell-inducing factors, KLF4 and c-Myc.", "Our results indicate that MafB/c-MafB deficiency renders self-renewal compatible with terminal differentiation.", "It thus appears possible to amplify functional differentiated cells without malignant transformation or stem cell intermediates."], "structured": false}
{"doc_id": 6454371, "title": "Macropinocytosis: an endocytic pathway for internalising large gulps.", "abstract": ["Macropinocytosis is a regulated form of endocytosis that mediates the non-selective uptake of solute molecules, nutrients and antigens.", "It is an actin-dependent process initiated from surface membrane ruffles that give rise to large endocytic vacuoles called macropinosomes.", "Macropinocytosis is important in a range of physiological processes; it is highly active in macrophages and dendritic cells where it is a major pathway for the capture of antigens, it is relevant to cell migration and tumour metastasis and it represents a portal of cell entry exploited by a range of pathogens.", "The molecular basis for the formation and maturation of macropinosomes has only recently begun to be defined.", "Here, we review the general characteristics of macropinocytosis, describe some of the regulators of this pathway, which have been identified to date and highlight strategies to explore the relevance of this endocytosis pathway in vivo."], "structured": false}
{"doc_id": 6455142, "title": "KDM5B regulates embryonic stem cell self-renewal and represses cryptic intragenic transcription.", "abstract": ["Although regulation of histone methylation is believed to contribute to embryonic stem cell (ESC) self-renewal, the mechanisms remain obscure.", "We show here that the histone H3 trimethyl lysine 4 (H3K4me3) demethylase, KDM5B, is a downstream Nanog target and critical for ESC self-renewal.", "Although KDM5B is believed to function as a promoter-bound repressor, we find that it paradoxically functions as an activator of a gene network associated with self-renewal.", "ChIP-Seq reveals that KDM5B is predominantly targeted to intragenic regions and that it is recruited to H3K36me3 via an interaction with the chromodomain protein MRG15.", "Depletion of KDM5B or MRG15 increases intragenic H3K4me3, increases cryptic intragenic transcription, and inhibits transcriptional elongation of KDM5B target genes.", "We propose that KDM5B activates self-renewal-associated gene expression by repressing cryptic initiation and maintaining an H3K4me3 gradient important for productive transcriptional elongation."], "structured": false}
{"doc_id": 6472746, "title": "Increased CDK1 activity determines the timing of kinetochore-microtubule attachments in meiosis I", "abstract": ["Chromosome segregation during cell division depends on stable attachment of kinetochores to spindle microtubules.", "Mitotic spindle formation and kinetochore-microtubule (K-MT) capture typically occur within minutes of nuclear envelope breakdown.", "In contrast, during meiosis I in mouse oocytes, formation of the acentrosomal bipolar spindle takes 3-4 h, and stabilization of K-MT attachments is delayed an additional 3-4 h. The mechanism responsible for this delay, which likely prevents stabilization of erroneous attachments during spindle formation, is unknown.", "Here we show that during meiosis I, attachments are regulated by CDK1 activity, which gradually increases through prometaphase and metaphase I. Partial reduction of CDK1 activity delayed formation of stable attachments, whereas a premature increase in CDK1 activity led to precocious formation of stable attachments and eventually lagging chromosomes at anaphase I. These results indicate that the slow increase in CDK1 activity in meiosis I acts as a timing mechanism to allow stable K-MT attachments only after bipolar spindle formation, thus preventing attachment errors."], "structured": false}
{"doc_id": 6477536, "title": "Discontinuation and non-publication of surgical randomised controlled trials: observational study", "abstract": ["OBJECTIVE To determine the rate of early discontinuation and non-publication of randomised controlled trials involving patients undergoing surgery.   \n", "DESIGN Cross sectional observational study of registered and published trials.   \n", "SETTING Randomised controlled trials of interventions in patients undergoing a surgical procedure.   \n", "DATA SOURCES The ClinicalTrials.gov database was searched for interventional trials registered between January 2008 and December 2009 using the keyword \"surgery\".", "Recruitment status was extracted from the ClinicalTrials.gov database.", "A systematic search for studies published in peer reviewed journals was performed; if they were not found, results posted on the ClinicalTrials.gov results database were sought.", "Email queries were sent to trial investigators of discontinued and unpublished completed trials if no reason for the respective status was disclosed.   \n", "MAIN OUTCOME MEASURES Trial discontinuation before completion and non-publication after completion.", "Logistic regression was used to determine the effect of funding source on publication status, with adjustment for intervention type and trial size.   \n", "RESULTS Of 818 registered trials found using the keyword \"surgery\", 395 met the inclusion criteria.", "Of these, 21% (81/395) were discontinued early, most commonly owing to poor recruitment (44%, 36/81).", "The remaining 314 (79%) trials proceeded to completion, with a publication rate of 66% (208/314) at a median time of 4.9 (interquartile range 4.0-6.0) years from study completion to publication search.", "A further 6% (20/314) of studies presented results on ClinicalTrials.gov without a corresponding peer reviewed publication.", "Industry funding did not affect the rate of discontinuation (adjusted odds ratio 0.91, 95% confidence interval 0.54 to 1.55) but was associated with a lower odds of publication for completed trials (0.43, 0.26 to 0.72).", "Investigators' email addresses for trials with an uncertain fate were identified for 71.4% (10/14) of discontinued trials and 83% (101/122) of unpublished studies.", "Only 43% (6/14) and 20% (25/122) replies were received.", "Email responses for completed trials indicated 11 trials in press, five published studies (four in non-indexed peer reviewed journals), and nine trials remaining unpublished.   \n", "CONCLUSIONS One in five surgical randomised controlled trials are discontinued early, one in three completed trials remain unpublished, and investigators of unpublished studies are frequently not contactable.", "This represents a waste of research resources and raises ethical concerns regarding hidden clinical data and futile participation by patients with its attendant risks.", "To promote future efficiency and transparency, changes are proposed to research governance frameworks to overcome these concerns."], "structured": true}
{"doc_id": 6477740, "title": "Efficient Generation of Fully Reprogrammed Human iPS Cells via Polycistronic Retroviral Vector and a New Cocktail of Chemical Compounds", "abstract": ["Direct reprogramming of human somatic cells into induced pluripotent stem (iPS) cells by defined transcription factors (TFs) provides great potential for regenerative medicine and biomedical research.", "This procedure has many challenges, including low reprogramming efficiency, many partially reprogrammed colonies, somatic coding mutations in the genome, etc.", "Here, we describe a simple approach for generating fully reprogrammed human iPS cells by using a single polycistronic retroviral vector expressing four human TFs in a single open reading frame (ORF), combined with a cocktail containing three small molecules (Sodium butyrate, SB431542, and PD0325901).", "Our results demonstrate that human iPS cells generated by this approach express human ES cells markers and exhibit pluripotency demonstrated by their abilities to differentiate into the three germ layers in vitro and in vivo.", "Notably, this approach not only provides a much faster reprogramming process but also significantly diminishes partially reprogrammed iPS cell colonies, thus facilitating efficient isolation of desired fully reprogrammed iPS cell colonies."], "structured": false}
{"doc_id": 6490571, "title": "Prevalence, severity, and unmet need for treatment of mental disorders in the World Health Organization World Mental Health Surveys.", "abstract": ["CONTEXT Little is known about the extent or severity of untreated mental disorders, especially in less-developed countries.   \n", "OBJECTIVE To estimate prevalence, severity, and treatment of Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition (DSM-IV) mental disorders in 14 countries (6 less developed, 8 developed) in the World Health Organization (WHO) World Mental Health (WMH) Survey Initiative.   \n", "DESIGN, SETTING, AND PARTICIPANTS Face-to-face household surveys of 60 463 community adults conducted from 2001-2003 in 14 countries in the Americas, Europe, the Middle East, Africa, and Asia.   \n", "MAIN OUTCOME MEASURES The DSM-IV disorders, severity, and treatment were assessed with the WMH version of the WHO Composite International Diagnostic Interview (WMH-CIDI), a fully structured, lay-administered psychiatric diagnostic interview.   \n", "RESULTS The prevalence of having any WMH-CIDI/DSM-IV disorder in the prior year varied widely, from 4.3% in Shanghai to 26.4% in the United States, with an interquartile range (IQR) of 9.1%-16.9%.", "Between 33.1% (Colombia) and 80.9% (Nigeria) of 12-month cases were mild (IQR, 40.2%-53.3%).", "Serious disorders were associated with substantial role disability.", "Although disorder severity was correlated with probability of treatment in almost all countries, 35.5% to 50.3% of serious cases in developed countries and 76.3% to 85.4% in less-developed countries received no treatment in the 12 months before the interview.", "Due to the high prevalence of mild and subthreshold cases, the number of those who received treatment far exceeds the number of untreated serious cases in every country.   \n", "CONCLUSIONS Reallocation of treatment resources could substantially decrease the problem of unmet need for treatment of mental disorders among serious cases.", "Structural barriers exist to this reallocation.", "Careful consideration needs to be given to the value of treating some mild cases, especially those at risk for progressing to more serious disorders."], "structured": true}
{"doc_id": 6491532, "title": "Successful '9-month Bangladesh regimen' for multidrug-resistant tuberculosis among over 500 consecutive patients.", "abstract": ["SETTING Tuberculosis (TB) program, Damien Foundation Projects, Bangladesh.   \n", "OBJECTIVE To summarize the outcome and its determinants of the first treatment for multidrug-resistant TB using a standardized regimen consisting of a minimum 9 months.   \n", "DESIGN This was a prospective, observational study of a gatifloxacin (GFX) based directly observed regimen, mainly with initial hospitalization.", "The 4-month intensive phase was extended until sputum smear conversion.", "Patients were monitored using culture for up to 2 years after treatment completion.   \n", "RESULTS Of the 515 patients who met the study inclusion criteria and were successively enrolled from 2005 to 2011, 84.4% had a bacteriologically favorable outcome.", "Due to extensive disease with delayed sputum conversion, only half of the patients completed treatment within 9 months; however, 95% were able to complete treatment within 12 months.", "Eleven patients failed or relapsed, and 93.1% of the 435 patients who were successfully treated completed at least 12 months post-treatment follow-up.", "The strongest risk factor for a bacteriologically unfavorable outcome was high-level fluoroquinolone (FQ) resistance, particularly when compounded by initial pyrazinamide (PZA) resistance.", "Low-level FQ resistance had no unfavorable effect on treatment outcome.", "Amplification of drug resistance occurred only once, in a patient strain that was initially only susceptible to kanamycin and clofazimine.   \n", "CONCLUSION The excellent outcome of the Bangladesh regimen was largely maintained.", "Bacteriological treatment failures and relapses were rare, except among patients with high-level GFX resistance, notably in the presence of PZA resistance."], "structured": true}
{"doc_id": 6492658, "title": "A Null Mutation in Inositol Polyphosphate 4-Phosphatase Type I Causes Selective Neuronal Loss in Weeble Mutant Mice", "abstract": ["Weeble mutant mice have severe locomotor instability and significant neuronal loss in the cerebellum and in the hippocampal CA1 field.", "Genetic mapping was used to localize the mutation to the gene encoding inositol polyphosphate 4-phosphatase type I (Inpp4a), where a single nucleotide deletion results in a likely null allele.", "The substrates of INPP4A are intermediates in a pathway affecting intracellular Ca(2+) release but are also involved in cell cycle regulation through binding the Akt protooncogene; dysfunction in either may account for the neuronal loss of weeble mice.", "Although other mutations in phosphoinositide enzymes are associated with synaptic defects without neuronal loss, weeble shows that Inpp4a is critical for the survival of a subset of neurons during postnatal development in mice."], "structured": false}
{"doc_id": 6493422, "title": "The myeloid transcription factor KLF2 regulates the host response to polymicrobial infection and endotoxic shock.", "abstract": ["Precise control of myeloid cell activation is required for optimal host defense.", "However, this activation process must be under exquisite control to prevent uncontrolled inflammation.", "Herein, we identify the Kruppel-like transcription factor 2 (KLF2) as a potent regulator of myeloid cell activation in vivo.", "Exposure of myeloid cells to hypoxia and/or bacterial products reduced KLF2 expression while inducing hypoxia inducible factor-1\u03b1 (HIF-1\u03b1), findings that were recapitulated in human septic patients.", "Myeloid KLF2 was found to be a potent inhibitor of nuclear factor-kappaB (NF-\u03baB)-dependent HIF-1\u03b1 transcription and, consequently, a critical determinant of outcome in models of polymicrobial infection and endotoxemia.", "Collectively, these observations identify KLF2 as a tonic repressor of myeloid cell activation in vivo and an essential regulator of the innate immune system."], "structured": false}
{"doc_id": 6501747, "title": "PQBP1 Is a Proximal Sensor of the cGAS-Dependent Innate Response to HIV-1", "abstract": ["Dendritic cells (DCs) play a critical role in the immune response to viral infection through the facilitation of cell-intrinsic antiviral activity and the activation of adaptive immunity.", "HIV-1 infection of DCs triggers an IRF3-dependent innate immune response, which requires the activity of cyclic GAMP synthase (cGAS).", "We report the results of a targeted RNAi screen utilizing primary human monocyte-derived DCs (MDDCs) to identify immune regulators that directly interface with HIV-1-encoded features to initiate this innate response.", "Polyglutamine binding protein 1 (PQBP1) emerged as a strong candidate through this analysis.", "We found that PQBP1 directly binds to reverse-transcribed HIV-1 DNA and interacts with cGAS to initiate an IRF3-dependent innate response.", "MDDCs derived from Renpenning syndrome patients, who harbor mutations in the PQBP1 locus, possess a severely attenuated innate immune response to HIV-1 challenge, underscoring the role of PQBP1 as a proximal innate sensor of a HIV-1 infection."], "structured": false}
{"doc_id": 6503185, "title": "Malaria biology and disease pathogenesis: insights for new treatments", "abstract": ["Plasmodium falciparum malaria, an infectious disease caused by a parasitic protozoan, claims the lives of nearly a million children each year in Africa alone and is a top public health concern.", "Evidence is accumulating that resistance to artemisinin derivatives, the frontline therapy for the asexual blood stage of the infection, is developing in southeast Asia.", "Renewed initiatives to eliminate malaria will benefit from an expanded repertoire of antimalarials, including new drugs that kill circulating P. falciparum gametocytes, thereby preventing transmission.", "Our current understanding of the biology of asexual blood-stage parasites and gametocytes and the ability to culture them in vitro lends optimism that high-throughput screenings of large chemical libraries will produce a new generation of antimalarial drugs.", "There is also a need for new therapies to reduce the high mortality of severe malaria.", "An understanding of the pathophysiology of severe disease may identify rational targets for drugs that improve survival."], "structured": false}
{"doc_id": 6503534, "title": "Mutations among Italian mucopolysaccharidosis type I patients", "abstract": ["A group of 27 Italian patients was screened for \u03b1-L-iduronidase mucopolysaccharidosis type I mutations.", "Mutations were found in 18 patients, with 28 alleles identified.", "The two most common mutations in northern Europeans (W402X and Q70X) accounted for 11% and 13% of the alleles, respectively.", "The R89Q mutation, uncommon in Europeans, was found only in one patient, accounting for 1 of 54 alleles (1.9%).", "The other mutations, P533R, A327P and G51D, accounted for 11%, 5.6% and 9.3% of the total alleles, respectively.", "Interestingly, the high frequency of the P533R mutation seems to be confined to Sicily and is higher than the 3% reported in a British/Australian study."], "structured": false}
{"doc_id": 6504953, "title": "Radiation-Related Cancer Risks at Low Doses among Atomic Bomb Survivors", "abstract": ["Abstract Pierce, D. A. and Preston, D. L. Radiation-Related Cancer Risks at Low Doses among Atomic Bomb Survivors.", "To clarify the information in the Radiation Effects Research Foundation data regarding cancer risks of low radiation doses, we focus on survivors with doses less than 0.5 Sv.", "For reasons indicated, we also restrict attention mainly to survivors within 3,000 m of the hypocenter of the bombs.", "Analysis is of solid cancer incidence from 1958\u20131994, involving 7,000 cancer cases among 50,000 survivors in that dose and distance range.", "The results provide useful risk estimates for doses as low as 0.05\u20130.1 Sv, which are not overestimated by linear risk estimates computed from the wider dose ranges 0\u20132 Sv or 0\u20134 Sv.", "There is a statistically significant risk in the range 0\u20130.1 Sv, and an upper confidence limit on any possible threshold is computed as 0.06 Sv.", "It is indicated that modification of the neutron dose estimates currently under consideration would not markedly change the conclusions."], "structured": false}
{"doc_id": 6517267, "title": "Barriers and facilitators to implement shared decision making in multidisciplinary sciatica care: a qualitative study", "abstract": ["BACKGROUND The Dutch multidisciplinary sciatica guideline recommends that the team of professionals involved in sciatica care and the patient together decide on surgical or prolonged conservative treatment (shared decision making [SDM]).", "Despite this recommendation, SDM is not yet integrated in sciatica care.", "Existing literature concerning barriers and facilitators to SDM implementation mainly focuses on one discipline only, whereas multidisciplinary care may involve other barriers and facilitators, or make these more complex for both professionals and patients.", "Therefore, this qualitative study aims to identify barriers and facilitators perceived by patients and professionals for SDM implementation in multidisciplinary sciatica care.   \n", "METHODS We conducted 40 semi-structured interviews with professionals involved in sciatica care (general practitioners, physical therapists, neurologists, neurosurgeons, and orthopedic surgeons) and three focus groups among patients (six to eight per group).", "The interviews and focus groups were audiotaped and transcribed in full.", "Reported barriers and facilitators were classified according to the framework of Grol and Wensing.", "The software package Atlas.ti 7.0 was used for analysis.   \n", "RESULTS Professionals reported 53 barriers and 5 facilitators, and patients 35 barriers and 18 facilitators for SDM in sciatica care.", "Professionals perceived most barriers at the level of the organizational context, and facilitators at the level of the individual professional.", "Patients reported most barriers and facilitators at the level of the individual professional.", "Several barriers and facilitators correspond with barriers and facilitators found in the literature (e.g., lack of time, motivation) but also new barriers and facilitators were identified.", "Many of these new barriers mentioned by both professionals and patients were related to the multidisciplinary setting, such as lack of visibility, lack of trust in expertise of other disciplines, and lack of communication between disciplines.   \n", "CONCLUSIONS This study identified barriers and facilitators for SDM in the multidisciplinary sciatica setting, by both professionals and patients.", "It is clear that more barriers than facilitators are perceived for implementation of SDM in sciatica care.", "Newly identified barriers and facilitators are related to the multidisciplinary care setting.", "Therefore, an effective implementation strategy of SDM in a multidisciplinary setting such as in sciatica care should focus on these barriers and facilitators."], "structured": true}
{"doc_id": 6517763, "title": "Molecular characterization of long-term survivors of glioblastoma using genome- and transcriptome-wide profiling.", "abstract": ["The prognosis of glioblastoma, the most malignant type of glioma, is still poor, with only a minority of patients showing long-term survival of more than three years after diagnosis.", "To elucidate the molecular aberrations in glioblastomas of long-term survivors, we performed genome- and/or transcriptome-wide molecular profiling of glioblastoma samples from 94 patients, including 28 long-term survivors with >36 months overall survival (OS), 20 short-term survivors with <12 months OS and 46 patients with intermediate OS.", "Integrative bioinformatic analyses were used to characterize molecular aberrations in the distinct survival groups considering established molecular markers such as isocitrate dehydrogenase 1 or 2 (IDH1/2) mutations, and O(6) -methylguanine DNA methyltransferase (MGMT) promoter methylation.", "Patients with long-term survival were younger and more often had IDH1/2-mutant and MGMT-methylated tumors.", "Gene expression profiling revealed over-representation of a distinct (proneural-like) expression signature in long-term survivors that was linked to IDH1/2 mutation.", "However, IDH1/2-wildtype glioblastomas from long-term survivors did not show distinct gene expression profiles and included proneural, classical and mesenchymal glioblastoma subtypes.", "Genomic imbalances also differed between IDH1/2-mutant and IDH1/2-wildtype tumors, but not between survival groups of IDH1/2-wildtype patients.", "Thus, our data support an important role for MGMT promoter methylation and IDH1/2 mutation in glioblastoma long-term survival and corroborate the association of IDH1/2 mutation with distinct genomic and transcriptional profiles.", "Importantly, however, IDH1/2-wildtype glioblastomas in our cohort of long-term survivors lacked distinctive DNA copy number changes and gene expression signatures, indicating that other factors might have been responsible for long survival in this particular subgroup of patients."], "structured": false}
{"doc_id": 6525844, "title": "Impact of aortic stiffness on survival in end-stage renal disease.", "abstract": ["BACKGROUND Damage to large arteries is a major factor in the high cardiovascular morbidity and mortality of patients with end-stage renal disease (ESRD).", "Increased arterial stiffness and intima-media thickness, together with increased pulse pressure, are the principal arterial alterations.", "Whether increased aortic pulse-wave velocity (PWV), a classic marker of increased arterial stiffness, may predict all-cause and/or cardiovascular mortality has never been investigated.   \n", "METHODS AND RESULTS A cohort of 241 patients with ESRD undergoing hemodialysis was studied between April 1987 and April 1998.", "The mean duration of follow-up was 72+/-41 months (mean+/-SD).", "Mean age at entry was 51.5+/-16.3 years.", "Seventy-three deaths occurred, including 48 cardiovascular and 25 noncardiovascular fatal events.", "At entry, together with standard clinical and biochemical analyses, patients underwent echocardiography and aortic PWV measured by Doppler ultrasonography.", "On the basis of Cox analyses, 2 factors emerged as predictors of all-cause and cardiovascular mortality: age and aortic PWV.", "Hemoglobin and low diastolic pressure interfered to a smaller extent.", "After adjustment for all the confounding factors, an OR for PWV >12.", "0 versus <9.4 m/s was 5.4 (95% CI, 2.4 to 11.9) for all-cause mortality and 5.9 (95% CI, 2.3 to 15.5) for cardiovascular mortality.", "For each PWV increase of 1 m/s in our study population, all-cause mortality-adjusted OR was 1.39 (95% CI, 1.19 to 1.62).   \n", "CONCLUSIONS These results provide the first direct evidence that in patients with ESRD, increased aortic stiffness determined by measurement of aortic PWV is a strong independent predictor of all-cause and mainly cardiovascular mortality."], "structured": true}
{"doc_id": 6532806, "title": "An integrated database of genes responsive to the Myc oncogenic transcription factor: identification of direct genomic targets", "abstract": ["We report a database of genes responsive to the Myc oncogenic transcription factor.", "The database Myc Target Gene prioritizes candidate target genes according to experimental evidence and clusters responsive genes into functional groups.", "We coupled the prioritization of target genes with phylogenetic sequence comparisons to predict c-Myc target binding sites, which are in turn validated by chromatin immunoprecipitation assays.", "This database is essential for the understanding of the genetic regulatory networks underlying the genesis of cancers."], "structured": false}
{"doc_id": 6535392, "title": "siRNA specificity searching incorporating mismatch tolerance data.", "abstract": ["UNLABELLED Artificially synthesized short interfering RNAs (siRNAs) are widely used in functional genomics to knock down specific target genes.", "One ongoing challenge is to guarantee that the siRNA does not elicit off-target effects.", "Initial reports suggested that siRNAs were highly sequence-specific; however, subsequent data indicates that this is not necessarily the case.", "It is still uncertain what level of similarity and other rules are required for an off-target effect to be observed, and scoring schemes have not been developed to look beyond simple measures such as the number of mismatches or the number of consecutive matching bases present.", "We created design rules for predicting the likelihood of a non-specific effect and present a web server that allows the user to check the specificity of a given siRNA in a flexible manner using a combination of methods.", "The server finds potential off-target matches in the corresponding RefSeq database and ranks them according to a scoring system based on experimental studies of specificity.   ", "AVAILABILITY The server is available at http://informatics-eskitis.griffith.edu.au/SpecificityServer."], "structured": false}
{"doc_id": 6536598, "title": "The Ino80 chromatin-remodeling complex restores chromatin structure during UV DNA damage repair", "abstract": ["Chromatin structure is modulated during deoxyribonucleic acid excision repair, but how this is achieved is unclear.", "Loss of the yeast Ino80 chromatin-remodeling complex (Ino80-C) moderately sensitizes cells to ultraviolet (UV) light.", "In this paper, we show that INO80 acts in the same genetic pathway as nucleotide excision repair (NER) and that the Ino80-C contributes to efficient UV photoproduct removal in a region of high nucleosome occupancy.", "Moreover, Ino80 interacts with the early NER damage recognition complex Rad4-Rad23 and is recruited to chromatin by Rad4 in a UV damage-dependent manner.", "Using a modified chromatin immunoprecipitation assay, we find that chromatin disruption during UV lesion repair is normal, whereas the restoration of nucleosome structure is defective in ino80 mutant cells.", "Collectively, our work suggests that Ino80 is recruited to sites of UV lesion repair through interactions with the NER apparatus and is required for the restoration of chromatin structure after repair."], "structured": false}
{"doc_id": 6540064, "title": "Effects of PCSK9 Inhibition With Alirocumab on Lipoprotein Metabolism in Healthy Humans", "abstract": ["BACKGROUND Alirocumab, a monoclonal antibody to proprotein convertase subtilisin/kexin type 9 (PCSK9), lowers plasma low-density lipoprotein (LDL) cholesterol and apolipoprotein B100 (apoB).", "Although studies in mice and cells have identified increased hepatic LDL receptors as the basis for LDL lowering by PCSK9 inhibitors, there have been no human studies characterizing the effects of PCSK9 inhibitors on lipoprotein metabolism.", "In particular, it is not known whether inhibition of PCSK9 has any effects on very low-density lipoprotein or intermediate-density lipoprotein (IDL) metabolism.", "Inhibition of PCSK9 also results in reductions of plasma lipoprotein (a) levels.", "The regulation of plasma Lp(a) levels, including the role of LDL receptors in the clearance of Lp(a), is poorly defined, and no mechanistic studies of the Lp(a) lowering by alirocumab in humans have been published to date.   \n", "METHODS Eighteen (10 F, 8 mol/L) participants completed a placebo-controlled, 2-period study.", "They received 2 doses of placebo, 2 weeks apart, followed by 5 doses of 150 mg of alirocumab, 2 weeks apart.", "At the end of each period, fractional clearance rates (FCRs) and production rates (PRs) of apoB and apo(a) were determined.", "In 10 participants, postprandial triglycerides and apoB48 levels were measured.   \n", "RESULTS Alirocumab reduced ultracentrifugally isolated LDL-C by 55.1%, LDL-apoB by 56.3%, and plasma Lp(a) by 18.7%.", "The fall in LDL-apoB was caused by an 80.4% increase in LDL-apoB FCR and a 23.9% reduction in LDL-apoB PR.", "The latter was due to a 46.1% increase in IDL-apoB FCR coupled with a 27.2% decrease in conversion of IDL to LDL.", "The FCR of apo(a) tended to increase (24.6%) without any change in apo(a) PR.", "Alirocumab had no effects on FCRs or PRs of very low-density lipoproteins-apoB and very low-density lipoproteins triglycerides or on postprandial plasma triglycerides or apoB48 concentrations.   \n", "CONCLUSIONS Alirocumab decreased LDL-C and LDL-apoB by increasing IDL- and LDL-apoB FCRs and decreasing LDL-apoB PR.", "These results are consistent with increases in LDL receptors available to clear IDL and LDL from blood during PCSK9 inhibition.", "The increase in apo(a) FCR during alirocumab treatment suggests that increased LDL receptors may also play a role in the reduction of plasma Lp(a).   ", "CLINICAL TRIAL REGISTRATION URL: http://www.clinicaltrials.gov.", "Unique identifier: NCT01959971."], "structured": true}
{"doc_id": 6544701, "title": "A more efficient method to generate integration-free human iPS cells", "abstract": ["We report a simple method, using p53 suppression and nontransforming L-Myc, to generate human induced pluripotent stem cells (iPSCs) with episomal plasmid vectors.", "We generated human iPSCs from multiple donors, including two putative human leukocyte antigen (HLA)-homozygous donors who match \u223c20% of the Japanese population at major HLA loci; most iPSCs are integrated transgene-free.", "This method may provide iPSCs suitable for autologous and allologous stem-cell therapy in the future."], "structured": false}
{"doc_id": 6549091, "title": "Permanent cardiac pacing versus medical treatment for the prevention of recurrent vasovagal syncope: a multicenter, randomized, controlled trial.", "abstract": ["BACKGROUND This clinical investigation was performed to compare the effects of permanent dual-chamber cardiac pacing with pharmacological therapy in patients with recurrent vasovagal syncope.   \n", "METHODS AND RESULTS Patients from 14 centers were randomized to receive either a DDD pacemaker provided with rate-drop response function or the beta-blocker atenolol at the dosage of 100 mg once a day.", "Inclusion criteria were age >35 years, >/=3 syncopal spells in the preceding 2 years, and positive response to tilt table testing with syncope occurring in association with relative bradycardia.", "The primary outcome was the first recurrence of syncope after randomization.", "Enrollment was started in December 1997, and the first formal interim analysis was performed on July 30, 2000.", "By that time, 93 patients (38 men and 55 women; mean age, 58.1+/-14.3 years) had been enrolled and randomized, although follow-up data were available for all patients (46 patients in the pacemaker arm, 47 patients in the pharmacological arm).", "The interim analysis showed a significant effect in favor of permanent cardiac pacing (recurrence of syncope in 2 patients [4.3%] after a median of 390 days) compared with medical treatment (recurrence of syncope in 12 patients [25.5%] after a median of 135 days; OR, 0.133; 95% CI, 0.028 to 0.632; P=0.004).", "Consequently, enrollment and follow-up were terminated.   \n", "CONCLUSIONS DDD pacing with rate-drop response function is more effective than beta-blockade for the prevention of syncopal recurrences in highly symptomatic vasovagal fainters with relative bradycardia during tilt-induced syncope."], "structured": true}
{"doc_id": 6550579, "title": "A central role for HER3 in HER2-amplified breast cancer: implications for targeted therapy.", "abstract": ["Epidermal growth factor receptor (EGFR) and HER3 each form heterodimers with HER2 and have independently been implicated as key coreceptors that drive HER2-amplified breast cancer.", "Some studies suggest a dominant role for EGFR, a notion of renewed interest given the development of dual HER2/EGFR small-molecule inhibitors.", "Other studies point to HER3 as the primary coreceptor.", "To clarify the relative contributions of EGFR and HER3 to HER2 signaling, we studied receptor knockdown via small interfering RNA technology across a panel of six HER2-overexpressing cell lines.", "Interestingly, HER3 was as critical as HER2 for maintaining cell proliferation in most cell lines, whereas EGFR was dispensable.", "Induction of HER3 knockdown in the HER2-overexpressing BT474M1 cell line was found to inhibit growth in three-dimensional culture and induce rapid tumor regression of in vivo xenografts.", "Furthermore, preferential phosphorylation of HER3, but not EGFR, was observed in HER2-amplified breast cancer tissues.", "Given these data suggesting HER3 as an important therapeutic target, we examined the activity of pertuzumab, a HER2 antibody that inhibits HER3 signaling by blocking ligand-induced HER2/HER3 heterodimerization.", "Pertuzumab inhibited ligand-dependent morphogenesis in three-dimensional culture and induced tumor regression in the heregulin-dependent MDA-MB-175 xenograft model.", "Importantly, these activities of pertuzumab were distinct from those of trastuzumab, a monoclonal antibody currently used for treatment of HER2-amplified breast cancer patients.", "Our data suggest that inhibition of HER3 may be more clinically relevant than inhibition of EGFR in HER2-amplified breast cancer and also suggest that adding pertuzumab to trastuzumab may augment therapeutic benefit by blocking HER2/HER3 signaling."], "structured": false}
{"doc_id": 6559201, "title": "Mechanisms of astrocytogenesis in the mammalian brain.", "abstract": ["In the mammalian central nervous system, astrocytes are the most abundant cell type and play crucial roles in brain development and function.", "Astrocytes are known to be produced from multipotent neural stem cells (NSCs) at the late gestational stage during brain development, and accumulating evidence indicates that this stage-dependent generation of astrocytes from NSCs is achieved by systematic cooperation between environmental cues and cell-intrinsic programs.", "Exemplifying the former is cytokine signaling through the gp130-Janus kinase/signal transducer and activator of transcription 3 pathway, and exemplifying the latter is epigenetic modification of astrocyte-specific genes.", "Here, we introduce recent advances in our understanding of the mechanisms that coordinate astrocytogenesis from NSCs by modulating signaling pathways and epigenetic programs, with a particular focus on the developing mammalian forebrain."], "structured": false}
{"doc_id": 6559701, "title": "Regulation of the latent-lytic switch in Epstein-Barr virus.", "abstract": ["Epstein-Barr virus (EBV) infection contributes to the development of several different types of human malignancy, including Burkitt lymphoma, Hodgkin lymphoma, and nasopharyngeal carcinoma.", "As a herpesvirus, EBV can establish latent or lytic infection in cells.", "EBV-positive tumors are composed almost exclusively of cells with latent EBV infection.", "Strategies for inducing the lytic form of EBV infection in tumor cells are being investigated as a potential therapy for EBV-positive tumors.", "In this article, we review how cellular and viral proteins regulate the latent-lytic EBV switch in infected B cells and epithelial cells, and discuss how harnessing lytic viral reactivation might be used therapeutically."], "structured": false}
{"doc_id": 6561200, "title": "Efficacy of HPV DNA testing with cytology triage and/or repeat HPV DNA testing in primary cervical cancer screening.", "abstract": ["BACKGROUND Primary cervical screening with both human papillomavirus (HPV) DNA testing and cytological examination of cervical cells with a Pap test (cytology) has been evaluated in randomized clinical trials.", "Because the vast majority of women with positive cytology are also HPV DNA positive, screening strategies that use HPV DNA testing as the primary screening test may be more effective.   \n", "METHODS We used the database from the intervention arm (n = 6,257 women) of a population-based randomized trial of double screening with cytology and HPV DNA testing to evaluate the efficacy of 11 possible cervical screening strategies that are based on HPV DNA testing alone, cytology alone, and HPV DNA testing combined with cytology among women aged 32-38 years.", "The main outcome measures were sensitivity for detection of cervical intraepithelial neoplasia grade 3 or worse (CIN3+) within 6 months of enrollment or at colposcopy for women with a persistent type-specific HPV infection and the number of screening tests and positive predictive value (PPV) for each screening strategy.", "All statistical tests were two-sided.   \n", "RESULTS Compared with screening by cytology alone, double testing with cytology and for type-specific HPV persistence resulted in a 35% (95% confidence interval [CI] = 15% to 60%) increase in sensitivity to detect CIN3+, without a statistically significant reduction in the PPV (relative PPV = 0.76, 95% CI = 0.52 to 1.10), but with more than twice as many screening tests needed.", "Several strategies that incorporated screening for high-risk HPV subtypes were explored, but they resulted in reduced PPV compared with cytology.", "Compared with cytology, primary screening with HPV DNA testing followed by cytological triage and repeat HPV DNA testing of HPV DNA-positive women with normal cytology increased the CIN3+ sensitivity by 30% (95% CI = 9% to 54%), maintained a high PPV (relative PPV = 0.87, 95% CI = 0.60 to 1.26), and resulted in a mere 12% increase in the number of screening tests (from 6,257 to 7,019 tests).   \n", "CONCLUSIONS Primary HPV DNA-based screening with cytology triage and repeat HPV DNA testing of cytology-negative women appears to be the most feasible cervical screening strategy."], "structured": true}
{"doc_id": 6565037, "title": "Extrasynaptic Glutamate Spillover in the Hippocampus: Dependence on Temperature and the Role of Active Glutamate Uptake", "abstract": ["At excitatory synapses on CA1 pyramidal cells of the hippocampus, a larger quantal content is sensed by N-methyl-D-aspartic acid receptors (NMDARs) than by alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors (AMPARs).", "A novel explanation for this discrepancy is that glutamate released from terminals presynaptic to one cell can diffuse to and activate NMDARs, but not AMPARs, on a neighboring cell.", "If this occurs in the living brain, it could invalidate the view that glutamatergic synapses function as private communication channels between neurons.", "Here, we show that the discrepancy in quantal content mediated by the two receptors is greatly decreased at physiological temperature, compared with conventional recording conditions.", "This effect of temperature is not due to changes in release probability or uncovering of latent AMPARs.", "It is, however, partially reversed by the glutamate uptake inhibitor dihydrokainate.", "The results suggest that glutamate transporters play a critical role in limiting the extrasynaptic diffusion of glutamate, thereby minimizing cross-talk between neighboring excitatory synapses."], "structured": false}
{"doc_id": 6580081, "title": "Molecular mechanisms of hepatic ischemia-reperfusion injury and preconditioning.", "abstract": ["Ischemia-reperfusion injury is, at least in part, responsible for the morbidity associated with liver surgery under total vascular exclusion or after liver transplantation.", "The pathophysiology of hepatic ischemia-reperfusion includes a number of mechanisms that contribute to various degrees in the overall injury.", "Some of the topics discussed in this review include cellular mechanisms of injury, formation of pro- and anti-inflammatory mediators, expression of adhesion molecules, and the role of oxidant stress during the inflammatory response.", "Furthermore, the roles of nitric oxide in preventing microcirculatory disturbances and as a substrate for peroxynitrite formation are reviewed.", "In addition, emerging mechanisms of protection by ischemic preconditioning are discussed.", "On the basis of current knowledge, preconditioning or pharmacological interventions that mimic these effects have the greatest potential to improve clinical outcome in liver surgery involving ischemic stress and reperfusion."], "structured": false}
{"doc_id": 6588614, "title": "Characterization of a FGF19 Variant with Altered Receptor Specificity Revealed a Central Role for FGFR1c in the Regulation of Glucose Metabolism", "abstract": ["Diabetes and associated metabolic conditions have reached pandemic proportions worldwide, and there is a clear unmet medical need for new therapies that are both effective and safe.", "FGF19 and FGF21 are distinctive members of the FGF family that function as endocrine hormones.", "Both have potent effects on normalizing glucose, lipid, and energy homeostasis, and therefore, represent attractive potential next generation therapies for combating the growing epidemics of type 2 diabetes and obesity.", "The mechanism responsible for these impressive metabolic effects remains unknown.", "While both FGF19 and FGF21 can activate FGFRs 1c, 2c, and 3c in the presence of co-receptor \u03b2Klotho in vitro, which receptor is responsible for the metabolic activities observed in vivo remains unknown.", "Here we have generated a variant of FGF19, FGF19-7, that has altered receptor specificity with a strong bias toward FGFR1c.", "We show that FGF19-7 is equally efficacious as wild type FGF19 in regulating glucose, lipid, and energy metabolism in both diet-induced obesity and leptin-deficient mouse models.", "These results are the first direct demonstration of the central role of the \u03b2Klotho/FGFR1c receptor complex in glucose and lipid regulation, and also strongly suggest that activation of this receptor complex alone might be sufficient to achieve all the metabolic functions of endocrine FGF molecules."], "structured": false}
{"doc_id": 6599693, "title": "Empirical verification of evolutionary theories of aging", "abstract": ["We recently selected 3 long-lived mutant strains of Saccharomyces cerevisiae by a lasting exposure to exogenous lithocholic acid.", "Each mutant strain can maintain the extended chronological lifespan after numerous passages in medium without lithocholic acid.", "In this study, we used these long-lived yeast mutants for empirical verification of evolutionary theories of aging.", "We provide evidence that the dominant polygenic trait extending longevity of each of these mutants 1) does not affect such key features of early-life fitness as the exponential growth rate, efficacy of post-exponential growth and fecundity; and 2) enhances such features of early-life fitness as susceptibility to chronic exogenous stresses, and the resistance to apoptotic and liponecrotic forms of programmed cell death.", "These findings validate evolutionary theories of programmed aging.", "We also demonstrate that under laboratory conditions that imitate the process of natural selection within an ecosystem, each of these long-lived mutant strains is forced out of the ecosystem by the parental wild-type strain exhibiting shorter lifespan.", "We therefore concluded that yeast cells have evolved some mechanisms for limiting their lifespan upon reaching a certain chronological age.", "These mechanisms drive the evolution of yeast longevity towards maintaining a finite yeast chronological lifespan within ecosystems."], "structured": false}
{"doc_id": 6609935, "title": "Differential regulation of actin microfilaments by human MICAL proteins.", "abstract": ["The Drosophila melanogaster MICAL protein is essential for the neuronal growth cone machinery that functions through plexin- and semaphorin-mediated axonal signaling.", "Drosophila MICAL is also involved in regulating myofilament organization and synaptic structures, and serves as an actin disassembly factor downstream of plexin-mediated axonal repulsion.", "In mammalian cells there are three known isoforms, MICAL1, MICAL2 and MICAL3, as well as the MICAL-like proteins MICAL-L1 and MICAL-L2, but little is known of their function, and information comes almost exclusively from neural cells.", "In this study we show that in non-neural cells human MICALs are required for normal actin organization, and all three MICALs regulate actin stress fibers.", "Moreover, we provide evidence that the generation of reactive oxygen species by MICAL proteins is crucial for their actin-regulatory function.", "However, although MICAL1 is auto-inhibited by its C-terminal coiled-coil region, MICAL2 remains constitutively active and affects stress fibers.", "These data suggest differential but complementary roles for MICAL1 and MICAL2 in actin microfilament regulation."], "structured": false}
{"doc_id": 6625693, "title": "Suppression of inflammatory and neuropathic pain by uncoupling CRMP-2 from the presynaptic Ca2+ channel complex", "abstract": ["The use of N-type voltage-gated calcium channel (CaV2.2) blockers to treat pain is limited by many physiological side effects.", "Here we report that inflammatory and neuropathic hypersensitivity can be suppressed by inhibiting the binding of collapsin response mediator protein 2 (CRMP-2) to CaV2.2 and thereby reducing channel function.", "A peptide of CRMP-2 fused to the HIV transactivator of transcription (TAT) protein (TAT-CBD3) decreased neuropeptide release from sensory neurons and excitatory synaptic transmission in dorsal horn neurons, reduced meningeal blood flow, reduced nocifensive behavior induced by formalin injection or corneal capsaicin application and reversed neuropathic hypersensitivity produced by an antiretroviral drug.", "TAT-CBD3 was mildly anxiolytic without affecting memory retrieval, sensorimotor function or depression.", "At doses tenfold higher than that required to reduce hypersensitivity in vivo, TAT-CBD3 caused a transient episode of tail kinking and body contortion.", "By preventing CRMP-2\u2013mediated enhancement of CaV2.2 function, TAT-CBD3 alleviated inflammatory and neuropathic hypersensitivity, an approach that may prove useful in managing chronic pain."], "structured": false}
{"doc_id": 6636088, "title": "Identification and characterization of a common set of complex I assembly intermediates in mitochondria from patients with complex I deficiency.", "abstract": ["Deficiencies in the activity of complex I (NADH: ubiquinone oxidoreductase) are an important cause of human mitochondrial disease.", "Complex I is composed of at least 46 structural subunits that are encoded in both nuclear and mitochondrial DNA.", "Enzyme deficiency can result from either impaired catalytic efficiency or an inability to assemble the holoenzyme complex; however, the assembly process remains poorly understood.", "We have used two-dimensional Blue-Native/SDS gel electrophoresis and a panel of 11 antibodies directed against structural subunits of the enzyme to investigate complex I assembly in the muscle mitochondria from four patients with complex I deficiency caused by either mitochondrial or nuclear gene defects.", "Immunoblot analyses of second dimension denaturing gels identified seven distinct complex I subcomplexes in the patients studied, five of which could also be detected in nondenaturing gels in the first dimension.", "Although the abundance of these intermediates varied among the different patients, a common constellation of subcomplexes was observed in all cases.", "A similar profile of subcomplexes was present in a human/mouse hybrid fibroblast cell line with a severe complex I deficiency due to an almost complete lack of assembly of the holoenzyme complex.", "The finding that diverse causes of complex I deficiency produce a similar pattern of complex I subcomplexes suggests that these are intermediates in the assembly of the holoenzyme complex.", "We propose a possible assembly pathway for the complex, which differs significantly from that proposed for Neurospora, the current model for complex I assembly."], "structured": false}
{"doc_id": 6647414, "title": "Leisure time physical activity and mortality: a detailed pooled analysis of the dose-response relationship.", "abstract": ["IMPORTANCE The 2008 Physical Activity Guidelines for Americans recommended a minimum of 75 vigorous-intensity or 150 moderate-intensity minutes per week (7.5 metabolic-equivalent hours per week) of aerobic activity for substantial health benefit and suggested additional benefits by doing more than double this amount.", "However, the upper limit of longevity benefit or possible harm with more physical activity is unclear.   \n", "OBJECTIVE To quantify the dose-response association between leisure time physical activity and mortality and define the upper limit of benefit or harm associated with increased levels of physical activity.   \n", "DESIGN, SETTING, AND PARTICIPANTS We pooled data from 6 studies in the National Cancer Institute Cohort Consortium (baseline 1992-2003).", "Population-based prospective cohorts in the United States and Europe with self-reported physical activity were analyzed in 2014.", "A total of 661,137 men and women (median age, 62 years; range, 21-98 years) and 116,686 deaths were included.", "We used Cox proportional hazards regression with cohort stratification to generate multivariable-adjusted hazard ratios (HRs) and 95% CIs.", "Median follow-up time was 14.2 years.   ", "EXPOSURES Leisure time moderate- to vigorous-intensity physical activity.   \n", "MAIN OUTCOMES AND MEASURES The upper limit of mortality benefit from high levels of leisure time physical activity.   \n", "RESULTS Compared with individuals reporting no leisure time physical activity, we observed a 20% lower mortality risk among those performing less than the recommended minimum of 7.5 metabolic-equivalent hours per week (HR, 0.80 [95% CI, 0.78-0.82]), a 31% lower risk at 1 to 2 times the recommended minimum (HR, 0.69 [95% CI, 0.67-0.70]), and a 37% lower risk at 2 to 3 times the minimum (HR, 0.63 [95% CI, 0.62-0.65]).", "An upper threshold for mortality benefit occurred at 3 to 5 times the physical activity recommendation (HR, 0.61 [95% CI, 0.59-0.62]); however, compared with the recommended minimum, the additional benefit was modest (31% vs 39%).", "There was no evidence of harm at 10 or more times the recommended minimum (HR, 0.69 [95% CI, 0.59-0.78]).", "A similar dose-response relationship was observed for mortality due to cardiovascular disease and to cancer.   \n", "CONCLUSIONS AND RELEVANCE Meeting the 2008 Physical Activity Guidelines for Americans minimum by either moderate- or vigorous-intensity activities was associated with nearly the maximum longevity benefit.", "We observed a benefit threshold at approximately 3 to 5 times the recommended leisure time physical activity minimum and no excess risk at 10 or more times the minimum.", "In regard to mortality, health care professionals should encourage inactive adults to perform leisure time physical activity and do not need to discourage adults who already participate in high-activity levels."], "structured": true}
{"doc_id": 6650933, "title": "Green tea polyphenol causes differential oxidative environments in tumor versus normal epithelial cells.", "abstract": ["Green tea polyphenols (GTPPs) are considered beneficial to human health, especially as chemopreventive agents.", "Recently, cytotoxic reactive oxygen species (ROS) were identified in tumor and certain normal cell cultures incubated with high concentrations of the most abundant GTPP, (-)-epigallocatechin-3-gallate (EGCG).", "If EGCG also provokes the production of ROS in normal epithelial cells, it may preclude the topical use of EGCG at higher doses.", "The current study examined the oxidative status of normal epithelial, normal salivary gland, and oral carcinoma cells treated with EGCG, using ROS measurement and catalase and superoxide dismutase activity assays.", "The results demonstrated that high concentrations of EGCG induced oxidative stress only in tumor cells.", "In contrast, EGCG reduced ROS in normal cells to background levels.", "3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay and 5-bromodeoxyuridine incorporation data were also compared between the two oral carcinoma cell lines treated by EGCG, which suggest that a difference in the levels of endogenous catalase activity may play an important role in reducing oxidative stress provoked by EGCG in tumor cells.", "It is concluded that pathways activated by GTPPs or EGCG in normal epithelial versus tumor cells create different oxidative environments, favoring either normal cell survival or tumor cell destruction.", "This finding may lead to applications of naturally occurring polyphenols to enhance the effectiveness of chemo/radiation therapy to promote cancer cell death while protecting normal cells."], "structured": false}
{"doc_id": 6669242, "title": "Protein acetylation affects acetate metabolism, motility and acid stress response in Escherichia coli", "abstract": ["Although protein acetylation is widely observed, it has been associated with few specific regulatory functions making it poorly understood.", "To interrogate its functionality, we analyzed the acetylome in Escherichia coli knockout mutants of cobB, the only known sirtuin-like deacetylase, and patZ, the best-known protein acetyltransferase.", "For four growth conditions, more than 2,000 unique acetylated peptides, belonging to 809 proteins, were identified and differentially quantified.", "Nearly 65% of these proteins are related to metabolism.", "The global activity of CobB contributes to the deacetylation of a large number of substrates and has a major impact on physiology.", "Apart from the regulation of acetyl-CoA synthetase, we found that CobB-controlled acetylation of isocitrate lyase contributes to the fine-tuning of the glyoxylate shunt.", "Acetylation of the transcription factor RcsB prevents DNA binding, activating flagella biosynthesis and motility, and increases acid stress susceptibility.", "Surprisingly, deletion of patZ increased acetylation in acetate cultures, which suggests that it regulates the levels of acetylating agents.", "The results presented offer new insights into functional roles of protein acetylation in metabolic fitness and global cell regulation."], "structured": false}
{"doc_id": 6670101, "title": "Ribosome biogenesis: Achilles heel of cancer?", "abstract": ["It is long been known that cancer and non-cancer cells can be distinguished on the basis of their nucleolar morphologies.", "As early as the 19th century, it was reported that cancer cells have larger and more irregularly shaped nucleoli.", "Since then, pathologists have used nucleolar morphology to predict the clinical outcome [1].", "Nucleolar morphology is altered due to the up-regulation of ribosomal gene transcription.", "Within nucleoli, ribosomal genes (rDNA) are transcribed by RNA polymerase I (pol I).", "The pre-ribosomal RNA (pre-rRNA) transcripts are subsequently modified and processed into the mature 18S, 5.8S and 28S rRNAs.", "5S rRNA is transcribed by RNA polymerase III in the nucleoplasm.", "Together with the ribosomal proteins, the 5S rRNA is imported into the nucleolus where 40S and 60S ribosomal subunits are assembled prior to export to the cytoplasm [1, 2].    ", "Oncogenes such as c-Myc can both directly and indirectly upregulate rDNA transcription, while tumour suppressors like p53 and Rb suppress ribosome biogenesis.", "Mutations in these genes not only result in deregulated cell cycle control, but also upregulated ribosome biogenesis.", "In addition to ribosome biogenesis, the nucleolus is a key cellular stress sensor and plays a central role in p53 activation [1, 2].    ", "The increased translational capacity of cancer cells enables them to maintain higher proliferation rates.", "As stated by Ruggero, \u201ccompared with normal cells, cancer cells may be addicted to increases in ribosome biogenesis and number\u201d [1].", "This provides new therapeutic opportunities.", "As it turns out many chemotherapeutic drugs used in cancer treatment already inhibit ribosome biogenesis.", "In one recent survey it was shown that 20 out of 36 drugs in clinical use inhibit ribosome biogenesis [3].", "Most of these drugs were originally designed to target highly proliferating cells by damaging DNA, interfering with DNA synthesis or with mitosis.", "These targeting modalities of these drugs also lead to toxicity in normal highly proliferating tissues.", "An example is ActinomycinD (AMD), a DNA intercalator which has a preference for GC-rich DNA sequences.", "As rDNA has above average GC-richness and because of its open chromatin conformation, low concentrations of AMD preferentially inhibit RNA polymerase I transcription and upon prolonged exposure causes genome wide DNA damage.", "Alkylating drugs like cisplatin and oxaliplatin or topoisomerases poisons like camptothecin inhibit pol I transcription.", "The degree to which inhibition of ribosome biogenesis contributes to the efficacy of these drugs is difficult to establish [3].", "This raises an important question.", "Can targeting ribosome biogenesis without DNA damage offer any therapeutic potential?", "Two recently described drugs CX-5461 and BMH-21 are now providing evidence that inhibition of ribosome biogenesis by targeting transcription of rDNA by pol I has promising therapeutic potential.", "CX-5461 was designed to specifically inhibit pol I transcription by disrupting pre-initiation complex formation at the rDNA promoter.", "CX-5461 has been shown to activate p53 via nucleolar stress.", "It induces autophagy as well as senescence in a multiple types of cancer cells in a p53-dependent manner.", "Especially in leukaemia and lymphoma cells, treatment with CX-5461 induces p53-dependent apoptosis, while normal cells tolerate it [4, 5].    ", "Whether the drug also induces DNA damage was not fully addressed, but it was demonstrated that it could induce cell death in cells lacking ATM - a key mediator of DNA double strand break responses.", "However, more recently Laiho and colleagues have shown that at high concentrations, CX-5461 does induce a \u03b3H2AX response, raising concerns about DNA damage [6].    ", "BMH-21 was identified in a screen performed by Laiho and colleagues aimed at identifying novel p53 activators.", "Like AMD, BMH-21 is a DNA intercalator with preference for GC rich sequences [7].", "Continuing the parallel with AMD, BMH-21 is a potent and specific inhibitor rDNA transcription and induces nucleolar reorganisation often referred to as nucleolar capping.", "Interestingly, transcription inhibition was followed by the degradation of the main pol I subunit, RPA194, by the proteasome [6].", "In contrast with AMD, initial indications were that BMH-21 did not appear to induce DNA damage as evidenced by the lack of a \u03b3H2AX response [7].", "Inhibition of transcription by BMH-21 causes nucleolar stress, resulting in decreased proliferation and cell death.", "P53 is activated in BMH-21 treated cells but is not required for its anti-proliferative effects.", "Intriguingly, it appears that cancer cells with high demands for ribosome biogenesis are selectively targeted [6].    ", "The current publication in Oncotarget now rules out any role for DNA damage signalling and repair pathways in the BMH-21 response.", "Moreover, BMH-21 derivatives that can induce DNA damage display lower efficiency in inducing nucleolar stress and inhibiting proliferation [8].", "The central importance of this study is that it finally uncouples DNA damage and nucleolar stress and reveals an Achilles heel in cancer cells, their addiction to ribosome biogenesis."], "structured": false}
{"doc_id": 6673421, "title": "Cell and molecular mechanisms of insulin-induced angiogenesis", "abstract": ["Angiogenesis, the development of new blood vessel from pre-existing vessels, is a key process in the formation of the granulation tissue during wound healing.", "The appropriate development of new blood vessels, along with their subsequent maturation and differentiation, establishes the foundation for functional wound neovasculature.", "We performed studies in vivo and used a variety of cellular and molecular approaches in vitro to show that insulin stimulates angiogenesis and to elucidate the signalling mechanisms by which this protein stimulates microvessel development.", "Mice skin injected with insulin shows longer vessels with more branches, along with increased numbers of associated alpha-smooth muscle actin-expressing cells, suggesting the appropriate differentiation and maturation of the new vessels.", "We also found that insulin stimulates human microvascular endothelial cell migration and tube formation, and that these effects occur independently of VEGF/VEGFR signalling, but are dependent upon the insulin receptor itself.", "Downstream signalling pathways involve PI3K, Akt, sterol regulatory element-binding protein 1 (SREBP-1) and Rac1; inhibition of these pathways results in elimination of endothelial cell migration and tube formation and significantly decreases the development of microvessels.", "Our findings strongly suggest that insulin is a good candidate for the treatment of ischaemic wounds and other conditions in which blood vessel development is impaired."], "structured": false}
{"doc_id": 6690087, "title": "Inhibition of mammalian target of rapamycin potentiates thrombin-induced intercellular adhesion molecule-1 expression by accelerating and stabilizing NF-kappa B activation in endothelial cells.", "abstract": ["We addressed the regulatory function of mammalian target of rapamycin (mTOR) in the mechanism of thrombin-induced ICAM-1 gene expression in endothelial cells.", "Pretreatment of HUVECs with rapamycin, an inhibitor of mTOR, augmented thrombin-induced ICAM-1 expression.", "Inhibition of mTOR by this approach promoted whereas over-expression of mTOR inhibited thrombin-induced transcriptional activity of NF-kappaB, an essential regulator of ICAM-1 transcription.", "Analysis of the NF-kappaB signaling pathway revealed that inhibition of mTOR potentiated IkappaB kinase activation resulting in a rapid and persistent phosphorylation of IkappaBalpha on Ser32 and Ser36, a requirement for IkappaBalpha degradation.", "Consistent with these data, we observed a more efficient and stable nuclear localization of RelA/p65 and, subsequently, the DNA binding activity of NF-kappaB by thrombin following mTOR inhibition.", "These data define a novel role of mTOR in down-regulating thrombin-induced ICAM-1 expression in endothelial cells by controlling a delayed and transient activation of NF-kappaB."], "structured": false}
{"doc_id": 6710699, "title": "Homologous recombination resolution defect in werner syndrome.", "abstract": ["Werner syndrome (WRN) is an uncommon autosomal recessive disease whose phenotype includes features of premature aging, genetic instability, and an elevated risk of cancer.", "We used three different experimental strategies to show that WRN cellular phenotypes of limited cell division potential, DNA damage hypersensitivity, and defective homologous recombination (HR) are interrelated.", "WRN cell survival and the generation of viable mitotic recombinant progeny could be rescued by expressing wild-type WRN protein or by expressing the bacterial resolvase protein RusA. The dependence of WRN cellular phenotypes on RAD51-dependent HR pathways was demonstrated by using a dominant-negative RAD51 protein to suppress mitotic recombination in WRN and control cells: the suppression of RAD51-dependent recombination led to significantly improved survival of WRN cells following DNA damage.", "These results define a physiological role for the WRN RecQ helicase protein in RAD51-dependent HR and identify a mechanistic link between defective recombination resolution and limited cell division potential, DNA damage hypersensitivity, and genetic instability in human somatic cells."], "structured": false}
{"doc_id": 6710713, "title": "Risk factors at medical school for subsequent professional misconduct: multicentre retrospective case-control study", "abstract": ["OBJECTIVE To determine whether there are risk factors in a doctor's time at medical school that are associated with subsequent professional misconduct.   \n", "DESIGN Matched case-control study.", "Setting Records from medical schools and the General Medical Council (GMC).   \n", "PARTICIPANTS 59 doctors who had graduated from any one of eight medical schools in the United Kingdom in 1958-97 and had a proved finding of serious professional misconduct in GMC proceedings in 1999-2004 (cases); 236 controls (four for each case) were selected by systematic sampling from matching graduation cohorts.", "Case-control status was revealed by the GMC after completion of data entry.   \n", "MAIN OUTCOME MEASURE Odds ratios for being a \"case,\" with multivariable conditional logistic regression of potential risk factors including pre-admission characteristics and progress during the course.", "These data were obtained from anonymised copies of the students' progress files held by their original medical schools.   \n", "RESULTS Univariate conditional logistic regression analysis found that cases were more likely to be men, to be of lower estimated social class, and to have had academic difficulties during their medical course, especially in the early years.", "Multivariable analysis showed that male sex (odds ratio 9.80, 95% confidence interval 2.43 to 39.44, P=0.001), lower social class (4.28, 1.52 to 12.09, P=0.006), and failure of early or preclinical examinations (5.47, 2.17 to 13.79, P<0.001) were independently associated with being a case.   \n", "CONCLUSIONS This small study suggests that male sex, a lower socioeconomic background, and early academic difficulties at medical school could be risk factors for subsequent professional misconduct.", "The findings are preliminary and should be interpreted with caution.", "Most doctors with risk factors will not come before the GMC's disciplinary panels."], "structured": true}
{"doc_id": 6712836, "title": "MiD49 and MiD51, new components of the mitochondrial fission machinery.", "abstract": ["Mitochondria form intricate networks through fission and fusion events.", "Here, we identify mitochondrial dynamics proteins of 49 and 51 kDa (MiD49 and MiD51, respectively) anchored in the mitochondrial outer membrane.", "MiD49/51 form foci and rings around mitochondria similar to the fission mediator dynamin-related protein 1 (Drp1).", "MiD49/51 directly recruit Drp1 to the mitochondrial surface, whereas their knockdown reduces Drp1 association, leading to unopposed fusion.", "Overexpression of MiD49/51 seems to sequester Drp1 from functioning at mitochondria and cause fused tubules to associate with actin.", "Thus, MiD49/51 are new mediators of mitochondrial division affecting Drp1 action at mitochondria."], "structured": false}
{"doc_id": 6717533, "title": "Maximal activation of transcription by statl and stat3 requires both tyrosine and serine phosphorylation", "abstract": ["Stat1 and Stat3 are latent transcriptional factors activated initially through phosphorylation on single tyrosine residues induced by cytokine and growth factor occupation of cell surface receptors.", "Here we show that phosphorylation on a single serine (residue 727) in each protein is also required for maximal transcriptional activity.", "Both cytokines and growth factors are capable of inducing the serine phosphorylation of Stat1 and Stat3.", "These experiments show that gene activation by Stat1 and Stat3, which obligatorily require tyrosine phosphorylation to become active, also depends for maximal activation on one or more of the many serine kinases."], "structured": false}
{"doc_id": 6718824, "title": "Protein restriction during pregnancy affects maternal liver lipid metabolism and fetal brain lipid composition in the rat.", "abstract": ["Suboptimal developmental environments program offspring to lifelong metabolic problems.", "The aim of this study was to determine the impact of protein restriction in pregnancy on maternal liver lipid metabolism at 19 days of gestation (dG) and its effect on fetal brain development.", "Control (C) and restricted (R) mothers were fed with isocaloric diets containing 20 and 10% of casein.", "At 19 dG, maternal blood and livers and fetal livers and brains were collected.", "Serum insulin and leptin levels were determinate in mothers.", "Maternal and fetal liver lipid and fetal brain lipid quantification were performed.", "Maternal liver and fetal brain fatty acids were quantified by gas chromatography.", "In mothers, liver desaturase and elongase mRNAs were measured by RT-PCR.", "Maternal body and liver weights were similar in both groups.", "However, fat body composition, including liver lipids, was lower in R mothers.", "A higher fasting insulin at 19 dG in the R group was observed (C = 0.2 +/-", "0.04 vs. R = 0.9 +/-", "0.16 ng/ml, P < 0.01) and was inversely related to early growth retardation.", "Serum leptin in R mothers was significantly higher than that observed in C rats (C = 5 +/- 0.1 vs. R = 7 +/-", "0.7 ng/ml, P < 0.05).", "In addition, protein restriction significantly reduced gene expression in maternal liver of desaturases and elongases and the concentration of arachidonic (AA) and docosahexanoic (DHA) acids.", "In fetus from R mothers, a low body weight (C = 3 +/-", "0.3 vs. R = 2 +/-", "0.1 g, P < 0.05), as well as liver and brain lipids, including the content of DHA in the brain, was reduced.", "This study showed that protein restriction during pregnancy may negatively impact normal fetal brain development by changes in maternal lipid metabolism."], "structured": false}
{"doc_id": 6722522, "title": "Heparan sulfate proteoglycans mediate internalization and propagation of specific proteopathic seeds.", "abstract": ["Recent experimental evidence suggests that transcellular propagation of fibrillar protein aggregates drives the progression of neurodegenerative diseases in a prion-like manner.", "This phenomenon is now well described in cell and animal models and involves the release of protein aggregates into the extracellular space.", "Free aggregates then enter neighboring cells to seed further fibrillization.", "The mechanism by which aggregated extracellular proteins such as tau and \u03b1-synuclein bind and enter cells to trigger intracellular fibril formation is unknown.", "Prior work indicates that prion protein aggregates bind heparan sulfate proteoglycans (HSPGs) on the cell surface to transmit pathologic processes.", "Here, we find that tau fibril uptake also occurs via HSPG binding.", "This is blocked in cultured cells and primary neurons by heparin, chlorate, heparinase, and genetic knockdown of a key HSPG synthetic enzyme, Ext1.", "Interference with tau binding to HSPGs prevents recombinant tau fibrils from inducing intracellular aggregation and blocks transcellular aggregate propagation.", "In vivo, a heparin mimetic, F6, blocks neuronal uptake of stereotactically injected tau fibrils.", "Finally, uptake and seeding by \u03b1-synuclein fibrils, but not huntingtin fibrils, occurs by the same mechanism as tau.", "This work suggests a unifying mechanism of cell uptake and propagation for tauopathy and synucleinopathy."], "structured": false}
{"doc_id": 6723450, "title": "Effects of Bifidobacterium animalis administered during lactation on allergic and autoimmune responses in rodents.", "abstract": ["Probiotics are promoted as being beneficial to health and positive effects on the immune system have been reported.", "Beneficial immune effects have been attributed to several mechanisms, including stimulating T helper 1 (Th1) immunity.", "To explore the effects of the probiotic Bifidobacterium animalis on Th1- and Th2-mediated immune responses, two different animal models representing either Th1- or Th2-mediated immune responses were used: a rat model for experimental autoimmune encephalomyelitis (EAE) (Th1) and a mouse model for respiratory allergy induced by ovalbumin (OVA) (Th2).", "B. animalis administration started when the mice or rats were 2 weeks old.", "Respiratory allergy or EAE were induced when the animals were 6-7 weeks old.", "In the allergy model, B. animalis modestly reduced the number of infiltrating eosinophils and lymphocytes in the lungs, but no effects on allergen-specific serum immunoglobulin E levels were found.", "Cytokine profiles assessed after culturing spleen cells with the mitogen concanvalin A (ConA) showed that B. animalis skewed the Th1/Th2 balance towards Th1 in females.", "However, allergen-induced cytokine production in females was not affected by B. animalis.", "In males, B. animalis significantly decreased ConA-induced interleukin-13 and a trend towards lower levels of OVA-induced Th2 cytokines.", "In the EAE model, B. animalis significantly reduced the duration of clinical symptoms by almost 2 days in males and improved the body weight gain during the experimental period compared with the control group.", "Our data show that B. animalis reduced several immune parameters in the allergy as well as in the autoimmunity model."], "structured": false}
{"doc_id": 6729465, "title": "Planar Cell Polarity Signaling Pathway in Congenital Heart Diseases", "abstract": ["Congenital heart disease (CHD) is a common cardiac disorder in humans.", "Despite many advances in the understanding of CHD and the identification of many associated genes, the fundamental etiology for the majority of cases remains unclear.", "The planar cell polarity (PCP) signaling pathway, responsible for tissue polarity in Drosophila and gastrulation movements and cardiogenesis in vertebrates, has been shown to play multiple roles during cardiac differentiation and development.", "The disrupted function of PCP signaling is connected to some CHDs.", "Here, we summarize our current understanding of how PCP factors affect the pathogenesis of CHD."], "structured": false}
{"doc_id": 6748318, "title": "Cost-effectiveness of human papillomavirus vaccination and screening in Spain.", "abstract": ["BACKGROUND In Spain, prophylactic vaccination against human papillomavirus (HPV) types 16 and 18 is being offered free-of-charge to one birth cohort of girls aged 11-14.", "Screening is opportunistic (annual/biannual) contributing to social and geographical disparities.   \n", "METHODS A multi-HPV-type microsimulation model was calibrated to epidemiologic data from Spain utilising likelihood-based methods to assess the health and economic impact of adding HPV vaccination to cervical cancer screening.", "Strategies included (1) screening alone of women over age 25, varying frequency (every 1-5 years) and test (cytology, HPV DNA testing); (2) HPV vaccination of 11-year-old girls combined with screening.", "Outcomes included lifetime cancer risk, life expectancy, lifetime costs, number of clinical procedures and incremental cost-effectiveness ratios.   \n", "RESULTS After the introduction of HPV vaccination, screening will need to continue, and strategies that incorporated HPV testing are more effective and cost-effective than those with cytology alone.", "For vaccinated girls, 5-year organised cytology with HPV testing as triage from ages 30 to 65 costs 24,350\u20ac per year of life saved (YLS), assuming life-long vaccine immunity against HPV-16/18 by 3 doses with 90% coverage.", "Unvaccinated girls would benefit from organised cytology screening with HPV testing as triage; 5-year screening from ages 30 to 65 costs 16,060\u20ac/YLS and 4-year screening from ages 30 to 85 costs 38,250\u20ac/YLS.", "Interventions would be cost-effective depending on the cost-effectiveness threshold and the vaccine price.   \n", "CONCLUSIONS In Spain, inequitable coverage and overuse of cytology make screening programmes inefficient.", "If high vaccination coverage among pre-adolescent girls is achieved, organised cytology screening with HPV triage starting at ages 30 to at least 65 every 4-5 years represents the best balance between costs and benefits."], "structured": true}
{"doc_id": 6751418, "title": "Dosimetry and risk estimates of radioiodine therapy for large, multinodular goiters.", "abstract": ["UNLABELLED In patients with a large, multinodular goiter (> 100 g), radiation absorbed doses in the thyroid, surrounding tissues and remainder of the body were estimated after therapeutic administration of 131I(3.7 MBq or 100 microCi/g of thyroid tissue retained at 24 hr).   \n", "METHODS Thermoluminescent dosimeter (TLD) measurements were performed on 23 patients (12 euthyroid and 1I hyperthyroid; thyroid weight 222 +/-", "72 g; 2.1 +/-", "0.9 GBq 131I) on the skin over the thyroid, over the submandibular gland and over the parotid gland.", "Thyroid radioactivity measurements were done daily in 6 euthyroid and 6 hyperthyroid patients (thyroid weight 204 +/-", "69 g; 1.9 +/-", "0.9 GBq 131I).", "An iodine biokinetic model and the MIRD methodology were used to estimate absorbed doses in organs.", "Cancer risks were calculated using ICRP Publication 60.   \n", "RESULTS Cumulated absorbed doses on the skin (TLD measurements) were 4.2 +/-", "1.4 Gy (thyroid), 1.2 +/-", "0.6 Gy (submandibular) and 0.4 +/-", "0.2 Gy (parotid).", "All these values were significantly correlated with the amount of radioiodine retained in the thyroid at 24 hr (euthyroid versus hyperthyroid not significant).", "Absorbed doses in the thyroid of 94 +/-", "25 Gy for euthyroid and 93 +/-", "17 Gy for hyperthyroid patients were calculated (thyroid radioactivity measurements).", "Extrathyroidal absorbed doses (means of 12 patients) were 0.88 Gy in the urinary bladder, 0.57 Gy in the small intestine, 0.38 Gy in the stomach, and ranged from 0.05 to 0.30 Gy in other organs (euthyroid versus hyperthyroid not significant).", "A 1.6% life-time risk of development of cancer outside the thyroid gland was calculated.", "When applied to people of 65 yr and older the estimated risk is approximately 0.5%.   \n", "CONCLUSION These data may help in choosing the treatment regimen for individual patients with a large, multinodular goiter, who have to be treated for hyperthyroidism or compressive problems.", "In younger patients, surgery may be preferred.", "However, for elderly patients and patients with cardiopulmonary disease, the advantages of noninvasive radioiodine treatment will outweight the life-time risk of this mode of therapy."], "structured": true}
{"doc_id": 6766459, "title": "RBM3 regulates temperature sensitive miR-142\u20135p and miR-143 (thermomiRs), which target immune genes and control fever", "abstract": ["Fever is commonly used to diagnose disease and is consistently associated with increased mortality in critically ill patients.", "However, the molecular controls of elevated body temperature are poorly understood.", "We discovered that the expression of RNA-binding motif protein 3 (RBM3), known to respond to cold stress and to modulate microRNA (miRNA) expression, was reduced in 30 patients with fever, and in THP-1-derived macrophages maintained at a fever-like temperature (40 \u00b0C).", "Notably, RBM3 expression is reduced during fever whether or not infection is demonstrable.", "Reduced RBM3 expression resulted in increased expression of RBM3-targeted temperature-sensitive miRNAs, we termed thermomiRs.", "ThermomiRs such as miR-142-5p and miR-143 in turn target endogenous pyrogens including IL-6, IL6ST, TLR2, PGE2 and TNF to complete a negative feedback mechanism, which may be crucial to prevent pathological hyperthermia.", "Using normal PBMCs that were exogenously exposed to fever-like temperature (40 \u00b0C), we further demonstrate the trend by which decreased levels of RBM3 were associated with increased levels of miR-142-5p and miR-143 and vice versa over a 24 h time course.", "Collectively, our results indicate the existence of a negative feedback loop that regulates fever via reduced RBM3 levels and increased expression of miR-142-5p and miR-143."], "structured": false}
{"doc_id": 6767133, "title": "Patient preferences and expectations for care: determinants in patients with lumbar intervertebral disc herniation.", "abstract": ["STUDY DESIGN Prospective observational cohort.   \n", "OBJECTIVE To describe the baseline characteristics of patients with a diagnosis of intervertebral disc herniation who had different treatment preferences and the relationship of specific expectations with those preferences.   ", "SUMMARY OF BACKGROUND DATA Data were gathered from the observational cohort of the Spine Patient Outcomes Research Trial (SPORT).", "Patients in the observational cohort met eligibility requirements identical to those of the randomized cohort, but declined randomization, receiving instead the treatment of their choice.   \n", "METHODS Baseline preference and expectation data were acquired at the time of enrollment of the patient, before exposure to the informed consent process.", "Univariate analyses were performed using a t test for continuous variables and chi for categorical variables.", "Multivariate analyses were also performed with ANCOVA for continuous variables and logistic regression for categorical variables.", "Multiple logistic regression models were developed in a forward stepwise fashion using blocks of variables.   \n", "RESULTS More patients preferred operative care: 67% preferred surgery, 28% preferred nonoperative treatment, and 6% were unsure; 53% of those preferring surgery stated a definite preference, whereas only 18% of those preferring nonoperative care had a definite preference.", "Patients preferring surgery were younger, had lower levels of education, and higher levels of unemployment/disability.", "This group also reported higher pain, worse physical and mental functioning, more back pain related disability, a longer duration of symptoms, and more opiate use.", "Gender, race, comorbidities, and use of other therapies did not differ significantly across preference groups.", "Patients' expectations regarding improvement with nonoperative care was the strongest predictor of preference.   \n", "CONCLUSION Patient expectations, particularly regarding the benefit of nonoperative treatment, are the primary determinant of surgery preference among patients with lumbar intervertebral disc herniation.", "Demographic, functional status, and prior treatment experience had significant associations with patients' expectations and preferences."], "structured": true}
{"doc_id": 6767271, "title": "Cord factor and peptidoglycan recapitulate the Th17-promoting adjuvant activity of mycobacteria through mincle/CARD9 signaling and the inflammasome.", "abstract": ["Although adjuvants are critical vaccine components, their modes of action are poorly understood.", "In this study, we investigated the mechanisms by which the heat-killed mycobacteria in CFA promote Th17 CD4(+) T cell responses.", "We found that IL-17 secretion by CD4(+) T cells following CFA immunization requires MyD88 and IL-1\u03b2/IL-1R signaling.", "Through measurement of Ag-specific responses after adoptive transfer of OTII cells, we confirmed that MyD88-dependent signaling controls Th17 differentiation rather than simply production of IL-17.", "Additional experiments showed that CFA-induced Th17 differentiation involves IL-1\u03b2 processing by the inflammasome, as mice lacking caspase-1, ASC, or NLRP3 exhibit partially defective responses after immunization.", "Biochemical fractionation studies further revealed that peptidoglycan is the major component of heat-killed mycobacteria responsible for inflammasome activation.", "By assaying Il1b transcripts in the injection site skin of CFA-immunized mice, we found that signaling through the adaptor molecule caspase activation and recruitment domain 9 (CARD9) plays a major role in triggering pro-IL-1\u03b2 expression.", "Moreover, we demonstrated that recognition of the mycobacterial glycolipid trehalose dimycolate (cord factor) by the C-type lectin receptor mincle partially explains this CARD9 requirement.", "Importantly, purified peptidoglycan and cord factor administered in mineral oil synergized to recapitulate the Th17-promoting activity of CFA, and, as expected, this response was diminished in caspase-1- and CARD9-deficient mice.", "Taken together, these findings suggest a general strategy for the rational design of Th17-skewing adjuvants by combining agonists of the CARD9 pathway with inflammasome activators."], "structured": false}
{"doc_id": 6776834, "title": "OPA1 gene therapy prevents retinal ganglion cell loss in a Dominant Optic Atrophy mouse model", "abstract": ["Dominant optic atrophy (DOA) is a rare progressive and irreversible blinding disease which is one of the most frequent forms of hereditary optic neuropathy.", "DOA is mainly caused by dominant mutation in the OPA1 gene encoding a large mitochondrial GTPase with crucial roles in membrane dynamics and cell survival.", "Hereditary optic neuropathies are commonly characterized by the degeneration of retinal ganglion cells, leading to the optic nerve atrophy and the progressive loss of visual acuity.", "Up to now, despite increasing advances in the understanding of the pathological mechanisms, DOA remains intractable.", "Here, we tested the efficiency of gene therapy on a genetically-modified mouse model reproducing DOA vision loss.", "We performed intravitreal injections of an Adeno-Associated Virus carrying the human OPA1 cDNA under the control of the cytomegalovirus promotor.", "Our results provide the first evidence that gene therapy is efficient on a mouse model of DOA as the wild-type OPA1 expression is able to alleviate the OPA1-induced retinal ganglion cell degeneration, the hallmark of the disease.", "These results displayed encouraging effects of gene therapy for Dominant Optic Atrophy, fostering future investigations aiming at clinical trials in patients."], "structured": false}
{"doc_id": 6784372, "title": "Multiple degradation pathways regulate versatile CIP/KIP CDK inhibitors.", "abstract": ["The mammalian CIP/KIP family of cyclin-dependent kinase (CDK) inhibitors (CKIs) comprises three proteins--p21(Cip1/WAF1), p27(Kip1), and p57(Kip2)--that bind and inhibit cyclin-CDK complexes, which are key regulators of the cell cycle.", "CIP/KIP CKIs have additional independent functions in regulating transcription, apoptosis and actin cytoskeletal dynamics.", "These divergent functions are performed in distinct cellular compartments and contribute to the seemingly contradictory observation that the CKIs can both suppress and promote cancer.", "Multiple ubiquitin ligases (E3s) direct the proteasome-mediated degradation of p21, p27 and p57.", "This review analyzes recent data highlighting our current understanding of how distinct E3 pathways regulate subpopulations of the CKIs to control their diverse functions."], "structured": false}
{"doc_id": 6788835, "title": "Dislocation of a type I membrane protein requires interactions between membrane-spanning segments within the lipid bilayer.", "abstract": ["The human cytomegalovirus gene product US11 causes rapid degradation of class I major histocompatibility complex (MHCI) heavy chains by inducing their dislocation from the endoplasmic reticulum (ER) and subsequent degradation by the proteasome.", "This set of reactions resembles the endogenous cellular quality control pathway that removes misfolded or unassembled proteins from the ER.", "We show that the transmembrane domain (TMD) of US11 is essential for MHCI heavy chain dislocation, but dispensable for MHCI binding.", "A Gln residue at position 192 in the US11 TMD is crucial for the ubiquitination and degradation of MHCI heavy chains.", "Cells that express US11 TMD mutants allow formation of MHCI-beta2m complexes, but their rate of egress from the ER is significantly impaired.", "Further mutagenesis data are consistent with the presence of an alpha-helical structure in the US11 TMD essential for MHCI heavy chain dislocation.", "The failure of US11 TMD mutants to catalyze dislocation is a unique instance in which a polar residue in the TMD of a type I membrane protein is required for that protein's function.", "Targeting of MHCI heavy chains for dislocation by US11 thus requires the formation of interhelical hydrogen bonds within the ER membrane."], "structured": false}
{"doc_id": 6790197, "title": "Prostate cancer-associated gene expression alterations determined from needle biopsies.", "abstract": ["PURPOSE To accurately identify gene expression alterations that differentiate neoplastic from normal prostate epithelium using an approach that avoids contamination by unwanted cellular components and is not compromised by acute gene expression changes associated with tumor devascularization and resulting ischemia.   ", "EXPERIMENTAL DESIGN Approximately 3,000 neoplastic and benign prostate epithelial cells were isolated using laser capture microdissection from snap-frozen prostate biopsy specimens provided by 31 patients who subsequently participated in a clinical trial of preoperative chemotherapy.", "cDNA synthesized from amplified total RNA was hybridized to custom-made microarrays composed of 6,200 clones derived from the Prostate Expression Database.", "Expression differences for selected genes were verified using quantitative reverse transcription-PCR.   \n", "RESULTS Comparative analyses identified 954 transcript alterations associated with cancer (q < 0.01%), including 149 differentially expressed genes with no known functional roles.", "Gene expression changes associated with ischemia and surgical removal of the prostate gland were absent.", "Genes up-regulated in prostate cancer were statistically enriched in categories related to cellular metabolism, energy use, signal transduction, and molecular transport.", "Genes down-regulated in prostate cancers were enriched in categories related to immune response, cellular responses to pathogens, and apoptosis.", "A heterogeneous pattern of androgen receptor expression changes was noted.", "In exploratory analyses, androgen receptor down-regulation was associated with a lower probability of cancer relapse after neoadjuvant chemotherapy followed by radical prostatectomy.   \n", "CONCLUSIONS Assessments of tumor phenotypes based on gene expression for treatment stratification and drug targeting of oncogenic alterations may best be ascertained using biopsy-based analyses where the effects of ischemia do not complicate interpretation."], "structured": true}
{"doc_id": 6793674, "title": "Circulating trimethylamine N\u2010oxide and the risk of cardiovascular diseases: a systematic review and meta\u2010analysis of 11 prospective cohort studies", "abstract": ["Circulating trimethylamine N-oxide (TMAO), a canonical metabolite from gut flora, has been related to the risk of cardiovascular disorders.", "However, the association between circulating TMAO and the risk of cardiovascular events has not been quantitatively evaluated.", "We performed a systematic review and meta-analysis of all available cohort studies regarding the association between baseline circulating TMAO and subsequent cardiovascular events.", "Embase and PubMed databases were searched for relevant cohort studies.", "The overall hazard ratios for the developing of cardiovascular events (CVEs) and mortality were extracted.", "Heterogeneity among the included studies was evaluated with Cochran's Q Test and I2 statistics.", "A random-effect model or a fixed-effect model was applied depending on the heterogeneity.", "Subgroup analysis and meta-regression were used to evaluate the source of heterogeneity.", "Among the 11 eligible studies, three reported both CVE and mortality outcome, one reported only CVEs and the other seven provided mortality data only.", "Higher circulating TMAO was associated with a 23% higher risk of CVEs (HR = 1.23, 95% CI: 1.07-1.42, I2 = 31.4%) and a 55% higher risk of all-cause mortality (HR = 1.55, 95% CI: 1.19-2.02, I2 = 80.8%).", "Notably, the latter association may be blunted by potential publication bias, although sensitivity analysis by omitting one study at a time did not significantly change the results.", "Further subgroup analysis and meta-regression did not support that the location of the study, follow-up duration, publication year, population characteristics or the samples of TMAO affect the results significantly.", "Higher circulating TMAO may independently predict the risk of subsequent cardiovascular events and mortality."], "structured": false}
{"doc_id": 6796297, "title": "PDGF-BB secreted by preosteoclasts induces angiogenesis during coupling with osteogenesis", "abstract": ["Osteogenesis during bone modeling and remodeling is coupled with angiogenesis.", "A recent study showed that a specific vessel subtype, strongly positive for CD31 and endomucin (CD31hiEmcnhi), couples angiogenesis and osteogenesis.", "Here, we found that platelet-derived growth factor-BB (PDGF-BB) secreted by preosteoclasts induces CD31hiEmcnhi vessel formation during bone modeling and remodeling.", "Mice with depletion of PDGF-BB in the tartrate-resistant acid phosphatase\u2013positive cell lineage show significantly lower trabecular and cortical bone mass, serum and bone marrow PDGF-BB concentrations, and fewer CD31hiEmcnhi vessels compared to wild-type mice.", "In the ovariectomy (OVX)-induced osteoporotic mouse model, serum and bone marrow levels of PDGF-BB and numbers of CD31hiEmcnhi vessels are significantly lower compared to sham-operated controls.", "Treatment with exogenous PDGF-BB or inhibition of cathepsin K to increase the number of preosteoclasts, and thus the endogenous levels of PDGF-BB, increases CD31hiEmcnhi vessel number and stimulates bone formation in OVX mice.", "Thus, pharmacotherapies that increase PDGF-BB secretion from preosteoclasts offer a new therapeutic target for treating osteoporosis by promoting angiogenesis and thus bone formation."], "structured": false}
{"doc_id": 6807122, "title": "Discovery of endothelial to mesenchymal transition as a source for carcinoma-associated fibroblasts.", "abstract": ["Activated fibroblasts are associated with many different tumors.", "Myofibroblasts, activated fibroblasts, and perivascular mesenchymal cells such as pericytes play a role in cancer progression.", "Many studies suggest that myofibroblasts facilitate tumor growth and cancer progression.", "The source for myofibroblasts and other activated fibroblasts within the tumors is still debated.", "Although de novo activation of quiescent fibroblasts into alpha-smooth muscle actin (alpha SMA)-positive myofibroblasts is one likely source, epithelial to mesenchymal transition and bone marrow recruitment are also evolving as possible mechanisms for the emergence of a heterogeneous population of carcinoma-associated fibroblasts.", "Here, we show that transforming growth factor-beta1 could induce proliferating endothelial cells to undergo a phenotypic conversion into fibroblast-like cells.", "Such endothelial to mesenchymal transition (EndMT) is associated with the emergence of mesenchymal marker fibroblast-specific protein-1 (FSP1) and down-regulation of CD31/PECAM.", "Additionally, we show EndMT in tumors using the B16F10 melanoma model and the Rip-Tag2 spontaneous pancreatic carcinoma model.", "Crossing Tie2-Cre mice with R26Rosa-lox-Stop-lox-LacZ mice allows for irreversible tagging of endothelial cells.", "We provide unequivocal evidence for EndMT at the invasive front of the tumors in these transgenic mice.", "Collectively, our results show that EndMT is a unique mechanism for the accumulation of carcinoma-associated fibroblasts and suggest that antiangiogenic treatment of tumors may have a direct effect in decreasing activated fibroblasts that likely facilitate cancer progression."], "structured": false}
{"doc_id": 6812319, "title": "ERCC1 and MUS81\u2013EME1 promote sister chromatid separation by processing late replication intermediates at common fragile sites during mitosis", "abstract": ["Chromosomal instability (CIN) is a hallmark of tumour initiation and progression.", "Some genomic regions are particularly unstable under replication stress, notably common fragile sites (CFSs) whose rearrangements in tumour cells contribute to cancer development.", "Recent work has shown that the Fanconi anaemia (FANC) pathway plays a role in preventing defective chromosome segregation and CIN under conditions of replication stress.", "Strikingly, FANCD2 is recruited to regions hosting CFSs on metaphase chromosomes.", "To decipher the mechanisms protecting CFSs in G2/M, we searched for proteins that co-localize with FANCD2 on mitotic chromosomes, and identified XPF\u2013ERCC1 and MUS81\u2013EME1, two structure-specific endonucleases.", "We show that depletion of either ERCC1 or MUS81\u2013EME1 affects accurate processing of replication intermediates or under-replicated DNA that persist at CFSs until mitosis.", "Depletion of these endonucleases also leads to an increase in the frequency of chromosome bridges during anaphase that, in turn, favours accumulation of DNA damage in the following G1 phase."], "structured": false}
{"doc_id": 6820680, "title": "Engineered RNA viral synthesis of microRNAs.", "abstract": ["MicroRNAs (miRNAs) are short noncoding RNAs that exert posttranscriptional gene silencing and regulate gene expression.", "In addition to the hundreds of conserved cellular miRNAs that have been identified, miRNAs of viral origin have been isolated and found to modulate both the viral life cycle and the cellular transcriptome.", "Thus far, detection of virus-derived miRNAs has been largely limited to DNA viruses, suggesting that RNA viruses may be unable to exploit this aspect of transcriptional regulation.", "Lack of RNA virus-produced miRNAs has been attributed to the replicative constraints that would incur following RNase III processing of a genomic hairpin.", "To ascertain whether the generation of viral miRNAs is limited to DNA viruses, we investigated whether influenza virus could be designed to deliver functional miRNAs without affecting replication.", "Here, we describe a modified influenza A virus that expresses cellular microRNA-124 (miR-124).", "Insertion of the miR-124 hairpin into an intron of the nuclear export protein transcript resulted in endogenous processing and functional miR-124.", "We demonstrate that a viral RNA genome incorporating a hairpin does not result in segment instability or miRNA-mediated genomic targeting, thereby permitting the virus to produce a miRNA without having a negative impact on viral replication.", "This work demonstrates that RNA viruses can produce functional miRNAs and suggests that this level of transcriptional regulation may extend beyond DNA viruses."], "structured": false}
{"doc_id": 6826100, "title": "The developmental potential of iPSCs is greatly influenced by reprogramming factor selection.", "abstract": ["Induced pluripotent stem cells (iPSCs) are commonly generated by transduction of Oct4, Sox2, Klf4, and Myc (OSKM) into cells.", "Although iPSCs are pluripotent, they frequently exhibit high variation in terms of quality, as measured in mice by chimera contribution and tetraploid complementation.", "Reliably high-quality iPSCs will be needed for future therapeutic applications.", "Here, we show that one major determinant of iPSC quality is the combination of reprogramming factors used.", "Based on tetraploid complementation, we found that ectopic expression of Sall4, Nanog, Esrrb, and Lin28 (SNEL) in mouse embryonic fibroblasts (MEFs) generated high-quality iPSCs more efficiently than other combinations of factors including OSKM.", "Although differentially methylated regions, transcript number of master regulators, establishment of specific superenhancers, and global aneuploidy were comparable between high- and low-quality lines, aberrant gene expression, trisomy of chromosome 8, and abnormal H2A.X deposition were distinguishing features that could potentially also be applicable to human."], "structured": false}
{"doc_id": 6826636, "title": "GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis", "abstract": ["GiardiaDB (http://GiardiaDB.org) and TrichDB (http://TrichDB.org) house the genome databases for Giardia lamblia and Trichomonas vaginalis, respectively, and represent the latest additions to the EuPathDB (http://EuPathDB.org) family of functional genomic databases.", "GiardiaDB and TrichDB employ the same framework as other EuPathDB sites (CryptoDB, PlasmoDB and ToxoDB), supporting fully integrated and searchable databases.", "Genomic-scale data available via these resources may be queried based on BLAST searches, annotation keywords and gene ID searches, GO terms, sequence motifs and other protein characteristics.", "Functional queries may also be formulated, based on transcript and protein expression data from a variety of platforms.", "Phylogenetic relationships may also be interrogated.", "The ability to combine the results from independent queries, and to store queries and query results for future use facilitates complex, genome-wide mining of functional genomic data."], "structured": false}
{"doc_id": 6828370, "title": "A coding-independent function of gene and pseudogene mRNAs regulates tumour biology", "abstract": ["The canonical role of messenger RNA (mRNA) is to deliver protein-coding information to sites of protein synthesis.", "However, given that microRNAs bind to RNAs, we hypothesized that RNAs could possess a regulatory role that relies on their ability to compete for microRNA binding, independently of their protein-coding function.", "As a model for the protein-coding-independent role of RNAs, we describe the functional relationship between the mRNAs produced by the PTEN tumour suppressor gene and its pseudogene PTENP1 and the critical consequences of this interaction.", "We find that PTENP1 is biologically active as it can regulate cellular levels of PTEN and exert a growth-suppressive role.", "We also show that the PTENP1 locus is selectively lost in human cancer.", "We extended our analysis to other cancer-related genes that possess pseudogenes, such as oncogenic KRAS.", "We also demonstrate that the transcripts of protein-coding genes such as PTEN are biologically active.", "These findings attribute a novel biological role to expressed pseudogenes, as they can regulate coding gene expression, and reveal a non-coding function for mRNAs."], "structured": false}
{"doc_id": 6836086, "title": "Identification of a Multicomponent Complex Required for Outer Membrane Biogenesis in Escherichia coli", "abstract": ["Gram-negative bacteria have an outer membrane (OM) that functions as a barrier to protect the cell from toxic compounds such as antibiotics and detergents.", "The OM is a highly asymmetric bilayer composed of phospholipids, glycolipids, and proteins.", "Assembly of this essential organelle occurs outside the cytoplasm in an environment that lacks obvious energy sources such as ATP, and the mechanisms involved are poorly understood.", "We describe the identification of a multiprotein complex required for the assembly of proteins in the OM of Escherichia coli.", "We also demonstrate genetic interactions between genes encoding components of this protein assembly complex and imp, which encodes a protein involved in the assembly of lipopolysaccharides (LPS) in the OM.", "These genetic interactions suggest a role for YfgL, one of the lipoprotein components of the protein assembly complex, in a homeostatic control mechanism that coordinates the overall OM assembly process."], "structured": false}
{"doc_id": 6841927, "title": "Transtheoretical model-based multiple behavior intervention for weight management: effectiveness on a population basis.", "abstract": ["BACKGROUND The increasing prevalence of overweight and obesity underscores the need for evidence-based, easily disseminable interventions for weight management that can be delivered on a population basis.", "The Transtheoretical Model (TTM) offers a promising theoretical framework for multiple behavior weight management interventions.   \n", "METHODS Overweight or obese adults (BMI 25-39.9; n=1277) were randomized to no-treatment control or home-based, stage-matched multiple behavior interventions for up to three behaviors related to weight management at 0, 3, 6, and 9 months.", "All participants were re-assessed at 6, 12, and 24 months.   \n", "RESULTS Significant treatment effects were found for healthy eating (47.5% versus 34.3%), exercise (44.90% versus 38.10%), managing emotional distress (49.7% versus 30.30%), and untreated fruit and vegetable intake (48.5% versus 39.0%) progressing to Action/Maintenance at 24 months.", "The groups differed on weight lost at 24 months.", "Co-variation of behavior change occurred and was much more pronounced in the treatment group, where individuals progressing to Action/Maintenance for a single behavior were 2.5-5 times more likely to make progress on another behavior.", "The impact of the multiple behavior intervention was more than three times that of single behavior interventions.   \n", "CONCLUSIONS This study demonstrates the ability of TTM-based tailored feedback to improve healthy eating, exercise, managing emotional distress, and weight on a population basis.", "The treatment produced a high level of population impact that future multiple behavior interventions can seek to surpass."], "structured": true}
{"doc_id": 6847208, "title": "Autoinduction and signal transduction in the regulation of staphylococcal virulence.", "abstract": ["The accessory genes of Staphylococcus aureus, including those involved in pathogenesis, are controlled by a complex regulatory network that includes at least four two-component systems, one of which, agr, is a quorum sensor, an alternative sigma factor and a large set of transcription factors, including at least two of the superantigen genes, tst and seb.", "These regulatory genes are hypothesized to act in a time- and population density-dependent manner to integrate signals received from the external environment with the internal metabolic machinery of the cell, in order to achieve the production of particular subsets of accessory/virulence factors at the time and in quantities that are appropriate to the needs of the organism at any given location.", "From the standpoint of pathogenesis, the regulatory agenda is presumably tuned to particular sites in the host organism.", "To address this hypothesis, it will be necessary to understand in considerable detail the regulatory interactions among the organism's numerous controlling systems.", "This review is an attempt to integrate a large body of data into the beginnings of a model that will hopefully help to guide research towards a full-scale test."], "structured": false}
{"doc_id": 6853699, "title": "Macrophages in the Pathogenesis of Atherosclerosis", "abstract": ["In atherosclerosis, the accumulation of apolipoprotein B-lipoproteins in the matrix beneath the endothelial cell layer of blood vessels leads to the recruitment of monocytes, the cells of the immune system that give rise to macrophages and dendritic cells.", "Macrophages derived from these recruited monocytes participate in a maladaptive, nonresolving inflammatory response that expands the subendothelial layer due to the accumulation of cells, lipid, and matrix.", "Some lesions subsequently form a necrotic core, triggering acute thrombotic vascular disease, including myocardial infarction, stroke, and sudden cardiac death.", "This Review discusses the central roles of macrophages in each of these stages of disease pathogenesis."], "structured": false}
{"doc_id": 6863070, "title": "Three-dimensional superresolution colocalization of intracellular protein superstructures and the cell surface in live Caulobacter crescentus.", "abstract": ["Recently, single-molecule imaging and photocontrol have enabled superresolution optical microscopy of cellular structures beyond Abbe's diffraction limit, extending the frontier of noninvasive imaging of structures within living cells.", "However, live-cell superresolution imaging has been challenged by the need to image three-dimensional (3D) structures relative to their biological context, such as the cellular membrane.", "We have developed a technique, termed superresolution by power-dependent active intermittency and points accumulation for imaging in nanoscale topography (SPRAIPAINT) that combines imaging of intracellular enhanced YFP (eYFP) fusions (SPRAI) with stochastic localization of the cell surface (PAINT) to image two different fluorophores sequentially with only one laser.", "Simple light-induced blinking of eYFP and collisional flux onto the cell surface by Nile red are used to achieve single-molecule localizations, without any antibody labeling, cell membrane permeabilization, or thiol-oxygen scavenger systems required.", "Here we demonstrate live-cell 3D superresolution imaging of Crescentin-eYFP, a cytoskeletal fluorescent protein fusion, colocalized with the surface of the bacterium Caulobacter crescentus using a double-helix point spread function microscope.", "Three-dimensional colocalization of intracellular protein structures and the cell surface with superresolution optical microscopy opens the door for the analysis of protein interactions in living cells with excellent precision (20-40 nm in 3D) over a large field of view (12 12 \u03bcm)."], "structured": false}
{"doc_id": 6876224, "title": "Overweight prevalence among youth in the United States: Why so many different numbers?", "abstract": ["Several recent publications have presented different estimates for the prevalence of overweight among youth in the United States.", "Prevalence estimates range from 11\u201324%, despite describing the same results from the third National Health and Nutrition Examination Survey (NHANES III).", "This paper discusses the variety and evolution of different overweight prevalence estimates.", "Issues of definition, measurements, criteria selection and comparison groups are considered and implications for estimates of the prevalence of overweight among youth are explored.", "Reference percentiles for body mass index (BMI) from several publications are compared.", "The differences in published estimates from NHANES III are noted and explained."], "structured": false}
{"doc_id": 6896063, "title": "Senescence and aging: the critical roles of p53", "abstract": ["p53 functions as a transcription factor involved in cell-cycle control, DNA repair, apoptosis and cellular stress responses.", "However, besides inducing cell growth arrest and apoptosis, p53 activation also modulates cellular senescence and organismal aging.", "Senescence is an irreversible cell-cycle arrest that has a crucial role both in aging and as a robust physiological antitumor response, which counteracts oncogenic insults.", "Therefore, via the regulation of senescence, p53 contributes to tumor growth suppression, in a manner strictly dependent by its expression and cellular context.", "In this review, we focus on the recent advances on the contribution of p53 to cellular senescence and its implication for cancer therapy, and we will discuss p53\u2019s impact on animal lifespan.", "Moreover, we describe p53-mediated regulation of several physiological pathways that could mediate its role in both senescence and aging."], "structured": false}
{"doc_id": 6903077, "title": "Asymmetric cryo-EM reconstruction of phage MS2 reveals genome structure in situ", "abstract": ["In single-stranded ribonucleic acid (RNA) viruses, virus capsid assembly and genome packaging are intertwined processes.", "Using cryo-electron microscopy and single particle analysis we determined the asymmetric virion structure of bacteriophage MS2, which includes 178 copies of the coat protein, a single copy of the A-protein and the RNA genome.", "This reveals that in situ, the viral RNA genome can adopt a defined conformation.", "The RNA forms a branched network of stem-loops that almost all allocate near the capsid inner surface, while predominantly binding to coat protein dimers that are located in one-half of the capsid.", "This suggests that genomic RNA is highly involved in genome packaging and virion assembly."], "structured": false}
{"doc_id": 6910577, "title": "Harnessing transposons for cancer gene discovery", "abstract": ["Recently, it has become possible to mobilize the Tc1/mariner transposon, Sleeping Beauty (SB), in mouse somatic cells at frequencies high enough to induce cancer.", "Tumours result from SB insertional mutagenesis of cancer genes, thus facilitating the identification of the genes and signalling pathways that drive tumour formation.", "A conditional SB transposition system has also been developed that makes it possible to limit where SB mutagenesis occurs, providing a means to selectively model many types of human cancer.", "SB mutagenesis has already identified a large collection of known cancer genes in addition to a plethora of new candidate cancer genes and potential drug targets."], "structured": false}
{"doc_id": 6913227, "title": "MicroRNA-Containing T-Regulatory-Cell-Derived Exosomes Suppress Pathogenic T Helper 1 Cells", "abstract": ["Foxp3(+) T regulatory (Treg) cells prevent inflammatory disease but the mechanistic basis of suppression is not understood completely.", "Gene silencing by RNA interference can act in a cell-autonomous and non-cell-autonomous manner, providing mechanisms of intercellular regulation.", "Here, we demonstrate that non-cell-autonomous gene silencing, mediated by miRNA-containing exosomes, is a mechanism employed by Treg cells to suppress T-cell-mediated disease.", "Treg cells transferred microRNAs (miRNA) to various immune cells, including T helper 1 (Th1) cells, suppressing Th1 cell proliferation and cytokine secretion.", "Use of Dicer-deficient or Rab27a and Rab27b double-deficient Treg cells to disrupt miRNA biogenesis or the exosomal pathway, respectively, established a requirement for miRNAs and exosomes for Treg-cell-mediated suppression.", "Transcriptional analysis and miRNA inhibitor studies showed that exosome-mediated transfer of Let-7d from Treg cell to Th1 cells contributed to suppression and prevention of systemic disease.", "These studies reveal a mechanism of Treg-cell-mediated suppression mediated by miRNA-containing exosomes."], "structured": false}
{"doc_id": 6917133, "title": "Estimating risk curves for first-degree relatives of patients with Alzheimer\u2019s disease: The REVEAL study", "abstract": ["Purpose: The REVEAL study is a randomized, controlled study of the psychological and behavioral impact of APOE disclosure in a risk assessment protocol provided to first degree relatives of patients with Alzheimer\u2019s disease.", "The protocol presents risk information as cumulative incidence curves.", "This article describes how these curves were estimated.", "Methods: Curves were calculated using Bayes\u2019 rule to compute the posterior survival curves incorporating APOE information.", "Results: A combination of survival data from the MIRAGE study and gender- and age-specific APOE odds ratios were used to create risk curves for males and females within each of the 6 APOE genotypes.", "Conclusion: Utilizing comparative genotype relative risk information and survival data from family studies, estimates of gender-, age-, and genotype-specific risk can be generated for use in a risk assessment research study that features genotype disclosure."], "structured": false}
{"doc_id": 6923795, "title": "Up-regulation of endothelial nitric-oxide synthase by endothelium-derived hyperpolarizing factor involves mitogen-activated protein kinase and protein kinase C signaling pathways.", "abstract": ["Cytochrome P450 (P450)-dependent metabolites of arachidonic acid, the epoxyeicosatrienoic acids (EETs), are proposed to be endothelium-derived hyperpolarizing factors (EDHF) that affect vascular tone; however, the effects of EDHF on endothelial-derived nitric oxide biosynthesis remain unknown.", "We examined the regulation of endothelial nitric-oxide synthase (eNOS) by EDHF and investigated the relevant signaling pathways involved.", "The P450 epoxygenases CYP102 F87V mutant, CYP2C11-CYPOR, and CYP2J2 were transfected into cultured bovine aortic endothelial cells, and the effects of endogenously formed or exogenously applied EETs on eNOS expression and activity were assessed.", "Transfection with the P450 epoxygenases led to increased eNOS protein expression, an effect that was attenuated by cotreatment with the P450 inhibitor 17-ODYA.", "Northern analysis demonstrated that P450 transfection led to increased eNOS mRNA levels consistent with an effect at the pretranslational level.", "P450 epoxygenase transfection resulted in increased eNOS activity as measured by the conversion of L-arginine to L-citrulline.", "Addition of synthetic EETs (50-200 nM) to the culture media also increased eNOS expression and activity.", "Treatment with mitogen-activated protein kinase (MAPK), MAPK kinase, and protein kinase C inhibitors apigenin, 2'-amino-3'-methoxyflavone (PD98059), and 1-(5-isoquinolinesulfonyl)-2-methylpiperazine (H-7), respectively, significantly inhibited the effects of P450 transfection on eNOS expression.", "Overexpression of P450 epoxygenases or addition of synthetic EETs increased Thr495 phosphorylation of eNOS, an effect that was inhibited by both apigenin and PD98059.", "Overexpression of P450 epoxygenases in rats resulted in increased aortic eNOS expression, providing direct evidence that EDHF can influence vascular eNOS levels in vivo.", "Based on this data, we conclude that EDHF up-regulates eNOS via activation of MAPK and protein kinase C signaling pathways."], "structured": false}
{"doc_id": 6923961, "title": "Prostaglandin E2 promotes intestinal tumor growth via DNA methylation", "abstract": ["Although aberrant DNA methylation is considered to be one of the key ways by which tumor-suppressor and DNA-repair genes are silenced during tumor initiation and progression, the mechanisms underlying DNA methylation alterations in cancer remain unclear.", "Here we show that prostaglandin E(2) (PGE(2)) silences certain tumor-suppressor and DNA-repair genes through DNA methylation to promote tumor growth.", "These findings uncover a previously unrecognized role for PGE(2) in the promotion of tumor progression."], "structured": false}
{"doc_id": 6936141, "title": "Nef is physically recruited into the immunological synapse and potentiates T cell activation early after TCR engagement.", "abstract": ["The HIV-1 protein Nef enhances viral pathogenicity and accelerates disease progression in vivo.", "Nef potentiates T cell activation by an unknown mechanism, probably by optimizing the intracellular environment for HIV replication.", "Using a new T cell reporter system, we have found that Nef more than doubles the number of cells expressing the transcription factors NF-kappaB and NFAT after TCR stimulation.", "This Nef-induced priming of TCR signaling pathways occurred independently of calcium signaling and involved a very proximal step before protein kinase C activation.", "Engagement of the TCR by MHC-bound Ag triggers the formation of the immunological synapse by recruiting detergent-resistant membrane microdomains, termed lipid rafts.", "Approximately 5-10% of the total cellular pool of Nef is localized within lipid rafts.", "Using confocal and real-time microscopy, we found that Nef in lipid rafts was recruited into the immunological synapse within minutes after Ab engagement of the TCR/CD3 and CD28 receptors.", "This recruitment was dependent on the N-terminal domain of Nef encompassing its myristoylation.", "Nef did not increase the number of cell surface lipid rafts or immunological synapses.", "Recently, studies have shown a specific interaction of Nef with an active subpopulation of p21-activated kinase-2 found only in the lipid rafts.", "Thus, the corecruitment of Nef and key cellular partners (e.g., activated p21-activated kinase-2) into the immunological synapse may underlie the increased frequency of cells expressing transcriptionally active forms of NF-kappaB and NFAT and the resultant changes in T cell activation."], "structured": false}
{"doc_id": 6944800, "title": "Microenvironmental regulation of tumor progression and metastasis", "abstract": ["Cancers develop in complex tissue environments, which they depend on for sustained growth, invasion and metastasis.", "Unlike tumor cells, stromal cell types within the tumor microenvironment (TME) are genetically stable and thus represent an attractive therapeutic target with reduced risk of resistance and tumor recurrence.", "However, specifically disrupting the pro-tumorigenic TME is a challenging undertaking, as the TME has diverse capacities to induce both beneficial and adverse consequences for tumorigenesis.", "Furthermore, many studies have shown that the microenvironment is capable of normalizing tumor cells, suggesting that re-education of stromal cells, rather than targeted ablation per se, may be an effective strategy for treating cancer.", "Here we discuss the paradoxical roles of the TME during specific stages of cancer progression and metastasis, as well as recent therapeutic attempts to re-educate stromal cells within the TME to have anti-tumorigenic effects."], "structured": false}
{"doc_id": 6945285, "title": "Bezafibrate in men with lower extremity arterial disease: randomised controlled trial.", "abstract": ["OBJECTIVE To assess the effect of bezafibrate on the risk of coronary heart disease and stroke in men with lower extremity arterial disease.   \n", "DESIGN Double blind placebo controlled randomised trial.   \n", "SETTING 85 general practices and nine hospital vascular clinics.   \n", "PARTICIPANTS 1568 men, mean age 68.2 years (range 35 to 92) at recruitment.   \n", "INTERVENTIONS Bezafibrate 400 mg daily (783 men) or placebo (785 men).   \n", "MAIN OUTCOME MEASURES Combination of coronary heart disease and of stroke.", "All coronary events, fatal and non-fatal coronary events separately, and strokes alone (secondary end points).   \n", "RESULTS Bezafibrate did not reduce the incidence of coronary heart disease and stroke.", "There were 150 and 160 events in the active and placebo groups respectively (relative risk 0.96, 95% confidence interval 0.76 to 1.21).", "There were 90 and 111 major coronary events in the active and placebo groups respectively (0.81, 0.60 to 1.08), of which 64 and 65 were fatal (0.95, 0.66 to 1.37) and 26 and 46 non-fatal (0.60, 0.36 to 0.99).", "Beneficial effects on non-fatal events were greatest in men aged <65 years at entry, in whom benefit was also seen for all coronary events (0.38, 0.20 to 0.72).", "There were no significant effects in older men.", "There were 60 strokes in those on active treatment and 49 in those on placebo (1.34, 0.80 to 2.01).", "There were 204 and 195 deaths from all causes in the two groups respectively (1.03, 0.83 to 1.26).", "Bezafibrate reduced the severity of intermittent claudication for up to three years.   \n", "CONCLUSIONS Bezafibrate has no effect on the incidence of coronary heart disease and of stroke combined but may reduce the incidence of non-fatal coronary events, particularly in those aged <65 years at entry, in whom all coronary events may also be reduced."], "structured": true}
{"doc_id": 6945691, "title": "The modulation of human natural killer cell activity by prostaglandins.", "abstract": ["Prostaglandins (PGs) have been implicated as a regulator of tumor growth in mice and humans.", "Since natural killer cell (NK) cytotoxicity may be an important component of immune surveillance against cancer, it is appropriate to study whether the amount of PGs produced by tumors may be sufficient to suppress NK activity.", "Accordingly, the effect of various PGs on the NK activity of human peripheral mononuclear cells was investigated.", "The percentage cytotoxicity was measured by the release of Cr51 from labeled K562 and other target cells.", "At very high concentrations of PG (10(-6) M), suppression was seen with PGE2, PGD2, PGA2, and PGF2 alpha.", "However, at concentrations of PG in the physiologic range (10(-8) M), significant suppression was seen with PGE2 and PGD2 only.", "The percentage suppression with PGE2 ranged from 77% to 9.5% over a range of concentrations from 10(-5) to 10(-9) M (45% at 10(-8) M).", "Significant suppression was observed at 10(-8) M PGE2 with 4 different targets and at effector:target ratios varying from 50:1 to 12.5:1.", "To assess whether the suppressive effect of PGE2 was directed at the effector and/or target cell, K562 cells or effector cells were pretreated with PGE2.", "Significant suppression was seen with effector cell pretreatment but not with target cell pretreatment.", "Finally, the suppressive effects of supernatants obtained from tumor cell lines (polyoma virus-transformed murine fibroblast cell line, PY3T3) was determined.", "The marked suppressive effect of the supernatant could be attributed to its content of PGE.", "Thus, it appears that the production of PGE by tumor cells may be an important modulator of human NK activity."], "structured": false}
{"doc_id": 6947286, "title": "Association analysis between anterior-pharynx defective-1 genes polymorphisms and Alzheimer's disease.", "abstract": ["Recent biological studies indicate the importance of anterior-pharynx defective-1 (APH-1) proteins in Alzheimer's disease (AD) pathogenesis.", "We scanned APH-1 genes for the presence of sequence variations by denaturing high performance liquid chromatography and analyzed their distribution in an Italian sample of 113 AD patients and 132 controls.", "We found six different polymorphisms: three of them, all in APH-1b, predict an aminoacid substitution (T27I, V199L and F217L); the others are either silent or in non-coding regions.", "None of them is significantly associated with the disease; data stratification by the apolipoprotein E epsilon4 carrier status show a trend for coexistence of the transversion c+651T>G (F217L) with the epsilon4 allele.", "Our data suggest that polymorphisms in APH-1a/b coding regions are not linked with higher risk for sporadic AD in our Italian population sample."], "structured": false}
{"doc_id": 6948886, "title": "Dynamic epigenetic regulation of glioblastoma tumorigenicity through LSD1 modulation of MYC expression.", "abstract": ["The available evidence suggests that the lethality of glioblastoma is driven by small subpopulations of cells that self-renew and exhibit tumorigenicity.", "It remains unclear whether tumorigenicity exists as a static property of a few cells or as a dynamically acquired property.", "We used tumor-sphere and xenograft formation as assays for tumorigenicity and examined subclones isolated from established and primary glioblastoma lines.", "Our results indicate that glioblastoma tumorigenicity is largely deterministic, yet the property can be acquired spontaneously at low frequencies.", "Further, these dynamic transitions are governed by epigenetic reprogramming through the lysine-specific demethylase 1 (LSD1).", "LSD depletion increases trimethylation of histone 3 lysine 4 at the avian myelocytomatosis viral oncogene homolog (MYC) locus, which elevates MYC expression.", "MYC, in turn, regulates oligodendrocyte lineage transcription factor 2 (OLIG2), SRY (sex determining region Y)-box 2 (SOX2), and POU class 3 homeobox 2 (POU3F2), a core set of transcription factors required for reprogramming glioblastoma cells into stem-like states.", "Our model suggests epigenetic regulation of key transcription factors governs transitions between tumorigenic states and provides a framework for glioblastoma therapeutic development."], "structured": false}
{"doc_id": 6955746, "title": "Auditory Cortex Tracks Both Auditory and Visual Stimulus Dynamics Using Low-Frequency Neuronal Phase Modulation", "abstract": ["Integrating information across sensory domains to construct a unified representation of multi-sensory signals is a fundamental characteristic of perception in ecological contexts.", "One provocative hypothesis deriving from neurophysiology suggests that there exists early and direct cross-modal phase modulation.", "We provide evidence, based on magnetoencephalography (MEG) recordings from participants viewing audiovisual movies, that low-frequency neuronal information lies at the basis of the synergistic coordination of information across auditory and visual streams.", "In particular, the phase of the 2-7 Hz delta and theta band responses carries robust (in single trials) and usable information (for parsing the temporal structure) about stimulus dynamics in both sensory modalities concurrently.", "These experiments are the first to show in humans that a particular cortical mechanism, delta-theta phase modulation across early sensory areas, plays an important \"active\" role in continuously tracking naturalistic audio-visual streams, carrying dynamic multi-sensory information, and reflecting cross-sensory interaction in real time."], "structured": false}
{"doc_id": 6957332, "title": "The diagnosis and management of gastro-oesophageal reflux in infants.", "abstract": ["Gastro-oesophageal reflux (GOR) and gastro-oesophageal reflux disease (GORD) occur frequently during the first months of life.", "Gastro-oesophageal reflux may be a primary gastro-intestinal motility disorder, but it may also be secondary to other conditions such as cow's milk protein allergy.", "Objective diagnosis can be difficult because there may be absence of correlation between history, results of pH monitoring and histology.", "Severe GORD may cause minor symptoms, and minor GOR may cause severe symptoms.", "Several different therapeutic interventions exist.", "Simply stated, thickened formula reduces regurgitation and alginates and proton pump inhibitors can be used to decrease acid GOR, depending on the severity of the GORD.", "Efficacy data of prokinetic drugs are either lacking or disappointing.", "Regarding side-effects, interest has been focused on cisapride, although other molecules have similar effects.", "Long-term side-effects such as the nutritional consequence of therapeutic management have been insufficiently studied, especially for the acid-reducing molecules."], "structured": false}
{"doc_id": 6961811, "title": "Increased sensitivity of antigen-experienced T cells through the enrichment of oligomeric T cell receptor complexes.", "abstract": ["Although memory T cells respond more vigorously to stimulation and they are more sensitive to low doses of antigen than naive T cells, the molecular basis of this increased sensitivity remains unclear.", "We have previously shown that the T cell receptor (TCR) exists as different-sized oligomers on the surface of resting T cells and that large oligomers are preferentially activated in response to low antigen doses.", "Through biochemistry and electron microscopy, we now showed that previously stimulated and memory T cells have more and larger TCR oligomers at the cell surface than their naive counterparts.", "Reconstitution of cells and mice with a point mutant of the CD3\u03b6 subunit, which impairs TCR oligomer formation, demonstrated that the increased size of TCR oligomers was directly responsible for the increased sensitivity of antigen-experienced T cells.", "Thus, we propose that an \"avidity maturation\" mechanism underlies T cell antigenic memory."], "structured": false}
{"doc_id": 6962472, "title": "G*Power 3: a flexible statistical power analysis program for the social, behavioral, and biomedical sciences.", "abstract": ["G*Power (Erdfelder, Faul, & Buchner, 1996) was designed as a general stand-alone power analysis program for statistical tests commonly used in social and behavioral research.", "G*Power 3 is a major extension of, and improvement over, the previous versions.", "It runs on widely used computer platforms (i.e., Windows XP, Windows Vista, and Mac OS X 10.4) and covers many different statistical tests of the t, F, and chi2 test families.", "In addition, it includes power analyses for z tests and some exact tests.", "G*Power 3 provides improved effect size calculators and graphic options, supports both distribution-based and design-based input modes, and offers all types of power analyses in which users might be interested.", "Like its predecessors, G*Power 3 is free."], "structured": false}
{"doc_id": 6969753, "title": "Dynamic interactions of cortactin and membrane type 1 matrix metalloproteinase at invadopodia: defining the stages of invadopodia formation and function.", "abstract": ["Metastatic tumor cells that actively migrate and invade surrounding tissues rely on invadopodia to degrade extracellular matrix (ECM) barriers.", "Invadopodia are membrane protrusions that localize enzymes required for ECM degradation.", "Little is known about the formation, function, and regulation of invadopodia.", "Here, we show that invadopodia have two distinct aspects: (a) structural for organizing the cellular actin cytoskeleton to form membrane protrusions and (b) functional for using proteolytic enzyme(s) for ECM degradation.", "Small interfering RNA (siRNA) inhibition established that organization of invadopodia structure requires cortactin, whereas protease inhibitor studies identified membrane type 1 matrix metalloproteinase (MT1-MMP) as the key invadopodial enzyme responsible for gelatin matrix degradation in the breast carcinoma cell line MDA-MB-231.", "The inhibition of invadopodial structure assembly by cortactin depletion resulted in a block of matrix degradation due to failure of invadopodia formation.", "Either protease inhibition or MT1-MMP siRNA depletion moderately decreased the formation of invadopodial structures that were identified as actin-cortactin accumulations at the ventral cell membrane adherent to matrix.", "The invadopodia that were able to form upon MT1-MMP inhibition or depletion retained actin-cortactin accumulations but were unable to degrade matrix.", "Examination of cells at different time points as well as live-cell imaging revealed four distinct invadopodial stages: membrane cortactin aggregation at membranes adherent to matrix, MT1-MMP accumulation at the region of cortactin accumulation, matrix degradation at the invadopodia region, and subsequent cortactin dissociation from the area of continued MT1-MMP accumulation associated with foci of degraded matrix.", "Based on these results, we propose a stepwise model of invadopodia formation and function."], "structured": false}
{"doc_id": 6974477, "title": "PEP-FOLD: an updated de novo structure prediction server for both linear and disulfide bonded cyclic peptides", "abstract": ["In the context of the renewed interest of peptides as therapeutics, it is important to have an on-line resource for 3D structure prediction of peptides with well-defined structures in aqueous solution.", "We present an updated version of PEP-FOLD allowing the treatment of both linear and disulphide bonded cyclic peptides with 9-36 amino acids.", "The server makes possible to define disulphide bonds and any residue-residue proximity under the guidance of the biologists.", "Using a benchmark of 34 cyclic peptides with one, two and three disulphide bonds, the best PEP-FOLD models deviate by an average RMS of 2.75 \u00c5 from the full NMR structures.", "Using a benchmark of 37 linear peptides, PEP-FOLD locates lowest-energy conformations deviating by 3 \u00c5 RMS from the NMR rigid cores.", "The evolution of PEP-FOLD comes as a new on-line service to supersede the previous server.", "The server is available at: http://bioserv.rpbs.univ-paris-diderot.fr/PEP-FOLD."], "structured": false}
{"doc_id": 6985854, "title": "Discrimination of speech stimuli based on neuronal response phase patterns depends on acoustics but not comprehension.", "abstract": ["Speech stimuli give rise to neural activity in the listener that can be observed as waveforms using magnetoencephalography.", "Although waveforms vary greatly from trial to trial due to activity unrelated to the stimulus, it has been demonstrated that spoken sentences can be discriminated based on theta-band (3-7 Hz) phase patterns in single-trial response waveforms.", "Furthermore, manipulations of the speech signal envelope and fine structure that reduced intelligibility were found to produce correlated reductions in discrimination performance, suggesting a relationship between theta-band phase patterns and speech comprehension.", "This study investigates the nature of this relationship, hypothesizing that theta-band phase patterns primarily reflect cortical processing of low-frequency (<40 Hz) modulations present in the acoustic signal and required for intelligibility, rather than processing exclusively related to comprehension (e.g., lexical, syntactic, semantic).", "Using stimuli that are quite similar to normal spoken sentences in terms of low-frequency modulation characteristics but are unintelligible (i.e., their time-inverted counterparts), we find that discrimination performance based on theta-band phase patterns is equal for both types of stimuli.", "Consistent with earlier findings, we also observe that whereas theta-band phase patterns differ across stimuli, power patterns do not.", "We use a simulation model of the single-trial response to spoken sentence stimuli to demonstrate that phase-locked responses to low-frequency modulations of the acoustic signal can account not only for the phase but also for the power results.", "The simulation offers insight into the interpretation of the empirical results with respect to phase-resetting and power-enhancement models of the evoked response."], "structured": false}
{"doc_id": 6993046, "title": "Breathing more with weaker respiratory muscles in pulmonary arterial hypertension.", "abstract": ["Exertional fatigue and dyspnoea limit the daily activities of patients with pulmonary arterial hypertension 1.", "These symptoms are usually explained by the inability of the overloaded right ventricle to perfuse the lungs and to adapt systemic oxygen delivery to oxygen demand.", "Accordingly, pulmonary hypertension patients present with reductions in peak oxygen uptake, anaerobic threshold, oxygen pulse, ventilatory efficiency and 6-min walk distance 2\u20138.", "This ergospirometric profile is strikingly similar to that of congestive heart failure 8\u201312, further supporting the notion of impaired cardiac output adaptation to peripheral oxygen requirements as the main cause of decreased exercise capacity.", "However, in both pulmonary hypertension and heart failure, ergospirometric variables and walk distances are better correlated to functional class and prognosis than to haemodynamic function 3, 6, 7, 10\u201312.", "In addition, impaired skeletal muscle function has been repeatedly reported in heart failure, fuelling a \u201cmuscle hypothesis\u201d relating dyspnoea and fatigue symptoms to skeletal muscle metaboreceptor and/or ergoreceptor reflexes 13.", "The muscle hypothesis implies a persistent sympathetic nervous system activation, which has indeed been shown to occur in heart failure 14 and also, more recently, in pulmonary hypertension 15.", "Until now, there have been no studies on skeletal muscle function in pulmonary arterial hypertension.  ", "In the present issue of the European Respiratory Journal , Meyer et al. 16 report data suggesting that respiratory muscle strength is decreased in pulmonary arterial hypertension.", "In a prospective study on 37 patients with idiopathic pulmonary hypertension, significant decreases in maximal inspiratory (MIP) and expiratory pressures (MEP) were measured, together with an increased mouth occlusion pressure within first 0.1 s of inspiration ( P 0.1), suggesting inadequate muscle \u2026"], "structured": false}
{"doc_id": 7005276, "title": "Acetic Acid Activates the AMP-Activated Protein Kinase Signaling Pathway to Regulate Lipid Metabolism in Bovine Hepatocytes", "abstract": ["The effect of acetic acid on hepatic lipid metabolism in ruminants differs significantly from that in monogastric animals.", "Therefore, the aim of this study was to investigate the regulation mechanism of acetic acid on the hepatic lipid metabolism in dairy cows.", "The AMP-activated protein kinase (AMPK) signaling pathway plays a key role in regulating hepatic lipid metabolism.", "In vitro, bovine hepatocytes were cultured and treated with different concentrations of sodium acetate (neutralized acetic acid) and BML-275 (an AMPK\u03b1 inhibitor).", "Acetic acid consumed a large amount of ATP, resulting in an increase in AMPK\u03b1 phosphorylation.", "The increase in AMPK\u03b1 phosphorylation increased the expression and transcriptional activity of peroxisome proliferator-activated receptor \u03b1, which upregulated the expression of lipid oxidation genes, thereby increasing lipid oxidation in bovine hepatocytes.", "Furthermore, elevated AMPK\u03b1 phosphorylation reduced the expression and transcriptional activity of the sterol regulatory element-binding protein 1c and the carbohydrate responsive element-binding protein, which reduced the expression of lipogenic genes, thereby decreasing lipid biosynthesis in bovine hepatocytes.", "In addition, activated AMPK\u03b1 inhibited the activity of acetyl-CoA carboxylase.", "Consequently, the triglyceride content in the acetate-treated hepatocytes was significantly decreased.", "These results indicate that acetic acid activates the AMPK\u03b1 signaling pathway to increase lipid oxidation and decrease lipid synthesis in bovine hepatocytes, thereby reducing liver fat accumulation in dairy cows."], "structured": false}
{"doc_id": 7011850, "title": "Unawareness of hypoglycaemia and inadequate hypoglycaemic counterregulation: no causal relation with diabetic autonomic neuropathy.", "abstract": ["OBJECTIVE To examine the traditional view that unawareness of hypoglycaemia and inadequate hypoglycaemic counterregulation in insulin dependent diabetes mellitus are manifestations of autonomic neuropathy.   \n", "DESIGN Perspective assessment of unawareness of hypoglycaemia and detailed assessment of autonomic neuropathy in patients with insulin dependent diabetes according to the adequacy of their hypoglycaemic counterregulation.   \n", "SETTING One routine diabetic unit in a university teaching hospital.   \n", "PATIENTS 23 Patients aged 21-52 with insulin dependent diabetes mellitus (seven with symptoms suggesting autonomic neuropathy, nine with a serious clinical problem with hypoglycaemia, and seven without symptoms of autonomic neuropathy and without problems with hypoglycaemia) and 10 controls with a similar age distribution, without a personal or family history of diabetes.   \n", "MAIN OUTCOME MEASURES Presence of autonomic neuropathy as assessed with a test of the longest sympathetic fibres (acetylcholine sweatspot test), a pupil test, and a battery of seven cardiovascular autonomic function tests; adequacy of hypoglycaemic glucose counterregulation during a 40 mU/kg/h insulin infusion test; history of unawareness of hypoglycaemia; and response of plasma pancreatic polypeptide during hypoglycaemia, which depends on an intact and responding autonomic innervation of the pancreas.   \n", "RESULTS There was little evidence of autonomic neuropathy in either the 12 diabetic patients with a history of unawareness of hypoglycaemia or the seven patients with inadequate hypoglycaemic counterregulation.", "By contrast, in all seven patients with clear evidence of autonomic neuropathy there was no history of unawareness of hypoglycaemia and in six out of seven there was adequate hypoglycaemic counterregulation.", "Unawareness of hypoglycaemia and inadequate hypoglycaemic counterregulation were significantly associated (p less than 0.01).", "The response of plasma pancreatic polypeptide in the diabetic patients with adequate counterregulation but without autonomic neuropathy was not significantly different from that of the controls (change in plasma pancreatic polypeptide 226.8 v 414 pmol/l).", "The patients with autonomic neuropathy had a negligible plasma pancreatic polypeptide response (3.7 pmol/l), but this response was also blunted in the patients with inadequate hypoglycaemic counterregulation (72.4 pmol/l) compared with that of the controls (p less than 0.05).   \n", "CONCLUSIONS Unawareness of hypoglycaemia and inadequate glucose counterregulation during hypoglycaemia are related to each other but are not due to autonomic neuropathy.", "The blunted plasma pancreatic polypeptide responses of the patients with inadequate hypoglycaemic counterregulation may reflect diminished autonomic activity consequent upon reduced responsiveness of a central glucoregulatory centre, rather than classical autonomic neuropathy."], "structured": true}
{"doc_id": 7020505, "title": "Genetic Abnormalities in Chronic Lymphocytic Leukemia: Where We Are and Where We Go", "abstract": ["Chromosomal abnormalities in chronic lymphocytic leukemia (CLL) are detected in up to 80% of patients.", "Among them, deletions of 11q, 13q, 17p, and trisomy 12 have a known prognostic value and play an important role in CLL pathogenesis and evolution, determining patients outcome and therapeutic strategies.", "Standard methods used to identify these genomic aberrations include both conventional G-banding cytogenetics (CGC) and fluorescence in situ hybridization (FISH).", "Although FISH analyses have been implemented as the gold standard, CGC allows the identification of chromosomal translocations and complex karyotypes, the latest associated with poor outcome.", "Genomic arrays have a higher resolution that allows the detection of cryptic abnormalities, although these have not been fully implemented in routine laboratories.", "In the last years, next generation sequencing (NGS) methods have identified a wide range of gene mutations (e.g., TP53, NOTCH1, SF3B1, and BIRC3) which have improved our knowledge about CLL development, allowing us to refine both the prognostic subgroups and better therapeutic strategies.", "Clonal evolution has also recently arisen as a key point in CLL, integrating cytogenetic alterations and mutations in a dynamic model that improve our understanding about its clinical course and relapse."], "structured": false}
{"doc_id": 7028976, "title": "Epidermal growth factor receptor expression identifies functionally and molecularly distinct tumor-initiating cells in human glioblastoma multiforme and is required for gliomagenesis.", "abstract": ["Epidermal growth factor receptor (EGFR) is a known diagnostic and, although controversial, prognostic marker of human glioblastoma multiforme (GBM).", "However, its functional role and biological significance in GBM remain elusive.", "Here, we show that multiple GBM cell subpopulations could be purified from the specimens of patients with GBM and from cancer stem cell (CSC) lines based on the expression of EGFR and of other putative CSC markers.", "All these subpopulations are molecularly and functionally distinct, are tumorigenic, and need to express EGFR to promote experimental tumorigenesis.", "Among them, EGFR-expressing tumor-initiating cells (TIC) display the most malignant functional and molecular phenotype.", "Accordingly, modulation of EGFR expression by gain-of-function and loss-of-function strategies in GBM CSC lines enhances and reduces their tumorigenic ability, respectively, suggesting that EGFR plays a fundamental role in gliomagenesis.", "These findings open up the possibility of new therapeutically relevant scenarios, as the presence of functionally heterogeneous EGFR(pos) and EGFR(neg) TIC subpopulations within the same tumor might affect clinical response to treatment."], "structured": false}
{"doc_id": 7029990, "title": "Stress-induced apoptosis associated with null mutation of ADAR1 RNA editing deaminase gene.", "abstract": ["One type of RNA editing involves the conversion of adenosine residues into inosine in double-stranded RNA through the action of adenosine deaminases acting on RNA (ADAR).", "A-to-I RNA editing of the coding sequence could result in synthesis of proteins not directly encoded in the genome.", "ADAR edits also non-coding sequences of target RNAs, such as introns and 3'-untranslated regions, which may affect splicing, translation, and mRNA stability.", "Three mammalian ADAR gene family members (ADAR1-3) have been identified.", "Here we investigated phenotypes of mice homozygous for ADAR1 null mutation.", "Although live ADAR1-/- embryos with normal gross appearance could be recovered up to E11.5, widespread apoptosis was detected in many tissues.", "Fibroblasts derived from ADAR1-/- embryos were also prone to apoptosis induced by serum deprivation.", "Our results demonstrate an essential requirement for ADAR1 in embryogenesis and suggest that it functions to promote survival of numerous tissues by editing one or more double-stranded RNAs required for protection against stress-induced apoptosis."], "structured": false}
{"doc_id": 7034001, "title": "Outcome of multipair donor kidney exchange by a web-based algorithm.", "abstract": ["Donor kidney exchange is an established method to overcome incompatibility of donor-recipient pairs (DRP).", "A computerized algorithm was devised to exchange donor kidney and was tested in a multicenter setting.", "The algorithm was made according to the consensus of participating centers.", "It makes all possible exchange combinations not only between two incompatible DRP but also circularly among three DRP and selects an optimum set of exchange combinations, considering several factors that can affect the outcome of the exchanged transplant.", "The algorithm was implemented as a web-based program, and matching was performed five times.", "Fifty-three DRP were enrolled from five transplant centers.", "The numbers of DRP that were enrolled in each matching were 38 (25:13), 39 (34:5), 33 (31:2), 32 (28:4), and 34 (30:4) (carryover:newcomer).", "The numbers of generated exchange combinations were 4:11, 3:17, 2:12, 2:3, and 2:3 (two-pair exchange:three-pair exchange), and the numbers of DRP in selected exchange combinations were six, 12, six, five, and four in each matching.", "The numbers of DRP with blood type O recipient or AB donor were five and one, respectively, in selected exchange combinations.", "Six DRP of two-pair exchange combinations and six DRP of three-pair exchange combinations underwent transplantation successfully.", "Computerized algorithm of donor kidney exchange was tried not only between two incompatible DRP but also circularly among three DRP.", "It showed that the algorithm has potential to improve the outcome of donor kidney exchange, especially for disadvantaged DRP with blood type O recipients or AB donors."], "structured": false}
{"doc_id": 7036529, "title": "Light Activation of Channelrhodopsin-2 in Excitable Cells of Caenorhabditis elegans Triggers Rapid Behavioral Responses", "abstract": ["For studying the function of specific neurons in their native circuitry, it is desired to precisely control their activity.", "This often requires dissection to allow accurate electrical stimulation or neurotransmitter application , and it is thus inherently difficult in live animals, especially in small model organisms.", "Here, we employed channelrhodopsin-2 (ChR2), a directly light-gated cation channel from the green alga Chlamydomonas reinhardtii, in excitable cells of the nematode Caenorhabditis elegans, to trigger specific behaviors, simply by illumination.", "Channelrhodopsins are 7-transmembrane-helix proteins that resemble the light-driven proton pump bacteriorhodopsin , and they also utilize the chromophore all-trans retinal, but to open an intrinsic cation pore.", "In muscle cells, light-activated ChR2 evoked strong, simultaneous contractions, which were reduced in the background of mutated L-type, voltage-gated Ca2+-channels (VGCCs) and ryanodine receptors (RyRs).", "Electrophysiological analysis demonstrated rapid inward currents that persisted as long as the illumination.", "When ChR2 was expressed in mechanosensory neurons, light evoked withdrawal behaviors that are normally elicited by mechanical stimulation.", "Furthermore, ChR2 enabled activity of these neurons in mutants lacking the MEC-4/MEC-10 mechanosensory ion channel .", "Thus, specific neurons or muscles expressing ChR2 can be quickly and reversibly activated by light in live and behaving, as well as dissected, animals."], "structured": false}
{"doc_id": 7039855, "title": "Neuronal activity regulates remyelination via glutamate signalling to oligodendrocyte progenitors", "abstract": ["Myelin regeneration can occur spontaneously in demyelinating diseases such as multiple sclerosis (MS).", "However, the underlying mechanisms and causes of its frequent failure remain incompletely understood.", "Here we show, using an in-vivo remyelination model, that demyelinated axons are electrically active and generate de novo synapses with recruited oligodendrocyte progenitor cells (OPCs), which, early after lesion induction, sense neuronal activity by expressing AMPA (\u03b1-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid)/kainate receptors.", "Blocking neuronal activity, axonal vesicular release or AMPA receptors in demyelinated lesions results in reduced remyelination.", "In the absence of neuronal activity there is a \u223c6-fold increase in OPC number within the lesions and a reduced proportion of differentiated oligodendrocytes.", "These findings reveal that neuronal activity and release of glutamate instruct OPCs to differentiate into new myelinating oligodendrocytes that recover lost function.", "Co-localization of OPCs with the presynaptic protein VGluT2 in MS lesions implies that this mechanism may provide novel targets to therapeutically enhance remyelination."], "structured": false}
{"doc_id": 7042304, "title": "The threshold for polyglutamine-expansion protein aggregation and cellular toxicity is dynamic and influenced by aging in Caenorhabditis elegans.", "abstract": ["Studies of the mutant gene in Huntington's disease, and for eight related neurodegenerative disorders, have identified polyglutamine (polyQ) expansions as a basis for cellular toxicity.", "This finding has led to a disease hypothesis that protein aggregation and cellular dysfunction can occur at a threshold of approximately 40 glutamine residues.", "Here, we test this hypothesis by expression of fluorescently tagged polyQ proteins (Q29, Q33, Q35, Q40, and Q44) in the body wall muscle cells of Caenorhabditis elegans and show that young adults exhibit a sharp boundary at 35-40 glutamines associated with the appearance of protein aggregates and loss of motility.", "Surprisingly, genetically identical animals expressing near-threshold polyQ repeats exhibited a high degree of variation in the appearance of protein aggregates and cellular toxicity that was dependent on repeat length and exacerbated during aging.", "The role of genetically determined aging pathways in the progression of age-dependent polyQ-mediated aggregation and cellular toxicity was tested by expressing Q82 in the background of age-1 mutant animals that exhibit an extended lifespan.", "We observed a dramatic delay of polyQ toxicity and appearance of protein aggregates.", "These data provide experimental support for the threshold hypothesis of polyQ-mediated toxicity in an experimental organism and emphasize the importance of the threshold as a point at which genetic modifiers and aging influence biochemical environment and protein homeostasis in the cell."], "structured": false}
{"doc_id": 7046487, "title": "Inflammation meets cancer, with NF-\u03baB as the matchmaker", "abstract": ["Inflammation is a fundamental protective response that sometimes goes awry and becomes a major cofactor in the pathogenesis of many chronic human diseases, including cancer.", "Here we review the evolutionary relationship and opposing functions of the transcription factor NF-\u03baB in inflammation and cancer.", "Although it seems to fulfill a distinctly tumor-promoting role in many types of cancer, NF-\u03baB has a confounding role in certain tumors.", "Understanding the activity and function of NF-\u03baB in the context of tumorigenesis is critical for its successful taming, an important challenge for modern cancer biology."], "structured": false}
{"doc_id": 7059897, "title": "IgBLAST: an immunoglobulin variable domain sequence analysis tool", "abstract": ["The variable domain of an immunoglobulin (IG) sequence is encoded by multiple genes, including the variable (V) gene, the diversity (D) gene and the joining (J) gene.", "Analysis of IG sequences typically requires identification of each gene, as well as a comparison of sequence variations in the context of defined regions.", "General purpose tools, such as the BLAST program, have only limited use for such tasks, as the rearranged nature of an IG sequence and the variable length of each gene requires multiple rounds of BLAST searches for a single IG sequence.", "Additionally, manual assembly of different genes is difficult and error-prone.", "To address these issues and to facilitate other common tasks in analysing IG sequences, we have developed the sequence analysis tool IgBLAST (http://www.ncbi.nlm.nih.gov/igblast/).", "With this tool, users can view the matches to the germline V, D and J genes, details at rearrangement junctions, the delineation of IG V domain framework regions and complementarity determining regions.", "IgBLAST has the capability to analyse nucleotide and protein sequences and can process sequences in batches.", "Furthermore, IgBLAST allows searches against the germline gene databases and other sequence databases simultaneously to minimize the chance of missing possibly the best matching germline V gene."], "structured": false}
{"doc_id": 7074001, "title": "Evidence into practice. Application of psychological models of change in evidence-based implementation.", "abstract": ["Psychiatrists have long recognised that routine clinical practice needs to be shaped and informed by external evidence (Lewis, 1958).", "Psychiatric researchers were among the first to utilise multi-centre randomised controlled trials (demonstrating the effectiveness of antipsychotics), and psychologists were among the first in the health field to develop techniques of meta-analysis.", "Social workers, too, point to their tradition with the publication of one of the earliest controlled trials (Lehrman, 1949)."], "structured": false}
{"doc_id": 7093809, "title": "Wnt signaling establishes anteroposterior neuronal polarity and requires retromer in C. elegans.", "abstract": ["Secreted Wnt proteins influence neural connectivity by regulating axon guidance, dendritic morphogenesis and synapse formation.", "We report a new role for Wnt and Frizzled proteins in establishing the anteroposterior polarity of the mechanosensory neurons ALM and PLM in C. elegans.", "Disruption of Wnt signaling leads to a complete inversion of ALM and PLM polarity: the anterior process adopts the length, branching pattern and synaptic properties of the wild-type posterior process, and vice versa.", "Different but overlapping sets of Wnt proteins regulate neuronal polarity in different body regions.", "Wnts act directly on PLM via the Frizzled LIN-17.", "In addition, we show that they are needed for axon branching and anteriorly directed axon growth.", "We also find that the retromer, a conserved protein complex that mediates transcytosis and endosome-to-Golgi protein trafficking, plays a key role in Wnt signaling.", "Deletion mutations of retromer subunits cause ALM and PLM polarity, and other Wnt-related defects.", "We show that retromer protein VPS-35 is required in Wnt-expressing cells and propose that retromer activity is needed to generate a fully active Wnt signal."], "structured": false}
{"doc_id": 7098463, "title": "Adjustable gastric banding and conventional therapy for type 2 diabetes: a randomized controlled trial.", "abstract": ["CONTEXT Observational studies suggest that surgically induced loss of weight may be effective therapy for type 2 diabetes.   \n", "OBJECTIVE To determine if surgically induced weight loss results in better glycemic control and less need for diabetes medications than conventional approaches to weight loss and diabetes control.   \n", "DESIGN, SETTING, AND PARTICIPANTS Unblinded randomized controlled trial conducted from December 2002 through December 2006 at the University Obesity Research Center in Australia, with general community recruitment to established treatment programs.", "Participants were 60 obese patients (BMI >30 and <40) with recently diagnosed (<2 years) type 2 diabetes.   \n", "INTERVENTIONS Conventional diabetes therapy with a focus on weight loss by lifestyle change vs laparoscopic adjustable gastric banding with conventional diabetes care.   \n", "MAIN OUTCOME MEASURES Remission of type 2 diabetes (fasting glucose level <126 mg/dL [7.0 mmol/L] and glycated hemoglobin [HbA1c] value <6.2% while taking no glycemic therapy).", "Secondary measures included weight and components of the metabolic syndrome.", "Analysis was by intention-to-treat.   \n", "RESULTS Of the 60 patients enrolled, 55 (92%) completed the 2-year follow-up.", "Remission of type 2 diabetes was achieved by 22 (73%) in the surgical group and 4 (13%) in the conventional-therapy group.", "Relative risk of remission for the surgical group was 5.5 (95% confidence interval, 2.2-14.0).", "Surgical and conventional-therapy groups lost a mean (SD) of 20.7% (8.6%) and 1.7% (5.2%) of weight, respectively, at 2 years (P < .001).", "Remission of type 2 diabetes was related to weight loss (R2 = 0.46, P < .001) and lower baseline HbA1c levels (combined R2 = 0.52, P < .001).", "There were no serious complications in either group.   \n", "CONCLUSIONS Participants randomized to surgical therapy were more likely to achieve remission of type 2 diabetes through greater weight loss.", "These results need to be confirmed in a larger, more diverse population and have long-term efficacy assessed.   \n", "TRIAL REGISTRATION actr.org Identifier: ACTRN012605000159651."], "structured": true}
{"doc_id": 7111021, "title": "Integration of antiretroviral therapy with tuberculosis treatment.", "abstract": ["BACKGROUND We previously reported that integrating antiretroviral therapy (ART) with tuberculosis treatment reduces mortality.", "However, the timing for the initiation of ART during tuberculosis treatment remains unresolved.   \n", "METHODS We conducted a three-group, open-label, randomized, controlled trial in South Africa involving 642 ambulatory patients, all with tuberculosis (confirmed by a positive sputum smear for acid-fast bacilli), human immunodeficiency virus infection, and a CD4+ T-cell count of less than 500 per cubic millimeter.", "Findings in the earlier-ART group (ART initiated within 4 weeks after the start of tuberculosis treatment, 214 patients) and later-ART group (ART initiated during the first 4 weeks of the continuation phase of tuberculosis treatment, 215 patients) are presented here.   \n", "RESULTS At baseline, the median CD4+ T-cell count was 150 per cubic millimeter, and the median viral load was 161,000 copies per milliliter, with no significant differences between the two groups.", "The incidence rate of the acquired immunodeficiency syndrome (AIDS) or death was 6.9 cases per 100 person-years in the earlier-ART group (18 cases) as compared with 7.8 per 100 person-years in the later-ART group (19 cases) (incidence-rate ratio, 0.89; 95% confidence interval [CI], 0.44 to 1.79; P=0.73).", "However, among patients with CD4+ T-cell counts of less than 50 per cubic millimeter, the incidence rates of AIDS or death were 8.5 and 26.3 cases per 100 person-years, respectively (incidence-rate ratio, 0.32; 95% CI, 0.07 to 1.13; P=0.06).", "The incidence rates of the immune reconstitution inflammatory syndrome (IRIS) were 20.1 and 7.7 cases per 100 person-years, respectively (incidence-rate ratio, 2.62; 95% CI, 1.48 to 4.82; P<0.001).", "Adverse events requiring a switching of antiretroviral drugs occurred in 10 patients in the earlier-ART group and 1 patient in the later-ART group (P=0.006).   \n", "CONCLUSIONS Early initiation of ART in patients with CD4+ T-cell counts of less than 50 per cubic millimeter increased AIDS-free survival.", "Deferral of the initiation of ART to the first 4 weeks of the continuation phase of tuberculosis therapy in those with higher CD4+ T-cell counts reduced the risks of IRIS and other adverse events related to ART without increasing the risk of AIDS or death.", "(Funded by the U.S. President's Emergency Plan for AIDS Relief and others; SAPIT ClinicalTrials.gov number, NCT00398996.)."], "structured": true}
{"doc_id": 7114092, "title": "From bloodjournal.hematologylibrary.org at PENN STATE UNIVERSITY on February 23, 2013. For personal use only.", "abstract": ["Megakaryocyte (MK) is the naturally polyploid cell that gives rise to platelets.", "Polyploidization occurs by endomitosis, which was a process considered to be an incomplete mitosis aborted in anaphase.", "Here, we used time-lapse confocal video microscopy to visualize the endomitotic process of primary human megakaryocytes.", "Our results show that the switch from mitosis to endomitosis corresponds to a late failure of cytokinesis accompanied by a backward movement of the 2 daughter cells.", "No abnormality was observed in the central spindle of endomitotic MKs.", "A furrow formation was present, but the contractile ring was abnormal because accumulation of nonmuscle myosin IIA was lacking.", "In addition, a defect in cell elongation was observed in dipolar endomitotic MKs during telophase.", "RhoA and F-actin were partially concentrated at the site of furrowing.", "Inhibition of the Rho/Rock pathway caused the disappearance of F-actin at midzone and increased MK ploidy level.", "This inhibition was associated with a more pronounced defect in furrow formation as well as in spindle elongation.", "Our results suggest that the late failure of cytokinesis responsible for the endomitotic process is related to a partial defect in the Rho/Rock pathway activation."], "structured": false}
{"doc_id": 7115651, "title": "Key role for IL-21 in experimental autoimmune uveitis.", "abstract": ["IL-21 is a pleiotropic type 1 cytokine that shares the common cytokine receptor \u03b3-chain, \u03b3(c), with IL-2, IL-4, IL-7, IL-9, and IL-15.", "IL-21 is most homologous to IL-2.", "These cytokines are encoded by adjacent genes, but they are functionally distinct.", "Whereas IL-2 promotes development of regulatory T cells and confers protection from autoimmune disease, IL-21 promotes differentiation of Th17 cells and is implicated in several autoimmune diseases, including type 1 diabetes and systemic lupus erythematosus.", "However, the roles of IL-21 and IL-2 in CNS autoimmune diseases such as multiple sclerosis and uveitis have been controversial.", "Here, we generated Il21-mCherry/Il2-emGFP dual-reporter transgenic mice and showed that development of experimental autoimmune uveitis (EAU) correlated with the presence of T cells coexpressing IL-21 and IL-2 into the retina.", "Furthermore, Il21r(-/-) mice were more resistant to EAU development than wild-type mice, and adoptive transfer of Il21r(-/-) T cells induced much less severe EAU, underscoring the need for IL-21 in the development of this disease and suggesting that blocking IL-21/\u03b3(c)-signaling pathways may provide a means for controlling CNS auto-inflammatory diseases."], "structured": false}
{"doc_id": 7116734, "title": "Nicotinamide Phosphoribosyltransferase/Visfatin Does Not Catalyze Nicotinamide Mononucleotide Formation in Blood Plasma", "abstract": ["Nicotinamide (Nam) phosphoribosyltransferase (NAMPT) is the rate-limiting enzyme in mammalian NAD synthesis, catalyzing nicotinamide mononucleotide (NMN) formation from Nam and 5-phosphoribosyl 1-pyrophosphate (PRPP).", "NAMPT has also been described as an adipocytokine visfatin with a variety of actions, although physiological significance of this protein remains unclear.", "It has been proposed that possible actions of visfatin are mediated through the extracellular formation of NMN.", "However, we did not detect NMN in mouse blood plasma, even with a highly specific and sensitive liquid chromatography/tandem mass spectrometry.", "Furthermore, there is no or little ATP, the activator of NAMPT, in extracellular spaces.", "We thus questioned whether visfatin catalyzes the in situ formation of NMN under such extracellular milieus.", "To address this question, we here determined K(m) values for the substrates Nam and PRPP in the NAMPT reaction without or with ATP using a recombinant human enzyme and found that 1 mM ATP dramatically decreases K(m) values for the substrates, in particular PRPP to its intracellular concentration.", "Consistent with the kinetic data, only when ATP is present at millimolar levels, NAMPT efficiently catalyzed the NMN formation at the intracellular concentrations of the substrates.", "Much lower concentrations of Nam and almost the absence of PRPP and ATP in the blood plasma suggest that NAMPT should not efficiently catalyze its reaction under the extracellular milieu.", "Indeed, NAMPT did not form NMN in the blood plasma.", "From these kinetic analyses of the enzyme and quantitative determination of its substrates, activator, and product, we conclude that visfatin does not participate in NMN formation under the extracellular milieus.", "Together with the absence of NMN in the blood plasma, our conclusion does not support the concept of \"NAMPT-mediated systemic NAD biosynthesis.", "\"", "Our study would advance current understanding of visfatin physiology."], "structured": false}
{"doc_id": 7137057, "title": "Hepatitis B virus replication is regulated by the acetylation status of hepatitis B virus cccDNA-bound H3 and H4 histones.", "abstract": ["BACKGROUND & AIMS HBV covalently closed circular DNA (cccDNA), the replicative intermediate responsible for persistent HBV infection of hepatocytes, is the template for transcription of all viral mRNAs.", "Nuclear cccDNA accumulates as a stable episome organized into minichromosomes by histone and nonhistone proteins.", "In this study we investigated, by a newly developed sensitive and specific assay, the relationship between viral replication and HBV chromatin assembly, transcription, and interaction with viral and cellular regulatory proteins.   \n", "METHODS To achieve this aim we coupled a quantitative chromatin immunoprecipitation (ChIP) technique to an established method that allows the amplification of virion-encapsidated HBV genomes after transfection of linear HBV DNA into human hepatoma HuH7 cells.", "The cccDNA-ChIP technique was also applied to study HBV minichromosome transcriptional regulation in liver tissue from HBV-infected patients.   \n", "RESULTS The use of anti-acetyl-H4/-H3 specific antibodies to immunoprecipitate transcriptionally active chromatin revealed that HBV replication is regulated by the acetylation status of the cccDNA-bound H3/H4 histones.", "Class I histone deacetylases inhibitors induced an evident increase of both cccDNA-bound acetylated H4 and HBV replication.", "Finally, histones hypoacetylation and histone deacetylase 1 recruitment onto the cccDNA in liver tissue correlated with low HBV viremia in hepatitis B patients.   \n", "CONCLUSIONS We developed a ChIP-based assay to analyze, in vitro and ex vivo, the transcriptional regulation of HBV cccDNA minichromosome.", "Our results provide new insights on the regulation of HBV replication and identify the enzymatic activities that modulate the acetylation of cccDNA-bound histones as new therapeutic targets for anti-HBV drugs."], "structured": true}
{"doc_id": 7142113, "title": "Visualization of cell cycle in mouse embryos with Fucci2 reporter directed by Rosa26 promoter.", "abstract": ["Fucci technology makes possible the distinction between live cells in the G(1) and S/G(2)/M phases by dual-color imaging.", "This technology relies upon ubiquitylation-mediated proteolysis, and transgenic mice expressing Fucci provide a powerful model system with which to study the coordination of the cell cycle and development.", "The mice were initially generated using the CAG promoter; lines expressing the G(1) and S/G(2)/M phase probes that emitted orange (mKO2) and green (mAG) fluorescence, respectively, were separately constructed.", "Owing to cell type-biased strength of the CAG promoter as well as the positional effects of random transgenesis, however, we noticed some variability in Fucci expression levels.", "To control more reliably the expression of cell cycle probes, we used different genetic approaches to create two types of reporter mouse lines with Fucci2 and Rosa26 transcriptional machinery.", "Fucci2 is a recently developed Fucci derivative, which emits red (mCherry) and green (mVenus) fluorescence and provides better color contrast than Fucci.", "A new transgenic line, R26p-Fucci2, utilizes the Rosa26 promoter and harbors the G(1) and S/G(2)/M phase probes in a single transgene to preserve their co-inheritance.", "In the other R26R-Fucci2 approach, the two probes are incorporated into Rosa26 locus conditionally.", "The Cre-mediated loxP recombination technique thus allows researchers to design cell-type-specific Fucci2 expression.", "By performing time-lapse imaging experiments using R26p-Fucci2 and R26-Fucci2 in which R26R-Fucci2 had undergone germline loxP recombination, we demonstrated the great promise of these mouse reporters for studying cell cycle behavior in vivo."], "structured": false}
{"doc_id": 7145763, "title": "Tit-for-Tat: Type VI Secretion System Counterattack during Bacterial Cell-Cell Interactions", "abstract": ["The bacterial type VI secretion system (T6SS) is a dynamic organelle that bacteria use to target prey cells for inhibition via translocation of effector proteins.", "Time-lapse fluorescence microscopy has documented striking dynamics of opposed T6SS organelles in adjacent sister cells of Pseudomonas aeruginosa.", "Such cell-cell interactions have been termed \"T6SS dueling\" and likely reflect a biological process that is driven by T6SS antibacterial attack.", "Here, we show that T6SS dueling behavior strongly influences the ability of P. aeruginosa to prey upon heterologous bacterial species.", "We show that, in the case of P. aeruginosa, T6SS-dependent killing of either Vibrio cholerae or Acinetobacter baylyi is greatly stimulated by T6SS activity occurring in those prey species.", "Our data suggest that, in P. aeruginosa, T6SS organelle assembly and lethal counterattack are regulated by a signal that corresponds to the point of attack of the T6SS apparatus elaborated by a second aggressive T6SS(+) bacterial cell.", "PAPERFLICK:"], "structured": false}
{"doc_id": 7150238, "title": "The effects of LY2405319, an FGF21 analog, in obese human subjects with type 2 diabetes.", "abstract": ["Fibroblast growth factor 21 (FGF21) is a recently discovered metabolic regulator.", "Exogenous FGF21 produces beneficial metabolic effects in animal models; however, the translation of these observations to humans has not been tested.", "Here, we studied the effects of LY2405319 (LY), a variant of FGF21, in a randomized, placebo-controlled, double-blind proof-of-concept trial in patients with obesity and type 2 diabetes.", "Patients received placebo or 3, 10, or 20 mg of LY daily for 28 days.", "LY treatment produced significant improvements in dyslipidemia, including decreases in low-density lipoprotein cholesterol and triglycerides and increases in high-density lipoprotein cholesterol and a shift to a potentially less atherogenic apolipoprotein concentration profile.", "Favorable effects on body weight, fasting insulin, and adiponectin were also detected.", "However, only a trend toward glucose lowering was observed.", "These results indicate that FGF21 is bioactive in humans and suggest that FGF21-based therapies may be effective for the treatment of selected metabolic disorders."], "structured": false}
{"doc_id": 7151961, "title": "Visualization of recombination intermediates produced by RAD52-mediated single-strand annealing.", "abstract": ["Double-strand breaks (DSBs) occur frequently during DNA replication.", "They are also caused by ionizing radiation, chemical damage or as part of the series of programmed events that occur during meiosis.", "In yeast, DSB repair requires RAD52, a protein that plays a critical role in homologous recombination.", "Here we describe the actions of human RAD52 protein in a model system for single-strand annealing (SSA) using tailed (i.e. exonuclease resected) duplex DNA molecules.", "Purified human RAD52 protein binds resected DSBs and promotes associations between complementary DNA termini.", "Heteroduplex intermediates of these recombination reactions have been visualized by electron microscopy, revealing the specific binding of multiple rings of RAD52 to the resected termini and the formation of large protein complexes at heteroduplex joints formed by RAD52-mediated annealing."], "structured": false}
{"doc_id": 7155555, "title": "Crucial Role of Interferon Consensus Sequence Binding Protein, but neither of Interferon Regulatory Factor 1 nor of Nitric Oxide Synthesis for Protection Against Murine Listeriosis", "abstract": ["Listeria monocytogenes is widely used as a model to study immune responses against intracellular bacteria.", "It has been shown that neutrophils and macrophages play an important role to restrict bacterial replication in the early phase of primary infection in mice, and that the cytokines interferon-\u03b3 (IFN-\u03b3) and tumor necrosis factor-\u03b1 (TNF-\u03b1) are essential for protection.", "However, the involved signaling pathways and effector mechanisms are still poorly understood.", "This study investigated mouse strains deficient for the IFN-dependent transcription factors interferon consensus sequence binding protein (ICSBP), interferon regulatory factor (IRF)1 or 2 for their capacity to eliminate Listeria in vivo and in vitro and for production of inducible reactive nitrogen intermediates (RNI) or reactive oxygen intermediates (ROI) in macrophages.", "ICSBP\u2212/\u2212 and to a lesser degree also IRF2\u2212/\u2212 mice were highly susceptible to Listeria infection.", "This correlated with impaired elimination of Listeria from infected peritoneal macrophage (PEM) cultures stimulated with IFN-\u03b3 in vitro; in addition these cultures showed reduced and delayed oxidative burst upon IFN-\u03b3 stimulation, whereas nitric oxide production was normal.", "In contrast, mice deficient for IRF1 were not able to produce nitric oxide, but they efficiently controlled Listeria in vivo and in vitro.", "These results indicate that (a) the ICSBP/IRF2 complex is essential for IFN-\u03b3\u2013mediated protection against Listeria and that (b) ROI together with additional still unknown effector mechanisms may be responsible for the anti-Listeria activity of macrophages, whereas IRF1-induced RNI are not limiting."], "structured": false}
{"doc_id": 7157436, "title": "Neuronal replacement from endogenous precursors in the adult brain after stroke", "abstract": ["In the adult brain, new neurons are continuously generated in the subventricular zone and dentate gyrus, but it is unknown whether these neurons can replace those lost following damage or disease.", "Here we show that stroke, caused by transient middle cerebral artery occlusion in adult rats, leads to a marked increase of cell proliferation in the subventricular zone.", "Stroke-generated new neurons, as well as neuroblasts probably already formed before the insult, migrate into the severely damaged area of the striatum, where they express markers of developing and mature, striatal medium-sized spiny neurons.", "Thus, stroke induces differentiation of new neurons into the phenotype of most of the neurons destroyed by the ischemic lesion.", "Here we show that the adult brain has the capacity for self-repair after insults causing extensive neuronal death.", "If the new neurons are functional and their formation can be stimulated, a novel therapeutic strategy might be developed for stroke in humans."], "structured": false}
{"doc_id": 7165938, "title": "Overexpression of the circadian clock gene Bmal1 increases sensitivity to oxaliplatin in colorectal cancer.", "abstract": ["PURPOSE The circadian clock gene Bmal1 is involved in cancer cell proliferation and DNA damage sensitivity.", "The aim of this study was to explore the effect of Bmal1 on oxaliplatin sensitivity and to determine its clinical significance in colorectal cancer.   ", "EXPERIMENTAL DESIGN Three colorectal cancer cell lines, HCT116, THC8307 and HT29, were used.", "The Bmal1-mediated control of colorectal cancer cell proliferation was tested in vitro and in vivo.", "MTT and colony formation assays were performed to determine the sensitivity of colorectal cancer cells to oxaliplatin.", "Flow cytometry was used to examine changes in the cell-cycle distribution and apoptosis rate.", "Proteins expressed downstream of Bmal1 upon its overexpression were determined by Western blotting.", "Immunohistochemistry was used to analyze Bmal1 expression in 82 archived colorectal cancer tumors from patients treated with oxaliplatin-based regimens.   \n", "RESULTS Bmal1 overexpression inhibited colorectal cancer cell proliferation and increased colorectal cancer sensitivity to oxaliplatin in three colorectal cancer cell lines and HCT116 cells model in vivo.", "Furthermore, the overall survival of patients with colorectal cancer with high Bmal1 levels in their primary tumors was significantly longer than that of patients with low Bmal1 levels (27 vs. 19 months; P = 0.043).", "The progression-free survival of patients with high Bmal1 expression was also significantly longer than that of patients with low Bmal1 expression (11 vs. 5 months; P = 0.015).", "Mechanistically, the effect of Bmal1 was associated with its ability to regulate G2-M arrest by activating the ATM pathway.   \n", "CONCLUSION Bmal1 shows the potential as a novel prognostic biomarker and may represent a new therapeutic target in colorectal cancer."], "structured": true}
{"doc_id": 7177329, "title": "Evolution of an HIV glycan\u2013dependent broadly neutralizing antibody epitope through immune escape", "abstract": ["Neutralizing antibodies are likely to play a crucial part in a preventative HIV-1 vaccine.", "Although efforts to elicit broadly cross-neutralizing (BCN) antibodies by vaccination have been unsuccessful, a minority of individuals naturally develop these antibodies after many years of infection.", "How such antibodies arise, and the role of viral evolution in shaping these responses, is unknown.", "Here we show, in two HIV-1\u2013infected individuals who developed BCN antibodies targeting the glycan at Asn332 on the gp120 envelope, that this glycan was absent on the initial infecting virus.", "However, this BCN epitope evolved within 6 months, through immune escape from earlier strain-specific antibodies that resulted in a shift of a glycan to position 332.", "Both viruses that lacked the glycan at amino acid 332 were resistant to the Asn332-dependent BCN monoclonal antibody PGT128 (ref.", "8), whereas escaped variants that acquired this glycan were sensitive.", "Analysis of large sequence and neutralization data sets showed the 332 glycan to be significantly under-represented in transmitted subtype C viruses compared to chronic viruses, with the absence of this glycan corresponding with resistance to PGT128.", "These findings highlight the dynamic interplay between early antibodies and viral escape in driving the evolution of conserved BCN antibody epitopes."], "structured": false}
{"doc_id": 7185591, "title": "Sir2-Independent Life Span Extension by Calorie Restriction in Yeast", "abstract": ["Calorie restriction slows aging and increases life span in many organisms.", "In yeast, a mechanistic explanation has been proposed whereby calorie restriction slows aging by activating Sir2.", "Here we report the identification of a Sir2-independent pathway responsible for a majority of the longevity benefit associated with calorie restriction.", "Deletion of FOB1 and overexpression of SIR2 have been previously found to increase life span by reducing the levels of toxic rDNA circles in aged mother cells.", "We find that combining calorie restriction with either of these genetic interventions dramatically enhances longevity, resulting in the longest-lived yeast strain reported thus far.", "Further, calorie restriction results in a greater life span extension in cells lacking both Sir2 and Fob1 than in cells where Sir2 is present.", "These findings indicate that Sir2 and calorie restriction act in parallel pathways to promote longevity in yeast and, perhaps, higher eukaryotes."], "structured": false}
{"doc_id": 7198295, "title": "The Effect of Submaximal Exercise Preceded by Single Whole-Body Cryotherapy on the Markers of Oxidative Stress and Inflammation in Blood of Volleyball Players", "abstract": ["The aim of the study was to determine the effect of single whole-body cryotherapy (WBC) session applied prior to submaximal exercise on the activity of antioxidant enzymes, the concentration of lipid peroxidation products, total oxidative status, and the level of cytokines in blood of volleyball players.", "The study group consisted of 18 male professional volleyball players, who were subjected to extremely cold air (-130\u00b0C) prior to exercise performed on cycloergometer.", "Blood samples were taken five times: before WBC, after WBC procedure, after exercise preceded by cryotherapy (WBC exercise), and before and after exercise without WBC (control exercise).", "The activity of catalase statistically significantly increased after control exercise.", "Moreover, the activity of catalase and superoxide dismutase was lower after WBC exercise than after control exercise (P < 0.001).", "After WBC exercise, the level of IL-6 and IL-1\u03b2 was also lower (P < 0.001) than after control exercise.", "The obtained results may suggest that cryotherapy prior to exercise may have some antioxidant and anti-inflammatory properties.", "The relations between the level of studied oxidative stress and inflammatory markers may testify to the contribution of reactive oxygen species in cytokines release into the blood system in response to exercise and WBC."], "structured": false}
{"doc_id": 7209559, "title": "Incidence of childhood distal forearm fractures over 30 years: a population-based study.", "abstract": ["CONTEXT The incidence of distal forearm fractures in children peaks around the time of the pubertal growth spurt, possibly because physical activity increases at the time of a transient deficit in cortical bone mass due to the increased calcium demand during maximal skeletal growth.", "Changes in physical activity or diet may therefore influence risk of forearm fracture.   \n", "OBJECTIVE To determine whether there has been a change in the incidence of distal forearm fractures in children in recent years.   \n", "DESIGN, SETTING, AND PATIENTS Population-based study among Rochester, Minn, residents younger than 35 years with distal forearm fractures in 1969-1971, 1979-1981, 1989-1991, and 1999-2001.   \n", "MAIN OUTCOME MEASURE Estimated incidence of distal forearm fractures in 4 time periods.   \n", "RESULTS Comparably age- and sex-adjusted annual incidence rates per 100 000 increased from 263.3 (95% confidence interval [CI], 231.1-295.4) in 1969-1971 to 322.3 (95% CI, 285.3-359.4) in 1979-1981 and to 399.8 (95% CI, 361.0-438.6) in 1989-1991 before leveling off at 372.9 (95% CI, 339.1-406.7) in 1999-2001.", "Age-adjusted incidence rates per 100 000 were 32% greater among male residents in 1999-2001 compared with 1969-1971 (409.4 [95% CI, 359.9-459.0] vs 309.4 [95% CI, 259.3-359.5]; P =.01) and 56% greater among female residents in the same time periods (334.3 [95% CI, 288.6-380.1] vs 214.6 [95% CI, 174.9-254.4]; P<.001).", "The peak incidence and greatest increase occurred between ages 11 and 14 years in boys and 8 and 11 years in girls.   \n", "CONCLUSIONS There has been a statistically significant increase in the incidence of distal forearm fractures in children and adolescents, but whether this is due to changing patterns of physical activity, decreased bone acquisition due to poor calcium intake, or both is unclear at present.", "Given the large number of childhood fractures, however, studies are needed to define the cause(s) of this increase."], "structured": true}
{"doc_id": 7211056, "title": "Tolerance of whole-genome doubling propagates chromosomal instability and accelerates cancer genome evolution.", "abstract": ["UNLABELLED The contribution of whole-genome doubling to chromosomal instability (CIN) and tumor evolution is unclear.", "We use long-term culture of isogenic tetraploid cells from a stable diploid colon cancer progenitor to investigate how a genome-doubling event affects genome stability over time.", "Rare cells that survive genome doubling demonstrate increased tolerance to chromosome aberrations.", "Tetraploid cells do not exhibit increased frequencies of structural or numerical CIN per chromosome.", "However, the tolerant phenotype in tetraploid cells, coupled with a doubling of chromosome aberrations per cell, allows chromosome abnormalities to evolve specifically in tetraploids, recapitulating chromosomal changes in genomically complex colorectal tumors.", "Finally, a genome-doubling event is independently predictive of poor relapse-free survival in early-stage disease in two independent cohorts in multivariate analyses [discovery data: hazard ratio (HR), 4.70, 95% confidence interval (CI), 1.04-21.37; validation data: HR, 1.59, 95% CI, 1.05-2.42].", "These data highlight an important role for the tolerance of genome doubling in driving cancer genome evolution.   ", "SIGNIFICANCE Our work sheds light on the importance of whole-genome\u2013doubling events in colorectal cancer evolution.", "We show that tetraploid cells undergo rapid genomic changes and recapitulate the genetic alterations seen in chromosomally unstable tumors.", "Furthermore, we demonstrate that a genome-doubling event is prognostic of poor relapse-free survival in this disease type."], "structured": false}
{"doc_id": 7221410, "title": "Alzheimer\u2019s Disease Risk Gene CD33 Inhibits Microglial Uptake of Amyloid Beta", "abstract": ["The transmembrane protein CD33 is a sialic acid-binding immunoglobulin-like lectin that regulates innate immunity but has no known functions in the brain.", "We have previously shown that the CD33 gene is a risk factor for Alzheimer's disease (AD).", "Here, we observed increased expression of CD33 in microglial cells in AD brain.", "The minor allele of the CD33 SNP rs3865444, which confers protection against AD, was associated with reductions in both CD33 expression and insoluble amyloid beta 42 (A\u03b242) levels in AD brain.", "Furthermore, the numbers of CD33-immunoreactive microglia were positively correlated with insoluble A\u03b242 levels and plaque burden in AD brain.", "CD33 inhibited uptake and clearance of A\u03b242 in microglial cell cultures.", "Finally, brain levels of insoluble A\u03b242 as well as amyloid plaque burden were markedly reduced in APP(Swe)/PS1(\u0394E9)/CD33(-/-) mice.", "Therefore, CD33 inactivation mitigates A\u03b2 pathology and CD33 inhibition could represent a novel therapy for AD."], "structured": false}
{"doc_id": 7223604, "title": "Aluminum fluoride stimulates surface protrusions in cells overexpressing the ARF6 GTPase", "abstract": ["To study the effector function of the ADP- ribosylation factor (ARF) 6 GTP-binding protein, we transfected HeLa cells with wild-type, epitope-tagged ARF6.", "Previously shown to indirectly activate the ARF1 GTPase, aluminum fluoride (AIF) treatment of ARF6-transfected cells resulted in a redistribution of both ARF6 and actin to discrete sites on the plasma membrane, which became increasingly protrusive over time.", "The effects of AIF were reversible, specific to cells transfected with wild-type ARF6, and resembled the cellular protrusions observed in cells expressing the GTPase defective mutant of ARF6.", "Importantly, the protrusions observed in cells transfected with ARF6 were distinct from the enhanced stress fibers and membrane ruffles observed in cells transfected with RhoA and Rac1, respectively.", "In cells forming protrusions, there was an apparent stimulation of macropinocytosis and membrane recycling within the protrusive structures.", "In contrast, no block in transferrin uptake or alteration of the distribution of clathrin AP-2 complexes was detected in these cells.", "The AIF-induced, ARF6- dependent formation of protrusive structures was blocked by cytochalasin D and inhibitors of the lipoxygenase pathway.", "These observations support a novel role for the ARF6 GTPase in modeling the plasma membrane and underlying cytoskeleton."], "structured": false}
{"doc_id": 7224632, "title": "A longitudinal diffusion tensor imaging study assessing white matter fiber tracts after sports-related concussion.", "abstract": ["The extent of structural injury in sports-related concussion (SRC) is central to the course of recovery, long-term effects, and the decision to return to play.", "In the present longitudinal study, we used diffusion tensor imaging (DTI) to assess white matter (WM) fiber tract integrity within 2 days, 2 weeks, and 2 months of concussive injury.", "Participants were right-handed male varsity contact-sport athletes (20.2\u00b11.0 years of age) with a medically diagnosed SRC (no loss of consciousness).", "They were compared to right-handed male varsity non-contact-sport athletes serving as controls (19.9\u00b11.7 years).", "We found significantly increased radial diffusivity (RD) in concussed athletes (n=12; paired t-test, tract-based spatial statistics; p<0.025) at 2 days, when compared to the 2-week postinjury time point.", "The increase was found in a cluster of right hemisphere voxels, spanning the posterior limb of the internal capsule (IC), the retrolenticular part of the IC, the inferior longitudinal fasciculus, the inferior fronto-occipital fasciculus (sagittal stratum), and the anterior thalamic radiation.", "Post-hoc, univariate, between-group (controls vs. concussed), mixed-effects analysis of the cluster showed significantly higher RD at 2 days (p=0.002), as compared to the controls, with a trend in the same direction at 2 months (p=0.11).", "Results for fractional anisotropy (FA) in the same cluster showed a similar, but inverted, pattern; FA was decreased at 2 days and at 2 months postinjury, when compared to healthy controls.", "At 2 weeks postinjury, no statistical differences between concussed and control athletes were found with regard to either RD or FA.", "These results support the hypothesis of increased RD and reduced FA within 72 h postinjury, followed by recovery that may extend beyond 2 weeks.", "RD appears to be a sensitive measure of concussive injury."], "structured": false}
{"doc_id": 7224723, "title": "HIV\u20131 Infects Multipotent Progenitor Cells Causing Cell Death and Establishing Latent Cellular Reservoirs", "abstract": ["HIV causes a chronic infection characterized by depletion of CD4(+) T lymphocytes and the development of opportunistic infections.", "Despite drugs that inhibit viral spread, HIV infection has been difficult to cure because of uncharacterized reservoirs of infected cells that are resistant to highly active antiretroviral therapy (HAART) and the immune response.", "Here we used CD34(+) cells from infected people as well as in vitro studies of wild-type HIV to show infection and killing of CD34(+) multipotent hematopoietic progenitor cells (HPCs).", "In some HPCs, we detected latent infection that stably persisted in cell culture until viral gene expression was activated by differentiation factors.", "A unique reporter HIV that directly detects latently infected cells in vitro confirmed the presence of distinct populations of active and latently infected HPCs.", "These findings have major implications for understanding HIV bone marrow pathology and the mechanisms by which HIV causes persistent infection."], "structured": false}
{"doc_id": 7225911, "title": "The human long non-coding RNA-RoR is a p53 repressor in response to DNA damage", "abstract": ["It is well known that upon stress, the level of the tumor suppressor p53 is remarkably elevated.", "However, despite extensive studies, the underlying mechanism involving important inter-players for stress-induced p53 regulation is still not fully understood.", "We present evidence that the human lincRNA-RoR (RoR) is a strong negative regulator of p53.", "Unlike MDM2 that causes p53 degradation through the ubiquitin-proteasome pathway, RoR suppresses p53 translation through direct interaction with the heterogeneous nuclear ribonucleoprotein I (hnRNP I).", "Importantly, a 28-base RoR sequence carrying hnRNP I binding motifs is essential and sufficient for p53 repression.", "We further show that RoR inhibits p53-mediated cell cycle arrest and apoptosis.", "Finally, we demonstrate a RoR-p53 autoregulatory feedback loop where p53 transcriptionally induces RoR expression.", "Together, these results suggest that the RoR-hnRNP I-p53 axis may constitute an additional surveillance network for the cell to better respond to various stresses."], "structured": false}
{"doc_id": 7227763, "title": "Experimental and clinical studies on lactate and pyruvate as indicators of the severity of acute circulatory failure (shock).", "abstract": ["The increase in lactate (L) and pyruvate (P) content of arterial blood during experimental and clinical shock states and the extent to which such increases serve as measures of oxygen deficit and irreversible injury were investigated on an empirical basis.", "A standardized method for production of hemorrhagic shock in the Wistar rat was employed.", "During a 4-hour bleeding period, oxygen consumption of the rat was reduced to approximately 40% of control value, pH was reduced from 7.39 to 7.08, and a concurrent increase in L from 0.80 to 6.06 mm and in P from 0.07 to 0.18 mm were observed.", "Cumulative oxygen debt correlated with log L (r = 0.50; P < 0.0005) and both were significantly related to survival.", "Correlation of cumulative oxygen debt and survival, both with P and with computed values of the lactate pyruvate ratio (L/P) and excess lactate (XL), were of no higher magnitude.", "Partial correlation analysis demonstrated that neither the measurement of P nor the computation of L/P or XL improved predictability..."], "structured": false}
{"doc_id": 7228140, "title": "Virtual microdissection identifies distinct tumor- and stroma-specific subtypes of pancreatic ductal adenocarcinoma", "abstract": ["Pancreatic ductal adenocarcinoma (PDAC) remains a lethal disease with a 5-year survival rate of 4%.", "A key hallmark of PDAC is extensive stromal involvement, which makes capturing precise tumor-specific molecular information difficult.", "Here we have overcome this problem by applying blind source separation to a diverse collection of PDAC gene expression microarray data, including data from primary tumor, metastatic and normal samples.", "By digitally separating tumor, stromal and normal gene expression, we have identified and validated two tumor subtypes, including a 'basal-like' subtype that has worse outcome and is molecularly similar to basal tumors in bladder and breast cancers.", "Furthermore, we define 'normal' and 'activated' stromal subtypes, which are independently prognostic.", "Our results provide new insights into the molecular composition of PDAC, which may be used to tailor therapies or provide decision support in a clinical setting where the choice and timing of therapies are critical."], "structured": false}
{"doc_id": 7230315, "title": "Inducible nitric oxide synthase in pulmonary alveolar macrophages from patients with tuberculosis", "abstract": ["The high-output pathway of nitric oxide production helps protect mice from infection by several pathogens, including Mycobacterium tuberculosis.", "However, based on studies of cells cultured from blood, it is controversial whether human mononuclear phagocytes can express the corresponding inducible nitric oxide synthase (iNOS;NOS2).", "The present study examined alveolar macrophages fixed directly after bronchopulmonary lavage.", "An average of 65% of the macrophages from 11 of 11 patients with untreated, culture-positive pulmonary tuberculosis reacted with an antibody documented herein to be monospecific for human NOS2.", "In contrast, a mean of 10% of bronchoalveolar lavage cells were positive from each of five clinically normal subjects.", "Tuberculosis patients' macrophages displayed diaphorase activity in the same proportion that they stained for NOS2, under assay conditions wherein the diaphorase reaction was strictly dependent on NOS2 expression.", "Bronchoalveolar lavage specimens also contained NOS2 mRNA.", "Thus, macrophages in the lungs of people with clinically active Mycobacterium tuberculosis infection often express catalytically competent NOS2."], "structured": false}
{"doc_id": 7239105, "title": "The use of mouse models to understand and improve cognitive deficits in Down syndrome", "abstract": ["Remarkable advances have been made in recent years towards therapeutics for cognitive impairment in individuals with Down syndrome (DS) by using mouse models.", "In this review, we briefly describe the phenotypes of mouse models that represent outcome targets for drug testing, the behavioral tests used to assess impairments in cognition and the known mechanisms of action of several drugs that are being used in preclinical studies or are likely to be tested in clinical trials.", "Overlaps in the distribution of targets and in the pathways that are affected by these diverse drugs in the trisomic brain suggest new avenues for DS research and drug development."], "structured": false}
{"doc_id": 7260461, "title": "position-specific gap penalties", "abstract": ["The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved for the alignment of divergent protein sequences.", "Firstly, individual weights are assigned to each sequence in a partial alignment in order to down-weight near-duplicate sequences and up-weight the most divergent ones.", "Secondly, amino acid substitution matrices are varied at different alignment stages according to the divergence of the sequences to be aligned.", "Thirdly, residue-specific gap penalties and locally reduced gap penalties in hydrophilic regions encourage new gaps in potential loop regions rather than regular secondary structure.", "Fourthly, positions in early alignments where gaps have been opened receive locally reduced gap penalties to encourage the opening up of new gaps at these positions.", "These modifications are incorporated into a new program, CLUSTAL W which is freely available."], "structured": false}
{"doc_id": 7261402, "title": "Pedestrian Detection via Periodic Motion Analysis", "abstract": ["We describe algorithms for detecting pedestrians in videos acquired by infrared (and color) sensors.", "Two approaches are proposed based on gait.", "The first employs computationally efficient periodicity measurements.", "Unlike other methods, it estimates a periodic motion frequency using two cascading hypothesis testing steps to filter out non-cyclic pixels so that it works well for both radial and lateral walking directions.", "The extraction of the period is efficient and robust with respect to sensor noise and cluttered background.", "In order to integrate shape and motion, we convert the cyclic pattern into a binary sequence by Maximal Principal Gait Angle (MPGA) fitting in the second method.", "It does not require alignment and continuously estimates the period using a Phase-locked Loop.", "Both methods are evaluated by experimental results that measure performance as a function of size, movement direction, frame rate and sequence length."], "structured": false}
{"doc_id": 7264949, "title": "Seroepidemiological survey of feline retrovirus infections in cats in Taiwan in 1993 and 1994.", "abstract": ["In order to investigate the prevalence of infections with three feline retroviruses feline immunodeficiency virus (FIV), feline leukemia virus (FeLV) and feline syncytial virus (FSV) in Taiwan, we collected a total of 75 blood samples from cats from veterinary hospitals, a breeding cattery and a homeless shelter in 1993 and 1994.", "We examined the presences of anti-FIV and FSV antibodies and FeLV-p27 antigen in these samples by the indirect immunofluorescence and/or enzyme-linked immunosorbent assays.", "All of the serum samples positive for FIV were obtained from homeless cats and the overall FIV positive rate was 4%.", "The overall positive rates of FSV and FeLV were 28% and 1.3%, respectively.", "From these results, together with previous seroepidemiological surveys by others, it was revealed that the prevalence of FIV and FeLV infections appeared to be lower in Taiwan than in the United States or Japan.", "In contrast, the prevalence of FSV infection in Taiwan was as high as that in Japan."], "structured": false}
{"doc_id": 7268522, "title": "Notch targets and their regulation.", "abstract": ["The proteolytic cleavages elicited by activation of the Notch receptor release an intracellular fragment, Notch intracellular domain, which enters the nucleus to activate the transcription of targets.", "Changes in transcription are therefore a major output of this pathway.", "However, the Notch outputs clearly differ from cell type to cell type.", "In this review we discuss current understanding of Notch targets, the mechanisms involved in their transcriptional regulation, and what might underlie the activation of different sets of targets in different cell types."], "structured": false}
{"doc_id": 7277084, "title": "Extraction and Analysis of Multiple Periodic Motions in Video Sequences", "abstract": ["The analysis of periodic or repetitive motions is useful in many applications, such as the recognition and classification of human and animal activities.", "Existing methods for the analysis of periodic motions first extract motion trajectories using spatial information and then determine if they are periodic.", "These approaches are mostly based on feature matching or spatial correlation, which are often infeasible, unreliable, or computationally demanding.", "In this paper, we present a new approach, based on the time- frequency analysis of the video sequence as a whole.", "Multiple periodic trajectories are extracted and their periods are estimated simultaneously.", "The objects that are moving in a periodic manner are extracted using the spatial domain information.", "Experiments with synthetic and real sequences display the capabilities of this approach."], "structured": false}
{"doc_id": 7281161, "title": "MicroRNA-21 is up-regulated in allergic airway inflammation and regulates IL-12p35 expression.", "abstract": ["Allergic airway inflammation is characterized by marked in situ changes in gene and protein expression, yet the role of microRNAs (miRNAs), a new family of key mRNA regulatory molecules, in this process has not yet been reported.", "Using a highly sensitive microarray-based approach, we identified 21 miRNAs with differential expression between doxycycline-induced lung-specific IL-13 transgenic mice (with allergic airway inflammation) and control mice.", "In particular, we observed overexpression of miR-21 and underexpression of miR-1 in the induced IL-13 transgenic mice compared with control mice.", "These findings were validated in two independent models of allergen-induced allergic airway inflammation and in IL-4 lung transgenic mice.", "Although IL-13-induced miR-21 expression was IL-13Ralpha1 dependent, allergen-induced miR-21 expression was mediated mainly independent of IL-13Ralpha1 and STAT6.", "Notably, predictive algorithms identified potential direct miR-21 targets among IL-13-regulated lung transcripts, such as IL-12p35 mRNA, which was decreased in IL-13 transgenic mice.", "Introduction of pre-miR-21 dose dependently inhibited cellular expression of a reporter vector harboring the 3'-untranslated region of IL-12p35.", "Moreover, mutating miR-21 binding sites in IL-12p35 3'-untranslated region abrogated miR-21-mediated repression.", "In summary, we have identified a miRNA signature in allergic airway inflammation, which includes miR-21 that modulates IL-12, a molecule germane to Th cell polarization."], "structured": false}
{"doc_id": 7285256, "title": "COPD: epidemiology, prevalence, morbidity and mortality, and disease heterogeneity.", "abstract": ["COPD continues to cause a heavy health and economic burden both in the United States and around the world.", "Some of the risk factors for COPD are well-known and include smoking, occupational exposures, air pollution, airway hyperresponsiveness, asthma, and certain genetic variations, although many questions, such as why < 20% of smokers develop significant airway obstruction, remain.", "Precise definitions of COPD vary and are frequently dependent on an accurate diagnosis of the problem by a physician.", "These differences in the definition of COPD can have large effects on the estimates of COPD in the population.", "Furthermore, evidence that COPD represents several different disease processes with potentially different interventions continues to emerge.", "In most of the world, COPD prevalence and mortality are still increasing and likely will continue to rise in response to increases in smoking, particularly by women and adolescents.", "Resources aimed at smoking cessation and prevention, COPD education and early detection, and better treatment will be of the most benefit in our continuing efforts against this important cause of morbidity and mortality."], "structured": false}
{"doc_id": 7299977, "title": "Changing geographic ranges of ticks and tick-borne pathogens: drivers, mechanisms and consequences for pathogen diversity", "abstract": ["The geographic ranges of ticks and tick-borne pathogens are changing due to global and local environmental (including climatic) changes.", "In this review we explore current knowledge of the drivers for changes in the ranges of ticks and tick-borne pathogen species and strains via effects on their basic reproduction number (R 0), and the mechanisms of dispersal that allow ticks and tick-borne pathogens to invade suitable environments.", "Using the expanding geographic distribution of the vectors and agent of Lyme disease as an example we then investigate what could be expected of the diversity of tick-borne pathogens during the process of range expansion, and compare this with what is currently being observed.", "Lastly we explore how historic population and range expansions and contractions could be reflected in the phylogeography of ticks and tick-borne pathogens seen in recent years, and conclude that combined study of currently changing tick and tick-borne pathogen ranges and diversity, with phylogeographic analysis, may help us better predict future patterns of invasion and diversity."], "structured": false}
{"doc_id": 7317051, "title": "Mutant KRAS is a druggable target for pancreatic cancer.", "abstract": ["Pancreatic ductal adenocarcinoma (PDA) represents an unmet therapeutic challenge.", "PDA is addicted to the activity of the mutated KRAS oncogene which is considered so far an undruggable therapeutic target.", "We propose an approach to target KRAS effectively in patients using RNA interference.", "To meet this challenge, we have developed a local prolonged siRNA delivery system (Local Drug EluteR, LODER) shedding siRNA against the mutated KRAS (siG12D LODER).", "The siG12D LODER was assessed for its structural, release, and delivery properties in vitro and in vivo.", "The effect of the siG12D LODER on tumor growth was assessed in s.c.", "and orthotopic mouse models.", "KRAS silencing effect was further assessed on the KRAS downstream signaling pathway.", "The LODER-encapsulated siRNA was stable and active in vivo for 155 d. Treatment of PDA cells with siG12D LODER resulted in a significant decrease in KRAS levels, leading to inhibition of proliferation and epithelial-mesenchymal transition.", "In vivo, siG12D LODER impeded the growth of human pancreatic tumor cells and prolonged mouse survival.", "We report a reproducible and safe delivery platform based on a miniature biodegradable polymeric matrix, for the controlled and prolonged delivery of siRNA.", "This technology provides the following advantages: (i) siRNA is protected from degradation; (ii) the siRNA is slowly released locally within the tumor for prolonged periods; and (iii) the siG12D LODER elicits a therapeutic effect, thereby demonstrating that mutated KRAS is indeed a druggable target."], "structured": false}
{"doc_id": 7324039, "title": "Trimmomatic: a flexible trimmer for Illumina sequence data", "abstract": ["MOTIVATION Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance.", "We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data.   \n", "RESULTS The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks.", "Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested.   ", "AVAILABILITY AND IMPLEMENTATION Trimmomatic is licensed under GPL V3.", "It is cross-platform (Java 1.5+ required) and available at http://www.usadellab.org/cms/index.php?page=trimmomatic   CONTACT usadel@bio1.rwth-aachen.de   SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online."], "structured": true}
{"doc_id": 7343711, "title": "Basics of PD-1 in self-tolerance, infection, and cancer immunity", "abstract": ["Successful cancer treatment requires understanding host immune response against tumor cells.", "PD-1 belongs to the CD28 superfamily of receptors that work as \u201ccheckpoints\u201d of immune activation.", "PD-1 maintains immune self-tolerance to prevent autoimmunity and controls T-cell reaction during infection to prevent excessive tissue damage.", "Tumor cells that arise from normal tissue acquire mutations that can be targeted by lymphocytes.", "Accumulating lines of evidence suggest that tumor cells evade host immune attack by expressing physiological PD-1 ligands and stimulating PD-1 on the lymphocytes.", "Based on this idea, researchers have successfully demonstrated that systemic administration of monoclonal antibodies that inhibit the binding of PD-1 to the ligands reactivated T cells and augmented the anti-cancer immune response.", "In this review, I summarize the basics of T-cell biology and its regulation by PD-1 and discuss the current understanding and questions about this multifaceted molecule."], "structured": false}
{"doc_id": 7357135, "title": "Dissociation of \u03b21- and \u03b22-adrenergic receptor subtypes in the retrieval of cocaine-associated memory.", "abstract": ["Drug seeking is maintained by encounters with drug-associated cues, and disrupting retrieval of these drug-cue associations would reduce the risk of relapse.", "Retrieval of cocaine-associated memories is dependent on \u03b2-adrenergic receptor (\u03b2-AR) activation, and blockade of these receptors induces a persistent retrieval deficit.", "Whether retrieval of cocaine-associated memory is mediated by a specific \u03b2-AR subtype, however, remains unclear.", "Using a cocaine conditioned place preference (CPP) procedure, we examined whether retrieval of a cocaine CPP memory is mediated collectively by \u03b21- and \u03b22-ARs, or by one of these \u03b2-AR subtypes alone.", "We show that co-blockade of \u03b21- and \u03b22-ARs abolished CPP expression on that and subsequent drug-free CPP tests, resulting in a long-lasting retrieval deficit that prevented subsequent cocaine-induced reinstatement.", "To dissociate the necessity of either \u03b21- or \u03b22-ARs alone, we administered subtype-specific antagonists prior to retrieval.", "Administration of a \u03b21-AR antagonist before the initial CPP trial dose-dependently reduced expression of a CPP on that and subsequent drug-free trials as compared to vehicle administration.", "In contrast, administration of a \u03b22-AR antagonist had no effect on initial CPP expression, although the highest dose reduced subsequent CPP expression.", "Importantly, either \u03b21- or \u03b22-AR blockade prior to an initial retrieval trial prevented subsequent cocaine-induced reinstatement.", "Our findings indicate that the \u03b21-AR subtype mediates retrieval of a cocaine CPP, and that acutely blocking either \u03b21- or \u03b22-ARs can prevent subsequent cocaine-induced reinstatement.", "Thus, \u03b2-AR antagonists, particularly \u03b21-ARs antagonists, could serve as adjuncts for addiction therapies to prevent retrieval of drug-associated memories and provide protection against relapse."], "structured": false}
{"doc_id": 7370282, "title": "Podoplanin-Rich Stromal Networks Induce Dendritic Cell Motility via Activation of the C-type Lectin Receptor CLEC-2", "abstract": ["To initiate adaptive immunity, dendritic cells (DCs) move from parenchymal tissues to lymphoid organs by migrating along stromal scaffolds that display the glycoprotein podoplanin (PDPN).", "PDPN is expressed by lymphatic endothelial and fibroblastic reticular cells and promotes blood-lymph separation during development by activating the C-type lectin receptor, CLEC-2, on platelets.", "Here, we describe a role for CLEC-2 in the morphodynamic behavior and motility of DCs.", "CLEC-2 deficiency in DCs impaired their entry into lymphatics and trafficking to and within lymph nodes, thereby reducing T cell priming.", "CLEC-2 engagement of PDPN was necessary for DCs to spread and migrate along stromal surfaces and sufficient to induce membrane protrusions.", "CLEC-2 activation triggered cell spreading via downregulation of RhoA activity and myosin light-chain phosphorylation and triggered F-actin-rich protrusions via Vav signaling and Rac1 activation.", "Thus, activation of CLEC-2 by PDPN rearranges the actin cytoskeleton in DCs to promote efficient motility along stromal surfaces."], "structured": false}
{"doc_id": 7373120, "title": "The Public Health Responsibility Deal: brokering a deal for public health, but on whose terms?", "abstract": ["UNLABELLED Coalitions of multinational food and drink businesses have pledged to reformulate their products and to market them responsibly.", "Largely business-led and self-regulated, the integrity of these voluntary initiatives has been questioned.", "The Public Health Responsibility Deal in England is an example of a voluntary initiative that is government-led.", "Does this approach provide evidence that with public leadership there is potential for voluntary actions to deliver meaningful results for public health?   \n", "METHODS The subject of the research is the calorie reduction initiative of the Responsibility Deal.", "Source material was obtained primarily through a series of UK Freedom of Information requests and comprises previously unpublished Department of Health documentation relating to relevant meetings held during 2011 and 2012.   \n", "RESULTS The Responsibility Deal approach to calorie reduction deliberately involves the food industry in the specification of the measures it is to implement (reformulation and portion control).", "Finding the common ground between private and public interests has resulted in the deflection of public health objectives and the preclusion of adequate monitoring and evaluation.   \n", "CONCLUSIONS The Responsibility Deal approach is fundamentally flawed in its expectation that industry will take voluntary actions that prioritise public health interests above its own.", "Being government-led counts for little in the absence of sanctions to drive compliance.", "Instead the initiative affords private interests the opportunity to influence in their favour the public health policies and strategies that affect their products."], "structured": true}
{"doc_id": 7373453, "title": "Role of endothelial shear stress in the natural history of coronary atherosclerosis and vascular remodeling: molecular, cellular, and vascular behavior.", "abstract": ["Although the entire coronary tree is exposed to the atherogenic effect of the systemic risk factors, atherosclerotic lesions form at specific arterial regions, where low and oscillatory endothelial shear stress (ESS) occur.", "Low ESS modulates endothelial gene expression through complex mechanoreception and mechanotransduction processes, inducing an atherogenic endothelial phenotype and formation of an early atherosclerotic plaque.", "Each early plaque exhibits an individual natural history of progression, regression, or stabilization, which is dependent not only on the formation and progression of atherosclerosis but also on the vascular remodeling response.", "Although the pathophysiologic mechanisms involved in the remodeling of the atherosclerotic wall are incompletely understood, the dynamic interplay between local hemodynamic milieu, low ESS in particular, and the biology of the wall is likely to be important.", "In this review, we explore the molecular, cellular, and vascular processes supporting the role of low ESS in the natural history of coronary atherosclerosis and vascular remodeling and indicate likely mechanisms concerning the different natural history trajectories of individual coronary lesions.", "Atherosclerotic plaques associated with excessive expansive remodeling evolve to high-risk plaques, because low ESS conditions persist, thereby promoting continued local lipid accumulation, inflammation, oxidative stress, matrix breakdown, and eventually further plaque progression and excessive expansive remodeling.", "An enhanced understanding of the pathobiologic processes responsible for atherosclerosis and vascular remodeling might allow for early identification of a high-risk coronary plaque and thereby provide a rationale for innovative diagnostic and/or therapeutic strategies for the management of coronary patients and prevention of acute coronary syndromes."], "structured": false}
{"doc_id": 7386360, "title": "Schistosoma mansoni worms induce anergy of T cells via selective up-regulation of programmed death ligand 1 on macrophages.", "abstract": ["Infectious pathogens can selectively stimulate activation or suppression of T cells to facilitate their survival within humans.", "In this study we demonstrate that the trematode parasite Schistosoma mansoni has evolved with two distinct mechanisms to suppress T cell activation.", "During the initial 4- to 12-wk acute stages of a worm infection both CD4(+) and CD8(+) T cells are anergized.", "In contrast, infection with male and female worms induced T cell anergy at 4 wk, which was replaced after egg laying by T cell suppression via a known NO-dependent mechanism, that was detected for up to 40 wk after infection.", "Worm-induced anergy was mediated by splenic F4/80(+) macrophages (Mphi) via an IL-4-, IL-13-, IL-10-, TGF-beta-, and NO-independent, but cell contact-dependent, mechanism.", "F4/80(+) Mphi isolated from worm-infected mice were shown to induce anergy of naive T cells in vitro.", "Furthermore, naive Mphi exposed to live worms in vitro also induced anergy in naive T cells.", "Flow cytometry on in vivo and in vitro worm-modulated Mphi revealed that of the family of B7 costimulatory molecules, only programmed death ligand 1 (PD-L1) was selectively up-regulated.", "The addition of inhibitory mAb against PD-L1, but not PD-L2, to worm-modulated Mphi completely blocked the ability of these cells to anergize T cells.", "These data highlight a novel mechanism through which S. mansoni worms have usurped the natural function of PD-L1 to reduce T cell activation during early acute stages of infection before the subsequent emergence of egg-induced T cell suppression in the chronic stages of infection."], "structured": false}
{"doc_id": 7396492, "title": "Thawing Frozen Robust Multi-array Analysis (fRMA)", "abstract": ["BACKGROUND A novel method of microarray preprocessing--Frozen Robust Multi-array Analysis (fRMA)--has recently been developed.", "This algorithm allows the user to preprocess arrays individually while retaining the advantages of multi-array preprocessing methods.", "The frozen parameter estimates required by this algorithm are generated using a large database of publicly available arrays.", "Curation of such a database and creation of the frozen parameter estimates is time-consuming; therefore, fRMA has only been implemented on the most widely used Affymetrix platforms.   \n", "RESULTS We present an R package, frmaTools, that allows the user to quickly create his or her own frozen parameter vectors.", "We describe how this package fits into a preprocessing workflow and explore the size of the training dataset needed to generate reliable frozen parameter estimates.", "This is followed by a discussion of specific situations in which one might wish to create one's own fRMA implementation.", "For a few specific scenarios, we demonstrate that fRMA performs well even when a large database of arrays in unavailable.   \n", "CONCLUSIONS By allowing the user to easily create his or her own fRMA implementation, the frmaTools package greatly increases the applicability of the fRMA algorithm.", "The frmaTools package is freely available as part of the Bioconductor project."], "structured": true}
{"doc_id": 7399084, "title": "Transcriptional repressor Blimp-1 is essential for T cell homeostasis and self-tolerance", "abstract": ["T cell homeostasis is crucial for a functional immune system, as the accumulation of T cells resulting from lack of regulatory T cells or an inability to shut down immune responses can lead to inflammation and autoimmune pathology.", "Here we show that Blimp-1, a transcriptional repressor that is a 'master regulator' of terminal B cell differentiation, was expressed in a subset of antigen-experienced CD4+ and CD8+ T cells.", "Mice reconstituted with fetal liver stem cells expressing a mutant Blimp-1 lacking the DNA-binding domain developed a lethal multiorgan inflammatory disease caused by an accumulation of effector and memory T cells.", "These data identify Blimp-1 as an essential regulator of T cell homeostasis and suggest that Blimp-1 regulates both B cell and T cell differentiation."], "structured": false}
{"doc_id": 7416873, "title": "Nuclear repositioning of the VSG promoter during developmental silencing in Trypanosoma brucei", "abstract": ["Interphase nuclear repositioning of chromosomes has been implicated in the epigenetic regulation of RNA polymerase (pol) II transcription.", "However, little is known about the nuclear position\u2013dependent regulation of RNA pol I\u2013transcribed loci.", "Trypanosoma brucei is an excellent model system to address this question because its two main surface protein genes, procyclin and variant surface glycoprotein (VSG), are transcribed by pol I and undergo distinct transcriptional activation or downregulation events during developmental differentiation.", "Although the monoallelically expressed VSG locus is exclusively localized to an extranucleolar body in the bloodstream form, in this study, we report that nonmutually exclusive procyclin genes are located at the nucleolar periphery.", "Interestingly, ribosomal DNA loci and pol I transcription activity are restricted to similar perinucleolar positions.", "Upon developmental transcriptional downregulation, however, the active VSG promoter selectively undergoes a rapid and dramatic repositioning to the nuclear envelope.", "Subsequently, the VSG promoter region was subjected to chromatin condensation.", "We propose a model whereby the VSG expression site pol I promoter is selectively targeted by temporal nuclear repositioning during developmental silencing."], "structured": false}
{"doc_id": 7419612, "title": "An administrative claims measure suitable for profiling hospital performance on the basis of 30-day all-cause readmission rates among patients with heart failure.", "abstract": ["BACKGROUND Readmission soon after hospital discharge is an expensive and often preventable event for patients with heart failure.", "We present a model approved by the National Quality Forum for the purpose of public reporting of hospital-level readmission rates by the Centers for Medicare & Medicaid Services.   \n", "METHODS AND RESULTS We developed a hierarchical logistic regression model to calculate hospital risk-standardized 30-day all-cause readmission rates for patients hospitalized with heart failure.", "The model was derived with the use of Medicare claims data for a 2004 cohort and validated with the use of claims and medical record data.", "The unadjusted readmission rate was 23.6%.", "The final model included 37 variables, had discrimination ranging from 15% observed 30-day readmission rate in the lowest predictive decile to 37% in the upper decile, and had a c statistic of 0.60.", "The 25th and 75th percentiles of the risk-standardized readmission rates across 4669 hospitals were 23.1% and 24.0%, with 5th and 95th percentiles of 22.2% and 25.1%, respectively.", "The odds of all-cause readmission for a hospital 1 standard deviation above average was 1.30 times that of a hospital 1 standard deviation below average.", "State-level adjusted readmission rates developed with the use of the claims model are similar to rates produced for the same cohort with the use of a medical record model (correlation, 0.97; median difference, 0.06 percentage points).   \n", "CONCLUSIONS This claims-based model of hospital risk-standardized readmission rates for heart failure patients produces estimates that may serve as surrogates for those derived from a medical record model."], "structured": true}
{"doc_id": 7421677, "title": "Queueing up for enzymatic processing: correlated signaling through coupled degradation", "abstract": ["High-throughput technologies have led to the generation of complex wiring diagrams as a post-sequencing paradigm for depicting the interactions between vast and diverse cellular species.", "While these diagrams are useful for analyzing biological systems on a large scale, a detailed understanding of the molecular mechanisms that underlie the observed network connections is critical for the further development of systems and synthetic biology.", "Here, we use queueing theory to investigate how 'waiting lines' can lead to correlations between protein 'customers' that are coupled solely through a downstream set of enzymatic 'servers'.", "Using the E. coli ClpXP degradation machine as a model processing system, we observe significant cross-talk between two networks that are indirectly coupled through a common set of processors.", "We further illustrate the implications of enzymatic queueing using a synthetic biology application, in which two independent synthetic networks demonstrate synchronized behavior when common ClpXP machinery is overburdened.", "Our results demonstrate that such post-translational processes can lead to dynamic connections in cellular networks and may provide a mechanistic understanding of existing but currently inexplicable links."], "structured": false}
{"doc_id": 7426741, "title": "The histone demethylases Jhdm1a/1b enhance somatic cell reprogramming in a vitamin-C-dependent manner.", "abstract": ["Reprogramming of somatic cells into induced pluripotent stem cells (iPSCs) resets the epigenome to an embryonic-like state.", "Vitamin C enhances the reprogramming process, but the underlying mechanisms are unclear.", "Here we show that the histone demethylases Jhdm1a/1b are key effectors of somatic cell reprogramming downstream of vitamin C. We first observed that vitamin C induces H3K36me2/3 demethylation in mouse embryonic fibroblasts in culture and during reprogramming.", "We then identified Jhdm1a/1b, two known vitamin-C-dependent H3K36 demethylases, as potent regulators of reprogramming through gain- and loss-of-function approaches.", "Furthermore, we found that Jhdm1b accelerates cell cycle progression and suppresses cell senescence during reprogramming by repressing the Ink4/Arf locus.", "Jhdm1b also cooperates with Oct4 to activate the microRNA cluster 302/367, an integral component of the pluripotency machinery.", "Our results therefore reveal a role for H3K36me2/3 in cell fate determination and establish a link between histone demethylases and vitamin-C-induced reprogramming."], "structured": false}
{"doc_id": 7433668, "title": "Preexisting helminth infection induces inhibition of innate pulmonary anti-tuberculosis defense by engaging the IL-4 receptor pathway", "abstract": ["Tuberculosis and helminthic infections coexist in many parts of the world, yet the impact of helminth-elicited Th2 responses on the ability of the host to control Mycobacterium tuberculosis (Mtb) infection has not been fully explored.", "We show that mice infected with the intestinal helminth Nippostrongylus brasiliensis (Nb) exhibit a transitory impairment of resistance to airborne Mtb infection.", "Furthermore, a second dose of Nb infection substantially increases the bacterial burden in the lungs of co-infected mice.", "Interestingly, the Th2 response in the co-infected animals did not impair the onset and development of the protective Mtb-specific Th1 cellular immune responses.", "However, the helminth-induced Th2 environment resulted in the accumulation of alternatively activated macrophages (AAMs) in the lung.", "Co-infected mice lacking interleukin (IL) 4R\u03b1 exhibited improved ability to control Mtb infection, which was accompanied by significantly reduced accumulation of AAMs.", "Moreover, IL-4R\u03b1(-/-) mice adoptively transferred with wild-type macrophages had a significantly higher Mtb load in their lungs compared with those that received IL-4R\u03b1(-/-) macrophages, suggesting a direct contribution for the IL-4R pathway to the heightened susceptibility of co-infected animals.", "The Th2 response can thus enhance the intracellular persistence of Mtb, in part by mediating the alternative activation of macrophages via the IL-4R\u03b1 signaling pathway."], "structured": false}
{"doc_id": 7438803, "title": "Archaea in biogeochemical cycles.", "abstract": ["Archaea constitute a considerable fraction of the microbial biomass on Earth.", "Like Bacteria they have evolved a variety of energy metabolisms using organic and/or inorganic electron donors and acceptors, and many of them are able to fix carbon from inorganic sources.", "Archaea thus play crucial roles in the Earth's global geochemical cycles and influence greenhouse gas emissions.", "Methanogenesis and anaerobic methane oxidation are important steps in the carbon cycle; both are performed exclusively by anaerobic archaea.", "Oxidation of ammonia to nitrite is performed by Thaumarchaeota.", "They represent the only archaeal group that resides in large numbers in the global aerobic terrestrial and marine environments on Earth.", "Sulfur-dependent archaea are confined mostly to hot environments, but metal leaching by acidophiles and reduction of sulfate by anaerobic, nonthermophilic methane oxidizers have a potential impact on the environment.", "The metabolisms of a large number of archaea, in particular those dominating the subsurface, remain to be explored."], "structured": false}
{"doc_id": 7447120, "title": "Novel proteinaceous infectious particles cause scrapie.", "abstract": ["After infection and a prolonged incubation period, the scrapie agent causes a degenerative disease of the central nervous system in sheep and goats.", "Six lines of evidence including sensitivity to proteases demonstrate that this agent contains a protein that is required for infectivity.", "Although the scrapie agent is irreversibly inactivated by alkali, five procedures with more specificity for modifying nucleic acids failed to cause inactivation.", "The agent shows heterogeneity with respect to size, apparently a result of its hydrophobicity; the smallest form may have a molecular weight of 50,000 or less.", "Because the novel properties of the scrapie agent distinguish it from viruses, plasmids, and viroids, a new term \"prion\" is proposed to denote a small proteinaceous infectious particle which is resistant to inactivation by most procedures that modify nucleic acids.", "Knowledge of the scrapie agent structure may have significance for understanding the causes of several degenerative diseases."], "structured": false}
{"doc_id": 7451018, "title": "Viral Carcinogenesis.", "abstract": ["Cancer has been recognized for thousands of years.", "Egyptians believed that cancer occurred at the will of the gods.", "Hippocrates believed human disease resulted from an imbalance of the four humors: blood, phlegm, yellow bile, and black bile with cancer being caused by excess black bile.", "The lymph theory of cancer replaced the humoral theory and the blastema theory replaced the lymph theory.", "Rudolph Virchow was the first to recognize that cancer cells like all cells came from other cells and believed chronic irritation caused cancer.", "At the same time there was a belief that trauma caused cancer, though it never evolved after many experiments inducing trauma.", "The birth of virology occurred in 1892 when Dimitri Ivanofsky demonstrated that diseased tobacco plants remained infective after filtering their sap through a filter that trapped bacteria.", "Martinus Beijerinck would call the tiny infective agent a virus and both Dimitri Ivanofsky and Marinus Beijerinck would become the fathers of virology.", "Not to long thereafter, Payton Rous founded the field of tumor virology in 1911 with his discovery of a transmittable sarcoma of chickens by what would come to be called Rous sarcoma virus or RSV for short.", "The first identified human tumor virus was the Epstein-Barr virus (EBV), named after Tony Epstein and Yvonne Barr who visualized the virus particles in Burkitt's lymphoma cells by electron microscopy in 1965.", "Since that time, many viruses have been associated with carcinogenesis including the most studied, human papilloma virus associated with cervical carcinoma, many other anogenital carcinomas, and oropharyngeal carcinoma.", "The World Health Organization currently estimates that approximately 22% of worldwide cancers are attributable to infectious etiologies, of which viral etiologies is estimated at 15-20%.", "The field of tumor virology/viral carcinogenesis has not only identified viruses as etiologic agents of human cancers, but has also given molecular insights to all human cancers including the oncogene activation and tumor suppressor gene inactivation."], "structured": false}
{"doc_id": 7451607, "title": "Monitoring spatiotemporal biogenesis of macromolecular assemblies by pulse-chase epitope labeling.", "abstract": ["Many cellular proteins perform their roles within macromolecular assemblies.", "Hence, an understanding of how these multiprotein complexes form is a fundamental question in cell biology.", "We developed a translation-controlled pulse-chase system that allows time-resolved isolation of newly forming multiprotein complexes in chemical quantities suitable for biochemical and cell biological analysis.", "The \"pulse\" is triggered by an unnatural amino acid, which induces immediate translation of an amber stop codon repressed mRNA encoding the protein of interest with a built-in tag for detection and purification.", "The \"chase\" is elicited by stopping translation of this bait via a riboswitch in the respective mRNA.", "Over the course of validating our method, we discovered a distinct time-resolved assembly step during NPC biogenesis and could directly monitor the spatiotemporal maturation of preribosomes via immunofluorescence detection and purification of a pulse-labeled ribosomal protein.", "Thus, we provide an innovative strategy to study dynamic protein assembly within cellular networks."], "structured": false}
{"doc_id": 7454794, "title": "Statins in the primary prevention of cardiovascular disease", "abstract": ["Statins are widely used in the evidence-based lowering of cardiovascular disease (CVD) risk.", "The use of these drugs for secondary prevention of CVD is well founded, but their expanding use in primary prevention\u2014in individuals without documented CVD\u2014has raised some concerns.", "Firstly, evidence suggests that, in primary prevention, statins substantially decrease CVD morbidity, but only moderately reduce CVD mortality.", "Secondly, long-term statin use might cause adverse effects, such as incident diabetes mellitus.", "Thirdly, the cost-effectiveness of such a strategy is unclear, and has to be balanced against the risk of 'overmedicating' the general population.", "Data clearly support the use of statins for primary prevention in high-risk individuals, in whom the strategy is cost-effective and the benefits exceed the risks.", "Whether primary prevention is beneficial in individuals at low or moderate risk is not certain.", "Therefore, the prescription of statins for primary prevention should be individualized on the basis of clinical judgment, particularly for low-risk individuals.", "In appropriately selected individuals, statins should also be used for primary prevention of ischaemic stroke and transient ischaemic attack."], "structured": false}
{"doc_id": 7465900, "title": "Acetylation of apurinic/apyrimidinic endonuclease-1 regulates Helicobacter pylori-mediated gastric epithelial cell apoptosis.", "abstract": ["BACKGROUND & AIMS Helicobacter pylori-induced gastric epithelial cell (GEC) apoptosis is a complex process that includes activation of the tumor suppressor p53.", "p53-mediated apoptosis involves p53 activation, bax transcription, and cytochrome c release from mitochondria.", "Apurinic/apyrimidinic endonuclease-1 (APE-1) regulates transcriptional activity of p53, and H pylori induce APE-1 expression in human GECs.", "H pylori infection increases intracellular calcium ion concentration [Ca2+]i of GECs, which induces APE-1 acetylation.", "We investigated the effects of H pylori infection and APE-1 acetylation on GEC apoptosis.   \n", "METHODS AGS cells (wild-type or with suppressed APE-1), KATO III cells, and cells isolated from gastric biopsy specimens were infected with H pylori.", "Effects were examined by immunoblotting, real-time reverse-transcription polymerase chain reaction, immunoprecipitation, immunofluorescence microscopy, chromatin immunoprecipitation, mobility shift, DNA binding, and luciferase assays.   \n", "RESULTS H pylori infection increased [Ca2+]i and acetylation of APE-1 in GECs, but the acetylation status of APE-1 did not affect the transcriptional activity of p53.", "In GECs, expression of a form of APE-1 that could not be acetylated increased total and mitochondrial levels of Bax and induced release of cytochrome c and fragmentation of DNA; expression of wild-type APE-1 reduced these apoptotic events.", "We identified a negative calcium response element in the human bax promoter and found that poly (adenosine diphosphate-ribose) polymerase 1 recruited the acetylated APE-1/histone deacetylase-1 repressor complex to bax nCaRE.   \n", "CONCLUSIONS H pylori-mediated acetylation of APE-1 suppresses Bax expression; this prevents p53-mediated apoptosis when H pylori infect GECs."], "structured": true}
{"doc_id": 7468449, "title": "A beginning of the end: new insights into the functional organization of telomeres", "abstract": ["Ever since the first demonstration of their repetitive sequence and unique replication pathway, telomeres have beguiled researchers with how they function in protecting chromosome ends.", "Of course much has been learned over the years, and we now appreciate that telomeres are comprised of the multimeric protein/DNA shelterin complex and that the formation of t-loops provides protection from DNA damage machinery.", "Deriving their name from D-loops, t-loops are generated by the insertion of the 3' overhang into telomeric repeats facilitated by the binding of TRF2.", "Recent studies have uncovered novel forms of chromosome end-structure that may implicate telomere organization in cellular processes beyond its essential role in telomere protection and homeostasis.", "In particular, we have recently described that t-loops form in a TRF2-dependent manner at interstitial telomere repeat sequences, which we termed interstitial telomere loops (ITLs).", "These structures are also dependent on association of lamin A/C, a canonical component of the nucleoskeleton that is mutated in myriad human diseases, including human segmental progeroid syndromes.", "Since ITLs are associated with telomere stability and require functional lamin A/C, our study suggests a mechanistic link between cellular aging (replicative senescence induced by telomere shortening) and organismal aging (modeled by Hutchinson Gilford Progeria Syndrome).", "Here we speculate on other potential ramifications of ITL formation, from gene expression to genome stability to chromosome structure."], "structured": false}
{"doc_id": 7481159, "title": "Biochemical analysis of TssK, a core component of the bacterial Type VI secretion system, reveals distinct oligomeric states of TssK and identifies a TssK\u2013TssFG subcomplex", "abstract": ["Gram-negative bacteria use the Type VI secretion system (T6SS) to inject toxic proteins into rival bacteria or eukaryotic cells.", "However, the mechanism of the T6SS is incompletely understood.", "In the present study, we investigated a conserved component of the T6SS, TssK, using the antibacterial T6SS of Serratia marcescens as a model system.", "TssK was confirmed to be essential for effector secretion by the T6SS.", "The native protein, although not an integral membrane protein, appeared to localize to the inner membrane, consistent with its presence within a membrane-anchored assembly.", "Recombinant TssK purified from S. marcescens was found to exist in several stable oligomeric forms, namely trimer, hexamer and higher-order species.", "Native-level purification of TssK identified TssF and TssG as interacting proteins.", "TssF and TssG, conserved T6SS components of unknown function, were required for T6SS activity, but not for correct localization of TssK. A complex containing TssK, TssF and TssG was subsequently purified in vitro, confirming that these three proteins form a new subcomplex within the T6SS.", "Our findings provide new insight into the T6SS assembly, allowing us to propose a model whereby TssK recruits TssFG into the membrane-associated T6SS complex and different oligomeric states of TssK may contribute to the dynamic mechanism of the system."], "structured": false}
{"doc_id": 7482674, "title": "Involvement of ER Stress in Dysmyelination of Pelizaeus-Merzbacher Disease with PLP1 Missense Mutations Shown by iPSC-Derived Oligodendrocytes", "abstract": ["Pelizaeus-Merzbacher disease (PMD) is a form of X-linked leukodystrophy caused by mutations in the proteolipid protein 1 (PLP1) gene.", "Although PLP1 proteins with missense mutations have been shown to accumulate in the rough endoplasmic reticulum (ER) in disease model animals and cell lines transfected with mutant PLP1 genes, the exact pathogenetic mechanism of PMD has not previously been clarified.", "In this study, we established induced pluripotent stem cells (iPSCs) from two PMD patients carrying missense mutation and differentiated them into oligodendrocytes in vitro.", "In the PMD iPSC-derived oligodendrocytes, mislocalization of mutant PLP1 proteins to the ER and an association between increased susceptibility to ER stress and increased numbers of apoptotic oligodendrocytes were observed.", "Moreover, electron microscopic analysis demonstrated drastically reduced myelin formation accompanied by abnormal ER morphology.", "Thus, this study demonstrates the involvement of ER stress in pathogenic dysmyelination in the oligodendrocytes of PMD patients with the PLP1 missense mutation."], "structured": false}
{"doc_id": 7485455, "title": "Using Routine Surveillance Data to Estimate the Epidemic Potential of Emerging Zoonoses: Application to the Emergence of US Swine Origin Influenza A H3N2v Virus", "abstract": ["BACKGROUND Prior to emergence in human populations, zoonoses such as SARS cause occasional infections in human populations exposed to reservoir species.", "The risk of widespread epidemics in humans can be assessed by monitoring the reproduction number R (average number of persons infected by a human case).", "However, until now, estimating R required detailed outbreak investigations of human clusters, for which resources and expertise are not always available.", "Additionally, existing methods do not correct for important selection and under-ascertainment biases.", "Here, we present simple estimation methods that overcome many of these limitations.   \n", "METHODS AND FINDINGS Our approach is based on a parsimonious mathematical model of disease transmission and only requires data collected through routine surveillance and standard case investigations.", "We apply it to assess the transmissibility of swine-origin influenza A H3N2v-M virus in the US, Nipah virus in Malaysia and Bangladesh, and also present a non-zoonotic example (cholera in the Dominican Republic).", "Estimation is based on two simple summary statistics, the proportion infected by the natural reservoir among detected cases (G) and among the subset of the first detected cases in each cluster (F).", "If detection of a case does not affect detection of other cases from the same cluster, we find that R can be estimated by 1-G; otherwise R can be estimated by 1-F when the case detection rate is low.", "In more general cases, bounds on R can still be derived.   \n", "CONCLUSIONS We have developed a simple approach with limited data requirements that enables robust assessment of the risks posed by emerging zoonoses.", "We illustrate this by deriving transmissibility estimates for the H3N2v-M virus, an important step in evaluating the possible pandemic threat posed by this virus.", "Please see later in the article for the Editors' Summary."], "structured": true}
{"doc_id": 7486516, "title": "Independently Evolving Species in Asexual Bdelloid Rotifers", "abstract": ["Asexuals are an important test case for theories of why species exist.", "If asexual clades displayed the same pattern of discrete variation as sexual clades, this would challenge the traditional view that sex is necessary for diversification into species.", "However, critical evidence has been lacking: all putative examples have involved organisms with recent or ongoing histories of recombination and have relied on visual interpretation of patterns of genetic and phenotypic variation rather than on formal tests of alternative evolutionary scenarios.", "Here we show that a classic asexual clade, the bdelloid rotifers, has diversified into distinct evolutionary species.", "Intensive sampling of the genus Rotaria reveals the presence of well-separated genetic clusters indicative of independent evolution.", "Moreover, combined genetic and morphological analyses reveal divergent selection in feeding morphology, indicative of niche divergence.", "Some of the morphologically coherent groups experiencing divergent selection contain several genetic clusters, in common with findings of cryptic species in sexual organisms.", "Our results show that the main causes of speciation in sexual organisms, population isolation and divergent selection, have the same qualitative effects in an asexual clade.", "The study also demonstrates how combined molecular and morphological analyses can shed new light on the evolutionary nature of species."], "structured": false}
{"doc_id": 7487927, "title": "The Ribosome Biogenesis Factor Nol11 Is Required for Optimal rDNA Transcription and Craniofacial Development in Xenopus ", "abstract": ["The production of ribosomes is ubiquitous and fundamental to life.", "As such, it is surprising that defects in ribosome biogenesis underlie a growing number of symptomatically distinct inherited disorders, collectively called ribosomopathies.", "We previously determined that the nucleolar protein, NOL11, is essential for optimal pre-rRNA transcription and processing in human tissue culture cells.", "However, the role of NOL11 in the development of a multicellular organism remains unknown.", "Here, we reveal a critical function for NOL11 in vertebrate ribosome biogenesis and craniofacial development.", "Nol11 is strongly expressed in the developing cranial neural crest (CNC) of both amphibians and mammals, and knockdown of Xenopus nol11 results in impaired pre-rRNA transcription and processing, increased apoptosis, and abnormal development of the craniofacial cartilages.", "Inhibition of p53 rescues this skeletal phenotype, but not the underlying ribosome biogenesis defect, demonstrating an evolutionarily conserved control mechanism through which ribosome-impaired craniofacial cells are removed.", "Excessive activation of this mechanism impairs craniofacial development.", "Together, our findings reveal a novel requirement for Nol11 in craniofacial development, present the first frog model of a ribosomopathy, and provide further insight into the clinically important relationship between specific ribosome biogenesis proteins and craniofacial cell survival."], "structured": false}
{"doc_id": 7488455, "title": "Genomic Nucleosome Organization Reconstituted with Pure Proteins", "abstract": ["Chromatin remodelers regulate genes by organizing nucleosomes around promoters, but their individual contributions are obfuscated by the complex in vivo milieu of factor redundancy and indirect effects.", "Genome-wide reconstitution of promoter nucleosome organization with purified proteins resolves this problem and is therefore a critical goal.", "Here, we reconstitute four stages of nucleosome architecture using purified components: yeast genomic DNA, histones, sequence-specific Abf1/Reb1, and remodelers RSC, ISW2, INO80, and ISW1a.", "We identify direct, specific, and sufficient contributions that in vivo observations validate.", "First, RSC clears promoters by translating poly(dA:dT) into directional nucleosome removal.", "Second, partial redundancy is recapitulated where INO80 alone, or ISW2 at Abf1/Reb1sites, positions +1 nucleosomes.", "Third, INO80 and ISW2 each align downstream nucleosomal arrays.", "Fourth, ISW1a tightens the spacing to canonical repeat lengths.", "Such a minimal set of rules and proteins establishes core mechanisms by which promoter chromatin architecture arises through a blend of redundancy and specialization."], "structured": false}
{"doc_id": 7489663, "title": "Identification of splenic reservoir monocytes and their deployment to inflammatory sites.", "abstract": ["A current paradigm states that monocytes circulate freely and patrol blood vessels but differentiate irreversibly into dendritic cells (DCs) or macrophages upon tissue entry.", "Here we show that bona fide undifferentiated monocytes reside in the spleen and outnumber their equivalents in circulation.", "The reservoir monocytes assemble in clusters in the cords of the subcapsular red pulp and are distinct from macrophages and DCs.", "In response to ischemic myocardial injury, splenic monocytes increase their motility, exit the spleen en masse, accumulate in injured tissue, and participate in wound healing.", "These observations uncover a role for the spleen as a site for storage and rapid deployment of monocytes and identify splenic monocytes as a resource that the body exploits to regulate inflammation."], "structured": false}
{"doc_id": 7492250, "title": "Prox1 Is Required for Granule Cell Maturation and Intermediate Progenitor Maintenance During Brain Neurogenesis", "abstract": ["The dentate gyrus has an important role in learning and memory, and adult neurogenesis in the subgranular zone of the dentate gyrus may play a role in the acquisition of new memories.", "The homeobox gene Prox1 is expressed in the dentate gyrus during embryonic development and adult neurogenesis.", "Here we show that Prox1 is necessary for the maturation of granule cells in the dentate gyrus during development and for the maintenance of intermediate progenitors during adult neurogenesis.", "We also demonstrate that Prox1-expressing intermediate progenitors are required for adult neural stem cell self-maintenance in the subgranular zone; thus, we have identified a previously unknown non-cell autonomous regulatory feedback mechanism that controls adult neurogenesis in this region of the mammalian brain.", "Finally, we show that the ectopic expression of Prox1 induces premature differentiation of neural stem cells."], "structured": false}
{"doc_id": 7492420, "title": "The abbreviated pluripotent cell cycle.", "abstract": ["Human embryonic stem cells (hESCs) and induced pluripotent stem cells proliferate rapidly and divide symmetrically producing equivalent progeny cells.", "In contrast, lineage committed cells acquire an extended symmetrical cell cycle.", "Self-renewal of tissue-specific stem cells is sustained by asymmetric cell division where one progeny cell remains a progenitor while the partner progeny cell exits the cell cycle and differentiates.", "There are three principal contexts for considering the operation and regulation of the pluripotent cell cycle: temporal, regulatory, and structural.", "The primary temporal context that the pluripotent self-renewal cell cycle of hESCs is a short G1 period without reducing periods of time allocated to S phase, G2, and mitosis.", "The rules that govern proliferation in hESCs remain to be comprehensively established.", "However, several lines of evidence suggest a key role for the na\u00efve transcriptome of hESCs, which is competent to stringently regulate the embryonic stem cell (ESC) cell cycle.", "This supports the requirements of pluripotent cells to self-propagate while suppressing expression of genes that confer lineage commitment and/or tissue specificity.", "However, for the first time, we consider unique dimensions to the architectural organization and assembly of regulatory machinery for gene expression in nuclear microenviornments that define parameters of pluripotency.", "From both fundamental biological and clinical perspectives, understanding control of the abbreviated ESC cycle can provide options to coordinate control of proliferation versus differentiation.", "Wound healing, tissue engineering, and cell-based therapy to mitigate developmental aberrations illustrate applications that benefit from knowledge of the biology of the pluripotent cell cycle."], "structured": false}
{"doc_id": 7506409, "title": "Senescent growth arrest in mesenchymal stem cells is bypassed by Wip1-mediated downregulation of intrinsic stress signaling pathways.", "abstract": ["Human mesenchymal stem cells (hMSCs) have been widely studied as a source of primary adult stem cells for cell therapy because of their multidifferentiation potential; however, the growth arrest (also known as \"premature senescence\") often found in hMSCs cultured in vitro has been a major obstacle to the in-depth characterization of these cells.", "In addition, the inability to maintain constant cell growth hampers the development of additional genetic modifications aimed at achieving desired levels of differentiation to specific tissues; however, the molecular mechanisms that govern this phenomenon remain unclear, with the exception of a few studies demonstrating that induction of p16INK4a is responsible for this senescence-like event.", "Here, we observed that the premature growth arrest in hMSCs occurs in parallel with the induction of p16INK4a, following abrogation of inhibitory phosphorylation of retinoblastoma protein.", "These stress responses were concurrent with increased formation of reactive oxygen species (ROSs) from mitochondria and increased p38 mitogen-activated protein kinase (MAPK) activity.", "The introduction of Wip1 (wild-type p53 inducible phosphatase-1), a well-studied stress modulator, significantly lowered p16INK4a expression and led to p38 MAPK inactivation, although it failed to affect the levels of ROSs.", "Moreover, the suppression of stress responses by Wip1 apparently extended the life span of hMSCs, compared with control conditions, while maintaining their multilineage differentiation potential.", "Based on these results, we suggest that senescent growth arrest in hMSCs may result from activation of stress signaling pathways and consequent onset of stress responses, due in part to ROS production during prolonged in vitro culture."], "structured": false}
{"doc_id": 7514614, "title": "Understanding the Odd Science of Aging", "abstract": ["Evolutionary considerations suggest aging is caused not by active gene programming but by evolved limitations in somatic maintenance, resulting in a build-up of damage.", "Ecological factors such as hazard rates and food availability influence the trade-offs between investing in growth, reproduction, and somatic survival, explaining why species evolved different life spans and why aging rate can sometimes be altered, for example, by dietary restriction.", "To understand the cell and molecular basis of aging is to unravel the multiplicity of mechanisms causing damage to accumulate and the complex array of systems working to keep damage at bay."], "structured": false}
{"doc_id": 7521113, "title": "Fate mapping reveals origins and dynamics of monocytes and tissue macrophages under homeostasis.", "abstract": ["Mononuclear phagocytes, including monocytes, macrophages, and dendritic cells, contribute to tissue integrity as well as to innate and adaptive immune defense.", "Emerging evidence for labor division indicates that manipulation of these cells could bear therapeutic potential.", "However, specific ontogenies of individual populations and the overall functional organization of this cellular network are not well defined.", "Here we report a fate-mapping study of the murine monocyte and macrophage compartment taking advantage of constitutive and conditional CX(3)CR1 promoter-driven Cre recombinase expression.", "We have demonstrated that major tissue-resident macrophage populations, including liver Kupffer cells and lung alveolar, splenic, and peritoneal macrophages, are established prior to birth and maintain themselves subsequently during adulthood independent of replenishment by blood monocytes.", "Furthermore, we have established that short-lived Ly6C(+) monocytes constitute obligatory steady-state precursors of blood-resident Ly6C(-) cells and that the abundance of Ly6C(+) blood monocytes dynamically controls the circulation lifespan of their progeny."], "structured": false}
{"doc_id": 7547329, "title": "Dealing with substantial heterogeneity in Cochrane reviews. Cross-sectional study", "abstract": ["BACKGROUND Dealing with heterogeneity in meta-analyses is often tricky, and there is only limited advice for authors on what to do.", "We investigated how authors addressed different degrees of heterogeneity, in particular whether they used a fixed effect model, which assumes that all the included studies are estimating the same true effect, or a random effects model where this is not assumed.   \n", "METHODS We sampled randomly 60 Cochrane reviews from 2008, which presented a result in its first meta-analysis with substantial heterogeneity (I2 greater than 50%, i.e. more than 50% of the variation is due to heterogeneity rather than chance).", "We extracted information on choice of statistical model, how the authors had handled the heterogeneity, and assessed the methodological quality of the reviews in relation to this.   \n", "RESULTS The distribution of heterogeneity was rather uniform in the whole I2 interval, 50-100%.", "A fixed effect model was used in 33 reviews (55%), but there was no correlation between I2 and choice of model (P = 0.79).", "We considered that 20 reviews (33%), 16 of which had used a fixed effect model, had major problems.", "The most common problems were: use of a fixed effect model and lack of rationale for choice of that model, lack of comment on even severe heterogeneity and of reservations and explanations of its likely causes.", "The problematic reviews had significantly fewer included trials than other reviews (4.3 vs. 8.0, P = 0.024).", "The problems became less pronounced with time, as those reviews that were most recently updated more often used a random effects model.   \n", "CONCLUSION One-third of Cochrane reviews with substantial heterogeneity had major problems in relation to their handling of heterogeneity.", "More attention is needed to this issue, as the problems we identified can be essential for the conclusions of the reviews."], "structured": true}
{"doc_id": 7548577, "title": "Antagonistic Controls of Autophagy and Glycogen Accumulation by Snf1p, the Yeast Homolog of AMP-Activated Protein Kinase, and the Cyclin-Dependent", "abstract": ["In the yeast Saccharomyces cerevisiae, glycogen is accumulated as a carbohydrate reserve when cells are deprived of nutrients.", "Yeast mutated in SNF1, a gene encoding a protein kinase required for glucose derepression, has diminished glycogen accumulation and concomitant inactivation of glycogen synthase.", "Restoration of synthesis in an snf1 strain results only in transient glycogen accumulation, implying the existence of other SNF1-dependent controls of glycogen storage.", "A genetic screen revealed that two genes involved in autophagy, APG1 and APG13, may be regulated by SNF1.", "Increased autophagic activity was observed in wild-type cells entering the stationary phase, but this induction was impaired in an snf1 strain.", "Mutants defective for autophagy were able to synthesize glycogen upon approaching the stationary phase, but were unable to maintain their glycogen stores, because subsequent synthesis was impaired and degradation by phosphorylase, Gph1p, was enhanced.", "Thus, deletion of GPH1 partially reversed the loss of glycogen accumulation in autophagy mutants.", "Loss of the vacuolar glucosidase, SGA1, also protected glycogen stores, but only very late in the stationary phase.", "Gph1p and Sga1p may therefore degrade physically distinct pools of glycogen.", "Pho85p is a cyclin-dependent protein kinase that antagonizes SNF1 control of glycogen synthesis.", "Induction of autophagy in pho85 mutants entering the stationary phase was exaggerated compared to the level in wild-type cells, but was blocked in apg1 pho85 mutants.", "We propose that Snf1p and Pho85p are, respectively, positive and negative regulators of autophagy, probably via Apg1 and/or Apg13.", "Defective glycogen storage in snf1 cells can be attributed to both defective synthesis upon entry into stationary phase and impaired maintenance of glycogen levels caused by the lack of autophagy."], "structured": false}
{"doc_id": 7549811, "title": "Preferential binding of a kinesin-1 motor to GTP-tubulin\u2013rich microtubules underlies polarized vesicle transport", "abstract": ["Polarized transport in neurons is fundamental for the formation of neuronal circuitry.", "A motor domain-containing truncated KIF5 (a kinesin-1) recognizes axonal microtubules, which are enriched in EB1 binding sites, and selectively accumulates at the tips of axons.", "However, it remains unknown what cue KIF5 recognizes to result in this selective accumulation.", "We found that axonal microtubules were preferentially stained by the anti-GTP-tubulin antibody hMB11.", "Super-resolution microscopy combined with EM immunocytochemistry revealed that hMB11 was localized at KIF5 attachment sites.", "In addition, EB1, which binds preferentially to guanylyl-methylene-diphosphate (GMPCPP) microtubules in vitro, recognized hMB11 binding sites on axonal microtubules.", "Further, expression of hMB11 antibody in neurons disrupted the selective accumulation of truncated KIF5 in the axon tips.", "In vitro studies revealed approximately threefold stronger binding of KIF5 motor head to GMPCPP microtubules than to GDP microtubules.", "Collectively, these data suggest that the abundance of GTP-tubulin in axonal microtubules may underlie selective KIF5 localization and polarized axonal vesicular transport."], "structured": false}
{"doc_id": 7552147, "title": "Developmental biology of the pancreas.", "abstract": ["The pancreas is an organ containing two distinct populations of cells, the exocrine cells that secrete enzymes into the digestive tract, and the endocrine cells that secrete hormones into the bloodstream.", "It arises from the endoderm as a dorsal and a ventral bud which fuse together to form the single organ.", "Mammals, birds, reptiles and amphibians have a pancreas with similar histology and mode of development, while in some fish, the islet cells are segregated as Brockmann bodies.", "Invertebrates do not have a pancreas, but comparable endocrine cells may be found in the gut or the brain.", "The early pancreatic bud shows uniform expression of the homeobox gene IPF-1 (also known as IDX-1, STF-1 or PDX), which when mutated to inactivity leads to total absence of the organ.", "The occurrence of heterotopic pancreas in the embryo, and also the metaplasias that can be displayed by a regenerating pancreas in the adult, both suggest that only a few gene products distinguish the pancreatic cell state from that of the surrounding tissues of duodenum, gall bladder and liver.", "In the developing pancreatic buds, the endocrine cells start to differentiate before the exocrine cells, and co-expression of different hormones by the same cell is often observed at early stages.", "Although pancreatic endocrine cells produce many gene products also characteristic of neurons, evidence from in vitro cultures and from quailchick grafts shows that they are of endogenous and not of neural crest origin.", "Observational studies suggest strongly that both endocrine and exocrine cells arise from the same endodermal rudiment.", "Development of the pancreas in embryonic life requires a trophic stimulus from the associated mesenchyme.", "In postnatal life, all cell types in the pancreas continue to grow.", "Destruction of acinar tissue by duct ligation or ethionine treatment is followed by rapid regeneration.", "Surgical removal of parts of the pancreas is followed by moderate but incomplete regeneration of both acini and islets.", "Poisoning with alloxan or streptozotocin can lead to permanent depletion of beta cells.", "Although the cell kinetics of the pancreas are not understood, it seems likely that there is a continuous slow turnover of cells, fed from a stem cells population in the ducts, and that the controls on the production rate of each cell type are local rather than systemic."], "structured": false}
{"doc_id": 7552215, "title": "Long term pharmacotherapy for obesity and overweight: updated meta-analysis.", "abstract": ["OBJECTIVE To summarise the long term efficacy of anti-obesity drugs in reducing weight and improving health status.   \n", "DESIGN Updated meta-analysis of randomised trials.   \n", "DATA SOURCES Medline, Embase, the Cochrane controlled trials register, the Current Science meta-register of controlled trials, and reference lists of identified articles.", "All data sources were searched from December 2002 (end date of last search) to December 2006.   ", "STUDIES REVIEWED Double blind randomised placebo controlled trials of approved anti-obesity drugs used in adults (age over 18) for one year or longer.   \n", "RESULTS 30 trials of one to four years' duration met the inclusion criteria: 16 orlistat (n=10 631 participants), 10 sibutramine (n=2623), and four rimonabant (n=6365).", "Of these, 14 trials were new and 16 had previously been identified.", "Attrition rates averaged 30-40%.", "Compared with placebo, orlistat reduced weight by 2.9 kg (95% confidence interval 2.5 kg to 3.2 kg), sibutramine by 4.2 kg (3.6 kg to 4.7 kg), and rimonabant by 4.7 kg (4.1 kg to 5.3 kg).", "Patients receiving active drug treatment were significantly more likely to achieve 5% and 10% weight loss thresholds.", "Orlistat reduced the incidence of diabetes and improved concentrations of total cholesterol and low density lipoprotein cholesterol, blood pressure, and glycaemic control in patients with diabetes but increased rates of gastrointestinal side effects and slightly lowered concentrations of high density lipoprotein.", "Sibutramine improved [corrected] concentrations of high density lipoprotein cholesterol and triglycerides [corrected] Rimonabant improved concentrations of high density lipoprotein cholesterol and triglycerides, blood pressure, and glycaemic control in patients with diabetes but increased the risk of mood disorders.   \n", "CONCLUSIONS Orlistat, sibutramine, and rimonabant modestly reduce weight, have differing effects on cardiovascular risk profiles, and have specific adverse effects."], "structured": true}
{"doc_id": 7560876, "title": "The centrosome cycle: Centriole biogenesis, duplication and inherent asymmetries", "abstract": ["Centrosomes are microtubule-organizing centres of animal cells.", "They influence the morphology of the microtubule cytoskeleton, function as the base for the primary cilium and serve as a nexus for important signalling pathways.", "At the core of a typical centrosome are two cylindrical microtubule-based structures termed centrioles, which recruit a matrix of associated pericentriolar material.", "Cells begin the cell cycle with exactly one centrosome, and the duplication of centrioles is constrained such that it occurs only once per cell cycle and at a specific site in the cell.", "As a result of this duplication mechanism, the two centrioles differ in age and maturity, and thus have different functions; for example, the older of the two centrioles can initiate the formation of a ciliary axoneme.", "We discuss spatial aspects of the centrosome duplication cycle, the mechanism of centriole assembly and the possible consequences of the inherent asymmetry of centrioles and centrosomes."], "structured": false}
{"doc_id": 7568596, "title": "Osteoclasts control reactivation of dormant myeloma cells by remodelling the endosteal niche", "abstract": ["Multiple myeloma is largely incurable, despite development of therapies that target myeloma cell-intrinsic pathways.", "Disease relapse is thought to originate from dormant myeloma cells, localized in specialized niches, which resist therapy and repopulate the tumour.", "However, little is known about the niche, and how it exerts cell-extrinsic control over myeloma cell dormancy and reactivation.", "In this study, we track individual myeloma cells by intravital imaging as they colonize the endosteal niche, enter a dormant state and subsequently become activated to form colonies.", "We demonstrate that dormancy is a reversible state that is switched 'on' by engagement with bone-lining cells or osteoblasts, and switched 'off' by osteoclasts remodelling the endosteal niche.", "Dormant myeloma cells are resistant to chemotherapy that targets dividing cells.", "The demonstration that the endosteal niche is pivotal in controlling myeloma cell dormancy highlights the potential for targeting cell-extrinsic mechanisms to overcome cell-intrinsic drug resistance and prevent disease relapse."], "structured": false}
{"doc_id": 7581911, "title": "Human embryonic stem cells with biological and epigenetic characteristics similar to those of mouse ESCs.", "abstract": ["Human and mouse embryonic stem cells (ESCs) are derived from blastocyst-stage embryos but have very different biological properties, and molecular analyses suggest that the pluripotent state of human ESCs isolated so far corresponds to that of mouse-derived epiblast stem cells (EpiSCs).", "Here we rewire the identity of conventional human ESCs into a more immature state that extensively shares defining features with pluripotent mouse ESCs.", "This was achieved by ectopic induction of Oct4, Klf4, and Klf2 factors combined with LIF and inhibitors of glycogen synthase kinase 3beta (GSK3beta) and mitogen-activated protein kinase (ERK1/2) pathway.", "Forskolin, a protein kinase A pathway agonist which can induce Klf4 and Klf2 expression, transiently substitutes for the requirement for ectopic transgene expression.", "In contrast to conventional human ESCs, these epigenetically converted cells have growth properties, an X-chromosome activation state (XaXa), a gene expression profile, and a signaling pathway dependence that are highly similar to those of mouse ESCs.", "Finally, the same growth conditions allow the derivation of human induced pluripotent stem (iPS) cells with similar properties as mouse iPS cells.", "The generation of validated \"na\u00efve\" human ESCs will allow the molecular dissection of a previously undefined pluripotent state in humans and may open up new opportunities for patient-specific, disease-relevant research."], "structured": false}
{"doc_id": 7583104, "title": "IDEAL in meshes for prolapse, urinary incontinence, and hernia repair.", "abstract": ["PURPOSE Mesh surgeries are counted among the most frequently applied surgical procedures.", "Despite global spread of mesh applying surgeries, there is no current systematic analysis of incidence and possible prevention of adverse events after mesh implantation.   ", "MATERIALS AND METHODS Based on the recommendations of IDEAL an in vitro test system for biocompatibility of surgical meshes has been generated (Innovation).", "Coating strategies for biocompatibility optimization have been developed (Development).", "The native and modified alloplastic materials have been tested in an animal model over 2 years (Exploration and Assessment and Long-term study).   \n", "RESULTS In 3 meshes, implanted in sheep and explanted at 4 different time points (a, 3 months; b, 6 months; c, 12 months; and d, 24 months) over 24 months, thickness of inflammatory tissue (TVT a, 35 \u00b5m; b, 32 \u00b5m; c, 33 \u00b5m; d, 28 \u00b5m; UltraPro, a, 25 \u00b5m; b, 24 \u00b5m; c, 21 \u00b5m; d, 22 \u00b5m; PVDF a, 20 \u00b5m; b, 21 \u00b5m; c, 14 \u00b5m; d, 15\u00b5m), connective tissue (TVT a, 37 \u00b5m; b, 36 \u00b5m; c, 43 \u00b5m; d, 41 \u00b5m; UltraPro a, 33 \u00b5m; b, 32 \u00b5m; c, 40 \u00b5m; d, 38 \u00b5m; PVDF a, 25 \u00b5m; b, 22 \u00b5m; c, 22 \u00b5m; d, 24 \u00b5m), and macrophage infiltration (TVT a, 36%; b, 33%; c, 23%; d, 20%; UltraPro a, 34%; b, 28%; c, 25%; d, 22%; PVDF a, 24%; b, 18%; c, 18%; d, 16%) revealed comparable ranking characteristics at every time point after explantation.", "The in vivo performance of these meshes in a sheep model was predictable with a previously developed in vitro test system.", "Coating of meshes with autologous plasma prior to implantation seems to have a positive effect on the meshes biocompatibility.   \n", "CONCLUSION We have applied IDEAL criteria on a new innovation for surgical meshes.", "The results permit the generation of a ranking of currently available meshes with potential to optimize future meshes."], "structured": true}
{"doc_id": 7583161, "title": "Heterotopic of bone marrow. Analysis of precursor cells for osteogenic and hematopoietic tissues.", "abstract": ["In semisyngeneic heterotopic bone marrow transplants the donor or recipient origin of cells of osteogenic and hematopoietic tissues was identified by chromosome markers (T6) and by reverse transplantation into the initial donor line.", "In syngeneic and semisyngeneic grafts of bone marrow under the renal capsule bone and bone marrow are formed.", "In allogeneic grafts only bone is formed; this bone is subsequently resorbed.", "In 14-month semisyngeneic transplants the bone marrow consists of recipient cells.", "This is true for both the proliferating pool and the stem cells of hematopoietic tissue.", "At the same time, osteogenic precursor cells and bone tissue in these transplants are of donor origin.", "A discussion is presented of the interrelationship between determinated osteogenic precursor cells (preosteoblasts) and hematopoietic stem cells (or their descendants) in which osteogenesis is inducible."], "structured": false}
{"doc_id": 7583725, "title": "TRPM7 is required for breast tumor cell metastasis.", "abstract": ["TRPM7 encodes a Ca2+-permeable nonselective cation channel with kinase activity.", "TRPM7 has been implicated in control of cell adhesion and migration, but whether TRPM7 activity contributes to cancer progression has not been established.", "Here we report that high levels of TRPM7 expression independently predict poor outcome in breast cancer patients and that it is functionally required for metastasis formation in a mouse xenograft model of human breast cancer.", "Mechanistic investigation revealed that TRPM7 regulated myosin II-based cellular tension, thereby modifying focal adhesion number, cell-cell adhesion and polarized cell movement.", "Our findings therefore suggest that TRPM7 is part of a mechanosensory complex adopted by cancer cells to drive metastasis formation."], "structured": false}
{"doc_id": 7595742, "title": "Frailty Syndrome: A Transitional State in a Dynamic Process", "abstract": ["Frailty has long been considered synonymous with disability and comorbidity, to be highly prevalent in old age and to confer a high risk for falls, hospitalization and mortality.", "However, it is becoming recognized that frailty may be a distinct clinical syndrome with a biological basis.", "The frailty process appears to be a transitional state in the dynamic progression from robustness to functional decline.", "During this process, total physiological reserves decrease and become less likely to be sufficient for the maintenance and repair of the ageing body.", "Central to the clinical concept of frailty is that no single altered system alone defines it, but that multiple systems are involved.", "Clinical consensus regarding the phenotype which constitutes frailty, drawing upon the opinions of numerous authors, shows the characteristics to include wasting (loss of both muscle mass and strength and weight loss), loss of endurance, decreased balance and mobility, slowed performance, relative inactivity and, potentially, decreased cognitive function.", "Frailty is a distinct entity easily recognized by clinicians, with multiple manifestations and with no single symptom being sufficient or essential in its presentation.", "Manifestations include appearance (consistent or not with age), nutritional status (thin, weight loss), subjective health rating (health perception), performance (cognition, fatigue), sensory/physical impairments (vision, hearing, strength) and current care (medication, hospital).", "Although the early stages of the frailty process may be clinically silent, when depleted reserves reach an aggregate threshold leading to serious vulnerability, the syndrome may become detectable by looking at clinical, functional, behavioral and biological markers.", "Thus, a better understanding of these clinical changes and their underlying mechanisms, beginning in the pre-frail state, may confirm the impression held by many geriatricians that increasing frailty is distinguishable from ageing and in consequence is potentially reversible.", "We therefore provide an update of the physiopathology and clinical and biological characteristics of the frailty process and speculate on possible preventative approaches."], "structured": false}
{"doc_id": 7602348, "title": "Progression of preclinical diastolic dysfunction to the development of symptoms.", "abstract": ["BACKGROUND Preclinical diastolic dysfunction (PDD) has been defined as subjects with normal systolic function, diastolic dysfunction but no symptoms of heart failure (HF).", "The clinical phenotype and natural history of the syndrome remains poorly defined.", "This study's objective was to determine the clinical phenotype and progression to HF in a group of patients with normal systolic function and moderate or severe diastolic dysfunction as determinate by Doppler criteria without any clinical diagnosis of HF according to the Framingham criteria or any symptoms of HF, specifically dyspnoea, oedema or fatigue at the time of echocardiography.   \n", "METHODS The authors used resources of the Mayo Clinic echocardiography database to consecutively select among patients who had an echocardiogram in 2005, a cohort with moderate or severe diastolic dysfunction by Doppler criteria and EF >or=50%.", "Patients could not have a diagnosis of HF, or any HF symptoms-specifically dyspnoea, oedema or fatigue-at the time of echocardiography; nor grade 3 or greater valvular dysfunction (except tricuspid valve).", "A total of 82 patients had their medical chart reviewed.", "Primary endpoint was the time to the development of (1) HF according to the Framingham criteria or (2) any symptoms of dyspnoea, oedema or fatigue.   \n", "RESULTS The mean age of the cohort of PDD subjects was 69+/-10 years with a female (67%) preponderance.", "Presence of hypertension was 76%, coronary artery disease was 29%, paroxysmal atrial fibrillation was 26%, estimated creatinine clearance <60 ml/min was 51%.", "The 2-year cumulative probability of development of HF according to the Framingham criteria was 1.9%; however, the 2-year cumulative probability of development of any symptoms was 31.1%.", "The 2-year cumulative probability for cardiac hospitalisation was 21.2%.", "Peripheral vascular disease and hypertension were independently associated with increased likelihood for the development of symptoms.   \n", "CONCLUSION The study demonstrates that hypertension, hyperlipidaemia, CAD and renal dysfunction are prevalent in patients with PDD.", "More importantly, although the progression to the development of clinical HF over 2 years was low, there was a moderate degree of progression to development of symptoms and cardiac hospitalisations over 2 years.", "Based on the finding that only PVD and hypertension were independently associated with the progression to the development of symptoms in subject with PDD, the authors speculate that ventricular-arterial interaction may be important to the progression of diastolic dysfunction to the development of symptoms."], "structured": true}
{"doc_id": 7613033, "title": "Aspirin in the chemoprevention of colorectal neoplasia: an overview.", "abstract": ["Considerable evidence supports the effectiveness of aspirin for chemoprevention of colorectal cancer (CRC) in addition to its well-established benefits in the prevention of vascular disease.", "Epidemiologic studies have consistently observed an inverse association between aspirin use and risk of CRC.", "A recent pooled analysis of a long-term posttrial follow-up of nearly 14,000 patients from four randomized, cardiovascular disease prevention trials showed that daily aspirin treatment for about five years was associated with a 34% reduction in 20-year CRC mortality.", "A separate metaanalysis of nearly 3,000 patients with a history of colorectal adenoma or cancer in four randomized adenoma prevention trials showed that aspirin reduced the occurrence of advanced adenomas by 28% and any adenoma by 17%.", "Aspirin has also been shown to be beneficial in a clinical trial of patients with Lynch syndrome, a hereditary CRC syndrome; in those treated with aspirin for at least two years, there was a 50% or more reduction in the risk of CRC commencing five years after randomization and after aspirin had been discontinued.", "A few observational studies have shown an increase in survival among patients with CRC who use aspirin.", "Taken together, these findings strengthen the case for consideration of long-term aspirin use in CRC prevention.", "Despite these compelling data, there is a lack of consensus about the balance of risks and benefits associated with long-term aspirin use, particularly in low-risk populations.", "The optimal dose to use for cancer prevention and the precise mechanism underlying aspirin's anticancer effect require further investigation."], "structured": false}
{"doc_id": 7621534, "title": "Chemokine receptor trio: CXCR3, CXCR4 and CXCR7 crosstalk via CXCL11 and CXCL12.", "abstract": ["Although chemokines are well established to function in immunity and endothelial cell activation and proliferation, a rapidly growing literature suggests that CXC Chemokine receptors CXCR3, CXCR4 and CXCR7 are critical in the development and progression of solid tumors.", "The effect of these chemokine receptors in tumorigenesis is mediated via interactions with shared ligands I-TAC (CXCL11) and SDF-1 (CXCL12).", "Over the last decade, CXCR4 has been extensively reported to be overexpressed in most human solid tumors and has earned considerable attention toward elucidating its role in cancer metastasis.", "To enrich the existing armamentarium of anti-cancerous agents, many inhibitors of CXCL12-CXCR4 axis have emerged as additional or alternative agents for neo-adjuvant treatments and even many of them are in preclinical and clinical stages of their development.", "However, the discovery of CXCR7 as another receptor for CXCL12 with rather high binding affinity and recent reports about its involvement in cancer progression, has questioned the potential of \"selective blockade\" of CXCR4 as cancer chemotherapeutics.", "Interestingly, CXCR7 can also bind another chemokine CXCL11, which is an established ligand for CXCR3.", "Recent reports have documented that CXCR3 and their ligands are overexpressed in different solid tumors and regulate tumor growth and metastasis.", "Therefore, it is important to consider the interactions and crosstalk between these three chemokine receptors and their ligand mediated signaling cascades for the development of effective anti-cancer therapies.", "Emerging evidence also indicates that these receptors are differentially expressed in tumor endothelial cells as well as in cancer stem cells, suggesting their direct role in regulating tumor angiogenesis and metastasis.", "In this review, we will focus on the signals mediated by this receptor trio via their shared ligands and their role in tumor growth and progression."], "structured": false}
{"doc_id": 7622767, "title": "Human Cyclin a Is Required for Mitosis until Mid Prophase", "abstract": ["We have used microinjection and time-lapse video microscopy to study the role of cyclin A in mitosis.", "We have injected purified, active cyclin A/cyclin-dependent kinase 2 (CDK2) into synchronized cells at specific points in the cell cycle and assayed its effect on cell division.", "We find that cyclin A/CDK2 will drive G2 phase cells into mitosis within 30 min of microinjection, up to 4 h before control cells enter mitosis.", "Often this premature mitosis is abnormal; the chromosomes do not completely condense and daughter cells fuse.", "Remarkably, microinjecting cyclin A/CDK2 into S phase cells has no effect on progress through the following G2 phase or mitosis.", "In complementary experiments we have microinjected the amino terminus of p21Cip1/Waf1/Sdi1 (p21N) into cells to inhibit cyclin A/CDK2 activity.", "We find that p21N will prevent S phase or G2 phase cells from entering mitosis, and will cause early prophase cells to return to interphase.", "These results suggest that cyclin A/CDK2 is a rate-limiting component required for entry into mitosis, and for progress through mitosis until late prophase.", "They also suggest that cyclin A/CDK2 may be the target of the recently described prophase checkpoint."], "structured": false}
{"doc_id": 7627167, "title": "Brief, four-session group CBT reduces binge eating behaviors among bariatric surgery candidates.", "abstract": ["BACKGROUND The objective of this study was to evaluate the effectiveness of a brief, 4-session cognitive behavioral, group psychotherapy for binge eating among bariatric surgery candidates at an academic medical center.", "Binge eating behaviors have been linked to poorer outcomes among bariatric surgery patients, and binge eating disorder have be considered a contraindication in surgery programs, some of which have mandated preoperative binge eating treatment.", "However, no previous studies have examined whether a preoperative binge eating intervention could successfully reduce binge eating behaviors among severely obese bariatric surgery candidates.   \n", "METHODS A total of 243 bariatric surgery candidates completed a brief cognitive behavioral group treatment for binge eating behaviors and were administered the Binge Eating Scale and reported the number of weekly binge eating episodes at the initial psychological evaluation and again after the group sessions.", "The study used a pre-post intervention design.   \n", "RESULTS The results suggested significant reductions in both binge eating behaviors and cognitions and binge eating episodes after the group intervention.", "The intervention's effectiveness did not differ according to gender or ethnicity (black versus white).   \n", "CONCLUSION A brief cognitive behavioral intervention can reduce binge eating behaviors among bariatric surgery candidates.", "Given the potential influence of binge eating on outcomes, bariatric surgery programs could benefit by treating binge eating before surgery."], "structured": true}
{"doc_id": 7639744, "title": "Influence of smoking cessation after diagnosis of early stage lung cancer on prognosis: systematic review of observational studies with meta-analysis", "abstract": ["OBJECTIVE To systematically review the evidence that smoking cessation after diagnosis of a primary lung tumour affects prognosis.   \n", "DESIGN Systematic review with meta-analysis.   \n", "DATA SOURCES CINAHL (from 1981), Embase (from 1980), Medline (from 1966), Web of Science (from 1966), CENTRAL (from 1977) to December 2008, and reference lists of included studies.   ", "STUDY SELECTION Randomised controlled trials or observational longitudinal studies that measured the effect of quitting smoking after diagnosis of lung cancer on prognostic outcomes, regardless of stage at presentation or tumour histology, were included.   \n", "DATA EXTRACTION Two researchers independently identified studies for inclusion and extracted data.", "Estimates were combined by using a random effects model, and the I(2) statistic was used to examine heterogeneity.", "Life tables were used to model five year survival for early stage non-small cell lung cancer and limited stage small cell lung cancer, using death rates for continuing smokers and quitters obtained from this review.   \n", "RESULTS In 9/10 included studies, most patients studied were diagnosed as having an early stage lung tumour.", "Continued smoking was associated with a significantly increased risk of all cause mortality (hazard ratio 2.94, 95% confidence interval 1.15 to 7.54) and recurrence (1.86, 1.01 to 3.41) in early stage non-small cell lung cancer and of all cause mortality (1.86, 1.33 to 2.59), development of a second primary tumour (4.31, 1.09 to 16.98), and recurrence (1.26, 1.06 to 1.50) in limited stage small cell lung cancer.", "No study contained data on the effect of quitting smoking on cancer specific mortality or on development of a second primary tumour in non-small cell lung cancer.", "Life table modelling on the basis of these data estimated 33% five year survival in 65 year old patients with early stage non-small cell lung cancer who continued to smoke compared with 70% in those who quit smoking.", "In limited stage small cell lung cancer, an estimated 29% of continuing smokers would survive for five years compared with 63% of quitters on the basis of the data from this review.   \n", "CONCLUSIONS This review provides preliminary evidence that smoking cessation after diagnosis of early stage lung cancer improves prognostic outcomes.", "From life table modelling, the estimated number of deaths prevented is larger than would be expected from reduction of cardiorespiratory deaths after smoking cessation, so most of the mortality gain is likely to be due to reduced cancer progression.", "These findings indicate that offering smoking cessation treatment to patients presenting with early stage lung cancer may be beneficial."], "structured": true}
{"doc_id": 7640058, "title": "Epigenetic reprogramming and induced pluripotency.", "abstract": ["The cloning of animals from adult cells has demonstrated that the developmental state of adult cells can be reprogrammed into that of embryonic cells by uncharacterized factors within the oocyte.", "More recently, transcription factors have been identified that can induce pluripotency in somatic cells without the use of oocytes, generating induced pluripotent stem (iPS) cells.", "iPS cells provide a unique platform to dissect the molecular mechanisms that underlie epigenetic reprogramming.", "Moreover, iPS cells can teach us about principles of normal development and disease, and might ultimately facilitate the treatment of patients by custom-tailored cell therapy."], "structured": false}
{"doc_id": 7640792, "title": "Sex differences in mortality following acute coronary syndromes.", "abstract": ["CONTEXT Conflicting information exists about whether sex differences modulate short-term mortality following acute coronary syndromes (ACS).   \n", "OBJECTIVES To investigate the relationship between sex and 30-day mortality in ACS, and to determine whether this relationship was modified by clinical syndrome or coronary anatomy using a large database across the spectrum of ACS and adjusting for potentially confounding clinical covariates.   \n", "DESIGN, SETTING, AND PARTICIPANTS A convenience sample of patients pooled from 11 independent, international, randomized ACS clinical trials between 1993 and 2006 whose databases are maintained at the Duke Clinical Research Institute, Durham, North Carolina.", "Of 136 247 patients, 38 048 (28%) were women; 102 004 (26% women) with ST-segment elevation myocardial infarction (STEMI), 14 466 (29% women) with non-STEMI (NSTEMI), and 19 777 (40% women) with unstable angina.   \n", "MAIN OUTCOME MEASURE Thirty-day mortality following ACS.   \n", "RESULTS Thirty-day mortality was 9.6% in women and 5.3% in men (odds ratio [OR], 1.91; 95% confidence interval [CI], 1.83-2.00).", "After multivariable adjustment, mortality was not significantly different between women and men (adjusted OR, 1.06; 95% CI, 0.99-1.15).", "A significant sex by type of ACS interaction was demonstrated (P < .001).", "In STEMI, 30-day mortality was higher among women (adjusted OR, 1.15; 95% CI, 1.06-1.24), whereas in NSTEMI (adjusted OR, 0.77; 95% CI, 0.63-0.95) and unstable angina, mortality was lower among women (adjusted OR, 0.55; 95% CI, 0.43-0.70).", "In a cohort of 35 128 patients with angiographic data, women more often had nonobstructive (15% vs 8%) and less often had 2-vessel (25% vs 28%) and 3-vessel (23% vs 26%) coronary disease, regardless of ACS type.", "After additional adjustment for angiographic disease severity, 30-day mortality among women was not significantly different than men, regardless of ACS type.", "The relationship between sex and 30-day mortality was similar across the levels of angiographic disease severity (P for interaction = .70).   \n", "CONCLUSIONS Sex-based differences existed in 30-day mortality among patients with ACS and vary depending on clinical presentation.", "However, these differences appear to be largely explained by clinical differences at presentation and severity of angiographically documented disease."], "structured": true}
{"doc_id": 7643848, "title": "Membrane topology of the 60-kDa Oxa1p homologue from Escherichia coli.", "abstract": ["We have characterized the membrane topology of a 60-kDa inner membrane protein from Escherichia coli that is homologous to the recently identified Oxa1p protein in Saccharomyces cerevisiae mitochondria implicated in the assembly of mitochondrial inner membrane proteins.", "Hydrophobicity and alkaline phosphatase fusion analyses suggest a membrane topology with six transmembrane segments, including an N-terminal signal-anchor sequence not present in mitochondrial Oxa1p.", "In contrast to partial N-terminal fusion protein constructs, the full-length protein folds into a protease-resistant conformation, suggesting that important folding determinants are present in the C-terminal part of the molecule."], "structured": false}
{"doc_id": 7645565, "title": "Identifying and Characterizing Interplay between Hepatitis B Virus X Protein and Smc5/6", "abstract": ["Hepatitis B X protein (HBx) plays an essential role in the hepatitis B virus (HBV) replication cycle, but the function of HBx has been elusive until recently.", "It was recently shown that transcription from the HBV genome (covalently-closed circular DNA, cccDNA) is inhibited by the structural maintenance of chromosome 5/6 complex (Smc5/6), and that a key function of HBx is to redirect the DNA-damage binding protein 1 (DDB1) E3 ubiquitin ligase to target this complex for degradation.", "By doing so, HBx alleviates transcriptional repression by Smc5/6 and stimulates HBV gene expression.", "In this review, we discuss in detail how the interplay between HBx and Smc5/6 was identified and characterized.", "We also discuss what is known regarding the repression of cccDNA transcription by Smc5/6, the timing of HBx expression, and the potential role of HBx in promoting hepatocellular carcinoma (HCC)."], "structured": false}
{"doc_id": 7647224, "title": "Hepatitis C Virus (HCV) Vertical Transmission in 12-Month-Old Infants Born to HCV-Infected Women and Assessment of Maternal Risk Factors", "abstract": ["Background.  ", "Hepatitis C virus (HCV) is an underappreciated cause of pediatric liver disease, most frequently acquired by vertical transmission (VT).", "Current guidelines that include the option of screening infants for HCV RNA at 1-2 months are based on data prior to current real-time polymerase chain reaction (PCR)-based testing.", "Previous studies have demonstrated VT rates of 4%-15% and an association with high maternal viral load.", "We evaluated HCV RNA in infants with HCV VT and assessed maternal risk factors in a prospective cohort in Cairo, Egypt.", "Methods.  ", "Pregnant women were screened for HCV from December 2012 to March 2014.", "For those with HCV viremia, their infants were tested at 12 months for HCV RNA using real-time PCR.", "Maternal risk factors assessed for HCV VT association included HCV RNA levels, mode of delivery, and maternal IL28B genotype.", "Results.  ", "Of 2514 women screened, a total of 54 women were viremic (2.1%) and delivered 56 infants.", "Of those, 51 infants of 49 women were tested at 12 months of age.", "Only 7 infants were viremic, with an HCV VT rate of 14.3% (7 of 49).", "Median HCV RNA in the infants was 2100 IU/mL. None of the maternal risk factors analyzed were associated with transmission.", "Conclusions.  ", "In Egypt where HCV is highly endemic, we observed an overall 12-month HCV VT rate of 14.3%.", "Further studies should focus on better identification of pregnant women more likely to vertically transmit HCV and earlier testing of infants to identify those likely to develop chronicity."], "structured": false}
{"doc_id": 7650066, "title": "Long-term follow-up of cervical disease in women screened by cytology and HPV testing: results from the HART study", "abstract": ["BACKGROUND Several studies have shown that testing for high-risk human papillomavirus (HPV) types results in an improved sensitivity for CIN2+, compared with cytology, although with a somewhat lower specificity.   \n", "METHODS We obtained follow-up results, with at least one smear after participation in the HART study, which compared HPV testing (HC-II) with cytology as a primary screening modality.   \n", "RESULTS With a median follow-up of 6 years, 42 additional cases of CIN2+ were identified; women who were HPV positive at baseline were more likely to develop CIN2+ than those who were HPV negative (hazard ratio (HR) 17.2; 95% confidence interval (CI) (9.3-31.6)) and the risk increased with increasing viral load.", "Compared with HPV-negative women (relative light unit (RLU) <1), the HR (95% CI) was 5.4 (1.6, 18.2) for 1-10 RLU and 25.5 (13.6, 47.9) for RLU > or = 10.", "Positive cytology (borderline or worse compared with negative) was also predictive of developing CIN2, although to a lesser extent (HR 8.7; 95% CI (4.5-17.1)).", "Only one case of CIN3 and three cases of CIN2 were found in women who showed a positive cytology result but were HPV negative at baseline.   \n", "CONCLUSION After 5 years of follow-up, CIN2+ occurred in 0.23% of women who were HPV negative at baseline compared with 0.48% of women who showed a negative cytology result, indicating a much longer low-risk interval for CIN2+ after HPV testing."], "structured": true}
{"doc_id": 7655029, "title": "The Burden of Trachoma in Ayod County of Southern Sudan", "abstract": ["BACKGROUND Blindness due to trachoma is avoidable through Surgery, Antibiotics, Facial hygiene and Environmental improvements (SAFE).", "Recent surveys have shown trachoma to be a serious cause of blindness in Southern Sudan.", "We conducted this survey in Ayod County of Jonglei State to estimate the need for intervention activities to eliminate blinding trachoma.   \n", "METHODOLOGY AND FINDINGS A cross-sectional two-stage cluster random survey was conducted in November 2006.", "All residents of selected households were clinically assessed for trachoma using the World Health Organization (WHO) simplified grading scheme.", "A total of 2,335 people from 392 households were examined, of whom 1,107 were over 14 years of age.", "Prevalence of signs of active trachoma in children 1-9 years of age was: trachomatous inflammation follicular (TF) = 80.1% (95% confidence interval [CI], 73.9-86.3); trachomatous inflammation intense (TI) = 60.7% (95% CI, 54.6-66.8); and TF and/or TI (active trachoma) = 88.3% (95% CI, 83.7-92.9).", "Prevalence of trachomatous trichiasis (TT) was 14.6% (95% CI, 10.9-18.3) in adults over 14 years of age; 2.9% (95% CI, 0.4-5.3) in children 1-14 years of age; and 8.4% (95% CI, 5.5-11.3) overall.", "The prevalence of corneal opacity in persons over 14 years of age with TT was 6.4% (95% CI, 4.5-8.3).", "No statistically significant difference was observed in the prevalence of trachoma signs between genders.", "Trachoma affected almost all households surveyed: 384/392 (98.0%) had at least one person with active trachoma and 130 (33.2%) had at least one person with trichiasis.   \n", "CONCLUSIONS Trachoma is an unnecessary public health problem in Ayod.", "The high prevalence of active trachoma and trichiasis confirms the severe burden of blinding trachoma found in other post-conflict areas of Southern Sudan.", "Based on WHO recommended thresholds, all aspects of the SAFE strategy are indicated to eliminate blinding trachoma in Ayod."], "structured": true}
{"doc_id": 7662206, "title": "A Century of Cholesterol and Coronaries: From Plaques to Genes to Statins", "abstract": ["One-fourth of all deaths in industrialized countries result from coronary heart disease.", "A century of research has revealed the essential causative agent: cholesterol-carrying low-density lipoprotein (LDL).", "LDL is controlled by specific receptors (LDLRs) in liver that remove it from blood.", "Mutations that eliminate LDLRs raise LDL and cause heart attacks in childhood, whereas mutations that raise LDLRs reduce LDL and diminish heart attacks.", "If we are to eliminate coronary disease, lowering LDL should be the primary goal.", "Effective means to achieve this goal are currently available.", "The key questions are: who to treat, when to treat, and how long to treat."], "structured": false}
{"doc_id": 7662395, "title": "Perinatal mortality in rural China: retrospective cohort study.", "abstract": ["OBJECTIVES To explore the use of local civil registration data to assess the perinatal mortality in a typical rural county in a less developed province in China, 1999-2000.   \n", "DESIGN Retrospective cohort study.", "Pregnancies in a cohort of women followed from registration of pregnancy to outcome of infant seven days after birth.   \n", "SETTING Routine family planning records in 20 rural townships in eastern China.   ", "SUBJECTS 3697 pregnancies registered by the local family planning system during 1999.   \n", "MAIN OUTCOME MEASURES Abortions, stillbirths, early neonatal mortality, perinatal mortality.   \n", "RESULTS Only three cases were lost to follow up.", "The average age of the women at pregnancy was 25.9 years.", "Three hundred and twelve pregnancies were aborted and 240 ended in miscarriage (total 552, 15%).", "The perinatal mortality rate was 69 per 1000 births, the rate of stillbirth was 24 per 1000 births, and the early neonatal mortality was 46 per 1000 live births.", "The early neonatal mortality was 29 in boys and 69 in girls per 1000 live births.", "The perinatal mortality rate increased notably with parity and was higher in townships having lower income per capita.   \n", "CONCLUSIONS The family planning system at the most local level is a useful data source for studying perinatal mortality in rural China.", "The perinatal mortality rate in the study county was higher than previously reported for both rural and urban areas in China.", "The results by parity and sex of the infant raise concern over the impact of the one child policy."], "structured": true}
{"doc_id": 7666498, "title": "Genetic disruption of aurora B uncovers an essential role for aurora C during early mammalian development.", "abstract": ["Mitosis is controlled by multiple kinases that drive cell cycle progression and prevent chromosome mis-segregation.", "Aurora kinase B interacts with survivin, borealin and incenp to form the chromosomal passenger complex (CPC), which is involved in the regulation of microtubule-kinetochore attachments and cytokinesis.", "Whereas genetic ablation of survivin, borealin or incenp results in early lethality at the morula stage, we show here that aurora B is dispensable for CPC function during early cell divisions and aurora B-null embryos are normally implanted.", "This is due to a crucial function of aurora C during these early embryonic cycles.", "Expression of aurora C decreases during late blastocyst stages resulting in post-implantation defects in aurora B-null embryos.", "These defects correlate with abundant prometaphase figures and apoptotic cell death of the aurora B-deficient inner cell mass.", "Conditional deletion of aurora B in somatic cells that do not express aurora C results in chromosomal misalignment and lack of chromosome segregation.", "Re-expression of wild-type, but not kinase-dead, aurora C rescues this defect, suggesting functional overlap between these two kinases.", "Finally, aurora B-null cells partially arrest in the presence of nocodazole, suggesting that this kinase is not essential for the spindle assembly checkpoint."], "structured": false}
{"doc_id": 7681810, "title": "NuSAP is essential for chromatin-induced spindle formation during early embryogenesis.", "abstract": ["Mitotic spindle assembly is mediated by two processes: a centrosomal and a chromosomal pathway.", "RanGTP regulates the latter process by releasing microtubule-associated proteins from inhibitory complexes.", "NuSAP, a microtubule- and DNA-binding protein, is a target of RanGTP and promotes the formation of microtubules near chromosomes.", "However, the contribution of NuSAP to cell proliferation in vivo is unknown.", "Here, we demonstrate that the expression of NuSAP highly correlates with cell proliferation during embryogenesis and adult life, making it a reliable marker of proliferating cells.", "Additionally, we show that NuSAP deficiency in mice leads to early embryonic lethality.", "Spindle assembly in NuSAP-deficient cells is highly inefficient and chromosomes remain dispersed in the mitotic cytoplasm.", "As a result of sustained spindle checkpoint activity, the cells are unable to progress through mitosis, eventually leading to caspase activation and apoptotic cell death.", "Together, our findings demonstrate that NuSAP is essential for proliferation of embryonic cells and, simultaneously, they underscore the importance of chromatin-induced spindle assembly."], "structured": false}
{"doc_id": 7688110, "title": "E2F-6: a novel member of the E2F family is an inhibitor of E2F-dependent transcription", "abstract": ["The E2F family of transcription factors are essential for the regulation of genes required for appropriate progression through the cell cycle.", "Five members of the E2F family have been previously reported, namely E2F1-5.", "All five are key elements in transcriptional regulation of essential genes, and they can be divided into two functional groups, those that induce S-phase progression when overexpressed in quiescent cells (E2Fs 1\u20133), and those that do not (E2Fs 4\u20135).", "Here, we describe the identification of a novel member of this family, which we refer to as E2F-6.", "E2F-6 shares significant homology with E2Fs 1\u20135, especially within the DNA binding, heterodimerization and marked box domains.", "Unlike E2Fs 1\u20135, E2F-6 lacks a transactivation and a pocket protein binding domain, hence, forms a unique third group within the E2F family.", "E2F-6 is a nuclear protein that can form heterodimers with the DP proteins (both DP-1 and DP-2) in vitro and in vivo.", "Our results show that the complex formed between E2F-6 and the DP proteins, possesses high DNA binding activity, displaying a preference for a TTTCCCGC E2F recognition site, which is slightly different to the E2F consensus site derived from the E2 promoter (TTTCGCGC).", "In contrast to the other members of the E2F family, ectopic expression of E2F-6 inhibits transcription from promoters possessing E2F recognition sites rather than activating transcription.", "In addition, overexpression of E2F-6 suppresses the transactivational effects of co-expression of E2F-1 and DP-1.", "The inhibitory effect of E2F-6 is dependent on its DNA binding activity and its ability to form heterodimers with the DPs.", "Interestingly, ectopic expression of E2F-6 leads to accumulation of cells in S-phase.", "Our data suggest that E2F-6 expression delays the exit from S-phase rather than inducing S-phase, which further emphasizes the functional difference between E2F-6 and the previously known E2F family members."], "structured": false}
{"doc_id": 7708803, "title": "Enhancement of hippocampal pyramidal cell excitability by the novel selective slow-afterhyperpolarization channel blocker 3-(triphenylmethylaminomethyl)pyridine (UCL2077).", "abstract": ["The slow afterhyperpolarization (sAHP) in hippocampal neurons has been implicated in learning and memory.", "However, its precise role in cell excitability and central nervous system function has not been explicitly tested for 2 reasons: 1) there are, at present, no selective inhibitors that effectively reduce the underlying current in vivo or in intact in vitro tissue preparations, and 2) although it is known that a small conductance K(+) channel that activates after a rise in [Ca(2+)](i) underlies the sAHP, the exact molecular identity remains unknown.", "We show that 3-(triphenylmethylaminomethyl)pyridine (UCL2077), a novel compound, suppressed the sAHP present in hippocampal neurons in culture (IC(50) = 0.5 microM) and in the slice preparation (IC(50) approximately 10 microM).", "UCL2077 was selective, having minimal effects on Ca(2+) channels, action potentials, input resistance and the medium afterhyperpolarization.", "UCL2077 also had little effect on heterologously expressed small conductance Ca(2+)-activated K(+) (SK) channels.", "Moreover, UCL2077 and apamin, a selective SK channel blocker, affected spike firing in hippocampal neurons in different ways.", "These results provide further evidence that SK channels are unlikely to underlie the sAHP.", "This study also demonstrates that UCL2077, the most potent, selective sAHP blocker described so far, is a useful pharmacological tool for exploring the role of sAHP channels in the regulation of cell excitability in intact tissue preparations and, potentially, in vivo."], "structured": false}
{"doc_id": 7711685, "title": "Lessons from sudden coronary death: a comprehensive morphological classification scheme for atherosclerotic lesions.", "abstract": ["This review will reconsider the current paradigm for understanding the critical, final steps in the progression of atherosclerotic lesions.", "That scheme, largely an outgrowth of observations of autopsy tissues by Davies and colleagues,1 2 asserts that the cause of death in atherosclerotic coronary artery disease is rupture of an advanced atherosclerotic lesion.", "Although this assumption may be partially true, recent autopsy studies suggest that it is incomplete.  ", "To reconsider this paradigm, we reexamined the morphological classification scheme for lesions proposed by the American Heart Association (AHA).3 4 This scheme is difficult to use for 2 reasons.", "First, it uses a very long list of roman numerals modified by letter codes that are difficult to remember.", "Second, it implies an orderly, linear pattern of lesion progression.", "This tends to be ambiguous, because it is not clear whether there is a single sequence of events during the progression of all lesions.", "We have therefore tried to devise a simpler classification scheme that is consistent with the AHA categories but is easier to use, able to deal with a wide array of morphological variations, and not overly burdened by mechanistic implications.  ", "The current paradigm is based on the belief that type IV lesions, or \u201catheromas,\u201d described by the AHA are stable because the fatty, necrotic core is contained by a smooth muscle cell\u2013rich fibrous cap.", "Virchow\u2019s analysis5 in 1858 pointed out that historically, the term \u201catheroma\u201d refers to a dermal cyst (\u201cGrutzbalg\u201d), a fatty \u2026"], "structured": false}
{"doc_id": 7717468, "title": "Loss of allergen 1 confers a hypervirulent phenotype that resembles mucoid switch variants of Cryptococcus neoformans.", "abstract": ["Microbial survival in a host is usually dependent on the ability of a pathogen to undergo changes that promote escape from host defense mechanisms.", "The human-pathogenic fungus Cryptococcus neoformans undergoes phenotypic switching in vivo that promotes persistence in tissue.", "By microarray and real-time PCR analyses, the allergen 1 gene (ALL1) was found to be downregulated in the hypervirulent mucoid switch variant, both during logarithmic growth and during intracellular growth in macrophages.", "The ALL1 gene encodes a small cytoplasmic protein that is involved in capsule formation.", "Growth of an all1Delta gene deletion mutant was normal.", "Similar to cells of the mucoid switch variant, all1Delta cells produced a larger polysaccharide capsule than cells of the smooth parent and the complemented strain produced, and the enlarged capsule inhibited macrophage phagocytosis.", "The mutant exhibited a modest defect in capsule induction compared to all of the other variants.", "In animal models the phenotype of the all1Delta mutant mimicked the hypervirulent phenotype of the mucoid switch variant, which is characterized by decreased host survival and elevated intracranial pressure.", "Decreased survival is likely the result of both an ineffective cell-mediated immune response and impaired phagocytosis by macrophages.", "Consequently, we concluded that, unlike loss of most virulence-associated genes, where loss of gene function results in attenuated virulence, loss of the ALL1 gene enhances virulence by altering the host-pathogen interaction and thereby impairing clearance.", "Our data identified the first cryptococcal gene associated with elevated intracranial pressure and support the hypothesis that an environmental opportunistic pathogen has modified its virulence in vivo by epigenetic downregulation of gene function."], "structured": false}
{"doc_id": 7729656, "title": "Lessons from more than 80 structures of the GluA2 ligand-binding domain in complex with agonists, antagonists and allosteric modulators.", "abstract": ["Ionotropic glutamate receptors (iGluRs) constitute a family of ligand-gated ion channels that are essential for mediating fast synaptic transmission in the central nervous system.", "These receptors play an important role for the development and function of the nervous system, and are essential in learning and memory.", "However, iGluRs are also implicated in or have causal roles for several brain disorders, e.g. epilepsy, Alzheimer's disease, Parkinson's disease and schizophrenia.", "Their involvement in neurological diseases has stimulated widespread interest in their structure and function.", "Since the first publication in 1998 of the structure of a recombinant soluble protein comprising the ligand-binding domain of GluA2 extensive studies have afforded numerous crystal structures of wildtype and mutant proteins including different ligands.", "The structural information obtained combined with functional data have led to models for receptor activation and desensitization by agonists, inhibition by antagonists and block of desensitization by positive allosteric modulators.", "Furthermore, the structural and functional studies have formed a powerful platform for the design of new selective compounds."], "structured": false}
{"doc_id": 7734150, "title": "Diaphragm Atrophy and Contractile Dysfunction in a Murine Model of Pulmonary Hypertension", "abstract": ["Pulmonary hypertension (PH) causes loss of body weight and inspiratory (diaphragm) muscle dysfunction.", "A model of PH induced by drug (monocrotaline, MCT) has been extensively used in mice to examine the etiology of PH.", "However, it is unclear if PH induced by MCT in mice reproduces the loss of body weight and diaphragm muscle dysfunction seen in patients.", "This is a pre-requisite for widespread use of mice to examine mechanisms of cachexia and diaphragm abnormalities in PH.", "Thus, we measured body and soleus muscle weight, food intake, and diaphragm contractile properties in mice after 6-8 weeks of saline (control) or MCT (600 mg/kg) injections.", "Body weight progressively decreased in PH mice, while food intake was similar in both groups.", "PH decreased (P<0.05) diaphragm maximal isometric specific force, maximal shortening velocity, and peak power.", "Protein carbonyls in whole-diaphragm lysates and the abundance of select myofibrillar proteins were unchanged by PH.", "Our findings show diaphragm isometric and isotonic contractile abnormalities in a murine model of PH induced by MCT.", "Overall, the murine model of PH elicited by MCT mimics loss of body weight and diaphragm muscle weakness reported in PH patients."], "structured": false}
{"doc_id": 7735859, "title": "Identification of an anti-inflammatory protein from Faecalibacterium prausnitzii, a commensal bacterium deficient in Crohn's disease.", "abstract": ["BACKGROUND Crohn's disease (CD)-associated dysbiosis is characterised by a loss of Faecalibacterium prausnitzii, whose culture supernatant exerts an anti-inflammatory effect both in vitro and in vivo.", "However, the chemical nature of the anti-inflammatory compounds has not yet been determined.   \n", "METHODS Peptidomic analysis using mass spectrometry was applied to F. prausnitzii supernatant.", "Anti-inflammatory effects of identified peptides were tested in vitro directly on intestinal epithelial cell lines and on cell lines transfected with a plasmid construction coding for the candidate protein encompassing these peptides.", "In vivo, the cDNA of the candidate protein was delivered to the gut by recombinant lactic acid bacteria to prevent dinitrobenzene sulfonic acid (DNBS)-colitis in mice.   \n", "RESULTS The seven peptides, identified in the F. prausnitzii culture supernatants, derived from a single microbial anti-inflammatory molecule (MAM), a protein of 15 kDa, and comprising 53% of non-polar residues.", "This last feature prevented the direct characterisation of the putative anti-inflammatory activity of MAM-derived peptides.", "Transfection of MAM cDNA in epithelial cells led to a significant decrease in the activation of the nuclear factor (NF)-\u03baB pathway with a dose-dependent effect.", "Finally, the use of a food-grade bacterium, Lactococcus lactis, delivering a plasmid encoding MAM was able to alleviate DNBS-induced colitis in mice.   \n", "CONCLUSIONS A 15 kDa protein with anti-inflammatory properties is produced by F. prausnitzii, a commensal bacterium involved in CD pathogenesis.", "This protein is able to inhibit the NF-\u03baB pathway in intestinal epithelial cells and to prevent colitis in an animal model."], "structured": true}
{"doc_id": 7736860, "title": "Calcium store sensor stromal-interaction molecule 1-dependent signaling plays an important role in cervical cancer growth, migration, and angiogenesis.", "abstract": ["Store-operated Ca(2+) entry (SOCE) is the principal Ca(2+) entry mechanism in nonexcitable cells.", "Stromal-interaction molecule 1 (STIM1) is an endoplasmic reticulum Ca(2+) sensor that triggers SOCE activation.", "However, the role of STIM1 in regulating cancer progression remains controversial and its clinical relevance is unclear.", "Here we show that STIM1-dependent signaling is important for cervical cancer cell proliferation, migration, and angiogenesis.", "STIM1 overexpression in tumor tissue is noted in 71% cases of early-stage cervical cancer.", "In tumor tissues, the level of STIM1 expression is significantly associated with the risk of metastasis and survival.", "EGF-stimulated cancer cell migration requires STIM1 expression and EGF increases the interaction between STIM1 and Orai1 in juxta-membrane areas, and thus induces Ca(2+) influx.", "STIM1 involves the activation of Ca(2+)-regulated protease calpain, as well as Ca(2+)-regulated cytoplasmic kinase Pyk2, which regulate the focal-adhesion dynamics of migratory cervical cancer cells.", "Because of an increase of p21 protein levels and a decrease of Cdc25C protein levels, STIM1-silencing in cervical cancer cells significantly inhibits cell proliferation by arresting the cell cycle at the S and G2/M phases.", "STIM1 also regulates the production of VEGF in cervical cancer cells.", "Interference with STIM1 expression or blockade of SOCE activity inhibits tumor angiogenesis and growth in animal models, confirming the crucial role of STIM1-mediated Ca(2+) influx in aggravating tumor development in vivo.", "These results make STIM1-dependent signaling an attractive target for therapeutic intervention."], "structured": false}
{"doc_id": 7751726, "title": "A feasibility study for a randomised controlled trial of the Positive Reappraisal Coping Intervention, a novel supportive technique for recurrent miscarriage", "abstract": ["INTRODUCTION Recurrent miscarriage (RM) is diagnosed when a woman has had three or more miscarriages.", "Increased levels of distress and anxiety are common during the waiting period of any subsequent pregnancies, posing a significant threat to psychological well-being.", "However, only limited support and therapy are available for these women, and many are left to cope alone.", "The Positive Reappraisal Coping Intervention (PRCI) is a novel self-administered supportive technique which has been shown to be effective in patients awaiting the outcome of in vitro fertilisation treatment.", "The primary objective of this study is to assess the feasibility and effectiveness of the PRCI in improving quality of life in the difficult waiting period which women with previous RM endure before an ongoing pregnancy can be confirmed.   \n", "METHODS AND ANALYSIS A randomised controlled trial (RCT) feasibility study will establish the viability of conducting a multicentre RCT to definitively test the effects of the PRCI on the psychological well-being of women who have experienced RM during the initial waiting period of a subsequent pregnancy.", "A second component consists of a qualitative process evaluation exploring the initial experience of pregnancy following repeated miscarriages.", "Participants (n=50) will be randomised into one of two groups.", "The PRCI intervention group will receive the PRCI card and weekly questionnaires to assess their psychological well-being during the waiting period of their new pregnancy.", "The non-intervention group will be asked to complete the same weekly questionnaires.", "The qualitative process analysis will employ semistructured interviews (n=20) to address relevant aspects of the study objectives.   ", "ETHICS AND DISSEMINATION Ethics approval has been obtained from the National Research Ethics Service Committee South Central-Hampshire A. Participating centres have given National Health Service R&D approval.", "Study findings will be disseminated through peer reviewed journals, national and international conferences and lay user groups.   \n", "TRIAL REGISTRATION NUMBER ISRCTN43571276.", "This study was registered with the ISRCTN 18/02/2014 following adoption onto the United Kingdom Clinical Research Network (UKCRN) portfolio.", "Recruitment of the first participant occurred 04/02/2014."], "structured": true}
{"doc_id": 7757997, "title": "Report of the National Heart, Lung, and Blood Institute Workshop on Lipoprotein(a) and Cardiovascular Disease: recent advances and future directions.", "abstract": ["It has been estimated that approximately 37% of the US population judged to be at high risk for developing coronary artery disease (CAD), based on the National Cholesterol Education Program guidelines, have increased plasma lipoprotein(a) [Lp(a)], whereas Lp(a) is increased in only 14% of those judged to be at low risk.", "Therefore, the importance of establishing a better understanding of the relative contribution of Lp(a) to the risk burden for CAD and other forms of vascular disease, as well as the underlying mechanisms, is clearly evident.", "However, the structural complexity and size heterogeneity of Lp(a) have hindered the development of immunoassays to accurately measure Lp(a) concentrations in plasma.", "The large intermethod variation in Lp(a) values has made it difficult to compare data from different clinical studies and to achieve a uniform interpretation of clinical data.", "A workshop was recently convened by the National Heart, Lung, and Blood Institute (NHLBI) to evaluate our current understanding of Lp(a) as a risk factor for atherosclerotic disorders; to determine how future studies could be designed to more clearly define the extent to which, and mechanisms by which, Lp(a) participates in these processes; and to present the results of the NHLBI-supported program for the evaluation and standardization of Lp(a) immunoassays.", "This report includes the most recent data presented by the workshop participants and the resulting practical and research recommendations."], "structured": false}
{"doc_id": 7764903, "title": "Classification, functions, and clinical relevance of extracellular vesicles.", "abstract": ["Both eukaryotic and prokaryotic cells release small, phospholipid-enclosed vesicles into their environment.", "Why do cells release vesicles?", "Initial studies showed that eukaryotic vesicles are used to remove obsolete cellular molecules.", "Although this release of vesicles is beneficial to the cell, the vesicles can also be a danger to their environment, for instance in blood, where vesicles can provide a surface supporting coagulation.", "Evidence is accumulating that vesicles are cargo containers used by eukaryotic cells to exchange biomolecules as transmembrane receptors and genetic information.", "Because also bacteria communicate to each other via extracellular vesicles, the intercellular communication via extracellular cargo carriers seems to be conserved throughout evolution, and therefore vesicles are likely to be a highly efficient, robust, and economic manner of exchanging information between cells.", "Furthermore, vesicles protect cells from accumulation of waste or drugs, they contribute to physiology and pathology, and they have a myriad of potential clinical applications, ranging from biomarkers to anticancer therapy.", "Because vesicles may pass the blood-brain barrier, they can perhaps even be considered naturally occurring liposomes.", "Unfortunately, pathways of vesicle release and vesicles themselves are also being used by tumors and infectious diseases to facilitate spreading, and to escape from immune surveillance.", "In this review, the different types, nomenclature, functions, and clinical relevance of vesicles will be discussed."], "structured": false}
{"doc_id": 7766808, "title": "Estimating the sample mean and standard deviation from the sample size, median, range and/or interquartile range", "abstract": ["In systematic reviews and meta-analysis, researchers often pool the results of the sample mean and standard deviation from a set of similar clinical trials.", "A number of the trials, however, reported the study using the median, the minimum and maximum values, and/or the first and third quartiles.", "Hence, in order to combine results, one may have to estimate the sample mean and standard deviation for such trials.", "In this paper, we propose to improve the existing literature in several directions.", "First, we show that the sample standard deviation estimation in Hozo et al. (2005) has some serious limitations and is always less satisfactory in practice.", "Inspired by this, we propose a new estimation method by incorporating the sample size.", "Second, we systematically study the sample mean and standard deviation estimation problem under more general settings where the first and third quartiles are also available for the trials.", "Through simulation studies, we demonstrate that the proposed methods greatly improve the existing methods and enrich the literature.", "We conclude our work with a summary table that serves as a comprehensive guidance for performing meta-analysis in different situations."], "structured": false}
{"doc_id": 7795952, "title": "Fascin protein is critical for transforming growth factor \u03b2 protein-induced invasion and filopodia formation in spindle-shaped tumor cells.", "abstract": ["Fascin, an actin-bundling protein overexpressed in all carcinomas, has been associated with poor prognosis, shorter survival, and more metastatic diseases.", "It is believed that fascin facilitates tumor metastasis by promoting the formation of invasive membrane protrusions.", "However, the mechanisms by which fascin is overexpressed in tumors are not clear.", "TGF\u03b2 is a cytokine secreted by tumor and mesenchymal cells and promotes metastasis in many late stage tumors.", "The pro-metastasis mechanisms of TGF\u03b2 remain to be fully elucidated.", "Here we demonstrated that TGF\u03b2 induced fascin expression in spindle-shaped tumor cells through the canonical Smad-dependent pathway.", "Fascin was critical for TGF\u03b2-promoted filopodia formation, migration, and invasion in spindle tumor cells.", "More importantly, fascin expression significantly correlates with TGF\u03b21 and TGF\u03b2 receptor I levels in a cohort of primary breast tumor samples.", "Our results indicate that elevated TGF\u03b2 level in the tumor microenvironment may be responsible for fascin overexpression in some of the metastatic tumors.", "Our data also suggest that fascin could play a central role in TGF\u03b2-promoted tumor metastasis."], "structured": false}
{"doc_id": 7808055, "title": "DNA methylation age of human tissues and cell types", "abstract": ["BACKGROUND It is not yet known whether DNA methylation levels can be used to accurately predict age across a broad spectrum of human tissues and cell types, nor whether the resulting age prediction is a biologically meaningful measure.   \n", "RESULTS I developed a multi-tissue predictor of age that allows one to estimate the DNA methylation age of most tissues and cell types.", "The predictor, which is freely available, was developed using 8,000 samples from 82 Illumina DNA methylation array datasets, encompassing 51 healthy tissues and cell types.", "I found that DNA methylation age has the following properties: first, it is close to zero for embryonic and induced pluripotent stem cells; second, it correlates with cell passage number; third, it gives rise to a highly heritable measure of age acceleration; and, fourth, it is applicable to chimpanzee tissues.", "Analysis of 6,000 cancer samples from 32 datasets showed that all of the considered 20 cancer types exhibit significant age acceleration, with an average of 36 years.", "Low age-acceleration of cancer tissue is associated with a high number of somatic mutations and TP53 mutations, while mutations in steroid receptors greatly accelerate DNA methylation age in breast cancer.", "Finally, I characterize the 353 CpG sites that together form an aging clock in terms of chromatin states and tissue variance.   \n", "CONCLUSIONS I propose that DNA methylation age measures the cumulative effect of an epigenetic maintenance system.", "This novel epigenetic clock can be used to address a host of questions in developmental biology, cancer and aging research."], "structured": true}
{"doc_id": 7813993, "title": "Whole-body MR vascular screening detects unsuspected concomitant vascular disease in coronary heart disease patients", "abstract": ["Coronary heart disease (CHD) patients often show atherosclerotic vascular disease in other vascular territories.", "We evaluated how often whole-body MR imaging detects concomitant arterial pathologies in CHD patients, and how often these pathologies were not known to the patients previously.", "Of 4,814 participants in the population-based Heinz Nixdorf Recall Study, 327 reported CHD (i.e., previous coronary bypass surgery, angioplasty); of those, 160 patients (mean age 66.4 years) were examined using MR of the brain, the heart (excluding the coronary arteries), and whole-body MR angiography.", "The prevalence of each vascular pathology was assessed, correlated to the others and compared to patients\u2019 histories.", "Of the 160 CHD patients, 16 (10%) showed MR signs of stroke, and 77 (48.1%) had a stenosis >50% in at least one extracerebral peripheral artery (other than the coronaries), including 28 (17.5%) with relevant renal artery stenoses, and 20 (12.5%) with relevant extracerebral internal carotid artery stenoses.", "False negative histories were reported in 12 of 81 cases with myocardial infarctions, and in 11 of 16 cases with cerebrovascular infarctions.", "This whole-body atherosclerosis MR screening program allows previously unknown concomitant vascular disease to be detected in coronary heart disease patients.", "Its prospective value should be assessed in further studies."], "structured": false}
{"doc_id": 7820043, "title": "Key role of Ubc5 and lysine-63 polyubiquitination in viral activation of IRF3.", "abstract": ["The mitochondrial antiviral signaling protein (MAVS; also known as IPS-1, VISA, and CARDIF) is essential for innate immune response against RNA viruses.", "MAVS transduces signals from the cytosolic RIG-I-like receptors, which bind to viral RNAs.", "But how MAVS activates downstream transcription factors such as IRF3 to induce type-I interferons is not well understood.", "We have established a cell-free system in which mitochondria derived from virus-infected cells activate IRF3 in the cytosol.", "Fractionation of the cytosol led to the identification of Ubc5 as a ubiquitin-conjugating enzyme (E2) required for IRF3 activation.", "Using an inducible RNAi strategy, we demonstrate that catalytically active Ubc5 is required for IRF3 activation by viral infection.", "The activation of IRF3 also requires two ubiquitin-binding domains of NEMO.", "Furthermore, we show that replacement of endogenous ubiquitin with its K63R mutant abolishes viral activation of IRF3, demonstrating that K63 polyubiquitination plays a key role in IRF3 activation."], "structured": false}
{"doc_id": 7821634, "title": "Profiling of residual breast cancers after neoadjuvant chemotherapy identifies DUSP4 deficiency as a mechanism of drug resistance", "abstract": ["Neoadjuvant chemotherapy (NAC) induces a pathological complete response (pCR) in \u223c30% of patients with breast cancer.", "However, many patients have residual cancer after chemotherapy, which correlates with a higher risk of metastatic recurrence and poorer outcome than those who achieve a pCR.", "We hypothesized that molecular profiling of tumors after NAC would identify genes associated with drug resistance.", "Digital transcript counting was used to profile surgically resected breast cancers after NAC.", "Low concentrations of dual specificity protein phosphatase 4 (DUSP4), an ERK phosphatase, correlated with high post-NAC tumor cell proliferation and with basal-like breast cancer (BLBC) status.", "BLBC had higher DUSP4 promoter methylation and gene expression patterns of Ras-ERK pathway activation relative to other breast cancer subtypes.", "DUSP4 overexpression increased chemotherapy-induced apoptosis, whereas DUSP4 depletion dampened the response to chemotherapy.", "Reduced DUSP4 expression in primary tumors after NAC was associated with treatment-refractory high Ki-67 scores and shorter recurrence-free survival.", "Finally, inhibition of mitogen-activated protein kinase kinase (MEK) synergized with docetaxel treatment in BLBC xenografts.", "Thus, DUSP4 downregulation activates the Ras-ERK pathway in BLBC, resulting in an attenuated response to anti-cancer chemotherapy."], "structured": false}
{"doc_id": 7834603, "title": "Age-related behaviors have distinct transcriptional profiles in Caenorhabditis elegans.", "abstract": ["There has been a great deal of interest in identifying potential biomarkers of aging.", "Biomarkers of aging would be useful to predict potential vulnerabilities in an individual that may arise well before they are chronologically expected, due to idiosyncratic aging rates that occur between individuals.", "Prior attempts to identify biomarkers of aging have often relied on the comparisons of long-lived animals to a wild-type control.", "However, the effect of interventions in model systems that prolong lifespan (such as single gene mutations or caloric restriction) can sometimes be difficult to interpret due to the manipulation itself having multiple unforeseen consequences on physiology, unrelated to aging itself.", "The search for predictive biomarkers of aging therefore is problematic, and the identification of metrics that can be used to predict either physiological or chronological age would be of great value.", "One methodology that has been used to identify biomarkers for numerous pathologies is gene expression profiling.", "Here, we report whole-genome expression profiles of individual wild-type Caenorhabditis elegans covering the entire wild-type nematode lifespan.", "Individual nematodes were scored for either age-related behavioral phenotypes, or survival, and then subsequently associated with their respective gene expression profiles.", "This facilitated the identification of transcriptional profiles that were highly associated with either physiological or chronological age.", "Overall, our approach serves as a paradigm for identifying potential biomarkers of aging in higher organisms that can be repeatedly sampled throughout their lifespan."], "structured": false}
{"doc_id": 7837879, "title": "Synchronization of Diffusively-Connected Nonlinear Systems: Results Based on Contractions with Respect to General Norms", "abstract": ["Contraction theory provides an elegant way to analyze the behavior of certain nonlinear dynamical systems.", "In this paper, we discuss the application of contraction to synchronization of diffusively interconnected components described by nonlinear differential equations.", "We provide estimates of convergence of the difference in states between components, in the cases of line, complete, and star graphs, and Cartesian products of such graphs.", "We base our approach on contraction theory, using matrix measures derived from norms that are not induced by inner products.", "Such norms are the most appropriate in many applications, but proofs cannot rely upon Lyapunov-like linear matrix inequalities, and different techniques, such as the use of the Perron-Frobenious Theorem in the cases of L1 or L\u221e norms, must be introduced."], "structured": false}
{"doc_id": 7838799, "title": "GeneTrack--a genomic data processing and visualization framework.", "abstract": ["MOTIVATION High-throughput 'ChIP-chip' and 'ChIP-seq' methodologies generate sufficiently large data sets that analysis poses significant informatics challenges, particularly for research groups with modest computational support.", "To address this challenge, we devised a software platform for storing, analyzing and visualizing high resolution genome-wide binding data.", "GeneTrack automates several steps of a typical data processing pipeline, including smoothing and peak detection, and facilitates dissemination of the results via the web.", "Our software is freely available via the Google Project Hosting environment at http://genetrack.googlecode.com"], "structured": false}
{"doc_id": 7840442, "title": "Multisite optical recording of excitability in the enteric nervous system.", "abstract": ["A multisite optical recording technique consisting of an array of 464 photodiodes was used to measure dynamic changes in transmembrane potentials (Vm) of guinea-pig and mouse enteric neurones stained with the voltage-sensitive dye Di-8-ANEPPS.", "Optical recordings of Vm changes in enteric neurones which were evoked by depolarizing current pulses or synaptic activation mirrored the Vm changes measured intracellularly in the same neurone.", "Action potentials had fractional change in fluorescence of -0.09 +/-", "0.06% and their peak to peak noise level was 20 +/-", "14% of the action potential amplitude.", "Optical recordings after electrical stimulation of interganglionic nerve strands revealed slow EPSPs, nicotinergic supra- and subthreshold fast EPSPs as well as propagation of action potentials along interganglionic strands.", "Local application of acetylcholine onto a single ganglion induced reproducibly and dose dependently action potential discharge demonstrating the feasibility of neuropharmacological studies.", "The optical mapping made it possible to record action potentials simultaneously in a large number of neurones with high spatiotemporal resolution that is unattainable by conventional techniques.", "This technique presents a powerful tool to study excitability spread within enteric circuits and to assess differential activation of enteric populations in response to a number of stimuli which modulate neuronal activity directly or through synaptic mechanisms."], "structured": false}
{"doc_id": 7848113, "title": "Telomere-bound TRF1 and TRF2 stall the replication fork at telomeric repeats.", "abstract": ["Vertebrate telomeres consist of tandem repeats of T2AG3 and associated proteins including the telomeric DNA-binding proteins, TRF1 and TRF2.", "It has been proposed that telomeres assume two interswitchable states, the open state that is accessible to various trans-acting factors and the closed state that excludes those factors.", "TRF1 and TRF2 are believed to promote the formation of the closed state.", "However, little is known about how those two states influence DNA replication.", "We analyzed the effects of TRF1 and TRF2 on telomeric replication both in vitro and in vivo.", "By exploiting the in vitro replication system of linear SV40 DNA, we found that telomeric repeats are a poor replication template.", "Moreover, the addition of recombinant TRF1 and TRF2 significantly stalled the replication fork progression at telomeric repeats.", "When TRF1 was overexpressed in HeLa cells, cells with 4N DNA content were accumulated.", "Furthermore, cytological analyses revealed that the replication focus overlapped with telomere signals at a significantly higher frequency in TRF1-overexpressing cells than in control cells.", "The results suggest that TRF1 and TRF2 exert inhibitory effects on replication fork progression."], "structured": false}
{"doc_id": 7850867, "title": "Margination of white blood cells in microcapillary flow.", "abstract": ["Margination of white blood cells (WBCs) towards vessel walls is an essential precondition for their efficient adhesion to the vascular endothelium.", "We perform numerical simulations with a two-dimensional blood flow model to investigate the dependence of WBC margination on hydrodynamic interactions of blood cells with the vessel walls, as well as on their collective behavior and deformability.", "We find WBC margination to be optimal in intermediate ranges of red blood cell (RBC) volume fractions and flow rates, while, beyond these ranges, it is substantially attenuated.", "RBC aggregation enhances WBC margination, while WBC deformability reduces it.", "These results are combined in state diagrams, which identify WBC margination for a wide range of flow and cell suspension conditions."], "structured": false}
{"doc_id": 7852582, "title": "Lung cancer treatment waiting times and tumour growth.", "abstract": ["We report a single-centre prospective audit of 29 lung cancer patients who were awaiting radical (potentially curative) radiotherapy.", "This was the total number assessed as suitable for radical treatment by one consultant during 1999.", "At the time of assessment they had been newly diagnosed and staged with a computed tomographic (CT) scan of chest.", "They had a subsequent CT scan prior to starting treatment for the purpose of planning the radiation fields.", "We have now measured tumour size on the diagnostic scans and compared this with the size on the planning scans.", "We have documented the delay between diagnostic and planning CT scanning and the total time between first hospital visit and starting treatment.", "Two patients had progression of symptoms while on the waiting list, making them unfit for radical treatment, and another four had tumour progression on planning CT such that the tumour volume was too large for radical treatment.", "Therefore, 21% of potentially curable patients became incurable on the waiting list.", "The delay between diagnostic and planning CT scans ranged from 18 to 131 days (median 54), with increases in the cross-sectional tumour size over that period ranging zero to 373%.", "The delay between the first hospital visit and starting treatment was 35-187 days (median 94); between the date of the radiotherapy request and the starting date for treatment it was 23-61 days (median 44).", "Limited access to specialists is the reason most often advanced for the poor performance of the UK in treating lung cancer.", "This study demonstrates that, even for the select minority of patients who have specialist referral and are deemed suitable for potentially curative treatment, the outcome is prejudiced by waiting times that allow tumour progression."], "structured": false}
{"doc_id": 7860396, "title": "Functional coupling of RNAP II transcription to spliceosome assembly.", "abstract": ["The pathway of gene expression in higher eukaryotes involves a highly complex network of physical and functional interactions among the different machines involved in each step of the pathway.", "Here we established an efficient in vitro system to determine how RNA polymerase II (RNAP II) transcription is functionally coupled to pre-mRNA splicing.", "Strikingly, our data show that nascent pre-messenger RNA (pre-mRNA) synthesized by RNAP II is immediately and quantitatively directed into the spliceosome assembly pathway.", "In contrast, nascent pre-mRNA synthesized by T7 RNA polymerase is quantitatively assembled into the nonspecific H complex, which consists of heterogeneous nuclear ribonucleoprotein (hnRNP) proteins and is inhibitory for spliceosome assembly.", "Consequently, RNAP II transcription results in a dramatic increase in both the kinetics of splicing and overall yield of spliced mRNA relative to that observed for T7 transcription.", "We conclude that RNAP II mediates the functional coupling of transcription to splicing by directing the nascent pre-mRNA into spliceosome assembly, thereby bypassing interaction of the pre-mRNA with the inhibitory hnRNP proteins."], "structured": false}
{"doc_id": 7869794, "title": "Calicum microdomains form within neutrophils at the neutrophil\u2013tumor cell synapse: role in antibody-dependent target cell apoptosis", "abstract": ["Ca2+ messages are broadly important in cellular signal transduction.", "In immune cells, Ca2+ signaling is an essential step in many forms of activation.", "Neutrophil-mediated antibody-dependent cell-mediated cytotoxicity (ADCC) is one form of leukocyte activation that plays an important role in tumor cell killing in vitro and in patient care.", "Using fluorescence methodologies, we found that neutrophils exhibit Ca2+ signals during ADCC directed against breast fibrosarcoma cells.", "Importantly, these signals were localized to Ca2+ microdomains at the neutrophil-to-tumor cell interface where they display dynamic features such as movement, fusion, and fission.", "These signals were blocked by the intracellular Ca2+ buffer BAPTA.", "At the neutrophil\u2013tumor cell synapse, the neutrophil\u2019s cytoplasm was enriched in STIM1, a crucial mediator of Ca2+ signaling, whereas the Ca2+-binding proteins calbindin and parvalbumin were not affected.", "Our findings suggest that Ca2+ microdomains are due to an active signaling process.", "As Ca2+ signals within neutrophils were necessary for specific tumor cell apoptosis, a central role of microdomains in leukocyte-mediated tumor cell destruction is indicated."], "structured": false}
{"doc_id": 7873737, "title": "Platelet glycoprotein IIb/IIIa inhibitors reduce mortality in diabetic patients with non-ST-segment-elevation acute coronary syndromes.", "abstract": ["BACKGROUND Diabetes mellitus is a major risk factor for adverse outcomes after acute coronary syndromes (ACS).", "Because this disease may be associated with increased platelet aggregation, we investigated whether diabetic patients with ACS derive particular benefit from platelet glycoprotein (GP) IIb/IIIa receptor inhibition.   \n", "METHODS AND RESULTS We performed a meta-analysis of the diabetic populations enrolled in the 6 large-scale platelet GP IIb/IIIa inhibitor ACS trials: PRISM, PRISM-PLUS, PARAGON A, PARAGON B, PURSUIT, and GUSTO IV.", "Among 6458 diabetic patients, platelet GP IIb/IIIa inhibition was associated with a significant mortality reduction at 30 days, from 6.2% to 4.6% (OR 0.74; 95% CI 0.59 to 0.92; P=0.007).", "Conversely, 23 072 nondiabetic patients had no survival benefit (3.0% versus 3.0%).", "The interaction between platelet GP IIb/IIIa inhibition and diabetic status was statistically significant (P=0.036).", "Among 1279 diabetic patients undergoing percutaneous coronary intervention (PCI) during index hospitalization, the use of these agents was associated with a mortality reduction at 30 days from 4.0% to 1.2% (OR 0.30; 95% CI 0.14 to 0.69; P=0.002).   \n", "CONCLUSIONS This meta-analysis, including the entire large-scale trial experience of intravenous platelet GP IIb/IIIa inhibitors for the medical management of non-ST-segment-elevation ACS, shows that these agents may significantly reduce mortality at 30 days in diabetic patients.", "Although not based on a randomized assessment, the survival benefit appears to be of greater magnitude in patients undergoing PCI.", "Therefore, the use of platelet GP IIb/IIIa inhibitors should be strongly considered in diabetic patients with ACS."], "structured": true}
{"doc_id": 7875158, "title": "Glucose deprivation-induced cytotoxicity and alterations in mitogen-activated protein kinase activation are mediated by oxidative stress in multidrug-resistant human breast carcinoma cells.", "abstract": ["We previously observed that glucose deprivation induces cell death in multidrug-resistant human breast carcinoma cells (MCF-7/ADR).", "As a follow up we wished to test the hypothesis that metabolic oxidative stress was the causative process or at least the link between causative processes behind the cytotoxicity.", "In the studies described here, we demonstrate that mitogen-activated protein kinase (MAPK) was activated within 3 min of being in glucose-free medium and remained activated for 3 h. Glucose deprivation for 2-4 h also caused oxidative stress as evidenced by a 3-fold greater steady state concentration of oxidized glutathione and a 3-fold increase in pro-oxidant production.", "Glucose and glutamate treatment rapidly suppressed MAPK activation and rescued cells from cytotoxicity.", "Glutamate and the peroxide scavenger, pyruvate, rescued the cells from cell killing as well as suppressed pro-oxidant production.", "In addition the thiol antioxidant, N-acetyl-L-cysteine, rescued cells from glucose deprivation-induced cytotoxicity and suppressed MAPK activation.", "These results suggest that glucose deprivation-induced cytotoxicity and alterations in MAPK signal transduction are mediated by oxidative stress in MCF-7/ADR.", "These results also support the speculation that a common mechanism of glucose deprivation-induced cytotoxicity in mammalian cells may involve metabolic oxidative stress."], "structured": false}
{"doc_id": 7878807, "title": "A structural basis for kinetochore recruitment of the Ndc80 complex via two distinct centromere receptors.", "abstract": ["The Ndc80 complex is the key microtubule-binding element of the kinetochore.", "In contrast to the well-characterized interaction of Ndc80-Nuf2 heads with microtubules, little is known about how the Spc24-25 heterodimer connects to centromeric chromatin.", "Here, we present molecular details of Spc24-25 in complex with the histone-fold protein Cnn1/CENP-T illustrating how this connection ultimately links microtubules to chromosomes.", "The conserved Ndc80 receptor motif of Cnn1 is bound as an \u03b1 helix in a hydrophobic cleft at the interface between Spc24 and Spc25.", "Point mutations that disrupt the Ndc80-Cnn1 interaction also abrogate binding to the Mtw1 complex and are lethal in yeast.", "We identify a Cnn1-related motif in the Dsn1 subunit of the Mtw1 complex, necessary for Ndc80 binding and essential for yeast growth.", "Replacing this region with the Cnn1 peptide restores viability demonstrating functionality of the Ndc80-binding module in different molecular contexts.", "Finally, phosphorylation of the Cnn1 N-terminus coordinates the binding of the two competing Ndc80 interaction partners.", "Together, our data provide structural insights into the modular binding mechanism of the Ndc80 complex to its centromere recruiters."], "structured": false}
{"doc_id": 7898952, "title": "Feedback Circuit among INK4 Tumor Suppressors Constrains Human Glioblastoma Development", "abstract": ["We have developed a nonheuristic genome topography scan (GTS) algorithm to characterize the patterns of genomic alterations in human glioblastoma (GBM), identifying frequent p18(INK4C) and p16(INK4A) codeletion.", "Functional reconstitution of p18(INK4C) in GBM cells null for both p16(INK4A) and p18(INK4C) resulted in impaired cell-cycle progression and tumorigenic potential.", "Conversely, RNAi-mediated depletion of p18(INK4C) in p16(INK4A)-deficient primary astrocytes or established GBM cells enhanced tumorigenicity in vitro and in vivo.", "Furthermore, acute suppression of p16(INK4A) in primary astrocytes induced a concomitant increase in p18(INK4C).", "Together, these findings uncover a feedback regulatory circuit in the astrocytic lineage and demonstrate a bona fide tumor suppressor role for p18(INK4C) in human GBM wherein it functions cooperatively with other INK4 family members to constrain inappropriate proliferation."], "structured": false}
{"doc_id": 7915836, "title": "The SMC5/6 complex maintains telomere length in ALT cancer cells through SUMOylation of telomere-binding proteins", "abstract": ["Most cancer cells activate telomerase to elongate telomeres and achieve unlimited replicative potential.", "Some cancer cells cannot activate telomerase and use telomere homologous recombination (HR) to elongate telomeres, a mechanism termed alternative lengthening of telomeres (ALT).", "A hallmark of ALT cells is the recruitment of telomeres to PML bodies (termed APBs).", "Here, we show that the SMC5/6 complex localizes to APBs in ALT cells and is required for targeting telomeres to APBs.", "The MMS21 SUMO ligase of the SMC5/6 complex SUMOylates multiple telomere-binding proteins, including TRF1 and TRF2.", "Inhibition of TRF1 or TRF2 SUMOylation prevents APB formation.", "Depletion of SMC5/6 subunits by RNA interference inhibits telomere HR, causing telomere shortening and senescence in ALT cells.", "Thus, the SMC5/6 complex facilitates telomere HR and elongation in ALT cells by promoting APB formation through SUMOylation of telomere-binding proteins."], "structured": false}
{"doc_id": 7925817, "title": "Dynein pulls microtubules without rotating its stalk.", "abstract": ["Dynein is a microtubule motor that powers motility of cilia and flagella.", "There is evidence that the relative sliding of the doublet microtubules is due to a conformational change in the motor domain that moves a microtubule bound to the end of an extension known as the stalk.", "A predominant model for the movement involves a rotation of the head domain, with its stalk, toward the microtubule plus end.", "However, stalks bound to microtubules have been difficult to observe.", "Here, we present the clearest views so far of stalks in action, by observing sea urchin, outer arm dynein molecules bound to microtubules, with a new method, \"cryo-positive stain\" electron microscopy.", "The dynein molecules in the complex were shown to be active in in vitro motility assays.", "Analysis of the electron micrographs shows that the stalk angles relative to microtubules do not change significantly between the ADP.vanadate and no-nucleotide states, but the heads, together with their stalks, shift with respect to their A-tubule attachments.", "Our results disagree with models in which the stalk acts as a lever arm to amplify structural changes.", "The observed movement of the head and stalk relative to the tail indicates a new plausible mechanism, in which dynein uses its stalk as a grappling hook, catching a tubulin subunit 8 nm ahead and pulling on it by retracting a part of the tail (linker)."], "structured": false}
{"doc_id": 7929932, "title": "The INO80 chromatin remodeling complex in transcription, replication and repair.", "abstract": ["The Ino80 ATPase is a member of the SNF2 family of ATPases and functions as an integral component of a multisubunit ATP-dependent chromatin remodeling complex.", "Although INO80 complexes from yeast and higher eukaryotes share a common core of conserved subunits, the complexes have diverged substantially during evolution and have acquired new subunits with apparently species-specific functions.", "Recent studies have shown that the INO80 complex contributes to a wide variety of chromatin-dependent nuclear transactions, including transcription, DNA repair and DNA replication."], "structured": false}
{"doc_id": 7944381, "title": "VEX1 controls the allelic exclusion required for antigenic variation in trypanosomes.", "abstract": ["Allelic exclusion underpins antigenic variation and immune evasion in African trypanosomes.", "These bloodstream parasites use RNA polymerase-I (pol-I) to transcribe just one telomeric variant surface glycoprotein (VSG) gene at a time, producing superabundant and switchable VSG coats.", "We identified trypanosome VSG exclusion-1 (VEX1) using a genetic screen for defects in telomere-exclusive expression.", "VEX1 was sequestered by the active VSG and silencing of other VSGs failed when VEX1 was either ectopically expressed or depleted, indicating positive and negative regulation, respectively.", "Positive regulation affected VSGs and nontelomeric pol-I-transcribed genes, whereas negative regulation primarily affected VSGs.", "Negative regulation by VEX1 also affected telomeric pol-I-transcribed reporter constructs, but only when they contained blocks of sequence sharing homology with a pol-I-transcribed locus.", "We conclude that restricted positive regulation due to VEX1 sequestration, combined with VEX1-dependent, possibly homology-dependent silencing, drives a \"winner-takes-all\" mechanism of allelic exclusion."], "structured": false}
{"doc_id": 7948486, "title": "Kruppel-like factor 2 (KLF2) regulates monocyte differentiation and functions in mBSA and IL-1\u03b2-induced arthritis.", "abstract": ["Kruppel-like factor 2 (KLF2) plays an important role in the regulation of a variety of immune cells, including monocytes.", "We have previously shown that KLF2 inhibits proinflammatory activation of monocytes.", "However, the role of KLF2 in arthritis is yet to be investigated.", "In the current study, we show that recruitment of significantly greater numbers of inflammatory subset of CD11b(+)F4/80(+)Ly6C+ monocytes to the inflammatory sites in KLF2 hemizygous mice compared to the wild type littermate controls.", "In parallel, inflammatory mediators, MCP-1, Cox-2 and PAI-1 were significantly up-regulated in bone marrow-derived monocytes isolated from KLF2 hemizygous mice, in comparison to wild-type controls.", "Methylated-BSA and IL-1\u03b2-induced arthritis was more severe in KLF2 hemizygous mice as compared to the littermate wild type controls.", "Consistent with this observation, monocytes isolated from KLF2 hemizygous mice showed an increased number of cells matured and differentiated towards osteoclastic lineage, potentially contributing to the severity of cartilage and bone damage in induced arthritic mice.", "The severity of arthritis was associated with the higher expression of proteins such as HSP60, HSP90 and MMP13 and attenuated levels of pPTEN, p21, p38 and HSP25/27 molecules in bone marrow cells of arthritic KLF2 hemizygous mice compared to littermate wild type controls.", "The data provide new insights and evidences of KLF2-mediated transcriptional regulation of arthritis via modulation of monocyte differentiation and function."], "structured": false}
{"doc_id": 7965928, "title": "Relationship of collegiate football experience and concussion with hippocampal volume and cognitive outcomes.", "abstract": ["IMPORTANCE Concussion and subconcussive impacts have been associated with short-term disrupted cognitive performance in collegiate athletes, but there are limited data on their long-term neuroanatomic and cognitive consequences.   \n", "OBJECTIVE To assess the relationships of concussion history and years of football experience with hippocampal volume and cognitive performance in collegiate football athletes.   \n", "DESIGN, SETTING, AND PARTICIPANTS Cross-sectional study conducted between June 2011 and August 2013 at a US psychiatric research institute specializing in neuroimaging among collegiate football players with a history of clinician-diagnosed concussion (n = 25), collegiate football players without a history of concussion (n = 25), and non-football-playing, age-, sex-, and education-matched healthy controls (n = 25).   ", "EXPOSURES History of clinician-diagnosed concussion and years of football experience.   \n", "MAIN OUTCOMES AND MEASURES High-resolution anatomical magnetic resonance imaging was used to quantify brain volumes.", "Baseline scores on a computerized concussion-related cognitive battery were used for cognitive assessment in athletes.   \n", "RESULTS Players with and without a history of concussion had smaller hippocampal volumes relative to healthy control participants (with concussion: t48 = 7.58; P < .001; mean difference, 1788 \u03bcL; 95% CI, 1317-2258 \u03bcL; without concussion: t48 = 4.35; P < .001, mean difference, 1027 \u03bcL; 95% CI, 556-1498 \u03bcL).", "Players with a history of concussion had smaller hippocampal volumes than players without concussion (t48 = 3.15; P < .001; mean difference, 761 \u03bcL; 95% CI, 280-1242 \u03bcL).", "In both athlete groups, there was a statistically significant inverse relationship between left hippocampal volume and number of years of football played (t46 = -3.62; P < .001; coefficient = -43.54; 95% CI, -67.66 to -19.41).", "Behavioral testing demonstrated no differences between athletes with and without a concussion history on 5 cognitive measures but did show an inverse correlation between years of playing football and reaction time (\u03c142 = -0.43; 95% CI, -0.46 to -0.40; P = .005).   \n", "CONCLUSIONS AND RELEVANCE Among a group of collegiate football athletes, there was a significant inverse relationship of concussion and years of football played with hippocampal volume.", "Years of football experience also correlated with slower reaction time.", "Further research is needed to determine the temporal relationships of these findings."], "structured": true}
{"doc_id": 7968532, "title": "STING and the innate immune response to nucleic acids in the cytosol", "abstract": ["Cytosolic detection of pathogen-derived nucleic acids is critical for the initiation of innate immune defense against diverse bacterial, viral and eukaryotic pathogens.", "Conversely, inappropriate responses to cytosolic nucleic acids can produce severe autoimmune pathology.", "The host protein STING has been identified as a central signaling molecule in the innate immune response to cytosolic nucleic acids.", "STING seems to be especially critical for responses to cytosolic DNA and the unique bacterial nucleic acids called 'cyclic dinucleotides'.", "Here we discuss advances in the understanding of STING and highlight the many unresolved issues in the field."], "structured": false}
{"doc_id": 7970974, "title": "Global Assessment of Genomic Regions Required for Growth in Mycobacterium tuberculosis", "abstract": ["Identifying genomic elements required for viability is central to our understanding of the basic physiology of bacterial pathogens.", "Recently, the combination of high-density mutagenesis and deep sequencing has allowed for the identification of required and conditionally required genes in many bacteria.", "Genes, however, make up only a part of the complex genomes of important bacterial pathogens.", "Here, we use an unbiased analysis to comprehensively identify genomic regions, including genes, domains, and intergenic elements, required for the optimal growth of Mycobacterium tuberculosis, a major global health pathogen.", "We found that several proteins jointly contain both domains required for optimal growth and domains that are dispensable.", "In addition, many non-coding regions, including regulatory elements and non-coding RNAs, are critical for mycobacterial growth.", "Our analysis shows that the genetic requirements for growth are more complex than can be appreciated using gene-centric analysis."], "structured": false}
{"doc_id": 7975937, "title": "Cyclooxygenase-Dependent Tumor Growth through Evasion of Immunity", "abstract": ["The mechanisms by which melanoma and other cancer cells evade anti-tumor immunity remain incompletely understood.", "Here, we show that the growth of tumors formed by mutant Braf(V600E) mouse melanoma cells in an immunocompetent host requires their production of prostaglandin E2, which suppresses immunity and fuels tumor-promoting inflammation.", "Genetic ablation of cyclooxygenases (COX) or prostaglandin E synthases in Braf(V600E) mouse melanoma cells, as well as in Nras(G12D) melanoma or in breast or colorectal cancer cells, renders them susceptible to immune control and provokes a shift in the tumor inflammatory profile toward classic anti-cancer immune pathways.", "This mouse COX-dependent inflammatory signature is remarkably conserved in human cutaneous melanoma biopsies, arguing for COX activity as a driver of immune suppression across species.", "Pre-clinical data demonstrate that inhibition of COX synergizes with anti-PD-1 blockade in inducing eradication of tumors, implying that COX inhibitors could be useful adjuvants for immune-based therapies in cancer patients."], "structured": false}
{"doc_id": 7986878, "title": "Anti-alphav integrin monoclonal antibody intetumumab enhances the efficacy of radiation therapy and reduces metastasis of human cancer xenografts in nude rats.", "abstract": ["We previously reported that intetumumab (CNTO 95), a fully human anti-\u03b1v integrin monoclonal antibody, is a radiosensitizer in mice with xenograft tumors.", "Because intetumumab does not cross-react with mouse integrins, but has cross-reactivity with rat integrins, we next studied the potential combined use of radiation therapy and intetumumab in human cancer xenograft models in nude rats to assess effects on both tumor cells and the tumor microenvironment.", "Nude rats bearing human head and neck cancer and non-small cell lung cancer (NSCLC) xenografts were treated with intetumumab and fractionated local tumor radiotherapy.", "Effects on tumor growth and metastasis, blood perfusion, oxygenation, and gastrointestinal toxicity were studied.", "Intetumumab alone had a moderate effect on tumor growth.", "When combined with fractionated radiation therapy, intetumumab significantly inhibited tumor growth and produced a tumor response rate that was significantly better than with radiation therapy alone.", "Treatment with intetumumab also significantly reduced lung metastasis in the A549 NSCLC xenograft model.", "The oxygenation and blood perfusion in xenograft tumors measured by microbubble-enhanced ultrasound imaging were substantially increased after treatment with intetumumab.", "The combined use of intetumumab and radiation therapy reduced the microvessel density and increased apoptosis in tumor cells and the tumor microenvironment.", "Toxicity studies showed that treatment with intetumumab did not cause the histopathologic changes in the lungs and did not sensitize the sensitive gastrointestinal epithelium to the effect of radiation therapy.", "Intetumumab can potentiate the efficacy of fractionated radiation therapy in human cancer xenograft tumors in nude rats without increased toxicity."], "structured": false}
{"doc_id": 7988832, "title": "Methylomic trajectories across human fetal brain development.", "abstract": ["Epigenetic processes play a key role in orchestrating transcriptional regulation during development.", "The importance of DNA methylation in fetal brain development is highlighted by the dynamic expression of de novo DNA methyltransferases during the perinatal period and neurodevelopmental deficits associated with mutations in the methyl-CpG binding protein 2 (MECP2) gene.", "However, our knowledge about the temporal changes to the epigenome during fetal brain development has, to date, been limited.", "We quantified genome-wide patterns of DNA methylation at \u223c 400,000 sites in 179 human fetal brain samples (100 male, 79 female) spanning 23 to 184 d post-conception.", "We identified highly significant changes in DNA methylation across fetal brain development at >7% of sites, with an enrichment of loci becoming hypomethylated with fetal age.", "Sites associated with developmental changes in DNA methylation during fetal brain development were significantly underrepresented in promoter regulatory regions but significantly overrepresented in regions flanking CpG islands (shores and shelves) and gene bodies.", "Highly significant differences in DNA methylation were observed between males and females at a number of autosomal sites, with a small number of regions showing sex-specific DNA methylation trajectories across brain development.", "Weighted gene comethylation network analysis (WGCNA) revealed discrete modules of comethylated loci associated with fetal age that are significantly enriched for genes involved in neurodevelopmental processes.", "This is, to our knowledge, the most extensive study of DNA methylation across human fetal brain development to date, confirming the prenatal period as a time of considerable epigenomic plasticity."], "structured": false}
{"doc_id": 7997337, "title": "Synaptic Determinants of Rett Syndrome", "abstract": ["There is mounting evidence showing that the structural and molecular organization of synaptic connections is affected both in human patients and in animal models of neurological and psychiatric diseases.", "As a consequence of these experimental observations, it has been introduced the concept of synapsopathies, a notion describing brain disorders of synaptic function and plasticity.", "A close correlation between neurological diseases and synaptic abnormalities is especially relevant for those syndromes including also mental retardation in their symptomatology, such as Rett syndrome (RS).", "RS (MIM312750) is an X-linked dominant neurological disorder that is caused in the majority of cases by mutations in methyl-CpG-binding protein 2 (MeCP2).", "This review will focus on the current knowledge of the synaptic alterations produced by mutations of the gene MeCP2 in mouse models of RS and will highlight prospects experimental therapies currently in use.", "Different experimental approaches have revealed that RS could be the consequence of an impairment in the homeostasis of synaptic transmission in specific brain regions.", "Indeed, several forms of experience-induced neuronal plasticity are impaired in the absence of MeCP2.", "Based on the results presented in this review, it is reasonable to propose that understanding how the brain is affected by diseases such as RS is at reach.", "This effort will bring us closer to identify the neurobiological bases of human cognition."], "structured": false}
{"doc_id": 8002529, "title": "Depressive symptoms and physical decline in community-dwelling older persons.", "abstract": ["CONTEXT Significant symptoms of depression are common in the older community-dwelling population.", "Although depressive symptoms and disability may commonly occur in the same person, whether depressive symptoms contribute to subsequent functional decline has not been elucidated.   \n", "OBJECTIVE To determine whether depressive symptoms in older persons increase the risk of subsequent decline in physical function as measured by objective performance-based tests.   \n", "DESIGN A 4-year prospective cohort study.   \n", "SETTING The communities of Iowa and Washington counties, Iowa.   \n", "PARTICIPANTS A total of 1286 persons aged 71 years and older who completed a short battery of physical performance tests in 1988 and again 4 years later.   \n", "MAIN OUTCOME MEASURES Baseline depressive symptoms were assessed by the Center for Epidemiological Studies Depression Scale.", "Physical performance tests included an assessment of standing balance, a timed 2.4-m (8-ft) walk, and a timed test of 5 repetitions of rising from a chair and sitting down.   \n", "RESULTS After adjustment for baseline performance score, health status, and sociodemographic factors, increasing levels of depressive symptoms were predictive of greater decline in physical performance over 4 years (odds ratio for decline in those with depressed mood vs those without, 1.55; 95% confidence interval [CI], 1.02-2.34).", "Even among those at the high end of the functional spectrum, who reported no disability, the severity of depressive symptoms predicted subsequent decline in physical performance (odds ratio for decline, 1.03; 95% CI, 1.00-1.08).   \n", "CONCLUSIONS This study provides evidence that older persons who report depressive symptoms are at higher risk of subsequent physical decline.", "These results suggest that prevention or reduction of depressed mood could play a role in reducing functional decline in older persons."], "structured": true}
{"doc_id": 8002887, "title": "Foxk proteins repress the initiation of starvation-induced atrophy and autophagy programs", "abstract": ["Autophagy is the primary catabolic process triggered in response to starvation.", "Although autophagic regulation within the cytosolic compartment is well established, it is becoming clear that nuclear events also regulate the induction or repression of autophagy.", "Nevertheless, a thorough understanding of the mechanisms by which sequence-specific transcription factors modulate expression of genes required for autophagy is lacking.", "Here, we identify Foxk proteins (Foxk1 and Foxk2) as transcriptional repressors of autophagy in muscle cells and fibroblasts.", "Interestingly, Foxk1/2 serve to counter-balance another forkhead transcription factor, Foxo3, which induces an overlapping set of autophagic and atrophic targets in muscle.", "Foxk1/2 specifically recruits Sin3A-HDAC complexes to restrict acetylation of histone H4 and expression of critical autophagy genes.", "Remarkably, mTOR promotes the transcriptional activity of Foxk1 by facilitating nuclear entry to specifically limit basal levels of autophagy in nutrient-rich conditions.", "Our study highlights an ancient, conserved mechanism whereby nutritional status is interpreted by mTOR to restrict autophagy by repressing essential autophagy genes through Foxk-Sin3-mediated transcriptional control."], "structured": false}
{"doc_id": 8005007, "title": "PRRSV receptors and their roles in virus infection", "abstract": ["Porcine reproductive and respiratory syndrome virus (PRRSV) has a restricted cell tropism and prefers to invade well-differentiated cells of the monocyte/macrophage lineage, such as pulmonary alveolar macrophages and African green monkey kidney cell line MA-104 and its derivatives, such as Marc-145, Vero and CL-2621.", "PRRSV infection of the host cells actually is a receptor-mediated endocytosis and replication process.", "The presence and absence of the cellular receptors decide whether the cell lines are permissive or non-permissive to PRRSV infection.", "Several PRRSV non-permissive cell lines, such as BHK-21, PK-15 and CHO-K1, have been shown to become sensitive to the virus infection upon expression of the recombinant receptor proteins.", "Up to now, heparin sulfate, sialoadhesin, CD163, CD151 and vimentin have been identified as the important PRRSV receptors via their involvement in virus attachment, internalization or uncoating.", "Each receptor is characterized by the distribution in different cells, the function in virus different infection stages and the interaction model with the viral proteins or genes.", "Joint forces of the receptors recently attract attentions due to the specific function.", "PRRSV receptors have become the targets for designing the new anti-viral reagents or the recombinant cell lines used for isolating the viruses or developing more effective vaccines due to their more conserved sequences compared with the genetic variation of the virus.", "In this paper, the role of PRRSV receptors and the molecular mechanism of the interaction between the virus and the receptors are reviewed."], "structured": false}
{"doc_id": 8006440, "title": "Kinetic Analysis Reveals the Fate of a MicroRNA following Target Regulation in Mammalian Cells", "abstract": ["Considerable details about microRNA (miRNA) biogenesis and regulation have been uncovered, but little is known about the fate of the miRNA subsequent to target regulation.", "To gain insight into this process, we carried out kinetic analysis of a miRNA's turnover following termination of its biogenesis and during regulation of a target that is not subject to Ago2-mediated catalytic cleavage.", "By quantitating the number of molecules of the miRNA and its target in steady state and in the course of its decay, we found that each miRNA molecule was able to regulate at least two target transcripts, providing in vivo evidence that the miRNA is not irreversibly sequestered with its target and that the nonslicing pathway of miRNA regulation is multiple-turnover.", "Using deep sequencing, we further show that miRNA recycling is limited by target regulation, which promotes posttranscriptional modifications to the 3' end of the miRNA and accelerates the miRNA's rate of decay.", "These studies provide new insight into the efficiency of miRNA regulation that help to explain how a miRNA can regulate a vast number of transcripts and that identify one of the mechanisms that impart specificity to miRNA decay in mammalian cells."], "structured": false}
{"doc_id": 8025177, "title": "Estimation of nuclear DNA content in plants using flow cytometry", "abstract": ["Flow cytometry (FCM) using DNA-selective fluorochromes is now the prevailing method for the measurement of nuclear DNA content in plants.", "Ease of sample preparation and high sample throughput make it generally better suited than other methods such as Feulgen densitometry to estimate genome size, level of generative polyploidy, nuclear replication state and endopolyploidy (polysomaty).", "Here we present four protocols for sample preparation (suspensions of intact cell nuclei) and describe the analysis of nuclear DNA amounts using FCM.", "We consider the chemicals and equipment necessary, the measurement process, data analysis, and describe the most frequent problems encountered with plant material such as the interference of secondary metabolites.", "The purpose and requirement of internal and external standardization are discussed.", "The importance of using a correct terminology for DNA amounts and genome size is underlined, and its basic principles are explained."], "structured": false}
{"doc_id": 8037453, "title": "Predictive value of bone resorption and formation markers in cancer patients with bone metastases receiving the bisphosphonate zoledronic acid.", "abstract": ["PURPOSE Three large, randomized trials of patients with bone metastases recently demonstrated that zoledronic acid reduces the risk of skeletal-related events.", "These trials provide an opportunity for investigating the correlation between bone metabolism and clinical outcome during bisphosphonate therapy.   \n", "PATIENTS AND METHODS Urinary measurements of N-telopeptide (Ntx) and serum bone alkaline phosphatase (BAP) were obtained in 1,824 bisphosphonate-treated patients-1,462 with zoledronic acid (breast, 490; prostate, 411; myeloma, 210; non-small-cell lung, 183; other, 168) and 362 with pamidronate (breast, 254; myeloma, 108).", "This exploratory cohort analysis grouped patients by baseline and most recent levels of Ntx as low (< 50 nmol/mmol creatinine), moderate (50 to 99 nmol/mmol creatinine), or high (> or = 100 nmol/mmol creatinine), and BAP as low (< 146 U/L) or high (> or = 146 U/L).", "The relative risks for negative clinical outcomes were estimated for each group using multiple-event and Cox regression models with time-varying covariates.   \n", "RESULTS Patients with high and moderate Ntx levels had 2-fold increases in their risk of skeletal complications and disease progression compared with patients with low Ntx levels (P < .001 for all).", "High Ntx levels in each solid tumor category were associated with a 4- to 6-fold increased risk of death on study, and moderate Ntx levels a 2- to 4-fold increased risk compared with low Ntx levels (P < .001 for all).", "Bone alkaline phosphatase also showed some correlation with risk of negative clinical outcomes.   \n", "CONCLUSION The bone resorption marker Ntx provides valuable prognostic information in patients with bone metastases receiving bisphosphonates."], "structured": true}
{"doc_id": 8038329, "title": "Role of CD28-B7 interactions in generation and maintenance of CD8 T cell memory.", "abstract": ["Although the role of CD28-B7 interaction in the activation of naive T cells is well established, its importance in the generation and maintenance of T cell memory is not well understood.", "In this study, we examined the requirement for CD28-B7 interactions in primary T cell activation and immune memory.", "Ag-specific CD8 T cell responses were compared between wild-type (+/+) and CD28-deficient (CD28(-/-)) mice following an acute infection with lymphocytic choriomeningitis virus (LCMV).", "During the primary response, there was a substantial activation and expansion of LCMV-specific CD8 T cells in both +/+ and CD28(-/-) mice.", "However, the magnitude of the primary CD8 T cell response to both dominant and subdominant LCMV CTL epitopes was approximately 2- to 3-fold lower in CD28(-/-) mice compared with +/+ mice; the lack of CD28-mediated costimulation did not lead to preferential suppression of CD8 T cell responses to the weaker subdominant epitopes.", "As seen in CD28(-/-) mice, blockade of B7-mediated costimulation by CTLA4-Ig treatment of +/+ mice also resulted in a 2-fold reduction in the anti-LCMV CD8 T cell responses.", "Loss of CD28/B7 interactions did not significantly affect the generation and maintenance of CD8 T cell memory; the magnitude of CD8 T cell memory was approximately 2-fold lower in CD28(-/-) mice as compared with +/+ mice.", "Further, in CD28(-/-) mice, LCMV-specific memory CD8 T cells showed normal homeostatic proliferation in vivo and also conferred protective immunity.", "Therefore, CD28 signaling is not necessary for the proliferative renewal and maintenance of memory CD8 T cells."], "structured": false}
{"doc_id": 8042158, "title": "Systematic reviews from astronomy to zoology: myths and misconceptions.", "abstract": ["Systematic literature reviews are widely used as an aid to evidence based decision making.", "For example, reviews of randomised controlled trials are regularly used to answer questions about the effectiveness of healthcare interventions.", "The high profile of systematic reviews as a cornerstone of evidence based medicine, however, has led to several misconceptions about their purpose and methods.", "Among these is the belief that systematic reviews are applicable only to randomised controlled trials and that they are incapable of dealing with other forms of evidence, such as from non-randomised studies or qualitative research.  ", "The systematic literature review is a method of locating, appraising, and synthesising evidence.", "The value of regularly updated systematic reviews in the assessment of effectiveness of healthcare interventions was dramatically illustrated by Antman and colleagues, who showed that review articles failed to mention advances in treatment identified by an updated systematic review.1  It is nearly a quarter of a century since Gene Glass coined the term \u201cmeta-analysis\u201d to refer to the quantitative synthesis of the results of primary studies.2 The importance of making explicit efforts to limit bias in the review of literature, however, has been emphasised by social scientists at least since the 1960s.3 In recent years systematic reviews have found an important role in health services research, and the growing interest in evidence based approaches to decision making makes it likely that their use will increase.", "Not everybody accepts that systematic reviews are necessary or desirable, and as one moves further away from the clinical applications of systematic reviews cynicism about their utility grows.", "Several arguments are commonly used to reject a wider role for systematic reviews, and these arguments are often based on major misconceptions about the history, purpose, methods, and uses of systematic reviews.", "I have examined eight common myths about \u2026"], "structured": false}
{"doc_id": 8063697, "title": "Acellular pertussis vaccines protect against disease but fail to prevent infection and transmission in a nonhuman primate model.", "abstract": ["Pertussis is a highly contagious respiratory illness caused by the bacterial pathogen Bordetella pertussis.", "Pertussis rates in the United States have been rising and reached a 50-y high of 42,000 cases in 2012.", "Although pertussis resurgence is not completely understood, we hypothesize that current acellular pertussis (aP) vaccines fail to prevent colonization and transmission.", "To test our hypothesis, infant baboons were vaccinated at 2, 4, and 6 mo of age with aP or whole-cell pertussis (wP) vaccines and challenged with B. pertussis at 7 mo.", "Infection was followed by quantifying colonization in nasopharyngeal washes and monitoring leukocytosis and symptoms.", "Baboons vaccinated with aP were protected from severe pertussis-associated symptoms but not from colonization, did not clear the infection faster than na\u00efve animals, and readily transmitted B. pertussis to unvaccinated contacts.", "Vaccination with wP induced a more rapid clearance compared with na\u00efve and aP-vaccinated animals.", "By comparison, previously infected animals were not colonized upon secondary infection.", "Although all vaccinated and previously infected animals had robust serum antibody responses, we found key differences in T-cell immunity.", "Previously infected animals and wP-vaccinated animals possess strong B. pertussis-specific T helper 17 (Th17) memory and Th1 memory, whereas aP vaccination induced a Th1/Th2 response instead.", "The observation that aP, which induces an immune response mismatched to that induced by natural infection, fails to prevent colonization or transmission provides a plausible explanation for the resurgence of pertussis and suggests that optimal control of pertussis will require the development of improved vaccines."], "structured": false}
{"doc_id": 8065561, "title": "Specific and cooperative binding of E. coli single-stranded DNA binding protein to mRNA.", "abstract": ["Fluorometric titration of E. coli single-stranded DNA binding protein with various RNAs showed that the protein specifically and cooperatively binds to its own mRNA.", "The binding inhibited in vitro expression of ssb and bla but not nusA. This inhibition takes place at a physiological concentration of SSB.", "The function of the protein in gene regulation is discussed."], "structured": false}
{"doc_id": 8069939, "title": "ACAM2000\u2122: The new smallpox vaccine for United States Strategic National Stockpile", "abstract": ["Smallpox was eradicated more than 30 years ago, but heightened concerns over bioterrorism have brought smallpox and smallpox vaccination back to the forefront.", "The previously licensed smallpox vaccine in the United States, Dryvax (Wyeth Laboratories, Inc.), was highly effective, but the supply was insufficient to vaccinate the entire current US population.", "Additionally, Dryvax had a questionable safety profile since it consisted of a pool of vaccinia virus strains with varying degrees of virulence, and was grown on the skin of calves, an outdated technique that poses an unnecessary risk of contamination.", "The US government has therefore recently supported development of an improved live vaccinia virus smallpox vaccine.", "This initiative has resulted in the development of ACAM2000 (Acambis, Inc.), a single plaque-purified vaccinia virus derivative of Dryvax, aseptically propagated in cell culture.", "Preclinical and clinical trials reported in 2008 demonstrated that ACAM2000 has comparable immunogenicity to that of Dryvax, and causes a similar frequency of adverse events.", "Furthermore, like Dryvax, ACAM2000 vaccination has been shown by careful cardiac screening to result in an unexpectedly high rate of myocarditis and pericarditis.", "ACAM2000 received US Food and Drug Administration (FDA) approval in August 2007, and replaced Dryvax for all smallpox vaccinations in February 2008.", "Currently, over 200 million doses of ACAM2000 have been produced for the US Strategic National Stockpile.", "This review of ACAM2000 addresses the production, characterization, clinical trials, and adverse events associated with this new smallpox vaccine."], "structured": false}
{"doc_id": 8082528, "title": "Risk of malignant neoplasms in patients with pulmonary sarcoidosis.", "abstract": ["BACKGROUND For over 20 years the association between sarcoidosis and malignancy, particularly lymphoma and lung cancer, has been disputed with misclassification being the major concern.", "The aim of the present study was to analyse the incidence of malignancies in a cohort of patients with sarcoidosis by linkage to a nationwide population based cancer register.   \n", "METHODS The cohort comprised 254 patients followed for a median of 25 years until death, emigration, or 31 December 1992, whichever came first.", "The expected number of cancer cases was calculated using the annual age and sex specific cancer rates from the Danish Cancer Registry.   \n", "RESULTS Thirty six cancers were registered, three of which were misclassified as sarcoidosis, leaving 33 cancers compared with 23 expected (standardised incidence ratio (SIR) = 1.4; 95% CI 0.99 to 2.0).", "Five lung cancers were observed compared with 2.5 expected, yielding an SIR of 2.0 (95% CI 0.7 to 4.7).", "There was no incidence of lymphoma and only one case of leukaemia.", "There was a significant excess number of pharyngeal cancers based on two cases (SIR = 15.4; 95% CI 1.7 to 56).   \n", "CONCLUSIONS This study does not support the theory of an association between sarcoidosis and malignancy, and the main reason other studies have shown such an association is most likely to have been due to selection bias and misclassification."], "structured": true}
{"doc_id": 8083310, "title": "Rps14 haploinsufficiency causes a block in erythroid differentiation mediated by S100A8 and S100A9", "abstract": ["Impaired erythropoiesis in the deletion 5q (del(5q)) subtype of myelodysplastic syndrome (MDS) has been linked to heterozygous deletion of RPS14, which encodes the ribosomal protein small subunit 14.", "We generated mice with conditional inactivation of Rps14 and demonstrated an erythroid differentiation defect that is dependent on the tumor suppressor protein p53 (encoded by Trp53 in mice) and is characterized by apoptosis at the transition from polychromatic to orthochromatic erythroblasts.", "This defect resulted in age-dependent progressive anemia, megakaryocyte dysplasia and loss of hematopoietic stem cell (HSC) quiescence.", "As assessed by quantitative proteomics, mutant erythroblasts expressed higher levels of proteins involved in innate immune signaling, notably the heterodimeric S100 calcium-binding proteins S100a8 and S100a9.", "S100a8\u2014whose expression was increased in mutant erythroblasts, monocytes and macrophages\u2014is functionally involved in the erythroid defect caused by the Rps14 deletion, as addition of recombinant S100a8 was sufficient to induce a differentiation defect in wild-type erythroid cells, and genetic inactivation of S100a8 expression rescued the erythroid differentiation defect of Rps14-haploinsufficient HSCs.", "Our data link Rps14 haploinsufficiency in del(5q) MDS to activation of the innate immune system and induction of S100A8-S100A9 expression, leading to a p53-dependent erythroid differentiation defect."], "structured": false}
{"doc_id": 8087082, "title": "A Microtubule Interactome: Complexes with Roles in Cell Cycle and Mitosis", "abstract": ["The microtubule (MT) cytoskeleton is required for many aspects of cell function, including the transport of intracellular materials, the maintenance of cell polarity, and the regulation of mitosis.", "These functions are coordinated by MT-associated proteins (MAPs), which work in concert with each other, binding MTs and altering their properties.", "We have used a MT cosedimentation assay, combined with 1D and 2D PAGE and mass spectrometry, to identify over 250 MAPs from early Drosophila embryos.", "We have taken two complementary approaches to analyse the cellular function of novel MAPs isolated using this approach.", "First, we have carried out an RNA interference (RNAi) screen, identifying 21 previously uncharacterised genes involved in MT organisation.", "Second, we have undertaken a bioinformatics analysis based on binary protein interaction data to produce putative interaction networks of MAPs.", "By combining both approaches, we have identified and validated MAP complexes with potentially important roles in cell cycle regulation and mitosis.", "This study therefore demonstrates that biologically relevant data can be harvested using such a multidisciplinary approach, and identifies new MAPs, many of which appear to be important in cell division."], "structured": false}
{"doc_id": 8093935, "title": "Structure of the Guanine Nucleotide Exchange Factor Sec7 Domain of Human Arno and Analysis of the Interaction with ARF GTPase", "abstract": ["Sec7-related guanine nucleotide exchange factors (GEFs) initiate vesicle budding from the Golgi membrane surface by converting the GTPase ARF to a GTP-bound, membrane-associated form.", "Here we report the crystal structure of the catalytic Sec7 homology domain of Arno, a human GEF for ARF1, determined at 2.2 angstroms resolution.", "The Sec7 domain is an elongated, all-helical protein with a distinctive hydrophobic groove that is phylogenetically conserved.", "Structure-based mutagenesis identifies the groove and an adjacent conserved loop as the ARF-interacting surface.", "The sites of Sec7 domain interaction on ARF1 have subsequently been mapped, by protein footprinting experiments, to the switch 1 and switch 2 GTPase regions, leading to a model for the interaction between ARF GTPases and Sec7 domain exchange factors."], "structured": false}
{"doc_id": 8122346, "title": "Brief Communication Repeated Cocaine Administration Increases Voltage-Sensitive Calcium Currents in Response to Membrane Depolarization in Medial Prefrontal Cortex Pyramidal Neurons", "abstract": ["The medial prefrontal cortex (mPFC) plays a critical role in cocaine addiction.", "However, evidence to elucidate how the mPFC is functionally involved in cocaine addiction remains incomplete.", "Recent studies have revealed that repeated cocaine administration induces various neuroadaptations in pyramidal mPFC neurons, including a reduction in voltage-gated K+ currents (VGKCs) and a possible increase in voltage-sensitive Ca2+ currents (I(Ca)).", "Here, we performed both current-clamp recordings in brain slices and voltage-clamp recordings in freshly dissociated cells to determine whether I(Ca) is altered in mPFC pyramidal neurons after chronic cocaine treatment with a short-term or long-term withdrawal.", "In addition, a critical role of VGKCs in regulating the generation of Ca2+ plateau potential was also studied in mPFC neurons.", "Repeated cocaine administration significantly prolonged the duration of evoked Ca2+ plateau potentials and increased the whole-cell I(Ca) in mPFC neurons after a 3 d withdrawal.", "Selective blockade of L-type Ca2+ channels by nifedipine not only significantly increased the threshold but also reduced the duration and amplitude of Ca2+ plateau potentials in both saline- and cocaine-withdrawn mPFC neurons.", "However, there was no significant difference in the increased threshold, reduced duration, and decreased amplitude of Ca2+ potentials between saline- and cocaine-withdrawn neurons after blockade of L-type Ca2+ channels.", "Moreover, an increase in amplitude was also observed, whereas the prolonged duration persisted, in Ca2+ potentials after 2-3 weeks of withdrawal.", "These findings indicate that chronic exposure to cocaine facilitates the responsiveness of I(Ca), particularly via the activated L-type Ca2+ channels, to excitatory stimuli in rat mPFC pyramidal neurons."], "structured": false}
{"doc_id": 8126244, "title": "Rational Extension of the Ribosome Biogenesis Pathway Using Network-Guided Genetics", "abstract": ["Biogenesis of ribosomes is an essential cellular process conserved across all eukaryotes and is known to require >170 genes for the assembly, modification, and trafficking of ribosome components through multiple cellular compartments.", "Despite intensive study, this pathway likely involves many additional genes.", "Here, we employ network-guided genetics-an approach for associating candidate genes with biological processes that capitalizes on recent advances in functional genomic and proteomic studies-to computationally identify additional ribosomal biogenesis genes.", "We experimentally evaluated >100 candidate yeast genes in a battery of assays, confirming involvement of at least 15 new genes, including previously uncharacterized genes (YDL063C, YIL091C, YOR287C, YOR006C/TSR3, YOL022C/TSR4).", "We associate the new genes with specific aspects of ribosomal subunit maturation, ribosomal particle association, and ribosomal subunit nuclear export, and we identify genes specifically required for the processing of 5S, 7S, 20S, 27S, and 35S rRNAs.", "These results reveal new connections between ribosome biogenesis and mRNA splicing and add >10% new genes-most with human orthologs-to the biogenesis pathway, significantly extending our understanding of a universally conserved eukaryotic process."], "structured": false}
{"doc_id": 8133050, "title": "Quantifying Transmission Investment in Malaria Parasites", "abstract": ["Many microparasites infect new hosts with specialized life stages, requiring a subset of the parasite population to forgo proliferation and develop into transmission forms.", "Transmission stage production influences infectivity, host exploitation, and the impact of medical interventions like drug treatment.", "Predicting how parasites will respond to public health efforts on both epidemiological and evolutionary timescales requires understanding transmission strategies.", "These strategies can rarely be observed directly and must typically be inferred from infection dynamics.", "Using malaria as a case study, we test previously described methods for inferring transmission stage investment against simulated data generated with a model of within-host infection dynamics, where the true transmission investment is known.", "We show that existing methods are inadequate and potentially very misleading.", "The key difficulty lies in separating transmission stages produced by different generations of parasites.", "We develop a new approach that performs much better on simulated data.", "Applying this approach to real data from mice infected with a single Plasmodium chabaudi strain, we estimate that transmission investment varies from zero to 20%, with evidence for variable investment over time in some hosts, but not others.", "These patterns suggest that, even in experimental infections where host genetics and other environmental factors are controlled, parasites may exhibit remarkably different patterns of transmission investment."], "structured": false}
{"doc_id": 8133180, "title": "Roles of induced expression of MAPK phosphatase-2 in tumor development in RET-MEN2A transgenic mice", "abstract": ["Germline mutations in the RET tyrosine kinase gene are responsible for the development of multiple endocrine neoplasia 2A and 2B (MEN2A and MEN2B).", "However, knowledge of the fundamental principles that determine the mutant RET-mediated signaling remains elusive.", "Here, we report increased expression of mitogen-activated protein kinase phosphatase-2 (MKP-2) in carcinomas developed in transgenic mice carrying RET with the MEN2A mutation (RET-MEN2A).", "The expression of MKP-2 was not only induced by RET-MEN2A or RET-MEN2B mutant proteins but also by the activation of endogenous RET by its ligand, glial cell line-derived neurotrophic factor (GDNF).", "MKP-2 expression was also evident in the MKK-f cell line, which was established from a mammary tumor developed in a RET-MEN2A transgenic mouse.", "Inhibition of MKP-2 attenuated the in vitro and in vivo proliferation of MKK-f cells, which was mediated by the suppression of cyclin B1 expression.", "Furthermore, we found that MKP-2 is highly expressed in medullary thyroid carcinomas derived from MEN2A patients.", "These findings suggest that the increased expression of MKP-2 may play a crucial role in oncogenic signaling downstream of mutant RET, leading to deregulation of cell cycle."], "structured": false}
{"doc_id": 8137081, "title": "Effects of repeated social stress on leukocyte distribution in bone marrow, peripheral blood and spleen", "abstract": ["Leukocyte trafficking between the various body compartments has an important surveillance function that ensures the detection of antigen and enables the immune system to initiate a rapid and effective response.", "Repeated social defeat of group-housed male mice induced by daily, acute encounters with an aggressive conspecific substantially altered leukocyte trafficking and led to a gradual redistribution of immune cells in bone marrow, peripheral blood and spleen.", "Recurrent exposure to the stressor over a period of 2, 4 or 6 consecutive days was associated with cell mobilization and increased myelopoiesis in the bone marrow that was paralleled by an accumulation of neutrophils and monocytes in circulation and spleen.", "Substantial depletion of B cells in bone marrow and blood was associated with an increase in splenic B cells indicating a redirection of this cell type to the spleen.", "In contrast, T cells were markedly reduced in these immune compartments.", "The recruitment of CD11b+ leukocytes (i.e., monocytes/macrophages and neutrophils) from the bone marrow to the spleen might play a critical role in the development of functional glucocorticoid resistance in the murine spleen that was reported in context with repeated social defeat."], "structured": false}
{"doc_id": 8144920, "title": "Lentivirally transduced dendritic cells as a tool for cancer immunotherapy.", "abstract": ["BACKGROUND Dendritic cells (DC) are the professional antigen-presenting cells of the immune system, fully equipped to prime naive T cells and thus essential components for cancer immunotherapy.   \n", "METHODS We tested the influence of several elements (cPPT, trip, WPRE, SIN) on the transduction efficiency of human DC.", "Human and murine DC were transduced with tNGFR-encoding lentiviruses to assess the effect of transduction on phenotype and function.", "Human DC were transduced with lentiviruses encoding huIi80MAGE-A3 and murine DC with huIi80tOVA to test antigen presentation.   \n", "RESULTS A self-inactivating (SIN) lentiviral vector containing the trip element was most efficient in transducing human DC.", "The transduction of DC with trip/SIN tNGFR encoding lentiviral vectors at MOI 15 resulted in stable gene expression in up to 94.6% (murine) and 88.2% (human) of the mature DC, without perturbing viability, phenotype and function.", "Human huIi80MAGE-A3-transduced DC were able to stimulate MAGE-A3-specific CD4(+) and CD8(+) T cell clones and could prime both MAGE-A3-specific CD4(+) and CD8(+) T cells in vitro.", "Murine huIi80tOVA-transduced DC were able to present OVA peptides in the context of MHC class I and class II in vitro and induced a strong OVA-specific cytotoxic T lymphocyte response in vivo, that was protective against subsequent challenge with OVA-expressing tumor cells.   \n", "CONCLUSIONS We show that, using lentiviral vectors, efficient gene transfer in human and murine DC can be obtained and that these DC can elicit antigen-specific immune responses in vitro and in vivo.", "The composition of the transfer vector has a major impact on the transduction efficiency."], "structured": true}
{"doc_id": 8148122, "title": "Global Reorganization of Replication Domains During Embryonic Stem Cell Differentiation", "abstract": ["DNA replication in mammals is regulated via the coordinate firing of clusters of replicons that duplicate megabase-sized chromosome segments at specific times during S-phase.", "Cytogenetic studies show that these \"replicon clusters\" coalesce as subchromosomal units that persist through multiple cell generations, but the molecular boundaries of such units have remained elusive.", "Moreover, the extent to which changes in replication timing occur during differentiation and their relationship to transcription changes has not been rigorously investigated.", "We have constructed high-resolution replication-timing profiles in mouse embryonic stem cells (mESCs) before and after differentiation to neural precursor cells.", "We demonstrate that chromosomes can be segmented into multimegabase domains of coordinate replication, which we call \"replication domains,\" separated by transition regions whose replication kinetics are consistent with large originless segments.", "The molecular boundaries of replication domains are remarkably well conserved between distantly related ESC lines and induced pluripotent stem cells.", "Unexpectedly, ESC differentiation was accompanied by the consolidation of smaller differentially replicating domains into larger coordinately replicated units whose replication time was more aligned to isochore GC content and the density of LINE-1 transposable elements, but not gene density.", "Replication-timing changes were coordinated with transcription changes for weak promoters more than strong promoters, and were accompanied by rearrangements in subnuclear position.", "We conclude that replication profiles are cell-type specific, and changes in these profiles reveal chromosome segments that undergo large changes in organization during differentiation.", "Moreover, smaller replication domains and a higher density of timing transition regions that interrupt isochore replication timing define a novel characteristic of the pluripotent state."], "structured": false}
{"doc_id": 8148304, "title": "Molecular characterization of the yeast meiotic regulatory gene RIM1.", "abstract": ["In the yeast Saccharomyces cerevisiae, genetic studies suggest that the RIM1 gene encodes a positive regulator of meiosis.", "rim1 mutations cause reduced expression of IME1, which is required for expression of many meiotic genes, and thus lead to a partial defect in meiosis and spore formation.", "We report the sequence of RIM1 and functional analysis of its coding region.", "The RIM1 gene product (RIM1) contains three regions similar to C2H2 zinc fingers.", "Serine substitutions for cysteine in each of the putative zinc fingers abolish RIM1 function.", "The carboxyl-terminus of RIM1 is enriched in acidic amino acids and is required for full RIM1 activity.", "RIM1 also contains two putative cAMP-dependent protein kinase (cAPK) phosphorylation sites.", "At one site, substitution of alanine for serine does not affect RIM1 activity; at the other site, this substitution impairs activity.", "This analysis of RIM1 suggests that the protein may function as a transcriptional activator.", "We have used the cloned RIM1 gene to create a complete rim1 deletion.", "This null allele, like previously isolated rim1 mutations, causes a partial meiotic defect.", "In addition to RIM1, maximum IME1 expression requires the MCK1 and IME4 gene products.", "Defects associated with rim1, mck1, and ime4 mutations in expression of a meiotic reporter gene (ime2-lacZ) and in sporulation are additive.", "These findings suggest that RIM1 acts independently of MCK1 and IME4 to stimulate IME1 expression."], "structured": false}
{"doc_id": 8150638, "title": "Butyrate greatly enhances derivation of human induced pluripotent stem cells by promoting epigenetic remodeling and the expression of pluripotency-associated genes.", "abstract": ["We report here that butyrate, a naturally occurring fatty acid commonly used as a nutritional supplement and differentiation agent, greatly enhances the efficiency of induced pluripotent stem (iPS) cell derivation from human adult or fetal fibroblasts.", "After transient butyrate treatment, the iPS cell derivation efficiency is enhanced by 15- to 51-fold using either retroviral or piggyBac transposon vectors expressing 4 to 5 reprogramming genes.", "Butyrate stimulation is more remarkable (>100- to 200-fold) on reprogramming in the absence of either KLF4 or MYC transgene.", "Butyrate treatment did not negatively affect properties of iPS cell lines established by either 3 or 4 retroviral vectors or a single piggyBac DNA transposon vector.", "These characterized iPS cell lines, including those derived from an adult patient with sickle cell disease by either the piggyBac or retroviral vectors, show normal karyotypes and pluripotency.", "To gain insights into the underlying mechanisms of butyrate stimulation, we conducted genome-wide gene expression and promoter DNA methylation microarrays and other epigenetic analyses on established iPS cells and cells from intermediate stages of the reprogramming process.", "By days 6 to 12 during reprogramming, butyrate treatment enhanced histone H3 acetylation, promoter DNA demethylation, and the expression of endogenous pluripotency-associated genes, including DPPA2, whose overexpression partially substitutes for butyrate stimulation.", "Thus, butyrate as a cell permeable small molecule provides a simple tool to further investigate molecular mechanisms of cellular reprogramming.", "Moreover, butyrate stimulation provides an efficient method for reprogramming various human adult somatic cells, including cells from patients that are more refractory to reprogramming."], "structured": false}
{"doc_id": 8182950, "title": "Nanoparticle conjugation of CpG enhances adjuvancy for cellular immunity and memory recall at low dose.", "abstract": ["In subunit vaccines, strong CD8(+) T-cell responses are desired, yet they are elusive at reasonable adjuvant doses.", "We show that targeting adjuvant to the lymph node (LN) via ultrasmall polymeric nanoparticles (NPs), which rapidly drain to the LN after intradermal injection, greatly enhances adjuvant efficacy at low doses.", "Coupling CpG-B or CpG-C oligonucleotides to NPs led to better dual-targeting of adjuvant and antigen (codelivered on separate NPs) in cross-presenting dendritic cells compared with free adjuvant.", "This led to enhanced dendritic cell maturation and T helper 1 (Th1)-cytokine secretion, in turn driving stronger effector CD8(+) T-cell activation with enhanced cytolytic profiles and, importantly, more powerful memory recall.", "With only 4 \u03bcg CpG, NP-CpG-B could substantially protect mice from syngeneic tumor challenge, even after 4 mo of vaccination, compared with free CpG-B. Together, these results show that nanocarriers can enhance vaccine efficacy at a low adjuvant dose for inducing potent and long-lived cellular immunity."], "structured": false}
{"doc_id": 8185080, "title": "Induction of pluripotent stem cells by defined factors is greatly improved by small-molecule compounds", "abstract": ["Reprogramming of mouse and human somatic cells can be achieved by ectopic expression of transcription factors, but with low efficiencies.", "We report that DNA methyltransferase and histone deacetylase (HDAC) inhibitors improve reprogramming efficiency.", "In particular, valproic acid (VPA), an HDAC inhibitor, improves reprogramming efficiency by more than 100-fold, using Oct4-GFP as a reporter.", "VPA also enables efficient induction of pluripotent stem cells without introduction of the oncogene c-Myc."], "structured": false}
{"doc_id": 8190282, "title": "Noninvasive ventilation for treatment of acute respiratory failure in patients undergoing solid organ transplantation: a randomized trial.", "abstract": ["CONTEXT Noninvasive ventilation (NIV) has been associated with lower rates of endotracheal intubation in populations of patients with acute respiratory failure.   \n", "OBJECTIVE To compare NIV with standard treatment using supplemental oxygen administration to avoid endotracheal intubation in recipients of solid organ transplantation with acute hypoxemic respiratory failure.   \n", "DESIGN AND SETTING Prospective randomized study conducted at a 14-bed, general intensive care unit of a university hospital.   \n", "PATIENTS Of 238 patients who underwent solid organ transplantation from December 1995 to October 1997, 51 were treated for acute respiratory failure.", "Of these, 40 were eligible and 20 were randomized to each group.   \n", "INTERVENTION Noninvasive ventilation vs standard treatment with supplemental oxygen administration.   \n", "MAIN OUTCOME MEASURES The need for endotracheal intubation and mechanical ventilation at any time during the study, complications not present on admission, duration of ventilatory assistance, length of hospital stay, and intensive care unit mortality.   \n", "RESULTS The 2 groups were similar at study entry.", "Within the first hour of treatment, 14 patients (70%) in the NIV group, and 5 patients (25%) in the standard treatment group improved their ratio of the PaO2 to the fraction of inspired oxygen (FIO2).", "Over time, a sustained improvement in PaO2 to FIO2 was noted in 12 patients (60%) in the NIV group, and in 5 patients (25%) randomized to standard treatment (P = .03).", "The use of NIV was associated with a significant reduction in the rate of endotracheal intubation (20% vs 70%; P = .002), rate of fatal complications (20% vs 50%; P = .05), length of stay in the intensive care unit by survivors (mean [SD] days, 5.5 [3] vs 9 [4]; P = .03), and intensive care unit mortality (20% vs 50%; P = .05).", "Hospital mortality did not differ.   \n", "CONCLUSIONS These results indicate that transplantation programs should consider NIV in the treatment of selected recipients of transplantation with acute respiratory failure."], "structured": true}
{"doc_id": 8202880, "title": "BIOINFORMATICS APPLICATIONS NOTE", "abstract": ["SUMMARY MADE4, microarray ade4, is a software package that facilitates multivariate analysis of microarray gene-expression data.", "MADE4 accepts a wide variety of gene-expression data formats.", "MADE4 takes advantage of the extensive multivariate statistical and graphical functions in the R package ade4, extending these for application to microarray data.", "In addition, MADE4 provides new graphical and visualization tools that aid in interpretation of multivariate analysis of microarray data."], "structured": false}
{"doc_id": 8208212, "title": "Dual and opposing roles of primary cilia in medulloblastoma development", "abstract": ["Recent work has shown that primary cilia are essential for Hedgehog (Hh) signaling during mammalian development.", "It is also known that aberrant Hh signaling can lead to cancer, but the role of primary cilia in oncogenesis is not known.", "Cerebellar granule neuron precursors (GNPs) can give rise to medulloblastomas, the most common malignant brain tumor in children.", "The primary cilium and Hh signaling are required for GNP proliferation.", "We asked whether primary cilia in GNPs have a role in medulloblastoma growth in mice.", "Genetic ablation of primary cilia blocked medulloblastoma formation when this tumor was driven by a constitutively active Smoothened protein (Smo), an upstream activator of Hh signaling.", "In contrast, removal of cilia was required for medulloblastoma growth by a constitutively active glioma-associated oncogene family zinc finger-2 (GLI2), a downstream transcription factor.", "Thus, primary cilia are either required for or inhibit medulloblastoma formation, depending on the initiating oncogenic event.", "Remarkably, the presence or absence of cilia was associated with specific variants of human medulloblastomas; primary cilia were found in medulloblastomas with activation in HH or WNT signaling but not in most medulloblastomas in other distinct molecular subgroups.", "Primary cilia could serve as a diagnostic tool and provide new insights into the mechanism of tumorigenesis."], "structured": false}
{"doc_id": 8210189, "title": "RAS genes in Saccharomyces cerevisiae: signal transduction in search of a pathway.", "abstract": ["Ras proteins in budding yeasts initially appeared to regulate initiation of the cell cycle in response to nutrient availability.", "More recent work, while clarifying the mechanism of Ras-mediated signal transduction, has undermined our notion of the signal Ras transmits.", "We now suspect that Ras helps to coordinate cellular metabolism and mass accumulation, but what Ras responds to is not clear."], "structured": false}
{"doc_id": 8219248, "title": "Use of synthetic peptides to locate novel integrin alpha2beta1-binding motifs in human collagen III.", "abstract": ["A set of 57 synthetic peptides encompassing the entire triplehelical domain of human collagen III was used to locate binding sites for the collagen-binding integrin alpha(2)beta(1).", "The capacity of the peptides to support Mg(2+)-dependent binding of several integrin preparations was examined.", "Wild-type integrins (recombinant alpha(2) I-domain, alpha(2)beta(1) purified from platelet membranes, and recombinant soluble alpha(2)beta(1) expressed as an alpha(2)-Fos/beta(1)-Jun heterodimer) bound well to only three peptides, two containing GXX'GER motifs (GROGER and GMOGER, where O is hydroxyproline) and one containing two adjacent GXX'GEN motifs (GLKGEN and GLOGEN).", "Two mutant alpha(2) I-domains were tested: the inactive T221A mutant, which recognized no peptides, and the constitutively active E318W mutant, which bound a larger subset of peptides.", "Adhesion of activated human platelets to GER-containing peptides was greater than that of resting platelets, and HT1080 cells bound well to more of the peptides compared with platelets.", "Binding of cells and recombinant proteins was abolished by anti-alpha(2) monoclonal antibody 6F1 and by chelation of Mg(2+).", "We describe two novel high affinity integrin-binding motifs in human collagen III (GROGER and GLOGEN) and a third motif (GLKGEN) that displays intermediate activity.", "Each motif was verified using shorter synthetic peptides."], "structured": false}
{"doc_id": 8227227, "title": "Locations of cerebral infarctions in tuberculous meningitis", "abstract": ["The locations of cerebral infarctions were studied in 14 patients with tuberculous meningitis (TBM) and 173 patients with noninflammatory ischemic stroke (IS).", "In patients with TBM, 75% of infarctions occurred in the \u201cTB zone\u201d supplied by medial striate and thalamoperforating arteries; only 11% occurred in the \u201cIS zone\u201d supplied by lateral striate, anterior choroidal and thalamogeniculate arteries.", "In patients with IS 29% of infarctions occurred in the IS zone, 29% in the subcortical white matter, and 24% in (or involving) the cerebral cortex.", "Only 11% occurred in the TB zone.", "Bilaterally symmetrical infarctions of the TB zone were common with TMB (71%) but rare with IS (5%)."], "structured": false}
{"doc_id": 8246090, "title": "TRP channels of intracellular membranes.", "abstract": ["Ion channels are classically understood to regulate the flux of ions across the plasma membrane in response to a variety of environmental and intracellular cues.", "Ion channels serve a number of functions in intracellular membranes as well.", "These channels may be temporarily localized to intracellular membranes as a function of their biosynthetic or secretory pathways, i.e., en route to their destination location.", "Intracellular membrane ion channels may also be located in the endocytic pathways, either being recycled back to the plasma membrane or targeted to the lysosome for degradation.", "Several channels do participate in intracellular signal transduction; the most well known example is the inositol 1,4,5-trisphosphate receptor (IP(3)R) in the endoplasmic reticulum.", "Some organellar intracellular membrane channels are required for the ionic homeostasis of their residing organelles.", "Several newly-discovered intracellular membrane Ca(2+) channels actually play active roles in membrane trafficking.", "Transient receptor potential (TRP) proteins are a superfamily (28 members in mammal) of Ca(2+)-permeable channels with diverse tissue distribution, subcellular localization, and physiological functions.", "Almost all mammalian TRP channels studied thus far, like their ancestor yeast TRP channel (TRPY1) that localizes to the vacuole compartment, are also (in addition to their plasma membrane localization) found to be localized to intracellular membranes.", "Accumulated evidence suggests that intracellularly-localized TRP channels actively participate in regulating membrane traffic, signal transduction, and vesicular ion homeostasis.", "This review aims to provide a summary of these recent works.", "The discussion will also be extended to the basic membrane and electrical properties of the TRP-residing compartments."], "structured": false}
{"doc_id": 8246922, "title": "the Development of Autoimmune Myocarditis in Mice by an", "abstract": ["BACKGROUND Interleukin (IL)-12 exerts a potent proinflammatory effect by stimulating T-helper (Th) 1 responses.", "This effect is believed to be mediated primarily through the activation of STAT4 and subsequent production of interferon (IFN)-gamma.", "Methods and Results- We examined the role of IL-12 receptor (IL-12R) signaling in the development of murine experimental autoimmune myocarditis (EAM) induced by cardiac myosin immunization.", "Both IL-12Rbeta1-deficient mice and STAT4-deficient mice were resistant to the induction of myocarditis.", "Treatment with exogenous IL-12 exacerbated disease.", "We questioned whether IFN-gamma is required for the disease-promoting activity of IL-12.", "On the contrary, we found that IFN-gamma suppresses EAM.", "Lack of IFN-gamma due to either depletion with an antibody or a genetic deficiency exacerbated myocarditis.", "Spleens from IFN-gamma-deficient mice immunized with cardiac myosin showed increased cellularity; greater numbers of CD3+, CD4+, CD8+, and IL-2-producing cells; and heightened ability to produce cytokines on stimulation in vitro.", "Treatment of mice with recombinant IFN-gamma suppressed the development of myocarditis.   \n", "CONCLUSIONS IL-12/IL-12R/STAT4 signaling promotes the development of EAM.", "In contrast, IFN-gamma plays a protective role.", "The disease-limiting effects of IFN-gamma might be explained by its ability to control the expansion of activated T lymphocytes."], "structured": true}
{"doc_id": 8247469, "title": "The Viral and Cellular MicroRNA Targetome in Lymphoblastoid Cell Lines", "abstract": ["Epstein-Barr virus (EBV) is a ubiquitous human herpesvirus linked to a number of B cell cancers and lymphoproliferative disorders.", "During latent infection, EBV expresses 25 viral pre-microRNAs (miRNAs) and induces the expression of specific host miRNAs, such as miR-155 and miR-21, which potentially play a role in viral oncogenesis.", "To date, only a limited number of EBV miRNA targets have been identified; thus, the role of EBV miRNAs in viral pathogenesis and/or lymphomagenesis is not well defined.", "Here, we used photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP) combined with deep sequencing and computational analysis to comprehensively examine the viral and cellular miRNA targetome in EBV strain B95-8-infected lymphoblastoid cell lines (LCLs).", "We identified 7,827 miRNA-interaction sites in 3,492 cellular 3'UTRs.", "531 of these sites contained seed matches to viral miRNAs.", "24 PAR-CLIP-identified miRNA:3'UTR interactions were confirmed by reporter assays.", "Our results reveal that EBV miRNAs predominantly target cellular transcripts during latent infection, thereby manipulating the host environment.", "Furthermore, targets of EBV miRNAs are involved in multiple cellular processes that are directly relevant to viral infection, including innate immunity, cell survival, and cell proliferation.", "Finally, we present evidence that myc-regulated host miRNAs from the miR-17/92 cluster can regulate latent viral gene expression.", "This comprehensive survey of the miRNA targetome in EBV-infected B cells represents a key step towards defining the functions of EBV-encoded miRNAs, and potentially, identifying novel therapeutic targets for EBV-associated malignancies."], "structured": false}
{"doc_id": 8247597, "title": "Mitochondrial Dysfunction Leads to Nuclear Genome Instability via an Iron-Sulfur Cluster Defect", "abstract": ["Mutations and deletions in the mitochondrial genome (mtDNA), as well as instability of the nuclear genome, are involved in multiple human diseases.", "Here, we report that in Saccharomyces cerevisiae, loss of mtDNA leads to nuclear genome instability, through a process of cell-cycle arrest and selection we define as a cellular crisis.", "This crisis is not mediated by the absence of respiration, but instead correlates with a reduction in the mitochondrial membrane potential.", "Analysis of cells undergoing this crisis identified a defect in iron-sulfur cluster (ISC) biogenesis, which requires normal mitochondrial function.", "We found that downregulation of nonmitochondrial ISC protein biogenesis was sufficient to cause increased genomic instability in cells with intact mitochondrial function.", "These results suggest mitochondrial dysfunction stimulates nuclear genome instability by inhibiting the production of ISC-containing protein(s), which are required for maintenance of nuclear genome integrity.", "For a video summary of this article, see the PaperFlick file available with the online Supplemental Data."], "structured": false}
{"doc_id": 8250852, "title": "Replisome stall events have shaped the distribution of replication origins in the genomes of yeasts", "abstract": ["During S phase, the entire genome must be precisely duplicated, with no sections of DNA left unreplicated.", "Here, we develop a simple mathematical model to describe the probability of replication failing due to the irreversible stalling of replication forks.", "We show that the probability of complete genome replication is maximized if replication origins are evenly spaced, the largest inter-origin distances are minimized, and the end-most origins are positioned close to chromosome ends.", "We show that origin positions in the yeast Saccharomyces cerevisiae genome conform to all three predictions thereby maximizing the probability of complete replication if replication forks stall.", "Origin positions in four other yeasts-Kluyveromyces lactis, Lachancea kluyveri, Lachancea waltii and Schizosaccharomyces pombe-also conform to these predictions.", "Equating failure rates at chromosome ends with those in chromosome interiors gives a mean per nucleotide fork stall rate of \u223c5 \u00d7 10(-8), which is consistent with experimental estimates.", "Using this value in our theoretical predictions gives replication failure rates that are consistent with data from replication origin knockout experiments.", "Our theory also predicts that significantly larger genomes, such as those of mammals, will experience a much greater probability of replication failure genome-wide, and therefore will likely require additional compensatory mechanisms."], "structured": false}
{"doc_id": 8267678, "title": "Regulation of chromatin by histone modifications", "abstract": ["Chromatin is not an inert structure, but rather an instructive DNA scaffold that can respond to external cues to regulate the many uses of DNA.", "A principle component of chromatin that plays a key role in this regulation is the modification of histones.", "There is an ever-growing list of these modifications and the complexity of their action is only just beginning to be understood.", "However, it is clear that histone modifications play fundamental roles in most biological processes that are involved in the manipulation and expression of DNA.", "Here, we describe the known histone modifications, define where they are found genomically and discuss some of their functional consequences, concentrating mostly on transcription where the majority of characterisation has taken place."], "structured": false}
{"doc_id": 8290760, "title": "Single-Cell Expression Analyses during Cellular Reprogramming Reveal an Early Stochastic and a Late Hierarchic Phase", "abstract": ["During cellular reprogramming, only a small fraction of cells become induced pluripotent stem cells (iPSCs).", "Previous analyses of gene expression during reprogramming were based on populations of cells, impeding single-cell level identification of reprogramming events.", "We utilized two gene expression technologies to profile 48 genes in single cells at various stages during the reprogramming process.", "Analysis of early stages revealed considerable variation in gene expression between cells in contrast to late stages.", "Expression of Esrrb, Utf1, Lin28, and Dppa2 is a better predictor for cells to progress into iPSCs than expression of the previously suggested reprogramming markers Fbxo15, Fgf4, and Oct4.", "Stochastic gene expression early in reprogramming is followed by a late hierarchical phase with Sox2 being the upstream factor in a gene expression hierarchy.", "Finally, downstream factors derived from the late phase, which do not include Oct4, Sox2, Klf4, c-Myc, and Nanog, can activate the pluripotency circuitry."], "structured": false}
{"doc_id": 8290953, "title": "Scaffold-based three-dimensional human fibroblast culture provides a structural matrix that supports angiogenesis in infarcted heart tissue.", "abstract": ["BACKGROUND We have developed techniques to implant angiogenic patches onto the epicardium over regions of infarcted cardiac tissue to stimulate revascularization of the damaged tissue.", "These experiments used a scaffold-based 3D human dermal fibroblast culture (3DFC) as an epicardial patch.", "The 3DFC contains viable cells that secrete angiogenic growth factors and has previously been shown to stimulate angiogenic activity.", "The hypothesis tested was that a viable 3DFC cardiac patch would stimulate an angiogenic response within an area of infarcted cardiac tissue.   \n", "METHODS AND RESULTS A coronary occlusion of a branch of the left anterior descending coronary artery was performed by thermal ligation in severe combined immunodeficient mice.", "3DFCs with or without viable cells were sized to the damaged area, implanted in replicate mice onto the epicardium at the site of tissue injury, and compared with animals that received infarct surgery but no implant.", "Fourteen and 30 days after surgery, hearts were exposed and photographed, and tissue samples were prepared for histology and cytochemistry.", "Fourteen and 30 days after surgery, the damaged myocardium receiving viable 3DFC exhibited a significantly greater angiogenic response (including arterioles, venules, and capillaries) than nonviable and untreated control groups.   \n", "CONCLUSIONS In this animal model, viable 3DFC stimulates angiogenesis within a region of cardiac infarction and can augment a repair response in damaged tissue.", "Therefore, a potential use for 3DFC is the repair of myocardial tissue damaged by infarction."], "structured": true}
{"doc_id": 8294009, "title": "Global tuberculosis control: lessons learnt and future prospects", "abstract": ["Tuberculosis (TB) is an ancient disease, but not a disease of the past.", "After disappearing from the world public health agenda in the 1960s and 1970s, TB returned in the early 1990s for several reasons, including the emergence of the HIV/AIDS pandemic and increases in drug resistance.", "More than 100 years after the discovery of the tubercle bacillus by Robert Koch, what is the status of TB control worldwide?", "Here, we review the evolution of global TB control policies, including DOTS (directly observed therapy, short course) and the Stop TB Strategy, and assess whether the challenges and obstacles faced by the public health community worldwide in developing and implementing this strategy can aid future action towards the elimination of TB."], "structured": false}
{"doc_id": 8298120, "title": "Global prevalence of glaucoma and projections of glaucoma burden through 2040: a systematic review and meta-analysis.", "abstract": ["PURPOSE Glaucoma is the leading cause of global irreversible blindness.", "Present estimates of global glaucoma prevalence are not up-to-date and focused mainly on European ancestry populations.", "We systematically examined the global prevalence of primary open-angle glaucoma (POAG) and primary angle-closure glaucoma (PACG), and projected the number of affected people in 2020 and 2040.   \n", "DESIGN Systematic review and meta-analysis.   \n", "PARTICIPANTS Data from 50 population-based studies (3770 POAG cases among 140,496 examined individuals and 786 PACG cases among 112 398 examined individuals).   \n", "METHODS We searched PubMed, Medline, and Web of Science for population-based studies of glaucoma prevalence published up to March 25, 2013.", "Hierarchical Bayesian approach was used to estimate the pooled glaucoma prevalence of the population aged 40-80 years along with 95% credible intervals (CrIs).", "Projections of glaucoma were estimated based on the United Nations World Population Prospects.", "Bayesian meta-regression models were performed to assess the association between the prevalence of POAG and the relevant factors.   \n", "MAIN OUTCOME MEASURES Prevalence and projection numbers of glaucoma cases.   \n", "RESULTS The global prevalence of glaucoma for population aged 40-80 years is 3.54% (95% CrI, 2.09-5.82).", "The prevalence of POAG is highest in Africa (4.20%; 95% CrI, 2.08-7.35), and the prevalence of PACG is highest in Asia (1.09%; 95% CrI, 0.43-2.32).", "In 2013, the number of people (aged 40-80 years) with glaucoma worldwide was estimated to be 64.3 million, increasing to 76.0 million in 2020 and 111.8 million in 2040.", "In the Bayesian meta-regression model, men were more likely to have POAG than women (odds ratio [OR], 1.36; 95% CrI, 1.23-1.52), and after adjusting for age, gender, habitation type, response rate, and year of study, people of African ancestry were more likely to have POAG than people of European ancestry (OR, 2.80; 95% CrI, 1.83-4.06), and people living in urban areas were more likely to have POAG than those in rural areas (OR, 1.58; 95% CrI, 1.19-2.04).   \n", "CONCLUSIONS The number of people with glaucoma worldwide will increase to 111.8 million in 2040, disproportionally affecting people residing in Asia and Africa.", "These estimates are important in guiding the designs of glaucoma screening, treatment, and related public health strategies."], "structured": true}
{"doc_id": 8300657, "title": "Gastrointestinal tract as a major site of CD4+ T cell depletion and viral replication in SIV infection.", "abstract": ["Human and simian immunodeficiency virus (HIV and SIV) replicate optimally in activated memory CD4(+) T cells, a cell type that is abundant in the intestine.", "SIV infection of rhesus monkeys resulted in profound and selective depletion of CD4+ T cells in the intestine within days of infection, before any such changes in peripheral lymphoid tissues.", "The loss of CD4+ T cells in the intestine occurred coincident with productive infection of large numbers of mononuclear cells at this site.", "The intestine appears to be a major target for SIV replication and the major site of CD4+ T cell loss in early SIV infection."], "structured": false}
{"doc_id": 8305686, "title": "Interaction of streptavidin-based peptide-MHC oligomers (tetramers) with cell-surface TCRs.", "abstract": ["The binding of oligomeric peptide-MHC (pMHC) complexes to cell surface TCR can be considered to approximate TCR-pMHC interactions at cell-cell interfaces.", "In this study, we analyzed the equilibrium binding of streptavidin-based pMHC oligomers (tetramers) and their dissociation kinetics from CD8(pos) T cells from 2C-TCR transgenic mice and from T cell hybridomas that expressed the 2C TCR or a high-affinity mutant (m33) of this TCR.", "Our results show that the tetramers did not come close to saturating cell-surface TCR (binding only 10-30% of cell-surface receptors), as is generally assumed in deriving affinity values (K(D)), in part because of dissociative losses from tetramer-stained cells.", "Guided by a kinetic model, the oligomer dissociation rate and equilibrium constants were seen to depend not only on monovalent association and dissociation rates (k(off) and k(on)), but also on a multivalent association rate (\u03bc) and TCR cell-surface density.", "Our results suggest that dissociation rates could account for the recently described surprisingly high frequency of tetramer-negative, functionally competent T cells in some T cell responses."], "structured": false}
{"doc_id": 8317408, "title": "Human monocyte characteristics are altered in hypercholesterolaemia.", "abstract": ["Peripheral blood monocytes are involved during atherogenesis in adhering to endothelium, migrating into the subendothelial space and taking-up lipoproteins to become macrophage/foam cells.", "We have assessed whether peripheral blood monocyte characteristics are altered in human hyperlipidaemia in age/sex/smoking status matched pairs of patients and controls.", "Monocytes from the hypercholesterolaemic patients, as opposed to the controls, were more sensitive to stimulation by the agonist, N-formyl-methionyl-leucyl-phenylalanine, with respect to chemokinesis (stimulation index 1.48 +/-", "0.17 vs. 1.10 +/-", "0.14), chemotaxis (4.05 +/- 0.55 vs. 2.72 +/- 0.24) and adhesion to porcine aortic endothelial monolayers (1.26 +/- 0.05 vs. 1.17 +/- 0.06).", "The patients' monocyte total surface expression of the adhesion glycoprotein CD11b/CD18 (37.5 +/- 7.1 vs. 36.0 +/-", "7.1), but not CD11c/CD18 (31.6 +/- 7.2 vs. 31.4 +/-", "6.8), was increased; however, the monocytes in hyperlipidaemia were larger (9.15 +/-", "0.11 microns vs. 8.98 +/-", "0.11 microns) such that the surface density of CD11b/CD18 was not altered (0.144 +/- 0.029 vs. 0.142 +/-", "0.029).", "The data suggest that circulating monocytes are functionally different in hypercholesterolaemia.", "This may explain the increased involvement by monocytes in hypercholesterolaemia-related atherogenesis."], "structured": false}
{"doc_id": 8318286, "title": "Adult Mammalian Neural Stem Cells and Neurogenesis: Five Decades Later.", "abstract": ["Adult somatic stem cells in various organs maintain homeostatic tissue regeneration and enhance plasticity.", "Since its initial discovery five decades ago, investigations of adult neurogenesis and neural stem cells have led to an established and expanding field that has significantly influenced many facets of neuroscience, developmental biology, and regenerative medicine.", "Here we review recent progress and focus on questions related to adult mammalian neural stem cells that also apply to other somatic stem cells.", "We further discuss emerging topics that are guiding the field toward better understanding adult neural stem cells and ultimately applying these principles to improve human health."], "structured": false}
{"doc_id": 8318922, "title": "Relationship of ambulatory blood pressure and the heart rate profile with renal function parameters in hypertensive patients with chronic kidney disease.", "abstract": ["Strict blood pressure (BP) control is reportedly important for the management of hypertensive patients with chronic kidney disease (CKD).", "The purpose of this cross-sectional study was to examine whether the variables of ambulatory BP and the heart rate (HR) profile, central hemodynamics, and arterial stiffness were closely related to the renal function parameters (urine albumin excretion rate [UACR] and estimated glomerular filtration rate [eGFR]) observed in 25 consecutive hospitalized hypertensive patients with CKD.", "There were significant positive relationships between UACR and 24-hour, daytime, and nighttime ambulatory systolic BP.", "In addition, there were significant negative relationships between UACR and 24-hour and daytime HR variability.", "The circulating B-type natriuretic peptide level and hemoglobin A1c were also positively related to UACR.", "With respect to eGFR, although the 24-hour and nighttime HR variability were positively associated with eGFR, the circulating pentosidine and nighttime HR had a negative relationship with eGFR.", "On the other hand, central hemodynamics and arterial stiffness did not exhibit any significant association with renal function parameters.", "These results indicate that ambulatory BP and the HR profile are closely modulated by renal function deterioration.", "Further studies are needed to investigate the causal relationship between ambulatory BP and the HR profile and renal function parameters in hypertensive patients with CKD."], "structured": false}
{"doc_id": 8325952, "title": "The frequency and immunodominance of islet-specific CD8+ T-cell responses change after type 1 diabetes diagnosis and treatment.", "abstract": ["OBJECTIVE Islet-reactive CD8(+) T-cells play a key role in the pathogenesis of type 1 diabetes in the NOD mouse.", "The predominant T-cell specificities change over time, but whether similar shifts also occur after clinical diagnosis and insulin treatment in type 1 diabetic patients is unknown.   ", "RESEARCH DESIGN AND METHODS", "We took advantage of a recently validated islet-specific CD8(+) T-cell gamma-interferon enzyme-linked immunospot (ISL8Spot) assay to follow responses against preproinsulin (PPI), GAD, insulinoma-associated protein 2 (IA-2), and islet-specific glucose-6-phosphatase catalytic subunit-related protein (IGRP) epitopes in 15 HLA-A2(+) adult type 1 diabetic patients close to diagnosis and at a second time point 7-16 months later.   \n", "RESULTS CD8(+) T-cell reactivities were less frequent at follow-up, as 28.6% of responses tested positive at type 1 diabetes diagnosis vs. 13.2% after a median of 11 months (P = 0.003).", "While GAD and IA-2 autoantibody (aAb) titers were unchanged in 75% of cases, the fraction of patients responding to PPI and/or GAD epitopes by ISL8Spot decreased from 60-67 to 20% (P < 0.02).", "The previously subdominant IA-2(206-214) and IGRP(265-273) peptides were newly targeted, thus becoming the immunodominant epitopes.   \n", "CONCLUSIONS Shifts both in frequency and in immunodominance of CD8(+) T-cell responses occur more rapidly than do changes in aAb titers.", "These different kinetics may suggest complementary clinical applications for T-cell and aAb measurements."], "structured": true}
{"doc_id": 8327914, "title": "A Protein Inventory of Human Ribosome Biogenesis Reveals an Essential Function of Exportin 5 in 60S Subunit Export", "abstract": ["The assembly of ribosomal subunits in eukaryotes is a complex, multistep process so far mostly studied in yeast.", "In S. cerevisiae, more than 200 factors including ribosomal proteins and trans-acting factors are required for the ordered assembly of 40S and 60S ribosomal subunits.", "To date, only few human homologs of these yeast ribosome synthesis factors have been characterized.", "Here, we used a systematic RNA interference (RNAi) approach to analyze the contribution of 464 candidate factors to ribosomal subunit biogenesis in human cells.", "The screen was based on visual readouts, using inducible, fluorescent ribosomal proteins as reporters.", "By performing computer-based image analysis utilizing supervised machine-learning techniques, we obtained evidence for a functional link of 153 human proteins to ribosome synthesis.", "Our data show that core features of ribosome assembly are conserved from yeast to human, but differences exist for instance with respect to 60S subunit export.", "Unexpectedly, our RNAi screen uncovered a requirement for the export receptor Exportin 5 (Exp5) in nuclear export of 60S subunits in human cells.", "We show that Exp5, like the known 60S exportin Crm1, binds to pre-60S particles in a RanGTP-dependent manner.", "Interference with either Exp5 or Crm1 function blocks 60S export in both human cells and frog oocytes, whereas 40S export is compromised only upon inhibition of Crm1.", "Thus, 60S subunit export is dependent on at least two RanGTP-binding exportins in vertebrate cells."], "structured": false}
{"doc_id": 8331432, "title": "Binding of the winged-helix transcription factor HNF3 to a linker histone site on the nucleosome.", "abstract": ["The transcription factor HNF3 and linker histones H1 and H5 possess winged-helix DNA-binding domains, yet HNF3 and other fork head-related proteins activate genes during development whereas linker histones compact DNA in chromatin and repress gene expression.", "We compared how the two classes of factors interact with chromatin templates and found that HNF3 binds DNA at the side of nucleosome cores, similarly to what has been reported for linker histone.", "A nucleosome structural binding site for HNF3 is occupied at the albumin transcriptional enhancer in active and potentially active chromatin, but not in inactive chromatin in vivo.", "While wild-type HNF3 protein does not compact DNA extending from the nucleosome, as does linker histone, site-directed mutants of HNF3 can compact nucleosomal DNA if they contain basic amino acids at positions previously shown to be essential for nucleosomal DNA compaction by linker histones.", "The results illustrate how transcription factors can possess special nucleosome-binding activities that are not predicted from studies of factor interactions with free DNA."], "structured": false}
{"doc_id": 8352137, "title": "Rapid recent growth and divergence of rice nuclear genomes.", "abstract": ["By employing the nuclear DNA of the African rice Oryza glaberrima as a reference genome, the timing, natures, mechanisms, and specificities of recent sequence evolution in the indica and japonica subspecies of Oryza sativa were identified.", "The data indicate that the genome sizes of both indica and japonica have increased substantially, >2% and >6%, respectively, since their divergence from a common ancestor, mainly because of the amplification of LTR-retrotransposons.", "However, losses of all classes of DNA sequence through unequal homologous recombination and illegitimate recombination have attenuated the growth of the rice genome.", "Small deletions have been particularly frequent throughout the genome.", "In >1 Mb of orthologous regions that we analyzed, no cases of complete gene acquisition or loss from either indica or japonica were found, nor was any example of precise transposon excision detected.", "The sequences between genes were observed to have a very high rate of divergence, indicating a molecular clock for transposable elements that is at least 2-fold more rapid than synonymous base substitutions within genes.", "We found that regions prone to frequent insertions and deletions also exhibit higher levels of point mutation.", "These results indicate a highly dynamic rice genome with competing processes for the generation and removal of genetic variation."], "structured": false}
{"doc_id": 8354687, "title": "Detection of an autoreactive T-cell population within the polyclonal repertoire that undergoes distinct autoimmune regulator (Aire)-mediated selection.", "abstract": ["The autoimmune regulator (Aire) plays a critical role in central tolerance by promoting the display of tissue-specific antigens in the thymus.", "To study the influence of Aire on thymic selection in a physiological setting, we used tetramer reagents to detect autoreactive T cells specific for the Aire-dependent tissue-specific antigen interphotoreceptor retinoid-binding protein (IRBP), in the polyclonal repertoire.", "Two class II tetramer reagents were designed to identify T cells specific for two different peptide epitopes of IRBP.", "Analyses of the polyclonal T-cell repertoire showed a high frequency of activated T cells specific for both IRBP tetramers in Aire(-/-) mice, but not in Aire(+/+) mice.", "Surprisingly, although one tetramer-binding T-cell population was efficiently deleted in the thymus in an Aire-dependent manner, the second tetramer-binding population was not deleted and could be detected in both the Aire(-/-) and Aire(+/+) T-cell repertoires.", "We found that Aire-dependent thymic deletion of IRBP-specific T cells relies on intercellular transfer of IRBP between thymic stroma and bone marrow-derived antigen-presenting cells.", "Furthermore, our data suggest that Aire-mediated deletion relies not only on thymic expression of IRBP, but also on proper antigen processing and presentation of IRBP by thymic antigen-presenting cells."], "structured": false}
{"doc_id": 8373753, "title": "Spatial and temporal heterogeneity of Anopheles mosquitoes and Plasmodium falciparum transmission along the Kenyan coast.", "abstract": ["The seasonal dynamics and spatial distributions of Anopheles mosquitoes and Plasmodium falciparum parasites were studied for one year at 30 villages in Malindi, Kilifi, and Kwale Districts along the coast of Kenya.", "Anopheline mosquitoes were sampled inside houses at each site once every two months and malaria parasite prevalence in local school children was determined at the end of the entomologic survey.", "A total of 5,476 Anopheles gambiae s.l.", "and 3,461 An.", "funestus were collected.", "Species in the An.", "gambiae complex, identified by a polymerase chain reaction, included 81.9% An.", "gambiae s.s., 12.8% An.", "arabiensis, and 5.3% An.", "merus.", "Anopheles gambiae s.s.", "contributed most to the transmission of P. falciparum along the coast as a whole, while An.", "funestus accounted for more than 50% of all transmission in Kwale District.", "Large spatial heterogeneity of transmission intensity (< 1 up to 120 infective bites per person per year) resulted in correspondingly large and significantly related variations in parasite prevalence (range = 38-83%).", "Thirty-two percent of the sites (7 of 22 sites) with malaria prevalences ranging from 38% to 70% had annual entomologic inoculation rates (EIR) less than five infective bites per person per year.", "Anopheles gambiae s.l.", "and An.", "funestus densities in Kwale were not significantly influenced by rainfall.", "However, both were positively correlated with rainfall one and three months previously in Malindi and Kilifi Districts, respectively.", "These unexpected variations in the relationship between mosquito populations and rainfall suggest environmental heterogeneity in the predominant aquatic habitats in each district.", "One important conclusion is that the highly non-linear relationship between EIRs and prevalence indicates that the consistent pattern of high prevalence might be governed by substantial variation in transmission intensity measured by entomologic surveys.", "The field-based estimate of entomologic parameters on a district level does not provide a sensitive indicator of transmission intensity in this study."], "structured": false}
{"doc_id": 8385277, "title": "Myelodysplasia and leukemia of Fanconi anemia are associated with a specific pattern of genomic abnormalities that includes cryptic RUNX1/AML1 lesions.", "abstract": ["Fanconi anemia (FA) is a genetic condition associated with bone marrow (BM) failure, myelodysplasia (MDS), and acute myeloid leukemia (AML).", "We studied 57 FA patients with hypoplastic or aplastic anemia (n = 20), MDS (n = 18), AML (n = 11), or no BM abnormality (n = 8).", "BM samples were analyzed by karyotype, high-density DNA arrays with respect to paired fibroblasts, and by selected oncogene sequencing.", "A specific pattern of chromosomal abnormalities was found in MDS/AML, which included 1q+ (44.8%), 3q+ (41.4%), -7/7q (17.2%), and 11q- (13.8%).", "Moreover, cryptic RUNX1/AML1 lesions (translocations, deletions, or mutations) were observed for the first time in FA (20.7%).", "Rare mutations of NRAS, FLT3-ITD, MLL-PTD, ERG amplification, and ZFP36L2-PRDM16 translocation, but no TP53, TET2, CBL, NPM1, and CEBP\u03b1 mutations were found.", "Frequent homozygosity regions were related not to somatic copy-neutral loss of heterozygosity but to consanguinity, suggesting that homologous recombination is not a common progression mechanism in FA.", "Importantly, the RUNX1 and other chromosomal/genomic lesions were found at the MDS/AML stages, except for 1q+, which was found at all stages.", "These data have implications for staging and therapeutic managing in FA patients, and also to analyze the mechanisms of clonal evolution and oncogenesis in a background of genomic instability and BM failure."], "structured": false}
{"doc_id": 8386609, "title": "Molecular and Cellular Approaches for Diversifying and Extending Optogenetics", "abstract": ["Optogenetic technologies employ light to control biological processes within targeted cells in vivo with high temporal precision.", "Here, we show that application of molecular trafficking principles can expand the optogenetic repertoire along several long-sought dimensions.", "Subcellular and transcellular trafficking strategies now permit (1) optical regulation at the far-red/infrared border and extension of optogenetic control across the entire visible spectrum, (2) increased potency of optical inhibition without increased light power requirement (nanoampere-scale chloride-mediated photocurrents that maintain the light sensitivity and reversible, step-like kinetic stability of earlier tools), and (3) generalizable strategies for targeting cells based not only on genetic identity, but also on morphology and tissue topology, to allow versatile targeting when promoters are not known or in genetically intractable organisms.", "Together, these results illustrate use of cell-biological principles to enable expansion of the versatile fast optogenetic technologies suitable for intact-systems biology and behavior."], "structured": false}
{"doc_id": 8396189, "title": "An analysis of the Caenorhabditis elegans lipid raft proteome using geLC-MS/MS.", "abstract": ["Lipid rafts are microdomains of the phospholipid bilayer, proposed to form semi-stable \"islands\" that act as a platform for several important cellular processes; major classes of raft-resident proteins include signalling proteins and glycosylphosphatidylinositol (GPI)-anchored proteins.", "Proteomic studies into lipid rafts have been mainly carried out in mammalian cell lines and single cell organisms.", "The nematode Caenorhabditis elegans, the model organism with a well-defined developmental profile, is ideally suited for the study of this subcellular locale in a complex developmental context.", "A study of the lipid raft proteome of C. elegans is presented here.", "A total of 44 proteins were identified from the lipid raft fraction using geLC-MS/MS, of which 40 have been determined to be likely raft proteins after analysis of predicted functions.", "Prediction of GPI-anchoring of the proteins found 21 to be potentially modified in this way, two of which were experimentally confirmed to be GPI-anchored.", "This work is the first reported study of the lipid raft proteome in C. elegans.", "The results show that raft proteins, including numerous GPI-anchored proteins, may have a variety of potentially important roles within the nematode, and will hopefully lead to C. elegans becoming a useful model for the study of lipid rafts."], "structured": false}
{"doc_id": 8398627, "title": "Geographic distribution of community-acquired methicillin-resistant Staphylococcus aureus soft tissue infections.", "abstract": ["PURPOSE The goal of this study is to look at the geographic growth patterns of community-acquired methicillin-resistant Staphylococcus aureus (MRSA) infections in our local region and to determine if specific geographic areas are at increased risk.   \n", "METHODS After Institution Review Board approval (132603-3), a retrospective chart review was conducted of 614 patients who underwent incision and drainage of an abscess by a single pediatric surgical practice from January 2004 to December 2008.", "In addition, previously published data from 195 patients who underwent incision and drainage of an abscess from January 2000 to December 2003 were reviewed.   \n", "RESULTS The most commonly cultured organism found in the pediatric population undergoing incision and drainage was S aureus (n = 388), of which 258 (66%) were methicillin resistant.", "This is a 21% increase from the rate of MRSA cultures identified from 2000 to 2003.", "Geographic information system space-time analysis showed that a cluster of 14 MRSA cases was located within a 1.44-km radius between 2000 and 2003, and 5 separate clusters of more than 20 MRSA infection cases each were identified in 3 separate cities over the 8-year time span using geographic information system spatial analysis (P value = .001).   \n", "CONCLUSION Methicillin-resistant S aureus has now become the most prevalent organism isolated from cultures of community-acquired abscesses requiring incision and drainage in the pediatric population in our local region.", "Significant clustering of MRSA infections has appeared in several different cities within our geographic region."], "structured": true}
{"doc_id": 8411251, "title": "The right place at the right time: chaperoning core histone variants.", "abstract": ["Histone proteins dynamically regulate chromatin structure and epigenetic signaling to maintain cell homeostasis.", "These processes require controlled spatial and temporal deposition and eviction of histones by their dedicated chaperones.", "With the evolution of histone variants, a network of functionally specific histone chaperones has emerged.", "Molecular details of the determinants of chaperone specificity for different histone variants are only slowly being resolved.", "A complete understanding of these processes is essential to shed light on the genuine biological roles of histone variants, their chaperones, and their impact on chromatin dynamics."], "structured": false}
{"doc_id": 8417211, "title": "Phosphorylation site mutations in heterochromatin protein 1 (HP1) reduce or eliminate silencing activity.", "abstract": ["HP1 is an essential heterochromatin-associated protein in Drosophila.", "HP1 has dosage-dependent effects on the silencing of euchromatic genes that are mislocalized to heterochromatin and is required for the normal expression of at least two heterochromatic genes.", "HP1 is multiply phosphorylated in vivo, and HP1 hyperphosphorylation is correlated with heterochromatin assembly during development.", "The purpose of this study was to test whether HP1 phosphorylation modifies biological activity and biochemical properties of HP1.", "To determine sites of HP1 phosphorylation in vivo and whether phosphorylation affects any biochemical properties of HP1, we expressed Drosophila HP1 in lepidopteran cultured cells using a recombinant baculovirus vector.", "Phosphopeptides were identified by matrix-assisted laser desorption ionization/time of flight mass spectroscopy; these peptides contain target sites for casein kinase II, protein tyrosine kinase, and PIM-1 kinase.", "Purified HP1 from bacterial (unphosphorylated) and lepidopteran (phosphorylated) cells has similar secondary structure.", "Phosphorylation has no effect on HP1 self-association but alters the DNA binding properties of HP1, suggesting that phosphorylation could differentially regulate HP1-dependent interactions.", "Serine-to-alanine and serine-to-glutamate substitutions at consensus protein kinase motifs resulted in reduction or loss of silencing activity of mutant HP1 in transgenic flies.", "These results suggest that dynamic phosphorylation/dephosphorylation regulates HP1 activity in heterochromatic silencing."], "structured": false}
{"doc_id": 8425533, "title": "Elimination of paternal mitochondria in mouse embryos occurs through autophagic degradation dependent on PARKIN and MUL1", "abstract": ["A defining feature of mitochondria is their maternal mode of inheritance.", "However, little is understood about the cellular mechanism through which paternal mitochondria, delivered from sperm, are eliminated from early mammalian embryos.", "Autophagy has been implicated in nematodes, but whether this mechanism is conserved in mammals has been disputed.", "Here, we show that cultured mouse fibroblasts and pre-implantation embryos use a common pathway for elimination of mitochondria.", "Both situations utilize mitophagy, in which mitochondria are sequestered by autophagosomes and delivered to lysosomes for degradation.", "The E3 ubiquitin ligases PARKIN and MUL1 play redundant roles in elimination of paternal mitochondria.", "The process is associated with depolarization of paternal mitochondria and additionally requires the mitochondrial outer membrane protein FIS1, the autophagy adaptor P62, and PINK1 kinase.", "Our results indicate that strict maternal transmission of mitochondria relies on mitophagy and uncover a collaboration between MUL1 and PARKIN in this process."], "structured": false}
{"doc_id": 8426046, "title": "Ribosome Profiling Provides Evidence that Large Noncoding RNAs Do Not Encode Proteins", "abstract": ["Large noncoding RNAs are emerging as an important component in cellular regulation.", "Considerable evidence indicates that these transcripts act directly as functional RNAs rather than through an encoded protein product.", "However, a recent study of ribosome occupancy reported that many large intergenic ncRNAs (lincRNAs) are bound by ribosomes, raising the possibility that they are translated into proteins.", "Here, we show that classical noncoding RNAs and 5' UTRs show the same ribosome occupancy as lincRNAs, demonstrating that ribosome occupancy alone is not sufficient to classify transcripts as coding or noncoding.", "Instead, we define a metric based on the known property of translation whereby translating ribosomes are released upon encountering a bona fide stop codon.", "We show that this metric accurately discriminates between protein-coding transcripts and all classes of known noncoding transcripts, including lincRNAs.", "Taken together, these results argue that the large majority of lincRNAs do not function through encoded proteins."], "structured": false}
{"doc_id": 8427306, "title": "Isolation of a Fusion Transcript, AMLl IETO, With Similarity to", "abstract": ["We have developed a restriction map of the chromosome 21 breakpoint region involved in t(8;21)(q22;q22.3) acute myelogenous leukemia (AML) and have isolated a genomic junction clone containing chromosome 8 and 21 material.", "Using probes from these regions, rearrangements have been identified in each of nine cases of t(8;21) AML examined.", "In addition, we have isolated cDNA clones from a t(8;21) AML cDNA library that contain fused sequences from chromosome 8 and 21.", "The chromosome 8 component, referred to as ETO (for eight twenty-one), is encoded over a large genomic region, as suggested by the analysis of corresponding yeast artificial chromosomes (YACs).", "The DNA sequence of the chromosome 21 portion of the fusion transcript is derived from the normal AML1 gene.", "A striking similarity (67% identity over 387 bp, with a corresponding 69% amino acid identity) was detected between AML1 and the Drosophila segmentation gene, runt.", "The critical consequence of the translocation is the juxtaposition of 5' sequences of AML1 to 3' sequences of ETO, oriented telomere to centromere on the der(8) chromosome."], "structured": false}
{"doc_id": 8428837, "title": "Treatment of spondyloarthropathy with 5-aminosalicylic acid (mesalazine): an open trial.", "abstract": ["OBJECTIVE Ankylosing spondylitis (AS) and spondyloarthropathy (SpA) are inflammatory diseases of unknown etiology.", "Various exogenous and endogenous (inherited) factors play a role in their development.", "Sulfasalazine (SSZ) is generally accepted as a disease modifying drug in the treatment of AS and SpA. Which part of SSZ, 5-acetylsalicylic acid (5-ASA, mesalazine) or sulfapyridine (SP), is the effective moiety is unknown.", "As the bowel, colon, and the ileum play an important role in the development of AS and SpA, it may be possible that 5-ASA is the effective moiety, with a similar mode of action as in the treatment of inflammatory bowel disease.", "To determine the efficacy of 5-ASA an open pilot study was done in 2 groups of patients with SpA.   METHODS Twenty patients with SpA, who were taking SSZ, were switched to 5-ASA (Pentasa), and 19 patients with active SpA were treated with 5-ASA without previous administration of SSZ.   \n", "RESULTS In the first group, 17 (85%) patients responded with respect to the physician global clinical assessment compared to the previous SSZ treatment period; whereas in the second patient group a statistically significant improvement was obtained in erythrocyte sedimentation rate.   \n", "CONCLUSION The results support our hypothesis that 5-ASA might be the active moiety of SSZ in the treatment of SpA."], "structured": true}
{"doc_id": 8428935, "title": "Relationship of physical activity and television watching with body weight and level of fatness among children: results from the Third National Health and Nutrition Examination Survey.", "abstract": ["CONTEXT Physical inactivity contributes to weight gain in adults, but whether this relationship is true for children of different ethnic groups is not well established.   \n", "OBJECTIVE To assess participation in vigorous activity and television watching habits and their relationship to body weight and fatness in US children.   \n", "DESIGN Nationally representative cross-sectional survey with an in-person interview and medical examination.   \n", "SETTING AND PARTICIPANTS Between 1988 and 1994, 4063 children aged 8 through 16 years were examined as part of the National Health and Nutrition Examination Survey III.", "Mexican Americans and non-Hispanic blacks were oversampled to produce reliable estimates for these groups.   \n", "MAIN OUTCOME MEASURES Episodes of weekly vigorous activity and daily hours of television watched, and their relationship to body mass index and body fatness.   \n", "RESULTS Eighty percent of US children reported performing 3 or more bouts of vigorous activity each week.", "This rate was lower in non-Hispanic black and Mexican American girls (69% and 73%, respectively).", "Twenty percent of US children participated in 2 or fewer bouts of vigorous activity perweek, and the rate was higher in girls (26%) than in boys (17%).", "Overall, 26% of US children watched 4 or more hours of television per day and 67% watched at least 2 hours per day.", "Non-Hispanic black children had the highest rates of watching 4 or more hours of television per day (42%).", "Boys and girls who watch 4 or more hours of television each day had greater body fat (P<.001) and had a greater body mass index (P<.001) than those who watched less than 2 hours per day.   \n", "CONCLUSIONS Many US children watch a great deal of television and are inadequately vigorously active.", "Vigorous activity levels are lowest among girls, non-Hispanic blacks, and Mexican Americans.", "Intervention strategies to promote lifelong physical activity among US children are needed to stem the adverse health consequences of inactivity."], "structured": true}
{"doc_id": 8446259, "title": "Vascular Calcification in Chronic Kidney Disease is Induced by Bone Morphogenetic Protein-2 via a Mechanism Involving the Wnt/\u03b2-Catenin Pathway", "abstract": ["Background: Vascular calcification (VC), in which vascular smooth muscle cells (VSMCs) undergo a phenotypic transformation into osteoblast-like cells, is one of the emergent risk factors for the accelerated atherosclerosis process characteristic of chronic kidney disease (CKD).", "Phosphate is an important regulator of VC.", "Methods: The expression of different smooth muscle cell or osteogenesis markers in response to high concentrations of phosphate or exogenous bone morphogenetic protein 2 (BMP-2) was examined by qRT-PCR and western blotting in rat VSMCs.", "Osteocalcin secretion was measured by radioimmunoassay.", "Differentiation and calcification of VSMCs were examined by alkaline phosphatase (ALP) activity assay and Alizarin staining.", "Short hairpin RNA-mediated silencing of \u03b2-catenin was performed to examine the involvement of Wnt/\u03b2-catenin signaling in VSMC calcification and osteoblastic differentiation induced by high phosphate or BMP-2.", "Apoptosis was determined by TUNEL assay and immunofluorescence imaging.", "Results: BMP-2 serum levels were significantly higher in CKD patients than in controls.", "High phosphate concentrations and BMP-2 induced VSMC apoptosis and upregulated the expression of \u03b2-catenin, Msx2, Runx2 and the phosphate cotransporter Pit1, whereas a BMP-2 neutralization antibody reversed these effects.", "Knockdown of \u03b2-catenin abolished the effect of high phosphate and BMP-2 on VSMC apoptosis and calcification.", "Conclusions: BMP-2 plays a crucial role in calcium deposition in VSMCs and VC in CKD patients via a mechanism involving the Wnt/\u03b2-catenin pathway."], "structured": false}
{"doc_id": 8446324, "title": "Advances in brain tumor surgery.", "abstract": ["Advances in the fields of molecular and translational research, oncology, and surgery have emboldened the medical community to believe that intrinsic brain tumors may be treatable.", "Intraoperative imaging and brain mapping allow operations adjacent to eloquent cortex and more radical resection of tumors with increased confidence and safety.", "Despite these advances, the infiltrating edge of a neoplasm and distant microscopic satellite lesions will never be amendable to a surgical cure.", "Indeed, it is continued research into the delivery of an efficacious chemobiologic agent that will eventually allows us to manage this primary cause of treatment failure."], "structured": false}
{"doc_id": 8447873, "title": "Systematic review of controlled clinical trials of gastric lavage in acute organophosphorus pesticide poisoning.", "abstract": ["BACKGROUND Organophosphorus pesticide (OP) self-poisoning is a major problem in the developing rural world.", "There is little clinical trial data to guide therapy, hindering the identification of best therapy.", "Despite the recognition of adverse effects, gastric lavage is commonly done in Asia.", "We aimed to identify studies assessing its effectiveness.   \n", "METHOD We systematically searched the literature for controlled clinical studies that assessed the effect of gastric lavage in OP pesticide self-poisoning.   \n", "RESULTS All 56 studies identified were Chinese and reported benefit from the intervention studied, including multiple gastric lavages, use of norepinephrine or pralidoxime in the lavage fluid, concurrent treatment with naloxone or scopolamine, insertion of the gastric tube via a laparotomy incision, and lavage later than 12 h post-ingestion.", "However, only 23 were RCTs and none presented adequate methodology for their quality to be assessed.", "The patient population and study treatment protocol were not defined - large variation in case fatality in the control arm of the studies (from 4.5 to 93%) suggests marked variation between studies and likely between study arms.", "No study compared an intervention against a control group receiving no gastric lavage or provided any data to indicate whether a significant quantity of poison was removed.   \n", "CONCLUSION Despite widespread use of multiple gastric lavages for OP pesticide poisoning across Asia, there is currently no high-quality evidence to support its clinical effectiveness.", "There is a need for studies to identify in which patients and for what duration gastric lavage is able to remove significant quantities of poison.", "Following these studies, large clinical trials will be required to address the effectiveness and safety of gastric lavage (either single or multiple) in acute OP pesticide poisoning."], "structured": true}
{"doc_id": 8453819, "title": "Integrin activation by Fam38A uses a novel mechanism of R-Ras targeting to the endoplasmic reticulum.", "abstract": ["The integrin family of heterodimeric cell-surface receptors are fundamental in cell-cell and cell-matrix adhesion.", "Changes to either integrin-ligand affinity or integrin gene expression are central to a variety of disease processes, including inflammation, cardiovascular disease and cancer.", "In screening for novel activators of integrin-ligand affinity we identified the previously uncharacterised multi-transmembrane domain protein Fam38A, located at the endoplasmic reticulum (ER).", "siRNA knockdown of Fam38A in epithelial cells inactivates endogenous beta1 integrin, reducing cell adhesion.", "Fam38A mediates integrin activation by recruiting the small GTPase R-Ras to the ER, which activates the calcium-activated protease calpain by increasing Ca(2+) release from cytoplasmic stores.", "Fam38A-induced integrin activation is blocked by inhibition of either R-Ras or calpain activity, or by siRNA knockdown of talin, a well-described calpain substrate.", "This highlights a novel mechanism for integrin activation by Fam38A, utilising calpain and R-Ras signalling from the ER.", "These data represent the first description of a novel spatial regulator of R-Ras, of an alternative integrin activation-suppression pathway based on direct relocalisation of R-Ras to the ER, and of a mechanism linking R-Ras and calpain signalling from the ER with modulation of integrin-ligand affinity."], "structured": false}
{"doc_id": 8458567, "title": "Convergence of 9-cis retinoic acid and peroxisome proliferator signalling pathways through heterodimer formation of their receptors", "abstract": ["PEROXISOMES are cytoplasmic organelles which are important in mammals in modulation of lipid homeostasis, including the metabolism of long-chain fatty acids and conversion of cholesterol to bile salts (reviewed in refs 1 and 2).", "Amphipathic carboxylates such as clofibric acid have been used in man as hypolipidaemic agents and in rodents they stimulate the proliferation of peroxisomes.", "These agents, termed peroxisome proliferators, and all-trans retinoic acid activate genes involved in peroxisomal-mediated \u03b2-oxidation of fatty acids1\u20134.", "Here we show that the receptor activated by peroxisome proliferators5 and the retinoid X receptor-\u03b1 (ref.", "6) form a heterodimer that activates acyl-CoA oxidase gene expression in response to either clofibric acid or the retinoid X receptor-\u03b1 ligand, 9-cis retinoic acid, an all-trans retinoic acid metabolite7,8; simultaneous exposure to both activators results in a synergistic induction of gene expression.", "These data demonstrate the coupling of the peroxisome proliferator and retinoid signalling pathways and provide evidence for a physiological role for 9-cis retinoic acid in modulating lipid metabolism."], "structured": false}
{"doc_id": 8460275, "title": "The Utilization of Extracellular Proteins as Nutrients Is Suppressed by mTORC1", "abstract": ["Despite being surrounded by diverse nutrients, mammalian cells preferentially metabolize glucose and free amino acids.", "Recently, Ras-induced macropinocytosis of extracellular proteins was shown to reduce a transformed cell's dependence on extracellular glutamine.", "Here, we demonstrate that protein macropinocytosis can also serve as an essential amino acid source.", "Lysosomal degradation of extracellular proteins can sustain cell survival and induce activation of mTORC1 but fails to elicit significant cell accumulation.", "Unlike its growth-promoting activity under amino-acid-replete conditions, we discovered that mTORC1 activation suppresses proliferation when cells rely on extracellular proteins as an amino acid source.", "Inhibiting mTORC1 results in increased catabolism of endocytosed proteins and enhances cell proliferation during nutrient-depleted conditions in vitro and within vascularly compromised tumors in vivo.", "Thus, by preventing nutritional consumption of extracellular proteins, mTORC1 couples growth to availability of free amino acids.", "These results may have important implications for the use of mTOR inhibitors as therapeutics."], "structured": false}
{"doc_id": 8476213, "title": "A general model to explore complex dominance patterns in plant sporophytic self-incompatibility systems.", "abstract": ["We developed a general model of sporophytic self-incompatibility under negative frequency-dependent selection allowing complex patterns of dominance among alleles.", "We used this model deterministically to investigate the effects on equilibrium allelic frequencies of the number of dominance classes, the number of alleles per dominance class, the asymmetry in dominance expression between pollen and pistil, and whether selection acts on male fitness only or both on male and on female fitnesses.", "We show that the so-called \"recessive effect\" occurs under a wide variety of situations.", "We found emerging properties of finite population models with several alleles per dominance class such as that higher numbers of alleles are maintained in more dominant classes and that the number of dominance classes can evolve.", "We also investigated the occurrence of homozygous genotypes and found that substantial proportions of those can occur for the most recessive alleles.", "We used the model for two species with complex dominance patterns to test whether allelic frequencies in natural populations are in agreement with the distribution predicted by our model.", "We suggest that the model can be used to test explicitly for additional, allele-specific, selective forces."], "structured": false}
{"doc_id": 8477699, "title": "Metabolic Reprograming in Macrophage Polarization", "abstract": ["Studying the metabolism of immune cells in recent years has emphasized the tight link existing between the metabolic state and the phenotype of these cells.", "Macrophages in particular are a good example of this phenomenon.", "Whether the macrophage obtains its energy through glycolysis or through oxidative metabolism can give rise to different phenotypes.", "Classically activated or M1 macrophages are key players of the first line of defense against bacterial infections and are known to obtain energy through glycolysis.", "Alternatively activated or M2 macrophages on the other hand are involved in tissue repair and wound healing and use oxidative metabolism to fuel their longer-term functions.", "Metabolic intermediates, however, are not just a source of energy but can be directly implicated in a particular macrophage phenotype.", "In M1 macrophages, the Krebs cycle intermediate succinate regulates HIF1\u03b1, which is responsible for driving the sustained production of the pro-inflammatory cytokine IL1\u03b2.", "In M2 macrophages, the sedoheptulose kinase carbohydrate kinase-like protein is critical for regulating the pentose phosphate pathway.", "The potential to target these events and impact on disease is an exciting prospect."], "structured": false}
{"doc_id": 8494570, "title": "Characterization of constitutive CTCF/cohesin loci: a possible role in establishing topological domains in mammalian genomes", "abstract": ["BACKGROUND Recent studies suggested that human/mammalian genomes are divided into large, discrete domains that are units of chromosome organization.", "CTCF, a CCCTC binding factor, has a diverse role in genome regulation including transcriptional regulation, chromosome-boundary insulation, DNA replication, and chromatin packaging.", "It remains unclear whether a subset of CTCF binding sites plays a functional role in establishing/maintaining chromatin topological domains.   \n", "RESULTS We systematically analysed the genomic, transcriptomic and epigenetic profiles of the CTCF binding sites in 56 human cell lines from ENCODE.", "We identified ~24,000 CTCF sites (referred to as constitutive sites) that were bound in more than 90% of the cell lines.", "Our analysis revealed: 1) constitutive CTCF loci were located in constitutive open chromatin and often co-localized with constitutive cohesin loci; 2) most constitutive CTCF loci were distant from transcription start sites and lacked CpG islands but were enriched with the full-spectrum CTCF motifs: a recently reported 33/34-mer and two other potentially novel (22/26-mer); 3) more importantly, most constitutive CTCF loci were present in CTCF-mediated chromatin interactions detected by ChIA-PET and these pair-wise interactions occurred predominantly within, but not between, topological domains identified by Hi-C.   CONCLUSIONS Our results suggest that the constitutive CTCF sites may play a role in organizing/maintaining the recently identified topological domains that are common across most human cells."], "structured": true}
{"doc_id": 8496132, "title": "Regulation of Bcl-2 expression by HuR in HL60 leukemia cells and A431 carcinoma cells.", "abstract": ["Overexpression of the proto-oncogene bcl-2 promotes abnormal cell survival by inhibiting apoptosis.", "Expression of bcl-2 is determined, in part, by regulatory mechanisms that control the stability of bcl-2 mRNA.", "Elements in the 3'-untranslated region of bcl-2 mRNA have been shown to play a role in regulating the stability of the message.", "Previously, it was found that the RNA binding proteins nucleolin and Ebp1 have a role in stabilizing bcl-2 mRNA in HL60 cells.", "Here, we have identified HuR as a component of bcl-2 messenger ribonucleoprotein (mRNP) complexes.", "RNA coimmunoprecipitation assays showed that HuR binds to bcl-2 mRNA in vivo.", "We also observed an RNA-dependent coprecipitation of HuR and nucleolin, suggesting that the two proteins are present in common mRNP complexes.", "Moreover, nucleolin and HuR bind concurrently to bcl-2 AU-rich element (ARE) RNA in vitro, suggesting separate binding sites for these proteins on bcl-2 mRNA.", "Knockdown of HuR in A431 cells leads to down-regulation of bcl-2 mRNA and protein levels.", "Observation of a decreased ratio of bcl-2 mRNA to heterogeneous nuclear RNA in HuR knockdown cells confirmed a positive role for HuR in regulating bcl-2 stability.", "Recombinant HuR retards exosome-mediated decay of bcl-2 ARE RNA in extracts of HL60 cells.", "This supports a role for HuR in the regulation of bcl-2 mRNA stability in HL60 cells, as well as in A431 cells.", "Addition of nucleolin and HuR to HL60 cell extracts produced a synergistic protective effect on decay of bcl-2 ARE RNA.", "HuR knockdown also leads to redistribution of bcl-2 mRNA from polysomes to monosomes.", "Thus, HuR seems to play a positive role in both regulation of bcl-2 mRNA translation and mRNA stability."], "structured": false}
{"doc_id": 8502193, "title": "The Worldwide Variation in Avian Clutch Size across Species and Space", "abstract": ["Traits such as clutch size vary markedly across species and environmental gradients but have usually been investigated from either a comparative or a geographic perspective, respectively.", "We analyzed the global variation in clutch size across 5,290 bird species, excluding brood parasites and pelagic species.", "We integrated intrinsic (morphological, behavioural), extrinsic (environmental), and phylogenetic effects in a combined model that predicts up to 68% of the interspecific variation in clutch size.", "We then applied the same species-level model to predict mean clutch size across 2,521 assemblages worldwide and found that it explains the observed eco-geographic pattern very well.", "Clutches are consistently largest in cavity nesters and in species occupying seasonal environments, highlighting the importance of offspring and adult mortality that is jointly expressed in intrinsic and extrinsic correlates.", "The findings offer a conceptual bridge between macroecology and comparative biology and provide a global and integrative understanding of the eco-geographic and cross-species variation in a core life-history trait."], "structured": false}
{"doc_id": 8509018, "title": "Diastolic heart failure--abnormalities in active relaxation and passive stiffness of the left ventricle.", "abstract": ["BACKGROUND Patients with signs and symptoms of heart failure and a normal left ventricular ejection fraction are said to have diastolic heart failure.", "It has traditionally been thought that the pathophysiological cause of heart failure in these patients is an abnormality in the diastolic properties of the left ventricle; however, this hypothesis remains largely unproven.   \n", "METHODS We prospectively identified 47 patients who met the diagnostic criteria for definite diastolic heart failure; all the patients had signs and symptoms of heart failure, a normal ejection fraction, and an increased left ventricular end-diastolic pressure.", "Ten patients who had no evidence of cardiovascular disease served as controls.", "Left ventricular diastolic function was assessed by means of cardiac catheterization and echocardiography.   \n", "RESULTS The patients with diastolic heart failure had abnormal left ventricular relaxation and increased left ventricular chamber stiffness.", "The mean (+/-SD) time constant for the isovolumic-pressure decline (tau) was longer in the group with diastolic heart failure than in the control group (59+/-14 msec vs. 35+/-10 msec, P=0.01).", "The diastolic pressure-volume relation was shifted up and to the left in the patients with diastolic heart failure as compared with the controls.", "The corrected left ventricular passive-stiffness constant was significantly higher in the group with diastolic heart failure than in the control group (0.03+/-0.01 vs. 0.01+/-0.01, P<0.001).   \n", "CONCLUSIONS Patients with heart failure and a normal ejection fraction have significant abnormalities in active relaxation and passive stiffness.", "In these patients, the pathophysiological cause of elevated diastolic pressures and heart failure is abnormal diastolic function."], "structured": true}
{"doc_id": 8512633, "title": "The lncRNAs PCGEM1 and PRNCR1 are not implicated in castration resistant prostate cancer", "abstract": ["Long noncoding RNAs (IncRNAs) are increasingly implicated in cancer biology, contributing to essential cancer cell functions such as proliferation, invasion, and metastasis.", "In prostate cancer, several lncRNAs have been nominated as critical actors in disease pathogenesis.", "Among these, expression of PCGEM1 and PRNCR1 has been identified as a possible component in disease progression through the coordination of androgen receptor (AR) signaling (Yang et al., Nature 2013, see ref.", "[1]).", "However, concerns regarding the robustness of these findings have been suggested.", "Here, we sought to evaluate whether PCGEM1 and PRNCR1 are associated with prostate cancer.", "Through a comprehensive analysis of RNA-sequencing data (RNA-seq), we find evidence that PCGEM1 but not PRNCR1 is associated with prostate cancer.", "We employ a large cohort of >230 high-risk prostate cancer patients with long-term outcomes data to show that, in contrast to prior reports, neither gene is associated with poor patient outcomes.", "We further observe no evidence that PCGEM1 nor PRNCR1 interact with AR, and neither gene is a component of AR signaling.", "Thus, we conclusively demonstrate that PCGEM1 and PRNCR1 are not prognostic lncRNAs in prostate cancer and we refute suggestions that these lncRNAs interact in AR signaling."], "structured": false}
{"doc_id": 8519911, "title": "p38MAPK controls expression of multiple cell cycle inhibitors and islet proliferation with advancing age.", "abstract": ["Aging is a complex organismal process that is controlled by genetic, environmental, and behavioral factors.", "Accumulating evidence supports a role for different cell cycle inhibitors in mammalian aging.", "Little is known, however, about the upstream signals that induce their expression.", "Here, we explore the role of p38MAPK by generating a dominant-negative allele (p38(AF)) in which activating phosphorylation sites Thr180 and Tyr182 are mutated.", "Heterozygous p38(AF) mice show a marked attenuation of p38-dependent signaling and age-induced expression of multiple cell cycle inhibitors in different organs, including pancreatic islets.", "As a result, aged p38(AF/+) mice show enhanced proliferation and regeneration of islets when compared to wild-type littermates.", "We further find an age-related reduction in expression of the p38-specific phosphatase Wip1.", "Wip1-deficient mice demonstrate decreased islet proliferation, while Wip1 overexpression rescues aging-related decline in proliferation and regenerative capacity.", "We propose that modulation of p38MAPK activity may provide new avenues for treating certain age-related degenerative diseases."], "structured": false}
{"doc_id": 8520041, "title": "ACTA PSYCHIATRICA", "abstract": ["OBJECTIVE We explored the subjective effects associated with olanzapine, risperidone and older antipsychotics.   \n", "METHOD We conducted a content analysis of an Internet database of comments about prescribed medications.   \n", "RESULTS We analysed 223 comments on risperidone, 170 on olanzapine and 46 relating to three older antipsychotics.", "The predominant subjective effects produced by all drugs consisted of sedation, cognitive impairment and emotional flattening or indifference.", "Connections appeared between these effects and Parkinsonian-like symptoms with the older drugs, sexual impairment with risperidone and metabolic effects with olanzapine.", "The experience of akathisia was frequently linked to suicidal thoughts.", "Some respondents described how the drugs' subjective effects helped to reduce symptoms of mania, psychosis and anxiety.   \n", "CONCLUSION The generalisability of Internet data is uncertain.", "However, the data suggest that adverse subjective effects play a central role in the experience of taking antipsychotic drugs and may be related to the drugs' desired benefits."], "structured": true}
{"doc_id": 8524891, "title": "White matter hyperintensities are a core feature of Alzheimer's disease: Evidence from the dominantly inherited Alzheimer network.", "abstract": ["OBJECTIVE White matter hyperintensities (WMHs) are areas of increased signal on T2-weighted magnetic resonance imaging (MRI) scans that most commonly reflect small vessel cerebrovascular disease.", "Increased WMH volume is associated with risk and progression of Alzheimer's disease (AD).", "These observations are typically interpreted as evidence that vascular abnormalities play an additive, independent role contributing to symptom presentation, but not core features of AD.", "We examined the severity and distribution of WMH in presymptomatic PSEN1, PSEN2, and APP mutation carriers to determine the extent to which WMH manifest in individuals genetically determined to develop AD.   \n", "METHODS The study comprised participants (n = 299; age = 39.03 \u00b1 10.13) from the Dominantly Inherited Alzheimer Network, including 184 (61.5%) with a mutation that results in AD and 115 (38.5%) first-degree relatives who were noncarrier controls.", "We calculated the estimated years from expected symptom onset (EYO) by subtracting the affected parent's symptom onset age from the participant's age.", "Baseline MRI data were analyzed for total and regional WMH.", "Mixed-effects piece-wise linear regression was used to examine WMH differences between carriers and noncarriers with respect to EYO.   \n", "RESULTS Mutation carriers had greater total WMH volumes, which appeared to increase approximately 6 years before expected symptom onset.", "Effects were most prominent for the parietal and occipital lobe, which showed divergent effects as early as 22 years before estimated onset.   \n", "INTERPRETATION Autosomal-dominant AD is associated with increased WMH well before expected symptom onset.", "The findings suggest the possibility that WMHs are a core feature of AD, a potential therapeutic target, and a factor that should be integrated into pathogenic models of the disease.", "Ann Neurol 2016;79:929-939."], "structured": true}
{"doc_id": 8529693, "title": "Maternal and child undernutrition: consequences for adult health and human capital", "abstract": ["In this paper we review the associations between maternal and child undernutrition with human capital and risk of adult diseases in low-income and middle-income countries.", "We analysed data from five long-standing prospective cohort studies from Brazil, Guatemala, India, the Philippines, and South Africa and noted that indices of maternal and child undernutrition (maternal height, birthweight, intrauterine growth restriction, and weight, height, and body-mass index at 2 years according to the new WHO growth standards) were related to adult outcomes (height, schooling, income or assets, offspring birthweight, body-mass index, glucose concentrations, blood pressure).", "We undertook systematic reviews of studies from low-income and middle-income countries for these outcomes and for indicators related to blood lipids, cardiovascular disease, lung and immune function, cancers, osteoporosis, and mental illness.", "Undernutrition was strongly associated, both in the review of published work and in new analyses, with shorter adult height, less schooling, reduced economic productivity, and--for women--lower offspring birthweight.", "Associations with adult disease indicators were not so clear-cut.", "Increased size at birth and in childhood were positively associated with adult body-mass index and to a lesser extent with blood pressure values, but not with blood glucose concentrations.", "In our new analyses and in published work, lower birthweight and undernutrition in childhood were risk factors for high glucose concentrations, blood pressure, and harmful lipid profiles once adult body-mass index and height were adjusted for, suggesting that rapid postnatal weight gain--especially after infancy--is linked to these conditions.", "The review of published works indicates that there is insufficient information about long-term changes in immune function, blood lipids, or osteoporosis indicators.", "Birthweight is positively associated with lung function and with the incidence of some cancers, and undernutrition could be associated with mental illness.", "We noted that height-for-age at 2 years was the best predictor of human capital and that undernutrition is associated with lower human capital.", "We conclude that damage suffered in early life leads to permanent impairment, and might also affect future generations.", "Its prevention will probably bring about important health, educational, and economic benefits.", "Chronic diseases are especially common in undernourished children who experience rapid weight gain after infancy."], "structured": false}
{"doc_id": 8533245, "title": "Ubiquitin-dependent intramembrane rhomboid protease promotes ERAD of membrane proteins.", "abstract": ["The ER-associated degradation (ERAD) pathway serves as an important cellular safeguard by directing incorrectly folded and unassembled proteins from the ER to the proteasome.", "Still, however, little is known about the components mediating ERAD of membrane proteins.", "Here we show that the evolutionary conserved rhomboid family protein RHBDL4 is a ubiquitin-dependent ER-resident intramembrane protease that is upregulated upon ER stress.", "RHBDL4 cleaves single-spanning and polytopic membrane proteins with unstable transmembrane helices, leading to their degradation by the canonical ERAD machinery.", "RHBDL4 specifically binds the AAA+-ATPase p97, suggesting that proteolytic processing and dislocation into the cytosol are functionally linked.", "The phylogenetic relationship between rhomboids and the ERAD factor derlin suggests that substrates for intramembrane proteolysis and protein dislocation are recruited by a shared mechanism."], "structured": false}
{"doc_id": 8536018, "title": "Detection and function of nitric oxide during the hypersensitive response in Arabidopsis thaliana: where there's a will there's a way.", "abstract": ["Nitric oxide (NO) was identified as a key player in plant defence responses approximately 20 years ago and a large body of evidence has accumulated since then supporting its role as a signalling molecule.", "However, there are many discrepancies in current NO detection assays and the enzymatic pathways responsible for its synthesis have yet to be determined.", "This has provoked strong debates concerning the function of NO in plants, even questioning its existence in planta.", "Here we gather data obtained using the model pathosystem Arabidopsis/Pseudomonas, which confirms the production of NO during the hypersensitive response and supports is role as a trigger of hypersensitive cell death and a mediator of defence gene expression.", "Finally, we discuss potential sources of NO synthesis, focusing on the role of nitrite as major substrate for NO production during incompatible interactions."], "structured": false}
{"doc_id": 8538916, "title": "The Cytosolic Chaperonin CCT/TRiC and Cancer Cell Proliferation", "abstract": ["The molecular chaperone CCT/TRiC plays a central role in maintaining cellular proteostasis as it mediates the folding of the major cytoskeletal proteins tubulins and actins.", "CCT/TRiC is also involved in the oncoprotein cyclin E, the Von Hippel-Lindau tumour suppressor protein, cyclin B and p21(ras) folding which strongly suggests that it is involved in cell proliferation and tumor genesis.", "To assess the involvement of CCT/TRiC in tumor genesis, we quantified its expression levels and activity in 18 cancer, one non-cancer human cell lines and a non-cancer human liver.", "We show that the expression levels of CCT/TRiC in cancer cell lines are higher than that in normal cells.", "However, CCT/TRiC activity does not always correlate with its expression levels.", "We therefore documented the expression levels of CCT/TRiC modulators and partners PhLP3, Hop/P60, prefoldin and Hsc/Hsp70.", "Our analysis reveals a functional interplay between molecular chaperones that might account for a precise modulation of CCT/TRiC activity in cell proliferation through changes in the cellular levels of prefoldin and/or Hsc/p70 and CCT/TRiC client protein availability.", "Our observation and approaches bring novel insights in the role of CCT/TRiC-mediated protein folding machinery in cancer cell development."], "structured": false}
{"doc_id": 8548635, "title": "RBP2 Belongs to a Family of Demethylases, Specific for Tri-and Dimethylated Lysine 4 on Histone 3", "abstract": ["Methylation of histones has been regarded as a stable modification defining the epigenetic program of the cell, which regulates chromatin structure and transcription.", "However, the recent discovery of histone demethylases has challenged the stable nature of histone methylation.", "Here we demonstrate that the JARID1 proteins RBP2, PLU1, and SMCX are histone demethylases specific for di- and trimethylated histone 3 lysine 4 (H3K4).", "Consistent with a role for the JARID1 Drosophila homolog Lid in regulating expression of homeotic genes during development, we show that RBP2 is displaced from Hox genes during embryonic stem (ES) cell differentiation correlating with an increase of their H3K4me3 levels and expression.", "Furthermore, we show that mutation or RNAi depletion of the C. elegans JARID1 homolog rbr-2 leads to increased levels of H3K4me3 during larval development and defects in vulva formation.", "Taken together, these results suggest that H3K4me3/me2 demethylation regulated by the JARID1 family plays an important role during development."], "structured": false}
{"doc_id": 8551160, "title": "Mitochondria: Dynamic Organelles in Disease, Aging, and Development", "abstract": ["Mitochondria are the primary energy-generating system in most eukaryotic cells.", "Additionally, they participate in intermediary metabolism, calcium signaling, and apoptosis.", "Given these well-established functions, it might be expected that mitochondrial dysfunction would give rise to a simple and predictable set of defects in all tissues.", "However, mitochondrial dysfunction has pleiotropic effects in multicellular organisms.", "Clearly, much about the basic biology of mitochondria remains to be understood.", "Here we discuss recent work that suggests that the dynamics (fusion and fission) of these organelles is important in development and disease."], "structured": false}
{"doc_id": 8563659, "title": "Persistence of HIV-1 Receptor-Positive Cells after HSV-2 Reactivation: A Potential Mechanism for Increased HIV-1 Acquisition", "abstract": ["To explore the mechanism by which herpes simplex virus (HSV)-2 infection is related to HIV-1 acquisition, we conducted in situ analysis of the cellular infiltrate from sequential biopsies of HSV-2 lesions from patients on and off antiviral therapy.", "CD4(+) and CD8(+) T cells and a mixed population of plasmacytoid and myeloid dendritic cells (DCs), including cells expressing the C-type lectin receptor DC-SIGN, persisted at sites of HSV-2 reactivation for months after healing, even with daily antiviral therapy.", "The CD4(+) T cells that persisted reacted to HSV-2 antigen, were enriched for expression of the chemokine receptor CCR5, and were contiguous to DCs expressing the interleukin-3 receptor CD123 or DC-SIGN.", "Ex vivo infection with a CCR5-tropic strain of HIV-1 revealed greater concentrations of integrated HIV-1 DNA in cells derived from healed genital lesion biopsies than in cells from control skin biopsies.", "The persistence and enrichment of HIV receptor-positive inflammatory cells in the genitalia help explain the inability of anti-HSV-2 therapy to reduce HIV acquisition."], "structured": false}
{"doc_id": 8570317, "title": "Chronic daily headache in Taipei, Taiwan: prevalence, follow-up and outcome predictors.", "abstract": ["We conducted a two-stage population-based headache survey among subjects aged > or = 15 in Taipei, Taiwan.", "Subjects with chronic daily headache (CDH) in the past year were identified, interviewed and followed-up.", "CDH was defined as a headache frequency > 15 days/month, with a duration > 4 h/day.", "Of the 3377 participants, 108 (3.2%) fulfilled the criteria for CDH, with a higher prevalence in women (4.3%) than men (1.9%).", "TM was the most common subtype (55%), followed by CTTH (44%).", "Thirty-four per cent of the CDH subjects overused analgesics.", "At the 2-year follow-up, 35% of the CDH subjects still had CDH.", "The significant predictors for persistent CDH at follow-up included: older age ( > or = 40 years) (RR = 2.4), CDH onset after 32 years (RR = 1.8), CDH duration > or = 6 years (RR = 2.0), medication overuse (RR = 1.8), and \"daily\" headache (RR = 2.1).", "We found that CDH is not uncommon in the community and its prevalence is similar among different populations.", "Older subjects and those with medication overuse may have a more protracted course of illness."], "structured": false}
{"doc_id": 8570478, "title": "In vivo microtubules are copolymers of available beta-tubulin isotypes: localization of each of six vertebrate beta-tubulin isotypes using polyclonal antibodies elicited by synthetic peptide antigens", "abstract": ["beta-Tubulin is encoded in the genomes of higher animals by a small multigene family comprising approximately seven functional genes.", "These genes produce a family of closely related, but distinct polypeptide isotypes that are distinguished principally by sequences within the approximately 15 carboxy-terminal amino acid residues.", "By immunizing rabbits with chemically synthesized peptides corresponding to these variable domain sequences, we have now prepared polyclonal antibodies specific for each of six distinct isotypes.", "Specificity of each antiserum has been demonstrated unambiguously by antibody binding to bacterially produced, cloned proteins representing each isotype and by the inhibition of such binding by preincubation of each antiserum only with the immunizing peptide and not with heterologous peptides.", "Protein blotting of known amounts of cloned, isotypically pure polypeptides has permitted accurate quantitative measurement of the amount of each beta-tubulin isotype present in the soluble and polymer forms in various cells, but has not revealed a bias for preferential assembly of any isotype.", "Localization of each isotype in three different cell types using indirect immunofluorescence has demonstrated that in vivo each class of microtubules distinguishable by light microscopy is assembled as copolymers of all isotypes expressed in a single cell."], "structured": false}
{"doc_id": 8570690, "title": "Topiramate for smoking cessation: a randomized, placebo-controlled pilot study.", "abstract": ["INTRODUCTION Topiramate (TOP) blocks glutamate receptors and facilitates GABA (\u03b3-aminobutyric acid) neurotransmission, effects that may facilitate smoking cessation.", "We compared the effects of behavioral counseling combined with (a) TOP, (b) TOP/nicotine patch (TOP/NIC), or (c) placebo (PLC) for smoking cessation.   \n", "METHODS We conducted a 10-week randomized trial in which subjects and research personnel were blinded to TOP versus PLC but not to the TOP/NIC patch condition.", "In groups receiving TOP, the medication dosage was titrated gradually up to 200 mg/day.", "The smoking quit date (QD) was scheduled after 2 weeks of medication treatment.", "NIC (21 mg) was started on the QD in subjects randomized to the TOP/NIC condition.", "The main outcome measure was the end-of-treatment, 4-week continuous abstinence rate (CAR; biochemically confirmed).   \n", "RESULTS Fifty-seven subjects were randomized to treatment.", "The 4-week CAR was 1 of 19 (5%) in the PLC group, 5 of 19 (26%) in the TOP group, and 7 of 19 (37%) in the TOP/NIC group (p = .056).", "Pairwise comparisons showed a difference between TOP/NIC and PLC (p = .042) and a nonsignificant difference between TOP and PLC (p = .18).", "The PLC group gained 0.37 lb/week, the TOP group lost 0.41 lb/week, and the TOP/NIC group lost 0.07 lb/week (p = .004).", "Pairwise comparisons showed a difference between TOP and PLC (p < .001) and between TOP/NIC and PLC groups (p = .035).", "Paresthesia was more frequent in subjects on TOP than PLC (p = .011).   \n", "CONCLUSIONS TOP, alone or in combination with the NIC, resulted in a numerically higher quit rate than PLC and decreased weight.", "A larger, PLC-controlled trial is needed to confirm these findings."], "structured": true}
{"doc_id": 8577229, "title": "Break-induced DNA replication.", "abstract": ["Recombination-dependent DNA replication, often called break-induced replication (BIR), was initially invoked to explain recombination events in bacteriophage but it has recently been recognized as a fundamentally important mechanism to repair double-strand chromosome breaks in eukaryotes.", "This mechanism appears to be critically important in the restarting of stalled and broken replication forks and in maintaining the integrity of eroded telomeres.", "Although BIR helps preserve genome integrity during replication, it also promotes genome instability by the production of loss of heterozygosity and the formation of nonreciprocal translocations, as well as in the generation of complex chromosomal rearrangements."], "structured": false}
{"doc_id": 8582337, "title": "The state of US health, 1990-2010: burden of diseases, injuries, and risk factors.", "abstract": ["IMPORTANCE Understanding the major health problems in the United States and how they are changing over time is critical for informing national health policy.   \n", "OBJECTIVES To measure the burden of diseases, injuries, and leading risk factors in the United States from 1990 to 2010 and to compare these measurements with those of the 34 countries in the Organisation for Economic Co-operation and Development (OECD) countries.   \n", "DESIGN We used the systematic analysis of descriptive epidemiology of 291 diseases and injuries, 1160 sequelae of these diseases and injuries, and 67 risk factors or clusters of risk factors from 1990 to 2010 for 187 countries developed for the Global Burden of Disease 2010 Study to describe the health status of the United States and to compare US health outcomes with those of 34 OECD countries.", "Years of life lost due to premature mortality (YLLs) were computed by multiplying the number of deaths at each age by a reference life expectancy at that age.", "Years lived with disability (YLDs) were calculated by multiplying prevalence (based on systematic reviews) by the disability weight (based on population-based surveys) for each sequela; disability in this study refers to any short- or long-term loss of health.", "Disability-adjusted life-years (DALYs) were estimated as the sum of YLDs and YLLs.", "Deaths and DALYs related to risk factors were based on systematic reviews and meta-analyses of exposure data and relative risks for risk-outcome pairs.", "Healthy life expectancy (HALE) was used to summarize overall population health, accounting for both length of life and levels of ill health experienced at different ages.   \n", "RESULTS US life expectancy for both sexes combined increased from 75.2 years in 1990 to 78.2 years in 2010; during the same period, HALE increased from 65.8 years to 68.1 years.", "The diseases and injuries with the largest number of YLLs in 2010 were ischemic heart disease, lung cancer, stroke, chronic obstructive pulmonary disease, and road injury.", "Age-standardized YLL rates increased for Alzheimer disease, drug use disorders, chronic kidney disease, kidney cancer, and falls.", "The diseases with the largest number of YLDs in 2010 were low back pain, major depressive disorder, other musculoskeletal disorders, neck pain, and anxiety disorders.", "As the US population has aged, YLDs have comprised a larger share of DALYs than have YLLs.", "The leading risk factors related to DALYs were dietary risks, tobacco smoking, high body mass index, high blood pressure, high fasting plasma glucose, physical inactivity, and alcohol use.", "Among 34 OECD countries between 1990 and 2010, the US rank for the age-standardized death rate changed from 18th to 27th, for the age-standardized YLL rate from 23rd to 28th, for the age-standardized YLD rate from 5th to 6th, for life expectancy at birth from 20th to 27th, and for HALE from 14th to 26th.   \n", "CONCLUSIONS AND RELEVANCE From 1990 to 2010, the United States made substantial progress in improving health.", "Life expectancy at birth and HALE increased, all-cause death rates at all ages decreased, and age-specific rates of years lived with disability remained stable.", "However, morbidity and chronic disability now account for nearly half of the US health burden, and improvements in population health in the United States have not kept pace with advances in population health in other wealthy nations."], "structured": true}
{"doc_id": 8593263, "title": "Malaria risk perception, knowledge and prophylaxis practices among travellers of African ethnicity living in Paris and visiting their country of origin in sub-Saharan Africa.", "abstract": ["An observational prospective cohort study assessed malaria risk perception, knowledge and prophylaxis practices among individuals of African ethnicity living in Paris and travelling to their country of origin to visit friends or relatives (VFR).", "The study compared two groups of VFR who had visited a travel clinic (TC; n=122) or a travel agency (TA; n=69) before departure.", "Of the 47% of VFR citing malaria as a health concern, 75% knew that malaria is mosquito-borne and that bed nets are an effective preventive measure.", "Perception of high malaria risk was greater in the TA group (33%) than in the TC group (7%).", "The availability of a malaria vaccine was mentioned by 35% of VFR, with frequent confusion between yellow fever vaccine and malaria prevention.", "Twenty-nine percent took adequate chemoprophylaxis with complete adherence, which was higher among the TC group (41%) than the TA group (12%).", "Effective antivector protection measures used were bed nets (16%), wearing long clothes at night (14%) and air conditioning (8%), with no differences between the study groups except in the use of impregnated bed nets (11% of the TC group and none of the TA group).", "Media coverage, malaria chemoprophylaxis repayment and cultural adaptation of preventive messages should be improved to reduce the high rate of inadequate malaria prophylaxis in VFR."], "structured": false}
{"doc_id": 8595678, "title": "Effect modification by population dietary folate on the association between MTHFR genotype, homocysteine, and stroke risk: a meta-analysis of genetic studies and randomised trials", "abstract": ["BACKGROUND The MTHFR 677C\u2192T polymorphism has been associated with raised homocysteine concentration and increased risk of stroke.", "A previous overview showed that the effects were greatest in regions with low dietary folate consumption, but differentiation between the effect of folate and small-study bias was difficult.", "A meta-analysis of randomised trials of homocysteine-lowering interventions showed no reduction in coronary heart disease events or stroke, but the trials were generally set in populations with high folate consumption.", "We aimed to reduce the effect of small-study bias and investigate whether folate status modifies the association between MTHFR 677C\u2192T and stroke in a genetic analysis and meta-analysis of randomised controlled trials.   \n", "METHODS We established a collaboration of genetic studies consisting of 237 datasets including 59,995 individuals with data for homocysteine and 20,885 stroke events.", "We compared the genetic findings with a meta-analysis of 13 randomised trials of homocysteine-lowering treatments and stroke risk (45,549 individuals, 2314 stroke events, 269 transient ischaemic attacks).   \n", "FINDINGS The effect of the MTHFR 677C\u2192T variant on homocysteine concentration was larger in low folate regions (Asia; difference between individuals with TT versus CC genotype, 3\u00b712 \u03bcmol/L, 95% CI 2\u00b723 to 4\u00b701) than in areas with folate fortification (America, Australia, and New Zealand, high; 0\u00b713 \u03bcmol/L, -0\u00b785 to 1\u00b711).", "The odds ratio (OR) for stroke was also higher in Asia (1\u00b768, 95% CI 1\u00b744 to 1\u00b797) than in America, Australia, and New Zealand, high (1\u00b703, 0\u00b784 to 1\u00b725).", "Most randomised trials took place in regions with high or increasing population folate concentrations.", "The summary relative risk (RR) of stroke in trials of homocysteine-lowering interventions (0\u00b794, 95% CI 0\u00b785 to 1\u00b704) was similar to that predicted for the same extent of homocysteine reduction in large genetic studies in populations with similar folate status (predicted RR 1\u00b700, 95% CI 0\u00b790 to 1\u00b711).", "Although the predicted effect of homocysteine reduction from large genetic studies in low folate regions (Asia) was larger (RR 0\u00b778, 95% CI 0\u00b768 to 0\u00b790), no trial has evaluated the effect of lowering of homocysteine on stroke risk exclusively in a low folate region.   \n", "INTERPRETATION In regions with increasing levels or established policies of population folate supplementation, evidence from genetic studies and randomised trials is concordant in suggesting an absence of benefit from lowering of homocysteine for prevention of stroke.", "Further large-scale genetic studies of the association between MTHFR 677C\u2192T and stroke in low folate settings are needed to distinguish effect modification by folate from small-study bias.", "If future randomised trials of homocysteine-lowering interventions for stroke prevention are undertaken, they should take place in regions with low folate consumption.   \n", "FUNDING Full funding sources listed at end of paper (see Acknowledgments)."], "structured": true}
{"doc_id": 8596357, "title": "Porcine circovirus type 2 DNA influences cytoskeleton rearrangements in plasmacytoid and monocyte-derived dendritic cells.", "abstract": ["Functional disruption of dendritic cells (DC) is an important strategy for viral pathogens to evade host defences.", "In this context, porcine circovirus type 2 (PCV2), a single-stranded DNA virus, impairs plasmacytoid DC (pDC) and conventional DC activation by certain viruses or Toll-like receptor (TLR) ligands.", "This inhibitory capacity is associated with the viral DNA, but the impairment does not affect all signalling cascades; TLR7 ligation by small chemical molecules will still induce interleukin-6 (IL-6) and tumour necrosis factor-\u03b1 secretion, but not interferon-\u03b1 or IL-12.", "In this study, the molecular mechanisms by which silencing occurs were investigated.", "PP2, a potent inhibitor of the Lyn and Hck kinases, produced a similar profile to the PCV2 DNA interference with cytokine secretion by pDC, efficiently inhibiting cell activation induced through TLR9, but not TLR7, ligation.", "Confocal microscopy and cytometry analysis strongly suggested that PCV2 DNA impairs actin polymerization and endocytosis in pDC and monocyte-derived DC, respectively.", "Altogether, this study delineates for the first time particular molecular mechanisms involved in PCV2 interference with DC danger recognition, which may be responsible for the virus-induced immunosuppression observed in infected pigs."], "structured": false}
{"doc_id": 8596837, "title": "Sympathetic neural and cardiovascular responses during static handgrip exercise in women with a history of hypertensive pregnancy", "abstract": ["Women with a history of hypertensive pregnancy are at greater risk for future cardiovascular events; however, the mechanisms for this increased risk are unknown.", "Evidence suggests that an exercise stimulus unmasks latent hypertensive tendencies, identifying individuals at the greatest risk for developing cardiovascular disease.", "The current study examined the hypothesis that women with a hypertensive pregnancy history exhibit an augmented exercise pressor response.", "Normotensive women with a history of healthy pregnancy (CON; n = 9) and hypertensive pregnancy (HP+; n = 12) were studied during the mid-luteal phase of the menstrual cycle.", "Heart rate (HR), systolic and diastolic blood pressure (SBP, DBP), and muscle sympathetic nerve activity (MSNA) were measured during a cold pressor test (CPT), and, following a sufficient period of recovery, during static handgrip to fatigue (SHG) and post-exercise circulatory arrest (PECA).", "The BP, HR, and MSNA responses to the CPT were similar between groups.", "The SBP response to SHG and PECA was similar between groups, but DBP and HR were significantly greater in HP+ women (both p < 0.05).", "MSNA burst frequency, but not burst incidence or total activity, tended to be elevated in HP+ women during the stressor (peak \u0394 from baseline 31 \u00b1 13 vs. 23 \u00b1 13 bursts/min; p for group = 0.06).", "Despite no clinical signs of cardiovascular disease or hypertension, women with a history of hypertensive pregnancy display an enhanced cardiovascular reactivity to an exercise stimulus compared to women with a healthy pregnancy history.", "This response may be indicative of impaired cardiovascular control that precedes the clinical manifestation of hypertension or cardiovascular events."], "structured": false}
{"doc_id": 8604837, "title": "Exercise and the immune system: regulation, integration, and adaptation.", "abstract": ["Stress-induced immunological reactions to exercise have stimulated much research into stress immunology and neuroimmunology.", "It is suggested that exercise can be employed as a model of temporary immunosuppression that occurs after severe physical stress.", "The exercise-stress model can be easily manipulated experimentally and allows for the study of interactions between the nervous, the endocrine, and the immune systems.", "This review focuses on mechanisms underlying exercise-induced immune changes such as neuroendocrinological factors including catecholamines, growth hormone, cortisol, beta-endorphin, and sex steroids.", "The contribution of a metabolic link between skeletal muscles and the lymphoid system is also reviewed.", "The mechanisms of exercise-associated muscle damage and the initiation of the inflammatory cytokine cascade are discussed.", "Given that exercise modulates the immune system in healthy individuals, considerations of the clinical ramifications of exercise in the prevention of diseases for which the immune system has a role is of importance.", "Accordingly, drawing on the experimental, clinical, and epidemiological literature, we address the interactions between exercise and infectious diseases as well as exercise and neoplasia within the context of both aging and nutrition."], "structured": false}
{"doc_id": 8610932, "title": "Positive feedback between PU.1 and the cell cycle controls myeloid differentiation.", "abstract": ["Regulatory gene circuits with positive-feedback loops control stem cell differentiation, but several mechanisms can contribute to positive feedback.", "Here, we dissect feedback mechanisms through which the transcription factor PU.1 controls lymphoid and myeloid differentiation.", "Quantitative live-cell imaging revealed that developing B cells decrease PU.1 levels by reducing PU.1 transcription, whereas developing macrophages increase PU.1 levels by lengthening their cell cycles, which causes stable PU.1 accumulation.", "Exogenous PU.1 expression in progenitors increases endogenous PU.1 levels by inducing cell cycle lengthening, implying positive feedback between a regulatory factor and the cell cycle.", "Mathematical modeling showed that this cell cycle-coupled feedback architecture effectively stabilizes a slow-dividing differentiated state.", "These results show that cell cycle duration functions as an integral part of a positive autoregulatory circuit to control cell fate."], "structured": false}
{"doc_id": 8629328, "title": "Peripheral B cell subsets.", "abstract": ["Our understanding of the origins and the biological functions of different peripheral B cell subsets continues to evolve.", "Some understanding has been obtained regarding the synergy between BCR-derived signals and other receptors and signaling pathways that drive the development of follicular, marginal zone, and B-1 B cells, but this remains a complex and poorly understood issue.", "More recent information regarding the origins of B-1 and B-2 B cells, the ability of follicular B cells to mature both in the bone marrow and the spleen, the existence of a definable precursor for MZ B cells, and the ability of follicular B cells to occupy two distinct niches are all highlighted in this review."], "structured": false}
{"doc_id": 8639034, "title": "Human IL-10 is produced by both type 1 helper (Th1) and type 2 helper (Th2) T cell clones and inhibits their antigen-specific proliferation and cytokine production.", "abstract": ["IL-10 gene transcription and IL-10 protein production was assessed in both type 1 (Th1) and type 2 (Th2) CD4+ human T cell clones by polymerase chain reaction and ELISA, respectively.", "Although Th2 clones apparently showed higher IL-10 mRNA levels, IL-10 mRNA expression was consistently found in Th1 clones, as well.", "Likewise, measurable IL-10 levels were found in the supernatants of both Th1 and Th2 clones.", "The effect of human IL-10 (h-IL-10) and viral IL-10 (v-IL-10) on the proliferative response and cytokine production by Th1 and Th2 human clones was also investigated.", "Addition in culture of h-IL-10 and v-IL-10 significantly reduced the proliferation of both Th1 and Th2 clones in response to the specific Ag and to PHA, but it had no inhibitory effect on the proliferative response of Th1 and Th2 clones to IL-2.", "h-IL-10 and v-IL-10 also inhibited the Ag-induced production of gamma-interferon (IFN-gamma) by Th1 clones and the production of IL-4 and IL-5 by Th2 clones, whereas they had no effect on the cytokine synthesis by the same clones stimulated with PMA plus anti-CD3 antibody.", "Preincubation of APC, but not of clonal T blasts, with h-IL-10 resulted in the inhibition of Ag-induced proliferation of both Th1 and Th2 clones, supporting the view that h-IL-10 primarily affects APC.", "These data demonstrate that, unlike the murine system where IL-10 is a product of Th2 (but not Th1) cells and seems to mainly down-regulate the Th1 response, in the human system, IL-10 is produced by, and down-regulates the function of, both Th1 and Th2 cells."], "structured": false}
{"doc_id": 8642784, "title": "Evaluating strategies for improving ovarian response of the poor responder undergoing assisted reproductive techniques.", "abstract": ["OBJECTIVE To assess the efficacy of various controlled ovarian hyperstimulation (COH) regimens in the prior poor-responder patient preparing for assisted reproductive techniques.   \n", "DESIGN English-language literature review.   \n", "PATIENT(S) Candidates for assisted reproductive techniques who had been defined as having a prior suboptimal response to standard COH regimens.   \n", "INTERVENTION(S) A variety of regimes are reviewed, including increased gonadotropin doses, change of gonadotropins, adjunctive growth hormone (GH), luteal phase (long) GnRH agonist (GnRH-a) initiation, early follicular phase (flare) GnRH-a initiation, low-dose luteal phase (ultrashort) GnRH-a initiation, progestin pretreatment, and microdose flare GnRH-a initiation.   \n", "MAIN OUTCOME MEASURE(S)", "Maximal serum E(2) levels, follicular development, dose, and duration of gonadotropin therapy, cycle cancellation rates, oocytes retrieved, embryos transferred, and clinical and ongoing pregnancy rates.   \n", "RESULT(S) A lack of uniformity in definition of the poor responder and of prospective randomized trials make data interpretation somewhat difficult.", "Of the varied strategies proposed, those that seem to be more uniformly beneficial are microdose GnRH-a flare and late luteal phase initiation of a short course of low-dose GnRH-a discontinued before COH.   \n", "CONCLUSION(S) No single regimen will benefit all poor responders.", "General acceptance of uniform definitions and performance of large-scale prospective randomized trials are critical.", "Development of a reliable precycle screen will allow effective differentiation among normal responders, poor responders, and those who will not conceive with their own oocytes."], "structured": true}
{"doc_id": 8646760, "title": "Identification and Functional Characterization of N-Terminally Acetylated Proteins in Drosophila melanogaster", "abstract": ["Protein modifications play a major role for most biological processes in living organisms.", "Amino-terminal acetylation of proteins is a common modification found throughout the tree of life: the N-terminus of a nascent polypeptide chain becomes co-translationally acetylated, often after the removal of the initiating methionine residue.", "While the enzymes and protein complexes involved in these processes have been extensively studied, only little is known about the biological function of such N-terminal modification events.", "To identify common principles of N-terminal acetylation, we analyzed the amino-terminal peptides from proteins extracted from Drosophila Kc167 cells.", "We detected more than 1,200 mature protein N-termini and could show that N-terminal acetylation occurs in insects with a similar frequency as in humans.", "As the sole true determinant for N-terminal acetylation we could extract the (X)PX rule that indicates the prevention of acetylation under all circumstances.", "We could show that this rule can be used to genetically engineer a protein to study the biological relevance of the presence or absence of an acetyl group, thereby generating a generic assay to probe the functional importance of N-terminal acetylation.", "We applied the assay by expressing mutated proteins as transgenes in cell lines and in flies.", "Here, we present a straightforward strategy to systematically study the functional relevance of N-terminal acetylations in cells and whole organisms.", "Since the (X)PX rule seems to be of general validity in lower as well as higher eukaryotes, we propose that it can be used to study the function of N-terminal acetylation in all species."], "structured": false}
{"doc_id": 8654183, "title": "Bax translocation and mitochondrial fragmentation induced by Helicobacter pylori.", "abstract": ["BACKGROUND AND AIMS Previous in vitro and in vivo studies have revealed an association between Helicobacter pylori infection and apoptosis in gastric epithelial cells.", "Although involvement of the Bcl-2 family of proteins as well as cytochrome c release has been demonstrated in H pylori induced cell death, the exact role of the mitochondria during this type of programmed cell death has not been fully elucidated.", "Therefore, we sought to determine whether or not Bax translocation and mitochondrial fragmentation occur on exposure of gastric epithelial cells to H pylori, resulting in cell death.   \n", "METHODS Experiments were performed with human gastric adenocarcinoma (AGS) cells, AGS cells transfected with the HPV-E6 gene (which inactivates p53 function), AGS-neo cells (transfected with the backbone construct), mouse embryonic fibroblasts (MEFs), and p19(ARF) null (ARF(-/-)) MEFs.", "Cells were incubated with a cag positive H pylori strain for up to 24 hours, lysed, and cytoplasmic and mitochondrial membrane fractions were analysed by western blot for Bax translocation.   \n", "RESULTS Bax translocation was detected in AGS, AGS-neo, and normal MEF cells after exposure to H pylori for three hours, but not in ARF(-/-) MEFs cells.", "Translocation of Bax after H pylori incubation was also detected in AGS-E6 cells (inactive p53 gene) but to a lesser degree than in AGS-neo cells.", "In parallel studies, the mitochondrial morphology of living cells infected with H pylori was assessed by confocal microscopy.", "Mitochondrial fragmentation was detectable after 10 hours of H pylori incubation with AGS cells and after seven hours with MEF cells.", "In wild-type MEFs, mitochondrial fragmentation was significantly increased in comparison with ARF null MEFs (43% v 10.4%, respectively).", "Furthermore, mitochondrial depolarisation and caspase-3 activity were initiated within four hours in cells incubated with H pylori, and these events were inhibited by forced expression of Bcl-2.   \n", "CONCLUSIONS These data suggest that during H pylori induced apoptosis, Bax translocates to the mitochondria which subsequently undergo depolarisation and profound fragmentation.", "Functional ARF and p53 proteins may play an important role in H pylori induced mitochondrial modification."], "structured": true}
{"doc_id": 8659426, "title": "Cancer chemoprevention: a rapidly evolving field", "abstract": ["Cancer chemoprevention involves the chronic administration of a synthetic, natural or biological agent to reduce or delay the occurrence of malignancy.", "The potential value of this approach has been demonstrated with trials in breast, prostate and colon cancer.", "The paradigm for developing new chemopreventive agents has changed markedly in the last decade and now involves extensive preclinical mechanistic evaluation of agents before clinical trials are instituted and a focus on defining biomarkers of activity that can be used as early predictors of efficacy.", "This review will summarise the current status of the field of chemoprevention and highlight potential new developments."], "structured": false}
{"doc_id": 8665891, "title": "Dengue is still an imported disease in China: a case study in Guangzhou.", "abstract": ["Dengue virus and its four serotypes (DENV 1-4) infect approximately 390 million people worldwide each year, with most cases in tropical and subtropical regions.", "Because of repeated introduction of DENV from epidemic regions and suitable weather conditions, many regions have shifted from hypo-endemicity to hyper-endemicity over recent decades.", "Since the first dengue outbreak in 1978, it is crucial to understand the current situation in China over nearly 40 years.", "The purpose of the study was to examine whether dengue in China was endemic or not, which is essential for relevant dengue control and prevention strategy implementation in China.", "The study, combining epidemiological characteristics of dengue from the disease notification system, phylogenetic and phylogeographic analyses, showed that all four serotypes had been detected in Guangzhou, China, which was dominated by DENV 1-2.", "The Maximum Likelihood tree analytic results showed that the virus detected in Guangzhou localized in different clades, except of virus of 2002 and 2003 clustered together.", "There existed the mutual introductions between Guangzhou and Southeast Asia.", "Most of the viruses were imported from Southeast Asia and the sources of outbreaks in Guangzhou mainly originated from Thailand, Indonesia, and the Philippines.", "The study indicates that dengue in China still remains as an imported disease, with the possibility of localization."], "structured": false}
{"doc_id": 8670178, "title": "The UNAIDS Estimation and Projection Package: a software package to estimate and project national HIV epidemics.", "abstract": ["This paper describes the Estimation and Projection Package (EPP) for estimating and projecting HIV prevalence levels in countries with generalised epidemics.", "The paper gives an overall summary of the software and interface.", "It describes the process of defining and modelling a national epidemic in terms of locally relevant sub-epidemics and the four epidemiological parameters used to fit a curve to produce the prevalence trends in the epidemic.", "It also provides an example of using the EPP in a country with a generalised epidemic.", "The paper discusses the strengths and weaknesses of the software and its envisaged future developments."], "structured": false}
{"doc_id": 8671456, "title": "Oncolytic adenovirus armed with IL-24 Inhibits the growth of breast cancer in vitro and in vivo", "abstract": ["BACKGROUND Interleukin-24 (IL-24) is a cytokine that belongs to the IL-10 family.", "It can selectively induce cancer cell apoptosis which has been utilized as a cancer gene therapy strategy.   \n", "METHODS A recombinant type five adenovirus containing IL-24 gene (designated CNHK600-IL24) was constructed, whose replication is activated only in tumor cells.", "The replication of CNHK600-IL24 in breast tumor cells and fibroblasts were assessed by TCID50 and MTT assay; the secretion of IL-24 was measured by ELISA and western blotting.", "The in vivo anti-tumor effect of CNHK600-IL24 was investigated in nude mice carrying orthotopic or metastatic breast tumor.   \n", "RESULTS We observed that CNHK600-IL24 could replicate efficiently and resulted in high level IL-24 expression and massive cell death in human breast cancer cell MDA-MB-231 but not in normal fibroblast cell MRC-5.", "In addition, orthotopic breast tumor growth in the nude mice model was significantly suppressed when CNHK600-IL24 was administered.", "In the metastatic model generated by tail vein injection, CNHK600-IL24 virotherapy significantly improved survival compared with the same virus expressing EGFP (median survival CNHK600-IL24, 55 days vs. CNHK600-EGFP, 41 day, p < 0.05 Mantal-Cox test).", "A similar phenomenon was observed in the metastatic model achieved by left ventricular injection as suggested by in vivo luminescence imaging of tumor growth.   \n", "CONCLUSION The oncolytic adenovirus armed with IL-24, which exhibited enhanced anti-tumor activity and improved survival, is a promising candidate for virotherapy of breast cancer."], "structured": true}
{"doc_id": 8672737, "title": "Brain stem and cerebellar hyperintense lesions in migraine.", "abstract": ["BACKGROUND AND PURPOSE Migraineurs are at increased risk of cerebellar infarcts and supratentorial white matter lesions.", "The prevalence, frequency, and distribution of infratentorial hyperintense lesions in migraine are unknown.   \n", "METHODS Migraineurs with aura (n=161), without aura (n=134), and controls (n=140) from a population-based sample of adults (30 to 60 years of age) were evaluated with MRI.   \n", "RESULTS Infratentorial hyperintensities were identified in 13 of 295 (4.4%) migraineurs and in 1 of 140 (0.7%) controls (P=0.04).", "Twelve cases had hyperintensities, mostly bilaterally, in the dorsal basis pontis.", "Those with infratentorial hyperintensities also had supratentorial white matter lesions more often.   \n", "CONCLUSIONS We found an increased prevalence of infratentorial (mostly pontine) hyperintensities in migraineurs from the general population.", "This extends the knowledge about vulnerable brain regions and type of lesions in migraine brains.", "A hemodynamic ischemic pathogenesis is likely, but further research is needed."], "structured": true}
{"doc_id": 8677721, "title": "NDRG1 promotes growth of hepatocellular carcinoma cells by directly interacting with GSK-3\u03b2 and Nur77 to prevent \u03b2-catenin degradation", "abstract": ["The N-myc downstream regulated gene 1 (NDRG1) is significantly associated with advanced tumor stages and poor survival of hepatocellular carcinoma (HCC), thereby implicating it as a potential target for HCC treatment.", "We aim to further understand its biological roles in hepatocarcinogenesis, as a means to exploit it for therapeutic purposes.", "By screening using the ProtoArray\u00ae Human Protein Microarrays, we identified glycogen synthase kinase 3\u03b2 (GSK-3\u03b2) and the orphan nuclear receptor (Nur77) as potential interaction partners of NDRG1.", "These interactions were confirmed in HCC cell lines in vitro by co-immunoprecipitation; and co-localizations of NDRG1 with GSK-3\u03b2 and Nur77 were observed by immunofluorescence staining.", "Additionally, high levels of NDRG1 competitively bind to GSK-3\u03b2 and Nur77 to allow \u03b2-catenin to escape degradation, with consequent elevated levels of downstream oncogenic genes.", "In vivo, we consistently observed that NDRG1 suppression in HCC xenografts decreased \u03b2-catenin levels and its downstream target Cyclin D1, with concomitant tumor growth inhibition.", "Clinically, the over-expression of NDRG1 in HCC patient samples is positively correlated with GSK-3\u03b2-9ser (|\u0094\u0082 R | = 0.28, p = 0.01), Nur77 (|\u0094\u0082 R | = 0.42, p < 0.001), and \u03b2-catenin (| R |= 0.32, p = 0.003) expressions.", "In conclusion, we identified GSK-3\u03b2 and Nur77 as novel interaction partners of NDRG1.", "These protein-protein interactions regulate the turnover of \u03b2-catenin and subsequent downstream signaling mediated by \u03b2-catenin in HCC cells, and provides potential targets for future therapeutic interventions."], "structured": false}
{"doc_id": 8690595, "title": "A tutorial on statistical methods for population association studies", "abstract": ["Although genetic association studies have been with us for many years, even for the simplest analyses there is little consensus on the most appropriate statistical procedures.", "Here I give an overview of statistical approaches to population association studies, including preliminary analyses (Hardy\u2013Weinberg equilibrium testing, inference of phase and missing data, and SNP tagging), and single-SNP and multipoint tests for association.", "My goal is to outline the key methods with a brief discussion of problems (population structure and multiple testing), avenues for solutions and some ongoing developments."], "structured": false}
{"doc_id": 8692744, "title": "Identification and Characterization of Multiple TRIM Proteins That Inhibit Hepatitis B Virus Transcription", "abstract": ["Tripartite motif (TRIM) proteins constitute a family of over 100 members that share conserved tripartite motifs and exhibit diverse biological functions.", "Several TRIM proteins have been shown to restrict viral infections and regulate host cellular innate immune responses.", "In order to identify TRIM proteins that modulate the infection of hepatitis B virus (HBV), we tested 38 human TRIMs for their effects on HBV gene expression, capsid assembly and DNA synthesis in human hepatoma cells (HepG2).", "The study revealed that ectopic expression of 8 TRIM proteins in HepG2 cells potently reduced the amounts of secreted HBV surface and e antigens as well as intracellular capsid and capsid DNA.", "Mechanistic analyses further demonstrated that the 8 TRIMs not only reduced the expression of HBV mRNAs, but also inhibited HBV enhancer I and enhancer II activities.", "Studies focused on TRIM41 revealed that a HBV DNA segment spanning nucleotide 1638 to nucleotide 1763 was essential for TRIM41-mediated inhibition of HBV enhancer II activity and the inhibitory effect depended on the E3 ubiquitin ligase activity of TRIM41 as well as the integrity of TRIM41 C-terminal domain.", "Moreover, knockdown of endogenous TRIM41 in a HepG2-derived stable cell line significantly increased the level of HBV preC/C RNA, leading to an increase in viral core protein, capsid and capsid DNA.", "Our studies have thus identified eight TRIM proteins that are able to inhibit HBV transcription and provided strong evidences suggesting the endogenous role of TRIM41 in regulating HBV transcription in human hepatoma cells."], "structured": false}
{"doc_id": 8698208, "title": "A mouse Mecp2-null mutation causes neurological symptoms that mimic Rett syndrome", "abstract": ["Rett syndrome (RTT) is an inherited neurodevelopmental disorder of females that occurs once in 10,000\u201315,000 births.", "Affected females develop normally for 6\u201318 months, but then lose voluntary movements, including speech and hand skills.", "Most RTT patients are heterozygous for mutations in the X-linked gene MECP2 (refs.", "3\u201312), encoding a protein that binds to methylated sites in genomic DNA and facilitates gene silencing.", "Previous work with Mecp2-null embryonic stem cells indicated that MeCP2 is essential for mouse embryogenesis.", "Here we generate mice lacking Mecp2 using Cre-loxP technology.", "Both Mecp2-null mice and mice in which Mecp2 was deleted in brain showed severe neurological symptoms at approximately six weeks of age.", "Compensation for absence of MeCP2 in other tissues by MeCP1 (refs.", "19,20) was not apparent in genetic or biochemical tests.", "After several months, heterozygous female mice also showed behavioral symptoms.", "The overlapping delay before symptom onset in humans and mice, despite their profoundly different rates of development, raises the possibility that stability of brain function, not brain development per se, is compromised by the absence of MeCP2."], "structured": false}
{"doc_id": 8698857, "title": "The p38/MK2-Driven Exchange between Tristetraprolin and HuR Regulates AU\u2013Rich Element\u2013Dependent Translation", "abstract": ["TNF expression of macrophages is under stringent translational control that depends on the p38 MAPK/MK2 pathway and the AU-rich element (ARE) in the TNF mRNA.", "Here, we elucidate the molecular mechanism of phosphorylation-regulated translation of TNF.", "We demonstrate that translation of the TNF-precursor at the ER requires expression of the ARE-binding and -stabilizing factor human antigen R (HuR) together with either activity of the p38 MAPK/MK2 pathway or the absence of the ARE-binding and -destabilizing factor tristetraprolin (TTP).", "We show that phosphorylation of TTP by MK2 decreases its affinity to the ARE, inhibits its ability to replace HuR, and permits HuR-mediated initiation of translation of TNF mRNA.", "Since translation of TTP's own mRNA is also regulated by this mechanism, an intrinsic feedback control of the inflammatory response is ensured.", "The phosphorylation-regulated TTP/HuR exchange at target mRNAs provides a reversible switch between unstable/non-translatable and stable/efficiently translated mRNAs."], "structured": false}
{"doc_id": 8702697, "title": "miR-205 hinders the malignant interplay between prostate cancer cells and associated fibroblasts.", "abstract": ["AIMS Tumor microenvironment is a strong determinant for the acquisition of metastatic potential of cancer cells.", "We have recently demonstrated that cancer-associated fibroblasts (CAFs) elicit a redox-dependent epithelial-mesenchymal transition (EMT) in prostate cancer (PCa) cells, driven by cycloxygenase-2/hypoxia-inducible factor-1 (HIF-1)/nuclear factor-\u03baB pathway and enhancing tumor aggressiveness.", "Here, we investigated the involvement of microRNAs (miRNAs) in tumor-stroma interplay to identify possible tools to counteract oxidative stress and metastasis dissemination.   \n", "RESULTS We found that miR-205 is the most downmodulated miRNA in PCa cells upon CAF stimulation, due to direct transcriptional repression by HIF-1, a known redox-sensitive transcription factor.", "Rescue experiments demonstrated that ectopic miR-205 overexpression in PCa cells counteracts CAF-induced EMT, thus impairing enhancement of cell invasion, acquisition of stem cell traits, tumorigenicity, and metastatic dissemination.", "In addition, miR-205 blocks tumor-driven activation of surrounding fibroblasts by reducing pro-inflammatory cytokine secretion.   ", "INNOVATION Overall, such findings suggest miR-205 as a brake against PCa metastasis by blocking both the afferent and efferent arms of the circuit between tumor cells and associated fibroblasts, thus interrupting the pro-oxidant and pro-inflammatory circuitries engaged by reactive stroma.   \n", "CONCLUSION The evidence that miR-205 replacement in PCa cells is able not only to prevent but also to revert the oxidative/pro-inflammatory axis leading to EMT induced by CAFs sets the rationale for developing miRNA-based approaches to prevent and treat metastatic disease."], "structured": true}
{"doc_id": 8708082, "title": "The prevention of type 2 diabetes", "abstract": ["Type 2 diabetes mellitus (T2DM) affects more than 7% of adults in the US and leads to substantial personal and economic burden.", "In prediabetic states insulin secretion and action\u2014potential targets of preventive interventions\u2014are impaired.", "In trials lifestyle modification (i.e. weight loss and exercise) has proven effective in preventing incident T2DM in high-risk groups, although weight loss has the greatest effect.", "Various medications (e.g. metformin, thiazolidinediones and acarbose) can also prevent or delay T2DM.", "Whether diabetes-prevention strategies also ultimately prevent the development of diabetic vascular complications is unknown, but cardiovascular risk factors are favorably affected.", "Preventive strategies that can be implemented in routine clinical settings have been developed and evaluated.", "Widespread application has, however, been limited by local financial considerations, even though cost-effectiveness might be achieved at the population level."], "structured": false}
{"doc_id": 8712839, "title": "The transcriptional landscape of the mammalian genome.", "abstract": ["This study describes comprehensive polling of transcription start and termination sites and analysis of previously unidentified full-length complementary DNAs derived from the mouse genome.", "We identify the 5' and 3' boundaries of 181,047 transcripts with extensive variation in transcripts arising from alternative promoter usage, splicing, and polyadenylation.", "There are 16,247 new mouse protein-coding transcripts, including 5154 encoding previously unidentified proteins.", "Genomic mapping of the transcriptome reveals transcriptional forests, with overlapping transcription on both strands, separated by deserts in which few transcripts are observed.", "The data provide a comprehensive platform for the comparative analysis of mammalian transcriptional regulation in differentiation and development."], "structured": false}
{"doc_id": 8721150, "title": "The Protein Data Bank", "abstract": ["The Protein Data Bank [PDB; Berman, Westbrook et al. (2000), Nucleic Acids Res. 28, 235-242; http://www.pdb.org/] is the single worldwide archive of primary structural data of biological macromolecules.", "Many secondary sources of information are derived from PDB data.", "It is the starting point for studies in structural bioinformatics.", "This article describes the goals of the PDB, the systems in place for data deposition and access, how to obtain further information and plans for the future development of the resource.", "The reader should come away with an understanding of the scope of the PDB and what is provided by the resource."], "structured": false}
{"doc_id": 8724666, "title": "Cell-State-Specific Metabolic Dependency in Hematopoiesis and Leukemogenesis", "abstract": ["The balance between oxidative and nonoxidative glucose metabolism is essential for a number of pathophysiological processes.", "By deleting enzymes that affect aerobic glycolysis with different potencies, we examine how modulating glucose metabolism specifically affects hematopoietic and leukemic cell populations.", "We find that a deficiency in the M2 pyruvate kinase isoform (PKM2) reduces the levels of metabolic intermediates important for biosynthesis and impairs progenitor function without perturbing hematopoietic stem cells (HSCs), whereas lactate dehydrogenase A (LDHA) deletion significantly inhibits the function of both HSCs and progenitors during hematopoiesis.", "In contrast, leukemia initiation by transforming alleles putatively affecting either HSCs or progenitors is inhibited in the absence of either PKM2 or LDHA, indicating that the cell-state-specific responses to metabolic manipulation in hematopoiesis do not apply to the setting of leukemia.", "This finding suggests that fine-tuning the level of glycolysis may be explored therapeutically for treating leukemia while preserving HSC function."], "structured": false}
{"doc_id": 8734695, "title": "A transition in brain state during propofol-induced unconsciousness.", "abstract": ["Rhythmic oscillations shape cortical dynamics during active behavior, sleep, and general anesthesia.", "Cross-frequency phase-amplitude coupling is a prominent feature of cortical oscillations, but its role in organizing conscious and unconscious brain states is poorly understood.", "Using high-density EEG and intracranial electrocorticography during gradual induction of propofol general anesthesia in humans, we discovered a rapid drug-induced transition between distinct states with opposite phase-amplitude coupling and different cortical source distributions.", "One state occurs during unconsciousness and may be similar to sleep slow oscillations.", "A second state occurs at the loss or recovery of consciousness and resembles an enhanced slow cortical potential.", "These results provide objective electrophysiological landmarks of distinct unconscious brain states, and could be used to help improve EEG-based monitoring for general anesthesia."], "structured": false}
{"doc_id": 8747771, "title": "Cohesins and condensins orchestrate the 4D dynamics of yeast chromosomes during the cell cycle", "abstract": ["Duplication and segregation of chromosomes involves dynamic reorganization of their internal structure by conserved architectural proteins, including the structural maintenance of chromosomes (SMC) complexes cohesin and condensin.", "Despite active investigation of the roles of these factors, a genome-wide view of dynamic chromosome architecture at both small and large scale during cell division is still missing.", "Here, we report the first comprehensive 4D analysis of the higher-order organization of the Saccharomyces cerevisiae genome throughout the cell cycle and investigate the roles of SMC complexes in controlling structural transitions.", "During replication, cohesion establishment promotes numerous long-range intra-chromosomal contacts and correlates with the individualization of chromosomes, which culminates at metaphase.", "In anaphase, mitotic chromosomes are abruptly reorganized depending on mechanical forces exerted by the mitotic spindle.", "Formation of a condensin-dependent loop bridging the centromere cluster with the rDNA loci suggests that condensin-mediated forces may also directly facilitate segregation.", "This work therefore comprehensively recapitulates cell cycle-dependent chromosome dynamics in a unicellular eukaryote, but also unveils new features of chromosome structural reorganization during highly conserved stages of cell division."], "structured": false}
{"doc_id": 8748720, "title": "Genome-wide patterns of divergence and gene flow across a butterfly radiation.", "abstract": ["The Heliconius butterflies are a diverse recent radiation comprising multiple levels of divergence with ongoing gene flow between species.", "The recently sequenced genome of Heliconius melpomene allowed us to investigate the genomic evolution of this group using dense RAD marker sequencing.", "Phylogenetic analysis of 54 individuals robustly supported reciprocal monophyly of H. melpomene and Heliconius cydno and refuted previous phylogenetic hypotheses that H. melpomene may be paraphylectic with respect to H. cydno.", "Heliconius timareta also formed a monophyletic clade closely related but distinct from H. cydno with Heliconius heurippa falling within this clade.", "We find evidence for genetic admixture between sympatric populations of the sister clades H. melpomene and H. cydno/timareta, particularly between H. cydno and H. melpomene from Central America and between H. timareta and H. melpomene from the eastern slopes of the Andes.", "Between races, divergence is primarily explained by isolation by distance and there is no detectable genetic population structure between parapatric races, suggesting that hybrid zones between races are not zones of secondary contact.", "Our results also support previous findings that colour pattern loci are shared between populations and species with similar colour pattern elements.", "Furthermore, this pattern is almost unique to these genomic regions, with only a very small number of other loci showing significant similarity between populations and species with similar colour patterns."], "structured": false}
{"doc_id": 8756719, "title": "Randomized, double-blind study of the safety, tolerability, and efficacy of tafenoquine versus mefloquine for malaria prophylaxis in nonimmune subjects.", "abstract": ["This study represents the first phase III trial of the safety, tolerability, and effectiveness of tafenoquine for malaria prophylaxis.", "In a randomized (3:1), double-blinded study, Australian soldiers received weekly malaria prophylaxis with 200 mg tafenoquine (492 subjects) or 250 mg mefloquine (162 subjects) for 6 months on a peacekeeping deployment to East Timor.", "After returning to Australia, tafenoquine-receiving subjects received a placebo and mefloquine-receiving subjects received 30 mg primaquine daily for 14 days.", "There were no clinically significant differences between hematological and biochemical parameters of the treatment groups.", "Treatment-related adverse events for the two groups were similar (tafenoquine, 13.4%; mefloquine, 11.7%).", "Three subjects on tafenoquine (0.6%) and none on mefloquine discontinued prophylaxis because of possible drug-related adverse events.", "No diagnoses of malaria occurred for either group during deployment, but 4 cases (0.9%) and 1 case (0.7%) of Plasmodium vivax infection occurred among the tafenoquine and mefloquine groups, respectively, up to 20 weeks after discontinuation of medication.", "In a subset of subjects recruited for detailed safety assessments, treatment-related mild vortex keratopathy was detected in 93% (69 of 74) of tafenoquine subjects but none of the 21 mefloquine subjects.", "The vortex keratopathy was not associated with any effect on visual acuity and was fully resolved in all subjects by 1 year.", "Tafenoquine appears to be safe and well tolerated as malaria prophylaxis.", "Although the volunteers' precise exposure to malaria could not be proven in this study, tafenoquine appears to be a highly efficacious drug for malaria prophylaxis."], "structured": false}
{"doc_id": 8759633, "title": "Domain-wide regulation of DNA replication timing during mammalian development", "abstract": ["Studies of replication timing provide a handle into previously impenetrable higher-order levels of chromosome organization and their plasticity during development.", "Although mechanisms regulating replication timing are not clear, novel genome-wide studies provide a thorough survey of the extent to which replication timing is regulated during most of the early cell fate transitions in mammals, revealing coordinated changes of a defined set of 400\u2013800 kb chromosomal segments that involve at least half the genome.", "Furthermore, changes in replication time are linked to changes in sub-nuclear organization and domain-wide transcriptional potential, and tissue-specific replication timing profiles are conserved from mouse to human, suggesting that the program has developmental significance.", "Hence, these studies have provided a solid foundation for linking megabase level chromosome structure to function, and suggest a central role for replication in domain-level genome organization."], "structured": false}
{"doc_id": 8764879, "title": "PU.1-mediated upregulation of CSF1R is crucial for leukemia stem cell potential induced by MOZ-TIF2", "abstract": ["Leukemias and other cancers possess self-renewing stem cells that help to maintain the cancer.", "Cancer stem cell eradication is thought to be crucial for successful anticancer therapy.", "Using an acute myeloid leukemia (AML) model induced by the leukemia-associated monocytic leukemia zinc finger (MOZ)-TIF2 fusion protein, we show here that AML can be cured by the ablation of leukemia stem cells.", "The MOZ fusion proteins MOZ-TIF2 and MOZ-CBP interacted with the transcription factor PU.1 to stimulate the expression of macrophage colony\u2013stimulating factor receptor (CSF1R, also known as M-CSFR, c-FMS or CD115).", "Studies using PU.1-deficient mice showed that PU.1 is essential for the ability of MOZ-TIF2 to establish and maintain AML stem cells.", "Cells expressing high amounts of CSF1R (CSF1Rhigh cells), but not those expressing low amounts of CSF1R (CSF1Rlow cells), showed potent leukemia-initiating activity.", "Using transgenic mice expressing a drug-inducible suicide gene controlled by the CSF1R promoter, we cured AML by ablation of CSF1Rhigh cells.", "Moreover, induction of AML was suppressed in CSF1R-deficient mice and CSF1R inhibitors slowed the progression of MOZ-TIF2\u2013induced leukemia.", "Thus, in this subtype of AML, leukemia stem cells are contained within the CSF1Rhigh cell population, and we suggest that targeting of PU.1-mediated upregulation of CSF1R expression might be a useful therapeutic approach."], "structured": false}
{"doc_id": 8771704, "title": "Pharmacological blockage of fibro/adipogenic progenitor expansion and suppression of regenerative fibrogenesis is associated with impaired skeletal muscle regeneration.", "abstract": ["Acute skeletal muscle injury triggers an expansion of fibro/adipogenic progenitors (FAPs) and a transient stage of fibrogenesis characterized by extracellular matrix deposition.", "While the perpetuation of such phase can lead to permanent tissue scarring, the consequences of its suppression remain to be studied.", "Using a model of acute muscle damage we were able to determine that pharmacological inhibition of FAP expansion by Nilotinib, a tyrosine kinase inhibitor with potent antifibrotic activity, exerts a detrimental effect on myogenesis during regeneration.", "We found that Nilotinib inhibits the damage-induced expansion of satellite cells in vivo, but it does not affect in vitro proliferation, suggesting a non cell-autonomous effect.", "Nilotinib impairs regenerative fibrogenesis by preventing the injury-triggered expansion and differentiation of resident CD45(-):CD31(-):\u03b17integrin(-):Sca1(+) mesenchymal FAPs.", "Our data support the notion that the expansion of FAPs and transient fibrogenesis observed during regeneration play an important trophic role toward tissue-specific stem cells."], "structured": false}
{"doc_id": 8774475, "title": "Deregulation of Scribble Promotes Mammary Tumorigenesis and Reveals a Role for Cell Polarity in Carcinoma", "abstract": ["Loss of cell polarity proteins such as Scribble induces neoplasia in Drosophila by promoting uncontrolled proliferation.", "In mammals, the role that polarity proteins play during tumorigenesis is not well understood.", "Here, we demonstrate that depletion of Scribble in mammary epithelia disrupts cell polarity, blocks three-dimensional morphogenesis, inhibits apoptosis, and induces dysplasia in vivo that progress to tumors after long latency.", "Loss of Scribble cooperates with oncogenes such as c-myc to transform epithelial cells and induce tumors in vivo by blocking activation of an apoptosis pathway.", "Like depletion, mislocalization of Scribble from cell-cell junction was sufficient to promote cell transformation.", "Interestingly, spontaneous mammary tumors in mice and humans possess both downregulated and mislocalized Scribble.", "Thus, we demonstrate that scribble inhibits breast cancer formation and that deregulation of polarity pathways promotes dysplastic and neoplastic growth in mammals by disrupting morphogenesis and inhibiting cell death."], "structured": false}
{"doc_id": 8780599, "title": "The Polymeal: a more natural, safer, and probably tastier (than the Polypill) strategy to reduce cardiovascular disease by more than 75%.", "abstract": ["OBJECTIVE Although the Polypill concept (proposed in 2003) is promising in terms of benefits for cardiovascular risk management, the potential costs and adverse effects are its main pitfalls.", "The objective of this study was to identify a tastier and safer alternative to the Polypill: the Polymeal.   \n", "METHODS Data on the ingredients of the Polymeal were taken from the literature.", "The evidence based recipe included wine, fish, dark chocolate, fruits, vegetables, garlic, and almonds.", "Data from the Framingham heart study and the Framingham offspring study were used to build life tables to model the benefits of the Polymeal in the general population from age 50, assuming multiplicative correlations.   \n", "RESULTS Combining the ingredients of the Polymeal would reduce cardiovascular disease events by 76%.", "For men, taking the Polymeal daily represented an increase in total life expectancy of 6.6 years, an increase in life expectancy free from cardiovascular disease of 9.0 years, and a decrease in life expectancy with cardiovascular disease of 2.4 years.", "The corresponding differences for women were 4.8, 8.1, and 3.3 years.   \n", "CONCLUSION The Polymeal promises to be an effective, non-pharmacological, safe, cheap, and tasty alternative to reduce cardiovascular morbidity and increase life expectancy in the general population."], "structured": true}
{"doc_id": 8790729, "title": "Islet-Like Clusters Derived from Mesenchymal Stem Cells in Wharton's Jelly of the Human Umbilical Cord for Transplantation to Control Type 1 Diabetes", "abstract": ["BACKGROUND There is a widespread interest in developing renewable sources of islet-replacement tissue for type I diabetes mellitus.", "Human mesenchymal cells isolated from the Wharton's jelly of the umbilical cord (HUMSCs), which can be easily obtained and processed compared with embryonic and bone marrow stem cells, possess stem cell properties.", "HUMSCs may be a valuable source for the generation of islets.   \n", "METHODOLOGY AND PRINCIPAL FINDINGS HUMSCs were induced to transform into islet-like cell clusters in vitro through stepwise culturing in neuron-conditioned medium.", "To assess the functional stability of the islet-like cell clusters in vivo, these cell clusters were transplanted into the liver of streptozotocin-induced diabetic rats via laparotomy.", "Glucose tolerance was measured on week 12 after transplantation accompanied with immunohistochemistry and electron microscopy analysis.", "These islet-like cell clusters were shown to contain human C-peptide and release human insulin in response to physiological glucose levels.", "Real-time RT-PCR detected the expressions of insulin and other pancreatic beta-cell-related genes (Pdx1, Hlxb9, Nkx2.2, Nkx6.1, and Glut-2) in these islet-like cell clusters.", "The hyperglycemia and glucose intolerance in streptozotocin-induced diabetic rats was significantly alleviated after xenotransplantation of islet-like cell clusters, without the use of immunosuppressants.", "In addition to the existence of islet-like cell clusters in the liver, some special fused liver cells were also found, which characterized by human insulin and nuclei-positive staining and possessing secretory granules.   \n", "CONCLUSIONS AND SIGNIFICANCE In this study, we successfully differentiate HUMSCs into mature islet-like cell clusters, and these islet-like cell clusters possess insulin-producing ability in vitro and in vivo.", "HUMSCs in Wharton's Jelly of the umbilical cord seem to be the preferential source of stem cells to convert into insulin-producing cells, because of the large potential donor pool, its rapid availability, no risk of discomfort for the donor, and low risk of rejection."], "structured": true}
{"doc_id": 8814634, "title": "Use of perioperative hydroxyethyl starch 6% and albumin 5% in elective joint arthroplasty and association with adverse outcomes: a retrospective population based analysis", "abstract": ["OBJECTIVE To determine whether the perioperative use of hydroxyethyl starch 6% and albumin 5% in elective joint arthroplasties are associated with an increased risk for perioperative complications.   \n", "DESIGN Retrospective cohort study of population based data between 2006 and 2013.   \n", "SETTING Data from 510 different hospitals across the United States participating in the Premier Perspective database.   \n", "PARTICIPANTS 1,051,441 patients undergoing elective total hip and knee arthroplasties.   ", "EXPOSURES Perioperative fluid resuscitation with hydroxyethyl starch 6% or albumin 5%, or neither.   \n", "MAIN OUTCOME MEASURES Acute renal failure and thromboembolic, cardiac, and pulmonary complications.   \n", "RESULTS Compared with patients who received neither colloid, perioperative fluid resuscitation with hydroxyethyl starch 6% or albumin 5% was associated with an increased risk of acute renal failure (odds ratios 1.23 (95% confidence interval 1.13 to 1.34) and 1.56 (1.36 to 1.78), respectively) and most other complications.", "A recent decrease in hydroxyethyl starch 6% use was noted, whereas that of albumin 5% increased.   \n", "CONCLUSIONS Similar to studies in critically ill patients, we showed that use of hydroxyethyl starch 6% was associated with an increased risk of acute renal failure and other complications in the elective perioperative orthopedic setting.", "This increased risk also applied to albumin 5%.", "These findings raise questions regarding the widespread use of these colloids in elective joint arthroplasty procedures."], "structured": true}
{"doc_id": 8816869, "title": "BMAL1 and CLOCK, Two Essential Components of the Circadian Clock, Are Involved in Glucose Homeostasis", "abstract": ["Circadian timing is generated through a unique series of autoregulatory interactions termed the molecular clock.", "Behavioral rhythms subject to the molecular clock are well characterized.", "We demonstrate a role for Bmal1 and Clock in the regulation of glucose homeostasis.", "Inactivation of the known clock components Bmal1 (Mop3) and Clock suppress the diurnal variation in glucose and triglycerides.", "Gluconeogenesis is abolished by deletion of Bmal1 and is depressed in Clock mutants, but the counterregulatory response of corticosterone and glucagon to insulin-induced hypoglycaemia is retained.", "Furthermore, a high-fat diet modulates carbohydrate metabolism by amplifying circadian variation in glucose tolerance and insulin sensitivity, and mutation of Clock restores the chow-fed phenotype.", "Bmal1 and Clock, genes that function in the core molecular clock, exert profound control over recovery from insulin-induced hypoglycaemia.", "Furthermore, asynchronous dietary cues may modify glucose homeostasis via their interactions with peripheral molecular clocks."], "structured": false}
{"doc_id": 8839502, "title": "Mechanisms of progression and regression of renal lesions of chronic nephropathies and diabetes.", "abstract": ["The incidence of chronic kidney diseases is increasing worldwide, and these conditions are emerging as a major public health problem.", "While genetic factors contribute to susceptibility and progression of renal disease, proteinuria has been claimed as an independent predictor of outcome.", "Reduction of urinary protein levels by various medications and a low-protein diet limits renal function decline in individuals with nondiabetic and diabetic nephropathies to the point that remission of the disease and regression of renal lesions have been observed in experimental animals and even in humans.", "In animal models, regression of glomerular structural changes is associated with remodeling of the glomerular architecture.", "Instrumental to this discovery were 3D reconstruction studies of the glomerular capillary tuft, which allowed the quantification of sclerosis volume reduction and capillary regeneration upon treatment.", "Regeneration of capillary segments might result from the contribution of resident cells, but progenitor cells of renal or extrarenal origin may also have a role.", "This review describes recent advances in our understanding of the mechanisms and mediators underlying renal tissue repair ultimately responsible for regression of renal injury."], "structured": false}
{"doc_id": 8842332, "title": "Contemporary type 1 diabetes pregnancy outcomes: impact of obesity and glycaemic control.", "abstract": ["OBJECTIVE To compare contemporary pregnancy outcomes in women with and without type 1 diabetes, and to examine the effects of obesity and glycaemic control on these outcomes.   \n", "DESIGN AND SETTING Historical cohort study in a specialist diabetes and maternity network in Victoria.   \n", "PARTICIPANTS All singleton births (at least 20 weeks' gestation), 2010-2013, were analysed: 107 pregnancies to women with type 1 diabetes and 27 075 pregnancies to women without diabetes.", "Women with type 2 diabetes or gestational diabetes were excluded.   \n", "METHODS Data were extracted from the Birthing Outcomes System database; associations between type 1 diabetes and pregnancy outcomes were analysed by multivariable regression.   \n", "MAIN OUTCOME MEASURES Mode of birth; maternal and neonatal outcomes.   \n", "RESULTS The mean body mass index was higher for women with type 1 diabetes than for women without diabetes (mean, 27.3 kg/m(2) [SD, 5.0] v 25.7 kg/m(2) [SD, 5.9]; P = 0.01); the median gestation period for their babies was shorter (median, 37.3 weeks [IQR, 34.6-38.1] v 39.4 weeks [IQR, 38.4-40.4]; P < 0.001) and they were more likely to be large for gestational age (LGA) (adjusted odds ratio [aOR], 7.9; 95% CI, 5.3-11.8).", "Women with type 1 diabetes were more likely to have had labour induced (aOR, 3.0; 95% CI, 2.0-4.5), a caesarean delivery (aOR, 4.6; 95% CI, 3.1-7.0), or a pre-term birth (aOR, 6.7; 95% CI, 4.5-10.0); their babies were more likely to have shoulder dystocia (aOR, 8.2; 95% CI, 3.6-18.7), hypoglycaemia (aOR, 10.3; 95% CI, 6.8-15.6), jaundice (aOR, 5.1; 95% CI, 3.3-7.7), respiratory distress (aOR, 2.5; 95% CI, 1.4-4.4) or to suffer perinatal death (aOR, 4.3; 95% CI, 1.9-9.9).", "In women with type 1 diabetes, greater obesity was associated with increased odds for an LGA baby or congenital malformation, and increased HbA1c levels were associated with pre-term birth and perinatal death.   \n", "CONCLUSION Women with type 1 diabetes, even when managed in a specialist setting, still experience adverse obstetric and neonatal outcomes.", "Poor glycaemic control is not wholly responsible for adverse outcomes, reinforcing the importance of other risk factors, such as obesity and weight gain."], "structured": true}
{"doc_id": 8856690, "title": "Molecular Mechanisms of Vitamin D Action", "abstract": ["The hormonal metabolite of vitamin D, 1\u03b1,25-dihydroxyvitamin D3 (1,25D), initiates biological responses via binding to the vitamin D receptor (VDR).", "When occupied by 1,25D, VDR interacts with the retinoid X receptor (RXR) to form a heterodimer that binds to vitamin D responsive elements in the region of genes directly controlled by 1,25D.", "By recruiting complexes of either coactivators or corepressors, ligand-activated VDR-RXR modulates the transcription of genes encoding proteins that promulgate the traditional functions of vitamin D, including signaling intestinal calcium and phosphate absorption to effect skeletal and calcium homeostasis.", "Thus, vitamin D action in a particular cell depends upon the metabolic production or delivery of sufficient concentrations of the 1,25D ligand, expression of adequate VDR and RXR coreceptor proteins, and cell-specific programming of transcriptional responses to regulate select genes that encode proteins that function in mediating the effects of vitamin D. For example, 1,25D induces RANKL, SPP1 (osteopontin), and BGP (osteocalcin) to govern bone mineral remodeling; TRPV6, CaBP9k, and claudin 2 to promote intestinal calcium absorption; and TRPV5, klotho, and Npt2c to regulate renal calcium and phosphate reabsorption.", "VDR appears to function unliganded by 1,25D in keratinocytes to drive mammalian hair cycling via regulation of genes such as CASP14, S100A8, SOSTDC1, and others affecting Wnt signaling.", "Finally, alternative, low-affinity, non-vitamin D VDR ligands, e.g., lithocholic acid, docosahexaenoic acid, and curcumin, have been reported.", "Combined alternative VDR ligand(s) and 1,25D/VDR control of gene expression may delay chronic disorders of aging such as osteoporosis, type 2 diabetes, cardiovascular disease, and cancer."], "structured": false}
{"doc_id": 8858602, "title": "Quantitative Temporal Viromics: An Approach to Investigate Host-Pathogen Interaction", "abstract": ["A systematic quantitative analysis of temporal changes in host and viral proteins throughout the course of a productive infection could provide dynamic insights into virus-host interaction.", "We developed a proteomic technique called \"quantitative temporal viromics\" (QTV), which employs multiplexed tandem-mass-tag-based mass spectrometry.", "Human cytomegalovirus (HCMV) is not only an important pathogen but a paradigm of viral immune evasion.", "QTV detailed how HCMV orchestrates the expression of >8,000 cellular proteins, including 1,200 cell-surface proteins to manipulate signaling pathways and counterintrinsic, innate, and adaptive immune defenses.", "QTV predicted natural killer and T cell ligands, as well as 29 viral proteins present at the cell surface, potential therapeutic targets.", "Temporal profiles of >80% of HCMV canonical genes and 14 noncanonical HCMV open reading frames were defined.", "QTV is a powerful method that can yield important insights into viral infection and is applicable to any virus with a robust in vitro model."], "structured": false}
{"doc_id": 8868863, "title": "Interactions between sleep, circadian function, and glucose metabolism: implications for risk and severity of diabetes.", "abstract": ["Sleep disturbances, including sleep insufficiency and sleep fragmentation, have been linked to abnormal glucose metabolism and increased diabetes risk.", "Well-controlled laboratory studies have provided insights regarding the underlying mechanisms.", "Several large prospective studies suggest that these sleep disturbances are associated with an increased risk of incident diabetes.", "Obstructive sleep apnea, which combines sleep fragmentation and hypoxemia, is a major risk factor for insulin resistance and possibly diabetes.", "Whether glycemic control in type 2 diabetes patients can be improved by treating sleep apnea remains controversial.", "Recently, sleep disturbances during pregnancy and their relationship to gestational diabetes and hyperglycemia have received considerable attention owing to potential adverse effects on maternal and fetal health.", "Additionally, evidence from animal models has identified disruption of the circadian system as a putative risk factor for adverse metabolic outcomes.", "The purpose of this review is to provide an update on the current state of knowledge linking sleep disturbances, circadian dysfunction, and glucose metabolism.", "Experimental, prospective, and interventional studies are discussed."], "structured": false}
{"doc_id": 8883846, "title": "Antibody-Based HIV-1 Vaccines: Recent Developments and Future Directions", "abstract": ["The Global HIV Vaccine Enterprise convened a two-day workshop in May of 2007 to discuss humoral immune responses to HIV and approaches to design vaccines that induce viral neutralizing and other potentially protective antibody responses.", "The goals of this workshop were to identify key scientific issues, gaps, and opportunities that have emerged since the Enterprise Strategic Plan was first published in 2005 [1], and to make recommendations that Enterprise stakeholders can use to plan new activities.    ", "Most effective viral vaccines work, at least in part, by generating antibodies that inactivate or neutralize the invading virus, and the existing data strongly suggest that an optimally effective HIV-1 vaccine should elicit potent antiviral neutralizing antibodies.", "However, unlike acute viral pathogens, HIV-1 chronically replicates in the host and evades the antibody response.", "This immune evasion, along with the large genetic variation among HIV-1 strains worldwide, has posed major obstacles to vaccine development.", "Current HIV vaccine candidates do not elicit neutralizing antibodies against most circulating virus strains, and thus the induction of a protective antibody response remains a major priority for HIV-1 vaccine development.", "For an antibody-based HIV-1 vaccine, progress in vaccine design is generally gauged by in vitro assays that measure the ability of vaccine-induced antibodies to neutralize a broad spectrum of viral isolates representing the major genetic subtypes (clades) of HIV-1 [2].", "Although it is not known what magnitude and breadth of neutralization will predict protection in vaccine recipients, it is clear that current vaccine immunogens elicit antibodies that neutralize only a minority of circulating isolates.", "Thus, much progress needs to be made in this area.", "Also, though virus neutralization is considered a critical benchmark for a vaccine, this may not be the only benchmark for predicting success with antibody-based HIV-1 vaccine immunogens.    ", "The main targets for neutralizing antibodies to HIV-1 are the surface gp120 and trans-membrane gp41 envelope glycoproteins (Env) that mediate receptor and coreceptor binding and the subsequent membrane fusion events that allow the virus to gain entry into cells [3].", "Antibodies neutralize the virus by binding these viral spikes and blocking virus entry into susceptible cells, such as CD4+ T cells [4,5].", "In order to chronically replicate in the host, the virus exploits several mechanisms to shield itself against antibody recognition, including a dense outer coating of sugar molecules (N-linked glycans) and the strategic positioning of cysteine\u2013cysteine loop structures on the gp120 molecule [6\u20138].", "These shielding mechanisms, although highly effective, have vulnerabilities imposed by fitness constraints.", "Information on the precise location and molecular structure of these vulnerable regions could be valuable for the rational design of improved vaccine immunogens.    ", "Participants in the workshop identified four areas that, if given proper attention, could provide key information that would bring the field closer to an effective antibody-based HIV-1 vaccine: (1) structure-assisted immunogen design, (2) role of Fc receptors and complement, (3) assay standardization and validation, and (4) immunoregulation of B cell responses."], "structured": false}
{"doc_id": 8891333, "title": "Targeted therapy for cancer stem cells: the patched pathway and ABC transporters", "abstract": ["Data from certain leukemias as well as brain and breast cancer indicate that there is a small population of tumor cells with \u2018stem cell\u2019 characteristics and the capacity for self-renewal.", "The self-renewing cells have many of the properties of normal stem cells and have been termed \u2018cancer stem cells\u2019.", "These cancer stem cells make up as few as 1% of the cells in a tumor, making them difficult to detect and study.", "Like normal stem cells, cancer stem cells have a number of properties permitting them to survive traditional cancer chemotherapy and radiation therapy.", "These cells express high levels of ATP-binding cassette (ABC) drug transporters, providing for a level of resistance; are relatively quiescent; have higher levels of DNA repair and a lowered ability to enter apoptosis.", "Combined cancer therapy approaches targeting the cancer stem cells and the non-stem cells may be developed with increased efficacy.", "Efforts to target the Hedgehog/Patched pathway, critical to embryonic growth and differentiation, and the ABCG2 drug efflux transporter will be presented."], "structured": false}
{"doc_id": 8892905, "title": "Increased in vivo amyloid-\u03b242 production, exchange, and loss in presenilin mutation carriers.", "abstract": ["Alzheimer's disease (AD) is hypothesized to be caused by an overproduction or reduced clearance of amyloid-\u03b2 (A\u03b2) peptide.", "Autosomal dominant AD (ADAD) caused by mutations in the presenilin (PSEN) gene have been postulated to result from increased production of A\u03b242 compared to A\u03b240 in the central nervous system (CNS).", "This has been demonstrated in rodent models of ADAD but not in human mutation carriers.", "We used compartmental modeling of stable isotope labeling kinetic (SILK) studies in human carriers of PSEN mutations and related noncarriers to evaluate the pathophysiological effects of PSEN1 and PSEN2 mutations on the production and turnover of A\u03b2 isoforms.", "We compared these findings by mutation status and amount of fibrillar amyloid deposition as measured by positron emission tomography (PET) using the amyloid tracer Pittsburgh compound B (PIB).", "CNS A\u03b242 to A\u03b240 production rates were 24% higher in mutation carriers compared to noncarriers, and this was independent of fibrillar amyloid deposits quantified by PET PIB imaging.", "The fractional turnover rate of soluble A\u03b242 relative to A\u03b240 was 65% faster in mutation carriers and correlated with amyloid deposition, consistent with increased deposition of A\u03b242 into plaques, leading to reduced recovery of A\u03b242 in cerebrospinal fluid (CSF).", "Reversible exchange of A\u03b242 peptides with preexisting unlabeled peptide was observed in the presence of plaques.", "These findings support the hypothesis that A\u03b242 is overproduced in the CNS of humans with PSEN mutations that cause AD, and demonstrate that soluble A\u03b242 turnover and exchange processes are altered in the presence of amyloid plaques, causing a reduction in A\u03b242 concentrations in the CSF."], "structured": false}
{"doc_id": 8903143, "title": "Basic residues in the T-cell receptor \u03b6 cytoplasmic domain mediate membrane association and modulate signaling.", "abstract": ["The T-cell receptor (TCR) consists of a TCR\u03b1\u03b2 heterodimer, a TCR\u03b6 homodimer, and CD3\u03b3\u03b5 and CD3\u03b4\u03b5 heterodimers.", "The precise mechanism of T-cell triggering following TCR ligand engagement remains elusive.", "Previous studies reported that the cytoplasmic tail of CD3\u03b5 binds to the plasma membrane through a basic residue-rich stretch (BRS) and proposed that dissociation from the membrane is required for phosphorylation thereof.", "In this report we show that BRS motifs within the cytoplasmic tail of TCR\u03b6 mediate association with the plasma membrane and that TCR engagement results in TCR\u03b6 dissociation from the membrane.", "This dissociation requires phosphorylation of the TCR\u03b6 immunoreceptor tyrosine-based activation motifs by lymphocyte cell-specificprotein tyrosine kinase (Lck) but not \u03b6-chain-associated protein kinase 70 binding.", "Mutations of the TCR\u03b6 BRS motifs that disrupt this membrane association attenuate proximal and distal responses induced by TCR engagement.", "These mutations appear to alter the localization of TCR\u03b6 with respect to Lck as well as the mobility of the TCR complex.", "This study reveals that tyrosine phosphorylation of the TCR\u03b6 cytoplasmic domain regulates its association with the plasma membrane and highlights the functional importance of TCR\u03b6 BRS motifs."], "structured": false}
{"doc_id": 8906858, "title": "Policies for alcohol restriction and their association with interpersonal violence: a time-series analysis of homicides in Cali, Colombia.", "abstract": ["BACKGROUND Cali, Colombia, has a high incidence of interpersonal violence deaths.", "Various alcohol control policies have been implemented to reduce alcohol-related problems.", "The objective of this study was to determine whether different alcohol control policies were associated with changes in the incidence rate of homicides.   \n", "METHODS Ecologic study conducted during 2004-08 using a time-series design.", "Policies were implemented with variations in hours of restriction of sales and consumption of alcohol.", "Most restrictive policies prohibited alcohol between 2 a.m. and 10 a.m. for 446 non-consecutive days.", "Moderately restrictive policies prohibited alcohol between 3 a.m. and 10 a.m. for 1277 non-consecutive days.", "Lax policies prohibited alcohol between 4 a.m. and 10 a.m. for 104 non-consecutive days.", "In conditional autoregressive negative binomial regressions, rates of homicides and unintentional injury deaths (excluding traffic events) were compared between different periods of days when different policies were in effect.   \n", "RESULTS There was an increased risk of homicides in periods when the moderately restrictive policies were in effect compared with periods when the most restrictive policies were in effect [incidence rate ratio (IRR) 1.15, 90% confidence interval (CI) 1.05-1.26, P = 0.012], and there was an even higher risk of homicides in periods when the lax policies were in effect compared with periods when the most restrictive policies were in effect (IRR 1.42, 90% CI 1.26-1.61, P < 0.001).", "Less restrictive policies were not associated with increased risk of unintentional injury deaths.   \n", "CONCLUSION Extended hours of sales and consumption of alcohol were associated with increased risk of homicides.", "Strong restrictions on alcohol availability could reduce the incidence of interpersonal violence events in communities where homicides are high."], "structured": true}
{"doc_id": 8909176, "title": "Effects of SNF1 on Maltose Metabolism and Leavening Ability of Baker's Yeast in Lean Dough.", "abstract": ["Maltose metabolism of baker's yeast (Saccharomyces cerevisiae) in lean dough is negatively influenced by glucose repression, thereby delaying the dough fermentation.", "To improve maltose metabolism and leavening ability, it is necessary to alleviate glucose repression.", "The Snf1 protein kinase is well known to be essential for the response to glucose repression and required for transcription of glucose-repressed genes including the maltose-utilization genes (MAL).", "In this study, the SNF1 overexpression and deletion industrial baker's yeast strains were constructed and characterized in terms of maltose utilization, growth and fermentation characteristics, mRNA levels of MAL genes (MAL62 encoding the maltase and MAL61 encoding the maltose permease) and maltase and maltose permease activities.", "Our results suggest that overexpression of SNF1 was effective to glucose derepression for enhancing MAL expression levels and enzymes (maltase and maltose permease) activities.", "These enhancements could result in an 18% increase in maltose metabolism of industrial baker's yeast in LSMLD medium (the low sugar model liquid dough fermentation medium) containing glucose and maltose and a 15% increase in leavening ability in lean dough.", "These findings provide a valuable insight of breeding industrial baker's yeast for rapid fermentation."], "structured": false}
{"doc_id": 8925851, "title": "Review article", "abstract": ["Ribosomopathies compose a collection of disorders in which genetic abnormalities cause impaired ribosome biogenesis and function, resulting in specific clinical phenotypes.", "Congenital mutations in RPS19 and other genes encoding ribosomal proteins cause Diamond-Blackfan anemia, a disorder characterized by hypoplastic, macrocytic anemia.", "Mutations in other genes required for normal ribosome biogenesis have been implicated in other rare congenital syndromes, Schwachman-Diamond syndrome, dyskeratosis congenita, cartilage hair hypoplasia, and Treacher Collins syndrome.", "In addition, the 5q- syndrome, a subtype of myelodysplastic syndrome, is caused by a somatically acquired deletion of chromosome 5q, which leads to haploinsufficiency of the ribosomal protein RPS14 and an erythroid phenotype highly similar to Diamond-Blackfan anemia.", "Acquired abnormalities in ribosome function have been implicated more broadly in human malignancies.", "The p53 pathway provides a surveillance mechanism for protein translation as well as genome integrity and is activated by defects in ribosome biogenesis; this pathway appears to be a critical mediator of many of the clinical features of ribosomopathies.", "Elucidation of the mechanisms whereby selective abnormalities in ribosome biogenesis cause specific clinical syndromes will hopefully lead to novel therapeutic strategies for these diseases."], "structured": false}
{"doc_id": 8963413, "title": "PD-L1 expression in human cancers and its association with clinical outcomes", "abstract": ["PD-L1 is an immunoinhibitory molecule that suppresses the activation of T cells, leading to the progression of tumors.", "Overexpression of PD-L1 in cancers such as gastric cancer, hepatocellular carcinoma, renal cell carcinoma, esophageal cancer, pancreatic cancer, ovarian cancer, and bladder cancer is associated with poor clinical outcomes.", "In contrast, PD-L1 expression correlates with better clinical outcomes in breast cancer and merkel cell carcinoma.", "The prognostic value of PD-L1 expression in lung cancer, colorectal cancer, and melanoma is controversial.", "Blocking antibodies that target PD-1 and PD-L1 have achieved remarkable response rates in cancer patients who have PD-L1-overexpressing tumors.", "However, using PD-L1 as an exclusive predictive biomarker for cancer immunotherapy is questionable due to the low accuracy of PD-L1 immunohistochemistry staining.", "Factors that affect the accuracy of PD-L1 immunohistochemistry staining are as follows.", "First, antibodies used in different studies have different sensitivity.", "Second, in different studies, the cut-off value of PD-L1 staining positivity is different.", "Third, PD-L1 expression in tumors is not uniform, and sampling time and location may affect the results of PD-L1 staining.", "Therefore, better understanding of tumor microenvironment and use of other biomarkers such as gene marker and combined index are necessary to better identify patients who will benefit from PD-1/PD-L1 checkpoint blockade therapy."], "structured": false}
{"doc_id": 8979167, "title": "Primate cytomegaloviruses encode and express an IL-10-like protein.", "abstract": ["An open reading frame (ORF) with homology to interleukin-10 (IL-10) has been identified in rhesus cytomegalovirus (RhCMV).", "The IL-10-like protein is generated from a multispliced, polyadenylated early gene transcript encompassing part of the corresponding UL111A ORF of human CMV (HCMV).", "Immunological analyses confirm expression of the IL-10-like protein both in tissue culture and in RhCMV-infected rhesus macaques.", "Conserved ORFs were subsequently identified in human, baboon, and African green monkey CMV, and a fully processed transcript has been mapped in fibroblasts infected with the Towne strain of HCMV.", "The conservation of this previously unrecognized ORF suggests that the protein may play an essential role in primate CMV persistence and pathogenesis."], "structured": false}
{"doc_id": 8989616, "title": "Genome Sequencing and Analysis of the Tasmanian Devil and Its Transmissible Cancer", "abstract": ["The Tasmanian devil (Sarcophilus harrisii), the largest marsupial carnivore, is endangered due to a transmissible facial cancer spread by direct transfer of living cancer cells through biting.", "Here we describe the sequencing, assembly, and annotation of the Tasmanian devil genome and whole-genome sequences for two geographically distant subclones of the cancer.", "Genomic analysis suggests that the cancer first arose from a female Tasmanian devil and that the clone has subsequently genetically diverged during its spread across Tasmania.", "The devil cancer genome contains more than 17,000 somatic base substitution mutations and bears the imprint of a distinct mutational process.", "Genotyping of somatic mutations in 104 geographically and temporally distributed Tasmanian devil tumors reveals the pattern of evolution and spread of this parasitic clonal lineage, with evidence of a selective sweep in one geographical area and persistence of parallel lineages in other populations."], "structured": false}
{"doc_id": 8994465, "title": "A Temporarily Distinct Subpopulation of Slow-Cycling Melanoma Cells Is Required for Continuous Tumor Growth", "abstract": ["Melanomas are highly heterogeneous tumors, but the biological significance of their different subpopulations is not clear.", "Using the H3K4 demethylase JARID1B (KDM5B/PLU-1/RBP2-H1) as a biomarker, we have characterized a small subpopulation of slow-cycling melanoma cells that cycle with doubling times of >4 weeks within the rapidly proliferating main population.", "Isolated JARID1B-positive melanoma cells give rise to a highly proliferative progeny.", "Knockdown of JARID1B leads to an initial acceleration of tumor growth followed by exhaustion which suggests that the JARID1B-positive subpopulation is essential for continuous tumor growth.", "Expression of JARID1B is dynamically regulated and does not follow a hierarchical cancer stem cell model because JARID1B-negative cells can become positive and even single melanoma cells irrespective of selection are tumorigenic.", "These results suggest a new understanding of melanoma heterogeneity with tumor maintenance as a dynamic process mediated by a temporarily distinct subpopulation."], "structured": false}
{"doc_id": 8995263, "title": "A map of human circular RNAs in clinically relevant tissues", "abstract": ["Cellular circular RNAs (circRNAs) are generated by head-to-tail splicing and are present in all multicellular organisms studied so far.", "Recently, circRNAs have emerged as a large class of RNA which can function as post-transcriptional regulators.", "It has also been shown that many circRNAs are tissue- and stage-specifically expressed.", "Moreover, the unusual stability and expression specificity make circRNAs important candidates for clinical biomarker research.", "Here, we present a circRNA expression resource of 20 human tissues highly relevant to disease-related research: vascular smooth muscle cells (VSMCs), human umbilical vein cells (HUVECs), artery endothelial cells (HUAECs), atrium, vena cava, neutrophils, platelets, cerebral cortex, placenta, and samples from mesenchymal stem cell differentiation.", "In eight different samples from a single donor, we found highly tissue-specific circRNA expression.", "Circular-to-linear RNA ratios revealed that many circRNAs were expressed higher than their linear host transcripts.", "Among the 71 validated circRNAs, we noticed potential biomarkers.", "In adenosine deaminase-deficient, severe combined immunodeficiency (ADA-SCID) patients and in Wiskott-Aldrich-Syndrome (WAS) patients' samples, we found evidence for differential circRNA expression of genes that are involved in the molecular pathogenesis of both phenotypes.", "Our findings underscore the need to assess circRNAs in mechanisms of human disease.", "KEY MESSAGES: circRNA resource catalog of 20 clinically relevant tissues.", "circRNA expression is highly tissue-specific.", "circRNA transcripts are often more abundant than their linear host RNAs.", "circRNAs can be differentially expressed in disease-associated genes."], "structured": false}
{"doc_id": 8997410, "title": "Arp2/3 complex inhibition radically alters lamellipodial actin architecture, suspended cell shape, and the cell spreading process", "abstract": ["Recent studies have investigated the dendritic actin cytoskeleton of the cell edge's lamellipodial (LP) region by experimentally decreasing the activity of the actin filament nucleator and branch former, the Arp2/3 complex.", "Here we extend these studies via pharmacological inhibition of the Arp2/3 complex in sea urchin coelomocytes, cells that possess an unusually broad LP region and display correspondingly exaggerated centripetal flow.", "Using light and electron microscopy, we demonstrate that Arp2/3 complex inhibition via the drug CK666 dramatically altered LP actin architecture, slowed centripetal flow, drove a lamellipodial-to-filopodial shape change in suspended cells, and induced a novel actin structural organization during cell spreading.", "A general feature of the CK666 phenotype in coelomocytes was transverse actin arcs, and arc generation was arrested by a formin inhibitor.", "We also demonstrate that CK666 treatment produces actin arcs in other cells with broad LP regions, namely fish keratocytes and Drosophila S2 cells.", "We hypothesize that the actin arcs made visible by Arp2/3 complex inhibition in coelomocytes may represent an exaggerated manifestation of the elongate mother filaments that could possibly serve as the scaffold for the production of the dendritic actin network."], "structured": false}
{"doc_id": 9021186, "title": "Synergistic Activation of HIV-1 Expression by Deacetylase Inhibitors and Prostratin: Implications for Treatment of Latent Infection", "abstract": ["The persistence of transcriptionally silent but replication-competent HIV-1 reservoirs in Highly Active Anti-Retroviral Therapy (HAART)-treated infected individuals, represents a major hurdle to virus eradication.", "Activation of HIV-1 gene expression in these cells together with an efficient HAART has been proposed as an adjuvant therapy aimed at decreasing the pool of latent viral reservoirs.", "Using the latently-infected U1 monocytic cell line and latently-infected J-Lat T-cell clones, we here demonstrated a strong synergistic activation of HIV-1 production by clinically used histone deacetylase inhibitors (HDACIs) combined with prostratin, a non-tumor-promoting nuclear factor (NF)- kappaB inducer.", "In J-Lat cells, we showed that this synergism was due, at least partially, to the synergistic recruitment of unresponsive cells into the expressing cell population.", "A combination of prostratin+HDACI synergistically activated the 5' Long Terminal Repeat (5'LTR) from HIV-1 Major group subtypes representing the most prevalent viral genetic forms, as shown by transient transfection reporter assays.", "Mechanistically, HDACIs increased prostratin-induced DNA-binding activity of nuclear NF-kappaB and degradation of cytoplasmic NF-kappaB inhibitor, IkappaBalpha .", "Moreover, the combined treatment prostratin+HDACI caused a more pronounced nucleosomal remodeling in the U1 viral promoter region than the treatments with the compounds alone.", "This more pronounced remodeling correlated with a synergistic reactivation of HIV-1 transcription following the combined treatment prostratin+HDACI, as demonstrated by measuring recruitment of RNA polymerase II to the 5'LTR and both initiated and elongated transcripts.", "The physiological relevance of the prostratin+HDACI synergism was shown in CD8(+)-depleted peripheral blood mononuclear cells from HAART-treated patients with undetectable viral load.", "Moreover, this combined treatment reactivated viral replication in resting CD4(+) T cells isolated from similar patients.", "Our results suggest that combinations of different kinds of proviral activators may have important implications for reducing the size of latent HIV-1 reservoirs in HAART-treated patients."], "structured": false}
{"doc_id": 9038803, "title": "Centrosome aberrations: cause or consequence of cancer progression?", "abstract": ["Many human tumours show centrosome aberrations, indicating an underlying deregulation of centrosome structure, duplication or segregation.", "Centrosomes organize microtubule arrays throughout the cell cycle, thereby influencing both tissue architecture and the accuracy of chromosome segregation.", "But what are the origins of centrosomal abnormalities in tumours, and what impact do they have on the generation of invasive, genetically unbalanced cells during cancer progression?"], "structured": false}
{"doc_id": 9047718, "title": "Autonomic neuropathy, QT interval lengthening, and unexpected deaths in male diabetic patients", "abstract": ["QT intervals were measured over RR intervals ranging from 500 ms to 1000 ms in 13 normal male subjects, 13 male diabetic subjects without and 13 with autonomic neuropathy.", "There was a close linear relationship between QT and RR in all subjects.", "The slope of the regression line was significantly greater in the autonomic neuropathy group than the normal group.", "Thirty-two male diabetic subjects with varying degrees of autonomic dysfunction had repeat QT measurements 3 (range 2\u20136) years later.", "QT and QTC lengthened significantly at the second visit, unrelated to age or time between recordings, but which corresponded with changes in autonomic function.", "Of 71 male diabetic subjects under 60 years followed for 3 years, 13 had died, 8 unexpectedly.", "Of those with autonomic neuropathy, QT and QTC were significantly longer in those who subsequently died, despite similar ages and duration of diabetes.", "We conclude that QT/RR interval relationships are altered in diabetic autonomic neuropathy, and that changes in QT length with time parallel changese in autonomic function.", "There may be an association between QT interval prolongation and the risk of dying unexpectedly in diabetic autonomic neuropathy."], "structured": false}
{"doc_id": 9056874, "title": "Incidence of cancer after immunosuppressive treatment for heart transplantation.", "abstract": ["Prolonged or intensive immunosuppressive therapy used after organ transplantation is complicated by an increased incidence of cancer.", "Striking differences in incidence are observed in heart and heart-lung transplant recipients when compared with renal transplant patients.", "The most significant increase was in the incidence of lymphomas in cardiac versus renal patients.", "Moreover, a two-fold greater increase of all neoplasms was found in cardiac recipients, with nearly a six-fold increase in visceral tumors.", "Several factors may account for these differences.", "In cardiac allograft recipients, intensive immunosuppression is frequently used to reverse acute rejection and the highest number of cardiac transplants was performed in the era of polypharmacy, usually consisting of triple therapy."], "structured": false}
{"doc_id": 9063688, "title": "Nucleating actin for invasion", "abstract": ["The invasion of cancer cells into the surrounding tissue is a prerequisite and initial step in metastasis, which is the leading cause of death from cancer.", "Invasive cell migration requires the formation of various structures, such as invadopodia and pseudopodia, which require actin assembly that is regulated by specialized actin nucleation factors.", "There is a large variety of different actin nucleators in human cells, such as formins, spire and Arp2/3-regulating proteins, and the list is likely to grow.", "Studies of the mechanisms of various actin nucleation factors that are involved in cancer cell function may ultimately provide new treatments for invasive and metastatic disease."], "structured": false}
{"doc_id": 9076196, "title": "GFI1 and GFI1B control the loss of endothelial identity of hemogenic endothelium during hematopoietic commitment.", "abstract": ["Recent studies have established that during embryonic development, hematopoietic progenitors and stem cells are generated from hemogenic endothelium precursors through a process termed endothelial to hematopoietic transition (EHT).", "The transcription factor RUNX1 is essential for this process, but its main downstream effectors remain largely unknown.", "Here, we report the identification of Gfi1 and Gfi1b as direct targets of RUNX1 and critical regulators of EHT.", "GFI1 and GFI1B are able to trigger, in the absence of RUNX1, the down-regulation of endothelial markers and the formation of round cells, a morphologic change characteristic of EHT.", "Conversely, blood progenitors in Gfi1- and Gfi1b-deficient embryos maintain the expression of endothelial genes.", "Moreover, those cells are not released from the yolk sac and disseminated into embryonic tissues.", "Taken together, our findings demonstrate a critical and specific role of the GFI1 transcription factors in the first steps of the process leading to the generation of hematopoietic progenitors from hemogenic endothelium."], "structured": false}
{"doc_id": 9091863, "title": "An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells.", "abstract": ["In a diverse group of organisms that includes Caenorhabditis elegans, Drosophila, planaria, hydra, trypanosomes, fungi and plants, the introduction of double-stranded RNAs inhibits gene expression in a sequence-specific manner.", "These responses, called RNA interference or post-transcriptional gene silencing, may provide anti-viral defence, modulate transposition or regulate gene expression.", "We have taken a biochemical approach towards elucidating the mechanisms underlying this genetic phenomenon.", "Here we show that 'loss-of-function' phenotypes can be created in cultured Drosophila cells by transfection with specific double-stranded RNAs.", "This coincides with a marked reduction in the level of cognate cellular messenger RNAs.", "Extracts of transfected cells contain a nuclease activity that specifically degrades exogenous transcripts homologous to transfected double-stranded RNA.", "This enzyme contains an essential RNA component.", "After partial purification, the sequence-specific nuclease co-fractionates with a discrete, approximately 25-nucleotide RNA species which may confer specificity to the enzyme through homology to the substrate mRNAs."], "structured": false}
{"doc_id": 9095394, "title": "Expression of basal cell keratin 15 and keratin 19 in oral squamous neoplasms represents diverse pathophysiologies.", "abstract": ["Human epithelium contains keratin, which is expressed during differentiation.", "Depending on the target cell type, different types of keratin are expressed, and their alterations seem to represent changes in cell properties.", "The basal cells of oral epithelium express keratin 5 (K5), K14, K15 and K19, but their alterations in tumors are unclear.", "To address this issue and to seek possible diagnostic application, we examined the expression of these keratins in oral squamous cell carcinoma (OSCC) and squamous intraepithelial neoplasm (SIN).", "cDNA microarray analysis of 43 OSCC revealed slight upregulation of KRT14, downregulation of KRT15 and KRT19, and unaltered KRT5 expression.", "There were great variations in KRT15 and KRT19 expression across each cancer.", "Well-differentiated OSCC tended to express more KRT15 and less KRT19 compared to moderately- or poorly-differentiated OSCC.", "KRT15 was positively correlated with differentiation-related keratin, KRT13.", "These observations were further investigated by immunohistochemical examination.", "K5 and K14 were ubiquitously expressed in all 50 OSCC and 50 SIN examined.", "K15 and K19 were generally downregulated, but were considerably retained in about half of the cases and showed diverse expression patterns.", "K15-positive cancers tended to show a well-differentiated phenotype, and K19-positive cancers tended to show more invasive tumor fronts.", "Most K19-positive cancers appeared to develop with little associating SIN.", "K19 was consistently downregulated in SIN, while K15 was downregulated mainly in high grade SIN.", "In summary, K15 and K19, unlike K5 or K14, are expressed variably in both SIN and OSCC, which reflects the differences in their pathogenesis and biological behaviors, suggesting their prospective applications as markers for subclassifying OSCC and SIN."], "structured": false}
{"doc_id": 9095943, "title": "Exosomes in Plasma of Patients with Ovarian Carcinoma: Potential Biomarkers of Tumor Progression and Response to Therapy.", "abstract": ["BACKGROUND In patients with Ovarian Cancer (OvCa) exosomes released by tumor cells are present in the plasma and could be involved in tumor progression.", "This study examines the association between the exosome presence/protein content in plasma of OvCa patients and disease outcome, response to standard therapy and/or tumorresistance to therapies in patients studied at diagnosis and also serially during and after therapy.   \n", "DESIGN AND METHODS Exosomes were purified from OvCa patients' plasma (n=22), patients with benign tumors (n=10) or (n=10) healthy controls (NC) using ultracentrifugation.", "Exosomes were visualized by scanning electron microscopy.", "Their protein content was measured.", "The presence of MAGE 3/6 and TGF-\u03b21 in exosomes was evaluated in Western blots.   \n", "RESULTS The OvCa patients' plasma contained higher levels of exosomal proteins (p<0.05) compared to those isolated from plasma of patients with benign tumors or NC.", "Exosomes isolated from OvCa patients's plasma carried TGF-\u03b21 and MAGE3/6, which distinguished OvCa patients from those with benign tumors and NC.", "High protein levels of exosomes were seen in newly diagnosed patients; however in advanced stages of OvCa patients the protein content of isolated exosomes was significantly higher than that of early stages.", "The exosome levels variably changed during/after chemotherapy, and correlations between the changes in exosomal protein levels and clinical data suggested that the protein content of exosomes might be useful in predicting responses to therapy and prognosis in OvCa patients.   \n", "CONCLUSION Analysis of plasma exosomes levels offers a novel approach to diagnosis and monitoring response to therapies in OvCa patients."], "structured": true}
{"doc_id": 9110810, "title": "Insecticide impregnated curtains to control domestic transmission of cutaneous leishmaniasis in Venezuela: cluster randomised trial.", "abstract": ["OBJECTIVE To measure the impact on transmission of leishmaniasis of curtains impregnated with insecticide.   \n", "DESIGN Cluster randomised controlled trial: household interview survey, observational study of people's behaviour, entomological study with light trap captures of sandflies inside houses.   \n", "SETTING 14 urban sectors in Trujillo, Venezuela.   \n", "PARTICIPANTS 2913 inhabitants of 569 houses.   \n", "INTERVENTION Sectors were paired according to their 12 month cumulative incidence of cutaneous leishmaniasis, one sector in each pair was randomly allocated to receive polyester curtains impregnated with lambdacyhalothrin (intervention group) while the other sector received curtains without insecticide or no curtains (control groups).", "After 12 months a follow up household survey was conducted.   \n", "MAIN OUTCOME MEASURES Reduction in abundance of sandflies indoors and 12 month incidence of clinical cases of cutaneous leishmaniasis.   \n", "RESULTS Transmission of cutaneous leishmaniasis occurred mainly in the domestic setting, with the incidence over 12 months of 4%.", "The mean number of sandflies per trap per night was 16.", "After follow up the 12 month incidence of cutaneous leishmaniasis was 0% in the intervention group and 8% in the six pairs in the control group that received unimpregnated curtains (mean difference 8, 95% confidence interval 4.22 to 11.78; P=0.001).", "There were significantly fewer sandflies in the intervention group (2 v 15, mean difference 13 sandflies per trap; 9 to 17; P<0.001).   \n", "CONCLUSION Curtains impregnated with insecticide provide a high degree of protection against indoor transmission of cutaneous leishmaniasis."], "structured": true}
{"doc_id": 9113824, "title": "Chronic pancreatitis is essential for induction of pancreatic ductal adenocarcinoma by K-Ras oncogenes in adult mice.", "abstract": ["Pancreatic ductal adenocarcinoma (PDA), one of the deadliest human cancers, often involves somatic activation of K-Ras oncogenes.", "We report that selective expression of an endogenous K-Ras(G12V) oncogene in embryonic cells of acinar/centroacinar lineage results in pancreatic intraepithelial neoplasias (PanINs) and invasive PDA, suggesting that PDA originates by differentiation of acinar/centroacinar cells or their precursors into ductal-like cells.", "Surprisingly, adult mice become refractory to K-Ras(G12V)-induced PanINs and PDA.", "However, if these mice are challenged with a mild form of chronic pancreatitis, they develop the full spectrum of PanINs and invasive PDA.", "These observations suggest that, during adulthood, PDA stems from a combination of genetic (e.g., somatic K-Ras mutations) and nongenetic (e.g., tissue damage) events."], "structured": false}
{"doc_id": 9122283, "title": "Relative roles of direct regeneration versus paracrine effects of human cardiosphere-derived cells transplanted into infarcted mice.", "abstract": ["RATIONALE Multiple biological mechanisms contribute to the efficacy of cardiac cell therapy.", "Most prominent among these are direct heart muscle and blood vessel regeneration from transplanted cells, as opposed to paracrine enhancement of tissue preservation and/or recruitment of endogenous repair.   \n", "OBJECTIVE Human cardiac progenitor cells, cultured as cardiospheres (CSps) or as CSp-derived cells (CDCs), have been shown to be capable of direct cardiac regeneration in vivo.", "Here we characterized paracrine effects in CDC transplantation and investigated their relative importance versus direct differentiation of surviving transplanted cells.   \n", "METHODS AND RESULTS In vitro, many growth factors were found in media conditioned by human adult CSps and CDCs; CDC-conditioned media exerted antiapoptotic effects on neonatal rat ventricular myocytes, and proangiogenic effects on human umbilical vein endothelial cells.", "In vivo, human CDCs secreted vascular endothelial growth factor, hepatocyte growth factor, and insulin-like growth factor 1 when transplanted into the same SCID mouse model of acute myocardial infarction where they were previously shown to improve function and to produce tissue regeneration.", "Injection of CDCs in the peri-infarct zone increased the expression of Akt, decreased apoptotic rate and caspase 3 level, and increased capillary density, indicating overall higher tissue resilience.", "Based on the number of human-specific cells relative to overall increases in capillary density and myocardial viability, direct differentiation quantitatively accounted for 20% to 50% of the observed effects.   \n", "CONCLUSIONS Together with their spontaneous commitment to cardiac and angiogenic differentiation, transplanted CDCs serve as \"role models,\" recruiting endogenous regeneration and improving tissue resistance to ischemic stress.", "The contribution of the role model effect rivals or exceeds that of direct regeneration."], "structured": true}
{"doc_id": 9142761, "title": "The IC(50) of anti-Pfs25 antibody in membrane-feeding assay varies among species.", "abstract": ["Plasmodium falciparum surface protein 25 (Pfs25) is a candidate for transmission-blocking vaccines (TBVs).", "Anti-Pfs25 antibodies block the development of oocysts in membrane-feeding assays and we have shown the activity correlates with antibody titer.", "In this study, we purified Pfs25-specific IgGs to convert antibody titer to microg/mL and determined the amount of antibody required to inhibit 50% of oocyst development (IC(50)).", "The IC(50) were, 15.9, 4.2, 41.2, and 85.6microg/mL for mouse, rabbit, monkey and human, respectively, and the differences among species were significant.", "Anti-Pfs25 sera from rabbit, monkey and human showed different patterns of competition against 6 mouse monoclonal antibodies, and the avidity of antibodies among four species were also different.", "These data suggests that information obtained from animal studies which assess efficacy of TBV candidates may be difficult to translate to human immunization."], "structured": false}
{"doc_id": 9154703, "title": "Single-Cell RNA-Seq Reveals Dynamic, Random Monoallelic Gene Expression in Mammalian Cells", "abstract": ["Expression from both alleles is generally observed in analyses of diploid cell populations, but studies addressing allelic expression patterns genome-wide in single cells are lacking.", "Here, we present global analyses of allelic expression across individual cells of mouse preimplantation embryos of mixed background (CAST/EiJ \u00d7 C57BL/6J).", "We discovered abundant (12 to 24%) monoallelic expression of autosomal genes and that expression of the two alleles occurs independently.", "The monoallelic expression appeared random and dynamic because there was considerable variation among closely related embryonic cells.", "Similar patterns of monoallelic expression were observed in mature cells.", "Our allelic expression analysis also demonstrates the de novo inactivation of the paternal X chromosome.", "We conclude that independent and stochastic allelic transcription generates abundant random monoallelic expression in the mammalian cell."], "structured": false}
{"doc_id": 9159125, "title": "Lipopolysaccharide-dependent prostaglandin E(2) production is regulated by the glutathione-dependent prostaglandin E(2) synthase gene induced by the Toll-like receptor 4/MyD88/NF-IL6 pathway.", "abstract": ["Macrophages produce a large amount of PGE(2) during inflammation.", "This lipid mediator modulates various immune responses.", "PGE(2) acts on macrophages and inhibits production of cytokines such as TNF-alpha and IL-12.", "Membrane-bound glutathione-dependent PGE(2) synthase (mPGES) has been shown to be a terminal enzyme of the cyclooxygenase-2-mediated PGE(2) biosynthesis.", "Here we identified mPGES as a molecule that is induced by LPS in macrophages.", "The expression of mPGES was not induced by LPS in mice lacking Toll-like receptor 4 or MyD88.", "Furthermore, mice deficient in NF-IL6 showed neither induction of mPGES nor biosynthesis of PGE(2) in response to LPS, indicating that mPGES expression in response to LPS is regulated by a Toll-like receptor 4/MyD88/NF-IL6-dependent signaling pathway.", "We generated mPGES-deficient mice and investigated the role of mPGES in vivo.", "The mice showed no augmentation of the PGE(2) production in response to LPS.", "However, they were not impaired in the LPS-induced production of inflammatory cytokines and showed normal response to the LPS-induced shock.", "Thus, mPGES is critically involved in the biosynthesis of PGE(2) induced by LPS, but is dispensable for the modulation of inflammatory responses."], "structured": false}
{"doc_id": 9159495, "title": "A microRNA feedback loop regulates global microRNA abundance during aging.", "abstract": ["Expression levels of many microRNAs (miRNAs) change during aging, notably declining globally in a number of organisms and tissues across taxa.", "However, little is known about the mechanisms or the biological relevance for this change.", "We investigated the network of genes that controls miRNA transcription and processing during C. elegans aging.", "We found that miRNA biogenesis genes are highly networked with transcription factors and aging-associated miRNAs.", "In particular, miR-71, known to influence life span and itself up-regulated during aging, represses alg-1/Argonaute expression post-transcriptionally during aging.", "Increased ALG-1 abundance in mir-71 loss-of-function mutants led to globally increased miRNA expression.", "Interestingly, these mutants demonstrated widespread mRNA expression dysregulation and diminished levels of variability both in gene expression and in overall life span.", "Thus, the progressive molecular decline often thought to be the result of accumulated damage over an organism's life may be partially explained by a miRNA-directed mechanism of age-associated decline."], "structured": false}
{"doc_id": 9160947, "title": "Early lymphocyte expansion is severely impaired in interleukin 7 receptor-deficient mice", "abstract": ["Interleukin 7 (IL-7) stimulates the proliferation of B cell progenitors, thymocytes, and mature T cells through an interaction with a high affinity receptor (IL-7R) belonging to the hematopoietin receptor superfamily.", "We have further addressed the role of IL-7 and its receptor during B and T cell development by generating mice genetically deficient in IL-7R.", "Mutant mice display a profound reduction in thymic and peripheral lymphoid cellularity.", "Analyses of lymphoid progenitor populations in IL-7R-deficient mice define precisely those developmental stages affected by the mutation and reveal a critical role for IL-7R during early lymphoid development.", "Significantly, these studies indicate that the phase of thymocyte expansion occurring before the onset of T cell receptor gene rearrangement is critically dependent upon, and mediated by the high affinity receptor for IL-7."], "structured": false}
{"doc_id": 9161988, "title": "Immune Activation with HIV Vaccines", "abstract": ["The development of a safe and effective HIV vaccine is perhaps the most important and challenging goal remaining in HIV-AIDS research.", "Recent progress using a poxvirus vector prime and envelope protein boost strategy demonstrated a modest but statistically significant level of efficacy and established the concept that a vaccine could prevent HIV infection (1), and approaches to boost durability and efficacy are currently in the planning stages (2).", "But the results of two vaccine concepts based on recombinant adenovirus serotype-5 (rAd5) (3\u20135) pointed to a potential major problem\u2014that such vaccines might increase susceptibility to HIV infection.", "This also raised the question of whether the problem extends to some or all of the other recombinant adenovirus vectors currently in development or to other vector-based vaccines."], "structured": false}
{"doc_id": 9164724, "title": "Distribution of dystrophin- and utrophin-associated protein complexes during activation of human neutrophils.", "abstract": ["OBJECTIVE Dystrophins, utrophins, and their associated proteins are involved in structural and signaling roles in nonmuscle tissues; however, description of these proteins in neutrophils remained unexplored.", "Therefore we characterize the pattern expression, and the cellular distribution of dystrophin and utrophin gene products and dystrophin-associated proteins (i.e., beta-dystroglycan, alpha-syntrophin, and alpha-dystrobrevins) in relation to actin filaments in resting and activated with formyl-methionyl-leucyl-phenylalanine human neutrophils.   ", "MATERIALS AND METHODS Resting and fMLP-activated human neutrophils were analyzed by immunoblot and by confocal microscopy analysis.", "Immunoprecipitation assays were performed to corroborate the presence of protein complexes.   \n", "RESULTS Immunoprecipitation assays and confocal analysis demonstrated the presence of two dystrophin-associated protein complexes in resting and activated neutrophils: the former formed by Dp71d/Dp71Delta(110)(m) and dystrophin-associated proteins (beta-dystroglycan, alpha-syntrophin, alpha-dystrobrevin-1, and -2), while the latter contains Up400, instead of Dp71d/Dp71Delta(110)(m), as a central component of the dystrophin-associated protein complexes (DAPC).", "Confocal analysis also showed the subcellular redistribution of Dp71d/Dp71Delta(110)(m) approximately DAPC and Up400 approximately DAPC in F-actin-based structures displayed during activation process with fMLP.   \n", "CONCLUSIONS Our study showed the existence of two protein complexes formed by Dp71d/Dp71Delta(110)(m) or Up400 associated with DAPs in resting and fMLP-treated human polymorphonuclears.", "The interaction of these complexes with the actin cytoskeleton is indicative of their dynamic participation in the chemotaxis process."], "structured": true}
{"doc_id": 9167230, "title": "Global and regional burden of hospital admissions for severe acute lower respiratory infections in young children in 2010: a systematic analysis", "abstract": ["BACKGROUND The annual number of hospital admissions and in-hospital deaths due to severe acute lower respiratory infections (ALRI) in young children worldwide is unknown.", "We aimed to estimate the incidence of admissions and deaths for such infections in children younger than 5 years in 2010.   \n", "METHODS We estimated the incidence of admissions for severe and very severe ALRI in children younger than 5 years, stratified by age and region, with data from a systematic review of studies published between Jan 1, 1990, and March 31, 2012, and from 28 unpublished population-based studies.", "We applied these incidence estimates to population estimates for 2010, to calculate the global and regional burden in children admitted with severe ALRI in that year.", "We estimated in-hospital mortality due to severe and very severe ALRI by combining incidence estimates with case fatality ratios from hospital-based studies.   \n", "FINDINGS We identified 89 eligible studies and estimated that in 2010, 11\u00b79 million (95% CI 10\u00b73-13\u00b79 million) episodes of severe and 3\u00b70 million (2\u00b71-4\u00b72 million) episodes of very severe ALRI resulted in hospital admissions in young children worldwide.", "Incidence was higher in boys than in girls, the sex disparity being greatest in South Asian studies.", "On the basis of data from 37 hospital studies reporting case fatality ratios for severe ALRI, we estimated that roughly 265,000 (95% CI 160,000-450,000) in-hospital deaths took place in young children, with 99% of these deaths in developing countries.", "Therefore, the data suggest that although 62% of children with severe ALRI are treated in hospitals, 81% of deaths happen outside hospitals.   \n", "INTERPRETATION Severe ALRI is a substantial burden on health services worldwide and a major cause of hospital referral and admission in young children.", "Improved hospital access and reduced inequities, such as those related to sex and rural status, could substantially decrease mortality related to such infection.", "Community-based management of severe disease could be an important complementary strategy to reduce pneumonia mortality and health inequities.   \n", "FUNDING WHO."], "structured": true}
{"doc_id": 9169645, "title": "Identification of a novel p53 functional domain that is necessary for mediating apoptosis.", "abstract": ["The ability of p53 to induce apoptosis requires its sequence-specific DNA binding activity; however, the transactivation-deficient p53(Gln22-Ser23) can still induce apoptosis.", "Previously, we have shown that the region between residues 23 and 97 in p53 is necessary for such activity.", "In an effort to more precisely map a domain necessary for apoptosis within the N terminus, we found that deletion of the N-terminal 23 amino acids compromises, but does not abolish, p53 induction of apoptosis.", "Surprisingly, p53(Delta1-42), which lacks the N-terminal 42 amino acids and the previously defined activation domain, retains the ability to induce apoptosis to an even higher level than wild-type p53.", "A more extensive deletion, which eliminates the N-terminal 63 amino acids, renders p53 completely inert in mediating apoptosis.", "In addition, we found that both p53(Delta1-42) and p53(Gln22-Ser23) can activate a subset of cellular p53 targets.", "Furthermore, we showed that residues 53 and 54 are critical for the apoptotic and transcriptional activities of both p53(Delta1-42) and p53(Gln22-Ser23).", "Taken together, these data suggest that within residues 43-63 lie an apoptotic domain as well as another transcriptional activation domain.", "We therefore postulate that the apoptotic activity in p53(Gln22-Ser23) and p53(Delta1-42) is still transcription-dependent."], "structured": false}
{"doc_id": 9171913, "title": "Risk of breast cancer in relation to blood lipids: a prospective study of 31,209 Norwegian women", "abstract": ["In this prospective study, the relationship between blood lipids and breast cancer risk was examined.", "Between 1977 and 1983, 31,209 Norwegian women, 20 to 54 years of age, attended a health screening carried out by the Norwegian National Health Screening Services.", "The screening consisted of a questionnaire, anthropometric measurements, and nonfasting blood drawn for analysis of total serum cholesterol (TC), triglyceride (TG), and high density lipoprotein (HDL) cholesterol.", "Low density lipoprotein (LDL) cholesterol was calculated by the Friedewald's formula.", "During the seven to 13 years of follow-up, 302 breast cancer cases were identified by linkage to the Norwegian Cancer Registry.", "After adjustment for some of the known risk factors of breast cancer, the relative risk of women in the highest quartile of TC compared with women in the lowest quartile was 0.87 (95 percent confidence interval [CI]=0.61\u20131.23).", "The corresponding relative risks and CIs were 0.82 (CI=0.58\u20131.16) for TG, 1.02 (CI=0.73\u20131.42) for HDL, and 0.93 (CI=0.67\u20131.29) for LDL.", "No association between breast cancer risk and blood lipids was found in the total population, nor when the data were divided into those diagnosed before or after the age of 50 as a dividing line between pre- and postmenopausal diagnosis."], "structured": false}
{"doc_id": 9178310, "title": "Involvement of lysosomal dysfunction in autophagosome accumulation and early pathologies in adipose tissue of obese mice", "abstract": ["Whether obesity accelerates or suppresses autophagy in adipose tissue is still debatable.", "To clarify dysregulation of autophagy and its role in pathologies of obese adipose tissue, we focused on lysosomal function, protease maturation and activity, both in vivo and in vitro.", "First, we showed that autophagosome formation was accelerated, but autophagic clearance was impaired in obese adipose tissue.", "We also found protein and activity levels of CTSL (cathepsin L) were suppressed in obese adipose tissue, while the activity of CTSB (cathepsin B) was significantly enhanced.", "Moreover, cellular senescence and inflammasomes were activated in obese adipose tissue.", "In 3T3L1 adipocytes, downregulation of CTSL deteriorated autophagic clearance, upregulated expression of CTSB, promoted cellular senescence and activated inflammasomes.", "Upregulation of CTSB promoted additional activation of inflammasomes.", "Therefore, we suggest lysosomal dysfunction observed in obese adipose tissue leads to lower autophagic clearance, resulting in autophagosome accumulation.", "Simultaneously, lysosomal abnormalities, including deteriorated CTSL function and compensatory activation of CTSB, caused cellular senescence and inflammasome activation.", "Our findings strongly suggest lysosomal dysfunction is involved in early pathologies of obese adipose tissue."], "structured": false}
{"doc_id": 9185195, "title": "ARNO regulates VEGF-dependent tissue responses by stabilizing endothelial VEGFR-2 surface expression.", "abstract": ["AIMS The vascular endothelial growth factor (VEGF) stimulates angiogenesis by induction of vessel permeability, proliferation, and migration of endothelial cells, an important process in ischaemic diseases.", "ADP-ribosylation factor (ARF) nucleotide-binding site opener (ARNO) (cytohesin-2) is a guanine exchange factor important for cellular signalling through ARF GTPases.", "However, a role for ARNO in VEGF-dependent endothelial processes has so far not been documented.", "Therefore, we investigated whether ARNO has a role in VEGF-dependent activation of endothelial cells and thus vessel permeability.   \n", "METHODS AND RESULTS ARNO expression was observed in endothelial cells in vitro by RT-PCR, western blotting, and immunofluorescence as well as ex vivo by immunohistochemical staining of mouse aorta.", "Treatment with the cytohesin inhibitor SecinH3 or with an ARNO siRNA prevented VEGF-dependent Akt activation, assessed by detection of phosphorylated Akt, and proliferation of endothelial cells in vitro, measured by methylthiazoletetrazolium (MTT) reduction.", "In addition, ARNO suppression reduced VEGF-induced permeability in vessels of the mouse (C57BL/6) cremaster muscle in vivo, as measured by extravasation of fluorescein isothiocyanate (FITC)-dextran.", "Moreover, ARNO knock-down accelerated ligand-induced reduction in vascular endothelial growth factor receptor-2 (VEGFR-2) surface expression, internalization, and degradation, as assessed by flow cytometry and western blotting, respectively.   \n", "CONCLUSION Our findings indicate an important and novel role for endothelial ARNO in VEGF-dependent initiation of angiogenesis by regulation of VEGFR-2 internalization in endothelial cells, resulting in the activation of the Akt pathway, vessel permeability, and ultimately endothelial proliferation.", "Thus, ARNO may be a new essential player in endothelial signalling and angiogenesis."], "structured": true}
{"doc_id": 9194077, "title": "Effects of Hypoxia and Oxidative Stress on Expression of Neprilysin in Human Neuroblastoma Cells and Rat Cortical Neurones and Astrocytes", "abstract": ["Pathogenesis of Alzheimer\u2019s disease (AD), which is characterised by accumulation of extracellular deposits of \u03b2-amyloid peptide (A\u03b2) in the brain, has recently been linked to vascular disorders such as ischemia and stroke.", "A\u03b2 is constantly produced in the brain from amyloid precursor protein (APP) through its cleavage by \u03b2- and \u03b3-secretases and certain A\u03b2 species are toxic for neurones.", "The brain has an endogenous mechanism of A\u03b2 removal via proteolytic degradation and the zinc metalloproteinase neprilysin (NEP) is a critical regulator of A\u03b2 concentration.", "Down-regulation of NEP could predispose to AD.", "By comparing the effects of hypoxia and oxidative stress on expression and activity of the A\u03b2-degrading enzyme NEP in human neuroblastoma NB7 cells and rat primary cortical neurones we have demonstrated that hypoxia reduced NEP expression at the protein and mRNA levels as well as its activity.", "On contrary in astrocytes hypoxia increased NEP mRNA expression."], "structured": false}
{"doc_id": 9196472, "title": "Genetics and Beyond \u2013 The Transcriptome of Human Monocytes and Disease Susceptibility", "abstract": ["BACKGROUND Variability of gene expression in human may link gene sequence variability and phenotypes; however, non-genetic variations, alone or in combination with genetics, may also influence expression traits and have a critical role in physiological and disease processes.   \n", "METHODOLOGY/PRINCIPAL FINDINGS To get better insight into the overall variability of gene expression, we assessed the transcriptome of circulating monocytes, a key cell involved in immunity-related diseases and atherosclerosis, in 1,490 unrelated individuals and investigated its association with >675,000 SNPs and 10 common cardiovascular risk factors.", "Out of 12,808 expressed genes, 2,745 expression quantitative trait loci were detected (P<5.78x10(-12)), most of them (90%) being cis-modulated.", "Extensive analyses showed that associations identified by genome-wide association studies of lipids, body mass index or blood pressure were rarely compatible with a mediation by monocyte expression level at the locus.", "At a study-wide level (P<3.9x10(-7)), 1,662 expression traits (13.0%) were significantly associated with at least one risk factor.", "Genome-wide interaction analyses suggested that genetic variability and risk factors mostly acted additively on gene expression.", "Because of the structure of correlation among expression traits, the variability of risk factors could be characterized by a limited set of independent gene expressions which may have biological and clinical relevance.", "For example expression traits associated with cigarette smoking were more strongly associated with carotid atherosclerosis than smoking itself.   \n", "CONCLUSIONS/SIGNIFICANCE This study demonstrates that the monocyte transcriptome is a potent integrator of genetic and non-genetic influences of relevance for disease pathophysiology and risk assessment."], "structured": true}
{"doc_id": 9197092, "title": "Molecular mechanisms of (-)-epicatechin and chlorogenic acid on the regulation of the apoptotic and survival/proliferation pathways in a human hepatoma cell line.", "abstract": ["Dietary polyphenols have been associated with reduced risk of chronic diseases, but the precise molecular mechanisms of protection remain unclear.", "This work was aimed at studying the effect of (-)-epicatechin (EC) and chlorogenic acid (CGA) on the regulation of apoptotic and survival/proliferation pathways in a human hepatoma cell line (HepG2).", "EC or CGA treatment for 18 h had a slight effect on cell viability and decreased reactive oxygen species formation, and EC alone promoted cell proliferation, whereas CGA increased glutathione levels.", "Phenols neither induced the caspase cascade for apoptosis nor affected expression levels of Bcl-xL or Bax.", "A sustained activation of the major survival signals AKT/PI-3-kinase and ERK was shown in EC-treated cells, rather than in CGA-exposed cells.", "These data suggest that EC and CGA have no effect on apoptosis and enhance the intrinsic cellular tolerance against oxidative insults either by activating survival/proliferation pathways or by increasing antioxidant potential in HepG2."], "structured": false}
{"doc_id": 9197786, "title": "Wnt5a mediates nerve growth factor-dependent axonal branching and growth in developing sympathetic neurons.", "abstract": ["Nerve growth factor (NGF) is a potent survival and axon growth factor for neuronal populations in the peripheral nervous system.", "Although the mechanisms by which target-derived NGF influences survival of innervating neurons have been extensively investigated, its regulation of axonal growth and target innervation are just being elucidated.", "Here, we identify Wnt5a, a member of the Wnt family of secreted growth factors, as a key downstream effector of NGF in mediating axonal branching and growth in developing sympathetic neurons.", "Wnt5a is robustly expressed in sympathetic neurons when their axons are innervating NGF-expressing targets.", "NGF:TrkA signaling enhances neuronal expression of Wnt5a.", "Wnt5a rapidly induces axon branching while it has a long-term effect on promoting axon extension.", "Loss of Wnt5a function revealed that it is necessary for NGF-dependent axonal branching and growth, but not survival, in vitro.", "Furthermore, Wnt5a(-/-) mice display reduced innervation of NGF-expressing target tissues, and a subsequent increase in neuronal apoptosis, in vivo.", "Wnt5a functions in developing sympathetic neurons by locally activating protein kinase C in axons.", "Together, our findings define a novel regulatory pathway in which Wnt5a, expressed in sympathetic neurons in response to target-derived NGF, regulates innervation of peripheral targets."], "structured": false}
{"doc_id": 9199796, "title": "The Snf1 kinase controls glucose repression in yeast by modulating interactions between the Mig1 repressor and the Cyc8-Tup1 co-repressor.", "abstract": ["Among lower eukaryotes, glucose repression is a conserved, widely spread mechanism regulating carbon catabolism.", "The yeast Snf1 kinase, the Mig1 DNA-binding repressor and the Mig1-interacting co-repressor complex Cyc8(Ssn6)-Tup1 are central components of this pathway.", "Previous experiments suggested that cytoplasmic translocation of Mig1, upon its phosphorylation by Snf1 in the nucleus, is the key regulatory step for releasing glucose repression.", "In this report we re-evaluate this model.", "We establish the coordinated repressive action of Mig1 and Cyc8-Tup1 on GAL1 transcription, but we find that Cyc8-Tup1 is not tethered by Mig1 to the promoter DNA.", "We demonstrate that both negative regulators occupy GAL1 continuously under either repression or activation conditions, although the majority of the Mig1 is redistributed to the cytoplasm upon activation.", "We show that Snf1-dependent phosphorylation of Mig1 abolishes interaction with Cyc8-Tup1, and we propose that regulation of this interaction, not the Mig1 cytoplasmic localization, is the molecular switch that controls transcriptional repression/de-repression."], "structured": false}
{"doc_id": 9211173, "title": "ARID1A mutations in endometriosis-associated ovarian carcinomas.", "abstract": ["BACKGROUND Ovarian clear-cell and endometrioid carcinomas may arise from endometriosis, but the molecular events involved in this transformation have not been described.   \n", "METHODS We sequenced the whole transcriptomes of 18 ovarian clear-cell carcinomas and 1 ovarian clear-cell carcinoma cell line and found somatic mutations in ARID1A (the AT-rich interactive domain 1A [SWI-like] gene) in 6 of the samples.", "ARID1A encodes BAF250a, a key component of the SWI\u2013SNF chromatin remodeling complex.", "We sequenced ARID1A in an additional 210 ovarian carcinomas and a second ovarian clear-cell carcinoma cell line and measured BAF250a expression by means of immunohistochemical analysis in an additional 455 ovarian carcinomas.   \n", "RESULTS ARID1A mutations were seen in 55 of 119 ovarian clear-cell carcinomas (46%), 10 of 33 endometrioid carcinomas (30%), and none of the 76 high-grade serous ovarian carcinomas.", "Seventeen carcinomas had two somatic mutations each.", "Loss of the BAF250a protein correlated strongly with the ovarian clear-cell carcinoma and endometrioid carcinoma subtypes and the presence of ARID1A mutations.", "In two patients, ARID1A mutations and loss of BAF250a expression were evident in the tumor and contiguous atypical endometriosis but not in distant endometriotic lesions.   \n", "CONCLUSIONS These data implicate ARID1A as a tumor-suppressor gene frequently disrupted in ovarian clear-cell and endometrioid carcinomas.", "Since ARID1A mutation and loss of BAF250a can be seen in the preneoplastic lesions, we speculate that this is an early event in the transformation of endometriosis into cancer.", "(Funded by the British Columbia Cancer Foundation and the Vancouver General Hospital\u2013University of British Columbia Hospital Foundation.)."], "structured": true}
{"doc_id": 9217800, "title": "The ALS-associated proteins FUS and TDP-43 function together to affect Drosophila locomotion and life span.", "abstract": ["The fatal adult motor neuron disease amyotrophic lateral sclerosis (ALS) shares some clinical and pathological overlap with frontotemporal dementia (FTD), an early-onset neurodegenerative disorder.", "The RNA/DNA-binding proteins fused in sarcoma (FUS; also known as TLS) and TAR DNA binding protein-43 (TDP-43) have recently been shown to be genetically and pathologically associated with familial forms of ALS and FTD.", "It is currently unknown whether perturbation of these proteins results in disease through mechanisms that are independent of normal protein function or via the pathophysiological disruption of molecular processes in which they are both critical.", "Here, we report that Drosophila mutants in which the homolog of FUS is disrupted exhibit decreased adult viability, diminished locomotor speed, and reduced life span compared with controls.", "These phenotypes were fully rescued by wild-type human FUS, but not ALS-associated mutant FUS proteins.", "A mutant of the Drosophila homolog of TDP-43 had similar, but more severe, deficits.", "Through cross-rescue analysis, we demonstrated that FUS acted together with and downstream of TDP-43 in a common genetic pathway in neurons.", "Furthermore, we found that these proteins associated with each other in an RNA-dependent complex.", "Our results establish that FUS and TDP-43 function together in vivo and suggest that molecular pathways requiring the combined activities of both of these proteins may be disrupted in ALS and FTD."], "structured": false}
{"doc_id": 9225850, "title": "Non-canonical PI3K-Cdc42-Pak-Mek-Erk Signaling Promotes Immune-Complex-Induced Apoptosis in Human Neutrophils", "abstract": ["Neutrophils are peripheral blood leukocytes that represent the first line of immune cell defense against bacterial and fungal infections but are also crucial players in the generation of the inflammatory response.", "Many neutrophil cell surface receptors regulate important cellular processes via activation of agonist-activated PI3Ks.", "We show here that activation of human neutrophils with insoluble immune complexes drives a previously uncharacterized, PI3K-dependent, non-canonical, pro-apoptotic signaling pathway, Fc\u03b3R-PI3K\u03b2/\u03b4-Cdc42-Pak-Mek-Erk.", "This is a rare demonstration of Ras/Raf-independent activation of Erk and of PI3K-mediated activation of Cdc42.", "In addition, comparative analysis of immune-complex- and fMLF-induced signaling uncovers key differences in pathways used by human and murine neutrophils.", "The non-canonical pathway we identify in this study may be important for the resolution of inflammation in chronic inflammatory diseases that rely on immune-complex-driven neutrophil activation."], "structured": false}
{"doc_id": 9226649, "title": "Inflammation-induced tumorigenesis in the colon is regulated by caspase-1 and NLRC4.", "abstract": ["Chronic inflammation is a known risk factor for tumorigenesis, yet the precise mechanism of this association is currently unknown.", "The inflammasome, a multiprotein complex formed by NOD-like receptor (NLR) family members, has recently been shown to orchestrate multiple innate and adaptive immune responses, yet its potential role in inflammation-induced cancer has been little studied.", "Using the azoxymethane and dextran sodium sulfate colitis-associated colorectal cancer model, we show that caspase-1-deficient (Casp1(-/-)) mice have enhanced tumor formation.", "Surprisingly, the role of caspase-1 in tumorigenesis was not through regulation of colonic inflammation, but rather through regulation of colonic epithelial cell proliferation and apoptosis.", "Consequently, caspase-1-deficient mice demonstrate increased colonic epithelial cell proliferation in early stages of injury-induced tumor formation and reduced apoptosis in advanced tumors.", "We suggest a model in which the NLRC4 inflammasome is central to colonic inflammation-induced tumor formation through regulation of epithelial cell response to injury."], "structured": false}
{"doc_id": 9239963, "title": "The nuclear receptors SF1 and LRH1 are expressed in endometrial cancer cells and regulate steroidogenic gene transcription by cooperating with AP-1 factors.", "abstract": ["Excessive exposure to estradiol represents the main risk factor for endometrial cancer.", "The abnormally high estradiol levels in the endometrium of women with endometrial cancer are most likely due to overproduction by the tumour itself.", "Endometrial cancer cells express the genes encoding the steroidogenic enzymes involved in estradiol synthesis.", "Here we used RT-PCR and Western blot to show that the nuclear receptors SF1 and LRH1, two well-known regulators of steroidogenic gene expression in gonadal and adrenal cells, are also expressed in endometrial cancer cell lines.", "By transient transfections, we found that SF1 and LRH1, but not the related nuclear receptor NUR77, can activate the promoters of three human steroidogenic genes: STAR, HSD3B2, and CYP19A1 PII.", "Similarly, forskolin but not PMA, could activate all three promoters.", "In addition, we found that both SF1 and LRH1 can transcriptionally cooperate with the AP-1 family members c-JUN and c-FOS, known to be associated with enhanced proliferation of endometrial carcinoma cells, to further enhance activation of the STAR, HSD3B2, and CYP19A1 PII promoters.", "All together, our data provide novel insights into the mechanisms of steroidogenic gene expression in endometrial cancer cells and thus in the regulation of estradiol biosynthesis by tumour cells."], "structured": false}
{"doc_id": 9244474, "title": "Dietary factors in chronic inflammation: food tolerances and intolerances of a New Zealand Caucasian Crohn's disease population.", "abstract": ["Diet is known to play a major role in the symptoms of the inflammatory bowel disease, Crohn's disease (CD).", "Although no single diet is appropriate to all individuals, most CD patients are aware of foods that provide adverse or beneficial effects.", "This study seeks to categorise foods in relation to their effects on symptoms of CD, in a New Zealand Caucasian population.", "Four hundred and forty-six subjects from two different centres in New Zealand were recruited into the study.", "An extensive dietary questionnaire (257 food items in 15 groups) recorded self-reported dietary tolerances and intolerances.", "Across each of the food groups, there were statistically significant differences among responses to foods.", "A two-dimensional graphical summary enabled stratification of foods according to the probability that they will be either beneficial or detrimental.", "A small number of foods are frequently considered to be beneficial, including white fish, salmon and tuna, gluten-free products, oatmeal, bananas, boiled potatoes, sweet potatoes (kumara), pumpkin, soya milk, goat's milk and yoghurt.", "Foods that are typically considered detrimental include grapefruit, chilli or chilli sauce, corn and corn products, peanuts, cream, salami, curried foods, cola drinks, high energy drinks, beer, and red wine.", "For a number of the food items, the same item that was beneficial for one group of subjects was detrimental to others; in particular soya milk, goat's milk, yoghurt, oatmeal, kiwifruit, prunes, apple, broccoli, cauliflower, linseed, pumpkin seed, sunflower seed, ginger and ginger products, beef, lamb, liver, and oily fish.", "It was not possible to identify a specific group of food items that should be avoided by all CD patients.", "The wide range of detrimental items suggests that dietary maintenance of remission is likely to be difficult, and to exclude a substantial number of foods.", "Personalised diets may be especially important to these individuals."], "structured": false}
{"doc_id": 9254550, "title": "Age as a risk factor for thrombocytopenia and anaemia in children treated for acute uncomplicated falciparum malaria.", "abstract": ["BACKGROUND & OBJECTIVES Anaemia is commonly observed in children with malaria, but reports on leucocyte and platelet count abnormalities associated with malaria are inconsistent.", "This study examined the effect of age, gender, parasite density and temperature on haematological parameters in children with acute uncomplicated malaria.   \n", "METHODS Haematological parameters were determined in children with acute uncomplicated malaria, and these were correlated with age, sex, temperature and parasite density.", "Statistical analysis was done using SAS 9.1.   \n", "RESULTS Six hundred and ninety five children with acute uncomplicated malaria participated in the study.", "The mean age was 51.7 months +/-", "33.8.", "At presentation, anaemia occurred in 43.8% of the patients and children <5 yr had a significantly lower haematocrit (28.4% +/- 4.8) than that of older children (32.8% +/-", "4.8) (p <0.001), but the haematocrit was not significantly different by days 14 and 28.", "There was no difference between both sexes.", "Leucocytosis was more frequently seen than leucopenia (9.5% vs 3%).", "Thrombocytopenia was found in 59.3% of enrolled patients.", "More than half of the patients with thrombocytopenia had recovered by Day 28.", "Baseline platelet count was related to Day 14 (r = 0.6, p < 0.0001) and Day 28 (r = 0.2, p = 0.0015) and the haematocrit on Day 28 (r = 0.12, p = 0.00197).", "Platelet count showed no correlation with temperature, parasite density and leucocyte count.", "Haematocrit correlated with age (r = 0.4, p < 0.0001); but not with parasite density or temperature.", "Leucocyte count showed no correlation with age or parasite density.   \n", "CONCLUSION While thrombocytopenia was the most common haematological finding and may be of diagnostic importance, anaemia and leucocytosis were more common in the under fives."], "structured": true}
{"doc_id": 9257019, "title": "Discovery of endogenous catecholamines in lymphocytes and evidence for catecholamine regulation of lymphocyte function via an autocrine loop.", "abstract": ["Evidence has been obtained that catecholamines and their metabolites are present in single lymphocytes and extracts of T- and B-cell clones by use of capillary electrophoresis with electrochemical detection.", "Pharmacological inhibition of tyrosine hydroxylase reduces observed catecholamine levels, suggesting catecholamine synthesis by lymphocytes.", "Intracellular dopamine levels are shown to be increased by extra-cellular dopamine, suggesting a cellular-uptake mechanism.", "Furthermore, incubation with either dopamine or L-dihydroxyphenylalanine, a precursor of dopamine, results in a dose-dependent inhibition of lymphocyte proliferation and differentiation.", "Together, these results suggest the presence of an autocrine loop whereby lymphocytes down-regulate their own activity."], "structured": false}
{"doc_id": 9272598, "title": "Structure-based drug design identifies polythiophenes as antiprion compounds", "abstract": ["Prions cause transmissible spongiform encephalopathies for which no treatment exists.", "Prions consist of PrPSc, a misfolded and aggregated form of the cellular prion protein (PrPC).", "We explore the antiprion properties of luminescent conjugated polythiophenes (LCPs) that bind and stabilize ordered protein aggregates.", "By administering a library of structurally diverse LCPs to the brains of prion-infected mice via osmotic minipumps, we found that antiprion activity required a minimum of five thiophene rings bearing regularly spaced carboxyl side groups.", "Solid-state nuclear magnetic resonance analyses and molecular dynamics simulations revealed that anionic side chains interacted with complementary, regularly spaced cationic amyloid residues of model prions.", "These findings allowed us to extract structural rules governing the interaction between LCPs and protein aggregates, which we then used to design a new set of LCPs with optimized binding.", "The new set of LCPs showed robust prophylactic and therapeutic potency in prion-infected mice, with the lead compound extending survival by >80% and showing activity against both mouse and hamster prions as well as efficacy upon intraperitoneal administration into mice.", "These results demonstrate the feasibility of targeted chemical design of compounds that may be useful for treating diseases of aberrant protein aggregation such as prion disease."], "structured": false}
{"doc_id": 9274291, "title": "Comparisons of patient and physician expectations for cancer survivorship care.", "abstract": ["PURPOSE To compare expectations for cancer survivorship care between patients and their physicians and between primary care providers (PCPs) and oncologists.   \n", "METHODS Survivors and their physicians were surveyed to evaluate for expectations regarding physician participation in primary cancer follow-up, screening for other cancers, general preventive health, and management of comorbidities.   \n", "RESULTS Of 992 eligible survivors and 607 physicians surveyed, 535 (54%) and 378 (62%) were assessable, respectively.", "Among physician respondents, 255 (67%) were PCPs and 123 (33%) were oncologists.", "Comparing patients with their oncologists, expectations were highly discrepant for screening for cancers other than the index one (agreement rate, 29%), with patients anticipating significantly more oncologist involvement.", "Between patients and their PCPs, expectations were most incongruent for primary cancer follow-up (agreement rate, 35%), with PCPs indicating they should contribute a much greater part to this aspect of care.", "Expectations between patients and their PCPs were generally more concordant than between patients and their oncologists.", "PCPs and oncologists showed high discordances in perceptions of their own roles for primary cancer follow-up, cancer screening, and general preventive health (agreement rates of 3%, 44%, and 51%, respectively).", "In the case of primary cancer follow-up, both PCPs and oncologists indicated they should carry substantial responsibility for this task.   \n", "CONCLUSION Patients and physicians have discordant expectations with respect to the roles of PCPs and oncologists in cancer survivorship care.", "Uncertainties around physician roles and responsibilities can lead to deficiencies in care, supporting the need to make survivorship care planning a standard component in cancer management."], "structured": true}
{"doc_id": 9278263, "title": "MHC class I antigen presentation: learning from viral evasion strategies", "abstract": ["The cell surface display of peptides by MHC class I molecules to lymphocytes provides the host with an important surveillance mechanism to protect against invading pathogens.", "However, in turn, viruses have evolved elegant strategies to inhibit various stages of the MHC class I antigen presentation pathway and prevent the display of viral peptides.", "This Review highlights how the elucidation of mechanisms of viral immune evasion is important for advancing our understanding of virus\u2013host interactions and can further our knowledge of the MHC class I presentation pathway as well as other cellular pathways."], "structured": false}
{"doc_id": 9283422, "title": "T cell receptor-proximal signals are sustained in peripheral microclusters and terminated in the central supramolecular activation cluster.", "abstract": ["T cell receptor (TCR) signaling is initiated and sustained in microclusters; however, it's not known whether signaling also occurs in the TCR-rich central supramolecular activation cluster (cSMAC).", "We showed that the cSMAC formed by fusion of microclusters contained more CD45 than microclusters and is a site enriched in lysobisphosphatidic acid, a lipid involved in sorting ubiquitinated membrane proteins for degradation.", "Calcium signaling via TCR was blocked within 2 min by anti-MHCp treatment and 1 min by latrunculin-A treatment.", "TCR-MHCp interactions in the cSMAC survived these perturbations for 10 min and hence were not sufficient to sustain signaling.", "TCR microclusters were also resistant to disruption by anti-MHCp and latrunculin-A treatments.", "We propose that TCR signaling is sustained by stabilized microclusters and is terminated in the cSMAC, a structure from which TCR are sorted for degradation.", "Our studies reveal a role for F-actin in TCR signaling beyond microcluster formation."], "structured": false}
{"doc_id": 9285396, "title": "The role of red cell distribution width in the prognosis of patients with gastric cancer.", "abstract": ["BACKGROUND Although the red cell distribution width (RDW) has been reported as a reliable predictor of prognosis in several types of cancer, to our knowledge the prognostic value of RDW in gastric carcinoma has not been studied, so far.   \n", "OBJECTIVE We aimed to investigate the role of red cell distribution width (RDW) in predicting prognosis in gastric cancer patients.   \n", "METHODS All gastric cancer patients who underwent curative surgery (n= 172, 110M/62F) over a five-year study period were evaluated.", "Data on demographics, preoperative RDW levels, tumor characteristics (early stage: I and II, advanced stage: IIIA-B-C), disease-free (DFS) and overall survival (OS) were retrospectively reviewed.", "Patients were classified as high RDW group (RDW \u2265 16, n= 62) or low RDW group (RDW < 16, n= 110).   \n", "RESULTS Overall mortality and postoperative 60-day mortality in both groups were 55% and 14%, respectively.", "A borderline significant association between RDW (0.063) and mortality was noted.", "Preoperative RDW levels were significantly higher in patients with short-term mortality (17.9 \u00b1 4.3 vs. 16 \u00b1 3.2, p= 0.015).", "In high RDW group, the incidence of advanced gastric cancer was significantly higher (75 vs. 51%, p= 0.002), whereas DFS (0.035) and OS (p= 0.04) were lower.   \n", "CONCLUSION The frequency of advanced cancer was high in patients with high RDWvalues.", "High RDW values were strongly associated with short-term mortality although only a borderline relationship with overall survival was observed."], "structured": true}
{"doc_id": 9288638, "title": "Vascular responsiveness in isolated perfused kidneys of diabetic hypertensive rats.", "abstract": ["OBJECTIVE The aim of this study was to investigate whether diabetes and hypertension cause additive effects in the responses to various vasoconstrictor and vasodilator agents, in isolated perfused kidneys obtained from streptozotocin (STZ)-diabetic Wistar-Kyoto (WKY) rats and from diabetic spontaneously hypertensive rats (SHR).   \n", "METHODS SHR and WKY rats were administered STZ 55 mg/kg by intravenous injection into a lateral tail vein at age 12 weeks.", "Eight weeks later the kidneys were isolated and perfused via the left renal artery with a physiological salt solution.", "Renal perfusion pressure was measured continuously.", "Concentration response curves were plotted for various vasoconstrictor and vasodilator agents.   \n", "RESULTS Both the diabetic and the hypertensive state were associated with an increased wet kidney weight.", "The contractile responses of the renal arterial system to phenylephrine (PhE), serotonin (5-HT) and angiotensin II (Ang II) in terms both of the maximal rise in perfusion pressure (mmHg) and of the sensitivity (log EC50) were the same in preparations from diabetic WKY rats and in those from normoglycaemic WKY rats.", "The maximal contractile responses both to PhE and to Ang II were enhanced in kidneys from SHR compared with those in kidneys from their normotensive controls, whereas simultaneously occurring diabetes impaired this sensitization.", "After precontraction with 3 x 10(-6) mol/l PhE both endothelium-dependent (methacholine) and endothelium-independent (sodium nitroprusside) vasodilator drugs caused the same vasodilator response in the preparations taken from the four groups of animals.   \n", "CONCLUSION In isolated perfused kidneys obtained from STZ-diabetic WKY rats and SHR, the isolated diabetic state did not influence the vasoconstriction caused by various agonists.", "However, the enhanced vascular reactivity in the hypertensive state was blunted by simultaneously occurring diabetes mellitus.", "Endothelium-dependent and -independent vasorelaxation in this model was not affected neither by the hypertensive nor by the diabetic state."], "structured": true}
{"doc_id": 9291596, "title": "DNA replication is required To elicit cellular responses to psoralen-induced DNA interstrand cross-links.", "abstract": ["Following introduction of DNA interstrand cross-links (ICLs), mammalian cells display chromosome breakage or cell cycle delay with a 4N DNA content.", "To further understand the nature of the delay, previously described as a G(2)/M arrest, we developed a protocol to generate ICLs during specific intervals of the cell cycle.", "Synchronous populations of G(1), S, and G(2) cells were treated with photoactivated 4'-hydroxymethyl-4,5',8-trimethylpsoralen (HMT) and scored for normal passage into mitosis.", "In contrast to what was found for ionizing radiation, ICLs introduced during G(2) did not result in a G(2)/M arrest, mitotic arrest, or chromosome breakage.", "Rather, subsequent passage through S phase was required to trigger both chromosome breakage and arrest in the next cell cycle.", "Similarly, ICLs introduced during G(1) did not cause a G(1)/S arrest.", "We conclude that DNA replication is required to elicit the cellular responses of cell cycle arrest and genomic instability after psoralen-induced ICLs.", "In primary human fibroblasts, the 4N DNA content cell cycle arrest triggered by ICLs was long lasting but reversible.", "Kinetic analysis suggested that these cells could remove up to approximately 2,500 ICLs/genome at an average rate of 11 ICLs/genome/h."], "structured": false}
{"doc_id": 9291668, "title": " DNA methylation and healthy human aging", "abstract": ["The process of aging results in a host of changes at the cellular and molecular levels, which include senescence, telomere shortening, and changes in gene expression.", "Epigenetic patterns also change over the lifespan, suggesting that epigenetic changes may constitute an important component of the aging process.", "The epigenetic mark that has been most highly studied is DNA methylation, the presence of methyl groups at CpG dinucleotides.", "These dinucleotides are often located near gene promoters and associate with gene expression levels.", "Early studies indicated that global levels of DNA methylation increase over the first few years of life and then decrease beginning in late adulthood.", "Recently, with the advent of microarray and next-generation sequencing technologies, increases in variability of DNA methylation with age have been observed, and a number of site-specific patterns have been identified.", "It has also been shown that certain CpG sites are highly associated with age, to the extent that prediction models using a small number of these sites can accurately predict the chronological age of the donor.", "Together, these observations point to the existence of two phenomena that both contribute to age-related DNA methylation changes: epigenetic drift and the epigenetic clock.", "In this review, we focus on healthy human aging throughout the lifetime and discuss the dynamics of DNA methylation as well as how interactions between the genome, environment, and the epigenome influence aging rates.", "We also discuss the impact of determining 'epigenetic age' for human health and outline some important caveats to existing and future studies."], "structured": false}
{"doc_id": 9301606, "title": "Parathyroid hormone-induced E4BP4/NFIL3 down-regulates transcription in osteoblasts.", "abstract": ["Parathyroid hormone (PTH), a major regulator of bone metabolism, activates the PTHR1 receptor on the osteoblast plasma membrane to initiate signaling and induce transcription of primary response genes.", "Subsequently, primary genes with transcriptional activity regulate expression of downstream PTH targets.", "We have identified the adenovirus E4 promoter-binding protein/nuclear factor regulated by IL-3 (E4bp4) as a PTH-induced primary gene in osteoblasts.", "E4BP4 is a basic leucine zipper (bZIP) transcription factor that represses or activates transcription in non-osteoblastic cells.", "We report here that PTH rapidly and transiently induced E4bp4 mRNA in osteoblastic cells and that this induction did not require protein synthesis.", "PTH also induced E4BP4 protein synthesis and E4BP4 binding to a consensus but not to a mutant E4BP4 response element (EBPRE).", "E4BP4 overexpression inhibited an EBPRE-containing promoter-reporter construct, whereas PTH treatment attenuated activity of the same construct in primary mouse osteoblasts.", "Finally, E4BP4 overexpression inhibited PTH-induced activity of a cyclooxygenase-2 promoter-reporter construct.", "Our data suggest a role for E4BP4 in attenuation of PTH target gene transcription in osteoblasts."], "structured": false}
{"doc_id": 9304312, "title": "Molecular basis of synaptic vesicle cargo recognition by the endocytic sorting adaptor stonin 2", "abstract": ["Synaptic transmission depends on clathrin-mediated recycling of synaptic vesicles (SVs).", "How select SV proteins are targeted for internalization has remained elusive.", "Stonins are evolutionarily conserved adaptors dedicated to endocytic sorting of the SV protein synaptotagmin.", "Our data identify the molecular determinants for recognition of synaptotagmin by stonin 2 or its Caenorhabditis elegans orthologue UNC-41B.", "The interaction involves the direct association of clusters of basic residues on the surface of the cytoplasmic domain of synaptotagmin 1 and a beta strand within the mu-homology domain of stonin 2.", "Mutation of K783, Y784, and E785 to alanine within this stonin 2 beta strand results in failure of the mutant stonin protein to associate with synaptotagmin, to accumulate at synapses, and to facilitate synaptotagmin internalization.", "Synaptotagmin-binding-defective UNC-41B is unable to rescue paralysis in C. elegans stonin mutant animals, suggesting that the mechanism of stonin-mediated SV cargo recognition is conserved from worms to mammals."], "structured": false}
{"doc_id": 9306247, "title": "Size separation of circulatory DNA in maternal plasma permits ready detection of fetal DNA polymorphisms.", "abstract": ["BACKGROUND Analysis of fetal DNA in maternal plasma has recently been introduced as a new method for noninvasive prenatal diagnosis, particularly for the analysis of fetal genetic traits, which are absent from the maternal genome, e.g., RHD or Y-chromosome-specific sequences.", "To date, the analysis of other fetal genetic traits has been more problematic because of the overwhelming presence of maternal DNA sequences in the circulation.", "We examined whether different biochemical properties can be discerned between fetal and maternal circulatory DNA.   \n", "METHODS Plasma DNA was examined by agarose gel electrophoresis.", "The fractions of fetal and maternal DNA in size-fractionated fragments were assayed by real-time PCR.", "The determination of paternally and maternally inherited fetal genetic traits was examined by use of highly polymorphic chromosome-21-specific microsatellite markers.   \n", "RESULTS Size fractionation of circulatory DNA indicated that the major portion of cell-free fetal DNA had an approximate molecular size of <0.3 kb, whereas maternally derived sequences were, on average, considerably larger than 1 kb.", "Analysis of size-fractionated DNA (</=0.3 kb) from maternal plasma samples facilitated the ready detection of paternally and maternally inherited microsatellite markers.   \n", "CONCLUSIONS Circulatory fetal DNA can be enriched by size selection of fragment sizes less than approximately 0.3 kb.", "Such selection permits easier analysis of both paternally and maternally inherited DNA polymorphisms."], "structured": true}
{"doc_id": 9310407, "title": "The intravascular volume effect of Ringer's lactate is below 20%: a prospective study in humans", "abstract": ["INTRODUCTION Isotonic crystalloids play a central role in perioperative fluid management.", "Isooncotic preparations of colloids (for example, human albumin or hydroxyethyl starch) remain nearly completely intravascular when infused to compensate for acute blood losses.", "Recent data were interpreted to indicate a comparable intravascular volume effect for crystalloids, challenging the occasionally suggested advantage of using colloids to treat hypovolemia.", "General physiological knowledge and clinical experience, however, suggest otherwise.   \n", "METHODS In a prospective study, double-tracer blood volume measurements were performed before and after intended normovolemic hemodilution in ten female adults, simultaneously substituting the three-fold amount of withdrawn blood with Ringer's lactate.", "Any originated deficits were substituted with half the volume of 20% human albumin, followed by a further assessment of blood volume.", "To assess significance between the measurements, repeated measures analysis of variance (ANOVA) according to Fisher were performed.", "If significant results were shown, paired t tests (according to Student) for the singular measurements were taken.", "P < 0.05 was considered to be significant.   \n", "RESULTS A total of 1,097 \u00b1 285 ml of whole blood were withdrawn (641 \u00b1 155 ml/m(2) body surface area) and simultaneously replaced by 3,430 \u00b1 806 ml of Ringer's lactate.", "All patients showed a significant decrease in blood volume after hemodilution (-459 \u00b1 185 ml; P < 0.05) that did not involve relevant hemodynamical changes, and a significant increase in interstitial water content (+2,157 \u00b1 606 ml; P < 0.05).", "The volume effect of Ringer's lactate was 17 \u00b1 10%.", "The infusion of 245 \u00b1 64 ml of 20% human albumin in this situation restored blood volume back to baseline values, the volume effect being 184 \u00b1 63%.   \n", "CONCLUSIONS Substitution of isolated intravascular deficits in cardiopulmonary healthy adults with the three-fold amount of Ringer's lactate impedes maintenance of intravascular normovolemia.", "The main side effect was an impressive interstitial fluid accumulation, which was partly restored by the intravenous infusion of 20% human albumin.", "We recommend to substitute the five-fold amount of crystalloids or to use an isooncotic preparation in the face of acute bleeding in patients where edema prevention might be advantageous."], "structured": true}
{"doc_id": 9315213, "title": "Fibroblast Growth Factor 21 Prevents Atherosclerosis by Suppression of Hepatic Sterol Regulatory Element-Binding Protein-2 and Induction of Adiponectin in Mice", "abstract": ["BACKGROUND Fibroblast growth factor 21 (FGF21) is a metabolic hormone with pleiotropic effects on glucose and lipid metabolism and insulin sensitivity.", "It acts as a key downstream target of both peroxisome proliferator-activated receptor \u03b1 and \u03b3, the agonists of which have been used for lipid lowering and insulin sensitization, respectively.", "However, the role of FGF21 in the cardiovascular system remains elusive.   \n", "METHODS AND RESULTS The roles of FGF21 in atherosclerosis were investigated by evaluating the impact of FGF21 deficiency and replenishment with recombinant FGF21 in apolipoprotein E(-/-) mice.", "FGF21 deficiency causes a marked exacerbation of atherosclerotic plaque formation and premature death in apolipoprotein E(-/-) mice, which is accompanied by hypoadiponectinemia and severe hypercholesterolemia.", "Replenishment of FGF21 protects against atherosclerosis in apolipoprotein E(-/-)mice via 2 independent mechanisms, inducing the adipocyte production of adiponectin, which in turn acts on the blood vessels to inhibit neointima formation and macrophage inflammation, and suppressing the hepatic expression of the transcription factor sterol regulatory element-binding protein-2, thereby leading to reduced cholesterol synthesis and attenuation of hypercholesterolemia.", "Chronic treatment with adiponectin partially reverses atherosclerosis without obvious effects on hypercholesterolemia in FGF21-deficient apolipoprotein E(-/-) mice.", "By contrast, the cholesterol-lowering effects of FGF21 are abrogated by hepatic expression of sterol regulatory element-binding protein-2.   \n", "CONCLUSIONS FGF21 protects against atherosclerosis via fine tuning the multiorgan crosstalk among liver, adipose tissue, and blood vessels."], "structured": true}
{"doc_id": 9317504, "title": "VARNA: Interactive drawing and editing of the RNA secondary structure", "abstract": ["DESCRIPTION VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases.   ", "FEATURES VARNA implements four drawing algorithms, supports input/output using the classic formats dbn, ct, bpseq and RNAML and exports the drawing as five picture formats, either pixel-based (JPEG, PNG) or vector-based (SVG, EPS and XFIG).", "It also allows manual modification and structural annotation of the resulting drawing using either an interactive point and click approach, within a web server or through command-line arguments.   ", "AVAILABILITY VARNA is a free software, released under the terms of the GPLv3.0 license and available at http://varna.lri.fr.   ", "SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online."], "structured": false}
{"doc_id": 9334631, "title": "C-reactive protein decreases interleukin-10 secretion in activated human monocyte-derived macrophages via inhibition of cyclic AMP production.", "abstract": ["OBJECTIVE C-Reactive protein (CRP), a cardiovascular risk marker, could also participate in atherosclerosis.", "Atherosclerotic plaques express CRP and interleukin (IL)-10, a major antiinflammatory cytokine.", "IL-10 deficiency results in increased lesion formation, whereas IL-10 delivery attenuates lesions.", "We tested the effect of CRP on lipopolysaccharide (LPS)-induced IL-10 secretion in human monocyte-derived macrophages (HMDMs).   \n", "METHODS AND RESULTS Incubation of HMDMs with CRP significantly decreased LPS-induced IL-10 mRNA and intracellular and secreted IL-10 protein and destabilized IL-10 mRNA.", "Also, CRP alone increased secretion of IL-8, IL-6, and tumor necrosis factor from HMDMs and did not inhibit LPS-induced secretion of these cytokines.", "Fc gamma receptor I antibodies significantly reversed CRP-mediated IL-10 inhibition.", "CRP significantly decreased intracellular cAMP, phospho-cAMP response element binding protein (pCREB), and adenyl cyclase activity.", "cAMP agonists reversed CRP-mediated IL-10 inhibition.", "Overexpression of wild-type and constitutively active CREB in THP-1 cells revealed attenuation of the inhibitory effect of CRP on LPS-induced IL-10 levels.", "CRP also inhibited hemoglobin:haptoglobin-induced IL-10 and heme oxygenase-1.", "Furthermore, administration of human CRP to rats significantly decreased IL-10 levels.   \n", "CONCLUSIONS This study provides novel evidence that CRP, by decreasing IL-10 alters the antiinflammatory/proinflammatory balance, accentuating inflammation, which is pivotal in atherothrombosis."], "structured": true}
{"doc_id": 9379687, "title": "The DNA polymerase activity of Pol \u03b5 holoenzyme is required for rapid and efficient chromosomal DNA replication in Xenopus egg extracts", "abstract": ["DNA polymerase \u03b5 (Pol \u03b5) is involved in DNA replication, repair, and cell-cycle checkpoint control in eukaryotic cells.", "Although the roles of replicative Pol \u03b1 and Pol \u03b4 in chromosomal DNA replication are relatively well understood and well documented, the precise role of Pol \u03b5 in chromosomal DNA replication is not well understood.", "This study uses a Xenopus egg extract DNA replication system to further elucidate the replicative role(s) played by Pol \u03b5.", "Previous studies show that the initiation timing and elongation of chromosomal DNA replication are markedly impaired in Pol \u03b5-depleted Xenopus egg extracts, with reduced accumulation of replicative intermediates and products.", "This study shows that normal replication is restored by addition of Pol \u03b5 holoenzyme to Pol \u03b5-depleted extracts, but not by addition of polymerase-deficient forms of Pol \u03b5, including polymerase point or deletion mutants or incomplete enzyme complexes.", "Evidence is also provided that Pol \u03b5 holoenzyme interacts directly with GINS, Cdc45p and Cut5p, each of which plays an important role in initiation of chromosomal DNA replication in eukaryotic cells.", "These results indicate that the DNA polymerase activity of Pol \u03b5 holoenzyme plays an essential role in normal chromosomal DNA replication in Xenopus egg extracts.", "These are the first biochemical data to show the DNA polymerase activity of Pol \u03b5 holoenzyme is essential for chromosomal DNA replication in higher eukaryotes, unlike in yeasts."], "structured": false}
{"doc_id": 9393969, "title": "DAF-16/FOXO employs the chromatin remodeller SWI/SNF to promote stress resistance and longevity", "abstract": ["Organisms are constantly challenged by stresses and privations and require adaptive responses for their survival.", "The forkhead box O (FOXO) transcription factor DAF-16 (hereafter referred to as DAF-16/FOXO) is a central nexus in these responses, but despite its importance little is known about how it regulates its target genes.", "Proteomic identification of DAF-16/FOXO-binding partners in Caenorhabditis elegans and their subsequent functional evaluation by RNA interference revealed several candidate DAF-16/FOXO cofactors, most notably the chromatin remodeller SWI/SNF.", "DAF-16/FOXO and SWI/SNF form a complex and globally co-localize at DAF-16/FOXO target promoters.", "We show that specifically for gene activation, DAF-16/FOXO depends on SWI/SNF, facilitating SWI/SNF recruitment to target promoters, to activate transcription by presumed remodelling of local chromatin.", "For the animal, this translates into an essential role for SWI/SNF in DAF-16/FOXO-mediated processes, in particular dauer formation, stress resistance and the promotion of longevity.", "Thus, we give insight into the mechanisms of DAF-16/FOXO-mediated transcriptional regulation and establish a critical link between ATP-dependent chromatin remodelling and lifespan regulation."], "structured": false}
{"doc_id": 9394119, "title": "Association of type and location of BRCA1 and BRCA2 mutations with risk of breast and ovarian cancer.", "abstract": ["IMPORTANCE Limited information about the relationship between specific mutations in BRCA1 or BRCA2 (BRCA1/2) and cancer risk exists.   \n", "OBJECTIVE To identify mutation-specific cancer risks for carriers of BRCA1/2.   \n", "DESIGN, SETTING, AND PARTICIPANTS Observational study of women who were ascertained between 1937 and 2011 (median, 1999) and found to carry disease-associated BRCA1 or BRCA2 mutations.", "The international sample comprised 19,581 carriers of BRCA1 mutations and 11,900 carriers of BRCA2 mutations from 55 centers in 33 countries on 6 continents.", "We estimated hazard ratios for breast and ovarian cancer based on mutation type, function, and nucleotide position.", "We also estimated RHR, the ratio of breast vs ovarian cancer hazard ratios.", "A value of RHR greater than 1 indicated elevated breast cancer risk; a value of RHR less than 1 indicated elevated ovarian cancer risk.   ", "EXPOSURES Mutations of BRCA1 or BRCA2.   \n", "MAIN OUTCOMES AND MEASURES Breast and ovarian cancer risks.   \n", "RESULTS Among BRCA1 mutation carriers, 9052 women (46%) were diagnosed with breast cancer, 2317 (12%) with ovarian cancer, 1041 (5%) with breast and ovarian cancer, and 7171 (37%) without cancer.", "Among BRCA2 mutation carriers, 6180 women (52%) were diagnosed with breast cancer, 682 (6%) with ovarian cancer, 272 (2%) with breast and ovarian cancer, and 4766 (40%) without cancer.", "In BRCA1, we identified 3 breast cancer cluster regions (BCCRs) located at c.179 to c.505 (BCCR1; RHR = 1.46; 95% CI, 1.22-1.74; P = 2 \u00d7 10(-6)), c.4328 to c.4945 (BCCR2; RHR = 1.34; 95% CI, 1.01-1.78; P = .04), and c. 5261 to c.5563 (BCCR2', RHR = 1.38; 95% CI, 1.22-1.55; P = 6 \u00d7 10(-9)).", "We also identified an ovarian cancer cluster region (OCCR) from c.1380 to c.4062 (approximately exon 11) with RHR = 0.62 (95% CI, 0.56-0.70; P = 9 \u00d7 10(-17)).", "In BRCA2, we observed multiple BCCRs spanning c.1 to c.596 (BCCR1; RHR = 1.71; 95% CI, 1.06-2.78; P = .03), c.772 to c.1806 (BCCR1'; RHR = 1.63; 95% CI, 1.10-2.40; P = .01), and c.7394 to c.8904 (BCCR2; RHR = 2.31; 95% CI, 1.69-3.16; P = .00002).", "We also identified 3 OCCRs: the first (OCCR1) spanned c.3249 to c.5681 that was adjacent to c.5946delT (6174delT; RHR = 0.51; 95% CI, 0.44-0.60; P = 6 \u00d7 10(-17)).", "The second OCCR spanned c.6645 to c.7471 (OCCR2; RHR = 0.57; 95% CI, 0.41-0.80; P = .001).", "Mutations conferring nonsense-mediated decay were associated with differential breast or ovarian cancer risks and an earlier age of breast cancer diagnosis for both BRCA1 and BRCA2 mutation carriers.   \n", "CONCLUSIONS AND RELEVANCE Breast and ovarian cancer risks varied by type and location of BRCA1/2 mutations.", "With appropriate validation, these data may have implications for risk assessment and cancer prevention decision making for carriers of BRCA1 and BRCA2 mutations."], "structured": true}
{"doc_id": 9412420, "title": "Endogenous bone marrow MSCs are dynamic, fate-restricted participants in bone maintenance and regeneration.", "abstract": ["Mesenchymal stem cells (MSCs) commonly defined by in vitro functions have entered clinical application despite little definition of their function in residence.", "Here, we report genetic pulse-chase experiments that define osteoblastic cells as short-lived and nonreplicative, requiring replenishment from bone-marrow-derived, Mx1(+) stromal cells with \"MSC\" features.", "These cells respond to tissue stress and migrate to sites of injury, supplying new osteoblasts during fracture healing.", "Single cell transplantation yielded progeny that both preserve progenitor function and differentiate into osteoblasts, producing new bone.", "They are capable of local and systemic translocation and serial transplantation.", "While these cells meet current definitions of MSCs in vitro, they are osteolineage restricted in vivo in growing and adult animals.", "Therefore, bone-marrow-derived MSCs may be a heterogeneous population with the Mx1(+) population, representing a highly dynamic and stress responsive stem/progenitor cell population of fate-restricted potential that feeds the high cell replacement demands of the adult skeleton."], "structured": false}
{"doc_id": 9420732, "title": "Dscam and DSCAM: complex genes in simple animals, complex animals yet simple genes.", "abstract": ["Cadherins and the immunoglobulin (Ig) proteins give rise to a multitude of surface receptors, which function as diverse cell adhesion molecules (CAMs) or signal-transducing receptors.", "These functions are often interdependent, and rely on a high degree of specificity in homophilic binding as well as heterophilic interactions.", "The Drosophila receptor Dscam is an exceptional example of homophilic binding specificity involved in a number of important biological processes, such as neural wiring and innate immunity.", "Combinatorial use of alternatively spliced Ig-domains enables the generation of an estimated 18,000 isoform-specific homophilic receptor pairs.", "Although isoform diversity of Dscam is unique to arthropods, recent genetic analysis of vertebrate DSCAM (Down Syndrome Cell Adhesion Molecule) genes has revealed an intriguing conservation of molecular functions underlying neural wiring.", "This review covers the multiple functions of Dscam across different species highlighting its remarkable versatility as well as its conserved basic functions in neural development.", "We discuss how an unprecedented expansion of complex alternative splicing has been uniquely employed by arthropods to generate diverse surface receptors, important for cell-cell communication, molecular self-recognition in neurons, and innate immune defenses.", "We end with a speculative hypothesis reconciling the striking differences in Dscam and DSCAM gene structures with their conserved functions in molecular recognition underlying neural circuit formation."], "structured": false}
{"doc_id": 9433958, "title": "Differential innate immune response programs in neuronal subtypes determine susceptibility to infection in the brain by positive stranded RNA viruses", "abstract": ["Although susceptibility of neurons in the brain to microbial infection is a major determinant of clinical outcome, little is known about the molecular factors governing this vulnerability.", "Here we show that two types of neurons from distinct brain regions showed differential permissivity to replication of several positive-stranded RNA viruses.", "Granule cell neurons of the cerebellum and cortical neurons from the cerebral cortex have unique innate immune programs that confer differential susceptibility to viral infection ex vivo and in vivo.", "By transducing cortical neurons with genes that were expressed more highly in granule cell neurons, we identified three interferon-stimulated genes (ISGs; Ifi27, Irg1 and Rsad2 (also known as Viperin)) that mediated the antiviral effects against different neurotropic viruses.", "Moreover, we found that the epigenetic state and microRNA (miRNA)-mediated regulation of ISGs correlates with enhanced antiviral response in granule cell neurons.", "Thus, neurons from evolutionarily distinct brain regions have unique innate immune signatures, which probably contribute to their relative permissiveness to infection."], "structured": false}
{"doc_id": 9440748, "title": "Small-airway obstruction and emphysema in chronic obstructive pulmonary disease.", "abstract": ["BACKGROUND The major sites of obstruction in chronic obstructive pulmonary disease (COPD) are small airways (<2 mm in diameter).", "We wanted to determine whether there was a relationship between small-airway obstruction and emphysematous destruction in COPD.   \n", "METHODS We used multidetector computed tomography (CT) to compare the number of airways measuring 2.0 to 2.5 mm in 78 patients who had various stages of COPD, as judged by scoring on the Global Initiative for Chronic Obstructive Lung Disease (GOLD) scale, in isolated lungs removed from patients with COPD who underwent lung transplantation, and in donor (control) lungs.", "MicroCT was used to measure the extent of emphysema (mean linear intercept), the number of terminal bronchioles per milliliter of lung volume, and the minimum diameters and cross-sectional areas of terminal bronchioles.   \n", "RESULTS On multidetector CT, in samples from patients with COPD, as compared with control samples, the number of airways measuring 2.0 to 2.5 mm in diameter was reduced in patients with GOLD stage 1 disease (P=0.001), GOLD stage 2 disease (P=0.02), and GOLD stage 3 or 4 disease (P<0.001).", "MicroCT of isolated samples of lungs removed from patients with GOLD stage 4 disease showed a reduction of 81 to 99.7% in the total cross-sectional area of terminal bronchioles and a reduction of 72 to 89% in the number of terminal bronchioles (P<0.001).", "A comparison of the number of terminal bronchioles and dimensions at different levels of emphysematous destruction (i.e., an increasing value for the mean linear intercept) showed that the narrowing and loss of terminal bronchioles preceded emphysematous destruction in COPD (P<0.001).   \n", "CONCLUSIONS These results show that narrowing and disappearance of small conducting airways before the onset of emphysematous destruction can explain the increased peripheral airway resistance reported in COPD.", "(Funded by the National Heart, Lung, and Blood Institute and others.)."], "structured": true}
{"doc_id": 9451052, "title": "Stepwise Histone Replacement by SWR1 Requires Dual Activation with Histone H2A.Z and Canonical Nucleosome", "abstract": ["Histone variant H2A.Z-containing nucleosomes are incorporated at most eukaryotic promoters.", "This incorporation is mediated by the conserved SWR1 complex, which replaces histone H2A in canonical nucleosomes with H2A.Z in an ATP-dependent manner.", "Here, we show that promoter-proximal nucleosomes are highly heterogeneous for H2A.Z in Saccharomyces cerevisiae, with substantial representation of nucleosomes containing one, two, or zero H2A.Z molecules.", "SWR1-catalyzed H2A.Z replacement in vitro occurs in a stepwise and unidirectional fashion, one H2A.Z-H2B dimer at a time, producing heterotypic nucleosomes as intermediates and homotypic H2A.Z nucleosomes as end products.", "The ATPase activity of SWR1 is specifically stimulated by H2A-containing nucleosomes without ensuing histone H2A eviction.", "Remarkably, further addition of free H2A.Z-H2B dimer leads to hyperstimulation of ATPase activity, eviction of nucleosomal H2A-H2B, and deposition of H2A.Z-H2B.", "These results suggest that the combination of H2A-containing nucleosome and free H2A.Z-H2B dimer acting as both effector and substrate for SWR1 governs the specificity and outcome of the replacement reaction."], "structured": false}
{"doc_id": 9451684, "title": "Logic of the yeast metabolic cycle: temporal compartmentalization of cellular processes.", "abstract": ["Budding yeast grown under continuous, nutrient-limited conditions exhibit robust, highly periodic cycles in the form of respiratory bursts.", "Microarray studies reveal that over half of the yeast genome is expressed periodically during these metabolic cycles.", "Genes encoding proteins having a common function exhibit similar temporal expression patterns, and genes specifying functions associated with energy and metabolism tend to be expressed with exceptionally robust periodicity.", "Essential cellular and metabolic events occur in synchrony with the metabolic cycle, demonstrating that key processes in a simple eukaryotic cell are compartmentalized in time."], "structured": false}
{"doc_id": 9460704, "title": "Molecular pathways: induction of polyploidy as a novel differentiation therapy for leukemia.", "abstract": ["Differentiation therapy has emerged as a powerful way to target specific hematologic malignancies.", "One of the best examples is the use of all-trans retinoic acid (ATRA) in acute promyelocytic leukemia (APL), which has significantly improved the outcome for patients with this specific form of acute myeloid leukemia (AML).", "In considering how differentiation therapy could be used in other forms of AML, we predicted that compounds that induce terminal differentiation of megakaryocytes would be effective therapies for the megakaryocytic form of AML, named acute megakaryocytic leukemia (AMKL).", "We also speculated that such agents would reduce the burden of abnormal hematopoietic cells in primary myelofibrosis and alter the differentiation of megakaryocytes in myelodysplastic syndromes.", "Using a high-throughput chemical screening approach, we identified small molecules that promoted many features of terminal megakaryocyte differentiation, including the induction of polyploidization, the process by which cells accumulate DNA to 32N or greater.", "As the induction of polyploidization is an irreversible process, cells that enter this form of the cell cycle do not divide again.", "Thus, this would be an effective way to reduce the tumor burden.", "Clinical studies with polyploidy inducers, such as aurora kinase A inhibitors, are under way for a wide variety of malignancies, whereas trials specifically for AMKL and PMF are in development.", "This novel form of differentiation therapy may be clinically available in the not-too-distant future.", "Clin Cancer Res; 19(22); 6084-8.", "\u00a92013 AACR."], "structured": false}
{"doc_id": 9478135, "title": "Dual mutations in the AML1 and FLT3 genes are associated with leukemogenesis in acute myeloblastic leukemia of the M0 subtype", "abstract": ["Point mutations of the transcription factor AML1 are associated with leukemogenesis in acute myeloblastic leukemia (AML).", "Internal tandem duplications (ITDs) in the juxtamembrane domain and mutations in the second tyrosine kinase domain of the Fms-like tyrosine kinase 3 (FLT3) gene represent the most frequent genetic alterations in AML.", "However, such mutations per se appear to be insufficient for leukemic transformation.", "To evaluate whether both AML1 and FLT3 mutations contribute to leukemogenesis, we analyzed mutations of these genes in AML M0 subtype in whom AML1 mutations were predominantly observed.", "Of 51 patients, eight showed a mutation in the Runt domain of the AML1 gene: one heterozygous missense mutation with normal function, five heterozygous frameshift mutations and two biallelic nonsense or frameshift mutations, resulting in haploinsufficiency or complete loss of the AML1 activities.", "On the other hand, a total of 10 of 49 patients examined had the FLT3 mutation.", "We detected the FLT3 mutation in five of eight (63%) patients with AML1 mutation, whereas five of 41 (12%) without AML1 mutation showed the FLT3 mutation (P=0.0055).", "These observations suggest that reduced AML1 activities predispose cells to the acquisition of the activating FLT3 mutation as a secondary event leading to full transformation in AML M0."], "structured": false}
{"doc_id": 9483851, "title": "Unravelling mechanisms of p53-mediated tumour suppression", "abstract": ["p53 is a crucial tumour suppressor that responds to diverse stress signals by orchestrating specific cellular responses, including transient cell cycle arrest, cellular senescence and apoptosis, which are all processes associated with tumour suppression.", "However, recent studies have challenged the relative importance of these canonical cellular responses for p53-mediated tumour suppression and have highlighted roles for p53 in modulating other cellular processes, including metabolism, stem cell maintenance, invasion and metastasis, as well as communication within the tumour microenvironment.", "In this Opinion article, we discuss the roles of classical p53 functions, as well as emerging p53-regulated processes, in tumour suppression."], "structured": false}
{"doc_id": 9486930, "title": "Stem cell-related \"self-renewal\" signature and high epidermal growth factor receptor expression associated with resistance to concomitant chemoradiotherapy in glioblastoma.", "abstract": ["PURPOSE Glioblastomas are notorious for resistance to therapy, which has been attributed to DNA-repair proficiency, a multitude of deregulated molecular pathways, and, more recently, to the particular biologic behavior of tumor stem-like cells.", "Here, we aimed to identify molecular profiles specific for treatment resistance to the current standard of care of concomitant chemoradiotherapy with the alkylating agent temozolomide.   \n", "PATIENTS AND METHODS Gene expression profiles of 80 glioblastomas were interrogated for associations with resistance to therapy.", "Patients were treated within clinical trials testing the addition of concomitant and adjuvant temozolomide to radiotherapy.   \n", "RESULTS An expression signature dominated by HOX genes, which comprises Prominin-1 (CD133), emerged as a predictor for poor survival in patients treated with concomitant chemoradiotherapy (n = 42; hazard ratio = 2.69; 95% CI, 1.38 to 5.26; P = .004).", "This association could be validated in an independent data set.", "Provocatively, the HOX cluster was reminiscent of a \"self-renewal\" signature (P = .008; Gene Set Enrichment Analysis) recently characterized in a mouse leukemia model.", "The HOX signature and EGFR expression were independent prognostic factors in multivariate analysis, adjusted for the O-6-methylguanine-DNA methyltransferase (MGMT) methylation status, a known predictive factor for benefit from temozolomide, and age.", "Better outcome was associated with gene clusters characterizing features of tumor-host interaction including tumor vascularization and cell adhesion, and innate immune response.   \n", "CONCLUSION This study provides first clinical evidence for the implication of a \"glioma stem cell\" or \"self-renewal\" phenotype in treatment resistance of glioblastoma.", "Biologic mechanisms identified here to be relevant for resistance will guide future targeted therapies and respective marker development for individualized treatment and patient selection."], "structured": true}
{"doc_id": 9498458, "title": "Heterogeneity Underlies the Emergence of EGFRT790 Wild-Type Clones Following Treatment of T790M-Positive Cancers with a Third-Generation EGFR Inhibitor.", "abstract": ["UNLABELLED Rociletinib is a third-generation EGFR inhibitor active in lung cancers with T790M, the gatekeeper mutation underlying most first-generation EGFR drug resistance.", "We biopsied patients at rociletinib progression to explore resistance mechanisms.", "Among 12 patients with T790M-positive cancers at rociletinib initiation, six had T790-wild-type rociletinib-resistant biopsies.", "Two T790-wild-type cancers underwent small cell lung cancer transformation; three T790M-positive cancers acquired EGFR amplification.", "We documented T790-wild-type and T790M-positive clones coexisting within a single pre-rociletinib biopsy.", "The pretreatment fraction of T790M-positive cells affected response to rociletinib.", "Longitudinal circulating tumor DNA (ctDNA) analysis revealed an increase in plasma EGFR-activating mutation, and T790M heralded rociletinib resistance in some patients, whereas in others the activating mutation increased but T790M remained suppressed.", "Together, these findings demonstrate the role of tumor heterogeneity when therapies targeting a singular resistance mechanism are used.", "To further improve outcomes, combination regimens that also target T790-wild-type clones are required.   ", "SIGNIFICANCE This report documents that half of T790M-positive EGFR-mutant lung cancers treated with rociletinib are T790-wild-type upon progression, suggesting that T790-wild-type clones can emerge as the dominant source of resistance.", "We show that tumor heterogeneity has important clinical implications and that plasma ctDNA analyses can sometimes predict emerging resistance mechanisms."], "structured": false}
{"doc_id": 9500590, "title": "Extrathymic Generation of Regulatory T Cells in Placental Mammals Mitigates Maternal-Fetal Conflict", "abstract": ["Regulatory T (Treg) cells, whose differentiation and function are controlled by X chromosome-encoded transcription factor Foxp3, are generated in the thymus (tTreg) and extrathymically (peripheral, pTreg), and their deficiency results in fatal autoimmunity.", "Here, we demonstrate that a Foxp3 enhancer, conserved noncoding sequence 1 (CNS1), essential for pTreg but dispensable for tTreg cell generation, is present only in placental mammals.", "CNS1 is largely composed of mammalian-wide interspersed repeats (MIR) that have undergone retrotransposition during early mammalian radiation.", "During pregnancy, pTreg cells specific to a model paternal alloantigen were generated in a CNS1-dependent manner and accumulated in the placenta.", "Furthermore, when mated with allogeneic, but not syngeneic, males, CNS1-deficient females showed increased fetal resorption accompanied by increased immune cell infiltration and defective remodeling of spiral arteries.", "Our results suggest that, during evolution, a CNS1-dependent mechanism of extrathymic differentiation of Treg cells emerged in placental animals to enforce maternal-fetal tolerance."], "structured": false}
{"doc_id": 9505402, "title": "Acquired EGFR C797S mutation mediates resistance to AZD9291 in non\u2013small cell lung cancer harboring EGFR T790M", "abstract": ["Here we studied cell-free plasma DNA (cfDNA) collected from subjects with advanced lung cancer whose tumors had developed resistance to the epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor (TKI) AZD9291.", "We first performed next-generation sequencing of cfDNA from seven subjects and detected an acquired EGFR C797S mutation in one; expression of this mutant EGFR construct in a cell line rendered it resistant to AZD9291.", "We then performed droplet digital PCR on serial cfDNA specimens collected from 15 AZD9291-treated subjects.", "All were positive for the T790M mutation before treatment, but upon developing AZD9291 resistance three molecular subtypes emerged: six cases acquired the C797S mutation, five cases maintained the T790M mutation but did not acquire the C797S mutation and four cases lost the T790M mutation despite the presence of the underlying EGFR activating mutation.", "Our findings provide insight into the diversity of mechanisms through which tumors acquire resistance to AZD9291 and highlight the need for therapies that are able to overcome resistance mediated by the EGFR C797S mutation."], "structured": false}
{"doc_id": 9505448, "title": "The Translation Initiation Factor 3f (eIF3f) Exhibits a Deubiquitinase Activity Regulating Notch Activation", "abstract": ["Activation of the mammalian Notch receptor after ligand binding relies on a succession of events including metalloprotease-cleavage, endocytosis, monoubiquitination, and eventually processing by the gamma-secretase, giving rise to a soluble, transcriptionally active molecule.", "The Notch1 receptor was proposed to be monoubiquitinated before its gamma-secretase cleavage; the targeted lysine has been localized to its submembrane domain.", "Investigating how this step might be regulated by a deubiquitinase (DUB) activity will provide new insight for understanding Notch receptor activation and downstream signaling.", "An immunofluorescence-based screening of an shRNA library allowed us to identify eIF3f, previously known as one of the subunits of the translation initiation factor eIF3, as a DUB targeting the activated Notch receptor.", "We show that eIF3f has an intrinsic DUB activity.", "Knocking down eIF3f leads to an accumulation of monoubiquitinated forms of activated Notch, an effect counteracted by murine WT eIF3f but not by a catalytically inactive mutant.", "We also show that eIF3f is recruited to activated Notch on endocytic vesicles by the putative E3 ubiquitin ligase Deltex1, which serves as a bridging factor.", "Finally, catalytically inactive forms of eIF3f as well as shRNAs targeting eIF3f repress Notch activation in a coculture assay, showing that eIF3f is a new positive regulator of the Notch pathway.", "Our results support two new and provocative conclusions: (1) The activated form of Notch needs to be deubiquitinated before being processed by the gamma-secretase activity and entering the nucleus, where it fulfills its transcriptional function.", "(2) The enzyme accounting for this deubiquitinase activity is eIF3f, known so far as a translation initiation factor.", "These data improve our knowledge of Notch signaling but also open new avenues of research on the Zomes family and the translation initiation factors."], "structured": false}
{"doc_id": 9507605, "title": "Focal contacts as mechanosensors: externally applied local mechanical force induces growth of focal contacts by an mDia1-dependent and ROCKindependent mechanism", "abstract": ["The transition of cell\u2013matrix adhesions from the initial punctate focal complexes into the mature elongated form, known as focal contacts, requires GTPase Rho activity.", "In particular, activation of myosin II\u2013driven contractility by a Rho target known as Rho-associated kinase (ROCK) was shown to be essential for focal contact formation.", "To dissect the mechanism of Rho-dependent induction of focal contacts and to elucidate the role of cell contractility, we applied mechanical force to vinculin-containing dot-like adhesions at the cell edge using a micropipette.", "Local centripetal pulling led to local assembly and elongation of these structures and to their development into streak-like focal contacts, as revealed by the dynamics of green fluorescent protein\u2013tagged vinculin or paxillin and interference reflection microscopy.", "Inhibition of Rho activity by C3 transferase suppressed this force-induced focal contact formation.", "However, constitutively active mutants of another Rho target, the formin homology protein mDia1 (Watanabe, N., T. Kato, A. Fujita, T. Ishizaki, and S. Narumiya.", "1999.", "Nat.", "Cell Biol.", "1:136\u2013143), were sufficient to restore force-induced focal contact formation in C3 transferase-treated cells.", "Force-induced formation of the focal contacts still occurred in cells subjected to myosin II and ROCK inhibition.", "Thus, as long as mDia1 is active, external tension force bypasses the requirement for ROCK-mediated myosin II contractility in the induction of focal contacts.", "Our experiments show that integrin-containing focal complexes behave as individual mechanosensors exhibiting directional assembly in response to local force."], "structured": false}
{"doc_id": 9513785, "title": "Maternal Protein Restriction Affects Postnatal Growth and the Expression of Key Proteins Involved in Lifespan Regulation in Mice", "abstract": ["We previously reported that maternal protein restriction in rodents influenced the rate of growth in early life and ultimately affected longevity.", "Low birth weight caused by maternal protein restriction followed by catch-up growth (recuperated animals) was associated with shortened lifespan whereas protein restriction and slow growth during lactation (postnatal low protein: PLP animals) increased lifespan.", "We aim to explore the mechanistic basis by which these differences arise.", "Here we investigated effects of maternal diet on organ growth, metabolic parameters and the expression of insulin/IGF1 signalling proteins and Sirt1 in muscle of male mice at weaning.", "PLP mice which experienced protein restriction during lactation had lower fasting glucose (P = 0.038) and insulin levels (P = 0.046) suggesting improved insulin sensitivity.", "PLP mice had higher relative weights (adjusted by body weight) of brain (P = 0.0002) and thymus (P = 0.031) compared to controls suggesting that enhanced functional capacity of these two tissues is beneficial to longevity.", "They also had increased expression of insulin receptor substrate 1 (P = 0.021) and protein kinase C zeta (P = 0.046).", "Recuperated animals expressed decreased levels of many insulin signalling proteins including PI3 kinase subunits p85alpha (P = 0.018), p110beta (P = 0.048) and protein kinase C zeta (P = 0.006) which may predispose these animals to insulin resistance.", "Sirt1 protein expression was reduced in recuperated offspring.", "These observations suggest that maternal protein restriction can affect major metabolic pathways implicated in regulation of lifespan at a young age which may explain the impact of maternal diet on longevity."], "structured": false}
{"doc_id": 9538708, "title": "\u2018Short stature in children - a questionnaire for parents\u2019: a new instrument for growth disorder-specific psychosocial adaptation in children", "abstract": ["Recent studies report comparable psychosocial adaptation in children with or without a growth disorder.", "These findings may be due to a general lack of sensitive and specific techniques for analysing and comparing their respective qualities of life.", "In this study we present a new questionnaire for parents of short-statured children.", "We suggest both a qualitative and quantitative approach providing specific information about the relative extent of individual stress factors and sources of help.", "The parents of 442 children with growth retardation resulting from different aetiologies completed the questionnaire.", "Aprincipal component analysis of the scaled items revealed four dimensions of psychosocial adaptation: suffering, future anxieties, behavioural problems and coping efforts.", "The index of internal consistency reliability was sufficient for all scales.", "The comparison of two selected growth disorder groups (achondroplasia versus growth hormone deficiency) demonstrated growth disorder-specific but not very different profiles of psychosocial adaptation.", "The qualitative analysis revealed a shift in the stress factor patterns (achondroplasia, more physical restrictions).", "These findings give evidence for both the specificity and construct validity of the new instrument.", "Therefore, we may conclude that this questionnaire is a helpful method in attaining growth disorder-specific information about individual stress factors, resources and psychosocial adaptation."], "structured": false}
{"doc_id": 9539248, "title": "Alphavirus-derived small RNAs modulate pathogenesis in disease vector mosquitoes.", "abstract": ["Mosquito-borne viruses cause significant levels of morbidity and mortality in humans and domesticated animals.", "Maintenance of mosquito-borne viruses in nature requires a biological transmission cycle that involves alternating virus replication in a susceptible vertebrate and mosquito host.", "Although the vertebrate infection is acute and often associated with disease, continual transmission of these viruses in nature depends on the establishment of a persistent, nonpathogenic infection in the mosquito vector.", "An antiviral RNAi response has been shown to limit the replication of RNA viruses in flies.", "However, the importance of the RNAi pathway as an antiviral defense in mammals is unclear.", "Differences in the immune responses of mammals and mosquitoes may explain why these viruses are not generally associated with pathology in the invertebrate host.", "We identified virus-derived small interfering RNAs (viRNAs), 21 nt in length, in Aedes aegypti infected with the mosquito-borne virus, Sindbis (SINV).", "viRNAs had an asymmetric distribution that spanned the length of the SINV genome.", "To determine the role of viRNAs in controlling pathogenic potential, mosquitoes were infected with recombinant alphaviruses expressing suppressors of RNA silencing.", "Decreased survival was observed in mosquitoes in which the accumulation of viRNAs was suppressed.", "These results suggest that an exogenous siRNA pathway is essential to the survival of mosquitoes infected with alphaviruses and, thus, the maintenance of these viruses in nature."], "structured": false}
{"doc_id": 9539753, "title": "Nuclear RNAi maintains heritable gene silencing in Caenorhabditis elegans.", "abstract": ["RNA interference (RNAi) is heritable in Caenorhabditis elegans; the progeny of C. elegans exposed to dsRNA inherit the ability to silence genes that were targeted by RNAi in the previous generation.", "Here we investigate the mechanism of RNAi inheritance in C. elegans.", "We show that exposure of animals to dsRNA results in the heritable expression of siRNAs and the heritable deposition of histone 3 lysine 9 methylation (H3K9me) marks in progeny.", "siRNAs are detectable before the appearance of H3K9me marks, suggesting that chromatin marks are not directly inherited but, rather, reestablished in inheriting progeny.", "Interestingly, H3K9me marks appear more prominently in inheriting progeny than in animals directly exposed to dsRNA, suggesting that germ-line transmission of silencing signals may enhance the efficiency of siRNA-directed H3K9me.", "Finally, we show that the nuclear RNAi (Nrde) pathway maintains heritable RNAi silencing in C. elegans.", "The Argonaute (Ago) NRDE-3 associates with heritable siRNAs and, acting in conjunction with the nuclear RNAi factors NRDE-1, NRDE-2, and NRDE-4, promotes siRNA expression in inheriting progeny.", "These results demonstrate that siRNA expression is heritable in C. elegans and define an RNAi pathway that promotes the maintenance of RNAi silencing and siRNA expression in the progeny of animals exposed to dsRNA."], "structured": false}
{"doc_id": 9547722, "title": "Cancer survivors in the United States: prevalence across the survivorship trajectory and implications for care.", "abstract": ["BACKGROUND Cancer survivors represent a growing population, heterogeneous in their need for medical care, psychosocial support, and practical assistance.", "To inform survivorship research and practice, this manuscript will describe the prevalent population of cancer survivors in terms of overall numbers and prevalence by cancer site and time since diagnosis.   \n", "METHODS Incidence and survival data from 1975-2007 were obtained from the Surveillance, Epidemiology, and End Results Program and population projections from the United States Census Bureau.", "Cancer prevalence for 2012 and beyond was estimated using the Prevalence Incidence Approach Model, assuming constant future incidence and survival trends but dynamic projections of the U.S. population.   \n", "RESULTS As of January 1, 2012, approximately 13.7 million cancer survivors were living in the United States with prevalence projected to approach 18 million by 2022.", "Sixty-four percent of this population have survived 5 years or more; 40% have survived 10 years or more; and 15% have survived 20 years or more after diagnosis.", "Over the next decade, the number of people who have lived 5 years or more after their cancer diagnosis is projected to increase approximately 37% to 11.9 million.   \n", "CONCLUSIONS A coordinated agenda for research and practice is needed to address cancer survivors' long-term medical, psychosocial, and practical needs across the survivorship trajectory.   ", "IMPACT Prevalence estimates for cancer survivors across the survivorship trajectory will inform the national research agenda as well as future projections about the health service needs of this population."], "structured": true}
{"doc_id": 9548440, "title": "Human aneuploidy: mechanisms and new insights into an age-old problem", "abstract": ["Trisomic and monosomic (aneuploid) embryos account for at least 10% of human pregnancies and, for women nearing the end of their reproductive lifespan, the incidence may exceed 50%.", "The errors that lead to aneuploidy almost always occur in the oocyte but, despite intensive investigation, the underlying molecular basis has remained elusive.", "Recent studies of humans and model organisms have shed new light on the complexity of meiotic defects, providing evidence that the age-related increase in errors in the human female is not attributable to a single factor but to an interplay between unique features of oogenesis and a host of endogenous and exogenous factors."], "structured": false}
{"doc_id": 9550981, "title": "The Drosophila hindgut lacks constitutively active adult stem cells but proliferates in response to tissue damage.", "abstract": ["The adult Drosophila hindgut was recently reported to contain active, tissue-replenishing stem cells, like those of the midgut, but located within an anterior ring so as to comprise a single giant crypt.", "In contrast to this view, we observed no active stem cells and little cell turnover in adult hindgut tissue based on clonal marking and BrdU incorporation studies.", "Again contradicting the previous proposal, we showed that the adult hindgut is not generated by anterior stem cells during larval/pupal development.", "However, severe tissue damage within the hindgut elicits cell proliferation within a ring of putative quiescent stem cells at the anterior of the pylorus.", "Thus, the hindgut does not provide a model of tissue maintenance by constitutively active stem cells, but has great potential to illuminate mechanisms of stress-induced tissue repair."], "structured": false}
{"doc_id": 9555784, "title": "Vitamin d deficiency in postmenopausal women - biological correlates.", "abstract": ["INTRODUCTION Low vitamin D (VD) is associated with secondary hyperparathyroidism and both contribute to deleterious consequences (reduced bone mineral density (BMD), risk of fractures and falls).   \n", "OBJECTIVE To study the VD status and biological correlates in a group of postmenopausal women.   ", "MATERIAL AND METHODS We studied 123 postmenopausal women evaluated in the C.I.Parhon National Institute of Endocrinology, the Pituitary and Neuroendocrine Diseases department.", "All cases had been reffered for the evaluation of BMD by the general practitioner.", "The evaluation included serum measurements of total and ionised calcium, phosphorus, alkaline phosphatase (ALP), 25 hydroxi vitaminD (25OHD), parathyroid hormone (PTH), osteocalcin, betacrosslaps.", "Central DXA osteodensitometry was performed.   \n", "RESULTS 91.9% of cases had 25OHD serum levels below 30 ng/ml (74.8% had VD deficiency, 17.1% VD insufficiency).", "Only 8.1% had sufficient VD levels.", "A history of fragility fractures was present in 45.83% of the osteoporotic patients, 27.27% of the osteopenic ones and 15.15% of the women with normal BMD.", "32 women (26%) were on VD supplementation at the time of evaluation.", "Among these subjects, the 25OHD level was significantly higher in those with prior fragility fractures (p=0.018) and osteoporosis (p=0.008).", "25OHD concentration negatively correlated with PTH, alkaline phosphatase (ALP) and osteocalcin.", "The bone markers evaluated had a significant inverse correlation with the radius BMD, T and Z scores (p=0.004).", "27.17% of the cases with VD deficiency had secondary hyperparathyroidism.", "The 25OHD concentration was significantly lower in these cases (p=0.000).   \n", "CONCLUSIONS VD insufficiency is widely prevalent but still under-recognized and under-treated, possibly leading to secondary hyperparathyroidism.", "The compliance to VD supplementation is lower in subjects without osteoporosis or fragility fractures.", "Primary prevention measures should be more actively implemented."], "structured": true}
{"doc_id": 9558539, "title": "CD44v6 is a marker of constitutive and reprogrammed cancer stem cells driving colon cancer metastasis.", "abstract": ["Cancer stem cells drive tumor formation and metastasis, but how they acquire metastatic traits is not well understood.", "Here, we show that all colorectal cancer stem cells (CR-CSCs) express CD44v6, which is required for their migration and generation of metastatic tumors.", "CD44v6 expression is low in primary tumors but demarcated clonogenic CR-CSC populations.", "Cytokines hepatocyte growth factor (HGF), osteopontin (OPN), and stromal-derived factor 1\u03b1 (SDF-1), secreted from tumor associated cells, increase CD44v6 expression in CR-CSCs by activating the Wnt/\u03b2-catenin pathway, which promotes migration and metastasis.", "CD44v6(-) progenitor cells do not give rise to metastatic lesions but, when treated with cytokines, acquire CD44v6 expression and metastatic capacity.", "Importantly, phosphatidylinositol 3-kinase (PI3K) inhibition selectively killed CD44v6 CR-CSCs and reduced metastatic growth.", "In patient cohorts, low levels of CD44v6 predict increased probability of survival.", "Thus, the metastatic process in colorectal cancer is initiated by CSCs through the expression of CD44v6, which is both a functional biomarker and therapeutic target."], "structured": false}
{"doc_id": 9559146, "title": "Senescent Cells, Tumor Suppression, and Organismal Aging: Good Citizens, Bad Neighbors", "abstract": ["Cells from organisms with renewable tissues can permanently withdraw from the cell cycle in response to diverse stress, including dysfunctional telomeres, DNA damage, strong mitogenic signals, and disrupted chromatin.", "This response, termed cellular senescence, is controlled by the p53 and RB tumor suppressor proteins and constitutes a potent anticancer mechanism.", "Nonetheless, senescent cells acquire phenotypic changes that may contribute to aging and certain age-related diseases, including late-life cancer.", "Thus, the senescence response may be antagonistically pleiotropic, promoting early-life survival by curtailing the development of cancer but eventually limiting longevity as dysfunctional senescent cells accumulate."], "structured": false}
{"doc_id": 9580772, "title": "Advances in high-resolution imaging--techniques for three-dimensional imaging of cellular structures.", "abstract": ["A fundamental goal in biology is to determine how cellular organization is coupled to function.", "To achieve this goal, a better understanding of organelle composition and structure is needed.", "Although visualization of cellular organelles using fluorescence or electron microscopy (EM) has become a common tool for the cell biologist, recent advances are providing a clearer picture of the cell than ever before.", "In particular, advanced light-microscopy techniques are achieving resolutions below the diffraction limit and EM tomography provides high-resolution three-dimensional (3D) images of cellular structures.", "The ability to perform both fluorescence and electron microscopy on the same sample (correlative light and electron microscopy, CLEM) makes it possible to identify where a fluorescently labeled protein is located with respect to organelle structures visualized by EM.", "Here, we review the current state of the art in 3D biological imaging techniques with a focus on recent advances in electron microscopy and fluorescence super-resolution techniques."], "structured": false}
{"doc_id": 9588931, "title": "Quercetin attenuates vascular calcification by inhibiting oxidative stress and mitochondrial fission.", "abstract": ["Vascular calcification is a strong independent predictor of increased cardiovascular morbidity and mortality and has a high prevalence among patients with chronic kidney disease.", "The present study investigated the effects of quercetin on vascular calcification caused by oxidative stress and abnormal mitochondrial dynamics both in vitro and in vivo.", "Calcifying vascular smooth muscle cells (VSMCs) treated with inorganic phosphate (Pi) exhibited mitochondrial dysfunction, as demonstrated by decreased mitochondrial potential and ATP production.", "Disruption of mitochondrial structural integrity was also observed in a rat model of adenine-induced aortic calcification.", "Increased production of reactive oxygen species, enhanced expression and phosphorylation of Drp1, and excessive mitochondrial fragmentation were also observed in Pi-treated VSMCs.", "These effects were accompanied by mitochondria-dependent apoptotic events, including release of cytochrome c from the mitochondria into the cytosol and subsequent activation of caspase-3.", "Quercetin was shown to block Pi-induced apoptosis and calcification of VSMCs by inhibiting oxidative stress and decreasing mitochondrial fission by inhibiting the expression and phosphorylation of Drp1.", "Quercetin also significantly ameliorated adenine-induced aortic calcification in rats.", "In summary, our findings suggest that quercetin attenuates calcification by reducing apoptosis of VSMCs by blocking oxidative stress and inhibiting mitochondrial fission."], "structured": false}
{"doc_id": 9591368, "title": "The M/GP5 Glycoprotein Complex of Porcine Reproductive and Respiratory Syndrome Virus Binds the Sialoadhesin Receptor in a Sialic Acid-Dependent Manner", "abstract": ["The porcine reproductive and respiratory syndrome virus (PRRSV) is a major threat to swine health worldwide and is considered the most significant viral disease in the swine industry today.", "In past years, studies on the entry of the virus into its host cell have led to the identification of a number of essential virus receptors and entry mediators.", "However, viral counterparts for these molecules have remained elusive and this has made rational development of new generation vaccines impossible.", "The main objective of this study was to identify the viral counterparts for sialoadhesin, a crucial PRRSV receptor on macrophages.", "For this purpose, a soluble form of sialoadhesin was constructed and validated.", "The soluble sialoadhesin could bind PRRSV in a sialic acid-dependent manner and could neutralize PRRSV infection of macrophages, thereby confirming the role of sialoadhesin as an essential PRRSV receptor on macrophages.", "Although sialic acids are present on the GP(3), GP(4) and GP(5) envelope glycoproteins, only the M/GP(5) glycoprotein complex of PRRSV was identified as a ligand for sialoadhesin.", "The interaction was found to be dependent on the sialic acid binding capacity of sialoadhesin and on the presence of sialic acids on GP(5).", "These findings not only contribute to a better understanding of PRRSV biology, but the knowledge and tools generated in this study also hold the key to the development of a new generation of PRRSV vaccines."], "structured": false}
{"doc_id": 9599194, "title": "A versatile zero background T-vector system for gene cloning and functional genomics.", "abstract": ["With the recent availability of complete genomic sequences of many organisms, high-throughput and cost-efficient systems for gene cloning and functional analysis are in great demand.", "Although site-specific recombination-based cloning systems, such as Gateway cloning technology, are extremely useful for efficient transfer of DNA fragments into multiple destination vectors, the two-step cloning process is time consuming and expensive.", "Here, we report a zero background TA cloning system that provides simple and high-efficiency direct cloning of PCR-amplified DNA fragments with almost no self-ligation.", "The improved T-vector system takes advantage of the restriction enzyme XcmI to generate a T-overhang after digestion and the negative selection marker gene ccdB to eliminate the self-ligation background after transformation.", "We demonstrate the feasibility and flexibility of the technology by developing a set of transient and stable transformation vectors for constitutive gene expression, gene silencing, protein tagging, protein subcellular localization detection, and promoter fragment activity analysis in plants.", "Because the system can be easily adapted for developing specialized expression vectors for other organisms, zero background TA provides a general, cost-efficient, and high-throughput platform that complements the Gateway cloning system for gene cloning and functional genomics."], "structured": false}
{"doc_id": 9600826, "title": "GEP100-Arf6-AMAP1-Cortactin Pathway Frequently Used in Cancer Invasion Is Activated by VEGFR2 to Promote Angiogenesis", "abstract": ["Angiogenesis and cancer invasiveness greatly contribute to cancer malignancy.", "Arf6 and its effector, AMAP1, are frequently overexpressed in breast cancer, and constitute a central pathway to induce the invasion and metastasis.", "In this pathway, Arf6 is activated by EGFR via GEP100.", "Arf6 is highly expressed also in human umbilical vein endothelial cells (HUVECs) and is implicated in angiogenesis.", "Here, we found that HUVECs also highly express AMAP1, and that vascular endothelial growth factor receptor-2 (VEGFR2) recruits GEP100 to activate Arf6.", "AMAP1 functions by binding to cortactin in cancer invasion and metastasis.", "We demonstrate that the same GEP100-Arf6-AMAP1-cortactin pathway is essential for angiogenesis activities, including cell migration and tubular formation, as well as for the enhancement of cell permeability and VE-cadherin endocytosis of VEGF-stimulated HUVECs.", "Components of this pathway are highly expressed in pathologic angiogenesis, and blocking of this pathway effectively inhibits VEGF- or tumor-induced angiogenesis and choroidal neovascularization.", "The GEP100-Arf6-AMAP1-cortactin pathway, activated by receptor tyrosine kinases, appears to be common in angiogenesis and cancer invasion and metastasis, and provides their new therapeutic targets."], "structured": false}
{"doc_id": 9604301, "title": "Dynamics of Cryptococcus neoformans-Macrophage Interactions Reveal that Fungal Background Influences Outcome during Cryptococcal Meningoencephalitis in Humans", "abstract": ["UNLABELLED Cryptococcosis is a multifaceted fungal infection with variable clinical presentation and outcome.", "As in many infectious diseases, this variability is commonly assigned to host factors.", "To investigate whether the diversity of Cryptococcus neoformans clinical (ClinCn) isolates influences the interaction with host cells and the clinical outcome, we developed and validated new quantitative assays using flow cytometry and J774 macrophages.", "The phenotype of ClinCn-macrophage interactions was determined for 54 ClinCn isolates recovered from cerebrospinal fluids (CSF) from 54 unrelated patients, based on phagocytic index (PI) and 2-h and 48-h intracellular proliferation indexes (IPH2 and IPH48, respectively).", "Their phenotypes were highly variable.", "Isolates harboring low PI/low IPH2 and high PI/high IPH2 values were associated with nonsterilization of CSF at week 2 and death at month 3, respectively.", "A subset of 9 ClinCn isolates with different phenotypes exhibited variable virulence in mice and displayed intramacrophagic expression levels of the LAC1, APP1, VAD1, IPC1, PLB1, and COX1 genes that were highly variable among the isolates and correlated with IPH48.", "Variation in the expression of virulence factors is thus shown here to depend on not only experimental conditions but also fungal background.", "These results suggest that, in addition to host factors, the patient's outcome can be related to fungal determinants.", "Deciphering the molecular events involved in C. neoformans fate inside host cells is crucial for our understanding of cryptococcosis pathogenesis.   ", "IMPORTANCE Cryptococcus neoformans is a life-threatening human fungal pathogen that is responsible for an estimated 1 million cases of meningitis/year, predominantly in HIV-infected patients.", "The diversity of infecting isolates is well established, as is the importance of the host factors.", "Interaction with macrophages is a major step in cryptococcosis pathogenesis.", "How the diversity of clinical isolates influences macrophages' interactions and impacts cryptococcosis outcome in humans remains to be elucidated.", "Using new assays, we uncovered how yeast-macrophage interactions were highly variable among clinical isolates and found an association between specific behaviors and cryptococcosis outcome.", "In addition, gene expression of some virulence factors and intracellular proliferation were correlated.", "While many studies have established that virulence factors can be differentially expressed as a function of experimental conditions, our study demonstrates that, under the same experimental conditions, clinical isolates behaved differently, a diversity that could participate in the variable outcome of infection in humans."], "structured": false}
{"doc_id": 9612317, "title": "Angiopoietin-2 at high concentration can enhance endothelial cell survival through the phosphatidylinositol 3\u2032-kinase/Akt signal transduction pathway", "abstract": ["The angiopoietin-Tie2 system in endothelial cells is an important regulator of vasculogenesis and vascular integrity.", "High levels of angiopoietin-2 (Ang2) mRNA are observed in vascular activation during tumorigenesis.", "Although Ang2 is known to be a naturally occurring antagonist of angiopoietin-1 (Ang1) in vivo, the exact function of Ang2 itself is not known.", "Here, we found that a high concentration of Ang2 (800 ng/ml) acts as an apoptosis survival factor for endothelial cells during serum deprivation apoptosis.", "The survival effect of high concentration Ang2 was blocked by pre-treatment with soluble Tie2 receptor and the PI 3\u2032-kinase-specific inhibitors, wortmannin and LY294002.", "Accordingly, 800 ng/ml of Ang2 induced phosphorylation of Tie2, the p85 subunit of phosphatidylinositol 3\u2032-kinase (PI 3\u2032-kinase), and serine-threonine kinase Akt at Ser473 in the human umbilical vein endothelial cells; lower concentrations of Ang2 (50\u2013400 ng/ml) did not produce notable effects.", "These findings indicate that at high concentrations, Ang2, like Ang1, can be an apoptosis survival factor for endothelial cells through the activation of the Tie2 receptor, PI 3\u2032-kinase and Akt, and thus may be a positive regulator of tumor angiogenesis."], "structured": false}
{"doc_id": 9614443, "title": "Lipoxin a4 analogs attenuate induction of intestinal epithelial proinflammatory gene expression and reduce the severity of dextran sodium sulfate-induced colitis.", "abstract": ["The anti-inflammatory eicosanoid lipoxin A(4) (LXA(4)), aspirin-triggered 15-epi-LXA(4), and their stable analogs down-regulate IL-8 secretion and subsequent recruitment of neutrophils by intestinal epithelia.", "In an effort to elucidate the mechanism by which these lipid mediators modulate cellular proinflammatory programs, we surveyed global epithelial gene expression using cDNA microarrays.", "LXA(4) analog alone did not significantly affect expression of any of the >7000 genes analyzed.", "However, LXA(4) analog pretreatment attenuated induction of approximately 50% of the 125 genes up-regulated in response to the gastroenteritis-causing pathogen Salmonella typhimurium.", "A major subset of genes whose induction was reduced by LXA(4) analog pretreatment is regulated by NF-kappaB, suggesting that LXA(4) analog was influencing the activity of this transcription factor.", "Nanomolar concentrations of LXA(4) analog reduced NF-kappaB-mediated transcriptional activation in a LXA(4) receptor-dependent manner and inhibited induced degradation of IkappaBalpha.", "LXA(4) analog did not affect earlier stimulus-induced signaling events that lead to IkappaBalpha degradation, such as S. typhimurium-induced epithelial Ca(2+) mobilization or TNF-alpha-induced phosphorylation of IkappaBalpha.", "To establish the in vivo relevance of these findings, we examined whether LXA(4) analogs could affect intestinal inflammation in vivo using the mouse model of DSS-induced inflammatory colitis.", "Oral administration of LXA(4) analog (15-epi-16-para-fluoro-phenoxy-LXA(4), 10 microg/day) significantly reduced the weight loss, hematochezia, and mortality that characterize DSS colitis.", "Thus, LXA(4) analog-mediated down-regulation of proinflammatory gene expression via inhibition of the NF-kappaB pathway can be therapeutic for diseases characterized by mucosal inflammation."], "structured": false}
{"doc_id": 9617381, "title": "Serum plant and other noncholesterol sterols, cholesterol metabolism and 22-year mortality among middle-aged men.", "abstract": ["OBJECTIVE To evaluate long-term prognostic effect of serum noncholesterol sterols, including plant sterols, in middle-aged men with high cardiovascular disease (CVD) risk, without statins at baseline.   \n", "METHODS This was a prospective study of 232 men (mean age 60 years) at high risk of CVD in 1985-1986.", "Most were hypercholesterolemic, 29 (12%) had a history of CVD or cancer, 6 (3%) had diabetes, and 46 (20%) had metabolic syndrome (MS).", "Measured noncholesterol sterols (expressed as absolute concentrations or ratios to serum cholesterol to standardize for cholesterol concentrations) included lathosterol and desmosterol (reflect cholesterol synthesis), and plant sterols (campesterol and sitosterol) and cholestanol (reflect cholesterol absorption).", "Main outcome measure was total mortality.   \n", "RESULTS At baseline, markers of cholesterol synthesis and absorption showed expected inverse associations.", "During the 22-year follow-up 101 men (43%) died.", "At baseline, nonsurvivors smoked more, exercised less and had more components of MS (although not filling strict criteria), whereas traditional risk factors of CVD were not significantly different.", "Of the noncholesterol sterols (either absolute or ratio), only sitosterol was significantly higher in survivors than in nonsurvivors (P=0.02).", "In multivariable analyses, highest sitosterol-to-cholesterol tertile was associated with significantly lower mortality risk (HR 0.51, 95% CI 0.30-0.87) as compared to lowest tertile.", "Other associations were nonsignificant, although a \"global\" index of cholesterol metabolism (desmosterol-to-sitosterol ratio) suggested higher cholesterol synthesis and lower absorption to be associated with higher total and CVD mortality.   \n", "CONCLUSION Higher serum plant sterol levels in middle-aged men predicted lower long-term mortality risk, possibly reflecting an association between higher synthesis/lower absorption of cholesterol and mortality."], "structured": true}
{"doc_id": 9622258, "title": "Intracoronary autologous cardiac progenitor cell transfer in patients with hypoplastic left heart syndrome: the TICAP prospective phase 1 controlled trial.", "abstract": ["RATIONALE Hypoplastic left heart syndrome (HLHS) remains a lethal congenital cardiac defect.", "Recent studies have suggested that intracoronary administration of autologous cardiosphere-derived cells (CDCs) may improve ventricular function.   \n", "OBJECTIVE The aim of this study was to test whether intracoronary delivery of CDCs is feasible and safe in patients with hypoplastic left heart syndrome.   \n", "METHODS AND RESULTS Between January 5, 2011, and January 16, 2012, 14 patients (1.8\u00b11.5 years) were prospectively assigned to receive intracoronary infusion of autologous CDCs 33.4\u00b18.1 days after staged procedures (n=7), followed by 7 controls with standard palliation alone.", "The primary end point was to assess the safety, and the secondary end point included the preliminary efficacy to verify the right ventricular ejection fraction improvements between baseline and 3 months.", "Manufacturing and intracoronary delivery of CDCs were feasible, and no serious adverse events were reported within the 18-month follow-up.", "Patients treated with CDCs showed right ventricular ejection fraction improvement from baseline to 3-month follow-up (46.9%\u00b14.6% to 52.1%\u00b12.4%; P=0.008).", "Compared with controls at 18 months, cardiac MRI analysis of CDC-treated patients showed a higher right ventricular ejection fraction (31.5%\u00b16.8% versus 40.4%\u00b17.6%; P=0.049), improved somatic growth (P=0.0005), reduced heart failure status (P=0.003), and lower incidence of coil occlusion for collaterals (P=0.007).   \n", "CONCLUSIONS Intracoronary infusion of autologous CDCs seems to be feasible and safe in children with hypoplastic left heart syndrome after staged surgery.", "Large phase 2 trials are warranted to examine the potential effects of cardiac function improvements and the long-term benefits of clinical outcomes.   ", "CLINICAL TRIAL REGISTRATION URL http://www.clinicaltrials.gov.", "Unique identifier: NCT01273857."], "structured": true}
{"doc_id": 9629682, "title": "A Whole Brain Staining, Embedding, and Clearing Pipeline for Adult Zebrafish to Visualize Cell Proliferation and Morphology in 3-Dimensions", "abstract": ["The field of macro-imaging has grown considerably with the appearance of innovative clearing methods and confocal microscopes with lasers capable of penetrating increasing tissue depths.", "The ability to visualize and model the growth of whole organs as they develop from birth, or with manipulation, disease or injury, provides new ways of thinking about development, tissue-wide signaling, and cell-to-cell interactions.", "The zebrafish (Danio rerio) has ascended from a predominantly developmental model to a leading adult model of tissue regeneration.", "The unmatched neurogenic and regenerative capacity of the mature central nervous system, in particular, has received much attention, however tools to interrogate the adult brain are sparse.", "At present there exists no straightforward methods of visualizing changes in the whole adult brain in 3-dimensions (3-D) to examine systemic patterns of cell proliferation or cell populations of interest under physiological, injury, or diseased conditions.", "The method presented here is the first of its kind to offer an efficient step-by-step pipeline from intraperitoneal injections of the proliferative marker, 5-ethynyl-2'-deoxyuridine (EdU), to whole brain labeling, to a final embedded and cleared brain sample suitable for 3-D imaging using optical projection tomography (OPT).", "Moreover, this method allows potential for imaging GFP-reporter lines and cell-specific antibodies in the presence or absence of EdU. The small size of the adult zebrafish brain, the highly consistent degree of EdU labeling, and the use of basic clearing agents, benzyl benzoate, and benzyl alcohol, makes this method highly tractable for most laboratories interested in understanding the vertebrate central nervous system in health and disease.", "Post-processing of OPT-imaged adult zebrafish brains injected with EdU illustrate that proliferative patterns in EdU can readily be observed and analyzed using IMARIS and/or FIJI/IMAGEJ software.", "This protocol will be a valuable tool to unlock new ways of understanding systemic patterns in cell proliferation in the healthy and injured brain, brain-wide cellular interactions, stem cell niche development, and changes in brain morphology."], "structured": false}
{"doc_id": 9634465, "title": "Single-Construct Polycistronic Doxycycline-Inducible Vectors Improve Direct Cardiac Reprogramming and Can Be Used to Identify the Critical Timing of Transgene Expression", "abstract": ["Direct reprogramming is a promising approach in regenerative medicine.", "Overexpression of the cardiac transcription factors Gata4, Mef2c, and Tbx5 (GMT) or GMT plus Hand2 (GHMT) directly reprogram fibroblasts into cardiomyocyte-like cells (iCMs).", "However, the critical timing of transgene expression and the molecular mechanisms for cardiac reprogramming remain unclear.", "The conventional doxycycline (Dox)-inducible temporal transgene expression systems require simultaneous transduction of two vectors (pLVX-rtTA/pLVX-cDNA) harboring the reverse tetracycline transactivator (rtTA) and the tetracycline response element (TRE)-controlled transgene, respectively, leading to inefficient cardiac reprogramming.", "Herein, we developed a single-construct-based polycistronic Dox-inducible vector (pDox-cDNA) expressing both the rtTA and TRE-controlled transgenes.", "Fluorescence activated cell sorting (FACS) analyses, quantitative RT-PCR, and immunostaining revealed that pDox-GMT increased cardiac reprogramming three-fold compared to the conventional pLVX-rtTA/pLVX-GMT.", "After four weeks, pDox-GMT-induced iCMs expressed multiple cardiac genes, produced sarcomeric structures, and beat spontaneously.", "Co-transduction of pDox-Hand2 with retroviral pMX-GMT increased cardiac reprogramming three-fold compared to pMX-GMT alone.", "Temporal Dox administration revealed that Hand2 transgene expression is critical during the first two weeks of cardiac reprogramming.", "Microarray analyses demonstrated that Hand2 represses cell cycle-promoting genes and enhances cardiac reprogramming.", "Thus, we have developed an efficient temporal transgene expression system, which could be invaluable in the study of cardiac reprogramming."], "structured": false}
{"doc_id": 9638032, "title": "Increasing microtubule acetylation rescues axonal transport and locomotor deficits caused by LRRK2 Roc-COR domain mutations", "abstract": ["Leucine-rich repeat kinase 2 (LRRK2) mutations are the most common genetic cause of Parkinson's disease.", "LRRK2 is a multifunctional protein affecting many cellular processes and has been described to bind microtubules.", "Defective microtubule-based axonal transport is hypothesized to contribute to Parkinson's disease, but whether LRRK2 mutations affect this process to mediate pathogenesis is not known.", "Here we find that LRRK2 containing pathogenic Roc-COR domain mutations (R1441C, Y1699C) preferentially associates with deacetylated microtubules, and inhibits axonal transport in primary neurons and in Drosophila, causing locomotor deficits in vivo.", "In vitro, increasing microtubule acetylation using deacetylase inhibitors or the tubulin acetylase \u03b1TAT1 prevents association of mutant LRRK2 with microtubules, and the deacetylase inhibitor trichostatin A (TSA) restores axonal transport.", "In vivo knockdown of the deacetylases HDAC6 and Sirt2, or administration of TSA rescues both axonal transport and locomotor behavior.", "Thus, this study reveals a pathogenic mechanism and a potential intervention for Parkinson's disease."], "structured": false}
{"doc_id": 9641846, "title": "G1 arrest and differentiation can occur independently of Rb family function", "abstract": ["The ability of progenitor cells to exit the cell cycle is essential for proper embryonic development and homeostasis, but the mechanisms governing cell cycle exit are still not fully understood.", "Here, we tested the requirement for the retinoblastoma (Rb) protein and its family members p107 and p130 in G0/G1 arrest and differentiation in mammalian cells.", "We found that Rb family triple knockout (TKO) mouse embryos survive until days 9-11 of gestation.", "Strikingly, some TKO cells, including in epithelial and neural lineages, are able to exit the cell cycle in G0/G1 and differentiate in teratomas and in culture.", "This ability of TKO cells to arrest in G0/G1 is associated with the repression of key E2F target genes.", "Thus, G1 arrest is not always dependent on Rb family members, which illustrates the robustness of cell cycle regulatory networks during differentiation and allows for the identification of candidate pathways to inhibit the expansion of cancer cells with mutations in the Rb pathway."], "structured": false}
{"doc_id": 9646449, "title": "Induction of ectopic eyes by targeted expression of the eyeless gene in Drosophila.", "abstract": ["The Drosophila gene eyeless (ey) encodes a transcription factor with both a paired domain and a homeodomain.", "It is homologous to the mouse Small eye (Pax-6) gene and to the Aniridia gene in humans.", "These genes share extensive sequence identity, the position of three intron splice sites is conserved, and these genes are expressed similarly in the developing nervous system and in the eye during morphogenesis.", "Loss-of-function mutations in both the insect and in the mammalian genes have been shown to lead to a reduction or absence of eye structures, which suggests that ey functions in eye morphogenesis.", "By targeted expression of the ey complementary DNA in various imaginal disc primordia of Drosophila, ectopic eye structures were induced on the wings, the legs, and on the antennae.", "The ectopic eyes appeared morphologically normal and consisted of groups of fully differentiated ommatidia with a complete set of photoreceptor cells.", "These results support the proposition that ey is the master control gene for eye morphogenesis.", "Because homologous genes are present in vertebrates, ascidians, insects, cephalopods, and nemerteans, ey may function as a master control gene throughout the metazoa."], "structured": false}
{"doc_id": 9648896, "title": "mir-1-mediated paracrine effect of cancer-associated fibroblasts on lung cancer cell proliferation and chemoresistance.", "abstract": ["Lung cancer is the leading cause of cancer-related mortality in humans worldwide.", "Moreover, the overall 5-year survival rate is only 15%.", "Pathologically almost 80% of all lung cancer cases are non-small cell lung cancer (NSCLC).", "Cancer-associated fibroblasts (CAFs) have been found to exist in a large number of NSCLCs.", "CAFs have been proven to promote tumor progression, metastasis and resistance to therapy through paracrine effects in most solid tumors.", "In the present study, firstly we isolated CAFs from patient tissues and demonstrated that they promoted cell proliferation and chemoresistance to cisplatin in the lung cancer cell lines A549 and 95D in a paracrine manner.", "Secondly, using ELISA and quantative PCR, we found that a higher amount of stromal cell-derived factor 1 (SDF-1) existed in the CAFs rather than that observed in the normal fibroblasts (NFs).", "Thirdly, we detected that SDF-1 facilitated lung cancer cell proliferation and drug resistance via the CXCR4-mediated signaling pathway which involved NF-\u03baB and Bcl-xL. Moreover, we also confirmed that the expression level of SDF-1 in the CAFs was negatively regulated by microRNA mir-1 through microRNA overexpression and quantitative PCR.", "Overall, our data provide one explanation for the effects of CAFs on lung cancer cells.", "Meanwhile, our results also suggest CAFs as a potential therapeutic target in tumor treatment."], "structured": false}
{"doc_id": 9650982, "title": "Genome-wide association analyses in East Asians identify new susceptibility loci for colorectal cancer", "abstract": ["To identify new genetic factors for colorectal cancer (CRC), we conducted a                 genome-wide association study in east Asians.", "By analyzing genome-wide data in 2,098                 cases and 5,749 controls, we selected 64 promising SNPs for replication in an                 independent set of samples, including up to 5,358 cases and 5,922 controls.", "We                 identified four SNPs with association P values of 8.58 \u00d7                     10(-7) to 3.77 \u00d7 10(-10)                 in the combined analysis of all east Asian samples.", "Three of the four were                 replicated in a study conducted in 26,060 individuals of European descent, with                 combined P values of 1.22 \u00d7 10(-10) for                 rs647161 (5q31.1), 6.64 \u00d7 10(-9) for rs2423279                 (20p12.3) and 3.06 \u00d7 10(-8) for rs10774214                 (12p13.32 near the CCND2 gene), derived from meta-analysis of data from both                 east Asian and European-ancestry populations.", "This study identified three new CRC                 susceptibility loci and provides additional insight into the genetics and biology of                 CRC."], "structured": false}
{"doc_id": 9655347, "title": "Long non-coding RNAs as novel players in \u03b2 cell function and type 1 diabetes", "abstract": ["BACKGROUND Long non-coding RNAs (lncRNAs) are a sub-class within non-coding RNA repertoire that have emerged as crucial regulators of the gene expression in various pathophysiological conditions.", "lncRNAs display remarkable versatility and wield their functions through interactions with RNA, DNA, or proteins.", "Accumulating body of evidence based on multitude studies has highlighted the role of lncRNAs in many autoimmune and inflammatory diseases, including type 1 diabetes (T1D).", "This review highlights emerging roles of lncRNAs in immune and islet \u03b2 cell function as well as some of the challenges and opportunities in understanding the pathogenesis of T1D and its complications.   \n", "CONCLUSION We accentuate that the lncRNAs within T1D-loci regions in consort with regulatory variants and enhancer clusters orchestrate the chromatin remodeling in \u03b2 cells and thereby act as cis/trans-regulatory determinants of islet cell transcriptional programs."], "structured": true}
{"doc_id": 9658390, "title": "Costs of the COPD. Differences between intensive care unit and respiratory intermediate care unit.", "abstract": ["INTRODUCTION To assess whether respiratory intermediate care units (RICUs) are cost effective alternatives to intensive care units (ICUs) for patients with exacerbation of chronic obstructive pulmonary disease (COPD).   \n", "PATIENTS AND METHODS Multi-centre, prospective, bottom-up cost study performed in 15 ICUs and 6 RICUs.", "COPD patients staying longer than 48 h were recruited; those coming from other ICUs/RICUs, with immune-deficiency or stroke, were excluded.", "After the ICU sample was standardised to the RICU distribution of the reason-for-admission and infusion of a vasoactive drug on admission, 60 ICU patients and 65 RICU patients remained, of the original 164 recruited.", "For each patient, besides clinical data on admission and discharge, daily information about the resources consumed were recorded and analysed in terms of their costs.   \n", "RESULTS Total cost per patient was lower in RICUs than in ICUs (754 vs. 1507 Euro; P < 0.0001).", "In all items, except drugs and nutrition, we found a significant lower cost in RICUs.", "Dead patients were noticeably different in terms of disease severity between ICUs and RICUs, while surviving ones were not.   \n", "CONCLUSIONS Our study suggests that some COPD patients, less severe and with pure respiratory failure, could be successfully and less costly treated in RICUs."], "structured": true}
{"doc_id": 9669099, "title": "eRNAs are required for p53-dependent enhancer activity and gene transcription.", "abstract": ["Binding within or nearby target genes involved in cell proliferation and survival enables the p53 tumor suppressor gene to regulate their transcription and cell-cycle progression.", "Using genome-wide chromatin-binding profiles, we describe binding of p53 also to regions located distantly from any known p53 target gene.", "Interestingly, many of these regions possess conserved p53-binding sites and all known hallmarks of enhancer regions.", "We demonstrate that these p53-bound enhancer regions (p53BERs) indeed contain enhancer activity and interact intrachromosomally with multiple neighboring genes to convey long-distance p53-dependent transcription regulation.", "Furthermore, p53BERs produce, in a p53-dependent manner, enhancer RNAs (eRNAs) that are required for efficient transcriptional enhancement of interacting target genes and induction of a p53-dependent cell-cycle arrest.", "Thus, our results ascribe transcription enhancement activity to p53 with the capacity to regulate multiple genes from a single genomic binding site.", "Moreover, eRNA production from p53BERs is required for efficient p53 transcription enhancement."], "structured": false}
{"doc_id": 9675944, "title": "Induction of pluripotent stem cells from mouse embryonic fibroblasts by Oct4 and Klf4 with small-molecule compounds.", "abstract": ["Somatic cells can be induced into pluripotent stem cells (iPSCs) with a combination of four transcription factors, Oct4/Sox2/Klf4/c-Myc or Oct4/Sox2/Nanog/LIN28.", "This provides an enabling platform to obtain patient-specific cells for various therapeutic and research applications.", "However, several problems remain for this approach to be therapeutically relevant due to drawbacks associated with efficiency and viral genome integration.", "Recently, it was shown that neural progenitor cells (NPCs) transduced with Oct4/Klf4 can be reprogrammed into iPSCs.", "However, NPCs express Sox2 endogenously, possibly facilitating reprogramming in the absence of exogenous Sox2.", "In this study, we identified a small-molecule combination, BIX-01294 and BayK8644, that enables reprogramming of Oct4/Klf4-transduced mouse embryonic fibroblasts, which do not endogenously express the factors essential for reprogramming.", "This study demonstrates that small molecules identified through a phenotypic screen can compensate for viral transduction of critical factors, such as Sox2, and improve reprogramming efficiency."], "structured": false}
{"doc_id": 9680193, "title": "Vps22/EAP30 in ESCRT-II mediates endosomal sorting of growth factor and chemokine receptors destined for lysosomal degradation.", "abstract": ["The ubiquitin-binding protein Hrs and endosomal sorting complex required for transport (ESCRT)-I and ESCRT-III are involved in sorting endocytosed and ubiquitinated receptors to lysosomes for degradation and efficient termination of signaling.", "In this study, we have investigated the role of the ESCRT-II subunit Vps22/EAP30 in degradative protein sorting of ubiquitinated receptors.", "Vps22 transiently expressed in HeLa cells was detected in endosomes containing endocytosed epidermal growth factor receptors (EGFRs) as well as Hrs and ESCRT-I and ESCRT-III.", "Depletion of Vps22 by small interfering RNA, which was accompanied by decreased levels of other ESCRT-II subunits, greatly reduced degradation of EGFR and its ligand EGF as well as the chemokine receptor CXCR4.", "EGFR accumulated on the limiting membranes of early endosomes and aberrantly small multivesicular bodies in Vps22-depleted cells.", "Phosphorylation and nuclear translocation of extracellular-signal-regulated kinase1/2 downstream of the EGF-activated receptor were sustained by depletion of Hrs or the ESCRT-I subunit Tsg101.", "In contrast, this was not the case when Vps22 was depleted.", "These results indicate an important role for Vps22 in ligand-induced EGFR and CXCR4 turnover and suggest that termination of EGF signaling occurs prior to ESCRT-II engagement."], "structured": false}
{"doc_id": 9687772, "title": "XPG stabilizes TFIIH, allowing transactivation of nuclear receptors: implications for Cockayne syndrome in XP-G/CS patients.", "abstract": ["Mutations in the human XPG gene give rise to an inherited photosensitive disorder, xeroderma pigmentosum (XP) associated with Cockayne syndrome (XP-G/CS).", "The clinical features of CS in XP-G/CS patients are difficult to explain on the basis of a defect in nucleotide excision repair (NER).", "We found that XPG forms a stable complex with TFIIH, which is active in transcription and NER.", "Mutations in XPG found in XP-G/CS patient cells that prevent the association with TFIIH also resulted in the dissociation of CAK and XPD from the core TFIIH.", "As a consequence, the phosphorylation and transactivation of nuclear receptors were disturbed in XP-G/CS as well as xpg(-/-) MEF cells and could be restored by expression of wild-type XPG.", "These results provide an insight into the role of XPG in the stabilization of TFIIH and the regulation of gene expression and provide an explanation of some of the clinical features of XP-G/CS."], "structured": false}
{"doc_id": 9696379, "title": "Metabolic cycling in single yeast cells from unsynchronized steady-state populations limited on glucose or phosphate.", "abstract": ["Oscillations in patterns of expression of a large fraction of yeast genes are associated with the \"metabolic cycle,\" usually seen only in prestarved, continuous cultures of yeast.", "We used FISH of mRNA in individual cells to test the hypothesis that these oscillations happen in single cells drawn from unsynchronized cultures growing exponentially in chemostats.", "Gene-expression data from synchronized cultures were used to predict coincident appearance of mRNAs from pairs of genes in the unsynchronized cells.", "Quantitative analysis of the FISH results shows that individual unsynchronized cells growing slowly because of glucose limitation or phosphate limitation show the predicted oscillations.", "We conclude that the yeast metabolic cycle is an intrinsic property of yeast metabolism and does not depend on either synchronization or external limitation of growth by the carbon source."], "structured": false}
{"doc_id": 9704467, "title": "in polyploid species", "abstract": ["We developed the Yeast Gene Order Browser (YGOB; http://wolfe.gen.tcd.ie/ygob) to facilitate visual comparisons and computational analysis of synteny relationships in yeasts.", "The data presented in YGOB, currently covering seven species, are based on sets of homologous genes that have been intensively manually curated based on both sequence similarity and genomic context (synteny).", "We reconciled different laboratories' lists of paralogous Saccharomyces cerevisiae gene pairs formed by genome duplication (ohnologs), and present near-exhaustive lists of the ohnolog pairs retained in S. cerevisiae (551, including 22 previously unidentified), Saccharomyces castellii (599), and Candida glabrata (404)."], "structured": false}
{"doc_id": 9705208, "title": "Immune complex relay by subcapsular sinus macrophages and non-cognate B cells drives antibody affinity maturation", "abstract": ["Subcapsular sinus (SCS) macrophages capture antigens from lymph and present them intact for B cell encounter and follicular delivery.", "However, the properties of SCS macrophages are poorly defined.", "Here we show SCS macrophage development depended on lymphotoxin-alpha1beta2, and the cells had low lysosomal enzyme expression and retained opsonized antigens on their surface.", "Intravital imaging revealed immune complexes moving along macrophage processes into the follicle.", "Moreover, noncognate B cells relayed antigen opsonized by newly produced antibodies from the subcapsular region to the germinal center, and affinity maturation was impaired when this transport process was disrupted.", "Thus, we characterize SCS macrophages as specialized antigen-presenting cells functioning at the apex of an antigen transport chain that promotes humoral immunity."], "structured": false}
{"doc_id": 9724974, "title": "Promoter decoding of transcription factor dynamics involves a trade-off between noise and control of gene expression", "abstract": ["Numerous transcription factors (TFs) encode information about upstream signals in the dynamics of their activation, but how downstream genes decode these dynamics remains poorly understood.", "Using microfluidics to control the nucleocytoplasmic translocation dynamics of the budding yeast TF Msn2, we elucidate the principles that govern how different promoters convert dynamical Msn2 input into gene expression output in single cells.", "Combining modeling and experiments, we classify promoters according to their signal-processing behavior and reveal that multiple, distinct gene expression programs can be encoded in the dynamics of Msn2.", "We show that both oscillatory TF dynamics and slow promoter kinetics lead to higher noise in gene expression.", "Furthermore, we show that the promoter activation timescale is related to nucleosome remodeling.", "Our findings imply a fundamental trade-off: although the cell can exploit different promoter classes to differentially control gene expression using TF dynamics, gene expression noise fundamentally limits how much information can be encoded in the dynamics of a single TF and reliably decoded by promoters."], "structured": false}
{"doc_id": 9730755, "title": "GaAs nanopillar-array solar cells employing in situ surface passivation", "abstract": ["Arrays of III-V direct-bandgap semiconductor nanopillars represent promising photovoltaic candidates due to their inherent high optical absorption coefficients and minimized reflection arising from light trapping, efficient charge collection in the radial direction and the ability to synthesize them on low-cost platforms.", "However, the increased surface area results in surface states that hamper the power conversion efficiency.", "Here, we report the first demonstration of GaAs nanopillar-array photovoltaics employing epitaxial passivation with air mass 1.5 global power conversion efficiencies of 6.63%.", "High-bandgap epitaxial InGaP shells are grown in situ and cap the radial p-n junctions to alleviate surface-state effects.", "Under light, the photovoltaic devices exhibit open-circuit voltages of 0.44 V, short-circuit current densities of 24.3 mA cm(-2) and fill factors of 62% with high external quantum efficiencies >70% across the spectral regime of interest.", "A novel titanium/indium tin oxide annealed alloy is exploited as transparent ohmic anode."], "structured": false}
{"doc_id": 9732010, "title": "Roles of histone acetylation and chromatin remodeling factor in a meiotic recombination hotspot.", "abstract": ["Histone acetyltransferases (HATs) and ATP-dependent chromatin remodeling factors (ADCRs) are involved in selective gene regulation via modulation of local chromatin configuration.", "Activation of the recombination hotspot ade6-M26 of Schizosaccharomyces pombe is mediated by a cAMP responsive element (CRE)-like sequence, M26, and a heterodimeric ATF/CREB transcription factor, Atf1.Pcr1.", "Chromatin remodeling occurs meiotically around M26.", "We examined the roles of HATs and ADCRs in chromatin remodeling around M26.", "Histones H3 and H4 around M26 were hyperacetylated in an M26- and Atf1-dependent manner early in meiosis.", "SpGcn5, the S. pombe homolog of Gcn5p, was required for the majority of histone H3 acetylation around M26 in vivo.", "Deletion of gcn5+ caused a significant delay in chromatin remodeling but only partial reduction of M26 meiotic recombination frequency.", "The snf22+ (a Swi2/Snf2-ADCR homologue) deletion and snf22+ gcn5+ double deletion abolished chromatin remodeling and significant reduction of meiotic recombination around M26.", "These results suggest that HATs and ADCRs cooperatively alter local chromatin structure, as in selective transcription activation, to activate meiotic recombination at M26 in a site-specific manner."], "structured": false}
{"doc_id": 9737083, "title": "The Somatic Genomic Landscape of Glioblastoma", "abstract": ["We describe the landscape of somatic genomic alterations based on multidimensional and comprehensive characterization of more than 500 glioblastoma tumors (GBMs).", "We identify several novel mutated genes as well as complex rearrangements of signature receptors, including EGFR and PDGFRA.", "TERT promoter mutations are shown to correlate with elevated mRNA expression, supporting a role in telomerase reactivation.", "Correlative analyses confirm that the survival advantage of the proneural subtype is conferred by the G-CIMP phenotype, and MGMT DNA methylation may be a predictive biomarker for treatment response only in classical subtype GBM.", "Integrative analysis of genomic and proteomic profiles challenges the notion of therapeutic inhibition of a pathway as an alternative to inhibition of the target itself.", "These data will facilitate the discovery of therapeutic and diagnostic target candidates, the validation of research and clinical observations and the generation of unanticipated hypotheses that can advance our molecular understanding of this lethal cancer."], "structured": false}
{"doc_id": 9745001, "title": "Radioiodine treatment of multinodular non-toxic goitre.", "abstract": ["OBJECTIVE To investigate the long term effect of radioactive iodine on thyroid function and size in patients with non-toxic multinodular goitre.   \n", "DESIGN Consecutive patients with multinodular non-toxic goitre selected for radioactive iodine treatment and followed for a minimum of 12 months (median 48 months) after an intended dose of 3.7 MBq/g thyroid tissue corrected to a 100% uptake of iodine-131 in 24 hours.   \n", "PATIENTS 69 patients with a growing multinodular non-toxic goitre causing local compression symptoms or cosmetic inconveniences.", "The treatment was chosen because of a high operative risk, previous thyroidectomy, or refusal to be operated on.   \n", "MAIN OUTCOME MEASUREMENTS Standard thyroid function variables and ultrasonically determined thyroid volume before treatment as well as 1, 2, 3, 6, and 12 months after treatment and then once a year.   \n", "RESULTS 56 patients were treated with a single dose of 131I, 12 with two doses, and one with four doses.", "In 45 patients treated with one dose and remaining euthyroid the median thyroid volume was reduced from 73 (interquartile range 50-106) ml to 29 (23-48) ml at 24 months in the 39 patients in whom this was measured during follow up.", "The median reduction was 40 (22-48) ml (60% reduction, p < 0.0001), half of which occurred within three months.", "Patients treated with two doses as well as those developing hypothyroidism and hyperthyroidism had a significant reduction in thyroid volume.", "Eleven patients developed hypothyroidism (cumulative five year risk 22%, 95% confidence interval 4.8% to 38.4%).", "Side effects were few: three cases of hyperthyroidism and two cases of radiation thyroiditis.", "Only one patient was dissatisfied with the result; she was referred for operation six months after treatment.   \n", "CONCLUSIONS A substantial reduction in thyroid volume accompanied by a low incidence of hypothyroidism and few side effects makes the use of radioactive iodine an attractive alternative to surgery in selected cases of non-toxic multinodular goitre."], "structured": true}
{"doc_id": 9748934, "title": "Alterations in microRNA-124 and AMPA receptors contribute to social behavioral deficits in frontotemporal dementia", "abstract": ["Neurodegenerative diseases, such as frontotemporal dementia (FTD), are often associated with behavioral deficits, but the underlying anatomical and molecular causes remain poorly understood.", "Here we show that forebrain-specific expression of FTD-associated mutant CHMP2B in mice causes several age-dependent neurodegenerative phenotypes, including social behavioral impairments.", "The social deficits were accompanied by a change in AMPA receptor (AMPAR) composition, leading to an imbalance between Ca(2+)-permeable and Ca(2+)-impermeable AMPARs.", "Expression of most AMPAR subunits was regulated by the brain-enriched microRNA miR-124, whose abundance was markedly decreased in the superficial layers of the cerebral cortex of mice expressing the mutant CHMP2B.", "We found similar changes in miR-124 and AMPAR levels in the frontal cortex and induced pluripotent stem cell-derived neurons from subjects with behavioral variant FTD.", "Moreover, ectopic miR-124 expression in the medial prefrontal cortex of mutant mice decreased AMPAR levels and partially rescued behavioral deficits.", "Knockdown of the AMPAR subunit Gria2 also alleviated social impairments.", "Our results identify a previously undescribed mechanism involving miR-124 and AMPARs in regulating social behavior in FTD and suggest a potential therapeutic avenue."], "structured": false}
{"doc_id": 9752604, "title": "Activated AMPK boosts the Nrf2/HO-1 signaling axis\u2014A role for the unfolded protein response", "abstract": ["In light of the emerging interplay between redox and metabolic signaling pathways we investigated the potential cross talk between nuclear factor E2-related factor 2 (Nrf2) and AMP-activated kinase (AMPK), central regulators of the cellular redox and energy balance, respectively.", "Making use of xanthohumol (XN) as an activator of both the AMPK and the Nrf2 signaling pathway we show that AMPK exerts a positive influence on Nrf2/heme oxygenase (HO)-1 signaling in mouse embryonic fibroblasts.", "Genetic ablation and pharmacological inhibition of AMPK blunts Nrf2-dependent HO-1 expression by XN already at the mRNA level.", "XN leads to AMPK activation via interference with mitochondrial function and activation of liver kinase B1 as upstream AMPK kinase.", "The subsequent AMPK-mediated enhancement of the Nrf2/HO-1 response does not depend on inhibition of the mammalian target of rapamycin, inhibition of glycogen synthase kinase 3\u03b2, or altered abundance of Nrf2 (total and nuclear).", "However, reduced endoplasmic reticulum stress was identified and elaborated as a step in the AMPK-augmented Nrf2/HO-1 response.", "Overall, we shed more light on the hitherto incompletely understood cross talk between the LKB1/AMPK and the Nrf2/HO-1 axis revealing for the first time involvement of the unfolded protein response as an additional player and suggesting tight cooperation between signaling pathways controlling cellular redox, energy, or protein homeostasis."], "structured": false}
{"doc_id": 9754530, "title": "The IDEAL recommendations and urological innovation", "abstract": ["Like other branches of surgery, Urology has encountered major challenges in aligning the research processes by which new interventions are assessed with the principles of Evidence-Based Medicine.", "This article explains the IDEAL framework and recommendations and illustrates how they might affect the evaluation of current controversial urological procedures.", "From an inside perspective, we provide an overview of the efforts of the IDEAL Working Group to date with special emphasis on the field of Urology.", "There are clear differences between drugs and interventions in the natural history of innovations.", "Since the conventional framework for conducting trials of new treatments is largely based on the former, the evaluation of surgical innovations using the same template can encounter significant problems.", "Difficulties in performing randomized controlled trials of surgical techniques and the persistence of the case series as an important feature of the scientific literature have been the two most controversial aspects of this mismatch between the subject of research and the methodology used.", "The IDEAL framework provides a description of the process of innovation and development for surgical trials, and the associated recommendations provide a suggested alternative approach to developing study designs, which are appropriate for the specific problems of new techniques.", "IDEAL provides a new framework for surgical innovation that was developed with broad stakeholder input from the surgical community and is expected to have a transformative impact on the way that urologists perform clinical research."], "structured": false}
{"doc_id": 9754833, "title": "Prolonged conservative care versus early surgery in patients with sciatica caused by lumbar disc herniation: two year results of a randomised controlled trial.", "abstract": ["OBJECTIVES To evaluate the effects of early lumbar disc surgery compared with prolonged conservative care for patients with sciatica over two years of follow-up.   \n", "DESIGN Randomised controlled trial.   \n", "SETTING Nine Dutch hospitals.   \n", "PARTICIPANTS 283 patients with 6-12 weeks of sciatica.   \n", "INTERVENTIONS Early surgery or an intended six months of continued conservative treatment, with delayed surgery if needed.   \n", "MAIN OUTCOME MEASURES Scores from Roland disability questionnaire for sciatica, visual analogue scale for leg pain, and Likert self rating scale of global perceived recovery.   \n", "RESULTS Of the 141 patients assigned to undergo early surgery, 125 (89%) underwent microdiscectomy.", "Of the 142 patients assigned to conservative treatment, 62 (44%) eventually required surgery, seven doing so in the second year of follow-up.", "There was no significant overall difference between treatment arms in disability scores during the first two years (P=0.25).", "Improvement in leg pain was faster for patients randomised to early surgery, with a significant difference between \"areas under the curves\" over two years (P=0.05).", "This short term benefit of early surgery was no longer significant by six months and continued to narrow between six months and 24 months.", "Patient satisfaction decreased slightly between one and two years for both groups.", "At two years 20% of all patients reported an unsatisfactory outcome.   \n", "CONCLUSIONS Early surgery achieved more rapid relief of sciatica than conservative care, but outcomes were similar by one year and these did not change during the second year.   \n", "TRIAL REGISTRY ISRCT", "No 26872154."], "structured": true}
{"doc_id": 9764256, "title": "Human papillomavirus testing for the detection of high-grade cervical intraepithelial neoplasia and cancer: final results of the POBASCAM randomised controlled trial.", "abstract": ["BACKGROUND Human papillomavirus (HPV) testing is more sensitive for the detection of high-grade cervical lesions than is cytology, but detection of HPV by DNA screening in two screening rounds 5 years apart has not been assessed.", "The aim of this study was to assess whether HPV DNA testing in the first screen decreases detection of cervical intraepithelial neoplasia (CIN) grade 3 or worse, CIN grade 2 or worse, and cervical cancer in the second screening.   \n", "METHODS In this randomised trial, women aged 29-56 years participating in the cervical screening programme in the Netherlands were randomly assigned to receive HPV DNA (GP5+/6+-PCR method) and cytology co-testing or cytology testing alone, from January, 1999, to September, 2002.", "Randomisation (in a 1:1 ratio) was done with computer-generated random numbers after the cervical specimen had been taken.", "At the second screening 5 years later, HPV DNA and cytology co-testing was done in both groups; researchers were masked to the patient's assignment.", "The primary endpoint was the number of CIN grade 3 or worse detected.", "Analysis was done by intention to screen.", "The trial is now finished and is registered, number ISRCTN20781131.   \n", "FINDINGS 22,420 women were randomly assigned to the intervention group and 22 518 to the control group; 19 999 in the intervention group and 20,106 in the control group were eligible for analysis at the first screen.", "At the second screen, 19 579 women in the intervention group and 19,731 in the control group were eligible, of whom 16,750 and 16,743, respectively, attended the second screen.", "In the second round, CIN grade 3 or worse was less common in the intervention group than in the control group (88 of 19 579 in the intervention group vs 122 of 19,731 in the control group; relative risk 0\u00b773, 95% CI 0\u00b755-0\u00b796; p=0\u00b7023).", "Cervical cancer was also less common in the intervention group than in the control group (four of 19 579 in the intervention group vs 14 of 19,731; 0\u00b729, 0\u00b710-0\u00b787; p=0\u00b7031).", "In the baseline round, detection of CIN grade 3 or worse did not differ significantly between groups (171 of 19 999 vs 150 of 20,106; 1\u00b715, 0\u00b792-1\u00b743; p=0\u00b7239) but was significantly more common in women with normal cytology (34 of 19,286 vs 12 of 19,373; 2\u00b785, 1\u00b747-5\u00b749; p=0\u00b7001).", "Furthermore, significantly more cases of CIN grade 2 or worse were detected in the intervention group than in the control group (267 of 19 999 vs 215 of 20,106; 1\u00b725, 1\u00b705-1\u00b750; p=0\u00b7015).", "In the second screen, fewer HPV16-positive CIN grade 3 or worse were detected in the intervention group than in the control group (17 of 9481 vs 35 of 9354; 0\u00b748, 0\u00b727-0\u00b785; p=0\u00b7012); detection of non-HPV16-positive CIN grade 3 or worse did not differ between groups (25 of 9481 vs 25 of 9354; 0\u00b799, 0\u00b757-1\u00b772; p=1\u00b700).", "The cumulative detection of CIN grade 3 or worse and CIN grade 2 or worse did not differ significantly between study arms, neither for the whole study group (CIN grade 3 or worse: 259 of 19 999 vs 272 of 20,106; 0\u00b796, 0\u00b781-1\u00b714, p=0\u00b7631; CIN grade 2 or worse: 427 of 19 999 vs 399 of 20,106; 1\u00b708, 0\u00b794-1\u00b724; p=0\u00b7292), nor for subgroups of women invited for the first time (CIN grade 3 or worse in women aged 29-33 years: 102 of 3139 vs 105 of 3128; 0\u00b797, 0\u00b774-1\u00b727; CIN grade 2 or worse in women aged 29-33 years: 153 of 3139 vs 151 of 3128; 1\u00b701, 0\u00b781-1\u00b726; CIN grade 3 or worse in women aged 34-56 years: 157 of 16,860 vs 167 of 16 978; 0\u00b795, 0\u00b776-1\u00b718; CIN grade 2 or worse in women aged 34-56 years: 274 of 16,860 vs 248 of 16 978; 1\u00b711, 0\u00b794-1\u00b732).   \n", "INTERPRETATION Implementation of HPV DNA testing in cervical screening leads to earlier detection of clinically relevant CIN grade 2 or worse, which when adequately treated, improves protection against CIN grade 3 or worse and cervical cancer.", "Early detection of high-grade cervical legions caused by HPV16 was a major component of this benefit.", "Our results lend support to the use of HPV DNA testing for all women aged 29 years and older.   \n", "FUNDING Zorg Onderzoek Nederland (Netherlands Organisation for Health Research and Development)."], "structured": true}
{"doc_id": 9767444, "title": "Epigenetic therapy activates type I interferon signaling in murine ovarian cancer to reduce immunosuppression and tumor burden.", "abstract": ["Ovarian cancer is the most lethal of all gynecological cancers, and there is an urgent unmet need to develop new therapies.", "Epithelial ovarian cancer (EOC) is characterized by an immune suppressive microenvironment, and response of ovarian cancers to immune therapies has thus far been disappointing.", "We now find, in a mouse model of EOC, that clinically relevant doses of DNA methyltransferase and histone deacetylase inhibitors (DNMTi and HDACi, respectively) reduce the immune suppressive microenvironment through type I IFN signaling and improve response to immune checkpoint therapy.", "These data indicate that the type I IFN response is required for effective in vivo antitumorigenic actions of the DNMTi 5-azacytidine (AZA).", "Through type I IFN signaling, AZA increases the numbers of CD45+ immune cells and the percentage of active CD8+ T and natural killer (NK) cells in the tumor microenvironment, while reducing tumor burden and extending survival.", "AZA also increases viral defense gene expression in both tumor and immune cells, and reduces the percentage of macrophages and myeloid-derived suppressor cells in the tumor microenvironment.", "The addition of an HDACi to AZA enhances the modulation of the immune microenvironment, specifically increasing T and NK cell activation and reducing macrophages over AZA treatment alone, while further increasing the survival of the mice.", "Finally, a triple combination of DNMTi/HDACi plus the immune checkpoint inhibitor \u03b1-PD-1 provides the best antitumor effect and longest overall survival, and may be an attractive candidate for future clinical trials in ovarian cancer."], "structured": false}
{"doc_id": 9769310, "title": "IGF2 is parentally imprinted during human embryogenesis and in the Beckwith\u2013Wiedemann syndrome", "abstract": ["The phenomenon of parental imprinting involves the preferential expression of one parental allele of a subset of chromosomal genes and has so far only been documented in the mouse.", "We show here, by exploiting sequence polymorphisms in exon nine of the human insulin\u2013like growth factor 2 (IGF2) gene, that only the paternally\u2013inherited allele is active in embryonic and extra\u2013embryonic cells from first trimester pregnancies.", "In addition, only the paternal allele is expressed in tissues from a patient who suffered from Beckwith\u2013Wiedemann syndrome.", "Thus the parental imprinting of IGF2 appears to be evolutionarily conserved from mouse to man and has implications for the generation of the Beckwith\u2013Wiedemann syndrome."], "structured": false}
{"doc_id": 9769684, "title": "Safety and reliability of Radio Frequency Identification Devices in Magnetic Resonance Imaging and Computed Tomography", "abstract": ["BACKGROUND Radio Frequency Identification (RFID) devices are becoming more and more essential for patient safety in hospitals.", "The purpose of this study was to determine patient safety, data reliability and signal loss wearing on skin RFID devices during magnetic resonance imaging (MRI) and computed tomography (CT) scanning.   \n", "METHODS Sixty RFID tags of the type I-Code SLI, 13.56 MHz, ISO 18000-3.1 were tested: Thirty type 1, an RFID tag with a 76 x 45 mm aluminum-etched antenna and 30 type 2, a tag with a 31 x 14 mm copper-etched antenna.", "The signal loss, material movement and heat tests were performed in a 1.5 T and a 3 T MR system.", "For data integrity, the tags were tested additionally during CT scanning.", "Standardized function tests were performed with all transponders before and after all imaging studies.   \n", "RESULTS There was no memory loss or data alteration in the RFID tags after MRI and CT scanning.", "Concerning heating (a maximum of 3.6 degrees C) and device movement (below 1 N/kg) no relevant influence was found.", "Concerning signal loss (artifacts 2 - 4 mm), interpretability of MR images was impaired when superficial structures such as skin, subcutaneous tissues or tendons were assessed.   \n", "CONCLUSIONS Patients wearing RFID wristbands are safe in 1.5 T and 3 T MR scanners using normal operation mode for RF-field.", "The findings are specific to the RFID tags that underwent testing."], "structured": true}
{"doc_id": 9784254, "title": "LXR-Dependent Gene Expression Is Important for Macrophage Survival and the Innate Immune Response", "abstract": ["The liver X receptors (LXRs) are nuclear receptors with established roles in the regulation of lipid metabolism.", "We now show that LXR signaling not only regulates macrophage cholesterol metabolism but also impacts antimicrobial responses.", "Mice lacking LXRs are highly susceptible to infection with the intracellular bacteria Listeria monocytogenes (LM).", "Bone marrow transplant studies point to altered macrophage function as the major determinant of susceptibility.", "LXR-null macrophages undergo accelerated apoptosis when challenged with LM and exhibit defective bacterial clearance in vivo.", "These defects result, at least in part, from loss of regulation of the antiapoptotic factor SPalpha, a direct target for regulation by LXRalpha.", "Expression of LXRalpha or SPalpha in macrophages inhibits apoptosis in the setting of LM infection.", "Our results demonstrate that LXR-dependent gene expression plays an unexpected role in innate immunity and suggest that common nuclear receptor pathways mediate macrophage responses to modified lipoproteins and intracellular pathogens."], "structured": false}
{"doc_id": 9787715, "title": "Alterations on peripheral B cell subsets following an acute uncomplicated clinical malaria infection in children", "abstract": ["BACKGROUND The effects of Plasmodium falciparum on B-cell homeostasis have not been well characterized.", "This study investigated whether an episode of acute malaria in young children results in changes in the peripheral B cell phenotype.   \n", "METHODS Using flow-cytofluorimetric analysis, the B cell phenotypes found in the peripheral blood of children aged 2-5 years were characterized during an episode of acute uncomplicated clinical malaria and four weeks post-recovery and in healthy age-matched controls.   \n", "RESULTS There was a significant decrease in CD19+ B lymphocytes during acute malaria.", "Characterization of the CD19+ B cell subsets in the peripheral blood based on expression of IgD and CD38 revealed a significant decrease in the numbers of naive 1 CD38-IgD+ B cells while there was an increase in CD38+IgD- memory 3 B cells during acute malaria.", "Further analysis of the peripheral B cell phenotype also identified an expansion of transitional CD10+CD19+ B cells in children following an episode of acute malaria with up to 25% of total CD19+ B cell pool residing in this subset.   \n", "CONCLUSION Children experiencing an episode of acute uncomplicated clinical malaria experienced profound disturbances in B cell homeostasis."], "structured": true}
{"doc_id": 9791313, "title": "SETD2: an epigenetic modifier with tumor suppressor functionality", "abstract": ["In the past decade important progress has been made in our understanding of the epigenetic regulatory machinery.", "It has become clear that genetic aberrations in multiple epigenetic modifier proteins are associated with various types of cancer.", "Moreover, targeting the epigenome has emerged as a novel tool to treat cancer patients.", "Recently, the first drugs have been reported that specifically target SETD2-negative tumors.", "In this review we discuss the studies on the associated protein, Set domain containing 2 (SETD2), a histone modifier for which mutations have only recently been associated with cancer development.", "Our review starts with the structural characteristics of SETD2 and extends to its corresponding function by combining studies on SETD2 function in yeast, Drosophila, Caenorhabditis elegans, mice, and humans.", "SETD2 is now generally known as the single human gene responsible for trimethylation of lysine 36 of Histone H3 (H3K36).", "H3K36me3 readers that recruit protein complexes to carry out specific processes, including transcription elongation, RNA processing, and DNA repair, determine the impact of this histone modification.", "Finally, we describe the prevalence of SETD2-inactivating mutations in cancer, with the highest frequency in clear cell Renal Cell Cancer, and explore how SETD2-inactivation might contribute to tumor development."], "structured": false}
{"doc_id": 9796495, "title": "Updated energy budgets for neural computation in the neocortex and cerebellum.", "abstract": ["The brain's energy supply determines its information processing power, and generates functional imaging signals.", "The energy use on the different subcellular processes underlying neural information processing has been estimated previously for the grey matter of the cerebral and cerebellar cortex.", "However, these estimates need reevaluating following recent work demonstrating that action potentials in mammalian neurons are much more energy efficient than was previously thought.", "Using this new knowledge, this paper provides revised estimates for the energy expenditure on neural computation in a simple model for the cerebral cortex and a detailed model of the cerebellar cortex.", "In cerebral cortex, most signaling energy (50%) is used on postsynaptic glutamate receptors, 21% is used on action potentials, 20% on resting potentials, 5% on presynaptic transmitter release, and 4% on transmitter recycling.", "In the cerebellar cortex, excitatory neurons use 75% and inhibitory neurons 25% of the signaling energy, and most energy is used on information processing by non-principal neurons: Purkinje cells use only 15% of the signaling energy.", "The majority of cerebellar signaling energy use is on the maintenance of resting potentials (54%) and postsynaptic receptors (22%), while action potentials account for only 17% of the signaling energy use."], "structured": false}
{"doc_id": 9813098, "title": "Plasma homocysteine is a risk factor for recurrent vascular events in young patients with an ischaemic stroke or TIA", "abstract": ["Young patients with an ischaemic stroke or transient ischaemic attack (TIA) often have no vascular risk factors.", "Hyperhomocysteinaemia is an established risk factor for stroke in elderly patients but it is uncertain whether it is also important for the prognosis of young ischaemic stroke and TIA patients.", "We examined the possible effect of the plasma homocysteine level on the risk of recurrent vascular events in patients between 18 and 45 years of age.", "The study population consisted of 161 consecutive patients with a recent cerebral infarction or TIA.", "Data on the primary event and the homocysteine level were collected retrospectively from hospital records.", "General practitioners and patients were contacted by telephone to record vascular events and the type of medication used during the follow\u2013up period.", "Vascular events included cerebral infarction, TIA, pulmonary embolism, venous thrombosis, myocardial infarction and peripheral arterial disease.", "A Kaplan- Meier curve showed a dose effect relationship between event-free survival time and tertiles of the homocysteine level (Log rank statistic 5.91; p = 0.05).", "The Cox hazard ratio, after adjustment for homocysteine lowering treatment, was 1.7 (95 % CI, 1.1 to 2.8) for any vascular outcome event, 1.9 (95% CI, 1.1 to 3.0) for arterial outcome events and 1.8 (95 % CI, 1.1 to 2.9) for cerebral outcome events.", "In spite of our small number of outcome events we found a significant association at the 95% confidence level between homocysteine level and the risk of recurrent vascular events in young patients with an ischaemic stroke or TIA.", "The association is of the same magnitude as in elderly people."], "structured": false}
{"doc_id": 9814332, "title": "LDL inhibits the mediation of cholesterol efflux from macrophage foam cells by apoA-I-containing lipoproteins. A putative mechanism for foam cell formation.", "abstract": ["Although the accumulation of cholesterol in macrophages appears to be an initial step in atherogenesis, low-density lipoprotein (LDL), a major risk factor for atherosclerosis, does not promote cholesterol accumulation in macrophages in its native form.", "On the other hand, apolipoprotein (apo) A-I-containing lipoprotein removes cholesterol from cholesterol-loaded macrophages (foam cells) and prevents cholesterol from accumulating in the cells.", "We examined the effect of LDL on cholesterol removal by two species of apoA-I-containing lipoproteins, one containing only apoA-I (LpA-I) and the other containing apoA-I and apoA-II (LpA-I/A-II).", "When foam cells were incubated with LpA-I or LpA-I/A-II, cellular cholesterol mass was reduced.", "In contrast, when LDL was added, the cholesterol-reducing capacities of these lipoproteins were dose-dependently inhibited by LDL.", "In the presence of LDL, LpA-I and LpA-I/A-II removed free cholesterol preferentially from LDL rather than from the plasma membrane of foam cells.", "In addition, a fair amount of cellular cholesterol was directly moved to LDL rather than to LpA-I or LpA-I/A-II.", "The cellular cholesterol that moved to LDL was completely compensated for by the cholesterol influx from LDL to foam cells.", "Thus, net cholesterol efflux (a combination of influx and efflux) from foam cells was inhibited by LDL.", "These results, taken together, indicate that LDL may accelerate foam cell formation by inhibiting cholesterol removal from the cells and that elevated levels of plasma LDL may become a risk factor for atherosclerosis by inhibiting the function of LpA-I and LpA-I/A-II at the cellular level."], "structured": false}
{"doc_id": 9822397, "title": "Sugar-sweetened beverages, weight gain, and incidence of type 2 diabetes in young and middle-aged women.", "abstract": ["CONTEXT Sugar-sweetened beverages like soft drinks and fruit punches contain large amounts of readily absorbable sugars and may contribute to weight gain and an increased risk of type 2 diabetes, but these relationships have been minimally addressed in adults.   \n", "OBJECTIVE To examine the association between consumption of sugar-sweetened beverages and weight change and risk of type 2 diabetes in women.   \n", "DESIGN, SETTING, AND PARTICIPANTS Prospective cohort analyses conducted from 1991 to 1999 among women in the Nurses' Health Study II.", "The diabetes analysis included 91,249 women free of diabetes and other major chronic diseases at baseline in 1991.", "The weight change analysis included 51,603 women for whom complete dietary information and body weight were ascertained in 1991, 1995, and 1999.", "We identified 741 incident cases of confirmed type 2 diabetes during 716,300 person-years of follow-up.   \n", "MAIN OUTCOME MEASURES Weight gain and incidence of type 2 diabetes.   \n", "RESULTS Those with stable consumption patterns had no difference in weight gain, but weight gain over a 4-year period was highest among women who increased their sugar-sweetened soft drink consumption from 1 or fewer drinks per week to 1 or more drinks per day (multivariate-adjusted means, 4.69 kg for 1991 to 1995 and 4.20 kg for 1995 to 1999) and was smallest among women who decreased their intake (1.34 and 0.15 kg for the 2 periods, respectively) after adjusting for lifestyle and dietary confounders.", "Increased consumption of fruit punch was also associated with greater weight gain compared with decreased consumption.", "After adjustment for potential confounders, women consuming 1 or more sugar-sweetened soft drinks per day had a relative risk [RR] of type 2 diabetes of 1.83 (95% confidence interval [CI], 1.42-2.36; P<.001 for trend) compared with those who consumed less than 1 of these beverages per month.", "Similarly, consumption of fruit punch was associated with increased diabetes risk (RR for > or =1 drink per day compared with <1 drink per month, 2.00; 95% CI, 1.33-3.03; P =.001).   \n", "CONCLUSION Higher consumption of sugar-sweetened beverages is associated with a greater magnitude of weight gain and an increased risk for development of type 2 diabetes in women, possibly by providing excessive calories and large amounts of rapidly absorbable sugars."], "structured": true}
{"doc_id": 9831859, "title": "Pancreatic stellate cells: partners in crime with pancreatic cancer cells.", "abstract": ["Pancreatic stellate cells (PSC) produce the stromal reaction in pancreatic cancer, but their role in cancer progression is not fully elucidated.", "We examined the influence of PSCs on pancreatic cancer growth using (a) an orthotopic model of pancreatic cancer and (b) cultured human PSCs (hPSC) and human pancreatic cancer cell lines MiaPaCa-2 and Panc-1.", "Athymic mice received an intrapancreatic injection of saline, hPSCs, MiaPaCa-2 cells, or hPSCs + MiaPaCa-2.", "After 7 weeks, tumor size, metastases, and tumor histology were assessed.", "In vitro studies assessed the effect of cancer cell secretions on PSC migration and the effect of hPSC secretions on cancer cell proliferation, apoptosis, and migration.", "Possible mediators of the effects of hPSC secretions on cancer cell proliferation were examined using neutralizing antibodies.", "Compared with mice receiving MiaPaCa-2 cells alone, mice injected with hPSCs + MiaPaCa-2 exhibited (a) increased tumor size and regional and distant metastasis, (b) fibrotic bands (desmoplasia) containing activated PSCs within tumors, and (c) increased tumor cell numbers.", "In vitro studies showed that, in the presence of pancreatic cancer cells, PSC migration was significantly increased.", "Furthermore, hPSC secretions induced the proliferation and migration, but inhibited the apoptosis, of MiaPaCa-2 and Panc-1 cells.", "The proliferative effect of hPSC secretions on pancreatic cancer cells was inhibited in the presence of neutralizing antibody to platelet-derived growth factor.", "Our studies indicate a significant interaction between pancreatic cancer cells and stromal cells (PSCs) and imply that pancreatic cancer cells recruit stromal cells to establish an environment that promotes cancer progression."], "structured": false}
{"doc_id": 9846940, "title": "Preoperative statin treatment reduces systemic inflammatory response and myocardial damage in cardiac surgery.", "abstract": ["OBJECTIVE To determine if preoperative statin treatment is associated with a reduction in systemic inflammatory response (SIR) and myocardial damage markers following cardiac surgery with cardiopulmonary bypass (CPB).   \n", "METHODS We study a prospective cohort of 138 patients who underwent coronary and valvular surgery with CPB.", "We differentiate two study groups: patients with (group A, n=72) or without (group B, n=66) statins.", "Plasma levels of pro-inflammatory interleukins (tumour necrosis factor-alpha (TNF-alpha), interleukin (IL)-6, IL-8 and IL-2R), creatine phosphokinase (CPK), CPK-MB and troponin I were measured before and 1, 6, 24 and >72 h after surgery.   \n", "RESULTS The baseline, operative and postoperative morbidity and mortality characteristics were similar for both the groups.", "Group A had significantly lower postoperative levels of IL-6 than group B at 6h (68.8+/-5 pg ml(-1) vs 108.9+/-108 pg ml(-1), p=0.01), 24h (71.7+/-7 pg ml(-1) vs 110.4+/-106 pg ml(-1), p=0.01) and before hospital discharge (21.6+/-12 pg ml(-1) vs 32.8+/-27 pg ml(-1), p=0.005), as well as significantly lower average IL-6 levels in the first 24h following surgery (71.8+/-5 pgml(-1) vs 112.8+/-82 pg ml(-1), p=0.002).", "The postoperative CPK-MB at 24h (19.7+/-23 ng ml(-1) vs 33.1+/-32 ng ml(-1), p=0.02) and troponin I levels at the end of the intervention (2.2+/-2.2 ng ml(-1) vs 3.3+/-3.1 ng ml(-1), p=0.03) and at 24h (4.1+/-3.5 ng ml(-1) vs 6.6+/-8 ng ml(-1), p=0.04) were also significantly lower in the group treated with statins prior to surgery.   \n", "CONCLUSIONS Preoperative treatment with statins is associated with a lower biochemical parameters of SIR and myocardial damage following cardiac surgery with CPB, regardless of it being coronary bypass grafting (CABG) or valvular surgery."], "structured": true}
{"doc_id": 9872468, "title": "MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.", "abstract": ["We present the latest version of the Molecular Evolutionary Genetics Analysis (Mega) software, which contains many sophisticated methods and tools for phylogenomics and phylomedicine.", "In this major upgrade, Mega has been optimized for use on 64-bit computing systems for analyzing larger datasets.", "Researchers can now explore and analyze tens of thousands of sequences in Mega The new version also provides an advanced wizard for building timetrees and includes a new functionality to automatically predict gene duplication events in gene family trees.", "The 64-bit Mega is made available in two interfaces: graphical and command line.", "The graphical user interface (GUI) is a native Microsoft Windows application that can also be used on Mac OS X. The command line Mega is available as native applications for Windows, Linux, and Mac OS X. They are intended for use in high-throughput and scripted analysis.", "Both versions are available from www.megasoftware.net free of charge."], "structured": false}
{"doc_id": 9875570, "title": "DNA replication fidelity", "abstract": ["DNA replication fidelity is a key determinant of genome stability and is central to the evolution of species and to the origins of human diseases.", "Here we review our current understanding of replication fidelity, with emphasis on structural and biochemical studies of DNA polymerases that provide new insights into the importance of hydrogen bonding, base pair geometry, and substrate-induced conformational changes to fidelity.", "These studies also reveal polymerase interactions with the DNA minor groove at and upstream of the active site that influence nucleotide selectivity, the efficiency of exonucleolytic proofreading, and the rate of forming errors via strand misalignments.", "We highlight common features that are relevant to the fidelity of any DNA synthesis reaction, and consider why fidelity varies depending on the enzymes, the error, and the local sequence environment."], "structured": false}
{"doc_id": 9878167, "title": "Viable neutrophils release mitochondrial DNA to form neutrophil extracellular traps", "abstract": ["Neutrophil extracellular traps (NETs) represent extracellular structures able to bind and kill microorganisms.", "It is believed that they are generated by neutrophils undergoing cell death, allowing these dying or dead cells to kill microbes.", "We show that, following priming with granulocyte/macrophage colony-stimulating factor (GM-CSF) and subsequent short-term toll-like receptor 4 (TLR4) or complement factor 5a (C5a) receptor stimulation, viable neutrophils are able to generate NETs.", "Strikingly, NETs formed by living cells contain mitochondrial, but no nuclear, DNA.", "Pharmacological or genetic approaches to block reactive oxygen species (ROS) production suggested that NET formation is ROS dependent.", "Moreover, neutrophil populations stimulated with GM-CSF and C5a showed increased survival compared with resting neutrophils, which did not generate NETs.", "In conclusion, mitochondrial DNA release by neutrophils and NET formation do not require neutrophil death and do also not limit the lifespan of these cells."], "structured": false}
{"doc_id": 9881829, "title": "ATP-driven exchange of histone H2AZ variant catalyzed by SWR1 chromatin remodeling complex.", "abstract": ["The conserved histone variant H2AZ has an important role in the regulation of gene expression and the establishment of a buffer to the spread of silent heterochromatin.", "How histone variants such as H2AZ are incorporated into nucleosomes has been obscure.", "We have found that Swr1, a Swi2/Snf2-related adenosine triphosphatase, is the catalytic core of a multisubunit, histone-variant exchanger that efficiently replaces conventional histone H2A with histone H2AZ in nucleosome arrays.", "Swr1 is required for the deposition of histone H2AZ at specific chromosome locations in vivo, and Swr1 and H2AZ commonly regulate a subset of yeast genes.", "These findings define a previously unknown role for the adenosine triphosphate-dependent chromatin remodeling machinery."], "structured": false}
{"doc_id": 9889151, "title": "FACT Disrupts Nucleosome Structure by Binding H2A-H2B with Conserved Peptide Motifs.", "abstract": ["FACT, a heterodimer of Spt16 and Pob3, is an essential histone chaperone.", "We show that the H2A-H2B binding activity that is central to FACT function resides in short acidic regions near the C termini of each subunit.", "Mutations throughout these regions affect binding and cause correlated phenotypes that range from mild to lethal, with the largest individual contributions unexpectedly coming from an aromatic residue and a nearby carboxylate residue within each domain.", "Spt16 and Pob3 bind overlapping sites on H2A-H2B, and Spt16-Pob3 heterodimers simultaneously bind two H2A-H2B dimers, the same stoichiometry as the components of a nucleosome.", "An Spt16:H2A-H2B crystal structure explains the biochemical and genetic data, provides a model for Pob3 binding, and implies a mechanism for FACT reorganization that we confirm biochemically.", "Moreover, unexpected similarity to binding of ANP32E and Swr1 with H2A.Z-H2B reveals that diverse H2A-H2B chaperones use common mechanisms of histone binding and regulating nucleosome functions."], "structured": false}
{"doc_id": 9899292, "title": "Role of AMP-activated protein kinase in mechanism of metformin action.", "abstract": ["Metformin is a widely used drug for treatment of type 2 diabetes with no defined cellular mechanism of action.", "Its glucose-lowering effect results from decreased hepatic glucose production and increased glucose utilization.", "Metformin's beneficial effects on circulating lipids have been linked to reduced fatty liver.", "AMP-activated protein kinase (AMPK) is a major cellular regulator of lipid and glucose metabolism.", "Here we report that metformin activates AMPK in hepatocytes; as a result, acetyl-CoA carboxylase (ACC) activity is reduced, fatty acid oxidation is induced, and expression of lipogenic enzymes is suppressed.", "Activation of AMPK by metformin or an adenosine analogue suppresses expression of SREBP-1, a key lipogenic transcription factor.", "In metformin-treated rats, hepatic expression of SREBP-1 (and other lipogenic) mRNAs and protein is reduced; activity of the AMPK target, ACC, is also reduced.", "Using a novel AMPK inhibitor, we find that AMPK activation is required for metformin's inhibitory effect on glucose production by hepatocytes.", "In isolated rat skeletal muscles, metformin stimulates glucose uptake coincident with AMPK activation.", "Activation of AMPK provides a unified explanation for the pleiotropic beneficial effects of this drug; these results also suggest that alternative means of modulating AMPK should be useful for the treatment of metabolic disorders."], "structured": false}
{"doc_id": 9904546, "title": "Interferon alfa therapy for chronic hepatitis B in children: a multinational randomized controlled trial.", "abstract": ["BACKGROUND & AIMS Treatment of chronic hepatitis B with interferon alfa is not approved in children.", "The aim of this study was to evaluate the safety and efficacy of interferon alfa (IFN-alpha) in children with chronic hepatitis B and increased transaminase levels.   \n", "METHODS Children were given either IFN-alpha2b (6 megaunits/m2 thrice weekly for 24 weeks) or no treatment.", "Clearance of markers of viral replication was evaluated 24 weeks after therapy and after 48 weeks of observation in controls.   \n", "RESULTS Of 149 children enrolled, 144 were evaluable (70 treated and 74 controls).", "Serum hepatitis B e antigen and viral DNA became negative in 26% of treated children and 11% of controls (P < 0.05).", "Serum aminotransferase levels normalized and liver histology improved among responders.", "Hepatitis B surface antigen became undetectable in 10% of treated patients and 1% of controls.", "Female gender and interferon treatment were the only significant predictors of response.", "Ethnic origin, baseline aminotransferase level, initial DNA levels, and histology did not correlate with response.", "Most adverse reactions were mild or moderate, and dose was reduced in 24% of children.   \n", "CONCLUSIONS In children with chronic hepatitis B, INF-alpha promotes loss of viral replication markers and surface antigen and improves aminotransferases and histology."], "structured": true}
{"doc_id": 9909405, "title": "ImmTACs for targeted cancer therapy: Why, what, how, and which.", "abstract": ["Overcoming immunosuppression and activating a cytotoxic T cell response has the potential to halt the progression of cancer and, in some circumstances, eradicate it.", "Designing therapeutic interventions that achieve this goal has proven challenging, but now a greater understanding of the complexities of immune responses is beginning to produce some notable breakthroughs.", "ImmTACs (immune-mobilising monoclonal TCRs against cancer) are a new class of bispecific reagents, based on soluble monoclonal T cell receptors, which have been engineered to possess extremely high affinity for cognate tumour antigen.", "In this way, ImmTACs overcome the problem of low affinity tumour-specific T cells imposed by thymic selection and provide access to the large number of antigens presented as peptide-HLA complexes.", "Once bound to tumour cells the anti-CD3 effector end of the ImmTAC drives recruitment of polyclonal T cells to the tumour site, leading to a potent redirected T cell response and tumour cell destruction.", "Extensive in vitro testing coupled with promising early clinical data has provided an enhanced appreciation of ImmTAC function in vivo and indicates their potential therapeutic benefit in terms of a durable response and ultimately the breaking of T cell tolerance.", "This review introduces ImmTACs in the context of immunotherapy, and outlines their design, construction and mechanism of action, as well as examining target selection and aspects of preclinical safety testing."], "structured": false}
{"doc_id": 9911547, "title": "Angiopoietin-like protein 3 supports the activity of hematopoietic stem cells in the bone marrow niche.", "abstract": ["The physiologic roles of angiopoietin-like proteins (Angptls) in the hematopoietic system remain unknown.", "Here we show that hematopoietic stem cells (HSCs) in Angptl3-null mice are decreased in number and quiescence.", "HSCs transplanted into Angptl3-null recipient mice exhibited impaired repopulation.", "Bone marrow sinusoidal endothelial cells express high levels of Angptl3 and are adjacent to HSCs.", "Importantly, bone marrow stromal cells or endothelium deficient in Angptl3 have a significantly decreased ability to support the expansion of repopulating HSCs.", "Angptl3 represses the expression of the transcription factor Ikaros, whose unregulated overexpression diminishes the repopulation activity of HSCs.", "Angptl3, as an extrinsic factor, thus supports the stemness of HSCs in the bone marrow niche."], "structured": false}
{"doc_id": 9929089, "title": "Subsequent chemotherapy reverses acquired tyrosine kinase inhibitor resistance and restores response to tyrosine kinase inhibitor in advanced non-small-cell lung cancer", "abstract": ["BACKGROUND Patients with advanced or metastatic non-small cell lung cancer (NSCLC) can develop acquired resistance to epidermal growth factor receptor tyrosine kinase inhibitors (TKIs) erlotinib and gefitinib.", "Here, we report the successful treatment with alternating chemotherapy and TKIs of two cases of advanced NSCLC who developed resistance to TKI.   ", "CASE PRESENTATION Two patients with advanced or metastatic NSCLC were treated with palliative chemotherapy followed by erlotinib/gefitinib.", "When TKI therapy failed, two cycles of chemotherapy were provided, which were followed by re-challenge with erlotinib or gefitinib.   \n", "CONCLUSION NSCLC patients with acquired TKI resistance should be managed aggressively whenever possible.", "Subsequent chemotherapy and target treatment is one of the reasonable choices for those with an initial dramatic clinical response with erlotinib/gefitinib treatment.", "Further studies are warranted to substantiate the association of erlotinib /gefitinib treatment with the efficacy of NSCLC patients with acquired TKI failure."], "structured": true}
{"doc_id": 9955779, "title": "Epigenetic Therapy Ties MYC Depletion to Reversing Immune Evasion and Treating Lung Cancer", "abstract": ["Combining DNA-demethylating agents (DNA methyltransferase inhibitors [DNMTis]) with histone deacetylase inhibitors (HDACis) holds promise for enhancing cancer immune therapy.", "Herein, pharmacologic and isoform specificity of HDACis are investigated to guide their addition to a DNMTi, thus devising a new, low-dose, sequential regimen that imparts a robust anti-tumor effect for non-small-cell lung cancer (NSCLC).", "Using in-vitro-treated NSCLC cell lines, we elucidate an interferon \u03b1/\u03b2-based transcriptional program with accompanying upregulation of antigen presentation machinery, mediated in part through double-stranded RNA (dsRNA) induction.", "This is accompanied by suppression of MYC signaling and an increase in the T cell chemoattractant CCL5.", "Use of this combination treatment schema in mouse models of NSCLC reverses tumor immune evasion and modulates T cell exhaustion state towards memory and effector T cell phenotypes.", "Key correlative science metrics emerge for an upcoming clinical trial, testing enhancement of immune checkpoint therapy for NSCLC."], "structured": false}
{"doc_id": 9956893, "title": "The Role of PPAR\u03b3 in Advanced Glycation End Products-Induced Inflammatory Response in Human Chondrocytes", "abstract": ["OBJECTIVE Advances made in the past ten years highlight the notion that peroxisome proliferator-activated receptors gamma (PPAR\u03b3) has protective properties in the pathophysiology of osteoarthritis (OA).", "The aim of this study was to define the roles of PPAR\u03b3 in AGEs-induced inflammatory response in human chondrocytes.   \n", "METHODS Primary human chondrocytes were stimulated with AGEs in the presence or absence of neutralizing antibody against RAGE (anti-RAGE), MAPK specific inhibitors and PPAR\u03b3 agonist pioglitazone.", "The expression of IL-1, MMP-13, TNF-\u03b1, PPAR\u03b3, nuclear NF-\u03baB p65 and cytosol I\u03baB\u03b1 was determined by western blotting and real-time PCR.   \n", "RESULTS AGEs could enhance the expression of IL-1, TNF-\u03b1, and MMP-13, but the level of PPAR\u03b3 was decreased in a time- and dose-dependent manner, which was inhibited by anti-RAGE, SB203580 (P38 MAPK specific inhibitor) and SP600125 (a selective inhibitor of JNK).", "PPAR\u03b3 agonist pioglitazone could inhibit the effects of AGEs-induced inflammatory response and PPAR\u03b3 down-regulation.", "In human chondrocytes, AGEs could induce cytosol I\u03baB\u03b1 degradation and increase the level of nuclear NF-\u03baB p65, which was inhibited by PPAR\u03b3 agonist pioglitazone.   \n", "CONCLUSIONS In primary human chondrocytes, AGEs could down-regulate PPAR\u03b3 expression and increase the inflammatory mediators, which could be reversed by PPAR\u03b3 agonist pioglitazone.", "Activation of RAGE by AGEs triggers a cascade of downstream signaling, including MAPK JNK/ p38, PPAR\u03b3 and NF-\u03baB. Taken together, PPAR\u03b3 could be a potential target for pharmacologic intervention in the treatment of OA."], "structured": true}
{"doc_id": 9967265, "title": "Surgical versus medical treatment with cyclooxygenase inhibitors for symptomatic patent ductus arteriosus in preterm infants.", "abstract": ["BACKGROUND Patent ductus arteriosus (PDA) with significant left to right shunt in preterm infants increases morbidity and mortality.", "Early closure of the ductus arteriosus may be achieved pharmacologically using cyclooxygenase inhibitors or by surgery.", "The efficacy of both treatment modalities is well established.", "However, the preferred initial treatment of a symptomatic PDA in a preterm infant, surgical ligation or treatment with indomethacin, has not been well established.   \n", "OBJECTIVES To compare the effect of surgical ligation of PDA vs. medical treatment with cyclooxygenase inhibitors (using indomethacin, ibuprofen, or mefenamic acid), each used as the initial treatment, on neonatal mortality in preterm infants with a symptomatic PDA.   ", "SEARCH STRATEGY The standard search strategy of the Cochrane Neonatal Review Group was used.", "This included search of electronic databases: Cochrane Central Register of Controlled Trials (CENTRAL, The Cochrane Library, Issue 2, 2007), MEDLINE (1966 - July 2007), CINAHL (1982 - July 2007), EMBASE (1980 - July 2007); and hand search of abstracts of Pediatric Academic Societies annual meetings published in Pediatric Research (1990 - April 2002) or on line from May 2002 -July 2007.", "No language restrictions were applied.   ", "SELECTION CRITERIA All trials 1) using randomized or quasi-randomized patient allocation, 2) in preterm infants < 37 weeks gestational age or low-birth-weight infants (< 2500 grams) with symptomatic PDA in the neonatal period (< 28 days) and 3) comparing surgical ligation with medical treatment with cyclooxygenase inhibitors, each used as the initial treatment for closure of PDA.   \n", "DATA COLLECTION AND ANALYSIS Assessment of methodological quality and extraction of data for included trials was undertaken independently by the authors.", "RevMan 4.1 was used for analysis of the data.   \n", "MAIN RESULTS Only one study, trial B in the report of Gersony 1983, was found eligible.", "No additional studies were identified in the literature searches performed in July 2007.", "The trial compared the effect of surgical ligation of PDA vs. medical treatment with indomethacin, each used as the primary treatment.", "No trials comparing surgery to other cyclooxygenase inhibitors (ibuprofen, mefenamic acid) were found.", "Trial B of Gersony 1983 enrolled 154 infants.", "The study found no statistically significant difference between surgical closure and indomethacin treatment in mortality during hospital stay, chronic lung disease, other bleeding, necrotizing enterocolitis, sepsis, creatinine level, or intraventricular hemorrhage.", "There was a statistically significant increase in the surgical group in incidence of pneumothorax [RR 2.68 (95% CI 1.45, 4.93); RD 0.25 (95% CI 0.11, 0.38); NNH 4 (95% CI 3, 9)] and retinopathy of prematurity stage III and IV [RR 3.80 (95% CI 1.12, 12.93); RD 0.11 (95% CI 0.02, 0.20), NNH 9 (95% CI 5, 50] compared to the indomethacin group.", "There was as expected a statistically significant decrease in failure of ductal closure rate in the surgical group as compared to the indomethacin group: [RR 0.04 (95% CI 0.01, 0.27); RD -0.32 (95% CI -0.43, -0.21), NNT 3 (95% CI 2, 4)].   ", "AUTHORS' CONCLUSIONS The data regarding net benefit/harm are insufficient to make a conclusion as to whether surgical ligation or medical treatment with indomethacin is preferred as initial treatment for symptomatic PDA in preterm infants.", "It should be noted that three recent observational studies indicated an increased risk for one or more of the following outcomes associated with PDA ligation; chronic lung disease, retinopathy of prematurity and neurosensory impairment .", "It is possible that the duration of the \"waiting-time\" and transport to another facility with surgical capacity to have the PDA ligated could adversely affect outcomes, as could the perioperative care."], "structured": true}
{"doc_id": 9973014, "title": "The Effect of Collinearity on Parameter Estimates in Nonlinear Mixed Effect Models", "abstract": ["Purpose.", "To demonstrate how correlations among predictor variables in a population pharmacokinetic model affect the ability to discern which covariates should enter into the structural pharmacokinetic model.", "Methods.", "Monte Carlo simulation was used to generate multiple-dose concentration-time data similar to that seen in a Phase III clinical trial.", "The drugs' pharmacokinetics were dependent on two covariates.", "Five data sets were simulated with increasing correlation between the two covariates.", "All data sets were analyzed using NONMEM both with and without inclusion of the covariates in the structural pharmacokinetic model.", "Summary measures for ill-conditioning and sensitivity analysis were used to examine how increasing correlation among covariates affects the accuracy and precision of the parameter estimates.", "Results.", "When covariates were included in the structural pharmacokinetic model and the correlation between covariates increased, the standard error of the parameter estimates increased and the value of parameter estimates themselves became increasingly biased.", "When the correlation between predictor variables was 0.75, the standard errors of the parameter estimates were too large to declare statistical significance.", "Conclusions.", "Correlations among predictor variables greater than 0.5 when entered into the model simultaneously should be a warning to researchers because the (1) the accuracy of the parameter estimates themselves may be biased and (2) the precision of the estimates may be inflated due to ill-conditioning."], "structured": false}
{"doc_id": 9976969, "title": "An analysis of age and gender influences on the relative risk for suicide and psychotropic drug self-poisoning.", "abstract": ["Psychiatric illness is a significant risk factor for both attempted and completed suicide and psychotropic medications account for 80% of all drug overdoses involving prescription medications.", "One challenge facing clinicians is to balance the benefit of treatment against the risk of drug overdose.", "The aim of the present study was to compare the age and gender distribution of patients prescribed psychotropic drugs with patients attempting and completing suicide with these drugs.", "Data were obtained from the Australian census and studies of general practitioner prescribing, patients who committed suicide or presented with self-poisoning within a defined geographic area.", "The characteristics of these populations were compared to calculate odds ratios for attempting or completing suicide with psychotropic drugs, before and after correction for rates of prescription, in different age and gender groups.", "The odds ratios (ORs) for self-poisoning were higher for those aged less than 45 years and yet this group was least likely to be prescribed psychotropic drugs.", "Men had a much higher rate of completed suicide using more lethal methods.", "The ORs for self-poisoning and suicide with psychotropic drugs, after correction for prescription rates, for those aged 15 to 24 years were 11.1 and 1.7, respectively.", "Those aged 25 to 44 years had ORs of 4.9 and 4.3, and, by contrast, those over 75 years had ORs of 0.03 and 0.", "Women were slightly more likely to poison themselves with psychotropic drugs (OR 1.2).", "However, the situation reversed after correction for prescription rates (OR 0.69).", "It is concluded that greater caution should be exercised in prescribing for those under 45 years of age, given their relatively higher risk of drug overdose, and that the least toxic compounds should be used.", "The risk (of self-poisoning) among the elderly may have been overstated, so that some patients may have been denied the benefit of adequate treatment."], "structured": false}
{"doc_id": 9977329, "title": "Cell death and immune privilege.", "abstract": ["The host response to pathogens involves complex inflammatory responses and immune reactions.", "While these are central to host defense and vital to clearing infections, they are often accompanied by injury to surrounding tissue.", "Most organ systems can tolerate these responses without permanent consequences.", "However, there are sites that limit the spread of inflammation because it can threaten organ function.", "The most prominent examples of these are the eye, brain, and reproductive organs (testis, ovary), where even minor bouts of inflammation can have long-term consequences for the survival of the organism.", "In these organs immune responses either do not proceed, or proceed in a manner different from other areas; thus, they are called \"immunologically privileged.", "\"", "Here a functioning immune response can be the culprit that leads to disease."], "structured": false}
{"doc_id": 9988425, "title": "Niche-Independent Symmetrical Self-Renewal of a Mammalian Tissue Stem Cell", "abstract": ["Pluripotent mouse embryonic stem (ES) cells multiply in simple monoculture by symmetrical divisions.", "In vivo, however, stem cells are generally thought to depend on specialised cellular microenvironments and to undergo predominantly asymmetric divisions.", "Ex vivo expansion of pure populations of tissue stem cells has proven elusive.", "Neural progenitor cells are propagated in combination with differentiating progeny in floating clusters called neurospheres.", "The proportion of stem cells in neurospheres is low, however, and they cannot be directly observed or interrogated.", "Here we demonstrate that the complex neurosphere environment is dispensable for stem cell maintenance, and that the combination of fibroblast growth factor 2 (FGF-2) and epidermal growth factor (EGF) is sufficient for derivation and continuous expansion by symmetrical division of pure cultures of neural stem (NS) cells.", "NS cells were derived first from mouse ES cells.", "Neural lineage induction was followed by growth factor addition in basal culture media.", "In the presence of only EGF and FGF-2, resulting NS cells proliferate continuously, are diploid, and clonogenic.", "After prolonged expansion, they remain able to differentiate efficiently into neurons and astrocytes in vitro and upon transplantation into the adult brain.", "Colonies generated from single NS cells all produce neurons upon growth factor withdrawal.", "NS cells uniformly express morphological, cell biological, and molecular features of radial glia, developmental precursors of neurons and glia.", "Consistent with this profile, adherent NS cell lines can readily be established from foetal mouse brain.", "Similar NS cells can be generated from human ES cells and human foetal brain.", "The extrinsic factors EGF plus FGF-2 are sufficient to sustain pure symmetrical self-renewing divisions of NS cells.", "The resultant cultures constitute the first known example of tissue-specific stem cells that can be propagated without accompanying differentiation.", "These homogenous cultures will enable delineation of molecular mechanisms that define a tissue-specific stem cell and allow direct comparison with pluripotent ES cells."], "structured": false}
{"doc_id": 9993008, "title": "A Bivalent Chromatin Structure Marks Key Developmental Genes in Embryonic Stem Cells", "abstract": ["The most highly conserved noncoding elements (HCNEs) in mammalian genomes cluster within regions enriched for genes encoding developmentally important transcription factors (TFs).", "This suggests that HCNE-rich regions may contain key regulatory controls involved in development.", "We explored this by examining histone methylation in mouse embryonic stem (ES) cells across 56 large HCNE-rich loci.", "We identified a specific modification pattern, termed \"bivalent domains,\" consisting of large regions of H3 lysine 27 methylation harboring smaller regions of H3 lysine 4 methylation.", "Bivalent domains tend to coincide with TF genes expressed at low levels.", "We propose that bivalent domains silence developmental genes in ES cells while keeping them poised for activation.", "We also found striking correspondences between genome sequence and histone methylation in ES cells, which become notably weaker in differentiated cells.", "These results highlight the importance of DNA sequence in defining the initial epigenetic landscape and suggest a novel chromatin-based mechanism for maintaining pluripotency."], "structured": false}
{"doc_id": 9997636, "title": "Ovarian Surface Epithelium in Patients with Severe Ovarian Infertility: A Potential Source of Cells Expressing Markers of Pluripotent/Multipotent Stem Cells", "abstract": ["The aim of this study was to confirm the presence of stem cells in the ovarian surface epithelium of patients with premature ovarian failure and no mature follicles and oocytes.", "In these patients, small round cells of unknown origin expressing SOX-2 marker of pluripotency were observed among the epithelial cells just after the ovarian surface epithelium scraping.", "These cells were an integral part of the ovarian surface epithelium.", "When the scraped cells were cultured in a medium with added follicular fluid to provide some ovarian niche, primitive oocyte-like cells and typical round-shaped cell clusters positively stained on alkaline phosphatase, and markers of pluripotency, such as SOX-2 and SSEA-4, were developed.", "These markers were expressed early and also later in the culture.", "Single oocyte-like cells expressed genes OCT4A, SOX-2, NANOG, NANOS, STELLA, CD9, LIN28, KLF4, GDF3, and MYC, characteristic for pluripotent stem cells.", "The results of this study confirmed the presence of putative stem cells in the ovarian surface epithelium of these patients and provided some basis to create a stem cell line in the future."], "structured": false}
{"doc_id": 10009203, "title": "Structural Homeostasis: Compensatory Adjustments of Dendritic Arbor Geometry in Response to Variations of Synaptic Input ", "abstract": ["As the nervous system develops, there is an inherent variability in the connections formed between differentiating neurons.", "Despite this variability, neural circuits form that are functional and remarkably robust.", "One way in which neurons deal with variability in their inputs is through compensatory, homeostatic changes in their electrical properties.", "Here, we show that neurons also make compensatory adjustments to their structure.", "We analysed the development of dendrites on an identified central neuron (aCC) in the late Drosophila embryo at the stage when it receives its first connections and first becomes electrically active.", "At the same time, we charted the distribution of presynaptic sites on the developing postsynaptic arbor.", "Genetic manipulations of the presynaptic partners demonstrate that the postsynaptic dendritic arbor adjusts its growth to compensate for changes in the activity and density of synaptic sites.", "Blocking the synthesis or evoked release of presynaptic neurotransmitter results in greater dendritic extension.", "Conversely, an increase in the density of presynaptic release sites induces a reduction in the extent of the dendritic arbor.", "These growth adjustments occur locally in the arbor and are the result of the promotion or inhibition of growth of neurites in the proximity of presynaptic sites.", "We provide evidence that suggest a role for the postsynaptic activity state of protein kinase A in mediating this structural adjustment, which modifies dendritic growth in response to synaptic activity.", "These findings suggest that the dendritic arbor, at least during early stages of connectivity, behaves as a homeostatic device that adjusts its size and geometry to the level and the distribution of input received.", "The growing arbor thus counterbalances naturally occurring variations in synaptic density and activity so as to ensure that an appropriate level of input is achieved."], "structured": false}
{"doc_id": 10010651, "title": "Nutrition and physical activity guidelines for cancer survivors.", "abstract": ["Cancer survivors are often highly motivated to seek information about food choices, physical activity, and dietary supplements to improve their treatment outcomes, quality of life, and overall survival.", "To address these concerns, the American Cancer Society (ACS) convened a group of experts in nutrition, physical activity, and cancer survivorship to evaluate the scientific evidence and best clinical practices related to optimal nutrition and physical activity after the diagnosis of cancer.", "This report summarizes their findings and is intended to present health care providers with the best possible information with which to help cancer survivors and their families make informed choices related to nutrition and physical activity.", "The report discusses nutrition and physical activity guidelines during the continuum of cancer care, briefly highlighting important issues during cancer treatment and for patients with advanced cancer, but focusing largely on the needs of the population of individuals who are disease free or who have stable disease following their recovery from treatment.", "It also discusses select nutrition and physical activity issues such as body weight, food choices, food safety, and dietary supplements; issues related to selected cancer sites; and common questions about diet, physical activity, and cancer survivorship."], "structured": false}
{"doc_id": 10012166, "title": "The role of protein clearance mechanisms in organismal ageing and age-related diseases.", "abstract": ["The ability to maintain a functional proteome, or proteostasis, declines during the ageing process.", "Damaged and misfolded proteins accumulate with age, impairing cell function and tissue homeostasis.", "The accumulation of damaged proteins contributes to multiple age-related diseases such as Alzheimer's, Parkinson's or Huntington's disease.", "Damaged proteins are degraded by the ubiquitin-proteasome system or through autophagy-lysosome, key components of the proteostasis network.", "Modulation of either proteasome activity or autophagic-lysosomal potential extends lifespan and protects organisms from symptoms associated with proteostasis disorders, suggesting that protein clearance mechanisms are directly linked to ageing and age-associated diseases."], "structured": false}
{"doc_id": 10015292, "title": "A distinctive DNA damage response in human hematopoietic stem cells reveals an apoptosis-independent role for p53 in self-renewal.", "abstract": ["Highly regenerative tissues such as blood must possess effective DNA damage responses (DDR) that balance long-term regeneration with protection from leukemogenesis.", "Hematopoietic stem cells (HSCs) sustain life-long blood production, yet their response to DNA damage remains largely unexplored.", "We report that human HSCs exhibit delayed DNA double-strand break rejoining, persistent gammaH2AX foci, and enhanced p53- and ASPP1-dependent apoptosis after gamma-radiation compared to progenitors.", "p53 inactivation or Bcl-2 overexpression reduced radiation-induced apoptosis and preserved in vivo repopulating HSC function.", "Despite similar protection from irradiation-induced apoptosis, only Bcl-2-overexpressing HSCs showed higher self-renewal capacity, establishing that intact p53 positively regulates self-renewal independently from apoptosis.", "The reduced self-renewal of HSCs with inactivated p53 was associated with increased spontaneous gammaH2AX foci in secondary transplants of HSCs.", "Our data reveal distinct physiological roles of p53 that together ensure optimal HSC function: apoptosis regulation and prevention of gammaH2AX foci accumulation upon HSC self-renewal."], "structured": false}
{"doc_id": 10017612, "title": "Behavioral characterization of neuropeptide Y knockout mice.", "abstract": ["An extensive behavioral characterization was conducted with mice lacking the gene for neuropeptide Y (NPY) including response to 24 and 48 h fast and challenge with small molecule antagonists of NPY receptors implicated in mediating the feeding effects of NPY (i.e., Y1 and Y5).", "In addition, wildtype (WT) and NPY knockout (KO) mice were tested in locomotor monitors, elevated plus maze, inhibitory avoidance, acoustic startle, prepulse inhibition, and hot plate assays.", "One of the major findings was that the NPY KO mice have a reduced food intake relative to WT controls in response to fasting.", "Also, based on data from the behavioral models, the NPY KO mice may have an anxiogenic-like phenotype, and appear to be hypoalgesic in the hot plate paradigm.", "The data from these studies provide further evidence of involvement of NPY in energy balance, anxiety, and possibly nociception."], "structured": false}
{"doc_id": 10024681, "title": "Epigenetic-induced repression of microRNA-205 is associated with MED1 activation and a poorer prognosis in localized prostate cancer", "abstract": ["Deregulation of microRNA (miRNA) expression can have a critical role in carcinogenesis.", "Here we show in prostate cancer that miRNA-205 (miR-205) transcription is commonly repressed and the MIR-205 locus is hypermethylated.", "LOC642587, the MIR-205 host gene of unknown function, is also concordantly inactivated.", "We show that miR-205 targets mediator 1 (MED1, also called TRAP220 and PPARBP) for transcriptional silencing in normal prostate cells, leading to reduction in MED1 mRNA levels, and in total and active phospho-MED1 protein.", "Overexpression of miR-205 in prostate cancer cells negatively affects cell viability, consistent with a tumor suppressor function.", "We found that hypermethylation of the MIR-205 locus was strongly related with a decrease in miR-205 expression and an increase in MED1 expression in primary tumor samples (n=14), when compared with matched normal prostate (n=7).", "An expanded patient cohort (tumor n=149, matched normal n=30) also showed significant MIR-205 DNA methylation in tumors compared with normal, and MIR-205 hypermethylation is significantly associated with biochemical recurrence (hazard ratio=2.005, 95% confidence interval (1.109, 3.625), P=0.02), in patients with low preoperative prostate specific antigen.", "In summary, these results suggest that miR-205 is an epigenetically regulated tumor suppressor that targets MED1 and may provide a potential biomarker in prostate cancer management."], "structured": false}
{"doc_id": 10029891, "title": "Th2 cytokine response in Major Depressive Disorder patients before treatment", "abstract": ["In Major Depressive Disorder (MDD), the neuroendocrine and immune systems interactions are impaired.", "We investigated the pro/anti-inflammatory Th1/Th2 cytokine balance in MDD patients and in non-depressed control group.", "The MDD subjects showed higher levels of cortisol and TNF-alpha, increased CD3+CD8+ and NK percentages, diminished B cell counts and no significant variations in CD3+CD4+ lymphocyte.", "Moreover, higher levels of IL-4 and IL-13 (Th2) and significantly lower measurements of IL-2 and IFN-gamma (Th1) cytokines were also observed in the MDD group.", "Overall, we propose that all these changes could be related to the elevated cortisol levels seen in the MDD patients.", "Further studies are necessary to explore these findings and its implication in future therapeutic approach of MDD patients."], "structured": false}
{"doc_id": 10029970, "title": "CDD: conserved domains and protein three-dimensional structure", "abstract": ["CDD, the Conserved Domain Database, is part of NCBI's Entrez query and retrieval system and is also accessible via http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml.", "CDD provides annotation of protein sequences with the location of conserved domain footprints and functional sites inferred from these footprints.", "Pre-computed annotation is available via Entrez, and interactive search services accept single protein or nucleotide queries, as well as batch submissions of protein query sequences, utilizing RPS-BLAST to rapidly identify putative matches.", "CDD incorporates several protein domain and full-length protein model collections, and maintains an active curation effort that aims at providing fine grained classifications for major and well-characterized protein domain families, as supported by available protein three-dimensional (3D) structure and the published literature.", "To this date, the majority of protein 3D structures are represented by models tracked by CDD, and CDD curators are characterizing novel families that emerge from protein structure determination efforts."], "structured": false}
{"doc_id": 10039688, "title": "Extensive diversity of Ig-superfamily proteins in the immune system of insects.", "abstract": ["The extensive somatic diversification of immune receptors is a hallmark of higher vertebrates.", "However, whether molecular diversity contributes to immune protection in invertebrates is unknown.", "We present evidence that Drosophila immune-competent cells have the potential to express more than 18,000 isoforms of the immunoglobulin (Ig)-superfamily receptor Down syndrome cell adhesion molecule (Dscam).", "Secreted protein isoforms of Dscam were detected in the hemolymph, and hemocyte-specific loss of Dscam impaired the efficiency of phagocytic uptake of bacteria, possibly due to reduced bacterial binding.", "Importantly, the molecular diversity of Dscam transcripts generated through a mechanism of alternative splicing is highly conserved across major insect orders, suggesting an unsuspected molecular complexity of the innate immune system of insects."], "structured": false}
{"doc_id": 10068634, "title": "Preparing the outbreak assistance laboratory network in the Netherlands for the detection of the influenza virus A(H1N1) variant.", "abstract": ["BACKGROUND Late April 2009, human infection with variant influenza virus A(H1N1)v emerged in the Northern Americas posing a threat that this virus may become the next pandemic influenza virus.   \n", "OBJECTIVES To prepare laboratories for surge capacity for molecular diagnosis of patients suspected for A(H1N1)v infection in the Netherlands.   ", "STUDY DESIGN A panel of 10 blinded specimens containing seasonal A(H1N1) or A(H3N2), or A/Netherlands/602/2009(H1N1)v influenza virus, or negative control was distributed to the outbreak assistance laboratories (OAL) together with influenza virus A (M-gene), swine influenza virus A (NP-gene) and influenza virus A(H1N1)v (H1v-gene) specific primers and probes and protocol (CDC Atlanta, USA).", "Laboratories were asked to implement and test this protocol.   \n", "RESULTS All OAL were able to detect A(H1N1)v using the CDC M-gene reagents, the majority with similar sensitivity as the in-house M-gene based assays.", "RT-PCRs used in routine diagnostic setting in the OAL specifically designed to detect H1, H3, or NS1 from seasonal influenza A viruses, did not or at very low level cross-react with A(H1N1)v.", "The CDC swine NP-gene and H1v-gene RT-PCRs showed somewhat reduced sensitivity compared to the CDC and in-house M-gene RT-PCRs.", "In contrast, in-house developed A(H1N1)v specific H1v-gene and N1v-gene RT-PCRs showed equal sensitivity to CDC and in-house M-gene RT-PCRs.   \n", "CONCLUSIONS The Dutch OAL are prepared for detection and specific identification of A(H1N1)v, although some level of cross-reactivity was observed with seasonal influenza viruses.", "Additionally, M-gene based generic influenza A virus detection is recommended to be able to detect emerging influenza A viruses in routine settings."], "structured": true}
{"doc_id": 10071552, "title": "Averting Obesity and Type 2 Diabetes in India through Sugar-Sweetened Beverage Taxation: An Economic-Epidemiologic Modeling Study", "abstract": ["BACKGROUND Taxing sugar-sweetened beverages (SSBs) has been proposed in high-income countries to reduce obesity and type 2 diabetes.", "We sought to estimate the potential health effects of such a fiscal strategy in the middle-income country of India, where there is heterogeneity in SSB consumption, patterns of substitution between SSBs and other beverages after tax increases, and vast differences in chronic disease risk within the population.   \n", "METHODS AND FINDINGS Using consumption and price variations data from a nationally representative survey of 100,855 Indian households, we first calculated how changes in SSB price alter per capita consumption of SSBs and substitution with other beverages.", "We then incorporated SSB sales trends, body mass index (BMI), and diabetes incidence data stratified by age, sex, income, and urban/rural residence into a validated microsimulation of caloric consumption, glycemic load, overweight/obesity prevalence, and type 2 diabetes incidence among Indian subpopulations facing a 20% SSB excise tax.", "The 20% SSB tax was anticipated to reduce overweight and obesity prevalence by 3.0% (95% CI 1.6%-5.9%) and type 2 diabetes incidence by 1.6% (95% CI 1.2%-1.9%) among various Indian subpopulations over the period 2014-2023, if SSB consumption continued to increase linearly in accordance with secular trends.", "However, acceleration in SSB consumption trends consistent with industry marketing models would be expected to increase the impact efficacy of taxation, averting 4.2% of prevalent overweight/obesity (95% CI 2.5-10.0%) and 2.5% (95% CI 1.0-2.8%) of incident type 2 diabetes from 2014-2023.", "Given current consumption and BMI distributions, our results suggest the largest relative effect would be expected among young rural men, refuting our a priori hypothesis that urban populations would be isolated beneficiaries of SSB taxation.", "Key limitations of this estimation approach include the assumption that consumer expenditure behavior from prior years, captured in price elasticities, will reflect future behavior among consumers, and potential underreporting of consumption in dietary recall data used to inform our calculations.   \n", "CONCLUSION Sustained SSB taxation at a high tax rate could mitigate rising obesity and type 2 diabetes in India among both urban and rural subpopulations."], "structured": true}
{"doc_id": 10071590, "title": "Acute myopericarditis after multiple vaccinations in an adolescent: case report and review of the literature.", "abstract": ["We report a case of postvaccination acute myopericarditis in an adolescent.", "The patient presented with acute chest pain, diffuse ST-segment elevation, and elevated cardiac enzyme levels.", "Cardiac MRI was consistent with acute myocarditis.", "He recovered within a few days with nonsteroidal antiinflammatory treatment and remains clinically stable, with improvement of MRI findings at the 10-week follow-up.", "Postvaccination cases of myopericarditis reported in the pediatric literature are also reviewed."], "structured": false}
{"doc_id": 10072941, "title": "Cardiovascular protection with antihypertensive drugs in dialysis patients: systematic review and meta-analysis.", "abstract": ["Epidemiological studies demonstrate that a lower blood pressure and decline in blood pressure over months or years are associated with higher mortality in dialysis patients.", "In contrast, randomized, controlled trials lack power to establish benefits of antihypertensive therapy.", "Patients on long-term dialysis participating in randomized, controlled trials and receiving antihypertensive drug therapy were the subject of this meta-analysis.", "Outcomes assessed were the hazard ratio of cardiovascular events and all-cause mortality in treated group compared with controls.", "Among 1202 patients who we identified in 5 studies, the overall benefit of antihypertensive therapy compared with the control or placebo group had a combined hazard ratio for cardiovascular events of 0.69 (95% CI: 0.56 to 0.84) using a fixed-effects model and 0.62 (95% CI: 0.45 to 0.86) using a random-effects model.", "In a sensitivity analysis, we found that the hypertensive group had a pooled hazard ratio of 0.49 (95% CI: 0.35 to 0.67), but when normotensives were included in the trial, lesser cardiovascular protection was seen (pooled hazard ratio of 0.86 [95% CI: 0.67 to 1.12]).", "Test for heterogeneity between hypertensive and \"normotensive-included\" groups was significant (P<0.006).", "Similar results were seen for risk ratio for death and cardiovascular events.", "There was evidence of publication bias based on Egger's test and funnel plot.", "Randomized trials suggested a benefit of antihypertensive therapy among hemodialysis patients.", "Adequately powered randomized trials are required to confirm these observations, especially among those with hypertension."], "structured": false}
{"doc_id": 10074251, "title": "Protoplasmic astrocytes in CA1 stratum radiatum occupy separate anatomical domains.", "abstract": ["Protoplasmic astrocytes are increasingly thought to interact extensively with neuronal elements in the brain and to influence their activity.", "Recent reports have also begun to suggest that physiologically, and perhaps functionally, diverse forms of these cells may be present in the CNS.", "Our current understanding of astrocyte form and distribution is based predominantly on studies that used the astrocytic marker glial fibrillary acidic protein (GFAP) and on studies using metal-impregnation techniques.", "The prevalent opinion, based on studies using these methods, is that astrocytic processes overlap extensively and primarily share the underlying neuropil.", "However, both of these techniques have serious shortcomings for visualizing the interactions among these structurally complex cells.", "In the present study, intracellular injection combined with immunohistochemistry for GFAP show that GFAP delineates only approximately 15% of the total volume of the astrocyte.", "As a result, GFAP-based images have led to incorrect conclusions regarding the interaction of processes of neighboring astrocytes.", "To investigate these interactions in detail, groups of adjacent protoplasmic astrocytes in the CA1 stratum radiatum were injected with fluorescent intracellular tracers of distinctive emissive wavelengths and analyzed using three-dimensional (3D) confocal analysis and electron microscopy.", "Our findings show that protoplasmic astrocytes establish primarily exclusive territories.", "The knowledge of how the complex morphology of protoplasmic astrocytes affects their 3D relationships with other astrocytes, oligodendroglia, neurons, and vasculature of the brain should have important implications for our understanding of nervous system function."], "structured": false}
{"doc_id": 10078024, "title": "Leptin-receptor-expressing mesenchymal stromal cells represent the main source of bone formed by adult bone marrow.", "abstract": ["Studies of the identity and physiological function of mesenchymal stromal cells (MSCs) have been hampered by a lack of markers that permit both prospective identification and fate mapping in vivo.", "We found that Leptin Receptor (LepR) is a marker that highly enriches bone marrow MSCs.", "Approximately 0.3% of bone marrow cells were LepR(+)", ", 10% of which were CFU-Fs, accounting for 94% of bone marrow CFU-Fs.", "LepR(+) cells formed bone, cartilage, and adipocytes in culture and upon transplantation in vivo.", "LepR(+) cells were Scf-GFP(+), Cxcl12-DsRed(high), and Nestin-GFP(low), markers which also highly enriched CFU-Fs, but negative for Nestin-CreER and NG2-CreER, markers which were unlikely to be found in CFU-Fs.", "Fate-mapping showed that LepR(+) cells arose postnatally and gave rise to most bone and adipocytes formed in adult bone marrow, including bone regenerated after irradiation or fracture.", "LepR(+) cells were quiescent, but they proliferated after injury.", "Therefore, LepR(+) cells are the major source of bone and adipocytes in adult bone marrow."], "structured": false}
{"doc_id": 10086360, "title": "High-resolution sperm typing of meiotic recombination in the mouse MHC Ebeta gene.", "abstract": ["Meiotic crossovers detected by pedigree analysis in the mouse MHC cluster into hotspots.", "To explore the properties of hotspots, we subjected the class II E(beta) gene to high-resolution sperm crossover analysis.", "We confirm the presence of a highly localized hotspot 1.0-1.6 kb wide in the second intron of E(beta) and show that it is flanked by DNA which is almost completely recombinationally inert.", "Mice heterozygous for haplotype s and another MHC haplotype show major haplotype-dependant variation in crossover rate but always the same hotspot, even in crosses including the highly diverged p haplotype.", "Crossovers in reciprocal orientations occur at similar rates but show different distributions across the hotspot, with the position of centre points in the two orientations shifted on average by 400 bp.", "This asymmetry results in crossover products showing biased gene conversion in favour of hotspot markers from the non-initiating haplotype, and supports the double-strand break repair model of recombination, with haplotype s as the most efficient crossover initiator.", "The detailed behaviour of the E(beta) hotspot, including evidence for highly localized recombination initiation, is strikingly similar to human hotspots."], "structured": false}
{"doc_id": 10128893, "title": "Long-term survival of beta thalassemia major patients treated with hematopoietic stem cell transplantation compared with survival with conventional treatment.", "abstract": ["Allogeneic hematopoietic stem cell transplantation (HSCT) in thalassemia remains a challenge.", "We reported a single-centre case-control study of a large cohort of 516 children and adult patients treated with HSCT or blood transfusion support and iron chelation therapy; 258 patients (median age 12, range 1-45) underwent sibling (67%) or unrelated (33%) HSCT; 97 patients were adults (age \u2265 16 years).", "The median follow-up after HSCT was 11 years (range 1-30).", "The conditioning regimen was busulfan (80.6%) or treosulfan-based (19.4%).", "A cohort of 258 age-sex matched conventionally treated (CT) patients was randomly selected.", "In transplanted patients the 30-year overall survival (OS) and thalassemia-free survival (TFS) were 82.6 \u00b1 2.7% and 77.8 \u00b1 2.9%, compared to the OS of 85.3 \u00b1 2.7% in CT patients (P = NS); The incidence of grade II-IV acute and chronic graft versus host disease (GvHD) was 23.6% and 12.9% respectively.", "The probability of rejection was 6.9%.", "Transplant-related mortality (TRM) (13.8%) was similar to the probability of dying of cardiovascular events in CT patients (12.2%).", "High-risk Pesaro score (class 3) was associated with lower OS (OR = 1.99, 95% C.I.=1.31-3.03) and TFS (OR = 1.54, 95% C.I.=1.12-2.12).", "In adult patients, the 23-years OS and TFS after HSCT were 70 \u00b1 5% and 67.3 \u00b1 5%, compared to 71.2 \u00b1 5% of OS in CT (P = NS).", "Finally, treosulfan was associated with lower risk of acute GvHD (P = .004; OR = 0.28, 95% C.I.=0.12-0.67).", "In conclusion, the 30-year survival rate of ex-thalassemia patients after HSCT was similar to that expected in CT thalassemia patients, with the vast majority of HSCT survivors cured from thalassemia."], "structured": false}
{"doc_id": 10145528, "title": "Global analysis of ATM polymorphism reveals significant functional constraint.", "abstract": ["ATM, the gene that is mutated in ataxia-telangiectasia, is associated with cerebellar degeneration, abnormal proliferation of small blood vessels, and cancer.", "These clinically important manifestations have stimulated interest in defining the sequence variation in the ATM gene.", "Therefore, we undertook a comprehensive survey of sequence variation in ATM in diverse human populations.", "The protein-encoding exons of the gene (9,168 bp) and the adjacent intron and untranslated sequences (14,661 bp) were analyzed in 93 individuals from seven major human populations.", "In addition, the coding sequence was analyzed in one chimpanzee, one gorilla, one orangutan, and one Old World monkey.", "In human ATM, 88 variant sites were discovered by denaturing high-performance liquid chromatography, which is 96%-100% sensitive for detection of DNA sequence variation.", "ATM was compared to 14 other autosomal genes for nucleotide diversity.", "The noncoding regions of ATM had diversity values comparable to other genes, but the coding regions had very low diversity, especially in the last 29% of the protein sequence.", "A test of the neutral evolution hypothesis, through use of the Hudson/Kreitman/Aguad\u00e9 statistic, revealed that this region of the human ATM gene was significantly constrained relative to that of the orangutan, the Old World monkey, and the mouse, but not relative to that of the chimpanzee or the gorilla.", "ATM displayed extensive linkage disequilibrium, consistent with suppression of meiotic recombination at this locus.", "Seven haplotypes were defined.", "Two haplotypes accounted for 82% of all chromosomes analyzed in all major populations; two others carrying the same D126E missense polymorphism accounted for 33% of chromosomes in Africa but were never observed outside of Africa.", "The high frequency of this polymorphism may be due either to a population expansion within Africa or to selective pressure."], "structured": false}
{"doc_id": 10162553, "title": "Ablation and regeneration of tolerance-inducing medullary thymic epithelial cells after cyclosporine, cyclophosphamide, and dexamethasone treatment.", "abstract": ["Immunosuppressive drugs and cytotoxic chemotherapy agents are designed to kill or suppress autoreactive, alloaggressive, or hyperinflammatory T cells, or disseminated malignancies.", "However, they also cause severe immunological side effects ranging from interrupted thymopoiesis and general immunodeficiency to, paradoxically, autoimmunity.", "Consistent with the cross-talk between thymocytes and stromal cells, we now show that these common therapeutic agents have major effects on murine thymic epithelial cells (TEC), crucially required to rebuild immunity posttreatment.", "We show that the immunosuppressant cyclosporine A, which has been linked to a thymus-dependent autoimmune syndrome in some patients, causes extensive loss of autoimmune regulator (Aire(+)) tolerance-inducing MHC class II(high) medullary TEC (mTEC(high)).", "Post-cyclosporine A, Aire expression was restored within 7 days.", "Full recovery of the mTEC(high) subset occurred within 10 days and was linked to a decrease in a relatively resistant MHC class II(low) mTEC subset (mTEC(low)), consistent with a previously described precursor-product relationship.", "Cyclophosphamide and dexamethasone caused more extensive ablation of thymocytes and stromal cells but again severely depleted tolerance-inducing mTEC(high).", "Together, these data show that Aire(+) mTECs are highly sensitive to damage and that mTEC regeneration follows a conserved pattern regardless of the treatment regimen used."], "structured": false}
{"doc_id": 10165258, "title": "GATA-3 regulates hematopoietic stem cell maintenance and cell-cycle entry.", "abstract": ["Maintaining hematopoietic stem cell (HSC) quiescence is a critical property for the life-long generation of blood cells.", "Approximately 75% of cells in a highly enriched long-term repopulating HSC (LT-HSC) pool (Lin(-)Sca1(+)c-Kit(hi)CD150(+)CD48(-)) are quiescent, with only a small percentage of the LT-HSCs in cycle.", "Transcription factor GATA-3 is known to be vital for the development of T cells at multiple stages in the thymus and for Th2 differentiation in the peripheral organs.", "Although it is well documented that GATA-3 is expressed in HSCs, a role for GATA-3 in any prethymic progenitor cell has not been established.", "In the present study, we show that Gata3-null mutant mice generate fewer LT-HSCs and that fewer Gata3-null LT-HSCs are in cycle.", "Furthermore, Gata3 mutant hematopoietic progenitor cells fail to be recruited into an increased cycling state after 5-fluorouracil-induced myelosuppression.", "Therefore, GATA-3 is required for the maintenance of a normal number of LT-HSCs and for their entry into the cell cycle."], "structured": false}
{"doc_id": 10165723, "title": "CpG island methylator phenotype predicts progression of malignant melanoma.", "abstract": ["PURPOSE The CpG island methylator phenotype (CIMP) may be associated with development of malignancy through coordinated inactivation of tumor suppressor and tumor-related genes (TRG) and methylation of multiple noncoding, methylated-in-tumor (MINT) loci.", "These epigenetic changes create a distinct CIMP pattern that has been linked to recurrence and survival in gastrointestinal cancers.", "Because epigenetic inactivation of TRGs also has been shown in malignant melanoma, we hypothesized the existence of a clinically significant CIMP in cutaneous melanoma progression.   ", "EXPERIMENTAL DESIGN The methylation status of the CpG island promoter region of TRGs related to melanoma pathophysiology (WIF1, TFPI2, RASSF1A, RARbeta2, SOCS1, and GATA4) and a panel of MINT loci (MINT1, MINT2, MINT3, MINT12, MINT17, MINT25, and MINT31) in primary and metastatic tumors of different clinical stages (n=122) was assessed.   \n", "RESULTS Here, we show an increase in hypermethylation of the TRGs WIF1, TFPI2, RASSF1A, and SOCS1 with advancing clinical tumor stage.", "Furthermore, we find a significant positive association between the methylation status of MINT17, MINT31, and TRGs.", "The methylation status of MINT31 is associated with disease outcome in stage III melanoma.   \n", "CONCLUSIONS These findings show the significance of a CIMP pattern that is associated with advancing clinical stage of malignant melanoma.", "Future prospective large-scale studies may determine if CIMP-positive primary melanomas are at high risk of metastasis or recurrence."], "structured": true}
{"doc_id": 10169908, "title": "SLC1A5 mediates glutamine transport required for lung cancer cell growth and survival.", "abstract": ["PURPOSE We have previously identified solute-linked carrier family A1 member 5 (SLC1A5) as an overexpressed protein in a shotgun proteomic analysis of stage I non-small cell lung cancer (NSCLC) when compared with matched controls.", "We hypothesized that overexpression of SLC1A5 occurs to meet the metabolic demand for lung cancer cell growth and survival.   ", "EXPERIMENTAL DESIGN To test our hypothesis, we first analyzed the protein expression of SLC1A5 in archival lung cancer tissues by immunohistochemistry and immunoblotting (N = 98) and in cell lines (N = 36).", "To examine SLC1A5 involvement in amino acid transportation, we conducted kinetic analysis of l-glutamine (Gln) uptake in lung cancer cell lines in the presence and absence of a pharmacologic inhibitor of SLC1A5, gamma-l-Glutamyl-p-Nitroanilide (GPNA).", "Finally, we examined the effect of Gln deprivation and uptake inhibition on cell growth, cell-cycle progression, and growth signaling pathways of five lung cancer cell lines.   \n", "RESULTS Our results show that (i) SLC1A5 protein is expressed in 95% of squamous cell carcinomas (SCC), 74% of adenocarcinomas (ADC), and 50% of neuroendocrine tumors; (ii) SLC1A5 is located at the cytoplasmic membrane and is significantly associated with SCC histology and male gender; (iii) 68% of Gln is transported in a Na(+)-dependent manner, 50% of which is attributed to SLC1A5 activity; and (iv) pharmacologic and genetic targeting of SLC1A5 decreased cell growth and viability in lung cancer cells, an effect mediated in part by mTOR signaling.   \n", "CONCLUSIONS These results suggest that SLC1A5 plays a key role in Gln transport controlling lung cancer cells' metabolism, growth, and survival."], "structured": true}
{"doc_id": 10189634, "title": "Eic1 links Mis18 with the CCAN/Mis6/Ctf19 complex to promote CENP-A assembly", "abstract": ["CENP-A chromatin forms the foundation for kinetochore assembly.", "Replication-independent incorporation of CENP-A at centromeres depends on its chaperone HJURP(Scm3), and Mis18 in vertebrates and fission yeast.", "The recruitment of Mis18 and HJURP(Scm3) to centromeres is cell cycle regulated.", "Vertebrate Mis18 associates with Mis18BP1(KNL2), which is critical for the recruitment of Mis18 and HJURP(Scm3).", "We identify two novel fission yeast Mis18-interacting proteins (Eic1 and Eic2), components of the Mis18 complex.", "Eic1 is essential to maintain Cnp1(CENP-A) at centromeres and is crucial for kinetochore integrity; Eic2 is dispensable.", "Eic1 also associates with Fta7(CENP-Q/Okp1), Cnl2(Nkp2) and Mal2(CENP-O/Mcm21), components of the constitutive CCAN/Mis6/Ctf19 complex.", "No Mis18BP1(KNL2) orthologue has been identified in fission yeast, consequently it remains unknown how the key Cnp1(CENP-A) loading factor Mis18 is recruited.", "Our findings suggest that Eic1 serves a function analogous to that of Mis18BP1(KNL2), thus representing the functional counterpart of Mis18BP1(KNL2) in fission yeast that connects with a module within the CCAN/Mis6/Ctf19 complex to allow the temporally regulated recruitment of the Mis18/Scm3(HJURP) Cnp1(CENP-A) loading factors.", "The novel interactions identified between CENP-A loading factors and the CCAN/Mis6/Ctf19 complex are likely to also contribute to CENP-A maintenance in other organisms."], "structured": false}
{"doc_id": 10190462, "title": "INTRANASAL INSULIN IMPROVES COGNITION AND MODULATES \u03b2-AMYLOID IN EARLY AD", "abstract": ["Background: Reduced brain insulin signaling and low CSF-to-plasma insulin ratios have been observed in patients with Alzheimer disease (AD).", "Furthermore, intracerebroventricular or IV insulin administration improve memory, alter evoked potentials, and modulate neurotransmitters, possibly by augmenting low brain levels.", "After intranasal administration, insulin-like peptides follow extracellular pathways to the brain within 15 minutes.", "Objective: We tested the hypothesis that daily intranasal insulin treatment would facilitate cognition in patients with early AD or its prodrome, amnestic mild cognitive impairment (MCI).", "The proportion of verbal information retained after a delay period was the planned primary outcome measure.", "Secondary outcome measures included attention, caregiver rating of functional status, and plasma levels of insulin, glucose, \u03b2-amyloid, and cortisol.", "Methods: Twenty-five participants were randomly assigned to receive either placebo (n = 12) or 20 IU BID intranasal insulin treatment (n = 13) using an electronic atomizer, and 24 participants completed the study.", "Participants, caregivers, and all clinical evaluators were blinded to treatment assignment.", "Cognitive measures and blood were obtained at baseline and after 21 days of treatment.", "Results: Fasting plasma glucose and insulin were unchanged with treatment.", "The insulin-treated group retained more verbal information after a delay compared with the placebo-assigned group ( p = 0.0374).", "Insulin-treated subjects also showed improved attention ( p = 0.0108) and functional status ( p = 0.0410).", "Insulin treatment raised fasting plasma concentrations of the short form of the \u03b2-amyloid peptide (A\u03b240; p = 0.0471) without affecting the longer isoform (A\u03b242), resulting in an increased A\u03b240/42 ratio ( p = 0.0207).", "Conclusions: The results of this pilot study support further investigation of the benefits of intranasal insulin for patients with Alzheimer disease, and suggest that intranasal peptide administration may be a novel approach to the treatment of neurodegenerative disorders."], "structured": false}
{"doc_id": 10190778, "title": "Maternal alloantigens promote the development of tolerogenic fetal regulatory T cells in utero.", "abstract": ["As the immune system develops, T cells are selected or regulated to become tolerant of self antigens and reactive against foreign antigens.", "In mice, the induction of such tolerance is thought to be attributable to the deletion of self-reactive cells.", "Here, we show that the human fetal immune system takes advantage of an additional mechanism: the generation of regulatory T cells (Tregs) that suppress fetal immune responses.", "We find that substantial numbers of maternal cells cross the placenta to reside in fetal lymph nodes, inducing the development of CD4+CD25highFoxP3+ Tregs that suppress fetal antimaternal immunity and persist at least until early adulthood.", "These findings reveal a form of antigen-specific tolerance in humans, induced in utero and probably active in regulating immune responses after birth."], "structured": false}
{"doc_id": 10207180, "title": "\u03b2-site amyloid precursor protein-cleaving enzyme 1(BACE1) inhibitor treatment induces A\u03b25-X peptides through alternative amyloid precursor protein cleavage", "abstract": ["INTRODUCTION The \u03b2-secretase enzyme, \u03b2-site amyloid precursor protein-cleaving enzyme 1 (BACE1), cleaves amyloid precursor protein (APP) in the first step in \u03b2-amyloid (A\u03b2) peptide production.", "Thus, BACE1 is a key target for candidate disease-modifying treatment of Alzheimer's disease.", "In a previous exploratory A\u03b2 biomarker study, we found that BACE1 inhibitor treatment resulted in decreased levels of A\u03b21-34 together with increased A\u03b25-40, suggesting that these A\u03b2 species may be novel pharmacodynamic biomarkers in clinical trials.", "We have now examined whether the same holds true in humans.   \n", "METHODS In an investigator-blind, placebo-controlled and randomized study, healthy subjects (n =18) were randomly assigned to receive a single dose of 30 mg of LY2811376 (n =6), 90 mg of LY2811376 (n =6), or placebo (n =6).", "We used hybrid immunoaffinity-mass spectrometry (HI-MS) and enzyme-linked immunosorbent assays to monitor a variety of A\u03b2 peptides.   \n", "RESULTS Here, we demonstrate dose-dependent changes in cerebrospinal fluid (CSF) A\u03b21-34, A\u03b25-40 and A\u03b25-X after treatment with the BACE1-inhibitor LY2811376.", "A\u03b25-40 and A\u03b25-X increased dose-dependently, as reflected by two independent methods, while A\u03b21-34 dose-dependently decreased.   \n", "CONCLUSION Using HI-MS for the first time in a study where subjects have been treated with a BACE inhibitor, we confirm that CSF A\u03b21-34 may be useful in clinical trials on BACE1 inhibitors to monitor target engagement.", "Since it is less hydrophobic than longer A\u03b2 species, it is less susceptible to preanalytical confounding factors and may thus be a more stable marker.", "By independent measurement techniques, we also show that BACE1 inhibition in humans is associated with APP-processing into N-terminally truncated A\u03b2 peptides via a BACE1-independent pathway.   \n", "TRIAL REGISTRATION ClinicalTrials.gov NCT00838084.", "Registered: First received: January 23, 2009, Last updated: July 14, 2009, Last verified: July 2009."], "structured": true}
{"doc_id": 10209731, "title": "Cardiovascular diseases in Chinese, Malays, and Indians in Singapore. I. Differences in mortality.", "abstract": ["STUDY OBJECTIVE The aim of the study was to analyse differences in mortality from the main cardiovascular diseases (ischaemic heart disease, hypertensive disease, and cerebrovascular disease) among Chinese, Malays, and Indians in Singapore.   \n", "DESIGN", "The study was a survey using national death registration data in Singapore for the five years 1980 to 1984.", "The underlying cause of death, coded according to the ninth revision of the International Classification of Diseases, was taken for the analyses.   \n", "SETTING The study was confined to the independent island state of Singapore, population 2.53 million (Chinese 76.5%, Malays 14.8%, Indians 6.4%, Others 2.3%).", "Death registration is thought to be complete.   ", "SUBJECTS All registered deaths in the age range 30-69 years during the study period were analysed by ethnic group.   \n", "MEASUREMENT AND MAIN RESULTS Indians had higher mortality from ischaemic heart disease than the other ethnic groups in both sexes, with age-standardised relative risks of Indian v Chinese (males 3.8, females 3.4), Indian v Malay (males 1.9, females 1.6), and Malay v Chinese (males 2.0, females 2.2).", "The excess mortality in Indians declined with age.", "For hypertensive disease Malays had the highest mortality, with age-standardised relative risks of Malay v Chinese (males 3.4, females 4.4), Malay v Indian (males 2.0, females 2.5), and Indian v Chinese (males 1.6, females 1.6).", "For cerebrovascular disease there was little ethnic difference except for lower rates in Chinese females, with age-standardised relative risks of Malay v Chinese (males 1.1, females 1.9), Malay v Indian (males 1.0, females 1.1), and Indian v Chinese (males 1.1, females 1.7).   \n", "CONCLUSIONS There are significant differences in mortality from the three main cardiovascular diseases in the different ethnic groups in Singapore."], "structured": true}
{"doc_id": 10212612, "title": "Protein localization in electron micrographs using fluorescence nanoscopy", "abstract": ["A complete portrait of a cell requires a detailed description of its molecular topography: proteins must be linked to particular organelles.", "Immunocytochemical electron microscopy can reveal locations of proteins with nanometer resolution but is limited by the quality of fixation, the paucity of antibodies and the inaccessibility of antigens.", "Here we describe correlative fluorescence electron microscopy for the nanoscopic localization of proteins in electron micrographs.", "We tagged proteins with the fluorescent proteins Citrine or tdEos and expressed them in Caenorhabditis elegans, fixed the worms and embedded them in plastic.", "We imaged the tagged proteins from ultrathin sections using stimulated emission depletion (STED) microscopy or photoactivated localization microscopy (PALM).", "Fluorescence correlated with organelles imaged in electron micrographs from the same sections.", "We used these methods to localize histones, a mitochondrial protein and a presynaptic dense projection protein in electron micrographs."], "structured": false}
{"doc_id": 10218447, "title": "The flavonoid component isorhamnetin in vitro inhibits proliferation and induces apoptosis in Eca-109 cells.", "abstract": ["Isorhamnetin is one member of flavonoid components which has been used in the treatment of heart disease.", "Recently the in vitro anti-cancer effect of isorhamnetin on human esophageal squamous carcinoma cell line Eca-109 was investigated in our lab.", "When Eca-109 cells were in vitro exposed to the graded doses of isorhamnetin (0-80 microg/ml) for 48 h, respectively, isorhamnetin exhibited cytostatic effect on the treated cells, with an IC(50) of 40+/-0.08 microg/ml as estimated by MTT assay.", "Inhibition on proliferation by isorhamnetin was detected by trypan blue exclusion assay, clone formation test, immunocytochemical assay of PCNA and (3)H-thymidine uptake analysis.", "Cell cycle distribution was measured by FCM.", "It was found that the viability of Eca-109 cells was significantly hampered by isorhamnetin.", "Compared with the negative control group, the treated group which was exposed to isorhamnetin had increased population in G(0)/G(1) phase from 74.6 to 84 while had a significant reduction in G(2)/M phase from 11.9 to 5.8.", "In addition to its cytostatic effect, isorhamnetin also showed stimulatory effect on apoptosis.", "Typical apoptotic morphology such as condensation and fragmentation of nuclei and blebbing membrane of the apoptotic cells could be observed through transmission electron microscope.", "Moreover, the sharp increase in apoptosis rate between the control and treated group were detected by FCM from 6.3 to 16.3.", "To explore the possible molecular mechanisms that underlie the growth inhibition and apoptosis stimulatory effects of isorhamnetin, the expressions of six proliferation- and death-related genes were detected by FCM.", "Expressions of bcl-2, c-myc and H-ras were downregulated whereas Bax, c-fos and p53 were upregulated.", "However, the in vivo experiments were required to further confirm the anti-cancer effects of isorhamnetin.", "In conclusion, isorhamnetin appears to be a potent drug against esophageal cancer due to its in vitro potential to not only inhibit proliferation but also induce apoptosis of Eca-109 cells."], "structured": false}
{"doc_id": 10247282, "title": "Arachidonic Acid in the Diabetic Rat Kidney", "abstract": ["In the rat isolated perfused kidney, arachidonic acid elicits cyclooxygenase-dependent vasoconstriction through activation of PGH2/TxA2 receptors; responses are enhanced in kidneys from diabetic rats.", "This study examined the roles of cyclooxygenase-1/cyclooxygenase-2 in the enhanced renal vasoconstrictor effect of arachidonic acid in streptozotocin-diabetic rats.", "Release of 20-HETE was also determined, as this eicosanoid has been reported to elicit cyclooxygenase-dependent vasoconstriction.", "We confirmed that vasoconstrictor responses to arachidonic acid were enhanced in the diabetic rat kidney associated with a 2-fold-greater increase in the release of 6-ketoPGF1alpha, which was used as an index of cyclooxygenase activity.", "One and three micrograms of arachidonic acid increased perfusion pressure by 85+/-37 and 186+/-6 mm Hg, respectively, in diabetic rat kidneys compared with 3+/-1 and 17+/-8 mm Hg, respectively, in control rat kidneys.", "Inhibition of both cyclooxygenase isoforms with indomethacin (10 micromol/L) abolished the vasoconstrictor response to arachidonic acid in both diabetic and control rat kidneys, whereas inhibition of cyclooxygenase-2 with nimesulide (5 micromol/L) reduced perfusion pressure responses to 1 and 3 microg arachidonic acid only in the diabetic rat kidney to 15+/-8 and 108+/-26 mm Hg, respectively, consistent with a 3-fold increase in the renal cortical expression of cyclooxygenase-2.", "20-HETE release from the diabetic rat kidney was reduced almost 6-fold and was not increased in response to arachidonic acid.", "These results demonstrate that the renal vasoconstrictor effect of arachidonic acid is solely dependent on cyclooxygenase activity, with no evidence for a contribution from 20-HETE; in the diabetic rat, cyclooxygenase-2 activity contributes to the renal vasoconstrictor effect of arachidonic acid."], "structured": false}
{"doc_id": 10247314, "title": "Two sequence motifs from HIF-1alpha bind to the DNA-binding site of p53.", "abstract": ["There is evidence that hypoxia-inducible factor-1alpha (HIF-1alpha) interacts with the tumor suppressor p53.", "To characterize the putative interaction, we mapped the binding of the core domain of p53 (p53c) to an array of immobilized HIF-1alpha-derived peptides and found two peptide-sequence motifs that bound to p53c with micromolar affinity in solution.", "One sequence was adjacent to and the other coincided with the two proline residues of the oxygen-dependent degradation domain (P402 and P564) that act as switches for the oxygen-dependent regulation of HIF-1alpha.", "The binding affinity was independent of the hydroxylation state of P564.", "We found from NMR spectroscopy that these sequence motifs bind to the DNA-binding site of p53c.", "Because the two sequences are homologous and separated by 120 residues, and one is in a largely unstructured transactivation domain, we speculate that each sequence motif in HIF-1alpha binds to a different subunit of the p53 tetramer, leading to very tight binding.", "The binding data support the proposal that p53 provides a route for the degradation in hypoxic tumor cells of HIF-1alpha that is not hydroxylated at the two proline residues."], "structured": false}
{"doc_id": 10273147, "title": "A functionally characterized test set of human induced pluripotent stem cells", "abstract": ["Human induced pluripotent stem cells (iPSCs) present exciting opportunities for studying development and for in vitro disease modeling.", "However, reported variability in the behavior of iPSCs has called their utility into question.", "We established a test set of 16 iPSC lines from seven individuals of varying age, sex and health status, and extensively characterized the lines with respect to pluripotency and the ability to terminally differentiate.", "Under standardized procedures in two independent laboratories, 13 of the iPSC lines gave rise to functional motor neurons with a range of efficiencies similar to that of human embryonic stem cells (ESCs).", "Although three iPSC lines were resistant to neural differentiation, early neuralization rescued their performance.", "Therefore, all 16 iPSC lines passed a stringent test of differentiation capacity despite variations in karyotype and in the expression of early pluripotency markers and transgenes.", "This iPSC and ESC test set is a robust resource for those interested in the basic biology of stem cells and their applications."], "structured": false}
{"doc_id": 10279084, "title": "Differential regulation of MAP kinase activation by a novel splice variant of human MAP kinase phosphatase-2.", "abstract": ["MAP kinase phosphatase-2 (MKP-2) is a member of the family of dual specificity phosphatases that functions to inactivate the ERK and JNK MAP kinase signalling pathways.", "Here, we identify a novel human MKP-2 variant (MKP-2-S) lacking the MAP kinase binding site but retaining the phosphatase catalytic domain.", "Endogenous MKP-2-S transcripts and proteins were found in PC3 prostate and MDA-MB-231 breast cancer cells and also human prostate biopsies.", "Cellular transfection of MKP-2-S gave rise to a nuclear protein of 33kDa which displayed phosphatase activity comparable to the formerly described long form of MKP-2 (MKP-2-L).", "Due to its lack of a kinase interacting motif (KIM), MKP-2-S did not bind to JNK or ERK; MKP-2-L bound ERK and to a lesser extent JNK.", "Protein turnover of adenoviral expressed MKP-2-S was accelerated relative to MKP-2-L, with a greater susceptibility to proteosomal-mediated degradation.", "MKP-2-S retained its ability to deactivate JNK in a similar manner as MKP-2-L and was an effective inhibitor of LPS-stimulated COX-2 induction.", "However, unlike MKP-2-L, MKP-2-S was unable to reverse serum-induced ERK activation or significantly inhibit endothelial cell proliferation.", "These findings reveal the occurrence of a novel splice variant of MKP-2 which is unable to bind ERK and may be significant in the dysregulation of MAP kinase activity in certain disease states, particularly in breast and prostate cancers."], "structured": false}
{"doc_id": 10284593, "title": "Myeloperoxidase acts as a profibrotic mediator of atrial fibrillation", "abstract": ["Observational clinical and ex vivo studies have established a strong association between atrial fibrillation and inflammation.", "However, whether inflammation is the cause or the consequence of atrial fibrillation and which specific inflammatory mediators may increase the atria's susceptibility to fibrillation remain elusive.", "Here we provide experimental and clinical evidence for the mechanistic involvement of myeloperoxidase (MPO), a heme enzyme abundantly expressed by neutrophils, in the pathophysiology of atrial fibrillation.", "MPO-deficient mice pretreated with angiotensin II (AngII) to provoke leukocyte activation showed lower atrial tissue abundance of the MPO product 3-chlorotyrosine, reduced activity of matrix metalloproteinases and blunted atrial fibrosis as compared to wild-type mice.", "Upon right atrial electrophysiological stimulation, MPO-deficient mice were protected from atrial fibrillation, which was reversed when MPO was restored.", "Humans with atrial fibrillation had higher plasma concentrations of MPO and a larger MPO burden in right atrial tissue as compared to individuals devoid of atrial fibrillation.", "In the atria, MPO colocalized with markedly increased formation of 3-chlorotyrosine.", "Our data demonstrate that MPO is a crucial prerequisite for structural remodeling of the myocardium, leading to an increased vulnerability to atrial fibrillation."], "structured": false}
{"doc_id": 10300000, "title": "Knowledge and use of secondary contraception among patients requesting termination of pregnancy.", "abstract": ["The results of a survey of 769 patients attending the St. James's University Fertility Control Clinic, England, for abortion services showed that patients seeing general practitioners were less knowledgeable than those attending specialist clinics.", "There was a demonstrated need for counseling on pill and condom use and protection against sexually transmitted diseases.", "Knowledge of postcoital methods was also found to be lacking.", "The survey was conducted between April 1, 1991, and January 31, 1992.", "Respondents included minorities such as Afro-Caribbean (8%) and Asian (9%).", "307 of the cases were using a less effective form of contraception at the time of conception, usually a change from the pill to condoms.", "Of the 171 people reporting failure of contraception, 93 noted a split or leaking condom; 13, a condom falling off during intercourse; 32, inconsistent use of condoms;l 32, forgetting to take contraceptive pills or using antibiotics with the pill; and 1, a late injection of medroxyprogesterone acetate.", "45 of the 309 people who had conceived while using condoms recognized a potential condom failure, and only 20 attempted any emergency contraceptive method such as the postcoital pill.", "Only 30% of the 171 patients with recognized condom failure and 12% of the 210 who had not used any contraception had adequate knowledge of the existence, timing, and source of postcoital pills; i.e., 20% of 381.", "Only 2% of the 171 nd 2% of the 381 patients, had knowledge of postcoital insertion of an intrauterine contraceptive device.", "Given the choice between and unplanned pregnancy and postcoital contraceptive, most (718 out of 769) preferred using postcoital contraception.", "Contraceptive information was given to 501 by a general practitioner, to 102 by a community family planning clinic, and 163 had no medical advice.", "There was a range of knowledge of postcoital contraceptive methods.", "Knowledge of how to deal with forgotten pills, severe vomiting, severe diarrhea, and concurrent antibiotic treatment among the 422 patients who had ever used the combined pill also was variable.", "19% of the 372 patients treated by general practitioners knew 4 correct answers, but 50% of the 50 patients in community family planning clinics answered correctly 4 times.", "Differences could not be explained by other demographic characteristics."], "structured": false}
{"doc_id": 10300888, "title": "Domestication and Divergence of Saccharomyces cerevisiae Beer Yeasts", "abstract": ["Whereas domestication of livestock, pets, and crops is well documented, it is still unclear to what extent microbes associated with the production of food have also undergone human selection and where the plethora of industrial strains originates from.", "Here, we present the genomes and phenomes of 157 industrial Saccharomyces cerevisiae yeasts.", "Our analyses reveal that today's industrial yeasts can be divided into five sublineages that are genetically and phenotypically separated from wild strains and originate from only a few ancestors through complex patterns of domestication and local divergence.", "Large-scale phenotyping and genome analysis further show strong industry-specific selection for stress tolerance, sugar utilization, and flavor production, while the sexual cycle and other phenotypes related to survival in nature show decay, particularly in beer yeasts.", "Together, these results shed light on the origins, evolutionary history, and phenotypic diversity of industrial yeasts and provide a resource for further selection of superior strains.", "PAPERCLIP."], "structured": false}
{"doc_id": 10314816, "title": "The ascendancy of Amblyomma americanum as a vector of pathogens affecting humans in the United States.", "abstract": ["Until the 1990s, Amblyomma americanum was regarded primarily as a nuisance species, but a tick of minor importance as a vector of zoonotic pathogens affecting humans.", "With the recent discoveries of Ehrlichia chaffeensis, Ehrlichia ewingii, and \"Borrelia lonestari,\" the public health relevance of lone star ticks is no longer in question.", "During the next 25 years, the number of cases of human disease caused by A. americanum-associated pathogens will probably increase.", "Based on current trajectories and historic precedents, the increase will be primarily driven by biological and environmental factors that alter the geographic distribution and intensity of transmission of zoonotic pathogens.", "Sociologic and demographic changes that influence the likelihood of highly susceptible humans coming into contact with infected lone star ticks, in addition to advances in diagnostic capabilities and national surveillance efforts, will also contribute to the anticipated increase in the number of recognized cases of disease."], "structured": false}
{"doc_id": 10326242, "title": "Biallelic mutations in PALB2 cause Fanconi anemia subtype FA-N and predispose to childhood cancer", "abstract": ["PALB2 was recently identified as a nuclear binding partner of BRCA2.", "Biallelic BRCA2 mutations cause Fanconi anemia subtype FA-D1 and predispose to childhood malignancies.", "We identified pathogenic mutations in PALB2 (also known as FANCN) in seven families affected with Fanconi anemia and cancer in early childhood, demonstrating that biallelic PALB2 mutations cause a new subtype of Fanconi anemia, FA-N, and, similar to biallelic BRCA2 mutations, confer a high risk of childhood cancer."], "structured": false}
{"doc_id": 10335603, "title": "Long tandem arrays of complex repeat units in Chironomus telomeres.", "abstract": ["A cloned 340-bp DNA fragment excised by EcoRI from the Chironomus pallividittatus genome has been localized to the telomeres by in situ hybridization as well as to connectives between telomeres.", "No hybridization was observed in other regions of the chromosomes.", "Another cloned EcoRI fragment, 525 bp long has also been studied.", "This represents a partial duplication of the 340-bp sequence.", "Genomic blot hybridization experiments show that the 340-bp sequence is a representative monomeric unit of tandemly repeated arrays which account for 1.2% of the Chironomus genome, on average 300 kb per telomere.", "The repeat unit contains two types of subrepeats each present twice per repeat unit.", "Northern blot hybridization experiments show that the telomere-associated sequences are transcribed into a discrete RNA species approximately 20 kb in size.", "The evolution of this telomere-associated DNA is discussed."], "structured": false}
{"doc_id": 10342807, "title": "Localization of Na+ channel isoforms at the atrioventricular junction and atrioventricular node in the rat.", "abstract": ["BACKGROUND The electrical activity of the atrioventricular node (AVN) is functionally heterogeneous, but how this relates to distinct cell types and the 3-dimensional structure of the AVN is unknown.", "To address this, we have studied the expression of Na(V)1.5 and other Na+ channel isoforms in the AVN.   \n", "METHODS AND RESULTS The rat AVN was identified by Masson's trichrome staining together with immunolabeling of marker proteins: connexin40, connexin43, desmoplakin, atrial natriuretic peptide, and hyperpolarization-activated and cyclic nucleotide-gated channel 4.", "Na+ channel expression was investigated with immunohistochemistry with isoform-specific Na+ channel antibodies.", "Na(V)1.1 was distributed in a similar manner to Na(V)1.5.", "Na(V)1.2 was not detected.", "Na(V)1.3 labeling was present in nerve fibers and cell bodies (but not myocytes) and was abundant in the penetrating atrioventricular (AV) bundle and the common bundle but was much less abundant in other regions.", "Na(V)1.5 labeling was abundant in the atrial and ventricular myocardium and the left bundle branch.", "Na(V)1.5 labeling was absent in the open node, penetrating AV bundle, AV ring bundle, and common bundle but present at a reduced level in the inferior nodal extension and transitional zone.", "Na(V)1.6 was not detected.   \n", "CONCLUSIONS Our findings provide molecular evidence of multiple electrophysiological cell types at the AV junction.", "Impaired AV conduction as a result of mutations in or loss of Na(V)1.5 must be the result of impaired conduction in the AVN inputs (inferior nodal extension and transitional zone) or output (bundle branches) rather than the AVN itself (open node and penetrating AV bundle)."], "structured": true}
{"doc_id": 10354110, "title": "Follicular B cell trafficking within the spleen actively restricts humoral immune responses.", "abstract": ["Follicular (FO) and marginal zone (MZ) B cells are maintained in distinct locations within the spleen, but the genetic basis for this separation is still enigmatic.", "We now report that B cell sequestration requires lineage-specific regulation of migratory receptors by the transcription factor Klf2.", "Moreover, using gene-targeted mice we show that altered splenic B cell migration confers a significant in vivo gain-of-function phenotype to FO B cells, including the ability to quickly respond to MZ-associated antigens and pathogens in a T cell-dependent manner.", "This work demonstrates that in wild-type animals, naive FO B cells are actively removed from the MZ, thus restricting their capacity to respond to blood-borne pathogens."], "structured": false}
{"doc_id": 10359591, "title": "Interleukin-2 and inflammation induce distinct transcriptional programs that promote the differentiation of effector cytolytic T cells.", "abstract": ["Interleukin(IL)-2 and inflammation regulate effector and memory cytolytic T-lymphocyte (CTL) generation during infection.", "We demonstrate a complex interplay between IL-2 and inflammatory signals during CTL differentiation.", "IL-2 stimulation induced the transcription factor eomesodermin (Eomes), upregulated perforin (Prf1) transcription, and repressed re-expression of memory CTL markers Bcl6 and IL-7Ralpha.", "Binding of Eomes and STAT5 to Prf1 cis-regulatory regions correlated with transcriptional initiation (increased recruitment of RNA polymerase II to the Prf1 promoter).", "Inflammation (CpG, IL-12) enhanced expression of IL-2Ralpha and the transcription factor T-bet, but countered late Eomes and perforin induction while preventing IL-7Ralpha repression by IL-2.", "After infection of mice with lymphocytic choriomeningitis virus, IL-2Ralpha-deficient effector CD8(+) T cells expressed more Bcl6 but less perforin and granzyme B, formed fewer KLRG-1(+) and T-bet-expressing CTL, and killed poorly.", "Thus, inflammation influences both effector and memory CTL differentiation, whereas persistent IL-2 stimulation promotes effector at the expense of memory CTL development."], "structured": false}
{"doc_id": 10365749, "title": "Neighbourhood risk factors for tuberculosis in Hong Kong.", "abstract": ["BACKGROUND Tuberculosis (TB) has been reported to be associated with poverty, especially in developing countries.", "Hong Kong is one of the few industrialised areas with a high incidence of TB where previous reports on the effect of poverty at neighbourhood level have been conflicting.   \n", "OBJECTIVE To examine the spatial distribution of TB and its association with neighbourhood risk factors.   \n", "METHOD A total of 17 294 TB cases notified from 2005 to 2007 were mapped down to the District Council Constituency Area (DCCA) level, and were indirectly standardised by age and sex using 2006 census population data.", "The standardised TB ratio was correlated with neighbourhood risk factors classified by family, ethnicity, economic and environmental domains.   \n", "RESULTS The indirect age- and sex-standardised ratio demonstrated a spatially varied pattern, and was significantly associated with all neighbourhood factors on univariate analysis.", "Only marital status, place of birth and low household income were independently associated with the standardised TB ratio on multivariate analysis.   \n", "CONCLUSION Despite the virtual elimination of absolute poverty by a well-developed social assistance scheme, low household income in the neighbourhood was significantly associated with TB, independently of place of birth, marital status and other risk factors."], "structured": true}
{"doc_id": 10365787, "title": "Genomic stability and tumour suppression by the APC/C cofactor Cdh1", "abstract": ["The anaphase promoting complex or cyclosome (APC/C) is a ubiquitin protein ligase that, together with Cdc20 or Cdh1, targets cell-cycle proteins for degradation.", "APC/C\u2013Cdh1 specifically promotes protein degradation in late mitosis and G1.", "Mutant embryos lacking Cdh1 die at E9.5\u2013E10.5 due to defects in the endoreduplication of trophoblast cells and placental malfunction.", "This lethality is prevented when Cdh1 is expressed in the placenta.", "Cdh1-deficient cells proliferate inefficiently and accumulate numeric and structural chromosomal aberrations, indicating that Cdh1 contributes to the maintenance of genomic stability.", "Cdh1 heterozygous animals show increased susceptibility to spontaneous tumours, suggesting that Cdh1 functions as a haploinsufficient tumour suppressor.", "These heterozygous mice also show several defects in behaviour associated with increased proliferation of stem cells in the nervous system.", "These results indicate that Cdh1 is required for preventing unscheduled proliferation of specific progenitor cells and protecting mammalian cells from genomic instability."], "structured": false}
{"doc_id": 10374686, "title": "Developing primary palliative care.", "abstract": ["Although 65% of people with cancer want to die at home, only about 30% are successful in doing so.1,2 A government committed to choice for patients must improve this figure.3 Developing palliative care services in primary care is essential for realising the expectations of dying people.", "Such services could also offer important opportunities for extending supportive humane care at an earlier stage, and to people not only with cancer but with chronic obstructive pulmonary disease, motor neurone disease, and cardiac failure, for example, who also often have palliative care needs.    ", "Primary care professionals have the potential and ability to provide end of life care for most patients, given adequate training, resources, and, when needed, specialist advice.4,5 They share common values with palliative care specialists\u2014holistic, patient centred care, delivered in the context of families and friends.6 However, until recently, apart from Macmillan general practitioners and nurse facilitators, few comprehensive workforce initiatives have been undertaken in primary care that focus on end of life care.    ", "Many cancer patients and their carers experience existential distress long before they die.7 Recognising and alleviating such suffering is important, but it often goes unrecognised or is overlooked by services focusing on the terminal phase of illnesses.", "Primary care teams may know patients over long periods of time.", "They can readily identify patients from cancer and chronic disease registers who might benefit from an early palliative care approach.", "Such patients could be identified by clinicians asking one simple question of themselves: \u201cWould I be surprised if my patient were to die in the next 12 months?\u201d8 By identifying such patients proactively we could deliver, simultaneously, active treatment and patient centred supportive care, through a team with whom many patients have a valued long term relationship.    ", "Palliative care services need to be extended to patients with non-malignant conditions who have comparable concerns to and in some cases even greater unmet needs than cancer patients.9 Progress by palliative medicine specialists is hampered by issues such as uncertainty about the most effective models of care, lack of non-cancer expertise, and concerns about pressure on specialist services.", "General practitioners and community nurses can lead the way in providing a palliative care approach for patients with terminal organ failure illness.", "The first step in such an approach is for the goals of care to be discussed and agreed.", "Management plans are adjusted accordingly.", "Effective control of symptoms and maintaining quality of life are prioritised.    ", "In the light of these important opportunities it is regrettable that the new general medical services contract has not prioritised palliative care.", "By day, other developments to achieve the quality indicators are taking precedence.", "By night and at weekends, the new unscheduled care services (which are responsible for providing care for 75% of the hours in the week) are even less well configured than previous out of hours provision to facilitate dying at home.", "Such services specialise in dealing with acute emergencies and, as such, often struggle to meet the medical, nursing, and social care needs of dying people and their families.", "These changes will greatly affect care for dying people and may increase the number of hospital admissions.    ", "However, one important initiative is gaining momentum within primary care.", "The Gold Standards Framework is a resource for organising proactive palliative care in the community and is supported by funding from the Cancer Services Collaborative, Macmillan Cancer Relief, and the National Lottery.10 The framework provides a detailed guide to providing holistic, patient centred care and thereby facilitates effective care in the community.", "Other recently initiated mechanisms for developing primary palliative care include the training of general practitioners with a special interest in palliative care and the new end of life initiative in England to improve palliative care provision by generalists and to share examples of good practice.    ", "To support such developments it is essential that primary palliative care is supported by an adequate academic base.11 This is admittedly a challenging arena in which to undertake research, but progress has been made in recent years in developing conceptual models and research architectures for studying end of life issues.", "Now we need to build on this work to ensure that the understanding and insights gleaned can be translated into effective interventions.    ", "Every person with a progressive illness has a right to palliative care.12 Patients desire a reassuring professional presence in the face of death.", "General practitioners and community nurses are trusted by patients and are in a position to provide effective, equitable, and accessible palliative care.", "This will happen only if they have adequate time and resources and work in a system that encourages such care.", "Patients who receive holistic support in the community may be less likely to require expensive admission to hospital and often futile treatments at the end of their lives."], "structured": false}
{"doc_id": 10408324, "title": "The effects of self-administering emergency contraception.", "abstract": ["BACKGROUND Emergency postcoital contraception prevents pregnancy, but it must be prescribed by a doctor and taken within 72 hours of intercourse.", "It has been proposed that emergency contraception be made available without a prescription.", "We undertook a study to learn how women might behave if given a supply of emergency contraceptive pills to keep at home.   \n", "METHODS We assigned 553 women to be given a replaceable supply of hormonal emergency contraceptive pills to take home (the treatment group) and 530 women to use emergency contraception obtained by visiting a doctor (the control group).", "The frequency of use of emergency contraception, the use of other contraceptives, and the incidence of unwanted pregnancy were determined in both groups of women one year later.   \n", "RESULTS The results for 549 women in the treatment group and 522 women in the control group were available for analysis.", "Three hundred seventy-nine of the women in the treatment group (69 percent) and 326 of the women in the control group (62 percent) contributed detailed information at follow-up.", "One hundred eighty of the women in the treatment group (47 percent) used emergency contraception at least once.", "Among those who returned the study questionnaire, 98 percent used emergency contraception correctly.", "There were no serious adverse effects.", "Eighty-seven women in the control group (27 percent) used emergency contraception at least once (P<0.001 for the comparison with the treatment group).", "The women in the treatment group were not more likely to use emergency contraception repeatedly.", "Their use of other methods of contraception was no different from that of the women in the control group.", "There were 18 unintended pregnancies in the treatment group and 25 in the control group (relative risk, 0.7; 95 percent confidence interval, 0.4 to 1.2).   \n", "CONCLUSIONS Making emergency contraception more easily obtainable does no harm and may reduce the rate of unwanted pregnancies."], "structured": true}
{"doc_id": 10423989, "title": "A coactivator of pre-mRNA splicing.", "abstract": ["The nuclear matrix antigen recognized by the monoclonal antibody (mAb) B1C8 is a novel serine (S) and arginine (R)-rich protein associated with splicing complexes and is named here SRm160 (SR-related matrix protein of 160 kD).", "SRm160 contains multiple SR repeats, but unlike proteins of the SR family of splicing factors, lacks an RNA recognition motif.", "SRm160 and a related protein SRm300 (the 300-kD nuclear matrix antigen recognized by mAb B4A11) form a complex that is required for the splicing of specific pre-mRNAs.", "The SRm160/300 complex associates with splicing complexes and promotes splicing through interactions with SR family proteins.", "Binding of SRm160/300 to pre-mRNA is normally also dependent on U1 snRNP and is stabilized by U2 snRNP.", "Thus, SRm160/300 forms multiple interactions with components bound directly to important sites within pre-mRNA.", "The results suggest that a complex of the nuclear matrix proteins SRm160 and SRm300 functions as a coactivator of pre-mRNA splicing."], "structured": false}
{"doc_id": 10430148, "title": "Comparison of pioglitazone vs glimepiride on progression of coronary atherosclerosis in patients with type 2 diabetes: the PERISCOPE randomized controlled trial.", "abstract": ["CONTEXT No antidiabetic regimen has demonstrated the ability to reduce progression of coronary atherosclerosis.", "Commonly used oral glucose-lowering agents include sulfonylureas, which are insulin secretagogues, and thiazolidinediones, which are insulin sensitizers.   \n", "OBJECTIVE To compare the effects of an insulin sensitizer, pioglitazone, with an insulin secretagogue, glimepiride, on the progression of coronary atherosclerosis in patients with type 2 diabetes.   \n", "DESIGN, SETTING, AND PARTICIPANTS Double-blind, randomized, multicenter trial at 97 academic and community hospitals in North and South America (enrollment August 2003-March 2006) in 543 patients with coronary disease and type 2 diabetes.   \n", "INTERVENTIONS A total of 543 patients underwent coronary intravascular ultrasonography and were randomized to receive glimepiride, 1 to 4 mg, or pioglitazone, 15 to 45 mg, for 18 months with titration to maximum dosage, if tolerated.", "Atherosclerosis progression was measured by repeat intravascular ultrasonography examination in 360 patients at study completion.   \n", "MAIN OUTCOME MEASURE Change in percent atheroma volume (PAV) from baseline to study completion.   \n", "RESULTS Least squares mean PAV increased 0.73% (95% CI, 0.33% to 1.12%) with glimepiride and decreased 0.16% (95% CI, -0.57% to 0.25%) with pioglitazone(P = .002).", "An alternative analysis imputing values for noncompleters based on baseline characteristics showed an increase in PAV of 0.64% (95% CI, 0.23% to 1.05%) for glimepiride and a decrease of 0.06% (-0.47% to 0.35%) for pioglitazone (between-group P = .02).", "Mean (SD) baseline HbA(1c) levels were 7.4% (1.0%) in both groups and declined during treatment an average 0.55% (95% CI, -0.68% to -0.42%) with pioglitazone and 0.36% (95% CI, -0.48% to -0.24%) with glimepiride (between-group P = .03).", "In the pioglitazone group, compared with glimepiride, high-density lipoprotein levels increased 5.7 mg/dL (95% CI, 4.4 to 7.0 mg/dL; 16.0%) vs 0.9 mg/dL (95% CI, -0.3 to 2.1 mg/dL; 4.1%), and median triglyceride levels decreased 16.3 mg/dL (95% CI, -27.7 to -11.0 mg/dL; 15.3%) vs an increase of 3.3 mg/dL (95% CI, -10.7 to 11.7 mg/dL; 0.6%) (P < .001 for both comparisons).", "Median fasting insulin levels decreased with pioglitazone and increased with glimepiride (P < .001).", "Hypoglycemia was more common in the glimepiride group and edema, fractures, and decreased hemoglobin levels occurred more frequently in the pioglitazone group.   \n", "CONCLUSION In patients with type 2 diabetes and coronary artery disease, treatment with pioglitazone resulted in a significantly lower rate of progression of coronary atherosclerosis compared with glimepiride.   \n", "TRIAL REGISTRATION clinicaltrials.gov Identifier: NCT00225277."], "structured": true}
{"doc_id": 10443642, "title": "Staphylococcus aureus RNAIII coordinately represses the synthesis of virulence factors and the transcription regulator Rot by an antisense mechanism.", "abstract": ["RNAIII is the intracellular effector of the quorum-sensing system in Staphylococcus aureus.", "It is one of the largest regulatory RNAs (514 nucleotides long) that are known to control the expression of a large number of virulence genes.", "Here, we show that the 3' domain of RNAIII coordinately represses at the post-transcriptional level, the expression of mRNAs that encode a class of virulence factors that act early in the infection process.", "We demonstrate that the 3' domain acts primarily as an antisense RNA and rapidly anneals to these mRNAs, forming long RNA duplexes.", "The interaction between RNAIII and the mRNAs results in repression of translation initiation and triggers endoribonuclease III hydrolysis.", "These processes are followed by rapid depletion of the mRNA pool.", "In addition, we show that RNAIII and its 3' domain mediate translational repression of rot mRNA through a limited number of base pairings involving two loop-loop interactions.", "Since Rot is a transcriptional regulatory protein, we proposed that RNAIII indirectly acts on many downstream genes, resulting in the activation of the synthesis of several exoproteins.", "These data emphasize the multitude of regulatory steps affected by RNAIII and its 3' domain in establishing a network of S. aureus virulence factors."], "structured": false}
{"doc_id": 10450300, "title": "Human Cytomegalovirus Latency-Associated Proteins Elicit Immune-Suppressive IL-10 Producing CD4+ T Cells", "abstract": ["Human cytomegalovirus (HCMV) is a widely prevalent human herpesvirus, which, after primary infection, persists in the host for life.", "In healthy individuals, the virus is well controlled by the HCMV-specific T cell response.", "A key feature of this persistence, in the face of a normally robust host immune response, is the establishment of viral latency.", "In contrast to lytic infection, which is characterised by extensive viral gene expression and virus production, long-term latency in cells of the myeloid lineage is characterised by highly restricted expression of viral genes, including UL138 and LUNA.", "Here we report that both UL138 and LUNA-specific T cells were detectable directly ex vivo in healthy HCMV seropositive subjects and that this response is principally CD4\u207a T cell mediated.", "These UL138-specific CD4\u207a T cells are able to mediate MHC class II restricted cytotoxicity and, importantly, show IFN\u03b3 effector function in the context of both lytic and latent infection.", "Furthermore, in contrast to CDCD4\u207a T cells specific to antigens expressed solely during lytic infection, both the UL138 and LUNA-specific CD4\u207a T cell responses included CD4\u207a T cells that secreted the immunosuppressive cytokine cIL-10.", "We also show that cIL-10 expressing CD4\u207a T-cells are directed against latently expressed US28 and UL111A.", "Taken together, our data show that latency-associated gene products of HCMV generate CD4\u207a T cell responses in vivo, which are able to elicit effector function in response to both lytic and latently infected cells.", "Importantly and in contrast to CD4\u207a T cell populations, which recognise antigens solely expressed during lytic infection, include a subset of cells that secrete the immunosuppressive cytokine cIL-10.", "This suggests that HCMV skews the T cell responses to latency-associated antigens to one that is overall suppressive in order to sustain latent carriage in vivo."], "structured": false}
{"doc_id": 10450725, "title": "Pamidronate induced anti-proliferative, apoptotic, and anti-migratory effects in hepatocellular carcinoma.", "abstract": ["BACKGROUND/AIMS The small GTPase of Ras and Rho families are widely involved in human tumorgenesis and metastasis.", "It has recently been reported that pamidronate inhibits the mevalonate pathway, which is required for the prenylation of the small GTPase.", "We demonstrated a possible beneficial use of pamidronate in the treatment of hepatocellular carcinoma (HCC).   \n", "METHODS The effect of pamidronate on cell proliferation was analyzed with five hepatoma cell lines using MTT assay.", "Apoptosis was evaluated by staining with DAPI and a histon ELISA assay.", "A cell migration assay was performed using the Modified Boyden Chamber.", "To analyze anti-proliferation effect of pamidronate in vivo, tumor volumes were monitored with the intraperitoneal injection of pamidronate after subcutaneous inoculation of PLC/PRF/5 cells into nude mice.   \n", "RESULTS Pamidronate inhibited cell growth for all hepatoma cell lines.", "The amount of membrane associated Ras and phosphorylated extracellular signal-regulated kinase 2 (ERK 2) were reduced after pamidronate treatment.", "Pamidronate increased apoptosis and cleavage of Caspase-3, and -9.", "Pamidronate suppressed membrane associated RhoA and cell motility.", "In vivo, tumor volumes were significantly suppressed by pamidronate at three weeks (P<0.03).   \n", "CONCLUSIONS We conclude that pamidronate has therapeutic potential in inducing anti-proliferative, apoptotic, and anti-migratory effects in HCC."], "structured": true}
{"doc_id": 10463997, "title": "Defective regulation of adipose tissue autophagy in obesity", "abstract": ["Objectives:", "Autophagy is a highly regulated process that has an important role in the control of a wide range of cellular functions, such as organelle recycling, nutrient availability and tissue differentiation.", "A recent study has shown an increased autophagic activity in the adipose tissue of obese subjects, and a role for autophagy in obesity-associated insulin resistance was proposed.", "Body mass reduction is the most efficient approach to tackle insulin resistance in over-weight subjects; however, the impact of weight loss in adipose tissue autophagy is unknown.", "Subjects:Adipose tissue autophagy was evaluated in mice and humans.", "Results:First, a mouse model of diet-induced obesity and diabetes was maintained on a 15-day, 40% caloric restriction.", "At baseline, markers of autophagy were increased in obese mice as compared with lean controls.", "Upon caloric restriction, autophagy increased in the lean mice, whereas it decreased in the obese mice.", "The reintroduction of ad libitum feeding was sufficient to rapidly reduce autophagy in the lean mice and increase autophagy in the obese mice.", "In the second part of the study, autophagy was evaluated in the subcutaneous adipose tissue of nine obese-non-diabetic and six obese-diabetic subjects undergoing bariatric surgery for body mass reduction.", "Specimens were collected during the surgery and approximately 1 year later.", "Markers of systemic inflammation, such as tumor necrosis factor-1\u03b1, interleukin (IL)-6 and IL-1\u03b2 were evaluated.", "As in the mouse model, human obesity was associated with increased autophagy, and body mass reduction led to an attenuation of autophagy in the adipose tissue.", "Conclusion:Obesity and caloric overfeeding are associated with the defective regulation of autophagy in the adipose tissue.", "The studies in obese-diabetic subjects undergoing improved metabolic control following calorie restriction suggest that autophagy and inflammation are regulated independently."], "structured": false}
{"doc_id": 10474873, "title": "Recovery of visual response of injured adult rat optic nerves treated with transglutaminase.", "abstract": ["Failure of axons of the central nervous system in adult mammals to regenerate spontaneously after injury is attributed in part to inhibitory molecules associated with oligodendrocytes.", "Regeneration of central nervous system axons in fish is correlated with the presence of a transglutaminase.", "This enzyme dimerizes interleukin-2, and the product is cytotoxic to oligodendrocytes in vitro.", "Application of this nerve-derived transglutaminase to rat optic nerves, in which the injury had caused the loss of visual evoked potential response to light, promoted the recovery of that response within 6 weeks after injury.", "Transmission electron microscopy analysis revealed the concomitant appearance of axons in the distal stump of the optic nerve."], "structured": false}
{"doc_id": 10482574, "title": "Cell survival during complete nutrient deprivation depends on lipid droplet-fueled \u03b2-oxidation of fatty acids.", "abstract": ["Cells exposed to stress of different origins synthesize triacylglycerols and generate lipid droplets (LD), but the physiological relevance of this response is uncertain.", "Using complete nutrient deprivation of cells in culture as a simple model of stress, we have addressed whether LD biogenesis has a protective role in cells committed to die.", "Complete nutrient deprivation induced the biogenesis of LD in human LN18 glioblastoma and HeLa cells and also in CHO and rat primary astrocytes.", "In all cell types, death was associated with LD depletion and was accelerated by blocking LD biogenesis after pharmacological inhibition of Group IVA phospholipase A2 (cPLA2\u03b1) or down-regulation of ceramide kinase.", "Nutrient deprivation also induced \u03b2-oxidation of fatty acids that was sensitive to cPLA2\u03b1 inhibition, and cell survival in these conditions became strictly dependent on fatty acid catabolism.", "These results show that, during nutrient deprivation, cell viability is sustained by \u03b2-oxidation of fatty acids that requires biogenesis and mobilization of LD."], "structured": false}
{"doc_id": 10485142, "title": "Molecular and cytogenetic changes involved in the immortalization of nasopharyngeal epithelial cells by telomerase.", "abstract": ["Nasopharyngeal carcinoma (NPC) is a common disease in Hong Kong and southern provinces of China.", "EBV infection is believed to play a critical role in the development of NPC.", "Previous studies on the transformation mechanism of EBV genes were mostly performed in either NPC or nonnasopharyngeal epithelial cells which may not be representative of premalignant nasopharyngeal epithelial cells.", "Establishment of a representative cell system would greatly facilitate the elucidation of the role of EBV infection in the development of NPC.", "Using telomerase alone, we were able to establish an immortalized nasopharyngeal epithelial cell line from primary nonmalignant nasopharyngeal biopsies.", "The telomerase-immortalized nasopharyngeal epithelial cells are largely diploid in karyotype.", "Interestingly, this newly immortalized nasopharyngeal epithelial cell line, referred as NP460hTert, harbors genetic alterations previously identified in premalignant and malignant nasopharyngeal epithelial cells.", "These include inactivation of p16 by homozygous deletion of the p16(INK4A) locus and downregulation of RASSF1A expression.", "The deletion of the p16(INK4A) locus appears to be the most crucial event for the immortalization of nasopharyngeal epithelial cells by telomerase and precedes RASSF1A downregulation.", "In addition, detailed analysis of the cytogenetic changes by conventional cytogenetics, spectral karyotyping (SKY) and array-based CGH revealed a gain of a 17q21-q25 fragment on 11p15 chromosome in all NP460hTert cells which occurred before deletion of the p16(INK4A) locus.", "Gain of 17q has been previously reported in NPC.", "In addition, activation of NF-kappaB was observed in immortalized NP460hTert cells at the later population doublings, and may play a role in the survival of immortalized NP epithelial cells.", "Id1 which is commonly expressed in various human cancers, including NPC, was also upregulated in the immortalized NP460hTert cells.", "Thus, the establishment of an immortalized nasopharyngeal epithelial cell line harboring common genetic alterations present in premalignant and cancerous nasopharyngeal epithelial cells may provide a valuable cell system to examine for early events involved in NPC carcinogenesis, particularly in elucidating the role of EBV infection in NPC development."], "structured": false}
{"doc_id": 10486817, "title": "Cellular nucleic acid binding protein suppresses tumor cell metastasis and induces tumor cell death by downregulating heterogeneous ribonucleoprotein K in fibrosarcoma cells.", "abstract": ["BACKGROUND Cellular nucleic acid binding protein (CNBP) has been implicated in vertebrate craniofacial development and in myotonic dystrophy type 2 (DM2) and sporadic inclusion body myositis (sIBM) human diseases by controlling cell proliferation and survival to mediate neural crest expansion.", "CNBP has been found to bind single-stranded nucleic acid and promote rearrangements of nucleic acid secondary structure in an ATP-independent manner, acting as a nucleic acid chaperone.   \n", "METHODS A variety of methods were used, including cell viability assays, wound-scratch assays, chemotaxis assays, invasion assays, circular dichroic (CD) spectroscopy, NMR spectroscopy, chromatin immunoprecipitation, expression and purification of recombinant human CNBP, electrophoretic mobility shift assay (EMSA), surface plasmon resonance (SPR), fluorescence resonance energy transfer (FRET) analyses, luciferase reporter assay, Western blotting, and isothermal titration calorimetry (ITC).   \n", "RESULTS Up-regulation of CNBP induced human fibrosarcoma cell death and suppressed fibrosarcoma cell motility and invasiveness.", "It was found that CNBP transcriptionally down-regulated the expression of heterogeneous ribonucleoprotein K (hnRNP K) through its conversion of a G-rich sequence into G-quadruplex in the promoter of hnRNP K. G-quadruplex stabilizing ligand tetra-(N-methyl-4-pyridyl) porphyrin (TMPyP4) could interact with and stabilize the G-quadruplex, resulting in downregulation of hnRNP K transcription.   \n", "CONCLUSIONS CNBP overexpression caused increase of cell death and suppression of cell metastasis through its induction of G-quadruplex formation in the promoter of hnRNP K resulting in hnRNP K down-regulation.   ", "GENERAL SIGNIFICANCE The present result provided a new solution for controlling hnRNP K expression, which should shed light on new anticancer drug design and development."], "structured": true}
{"doc_id": 10491220, "title": "The DHR96 nuclear receptor regulates xenobiotic responses in Drosophila.", "abstract": ["Exposure to xenobiotics such as plant toxins, pollutants, or prescription drugs triggers a defense response, inducing genes that encode key detoxification enzymes.", "Although xenobiotic responses have been studied in vertebrates, little effort has been made to exploit a simple genetic system for characterizing the molecular basis of this coordinated transcriptional response.", "We show here that approximately 1000 transcripts are significantly affected by phenobarbital treatment in Drosophila.", "We also demonstrate that the Drosophila ortholog of the human SXR and CAR xenobiotic receptors, DHR96, plays a role in this response.", "A DHR96 null mutant displays increased sensitivity to the sedative effects of phenobarbital and the pesticide DDT as well as defects in the expression of many phenobarbital-regulated genes.", "Metabolic and stress-response genes are also controlled by DHR96, implicating its role in coordinating multiple response pathways.", "This work establishes a new model system for defining the genetic control of xenobiotic stress responses."], "structured": false}
{"doc_id": 10494012, "title": "A primate virus generates transformed human cells by fusion", "abstract": ["Amodel that explains both the origin and sporadic nature of cancer argues that cancer cells are a chance result of events that cause genomic and epigenetic variability.", "The prevailing view is that these events are mutations that affect chromosome segregation or stability.", "However, genomic and epigenetic variability is also triggered by cell fusion, which is often caused by viruses.", "Yet, cells fused by viruses are considered harmless because they die.", "We provide evidence that a primate virus uses both viral and exosomal proteins involved in cell fusion to produce transformed proliferating human cells.", "Although normal cells indeed fail to proliferate after fusion, expression of an oncogene or a mutated tumor suppressor p53 in just one of the fusion partners is sufficient to produce heterogeneous progeny.", "We also show that this virus can produce viable oncogenically transformed cells by fusing cells that are otherwise destined to die.", "Therefore, we argue that viruses can contribute to carcinogenesis by fusing cells."], "structured": false}
{"doc_id": 10504681, "title": "TAA1-Mediated Auxin Biosynthesis Is Essential for Hormone Crosstalk and Plant Development", "abstract": ["Plants have evolved a tremendous ability to respond to environmental changes by adapting their growth and development.", "The interaction between hormonal and developmental signals is a critical mechanism in the generation of this enormous plasticity.", "A good example is the response to the hormone ethylene that depends on tissue type, developmental stage, and environmental conditions.", "By characterizing the Arabidopsis wei8 mutant, we have found that a small family of genes mediates tissue-specific responses to ethylene.", "Biochemical studies revealed that WEI8 encodes a long-anticipated tryptophan aminotransferase, TAA1, in the essential, yet genetically uncharacterized, indole-3-pyruvic acid (IPA) branch of the auxin biosynthetic pathway.", "Analysis of TAA1 and its paralogues revealed a link between local auxin production, tissue-specific ethylene effects, and organ development.", "Thus, the IPA route of auxin production is key to generating robust auxin gradients in response to environmental and developmental cues."], "structured": false}
{"doc_id": 10509344, "title": "A research agenda for public health workforce development.", "abstract": ["In the past decades, public health research has focused on categorical rather than cross-cutting or systems issues.", "Little research has been carried out on the infrastructure required to support public health programs.", "This article describes the results of an interactive process to develop a research agenda for public health workforce development to inform all those with stakes in the public health system.", "This research is defined as a multidisciplinary field of inquiry, both basic and applied, that examines the workforce in terms of costs, quality, accessibility, delivery, organization, financing, and outcomes of public health services to increase knowledge and understanding of the relationships among workforce and structure, processes, and effects of public health services.", "A logic model and five priority research areas resulted from meetings of expert panels during 2000 to 2003.", "Innovative public and private partnerships will be required to advance cross-cutting and systems-focused research."], "structured": false}
{"doc_id": 10518721, "title": "Parallel processing in the mammalian retina", "abstract": ["Our eyes send different 'images' of the outside world to the brain \u2014 an image of contours (line drawing), a colour image (watercolour painting) or an image of moving objects (movie).", "This is commonly referred to as parallel processing, and starts as early as the first synapse of the retina, the cone pedicle.", "Here, the molecular composition of the transmitter receptors of the postsynaptic neurons defines which images are transferred to the inner retina.", "Within the second synaptic layer \u2014 the inner plexiform layer \u2014 circuits that involve complex inhibitory and excitatory interactions represent filters that select 'what the eye tells the brain'."], "structured": false}
{"doc_id": 10526279, "title": "Oxymetholone Therapy of Fanconi Anemia Suppresses Osteopontin Transcription and Induces Hematopoietic Stem Cell Cycling", "abstract": ["Androgens are widely used for treating Fanconi anemia (FA) and other human bone marrow failure syndromes, but their mode of action remains incompletely understood.", "Aged Fancd2(-/-) mice were used to assess the therapeutic efficacy of oxymetholone (OXM) and its mechanism of action.", "Eighteen-month-old Fancd2(-/-) mice recapitulated key human FA phenotypes, including reduced bone marrow cellularity, red cell macrocytosis, and peripheral pancytopenia.", "As in humans, chronic OXM treatment significantly improved these hematological parameters and stimulated the proliferation of hematopoietic stem and progenitor cells.", "RNA-Seq analysis implicated downregulation of osteopontin as an important potential mechanism for the drug's action.", "Consistent with the increased stem cell proliferation, competitive repopulation assays demonstrated that chronic OXM therapy eventually resulted in stem cell exhaustion.", "These results expand our knowledge of the regulation of hematopoietic stem cell proliferation and have direct clinical implications for the treatment of bone marrow failure."], "structured": false}
{"doc_id": 10530014, "title": "A point mutation in KINDLIN3 ablates activation of three integrin subfamilies in humans", "abstract": ["Monogenic deficiency diseases provide unique opportunities to define the contributions of individual molecules to human physiology and to identify pathologies arising from their dysfunction.", "Here we describe a deficiency disease in two human siblings that presented with severe bleeding, frequent infections and osteopetrosis at an early age.", "These symptoms are consistent with but more severe than those reported for people with leukocyte adhesion deficiency III (LAD-III).", "Mechanistically, these symptoms arose from an inability to activate the integrins expressed on hematopoietic cells, including platelets and leukocytes.", "Immortalized lymphocyte cell lines isolated from the two individuals showed integrin activation defects.", "Several proteins previously implicated in integrin activation, including Ras-associated protein-1 (RAP1) and calcium and diacylglycerol-regulated guanine nucleotide exchange factor-1 (CALDAG-GEF1), were present and functional in these cell lines.", "The genetic basis for this disease was traced to a point mutation in the coding region of the KINDLIN3 (official gene symbol FERMT3) gene.", "When wild-type KINDLIN-3 was expressed in the immortalized lymphocytes, their integrins became responsive to activation signals.", "These results identify a genetic disease that severely compromises the health of the affected individuals and establish an essential role of KINDLIN-3 in integrin activation in humans.", "Furthermore, allogeneic bone marrow transplantation was shown to alleviate the symptoms of the disease."], "structured": false}
{"doc_id": 10534299, "title": "Fasting Activation of AgRP Neurons Requires NMDA Receptors and Involves Spinogenesis and Increased Excitatory Tone", "abstract": ["AgRP neuron activity drives feeding and weight gain whereas that of nearby POMC neurons does the opposite.", "However, the role of excitatory glutamatergic input in controlling these neurons is unknown.", "To address this question, we generated mice lacking NMDA receptors (NMDARs) on either AgRP or POMC neurons.", "Deletion of NMDARs from AgRP neurons markedly reduced weight, body fat and food intake whereas deletion from POMC neurons had no effect.", "Activation of AgRP neurons by fasting, as assessed by c-Fos, Agrp and Npy mRNA expression, AMPA receptor-mediated EPSCs, depolarization and firing rates, required NMDARs.", "Furthermore, AgRP but not POMC neurons have dendritic spines and increased glutamatergic input onto AgRP neurons caused by fasting was paralleled by an increase in spines, suggesting fasting induced synaptogenesis and spinogenesis.", "Thus glutamatergic synaptic transmission and its modulation by NMDARs play key roles in controlling AgRP neurons and determining the cellular and behavioral response to fasting."], "structured": false}
{"doc_id": 10536636, "title": "Prevalence and Causes of Blindness and Low Vision in Southern Sudan ", "abstract": ["Background Blindness and low vision are thought to be common in southern Sudan.", "However, the magnitude and geographical distribution are largely unknown.", "We aimed to estimate the prevalence of blindness and low vision, identify the main causes of blindness and low vision, and estimate targets for blindness prevention programs in Mankien payam (district), southern Sudan."], "structured": false}
{"doc_id": 10538985, "title": "Origin of nitrite and nitrate in nasal and exhaled breath condensate and relation to nitric oxide formation.", "abstract": ["BACKGROUND Raised concentrations of nitrate and nitrite have been found in exhaled breath condensate (EBC) in airway disease, and it has been postulated that this reflects increased nitric oxide (NO) metabolism.", "However, the chemical and anatomical origin of nitrate and nitrite in the airways has not yet been sufficiently studied.   \n", "METHODS The fraction of exhaled NO at an exhalation flow rate of 50 ml/s (FE(NO)) and nitrite and nitrate in EBC, nasal condensate, and saliva were measured in 17 tracheostomised and 15 non-tracheostomised subjects, all of whom were non-smokers without respiratory disease.", "Tracheal and oral samples were taken from the tracheostomised subjects and nasal (during velum closure) and oral samples from the non-tracheostomised subjects.", "Measurements were performed before and after sodium nitrate ingestion (10 mg/kg) and use of antibacterial mouthwash (chlorhexidine 0.2%).   \n", "RESULTS In tracheostomised subjects oral FE(NO) increased by 90% (p<0.01) while tracheal FE(NO) was not affected 60 minutes after nitrate ingestion.", "Oral EBC nitrite levels were increased 23-fold at 60 minutes (p<0.001) whereas the nitrite levels in tracheal EBC showed only a minor increase (fourfold, p<0.05).", "Nitrate was increased the same amount in oral and tracheal EBC at 60 minutes (2.5-fold, p<0.05).", "In non-tracheostomised subjects oral FE(NO) and EBC nitrite increased after nitrate ingestion and after chlorhexidine mouthwash they approached baseline levels again (p<0.001).", "Nasal NO, nitrate, and nitrite were not affected by nitrate intake or mouthwash.", "At baseline, mouthwash with deionised water did not affect nitrite in oral EBC or saliva, whereas significant reductions were seen after antibacterial mouthwash (p<0.05 and p<0.001, respectively).   \n", "CONCLUSIONS Besides the salivary glands, plasma nitrate is taken up by the lower airways but not the nasal airways.", "Nitrate levels in EBC are thus influenced by dietary intake.", "Nitrate is reduced to nitrite by bacterial activity which takes place primarily in the oropharyngeal tract of healthy subjects.", "Only oropharyngeal nitrite seems to contribute to exhaled NO in non-inflamed airways, and there is also a substantial contribution of nitrite from the oropharyngeal tract during standard collection of EBC."], "structured": true}
{"doc_id": 10542877, "title": "AZD9150, a next-generation antisense oligonucleotide inhibitor of STAT3 with early evidence of clinical activity in lymphoma and lung cancer", "abstract": ["Next-generation sequencing technologies have greatly expanded our understanding of cancer genetics.", "Antisense technology is an attractive platform with the potential to translate these advances into improved cancer therapeutics, because antisense oligonucleotide (ASO) inhibitors can be designed on the basis of gene sequence information alone.", "Recent human clinical data have demonstrated the potent activity of systemically administered ASOs targeted to genes expressed in the liver.", "We describe the preclinical activity and initial clinical evaluation of a class of ASOs containing constrained ethyl modifications for targeting the gene encoding the transcription factor STAT3, a notoriously difficult protein to inhibit therapeutically.", "Systemic delivery of the unformulated ASO, AZD9150, decreased STAT3 expression in a broad range of preclinical cancer models and showed antitumor activity in lymphoma and lung cancer models.", "AZD9150 preclinical activity translated into single-agent antitumor activity in patients with highly treatment-refractory lymphoma and non\u2013small cell lung cancer in a phase 1 dose-escalation study."], "structured": false}
{"doc_id": 10546779, "title": "Evidence of a pluripotent human embryonic stem cell line derived from a cloned blastocyst.", "abstract": ["Somatic cell nuclear transfer (SCNT) technology has recently been used to generate animals with a common genetic composition.", "In this study, we report the derivation of a pluripotent embryonic stem (ES) cell line (SCNT-hES-1) from a cloned human blastocyst.", "The SCNT-hES-1 cells displayed typical ES cell morphology and cell surface markers and were capable of differentiating into embryoid bodies in vitro and of forming teratomas in vivo containing cell derivatives from all three embryonic germ layers in severe combined immunodeficient mice.", "After continuous proliferation for more than 70 passages, SCNT-hES-1 cells maintained normal karyotypes and were genetically identical to the somatic nuclear donor cells.", "Although we cannot completely exclude the possibility that the cells had a parthenogenetic origin, imprinting analyses support a SCNT origin of the derived human ES cells."], "structured": false}
{"doc_id": 10548391, "title": "Ultrarapid drug metabolism: PCR-based detection of CYP2D6 gene duplication.", "abstract": ["The enzyme debrisoquine 4-hydroxylase (CYP2D6), which metabolizes many widely used drugs, is highly polymorphic.", "The activity of the enzyme ranges between subjects from ultrafast to a complete absence.", "Therefore, metabolic capacity varies, producing intersubject differences in therapeutic efficacy and side effects at standard recommended doses.", "Up to 7% of Caucasians may demonstrate ultrarapid drug metabolism (UM) because of inherited alleles with multiplicate functional CYP2D6 genes, causing an increased amount of enzyme to be expressed.", "Identification of UM subjects is of potential clinical importance for adjustment of doses in drug therapy, as well as to avoid misidentification of noncompliance.", "In our study, we tested recently designed PCR assays for the detection of the UM genotype.", "We found a 3.5% prevalence of UMs carrying duplicate active CYP2D6 genes in a population consisting of 202 psychiatric patients."], "structured": false}
{"doc_id": 10555591, "title": "The Actions of Synaptically Released Zinc at Hippocampal Mossy Fiber Synapses", "abstract": ["Zn2+ is present at high concentrations in the synaptic vesicles of hippocampal mossy fibers.", "We have used Zn2+ chelators and the mocha mutant mouse to address the physiological role of Zn2+ in this pathway.", "Zn2+ is not involved in the unique presynaptic plasticities observed at mossy fiber synapses but is coreleased with glutamate from these synapses, both spontaneously and with electrical stimulation, where it exerts a strong modulatory effect on the NMDA receptors.", "Zn2+ tonically occupies the high-affinity binding site of NMDA receptors at mossy fiber synapses, whereas the lower affinity voltage-dependent Zn2+ binding site is occupied during action potential driven-release.", "We conclude that Zn2+ is a modulatory neurotransmitter released from mossy fiber synapses and plays an important role in shaping the NMDA receptor response at these synapses."], "structured": false}
{"doc_id": 10557471, "title": "Association between folate intake from different food sources in Norway and homocysteine status in a dietary intervention among young male adults.", "abstract": ["The aim of the present investigation was to study the effect of a dietary intervention which combined nutrition information with increased availability of vegetables, fruits and wholegrain bread.", "The effect of the intervention was determined by changes in the intake of vegetables, fruits, wholegrain bread and estimated nutrients.", "Furthermore, the study investigated whether changes in relative contribution from different food sources of folate were related to changes in the concentration of plasma total homocysteine (p-tHcy).", "The 5-month intervention study included 376 male recruits from the Norwegian National Guard, Vaernes (intervention group) and 105 male recruits from the Norwegian National Guard, Heggelia (control group).", "The study resulted in an increase in the total consumption of vegetables, fruits, berries and juice (P < 0.001) and of wholegrain bread (P < 0.001).", "The participants in the intervention group showed a higher increase in the intake of dietary fibre (P < 0.001) and folate (P < 0.001) compared with the control group.", "The relative contribution of folate intake from fruits, vegetables and wholegrain bread was higher in the intervention group compared with the control group (P < 0.001 for all).", "The increased intake of folate from wholegrain bread was inversely associated with a reduced concentration of p-tHcy (P = 0.017).", "In summary, the dietary intervention resulted in an increased intake of vegetables, fruits and wholegrain bread and a subsequent increase in folate intake from these food components.", "Reduction in the concentration of p-tHcy was significantly related to an increased folate intake due to an increased consumption of wholegrain bread."], "structured": false}
{"doc_id": 10559501, "title": "Beta interferon controls West Nile virus infection and pathogenesis in mice.", "abstract": ["Studies with mice lacking the common plasma membrane receptor for type I interferon (IFN-\u03b1\u03b2R(-)(/)(-)) have revealed that IFN signaling restricts tropism, dissemination, and lethality after infection with West Nile virus (WNV) or several other pathogenic viruses.", "However, the specific functions of individual IFN subtypes remain uncertain.", "Here, using IFN-\u03b2(-)(/)(-) mice, we defined the antiviral and immunomodulatory function of this IFN subtype in restricting viral infection.", "IFN-\u03b2(-)(/)(-) mice were more vulnerable to WNV infection than wild-type mice, succumbing more quickly and with greater overall mortality, although the phenotype was less severe than that of IFN-\u03b1\u03b2R(-)(/)(-) mice.", "The increased susceptibility of IFN-\u03b2(-)(/)(-) mice was accompanied by enhanced viral replication in different tissues.", "Consistent with a direct role for IFN-\u03b2 in control of WNV replication, viral titers in ex vivo cultures of macrophages, dendritic cells, fibroblasts, and cerebellar granule cell neurons, but not cortical neurons, from IFN-\u03b2(-)(/)(-) mice were greater than in wild-type cells.", "Although detailed immunological analysis revealed no major deficits in the quality or quantity of WNV-specific antibodies or CD8(+) T cells, we observed an altered CD4(+) CD25(+) FoxP3(+) regulatory T cell response, with greater numbers after infection.", "Collectively, these results suggest that IFN-\u03b2 controls WNV pathogenesis by restricting infection in key cell types and by modulating T cell regulatory networks."], "structured": false}
{"doc_id": 10562341, "title": "Frontrunners of T cell activation: Initial, localized Ca2+ signals mediated by NAADP and the type 1 ryanodine receptor", "abstract": ["The activation of T cells is the fundamental on switch for the adaptive immune system.", "Ca2+ signaling is essential for T cell activation and starts as initial, short-lived, localized Ca2+ signals.", "The second messenger nicotinic acid adenine dinucleotide phosphate (NAADP) forms rapidly upon T cell activation and stimulates early Ca2+ signaling.", "We developed a high-resolution imaging technique using multiple fluorescent Ca2+ indicator dyes to characterize these early signaling events and investigate the channels involved in NAADP-dependent Ca2+ signals.", "In the first seconds of activation of either primary murine T cells or human Jurkat cells with beads coated with an antibody against CD3, we detected Ca2+ signals with diameters close to the limit of detection and that were close to the activation site at the plasma membrane.", "In Jurkat cells in which the ryanodine receptor (RyR) was knocked down or in primary T cells from RyR1\u2212/\u2212 mice, either these early Ca2+ signals were not detected or the number of signals was markedly reduced.", "Local Ca2+ signals observed within 20 ms upon microinjection of Jurkat cells with NAADP were also sensitive to RyR knockdown.", "In contrast, TRPM2 (transient receptor potential channel, subtype melastatin 2), a potential NAADP target channel, was not required for the formation of initial Ca2+ signals in primary T cells.", "Thus, through our high-resolution imaging method, we characterized early Ca2+ release events in T cells and obtained evidence for the involvement of RyR and NAADP in such signals."], "structured": false}
{"doc_id": 10574949, "title": "A missense LAMB2 mutation causes congenital nephrotic syndrome by impairing laminin secretion.", "abstract": ["Laminin \u03b22 is a component of laminin-521, which is an important constituent of the glomerular basement membrane (GBM).", "Null mutations in laminin \u03b22 (LAMB2) cause Pierson syndrome, a severe congenital nephrotic syndrome with ocular and neurologic defects.", "In contrast, patients with LAMB2 missense mutations, such as R246Q, can have less severe extrarenal defects but still exhibit congenital nephrotic syndrome.", "To investigate how such missense mutations in LAMB2 cause proteinuria, we generated three transgenic lines of mice in which R246Q-mutant rat laminin \u03b22 replaced the wild-type mouse laminin \u03b22 in the GBM.", "These transgenic mice developed much less severe proteinuria than their nontransgenic Lamb2-deficient littermates; the level of proteinuria correlated inversely with R246Q-LAMB2 expression.", "At the onset of proteinuria, expression and localization of proteins associated with the slit diaphragm and foot processes were normal, and there were no obvious ultrastructural abnormalities.", "Low transgene expressors developed heavy proteinuria, foot process effacement, GBM thickening, and renal failure by 3 months, but high expressors developed only mild proteinuria by 9 months.", "In vitro studies demonstrated that the R246Q mutation results in impaired secretion of laminin.", "Taken together, these results suggest that the R246Q mutation causes nephrotic syndrome by impairing secretion of laminin-521 from podocytes into the GBM; however, increased expression of the mutant protein is able to overcome this secretion defect and improve glomerular permselectivity."], "structured": false}
{"doc_id": 10576136, "title": "Interleukin-33 prevents apoptosis and improves survival after experimental myocardial infarction through ST2 signaling.", "abstract": ["BACKGROUND ST2 is an interleukin (IL)-1 receptor family member with membrane-bound (ST2L) and soluble (sST2) isoforms, and sST2 is a biomarker for poor outcome in patients with myocardial infarction (MI).", "IL-33, the recently discovered ligand for ST2, activates nuclear factor kappaB and thus may regulate apoptotic cell death.", "We tested the hypothesis that IL-33 is cardioprotective after MI through ST2 signaling.   \n", "METHODS AND RESULTS IL-33 protected cultured cardiomyocytes from hypoxia-induced apoptosis, and this cardioprotection was partially inhibited by sST2.", "IL-33 induced expression of the antiapoptotic factors XIAP, cIAP1, and survivin.", "To define the cardioprotective role of IL-33 in vivo, we performed a blinded and randomized study of ischemia/reperfusion in rats.", "IL-33 reduced cardiomyocyte apoptosis, suppressed caspase-3 activity, and increased expression of IAP family member proteins.", "IL-33 decreased both infarct and fibrosis volumes at 15 days; furthermore, both echocardiographic and hemodynamic studies revealed that IL-33 improved ventricular function.", "To determine whether cardioprotection by IL-33 is mediated through ST2 signaling, a randomized and blinded study of ST2(-/-) versus wild-type littermate mice was performed in 98 mice subjected to MI.", "At 4 weeks after MI, IL-33 reduced ventricular dilation and improved contractile function in wild-type mice but not in ST2(-/-) mice.", "Finally, IL-33 improved survival after MI in wild-type but not in ST2(-/-) mice.   \n", "CONCLUSIONS IL-33 prevents cardiomyocyte apoptosis and improves cardiac function and survival after MI through ST2 signaling."], "structured": true}
{"doc_id": 10577574, "title": "The impact of open versus closed format ICU admission practices on the outcome of high risk surgical patients: a cohort analysis", "abstract": ["BACKGROUND In the year 2000, the organizational structure of the ICU in the Zaandam Medical Centre (ZMC) changed from an open to a closed format ICU.", "The objective of this study was to evaluate the effect of this organizational change on outcome in high risk surgical patients.   \n", "METHODS The medical records of all consecutive high risk surgical patients admitted to the ICU from 1996 to 1998 (open format) and from 2003 to 2005 (closed format), were reviewed.", "High-risk patients were defined according to the Identification of Risk in Surgical patients (IRIS) score.", "Parameters studied were: mortality, morbidity, ICU length of stay (LOS) and hospital LOS.   \n", "RESULTS Mortality of ICU patients was 25.7% in the open format group and 15.8% in the closed format group (p = 0.01).", "Morbidity decreased from 48.6% to 46.1% (p = 0.6).", "The average length of hospital stay was 17 days in the open format group, and 21 days in the closed format group (p = 0.03).   \n", "CONCLUSIONS High risk surgical patients in the ICU are patients that have undergone complex and often extensive surgery.", "These patients are in need of specialized treatment and careful monitoring for maximum safety and optimal care.", "Our results suggest that closed format is a more favourable setting than open format to minimize the effects of high risk surgery, and to warrant safe outcome in this patient group."], "structured": true}
{"doc_id": 10582939, "title": "Induction therapy with autologous mesenchymal stem cells in living-related kidney transplants: a randomized controlled trial.", "abstract": ["CONTEXT Antibody-based induction therapy plus calcineurin inhibitors (CNIs) reduce acute rejection rates in kidney recipients; however, opportunistic infections and toxic CNI effects remain challenging.", "Reportedly, mesenchymal stem cells (MSCs) have successfully treated graft-vs-host disease.   \n", "OBJECTIVE To assess autologous MSCs as replacement of antibody induction for patients with end-stage renal disease who undergo ABO-compatible, cross-match-negative kidney transplants from a living-related donor.   \n", "DESIGN, SETTING, AND PATIENTS One hundred fifty-nine patients were enrolled in this single-site, prospective, open-label, randomized study from February 2008-May 2009, when recruitment was completed.   \n", "INTERVENTION Patients were inoculated with marrow-derived autologous MSC (1-2 x 10(6)/kg) at kidney reperfusion and two weeks later.", "Fifty-three patients received standard-dose and 52 patients received low-dose CNIs (80% of standard); 51 patients in the control group received anti-IL-2 receptor antibody plus standard-dose CNIs.   \n", "MAIN OUTCOME MEASURES The primary measure was 1-year incidence of acute rejection and renal function (estimated glomerular filtration rate [eGFR]); the secondary measure was patient and graft survival and incidence of adverse events.   \n", "RESULTS Patient and graft survival at 13 to 30 months was similar in all groups.", "After 6 months, 4 of 53 patients (7.5%) in the autologous MSC plus standard-dose CNI group (95% CI, 0.4%-14.7%; P = .04) and 4 of 52 patients (7.7%) in the low-dose group (95% CI, 0.5%-14.9%; P = .046) compared with 11 of 51 controls (21.6%; 95% CI, 10.5%-32.6%) had biopsy-confirmed acute rejection.", "None of the patients in either autologous MSC group had glucorticoid-resistant rejection, whereas 4 patients (7.8%) in the control group did (95% CI, 0.6%-15.1%; overall P = .02).", "Renal function recovered faster among both MSC groups showing increased eGFR levels during the first month after surgery than the control group.", "Patients receiving standard-dose CNI had a mean difference of 6.2 mL/min per 1.73 m(2) (95% CI, 0.4-11.9; P=.04) and those in the low-dose CNI of 10.0 mL/min per 1.73 m(2) (95% CI, 3.8-16.2; P=.002).", "Also, during the 1-year follow-up, combined analysis of MSC-treated groups revealed significantly decreased risk of opportunistic infections than the control group (hazard ratio, 0.42; 95% CI, 0.20-0.85, P=.02)   CONCLUSION Among patients undergoing renal transplant, the use of autologous MSCs compared with anti-IL-2 receptor antibody induction therapy resulted in lower incidence of acute rejection, decreased risk of opportunistic infection, and better estimated renal function at 1 year.   \n", "TRIAL REGISTRATION clinicaltrials.gov Identifier: NCT00658073."], "structured": true}
{"doc_id": 10605189, "title": "Cerebral cortex assembly: generating and reprogramming projection neuron diversity", "abstract": ["The mammalian cerebral cortex is responsible for the highest levels of associative, cognitive and motor functions.", "In the central nervous system (CNS) the cortex stands as a prime example of extreme neuronal diversity, broadly classified into excitatory projection neurons (PNs) and inhibitory interneurons (INs).", "We review here recent progress made in understanding the strategies and mechanisms that shape PN diversity during embryogenesis, and discuss how PN classes may be maintained, postnatally, for the life of the organism.", "In addition, we consider the intriguing possibility that PNs may be amenable to directed reprogramming of their class-specific features to allow enhanced cortical plasticity in the adult."], "structured": false}
{"doc_id": 10607877, "title": "Mechanical modulation of receptor-ligand interactions at cell-cell interfaces.", "abstract": ["Cell surface receptors have been extensively studied because they initiate and regulate signal transduction cascades leading to a variety of functional cellular outcomes.", "An important class of immune receptors (e.g., T-cell antigen receptors) whose ligands are anchored to the surfaces of other cells remain poorly understood.", "The mechanism by which ligand binding initiates receptor phosphorylation, a process termed \"receptor triggering\", remains controversial.", "Recently, direct measurements of the (two-dimensional) receptor-ligand complex lifetimes at cell-cell interface were found to be smaller than (three-dimensional) lifetimes in solution but the underlying mechanism is unknown.", "At the cell-cell interface, the receptor-ligand complex spans a short intermembrane distance (15 nm) compared to long surface molecules (LSMs) whose ectodomains span >40 nm and these LSMs include phosphatases (e.g., CD45) that dephosphorylate the receptor.", "It has been proposed that size-based segregation of LSMs from a receptor-ligand complex is a mechanism of receptor triggering but it is unclear whether the mechanochemistry supports such small-scale segregation.", "Here we present a nanometer-scale mathematical model that couples membrane elasticity with the compressional stiffness and lateral mobility of LSMs.", "We find robust supradiffusive segregation of LSMs from a single receptor-ligand complex.", "The model predicts that LSM redistribution will result in a time-dependent tension on the complex leading to a decreased two-dimensional lifetime.", "Interestingly, the model predicts a nonlinear relationship between the three- and two-dimensional lifetimes, which can enhance the ability of receptors to discriminate between similar ligands."], "structured": false}
{"doc_id": 10608397, "title": "High-performance neuroprosthetic control by an individual with tetraplegia.", "abstract": ["BACKGROUND Paralysis or amputation of an arm results in the loss of the ability to orient the hand and grasp, manipulate, and carry objects, functions that are essential for activities of daily living.", "Brain-machine interfaces could provide a solution to restoring many of these lost functions.", "We therefore tested whether an individual with tetraplegia could rapidly achieve neurological control of a high-performance prosthetic limb using this type of an interface.   \n", "METHODS We implanted two 96-channel intracortical microelectrodes in the motor cortex of a 52-year-old individual with tetraplegia.", "Brain-machine-interface training was done for 13 weeks with the goal of controlling an anthropomorphic prosthetic limb with seven degrees of freedom (three-dimensional translation, three-dimensional orientation, one-dimensional grasping).", "The participant's ability to control the prosthetic limb was assessed with clinical measures of upper limb function.", "This study is registered with ClinicalTrials.gov, NCT01364480.   \n", "FINDINGS The participant was able to move the prosthetic limb freely in the three-dimensional workspace on the second day of training.", "After 13 weeks, robust seven-dimensional movements were performed routinely.", "Mean success rate on target-based reaching tasks was 91\u00b76% (SD 4\u00b74) versus median chance level 6\u00b72% (95% CI 2\u00b70-15\u00b73).", "Improvements were seen in completion time (decreased from a mean of 148 s [SD 60] to 112 s [6]) and path efficiency (increased from 0\u00b730 [0\u00b704] to 0\u00b738 [0\u00b702]).", "The participant was also able to use the prosthetic limb to do skilful and coordinated reach and grasp movements that resulted in clinically significant gains in tests of upper limb function.", "No adverse events were reported.   \n", "INTERPRETATION With continued development of neuroprosthetic limbs, individuals with long-term paralysis could recover the natural and intuitive command signals for hand placement, orientation, and reaching, allowing them to perform activities of daily living.   \n", "FUNDING Defense Advanced Research Projects Agency, National Institutes of Health, Department of Veterans Affairs, and UPMC Rehabilitation Institute."], "structured": true}
{"doc_id": 10608822, "title": "Phase locking and multiple oscillating attractors for the coupled mammalian clock and cell cycle.", "abstract": ["Daily synchronous rhythms of cell division at the tissue or organism level are observed in many species and suggest that the circadian clock and cell cycle oscillators are coupled.", "For mammals, despite known mechanistic interactions, the effect of such coupling on clock and cell cycle progression, and hence its biological relevance, is not understood.", "In particular, we do not know how the temporal organization of cell division at the single-cell level produces this daily rhythm at the tissue level.", "Here we use multispectral imaging of single live cells, computational methods, and mathematical modeling to address this question in proliferating mouse fibroblasts.", "We show that in unsynchronized cells the cell cycle and circadian clock robustly phase lock each other in a 1:1 fashion so that in an expanding cell population the two oscillators oscillate in a synchronized way with a common frequency.", "Dexamethasone-induced synchronization reveals additional clock states.", "As well as the low-period phase-locked state there are distinct coexisting states with a significantly higher period clock.", "Cells transition to these states after dexamethasone synchronization.", "The temporal coordination of cell division by phase locking to the clock at a single-cell level has significant implications because disordered circadian function is increasingly being linked to the pathogenesis of many diseases, including cancer."], "structured": false}
{"doc_id": 10617916, "title": "Moderate effect of artemisinin-based combination therapy on transmission of Plasmodium falciparum.", "abstract": ["Background.", "Artemisinin-based combination therapy (ACT) reduces microscopically confirmed gametocytemia and mosquito infection.", "However, molecular techniques have recently revealed high prevalences of submicroscopic gametocytemia.", "Our objective here was to determine the effect of sulfadoxine-pyrimethamine (SP) monotherapy and treatment with SP plus amodiaquine (AQ), SP plus artesunate (AS), and artemether-lumefantrine (AL; Coartem) on submicroscopic gametocytemia and infectiousness.", "Methods.", "Kenyan children (n=528) 6 months-10 years of age were randomized to 4 treatment arms.", "Gametocytemia was determined by both microscopy and Pfs25 RNA-based quantitative nucleic acid sequence-based amplification (Pfs25 QT-NASBA).", "Transmission was determined by membrane-feeding assays.", "Results.", "Gametocyte prevalence, as determined by Pfs25 QT-NASBA, was 89.4% (219/245) at enrollment and decreased after treatment with SP plus AS, SP plus AQ, and AL.", "Membrane-feeding assays for a group of randomly selected children revealed that the proportion of infectious children was as much as 4-fold higher than expected when based on microscopy.", "ACT did not significantly reduce the proportion of infectious children but did reduce the proportion of infected mosquitoes.", "Conclusions.", "Submicroscopic gametocytemia is common after treatment and contributes considerably to mosquito infection.", "Our findings should be interpreted in the context of transmission intensity, but the effect of ACT on malaria transmission appears to be moderate and restricted to the duration of gametocyte carriage and the proportion of mosquitoes that are infected by carriers."], "structured": false}
{"doc_id": 10624000, "title": "Lip movements entrain the observers\u2019 low-frequency brain oscillations to facilitate speech intelligibility", "abstract": ["During continuous speech, lip movements provide visual temporal signals that facilitate speech processing.", "Here, using MEG we directly investigated how these visual signals interact with rhythmic brain activity in participants listening to and seeing the speaker.", "First, we investigated coherence between oscillatory brain activity and speaker's lip movements and demonstrated significant entrainment in visual cortex.", "We then used partial coherence to remove contributions of the coherent auditory speech signal from the lip-brain coherence.", "Comparing this synchronization between different attention conditions revealed that attending visual speech enhances the coherence between activity in visual cortex and the speaker's lips.", "Further, we identified a significant partial coherence between left motor cortex and lip movements and this partial coherence directly predicted comprehension accuracy.", "Our results emphasize the importance of visually entrained and attention-modulated rhythmic brain activity for the enhancement of audiovisual speech processing."], "structured": false}
{"doc_id": 10627801, "title": "Loss of DExD/H box RNA helicase LGP2 manifests disparate antiviral responses.", "abstract": ["The DExD/H box RNA helicase retinoic acid-inducible gene I (RIG-I) and the melanoma differentiation-associated gene 5 (MDA5) are key intracellular receptors that recognize virus infection to produce type I IFN.", "A third helicase gene, Lgp2, is homologous to Rig-I and Mda5 but lacks a caspase activation and recruitment domain.", "We generated Lgp2-deficient mice and report that the loss of this gene greatly sensitizes cells to cytosolic polyinosinic/polycytidylic acid-mediated induction of type I IFN.", "However, negative feedback inhibition of IFN-beta transcription was found to be normal in the absence of LGP2, indicating that LGP2 is not the primary negative regulator of type I IFN production.", "Our data further indicate that Lgp2-/- mice exhibited resistance to lethal vesicular stomatitis virus infection, a virus whose replicative RNA intermediates are recognized specifically by RIG-I rather than by MDA5 to trigger the production of type I IFN.", "However, mice lacking LGP2 were observed to exhibit a defect in type I IFN production in response to infection by the encephalomyocarditis virus, the replication of which activates MDA5-dependent innate immune responses.", "Collectively, our data indicate a disparate regulatory role for LGP2 in the triggering of innate immune signaling pathways following RNA virus infection."], "structured": false}
{"doc_id": 10628767, "title": "Three-dimensional, single-molecule fluorescence imaging beyond the diffraction limit by using a double-helix point spread function.", "abstract": ["We demonstrate single-molecule fluorescence imaging beyond the optical diffraction limit in 3 dimensions with a wide-field microscope that exhibits a double-helix point spread function (DH-PSF).", "The DH-PSF design features high and uniform Fisher information and has 2 dominant lobes in the image plane whose angular orientation rotates with the axial (z) position of the emitter.", "Single fluorescent molecules in a thick polymer sample are localized in single 500-ms acquisitions with 10- to 20-nm precision over a large depth of field (2 microm) by finding the center of the 2 DH-PSF lobes.", "By using a photoactivatable fluorophore, repeated imaging of sparse subsets with a DH-PSF microscope provides superresolution imaging of high concentrations of molecules in all 3 dimensions.", "The combination of optical PSF design and digital postprocessing with photoactivatable fluorophores opens up avenues for improving 3D imaging resolution beyond the Rayleigh diffraction limit."], "structured": false}
{"doc_id": 10641162, "title": "A unique cell division machinery in the Archaea.", "abstract": ["In contrast to the cell division machineries of bacteria, euryarchaea, and eukaryotes, no division components have been identified in the second main archaeal phylum, Crenarchaeota.", "Here, we demonstrate that a three-gene operon, cdv, in the crenarchaeon Sulfolobus acidocaldarius, forms part of a unique cell division machinery.", "The operon is induced at the onset of genome segregation and division, and the Cdv proteins then polymerize between segregating nucleoids and persist throughout cell division, forming a successively smaller structure during constriction.", "The cdv operon is dramatically down-regulated after UV irradiation, indicating division inhibition in response to DNA damage, reminiscent of eukaryotic checkpoint systems.", "The cdv genes exhibit a complementary phylogenetic range relative to FtsZ-based archaeal division systems such that, in most archaeal lineages, either one or the other system is present.", "Two of the Cdv proteins, CdvB and CdvC, display homology to components of the eukaryotic ESCRT-III sorting complex involved in budding of luminal vesicles and HIV-1 virion release, suggesting mechanistic similarities and a common evolutionary origin."], "structured": false}
{"doc_id": 10641715, "title": "Modelling and rescuing neurodevelopmental defect of Down syndrome using induced pluripotent stem cells from monozygotic twins discordant for trisomy 21", "abstract": ["Down syndrome (trisomy 21) is the most common viable chromosomal disorder with intellectual impairment and several other developmental abnormalities.", "Here, we report the generation and characterization of induced pluripotent stem cells (iPSCs) derived from monozygotic twins discordant for trisomy 21 in order to eliminate the effects of the variability of genomic background.", "The alterations observed by genetic analysis at the iPSC level and at first approximation in early development illustrate the developmental disease transcriptional signature of Down syndrome.", "Moreover, we observed an abnormal neural differentiation of Down syndrome iPSCs in vivo when formed teratoma in NOD-SCID mice, and in vitro when differentiated into neuroprogenitors and neurons.", "These defects were associated with changes in the architecture and density of neurons, astroglial and oligodendroglial cells together with misexpression of genes involved in neurogenesis, lineage specification and differentiation.", "Furthermore, we provide novel evidence that dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A (DYRK1A) on chromosome 21 likely contributes to these defects.", "Importantly, we found that targeting DYRK1A pharmacologically or by shRNA results in a considerable correction of these defects."], "structured": false}
{"doc_id": 10648422, "title": "Programmed death-1\u2013induced interleukin-10 production by monocytes impairs CD4+ T cell activation during HIV infection", "abstract": ["Viral replication and microbial translocation from the gut to the blood during HIV infection lead to hyperimmune activation, which contributes to the decline in CD4+ T cell numbers during HIV infection.", "Programmed death-1 (PD-1) and interleukin-10 (IL-10) are both upregulated during HIV infection.", "Blocking interactions between PD-1 and programmed death ligand-1 (PD-L1) and between IL-10 and IL-10 receptor (IL-10R) results in viral clearance and improves T cell function in animal models of chronic viral infections.", "Here we show that high amounts of microbial products and inflammatory cytokines in the plasma of HIV-infected subjects lead to upregulation of PD-1 expression on monocytes that correlates with high plasma concentrations of IL-10.", "Triggering of PD-1 expressed on monocytes by PD-L1 expressed on various cell types induced IL-10 production and led to reversible CD4+ T cell dysfunction.", "We describe a new function for PD-1 whereby microbial products inhibit T cell expansion and function by upregulating PD-1 levels and IL-10 production by monocytes after binding of PD-1 by PD-L1."], "structured": false}
{"doc_id": 10650521, "title": "A general role for splicing enhancers in exon definition.", "abstract": ["Exonic splicing enhancers (ESEs) facilitate exon definition by assisting in the recruitment of splicing factors to the adjacent intron.", "Here we demonstrate that suboptimal 5' and 3' splice sites are activated independently by ESEs when they are located on different exons.", "However, when they are situated within a single exon, the same weak 5' and 3' splice sites are activated simultaneously by a single ESE.", "These findings demonstrate that a single ESE promotes the recognition of both exon/intron junctions within the same step during exon definition.", "Our results suggest that ESEs recruit a multicomponent complex that minimally contains components of the splicing machinery required for 5' and 3' splice site selection."], "structured": false}
{"doc_id": 10660080, "title": "SecDFyajC is not required for the maintenance of the proton motive force.", "abstract": ["SecDFyajC of Escherichia coli is required for efficient export of proteins in vivo.", "However, the functional role of SecDFyajC in protein translocation is unclear.", "We evaluated the postulated function of SecDFyajC in the maintenance of the proton motive force.", "As previously reported, inner membrane vesicles (IMVs) lacking SecDFyajC are defective in the generation of a stable proton motive force when energized with succinate.", "This phenomenon is, however, not observed when NADH is used as an electron donor.", "Moreover, the proton motive force generated in SecDFyajC-depleted vesicles stimulated translocation to the same extent as seen with IMVs containing SecDFyajC. Further analysis demonstrates that the reduced proton motive force with succinate in IMVs lacking SecDFyajC is due to a lower amount of the enzyme succinate dehydrogenase.", "The expression of this enzyme complex is repressed by growth on glucose media, the condition used to deplete SecDFyajC.", "These results demonstrate that SecDFyajC is not required for proton motive force-driven protein translocation."], "structured": false}
{"doc_id": 10666475, "title": "The serine protease inhibitor SerpinA3N attenuates neuropathic pain by inhibiting T cell-derived leukocyte elastase", "abstract": ["Neuropathic pain is a major, intractable clinical problem and its pathophysiology is not well understood.", "Although recent gene expression profiling studies have enabled the identification of novel targets for pain therapy, classical study designs provide unclear results owing to the differential expression of hundreds of genes across sham and nerve-injured groups, which can be difficult to validate, particularly with respect to the specificity of pain modulation.", "To circumvent this, we used two outbred lines of rats, which are genetically similar except for being genetically segregated as a result of selective breeding for differences in neuropathic pain hypersensitivity.", "SerpinA3N, a serine protease inhibitor, was upregulated in the dorsal root ganglia (DRG) after nerve injury, which was further validated for its mouse homolog.", "Mice lacking SerpinA3N developed more neuropathic mechanical allodynia than wild-type (WT) mice, and exogenous delivery of SerpinA3N attenuated mechanical allodynia in WT mice.", "T lymphocytes infiltrate the DRG after nerve injury and release leukocyte elastase (LE), which was inhibited by SerpinA3N derived from DRG neurons.", "Genetic loss of LE or exogenous application of a LE inhibitor (Sivelastat) in WT mice attenuated neuropathic mechanical allodynia.", "Overall, we reveal a novel and clinically relevant role for a member of the serpin superfamily and a leukocyte elastase and crosstalk between neurons and T cells in the modulation of neuropathic pain."], "structured": false}
{"doc_id": 10669582, "title": "Tissue Transglutaminase Is an Integrin-Binding Adhesion Coreceptor for Fibronectin", "abstract": ["The protein cross-linking enzyme tissue transglutaminase binds in vitro with high affinity to fibronectin via its 42-kD gelatin-binding domain.", "Here we report that cell surface transglutaminase mediates adhesion and spreading of cells on the 42-kD fibronectin fragment, which lacks integrin-binding motifs.", "Overexpression of tissue transglutaminase increases its amount on the cell surface, enhances adhesion and spreading on fibronectin and its 42-kD fragment, enlarges focal adhesions, and amplifies adhesion-dependent phosphorylation of focal adhesion kinase.", "These effects are specific for tissue transglutaminase and are not shared by its functional homologue, a catalytic subunit of factor XIII.", "Adhesive function of tissue transglutaminase does not require its cross-linking activity but depends on its stable noncovalent association with integrins.", "Transglutaminase interacts directly with multiple integrins of \u03b21 and \u03b23 subfamilies, but not with \u03b22 integrins.", "Complexes of transglutaminase with integrins are formed inside the cell during biosynthesis and accumulate on the surface and in focal adhesions.", "Together our results demonstrate that tissue transglutaminase mediates the interaction of integrins with fibronectin, thereby acting as an integrin-associated coreceptor to promote cell adhesion and spreading."], "structured": false}
{"doc_id": 10669939, "title": "Imaging the expression of transfected genes in vivo.", "abstract": ["Imaging the expression of successful gene transduction has been demonstrated in vivo for the first time by using an appropriate combination of \"marker gene\" and \"marker substrate\" in an experimental animal model.", "The herpes simplex virus 1 thymidine kinase (HSV1-tk) gene was selected as an example of a marker gene, and the recombinant STK retrovirus containing HSV1-tk was used to transduce RG2 glioma cells in vitro and in vivo.", "RG2TK+ cell lines expressing the HSV1-tk gene and three potential marker substrates for the HSV1-TK enzyme were evaluated.", "Radiolabeled 5-iodo-2'-fluoro-2'deoxy-1-beta-D-arabinofuranosyluracil (FIAU) was shown to be a substantially better marker substrate for the HSV1-TK enzyme than 5-iodo-2'-deoxyuridine or ganciclovir.", "The magnitude of FIAU accumulation in different RG2TK+ clones corresponded to their sensitivity to ganciclovir and to the level of HSV1-tk mRNA expression.", "Imaging the expression of HSV1-tk in transduced RG2 tumor cells was demonstrated in animals using quantitative autoradiography; 2-[14C]FIAU accumulation was shown to be high in RG2TK+ brain tumors growing in one hemisphere and very low in nontransduced RG2 tumors in the contralateral hemisphere.", "Transduction of RG2 tumor cells with the HSV-tk gene in vivo resulted in tumors which accumulated FIAU to high levels and produced clearly defined images.", "Given the level of FIAU accumulation in the transduced tumors, it is likely that a clinically applicable method for imaging HSV1-tk gene expression can be implemented using existing clinical imaging techniques."], "structured": false}
{"doc_id": 10670430, "title": "Engulfment of apoptotic cells: signals for a good meal", "abstract": ["The clearance of apoptotic cells by phagocytes is an integral component of normal life, and defects in this process can have significant implications for self tolerance and autoimmunity.", "Recent studies have provided new insights into the engulfment process, including how phagocytes seek apoptotic cells, how they recognize and ingest these targets and how they maintain cellular homeostasis after the 'meal'.", "Several new factors that regulate engulfment have been identified, whereas the roles of some of the older players require revision.", "This Review focuses on these recent developments and attempts to highlight some of the important questions in this field."], "structured": false}
{"doc_id": 10675756, "title": "Related IgA1 and IgG producing cells in blood and diseased mucosa in ulcerative colitis.", "abstract": ["BACKGROUND Ulcerative colitis (UC) is a chronic inflammatory bowel disease in which the colonic mucosa is infiltrated with plasma cells producing IgG autoantibodies.", "It is not known whether this represents a local mucosal response which has switched to IgG or a peripheral response which may have been initiated by peripheral antigen which homed to the colonic mucosa.", "The clonal distribution of IgG secreting cells and isotype switched variants in UC is not known.   ", "AIMS To investigate the clonal distribution of mucosal IgG in UC and to search for related IgG and IgA secreting cells in normal and diseased mucosa and blood in UC.", "To investigate characteristics which may discriminate between the mucosal and peripheral repertoire in the normal mucosa and in UC.   \n", "PATIENTS Blood and normal and diseased mucosa from two patients with UC were studied.   \n", "METHODS Immunoglobulin gene analysis and clone specific polymerase chain reaction were used to study the clonal distribution and characteristics of IgG and related IgA in the mucosa and blood of patients with UC.   \n", "RESULTS The IgG response in the mucosa of UC patients included widespread clones of cells that were present in both the diseased mucosa and blood but that were scarce in normal mucosa.", "Clonally related IgA class switch variants, all IgA1, were detected but also only in the diseased mucosa and blood.", "This suggests that these clones home preferentially to the diseased mucosa.", "We showed that J(H)1 usage was characteristic of the peripheral repertoire, and that examples of J(H)1 usage were observed in mucosal IgG in UC.   \n", "CONCLUSIONS Overall, these data are consistent with a model of UC in which a peripheral response is expressed and expanded in the colonic mucosa."], "structured": true}
{"doc_id": 10692412, "title": "Geovisual analytics to enhance spatial scan statistic interpretation: an analysis of U.S. cervical cancer mortality", "abstract": ["BACKGROUND Kulldorff's spatial scan statistic and its software implementation - SaTScan - are widely used for detecting and evaluating geographic clusters.", "However, two issues make using the method and interpreting its results non-trivial: (1) the method lacks cartographic support for understanding the clusters in geographic context and (2) results from the method are sensitive to parameter choices related to cluster scaling (abbreviated as scaling parameters), but the system provides no direct support for making these choices.", "We employ both established and novel geovisual analytics methods to address these issues and to enhance the interpretation of SaTScan results.", "We demonstrate our geovisual analytics approach in a case study analysis of cervical cancer mortality in the U.S.   RESULTS We address the first issue by providing an interactive visual interface to support the interpretation of SaTScan results.", "Our research to address the second issue prompted a broader discussion about the sensitivity of SaTScan results to parameter choices.", "Sensitivity has two components: (1) the method can identify clusters that, while being statistically significant, have heterogeneous contents comprised of both high-risk and low-risk locations and (2) the method can identify clusters that are unstable in location and size as the spatial scan scaling parameter is varied.", "To investigate cluster result stability, we conducted multiple SaTScan runs with systematically selected parameters.", "The results, when scanning a large spatial dataset (e.g., U.S. data aggregated by county), demonstrate that no single spatial scan scaling value is known to be optimal to identify clusters that exist at different scales; instead, multiple scans that vary the parameters are necessary.", "We introduce a novel method of measuring and visualizing reliability that facilitates identification of homogeneous clusters that are stable across analysis scales.", "Finally, we propose a logical approach to proceed through the analysis of SaTScan results.   \n", "CONCLUSION The geovisual analytics approach described in this manuscript facilitates the interpretation of spatial cluster detection methods by providing cartographic representation of SaTScan results and by providing visualization methods and tools that support selection of SaTScan parameters.", "Our methods distinguish between heterogeneous and homogeneous clusters and assess the stability of clusters across analytic scales.   \n", "METHOD We analyzed the cervical cancer mortality data for the United States aggregated by county between 2000 and 2004.", "We ran SaTScan on the dataset fifty times with different parameter choices.", "Our geovisual analytics approach couples SaTScan with our visual analytic platform, allowing users to interactively explore and compare SaTScan results produced by different parameter choices.", "The Standardized Mortality Ratio and reliability scores are visualized for all the counties to identify stable, homogeneous clusters.", "We evaluated our analysis result by comparing it to that produced by other independent techniques including the Empirical Bayes Smoothing and Kafadar spatial smoother methods.", "The geovisual analytics approach introduced here is developed and implemented in our Java-based Visual Inquiry Toolkit."], "structured": true}
{"doc_id": 10692948, "title": "Neurological development of 5-year-old children receiving a low-saturated fat, low-cholesterol diet since infancy: A randomized controlled trial.", "abstract": ["CONTEXT Early childhood introduction of nutritional habits aimed at atherosclerosis prevention is compatible with normal growth, but its effect on neurological development is unknown.   \n", "OBJECTIVE To analyze how parental counseling aimed at keeping children's diets low in saturated fat and cholesterol influences neurodevelopment during the first 5 years of life.   \n", "DESIGN Randomized controlled trial conducted between February 1990 and November 1996.   \n", "SETTING Outpatient clinic of a university department in Turku, Finland.   \n", "PARTICIPANTS A total of 1062 seven-month-old infants and their parents, recruited at well-baby clinics between 1990 and 1992.", "At age 5 years, 496 children still living in the city of Turku were available to participate in neurodevelopmental testing.   \n", "INTERVENTION Participants were randomly assigned to receive individualized counseling aimed at limiting the child's fat intake to 30% to 35% of daily energy, with a saturated:monounsaturated:polyunsaturated fatty acid ratio of 1:1:1 and a cholesterol intake of less than 200 mg/d (n = 540) or usual health education (control group, n = 522).   \n", "MAIN OUTCOME MEASURES Nutrient intake, serum lipid concentrations, and neurological development at 5 years, among children in the intervention vs control groups.   \n", "RESULTS Absolute and relative intakes of fat, saturated fatty acids, and cholesterol among children in the intervention group were markedly less than the respective values of control children.", "Mean (SD) percentages of daily energy at age 5 years for the intervention vs control groups were as follows: for total fat, 30.6% (4.5%) vs 33.4% (4.4%) (P<. 001); and for saturated fat, 11.7% (2.3%) vs 14.5% (2.4%) (P<.001).", "Mean intakes of cholesterol were 164.2 mg (60.1 mg) and 192.5 mg (71. 9 mg) (P<.001) for the intervention and control groups, respectively.", "Serum cholesterol concentrations were continuously 3% to 5% lower in children in the intervention group than in children in the control group.", "At age 5 years, mean (SD) serum cholesterol concentration of the intervention group was 4.27 (0.63) mmol/L (165 [24] mg/dL) and of the control group, 4.41 (0.74) mmol/L (170 [29] mg/dL) (P =.04).", "Neurological development of children in the intervention group was at least as good as that of children in the control group.", "Relative risks for children in the intervention group to fail tests of speech and language skills, gross motor functioning plus perception, and visual motor skills were 0.95 (90% confidence interval [CI], 0.60-1.49), 0.95 (90% CI, 0.58-1.55), and 0.65 (90% CI, 0.39-1.08), respectively (P =.85,.86, and.16, respectively, vs control children).   \n", "CONCLUSION Our data indicate that repeated child-targeted dietary counseling of parents during the first 5 years of a child's life lessens age-associated increases in children's serum cholesterol and is compatible with normal neurological development.", "JAMA.", "2000;284:993-1000"], "structured": true}
{"doc_id": 10697096, "title": "Vasodilator responses of coronary resistance arteries of exercise-trained pigs.", "abstract": ["BACKGROUND The purpose of this study was to test the hypothesis that vasodilator responses of porcine coronary resistance arteries are increased by exercise training.   \n", "METHODS AND RESULTS Yucatan miniature swine were randomly divided into groups of exercise-trained (ET) and sedentary (SED) control pigs.", "ET pigs were placed on a progressive treadmill training program lasting 16 to 20 weeks, and SED pigs remained inactive during the same time period.", "Coronary resistance arteries 64 to 157 microns in diameter were isolated for in vitro evaluation of relaxation responses to the endothelium-independent dilators sodium nitroprusside (1 x 10(-10) to 1 x 10(-4) mol/L) and adenosine (1 x 10(-10) to 1 x 10(-5) mol/L) and to bradykinin (1 x 10(-13) to 3 x 10(-7) mol/L), an endothelium-dependent agent.", "Relaxation responses to adenosine and sodium nitroprusside were not altered by exercise training.", "Endothelium-dependent relaxation to bradykinin was enhanced in coronary resistance arteries from ET pigs (IC50: ET, 0.07 +/-", "0.02 nmol/L; SED, 1.59 +/-", "0.09 nmol/L).", "To determine whether prostanoids and/or the nitric oxide synthase pathway were involved in the ET-induced changes in bradykinin-induced vasodilation, responses to bradykinin were examined in coronary resistance arteries from both ET and SED pigs in the presence of indomethacin and in the presence of nitro-monomethyl L-arginine (L-NMMA).", "Both indomethacin and L-NMMA produced significant inhibition of the bradykinin-induced relaxation in vessels from both groups.", "Despite decreased bradykinin-induced relaxation after indomethacin, bradykinin-induced vasodilation was still enhanced in vessels from the ET group.", "L-NMMA caused greater inhibition of the bradykinin-induced relaxation in coronary resistance arteries from ET pigs relative to arteries from SED pigs and eliminated the training-induced enhancement of the bradykinin responses.   \n", "CONCLUSIONS These results suggest that exercise training enhances bradykinin-induced vasodilation through increased endothelium-derived relaxing factor/nitric oxide production by the L-arginine/nitric oxide synthase pathway."], "structured": true}
{"doc_id": 10698739, "title": "Modulation of mitochondrial function and morphology by interaction of Omi/HtrA2 with the mitochondrial fusion factor OPA1.", "abstract": ["Loss of Omi/HtrA2 function leads to nerve cell loss in mouse models and has been linked to neurodegeneration in Parkinson's and Huntington's disease.", "Omi/HtrA2 is a serine protease released as a pro-apoptotic factor from the mitochondrial intermembrane space into the cytosol.", "Under physiological conditions, Omi/HtrA2 is thought to be involved in protection against cellular stress, but the cytological and molecular mechanisms are not clear.", "Omi/HtrA2 deficiency caused an accumulation of reactive oxygen species and reduced mitochondrial membrane potential.", "In Omi/HtrA2 knockout mouse embryonic fibroblasts, as well as in Omi/HtrA2 silenced human HeLa cells and Drosophila S2R+ cells, we found elongated mitochondria by live cell imaging.", "Electron microscopy confirmed the mitochondrial morphology alterations and showed abnormal cristae structure.", "Examining the levels of proteins involved in mitochondrial fusion, we found a selective up-regulation of more soluble OPA1 protein.", "Complementation of knockout cells with wild-type Omi/HtrA2 but not with the protease mutant [S306A]Omi/HtrA2 reversed the mitochondrial elongation phenotype and OPA1 alterations.", "Finally, co-immunoprecipitation showed direct interaction of Omi/HtrA2 with endogenous OPA1.", "Thus, we show for the first time a direct effect of loss of Omi/HtrA2 on mitochondrial morphology and demonstrate a novel role of this mitochondrial serine protease in the modulation of OPA1.", "Our results underscore a critical role of impaired mitochondrial dynamics in neurodegenerative disorders."], "structured": false}
{"doc_id": 10699587, "title": "Four prognostic groups predict long-term survival from prostate cancer following radiotherapy alone on Radiation Therapy Oncology Group clinical trials.", "abstract": ["PURPOSE Gleason score (GS), T stage, and pathologic lymph node status have been described as major independent predictors of death due to prostate cancer in men treated with external beam radiotherapy (XRT).", "In this analysis we combine these three factors to define prognostic subgroups that correlate with disease-specific survival (DSS) death from prostate cancer.   \n", "METHODS AND MATERIALS Men entered on one of four Radiation Therapy Oncology Group (RTOG) Phase III randomized trials between 1975 and 1992, for clinically localized prostate cancer (CAP) (n = 1557), were selected for this analysis.", "Patients were included if: 1) they were evaluable, and eligible for the trial; 2) they received no hormonal therapy with their initial treatment; and 3) follow-up was available.", "For this study a DSS event was declared if: 1) death was certified as due to CAP; 2) death was due to complications of treatment; or 3) death was from unknown causes with active malignancy.", "The median follow-up for patients treated on early and late RTOG studies exceeded 11 and 6 years respectively.", "Subgroups were identified based on their pretreatment GS, T-stage, and lymph node such that patients with similar risk of dying from prostate cancer were combined.   \n", "RESULTS By combining patients with similar DSS, four subgroups were identified.", "Risk Group 1 patients had a GS = 2-6, and T1-2Nx; Group 2: GS = 2-6, T3Nx; or GS = 2-6, N+, or GS = 7, T1-2Nx; Group 3: T3Nx, GS = 7; or N+, GS = 7, or T1-2Nx, GS = 8-10; and Group 4 patients were T3Nx, GS = 8-10, or N+, GS = 8-10.", "The 5-, 10-, and 15-year DSS was 96%, 86%, and 72%; 94%, 75%, and 61%; 83%, 62%, and 39%; and 64%, 34%, and 27% for Groups 1 through 4, respectively.   \n", "CONCLUSIONS Recognition of these four risk groups provides a basis for estimating the long-term DSS for men treated with XRT alone and should facilitate the design of future prospective randomized trials."], "structured": true}
{"doc_id": 10703001, "title": "The pathogenesis of bleomycin-induced pulmonary fibrosis in mice.", "abstract": ["Administration of 0.5 mg bleomycin to mice twice weekly for 4 weeks induced pulmonary fibrosis.", "The initial site of injury was the intima of pulmonary arteries and veins where endothelial cells became edematous and were separated from the underlying basement membrane by large blebs.", "These lesions occurred after 2 weeks and were associated with infiltration of perivascular spaces by lymphocytes and plasma cells.", "Capillary endothelial blebbing and interstitial edema were observed after 4 weeks, when multifocal necrosis of type 1 alveolar epithelial cells was accompanied by fibrinous exudation into the alveoli.", "The process of repair was characterized by proliferation and metaplasia of type 2 epithelial cells, fibroblastic organization of alveolar fibrin and fibrosis of the interstitium within 8 to 12 weeks.", "The consistent induction of changes similar to those of diffuse pulmonary fibrosis or fibrosing alveolitis in man suggests that bleomycin-induced injury may provide a suitable model for the investigation of this ill-defined group of diseases."], "structured": false}
{"doc_id": 10704438, "title": "The DNA damage response during mitosis.", "abstract": ["Cells are equipped with a cell-intrinsic signaling network called the DNA damage response (DDR).", "This signaling network recognizes DNA lesions and initiates various downstream pathways to coordinate a cell cycle arrest with the repair of the damaged DNA.", "Alternatively, the DDR can mediate clearance of affected cells that are beyond repair through apoptosis or senescence.", "The DDR can be activated in response to DNA damage throughout the cell cycle, although the extent of DDR signaling is different in each cell cycle phase.", "Especially in response to DNA double strand breaks, only a very marginal response was observed during mitosis.", "Early on it was recognized that cells which are irradiated during mitosis continued division without repairing broken chromosomes.", "Although these initial observations indicated diminished DNA repair and lack of an acute DNA damage-induced cell cycle arrest, insight into the mechanistic re-wiring of DDR signaling during mitosis was only recently provided.", "Different mechanisms appear to be at play to inactivate specific signaling axes of the DDR network in mitosis.", "Importantly, mitotic cells not simply inactivate the entire DDR, but appear to mark their DNA damage for repair after mitotic exit.", "Since the treatment of cancer frequently involves agents that induce DNA damage as well as agents that block mitotic progression, it is clinically relevant to obtain a better understanding of how cancer cells deal with DNA damage during interphase versus mitosis.", "In this review, the molecular details concerning DDR signaling during mitosis as well as the consequences of encountering DNA damage during mitosis for cellular fate are discussed."], "structured": false}
{"doc_id": 10743131, "title": "Model-based Geostatistics", "abstract": ["Geostatistics is concerned with estimation and prediction problems for spatially continuous phenomena, using data obtained at a limited number of spatial locations.", "Model-based geostatistics refers to the application of general statistical principles of modelling and inference to geostatisatical problems.", "This volume is the first book-length treatment of model-based geostatistics."], "structured": false}
{"doc_id": 10749308, "title": "Placebo-Controlled Trials and Active-Control Trials in the Evaluation of New Treatments. Part 1: Ethical and Scientific Issues", "abstract": ["Placebo-controlled trials are used extensively in the development of new pharmaceuticals.", "They are sometimes challenged as unethical in settings in which patients could be treated with an existing therapy (1-7).", "The issues of when placebo controls are ethically acceptable and when they are scientifically necessary are important and worthy of discussion.", "The Ethics of Placebo Controls The Declaration of Helsinki The Declaration of Helsinki (8) is an international document that describes ethical principles for clinical investigation.", "Those who contend that placebo controls are unethical whenever known effective therapy exists for a condition usually cite the following sentence in the Declaration as support for that position: In any medical study, every patientincluding those of a control group, if anyshould be assured of the best proven diagnostic and therapeutic method.", "We believe that an interpretation of this sentence as barring placebo controls whenever an effective treatment exists is untenable.", "First, the requirement that all patients receive the best proven diagnostic and therapeutic method would bar not only placebo-controlled trials but also active-control and historically controlled trials.", "When effective treatment exists, the patient receiving the investigational treatment instead of the established therapy is clearly not getting the best proven treatment.", "Second, it does not seem reasonable to consider as equivalent all failures to use known effective therapy.", "Historically, concerns about placebo use have usually arisen in the context of serious illness.", "There is universal agreement that use of placebo or otherwise untreated controls is almost always unethical when therapy shown to improve survival or decrease serious morbidity is available.", "But in cases in which the treatment does not affect the patient's long-term health, an ethical imperative to use existing therapy is not plausible.", "Can it be, for example, that because topical minoxidil or oral finasteride can grow hair, a placebo-controlled trial of a new remedy for baldness is unethical?", "Is it really unethical to use placebos in short-term studies of drugs for allergic rhinitis, insomnia, anxiety, dermatoses, heartburn, or headaches in fully informed patients?", "We do not believe that there is a reasonable basis for arguing that such studies and many other placebo-controlled studies of symptom relief are unethical and that an informed patient cannot properly be asked to participate in them.", "Third, there is good reason to doubt that the cited phrase was intended to discourage placebo-controlled trials.", "The phrase under discussion was not part of the original 1964 Declaration but was added in 1975 to reinforce the idea that the physicianpatient relationship must be respected just as it would be in a purely therapeutic situation not involving research objectives (8).", "In the explanation accompanying the 1975 change, the issue of placebo-controlled trials was not even mentioned (9).", "The American Medical Association (10), the World Health Organization (11), and the Council for International Organizations of Medical Sciences (12) have rejected the position that the Declaration uniformly bars placebo-controlled trials when proven therapy is available.", "Informed Consent in Placebo-Controlled Trials Patients asked to participate in a placebo-controlled trial must be informed of the existence of any effective therapy, must be able to explore the consequences of deferring such therapy with the investigator, and must provide fully informed consent.", "Concern about whether consent to participate in trials is as informed as we would like to believe is valid, but these concerns apply as much to the patient's decision to forgo known effective treatment and risk exposure to a potentially ineffective or even harmful new agent in an active-control trial as to a decision to accept possible persistence of symptoms in a placebo-controlled trial.", "Thus, this problem is not unique to placebo-controlled trials.", "For the above reasons, we conclude that placebo-controlled trials may be ethically conducted even when effective therapy exists, as long as patients will not be harmed by participation and are fully informed about their alternatives.", "Although in many cases application of this standard will be fairly straightforward, in others it will not, and there may be debate about the consequences of deferring treatment (13).", "Assessment of Effectiveness with Active-Control Trials Clinical trials that, because of deficiencies in study design or conduct, are unlikely to provide scientifically valid and clinically meaningful results raise their own ethical concerns (12, 14).", "The remainder of this paper will address the inability of commonly proposed alternatives to placebo-controlled trials to evaluate the effectiveness of new treatments in many medical settings.", "Active-Control Equivalence Trials (Noninferiority Trials)", "The ability to conduct a placebo-controlled trial ethically in a given situation does not necessarily mean that placebo-controlled trials should be carried out when effective therapy exists.", "Patients and physicians might still prefer a trial in which every participant is given an active treatment.", "What remains to be examined is why placebo-controlled trials (or, more generally, trials intended to show an advantage of one treatment over another) are frequently needed to demonstrate the effectiveness of new treatments and often cannot be replaced by active-control trials showing that a new drug is equivalent or noninferior to a known effective agent.", "The limitations of active-control equivalence trials (ACETs) that are intended to show the effectiveness of a new drug have long been recognized and are well described (15-33) but are perhaps not as widely appreciated as they should be.", "A recent proposed international guideline on choice of control group addresses this issue in detail (33).", "The Fundamental Problem: Need for Assay Sensitivity", "There are two distinct ways to show that a new therapy is effective.", "One can show that the new therapy is superior to a control treatment, or one can show that the new therapy is equivalent to or not worse by some defined amount than a known effective treatment.", "Each method can be valid, but each requires entirely different inferential approaches.", "A well-designed study that shows superiority of a treatment to a control (placebo or active therapy) provides strong evidence of the effectiveness of the new treatment, limited only by the statistical uncertainty of the result.", "No information external to the trial is needed to support the conclusion of effectiveness.", "In contrast, a study that successfully shows equivalencethat is, little difference between a new drug and known active treatmentdoes not by itself demonstrate that the new treatment is effective.", "Equivalence could mean that the treatments were both effective in the study, but it could also mean that both treatments were ineffective in the study.", "To conclude from an ACET that a new treatment is effective on the basis of its similarity to the active control, one must make the critical (and untestable within the study) assumption that the active control had an effect in that particular study.", "In other words, one must assume that if a placebo group had been included, the placebo would have been inferior to the active control (15-33).", "Support for this assumption must come from sources external to the trial.", "Although it might appear reasonable to expect a known active agent to be superior to placebo in any given appropriately designed trial, experience has shown that this is not the case for many types of drugs.", "The ability of a study to distinguish between active and inactive treatments is termed assay sensitivity.", "If assay sensitivity cannot be assumed, then even if the new and standard treatments appear virtually identical and the confidence interval for their comparison is exquisitely narrow, the study cannot demonstrate effectiveness of the new drug.", "(Note that in practice, ACETs are not designed simply to show lack of a statistically significant difference between treatments.", "Rather, such trials are designed to show noninferioritythat the new treatment is not inferior to the control by more than a specified margin.", "This approach is described in the Appendix.)", "The best evidence that an active drug would have an effect superior to that of placebo in a given study would be a series of trials of similar design in which the active drug has reliably outperformed placebo.", "The ACET thus requires information external to the trial (the information about past placebo-controlled studies of the active control) to interpret the results.", "In this respect, an ACET is similar to a historically controlled trial.", "In some settings, such as highly responsive cancers, most infectious diseases, and some cardiovascular conditions, such external information is available and ACETs can and do provide a valid and reliable basis for evaluating new treatments.", "In many cases, however, the historically based assumption of assay sensitivity cannot be made; for many types of effective drugs, studies of apparently adequate size and design do not regularly distinguish drugs from placebo (16-18, 25, 34).", "More than 20 years ago, Lasagna (19) described this difficulty particularly well (reflecting long recognition of the problem among analgesiologists): a comparison between new drug and standard is convincing only when the new remedy is superior to standard treatment.", "If it is inferior, or even indistinguishable from a standard remedy, the results are not readily interpretable.", "In the absence of placebo controls, one does not know if the inferior new medicine has any efficacy at all, and equivalent performance may reflect simply a patient population that cannot distinguish between two active treatments that differ considerably from each other, or between active drug and placebo.", "Certain clinical conditions, such as seri"], "structured": false}
{"doc_id": 10761515, "title": "Breath-methane in patients with cancer of the large bowel.", "abstract": ["In 30 patients with cancer of the large bowel, 24 (80%) had detectable levels of methane in their breath, compared with 25 (39%) of 64 patients with non-malignant large-bowel disease and 83 (40%) of 208 subjects without large-bowel disease.", "These findings suggest that there may be a difference in anaerobic intestinal flora between patients with cancer of the large bowel and those without the disease.", "This difference may antedate the development of the tumour or, alternatively, result from the tumour."], "structured": false}
{"doc_id": 10765888, "title": "Immune cells contribute to the maintenance of neurogenesis and spatial learning abilities in adulthood", "abstract": ["Neurogenesis is known to take place in the adult brain.", "This work identifies T lymphocytes and microglia as being important to the maintenance of hippocampal neurogenesis and spatial learning abilities in adulthood.", "Hippocampal neurogenesis induced by an enriched environment was associated with the recruitment of T cells and the activation of microglia.", "In immune-deficient mice, hippocampal neurogenesis was markedly impaired and could not be enhanced by environmental enrichment, but was restored and boosted by T cells recognizing a specific CNS antigen.", "CNS-specific T cells were also found to be required for spatial learning and memory and for the expression of brain-derived neurotrophic factor in the dentate gyrus, implying that a common immune-associated mechanism underlies different aspects of hippocampal plasticity and cell renewal in the adult brain."], "structured": false}
{"doc_id": 10766688, "title": "Sperm cross-over activity in regions of the human genome showing extreme breakdown of marker association.", "abstract": ["Population diversity data have recently provided profound, albeit inferential, insights into meiotic recombination across the human genome, revealing a landscape dominated by thousands of cross-over hotspots.", "However, very few of these putative hotspots have been directly analyzed for cross-over activity.", "We now describe a search for very active hotspots, by using extreme breakdown of marker association as a guide for high-resolution sperm cross-over analysis.", "This strategy has led to the isolation of the most active cross-over hotspots yet described.", "Their morphology, sequence attributes, and cross-over processes are very similar to those seen at less active hotspots, but their activity in sperm is poorly predicted from population diversity information.", "Several of these hotspots showed evidence for biased gene conversion accompanying cross-over, in some cases associated with variation between men in cross-over activity and with two hotspots showing complete presence/absence polymorphism in different men.", "Hotspot polymorphism is very common at less active hotspots but curiously was not seen at any of the most active hotspots.", "This contrasts with the prediction that extreme hotspots should be the most vulnerable to attenuation by meiotic drive in favor of mutations that suppress recombination and should therefore show rapid rate evolution and thus variation in activity between men.", "Finally, these very intense hotspots provide a valuable resource for dissecting meiotic recombination processes and pathways in humans."], "structured": false}
{"doc_id": 10786948, "title": "An efficient nonviral method to generate integration-free human-induced pluripotent stem cells from cord blood and peripheral blood cells.", "abstract": ["The generation of induced pluripotent stem cells (iPSCs) provides the opportunity to use patient-specific somatic cells, which are a valuable source for disease modeling and drug discovery.", "To promote research involving these cells, it is important to make iPSCs from easily accessible and less invasive tissues, like blood.", "We have recently reported the efficient generation of human iPSCs from adult fibroblasts using a combination of plasmids encoding OCT3/4, SOX2, KLF4, L-MYC, LIN28, and shRNA for TP53.", "We herein report a modified protocol enabling efficient iPSC induction from CD34+ cord blood cells and from peripheral blood isolated from healthy donors using these plasmid vectors.", "The original plasmid mixture could induce iPSCs; however, the efficiency was low.", "The addition of EBNA1, an essential factor for episomal amplification of the vectors, by an extra plasmid greatly increased the efficiency of iPSC induction, especially when the induction was performed from \u03b1\u03b2T cells.", "This improvement enabled the establishment of blood-derived iPSCs from seven healthy donors ranging in age from their 20s to their 60s.", "This induction method will be useful for the derivation of patient-specific integration-free iPSCs and would also be applicable to the generation of clinical-grade iPSCs in the future."], "structured": false}
{"doc_id": 10790846, "title": "A rapamycin-sensitive signaling pathway contributes to long-term synaptic plasticity in the hippocampus.", "abstract": ["Many forms of long-lasting behavioral and synaptic plasticity require the synthesis of new proteins.", "For example, long-term potentiation (LTP) that endures for more than an hour requires both transcription and translation.", "The signal-transduction mechanisms that couple synaptic events to protein translational machinery during long-lasting synaptic plasticity, however, are not well understood.", "One signaling pathway that is stimulated by growth factors and results in the translation of specific mRNAs includes the rapamycin-sensitive kinase mammalian target of rapamycin (mTOR, also known as FRAP and RAFT-1).", "Several components of this translational signaling pathway, including mTOR, eukaryotic initiation factor-4E-binding proteins 1 and 2, and eukaryotic initiation factor-4E, are present in the rat hippocampus as shown by Western blot analysis, and these proteins are detected in the cell bodies and dendrites in the hippocampal slices by immunostaining studies.", "In cultured hippocampal neurons, these proteins are present in dendrites and are often found near the presynaptic protein, synapsin I. At synaptic sites, their distribution completely overlaps with a postsynaptic protein, PSD-95.", "These observations suggest the postsynaptic localization of these proteins.", "Disruption of mTOR signaling by rapamycin results in a reduction of late-phase LTP expression induced by high-frequency stimulation; the early phase of LTP is unaffected.", "Rapamycin also blocks the synaptic potentiation induced by brain-derived neurotrophic factor in hippocampal slices.", "These results demonstrate an essential role for rapamycin-sensitive signaling in the expression of two forms of synaptic plasticity that require new protein synthesis.", "The localization of this translational signaling pathway at postsynaptic sites may provide a mechanism that controls local protein synthesis at potentiated synapses."], "structured": false}
{"doc_id": 10795063, "title": "The FASEB Journal express article 10.1096/fj.00-0815fje. Published online June 27, 2001. Essential role for cholesterol in synaptic plasticity and neuronal degeneration", "abstract": ["SPECIFIC AIMSOur previous studies implied the relation between lipid metabolism and amyloid beta protein (A\u03b2) as \u2018a missing link in Alzheimer\u2019s puzzle\u2019 [FASEB J., vol.", "12, p. 1097 (1998)].", "In the present study, we evaluated the role of cholesterol in synaptic plasticity and neuronal degeneration by a combination of adult rat hippocampal slice technology, a well-established procedure for limited cholesterol efflux, lipid metabolic labeling, extracellular recording of CA1 field excitatory postsynaptic potentials (fEPSPs), and immunofluorescence.", "PRINCIPAL FINDINGS1.", "Increased cholesterol efflux impairs short- and long-term synaptic plasticitySynaptic plasticity is a fundamental feature of the central nervous system (CNS) that allows synapses to \u2018remember\u2019 previous activity and express plastic changes to fine-tune current synaptic action.", "In this study, we asked whether an increased cholesterol efflux induced ex vivo by normal human CSF-HDL3 and methyl-\u03b2-cyclodextrin (M\u03b2CD) (a natural and model cholesterol ac..."], "structured": true}
{"doc_id": 10795340, "title": "Functional inhibition of osteoblastic cells in an in vivo mouse model of myeloid leukemia.", "abstract": ["Pancytopenia is a major cause of morbidity in acute myeloid leukemia (AML), yet its cause is unclear.", "Normal osteoblastic cells have been shown to support hematopoiesis.", "To define the effects of leukemia on osteoblastic cells, we used an immunocompetent murine model of AML.", "Leukemic mice had inhibition of osteoblastic cells, with decreased serum levels of the bone formation marker osteocalcin.", "Osteoprogenitor cells and endosteal-lining osteopontin(+) cells were reduced, and osteocalcin mRNA in CD45(-) marrow cells was diminished.", "This resulted in severe loss of mineralized bone.", "Osteoclasts were only transiently increased without significant increases in bone resorption, and their inhibition only partially rescued leukemia-induced bone loss.", "In vitro data suggested that a leukemia-derived secreted factor inhibited osteoblastic cells.", "Because the chemokine CCL-3 was recently reported to inhibit osteoblastic function in myeloma, we tested its expression in our model and in AML patients.", "Consistent with its potential novel role in leukemic-dependent bone loss, CCL-3 mRNA was significantly increased in malignant marrow cells from leukemic mice and from samples from AML patients.", "Based on these results, we propose that therapeutic mitigation of leukemia-induced uncoupling of osteoblastic and osteoclastic cells may represent a novel approach to promote normal hematopoiesis in patients with myeloid neoplasms."], "structured": false}
{"doc_id": 10812605, "title": "Fibroblast heterogeneity in the cancer wound", "abstract": ["Fibroblasts regulate the structure and function of healthy tissues, participate transiently in tissue repair after acute inflammation, and assume an aberrant stimulatory role during chronic inflammatory states including cancer.", "Such cancer-associated fibroblasts (CAFs) modulate the tumor microenvironment and influence the behavior of neoplastic cells in either a tumor-promoting or tumor-inhibiting manner.", "These pleiotropic functions highlight the inherent plasticity of fibroblasts and may provide new avenues to understand and therapeutically intervene in malignancies.", "We discuss the emerging themes of CAF biology in the context of tumorigenesis and therapy."], "structured": false}
{"doc_id": 10827901, "title": "Cohort profile: the China Health and Retirement Longitudinal Study (CHARLS).", "abstract": ["The China Health and Retirement Longitudinal Study (CHARLS) is a nationally representative longitudinal survey of persons in China 45 years of age or older and their spouses, including assessments of social, economic, and health circumstances of community-residents.", "CHARLS examines health and economic adjustments to rapid ageing of the population in China.", "The national baseline survey for the study was conducted between June 2011 and March 2012 and involved 17 708 respondents.", "CHARLS respondents are followed every 2 years, using a face-to-face computer-assisted personal interview (CAPI).", "Physical measurements are made at every 2-year follow-up, and blood sample collection is done once in every two follow-up periods.", "A pilot survey for CHARLS was conducted in two provinces of China in 2008, on 2685 individuals, who were resurveyed in 2012.", "To ensure the adoption of best practices and international comparability of results, CHARLS was harmonized with leading international research studies in the Health and Retirement Study (HRS) model.", "Requests for collaborations should be directed to Dr Yaohui Zhao (yhzhao@nsd.edu.cn).", "All data in CHARLS are maintained at the National School of Development of Peking University and will be accessible to researchers around the world at the study website.", "The 2008 pilot data for CHARLS are available at: http://charls.ccer.edu.cn/charls/. National baseline data for the study are expected to be released in January 2013."], "structured": false}
{"doc_id": 10831818, "title": "Central role of Th2/Tc2 lymphocytes in pattern II multiple sclerosis lesions", "abstract": ["OBJECTIVE Multiple sclerosis (MS) is a disease of the central nervous system with marked heterogeneity in several aspects including pathological processes.", "Based on infiltrating immune cells, deposition of humoral factors and loss of oligodendrocytes and/or myelin proteins, four lesion patterns have been described.", "Pattern II is characterized by antibody and complement deposition in addition to T-cell infiltration.", "MS is considered a T-cell-mediated disease, but until now the study of pathogenic T cells has encountered major challenges, most importantly the limited access of brain-infiltrating T cells.", "Our objective was to identify, isolate, and characterize brain-infiltrating clonally expanded T cells in pattern II MS lesions.   \n", "METHODS We used next-generation sequencing to identify clonally expanded T cells in demyelinating pattern II brain autopsy lesions, subsequently isolated these as T-cell clones from autologous cerebrospinal fluid and functionally characterized them.   \n", "RESULTS We identified clonally expanded CD8(+) but also CD4(+) T cells in demyelinating pattern II lesions and for the first time were able to isolate these as live T-cell clones.", "The functional characterization shows that T cells releasing Th2 cytokines and able to provide B cell help dominate the T-cell infiltrate in pattern II brain lesions.   \n", "INTERPRETATION Our data provide the first functional evidence for a putative role of Th2/Tc2 cells in pattern II MS supporting the existence of this pathogenic phenotype and questioning the protective role that is generally ascribed to Th2 cells.", "Our observations are important to consider for future treatments of pattern II MS patients."], "structured": true}
{"doc_id": 10846815, "title": "Coordinated oscillations in cortical actin and Ca2+ correlate with cycles of vesicle secretion", "abstract": ["The actin cortex both facilitates and hinders the exocytosis of secretory granules.", "How cells consolidate these two opposing roles was not well understood.", "Here we show that antigen activation of mast cells induces oscillations in Ca(2+) and PtdIns(4,5)P(2) lipid levels that in turn drive cyclic recruitment of N-WASP and cortical actin level oscillations.", "Experimental and computational analysis argues that vesicle fusion correlates with the observed actin and Ca(2+) level oscillations.", "A vesicle secretion cycle starts with the capture of vesicles by actin when cortical F-actin levels are high, followed by vesicle passage through the cortex when F-actin levels are low, and vesicle fusion with the plasma membrane when Ca(2+) levels subsequently increase.", "Thus, cells employ oscillating levels of Ca(2+), PtdIns(4,5)P(2) and cortical F-actin to increase secretion efficiency, explaining how the actin cortex can function as a carrier as well as barrier for vesicle secretion."], "structured": false}
{"doc_id": 10852047, "title": "WK175, a novel antitumor agent, decreases the intracellular nicotinamide adenine dinucleotide concentration and induces the apoptotic cascade in human leukemia cells.", "abstract": ["We recently developed a class of novel antitumor agents that elicit a potent growth-inhibitory response in many tumor cells cultured in vitro.", "WK175, a member of this class, was chosen as a model compound that showed strong in vitro efficacy.", "WK175 interferes with the intracellular steady-state level of NAD(+), resulting in a decreased cellular NAD(+) concentration.", "We found that WK175 induces apoptotic cell death without any DNA-damaging effect.", "The apoptotic death signaling pathway initiated by WK175 was examined in detail: mitochondrial membrane potential, cytochrome c release, caspase 3 activation, caspase 3 and poly(ADP-ribose) polymerase cleavage, and the appearance of a sub-G(1) cell cycle population were determined in time course studies in THP-1 (a human monocytic leukemia cell line) cells.", "We found activation of this cascade after 24 h of treatment with 10 nM WK175.", "Induction of apoptosis was prevented by bongkrekic acid, Z-Asp-Glu-Val-Asp-fluoromethylketone, and Z-Leu-Glu-His-Asp-fluoromethylketone, inhibitors of the mitochondrial permeability transition and of caspase 3 and 9, respectively, but not by Ac-Tyr-Val-Ala-Asp-CHO, a specific caspase 1 inhibitor, suggesting the involvement of the permeability transition pore, caspase 3, and caspase 9 in the WK175-induced apoptotic cascade.", "These results imply that decreased NAD(+) concentration initiates the apoptotic cascade, resulting in the antitumor effect of WK175."], "structured": false}
{"doc_id": 10854174, "title": "Husbands' involvement in delivery care utilization in rural Bangladesh: A qualitative study", "abstract": ["BACKGROUND A primary cause of high maternal mortality in Bangladesh is lack of access to professional delivery care.", "Examining the role of the family, particularly the husband, during pregnancy and childbirth is important to understanding women's access to and utilization of professional maternal health services that can prevent maternal mortality.", "This qualitative study examines husbands' involvement during childbirth and professional delivery care utilization in a rural sub-district of Netrokona district, Bangladesh.   \n", "METHODS Using purposive sampling, ten households utilizing a skilled attendant during the birth of the youngest child were selected and matched with ten households utilizing an untrained traditional birth attendant, or dhatri.", "Households were selected based on a set of inclusion criteria, such as approximate household income, ethnicity, and distance to the nearest hospital.", "Twenty semi-structured interviews were conducted in Bangla with husbands in these households in June 2010.", "Interviews were transcribed, translated into English, and analyzed using NVivo 9.0.   \n", "RESULTS By purposefully selecting households that differed on the type of provider utilized during delivery, common themes--high costs, poor transportation, and long distances to health facilities--were eliminated as sufficient barriers to the utilization of professional delivery care.", "Divergent themes, namely husbands' social support and perceived social norms, were identified as underlying factors associated with delivery care utilization.", "We found that husbands whose wives utilized professional delivery care provided emotional, instrumental and informational support to their wives during delivery and believed that medical intervention was necessary.", "By contrast, husbands whose wives utilized an untrained dhatri at home were uninvolved during delivery and believed childbirth should take place at home according to local traditions.   \n", "CONCLUSIONS This study provides novel evidence about male involvement during childbirth in rural Bangladesh.", "These findings have important implications for program planners, who should pursue culturally sensitive ways to involve husbands in maternal health interventions and assess the effectiveness of education strategies targeted at husbands."], "structured": true}
{"doc_id": 10874408, "title": "Mapping Meiotic Single-Strand DNA Reveals a New Landscape of DNA Double-Strand Breaks in Saccharomyces cerevisiae", "abstract": ["DNA double-strand breaks (DSBs), which are formed by the Spo11 protein, initiate meiotic recombination.", "Previous DSB-mapping studies have used rad50S or sae2\u0394 mutants, which are defective in break processing, to accumulate Spo11-linked DSBs, and report large (\u2265 50 kb) \u201cDSB-hot\u201d regions that are separated by \u201cDSB-cold\u201d domains of similar size.", "Substantial recombination occurs in some DSB-cold regions, suggesting that DSB patterns are not normal in rad50S or sae2\u0394 mutants.", "We therefore developed a novel method to map genome-wide, single-strand DNA (ssDNA)\u2013associated DSBs that accumulate in processing-capable, repair-defective dmc1\u0394 and dmc1\u0394 rad51\u0394 mutants.", "DSBs were observed at known hot spots, but also in most previously identified \u201cDSB-cold\u201d regions, including near centromeres and telomeres.", "Although approximately 40% of the genome is DSB-cold in rad50S mutants, analysis of meiotic ssDNA from dmc1\u0394 shows that most of these regions have substantial DSB activity.", "Southern blot assays of DSBs in selected regions in dmc1\u0394, rad50S, and wild-type cells confirm these findings.", "Thus, DSBs are distributed much more uniformly than was previously believed.", "Comparisons of DSB signals in dmc1, dmc1 rad51, and dmc1 spo11 mutant strains identify Dmc1 as a critical strand-exchange activity genome-wide, and confirm previous conclusions that Spo11-induced lesions initiate all meiotic recombination."], "structured": false}
{"doc_id": 10883736, "title": "Alterations in liver ATP homeostasis in human nonalcoholic steatohepatitis: a pilot study.", "abstract": ["CONTEXT The mechanisms that drive progression from fatty liver to steatohepatitis and cirrhosis are unknown.", "In animal models, obese mice with fatty livers are vulnerable to liver adenosine triphosphate (ATP) depletion and necrosis, suggesting that altered hepatic energy homeostasis may be involved.   \n", "OBJECTIVE To determine if patients with fatty liver disease exhibit impaired recovery from hepatic ATP depletion.   \n", "DESIGN Laboratory analysis of liver ATP stores monitored by nuclear magnetic resonance spectroscopy before and after transient hepatic ATP depletion was induced by fructose injection.", "The study was conducted between July 15 and August 30, 1998.   \n", "SETTING University hospital.   \n", "PATIENTS Eight consecutive adults with biopsy-proven nonalcoholic steatohepatitis and 7 healthy age- and sex-matched controls.   \n", "MAIN OUTCOME MEASURE Level of ATP 1 hour after fructose infusion in patients vs controls.   \n", "RESULTS In patients, serum aminotransferase levels were increased (P = .02 vs controls); albumin and bilirubin values were normal and clinical evidence of portal hypertension was absent in both groups.", "However, 2 patients had moderate fibrosis and 1 had cirrhosis on liver biopsy.", "Mean serum glucose, cholesterol, and triglyceride levels were similar between groups but patients weighed significantly more than controls (P = .02).", "Liver ATP levels were similar in the 2 groups before fructose infusion and decreased similarly in both after fructose infusion (P = .01 vs initial ATP levels).", "However, controls replenished their hepatic ATP stores during the 1-hour follow-up period (P<.02 vs minimum ATP) but patients did not.", "Hence, patients' hepatic ATP levels were lower than those of controls at the end of the study (P = .04).", "Body mass index (BMI) correlated inversely with ATP recovery, even in controls (R = -0.768; P = .07).", "Although BMI was greater in patients than controls (P = .02) and correlated strongly with fatty liver and serum aminotransferase elevations, neither of the latter 2 parameters nor the histologic severity of fibrosis strongly predicted hepatic ATP recovery.   \n", "CONCLUSIONS These data suggest that recovery from hepatic ATP depletion becomes progressively less efficient as body mass increases in healthy controls and is severely impaired in patients with obesity-related nonalcoholic steatohepatitis."], "structured": true}
{"doc_id": 10889845, "title": "Blockade of class IB phosphoinositide-3 kinase ameliorates obesity-induced inflammation and insulin resistance.", "abstract": ["Obesity and insulin resistance, the key features of metabolic syndrome, are closely associated with a state of chronic, low-grade inflammation characterized by abnormal macrophage infiltration into adipose tissues.", "Although it has been reported that chemokines promote leukocyte migration by activating class IB phosphoinositide-3 kinase (PI3K\u03b3) in inflammatory states, little is known about the role of PI3K\u03b3 in obesity-induced macrophage infiltration into tissues, systemic inflammation, and the development of insulin resistance.", "In the present study, we used murine models of both diet-induced and genetically induced obesity to examine the role of PI3K\u03b3 in the accumulation of tissue macrophages and the development of obesity-induced insulin resistance.", "Mice lacking p110\u03b3 (Pik3cg(-/-)), the catalytic subunit of PI3K\u03b3, exhibited improved systemic insulin sensitivity with enhanced insulin signaling in the tissues of obese animals.", "In adipose tissues and livers of obese Pik3cg(-/-) mice, the numbers of infiltrated proinflammatory macrophages were markedly reduced, leading to suppression of inflammatory reactions in these tissues.", "Furthermore, bone marrow-specific deletion and pharmacological blockade of PI3K\u03b3 also ameliorated obesity-induced macrophage infiltration and insulin resistance.", "These data suggest that PI3K\u03b3 plays a crucial role in the development of both obesity-induced inflammation and systemic insulin resistance and that PI3K\u03b3 can be a therapeutic target for type 2 diabetes."], "structured": false}
{"doc_id": 10893238, "title": "Identifying common impairments in frail and dependent older people: validation of the COPE assessment for non-specialised health workers in low resource primary health care settings", "abstract": ["BACKGROUND Frail and dependent older people in resource-poor settings are poorly served by health systems that lack outreach capacity.", "The COPE (Caring for Older PEople) multidimensional assessment tool is designed to help community health workers (CHWs) identify clinically significant impairments and deliver evidence-based interventions   METHODS Older people (n = 150) identified by CHWs as frail or dependent, were assessed at home by the CHW using the structured COPE assessment tool, generating information on impairments in nutrition, mobility, vision, hearing, continence, cognition, mood and behaviour.", "The older people were reassessed by local physicians who reached a clinical judgment regarding the presence or absence of the same impairments based upon clinical examination guided by the EASY-Care assessment tool.   \n", "RESULTS The COPE tool was considered easy to administer, and gave CHWs a sense of empowerment to understand and act upon the needs of older people.", "Agreement between COPE assessment by CHW and clinician assessors was modest (ranged from 45.8 to 91.3 %) for most impairments.", "However, the prevalence of impairments was generally higher according to clinicians, particularly for visual impairment (98.7 vs 45.8 %), cognitive impairment (78.4 vs. 38.2 %) and depression (82.0 vs. 59.9 %).", "Most cases identified by WHO-COPE were clinician confirmed (positive predictive values - 72.2 to 98.5 %), and levels of disability and needs for care among those identified by COPE were higher than those additionally identified by the clinician alone.   \n", "CONCLUSIONS The COPE is a feasible tool for the identification of specific impairments in frail dependent older people in the community.", "Those identified are likely to be confirmed as having clinically relevant problems by clinicians working in the same service, and the COPE may be particularly effective at targeting attention upon those with the most substantial unmet needs."], "structured": true}
{"doc_id": 10906636, "title": "The carboxyl terminus of human cytomegalovirus-encoded 7 transmembrane receptor US28 camouflages agonism by mediating constitutive endocytosis.", "abstract": ["US28 is one of four 7 transmembrane (7TM) chemokine receptors encoded by human cytomegalovirus and has been shown to both signal and endocytose in a ligand-independent, constitutively active manner.", "Here we show that the constitutive activity and constitutive endocytosis properties of US28 are separable entities in this viral chemokine receptor.", "We generated chimeric and mutant US28 proteins that were altered in either their constitutive endocytic (US28 Delta 300, US28 Delta 317, US28-NK1-ctail, and US28-ORF74-ctail) or signaling properties (US28R129A).", "By using this series of mutants, we show that the cytoplasmic tail domain of US28 per se regulates receptor endocytosis, independent of the signaling ability of the core domain of US28.", "The constitutive endocytic property of the US28 c-tail was transposable to other 7TM receptors, the herpes virus 8-encoded ORF74 and the tachykinin NK1 receptor (ORF74-US28-ctail and NK1-US28-ctail).", "Deletion of the US28 C terminus resulted in reduced constitutive endocytosis and consequently enhanced signaling capacity of all receptors tested as assessed by inositol phosphate turnover, NF-kappa B, and cAMP-responsive element-binding protein transcription assays.", "We further show that the constitutive endocytic property of US28 affects the action of its chemokine ligand fractalkine/CX3CL1 and show that in the absence of the US28 C terminus, fractalkine/CX3CL1 acts as an agonist on US28.", "This demonstrates for the first time that the endocytic properties of a 7TM receptor can camouflage the agonist properties of a ligand."], "structured": false}
{"doc_id": 10931595, "title": "Geometry, epistasis, and developmental patterning.", "abstract": ["Developmental signaling networks are composed of dozens of components whose interactions are very difficult to quantify in an embryo.", "Geometric reasoning enumerates a discrete hierarchy of phenotypic models with a few composite variables whose parameters may be defined by in vivo data.", "Vulval development in the nematode Caenorhabditis elegans is a classic model for the integration of two signaling pathways; induction by EGF and lateral signaling through Notch.", "Existing data for the relative probabilities of the three possible terminal cell types in diverse genetic backgrounds as well as timed ablation of the inductive signal favor one geometric model and suffice to fit most of its parameters.", "The model is fully dynamic and encompasses both signaling and commitment.", "It then predicts the correlated cell fate probabilities for a cross between any two backgrounds/conditions.", "The two signaling pathways are combined additively, without interactions, and epistasis only arises from the nonlinear dynamical flow in the landscape defined by the geometric model.", "In this way, the model quantitatively fits genetic experiments purporting to show mutual pathway repression.", "The model quantifies the contributions of extrinsic vs. intrinsic sources of noise in the penetrance of mutant phenotypes in signaling hypomorphs and explains available experiments with no additional parameters.", "Data for anchor cell ablation fix the parameters needed to define Notch autocrine signaling."], "structured": false}
{"doc_id": 10937190, "title": "Table of Contents", "abstract": ["The morphogenesis of the C. elegans embryo is largely controlled by the development of the epidermis, also known as the hypodermis, a single epithelial layer that surrounds the animal.", "Morphogenesis of the epidermis involves cell-cell interactions with internal tissues, such as the developing nervous system and musculature.", "Genetic analysis of mutants with aberrant epidermal morphology has defined multiple steps in epidermal morphogenesis.", "In the wild type, epidermal cells are generated on the dorsal side of the embryo among the progeny of four early embryonic blastomeres.", "Specification of epidermal fate is regulated by a hierarchy of transcription factors.", "After specification, dorsal epidermal cells rearrange, a process known as dorsal intercalation.", "Most epidermal cells fuse to generate multinucleate syncytia.", "The dorsally located epidermal sheet undergoes epiboly to enclose the rest of the embryo in a process known as ventral enclosure; this movement requires both an intact epidermal layer and substrate neuroblasts.", "At least three distinct types of cellular behavior underlie the enclosure of different regions of the epidermis.", "Following enclosure, the epidermis elongates, a process driven by coordinated cell shape changes.", "Epidermal actin microfilaments, microtubules, and intermediate filaments all play roles in elongation, as do body wall muscles.", "The final shape of the epidermis is maintained by the collagenous exoskeleton, secreted by the apical surface of the epidermis."], "structured": false}
{"doc_id": 10944947, "title": "High-throughput sequencing reveals extensive variation in human-specific L1 content in individual human genomes.", "abstract": ["Using high-throughput sequencing, we devised a technique to determine the insertion sites of virtually all members of the human-specific L1 retrotransposon family in any human genome.", "Using diagnostic nucleotides, we were able to locate the approximately 800 L1Hs copies corresponding specifically to the pre-Ta, Ta-0, and Ta-1 L1Hs subfamilies, with over 90% of sequenced reads corresponding to human-specific elements.", "We find that any two individual genomes differ at an average of 285 sites with respect to L1 insertion presence or absence.", "In total, we assayed 25 individuals, 15 of which are unrelated, at 1139 sites, including 772 shared with the reference genome and 367 nonreference L1 insertions.", "We show that L1Hs profiles recapitulate genetic ancestry, and determine the chromosomal distribution of these elements.", "Using these data, we estimate that the rate of L1 retrotransposition in humans is between 1/95 and 1/270 births, and the number of dimorphic L1 elements in the human population with gene frequencies greater than 0.05 is between 3000 and 10,000."], "structured": false}
{"doc_id": 10958594, "title": "Nationwide trends in incidence, treatment and survival of colorectal cancer patients with synchronous metastases", "abstract": ["The aim of this study was to determine trends in incidence, treatment and survival of colorectal cancer (CRC) patients with synchronous metastases (Stage IV) in the Netherlands.", "This nationwide population-based study included 160,278 patients diagnosed with CRC between 1996 and 2011.", "We evaluated changes in stage distribution, location of synchronous metastases and treatment in four consecutive periods, using Chi square tests for trend.", "Median survival in months was determined, using Kaplan\u2013Meier analysis.", "The proportion of Stage IV CRC patients (n = 33,421) increased from 19 % (1996\u20131999) to 23 % (2008\u20132011, p < 0.001).", "This was predominantly due to a major increase in the incidence of lung metastases (1.7\u20135.0 % of all CRC patients).", "During the study period, the primary tumor was resected less often in Stage IV patients (65\u201346 %) and the use of systemic treatment has increased (29\u201360 %).", "Also an increase in metastasectomy was found in patients with one metastatic site, especially in patients with liver-only disease (5\u201318 %, p < 0.001).", "Median survival of all Stage IV CRC patients increased from 7 to 12 months.", "Especially in patients with metastases confined to the liver or lungs this improvement in survival was apparent (9\u201316 and 12\u201324 months respectively, both p < 0.001).", "In the last two decades, more lung metastases were detected and an increasing proportion of Stage IV CRC patients was treated with systemic therapy and/or metastasectomy.", "Survival of patients has significantly improved.", "However, the prognosis of Stage IV patients becomes increasingly diverse."], "structured": false}
{"doc_id": 10976596, "title": "The curious case of the tumour virus: 50 years of Burkitt's lymphoma", "abstract": ["Burkitt's lymphoma (BL) was first described 50 years ago, and the first human tumour virus Epstein\u2013Barr virus (EBV) was discovered in BL tumours soon after.", "Since then, the role of EBV in the development of BL has become more and more enigmatic.", "Only recently have we finally begun to understand, at the cellular and molecular levels, the complex and interesting interaction of EBV with B cells that creates a predisposition for the development of BL.", "Here, we discuss the intertwined histories of EBV and BL and their relationship to the cofactors in BL pathogenesis: malaria and the MYC translocation."], "structured": false}
{"doc_id": 10982689, "title": "Nanotoxicology: An Emerging Discipline Evolving from Studies of Ultrafine Particles", "abstract": ["Although humans have been exposed to airborne nanosized particles (NSPs; < 100 nm) throughout their evolutionary stages, such exposure has increased dramatically over the last century due to anthropogenic sources.", "The rapidly developing field of nanotechnology is likely to become yet another source through inhalation, ingestion, skin uptake, and injection of engineered nanomaterials.", "Information about safety and potential hazards is urgently needed.", "Results of older biokinetic studies with NSPs and newer epidemiologic and toxicologic studies with airborne ultrafine particles can be viewed as the basis for the expanding field of nanotoxicology, which can be defined as safety evaluation of engineered nanostructures and nanodevices.", "Collectively, some emerging concepts of nanotoxicology can be identified from the results of these studies.", "When inhaled, specific sizes of NSPs are efficiently deposited by diffusional mechanisms in all regions of the respiratory tract.", "The small size facilitates uptake into cells and transcytosis across epithelial and endothelial cells into the blood and lymph circulation to reach potentially sensitive target sites such as bone marrow, lymph nodes, spleen, and heart.", "Access to the central nervous system and ganglia via translocation along axons and dendrites of neurons has also been observed.", "NSPs penetrating the skin distribute via uptake into lymphatic channels.", "Endocytosis and biokinetics are largely dependent on NSP surface chemistry (coating) and in vivo surface modifications.", "The greater surface area per mass compared with larger-sized particles of the same chemistry renders NSPs more active biologically.", "This activity includes a potential for inflammatory and pro-oxidant, but also antioxidant, activity, which can explain early findings showing mixed results in terms of toxicity of NSPs to environmentally relevant species.", "Evidence of mitochondrial distribution and oxidative stress response after NSP endocytosis points to a need for basic research on their interactions with subcellular structures.", "Additional considerations for assessing safety of engineered NSPs include careful selections of appropriate and relevant doses/concentrations, the likelihood of increased effects in a compromised organism, and also the benefits of possible desirable effects.", "An interdisciplinary team approach (e.g., toxicology, materials science, medicine, molecular biology, and bioinformatics, to name a few) is mandatory for nanotoxicology research to arrive at an appropriate risk assessment."], "structured": false}
{"doc_id": 10984005, "title": "ADHD medications and risk of serious cardiovascular events in young and middle-aged adults.", "abstract": ["CONTEXT More than 1.5 million US adults use stimulants and other medications labeled for treatment of attention-deficit/hyperactivity disorder (ADHD).", "These agents can increase heart rate and blood pressure, raising concerns about their cardiovascular safety.   \n", "OBJECTIVE To examine whether current use of medications prescribed primarily to treat ADHD is associated with increased risk of serious cardiovascular events in young and middle-aged adults.   \n", "DESIGN, SETTING, AND PARTICIPANTS Retrospective, population-based cohort study using electronic health care records from 4 study sites (OptumInsight Epidemiology, Tennessee Medicaid, Kaiser Permanente California, and the HMO Research Network), starting in 1986 at 1 site and ending in 2005 at all sites, with additional covariate assessment using 2007 survey data.", "Participants were adults aged 25 through 64 years with dispensed prescriptions for methylphenidate, amphetamine, or atomoxetine at baseline.", "Each medication user (n = 150,359) was matched to 2 nonusers on study site, birth year, sex, and calendar year (443,198 total users and nonusers).   \n", "MAIN OUTCOME MEASURES Serious cardiovascular events, including myocardial infarction (MI), sudden cardiac death (SCD), or stroke, with comparison between current or new users and remote users to account for potential healthy-user bias.   \n", "RESULTS During 806,182 person-years of follow-up (median, 1.3 years per person), 1357 cases of MI, 296 cases of SCD, and 575 cases of stroke occurred.", "There were 107,322 person-years of current use (median, 0.33 years), with a crude incidence per 1000 person-years of 1.34 (95% CI, 1.14-1.57) for MI, 0.30 (95% CI, 0.20-0.42) for SCD, and 0.56 (95% CI, 0.43-0.72) for stroke.", "The multivariable-adjusted rate ratio (RR) of serious cardiovascular events for current use vs nonuse of ADHD medications was 0.83 (95% CI, 0.72-0.96).", "Among new users of ADHD medications, the adjusted RR was 0.77 (95% CI, 0.63-0.94).", "The adjusted RR for current use vs remote use was 1.03 (95% CI, 0.86-1.24); for new use vs remote use, the adjusted RR was 1.02 (95% CI, 0.82-1.28); the upper limit of 1.28 corresponds to an additional 0.19 events per 1000 person-years at ages 25-44 years and 0.77 events per 1000 person-years at ages 45-64 years.   \n", "CONCLUSIONS Among young and middle-aged adults, current or new use of ADHD medications, compared with nonuse or remote use, was not associated with an increased risk of serious cardiovascular events.", "Apparent protective associations likely represent healthy-user bias."], "structured": true}
{"doc_id": 10991183, "title": "The Rho GEFs LARG and GEF-H1 regulate the mechanical response to force on integrins", "abstract": ["How individual cells respond to mechanical forces is of considerable interest to biologists as force affects many aspects of cell behaviour.", "The application of force on integrins triggers cytoskeletal rearrangements and growth of the associated adhesion complex, resulting in increased cellular stiffness, also known as reinforcement.", "Although RhoA has been shown to play a role during reinforcement, the molecular mechanisms that regulate its activity are unknown.", "By combining biochemical and biophysical approaches, we identified two guanine nucleotide exchange factors (GEFs), LARG and GEF-H1, as key molecules that regulate the cellular adaptation to force.", "We show that stimulation of integrins with tensional force triggers activation of these two GEFs and their recruitment to adhesion complexes.", "Surprisingly, activation of LARG and GEF-H1 involves distinct signalling pathways.", "Our results reveal that LARG is activated by the Src family tyrosine kinase Fyn, whereas GEF-H1 catalytic activity is enhanced by ERK downstream of a signalling cascade that includes FAK and Ras."], "structured": false}
{"doc_id": 10993232, "title": "Cell death from antibiotics without the involvement of reactive oxygen species.", "abstract": ["Recent observations have suggested that classic antibiotics kill bacteria by stimulating the formation of reactive oxygen species (ROS).", "If true, this notion might guide new strategies to improve antibiotic efficacy.", "In this study, the model was directly tested.", "Contrary to the hypothesis, antibiotic treatment did not accelerate the formation of hydrogen peroxide in Escherichia coli and did not elevate intracellular free iron, an essential reactant for the production of lethal damage.", "Lethality persisted in the absence of oxygen, and DNA repair mutants were not hypersensitive, undermining the idea that toxicity arose from oxidative DNA lesions.", "We conclude that these antibiotic exposures did not produce ROS and that lethality more likely resulted from the direct inhibition of cell-wall assembly, protein synthesis, and DNA replication."], "structured": false}
{"doc_id": 11011905, "title": "Pioneer Transcription Factors Target Partial DNA Motifs on Nucleosomes to Initiate Reprogramming", "abstract": ["Pioneer transcription factors (TFs) access silent chromatin and initiate cell-fate changes, using diverse types of DNA binding domains (DBDs).", "FoxA, the paradigm pioneer TF, has a winged helix DBD that resembles linker histone and thereby binds its target sites on nucleosomes and in compacted chromatin.", "Herein, we compare the nucleosome and chromatin targeting activities of Oct4 (POU DBD), Sox2 (HMG box DBD), Klf4 (zinc finger DBD), and c-Myc (bHLH DBD), which together reprogram somatic cells to pluripotency.", "Purified Oct4, Sox2, and Klf4 proteins can bind nucleosomes in vitro, and in vivo they preferentially target silent sites enriched for nucleosomes.", "Pioneer activity relates simply to the ability of a given DBD to target partial motifs displayed on the nucleosome surface.", "Such partial motif recognition can occur by coordinate binding between factors.", "Our findings provide insight into how pioneer factors can target naive chromatin sites."], "structured": false}
{"doc_id": 11016410, "title": "Experimental Evolution of an RNA Virus in Wild Birds: Evidence for Host-Dependent Impacts on Population Structure and Competitive Fitness", "abstract": ["Within hosts, RNA viruses form populations that are genetically and phenotypically complex.", "Heterogeneity in RNA virus genomes arises due to error-prone replication and is reduced by stochastic and selective mechanisms that are incompletely understood.", "Defining how natural selection shapes RNA virus populations is critical because it can inform treatment paradigms and enhance control efforts.", "We allowed West Nile virus (WNV) to replicate in wild-caught American crows, house sparrows and American robins to assess how natural selection shapes RNA virus populations in ecologically relevant hosts that differ in susceptibility to virus-induced mortality.", "After five sequential passages in each bird species, we examined the phenotype and population diversity of WNV through fitness competition assays and next generation sequencing.", "We demonstrate that fitness gains occur in a species-specific manner, with the greatest replicative fitness gains in robin-passaged WNV and the least in WNV passaged in crows.", "Sequencing data revealed that intrahost WNV populations were strongly influenced by purifying selection and the overall complexity of the viral populations was similar among passaged hosts.", "However, the selective pressures that control WNV populations seem to be bird species-dependent.", "Specifically, crow-passaged WNV populations contained the most unique mutations (~1.7\u00d7 more than sparrows, ~3.4\u00d7 more than robins) and defective genomes (~1.4\u00d7 greater than sparrows, ~2.7\u00d7 greater than robins), but the lowest average mutation frequency (about equal to sparrows, ~2.6\u00d7 lower than robins).", "Therefore, our data suggest that WNV replication in the most disease-susceptible bird species is positively associated with virus mutational tolerance, likely via complementation, and negatively associated with the strength of selection.", "These differences in genetic composition most likely have distinct phenotypic consequences for the virus populations.", "Taken together, these results reveal important insights into how different hosts may contribute to the emergence of RNA viruses."], "structured": false}
{"doc_id": 11016788, "title": "sasCIF: an extension of core Crystallographic Information File for SAS", "abstract": ["Data acquisition packages developed at different small angle scattering facilities use different formats both for raw and processed data storage.", "To facilitate the data exchange between laboratories, a consensus in the small angle scattering community has been reached on an ASCII format for one-dimensional data which includes a self-describing header containing relevant information about the sample and instrumental conditions followed by raw or reduced data in a tabular form.", "This format called sasCIF was implemented as an extension of core CIF (Crystallographic Information File) dictionary."], "structured": false}
{"doc_id": 11020556, "title": "Migratory dendritic cells transfer antigen to a lymph node-resident dendritic cell population for efficient CTL priming.", "abstract": ["Skin dendritic cells (DCs) are thought to act as key initiators of local T cell immunity.", "Here we show that after skin infection with herpes simplex virus (HSV), cytotoxic T lymphocyte (CTL) activation required MHC class I-restricted presentation by nonmigratory CD8(+) DCs rather than skin-derived DCs.", "Despite a lack of direct presentation by migratory DCs, blocking their egress from infected skin substantially inhibited class I-restricted presentation and HSV-specific CTL responses.", "These results support the argument for initial transport of antigen by migrating DCs, followed by its transfer to the lymphoid-resident DCs for presentation and CTL priming.", "Given that relatively robust CTL responses were seen with small numbers of skin-emigrant DCs, we propose that this inter-DC antigen transfer functions to amplify presentation across a larger network of lymphoid-resident DCs for efficient T cell activation."], "structured": false}
{"doc_id": 11020675, "title": "Thrombopoietin-induced Polyploidization of Bone Marrow Megakaryocytes Is Due to a Unique Regulatory Mechanism in Late Mitosis ", "abstract": ["Megakaryocytes undergo a unique differentiation program, becoming polyploid through repeated cycles of DNA synthesis without concomitant cell division.", "However, the mechanism underlying this polyploidization remains totally unknown.", "It has been postulated that polyploidization is due to a skipping of mitosis after each round of DNA replication.", "We carried out immunohistochemical studies on mouse bone marrow megakaryocytes during thrombopoietin- induced polyploidization and found that during this process megakaryocytes indeed enter mitosis and progress through normal prophase, prometaphase, metaphase, and up to anaphase A, but not to anaphase B, telophase, or cytokinesis.", "It was clearly observed that multiple spindle poles were formed as the polyploid megakaryocytes entered mitosis; the nuclear membrane broke down during prophase; the sister chromatids were aligned on a multifaced plate, and the centrosomes were symmetrically located on either side of each face of the plate at metaphase; and a set of sister chromatids moved into the multiple centrosomes during anaphase A. We further noted that the pair of spindle poles in anaphase were located in close proximity to each other, probably because of the lack of outward movement of spindle poles during anaphase B. Thus, the reassembling nuclear envelope may enclose all the sister chromatids in a single nucleus at anaphase and then skip telophase and cytokinesis.", "These observations clearly indicate that polyploidization of megakaryocytes is not simply due to a skipping of mitosis, and that the megakaryocytes must have a unique regulatory mechanism in anaphase, e.g., factors regulating anaphase such as microtubule motor proteins might be involved in this polyploidization process."], "structured": false}
{"doc_id": 11026600, "title": "Unifying Viral Genetics and Human Transportation Data to Predict the Global Transmission Dynamics of Human Influenza H3N2", "abstract": ["Information on global human movement patterns is central to spatial epidemiological models used to predict the behavior of influenza and other infectious diseases.", "Yet it remains difficult to test which modes of dispersal drive pathogen spread at various geographic scales using standard epidemiological data alone.", "Evolutionary analyses of pathogen genome sequences increasingly provide insights into the spatial dynamics of influenza viruses, but to date they have largely neglected the wealth of information on human mobility, mainly because no statistical framework exists within which viral gene sequences and empirical data on host movement can be combined.", "Here, we address this problem by applying a phylogeographic approach to elucidate the global spread of human influenza subtype H3N2 and assess its ability to predict the spatial spread of human influenza A viruses worldwide.", "Using a framework that estimates the migration history of human influenza while simultaneously testing and quantifying a range of potential predictive variables of spatial spread, we show that the global dynamics of influenza H3N2 are driven by air passenger flows, whereas at more local scales spread is also determined by processes that correlate with geographic distance.", "Our analyses further confirm a central role for mainland China and Southeast Asia in maintaining a source population for global influenza diversity.", "By comparing model output with the known pandemic expansion of H1N1 during 2009, we demonstrate that predictions of influenza spatial spread are most accurate when data on human mobility and viral evolution are integrated.", "In conclusion, the global dynamics of influenza viruses are best explained by combining human mobility data with the spatial information inherent in sampled viral genomes.", "The integrated approach introduced here offers great potential for epidemiological surveillance through phylogeographic reconstructions and for improving predictive models of disease control."], "structured": false}
{"doc_id": 11041152, "title": "Microtubule sliding activity of a kinesin-8 promotes spindle assembly and spindle length control", "abstract": ["Molecular motors play critical roles in the formation of mitotic spindles, either through controlling the stability of individual microtubules, or by crosslinking and sliding microtubule arrays.", "Kinesin-8 motors are best known for their regulatory roles in controlling microtubule dynamics.", "They contain microtubule-destabilizing activities, and restrict spindle length in a wide variety of cell types and organisms.", "Here, we report an antiparallel microtubule-sliding activity of the budding yeast kinesin-8, Kip3.", "The in vivo importance of this sliding activity was established through the identification of complementary Kip3 mutants that separate the sliding activity and microtubule-destabilizing activity.", "In conjunction with Cin8, a kinesin-5 family member, the sliding activity of Kip3 promotes bipolar spindle assembly and the maintenance of genome stability.", "We propose a slide-disassemble model where the sliding and destabilizing activity of Kip3 balance during pre-anaphase.", "This facilitates normal spindle assembly.", "However, the destabilizing activity of Kip3 dominates in late anaphase, inhibiting spindle elongation and ultimately promoting spindle disassembly."], "structured": false}
{"doc_id": 11043831, "title": "A Pharmacological Map of the PI3-K Family Defines a Role for p110\u03b1 in Insulin Signaling", "abstract": ["Phosphoinositide 3-kinases (PI3-Ks) are an important emerging class of drug targets, but the unique roles of PI3-K isoforms remain poorly defined.", "We describe here an approach to pharmacologically interrogate the PI3-K family.", "A chemically diverse panel of PI3-K inhibitors was synthesized, and their target selectivity was biochemically enumerated, revealing cryptic homologies across targets and chemotypes.", "Crystal structures of three inhibitors bound to p110gamma identify a conformationally mobile region that is uniquely exploited by selective compounds.", "This chemical array was then used to define the PI3-K isoforms required for insulin signaling.", "We find that p110alpha is the primary insulin-responsive PI3-K in cultured cells, whereas p110beta is dispensable but sets a phenotypic threshold for p110alpha activity.", "Compounds targeting p110alpha block the acute effects of insulin treatment in vivo, whereas a p110beta inhibitor has no effect.", "These results illustrate systematic target validation using a matrix of inhibitors that span a protein family."], "structured": false}
{"doc_id": 11048759, "title": "Identification of Epstein-Barr virus nuclear antigen 1 protein domains that direct interactions at a distance between DNA-bound proteins.", "abstract": ["The EBNA1 protein of Epstein-Barr virus (EBV) binds to and activates DNA replication from the EBV latent origin of replication, oriP, via a direct interaction with the two noncontiguous subelements of oriP. The EBNA1 molecules bound to the oriP subelements interact efficiently with each other by a DNA looping mechanism.", "We have previously mapped a region of EBNA1 (termed the looping region) that is required to mediate the interaction of the EBNA1 molecules bound to the oriP subelements.", "We now demonstrate that two fragments of this region of EBNA1, which consist largely of an eight amino acid repeat, can mediate homotypic interactions when transferred to another DNA-binding protein.", "Protein interactions mediated by the EBNA1 looping region appear to be dependent on DNA binding since these interactions were detected between DNA-bound forms of the proteins only."], "structured": false}
{"doc_id": 11071351, "title": "Primary prevention of hypertension: clinical and public health advisory from The National High Blood Pressure Education Program.", "abstract": ["The National High Blood Pressure Education Program Coordinating Committee published its first statement on the primary prevention of hypertension in 1993.", "This article updates the 1993 report, using new and further evidence from the scientific literature.", "Current recommendations for primary prevention of hypertension involve a population-based approach and an intensive targeted strategy focused on individuals at high risk for hypertension.", "These 2 strategies are complementary and emphasize 6 approaches with proven efficacy for prevention of hypertension: engage in moderate physical activity; maintain normal body weight; limit alcohol consumption; reduce sodium intake; maintain adequate intake of potassium; and consume a diet rich in fruits, vegetables, and low-fat dairy products and reduced in saturated and total fat.", "Applying these approaches to the general population as a component of public health and clinical practice can help prevent blood pressure from increasing and can help decrease elevated blood pressure levels for those with high normal blood pressure or hypertension."], "structured": false}
{"doc_id": 11083121, "title": "Formins: intermediates in signal-transduction cascades that affect cytoskeletal reorganization.", "abstract": ["The control of cell growth and polarity depends on a dynamic actin cytoskeleton that has the ability to reorganize in response to developmental and environmental stimuli.", "In animals and fungi, formins are just one of the four major classes of poly-L-proline-containing (PLP) proteins that form part of the signal-transduction cascade that leads to rearrangement of the actin cytoskeleton.", "Analysis of the Arabidopsis genome sequence indicates that, unlike animals and fungi, formins are the only class of conserved profilin-binding PLP proteins in plants.", "Moreover, plant formins show significant structural differences compared with their animal and fungal counterparts, raising the possibility that plant formins are subject to novel mechanisms of control or perform unique roles in plants."], "structured": false}
{"doc_id": 11090688, "title": "Genetic variability in GLP-1 receptor is associated with inter-individual differences in weight lowering potential of liraglutide in obese women with PCOS: a pilot study", "abstract": ["The weight lowering potential of glucagon-like peptide 1 (GLP-1) receptor agonists (RAs) is inter-individually different and clinically unpredictable.", "The potential role of genetic variability of GLP-1R on body weight response to GLP-1 RAs in obese women with polycystic ovary syndrome (PCOS) has not yet been evaluated.", "Fifty-seven obese women with PCOS (aged 30.7 \u00b1 7.0, BMI 38.6 \u00b1 5.3 kg/m2) were assigned to liraglutide 1.2 mg QD s.c.", "for 12 weeks and classified as strong responders regarding weight loss if they lost 5 % or more of their initial body weight.", "They were genotyped for common GLP-1R single nucleotide polymorphisms (SNPs) rs6923761 and rs10305420.", "Changes of measures of obesity were measured before and at the end of the treatment.", "Twenty out of 57 subjects were strong responders and lost 7.38 \u00b1 1.74 compared to 2.11 \u00b1 2.17 kg lost in poor responders.", "Carriers of at least one polymorphic rs10305420 allele had poor treatment response compared to carriers of two wild type alleles (OR = 0.27, 95 % CI = 0.09\u20130.85, P = 0.025).", "Carriers of at least one polymorphic rs6923761 allele tended to have stronger treatment response compared to carriers of two wild type alleles (OR = 3.06, 95 % CI = 0.96\u20139.74, P = 0.058).", "Fasting glucose and glucose after oral glucose tolerance test (OGTT) comparably decreased in both groups when compared to baseline, whereas no within treatment differences were found in androgen profile.", "Gastrointestinal adverse events were transit and balanced between strong and poor responders.", "GLP-1R rs10305420 polymorphism explained some of the inter-individual differences in response to liraglutide regarding weight loss in obese PCOS women."], "structured": false}
{"doc_id": 11109043, "title": "Cost-effectiveness of aromatase inhibitor co-treatment for controlled ovarian stimulation.", "abstract": ["BACKGROUND To compare the clinical results and the cost-effectiveness of using the aromatase inhibitor, letrozole, in conjunction with FSH and FSH alone for controlled ovarian stimulation (COS) in patients undergoing intrauterine insemination (IUI) for a variety of indications.   \n", "METHODS Four hundred and thirty-two consecutive patients who underwent 872 IUI cycles were included.", "The study population was composed of two groups.", "Group I included 308 patients who underwent 589 IUI cycles with letrozole and FSH for the following indications: anovulation (143 cycles), male factor infertility (147 cycles), unexplained infertility (250 cycles), endometriosis (18 cycles) and combined indications (31 cycles).", "Group II included 124 patients who underwent 283 IUI cycles who received FSH only for the following indications: ovarian factor infertility (82 cycles), male factor infertility (66 cycles), unexplained infertility (114 cycles), endometriosis (13 cycles) and other indications (8 cycles).", "Main outcome measures included number of mature follicles >16 mm in diameter, dose of FSH used per cycle, clinical pregnancy rate and cost-effectiveness ratio per pregnancy.   \n", "RESULTS FSH dose required for ovarian stimulation was significantly lower when letrozole was used (P < 0.0001).", "Although a significantly higher number of follicles >16 mm and endometrial thickness at the day of hCG administration (P < 0.0001) were observed in Group II, pregnancy rate per started (14.4 versus 15.9%) and per completed cycles (15.77 versus 18.07%) was the same in Group I and Group II, respectively.", "IUI cancellation rate was significantly lower with letrozole treatment (P = 0.05%).", "The cost per cycle was significantly lower in Group I versus Group II (468.93 Can dollars +/-", "418.18 versus 1067.28 +/-", "921.43; P < 0.0001).", "The cost-effectiveness ratio was 3249.42 dollars in the letrozole group and 6712.00 dollars in the FSH-only group.   \n", "CONCLUSION A letrozole-FSH combination could be an effective ovarian stimulation protocol in IUI cycles.", "Such a protocol may be more cost-effective than FSH alone because of the difference of FSH dose and cost.", "A randomized controlled trial is needed to further substantiate this finding."], "structured": true}
{"doc_id": 11117498, "title": "The cost effectiveness of stereotactic radiosurgery versus surgical resection in the treatment of solitary metastatic brain tumors.", "abstract": ["Solitary metastatic brain tumors are the most common intracranial neoplasms encountered by neurosurgeons.", "Surgical resection of brain metastasis with whole brain radiotherapy (WBR) significantly increases survival in comparison with WBR alone.", "Stereotactic radiosurgery (SR) seems to provide results that are similar to those of surgical resection.", "To analyze the economic efficiency of these different treatments, we compared the results of surgical resection and SR as reported in the medical literature between 1974 and 1994.", "We included studies in which: 1) at least 75% of patients received WBR; 2) study dates were in the computed tomography era (after 1975); 3) operative morbidity, mortality, and median survival were reported; 4) study dates were not included in a more recent update or review; 5) tumor histologies were reported; and 6) the cobalt-60 gamma unit was used for SR.", "Three surgical resection studies and one SR study met all entry requirements.", "The WBR baseline was developed from two prospective, randomized trials and used for incremental cost effectiveness analysis.", "We developed a model of typical resource usage for uncomplicated procedures, reported complications, and subsequent craniotomies (for recurrent tumor or radiation necrosis) for both treatment options.", "Costs were estimated from the societal viewpoint using the 1992 Medicare Provider Analysis and Review database with average cost:charge ratios for surgery and WBR.", "A survey of capital and operating costs from five sites was used for radiosurgery.", "Our analysis revealed that radiosurgery had a lower uncomplicated procedure cost ($20,209 versus $27,587), a lower average complication cost per case ($2,534 versus $2,874), and a lower total cost per procedure ($22,743 versus $30,461), was more cost effective ($24,811 versus $32,149 per life year), and had a better incremental cost effectiveness ($40,648 versus $52,384 per life year) than surgical resection.", "A sensitivity analysis revealed that large changes in key assumptions would be required to change the analysis outcome.", "Equalization of the incremental cost effectiveness of the two treatments would require one of the following: 1) a 38.7% reduction in SR annual case volume, 2) a 34.7% increase in SR procedure cost, 3) a 18.8% reduction in surgical resection procedure cost, 4) a 240.5% increase in SR morbidity cost, 5) a 12.7% reduction in SR median survival, 6) a 16.8% increase in surgical resection median survival.", "Elimination of all surgical resection morbidity cost would still result in superior incremental cost effectiveness for SR.(ABSTRACT TRUNCATED AT 400 WORDS)"], "structured": false}
{"doc_id": 11117679, "title": "Trans-ancestry mutational landscape of hepatocellular carcinoma genomes", "abstract": ["Diverse epidemiological factors are associated with hepatocellular carcinoma (HCC) prevalence in different populations.", "However, the global landscape of the genetic changes in HCC genomes underpinning different epidemiological and ancestral backgrounds still remains uncharted.", "Here a collection of data from 503 liver cancer genomes from different populations uncovered 30 candidate driver genes and 11 core pathway modules.", "Furthermore, a collaboration of two large-scale cancer genome projects comparatively analyzed the trans-ancestry substitution signatures in 608 liver cancer cases and identified unique mutational signatures that predominantly contribute to Asian cases.", "This work elucidates previously unexplored ancestry-associated mutational processes in HCC development.", "A combination of hotspot TERT promoter mutation, TERT focal amplification and viral genome integration occurs in more than 68% of cases, implicating TERT as a central and ancestry-independent node of hepatocarcinogenesis.", "Newly identified alterations in genes encoding metabolic enzymes, chromatin remodelers and a high proportion of mTOR pathway activations offer potential therapeutic and diagnostic opportunities."], "structured": false}
{"doc_id": 11141995, "title": "Organization of the mitotic chromosome.", "abstract": ["Mitotic chromosomes are among the most recognizable structures in the cell, yet for over a century their internal organization remains largely unsolved.", "We applied chromosome conformation capture methods, 5C and Hi-C, across the cell cycle and revealed two distinct three-dimensional folding states of the human genome.", "We show that the highly compartmentalized and cell type-specific organization described previously for nonsynchronous cells is restricted to interphase.", "In metaphase, we identified a homogenous folding state that is locus-independent, common to all chromosomes, and consistent among cell types, suggesting a general principle of metaphase chromosome organization.", "Using polymer simulations, we found that metaphase Hi-C data are inconsistent with classic hierarchical models and are instead best described by a linearly organized longitudinally compressed array of consecutive chromatin loops."], "structured": false}
{"doc_id": 11156883, "title": "Compensatory anti-inflammatory response syndrome.", "abstract": ["The concept of 'Compensatory anti-inflammatory response syndrome' (CARS) was proposed in 1997 by Roger Bone (1941-1997) to qualify the consequences of the counter-regulatory mechanisms initiated to limit the overzealous inflammatory process in patients with infectious (sepsis) or non-infectious systemic inflammatory response syndrome (SIRS).", "One major consequence of CARS is the modification of the immune status that could favour the enhanced susceptibility of intensive care patients to nosocomial infections.", "Indeed, most animal 'two-hit' models illustrate an enhanced sensitivity to infection after a first insult.", "However, this observation is highly dependent on the experimental procedure.", "Numerous functions of circulating leukocytes are altered in sepsis and SIRS patients, as well as in animal models of sepsis or SIRS.", "However, this is rather a reprogramming of circulating leukocytes, since there is not a global defect of the immune cells functions.", "Furthermore, within tissues, leukocytes are rather primed or activated than immunosuppressed.", "Thus, CARS may be considered as an adapted compartmentalized response with the aim to silence some acute proinflammatory genes, and to maintain the possible expression of certain genes involved in the anti-infectious process."], "structured": false}
{"doc_id": 11172205, "title": "Quantum dots spectrally distinguish multiple species within the tumor milieu in vivo", "abstract": ["A solid tumor is an organ composed of cancer and host cells embedded in an extracellular matrix and nourished by blood vessels.", "A prerequisite to understanding tumor pathophysiology is the ability to distinguish and monitor each component in dynamic studies.", "Standard fluorophores hamper simultaneous intravital imaging of these components.", "Here, we used multiphoton microscopy techniques and transgenic mice that expressed green fluorescent protein, and combined them with the use of quantum dot preparations.", "We show that these fluorescent semiconductor nanocrystals can be customized to concurrently image and differentiate tumor vessels from both the perivascular cells and the matrix.", "Moreover, we used them to measure the ability of particles of different sizes to access the tumor.", "Finally, we successfully monitored the recruitment of quantum dot\u2013labeled bone marrow\u2013derived precursor cells to the tumor vasculature.", "These examples show the versatility of quantum dots for studying tumor pathophysiology and creating avenues for treatment."], "structured": false}
{"doc_id": 11181416, "title": "Arginase I: a limiting factor for nitric oxide and polyamine synthesis by activated macrophages?", "abstract": ["Because arginase hydrolyzes arginine to produce ornithine and urea, it has the potential to regulate nitric oxide (NO) and polyamine synthesis.", "We tested whether expression of the cytosolic isoform of arginase (arginase I) was limiting for NO or polyamine production by activated RAW 264.7 macrophage cells.", "RAW 264.7 cells, stably transfected to overexpress arginase I or beta-galactosidase, were treated with interferon-gamma to induce type 2 NO synthase or with lipopolysaccharide or 8-bromo-cAMP (8-BrcAMP) to induce ornithine decarboxylase.", "Overexpression of arginase I had no effect on NO synthesis.", "In contrast, cells overexpressing arginase I produced twice as much putrescine after activation than did cells expressing beta-galactosidase.", "Cells overexpressing arginase I also produced more spermidine after treatment with 8-BrcAMP than did cells expressing beta-galactosidase.", "Thus endogenous levels of arginase I are limiting for polyamine synthesis, but not for NO synthesis, by activated macrophage cells.", "This study also demonstrates that it is possible to alter arginase I levels sufficiently to affect polyamine synthesis without affecting induced NO synthesis."], "structured": false}
{"doc_id": 11195653, "title": "Opposing Effects of PKC\u03b8 and WASp on Symmetry Breaking and Relocation of the Immunological Synapse", "abstract": ["The immunological synapse (IS) is a junction between the T cell and antigen-presenting cell and is composed of supramolecular activation clusters (SMACs).", "No studies have been published on naive T cell IS dynamics.", "Here, we find that IS formation during antigen recognition comprises cycles of stable IS formation and autonomous naive T cell migration.", "The migration phase is driven by PKCtheta, which is localized to the F-actin-dependent peripheral (p)SMAC.", "PKCtheta(-/-) T cells formed hyperstable IS in vitro and in vivo and, like WT cells, displayed fast oscillations in the distal SMAC, but they showed reduced slow oscillations in pSMAC integrity.", "IS reformation is driven by the Wiscott Aldrich Syndrome protein (WASp).", "WASp(-/-) T cells displayed normal IS formation but were unable to reform IS after migration unless PKCtheta was inhibited.", "Thus, opposing effects of PKCtheta and WASp control IS stability through pSMAC symmetry breaking and reformation."], "structured": false}
{"doc_id": 11200685, "title": "Integrins regulate microtubule nucleating activity of centrosome through mitogen-activated protein kinase/extracellular signal-regulated kinase kinase/extracellular signal-regulated kinase (MEK/ERK) signaling.", "abstract": ["Microtubule nucleation is an essential step in the formation of the microtubule cytoskeleton.", "We recently showed that androgen and Src promote microtubule nucleation and \u03b3-tubulin accumulation at the centrosome.", "Here, we explore the mechanisms by which androgen and Src regulate these processes and ask whether integrins play a role.", "We perturb integrin function by a tyrosine-to-alanine substitution in membrane-proximal NPIY motif in the integrin \u03b21 tail and show that this mutant substantially decreases microtubule nucleation and \u03b3-tubulin accumulation at the centrosome.", "Because androgen stimulation promotes the interaction of the androgen receptor with Src, resulting in PI3K/AKT and MEK/ERK signaling, we asked whether these pathways are inhibited by the mutant integrin and whether they regulate microtubule nucleation.", "Our results indicate that the formation of the androgen receptor-Src complex and the activation of downstream pathways are significantly suppressed when cells are adhered by the mutant integrin.", "Inhibitor studies indicate that microtubule nucleation requires MEK/ERK but not PI3K/AKT signaling.", "Importantly, the expression of activated RAF-1 is sufficient to rescue microtubule nucleation inhibited by the mutant integrin by promoting the centrosomal accumulation of \u03b3-tubulin.", "Our data define a novel paradigm of integrin signaling, where integrins regulate microtubule nucleation by promoting the formation of androgen receptor-Src signaling complexes to activate the MEK/ERK signaling pathway."], "structured": false}
{"doc_id": 11201004, "title": "Consumption of added sugars from liquid but not solid sources predicts impaired glucose homeostasis and insulin resistance among youth at risk of obesity.", "abstract": ["Little is known about longitudinal associations between added sugar consumption (solid and liquid sources) and glucose-insulin homeostasis among youth.", "Caucasian children (8-10 y) with at least one obese biological parent were recruited in the QU\u00e9bec Adipose and Lifestyle InvesTigation in Youth (QUALITY) cohort (n = 630) and followed-up 2 y later (n = 564).", "Added sugars were assessed by 3 24-h dietary recalls at baseline.", "Two-year changes were examined in multivariate linear regression models, adjusting for baseline level, age, sex, Tanner stage, energy intake, fat mass (dual-energy X-ray absorptiometry), and physical activity (7 d accelerometer).", "Added sugar intake in either liquid or solid sources was not related to changes in adiposity measures (fat mass, body mass index, or waist circumference).", "However, a higher consumption (10 g/d) of added sugars from liquid sources was associated with 0.04 mmol/L higher fasting glucose, 2.3 pmol/L higher fasting insulin, 0.1 unit higher homeostasis model assessment of insulin resistance (HOMA-IR), and 0.4 unit lower Matsuda-insulin sensitivity index (Matsuda-ISI) in all participants (P < 0.01).", "No associations were observed with consumption of added sugars from solid sources.", "Overweight/obese children at baseline had greater increases in adiposity indicators, fasting insulin, and HOMA-IR and decreases in Matsuda-ISI during those 2 y than normal-weight children.", "Consumption of added sugars from liquid or solid sources was not associated with changes in adiposity, but liquid added sugars were a risk factor for the development of impaired glucose homeostasis and insulin resistance over 2 y among youth at risk of obesity."], "structured": false}
{"doc_id": 11230569, "title": "Towards an improved investment approach for an effective response to HIV/AIDS.", "abstract": ["Substantial changes are needed to achieve a more targeted and strategic approach to investment in the response to the HIV/AIDS epidemic that will yield long-term dividends.", "Until now, advocacy for resources has been done on the basis of a commodity approach that encouraged scaling up of numerous strategies in parallel, irrespective of their relative effects.", "We propose a strategic investment framework that is intended to support better management of national and international HIV/AIDS responses than exists with the present system.", "Our framework incorporates major efficiency gains through community mobilisation, synergies between programme elements, and benefits of the extension of antiretroviral therapy for prevention of HIV transmission.", "It proposes three categories of investment, consisting of six basic programmatic activities, interventions that create an enabling environment to achieve maximum effectiveness, and programmatic efforts in other health and development sectors related to HIV/AIDS.", "The yearly cost of achievement of universal access to HIV prevention, treatment, care, and support by 2015 is estimated at no less than US$22 billion.", "Implementation of the new investment framework would avert 12\u00b72 million new HIV infections and 7\u00b74 million deaths from AIDS between 2011 and 2020 compared with continuation of present approaches, and result in 29\u00b74 million life-years gained.", "The framework is cost effective at $1060 per life-year gained, and the additional investment proposed would be largely offset from savings in treatment costs alone."], "structured": false}
{"doc_id": 11233339, "title": "Pivotal Roles of T-Helper 17-Related Cytokines, IL-17, IL-22, and IL-23, in Inflammatory Diseases", "abstract": ["T-helper 17 (Th17) cells are characterized by producing interleukin-17 (IL-17, also called IL-17A), IL-17F, IL-21, and IL-22 and potentially TNF- \u03b1 and IL-6 upon certain stimulation.", "IL-23, which promotes Th17 cell development, as well as IL-17 and IL-22 produced by the Th17 cells plays essential roles in various inflammatory diseases, such as experimental autoimmune encephalomyelitis, rheumatoid arthritis, colitis, and Concanavalin A-induced hepatitis.", "In this review, we summarize the characteristics of the functional role of Th17 cells, with particular focus on the Th17 cell-related cytokines such as IL-17, IL-22, and IL-23, in mouse models and human inflammatory diseases."], "structured": false}
{"doc_id": 11238784, "title": "LXRS and FXR: the yin and yang of cholesterol and fat metabolism.", "abstract": ["Liver X receptors (LXRs) and farnesoid X receptor (FXR) are nuclear receptors that function as intracellular sensors for sterols and bile acids, respectively.", "In response to their ligands, these receptors induce transcriptional responses that maintain a balanced, finely tuned regulation of cholesterol and bile acid metabolism.", "LXRs also permit the efficient storage of carbohydrate- and fat-derived energy, whereas FXR activation results in an overall decrease in triglyceride levels and modulation of glucose metabolism.", "The elegant, dual interplay between these two receptor systems suggests that they coevolved to constitute a highly sensitive and efficient system for the maintenance of total body fat and cholesterol homeostasis.", "Emerging evidence suggests that the tissue-specific action of these receptors is also crucial for the proper function of the cardiovascular, immune, reproductive, endocrine pancreas, renal, and central nervous systems.", "Together, LXRs and FXR represent potential therapeutic targets for the treatment and prevention of numerous metabolic and lipid-related diseases."], "structured": false}
{"doc_id": 11238951, "title": "Kaposi's sarcoma-associated herpesvirus/human herpesvirus type 8-positive solid lymphomas: a tissue-based variant of primary effusion lymphoma.", "abstract": ["Kaposi's sarcoma-associated herpesvirus (KSHV), also termed human herpesvirus type 8, is consistently identified in Kaposi's sarcoma, primary effusion lymphoma (PEL), and multicentric Castleman's disease.", "Here we report four cases of KSHV-bearing solid lymphomas that occurred in AIDS patients (cases 1 to 3) and in a human immunodeficiency virus (HIV)-seronegative person (case 4).", "The patients presented extranodal masses in the abdomen (cases 1, 3, and 4) or skin (case 2), and nodal involvement, together with Kaposi's sarcoma (case 3).", "The gastrointestinal tract was involved in two patients (cases 1 and 3).", "The patients did not develop a lymphomatous effusion.", "KSHV was detected in the tumor cells of all cases by immunohistochemistry and by polymerase chain reaction.", "Epstein-Barr virus was detected in two of the HIV-related cases.", "All KSHV-positive solid lymphomas exhibited PEL-like cell morphology.", "To investigate the relationship of these disorders to PEL and to other AIDS-associated diffuse large cell lymphomas, KSHV-positive solid lymphomas were tested for the expression of a set of genes that were previously shown by gene profiling analysis to define PEL tumor cells.", "The results showed that expression of this set of genes in KSHV-positive lymphomas is similar to that of PEL but distinct from KSHV-negative AIDS-associated diffuse large cell lymphomas.", "Because pathobiological features of KSHV-positive solid lymphomas closely mimic those of PEL, our results suggest that KSHV-positive solid lymphomas should be considered as a tissue-based variant of classical PEL, irrespective of HIV status."], "structured": false}
{"doc_id": 11244195, "title": "STAR: ultrafast universal RNA-seq aligner.", "abstract": ["MOTIVATION Accurate alignment of high-throughput RNA-seq data is a challenging and yet unsolved problem because of the non-contiguous transcript structure, relatively short read lengths and constantly increasing throughput of the sequencing technologies.", "Currently available RNA-seq aligners suffer from high mapping error rates, low mapping speed, read length limitation and mapping biases.   \n", "RESULTS To align our large (>80 billon reads) ENCODE Transcriptome RNA-seq dataset, we developed the Spliced Transcripts Alignment to a Reference (STAR) software based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure.", "STAR outperforms other aligners by a factor of >50 in mapping speed, aligning to the human genome 550 million 2 \u00d7 76 bp paired-end reads per hour on a modest 12-core server, while at the same time improving alignment sensitivity and precision.", "In addition to unbiased de novo detection of canonical junctions, STAR can discover non-canonical splices and chimeric (fusion) transcripts, and is also capable of mapping full-length RNA sequences.", "Using Roche 454 sequencing of reverse transcription polymerase chain reaction amplicons, we experimentally validated 1960 novel intergenic splice junctions with an 80-90% success rate, corroborating the high precision of the STAR mapping strategy.   ", "AVAILABILITY AND IMPLEMENTATION STAR is implemented as a standalone C++ code.", "STAR is free open source software distributed under GPLv3 license and can be downloaded from http://code.google.com/p/rna-star/."], "structured": true}
{"doc_id": 11246427, "title": "Effect of alendronate on risk of fracture in women with low bone density but without vertebral fractures: results from the Fracture Intervention Trial.", "abstract": ["CONTEXT Alendronate sodium reduces fracture risk in postmenopausal women who have vertebral fractures, but its effects on fracture risk have not been studied for women without vertebral fractures.   \n", "OBJECTIVE To test the hypothesis that 4 years of alendronate would decrease the risk of clinical and vertebral fractures in women who have low bone mineral density (BMD) but no vertebral fractures.   \n", "DESIGN Randomized, blinded, placebo-controlled trial.   \n", "SETTING Eleven community-based clinical research centers.   ", "SUBJECTS Women aged 54 to 81 years with a femoral neck BMD of 0.68 g/cm2 or less (Hologic Inc, Waltham, Mass) but no vertebral fracture; 4432 were randomized to alendronate or placebo and 4272 (96%) completed outcome measurements at the final visit (an average of 4.2 years later).   \n", "INTERVENTION All participants reporting calcium intakes of 1000 mg/d or less received a supplement containing 500 mg of calcium and 250 IU of cholecalciferol.", "Subjects were randomly assigned to either placebo or 5 mg/d of alendronate sodium for 2 years followed by 10 mg/d for the remainder of the trial.   \n", "MAIN OUTCOME MEASURES Clinical fractures confirmed by x-ray reports, new vertebral deformities detected by morphometric measurements on radiographs, and BMD measured by dual x-ray absorptiometry.   \n", "RESULTS Alendronate increased BMD at all sites studied (P<.001) and reduced clinical fractures from 312 in the placebo group to 272 in the intervention group, but not significantly so (14% reduction; relative hazard [RH], 0.86; 95% confidence interval [CI], 0.73-1.01).", "Alendronate reduced clinical fractures by 36% in women with baseline osteoporosis at the femoral neck (>2.5 SDs below the normal young adult mean; RH, 0.64; 95% CI, 0.50-0.82; treatment-control difference, 6.5%; number needed to treat [NNT], 15), but there was no significant reduction among those with higher BMD (RH, 1.08; 95% CI, 0.87-1.35).", "Alendronate decreased the risk of radiographic vertebral fractures by 44% overall (relative risk, 0.56; 95% CI, 0.39-0.80; treatment-control difference, 1.7%; NNT, 60).", "Alendronate did not increase the risk of gastrointestinal or other adverse effects.   \n", "CONCLUSIONS In women with low BMD but without vertebral fractures, 4 years of alendronate safely increased BMD and decreased the risk of first vertebral deformity.", "Alendronate significantly reduced the risk of clinical fractures among women with osteoporosis but not among women with higher BMD."], "structured": true}
{"doc_id": 11250124, "title": "AP-1/sigma1B-adaptin mediates endosomal synaptic vesicle recycling, learning and memory.", "abstract": ["Synaptic vesicle recycling involves AP-2/clathrin-mediated endocytosis, but it is not known whether the endosomal pathway is also required.", "Mice deficient in the tissue-specific AP-1-sigma1B complex have impaired synaptic vesicle recycling in hippocampal synapses.", "The ubiquitously expressed AP-1-sigma1A complex mediates protein sorting between the trans-Golgi network and early endosomes.", "Vertebrates express three sigma1 subunit isoforms: A, B and C. The expressions of sigma1A and sigma1B are highest in the brain.", "Synaptic vesicle reformation in cultured neurons from sigma1B-deficient mice is reduced upon stimulation, and large endosomal intermediates accumulate.", "The sigma1B-deficient mice have reduced motor coordination and severely impaired long-term spatial memory.", "These data reveal a molecular mechanism for a severe human X-chromosome-linked mental retardation."], "structured": false}
{"doc_id": 11253758, "title": "Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals", "abstract": ["Upon the first publication of the fifth iteration of the Functional Annotation of Mammalian Genomes collaborative project, FANTOM5, we gathered a series of primary data and database systems into the FANTOM web resource (http://fantom.gsc.riken.jp) to facilitate researchers to explore transcriptional regulation and cellular states.", "In the course of the collaboration, primary data and analysis results have been expanded, and functionalities of the database systems enhanced.", "We believe that our data and web systems are invaluable resources, and we think the scientific community will benefit for this recent update to deepen their understanding of mammalian cellular organization.", "We introduce the contents of FANTOM5 here, report recent updates in the web resource and provide future perspectives."], "structured": false}
{"doc_id": 11254040, "title": "Adverse Events Associated With the Treatment of Multidrug-Resistant Tuberculosis: A Systematic Review and Meta-analysis.", "abstract": ["Multidrug-resistant tuberculosis (MDR-TB) is a growing public health problem.", "Due to long duration of therapy and concurrent use of multiple second-line drugs, adverse drug events (ADEs) are regarded as the most important clinical consideration in patients undergoing anti-MDR-TB treatment.", "To evaluate the frequency and type of treatment-related ADEs owing to MDR-TB therapy.", "The Cochrane Library, MEDLINE, and EMBASE were searched from inception through October 1, 2012, with additional manual search of International Journal of Tuberculosis and Lung Disease.", "Studies with available ADEs were selected if MDR-TB patients were treated with regimen including second-line drugs.", "Pooled estimations of incidence for each specific type of ADEs were calculated with 95% confidence intervals using random-effects model.", "Of the 5346 patients included, 2602 (57.3%) experienced at least 1 kind of ADE.", "The 3 most common side effects were gastrointestinal disorders (32.1%), ototoxicity (14.6%), and psychiatric disorders (13.2%).", "Subgroup analyses based on each characteristic (study population, previous tuberculosis treated, human immunodeficiency virus prevalence, and length of treatment) did not show any significant difference between groups.", "Additionally, among 1519 patients who developed ADEs with available data of impact on MDR-TB therapy, 70.4% required change of MDR-TB treatment.", "Adverse events were common among MDR-TB cases, occurring in more than half of the cases, with over two-thirds requiring change of anti-MDR-TB treatment.", "MDR-TB patients should be monitored closely and managed aggressively for side effects during therapy, especially for ototoxicity and psychiatric disorders."], "structured": false}
{"doc_id": 11254556, "title": "Presynaptically Localized Cyclic GMP-Dependent Protein Kinase 1 Is a Key Determinant of Spinal Synaptic Potentiation and Pain Hypersensitivity", "abstract": ["Synaptic long-term potentiation (LTP) at spinal neurons directly communicating pain-specific inputs from the periphery to the brain has been proposed to serve as a trigger for pain hypersensitivity in pathological states.", "Previous studies have functionally implicated the NMDA receptor-NO pathway and the downstream second messenger, cGMP, in these processes.", "Because cGMP can broadly influence diverse ion-channels, kinases, and phosphodiesterases, pre- as well as post-synaptically, the precise identity of cGMP targets mediating spinal LTP, their mechanisms of action, and their locus in the spinal circuitry are still unclear.", "Here, we found that Protein Kinase G1 (PKG-I) localized presynaptically in nociceptor terminals plays an essential role in the expression of spinal LTP.", "Using the Cre-lox P system, we generated nociceptor-specific knockout mice lacking PKG-I specifically in presynaptic terminals of nociceptors in the spinal cord, but not in post-synaptic neurons or elsewhere (SNS-PKG-I(-/-) mice).", "Patch clamp recordings showed that activity-induced LTP at identified synapses between nociceptors and spinal neurons projecting to the periaqueductal grey (PAG) was completely abolished in SNS-PKG-I(-/-) mice, although basal synaptic transmission was not affected.", "Analyses of synaptic failure rates and paired-pulse ratios indicated a role for presynaptic PKG-I in regulating the probability of neurotransmitter release.", "Inositol 1,4,5-triphosphate receptor 1 and myosin light chain kinase were recruited as key phosphorylation targets of presynaptic PKG-I in nociceptive neurons.", "Finally, behavioural analyses in vivo showed marked defects in SNS-PKG-I(-/-) mice in several models of activity-induced nociceptive hypersensitivity, and pharmacological studies identified a clear contribution of PKG-I expressed in spinal terminals of nociceptors.", "Our results thus indicate that presynaptic mechanisms involving an increase in release probability from nociceptors are operational in the expression of synaptic LTP on spinal-PAG projection neurons and that PKG-I localized in presynaptic nociceptor terminals plays an essential role in this process to regulate pain sensitivity."], "structured": false}
{"doc_id": 11255504, "title": "A Sleeping Beauty mutagenesis screen reveals a tumor suppressor role for Ncoa2/Src-2 in liver cancer.", "abstract": ["The Sleeping Beauty (SB) transposon mutagenesis system is a powerful tool that facilitates the discovery of mutations that accelerate tumorigenesis.", "In this study, we sought to identify mutations that cooperate with MYC, one of the most commonly dysregulated genes in human malignancy.", "We performed a forward genetic screen with a mouse model of MYC-induced liver cancer using SB-mediated mutagenesis.", "We sequenced insertions in 63 liver tumor nodules and identified at least 16 genes/loci that contribute to accelerated tumor development.", "RNAi-mediated knockdown in a liver progenitor cell line further validate three of these genes, Ncoa2/Src-2, Zfx, and Dtnb, as tumor suppressors in liver cancer.", "Moreover, deletion of Ncoa2/Src-2 in mice predisposes to diethylnitrosamine-induced liver tumorigenesis.", "These findings reveal genes and pathways that functionally restrain MYC-mediated liver tumorigenesis and therefore may provide targets for cancer therapy."], "structured": false}
{"doc_id": 11256632, "title": "Protein-Protein Interaction Inhibition (2P2I)-Oriented Chemical Library Accelerates Hit Discovery.", "abstract": ["Protein-protein interactions (PPIs) represent an enormous source of opportunity for therapeutic intervention.", "We and others have recently pinpointed key rules that will help in identifying the next generation of innovative drugs to tackle this challenging class of targets within the next decade.", "We used these rules to design an oriented chemical library corresponding to a set of diverse \"PPI-like\" modulators with cores identified as privileged structures in therapeutics.", "In this work, we purchased the resulting 1664 structurally diverse compounds and evaluated them on a series of representative protein-protein interfaces with distinct \"druggability\" potential using homogeneous time-resolved fluorescence (HTRF) technology.", "For certain PPI classes, analysis of the hit rates revealed up to 100 enrichment factors compared with nonoriented chemical libraries.", "This observation correlates with the predicted \"druggability\" of the targets.", "A specific focus on selectivity profiles, the three-dimensional (3D) molecular modes of action resolved by X-ray crystallography, and the biological activities of identified hits targeting the well-defined \"druggable\" bromodomains of the bromo and extraterminal (BET) family are presented as a proof-of-concept.", "Overall, our present study illustrates the potency of machine learning-based oriented chemical libraries to accelerate the identification of hits targeting PPIs.", "A generalization of this method to a larger set of compounds will accelerate the discovery of original and potent probes for this challenging class of targets."], "structured": false}
{"doc_id": 11271123, "title": "Molecular characterization of endometrial cancer: a correlative study assessing microsatellite instability, MLH1 hypermethylation, DNA mismatch repair protein expression, and PTEN, PIK3CA, KRAS, and BRAF mutation analysis.", "abstract": ["Endometrial cancer is associated with numeric and structural chromosomal abnormalities, microsatellite instability (MSI), and alterations that activate oncogenes and inactivate tumor suppressor genes.", "The aim of this study was to characterize a set of endometrial cancers using multiple molecular genetic and immunohistochemical techniques.", "Ninety-six cases were examined for genomic alterations by MSI, MLH1 promoter hypermethylation, p53 and mismatch repair protein expression (MLH1, MSH2, MSH6, PMS2), and PTEN, PIK3CA, KRAS, and BRAF mutation analysis.", "At least 1 alteration was identified in 48 of 87 (55%) specimens tested for PTEN, making it the most common abnormality in this study.", "A PIK3CA alteration was observed in 16 (17%) specimens.", "Twenty-nine of 94 (31%) MSI tested tumors exhibited an MSI-H phenotype.", "Of the 29 MSI-H cases, 24 (83%) were positive for methylation of the MLH1 promoter region.", "Twenty-three (82%) of the 28 MSI-H cases with immunohistochemistry results showed loss of expression of MLH1/PMS2 (n=19), MSH2/MSH6 (n=2), or MSH6 only (n=2).", "Of the 19 MSI-H cases with loss of MLH1/PMS2 on immunohistochemistry, 18 were positive, and 1 was equivocal for MLH1 promoter hypermethylation.", "Twelve of 94 cases (13%) analyzed for KRAS mutations were found to have a mutation.", "No BRAF V600E mutations were indentified.", "This study provides a comprehensive molecular genetic analysis of commonly analyzed targets in a large cohort of endometrial cancers."], "structured": false}
{"doc_id": 11280569, "title": "Identification of indole-3-carboxylic acid as mediator of priming against Plectosphaerella cucumerina.", "abstract": ["Plant resistance against the necrotrophic pathogen Plectosphaerella cucumerina is mediated by a combination of several hormonal-controlled signalling pathways.", "The priming agent \u03b2-aminobutyric acid (BABA) is able to induce effective resistance against this pathogen by stimulating callose-rich cell wall depositions.", "In the present research it is demonstrated that BABA-Induced Resistance (BABA-IR) against P. cucumerina in Arabidopsis has additional components such as the induction of defences mediated by indolic derivatives.", "Chromatographic approach for the detection and characterization of metabolites enhanced by BABA compared with water-treated plants only when the challenge is present has been developed.", "The metabolites matching this criteria are considered to be primed by BABA.", "The analytic procedure is based on the combination of liquid chromatography (LC) with a triple quadrupole (TQD) detector in a precursor ion scanning mode.", "Using this analytical system a signal in negative electro-spray mode of 160 m/z is primed by BABA in infected plants.", "A subsequent exact mass analysis in a quadrupole time-of-flight mass spectrometer demonstrated that this ion was the indole-derivative metabolite indole-3-carboxylic acid (I3CA).", "The identity of indole-3-carboxilic acid was definitively confirmed by comparing its retention time and fragmentation spectra with a commercial standard.", "Quantification of I3CA in primed plants showed that this indolic metabolite is specifically primed by BABA upon P. cucumerina infection, while other indolic compounds such as IAA and camalexin are not.", "Taking together these observations with the known role of callose in priming against this pathogen, suggests that priming is not a single mechanism but rather a multicomponent defence."], "structured": false}
{"doc_id": 11288846, "title": "Evaluation of networks of randomized trials.", "abstract": ["Randomized trials may be designed and interpreted as single experiments or they may be seen in the context of other similar or relevant evidence.", "The amount and complexity of available randomized evidence vary for different topics.", "Systematic reviews may be useful in identifying gaps in the existing randomized evidence, pointing to discrepancies between trials, and planning future trials.", "A new, promising, but also very much debated extension of systematic reviews, mixed treatment comparison (MTC) meta-analysis, has become increasingly popular recently.", "MTC meta-analysis may have value in interpreting the available randomized evidence from networks of trials and can rank many different treatments, going beyond focusing on simple pairwise-comparisons.", "Nevertheless, the evaluation of networks also presents special challenges and caveats.", "In this article, we review the statistical methodology for MTC meta-analysis.", "We discuss the concept of inconsistency and methods that have been proposed to evaluate it as well as the methodological gaps that remain.", "We introduce the concepts of network geometry and asymmetry, and propose metrics for the evaluation of the asymmetry.", "Finally, we discuss the implications of inconsistency, network geometry and asymmetry in informing the planning of future trials."], "structured": false}
{"doc_id": 11289247, "title": "Metabolic regulation by the mitochondrial phosphatase PTPMT1 is required for hematopoietic stem cell differentiation.", "abstract": ["The regulation and coordination of mitochondrial metabolism with hematopoietic stem cell (HSC) self-renewal and differentiation is not fully understood.", "Here we report that depletion of PTPMT1, a PTEN-like mitochondrial phosphatase, in inducible or hematopoietic-cell-specific knockout mice resulted in hematopoietic failure due to changes in the cell cycle and a block in the differentiation of HSCs.", "Surprisingly, the HSC pool was increased by \u223c40-fold in PTPMT1 knockout mice.", "Reintroduction of wild-type PTPMT1, but not catalytically deficient PTPMT1 or truncated PTPMT1 lacking mitochondrial localization, restored differentiation capabilities of PTPMT1 knockout HSCs.", "Further analyses demonstrated that PTPMT1 deficiency altered mitochondrial metabolism and that phosphatidylinositol phosphate substrates of PTPMT1 directly enhanced fatty-acid-induced activation of mitochondrial uncoupling protein 2.", "Intriguingly, depletion of PTPMT1 from myeloid, T lymphoid, or B lymphoid progenitors did not cause any defects in lineage-specific knockout mice.", "This study establishes a crucial role of PTPMT1 in the metabolic regulation of HSC function."], "structured": false}
{"doc_id": 11291348, "title": "GSK-3-mediated phosphorylation enhances Maf-transforming activity.", "abstract": ["The Maf oncoproteins are b-Zip transcription factors of the AP-1 superfamily.", "They are involved in developmental, metabolic, and tumorigenic processes.", "Maf proteins are overexpressed in about 50% of human multiple myelomas.", "Here, we show that Maf-transforming activity is controlled by GSK-3-dependent phosphorylation and that phosphorylation by GSK-3 can increase the oncogenic activity of a protein.", "Using microarray analysis, we identify a gene-expression subprogram regulated by GSK-3-mediated Maf phosphorylation involved in extracellular matrix remodeling and relevant to cancer progression.", "We also demonstrate that GSK-3 triggers MafA sequential phosphorylation on residues S61, T57, T53, and S49, inducing its ubiquitination and degradation.", "Paradoxically, this phosphorylation increases MafA-transcriptional activity through the recruitment of the coactivator P/CAF.", "We further demonstrate that P/CAF protects MafA from ubiquitination and degradation, suggesting that, upon the release of the coactivator complex, MafA becomes polyubiquitinated and degraded to allow the response to terminate."], "structured": false}
{"doc_id": 11328820, "title": "NETs are a source of citrullinated autoantigens and stimulate inflammatory responses in rheumatoid arthritis.", "abstract": ["The early events leading to the development of rheumatoid arthritis (RA) remain unclear, but formation of autoantibodies to citrullinated protein antigens (ACPAs) is considered a key pathogenic event.", "Neutrophils isolated from patients with various autoimmune diseases display enhanced neutrophil extracellular trap (NET) formation, a phenomenon that exposes autoantigens in the context of immunostimulatory molecules.", "We investigated whether aberrant NETosis occurs in RA, determined its triggers, and examined its deleterious inflammatory consequences.", "Enhanced NETosis was observed in circulating and RA synovial fluid neutrophils compared to neutrophils from healthy controls and from patients with osteoarthritis (OA).", "Further, netting neutrophils infiltrated RA synovial tissue, rheumatoid nodules, and skin.", "NETosis correlated with ACPA presence and levels and with systemic inflammatory markers.", "RA sera and immunoglobulin fractions from RA patients with high levels of ACPA and/or rheumatoid factor significantly enhanced NETosis, and the NETs induced by these autoantibodies displayed distinct protein content.", "Indeed, during NETosis, neutrophils externalized the citrullinated autoantigens implicated in RA pathogenesis, and anti-citrullinated vimentin antibodies potently induced NET formation.", "Moreover, the inflammatory cytokines interleukin-17A (IL-17A) and tumor necrosis factor-\u03b1 (TNF-\u03b1) induced NETosis in RA neutrophils.", "In turn, NETs significantly augmented inflammatory responses in RA and OA synovial fibroblasts, including induction of IL-6, IL-8, chemokines, and adhesion molecules.", "These observations implicate accelerated NETosis in RA pathogenesis, through externalization of citrullinated autoantigens and immunostimulatory molecules that may promote aberrant adaptive and innate immune responses in the joint and in the periphery, and perpetuate pathogenic mechanisms in this disease."], "structured": false}
{"doc_id": 11335781, "title": "Is autoimmunity the Achilles' heel of cancer immunotherapy?", "abstract": ["The emergence of immuno-oncology as the first broadly successful strategy for metastatic cancer will require clinicians to integrate this new pillar of medicine with chemotherapy, radiation, and targeted small-molecule compounds.", "Of equal importance is gaining an understanding of the limitations and toxicities of immunotherapy.", "Immunotherapy was initially perceived to be a relatively less toxic approach to cancer treatment than other available therapies\u2014and surely it is, when compared to those.", "However, as the use of immunotherapy becomes more common, especially as first- and second-line treatments, immunotoxicity and autoimmunity are emerging as the Achilles' heel of immunotherapy.", "In this Perspective, we discuss evidence that the occurrence of immunotoxicity bodes well for the patient, and describe mechanisms that might be related to the induction of autoimmunity.", "We then explore approaches to limit immunotoxicity, and discuss the future directions of research and reporting that are needed to diminish it."], "structured": false}
{"doc_id": 11335860, "title": "Trophoblast differentiation defect in human embryonic stem cells lacking PIG-A and GPI-anchored cell-surface proteins.", "abstract": ["Pluripotent human embryonic stem (hES) cells can differentiate into various cell types derived from the three embryonic germ layers and extraembryonic tissues such as trophoblasts.", "The mechanisms governing lineage choices of hES cells are largely unknown.", "Here, we report that we established two independent hES cell clones lacking a group of cell surface molecules, glycosyl-phosphatidyl-inositol-anchored proteins (GPI-APs).", "The GPI-AP deficiency in these two hES clones is due to the deficiency in the gene expression of PIG-A (phosphatidyl-inositol-glycan class A), which is required for the first step of GPI synthesis.", "GPI-AP-deficient hES cells were capable of forming embryoid bodies and initiating cell differentiation into the three embryonic germ layers.", "However, GPI-AP-deficient hES cells failed to form trophoblasts after differentiation induction by embryoid body formation or by adding exogenous BMP4.", "The defect in trophoblast formation was due to the lack of GPI-anchored BMP coreceptors, resulting in the impairment of full BMP4 signaling activation in the GPI-AP-deficient hES cells.", "These data reveal that GPI-AP-enhanced full activation of BMP signaling is required for human trophoblast formation."], "structured": false}
{"doc_id": 11336632, "title": "CRISPR Interference Limits Horizontal Gene Transfer in Staphylococci by Targeting DNA", "abstract": ["Horizontal gene transfer (HGT) in bacteria and archaea occurs through phage transduction, transformation, or conjugation, and the latter is particularly important for the spread of antibiotic resistance.", "Clustered, regularly interspaced, short palindromic repeat (CRISPR) loci confer sequence-directed immunity against phages.", "A clinical isolate of Staphylococcus epidermidis harbors a CRISPR spacer that matches the nickase gene present in nearly all staphylococcal conjugative plasmids.", "Here we show that CRISPR interference prevents conjugation and plasmid transformation in S. epidermidis.", "Insertion of a self-splicing intron into nickase blocks interference despite the reconstitution of the target sequence in the spliced mRNA, which indicates that the interference machinery targets DNA directly.", "We conclude that CRISPR loci counteract multiple routes of HGT and can limit the spread of antibiotic resistance in pathogenic bacteria."], "structured": false}
{"doc_id": 11344428, "title": "Development of leukemia in donor cells after allogeneic stem cell transplantation--a survey of the European Group for Blood and Marrow Transplantation (EBMT).", "abstract": ["Leukemia in donor cells (donor cell leukemia; DCL) has been reported as a rare but severe complication of allogeneic stem cell transplantation (SCT).", "However, the incidence, potential pathogenetic factors, therapeutic options and outcome of patients suffering from DCL and the leukemia risk of their donors are not well defined.", "A questionnaire survey was carried out within European Blood and Marrow Transplantation Group (EBMT) centers.", "Ninety-one EBMT centers participated in this survey, covering 10489 allogeneic SCT between 12/1982 and 09/2003.", "Fourteen cases of DCL, most with a myeloid phenotype (7 cases of acute myeloid leukemia, 3 each of acute lymphocytic leukemia and 1 case of chronic myeloid leukemia) were identified.", "Demonstration of donor cell origin included molecular analysis of chimerism in most cases.", "DCL type and cytogenetic alterations were independent from the original disease.", "The median time between transplantation and diagnosis of DCL was 17 months (4-164).", "No type of conditioning, donor, graft manipulation, graft-versus-host disease prophylaxis or subsequent complications were identified as risk factors for DCL.", "Chemotherapy induced remissions in DCL and 2 of 5 patients remain alive in remission after a second transplant.", "None of the stem cell donors developed hematologic malignancies (median follow-up period of 9 years; range 6-30 years).", "DCL is an extremely rare complication of allogeneic SCT in which treatment attempts with chemotherapy and a second SCT are justified.", "Donors are not at an increased risk of developing hematologic malignancies."], "structured": false}
{"doc_id": 11349166, "title": "Lack of evidence of transfusion transmission of Creutzfeldt-Jakob disease in a US surveillance study.", "abstract": ["BACKGROUND Since 2004, several reported transfusion transmissions of variant Creutzfeldt-Jakob disease (vCJD) in the United Kingdom have reawakened concerns about the possible risk of similar transmissions of nonvariant or classic forms of CJD.   ", "STUDY DESIGN AND METHODS Patients with a CJD diagnosis and a history of donating blood were reported to the study coordinator.", "Through review of blood distribution and hospital records, the recipients of blood components from these donors were identified.", "We then determined each recipient's vital status and, if deceased, the cause(s) of death identified by matching the recipient's personal identifiers with the Centers for Disease Control and Prevention's National Death Index database.", "We conducted such searches after recipients were enrolled in this study and annually thereafter for those who remained alive.   \n", "RESULTS The study included a total of 36 blood donors who subsequently developed CJD and 436 recipients.", "Through 2006, 91 of these recipients were still alive, 329 were deceased, and 16 were lost to follow-up.", "After transfusion, these three groups had survived a total of 2096.0 person-years.", "A total of 144 recipients survived 5 years or longer after transfusion and 68 of them had received blood donated 60 or fewer months before the onset of CJD in the donor.", "We identified no recipient with CJD.   \n", "CONCLUSIONS The current results of this large, ongoing lookback study show no evidence of transfusion transmission of CJD.", "They reinforce the conclusion that the risk, if any, of transfusion transmission of prion disease by CJD donors is significantly lower than the comparable risk of such transmission by vCJD donors."], "structured": true}
{"doc_id": 11359243, "title": "Large-scale hypomethylated blocks associated with Epstein-Barr virus-induced B-cell immortalization.", "abstract": ["Altered DNA methylation occurs ubiquitously in human cancer from the earliest measurable stages.", "A cogent approach to understanding the mechanism and timing of altered DNA methylation is to analyze it in the context of carcinogenesis by a defined agent.", "Epstein-Barr virus (EBV) is a human oncogenic herpesvirus associated with lymphoma and nasopharyngeal carcinoma, but also used commonly in the laboratory to immortalize human B-cells in culture.", "Here we have performed whole-genome bisulfite sequencing of normal B-cells, activated B-cells, and EBV-immortalized B-cells from the same three individuals, in order to identify the impact of transformation on the methylome.", "Surprisingly, large-scale hypomethylated blocks comprising two-thirds of the genome were induced by EBV immortalization but not by B-cell activation per se.", "These regions largely corresponded to hypomethylated blocks that we have observed in human cancer, and they were associated with gene-expression hypervariability, similar to human cancer, and consistent with a model of epigenomic change promoting tumor cell heterogeneity.", "We also describe small-scale changes in DNA methylation near CpG islands.", "These results suggest that methylation disruption is an early and critical step in malignant transformation."], "structured": false}
{"doc_id": 11360430, "title": "Stem cell self-renewal specified by JAK-STAT activation in response to a support cell cue.", "abstract": ["Stem cells generate many differentiated, short-lived cell types, such as blood, skin, and sperm, throughout adult life.", "Stem cells maintain a long-term capacity to divide, producing daughter cells that either self-renew or initiate differentiation.", "Although the surrounding microenvironment or \"niche\" influences stem cell fate decisions, few signals that emanate from the niche to specify stem cell self-renewal have been identified.", "Here we demonstrate that the apical hub cells in the Drosophila testis act as a cellular niche that supports stem cell self-renewal.", "Hub cells express the ligand Unpaired (Upd), which activates the Janus kinase-signal transducer and activator of transcription (JAK-STAT) pathway in adjacent germ cells to specify self-renewal and continual maintenance of the germ line stem cell population."], "structured": false}
{"doc_id": 11360768, "title": "Effects of interventions in pregnancy on maternal weight and obstetric outcomes: meta-analysis of randomised evidence", "abstract": ["OBJECTIVE To evaluate the effects of dietary and lifestyle interventions in pregnancy on maternal and fetal weight and to quantify the effects of these interventions on obstetric outcomes.   \n", "DESIGN Systematic review and meta-analysis.   \n", "DATA SOURCES Major databases from inception to January 2012 without language restrictions.   ", "STUDY SELECTION Randomised controlled trials that evaluated any dietary or lifestyle interventions with potential to influence maternal weight during pregnancy and outcomes of pregnancy.   \n", "DATA SYNTHESIS Results summarised as relative risks for dichotomous data and mean differences for continuous data.   \n", "RESULTS We identified 44 relevant randomised controlled trials (7278 women) evaluating three categories of interventions: diet, physical activity, and a mixed approach.", "Overall, there was 1.42 kg reduction (95% confidence interval 0.95 to 1.89 kg) in gestational weight gain with any intervention compared with control.", "With all interventions combined, there were no significant differences in birth weight (mean difference -50 g, -100 to 0 g) and the incidence of large for gestational age (relative risk 0.85, 0.66 to 1.09) or small for gestational age (1.00, 0.78 to 1.28) babies between the groups, though by itself physical activity was associated with reduced birth weight (mean difference -60 g, -120 to -10 g).", "Interventions were associated with a reduced the risk of pre-eclampsia (0.74, 0.60 to 0.92) and shoulder dystocia (0.39, 0.22 to 0.70), with no significant effect on other critically important outcomes.", "Dietary intervention resulted in the largest reduction in maternal gestational weight gain (3.84 kg, 2.45 to 5.22 kg), with improved pregnancy outcomes compared with other interventions.", "The overall evidence rating was low to very low for important outcomes such as pre-eclampsia, gestational diabetes, gestational hypertension, and preterm delivery.   \n", "CONCLUSIONS Dietary and lifestyle interventions in pregnancy can reduce maternal gestational weight gain and improve outcomes for both mother and baby.", "Among the interventions, those based on diet are the most effective and are associated with reductions in maternal gestational weight gain and improved obstetric outcomes."], "structured": true}
{"doc_id": 11369420, "title": "Tetraspanin 3 Is Required for the Development and Propagation of Acute Myelogenous Leukemia.", "abstract": ["Acute Myelogenous Leukemia (AML) is an aggressive cancer that strikes both adults and children and is frequently resistant to therapy.", "Thus, identifying signals needed for AML propagation is a critical step toward developing new approaches for treating this disease.", "Here, we show that Tetraspanin 3 is a target of the RNA binding protein Musashi 2, which plays a key role in AML.", "We generated Tspan3 knockout mice that were born without overt defects.", "However, Tspan3 deletion impaired leukemia stem cell self-renewal and disease propagation and markedly improved survival in mouse models of AML.", "Additionally, Tspan3 inhibition blocked growth of AML patient samples, suggesting that Tspan3 is also important in human disease.", "As part of the mechanism, we show that Tspan3 deficiency disabled responses to CXCL12/SDF-1 and led to defects in AML localization within the niche.", "These identify Tspan3 as an important regulator of aggressive leukemias and highlight a role for Tspan3 in oncogenesis."], "structured": false}
{"doc_id": 11390393, "title": "Reorganization of enhancer patterns in transition from naive to primed pluripotency.", "abstract": ["Naive and primed pluripotency is characterized by distinct signaling requirements, transcriptomes, and developmental properties, but both cellular states share key transcriptional regulators: Oct4, Sox2, and Nanog.", "Here, we demonstrate that transition between these two pluripotent states is associated with widespread Oct4 relocalization, mirrored by global rearrangement of enhancer chromatin landscapes.", "Our genomic and biochemical analyses identified candidate mediators of primed state-specific Oct4 binding, including Otx2 and Zic2/3.", "Even when differentiation cues are blocked, premature Otx2 overexpression is sufficient to exit the naive state, induce transcription of a substantial subset of primed pluripotency-associated genes, and redirect Oct4 to previously inaccessible enhancer sites.", "However, the ability of Otx2 to engage new enhancer regions is determined by its levels, cis-encoded properties of the sites, and the signaling environment.", "Our results illuminate regulatory mechanisms underlying pluripotency and suggest that the capacity of transcription factors such as Otx2 and Oct4 to pioneer new enhancer sites is highly context dependent."], "structured": false}
{"doc_id": 11401602, "title": "Topoisomerase II plays an essential role as a swivelase in the late stage of SV40 chromosome replication in vitro.", "abstract": ["The effects of topoisomerases I and II on the replication of SV40 DNA were examined using an in vitro replication system of purified proteins that constitutes the monopolymerase system.", "In the presence of the two topoisomerases, two distinct nascent DNAs were formed.", "One product arising from the replication of the leading template strand was approximately half the size of the template DNA, whereas the other product derived from the lagging template strand consisted of short DNAs.", "These products were synthesized from both SV40 naked DNA and SV40 chromosomes.", "For the replication of SV40 naked DNA, either topoisomerase I or II maintained replication fork movement and supported complete leading strand synthesis.", "When SV40 chromosomes were replicated with the same proteins, reactions containing only topoisomerase I produced shorter leading strands.", "However, mature size DNA products accumulated in reactions supplemented with topoisomerase II, as well as in reactions containing only topoisomerase II.", "In the presence of crude extracts of HeLa cells, VP-16, a specific inhibitor of topoisomerase II, blocked elongation of the nascent DNA during the replication of SV40 chromosomes.", "These results indicate that topoisomerase II plays a crucial role as a swivelase in the late stage of SV40 chromosome replication in vitro."], "structured": false}
{"doc_id": 11411060, "title": "Bromodomain Proteins Contribute to Maintenance of Bloodstream Form Stage Identity in the African Trypanosome", "abstract": ["Trypanosoma brucei, the causative agent of African sleeping sickness, is transmitted to its mammalian host by the tsetse.", "In the fly, the parasite's surface is covered with invariant procyclin, while in the mammal it resides extracellularly in its bloodstream form (BF) and is densely covered with highly immunogenic Variant Surface Glycoprotein (VSG).", "In the BF, the parasite varies this highly immunogenic surface VSG using a repertoire of ~2500 distinct VSG genes.", "Recent reports in mammalian systems point to a role for histone acetyl-lysine recognizing bromodomain proteins in the maintenance of stem cell fate, leading us to hypothesize that bromodomain proteins may maintain the BF cell fate in trypanosomes.", "Using small-molecule inhibitors and genetic mutants for individual bromodomain proteins, we performed RNA-seq experiments that revealed changes in the transcriptome similar to those seen in cells differentiating from the BF to the insect stage.", "This was recapitulated at the protein level by the appearance of insect-stage proteins on the cell surface.", "Furthermore, bromodomain inhibition disrupts two major BF-specific immune evasion mechanisms that trypanosomes harness to evade mammalian host antibody responses.", "First, monoallelic expression of the antigenically varied VSG is disrupted.", "Second, rapid internalization of antibodies bound to VSG on the surface of the trypanosome is blocked.", "Thus, our studies reveal a role for trypanosome bromodomain proteins in maintaining bloodstream stage identity and immune evasion.", "Importantly, bromodomain inhibition leads to a decrease in virulence in a mouse model of infection, establishing these proteins as potential therapeutic drug targets for trypanosomiasis.", "Our 1.25\u00c5 resolution crystal structure of a trypanosome bromodomain in complex with I-BET151 reveals a novel binding mode of the inhibitor, which serves as a promising starting point for rational drug design."], "structured": false}
{"doc_id": 11414664, "title": "Timing requirements for insulin/IGF-1 signaling in C. elegans.", "abstract": ["The insulin/IGF-1 (where IGF-1 is insulin-like growth factor-1) signaling pathway influences longevity, reproduction, and diapause in many organisms.", "Because of the fundamental importance of this system in animal physiology, we asked when during the animal's life it is required to regulate these different processes.", "We find that in Caenorhabditis elegans, the pathway acts during adulthood, to relatively advanced ages, to influence aging.", "In contrast, it regulates diapause during development.", "In addition, the pathway controls longevity and reproduction independently of one another.", "Together our findings show that life-span regulation can be dissociated temporally from phenotypes that might seem to decrease the quality of life."], "structured": false}
{"doc_id": 11415809, "title": "Predominance of Type 1 Innate Lymphoid Cells in the Rectal Mucosa of Patients With Non-Celiac Wheat Sensitivity: Reversal After a Wheat-Free Diet", "abstract": ["OBJECTIVES Non-celiac wheat sensitivity (NCWS) is defined as a reaction to ingested wheat after exclusion of celiac disease and wheat allergy.", "As its pathogenesis is incompletely understood, we evaluated the inflammatory response in the rectal mucosa of patients with well-defined NCWS.   \n", "METHODS The prospective study included 22 patients with irritable bowel syndrome (IBS)-like clinical presentation, diagnosed with NCWS by double-blind placebo-controlled challenge.", "Eight IBS patients not improving on wheat-free diet were used as controls.", "Two weeks after oral challenge was performed with 80 grams of wheat daily, cells were isolated from rectal biopsies and thoroughly characterized by fluorescence-activated cell sorting analysis for intracellular cytokines and surface markers.   \n", "RESULTS Rectal biopsies from wheat-challenged NCWS patients showed that a significant mucosal CD45(+) infiltrate consisted of CD3(+) and CD3(-) lymphocytes, with the latter spontaneously producing more interferon (IFN)-\u03b3 than IBS controls.", "About 30% of IFN-\u03b3-producing CD45(+) cells were T-bet(+), CD56(-), NKP44(-), and CD117(-), defining them as a type-1 innate lymphoid cells (ILC1).", "IFN-\u03b3-producing ILC1 cells significantly decreased in 10 patients analyzed 2 weeks after they resumed a wheat-free diet.   \n", "CONCLUSIONS These data indicate that, in patients with active NCWS, IFN-\u03b3-producing ILC1 cells infiltrate rectal mucosa and support a role for this innate lymphoid cell population in the pathogenesis of NCWS."], "structured": true}
{"doc_id": 11419230, "title": "Folding and Self-Assembly of the TatA Translocation Pore Based on a Charge Zipper Mechanism", "abstract": ["We propose a concept for the folding and self-assembly of the pore-forming TatA complex from the Twin-arginine translocase and of other membrane proteins based on electrostatic \"charge zippers.", "\"", "Each subunit of TatA consists of a transmembrane segment, an amphiphilic helix (APH), and a C-terminal densely charged region (DCR).", "The sequence of charges in the DCR is complementary to the charge pattern on the APH, suggesting that the protein can be \"zipped up\" by a ladder of seven salt bridges.", "The length of the resulting hairpin matches the lipid bilayer thickness, hence a transmembrane pore could self-assemble via intra- and intermolecular salt bridges.", "The steric feasibility was rationalized by molecular dynamics simulations, and experimental evidence was obtained by monitoring the monomer-oligomer equilibrium of specific charge mutants.", "Similar \"charge zippers\" are proposed for other membrane-associated proteins, e.g., the biofilm-inducing peptide TisB, the human antimicrobial peptide dermcidin, and the pestiviral E(RNS) protein."], "structured": false}
{"doc_id": 11420613, "title": "Molecular mechanisms of ribosomal protein gene coregulation.", "abstract": ["The 137 ribosomal protein genes (RPGs) of Saccharomyces provide a model for gene coregulation.", "We examined the positional and functional organization of their regulators (Rap1 [repressor activator protein 1], Fhl1, Ifh1, Sfp1, and Hmo1), the transcription machinery (TFIIB, TFIID, and RNA polymerase II), and chromatin at near-base-pair resolution using ChIP-exo, as RPGs are coordinately reprogrammed.", "Where Hmo1 is enriched, Fhl1, Ifh1, Sfp1, and Hmo1 cross-linked broadly to promoter DNA in an RPG-specific manner and demarcated by general minor groove widening.", "Importantly, Hmo1 extended 20-50 base pairs (bp) downstream from Fhl1.", "Upon RPG repression, Fhl1 remained in place.", "Hmo1 dissociated, which was coupled to an upstream shift of the +1 nucleosome, as reflected by the Hmo1 extension and core promoter region.", "Fhl1 and Hmo1 may create two regulatable and positionally distinct barriers, against which chromatin remodelers position the +1 nucleosome into either an activating or a repressive state.", "Consistent with in vitro studies, we found that specific TFIID subunits, in addition to cross-linking at the core promoter, made precise cross-links at Rap1 sites, which we interpret to reflect native Rap1-TFIID interactions.", "Our findings suggest how sequence-specific DNA binding regulates nucleosome positioning and transcription complex assembly >300 bp away and how coregulation coevolved with coding sequences."], "structured": false}
{"doc_id": 11428884, "title": "Lipoatrophy and severe metabolic disturbance in mice with fat-specific deletion of PPAR\u03b3.", "abstract": ["Adipose tissue is an important metabolic organ, the dysfunction of which is associated with the development of obesity, diabetes mellitus, and cardiovascular disease.", "The nuclear receptor peroxisome proliferator-activated receptor gamma (PPAR\u03b3) is considered the master regulator of adipocyte differentiation and function.", "Although its cell-autonomous role in adipogenesis has been clearly demonstrated in cell culture, previous fat-specific knockouts of the murine PPAR\u03b3 gene did not demonstrate a dramatic phenotype in vivo.", "Here, using Adipoq-Cre mice to drive adipose-specific recombination, we report a unique fat-specific PPAR\u03b3 knockout (PPAR\u03b3 FKO) mouse model with almost no visible brown and white adipose tissue at age 3 mo.", "As a consequence, PPAR\u03b3 FKO mice had hugely enlarged pancreatic islets, massive fatty livers, and dramatically elevated levels of blood glucose and serum insulin accompanied by extreme insulin resistance.", "PPAR\u03b3 FKO mice also exhibited delayed hair coat formation associated with absence of dermal fat, disrupted mammary gland development with loss of mammary fat pads, and high bone mass with loss of bone marrow fat, indicating the critical roles of adipose PPAR\u03b3 in these tissues.", "Together, our data reveal the necessity of fat PPAR\u03b3 in adipose formation, whole-body metabolic homeostasis, and normal development of fat-containing tissues."], "structured": false}
{"doc_id": 11441172, "title": "Fluconazole prophylaxis: can we eliminate invasive Candida infections in the neonatal ICU?", "abstract": ["PURPOSE OF REVIEW Owing to the high mortality, risk of neurodevelopmental impairment and end-organ involvement with fungal infections in the neonate, prevention of invasive Candida infections in extremely preterm infants should be a priority for each neonatal ICU.   ", "RECENT FINDINGS Even with prompt or empiric treatment, mortality and neurodevelopmental impairment is high (57%) in infants <1000 g. Multiple studies have been performed with fluconazole prophylaxis, including a recent multicenter randomized controlled trial.", "All of the studies have demonstrated efficacy and safety with no increase or emergence of fungal resistance.", "Analysis of these studies demonstrates that fluconazole prophylaxis decreased the incidence of invasive Candida infections in high-risk infants <1000 g by 91% (P = 0.0004) and all infants <1500 g by 85% (P < 0.0001).", "The mortality rate from all causes was 25% lower (P = 0.029).", "Furthermore, studies have demonstrated that all Candida-related mortality can be eliminated in an entire neonatal ICU by targeting fluconazole prophylaxis in infants <1000 g.   SUMMARY Targeting fluconazole prophylaxis to infants who are either <1000 g or < or =27 weeks is highly effective, safe and inexpensive, and can eliminate these infections as a cause of neurodevelopmental impairment and mortality."], "structured": true}
{"doc_id": 11457219, "title": "Fumarase deficiency in dichorionic diamniotic twins.", "abstract": ["Fumarase deficiency is a rare autosomal recessive inborn error of metabolism of the Krebs Tricarboxylic Acid cycle.", "A heavy neurological disease burden is imparted by fumarase deficiency, commonly manifesting as microcephaly, dystonia, global developmental delay, seizures, and lethality in the infantile period.", "Heterozygous carriers also carry an increased risk of developing hereditary leiomyomatosis and renal cell carcinoma.", "We describe a non-consanguineous family in whom a dichorionic diamniotic twin pregnancy resulted in twin boys with fumarase deficiency proven at the biochemical, enzymatic, and molecular levels.", "Their clinical phenotype included hepatic involvement.", "A novel mutation in the fumarate hydratase gene was identified in this family."], "structured": false}
{"doc_id": 11459139, "title": "Angiopoietin-2 is increased in sepsis and inversely associated with nitric oxide-dependent microvascular reactivity", "abstract": ["INTRODUCTION Angiopoietin-2 (ang-2), an angiogenic peptide released by endothelial cell Weibel-Palade bodies (WPBs), increases endothelial activation and vascular permeability.", "Ang-2 is raised in severe sepsis but the mechanisms underlying this are not known.", "Nitric oxide (NO) inhibits WPB exocytosis, and bioavailability of endothelial NO is decreased in sepsis.", "We hypothesized that endothelial NO bioavailability would be inversely correlated with ang-2 concentrations in sepsis.   \n", "METHODS Plasma ang-2, vascular endothelial growth factor (VEGF) and endothelial-active cytokines were assessed in 83 patients with early sepsis and 41 hospital controls, and related to reactive hyperaemia-peripheral arterial tonometry, RH-PAT, a measure of endothelial NO bioavailability.   \n", "RESULTS Plasma Ang-2 was elevated in sepsis (median [interquartile range (IQR)], ng/ml: severe sepsis 12.4 [8.5-33.4], sepsis without organ failure 6.1 [5.0-10.4], controls 2.7 [2.2-3.6], P < 0.0001).", "It correlated inversely with RH-PAT (r = -0.38, P < 0.0001) and positively with IL-6 (r = 0.57, P < 0.0001) and degree of organ failure (sequential organ function assessment score) (r = 0.58, P < 0.0001).", "The correlation of ang-2 with RH-PAT persisted after controlling for sepsis severity.", "In a longitudinal mixed-effects model, recovery of RH-PAT over time was associated with decline in ang-2.   \n", "CONCLUSIONS Ang-2 is elevated in proportion to sepsis severity, and inversely correlated with NO-dependent microvascular reactivity.", "Impaired endothelial NO bioavailability may contribute to increased endothelial cell release of ang-2, endothelial activation and capillary leak.", "Agents that increase endothelial NO bioavailability or inhibit WPB exocytosis and/or Ang-2 activity may have therapeutic potential in sepsis."], "structured": true}
{"doc_id": 11469078, "title": "Ecologic versus individual-level sources of bias in ecologic estimates of contextual health effects.", "abstract": ["A number of authors have attempted to defend ecologic (aggregate) studies by claiming that the goal of those studies is estimation of ecologic (contextual or group-level) effects rather than individual-level effects.", "Critics of these attempts point out that ecologic effect estimates are inevitably used as estimates of individual effects, despite disclaimers.", "A more subtle problem is that ecologic variation in the distribution of individual effects can bias ecologic estimates of contextual effects.", "The conditions leading to this bias are plausible and perhaps even common in studies of ecosocial factors and health outcomes because social context is not randomized across typical analysis units (administrative regions).", "By definition, ecologic data contain only marginal observations on the joint distribution of individually defined confounders and outcomes, and so identify neither contextual nor individual-level effects.", "While ecologic studies can still be useful given appropriate caveats, their problems are better addressed by multilevel study designs, which obtain and use individual as well as group-level data.", "Nonetheless, such studies often share certain special problems with ecologic studies, including problems due to inappropriate aggregation and problems due to temporal changes in covariate distributions."], "structured": false}
{"doc_id": 11475379, "title": "Left\u2013right asymmetry in the vertebrate embryo: from early information to higher-level integration", "abstract": ["Although vertebrates seem to be essentially bilaterally symmetrical on the exterior, there are numerous interior left\u2013right asymmetries in the disposition and placement of internal organs.", "These asymmetries are established during embryogenesis by complex epigenetic and genetic cascades.", "Recent studies in a range of model organisms have made important progress in understanding how this laterality information is generated and conveyed to large regions of the embryo.", "Both commonalities and divergences are emerging in the mechanisms that different vertebrates use in left\u2013right axis specification.", "Recent evidence also provides intriguing links between the establishment of left\u2013right asymmetries and the symmetrical elongation of the anterior\u2013posterior axis."], "structured": false}
{"doc_id": 11481946, "title": "Obesity, type 2 diabetes, and cancer: the insulin and IGF connection.", "abstract": ["Epidemiological studies suggest a positive association between obesity and type 2 diabetes mellitus (T2D) with the risk of cancer and cancer-related mortality.", "Insulin resistance, hyperinsulinemia, increased levels of IGF, elevated levels of steroid and peptide hormones, and inflammatory markers appear to play a role in the connection between these different diseases.", "Medications, such as metformin and exogenous insulin, used to treat T2D may affect the risk of cancer and cancer-related mortality.", "Newer therapies targeting the insulin and IGF1 systems are being developed for use in cancer therapy."], "structured": false}
{"doc_id": 11484808, "title": "Non-coding RNAs: Functions and applications in endocrine-related cancer.", "abstract": ["A significant fraction of the human genome is transcribed as non-coding RNAs (ncRNAs).", "This non-coding transcriptome has challenged the notion of the central dogma and its involvement in transcriptional and post-transcriptional regulation of gene expression is well established.", "Interestingly, several ncRNAs are dysregulated in cancer and current non-coding transcriptome research aims to use our increasing knowledge of these ncRNAs for the development of cancer biomarkers and anti-cancer drugs.", "In endocrine-related cancers, for which survival rates can be relatively low, there is a need for such advancements.", "In this review, we aimed to summarize the roles and clinical implications of recently discovered ncRNAs, including long ncRNAs, PIWI-interacting RNAs, tRNA- and Y RNA-derived ncRNAs, and small nucleolar RNAs, in endocrine-related cancers affecting both sexes.", "We focus on recent studies highlighting discoveries in ncRNA biology and expression in cancer, and conclude with a discussion on the challenges and future directions, including clinical application.", "ncRNAs show great promise as diagnostic tools and therapeutic targets, but further work is necessary to realize the potential of these unconventional transcripts."], "structured": false}
{"doc_id": 11498670, "title": "NMR structural and kinetic characterization of a homeodomain diffusing and hopping on nonspecific DNA.", "abstract": ["Nonspecific protein-DNA interactions are inherently dynamic and involve both diffusion of the protein along the DNA and hopping of the protein from one DNA molecule or segment to another.", "Understanding how gene regulatory proteins interact nonspecifically with DNA in terms of both structure and dynamics is challenging because the experimental observables are an ensemble average of many rapidly exchanging states.", "By using a variety of NMR spectroscopic techniques, including relaxation analysis, paramagnetic relaxation enhancement, and residual dipolar couplings, we have characterized structural and kinetic aspects of the interaction of the HoxD9 homeodomain with a nonspecific, 24-bp DNA duplex in a system in which the protein is not constrained to any particular site.", "The data reveal that HoxD9 binds to nonspecific DNA with the same binding mode and orientation as that observed in the specific complex.", "The mobility, however, of Arg side-chains contacting the DNA is increased in the nonspecific complex relative to the specific one.", "The kinetics of intermolecular translocation between two different nonspecific DNA molecules have also been analyzed and reveal that at high DNA concentrations (such as those present in vivo) direct transfer from one nonspecific complex to another nonspecific DNA molecule occurs without going through the intermediary of free protein.", "This finding provides a simple mechanism for accelerating the target search in vivo for the specific site in a sea of nonspecific sites by permitting more effective sampling of available DNA sites as the protein jumps from one segment to another."], "structured": false}
{"doc_id": 11527199, "title": "MHC Haplotype Matching for Unrelated Hematopoietic Cell Transplantation", "abstract": ["Background  Current criteria for the selection of unrelated donors for hematopoietic cell transplantation (HCT) include matching for the alleles of each human leukocyte antigen (HLA) locus within the major histocompatibility complex (MHC).", "Graft-versus-host disease (GVHD), however, remains a significant and potentially life-threatening complication even after HLA-identical unrelated HCT.", "The MHC harbors more than 400 genes, but the total number of transplantation antigens is unknown.", "Genes that influence transplantation outcome could be identified by using linkage disequilibrium (LD)-mapping approaches, if the extended MHC haplotypes of the unrelated donor and recipient could be defined."], "structured": false}
{"doc_id": 11527822, "title": "The SIR2/3/4 complex and SIR2 alone promote longevity in Saccharomyces cerevisiae by two different mechanisms. Genes Dev 13", "abstract": ["The SIR genes are determinants of life span in yeast mother cells.", "Here we show that life span regulation by the Sir proteins is independent of their role in nonhomologous end joining.", "The short life span of a sir3 or sir4 mutant is due to the simultaneous expression of a and alpha mating-type information, which indirectly causes an increase in rDNA recombination and likely increases the production of extrachromosomal rDNA circles.", "The short life span of a sir2 mutant also reveals a direct failure to repress recombination generated by the Fob1p-mediated replication block in the rDNA.", "Sir2p is a limiting component in promoting yeast longevity, and increasing the gene dosage extends the life span in wild-type cells.", "A possible role of the conserved SIR2 in mammalian aging is discussed."], "structured": false}
{"doc_id": 11532028, "title": "Meta-analysis identifies common variants associated with body mass index in East Asians", "abstract": ["Multiple genetic loci associated with obesity or body mass index (BMI) have been identified through genome-wide association studies conducted predominantly in populations of European ancestry.", "We performed a meta-analysis of associations between BMI and approximately 2.4 million SNPs in 27,715 east Asians, which was followed by in silico and de novo replication studies in 37,691 and 17,642 additional east Asians, respectively.", "We identified ten BMI-associated loci at genome-wide significance (P < 5.0 \u00d7 10(-8)), including seven previously identified loci (FTO, SEC16B, MC4R, GIPR-QPCTL, ADCY3-DNAJC27, BDNF and MAP2K5) and three novel loci in or near the CDKAL1, PCSK1 and GP2 genes.", "Three additional loci nearly reached the genome-wide significance threshold, including two previously identified loci in the GNPDA2 and TFAP2B genes and a newly identified signal near PAX6, all of which were associated with BMI with P < 5.0 \u00d7 10(-7).", "Findings from this study may shed light on new pathways involved in obesity and demonstrate the value of conducting genetic studies in non-European populations."], "structured": false}
{"doc_id": 11532659, "title": "Phosphorylation of histone H3(T118) alters nucleosome dynamics and remodeling", "abstract": ["Nucleosomes, the fundamental units of chromatin structure, are regulators and barriers to transcription, replication and repair.", "Post-translational modifications (PTMs) of the histone proteins within nucleosomes regulate these DNA processes.", "Histone H3(T118) is a site of phosphorylation [H3(T118ph)] and is implicated in regulation of transcription and DNA repair.", "We prepared H3(T118ph) by expressed protein ligation and determined its influence on nucleosome dynamics.", "We find H3(T118ph) reduces DNA-histone binding by 2  kcal/mol, increases nucleosome mobility by 28-fold and increases DNA accessibility near the dyad region by 6-fold.", "Moreover, H3(T118ph) increases the rate of hMSH2-hMSH6 nucleosome disassembly and enables nucleosome disassembly by the SWI/SNF chromatin remodeler.", "These studies suggest that H3(T118ph) directly enhances and may reprogram chromatin remodeling reactions."], "structured": false}
{"doc_id": 11535539, "title": "Mechanosignaling through YAP and TAZ drives fibroblast activation and fibrosis.", "abstract": ["Pathological fibrosis is driven by a feedback loop in which the fibrotic extracellular matrix is both a cause and consequence of fibroblast activation.", "However, the molecular mechanisms underlying this process remain poorly understood.", "Here we identify yes-associated protein (YAP) (homolog of drosophila Yki) and transcriptional coactivator with PDZ-binding motif (TAZ) (also known as Wwtr1), transcriptional effectors of the Hippo pathway, as key matrix stiffness-regulated coordinators of fibroblast activation and matrix synthesis.", "YAP and TAZ are prominently expressed in fibrotic but not healthy lung tissue, with particularly pronounced nuclear expression of TAZ in spindle-shaped fibroblastic cells.", "In culture, both YAP and TAZ accumulate in the nuclei of fibroblasts grown on pathologically stiff matrices but not physiologically compliant matrices.", "Knockdown of YAP and TAZ together in vitro attenuates key fibroblast functions, including matrix synthesis, contraction, and proliferation, and does so exclusively on pathologically stiff matrices.", "Profibrotic effects of YAP and TAZ operate, in part, through their transcriptional target plasminogen activator inhibitor-1, which is regulated by matrix stiffness independent of transforming growth factor-\u03b2 signaling.", "Immortalized fibroblasts conditionally expressing active YAP or TAZ mutant proteins overcome soft matrix limitations on growth and promote fibrosis when adoptively transferred to the murine lung, demonstrating the ability of fibroblast YAP/TAZ activation to drive a profibrotic response in vivo.", "Together, these results identify YAP and TAZ as mechanoactivated coordinators of the matrix-driven feedback loop that amplifies and sustains fibrosis."], "structured": false}
{"doc_id": 11557602, "title": "Control of cellular cholesterol efflux by the nuclear oxysterol receptor LXR alpha.", "abstract": ["LXR alpha is a nuclear receptor that has previously been shown to regulate the metabolic conversion of cholesterol to bile acids.", "Here we define a role for this transcription factor in the control of cellular cholesterol efflux.", "We demonstrate that retroviral expression of LXR alpha in NIH 3T3 fibroblasts or RAW264.7 macrophages and/or treatment of these cells with oxysterol ligands of LXR results in 7- to 30-fold induction of the mRNA encoding the putative cholesterol/phospholipid transporter ATP-binding cassette (ABC)A1.", "In contrast, induction of ABCA1 mRNA in response to oxysterols is attenuated in cells that constitutively express dominant-negative forms of LXR alpha or LXR beta that lack the AF2 transcriptional activation domain.", "We further demonstrate that expression of LXR alpha in NIH 3T3 fibroblasts and/or treatment of these cells with oxysterols is sufficient to stimulate cholesterol efflux to extracellular apolipoprotein AI.", "The ability of oxysterol ligands of LXR to stimulate efflux is dramatically reduced in Tangier fibroblasts, which carry a loss of function mutation in the ABCA1 gene.", "Taken together, these results indicate that cellular cholesterol efflux is controlled, at least in part, at the level of transcription by a nuclear receptor-signaling pathway.", "They suggest a model in which activation of LXRs by oxysterols in response to cellular sterol loading leads to induction of the ABCA1 transporter and the stimulation of lipid efflux to extracellular acceptors.", "These findings have important implications for our understanding of mammalian cholesterol homeostasis and suggest new opportunities for pharmacological regulation of cellular lipid metabolism."], "structured": false}
{"doc_id": 11565780, "title": "Circadian regulation of intracellular G-protein signalling mediates intercellular synchrony and rhythmicity in the suprachiasmatic nucleus", "abstract": ["Synchronous oscillations of thousands of cellular clocks in the suprachiasmatic nucleus (SCN), the circadian centre, are coordinated by precisely timed cell-cell communication, the principle of which is largely unknown.", "Here we show that the amount of RGS16 (regulator of G protein signalling 16), a protein known to inactivate G\u03b1i, increases at a selective circadian time to allow time-dependent activation of intracellular cyclic AMP signalling in the SCN.", "Gene ablation of Rgs16 leads to the loss of circadian production of cAMP and as a result lengthens circadian period of behavioural rhythm.", "The temporally precise regulation of the cAMP signal by clock-controlled RGS16 is needed for the dorsomedial SCN to maintain a normal phase-relationship to the ventrolateral SCN.", "Thus, RGS16-dependent temporal regulation of intracellular G protein signalling coordinates the intercellular synchrony of SCN pacemaker neurons and thereby defines the 24 h rhythm in behaviour."], "structured": false}
{"doc_id": 11568270, "title": "MDC1 collaborates with TopBP1 in DNA replication checkpoint control", "abstract": ["Human TopBP1 is a major player in the control of the DNA replication checkpoint.", "In this study, we identified MDC1, a key checkpoint protein involved in the cellular response to DNA double-strand breaks, as a TopBP1-associated protein.", "The specific TopBP1-MDC1 interaction is mediated by the fifth BRCT domain of TopBP1 and the Ser-Asp-Thr (SDT) repeats of MDC1.", "In addition, we demonstrated that TopBP1 accumulation at stalled replication forks is promoted by the H2AX/MDC1 signaling cascade.", "Moreover, MDC1 is important for ATR-dependent Chk1 activation in response to replication stress.", "Collectively, our data suggest that MDC1 facilitates several important steps in both cellular DNA damage response and the DNA replication checkpoint."], "structured": false}
{"doc_id": 11569583, "title": "Deregulated DNA polymerase \u03b2 strengthens ionizing radiation-induced nucleotidic and chromosomal instabilities", "abstract": ["DNA polymerase \u03b2 (Pol \u03b2) is an error-prone enzyme which has been found to be overexpressed in several human tumors.", "By using a couple of recombinant CHO cells differing only from the exogenous expression of Pol \u03b2, we showed here that cells overexpressing Pol \u03b2 are much more sensitive to IR treatments by increasing apoptosis.", "We also found that the surviving cells displayed an hypermutator phenotype which could be explained by different pathways involving Pol \u03b2, such as (i) an increased capacity to incorporate into DNA the mutagenic dGTP analog, 8-oxo-dGTP, one of the most abundant purine-derived nucleotides exposed to \u03b3-irradiation, (ii) the induction of IR-induced DNA breaks and (iii) accumulation of chromosome aberrations induced by radiation.", "Alteration of Pol \u03b2 expression in irradiated cells thus appears to strengthen both cell death and genetic changes associated with a malignant phenotype.", "These data provide new insights into the cellular response to radiations and the associated carcinogenic consequences."], "structured": false}
{"doc_id": 11578459, "title": "Chromosome 7 gain and DNA hypermethylation at the HOXA10 locus are associated with expression of a stem cell related HOX-signature in glioblastoma", "abstract": ["BACKGROUND HOX genes are a family of developmental genes that are expressed neither in the developing forebrain nor in the normal brain.", "Aberrant expression of a HOX-gene dominated stem-cell signature in glioblastoma has been linked with increased resistance to chemo-radiotherapy and sustained proliferation of glioma initiating cells.", "Here we describe the epigenetic and genetic alterations and their interactions associated with the expression of this signature in glioblastoma.   \n", "RESULTS We observe prominent hypermethylation of the HOXA locus 7p15.2 in glioblastoma in contrast to non-tumoral brain.", "Hypermethylation is associated with a gain of chromosome 7, a hallmark of glioblastoma, and may compensate for tumor-driven enhanced gene dosage as a rescue mechanism by preventing undue gene expression.", "We identify the CpG island of the HOXA10 alternative promoter that appears to escape hypermethylation in the HOX-high glioblastoma.", "An additive effect of gene copy gain at 7p15.2 and DNA methylation at key regulatory CpGs in HOXA10 is significantly associated with HOX-signature expression.", "Additionally, we show concordance between methylation status and presence of active or inactive chromatin marks in glioblastoma-derived spheres that are HOX-high or HOX-low, respectively.   \n", "CONCLUSIONS Based on these findings, we propose co-evolution and interaction between gene copy gain, associated with a gain of chromosome 7, and additional epigenetic alterations as key mechanisms triggering a coordinated, but inappropriate, HOX transcriptional program in glioblastoma."], "structured": true}
{"doc_id": 11581157, "title": "Probing the phenomenon of trained immunity in invertebrates during a transgenerational study, using brine shrimp Artemia as a model system", "abstract": ["The invertebrate's innate immune system was reported to show some form of adaptive features, termed trained immunity.", "However, the memory characteristics of innate immune system and the mechanisms behind such phenomena remain unclear.", "Using the invertebrate model Artemia, we verified the possibility or impossibility of trained immunity, examining the presence or absence of enduring memory against homologous and heterologous antigens (Vibrio spp.) during a transgenerational study.", "We also determined the mechanisms behind such phenomenon.", "Our results showed the occurrence of memory and partial discrimination in Artemia's immune system, as manifested by increased resistance, for three successive generations, of the progenies of Vibrio-exposed ancestors towards a homologous bacterial strain, rather than to a heterologous strain.", "This increased resistance phenotype was associated with elevated levels of hsp70 and hmgb1 signaling molecules and alteration in the expression of key innate immunity-related genes.", "Our results also showed stochastic pattern in the acetylation and methylation levels of H4 and H3K4me3 histones, respectively, in the progenies whose ancestors were challenged.", "Overall results suggest that innate immune responses in invertebrates have the capacity to be trained, and epigenetic reprogramming of (selected) innate immune effectors is likely to have central place in the mechanisms leading to trained immunity."], "structured": false}
{"doc_id": 11603066, "title": "Using Structural Information to Change the Phosphotransfer Specificity of a Two-Component Chemotaxis Signalling Complex", "abstract": ["Two-component signal transduction pathways comprising histidine protein kinases (HPKs) and their response regulators (RRs) are widely used to control bacterial responses to environmental challenges.", "Some bacteria have over 150 different two-component pathways, and the specificity of the phosphotransfer reactions within these systems is tightly controlled to prevent unwanted crosstalk.", "One of the best understood two-component signalling pathways is the chemotaxis pathway.", "Here, we present the 1.40 A crystal structure of the histidine-containing phosphotransfer domain of the chemotaxis HPK, CheA(3), in complex with its cognate RR, CheY(6).", "A methionine finger on CheY(6) that nestles in a hydrophobic pocket in CheA(3) was shown to be important for the interaction and was found to only occur in the cognate RRs of CheA(3), CheY(6), and CheB(2).", "Site-directed mutagenesis of this methionine in combination with two adjacent residues abolished binding, as shown by surface plasmon resonance studies, and phosphotransfer from CheA(3)-P to CheY(6).", "Introduction of this methionine and an adjacent alanine residue into a range of noncognate CheYs, dramatically changed their specificity, allowing protein interaction and rapid phosphotransfer from CheA(3)-P. The structure presented here has allowed us to identify specificity determinants for the CheA-CheY interaction and subsequently to successfully reengineer phosphotransfer signalling.", "In summary, our results provide valuable insight into how cells mediate specificity in one of the most abundant signalling pathways in biology, two-component signal transduction."], "structured": false}
{"doc_id": 11614737, "title": "Combination varenicline and bupropion SR for tobacco-dependence treatment in cigarette smokers: a randomized trial.", "abstract": ["IMPORTANCE Combining pharmacotherapies for tobacco-dependence treatment may increase smoking abstinence.   \n", "OBJECTIVE To determine efficacy and safety of varenicline and bupropion sustained-release (SR; combination therapy) compared with varenicline (monotherapy) in cigarette smokers.   \n", "DESIGN, SETTING, AND PARTICIPANTS Randomized, blinded, placebo-controlled multicenter clinical trial with a 12-week treatment period and follow-up through week 52 conducted between October 2009 and April 2013 at 3 midwestern clinical research sites.", "Five hundred six adult (\u226518 years) cigarette smokers were randomly assigned and 315 (62%) completed the study.   \n", "INTERVENTIONS Twelve weeks of varenicline and bupropion SR or varenicline and placebo.   \n", "MAIN OUTCOMES AND MEASURES Primary outcome was abstinence rates at week 12, defined as prolonged (no smoking from 2 weeks after the target quit date) abstinence and 7-day point-prevalence (no smoking past 7 days) abstinence.", "Secondary outcomes were prolonged and point-prevalence smoking abstinence rates at weeks 26 and 52.", "Outcomes were biochemically confirmed.   \n", "RESULTS At 12 weeks, 53.0% of the combination therapy group achieved prolonged smoking abstinence and 56.2% achieved 7-day point-prevalence smoking abstinence compared with 43.2% and 48.6% in varenicline monotherapy (odds ratio [OR], 1.49; 95% CI, 1.05-2.12; P = .03 and OR, 1.36; 95% CI, 0.95-1.93; P = .09, respectively).", "At 26 weeks, 36.6% of the combination therapy group achieved prolonged and 38.2% achieved 7-day point-prevalence smoking abstinence compared with 27.6% and 31.9% in varenicline monotherapy (OR, 1.52; 95% CI, 1.04-2.22; P = .03 and OR, 1.32; 95% CI, 0.91-1.91; P = .14, respectively).", "At 52 weeks, 30.9% of the combination therapy group achieved prolonged and 36.6% achieved 7-day point-prevalence smoking abstinence compared with 24.5% and 29.2% in varenicline monotherapy (OR, 1.39; 95% CI, 0.93-2.07; P = .11 and OR, 1.40; 95% CI, 0.96-2.05; P = .08, respectively).", "Participants receiving combination therapy reported more anxiety (7.2% vs 3.1%; P = .04) and depressive symptoms (3.6% vs 0.8%; P = .03).   \n", "CONCLUSIONS AND RELEVANCE Among cigarette smokers, combined use of varenicline and bupropion, compared with varenicline alone, increased prolonged abstinence but not 7-day point prevalence at 12 and 26 weeks.", "Neither outcome was significantly different at 52 weeks.", "Further research is required to determine the role of combination therapy in smoking cessation.   \n", "TRIAL REGISTRATION clinicaltrials.gov Identifier: http://clinicaltrials.gov/show/NCT00935818."], "structured": true}
{"doc_id": 11615242, "title": "Effect of a C/EBP gene replacement on mitochondrial biogenesis in fat cells.", "abstract": ["CCAAT/enhancer-binding proteins, C/EBPalpha and C/EBPbeta, are required for fat cell differentiation and maturation.", "Previous studies showed that replacement of C/EBPalpha with C/EBPbeta, generating the beta/beta alleles in the mouse genome, prevents lipid accumulation in white adipose tissue (WAT).", "In this study, beta/beta mice lived longer and had higher energy expenditure than their control littermates due to increased WAT energy oxidation.", "The WAT of beta/beta mice was enriched with metabolically active, thermogenic mitochondria known for energy burning.", "The beta/beta allele exerted its effect through the elevated expression of the G protein alpha stimulatory subunit (Galphas) in WAT.", "Galphas, when overexpressed in fat-laden 3T3-L1 cells, stimulated mitochondrial biogenesis similar to that seen in the WAT of beta/beta mice, and effectively diminished the stored lipid pool."], "structured": false}
{"doc_id": 11615422, "title": "Variable breakpoints target PAX5 in patients with dicentric chromosomes: a model for the basis of unbalanced translocations in cancer.", "abstract": ["The search for target genes involved in unbalanced acquired chromosomal abnormalities has been largely unsuccessful, because the breakpoints of these rearrangements are too variable.", "Here, we use the example of dicentric chromosomes in B cell precursor acute lymphoblastic leukemia to show that, despite this heterogeneity, single genes are targeted through a variety of mechanisms.", "FISH showed that, although they were heterogeneous, breakpoints on 9p resulted in the partial or complete deletion of PAX5.", "Molecular copy number counting further delineated the breakpoints and facilitated cloning with long-distance inverse PCR.", "This approach identified 5 fusion gene partners with PAX5: LOC392027 (7p12.1), SLCO1B3 (12p12), ASXL1 (20q11.1), KIF3B (20q11.21), and C20orf112 (20q11.1).", "In each predicted fusion protein, the DNA-binding paired domain of PAX5 was present.", "Using quantitative PCR, we demonstrated that both the deletion and gene fusion events resulted in the same underexpression of PAX5, which extended to the differential expression of the PAX5 target genes, EBF1, ALDH1A1, ATP9A, and FLT3.", "Further molecular analysis showed deletion and mutation of the homologous PAX5 allele, providing further support for the key role of PAX5.", "Here, we show that specific gene loci may be the target of heterogeneous translocation breakpoints in human cancer, acting through a variety of mechanisms.", "This approach indicates an application for the identification of cancer genes in solid tumours, where unbalanced chromosomal rearrangements are particularly prevalent and few genes have been identified.", "It can be extrapolated that this strategy will reveal that the same mechanisms operate in cancer pathogenesis in general."], "structured": false}
{"doc_id": 11616424, "title": "Copyright \ufffd 1996, American Society for Microbiology Endotoxin-Induced Enhancement of Glucose Influx into", "abstract": ["Hypoglycemia is among the most injurious metabolic disorders caused by endotoxemia.", "In experimental endotoxemia with lipopolysaccharide (LPS) in animals, a marked glucose consumption is observed in macrophage-rich organs.", "However, the direct effect of LPS on the uptake of glucose by macrophages has not been fully understood, and the present study was undertaken to shed light on this point.", "The consumption and uptake of glucose, as measured with 2-deoxy-D-[3H]glucose, by murine peritoneal exudate macrophages in culture were accelerated two- to threefold by stimulation with 3 ng of LPS per ml.", "The rate of glucose uptake reached a plateau after 20 min of stimulation and remained at the maximum as long as LPS was present.", "Northern (RNA) blot analysis with cDNA probes for five known isoforms of glucose transporter (GLUT) revealed that the expression of GLUT by macrophages was restricted to the GLUT1 isoform during LPS stimulation and the amount of GLUT1 mRNA was increased by the stimulation.", "These results suggest that macrophage responses to LPS are supported by a rapid and sustained glucose influx via GLUT1 and that this is a participating factor in the development of systemic hypoglycemia when endotoxemia is prolonged."], "structured": false}
{"doc_id": 11624482, "title": "Factors associated with American Board of Medical Specialties member board certification among US medical school graduates.", "abstract": ["CONTEXT Certification by an American Board of Medical Specialties (ABMS) member board is emerging as a measure of physician quality.   \n", "OBJECTIVE To identify demographic and educational factors associated with ABMS member board certification of US medical school graduates.   \n", "DESIGN, SETTING, AND PARTICIPANTS Retrospective study of a national cohort of 1997-2000 US medical school graduates, grouped by specialty choice at graduation and followed up through March 2, 2009.", "In separate multivariable logistic regression models for each specialty category, factors associated with ABMS member board certification were identified.   \n", "MAIN OUTCOME MEASURE ABMS member board certification.   \n", "RESULTS Of 42,440 graduates in the study sample, 37,054 (87.3%) were board certified.", "Graduates in all specialty categories with first-attempt passing scores in the highest tertile (vs first-attempt failing scores) on US Medical Licensing Examination Step 2 Clinical Knowledge were more likely to be board certified; adjusted odds ratios (AORs) varied by specialty category, with the lowest odds for emergency medicine (87.4% vs 73.6%; AOR, 1.82; 95% CI, 1.03-3.20) and highest odds for radiology (98.1% vs 74.9%; AOR, 13.19; 95% CI, 5.55-31.32).", "In each specialty category except family medicine, graduates self-identified as underrepresented racial/ethnic minorities (vs white) were less likely to be board certified, ranging from 83.5% vs 95.6% in the pediatrics category (AOR, 0.44; 95% CI, 0.33-0.58) to 71.5% vs 83.7% in the other nongeneralist specialties category (AOR, 0.79; 95% CI, 0.64-0.96).", "With each $50,000 unit increase in debt (vs no debt), graduates choosing obstetrics/gynecology were less likely to be board certified (AOR, 0.89; 95% CI, 0.83-0.96), and graduates choosing family medicine were more likely to be board certified (AOR, 1.13; 95% CI, 1.01-1.26).   \n", "CONCLUSION Demographic and educational factors were associated with board certification among US medical school graduates in every specialty category examined; findings varied among specialty categories."], "structured": true}
{"doc_id": 11630388, "title": "Body-mass index and mortality in Korean men and women.", "abstract": ["BACKGROUND Obesity is associated with diverse health risks, but the role of body weight as a risk factor for death remains controversial.   \n", "METHODS We examined the association between body weight and the risk of death in a 12-year prospective cohort study of 1,213,829 Koreans between the ages of 30 and 95 years.", "We examined 82,372 deaths from any cause and 48,731 deaths from specific diseases (including 29,123 from cancer, 16,426 from atherosclerotic cardiovascular disease, and 3362 from respiratory disease) in relation to the body-mass index (BMI) (the weight in kilograms divided by the square of the height in meters).   \n", "RESULTS In both sexes, the average baseline BMI was 23.2, and the rate of death from any cause had a J-shaped association with the BMI, regardless of cigarette-smoking history.", "The risk of death from any cause was lowest among patients with a BMI of 23.0 to 24.9.", "In all groups, the risk of death from respiratory causes was higher among subjects with a lower BMI, and the risk of death from atherosclerotic cardiovascular disease or cancer was higher among subjects with a higher BMI.", "The relative risk of death associated with BMI declined with increasing age.   \n", "CONCLUSIONS Underweight, overweight, and obese men and women had higher rates of death than men and women of normal weight.", "The association of BMI with death varied according to the cause of death and was modified by age, sex, and smoking history."], "structured": true}
{"doc_id": 11659421, "title": "Human iPSC-based modeling of late-onset disease via progerin-induced aging.", "abstract": ["Reprogramming somatic cells to induced pluripotent stem cells (iPSCs) resets their identity back to an embryonic age and, thus, presents a significant hurdle for modeling late-onset disorders.", "In this study, we describe a strategy for inducing aging-related features in human iPSC-derived lineages and apply it to the modeling of Parkinson's disease (PD).", "Our approach involves expression of progerin, a truncated form of lamin A associated with premature aging.", "We found that expression of progerin in iPSC-derived fibroblasts and neurons induces multiple aging-related markers and characteristics, including dopamine-specific phenotypes such as neuromelanin accumulation.", "Induced aging in PD iPSC-derived dopamine neurons revealed disease phenotypes that require both aging and genetic susceptibility, such as pronounced dendrite degeneration, progressive loss of tyrosine hydroxylase (TH) expression, and enlarged mitochondria or Lewy-body-precursor inclusions.", "Thus, our study suggests that progerin-induced aging can be used to reveal late-onset age-related disease features in hiPSC-based disease models."], "structured": false}
{"doc_id": 11661377, "title": "SNAREs \u2014 engines for membrane fusion", "abstract": ["Since the discovery of SNARE proteins in the late 1980s, SNAREs have been recognized as key components of protein complexes that drive membrane fusion.", "Despite considerable sequence divergence among SNARE proteins, their mechanism seems to be conserved and is adaptable for fusion reactions as diverse as those involved in cell growth, membrane repair, cytokinesis and synaptic transmission.", "A fascinating picture of these robust nanomachines is emerging."], "structured": false}
{"doc_id": 11666252, "title": "Maintaining the norm: T-cell homeostasis", "abstract": ["The persistence of naive and memory T cells has long been of interest to immunologists, but the factors that influence the survival and homeostasis of these subsets have remained obscure.", "In recent years, it has become evident that the homeostasis of both naive and memory T-cell pools is highly dynamic and tightly regulated by internal stimuli, including cytokines and self-peptide\u2013MHC ligands for the T-cell receptor.", "These homeostatic mechanisms might have a vital influence on the capacity of the T-cell pool to respond to both foreign and self-antigens."], "structured": false}
{"doc_id": 11674288, "title": "Cell type of origin influences the molecular and functional properties of mouse induced pluripotent stem cells", "abstract": ["Induced pluripotent stem cells (iPSCs) have been derived from various somatic cell populations through ectopic expression of defined factors.", "It remains unclear whether iPSCs generated from different cell types are molecularly and functionally similar.", "Here we show that iPSCs obtained from mouse fibroblasts, hematopoietic and myogenic cells exhibit distinct transcriptional and epigenetic patterns.", "Moreover, we demonstrate that cellular origin influences the in vitro differentiation potentials of iPSCs into embryoid bodies and different hematopoietic cell types.", "Notably, continuous passaging of iPSCs largely attenuates these differences.", "Our results suggest that early-passage iPSCs retain a transient epigenetic memory of their somatic cells of origin, which manifests as differential gene expression and altered differentiation capacity.", "These observations may influence ongoing attempts to use iPSCs for disease modeling and could also be exploited in potential therapeutic applications to enhance differentiation into desired cell lineages."], "structured": false}
{"doc_id": 11674596, "title": "Spatiotemporal control of mitosis by the conserved spindle matrix protein Megator", "abstract": ["A putative spindle matrix has been hypothesized to mediate chromosome motion, but its existence and functionality remain controversial.", "In this report, we show that Megator (Mtor), the Drosophila melanogaster counterpart of the human nuclear pore complex protein translocated promoter region (Tpr), and the spindle assembly checkpoint (SAC) protein Mad2 form a conserved complex that localizes to a nuclear derived spindle matrix in living cells.", "Fluorescence recovery after photobleaching experiments supports that Mtor is retained around spindle microtubules, where it shows distinct dynamic properties.", "Mtor/Tpr promotes the recruitment of Mad2 and Mps1 but not Mad1 to unattached kinetochores (KTs), mediating normal mitotic duration and SAC response.", "At anaphase, Mtor plays a role in spindle elongation, thereby affecting normal chromosome movement.", "We propose that Mtor/Tpr functions as a spatial regulator of the SAC, which ensures the efficient recruitment of Mad2 to unattached KTs at the onset of mitosis and proper spindle maturation, whereas enrichment of Mad2 in a spindle matrix helps confine the action of a diffusible \"wait anaphase\" signal to the vicinity of the spindle."], "structured": false}
{"doc_id": 11705328, "title": "Randomized trial of folic acid supplementation and serum homocysteine levels.", "abstract": ["BACKGROUND Lowering serum homocysteine levels with folic acid is expected to reduce mortality from ischemic heart disease.", "Homocysteine reduction is known to be maximal at a folic acid dosage of 1 mg/d, but the effect of lower doses (relevant to food fortification) is unclear.   \n", "METHODS We randomized 151 patients with ischemic heart disease to 1 of 5 dosages of folic acid (0.2, 0.4, 0.6, 0.8, and 1.0 mg/d) or placebo.", "Fasting blood samples for serum homocysteine and serum folate analysis were taken initially, after 3 months of supplementation, and 3 months after folic acid use was discontinued.   \n", "RESULTS Median serum homocysteine level decreased with increasing folic acid dosage, to a maximum at 0.8 mg of folic acid per day, when the homocysteine reduction (placebo adjusted) was 2.7 micromol/L (23%), similar to the known effect of folic acid dosages of 1 mg/d and above.", "The higher a person's initial serum homocysteine level, the greater was the response to folic acid, but there were statistically significant reductions regardless of the initial level.", "Serum folate level increased approximately linearly (5.5 nmol/L for every 0.1 mg of folic acid).", "Within-person fluctuations over time in serum homocysteine levels, measured in the placebo group, were large compared with the effect of folic acid, indicating that monitoring of the reduction in an individual is impractical.   \n", "CONCLUSIONS A dosage of folic acid of 0.8 mg/d appears necessary to achieve the maximum reduction in serum homocysteine level across the range of homocysteine levels in the population.", "Current US food fortification levels will achieve only a small proportion of the achievable homocysteine reduction."], "structured": true}
{"doc_id": 11710511, "title": "Adherens junctions in Drosophila retinal morphogenesis.", "abstract": ["Adherens junctions and their core molecular components, classic cadherins, make major contributions to animal morphogenesis.", "Although the significance of cadherins in development is generally accepted, the mechanisms regulating adherens junction function during morphogenesis remain a subject of intense research.", "Adherens junctions are involved in the organization of simple cellular patterns, and more complex cell shape changes and cell movements that depend on the dynamic modulation of adherens junctions."], "structured": false}
{"doc_id": 11716783, "title": "Multiple roles of vascular endothelial growth factor (VEGF) in skeletal development, growth, and repair.", "abstract": ["Publisher Summary This chapter discusses the developmental roles of vascular endothelial growth factor (VEGF) in skeletal morphogenesis, speculates on the future directions of research in this area, and describes some of the challenges in the field.", "VEGF regulates osteoclastic differentiation, migration, and activity.", "VEGF is, therefore, a key coordinator of the entire process.", "VEGF is necessary for osteoclastic activity both at the stage when the primary ossification center is established and later during bone growth.", "A number of studies have led to the identification of VEGF as a critical factor for the survival of chondrocytes.", "Several factors with important roles in regulating bone formation also induce the expression of VEGF by osteoblasts.", "Prostaglandins E1 and E2, BMP-4, BMP-6, BMP-7, FGF-2, TGF-\u03b2, endothelin-1, IGF-1, and vitamin D3 can all induce VEGF expression in osteoblasts by activating a variety of signaling pathways.", "Bone fractures can heal in two divergent ways, similar to the two ways of forming bone during embryonic development.", "Stabilized fractures heal by intramembranous ossification, and unstable fractures undergo endochondral ossification.", "The similarity between the embryonic bone development and repair of fractured bones, coupled with the finding that VEGF is expressed at sites of bone fracture, suggests that VEGF is involved in bone repair as it is in bone development."], "structured": false}
{"doc_id": 11718220, "title": "Effectiveness of thigh-length graduated compression stockings to reduce the risk of deep vein thrombosis after stroke (CLOTS trial 1): a multicentre, randomised controlled trial", "abstract": ["BACKGROUND Deep vein thrombosis (DVT) and pulmonary embolism are common after stroke.", "In small trials of patients undergoing surgery, graduated compression stockings (GCS) reduce the risk of DVT.", "National stroke guidelines extrapolating from these trials recommend their use in patients with stroke despite insufficient evidence.", "We assessed the effectiveness of thigh-length GCS to reduce DVT after stroke.   \n", "METHODS In this outcome-blinded, randomised controlled trial, 2518 patients who were admitted to hospital within 1 week of an acute stroke and who were immobile were enrolled from 64 centres in the UK, Italy, and Australia.", "Patients were allocated via a central randomisation system to routine care plus thigh-length GCS (n=1256) or to routine care plus avoidance of GCS (n=1262).", "A technician who was blinded to treatment allocation undertook compression Doppler ultrasound of both legs at about 7-10 days and, when practical, again at 25-30 days after enrolment.", "The primary outcome was the occurrence of symptomatic or asymptomatic DVT in the popliteal or femoral veins.", "Analyses were by intention to treat.", "This study is registered, number ISRCTN28163533.   \n", "FINDINGS All patients were included in the analyses.", "The primary outcome occurred in 126 (10.0%) patients allocated to thigh-length GCS and in 133 (10.5%) allocated to avoid GCS, resulting in a non-significant absolute reduction in risk of 0.5% (95% CI -1.9% to 2.9%).", "Skin breaks, ulcers, blisters, and skin necrosis were significantly more common in patients allocated to GCS than in those allocated to avoid their use (64 [5%] vs 16 [1%]; odds ratio 4.18, 95% CI 2.40-7.27).   \n", "INTERPRETATION These data do not lend support to the use of thigh-length GCS in patients admitted to hospital with acute stroke.", "National guidelines for stroke might need to be revised on the basis of these results.   \n", "FUNDING Medical Research Council (UK), Chief Scientist Office of Scottish Government, Chest Heart and Stroke Scotland, Tyco Healthcare (Covidien) USA, and UK Stroke Research Network."], "structured": true}
{"doc_id": 11721286, "title": "Streptococcus pneumoniae early response genes to human lung epithelial cells", "abstract": ["BACKGROUND Streptococcus pneumoniae infection starts from colonization of the host respiratory tract where interaction with host respiratory tract epithelial cells occurs.", "To investigate pneumococcal genes that are involved in the early stage of interaction with host epithelial cells, transcriptional responses of an encapsulated pathogenic pneumococcal strain TIGR4 upon exposure to human lung epithelial cells A549 for 0.5 h and 1 h time periods were investigated by using TIGR (JCVI) microarray technology.", "Gene expression changes were validated by quantitative real-time PCR (qRT-PCR) analysis.   \n", "FINDINGS We observed different transcriptional profiles at two incubation time periods in which most gene expressions were down-regulated at 0.5 h but up-regulated at 1 h. Many genes associated with ribonucleotide biosynthesis were down-regulated at both time points, whereas the genes associated with cell envelope, energy metabolism, transport and protein synthesis were mostly up-regulated at 1 h. Furthermore, these profiles were compared to the transcriptomes of a TIGR4-derived strain in response to human macrophages for the same time periods.", "We found one set of genes that exhibited similar expression changes upon exposure to both types of host cells, including cell envelope-associated bgaA (SP0648) and nanA (SP1693), and uncharacterized gene clusters such as SP1677-SP1680 and SP1688-SP1690.   \n", "CONCLUSION These data indicate that at the early stage of interaction with host epithelial cells, a complex gene regulation and expression change occur in bacteria.", "Some of them might play an essential role during pathogen-host interactions and for the establishment of infection."], "structured": true}
{"doc_id": 11721676, "title": "Proteomic identification of a novel isoform of collapsin response mediator protein-2 in spinal nerves peripheral to dorsal root ganglia.", "abstract": ["Primary afferent fibers are originated from pseudounipolar sensory cells in dorsal root ganglia (DRG) and transmit external stimuli received in the skin to the spinal cord.", "Here we undertook a proteomic approach to uncover the polarity of primary afferent fibers.", "Lumbar spinal nerve segments, peripheral and central to DRG, were dissected from 5-wk-old Wistar rats and the lysates were subjected to large-sized 2-DE at pH 5-6.", "Among approximately 800 protein spots detected in the central and peripheral fractions, one of the unique spots in the peripheral fraction with MW of 60 kDa and pI of 5.6 was identified as an isoform of collapsin response mediator protein-2 (CRMP-2) by MALDI-TOF MS and Western blots with anti-CRMP-2 antibodies that recognize 1-17 and 486-528 residues.", "Since this novel spot was detected only in the peripheral fraction, but not in the central fraction, DRG, and other regions of the brain, it was named periCRMP-2.", "The C-terminal fragment of CRMP-2 was not detected in periCRMP-2 by MS analyses.", "Expression of periCRMP-2 decreased following sciatic nerve injury.", "These results suggest that periCRMP-2 is a C-terminal truncated isoform polarized in the peripheral side of spinal nerves and may be involved in nerve degeneration and regeneration."], "structured": false}
{"doc_id": 11728637, "title": "Empirical statistical estimates for sequence similarity searches", "abstract": ["The FASTA package of sequence comparison programs has been modified to provide accurate statistical estimates for local sequence similarity scores with gaps.", "These estimates are derived using the extreme value distribution from the mean and variance of the local similarity scores of unrelated sequences after the scores have been corrected for the expected effect of library sequence length.", "This approach allows accurate estimates to be calculated for both FASTA and Smith-Waterman similarity scores for protein/protein, DNA/DNA, and protein/translated-DNA comparisons.", "The accuracy of the statistical estimates is summarized for 54 protein families using FASTA and Smith-Waterman scores.", "Probability estimates calculated from the distribution of similarity scores are generally conservative, as are probabilities calculated using the Altschul-Gish lambda, kappa, and eta parameters.", "The performance of several alternative methods for correcting similarity scores for library-sequence length was evaluated using 54 protein superfamilies from the PIR39 database and 110 protein families from the Prosite/SwissProt rel.", "34 database.", "Both regression-scaled and Altschul-Gish scaled scores perform significantly better than unscaled Smith-Waterman or FASTA similarity scores.", "When the Prosite/ SwissProt test set is used, regression-scaled scores perform slightly better; when the PIR database is used, Altschul-Gish scaled scores perform best.", "Thus, length-corrected similarity scores improve the sensitivity of database searches.", "Statistical parameters that are derived from the distribution of similarity scores from the thousands of unrelated sequences typically encountered in a database search provide accurate estimates of statistical significance that can be used to infer sequence homology."], "structured": false}
{"doc_id": 11738716, "title": "Steroid hormone signalling links reproduction to lifespan in dietary-restricted Caenorhabditis elegans.", "abstract": ["Dietary restriction (DR) increases healthspan and longevity in many species, including primates, but it is often accompanied by impaired reproductive function.", "Whether signals associated with the reproductive system contribute to or are required for DR effects on lifespan has not been established.", "Here we show that expression of the cytochrome P450 DAF-9/CYP450 and production of the steroid hormone \u0394(7)-dafachronic acid (DA) are increased in C. elegans subjected to DR.", "DA signalling through the non-canonical nuclear hormone receptor NHR-8/NHR and the nutrient-responsive kinase let-363/mTOR is essential for DR-mediated longevity.", "Steroid signalling also affects germline plasticity in response to nutrient deprivation and this is required to achieve lifespan extension.", "These data demonstrate that steroid signalling links germline physiology to lifespan when nutrients are limited, and establish a central role for let-363/mTOR in integrating signals derived from nutrients and steroid hormones."], "structured": false}
{"doc_id": 11742219, "title": "Regulation and effects of hypothalamic galanin: relation to dietary fat, alcohol ingestion, circulating lipids and energy homeostasis.", "abstract": ["Galanin (GAL) is known to stimulate feeding behavior.", "This peptide has different properties and functions from other feeding stimulants, e.g., neuropeptide Y and agouti-related protein.", "Hypothalamic GAL is relatively unresponsive to food deprivation and to changes in corticosterone, glucose utilization, dietary carbohydrate and leptin.", "This indicates that this peptide is not essential under conditions when food is scarce or low-energy, high-carbohydrate diets are being consumed.", "In contrast, recent evidence suggests that GAL in the paraventricular nucleus (PVN) functions in close relation to dietary fat and alcohol.", "In particular, it mediates functions that allow animals to adapt to conditions of positive energy balance involving excess consumption of these nutrients.", "This peptide in the PVN is stimulated by a high-fat diet and also by alcohol.", "It is stimulated by an increase in circulating lipids caused by a fat-rich meal or alcohol consumption, and it rises during the middle of the active feeding cycle, when fat consumption and triglycerides naturally rise.", "When centrally injected, GAL in the PVN increases the consumption of food and alcohol.", "Moreover, it produces a significantly stronger feeding response in rats maintained on a fat-rich diet, which also promotes alcohol intake.", "This evidence supports the existence of non-homeostatic, positive feedback circuits between GAL and both dietary fat and alcohol.", "These circuits are believed to contribute to the large meal size, over-consumption of alcohol, and obesity which are generally associated with fat-rich foods."], "structured": false}
{"doc_id": 11748341, "title": "Evidence-based interventions for improvement of maternal and child nutrition: what can be done and at what cost?", "abstract": ["Maternal undernutrition contributes to 800,000 neonatal deaths annually through small for gestational age births; stunting, wasting, and micronutrient deficiencies are estimated to underlie nearly 3\u00b71 million child deaths annually.", "Progress has been made with many interventions implemented at scale and the evidence for effectiveness of nutrition interventions and delivery strategies has grown since The Lancet Series on Maternal and Child Undernutrition in 2008.", "We did a comprehensive update of interventions to address undernutrition and micronutrient deficiencies in women and children and used standard methods to assess emerging new evidence for delivery platforms.", "We modelled the effect on lives saved and cost of these interventions in the 34 countries that have 90% of the world's children with stunted growth.", "We also examined the effect of various delivery platforms and delivery options using community health workers to engage poor populations and promote behaviour change, access and uptake of interventions.", "Our analysis suggests the current total of deaths in children younger than 5 years can be reduced by 15% if populations can access ten evidence-based nutrition interventions at 90% coverage.", "Additionally, access to and uptake of iodised salt can alleviate iodine deficiency and improve health outcomes.", "Accelerated gains are possible and about a fifth of the existing burden of stunting can be averted using these approaches, if access is improved in this way.", "The estimated total additional annual cost involved for scaling up access to these ten direct nutrition interventions in the 34 focus countries is Int$9\u00b76 billion per year.", "Continued investments in nutrition-specific interventions to avert maternal and child undernutrition and micronutrient deficiencies through community engagement and delivery strategies that can reach poor segments of the population at greatest risk can make a great difference.", "If this improved access is linked to nutrition-sensitive approaches--ie, women's empowerment, agriculture, food systems, education, employment, social protection, and safety nets--they can greatly accelerate progress in countries with the highest burden of maternal and child undernutrition and mortality."], "structured": false}
{"doc_id": 11771811, "title": "FGF regulates TGF-\u03b2 signaling and endothelial-to-mesenchymal transition via control of let-7 miRNA expression.", "abstract": ["Maintenance of normal endothelial function is critical to various aspects of blood vessel function, but its regulation is poorly understood.", "In this study, we show that disruption of baseline fibroblast growth factor (FGF) signaling to the endothelium leads to a dramatic reduction in let-7 miRNA levels that, in turn, increases expression of transforming growth factor (TGF)-\u03b2 ligands and receptors and activation of TGF-\u03b2 signaling, leading to endothelial-to-mesenchymal transition (Endo-MT).", "We also find that Endo-MT is an important driver of neointima formation in a murine transplant arteriopathy model and in rejection of human transplant lesions.", "The decline in endothelial FGF signaling input is due to the appearance of an FGF resistance state that is characterized by inflammation-dependent reduction in expression and activation of key components of the FGF signaling cascade.", "These results establish FGF signaling as a critical factor in maintenance of endothelial homeostasis and point to an unexpected role of Endo-MT in vascular pathology."], "structured": false}
{"doc_id": 11774598, "title": "Nuclear Receptors, RXR, and the Big Bang", "abstract": ["Isolation of genes encoding the receptors for steroids, retinoids, vitamin D, and thyroid hormone and their structural and functional analysis revealed an evolutionarily conserved template for nuclear hormone receptors.", "This discovery sparked identification of numerous genes encoding related proteins, termed orphan receptors.", "Characterization of these orphan receptors and, in particular, of the retinoid X receptor (RXR) positioned nuclear receptors at the epicenter of the \"Big Bang\" of molecular endocrinology.", "This Review provides a personal perspective on nuclear receptors and explores their integrated and coordinated signaling networks that are essential for multicellular life, highlighting the RXR heterodimer and its associated ligands and transcriptional mechanism."], "structured": false}
{"doc_id": 11784947, "title": "A genome-wide short hairpin RNA screening of jurkat T-cells for human proteins contributing to productive HIV-1 replication.", "abstract": ["Short interfering RNAs (siRNAs) have been used to inhibit HIV-1 replication.", "The durable inhibition of HIV-1 replication by RNA interference has been impeded, however, by a high mutation rate when viral sequences are targeted and by cytotoxicity when cellular genes are knocked down.", "To identify cellular proteins that contribute to HIV-1 replication that can be chronically silenced without significant cytotoxicity, we employed a shRNA library that targets 54,509 human transcripts.", "We used this library to select a comprehensive population of Jurkat T-cell clones, each expressing a single discrete shRNA.", "The Jurkat clones were then infected with HIV-1.", "Clones that survived viral infection represent moieties silenced for a human mRNA needed for virus replication, but whose chronic knockdown did not cause cytotoxicity.", "Overall, 252 individual Jurkat mRNAs were identified.", "Twenty-two of these mRNAs were secondarily verified for their contributions to HIV-1 replication.", "Five mRNAs, NRF1, STXBP2, NCOA3, PRDM2, and EXOSC5, were studied for their effect on steps of the HIV-1 life cycle.", "We discuss the similarities and differences between our shRNA findings for HIV-1 using a spreading infection assay in human Jurkat T-cells and results from other investigators who used siRNA-based screenings in HeLa or 293T cells."], "structured": false}
{"doc_id": 11822354, "title": "UNR facilitates the interaction of MLE with the lncRNA roX2 during Drosophila dosage compensation.", "abstract": ["Dosage compensation is a regulatory process that balances the expression of X-chromosomal genes between males (XY) and females (XX).", "In Drosophila, this requires non-coding RNAs and RNA-binding proteins (RBPs) whose specific functions remain elusive.", "Here we show that the Drosophila RBP UNR promotes the targeting of the activating male-specific-lethal complex to the X-chromosome by facilitating the interaction of two crucial subunits: the RNA helicase MLE and the long non-coding RNA roX2."], "structured": false}
{"doc_id": 11831598, "title": "BMP/SMAD1 signaling sets a threshold for the left/right pathway in lateral plate mesoderm and limits availability of SMAD4.", "abstract": ["Bistability in developmental pathways refers to the generation of binary outputs from graded or noisy inputs.", "Signaling thresholds are critical for bistability.", "Specification of the left/right (LR) axis in vertebrate embryos involves bistable expression of transforming growth factor beta (TGFbeta) member NODAL in the left lateral plate mesoderm (LPM) controlled by feed-forward and feedback loops.", "Here we provide evidence that bone morphogenetic protein (BMP)/SMAD1 signaling sets a repressive threshold in the LPM essential for the integrity of LR signaling.", "Conditional deletion of Smad1 in the LPM led to precocious and bilateral pathway activation.", "NODAL expression from both the left and right sides of the node contributed to bilateral activation, indicating sensitivity of mutant LPM to noisy input from the LR system.", "In vitro, BMP signaling inhibited NODAL pathway activation and formation of its downstream SMAD2/4-FOXH1 transcriptional complex.", "Activity was restored by overexpression of SMAD4 and in embryos, elevated SMAD4 in the right LPM robustly activated LR gene expression, an effect reversed by superactivated BMP signaling.", "We conclude that BMP/SMAD1 signaling sets a bilateral, repressive threshold for NODAL-dependent Nodal activation in LPM, limiting availability of SMAD4.", "This repressive threshold is essential for bistable output of the LR system."], "structured": false}
{"doc_id": 11837657, "title": "Human Macrophages Infected with a High Burden of ESAT-6-Expressing M. tuberculosis Undergo Caspase-1- and Cathepsin B-Independent Necrosis", "abstract": ["Mycobacterium tuberculosis (Mtb) infects lung macrophages, which instead of killing the pathogen can be manipulated by the bacilli, creating an environment suitable for intracellular replication and spread to adjacent cells.", "The role of host cell death during Mtb infection is debated because the bacilli have been shown to be both anti-apoptotic, keeping the host cell alive to avoid the antimicrobial effects of apoptosis, and pro-necrotic, killing the host macrophage to allow infection of neighboring cells.", "Since mycobacteria activate the NLRP3 inflammasome in macrophages, we investigated whether Mtb could induce one of the recently described inflammasome-linked cell death modes pyroptosis and pyronecrosis.", "These are mediated through caspase-1 and cathepsin-B, respectively.", "Human monocyte-derived macrophages were infected with virulent (H37Rv) Mtb at a multiplicity of infection (MOI) of 1 or 10.", "The higher MOI resulted in strongly enhanced release of IL-1\u03b2, while a low MOI gave no IL-1\u03b2 response.", "The infected macrophages were collected and cell viability in terms of the integrity of DNA, mitochondria and the plasma membrane was determined.", "We found that infection with H37Rv at MOI 10, but not MOI 1, over two days led to extensive DNA fragmentation, loss of mitochondrial membrane potential, loss of plasma membrane integrity, and HMGB1 release.", "Although we observed plasma membrane permeabilization and IL-1\u03b2 release from infected cells, the cell death induced by Mtb was not dependent on caspase-1 or cathepsin B. It was, however, dependent on mycobacterial expression of ESAT-6.", "We conclude that as virulent Mtb reaches a threshold number of bacilli inside the human macrophage, ESAT-6-dependent necrosis occurs, activating caspase-1 in the process."], "structured": false}
{"doc_id": 11840194, "title": "Differentiation of Human Induced-Pluripotent Stem Cells into Smooth-Muscle Cells: Two Novel Protocols", "abstract": ["Conventional protocols for differentiating human induced-pluripotent stem cells (hiPSCs) into smooth-muscle cells (SMCs) can be inefficient and generally fail to yield cells with a specific SMC phenotype (i.e., contractile or synthetic SMCs).", "Here, we present two novel hiPSC-SMC differentiation protocols that yield SMCs with predominantly contractile or synthetic phenotypes.", "Flow cytometry analyses of smooth-muscle actin (SMA) expression indicated that ~45% of the cells obtained with each protocol assumed an SMC phenotype, and that the populations could be purified to ~95% via metabolic selection.", "Assessments of cellular mRNA and/or protein levels indicated that SMA, myosin heavy chain II, collagen 1, calponin, transgelin, connexin 43, and vimentin expression in the SMCs obtained via the Contractile SMC protocol and in SMCs differentiated via a traditional protocol were similar, while SMCs produced via the Sythetic SMC protocol expressed less calponin, more collagen 1, and more connexin 43.", "Differences were also observed in functional assessments of the two SMC populations: the two-dimensional surface area of Contractile SMCs declined more extensively (to 12% versus 44% of original size) in response to carbachol treatment, while quantification of cell migration and proliferation were greater in Synthetic SMCs.", "Collectively, these data demonstrate that our novel differentiation protocols can efficiently generate SMCs from hiPSCs."], "structured": false}
{"doc_id": 11844791, "title": "Conserved Histone Variant H2A.Z Protects Euchromatin from the Ectopic Spread of Silent Heterochromatin", "abstract": ["Boundary elements hinder the spread of heterochromatin, yet these sites do not fully account for the preservation of adjacent euchromatin.", "Histone variant H2A.Z (Htz1 in yeast) replaces conventional H2A in many nucleosomes.", "Microarray analysis revealed that HTZ1-activated genes cluster near telomeres.", "The reduced expression of most of these genes in htz1Delta cells was reversed by the deletion of SIR2 (sir2Delta) suggesting that H2A.Z antagonizes telomeric silencing.", "Other Htz1-activated genes flank the silent HMR mating-type locus.", "Their requirement for Htz1 can be bypassed by sir2Delta or by a deletion encompassing the silencing nucleation sites in HMR.", "In htz1Delta cells, Sir2 and Sir3 spread into flanking euchromatic regions, producing changes in histone H4 acetylation and H3 4-methylation indicative of ectopic heterochromatin formation.", "Htz1 is enriched in these euchromatic regions and acts synergistically with a boundary element to prevent the spread of heterochromatin.", "Thus, euchromatin and heterochromatin each contains components that antagonize switching to the opposite chromatin state."], "structured": false}
{"doc_id": 11844826, "title": "COMMD proteins, a novel family of structural and functional homologs of MURR1.", "abstract": ["MURR1 is a multifunctional protein that inhibits nuclear factor kappaB (NF-kappaB), a transcription factor with pleiotropic functions affecting innate and adaptive immunity, apoptosis, cell cycle regulation, and oncogenesis.", "Here we report the discovery of a new family of proteins with homology to MURR1.", "These proteins form multimeric complexes and were identified in a biochemical screen for MURR1-associated factors.", "The family is defined by the presence of a conserved and unique motif termed the COMM (copper metabolism gene MURR1) domain, which functions as an interface for protein-protein interactions.", "Like MURR1, several of these factors also associate with and inhibit NF-kappaB. The proteins designated as COMMD or COMM domain containing 1-10 are extensively conserved in multicellular eukaryotic organisms and define a novel family of structural and functional homologs of MURR1.", "The prototype of this family, MURR1/COMMD1, suppresses NF-kappaB not by affecting nuclear translocation or binding of NF-kappaB to cognate motifs; rather, it functions in the nucleus by affecting the association of NF-kappaB with chromatin."], "structured": false}
{"doc_id": 11861374, "title": "Occurrence of chromosome 9 and p53 alterations in multifocal dysplasia and carcinoma in situ of human urinary bladder", "abstract": ["To define the genetic changes of flat urothelial lesions, carcinoma in situ (CIS) and moderate dysplasias (DII) were investigated for alterations in the two chromosomal regions most frequently involved in bladder cancer.", "Overall, 33 CIS and 16 DII from 21 patients were used to microdissect urothelium.", "Dual color fluorescence in situ hybridization (FISH) using gene locus probes of 9q22 (FACC), 9p21 (CDK), 17p13 (p53), and related centromeric probes was applied on interphase nuclei.", "In parallel, preamplified DNA of these samples was used for loss of heterozygosity (LOH) analyses with eight microsatellite markers on chromosomes 9p, 9q and 17p, and for sequencing of exons 5-9 of p53.", "Data indicated nearly identical deletion frequencies for chromosomes 9 and 17 for CIS (chromosome 9, 86%; p53, 84%).", "DII showed a lower deletion rate in comparison with CIS (chromosome 9, 75%; p53, 53%).", "A very high correlation between the results of FISH and LOH analyses was found.", "p53 mutations were detected in 12 of 15 patients (CIS, 72%; DII, 67%).", "In three of 16 patients with multifocal tumors, oligoclonal lesions were identified by LOH analyses, a finding further supported by sequencing of p53, by which two different p53 deletions were detected in two cases.", "In conclusion, data from microdissected flat urothelial lesions indicate that chromosome 9 deletions cannot be regarded as indicators of papillary growth, because they are found frequently in both types of flat lesions of the urothelium: those associated with papillary tumors and those that are not.", "The similar distribution and lower amount of genetic changes in DII render DII a possible precursor lesion of CIS."], "structured": false}
{"doc_id": 11862753, "title": "Fresh meat and further processing characteristics of ham muscles from finishing pigs fed ractopamine hydrochloride.", "abstract": ["Ractopamine hydrochloride (RAC) has consistently led to an advantage in carcass cutting yields of finishing pigs and remains a common feed additive in US finishing pig diets.", "Less is known about the effect of RAC on further processing characteristics.", "Some researchers have reported advantages in ultimate pH of the LM in pigs fed RAC.", "If a greater ultimate pH was also observed in hams, the increased pH could affect further processing characteristics and lead to better protein interaction and improved textural properties.", "The objective of this experiment was to determine if RAC-fed pigs yielded hams with a greater ultimate pH, and if so, whether or not that advantage improves textural properties and water retention of further processed hams.", "Two hundred hams from barrows and gilts fed RAC or control diets were selected based on HCW.", "Hams were fabricated into 5 separate pieces to determine cutting yields, and 6 muscles were evaluated for ultimate pH. Hams were processed to make cured and smoked hams.", "Ractopamine increased cutting yields of the whole ham (P < 0.0001), inside (P < 0.01), outside (P < 0.01), and knuckle (P < 0.01) when expressed as a percentage of chilled side weight.", "Ultimate pH of the rectus femoris, vastus lateralis, and semitendinosus were all 0.06 pH units greater (P < 0.05), the biceps femoris was 0.04 pH units greater (P = 0.02), and the semimembranosus and adductor muscles were 0.03 pH units greater in pigs fed 7.4 mg/kg of RAC when compared with control pigs.", "Cured hams from RAC-fed pigs were heavier at all stages of production.", "No differences were detected in binding strengths (P = 0.88) or protein fat-free values (P = 0.13) between RAC (9.06 kg and 20.37) and control hams (9.01 kg and 20.13).", "Ractopamine increased cutting yields, total weight of cured hams, and ultimate muscle pH. Ractopamine can be fed to pigs to achieve the desired growth characteristic advantages and cutting yields without affecting further processed ham characteristics."], "structured": false}
{"doc_id": 11868606, "title": "Translocated LPS Might Cause Endotoxin Tolerance in Circulating Monocytes of Cystic Fibrosis Patients", "abstract": ["Cystic Fibrosis (CF) is an inherited pleiotropic disease that results from abnormalities in the gene codes of a chloride channel.", "The lungs of CF patients are chronically infected by several pathogens but bacteraemia have rarely been reported in this pathology.", "Besides that, circulating monocytes in CF patients exhibit a patent Endotoxin Tolerance (ET) state since they show a significant reduction of the inflammatory response to bacterial stimulus.", "Despite a previous description of this phenomenon, the direct cause of ET in CF patients remains unknown.", "In this study we have researched the possible role of microbial/endotoxin translocation from a localized infection to the bloodstream as a potential cause of ET induction in CF patients.", "Plasma analysis of fourteen CF patients revealed high levels of LPS compared to healthy volunteers and patients who suffer from Chronic Obstructive Pulmonary Disease.", "Experiments in vitro showed that endotoxin concentrations found in plasma of CF patients were enough to induce an ET phenotype in monocytes from healthy controls.", "In agreement with clinical data, we failed to detect bacterial DNA in CF plasma.", "Our results suggest that soluble endotoxin present in bloodstream of CF patients causes endotoxin tolerance in their circulating monocytes."], "structured": false}
{"doc_id": 11880289, "title": "Effect of mammographic screening from age 40 years on breast cancer mortality in the UK Age trial at 17 years' follow-up: a randomised controlled trial.", "abstract": ["BACKGROUND Age-specific effects of mammographic screening, and the timing of such effects, are a matter of debate.", "The results of the UK Age trial, which compared the effect of invitation to annual mammographic screening from age 40 years with commencement of screening at age 50 years on breast cancer mortality, have been reported at 10 years of follow-up and showed no significant difference in mortality between the trial groups.", "Here, we report the results of the UK Age trial after 17 years of follow-up.   \n", "METHODS Women aged 39-41 from 23 UK NHS Breast Screening Programme units years were randomly assigned by individual randomisation (1:2) to either an intervention group offered annual screening by mammography up to and including the calendar year of their 48th birthday or to a control group receiving usual medical care (invited for screening at age 50 years and every 3 years thereafter).", "Both groups were stratified by general practice.", "We compared breast cancer incidence and mortality by time since randomisation.", "Analyses included all women randomly assigned who could be traced with the National Health Service Central Register and who had not died or emigrated before entry.", "The primary outcome measures were mortality from breast cancer (defined as deaths with breast cancer coded as the underlying cause of death) and breast cancer incidence, including in-situ, invasive, and total incidence.", "Because there is an interest in the timing of the mortality effect, we analysed the results in different follow-up periods.", "This trial is registered, number ISRCTN24647151.   \n", "FINDINGS Between Oct 14, 1990, and Sept 25, 1997, 160 921 participants were randomly assigned; 53 883 women in the intervention group and 106 953 assigned to usual medical care were included in this analysis.", "After a median follow-up of 17 years (IQR 16\u00b78-18\u00b78), the rate ratio (RR) for breast cancer mortality was 0\u00b788 (95% CI 0\u00b774-1\u00b704) from tumours diagnosed during the intervention phase.", "A significant reduction in breast cancer mortality was noted in the intervention group compared with the control group in the first 10 years after diagnosis (RR 0\u00b775, 0\u00b758-0\u00b797) but not thereafter (RR 1\u00b702, 0\u00b780-1\u00b730) from tumours diagnosed during the intervention phase.", "The overall breast cancer incidence during 17 year follow-up was similar between the intervention group and the control group (RR 0\u00b798, 0\u00b793-1\u00b704).   \n", "INTERPRETATION Our results support an early reduction in mortality from breast cancer with annual mammography screening in women aged 40-49 years.", "Further data are needed to fully understand long-term effects.", "Cumulative incidence figures suggest at worst a small amount of overdiagnosis.   \n", "FUNDING National Institute for Health Research Health Technology Assessment programme and the American Cancer Society.", "Past funding was received from the Medical Research Council, Cancer Research UK, the UK Department of Health, and the US National Cancer Institute."], "structured": true}
{"doc_id": 11884292, "title": "Concordance, disease progression, and heritability of coeliac disease in Italian twins.", "abstract": ["BACKGROUND AND AIMS We adopted the twin method to disentangle the genetic and environmental components of susceptibility to coeliac disease (CD).", "We estimated disease concordance rate by zygosity and HLA genotypes, discordance times, progression rates to disease, and heritability.   \n", "METHODS We crosslinked the Italian Twin Registry with the membership lists of the Italian Coeliac Disease Association and recruited 23 monozygotic (MZ) and 50 dizygotic (DZ) twin pairs with at least one affected member.", "Zygosity was assigned by DNA fingerprinting, and HLA-DQ and DR alleles were genotyped.", "Disease status was ascertained by antiendomysial, anti-human tissue transglutaminase antibodies, and bowel biopsy.   \n", "RESULTS Concordance was significantly higher in MZ (83.3% probandwise, 71.4% pairwise) than in DZ (16.7% probandwise, 9.1% pairwise) pairs.", "Concordance was not affected by sex or HLA genotype of the co-twin and being MZ was significantly associated with the occurrence of CD (Cox adjusted hazard ratio 14.3 (95% confidence interval 4.0-50.3)).", "In 90% of concordant pairs the discordance time was <or=2 years.", "MZ and DZ co-twins had 70% and 9% cumulative probability of having symptomatic or silent forms of CD, respectively, within five years.", "Under ACE (additive genetic, common, and unshared environmental factors) models, with CD population prevalences of 1/91 and 1/1000, heritability estimates were 87% and 57%, respectively.   \n", "CONCLUSION MZ pairs have a high probability of being concordant, regardless of sex or HLA genotype.", "Most of the affected co-twins receive a diagnosis within two years.", "A remarkable proportion of phenotypic variance is due to genetic factors."], "structured": true}
{"doc_id": 11884867, "title": "A literature review of the safety of medical body area network devices in magnetic resonance imaging", "abstract": ["Electro-magnetic fields and wireless technology are part of modern life.", "The use of Magnetic Resonance Imaging (MRI) machines for clarification of internal human structures and function in healthcare is increasing.", "The rapid development of wireless devices, their miniaturization and their application as clinical tools creates an expanding intersection zone.", "Although safety standards for devices in MRI machines have been previously published, it is not clear that newer wireless technologies, including devices used in Medical Body Area Networks (MBAN) have been rigorously tested or disclosed.", "We undertook a review of the clinical scientific literature and the United States Food and Drug Administration adverse events database to discover whether this is a significant issue.", "There are currently no published studies specifically addressing the safety of wireless devices potentially used in MBAN in MRI machines.", "We suggest the addition of a research track to clarify the safety of MBAN devices in MRI machines.", "Informed design of current and future MBAN components, devices and systems can avoid potential patient adverse events due to the un-intended consequences of the concurrent use of these technologies in MRI machines."], "structured": false}
{"doc_id": 11886686, "title": "Synaptic glutamate release by ventromedial hypothalamic neurons is part of the neurocircuitry that prevents hypoglycemia.", "abstract": ["The importance of neuropeptides in the hypothalamus has been experimentally established.", "Due to difficulties in assessing function in vivo, the roles of the fast-acting neurotransmitters glutamate and GABA are largely unknown.", "Synaptic vesicular transporters (VGLUTs for glutamate and VGAT for GABA) are required for vesicular uptake and, consequently, synaptic release of neurotransmitters.", "Ventromedial hypothalamic (VMH) neurons are predominantly glutamatergic and express VGLUT2.", "To evaluate the role of glutamate release from VMH neurons, we generated mice lacking VGLUT2 selectively in SF1 neurons (a major subset of VMH neurons).", "These mice have hypoglycemia during fasting secondary to impaired fasting-induced increases in the glucose-raising pancreatic hormone glucagon and impaired induction in liver of mRNAs encoding PGC-1alpha and the gluconeogenic enzymes PEPCK and G6Pase.", "Similarly, these mice have defective counterregulatory responses to insulin-induced hypoglycemia and 2-deoxyglucose (an antimetabolite).", "Thus, glutamate release from VMH neurons is an important component of the neurocircuitry that functions to prevent hypoglycemia."], "structured": false}
{"doc_id": 11887584, "title": "c-Src and cooperating partners in human cancer.", "abstract": ["The proto-oncogene c-src is rarely mutated in human cancers, and when overexpressed in normal cells is non- or weakly oncogenic.", "These observations have raised doubts about the involvement of c-src in the etiology of human tumors.", "However, recent studies have shown that c-Src, a non-receptor tyrosine kinase, exhibits elevated protein levels and activity in numerous types of human cancers.", "Furthermore, it has been found to be a critical component of multiple signaling pathways that regulate proliferation, survival, metastasis, and angiogenesis.", "Because of its important role in these oncogenic processes, it represents a therapeutic target ripe for exploitation."], "structured": false}
{"doc_id": 11899391, "title": "Type 1 diabetes-associated IL2RA variation lowers IL-2 signaling and contributes to diminished CD4+CD25+ regulatory T cell function.", "abstract": ["Numerous reports have demonstrated that CD4(+)CD25(+) regulatory T cells (Tregs) from individuals with a range of human autoimmune diseases, including type 1 diabetes, are deficient in their ability to control autologous proinflammatory responses when compared with nondiseased, control individuals.", "Treg dysfunction could be a primary, causal event or may result from perturbations in the immune system during disease development.", "Polymorphisms in genes associated with Treg function, such as IL2RA, confer a higher risk of autoimmune disease.", "Although this suggests a primary role for defective Tregs in autoimmunity, a link between IL2RA gene polymorphisms and Treg function has not been examined.", "We addressed this by examining the impact of an IL2RA haplotype associated with type 1 diabetes on Treg fitness and suppressive function.", "Studies were conducted using healthy human subjects to avoid any confounding effects of disease.", "We demonstrated that the presence of an autoimmune disease-associated IL2RA haplotype correlates with diminished IL-2 responsiveness in Ag-experienced CD4(+) T cells, as measured by phosphorylation of STAT5a, and is associated with lower levels of FOXP3 expression by Tregs and a reduction in their ability to suppress proliferation of autologous effector T cells.", "These data offer a rationale that contributes to the molecular and cellular mechanisms through which polymorphisms in the IL-2RA gene affect immune regulation, and consequently upon susceptibility to autoimmune and inflammatory diseases."], "structured": false}
{"doc_id": 11900630, "title": "Hematopoietic stem cells and other hematopoietic cells show broad resistance to chemotherapeutic agents in vivo when overexpressing bcl-2.", "abstract": ["Objective.", "Chemotherapeutic agents function by inducing apoptosis and their effectiveness depends on the balance of pro- and anti-apoptotic proteins in cells.", "Due to the complicated interactions of the many proteins involved, it has been difficult to determine in tumors whether overexpression of single genes is prognostic for increased resistance.", "Therefore, we studied the influence of bcl-2 overexpression on resistance to chemotherapeutics in a transgenic mouse system.", "This allowed us to study a wide variety of cells, including important but rare populations such as hematopoietic stem cells (HSC).Methods.", "H2K-bcl-2 transgenic and wild-type (WT) mice were treated with several agents(5-fluoruracil, cyclophosphamide, and busulfan) to determine the contribution of increased amounts of bcl-2 to the response to these chemotherapeutics in vivo.", "Populations were enumerated using flow cytometry.", "HSC were studied by FACS purification and long-term reconstitution assays in vivo and resistance was confirmed by short-term proliferation assays with different amounts of chemotherapeutics in vitro.", "Results.", "bcl-2 overexpression alone protects many cell types, though protection levels differ between populations and agents.", "However, even sensitive populations return to pretreatment levels faster in transgenic mice.", "bcl-2 overexpression also prevents the dramatic changes in HSC following 5-FU treatment (downregulation of c-kit, upregulation of Lin, less efficient long-term reconstitution).", "In vitro studies directly demonstrate increased resistance of bcl-2 overexpressing HSC to chemotherapeutic agents.", "Conclusions.", "Increased expression of bcl-2 in HSC and their progeny endows these cells with broad resistance to chemotherapeutic agents.", "The ability to (differentially) regulate sensitivity to apoptosis of bystander and tumor cells is clinically important."], "structured": false}
{"doc_id": 11902109, "title": "Direct sensing of systemic and nutritional signals by hematopoietic progenitors in Drosophila", "abstract": ["The Drosophila lymph gland is a haematopoietic organ in which progenitor cells, which are most akin to the common myeloid progenitor in mammals, proliferate and differentiate into three types of mature cell--plasmatocytes, crystal cells and lamellocytes--the functions of which are reminiscent of mammalian myeloid cells.", "During the first and early second instars of larval development, the lymph gland contains only progenitors, whereas in the third instar, a medial region of the primary lobe of the lymph gland called the medullary zone contains these progenitors, and maturing blood cells are found juxtaposed in a peripheral region designated the cortical zone.", "A third group of cells referred to as the posterior signalling centre functions as a haematopoietic niche.", "Similarly to mammalian myeloid cells, Drosophila blood cells respond to multiple stresses including hypoxia, infection and oxidative stress.", "However, how systemic signals are sensed by myeloid progenitors to regulate cell-fate determination has not been well described.", "Here, we show that the haematopoietic progenitors of Drosophila are direct targets of systemic (insulin) and nutritional (essential amino acid) signals, and that these systemic signals maintain the progenitors by promoting Wingless (WNT in mammals) signalling.", "We expect that this study will promote investigation of such possible direct signal sensing mechanisms by mammalian myeloid progenitors."], "structured": false}
{"doc_id": 11903247, "title": "Regulation of autophagy by cytoplasmic p53", "abstract": ["Multiple cellular stressors, including activation of the tumour suppressor p53, can stimulate autophagy.", "Here we show that deletion, depletion or inhibition of p53 can induce autophagy in human, mouse and nematode cells subjected to knockout, knockdown or pharmacological inhibition of p53.", "Enhanced autophagy improved the survival of p53-deficient cancer cells under conditions of hypoxia and nutrient depletion, allowing them to maintain high ATP levels.", "Inhibition of p53 led to autophagy in enucleated cells, and cytoplasmic, not nuclear, p53 was able to repress the enhanced autophagy of p53\u2212/\u2212 cells.", "Many different inducers of autophagy (for example, starvation, rapamycin and toxins affecting the endoplasmic reticulum) stimulated proteasome-mediated degradation of p53 through a pathway relying on the E3 ubiquitin ligase HDM2.", "Inhibition of p53 degradation prevented the activation of autophagy in several cell lines, in response to several distinct stimuli.", "These results provide evidence of a key signalling pathway that links autophagy to the cancer-associated dysregulation of p53."], "structured": false}
{"doc_id": 11913139, "title": "The Neurobiology of Sleep: Genetics, cellular physiology and subcortical networks", "abstract": ["To appreciate the neural underpinnings of sleep, it is important to view this universal mammalian behaviour at multiple levels of its biological organization.", "Molecularly, the circadian rhythm of sleep involves interlocking positive- and negative-feedback mechanisms of circadian genes and their protein products in cells of the suprachiasmatic nucleus that are entrained to ambient conditions by light.", "Circadian information is integrated with information on homeostatic sleep need in nuclei of the anterior hypothalamus.", "These nuclei interact with arousal systems in the posterior hypothalamus, basal forebrain and brainstem to control sleep onset.", "During sleep, an ultradian oscillator in the mesopontine junction controls the regular alternation of rapid eye movement (REM) and non-REM sleep.", "Sleep cycles are accompanied by neuromodulatory influences on forebrain structures that influence behaviour, consciousness and cognition."], "structured": false}
{"doc_id": 11915280, "title": "Suppression of intestinal neoplasia by deletion of Dnmt3b", "abstract": ["Aberrant gene silencing accompanied by DNA methylation is associated with neoplastic progression in many tumors that also show global loss of DNA methylation.", "Using conditional inactivation of de novo methyltransferase Dnmt3b in Apc(Min/+) mice, we demonstrate that the loss of Dnmt3b has no impact on microadenoma formation, which is considered the earliest stage of intestinal tumor formation.", "Nevertheless, we observed a significant decrease in the formation of macroscopic colonic adenomas.", "Interestingly, many large adenomas showed regions with Dnmt3b inactivation, indicating that Dnmt3b is required for initial outgrowth of macroscopic adenomas but is not required for their maintenance.", "These results support a role for Dnmt3b in the transition stage between microadenoma formation and macroscopic colonic tumor growth and further suggest that Dnmt3b, and by extension de novo methylation, is not required for maintaining tumor growth after this transition stage has occurred."], "structured": false}
{"doc_id": 11921405, "title": "Epithelium-intrinsic NAIP/NLRC4 inflammasome drives infected enterocyte expulsion to restrict Salmonella replication in the intestinal mucosa.", "abstract": ["The gut mucosal epithelium separates the host from the microbiota, but enteropathogens such as Salmonella Typhimurium (S.Tm) can invade and breach this barrier.", "Defenses against such acute insults remain incompletely understood.", "Using a murine model of Salmonella enterocolitis, we analyzed mechanisms limiting pathogen loads in the epithelium during early infection.", "Although the epithelium-invading S.Tm replicate initially, this intraepithelial replicative niche is restricted by expulsion of infected enterocytes into the lumen.", "This mechanism is compromised if inflammasome components (NAIP1-6, NLRC4, caspase-1/-11) are deleted, or ablated specifically in the epithelium, resulting in \u223c100-fold higher intraepithelial loads and accelerated lymph node colonization.", "Interestingly, the cytokines downstream of inflammasome activation, interleukin (IL)-1\u03b1/\u03b2 and IL-18, appear dispensable for epithelial restriction of early infection.", "These data establish the role of an epithelium-intrinsic inflammasome, which drives expulsion of infected cells to restrict the pathogen's intraepithelial proliferation.", "This may represent a general defense mechanism against mucosal infections."], "structured": false}
{"doc_id": 11922370, "title": "GEMC1 is a TopBP1 interacting protein required for chromosomal DNA replication", "abstract": ["Many of the factors required for chromosomal DNA replication have been identified in unicellular eukaryotes.", "However, DNA replication is poorly understood in multicellular organisms.", "Here, we report the identification of GEMC1 (geminin coiled-coil containing protein 1), a novel vertebrate protein required for chromosomal DNA replication.", "GEMC1 is highly conserved in vertebrates and is preferentially expressed in proliferating cells.", "Using Xenopus laevis egg extract we show that Xenopus GEMC1 (xGEMC1) binds to the checkpoint and replication factor TopBP1, which promotes binding of xGEMC1 to chromatin during pre-replication complex (pre-RC) formation.", "We demonstrate that xGEMC1 interacts directly with replication factors such as Cdc45 and the kinase Cdk2-CyclinE, through which it is heavily phosphorylated.", "Phosphorylated xGEMC1 stimulates initiation of DNA replication, whereas depletion of xGEMC1 prevents the onset of DNA replication owing to the impairment of Cdc45 loading onto chromatin.", "Similarly, inhibition of GEMC1 expression with morpholino and siRNA oligos prevents DNA replication in embryonic and somatic vertebrate cells.", "These data suggest that GEMC1 promotes initiation of chromosomal DNA replication in multicellular organisms by mediating TopBP1- and Cdk2-dependent recruitment of Cdc45 onto replication origins."], "structured": false}
{"doc_id": 11933721, "title": "Does an arthroscopic suture bridge technique maintain repair integrity?: a serial evaluation by ultrasonography.", "abstract": ["UNLABELLED Biomechanical studies suggest a suture bridge technique enhances rotator cuff tendon footprint contact area, holding strength, and mean contact pressure.", "Based on these studies, we asked whether (1) the suture bridge technique would provide a high rate of cuff integrity after surgery, (2) the status of the repaired cuff would change with time, (3) preoperative factors could predict postoperative cuff integrity, and (4) patients with retears had less favorable pain, functional scores, range of motion (ROM), and muscle strength compared with those with intact repairs.", "We prospectively followed 78 patients with arthroscopic repairs in whom we used the suture bridge technique.", "The integrity of the rotator cuff repair was determined using ultrasonographic evaluation at 4.5 and 12 months after surgery.", "Ultrasonography revealed intact cuffs in 91% at 4.5 months postoperatively, all of which were maintained at the 12-month followup.", "Failure rates were 17.6% (three of 17) for massive tears, 11.1% (two of 18) for large tears, 6.3% (two of 32) for medium tears, and no failures for small tears.", "Preoperative fatty degeneration of the supraspinatus muscle was a strong predictor of cuff integrity.", "We found no correlation between the integrity and clinical outcomes except for a temporary decrease of abduction strength at 6 months.", "Arthroscopic repair using suture bridge technique can achieve a low retear rate in shoulders treated for rotator cuff tears, but the occurrence of retear did not influence the outcome.   ", "LEVEL OF EVIDENCE Level IV, therapeutic study.", "See Guidelines for Authors for a complete description of levels of evidence."], "structured": false}
{"doc_id": 11935250, "title": "Widespread and tissue specific age-related DNA methylation changes in mice.", "abstract": ["Aberrant methylation of promoter CpG islands in cancer is associated with silencing of tumor-suppressor genes, and age-dependent hypermethylation in normal appearing mucosa may be a risk factor for human colon cancer.", "It is not known whether this age-related DNA methylation phenomenon is specific to human tissues.", "We performed comprehensive DNA methylation profiling of promoter regions in aging mouse intestine using methylated CpG island amplification in combination with microarray analysis.", "By comparing C57BL/6 mice at 3-mo-old versus 35-mo-old for 3627 detectable autosomal genes, we found 774 (21%) that showed increased methylation and 466 (13%) that showed decreased methylation.", "We used pyrosequencing to quantitatively validate the microarray data and confirmed linear age-related methylation changes for all 12 genomic regions examined.", "We then examined 11 changed genomic loci for age-related methylation in other tissues.", "Of these, three of 11 showed similar changes in lung, seven of 11 changed in liver, and six of 11 changed in spleen, though to a lower degree than the changes seen in colon.", "There was partial conservation between age-related hypermethylation in human and mouse intestines, and Polycomb targets in embryonic stem cells were enriched among the hypermethylated genes.", "Our findings demonstrate a surprisingly high rate of hyper- and hypomethylation as a function of age in normal mouse small intestine tissues and a strong tissue-specificity to the process.", "We conclude that epigenetic deregulation is a common feature of aging in mammals."], "structured": false}
{"doc_id": 11936877, "title": "Environmental and economic costs of soil erosion and conservation benefits.", "abstract": ["Soil erosion is a major environmental threat to the sustainability and productive capacity of agriculture.", "During the last 40 years, nearly one-third of the world's arable land has been lost by erosion and continues to be lost at a rate of more than 10 million hectares per year.", "With the addition of a quarter of a million people each day, the world population's food demand is increasing at a time when per capita food productivity is beginning to decline."], "structured": false}
{"doc_id": 11939159, "title": "Association between influenza vaccination and cardiovascular outcomes in high-risk patients: a meta-analysis.", "abstract": ["IMPORTANCE Among nontraditional cardiovascular risk factors, recent influenzalike infection is associated with fatal and nonfatal atherothrombotic events.   \n", "OBJECTIVES To determine if influenza vaccination is associated with prevention of cardiovascular events.   \n", "DATA SOURCES AND STUDY SELECTION A systematic review and meta-analysis of MEDLINE (1946-August 2013), EMBASE (1947-August 2013), and the Cochrane Library Central Register of Controlled Trials (inception-August 2013) for randomized clinical trials (RCTs) comparing influenza vaccine vs placebo or control in patients at high risk of cardiovascular disease, reporting cardiovascular outcomes either as efficacy or safety events.   \n", "DATA EXTRACTION AND SYNTHESIS Two investigators extracted data independently on trial design, baseline characteristics, outcomes, and safety events from published manuscripts and unpublished supplemental data.", "High-quality studies were considered those that described an appropriate method of randomization, allocation concealment, blinding, and completeness of follow-up.   \n", "MAIN OUTCOMES AND MEASURES Random-effects Mantel-Haenszel risk ratios (RRs) and 95% CIs were derived for composite cardiovascular events, cardiovascular mortality, all-cause mortality, and individual cardiovascular events.", "Analyses were stratified by subgroups of patients with and without a history of acute coronary syndrome (ACS) within 1 year of randomization.   \n", "RESULTS Five published and 1 unpublished randomized clinical trials of 6735 patients (mean age, 67 years; 51.3% women; 36.2% with a cardiac history; mean follow-up time, 7.9 months) were included.", "Influenza vaccine was associated with a lower risk of composite cardiovascular events (2.9% vs 4.7%; RR, 0.64 [95% CI, 0.48-0.86], P = .003) in published trials.", "A treatment interaction was detected between patients with (RR, 0.45 [95% CI, 0.32-0.63]) and without (RR, 0.94 [95% CI, 0.55-1.61]) recent ACS (P for interaction = .02).", "Results were similar with the addition of unpublished data.   \n", "CONCLUSIONS AND RELEVANCE In a meta-analysis of RCTs, the use of influenza vaccine was associated with a lower risk of major adverse cardiovascular events.", "The greatest treatment effect was seen among the highest-risk patients with more active coronary disease.", "A large, adequately powered, multicenter trial is warranted to address these findings and assess individual cardiovascular end points."], "structured": true}
{"doc_id": 11943989, "title": "Baby hands that move to the rhythm of language: hearing babies acquiring sign languages babble silently on the hands", "abstract": ["The \"ba, ba, ba\" sound universal to babies' babbling around 7 months captures scientific attention because it provides insights into the mechanisms underlying language acquisition and vestiges of its evolutionary origins.", "Yet the prevailing mystery is what is the biological basis of babbling, with one hypothesis being that it is a non-linguistic motoric activity driven largely by the baby's emerging control over the mouth and jaw, and another being that it is a linguistic activity reflecting the babies' early sensitivity to specific phonetic-syllabic patterns.", "Two groups of hearing babies were studied over time (ages 6, 10, and 12 months), equal in all developmental respects except for the modality of language input (mouth versus hand): three hearing babies acquiring spoken language (group 1: \"speech-exposed\") and a rare group of three hearing babies acquiring sign language only, not speech (group 2: \"sign-exposed\").", "Despite this latter group's exposure to sign, the motoric hypothesis would predict similar hand activity to that seen in speech-exposed hearing babies because language acquisition in sign-exposed babies does not involve the mouth.", "Using innovative quantitative Optotrak 3-D motion-tracking technology, applied here for the first time to study infant language acquisition, we obtained physical measurements similar to a speech spectrogram, but for the hands.", "Here we discovered that the specific rhythmic frequencies of the hands of the sign-exposed hearing babies differed depending on whether they were producing linguistic activity, which they produced at a low frequency of approximately 1 Hz, versus non-linguistic activity, which they produced at a higher frequency of approximately 2.5 Hz - the identical class of hand activity that the speech-exposed hearing babies produced nearly exclusively.", "Surprisingly, without benefit of the mouth, hearing sign-exposed babies alone babbled systematically on their hands.", "We conclude that babbling is fundamentally a linguistic activity and explain why the differentiation between linguistic and non-linguistic hand activity in a single manual modality (one distinct from the human mouth) could only have resulted if all babies are born with a sensitivity to specific rhythmic patterns at the heart of human language and the capacity to use them."], "structured": false}
{"doc_id": 11951999, "title": "The Ten-Eleven Translocation-2 (TET2) gene in hematopoiesis and hematopoietic diseases", "abstract": ["Ten-Eleven Translocation-2 (TET2) inactivation through loss-of-function mutation, deletion and IDH1/2 (Isocitrate Dehydrogenase 1 and 2) gene mutation is a common event in myeloid and lymphoid malignancies.", "TET2 gene mutations similar to those observed in myeloid and lymphoid malignancies also accumulate with age in otherwise healthy subjects with clonal hematopoiesis.", "TET2 is one of the three proteins of the TET (Ten-Eleven Translocation) family, which are evolutionarily conserved dioxygenases that catalyze the conversion of 5-methyl-cytosine (5-mC) to 5-hydroxymethyl-cytosine (5-hmC) and promote DNA demethylation.", "TET dioxygenases require 2-oxoglutarate, oxygen and Fe(II) for their activity, which is enhanced in the presence of ascorbic acid.", "TET2 is the most expressed TET gene in the hematopoietic tissue, especially in hematopoietic stem cells.", "In addition to their hydroxylase activity, TET proteins recruit the O-linked \u03b2-D-N-acetylglucosamine (O-GlcNAc) transferase (OGT) enzyme to chromatin, which promotes post-transcriptional modifications of histones and facilitates gene expression.", "The TET2 level is regulated by interaction with IDAX, originating from TET2 gene fission during evolution, and by the microRNA miR-22.", "TET2 has pleiotropic roles during hematopoiesis, including stem-cell self-renewal, lineage commitment and terminal differentiation of monocytes.", "Analysis of Tet2 knockout mice, which are viable and fertile, demonstrated that Tet2 functions as a tumor suppressor whose haploinsufficiency initiates myeloid and lymphoid transformations.", "This review summarizes the recently identified TET2 physiological and pathological functions and discusses how this knowledge influences our therapeutic approaches in hematological malignancies and possibly other tumor types."], "structured": false}
{"doc_id": 11953232, "title": "Impaired Awareness of Hypoglycemia in a Population-Based Sample of Children and Adolescents With Type 1 Diabetes", "abstract": ["OBJECTIVE To determine the prevalence and clinical associations of impaired awareness of hypoglycemia in a population-based sample of children and adolescents with type 1 diabetes.   ", "RESEARCH DESIGN AND METHODS A validated questionnaire was administered to 656 patients with type 1 diabetes over a 6-month period to determine hypoglycemia awareness status.", "Case ascertainment was 79% of the clinic population.", "The rate of severe hypoglycemia was determined by data collected prospectively in the preceding year.   \n", "RESULTS Impaired awareness of hypoglycemia was present in 29% of patients.", "Patients with impaired awareness of hypoglycemia had an earlier onset of diabetes (P < 0.001), were younger (P < 0.001), and had lower mean levels of A1C since diabetes onset (P = 0.006) and at their last visit (P = 0.001).", "The overall rate of severe hypoglycemia was 24.5 episodes per 100 patient-years in the preceding year.", "The severe hypoglycemia rate was higher in those with impaired awareness of hypoglycemia (37.1 vs. 19.3 episodes per 100 patient-years, P < 0.001).", "Among patients aged <6 years (n = 46), 59% of care providers reported impaired awareness of hypoglycemia, and the rate of severe hypoglycemia was significantly higher in those reporting impaired awareness (33.3 vs. 52 episodes per 100 patient-years, P = 0.02).", "More patients with recurrent hypoglycemia reported impaired awareness of hypoglycemia (47 vs. 28%, P = 0.03).   \n", "CONCLUSIONS A significant proportion of children and adolescents with type 1 diabetes have impaired awareness of hypoglycemia.", "Screening for impaired awareness is an important component of routine diabetes care and can identify patients at increased risk of a severe hypoglycemic event."], "structured": true}
{"doc_id": 11968641, "title": "Enhancing circadian clock function in cancer cells inhibits tumor growth", "abstract": ["BACKGROUND Circadian clocks control cell cycle factors, and circadian disruption promotes cancer.", "To address whether enhancing circadian rhythmicity in tumor cells affects cell cycle progression and reduces proliferation, we compared growth and cell cycle events of B16 melanoma cells and tumors with either a functional or dysfunctional clock.   \n", "RESULTS We found that clock genes were suppressed in B16 cells and tumors, but treatments inducing circadian rhythmicity, such as dexamethasone, forskolin and heat shock, triggered rhythmic clock and cell cycle gene expression, which resulted in fewer cells in S phase and more in G1 phase.", "Accordingly, B16 proliferation in vitro and tumor growth in vivo was slowed down.", "Similar effects were observed in human colon carcinoma HCT-116 cells.", "Notably, the effects of dexamethasone were not due to an increase in apoptosis nor to an enhancement of immune cell recruitment to the tumor.", "Knocking down the essential clock gene Bmal1 in B16 tumors prevented the effects of dexamethasone on tumor growth and cell cycle events.   \n", "CONCLUSIONS Here we demonstrated that the effects of dexamethasone on cell cycle and tumor growth are mediated by the tumor-intrinsic circadian clock.", "Thus, our work reveals that enhancing circadian clock function might represent a novel strategy to control cancer progression."], "structured": true}
{"doc_id": 11983390, "title": "Distinct functions of nucleotide-binding/hydrolysis sites in the four AAA modules of cytoplasmic dynein.", "abstract": ["Cytoplasmic dynein is a microtubule-based motor protein that is responsible for most intracellular retrograde transports along microtubule filaments.", "The motor domain of dynein contains six tandemly linked AAA (ATPases associated with diverse cellular activities) modules, with the first four containing predicted nucleotide-binding/hydrolysis sites (P1-P4).", "To dissect the functions of these multiple nucleotide-binding/hydrolysis sites, we expressed and purified Dictyostelium dynein motor domains in which mutations were introduced to block nucleotide binding at each of the four AAA modules, and then examined their detailed biochemical properties.", "The P1 mutant was trapped in a strong-binding state even in the presence of ATP and lost its motile activity.", "The P3 mutant also showed a high affinity for microtubules in the presence of ATP and lost most of the microtubule-activated ATPase activity, but retained microtubule sliding activity, although the sliding velocity of the mutant was more than 20-fold slower than that of the wild type.", "In contrast, mutation in the P2 or P4 site did not affect the apparent binding affinity of the mutant for microtubules in the presence of ATP, but reduced ATPase and microtubule sliding activities.", "These results indicate that ATP binding and its hydrolysis only at the P1 site are essential for the motor activities of cytoplasmic dynein, and suggest that the other nucleotide-binding/hydrolysis sites regulate the motor activities.", "Among them, nucleotide binding at the P3 site is not essential but is critical for microtubule-activated ATPase and motile activities of cytoplasmic dynein."], "structured": false}
{"doc_id": 11992632, "title": "Over-expression of RCAN1 causes Down syndrome-like hippocampal deficits that alter learning and memory.", "abstract": ["People with Down syndrome (DS) exhibit abnormal brain structure.", "Alterations affecting neurotransmission and signalling pathways that govern brain function are also evident.", "A large number of genes are simultaneously expressed at abnormal levels in DS; therefore, it is a challenge to determine which gene(s) contribute to specific abnormalities, and then identify the key molecular pathways involved.", "We generated RCAN1-TG mice to study the consequences of RCAN1 over-expression and investigate the contribution of RCAN1 to the brain phenotype of DS.", "RCAN1-TG mice exhibit structural brain abnormalities in those areas affected in DS.", "The volume and number of neurons within the hippocampus is reduced and this correlates with a defect in adult neurogenesis.", "The density of dendritic spines on RCAN1-TG hippocampal pyramidal neurons is also reduced.", "Deficits in hippocampal-dependent learning and short- and long-term memory are accompanied by a failure to maintain long-term potentiation (LTP) in hippocampal slices.", "In response to LTP induction, we observed diminished calcium transients and decreased phosphorylation of CaMKII and ERK1/2-proteins that are essential for the maintenance of LTP and formation of memory.", "Our data strongly suggest that RCAN1 plays an important role in normal brain development and function and its up-regulation likely contributes to the neural deficits associated with DS."], "structured": false}
{"doc_id": 12009265, "title": "Vitamins E and C in the prevention of prostate and total cancer in men: the Physicians' Health Study II randomized controlled trial.", "abstract": ["CONTEXT Many individuals take vitamins in the hopes of preventing chronic diseases such as cancer, and vitamins E and C are among the most common individual supplements.", "A large-scale randomized trial suggested that vitamin E may reduce risk of prostate cancer; however, few trials have been powered to address this relationship.", "No previous trial in men at usual risk has examined vitamin C alone in the prevention of cancer.   \n", "OBJECTIVE To evaluate whether long-term vitamin E or C supplementation decreases risk of prostate and total cancer events among men.   \n", "DESIGN, SETTING, AND PARTICIPANTS The Physicians' Health Study II is a randomized, double-blind, placebo-controlled factorial trial of vitamins E and C that began in 1997 and continued until its scheduled completion on August 31, 2007.", "A total of 14,641 male physicians in the United States initially aged 50 years or older, including 1307 men with a history of prior cancer at randomization, were enrolled.   \n", "INTERVENTION Individual supplements of 400 IU of vitamin E every other day and 500 mg of vitamin C daily.   \n", "MAIN OUTCOME MEASURES Prostate and total cancer.   \n", "RESULTS During a mean follow-up of 8.0 years, there were 1008 confirmed incident cases of prostate cancer and 1943 total cancers.", "Compared with placebo, vitamin E had no effect on the incidence of prostate cancer (active and placebo vitamin E groups, 9.1 and 9.5 events per 1000 person-years; hazard ratio [HR], 0.97; 95% confidence interval [CI], 0.85-1.09; P = .58) or total cancer (active and placebo vitamin E groups, 17.8 and 17.3 cases per 1000 person-years; HR, 1.04; 95% CI, 0.95-1.13; P = .41).", "There was also no significant effect of vitamin C on total cancer (active and placebo vitamin C groups, 17.6 and 17.5 events per 1000 person-years; HR, 1.01; 95% CI, 0.92-1.10; P = .86) or prostate cancer (active and placebo vitamin C groups, 9.4 and 9.2 cases per 1000 person-years; HR, 1.02; 95% CI, 0.90-1.15; P = .80).", "Neither vitamin E nor vitamin C had a significant effect on colorectal, lung, or other site-specific cancers.", "Adjustment for adherence and exclusion of the first 4 or 6 years of follow-up did not alter the results.", "Stratification by various cancer risk factors demonstrated no significant modification of the effect of vitamin E on prostate cancer risk or either agent on total cancer risk.   \n", "CONCLUSIONS In this large, long-term trial of male physicians, neither vitamin E nor C supplementation reduced the risk of prostate or total cancer.", "These data provide no support for the use of these supplements for the prevention of cancer in middle-aged and older men.   \n", "TRIAL REGISTRATION clinicaltrials.gov Identifier: NCT00270647."], "structured": true}
{"doc_id": 12014458, "title": "Micromanagers of gene expression: the potentially widespread influence of metazoan microRNAs", "abstract": ["We propose that the microRNA milieu, unique to each cell type, productively dampens the expression of thousands of mRNAs and provides important context for the evolution of all metazoan mRNA sequences.", "For genes that should not be expressed in a particular cell type, protein output is lowered to inconsequential levels.", "For other genes, dosage is adjusted in a manner that allows for customized expression in different cell types while achieving a more uniform level within each cell type.", "In these ways, the microRNAs add an extensive layer of gene control that integrates with transcriptional and other regulatory processes to expand the complexity of metazoan gene expression."], "structured": false}
{"doc_id": 12030318, "title": "The Kinase Regulator Mob1 Acts as a Patterning Protein for Stentor Morphogenesis", "abstract": ["Morphogenesis and pattern formation are vital processes in any organism, whether unicellular or multicellular.", "But in contrast to the developmental biology of plants and animals, the principles of morphogenesis and pattern formation in single cells remain largely unknown.", "Although all cells develop patterns, they are most obvious in ciliates; hence, we have turned to a classical unicellular model system, the giant ciliate Stentor coeruleus.", "Here we show that the RNA interference (RNAi) machinery is conserved in Stentor.", "Using RNAi, we identify the kinase coactivator Mob1--with conserved functions in cell division and morphogenesis from plants to humans-as an asymmetrically localized patterning protein required for global patterning during development and regeneration in Stentor.", "Our studies reopen the door for Stentor as a model regeneration system."], "structured": false}
{"doc_id": 12030680, "title": "Measurement and clinical monitoring of human lymphocyte clonality by massively parallel VDJ pyrosequencing.", "abstract": ["The complex repertoire of immune receptors generated by B and T cells enables recognition of diverse threats to the host organism.", "In this work, we show that massively parallel DNA sequencing of rearranged immune receptor loci can provide direct detection and tracking of immune diversity and expanded clonal lymphocyte populations in physiological and pathological contexts.", "DNA was isolated from blood and tissue samples, a series of redundant primers was used to amplify diverse DNA rearrangements, and the resulting mixtures of barcoded amplicons were sequenced using long-read ultra deep sequencing.", "Individual DNA molecules were then characterized on the basis of DNA segments that had been joined to make a functional (or nonfunctional) immune effector.", "Current experimental designs can accommodate up to 150 samples in a single sequence run, with the depth of sequencing sufficient to identify stable and dynamic aspects of the immune repertoire in both normal and diseased circumstances.", "These data provide a high-resolution picture of immune spectra in normal individuals and in patients with hematological malignancies, illuminating, in the latter case, both the initial behavior of clonal tumor populations and the later suppression or re-emergence of such populations after treatment."], "structured": false}
{"doc_id": 12030735, "title": "Can we apply the National Cholesterol Education Program Adult Treatment Panel definition of the metabolic syndrome to Asians?", "abstract": ["OBJECTIVE Limited information is available about the metabolic syndrome in Asians.", "Furthermore, the definition of central obesity using waist circumference may not be appropriate for Asians.", "The objectives of this study were to determine the optimal waist circumference for diagnosing central obesity in Asians and to estimate the prevalence of the metabolic syndrome in an Asian population.   ", "RESEARCH DESIGN AND METHODS We used data from the 1998 Singapore National Health Survey, a cross-sectional survey involving 4,723 men and women of Chinese, Malay, and Asian-Indian ethnicity aged 18-69 years.", "Receiver operating characteristic analysis suggested that waist circumference >80 cm in women and >90 cm in men was a more appropriate definition of central obesity in this population.", "The prevalence of the metabolic syndrome was then determined using the National Cholesterol Education Program Adult Treatment Panel III (NCEP ATP III) criteria with and without the modified waist circumference criteria.   \n", "RESULTS In Asians, decreasing waist circumference increased the crude prevalence of the metabolic syndrome from 12.2 to 17.9%.", "Using the modified Asian criteria, the prevalence of the metabolic syndrome increased from 2.9% in those aged 18-30 years to 31.0% in those aged 60-69 years.", "It was more common in men (prevalence 20.9% in men versus 15.5% in women; P < 0.001) and Asian Indians (prevalence 28.8% in Asian-Indians, 24.2% in Malays, and 14.8% in Chinese; P < 0.001).   \n", "CONCLUSIONS NCEP ATP III criteria, applied to an Asian population, will underestimate the population at risk.", "With a lower waist circumference cutoff, the prevalence of the metabolic syndrome is comparable to that in Western populations.", "Ethnic differences are likely to exist between populations across Asia."], "structured": true}
{"doc_id": 12039953, "title": "Serotonin and fluoxetine levels in plasma and platelets after fluoxetine treatment in depressive patients.", "abstract": ["Depression is a mood disorder characterized by complex alterations of neurotransmitters such as serotonin, norepinephrine, and dopamine.", "In particular, there is substantial evidence of abnormalities in serotonin neurotransmission.", "Peripheral parameters of serotoninergic transmission, such as the 5-hydroxytryptamine content of plasma and platelets, have been used to identify biochemical alterations related to depression.", "In recent years, these parameters have also been used to examine the mechanism of action of antidepressive drugs such as the selective serotonin reuptake inhibitors.", "This study investigated the interaction between the plasma and platelet levels of fluoxetine and serotonin after fluoxetine administration to depressed patients.", "Twelve patients affected by major depression (according to the DSM-IV criteria) received a single oral dose of fluoxetine in the morning: 5 mg in the first 5 days, 10 mg from day 6 to day 10, and 20 mg from day 11 to day 40.", "Blood samples were collected at 0, 7, 10, and 24 hours after drug administration on the day 1 of fluoxetine 5 mg and on the 1st and the 30th day of fluoxetine 20 mg (days 11 and 40 of treatment, respectively).", "Plasma fluoxetine and serotonin levels increased after drug administration, reaching the highest levels on the 30th day of fluoxetine 20 mg.", "Fluoxetine levels were also detectable in platelets, with a time variation similar to plasma values.", "Platelet serotonin levels decreased after drug administration, and the lowest values were observed on the 30th day of fluoxetine 20 mg."], "structured": false}
{"doc_id": 12040627, "title": "The histone acetyltransferase MOF is a key regulator of the embryonic stem cell core transcriptional network.", "abstract": ["Pluripotent embryonic stem cells (ESCs) maintain self-renewal and the potential for rapid response to differentiation cues.", "Both ESC features are subject to epigenetic regulation.", "Here we show that the histone acetyltransferase Mof plays an essential role in the maintenance of ESC self-renewal and pluripotency.", "ESCs with Mof deletion lose characteristic morphology, alkaline phosphatase (AP) staining, and differentiation potential.", "They also have aberrant expression of the core transcription factors Nanog, Oct4, and Sox2.", "Importantly, the phenotypes of Mof null ESCs can be partially suppressed by Nanog overexpression, supporting the idea that Mof functions as an upstream regulator of Nanog in ESCs.", "Genome-wide ChIP-sequencing and transcriptome analyses further demonstrate that Mof is an integral component of the ESC core transcriptional network and that Mof primes genes for diverse developmental programs.", "Mof is also required for Wdr5 recruitment and H3K4 methylation at key regulatory loci, highlighting the complexity and interconnectivity of various chromatin regulators in ESCs."], "structured": false}
{"doc_id": 12058271, "title": "Role of the CXCR4/SDF-1 chemokine axis in circulating neutrophil homeostasis.", "abstract": ["The bone marrow is the primary site for neutrophil production and release into the circulation.", "Because the CXC chemokine receptor-4/stromal derived factor-1 (CXCR4/SDF-1) axis plays a central role in the interactions of hematopoietic stem cells, lymphocytes, and developing neutrophils in the marrow, we investigated whether reciprocal CXCR4-dependent mechanisms might be involved in neutrophil release and subsequent return to the marrow following circulation.", "Neutralizing antibody to CXCR4 reduced marrow retention of infused neutrophils (45.7% +/-", "0.5% to 6.9% +/-", "0.5%) and was found to mobilize neutrophils from marrow (34.4% +/-", "4.4%).", "Neutrophil CXCR4 expression and SDF-1-induced calcium flux decreased with maturation and activation of the cells, corresponding to the decreased marrow homing associated with these characteristics in vivo.", "Infusion of the inflammatory mediator and CXCR2 ligand KC led to mobilization of neutrophils from marrow by itself and was augmented 3-fold by low doses of CXCR4-blocking antibody that otherwise had no mobilizing effect.", "Examination of KC and SDF-1 calcium signaling demonstrated that the effect of KC may, in part, be due to heterologous desensitization to SDF-1.", "These results suggest that the CXCR4/SDF-1 axis is critical in circulating neutrophil homeostasis and that it may participate in the rapid release of neutrophils from the marrow during inflammation through a novel interaction with inflammatory CXC chemokines."], "structured": false}
{"doc_id": 12074066, "title": "Vitamin D and prevention of colorectal cancer.", "abstract": ["BACKGROUND Inadequate photosynthesis or oral intake of Vitamin D are associated with high incidence rates of colorectal cancer, but the dose-response relationship has not been adequately studied.   \n", "METHODS Dose-response gradients from observational studies of Vitamin D intake and serum 25-hydroxyvitamin D were plotted as trend lines.", "The point on each linear trend line corresponding to an odds ratio of 0.50 provided the prediagnostic Vitamin D intake or 25-hydroxyvitamin D concentration associated with 50% lower risk compared to <100IU/day Vitamin D or <13ng/ml serum 25-hydroxyvitamin D. Medians of these values were determined.   \n", "RESULTS Overall, individuals with >or=1000IU/day oral Vitamin D (p<0.0001) or >or=33ng/ml (82nmol/l) serum 25-hydroxyvitamin D (p<0.01) had 50% lower incidence of colorectal cancer compared to reference values.   \n", "CONCLUSIONS Intake of 1000IU/day of Vitamin D, half the safe upper intake established by the National Academy of Sciences, was associated with 50% lower risk.", "Serum 25-hydroxyvitamin D of 33ng/ml, which is known to be safe, also was associated with 50% lower risk.", "Prompt public health action is needed to increase intake of Vitamin D(3) to 1000IU/day, and to raise 25-hydroxyvitamin D by encouraging a modest duration of sunlight exposure."], "structured": true}
{"doc_id": 12086599, "title": "Repeat expansion in the budding yeast ribosomal DNA can occur independently of the canonical homologous recombination machinery", "abstract": ["Major eukaryotic genomic elements, including the ribosomal DNA (rDNA), are composed of repeated sequences with well-defined copy numbers that must be maintained by regulated recombination.", "Although mechanisms that instigate rDNA recombination have been identified, none are directional and they therefore cannot explain precise repeat number control.", "Here, we show that yeast lacking histone chaperone Asf1 undergo reproducible rDNA repeat expansions.", "These expansions do not require the replication fork blocking protein Fob1 and are therefore independent of known rDNA expansion mechanisms.", "We propose the existence of a regulated rDNA repeat gain pathway that becomes constitutively active in asf1\u0394 mutants.", "Cells lacking ASF1 accumulate rDNA repeats with high fidelity in a processive manner across multiple cell divisions.", "The mechanism of repeat gain is dependent on highly repetitive sequence but, surprisingly, is independent of the homologous recombination proteins Rad52, Rad51 and Rad59.", "The expansion mechanism is compromised by mutations that decrease the processivity of DNA replication, which leads to progressive loss of rDNA repeats.", "Our data suggest that a novel mode of break-induced replication occurs in repetitive DNA that is dependent on high homology but does not require the canonical homologous recombination machinery."], "structured": false}
{"doc_id": 12086818, "title": "cDNA and genomic cloning of lacritin, a novel secretion enhancing factor from the human lacrimal gland.", "abstract": ["Multiple extracellular factors are hypothesized to promote the differentiation of unstimulated and/or stimulated secretory pathways in exocrine secretory cells, but the identity of differentiation factors, particularly those organ-specific, remain largely unknown.", "Here, we report on the identification of a novel secreted glycoprotein, lacritin, that enhances exocrine secretion in overnight cultures of lacrimal acinar cells which otherwise display loss of secretory function.", "Lacritin mRNA and protein are highly expressed in human lacrimal gland, moderately in major and minor salivary glands and slightly in thyroid.", "No lacritin message or protein is detected elsewhere among more than 50 human tissues examined.", "Lacritin displays partial similarity to the glycosaminoglycan-binding region of brain-specific neuroglycan C (32 % identity over 102 amino acid residues) and to the possibly mucin-like amino globular region of fibulin-2 (30 % identity over 81 amino acid residues), and localizes primarily to secretory granules and secretory fluid.", "The lacritin gene consists of five exons, displays no alternative splicing and maps to 12q13.", "Recombinant lacritin augments unstimulated but not stimulated acinar cell secretion, promotes ductal cell proliferation, and stimulates signaling through tyrosine phosphorylation and release of calcium.", "It binds collagen IV, laminin-1, entactin/nidogen-1, fibronectin and vitronectin, but not collagen I, heparin or EGF.", "As an autocrine/paracrine enhancer of the lacrimal constitutive secretory pathway, ductal cell mitogen and stimulator of corneal epithelial cells, lacritin may play a key role in the function of the lacrimal gland-corneal axis."], "structured": false}
{"doc_id": 12087063, "title": "The structure of informal care: are there differences by race?", "abstract": ["This study investigated whether there are race differences in the structure of informal caregiving networks.", "Data on 3,793 functionally impaired persons age 65 and over from the 1989 National Long-Term Care Survey were analyzed.", "The size of the total caregiver network and the unpaid network did not differ by race, but the likelihood of there being a non-immediate family member among unpaid caregivers was higher among disabled older blacks.", "These findings raise questions about whether race differences in nursing home utilization and paid long-term care services, documented in other studies, can be explained by differences in caregiving arrangements."], "structured": false}
{"doc_id": 12100854, "title": "Proteomic and genomic approaches reveal critical functions of H3K9 methylation and Heterochromatin Protein-1\u03b3 in reprogramming to pluripotency", "abstract": ["Reprogramming of somatic cells into induced pluripotent stem cells (iPSCs) involves a marked reorganization of chromatin.", "To identify post-translational histone modifications that change in global abundance during this process, we have applied a quantitative mass-spectrometry-based approach.", "We found that iPSCs, compared with both the starting fibroblasts and a late reprogramming intermediate (pre-iPSCs), are enriched for histone modifications associated with active chromatin, and depleted for marks of transcriptional elongation and a subset of repressive modifications including H3K9me2/me3.", "Dissecting the contribution of H3K9 methylation to reprogramming, we show that the H3K9 methyltransferases Ehmt1, Ehmt2 and Setdb1 regulate global H3K9me2/me3 levels and that their depletion increases iPSC formation from both fibroblasts and pre-iPSCs.", "Similarly, we find that inhibition of heterochromatin protein-1\u03b3 (Cbx3), a protein known to recognize H3K9 methylation, enhances reprogramming.", "Genome-wide location analysis revealed that Cbx3 predominantly binds active genes in both pre-iPSCs and pluripotent cells but with a strikingly different distribution: in pre-iPSCs, but not in embryonic stem cells, Cbx3 associates with active transcriptional start sites, suggesting a developmentally regulated role for Cbx3 in transcriptional activation.", "Despite largely non-overlapping functions and the predominant association of Cbx3 with active transcription, the H3K9 methyltransferases and Cbx3 both inhibit reprogramming by repressing the pluripotency factor Nanog.", "Together, our findings demonstrate that Cbx3 and H3K9 methylation restrict late reprogramming events, and suggest that a marked change in global chromatin character constitutes an epigenetic roadblock for reprogramming."], "structured": false}
{"doc_id": 12100963, "title": "Tissue exit: a novel control point in the accumulation of antigen-specific CD8 T cells in the influenza a virus-infected lung.", "abstract": ["Memory/effector T cells efficiently migrate into extralymphoid tissues and sites of infection, providing immunosurveillance and a first line of defense against invading pathogens.", "Even though it is a potential means to regulate the size, quality, and duration of a tissue infiltrate, T cell egress from infected tissues is poorly understood.", "Using a mouse model of influenza A virus infection, we found that CD8 effector T cells egressed from the infected lung in a CCR7-dependent manner.", "In contrast, following antigen recognition, effector CD8 T cell egress decreased and CCR7 function was reduced in vivo and in vitro, indicating that the exit of CD8 T cells from infected tissues is tightly regulated.", "Our data suggest that the regulation of T cell egress is a mechanism to retain antigen-specific effectors at the site of infection to promote viral clearance, while decreasing the numbers of bystander T cells and preventing overt inflammation."], "structured": false}
{"doc_id": 12102963, "title": "The relation between dietary flavonol intake and coronary heart disease mortality: a meta-analysis of prospective cohort studies", "abstract": ["Objective: To assess the association of dietary flavonol intake with the subsequent risk of coronary heart disease (CHD) mortality.", "Design: Meta-analysis of prospective cohort studies published before September 2001.", "Studies were identified by MEDLINE and EMBASE searches and by scanning relevant reference lists.", "The following information was extracted from published reports: size of cohort, mean age, mean duration of follow-up, number of fatal CHD events, mean flavonol intake, main sources of flavonol intake, degree of adjustment for potential confounders, and the relation of CHD mortality to dietary flavonol intake measured at baseline.", "Results: Seven prospective cohorts of men and women were identified including a total of 2087 fatal CHD events.", "Comparison of individuals in the top third with those in the bottom third of dietary flavonol intake yielded a combined risk ratio of 0.80 (95% CI 0.69\u20130.93) after adjustment for known CHD risk factors and other dietary components.", "Conclusion: This overview of prospective cohort studies indicates that high dietary intake of flavonols from a small number of fruits and vegetables, tea and red wine may be associated with a reduced risk from CHD mortality in free-living populations.", "Sponsorship: Institute for International Health, University of Sydney."], "structured": false}
{"doc_id": 12122482, "title": "MRI in the diagnosis of MS: a prospective study with comparison of clinical evaluation, evoked potentials, oligoclonal banding, and CT.", "abstract": ["We compared the diagnostic capabilities of MRI to CT, evoked potentials (EP), and CSF oligoclonal banding analysis in a prospective evaluation of 200 patients with suspected multiple sclerosis (MS).", "MRI was the best method for demonstrating dissemination in space.", "An abnormal appropriate EP in monosymptomatic disease was usually supported by MRI and CSF analysis as being predictive of MS as a clinical diagnosis.", "A normal appropriate EP study was not satisfactory because MRI and CSF analysis often did not support a diagnosis of non-MS.", "When there is agreement between three of these paraclinical studies, the diagnosis of MS is probably unequivocal.", "For use in research studies, laboratory-supported definite MS (LSDMS) could be diagnosed in 85 patients of the total 200 (42.5%), in 19/38 (50%) of optic neuritis (ON) patients, and in 24/52 (46%) of chronic progressive myelopathy (CPM) patients.", "MRI was 100% successful in identifying patients who qualified for LSDMS in the ON and CPM groups.", "In a short follow-up (less than 1 year), 19/200 (10%) went on to develop clinically definite MS (CDMS), and MRI predicted that diagnosis in 18/19 (95%).", "Only long-term follow-up will show how well these studies and the category of LSDMS predict the development of CDMS.", "The clinical diagnosis of MS (CDMS), even though only 95% accurate, must remain the gold standard."], "structured": false}
{"doc_id": 12130067, "title": "Osteoclasts promote the formation of hematopoietic stem cell niches in the bone marrow", "abstract": ["Formation of the hematopoietic stem cell (HSC) niche in bone marrow (BM) is tightly associated with endochondral ossification, but little is known about the mechanisms involved.", "We used the oc/oc mouse, a mouse model with impaired endochondral ossification caused by a loss of osteoclast (OCL) activity, to investigate the role of osteoblasts (OBLs) and OCLs in the HSC niche formation.", "The absence of OCL activity resulted in a defective HSC niche associated with an increased proportion of mesenchymal progenitors but reduced osteoblastic differentiation, leading to impaired HSC homing to the BM.", "Restoration of OCL activity reversed the defect in HSC niche formation.", "Our data demonstrate that OBLs are required for establishing HSC niches and that osteoblastic development is induced by OCLs.", "These findings broaden our knowledge of the HSC niche formation, which is critical for understanding normal and pathological hematopoiesis."], "structured": false}
{"doc_id": 12130200, "title": "A prospective study of plasma homocyst(e)ine and risk of myocardial infarction in US physicians.", "abstract": ["OBJECTIVE To assess prospectively the risk of coronary heart disease associated with elevated plasma levels of homocyst(e)ine.   \n", "DESIGN Nested case-control study using prospectively collected blood samples.   \n", "SETTING Participants in the Physicians' Health Study.   \n", "PARTICIPANTS A total of 14,916 male physicians, aged 40 to 84 years, with no prior myocardial infarction (MI) or stroke provided plasma samples at baseline and were followed up for 5 years.", "Samples from 271 men who subsequently developed MI were analyzed for homocyst(e)ine levels together with paired controls, matched by age and smoking.   \n", "MAIN OUTCOME MEASURE Acute MI or death due to coronary disease.   \n", "RESULTS Levels of homocyst(e)ine were higher in cases than in controls (11.1 +/- 4.0 [SD] vs 10.5 +/-", "2.8 nmol/mL; P = .03).", "The difference was attributable to an excess of high values among men who later had MIs.", "The relative risk for the highest 5% vs the bottom 90% of homocyst(e)ine levels was 3.1 (95% confidence interval, 1.4 to 6.9; P = .005).", "After additional adjustment for diabetes, hypertension, aspirin assignment, Quetelet's Index, and total/high-density lipoprotein cholesterol, this relative risk was 3.4 (95% confidence interval, 1.3 to 8.8) (P = .01).", "Thirteen controls and 31 cases (11%) had values above the 95th percentile of the controls.   \n", "CONCLUSIONS Moderately high levels of plasma homocyst(e)ine are associated with subsequent risk of MI independent of other coronary risk factors.", "Because high levels can often be easily treated with vitamin supplements, homocyst(e)ine may be an independent, modifiable risk factor."], "structured": true}
{"doc_id": 12130690, "title": "Involvement of transient receptor potential vanilloid 1 receptors in protease-activated receptor-2-induced joint inflammation and nociception.", "abstract": ["Protease-activated receptor-2 (PAR-2) is a G-protein-coupled receptor activated through proteolytic cleavage.", "It is localized on epithelial, endothelial and inflammatory cells, as well as on transient receptor potential vanilloid 1 (TRPV1) receptor-expressing neurones.", "It plays an important role in inflammatory/nociceptive processes.", "Since there are few reports concerning PAR-2 function in joints, the effects of intraarticular PAR-2 activation on joint pain and inflammation were studied.", "Secondary hyperalgesia/allodynia, spontaneous weight distribution, swelling and inflammatory cytokine production were measured and the involvement of TRPV1 ion channels was investigated in rats and mice.", "Injection of the PAR-2 receptor agonist SLIGRL-NH(2) into the knee decreased touch sensitivity and weight bearing of the ipsilateral hindlimb in both species.", "Secondary mechanical allodynia/hyperalgesia and impaired weight distribution were significantly reduced by the TRPV1 antagonist SB366791 in rats and by the genetic deletion of this receptor in mice.", "PAR-2 activation did not cause significant joint swelling, but increased IL-1beta concentration which was not influenced by the lack of the TRPV1 channel.", "For comparison, intraplantar SLIGRL-NH(2) evoked similar primary mechanical hyperalgesia and impaired weight distribution in both WT and TRPV1 deficient mice, but oedema was smaller in the knockouts.", "The inactive peptide, LRGILS-NH(2), injected into either site did not induce any inflammatory or nociceptive changes.", "These data provide evidence for a significant role of TRPV1 receptors in secondary mechanical hyperalgesia/allodynia and spontaneous pain induced by PAR-2 receptor activation in the knee joint.", "Although intraplantar PAR-2 activation-induced oedema is also TRPV1 receptor-mediated, primary mechanical hyperalgesia, impaired weight distribution and IL-1beta production are independent of this channel."], "structured": false}
{"doc_id": 12145359, "title": "Relationship between reduced forced expiratory volume in one second and the risk of lung cancer: a systematic review and meta-analysis.", "abstract": ["BACKGROUND Individuals with severely impaired lung function have an increased risk of lung cancer.", "Whether milder reductions in forced expiratory volume in 1 second (FEV(1)) also increase the risk of lung cancer is controversial.", "Moreover, there is little consensus on whether men and women have similar risks for lung cancer for similar decreases in FEV(1).   \n", "METHODS A search was conducted of PubMed and EMBASE from January 1966 to January 2005 and studies that examined the relationship between FEV1 and lung cancer were identified.", "The search was limited to studies that were population based, employed a prospective design, were large in size (> or = 5000 participants), and adjusted for cigarette smoking status.   \n", "RESULTS Twenty eight abstracts were identified, six of which did not report FEV1 and eight did not adjust for smoking.", "Included in this report are four studies that reported FEV1 in quintiles.", "The risk of lung cancer increased with decreasing FEV1.", "Compared with the highest quintile of FEV1 (> 100% of predicted), the lowest quintile of FEV1 (< approximately 70% of predicted) was associated with a 2.23 fold (95% confidence interval (CI) 1.73 to 2.86) increase in the risk for lung cancer in men and a 3.97 fold increase in women (95% CI 1.93 to 8.25).", "Even relatively small decrements in FEV1 ( approximately 90% of predicted) increased the risk for lung cancer by 30% in men (95% CI 1.05 to 1.62) and 2.64 fold in women (95% CI 1.30 to 5.31).   \n", "CONCLUSION Reduced FEV1 is strongly associated with lung cancer.", "Even a relatively modest reduction in FEV1 is a significant predictor of lung cancer, especially among women."], "structured": true}
{"doc_id": 12149169, "title": "Functional Architecture of RNA Polymerase I", "abstract": ["Synthesis of ribosomal RNA (rRNA) by RNA polymerase (Pol) I is the first step in ribosome biogenesis and a regulatory switch in eukaryotic cell growth.", "Here we report the 12 A cryo-electron microscopic structure for the complete 14-subunit yeast Pol I, a homology model for the core enzyme, and the crystal structure of the subcomplex A14/43.", "In the resulting hybrid structure of Pol I, A14/43, the clamp, and the dock domain contribute to a unique surface interacting with promoter-specific initiation factors.", "The Pol I-specific subunits A49 and A34.5 form a heterodimer near the enzyme funnel that acts as a built-in elongation factor and is related to the Pol II-associated factor TFIIF.", "In contrast to Pol II, Pol I has a strong intrinsic 3'-RNA cleavage activity, which requires the C-terminal domain of subunit A12.2 and, apparently, enables ribosomal RNA proofreading and 3'-end trimming."], "structured": false}
{"doc_id": 12152977, "title": "SWI/SNF-Brg1 regulates self-renewal and occupies core pluripotency-related genes in embryonic stem cells.", "abstract": ["The SWI/SNF-Brg1 chromatin remodeling protein plays critical roles in cell-cycle control and differentiation through regulation of gene expression.", "Loss of Brg1 in mice results in early embryonic lethality, and recent studies have implicated a role for Brg1 in somatic stem cell self-renewal and differentiation.", "However, little is known about Brg1 function in preimplantation embryos and embryonic stem (ES) cells.", "Here we report that Brg1 is required for ES cell self-renewal and pluripotency.", "RNA interference-mediated knockdown of Brg1 in blastocysts caused aberrant expression of Oct4 and Nanog.", "In ES cells, knockdown of Brg1 resulted in phenotypic changes indicative of differentiation, downregulation of self-renewal and pluripotency genes (e.g., Oct4, Sox2, Sall4, Rest), and upregulation of differentiation genes.", "Using genome-wide promoter analysis (chromatin immunoprecipitation) we found that Brg1 occupied the promoters of key pluripotency-related genes, including Oct4, Sox2, Nanog, Sall4, Rest, and Polycomb group (PcG) proteins.", "Moreover, Brg1 co-occupied a subset of Oct4, Sox2, Nanog, and PcG protein target genes.", "These results demonstrate an important role for Brg1 in regulating self-renewal and pluripotency in ES cells."], "structured": false}
{"doc_id": 12156187, "title": "Rapid induction of Alternative Lengthening of Telomeres by depletion of the histone chaperone ASF1", "abstract": ["The mechanism of activation of the alternative lengthening of telomeres (ALT) pathway of mammalian chromosome-end maintenance has been unclear.", "We have now discovered that co-depletion of the histone chaperones ASF1a and ASF1b in human cells induced all hallmarks of ALT in both primary and cancer cells.", "These included the formation of ALT-associated PML (promyelocytic leukemia) bodies (APBs), the presence of extrachromosomal telomeric DNA species, an elevated frequency of telomeric sister chromatid exchanges (t-SCE) events and intertelomeric exchange of an integrated tag.", "The induction of ALT characteristics in this setting led to the simultaneous suppression of telomerase.", "We determined that ALT induction is positively regulated by the proteins RAD17 and BLM and negatively regulated by EXO1 and DNA2.", "The induction of ALT phenotypes as a consequence of ASF1 depletion strongly supports the hypothesis that ALT is a consequence of histone management dysfunction."], "structured": false}
{"doc_id": 12172346, "title": "Targeting bromodomains: epigenetic readers of lysine acetylation", "abstract": ["Lysine acetylation is a key mechanism that regulates chromatin structure; aberrant acetylation levels have been linked to the development of several diseases.", "Acetyl-lysine modifications create docking sites for bromodomains, which are small interaction modules found on diverse proteins, some of which have a key role in the acetylation-dependent assembly of transcriptional regulator complexes.", "These complexes can then initiate transcriptional programmes that result in phenotypic changes.", "The recent discovery of potent and highly specific inhibitors for the BET (bromodomain and extra-terminal) family of bromodomains has stimulated intensive research activity in diverse therapeutic areas, particularly in oncology, where BET proteins regulate the expression of key oncogenes and anti-apoptotic proteins.", "In addition, targeting BET bromodomains could hold potential for the treatment of inflammation and viral infection.", "Here, we highlight recent progress in the development of bromodomain inhibitors, and their potential applications in drug discovery."], "structured": false}
{"doc_id": 12197393, "title": "Arachidonic acid cytochrome P450 epoxygenase pathway.", "abstract": ["Cytochrome P450 (CYP) epoxygenases convert arachidonic acid to four epoxyeicosatrienoic acid (EET) regioisomers, 5,6-, 8,9-, 11,12-, and 14,15-EET, that function as autacrine and paracrine mediators.", "EETs produce vascular relaxation by activating smooth muscle large-conductance Ca2+-activated K+ channels (BKCa).", "In addition, they have anti-inflammatory effects on blood vessels and in the kidney, promote angiogenesis, and protect ischemic myocardium and brain.", "CYP epoxygenases also convert eicosapentaenoic acid to vasoactive epoxy-derivatives, and endocannabinoids containing 11,12- and 14,15-EET are formed.", "Many EET actions appear to be initiated by EET binding to a membrane receptor that activates ion channels and intracellular signal transduction pathways.", "However, EETs also are taken up by cells, are incorporated into phospholipids, and bind to cytosolic proteins and nuclear receptors, suggesting that some functions may occur through direct interaction of the EET with intracellular effector systems.", "Soluble epoxide hydrolase (sEH) converts EETs to dihydroxyeicosatrienoic acids (DHETs).", "Because this attenuates many of the functional effects of EETs, sEH inhibition is being evaluated as a mechanism for increasing and prolonging the beneficial actions of EETs."], "structured": false}
{"doc_id": 12205576, "title": "Physical activity at 36 years: patterns and childhood predictors in a longitudinal study.", "abstract": ["OBJECTIVE The aim was to describe the sex and socioeconomic differences in patterns of physical activity at work and in leisure time of men and women aged 36 years, and to investigate factors in childhood and adolescence which predict high rates of participation in sports and recreational activities in later life.   \n", "DESIGN Data collected in childhood, adolescence, and at 36 years on members of a national prospective birth cohort study were used.   \n", "SETTING", "The population sample was resident in England, Scotland, and Wales.   ", "SUBJECTS A stratified sample of about 3500 men and women was studied regularly from birth until 43 years.   \n", "MEASUREMENTS AND MAIN RESULTS More men than women reported high rates of sports and recreational activities, gardening, and do-it-yourself.", "In contrast women reported higher rates of bicycling and walking.", "Higher levels of education were associated with frequent participation in sports.", "Individuals often engaged in one type of activity without necessarily engaging in other types.", "Those who were most active in sport had been above average at sports in school, more outgoing socially in adolescence, had fewer health problems in childhood, were better educated, and had more mothers with a secondary education than those who were less active.   \n", "CONCLUSIONS Studies that examine the relationship between physical activity and chronic disease should consider a broad range of pursuits rather than extrapolating from only one area of physical activity, and in their explanations should take account of the possible role of childhood characteristics.", "The findings suggest the importance of developing skills and habits in childhood as well as of encouraging healthier exercise habits in adults who may have had few opportunities or low motivation previously."], "structured": true}
{"doc_id": 12206390, "title": "Residual lifetime risk for developing hypertension in middle-aged women and men: The Framingham Heart Study.", "abstract": ["CONTEXT The long-term risk for developing hypertension is best described by the lifetime risk statistic.", "The lifetime risk for hypertension and trends in this risk over time are unknown.   \n", "OBJECTIVES To estimate the residual lifetime risk for hypertension in older US adults and to evaluate temporal trends in this risk.   \n", "DESIGN, SETTING, AND PARTICIPANTS Community-based prospective cohort study of 1298 participants from the Framingham Heart Study who were aged 55 to 65 years and free of hypertension at baseline (1976-1998).   \n", "MAIN OUTCOME MEASURES Residual lifetime risk (lifetime cumulative incidence not adjusted for competing causes of mortality) for hypertension, defined as blood pressure of 140/90 mm Hg or greater or use of antihypertensive medications.   \n", "RESULTS The residual lifetime risks for developing hypertension and stage 1 high blood pressure or higher (greater-than-or-equal to 140/90 mm Hg regardless of treatment) were 90% in both 55- and 65-year-old participants.", "The lifetime probability of receiving antihypertensive medication was 60%.", "The risk for hypertension remained unchanged for women, but it was approximately 60% higher for men in the contemporary 1976-1998 period compared with an earlier 1952-1975 period.", "In contrast, the residual lifetime risk for stage 2 high blood pressure or higher (greater-than-or-equal to 160/100 mm Hg regardless of treatment) was considerably lower in both sexes in the recent period (35%-57% in 1952-1975 vs 35%-44% in 1976-1998), likely due to a marked increase in treatment of individuals with substantially elevated blood pressure.   \n", "CONCLUSION The residual lifetime risk for hypertension for middle-aged and elderly individuals is 90%, indicating a huge public health burden.", "Although the decline in lifetime risk for stage 2 high blood pressure or higher represents a major achievement, efforts should be directed at the primary prevention of hypertension."], "structured": true}
{"doc_id": 12207167, "title": "Adverse effects of excessive consumption of amino acids.", "abstract": ["PHENYLALANINE TOXICITY 158 Developing the 0.", "-M ethylphenylalanine Model. . . . . .", ".. .", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", "160 Use of the a-Methyl phenylalanine Model in Brain Protein Synthesis . . . . . . . . . . . . . . . . . . .", "161 TYROSINE TOXICITY 162 General Nutritional Observations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .", "162 Factors Affecting Tissue Concentrations of Tyrosine .", "...", ".. ..", ".. ...... .", ".", ".", ".", ".", ".", ".. . .", "163 Probable Cause of Tyrosine Toxicity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .", "164 A New Animal Model for Human Tyrosinemia II 165 TRYPTOPHAN TOXICITy 165 General Nutritional Observations . ..", "....... .", "....... .", ".... .", ".", ".. .", ".", ".", ".. .", ".. .", ".. .....", ".........", "165 Factors Affecting Tryptophan Toxicity . . .", ".. .", ".", ".", ".", ".", ".", ".", ".... .", "........", "166 Tryptophan and Ruminant Interstitial Pulmonary Emphysema and Edema ..... . . . . . . .", "167 HISTIDINE TOXICITY 168 General Nutritional Observations ...... ........ . . . .", "..... .", "...... .. .", "168 Metabolic Aspects. . . . . . . . . . . . . . . . . . . . . . . . . . . . . .", ".. .", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".. .", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", "169 Alleviation of Histidine Toxicity . . . . . . . . . . . . . . . . . . . . . . . . . . . . .", "... .", ". .", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", "170 METHIONINE TOXICITY 171 General Nutritional Observations . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .", "171 Tissue Damage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .", ".. .", ".", ".", ".", ".", ".", ".", ".", ".", "172 Protective Effect of Glycine, Serine, or Retinol . . .", "..", "....... .", "......... .", "......... .. .", ".. .", ".", "......", "172 Chemical Characteristics Related to the Toxicity of Methionine . .", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", "173 Damaging Effects of Methanethiol. .", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".. .", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".. .", ".", ".", ".", ".", ".", ".", ".", ".", "173 Met\ufffdio,!ine To\ufffdi.city in Chickens 174 EthlOnme TOxIcIty . .", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".. .", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", "... .", "174"], "structured": false}
{"doc_id": 12207340, "title": "Mechanism and regulation of DNA end resection in eukaryotes.", "abstract": ["The repair of DNA double-strand breaks (DSBs) by homologous recombination (HR) is initiated by nucleolytic degradation of the 5'-terminated strands in a process termed end resection.", "End resection generates 3'-single-stranded DNA tails, substrates for Rad51 to catalyze homologous pairing and DNA strand exchange, and for activation of the DNA damage checkpoint.", "The commonly accepted view is that end resection occurs by a two-step mechanism.", "In the first step, Sae2/CtIP activates the Mre11-Rad50-Xrs2/Nbs1 (MRX/N) complex to endonucleolytically cleave the 5'-terminated DNA strands close to break ends, and in the second step Exo1 and/or Dna2 nucleases extend the resected tracts to produce long 3'-ssDNA-tailed intermediates.", "Initiation of resection commits a cell to repair a DSB by HR because long ssDNA overhangs are poor substrates for non-homologous end joining (NHEJ).", "Thus, the initiation of end resection has emerged as a critical control point for repair pathway choice.", "Here, I review recent studies on the mechanism of end resection and how this process is regulated to ensure the most appropriate repair outcome."], "structured": false}
{"doc_id": 12209494, "title": "Multiple-dose activated charcoal in acute self-poisoning: a randomised controlled trial", "abstract": ["BACKGROUND The case-fatality for intentional self-poisoning in the rural developing world is 10-50-fold higher than that in industrialised countries, mostly because of the use of highly toxic pesticides and plants.", "We therefore aimed to assess whether routine treatment with multiple-dose activated charcoal, to interrupt enterovascular or enterohepatic circulations, offers benefit compared with no charcoal in such an environment.   \n", "METHODS We did an open-label, parallel group, randomised, controlled trial of six 50 g doses of activated charcoal at 4-h intervals versus no charcoal versus one 50 g dose of activated charcoal in three Sri Lankan hospitals.", "4632 patients were randomised to receive no charcoal (n=1554), one dose of charcoal (n=1545), or six doses of charcoal (n=1533); outcomes were available for 4629 patients.", "2338 (51%) individuals had ingested pesticides, whereas 1647 (36%) had ingested yellow oleander (Thevetia peruviana) seeds.", "Mortality was the primary outcome measure.", "Analysis was by intention to treat.", "The trial is registered with controlled-trials.com as ISRCTN02920054.   \n", "FINDINGS Mortality did not differ between the groups.", "97 (6.3%) of 1531 participants in the multiple-dose group died, compared with 105 (6.8%) of 1554 in the no charcoal group (adjusted odds ratio 0.96, 95% CI 0.70-1.33).", "No differences were noted for patients who took particular poisons, were severely ill on admission, or who presented early.   \n", "INTERPRETATION We cannot recommend the routine use of multiple-dose activated charcoal in rural Asia Pacific; although further studies of early charcoal administration might be useful, effective affordable treatments are urgently needed."], "structured": true}
{"doc_id": 12217662, "title": "Post-prenylation-processing enzymes as new targets in oncogenesis", "abstract": ["RAS and many other oncogenic proteins undergo a complex series of post-translational modifications that are initiated by the addition of an isoprenoid lipid through a process known as prenylation.", "Following prenylation, these proteins usually undergo endoproteolytic processing by the RCE1 protease and then carboxyl methylation by a unique methyltransferase known as isoprenylcysteine carboxyl methyltransferase (ICMT).", "Although inhibitors that have been designed to target the prenylation step are now in advanced-stage clinical trials, their utility and efficacy seem to be limited.", "Recent findings, however, indicate that the inhibition of these post-prenylation-processing steps \u2014 particularly that of ICMT-catalysed methylation \u2014 might provide a better approach to the control of cancer-cell proliferation."], "structured": false}
{"doc_id": 12224536, "title": "Trends in sugar-sweetened beverage consumption among youth and adults in the United States: 1999-2010.", "abstract": ["BACKGROUND Reducing sugar-sweetened beverage (SSB) consumption is a recommended strategy to promote optimal health.   \n", "OBJECTIVE The objective was to describe trends in SSB consumption among youth and adults in the United States.   \n", "DESIGN We analyzed energy intake from SSBs among 22,367 youth aged 2-19 y and 29,133 adults aged \u226520 y who participated in a 24-h dietary recall as part of NHANES, a nationally representative sample of the US population with a cross-sectional design, between 1999 and 2010.", "SSBs included soda, fruit drinks, sports and energy drinks, sweetened coffee and tea, and other sweetened beverages.", "Patterns of SSB consumption, including location of consumption and meal occasion associated with consumption, were also examined.   \n", "RESULTS In 2009-2010, youth consumed a mean (\u00b1SE) of 155 \u00b1 7 kcal/d from SSBs, and adults consumed an age-adjusted mean (\u00b1SE) of 151 \u00b1 5 kcal/d from SSBs--a decrease from 1999 to 2000 of 68 kcal/d and 45 kcal/d, respectively (P-trend < 0.001 for each).", "In 2009-2010, SSBs contributed 8.0% \u00b1 0.4% and 6.9% \u00b1 0.2% of daily energy intake among youth and adults, respectively, which reflected a decrease compared with 1999-2000 (P-trend < 0.001 for both).", "Decreases in SSB consumption, both in the home and away from home and also with both meals and snacks, occurred over the 12-y study duration (P-trend < 0.01 for each).   \n", "CONCLUSION A decrease in SSB consumption among youth and adults in the United States was observed between 1999 and 2010."], "structured": true}
{"doc_id": 12225214, "title": "Ubiquitination on nonlysine residues by a viral E3 ubiquitin ligase.", "abstract": ["Ubiquitination controls a broad range of cellular functions.", "The last step of the ubiquitination pathway is regulated by enzyme type 3 (E3) ubiquitin ligases.", "E3 enzymes are responsible for substrate specificity and catalyze the formation of an isopeptide bond between a lysine residue of the substrate (or the N terminus of the substrate) and ubiquitin.", "MIR1 and MIR2 are two E3 ubiquitin ligases encoded by Kaposi's sarcoma-associated herpesvirus that mediate the ubiquitination of major histocompatibility complex class I (MHC I) molecules and subsequent internalization.", "Here, we found that MIR1, but not MIR2, promoted down-regulation of MHC I molecules lacking lysine residues in their intracytoplasmic domain.", "In the presence of MIR1, these MHC I molecules were ubiquitinated, and their association with ubiquitin was sensitive to beta2-mercaptoethanol, unlike lysine-ubiquitin bonds.", "This form of ubiquitination required a cysteine residue in the intracytoplasmic tail of MHC I molecules.", "An MHC I molecule containing a single cysteine residue in an artificial glycine and alanine intracytoplasmic domain was endocytosed and degraded in the presence of MIR1.", "Thus, ubiquitination can occur on proteins lacking accessible lysines or an accessible N terminus."], "structured": false}
{"doc_id": 12232678, "title": "All dosage compensation is local: Gene-by-gene regulation of sex-biased expression on the chicken Z chromosome", "abstract": ["Recent reports have suggested that birds lack a mechanism of wholesale dosage compensation for the Z sex chromosome.", "This discovery was rather unexpected, as all other animals investigated with chromosomal mechanisms of sex determination have some method to counteract the effects of gene dosage of the dominant sex chromosome in males and females.", "Despite the lack of a global mechanism of avian dosage compensation, the pattern of gene expression difference between males and females varies a great deal for individual Z-linked genes.", "This suggests that some genes may be individually dosage compensated, and that some less-than-global pattern of dosage compensation, such as local or temporal, exists on the avian Z chromosome.", "We used global gene expression profiling in males and females for both somatic and gonadal tissue at several time points in the life cycle of the chicken to assess the pattern of sex-biased gene expression on the Z chromosome.", "Average fold-change between males and females varied somewhat among tissue time-point combinations, with embryonic brain samples having the smallest gene dosage effects, and adult gonadal tissue having the largest degree of male bias.", "Overall, there were no neighborhoods of overall dosage compensation along the Z. Taken together, this suggests that dosage compensation is regulated on the Z chromosome entirely on a gene-by-gene level, and can vary during the life cycle and by tissue type.", "This regulation may be an indication of how critical a given gene's functionality is, as the expression level for essential genes will be tightly regulated in order to avoid perturbing important pathways and networks with differential expression levels in males and females."], "structured": false}
{"doc_id": 12236208, "title": "Hormone replacement therapy prevents bone loss in patients with inflammatory bowel disease.", "abstract": ["Patients with inflammatory bowel disease have an increased prevalence of osteoporosis, and suffer high rates of spinal bone loss.", "Hormone replacement therapy (HRT) is effective in the treatment and prevention of osteoporosis but has not been studied in patients with inflammatory bowel disease.", "A two year prospective study of HRT in inflammatory bowel disease was performed in 47 postmenopausal women aged 44 to 67 years with ulcerative colitis (25) or Crohn's disease (22).", "Patients had radial and spinal bone density measured annually by single photon absorptiometry and quantitative computed tomography respectively.", "The mean (95% confidence intervals) annual change in radial bone density was +1.42%/yr (+0.58 to +2.26; P < 0.005) and for spinal bone +2.60%/yr (+1.06 to +4.15; p < 0.005).", "There was no significant correlation between rates of change of bone density at the two sites, or between the rates of change and the initial bone density either in the radius or spine.", "Twelve patients were given prednisolone during the study, and their rates of change for spinal bone density were lower, but values were not statistically significantly different from those who did not receive corticosteroids.", "Changes in bone density for patients with ulcerative colitis and Crohn's disease were not significantly different.", "The change in bone density did not correlate with the patients' age or number of years after the menopause.", "It is concluded that HRT is effective in prevention of bone loss in postmenopausal women with inflammatory bowel disease."], "structured": false}
{"doc_id": 12240507, "title": "Disruption of the 5S RNP\u2013Mdm2 interaction significantly improves the erythroid defect in a mouse model for Diamond-Blackfan anemia", "abstract": ["Diamond-Blackfan anemia (DBA) is a congenital erythroid hypoplasia caused by haploinsufficiency of genes encoding ribosomal proteins (RPs).", "Perturbed ribosome biogenesis in DBA has been shown to induce a p53-mediated ribosomal stress response.", "However, the mechanisms of p53 activation and its relevance for the erythroid defect remain elusive.", "Previous studies have indicated that activation of p53 is caused by the inhibition of mouse double minute 2 (Mdm2), the main negative regulator of p53, by the 5S ribonucleoprotein particle (RNP).", "Meanwhile, it is not clear whether this mechanism solely mediates the p53-dependent component found in DBA.", "To approach this question, we crossed our mouse model for RPS19-deficient DBA with Mdm2C305F knock-in mice that have a disrupted 5S RNP\u2013Mdm2 interaction.", "Upon induction of the Rps19 deficiency, Mdm2C305F reversed the p53 response and improved expansion of hematopoietic progenitors in vitro, and ameliorated the anemia in vivo.", "Unexpectedly, disruption of the 5S RNP\u2013Mdm2 interaction also led to selective defect in erythropoiesis.", "Our findings highlight the sensitivity of erythroid progenitor cells to aberrations in p53 homeostasis mediated by the 5S RNP\u2013Mdm2 interaction.", "Finally, we provide evidence indicating that physiological activation of the 5S RNP-Mdm2-p53 pathway may contribute to functional decline of the hematopoietic system in a cell-autonomous manner over time."], "structured": false}
{"doc_id": 12258338, "title": "Pharmacist participation on physician rounds and adverse drug events in the intensive care unit.", "abstract": ["CONTEXT Pharmacist review of medication orders in the intensive care unit (ICU) has been shown to prevent errors, and pharmacist consultation has reduced drug costs.", "However, whether pharmacist participation in the ICU at the time of drug prescribing reduces adverse events has not been studied.   \n", "OBJECTIVE To measure the effect of pharmacist participation on medical rounds in the ICU on the rate of preventable adverse drug events (ADEs) caused by ordering errors.   \n", "DESIGN Before-after comparison between phase 1 (baseline) and phase 2 (after intervention implemented) and phase 2 comparison with a control unit that did not receive the intervention.   \n", "SETTING A medical ICU (study unit) and a coronary care unit (control unit) in a large urban teaching hospital.   \n", "PATIENTS Seventy-five patients randomly selected from each of 3 groups: all admissions to the study unit from February 1, 1993, through July 31, 1993 (baseline) and all admissions to the study unit (postintervention) and control unit from October 1, 1994, through July 7, 1995.", "In addition, 50 patients were selected at random from the control unit during the baseline period.   \n", "INTERVENTION A senior pharmacist made rounds with the ICU team and remained in the ICU for consultation in the morning, and was available on call throughout the day.   \n", "MAIN OUTCOME MEASURES Preventable ADEs due to ordering (prescribing) errors and the number, type, and acceptance of interventions made by the pharmacist.", "Preventable ADEs were identified by review of medical records of the randomly selected patients during both preintervention and postintervention phases.", "Pharmacists recorded all recommendations, which were then analyzed by type and acceptance.   \n", "RESULTS The rate of preventable ordering ADEs decreased by 66% from 10.4 per 1000 patient-days (95% confidence interval [CI], 7-14) before the intervention to 3.5 (95% CI, 1-5; P<.001) after the intervention.", "In the control unit, the rate was essentially unchanged during the same time periods: 10.9 (95% CI, 6-16) and 12.4 (95% CI, 8-17) per 1000 patient-days.", "The pharmacist made 366 recommendations related to drug ordering, of which 362 (99%) were accepted by physicians.   \n", "CONCLUSIONS The presence of a pharmacist on rounds as a full member of the patient care team in a medical ICU was associated with a substantially lower rate of ADEs caused by prescribing errors.", "Nearly all the changes were readily accepted by physicians."], "structured": true}
{"doc_id": 12265561, "title": "Ligand-target interactions: what can we learn from NMR?", "abstract": ["The conformation of the ligand in complex with a macromolecular target can be studied by nuclear magnetic resonance (NMR) in solution for both tightly and weakly forming complexes.", "In the weak binding regime (k(off) > 10(4) Hz), the structure of the bound ligand is accessible also for very large complexes (>100 kDa), which are not amenable to NMR studies in the tight binding regime.", "Here I review the state-of-the-art NMR methodology used for screening ligands and for the structural investigation of bound ligand conformations, in both tight and weak binding regimes.", "The advantages and disadvantages of each approach are critically described.", "The NMR methodology used to investigate transiently forming complexes has expanded considerably in the past few years, opening new possibilities for a detailed description of ligand-target interactions.", "Novel methods for the determination of the bound ligand conformation, in particular transferred cross-correlated relaxation, are thoroughly reviewed, and their advantages with respect to established methodology are discussed, using the epothilone-tubulin complex as a primary example."], "structured": false}
{"doc_id": 12271486, "title": "MotifMap: integrative genome-wide maps of regulatory motif sites for model species", "abstract": ["BACKGROUND A central challenge of biology is to map and understand gene regulation on a genome-wide scale.", "For any given genome, only a small fraction of the regulatory elements embedded in the DNA sequence have been characterized, and there is great interest in developing computational methods to systematically map all these elements and understand their relationships.", "Such computational efforts, however, are significantly hindered by the overwhelming size of non-coding regions and the statistical variability and complex spatial organizations of regulatory elements and interactions.", "Genome-wide catalogs of regulatory elements for all model species simply do not yet exist.   \n", "RESULTS The MotifMap system uses databases of transcription factor binding motifs, refined genome alignments, and a comparative genomic statistical approach to provide comprehensive maps of candidate regulatory elements encoded in the genomes of model species.", "The system is used to derive new genome-wide maps for yeast, fly, worm, mouse, and human.", "The human map contains 519,108 sites for 570 matrices with a False Discovery Rate of 0.1 or less.", "The new maps are assessed in several ways, for instance using high-throughput experimental ChIP-seq data and AUC statistics, providing strong evidence for their accuracy and coverage.", "The maps can be usefully integrated with many other kinds of omic data and are available at http://motifmap.igb.uci.edu/.   CONCLUSIONS MotifMap and its integration with other data provide a foundation for analyzing gene regulation on a genome-wide scale, and for automatically generating regulatory pathways and hypotheses.", "The power of this approach is demonstrated and discussed using the P53 apoptotic pathway and the Gli hedgehog pathways as examples."], "structured": true}
{"doc_id": 12280462, "title": "Inhibition of apical sodium-dependent bile acid transporter as a novel treatment for diabetes.", "abstract": ["Bile acids are recognized as metabolic modulators.", "The present study was aimed at evaluating the effects of a potent Asbt inhibitor (264W94), which blocks intestinal absorption of bile acids, on glucose homeostasis in Zucker Diabetic Fatty (ZDF) rats.", "Oral administration of 264W94 for two wk increased fecal bile acid concentrations and elevated non-fasting plasma total Glp-1.", "Treatment of 264W94 significantly decreased HbA1c and glucose, and prevented the drop of insulin levels typical of ZDF rats in a dose-dependent manner.", "An oral glucose tolerance test revealed up to two-fold increase in plasma total Glp-1 and three-fold increase in insulin in 264W94 treated ZDF rats at doses sufficient to achieve glycemic control.", "Tissue mRNA analysis indicated a decrease in farnesoid X receptor (Fxr) activation in small intestines and the liver but co-administration of a Fxr agonist (GW4064) did not attenuate 264W94 induced glucose lowering effects.", "In summary, our results demonstrate that inhibition of Asbt increases bile acids in the distal intestine, promotes Glp-1 release and may offer a new therapeutic strategy for type 2 diabetes mellitus."], "structured": false}
{"doc_id": 12315072, "title": "Early chromatin unfolding by RUNX1: a molecular explanation for differential requirements during specification versus maintenance of the hematopoietic gene expression program.", "abstract": ["At the cellular level, development progresses through successive regulatory states, each characterized by their specific gene expression profile.", "However, the molecular mechanisms regulating first the priming and then maintenance of gene expression within one developmental pathway are essentially unknown.", "The hematopoietic system represents a powerful experimental model to address these questions and here we have focused on a regulatory circuit playing a central role in myelopoiesis: the transcription factor PU.1, its target gene colony-stimulating-factor 1 receptor (Csf1r), and key upstream regulators such as RUNX1.", "We find that during ontogeny, chromatin unfolding precedes the establishment of active histone marks and the formation of stable transcription factor complexes at the Pu.1 locus and we show that chromatin remodeling is mediated by the transient binding of RUNX1 to Pu.1 cis-elements.", "By contrast, chromatin reorganization of Csf1r requires prior expression of PU.1 together with RUNX1 binding.", "Once the full hematopoietic program is established, stable transcription factor complexes and active chromatin can be maintained without RUNX1.", "Our experiments therefore demonstrate how individual transcription factors function in a differentiation stage-specific manner to differentially affect the initiation versus maintenance of a developmental program."], "structured": false}
{"doc_id": 12324049, "title": "Whole-genome fingerprint of the DNA methylome during human B cell differentiation", "abstract": ["We analyzed the DNA methylome of ten subpopulations spanning the entire B cell differentiation program by whole-genome bisulfite sequencing and high-density microarrays.", "We observed that non-CpG methylation disappeared upon B cell commitment, whereas CpG methylation changed extensively during B cell maturation, showing an accumulative pattern and affecting around 30% of all measured CpG sites.", "Early differentiation stages mainly displayed enhancer demethylation, which was associated with upregulation of key B cell transcription factors and affected multiple genes involved in B cell biology.", "Late differentiation stages, in contrast, showed extensive demethylation of heterochromatin and methylation gain at Polycomb-repressed areas, and genes with apparent functional impact in B cells were not affected.", "This signature, which has previously been linked to aging and cancer, was particularly widespread in mature cells with an extended lifespan.", "Comparing B cell neoplasms with their normal counterparts, we determined that they frequently acquire methylation changes in regions already undergoing dynamic methylation during normal B cell differentiation."], "structured": false}
{"doc_id": 12337611, "title": "LIN28B induces neuroblastoma and enhances MYCN levels via let-7 suppression", "abstract": ["LIN28B regulates developmental processes by modulating microRNAs (miRNAs) of the let-7 family.", "A role for LIN28B in cancer has been proposed but has not been established in vivo.", "Here, we report that LIN28B showed genomic aberrations and extensive overexpression in high-risk neuroblastoma compared to several other tumor entities and normal tissues.", "High LIN28B expression was an independent risk factor for adverse outcome in neuroblastoma.", "LIN28B signaled through repression of the let-7 miRNAs and consequently resulted in elevated MYCN protein expression in neuroblastoma cells.", "LIN28B\u2013let-7\u2013MYCN signaling blocked differentiation of normal neuroblasts and neuroblastoma cells.", "These findings were fully recapitulated in a mouse model in which LIN28B expression in the sympathetic adrenergic lineage induced development of neuroblastomas marked by low let-7 miRNA levels and high MYCN protein expression.", "Interference with this pathway might offer therapeutic perspectives."], "structured": false}
{"doc_id": 12358173, "title": "Platelet-derived endothelial cell growth factor expression correlates with tumour angiogenesis and prognosis in non-small-cell lung cancer.", "abstract": ["Angiogenesis is a recently described prognostic factor in non-small-cell lung cancer.", "Platelet-derived endothelial cell growth factor (PD-ECGF), shown to be the enzyme thymidine phosphorylase (TP), induces angiogenesis in vitro and in vivo.", "High intracellular levels of the enzyme are associated with increased chemosensitivity to pyrimidine antimetabolites.", "PD-ECGF/TP expression was evaluated immunohistochemically in surgically resected specimens from 107 patients with operable non-small-cell lung cancer using the P-GF,44C monoclonal antibody.", "High expression of PD-ECGF/TP was found in 25% of cases and was associated with high vascular grade (P = 0.01).", "Fourteen of 32 (44%) high vascular grade tumours showed a positive reactivity for PD-ECGF/TP vs 13/75 (17%) of low/medium vascular grade.", "Positive expression was observed more frequently in T2-staged cases than in T1 (P = 0.04).", "While overall survival was not affected (P = 0.09), subset analysis revealed that node-negative patients with positive PD-ECGF/TP expression had a worse prognosis (P = 0.04).", "The results suggest that PD-ECGF/TP may be an important molecule involved in angiogenesis in non-small-cell lung cancer.", "Up-regulation of the enzyme defines a more aggressive tumour phenotype in patients with node-negative disease.", "Assessment of vascular grade and PD-ECGF/TP expression should be taken into account in the design of randomized trials assessing the role of adjuvant chemotherapy in non-small-cell lung cancer."], "structured": false}
{"doc_id": 12364109, "title": "The association between psychological distance and construal level: evidence from an implicit association test.", "abstract": ["According to construal level theory (N. Liberman, Y. Trope, & E. Stephan, in press; Y. Trope & N. Liberman, 2003), people use a more abstract, high construal level when judging, perceiving, and predicting more psychologically distal targets, and they judge more abstract targets as being more psychologically distal.", "The present research demonstrated that associations between more distance and higher level of construal also exist on a pure conceptual level.", "Eight experiments used the Implicit Association Test (IAT; A. G. Greenwald, D. E. McGhee, & J. L. K. Schwartz, 1998) to demonstrate an association between words related to construal level (low vs. high) and words related to four dimensions of distance (proximal vs. distal): temporal distance, spatial distance, social distance, and hypotheticality.", "In addition to demonstrating an association between level of construal and psychological distance, these findings also corroborate the assumption that all 4 dimensions of psychological distance are related to level of construal in a similar way and support the notion that they all are forms of psychological distance."], "structured": false}
{"doc_id": 12370190, "title": "A load driver device for engineering modularity in biological networks", "abstract": ["The behavior of gene modules in complex synthetic circuits is often unpredictable.", "After joining modules to create a circuit, downstream elements (such as binding sites for a regulatory protein) apply a load to upstream modules that can negatively affect circuit function.", "Here we devised a genetic device named a load driver that mitigates the impact of load on circuit function, and we demonstrate its behavior in Saccharomyces cerevisiae.", "The load driver implements the design principle of timescale separation: inclusion of the load driver's fast phosphotransfer processes restores the capability of a slower transcriptional circuit to respond to time-varying input signals even in the presence of substantial load.", "Without the load driver, we observed circuit behavior that suffered from a 76% delay in response time and a 25% decrease in system bandwidth due to load.", "With the addition of a load driver, circuit performance was almost completely restored.", "Load drivers will serve as fundamental building blocks in the creation of complex, higher-level genetic circuits."], "structured": false}
{"doc_id": 12370881, "title": "Inflammatory monocyte/macrophage modulation by liposome-entrapped spironolactone ameliorates acute lung injury in mice.", "abstract": ["AIM To examine the therapeutic/preventive potential of liposome-encapsulated spironolactone (SP; Lipo-SP) for acute lung injury (ALI) and fibrosis.   ", "MATERIALS & METHODS Lipo-SP was prepared by the film-ultrasonic method, and physicochemical and pharmacokinetic characterized for oral administration (10 and 20 mg/kg for SP-loaded liposome; 20 mg/kg for free SP) in a mouse model bleomycin-induced ALI.   \n", "RESULTS Lipo-SP enhanced bioavailability of SP with significant amelioration in lung pathology.", "Mechanistically, SP-mediated mineralocorticoid receptor antagonism contributes to inflammatory monocyte/macrophage modulation via an inhibitory effect on Ly6C(hi) monocytosis-directed M2 polarization of alveolar macrophages.", "Moreover, Lipo-SP at lower dose (10 mg/kg) exhibited more improvement in body weight gain.   \n", "CONCLUSION Our data highlight Lipo-SP as a promising approach with therapeutic/preventive potential for ALI and fibrosis."], "structured": true}
{"doc_id": 12383365, "title": "Passive Surveillance for I. scapularis Ticks: Enhanced Analysis for Early Detection of Emerging Lyme Disease Risk", "abstract": ["ABSTRACT Lyme disease (LD) is emerging in Canada because of the northward expansion of the geographic range of the tick vector Ixodes scapularis (Say).", "Early detection of emerging areas of LD risk is critical to public health responses, but the methods to do so on a local scale are lacking.", "Passive tick surveillance has operated in Canada since 1990 but this method lacks specificity for identifying areas where tick populations are established because of dispersion of ticks from established LD risk areas by migratory birds.", "Using data from 70 field sites in Quebec visited previously, we developed a logistic regression model for estimating the risk of I. scapularis population establishment based on the number of ticks submitted in passive surveillance and a model-derived environmental suitability index.", "Sensitivity-specificity plots were used to select an optimal threshold value of the linear predictor from the model as the signal for tick population establishment.", "This value was used to produce an \u201cAlert Map\u201d identifying areas where the passive surveillance data suggested ticks were establishing in Quebec.", "Alert Map predictions were validated by field surveillance at 76 sites: the prevalence of established I. scapularis populations was significantly greater in areas predicted as high-risk by the Alert map (29 out of 48) than in areas predicted as moderate-risk (4 out of 30) (P < 0.001).", "This study suggests that Alert Maps created using this approach can provide a usefully rapid and accurate tool for early identification of emerging areas of LD risk at a geographic scale appropriate for local disease control and prevention activities."], "structured": false}
{"doc_id": 12409683, "title": "Reduction of transmission from malaria patients by artemisinin combination therapies: a pooled analysis of six randomized trials", "abstract": ["BACKGROUND Artemisinin combination therapies (ACT), which are increasingly being introduced for treatment of Plasmodium falciparum malaria, are more effective against sexual stage parasites (gametocytes) than previous first-line antimalarials and therefore have the potential to reduce parasite transmission.", "The size of this effect is estimated in symptomatic P. falciparum infections.   \n", "METHODS Data on 3,174 patients were pooled from six antimalarial trials conducted in The Gambia and Kenya.", "Multivariable regression was used to investigate the role of ACT versus non-artemisinin antimalarial treatment, treatment failure, presence of pre-treatment gametocytes and submicroscopic gametocytaemia on transmission to mosquitoes and the area under the curve (AUC) of gametocyte density during the 28 days of follow up.   \n", "RESULTS ACT treatment was associated with a significant reduction in the probability of being gametocytaemic on the day of transmission experiments (OR 0.20 95% CI 0.16-0.26), transmission to mosquitoes by slide-positive gametocyte carriers (OR mosquito infection 0.49 95% CI 0.33-0.73) and AUC of gametocyte density (ratio of means 0.35 95% CI 0.31-0.41).", "Parasitological treatment failure did not account for the difference between ACT and non-artemisinin impact.", "The presence of slide-positive gametocytaemia prior to treatment significantly reduced ACT impact on gametocytaemia (p < 0.001).", "Taking account of submicroscopic gametocytaemia reduced estimates of ACT impact in a high transmission setting in Kenya, but not in a lower transmission setting in the Gambia.   \n", "CONCLUSION Treatment with ACT significantly reduces infectiousness of individual patients with uncomplicated falciparum malaria compared to previous first line treatments.", "Rapid treatment of cases before gametocytaemia is well developed may enhance the impact of ACT on transmission."], "structured": true}
{"doc_id": 12411274, "title": "Skeletal Myogenic Progenitors Originating from Embryonic Dorsal Aorta Coexpress Endothelial and Myogenic Markers and Contribute to Postnatal Muscle Growth and Regeneration", "abstract": ["Skeletal muscle in vertebrates is derived from somites, epithelial structures of the paraxial mesoderm, yet many unrelated reports describe the occasional appearance of myogenic cells from tissues of nonsomite origin, suggesting either transdifferentiation or the persistence of a multipotent progenitor.", "Here, we show that clonable skeletal myogenic cells are present in the embryonic dorsal aorta of mouse embryos.", "This finding is based on a detailed clonal analysis of different tissue anlagen at various developmental stages.", "In vitro, these myogenic cells show the same morphology as satellite cells derived from adult skeletal muscle, and express a number of myogenic and endothelial markers.", "Surprisingly, the latter are also expressed by adult satellite cells.", "Furthermore, it is possible to clone myogenic cells from limbs of mutant c-Met-/- embryos, which lack appendicular muscles, but have a normal vascular system.", "Upon transplantation, aorta-derived myogenic cells participate in postnatal muscle growth and regeneration, and fuse with resident satellite cells.    ", "The potential of the vascular system to generate skeletal muscle cells may explain observations of nonsomite skeletal myogenesis and raises the possibility that a subset of satellite cells may derive from the vascular system."], "structured": false}
{"doc_id": 12428137, "title": "Mapping of a gene for severe pediatric gastroesophageal reflux to chromosome 13q14.", "abstract": ["CONTEXT Gastroesophageal reflux (GER) has not previously been widely regarded as a hereditary disease.", "A few reports have suggested, however, that a genetic component may contribute to the incidence of GER, especially in its severe or chronic forms.   \n", "OBJECTIVE To identify a genetic locus that cosegregates with a severe pediatric GER phenotype in families with multiple affected members.   \n", "DESIGN A genome-wide scan of families affected by severe pediatric GER using polymorphic microsatellite markers spaced at an average of 8 centimorgans (cM), followed by haplotyping and by pairwise and multipoint linkage analyses.   \n", "SETTING General US community, with research performed in a university tertiary care hospital.   ", "SUBJECTS Affected and unaffected family members from 5 families having multiple individuals affected by severe pediatric GER, identified through a patient support group.   \n", "MAIN OUTCOME MEASURES Determination of inheritance patterns and linkage of a genetic locus with the severe pediatric GER phenotype by logarithm-of-odds (lod) score analysis, considering a lod score of 3 or greater as evidence of linkage.   \n", "RESULTS In these families, severe pediatric GER followed an autosomal dominant hereditary pattern with high penetrance.", "A gene for severe pediatric GER was mapped to a 13-cM region on chromosome 13q between microsatellite markers D13S171 and D13S263.", "A maximum multifamily 2-point lod score of 5.58 and a maximum multifamily multipoint lod score of 7.15 were obtained for marker D13S1253 at map position 35 cM when presumptively affected persons were modeled as unknown (a maximum multipoint score of 4.88 was obtained when presumptively affected persons were modeled as unaffected).   \n", "CONCLUSION These data suggest that a gene for severe pediatric GER maps to chromosome 13q14.", "JAMA.", "2000;284:325-334"], "structured": true}
{"doc_id": 12428497, "title": "Accelerating Policy Decisions to Adopt Haemophilus influenzae Type b Vaccine: A Global, Multivariable Analysis", "abstract": ["BACKGROUND Adoption of new and underutilized vaccines by national immunization programs is an essential step towards reducing child mortality.", "Policy decisions to adopt new vaccines in high mortality countries often lag behind decisions in high-income countries.", "Using the case of Haemophilus influenzae type b (Hib) vaccine, this paper endeavors to explain these delays through the analysis of country-level economic, epidemiological, programmatic and policy-related factors, as well as the role of the Global Alliance for Vaccines and Immunisation (GAVI Alliance).   \n", "METHODS AND FINDINGS Data for 147 countries from 1990 to 2007 were analyzed in accelerated failure time models to identify factors that are associated with the time to decision to adopt Hib vaccine.", "In multivariable models that control for Gross National Income, region, and burden of Hib disease, the receipt of GAVI support speeded the time to decision by a factor of 0.37 (95% CI 0.18-0.76), or 63%.", "The presence of two or more neighboring country adopters accelerated decisions to adopt by a factor of 0.50 (95% CI 0.33-0.75).", "For each 1% increase in vaccine price, decisions to adopt are delayed by a factor of 1.02 (95% CI 1.00-1.04).", "Global recommendations and local studies were not associated with time to decision.   \n", "CONCLUSIONS This study substantiates previous findings related to vaccine price and presents new evidence to suggest that GAVI eligibility is associated with accelerated decisions to adopt Hib vaccine.", "The influence of neighboring country decisions was also highly significant, suggesting that approaches to support the adoption of new vaccines should consider supply- and demand-side factors."], "structured": true}
{"doc_id": 12428814, "title": "Haemolysin coregulated protein is an exported receptor and chaperone of type VI secretion substrates.", "abstract": ["Secretion systems require high-fidelity mechanisms to discriminate substrates among the vast cytoplasmic pool of proteins.", "Factors mediating substrate recognition by the type VI secretion system (T6SS) of Gram-negative bacteria, a widespread pathway that translocates effector proteins into target bacterial cells, have not been defined.", "We report that haemolysin coregulated protein (Hcp), a ring-shaped hexamer secreted by all characterized T6SSs, binds specifically to cognate effector molecules.", "Electron microscopy analysis of an Hcp-effector complex from Pseudomonas aeruginosa revealed the effector bound to the inner surface of Hcp.", "Further studies demonstrated that interaction with the Hcp pore is a general requirement for secretion of diverse effectors encompassing several enzymatic classes.", "Though previous models depict Hcp as a static conduit, our data indicate it is a chaperone and receptor of substrates.", "These unique functions of a secreted protein highlight fundamental differences between the export mechanism of T6 and other characterized secretory pathways."], "structured": false}
{"doc_id": 12438901, "title": "Long-term effects of continuing adjuvant tamoxifen to 10 years versus stopping at 5 years after diagnosis of oestrogen receptor-positive breast cancer: ATLAS, a randomised trial", "abstract": ["BACKGROUND For women with oestrogen receptor (ER)-positive early breast cancer, treatment with tamoxifen for 5 years substantially reduces the breast cancer mortality rate throughout the first 15 years after diagnosis.", "We aimed to assess the further effects of continuing tamoxifen to 10 years instead of stopping at 5 years.   \n", "METHODS In the worldwide Adjuvant Tamoxifen: Longer Against Shorter (ATLAS) trial, 12,894 women with early breast cancer who had completed 5 years of treatment with tamoxifen were randomly allocated to continue tamoxifen to 10 years or stop at 5 years (open control).", "Allocation (1:1) was by central computer, using minimisation.", "After entry (between 1996 and 2005), yearly follow-up forms recorded any recurrence, second cancer, hospital admission, or death.", "We report effects on breast cancer outcomes among the 6846 women with ER-positive disease, and side-effects among all women (with positive, negative, or unknown ER status).", "Long-term follow-up still continues.", "This study is registered, number ISRCTN19652633.   \n", "FINDINGS Among women with ER-positive disease, allocation to continue tamoxifen reduced the risk of breast cancer recurrence (617 recurrences in 3428 women allocated to continue vs 711 in 3418 controls, p=0\u00b7002), reduced breast cancer mortality (331 deaths vs 397 deaths, p=0\u00b701), and reduced overall mortality (639 deaths vs 722 deaths, p=0\u00b701).", "The reductions in adverse breast cancer outcomes appeared to be less extreme before than after year 10 (recurrence rate ratio [RR] 0\u00b790 [95% CI 0\u00b779\u20131\u00b702] during years 5\u20139 and 0\u00b775 [0\u00b762\u20130\u00b790] in later years; breast cancer mortality RR 0\u00b797 [0\u00b779\u20131\u00b718] during years 5\u20139 and 0\u00b771 [0\u00b758\u20130\u00b788] in later years).", "The cumulative risk of recurrence during years 5\u201314 was 21\u00b74% for women allocated to continue versus 25\u00b71% for controls; breast cancer mortality during years 5\u201314 was 12\u00b72% for women allocated to continue versus 15\u00b70% for controls (absolute mortality reduction 2\u00b78%).", "Treatment allocation seemed to have no effect on breast cancer outcome among 1248 women with ER-negative disease, and an intermediate effect among 4800 women with unknown ER status.", "Among all 12,894 women, mortality without recurrence from causes other than breast cancer was little affected (691 deaths without recurrence in 6454 women allocated to continue versus 679 deaths in 6440 controls; RR 0\u00b799 [0\u00b789\u20131\u00b710]; p=0\u00b784).", "For the incidence (hospitalisation or death) rates of specific diseases, RRs were as follows: pulmonary embolus 1\u00b787 (95% CI 1\u00b713\u20133\u00b707, p=0\u00b701 [including 0\u00b72% mortality in both treatment groups]), stroke 1\u00b706 (0\u00b783\u20131\u00b736), ischaemic heart disease 0\u00b776 (0\u00b760\u20130\u00b795, p=0\u00b702), and endometrial cancer 1\u00b774 (1\u00b730\u20132\u00b734, p=0\u00b70002).", "The cumulative risk of endometrial cancer during years 5\u201314 was 3\u00b71% (mortality 0\u00b74%) for women allocated to continue versus 1\u00b76% (mortality 0\u00b72%) for controls (absolute mortality increase 0\u00b72%).   \n", "INTERPRETATION For women with ER-positive disease, continuing tamoxifen to 10 years rather than stopping at 5 years produces a further reduction in recurrence and mortality, particularly after year 10.", "These results, taken together with results from previous trials of 5 years of tamoxifen treatment versus none, suggest that 10 years of tamoxifen treatment can approximately halve breast cancer mortality during the second decade after diagnosis.   \n", "FUNDING Cancer Research UK, UK Medical Research Council, AstraZeneca UK, US Army, EU-Biomed."], "structured": true}
{"doc_id": 12440953, "title": "Roles for MicroRNAs in Conferring Robustness to Biological Processes", "abstract": ["Biological systems use a variety of mechanisms to maintain their functions in the face of environmental and genetic perturbations.", "Increasing evidence suggests that, among their roles as posttranscriptional repressors of gene expression, microRNAs (miRNAs) help to confer robustness to biological processes by reinforcing transcriptional programs and attenuating aberrant transcripts, and they may in some network contexts help suppress random fluctuations in transcript copy number.", "These activities have important consequences for normal development and physiology, disease, and evolution.", "Here, we will discuss examples and principles of miRNAs that contribute to robustness in animal systems."], "structured": false}
{"doc_id": 12442311, "title": "Six-Year Follow-Up of Impact of Co-proxamol Withdrawal in England and Wales on Prescribing and Deaths: Time-Series Study", "abstract": ["BACKGROUND The analgesic co-proxamol (paracetamol/dextropropoxyphene combination) has been widely involved in fatal poisoning.", "Concerns about its safety/effectiveness profile and widespread use for suicidal poisoning prompted its withdrawal in the UK in 2005, with partial withdrawal between 2005 and 2007, and full withdrawal in 2008.", "Our objective in this study was to assess the association between co-proxamol withdrawal and prescribing and deaths in England and Wales in 2005-2010 compared with 1998-2004, including estimation of possible substitution effects by other analgesics.   \n", "METHODS AND FINDINGS We obtained prescribing data from the NHS Health and Social Care Information Centre (England) and Prescribing Services Partneriaeth Cydwasanaethau GIG Cymru (Wales), and mortality data from the Office for National Statistics.", "We carried out an interrupted time-series analysis of prescribing and deaths (suicide, open verdicts, accidental poisonings) involving single analgesics.", "The reduction in prescribing of co-proxamol following its withdrawal in 2005 was accompanied by increases in prescribing of several other analgesics (co-codamol, paracetamol, codeine, co-dydramol, tramadol, oxycodone, and morphine) during 2005-2010 compared with 1998-2004.", "These changes were associated with major reductions in deaths due to poisoning with co-proxamol receiving verdicts of suicide and undetermined cause of -21 deaths (95% CI -34 to -8) per quarter, equating to approximately 500 fewer suicide deaths (-61%) over the 6 years 2005-2010, and -25 deaths (95% CI -38 to -12) per quarter, equating to 600 fewer deaths (-62%) when accidental poisoning deaths were included.", "There was little observed change in deaths involving other analgesics, apart from an increase in oxycodone poisonings, but numbers were small.", "Limitations were that the study was based on deaths involving single drugs alone and changes in deaths involving prescribed morphine could not be assessed.   \n", "CONCLUSIONS During the 6 years following the withdrawal of co-proxamol in the UK, there was a major reduction in poisoning deaths involving this drug, without apparent significant increase in deaths involving other analgesics."], "structured": true}
{"doc_id": 12443371, "title": "Apolipoprotein E genotype and concussion in college athletes.", "abstract": ["OBJECTIVE To evaluate the association between apolipoprotein E (APOE) polymorphisms (E2, C/T Arg158Cys; E4, T/C Cys112Arg; and promoter, g-219t) and the history of concussion in college athletes.", "We hypothesized that carrying 1 or more APOE rare (or minor) allele assessed in this study would be associated with having a history of 1 or more concussions.   \n", "DESIGN Multicenter cross-sectional study.   \n", "SETTING University athletic facilities.   \n", "PARTICIPANTS One hundred ninety-six male football (n = 163) and female soccer (n = 33) college athletes volunteered.   \n", "INTERVENTIONS Written concussion history questionnaire and saliva samples for genotyping.   \n", "MAIN OUTCOME MEASURES Self-reported history of a documented concussion and rare APOE genotype (E2, E4, promoter).   \n", "RESULTS There was a significant association (Wald \u03c7\u00b2 = 3.82; P = 0.05; odds ratio = 9.8) between carrying all APOE rare alleles and the history of a previous concussion.", "There was also a significant association (Wald \u03c7\u00b2 = 3.96, P = 0.04, odds ratio = 8.4) between carrying the APOE promoter minor allele and experiencing 2 or more concussions.   \n", "CONCLUSIONS Carriers of all 3 APOE rare (or minor) alleles assessed in this study were nearly 10 times more likely to report a previous concussion and may be at a greater risk of concussion versus noncarriers.", "Promoter minor allele carriers were 8.4 times more likely to report multiple concussions and may be at a greater risk of multiple concussions versus noncarriers.", "Research involving larger samples of individuals with multiple concussions and carriers of multiple APOE rare alleles is warranted."], "structured": true}
{"doc_id": 12451492, "title": "Plasma soluble corin and N-terminal pro-atrial natriuretic peptide levels in pregnancy induced hypertension.", "abstract": ["OBJECTIVE One of the theories involved in the pathogenesis of pregnancy induced hypertension involves salt and water retention.", "We aimed to measure the proenzyme convertase corin, responsible for pro-atrial natriuretic peptide (ANP) cleavage to active ANP, in plasma of hypertensive pregnant females.   ", "STUDY DESIGN Sixty pregnant females suffering from pregnancy induced hypertension in second and third trimesters of pregnancy were compared to twenty eight healthy pregnant females of the same gestational period.", "Concomitant urine and plasma samples were collected for the determination of some biochemical parameters.", "Plasma soluble corin and N-terminal (NT) pro-ANP (1-98) values were determined in both groups using enzyme immunoassays.   \n", "RESULTS Plasma soluble corin mean value was significantly higher in the patient group compared to the control group.", "Upon dividing the patient group according to blood pressure, plasma NT pro-ANP showed significantly higher mean value in the group with blood pressure\u2a7e140/90mmHg compared to the group with blood pressure<140/90mmHg and control group.   \n", "CONCLUSIONS High plasma soluble corin and NT pro-ANP values in hypertensive pregnant females particularly those with blood pressure\u2a7e140/90mmHg speculates an ANP receptor/ post receptor signaling defect, which would aggravate the pregnancy induced hypertensive state."], "structured": true}
{"doc_id": 12462961, "title": "GATA-4 and GATA-6 modulate tissue-specific transcription of the human gene for P450c17 by direct interaction with Sp1.", "abstract": ["Cytochrome P450c17 catalyzes steroidogenic 17alpha-hydroxylase and 17,20 lyase activities.", "Expression of the gene for P450c17 is cAMP dependent, tissue specific, developmentally programmed, and varies among species.", "Binding of Sp1, Sp3, and NF1-C (nuclear factor 1-C) to the first 227 bp of 5'flanking DNA (-227/LUC) is crucial for basal transcription in human NCI-H295A adrenal cells.", "Human placental JEG-3 cells contain Sp1, Sp3, and NF1, but do not express -227/LUC, even when transfected with a vector expressing steroidogenic factor 1 (SF-1).", "Therefore, other factors are essential for basal expression of P450c17.", "Deoxyribonuclease I footprinting and EMSAs identified a GATA consensus site at -64/-58 and an SF-1 site at -58/-50.", "RT-PCR identified GATA-4, GATA-6, and SF-1 in NCI-H295A cells and GATA-2 and GATA-3, but not GATA-4, GATA-6, or SF-1 in JEG-3 cells.", "Cotransfection of either GATA-4 or GATA-6 without SF-1 activated -227/LUC in JEG-3 cells, but cotransfection of GATA-2 or GATA-3 with or without SF-1 did not.", "Surprisingly, mutation of the GATA binding site in -227/LUC increased GATA-4 or GATA-6 induced activity, whereas mutation of the Sp1/Sp3 site decreased it.", "Furthermore, promoter constructs including the GATA site, but excluding the Sp1/Sp3 site at -196/-188, were not activated by GATA-4 or GATA-6, suggesting an interaction between Sp1/Sp3 and GATA-4 or GATA-6.", "Glutathione-S-transferase pull-down experiments and coimmunoprecipitation demonstrated interaction between GATA-4 or GATA-6 and Sp1, but not Sp3.", "Chromatin immunoprecipitation assays confirmed that this GATA-4/6 interaction with Sp1 occurred at the Sp site in the P450c17 promoter in NCI-H295A cells.", "Demethylation with 5-aza-2-deoxycytidine permitted JEG-3 cells to express endogenous P450c17, SF-1, GATA-4, GATA-6, and transfected -227/LUC.", "Thus, GATA-4 or GATA-6 and Sp1 together regulate expression of P450c17 in adrenal NCI-H295A cells and methylation of P450c17, GATA-4 and GATA-6 silence the expression of P450c17 in placental JEG-3 cells."], "structured": false}
{"doc_id": 12470783, "title": "Performance of an abbreviated version of the Lubben Social Network Scale among three European community-dwelling older adult populations.", "abstract": ["PURPOSE There is a need for valid and reliable short scales that can be used to assess social networks and social supports and to screen for social isolation in older persons.   \n", "DESIGN AND METHODS The present study is a cross-national and cross-cultural evaluation of the performance of an abbreviated version of the Lubben Social Network Scale (LSNS-6), which was used to screen for social isolation among community-dwelling older adult populations in three European countries.", "Based on the concept of lack of redundancy of social ties we defined clinical cut-points of the LSNS-6 for identifying persons deemed at risk for social isolation.   \n", "RESULTS Among all three samples, the LSNS-6 and two subscales (Family and Friends) demonstrated high levels of internal consistency, stable factor structures, and high correlations with criterion variables.", "The proposed clinical cut-points showed good convergent validity, and classified 20% of the respondents in Hamburg, 11% of those in Solothurn (Switzerland), and 15% of those in London as at risk for social isolation.   ", "IMPLICATIONS We conclude that abbreviated scales such as the LSNS-6 should be considered for inclusion in practice protocols of gerontological practitioners.", "Screening older persons based on the LSNS-6 provides quantitative information on their family and friendship ties, and identifies persons at increased risk for social isolation who might benefit from in-depth assessment and targeted interventions."], "structured": true}
{"doc_id": 12471115, "title": "The PneuCarriage Project: A Multi-Centre Comparative Study to Identify the Best Serotyping Methods for Examining Pneumococcal Carriage in Vaccine Evaluation Studies", "abstract": ["BACKGROUND The pneumococcus is a diverse pathogen whose primary niche is the nasopharynx.", "Over 90 different serotypes exist, and nasopharyngeal carriage of multiple serotypes is common.", "Understanding pneumococcal carriage is essential for evaluating the impact of pneumococcal vaccines.", "Traditional serotyping methods are cumbersome and insufficient for detecting multiple serotype carriage, and there are few data comparing the new methods that have been developed over the past decade.", "We established the PneuCarriage project, a large, international multi-centre study dedicated to the identification of the best pneumococcal serotyping methods for carriage studies.   \n", "METHODS AND FINDINGS Reference sample sets were distributed to 15 research groups for blinded testing.", "Twenty pneumococcal serotyping methods were used to test 81 laboratory-prepared (spiked) samples.", "The five top-performing methods were used to test 260 nasopharyngeal (field) samples collected from children in six high-burden countries.", "Sensitivity and positive predictive value (PPV) were determined for the test methods and the reference method (traditional serotyping of >100 colonies from each sample).", "For the alternate serotyping methods, the overall sensitivity ranged from 1% to 99% (reference method 98%), and PPV from 8% to 100% (reference method 100%), when testing the spiked samples.", "Fifteen methods had \u226570% sensitivity to detect the dominant (major) serotype, whilst only eight methods had \u226570% sensitivity to detect minor serotypes.", "For the field samples, the overall sensitivity ranged from 74.2% to 95.8% (reference method 93.8%), and PPV from 82.2% to 96.4% (reference method 99.6%).", "The microarray had the highest sensitivity (95.8%) and high PPV (93.7%).", "The major limitation of this study is that not all of the available alternative serotyping methods were included.   \n", "CONCLUSIONS Most methods were able to detect the dominant serotype in a sample, but many performed poorly in detecting the minor serotype populations.", "Microarray with a culture amplification step was the top-performing method.", "Results from this comprehensive evaluation will inform future vaccine evaluation and impact studies, particularly in low-income settings, where pneumococcal disease burden remains high."], "structured": true}
{"doc_id": 12486491, "title": "Ribosome-Mediated Specificity in Hox mRNA Translation and Vertebrate Tissue Patterning", "abstract": ["Historically, the ribosome has been viewed as a complex ribozyme with constitutive rather than regulatory capacity in mRNA translation.", "Here we identify mutations of the Ribosomal Protein L38 (Rpl38) gene in mice exhibiting surprising tissue-specific patterning defects, including pronounced homeotic transformations of the axial skeleton.", "In Rpl38 mutant embryos, global protein synthesis is unchanged; however the translation of a select subset of Homeobox mRNAs is perturbed.", "Our data reveal that RPL38 facilitates 80S complex formation on these mRNAs as a regulatory component of the ribosome to confer transcript-specific translational control.", "We further show that Rpl38 expression is markedly enriched in regions of the embryo where loss-of-function phenotypes occur.", "Unexpectedly, a ribosomal protein (RP) expression screen reveals dynamic regulation of individual RPs within the vertebrate embryo.", "Collectively, these findings suggest that RP activity may be highly regulated to impart a new layer of specificity in the control of gene expression and mammalian development."], "structured": false}
{"doc_id": 12489130, "title": "Growth and invasion of human melanomas in human skin grafted to immunodeficient mice.", "abstract": ["An orthotopic model of human melanoma was developed in which malignant cells were injected into human skin grafted to nude and SCID mice.", "Melanoma cells proliferated and invaded the human skin grafts with characteristic patterns.", "Three of six melanomas grew as multiple nodules and infiltered the grafts without major architectural changes in the dermis, whereas the others invaded the dermis along collagen fibers with prominent endothelial vessels.", "By contrast, melanoma cells inoculated into mouse skin grew as diffusely expanding nodules that did not invade the murine dermis.", "In human skin grafts, human melanoma cells were angiogenic for human blood vessels, and murine vessels were only found at the periphery of grafts.", "Tumor cells invaded the human vessels, and four out of seven cell lines metastasized to lungs, suggesting that this model is useful to determine in vivo the interactions between normal and malignant human cells."], "structured": false}
{"doc_id": 12489688, "title": "Myeloperoxidase: friend and foe.", "abstract": ["Neutrophilic polymorphonuclear leukocytes (neutrophils) are highly specialized for their primary function, the phagocytosis and destruction of microorganisms.", "When coated with opsonins (generally complement and/or antibody), microorganisms bind to specific receptors on the surface of the phagocyte and invagination of the cell membrane occurs with the incorporation of the microorganism into an intracellular phagosome.", "There follows a burst of oxygen consumption, and much, if not all, of the extra oxygen consumed is converted to highly reactive oxygen species.", "In addition, the cytoplasmic granules discharge their contents into the phagosome, and death of the ingested microorganism soon follows.", "Among the antimicrobial systems formed in the phagosome is one consisting of myeloperoxidase (MPO), released into the phagosome during the degranulation process, hydrogen peroxide (H2O2), formed by the respiratory burst and a halide, particularly chloride.", "The initial product of the MPO-H2O2-chloride system is hypochlorous acid, and subsequent formation of chlorine, chloramines, hydroxyl radicals, singlet oxygen, and ozone has been proposed.", "These same toxic agents can be released to the outside of the cell, where they may attack normal tissue and thus contribute to the pathogenesis of disease.", "This review will consider the potential sources of H2O2 for the MPO-H2O2-halide system; the toxic products of the MPO system; the evidence for MPO involvement in the microbicidal activity of neutrophils; the involvement of MPO-independent antimicrobial systems; and the role of the MPO system in tissue injury.", "It is concluded that the MPO system plays an important role in the microbicidal activity of phagocytes."], "structured": false}
{"doc_id": 12513042, "title": "Role of microsomal prostaglandin E synthase-1 in the facilitation of angiogenesis and the healing of gastric ulcers.", "abstract": ["The importance of prostaglandin E(2) in various pathophysiological events emphasizes the necessity of understanding the role of PGE synthases (PGESs) in vivo.", "However, there has been no report on the functional relevance of microsomal PGES-1 (mPGES-1) to the physiological healing processes of gastric ulcers, or to angiogenesis, which is indispensable to the healing processes.", "In this report, we tested whether mPGES-1 plays a role in the healing of gastric ulcers and in the enhancement of angiogenesis using mPGES-1 knockout mice (mPGES-1 KO mice) and their wild-type (WT) counterparts.", "Gastric ulcers were induced by the serosal application of 100% acetic acid, and the areas of the ulcers were measured thereafter.", "mPGES-1 together with cyclooxygenase-2 were induced in the granulation tissues compared with normal stomach tissues.", "The healing of acetic acid-induced ulcers was significantly delayed in mPGES-1 KO mice compared with WT.", "This was accompanied with reduced angiogenesis in ulcer granulation tissues, as estimated by CD31 mRNA levels determined by real-time PCR and the microvessel density in granulation tissues.", "The mRNA levels of proangiogenic growth factors, such as transforming growth factor-\u03b2, basic fibroblast growth factor, and connective tissue growth factor in ulcer granulation tissues determined were reduced in mPGES-1 KO mice compared with WT.", "The present results suggest that mPGES-1 enhances the ulcer-healing processes and the angiogenesis indispensable to ulcer healing, and that a selective mPGES-1 inhibitor should be used with care in patients with gastric ulcers."], "structured": false}
{"doc_id": 12513972, "title": "Echocardiographic Evidence of Innate Aortopathy in the Human Intracranial Aneurysm", "abstract": ["BACKGROUND Intracranial aneurysm (IA) is significantly more prevalent in patients with coarctation of the aorta or bicuspid aortic valve than in the general population, suggesting a common pathophysiology connecting IA and aortopathy.", "Here, we analyzed echocardiographic aortic root dimension (ARD) in patients with IA to confirm this possibility.   \n", "METHODS From January 2008 to December 2010, 260 consecutive patients with IA who were admitted to our institution for coil embolization or for acute stroke management and who also underwent echocardiography were enrolled.", "We hypothesized that patients with large, ruptured, or multiple IAs are more likely to harbor co-prevalent aortopathy as measured by ARD compared to patients with small, isolated, unruptured IAs.", "Eccentric group was defined as patients aged <55 years with at least one ruptured aneurysm, an aneurysm \u22657 mm in size, or multiple aneurysms; the remainder was classified into a non-eccentric group.", "Clinical, angiographic, and echocardiographic findings of the two groups were compared.   \n", "RESULTS ARD was significantly larger in the eccentric group than in the non-eccentric group (P = 0.049), and the difference was confirmed by multivariable analysis (P = 0.02).", "Subgroup analysis of patients aged <55 years showed similar result for ARD (P = 0.03), whereas hypertension was more associated with the non-eccentric group (P = 0.01).", "In addition, height was inversely related to aneurysm size after adjustment for age, sex, weight, ARD, smoking status, and number of aneurysms (P = 0.004).   \n", "CONCLUSIONS A certain group of IA patients share a common intrinsic wall defect with aortopathy.", "Shared neural crest cell origin may give rise to this phenomenon."], "structured": true}
{"doc_id": 12549585, "title": "Aortic and large artery compliance in end-stage renal failure.", "abstract": ["Pulse wave velocity (PWV) was measured in the aorta, right leg and arm of 90 control subjects (CS) and 92 hemodialysis patients (HD) of the same age and mean arterial pressure (MAP).", "Blood chemistry, including blood lipids, and echographic dimensions of the aorta, were measured in all subjects.", "Presence of aortic calcification was evaluated by abdominal X-ray and echography.", "Whereas femoral and brachial PWV were only slightly increased in HD (P less than 0.05), the aortic PWV was significantly elevated (1113 +/-", "319 cm/sec) in comparison with CS (965 +/- 216 cm/sec; P = 0.0016).", "Aortic diameters were larger in HD, both at the root of aorta (32.7 +/- 4 vs. 28.2 +/-", "2.8 mm; P less than 0.0001) and aortic bifurcation (16.9 +/- 3.1 vs. 14.6 +/-", "2.2 mm; P less than 0.0001).", "Although the MAP was similar in HD (109.9 +/-", "19.3 mm Hg) and CS (110.2 +/-", "17.2 mm Hg), the pulse pressure was significantly increased in HD patients (76.6 +/- 23.7 vs. 63.9 +/-", "22 mm Hg; P = 0.007).", "In the two populations, aortic PWV was found to increase with age (P less than 0.0001) and MAP (P less than 0.0001).", "The presence of aortic calcification showed only a borderline relationship with the increase in aortic PWV (P = 0.050 in CS and P = 0.069 in HD).", "As change in PWV is directly related to change in distensibility, and the aortic diameters were increased in HD, these results indicate that aortic wall compliance is decreased in HD, resulting in an increase in the pulsatile component of arterial pressure.(ABSTRACT TRUNCATED AT 250 WORDS)"], "structured": false}
{"doc_id": 12552297, "title": "The DNA polymerase \u03bb is required for the repair of non-compatible DNA double strand breaks by NHEJ in mammalian cells", "abstract": ["DNA polymerase lambda (pol\u03bb) is a recently identified DNA polymerase whose cellular function remains elusive.", "Here we show, that pol\u03bb participates at the molecular level in a chromosomal context, in the repair of DNA double strand breaks (DSB) via non-homologous end joining (NHEJ) in mammalian cells.", "The expression of a catalytically inactive form of pol\u03bb (pol\u03bbDN) decreases the frequency of NHEJ events in response to I-Sce-I-induced DSB whereas inactivated forms of its homologues pol\u03b2 and pol\u03bc do not.", "Only events requiring DNA end processing before ligation are affected; this defect is associated with large deletions arising in the vicinity of the induced DSB.", "Furthermore, pol\u03bbDN-expressing cells exhibit increased sensitization and genomic instability in response to ionizing radiation similar to that of NHEJ-defective cells.", "Our data support a requirement for pol\u03bb in repairing a subset of DSB in genomic DNA, thereby contributing to the maintenance of genetic stability mediated by the NHEJ pathway."], "structured": false}
{"doc_id": 12561083, "title": "Angina with \"normal\" coronary arteries: sex differences in outcomes.", "abstract": ["BACKGROUND Several studies have demonstrated that women with nonobstructive coronary disease have a high rate of subsequent investigations, rehospitalizations for recurrent chest pain, and repeat coronary angiography.", "The sex specificity of this finding is unclear.", "We therefore undertook an evaluation of sex differences in rehospitalization for acute coronary syndrome (ACS) or chest pain in patients with \"angiographically normal\" coronaries.   \n", "METHODS A retrospective cohort study using prospectively collected angiographic and clinical data on all patients in British Columbia, Canada, presenting for their first cardiac catheterization with suspected ischemic heart disease but angiographically normal coronaries.   \n", "RESULTS Among 32,856 patients, 7.1% of men versus 23.3% of women were angiographically normal (P < .001).", "Among angiographically normal patients, women were older and more likely to present with hypertension, prior stroke, chronic obstructive pulmonary disease, and peripheral vascular disease than men, but Canadian Cardiovascular Society class of angina did not vary by sex.", "Within 1 year, 1.0% died, (19 women, 18 men, P = .27) and 0.6% had a stroke (13 women, 9 men, P = .91).", "Readmission to hospital for ACS or chest pain requiring catheterization was significantly higher in women compared to men (adjusted OR 4.06; 95% CI 1.15-14.31).   \n", "CONCLUSIONS In a contemporary, population-based cohort presenting for cardiac catheterization for suspected ischemia, women with angiographically normal coronaries were >4 times more likely to be readmitted to hospital for ACS/chest pain within 180 days compared to men.", "The observed sex difference has important social and economic implications and suggests that traditional diagnostic methods may not be optimal for women."], "structured": true}
{"doc_id": 12580014, "title": "Keratin-dependent regulation of Aire and gene expression in skin tumor keratinocytes", "abstract": ["Expression of the intermediate filament protein keratin 17 (K17) is robustly upregulated in inflammatory skin diseases and in many tumors originating in stratified and pseudostratified epithelia.", "We report that autoimmune regulator (Aire), a transcriptional regulator, is inducibly expressed in human and mouse tumor keratinocytes in a K17-dependent manner and is required for timely onset of Gli2-induced skin tumorigenesis in mice.", "The induction of Aire mRNA in keratinocytes depends on a functional interaction between K17 and the heterogeneous nuclear ribonucleoprotein hnRNP K. Further, K17 colocalizes with Aire protein in the nucleus of tumor-prone keratinocytes, and each factor is bound to a specific promoter region featuring an NF-\u03baB consensus sequence in a relevant subset of K17- and Aire-dependent proinflammatory genes.", "These findings provide radically new insight into keratin intermediate filament and Aire function, along with a molecular basis for the K17-dependent amplification of inflammatory and immune responses in diseased epithelia."], "structured": false}
{"doc_id": 12582729, "title": "Flow-Dependent Regulation of Kruppel-Like Factor 2 Is Mediated by MicroRNA-92a.", "abstract": ["BACKGROUND Upregulated by atheroprotective flow, the transcription factor Kr\u00fcppel-like factor 2 (KLF2) is crucial for maintaining endothelial function.", "MicroRNAs (miRNAs) are noncoding small RNAs that regulate gene expression at the posttranscriptional level.", "We examined the role of miRNAs, particularly miR-92a, in the atheroprotective flow-regulated KLF2.   \n", "METHODS AND RESULTS Dicer knockdown increased the level of KLF2 mRNA in human umbilical vein endothelial cells, suggesting that KLF2 is regulated by miRNA.", "In silico analysis predicted that miR-92a could bind to the 3' untranslated region of KLF2 mRNA.", "Overexpression of miR-92a decreased the expression of KLF2 and the KLF2-regulated endothelial nitric oxide synthase and thrombomodulin at mRNA and protein levels.", "A complementary finding is that miR-92a inhibitor increased the mRNA and protein expression of KLF2, endothelial nitric oxide synthase, and thrombomodulin.", "Subsequent studies revealed that atheroprotective laminar flow downregulated the level of miR-92a precursor to induce KLF2, and the level of this flow-induced KLF2 was reduced by miR-92a precursor.", "Furthermore, miR-92a level was lower in human umbilical vein endothelial cells exposed to the atheroprotective pulsatile shear flow than under atheroprone oscillatory shear flow.", "Anti-Ago1/2 immunoprecipitation coupled with real-time polymerase chain reaction revealed that pulsatile shear flow decreased the functional targeting of miR-92a precursor/KLF2 mRNA in human umbilical vein endothelial cells.", "Consistent with these findings, mouse carotid arteries receiving miR-92a precursor exhibited impaired vasodilatory response to flow.   \n", "CONCLUSIONS Atheroprotective flow patterns decrease the level of miR-92a, which in turn increases KLF2 expression to maintain endothelial homeostasis."], "structured": true}
{"doc_id": 12584053, "title": "Effectiveness of a diabetes education and self management programme (DESMOND) for people with newly diagnosed type 2 diabetes mellitus: three year follow-up of a cluster randomised controlled trial in primary care", "abstract": ["OBJECTIVE To measure whether the benefits of a single education and self management structured programme for people with newly diagnosed type 2 diabetes mellitus are sustained at three years.   \n", "DESIGN Three year follow-up of a multicentre cluster randomised controlled trial in primary care, with randomisation at practice level.   \n", "SETTING 207 general practices in 13 primary care sites in the United Kingdom.   \n", "PARTICIPANTS 731 of the 824 participants included in the original trial were eligible for follow-up.", "Biomedical data were collected on 604 (82.6%) and questionnaire data on 513 (70.1%) participants.   \n", "INTERVENTION A structured group education programme for six hours delivered in the community by two trained healthcare professional educators compared with usual care.   \n", "MAIN OUTCOME MEASURES The primary outcome was glycated haemoglobin (HbA(1c)) levels.", "The secondary outcomes were blood pressure, weight, blood lipid levels, smoking status, physical activity, quality of life, beliefs about illness, depression, emotional impact of diabetes, and drug use at three years.   \n", "RESULTS HbA(1c) levels at three years had decreased in both groups.", "After adjusting for baseline and cluster the difference was not significant (difference -0.02, 95% confidence interval -0.22 to 0.17).", "The groups did not differ for the other biomedical and lifestyle outcomes and drug use.", "The significant benefits in the intervention group across four out of five health beliefs seen at 12 months were sustained at three years (P<0.01).", "Depression scores and quality of life did not differ at three years.   \n", "CONCLUSION A single programme for people with newly diagnosed type 2 diabetes mellitus showed no difference in biomedical or lifestyle outcomes at three years although there were sustained improvements in some illness beliefs.   \n", "TRIAL REGISTRATION Current Controlled Trials ISRCTN17844016."], "structured": true}
{"doc_id": 12588500, "title": "Acetylation of Histone H3 Lysine 56 Regulates Replication-Coupled Nucleosome Assembly", "abstract": ["Chromatin assembly factor 1 (CAF-1) and Rtt106 participate in the deposition of newly synthesized histones onto replicating DNA to form nucleosomes.", "This process is critical for the maintenance of genome stability and inheritance of functionally specialized chromatin structures in proliferating cells.", "However, the molecular functions of the acetylation of newly synthesized histones in this DNA replication-coupled nucleosome assembly pathway remain enigmatic.", "Here we show that histone H3 acetylated at lysine 56 (H3K56Ac) is incorporated onto replicating DNA and, by increasing the binding affinity of CAF-1 and Rtt106 for histone H3, H3K56Ac enhances the ability of these histone chaperones to assemble DNA into nucleosomes.", "Genetic analysis indicates that H3K56Ac acts in a nonredundant manner with the acetylation of the N-terminal residues of H3 and H4 in nucleosome assembly.", "These results reveal a mechanism by which H3K56Ac regulates replication-coupled nucleosome assembly mediated by CAF-1 and Rtt106."], "structured": false}
{"doc_id": 12622860, "title": "Selective inhibition of Ras-dependent cell growth by farnesylthiosalisylic acid.", "abstract": ["S-trans,trans-Farnesylthiosalicylic acid (FTS) is a novel farnesylated rigid carboxylic acid derivative.", "In cell-free systems, it acts as a potent competitive inhibitor (Ki = 2.6 microM) of the enzyme prenylated protein methyltransferase (PPMTase), which methylates the carboxyl-terminal S-prenylcysteine in a large number of prenylated proteins including Ras.", "In such systems, FTS inhibits Ras methylation but not Ras farnesylation.", "Inhibition of the PPMTase by FTS in homogenates or membranes of a variety of tissues and cell lines is inferred from a block in the methylation of exogenously added substrates such as N-acetyl-S-trans,trans-farnesyl-L-cysteine and of endogenous substrates including small GTP-binding proteins.", "FTS can also inhibit methylation of these proteins in intact cells (e.g. in Rat-1 fibroblasts, Ras-transformed Rat-1, and B16 melanoma cells).", "Unlike in cell-free systems, however, relatively high concentrations of FTS (50-100 microM) are required for partial blocking (10-40%) of protein methylation in the intact cells.", "Thus, FTS is a weak inhibitor of methylation in intact cells.", "Because methylation is the last step in the processing of Ras and related proteins, FTS is not likely to affect steps that precede it, e.g. protein prenylation.", "This may explain why the growth and gross morphology of a variety of cultured cell types (including Chinese hamster ovary, NIH3T3, Rat1, B16 melanoma, and PC12) is not affected by up to 25 microM FTS and is consistent with the observed lack of FTS-induced cytotoxicity.", "Nevertheless, FTS reduces the levels of Ras in cell membranes and can inhibit Ras-dependent cell growth in vitro, independently of methylation.", "It inhibits the growth of human Ha-ras-transformed cells (EJ cells) and reverses their transformed morphology in a dose-dependent manner (0.1-10 microM).", "The drug does not interfere with the growth of cells transformed by v-Raf or T-antigen but inhibits the growth of ErbB2-transformed cells and blocks the mitogenic effects of epidermal and basic fibroblast growth factors, thus implying its selectivity toward Ras growth signaling, possibly via modulation of Ras-Raf communication.", "Taken together, the results raise the possibility that FTS may specifically interfere with the interaction of Ras with a farnesylcysteine recognition domain in the cell membrane.(ABSTRACT TRUNCATED AT 400 WORDS)"], "structured": false}
{"doc_id": 12631182, "title": "NADPH oxidase controls phagosomal pH and antigen cross-presentation in human dendritic cells.", "abstract": ["The phagocyte NADPH oxidase (NOX2) is critical for the bactericidal activity of phagocytic cells and plays a major role in innate immunity.", "We showed recently that NOX2 activity in mouse dendritic cells (DCs) prevents acidification of phagosomes, promoting antigen cross-presentation.", "In order to investigate the role of NOX2 in the regulation of the phagosomal pH in human DCs, we analyzed the production of reactive oxygen species (ROS) and the phagosomal/endosomal pH in monocyte-derived DCs and macrophages (M(diameter)s) from healthy donors or patients with chronic granulomatous disease (CGD).", "As expected, we found that human M(diameter)s acidify their phagosomes more efficiently than human DCs.", "Accordingly, the expression of the vacuolar proton ATPase (V-H(+)-ATPase) was higher in M(diameter)s than in DCs.", "Phagosomal ROS production, however, was also higher in M(diameter)s than in DCs, due to higher levels of gp91phox expression and recruitment to phagosomes.", "In contrast, in the absence of active NOX2, the phagosomal and endosomal pH decreased.", "Both in the presence of a NOX2 inhibitor and in DCs derived from patients with CGD, the cross-presentation of 2 model tumor antigens was impaired.", "We conclude that NOX2 activity participates in the regulation of the phagosomal and endosomal pH in human DCs, and is required for efficient antigen cross-presentation."], "structured": false}
{"doc_id": 12631697, "title": "Activation of fast skeletal muscle troponin as a potential therapeutic approach for treating neuromuscular diseases", "abstract": ["Limited neural input results in muscle weakness in neuromuscular disease because of a reduction in the density of muscle innervation, the rate of neuromuscular junction activation or the efficiency of synaptic transmission.", "We developed a small-molecule fast-skeletal-troponin activator, CK-2017357, as a means to increase muscle strength by amplifying the response of muscle when neural input is otherwise diminished secondary to neuromuscular disease.", "Binding selectively to the fast-skeletal-troponin complex, CK-2017357 slows the rate of calcium release from troponin C and sensitizes muscle to calcium.", "As a consequence, the force-calcium relationship of muscle fibers shifts leftwards, as does the force-frequency relationship of a nerve-muscle pair, so that CK-2017357 increases the production of muscle force in situ at sub-maximal nerve stimulation rates.", "Notably, we show that sensitization of the fast-skeletal-troponin complex to calcium improves muscle force and grip strength immediately after administration of single doses of CK-2017357 in a model of the neuromuscular disease myasthenia gravis.", "Troponin activation may provide a new therapeutic approach to improve physical activity in diseases where neuromuscular function is compromised."], "structured": false}
{"doc_id": 12640810, "title": "Cortactin regulates cofilin and N-WASp activities to control the stages of invadopodium assembly and maturation", "abstract": ["Invadopodia are matrix-degrading membrane protrusions in invasive carcinoma cells.", "The mechanisms regulating invadopodium assembly and maturation are not understood.", "We have dissected the stages of invadopodium assembly and maturation and show that invadopodia use cortactin phosphorylation as a master switch during these processes.", "In particular, cortactin phosphorylation was found to regulate cofilin and Arp2/3 complex-dependent actin polymerization.", "Cortactin directly binds cofilin and inhibits its severing activity.", "Cortactin phosphorylation is required to release this inhibition so cofilin can sever actin filaments to create barbed ends at invadopodia to support Arp2/3-dependent actin polymerization.", "After barbed end formation, cortactin is dephosphorylated, which blocks cofilin severing activity thereby stabilizing invadopodia.", "These findings identify novel mechanisms for actin polymerization in the invadopodia of metastatic carcinoma cells and define four distinct stages of invadopodium assembly and maturation consisting of invadopodium precursor formation, actin polymerization, stabilization, and matrix degradation."], "structured": false}
{"doc_id": 12641252, "title": "Calreticulin exposure dictates the immunogenicity of cancer cell death", "abstract": ["Anthracyclin-treated tumor cells are particularly effective in eliciting an anticancer immune response, whereas other DNA-damaging agents such as etoposide and mitomycin C do not induce immunogenic cell death.", "Here we show that anthracyclins induce the rapid, preapoptotic translocation of calreticulin (CRT) to the cell surface.", "Blockade or knockdown of CRT suppressed the phagocytosis of anthracyclin-treated tumor cells by dendritic cells and abolished their immunogenicity in mice.", "The anthracyclin-induced CRT translocation was mimicked by inhibition of the protein phosphatase 1/GADD34 complex.", "Administration of recombinant CRT or inhibitors of protein phosphatase 1/GADD34 restored the immunogenicity of cell death elicited by etoposide and mitomycin C, and enhanced their antitumor effects in vivo.", "These data identify CRT as a key feature determining anticancer immune responses and delineate a possible strategy for immunogenic chemotherapy."], "structured": false}
{"doc_id": 12642224, "title": "In vivo disruption of Xenopus U3 snRNA affects ribosomal RNA processing.", "abstract": ["DNA oligonucleotide complementary to sequences in the 5' third of U3 snRNA were injected into Xenopus oocyte nuclei to disrupt endogenous U3 snRNA.", "The effect of this treatment on rRNA processing was examined.", "We found that some toads have a single rRNA processing pathway, whereas in other toads, two rRNA processing pathways can coexist in a single oocyte.", "U3 snRNA disruption in toads with the single rRNA processing pathway caused a reduction in 20S and '32S' pre-rRNA.", "In addition, in toads with two rRNA processing pathways, an increase in '36S' pre-rRNA of the second pathway is observed.", "This is the first in vivo demonstration that U3 snRNA plays a role in rRNA processing.", "Cleavage site #3 is at the boundary of ITS 1 and 5.8S and links all of the affected rRNA intermediates: 20S and '32S' are the products of site #3 cleavage in the first pathway and '36S' is the substrate for cleavage at site #3 in the second pathway.", "We postulate that U3 snRNP folds pre-rRNA into a conformation dictating correct cleavage at processing site #3."], "structured": false}
{"doc_id": 12643937, "title": "A genome-wide siRNA screen reveals diverse cellular processes and pathways that mediate genome stability.", "abstract": ["Signaling pathways that respond to DNA damage are essential for the maintenance of genome stability and are linked to many diseases, including cancer.", "Here, a genome-wide siRNA screen was employed to identify additional genes involved in genome stabilization by monitoring phosphorylation of the histone variant H2AX, an early mark of DNA damage.", "We identified hundreds of genes whose downregulation led to elevated levels of H2AX phosphorylation (gammaH2AX) and revealed links to cellular complexes and to genes with unclassified functions.", "We demonstrate a widespread role for mRNA-processing factors in preventing DNA damage, which in some cases is caused by aberrant RNA-DNA structures.", "Furthermore, we connect increased gammaH2AX levels to the neurological disorder Charcot-Marie-Tooth (CMT) syndrome, and we find a role for several CMT proteins in the DNA-damage response.", "These data indicate that preservation of genome stability is mediated by a larger network of biological processes than previously appreciated."], "structured": false}
{"doc_id": 12650610, "title": "Alphavbeta6-Fyn signaling promotes oral cancer progression.", "abstract": ["We have previously shown that the integrin beta6 is neo-expressed in invasive oral squamous cell carcinoma (SCC) and is correlated with oral tumor progression.", "However, the mechanism by which the integrin beta6 promotes oral tumor progression is not well understood.", "The purpose of the present study was to determine whether integrin beta6 signaling activates Fyn and thus promotes oral squamous cell carcinoma progression.", "We analyzed the integrin beta6 signaling complex and investigated the function of these signaling molecules in oral SCC cells.", "We found that, upon ligation of the integrin beta6 with fibronectin, beta6 complexed with Fyn and activated it.", "The activation of Fyn recruited and activated focal adhesion kinase to this complex.", "This complex was necessary to activate Shc and to couple beta6 signaling to the Raf-ERK/MAPK pathway.", "This pathway transcriptionally activated the matrix metalloproteinase-3 gene and promoted oral SCC cell proliferation and experimental metastasis in vivo.", "These findings indicate that integrin beta6 signaling activates Fyn and thus promotes oral cancer progression."], "structured": false}
{"doc_id": 12652963, "title": "miRNA-dependent gene silencing involving Ago2-mediated cleavage of a circular antisense RNA.", "abstract": ["MicroRNAs (miRNAs) are \u223c22 nt non-coding RNAs that typically bind to the 3' UTR of target mRNAs in the cytoplasm, resulting in mRNA destabilization and translational repression.", "Here, we report that miRNAs can also regulate gene expression by targeting non-coding antisense transcripts in human cells.", "Specifically, we show that miR-671 directs cleavage of a circular antisense transcript of the Cerebellar Degeneration-Related protein 1 (CDR1) locus in an Ago2-slicer-dependent manner.", "The resulting downregulation of circular antisense has a concomitant decrease in CDR1 mRNA levels, independently of heterochromatin formation.", "This study provides the first evidence for non-coding antisense transcripts as functional miRNA targets, and a novel regulatory mechanism involving a positive correlation between mRNA and antisense circular RNA levels."], "structured": false}
{"doc_id": 12658073, "title": "Regulation of Serum Amyloid A3 (SAA3) in Mouse Colonic Epithelium and Adipose Tissue by the Intestinal Microbiota", "abstract": ["The gut microbiota has been proposed as an environmental factor that affects the development of metabolic and inflammatory diseases in mammals.", "Recent reports indicate that gut bacteria-derived lipopolysaccharide (LPS) can initiate obesity and insulin resistance in mice; however, the molecular interactions responsible for microbial regulation of host metabolism and mediators of inflammation have not been studied in detail.", "Hepatic serum amyloid A (SAA) proteins are markers and proposed mediators of inflammation that exhibit increased levels in serum of insulin-resistant mice.", "Adipose tissue-derived SAA3 displays monocyte chemotactic activity and may play a role in metabolic inflammation associated with obesity and insulin resistance.", "To investigate a potential mechanistic link between the intestinal microbiota and induction of proinflammatory host factors, we performed molecular analyses of germ-free, conventionally raised and genetically modified Myd88-/- mouse models.", "SAA3 expression was determined to be significantly augmented in adipose (9.9+/-1.9-fold; P<0.001) and colonic tissue (7.0+/-2.3-fold; P<0.05) by the presence of intestinal microbes.", "In the colon, we provided evidence that SAA3 is partially regulated through the Toll-like receptor (TLR)/MyD88/NF-kappaB signaling axis.", "We identified epithelial cells and macrophages as cellular sources of SAA3 in the colon and found that colonic epithelial expression of SAA3 may be part of an NF-kappaB-dependent response to LPS from gut bacteria.", "In vitro experiments showed that LPS treatments of both epithelial cells and macrophages induced SAA3 expression (27.1+/-2.5-fold vs. 1.6+/-0.1-fold, respectively).", "Our data suggest that LPS, and potentially other products of the indigenous gut microbiota, might elevate cytokine expression in tissues and thus exacerbate chronic low-grade inflammation observed in obesity."], "structured": false}
{"doc_id": 12662435, "title": "Reversing the tide \u2014 diagnosis and prevention of T2DM in populations of African descent", "abstract": ["Abstract | Populations of African descent are at the forefront of the worldwide epidemic of type 2 diabetes mellitus (T2DM).", "The burden of T2DM is amplified by diagnosis after preventable complications of the disease have occurred.", "Earlier detection would result in a reduction in undiagnosed T2DM, more accurate statistics, more informed resource allocation and better health.", "An underappreciated factor contributing to undiagnosed T2DM in populations of African descent is that screening tests for hyperglycaemia, specifically, fasting plasma glucose and HbA1c, perform sub\u2010optimally in these populations.", "To offset this problem, combining tests or adding glycated albumin (a nonfasting marker of glycaemia), might be the way forward.", "However, differences in diet, exercise, BMI, environment, gene\u2010environment interactions and the prevalence of sickle cell trait mean that neither diagnostic tests nor interventions will be uniformly effective in individuals of African, Caribbean or African\u2010American descent.", "Among these three populations of African descent, intensive lifestyle interventions have been reported in only the African\u2010American population, in which they have been found to provide effective primary prevention of T2DM but not secondary prevention.", "Owing to a lack of health literacy and poor glycaemic control in Africa and the Caribbean, customized lifestyle interventions might achieve both secondary and primary prevention.", "Overall, diagnosis and prevention of T2DM requires innovative strategies that are sensitive to the diversity that exists within populations of African descent."], "structured": false}
{"doc_id": 12667988, "title": "Biofeedback and relaxation in the treatment of migraine headaches: comparative effectiveness and physiological correlates.", "abstract": ["Twenty-seven migraine headache patients were divided into three equal groups which received thermal biofeedback, frontalis EMG biofeedback, or relaxation training.", "Training was given under \"massed\" practice conditions (nine sessions per week) and consisted of 18 training sessions and six test-generalisation sessions.", "While improvements in headaches were observed in all groups, the best improvements took place in the thermal biofeedback group, which had almost complete elimination of migraine attacks by the end of training, and maintained that performance as long as six months after training.", "Examination of the patterns of skin temperature and EMG changes in the three groups over the course of training also points to a relationship between skin temperature control and reduction in migraine headache symptomatology, and suggests that this relationship is worthy of further investigation."], "structured": false}
{"doc_id": 12669325, "title": "Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes", "abstract": ["High-throughput methods based on chromosome conformation capture have greatly advanced our understanding of the three-dimensional (3D) organization of genomes but are limited in resolution by their reliance on restriction enzymes.", "Here we describe a method called DNase Hi-C for comprehensively mapping global chromatin contacts.", "DNase Hi-C uses DNase I for chromatin fragmentation, leading to greatly improved efficiency and resolution over that of Hi-C. Coupling this method with DNA-capture technology provides a high-throughput approach for targeted mapping of fine-scale chromatin architecture.", "We applied targeted DNase Hi-C to characterize the 3D organization of 998 large intergenic noncoding RNA (lincRNA) promoters in two human cell lines.", "Our results revealed that expression of lincRNAs is tightly controlled by complex mechanisms involving both super-enhancers and the Polycomb repressive complex.", "Our results provide the first glimpse of the cell type-specific 3D organization of lincRNA genes."], "structured": false}
{"doc_id": 12670680, "title": "BASOPHILS AND THE T HELPER 2 ENVIRONMENT CAN PROMOTE THE DEVELOPMENT OF LUPUS NEPHRITIS", "abstract": ["In systemic lupus erythematosus (SLE), self-reactive antibodies can target the kidney (lupus nephritis), leading to functional failure and possible mortality.", "We report that activation of basophils by autoreactive IgE causes their homing to lymph nodes, promoting T helper type 2 (T(H)2) cell differentiation and enhancing the production of self-reactive antibodies that cause lupus-like nephritis in mice lacking the Src family protein tyrosine kinase Lyn (Lyn(-/-) mice).", "Individuals with SLE also have elevated serum IgE, self-reactive IgEs and activated basophils that express CD62 ligand (CD62L) and the major histocompatibility complex (MHC) class II molecule human leukocyte antigen-DR (HLA-DR), parameters that are associated with increased disease activity and active lupus nephritis.", "Basophils were also present in the lymph nodes and spleen of subjects with SLE.", "Thus, in Lyn(-/-) mice, basophils and IgE autoantibodies amplify autoantibody production that leads to lupus nephritis, and in individuals with SLE IgE autoantibodies and activated basophils are factors associated with disease activity and nephritis."], "structured": false}
{"doc_id": 12672066, "title": "Behavioral treatment of obesity in patients encountered in primary care settings: a systematic review.", "abstract": ["IMPORTANCE In 2011, the Centers for Medicare & Medicaid Services (CMS) approved intensive behavioral weight loss counseling for approximately 14 face-to-face, 10- to 15-minute sessions over 6 months for obese beneficiaries in primary care settings, when delivered by physicians and other CMS-defined primary care practitioners.   \n", "OBJECTIVE To conduct a systematic review of behavioral counseling for overweight and obese patients recruited from primary care, as delivered by primary care practitioners working alone or with trained interventionists (eg, medical assistants, registered dietitians), or by trained interventionists working independently.   ", "EVIDENCE REVIEW We searched PubMed, CINAHL, and EMBASE for randomized controlled trials published between January 1980 and June 2014 that recruited overweight and obese patients from primary care; provided behavioral counseling (ie, diet, exercise, and behavioral therapy) for at least 3 months, with at least 6 months of postrandomization follow-up; included at least 15 participants per treatment group and objectively measured weights; and had a comparator, an intention-to-treat analysis, and attrition of less than 30% at 1 year or less than 40% at longer follow-up.   \n", "FINDINGS Review of 3304 abstracts yielded 12 trials, involving 3893 participants, that met inclusion-exclusion criteria and prespecified quality ratings.", "No studies were found in which primary care practitioners delivered counseling that followed the CMS guidelines.", "Mean 6-month weight changes from baseline in the intervention groups ranged from a loss of 0.3 kg to 6.6 kg.", "In the control group, mean change ranged from a gain of 0.9 kg to a loss of 2.0 kg.", "Weight loss in both groups generally declined with longer follow-up (12-24 months).", "Interventions that prescribed both reduced energy intake (eg, \u2265 500 kcal/d) and increased physical activity (eg, \u2265150 minutes a week of walking), with traditional behavioral therapy, generally produced larger weight loss than interventions without all 3 specific components.", "In the former trials, more treatment sessions, delivered in person or by telephone by trained interventionists, were associated with greater mean weight loss and likelihood of patients losing 5% or more of baseline weight.   \n", "CONCLUSIONS AND RELEVANCE Intensive behavioral counseling can induce clinically meaningful weight loss, but there is little research on primary care practitioners providing such care.", "The present findings suggest that a range of trained interventionists, who deliver counseling in person or by telephone, could be considered for treating overweight or obesity in patients encountered in primary care settings."], "structured": true}
{"doc_id": 12685434, "title": "Guanylate binding protein 1 is a novel effector of EGFR-driven invasion in glioblastoma", "abstract": ["Although GBP1 (guanylate binding protein 1) was among the first interferon-inducible proteins identified, its function is still largely unknown.", "Epidermal growth factor receptor (EGFR) activation by amplification or mutation is one of the most frequent genetic lesions in a variety of human tumors.", "These include glioblastoma multiforme (GBM), which is characterized by independent but interrelated features of extensive invasion into normal brain parenchyma, rapid growth, necrosis, and angiogenesis.", "In this study, we show that EGFR activation promoted GBP1 expression in GBM cell lines through a signaling pathway involving Src and p38 mitogen-activated protein kinase.", "Moreover, we identified YY1 (Yin Yang 1) as the downstream transcriptional regulator regulating EGFR-driven GBP1 expression.", "GBP1 was required for EGFR-mediated MMP1 (matrix metalloproteinase 1) expression and glioma cell invasion in vitro.", "Although deregulation of GBP1 expression did not affect glioma cell proliferation, overexpression of GBP1 enhanced glioma cell invasion through MMP1 induction, which required its C-terminal helical domain and was independent of its GTPase activity.", "Reducing GBP1 levels by RNA interference in invasive GBM cells also markedly inhibited their ability to infiltrate the brain parenchyma of mice.", "GBP1 expression was high and positively correlated with EGFR expression in human GBM tumors and cell lines, particularly those of the neural subtype.", "Together, these findings establish GBP1 as a previously unknown link between EGFR activity and MMP1 expression and nominate it as a novel potential therapeutic target for inhibiting GBM invasion."], "structured": false}
{"doc_id": 12691537, "title": "ATP binding to PAN or the 26S ATPases causes association with the 20S proteasome, gate opening, and translocation of unfolded proteins.", "abstract": ["The archaeal ATPase complex PAN, the homolog of the eukaryotic 26S proteasome-regulatory ATPases, was shown to associate transiently with the 20S proteasome upon binding of ATP or ATPgammaS, but not ADP.", "By electron microscopy (EM), PAN appears as a two-ring structure, capping the 20S, and resembles two densities in the 19S complex.", "The N termini of the archaeal 20S alpha subunits were found to function as a gate that prevents entry of seven-residue peptides but allows entry of tetrapeptides.", "Upon association with the 20S particle, PAN stimulates gate opening.", "Although degradation of globular proteins requires ATP hydrolysis, the PAN-20S complex with ATPgammaS translocates and degrades unfolded and denatured proteins.", "Rabbit 26S proteasomes also degrade these unfolded proteins upon ATP binding, without hydrolysis.", "Thus, although unfolding requires energy from ATP hydrolysis, ATP binding alone supports ATPase-20S association, gate opening, and translocation of unfolded substrates into the proteasome, which can occur by facilitated diffusion through the ATPase."], "structured": false}
{"doc_id": 12705056, "title": "Cytokines and anti-cytokine biologicals in autoimmunity: present and future.", "abstract": ["The increasing understanding of the role of cytokines in autoimmunity, and the observation that tumour necrosis factor alpha (TNFalpha) is central to the inflammatory and destructive process common to several human autoimmune diseases, has led to a new generation of therapeutics, the TNFalpha blocking agents.", "In this article, we review the current knowledge of the role of cytokines in autoimmunity as unravelled by studies both in the laboratory and the clinic.", "In addition, we discuss future prospects of the anti-TNFalpha therapy that may involve combination therapy with other anti-cytokine or anti-T cell biologicals, or the use of small chemicals targeting molecules involved in TNFalpha production such as NF-kappaB and p38 MAPK.", "The future developments of anti-TNFalpha and anti-cytokine therapy in general will be interesting."], "structured": false}
{"doc_id": 12709184, "title": "Vegetarian dietary patterns and mortality in Adventist Health Study 2.", "abstract": ["IMPORTANCE Some evidence suggests vegetarian dietary patterns may be associated with reduced mortality, but the relationship is not well established.   \n", "OBJECTIVE To evaluate the association between vegetarian dietary patterns and mortality.   \n", "DESIGN Prospective cohort study; mortality analysis by Cox proportional hazards regression, controlling for important demographic and lifestyle confounders.   \n", "SETTING Adventist Health Study 2 (AHS-2), a large North American cohort.   \n", "PARTICIPANTS A total of 96,469 Seventh-day Adventist men and women recruited between 2002 and 2007, from which an analytic sample of 73,308 participants remained after exclusions.   ", "EXPOSURES Diet was assessed at baseline by a quantitative food frequency questionnaire and categorized into 5 dietary patterns: nonvegetarian, semi-vegetarian, pesco-vegetarian, lacto-ovo-vegetarian, and vegan.   \n", "MAIN OUTCOME AND MEASURE The relationship between vegetarian dietary patterns and all-cause and cause-specific mortality; deaths through 2009 were identified from the National Death Index.   \n", "RESULTS There were 2570 deaths among 73,308 participants during a mean follow-up time of 5.79 years.", "The mortality rate was 6.05 (95% CI, 5.82-6.29) deaths per 1000 person-years.", "The adjusted hazard ratio (HR) for all-cause mortality in all vegetarians combined vs nonvegetarians was 0.88 (95% CI, 0.80-0.97).", "The adjusted HR for all-cause mortality in vegans was 0.85 (95% CI, 0.73-1.01); in lacto-ovo-vegetarians, 0.91 (95% CI, 0.82-1.00); in pesco-vegetarians, 0.81 (95% CI, 0.69-0.94); and in semi-vegetarians, 0.92 (95% CI, 0.75-1.13) compared with nonvegetarians.", "Significant associations with vegetarian diets were detected for cardiovascular mortality, noncardiovascular noncancer mortality, renal mortality, and endocrine mortality.", "Associations in men were larger and more often significant than were those in women.   \n", "CONCLUSIONS AND RELEVANCE Vegetarian diets are associated with lower all-cause mortality and with some reductions in cause-specific mortality.", "Results appeared to be more robust in males.", "These favorable associations should be considered carefully by those offering dietary guidance."], "structured": true}
{"doc_id": 12737132, "title": "TEAD mediates YAP-dependent gene induction and growth control.", "abstract": ["The YAP transcription coactivator has been implicated as an oncogene and is amplified in human cancers.", "Recent studies have established that YAP is phosphorylated and inhibited by the Hippo tumor suppressor pathway.", "Here we demonstrate that the TEAD family transcription factors are essential in mediating YAP-dependent gene expression.", "TEAD is also required for YAP-induced cell growth, oncogenic transformation, and epithelial-mesenchymal transition.", "CTGF is identified as a direct YAP target gene important for cell growth.", "Moreover, the functional relationship between YAP and TEAD is conserved in Drosophila Yki (the YAP homolog) and Scalloped (the TEAD homolog).", "Our study reveals TEAD as a new component in the Hippo pathway playing essential roles in mediating biological functions of YAP."], "structured": false}
{"doc_id": 12742164, "title": "Direct isolation of human central nervous system stem cells.", "abstract": ["Stem cells, which are clonogenic cells with self-renewal and multilineage differentiation properties, have the potential to replace or repair damaged tissue.", "We have directly isolated clonogenic human central nervous system stem cells (hCNS-SC) from fresh human fetal brain tissue, using antibodies to cell surface markers and fluorescence-activated cell sorting.", "These hCNS-SC are phenotypically 5F3 (CD133)(+), 5E12(+), CD34(-), CD45(-), and CD24(-/lo).", "Single CD133(+) CD34(-) CD45(-) sorted cells initiated neurosphere cultures, and the progeny of clonogenic cells could differentiate into both neurons and glial cells.", "Single cells from neurosphere cultures initiated from CD133(+) CD34(-) CD45(-) cells were again replated as single cells and were able to reestablish neurosphere cultures, demonstrating the self-renewal potential of this highly enriched population.", "Upon transplantation into brains of immunodeficient neonatal mice, the sorted/expanded hCNS-SC showed potent engraftment, proliferation, migration, and neural differentiation."], "structured": false}
{"doc_id": 12762485, "title": "p53 mutation in breast cancer. Correlation with cell kinetics and cell of origin.", "abstract": ["AIM Several studies have investigated the expression of the cytokeratins (CKs), vimentin, the epithelial growth factor receptor (EGFR), the oestrogen receptor (ER), and the progesterone receptor (PgR), in breast cancer, but no study has directly compared p53 mutations with these phenotypic and differentiation markers in the same case.", "The present study was designed to provide some of this information.   \n", "METHODS The expression of the p53 and bcl-2 proteins was evaluated by immunohistochemistry in relation to phenotypic characteristics and cellular kinetic parameters (mitotic index and apoptotic index) in 37 cases of ductal carcinoma in situ (DCIS) and 27 cases of infiltrating ductal carcinoma (IDC) of the breast.", "In addition, p53 gene mutation was examined by polymerase chain reaction single strand conformation polymorphism analysis (SSCP).   \n", "RESULTS Thirteen cases (eight DCIS and five IDC) showed expression of CK8, CK14, CK18, vimentin, and EGFR, consistent with a stem cell phenotype, whereas 44 cases (27 DCIS and 17 IDC) showed expression of CK8 and CK1, weak or negative expression of CK18, but were negative for vimentin and EGFR, consistent with a luminal cell phenotype.", "DCIS and IDC cases with a stem cell phenotype were ER/PgR negative and intermediately or poorly differentiated.", "In contrast, the cases with luminal cell phenotype were ER/PgR positive and well or intermediately differentiated.", "In addition, intermediately or poorly differentiated cases with a stem cell phenotype showed higher proliferative activity (per cent of MIB-l positive cells) than did intermediately or well differentiated cases with a luminal cell phenotype.", "Both DCIS and IDC cases with a stem cell phenotype were p53 positive and bcl-2 negative by immunohistochemistry.", "In IDC, p53 expression was associated with a reduction of both mitotic index and apoptotic index compared with DCIS.", "Most of the tumours showing a more differentiated phenotype (luminal) were p53 negative and bcl-2 positive.", "In these cases, cell kinetic parameters increased from DCIS to IDC.", "These data suggest the existence of subsets of DCIS and IDC that, because of their phenotypic characteristics, could be derived from subpopulations of normal breast cells having different control mechanisms of cell proliferation and neoplastic progression.   \n", "CONCLUSIONS These results are compatible with the hypothesis that the phenotype of the cell of origin constrains both tumour phenotype and the choice of genetic events; however, the occurrence of p53 mutants by chance during neoplastic transformation cannot be excluded."], "structured": true}
{"doc_id": 12770738, "title": "Cardiorespiratory fitness and body mass index as predictors of cardiovascular disease mortality among men with diabetes.", "abstract": ["BACKGROUND Questions remain as to whether higher levels of cardiorespiratory fitness, a measure of regular physical activity, are associated with lower risk of cardiovascular disease (CVD) mortality in overweight and obese individuals with diabetes.", "Our objective was to quantify the independent and joint relations of cardiorespiratory fitness (hereafter, fitness) and body mass index (BMI; calculated as weight in kilograms divided by the square of height in meters) with CVD mortality in men with diabetes.   \n", "METHODS This study was conducted using prospective observational data from the Aerobics Center Longitudinal Study.", "Study participants comprised 2316 men with no history of stroke or myocardial infarction and who were diagnosed as having diabetes (mean [SD] age, 50 [10] years); had a medical examination, including a maximal exercise test during 1970 to 1997 with mortality surveillance to December 31, 1998; and had a BMI of 18.5 or greater and less than 35.0.", "The main outcome measure was CVD mortality across levels of fitness with stratification by BMI.   \n", "RESULTS We identified 179 CVD deaths during a mean (SD) follow-up of 15.9 (7.9) years and 36,710 man-years of exposure.", "In a model containing age, examination year, fasting glucose level, systolic blood pressure, parental history of premature CVD, total cholesterol level, cigarette smoking, abnormal resting, and exercise electrocardiograms, a significantly higher adjusted risk of mortality was observed in men with a low fitness level who were normal weight (hazard ratio, 2.7 [95% confidence interval, 1.3-5.7]), overweight (hazard ratio, 2.7 [95% confidence interval, 1.4-5.1]), and class 1 obese (hazard ratio, 2.8 [95% confidence interval, 1.4-5.1]) compared with normal weight men with a high fitness level.   \n", "CONCLUSION In this cohort of men with diabetes, low fitness level was associated with increased risk of CVD mortality within normal weight, overweight, and class 1 obese weight categories."], "structured": true}
{"doc_id": 12779444, "title": "Effect of screening on cervical cancer mortality in England and Wales: analysis of trends with an age period cohort model.", "abstract": ["The number of women dying from cervical cancer in 1997 was 7% lower than in 1996 and has fallen by over 25% since 1992.1 Such rapid change must be at least partly due to cervical screening, although strong cohort effects have caused large fluctuations in cervical mortality in the past.2 We modelled mortality data, taking into account the effects of age and year of birth and looking for trends in time within four age groups to estimate the beneficial effects of cervical screening.  ", "We obtained mortality data, in 5 year age bands, from death registrations in England and Wales and calculated rates using mid-year population estimates.", "Mortality since 1993 was adjusted upwards by 4% because of changes in classification of cause of death.3  We modelled the data assuming that the age specific mortality is the product of a smoothly varying age effect, birth cohort effect, and age dependent \u2026"], "structured": false}
{"doc_id": 12785130, "title": "The regulation of N-methyl-D-aspartate receptors by Src kinase.", "abstract": ["Src family kinases (SFKs) play critical roles in the regulation of many cellular functions by growth factors, G-protein-coupled receptors and ligand-gated ion channels.", "Recent data have shown that SFKs serve as a convergent point of multiple signaling pathways regulating N-methyl-d-aspartate (NMDA) receptors in the central nervous system.", "Multiple SFK molecules, such as Src and Fyn, closely associate with their substrate, NMDA receptors, via indirect and direct binding mechanisms.", "The NMDA receptor is associated with an SFK signaling complex consisting of SFKs; the SFK-activating phosphatase, protein tyrosine phosphatase \u03b1; and the SFK-inactivating kinase, C-terminal Src kinase.", "Early studies have demonstrated that intramolecular interactions with the SH2 or SH3 domain lock SFKs in a closed conformation.", "Disruption of the interdomain interactions can induce the activation of SFKs with multiple signaling pathways involved in regulation of this process.", "The enzyme activity of SFKs appears 'graded', exhibiting different levels coinciding with activation states.", "It has also been proposed that the SH2 and SH3 domains may stimulate catalytic activity of protein tyrosine kinases, such as Abl.", "Recently, it has been found that the enzyme activity of neuronal Src protein is associated with its stability, and that the SH2 and SH3 domain interactions may act not only to constrain the activation of neuronal Src, but also to regulate the enzyme activity of active neuronal Src.", "Collectively, these findings demonstrate novel mechanisms underlying the regulation of SFKs."], "structured": false}
{"doc_id": 12787125, "title": "The art and design of genetic screens: RNA interference", "abstract": ["The remarkable gene knockdown technique of RNAi has opened exciting new avenues for genetic screens in model organisms and human cells.", "Here we describe the current state of the art for RNAi screening, and stress the importance of well-designed assays and of analytical approaches for large-scale screening experiments, from high-throughput screens using simplified homogenous assays to microscopy and whole-animal experiments.", "Like classical genetic screens in the past, the success of large-scale RNAi surveys depends on a careful development of phenotypic assays and their interpretation in a relevant biological context."], "structured": false}
{"doc_id": 12789595, "title": "Computer assisted learning in undergraduate medical education.", "abstract": ["It is becoming \u201ca truth universally acknowledged\u201d that the education of undergraduate medical students will be enhanced through the use of computer assisted learning.", "Access to the wide range of online options illustrated in the figure must surely make learning more exciting, effective, and likely to be retained.", "This assumption is potentially but by no means inevitably correct.  ", "### Box 1: Why fund computer assisted learning?  ", "Computer assisted learning is inevitable \u2014Individual lecturers and departments are already beginning to introduce a wide range of computer based applications, sometimes in a haphazard way.", "Planned and coordinated development is better than indiscriminate expansion  It is convenient and flexible \u2014Courses supported by computer assisted learning applications may require fewer face to face lectures and seminars and place fewer geographical and temporal constraints on staff and students.", "Students at peripheral hospitals or primary care centres may benefit in particular  Unique presentational benefits \u2014Computer presentation is particularly suited to subjects that are visually intensive, detail oriented, and difficult to conceptualise, such as complex biochemical processes or microscopic images.1 Furthermore, \u201cvirtual\u201d cases may reduce the need to use animal or human tissue in learning  Personalised learning \u2014Each learner can progress at his or her preferred pace.", "They can repeat, interrupt, and resume at will, which may have particular advantages for weaker students  Economies of scale \u2014Once an application has been set up, the incremental cost of offering it to additional students is relatively small  Competitive advantage \u2014Potential applicants may use the quality of information technology to discriminate between medical schools.", "A \u201cleading edge\u201d virtual campus is likely to attract good students  Achieves the ultimate goal of higher education \u2014The goal is to link people into learning communities.", "Computer applications, especially the internet and world wide web, are an extremely efficient way of doing this2  Expands pedagogical horizons \u2014The most controversial argument for \u2026 RETURN TO TEXT"], "structured": false}
{"doc_id": 12794099, "title": "Combined Impact of Health Behaviours and Mortality in Men and Women: The EPIC-Norfolk Prospective Population Study", "abstract": ["BACKGROUND There is overwhelming evidence that behavioural factors influence health, but their combined impact on the general population is less well documented.", "We aimed to quantify the potential combined impact of four health behaviours on mortality in men and women living in the general community.   \n", "METHODS AND FINDINGS We examined the prospective relationship between lifestyle and mortality in a prospective population study of 20,244 men and women aged 45-79 y with no known cardiovascular disease or cancer at baseline survey in 1993-1997, living in the general community in the United Kingdom, and followed up to 2006.", "Participants scored one point for each health behaviour: current non-smoking, not physically inactive, moderate alcohol intake (1-14 units a week) and plasma vitamin C >50 mmol/l indicating fruit and vegetable intake of at least five servings a day, for a total score ranging from zero to four.", "After an average 11 y follow-up, the age-, sex-, body mass-, and social class-adjusted relative risks (95% confidence intervals) for all-cause mortality(1,987 deaths) for men and women who had three, two, one, and zero compared to four health behaviours were respectively, 1.39 (1.21-1.60), 1.95 (1.70--2.25), 2.52 (2.13-3.00), and 4.04 (2.95-5.54) p < 0.001 trend.", "The relationships were consistent in subgroups stratified by sex, age, body mass index, and social class, and after excluding deaths within 2 y.", "The trends were strongest for cardiovascular causes.", "The mortality risk for those with four compared to zero health behaviours was equivalent to being 14 y younger in chronological age.   \n", "CONCLUSIONS Four health behaviours combined predict a 4-fold difference in total mortality in men and women, with an estimated impact equivalent to 14 y in chronological age."], "structured": true}
{"doc_id": 12800122, "title": "Increased Cell Bond Tension Governs Cell Sorting at the Drosophila Anteroposterior Compartment Boundary", "abstract": ["Subdividing proliferating tissues into compartments is an evolutionarily conserved strategy of animal development [1-6].", "Signals across boundaries between compartments can result in local expression of secreted proteins organizing growth and patterning of tissues [1-6].", "Sharp and straight interfaces between compartments are crucial for stabilizing the position of such organizers and therefore for precise implementation of body plans.", "Maintaining boundaries in proliferating tissues requires mechanisms to counteract cell rearrangements caused by cell division; however, the nature of such mechanisms remains unclear.", "Here we quantitatively analyzed cell morphology and the response to the laser ablation of cell bonds in the vicinity of the anteroposterior compartment boundary in developing Drosophila wings.", "We found that mechanical tension is approximately 2.5-fold increased on cell bonds along this compartment boundary as compared to the remaining tissue.", "Cell bond tension is decreased in the presence of Y-27632 [7], an inhibitor of Rho-kinase whose main effector is Myosin II [8].", "Simulations using a vertex model [9] demonstrate that a 2.5-fold increase in local cell bond tension suffices to guide the rearrangement of cells after cell division to maintain compartment boundaries.", "Our results provide a physical mechanism in which the local increase in Myosin II-dependent cell bond tension directs cell sorting at compartment boundaries."], "structured": false}
{"doc_id": 12801438, "title": "Plant products as antimicrobial agents.", "abstract": ["The use of and search for drugs and dietary supplements derived from plants have accelerated in recent years.", "Ethnopharmacologists, botanists, microbiologists, and natural-products chemists are combing the Earth for phytochemicals and \"leads\" which could be developed for treatment of infectious diseases.", "While 25 to 50% of current pharmaceuticals are derived from plants, none are used as antimicrobials.", "Traditional healers have long used plants to prevent or cure infectious conditions; Western medicine is trying to duplicate their successes.", "Plants are rich in a wide variety of secondary metabolites, such as tannins, terpenoids, alkaloids, and flavonoids, which have been found in vitro to have antimicrobial properties.", "This review attempts to summarize the current status of botanical screening efforts, as well as in vivo studies of their effectiveness and toxicity.", "The structure and antimicrobial properties of phytochemicals are also addressed.", "Since many of these compounds are currently available as unregulated botanical preparations and their use by the public is increasing rapidly, clinicians need to consider the consequences of patients self-medicating with these preparations."], "structured": false}
{"doc_id": 12804937, "title": "Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences", "abstract": ["Gene expression is a fundamentally stochastic process, with randomness in transcription and translation leading to cell-to-cell variations in mRNA and protein levels.", "This variation appears in organisms ranging from microbes to metazoans, and its characteristics depend both on the biophysical parameters governing gene expression and on gene network structure.", "Stochastic gene expression has important consequences for cellular function, being beneficial in some contexts and harmful in others.", "These situations include the stress response, metabolism, development, the cell cycle, circadian rhythms, and aging."], "structured": false}
{"doc_id": 12805683, "title": "Nuclear Hormone Receptor NHR-49 Controls Fat Consumption and Fatty Acid Composition in C. elegans", "abstract": ["Mammalian nuclear hormone receptors (NHRs), such as liver X receptor, farnesoid X receptor, and peroxisome proliferator-activated receptors (PPARs), precisely control energy metabolism.", "Consequently, these receptors are important targets for the treatment of metabolic diseases, including diabetes and obesity.", "A thorough understanding of NHR fat regulatory networks has been limited, however, by a lack of genetically tractable experimental systems.", "Here we show that deletion of the Caenorhabditis elegans NHR gene nhr-49 yielded worms with elevated fat content and shortened life span.", "Employing a quantitative RT-PCR screen, we found that nhr-49 influenced the expression of 13 genes involved in energy metabolism.", "Indeed, nhr-49 served as a key regulator of fat usage, modulating pathways that control the consumption of fat and maintain a normal balance of fatty acid saturation.", "We found that the two phenotypes of the nhr-49 knockout were linked to distinct pathways and were separable: The high-fat phenotype was due to reduced expression of enzymes in fatty acid \u03b2-oxidation, and the shortened adult life span resulted from impaired expression of a stearoyl-CoA desaturase.", "Despite its sequence relationship with the mammalian hepatocyte nuclear factor 4 receptor, the biological activities of nhr-49 were most similar to those of the mammalian PPARs, implying an evolutionarily conserved role for NHRs in modulating fat consumption and composition.", "Our findings in C. elegans provide novel insights into how NHR regulatory networks are coordinated to govern fat metabolism."], "structured": false}
{"doc_id": 12810152, "title": "Folate and vitamin B6 from diet and supplements in relation to risk of coronary heart disease among women.", "abstract": ["CONTEXT Hyperhomocysteinemia is caused by genetic and lifestyle influences, including low intakes of folate and vitamin B6.", "However, prospective data relating intake of these vitamins to risk of coronary heart disease (CHD) are not available.   \n", "OBJECTIVE To examine intakes of folate and vitamin B6 in relation to the incidence of nonfatal myocardial infarction (MI) and fatal CHD.   \n", "DESIGN Prospective cohort study.   \n", "SETTING AND PATIENTS In 1980, a total of 80082 women from the Nurses' Health Study with no previous history of cardiovascular disease, cancer, hypercholesterolemia, or diabetes completed a detailed food frequency questionnaire from which we derived usual intake of folate and vitamin B6.   \n", "MAIN OUTCOME MEASURE Nonfatal MI and fatal CHD confirmed by World Health Organization criteria.   \n", "RESULTS During 14 years of follow-up, we documented 658 incident cases of nonfatal MI and 281 cases of fatal CHD.", "After controlling for cardiovascular risk factors, including smoking and hypertension and intake of alcohol, fiber, vitamin E, and saturated, polyunsaturated, and trans fat, the relative risks (RRs) of CHD between extreme quintiles were 0.69 (95% confidence interval [CI], 0.55-0.87) for folate (median intake, 696 microg/d vs 158 microg/d) and 0.67 (95% CI, 0.53-0.85) for vitamin B6 (median intake, 4.6 mg/d vs 1.1 mg/d).", "Controlling for the same variables, the RR was 0.55 (95% CI, 0.41-0.74) among women in the highest quintile of both folate and vitamin B6 intake compared with the opposite extreme.", "Risk of CHD was reduced among women who regularly used multiple vitamins (RR=0.76; 95% CI, 0.65-0.90), the major source of folate and vitamin B6, and after excluding multiple vitamin users, among those with higher dietary intakes of folate and vitamin B6.", "In a subgroup analysis, compared with nondrinkers, the inverse association between a high-folate diet and CHD was strongest among women who consumed up to 1 alcoholic beverage per day (RR =0.69; 95% CI, 0.49-0.97) or more than 1 drink per day (RR=0.27; 95% CI, 0.13-0.58).   \n", "CONCLUSION These results suggest that intake of folate and vitamin B6 above the current recommended dietary allowance may be important in the primary prevention of CHD among women."], "structured": true}
{"doc_id": 12821938, "title": "Control of oocyte meiotic maturation and fertilization.", "abstract": ["Sexual reproduction depends upon meiosis for the generation of haploid gamete nuclei, which unite after fertilization to form the diploid zygote.", "The oocytes of most animal species arrest during meiotic prophase, and complete meiosis in response to intercellular signaling in a process called meiotic maturation.", "Oocyte meiotic maturation is defined by the transition between diakinesis and metaphase of meiosis I and is accompanied by nuclear envelope breakdown, rearrangement of the cortical cytoskeleton, and meiotic spindle assembly.", "Thus, the meiotic maturation process is essential for meiosis and prepares the oocyte for fertilization.", "In C. elegans, the processes of meiotic maturation, ovulation, and fertilization are temporally coupled: sperm utilize the major sperm protein as a hormone to trigger oocyte meiotic maturation, and in turn, the maturing oocyte signals its own ovulation thereby facilitating fertilization.", "This chapter highlights recent advances in understanding meiotic maturation signaling and gametic interactions required for fertilization."], "structured": false}
{"doc_id": 12824568, "title": "From Cell Differentiation to Cell Collectives: Bacillus subtilis Uses Division of Labor to Migrate", "abstract": ["The organization of cells, emerging from cell-cell interactions, can give rise to collective properties.", "These properties are adaptive when together cells can face environmental challenges that they separately cannot.", "One particular challenge that is important for microorganisms is migration.", "In this study, we show how flagellum-independent migration is driven by the division of labor of two cell types that appear during Bacillus subtilis sliding motility.", "Cell collectives organize themselves into bundles (called \"van Gogh bundles\") of tightly aligned cell chains that form filamentous loops at the colony edge.", "We show, by time-course microscopy, that these loops migrate by pushing themselves away from the colony.", "The formation of van Gogh bundles depends critically on the synergistic interaction of surfactin-producing and matrix-producing cells.", "We propose that surfactin-producing cells reduce the friction between cells and their substrate, thereby facilitating matrix-producing cells to form bundles.", "The folding properties of these bundles determine the rate of colony expansion.", "Our study illustrates how the simple organization of cells within a community can yield a strong ecological advantage.", "This is a key factor underlying the diverse origins of multicellularity."], "structured": false}
{"doc_id": 12827098, "title": "Tissue-resident macrophages self-maintain locally throughout adult life with minimal contribution from circulating monocytes.", "abstract": ["Despite accumulating evidence suggesting local self-maintenance of tissue macrophages in the steady state, the dogma remains that tissue macrophages derive from monocytes.", "Using parabiosis and fate-mapping approaches, we confirmed that monocytes do not show significant contribution to tissue macrophages in the steady state.", "Similarly, we found that after depletion of lung macrophages, the majority of repopulation occurred by stochastic cellular proliferation in situ in a macrophage colony-stimulating factor (M-Csf)- and granulocyte macrophage (GM)-CSF-dependent manner but independently of interleukin-4.", "We also found that after bone marrow transplantation, host macrophages retained the capacity to expand when the development of donor macrophages was compromised.", "Expansion of host macrophages was functional and prevented the development of alveolar proteinosis in mice transplanted with GM-Csf-receptor-deficient progenitors.", "Collectively, these results indicate that tissue-resident macrophages and circulating monocytes should be classified as mononuclear phagocyte lineages that are independently maintained in the steady state."], "structured": false}
{"doc_id": 12839939, "title": "Registration and real-time visualization of transcranial magnetic stimulation with 3-D MR images", "abstract": ["This paper describes a method for registering and visualizing in real-time the results of transcranial magnetic stimulations (TMS) in physical space on the corresponding anatomical locations in MR images of the brain.", "The method proceeds in three main steps.", "First, the patient scalp is digitized in physical space with a magnetic-field digitizer, following a specific digitization pattern.", "Second, a registration process minimizes the mean square distance between those points and a segmented scalp surface extracted from the magnetic resonance image.", "Following this registration, the physician can follow the change in coil position in real-time through the visualization interface and adjust the coil position to the desired anatomical location.", "Third, amplitude of motor evoked potentials can be projected onto the segmented brain in order to create functional brain maps.", "The registration has subpixel accuracy in a study with simulated data, while we obtain a point to surface root-mean-square error of 1.17/spl plusmn/0.38 mm in a 24 subject study."], "structured": false}
{"doc_id": 12866641, "title": "Enzymatic targeting of the stroma ablates physical barriers to treatment of pancreatic ductal adenocarcinoma.", "abstract": ["Pancreatic ductal adenocarcinomas (PDAs) are characterized by a robust fibroinflammatory response.", "We show here that this desmoplastic reaction generates inordinately high interstitial fluid pressures (IFPs), exceeding those previously measured or theorized for solid tumors, and induces vascular collapse, while presenting substantial barriers to perfusion, diffusion, and convection of small molecule therapeutics.", "We identify hyaluronan, or hyaluronic acid (HA), as the primary matrix determinant of these barriers and show that systemic administration of an enzymatic agent can ablate stromal HA from autochthonous murine PDA, normalize IFP, and re-expand the microvasculature.", "In combination with the standard chemotherapeutic, gemcitabine, the treatment permanently remodels the tumor microenvironment and consistently achieves objective tumor responses, resulting in a near doubling of overall survival."], "structured": false}
{"doc_id": 12869200, "title": "Circulating adiponectin, leptin and adiponectin-leptin ratio and endometrial cancer risk: Evidence from a meta-analysis of epidemiologic studies.", "abstract": ["We performed this meta-analysis of epidemiologic studies to investigate the associations between circulating adiponectin, leptin and adiponectin-leptin (A/L) ratio and endometrial cancer risk.", "Relevant manuscripts were identified by searching PubMed and ISI Web of Science databases as well as by manual searching the references cited in retrieved manuscripts.", "Random-effects models were used to estimate summary odds ratio (SOR) and 95% confidence intervals (CIs) for aforementioned associations.", "Fourteen manuscripts with 13 studies (five nested case-control and eight case-control studies) cumulatively involving a total of 1,963 endometrial cancer cases and 3,503 noncases were included in the analyses.", "Overall, comparing persons with circulating concentrations of adiponectin, leptin and A/L ratio in the top tertile with persons with concentrations of these biomarkers in the bottom tertile yielded SORs of 0.47 (95% CI: 0.34-0.65; I(2)  = 63.7%; n = 13), 2.19 (95% CI: 1.44-3.31; I(2)  = 64.2%; n = 7),and 0.45 (95% CI: 0.24-0.86; I(2)  = 90.1%; n = 5), respectively.", "Notably, there was an 18% reduction in risk for per each 5 \u03bcg/mL increment in circulating adiponectin concentrations (SOR = 0.82; 95% CI: 0.74-0.90; I(2)  = 49%; n = 8).", "Stratifying by study characteristics and whether these studies considered or adjusted for potential confounders, the findings were robust in the analyses of circulating adiponectin and leptin.", "No evidence of publication bias was detected.", "In conclusion, the findings from this meta-analysis suggest that increased circulating adiponectin and A/L ratio or decreased leptin concentrations were associated with reduced risk of endometrial cancer.", "Further prospective designed studies are warranted to confirm our findings."], "structured": false}
{"doc_id": 12871002, "title": "CDE-1 Affects Chromosome Segregation through Uridylation of CSR-1-Bound siRNAs", "abstract": ["We have studied the function of a conserved germline-specific nucleotidyltransferase protein, CDE-1, in RNAi and chromosome segregation in C. elegans.", "CDE-1 localizes specifically to mitotic chromosomes in embryos.", "This localization requires the RdRP EGO-1, which physically interacts with CDE-1, and the Argonaute protein CSR-1.", "We found that CDE-1 is required for the uridylation of CSR-1 bound siRNAs, and that in the absence of CDE-1 these siRNAs accumulate to inappropriate levels, accompanied by defects in both meiotic and mitotic chromosome segregation.", "Elevated siRNA levels are associated with erroneous gene silencing, most likely through the inappropriate loading of CSR-1 siRNAs into other Argonaute proteins.", "We propose a model in which CDE-1 restricts specific EGO-1-generated siRNAs to the CSR-1 mediated, chromosome associated RNAi pathway, thus separating it from other endogenous RNAi pathways.", "The conserved nature of CDE-1 suggests that similar sorting mechanisms may operate in other animals, including mammals."], "structured": false}
{"doc_id": 12871281, "title": "Localized diacylglycerol drives the polarization of the microtubule-organizing center in T cells", "abstract": ["The reorientation of the T cell microtubule-organizing center (MTOC) toward the antigen-presenting cell enables the directional secretion of cytokines and lytic factors.", "By single-cell photoactivation of the T cell antigen receptor, we show that MTOC polarization is driven by localized accumulation of diacylglycerol (DAG).", "MTOC reorientation was closely preceded first by production of DAG and then by recruitment of the microtubule motor protein dynein.", "Blocking DAG production or disrupting the localization of DAG impaired MTOC recruitment.", "Localized DAG accumulation was also required for cytotoxic T cell\u2013mediated killing.", "Furthermore, photoactivation of DAG itself was sufficient to induce transient polarization.", "Our data identify a DAG-dependent pathway that signals through dynein to control microtubule polarity in T cells."], "structured": false}
{"doc_id": 12880573, "title": "Dual roles of plcA in Listeria monocytogenes pathogenesis.", "abstract": ["The plcA gene of Listeria monocytogenes encodes a secreted phosphatidylinositol-specific phospholipase C (Pl-PLC).", "Recent studies have established that transposon mutations within plcA result in avirulence for mice and pleiotropic effects when examined in tissue-culture models of infection.", "Genetic analysis reveals that many of the effects of the transposon insertions are due to loss of readthrough transcription from plcA into the downstream gene prfA, which encodes an essential transcription factor of numerous L. monocytogenes virulence genes.", "Construction of an in-frame deletion within plcA had no effect on expression of prfA thus allowing direct assignment of a role of the Pl-PLC in pathogenesis.", "Pl-PLC was shown to play a significant role in mediating escape of L. monocytogenes from phagosomes of primary murine macrophages.", "Interestingly, this defect manifested itself in vivo in the liver but not in the spleen of infected mice."], "structured": false}
{"doc_id": 12881593, "title": "Fine-tuning in regulation of Clp protein content in Bacillus subtilis.", "abstract": ["Clp-controlled proteolysis in Bacillus subtilis seems to play a substantial role, particularly under stress conditions.", "Calibrated Western blot analyses were used to estimate the approximate numbers of heat-inducible Clp molecules within a single cell.", "According to these numbers, the different Clp ATPases do not seem to compete for the proteolytic subunit ClpP. Coimmunoprecipitation experiments revealed the predicted specific ClpX-ClpP, ClpC-ClpP, and ClpE-ClpP interactions.", "ClpE and ClpX are rapidly degraded in wild-type cells during permanent heat stress but remained almost stable in a clpP mutant, suggesting ClpP-dependent degradation.", "In particular, ClpCP appeared to be involved in the degradation of the short-lived ClpE ATPase, indicating a negative \"autoregulatory\" circuit for this particular Clp ATPase at the posttranslational level.", "Analysis of the half-life of stress-inducible clp mRNAs during exponential growth and heat shock revealed precise regulation of the synthesis of each Clp protein at the posttranscriptional level as well to meet the needs of B. subtilis."], "structured": false}
{"doc_id": 12885341, "title": "A C-Type Lectin Collaborates with a CD45 Phosphatase Homolog to Facilitate West Nile Virus Infection of Mosquitoes", "abstract": ["West Nile virus (WNV) is the most common arthropod-borne flavivirus in the United States; however, the vector ligand(s) that participate in infection are not known.", "We now show that an Aedes aegypti C-type lectin, mosGCTL-1, is induced by WNV, interacts with WNV in a calcium-dependent manner, and facilitates infection in vivo and in vitro.", "A mosquito homolog of human CD45 in A. aegypti, designated mosPTP-1, recruits mosGCTL-1 to enable viral attachment to cells and to enhance viral entry.", "In vivo experiments show that mosGCTL-1 and mosPTP-1 function as part of the same pathway and are critical for WNV infection of mosquitoes.", "A similar phenomenon was also observed in Culex quinquefasciatus, a natural vector of WNV, further demonstrating that these genes participate in WNV infection.", "During the mosquito blood-feeding process, WNV infection was blocked in vivo with mosGCTL-1 antibodies.", "A molecular understanding of flaviviral-arthropod interactions may lead to strategies to control viral dissemination in nature."], "structured": false}
{"doc_id": 12887068, "title": "Use of human embryonic stem cells to model pediatric gliomas with H3.3K27M histone mutation", "abstract": ["Over 70% of diffuse intrinsic pediatric gliomas, an aggressive brainstem tumor, harbor heterozygous mutations that create a K27M amino acid substitution (methionine replaces lysine 27) in the tail of histone H3.3.", "The role of the H3.3K27M mutation in tumorigenesis is not fully understood.", "Here, we use a human embryonic stem cell system to model this tumor.", "We show that H3.3K27M expression synergizes with p53 loss and PDGFRA activation in neural progenitor cells derived from human embryonic stem cells, resulting in neoplastic transformation.", "Genome-wide analyses indicate a resetting of the transformed precursors to a developmentally more primitive stem cell state, with evidence of major modifications of histone marks at several master regulator genes.", "Drug screening assays identified a compound targeting the protein menin as an inhibitor of tumor cell growth in vitro and in mice."], "structured": false}
{"doc_id": 12892137, "title": "Basis for avid homologous DNA strand exchange by human Rad51 and RPA.", "abstract": ["Human Rad51 (hRad51), a member of a conserved family of general recombinases, is shown here to have an avid capability to make DNA joints between homologous DNA molecules and promote highly efficient DNA strand exchange of the paired molecules over at least 5.4 kilobase pairs.", "Furthermore, maximal efficiency of homologous DNA pairing and strand exchange is strongly dependent on the heterotrimeric single-stranded DNA binding factor hRPA and requires conditions that lessen interactions of the homologous duplex with the hRad51-single-stranded DNA nucleoprotein filament.", "The homologous DNA pairing and strand exchange system described should be valuable for dissecting the action mechanism of hRad51 and for deciphering its functional interactions with other recombination factors."], "structured": false}
{"doc_id": 12899460, "title": "A multiple indicators multiple causes model of late-life depression in Latin American countries", "abstract": ["BACKGROUND The Euro-D depression scale consists of symptom clusters that may be differentially related to demographic and cognitive characteristics in older adults.", "This hypothesis needs further investigation and the role of measurement bias on substantive conclusions remains to be established.   \n", "METHOD The study sample comprised 10,405 community-dwelling older adults from six Latin American countries.", "We applied a Multiple Indicators Multiple Causes (MIMIC) model for a concurrent investigation of measurement bias and of the association between Euro-D symptom clusters and background variables.   \n", "RESULTS The factorial validity of Euro-D, with a two-dimensional structure--affective suffering and motivation disturbance, was consistently supported in all countries.", "Although complete measurement invariance could not be assumed across countries, measurement bias was minor.", "Both Euro-D factors were unrelated to age, but related to gender, as well as to impairment in memory and verbal fluency.", "Gender differences were larger for affective suffering than for motivation disturbance, whereas differences in verbal fluency impairment were more strongly related to motivation disturbance.   ", "LIMITATIONS Our analytic strategies could only examine invariance at the level of indicator thresholds.", "The generalisability of current findings needs to be examined in clinical populations.", "A wider set of cognitive tests is needed.", "We did not examine the compositional factors that could have accounted for the variation in Euro-D scores across countries, as this was beyond the aims of the paper.   \n", "CONCLUSION The current study adds evidence for the construct validity of Euro-D and for the possible differential association of depression symptom-clusters with gender and verbal fluency in older adults.", "An understanding of the heterogeneity of late-life depression may carry clinical implications for the diagnosis and treatment of depression in old age."], "structured": true}
{"doc_id": 12899612, "title": "Microvesicles derived from human umbilical cord mesenchymal stem cells stimulated by hypoxia promote angiogenesis both in vitro and in vivo.", "abstract": ["Although mesenchymal stem cells (MSCs) have been increasingly trialed to treat a variety of diseases, the underlying mechanisms remain still elusive.", "In this study, human umbilical cord (UC)-derived MSCs were stimulated by hypoxia, and the membrane microvesicles (MVs) in the supernatants were collected by ultracentrifugation, observed under an electron microscope, and the origin was identified with the flow cytometric technique.", "The results showed that upon hypoxic stimulus, MSCs released a large quantity of MVs of ~100 nm in diameter.", "The MVs were phenotypically similar to the parent MSCs, except that the majority of them were negative for the receptor of platelet-derived growth factor.", "DiI-labeling assay revealed that MSC-MVs could be internalized into human UC endothelial cells (UC-ECs) within 8 h after they were added into the culture medium.", "Carboxyfluorescein succinimidyl ester-labeling technique and MTT test showed that MSC-MVs promoted the proliferation of UC-ECs in a dose-dependent manner.", "Further, MVs could enhance in vitro capillary network formation of UC-ECs in a Matrigel matrix.", "In a rat hindlimb ischemia model, both MSCs and MSC-MVs were shown to improve significantly the blood flow recovery compared with the control medium (P<0.0001), as assessed by laser Doppler imaging analysis.", "These data indicate that MV releasing is one of the major mechanisms underlying the effectiveness of MSC therapy by promoting angiogenesis."], "structured": false}
{"doc_id": 12903921, "title": "Evaluation of oxidative status and depression-like responses in Brown Norway rats with acute myeloid leukemia", "abstract": ["It has been proved that oxidative stress increases when leukemia is accompanied by depression.", "This fact may indicate the role of oxidative stress in the development of depression in cancer patients.", "The aim of this study was to determine whether the acute myeloid leukemia of Brown Norway rats, which is accompanied by oxidative stress, evoked behavioral and receptor changes resembling alterations characteristic of rat models of depression.", "The rats were divided into two groups: leukemic rats and healthy control.", "Leukemia was induced through intraperitoneal injection of 10(7) promyelocytic leukemia cells to the Brown Norway rats.", "Depression-like behavior was evaluated in the forced swim test at 30 or 34 days after leukemic cells injection.", "The rats were killed after the evaluation and the spleen, brain cortex and hippocampus were excised.", "The red-ox state was assessed in homogenates of tissues by measuring total glutathione (GSH) content, the ferric ion reducing ability of plasma (FRAP) level, expression of heme oxygenase-1 (HO-1), biliverdin reductase (BvR) and ferritin mRNA, superoxide dismutase (SOD) activity, as well as malondialdehyde (MDA) concentration.", "Radioligand binding assay was used to assess of the effect of leukemia on cortical receptors.", "Leukemic cells were identified using RM-124 antibody by FACS Calibur flow cytometry.", "Leukemia influenced locomotory activity as well as forced swim test behavior in a 34-day series of experiments.", "Signs of oxidative stress in leukemic rats were observed in each examined stage of leukemia development.", "The FRAP values and glutathione contents, were significantly lowered whereas HO-1 mRNA expression, and malonodialdehyde concentrations were significantly increased in the spleen and brain structures of leukemic rats in comparison with the healthy controls.", "A significant increase in the potency of glycine to displace [(3)H]L-689,560 from the strychnine-insensitive glycine site of the N-methyl-D-aspartic (NMDA) receptors receptor complex in cortical homogenates of the leukemic rats in 30- and 34-day experimental series was observed in comparison with the control.", "Upregulation of 5-HT(2A) receptors was observed in rat cortex after 30 days of leukemia development but not in 34-days series compared with the control.", "It is concluded that disturbances in antioxidant system in brain cortex were accompanied by an activation of glycine sites of the NMDA receptor complex, regardless of stage of leukemia development, which are characteristic of model of depression.", "Findings of our study demonstrate the link between glutamatergic activity, oxidative stress and leukemia."], "structured": false}
{"doc_id": 12909503, "title": "Distinct roles for DNA-PK, ATM and ATR in RPA phosphorylation and checkpoint activation in response to replication stress", "abstract": ["DNA damage encountered by DNA replication forks poses risks of genome destabilization, a precursor to carcinogenesis.", "Damage checkpoint systems cause cell cycle arrest, promote repair and induce programed cell death when damage is severe.", "Checkpoints are critical parts of the DNA damage response network that act to suppress cancer.", "DNA damage and perturbation of replication machinery causes replication stress, characterized by accumulation of single-stranded DNA bound by replication protein A (RPA), which triggers activation of ataxia telangiectasia and Rad3 related (ATR) and phosphorylation of the RPA32, subunit of RPA, leading to Chk1 activation and arrest.", "DNA-dependent protein kinase catalytic subunit (DNA-PKcs) [a kinase related to ataxia telangiectasia mutated (ATM) and ATR] has well characterized roles in DNA double-strand break repair, but poorly understood roles in replication stress-induced RPA phosphorylation.", "We show that DNA-PKcs mutant cells fail to arrest replication following stress, and mutations in RPA32 phosphorylation sites targeted by DNA-PKcs increase the proportion of cells in mitosis, impair ATR signaling to Chk1 and confer a G2/M arrest defect.", "Inhibition of ATR and DNA-PK (but not ATM), mimic the defects observed in cells expressing mutant RPA32.", "Cells expressing mutant RPA32 or DNA-PKcs show sustained H2AX phosphorylation in response to replication stress that persists in cells entering mitosis, indicating inappropriate mitotic entry with unrepaired damage."], "structured": false}
{"doc_id": 12922760, "title": "The essential Schizosaccharomyces pombe Pfh1 DNA helicase promotes fork movement past G-quadruplex motifs to prevent DNA damage", "abstract": ["BACKGROUND G-quadruplexes (G4s) are stable non-canonical DNA secondary structures consisting of stacked arrays of four guanines, each held together by Hoogsteen hydrogen bonds.", "Sequences with the ability to form these structures in vitro, G4 motifs, are found throughout bacterial and eukaryotic genomes.", "The budding yeast Pif1 DNA helicase, as well as several bacterial Pif1 family helicases, unwind G4 structures robustly in vitro and suppress G4-induced DNA damage in S. cerevisiae in vivo.   \n", "RESULTS We determined the genomic distribution and evolutionary conservation of G4 motifs in four fission yeast species and investigated the relationship between G4 motifs and Pfh1, the sole S. pombe Pif1 family helicase.", "Using chromatin immunoprecipitation combined with deep sequencing, we found that many G4 motifs in the S. pombe genome were associated with Pfh1.", "Cells depleted of Pfh1 had increased fork pausing and DNA damage near G4 motifs, as indicated by high DNA polymerase occupancy and phosphorylated histone H2A, respectively.", "In general, G4 motifs were underrepresented in genes.", "However, Pfh1-associated G4 motifs were located on the transcribed strand of highly transcribed genes significantly more often than expected, suggesting that Pfh1 has a function in replication or transcription at these sites.   \n", "CONCLUSIONS In the absence of functional Pfh1, unresolved G4 structures cause fork pausing and DNA damage of the sort associated with human tumors."], "structured": true}
{"doc_id": 12932176, "title": "Wnt7a signaling promotes dendritic spine growth and synaptic strength through Ca\u00b2\u207a/Calmodulin-dependent protein kinase II.", "abstract": ["The balance between excitatory and inhibitory synapses is crucial for normal brain function.", "Wnt proteins stimulate synapse formation by increasing synaptic assembly.", "However, it is unclear whether Wnt signaling differentially regulates the formation of excitatory and inhibitory synapses.", "Here, we demonstrate that Wnt7a preferentially stimulates excitatory synapse formation and function.", "In hippocampal neurons, Wnt7a increases the number of excitatory synapses, whereas inhibitory synapses are unaffected.", "Wnt7a or postsynaptic expression of Dishevelled-1 (Dvl1), a core Wnt signaling component, increases the frequency and amplitude of miniature excitatory postsynaptic currents (mEPSCs), but not miniature inhibitory postsynaptic currents (mIPSCs).", "Wnt7a increases the density and maturity of dendritic spines, whereas Wnt7a-Dvl1-deficient mice exhibit defects in spine morphogenesis and mossy fiber-CA3 synaptic transmission in the hippocampus.", "Using a postsynaptic reporter for Ca(2+)/Calmodulin-dependent protein kinase II (CaMKII) activity, we demonstrate that Wnt7a rapidly activates CaMKII in spines.", "Importantly, CaMKII inhibition abolishes the effects of Wnt7a on spine growth and excitatory synaptic strength.", "These data indicate that Wnt7a signaling is critical to regulate spine growth and synaptic strength through the local activation of CaMKII at dendritic spines.", "Therefore, aberrant Wnt7a signaling may contribute to neurological disorders in which excitatory signaling is disrupted."], "structured": false}
{"doc_id": 12943966, "title": "Bitter taste receptors and \u03b1-gustducin regulate the secretion of ghrelin with functional effects on food intake and gastric emptying.", "abstract": ["Ghrelin is a hunger hormone with gastroprokinetic properties but the factors controlling ghrelin secretion from the stomach are unknown.", "Bitter taste receptors (T2R) and the gustatory G proteins, \u03b1-gustducin (gust) and \u03b1-transducin, are expressed in the gut and are involved in the chemosensation of nutrients.", "This study aimed to investigate whether T2R-agonists affect (i) ghrelin release via \u03b1-gustducin and (ii) food intake and gastric emptying via the release of ghrelin.", "The mouse stomach contains two ghrelin cell populations: cells containing octanoyl and desoctanoyl ghrelin, which were colocalized with \u03b1-gustducin and \u03b1-transducin, and cells staining for desoctanoyl ghrelin.", "Gavage of T2R-agonists increased plasma octanoyl ghrelin levels in WT mice but the effect was partially blunted in gust(-/-) mice.", "Intragastric administration of T2R-agonists increased food intake during the first 30 min in WT but not in gust(-/-) and ghrelin receptor knockout mice.", "This increase was accompanied by an increase in the mRNA expression of agouti-related peptide in the hypothalamus of WT but not of gust(-/-) mice.", "The temporary increase in food intake was followed by a prolonged decrease (next 4 h), which correlated with an inhibition of gastric emptying.", "The delay in emptying, which was partially counteracted by ghrelin, was not mediated by cholecystokinin and GLP-1 but involved a direct inhibitory effect of T2R-agonists on gastric contractility.", "This study is unique in providing functional evidence that activation of bitter taste receptors stimulates ghrelin secretion.", "Modulation of endogenous ghrelin levels by tastants may provide novel therapeutic applications for the treatment of weight -and gastrointestinal motility disorders."], "structured": false}
{"doc_id": 12948892, "title": "Ca2+-permeable AMPA receptors regulate growth of human glioblastoma via Akt activation.", "abstract": ["Evidence has been accumulated that glioblastoma cells release and exploit glutamate for proliferation and migration by autocrine or paracrine loops through Ca2+-permeable AMPA-type glutamate receptors.", "Here, we show that Ca2+ signaling mediated by AMPA receptor regulates the growth and motility of glioblastoma cells via activation of Akt.", "Ca2+ supplied through Ca2+-permeable AMPA receptor phosphorylated Akt at Ser-473, thereby facilitating proliferation and mobility.", "A dominant-negative form of Akt inhibited cell proliferation and migration accelerated by overexpression of Ca2+-permeable AMPA receptor.", "In contrast, introduction of a constitutively active form of Akt rescued tumor cells from apoptosis induced by the conversion of Ca2+-permeable AMPA receptor to Ca2+-impermeable receptors by the delivery of GluR2 cDNA.", "Therefore, Akt functions as downstream effectors for Ca2+-signaling mediated by AMPA receptor in glioblastoma cells.", "The activation of the glutamate-AMPA receptor-Akt pathway may contribute to the high degree of anaplasia and invasive growth of human glioblastoma.", "This novel pathway might give an alternative therapeutic target."], "structured": false}
{"doc_id": 12956194, "title": "The Extracellular Surface of the GLP-1 Receptor Is a Molecular Trigger for Biased Agonism", "abstract": ["Ligand-directed signal bias offers opportunities for sculpting molecular events, with the promise of better, safer therapeutics.", "Critical to the exploitation of signal bias is an understanding of the molecular events coupling ligand binding to intracellular signaling.", "Activation of class B G protein-coupled receptors is driven by interaction of the peptide N terminus with the receptor core.", "To understand how this drives signaling, we have used advanced analytical methods that enable separation of effects on pathway-specific signaling from those that modify agonist affinity and mapped the functional consequence of receptor modification onto three-dimensional models of a receptor-ligand complex.", "This yields molecular insights into the initiation of receptor activation and the mechanistic basis for biased agonism.", "Our data reveal that peptide agonists can engage different elements of the receptor extracellular face to achieve effector coupling and biased signaling providing a foundation for rational design of biased agonists."], "structured": false}
{"doc_id": 12966719, "title": "A local macrophage chemokine network sustains protective tissue-resident memory CD4 T cells", "abstract": ["CD8 tissue-resident memory T (TRM) cells provide efficient local control of viral infection, but the role of CD4 TRM is less clear.", "Here, by using parabiotic mice, we show that a preexisting pool of CD4 TRM cells in the genital mucosa was required for full protection from a lethal herpes simplex virus 2 (HSV-2) infection.", "Chemokines secreted by a local network of macrophages maintained vaginal CD4 TRM in memory lymphocyte clusters (MLCs), independently of circulating memory T cells.", "CD4 TRM cells within the MLCs were enriched in clones that expanded in response to HSV-2.", "Our results highlight the need for vaccine strategies that enable establishment of TRM cells for protection from a sexually transmitted virus and provide insights as to how such a pool might be established."], "structured": false}
{"doc_id": 12991445, "title": "Influence of smoking and plasma factors on patency of femoropopliteal vein grafts.", "abstract": ["OBJECTIVE To determine the effects of smoking, plasma lipids, lipoproteins, apolipoproteins, and fibrinogen on the patency of saphenous vein femoropopliteal bypass grafts at one year.   \n", "DESIGN Prospective study of patients with saphenous vein femoropopliteal bypass grafts entered into a multicentre trial.   \n", "SETTING Surgical wards, outpatient clinics, and home visits coordinated by two tertiary referral centres in London and Birmingham.   \n", "PATIENTS 157 Patients (mean age 66.6 (SD 8.2) years), 113 with patent grafts and 44 with occluded grafts one year after bypass.   \n", "MAIN OUTCOME MEASURE Cumulative percentage patency at one year.   \n", "RESULTS Markers for smoking (blood carboxyhaemoglobin concentration (p less than 0.05) and plasma thiocyanate concentration (p less than 0.01) and plasma concentrations of fibrinogen (p less than 0.001) and apolipoproteins AI (p less than 0.04) and (a) (p less than 0.05) were significantly higher in patients with occluded grafts.", "Serum cholesterol concentrations were significantly higher in patients with grafts that remained patent one year after bypass (p less than 0.005).", "Analysis of the smoking markers indicated that a quarter of patients (40) were untruthful in their claims to have stopped smoking.", "Based on smoking markers, patency of grafts in smokers was significantly lower at one year by life table analysis than in non-smokers (63% v 84%, p less than 0.02).", "Patency was significantly higher by life table analysis in patients with a plasma fibrinogen concentration below the median than in those with a concentration above (90% v 57%, p less than 0.0002).", "Surprisingly, increased plasma low density lipoprotein cholesterol concentration was significantly associated with improved patency at one year (85%) at values above the median compared with patency (only 68%) at values in the lower half of the range (p less than 0.02).   \n", "CONCLUSIONS Plasma fibrinogen concentration was the most important variable predicting graft occlusion, followed by smoking markers.", "A more forceful approach is needed to stop patients smoking; therapeutic measures to improve patency of vein grafts should focus on decreasing plasma fibrinogen concentration rather than serum cholesterol concentration."], "structured": true}
{"doc_id": 12994780, "title": "No effect of dietary fat on short-term weight gain in mice treated with atypical antipsychotic drugs", "abstract": ["Rationale:Atypical antipsychotic drugs (AAD) induce significant weight gain in female C57BL/6J mice.", "The effect of dietary fat on weight gain and serum lipids in this model is unknown.", "Objectives:", "Test the hypothesis that the obesigenic effects of these drugs are greater in the presence of a high-fat diet.", "Methods:Female C57BL/6J mice were treated with atypical antipsychotics for 3 weeks and fed either a low-fat or high-fat diet (4.6 vs 15.6% fat by wt).", "Food intake (FI), body weight (BW), body composition, and serum lipids were measured during treatment with optimized doses of olanzapine, quetiapine, and risperidone.", "Energy intake (EI) and feed efficiency (FE) were calculated.", "Group differences in change were analyzed via repeated measures analysis of variance (ANOVA).", "Serum lipid concentrations, EI and FE were compared using two-way ANOVA.Results:AAD-treated mice gained significantly more weight than controls after 3 weeks (P<0.001).", "Treatment and diet had significant effects on FI and EI over time (P<0.001).", "AAD-treated mice had significantly higher FE than controls (P<0.05); however, there was no significant drug by diet interaction (P=0.65).", "Risperidone low-fat mice gained significantly more absolute fat mass than placebo low-fat mice (P<0.05).", "All treatment groups, except quetiapine low-fat and olanzapine high-fat, gained significantly more absolute lean mass than placebo controls (P<0.05).", "Cholesterol levels were significantly lower in quetiapine and risperidone than placebo (P<0.05).", "Risperidone low-fat mice had significantly higher triglyceride levels than placebo and risperidone high-fat mice (P<0.05).Conclusions:A high-fat diet does not increase AAD-induced BW gain in female mice during a 3-week treatment period."], "structured": false}
{"doc_id": 13000926, "title": "The role of free radicals in cold injuries.", "abstract": ["Cold injury is a tissue trauma produced by exposure to freezing temperatures and even brief exposure to a severely cold and windy environment.", "Rewarming of frozen tissue is associated with blood reperfusion and the simultaneous generation of free oxygen radicals.", "In this review is discussed the current understanding of the mechanism of action of free oxygen radicals as related to cold injury during rewarming.", "Decreased energy stores during ischaemia lead to the accumulation of adenine nucleotides and liberation of free fatty acids due to the breakdown of lipid membranes.", "On rewarming, free fatty acids are metabolized via cyclo-oxygenase and adenine nucleotides are metabolized via the xanthine oxidase pathway.", "These may be the source of free oxygen radicals.", "Leukocytes may also play a major role in the pathogenesis of cold injury.", "Oxygen radical scavengers, such as superoxide dismutase and catalase, may help to reduce the cold induced injury but their action is limited due to the inability readily to cross the plasma membrane.", "Lipid soluble antioxidants are likely to be more effective scavengers because of their presence in membranes where peroxidative reactions can be arrested."], "structured": false}
{"doc_id": 13001323, "title": "SIRT1 deacetylase in SF1 neurons protects against metabolic imbalance.", "abstract": ["Chronic feeding on high-calorie diets causes obesity and type 2 diabetes mellitus (T2DM), illnesses that affect hundreds of millions.", "Thus, understanding the pathways protecting against diet-induced metabolic imbalance is of paramount medical importance.", "Here, we show that mice lacking SIRT1 in steroidogenic factor 1 (SF1) neurons are hypersensitive to dietary obesity owing to maladaptive energy expenditure.", "Also, mutant mice have increased susceptibility to developing dietary T2DM due to insulin resistance in skeletal muscle.", "Mechanistically, these aberrations arise, in part, from impaired metabolic actions of the neuropeptide orexin-A and the hormone leptin.", "Conversely, mice overexpressing SIRT1 in SF1 neurons are more resistant to diet-induced obesity and insulin resistance due to increased energy expenditure and enhanced skeletal muscle insulin sensitivity.", "Our results unveil important protective roles of SIRT1 in SF1 neurons against dietary metabolic imbalance."], "structured": false}
{"doc_id": 13002003, "title": "mTOR supports long-term self-renewal and suppresses mesoderm and endoderm activities of human embryonic stem cells.", "abstract": ["Despite the recent identification of the transcriptional regulatory circuitry involving SOX2, NANOG, and OCT-4, the intracellular signaling networks that control pluripotency of human embryonic stem cells (hESCs) remain largely undefined.", "Here, we demonstrate an essential role for the serine/threonine protein kinase mammalian target of rapamycin (mTOR) in regulating hESC long-term undifferentiated growth.", "Inhibition of mTOR impairs pluripotency, prevents cell proliferation, and enhances mesoderm and endoderm activities in hESCs.", "At the molecular level, mTOR integrates signals from extrinsic pluripotency-supporting factors and represses the transcriptional activities of a subset of developmental and growth-inhibitory genes, as revealed by genome-wide microarray analyses.", "Repression of the developmental genes by mTOR is necessary for the maintenance of hESC pluripotency.", "These results uncover a novel signaling mechanism by which mTOR controls fate decisions in hESCs.", "Our findings may contribute to effective strategies for tissue repair and regeneration."], "structured": false}
{"doc_id": 13007205, "title": "Intrinsic genetic characteristics determine tumor-modifying capacity of fibroblasts: matrix metalloproteinase-3 5A/5A genotype enhances breast cancer cell invasion", "abstract": ["Stromal fibroblasts can contribute to tumor invasion through the release of matrix metalloproteinases (MMPs).", "Population studies have suggested that single nucleotide polymorphisms (SNPs) in MMP genes influence levels of expression and may be associated with breast cancer risk and with disease progression.", "This study directly examined the impact of MMP SNP genotype on the ability of host fibroblasts to promote tumor cell invasion.", "Primary breast fibroblasts were isolated from patients with (n = 13) or without (n = 19) breast cancer, and their ability to promote breast cancer cell invasion was measured in in vitro invasion assays.", "Fibroblast invasion-promoting capacity (IPC) was analyzed in relation to donor type (tumor or non-tumor patient), MMP-1, MMP-3, and MMP-9 SNP genotype and MMP activity using independent samples t test and analysis of variance.", "All statistical tests were two-sided.", "Tumor-derived fibroblasts promoted higher levels of invasion than normal fibroblasts (p = 0.041).", "When IPC was related to genotype, higher levels of IPC were generated by tumor fibroblasts with the high-expressing MMP-3 5A/5A genotype compared with the 5A/6A and 6A/6A genotypes (p = 0.05 and 0.07, respectively), and this was associated with enhanced MMP-3 release.", "The functional importance of MMP-3 was demonstrated by enhanced invasion in the presence of recombinant MMP-3, whereas reduction occurred in the presence of a specific MMP-3 inhibitor.", "An inverse relationship was demonstrated between fibroblast IPC and the high-expressing MMP-1 genotype (p = 0.031), but no relationship was seen with MMP-9 SNP status.", "In contrast, normal fibroblasts showed no variation in IPC in relation to MMP genotype, with MMP-3 5A/5A fibroblasts exhibiting significantly lower levels of IPC than their tumor-derived counterparts (p = 0.04).", "This study has shown that tumor-derived fibroblasts exhibit higher levels of IPC than normal fibroblasts and that the MMP-3 5A/5A genotype contributes to this through enhanced MMP-3 release.", "Despite a high-expressing genotype, normal fibroblasts do not exhibit higher IPC or enhanced MMP release.", "This suggests that more complex changes occur in tumor-derived fibroblasts, enabling full expression of the MMP SNP genotype and these possibly are epigenetic in nature.", "The results do suggest that, in women with breast cancer, a high-expressing MMP-3 genotype may promote tumor progression more effectively."], "structured": false}
{"doc_id": 13011249, "title": "Hallmarks of Cancer: The Next Generation", "abstract": ["The hallmarks of cancer comprise six biological capabilities acquired during the multistep development of human tumors.", "The hallmarks constitute an organizing principle for rationalizing the complexities of neoplastic disease.", "They include sustaining proliferative signaling, evading growth suppressors, resisting cell death, enabling replicative immortality, inducing angiogenesis, and activating invasion and metastasis.", "Underlying these hallmarks are genome instability, which generates the genetic diversity that expedites their acquisition, and inflammation, which fosters multiple hallmark functions.", "Conceptual progress in the last decade has added two emerging hallmarks of potential generality to this list-reprogramming of energy metabolism and evading immune destruction.", "In addition to cancer cells, tumors exhibit another dimension of complexity: they contain a repertoire of recruited, ostensibly normal cells that contribute to the acquisition of hallmark traits by creating the \"tumor microenvironment.", "\"", "Recognition of the widespread applicability of these concepts will increasingly affect the development of new means to treat human cancer."], "structured": false}
{"doc_id": 13023410, "title": "BCR/ABL oncogenic kinase promotes unfaithful repair of the reactive oxygen species-dependent DNA double-strand breaks.", "abstract": ["The oncogenic BCR/ABL tyrosine kinase induces constitutive DNA damage in Philadelphia chromosome (Ph)-positive leukemia cells.", "We find that BCR/ABL-induced reactive oxygen species (ROSs) cause chronic oxidative DNA damage resulting in double-strand breaks (DSBs) in S and G(2)/M cell cycle phases.", "These lesions are repaired by BCR/ABL-stimulated homologous recombination repair (HRR) and nonhomologous end-joining (NHEJ) mechanisms.", "A high mutation rate is detected in HRR products in BCR/ABL-positive cells, but not in the normal counterparts.", "In addition, large deletions are found in NHEJ products exclusively in BCR/ABL cells.", "We propose that the following series of events may contribute to genomic instability of Ph-positive leukemias: BCR/ABL --> ROSs --> oxidative DNA damage --> DSBs in proliferating cells --> unfaithful HRR and NHEJ repair."], "structured": false}
{"doc_id": 13025574, "title": "Cancer risks attributable to low doses of ionizing radiation: assessing what we really know.", "abstract": ["High doses of ionizing radiation clearly produce deleterious consequences in humans, including, but not exclusively, cancer induction.", "At very low radiation doses the situation is much less clear, but the risks of low-dose radiation are of societal importance in relation to issues as varied as screening tests for cancer, the future of nuclear power, occupational radiation exposure, frequent-flyer risks, manned space exploration, and radiological terrorism.", "We review the difficulties involved in quantifying the risks of low-dose radiation and address two specific questions.", "First, what is the lowest dose of x- or gamma-radiation for which good evidence exists of increased cancer risks in humans?", "The epidemiological data suggest that it is approximately 10-50 mSv for an acute exposure and approximately 50-100 mSv for a protracted exposure.", "Second, what is the most appropriate way to extrapolate such cancer risk estimates to still lower doses?", "Given that it is supported by experimentally grounded, quantifiable, biophysical arguments, a linear extrapolation of cancer risks from intermediate to very low doses currently appears to be the most appropriate methodology.", "This linearity assumption is not necessarily the most conservative approach, and it is likely that it will result in an underestimate of some radiation-induced cancer risks and an overestimate of others."], "structured": false}
{"doc_id": 13027590, "title": "Laparoscopic uterosacral nerve ablation for alleviating chronic pelvic pain: a randomized controlled trial.", "abstract": ["CONTEXT Chronic pelvic pain is a common condition with a major effect on health-related quality of life, work productivity, and health care use.", "Operative interruption of nerve trunks in the uterosacral ligaments by laparoscopic uterosacral nerve ablation (LUNA) is a treatment option for patients with chronic pelvic pain.   \n", "OBJECTIVE To assess the effectiveness of LUNA in patients with chronic pelvic pain.   \n", "DESIGN, SETTING, AND PARTICIPANTS Randomized controlled trial of 487 women with chronic pelvic pain lasting longer than 6 months without or with minimal endometriosis, adhesions, or pelvic inflammatory disease, who were recruited to the study by consultant gynecological surgeons from 18 UK hospitals between February 1998 and December 2005.", "Follow-up was conducted by questionnaires mailed at 3 and 6 months and at 1, 2, 3, and 5 years.   \n", "INTERVENTION Bilateral LUNA or laparoscopy without pelvic denervation (no LUNA); participants were blinded to the treatment allocation.   \n", "MAIN OUTCOME MEASURES", "The primary outcome was pain, which was assessed by a visual analogue scale.", "Data concerning the 3 types of pain (noncyclical pain, dysmenorrhea, and dyspareunia) were analyzed separately as was the worst pain level experienced from any of these 3 types of pain.", "The secondary outcome was health-related quality of life, which was measured using a generic instrument (EuroQoL EQ-5D and EQ-VAS).   \n", "RESULTS After a median follow-up of 69 months, there were no significant differences reported on the visual analogue pain scales for the worst pain (mean difference between the LUNA group and the no LUNA group, -0.04 cm [95% confidence interval {CI}, -0.33 to 0.25 cm]; P = .80), noncyclical pain (-0.11 cm [95% CI, -0.50 to 0.29 cm]; P = .60), dysmenorrhea (-0.09 cm [95% CI, -0.49 to 0.30 cm]; P = .60), or dyspareunia (0.18 cm [95% CI, -0.22 to 0.62 cm]; P = .40).", "No differences were observed between the LUNA group and the no LUNA group for quality of life.   \n", "CONCLUSION Among women with chronic pelvic pain, LUNA did not result in improvements in pain, dysmenorrhea, dyspareunia, or quality of life compared with laparoscopy without pelvic denervation.   \n", "TRIAL REGISTRATION controlled-trials.com Identifier: ISRCTN41196151."], "structured": true}
{"doc_id": 13030852, "title": "Identification of bone and liver metastases from breast cancer by measurement of plasma alkaline phosphatase isoenzyme activity.", "abstract": ["Plasma alkaline phosphatase isoenzyme activities were determined in patients with breast cancer to diagnose and monitor bone and liver metastases.", "Bone alkaline phosphatase activity was increased in 21 of 50 patients (42%) with radiologically confirmed bone metastases, while total alkaline phosphatase activity was increased in only 10 of 50 (20%); liver alkaline phosphatase activity was raised in 12 of 25 patients (48%) with liver metastases.", "All patients with liver metastases had bone metastases.", "Bone alkaline phosphatase activity was significantly higher in patients with symptomatic bone disease.", "Isoenzyme determination provided additional information that would have changed patient management in five of 20 patients who were monitored serially.", "Measurement of alkaline phosphatase isoenzyme activity, though less sensitive than imaging procedures, can assist in screening for, and in early detection of, a high proportion of bone and liver metastases, and can provide useful objective evidence of their response to treatment."], "structured": false}
{"doc_id": 13031967, "title": "Recommendations on how to ensure the safety and effectiveness of biosimilars in Latin America: a point of view", "abstract": ["The use of biotechnology-derived medicines has significantly increased in recent decades.", "Although biosimilars undergo rigorous characterization as well as clinical studies to document their safety and effectiveness, they are highly complex molecules and small changes in the purification and production process of a biosimilar can have major implications in its safety and effectiveness profile.", "In Latin America, regulatory authorities have begun to establish well-described and standardized pathways that permit a biosimilar to gain commercial licensure.", "In order to be certain that a biosimilar reaches its potential in ordinary clinical use, an intensive post-licensing monitoring system must be established since it is the only means to ascertain the true similarity between the original biologic and its biosimilar.", "Pharmacovigilance allows national authorities to determine a drug's performance in the marketplace.", "An effective tracking and pharmacovigilance system for biological medicines has many steps and processes.", "To aid policy makers in Latin American in addressing the many issues surrounding the establishment of an effective pharmacovigilance system, the Americas Health Foundation convened a group of experts to discuss the topic and develop recommendations for implementation.", "The group discussed current challenges and gaps in pharmacovigilance in Latin America, paying close attention to the major issues associated with traceability and pharmacovigilance of biosimilars following their approval.", "The recommendations developed should enable countries to accurately document the safety and performance of a biosimilar as experienced by patients under real-life conditions and have a significant impact on the successful implementation of pharmacovigilance of biosimilars throughout the region."], "structured": false}
{"doc_id": 13036442, "title": "Coordinated regulation of sulfur and phospholipid metabolism reflects the importance of methylation in the growth of yeast", "abstract": ["A yeast strain lacking Met4p, the primary transcriptional regulator of the sulfur assimilation pathway, cannot synthesize methionine.", "This apparently simple auxotroph did not grow well in rich media containing excess methionine, forming small colonies on yeast extract/peptone/dextrose plates.", "Faster-growing large colonies were abundant when overnight cultures were plated, suggesting that spontaneous suppressors of the growth defect arise with high frequency.", "To identify the suppressor mutations, we used genome-wide single-nucleotide polymorphism and standard genetic analyses.", "The most common suppressors were loss-of-function mutations in OPI1, encoding a transcriptional repressor of phospholipid metabolism.", "Using a new system that allows rapid and specific degradation of Met4p, we could study the dynamic expression of all genes following loss of Met4p.", "Experiments using this system with and without Opi1p showed that Met4 activates and Opi1p represses genes that maintain levels of S-adenosylmethionine (SAM), the substrate for most methyltransferase reactions.", "Cells lacking Met4p grow normally when either SAM is added to the media or one of the SAM synthetase genes is overexpressed.", "SAM is used as a methyl donor in three Opi1p-regulated reactions to create the abundant membrane phospholipid, phosphatidylcholine.", "Our results show that rapidly growing cells require significant methylation, likely for the biosynthesis of phospholipids."], "structured": false}
{"doc_id": 13042119, "title": "Glossary of reference terms for alternative test methods and their validation.", "abstract": ["This glossary was developed to provide technical references to support work in the field of the alternatives to animal testing.", "It was compiled from various existing reference documents coming from different sources and is meant to be a point of reference on alternatives to animal testing.", "Giving the ever-increasing number of alternative test methods and approaches being developed over the last decades, a combination, revision, and harmonization of earlier published collections of terms used in the validation of such methods is required.", "The need to update previous glossary efforts came from the acknowledgement that new words have emerged with the development of new approaches, while others have become obsolete, and the meaning of some terms has partially changed over time.", "With this glossary we intend to provide guidance on issues related to the validation of new or updated testing methods consistent with current approaches.", "Moreover, because of new developments and technologies, a glossary needs to be a living, constantly updated document.", "An Internet-based version based on this compilation may be found at http://altweb.jhsph.edu/, allowing the addition of new material."], "structured": false}
{"doc_id": 13048272, "title": "Combinatorial transcriptional control in blood stem/progenitor cells: genome-wide analysis of ten major transcriptional regulators.", "abstract": ["Combinatorial transcription factor (TF) interactions control cellular phenotypes and, therefore, underpin stem cell formation, maintenance, and differentiation.", "Here, we report the genome-wide binding patterns and combinatorial interactions for ten key regulators of blood stem/progenitor cells (SCL/TAL1, LYL1, LMO2, GATA2, RUNX1, MEIS1, PU.1, ERG, FLI-1, and GFI1B), thus providing the most comprehensive TF data set for any adult stem/progenitor cell type to date.", "Genome-wide computational analysis of complex binding patterns, followed by functional validation, revealed the following: first, a previously unrecognized combinatorial interaction between a heptad of TFs (SCL, LYL1, LMO2, GATA2, RUNX1, ERG, and FLI-1).", "Second, we implicate direct protein-protein interactions between four key regulators (RUNX1, GATA2, SCL, and ERG) in stabilizing complex binding to DNA.", "Third, Runx1(+/-)::Gata2(+/-) compound heterozygous mice are not viable with severe hematopoietic defects at midgestation.", "Taken together, this study demonstrates the power of genome-wide analysis in generating novel functional insights into the transcriptional control of stem and progenitor cells."], "structured": false}
{"doc_id": 13069283, "title": "Influence of CYP2D6 Polymorphisms on Serum Levels of Tamoxifen Metabolites in Spanish Women with Breast Cancer", "abstract": ["BACKGROUND Estrogen receptor-positive breast cancer tumors depend on estrogen signaling for their growth and replication and can be treated by anti-estrogen therapy with tamoxifen.", "Polymorphisms of the CYP2D6 and CYP2C19 genes are associated with an impaired response to tamoxifen.", "The study objective was to investigate the impact of genetic polymorphisms in CYP2D6 and CYP2C19 on the pharmacokinetics of tamoxifen and its metabolites in Spanish women with estrogen receptor-positive breast cancer who were candidates for tamoxifen therapy.   \n", "METHODS We studied 90 women with estrogen receptor-positive breast cancer, using the AmpliChip CYP450 test to determine CYP2D6 and CYP2C19 gene variants.", "Plasma levels of tamoxifen and its metabolites were quantified by high-performance liquid chromatography.   \n", "RESULTS The CYP2D6 phenotype was extensive metabolizer in 80%, intermediate metabolizer in 12.2%, ultra-rapid metabolizer in 2.2%, and poor metabolizer in 5.6% of patients, and the allele frequency was 35.0% for allele (*)1, 21.0% for *2, and 18.9% for *4.", "All poor metabolizers in this series were *4/*4, and their endoxifen and 4-hydroxy tamoxifen levels were 25% lower than those of extensive metabolizers.", "CYP2C19*2 allele, which has been related to breast cancer outcomes, was detected in 15.6% of the studied alleles.   \n", "CONCLUSION CYP2D6*4/*4 genotype was inversely associated with 4-hydroxy tamoxifen and endoxifen levels.", "According to these results, CYP2D6 and CYP2C19 genotyping appears advisable before the prescription of tamoxifen therapy."], "structured": true}
{"doc_id": 13070316, "title": "Role of tumor associated macrophages in tumor angiogenesis and lymphangiogenesis", "abstract": ["Tumor angiogenesis is an essential process for supplying rapidly growing malignant tissues with essential nutrients and oxygen.", "An angiogenic switch allows tumor cells to survive and grow, and provides them access to vasculature resulting in metastatic disease.", "Monocyte-derived macrophages recruited and reprogrammed by tumor cells serve as a major source of angiogenic factors boosting the angiogenic switch.", "Tumor endothelium releases angiopoietin-2 and further facilitates recruitment of TIE2 receptor expressing monocytes (TEM) into tumor sites.", "Tumor-associated macrophages (TAM) sense hypoxia in avascular areas of tumors, and react by production of angiogenic factors such as VEGFA.", "VEGFA stimulates chemotaxis of endothelial cells (EC) and macrophages.", "In some tumors, TAM appeared to be a major source of MMP9.", "Elevated expression of MMP9 by TAM mediates extracellular matrix (ECM) degradation and the release of bioactive VEGFA.", "Other angiogenic factors released by TAM include basic fibroblast growth factor (bFGF), thymidine phosphorylase (TP), urokinase-type plasminogen activator (uPA), and adrenomedullin (ADM).", "The same factors used by macrophages for the induction of angiogenesis [like vascular endothelial growth factor A (VEGF-A) and MMP9] support lymphangiogenesis.", "TAM can express LYVE-1, one of the established markers of lymphatic endothelium.", "TAM support tumor lymphangiogenesis not only by secretion of pro-lymphangiogenic factors but also by trans-differentiation into lymphatic EC.", "New pro-angiogenic factor YKL-40 belongs to a family of mammalian chitinase-like proteins (CLP) that act as cytokines or growth factors.", "Human CLP family comprises YKL-40, YKL-39, and SI-CLP.", "Production of all three CLP in macrophages is antagonistically regulated by cytokines.", "It was recently established that YKL-40 induces angiogenesis in vitro and in animal tumor models.", "YKL-40-neutralizing monoclonal antibody blocks tumor angiogenesis and progression.", "The role of YKL-39 and SI-CLP in tumor angiogenesis and lymphangiogenesis remains to be investigated."], "structured": false}
{"doc_id": 13071728, "title": "The HIV Treatment Gap: Estimates of the Financial Resources Needed versus Available for Scale-Up of Antiretroviral Therapy in 97 Countries from 2015 to 2020", "abstract": ["BACKGROUND The World Health Organization (WHO) released revised guidelines in 2015 recommending that all people living with HIV, regardless of CD4 count, initiate antiretroviral therapy (ART) upon diagnosis.", "However, few studies have projected the global resources needed for rapid scale-up of ART.", "Under the Health Policy Project, we conducted modeling analyses for 97 countries to estimate eligibility for and numbers on ART from 2015 to 2020, along with the facility-level financial resources required.", "We compared the estimated financial requirements to estimated funding available.   \n", "METHODS AND FINDINGS Current coverage levels and future need for treatment were based on country-specific epidemiological and demographic data.", "Simulated annual numbers of individuals on treatment were derived from three scenarios: (1) continuation of countries' current policies of eligibility for ART, (2) universal adoption of aspects of the WHO 2013 eligibility guidelines, and (3) expanded eligibility as per the WHO 2015 guidelines and meeting the Joint United Nations Programme on HIV/AIDS \"90-90-90\" ART targets.", "We modeled uncertainty in the annual resource requirements for antiretroviral drugs, laboratory tests, and facility-level personnel and overhead.", "We estimate that 25.7 (95% CI 25.5, 26.0) million adults and 1.57 (95% CI 1.55, 1.60) million children could receive ART by 2020 if countries maintain current eligibility plans and increase coverage based on historical rates, which may be ambitious.", "If countries uniformly adopt aspects of the WHO 2013 guidelines, 26.5 (95% CI 26.0 27.0) million adults and 1.53 (95% CI 1.52, 1.55) million children could be on ART by 2020.", "Under the 90-90-90 scenario, 30.4 (95% CI 30.1, 30.7) million adults and 1.68 (95% CI 1.63, 1.73) million children could receive treatment by 2020.", "The facility-level financial resources needed for scaling up ART in these countries from 2015 to 2020 are estimated to be US$45.8 (95% CI 45.4, 46.2) billion under the current scenario, US$48.7 (95% CI 47.8, 49.6) billion under the WHO 2013 scenario, and US$52.5 (95% CI 51.4, 53.6) billion under the 90-90-90 scenario.", "After projecting recent external and domestic funding trends, the estimated 6-y financing gap ranges from US$19.8 billion to US$25.0 billion, depending on the costing scenario and the U.S. President's Emergency Plan for AIDS Relief contribution level, with the gap for ART commodities alone ranging from US$14.0 to US$16.8 billion.", "The study is limited by excluding above-facility and other costs essential to ART service delivery and by the availability and quality of country- and region-specific data.   \n", "CONCLUSIONS The projected number of people receiving ART across three scenarios suggests that countries are unlikely to meet the 90-90-90 treatment target (81% of people living with HIV on ART by 2020) unless they adopt a test-and-offer approach and increase ART coverage.", "Our results suggest that future resource needs for ART scale-up are smaller than stated elsewhere but still significantly threaten the sustainability of the global HIV response without additional resource mobilization from domestic or innovative financing sources or efficiency gains.", "As the world moves towards adopting the WHO 2015 guidelines, advances in technology, including the introduction of lower-cost, highly effective antiretroviral regimens, whose value are assessed here, may prove to be \"game changers\" that allow more people to be on ART with the resources available."], "structured": true}
{"doc_id": 13072112, "title": "Distinction and relationship between elongation rate and processivity of RNA polymerase II in vivo.", "abstract": ["A number of proteins and drugs have been implicated in the process of transcriptional elongation by RNA polymerase (Pol) II, but the factors that govern the elongation rate (nucleotide additions per min) and processivity (nucleotide additions per initiation event) in vivo are poorly understood.", "Here, we show that a mutation in the Rpb2 subunit of Pol II reduces both the elongation rate and processivity in vivo.", "In contrast, none of the putative elongation factors tested affect the elongation rate, although mutations in the THO complex and in Spt4 significantly reduce processivity.", "The drugs 6-azauracil and mycophenolic acid reduce both the elongation rate and processivity, and this processivity defect is aggravated by mutations in Spt4, TFIIS, and CTDK-1.", "Our results suggest that, in vivo, a reduced rate of Pol II elongation leads to premature dissociation along the chromatin template and that Pol II processivity can be uncoupled from elongation rate."], "structured": false}
{"doc_id": 13072113, "title": "Neurite sprouting and synapse deterioration in the aging Caenorhabditis elegans nervous system.", "abstract": ["Caenorhabditis elegans is a powerful model for analysis of the conserved mechanisms that modulate healthy aging.", "In the aging nematode nervous system, neuronal death and/or detectable loss of processes are not readily apparent, but because dendrite restructuring and loss of synaptic integrity are hypothesized to contribute to human brain decline and dysfunction, we combined fluorescence microscopy and electron microscopy (EM) to screen at high resolution for nervous system changes.", "We report two major components of morphological change in the aging C. elegans nervous system: (1) accumulation of novel outgrowths from specific neurons, and (2) physical decline in synaptic integrity.", "Novel outgrowth phenotypes, including branching from the main dendrite or new growth from somata, appear at a high frequency in some aging neurons, but not all.", "Mitochondria are often associated with age-associated branch sites.", "Lowered insulin signaling confers some maintenance of ALM and PLM neuron structural integrity into old age, and both DAF-16/FOXO and heat shock factor transcription factor HSF-1 exert neuroprotective functions.", "hsf-1 can act cell autonomously in this capacity.", "EM evaluation in synapse-rich regions reveals a striking decline in synaptic vesicle numbers and a diminution of presynaptic density size.", "Interestingly, old animals that maintain locomotory prowess exhibit less synaptic decline than same-age decrepit animals, suggesting that synaptic integrity correlates with locomotory healthspan.", "Our data reveal similarities between the aging C. elegans nervous system and mammalian brain, suggesting conserved neuronal responses to age.", "Dissection of neuronal aging mechanisms in C. elegans may thus influence the development of brain healthspan-extending therapies."], "structured": false}
{"doc_id": 13083189, "title": "Determinants of adolescent physical activity and inactivity patterns.", "abstract": ["OBJECTIVES Despite recognition of the important influence of environmental determinants on physical activity patterns, minimal empirical research has been done to assess the impact of environmental/contextual determinants of physical activity.", "This article aims to investigate environmental and sociodemographic determinants of physical activity and inactivity patterns among subpopulations of US adolescents.", "We define environmental determinants as modifiable factors in the physical environment that impose a direct influence on the opportunity to engage in physical activity.", "The present research examines environmental and sociodemographic determinants of physical activity and inactivity with the implication that these findings can point toward societal-level intervention strategies for increasing physical activity and decreasing inactivity among adolescents.   ", "STUDY DESIGN AND METHODOLOGY The study population consists of nationally representative data from the 1996 National Longitudinal Study of Adolescent Health on 17 766 US adolescents enrolled in US middle and high schools (including 3933 non-Hispanic blacks, 3148 Hispanics, and 1337 Asians).", "Hours/week of inactivity (TV/video viewing and video/computer games) and times/week of moderate to vigorous physical activity were collected by questionnaire.", "Outcome variables were moderate to vigorous physical activity and inactivity, which were broken into categories (physical activity: 0-2 times/week, 3-4 times/week, and >/=5 times/week; inactivity: 0-10 hours/week, 11-24 hours/week, and >/=25 hours/week).", "Sociodemographic and environmental correlates of physical activity and inactivity were used as exposure and control variables and included sex, age, urban residence, participation in school physical education program, use of community recreation center, total reported incidents of serious crime in neighborhood, socioeconomic status, ethnicity, generation of residence in the United States, presence of mother/father in household, pregnancy status, work status, in-school status, region, and month of interview.", "Logistic regression models of high versus low and medium physical activity and inactivity were used to investigate sex and ethnic interactions in relation to environmental and sociodemographic factors to examine evidence for the potential impact of physical education and recreation programs and sociodemographic factors on physical activity and inactivity patterns.   \n", "RESULTS Moderate to vigorous physical activity was lower and inactivity higher for non-Hispanic black and Hispanic adolescents.", "Participation in school physical education programs was considerably low for these adolescents and decreased with age.", "Participation in daily school physical education (PE) program classes (adjusted odds ratio [AOR]: 2.21; confidence interval [CI]: 1.82-2.68) and use of a community recreation center (AOR: 1.75; CI: 1.56-1.96) were associated with an increased likelihood of engaging in high level moderate to vigorous physical activity.", "Maternal education was inversely associated with high inactivity patterns; for example, having a mother with a graduate or professional degree was associated with an AOR of.61 (CI:.48-.76) for high inactivity.", "High family income was associated with increased moderate to vigorous physical activity (AOR: 1.43; CI: 1.22-1.67) and decreased inactivity (AOR:.70; CI:.59-.82).", "High neighborhood serious crime level was associated with a decreased likelihood of falling in the highest category of moderate to vigorous physical activity (AOR:.77; CI:.66-.91).   \n", "CONCLUSIONS These results show important associations between modifiable environmental factors, such as participation in school PE and community recreation programs, with activity patterns of adolescents.", "Despite the marked and significant impact of participation in school PE programs on physical activity patterns of US adolescents, few adolescents participated in such school PE programs; only 21.3% of all adolescents"], "structured": true}
{"doc_id": 13097856, "title": "Suicide prevention strategies: a systematic review.", "abstract": ["CONTEXT In 2002, an estimated 877,000 lives were lost worldwide through suicide.", "Some developed nations have implemented national suicide prevention plans.", "Although these plans generally propose multiple interventions, their effectiveness is rarely evaluated.   \n", "OBJECTIVES To examine evidence for the effectiveness of specific suicide-preventive interventions and to make recommendations for future prevention programs and research.   \n", "DATA SOURCES AND STUDY SELECTION Relevant publications were identified via electronic searches of MEDLINE, the Cochrane Library, and PsychINFO databases using multiple search terms related to suicide prevention.", "Studies, published between 1966 and June 2005, included those that evaluated preventative interventions in major domains; education and awareness for the general public and for professionals; screening tools for at-risk individuals; treatment of psychiatric disorders; restricting access to lethal means; and responsible media reporting of suicide.   \n", "DATA EXTRACTION Data were extracted on primary outcomes of interest: suicidal behavior (completion, attempt, ideation), intermediary or secondary outcomes (treatment seeking, identification of at-risk individuals, antidepressant prescription/use rates, referrals), or both.", "Experts from 15 countries reviewed all studies.", "Included articles were those that reported on completed and attempted suicide and suicidal ideation; or, where applicable, intermediate outcomes, including help-seeking behavior, identification of at-risk individuals, entry into treatment, and antidepressant prescription rates.", "We included 3 major types of studies for which the research question was clearly defined: systematic reviews and meta-analyses (n = 10); quantitative studies, either randomized controlled trials (n = 18) or cohort studies (n = 24); and ecological, or population- based studies (n = 41).", "Heterogeneity of study populations and methodology did not permit formal meta-analysis; thus, a narrative synthesis is presented.   \n", "DATA SYNTHESIS Education of physicians and restricting access to lethal means were found to prevent suicide.", "Other methods including public education, screening programs, and media education need more testing.   \n", "CONCLUSIONS Physician education in depression recognition and treatment and restricting access to lethal methods reduce suicide rates.", "Other interventions need more evidence of efficacy.", "Ascertaining which components of suicide prevention programs are effective in reducing rates of suicide and suicide attempt is essential in order to optimize use of limited resources."], "structured": true}
{"doc_id": 13106686, "title": "Oxidative damage of DNA confers resistance to cytosolic nuclease TREX1 degradation and potentiates STING-dependent immune sensing.", "abstract": ["Immune sensing of DNA is critical for antiviral immunity but can also trigger autoimmune diseases such as lupus erythematosus (LE).", "Here we have provided evidence for the involvement of a damage-associated DNA modification in the detection of cytosolic DNA.", "The oxidized base 8-hydroxyguanosine (8-OHG), a marker of oxidative damage in DNA, potentiated cytosolic immune recognition by decreasing its susceptibility to 3' repair exonuclease 1 (TREX1)-mediated degradation.", "Oxidizative modifications arose physiologically in pathogen DNA during lysosomal reactive oxygen species (ROS) exposure, as well as in neutrophil extracellular trap (NET) DNA during the oxidative burst.", "8-OHG was also abundant in UV-exposed skin lesions of LE patients and colocalized with type I interferon (IFN).", "Injection of oxidized DNA in the skin of lupus-prone mice induced lesions that closely matched respective lesions in patients.", "Thus, oxidized DNA represents a prototypic damage-associated molecular pattern (DAMP) with important implications for infection, sterile inflammation, and autoimmunity."], "structured": false}
{"doc_id": 13108582, "title": "IL-18 induction of osteopontin mediates cardiac fibrosis and diastolic dysfunction in mice.", "abstract": ["Osteopontin (OPN), a key component of the extracellular matrix, is associated with the fibrotic process during tissue remodeling.", "OPN and the cytokine interleukin (IL)-18 have been shown to be overexpressed in an array of human cardiac pathologies.", "In the present study, we determined the role of IL-18 in the regulation of cardiac OPN expression and the subsequent interstitial fibrosis and diastolic dysfunction.", "We demonstrated parallel increases in IL-18, OPN expression, and interstitial fibrosis in murine models of left ventricular pressure and volume overload.", "Exogenous recombinant (r)IL-18 administered for 2 wk increased cardiac OPN expression, interstitial fibrosis, and diastolic dysfunction.", "Stimulation of the T helper (Th)1 lymphocyte phenotype with a selective toll-like receptor (TLR)9 agonist induced cardiac IL-18 and OPN expression, which was associated with increased cardiac fibrillar collagen concentrations and interstitial fibrosis resulting in diastolic dysfunction.", "rIL-18 induced OPN expression and protein levels in primary of cardiac fibroblast cultures.", "Conditioned media from TLR9-stimulated T lymphocyte cultures induced IL-18 and OPN expression in cardiac fibroblasts, while blockade of the IL-18 receptor with a neutralizing antibody abolished the increase in OPN expression.", "Furthermore, a mutation in the transcriptional factor interferon regulatory factor (IRF)1 or IRF1 small interfering RNA (siRNA) resulted in the decreased expression of IL-18 and OPN in cardiac fibroblasts.", "With pressure overload, IRF1-mutant mice showed downregulation of IL-18 and OPN expression in cardiac tissue, reduced cardiac fibrotic development, and increased left ventricular function compared with wild type.", "These results provide direct evidence that the induction of IL-18 regulates OPN-mediated cardiac fibrosis and diastolic dysfunction."], "structured": false}
{"doc_id": 13116880, "title": "Hematopoietic stem cell: self-renewal versus differentiation.", "abstract": ["The mammalian blood system, containing more than 10 distinct mature cell types, stands on one specific cell type, hematopoietic stem cell (HSC).", "Within the system, only HSCs possess the ability of both multipotency and self-renewal.", "Multipotency is the ability to differentiate into all functional blood cells.", "Self-renewal is the ability to give rise to HSC itself without differentiation.", "Since mature blood cells (MBCs) are predominantly short-lived, HSCs continuously provide more differentiated progenitors while properly maintaining the HSC pool size throughout life by precisely balancing self-renewal and differentiation.", "Thus, understanding the mechanisms of self-renewal and differentiation of HSC has been a central issue.", "In this review, we focus on the hierarchical structure of the hematopoietic system, the current understanding of microenvironment and molecular cues regulating self-renewal and differentiation of adult HSCs, and the currently emerging systems approaches to understand HSC biology."], "structured": false}
{"doc_id": 13123189, "title": "RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome", "abstract": ["BACKGROUND RNA-Seq is revolutionizing the way transcript abundances are measured.", "A key challenge in transcript quantification from RNA-Seq data is the handling of reads that map to multiple genes or isoforms.", "This issue is particularly important for quantification with de novo transcriptome assemblies in the absence of sequenced genomes, as it is difficult to determine which transcripts are isoforms of the same gene.", "A second significant issue is the design of RNA-Seq experiments, in terms of the number of reads, read length, and whether reads come from one or both ends of cDNA fragments.   \n", "RESULTS We present RSEM, an user-friendly software package for quantifying gene and isoform abundances from single-end or paired-end RNA-Seq data.", "RSEM outputs abundance estimates, 95% credibility intervals, and visualization files and can also simulate RNA-Seq data.", "In contrast to other existing tools, the software does not require a reference genome.", "Thus, in combination with a de novo transcriptome assembler, RSEM enables accurate transcript quantification for species without sequenced genomes.", "On simulated and real data sets, RSEM has superior or comparable performance to quantification methods that rely on a reference genome.", "Taking advantage of RSEM's ability to effectively use ambiguously-mapping reads, we show that accurate gene-level abundance estimates are best obtained with large numbers of short single-end reads.", "On the other hand, estimates of the relative frequencies of isoforms within single genes may be improved through the use of paired-end reads, depending on the number of possible splice forms for each gene.   \n", "CONCLUSIONS RSEM is an accurate and user-friendly software tool for quantifying transcript abundances from RNA-Seq data.", "As it does not rely on the existence of a reference genome, it is particularly useful for quantification with de novo transcriptome assemblies.", "In addition, RSEM has enabled valuable guidance for cost-efficient design of quantification experiments with RNA-Seq, which is currently relatively expensive."], "structured": true}
{"doc_id": 13135544, "title": "A synthetic Escherichia coli predator\u2013prey ecosystem", "abstract": ["We have constructed a synthetic ecosystem consisting of two Escherichia coli populations, which communicate bi-directionally through quorum sensing and regulate each other's gene expression and survival via engineered gene circuits.", "Our synthetic ecosystem resembles canonical predator-prey systems in terms of logic and dynamics.", "The predator cells kill the prey by inducing expression of a killer protein in the prey, while the prey rescue the predators by eliciting expression of an antidote protein in the predator.", "Extinction, coexistence and oscillatory dynamics of the predator and prey populations are possible depending on the operating conditions as experimentally validated by long-term culturing of the system in microchemostats.", "A simple mathematical model is developed to capture these system dynamics.", "Coherent interplay between experiments and mathematical analysis enables exploration of the dynamics of interacting populations in a predictable manner."], "structured": false}
{"doc_id": 13162391, "title": "Funnel trap for the capture of phlebotomine sand flies (Diptera: Psychodidae) from tree holes.", "abstract": ["A funnel trap that fitted over holes leading into hollow trees was used to capture adult phlebotomine sand flies, Lutzomyia shannoni Dyar, on Ossabaw Island, Chatham County, Ga. These insects rested in hollow trees during the day and were collected by funnel traps as they egressed from the tree holes at night.", "The trap is lightweight, durable, inexpensive, waterproof, and selective.", "Using this trap, greater than 100 healthy L. shannoni ++were captured per night by a single investigator during July and August 1988 when adult flies were abundant on the island."], "structured": false}
{"doc_id": 13172737, "title": "Cystine/glutamate exchange regulates metabotropic glutamate receptor presynaptic inhibition of excitatory transmission and vulnerability to cocaine seeking.", "abstract": ["Withdrawal from chronic cocaine reduces extracellular glutamate levels in the nucleus accumbens by decreasing cystine/glutamate exchange (xc-).", "Activating xc- with N-acetylcysteine restores extracellular glutamate and prevents cocaine-induced drug seeking.", "It was hypothesized that the activation of xc- prevents drug seeking by increasing glutamatergic tone on presynaptic group II metabotropic glutamate receptors (mGluR2/3) and thereby inhibiting excitatory transmission.", "In the first experiment, the capacity of glutamate derived from xc- to regulate excitatory transmission via mGluR2/3 was determined.", "Physiological levels of cystine (100-300 nm) were restored to acute tissue slices from the nucleus accumbens or prefrontal cortex.", "Cystine increased glutamate efflux and decreased miniature EPSC (mEPSC) and spontaneous EPSC (sEPSC) frequency as well as evoked EPSC amplitude.", "These effects of cystine were presynaptic, because there was no change in mEPSC or sEPSC amplitude, and an increase in the evoked EPSC paired-pulse facilitation ratio.", "The cystine-induced reduction in EPSCs was reversed by blocking either xc- or mGluR2/3.", "In the second experiment, blocking mGluR2/3 prevented the ability of N-acetylcystine to inhibit the reinstatement of drug seeking in rats trained to self-administer cocaine.", "These data demonstrate that nonsynaptic glutamate derived from xc- modulates synaptic glutamate release and thereby regulates cocaine-induced drug seeking."], "structured": false}
{"doc_id": 13179318, "title": "Survival analysis: time-dependent effects and time-varying risk factors.", "abstract": ["In traditional Kaplan-Meier or Cox regression analysis, usually a risk factor measured at baseline is related to mortality thereafter.", "During follow-up, however, things may change: either the effect of a fixed baseline risk factor may vary over time, resulting in a weakening or strengthening of associations over time, or the risk factor itself may vary over time.", "In this paper, short-term versus long-term effects (so-called time-dependent effects) of a fixed baseline risk factor are addressed.", "An example is presented showing that underweight is a strong risk factor for mortality in dialysis patients, especially in the short run.", "In contrast, overweight is a risk factor for mortality, which is stronger in the long run than in the short run.", "In addition, the analysis of how time-varying risk factors (so-called time-dependent risk factors) are related to mortality is demonstrated by paying attention to the pitfall of adjusting for sequelae.", "The proper analysis of effects over time should be driven by a clear research question.", "Both kinds of research questions, that is those of time-dependent effects as well those of time-dependent risk factors, can be analyzed with time-dependent Cox regression analysis.", "It will be shown that using time-dependent risk factors usually implies focusing on short-term effects only."], "structured": false}
{"doc_id": 13189693, "title": "Control of interneuron dendritic growth through NRG1/erbB4-mediated kalirin-7 disinhibition", "abstract": ["Neuregulin 1 (NRG1) is a secreted trophic factor that activates the postsynaptic erbB4 receptor tyrosine kinase.", "Both NRG1 and erbB4 have been repeatedly associated with schizophrenia, but their downstream targets are not well characterized.", "ErbB4 is highly abundant in interneurons, and NRG1-mediated erbB4 activation has been shown to modulate interneuron function, but the role for NRG1-erbB4 signaling in regulating interneuron dendritic growth is not well understood.", "Here we show that NRG1/erbB4 promote the growth of dendrites in mature interneurons through kalirin, a major dendritic Rac1-GEF.", "Recent studies have shown associations of the KALRN gene with schizophrenia.", "Our data point to an essential role of phosphorylation in kalirin-7's C terminus as the critical site for these effects.", "As reduced interneuron dendrite length occurs in schizophrenia, understanding how NRG1-erbB4 signaling modulates interneuron dendritic morphogenesis might shed light on disease-related alterations in cortical circuits."], "structured": false}
{"doc_id": 13205096, "title": "Use of gene-expression profiling to identify prognostic subclasses in adult acute myeloid leukemia.", "abstract": ["BACKGROUND In patients with acute myeloid leukemia (AML), the presence or absence of recurrent cytogenetic aberrations is used to identify the appropriate therapy.", "However, the current classification system does not fully reflect the molecular heterogeneity of the disease, and treatment stratification is difficult, especially for patients with intermediate-risk AML with a normal karyotype.   \n", "METHODS We used complementary-DNA microarrays to determine the levels of gene expression in peripheral-blood samples or bone marrow samples from 116 adults with AML (including 45 with a normal karyotype).", "We used unsupervised hierarchical clustering analysis to identify molecular subgroups with distinct gene-expression signatures.", "Using a training set of samples from 59 patients, we applied a novel supervised learning algorithm to devise a gene-expression-based clinical-outcome predictor, which we then tested using an independent validation group comprising the 57 remaining patients.   \n", "RESULTS Unsupervised analysis identified new molecular subtypes of AML, including two prognostically relevant subgroups in AML with a normal karyotype.", "Using the supervised learning algorithm, we constructed an optimal 133-gene clinical-outcome predictor, which accurately predicted overall survival among patients in the independent validation group (P=0.006), including the subgroup of patients with AML with a normal karyotype (P=0.046).", "In multivariate analysis, the gene-expression predictor was a strong independent prognostic factor (odds ratio, 8.8; 95 percent confidence interval, 2.6 to 29.3; P<0.001).   \n", "CONCLUSIONS The use of gene-expression profiling improves the molecular classification of adult AML."], "structured": true}
{"doc_id": 13205803, "title": "Perspectives on public health workforce research.", "abstract": ["The Centers for Disease Control and Prevention Office of Workforce and Career Development is committed to developing a competent, sustainable, and diverse public health workforce through evidence-based training, career and leadership development, and strategic workforce planning to improve population health outcomes.", "This article reviews the previous efforts in identifying priorities of public health workforce research, which are summarized as eight major research themes.", "We outline a strategic framework for public health workforce research that includes six functional areas (ie, definition and standards, data, methodology, evaluation, policy, and dissemination and translation).", "To conceptualize and prioritize development of an actionable public health research agenda, we constructed a matrix of key challenges in workforce analysis by public health workforce categories.", "Extensive reviews were conducted to identify valuable methods, models, and approaches to public health workforce research.", "We explore new tools and approaches for addressing priority areas for public health workforce and career development research and assess how tools from multiple disciplines of social sciences can guide the development of a research framework for advancing public health workforce research and policy."], "structured": false}
{"doc_id": 13221399, "title": "Gene targeting using zinc finger nucleases", "abstract": ["The ability to achieve site-specific manipulation of the mammalian genome has widespread implications for basic and applied research.", "Gene targeting is a process in which a DNA molecule introduced into a cell replaces the corresponding chromosomal segment by homologous recombination, and thus presents a precise way to manipulate the genome.", "In the past, the application of gene targeting to mammalian cells has been limited by its low efficiency.", "Zinc finger nucleases (ZFNs) show promise in improving the efficiency of gene targeting by introducing DNA double-strand breaks in target genes, which then stimulate the cell's endogenous homologous recombination machinery.", "Recent results have shown that ZFNs can be used to create targeting frequencies of up to 20% in a human disease-causing gene.", "Future work will be needed to translate these in vitro findings to in vivo applications and to determine whether zinc finger nucleases create undesired genomic instability."], "structured": false}
{"doc_id": 13223806, "title": "relative expression results in real-time", "abstract": ["Real-time reverse transcription followed by polymerase chain reaction (RT-PCR) is the most suitable method for the detection and quantification of mRNA.", "It offers high sensitivity, good reproducibility and a wide quantification range.", "Today, relative expression is increasingly used, where the expression of a target gene is standardised by a non-regulated reference gene.", "Several mathematical algorithms have been developed to compute an expression ratio, based on real-time PCR efficiency and the crossing point deviation of an unknown sample versus a control.", "But all published equations and available models for the calculation of relative expression ratio allow only for the determination of a single transcription difference between one control and one sample.", "Therefore a new software tool was established, named REST (relative expression software tool), which compares two groups, with up to 16 data points in a sample and 16 in a control group, for reference and up to four target genes.", "The mathematical model used is based on the PCR efficiencies and the mean crossing point deviation between the sample and control group.", "Subsequently, the expression ratio results of the four investigated transcripts are tested for significance by a randomisation test.", "Herein, development and application of REST is explained and the usefulness of relative expression in real-time PCR using REST is discussed.", "The latest software version of REST and examples for the correct use can be downloaded at http://www.wzw.tum.de/gene-quantification/."], "structured": false}
{"doc_id": 13223957, "title": "Pain attacks in non-complicated and complicated gallstone disease have a characteristic pattern and are accompanied by dyspepsia in most patients: the results of a prospective study.", "abstract": ["OBJECTIVE The cardinal indication for surgical treatment of gallstones is pain attacks.", "However, following cholecystectomy, 20% of patients remain symptomatic.", "It is unclear to what extent post-cholecystectomy symptoms can be ascribed to persistence of preoperative symptoms or to new pathology.", "The pain and digestive pattern in gallstone patients has not been defined in a recent setting with ultrasonography as the diagnostic method.", "The aim of this study was to characterize a pain pattern that is typical for gallstone disease and to describe the extent of associated dyspepsia.   ", "MATERIAL AND METHODS A total of 220 patients with symptomatic gallstone disease including complicated disease (acute cholecystitis and common bile duct stones) were interviewed using detailed questionnaires to disclose pain patterns and symptoms of indigestion.   \n", "RESULTS All patients had pain in the right upper quadrant (RUQ) including the upper midline epigastrium.", "The pain was localized to the right subcostal area in 20% and to the upper epigastrium in 14%, and in the rest (66%) it was more evenly distributed.", "An area of maximal pain could be defined in 90%.", "Maximal pain was located under the costal arch in 51% of patients and in the epigastrium in 41%, but in 3% behind the sternum and in 5% in the back.", "The pain was referred to the back in 63% of the patients.", "The mean visual analogue scale (VAS) score was very high: 90 mm on a 0-100 scale.", "A pattern of incipient or low-grade warning pain with a subsequent relatively steady state until subsiding in the same fashion was present in 90% of the patients.", "An urge to walk around was experienced by 71%.", "Pain attacks usually occurred in the late evening or at night (77%), with 85% of the attacks lasting for more than one hour and almost never less than half an hour.", "Sixty-six percent of the patients were intolerant to at least one kind of food, but only 48% to fatty foods.", "Symptoms of functional indigestion (gastroesophageal reflux, dyspepsia or irritable bowel symptoms) were seen in the vast majority in association with attacks.   \n", "CONCLUSIONS Gallstone-associated pain follows a certain pattern in the majority of patients.", "The pain is located in a defined area with a point of maximum intensity, is usually referred, and occurs mainly at night with duration of more than one hour.", "The majority of patients experience functional indigestion, mainly of the reflux type or dyspepsia."], "structured": true}
{"doc_id": 13230773, "title": "Prevalence and cardiovascular disease correlates of low cardiorespiratory fitness in adolescents and adults.", "abstract": ["CONTEXT Population surveys indicate that physical activity levels are low in the United States.", "One consequence of inactivity, low cardiorespiratory fitness, is an established risk factor for cardiovascular disease (CVD) morbidity and mortality, but the prevalence of cardiorespiratory fitness has not been quantified in representative US population samples.   \n", "OBJECTIVES To describe the prevalence of low fitness in the US population aged 12 through 49 years and to relate low fitness to CVD risk factors in this population.   \n", "DESIGN, SETTING, AND PARTICIPANTS Inception cohort study using data from the cross-sectional nationally representative National Health and Nutrition Examination Survey 1999-2002.", "Participants were adolescents (aged 12-19 years; n = 3110) and adults (aged 20-49 years; n = 2205) free from previously diagnosed CVD who underwent submaximal graded exercise treadmill testing to achieve at least 75% to 90% of their age-predicted maximum heart rate.", "Maximal oxygen consumption (VO2max) was estimated by measuring the heart rate response to reference levels of submaximal work.   \n", "MAIN OUTCOME MEASURES Low fitness defined using percentile cut points of estimated VO2max from existing external referent populations; anthropometric and other CVD risk factors measured according to standard methods.   \n", "RESULTS Low fitness was identified in 33.6% of adolescents (approximately 7.5 million US adolescents) and 13.9% of adults (approximately 8.5 million US adults); the prevalence was similar in adolescent females (34.4%) and males (32.9%) (P = .40) but was higher in adult females (16.2%) than in males (11.8%) (P = .03).", "Non-Hispanic blacks and Mexican Americans were less fit than non-Hispanic whites.", "In all age-sex groups, body mass index and waist circumference were inversely associated with fitness; age- and race-adjusted odds ratios of overweight or obesity (body mass index > or =25) ranged from 2.1 to 3.7 (P<.01 for all), comparing persons with low fitness with those with moderate or high fitness.", "Total cholesterol levels and systolic blood pressure were higher and levels of high-density lipoprotein cholesterol were lower among participants with low vs high fitness.   \n", "CONCLUSION Low fitness in adolescents and adults is common in the US population and is associated with an increased prevalence of CVD risk factors."], "structured": true}
{"doc_id": 13231899, "title": "In situ regulation of DC subsets and T cells mediates tumor regression in mice.", "abstract": ["Vaccines are largely ineffective for patients with established cancer, as advanced disease requires potent and sustained activation of CD8(+) cytotoxic T lymphocytes (CTLs) to kill tumor cells and clear the disease.", "Recent studies have found that subsets of dendritic cells (DCs) specialize in antigen cross-presentation and in the production of cytokines, which regulate both CTLs and T regulatory (Treg) cells that shut down effector T cell responses.", "Here, we addressed the hypothesis that coordinated regulation of a DC network, and plasmacytoid DCs (pDCs) and CD8(+) DCs in particular, could enhance host immunity in mice.", "We used functionalized biomaterials incorporating various combinations of an inflammatory cytokine, immune danger signal, and tumor lysates to control the activation and localization of host DC populations in situ.", "The numbers of pDCs and CD8(+) DCs, and the endogenous production of interleukin-12, all correlated strongly with the magnitude of protective antitumor immunity and the generation of potent CD8(+) CTLs.", "Vaccination by this method maintained local and systemic CTL responses for extended periods while inhibiting FoxP3 Treg activity during antigen clearance, resulting in complete regression of distant and established melanoma tumors.", "The efficacy of this vaccine as a monotherapy against large invasive tumors may be a result of the local activity of pDCs and CD8(+) DCs induced by persistent danger and antigen signaling at the vaccine site.", "These results indicate that a critical pattern of DC subsets correlates with the evolution of therapeutic antitumor responses and provide a template for future vaccine design."], "structured": false}
{"doc_id": 13235609, "title": "VEGF inhibits tumor cell invasion and mesenchymal transition through a MET/VEGFR2 complex.", "abstract": ["Inhibition of VEGF signaling leads to a proinvasive phenotype in mouse models of glioblastoma multiforme (GBM) and in a subset of GBM patients treated with bevacizumab.", "Here, we demonstrate that vascular endothelial growth factor (VEGF) directly and negatively regulates tumor cell invasion through enhanced recruitment of the protein tyrosine phosphatase 1B (PTP1B) to a MET/VEGFR2 heterocomplex, thereby suppressing HGF-dependent MET phosphorylation and tumor cell migration.", "Consequently, VEGF blockade restores and increases MET activity in GBM cells in a hypoxia-independent manner, while inducing a program reminiscent of epithelial-to-mesenchymal transition highlighted by a T-cadherin to N-cadherin switch and enhanced mesenchymal features.", "Inhibition of MET in GBM mouse models blocks mesenchymal transition and invasion provoked by VEGF ablation, resulting in substantial survival benefit."], "structured": false}
{"doc_id": 13242763, "title": "Interaction between Oct3/4 and Cdx2 Determines Trophectoderm Differentiation", "abstract": ["Trophectoderm (TE), the first differentiated cell lineage of mammalian embryogenesis, forms the placenta, a structure unique to mammalian development.", "The differentiation of TE is a hallmark event in early mammalian development, but molecular mechanisms underlying this first differentiation event remain obscure.", "Embryonic stem (ES) cells can be induced to differentiate into the TE lineage by forced repression of the POU-family transcription factor, Oct3/4.", "We show here that this event can be mimicked by overexpression of Caudal-related homeobox 2 (Cdx2), which is sufficient to generate proper trophoblast stem (TS) cells.", "Cdx2 is dispensable for trophectoderm differentiation induced by Oct3/4 repression but essential for TS cell self-renewal.", "In preimplantation embryos, Cdx2 is initially coexpressed with Oct3/4 and they form a complex for the reciprocal repression of their target genes in ES cells.", "This suggests that reciprocal inhibition between lineage-specific transcription factors might be involved in the first differentiation event of mammalian development."], "structured": false}
{"doc_id": 13244602, "title": "SSEA-1 is an enrichment marker for tumor-initiating cells in human glioblastoma.", "abstract": ["CD133+ populations of human glioblastoma multiforme (GBM) cells are reportedly enriched for tumor stem cells (TSCs) or tumor-initiating cells (TICs).", "Approximately 40% of freshly isolated GBM specimens, however, do not contain CD133+ tumor cells, raising the possibility that CD133 may not be a universal enrichment marker for GBM TSCs/TICs.", "Here we demonstrate that stage-specific embryonic antigen 1(SSEA-1/LeX)+ GBM cells fulfill the functional criteria for TSC/TIC, since (1) SSEA-1+ cells are highly tumorigenic in vivo, unlike SSEA-1- cells; (2) SSEA-1+ cells can give rise to both SSEA-1+ and SSEA-1- cells, thereby establishing a cellular hierarchy; and (3) SSEA-1+ cells have self-renewal and multilineage differentiation potentials.", "A distinct subpopulation of SSEA-1+ cells was present in all but one of the primary GBMs examined (n = 24), and most CD133+ tumor cells were also SSEA-1+, suggesting that SSEA-1 may be a general TSC/TIC enrichment marker in human GBMs."], "structured": false}
{"doc_id": 13245542, "title": "Temporal regulation of topoisomerase IV activity in E. coli.", "abstract": ["We isolated a mutant allele of dnaX, encoding the tau and gamma subunits of the DNA polymerase III holoenzyme, that causes extreme cell filamentation but does not affect either cell growth or DNA replication.", "This phenotype results from a defect in daughter chromosome decatenation during rapid growth.", "In these cells, ParC, one subunit of topoisomerase IV, no longer associated with the replication factory, as occurs in wild-type cells, and was instead distributed uniformly on the nucleoid; the distribution of ParE, the other subunit of topoisomerase IV, was unaffected.", "In addition, the majority of topoisomerase IV activity in synchronized cell populations was restricted to late in the cell cycle, when replication was essentially complete.", "These observations suggest that topoisomerase IV activity in vivo might be dependent on release of ParC from the replication factory."], "structured": false}
{"doc_id": 13256155, "title": "Molecularly targeted therapy based on tumour molecular profiling versus conventional therapy for advanced cancer (SHIVA): a multicentre, open-label, proof-of-concept, randomised, controlled phase 2 trial.", "abstract": ["BACKGROUND Molecularly targeted agents have been reported to have anti-tumour activity for patients whose tumours harbour the matching molecular alteration.", "These results have led to increased off-label use of molecularly targeted agents on the basis of identified molecular alterations.", "We assessed the efficacy of several molecularly targeted agents marketed in France, which were chosen on the basis of tumour molecular profiling but used outside their indications, in patients with advanced cancer for whom standard-of-care therapy had failed.   \n", "METHODS The open-label, randomised, controlled phase 2 SHIVA trial was done at eight French academic centres.", "We included adult patients with any kind of metastatic solid tumour refractory to standard of care, provided they had an Eastern Cooperative Oncology Group performance status of 0 or 1, disease that was accessible for a biopsy or resection of a metastatic site, and at least one measurable lesion.", "The molecular profile of each patient's tumour was established with a mandatory biopsy of a metastatic tumour and large-scale genomic testing.", "We only included patients for whom a molecular alteration was identified within one of three molecular pathways (hormone receptor, PI3K/AKT/mTOR, RAF/MEK), which could be matched to one of ten regimens including 11 available molecularly targeted agents (erlotinib, lapatinib plus trastuzumab, sorafenib, imatinib, dasatinib, vemurafenib, everolimus, abiraterone, letrozole, tamoxifen).", "We randomly assigned these patients (1:1) to receive a matched molecularly targeted agent (experimental group) or treatment at physician's choice (control group) by central block randomisation (blocks of size six).", "Randomisation was done centrally with a web-based response system and was stratified according to the Royal Marsden Hospital prognostic score (0 or 1 vs 2 or 3) and the altered molecular pathway.", "Clinicians and patients were not masked to treatment allocation.", "Treatments in both groups were given in accordance with the approved product information and standard practice protocols at each institution and were continued until evidence of disease progression.", "The primary endpoint was progression-free survival in the intention-to-treat population, which was not assessed by independent central review.", "We assessed safety in any patients who received at least one dose of their assigned treatment.", "This trial is registered with ClinicalTrials.gov, number NCT01771458.   \n", "FINDINGS Between Oct 4, 2012, and July 11, 2014, we screened 741 patients with any tumour type.", "293 (40%) patients had at least one molecular alteration matching one of the 10 available regimens.", "At the time of data cutoff, Jan 20, 2015, 195 (26%) patients had been randomly assigned, with 99 in the experimental group and 96 in the control group.", "All patients in the experimental group started treatment, as did 92 in the control group.", "Two patients in the control group received a molecularly targeted agent: both were included in their assigned group for efficacy analyses, the patient who received an agent that was allowed in the experimental group was included in the experimental group for the purposes of safety analyses, while the other patient, who received a molecularly targeted agent and chemotherapy, was kept in the control group for safety analyses.", "Median follow-up was 11\u00b73 months (IQR 5\u00b78-11\u00b76) in the experimental group and 11\u00b73 months (8\u00b71-11\u00b76) in the control group at the time of the primary analysis of progression-free survival.", "Median progression-free survival was 2\u00b73 months (95% CI 1\u00b77-3\u00b78) in the experimental group versus 2\u00b70 months (1\u00b78-2\u00b71) in the control group (hazard ratio 0\u00b788, 95% CI 0\u00b765-1\u00b719, p=0\u00b741).", "In the safety population, 43 (43%) of 100 patients treated with a molecularly targeted agent and 32 (35%) of 91 patients treated with cytotoxic chemotherapy had grade 3-4 adverse events (p=0\u00b730).   \n", "INTERPRETATION The use of molecularly targeted agents outside their indications does not improve progression-free survival compared with treatment at physician's choice in heavily pretreated patients with cancer.", "Off-label use of molecularly targeted agents should be discouraged, but enrolment in clinical trials should be encouraged to assess predictive biomarkers of efficacy."], "structured": true}
{"doc_id": 13277039, "title": "CRTC2 (TORC2) contributes to the transcriptional response to fasting in the liver but is not required for the maintenance of glucose homeostasis.", "abstract": ["The liver contributes to glucose homeostasis by promoting either storage or production of glucose, depending on the physiological state.", "The cAMP response element-binding protein (CREB) is a principal regulator of genes involved in coordinating the hepatic response to fasting, but its mechanism of gene activation remains controversial.", "We derived CRTC2 (CREB-regulated transcription coactivator 2, previously TORC2)-deficient mice to assess the contribution of this cofactor to hepatic glucose metabolism in vivo.", "CRTC2 mutant hepatocytes showed reduced glucose production in response to glucagon, which correlated with decreased CREB binding to several gluconeogenic genes.", "However, despite attenuated expression of CREB target genes, including PEPCK, G6Pase, and PGC-1alpha, no hypoglycemia was observed in mutant mice.", "Collectively, these results provide genetic evidence supporting a role for CRTC2 in the transcriptional response to fasting, but indicate only a limited contribution of this cofactor to the maintenance of glucose homeostasis."], "structured": false}
{"doc_id": 13277118, "title": "Ancient Hybridization and an Irish Origin for the Modern Polar Bear Matriline", "abstract": ["BACKGROUND Polar bears (Ursus maritimus) are among those species most susceptible to the rapidly changing arctic climate, and their survival is of global concern.", "Despite this, little is known about polar bear species history.", "Future conservation strategies would significantly benefit from an understanding of basic evolutionary information, such as the timing and conditions of their initial divergence from brown bears (U. arctos) or their response to previous environmental change.   \n", "RESULTS We used a spatially explicit phylogeographic model to estimate the dynamics of 242 brown bear and polar bear matrilines sampled throughout the last 120,000 years and across their present and past geographic ranges.", "Our results show that the present distribution of these matrilines was shaped by a combination of regional stability and rapid, long-distance dispersal from ice-age refugia.", "In addition, hybridization between polar bears and brown bears may have occurred multiple times throughout the Late Pleistocene.   \n", "CONCLUSIONS The reconstructed matrilineal history of brown and polar bears has two striking features.", "First, it is punctuated by dramatic and discrete climate-driven dispersal events.", "Second, opportunistic mating between these two species as their ranges overlapped has left a strong genetic imprint.", "In particular, a likely genetic exchange with extinct Irish brown bears forms the origin of the modern polar bear matriline.", "This suggests that interspecific hybridization not only may be more common than previously considered but may be a mechanism by which species deal with marginal habitats during periods of environmental deterioration."], "structured": true}
{"doc_id": 13277623, "title": "FBW7 ubiquitin ligase: a tumour suppressor at the crossroads of cell division, growth and differentiation", "abstract": ["FBW7 (F-box and WD repeat domain-containing 7) is the substrate recognition component of an evolutionary conserved SCF (complex of SKP1, CUL1 and F-box protein)-type ubiquitin ligase.", "SCFFBW7 degrades several proto-oncogenes that function in cellular growth and division pathways, including MYC, cyclin E, Notch and JUN.", "FBW7 is also a tumour suppressor, the regulatory network of which is perturbed in many human malignancies.", "Numerous cancer-associated mutations in FBW7 and its substrates have been identified, and loss of FBW7 function causes chromosomal instability and tumorigenesis.", "This Review focuses on structural and functional aspects of FBW7 and its role in the development of cancer."], "structured": false}
{"doc_id": 13282296, "title": "Hypoglycemic episodes and risk of dementia in older patients with type 2 diabetes mellitus.", "abstract": ["CONTEXT Although acute hypoglycemia may be associated with cognitive impairment in children with type 1 diabetes, no studies to date have evaluated whether hypoglycemia is a risk factor for dementia in older patients with type 2 diabetes.   \n", "OBJECTIVE To determine if hypoglycemic episodes severe enough to require hospitalization are associated with an increased risk of dementia in a population of older patients with type 2 diabetes followed up for 27 years.   \n", "DESIGN, SETTING, AND PATIENTS A longitudinal cohort study from 1980-2007 of 16,667 patients with a mean age of 65 years and type 2 diabetes who are members of an integrated health care delivery system in northern California.   \n", "MAIN OUTCOME MEASURE Hypoglycemic events from 1980-2002 were collected and reviewed using hospital discharge and emergency department diagnoses.", "Cohort members with no prior diagnoses of dementia, mild cognitive impairment, or general memory complaints as of January 1, 2003, were followed up for a dementia diagnosis through January 15, 2007.", "Dementia risk was examined using Cox proportional hazard regression models, adjusted for age, sex, race/ethnicity, education, body mass index, duration of diabetes, 7-year mean glycated hemoglobin, diabetes treatment, duration of insulin use, hyperlipidemia, hypertension, cardiovascular disease, stroke, transient cerebral ischemia, and end-stage renal disease.   \n", "RESULTS At least 1 episode of hypoglycemia was diagnosed in 1465 patients (8.8%) and dementia was diagnosed in 1822 patients (11%) during follow-up; 250 patients had both dementia and at least 1 episode of hypoglycemia (16.95%).", "Compared with patients with no hypoglycemia, patients with single or multiple episodes had a graded increase in risk with fully adjusted hazard ratios (HRs): for 1 episode (HR, 1.26; 95% confidence interval [CI], 1.10-1.49); 2 episodes (HR, 1.80; 95% CI, 1.37-2.36); and 3 or more episodes (HR, 1.94; 95% CI, 1.42-2.64).", "The attributable risk of dementia between individuals with and without a history of hypoglycemia was 2.39% per year (95% CI, 1.72%-3.01%).", "Results were not attenuated when medical utilization rates, length of health plan membership, or time since initial diabetes diagnosis were added to the model.", "When examining emergency department admissions for hypoglycemia for association with risk of dementia (535 episodes), results were similar (compared with patients with 0 episodes) with fully adjusted HRs: for 1 episode (HR, 1.42; 95% CI, 1.12-1.78) and for 2 or more episodes (HR, 2.36; 95% CI, 1.57-3.55).   \n", "CONCLUSIONS Among older patients with type 2 diabetes, a history of severe hypoglycemic episodes was associated with a greater risk of dementia.", "Whether minor hypoglycemic episodes increase risk of dementia is unknown."], "structured": true}
{"doc_id": 13283919, "title": "Defective mast cell effector functions in mice lacking the CRACM1 pore subunit of store-operated calcium release\u2013activated calcium channels", "abstract": ["CRACM1 (also called Orai1) constitutes the pore subunit of store-operated calcium release\u2013activated calcium channels.", "A point mutation in the gene encoding CRACM1 is associated with severe combined immunodeficiency disease in humans.", "Here we generated CRACM1-deficient mice in which \u03b2-galactosidase activity 'reported' CRACM1 expression.", "CRACM1-deficient mice were smaller in size.", "Mast cells derived from CRACM1-deficient mice showed grossly defective degranulation and cytokine secretion, and the allergic reactions elicited in vivo were inhibited in CRACM1-deficient mice.", "We detected robust CRACM1 expression in skeletal muscles and some regions of the brain, heart and kidney but not in the lymphoid regions of thymus and spleen.", "In contrast, we found CRACM2 expression to be much higher in mouse T cells.", "In agreement with those findings, the store-operated calcium influx and development and proliferation of CRACM1-deficient T cells was unaffected.", "Thus, CRACM1 is crucial in mouse mast cell effector function, but mouse T cell calcium release\u2013activated calcium channels are functional in the absence of CRACM1."], "structured": false}
{"doc_id": 13290521, "title": "MicroRNA-7: A miRNA with expanding roles in development and disease.", "abstract": ["MicroRNAs (miRNAs) are a family of short, non-coding RNA molecules (\u223c22nt) involved in post-transcriptional control of gene expression.", "They act via base-pairing with mRNA transcripts that harbour target sequences, resulting in accelerated mRNA decay and/or translational attenuation.", "Given miRNAs mediate the expression of molecules involved in many aspects of normal cell development and functioning, it is not surprising that aberrant miRNA expression is closely associated with many human diseases.", "Their pivotal role in driving a range of normal cellular physiology as well as pathological processes has established miRNAs as potential therapeutics, as well as potential diagnostic and prognostic tools in human health.", "MicroRNA-7 (miR-7) is a highly conserved miRNA which displays restricted spatiotemporal expression during development and in maturity.", "In humans and mice, mature miR-7 is generated from three different genes, illustrating unexpected redundancy and also the importance of this miRNA in regulating key cellular processes.", "In this review we examine the expanding role of miR-7 in the context of health, with emphasis on organ differentiation and development, as well as in various mammalian diseases, particularly of the brain, heart, endocrine pancreas and skin, as well as in cancer.", "The more we learn about miR-7, the more we realise the complexity of its regulation and potential functional application both from a biomarker and therapeutic perspective."], "structured": false}
{"doc_id": 13293033, "title": "Integration-free induced pluripotent stem cells model genetic and neural developmental features of down syndrome etiology.", "abstract": ["Down syndrome (DS) is the most frequent cause of human congenital mental retardation.", "Cognitive deficits in DS result from perturbations of normal cellular processes both during development and in adult tissues, but the mechanisms underlying DS etiology remain poorly understood.", "To assess the ability of induced pluripotent stem cells (iPSCs) to model DS phenotypes, as a prototypical complex human disease, we generated bona fide DS and wild-type (WT) nonviral iPSCs by episomal reprogramming.", "DS iPSCs selectively overexpressed chromosome 21 genes, consistent with gene dosage, which was associated with deregulation of thousands of genes throughout the genome.", "DS and WT iPSCs were neurally converted at >95% efficiency and had remarkably similar lineage potency, differentiation kinetics, proliferation, and axon extension at early time points.", "However, at later time points DS cultures showed a twofold bias toward glial lineages.", "Moreover, DS neural cultures were up to two times more sensitive to oxidative stress-induced apoptosis, and this could be prevented by the antioxidant N-acetylcysteine.", "Our results reveal a striking complexity in the genetic alterations caused by trisomy 21 that are likely to underlie DS developmental phenotypes, and indicate a central role for defective early glial development in establishing developmental defects in DS brains.", "Furthermore, oxidative stress sensitivity is likely to contribute to the accelerated neurodegeneration seen in DS, and we provide proof of concept for screening corrective therapeutics using DS iPSCs and their derivatives.", "Nonviral DS iPSCs can therefore model features of complex human disease in vitro and provide a renewable and ethically unencumbered discovery platform."], "structured": false}
{"doc_id": 13296399, "title": "In Vivo CRISPR/Cas9 Gene Editing Corrects Retinal Dystrophy in the S334ter-3 Rat Model of Autosomal Dominant Retinitis Pigmentosa", "abstract": ["Reliable genome editing via Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)/Cas9 may provide a means to correct inherited diseases in patients.", "As proof of principle, we show that CRISPR/Cas9 can be used in vivo to selectively ablate the rhodopsin gene carrying the dominant S334ter mutation (Rho(S334)) in rats that model severe autosomal dominant retinitis pigmentosa.", "A single subretinal injection of guide RNA/Cas9 plasmid in combination with electroporation generated allele-specific disruption of Rho(S334), which prevented retinal degeneration and improved visual function."], "structured": false}
{"doc_id": 13312471, "title": "Vitamin D insufficiency and the blunted PTH response in established osteoporosis: the role of magnesium deficiency", "abstract": ["Vitamin D insufficiency is common, however within individuals, not all manifest the biochemical effects of PTH excess.", "This further extends to patients with established osteoporosis.", "The mechanism underlying the blunted PTH response is unclear but may be related to magnesium (Mg) deficiency.", "The aims of this study were to compare in patients with established osteoporosis and differing degrees of vitamin D and PTH status : (1) the presence of Mg deficiency using the standard Mg loading test (2) evaluate the effects of Mg loading on the calcium-PTH endocrine axis (3) determine the effects of oral, short term Mg supplementation on the calcium-PTH endocrine axis and bone turnover.", "30 patients (10 women in 3 groups) were evaluated prospectively measuring calcium, PTH, Mg retention (Mg loading test), dietary nutrient intake (calcium, vitamin D, Mg) and bone turnover markers (serum CTX & P1CP).", "Multivariate analysis controlling for potential confounding baseline variable was undertaken for the measured outcomes.", "All subjects, within the low vitamin D and low PTH group following the magnesium loading test had evidence of Mg depletion [mean(SD) retention 70.3%(12.5)] and showed an increase in calcium 0.06(0.01) mmol/l [95% CI 0.03, 0.09, p=0.007], together with a rise in PTH 13.3 ng/l (4.5) [95% CI 3.2, 23.4, p=0.016] compared to baseline.", "Following oral supplementation bone turnover increased: CTX 0.16 (0.06) mcg/l [95%CI 0.01, 0.32 p=0.047]; P1CP 13.1 (5.7) mcg/l [95% CI 0.29, 26.6 p=0.049].", "In subjects with a low vitamin D and raised PTH mean retention was 55.9%(14.8) and in the vitamin replete group 36.1%(14.4), with little change in both acute markers of calcium homeostasis and bone turnover markers following both the loading test and oral supplementation.", "This study confirms that in patients with established osteoporosis, there is also a distinct group with a low vitamin D and a blunted PTH level and that Mg deficiency (as measured by the Mg loading test) is an important contributing factor."], "structured": false}
{"doc_id": 13322804, "title": "Novel syndromes associated with JC virus infection of neurons and meningeal cells: no longer a gray area.", "abstract": ["PURPOSE OF REVIEW The availability of a growing number of immunomodulatory medications over the past few years has been associated with various JC virus (JCV)-associated brain syndromes in patients with autoimmune diseases, including multiple sclerosis, Crohn's disease, and psoriasis that had not been previously recognized as predisposing factors for progressive multifocal leukoencephalopathy.", "This review covers the three novel syndromes discovered in the last decade that are caused by JCV infection of neurons and meningeal cells.   ", "RECENT FINDINGS For more than 30 years, JCV was thought to exclusively infect oligodendrocytes and astrocytes in the white matter of the brain of immunosuppressed individuals.", "We now recognize that JCV-infected glial cells are frequently located at the gray-white matter junction or exclusively within the gray matter causing demyelination in the cortex.", "Mutations in JCV can trigger a change in tropism leading to involvement of other cell types, such as neurons and meningeal cells, causing clinically distinct entities.", "These new features of JCV infection provide challenges for clinicians taking care of affected patients and investigators studying the biology of this polyomavirus, its pathogenesis, and tropism.   ", "SUMMARY We hope that increasing awareness of these syndromes will lead to early diagnosis, and pave the way for new avenues of research to better understand all aspects of JCV pathogenesis and develop efficient therapies for our patients.", "However, we need to remain vigilant and open to the possibility that additional JC variants or yet unknown polyomaviruses may also be associated with neurological diseases."], "structured": true}
{"doc_id": 13329980, "title": "Phosphoinositide 3-kinase signalling pathways in tumor progression, invasion and angiogenesis.", "abstract": ["AIMS AND BACKGROUND The PI3 kinase signalling pathway is now accepted as being at least as important as the ras-MAP kinase pathway in cell survival and proliferation, and hence its potential role in cancer is of great interest.", "The purpose of this review is briefly to examine evidence for an involvement of PI3K in human cancers, discuss the mechanisms by which its activation promotes tumor progression, and consider its utility as a novel target for anticancer therapy.   \n", "METHODS AND STUDY DESIGN A Medline review of recent literature concerning the role of PI3 kinase in tumor progression--mechanisms of action and clinical implications.   \n", "RESULTS Evidence is presented that misregulation of the PI3 kinase pathway is a feature of many common cancers, either by loss of the suppressor protein PTEN, or by constitutive activation of PI3 kinase isoforms or downstream elements such as AKT and mTOR.", "This activation potentiates not only cell survival and proliferation, but also cytoskeletal deformability and motility; key elements in tumor invasion.", "In addition the PI3K pathway is implicated in many aspects of angiogenesis, including upregulation of angiogenic cytokines due to tumor hypoxia or oncogene activation and endothelial cell responses to them.", "These cytokines signal though receptors such as VEGF-R, FGF-R and Tie-2 and potentiate processes essential for neoangiogenesis including cell proliferation, migration, differentiation into tubules and \"invasion\" of these capillary sprouts into extracellular matrix (ECM).   \n", "CONCLUSIONS A more complete understanding of the role of the PI3 kinase pathway in cancer will lead the way to the development of more potent and selective inhibitors which should be a useful adjunct to conventional therapies, potentially interfering with tumor progression at several pivotal points; in particular cell survival, invasion and angiogenesis."], "structured": true}
{"doc_id": 13338820, "title": "Complementary foods for infant feeding in developing countries: their nutrient adequacy and improvement", "abstract": ["Objective: To assess the energy and nutrient adequacy of a variety of complementary foods used in parts of Africa, India, Papua New Guinea, the Philippines and Thailand.", "Method: The energy, nutrient and anti-nutrient (dietary fibre and phytic acid) content (per 100 g as eaten, per 100 kcal, and per day) of twenty-three plant-based complementary foods consumed in developing countries was calculated from food composition values based on chemical analysis for the trace minerals, non-starch polysaccharide and phytic acid, and the literature.", "Results were compared with the estimated nutrient needs (per day; per 100 kcal) from complementary foods for infants 9\u201311 months, assuming a breast milk intake of average volume and composition and three complementary feedings per day, each of 250 g.", "Results: Complementary foods should provide approximately 25\u201350% of total daily requirements for protein, riboflavin and copper; 50\u201375% for thiamin, calcium and manganese; and 75\u2013100% for phosphorus, zinc and iron.", "Most or all appear to meet the estimated daily nutrient needs (per day; per 100 kcal) from complementary foods for protein, thiamin and copper (per day), but not for calcium, iron, and in some cases zinc, even if moderate bioavailability for iron and zinc is assumed.", "Some of those based on rice are also inadequate in riboflavin (per day; per 100 kcal).Conclusions:", "Even if strategies to improve the bioavailability of iron and zinc are employed, they are probably insufficient to overcome the deficits in calcium, iron and zinc.", "Therefore, research on the feasibility of fortifying plant-based complementary foods in developing countries with calcium, iron and zinc is urgently required.", "Sponsorship: This study was supported by the Micronutrient Initiative through the Canadian International Development Agency."], "structured": false}
{"doc_id": 13350374, "title": "Early aging and age-related pathologies in mice deficient in BMAL1, the core componentof the circadian clock.", "abstract": ["Mice deficient in the circadian transcription factor BMAL1 (brain and muscle ARNT-like protein) have impaired circadian behavior and demonstrate loss of rhythmicity in the expression of target genes.", "Here we report that Bmal1(-/-) mice have reduced lifespans and display various symptoms of premature aging including sarcopenia, cataracts, less subcutaneous fat, organ shrinkage, and others.", "The early aging phenotype correlates with increased levels of reactive oxygen species in some tissues of the Bmal1(-/- )animals.", "These findings, together with data on CLOCK/BMAL1-dependent control of stress responses, may provide a mechanistic explanation for the early onset of age-related pathologies in the absence of BMAL1."], "structured": false}
{"doc_id": 13368032, "title": "A self-inactivating lentiviral vector for SCID-X1 gene therapy that does not activate LMO2 expression in human T cells.", "abstract": ["To develop safer and more effective vectors for gene therapy of X-linked severe combined immunodeficiency (SCID-X1), we have evaluated new self-inactivating lentiviral vectors based on the HIV virus.", "The CL20i4-hgamma(c)-Revgen vector contains the entire human common gamma chain (gamma(c)) genomic sequence driven by the gamma(c) promoter.", "The CL20i4-EF1alpha-hgamma(c)OPT vector uses a promoter fragment from the eukaryotic elongation factor alpha (EF1alpha) gene to express a codon-optimized human gamma(c) cDNA.", "Both vectors contain a 400-bp insulator fragment from the chicken beta-globin locus within the self-inactivating long-terminal repeat.", "Transduction of bone marrow cells using either of these vectors restored T, B, and natural killer lymphocyte development and function in a mouse SCID-X1 transplantation model.", "Transduction of human CD34(+) bone marrow cells from SCID-X1 patients with either vector restored T-cell development in an in vitro assay.", "In safety studies using a Jurkat LMO2 activation assay, only the CL20i4-EF1alpha-hgamma(c)OPT vector lacked the ability to transactivate LMO2 protein expression, whereas the CL20i4-hgamma(c)-Revgen vector significantly activated LMO2 protein expression.", "In addition, the CL20i4-EF1alpha-hgamma(c)OPT vector has not caused any tumors in transplanted mice.", "We conclude that the CL20i4-EF1alpha-hgamma(c)OPT vector may be suitable for testing in a clinical trial based on these preclinical demonstrations of efficacy and safety."], "structured": false}
{"doc_id": 13373629, "title": "Genetic Variants at Newly Identified Lipid Loci Are Associated with Coronary Heart Disease in a Chinese Han Population", "abstract": ["BACKGROUND Recent genome-wide association studies (GWAS) have mapped several novel loci influencing blood lipid levels in Caucasians.", "We sought to explore whether the genetic variants at newly identified lipid-associated loci were associated with CHD susceptibility in a Chinese Han population.   \n", "METHODOLOGY/PRINCIPAL FINDINGS We conducted a two-stage case-control study in a Chinese Han population.", "The first-stage, consisting of 1,376 CHD cases and 1,376 sex and age- frequency matched controls, examined 5 novel lipid-associated single-nucleotide polymorphisms (SNPs) identified from GWAS among Caucasians in relation to CHD risk in Chinese.", "We then validated significant SNPs in the second-stage, consisting of 1,269 cases and 2,745 controls.", "We also tested associations between SNPs within the five novel loci and blood lipid levels in 4,121 controls.", "We identified two novel SNPs (rs599839 in CELSR2-PSRC1-SORT1 and rs16996148 in NCAN-CILP2) that were significantly associated with reduced CHD risk in Chinese (odds ratios (95% confidence intervals) in the dominant model 0.76 (0.61-0.90; P = 0.001), 0.67 (0.57-0.77; P = 3.4\u00d710(-8)), respectively).", "Multiple linear regression analyses using dominant model showed that rs599839 was significantly associated with decreased LDL levels (P = 0.022) and rs16996148 was significantly associated with increased LDL and HDL levels (P = 2.9\u00d710(-4) and 0.001, respectively).   \n", "CONCLUSIONS/SIGNIFICANCE We identified two novel SNPs (rs599839 and rs16996148) at newly identified lipid-associated loci that were significantly associated with CHD susceptibility in a Chinese Han population."], "structured": true}
{"doc_id": 13380011, "title": "Spare respiratory capacity rather than oxidative stress regulates glutamate excitotoxicity after partial respiratory inhibition of mitochondrial complex I with rotenone.", "abstract": ["Partial inhibition of mitochondrial respiratory complex I by rotenone reproduces aspects of Parkinson's disease in rodents.", "The hypothesis that rotenone enhancement of neuronal cell death is attributable to oxidative stress was tested in an acute glutamate excitotoxicity model using primary cultures of rat cerebellar granule neurons.", "As little as 5 nM rotenone increased mitochondrial superoxide (O2*-) levels and potentiated glutamate-induced cytoplasmic Ca2+ deregulation, the first irreversible stage of necrotic cell death.", "However, the potent cell-permeant O2*- trap manganese tetrakis (N-ethylpyridinium-2yl) porphyrin failed to prevent the effects of the inhibitor.", "The bioenergetic consequences of rotenone addition were quantified by monitoring cell respiration.", "Glutamate activation of NMDA receptors used the full respiratory capacity of the in situ mitochondria, and >80% of the glutamate-stimulated respiration was attributable to increased cellular ATP demand.", "Rotenone at 20 nM inhibited basal and carbonyl cyanide p-trifluoromethoxyphenylhydrazone-stimulated cell respiration and caused respiratory failure in the presence of glutamate.", "ATP synthase inhibition by oligomycin was also toxic in the presence of glutamate.", "We conclude that the cell vulnerability in the rotenone model of partial complex I deficiency under these specific conditions is primarily determined by spare respiratory capacity rather than oxidative stress."], "structured": false}
{"doc_id": 13380980, "title": "Isolated liver perfusion for non-resectable liver tumours: a review.", "abstract": ["Many treatments have been proposed for non-resectable primary or secondary hepatic cancer but the results have generally been disappointing.", "Isolated Hepatic Perfusion (IHP) was first attempted four decades ago but it gained acceptance only recently, after spectacular tumour responses were obtained by isolated limb perfusion with melphalan and tumour necrosis factor (TNF) for melanomas and sarcomas.", "Surgical isolation of the liver is a technically demanding operation that allows the safe administration of high doses of chemotherapeutics and TNF.", "Percutaneous techniques using balloon occlusion catheters are simpler but result in higher leakage rates from the perfusion circuit into the systemic circulation.", "Several phase I-II trials indicate that IHP can yield high tumour response rates, even when there is resistance to systemic chemotherapy.", "However, no significant advantage in overall survival has been demonstrated so far.", "IHP offers unique pharmacokinetic advantages for locoregional chemotherapy and biotherapy.", "It might also allow gene therapy with limited systemic exposure and toxicity.", "At present, IHP nevertheless remains an experimental treatment modality which should therefore be used in controlled trials only."], "structured": false}
{"doc_id": 13384318, "title": "Combinatorial control of exon recognition.", "abstract": ["Pre-mRNA splicing is a fundamental process required for the expression of most metazoan genes.", "It is carried out by the spliceosome, which catalyzes the removal of noncoding intronic sequences to assemble exons into mature mRNAs prior to export and translation.", "Given the complexity of higher eukaryotic genes and the relatively low level of splice site conservation, the precision of the splicing machinery in recognizing and pairing splice sites is impressive.", "Introns ranging in size from <100 up to 100,000 bases are removed efficiently.", "At the same time, a large number of alternative splicing events are observed between different cell types, during development, or during other biological processes.", "This extensive alternative splicing implies a significant flexibility of the spliceosome to identify and process exons within a given pre-mRNA.", "To reach this flexibility, splice site selection in higher eukaryotes has evolved to depend on multiple parameters such as splice site strength, the presence or absence of splicing regulators, RNA secondary structures, the exon/intron architecture, and the process of pre-mRNA synthesis itself.", "The relative contributions of each of these parameters control how efficiently splice sites are recognized and flanking introns are removed."], "structured": false}
{"doc_id": 13398997, "title": "High CTLA-4 expression on Th17 cells results in increased sensitivity to CTLA-4 coinhibition and resistance to belatacept.", "abstract": ["The CD28/cytotoxic T-lymphocyte antigen 4 (CTLA-4)blocker belatacept selectively inhibits alloreactive T cell responses but is associated with a high incidence of acute rejection following renal transplantation,which led us to investigate the etiology of belatacept\u2013resistant graft rejection.", "T cells can differentiate into functionally distinct subsets of memory T cellsthat collectively enable protection against diverse classes of pathogens and can cross-react with allogeneicantigen and mediate graft rejection.", "T helper 17(Th17) cells are a pro-inflammatory CD4+ lineage that provides immunity to pathogens and are pathogenic in autoimmune disease.", "We found that T helper 1 (Th1)and Th17 memory compartments contained a similar frequency of divided cells following allogeneic stimulation.", "Compared to Th1 cells, Th17 memory cells expressed significantly higher levels of the coinhibitory molecule CTLA-4.", "Stimulation in the presence of belatacept inhibited Th1 responses but augmented Th17 cells due to greater sensitivity to coinhibition by CTLA-4.", "Th17 cells from renal transplant recipients were resistant to ex vivo CD28/CTLA-4 blockade with belatacept, and an elevated frequency of Th17 memory cells was associated with acute rejection during belatacept therapy.", "These data highlight important differences in costimulatory and coinhibitory requirements of CD4+ memory subsets, and demonstrate that the heterogeneity of pathogen-derived memory has implications for immunomodulation strategies."], "structured": false}
{"doc_id": 13400643, "title": "A small molecule modulates Jumonji histone demethylase activity and selectively inhibits cancer growth", "abstract": ["The pharmacological inhibition of general transcriptional regulators has the potential to block growth through targeting multiple tumorigenic signalling pathways simultaneously.", "Here, using an innovative cell-based screen, we identify a structurally unique small molecule (named JIB-04) that specifically inhibits the activity of the Jumonji family of histone demethylases in vitro, in cancer cells, and in tumours in vivo.", "Unlike known inhibitors, JIB-04 is not a competitive inhibitor of \u03b1-ketoglutarate.", "In cancer, but not in patient-matched normal cells, JIB-04 alters a subset of transcriptional pathways and blocks viability.", "In mice, JIB-04 reduces tumour burden and prolongs survival.", "Importantly, we find that patients with breast tumours that overexpress Jumonji demethylases have significantly lower survival.", "Thus, JIB-04, a novel inhibitor of Jumonji demethylases in vitro and in vivo, constitutes a unique potential therapeutic and research tool against cancer, and validates the use of unbiased cellular screens to discover chemical modulators with disease relevance."], "structured": false}
{"doc_id": 13411519, "title": "Gq protein alpha subunits Galphaq and Galpha11 are localized at postsynaptic extra-junctional membrane of cerebellar Purkinje cells and hippocampal pyramidal cells.", "abstract": ["Following cell surface receptor activation, the alpha subunit of the Gq subclass of GTP-binding proteins activates the phosphoinositide signalling pathway.", "Here we examined the expression and localization of Gq protein alpha subunits in the adult mouse brain by in situ hybridization and immunohistochemistry.", "Of the four members of the Gq protein alpha subunits, Galphaq and Galpha11 were transcribed predominantly in the brain.", "The highest transcriptional level of Galphaq was observed in cerebellar Purkinje cells (PCs) and hippocampal pyramidal cells, while that of Galpha11 was noted in hippocampal pyramidal cells.", "Antibody against the C-terminal peptide common to Galphaq and Galpha11 strongly labelled the cerebellar molecular layer and hippocampal neuropil layers.", "In these regions, immunogold preferentially labelled the cytoplasmic face of postsynaptic cell membrane of PCs and pyramidal cells.", "Immunoparticles were distributed along the extra-junctional cell membrane of spines, dendrites and somata, but were almost excluded from the junctional membrane.", "By double immunofluorescence, Galphaq/Galpha11 was extensively colocalized with metabotropic glutamate receptor mGluR1alpha in dendritic spines of PCs and with mGluR5 in those of hippocampal pyramidal cells.", "Together with concentrated localization of mGluR1alpha and mGluR5 in a peri-junctional annulus on PC and pyramidal cell synapses (Baude et al. 1993, Neuron, 11, 771-787; Luj\u00e1n et al. 1996, Eur.", "J. Neurosci., 8, 1488-1500), the present molecular-anatomical findings suggest that peri-junctional stimulation of the group I metabotropic glutamate receptors is mediated by Galphaq and/or Galpha11, leading to the activation of the intracellular effector, phospholipase Cbeta."], "structured": false}
{"doc_id": 13439128, "title": "The Bloom's syndrome gene product is homologous to RecQ helicases", "abstract": ["The Bloom's syndrome (BS) gene, BLM, plays an important role in the maintenance of genomic stability in somatic cells.", "A candidate for BLM was identified by direct selection of a cDNA derived from a 250 kb segment of the genome to which BLM had been assigned by somatic crossover point mapping.", "In this novel mapping method, cells were used from persons with BS that had undergone intragenic recombination within BLM.", "cDNA analysis of the candidate gene identified a 4437 bp cDNA that encodes a 1417 amino acid peptide with homology to the RecQ helicases, a subfamily of DExH box-containing DNA and RNA helicases.", "The presence of chain-terminating mutations in the candidate gene in persons with BS proved that it was BLM."], "structured": false}
{"doc_id": 13441037, "title": "Preventing obesity in children and adolescents.", "abstract": ["In this review, we address the natural history of obesity in children, the most promising family- and school-based approaches to the prevention of obesity, and the barriers and opportunities associated with secondary prevention.", "In childhood, the most important periods of risk appear to be the periods of adiposity rebound and adolescence.", "Caution regarding the period of adiposity rebound is still warranted, because it is not yet clear that early rebound is attributable to changes in body fat.", "Families and schools represent the most important foci for preventive efforts in children and adolescents.", "One productive approach is to proceed from an examination of factors that affect energy balance to the identification of more proximal influences on those factors.", "This approach may help to narrow the strategies necessary to prevent or treat childhood obesity.", "For example, television viewing affects both energy intake and energy expenditure, and therefore represents a logical target for interventions.", "Anticipatory guidance by pediatricians may offer an effective mechanism by which to change parental attitudes and practices regarding television viewing.", "A similar process is used to emphasize the potential influence of school-based interventions directed at changes in food choices and sedentary behavior."], "structured": false}
{"doc_id": 13441537, "title": "Culture of Preimplantation Mouse Embryos Affects Fetal Development and the Expression of Imprinted Genes1", "abstract": ["Abstract Culture of preimplantation mammalian embryos and cells can influence their subsequent growth and differentiation.", "Previously, we reported that culture of mouse embryonic stem cells is associated with deregulation of genomic imprinting and affects the potential for these cells to develop into normal fetuses.", "The purpose of our current study was to determine whether culture of preimplantation mouse embryos in a chemically defined medium (M16) with or without fetal calf serum (FCS) can affect their subsequent development and imprinted gene expression.", "Only one third of the blastocysts that had been cultured from two-cell embryos in M16 medium complemented with FCS developed into viable Day 14 fetuses after transfer into recipients.", "These M16 + FCS fetuses were reduced in weight as compared with controls and M16 fetuses and had decreased expression of the imprinted H19 and insulin-like growth factor 2 genes associated with a gain of DNA methylation at an imprinting control region upstream of H19.", "They also displayed increased expression of the imprinted gene Grb10.", "The growth factor receptor binding gene Grb7, in contrast, was strongly reduced in its expression in most of the M16 + FCS fetuses.", "No alterations were detected for the imprinted gene Mest.", "Preimplantation culture in the presence of serum can influence the regulation of multiple growth-related imprinted genes, thus leading to aberrant fetal growth and development."], "structured": false}
{"doc_id": 13445579, "title": "Results of screening for intracranial aneurysms in patients with coarctation of the aorta.", "abstract": ["BACKGROUND AND PURPOSE IAs are found in 2.3% of adults; the mean age at detection is 52 years.", "Prevalence is <0.5% in young adults.", "Early studies suggest that 10%-50% of patients with aortic coarctation have IAs.", "Screening recommendations are variable.", "We sought to examine the prevalence of IAs through screening with MRA.   ", "MATERIALS AND METHODS Consecutive patients older than 16 years of age with coarctation undergoing brain MRA between May 1999 and October 2007 were included.", "MRA was performed by using a 1.5T scanner with a 3D time-of-flight protocol; simultaneous MR imaging was performed of the heart and aorta.", "Cerebral MRAs were double-reported by a neuroradiologist.", "Statistics are described as mean \u00b1 SD and median \u00b1 range.", "Continuous variables were compared by using Student t tests and Mann-Whitney U tests (categoric variables, by using the Fisher exact test).   \n", "RESULTS One hundred seventeen MRAs were double-reported.", "The median age was 29 \u00b1 11 years (range, 16-59 years).", "IAs were found in 12 patients (10.3%).", "The mean diameter of IAs was 3.9 mm (range, 2.0-8.0 mm).", "Patients with aneurysms were older (median, 37 years; range, 16-50 years) than those without (median, 23 years; range, 16-59 years; Z = -2.01, P = .04).", "Hypertension was more common in those with IAs (IA 83% versus no IA 43%, P = .01).", "There was no association between ascending aortopathy, bicuspid aortic valves, and IAs.   \n", "CONCLUSIONS Patients with coarctation have a higher prevalence of IAs, occurring at an earlier age than in population studies.", "Whether routine screening is appropriate for this group of patients is unclear.", "Hypertension is likely to be an important pathophysiologic factor."], "structured": true}
{"doc_id": 13448422, "title": "A new look at the heart in diabetes mellitus: from ailing to failing", "abstract": ["This review discusses some of the mechanisms inherent in diabetes that predispose patients to increased cardiac morbidity and mortality.", "Single photon emission computerized tomography or photon emission tomography with radioactive labeled analogues of norepinephrine have shown that cardiac sympathetic dysfunction and incompetence are early and also late abnormalities in patients with Type I (insulin-dependent) and Type II (non-insulin-dependent) diabetes mellitus.", "Furthermore, myocardial blood flow assessment with photon emission tomography has shown that in patients without myocardial perfusion deficits, endothelial-dependent vasodilatation is severely reduced in relation to cardiac sympathetic dysfunction.", "In addition, signs of endothelial activation have also been found early in patients with Type I and Type II diabetes in whom vascular disease has not been clinically detected.", "This activation in conjunction with glycaemic control is important in determining macrovascular mortality.", "Cardiac sympathetic dysfunction is partially restored to normal with near normalisation of glycaemia.", "Interpretations.", "Recently unrecognized \u201csubtle\u201d changes predispose the heart to failure, after ischaemia-induced remodelling, and arteriosclerotic plaques to instability and rupture.", "These changes act in conjunction with effects, driven by hyperglycaemia and diabetes, on the endothelium of large blood vessels, e. g. on nitric oxide release or on protein kinase-C \u03b2 activation.", "Meticulous glucose control early on and rapid recompensation of hyperglycaemia in patients with acute coronary syndrome are part of a successful intensive multifactorial approach to prevent the heart in diabetes converting from ailing to failing.", "[Diabetologia (2000) 43: 1455\u20131469]"], "structured": false}
{"doc_id": 13450938, "title": "Genetic and epigenetic mutations affect the DNA binding capability of human ZFP57 in transient neonatal diabetes type 1", "abstract": ["In the mouse, ZFP57 contains three classical Cys2His2 zinc finger domains (ZF) and recognizes the methylated TGC(met)CGC target sequence using the first and the second ZFs.", "In this study, we demonstrate that the human ZFP57 (hZFP57) containing six Cys2His2 ZFs, binds the same methylated sequence through the third and the fourth ZFs, and identify the aminoacids critical for DNA interaction.", "In addition, we present evidences indicating that hZFP57 mutations and hypomethylation of the TNDM1 ICR both associated with Transient Neonatal Diabetes Mellitus type 1 result in loss of hZFP57 binding to the TNDM1 locus, likely causing PLAGL1 activation."], "structured": false}
{"doc_id": 13458119, "title": "Physiological astrocytic calcium levels stimulate glutamate release to modulate adjacent neurons.", "abstract": ["Astrocytes can release glutamate in a calcium-dependent manner and consequently signal to adjacent neurons.", "Whether this glutamate release pathway is used during physiological signaling or is recruited only under pathophysiological conditions is not well defined.", "One reason for this lack of understanding is the limited knowledge about the levels of calcium necessary to stimulate glutamate release from astrocytes and about how they compare with the range of physiological calcium levels in these cells.", "We used flash photolysis to raise internal calcium in astrocytes, while monitoring astrocytic calcium levels and glutamate, which evoked slow inward currents that were recorded electrophysiologically from single neurons grown on microislands of astrocytes.", "With this approach, we demonstrate that modest changes of astrocytic calcium, from 84 to 140 nM, evoke substantial glutamatergic currents in neighboring neurons (-391 pA), with a Hill coefficient of 2.1 to 2.7.", "Because the agonists glutamate, norepinephrine, and dopamine all raise calcium in astrocytes to levels exceeding 1.8 microM, these quantitative studies demonstrate that the astrocytic glutamate release pathway is engaged at physiological levels of internal calcium.", "Consequently, the calcium-dependent release of glutamate from astrocytes functions within an appropriate range of astrocytic calcium levels to be used as a signaling pathway within the functional nervous system."], "structured": false}
{"doc_id": 13464392, "title": "Albumin and furosemide therapy in hypoproteinemic patients with acute lung injury.", "abstract": ["OBJECTIVE Hypoproteinemia, fluid retention, and weight gain are associated with development of acute lung injury and mortality in critically ill patients, without proof of cause and effect.", "We designed a clinical trial to determine whether diuresis and colloid replacement in hypoproteinemic patients with acute lung injury would improve pulmonary physiology.   \n", "DESIGN Prospective, randomized, double-blind, placebo-controlled trial.   \n", "SETTING All adult intensive care units from two university hospitals.   \n", "PATIENTS Thirty-seven mechanically-ventilated patients with acute lung injury and serum total protein </=5.0 g/dL.   INTERVENTIONS Five-day protocolized regimen of 25 g of human serum albumin every 8 hrs with continuous infusion furosemide, or dual placebo, targeted to diuresis, weight loss, and serum total protein.   \n", "MEASUREMENTS AND MAIN RESULTS Measured outcomes included change in weight, serum total protein, fluid balance, hemodynamics, respiratory system compliance, and oxygenation.", "Baseline characteristics were similar between groups (treatment, n = 19; control, n = 18), with trauma being the major cause of acute lung injury.", "Diuresis and weight loss over 5 days (5.3 kg more in the treatment group, p =.04) was accompanied by improvements in the Pao2/Fio2 ratio in the treatment group within 24 hrs (from 171 to 236, p =.02).", "Respiratory mechanics were unchanged.", "Mean arterial pressure increased from 80 to 88 mm Hg (p =.10), and heart rate decreased from 110 to 95 beats/min (p =.008) over time in the treatment group.", "No difference in mortality was observed, with favorable trends in measures of intensive care.   \n", "CONCLUSIONS Albumin and furosemide therapy improves fluid balance, oxygenation, and hemodynamics in hypoproteinemic patients with acute lung injury.", "Determining the effect of this simple therapy on cost, outcomes, and other patient populations requires further study."], "structured": true}
{"doc_id": 13466517, "title": "Advances in functional and structural mr image analysis and implementation as fsl", "abstract": ["The techniques available for the interrogation and analysis of neuroimaging data have a large influence in determining the flexibility, sensitivity, and scope of neuroimaging experiments.", "The development of such methodologies has allowed investigators to address scientific questions that could not previously be answered and, as such, has become an important research area in its own right.", "In this paper, we present a review of the research carried out by the Analysis Group at the Oxford Centre for Functional MRI of the Brain (FMRIB).", "This research has focussed on the development of new methodologies for the analysis of both structural and functional magnetic resonance imaging data.", "The majority of the research laid out in this paper has been implemented as freely available software tools within FMRIB's Software Library (FSL)."], "structured": false}
{"doc_id": 13466622, "title": "Metformin\u2014mode of action and clinical implications for diabetes and cancer", "abstract": ["Metformin has been the mainstay of therapy for diabetes mellitus for many years; however, the mechanistic aspects of metformin action remained ill-defined.", "Recent advances revealed that this drug, in addition to its glucose-lowering action, might be promising for specifically targeting metabolic differences between normal and abnormal metabolic signalling.", "The knowledge gained from dissecting the principal mechanisms by which metformin works can help us to develop novel treatments.", "The centre of metformin's mechanism of action is the alteration of the energy metabolism of the cell.", "Metformin exerts its prevailing, glucose-lowering effect by inhibiting hepatic gluconeogenesis and opposing the action of glucagon.", "The inhibition of mitochondrial complex I results in defective cAMP and protein kinase A signalling in response to glucagon.", "Stimulation of 5\u2032-AMP-activated protein kinase, although dispensable for the glucose-lowering effect of metformin, confers insulin sensitivity, mainly by modulating lipid metabolism.", "Metformin might influence tumourigenesis, both indirectly, through the systemic reduction of insulin levels, and directly, via the induction of energetic stress; however, these effects require further investigation.", "Here, we discuss the updated understanding of the antigluconeogenic action of metformin in the liver and the implications of the discoveries of metformin targets for the treatment of diabetes mellitus and cancer."], "structured": false}
{"doc_id": 13469921, "title": "Characteristics of the Earliest Cross-Neutralizing Antibody Response to HIV-1", "abstract": ["Recent cross-sectional analyses of HIV-1+ plasmas have indicated that broadly cross-reactive neutralizing antibody responses are developed by 10%-30% of HIV-1+ subjects.", "The timing of the initial development of such anti-viral responses is unknown.", "It is also unknown whether the emergence of these responses coincides with the appearance of antibody specificities to a single or multiple regions of the viral envelope glycoprotein (Env).", "Here we analyzed the cross-neutralizing antibody responses in longitudinal plasmas collected soon after and up to seven years after HIV-1 infection.", "We find that anti-HIV-1 cross-neutralizing antibody responses first become evident on average at 2.5 years and, in rare cases, as early as 1 year following infection.", "If cross-neutralizing antibody responses do not develop during the first 2-3 years of infection, they most likely will not do so subsequently.", "Our results indicate a potential link between the development of cross-neutralizing antibody responses and specific activation markers on T cells, and with plasma viremia levels.", "The earliest cross-neutralizing antibody response targets a limited number of Env regions, primarily the CD4-binding site and epitopes that are not present on monomeric Env, but on the virion-associated trimeric Env form.", "In contrast, the neutralizing activities of plasmas from subjects that did not develop cross-neutralizing antibody responses target epitopes on monomeric gp120 other than the CD4-BS.", "Our study provides information that is not only relevant to better understanding the interaction of the human immune system with HIV but may guide the development of effective immunization protocols.", "Since antibodies to complex epitopes that are present on the virion-associated envelope spike appear to be key components of earliest cross-neutralizing activities of HIV-1+ plasmas, then emphasis should be made to elicit similar antibodies by vaccination."], "structured": false}
{"doc_id": 13481731, "title": "Gender, age, and heart failure with preserved left ventricular systolic function.", "abstract": ["OBJECTIVES This study was designed to determine if women are more likely than men to have heart failure (HF) with preserved systolic function after adjustment for potential confounders, including age.   \n", "BACKGROUND Although prior evidence suggests an independent association between female gender and preserved left ventricular systolic function (LVSF) in patients with HF, existing studies are limited by referral biases, small sample sizes, or the inability to adjust for a wide range of potential confounding variables.   \n", "METHODS This is a cross-sectional study using data from retrospective medical chart abstraction of a national sample of Medicare beneficiaries hospitalized with the principal discharge diagnosis of HF in acute-care nongovernmental hospitals in the U.S. between April 1998 and March 1999.", "Patients were eligible for this analysis if they were age 65 years or older, had documentation of LVSF, and corroboration of the diagnosis of HF.", "We used multivariable logistic regression to identify the correlates of preserved LVSF, which was defined as qualitatively normal function or quantitatively reported ejection fraction > or =0.50.", "Stratified regressions by gender were performed to identify significant interactions.   \n", "RESULTS Of the 19,710 patients in the analysis, preserved LVSF was present in 6,700 (35%), 79% of whom were women.", "In contrast, among the 12,956 patients with impaired LVSF, only 49% were women.", "Patients with preserved LVSF were 1.5 years older than those with impaired LVSF.", "After adjustment for age and other patient factors, female gender remained strongly associated with preserved LVSF (calculated risk ratio = 1.71; 95% confidence interval 1.63 to 1.78).", "The association was consistent in all age groups, and was similar in patients with or without coronary artery disease, hypertension, pulmonary disease, renal insufficiency, or atrial fibrillation.   \n", "CONCLUSIONS In elderly patients hospitalized with HF, preserved systolic function is primarily a condition of women, independent of important demographic and clinical characteristics."], "structured": true}
{"doc_id": 13481880, "title": "YAP/TAZ-Dependent Reprogramming of Colonic Epithelium Links ECM Remodeling to Tissue Regeneration", "abstract": ["Tissue regeneration requires dynamic cellular adaptation to the wound environment.", "It is currently unclear how this is orchestrated at the cellular level and how cell fate is affected by severe tissue damage.", "Here we dissect cell fate transitions during colonic regeneration in a mouse dextran sulfate sodium (DSS) colitis model, and we demonstrate that the epithelium is transiently reprogrammed into a primitive state.", "This is characterized by de novo expression of fetal markers as well as suppression of markers for adult stem and differentiated cells.", "The fate change is orchestrated by remodeling the extracellular matrix (ECM), increased FAK/Src signaling, and ultimately YAP/TAZ activation.", "In a defined cell culture system recapitulating the extracellular matrix remodeling observed in vivo, we show that a collagen 3D matrix supplemented with Wnt ligands is sufficient to sustain endogenous YAP/TAZ and induce conversion of cell fate.", "This provides a simple model for tissue regeneration, implicating cellular reprogramming as an essential element."], "structured": false}
{"doc_id": 13492264, "title": "Summary", "abstract": ["Glomerular basement membrane (GBM) and podocalyxin are essential for podocyte morphology.", "We provide evidence of functional interconnections between basement membrane components (collagen IV and laminin), the expression of podocalyxin and the morphology of human glomerular epithelial cells (podocytes).", "We demonstrated that GBM and laminin, but not collagen IV, up-regulated the expression of podocalyxin.", "Scanning electron microscopy revealed that laminin induced a modified morphology of podocytes with process formation, which was more extensive in the presence of GBM.", "Under high magnification, podocytes appeared ruffled.", "Using transmission electron microscopy we observed that raised areas occurred in the basal cell surface.", "Furthermore, the presence of anti-podocalyxin antibody increased the extent of adhesion and spreading of podocytes to both collagen IV and laminin, thus podocalyxin apparently inhibits cell-matrix interactions.", "We also performed adhesion and spreading assays on podocytes grown under increased glucose concentration (25 mM).", "Under these conditions, the expression of podocalyxin was almost totally suppressed.", "The cells adhered and spread to basement membrane components but there was no increase in the extent of adhesion and spreading in the presence of anti-podocalyxin antibody, or ruffling of the cell edges.", "Additionally, in podocytes expressing podocalyxin, the presence of anti-podocalyxin antibody partially reversed the inhibition of adhesion to collagen IV provoked by anti-beta1 integrin antibody, thus podocalyxin should compete with beta1-related cell adhesion.", "We suggest that the observed podocalyxin-mediated inhibition of binding to the matrix could be in part responsible for the specialized conformation of the basal surface of podocytes."], "structured": false}
{"doc_id": 13494853, "title": "Mfold web server for nucleic acid folding and hybridization prediction", "abstract": ["The abbreviated name, 'mfold web server', describes a number of closely related software applications available on the World Wide Web (WWW) for the prediction of the secondary structure of single stranded nucleic acids.", "The objective of this web server is to provide easy access to RNA and DNA folding and hybridization software to the scientific community at large.", "By making use of universally available web GUIs (Graphical User Interfaces), the server circumvents the problem of portability of this software.", "Detailed output, in the form of structure plots with or without reliability information, single strand frequency plots and 'energy dot plots', are available for the folding of single sequences.", "A variety of 'bulk' servers give less information, but in a shorter time and for up to hundreds of sequences at once.", "The portal for the mfold web server is http://www.bioinfo.rpi.edu/applications/mfold.", "This URL will be referred to as 'MFOLDROOT'."], "structured": false}
{"doc_id": 13496853, "title": "Grip strength in healthy caucasian adults: reference values.", "abstract": ["PURPOSE The aim of this study was to update reference data of handgrip strength for healthy adults of both genders spanning a wide age range and to analyze possible factors of influence.   \n", "METHODS Intraindividual and interindividual variations of grip strength and their relation to several anthropometric factors were analyzed in a standardized manner for 769 healthy adults (women, n = 403; men, n = 366) aged between 20 years and 95 years.", "Measurements were done in neutral position of arm, forearm, and wrist on setting II of a Baseline digital hydraulic dynamometer (NexGen Ergonomics Inc. Quebec, Canada).   \n", "RESULTS Mean strength was about 41% less in women (right 29 kg; left 27 kg) than in men (right 49 kg; left 47 kg) resulting in a ratio of left to right hand slightly above .95 in both genders.", "During the course of life, hand strength develops comparably in both genders peaking at 35 years of age and decreasing continuously further on.", "Anthropometric variables such as forearm circumference and length, hand size, or body mass showed a positive correlation with grip strength.", "Body mass index, type of work, and hand dominance showed only a partial positive correlation or no correlation with grip strength.", "Gender and age, followed by parameters representing body length and obesity, were observed to have the highest predictive value for handgrip strength and were therefore entered into the generation of prediction equations.   \n", "CONCLUSIONS We recommend side adjustment of measured values for intraindividual comparison and inclusion of information regarding anthropometric characteristics, as well as using gender- and age-adjusted reference values, whereas hand dominance can be neglected.", "The regression equations we generated might prove to be useful for clinicians or for those who use normative values within software to provide more accurate predictions of strength scores for specific applications."], "structured": true}
{"doc_id": 13497630, "title": "Association Between Biomarkers of Ovarian Reserve and Infertility Among Older Women of Reproductive Age", "abstract": ["Importance Despite lack of evidence of their utility, biomarkers of ovarian reserve are being promoted as potential markers of reproductive potential.", "Objective To determine the associations between biomarkers of ovarian reserve and reproductive potential among women of late reproductive age.", "Design, Setting, and Participants Prospective time-to-pregnancy cohort study (2008 to date of last follow-up in March 2016) of women (N = 981) aged 30 to 44 years without a history of infertility who had been trying to conceive for 3 months or less, recruited from the community in the Raleigh-Durham, North Carolina, area.", "Exposures Early-follicular-phase serum level of antim\u00fcllerian hormone (AMH), follicle-stimulating hormone (FSH), and inhibin B and urinary level of FSH.", "Main Outcomes and Measures The primary outcomes were the cumulative probability of conception by 6 and 12 cycles of attempt and relative fecundability (probability of conception in a given menstrual cycle).", "Conception was defined as a positive pregnancy test result.", "Results A total of 750 women (mean age, 33.3 [SD, 3.2] years; 77% white; 36% overweight or obese) provided a blood and urine sample and were included in the analysis.", "After adjusting for age, body mass index, race, current smoking status, and recent hormonal contraceptive use, women with low AMH values (<0.7 ng/mL [n = 84]) did not have a significantly different predicted probability of conceiving by 6 cycles of attempt (65%; 95% CI, 50%-75%) compared with women (n = 579) with normal values (62%; 95% CI, 57%-66%) or by 12 cycles of attempt (84% [95% CI, 70%-91%] vs 75% [95% CI, 70%-79%], respectively).", "Women with high serum FSH values (>10 mIU/mL [n = 83]) did not have a significantly different predicted probability of conceiving after 6 cycles of attempt (63%; 95% CI, 50%-73%) compared with women (n = 654) with normal values (62%; 95% CI, 57%-66%) or after 12 cycles of attempt (82% [95% CI, 70%-89%] vs 75% [95% CI, 70%-78%], respectively).", "Women with high urinary FSH values (>11.5 mIU/mg creatinine [n = 69]) did not have a significantly different predicted probability of conceiving after 6 cycles of attempt (61%; 95% CI, 46%-74%) compared with women (n = 660) with normal values (62%; 95% CI, 58%-66%) or after 12 cycles of attempt (70% [95% CI, 54%-80%] vs 76% [95% CI, 72%-80%], respectively).", "Inhibin B levels (n = 737) were not associated with the probability of conceiving in a given cycle (hazard ratio per 1-pg/mL increase, 0.999; 95% CI, 0.997-1.001).", "Conclusions and Relevance Among women aged 30 to 44 years without a history of infertility who had been trying to conceive for 3 months or less, biomarkers indicating diminished ovarian reserve compared with normal ovarian reserve were not associated with reduced fertility.", "These findings do not support the use of urinary or blood follicle-stimulating hormone tests or antim\u00fcllerian hormone levels to assess natural fertility for women with these characteristics."], "structured": false}
{"doc_id": 13509809, "title": "Matrix-embedded osteocytes regulate mobilization of hematopoietic stem/progenitor cells.", "abstract": ["The bone marrow (BM) niche comprises multiple cell types that regulate hematopoietic stem/progenitor cell (HSPC) migration out of the niche and into the circulation.", "Here, we demonstrate that osteocytes, the major cellular component of mature bone, are regulators of HSPC egress.", "Granulocyte colony-stimulating factor (G-CSF), used clinically to mobilize HSPCs, induces changes in the morphology and gene expression of the osteocytic network that precedes changes in osteoblasts.", "This rapid response is likely under control of the sympathetic nervous system, since osteocytes express the \u03b22-adrenergic receptor and surgical sympathectomy prevents it.", "Mice with targeted ablation of osteocytes or a disrupted osteocyte network have comparable numbers of HSPCs in the BM but fail to mobilize HSPCs in response to G-CSF.", "Taken together, these results indicate that the BM/bone niche interface is critically controlled from inside of the bone matrix and establish an important physiological role for skeletal tissues in hematopoietic function."], "structured": false}
{"doc_id": 13513790, "title": "Generation of Genetically Modified Mice by Oocyte Injection of Androgenetic Haploid Embryonic Stem Cells", "abstract": ["Haploid cells are amenable for genetic analysis.", "Recent success in the derivation of mouse haploid embryonic stem cells (haESCs) via parthenogenesis has enabled genetic screening in mammalian cells.", "However, successful generation of live animals from these haESCs, which is needed to extend the genetic analysis to the organism level, has not been achieved.", "Here, we report the derivation of haESCs from androgenetic blastocysts.", "These cells, designated as AG-haESCs, partially maintain paternal imprints, express classical ESC pluripotency markers, and contribute to various tissues, including the germline, upon injection into diploid blastocysts.", "Strikingly, live mice can be obtained upon injection of AG-haESCs into MII oocytes, and these mice bear haESC-carried genetic traits and develop into fertile adults.", "Furthermore, gene targeting via homologous recombination is feasible in the AG-haESCs.", "Our results demonstrate that AG-haESCs can be used as a genetically tractable fertilization agent for the production of live animals via injection into oocytes."], "structured": false}
{"doc_id": 13514898, "title": "The impact of hydroxyethyl starches in cardiac surgery: a meta-analysis", "abstract": ["INTRODUCTION Recent studies in septic patients showed that adverse effects of hydroxyethyl starches (HESs) possibly outweigh their benefits in severely impaired physiological haemostasis.", "It remains unclear whether this also applies to patient populations that are less vulnerable.", "In this meta-analysis, we evaluated the impact of various HES generations on safety and efficacy endpoints in patients undergoing cardiac surgery.   \n", "METHODS We searched the PubMed, Embase and Cochrane Central Register of Controlled Trials databases for randomised controlled trials (RCTs) in the English or German language comparing the use of HES to any other colloid or crystalloid during open heart surgery.   \n", "RESULTS Blood loss and transfusion requirements were higher for older starches with mean molecular weights more than 200 kDa compared to other volume substitutes.", "In contrast, this effect was not observed with latest-generation tetrastarches (130/0.4), which performed even better when compared to albumin (blood loss of tetrastarch versus albumin: standardised mean difference (SMD), -0.34; 95% CI, -0.63, -0.05; P = 0.02; versus gelatin: SMD, -0.06; 95% CI, -0.20, 0.08; P = 0.39; versus crystalloids: SMD, -0.05; 95% CI, -0.20, 0.10; P = 0.54).", "Similar results were found for transfusion needs.", "Lengths of stay in the intensive care unit or hospital were significantly shorter with tetrastarches compared to gelatin (intensive care unit: SMD, -0.10; 95% CI, -0.15, -0.05; P = 0.0002) and crystalloids (hospital: SMD, -0.52; 95% CI, -0.90, -0.14; P = 0.007).   \n", "CONCLUSIONS In this meta-analysis of RCTs, we could not identify safety issues with tetrastarches compared with other colloid or crystalloid solutions in terms of blood loss, transfusion requirements or hospital length of stay in patients undergoing cardiac surgery.", "The safety data on coagulation with older starches raise some issues that need to be addressed in future trials."], "structured": true}
{"doc_id": 13515165, "title": "Place of care in advanced cancer: a qualitative systematic literature review of patient preferences.", "abstract": ["BACKGROUND It is commonly written that more patients wish to die at home than currently achieve this.", "However, the evidence for preferences for place of terminal care and death has not been systematically reviewed.   ", "AIM To carry out a systematic literature review of the preferences for place of care and death among advanced cancer patients.   \n", "METHOD Studies were identified using systematic database searches of MEDLINE (1966-1999), PsychLit (1974-1999), and Bath Information Data Service (BIDS) (1981-1999).", "Studies were assessed and data extracted and synthesises following the NHS Centre for Reviews and Dissemination guidelines, grading studies according to design and rigor of methods.", "Studies of preferences in the general population and of groups including cancer patients and/or their caregivers were included.   \n", "RESULTS Eighteen studies determining preferences in either the general population or groups including cancer patients were identified.", "Views were obtained prospectively and retrospectively from patients, the general population, families, and professionals.", "Respondents indicated preferences for home death (range 49%-100%), except one study of patients in the care of a continuing care team in London where only 25%-29% of patients wanted a home death, and inpatient hospice was the most favored option.", "However, the response rate of this study was not known.", "Among the general public there was a higher preference for inpatient hospice care among in people with recent experience of a close friend or relative's death or dying.", "Where the views of patients, families, and professionals were compared, all respondents broadly agreed although patients expressed the strongest home preferences.", "Only 2 of the studies provided longitudinal data, and 9 of the 18 had major deficits in design or reporting, such as poor or unknown response rate, unclear or unsystematic methods of eliciting preferences or other sample or measurement bias.", "However, sensitivity analysis of only the more robust and larger studies did not alter the finding of a preference for home care at the end of life in over 50% of patients.   \n", "CONCLUSIONS Home care is the most common preference, with inpatient hospice care as second preference in advanced illness.", "Meeting these preferences could be important outcomes for services.", "Study designs in this area need to be improved."], "structured": true}
{"doc_id": 13519661, "title": "Linkage Disequilibrium Mapping of       CHEK2: Common Variation and Breast Cancer Risk     ", "abstract": ["Background Checkpoint kinase 2 (CHEK2) averts cancer development by promoting cell cycle arrest and activating DNA repair in genetically damaged cells.", "Previous investigation has established a role for the CHEK2 gene in breast cancer aetiology, but studies have largely been limited to the rare 1100delC mutation.", "Whether common polymorphisms in this gene influence breast cancer risk remains unknown.", "In this study, we aimed to assess the importance of common CHEK2 variants on population risk for breast cancer by capturing the majority of diversity in the gene using haplotype tagging single nucleotide polymorphisms (tagSNPs).", "Methods and Findings We analyzed 14 common SNPs spanning 52 kilobases (kb) of the CHEK2 gene in 92 Swedish women.", "Coverage evaluation indicated that these typed SNPs would efficiently convey association signal also from untyped SNPs in the same region.", "Six of the 14 SNPs predicted well both the haplotypic and single SNP variations within CHEK2.", "We genotyped these six tagSNPs in 1,577 postmenopausal breast cancer cases and 1,513 population controls, but found no convincing association between any common CHEK2 haplotype and breast cancer risk.", "The 1100delC mutation was rare in our Swedish population\u20140.7% in cases and 0.4% in controls\u2014 with a corresponding odds ratio for carriers versus noncarriers of 2.26 (95% confidence interval, 0.99\u20135.15).", "Estimates of the population frequency and the odds ratio of 1100delC indicate that our sample is representative of a Northern European population."], "structured": false}
{"doc_id": 13552682, "title": "Decoding Mammalian Ribosome-mRNA States by Translational GTPase Complexes", "abstract": ["In eukaryotes, accurate protein synthesis relies on a family of translational GTPases that pair with specific decoding factors to decipher the mRNA code on ribosomes.", "We present structures of the mammalian ribosome engaged with decoding factor\u22c5GTPase complexes representing intermediates of translation elongation (aminoacyl-tRNA\u22c5eEF1A), termination (eRF1\u22c5eRF3), and ribosome rescue (Pelota\u22c5Hbs1l).", "Comparative analyses reveal that each decoding factor exploits the plasticity of the ribosomal decoding center to differentially remodel ribosomal proteins and rRNA.", "This leads to varying degrees of large-scale ribosome movements and implies distinct mechanisms for communicating information from the decoding center to each GTPase.", "Additional structural snapshots of the translation termination pathway reveal the conformational changes that choreograph the accommodation of decoding factors into the peptidyl transferase center.", "Our results provide a structural framework for how different states of the mammalian ribosome are selectively recognized by the appropriate decoding factor\u22c5GTPase complex to ensure translational fidelity."], "structured": false}
{"doc_id": 13573143, "title": "Intestinal Cgi-58 Deficiency Reduces Postprandial Lipid Absorption", "abstract": ["Comparative Gene Identification-58 (CGI-58), a lipid droplet (LD)-associated protein, promotes intracellular triglyceride (TG) hydrolysis in vitro.", "Mutations in human CGI-58 cause TG accumulation in numerous tissues including intestine.", "Enterocytes are thought not to store TG-rich LDs, but a fatty meal does induce temporary cytosolic accumulation of LDs.", "Accumulated LDs are eventually cleared out, implying existence of TG hydrolytic machinery in enterocytes.", "However, identities of proteins responsible for LD-TG hydrolysis remain unknown.", "Here we report that intestine-specific inactivation of CGI-58 in mice significantly reduces postprandial plasma TG concentrations and intestinal TG hydrolase activity, which is associated with a 4-fold increase in intestinal TG content and large cytosolic LD accumulation in absorptive enterocytes during the fasting state.", "Intestine-specific CGI-58 knockout mice also display mild yet significant decreases in intestinal fatty acid absorption and oxidation.", "Surprisingly, inactivation of CGI-58 in intestine significantly raises plasma and intestinal cholesterol, and reduces hepatic cholesterol, without altering intestinal cholesterol absorption and fecal neutral sterol excretion.", "In conclusion, intestinal CGI-58 is required for efficient postprandial lipoprotein-TG secretion and for maintaining hepatic and plasma lipid homeostasis.", "Our animal model will serve as a valuable tool to further define how intestinal fat metabolism influences the pathogenesis of metabolic disorders, such as obesity and type 2 diabetes."], "structured": false}
{"doc_id": 13578199, "title": "Transglutaminase 2 Undergoes a Large Conformational Change upon Activation ", "abstract": ["Human transglutaminase 2 (TG2), a member of a large family of enzymes that catalyze protein crosslinking, plays an important role in the extracellular matrix biology of many tissues and is implicated in the gluten-induced pathogenesis of celiac sprue.", "Although vertebrate transglutaminases have been studied extensively, thus far all structurally characterized members of this family have been crystallized in conformations with inaccessible active sites.", "We have trapped human TG2 in complex with an inhibitor that mimics inflammatory gluten peptide substrates and have solved, at 2-A resolution, its x-ray crystal structure.", "The inhibitor stabilizes TG2 in an extended conformation that is dramatically different from earlier transglutaminase structures.", "The active site is exposed, revealing that catalysis takes place in a tunnel, bridged by two tryptophan residues that separate acyl-donor from acyl-acceptor and stabilize the tetrahedral reaction intermediates.", "Site-directed mutagenesis was used to investigate the acyl-acceptor side of the tunnel, yielding mutants with a marked increase in preference for hydrolysis over transamidation.", "By providing the ability to visualize this activated conformer, our results create a foundation for understanding the catalytic as well as the non-catalytic roles of TG2 in biology, and for dissecting the process by which the autoantibody response to TG2 is induced in celiac sprue patients."], "structured": false}
{"doc_id": 13580614, "title": "Lactic acidosis in patients with diabetes treated with metformin.", "abstract": ["To the Editor: From May 1995, when metformin was introduced in the United States, through June 30, 1996, the Food and Drug Administration (FDA) received reports of lactic acidosis in 66 patients treated with metformin.", "In 47 patients, the diagnosis was confirmed on the basis of circulating lactate values (>5 mmol per liter), in accordance with established criteria for the diagnosis of lactic acidosis (Table 1).1,2 Of the 47 patients with confirmed diagnoses, 43 had one or more risk factors for lactic acidosis.", "Thirty (64 percent) had preexisting cardiac disease, of whom 18 had histories of congestive heart failure. . . ."], "structured": false}
{"doc_id": 13583521, "title": "The Apaf-1 apoptosome induces formation of caspase-9 homo- and heterodimers with distinct activities", "abstract": ["According to dogma, initiator caspases are activated through proximity-induced homodimerization, but some studies infer that during apoptosis caspase-9 may instead form a holoenzyme with the Apaf-1 apoptosome.", "Using several biochemical approaches, including a novel site-specific crosslinking technique, we provide the first direct evidence that procaspase-9 homodimerizes within the apoptosome, markedly increasing its avidity for the complex and inducing selective intramolecular cleavage at Asp-315.", "Remarkably, however, procaspase-9 could also bind via its small subunit to the NOD domain in Apaf-1, resulting in the formation of a heterodimer that more efficiently activated procaspase-3.", "Following cleavage, the intersubunit linker (and associated conformational changes) in caspase-9-p35/p12 inhibited its ability to form homo- and heterodimers, but feedback cleavage by caspase-3 at Asp-330 removed the linker entirely and partially restored activity to caspase-9-p35/p10.", "Thus, the apoptosome mediates the formation of caspase-9 homo- and heterodimers, both of which are impacted by cleavage and contribute to its overall function."], "structured": false}
{"doc_id": 13583615, "title": "Repositioning of aurora B promoted by chiasmata ensures sister chromatid mono-orientation in meiosis I.", "abstract": ["During meiosis I, kinetochores of sister chromatids are juxtaposed or fused and mono-orient, while homologous chromosomes that are paired by chiasmata (bivalents) have to biorient.", "In the absence of chiasmata, biorientation of sister chromatids (univalents), which carries a risk of aneuploidy, has been occasionally detected in several species, including humans.", "We show in fission yeast that biorientation of fused sister kinetochores predominates during early prometaphase I. Without chiasmata, this undesirable biorientation of univalents persists and eventually evades the spindle assembly checkpoint, provoking abnormal anaphase.", "When univalents are connected by chiasmata or by an artificial tether, this erroneous attachment is converted to monopolar attachment and stabilized.", "This stabilization is apparently achieved by a chromosome configuration that brings kinetochores to the outer edge of the bivalent, while bringing Aurora B, a destabilizer of kinetochore-microtubule attachment, inward.", "Our results elucidate how chiasmata favor biorientation of bivalents over that of univalents at meiosis I."], "structured": false}
{"doc_id": 13592721, "title": "Biophysical Constraints Arising from Compositional Context in Synthetic Gene Networks.", "abstract": ["Synthetic gene expression is highly sensitive to intragenic compositional context (promoter structure, spacing regions between promoter and coding sequences, and ribosome binding sites).", "However, much less is known about the effects of intergenic compositional context (spatial arrangement and orientation of entire genes on DNA) on expression levels in synthetic gene networks.", "We compare expression of induced genes arranged in convergent, divergent, or tandem orientations.", "Induction of convergent genes yielded up to 400% higher expression, greater ultrasensitivity, and dynamic range than divergent- or tandem-oriented genes.", "Orientation affects gene expression whether one or both genes are induced.", "We postulate that transcriptional interference in divergent and tandem genes, mediated by supercoiling, can explain differences in expression and validate this hypothesis through modeling and in vitro supercoiling relaxation experiments.", "Treatment with gyrase abrogated intergenic context effects, bringing expression levels within 30% of each other.", "We rebuilt the toggle switch with convergent genes, taking advantage of supercoiling effects to improve threshold detection and switch stability."], "structured": false}
{"doc_id": 13613916, "title": "Glucose repression in Saccharomyces cerevisiae", "abstract": ["Glucose is the primary source of energy for the budding yeast Saccharomyces cerevisiae.", "Although yeast cells can utilize a wide range of carbon sources, presence of glucose suppresses molecular activities involved in the use of alternate carbon sources as well as it represses respiration and gluconeogenesis.", "This dominant effect of glucose on yeast carbon metabolism is coordinated by several signaling and metabolic interactions that mainly regulate transcriptional activity but are also effective at post-transcriptional and post-translational levels.", "This review describes effects of glucose repression on yeast carbon metabolism with a focus on roles of the Snf3/Rgt2 glucose-sensing pathway and Snf1 signal transduction in establishment and relief of glucose repression."], "structured": false}
{"doc_id": 13614794, "title": "The p21 Cdk-interacting protein Cip1 is a potent inhibitor of G1 cyclin-dependent kinases.", "abstract": ["The cyclin-dependent kinase Cdk2 associates with cyclins A, D, and E and has been implicated in the control of the G1 to S phase transition in mammals.", "To identify potential Cdk2 regulators, we have employed an improved two-hybrid system to isolate human genes encoding Cdk-interacting proteins (Cips).", "CIP1 encodes a novel 21 kd protein that is found in cyclin A, cyclin D1, cyclin E, and Cdk2 immunoprecipitates.", "p21CIP1 is a potent, tight-binding inhibitor of Cdks and can inhibit the phosphorylation of Rb by cyclin A-Cdk2, cyclin E-Cdk2, cyclin D1-Cdk4, and cyclin D2-Cdk4 complexes.", "Cotransfection experiments indicate that CIP1 and SV40 T antigen function in a mutually antagonistic manner to control cell cycle progression."], "structured": false}
{"doc_id": 13618987, "title": "Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen)", "abstract": ["Gene sequences sampled at different points in time can be used to infer molecular phylogenies on a natural timescale of months or years, provided that the sequences in question undergo measurable amounts of evolutionary change between sampling times.", "Data sets with this property are termed heterochronous and have become increasingly common in several fields of biology, most notably the molecular epidemiology of rapidly evolving viruses.", "Here we introduce the cross-platform software tool, TempEst (formerly known as Path-O-Gen), for the visualization and analysis of temporally sampled sequence data.", "Given a molecular phylogeny and the dates of sampling for each sequence, TempEst uses an interactive regression approach to explore the association between genetic divergence through time and sampling dates.", "TempEst can be used to (1) assess whether there is sufficient temporal signal in the data to proceed with phylogenetic molecular clock analysis, and (2) identify sequences whose genetic divergence and sampling date are incongruent.", "Examination of the latter can help identify data quality problems, including errors in data annotation, sample contamination, sequence recombination, or alignment error.", "We recommend that all users of the molecular clock models implemented in BEAST first check their data using TempEst prior to analysis."], "structured": false}
{"doc_id": 13619127, "title": "Diabetes treatments and risk of amputation, blindness, severe kidney failure, hyperglycaemia, and hypoglycaemia: open cohort study in primary care", "abstract": ["OBJECTIVE To assess the risks of amputation, blindness, severe kidney failure, hyperglycaemia, and hypoglycaemia in patients with type 2 diabetes associated with prescribed diabetes drugs, particularly newer agents including gliptins or glitazones (thiazolidinediones).   \n", "DESIGN Open cohort study in primary care.   \n", "SETTING 1243 practices contributing data to the QResearch database in England.   \n", "PARTICIPANTS 469,688 patients with type 2 diabetes aged 25-84 years between 1 April 2007 and 31 January 2015.   ", "EXPOSURES Hypoglycaemic agents (glitazones, gliptins, metformin, sulphonylureas, insulin, and other) alone and in combination.   \n", "MAIN OUTCOME MEASURES First recorded diagnoses of amputation, blindness, severe kidney failure, hyperglycaemia, and hypoglycaemia recorded on patients' primary care, mortality, or hospital records.", "Cox models estimated hazard ratios for diabetes treatments adjusting for potential confounders.   \n", "RESULTS 21,308 (4.5%) and 32,533 (6.9%) patients received prescriptions for glitazones and gliptins during follow-up, respectively.", "Compared with non-use, glitazones were associated with a decreased risk of blindness (adjusted hazard ratio 0.71, 95% confidence interval 0.57 to 0.89; rate 14.4 per 10,000 person years of exposure) and an increased risk of hypoglycaemia (1.22, 1.10 to 1.37; 65.1); gliptins were associated with a decreased risk of hypoglycaemia (0.86, 0.77 to 0.96; 45.8).", "Although the numbers of patients prescribed gliptin monotherapy or glitazones monotherapy were relatively low, there were significantly increased risks of severe kidney failure compared with metformin monotherapy (adjusted hazard ratio 2.55, 95% confidence interval 1.13 to 5.74).", "We found significantly lower risks of hyperglycaemia among patients prescribed dual therapy involving metformin with either gliptins (0.78, 0.62 to 0.97) or glitazones (0.60, 0.45 to 0.80) compared with metformin monotherapy.", "Patients prescribed triple therapy with metformin, sulphonylureas, and either gliptins (adjusted hazard ratio 5.07, 95% confidence interval 4.28 to 6.00) or glitazones (6.32, 5.35 to 7.45) had significantly higher risks of hypoglycaemia than those prescribed metformin monotherapy, but these risks were similar to those involving dual therapy with metformin and sulphonylureas (6.03, 5.47 to 6.63).", "Patients prescribed triple therapy with metformin, sulphonylureas, and glitazones had a significantly reduced risk of blindness compared with metformin monotherapy (0.67, 0.48 to 0.94).   \n", "CONCLUSIONS We have found lower risks of hyperglycaemia among patients prescribed dual therapy involving metformin with either gliptins or glitazones compared with metformin alone.", "Compared with metformin monotherapy, triple therapy with metformin, sulphonylureas, and either gliptins or glitazones was associated with an increased risk of hypoglycaemia, which was similar to the risk for dual therapy with metformin and sulphonylureas.", "Compared with metformin monotherapy, triple therapy with metformin, sulphonylureas, and glitazones was associated with a reduced risk of blindness.", "These results, while subject to residual confounding, could have implications for the prescribing of hypoglycaemic drugs."], "structured": true}
{"doc_id": 13621186, "title": "Vertebrate rod photoreceptors express both BK and IK calcium-activated potassium channels, but only BK channels are involved in receptor potential regulation.", "abstract": ["In salamander rods, Ca(2+)-activated K(+) current (I(KCa)) provides an effective \"clamp\" of the dark membrane potential to its normal resting level.", "By a combination of electrophysiological, pharmacological, and immunohistochemical approaches, we show that salamander rods functionally express large-conductance Ca(2+)- and voltage-dependent potassium (BK) channel and intermediate-conductance Ca(2+)-dependent potassium (IK) channel, but not small-conductance Ca(2+)-dependent potassium channel (SK) subtypes.", "Application of 100 nM iberiotoxin and 100 nM clotrimazole reduced net I(KCa) to 36% and 63%, respectively, whereas the current was unaffected by application of 1 microM apamin.", "Consistently, anti- SK1, -SK2, and -SK3 antibodies were unable to stain rod photoreceptors, whereas both anti-BK and -SK4/ IK1 antibodies heavily stained the ellipsoid region of the inner segments of the rods.", "Moreover, by using current-clamp experiments, it was clearly seen that the strong clamping effect of the total I(KCa) was lost when IbTx, but not CLTZ, was applied to the bath.", "This behavior strongly suggests that of BK and IK channels, only the former are responsible for the clamping effect on the photoreceptor membrane potential."], "structured": false}
{"doc_id": 13624704, "title": "Ondansetron reduces nausea and vomiting after paediatric adenotonsillectomy.", "abstract": ["The efficacy, safety and resource implications of a single intravenous dose of ondansetron (0.1 mg.kg-1, maximum 4 mg) were assessed in a multinational, multicentre, randomized, double-blind, placebo-controlled trial of 427 children aged 1-12 years, undergoing tonsillectomy with/without adenoidectomy.", "Emesis (retching and/or vomiting) and nausea were analysed separately.", "Significantly more ondansetron-treated children had no episodes of emesis (127/212 (60%) vs 100/215 (47%); P = 0.004) and experienced no postoperative nausea (135/211 (64%) vs 108/213 (51%); P = 0.004) in the first 24 h. Ondansetron also reduced the number of emetic episodes (P < 0.001), the time to the first emetic episode (P < 0.001) and overall nausea severity (P = 0.003).", "Significantly fewer ondansetron-treated children were rescued or withdrawn from the study (5% vs 10%; P = 0.042).", "Fewer ondansetron-treated patients required nursing intervention (34% vs 45%; P = 0.007) and the average intervention time was significantly shorter (4.6 vs 8.1 minutes; P = 0.001).", "Resources used to manage PONV were significantly reduced by ondansetron (43% vs 57%; P = 0.014)."], "structured": false}
{"doc_id": 13625993, "title": "Assessing the cost effectiveness of using prognostic biomarkers with decision models: case study in prioritising patients waiting for coronary artery surgery", "abstract": ["OBJECTIVE To determine the effectiveness and cost effectiveness of using information from circulating biomarkers to inform the prioritisation process of patients with stable angina awaiting coronary artery bypass graft surgery.   \n", "DESIGN Decision analytical model comparing four prioritisation strategies without biomarkers (no formal prioritisation, two urgency scores, and a risk score) and three strategies based on a risk score using biomarkers: a routinely assessed biomarker (estimated glomerular filtration rate), a novel biomarker (C reactive protein), or both.", "The order in which to perform coronary artery bypass grafting in a cohort of patients was determined by each prioritisation strategy, and mean lifetime costs and quality adjusted life years (QALYs) were compared.   \n", "DATA SOURCES Swedish Coronary Angiography and Angioplasty Registry (9935 patients with stable angina awaiting coronary artery bypass grafting and then followed up for cardiovascular events after the procedure for 3.8 years), and meta-analyses of prognostic effects (relative risks) of biomarkers.   \n", "RESULTS The observed risk of cardiovascular events while on the waiting list for coronary artery bypass grafting was 3 per 10,000 patients per day within the first 90 days (184 events in 9935 patients).", "Using a cost effectiveness threshold of pound20,000- pound30,000 (euro22,000-euro33,000; $32,000-$48,000) per additional QALY, a prioritisation strategy using a risk score with estimated glomerular filtration rate was the most cost effective strategy (cost per additional QALY was < pound410 compared with the Ontario urgency score).", "The impact on population health of implementing this strategy was 800 QALYs per 100,000 patients at an additional cost of pound 245,000 to the National Health Service.", "The prioritisation strategy using a risk score with C reactive protein was associated with lower QALYs and higher costs compared with a risk score using estimated glomerular filtration rate.   \n", "CONCLUSION Evaluating the cost effectiveness of prognostic biomarkers is important even when effects at an individual level are small.", "Formal prioritisation of patients awaiting coronary artery bypass grafting using a routinely assessed biomarker (estimated glomerular filtration rate) along with simple, routinely collected clinical information was cost effective.", "Prioritisation strategies based on the prognostic information conferred by C reactive protein, which is not currently measured in this context, or a combination of C reactive protein and estimated glomerular filtration rate, is unlikely to be cost effective.", "The widespread practice of using only implicit or informal means of clinically ordering the waiting list may be harmful and should be replaced with formal prioritisation approaches."], "structured": true}
{"doc_id": 13636631, "title": "Cytokine control of memory T-cell development and survival", "abstract": ["Evidence has accumulated that cytokines have a fundamental role in the differentiation of memory T cells.", "Here, we follow the CD8+ T cell from initial activation to memory-cell generation, indicating the checkpoints at which cytokines determine the fate of the T cell.", "Members of the common cytokine-receptor \u03b3-chain (\u03b3c)-cytokine family \u2014 in particular, interleukin-7 (IL-7) and IL-15 \u2014 act at each stage of the immune response to promote proliferation and survival.", "In this manner, a stable and protective, long-lived memory CD8+ T-cell pool can be propagated and maintained."], "structured": false}
{"doc_id": 13639330, "title": "Histone Methylation-Dependent Mechanisms Impose Ligand Dependency for Gene Activation by Nuclear Receptors", "abstract": ["Nuclear receptors undergo ligand-dependent conformational changes that are required for corepressor-coactivator exchange, but whether there is an actual requirement for specific epigenetic landmarks to impose ligand dependency for gene activation remains unknown.", "Here we report an unexpected and general strategy that is based on the requirement for specific cohorts of inhibitory histone methyltransferases (HMTs) to impose gene-specific gatekeeper functions that prevent unliganded nuclear receptors and other classes of regulated transcription factors from binding to their target gene promoters and causing constitutive gene activation in the absence of stimulating signals.", "This strategy, based at least in part on an HMT-dependent inhibitory histone code, imposes a requirement for specific histone demethylases, including LSD1, to permit ligand- and signal-dependent activation of regulated gene expression.", "These events link an inhibitory methylation component of the histone code to a broadly used strategy that circumvents pathological constitutive gene induction by physiologically regulated transcription factors."], "structured": false}
{"doc_id": 13651792, "title": "Human IRGM Regulates Autophagy and Its Cell-Autonomous Immunity Functions Through Mitochondria", "abstract": ["IRGM, a human immunity-related GTPase, confers autophagic defence against intracellular pathogens by an unknown mechanism.", "Here, we report an unexpected mode of IRGM action.", "IRGM demonstrated differential affinity for the mitochondrial lipid cardiolipin, translocated to mitochondria, affected mitochondrial fission and induced autophagy.", "Mitochondrial fission was necessary for autophagic control of intracellular mycobacteria by IRGM.", "IRGM influenced mitochondrial membrane polarization and cell death.", "Overexpression of IRGMd, but not IRGMb splice isoforms, caused mitochondrial depolarization and autophagy-independent, but Bax/Bak-dependent, cell death.", "By acting on mitochondria, IRGM confers autophagic protection or cell death, explaining IRGM action both in defence against tuberculosis and in the damaging inflammation caused by Crohn's disease."], "structured": false}
{"doc_id": 13702924, "title": "The Developmental Transcriptome of the Mosquito Aedes aegypti, an Invasive Species and Major Arbovirus Vector", "abstract": ["Mosquitoes are vectors of a number of important human and animal diseases.", "The development of novel vector control strategies requires a thorough understanding of mosquito biology.", "To facilitate this, we used RNA-seq to identify novel genes and provide the first high-resolution view of the transcriptome throughout development and in response to blood feeding in a mosquito vector of human disease, Aedes aegypti, the primary vector for Dengue and yellow fever.", "We characterized mRNA expression at 34 distinct time points throughout Aedes development, including adult somatic and germline tissues, by using polyA+ RNA-seq.", "We identify a total of 14,238 novel new transcribed regions corresponding to 12,597 new loci, as well as many novel transcript isoforms of previously annotated genes.", "Altogether these results increase the annotated fraction of the transcribed genome into long polyA+ RNAs by more than twofold.", "We also identified a number of patterns of shared gene expression, as well as genes and/or exons expressed sex-specifically or sex-differentially.", "Expression profiles of small RNAs in ovaries, early embryos, testes, and adult male and female somatic tissues also were determined, resulting in the identification of 38 new Aedes-specific miRNAs, and ~291,000 small RNA new transcribed regions, many of which are likely to be endogenous small-interfering RNAs and Piwi-interacting RNAs.", "Genes of potential interest for transgene-based vector control strategies also are highlighted.", "Our data have been incorporated into a user-friendly genome browser located at www.", "Aedes.caltech.edu, with relevant links to Vectorbase (www.vectorbase.org)."], "structured": false}
{"doc_id": 13714201, "title": "Gut microbial diversity is associated with lower arterial stiffness in women", "abstract": ["Aims The gut microbiome influences metabolic syndrome (MetS) and inflammation and is therapeutically modifiable.", "Arterial stiffness is poorly correlated with most traditional risk factors.", "Our aim was to examine whether gut microbial composition is associated with arterial stiffness.   ", "Methods and results We assessed the correlation between carotid-femoral pulse wave velocity (PWV), a measure of arterial stiffness, and gut microbiome composition in 617 middle-aged women from the TwinsUK cohort with concurrent serum metabolomics data.", "Pulse wave velocity was negatively correlated with gut microbiome alpha diversity (Shannon index, Beta(SE)= -0.25(0.07), P = 1 \u00d7 10-4) after adjustment for covariates.", "We identified seven operational taxonomic units associated with PWV after adjusting for covariates and multiple testing-two belonging to the Ruminococcaceae family.", "Associations between microbe abundances, microbe diversity, and PWV remained significant after adjustment for levels of gut-derived metabolites (indolepropionate, trimethylamine oxide, and phenylacetylglutamine).", "We linearly combined the PWV-associated gut microbiome-derived variables and found that microbiome factors explained 8.3% (95% confidence interval 4.3-12.4%) of the variance in PWV.", "A formal mediation analysis revealed that only a small proportion (5.51%) of the total effect of the gut microbiome on PWV was mediated by insulin resistance and visceral fat, c-reactive protein, and cardiovascular risk factors after adjusting for age, body mass index, and mean arterial pressure.   ", "Conclusions Gut microbiome diversity is inversely associated with arterial stiffness in women.", "The effect of gut microbiome composition on PWV is only minimally mediated by MetS. This first human observation linking the gut microbiome to arterial stiffness suggests that targeting the microbiome may be a way to treat arterial ageing."], "structured": false}
{"doc_id": 13717103, "title": "ALS-FUS pathology revisited: singleton FUS mutations and an unusual case with both a FUS and TARDBP mutation", "abstract": ["INTRODUCTION Mutations in the FUS gene have been shown to be a rare cause of amyotrophic lateral sclerosis (ALS-FUS) and whilst well documented clinically and genetically there have been relatively few neuropathological studies.", "Recent work suggested a possible correlation between pathological features such as frequency of basophilic inclusions in neurons and rate of clinical decline, other studies have revealed a discrepancy between the upper motor neuron features detected clinically and the associated pathology.", "The purpose of this study was to describe the pathological features associated with more recently discovered FUS mutations and reinvestigate those with well recognised mutations in an attempt to correlate the pathology with mutation and/or clinical phenotype.", "The brains and spinal cords of seven cases of ALS-FUS were examined neuropathologically, including cases with the newly described p.", "K510E mutation and a case with both a known p.", "P525L mutation in the FUS gene and a truncating p.", "Y374X mutation in the TARDBP gene.   \n", "RESULTS The neuropathology in all cases revealed basophilic and FUS inclusions in the cord.", "The density and type of inclusions varied markedly between cases, but did not allow a clear correlation with clinical progression.", "Only one case showed significant motor cortical pathology despite the upper motor neuron clinical features being evident in 4 patients.", "The case with both a FUS and TARDBP mutation revealed FUS positive inclusions but no TDP-43 pathology.", "Instead there were unusual p62 positive, FUS negative neuronal and glial inclusions as well as dot-like neurites.   \n", "CONCLUSIONS The study confirms cases of ALS-FUS to be mainly a lower motor neuron disease and to have pathology that does not appear to neatly correlate with clinical features or genetics.", "Furthermore, the case with both a FUS and TARDBP mutation reveals an intriguing pathological profile which at least in part involves a very unusual staining pattern for the ubiquitin-binding protein p62."], "structured": true}
{"doc_id": 13726379, "title": "Coronary heart disease in south Asians overseas: a review.", "abstract": ["Coronary heart disease rates have been reported in several parts of the world to be unusually high in people originating from the Indian subcontinent.", "High coronary disease rates appear to be common to South Asian groups of different geographical origin, religion, and language.", "This presents a challenge to the understanding of coronary heart disease: the high rates in South Asians are not explained on the basis of elevated serum cholesterol, smoking or hypertension.", "Low plasma HDL cholesterol, high plasma triglyceride levels and high prevalence of non-insulin-dependent diabetes have been consistently found in South Asians overseas: this probably reflects an underlying state of insulin resistance.", "Further studies are needed to determine whether this metabolic disturbance can account for the high rates of coronary heart disease in South Asians, and to identify possibilities for prevention."], "structured": false}
{"doc_id": 13732033, "title": "A systematic review of parent and clinician views and perceptions that influence prescribing decisions in relation to acute childhood infections in primary care", "abstract": ["OBJECTIVES To investigate the views of parents, clinicians, and children pertaining to prescribing decisions for acute childhood infection in primary care.   \n", "METHODS A systematic review of qualitative studies.", "Meta-ethnographic methods were used, with data drawn from the primary studies in an interpretive analysis.   \n", "RESULTS A total of 15 studies met the inclusion criteria.", "The literature was dominated by concerns about antibiotic over-prescription.", "Children's views were not reported.", "Clinicians prescribed antibiotics when they felt pressured by parents or others (e.g. employers) to do so, when they believed there was a clear clinical indication, but also when they felt uncertain of clinical or social outcomes they prescribed \"just in case\".", "Parents wanted antibiotics when they felt they would improve the current illness, and when they felt pressure from daycare providers or employers.", "Clinicians avoided antibiotics when they were concerned about adverse reactions or drug resistance, when certain they were not indicated, and when there was no perceived pressure from parents.", "Parents also wished to avoid adverse effects of antibiotics, and did not want antibiotics when they would not relieve current symptoms.", "Some parents preferred to avoid medication altogether.", "Within paediatric consultations, parents sought a medical evaluation and decision.", "Primary care clinicians want satisfied parents and short consultations.   \n", "CONCLUSIONS Antibiotic prescriptions for childhood infections in primary care often result from \"just in case\" prescribing.", "These findings suggest that interventions which reduce clinician uncertainty regarding social or clinical outcomes and provide strategies to meet parents' needs within a short consultation are most likely to reduce antibiotic prescribing."], "structured": true}
{"doc_id": 13734012, "title": "Prevalent abnormal prion protein in human appendixes after bovine spongiform encephalopathy epizootic: large scale survey", "abstract": ["OBJECTIVES To carry out a further survey of archived appendix samples to understand better the differences between existing estimates of the prevalence of subclinical infection with prions after the bovine spongiform encephalopathy epizootic and to see whether a broader birth cohort was affected, and to understand better the implications for the management of blood and blood products and for the handling of surgical instruments.   \n", "DESIGN Irreversibly unlinked and anonymised large scale survey of archived appendix samples.   \n", "SETTING Archived appendix samples from the pathology departments of 41 UK hospitals participating in the earlier survey, and additional hospitals in regions with lower levels of participation in that survey.   ", "SAMPLE 32,441 archived appendix samples fixed in formalin and embedded in paraffin and tested for the presence of abnormal prion protein (PrP).   \n", "RESULTS Of the 32,441 appendix samples 16 were positive for abnormal PrP, indicating an overall prevalence of 493 per million population (95% confidence interval 282 to 801 per million).", "The prevalence in those born in 1941-60 (733 per million, 269 to 1596 per million) did not differ significantly from those born between 1961 and 1985 (412 per million, 198 to 758 per million) and was similar in both sexes and across the three broad geographical areas sampled.", "Genetic testing of the positive specimens for the genotype at PRNP codon 129 revealed a high proportion that were valine homozygous compared with the frequency in the normal population, and in stark contrast with confirmed clinical cases of vCJD, all of which were methionine homozygous at PRNP codon 129.   \n", "CONCLUSIONS This study corroborates previous studies and suggests a high prevalence of infection with abnormal PrP, indicating vCJD carrier status in the population compared with the 177 vCJD cases to date.", "These findings have important implications for the management of blood and blood products and for the handling of surgical instruments."], "structured": true}
{"doc_id": 13757347, "title": "Involvement of cortical fast-spiking parvalbumin-positive basket cells in epilepsy.", "abstract": ["GABAergic interneurons of the parvalbumin-positive fast-spiking basket cells subtype (PV INs) are important regulators of cortical network excitability and of gamma oscillations, involved in signal processing and cognition.", "Impaired development or function of PV INs has been associated with epilepsy in various animal models of epilepsy, as well as in some genetic forms of epilepsy in humans.", "In this review, we provide an overview of some of the experimental data linking PV INs dysfunction with epilepsy, focusing on disorders of the specification, migration, maturation, synaptic function, or connectivity of PV INs.", "Furthermore, we reflect on the potential therapeutic use of cell-type specific stimulation of PV INs within active networks and on the transplantation of PV INs precursors in the treatment of epilepsy and its comorbidities."], "structured": false}
{"doc_id": 13759726, "title": "Dynamic Gene Regulatory Networks of Human Myeloid Differentiation.", "abstract": ["The reconstruction of gene regulatory networks underlying cell differentiation from high-throughput gene expression and chromatin data remains a challenge.", "Here, we derive dynamic gene regulatory networks for human myeloid differentiation using a 5-day time series of RNA-seq and ATAC-seq data.", "We profile HL-60 promyelocytes differentiating into macrophages, neutrophils, monocytes, and monocyte-derived macrophages.", "We find a rapid response in the expression of key transcription factors and lineage markers that only regulate a subset of their targets at a given time, which is followed by chromatin accessibility changes that occur later along with further gene expression changes.", "We observe differences between promyelocyte- and monocyte-derived macrophages at both the transcriptional and chromatin landscape level, despite using the same differentiation stimulus, which suggest that the path taken by cells in the differentiation landscape defines their end cell state.", "More generally, our approach of combining neighboring time points and replicates to achieve greater sequencing depth can efficiently infer footprint-based regulatory networks from long series data."], "structured": false}
{"doc_id": 13760557, "title": "Canonical transient receptor potential 5 channel in conjunction with Orai1 and STIM1 allows Sr2+ entry, optimal influx of Ca2+, and degranulation in a rat mast cell line.", "abstract": ["Degranulation of mast cells in response to Ag or the calcium mobilizing agent, thapsigargin, is dependent on emptying of intracellular stores of Ca(2+) and the ensuing influx of external Ca(2+), also referred to as store-operated calcium entry.", "However, it is unlikely that the calcium release-activated calcium channel is the sole mechanism for the entry of Ca(2+) because Sr(2+) and other divalent cations also permeate and support degranulation in stimulated mast cells.", "In this study we show that influx of Ca(2+) and Sr(2+) as well as degranulation are dependent on the presence of the canonical transient receptor potential (TRPC) channel protein TRPC5, in addition to STIM1 and Orai1, as demonstrated by knock down of each of these proteins by inhibitory RNAs in a rat mast cell (RBL-2H3) line.", "Overexpression of STIM1 and Orai1, which are known to be essential components of calcium release-activated calcium channel, allows entry of Ca(2+) but not Sr(2+), whereas overexpression of STIM1 and TRPC5 allows entry of both Ca(2+) and Sr(2+).", "These and other observations suggest that the Sr(2+)-permeable TRPC5 associates with STIM1 and Orai1 in a stoichiometric manner to enhance entry of Ca(2+) to generate a signal for degranulation."], "structured": false}
{"doc_id": 13763195, "title": "LincRNA-p21 suppresses target mRNA translation.", "abstract": ["Mammalian long intergenic noncoding RNAs (lincRNAs) are best known for modulating transcription.", "Here we report a posttranscriptional function for lincRNA-p21 as a modulator of translation.", "Association of the RNA-binding protein HuR with lincRNA-p21 favored the recruitment of let-7/Ago2 to lincRNA-p21, leading to lower lincRNA-p21 stability.", "Under reduced HuR levels, lincRNA-p21 accumulated in human cervical carcinoma HeLa cells, increasing its association with JUNB and CTNNB1 mRNAs and selectively lowering their translation.", "With elevated HuR, lincRNA-p21 levels declined, which in turn derepressed JunB and \u03b2-catenin translation and increased the levels of these proteins.", "We propose that HuR controls translation of a subset of target mRNAs by influencing lincRNA-p21 levels.", "Our findings uncover a role for lincRNA as a posttranscriptional inhibitor of translation."], "structured": false}
{"doc_id": 13764090, "title": "Large intestine-targeted nanoparticle-releasing oral vaccine to control genitorectal viral infection", "abstract": ["Both rectal and vaginal mucosal surfaces serve as transmission routes for pathogenic microorganisms.", "Vaccination through large intestinal mucosa, previously proven protective for both of these mucosal sites in animal studies, can be achieved successfully by direct intracolorectal (i.c.r.) administration, but this route is clinically impractical.", "Oral vaccine delivery seems preferable but runs the risk of the vaccine's destruction in the upper gastrointestinal tract.", "Therefore, we designed a large intestine-targeted oral delivery with pH-dependent microparticles containing vaccine nanoparticles, which induced colorectal immunity in mice comparably to colorectal vaccination and protected against rectal and vaginal viral challenge.", "Conversely, vaccine targeted to the small intestine induced only small intestinal immunity and provided no rectal or vaginal protection, demonstrating functional compartmentalization within the gut mucosal immune system.", "Therefore, using this oral vaccine delivery system to target the large intestine, but not the small intestine, may represent a feasible new strategy for immune protection of rectal and vaginal mucosa."], "structured": false}
{"doc_id": 13765757, "title": "Timing of menarche and first full-term birth in relation to breast cancer risk.", "abstract": ["Ages at menarche and first birth are established risk factors for breast cancer.", "The interval between these ages may also affect risk, since the breast is more susceptible to carcinogenic insults during this period than during the parous period.", "However, few investigators have studied this relation.", "Using logistic regression, the authors evaluated associations between the timing of reproductive events and breast cancer risk among 4,013 cases and 4,069 controls enrolled in a multicenter, population-based US case-control study of White and African-American women (1994-1998).", "For White, parous premenopausal and postmenopausal women, those who had an interval of > or =16 years between the ages of menarche and first birth had 1.5-fold (95% confidence interval (CI): 1.0, 2.2) and 1.4-fold (95% CI: 1.1, 1.8) increased risks of breast cancer, respectively, in comparison with those who had < or =5 years between these ages.", "Adjusting for age at first birth altered these risk estimates somewhat, to odds ratios of 1.5 (95% CI: 0.8, 2.9) and 1.0 (95% CI: 0.6, 1.5), respectively.", "These associations were stronger for lobular and hormone-receptor-positive tumors but were absent among premenopausal African-American women.", "The authors conclude that the interval between age at menarche and age at first birth is associated with the risk of hormonally sensitive types of breast cancer, particularly among White women."], "structured": false}
{"doc_id": 13768432, "title": "Prognostic Value of Late Gadolinium Enhancement Cardiovascular Magnetic Resonance in Cardiac Amyloidosis", "abstract": ["BACKGROUND The prognosis and treatment of the 2 main types of cardiac amyloidosis, immunoglobulin light chain (AL) and transthyretin (ATTR) amyloidosis, are substantially influenced by cardiac involvement.", "Cardiovascular magnetic resonance with late gadolinium enhancement (LGE) is a reference standard for the diagnosis of cardiac amyloidosis, but its potential for stratifying risk is unknown.   \n", "METHODS AND RESULTS Two hundred fifty prospectively recruited subjects, 122 patients with ATTR amyloid, 9 asymptomatic mutation carriers, and 119 patients with AL amyloidosis, underwent LGE cardiovascular magnetic resonance.", "Subjects were followed up for a mean of 24\u00b113 months.", "LGE was performed with phase-sensitive inversion recovery (PSIR) and without (magnitude only).", "These were compared with extracellular volume measured with T1 mapping.", "PSIR was superior to magnitude-only inversion recovery LGE because PSIR always nulled the tissue (blood or myocardium) with the longest T1 (least gadolinium).", "LGE was classified into 3 patterns: none, subendocardial, and transmural, which were associated with increasing amyloid burden as defined by extracellular volume (P<0.0001), with transitions from none to subendocardial LGE at an extracellular volume of 0.40 to 0.43 (AL) and 0.39 to 0.40 (ATTR) and to transmural at 0.48 to 0.55 (AL) and 0.47 to 0.59 (ATTR).", "Sixty-seven patients (27%) died.", "Transmural LGE predicted death (hazard ratio, 5.4; 95% confidence interval, 2.1-13.7; P<0.0001) and remained independent after adjustment for N-terminal pro-brain natriuretic peptide, ejection fraction, stroke volume index, E/E', and left ventricular mass index (hazard ratio, 4.1; 95% confidence interval, 1.3-13.1; P<0.05).   \n", "CONCLUSIONS There is a continuum of cardiac involvement in systemic AL and ATTR amyloidosis.", "Transmural LGE is determined reliably by PSIR and represents advanced cardiac amyloidosis.", "The PSIR technique provides incremental information on outcome even after adjustment for known prognostic factors."], "structured": true}
{"doc_id": 13770184, "title": "Global, regional, and national comparative risk assessment of 79 behavioural, environmental and occupational, and metabolic risks or clusters of risks, 1990\u20132015: a systematic analysis for the Global Burden of Disease Study 2015", "abstract": ["BACKGROUND The Global Burden of Diseases, Injuries, and Risk Factors Study 2015 provides an up-to-date synthesis of the evidence for risk factor exposure and the attributable burden of disease.", "By providing national and subnational assessments spanning the past 25 years, this study can inform debates on the importance of addressing risks in context.   \n", "METHODS We used the comparative risk assessment framework developed for previous iterations of the Global Burden of Disease Study to estimate attributable deaths, disability-adjusted life-years (DALYs), and trends in exposure by age group, sex, year, and geography for 79 behavioural, environmental and occupational, and metabolic risks or clusters of risks from 1990 to 2015.", "This study included 388 risk-outcome pairs that met World Cancer Research Fund-defined criteria for convincing or probable evidence.", "We extracted relative risk and exposure estimates from randomised controlled trials, cohorts, pooled cohorts, household surveys, census data, satellite data, and other sources.", "We used statistical models to pool data, adjust for bias, and incorporate covariates.", "We developed a metric that allows comparisons of exposure across risk factors-the summary exposure value.", "Using the counterfactual scenario of theoretical minimum risk level, we estimated the portion of deaths and DALYs that could be attributed to a given risk.", "We decomposed trends in attributable burden into contributions from population growth, population age structure, risk exposure, and risk-deleted cause-specific DALY rates.", "We characterised risk exposure in relation to a Socio-demographic Index (SDI).   \n", "FINDINGS Between 1990 and 2015, global exposure to unsafe sanitation, household air pollution, childhood underweight, childhood stunting, and smoking each decreased by more than 25%.", "Global exposure for several occupational risks, high body-mass index (BMI), and drug use increased by more than 25% over the same period.", "All risks jointly evaluated in 2015 accounted for 57\u00b78% (95% CI 56\u00b76-58\u00b78) of global deaths and 41\u00b72% (39\u00b78-42\u00b78) of DALYs.", "In 2015, the ten largest contributors to global DALYs among Level 3 risks were high systolic blood pressure (211\u00b78 million [192\u00b77 million to 231\u00b71 million] global DALYs), smoking (148\u00b76 million [134\u00b72 million to 163\u00b71 million]), high fasting plasma glucose (143\u00b71 million [125\u00b71 million to 163\u00b75 million]), high BMI (120\u00b71 million [83\u00b78 million to 158\u00b74 million]), childhood undernutrition (113\u00b73 million [103\u00b79 million to 123\u00b74 million]), ambient particulate matter (103\u00b71 million [90\u00b78 million to 115\u00b71 million]), high total cholesterol (88\u00b77 million [74\u00b76 million to 105\u00b77 million]), household air pollution (85\u00b76 million [66\u00b77 million to 106\u00b71 million]), alcohol use (85\u00b70 million [77\u00b72 million to 93\u00b70 million]), and diets high in sodium (83\u00b70 million [49\u00b73 million to 127\u00b75 million]).", "From 1990 to 2015, attributable DALYs declined for micronutrient deficiencies, childhood undernutrition, unsafe sanitation and water, and household air pollution; reductions in risk-deleted DALY rates rather than reductions in exposure drove these declines.", "Rising exposure contributed to notable increases in attributable DALYs from high BMI, high fasting plasma glucose, occupational carcinogens, and drug use.", "Environmental risks and childhood undernutrition declined steadily with SDI; low physical activity, high BMI, and high fasting plasma glucose increased with SDI.", "In 119 countries, metabolic risks, such as high BMI and fasting plasma glucose, contributed the most attributable DALYs in 2015.", "Regionally, smoking still ranked among the leading five risk factors for attributable DALYs in 109 countries; childhood underweight and unsafe sex remained primary drivers of early death and disability in much of sub-Saharan Africa.   \n", "INTERPRETATION Declines in some key environmental risks have contributed to declines in critical infectious diseases.", "Some risks appear to be invariant to SDI.", "Increasing risks, including high BMI, high fasting plasma glucose, drug use, and some occupational exposures, contribute to rising burden from some conditions, but also provide opportunities for intervention.", "Some highly preventable risks, such as smoking, remain major causes of attributable DALYs, even as exposure is declining.", "Public policy makers need to pay attention to the risks that are increasingly major contributors to global burden.   \n", "FUNDING Bill & Melinda Gates Foundation."], "structured": true}
{"doc_id": 13771184, "title": "Human RecQ helicases in DNA repair, recombination, and replication.", "abstract": ["RecQ helicases are an important family of genome surveillance proteins conserved from bacteria to humans.", "Each of the five human RecQ helicases plays critical roles in genome maintenance and stability, and the RecQ protein family members are often referred to as guardians of the genome.", "The importance of these proteins in cellular homeostasis is underscored by the fact that defects in BLM, WRN, and RECQL4 are linked to distinct heritable human disease syndromes.", "Each human RecQ helicase has a unique set of protein-interacting partners, and these interactions dictate its specialized functions in genome maintenance, including DNA repair, recombination, replication, and transcription.", "Human RecQ helicases also interact with each other, and these interactions have significant impact on enzyme function.", "Future research goals in this field include a better understanding of the division of labor among the human RecQ helicases and learning how human RecQ helicases collaborate and cooperate to enhance genome stability."], "structured": false}
{"doc_id": 13774178, "title": "Metabolomics study of the therapeutic mechanism of Schisandra Chinensis lignans in diet-induced hyperlipidemia mice", "abstract": ["BACKGROUND Schisandra, a globally distributed plant, has been widely applied for the treatment of diseases such as hyperlipidemia, fatty liver and obesity in China.", "In the present work, a rapid resolution liquid chromatography coupled with quadruple-time-of-flight mass spectrometry (RRLC-Q-TOF-MS)-based metabolomics was conducted to investigate the intervention effect of Schisandra chinensis lignans (SCL) on hyperlipidemia mice induced by high-fat diet (HFD).   \n", "METHODS Hyperlipidemia mice were orally administered with SCL (100 mg/kg) once a day for 4 weeks.", "Serum biochemistry assay of triglyceride (TG), total cholesterol (TC), low-density lipoprotein cholesterol (LDL-c) and high-density lipoprotein cholesterol (HDL-c) was conducted to confirm the treatment of SCL on lipid regulation.", "Metabolomics analysis on serum samples was carried out, and principal component analysis (PCA) and partial least squares-discriminant analysis (PLS-DA) were carried out for the pattern recognition and characteristic metabolites identification.", "The relative levels of critical regulatory factors of liver lipid metabolism, sterol regulatory element-binding proteins (SREBPs) and its related gene expressions were measured by quantitative real-time polymerase chain reaction (RT-PCR) for investigating the underlying mechanism.   \n", "RESULTS Oral administration of SCL significantly decreased the serum levels of TC, TG and LDL-c and increased the serum level of HDL-c in the hyperlipidemia mice, and no effect of SCL on blood lipid levels was observed in control mice.", "Serum samples were scattered in the PCA scores plots in response to the control, HFD and SCL group.", "Totally, thirteen biomarkers were identified and nine of them were recovered to the normal levels after SCL treatment.", "Based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis, the anti-hyperlipidemia mechanisms of SCL may be involved in the following metabolic pathways: tricarboxylic acid (TCA) cycle, synthesis of ketone body and cholesterol, choline metabolism and fatty acid metabolism.", "Meanwhile, SCL significantly inhibited the mRNA expression level of hepatic lipogenesis genes such as SREBP-1c, fatty acid synthase (FAS) and acetyl-CoA carboxylase (ACC), and decreased the mRNA expression of liver X receptor \u03b1 (LXR\u03b1).", "Moreover, SCL also significantly decreased the expression level of SREBP-2 and 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGCR) in the liver of hyperlipidemia mice.   \n", "CONCLUSION Anti-hyperlipidemia effect of SCL was confirmed by both serum biochemistry and metabolomics analysis.", "The mechanism may be related to the down-regulation of LXR\u03b1/SREBP-1c/FAS/ACC and SREBP2/HMGCR signaling pathways."], "structured": true}
{"doc_id": 13777138, "title": "Tet1 and Tet2 regulate 5-hydroxymethylcytosine production and cell lineage specification in mouse embryonic stem cells.", "abstract": ["TET family enzymes convert 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) in DNA.", "Here, we show that Tet1 and Tet2 are Oct4-regulated enzymes that together sustain 5hmC in mouse embryonic stem cells (ESCs) and are induced concomitantly with 5hmC during reprogramming of fibroblasts to induced pluripotent stem cells.", "ESCs depleted of Tet1 by RNAi show diminished expression of the Nodal antagonist Lefty1 and display hyperactive Nodal signaling and skewed differentiation into the endoderm-mesoderm lineage in embryoid bodies in vitro.", "In Fgf4- and heparin-supplemented culture conditions, Tet1-depleted ESCs activate the trophoblast stem cell lineage determinant Elf5 and can colonize the placenta in midgestation embryo chimeras.", "Consistent with these findings, Tet1-depleted ESCs form aggressive hemorrhagic teratomas with increased endoderm, reduced neuroectoderm, and ectopic appearance of trophoblastic giant cells.", "Thus, 5hmC is an epigenetic modification associated with the pluripotent state, and Tet1 functions to regulate the lineage differentiation potential of ESCs."], "structured": false}
{"doc_id": 13777706, "title": "Polycomb Associates Genome-wide with a Specific RNA Polymerase II Variant, and Regulates Metabolic Genes in ESCs", "abstract": ["Polycomb repressor complexes (PRCs) are important chromatin modifiers fundamentally implicated in pluripotency and cancer.", "Polycomb silencing in embryonic stem cells (ESCs) can be accompanied by active chromatin and primed RNA polymerase II (RNAPII), but the relationship between PRCs and RNAPII remains unclear genome-wide.", "We mapped PRC repression markers and four RNAPII states in ESCs using ChIP-seq, and found that PRC targets exhibit a range of RNAPII variants.", "First, developmental PRC targets are bound by unproductive RNAPII (S5p(+)S7p(-)S2p(-)) genome-wide.", "Sequential ChIP, Ring1B depletion, and genome-wide correlations show that PRCs and RNAPII-S5p physically bind to the same chromatin and functionally synergize.", "Second, we identify a cohort of genes marked by PRC and elongating RNAPII (S5p(+)S7p(+)S2p(+)); they produce mRNA and protein, and their expression increases upon PRC1 knockdown.", "We show that this group of PRC targets switches between active and PRC-repressed states within the ESC population, and that many have roles in metabolism."], "structured": false}
{"doc_id": 13778710, "title": "Chemokine-like receptor 1 (CMKLR1) and chemokine (C-C motif) receptor-like 2 (CCRL2); two multifunctional receptors with unusual properties.", "abstract": ["Chemokine-like receptor 1 (CMKLR1), also known as ChemR23, and chemokine (C-C motif) receptor-like 2 (CCRL2) are 7-transmembrane receptors that were cloned in the late 1990s based on their homology to known G-protein-coupled receptors.", "They were previously orphan receptors without any known biological roles; however, recent studies identified ligands for these receptors and their functions have begun to be unveiled.", "The plasma protein-derived chemoattractant chemerin is a ligand for CMKLR1 and activation of CMKLR1 with chemerin induces the migration of macrophages and dendritic cells (DCs) in vitro, suggesting a proinflammatory role.", "However, in vivo studies using CMKLR-deficient mice suggest an anti-inflammatory role for this receptor, possibly due to the recruitment of tolerogenic plasmacytoid DCs.", "Chemerin/CMKLR1 interaction also promotes adipogenesis and angiogenesis.", "The anti-inflammatory lipid mediator, resolving E1, is another CMKLR1 ligand and it inhibits leukocyte infiltration and proinflammatory gene expression.", "These divergent results suggest that CMKLR1 is a multifunctional receptor.", "The chemokine CCL5 and CCL19 are reported to bind to CCRL2.", "Like Duffy antigen for chemokine receptor (DARC), D6 and CCX-CKR, CCRL2 does not signal, but it constitutively recycles, potentially reducing local concentration of CCL5 and CCL19 and subsequent immune responses.", "Surprisingly, chemerin, a ligand for CMKLR1, is a ligand for CCRL2.", "CCRL2 binds chemerin and increases local chemerin concentration to efficiently present it to CMKLR1 on nearby cells, providing a link between CCRL2 and CMKLR1.", "Although these findings suggest an anti-inflammatory role, a recent study using CCRL2-deficient mice indicates a proinflammatory role; thus, CCRL2 may also be multifunctional.", "Further studies using CMKLR1- or CCRL2-deficient mice are needed to further define the role of these receptors in immune responses and other cellular processes."], "structured": false}
{"doc_id": 13779605, "title": "Identification of vitronectin as an extrinsic inducer of cancer stem cell differentiation and tumor formation.", "abstract": ["There is mounting evidence that tumors are initiated by a rare subset of cells called cancer stem cells (CSCs).", "CSCs are generally quiescent, self-renew, form tumors at low numbers, and give rise to the heterogeneous cell types found within a tumor.", "CSCs isolated from multiple tumor types differentiate both in vivo and in vitro when cultured in serum, yet the factors responsible for their differentiation have not yet been identified.", "Here we show that vitronectin is the component of human serum driving stem cell differentiation through an integrin alpha V beta 3-dependent mechanism.", "CSCs cultured on vitronectin result in downregulation of stem cell genes, modulation of differentiation markers, and loss of beta-catenin nuclear localization.", "Blocking integrin alpha V beta 3 inhibits differentiation and subsequently tumor formation.", "Thus, CSCs must be engaged by one or more extracellular signals to differentiate and initiate tumor formation, defining a new axis for future novel therapies aimed at both the extrinsic and intracellular pathways."], "structured": false}
{"doc_id": 13780287, "title": "STIM1 Is a Calcium Sensor Specialized for Digital Signaling", "abstract": ["When cells are activated by calcium-mobilizing agonists at low, physiological concentrations, the resulting calcium signals generally take the form of repetitive regenerative discharges of stored calcium, termed calcium oscillations [1].", "These intracellular calcium oscillations have long fascinated biologists as a mode of digitized intracellular signaling.", "Recent work has highlighted the role of calcium influx as an essential component of calcium oscillations [2].", "This influx occurs through a process known as store-operated calcium entry, which is initiated by calcium sensor proteins, STIM1 and STIM2, in the endoplasmic reticulum [3].", "STIM2 is activated by changes in endoplasmic reticulum calcium near the resting level, whereas a threshold of calcium depletion is required for STIM1 activation [4].", "Here we show that, surprisingly, it is STIM1 and not STIM2 that is exclusively involved in calcium entry during calcium oscillations.", "The implication is that each oscillation produces a transient drop in endoplasmic reticulum calcium and that this drop is sufficient to transiently activate STIM1.", "This transient activation of STIM1 can be observed in some cells by total internal reflection fluorescence microscopy.", "This arrangement nicely provides a clearly defined and unambiguous signaling system, translating a digital calcium release signal into calcium influx that can signal to downstream effectors."], "structured": false}
{"doc_id": 13782317, "title": "Trends in the use of complementary health approaches among adults: United States, 2002-2012.", "abstract": ["OBJECTIVE This report presents national estimates of the use of complementary health approaches among adults in the United States across three time points.", "Trends in the use of selected complementary health approaches are compared for 2002, 2007, and 2012, and differences by selected demographic characteristics are also examined.   \n", "METHODS Combined data from 88,962 adults aged 18 and over collected as part of the 2002, 2007, and 2012 National Health Interview Survey were analyzed for this report.", "Sample data were weighted to produce national estimates that are representative of the civilian noninstitutionalized U.S. adult population.", "Differences between percentages were evaluated using two-sided significance tests at the 0.05 level.   \n", "RESULTS Although the use of individual approaches varied across the three time points, nonvitamin, nonmineral dietary supplements remained the most popular complementary health approach used.", "The use of yoga, tai chi, and qi gong increased linearly across the three time points; among these three approaches, yoga accounted for approximately 80% of the prevalence.", "The use of any complementary health approach also differed by selected sociodemographic characteristics.", "The most notable observed differences in use were by age and Hispanic or Latino origin and race."], "structured": true}
{"doc_id": 13790144, "title": "Histone structure and nucleosome stability.", "abstract": ["Histone proteins play essential structural and functional roles in the transition between active and inactive chromatin states.", "Although histones have a high degree of conservation due to constraints to maintain the overall structure of the nucleosomal octameric core, variants have evolved to assume diverse roles in gene regulation and epigenetic silencing.", "Histone variants, post-translational modifications and interactions with chromatin remodeling complexes influence DNA replication, transcription, repair and recombination.", "The authors review recent findings on the structure of chromatin that confirm previous interparticle interactions observed in crystal structures."], "structured": false}
{"doc_id": 13791044, "title": "Cerebral palsy among term and postterm births.", "abstract": ["CONTEXT Although preterm delivery is a well-established risk factor for cerebral palsy (CP), preterm deliveries contribute only a minority of affected infants.", "There is little information on the relation of CP risk to gestational age in the term range, where most CP occurs.   \n", "OBJECTIVE To determine whether timing of birth in the term and postterm period is associated with risk of CP.   \n", "DESIGN, SETTING, AND PARTICIPANTS Population-based follow-up study using the Medical Birth Registry of Norway to identify 1,682,441 singleton children born in the years 1967-2001 with a gestational age of 37 through 44 weeks and no congenital anomalies.", "The cohort was followed up through 2005 by linkage to other national registries.   \n", "MAIN OUTCOME MEASURES Absolute and relative risk of CP for children surviving to at least 4 years of age.   \n", "RESULTS Of the cohort of term and postterm children, 1938 were registered with CP in the National Insurance Scheme.", "Infants born at 40 weeks had the lowest risk of CP, with a prevalence of 0.99/1000 (95% confidence interval [CI], 0.90-1.08).", "Risk for CP was higher with earlier or later delivery, with a prevalence at 37 weeks of 1.91/1000 (95% CI, 1.58-2.25) and a relative risk (RR) of 1.9 (95% CI, 1.6-2.4), a prevalence at 38 weeks of 1.25/1000 (95% CI, 1.07-1.42) and an RR of 1.3 (95% CI, 1.1-1.6), a prevalence at 42 weeks of 1.36/1000 (95% CI, 1.19-1.53) and an RR of 1.4 (95% CI, 1.2-1.6), and a prevalence after 42 weeks of 1.44 (95% CI, 1.15-1.72) and an RR of 1.4 (95% CI, 1.1-1.8).", "These associations were even stronger in a subset with gestational age based on ultrasound measurements: at 37 weeks the prevalence was 1.17/1000 (95% CI, 0.30-2.04) and the relative risk was 3.7 (95% CI, 1.5-9.1).", "At 42 weeks the prevalence was 0.85/1000 (95% CI, 0.33-1.38) and the relative risk was 2.4 (95% CI, 1.1-5.3).", "Adjustment for infant sex, maternal age, and various socioeconomic measures had little effect.   \n", "CONCLUSION Compared with delivery at 40 weeks' gestation, delivery at 37 or 38 weeks or at 42 weeks or later was associated with an increased risk of CP."], "structured": true}
{"doc_id": 13791206, "title": "53BP1 Inhibits Homologous Recombination in Brca1-Deficient Cells by Blocking Resection of DNA Breaks", "abstract": ["Defective DNA repair by homologous recombination (HR) is thought to be a major contributor to tumorigenesis in individuals carrying Brca1 mutations.", "Here, we show that DNA breaks in Brca1-deficient cells are aberrantly joined into complex chromosome rearrangements by a process dependent on the nonhomologous end-joining (NHEJ) factors 53BP1 and DNA ligase 4.", "Loss of 53BP1 alleviates hypersensitivity of Brca1 mutant cells to PARP inhibition and restores error-free repair by HR.", "Mechanistically, 53BP1 deletion promotes ATM-dependent processing of broken DNA ends to produce recombinogenic single-stranded DNA competent for HR.", "In contrast, Lig4 deficiency does not rescue the HR defect in Brca1 mutant cells but prevents the joining of chromatid breaks into chromosome rearrangements.", "Our results illustrate that HR and NHEJ compete to process DNA breaks that arise during DNA replication and that shifting the balance between these pathways can be exploited to selectively protect or kill cells harboring Brca1 mutations."], "structured": false}
{"doc_id": 13791788, "title": "The genetics of Mexico recapitulates Native American substructure and affects biomedical traits", "abstract": ["Mexico harbors great cultural and ethnic diversity, yet fine-scale patterns of human genome-wide variation from this region remain largely uncharacterized.", "We studied genomic variation within Mexico from over 1000 individuals representing 20 indigenous and 11 mestizo populations.", "We found striking genetic stratification among indigenous populations within Mexico at varying degrees of geographic isolation.", "Some groups were as differentiated as Europeans are from East Asians.", "Pre-Columbian genetic substructure is recapitulated in the indigenous ancestry of admixed mestizo individuals across the country.", "Furthermore, two independently phenotyped cohorts of Mexicans and Mexican Americans showed a significant association between subcontinental ancestry and lung function.", "Thus, accounting for fine-scale ancestry patterns is critical for medical and population genetic studies within Mexico, in Mexican-descent populations, and likely in many other populations worldwide."], "structured": false}
{"doc_id": 13794374, "title": "COPI Complex Is a Regulator of Lipid Homeostasis", "abstract": ["Lipid droplets are ubiquitous triglyceride and sterol ester storage organelles required for energy storage homeostasis and biosynthesis.", "Although little is known about lipid droplet formation and regulation, it is clear that members of the PAT (perilipin, adipocyte differentiation related protein, tail interacting protein of 47 kDa) protein family coat the droplet surface and mediate interactions with lipases that remobilize the stored lipids.", "We identified key Drosophila candidate genes for lipid droplet regulation by RNA interference (RNAi) screening with an image segmentation-based optical read-out system, and show that these regulatory functions are conserved in the mouse.", "Those include the vesicle-mediated Coat Protein Complex I (COPI) transport complex, which is required for limiting lipid storage.", "We found that COPI components regulate the PAT protein composition at the lipid droplet surface, and promote the association of adipocyte triglyceride lipase (ATGL) with the lipid droplet surface to mediate lipolysis.", "Two compounds known to inhibit COPI function, Exo1 and Brefeldin A, phenocopy COPI knockdowns.", "Furthermore, RNAi inhibition of ATGL and simultaneous drug treatment indicate that COPI and ATGL function in the same pathway.", "These data indicate that the COPI complex is an evolutionarily conserved regulator of lipid homeostasis, and highlight an interaction between vesicle transport systems and lipid droplets."], "structured": false}
{"doc_id": 13798951, "title": "Differentiation of effector CD4 T cell populations (*).", "abstract": ["CD4 T cells play critical roles in mediating adaptive immunity to a variety of pathogens.", "They are also involved in autoimmunity, asthma, and allergic responses as well as in tumor immunity.", "During TCR activation in a particular cytokine milieu, naive CD4 T cells may differentiate into one of several lineages of T helper (Th) cells, including Th1, Th2, Th17, and iTreg, as defined by their pattern of cytokine production and function.", "In this review, we summarize the discovery, functions, and relationships among Th cells; the cytokine and signaling requirements for their development; the networks of transcription factors involved in their differentiation; the epigenetic regulation of their key cytokines and transcription factors; and human diseases involving defective CD4 T cell differentiation."], "structured": false}
{"doc_id": 13801259, "title": "Homocysteine and other thiols in plasma and urine: automated determination and sample stability.", "abstract": ["We have developed a modified version of our fully automated column-switching HPLC method for determining total plasma homocysteine based on single-column (reversed-phase) separation.", "Homocysteine, cysteine, and cysteinylglycine in plasma (total concentrations), acid-precipitated plasma (non-protein-bound concentrations), and urine can be determined.", "The derivatization and chromatography were performed automatically by a sample processor.", "The successful separation of all thiol species (within 15 min) was accomplished by accurate adjustment of the pH of the mobile phase to 3.65 (plasma) or 3.50 (acid-precipitated plasma, urine).", "Maximal fluorescence yield of cysteine, cysteinylglycine, and, to a lesser degree, homocysteine was dependent on optimal concentrations of EDTA and dithioerythritol during reduction (with NaBH4) and derivatization (with monobromobimane).", "The method is sensitive (detection limit approximately 0.05 pmol) and has a high degree of precision (CV < 5%).", "The sample output is approximately 70 samples in 24 h. Serum and heparin plasma can also be analyzed.", "Hemolysis up to approximately 2.0 g/L of hemoglobin did not interfere with the analytical recovery of homocysteine or cysteine.", "Collection of blood, separation of plasma from whole blood, and acid precipitation must be standardized to obtain reproducible thiol results.", "Our modifications and the standardization of blood-sampling procedures have substantially improved the method and broadened its applications."], "structured": false}
{"doc_id": 13814480, "title": "Induced pluripotent stem cells in Alzheimer\u2019s disease: applications for disease modeling and cell-replacement therapy", "abstract": ["Alzheimer's disease (AD) is the most common cause of dementia in those over the age of 65.", "While a numerous of disease-causing genes and risk factors have been identified, the exact etiological mechanisms of AD are not yet completely understood, due to the inability to test theoretical hypotheses on non-postmortem and patient-specific research systems.", "The use of recently developed and optimized induced pluripotent stem cells (iPSCs) technology may provide a promising platform to create reliable models, not only for better understanding the etiopathological process of AD, but also for efficient anti-AD drugs screening.", "More importantly, human-sourced iPSCs may also provide a beneficial tool for cell-replacement therapy against AD.", "Although considerable progress has been achieved, a number of key challenges still require to be addressed in iPSCs research, including the identification of robust disease phenotypes in AD modeling and the clinical availabilities of iPSCs-based cell-replacement therapy in human.", "In this review, we highlight recent progresses of iPSCs research and discuss the translational challenges of AD patients-derived iPSCs in disease modeling and cell-replacement therapy."], "structured": false}
{"doc_id": 13823200, "title": "Nitrite protects against morbidity and mortality associated with TNF- or LPS-induced shock in a soluble guanylate cyclase\u2013dependent manner", "abstract": ["Nitrite (NO(2)(-)), previously viewed as a physiologically inert metabolite and biomarker of the endogenous vasodilator NO, was recently identified as an important biological NO reservoir in vasculature and tissues, where it contributes to hypoxic signaling, vasodilation, and cytoprotection after ischemia-reperfusion injury.", "Reduction of nitrite to NO may occur enzymatically at low pH and oxygen tension by deoxyhemoglobin, deoxymyoglobin, xanthine oxidase, mitochondrial complexes, or NO synthase (NOS).", "We show that nitrite treatment, in sharp contrast with the worsening effect of NOS inhibition, significantly attenuates hypothermia, mitochondrial damage, oxidative stress and dysfunction, tissue infarction, and mortality in a mouse shock model induced by a lethal tumor necrosis factor challenge.", "Mechanistically, nitrite-dependent protection was not associated with inhibition of mitochondrial complex I activity, as previously demonstrated for ischemia-reperfusion, but was largely abolished in mice deficient for the soluble guanylate cyclase (sGC) alpha1 subunit, one of the principal intracellular NO receptors and signal transducers in the cardiovasculature.", "Nitrite could also provide protection against toxicity induced by Gram-negative lipopolysaccharide, although higher doses were required.", "In conclusion, we show that nitrite can protect against toxicity in shock via sGC-dependent signaling, which may include hypoxic vasodilation necessary to maintain microcirculation and organ function, and cardioprotection."], "structured": false}
{"doc_id": 13831558, "title": "Mammographic density and the risk and detection of breast cancer.", "abstract": ["BACKGROUND Extensive mammographic density is associated with an increased risk of breast cancer and makes the detection of cancer by mammography difficult, but the influence of density on risk according to method of cancer detection is unknown.   \n", "METHODS We carried out three nested case-control studies in screened populations with 1112 matched case-control pairs.", "We examined the association of the measured percentage of density in the baseline mammogram with risk of breast cancer, according to method of cancer detection, time since the initiation of screening, and age.   \n", "RESULTS As compared with women with density in less than 10% of the mammogram, women with density in 75% or more had an increased risk of breast cancer (odds ratio, 4.7; 95% confidence interval [CI], 3.0 to 7.4), whether detected by screening (odds ratio, 3.5; 95% CI, 2.0 to 6.2) or less than 12 months after a negative screening examination (odds ratio, 17.8; 95% CI, 4.8 to 65.9).", "Increased risk of breast cancer, whether detected by screening or other means, persisted for at least 8 years after study entry and was greater in younger than in older women.", "For women younger than the median age of 56 years, 26% of all breast cancers and 50% of cancers detected less than 12 months after a negative screening test were attributable to density in 50% or more of the mammogram.   \n", "CONCLUSIONS Extensive mammographic density is strongly associated with the risk of breast cancer detected by screening or between screening tests.", "A substantial fraction of breast cancers can be attributed to this risk factor."], "structured": true}
{"doc_id": 13831842, "title": "Pooled analysis of prospective cohort studies on height, weight, and breast cancer risk.", "abstract": ["The association between anthropometric indices and the risk of breast cancer was analyzed using pooled data from seven prospective cohort studies.", "Together, these cohorts comprise 337,819 women and 4,385 incident invasive breast cancer cases.", "In multivariate analyses controlling for reproductive, dietary, and other risk factors, the pooled relative risk (RR) of breast cancer per height increment of 5 cm was 1.02 (95% confidence interval (CI): 0.96, 1.10) in premenopausal women and 1.07 (95% CI: 1.03, 1.12) in postmenopausal women.", "Body mass index (BMI) showed significant inverse and positive associations with breast cancer among pre- and postmenopausal women, respectively; these associations were nonlinear.", "Compared with premenopausal women with a BMI of less than 21 kg/m2, women with a BMI exceeding 31 kg/m2 had an RR of 0.54 (95% CI: 0.34, 0.85).", "In postmenopausal women, the RRs did not increase further when BMI exceeded 28 kg/m2; the RR for these women was 1.26 (95% CI: 1.09, 1.46).", "The authors found little evidence for interaction with other breast cancer risk factors.", "Their data indicate that height is an independent risk factor for postmenopausal breast cancer; in premenopausal women, this relation is less clear.", "The association between BMI and breast cancer varies by menopausal status.", "Weight control may reduce the risk among postmenopausal women."], "structured": false}
{"doc_id": 13843341, "title": "Cost effectiveness of ward based non-invasive ventilation for acute exacerbations of chronic obstructive pulmonary disease: economic analysis of randomised controlled trial.", "abstract": ["OBJECTIVE To evaluate the cost effectiveness of standard treatment with and without the addition of ward based non-invasive ventilation in patients admitted to hospital with an acute exacerbation of chronic obstructive pulmonary disease.   \n", "DESIGN Incremental cost effectiveness analysis of a randomised controlled trial.   \n", "SETTING Medical wards in 14 hospitals in the United Kingdom.   \n", "PARTICIPANTS The trial comprised 236 patients admitted to hospital with an acute exacerbation of chronic obstructive pulmonary disease and mild to moderate acidosis (pH 7.25-7.35) secondary to respiratory failure.", "The economic analysis compared the costs of treatment that these patients received after randomisation.   \n", "MAIN OUTCOME MEASURE Incremental cost per in-hospital death.   \n", "RESULTS 24/118 died in the group receiving standard treatment and 12/118 in the group receiving non-invasive ventilation (P=0.05).", "Allocation to the group receiving non-invasive ventilation was associated with a reduction in costs of 49362 pounds sterling (78741 dollars; 73109 euros), mainly through reduced use of intensive care units.", "The incremental cost effectiveness ratio was -645 pounds sterling per death avoided (95% confidence interval -2310 pounds sterling to 386 pounds sterling), indicating a dominant (more effective and less costly) strategy.", "Modelling of these data indicates that a typical UK hospital providing a non-invasive ventilation service will avoid six deaths and three to nine admissions to intensive care units per year, with an associated cost reduction of 12000-53000 pounds sterling per year.   \n", "CONCLUSIONS Non-invasive ventilation is a highly cost effective treatment that both reduced total costs and improved mortality in hospital."], "structured": true}
{"doc_id": 13857083, "title": "Persistent human papillomavirus infection and cervical neoplasia: a systematic review and meta-analysis.", "abstract": ["Detection of persistent cervical carcinogenic human papillomavirus (HPV) DNA is used as a marker for cervical cancer risk in clinical trials.", "The authors performed a systematic review and meta-analysis of the association between persistent HPV DNA and high-grade cervical intraepithelial neoplasia (CIN2-3), high-grade squamous intraepithelial lesions (HSIL), and invasive cervical cancer (together designated CIN2-3/HSIL+) to evaluate the robustness of HPV persistence for clinical use.", "MEDLINE and Current Contents were searched through January 30, 2006.", "Relative risks (RRs) were stratified by HPV comparison group.", "Of 2,035 abstracts, 41 studies were eligible for inclusion in the meta-analysis.", "Over 22,500 women were included in calculation of RRs for persistent HPV DNA detection and cervical neoplasia.", "RRs ranged from 1.3 (95% confidence interval: 1.1, 1.5) to 813.0 (95% confidence interval: 168.2, 3,229.2) for CIN2-3/HSIL+ versus 12 months), wider testing intervals, CIN2-3/HSIL+, and use of an HPV-negative reference group were consistently associated with higher RRs.", "Thus, HPV persistence was consistently and strongly associated with CIN2-3/HSIL+, despite wide variation in definitions and study methods.", "The magnitude of association varied by duration of persistence and testing interval.", "Precise definition and standardization of HPV testing, sampling procedure, and test interval are needed for reliable clinical testing.", "These findings validate HPV persistence as a clinical marker and endpoint."], "structured": false}
{"doc_id": 13867350, "title": "Post-transcriptional Wnt Signaling Governs Epididymal Sperm Maturation", "abstract": ["The canonical Wnt signaling pathway is of paramount importance in development and disease.", "An emergent question is whether the upstream cascade of the canonical Wnt pathway has physiologically relevant roles beyond \u03b2-catenin-mediated transcription, which is difficult to study due to the pervasive role of this protein.", "Here, we show that transcriptionally silent spermatozoa respond to Wnt signals released from the epididymis and that mice mutant for the Wnt regulator Cyclin Y-like 1 are male sterile due to immotile and malformed spermatozoa.", "Post-transcriptional Wnt signaling impacts spermatozoa through GSK3 by (1) reducing global protein poly-ubiquitination to maintain protein homeostasis; (2) inhibiting septin 4 phosphorylation to establish a membrane diffusion barrier in the sperm tail; and (3) inhibiting protein phosphatase 1 to initiate sperm motility.", "The results indicate that Wnt signaling orchestrates a rich post-transcriptional sperm maturation program and invite revisiting transcription-independent Wnt signaling in somatic cells as well."], "structured": false}
{"doc_id": 13868795, "title": "CD28 Costimulation: From Mechanism to Therapy.", "abstract": ["Ligation of the CD28 receptor on T cells provides a critical second signal alongside T cell receptor (TCR) ligation for naive T cell activation.", "Here, we discuss the expression, structure, and biochemistry of CD28 and its ligands.", "CD28 signals play a key role in many T cell processes, including cytoskeletal remodeling, production of cytokines, survival, and differentiation.", "CD28 ligation leads to unique epigenetic, transcriptional, and post-translational changes in T cells that cannot be recapitulated by TCR ligation alone.", "We discuss the function of CD28 and its ligands in both effector and regulatory T cells.", "CD28 is critical for regulatory T cell survival and the maintenance of immune homeostasis.", "We outline the roles that CD28 and its family members play in human disease and we review the clinical efficacy of drugs that block CD28 ligands.", "Despite the centrality of CD28 and its family members and ligands to immune function, many aspects of CD28 biology remain unclear.", "Translation of a basic understanding of CD28 function into immunomodulatory therapeutics has been uneven, with both successes and failures.", "Such real-world results might stem from multiple factors, including complex receptor-ligand interactions among CD28 family members, differences between the mouse and human CD28 families, and cell-type specific roles of CD28 family members."], "structured": false}
{"doc_id": 13870943, "title": "Recommended diagnostic criteria for multiple sclerosis: guidelines from the International Panel on the diagnosis of multiple sclerosis.", "abstract": ["The International Panel on MS Diagnosis presents revised diagnostic criteria for multiple sclerosis (MS).", "The focus remains on the objective demonstration of dissemination of lesions in both time and space.", "Magnetic resonance imaging is integrated with dinical and other paraclinical diagnostic methods.", "The revised criteria facilitate the diagnosis of MS in patients with a variety of presentations, including \"monosymptomatic\" disease suggestive of MS, disease with a typical relapsing-remitting course, and disease with insidious progression, without clear attacks and remissions.", "Previously used terms such as \"clinically definite\" and \"probable MS\" are no longer recommended.", "The outcome of a diagnostic evaluation is either MS, \"possible MS\" (for those at risk for MS, but for whom diagnostic evaluation is equivocal), or \"not MS.", "\""], "structured": false}
{"doc_id": 13878124, "title": "Regulation of radial glial survival by signals from the meninges.", "abstract": ["Radial glial cells (RGCs) in the developing cerebral cortex are progenitors for neurons and glia, and their processes serve as guideposts for migrating neurons.", "So far, it has remained unclear whether RGC processes also control the function of RGCs more directly.", "Here, we show that RGC numbers and cortical size are reduced in mice lacking beta1 integrins in RGCs.", "TUNEL stainings and time-lapse video recordings demonstrate that beta1-deficient RGCs processes detach from the meningeal basement membrane (BM) followed by apoptotic death of RGCs.", "Apoptosis is also induced by surgical removal of the meninges.", "Finally, mice lacking the BM components laminin alpha2 and alpha4 show defects in the attachment of RGC processes at the meninges, a reduction in cortical size, and enhanced apoptosis of RGC cells.", "Our findings demonstrate that attachment of RGC processes at the meninges is important for RGC survival and the control of cortical size."], "structured": false}
{"doc_id": 13878643, "title": "The sterol regulatory element binding proteins are essential for the metabolic programming of effector T cells and adaptive immunity", "abstract": ["Newly activated CD8(+) T cells reprogram their metabolism to meet the extraordinary biosynthetic demands of clonal expansion; however, the signals that mediate metabolic reprogramming remain poorly defined.", "Here we demonstrate an essential role for sterol regulatory element-binding proteins (SREBPs) in the acquisition of effector-cell metabolism.", "Without SREBP signaling, CD8(+) T cells were unable to blast, which resulted in attenuated clonal expansion during viral infection.", "Mechanistic studies indicated that SREBPs were essential for meeting the heightened lipid requirements of membrane synthesis during blastogenesis.", "SREBPs were dispensable for homeostatic proliferation, which indicated a context-specific requirement for SREBPs in effector responses.", "Our studies provide insights into the molecular signals that underlie the metabolic reprogramming of CD8(+) T cells during the transition from quiescence to activation."], "structured": false}
{"doc_id": 13882658, "title": "Human contribution to the European heatwave of 2003", "abstract": ["The summer of 2003 was probably the hottest in Europe since at latest ad 1500, and unusually large numbers of heat-related deaths were reported in France, Germany and Italy.", "It is an ill-posed question whether the 2003 heatwave was caused, in a simple deterministic sense, by a modification of the external influences on climate\u2014for example, increasing concentrations of greenhouse gases in the atmosphere\u2014because almost any such weather event might have occurred by chance in an unmodified climate.", "However, it is possible to estimate by how much human activities may have increased the risk of the occurrence of such a heatwave.", "Here we use this conceptual framework to estimate the contribution of human-induced increases in atmospheric concentrations of greenhouse gases and other pollutants to the risk of the occurrence of unusually high mean summer temperatures throughout a large region of continental Europe.", "Using a threshold for mean summer temperature that was exceeded in 2003, but in no other year since the start of the instrumental record in 1851, we estimate it is very likely (confidence level >90%) that human influence has at least doubled the risk of a heatwave exceeding this threshold magnitude."], "structured": false}
{"doc_id": 13883546, "title": "Do Antidepressants Cure or Create Abnormal Brain States?", "abstract": ["The term antidepressant refers to a drug that helps to rectify specific biological abnormalities that give rise to the symptoms of depression.", "This exemplifies what we have called the \u201cdisease-centred\u201d model of psychotropic drug action [ 1].", "Modelled on paradigmatic situations in general medicine\u2014such as the use of insulin in diabetes, antibiotics in infectious disease, chemotherapy in cancer\u2014the disease-centred model suggests that antidepressants help restore normal functioning by acting on the neuropathology of depression or of depressive symptoms.    ", "In contrast, we propose in this Essay that an alternative \u201cdrug-centred\u201d model can better explain observed drug effects in psychiatric conditions.", "This drug-centred model suggests that instead of relieving a hypothetical biochemical abnormality, drugs themselves cause abnormal states, which may coincidentally relieve psychiatric symptoms ( Table 1).", "Alcohol's disinhibiting effects may relieve symptoms of social phobia, but that does not imply that alcohol corrects a chemical imbalance underlying social phobia.", "Sedation may lessen high arousal, present in many acute psychiatric situations.", "Drugs that induce indifference, such as neuroleptics or opiates, may help reduce the distress of acute psychotic symptoms.", "Low-dose stimulants may help improve attention and concentration in the short term.        ", "Table 1    Main Assumptions of Two Models of Psychotropic Drug Action        ", "The disease-centred model in psychiatry leads researchers to infer antidepressant effects from patients' scores on symptom rating scales presumed to assess the manifestations of the disease.", "The drug-centred model, on the other hand, suggests that physiological and subjective effects of drugs should be examined in their own right.", "These effects include various forms of sedation, stimulation, and a plethora of biopsychological states.", "Depending on individual inclination and context (including a person's emotional state upon drug ingestion), intoxication with some drugs produces euphoria or mood elevation.", "Because tolerance develops, however, euphoriant effects do not persist with long-term use.", "If antidepressants or any other psychotropic drugs could be shown to have mood-elevating effects that were long-term and not diminished by being in a depressed emotional state, this would distinguish them from psychotropic drugs that cause euphoria and might prove uniquely useful in depressed patients (see Sidebar)."], "structured": false}
{"doc_id": 13889430, "title": "Cancer exosomes trigger fibroblast to myofibroblast differentiation.", "abstract": ["There is a growing interest in the cell-cell communication roles in cancer mediated by secreted vesicles termed exosomes.", "In this study, we examined whether exosomes produced by cancer cells could transmit information to normal stromal fibroblasts and trigger a cellular response.", "We found that some cancer-derived exosomes could trigger elevated \u03b1-smooth muscle actin expression and other changes consistent with the process of fibroblast differentiation into myofibroblasts.", "We show that TGF-\u03b2 is expressed at the exosome surface in association with the transmembrane proteoglycan betaglycan.", "Although existing in a latent state, this complex was fully functional in eliciting SMAD-dependent signaling.", "Inhibiting either signaling or betaglycan expression attenuated differentiation.", "While the kinetics and overall magnitude of the response were similar to that achieved with soluble TGF-\u03b2, we identified important qualitative differences unique to the exosomal route of TGF-\u03b2 delivery, as exemplified by a significant elevation in fibroblast FGF2 production.", "This hitherto unknown trigger for instigating cellular differentiation in a distinctive manner has major implications for mechanisms underlying cancer-recruited stroma, fibrotic diseases, and wound-healing responses."], "structured": false}
{"doc_id": 13889962, "title": "A model of multiple myeloma: culture of 5T33 murine myeloma cells and evaluation of tumorigenicity in the C57BL/KaLwRij mouse.", "abstract": ["The 5T33 multiple myeloma is one of a series of transplantable murine myelomas arising spontaneously in C57BL/KaLwRij mice.", "This study describes the establishment and characterisation of the 5T33 murine myeloma in vitro as a cultured cell line in terms of its morphology, growth rate, expression of paraprotein (IgG2b) and tumorigenicity in syngeneic animals.", "The 5T33 cell line has been in continuous culture for over 10 months and has achieved more than passage 34.", "In culture, 5T33 myeloma grows as single cells or in small clusters of loosely adherent cells on an adherent stromal cell layer.", "Maximum doubling time is approximately 25 h, and over 90% of the cells express cytoplasmic IgG2b paraprotein.", "The cultured 5T33 myeloma cells are highly tumorigenic in C57BL/KaLwRij mice with as few as 500 cells inducing paralysis and death as early as day 36 post-tumour inoculation.", "Kinetics of tumour development and detection of IgG2b paraprotein are dose dependent.", "Two weeks following intravenous inoculation of 5 x 10(5) cultured 5T33 myeloma cells, tumour cells were readily identified in the bone marrow.", "By 3 weeks post-tumour inoculation, 5T33 myeloma cells were found in various tissues throughout the animal.", "Studies are now underway to determine the sensitivity of this cell line to various therapeutic modalities."], "structured": false}
{"doc_id": 13899137, "title": "HIV Treatment as Prevention: Systematic Comparison of Mathematical Models of the Potential Impact of Antiretroviral Therapy on HIV Incidence in South Africa", "abstract": ["BACKGROUND Many mathematical models have investigated the impact of expanding access to antiretroviral therapy (ART) on new HIV infections.", "Comparing results and conclusions across models is challenging because models have addressed slightly different questions and have reported different outcome metrics.", "This study compares the predictions of several mathematical models simulating the same ART intervention programmes to determine the extent to which models agree about the epidemiological impact of expanded ART.   \n", "METHODS AND FINDINGS Twelve independent mathematical models evaluated a set of standardised ART intervention scenarios in South Africa and reported a common set of outputs.", "Intervention scenarios systematically varied the CD4 count threshold for treatment eligibility, access to treatment, and programme retention.", "For a scenario in which 80% of HIV-infected individuals start treatment on average 1 y after their CD4 count drops below 350 cells/\u00b5l and 85% remain on treatment after 3 y, the models projected that HIV incidence would be 35% to 54% lower 8 y after the introduction of ART, compared to a counterfactual scenario in which there is no ART.", "More variation existed in the estimated long-term (38 y) reductions in incidence.", "The impact of optimistic interventions including immediate ART initiation varied widely across models, maintaining substantial uncertainty about the theoretical prospect for elimination of HIV from the population using ART alone over the next four decades.", "The number of person-years of ART per infection averted over 8 y ranged between 5.8 and 18.7.", "Considering the actual scale-up of ART in South Africa, seven models estimated that current HIV incidence is 17% to 32% lower than it would have been in the absence of ART.", "Differences between model assumptions about CD4 decline and HIV transmissibility over the course of infection explained only a modest amount of the variation in model results.   \n", "CONCLUSIONS Mathematical models evaluating the impact of ART vary substantially in structure, complexity, and parameter choices, but all suggest that ART, at high levels of access and with high adherence, has the potential to substantially reduce new HIV infections.", "There was broad agreement regarding the short-term epidemiologic impact of ambitious treatment scale-up, but more variation in longer term projections and in the efficiency with which treatment can reduce new infections.", "Differences between model predictions could not be explained by differences in model structure or parameterization that were hypothesized to affect intervention impact."], "structured": true}
{"doc_id": 13900610, "title": "Self-harm in prisons in England and Wales: an epidemiological study of prevalence, risk factors, clustering, and subsequent suicide", "abstract": ["BACKGROUND Self-harm and suicide are common in prisoners, yet robust information on the full extent and characteristics of people at risk of self-harm is scant.", "Furthermore, understanding how frequently self-harm is followed by suicide, and in which prisoners this progression is most likely to happen, is important.", "We did a case-control study of all prisoners in England and Wales to ascertain the prevalence of self-harm in this population, associated risk factors, clustering effects, and risk of subsequent suicide after self-harm.   \n", "METHODS Records of self-harm incidents in all prisons in England and Wales were gathered routinely between January, 2004, and December, 2009.", "We did a case-control comparison of prisoners who self-harmed and those who did not between January, 2006, and December, 2009.", "We also used a Bayesian approach to look at clustering of people who self-harmed.", "Prisoners who self-harmed and subsequently died by suicide in prison were compared with other inmates who self-harmed.   \n", "FINDINGS 139,195 self-harm incidents were recorded in 26,510 individual prisoners between 2004 and 2009; 5-6% of male prisoners and 20-24% of female inmates self-harmed every year.", "Self-harm rates were more than ten times higher in female prisoners than in male inmates.", "Repetition of self-harm was common, particularly in women and teenage girls, in whom a subgroup of 102 prisoners accounted for 17,307 episodes.", "In both sexes, self-harm was associated with younger age, white ethnic origin, prison type, and a life sentence or being unsentenced; in female inmates, committing a violent offence against an individual was also a factor.", "Substantial evidence was noted of clustering in time and location of prisoners who self-harmed (adjusted intra-class correlation 0\u00b715, 95% CI 0\u00b711-0\u00b718).", "109 subsequent suicides in prison were reported in individuals who self-harmed; the risk was higher in those who self-harmed than in the general prison population, and more than half the deaths occurred within a month of self-harm.", "Risk factors for suicide after self-harm in male prisoners were older age and a previous self-harm incident of high or moderate lethality; in female inmates, a history of more than five self-harm incidents within a year was associated with subsequent suicide.   \n", "INTERPRETATION The burden of self-harm in prisoners is substantial, particularly in women.", "Self-harm in prison is associated with subsequent suicide in this setting.", "Prevention and treatment of self-harm in prisoners is an essential component of suicide prevention in prisons.   \n", "FUNDING Wellcome Trust, National Institute for Health Research, National Offender Management Service, and Department of Health."], "structured": true}
{"doc_id": 13901073, "title": "Elimination of HIV in South Africa through Expanded Access to Antiretroviral Therapy: A Model Comparison Study", "abstract": ["BACKGROUND Expanded access to antiretroviral therapy (ART) using universal test and treat (UTT) has been suggested as a strategy to eliminate HIV in South Africa within 7 y based on an influential mathematical modeling study.", "However, the underlying deterministic model was criticized widely, and other modeling studies did not always confirm the study's finding.", "The objective of our study is to better understand the implications of different model structures and assumptions, so as to arrive at the best possible predictions of the long-term impact of UTT and the possibility of elimination of HIV.   \n", "METHODS AND FINDINGS We developed nine structurally different mathematical models of the South African HIV epidemic in a stepwise approach of increasing complexity and realism.", "The simplest model resembles the initial deterministic model, while the most comprehensive model is the stochastic microsimulation model STDSIM, which includes sexual networks and HIV stages with different degrees of infectiousness.", "We defined UTT as annual screening and immediate ART for all HIV-infected adults, starting at 13% in January 2012 and scaled up to 90% coverage by January 2019.", "All models predict elimination, yet those that capture more processes underlying the HIV transmission dynamics predict elimination at a later point in time, after 20 to 25 y. Importantly, the most comprehensive model predicts that the current strategy of ART at CD4 count \u2264350 cells/\u00b5l will also lead to elimination, albeit 10 y later compared to UTT.", "Still, UTT remains cost-effective, as many additional life-years would be saved.", "The study's major limitations are that elimination was defined as incidence below 1/1,000 person-years rather than 0% prevalence, and drug resistance was not modeled.   \n", "CONCLUSIONS Our results confirm previous predictions that the HIV epidemic in South Africa can be eliminated through universal testing and immediate treatment at 90% coverage.", "However, more realistic models show that elimination is likely to occur at a much later point in time than the initial model suggested.", "Also, UTT is a cost-effective intervention, but less cost-effective than previously predicted because the current South African ART treatment policy alone could already drive HIV into elimination.", "Please see later in the article for the Editors' Summary."], "structured": true}
{"doc_id": 13902570, "title": "Bile acid receptor TGR5 agonism induces NO production and reduces monocyte adhesion in vascular endothelial cells.", "abstract": ["OBJECTIVE TGR5 is a G-protein-coupled receptor for bile acids.", "So far, little is known about the function of TGR5 in vascular endothelial cells.   ", "APPROACH AND RESULTS In bovine aortic endothelial cells, treatment with a bile acid having a high affinity to TGR5, taurolithocholic acid (TLCA), significantly increased NO production.", "This effect was abolished by small interfering RNA-mediated depletion of TGR5.", "TLCA-induced NO production was also observed in human umbilical vein endothelial cells measured via intracellular cGMP accumulation.", "TLCA increased endothelial NO synthase(ser1177) phosphorylation in human umbilical vein endothelial cells.", "This response was accompanied by increased Akt(ser473) phosphorylation and intracellular Ca(2+).", "Inhibition of these signals significantly decreased TLCA-induced NO production.", "We next examined whether TGR5-mediated NO production affects inflammatory responses of endothelial cells.", "In human umbilical vein endothelial cells, TLCA significantly reduced tumor necrosis factor-\u03b1-induced adhesion of monocytes, vascular cell adhesion molecule-1 expression, and activation of nuclear factor-\u03baB. TLCA also inhibited lipopolysaccharide-induced monocyte adhesion to mesenteric venules in vivo.", "These inhibitory effects of TLCA were abrogated by NO synthase inhibition.   \n", "CONCLUSIONS TGR5 agonism induces NO production via Akt activation and intracellular Ca(2+) increase in vascular endothelial cells, and this function inhibits monocyte adhesion in response to inflammatory stimuli."], "structured": true}
{"doc_id": 13903052, "title": "Structural insights into calicivirus attachment and uncoating.", "abstract": ["The Caliciviridae family comprises positive-sense RNA viruses of medical and veterinary significance.", "In humans, caliciviruses are a major cause of acute gastroenteritis, while in animals respiratory illness, conjunctivitis, stomatitis, and hemorrhagic disease are documented.", "Investigation of virus-host interactions is limited by a lack of culture systems for many viruses in this family.", "Feline calicivirus (FCV), a member of the Vesivirus genus, provides a tractable model, since it may be propagated in cell culture.", "Feline junctional adhesion molecule 1 (fJAM-1) was recently identified as a functional receptor for FCV.", "We have analyzed the structure of this virus-receptor complex by cryo-electron microscopy and three-dimensional image reconstruction, combined with fitting of homology modeled high-resolution coordinates.", "We show that domain 1 of fJAM-1 binds to the outer face of the P2 domain of the FCV capsid protein VP1, inducing conformational changes in the viral capsid.", "This study provides the first structural view of a native calicivirus-protein receptor complex and insights into the mechanisms of virus attachment and uncoating."], "structured": false}
{"doc_id": 13905670, "title": "Human SNP Links Differential Outcomes in Inflammatory and Infectious Disease to a FOXO3-Regulated Pathway", "abstract": ["The clinical course and eventual outcome, or prognosis, of complex diseases varies enormously between affected individuals.", "This variability critically determines the impact a disease has on a patient's life but is very poorly understood.", "Here, we exploit existing genome-wide association study data to gain insight into the role of genetics in prognosis.", "We identify a noncoding polymorphism in FOXO3A (rs12212067: T > G) at which the minor (G) allele, despite not being associated with disease susceptibility, is associated with a milder course of Crohn's disease and rheumatoid arthritis and with increased risk of severe malaria.", "Minor allele carriage is shown to limit inflammatory responses in monocytes via a FOXO3-driven pathway, which through TGF\u03b21 reduces production of proinflammatory cytokines, including TNF\u03b1, and increases production of anti-inflammatory cytokines, including IL-10.", "Thus, we uncover a shared genetic contribution to prognosis in distinct diseases that operates via a FOXO3-driven pathway modulating inflammatory responses."], "structured": false}
{"doc_id": 13906581, "title": "Patient Outcomes with Teaching Versus Nonteaching Healthcare: A Systematic Review", "abstract": ["Background  Extensive debate exists in the healthcare community over whether outcomes of medical care at teaching hospitals and other healthcare units are better or worse than those at the respective nonteaching ones.", "Thus, our goal was to systematically evaluate the evidence pertaining to this question.      ", "Methods and Findings  We reviewed all studies that compared teaching versus nonteaching healthcare structures for mortality or any other patient outcome, regardless of health condition.", "Studies were retrieved from PubMed, contact with experts, and literature cross-referencing.", "Data were extracted on setting, patients, data sources, author affiliations, definition of compared groups, types of diagnoses considered, adjusting covariates, and estimates of effect for mortality and for each other outcome.", "Overall, 132 eligible studies were identified, including 93 on mortality and 61 on other eligible outcomes (22 addressed both).", "Synthesis of the available adjusted estimates on mortality yielded a summary relative risk of 0.96 (95% confidence interval [CI], 0.93\u20131.00) for teaching versus nonteaching healthcare structures and 1.04 (95% CI, 0.99\u20131.10) for minor teaching versus nonteaching ones.", "There was considerable heterogeneity between studies (I2 = 72% for the main analysis).", "Results were similar in studies using clinical and those using administrative databases.", "No differences were seen in the 14 studies fully adjusting for volume/experience, severity, and comorbidity (relative risk 1.01).", "Smaller studies did not differ in their results from larger studies.", "Differences were seen for some diagnoses (e.g., significantly better survival for breast cancer and cerebrovascular accidents in teaching hospitals and significantly better survival from cholecystectomy in nonteaching hospitals), but these were small in magnitude.", "Other outcomes were diverse, but typically teaching healthcare structures did not do better than nonteaching ones.      ", "Conclusions  The available data are limited by their nonrandomized design, but overall they do not suggest that a healthcare facility's teaching status on its own markedly improves or worsens patient outcomes.", "Differences for specific diseases cannot be excluded, but are likely to be small."], "structured": false}
{"doc_id": 13906892, "title": "DNA damage and Repair Modify DNA methylation and Chromatin Domain of the Targeted Locus: Mechanism of allele methylation polymorphism", "abstract": ["We characterize the changes in chromatin structure, DNA methylation and transcription during and after homologous DNA repair (HR).", "We find that HR modifies the DNA methylation pattern of the repaired segment.", "HR also alters local histone H3 methylation as well chromatin structure by inducing DNA-chromatin loops connecting the 5' and 3' ends of the repaired gene.", "During a two-week period after repair, transcription-associated demethylation promoted by Base Excision Repair enzymes further modifies methylation of the repaired DNA.", "Subsequently, the repaired genes display stable but diverse methylation profiles.", "These profiles govern the levels of expression in each clone.", "Our data argue that DNA methylation and chromatin remodelling induced by HR may be a source of permanent variation of gene expression in somatic cells."], "structured": false}
{"doc_id": 13907427, "title": "DNA repair factor APLF is a histone chaperone.", "abstract": ["Poly(ADP-ribosyl)ation plays a major role in DNA repair, where it regulates chromatin relaxation as one of the critical events in the repair process.", "However, the molecular mechanism by which poly(ADP-ribose) modulates chromatin remains poorly understood.", "Here we identify the poly(ADP-ribose)-regulated protein APLF as a DNA-damage-specific histone chaperone.", "APLF preferentially binds to the histone H3/H4 tetramer via its C-terminal acidic motif, which is homologous to the motif conserved in the histone chaperones of the NAP1L family (NAP1L motif).", "We further demonstrate that APLF exhibits histone chaperone activities in a manner that is dependent on its acidic domain and that the NAP1L motif is critical for the repair capacity of APLF in vivo.", "Finally, we identify structural analogs of APLF in lower eukaryotes with the ability to bind histones and localize to the sites of DNA-damage-induced poly(ADP-ribosyl)ation.", "Collectively, these findings define the involvement of histone chaperones in poly(ADP-ribose)-regulated DNA repair reactions."], "structured": false}
{"doc_id": 13907928, "title": "Regulation of sympathetic nerve activity during the cold pressor test in normotensive pregnant and nonpregnant women.", "abstract": ["Baseline neurovascular transduction is reduced in normotensive pregnancy; however, little is known about changes to neurovascular transduction during periods of heightened sympathetic activation.", "We tested the hypothesis that, despite an exacerbated muscle sympathetic nerve activity (microneurography) response to cold pressor stimulation, the blunting of neurovascular transduction in normotensive pregnant women would result in similar changes in vascular resistance and mean arterial pressure (Finometer) relative to nonpregnant controls.", "Baseline neurovascular transduction was reduced in pregnant women relative to controls when expressed as the quotient of both total resistance and mean arterial pressure and sympathetic burst frequency (0.32\u00b10.07 versus 0.58\u00b10.16 mm Hg/L/min/bursts/min, P<0.001 and 2.4\u00b10.7 versus 3.6\u00b10.8 mm Hg/bursts/min, P=0.001).", "Sympathetic activation was greater across all 3 minutes of cold pressor stimulation in the pregnant women relative to the nonpregnant controls.", "Peak sympathoexcitation was also greater in pregnant than in nonpregnant women, whether expressed as sympathetic burst frequency (+17\u00b113 versus +7\u00b18 bursts/min, P=0.049), burst incidence (+17\u00b19 versus +6\u00b111 bursts/100 hb, P=0.03), or total activity (+950\u00b1660 versus +363\u00b1414 arbitrary units, P=0.04).", "However, neurovascular transduction during peak cold pressor-induced sympathoexcitation remained blunted in pregnant women (0.25\u00b10.11 versus 0.45\u00b10.08 mm Hg/L/min/bursts/min, P<0.001 and 1.9\u00b11.0 versus 3.2\u00b10.9 mm Hg/bursts/min, P=0.006).", "Therefore, mean arterial pressure (93\u00b121 versus 99\u00b16 mm Hg, P=0.4) and total peripheral resistance (12\u00b13 versus 14\u00b13 mm Hg/L/min) were not different between pregnant and nonpregnant women during peak sympathoexcitation.", "These data indicate that the third trimester of normotensive pregnancy is associated with reductions in neurovascular transduction, which result in the dissociation of sympathetic outflow from hemodynamic outcomes, even during cold pressor-induced sympathoexcitation."], "structured": false}
{"doc_id": 13910150, "title": "The Germ Cell Determinant Blimp1 Is Not Required for Derivation of Pluripotent Stem Cells", "abstract": ["Blimp1 (Prdm1), the key determinant of primordial germ cells (PGCs), plays a combinatorial role with Prdm14 during PGC specification from postimplantation epiblast cells.", "They together initiate epigenetic reprogramming in early germ cells toward an underlying pluripotent state, which is equivalent to embryonic stem cells (ESCs).", "Whereas Prdm14 alone can promote reprogramming and is important for the propagation of the pluripotent state, it is not known whether Blimp1 is similarly involved.", "By using a genetic approach, we demonstrate that Blimp1 is dispensable for the derivation and maintenance of ESCs and postimplantation epiblast stem cells (epiSCs).", "Notably, Blimp1 is also dispensable for reprogramming epiSCs to ESCs.", "Thus, although Blimp1 is obligatory for PGC specification, it is not required for the reversion of epiSCs to ESCs and for their maintenance thereafter.", "This study suggests that reprogramming, including that of somatic cells to ESCs, may not entail an obligatory route through a Blimp1-positive PGC-like state."], "structured": false}
{"doc_id": 13912224, "title": "A Nexus for Gene Expression\u2014Molecular Mechanisms of Spt5 and NusG in the Three Domains of Life", "abstract": ["Evolutionary related multisubunit RNA polymerases (RNAPs) transcribe the genomes of all living organisms.", "Whereas the core subunits of RNAPs are universally conserved in all three domains of life-indicative of a common evolutionary descent-this only applies to one RNAP-associated transcription factor-Spt5, also known as NusG in bacteria.", "All other factors that aid RNAP during the transcription cycle are specific for the individual domain or only conserved between archaea and eukaryotes.", "Spt5 and its bacterial homologue NusG regulate gene expression in several ways by (i) modulating transcription processivity and promoter proximal pausing, (ii) coupling transcription and RNA processing or translation, and (iii) recruiting termination factors and thereby silencing laterally transferred DNA and protecting the genome against double-stranded DNA breaks.", "This review discusses recent discoveries that identify Spt5-like factors as evolutionary conserved nexus for the regulation and coordination of the machineries responsible for information processing in the cell."], "structured": false}
{"doc_id": 13914198, "title": "Haplotype estimation using sequencing reads.", "abstract": ["High-throughput sequencing technologies produce short sequence reads that can contain phase information if they span two or more heterozygote genotypes.", "This information is not routinely used by current methods that infer haplotypes from genotype data.", "We have extended the SHAPEIT2 method to use phase-informative sequencing reads to improve phasing accuracy.", "Our model incorporates the read information in a probabilistic model through base quality scores within each read.", "The method is primarily designed for high-coverage sequence data or data sets that already have genotypes called.", "One important application is phasing of single samples sequenced at high coverage for use in medical sequencing and studies of rare diseases.", "Our method can also use existing panels of reference haplotypes.", "We tested the method by using a mother-father-child trio sequenced at high-coverage by Illumina together with the low-coverage sequence data from the 1000 Genomes Project (1000GP).", "We found that use of phase-informative reads increases the mean distance between switch errors by 22% from 274.4 kb to 328.6 kb.", "We also used male chromosome X haplotypes from the 1000GP samples to simulate sequencing reads with varying insert size, read length, and base error rate.", "When using short 100 bp paired-end reads, we found that using mixtures of insert sizes produced the best results.", "When using longer reads with high error rates (5-20 kb read with 4%-15% error per base), phasing performance was substantially improved."], "structured": false}
{"doc_id": 13914633, "title": "Time and Money: The True Costs of Health Care Utilization for Patients Receiving \"Free\" HIV/Tuberculosis Care and Treatment in Rural KwaZulu-Natal.", "abstract": ["BACKGROUND HIV and tuberculosis (TB) services are provided free of charge in many sub-Saharan African countries, but patients still incur costs.   \n", "METHODS Patient-exit interviews were conducted in primary health care clinics in rural South Africa with representative samples of 200 HIV-infected patients enrolled in a pre-antiretroviral treatment (pre-ART) program, 300 patients receiving antiretroviral treatment (ART), and 300 patients receiving TB treatment.", "For each group, we calculated health expenditures across different spending categories, time spent traveling to and using services, and how patients financed their spending.", "Associations between patient group and costs were assessed in multivariate regression models.   \n", "RESULTS Total monthly health expenditures [1 USD = 7.3 South African Rand (ZAR)] were ZAR 171 [95% confidence interval (CI): 134 to 207] for pre-ART, ZAR 164 (95% CI: 141 to 187) for ART, and ZAR 122 (95% CI: 105 to 140) for TB patients (P = 0.01).", "Total monthly time costs (in hours) were 3.4 (95% CI: 3.3 to 3.5) for pre-ART, 5.0 (95% CI: 4.7 to 5.3) for ART, and 3.2 (95% CI: 2.9 to 3.4) for TB patients (P < 0.01).", "Although overall patient costs were similar across groups, pre-ART patients spent on average ZAR 29.2 more on traditional healers and ZAR 25.9 more on chemists and private doctors than ART patients, whereas ART patients spent ZAR 34.0 more than pre-ART patients on transport to clinics (P < 0.05 for all results).", "Thirty-one percent of pre-ART, 39% of ART, and 41% of TB patients borrowed money or sold assets to finance health care.   \n", "CONCLUSIONS Patients receiving nominally free care for HIV/TB face large private costs, commonly leading to financial distress.", "Subsidized transport, fewer clinic visits, and drug pick-up points closer to home could reduce costs for ART patients, potentially improving retention and adherence.", "Large expenditure on alternative care among pre-ART patients suggests that transitioning patients to ART earlier, as under HIV treatment-as-prevention policies, may not substantially increase patients' financial burden."], "structured": true}
{"doc_id": 13915464, "title": "A new system for naming ribosomal proteins.", "abstract": ["A system for naming ribosomal proteins is described that the authors intend to use in the future.", "They urge others to adopt it.", "The objective is to eliminate the confusion caused by the assignment of identical names to ribosomal proteins from different species that are unrelated in structure and function.", "In the system proposed here, homologous ribosomal proteins are assigned the same name, regardless of species.", "It is designed so that new names are similar enough to old names to be easily recognized, but are written in a format that unambiguously identifies them as 'new system' names."], "structured": false}
{"doc_id": 13916484, "title": "COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer", "abstract": ["COSMIC (http://www.sanger.ac.uk/cosmic) curates comprehensive information on somatic mutations in human cancer.", "Release v48 (July 2010) describes over 136,000 coding mutations in almost 542,000 tumour samples; of the 18,490 genes documented, 4803 (26%) have one or more mutations.", "Full scientific literature curations are available on 83 major cancer genes and 49 fusion gene pairs (19 new cancer genes and 30 new fusion pairs this year) and this number is continually increasing.", "Key amongst these is TP53, now available through a collaboration with the IARC p53 database.", "In addition to data from the Cancer Genome Project (CGP) at the Sanger Institute, UK, and The Cancer Genome Atlas project (TCGA), large systematic screens are also now curated.", "Major website upgrades now make these data much more mineable, with many new selection filters and graphics.", "A Biomart is now available allowing more automated data mining and integration with other biological databases.", "Annotation of genomic features has become a significant focus; COSMIC has begun curating full-genome resequencing experiments, developing new web pages, export formats and graphics styles.", "With all genomic information recently updated to GRCh37, COSMIC integrates many diverse types of mutation information and is making much closer links with Ensembl and other data resources."], "structured": false}
{"doc_id": 13916951, "title": "Quantitative imaging assay for NF-\u03baB nuclear translocation in primary human macrophages", "abstract": ["Quantitative measurement of NF-kappaB nuclear translocation is an important research tool in cellular immunology.", "Established methodologies have a number of limitations, such as poor sensitivity, high cost or dependence on cell lines.", "Novel imaging methods to measure nuclear translocation of transcriptionally active components of NF-kappaB are being used but are also partly limited by the need for specialist imaging equipment or image analysis software.", "Herein we present a method for quantitative detection of NF-kappaB rel A nuclear translocation, using immunofluorescence microscopy and the public domain image analysis software ImageJ that can be easily adopted for cellular immunology research without the need for specialist image analysis expertise and at low cost.", "The method presented here is validated by demonstrating the time course and dose response of NF-kappaB nuclear translocation in primary human macrophages stimulated with LPS, and by comparison with a commercial NF-kappaB activation reporter cell line."], "structured": false}
{"doc_id": 13921526, "title": "An RNA-sequencing transcriptome and splicing database of glia, neurons, and vascular cells of the cerebral cortex.", "abstract": ["The major cell classes of the brain differ in their developmental processes, metabolism, signaling, and function.", "To better understand the functions and interactions of the cell types that comprise these classes, we acutely purified representative populations of neurons, astrocytes, oligodendrocyte precursor cells, newly formed oligodendrocytes, myelinating oligodendrocytes, microglia, endothelial cells, and pericytes from mouse cerebral cortex.", "We generated a transcriptome database for these eight cell types by RNA sequencing and used a sensitive algorithm to detect alternative splicing events in each cell type.", "Bioinformatic analyses identified thousands of new cell type-enriched genes and splicing isoforms that will provide novel markers for cell identification, tools for genetic manipulation, and insights into the biology of the brain.", "For example, our data provide clues as to how neurons and astrocytes differ in their ability to dynamically regulate glycolytic flux and lactate generation attributable to unique splicing of PKM2, the gene encoding the glycolytic enzyme pyruvate kinase.", "This dataset will provide a powerful new resource for understanding the development and function of the brain.", "To ensure the widespread distribution of these datasets, we have created a user-friendly website (http://web.stanford.edu/group/barres_lab/brain_rnaseq.html) that provides a platform for analyzing and comparing transciption and alternative splicing profiles for various cell classes in the brain."], "structured": false}
{"doc_id": 13921783, "title": "C9orf72 repeat expansions cause neurodegeneration in Drosophila through arginine-rich proteins", "abstract": ["An expanded GGGGCC repeat in C9orf72 is the most common genetic cause of frontotemporal dementia and amyotrophic lateral sclerosis.", "A fundamental question is whether toxicity is driven by the repeat RNA itself and/or by dipeptide repeat proteins generated by repeat-associated, non-ATG translation.", "To address this question, we developed in vitro and in vivo models to dissect repeat RNA and dipeptide repeat protein toxicity.", "Expression of pure repeats, but not stop codon\u2013interrupted \u201cRNA-only\u201d repeats in Drosophila caused adult-onset neurodegeneration.", "Thus, expanded repeats promoted neurodegeneration through dipeptide repeat proteins.", "Expression of individual dipeptide repeat proteins with a non-GGGGCC RNA sequence revealed that both poly-(glycine-arginine) and poly-(proline-arginine) proteins caused neurodegeneration.", "These findings are consistent with a dual toxicity mechanism, whereby both arginine-rich proteins and repeat RNA contribute to C9orf72-mediated neurodegeneration."], "structured": false}
{"doc_id": 13923069, "title": "Targeted nanoparticles containing the proresolving peptide Ac2-26 protect against advanced atherosclerosis in hypercholesterolemic mice", "abstract": ["Chronic, nonresolving inflammation is a critical factor in the clinical progression of advanced atherosclerotic lesions.", "In the normal inflammatory response, resolution is mediated by several agonists, among which is the glucocorticoid-regulated protein called annexin A1.", "The proresolving actions of annexin A1, which are mediated through its receptor N-formyl peptide receptor 2 (FPR2/ALX), can be mimicked by an amino-terminal peptide encompassing amino acids 2\u201326 (Ac2-26).", "Collagen IV (Col IV)\u2013targeted nanoparticles (NPs) containing Ac2-26 were evaluated for their therapeutic effect on chronic, advanced atherosclerosis in fat-fed Ldlr\u2212/\u2212 mice.", "When administered to mice with preexisting lesions, Col IV\u2013Ac2-26 NPs were targeted to lesions and led to a marked improvement in key advanced plaque properties, including an increase in the protective collagen layer overlying lesions (which was associated with a decrease in lesional collagenase activity), suppression of oxidative stress, and a decrease in plaque necrosis.", "In mice lacking FPR2/ALX in myeloid cells, these improvements were not seen.", "Thus, administration of a resolution-mediating peptide in a targeted NP activates its receptor on myeloid cells to stabilize advanced atherosclerotic lesions.", "These findings support the concept that defective inflammation resolution plays a role in advanced atherosclerosis, and suggest a new form of therapy."], "structured": false}
{"doc_id": 13923140, "title": "Interleukin-2 gene variation impairs regulatory T cell function and causes autoimmunity", "abstract": ["Autoimmune diseases are thought to result from imbalances in normal immune physiology and regulation.", "Here, we show that autoimmune disease susceptibility and resistance alleles on mouse chromosome 3 (Idd3) correlate with differential expression of the key immunoregulatory cytokine interleukin-2 (IL-2).", "In order to test directly that an approximately twofold reduction in IL-2 underpins the Idd3-linked destabilization of immune homeostasis, we show that engineered haplodeficiency of Il2 gene expression not only reduces T cell IL-2 production by twofold but also mimics the autoimmune dysregulatory effects of the naturally occurring susceptibility alleles of Il2.", "Reduced IL-2 production achieved by either genetic mechanism correlates with reduced function of CD4+ CD25+ regulatory T cells, which are critical for maintaining immune homeostasis."], "structured": false}
{"doc_id": 13931771, "title": "GRSF1 Regulates RNA Processing in Mitochondrial RNA Granules", "abstract": ["Various specialized domains have been described in the cytosol and the nucleus; however, little is known about compartmentalization within the mitochondrial matrix.", "GRSF1 (G-rich sequence factor 1) is an RNA binding protein that was previously reported to localize in the cytosol.", "We found that an isoform of GRSF1 accumulates in discrete foci in the mitochondrial matrix.", "These foci are composed of nascent mitochondrial RNA and also contain RNase P, an enzyme that participates in mitochondrial RNA processing.", "GRSF1 was found to interact with RNase P and to be required for processing of both classical and tRNA-less RNA precursors.", "In its absence, cleavage of primary RNA transcripts is abnormal, leading to decreased expression of mitochondrially encoded proteins and mitochondrial dysfunction.", "Our findings suggest that the foci containing GRSF1 and RNase P correspond to sites where primary RNA transcripts converge to be processed.", "We have termed these large ribonucleoprotein structures \"mitochondrial RNA granules.", "\""], "structured": false}
{"doc_id": 13933299, "title": "Midlife Serum Cholesterol and Increased Risk of Alzheimer\u2019s and Vascular Dementia Three Decades Later", "abstract": ["Aims:", "To investigate midlife cholesterol in relation to Alzheimer\u2019s disease (AD) and vascular dementia (VaD) in a large multiethnic cohort of women and men.", "Methods: The Kaiser Permanente Northern California Medical Group (healthcare delivery organization) formed the database for this study.", "The 9,844 participants underwent detailed health evaluations during 1964\u20131973 at ages 40\u201345 years; they were still members of the health plan in 1994.", "AD and VaD were ascertained by medical records between 1 January 1994 and 1 June 2007.", "Cox proportional hazards models \u2013 adjusted for age, education, race/ethnic group, sex, midlife diabetes, hypertension, BMI and late-life stroke \u2013 were conducted.", "Results:", "In total, 469 participants had AD and 127 had VaD. With desirable cholesterol levels (<200 mg/dl) as a reference, hazard ratios (HR) and 95% CI for AD were 1.23 (0.97\u20131.55) and 1.57 (1.23\u20132.01) for borderline (200\u2013239 mg/dl) and high cholesterol (\u2265240 mg/dl), respectively.", "HR and 95% CI for VaD were 1.50 (1.01\u20132.23) for borderline and 1.26 (0.82\u20131.96) for high cholesterol.", "Further analyses for AD (cholesterol quartiles, 1st quartile reference) indicated that cholesterol levels >220 mg/dl were a significant risk factor: HR were 1.31 (1.01\u20131.71; 3rd quartile, 221\u2013248 mg/dl) and 1.58 (1.22\u20132.06; 4th quartile, 249\u2013500 mg/dl).", "Conclusion: Midlife serum total cholesterol was associated with an increased risk of AD and VaD. Even moderately elevated cholesterol increased dementia risk.", "Dementia risk factors need to be addressed as early as midlife, before underlying disease(s) or symptoms appear."], "structured": false}
{"doc_id": 13934676, "title": "\"The contribution of chronic diseases to the prevalence of dependence among older people in Latin America, China and India: a 10/66 Dementia Research Group population-based survey\"", "abstract": ["BACKGROUND The number of older people is set to increase dramatically worldwide.", "Demographic changes are likely to result in the rise of age-related chronic diseases which largely contribute to years lived with a disability and future dependence.", "However dependence is much less studied although intrinsically linked to disability.", "We investigated the prevalence and correlates of dependence among older people from middle income countries.   \n", "METHODS A one-phase cross-sectional survey was carried out at 11 sites in seven countries (urban sites in Cuba, Venezuela, and Dominican Republic, urban and rural sites in Peru, Mexico, China and India).", "All those aged 65 years and over living in geographically defined catchment areas were eligible.", "In all, 15,022 interviews were completed with an informant interview for each participant.", "The full 10/66 Dementia Research Group survey protocol was applied, including ascertainment of depression, dementia, physical impairments and self-reported diagnoses.", "Dependence was interviewer-rated based on a key informant's responses to a set of open-ended questions on the participant's needs for care.", "We estimated the prevalence of dependence and the independent contribution of underlying health conditions.", "Site-specific prevalence ratios were meta-analysed, and population attributable prevalence fractions (PAPF) calculated.   \n", "RESULTS The prevalence of dependence increased with age at all sites, with a tendency for the prevalence to be lower in men than in women.", "Age-standardised prevalence was lower in all sites than in the USA.", "Other than in rural China, dementia made the largest independent contribution to dependence, with a median PAPF of 34% (range 23%-59%).", "Other substantial contributors were limb impairment (9%, 1%-46%), stroke (8%, 2%-17%), and depression (8%, 1%-27%).   \n", "CONCLUSION The demographic and health transitions will lead to large and rapid increases in the numbers of dependent older people particularly in middle income countries (MIC).", "The prevention and control of chronic neurological and neuropsychiatric diseases and the development of long-term care policies and plans should be urgent priorities."], "structured": true}
{"doc_id": 13936152, "title": "An actomyosin-based barrier inhibits cell mixing at compartmental boundaries in Drosophila embryos", "abstract": ["Partitioning tissues into compartments that do not intermix is essential for the correct morphogenesis of animal embryos and organs.", "Several hypotheses have been proposed to explain compartmental cell sorting, mainly differential adhesion, but also regulation of the cytoskeleton or of cell proliferation.", "Nevertheless, the molecular and cellular mechanisms that keep cells apart at boundaries remain unclear.", "Here we demonstrate, in early Drosophila melanogaster embryos, that actomyosin-based barriers stop cells from invading neighbouring compartments.", "Our analysis shows that cells can transiently invade neighbouring compartments, especially when they divide, but are then pushed back into their compartment of origin.", "Actomyosin cytoskeletal components are enriched at compartmental boundaries, forming cable-like structures when the epidermis is mitotically active.", "When MyoII (non-muscle myosin II) function is inhibited, including locally at the cable by chromophore-assisted laser inactivation (CALI), in live embryos, dividing cells are no longer pushed back, leading to compartmental cell mixing.", "We propose that local regulation of actomyosin contractibility, rather than differential adhesion, is the primary mechanism sorting cells at compartmental boundaries."], "structured": false}
{"doc_id": 13938878, "title": "Clinical algorithms for malaria diagnosis lack utility among people of different age groups.", "abstract": ["We conducted a study to determine whether clinical algorithms would be useful in malaria diagnosis among people living in an area of moderate malaria transmission within Kilifi District in Kenya.", "A total of 1602 people of all age groups participated.", "We took smears and recorded clinical signs and symptoms (prompted or spontaneous) of all those presenting to the study clinic with a history of fever.", "A malaria case was defined as a person presenting to the clinic with a history of fever and concurrent parasitaemia.", "A set of clinical signs and symptoms (algorithms) with the highest sensitivity and specificity for diagnosing a malaria case was selected for the age groups </=5 years, 6-14 years and >/=15 years.", "These age-optimized derived algorithms were able to identify about 66% of the cases among those <15 years of age but only 23% of cases among adults.", "Were these algorithms to be used as a basis for a decision on treatment among those presenting to the clinic, 16% of children </=5 years, 44% of those 6-14 years of age and 66% of the adults who had a history of fever and parasitaemia >/=5000 parasites/microl of blood would be sent home without treatment.", "Clinical algorithms therefore appear to have little utility in malaria diagnosis, performing even worse in the older age groups, where avoiding unnecessary use of anti-malarials would make more drugs available to the really needy population of children under 5 years of age."], "structured": false}
{"doc_id": 13940200, "title": "Large-scale genetic fine mapping and genotype-phenotype associations implicate polymorphism in the IL2RA region in type 1 diabetes", "abstract": ["Genome-wide association studies are now identifying disease-associated chromosome regions.", "However, even after convincing replication, the localization of the causal variant(s) requires comprehensive resequencing, extensive genotyping and statistical analyses in large sample sets leading to targeted functional studies.", "Here, we have localized the type 1 diabetes (T1D) association in the interleukin 2 receptor alpha (IL2RA) gene region to two independent groups of SNPs, spanning overlapping regions of 14 and 40 kb, encompassing IL2RA intron 1 and the 5\u2032 regions of IL2RA and RBM17 (odds ratio = 2.04, 95% confidence interval = 1.70\u20132.45; P = 1.92 \u00d7 10\u221228; control frequency = 0.635).", "Furthermore, we have associated IL2RA T1D susceptibility genotypes with lower circulating levels of the biomarker, soluble IL-2RA (P = 6.28 \u00d7 10\u221228), suggesting that an inherited lower immune responsiveness predisposes to T1D."], "structured": false}
{"doc_id": 13944805, "title": "Maternal obesity epigenetically alters visceral fat progenitor cell properties in male offspring mice.", "abstract": ["KEY POINTS Maternal obesity reduces adipogenic progenitor density in offspring adipose tissue.", "The ability of adipose tissue expansion in the offspring of obese mothers is limited and is associated with metabolic dysfunction of adipose tissue when challenged with a high-fat diet.", "Maternal obesity induces DNA demethylation in the promoter of zinc finger protein 423, which renders progenitor cells with a high adipogenic capacity.", "Maternal obesity demonstrates long-term effects on the adipogenic capacity of progenitor cells in offspring adipose tissue, demonstrating a developmental programming effect.   ", "ABSTRACT Maternal obesity (MO) programs offspring obesity and metabolic disorders, although the underlying mechanisms remain poorly defined.", "Progenitor cells are the source of new adipocytes.", "The present study aimed to test whether MO epigenetically predisposes adipocyte progenitors in the fat of offspring to adipogenic differentiation and subsequent depletion, which leads to a failure of adipose tissue plasticity under positive energy balance, contributing to adipose tissue metabolic dysfunction.", "C57BL/6 female mice were fed either a control diet (10% energy from fat) or a high-fat diet (45% energy from fat) for 8 weeks before mating.", "Male offspring of control (Con) and obese (OB) dams were weaned onto a regular (Reg) or obesogenic (Obe) diet until 3 months of age.", "At weaning, male OB offspring had a higher expression of Zinc finger protein 423 (zfp423), a key transcription factor in adipogenesis, as well as lower DNA methylation of its promoter in progenitors of epididymal fat compared to Con offspring, which was correlated with enhanced adipogenic differentiation.", "At 3 months of age, progenitor density was 30.9 \u00b1 9.7% lower in OB/Obe compared to Con/Obe mice, accompanied by a limited expansion of the adipocyte number when challenged with a high-energy diet.", "This difference was associated with lower DNA methylation in the zfp423 promoter in the epididymal fat of OB/Obe offspring, which was correlated with greater macrophage chemotactic protein-1 and hypoxia-inducible factor 1\u03b1 expression.", "In summary, MO epigenetically limits the expansion capacity of offspring adipose tissue, providing an explanation for the adipose metabolic dysfunction of male offspring in the setting of MO."], "structured": false}
{"doc_id": 13948920, "title": "Quality Testing of Artemisinin-Based Antimalarial Drugs in Myanmar.", "abstract": ["Artemisinin-based combination therapies are the frontline treatment of Plasmodium falciparum malaria.", "The circulation of falsified and substandard artemisinin-based antimalarials in Southeast Asia has been a major predicament for the malaria elimination campaign.", "To provide an update of this situation, we purchased 153 artemisinin-containing antimalarials, as convenience samples, in private drug stores from different regions of Myanmar.", "The quality of these drugs in terms of their artemisinin derivative content was tested using specific dipsticks for these artemisinin derivatives, as point-of-care devices.", "A subset of these samples was further tested by high-performance liquid chromatography (HPLC).", "This survey identified that > 35% of the collected drugs were oral artesunate and artemether monotherapies.", "When tested with the dipsticks, all but one sample passed the assays, indicating that the detected artemisinin derivative content corresponded approximately to the labeled contents.", "However, one artesunate injection sample was found to contain no active ingredient at all by the dipstick assay and subsequent HPLC analysis.", "The continued circulation of oral monotherapies and the description, for the first time, of falsified parenteral artesunate provides a worrisome picture of the antimalarial drug quality in Myanmar during the malaria elimination phase, a situation that deserves more oversight from regulatory authorities."], "structured": false}
{"doc_id": 13949015, "title": "LINE-1 Retrotransposition Activity in Human Genomes", "abstract": ["Highly active (i.e., \"hot\") long interspersed element-1 (LINE-1 or L1) sequences comprise the bulk of retrotransposition activity in the human genome; however, the abundance of hot L1s in the human population remains largely unexplored.", "Here, we used a fosmid-based, paired-end DNA sequencing strategy to identify 68 full-length L1s that are differentially present among individuals but are absent from the human genome reference sequence.", "The majority of these L1s were highly active in a cultured cell retrotransposition assay.", "Genotyping 26 elements revealed that two L1s are only found in Africa and that two more are absent from the H952 subset of the Human Genome Diversity Panel.", "Therefore, these results suggest that hot L1s are more abundant in the human population than previously appreciated, and that ongoing L1 retrotransposition continues to be a major source of interindividual genetic variation."], "structured": false}
{"doc_id": 13952658, "title": "Immune cell promotion of metastasis", "abstract": ["Metastatic disease is the major cause of death from cancer, and immunotherapy and chemotherapy have had limited success in reversing its progression.", "Data from mouse models suggest that the recruitment of immunosuppressive cells to tumours protects metastatic cancer cells from surveillance by killer cells, which nullifies the effects of immunotherapy and thus establishes metastasis.", "Furthermore, in most cases, tumour-infiltrating immune cells differentiate into cells that promote each step of the metastatic cascade and thus are novel targets for therapy.", "In this Review, we describe how tumour-infiltrating immune cells contribute to the metastatic cascade and we discuss potential therapeutic strategies to target these cells."], "structured": false}
{"doc_id": 13953762, "title": "PICH: a DNA translocase specially adapted for processing anaphase bridge DNA.", "abstract": ["The Plk1-interacting checkpoint helicase (PICH) protein localizes to ultrafine anaphase bridges (UFBs) in mitosis alongside a complex of DNA repair proteins, including the Bloom's syndrome protein (BLM).", "However, very little is known about the function of PICH or how it is recruited to UFBs.", "Using a combination of microfluidics, fluorescence microscopy, and optical tweezers, we have defined the properties of PICH in an in vitro model of an anaphase bridge.", "We show that PICH binds with a remarkably high affinity to duplex DNA, resulting in ATP-dependent protein translocation and extension of the DNA.", "Most strikingly, the affinity of PICH for binding DNA increases with tension-induced DNA stretching, which mimics the effect of the mitotic spindle on a UFB.", "PICH binding also appears to diminish force-induced DNA melting.", "We propose a model in which PICH recognizes and stabilizes DNA under tension during anaphase, thereby facilitating the resolution of entangled sister chromatids."], "structured": false}
{"doc_id": 13955536, "title": "The Dynamics of Genome-wide DNA Methylation Reprogramming in Mouse Primordial Germ Cells", "abstract": ["Genome-wide DNA methylation reprogramming occurs in mouse primordial germ cells (PGCs) and preimplantation embryos, but the precise dynamics and biological outcomes are largely unknown.", "We have carried out whole-genome bisulfite sequencing (BS-Seq) and RNA-Seq across key stages from E6.5 epiblast to E16.5 PGCs.", "Global loss of methylation takes place during PGC expansion and migration with evidence for passive demethylation, but sequences that carry long-term epigenetic memory (imprints, CpG islands on the X chromosome, germline-specific genes) only become demethylated upon entry of PGCs into the gonads.", "The transcriptional profile of PGCs is tightly controlled despite global hypomethylation, with transient expression of the pluripotency network, suggesting that reprogramming and pluripotency are inextricably linked.", "Our results provide a framework for the understanding of the epigenetic ground state of pluripotency in the germline."], "structured": false}
{"doc_id": 13956305, "title": "Major histocompatibility complex associations of ankylosing spondylitis are complex and involve further epistasis with ERAP1", "abstract": ["Ankylosing spondylitis (AS) is a common, highly heritable, inflammatory arthritis for which HLA-B*27 is the major genetic risk factor, although its role in the aetiology of AS remains elusive.", "To better understand the genetic basis of the MHC susceptibility loci, we genotyped 7,264 MHC SNPs in 22,647 AS cases and controls of European descent.", "We impute SNPs, classical HLA alleles and amino-acid residues within HLA proteins, and tested these for association to AS status.", "Here we show that in addition to effects due to HLA-B*27 alleles, several other HLA-B alleles also affect susceptibility.", "After controlling for the associated haplotypes in HLA-B, we observe independent associations with variants in the HLA-A, HLA-DPB1 and HLA-DRB1 loci.", "We also demonstrate that the ERAP1 SNP rs30187 association is not restricted only to carriers of HLA-B*27 but also found in HLA-B*40:01 carriers independently of HLA-B*27 genotype."], "structured": false}
{"doc_id": 13958154, "title": "RNA sequencing identifies dysregulation of the human pancreatic islet transcriptome by the saturated fatty acid palmitate.", "abstract": ["Pancreatic \u03b2-cell dysfunction and death are central in the pathogenesis of type 2 diabetes (T2D).", "Saturated fatty acids cause \u03b2-cell failure and contribute to diabetes development in genetically predisposed individuals.", "Here we used RNA sequencing to map transcripts expressed in five palmitate-treated human islet preparations, observing 1,325 modified genes.", "Palmitate induced fatty acid metabolism and endoplasmic reticulum (ER) stress.", "Functional studies identified novel mediators of adaptive ER stress signaling.", "Palmitate modified genes regulating ubiquitin and proteasome function, autophagy, and apoptosis.", "Inhibition of autophagic flux and lysosome function contributed to lipotoxicity.", "Palmitate inhibited transcription factors controlling \u03b2-cell phenotype, including PAX4 and GATA6.", "Fifty-nine T2D candidate genes were expressed in human islets, and 11 were modified by palmitate.", "Palmitate modified expression of 17 splicing factors and shifted alternative splicing of 3,525 transcripts.", "Ingenuity Pathway Analysis of modified transcripts and genes confirmed that top changed functions related to cell death.", "Database for Annotation, Visualization and Integrated Discovery (DAVID) analysis of transcription factor binding sites in palmitate-modified transcripts revealed a role for PAX4, GATA, and the ER stress response regulators XBP1 and ATF6.", "This human islet transcriptome study identified novel mechanisms of palmitate-induced \u03b2-cell dysfunction and death.", "The data point to cross talk between metabolic stress and candidate genes at the \u03b2-cell level."], "structured": false}
{"doc_id": 13959707, "title": "The Ratio of Monocytes to Lymphocytes in Peripheral Blood Correlates with Increased Susceptibility to Clinical Malaria in Kenyan Children", "abstract": ["BACKGROUND Plasmodium falciparum malaria remains a major cause of illness and death in sub-Saharan Africa.", "Young children bear the brunt of the disease and though older children and adults suffer relatively fewer clinical attacks, they remain susceptible to asymptomatic P. falciparum infection.", "A better understanding of the host factors associated with immunity to clinical malaria and the ability to sustain asymptomatic P. falciparum infection will aid the development of improved strategies for disease prevention.   \n", "METHODS AND FINDINGS Here we investigate whether full differential blood counts can predict susceptibility to clinical malaria among Kenyan children sampled at five annual cross-sectional surveys.", "We find that the ratio of monocytes to lymphocytes, measured in peripheral blood at the time of survey, directly correlates with risk of clinical malaria during follow-up.", "This association is evident among children with asymptomatic P. falciparum infection at the time the cell counts are measured (Hazard ratio (HR)  =  2.7 (95% CI 1.42, 5.01, P  =  0.002) but not in those without detectable parasitaemia (HR  =  1.0 (95% CI 0.74, 1.42, P  =  0.9).   \n", "CONCLUSIONS We propose that the monocyte to lymphocyte ratio, which is easily derived from routine full differential blood counts, reflects an individual's capacity to mount an effective immune response to P. falciparum infection."], "structured": true}
{"doc_id": 13963620, "title": "Dynamic analysis of filopodial interactions during the zippering phase of Drosophila dorsal closure.", "abstract": ["Dorsal closure is a paradigm epithelial fusion episode that occurs late in Drosophila embryogenesis and leads to sealing of a midline hole by bonding of two opposing epithelial sheets.", "The leading edge epithelial cells express filopodia and fusion is dependent on interdigitation of these filopodia to prime formation of adhesions.", "Since the opposing epithelia are molecularly patterned there must exist some mechanism for accurately aligning the two sheets across this fusion seam.", "To address this, we generated a fly in which RFP-Moesin and GFP-Moesin are expressed in mutually exclusive stripes within each segment using the engrailed and patched promoters.", "We observe mutually exclusive interactions between the filopodia of engrailed and patched cells.", "Interactions between filopodia from matching cells leads to formation of tethers between them, and these tethers can pull misaligned epithelial sheets into alignment.", "Filopodial matching also occurs during repair of laser wounds in the ventral epithelium, and so this behaviour is not restricted to leading edge cells during dorsal closure.", "Finally, we characterise the behaviour of a patched-expressing cell that we observe within the engrailed region of segments A1-A5, and provide evidence that this cell contributes to cell matching."], "structured": false}
{"doc_id": 13964633, "title": "Expression of Versican 3\u2032-Untranslated Region Modulates Endogenous MicroRNA Functions", "abstract": ["BACKGROUND Mature microRNAs (miRNAs) are single-stranded RNAs that regulate post-transcriptional gene expression.", "In our previous study, we have shown that versican 3'UTR, a fragment of non-coding transcript, has the ability to antagonize miR-199a-3p function thereby regulating expression of the matrix proteins versican and fibronectin, and thus resulting in enhanced cell-cell adhesion and organ adhesion.", "However, the impact of this non-coding fragment on tumorigenesis is yet to be determined.   \n", "METHODS AND FINDINGS Using computational prediction confirmed with in vitro and in vivo experiments, we report that the expression of versican 3'UTR not only antagonizes miR-199a-3p but can also lower its steady state expression.", "We found that expression of versican 3'UTR in a mouse breast carcinoma cell line, 4T1, decreased miR-199a-3p levels.", "The decrease in miRNA activity consequently translated into differences in tumor growth.", "Computational analysis indicated that both miR-199a-3p and miR-144 targeted a cell cycle regulator, Rb1.", "In addition, miR-144 and miR-136, which have also been shown to interact with versican 3'UTR, was found to target PTEN.", "Expression of Rb1 and PTEN were up-regulated synergistically in vitro and in vivo, suggesting that the 3'UTR binds and modulates miRNA activities, freeing Rb1 and PTEN mRNAs for translation.", "In tumor formation assays, cells transfected with the 3'UTR formed smaller tumors compared with cells transfected with a control vector.   \n", "CONCLUSION Our results demonstrated that a 3'UTR fragment can be used to modulate miRNA functions.", "Our study also suggests that miRNAs in the cancer cells are more susceptible to degradation, due to its interaction with a non-coding 3'UTR.", "This non-coding component of mRNA may be used retrospectively to modulate miRNA activities."], "structured": true}
{"doc_id": 13965483, "title": "Prophylactic and therapeutic efficacy of the epitope vaccine CTB-UA against Helicobacter pylori infection in a BALB/c mice model", "abstract": ["Epitope vaccine based on the enzyme urease of Helicobacter pylori is a promising option for prophylactic and therapeutic vaccination against H. pylori infection.", "In our previous study, the epitope vaccine CTB-UA, which was composed of the mucosal adjuvant cholera toxin B subunit (CTB) and an epitope (UreA183\u2013203) from the H. pylori urease A subunit (UreA) was constructed.", "This particular vaccine was shown to have good immunogenicity and immunoreactivity and could induce specific neutralizing antibodies, which exhibited effectively inhibitory effects on the enzymatic activity of H. pylori urease.", "In this study, the prophylactic and therapeutic efficacy of the epitope vaccine CTB-UA was evaluated in a BALB/c mice model.", "The experimental results indicated that oral prophylactic or therapeutic immunization with CTB-UA significantly decreased H. pylori colonization compared with oral immunization with PBS.", "The results also revealed that the protection was correlated with antigen-specific IgG, IgA, and mucosal secretory IgA antibody responses.", "CTB-UA may be a promising vaccine candidate for the control of H. pylori infection."], "structured": false}
{"doc_id": 13966946, "title": "Spatial co-distribution of neglected tropical diseases in the east African great lakes region: revisiting the justification for integrated control.", "abstract": ["OBJECTIVE To determine spatial patterns of co-endemicity of schistosomiasis mansoni and the soil-transmitted helminths (STHs) Ascaris lumbricoides, Trichuris trichiura and hookworm in the Great Lakes region of East Africa, to help plan integrated neglected tropical disease programmes in this region.   \n", "METHOD Parasitological surveys were conducted in Uganda, Tanzania, Kenya and Burundi in 28 213 children in 404 schools.", "Bayesian geostatistical models were used to interpolate prevalence of these infections across the study area.", "Interpolated prevalence maps were overlaid to determine areas of co-endemicity.   \n", "RESULTS In the Great Lakes region, prevalence was 18.1% for Schistosoma mansoni, 50.0% for hookworm, 6.8% for A. lumbricoides and 6.8% for T. trichiura.", "Hookworm infection was ubiquitous, whereas S. mansoni, A. lumbricoides and T. trichiura were highly focal.", "Most areas were endemic (prevalence >or=10%) or hyperendemic (prevalence >or=50%) for one or more STHs, whereas endemic areas for schistosomiasis mansoni were restricted to foci adjacent large perennial water bodies.   \n", "CONCLUSION Because of the ubiquity of hookworm, treatment programmes are required for STH throughout the region but efficient schistosomiasis control should only be targeted at limited high-risk areas.", "Therefore, integration of schistosomiasis with STH control is only indicated in limited foci in East Africa."], "structured": true}
{"doc_id": 13969173, "title": "Direct conversion of patient fibroblasts demonstrates non-cell autonomous toxicity of astrocytes to motor neurons in familial and sporadic ALS.", "abstract": ["Amyotrophic lateral sclerosis (ALS) causes motor neuron degeneration, paralysis, and death.", "Accurate disease modeling, identifying disease mechanisms, and developing therapeutics is urgently needed.", "We previously reported motor neuron toxicity through postmortem ALS spinal cord-derived astrocytes.", "However, these cells can only be harvested after death, and their expansion is limited.", "We now report a rapid, highly reproducible method to convert adult human fibroblasts from living ALS patients to induced neuronal progenitor cells and subsequent differentiation into astrocytes (i-astrocytes).", "Non-cell autonomous toxicity to motor neurons is found following coculture of i-astrocytes from familial ALS patients with mutation in superoxide dismutase or hexanucleotide expansion in C9orf72 (ORF 72 on chromosome 9) the two most frequent causes of ALS.", "Remarkably, i-astrocytes from sporadic ALS patients are as toxic as those with causative mutations, suggesting a common mechanism.", "Easy production and expansion of i-astrocytes now enables rapid disease modeling and high-throughput drug screening to alleviate astrocyte-derived toxicity."], "structured": false}
{"doc_id": 13980338, "title": "Combined Single-Cell Functional and Gene Expression Analysis Resolves Heterogeneity within Stem Cell Populations", "abstract": ["Heterogeneity within the self-renewal durability of adult hematopoietic stem cells (HSCs) challenges our understanding of the molecular framework underlying HSC function.", "Gene expression studies have been hampered by the presence of multiple HSC subtypes and contaminating non-HSCs in bulk HSC populations.", "To gain deeper insight into the gene expression program of murine HSCs, we combined single-cell functional assays with flow cytometric index sorting and single-cell gene expression assays.", "Through bioinformatic integration of these datasets, we designed an unbiased sorting strategy that separates non-HSCs away from HSCs, and single-cell transplantation experiments using the enriched population were combined with RNA-seq data to identify key molecules that associate with long-term durable self-renewal, producing a single-cell molecular dataset that is linked to functional stem cell activity.", "Finally, we demonstrated the broader applicability of this approach for linking key molecules with defined cellular functions in another stem cell system."], "structured": false}
{"doc_id": 13989491, "title": "Acids: Structures, Properties, and Functions (University Science Books, Sausalito, CA, 2000).", "abstract": ["Humans expressing a defective form of the transcription factor AIRE (autoimmune regulator) develop multiorgan autoimmune disease.", "We used aire- deficient mice to test the hypothesis that this transcription factor regulates autoimmunity by promoting the ectopic expression of peripheral tissue- restricted antigens in medullary epithelial cells of the thymus.", "This hypothesis proved correct.", "The mutant animals exhibited a defined profile of autoimmune diseases that depended on the absence of aire in stromal cells of the thymus.", "Aire-deficient thymic medullary epithelial cells showed a specific reduction in ectopic transcription of genes encoding peripheral antigens.", "These findings highlight the importance of thymically imposed \"central\" tolerance in controlling autoimmunity."], "structured": false}
{"doc_id": 13992047, "title": "Directed Actin Polymerization Is the Driving Force for Epithelial Cell\u2013Cell Adhesion", "abstract": ["We have found that epithelial cells engage in a process of cadherin-mediated intercellular adhesion that utilizes calcium and actin polymerization in unexpected ways.", "Calcium stimulates filopodia, which penetrate and embed into neighboring cells.", "E-cadherin complexes cluster at filopodia tips, generating a two-rowed zipper of embedded puncta.", "Opposing cell surfaces are clamped by desmosomes, while vinculin, zyxin, VASP, and Mena are recruited to adhesion zippers by a mechanism that requires alpha-catenin.", "Actin reorganizes and polymerizes to merge puncta into a single row and seal cell borders.", "In keratinocytes either null for alpha-catenin or blocked in VASP/Mena function, filopodia embed, but actin reorganization/polymerization is prevented, and membranes cannot seal.", "Taken together, a dynamic mechanism for intercellular adhesion is unveiled involving calcium-activated filopodia penetration and VASP/Mena-dependent actin reorganization/polymerization."], "structured": false}
{"doc_id": 14019636, "title": "Ribosomal DNA copy number loss and sequence variation in cancer", "abstract": ["Ribosomal DNA is one of the most variable regions in the human genome with respect to copy number.", "Despite the importance of rDNA for cellular function, we know virtually nothing about what governs its copy number, stability, and sequence in the mammalian genome due to challenges associated with mapping and analysis.", "We applied computational and droplet digital PCR approaches to measure rDNA copy number in normal and cancer states in human and mouse genomes.", "We find that copy number and sequence can change in cancer genomes.", "Counterintuitively, human cancer genomes show a loss of copies, accompanied by global copy number co-variation.", "The sequence can also be more variable in the cancer genome.", "Cancer genomes with lower copies have mutational evidence of mTOR hyperactivity.", "The PTEN phosphatase is a tumor suppressor that is critical for genome stability and a negative regulator of the mTOR kinase pathway.", "Surprisingly, but consistent with the human cancer genomes, hematopoietic cancer stem cells from a Pten-/- mouse model for leukemia have lower rDNA copy number than normal tissue, despite increased proliferation, rRNA production, and protein synthesis.", "Loss of copies occurs early and is associated with hypersensitivity to DNA damage.", "Therefore, copy loss is a recurrent feature in cancers associated with mTOR activation.", "Ribosomal DNA copy number may be a simple and useful indicator of whether a cancer will be sensitive to DNA damaging treatments."], "structured": false}
{"doc_id": 14021596, "title": "The association of Red cell distribution width and in-hospital mortality in older adults admitted to the emergency department", "abstract": ["BACKGROUND The objective of the study was to test the hypothesis that elevated red cell distribution width (RDW) at admission increases the risk of mortality in older patients admitted to the emergency department (ED).   \n", "METHODS We performed a retrospective analysis of patients admitted to the ED between May 2013 and October 2013.", "We included patients who were older than 65 years who visited the ED with any medical problems.", "Baseline RDW values were measured at the time of admission to the ED.", "The primary outcome was all-cause in-hospital mortality.", "Multivariate logistic analysis was performed.   \n", "RESULTS A total of 1,990 patients were finally included in this study.", "The mean age was 75 years (SD 7), and 936 (47 %) subjects were male.", "The in-hospital mortality rate was 3.76 % (74 patients).", "RDW values higher in non-survivors than in survivors (15.9 \u00b1 2.5 vs. 13.8 \u00b1 1.7, p < 0.001).", "Multivariate logistic analysis showed that RDW was associated with all-cause in-hospital mortality after adjusting for other confounding factors.   ", "DISCUSSION RDW value at admission is an independent predictor of all-cause in-hospital mortality among patients older than 65 years.", "After adjustment for multiple confounders, the all-cause in-hospital mortality rate increased by 21.8% for each 1% increase in RDW.   \n", "CONCLUSION These results show that RDW at admission is associated with in-hospital mortality among patients older than 65.", "Thus, RDW at admission may represent a surrogate marker of disease severity.", "We caution against using these findings to aid clinical decision-making process until they are externally validated."], "structured": true}
{"doc_id": 14050257, "title": "Gene regulation by the act of long non-coding RNA transcription", "abstract": ["Long non-protein-coding RNAs (lncRNAs) are proposed to be the largest transcript class in the mouse and human transcriptomes.", "Two important questions are whether all lncRNAs are functional and how they could exert a function.", "Several lncRNAs have been shown to function through their product, but this is not the only possible mode of action.", "In this review we focus on a role for the process of lncRNA transcription, independent of the lncRNA product, in regulating protein-coding-gene activity in cis.", "We discuss examples where lncRNA transcription leads to gene silencing or activation, and describe strategies to determine if the lncRNA product or its transcription causes the regulatory effect."], "structured": false}
{"doc_id": 14060030, "title": "Life and death of cardiac stem cells: a paradigm shift in cardiac biology.", "abstract": ["The recognition that myocyte mitosis occurs in the fetal, neonatal, adult, and hypertrophied heart and that a pool of primitive, undifferentiated cells is present in the myocardium has put forward a different view of the biology of the heart.", "The new paradigm suggests that myocyte formation is preserved during postnatal life, in adulthood or senescence, pointing to a remarkable growth reserve of the heart throughout the course of life of the organism.", "This article reviews a large body of novel information, which has been obtained in the last 2 decades, in favor of the notion that the mammalian heart has the inherent ability to continuously replace its parenchymal cells and that this unexpected characteristic has important implications in understanding myocardial homeostasis, cardiac aging, and tissue repair.  ", "The paradigm that the heart is a postmitotic organ incapable of regenerating parenchymal cells was established in the 1970s, and this dogma has profoundly conditioned basic and clinical research in cardiology for the last 3 decades.", "On the basis of this paradigm, cardiomyocytes undergo cellular hypertrophy1,2 but cannot be replaced either by entry into the cell cycle of a subpopulation of nonterminally differentiated myocytes or by activation of a pool of primitive cells that become committed to the myocyte lineage.", "The only response of cardiomyocytes to stress is hypertrophy and/or death.", "Therefore, a tremendous effort was made to identify the molecular mechanisms of myocyte hypertrophy and their genetic control.", "A sophisticated knowledge of various signaling pathways has been achieved, and our understanding of the biology of hypertrophic myocyte growth has advanced markedly.3 An array of new technologies has been introduced that has led to a scientific revolution in terms of questions, approaches, and interpretation of experimental results.", "Despite this enormous progress in our understanding of basic mechanisms of hypertrophy, however, very little \u2026"], "structured": false}
{"doc_id": 14075252, "title": "Paraneoplastic thrombocytosis: the secrets of tumor self-promotion.", "abstract": ["Paraneoplastic thrombocytosis is associated with many solid tumors and often correlates with reduced survival.", "Recent studies suggest that a pathogenic feed back loop may be operative between platelets and tumor cells, with reciprocal interactions between tumor growth/metastasis and thrombocytosis/platelet activation.", "Specific molecular pathways have been identified in which tumors can stimulate platelet production and activation; activated platelets can, in turn, promote tumor growth and metastasis.", "Taken together, these findings provide exciting new potential targets for therapeutic intervention."], "structured": false}
{"doc_id": 14079881, "title": "Perceived age as clinically useful biomarker of ageing: cohort study.", "abstract": ["OBJECTIVE To determine whether perceived age correlates with survival and important age related phenotypes.   \n", "DESIGN Follow-up study, with survival of twins determined up to January 2008, by which time 675 (37%) had died.   \n", "SETTING Population based twin cohort in Denmark.   \n", "PARTICIPANTS 20 nurses, 10 young men, and 11 older women (assessors); 1826 twins aged >or=70.   \n", "MAIN OUTCOME MEASURES Assessors: perceived age of twins from photographs.", "Twins: physical and cognitive tests and molecular biomarker of ageing (leucocyte telomere length).   \n", "RESULTS For all three groups of assessors, perceived age was significantly associated with survival, even after adjustment for chronological age, sex, and rearing environment.", "Perceived age was still significantly associated with survival after further adjustment for physical and cognitive functioning.", "The likelihood that the older looking twin of the pair died first increased with increasing discordance in perceived age within the twin pair-that is, the bigger the difference in perceived age within the pair, the more likely that the older looking twin died first.", "Twin analyses suggested that common genetic factors influence both perceived age and survival.", "Perceived age, controlled for chronological age and sex, also correlated significantly with physical and cognitive functioning as well as with leucocyte telomere length.   \n", "CONCLUSION Perceived age-which is widely used by clinicians as a general indication of a patient's health-is a robust biomarker of ageing that predicts survival among those aged >or=70 and correlates with important functional and molecular ageing phenotypes."], "structured": true}
{"doc_id": 14082855, "title": "Inflammatory Reaction as Determinant of Foreign Body Reaction Is an Early and Susceptible Event after Mesh Implantation", "abstract": ["PURPOSE To investigate and relate the ultrashort-term and long-term courses of determinants for foreign body reaction as biocompatibility predictors for meshes in an animal model.   ", "MATERIALS AND METHODS Three different meshes (TVT, UltraPro, and PVDF) were implanted in sheep.", "Native and plasma coated meshes were placed bilaterally: (a) interaperitoneally, (b) as fascia onlay, and (c) as muscle onlay (fascia sublay).", "At 5 min, 20 min, 60 min, and 120 min meshes were explanted and histochemically investigated for inflammatory infiltrate, macrophage infiltration, vessel formation, myofibroblast invasion, and connective tissue accumulation.", "The results were related to long-term values over 24 months.   \n", "RESULTS Macrophage invasion reached highest extents with up to 60% in short-term and decreased within 24 months to about 30%.", "Inflammatory infiltrate increased within the first 2 hours, the reached levels and the different extents and ranking among the investigated meshes remained stable during long-term follow up.", "For myofibroblasts, connective tissue, and CD31+ cells, no activity was detected during the first 120 min.   \n", "CONCLUSION The local inflammatory reaction is an early and susceptible event after mesh implantation.", "It cannot be influenced by prior plasma coating and does not depend on the localisation of implantation."], "structured": true}
{"doc_id": 14083283, "title": "Riesz pyramids for fast phase-based video magnification", "abstract": ["We present a new compact image pyramid representation, the Riesz pyramid, that can be used for real-time phase-based motion magnification.", "Our new representation is less overcomplete than even the smallest two orientation, octave-bandwidth complex steerable pyramid, and can be implemented using compact, efficient linear filters in the spatial domain.", "Motion-magnified videos produced with this new representation are of comparable quality to those produced with the complex steerable pyramid.", "When used with phase-based video magnification, the Riesz pyramid phase-shifts image features along only their dominant orientation rather than every orientation like the complex steerable pyramid."], "structured": false}
{"doc_id": 14092737, "title": "Alpha-Synuclein Induces Lysosomal Rupture and Cathepsin Dependent Reactive Oxygen Species Following Endocytosis", "abstract": ["\u03b1-synuclein dysregulation is a critical aspect of Parkinson's disease pathology.", "Recent studies have observed that \u03b1-synuclein aggregates are cytotoxic to cells in culture and that this toxicity can be spread between cells.", "However, the molecular mechanisms governing this cytotoxicity and spread are poorly characterized.", "Recent studies of viruses and bacteria, which achieve their cytoplasmic entry by rupturing intracellular vesicles, have utilized the redistribution of galectin proteins as a tool to measure vesicle rupture by these organisms.", "Using this approach, we demonstrate that \u03b1-synuclein aggregates can induce the rupture of lysosomes following their endocytosis in neuronal cell lines.", "This rupture can be induced by the addition of \u03b1-synuclein aggregates directly into cells as well as by cell-to-cell transfer of \u03b1-synuclein.", "We also observe that lysosomal rupture by \u03b1-synuclein induces a cathepsin B dependent increase in reactive oxygen species (ROS) in target cells.", "Finally, we observe that \u03b1-synuclein aggregates can induce inflammasome activation in THP-1 cells.", "Lysosomal rupture is known to induce mitochondrial dysfunction and inflammation, both of which are well established aspects of Parkinson's disease, thus connecting these aspects of Parkinson's disease to the propagation of \u03b1-synuclein pathology in cells."], "structured": false}
{"doc_id": 14103509, "title": "Mechanistic Fracture Criteria For The Failure Of Human Cortical Bone", "abstract": ["A mechanistic understanding of fracture in human bone is critical to predicting fracture risk associated with age and disease.", "Despite extensive work, a mechanistic framework for describing how the microstructure affects the failure of bone is lacking.", "Although micromechanical models incorporating local failure criteria have been developed for metallic and ceramic materials, few such models exist for biological materials.", "In fact, there is no proof to support the widely held belief that fracture in bone is locally strain-controlled, as for example has been shown for ductile fracture in metallic materials.", "In the present study, we provide such evidence through a novel series of experiments involving a double-notch-bend geometry, designed to shed light on the nature of the critical failure events in bone.", "We examine how the propagating crack interacts with the bone microstructure to provide some mechanistic understanding of fracture and to define how properties vary with orientation.", "It was found that fracture in human cortical bone is consistent with strain-controlled failure, and the influence of microstructure can be described in terms of several toughening mechanisms.", "We provide estimates of the relative importance of these mechanisms, such as uncracked-ligament bridging."], "structured": false}
{"doc_id": 14105446, "title": "Inhibition of limb regeneration in the axolotl after treatment of the skin with actinomycin D.", "abstract": ["In this experiment actinomycin D was used to explore the action of the wound epidermis on underlying tissues during limb regeneration.", "In axolotl forelimbs the skin was removed from the elbow to the shoulder.", "Skin from the right limbs was soaked for three hours in actinomycin D (5.0 or 10.0 \u03bcg/ml 0.6% NaCl).", "For controls, skin from left limbs was soaked in 0.6% NaCl for the same period of time.", "Each piece of skin was orthotopically replanted, and both limbs were amputated through the treated skin, proximal to the elbow.", "After an initial healing period, the control limbs regenerated normally.", "Except for a slightly paler color, limbs bearing actinomycin-treated skin were indistinguishable from the controls, both grossly and histologically, during the first week following amputation.", "While the control limbs formed early blastemas, no grossly visible evidence of regeneration was apparent in the experimental limbs, but histologically some dedifferentiation was occurring.", "Normally three to four digits were seen in the control regenerates before blastemas appeared on the experimental limbs.", "By 35\u201340 days blastemas had appeared on most experimental limbs.", "These developed very rapidly, and within a short time many of them had attained levels of development close to the controls.", "Actinomycin D temporarily suppresses formation of the apical epidermal cap and the subsequent aggregation of dedifferentiated cells into a blastema.", "When the effect wears off, an apical cap forms and the dedifferentiated cells quickly organize into a blastema and begin to differentiate."], "structured": false}
{"doc_id": 14116046, "title": "Retinoic acid-related orphan receptors \u03b1 and \u03b3: key regulators of lipid/glucose metabolism, inflammation, and insulin sensitivity", "abstract": ["Retinoic acid-related orphan receptors ROR\u03b1 and ROR\u03b3 play a regulatory role in lipid/glucose homeostasis and various immune functions, and have been implicated in metabolic syndrome and several inflammatory diseases.", "ROR\u03b1-deficient mice are protected against age- and diet-induced obesity, hepatosteatosis, and insulin resistance.", "The resistance to hepatosteatosis in ROR\u03b1-deficient mice is related to the reduced expression of several genes regulating lipid synthesis, transport, and storage.", "Adipose tissue-associated inflammation, which plays a critical role in the development of insulin resistance, is considerably diminished in ROR\u03b1-deficient mice as indicated by the reduced infiltration of M1 macrophages and decreased expression of many proinflammatory genes.", "Deficiency in ROR\u03b3 also protects against diet-induced insulin resistance by a mechanism that appears different from that in ROR\u03b1 deficiency.", "Recent studies indicated that RORs provide an important link between the circadian clock machinery and its regulation of metabolic genes and metabolic syndrome.", "As ligand-dependent transcription factors, RORs may provide novel therapeutic targets in the management of obesity and associated metabolic diseases, including hepatosteatosis, adipose tissue-associated inflammation, and insulin resistance."], "structured": false}
{"doc_id": 14118484, "title": "ERS/ESTS clinical guidelines on fitness for radical therapy in lung cancer patients (surgery and chemo-radiotherapy).", "abstract": ["A collaboration of multidisciplinary experts on the functional evaluation of lung cancer patients has been facilitated by the European Respiratory Society (ERS) and the European Society of Thoracic Surgery (ESTS), in order to draw up recommendations and provide clinicians with clear, up-to-date guidelines on fitness for surgery and chemo-radiotherapy.", "The subject was divided into different topics, which were then assigned to at least two experts.", "The authors searched the literature according to their own strategies, with no central literature review being performed.", "The draft reports written by the experts on each topic were reviewed, discussed and voted on by the entire expert panel.", "The evidence supporting each recommendation was summarised, and graded as described by the Scottish Intercollegiate Guidelines Network Grading Review Group.", "Clinical practice guidelines were generated and finalized in a functional algorithm for risk stratification of the lung resection candidates, emphasising cardiological evaluation, forced expiratory volume in 1 s, systematic carbon monoxide lung diffusion capacity and exercise testing.", "Contrary to lung resection, for which the scientific evidences are more robust, we were unable to recommend any specific test, cut-off value, or algorithm before chemo-radiotherapy due to the lack of data.", "We recommend that lung cancer patients should be managed in specialised settings by multidisciplinary teams."], "structured": false}
{"doc_id": 14119470, "title": "The Ran GTPase regulates mitotic spindle assembly", "abstract": ["Ran is an abundant nuclear GTPase with a clear role in nuclear transport during interphase but with roles in mitotic regulation that are less well understood.", "The nucleotide-binding state of Ran is regulated by a GTPase activating protein, RanGAP1, and by a guanine nucleotide exchange factor, RCC1.", "Ran also interacts with a guanine nucleotide dissociation inhibitor, RanBP1.", "RanBP1 has a high affinity for GTP-bound Ran, and it acts as a cofactor for RanGAP1, increasing the rate of GAP-mediated GTP hydrolysis on Ran approximately tenfold.", "RanBP1 levels oscillate during the cell cycle [4], and increased concentrations of RanBP1 prolong mitosis in mammalian cells and in Xenopus egg extracts (our unpublished observations).", "We investigated how increased concentrations of RanBP1 disturb mitosis.", "We found that spindle assembly is dramatically disrupted when exogenous RanBP1 is added to M phase Xenopus egg extracts.", "We present evidence that the role of Ran in spindle assembly is independent of nuclear transport and is probably mediated through changes in microtubule dynamics."], "structured": false}
{"doc_id": 14121786, "title": "A summary of the effects of antihypertensive medications on measured blood pressure.", "abstract": ["BACKGROUND Epidemiologic analysis of family data on blood pressure (BP) is often compromised by the effects of antihypertensive medications.", "A review of numerous clinical trials that investigated the effects of BP-lowering medications is summarized here.   \n", "METHODS Published clinical trials, including 137 clinical trials with monodrug therapies and 28 clinical trials of combination drug therapies with a total of 11,739 participants, were reviewed from PubMed.", "Six major classes/groups of antihypertensive medications were categorized by ethnicity, including angiotensin-converting enzyme (ACE) inhibitors, alpha1-blockers, cardioselective beta-blockers (beta1-blockers), calcium channel blockers, thiazide and thiazide-like diuretics, and loop diuretics.   \n", "RESULTS Using sitting or supine BP, for ethnic groups combined, monodrug therapy with ACE inhibitors showed a weighted average effect of lowering the systolic and diastolic BP by 12.5/9.5 mm Hg; alpha1-blockers by 15.5/11.7 mm Hg; beta1-blockers by 14.8/12.2 mm Hg; calcium channel blockers by 15.3/10.5 mm Hg; thiazide diuretics by 15.3/9.8 mm Hg; and loop diuretics by 15.8/8.2 mm Hg.", "However, ACE inhibitors, alpha1-blockers, and beta1-blockers were less effective in African Americans than in non-African Americans, whereas calcium channel blockers, thiazide diuretics, and loop diuretics were more effective in African Americans than in non-African Americans.", "For two-drug combination therapy with ethnic groups combined, the BP-lowering effect of the second medication, when compared to its effect as monodrug therapy, was 84% and 65% for systolic and diastolic BP, respectively.   \n", "CONCLUSIONS The BP-lowering effects reported here may be used to impute the pretreatment BP levels, which can improve the information content and hence the power of epidemiologic analysis in studies where use of antihypertensive medications is a confounding factor in the BP measurements."], "structured": true}
{"doc_id": 14128314, "title": "Stem Cells and Early Lineage Development", "abstract": ["The recent derivation of pluripotent stem cell lines from a number of different sources, including reprogrammed adult somatic cells, raises the issue of the developmental equivalence of these different pluripotent states.", "At least two different states representing the epiblast progenitors in the blastocyst and the pluripotent progenitors of the later gastrulating embryo have been recognized.", "Understanding the initial developmental status of the different pluripotent lines is critical for defining starting conditions for differentiation toward therapeutically relevant cell types."], "structured": false}
{"doc_id": 14131683, "title": "Divergent clonal evolution of castration resistant neuroendocrine prostate cancer", "abstract": ["An increasingly recognized resistance mechanism to androgen receptor (AR)-directed therapy in prostate cancer involves epithelial plasticity, in which tumor cells demonstrate low to absent AR expression and often have neuroendocrine features.", "The etiology and molecular basis for this 'alternative' treatment-resistant cell state remain incompletely understood.", "Here, by analyzing whole-exome sequencing data of metastatic biopsies from patients, we observed substantial genomic overlap between castration-resistant tumors that were histologically characterized as prostate adenocarcinomas (CRPC-Adeno) and neuroendocrine prostate cancer (CRPC-NE); analysis of biopsy samples from the same individuals over time points to a model most consistent with divergent clonal evolution.", "Genome-wide DNA methylation analysis revealed marked epigenetic differences between CRPC-NE tumors and CRPC-Adeno, and also designated samples of CRPC-Adeno with clinical features of AR independence as CRPC-NE, suggesting that epigenetic modifiers may play a role in the induction and/or maintenance of this treatment-resistant state.", "This study supports the emergence of an alternative, 'AR-indifferent' cell state through divergent clonal evolution as a mechanism of treatment resistance in advanced prostate cancer."], "structured": false}
{"doc_id": 14145440, "title": "S-phase-promoting cyclin-dependent kinases prevent re-replication by inhibiting the transition of replication origins to a pre-replicative state", "abstract": ["BACKGROUND DNA replication and mitosis are triggered by activation of kinase complexes, each made up of a cyclin and a cyclin-dependent kinase (Cdk).", "It had seemed possible that the association of Cdks with different classes of cyclins specifies whether S phase (replication) or M phase (mitosis) will occur.", "The recent finding that individual B-type cyclins (encoded by the genes CLB1-CLB6) can have functions in both processes in the budding yeast Saccharomyces cerevisiae casts doubt on this notion.   \n", "RESULTS S. cerevisiae strains lacking C1b1-C1b4 undergo DNA replication once but fail to enter mitosis.", "We have isolated mutations in two genes, SIM1 and SIM2 (SIM2 is identical to SEC72), which allow such cells to undergo an extra round of DNA replication without mitosis.", "The Clb5 kinase, which promotes S phase, remains active during the G2-phase arrest of cells of the parental strain, but its activity declines rapidly in sim mutants.", "Increased expression of the CLB5 gene prevents re-replication.", "Thus, a cyclin B-kinase that promotes DNA replication in G1-phase cells can prevent re-replication in G2-phase cells.", "Inactivation of C1b kinases by expression of the specific C1b-Cdk1 inhibitor p40SIC1 is sufficient to induce a prereplicative state at origins of replication in cells blocked in G2/M phase by nocodazole.", "Re-activation of C1b-Cdk1 kinases induces a second round of DNA replication.   \n", "CONCLUSIONS We propose that S-phase-promoting cyclin B--Cdk complexes prevent re-replication during S, G2 and M phases by inhibiting the transition of replication origins to a pre-replicative state.", "This model can explain both why origins 'fire' only once per S phase and why S phase is dependent on completion of the preceding M phase."], "structured": true}
{"doc_id": 14149065, "title": "E-cadherin engagement stimulates proliferation via Rac1", "abstract": ["E-cadherin has been linked to the suppression of tumor growth and the inhibition of cell proliferation in culture.", "We observed that progressively decreasing the seeding density of normal rat kidney-52E (NRK-52E) or MCF-10A epithelial cells from confluence, indeed, released cells from growth arrest.", "Unexpectedly, a further decrease in seeding density so that cells were isolated from neighboring cells decreased proliferation.", "Experiments using microengineered substrates showed that E-cadherin engagement stimulated the peak in proliferation at intermediate seeding densities, and that the proliferation arrest at high densities did not involve E-cadherin, but rather resulted from a crowding-dependent decrease in cell spreading against the underlying substrate.", "Rac1 activity, which was induced by E-cadherin engagement specifically at intermediate seeding densities, was required for the cadherin-stimulated proliferation, and the control of Rac1 activation by E-cadherin was mediated by p120-catenin.", "Together, these findings demonstrate a stimulatory role for E-cadherin in proliferative regulation, and identify a simple mechanism by which cell\u2013cell contact may trigger or inhibit epithelial cell proliferation in different settings."], "structured": false}
{"doc_id": 14155726, "title": "Structure of Actin-related protein 8 and its contribution to nucleosome binding", "abstract": ["Nuclear actin-related proteins (Arps) are subunits of several chromatin remodelers, but their molecular functions within these complexes are unclear.", "We report the crystal structure of the INO80 complex subunit Arp8 in its ATP-bound form.", "Human Arp8 has several insertions in the conserved actin fold that explain its inability to polymerize.", "Most remarkably, one insertion wraps over the active site cleft and appears to rigidify the domain architecture, while active site features shared with actin suggest an allosterically controlled ATPase activity.", "Quantitative binding studies with nucleosomes and histone complexes reveal that Arp8 and the Arp8-Arp4-actin-HSA sub-complex of INO80 strongly prefer nucleosomes and H3-H4 tetramers over H2A-H2B dimers, suggesting that Arp8 functions as a nucleosome recognition module.", "In contrast, Arp4 prefers free (H3-H4)(2) over nucleosomes and may serve remodelers through binding to (dis)assembly intermediates in the remodeling reaction."], "structured": false}
{"doc_id": 14171859, "title": "Regulation of \u03b2-Adrenergic Receptor Signaling by S-Nitrosylation of G-Protein-Coupled Receptor Kinase 2", "abstract": ["beta-adrenergic receptors (beta-ARs), prototypic G-protein-coupled receptors (GPCRs), play a critical role in regulating numerous physiological processes.", "The GPCR kinases (GRKs) curtail G-protein signaling and target receptors for internalization.", "Nitric oxide (NO) and/or S-nitrosothiols (SNOs) can prevent the loss of beta-AR signaling in vivo, but the molecular details are unknown.", "Here we show in mice that SNOs increase beta-AR expression and prevent agonist-stimulated receptor downregulation; and in cells, SNOs decrease GRK2-mediated beta-AR phosphorylation and subsequent recruitment of beta-arrestin to the receptor, resulting in the attenuation of receptor desensitization and internalization.", "In both cells and tissues, GRK2 is S-nitrosylated by SNOs as well as by NO synthases, and GRK2 S-nitrosylation increases following stimulation of multiple GPCRs with agonists.", "Cys340 of GRK2 is identified as a principal locus of inhibition by S-nitrosylation.", "Our studies thus reveal a central molecular mechanism through which GPCR signaling is regulated."], "structured": false}
{"doc_id": 14174055, "title": "Electroporation enables the efficient mRNA delivery into the mouse zygotes and facilitates CRISPR/Cas9-based genome editing", "abstract": ["Recent use of the CRISPR/Cas9 system has dramatically reduced the time required to produce mutant mice, but the involvement of a time-consuming microinjection step still hampers its application for high-throughput genetic analysis.", "Here we developed a simple, highly efficient, and large-scale genome editing method, in which the RNAs for the CRISPR/Cas9 system are electroporated into zygotes rather than microinjected.", "We used this method to perform single-stranded oligodeoxynucleotide (ssODN)-mediated knock-in in mouse embryos.", "This method facilitates large-scale genetic analysis in the mouse."], "structured": false}
{"doc_id": 14178995, "title": "Summary", "abstract": ["The genetic diseases Hutchinson-Gilford progeria syndrome (HGPS) and restrictive dermopathy (RD) arise from accumulation of farnesylated prelamin A because of defects in the lamin A maturation pathway.", "Both of these diseases exhibit symptoms that can be viewed as accelerated aging.", "The mechanism by which accumulation of farnesylated prelamin A leads to these accelerated aging phenotypes is not understood.", "Here we present evidence that in HGPS and RD fibroblasts, DNA damage checkpoints are persistently activated because of the compromise in genomic integrity.", "Inactivation of checkpoint kinases Ataxia-telangiectasia-mutated (ATM) and ATR (ATM- and Rad3-related) in these patient cells can partially overcome their early replication arrest.", "Treatment of patient cells with a protein farnesyltransferase inhibitor (FTI) did not result in reduction of DNA double-strand breaks and damage checkpoint signaling, although the treatment significantly reversed the aberrant shape of their nuclei.", "This suggests that DNA damage accumulation and aberrant nuclear morphology are independent phenotypes arising from prelamin A accumulation in these progeroid syndromes.", "Since DNA damage accumulation is an important contributor to the symptoms of HGPS, our results call into question the possibility of treatment of HGPS with FTIs alone."], "structured": false}
{"doc_id": 14180217, "title": "The Buccaneer software for automated model building. 1. Tracing protein chains.", "abstract": ["A new technique for the automated tracing of protein chains in experimental electron-density maps is described.", "The technique relies on the repeated application of an oriented electron-density likelihood target function to identify likely C(alpha) positions.", "This function is applied both in the location of a few promising ;seed' positions in the map and to grow those initial C(alpha) positions into extended chain fragments.", "Techniques for assembling the chain fragments into an initial chain trace are discussed."], "structured": false}
{"doc_id": 14180565, "title": "Expression profile of genes modulated by Aloe emodin in human U87 glioblastoma cells.", "abstract": ["Glioblastoma, the most aggressive and malignant form of glioma, appears to be resistant to various chemotherapeutic agents.", "Hence, approaches have been intensively investigated to targeti specific molecular pathways involved in glioblastoma development and progression.", "Aloe emodin is believed to modulate the expression of several genes in cancer cells.", "We aimed to understand the molecular mechanisms underlying the therapeutic effect of Aloe emodin on gene expression profiles in the human U87 glioblastoma cell line utilizing microarray technology.", "The gene expression analysis revealed that a total of 8,226 gene alterations out of 28,869 genes were detected after treatment with 58.6 \u03bcg/ml for 24 hours.", "Out of this total, 34 genes demonstrated statistically significant change (p<0.05) ranging from 1.07 to 1.87 fold.", "The results revealed that 22 genes were up-regulated and 12 genes were down-regulated in response to Aloe emodin treatment.", "These genes were then grouped into several clusters based on their biological functions, revealing induction of expression of genes involved in apoptosis (programmed cell death) and tissue remodelling in U87 cells (p<0.01).", "Several genes with significant changes of the expression level e.g. SHARPIN, BCAP31, FIS1, RAC1 and TGM2 from the apoptotic cluster were confirmed by quantitative real-time PCR (qRT-PCR).", "These results could serve as guidance for further studies in order to discover molecular targets for the cancer therapy based on Aloe emodin treatment."], "structured": false}
{"doc_id": 14185503, "title": "The miniature genome of a carnivorous plant Genlisea aurea contains a low number of genes and short non-coding sequences", "abstract": ["BACKGROUND Genlisea aurea (Lentibulariaceae) is a carnivorous plant with unusually small genome size - 63.6 Mb - one of the smallest known among higher plants.", "Data on the genome sizes and the phylogeny of Genlisea suggest that this is a derived state within the genus.", "Thus, G. aurea is an excellent model organism for studying evolutionary mechanisms of genome contraction.   \n", "RESULTS Here we report sequencing and de novo draft assembly of G. aurea genome.", "The assembly consists of 10,687 contigs of the total length of 43.4 Mb and includes 17,755 complete and partial protein-coding genes.", "Its comparison with the genome of Mimulus guttatus, another representative of higher core Lamiales clade, reveals striking differences in gene content and length of non-coding regions.   \n", "CONCLUSIONS Genome contraction was a complex process, which involved gene loss and reduction of lengths of introns and intergenic regions, but not intron loss.", "The gene loss is more frequent for the genes that belong to multigenic families indicating that genetic redundancy is an important prerequisite for genome size reduction."], "structured": true}
{"doc_id": 14188138, "title": "Abnormal Spine Morphology and Enhanced LTP in LIMK-1 Knockout Mice", "abstract": ["In vitro studies indicate a role for the LIM kinase family in the regulation of cofilin phosphorylation and actin dynamics.", "In addition, abnormal expression of LIMK-1 is associated with Williams syndrome, a mental disorder with profound deficits in visuospatial cognition.", "However, the in vivo function of this family of kinases remains elusive.", "Using LIMK-1 knockout mice, we demonstrate a significant role for LIMK-1 in vivo in regulating cofilin and the actin cytoskeleton.", "Furthermore, we show that the knockout mice exhibited significant abnormalities in spine morphology and in synaptic function, including enhanced hippocampal long-term potentiation.", "The knockout mice also showed altered fear responses and spatial learning.", "These results indicate that LIMK-1 plays a critical role in dendritic spine morphogenesis and brain function."], "structured": false}
{"doc_id": 14191255, "title": "Wdr5 Mediates Self-Renewal and Reprogramming via the Embryonic Stem Cell Core Transcriptional Network", "abstract": ["The embryonic stem (ES) cell transcriptional and chromatin-modifying networks are critical for self-renewal maintenance.", "However, it remains unclear whether these networks functionally interact and, if so, what factors mediate such interactions.", "Here, we show that WD repeat domain 5 (Wdr5), a core member of the mammalian Trithorax (trxG) complex, positively correlates with the undifferentiated state and is a regulator of ES cell self-renewal.", "We demonstrate that Wdr5, an \"effector\" of H3K4 methylation, interacts with the pluripotency transcription factor Oct4.", "Genome-wide protein localization and transcriptome analyses demonstrate overlapping gene regulatory functions between Oct4 and Wdr5.", "The Oct4-Sox2-Nanog circuitry and trxG cooperate in activating transcription of key self-renewal regulators, and furthermore, Wdr5 expression is required for the efficient formation of induced pluripotent stem (iPS) cells.", "We propose an integrated model of transcriptional and epigenetic control, mediated by select trxG members, for the maintenance of ES cell self-renewal and somatic cell reprogramming."], "structured": false}
{"doc_id": 14192687, "title": "Neurons derived from reprogrammed fibroblasts functionally integrate into the fetal brain and improve symptoms of rats with Parkinson's disease.", "abstract": ["The long-term goal of nuclear transfer or alternative reprogramming approaches is to create patient-specific donor cells for transplantation therapy, avoiding immunorejection, a major complication in current transplantation medicine.", "It was recently shown that the four transcription factors Oct4, Sox2, Klf4, and c-Myc induce pluripotency in mouse fibroblasts.", "However, the therapeutic potential of induced pluripotent stem (iPS) cells for neural cell replacement strategies remained unexplored.", "Here, we show that iPS cells can be efficiently differentiated into neural precursor cells, giving rise to neuronal and glial cell types in culture.", "Upon transplantation into the fetal mouse brain, the cells migrate into various brain regions and differentiate into glia and neurons, including glutamatergic, GABAergic, and catecholaminergic subtypes.", "Electrophysiological recordings and morphological analysis demonstrated that the grafted neurons had mature neuronal activity and were functionally integrated in the host brain.", "Furthermore, iPS cells were induced to differentiate into dopamine neurons of midbrain character and were able to improve behavior in a rat model of Parkinson's disease upon transplantation into the adult brain.", "We minimized the risk of tumor formation from the grafted cells by separating contaminating pluripotent cells and committed neural cells using fluorescence-activated cell sorting.", "Our results demonstrate the therapeutic potential of directly reprogrammed fibroblasts for neuronal cell replacement in the animal model."], "structured": false}
{"doc_id": 14195528, "title": "Responses of primate frontal cortex neurons during natural vocal communication.", "abstract": ["The role of primate frontal cortex in vocal communication and its significance in language evolution have a controversial history.", "While evidence indicates that vocalization processing occurs in ventrolateral prefrontal cortex neurons, vocal-motor activity has been conjectured to be primarily subcortical and suggestive of a distinctly different neural architecture from humans.", "Direct evidence of neural activity during natural vocal communication is limited, as previous studies were performed in chair-restrained animals.", "Here we recorded the activity of single neurons across multiple regions of prefrontal and premotor cortex while freely moving marmosets engaged in a natural vocal behavior known as antiphonal calling.", "Our aim was to test whether neurons in marmoset frontal cortex exhibited responses during vocal-signal processing and/or vocal-motor production in the context of active, natural communication.", "We observed motor-related changes in single neuron activity during vocal production, but relatively weak sensory responses for vocalization processing during this natural behavior.", "Vocal-motor responses occurred both prior to and during call production and were typically coupled to the timing of each vocalization pulse.", "Despite the relatively weak sensory responses a population classifier was able to distinguish between neural activity that occurred during presentations of vocalization stimuli that elicited an antiphonal response and those that did not.", "These findings are suggestive of the role that nonhuman primate frontal cortex neurons play in natural communication and provide an important foundation for more explicit tests of the functional contributions of these neocortical areas during vocal behaviors."], "structured": false}
{"doc_id": 14198646, "title": "Salt-inducible kinase 2 links transcriptional coactivator p300 phosphorylation to the prevention of ChREBP-dependent hepatic steatosis in mice.", "abstract": ["Obesity and type 2 diabetes are associated with increased lipogenesis in the liver.", "This results in fat accumulation in hepatocytes, a condition known as hepatic steatosis, which is a form of nonalcoholic fatty liver disease (NAFLD), the most common cause of liver dysfunction in the United States.", "Carbohydrate-responsive element-binding protein (ChREBP), a transcriptional activator of glycolytic and lipogenic genes, has emerged as a major player in the development of hepatic steatosis in mice.", "However, the molecular mechanisms enhancing its transcriptional activity remain largely unknown.", "In this study, we have identified the histone acetyltransferase (HAT) coactivator p300 and serine/threonine kinase salt-inducible kinase 2 (SIK2) as key upstream regulators of ChREBP activity.", "In cultured mouse hepatocytes, we showed that glucose-activated p300 acetylated ChREBP on Lys672 and increased its transcriptional activity by enhancing its recruitment to its target gene promoters.", "SIK2 inhibited p300 HAT activity by direct phosphorylation on Ser89, which in turn decreased ChREBP-mediated lipogenesis in hepatocytes and mice overexpressing SIK2.", "Moreover, both liver-specific SIK2 knockdown and p300 overexpression resulted in hepatic steatosis, insulin resistance, and inflammation, phenotypes reversed by SIK2/p300 co-overexpression.", "Finally, in mouse models of type 2 diabetes and obesity, low SIK2 activity was associated with increased p300 HAT activity, ChREBP hyperacetylation, and hepatic steatosis.", "Our findings suggest that inhibition of hepatic p300 activity may be beneficial for treating hepatic steatosis in obesity and type 2 diabetes and identify SIK2 activators and specific p300 inhibitors as potential targets for pharmaceutical intervention."], "structured": false}
{"doc_id": 14205246, "title": "A Role for NuSAP in Linking Microtubules to Mitotic Chromosomes", "abstract": ["The spindle apparatus is a microtubule (MT)-based machinery that attaches to and segregates the chromosomes during mitosis and meiosis.", "Self-organization of the spindle around chromatin involves the assembly of MTs, their attachment to the chromosomes, and their organization into a bipolar array.", "One regulator of spindle self-organization is RanGTP.", "RanGTP is generated at chromatin and activates a set of soluble, Ran-regulated spindle factors such as TPX2, NuMA, and NuSAP .", "How the spindle factors direct and attach MTs to the chromosomes are key open questions.", "Nucleolar and Spindle-Associated Protein (NuSAP) was recently identified as an essential MT-stabilizing and bundling protein that is enriched at the central part of the spindle .", "Here, we show by biochemical reconstitution that NuSAP efficiently adsorbs to isolated chromatin and DNA and that it can directly produce and retain high concentrations of MTs in the immediate vicinity of chromatin or DNA.", "Moreover, our data reveal that NuSAP-chromatin interaction is subject to Ran regulation and can be suppressed by Importin alpha (Impalpha) and Imp7.", "We propose that the presence of MT binding agents such as NuSAP, which can be directly immobilized on chromatin, are critical for targeting MT production to vertebrate chromosomes during spindle self-organization."], "structured": false}
{"doc_id": 14225271, "title": "Molecular features of cellular reprogramming and development", "abstract": ["Differentiating somatic cells are progressively restricted to specialized functions during ontogeny, but they can be experimentally directed to form other cell types, including those with complete embryonic potential.", "Early nuclear reprogramming methods, such as somatic cell nuclear transfer (SCNT) and cell fusion, posed significant technical hurdles to precise dissection of the regulatory programmes governing cell identity.", "However, the discovery of reprogramming by ectopic expression of a defined set of transcription factors, known as direct reprogramming, provided a tractable platform to uncover molecular characteristics of cellular specification and differentiation, cell type stability and pluripotency.", "We discuss the control and maintenance of cellular identity during developmental transitions as they have been studied using direct reprogramming, with an emphasis on transcriptional and epigenetic regulation."], "structured": false}
{"doc_id": 14240343, "title": "Small molecule modifiers of circadian clocks", "abstract": ["Circadian clocks orchestrate 24-h oscillations of essential physiological and behavioral processes in response to daily environmental changes.", "These clocks are remarkably precise under constant conditions yet highly responsive to resetting signals.", "With the molecular composition of the core oscillator largely established, recent research has increasingly focused on clock-modifying mechanisms/molecules.", "In particular, small molecule modifiers, intrinsic or extrinsic, are emerging as powerful tools for understanding basic clock biology as well as developing putative therapeutic agents for clock-associated diseases.", "In this review, we will focus on synthetic compounds capable of modifying the period, phase, or amplitude of circadian clocks, with particular emphasis on the mammalian clock.", "We will discuss the potential of exploiting these small molecule modifiers in both basic and translational research."], "structured": false}
{"doc_id": 14241418, "title": "NVP-BEZ235, a dual PI3K/mTOR inhibitor, prevents PI3K signaling and inhibits the growth of cancer cells with activating PI3K mutations.", "abstract": ["Phosphatidylinositol-3-kinase (PI3K) pathway deregulation is a common event in human cancer, either through inactivation of the tumor suppressor phosphatase and tensin homologue deleted from chromosome 10 or activating mutations of p110-alpha.", "These hotspot mutations result in oncogenic activity of the enzyme and contribute to therapeutic resistance to the anti-HER2 antibody trastuzumab.", "The PI3K pathway is, therefore, an attractive target for cancer therapy.", "We have studied NVP-BEZ235, a dual inhibitor of the PI3K and the downstream mammalian target of rapamycin (mTOR).", "NVP-BEZ235 inhibited the activation of the downstream effectors Akt, S6 ribosomal protein, and 4EBP1 in breast cancer cells.", "The antiproliferative activity of NVP-BEZ235 was superior to the allosteric selective mTOR complex inhibitor everolimus in a panel of 21 cancer cell lines of different origin and mutation status.", "The described Akt activation due to mTOR inhibition was prevented by higher doses of NVP-BEZ235.", "NVP-BEZ235 reversed the hyperactivation of the PI3K/mTOR pathway caused by the oncogenic mutations of p110-alpha, E545K, and H1047R, and inhibited the proliferation of HER2-amplified BT474 cells exogenously expressing these mutations that render them resistant to trastuzumab.", "In trastuzumab-resistant BT474 H1047R breast cancer xenografts, NVP-BEZ235 inhibited PI3K signaling and had potent antitumor activity.", "In treated animals, there was complete inhibition of PI3K signaling in the skin at pharmacologically active doses, suggesting that skin may serve as surrogate tissue for pharmacodynamic studies.", "In summary, NVP-BEZ235 inhibits the PI3K/mTOR axis and results in antiproliferative and antitumoral activity in cancer cells with both wild-type and mutated p110-alpha."], "structured": false}
{"doc_id": 14252892, "title": "Pharmacokinetic, pharmacodynamic, and pharmacogenetic determinants of osteonecrosis in children with acute lymphoblastic leukemia.", "abstract": ["Osteonecrosis is a severe glucocorticoid-induced complication of acute lymphoblastic leukemia treatment.", "We prospectively screened children (n = 364) with magnetic resonance imaging of hips and knees, regardless of symptoms; the cumulative incidence of any (grade 1-4) versus symptomatic (grade 2-4) osteonecrosis was 71.8% versus 17.6%, respectively.", "We investigated whether age, race, sex, acute lymphoblastic leukemia treatment arm, body mass, serum lipids, albumin and cortisol levels, dexamethasone pharmacokinetics, and genome-wide germline genetic polymorphisms were associated with symptomatic osteonecrosis.", "Age more than 10 years (odds ratio, = 4.85; 95% confidence interval, 2.5-9.2; P = .00001) and more intensive treatment (odds ratio = 2.5; 95% confidence interval, 1.2-4.9; P = .011) were risk factors and included as covariates in all analyses.", "Lower albumin (P = .05) and elevated cholesterol (P = .02) associated with symptomatic osteonecrosis, and severe (grade 3 or 4) osteonecrosis was linked to poor dexamethasone clearance (P = .0005).", "Adjusting for clinical features, polymorphisms of ACP1 (eg, rs12714403, P = 1.9 \u00d7 10(-6), odds ratio = 5.6; 95% confidence interval, 2.7-11.3), which regulates lipid levels and osteoblast differentiation, were associated with risk of osteonecrosis as well as with lower albumin and higher cholesterol.", "Overall, older age, lower albumin, higher lipid levels, and dexamethasone exposure were associated with osteonecrosis and may be linked by inherited genomic variation."], "structured": false}
{"doc_id": 14260013, "title": "Prevention of Rectal SHIV Transmission in Macaques by Daily or Intermittent Prophylaxis with Emtricitabine and Tenofovir ", "abstract": ["BACKGROUND In the absence of an effective vaccine, HIV continues to spread globally, emphasizing the need for novel strategies to limit its transmission.", "Pre-exposure prophylaxis (PrEP) with antiretroviral drugs could prove to be an effective intervention strategy if highly efficacious and cost-effective PrEP modalities are identified.", "We evaluated daily and intermittent PrEP regimens of increasing antiviral activity in a macaque model that closely resembles human transmission.   \n", "METHODS AND FINDINGS We used a repeat-exposure macaque model with 14 weekly rectal virus challenges.", "Three drug treatments were given once daily, each to a different group of six rhesus macaques.", "Group 1 was treated subcutaneously with a human-equivalent dose of emtricitabine (FTC), group 2 received orally the human-equivalent dosing of both FTC and tenofovir-disoproxil fumarate (TDF), and group 3 received subcutaneously a similar dosing of FTC and a higher dose of tenofovir.", "A fourth group of six rhesus macaques (group 4) received intermittently a PrEP regimen similar to group 3 only 2 h before and 24 h after each weekly virus challenge.", "Results were compared to 18 control macaques that did not receive any drug treatment.", "The risk of infection in macaques treated in groups 1 and 2 was 3.8- and 7.8-fold lower than in untreated macaques (p = 0.02 and p = 0.008, respectively).", "All six macaques in group 3 were protected.", "Breakthrough infections had blunted acute viremias; drug resistance was seen in two of six animals.", "All six animals in group 4 that received intermittent PrEP were protected.   \n", "CONCLUSIONS This model suggests that single drugs for daily PrEP can be protective but a combination of antiretroviral drugs may be required to increase the level of protection.", "Short but potent intermittent PrEP can provide protection comparable to that of daily PrEP in this SHIV/macaque model.", "These findings support PrEP trials for HIV prevention in humans and identify promising PrEP modalities."], "structured": true}
{"doc_id": 14275671, "title": "Direct-coupling analysis of residue co-evolution captures native contacts across many protein families", "abstract": ["The similarity in the three-dimensional structures of homologous proteins imposes strong constraints on their sequence variability.", "It has long been suggested that the resulting correlations among amino acid compositions at different sequence positions can be exploited to infer spatial contacts within the tertiary protein structure.", "Crucial to this inference is the ability to disentangle direct and indirect correlations, as accomplished by the recently introduced Direct Coupling Analysis (DCA) (Weigt et al. (2009) Proc Natl Acad Sci 106:67).", "Here we develop a computationally efficient implementation of DCA, which allows us to evaluate the accuracy of contact prediction by DCA for a large number of protein domains, based purely on sequence information.", "DCA is shown to yield a large number of correctly predicted contacts, recapitulating the global structure of the contact map for the majority of the protein domains examined.", "Furthermore, our analysis captures clear signals beyond intra- domain residue contacts, arising, e.g., from alternative protein conformations, ligand- mediated residue couplings, and inter-domain interactions in protein oligomers.", "Our findings suggest that contacts predicted by DCA can be used as a reliable guide to facilitate computational predictions of alternative protein conformations, protein complex formation, and even the de novo prediction of protein domain structures, provided the existence of a large number of homologous sequences which are being rapidly made available due to advances in genome sequencing."], "structured": false}
{"doc_id": 14290854, "title": "Variation in antibiotic prescribing and its impact on recovery in patients with acute cough in primary care: prospective study in 13 countries.", "abstract": ["OBJECTIVE To describe variation in antibiotic prescribing for acute cough in contrasting European settings and the impact on recovery.   \n", "DESIGN Cross sectional observational study with clinicians from 14 primary care research networks in 13 European countries who recorded symptoms on presentation and management.", "Patients followed up for 28 days with patient diaries.   \n", "SETTING Primary care.   \n", "PARTICIPANTS Adults with a new or worsening cough or clinical presentation suggestive of lower respiratory tract infection.   \n", "MAIN OUTCOME MEASURES Prescribing of antibiotics by clinicians and total symptom severity scores over time.   \n", "RESULTS 3402 patients were recruited (clinicians completed a case report form for 99% (3368) of participants and 80% (2714) returned a symptom diary).", "Mean symptom severity scores at presentation ranged from 19 (scale range 0 to 100) in networks based in Spain and Italy to 38 in the network based in Sweden.", "Antibiotic prescribing by networks ranged from 20% to nearly 90% (53% overall), with wide variation in classes of antibiotics prescribed.", "Amoxicillin was overall the most common antibiotic prescribed, but this ranged from 3% of antibiotics prescribed in the Norwegian network to 83% in the English network.", "While fluoroquinolones were not prescribed at all in three networks, they were prescribed for 18% in the Milan network.", "After adjustment for clinical presentation and demographics, considerable differences remained in antibiotic prescribing, ranging from Norway (odds ratio 0.18, 95% confidence interval 0.11 to 0.30) to Slovakia (11.2, 6.20 to 20.27) compared with the overall mean (proportion prescribed: 0.53).", "The rate of recovery was similar for patients who were and were not prescribed antibiotics (coefficient -0.01, P<0.01) once clinical presentation was taken into account.   \n", "CONCLUSIONS Variation in clinical presentation does not explain the considerable variation in antibiotic prescribing for acute cough in Europe.", "Variation in antibiotic prescribing is not associated with clinically important differences in recovery.   \n", "TRIAL REGISTRATION Clinicaltrials.gov NCT00353951."], "structured": true}
{"doc_id": 14296612, "title": "Dorsomorphin, a Selective Small Molecule Inhibitor of BMP Signaling, Promotes Cardiomyogenesis in Embryonic Stem Cells", "abstract": ["BACKGROUND Pluripotent embryonic stem (ES) cells, which have the capacity to give rise to all tissue types in the body, show great promise as a versatile source of cells for regenerative therapy.", "However, the basic mechanisms of lineage specification of pluripotent stem cells are largely unknown, and generating sufficient quantities of desired cell types remains a formidable challenge.", "Small molecules, particularly those that modulate key developmental pathways like the bone morphogenetic protein (BMP) signaling cascade, hold promise as tools to study in vitro lineage specification and to direct differentiation of stem cells toward particular cell types.   \n", "METHODOLOGY/ PRINCIPAL FINDINGS We describe the use of dorsomorphin, a selective small molecule inhibitor of BMP signaling, to induce myocardial differentiation in mouse ES cells.", "Cardiac induction is very robust, increasing the yield of spontaneously beating cardiomyocytes by at least 20 fold.", "Dorsomorphin, unlike the endogenous BMP antagonist Noggin, robustly induces cardiomyogenesis when treatment is limited to the initial 24-hours of ES cell differentiation.", "Quantitative-PCR analyses of differentiating ES cells indicate that pharmacological inhibition of BMP signaling during the early critical stage promotes the development of the cardiomyocyte lineage, but reduces the differentiation of endothelial, smooth muscle, and hematopoietic cells.   \n", "CONCLUSIONS/ SIGNIFICANCE Administration of a selective small molecule BMP inhibitor during the initial stages of ES cell differentiation substantially promotes the differentiation of primitive pluripotent cells toward the cardiomyocytic lineage, apparently at the expense of other mesodermal lineages.", "Small molecule modulators of developmental pathways like dorsomorphin could become versatile pharmacological tools for stem cell research and regenerative medicine."], "structured": true}
{"doc_id": 14300799, "title": "Cineradiography of Monkey Lip-Smacking Reveals Putative Precursors of Speech Dynamics", "abstract": ["A key feature of speech is its stereotypical 5 Hz rhythm.", "One theory posits that this rhythm evolved through the modification of rhythmic facial movements in ancestral primates.", "If the hypothesis has any validity, then a comparative approach may shed some light.", "We tested this idea by using cineradiography (X-ray movies) to characterize and quantify the internal dynamics of the macaque monkey vocal tract during lip-smacking (a rhythmic facial expression) versus chewing.", "Previous human studies showed that speech movements are faster than chewing movements, and the functional coordination between vocal tract structures is different between the two behaviors.", "If rhythmic speech evolved through a rhythmic ancestral facial movement, then one hypothesis is that monkey lip-smacking versus chewing should also exhibit these differences.", "We found that the lips, tongue, and hyoid move with a speech-like 5 Hz rhythm during lip-smacking, but not during chewing.", "Most importantly, the functional coordination between these structures was distinct for each behavior.", "These data provide empirical support for the idea that the human speech rhythm evolved from the rhythmic facial expressions of ancestral primates."], "structured": false}
{"doc_id": 14308244, "title": "Interneuronal DISC1 regulates NRG1-ErbB4 signalling and excitatory-inhibitory synapse formation in the mature cortex.", "abstract": ["Neuregulin-1 (NRG1) and its receptor ErbB4 influence several processes of neurodevelopment, but the mechanisms regulating this signalling in the mature brain are not well known.", "DISC1 is a multifunctional scaffold protein that mediates many cellular processes.", "Here we present a functional relationship between DISC1 and NRG1-ErbB4 signalling in mature cortical interneurons.", "By cell type-specific gene modulation in vitro and in vivo including in a mutant DISC1 mouse model, we demonstrate that DISC1 inhibits NRG1-induced ErbB4 activation and signalling.", "This effect is likely mediated by competitive inhibition of binding of ErbB4 to PSD95.", "Finally, we show that interneuronal DISC1 affects NRG1-ErbB4-mediated phenotypes in the fast spiking interneuron-pyramidal neuron circuit.", "Post-mortem brain analyses and some genetic studies have reported interneuronal deficits and involvement of the DISC1, NRG1 and ErbB4 genes in schizophrenia, respectively.", "Our results suggest a mechanism by which cross-talk between DISC1 and NRG1-ErbB4 signalling may contribute to these deficits."], "structured": false}
{"doc_id": 14311986, "title": "The Proto-Oncogene c-maf Is Responsible for Tissue-Specific Expression of Interleukin-4", "abstract": ["The molecular basis for the distinctive cytokine expression of CD4+ T helper 1 (Th1) and T helper 2 (Th2) subsets remains elusive.", "Here, we report that the proto-oncogene c-maf, a basic region/leucine zipper transcription factor, controls tissue-specific expression of IL-4.", "c-Maf is expressed in Th2 but not Th1 clones and is induced during normal precursor cell differentiation along a Th2 but not Th1 lineage.", "c-Maf binds to a c-Maf response element (MARE) in the proximal IL-4 promoter adjacent to a site footprinted by extracts from Th2 but not Th1 clones.", "Ectopic expression of c-Maf transactivates the IL-4 promoter in Th1 cells, B cells, and nonlymphoid cells, a function that maps to the MARE and Th2-specific footprint.", "Furthermore, c-Maf acts in synergy with the nuclear factor of activated T cells (NF-ATp) to initiate endogeneous IL-4 production by B cells.", "Manipulation of c-Maf may alter Th subset ratios in human disease."], "structured": false}
{"doc_id": 14315749, "title": "hClock gene expression in human colorectal carcinoma.", "abstract": ["In this study, we aimed to investigate changes in the expression of human Clock (hClock), a gene at the core of the circadian gene family, in colorectal carcinomas (CRCs) and to discuss the possible effects.", "Previous studies have revealed that the disruption of circadian rhythms is one of the endogenous factors that contribute to the initiation and development of CRCs.", "However, the underlying molecular changes to the circadian genes associated with CRCs have not been explored.", "Immunofluorescence and quantitative polymerase chain reaction (qPCR) analysis of the hCLOCK protein and gene expression were performed in 30 cases of CRC.", "The hCLOCK protein was expressed in all specimens obtained from 30 CRC patients.", "Higher levels of hCLOCK expression were observed in human CRC tissues compared with the paired non-cancerous tissues.", "hCLOCK expression was significantly higher in poorly differentiated, or late-stage, Dukes' grade tumors and in 64.3% of tumor cases with lymph node metastasis.", "The hClock gene was expressed in all specimens.", "A significantly higher expression of hClock was found in human CRC cases compared with paired non-cancerous tissues.", "There was a strong positive linear correlation between hClock gene expression and protein expression in human CRCs.", "A strong positive linear correlation was also found between hClock gene expression and ARNT, HIF-1\u03b1 and VEGF expression in human CRCs.", "There was no significant correlation between hClock and Bak, Bax, Bid, tumor necrosis factor receptor I (TNFR I) and TNFR II.", "The circadian gene hClock was stably expressed in human colorectal mucosa and was important in regulating the expression of downstream clock-controlled genes.", "hCLOCK may interact with HIF-1\u03b1/ARNT and activate VEGF to stimulate tumor angiogenesis and metastasis."], "structured": false}
{"doc_id": 14319754, "title": "The Antiretroviral Therapy in Lower Income Countries (ART-LINC) Collaboration and ART Cohort Collaboration (ART-CC) groups Summary", "abstract": ["BACKGROUND Highly active antiretroviral therapy (HAART) is being scaled up in developing countries.", "We compared baseline characteristics and outcomes during the first year of HAART between HIV-1-infected patients in low-income and high-income settings.   \n", "METHODS 18 HAART programmes in Africa, Asia, and South America (low-income settings) and 12 HIV cohort studies from Europe and North America (high-income settings) provided data for 4810 and 22,217, respectively, treatment-na\u00efve adult patients starting HAART.", "All patients from high-income settings and 2725 (57%) patients from low-income settings were actively followed-up and included in survival analyses.   \n", "FINDINGS Compared with high-income countries, patients starting HAART in low-income settings had lower CD4 cell counts (median 108 cells per muL vs 234 cells per muL), were more likely to be female (51%vs 25%), and more likely to start treatment with a non-nucleoside reverse transcriptase inhibitor (NNRTI) (70%vs 23%).", "At 6 months, the median number of CD4 cells gained (106 cells per muL vs 103 cells per muL) and the percentage of patients reaching HIV-1 RNA levels lower than 500 copies/mL (76%vs 77%) were similar.", "Mortality was higher in low-income settings (124 deaths during 2236 person-years of follow-up) than in high-income settings (414 deaths during 20,532 person-years).", "The adjusted hazard ratio (HR) of mortality comparing low-income with high-income settings fell from 4.3 (95% CI 1.6-11.8) during the first month to 1.5 (0.7-3.0) during months 7-12.", "The provision of treatment free of charge in low-income settings was associated with lower mortality (adjusted HR 0.23; 95% CI 0.08-0.61).   \n", "INTERPRETATION Patients starting HAART in resource-poor settings have increased mortality rates in the first months on therapy, compared with those in developed countries.", "Timely diagnosis and assessment of treatment eligibility, coupled with free provision of HAART, might reduce this excess mortality."], "structured": true}
{"doc_id": 14328288, "title": "A family of phosphoinositide 3-kinases in Drosophila identifies a new mediator of signal transduction", "abstract": ["BACKGROUND Mammalian phosphoinositide 3-kinases (PI 3-kinases) are involved in receptor-mediated signal transduction and have been implicated in processes such as transformation and mitogenesis through their role in elevating cellular phosphatidylinositol (3,4,5)-trisphosphate.", "Additionally, a PI 3-kinase activity which generates phosphatidylinositol 3-phosphate has been shown to be required for protein trafficking in yeast.   \n", "RESULTS We have identified a family of three distinct PI 3-kinases in Drosophila, using an approach based on the polymerase chain reaction to amplify a region corresponding to the conserved catalytic domain of PI 3-kinases.", "One of these family members, PI3K_92D, is closely related to the prototypical PI 3-kinase, p110 alpha; PI3K_59F is homologous to Vps34p, whereas the third, PI3K_68D, is a novel PI 3-kinase which is widely expressed throughout the Drosophila life cycle.", "The PI3K_68D cDNA encodes a protein of 210 kDa, which lacks sequences implicated in linking p110 PI 3-kinases to p85 adaptor proteins, but contains an amino-terminal proline-rich sequence, which could bind to SH3 domains, and a carboxy-terminal C2 domain.", "Biochemical analyses demonstrate that PI3K_68D has a novel substrate specificity in vitro, restricted to phosphatidylinositol and phosphatidylinositol 4-phosphate, and is unable to phosphorylate phosphatidylinositol (4,5)-bisphosphate, the implied in vivo substrate for p110.   \n", "CONCLUSIONS A family of PI 3-kinases in Drosophila, including a novel class represented by PI3K_68D, is described.", "PI3K_68D has the potential to bind to signalling molecules containing SH3 domains, lacks p85-adaptor-binding sequences, has a Ca(2+)-independent phospholipid-binding domain and displays a restricted in vitro substrate specificity, so it could define a novel signal transduction pathway."], "structured": true}
{"doc_id": 14332945, "title": "Mammalian RAD52 Functions in Break-Induced Replication Repair of Collapsed DNA Replication Forks", "abstract": ["Human cancers are characterized by the presence of oncogene-induced DNA replication stress (DRS), making them dependent on repair pathways such as break-induced replication (BIR) for damaged DNA replication forks.", "To better understand BIR, we performed a targeted siRNA screen for genes whose depletion inhibited G1 to S phase progression when oncogenic cyclin E was overexpressed.", "RAD52, a gene dispensable for normal development in mice, was among the top hits.", "In cells in which fork collapse was induced by oncogenes or chemicals, the Rad52 protein localized to DRS foci.", "Depletion of Rad52 by siRNA or knockout of the gene by CRISPR/Cas9 compromised restart of collapsed forks and led to DNA damage in cells experiencing DRS.", "Furthermore, in cancer-prone, heterozygous APC mutant mice, homozygous deletion of the Rad52 gene suppressed tumor growth and prolonged lifespan.", "We therefore propose that mammalian RAD52 facilitates repair of collapsed DNA replication forks in cancer cells."], "structured": false}
{"doc_id": 14333540, "title": "Neural crest cell lineage segregation in the mouse neural tube.", "abstract": ["Neural crest (NC) cells arise in the dorsal neural tube (NT) and migrate into the embryo to develop into many different cell types.", "A major unresolved question is when and how the fate of NC cells is decided.", "There is widespread evidence for multipotential NC cells, whose fates are decided during or after migration.", "There is also some evidence that the NC is already divided into subpopulations of discrete precursors within the NT.", "We have investigated this question in the mouse embryo.", "We find that a subpopulation of cells on the most dorsomedial aspect of the NT express the receptor tyrosine kinase Kit (previously known as c-kit), emigrate exclusively into the developing dermis, and then express definitive markers of the melanocyte lineage.", "These are thus melanocyte progenitor cells.", "They are generated predominantly at the midbrain-hindbrain junction and cervical trunk, with significant numbers also in lower trunk.", "Other cells within the dorsal NT are Kit-, migrate ventrally, and, from embryonic day 9.5, express the neurotrophin receptor p75.", "These cells most likely only give rise to ventral NC derivatives such as neurons and glia.", "The p75+ cells are located ventrolateral to the Kit+ cells in areas of the NT where these two cell types are found.", "These data provide direct in vivo evidence for NC lineage segregation within the mouse neural tube."], "structured": false}
{"doc_id": 14337960, "title": "How absolute is zero? An evaluation of historical and current definitions of malaria elimination", "abstract": ["Decisions to eliminate malaria from all or part of a country involve a complex set of factors, and this complexity is compounded by ambiguity surrounding some of the key terminology, most notably \"control\" and \"elimination.", "\"", "It is impossible to forecast resource and operational requirements accurately if endpoints have not been defined clearly, yet even during the Global Malaria Eradication Program, debate raged over the precise definition of \"eradication.", "\"", "Analogous deliberations regarding the meaning of \"elimination\" and \"control\" are basically nonexistent today despite these terms' core importance to programme planning.", "To advance the contemporary debate about these issues, this paper presents a historical review of commonly used terms, including control, elimination, and eradication, to help contextualize current understanding of these concepts.", "The review has been supported by analysis of the underlying mathematical concepts on which these definitions are based through simple branching process models that describe the proliferation of malaria cases following importation.", "Through this analysis, the importance of pragmatic definitions that are useful for providing malaria control and elimination programmes with a practical set of strategic milestones is emphasized, and it is argued that current conceptions of elimination in particular fail to achieve these requirements.", "To provide all countries with precise targets, new conceptual definitions are suggested to more precisely describe the old goals of \"control\" - here more exactly named \"controlled low-endemic malaria\" - and \"elimination.", "\"", "Additionally, it is argued that a third state, called \"controlled non-endemic malaria,\" is required to describe the epidemiological condition in which endemic transmission has been interrupted, but malaria resulting from onwards transmission from imported infections continues to occur at a sufficiently high level that elimination has not been achieved.", "Finally, guidelines are discussed for deriving the separate operational definitions and metrics that will be required to make these concepts relevant, measurable, and achievable for a particular environment."], "structured": false}
{"doc_id": 14338915, "title": "Fission Yeast Scm3: A CENP-A Receptor Required for Integrity of Subkinetochore Chromatin", "abstract": ["The mechanisms ensuring specific incorporation of CENP-A at centromeres are poorly understood.", "Mis16 and Mis18 are required for CENP-A localization at centromeres and form a complex that is conserved from fission yeast to human.", "Fission yeast sim1 mutants that alleviate kinetochore domain silencing are defective in Scm3(Sp), the ortholog of budding yeast Scm3(Sc).", "Scm3(Sp) depends on Mis16/18 for its centromere localization and like them is recruited to centromeres in late anaphase.", "Importantly, Scm3(Sp) coaffinity purifies with CENP-A(Cnp1) and associates with CENP-A(Cnp1) in vitro, yet localizes independently of intact CENP-A(Cnp1) chromatin and is differentially released from chromatin.", "While Scm3(Sc) has been proposed to form a unique hexameric nucleosome with CENP-A(Cse4) and histone H4 at budding yeast point centromeres, we favor a model in which Scm3(Sp) acts as a CENP-A(Cnp1) receptor/assembly factor, cooperating with Mis16 and Mis18 to receive CENP-A(Cnp1) from the Sim3 escort and mediate assembly of CENP-A(Cnp1) into subkinetochore chromatin."], "structured": false}
{"doc_id": 14340571, "title": "The Molecular Basis for Oat Intolerance in Patients with Celiac Disease", "abstract": ["Background  Celiac disease is a small intestinal inflammatory disorder characterized by malabsorption, nutrient deficiency, and a range of clinical manifestations.", "It is caused by an inappropriate immune response to dietary gluten and is treated with a gluten-free diet.", "Recent feeding studies have indicated oats to be safe for celiac disease patients, and oats are now often included in the celiac disease diet.", "This study aimed to investigate whether oat intolerance exists in celiac disease and to characterize the cells and processes underlying this intolerance.      ", "Methods and Findings  We selected for study nine adults with celiac disease who had a history of oats exposure.", "Four of the patients had clinical symptoms on an oats-containing diet, and three of these four patients had intestinal inflammation typical of celiac disease at the time of oats exposure.", "We established oats-avenin-specific and -reactive intestinal T-cell lines from these three patients, as well as from two other patients who appeared to tolerate oats.", "The avenin-reactive T-cell lines recognized avenin peptides in the context of HLA-DQ2.", "These peptides have sequences rich in proline and glutamine residues closely resembling wheat gluten epitopes.", "Deamidation (glutamine\u2192glutamic acid conversion) by tissue transglutaminase was involved in the avenin epitope formation.      ", "Conclusions  We conclude that some celiac disease patients have avenin-reactive mucosal T-cells that can cause mucosal inflammation.", "Oat intolerance may be a reason for villous atrophy and inflammation in patients with celiac disease who are eating oats but otherwise are adhering to a strict gluten-free diet.", "Clinical follow-up of celiac disease patients eating oats is advisable."], "structured": false}
{"doc_id": 14361849, "title": "A comparison of continuous and bi-level positive airway pressure non-invasive ventilation in patients with acute cardiogenic pulmonary oedema: a meta-analysis", "abstract": ["IntroductionWe conducted the present study to investigate the potential beneficial and adverse effects of continuous positive airway pressure (CPAP) compared with bi-level positive airway pressure (BiPAP) noninvasive ventilation in patients with cardiogenic pulmonary oedema.", "MethodWe included randomized controlled studies comparing CPAP and BiPAP treatment in patients with cardiogenic pulmonary oedema from the Cochrane Controlled Trials Register (2005 issue 3), and EMBASE and MEDLINE databases (1966 to 1 December 2005), without language restriction.", "Two reviewers reviewed the quality of the studies and independently performed data extraction.", "ResultsSeven randomized controlled studies, including a total of 290 patients with cardiogenic pulmonary oedema, were considered.", "The hospital mortality (relative risk [RR] 0.76, 95% confidence interval [CI] 0.32\u20131.78; P = 0.52; I2 = 0%) and risk for requiring invasive ventilation (RR 0.80, 95% CI 0.33\u20131.94; P = 0.62; I2 = 0%) were not significantly different between patients treated with CPAP and those treated with BiPAP.", "Stratifying studies that used either fixed or titrated pressure during BiPAP treatment and studies involving patients with or without hypercapnia did not change the results.", "The duration of noninvasive ventilation required until the pulmonary oedema resolved (weighted mean difference [WMD] in hours = 3.65, 95% CI -12.12 to +19.43; P = 0.65, I2 = 0%) and length of hospital stay (WMD in days = -0.04, 95% CI -2.57 to +2.48; P = 0.97, I2 = 0%) were also not significantly different between the two groups.", "Based on the limited data available, there was an insignificant trend toward an increase in new onset acute myocardial infarction in patients treated with BiPAP (RR 2.10, 95% CI 0.91\u20134.84; P = 0.08; I2 = 25.3%).ConclusionBiPAP does not offer any significant clinical benefits over CPAP in patients with acute cardiogenic pulmonary oedema.", "Until a large randomized controlled trial shows significant clinical benefit and cost-effectiveness of BiPAP versus CPAP in patients with acute cardiogenic pulmonary oedema, the choice of modality will depend mainly on the equipment available."], "structured": false}
{"doc_id": 14362678, "title": "CaMKII induces permeability transition through Drp1 phosphorylation during chronic \u03b2-AR stimulation", "abstract": ["Mitochondrial permeability transition pore (mPTP) is involved in cardiac dysfunction during chronic \u03b2-adrenergic receptor (\u03b2-AR) stimulation.", "The mechanism by which chronic \u03b2-AR stimulation leads to mPTP openings is elusive.", "Here, we show that chronic administration of isoproterenol (ISO) persistently increases the frequency of mPTP openings followed by mitochondrial damage and cardiac dysfunction.", "Mechanistically, this effect is mediated by phosphorylation of mitochondrial fission protein, dynamin-related protein 1 (Drp1), by Ca2+/calmodulin-dependent kinase II (CaMKII) at a serine 616 (S616) site.", "Mutating this phosphorylation site or inhibiting Drp1 activity blocks CaMKII- or ISO-induced mPTP opening and myocyte death in vitro and rescues heart hypertrophy in vivo.", "In human failing hearts, Drp1 phosphorylation at S616 is increased.", "These results uncover a pathway downstream of chronic \u03b2-AR stimulation that links CaMKII, Drp1 and mPTP to bridge cytosolic stress signal with mitochondrial dysfunction in the heart."], "structured": false}
{"doc_id": 14362780, "title": "MicroRNA Response of Primary Human Macrophages to Arcobacter Butzleri Infection", "abstract": ["The role of microRNAs (miRNAs) in infectious diseases is becoming more and more apparent, and the use of miRNAs as a diagnostic tool and their therapeutic application has become the major focus of investigation.", "The aim of this study was to identify miRNAs involved in the immune signaling of macrophages in response to Arcobacter (A.) butzleri infection, an emerging foodborne pathogen causing gastroenteritis.", "Therefore, primary human macrophages were isolated and infected, and miRNA expression was studied by means of RNAseq.", "Analysis of the data revealed the expression of several miRNAs, which were previously associated with bacterial infections such as miR-155, miR-125, and miR-212.", "They were shown to play a key role in Toll-like receptor signaling where they act as fine-tuners to establish a balanced immune response.", "In addition, miRNAs which have yet not been identified during bacterial infections such as miR-3613, miR-2116, miR-671, miR-30d, and miR-629 were differentially regulated in A. butzleri-infected cells.", "Targets of these miRNAs accumulated in pathways such as apoptosis and endocytosis - processes that might be involved in A. butzleri pathogenesis.", "Our study contributes new findings about the interaction of A. butzleri with human innate immune cells helping to understand underlying regulatory mechanisms in macrophages during infection."], "structured": false}
{"doc_id": 14367469, "title": "The circadian factor Period 2 modulates p53 stability and transcriptional activity in unstressed cells", "abstract": ["Human Period 2 (hPer2) is a transcriptional regulator at the core of the circadian clock mechanism that is responsible for generating the negative feedback loop that sustains the clock.", "Its relevance to human disease is underlined by alterations in its function that affect numerous biochemical and physiological processes.", "When absent, it results in the development of various cancers and an increase in the cell's susceptibility to genotoxic stress.", "Thus we sought to define a yet-uncharacterized checkpoint node in which circadian components integrate environmental stress signals to the DNA-damage response.", "We found that hPer2 binds the C-terminal half of human p53 (hp53) and forms a stable trimeric complex with hp53's negative regulator, Mdm2.", "We determined that hPer2 binding to hp53 prevents Mdm2 from being ubiquitinated and targeting hp53 by the proteasome.", "Down-regulation of hPer2 expression directly affects hp53 levels, whereas its overexpression influences both hp53 protein stability and transcription of targeted genes.", "Overall our findings place hPer2 directly at the heart of the hp53-mediated response by ensuring that basal levels of hp53 are available to precondition the cell when a rapid, hp53-mediated, transcriptional response is needed."], "structured": false}
{"doc_id": 14376683, "title": "Properties of Commelina yellow mottle virus's complete DNA sequence, genomic discontinuities and transcript suggest that it is a pararetrovirus.", "abstract": ["The non-enveloped bacilliform viruses are the second group of plant viruses known to possess a genome consisting of circular double-stranded DNA.", "We have characterized the viral transcript and determined the complete sequence of the genome of Commelina mellow mottle virus (CoYMV), a member of this group.", "Analysis of the viral transcript indicates that the virus encodes a single terminally-redundant genome-length plus 120 nucleotide transcript.", "A fraction of the transcripts is polyadenylated, although the majority of the transcript is not polyadenylated.", "Analysis of the genome sequence indicates that the genome is 7489 bp in size and that the transcribed strand contains three open reading frames capable of encoding proteins of 23, 15 and 216 kd.", "The function of the 25 and 15 kd proteins is unknown.", "Similarities between the 216 kd polypeptide and the cauliflower mosaic virus coat protein and protease/reverse transcriptase polyprotein suggest that the 216 kd polypeptide is a polyprotein that is proteolytically processed to yield the virion coat protein, a protease, and replicase (reverse transcriptase and ribonuclease H).", "Each strand of the CoYMV genome is interrupted by site-specific discontinuities.", "The locations of the 5'-ends of these discontinuities, and the presence and location of a region on the CoYMV transcript capable of annealing with the 3'-end of cytosolic initiator methionine tRNA are consistent with replication by reverse transcription.", "We have demonstrated that a construct containing 1.3 CoYMV genomes is infective when introduced into Commelina diffusa, the host for CoYMV, using Agrobacterium-mediated infection."], "structured": false}
{"doc_id": 14380875, "title": "The Glucocorticoid Receptor Inhibits", "abstract": ["Glucocorticoids repress NFkappaB-mediated activation of proinflammatory genes such as interleukin-8 (IL-8) and ICAM-1.", "Our experiments suggest that the glucocorticoid receptor (GR) confers this effect by associating through protein-protein interactions with NFkappaB bound at each of these genes.", "That is, we show that the GR zinc binding region (ZBR), which includes the DNA binding and dimerization functions of the receptor, binds directly to the dimerization domain of the RelA subunit of NFkappaB in vitro and that the ZBR is sufficient to associate with RelA bound at NFkappaB response elements in vivo.", "Moreover, we demonstrate in vivo and in vitro that GR does not disrupt DNA binding by NFkappaB. In transient transfections, we found that the GR ligand binding domain is essential for repression of NFkappaB but not for association with it and that GR can repress an NFkappaB derivative bearing a heterologous activation domain.", "We used chromatin immunoprecipitation assays in untransfected A549 cells to infer the mechanism by which the tethered GR represses NFkappaB-activated transcription.", "As expected, we found that the inflammatory signal TNFalpha stimulated preinitiation complex (PIC) assembly at the IL-8 and ICAM-1 promoters and that the largest subunit of RNA polymerase II (pol II) in those complexes became phosphorylated at serines 2 and 5 in its carboxy-terminal domain (CTD) heptapeptide repeats (YSPTSPS); these modifications are required for transcription initiation.", "Remarkably, GR did not inhibit PIC assembly under repressing conditions, but rather interfered with phosphorylation of serine 2 of the pol II CTD."], "structured": false}
{"doc_id": 14386505, "title": "Regulation of myeloid cell function through the CD200 receptor.", "abstract": ["Myeloid cells play pivotal roles in chronic inflammatory diseases through their broad proinflammatory, destructive, and remodeling capacities.", "CD200 is widely expressed on a variety of cell types, while the recently identified CD200R is expressed on myeloid cells and T cells.", "CD200 deletion in vivo results in myeloid cell dysregulation and enhanced susceptibility to autoimmune inflammation, suggesting that the CD200-CD200R interaction is involved in immune suppression.", "We demonstrate in this study that CD200R agonists suppress mouse and human myeloid cell function in vitro, and also define a dose relationship between receptor expression and cellular inhibition.", "IFN-gamma- and IL-17-stimulated cytokine secretion from mouse peritoneal macrophages was inhibited by CD200R engagement.", "Inhibitory effects were not universal, as LPS-stimulated responses were unaffected.", "Inhibition of U937 cell cytokine production correlated with CD200R expression levels, and inhibition was only observed in low CD200R expressing cells, if the CD200R agonists were further cross-linked.", "Tetanus toxoid-induced human PBMC IL-5 and IL-13 secretion was inhibited by CD200R agonists.", "This inhibition was dependent upon cross-linking the CD200R on monocytes, but not on cross-linking the CD200R on CD4+ T cells.", "In all, we provide direct evidence that the CD200-CD200R interaction controls monocyte/macrophage function in both murine and human systems, further supporting the potential clinical application of CD200R agonists for the treatment of chronic inflammatory diseases."], "structured": false}
{"doc_id": 14390137, "title": "Management of hepatitis C disease among VA patients with schizophrenia and substance use disorders.", "abstract": ["OBJECTIVE Rates of hepatitis C (HCV) infection, testing, and treatment were compared among patients with schizophrenia, a substance use disorder, or co-occurring schizophrenia or schizoaffective disorder and a substance use disorder and a control group.   \n", "METHODS Information about 293,445 patients of the Northwest Veterans Healthcare Administration was obtained.   \n", "RESULTS The substance use disorder group constituted 13.6 percent of the sample; the schizophrenia group, 1.6 percent; and the co-occurring-disorders group, 1.4 percent.", "Respectively, these groups were approximately four, two, and six times as likely as the control group to receive HCV testing and about seven, two, and eight times as likely to be infected.", "The rate of interferon (IFN) therapy was significantly lower for the substance use group and the group with co-occurring disorders.", "However, the magnitude of the differences was not substantial, suggesting that these high-risk groups were not excluded from IFN therapy."], "structured": true}
{"doc_id": 14395738, "title": "Equity in adherence to antiretroviral therapy among economically vulnerable adolescents living with HIV in Uganda", "abstract": ["Studies from sub-Saharan Africa indicate that children made vulnerable by poverty have been disproportionately affected by HIV with many exposed via mother-to-child transmission.", "For youth living with HIV, adherence to life-saving treatment regimens are likely to be affected by the complex set of economic and social circumstances that challenge their families and also exacerbate health problems.", "Using baseline data from the National Institute of Child and Human Development (NICHD) funded Suubi+Adherence study, we examined the extent to which individual and composite measures of equity predict self-reported adherence among Ugandan adolescents aged 10-16 (n = 702) living with HIV.", "Results showed that greater asset ownership, specifically familial possession of seven or more tangible assets, was associated with greater odds of self-reported adherence (OR 1.69, 95% CI: 1.00-2.85).", "Our analyses also indicated that distance to the nearest health clinic impacts youth's adherence to an ARV regimen.", "Youth who reported living nearest to a clinic were significantly more likely to report optimal adherence (OR 1.49, 95% CI: 0.92-2.40).", "Moreover, applying the composite equity scores, we found that adolescents with greater economic advantage in ownership of household assets, financial savings, and caregiver employment had higher odds of adherence by a factor of 1.70 (95% CI: 1.07-2.70).", "These findings suggest that interventions addressing economic and social inequities may be beneficial to increase antiretroviral therapy (ART) uptake among economically vulnerable youth, especially in sub-Saharan Africa.", "This is one of the first studies to address the question of equity in adherence to ART among economically vulnerable youth with HIV."], "structured": false}
{"doc_id": 14402338, "title": "High-Resolution Phenotypic Profiling Defines Genes Essential for Mycobacterial Growth and Cholesterol Catabolism", "abstract": ["The pathways that comprise cellular metabolism are highly interconnected, and alterations in individual enzymes can have far-reaching effects.", "As a result, global profiling methods that measure gene expression are of limited value in predicting how the loss of an individual function will affect the cell.", "In this work, we employed a new method of global phenotypic profiling to directly define the genes required for the growth of Mycobacterium tuberculosis.", "A combination of high-density mutagenesis and deep-sequencing was used to characterize the composition of complex mutant libraries exposed to different conditions.", "This allowed the unambiguous identification of the genes that are essential for Mtb to grow in vitro, and proved to be a significant improvement over previous approaches.", "To further explore functions that are required for persistence in the host, we defined the pathways necessary for the utilization of cholesterol, a critical carbon source during infection.", "Few of the genes we identified had previously been implicated in this adaptation by transcriptional profiling, and only a fraction were encoded in the chromosomal region known to encode sterol catabolic functions.", "These genes comprise an unexpectedly large percentage of those previously shown to be required for bacterial growth in mouse tissue.", "Thus, this single nutritional change accounts for a significant fraction of the adaption to the host.", "This work provides the most comprehensive genetic characterization of a sterol catabolic pathway to date, suggests putative roles for uncharacterized virulence genes, and precisely maps genes encoding potential drug targets."], "structured": false}
{"doc_id": 14405193, "title": "Tyrosine phosphorylation regulates the endocytosis and surface expression of GluN3A-containing NMDA receptors.", "abstract": ["Selective control of receptor trafficking provides a mechanism for remodeling the receptor composition of excitatory synapses, and thus supports synaptic transmission, plasticity, and development.", "GluN3A (formerly NR3A) is a nonconventional member of the NMDA receptor (NMDAR) subunit family, which endows NMDAR channels with low calcium permeability and reduced magnesium sensitivity compared with NMDARs comprising only GluN1 and GluN2 subunits.", "Because of these special properties, GluN3A subunits act as a molecular brake to limit the plasticity and maturation of excitatory synapses, pointing toward GluN3A removal as a critical step in the development of neuronal circuitry.", "However, the molecular signals mediating GluN3A endocytic removal remain unclear.", "Here we define a novel endocytic motif (YWL), which is located within the cytoplasmic C-terminal tail of GluN3A and mediates its binding to the clathrin adaptor AP2.", "Alanine mutations within the GluN3A endocytic motif inhibited clathrin-dependent internalization and led to accumulation of GluN3A-containing NMDARs at the cell surface, whereas mimicking phosphorylation of the tyrosine residue promoted internalization and reduced cell-surface expression as shown by immunocytochemical and electrophysiological approaches in recombinant systems and rat neurons in primary culture.", "We further demonstrate that the tyrosine residue is phosphorylated by Src family kinases, and that Src-activation limits surface GluN3A expression in neurons.", "Together, our results identify a new molecular signal for GluN3A internalization that couples the functional surface expression of GluN3A-containing receptors to the phosphorylation state of GluN3A subunits, and provides a molecular framework for the regulation of NMDAR subunit composition with implications for synaptic plasticity and neurodevelopment."], "structured": false}
{"doc_id": 14407673, "title": "Myeloid-specific Kr\u00fcppel-like factor 2 inactivation increases macrophage and neutrophil adhesion and promotes atherosclerosis.", "abstract": ["RATIONALE Hemizygous deficiency of the transcription factor Kr\u00fcppel-like factor 2 (KLF2) has been shown previously to augment atherosclerosis in hypercholesterolemic mice.", "However, the cell type responsible for the increased atherosclerosis due to KLF2 deficiency has not been identified.", "This study examined the consequence of myeloid cell-specific KLF2 inactivation in atherosclerosis.   \n", "METHODS AND RESULTS Cell-specific knockout mice were generated by Cre/loxP recombination.", "Macrophages isolated from myeloid-specific Klf2 knockout (myeKlf2(-/-)) mice were similar to myeKlf2(+/+) macrophages in response to activation, polarization, and lipid accumulation.", "However, in comparison to myeKlf2(+/+) macrophages, myeKlf2(-/-) macrophages adhered more robustly to endothelial cells.", "Neutrophils from myeKlf2(-/-) mice also adhered more robustly to endothelial cells, and fewer myeKlf2(-/-) neutrophils survived in culture over a 24-hour period in comparison with myeKlf2(+/+) neutrophils.", "When myeKlf2(-/-) mice were mated to Ldlr(-/-) mice and then fed a high fat and high cholesterol diet, significant increase in atherosclerosis was observed in the myeKlf2(-/-)Ldlr(-/-) mice compared with myeKlf2(+/+)Ldlr(-/-) littermates.", "The increased atherosclerosis in myeKlf2(-/-)Ldlr(-/-) mice was associated with elevated presence of neutrophils and macrophages, with corresponding increase of myeloperoxidase as well as chlorinated and nitrosylated tyrosine epitopes in their lesion areas compared with myeKlf2(+/+)Ldlr(-/-) mice.   \n", "CONCLUSIONS This study documents a role for myeloid KLF2 expression in modulating atherosclerosis.", "The increased neutrophil accumulation and atherosclerosis progression with myeloid-specific KLF2 deficiency also underscores the importance of neutrophils in promoting vascular oxidative stress and atherosclerosis.", "Collectively, these results suggest that elevating KLF2 expression may be a novel strategy for prevention and treatment of atherosclerosis."], "structured": true}
{"doc_id": 14408200, "title": "Epidemiology of Staphylococcus aureus blood and skin and soft tissue infections in the US military health system, 2005-2010.", "abstract": ["CONTEXT Rates of hospital-onset methicillin-resistant Staphylococcus aureus (MRSA) infections are reported as decreasing, but recent rates of community-onset S. aureus infections are less known.   \n", "OBJECTIVES To characterize the overall and annual incidence rates of community-onset and hospital-onset S. aureus bacteremia and skin and soft tissue infections (SSTIs) in a national health care system and to evaluate trends in the incidence rates of S. aureus bacteremia and SSTIs and the proportion due to MRSA.   \n", "DESIGN, SETTING, AND PARTICIPANTS Observational study of all Department of Defense TRICARE beneficiaries from January 2005 through December 2010.", "Medical record databases were used to identify and classify all annual first-positive S. aureus blood and wound or abscess cultures as methicillin-susceptible S. aureus or MRSA, and as community-onset or hospital-onset infections (isolates collected >3 days after hospital admission).   \n", "MAIN OUTCOME MEASURES Unadjusted incidence rates per 100,000 person-years of observation, the proportion of infections that was due to MRSA, and annual trends for 2005 through 2010 (examined using the Spearman rank correlation test or the Mantel-Haenszel \u03c72 test for linear trend).   \n", "RESULTS During 56 million person-years (nonactive duty: 47 million person-years; active duty: 9 million person-years), there were 2643 blood and 80,281 wound or abscess annual first-positive S. aureus cultures.", "Annual incidence rates varied from 3.6 to 6.0 per 100,000 person-years for S. aureus bacteremia and 122.7 to 168.9 per 100,000 person-years for S. aureus SSTIs.", "The annual incidence rates for community-onset MRSA bacteremia decreased from 1.7 per 100,000 person-years (95% CI, 1.5-2.0 per 100,000 person-years) in 2005 to 1.2 per 100,000 person-years (95% CI, 0.9-1.4 per 100,000 person-years) in 2010 (P = .005 for trend).", "The annual incidence rates for hospital-onset MRSA bacteremia also decreased from 0.7 per 100,000 person-years (95% CI, 0.6-0.9 per 100,000 person-years) in 2005 to 0.4 per 100,000 person-years (95% CI, 0.3-0.5 per 100,000 person-years) in 2010 (P = .005 for trend).", "Concurrently, the proportion of community-onset SSTI due to MRSA peaked at 62% in 2006 before decreasing annually to 52% in 2010 (P < .001 for trend).   \n", "CONCLUSION In the Department of Defense population consisting of men and women of all ages from across the United States, the rates of both community-onset and hospital-onset MRSA bacteremia decreased in parallel, while the proportion of community-onset SSTIs due to MRSA has more recently declined."], "structured": true}
{"doc_id": 14419116, "title": "Potentiation of NMDA currents by pituitary adenylate cyclase activating polypeptide in neonatal rat sympathetic preganglionic neurons.", "abstract": ["Whole cell patch-clamp recordings were made from sympathetic preganglionic neurons (SPNs) in the intermediolateral cell column of thoracolumbar spinal cord slices of 12- to 16-day-old rats, and the effects of pituitary adenylate cyclase activating polypeptide (PACAP)-38 on N-methyl-D-aspartate (NMDA)- and kainate (KA)-induced inward currents were examined.", "PACAP, in concentrations (10-30 nM) that caused no significant change of holding currents, reversibly increased NMDA-induced currents but not KA-induced currents.", "At higher concentrations (>30 nM), the peptide produced a sustained inward current.", "The potentiating effect of PACAP was nullified by prior incubation of the slices with the adenylate cyclase inhibitor MDL-12,330A (25 microM).", "Further, superfusing the slices with the membrane-permeable cyclic AMP analogue N6,2'-O-dibutyryladenosine 3':5'-cyclic monophosphate (100-300 microM) in the presence of the phosphodiesterase inhibitor 3-isobutyl-1-methylxanthine (700 microM) increased the NMDA currents.", "This result suggests that PACAP selectively increases NMDA-receptor-mediated responses in the rat SPNs, probably via a cyclic-AMP-dependent mechanism, providing evidence that the peptide may be involved in synaptic plasticity."], "structured": false}
{"doc_id": 14434123, "title": "Aberrant Expression of RCAN1 in Alzheimer\u2019s Pathogenesis: A New Molecular Mechanism and a Novel Drug Target", "abstract": ["AD, a devastating neurodegenerative disorder, is the most common cause of dementia in the elderly.", "Patients with AD are characterized by three hallmarks of neuropathology including neuritic plaque deposition, neurofibrillary tangle formation, and neuronal loss.", "Growing evidences indicate that dysregulation of regulator of calcineurin 1 (RCAN1) plays an important role in the pathogenesis of AD.", "Aberrant RCAN1 expression facilitates neuronal apoptosis and Tau hyperphosphorylation, leading to neuronal loss and neurofibrillary tangle formation.", "This review aims to describe the recent advances of the regulation of RCAN1 expression and its physiological functions.", "Moreover, the AD risk factors-induced RCAN1 dysregulation and its role in promoting neuronal loss, synaptic impairments and neurofibrillary tangle formation are summarized.", "Furthermore, we provide an outlook into the effects of RCAN1 dysregulation on APP processing, A\u03b2 generation and neuritic plaque formation, and the possible underlying mechanisms, as well as the potential of targeting RCAN1 as a new therapeutic approach."], "structured": false}
{"doc_id": 14437255, "title": "Congruent Visual Speech Enhances Cortical Entrainment to Continuous Auditory Speech in Noise-Free Conditions.", "abstract": ["UNLABELLED Congruent audiovisual speech enhances our ability to comprehend a speaker, even in noise-free conditions.", "When incongruent auditory and visual information is presented concurrently, it can hinder a listener's perception and even cause him or her to perceive information that was not presented in either modality.", "Efforts to investigate the neural basis of these effects have often focused on the special case of discrete audiovisual syllables that are spatially and temporally congruent, with less work done on the case of natural, continuous speech.", "Recent electrophysiological studies have demonstrated that cortical response measures to continuous auditory speech can be easily obtained using multivariate analysis methods.", "Here, we apply such methods to the case of audiovisual speech and, importantly, present a novel framework for indexing multisensory integration in the context of continuous speech.", "Specifically, we examine how the temporal and contextual congruency of ongoing audiovisual speech affects the cortical encoding of the speech envelope in humans using electroencephalography.", "We demonstrate that the cortical representation of the speech envelope is enhanced by the presentation of congruent audiovisual speech in noise-free conditions.", "Furthermore, we show that this is likely attributable to the contribution of neural generators that are not particularly active during unimodal stimulation and that it is most prominent at the temporal scale corresponding to syllabic rate (2-6 Hz).", "Finally, our data suggest that neural entrainment to the speech envelope is inhibited when the auditory and visual streams are incongruent both temporally and contextually.   ", "SIGNIFICANCE STATEMENT Seeing a speaker's face as he or she talks can greatly help in understanding what the speaker is saying.", "This is because the speaker's facial movements relay information about what the speaker is saying, but also, importantly, when the speaker is saying it.", "Studying how the brain uses this timing relationship to combine information from continuous auditory and visual speech has traditionally been methodologically difficult.", "Here we introduce a new approach for doing this using relatively inexpensive and noninvasive scalp recordings.", "Specifically, we show that the brain's representation of auditory speech is enhanced when the accompanying visual speech signal shares the same timing.", "Furthermore, we show that this enhancement is most pronounced at a time scale that corresponds to mean syllable length."], "structured": false}
{"doc_id": 14446279, "title": "Telomere tethering at the nuclear periphery is essential for efficient DNA double strand break repair in subtelomeric region", "abstract": ["In the yeast Saccharomyces cerevisiae that lacks lamins, the nuclear pore complex (NPC) has been proposed to serve a role in chromatin organization.", "Here, using fluorescence microscopy in living cells, we show that nuclear pore proteins of the Nup84 core complex, Nup84p, Nup145Cp, Nup120p, and Nup133p, serve to anchor telomere XI-L at the nuclear periphery.", "The integrity of this complex is shown to be required for repression of a URA3 gene inserted in the subtelomeric region of this chromosome end.", "Furthermore, altering the integrity of this complex decreases the efficiency of repair of a DNA double-strand break (DSB) only when it is generated in the subtelomeric region, even though the repair machinery is functional.", "These effects are specific to the Nup84 complex.", "Our observations thus confirm and extend the role played by the NPC, through the Nup84 complex, in the functional organization of chromatin.", "They also indicate that anchoring of telomeres is essential for efficient repair of DSBs occurring therein and is important for preserving genome integrity."], "structured": false}
{"doc_id": 14460402, "title": "p63 Regulates adult neural precursor and newly born neuron survival to control hippocampal-dependent Behavior.", "abstract": ["The molecular mechanisms that regulate adult neural precursor cell (NPC) survival, and thus maintain adult neurogenesis, are not well defined.", "Here, we investigate the role of p63, a p53 family member, in adult NPC function in mice.", "Conditional ablation of p63 in adult NPCs or p63 haploinsufficiency led to reduced numbers of NPCs and newborn neurons in the neurogenic zones of the hippocampus and lateral ventricles and in the olfactory bulb.", "These reductions were attributable to enhanced apoptosis of NPCs and newborn neurons and were rescued by inhibition of caspase activity, p53, or the p53 apoptotic effector PUMA (p53-upregulated modulator of apoptosis).", "Moreover, these cellular deficits were functionally important because they led to perturbations in hippocampus-dependent memory formation.", "These results indicate that p63 regulates the numbers of adult NPCs and adult-born neurons as well as neural stem cell-dependent cognitive functions, and that it does so, at least in part, by inhibiting p53-dependent cell death."], "structured": false}
{"doc_id": 14461101, "title": "Tyrosine-Phosphorylated Caveolin-1 Blocks Bacterial Uptake by Inducing Vav2-RhoA-Mediated Cytoskeletal Rearrangements", "abstract": ["Certain bacterial adhesins appear to promote a pathogen's extracellular lifestyle rather than its entry into host cells.", "However, little is known about the stimuli elicited upon such pathogen host-cell interactions.", "Here, we report that type IV pili (Tfp)-producing Neisseria gonorrhoeae (P(+)GC) induces an immediate recruitment of caveolin-1 (Cav1) in the host cell, which subsequently prevents bacterial internalization by triggering cytoskeletal rearrangements via downstream phosphotyrosine signaling.", "A broad and unbiased analysis of potential interaction partners for tyrosine-phosphorylated Cav1 revealed a direct interaction with the Rho-family guanine nucleotide exchange factor Vav2.", "Both Vav2 and its substrate, the small GTPase RhoA, were found to play a direct role in the Cav1-mediated prevention of bacterial uptake.", "Our findings, which have been extended to enteropathogenic Escherichia coli, highlight how Tfp-producing bacteria avoid host cell uptake.", "Further, our data establish a mechanistic link between Cav1 phosphorylation and pathogen-induced cytoskeleton reorganization and advance our understanding of caveolin function."], "structured": false}
{"doc_id": 14464451, "title": "Effects of GC Bias in Next-Generation-Sequencing Data on De Novo Genome Assembly", "abstract": ["Next-generation-sequencing (NGS) has revolutionized the field of genome assembly because of its much higher data throughput and much lower cost compared with traditional Sanger sequencing.", "However, NGS poses new computational challenges to de novo genome assembly.", "Among the challenges, GC bias in NGS data is known to aggravate genome assembly.", "However, it is not clear to what extent GC bias affects genome assembly in general.", "In this work, we conduct a systematic analysis on the effects of GC bias on genome assembly.", "Our analyses reveal that GC bias only lowers assembly completeness when the degree of GC bias is above a threshold.", "At a strong GC bias, the assembly fragmentation due to GC bias can be explained by the low coverage of reads in the GC-poor or GC-rich regions of a genome.", "This effect is observed for all the assemblers under study.", "Increasing the total amount of NGS data thus rescues the assembly fragmentation because of GC bias.", "However, the amount of data needed for a full rescue depends on the distribution of GC contents.", "Both low and high coverage depths due to GC bias lower the accuracy of assembly.", "These pieces of information provide guidance toward a better de novo genome assembly in the presence of GC bias."], "structured": false}
{"doc_id": 14471161, "title": "Cancer inhibition through circadian reprogramming of tumor transcriptome with meal timing.", "abstract": ["Circadian disruption accelerates cancer progression, whereas circadian reinforcement could halt it.", "Mice with P03 pancreatic adenocarcinoma (n = 77) were synchronized and fed ad libitum (AL) or with meal timing (MT) from Zeitgeber time (ZT) 2 to ZT6 with normal or fat diet.", "Tumor gene expression profiling was determined with DNA microarrays at endogenous circadian time (CT) 4 and CT16.", "Circadian mRNA expression patterns were determined for clock genes Rev-erbalpha, Per2, and Bmal1, cellular stress genes Hspa8 and Cirbp, and cyclin A2 gene Ccna2 in liver and tumor.", "The 24-hour patterns in telemetered rest-activity and body temperature and plasma corticosterone and insulin-like growth factor-I (IGF-I) were assessed.", "We showed that MT inhibited cancer growth by approximately 40% as compared with AL (P = 0.011) irrespective of calorie intake.", "Clock gene transcription remained arrhythmic in tumors irrespective of feeding schedule or diet.", "Yet, MT upregulated or downregulated the expression of 423 tumor genes, according to CT.", "Moreover, 36 genes involved in cellular stress, cell cycle, and metabolism were upregulated at one CT and downregulated 12 h apart.", "MT induced >10-fold circadian expression of Hspa8, Cirbp, and Ccna2 in tumors.", "Corticosterone or IGF-I patterns played no role in tumor growth inhibition.", "In contrast, MT consistently doubled the circadian amplitude of body temperature.", "Peak and trough respectively corresponded to peak expressions of Hspa8 and Cirbp in tumors.", "The reinforcement of the host circadian timing system with MT induced 24-hour rhythmic expression of critical genes in clock-deficient tumors, which translated into cancer growth inhibition.", "Targeting circadian clocks represents a novel potential challenge for cancer therapeutics."], "structured": false}
{"doc_id": 14474178, "title": "Role of chicken melanoma differentiation-associated gene 5 in induction and activation of innate and adaptive immune responses to infectious bursal disease virus in cultured macrophages", "abstract": ["The objective of the present study was to determine if chicken melanoma-differentiation-associated gene 5 (MDA5) senses infectious bursal disease virus infection to induce innate immunity that bridges to adaptive immunity.", "During IBDV infection in HD11 cells, IBDV titers and RNA loads increased up to 3.4 \u00d7 107 plaque-forming units (PFU)/mL and 1114 ng/\u00b5L, respectively, at 24 hours postinfection (hpi).", "IBDV infection in HD11 cells induced significantly upregulated (p < 0.05) expression levels of chicken MDA5 (59-fold), interferon-\u03b2 (IFN-\u03b2) (693-fold), dsRNA-dependent protein kinase (PKR) (4-fold), 2\u2019, 5\u2019-oligoadenylate synthetase (OAS) (286-fold), myxovirus resistance gene (Mx) (22-fold), interleukin-1\u03b2 (IL-1\u03b2) (5-fold), IL-6 (146-fold), IL-8 (4-fold), IL-10 (4-fold), inducible nitric oxide synthase (iNOS) (15-fold), and major histocompatibility complex class I (MHC class I) (4-fold).", "Nitric oxide production in the culture supernatants increased significantly (p < 0.05) up to 6.5 \u03bcM at 24 hpi.", "The expressed chMDA5 and IBDV-derived dsRNA were localized in the cytoplasm of HD11 cells during IBDV infection.", "ChMDA5-knockdown HD11 cells had significantly higher (p < 0.05) IBDV RNA loads at 24 hpi and significantly lower (p < 0.05) nitric oxide production and expression levels of chicken MDA5, IFN-\u03b2, PKR, OAS, Mx, IL-1\u03b2, IL-6, IL-8, IL-12(p40), IL-18, IL-10, iNOS, MHC class I and CD86 at 24 hpi.", "In addition, chMDA5 overexpression in HD11 cells resulted in significantly reduced (p < 0.05) IBDV titers and RNA loads and significantly increased (p < 0.05) nitric oxide production at 16 and 24 hpi.", "It also resulted in significantly higher (p < 0.05) expression levels of chicken MDA5, IFN-\u03b2, PKR, OAS, Mx, IL-1\u03b2, IL-6, IL-8, IL-12(p40), IL-10 and iNOS at 2 hpi.", "In conclusion, the results indicate that chMDA5 senses IBDV infection in chicken macrophages, and this is associated with IBDV-induced expression of IFN-\u03b2 and initiation of an innate immune response that in turn activates the adaptive immune response and limits IBDV replication."], "structured": false}
{"doc_id": 14475235, "title": "Age-Associated Sperm DNA Methylation Alterations: Possible Implications in Offspring Disease Susceptibility", "abstract": ["Recent evidence demonstrates a role for paternal aging on offspring disease susceptibility.", "It is well established that various neuropsychiatric disorders (schizophrenia, autism, etc.), trinucleotide expansion associated diseases (myotonic dystrophy, Huntington's, etc.) and even some forms of cancer have increased incidence in the offspring of older fathers.", "Despite strong epidemiological evidence that these alterations are more common in offspring sired by older fathers, in most cases the mechanisms that drive these processes are unclear.", "However, it is commonly believed that epigenetics, and specifically DNA methylation alterations, likely play a role.", "In this study we have investigated the impact of aging on DNA methylation in mature human sperm.", "Using a methylation array approach we evaluated changes to sperm DNA methylation patterns in 17 fertile donors by comparing the sperm methylome of 2 samples collected from each individual 9-19 years apart.", "With this design we have identified 139 regions that are significantly and consistently hypomethylated with age and 8 regions that are significantly hypermethylated with age.", "A representative subset of these alterations have been confirmed in an independent cohort.", "A total of 117 genes are associated with these regions of methylation alterations (promoter or gene body).", "Intriguingly, a portion of the age-related changes in sperm DNA methylation are located at genes previously associated with schizophrenia and bipolar disorder.", "While our data does not establish a causative relationship, it does raise the possibility that the age-associated methylation of the candidate genes that we observe in sperm might contribute to the increased incidence of neuropsychiatric and other disorders in the offspring of older males.", "However, further study is required to determine whether, and to what extent, a causative relationship exists."], "structured": false}
{"doc_id": 14479433, "title": "Mutations in the nuclear bile acid receptor FXR cause progressive familial intrahepatic cholestasis", "abstract": ["Neonatal cholestasis is a potentially life-threatening condition requiring prompt diagnosis.", "Mutations in several different genes can cause progressive familial intrahepatic cholestasis, but known genes cannot account for all familial cases.", "Here we report four individuals from two unrelated families with neonatal cholestasis and mutations in NR1H4, which encodes the farnesoid X receptor (FXR), a bile acid-activated nuclear hormone receptor that regulates bile acid metabolism.", "Clinical features of severe, persistent NR1H4-related cholestasis include neonatal onset with rapid progression to end-stage liver disease, vitamin K-independent coagulopathy, low-to-normal serum gamma-glutamyl transferase activity, elevated serum alpha-fetoprotein and undetectable liver bile salt export pump (ABCB11) expression.", "Our findings demonstrate a pivotal function for FXR in bile acid homeostasis and liver protection."], "structured": false}
{"doc_id": 14482051, "title": "Phase II study of panobinostat in combination with bevacizumab for recurrent glioblastoma and anaplastic glioma.", "abstract": ["BACKGROUND Panobinostat is a histone deacetylase inhibitor with antineoplastic and antiangiogenic effects in glioma that may work synergistically with bevacizumab.", "We conducted a multicenter phase II trial of panobinostat combined with bevacizumab in patients with recurrent high-grade glioma (HGG).   \n", "METHODS Patients with recurrent HGG were treated with oral panobinostat 30 mg 3 times per week, every other week, in combination with bevacizumab 10 mg/kg every other week.", "The primary endpoint was a 6-month progression-fee survival (PFS6) rate for participants with recurrent glioblastoma (GBM).", "Patients with recurrent anaplastic glioma (AG) were evaluated as an exploratory arm of the study.   \n", "RESULTS At interim analysis, the GBM arm did not meet criteria for continued accrual, and the GBM arm was closed.", "A total of 24 patients with GBM were accrued prior to closure.", "The PFS6 rate was 30.4% (95%, CI 12.4%-50.7%), median PFS was 5 months (range, 3-9 months), and median overall survival (OS) was 9 months (range, 6-19 months).", "Accrual in the AG arm continued to completion, and a total of 15 patients were enrolled.", "The PFS6 rate was 46.7% (range, 21%-73%), median PFS was 7 months (range, 2-10 months), and median OS was 17 months (range, 5 months-27 months).   \n", "CONCLUSIONS This phase II study of panobinostat and bevacizumab in participants with recurrent GBM did not meet criteria for continued accrual, and the GBM cohort of the study was closed.", "Although it was reasonably well tolerated, the addition of panobinostat to bevacizumab did not significantly improve PFS6 compared with historical controls of bevacizumab monotherapy in either cohort."], "structured": true}
{"doc_id": 14492339, "title": "Blood monocytes consist of two principal subsets with distinct migratory properties", "abstract": ["Peripheral blood monocytes are a heterogeneous population of circulating leukocytes.", "Using a murine adoptive transfer system to probe monocyte homing and differentiation in vivo, we identified two functional subsets among murine blood monocytes: a short-lived CX(3)CR1(lo)CCR2(+)Gr1(+) subset that is actively recruited to inflamed tissues and a CX(3)CR1(hi)CCR2(-)Gr1(-) subset characterized by CX(3)CR1-dependent recruitment to noninflamed tissues.", "Both subsets have the potential to differentiate into dendritic cells in vivo.", "The level of CX(3)CR1 expression also defines the two major human monocyte subsets, the CD14(+)CD16(-) and CD14(lo)CD16(+) monocytes, which share phenotype and homing potential with the mouse subsets.", "These findings raise the potential for novel therapeutic strategies in inflammatory diseases."], "structured": false}
{"doc_id": 14492964, "title": "The Spemann Organizer Signal noggin Binds and Inactivates Bone Morphogenetic Protein 4", "abstract": ["Signals released by the Spemann organizer of the amphibian gastrula can directly induce neural tissue from ectoderm and can dorsalize ventral mesoderm to form muscle.", "The secreted polypeptide noggin mimics these activities and is expressed at the appropriate time and place to participate in the organizer signal.", "Neural induction and mesoderm dorsalization are antagonized by bone morphogenetic proteins (BMPs), which induce epidermis and ventral mesoderm instead.", "Here we report that noggin protein binds BMP4 with high affinity and can abolish BMP4 activity by blocking binding to cognate cell-surface receptors.", "These data suggest that noggin secreted by the organizer patterns the embryo by interrupting BMP signaling."], "structured": false}
{"doc_id": 14496749, "title": "A Conserved MST-FOXO Signaling Pathway Mediates Oxidative-Stress Responses and Extends Life Span", "abstract": ["Oxidative stress influences cell survival and homeostasis, but the mechanisms underlying the biological effects of oxidative stress remain to be elucidated.", "Here, we demonstrate that the protein kinase MST1 mediates oxidative-stress-induced cell death in primary mammalian neurons by directly activating the FOXO transcription factors.", "MST1 phosphorylates FOXO proteins at a conserved site within the forkhead domain that disrupts their interaction with 14-3-3 proteins, promotes FOXO nuclear translocation, and thereby induces cell death in neurons.", "We also extend the MST-FOXO signaling link to nematodes.", "Knockdown of the C. elegans MST1 ortholog CST-1 shortens life span and accelerates tissue aging, while overexpression of cst-1 promotes life span and delays aging.", "The cst-1-induced life-span extension occurs in a daf-16-dependent manner.", "The identification of the FOXO transcription factors as major and evolutionarily conserved targets of MST1 suggests that MST kinases play important roles in diverse biological processes including cellular responses to oxidative stress and longevity."], "structured": false}
{"doc_id": 14500725, "title": "Physician Emigration from Sub-Saharan Africa to the United States: Analysis of the 2011 AMA Physician Masterfile", "abstract": ["BACKGROUND The large-scale emigration of physicians from sub-Saharan Africa (SSA) to high-income nations is a serious development concern.", "Our objective was to determine current emigration trends of SSA physicians found in the physician workforce of the United States.   \n", "METHODS AND FINDINGS We analyzed physician data from the World Health Organization (WHO) Global Health Workforce Statistics along with graduation and residency data from the 2011 American Medical Association Physician Masterfile (AMA-PM) on physicians trained or born in SSA countries who currently practice in the US.", "We estimated emigration proportions, year of US entry, years of practice before emigration, and length of time in the US.", "According to the 2011 AMA-PM, 10,819 physicians were born or trained in 28 SSA countries.", "Sixty-eight percent (n = 7,370) were SSA-trained, 20% (n = 2,126) were US-trained, and 12% (n = 1,323) were trained outside both SSA and the US.", "We estimated active physicians (age \u2264 70 years) to represent 96% (n = 10,377) of the total.", "Migration trends among SSA-trained physicians increased from 2002 to 2011 for all but one principal source country; the exception was South Africa whose physician migration to the US decreased by 8% (-156).", "The increase in last-decade migration was >50% in Nigeria (+1,113) and Ghana (+243), >100% in Ethiopia (+274), and >200% (+244) in Sudan.", "Liberia was the most affected by migration to the US with 77% (n = 175) of its estimated physicians in the 2011 AMA-PM.", "On average, SSA-trained physicians have been in the US for 18 years.", "They practiced for 6.5 years before US entry, and nearly half emigrated during the implementation years (1984-1999) of the structural adjustment programs.   \n", "CONCLUSION Physician emigration from SSA to the US is increasing for most SSA source countries.", "Unless far-reaching policies are implemented by the US and SSA countries, the current emigration trends will persist, and the US will remain a leading destination for SSA physicians emigrating from the continent of greatest need.", "Please see later in the article for the Editors' Summary."], "structured": true}
{"doc_id": 14501880, "title": "Kynurenic Acid Is a Nutritional Cue that Enables Behavioral Plasticity", "abstract": ["The kynurenine pathway of tryptophan metabolism is involved in the pathogenesis of several brain diseases, but its physiological functions remain unclear.", "We report that kynurenic acid, a metabolite in this pathway, functions as a regulator of food-dependent behavioral plasticity in C. elegans.", "The experience of fasting in C. elegans alters a variety of behaviors, including feeding rate, when food is encountered post-fast.", "Levels of neurally produced kynurenic acid are depleted by fasting, leading to activation of NMDA-receptor-expressing interneurons and initiation of a neuropeptide-y-like signaling axis that promotes elevated feeding through enhanced serotonin release when animals re-encounter food.", "Upon refeeding, kynurenic acid levels are eventually replenished, ending the elevated feeding period.", "Because tryptophan is an essential amino acid, these findings suggest that a physiological role of kynurenic acid is in directly linking metabolism to activity of NMDA and serotonergic circuits, which regulate a broad range of behaviors and physiologies."], "structured": false}
{"doc_id": 14530534, "title": "Comprehensive Identification and Annotation of Cell Type-Specific and Ubiquitous CTCF-Binding Sites in the Human Genome", "abstract": ["Chromatin insulators are DNA elements that regulate the level of gene expression either by preventing gene silencing through the maintenance of heterochromatin boundaries or by preventing gene activation by blocking interactions between enhancers and promoters.", "CCCTC-binding factor (CTCF), a ubiquitously expressed 11-zinc-finger DNA-binding protein, is the only protein implicated in the establishment of insulators in vertebrates.", "While CTCF has been implicated in diverse regulatory functions, CTCF has only been studied in a limited number of cell types across human genome.", "Thus, it is not clear whether the identified cell type-specific differences in CTCF-binding sites are functionally significant.", "Here, we identify and characterize cell type-specific and ubiquitous CTCF-binding sites in the human genome across 38 cell types designated by the Encyclopedia of DNA Elements (ENCODE) consortium.", "These cell type-specific and ubiquitous CTCF-binding sites show uniquely versatile transcriptional functions and characteristic chromatin features.", "In addition, we confirm the insulator barrier function of CTCF-binding and explore the novel function of CTCF in DNA replication.", "These results represent a critical step toward the comprehensive and systematic understanding of CTCF-dependent insulators and their versatile roles in the human genome."], "structured": false}
{"doc_id": 14535322, "title": "Experimental and Theoretical Approaches to Conscious Processing", "abstract": ["Recent experimental studies and theoretical models have begun to address the challenge of establishing a causal link between subjective conscious experience and measurable neuronal activity.", "The present review focuses on the well-delimited issue of how an external or internal piece of information goes beyond nonconscious processing and gains access to conscious processing, a transition characterized by the existence of a reportable subjective experience.", "Converging neuroimaging and neurophysiological data, acquired during minimal experimental contrasts between conscious and nonconscious processing, point to objective neural measures of conscious access: late amplification of relevant sensory activity, long-distance cortico-cortical synchronization at beta and gamma frequencies, and \"ignition\" of a large-scale prefronto-parietal network.", "We compare these findings to current theoretical models of conscious processing, including the Global Neuronal Workspace (GNW) model according to which conscious access occurs when incoming information is made globally available to multiple brain systems through a network of neurons with long-range axons densely distributed in prefrontal, parieto-temporal, and cingulate cortices.", "The clinical implications of these results for general anesthesia, coma, vegetative state, and schizophrenia are discussed."], "structured": false}
{"doc_id": 14541844, "title": "Reconstruction of the yeast Snf1 kinase regulatory network reveals its role as a global energy regulator", "abstract": ["Highly conserved among eukaryotic cells, the AMP-activated kinase (AMPK) is a central regulator of carbon metabolism.", "To map the complete network of interactions around AMPK in yeast (Snf1) and to evaluate the role of its regulatory subunit Snf4, we measured global mRNA, protein and metabolite levels in wild type, Deltasnf1, Deltasnf4, and Deltasnf1Deltasnf4 knockout strains.", "Using four newly developed computational tools, including novel DOGMA sub-network analysis, we showed the benefits of three-level ome-data integration to uncover the global Snf1 kinase role in yeast.", "We for the first time identified Snf1's global regulation on gene and protein expression levels, and showed that yeast Snf1 has a far more extensive function in controlling energy metabolism than reported earlier.", "Additionally, we identified complementary roles of Snf1 and Snf4.", "Similar to the function of AMPK in humans, our findings showed that Snf1 is a low-energy checkpoint and that yeast can be used more extensively as a model system for studying the molecular mechanisms underlying the global regulation of AMPK in mammals, failure of which leads to metabolic diseases."], "structured": false}
{"doc_id": 14544564, "title": "Influence of Steroid Hormone Signaling on Life Span Control by Caenorhabditis elegans Insulin-Like Signaling", "abstract": ["Sterol-sensing nuclear receptors and insulin-like growth factor signaling play evolutionarily conserved roles in the control of aging.", "In the nematode Caenorhabditis elegans, bile acid-like steroid hormones known as dafachronic acids (DAs) influence longevity by binding to and regulating the activity of the conserved nuclear receptor DAF-12, and the insulin receptor (InsR) ortholog DAF-2 controls life span by inhibiting the FoxO transcription factor DAF-16.", "How the DA/DAF-12 pathway interacts with DAF-2/InsR signaling to control life span is poorly understood.", "Here we specifically investigated the roles of liganded and unliganded DAF-12 in life span control in the context of reduced DAF-2/InsR signaling.", "In animals with reduced daf-2/InsR activity, mutations that either reduce DA biosynthesis or fully abrogate DAF-12 activity shorten life span, suggesting that liganded DAF-12 promotes longevity.", "In animals with reduced DAF-2/InsR activity induced by daf-2/InsR RNAi, both liganded and unliganded DAF-12 promote longevity.", "However, in daf-2/InsR mutants, liganded and unliganded DAF-12 act in opposition to control life span.", "Thus, multiple DAF-12 activities influence life span in distinct ways in contexts of reduced DAF-2/InsR signaling.", "Our findings establish new roles for a conserved steroid signaling pathway in life span control and elucidate interactions among DA biosynthetic pathways, DAF-12, and DAF-2/InsR signaling in aging."], "structured": false}
{"doc_id": 14550841, "title": "Asymmetric Cell Divisions Sustain Long-Term  Hematopoiesis from Single-sorted Human Fetal Liver Cells ", "abstract": ["Hematopoietic stem cells (HSCs) in adult marrow are believed to be derived from fetal liver precursors.", "To study cell kinetics involved in long-term hematopoiesis, we studied single-sorted candidate HSCs from fetal liver that were cultured in the presence of a mixture of stimulatory cytokines.", "After 8\u201310 d, the number of cells in primary cultures varied from 10,000 cells.", "Single cells in slow growing colonies were recloned upon reaching a 100\u2013200 cell stage.", "Strikingly, the number of cells in subclones varied widely again.", "These results are indicative of asymmetric divisions in primitive hematopoietic cells in which proliferative potential and cell cycle properties are unevenly distributed among daughter cells.", "The continuous generation of functional heterogeneity among the clonal progeny of HSCs is in support of intrinsic control of stem cell fate and provides a model for the long-term maintenance of hematopoiesis in vitro and in vivo."], "structured": false}
{"doc_id": 14555750, "title": "Reprogramming factor expression initiates widespread targeted chromatin remodeling.", "abstract": ["Despite rapid progress in characterizing transcription factor-driven reprogramming of somatic cells to an induced pluripotent stem cell (iPSC) state, many mechanistic questions still remain.", "To gain insight into the earliest events in the reprogramming process, we systematically analyzed the transcriptional and epigenetic changes that occur during early factor induction after discrete numbers of divisions.", "We observed rapid, genome-wide changes in the euchromatic histone modification, H3K4me2, at more than a thousand loci including large subsets of pluripotency-related or developmentally regulated gene promoters and enhancers.", "In contrast, patterns of the repressive H3K27me3 modification remained largely unchanged except for focused depletion specifically at positions where H3K4 methylation is gained.", "These chromatin regulatory events precede transcriptional changes within the corresponding loci.", "Our data provide evidence for an early, organized, and population-wide epigenetic response to ectopic reprogramming factors that clarify the temporal order through which somatic identity is reset during reprogramming."], "structured": false}
{"doc_id": 14566771, "title": "Stroke and migraine--the spectrum of cause and effect.", "abstract": ["The relationship of migraine and stroke is complex.", "Stroke may be coincidental with migraine but migraine may confer an increased risk of stroke in women under 45 years of age and possibly in men who have migraine with aura.", "Stroke may mimic migraine but migraine syndromes may be symptomatic of underlying cerebrovascular disorders.", "True migraine-induced stroke is rare.", "The mechanisms of stroke induced during a migraine attack remain to be determined but probably involve an interaction between the dynamic shifts in cerebral blood flow and stroke risk factors."], "structured": false}
{"doc_id": 14581009, "title": "MicroRNA Regulation of Cbx7 Mediates a Switch of Polycomb Orthologs during ESC Differentiation", "abstract": ["The Polycomb Group (PcG) of chromatin modifiers regulates pluripotency and differentiation.", "Mammalian genomes encode multiple homologs of the Polycomb repressive complex 1 (PRC1) components, including five orthologs of the Drosophila Polycomb protein (Cbx2, Cbx4, Cbx6, Cbx7, and Cbx8).", "We have identified Cbx7 as the primary Polycomb ortholog of PRC1 complexes in embryonic stem cells (ESCs).", "The expression of Cbx7 is downregulated during ESC differentiation, preceding the upregulation of Cbx2, Cbx4, and Cbx8, which are directly repressed by Cbx7.", "Ectopic expression of Cbx7 inhibits differentiation and X chromosome inactivation and enhances ESC self-renewal.", "Conversely, Cbx7 knockdown induces differentiation and derepresses lineage-specific markers.", "In a functional screen, we identified the miR-125 and miR-181 families as regulators of Cbx7 that are induced during ESC differentiation.", "Ectopic expression of these miRNAs accelerates ESC differentiation via regulation of Cbx7.", "These observations establish a critical role for Cbx7 and its regulatory miRNAs in determining pluripotency."], "structured": false}
{"doc_id": 14584755, "title": "Differences in the Clinical Effects of Angiotensin-Converting Enzyme Inhibitors and Angiotensin Receptor Blockers: A Critical Review of the Evidence", "abstract": ["The renin-angiotensin-aldosterone system plays a major role in the pathophysiology of hypertension and closely related cardio- and cerebrovascular events.", "Although both angiotensin-converting enzyme (ACE) inhibitors and angiotensin receptor antagonists (angiotensin receptor blockers; ARBs) are equally important in the treatment of hypertension, according to the results of recent years, there might be substantial differences in their cardiovascular protective effects, and these differences might be explained by our increasing knowledge of their non-overlapping mechanisms of action.", "The number of studies investigating how ACE inhibitors and ARB agents differ will certainly be increasing in the future.", "ACE inhibitors are the safe therapeutic opportunity for hypertensive patients at high risk, with a cardiological comorbidity."], "structured": false}
{"doc_id": 14591894, "title": "A talin-dependent LFA-1 focal zone is formed by rapidly migrating T lymphocytes", "abstract": ["Cells such as fibroblasts and endothelial cells migrate through the coordinated responses of discrete integrin-containing focal adhesions and complexes.", "In contrast, little is known about the organization of integrins on the highly motile T lymphocyte.", "We have investigated the distribution, activity, and cytoskeletal linkage of the integrin lymphocyte function associated antigen-1 (LFA-1) on human T lymphocytes migrating on endothelial cells and on ligand intercellular adhesion molecule-1 (ICAM-1).", "The pattern of total LFA-1 varies from low expression in the lamellipodia to high expression in the uropod.", "However, high affinity, clustered LFA-1 is restricted to a mid-cell zone that remains stable over time and over a range of ICAM-1 densities.", "Talin is essential for the stability and formation of the LFA-1 zone.", "Disruption of the talin\u2013integrin link leads to loss of zone integrity and a substantial decrease in speed of migration on ICAM-1.", "This adhesive structure, which differs from the previously described integrin-containing attachments displayed by many other cell types, we have termed the \u201cfocal zone.", "\u201d"], "structured": false}
{"doc_id": 14606752, "title": "Tricyclic antidepressants and headaches: systematic review and meta-analysis", "abstract": ["OBJECTIVE To evaluate the efficacy and relative adverse effects of tricyclic antidepressants in the treatment of migraine, tension-type, and mixed headaches.   \n", "DESIGN Meta-analysis.   \n", "DATA SOURCES Medline, Embase, the Cochrane Trials Registry, and PsycLIT.", "Studies reviewed Randomised trials of adults receiving tricyclics as only treatment for a minimum of four weeks.   \n", "DATA EXTRACTION Frequency of headaches (number of headache attacks for migraine and number of days with headache for tension-type headaches), intensity of headache, and headache index.   \n", "RESULTS 37 studies met the inclusion criteria.", "Tricyclics significantly reduced the number of days with tension-type headache and number of headache attacks from migraine than placebo (average standardised mean difference -1.29, 95% confidence interval -2.18 to -0.39 and -0.70, -0.93 to -0.48) but not compared with selective serotonin reuptake inhibitors (-0.80, -2.63 to 0.02 and -0.20, -0.60 to 0.19).", "The effect of tricyclics increased with longer duration of treatment (\u03b2=-0.11, 95% confidence interval -0.63 to -0.15; P<0.0005).", "Tricyclics were also more likely to reduce the intensity of headaches by at least 50% than either placebo (tension-type: relative risk 1.41, 95% confidence interval 1.02 to 1.89; migraine: 1.80, 1.24 to 2.62) or selective serotonin reuptake inhibitors (1.73, 1.34 to 2.22 and 1.72, 1.15 to 2.55).", "Tricyclics were more likely to cause adverse effects than placebo (1.53, 95% confidence interval 1.11 to 2.12) and selective serotonin reuptake inhibitors (2.22, 1.52 to 3.32), including dry mouth (P<0.0005 for both), drowsiness (P<0.0005 for both), and weight gain (P<0.001 for both), but did not increase dropout rates (placebo: 1.22, 0.83 to 1.80, selective serotonin reuptake inhibitors: 1.16, 0.81 to 2.97).   \n", "CONCLUSIONS Tricyclic antidepressants are effective in preventing migraine and tension-type headaches and are more effective than selective serotonin reuptake inhibitors, although with greater adverse effects.", "The effectiveness of tricyclics seems to increase over time."], "structured": true}
{"doc_id": 14610165, "title": "Functional Consequences of Splicing of the Antisense Transcript COOLAIR on FLC Transcription", "abstract": ["Antisense transcription is widespread in many genomes; however, how much is functional is hotly debated.", "We are investigating functionality of a set of long noncoding antisense transcripts, collectively called COOLAIR, produced at Arabidopsis FLOWERING LOCUS C (FLC).", "COOLAIR initiates just downstream of the major sense transcript poly(A) site and terminates either early or extends into the FLC promoter region.", "We now show that splicing of COOLAIR is functionally important.", "This was revealed through analysis of a hypomorphic mutation in the core spliceosome component PRP8.", "The prp8 mutation perturbs a cotranscriptional feedback mechanism linking COOLAIR processing to FLC gene body histone demethylation and reduced FLC transcription.", "The importance of COOLAIR splicing in this repression mechanism was confirmed by disrupting COOLAIR production and mutating the COOLAIR proximal splice acceptor site.", "Our findings suggest that altered splicing of a long noncoding transcript can quantitatively modulate gene expression through cotranscriptional coupling mechanisms."], "structured": false}
{"doc_id": 14615911, "title": "Nuclear Factor-\ufffdB Affects Tumor Progression in a Mouse Model of Malignant Pleural Effusion", "abstract": ["We developed a novel mouse model of malignant pleural effusion (MPE) by injecting Lewis lung cancer (LLC) cells directly into the pleural space of syngeneic C57B/6 mice.", "The pleural effusions in this model share common cellular and biochemical features with human MPEs.", "Implantation and growth of pleural tumors triggers a host inflammatory response characterized by a mixed inflammatory cell influx into the pleural fluid.", "LLC cells exhibited high basal nuclear factor (NF)-\u03baB activity in vitro and in vivo, which we used to drive expression of a NF-\u03baB\u2013dependent green fluorescent protein-firefly luciferase fusion reporter construct.", "NF-\u03baB\u2013dependent reporter expression allowed intravital tracing of pleural tumors.", "Inhibition of NF-\u03baB in LLC cells did not affect cell viability in culture; however, injection of LLC cells expressing a dominant NF-\u03baB inhibitor resulted in decreased tumor burden, decreased pleural effusion volume, and decreased pleural effusion TNF-\u03b1 levels.", "These studies indicate that tumor NF-\u03baB a..."], "structured": false}
{"doc_id": 14626540, "title": "A phase I study of PF-04449913, an oral hedgehog inhibitor, in patients with advanced solid tumors.", "abstract": ["PURPOSE To estimate the maximum tolerated dose (MTD) of single-agent PF-04449913, and to evaluate safety, tolerability, pharmacokinetics, pharmacodynamics, and preliminary antitumor activity in patients with advanced tumors.   ", "EXPERIMENTAL DESIGN A 3+3 design was used in this open-label, multicenter, phase I study and dose escalation/de-escalation applied until identification of the MTD.", "PF-04449913 was orally administered once daily in continuous 28-day treatment cycles.", "The starting dose was 80 mg.   \n", "RESULTS A total of 23 patients were enrolled; 19 were evaluable for first-cycle dose-limiting toxicity (DLT).", "The first-cycle DLT rate at the 640 mg dose level was 33.3%, and the MTD was estimated to be 320 mg once daily.", "The recommended phase II dose was not determined.", "PF-04449913 was generally well tolerated at doses of 80 to 320 mg once daily.", "The most common treatment-related adverse events (AE) were grade 1-2 dysgeusia, fatigue, decreased appetite, nausea, dizziness, dehydration, and diarrhea.", "Treatment-related grade 3 AEs only occurred in patients receiving PF-04449913 640 mg once daily.", "No treatment-related grade 4-5 AEs were reported.", "Pharmacokinetic analysis indicated a generally dose-proportional kinetics with biphasic elimination, supporting once-daily dosing.", "PF-04449913 modulated hedgehog signaling at the dose levels tested, as demonstrated by >80% downregulation of GLI1 expression in the skin of treated patients.", "Eight patients (34.8%) achieved stable disease; none had complete or partial response.", "Three patients with disease progression at enrollment had prolonged disease stabilization (\u22656 months).   \n", "CONCLUSIONS The results obtained in this study support further evaluation of PF-04449913 in patients with advanced solid tumors."], "structured": true}
{"doc_id": 14637235, "title": "Histone levels are regulated by phosphorylation and ubiquitylation dependent proteolysis", "abstract": ["Histone levels are tightly regulated to prevent harmful effects such as genomic instability and hypersensitivity to DNA-damaging agents due to the accumulation of these highly basic proteins when DNA replication slows down or stops.", "Although chromosomal histones are stable, excess (non-chromatin bound) histones are rapidly degraded in a Rad53 (radiation sensitive 53) kinase-dependent manner in Saccharomyces cerevisiae.", "Here we demonstrate that excess histones associate with Rad53 in vivo and seem to undergo modifications such as tyrosine phosphorylation and polyubiquitylation, before their proteolysis by the proteasome.", "We have identified the Tyr 99 residue of histone H3 as being critical for the efficient ubiquitylation and degradation of this histone.", "We have also identified the ubiquitin conjugating enzymes (E2) Ubc4 and Ubc5, as well as the ubiquitin ligase (E3) Tom1 (temperature dependent organization in mitotic nucleus 1), as enzymes involved in the ubiquitylation of excess histones.", "Regulated histone proteolysis has major implications for the maintenance of epigenetic marks on chromatin, genomic stability and the packaging of sperm DNA."], "structured": false}
{"doc_id": 14644164, "title": "TLR-activated B cells suppress T cell-mediated autoimmunity.", "abstract": ["TLR sense microbial infections, and control activation of immune responses.", "Dendritic cells, macrophages, and B lymphocytes express TLR and the TLR-signaling adaptor protein MyD88.", "The impact of TLR-activated B cells on T cell-mediated inflammation is unknown.", "In this study, we have used mice carrying B cell-restricted deficiencies in MyD88 or in distinct TLR to examine the impact of TLR-activated B cells on a T cell-mediated autoimmune disease, experimental autoimmune encephalomyelitis (EAE).", "We demonstrate that TLR-signaling in B cells suppresses inflammatory T cell responses (both Th1 and Th17), and stimulates recovery from EAE.", "Only certain TLR are required on B cells for resolution of EAE, and these are dispensable for disease initiation, indicating that a category of TLR agonists preferentially triggers a suppressive function in B cells and thereby limits autoimmune disease.", "The TLR agonists controlling the regulatory function of B cells are provided by components of Mycobacterium tuberculosis present in the adjuvant.", "Thus, MyD88 signaling in B cells antagonizes MyD88 signaling in other cells, which drives differentiation of Th17 cells and is required for induction of EAE.", "Altogether, our data indicate that B cells link recognition of microbial products via TLR to suppression of a T cell-mediated autoimmune disease."], "structured": false}
{"doc_id": 14647747, "title": "Successful expansion of functional and stable regulatory T cells for immunotherapy in liver transplantation", "abstract": ["Strategies to prevent organ transplant rejection whilst minimizing long-term immunosuppression are currently under intense investigation with regulatory T cells (Tregs) nearing clinical application.", "The clinical trial, ThRIL, recently commenced at King's College London, proposes to use Treg cell therapy to induce tolerance in liver transplant recipients, the success of which has the potential to revolutionize the management of these patients and enable a future of drug-free transplants.", "This is the first report of the manufacture of clinical grade Tregs from prospective liver transplant recipients via a CliniMACS-based GMP isolation technique and expanded using anti-CD3/CD28 beads, IL-2 and rapamycin.", "We report the enrichment of a pure, stable population of Tregs (>95% CD4(+)CD25(+)FOXP3(+)), reaching adequate numbers for their clinical application.", "Our protocol proved successful in, influencing the expansion of superior functional Tregs, as compared to freshly isolated cells, whilst also preventing their conversion to Th17 cells under pro-inflammatory conditions.", "We conclude with the manufacture of the final Treg product in the clinical research facility (CRF), a prerequisite for the clinical application of these cells.", "The data presented in this manuscript together with the much-anticipated clinical results from ThRIL, will undoubtedly inform the improved management of the liver transplant recipient."], "structured": false}
{"doc_id": 14652521, "title": "A framework for improving microRNA prediction in non-human genomes", "abstract": ["The prediction of novel pre-microRNA (miRNA) from genomic sequence has received considerable attention recently.", "However, the majority of studies have focused on the human genome.", "Previous studies have demonstrated that sensitivity (correctly detecting true miRNA) is sustained when human-trained methods are applied to other species, however they have failed to report the dramatic drop in specificity (the ability to correctly reject non-miRNA sequences) in non-human genomes.", "Considering the ratio of true miRNA sequences to pseudo-miRNA sequences is on the order of 1:1000, such low specificity prevents the application of most existing tools to non-human genomes, as the number of false positives overwhelms the true predictions.", "We here introduce a framework (SMIRP) for creating species-specific miRNA prediction systems, leveraging sequence conservation and phylogenetic distance information.", "Substantial improvements in specificity and precision are obtained for four non-human test species when our framework is applied to three different prediction systems representing two types of classifiers (support vector machine and Random Forest), based on three different feature sets, with both human-specific and taxon-wide training data.", "The SMIRP framework is potentially applicable to all miRNA prediction systems and we expect substantial improvement in precision and specificity, while sustaining sensitivity, independent of the machine learning technique chosen."], "structured": false}
{"doc_id": 14657344, "title": "CD8 Cells of Patients with Diffuse Cutaneous Leishmaniasis Display Functional Exhaustion: The Latter Is Reversed, In Vitro, by TLR2 Agonists", "abstract": ["Leishmania mexicana (Lm) causes localized (LCL) and diffuse (DCL) cutaneous leishmaniasis.", "DCL patients have a poor cellular immune response leading to chronicity.", "It has been proposed that CD8 T lymphocytes (CD8) play a crucial role in infection clearance, although the role of CD8 cytotoxicity in disease control has not been elucidated.", "Lesions of DCL patients have been shown to harbor low numbers of CD8, as compared to patients with LCL, and leishmanicidal treatment restores CD8 numbers.", "The marked response of CD8 towards Leishmania parasites led us to analyze possible functional differences between CD8 from patients with LCL and DCL.", "We compared IFN\u03b3 production, antigen-specific proliferation, and cytotoxicity of CD8 purified from PBMC against autologous macrophages (MO) infected with Leishmania mexicana (MOi).", "Additionally, we analyzed tissue biopsies from both groups of patients for evidence of cytotoxicity associated with apoptotic cells in the lesions.", "We found that CD8 cell of DCL patients exhibited low cytotoxicity, low antigen-specific proliferation and low IFN\u03b3 production when stimulated with MOi, as compared to LCL patients.", "Additionally, DCL patients had significantly less TUNEL+ cells in their lesions.", "These characteristics are similar to cellular \"exhaustion\" described in chronic infections.", "We intended to restore the functional capacity of CD8 cells of DCL patients by preincubating them with TLR2 agonists: Lm lipophosphoglycan (LPG) or Pam3Cys.", "Cytotoxicity against MOi, antigen-specific proliferation and IFN\u03b3 production were restored with both stimuli, whereas PD-1 (a molecule associated with cellular exhaustion) expression, was reduced.", "Our work suggests that CD8 response is associated with control of Lm infection in LCL patients and that chronic infection in DCL patients leads to a state of CD8 functional exhaustion, which could facilitate disease spread.", "This is the first report that shows the presence of functionally exhausted CD8 T lymphocytes in DCL patients and, additionally, that pre-stimulation with TLR2 ligands can restore the effector mechanisms of CD8 T lymphocytes from DCL patients against Leishmania mexicana-infected macrophages."], "structured": false}
{"doc_id": 14658685, "title": "Enhancer Evolution across 20 Mammalian Species", "abstract": ["The mammalian radiation has corresponded with rapid changes in noncoding regions of the genome, but we lack a comprehensive understanding of regulatory evolution in mammals.", "Here, we track the evolution of promoters and enhancers active in liver across 20 mammalian species from six diverse orders by profiling genomic enrichment of H3K27 acetylation and H3K4 trimethylation.", "We report that rapid evolution of enhancers is a universal feature of mammalian genomes.", "Most of the recently evolved enhancers arise from ancestral DNA exaptation, rather than lineage-specific expansions of repeat elements.", "In contrast, almost all liver promoters are partially or fully conserved across these species.", "Our data further reveal that recently evolved enhancers can be associated with genes under positive selection, demonstrating the power of this approach for annotating regulatory adaptations in genomic sequences.", "These results provide important insight into the functional genetics underpinning mammalian regulatory evolution."], "structured": false}
{"doc_id": 14663842, "title": "IDH1 mutations alter citric acid cycle metabolism and increase dependence on oxidative mitochondrial metabolism.", "abstract": ["Oncogenic mutations in isocitrate dehydrogenase 1 and 2 (IDH1/2) occur in several types of cancer, but the metabolic consequences of these genetic changes are not fully understood.", "In this study, we performed (13)C metabolic flux analysis on a panel of isogenic cell lines containing heterozygous IDH1/2 mutations.", "We observed that under hypoxic conditions, IDH1-mutant cells exhibited increased oxidative tricarboxylic acid metabolism along with decreased reductive glutamine metabolism, but not IDH2-mutant cells.", "However, selective inhibition of mutant IDH1 enzyme function could not reverse the defect in reductive carboxylation activity.", "Furthermore, this metabolic reprogramming increased the sensitivity of IDH1-mutant cells to hypoxia or electron transport chain inhibition in vitro.", "Lastly, IDH1-mutant cells also grew poorly as subcutaneous xenografts within a hypoxic in vivo microenvironment.", "Together, our results suggest therapeutic opportunities to exploit the metabolic vulnerabilities specific to IDH1 mutation."], "structured": false}
{"doc_id": 14664424, "title": "The assessment of the prognostic value of tumor markers and cytokines as SCCAg, CYFRA 21.1, IL-6, VEGF and sTNF receptors in patients with squamous cell cervical cancer, particularly with early stage of the disease", "abstract": ["The aim of this study is to determine the prognostic value of tumor markers, as squamous cell carcinoma antigen (SCCAg) and cytokeratin-19 fragment (CYFRA 21.1) and interleukin 6 (IL-6), vascular endothelial growth factor (VEGF), soluble tumor necrosis factor receptor I (sTNF RI), and sTNF RII in patients with squamous cell carcinoma of the cervix.", "The subjects of analysis were 138 patients with stage I-IVA according to the International Federation of Gynecology and Obstetrics (FIGO) classification.", "The collected research material comes from one oncology center.", "During the 10 years of follow-up, 56 relapses and 53 deaths were observed, and recurrent disease in early stage was confirmed in 45 % of patients.", "The pretreatment serum levels of SCCAg and CYFRA 21.1, and cytokines IL-6, VEGF, sTNF RI, and sTNF RII were determined in all patients.", "The probability of disease-free survival (DFS) and overall survival (OS) was evaluated using the log-rank test and the Cox regression model.", "Based on the ROC curve analysis for patients with recurrence, the largest area under the curve was demonstrated for SCCAg and IL-6 and for patients who died, for SCCAg and VEGF.", "Cox analysis demonstrated that independent prognostic factor for DFS was only SCCAg and for OS cytokine IL-6 and SCCAg, but in patients with early stage the prognostic value for DFS was VEGF, whereas IL-6 and CYFRA 21.1 for OS.", "Serum level of VEGF, CYFRA 21.1 and IL-6 before treatment in patients with early stage cervical cancer appears to be an important prognostic factor."], "structured": false}
{"doc_id": 14672919, "title": "Combination of platelet count and mean platelet volume (COP-MPV) predicts postoperative prognosis in both resectable early and advanced stage esophageal squamous cell cancer patients", "abstract": ["The aim of this study is to search the most powerful prognostic factor from routine blood test for esophageal squamous cell cancer (ESCC) patients.", "Multiple laboratory tests were evaluated including those reflecting red blood cell parameters (hemoglobin (Hb), mean corpuscular volume (MCV), mean corpuscular hemoglobin concentration (MCHC), and red blood cell distribution width (RDW)), platelet morphological parameters (mean platelet volume (MPV) and platelet count (PLT)), blood coagulation status (D-dimer), and tumor biomarker (CA19-9).", "Known inflammatory indices (NLR and PLR) were also calculated.", "A total of 468 patients who were diagnosed with ESCC between December 2005 and December 2008 were retrospectively analyzed in this study.", "By utilizing univariate and multivariate Cox proportional hazard analyses, we found that PLT and MPV were significantly associated with overall survival (OS) and disease-free survival (DFS) of ESCC patients, with optimal cutoff values of 212 and 10.6, respectively.", "Moreover, the combination of the preoperative PLT and MPV (COP-MPV) was calculated as follows: patients with both PLT (\u2265212 \u00d7 10(9) L(-1)) and MPV (\u226510.6 fL) elevation were assigned a score of 2, and patients with one or neither were assigned a score of 1 and 0.", "The COP-MPV was an independent prognostic factor for OS (hazard ratio (HR) 0.378, 95 % confidence interval (CI) 0.241 to 0.593, P < 0.001, 0/2) and DFS (HR 0.341, 95 % CI 0.218 to 0.534, P < 0.001, 0/2) in multivariate analyses.", "In subgroup analyses for early (stages I and II) and locally (stage III) advanced stage patients, COP-MPV was found significantly associated with OS and DFS in each group (P = 0.025 and P = 0.018 for OS and P = 0.029 and P = 0.002 for DFS).", "In conclusion, we considered that COP-MPV is a promising predictor for postoperative survival in ESCC patients."], "structured": false}
{"doc_id": 14682243, "title": "Dementia incidence and mortality in middle-income countries, and associations with indicators of cognitive reserve: a 10/66 Dementia Research Group population-based cohort study", "abstract": ["BACKGROUND Results of the few cohort studies from countries with low incomes or middle incomes suggest a lower incidence of dementia than in high-income countries.", "We assessed incidence of dementia according to criteria from the 10/66 Dementia Research Group and Diagnostic and Statistical Manual of Mental Disorders (DSM) IV, the effect of dementia at baseline on mortality, and the independent effects of age, sex, socioeconomic position, and indicators of cognitive reserve.   \n", "METHODS We did a population-based cohort study of all people aged 65 years and older living in urban sites in Cuba, the Dominican Republic, and Venezuela, and rural and urban sites in Peru, Mexico, and China, with ascertainment of incident 10/66 and DSM-IV dementia 3-5 years after cohort inception.", "We used questionnaires to obtain information about age in years, sex, educational level, literacy, occupational attainment, and number of household assets.", "We obtained information about mortality from all sites.", "For participants who had died, we interviewed a friend or relative to ascertain the likelihood that they had dementia before death.   \n", "FINDINGS 12,887 participants were interviewed at baseline.", "11,718 were free of dementia, of whom 8137 (69%) were reinterviewed, contributing 34,718 person-years of follow-up.", "Incidence for 10/66 dementia varied between 18\u00b72 and 30\u00b74 per 1000 person-years, and were 1\u00b74-2\u00b77 times higher than were those for DSM-IV dementia (9\u00b79-15\u00b77 per 1000 person-years).", "Mortality hazards were 1\u00b756-5\u00b769 times higher in individuals with dementia at baseline than in those who were dementia-free.", "Informant reports suggested a high incidence of dementia before death; overall incidence might be 4-19% higher if these data were included.", "10/66 dementia incidence was independently associated with increased age (HR 1\u00b767; 95% CI 1\u00b756-1\u00b779), female sex (0\u00b772; 0\u00b761-0\u00b784), and low education (0\u00b789; 0\u00b781-0\u00b797), but not with occupational attainment (1\u00b704; 0\u00b795-1\u00b713).   \n", "INTERPRETATION Our results provide supportive evidence for the cognitive reserve hypothesis, showing that in middle-income countries as in high-income countries, education, literacy, verbal fluency, and motor sequencing confer substantial protection against the onset of dementia.   \n", "FUNDING Wellcome Trust Health Consequences of Population Change Programme, WHO, US Alzheimer's Association, FONACIT/ CDCH/ UCV."], "structured": true}
{"doc_id": 14692646, "title": "Regulation of immune responses by extracellular vesicles", "abstract": ["Extracellular vesicles, including exosomes, are small membrane vesicles derived from multivesicular bodies or from the plasma membrane.", "Most, if not all, cell types release extracellular vesicles, which then enter the bodily fluids.", "These vesicles contain a subset of proteins, lipids and nucleic acids that are derived from the parent cell.", "It is thought that extracellular vesicles have important roles in intercellular communication, both locally and systemically, as they transfer their contents, including proteins, lipids and RNAs, between cells.", "Extracellular vesicles are involved in numerous physiological processes, and vesicles from both non-immune and immune cells have important roles in immune regulation.", "Moreover, extracellular vesicle-based therapeutics are being developed and clinically tested for the treatment of inflammatory diseases, autoimmune disorders and cancer.", "Given the tremendous therapeutic potential of extracellular vesicles, this Review focuses on their role in modulating immune responses, as well as their potential therapeutic applications."], "structured": false}
{"doc_id": 14700857, "title": "Risk of cancer after low doses of ionising radiation: retrospective cohort study in 15 countries.", "abstract": ["OBJECTIVES To provide direct estimates of risk of cancer after protracted low doses of ionising radiation and to strengthen the scientific basis of radiation protection standards for environmental, occupational, and medical diagnostic exposures.   \n", "DESIGN Multinational retrospective cohort study of cancer mortality.   \n", "SETTING Cohorts of workers in the nuclear industry in 15 countries.   \n", "PARTICIPANTS 407 391 workers individually monitored for external radiation with a total follow-up of 5.2 million person years.   \n", "MAIN OUTCOME MEASUREMENTS Estimates of excess relative risks per sievert (Sv) of radiation dose for mortality from cancers other than leukaemia and from leukaemia excluding chronic lymphocytic leukaemia, the main causes of death considered by radiation protection authorities.   \n", "RESULTS The excess relative risk for cancers other than leukaemia was 0.97 per Sv, 95% confidence interval 0.14 to 1.97.", "Analyses of causes of death related or unrelated to smoking indicate that, although confounding by smoking may be present, it is unlikely to explain all of this increased risk.", "The excess relative risk for leukaemia excluding chronic lymphocytic leukaemia was 1.93 per Sv (< 0 to 8.47).", "On the basis of these estimates, 1-2% of deaths from cancer among workers in this cohort may be attributable to radiation.   \n", "CONCLUSIONS These estimates, from the largest study of nuclear workers ever conducted, are higher than, but statistically compatible with, the risk estimates used for current radiation protection standards.", "The results suggest that there is a small excess risk of cancer, even at the low doses and dose rates typically received by nuclear workers in this study."], "structured": true}
{"doc_id": 14706752, "title": "Gamma-Secretase Represents a Therapeutic Target for the Treatment of Invasive Glioma Mediated by the p75 Neurotrophin Receptor", "abstract": ["The multifunctional signaling protein p75 neurotrophin receptor (p75(NTR)) is a central regulator and major contributor to the highly invasive nature of malignant gliomas.", "Here, we show that neurotrophin-dependent regulated intramembrane proteolysis (RIP) of p75(NTR) is required for p75(NTR)-mediated glioma invasion, and identify a previously unnamed process for targeted glioma therapy.", "Expression of cleavage-resistant chimeras of p75(NTR) or treatment of animals bearing p75(NTR)-positive intracranial tumors with clinically applicable gamma-secretase inhibitors resulted in dramatically decreased glioma invasion and prolonged survival.", "Importantly, proteolytic processing of p75(NTR) was observed in p75(NTR)-positive patient tumor specimens and brain tumor initiating cells.", "This work highlights the importance of p75(NTR) as a therapeutic target, suggesting that gamma-secretase inhibitors may have direct clinical application for the treatment of malignant glioma."], "structured": false}
{"doc_id": 14711483, "title": "Preliminary assessment of inhaled nitric oxide for acute vaso-occlusive crisis in pediatric patients with sickle cell disease.", "abstract": ["CONTEXT Vaso-occlusion is central to the painful crises and acute and chronic organ damage in sickle cell disease.", "Abnormal nitric oxide-dependent regulation of vascular tone, adhesion, platelet activation, and inflammation contributes to the pathophysiology of vaso-occlusion.", "Nitric oxide may have promise as a mechanism-of-disease-based therapy for treatment of vaso-occlusion.   \n", "OBJECTIVE To explore the efficacy and safety of inhaled nitric oxide (INO) for treatment of vaso-occlusive crisis in pediatric patients.   \n", "DESIGN Prospective, double-blind, placebo-controlled, randomized clinical trial with enrollment between September 1999 and October 2001.   \n", "SETTING Urban, tertiary care children's hospital in the United States.   \n", "PARTICIPANTS Twenty patients aged 10 to 21 years with sickle cell disease and severe acute vaso-occlusive crisis.   \n", "INTERVENTION Patients were randomly assigned to receive INO (80 ppm with 21% final concentration of inspired oxygen; n = 10), or placebo (21% inspired oxygen; n = 10) for 4 hours.   \n", "MAIN OUTCOME MEASURES Change in pain at 4 hours of inhalation compared with preinhalation pain, measured on a 10-cm visual analog scale (VAS); secondary outcome measures were pain over 6 hours, parenteral narcotic use over 24 hours, duration of hospitalization, blood pressure, oxygen saturation, and methemoglobin concentration.   \n", "RESULTS Preinhalation VAS pain scores were similar in the INO and placebo groups (P =.80).", "The decrease in VAS pain scores at 4 hours was 2.0 cm in the INO group and 1.2 cm in the placebo group (P =.37).", "Repeated-measures analysis of variance for hourly pain scores showed a 1-cm/h greater reduction in the INO group than the placebo group (P =.02).", "Morphine use over 6 hours was significantly less in the INO group (mean cumulative use, 0.29 vs 0.44 mg/kg; P =.03) but was not different over 4 hours (0.26 vs 0.32 mg/kg; P =.21) or 24 hours (0.63 vs 0.91 mg/kg; P =.15).", "Duration of hospitalization was 78 and 100 hours in the INO and placebo groups, respectively (P =.19).", "No INO toxicity was observed.   \n", "CONCLUSIONS Results of this exploratory study suggest that INO may be beneficial for acute vaso-occlusive crisis.", "These preliminary results warrant further investigation."], "structured": true}
{"doc_id": 14717213, "title": "Corresponding author:", "abstract": ["Over the years, methods of cytogenetic analysis evolved and became part of routine laboratory testing, providing valuable diagnostic and prognostic information in hematologic disorders.", "Karyotypic aberrations contribute to the understanding of the molecular pathogenesis of disease and thereby to rational application of therapeutic modalities.", "Most of the progress in this field stems from the application of metaphase cytogenetics (MC), but recently, novel molecular technologies have been introduced that complement MC and overcome many of the limitations of traditional cytogenetics, including a need for cell culture.", "Whole genome scanning using comparative genomic hybridization and single nucleotide polymorphism arrays (CGH-A; SNP-A) can be used for analysis of somatic or clonal unbalanced chromosomal defects.", "In SNP-A, the combination of copy number detection and genotyping enables diagnosis of copy-neutral loss of heterozygosity, a lesion that cannot be detected using MC but may have important pathogenetic implications.", "Overall, whole genome scanning arrays, despite the drawback of an inability to detect balanced translocations, allow for discovery of chromosomal defects in a higher proportion of patients with hematologic malignancies.", "Newly detected chromosomal aberrations, including somatic uniparental disomy, may lead to more precise prognostic schemes in many diseases."], "structured": false}
{"doc_id": 14717500, "title": "Rare Variants Create Synthetic Genome-Wide Associations", "abstract": ["Genome-wide association studies (GWAS) have now identified at least 2,000 common variants that appear associated with common diseases or related traits (http://www.genome.gov/gwastudies), hundreds of which have been convincingly replicated.", "It is generally thought that the associated markers reflect the effect of a nearby common (minor allele frequency >0.05) causal site, which is associated with the marker, leading to extensive resequencing efforts to find causal sites.", "We propose as an alternative explanation that variants much less common than the associated one may create \"synthetic associations\" by occurring, stochastically, more often in association with one of the alleles at the common site versus the other allele.", "Although synthetic associations are an obvious theoretical possibility, they have never been systematically explored as a possible explanation for GWAS findings.", "Here, we use simple computer simulations to show the conditions under which such synthetic associations will arise and how they may be recognized.", "We show that they are not only possible, but inevitable, and that under simple but reasonable genetic models, they are likely to account for or contribute to many of the recently identified signals reported in genome-wide association studies.", "We also illustrate the behavior of synthetic associations in real datasets by showing that rare causal mutations responsible for both hearing loss and sickle cell anemia create genome-wide significant synthetic associations, in the latter case extending over a 2.5-Mb interval encompassing scores of \"blocks\" of associated variants.", "In conclusion, uncommon or rare genetic variants can easily create synthetic associations that are credited to common variants, and this possibility requires careful consideration in the interpretation and follow up of GWAS signals."], "structured": false}
{"doc_id": 14719322, "title": "Decoding of Cytoplasmic Ca2+ Oscillations through the Spatial Signature Drives Gene Expression", "abstract": ["Cytoplasmic Ca(2+) oscillations are a universal signaling mode that activates numerous cellular responses [1, 2].", "Oscillations are considered the physiological mechanism of Ca(2+) signaling because they occur at low levels of stimulus intensity [3].", "Ca(2+) oscillations are proposed to convey information in their amplitude and frequency, leading to activation of specific downstream targets [4-6].", "Here, we report that the spatial Ca(2+) gradient within the oscillation is key.", "Ca(2+) oscillations in mast cells evoked over a range of agonist concentrations in the presence of external Ca(2+) were indistinguishable from those in the absence of Ca(2+) when plasmalemmal Ca(2+) extrusion was suppressed.", "Nevertheless, only oscillations with accompanying Ca(2+) entry through store-operated CRAC channels triggered gene expression.", "Increased cytoplasmic Ca(2+) buffering prevented oscillations but not gene activation.", "Local Ca(2+) influx and not global Ca(2+) oscillations therefore drives gene expression at physiological levels of stimulation.", "Rather than serving to maintain Ca(2+) oscillations by replenishing stores, we suggest that the role of oscillations might be to activate CRAC channels, thereby ensuring the generation of spatially restricted physiological Ca(2+) signals driving gene activation.", "Furthermore, we show that the spatial profile of a Ca(2+) oscillation provides a novel mechanism whereby a pleiotropic messenger specifically activates gene expression."], "structured": false}
{"doc_id": 14724693, "title": "Effect of glucosamine on pain-related disability in patients with chronic low back pain and degenerative lumbar osteoarthritis: a randomized controlled trial.", "abstract": ["CONTEXT Chronic low back pain (LBP) with degenerative lumbar osteoarthritis (OA) is widespread in the adult population.", "Although glucosamine is increasingly used by patients with chronic LBP, little is known about its effect in this setting.   \n", "OBJECTIVE To investigate the effect of glucosamine in patients with chronic LBP and degenerative lumbar OA.   \n", "DESIGN, SETTING, AND PARTICIPANTS A double-blind, randomized, placebo-controlled trial conducted at Oslo University Hospital Outpatient Clinic, Oslo, Norway, with 250 patients older than 25 years of age with chronic LBP (>6 months) and degenerative lumbar OA.   \n", "INTERVENTIONS Daily intake of 1500 mg of oral glucosamine (n = 125) or placebo (n = 125) for 6 months, with assessment of effect after the 6-month intervention period and at 1 year (6 months postintervention).   \n", "MAIN OUTCOME MEASURES The primary outcome was pain-related disability measured with the Roland Morris Disability Questionnaire (RMDQ).", "Secondary outcomes were numerical scores from pain-rating scales of patients at rest and during activity, and the quality-of-life EuroQol-5 Dimensions (EQ-5D) instrument.", "Data collection occurred during the intervention period at baseline, 6 weeks, 3 and 6 months, and again 6 months following the intervention at 1 year.", "Group differences were analyzed using linear mixed models analysis.   \n", "RESULTS At baseline, mean RMDQ scores were 9.2 (95% confidence interval [CI], 8.4-10.0) for glucosamine and 9.7 (95% CI, 8.9-10.5) for the placebo group (P = .37).", "At 6 months, the mean RMDQ score was the same for the glucosamine and placebo groups (5.0; 95% CI, 4.2-5.8).", "At 1 year, the mean RMDQ scores were 4.8 (95% CI, 3.9-5.6) for glucosamine and 5.5 (95% CI, 4.7-6.4) for the placebo group.", "No statistically significant difference in change between groups was found when assessed after the 6-month intervention period and at 1 year: RMDQ (P = .72), LBP at rest (P = .91), LBP during activity (P = .97), and quality-of-life EQ-5D (P = .20).", "Mild adverse events were reported in 40 patients in the glucosamine group and 46 in the placebo group (P = .48).   \n", "CONCLUSIONS Among patients with chronic LBP and degenerative lumbar OA, 6-month treatment with oral glucosamine compared with placebo did not result in reduced pain-related disability after the 6-month intervention and after 1-year follow-up.   \n", "TRIAL REGISTRATION clinicaltrials.gov Identifier: NCT00404079."], "structured": true}
{"doc_id": 14726759, "title": "Adult cervicocerebral artery dissection: a single-center study of 301 Finnish patients.", "abstract": ["BACKGROUND AND PURPOSE There are only few small studies assessing potential risk factors, comorbidity, and prognostic factors in adult spontaneous cervicocerebral artery dissection (CAD).   \n", "METHODS We conducted a retrospective, hospital-based analysis on the prognostic factors and association of CAD with vascular risk factors in 301 consecutive Finnish patients, diagnosed from 1994 to 2007.   \n", "RESULTS Two thirds of the patients were men (68%).", "Women were younger than men.", "Migraine (36% of all patients), especially with visual aura (63% of all migraineurs), and smoking were more common in patients with CAD compared with the general Finnish population.", "At 3 months, 247 (83%) patients reached a favorable outcome.", "Occlusion of the dissected artery, internal carotid artery dissection (ICAD), and recent infection in infarction patients were associated with a poorer outcome.", "ICAD patients had less often brain infarction, but the strokes they had were more severe.", "Seven (2.3%) patients died during the follow-up (mean 4.0 years, 1186 patient years).", "Six (2%) patients had verified CAD recurrence.   \n", "CONCLUSIONS This study provides evidence for the association of CAD with male sex, and possible association with smoking and migraine.", "Occlusion of the dissected artery, ICAD, and infection appear to be associated with poorer outcome."], "structured": true}
{"doc_id": 14729253, "title": "Genetic variation and gastric cancer risk: a field synopsis and meta-analysis.", "abstract": ["BACKGROUND Data on genetic susceptibility to sporadic gastric carcinoma have been published at a growing pace, but to date no comprehensive overview and quantitative summary has been available.   \n", "METHODS We conducted a systematic review and meta-analysis of the evidence on the association between DNA variation and risk of developing stomach cancer.", "To assess result credibility, summary evidence was graded according to the Venice criteria and false positive report probability (FPRP) was calculated to further validate result noteworthiness.", "Meta-analysis was also conducted for subgroups, which were defined by ethnicity (Asian vs Caucasian), tumour histology (intestinal vs diffuse), tumour site (cardia vs non-cardia) and Helicobacter pylori infection status (positive vs negative).   \n", "RESULTS Literature search identified 824 eligible studies comprising 2 530 706 subjects (cases: 261 386 (10.3%)) and investigating 2841 polymorphisms involving 952 distinct genes.", "Overall, we performed 456 primary and subgroup meta-analyses on 156 variants involving 101 genes.", "We identified 11 variants significantly associated with disease risk and assessed to have a high level of summary evidence: MUC1 rs2070803 at 1q22 (diffuse carcinoma subgroup), MTX1 rs2075570 at 1q22 (diffuse), PSCA rs2294008 at 8q24.2 (non-cardia), PRKAA1 rs13361707 5p13 (non-cardia), PLCE1 rs2274223 10q23 (cardia), TGFBR2 rs3087465 3p22 (Asian), PKLR rs3762272 1q22 (diffuse), PSCA rs2976392 (intestinal), GSTP1 rs1695 11q13 (Asian), CASP8 rs3834129 2q33 (mixed) and TNF rs1799724 6p21.3 (mixed), with the first nine variants characterised by a low FPRP.", "We also identified polymorphisms with lower quality significant associations (n=110).   \n", "CONCLUSIONS We have identified several high-quality biomarkers of gastric cancer susceptibility.", "These data will form the backbone of an annually updated online resource that will be integral to the study of gastric carcinoma genetics and may inform future screening programmes."], "structured": true}
{"doc_id": 14753395, "title": "Structure and function of the blood\u2013brain barrier", "abstract": ["Neural signalling within the central nervous system (CNS) requires a highly controlled microenvironment.", "Cells at three key interfaces form barriers between the blood and the CNS: the blood-brain barrier (BBB), blood-CSF barrier and the arachnoid barrier.", "The BBB at the level of brain microvessel endothelium is the major site of blood-CNS exchange.", "The structure and function of the BBB is summarised, the physical barrier formed by the endothelial tight junctions, and the transport barrier resulting from membrane transporters and vesicular mechanisms.", "The roles of associated cells are outlined, especially the endfeet of astrocytic glial cells, and pericytes and microglia.", "The embryonic development of the BBB, and changes in pathology are described.", "The BBB is subject to short and long-term regulation, which may be disturbed in pathology.", "Any programme for drug discovery or delivery, to target or avoid the CNS, needs to consider the special features of the BBB."], "structured": false}
{"doc_id": 14767844, "title": "Golli protein negatively regulates store depletion-induced calcium influx in T cells.", "abstract": ["Calcium influx is crucial for T cell activation and differentiation.", "The detailed regulation of this process remains unclear.", "We report here that golli protein, an alternatively spliced product of the myelin basic protein gene, plays a critical role in regulating calcium influx in T cells.", "Golli-deficient T cells were hyperproliferative and showed enhanced calcium entry upon T cell receptor stimulation.", "We further found that golli regulates calcium influx in T cells through the inhibition of the store depletion-induced calcium influx.", "Mutation of the myristoylation site on golli disrupted its association with the plasma membrane and reversed its inhibitory action on Ca2+ influx, indicating that membrane association of golli was essential for its inhibitory action.", "These results indicate that golli functions in a unique way to regulate T cell activation through a mechanism involving the modulation of the calcium homeostasis."], "structured": false}
{"doc_id": 14768471, "title": "Extracellular vesicles derived from renal cancer stem cells induce a pro-tumorigenic phenotype in mesenchymal stromal cells", "abstract": ["Renal carcinomas have been shown to contain a population of cancer stem cells (CSCs) that present self-renewing capacity and support tumor growth and metastasis.", "CSCs were shown to secrete large amount of extracellular vesicles (EVs) that can transfer several molecules (proteins, lipids and nucleic acids) and induce epigenetic changes in target cells.", "Mesenchymal Stromal Cells (MSCs) are susceptible to tumor signalling and can be recruited to tumor regions.", "The precise role of MSCs in tumor development is still under debate since both pro- and anti-tumorigenic effects have been reported.", "In this study we analysed the participation of renal CSC-derived EVs in the interaction between tumor and MSCs.", "We found that CSC-derived EVs promoted persistent phenotypical changes in MSCs characterized by an increased expression of genes associated with cell migration (CXCR4, CXCR7), matrix remodeling (COL4A3), angiogenesis and tumor growth (IL-8, Osteopontin and Myeloperoxidase).", "EV-stimulated MSCs exhibited in vitro an enhancement of migration toward the tumor conditioned medium.", "Moreover, EV-stimulated MSCs enhanced migration of renal tumor cells and induced vessel-like formation.", "In vivo, EV-stimulated MSCs supported tumor development and vascularization, when co-injected with renal tumor cells.", "In conclusion, CSC-derived EVs induced phenotypical changes in MSCs that are associated with tumor growth."], "structured": false}
{"doc_id": 14782049, "title": "In vivo effect of chronic hypoxia on the neurochemical profile of the developing rat hippocampus.", "abstract": ["The cognitive deficits observed in children with cyanotic congenital heart disease suggest involvement of the developing hippocampus.", "Chronic postnatal hypoxia present during infancy in these children may play a role in these impairments.", "To understand the biochemical mechanisms of hippocampal injury in chronic hypoxia, a neurochemical profile consisting of 15 metabolite concentrations and 2 metabolite ratios in the hippocampus was evaluated in a rat model of chronic postnatal hypoxia using in vivo 1H NMR spectroscopy at 9.4 T. Chronic hypoxia was induced by continuously exposing rats (n = 23) to 10% O2 from postnatal day (P) 3 to P28.", "Fifteen metabolites were quantified from a volume of 9-11 microl centered on the left hippocampus on P14, P21, and P28 and were compared with normoxic controls (n = 14).", "The developmental trajectory of neurochemicals in chronic hypoxia was similar to that seen in normoxia.", "However, chronic hypoxia had an effect on the concentrations of the following neurochemicals: aspartate, creatine, phosphocreatine, GABA, glutamate, glutamine, glutathione, myoinositol, N-acetylaspartate (NAA), phosphorylethanolamine, and phosphocreatine/creatine (PCr/Cr) and glutamate/glutamine (Glu/Gln) ratios (P < 0.001 each, except glutamate, P = 0.04).", "The increased PCr/Cr ratio is consistent with decreased brain energy consumption.", "Given the well-established link between excitatory neurotransmission and brain energy metabolism, we postulate that elevated glutamate, Glu/Gln ratio, and GABA indicate suppressed excitatory neurotransmission in an energy-limited environment.", "Decreased NAA and phosphorylethanolamine suggest reduced neuronal integrity and phospholipid metabolism.", "The altered hippocampal neurochemistry during its development may underlie some of the cognitive deficits present in human infants at risk of chronic hypoxia."], "structured": false}
{"doc_id": 14797520, "title": "Noncoding Transcription by RNA Polymerase Pol IVb/Pol V Mediates Transcriptional Silencing of Overlapping and Adjacent Genes", "abstract": ["Nuclear transcription is not restricted to genes but occurs throughout the intergenic and noncoding space of eukaryotic genomes.", "The functional significance of this widespread noncoding transcription is mostly unknown.", "We show that Arabidopsis RNA polymerase IVb/Pol V, a multisubunit nuclear enzyme required for siRNA-mediated gene silencing of transposons and other repeats, transcribes intergenic and noncoding sequences, thereby facilitating heterochromatin formation and silencing of overlapping and adjacent genes.", "Pol IVb/Pol V transcription requires the chromatin-remodeling protein DRD1 but is independent of siRNA biogenesis.", "However, Pol IVb/Pol V transcription and siRNA production are both required to silence transposons, suggesting that Pol IVb/Pol V generates RNAs or chromatin structures that serve as scaffolds for siRNA-mediated heterochromatin-forming complexes.", "Pol IVb/Pol V function provides a solution to a paradox of epigenetic control: the need for transcription in order to transcriptionally silence the same region."], "structured": false}
{"doc_id": 14803797, "title": "Intestinal microbiota metabolism of L-carnitine, a nutrient in red meat, promotes atherosclerosis", "abstract": ["Intestinal microbiota metabolism of choline and phosphatidylcholine produces trimethylamine (TMA), which is further metabolized to a proatherogenic species, trimethylamine-N-oxide (TMAO).", "We demonstrate here that metabolism by intestinal microbiota of dietary L-carnitine, a trimethylamine abundant in red meat, also produces TMAO and accelerates atherosclerosis in mice.", "Omnivorous human subjects produced more TMAO than did vegans or vegetarians following ingestion of L-carnitine through a microbiota-dependent mechanism.", "The presence of specific bacterial taxa in human feces was associated with both plasma TMAO concentration and dietary status.", "Plasma L-carnitine levels in subjects undergoing cardiac evaluation (n = 2,595) predicted increased risks for both prevalent cardiovascular disease (CVD) and incident major adverse cardiac events (myocardial infarction, stroke or death), but only among subjects with concurrently high TMAO levels.", "Chronic dietary L-carnitine supplementation in mice altered cecal microbial composition, markedly enhanced synthesis of TMA and TMAO, and increased atherosclerosis, but this did not occur if intestinal microbiota was concurrently suppressed.", "In mice with an intact intestinal microbiota, dietary supplementation with TMAO or either carnitine or choline reduced in vivo reverse cholesterol transport.", "Intestinal microbiota may thus contribute to the well-established link between high levels of red meat consumption and CVD risk."], "structured": false}
{"doc_id": 14806256, "title": "Hepatotoxicity associated with antiretroviral therapy in adults infected with human immunodeficiency virus and the role of hepatitis C or B virus infection.", "abstract": ["CONTEXT Use of antiretroviral drugs, including protease inhibitors, for treatment of human immunodeficiency virus (HIV) infection has been anecdotally associated with hepatotoxicity, particularly in persons coinfected with hepatitis C or B virus.   \n", "OBJECTIVES To ascertain if incidence of severe hepatotoxicity during antiretroviral therapy is similar for all antiretroviral drug combinations, and to define the role of chronic viral hepatitis in its development.   \n", "DESIGN Prospective cohort study.   \n", "SETTING University-based urban HIV clinic.   \n", "PATIENTS A total of 298 patients who were prescribed new antiretroviral therapies between January 1996 and January 1998, 211 (71%) of whom received protease inhibitors as part of combination therapy (median follow-up, 182 days) and 87 (29%) of whom received dual nucleoside analog regimens (median follow-up, 167 days).", "Chronic hepatitis C and B virus infection was present in 154 (52%) and 8 (2.7%) patients, respectively.   \n", "MAIN OUTCOME MEASURE Severe hepatotoxicity, defined as a grade 3 or 4 change in levels of serum alanine aminotransferase and aspartate aminotransferase, evaluated before and during therapy.   \n", "RESULTS Severe hepatotoxicity was observed in 31 (10.4%) of 298 patients (95% confidence interval [CI], 7.2%-14.4%).", "Ritonavir use was associated with a higher incidence of toxicity (30%; 95% CI, 17.9% -44.6%).", "However, no significant difference was detected in hepatotoxicity incidence in other treatment groups, ie, nucleoside analogs (5.7%; 95% CI, 1.2%-12.9%), nelfinavir (5.9%; 95% CI, 1.2%-16.2%), saquinavir (5.9%; 95% CI, 0.15%-28.7%), and indinavir(6.8%; 95% CI, 3.0%-13.1 %).", "Although chronicviral hepatitis was associated with an increased risk of severe hepatotoxicity among patients prescribed nonritonavir regimens (relative risk, 3.7; 95% CI, 1.0-11.8), most patients with chronic hepatitis C or B virus infection (88%) did not experience significant toxic effects.", "Rate of severe toxicity with use of any protease inhibitor in patients with hepatitis C infection was 12.2% (13/107; 95% CI, 6.6%-19.9%).", "In multivariate logistic regression, only ritonavir (adjusted odds ratio [AOR], 8.6; 95% CI, 3.0-24.6) and a CD4 cell count increase of more than 0.05 x 10(9)/L (AOR, 3.6; 95% CI, 1.0-12.9) were associated with severe hepatotoxicity.", "No irreversible outcomes were seen in patients with severe hepatotoxicity.   \n", "CONCLUSIONS Our data indicate that use of ritonavir may increase risk of severe hepatotoxicity.", "Although hepatotoxicity may be more common in persons with chronic viral hepatitis, these data do not support withholding protease inhibitor therapy from persons coinfected with hepatitis B or C virus."], "structured": true}
{"doc_id": 14819804, "title": "Mutations in the phosphatidylinositol-3-kinase pathway predict for antitumor activity of the inhibitor PX-866 whereas oncogenic Ras is a dominant predictor for resistance.", "abstract": ["The novel phosphatidylinositol-3-kinase (PI3K) inhibitor PX-866 was tested against 13 experimental human tumor xenografts derived from cell lines of various tissue origins.", "Mutant PI3K (PIK3CA) and loss of PTEN activity were sufficient, but not necessary, as predictors of sensitivity to the antitumor activity of the PI3K inhibitor PX-866 in the presence of wild-type Ras, whereas mutant oncogenic Ras was a dominant determinant of resistance, even in tumors with coexisting mutations in PIK3CA.", "The level of activation of PI3K signaling measured by tumor phosphorylated Ser(473)-Akt was insufficient to predict in vivo antitumor response to PX-866.", "Reverse-phase protein array revealed that the Ras-dependent downstream targets c-Myc and cyclin B were elevated in cell lines resistant to PX-866 in vivo.", "Studies using an H-Ras construct to constitutively and preferentially activate the three best-defined downstream targets of Ras, i.e., Raf, RalGDS, and PI3K, showed that mutant Ras mediates resistance through its ability to use multiple pathways for tumorigenesis.", "The identification of Ras and downstream signaling pathways driving resistance to PI3K inhibition might serve as an important guide for patient selection as inhibitors enter clinical trials and for the development of rational combinations with other molecularly targeted agents."], "structured": false}
{"doc_id": 14823313, "title": "Changing mortality patterns in East and West Germany and Poland. II: short-term trends during transition and in the 1990s.", "abstract": ["OBJECTIVES To examine trends in life expectancy at birth and age and cause specific patterns of mortality in the former German Democratic Republic (GDR) and Poland during political transition and throughout the 1990s in both parts of Germany and in Poland.   \n", "METHODS Decomposition of life expectancy by age and cause of death.", "Changes in life expectancy during transition by cause of death were examined using data for 1988/89 and 1990/91 for the former GDR and Poland; examination of life expectancy changes after transition were based on 1992-97 data for Germany and 1991-96 data for Poland.   \n", "RESULTS In both the former GDR and Poland male life expectancy at birth declined by almost one year during transition, mainly attributable to rising death rates from external causes and circulatory diseases.", "Female life expectancy in Poland deteriorated by 0.3 years, largely attributable to increasing circulatory mortality among the old, while in East German female rising death rates in children and young adults were nearly outbalanced by declining circulatory mortality among those over 70.", "Between 1991/92 and 1996/97, male life expectancy at birth increased by 2.4 years in the former GDR, 1.2 years in old Federal Republic, and 2.0 years in Poland (women: 2.3, 0.9, and 1.2 years).", "In East Germany and Poland, the overall improvement was largely attributable to falling mortality among men aged 40-64, while those over 65 contributed the largest proportion to life expectancy gains in women.", "The change in deaths among men aged 15-39 accounted for 0.4 of a year to life expectancy at birth in East Germany and Poland, attributable largely to greater decreases from external causes.", "Among those over 40, absolute contributions to changing life expectancy were greater in the former GDR than in the other two entities in both sexes, largely attributable to circulatory diseases.", "A persisting East-west life expectancy gap in Germany of 2.1 years in men in 1997 was largely attributable to external causes, diseases of the digestive system and circulatory diseases.", "Higher death rates from circulatory diseases among the elderly largely explain the female life expectancy gap of approximately one year.   \n", "CONCLUSIONS This study provides further insights into the health effects of political transition.", "Post-transition improvements in life expectancy and mortality have been much steeper in East Germany compared with Poland.", "Changes in dietary pattern and, in Germany, medical care may have been important factors in shaping post-transition mortality trends."], "structured": true}
{"doc_id": 14827874, "title": "0021-972X/06/$15.00/0 The Journal of Clinical Endocrinology & Metabolism 91(3):760\u2013771 Printed in U.S.A. Copyright \u00a9 2006 by The Endocrine Society doi: 10.1210/jc.2005-1923 REVIEW: Aromatase Inhibitors for Ovulation Induction", "abstract": ["CONTEXT For the last 40 yr, the first line of treatment for anovulation in infertile women has been clomiphene citrate (CC).", "CC is a safe, effective oral agent but is known to have relatively common antiestrogenic endometrial and cervical mucous side effects that could prevent pregnancy in the face of successful ovulation.", "In addition, there is a significant risk of multiple pregnancy with CC, compared with natural cycles.", "Because of these problems, we proposed the concept of aromatase inhibition as a new method of ovulation induction that could avoid many of the adverse effects of CC.", "The objective of this review was to describe the different physiological mechanisms of action for CC and aromatase inhibitors (AIs) and compare studies of efficacy for both agents for ovulation induction.   ", "EVIDENCE ACQUISITION We conducted a systematic review of all the published studies, both controlled and noncontrolled, comparing CC and AI treatment, either alone or in combination with gonadotropins, for ovulation induction or augmentation, identified through the Entrez-PubMed search engine.   ", "EVIDENCE SYNTHESIS Because of the recent acceptance of the concept of using AIs for ovulation induction, few controlled studies were identified, and the rest of the studies were pilot or preliminary comparisons.", "Based on these studies, it appears that AIs are as effective as CC in inducing ovulation, are devoid of any antiestrogenic side effects, result in lower serum estrogen concentrations, and are associated with good pregnancy rates with a lower incidence of multiple pregnancy than CC.", "When combined with gonadotropins for assisted reproductive technologies, AIs reduce the dose of FSH required for optimal follicle recruitment and improve the response to FSH in poor responders.   \n", "CONCLUSIONS Preliminary evidence suggests that AIs may replace CC in the future because of similar efficacy with a reduced side effect profile.", "Although worldwide experience with AIs for ovulation induction is increasing, at present, definitive studies in the form of randomized controlled trials comparing CC with AIs are lacking."], "structured": true}
{"doc_id": 14831629, "title": "Patent ductus arteriosus: lack of evidence for common treatments.", "abstract": ["Patent ductus arteriosus (PDA) is a common diagnosis among extremely premature infants, especially in those with lung disease.", "Treatments are often used to close the PDA.", "Despite nearly three decades of research, the question of whether the benefits of treatments to prevent ductal patency or promote closure outweigh the risks of these treatments remains unanswered.", "The authors rarely use treatments designed to close the PDA.", "This article reviews three considerations in support of this restrained approach: rates of spontaneous closure of the ductus arteriosus; adverse effect of persistent ductal patency; and benefits and risks of treatments for closure."], "structured": false}
{"doc_id": 14834714, "title": "Gene therapy of arthritis with TCR isolated from the inflamed paw.", "abstract": ["In recent years, the treatment of autoimmune diseases has been significantly advanced by the use of biological agents.", "However, some biologics are accompanied with severe side effects, including tuberculosis and other types of infection.", "There is thus a critical need for nonsystemic and lesion-specific methods of delivering these therapeutic agents.", "We attempted to treat a mouse model of arthritis by using T cells that expressed a regulatory molecule and were specifically directed to the inflamed paw.", "To this end, we first identified the TCR alphabeta genes accumulating in the inflamed paw of mice with collagen-induced arthritis (CIA) by a combination of single-strand chain polymorphism analysis of TCR and single-cell sorting.", "We identified an expanded clone B47 which is autoreactive but is not specific to type II collagen.", "In vivo, TCR genes from B47-transduced T cells accumulated in the inflamed paw.", "Injection of cells cotransduced with the B47 and soluble TNFRIg genes resulted in a significant suppression of CIA.", "The suppression was correlated with the amount of TNFRIg transcripts in the hind paw, not with the serum concentrations of TNFRIg.", "Moreover, T cells cotransduced with the B47 and intracellular Foxp3 genes significantly suppressed CIA with reductions in TNF-alpha, IL-17A, and IL-1beta expression and bone destruction.", "T cells cotransduced with B47 and Foxp3 genes also suppressed the progression of established CIA.", "Therefore, immunosuppressive therapy with autoreactive TCR is a promising therapeutic strategy for arthritis whether the TCRs are used to deliver either soluble or intracellular suppressive molecules."], "structured": false}
{"doc_id": 14835068, "title": "Melatonin: A Mitochondrial Targeting Molecule Involving Mitochondrial Protection and Dynamics", "abstract": ["Melatonin has been speculated to be mainly synthesized by mitochondria.", "This speculation is supported by the recent discovery that aralkylamine N-acetyltransferase/serotonin N-acetyltransferase (AANAT/SNAT) is localized in mitochondria of oocytes and the isolated mitochondria generate melatonin.", "We have also speculated that melatonin is a mitochondria-targeted antioxidant.", "It accumulates in mitochondria with high concentration against a concentration gradient.", "This is probably achieved by an active transportation via mitochondrial melatonin transporter(s).", "Melatonin protects mitochondria by scavenging reactive oxygen species (ROS), inhibiting the mitochondrial permeability transition pore (MPTP), and activating uncoupling proteins (UCPs).", "Thus, melatonin maintains the optimal mitochondrial membrane potential and preserves mitochondrial functions.", "In addition, mitochondrial biogenesis and dynamics is also regulated by melatonin.", "In most cases, melatonin reduces mitochondrial fission and elevates their fusion.", "Mitochondrial dynamics exhibit an oscillatory pattern which matches the melatonin circadian secretory rhythm in pinealeocytes and probably in other cells.", "Recently, melatonin has been found to promote mitophagy and improve homeostasis of mitochondria."], "structured": false}
{"doc_id": 14843502, "title": "Self-reported health status and access to health services in a sample of prisoners in Italy", "abstract": ["BACKGROUND Self-reported health status in underserved population of prisoners has not been extensively explored.", "The purposes of this cross-sectional study were to assess self-reported health, quality of life, and access to health services in a sample of male prisoners of Italy.   \n", "METHODS A total of 908 prisoners received a self-administered anonymous questionnaire pertaining on demographic and detention characteristics, self-reported health status and quality of life, access to health services, lifestyles, and participation to preventive, social, and rehabilitation programs.", "A total of 650 prisoners agreed to participate in the study and returned the questionnaire.   \n", "RESULTS Respectively, 31.6% and 43.5% of prisoners reported a poor perceived health status and a poor quality of life, and 60% admitted that their health was worsened or greatly worsened during the prison stay.", "Older age, lower education, psychiatric disorders, self-reported health problems on prison entry, and suicide attempts within prison were significantly associated with a perceived worse health status.", "At the time of the questionnaire delivery, 30% of the prisoners self-reported a health problem present on prison entry and 82% present at the time of the survey.", "Most frequently reported health problems included dental health problems, arthritis or joint pain, eye problems, gastrointestinal diseases, emotional problems, and high blood pressure.", "On average, prisoners encountered general practitioners six times during the previous year, and the frequency of medical encounters was significantly associated with older age, sentenced prisoners, psychiatric disorders, and self-reported health problems on prison entry.   \n", "CONCLUSIONS The findings suggest that prisoners have a perceived poor health status, specific care needs and health promotion programs are seldom offered.", "Programs for correction of risk behaviour and prevention of long-term effects of incarceration on prisoners' health are strongly needed."], "structured": true}
{"doc_id": 14848619, "title": "BH3-only Protein Noxa Is a Mediator of Hypoxic Cell Death Induced by Hypoxia-inducible Factor 1\u03b1", "abstract": ["Hypoxia is a common cause of cell death and is implicated in many disease processes including stroke and chronic degenerative disorders.", "In response to hypoxia, cells express a variety of genes, which allow adaptation to altered metabolic demands, decreased oxygen demands, and the removal of irreversibly damaged cells.", "Using polymerase chain reaction\u2013based suppression subtractive hybridization to find genes that are differentially expressed in hypoxia, we identified the BH3-only Bcl-2 family protein Noxa.", "Noxa is a candidate molecule mediating p53-induced apoptosis.", "We show that Noxa promoter responds directly to hypoxia via hypoxia-inducible factor (HIF)-1\u03b1.", "Suppression of Noxa expression by antisense oligonucleotides rescued cells from hypoxia-induced cell death and decreased infarction volumes in an animal model of ischemia.", "Further, we show that reactive oxygen species and resultant cytochrome c release participate in Noxa-mediated hypoxic cell death.", "Altogether, our results show that Noxa is induced by HIF-1\u03b1 and mediates hypoxic cell death."], "structured": false}
{"doc_id": 14853989, "title": "Neutrophil extracellular chromatin traps connect innate immune response to autoimmunity", "abstract": ["Autoantibodies to DNA and histones (chromatin) are the defining antigen specificity in systemic lupus erythematosus (SLE) and related musculoskeletal disorders but the mechanisms responsible for their induction remain mysterious.", "That situation rapidly changed once neutrophil extracellular chromatin traps (NETs) were discovered and observed to play a conserved role in innate immune responses to a broad variety of microbial pathogens.", "At the center of an infectious process, neutrophils exert various antimicrobial defenses, including the release of nuclear chromatin into the extracellular space.", "The externalized NETs, a complex meshwork of nuclear chromatin and antimicrobial proteins, serve to immobilize and degrade microbial pathogens.", "Here, we critically evaluate the evidence supporting NETs versus apoptotic bodies as a source for nuclear antigens in autoimmunity.", "We also discuss the possibility that NET chromatin forms an essential component of immune deposits in the pathogenesis of glomerulonephritis in SLE and other autoimmune immune complex diseases."], "structured": false}
{"doc_id": 14863011, "title": "Bcl2 Regulation by the Melanocyte Master Regulator Mitf Modulates Lineage Survival and Melanoma Cell Viability", "abstract": ["Kit/SCF signaling and Mitf-dependent transcription are both essential for melanocyte development and pigmentation.", "To identify Mitf-dependent Kit transcriptional targets in primary melanocytes, microarray studies were undertaken.", "Among identified targets was BCL2, whose germline deletion produces melanocyte loss and which exhibited phenotypic synergy with Mitf in mice.", "BCL2's regulation by Mitf was verified in melanocytes and melanoma cells and by chromatin immunoprecipitation of the BCL2 promoter.", "Mitf also regulates BCL2 in osteoclasts, and both Mitf(mi/mi) and Bcl2(-/-) mice exhibit severe osteopetrosis.", "Disruption of Mitf in melanocytes or melanoma triggered profound apoptosis susceptible to rescue by BCL2 overexpression.", "Clinically, primary human melanoma expression microarrays revealed tight nearest neighbor linkage for MITF and BCL2.", "This linkage helps explain the vital roles of both Mitf and Bcl2 in the melanocyte lineage and the well-known treatment resistance of melanoma."], "structured": false}
{"doc_id": 14864285, "title": "YOKO HONDA AND SHUJI HONDA 1", "abstract": ["Longevity is regulated by the daf-2 gene network in Caenorhabditis elegans.", "Mutations in the daf-2 gene, which encodes a member of the insulin receptor family, confer the life extension (Age) phenotype and the constitutive dauer (a growth-arrested larval form specialized for dispersal) formation phenotype.", "The Age phenotype is mutually potentiated by two life extension mutations in the daf-2 gene and the clk-1 gene, a homologue of yeast CAT5/COQ7 known to regulate ubiquinone biosynthesis.", "In this study, we demonstrated that the daf-2 mutation also conferred an oxidative stress resistance (Oxr) phenotype, which was also enhanced by the clk-1 mutation.", "Similar to the Age phenotype, the Oxr phenotype was regulated by the genetic pathway of insulin-like signaling from daf-2 to the daf-16 gene, a homologue of the HNF-3/forkhead transcription factor.", "These findings led us to examine whether the insulin-like signaling pathway regulates the gene expression of antioxidant defense enzymes.", "We found that the mRNA level of the sod-3 gene, which encodes Mn-superoxide dismutase (SOD), was much higher in daf-2 mutants than in the wild type.", "Moreover, the increased sod-3 gene expression phenotype is regulated by the insulin-like signaling pathway.", "Although the clk-1 mutant itself did not display Oxr and the increased sod-3 expression phenotypes, the clk-1 mutation enhanced them in the daf-2 mutant, suggesting that clk-1 is involved in longevity in two ways: clk-1 composes the original clk-1 longevity program and the daf-2 longevity program.", "These observations suggest that the daf-2 gene network controls longevity by regulating the Mn-SOD-associated antioxidant defense system.", "This system appears to play a role in efficient life maintenance at the dauer stage."], "structured": false}
{"doc_id": 14865329, "title": "Brown Fat and Browning for the Treatment of Obesity and Related Metabolic Disorders", "abstract": ["Brown fat is a specialized fat depot that can increase energy expenditure and produce heat.", "After the recent discovery of the presence of active brown fat in human adults and novel transcription factors controlling brown adipocyte differentiation, the field of the study of brown fat has gained great interest and is rapidly growing.", "Brown fat expansion and/or activation results in increased energy expenditure and a negative energy balance in mice and limits weight gain.", "Brown fat is also able to utilize blood glucose and lipid and results in improved glucose metabolism and blood lipid independent of weight loss.", "Prolonged cold exposure and beta adrenergic agonists can induce browning of white adipose tissue.", "The inducible brown adipocyte, beige adipocyte evolving by thermogenic activation of white adipose tissue have different origin and molecular signature from classical brown adipocytes but share the characteristics of high mitochondria content, UCP1 expression and thermogenic capacity when activated.", "Increasing browning may also be an efficient way to increase whole brown fat activity.", "Recent human studies have shown possibilities that findings in mice can be reproduced in human, making brown fat a good candidate organ to treat obesity and its related disorders."], "structured": false}
{"doc_id": 14874811, "title": "Hypoxia-induced energy stress regulates mRNA translation and cell growth.", "abstract": ["Oxygen (O2) deprivation, or hypoxia, has profound effects on cell metabolism and growth.", "Cells can adapt to low O2 in part through activation of hypoxia-inducible factor (HIF).", "We report here that hypoxia inhibits mRNA translation by suppressing multiple key regulators, including eIF2alpha, eEF2, and the mammalian target of rapamycin (mTOR) effectors 4EBP1, p70S6K, and rpS6, independent of HIF.", "Hypoxia results in energy starvation and activation of the AMPK/TSC2/Rheb/mTOR pathway.", "Hypoxic AMP-activated protein kinase (AMPK) activation also leads to eEF2 inhibition.", "Moreover, hypoxic effects on cellular bioenergetics and mTOR inhibition increase over time.", "Mutation of the TSC2 tumor suppressor gene confers a growth advantage to cells by repressing hypoxic mTOR inhibition and hypoxia-induced G1 arrest.", "Together, eIF2alpha, eEF2, and mTOR inhibition represent important HIF-independent mechanisms of energy conservation that promote survival under low O2 conditions."], "structured": false}
{"doc_id": 14893425, "title": "The dystonia-associated protein torsinA modulates synaptic vesicle recycling.", "abstract": ["The loss of a glutamic acid residue in the AAA-ATPase (ATPases associated with diverse cellular activities) torsinA is responsible for most cases of early onset autosomal dominant primary dystonia.", "In this study, we found that snapin, which binds SNAP-25 (synaptosome-associated protein of 25,000 Da) and enhances the association of the SNARE complex with synaptotagmin, is an interacting partner for both wild type and mutant torsinA. Snapin co-localized with endogenous torsinA on dense core granules in PC12 cells and was recruited to perinuclear inclusions containing mutant DeltaE-torsinA in neuroblastoma SH-SY5Y cells.", "In view of these observations, synaptic vesicle recycling was analyzed using the lipophilic dye FM1-43 and an antibody directed against an intravesicular epitope of synaptotagmin I. We found that overexpression of wild type torsinA negatively affects synaptic vesicle endocytosis.", "Conversely, overexpression of DeltaE-torsinA in neuroblastoma cells increases FM1-43 uptake.", "Knockdown of snapin and/or torsinA using small interfering RNAs had a similar inhibitory effect on the exo-endocytic process.", "In addition, down-regulation of torsinA causes the persistence of synaptotagmin I on the plasma membrane, which closely resembles the effect observed by the overexpression of the DeltaE-torsinA mutant.", "Altogether, these findings suggest that torsinA plays a role together with snapin in regulated exocytosis and that DeltaE-torsinA exerts its pathological effects through a loss of function mechanism.", "This may affect neuronal uptake of neurotransmitters, such as dopamine, playing a role in the development of dystonic movements."], "structured": false}
{"doc_id": 14893428, "title": "In vivo electroporation in the embryonic mouse central nervous system", "abstract": ["This protocol describes a basic method for in vivo electroporation in the nervous system of embryonic mice.", "Delivery of electric pulses following microinjection of DNA into the brain ventricle or the spinal cord central canal enables efficient transfection of genes into the nervous system.", "Transfection is facilitated by forceps-type electrodes, which hold the uterus and/or the yolk sac containing the embryo.", "More than ten embryos in a single pregnant mouse can be operated on within 30 min.", "More than 90% of operated embryos survive and more than 90% of these survivors express the transfected genes appropriately.", "Gene expression in neurons persists for a long time, even at postnatal stages, after electroporation.", "Thus, this method could be used to analyze roles of genes not only in embryonic development but also in higher order function of the nervous system, such as learning."], "structured": false}
{"doc_id": 14915566, "title": "Hierarchical phylogenetic models for analyzing multipartite sequence data.", "abstract": ["Debate exists over how to incorporate information from multipartite sequence data in phylogenetic analyses.", "Strict combined-data approaches argue for concatenation of all partitions and estimation of one evolutionary history, maximizing the explanatory power of the data.", "Consensus/independence approaches endorse a two-step procedure where partitions are analyzed independently and then a consensus is determined from the multiple results.", "Mixtures across the model space of a strict combined-data approach and a priori independent parameters are popular methods to integrate these methods.", "We propose an alternative middle ground by constructing a Bayesian hierarchical phylogenetic model.", "Our hierarchical framework enables researchers to pool information across data partitions to improve estimate precision in individual partitions while permitting estimation and testing of tendencies in across-partition quantities.", "Such across-partition quantities include the distribution from which individual topologies relating the sequences within a partition are drawn.", "We propose standard hierarchical priors on continuous evolutionary parameters across partitions, while the structure on topologies varies depending on the research problem.", "We illustrate our model with three examples.", "We first explore the evolutionary history of the guinea pig (Cavia porcellus) using alignments of 13 mitochondrial genes.", "The hierarchical model returns substantially more precise continuous parameter estimates than an independent parameter approach without losing the salient features of the data.", "Second, we analyze the frequency of horizontal gene transfer using 50 prokaryotic genes.", "We assume an unknown species-level topology and allow individual gene topologies to differ from this with a small estimable probability.", "Simultaneously inferring the species and individual gene topologies returns a transfer frequency of 17%.", "We also examine HIV sequences longitudinally sampled from HIV+ patients.", "We ask whether posttreatment development of CCR5 coreceptor virus represents concerted evolution from middisease CXCR4 virus or reemergence of initial infecting CCR5 virus.", "The hierarchical model pools partitions from multiple unrelated patients by assuming that the topology for each patient is drawn from a multinomial distribution with unknown probabilities.", "Preliminary results suggest evolution and not reemergence."], "structured": false}
{"doc_id": 14920021, "title": "Up-to-date catalogues of yeast protein complexes", "abstract": ["Gold standard datasets on protein complexes are key to inferring and validating protein-protein interactions.", "Despite much progress in characterizing protein complexes in the yeast Saccharomyces cerevisiae, numerous researchers still use as reference the manually curated complexes catalogued by the Munich Information Center of Protein Sequences database.", "Although this catalogue has served the community extremely well, it no longer reflects the current state of knowledge.", "Here, we report two catalogues of yeast protein complexes as results of systematic curation efforts.", "The first one, denoted as CYC2008, is a comprehensive catalogue of 408 manually curated heteromeric protein complexes reliably backed by small-scale experiments reported in the current literature.", "This catalogue represents an up-to-date reference set for biologists interested in discovering protein interactions and protein complexes.", "The second catalogue, denoted as YHTP2008, comprises 400 high-throughput complexes annotated with current literature evidence.", "Among them, 262 correspond, at least partially, to CYC2008 complexes.", "Evidence for interacting subunits is collected for 68 complexes that have only partial or no overlap with CYC2008 complexes, whereas no literature evidence was found for 100 complexes.", "Some of these partially supported and as yet unsupported complexes may be interesting candidates for experimental follow up.", "Both catalogues are freely available at: http://wodaklab.org/cyc2008/."], "structured": false}
{"doc_id": 14923462, "title": "Synergistic Mechanisms of DNA Demethylation during Transition to Ground-State Pluripotency", "abstract": ["Pluripotent stem cells (PSCs) occupy a spectrum of reversible molecular states ranging from a naive ground-state in 2i, to metastable embryonic stem cells (ESCs) in serum, to lineage-primed epiblast stem cells (EpiSCs).", "To investigate the role of DNA methylation (5mC) across distinct pluripotent states, we mapped genome-wide 5mC and 5-hydroxymethycytosine (5hmC) in multiple PSCs.", "Ground-state ESCs exhibit an altered distribution of 5mC and 5hmC at regulatory elements and dramatically lower absolute levels relative to ESCs in serum.", "By contrast, EpiSCs exhibit increased promoter 5mC coupled with reduced 5hmC, which contributes to their developmental restriction.", "Switch to 2i triggers rapid onset of both the ground-state gene expression program and global DNA demethylation.", "Mechanistically, repression of de novo methylases by PRDM14 drives DNA demethylation at slow kinetics, whereas TET1/TET2-mediated 5hmC conversion enhances both the rate and extent of hypomethylation.", "These processes thus act synergistically during transition to ground-state pluripotency to promote a robust hypomethylated state."], "structured": false}
{"doc_id": 14924526, "title": "Febrile seizures in the developing brain result in persistent modification of neuronal excitability in limbic circuits", "abstract": ["Febrile (fever-induced) seizures affect 3\u20135% of infants and young children.", "Despite the high incidence of febrile seizures, their contribution to the development of epilepsy later in life has remained controversial.", "Combining a new rat model of complex febrile seizures and patch clamp techniques, we determined that hyperthermia-induced seizures in the immature rat cause a selective presynaptic increase in inhibitory synaptic transmission in the hippocampus that lasts into adulthood.", "The long-lasting nature of these potent alterations in synaptic communication after febrile seizures does not support the prevalent view of the 'benign' nature of early-life febrile convulsions."], "structured": false}
{"doc_id": 14926162, "title": "Identification of an allele of VAM3/SYP22 that confers a semi-dwarf phenotype in Arabidopsis thaliana.", "abstract": ["The short stem and midrib (ssm) mutants of Arabidopsis thaliana show both semi-dwarf and wavy leaf phenotypes due to defects in the elongation of the stem internodes and leaves.", "Moreover, these abnormalities cannot be recovered by exogenous phytohormones.", "ssm was originally identified as a single recessive mutant of the ecotype Columbia (Col-0), but genetic crossing experiments have revealed that this mutant phenotype is restored by another gene that is functional in the ecotype Landsberg erecta (Ler) and not in Col-0.", "Map-based cloning of the gene that is defective in ssm mutants has uncovered a small deletion in the sixth intron of a gene encoding a syntaxin, VAM3/SYP22, which has been implicated in vesicle transport to the vacuole.", "This mutation appears to cause a peptide insertion in the deduced VAM3/SYP22 polypeptide sequence due to defective splicing of the shortened sixth intron.", "Significantly, when compared with the wild-type Ler genome, the wild-type Col-0 genome has a single base pair deletion causing a frameshift mutation in SYP23, a gene with the highest known homology to VAM3/SYP22.", "These findings suggest that VAM3/SYP22 and SYP23 have overlapping functions and that the vesicle transport mediated by these syntaxins is important for shoot morphogenesis."], "structured": false}
{"doc_id": 14934137, "title": "Class Ia MHC-deficient BALB/c mice generate CD8+ T cell-mediated protective immunity against Listeria monocytogenes infection.", "abstract": ["CD8(+) T cells are required for protective immunity against intracellular pathogens such as Listeria monocytogenes.", "In this study, we used class Ia MHC-deficient mice, which have a severe reduction in circulating CD8(+) T cells, to determine the protective capacity of class Ib MHC-restricted T cells during L. monocytogenes infection.", "The K(b-/-)D(b-/-) mutation was backcrossed onto a C.B10 (BALB/c congenic at H-2 locus with C57BL/10) background, because BALB/c mice are more susceptible to Listeria infection than other commonly studied mouse strains such as C57BL/6.", "C.B10 K(b-/-)D(b-/-) mice immunized with a sublethal dose of L. monocytogenes were fully protected against a subsequent lethal infection.", "Adoptive transfer of Listeria-immune splenocyte subsets into naive K(b-/-)D(b-/-) mice indicated that CD8(+) T cells were the major component of this protective immune response.", "A CD8(+) T cell line isolated from the spleen of a Listeria-infected class Ia MHC-deficient mouse was shown to specifically recognize Listeria-infected cells in vitro, as determined by IFN-gamma secretion and cytotoxicity assays.", "Adoptive transfer of this T cell line alone resulted in significant protection against L. monocytogenes challenge.", "These results suggest that even a limited number of class Ib MHC-restricted T cells are sufficient to generate the rapid recall response required for protection against secondary infection with L. monocytogenes."], "structured": false}
{"doc_id": 14938990, "title": "Upregulated PD-1 Expression Is Associated with the Development of Systemic Lupus Erythematosus, but Not the PD-1.1 Allele of the PDCD1 Gene", "abstract": ["Systemic lupus erythematosus (SLE) is a multisystem autoimmune disease with complicated genetic inheritance.", "Programmed death 1 (PD-1), a negative T cell regulator to maintain peripheral tolerance, induces negative signals to T cells during interaction with its ligands and is therefore a candidate gene in the development of SLE.", "In order to examine whether expression levels of PD-1 contribute to the pathogenesis of SLE, 30 patients with SLE and 30 controls were recruited and their PD-1 expression levels in peripheral blood mononuclear cells (PBMCs) were measured via flow cytometry and quantitative real-time-reverse transcription polymerase chain reaction (RT-PCR).", "Also, whether PD-1 expression levels are associated with the variant of the SNP rs36084323 and the SLE Disease Activity Index (SLEDAI) was studied in this work.", "The PD-1 expression levels of SLE patients were significantly increased compared with those of the healthy controls.", "The upregulated PD-1 expression levels in SLE patients were greatly associated with SLEDAI scores.", "No significant difference was found between PD-1 expression levels and SNP rs36084323.", "The results suggest that increased expression of PD-1 may correlate with the pathogenesis of SLE, upregulated PD-1 expression may be a biomarker for SLE diagnosis, and PD-1 inhibitor may be useful to SLE treatment."], "structured": false}
{"doc_id": 14965508, "title": "Endothelial cell membranes contain podocalyxin--the major sialoprotein of visceral glomerular epithelial cells", "abstract": ["Podocalyxin is the major sialoprotein in the glycocalyx of glomerular podocytes.", "Here we report on its extraglomerular localization, using a monospecific antibody which was obtained by affinity purification of IgG on nitrocellulose transfers of glomerular podocalyxin.", "By indirect immunofluorescence, podocalyxin was found in the blood vessels of several organs (lung, heart, kidney, small intestine, brain, pancreas, aorta, the periportal blood vessels in liver, and the central arteries of follicles of the spleen, but not in the endothelia that line the sinusoids of the latter organs).", "By immunoelectron microscopy--using immunogold conjugates in diffusion (\"pre-embedding\") and surface (\"postembedding\") procedures--podocalyxin was localized on the luminal membrane domain of endothelial cells, in a patchy distribution.", "The presence of podocalyxin was confirmed in SDS extracts of lung tissue by immunoblotting.", "We conclude that (a) podocalyxin is a widespread component of endothelial plasma membranes, (b) it is restricted to the luminal membrane domain, and (c) it is distributed unevenly on the endothelial cell surface."], "structured": false}
{"doc_id": 14972169, "title": "Teratogen-Induced Oxidative Stress Targets Glyceraldehyde-3-Phosphate Dehydrogenase in the Organogenesis Stage Mouse Embryo", "abstract": ["Exposure during the organogenesis stage of the mouse embryo to the model teratogen, hydroxyurea (HU), induces curly tail and limb malformations.", "Oxidative stress contributes to the developmental toxicity of HU.", "Reactive oxygen species (ROS) interact with polyunsaturated bilipid membranes to form \u03b1,\u03b2-unsaturated reactive aldehydes; 4-hydroxy-2-nonenal (4-HNE), one of the most cytotoxic of these aldehydes, covalently adducts with proteins, lipids, and nucleic acids.", "The goal of the current study is to determine if HU exposure of CD1 mice on gestation day 9 generates region-specific 4-HNE-protein adducts in the embryo and to identify the proteins targeted.", "The formation of 4-HNE-protein adducts was elevated in the caudal region of control embryos; HU exposure further increased 4-HNE-protein adduct formation in this area.", "Interestingly, three of the 4-HNE-modified proteins, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), glutamate oxaloacetate transaminase 2, and aldolase 1, A isoform, are involved in energy metabolism.", "The formation of 4-HNE-GAPDH protein adducts reduced GAPDH enzymatic activity by 20% and attenuated lactate production by 40%.", "Furthermore, HU exposure induced the nuclear translocation of GAPDH in the caudal region of exposed embryos; this nuclear translocation may be associated with the reactivation of oxidized proteins involved in DNA repair, such as apurinic/apyrimidinic endonuclease-1, and the stimulation of E1A-associated P300 protein/creb-binding protein (p300/CBP) activity, initiating cell death in a p53-dependent pathway.", "We propose that GAPDH is a redox-sensitive target in the embryo and may play a role in a stress response during development."], "structured": false}
{"doc_id": 14973286, "title": "Recurrent venous thromboembolism and bleeding complications during anticoagulant treatment in patients with cancer and venous thrombosis.", "abstract": ["A small proportion of patients with deep vein thrombosis develop recurrent venous thromboembolic complications or bleeding during anticoagulant treatment.", "These complications may occur more frequently if these patients have concomitant cancer.", "This prospective follow-up study sought to determine whether in thrombosis patients those with cancer have a higher risk for recurrent venous thromboembolism or bleeding during anticoagulant treatment than those without cancer.", "Of the 842 included patients, 181 had known cancer at entry.", "The 12-month cumulative incidence of recurrent thromboembolism in cancer patients was 20.7% (95% CI, 15.6%-25.8%) versus 6.8% (95% CI, 3.9%- 9.7%) in patients without cancer, for a hazard ratio of 3.2 (95% CI, 1.9-5.4) The 12-month cumulative incidence of major bleeding was 12.4% (95% CI, 6.5%-18.2%) in patients with cancer and 4.9% (95% CI, 2.5%-7.4%) in patients without cancer, for a hazard ratio of 2.2 (95% CI, 1.2-4.1).", "Recurrence and bleeding were both related to cancer severity and occurred predominantly during the first month of anticoagulant therapy but could not be explained by sub- or overanticoagulation.", "Cancer patients with venous thrombosis are more likely to develop recurrent thromboembolic complications and major bleeding during anticoagulant treatment than those without malignancy.", "These risks correlate with the extent of cancer.", "Possibilities for improvement using the current paradigms of anticoagulation seem limited and new treatment strategies should be developed."], "structured": false}
{"doc_id": 15040589, "title": "Fitting multilevel models in complex survey data with design weights: Recommendations", "abstract": ["BACKGROUND Multilevel models (MLM) offer complex survey data analysts a unique approach to understanding individual and contextual determinants of public health.", "However, little summarized guidance exists with regard to fitting MLM in complex survey data with design weights.", "Simulation work suggests that analysts should scale design weights using two methods and fit the MLM using unweighted and scaled-weighted data.", "This article examines the performance of scaled-weighted and unweighted analyses across a variety of MLM and software programs.   \n", "METHODS Using data from the 2005-2006 National Survey of Children with Special Health Care Needs (NS-CSHCN: n = 40,723) that collected data from children clustered within states, I examine the performance of scaling methods across outcome type (categorical vs. continuous), model type (level-1, level-2, or combined), and software (Mplus, MLwiN, and GLLAMM).   \n", "RESULTS Scaled weighted estimates and standard errors differed slightly from unweighted analyses, agreeing more with each other than with unweighted analyses.", "However, observed differences were minimal and did not lead to different inferential conclusions.", "Likewise, results demonstrated minimal differences across software programs, increasing confidence in results and inferential conclusions independent of software choice.   \n", "CONCLUSION If including design weights in MLM, analysts should scale the weights and use software that properly includes the scaled weights in the estimation."], "structured": true}
{"doc_id": 15041758, "title": "Functional outcomes of multi-condition collaborative care and successful ageing: results of randomised trial", "abstract": ["OBJECTIVE To evaluate the effectiveness of integrated care for chronic physical diseases and depression in reducing disability and improving quality of life.   \n", "DESIGN A randomised controlled trial of multi-condition collaborative care for depression and poorly controlled diabetes and/or risk factors for coronary heart disease compared with usual care among middle aged and elderly people   SETTING Fourteen primary care clinics in Seattle, Washington.   PARTICIPANTS Patients with diabetes or coronary heart disease, or both, and blood pressure above 140/90 mm Hg, low density lipoprotein concentration >3.37 mmol/L, or glycated haemoglobin 8.5% or higher, and PHQ-9 depression scores of \u2265 10.   \n", "INTERVENTION A 12 month intervention to improve depression, glycaemic control, blood pressure, and lipid control by integrating a \"treat to target\" programme for diabetes and risk factors for coronary heart disease with collaborative care for depression.", "The intervention combined self management support, monitoring of disease control, and pharmacotherapy to control depression, hyperglycaemia, hypertension, and hyperlipidaemia.   \n", "MAIN OUTCOME MEASURES Social role disability (Sheehan disability scale), global quality of life rating, and World Health Organization disability assessment schedule (WHODAS-2) scales to measure disabilities in activities of daily living (mobility, self care, household maintenance).   \n", "RESULTS Of 214 patients enrolled (106 intervention and 108 usual care), disability and quality of life measures were obtained for 97 intervention patients at six months (92%) and 92 at 12 months (87%), and for 96 usual care patients at six months (89%) and 92 at 12 months (85%).", "Improvements from baseline on the Sheehan disability scale (-0.9, 95% confidence interval -1.5 to -0.2; P = 0.006) and global quality of life rating (0.7, 0.2 to 1.2; P = 0.005) were significantly greater at six and 12 months in patients in the intervention group.", "There was a trend toward greater improvement in disabilities in activities of daily living (-1.5, -3.3 to 0.4; P = 0.10).   \n", "CONCLUSIONS Integrated care that covers chronic physical disease and comorbid depression can reduce social role disability and enhance global quality of life.", "Trial registration Clinical Trials NCT00468676."], "structured": true}
{"doc_id": 15048300, "title": "A Comparison of Cost Effectiveness Using Data from Randomized Trials or Actual Clinical Practice: Selective Cox-2 Inhibitors as an Example", "abstract": ["BACKGROUND Data on absolute risks of outcomes and patterns of drug use in cost-effectiveness analyses are often based on randomised clinical trials (RCTs).", "The objective of this study was to evaluate the external validity of published cost-effectiveness studies by comparing the data used in these studies (typically based on RCTs) to observational data from actual clinical practice.", "Selective Cox-2 inhibitors (coxibs) were used as an example.   \n", "METHODS AND FINDINGS The UK General Practice Research Database (GPRD) was used to estimate the exposure characteristics and individual probabilities of upper gastrointestinal (GI) events during current exposure to nonsteroidal anti-inflammatory drugs (NSAIDs) or coxibs.", "A basic cost-effectiveness model was developed evaluating two alternative strategies: prescription of a conventional NSAID or coxib.", "Outcomes included upper GI events as recorded in GPRD and hospitalisation for upper GI events recorded in the national registry of hospitalisations (Hospital Episode Statistics) linked to GPRD.", "Prescription costs were based on the prescribed number of tables as recorded in GPRD and the 2006 cost data from the British National Formulary.", "The study population included over 1 million patients prescribed conventional NSAIDs or coxibs.", "Only a minority of patients used the drugs long-term and daily (34.5% of conventional NSAIDs and 44.2% of coxibs), whereas coxib RCTs required daily use for at least 6-9 months.", "The mean cost of preventing one upper GI event as recorded in GPRD was US$104k (ranging from US$64k with long-term daily use to US$182k with intermittent use) and US$298k for hospitalizations.", "The mean costs (for GPRD events) over calendar time were US$58k during 1990-1993 and US$174k during 2002-2005.", "Using RCT data rather than GPRD data for event probabilities, the mean cost was US$16k with the VIGOR RCT and US$20k with the CLASS RCT.   \n", "CONCLUSIONS The published cost-effectiveness analyses of coxibs lacked external validity, did not represent patients in actual clinical practice, and should not have been used to inform prescribing policies.", "External validity should be an explicit requirement for cost-effectiveness analyses."], "structured": true}
{"doc_id": 15058155, "title": "7\u03b1, 25-dihydroxycholesterol-mediated activation of EBI2 in immune regulation and diseases", "abstract": ["EBI2, aka GPR183, is a G-couple receptor originally identified in 1993 as one of main genes induced in Burkitt's lymphoma cell line BL41 by Epstein-Barr virus (EBV) infection.", "After it was reported in 2009 that the receptor played a key role in regulating B cell migration and responses, we initiated an effort in looking for its endogenous ligand.", "In 2011 we and another group reported the identification of 7\u03b1, 25-dihydroxyxcholesterol (7\u03b1, 25-OHC), an oxysterol, as the likely physiological ligand of EBI2.", "A few subsequently published studies further elucidated how 7\u03b1, 25-OHC bound to EBI2, and how a gradient of 7\u03b1, 25-OHC could be generated in vivo and regulated migration, activation, and functions of B cells, T cells, dendritic cells (DCs), monocytes/macrophages, and astrocytes.", "The identification of 7\u03b1, 25-OHC as a G protein-coupled receptor ligand revealed a previously unknown signaling system of oxysterols, a class of molecules which exert profound biological functions.", "Dysregulation of the synthesis or functions of these molecules is believed to contribute to inflammation and autoimmune diseases, cardiovascular diseases, neurodegenerative diseases, cancer as well as metabolic diseases such as diabetes, obesity, and dyslipidemia.", "Therefore EBI2 may represent a promising target for therapeutic interventions for human diseases."], "structured": false}
{"doc_id": 15077696, "title": "PrimPol Bypasses UV Photoproducts during Eukaryotic Chromosomal DNA Replication", "abstract": ["DNA damage can stall the DNA replication machinery, leading to genomic instability.", "Thus, numerous mechanisms exist to complete genome duplication in the absence of a pristine DNA template, but identification of the enzymes involved remains incomplete.", "Here, we establish that Primase-Polymerase (PrimPol; CCDC111), an archaeal-eukaryotic primase (AEP) in eukaryotic cells, is involved in chromosomal DNA replication.", "PrimPol is required for replication fork progression on ultraviolet (UV) light-damaged DNA templates, possibly mediated by its ability to catalyze translesion synthesis (TLS) of these lesions.", "This PrimPol UV lesion bypass pathway is not epistatic with the Pol \u03b7-dependent pathway and, as a consequence, protects xeroderma pigmentosum variant (XP-V) patient cells from UV-induced cytotoxicity.", "In addition, we establish that PrimPol is also required for efficient replication fork progression during an unperturbed S phase.", "These and other findings indicate that PrimPol is an important player in replication fork progression in eukaryotic cells."], "structured": false}
{"doc_id": 15081770, "title": "The novel immunosuppressive enzyme IL4I1 is expressed by neoplastic cells of several B-cell lymphomas and by tumor-associated macrophages", "abstract": ["We previously reported a strong IL4I1 gene expression in primary mediastinal B-cell lymphoma (PMBL) and recently identified the protein as a secreted L-phenylalanine oxidase, physiologically expressed by myeloid cells, which inhibits T-cell proliferation in vitro.", "Here, we analyzed the pattern of IL4I1 protein expression in 315 human lymphoid and non-lymphoid malignancies.", "Besides PMBL, IL4I1 expression in tumors was very frequent.", "IL4I1 was detected in tumor-associated macrophages from most of the tumors and in neoplastic cells from follicular lymphoma, classic and nodular lymphocyte predominant Hodgkin lymphomas and small lymphocytic lymphoma, three of which are germinal center derived.", "IL4I1-positive tumor cells were also detected in rare cases of solid cancers, mainly mesothelioma.", "The enzymatic activity paralleled protein expression, suggesting that IL4I1 is functional in vivo.", "Depending on the tumor type, IL4I1 may impact on different infiltrating lymphocyte populations with consequences on tumor evolution.", "In the particular case of follicular lymphoma cells, which are susceptible to antitumor cytotoxic T cells killing but depend on interactions with local T helper cells for survival, a high level of IL4I1 expression seems associated with the absence of bone marrow involvement and a better outcome.", "These findings plead for an evaluation of IL4I1 as a prognosis factor."], "structured": false}
{"doc_id": 15113221, "title": "Poor prognosis in carcinoma is associated with a gene expression signature of aberrant PTEN tumor suppressor pathway activity.", "abstract": ["Pathway-specific therapy is the future of cancer management.", "The oncogenic phosphatidylinositol 3-kinase (PI3K) pathway is frequently activated in solid tumors; however, currently, no reliable test for PI3K pathway activation exists for human tumors.", "Taking advantage of the observation that loss of PTEN, the negative regulator of PI3K, results in robust activation of this pathway, we developed and validated a microarray gene expression signature for immunohistochemistry (IHC)-detectable PTEN loss in breast cancer (BC).", "The most significant signature gene was PTEN itself, indicating that PTEN mRNA levels are the primary determinant of PTEN protein levels in BC.", "Some PTEN IHC-positive BCs exhibited the signature of PTEN loss, which was associated to moderately reduced PTEN mRNA levels cooperating with specific types of PIK3CA mutations and/or amplification of HER2.", "This demonstrates that the signature is more sensitive than PTEN IHC for identifying tumors with pathway activation.", "In independent data sets of breast, prostate, and bladder carcinoma, prediction of pathway activity by the signature correlated significantly to poor patient outcome.", "Stathmin, encoded by the signature gene STMN1, was an accurate IHC marker of the signature and had prognostic significance in BC.", "Stathmin was also pathway-pharmacodynamic in vitro and in vivo.", "Thus, the signature or its components such as stathmin may be clinically useful tests for stratification of patients for anti-PI3K pathway therapy and monitoring therapeutic efficacy.", "This study indicates that aberrant PI3K pathway signaling is strongly associated with metastasis and poor survival across carcinoma types, highlighting the enormous potential impact on patient survival that pathway inhibition could achieve."], "structured": false}
{"doc_id": 15121114, "title": "Suppression of subtelomeric VSG switching by Trypanosoma brucei TRF requires its TTAGGG repeat-binding activity", "abstract": ["Trypanosoma brucei causes human African trypanosomiasis and regularly switches its major surface antigen, VSG, in the bloodstream of its mammalian host to evade the host immune response.", "VSGs are expressed exclusively from subtelomeric loci, and we have previously shown that telomere proteins TbTIF2 and TbRAP1 play important roles in VSG switching and VSG silencing regulation, respectively.", "We now discover that the telomere duplex DNA-binding factor, TbTRF, also plays a critical role in VSG switching regulation, as a transient depletion of TbTRF leads to significantly more VSG switching events.", "We solved the NMR structure of the DNA-binding Myb domain of TbTRF, which folds into a canonical helix-loop-helix structure that is conserved to the Myb domains of mammalian TRF proteins.", "The TbTRF Myb domain tolerates well the bulky J base in T. brucei telomere DNA, and the DNA-binding affinity of TbTRF is not affected by the presence of J both in vitro and in vivo.", "In addition, we find that point mutations in TbTRF Myb that significantly reduced its in vivo telomere DNA-binding affinity also led to significantly increased VSG switching frequencies, indicating that the telomere DNA-binding activity is critical for TbTRF's role in VSG switching regulation."], "structured": false}
{"doc_id": 15128866, "title": "CD4+ T cell-mediated cytotoxicity eliminates primary tumor cells in metastatic melanoma through high MHC class II expression and can be enhanced by inhibitory receptor blockade", "abstract": ["Metastatic melanoma is a rapidly progressing disease with high mortality rate and limited treatment options.", "Immunotherapy based on tumor-targeting cytotoxic T cell responses represents a promising strategy.", "To assist in its development, we examined the possibility and efficacy of using CD4+ cytotoxic T cells.", "The regulatory mechanisms controlling CD4+ T cell-mediated cytotoxicity were also investigated.", "We found that naturally occurring granzyme B and perforin-expressing CD4+ cytotoxic T cells can be recovered from metastatic melanoma patients at significantly elevated frequencies compared to those from healthy controls.", "These CD4+ cytotoxic T cells were also capable of killing autologous tumor cells harvested from metastatic melanoma, independent of CD8+ T cells or any other cell types.", "However, several restricting factors were observed.", "First, the cytolytic activity by CD4+ T cells required high MHC class II expression on melanoma cells, which was not satisfied in a subset of melanomas.", "Second, the granzyme B and perforin release by activated CD4+ cytotoxic T cells was reduced after coculturing with autologous melanoma cells, characterized by low LAMP-1 expression and low granzyme B and perforin secretion in the supernatant.", "This suggested that inhibitory mechanisms were present to suppress CD4+ cytotoxic T cells.", "Indeed, blockade of PD-1 and CTLA-4 had increased the cytolytic activity of CD4+ T cells but was only effective in MHC class II high but not MHC class II low melanomas.", "Together, our study showed that CD4+ T cell-mediated cytotoxicity could eliminate primary melanoma cells but the efficacy depended on MHC class II expression."], "structured": false}
{"doc_id": 15129362, "title": "The epidemiology and iatrogenic transmission of hepatitis C virus in Egypt: a Bayesian coalescent approach.", "abstract": ["Hepatitis C virus (HCV) is a leading cause of liver cancer and cirrhosis, and Egypt has possibly the highest HCV prevalence worldwide.", "In this article we use a newly developed Bayesian inference framework to estimate the transmission dynamics of HCV in Egypt from sampled viral gene sequences, and to predict the public health impact of the virus.", "Our results indicate that the effective number of HCV infections in Egypt underwent rapid exponential growth between 1930 and 1955.", "The timing and speed of this spread provides quantitative genetic evidence that the Egyptian HCV epidemic was initiated and propagated by extensive antischistosomiasis injection campaigns.", "Although our results show that HCV transmission has since decreased, we conclude that HCV is likely to remain prevalent in Egypt for several decades.", "Our combined population genetic and epidemiological analysis provides detailed estimates of historical changes in Egyptian HCV prevalence.", "Because our results are consistent with a demographic scenario specified a priori, they also provide an objective test of inference methods based on the coalescent process."], "structured": false}
{"doc_id": 15135001, "title": "Improving population representation through geographic health information systems: mapping the MURDOCK study.", "abstract": ["This paper highlights methods for using geospatial analysis to assess, enhance, and improve recruitment efforts to ensure representativeness in study populations.", "We apply these methods to the Measurement to Understand Reclassification of Disease of Cabarrus/Kannapolis (MURDOCK) study, a longitudinal population health study focused on the city of Kannapolis and Cabarrus County, NC.", "Although efforts have been made to recruit a participant registry that is representative of the 18 ZIP code catchment region inclusive of Cabarrus County and Kannapolis, bias in such recruitment is inevitable.", "Participants in the MURDOCK study are geospatially referenced at entry, providing information that can be used to monitor and guide recruitment efforts.", "MURDOCK participant population representativeness was assessed using chi-squared tests to compare the MURDOCK population with 2010 Census data, relative to both the entire 18 ZIP code catchment area and for individual Census tracts.", "A logistic regression model was fit to characterize Census tracts with low recruitment, defined by fewer than 56 participants from that tract.", "The distance to the site at which participants enrolled was calculated, and median distance to enrollment site was used in the logistic regression.", "Tracts with low recruitment rates contained higher minority and younger populations, suggesting specific strategies for improving recruitment in these areas.", "Areal units farther away from enrollment sites were also not well-sampled, despite being in the specified study area, indicating that distance traveled to enrollment may be a barrier.", "These results have implications for targeting recruitment efforts and representative samples more generally, including in other population-based studies."], "structured": false}
{"doc_id": 15153602, "title": "Haplotype-based variant detection from short-read sequencing", "abstract": ["The direct detection of haplotypes from short-read DNA sequencing data requires changes to existing small-variant detection methods.", "Here, we develop a Bayesian statistical framework which is capable of modeling multiallelic loci in sets of individuals with non-uniform copy number.", "We then describe our implementation of this framework in a haplotype-based variant detector, FreeBayes."], "structured": false}
{"doc_id": 15155862, "title": "Longitudinal Genome-Wide Association of Cardiovascular Disease Risk Factors in the Bogalusa Heart Study", "abstract": ["Cardiovascular disease (CVD) is the leading cause of death worldwide.", "Recent genome-wide association (GWA) studies have pinpointed many loci associated with CVD risk factors in adults.", "It is unclear, however, if these loci predict trait levels at all ages, if they are associated with how a trait develops over time, or if they could be used to screen individuals who are pre-symptomatic to provide the opportunity for preventive measures before disease onset.", "We completed a genome-wide association study on participants in the longitudinal Bogalusa Heart Study (BHS) and have characterized the association between genetic factors and the development of CVD risk factors from childhood to adulthood.", "We report 7 genome-wide significant associations involving CVD risk factors, two of which have been previously reported.", "Top regions were tested for replication in the Young Finns Study (YF) and two associations strongly replicated: rs247616 in CETP with HDL levels (combined P = 9.7 x 10(-24)), and rs445925 at APOE with LDL levels (combined P = 8.7 x 10(-19)).", "We show that SNPs previously identified in adult cross-sectional studies tend to show age-independent effects in the BHS with effect sizes consistent with previous reports.", "Previously identified variants were associated with adult trait levels above and beyond those seen in childhood; however, variants with time-dependent effects were also promising predictors.", "This is the first GWA study to evaluate the role of common genetic variants in the development of CVD risk factors in children as they advance through adulthood and highlights the utility of using longitudinal studies to identify genetic predictors of adult traits in children."], "structured": false}
{"doc_id": 15176526, "title": "Actin and serum response factor transduce physical cues from the microenvironment to regulate epidermal stem cell fate decisions", "abstract": ["Epidermal homeostasis depends on a balance between stem cell renewal and differentiation and is regulated by extrinsic signals from the extracellular matrix (ECM).", "A powerful approach to analysing the pathways involved is to engineer single-cell microenvironments in which individual variables are precisely and quantitatively controlled.", "Here, we employ micropatterned surfaces to identify the signalling pathways by which restricted ECM contact triggers human epidermal stem cells to initiate terminal differentiation.", "On small (20 \u03bcm diameter) circular islands, keratinocytes remained rounded, and differentiated at higher frequency than cells that could spread on large (50 \u03bcm diameter) islands.", "Differentiation did not depend on ECM composition or density.", "Rather, the actin cytoskeleton mediated shape-induced differentiation by regulating serum response factor (SRF) transcriptional activity.", "Knockdown of SRF or its co-factor MAL inhibited differentiation, whereas overexpression of MAL stimulated SRF activity and involucrin expression.", "SRF target genes FOS and JUNB were also required for differentiation: c-Fos mediated serum responsiveness, whereas JunB was regulated by actin and MAL.", "Our findings demonstrate how biophysical cues are transduced into transcriptional responses that determine epidermal cell fate."], "structured": false}
{"doc_id": 15194125, "title": "Reproducibility and automatic measurement of QT dispersion.", "abstract": ["This study investigated interobserver (two observers) and intrasubject (two measurements) reproducibility of QT dispersion from abnormal electrocardiograms in patients with previous myocardial infarction, and compared a user-interactive with an automatic measurement system.", "Standard 12-lead electrocardiograms, recorded at 25 mm.s-1, were randomly chosen from 70 patients following myocardial infarction.", "These were scanned into a personal computer, and specially designed software skeletonized and joined each image.", "The images were then available for user-interactive (mouse and computer screen), or automatic measurements using a specially designed algorithm.", "For all methods reproducibility of the RR interval was excellent (mean absolute errors 3-4 ms, relative errors 0.3-0.5%).", "Reproducibility of the mean QT interval was good; intrasubject error was 6 ms (relative error 1.4%), interobserver error was 7 ms (1.8%), and observers' vs automatic measurement errors were 10 and 11 ms (2.5, 2.8%).", "However QTc dispersion measurements had large errors for all methods; intrasubject error was 12 ms (17.3%), interobserver error was 15 ms (22.1%), and observers' vs automatic measurement were errors 30 and 28 ms (35.4, 31.9%).", "QT dispersion measurements rely on the most difficult to measure QT intervals, resulting in a problem of reproducibility.", "Any automatic system must not only recognize common T wave morphologies, but also these more difficult T waves, if it is to be useful for measuring QT dispersion.", "The poor reproducibility of QT dispersion limits its role as a useful clinical tool, particularly as a predictor of events."], "structured": false}
{"doc_id": 15215393, "title": "Inhibition of LSD1 sensitizes glioblastoma cells to histone deacetylase inhibitors.", "abstract": ["Glioblastoma multiforme (GBM) is a particularly aggressive brain tumor and remains a clinically devastating disease.", "Despite innovative therapies for the treatment of GBM, there has been no significant increase in patient survival over the past decade.", "Enzymes that control epigenetic alterations are of considerable interest as targets for cancer therapy because of their critical roles in cellular processes that lead to oncogenesis.", "Several inhibitors of histone deacetylases (HDACs) have been developed and tested in GBM with moderate success.", "We found that treatment of GBM cells with HDAC inhibitors caused the accumulation of histone methylation, a modification removed by the lysine specific demethylase 1 (LSD1).", "This led us to examine the effects of simultaneously inhibiting HDACs and LSD1 as a potential combination therapy.", "We evaluated induction of apoptosis in GBM cell lines after combined inhibition of LSD1 and HDACs.", "LSD1 was inhibited by targeted short hairpin RNA or pharmacological means and inhibition of HDACs was achieved by treatment with either vorinostat or PCI-24781.", "Caspase-dependent apoptosis was significantly increased (>2-fold) in LSD1-knockdown GBM cells treated with HDAC inhibitors.", "Moreover, pharmacologically inhibiting LSD1 with the monoamine oxidase inhibitor tranylcypromine, in combination with HDAC inhibitors, led to synergistic apoptotic cell death in GBM cells; this did not occur in normal human astrocytes.", "Taken together, these results indicate that LSD1 and HDACs cooperate to regulate key pathways of cell death in GBM cell lines but not in normal counterparts, and they validate the combined use of LSD1 and HDAC inhibitors as a therapeutic approach for GBM."], "structured": false}
{"doc_id": 15237660, "title": "Challenges for malaria elimination in Zanzibar: pyrethroid resistance in malaria vectors and poor performance of long-lasting insecticide nets", "abstract": ["BACKGROUND Long-lasting insecticide treated nets (LLINs) and indoor residual house spraying (IRS) are the main interventions for the control of malaria vectors in Zanzibar.", "The aim of the present study was to assess the susceptibility status of malaria vectors against the insecticides used for LLINs and IRS and to determine the durability and efficacy of LLINs on the island.   \n", "METHODS Mosquitoes were sampled from Pemba and Unguja islands in 2010-2011 for use in WHO susceptibility tests.", "One hundred and fifty LLINs were collected from households on Unguja, their physical state was recorded and then tested for efficacy as well as total insecticide content.   \n", "RESULTS Species identification revealed that over 90% of the Anopheles gambiae complex was An.", "arabiensis with a small number of An.", "gambiae s.s. and An.", "merus being present.", "Susceptibility tests showed that An.", "arabiensis on Pemba was resistant to the pyrethroids used for LLINs and IRS.", "Mosquitoes from Unguja Island, however, were fully susceptible to all pyrethroids tested.", "A physical examination of 150 LLINs showed that two thirds were damaged after only three years in use.", "All used nets had a significantly lower (p < 0.001) mean permethrin concentration of 791.6 mg/m2 compared with 944.2 mg/m2 for new ones.", "Their efficacy decreased significantly against both susceptible An.", "gambiae s.s.", "colony mosquitoes and wild-type mosquitoes from Pemba after just six washes (p < 0.001).   \n", "CONCLUSION The sustainability of the gains achieved in malaria control in Zanzibar is seriously threatened by the resistance of malaria vectors to pyrethroids and the short-lived efficacy of LLINs.", "This study has revealed that even in relatively well-resourced and logistically manageable places like Zanzibar, malaria elimination is going to be difficult to achieve with the current control measures."], "structured": true}
{"doc_id": 15248287, "title": "Proliferating cell nuclear antigen acts as a cytoplasmic platform controlling human neutrophil survival", "abstract": ["Neutrophil apoptosis is a highly regulated process essential for inflammation resolution, the molecular mechanisms of which are only partially elucidated.", "In this study, we describe a survival pathway controlled by proliferating cell nuclear antigen (PCNA), a nuclear factor involved in DNA replication and repairing of proliferating cells.", "We show that mature neutrophils, despite their inability to proliferate, express high levels of PCNA exclusively in their cytosol and constitutively associated with procaspases, presumably to prevent their activation.", "Notably, cytosolic PCNA abundance decreased during apoptosis, and increased during in vitro and in vivo exposure to the survival factor granulocyte colony-stimulating factor (G-CSF).", "Peptides derived from the cyclin-dependent kinase inhibitor p21, which compete with procaspases to bind PCNA, triggered neutrophil apoptosis thus demonstrating that specific modification of PCNA protein interactions affects neutrophil survival.", "Furthermore, PCNA overexpression rendered neutrophil-differentiated PLB985 myeloid cells significantly more resistant to TNF-related apoptosis-inducing ligand- or gliotoxin-induced apoptosis.", "Conversely, a decrease in PCNA expression after PCNA small interfering RNA transfection sensitized these cells to apoptosis.", "Finally, a mutation in the PCNA interdomain-connecting loop, the binding site for many partners, significantly decreased the PCNA-mediated antiapoptotic effect.", "These results identify PCNA as a regulator of neutrophil lifespan, thereby highlighting a novel target to potentially modulate pathological inflammation."], "structured": false}
{"doc_id": 15274349, "title": "Development of the Human Infant Intestinal Microbiota", "abstract": ["Almost immediately after a human being is born, so too is a new microbial ecosystem, one that resides in that person's gastrointestinal tract.", "Although it is a universal and integral part of human biology, the temporal progression of this process, the sources of the microbes that make up the ecosystem, how and why it varies from one infant to another, and how the composition of this ecosystem influences human physiology, development, and disease are still poorly understood.", "As a step toward systematically investigating these questions, we designed a microarray to detect and quantitate the small subunit ribosomal RNA (SSU rRNA) gene sequences of most currently recognized species and taxonomic groups of bacteria.", "We used this microarray, along with sequencing of cloned libraries of PCR-amplified SSU rDNA, to profile the microbial communities in an average of 26 stool samples each from 14 healthy, full-term human infants, including a pair of dizygotic twins, beginning with the first stool after birth and continuing at defined intervals throughout the first year of life.", "To investigate possible origins of the infant microbiota, we also profiled vaginal and milk samples from most of the mothers, and stool samples from all of the mothers, most of the fathers, and two siblings.", "The composition and temporal patterns of the microbial communities varied widely from baby to baby.", "Despite considerable temporal variation, the distinct features of each baby's microbial community were recognizable for intervals of weeks to months.", "The strikingly parallel temporal patterns of the twins suggested that incidental environmental exposures play a major role in determining the distinctive characteristics of the microbial community in each baby.", "By the end of the first year of life, the idiosyncratic microbial ecosystems in each baby, although still distinct, had converged toward a profile characteristic of the adult gastrointestinal tract."], "structured": false}
{"doc_id": 15282056, "title": "Combinatorial modulation of galP and glk gene expression for improved alternative glucose utilization", "abstract": ["Phosphoenolpyruvate (PEP) is an important precursor for anaerobic production of succinate and malate.", "Although inactivating PEP/carbohydrate phosphotransferase systems (PTS) could increase PEP supply, the resulting strain had a low glucose utilization rate.", "In order to improve anaerobic glucose utilization rate for efficient production of succinate and malate, combinatorial modulation of galactose permease (galP) and glucokinase (glk) gene expression was carried out in chromosome of an Escherichia coli strain with inactivated PTS.", "Libraries of artificial regulatory parts, including promoter and messenger RNA stabilizing region (mRS), were firstly constructed in front of \u03b2-galactosidase gene (lacZ) in E. coli chromosome through \u03bb-Red recombination.", "Most regulatory parts selected from mRS library had constitutive strengths under different cultivation conditions.", "A convenient one-step recombination method was then used to modulate galP and glk gene expression with different regulatory parts.", "Glucose utilization rates of strains modulated with either galP or glk all increased, and the rates had a positive relation with expression strength of both genes.", "Combinatorial modulation had a synergistic effect on glucose utilization rate.", "The highest rate (1.64 g/L h) was tenfold higher than PTS\u2212 strain and 39% higher than the wild-type E. coli.", "These modulated strains could be used for efficient anaerobic production of succinate and malate."], "structured": false}
{"doc_id": 15286783, "title": "Matrix eQTL: Ultra fast eQTL analysis via large matrix operations", "abstract": ["Expression quantitative trait loci (eQTL) mapping aims to determine genomic regions that regulate gene transcription.", "Expression QTL is used to study the regulatory structure of normal tissues and to search for genetic factors in complex diseases such as cancer, diabetes, and cystic fibrosis.", "A modern eQTL dataset contains millions of SNPs and thousands of transcripts measured for hundreds of samples.", "This makes the analysis computationally complex as it involves independent testing for association for every transcript-SNP pair.", "The heavy computational burden makes eQTL analysis less popular, often forces analysts to restrict their attention to just a subset of transcripts and SNPs.", "As larger genotype and gene expression datasets become available, the demand for fast tools for eQTL analysis increases.", "We present a new method for fast eQTL analysis via linear models, called Matrix eQTL.", "Matrix eQTL can model and test for association using both linear regression and ANOVA models.", "The models can include covariates to account for such factors as population structure, gender, and clinical variables.", "It also supports testing of heteroscedastic models and models with correlated errors.", "In our experiment on large datasets Matrix eQTL was thousands of times faster than the existing popular software for QTL/eQTL analysis.", "Matrix eQTL is implemented as both Matlab and R packages and thus can easily be run on Windows, Mac OS, and Linux systems.", "The software is freely available at the following address: http://www.bios.unc.edu/research/genomic_software/Matrix_eQTL"], "structured": false}
{"doc_id": 15305881, "title": "The structure of DdrB from Deinococcus: a new fold for single-stranded DNA binding proteins", "abstract": ["Deinococcus spp. are renowned for their amazing ability to recover rapidly from severe genomic fragmentation as a result of exposure to extreme levels of ionizing radiation or desiccation.", "Despite having been originally characterized over 50 years ago, the mechanism underlying this remarkable repair process is still poorly understood.", "Here, we report the 2.8 A structure of DdrB, a single-stranded DNA (ssDNA) binding protein unique to Deinococcus spp.", "that is crucial for recovery following DNA damage.", "DdrB forms a pentameric ring capable of binding single-stranded but not double-stranded DNA.", "Unexpectedly, the crystal structure reveals that DdrB comprises a novel fold that is structurally and topologically distinct from all other single-stranded binding (SSB) proteins characterized to date.", "The need for a unique ssDNA binding function in response to severe damage, suggests a distinct role for DdrB which may encompass not only standard SSB protein function in protection of ssDNA, but also more specialized roles in protein recruitment or DNA architecture maintenance.", "Possible mechanisms of DdrB action in damage recovery are discussed."], "structured": false}
{"doc_id": 15319019, "title": "N348I in the Connection Domain of HIV-1 Reverse Transcriptase Confers Zidovudine and Nevirapine Resistance", "abstract": ["Background The catalytically active 66-kDa subunit of the human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) consists of DNA polymerase, connection, and ribonuclease H (RNase H) domains.", "Almost all known RT inhibitor resistance mutations identified to date map to the polymerase domain of the enzyme.", "However, the connection and RNase H domains are not routinely analysed in clinical samples and none of the genotyping assays available for patient management sequence the entire RT coding region.", "The British Columbia Centre for Excellence in HIV/AIDS (the Centre) genotypes clinical isolates up to codon 400 in RT, and our retrospective statistical analyses of the Centre\u2019s database have identified an N348I mutation in the RT connection domain in treatment-experienced individuals.", "The objective of this multidisciplinary study was to establish the in vivo relevance of this mutation and its role in drug resistance.", "Methods and Findings The prevalence of N348I in clinical isolates, the time taken for it to emerge under selective drug pressure, and its association with changes in viral load, specific drug treatment, and known drug resistance mutations was analysed from genotypes, viral loads, and treatment histories from the Centre\u2019s database.", "N348I increased in prevalence from below 1% in 368 treatmentnao \u00a8ve individuals to 12.1% in 1,009 treatment-experienced patients (p \u00bc 7.7 3 10 \ufffd 12 ).", "N348I appeared early in therapy and was highly associated with thymidine analogue mutations (TAMs) M41L and T215Y/F (p , 0.001), the lamivudine resistance mutations M184V/I (p , 0.001), and non-nucleoside RTI (NNRTI) resistance mutations K103N and Y181C/I (p , 0.001).", "The association with TAMs and NNRTI resistance mutations was consistent with the selection of N348I in patients treated with regimens that included both zidovudine and nevirapine (odds ratio 2.62, 95% confidence interval 1.43\u20134.81).", "The appearance of N348I was associated with a significant increase in viral load (p , 0.001), which was as large as the viral load increases observed for any of the TAMs.", "However, this analysis did not account for the simultaneous selection of other RT or protease inhibitor resistance mutations on viral load.", "To delineate the role of this mutation in RT inhibitor resistance, N348I was introduced into HIV-1 molecular clones containing different genetic backbones.", "N348I decreased zidovudine susceptibility 2- to 4-fold in the context of wildtype HIV-1 or when combined with TAMs.", "N348I also decreased susceptibility to nevirapine (7.4fold) and efavirenz (2.5-fold) and significantly potentiated resistance to these drugs when combined with K103N.", "Biochemical analyses of recombinant RT containing N348I provide supporting evidence for the role of this mutation in zidovudine and NNRTI resistance and give some insight into the molecular mechanism of resistance.", "Conclusions"], "structured": false}
{"doc_id": 15322518, "title": "Dual Targeting of PDGFR\u03b1 and FGFR1 Displays Synergistic Efficacy in Malignant Rhabdoid Tumors", "abstract": ["Subunits of the SWI/SNF chromatin remodeling complex are mutated in a significant proportion of human cancers.", "Malignant rhabdoid tumors (MRTs) are lethal pediatric cancers characterized by a deficiency in the SWI/SNF subunit SMARCB1.", "Here, we employ an integrated molecular profiling and chemical biology approach to demonstrate that the receptor tyrosine kinases (RTKs) PDGFR\u03b1 and FGFR1 are coactivated in MRT cells and that dual blockade of these receptors has synergistic efficacy.", "Inhibitor combinations targeting both receptors and the dual inhibitor ponatinib suppress the AKT and ERK1/2 pathways leading to apoptosis.", "MRT cells that have acquired resistance to the PDGFR\u03b1 inhibitor pazopanib are susceptible to FGFR inhibitors.", "We show that PDGFR\u03b1 levels are regulated by SMARCB1 expression, and assessment of clinical specimens documents the expression of both PDGFR\u03b1 and FGFR1 in rhabdoid tumor patients.", "Our findings support a therapeutic approach in cancers with SWI/SNF deficiencies by exploiting RTK coactivation dependencies."], "structured": false}
{"doc_id": 15327601, "title": "A nano-positioning system for macromolecular structural analysis", "abstract": ["Very often, the positions of flexible domains within macromolecules as well as within macromolecular complexes cannot be determined by standard structural biology methods.", "To overcome this problem, we developed a method that uses probabilistic data analysis to combine single-molecule measurements with X-ray crystallography data.", "The method determines not only the most likely position of a fluorescent dye molecule attached to the domain but also the complete three-dimensional probability distribution depicting the experimental uncertainty.", "With this approach, single-pair fluorescence resonance energy transfer measurements can now be used as a quantitative tool for investigating the position and dynamics of flexible domains within macromolecular complexes.", "We applied this method to find the position of the 5\u2032 end of the nascent RNA exiting transcription elongation complexes of yeast (Saccharomyces cerevisiae) RNA polymerase II and studied the influence of transcription factor IIB on the position of the RNA."], "structured": false}
{"doc_id": 15335331, "title": "Tumor-associated macrophages correlate with the clinicopathological features and poor outcomes via inducing epithelial to mesenchymal transition in oral squamous cell carcinoma", "abstract": ["BACKGROUND Both tumor-associated macrophages (TAMs) and the epithelial to mesenchymal transition (EMT) of cancer cells play key roles in promoting tumor progression.", "However, whether TAMs could induce EMT in the progression of oral squamous cell carcinoma (OSCC) remains undefined.   \n", "RESULTS Here we detected the expression of macrophages markers CD68 and CD163, epithelial marker E-cadherin and mesenchymal marker vimentin in 127 OSCC patients by using semi-quantitative immunohistochemistry.", "CD68 and CD163 expression was not confined to the infiltrating TAMs, but also detected in cancer cells.", "The high number of CD68-positive macrophages was correlated with poor overall survival.", "Meanwhile, the expression of CD163 both in macrophages and in cancer cells was associated with poor overall survival and had a significant prognostic impact in OSCC.", "Importantly, the expression of CD163 in cancer cells had a significant relationship with E-cadherin and vimentin.", "Furthermore, the incubation of TAMs conditioned medium resulted in a fibroblast-like appearance of cancer cells (HN4, HN6 and SCC9) together with the decreased/increased expression of E-cadherin/ vimentin, which were correlated with the enhanced ability of migration and invasion.   \n", "CONCLUSIONS Our results indicate that TAMs could promote the EMT of cancer cells, thereby leading to the progression of oral cancer."], "structured": true}
{"doc_id": 15337254, "title": "Geometric cues for directing the differentiation of mesenchymal stem cells.", "abstract": ["Significant efforts have been directed to understanding the factors that influence the lineage commitment of stem cells.", "This paper demonstrates that cell shape, independent of soluble factors, has a strong influence on the differentiation of human mesenchymal stem cells (MSCs) from bone marrow.", "When exposed to competing soluble differentiation signals, cells cultured in rectangles with increasing aspect ratio and in shapes with pentagonal symmetry but with different subcellular curvature-and with each occupying the same area-display different adipogenesis and osteogenesis profiles.", "The results reveal that geometric features that increase actomyosin contractility promote osteogenesis and are consistent with in vivo characteristics of the microenvironment of the differentiated cells.", "Cytoskeletal-disrupting pharmacological agents modulate shape-based trends in lineage commitment verifying the critical role of focal adhesion and myosin-generated contractility during differentiation.", "Microarray analysis and pathway inhibition studies suggest that contractile cells promote osteogenesis by enhancing c-Jun N-terminal kinase (JNK) and extracellular related kinase (ERK1/2) activation in conjunction with elevated wingless-type (Wnt) signaling.", "Taken together, this work points to the role that geometric shape cues can play in orchestrating the mechanochemical signals and paracrine/autocrine factors that can direct MSCs to appropriate fates."], "structured": false}
{"doc_id": 15347087, "title": "Amyloid accumulation is a late event in sporadic Alzheimer's disease-like pathology in nontransgenic rats", "abstract": ["The amyloid cascade hypothesis posits that deposition of the amyloid \u03b2 (A\u03b2) peptide in the brain is a key event in the initiation of Alzheimer's disease (AD).", "Nonetheless, it now seems increasingly unlikely that amyloid toxicity is the cause of sporadic AD, which leads to cognitive decline.", "Here, using accelerated-senescence nontransgenic OXYS rats, we confirmed that aggregation of A\u03b2 is a later event in AD-like pathology.", "We showed that an age-dependent increase in the levels of A\u03b2\u2081\u208b\u2084\u2082 and extracellular A\u03b2 deposits in the brain of OXYS rats occur later than do synaptic losses, neuronal cell death, mitochondrial structural abnormalities, and hyperphosphorylation of the tau protein.", "We identified the variants of the genes that are strongly associated with the risk of either late-onset or early-onset AD, including App, Apoe4, Bace1, Psen1, Psen2, and Picalm.", "We found that in OXYS rats nonsynonymous SNPs were located only in the genes Casp3 and Sorl1.", "Thus, we present proof that OXYS rats may be a model of sporadic AD.", "It is possible that multiple age-associated pathological processes may precede the toxic amyloid accumulation, which in turn triggers the final stage of the sporadic form of AD and becomes a hallmark event of the disease."], "structured": false}
{"doc_id": 15360986, "title": "Estimating low-density lipoprotein cholesterol by the Friedewald equation is adequate for classifying patients on the basis of nationally recommended cutpoints.", "abstract": ["We compared low-density lipoprotein cholesterol (LDL) values obtained by the Friedewald formula--i.e., total cholesterol minus high-density lipoprotein (HDL) cholesterol minus very-low-density lipoprotein (VLDL) cholesterol (estimated as triglyceride divided by 5)--with those obtained by lipoprotein fractionation, using 4736 specimens.", "When triglycerides were less than 2.0 g/L, greater than 90% of estimated LDL cholesterol values were acceptable, within +/-", "10% of measured values.", "At triglyceride concentrations of 2.0-4.0 g/L and 4.0-6.0 g/L, only 72% and 39%, respectively, of the estimates were acceptable.", "LDL values derived from an alternative formula, estimating VLDL as triglycerides divided by 6, were even less accurate.", "Nevertheless, the use of estimated LDL for risk classification based on the National Cholesterol Education Program Adult Treatment Panel cutpoints of 1.30 and 1.60 g/L was considered acceptable.", "At triglyceride concentrations less than or equal to 5.0 g/L, 88% of classifications based on estimated LDL (using triglycerides divided by 5) were concordant with those by measured LDL.", "Eleven percent of classifications were shifted across one cutpoint, evenly distributed between high and low.", "Fewer than 1% of classifications, all with Type III hyperlipoproteinemia, were misclassified two cutpoints high.", "Refinements in the estimation model did not substantially improve LDL estimation or concordance of risk classification."], "structured": false}
{"doc_id": 15365719, "title": "Conditional Kif3a ablation causes abnormal hedgehog signaling topography, growth plate dysfunction, and excessive bone and cartilage formation during mouse skeletogenesis.", "abstract": ["The motor protein Kif3a and primary cilia regulate important developmental processes, but their roles in skeletogenesis remain ill-defined.", "Here we created mice deficient in Kif3a in cartilage and focused on the cranial base and synchondroses.", "Kif3a deficiency caused cranial base growth retardation and dysmorphogenesis, which were evident in neonatal animals by anatomical and micro-computed tomography (microCT) inspection.", "Kif3a deficiency also changed synchondrosis growth plate organization and function, and the severity of these changes increased over time.", "By postnatal day (P)7, mutant growth plates lacked typical zones of chondrocyte proliferation and hypertrophy, and were instead composed of chondrocytes with an unusual phenotype characterized by strong collagen II (Col2a1) gene expression but barely detectable expression of Indian hedgehog (Ihh), collagen X (Col10a1), Vegf (Vegfa), MMP-13 (Mmp13) and osterix (Sp7).", "Concurrently, unexpected developmental events occurred in perichondrial tissues, including excessive intramembranous ossification all along the perichondrial border and the formation of ectopic cartilage masses.", "Looking for possible culprits for these latter processes, we analyzed hedgehog signalling topography and intensity by monitoring the expression of the hedgehog effectors Patched 1 and Gli1, and of the hedgehog-binding cell-surface component syndecan 3.", "Compared with controls, hedgehog signaling was quite feeble within mutant growth plates as early as P0, but was actually higher and was widespread all along mutant perichondrial tissues.", "Lastly, we studied postnatal mice deficient in Ihh in cartilage; their cranial base defects only minimally resembled those in Kif3a-deficient mice.", "In summary, Kif3a and primary cilia make unique contributions to cranial base development and synchondrosis growth plate function.", "Their deficiency causes abnormal topography of hedgehog signaling, growth plate dysfunction, and un-physiologic responses and processes in perichondrial tissues, including ectopic cartilage formation and excessive intramembranous ossification."], "structured": false}
{"doc_id": 15381976, "title": "Morin Attenuates Ovalbumin-Induced Airway Inflammation by Modulating Oxidative Stress-Responsive MAPK Signaling.", "abstract": ["Asthma is one of the most common inflammatory diseases characterized by airway hyperresponsiveness, inflammation, and remodeling.", "Morin, an active ingredient obtained from Moraceae plants, has been demonstrated to have promising anti-inflammatory activities in a range of disorders.", "However, its impacts on pulmonary diseases, particularly on asthma, have not been clarified.", "This study was designed to investigate whether morin alleviates airway inflammation in chronic asthma with an emphasis on oxidative stress modulation.", "In vivo, ovalbumin- (OVA-) sensitized mice were administered with morin or dexamethasone before challenge.", "Bronchoalveolar lavage fluid (BALF) and lung tissues were obtained to perform cell counts, histological analysis, and enzyme-linked immunosorbent assay.", "In vitro, human bronchial epithelial cells (BECs) were challenged by tumor necrosis factor alpha (TNF-\u03b1).", "The supernatant was collected for the detection of the proinflammatory proteins, and the cells were collected for reactive oxygen species (ROS)/mitogen-activated protein kinase (MAPK) evaluations.", "Severe inflammatory responses and remodeling were observed in the airways of the OVA-sensitized mice.", "Treatment with morin dramatically attenuated the extensive trafficking of inflammatory cells into the BALF and inhibited their infiltration around the respiratory tracts and vessels.", "Morin administration also significantly suppressed goblet cell hyperplasia and collagen deposition/fibrosis and dose-dependently inhibited the OVA-induced increases in IgE, TNF-\u03b1, interleukin- (IL-) 4, IL-13, matrix metalloproteinase-9, and malondialdehyde.", "In human BECs challenged by TNF-\u03b1, the levels of proteins such as eotaxin-1, monocyte chemoattractant protein-1, IL-8 and intercellular adhesion molecule-1, were consistently significantly decreased by morin.", "Western blotting and the 2',7'-dichlorofluorescein assay revealed that the increases in intracellular ROS and MAPK phosphorylation were abolished by morin, implying that ROS/MAPK signaling contributes to the relief of airway inflammation.", "Our findings indicate for the first time that morin alleviates airway inflammation in chronic asthma, which probably occurs via the oxidative stress-responsive MAPK pathway, highlighting a novel profile of morin as a potent agent for asthma management."], "structured": false}
{"doc_id": 15405204, "title": "Spontaneous autoimmunity prevented by thymic expression of a single self-antigen", "abstract": ["The expression of self-antigen in the thymus is believed to be responsible for the deletion of autoreactive T lymphocytes, a critical process in the maintenance of unresponsiveness to self.", "The Autoimmune regulator (Aire) gene, which is defective in the disorder autoimmune polyglandular syndrome type 1, has been shown to promote the thymic expression of self-antigens.", "A clear link, however, between specific thymic self-antigens and a single autoimmune phenotype in this model has been lacking.", "We show that autoimmune eye disease in aire-deficient mice develops as a result of loss of thymic expression of a single eye antigen, interphotoreceptor retinoid-binding protein (IRBP).", "In addition, lack of IRBP expression solely in the thymus, even in the presence of aire expression, is sufficient to trigger spontaneous eye-specific autoimmunity.", "These results suggest that failure of thymic expression of selective single self-antigens can be sufficient to cause organ-specific autoimmune disease, even in otherwise self-tolerant individuals."], "structured": false}
{"doc_id": 15414628, "title": "Preventing bacterial DNA release and absent in melanoma 2 inflammasome activation by a Legionella effector functioning in membrane trafficking.", "abstract": ["Legionella pneumophila, the causative agent of Legionnaires' pneumonia, resides in a distinct vacuole structure called Legionella-containing vacuole (LCV).", "The LCV resists fusion with the lysosome and permits efficient bacterial replication in host macrophages, which requires a Dot/Icm type IVB secretion system.", "Dot/Icm-translocated effector SdhA is critical for L. pneumophila intracellular growth and functions to prevent host cell death.", "Here, we show that the absence of SdhA resulted in elevated caspase-1 activation and IL-1\u03b2 secretion as well as macrophage pyroptosis during Legionella infection.", "These inflammasome activation phenotypes were independent of the established flagellin-NAIP5-NLRC4 axis, but relied on the DNA-sensing AIM2 inflammasome.", "We further demonstrate that Legionella DNA was released into macrophage cytosol, and this effect was significantly exaggerated by the absence of SdhA. SdhA bears a functional Golgi-targeting GRIP domain that is required for preventing AIM2 inflammasome activation.", "Ectopically expressed SdhA formed a unique ring-shape membrane structure, further indicating a role in membrane trafficking and maintaining LCV membrane integrity.", "Our data together suggest a possible link, mediated by the function of SdhA, between LCV trafficking/maturation and suppression of host innate immune detection."], "structured": false}
{"doc_id": 15419873, "title": "Cytosolic viral sensor RIG-I is a 5'-triphosphate-dependent translocase on double-stranded RNA.", "abstract": ["Retinoic acid inducible-gene I (RIG-I) is a cytosolic multidomain protein that detects viral RNA and elicits an antiviral immune response.", "Two N-terminal caspase activation and recruitment domains (CARDs) transmit the signal, and the regulatory domain prevents signaling in the absence of viral RNA.", "5'-triphosphate and double-stranded RNA (dsRNA) are two molecular patterns that enable RIG-I to discriminate pathogenic from self-RNA.", "However, the function of the DExH box helicase domain that is also required for activity is less clear.", "Using single-molecule protein-induced fluorescence enhancement, we discovered a robust adenosine 5'-triphosphate-powered dsRNA translocation activity of RIG-I. The CARDs dramatically suppress translocation in the absence of 5'-triphosphate, and the activation by 5'-triphosphate triggers RIG-I to translocate preferentially on dsRNA in cis.", "This functional integration of two RNA molecular patterns may provide a means to specifically sense and counteract replicating viruses."], "structured": false}
{"doc_id": 15425958, "title": "Human Cytomegalovirus-Encoded Interleukin-10 Homolog Inhibits Maturation of Dendritic Cells and Alters Their Functionality", "abstract": ["Interleukin-10 (IL-10) suppresses the maturation and cytokine production of dendritic cells (DCs), key regulators of adaptive immunity, and prevents the activation and polarization of na\u00efve T cells towards protective gamma interferon-producing effectors.", "We hypothesized that human cytomegalovirus (HCMV) utilizes its viral IL-10 homolog (cmvIL-10) to attenuate DC functionality, thereby subverting the efficient induction of antiviral immune responses.", "RNA and protein analyses demonstrated that the cmvIL-10 gene was expressed with late gene kinetics.", "Treatment of immature DCs (iDCs) with supernatant from HCMV-infected cultures inhibited both the lipopolysaccharide-induced DC maturation and proinflammatory cytokine production.", "These inhibitory effects were specifically mediated through the IL-10 receptor and were not observed when DCs were treated with supernatant of cells infected with a cmvIL-10-knockout mutant.", "Incubation of iDCs with recombinant cmvIL-10 recapitulated the inhibition of maturation.", "Furthermore, cmvIL-10 had pronounced long-term effects on those DCs that could overcome this inhibition of maturation.", "It enhanced the migration of mature DCs (mDCs) towards the lymph node homing chemokine but greatly reduced their cytokine production.", "The inability of mDCs to secrete IL-12 was maintained, even when they were restimulated by the activated T-cell signal CD40 ligand in the absence of cmvIL-10.", "Importantly, cmvIL-10 potentiates these anti-inflammatory effects, at least partially, by inducing endogenous cellular IL-10 expression in DCs.", "Collectively, we show that cmvIL-10 causes long-term functional alterations at all stages of DC activation."], "structured": false}
{"doc_id": 15426878, "title": "Model for unidirectional movement of axonemal and cytoplasmic dynein molecules", "abstract": ["A model for the unidirectional movement of dynein is presented based on structural observations and biochemical experimental results available.", "In this model, the binding affinity of dynein for microtubule is independent of its nucleotide state and the change between strong and weak microtubule-binding is determined naturally by the variation of relative orientation between the stalk and microtubule as the stalk rotates following nucleotide-state transition.", "Thus the enigmatic communication from the ATP binding site in the globular domain to the far MT-binding site in the tip of the stalk, which is prerequisite in conventional models, is not required.", "Using the present model, the previous experimental results such as the effect of ATP and ADP bindings on dissociation of dynein from microtubule, the processive movement of single-headed axonemal dyneins at saturating ATP concentration, the load dependence of step size for the processive movement of two-headed cytoplasmic dyneins and the dependence of stall force on ATP concentration can be well explained."], "structured": false}
{"doc_id": 15435343, "title": "The inflammasome component NLRP3 impairs antitumor vaccine by enhancing the accumulation of tumor-associated myeloid-derived suppressor cells.", "abstract": ["The inflammasome is a proteolysis complex that generates the active forms of the proinflammatory cytokines interleukin (IL)-1\u03b2 and IL-18.", "Inflammasome activation is mediated by NLR proteins that respond to microbial and nonmicrobial stimuli.", "Among NLRs, NLRP3 senses the widest array of stimuli and enhances adaptive immunity.", "However, its role in antitumor immunity is unknown.", "Therefore, we evaluated the function of the NLRP3 inflammasome in the immune response using dendritic cell vaccination against the poorly immunogenic melanoma cell line B16-F10.", "Vaccination of Nlrp3(-/-) mice led to a relative 4-fold improvement in survival relative to control animals.", "Immunity depended on CD8(+) T cells and exhibited immune specificity and memory.", "Increased vaccine efficacy in Nlrp3(-/-) hosts did not reflect differences in dendritic cells but rather differences in myeloid-derived suppressor cells (MDSC).", "Although Nlrp3 was expressed in MDSCs, the absence of Nlrp3 did not alter either their functional capacity to inhibit T cells or their presence in peripheral lymphoid tissues.", "Instead, the absence of Nlrp3 caused a 5-fold reduction in the number of tumor-associated MDSCs found in host mice.", "Adoptive transfer experiments also showed that Nlrp3(-/-) MDSCs were less efficient in reaching the tumor site.", "Depleting MDSCs with an anti-Gr-1 antibody increased the survival of tumor-bearing wild-type mice but not Nlrp3(-/-) mice.", "We concluded that Nlrp3 was critical for accumulation of MDSCs in tumors and for inhibition of antitumor T-cell immunity after dendritic cell vaccination.", "Our findings establish an unexpected role for Nlrp3 in impeding antitumor immune responses, suggesting novel approaches to improve the response to antitumor vaccines by limiting Nlrp3 signaling."], "structured": false}
{"doc_id": 15462523, "title": "Natural Killer Cells for Immunotherapy \u2013 Advantages of the NK-92 Cell Line over Blood NK Cells", "abstract": ["Natural killer (NK) cells are potent cytotoxic effector cells for cancer therapy and potentially for severe viral infections.", "However, there are technical challenges to obtain sufficient numbers of functionally active NK cells from a patient's blood since they represent only 10% of the lymphocytes and are often dysfunctional.", "The alternative is to obtain cells from a healthy donor, which requires depletion of the allogeneic T cells to prevent graft-versus-host reactions.", "Cytotoxic cell lines have been established from patients with clonal NK-cell lymphoma.", "Those cells can be expanded in culture in the presence of IL-2.", "Except for the NK-92 cell line, though, none of the other six known NK cell lines has consistently and reproducibly shown high antitumor cytotoxicity.", "Only NK-92 cells can easily be genetically manipulated to recognize specific tumor antigens or to augment monoclonal antibody activity through antibody-dependent cellular cytotoxicity.", "NK-92 is also the only cell line product that has been infused into patients with advanced cancer with clinical benefit and minimal side effects."], "structured": false}
{"doc_id": 15472716, "title": "Differential activation of DNA-PK based on DNA strand orientation and sequence bias", "abstract": ["DNA-PKcs and Ku are essential components of the complex that catalyzes non-homologous end joining (NHEJ) of DNA double-strand breaks (DSBs).", "Ku, a heterodimeric protein, binds to DNA ends and facilitates recruitment of the catalytic subunit, DNA-PKcs.", "We have investigated the effect of DNA strand orientation and sequence bias on the activation of DNA-PK.", "In addition, we assessed the effect of the position and strand orientation of cisplatin adducts on kinase activation.", "A series of duplex DNA substrates with site-specific cisplatin\u2013DNA adducts placed in three different orientations on the duplex DNA were prepared.", "Terminal biotin modification and streptavidin (SA) blocking was employed to direct DNA-PK binding to the unblocked termini with a specific DNA strand orientation and cisplatin\u2013DNA adduct position.", "DNA-PK kinase activity was measured and the results reveal that DNA strand orientation and sequence bias dramatically influence kinase activation, only a portion of which could be attributed to Ku-DNA binding activity.", "In addition, cisplatin\u2013DNA adduct position resulted in differing degrees of inhibition depending on distance from the terminus as well as strand orientation.", "These results highlight the importance of how local variations in DNA structure, chemistry and sequence influence DNA-PK activation and potentially NHEJ."], "structured": false}
{"doc_id": 15473205, "title": "Regulators of Trypanosoma brucei Cell Cycle Progression and Differentiation Identified Using a Kinome-Wide RNAi Screen", "abstract": ["The African trypanosome, Trypanosoma brucei, maintains an integral link between cell cycle regulation and differentiation during its intricate life cycle.", "Whilst extensive changes in phosphorylation have been documented between the mammalian bloodstream form and the insect procyclic form, relatively little is known about the parasite's protein kinases (PKs) involved in the control of cellular proliferation and differentiation.", "To address this, a T. brucei kinome-wide RNAi cell line library was generated, allowing independent inducible knockdown of each of the parasite's 190 predicted protein kinases.", "Screening of this library using a cell viability assay identified \u226542 PKs that are required for normal bloodstream form proliferation in culture.", "A secondary screen identified 24 PKs whose RNAi-mediated depletion resulted in a variety of cell cycle defects including in G1/S, kinetoplast replication/segregation, mitosis and cytokinesis, 15 of which are novel cell cycle regulators.", "A further screen identified for the first time two PKs, named repressor of differentiation kinase (RDK1 and RDK2), depletion of which promoted bloodstream to procyclic form differentiation.", "RDK1 is a membrane-associated STE11-like PK, whilst RDK2 is a NEK PK that is essential for parasite proliferation.", "RDK1 acts in conjunction with the PTP1/PIP39 phosphatase cascade to block uncontrolled bloodstream to procyclic form differentiation, whilst RDK2 is a PK whose depletion efficiently induces differentiation in the absence of known triggers.", "Thus, the RNAi kinome library provides a valuable asset for functional analysis of cell signalling pathways in African trypanosomes as well as drug target identification and validation."], "structured": false}
{"doc_id": 15476777, "title": "Chemotherapy options in elderly and frail patients with metastatic colorectal cancer (MRC FOCUS2): an open-label, randomised factorial trial", "abstract": ["BACKGROUND Elderly and frail patients with cancer, although often treated with chemotherapy, are under-represented in clinical trials.", "We designed FOCUS2 to investigate reduced-dose chemotherapy options and to seek objective predictors of outcome in frail patients with advanced colorectal cancer.   \n", "METHODS We undertook an open, 2 \u00d7 2 factorial trial in 61 UK centres for patients with previously untreated advanced colorectal cancer who were considered unfit for full-dose chemotherapy.", "After comprehensive health assessment (CHA), patients were randomly assigned by minimisation to: 48-h intravenous fluorouracil with levofolinate (group A); oxaliplatin and fluorouracil (group B); capecitabine (group C); or oxaliplatin and capecitabine (group D).", "Treatment allocation was not masked.", "Starting doses were 80% of standard doses, with discretionary escalation to full dose after 6 weeks.", "The two primary outcome measures were: addition of oxaliplatin ([A vs B] + [C vs D]), assessed with progression-free survival (PFS); and substitution of fluorouracil with capecitabine ([A vs C] + [B vs D]), assessed by change from baseline to 12 weeks in global quality of life (QoL).", "Analysis was by intention to treat.", "Baseline clinical and CHA data were modelled against outcomes with a novel composite measure, overall treatment utility (OTU).", "This study is registered, number ISRCTN21221452.   \n", "FINDINGS 459 patients were randomly assigned (115 to each of groups A-C, 114 to group D).", "Factorial comparison of addition of oxaliplatin versus no addition suggested some improvement in PFS, but the finding was not significant (median 5\u00b78 months [IQR 3\u00b73-7\u00b75] vs 4\u00b75 months [2\u00b78-6\u00b74]; hazard ratio 0\u00b784, 95% CI 0\u00b769-1\u00b701, p=0\u00b707).", "Replacement of fluorouracil with capecitabine did not improve global QoL: 69 of 124 (56%) patients receiving fluorouracil reported improvement in global QoL compared with 69 of 123 (56%) receiving capecitabine.", "The risk of having any grade 3 or worse toxic effect was not significantly increased with oxaliplatin (83/219 [38%] vs 70/221 [32%]; p=0\u00b717), but was higher with capecitabine than with fluorouracil (88/222 [40%] vs 65/218 [30%]; p=0\u00b703).", "In multivariable analysis, fewer baseline symptoms (odds ratio 1\u00b732, 95% CI 1\u00b714-1\u00b752), less widespread disease (1\u00b751, 1\u00b705-2\u00b719), and use of oxaliplatin (0\u00b757, 0\u00b739-0\u00b782) were predictive of better OTU.   \n", "INTERPRETATION FOCUS2 shows that with an appropriate design, including reduced starting doses of chemotherapy, frail and elderly patients can participate in a randomised controlled trial.", "On balance, a combination including oxaliplatin was preferable to single-agent fluoropyrimidines, although the primary endpoint of PFS was not met.", "Capecitabine did not improve QoL compared with fluorouracil.", "Comprehensive baseline assessment holds promise as an objective predictor of treatment benefit.   \n", "FUNDING Cancer Research UK and the Medical Research Council."], "structured": true}
{"doc_id": 15478227, "title": "Whole-genome sequencing of Oryza brachyantha reveals mechanisms underlying Oryza genome evolution", "abstract": ["The wild species of the genus Oryza contain a largely untapped reservoir of agronomically important genes for rice improvement.", "Here we report the 261-Mb de novo assembled genome sequence of Oryza brachyantha.", "Low activity of long-terminal repeat retrotransposons and massive internal deletions of ancient long-terminal repeat elements lead to the compact genome of Oryza brachyantha.", "We model 32,038 protein-coding genes in the Oryza brachyantha genome, of which only 70% are located in collinear positions in comparison with the rice genome.", "Analysing breakpoints of non-collinear genes suggests that double-strand break repair through non-homologous end joining has an important role in gene movement and erosion of collinearity in the Oryza genomes.", "Transition of euchromatin to heterochromatin in the rice genome is accompanied by segmental and tandem duplications, further expanded by transposable element insertions.", "The high-quality reference genome sequence of Oryza brachyantha provides an important resource for functional and evolutionary studies in the genus Oryza."], "structured": false}
{"doc_id": 15482274, "title": "Ultrasound imaging for lumbar punctures and epidural catheterisations: systematic review and meta-analysis.", "abstract": ["OBJECTIVE To determine whether ultrasound imaging can reduce the risk of failed lumbar punctures or epidural catheterisations, when compared with standard palpation methods, and whether ultrasound imaging can reduce traumatic procedures, insertion attempts, and needle redirections.   \n", "DESIGN Systematic review and meta-analysis of randomised controlled trials.   \n", "DATA SOURCES Ovid Medline, Embase, and Cochrane Central Register of Controlled Trials up to May 2012, without restriction by language or publication status.   ", "REVIEW METHODS Randomised trials that compared ultrasound imaging with standard methods (no imaging) in the performance of a lumbar puncture or epidural catheterisation were identified.   \n", "RESULTS 14 studies with a total of 1334 patients were included (674 patients assigned to the ultrasound group, 660 to the control group).", "Five studies evaluated lumbar punctures and nine evaluated epidural catheterisations.", "Six of 624 procedures conducted in the ultrasound group failed; 44 of 610 procedures in the control group failed.", "Ultrasound imaging reduced the risk of failed procedures (risk ratio 0.21 (95% confidence interval 0.10 to 0.43), P<0.001).", "Risk reduction was similar when subgroup analysis was performed for lumbar punctures (risk ratio 0.19 (0.07 to 0.56), P=0.002) or epidural catheterisations (0.23 (0.09 to 0.60), P=0.003).", "Ultrasound imaging also significantly reduced the risk of traumatic procedures (risk ratio 0.27 (0.11 to 0.67), P=0.005), the number of insertion attempts (mean difference -0.44 (-0.64 to -0.24), P<0.001), and the number of needle redirections (mean difference -1.00 (-1.24 to -0.75), P<0.001).   \n", "CONCLUSIONS Ultrasound imaging can reduce the risk of failed or traumatic lumbar punctures and epidural catheterisations, as well as the number of needle insertions and redirections.", "Ultrasound may be a useful adjunct for these procedures."], "structured": true}
{"doc_id": 15488881, "title": "Guidance of B cells by the orphan G protein-coupled receptor EBI2 shapes humoral immune responses.", "abstract": ["Humoral immunity depends on both rapid and long-term antibody production against invading pathogens.", "This is achieved by the generation of spatially distinct extrafollicular plasmablast and follicular germinal center (GC) B cell populations, but the signals that guide responding B cells to these alternative compartments have not been fully elucidated.", "Here, we show that expression of the orphan G protein-coupled receptor Epstein-Barr virus-induced gene 2 (EBI2, also known as GPR183) by activated B cells was essential for their movement to extrafollicular sites and induction of early plasmablast responses.", "Conversely, downregulation of EBI2 enabled B cells to access the center of follicles and promoted efficient GC formation.", "EBI2 therefore provides a previously uncharacterized dimension to B cell migration that is crucial for coordinating rapid versus long-term antibody responses."], "structured": false}
{"doc_id": 15491308, "title": "SIRT1 is required for long-term growth of human mesenchymal stem cells", "abstract": ["Human mesenchymal stem cells (MSCs) have therapeutic potential because of their ability to self-renew and differentiate into multiple tissues.", "However, senescence often occurs in MSCs when they are cultured in vitro and the molecular mechanisms underlying this effect remain unclear.", "In this study, we found that NAD-dependent protein deacetylase SIRT1 is differentially expressed in both human bone marrow-derived MSCs (B-MSCs) and adipose tissue-derived MSCs after increasing passages of cell culture.", "Using lentiviral shRNA we demonstrated that selective knockdown of SIRT1 in human MSCs at early passage slows down cell growth and accelerates cellular senescence.", "Conversely, overexpression of SIRT1 delays senescence in B-MSCs that have undergone prolonged in vitro culturing and the cells do not lose adipogenic and osteogenic potential.", "In addition, we found that the delayed accumulation of the protein p16 is involved in the effect of SIRT1.", "However, resveratrol, which has been used as an activator of SIRT1 deacetylase activity, only transiently promotes proliferation of B-MSCs.", "Our findings will help us understand the role of SIRT1 in the aging of normal diploid cells and may contribute to the prevention of human MSCs senescence thus benefiting MSCs-based tissue engineering and therapies."], "structured": false}
{"doc_id": 15491404, "title": "Rapid and persistent modulation of actin dynamics regulates postsynaptic reorganization underlying bidirectional plasticity", "abstract": ["The synapse is a highly organized cellular specialization whose structure and composition are reorganized, both positively and negatively, depending on the strength of input signals.", "The mechanisms orchestrating these changes are not well understood.", "A plausible locus for the reorganization of synapse components and structure is actin, because it serves as both cytoskeleton and scaffold for synapses and exists in a dynamic equilibrium between F-actin and G-actin that is modulated bidirectionally by cellular signaling.", "Using a new FRET-based imaging technique to monitor F-actin/G-actin equilibrium, we show here that tetanic stimulation causes a rapid, persistent shift of actin equilibrium toward F-actin in the dendritic spines of rat hippocampal neurons.", "This enlarges the spines and increases postsynaptic binding capacity.", "In contrast, prolonged low-frequency stimulation shifts the equilibrium toward G-actin, resulting in a loss of postsynaptic actin and of structure.", "This bidirectional regulation of actin is actively involved in protein assembly and disassembly and provides a substrate for bidirectional synaptic plasticity."], "structured": false}
{"doc_id": 15493354, "title": "Sublime Microglia: Expanding Roles for the Guardians of the CNS", "abstract": ["Recent findings challenge the concept that microglia solely function in disease states in the central nervous system (CNS).", "Rather than simply reacting to CNS injury, infection, or pathology, emerging lines of evidence indicate that microglia sculpt the structure of the CNS, refine neuronal circuitry and network connectivity, and contribute to plasticity.", "These physiological functions of microglia in the normal CNS begin during development and persist into maturity.", "Here, we develop a conceptual framework for functions of microglia beyond neuroinflammation and discuss the rich repertoire of signaling and communication motifs in microglia that are critical both in pathology and for the normal physiology of the CNS."], "structured": false}
{"doc_id": 15512462, "title": "Cancer after pre-eclampsia: follow up of the Jerusalem perinatal study cohort.", "abstract": ["OBJECTIVE To compare the incidence of cancer among women with and without a history of pre-eclampsia.   \n", "DESIGN Cohort study.   \n", "SETTING Jerusalem perinatal study of women who delivered in three large hospitals in West Jerusalem during 1964-76.   \n", "PARTICIPANTS 37 033 women.   \n", "MAIN OUTCOME MEASURES Age adjusted and multivariable adjusted hazard ratios for cancer incidence for the entire cohort and for women who were primiparous at study entry.   \n", "RESULTS Cancer developed in 91 women who had pre-eclampsia and 2204 who did not (hazard ratio 1.27, 95% confidence interval 1.03 to 1.57).", "The risk of site specific cancers was increased, particularly of the stomach, ovary epithelium, breast, and lung or larynx.", "The incidence of cancer of the stomach, breast, ovary, kidney, and lung or larynx was increased in primiparous women at study entry who had a history pre-eclampsia.   \n", "CONCLUSIONS A history of pre-eclampsia is associated with increases in overall risk of cancer and incidence at several sites.", "This may be explained by environmental and genetic factors common to the development of pre-eclampsia and cancer in this population."], "structured": true}
{"doc_id": 15521377, "title": "Keeping your senescent cells under control", "abstract": ["Cellular senescence is a stable form of cell-cycle arrest which is thought to limit the proliferative potential of premalignant cells [1].", "The senescence phenotype was initially described by Hayflick and Moorhead in 1961 on human fibroblasts undergoing replicative exhaustion in culture [2].", "It has been shown that senescence can be triggered in different cell types in response to diverse forms of cellular damage or stress (for review see [1]).", "Importantly, while senescence was denounced as a tissue culture phenomenon for many years, recent in vivo studies demonstrated that cellular senescence represents a potent failsafe mechanism against tumorigenesis and contributes to the cytotoxicity of certain anticancer agents (see for example [3-7]).", "Interestingly, senescent cells have also been observed in certain aged or damaged tissues and there is growing evidence that senescence checkpoints can affect the regenerative reserve of tissues and organismal aging [8-11].", "However, senescence may also have positive effects on organ maintenance by limiting pathological responses to acute forms of injury such as fibrotic scarring in response to chemical induced liver injury [12].    ", "Over the past years it was also shown that senescent cells can communicate with their environment by secreting a myriad of cytokines and growth factors.", "Interestingly, this \"senescence associated secretory phenotype (SASP)\" seems to be a double edged sword regarding tumor initiation and maintenance:    i)    On the one hand, it has been shown that the SASP can have pro-tumorigenic effects.", "In an experimental system it was shown that senescent mesenchymal cells can enhance the tumorigenicity of surrounding breast cancer cells [13].    ", "ii)    Similarly, it is possible that the SASP enhances selection of transformed cell clones in aged organ systems.", "It has been shown that loss of proliferative competition of non-transformed cells can accelerate leukemogenesis [14].", "It remains to be seen whether aberrant secretion of cytokines and growth factors by the SASP can accelerated this process in aged and chronically damage organ systems.    ", "iii)    In contrast to its pro-tumorigenic aspect, the SASP could also have anti-tumor effects.", "A recent study showed that in a mosaic liver cancer mouse model the activation of p53 induced senescence, an upregulation of inflammatory cytokines, and activation of innate immune responses leading to tumour cell clearance [15].    ", "iv)    In further support that the SASP could have anti-tumor activities, a series of recent papers showed that components of the SASP can stabilize the senescence cell cycle arrest via an autoregulatory feedback loop [16,17] or induces apoptosis of tumor cells [18].    ", "In addition to its effects on tumorigenesis, the SASP could also influence tissue aging.", "Studies on aging telomere dysfunctional mice have provided direct experimental evidence for an in vivo activation of the SASP in response to telomere dysfunction [19].", "Interestingly, this in vivo SASP provoked alterations in stem cell differentiation (skewing of hematopoiesis towards reduction in lymphopoiesis and enhancement of myelopoiesis) that are also characteristic signs of human aging.        ", "Figure 1.    ", "Different cellular stresses can induce senescence including telomere shortening, DNA damage, and oncogene activation.", "Senescence of tumor cells ...        ", "In light of the many possible roles o the SASP in aging and carcinogenesis, it appears to be of utmost importance to decipher regulatory pathways controlling the SASP.", "In a current publication, Bhaumik et al. have identified 2 microRNAs (miR-146a/b) that negatively regulate the secretion of IL-6 and IL-8 - two of the SASP [20].", "The authors show that these microRNAs are up-regulated at late stages of senescence, many days after a permanent cell cycle arrest has been established.", "Interestingly, the inhibitory miRs are most strongly up-regulated in senescence of cell lines that show a strong SASP but not in cell lines characterized by a weak SASP.", "The authors propose a new concept indicating that miRs 146a and b function in a negative feedback loop preventing an over-activation of the SASP in senescent cells.", "The authors present some initial data suggesting that activation of this negative feedback loop involves IL-1 receptor, IRAK-1, and NF\u03baB signalling leading to an up-regulation of miRs-146a and b. A direct proof that this proposed feedback loop suppresses over-activation of the SASP remains to be demonstrated in future studies.", "The authors show that blockage of IL-1-receptor signalling prevents both the up-regulation of miRs-146a and b as well as Il-6 secretion.", "To confirm their new concept, it would be important to show that a selective blockage of miRs-146a and b results in over-activation of the SASP.    ", "The work by Bhaumik et al. places mir-146a/b as central players to control IL-6 and IL-8 expression within the SASP.", "MicroRNAs are emerging therapeutic targets because their expression levels can be effectively modulated via the use of antagomirs (see for example [21]).", "Also, for increasing microRNA expression, microRNAs can be delivered into cellsin vivo (see for example [22]).", "Therefore, it will be interesting to functionally test the impact of mir-146 inhibition on tumorigenesis and aging in relevant mouse models.", "Such studies will be of particular interest, as recent work showed that IL-6 secretion by senescent cells is relevant for initiating and maintaining the senescene response via an autocrine loop [17].", "A reduction of miR-146 could increase IL-6 levels in senescent cells, which should stabilize the senescence program and reduce the risk of malignant transformation.", "Furthermore, it can be speculated that reduction of mir-146 a/b will increase Nf\u03baB activation via IRAK1.", "As Nf\u03baB is modulating the expression of various inflammation associated genes, this may also lead to increased clearance of senescent tumor cells by the innate immune system.", "However, it should be mentioned that Il-6 secreted by senescent cells can also act as a mitogen for surrounding cells, thus potentially increasing the risk of malignant transformation [13,17].", "Besides its function in SASP modulation, miR-146 was also reported to target the mRNAs of the BRCA1 and BRCA2 tumor suppressors.", "In a recent study a G to C polymorphism in miR-146, which leads to an increased processing and release of the mature microRNA, can predict an early onset of breast cancer [23].    ", "Taken together, the study of Bhaumik et al. opens an interesting new research area dealing with the gene regulatory mechanisms that control activation of the SASP.", "Given the diverse roles of the SASP in modulating tumor progression, immune surveillance of damaged cells, and the stabilization of the senescence arrest itself, it will be of great interest to analyse the influence of SASP regulatory pathways during aging and cancer."], "structured": false}
{"doc_id": 15535511, "title": "Role for insulin signaling in catecholaminergic neurons in control of energy homeostasis.", "abstract": ["Dopaminergic midbrain neurons integrate signals on food palatability and food-associated reward into the complex control of energy homeostasis.", "To define the role of insulin receptor (IR) signaling in this circuitry, we inactivated IR signaling in tyrosine hydroxylase (Th)-expressing cells of mice (IR(\u0394Th)).", "IR inactivation in Th-expressing cells of mice resulted in increased body weight, increased fat mass, and hyperphagia.", "While insulin acutely stimulated firing frequency in 50% of dopaminergic VTA/SN neurons, this response was abolished in IR(\u0394Th) mice.", "Moreover, these mice exhibited an altered response to cocaine under food-restricted conditions.", "Taken together, these data provide in vivo evidence for a critical role of insulin signaling in catecholaminergic neurons to control food intake and energy homeostasis."], "structured": false}
{"doc_id": 15541119, "title": "[New guidelines to evaluate the response to treatment in solid tumors].", "abstract": ["Anticancer agents go through a process by which their antitumor activity, on the basis of the amount of tumor shrinkage they could generate, has been investigated.", "In the late 1970s, the International Union Against Cancer and the World Health Organization (WHO) introduced specific criteria for the codification of tumor response evaluation.", "In 1994, several organizations involved in clinical cancer research joined together to undertake the review of these response evaluation criteria on the basis of their experience and knowledge.", "After several years of intensive discussions, new guidelines are ready and will replace the previous WHO criteria.", "In parallel to this initiative, one of the participating groups developed a model by which response rates could be derived from unidimensional measurement of tumor lesions instead of the usual bidimensional approach.", "This new concept has been largely validated by the Response Evaluation Criteria in Solid Tumors (Recist) Group and integrated into the present guidelines.", "This special article provides some philosophic background to clarify the various purposes of response evaluation.", "It proposes a model by which a combined assessment of all existing lesions, characterized by target lesion (to be measured) and nontarget lesions, is used to extrapolate an overall response to treatment.", "Methods of assessing tumor lesions are better codified.", "All other aspects of response evaluation have been discussed, reviewed, and amended whenever suitable."], "structured": false}
{"doc_id": 15548965, "title": "Structural Rearrangements of NR1/NR2A NMDA Receptors during Allosteric Inhibition", "abstract": ["Ionotropic glutamate receptor (iGluR) subunits contain a large N-terminal domain (NTD) that precedes the agonist-binding domain (ABD) and participates in subunit oligomerization.", "In NMDA receptors (NMDARs), the NTDs of NR2A and NR2B subunits also form binding sites for the endogenous inhibitor Zn(2+) ion.", "Although these allosteric sites have been characterized in detail, the molecular mechanisms by which the NTDs communicate with the rest of the receptor to promote its inhibition remain unknown.", "Here, we identify the ABD dimer interface as a major structural determinant that permits coupling between the NTDs and the channel gate.", "The strength of this interface also controls proton inhibition, another form of allosteric modulation of NMDARs.", "Conformational rearrangements at the ABD dimer interface thus appear to be a key mechanism conserved in all iGluR subfamilies, but have evolved to fulfill different functions: fast desensitization at AMPA and kainate receptors, allosteric inhibition at NMDARs."], "structured": false}
{"doc_id": 15551129, "title": "The role of iron in Mycobacterium smegmatis biofilm formation: the exochelin siderophore is essential in limiting iron conditions for biofilm formation but not for planktonic growth", "abstract": ["Many species of mycobacteria form structured biofilm communities at liquid\u2013air interfaces and on solid surfaces.", "Full development of Mycobacterium smegmatis biofilms requires addition of supplemental iron above 1 \u03bcM ferrous sulphate, although addition of iron is not needed for planktonic growth.", "Microarray analysis of the M. smegmatis transcriptome shows that iron-responsive genes \u2013 especially those involved in siderophore synthesis and iron uptake \u2013 are strongly induced during biofilm formation reflecting a response to iron deprivation, even when 2 \u03bcM iron is present.", "The acquisition of iron under these conditions is specifically dependent on the exochelin synthesis and uptake pathways, and the strong defect of an iron\u2013exochelin uptake mutant suggests a regulatory role of iron in the transition to biofilm growth.", "In contrast, although the expression of mycobactin and iron ABC transport operons is highly upregulated during biofilm formation, mutants in these systems form normal biofilms in low-iron (2 \u03bcM) conditions.", "A close correlation between iron availability and matrix-associated fatty acids implies a possible metabolic role in the late stages of biofilm maturation, in addition to the early regulatory role.", "M. smegmatis surface motility is similarly dependent on iron availability, requiring both supplemental iron and the exochelin pathway to acquire it."], "structured": false}
{"doc_id": 15559582, "title": "Plasma lipids and prolactin in patients with breast cancer.", "abstract": ["In a comparative study of pre- and postmenopausal women with benign and malignant breast disease, a number of differences were observed in circulating plasma prolactin and lipid concentrations.", "Plasma lipids, phospholipids, triglycerides, cholesterol and free fatty acids were all higher in blood obtained from breast cancer patients prior to surgery.", "HDL-Cholesterol levels were significantly lower in these patients.", "These differences remained when the patient groups were sub-divided according to menopausal status.", "Plasma prolactin concentrations were also found to be higher in cancer compared with non-cancer patients, this effect being more marked in premenopausal than in postmenopausal patients.", "Premenopausal patients with invasive or poorly differentiated disease had significantly higher prolactin levels than those with non-invasive disease.", "No correlations were found between plasma prolactin and any of the lipid fractions."], "structured": false}
{"doc_id": 15561961, "title": "expression by oxidized linoleic", "abstract": ["Hypercholesterolemia is associated with impairments in endothelium-dependent vascular relaxations.", "Paradoxically, endothelial production of nitrogen oxides is increased in early stages of hypercholesterolemia.", "Prior work has shown that oxidized low density lipoprotein (LDL) has both stimulatory and inhibitory effects on endothelial nitric oxide synthase expression (eNOS) and has focused on lysophosphatidyl choline (LPC) as a component of oxidized LDL which may modulate this effect.", "Another biologically active component of oxidized LDL is 13-hydroperoxyoctadecadienoic acid (13-HPODE), an oxidized form of linoleic acid.", "The purpose of this study was to determine the effect of HPODE on the expression of eNOS in bovine aortic endothelial cells (BAECs).", "Twenty four hour treatment of endothelial cells with HPODE caused a dose-dependent increase in eNOS mRNA levels as assessed by Northern analysis.", "The time response studies show that HPODE treatment significantly increased eNOS mRNA levels at 12 and 24 h. Concomitant with the increase in eNOS mRNA levels, 20 microM HPODE treatment significantly increased eNOS protein content and enzyme activity.", "Nuclear run-on studies indicated that the rate of transcription of eNOS gene was significantly elevated 4 h after HPODE treatment when compared to control cultures.", "Also, actinomycin D studies demonstrated that the half-life of eNOS mRNA was increased from 6 h to 12 h by HPODE treatment.", "Thus, HPODE-induced up-regulation of eNOS expression is mediated by both transcriptional and posttranscriptional mechanisms.", "These observations suggest that endothelial cells may attempt to compensate for oxidative injury by increasing expression of eNOS in early stages of hypercholesterolemia."], "structured": false}
{"doc_id": 15563864, "title": "Specific killing of multiple myeloma cells by (-)-epigallocatechin-3-gallate extracted from green tea: biologic activity and therapeutic implications.", "abstract": ["Epigallocatechin-3-gallate (EGCG), a polyphenol extracted from green tea, is an antioxidant with chemopreventive and chemotherapeutic actions.", "Based on its ability to modulate growth factor-mediated cell proliferation, we evaluated its efficacy in multiple myeloma (MM).", "EGCG induced both dose- and time-dependent growth arrest and subsequent apoptotic cell death in MM cell lines including IL-6-dependent cells and primary patient cells, without significant effect on the growth of peripheral blood mononuclear cells (PBMCs) and normal fibroblasts.", "Treatment with EGCG also led to significant apoptosis in human myeloma cells grown as tumors in SCID mice.", "EGCG interacts with the 67-kDa laminin receptor 1 (LR1), which is significantly elevated in myeloma cell lines and patient samples relative to normal PBMCs.", "RNAi-mediated inhibition of LR1 resulted in abrogation of EGCG-induced apoptosis in myeloma cells, indicating that LR1 plays an important role in mediating EGCG activity in MM while sparing PBMCs.", "Evaluation of changes in gene expression profile indicates that EGCG treatment activates distinct pathways of growth arrest and apoptosis in MM cells by inducing the expression of death-associated protein kinase 2, the initiators and mediators of death receptor-dependent apoptosis (Fas ligand, Fas, and caspase 4), p53-like proteins (p73, p63), positive regulators of apoptosis and NF-kappaB activation (CARD10, CARD14), and cyclin-dependent kinase inhibitors (p16 and p18).", "Expression of related genes at the protein level were also confirmed by Western blot analysis.", "These data demonstrate potent and specific antimyeloma activity of EGCG and provide the rationale for its clinical evaluation."], "structured": false}
{"doc_id": 15570691, "title": "Pharmacologic inhibition of cyclin-dependent kinases 4 and 6 arrests the growth of glioblastoma multiforme intracranial xenografts.", "abstract": ["Activation of cyclin-dependent kinases 4 and 6 (cdk4/6) occurs in the majority of glioblastoma multiforme (GBM) tumors, and represents a promising molecular target for the development of small molecule inhibitors.", "In the current study, we investigated the molecular determinants and in vivo response of diverse GBM cell lines and xenografts to PD-0332991, a cdk4/6-specific inhibitor.", "In vitro testing of PD-0332991 against a panel of GBM cell lines revealed a potent G(1) cell cycle arrest and induction of senescence in each of 16 retinoblastoma protein (Rb)-proficient cell lines regardless of other genetic lesions, whereas 5 cell lines with homozygous inactivation of Rb were completely resistant to treatment.", "Short hairpin RNA depletion of Rb expression conferred resistance of GBM cells to PD-0332991, further demonstrating a requirement of Rb for sensitivity to cdk4/6 inhibition.", "PD-0332991 was found to efficiently cross the blood-brain barrier and proved highly effective in suppressing the growth of intracranial GBM xenograft tumors, including those that had recurred after initial therapy with temozolomide.", "Remarkably, no mice receiving PD-0332991 died as a result of disease progression while on therapy.", "Additionally, the combination of PD-0332991 and radiation therapy resulted in significantly increased survival benefit compared with either therapy alone.", "In total, our results support clinical trial evaluation of PD-0332991 against newly diagnosed as well as recurrent GBM, and indicate that Rb status is the primary determinant of potential benefit from this therapy."], "structured": false}
{"doc_id": 15570962, "title": "Choosing Haplotype-Tagging SNPS Based on Unphased Genotype Data Using a Preliminary Sample of Unrelated Subjects with an Example from the Multiethnic Cohort Study", "abstract": ["We describe an approach for picking haplotype-tagging single nucleotide polymorphisms (htSNPs) that is presently being taken in two large nested case-control studies within a multiethnic cohort (MEC), which are engaged in a search for associations between risk of prostate and breast cancer and common genetic variations in candidate genes.", "Based on a preliminary sample of 70 control subjects chosen at random from each of the 5 ethnic groups in the MEC we estimate haplotype frequencies using a variant of the Excoffier-Slatkin E-M algorithm after genotyping a high density of SNPs selected every 3\u20135 kb in and surrounding a candidate gene.", "In order to evaluate the performance of a candidate set of htSNPS (which will be genotyped in the much larger case-control sample) we treat the haplotype frequencies estimate above as known, and carry out a formal calculation of the uncertainty of the number of copies of common haplotypes carried by an individual, summarizing this calculation as a coefficient of determination, R2h.", "A candidate set of htSNPS of a given size is chosen so as to maximize the minimum value of R2h over the common haplotypes, h."], "structured": false}
{"doc_id": 15578265, "title": "A model for the role of gut bacteria in the development of autoimmunity for type 1 diabetes", "abstract": ["Several lines of evidence suggest a role for the gut microbiome in type 1 diabetes.", "Treating diabetes-prone rodents with probiotics or antibiotics prevents the development of the disorder.", "Diabetes-prone rodents also have a distinctly different gut microbiome compared with healthy rodents.", "Recent studies in children with a high genetic risk for type 1 diabetes demonstrate significant differences in the gut microbiome between children who develop autoimmunity for the disease and those who remain healthy.", "However, the differences in microbiome composition between autoimmune and healthy children are not consistent across all studies because of the strong environmental influences on microbiome composition, particularly diet and geography.", "Controlling confounding factors of microbiome composition uncovers bacterial associations with disease.", "For example, in a human cohort from a single Finnish city where geography is confined, a strong association between one dominant bacterial species, Bacteroides dorei, and type 1 diabetes was discovered (Davis-Richardson et al. Front Microbiol 2014;5:678).", "Beyond this, recent DNA methylation analyses suggest that a thorough epigenetic analysis of the gut microbiome may be warranted.", "These studies suggest a testable model whereby a diet high in fat and gluten and low in resistant starch may be the primary driver of gut dysbiosis.", "This dysbiosis may cause a lack of butyrate production by gut bacteria, which, in turn, leads to the development of a permeable gut followed by autoimmunity.", "The bacterial community responsible for these changes in butyrate production may vary around the world, but bacteria of the genus Bacteroides are thought to play a key role."], "structured": false}
{"doc_id": 15588516, "title": "METHODS AND RESULTS", "abstract": ["Cytoscape is an open source software project for integrating biomolecular interaction networks with high-throughput expression data and other molecular states into a unified conceptual framework.", "Although applicable to any system of molecular components and interactions, Cytoscape is most powerful when used in conjunction with large databases of protein-protein, protein-DNA, and genetic interactions that are increasingly available for humans and model organisms.", "Cytoscape's software Core provides basic functionality to layout and query the network; to visually integrate the network with expression profiles, phenotypes, and other molecular states; and to link the network to databases of functional annotations.", "The Core is extensible through a straightforward plug-in architecture, allowing rapid development of additional computational analyses and features.", "Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models."], "structured": false}
{"doc_id": 15590539, "title": "Dual Regulation of miRNA Biogenesis Generates Target Specificity in Neurotrophin-Induced Protein Synthesis", "abstract": ["Control of translation is a fundamental source of regulation in gene expression.", "The induction of protein synthesis by brain-derived neurotrophic factor (BDNF) critically contributes to enduring modifications of synaptic function, but how BDNF selectively affects only a minority of expressed mRNAs is poorly understood.", "We report that BDNF rapidly elevates Dicer, increasing mature miRNA levels and inducing RNA processing bodies in neurons.", "BDNF also rapidly induces Lin28, causing selective loss of Lin28-regulated miRNAs and a corresponding upregulation in translation of their target mRNAs.", "Binding sites for Lin28-regulated miRNAs are necessary and sufficient to confer BDNF responsiveness to a transcript.", "Lin28 deficiency, or expression of a Lin28-resistant Let-7 precursor miRNA, inhibits BDNF translation specificity and BDNF-dependent dendrite arborization.", "Our data establish that specificity in BDNF-regulated translation depends upon a two-part posttranscriptional control of miRNA biogenesis that generally enhances mRNA repression in association with GW182 while selectively derepressing and increasing translation of specific mRNAs."], "structured": false}
{"doc_id": 15593561, "title": "A Viral microRNA Cluster Strongly Potentiates the Transforming Properties of a Human Herpesvirus", "abstract": ["Epstein-Barr virus (EBV), an oncogenic human herpesvirus, induces cell proliferation after infection of resting B lymphocytes, its reservoir in vivo.", "The viral latent proteins are necessary for permanent B cell growth, but it is unknown whether they are sufficient.", "EBV was recently found to encode microRNAs (miRNAs) that are expressed in infected B cells and in some EBV-associated lymphomas.", "EBV miRNAs are grouped into two clusters located either adjacent to the BHRF1 gene or in introns contained within the viral BART transcripts.", "To understand the role of the BHRF1 miRNA cluster, we have constructed a virus mutant that lacks all its three members (\u0394123) and a revertant virus.", "Here we show that the B cell transforming capacity of the \u0394123 EBV mutant is reduced by more than 20-fold, relative to wild type or revertant viruses.", "B cells exposed to the knock-out virus displayed slower growth, and exhibited a two-fold reduction in the percentage of cells entering the cell cycle S phase.", "Furthermore, they displayed higher latent gene expression levels and latent protein production than their wild type counterparts.", "Therefore, the BHRF1 miRNAs accelerate B cell expansion at lower latent gene expression levels.", "Thus, this miRNA cluster simultaneously enhances expansion of the virus reservoir and reduces the viral antigenic load, two features that have the potential to facilitate persistence of the virus in the infected host.", "Thus, the EBV BHRF1 miRNAs may represent new therapeutic targets for the treatment of some EBV-associated lymphomas."], "structured": false}
{"doc_id": 15600979, "title": "EMSY overexpression disrupts the BRCA2/RAD51 pathway in the DNA-damage response: implications for chromosomal instability/recombination syndromes as checkpoint diseases", "abstract": ["EMSY links the BRCA2 pathway to sporadic breast/ovarian cancer.", "It encodes a nuclear protein that binds to the BRCA2 N-terminal domain implicated in chromatin/transcription regulation, but when sporadically amplified/overexpressed, increased EMSY level represses BRCA2 transactivation potential and induces chromosomal instability, mimicking the activity of BRCA2 mutations in the development of hereditary breast/ovarian cancer.", "In addition to chromatin/transcription regulation, EMSY may also play a role in the DNA-damage response, suggested by its ability to localize at chromatin sites of DNA damage/repair.", "This implies that EMSY overexpression may also repress BRCA2 in DNA-damage replication/checkpoint and recombination/repair, coordinated processes that also require its interacting proteins: PALB2, the partner and localizer of BRCA2; RPA, replication/checkpoint protein A; and RAD51, the inseparable recombination/repair enzyme.", "Here, using a well-characterized recombination/repair assay system, we demonstrate that a slight increase in EMSY level can indeed repress these two processes independently of transcriptional interference/repression.", "Since EMSY, RPA and PALB2 all bind to the same BRCA2 region, these findings further support a scenario wherein: (a) EMSY amplification may mimic BRCA2 deficiency, at least by overriding RPA and PALB2, crippling the BRCA2/RAD51 complex at DNA-damage and replication/transcription sites; and (b) BRCA2/RAD51 may coordinate these processes by employing at least EMSY, PALB2 and RPA.", "We extensively discuss the molecular details of how this can happen to ascertain its implications for a novel recombination mechanism apparently conceived as checkpoint rather than a DNA repair system for cell division, survival, death, and human diseases, including the tissue specificity of cancer predisposition, which may renew our thinking about targeted therapy and prevention."], "structured": false}
{"doc_id": 15615957, "title": "Original Article", "abstract": ["UNLABELLED Fruit and vegetable consumption has been inversely associated with the risk of chronic diseases including cancer and cardiovascular disease, with the beneficial effects attributed to a variety of protective antioxidants, carotenoids and phytonutrients.", "The objective of the present study was to determine the effect of supplementation with dehydrated concentrates from mixed fruit and vegetable juices (Juice Plus+R) on serum antioxidant and folate status, plasma homocysteine levels and markers for oxidative stress and DNA damage.", "Japanese subjects (n=60; age 27.8 yrs; BMI 22.1) were recruited to participate in a double-blind placebo controlled study and were randomized into 2 groups of 30, matched for sex, age, BMI and smoking status (39 males, 22 smokers; 21 females, 13 smokers).", "Subjects were given encapsulated supplements containing mixed fruit and vegetable juice concentrates or a matching placebo for 28 days, with blood and urine samples collected at baseline, day 14 and day 28 for analytical testing.", "Compared with the placebo, 28 day supplementation significantly increased the concentration of serum beta-carotene 528% (p<0.0001), lycopene 80.2% (p<0.0005), and alpha tocopherol 39.5% (p<0.0001).", "Serum folate increased 174.3% (p<0.0001) and correlated with a decrease in plasma homocysteine of -19.9% (p<0.03).", "Compared with baseline, measures of oxidative stress decreased with serum lipid peroxides declining -10.5% (p<0.02) and urine 8OHdG decreasing -21.1% (p<0.02).", "Evaluation of data from smokers only (n=17) after 28 days of active supplementation showed comparable changes.   \n", "CONCLUSION In the absence of dietary modification, supplementation with the fruit and vegetable juice concentrate capsules proved to be a highly bioavailable source of phytonutrients.", "Important antioxidants were elevated to desirable levels associated with decreased risk of disease while markers of oxidative stress were reduced, and folate status improved with a concomitant decrease in homocysteine, and these benefits occurred to a similar extent in smokers when compared to non-smokers."], "structured": true}
{"doc_id": 15617300, "title": "NCBI GEO: archive for functional genomics data sets\u2014update", "abstract": ["The Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) is an international public repository for high-throughput microarray and next-generation sequence functional genomic data sets submitted by the research community.", "The resource supports archiving of raw data, processed data and metadata which are indexed, cross-linked and searchable.", "All data are freely available for download in a variety of formats.", "GEO also provides several web-based tools and strategies to assist users to query, analyse and visualize data.", "This article reports current status and recent database developments, including the release of GEO2R, an R-based web application that helps users analyse GEO data."], "structured": false}
{"doc_id": 15617866, "title": "Viral Paratransgenesis in the Malaria Vector Anopheles gambiae", "abstract": ["Paratransgenesis, the genetic manipulation of insect symbiotic microorganisms, is being considered as a potential method to control vector-borne diseases such as malaria.", "The feasibility of paratransgenic malaria control has been hampered by the lack of candidate symbiotic microorganisms for the major vector Anopheles gambiae.", "In other systems, densonucleosis viruses (DNVs) are attractive agents for viral paratransgenesis because they infect important vector insects, can be genetically manipulated and are transmitted to subsequent generations.", "However, An.", "gambiae has been shown to be refractory to DNV dissemination.", "We discovered, cloned and characterized the first known DNV (AgDNV) capable of infection and dissemination in An.", "gambiae.", "We developed a flexible AgDNV-based expression vector to express any gene of interest in An.", "gambiae using a two-plasmid helper-transducer system.", "To demonstrate proof-of-concept of the viral paratransgenesis strategy, we used this system to transduce expression of an exogenous gene (enhanced green fluorescent protein; EGFP) in An.", "gambiae mosquitoes.", "Wild-type and EGFP-transducing AgDNV virions were highly infectious to An.", "gambiae larvae, disseminated to and expressed EGFP in epidemiologically relevant adult tissues such as midgut, fat body and ovaries and were transmitted to subsequent mosquito generations.", "These proof-of-principle data suggest that AgDNV could be used as part of a paratransgenic malaria control strategy by transduction of anti-Plasmodium peptides or insect-specific toxins in Anopheles mosquitoes.", "AgDNV will also be extremely valuable as an effective and easy-to-use laboratory tool for transient gene expression or RNAi in An.", "gambiae."], "structured": false}
{"doc_id": 15635366, "title": "The polycomb group protein L3mbtl2 assembles an atypical PRC1-family complex that is essential in pluripotent stem cells and early development.", "abstract": ["L3mbtl2 has been implicated in transcriptional repression and chromatin compaction but its biological function has not been defined.", "Here we show that disruption of L3mbtl2 results in embryonic lethality with failure of gastrulation.", "This correlates with compromised proliferation and abnormal differentiation of L3mbtl2(-/-) embryonic stem (ES) cells.", "L3mbtl2 regulates genes by recruiting a Polycomb Repressive Complex1 (PRC1)-related complex, resembling the previously described E2F6-complex, and including G9A, Hdac1, and Ring1b.", "The presence of L3mbtl2 at target genes is associated with H3K9 dimethylation, low histone acetylation, and H2AK119 ubiquitination, but the latter is neither dependent on L3mbtl2 nor sufficient for repression.", "Genome-wide studies revealed that the L3mbtl2-dependent complex predominantly regulates genes not bound by canonical PRC1 and PRC2.", "However, some developmental regulators are repressed by the combined activity of all three complexes.", "Together, we have uncovered a highly selective, essential role for an atypical PRC1-family complex in ES cells and early development."], "structured": false}
{"doc_id": 15648443, "title": "Long-term effect of aspirin on cancer risk in carriers of hereditary colorectal cancer: an analysis from the CAPP2 randomised controlled trial", "abstract": ["BACKGROUND Observational studies report reduced colorectal cancer in regular aspirin consumers.", "Randomised controlled trials have shown reduced risk of adenomas but none have employed prevention of colorectal cancer as a primary endpoint.", "The CAPP2 trial aimed to investigate the antineoplastic effects of aspirin and a resistant starch in carriers of Lynch syndrome, the major form of hereditary colorectal cancer; we now report long-term follow-up of participants randomly assigned to aspirin or placebo.   \n", "METHODS In the CAPP2 randomised trial, carriers of Lynch syndrome were randomly assigned in a two-by-two factorial design to 600 mg aspirin or aspirin placebo or 30 g resistant starch or starch placebo, for up to 4 years.", "Randomisation was in blocks of 16 with provision for optional single-agent randomisation and extended postintervention double-blind follow-up; participants and investigators were masked to treatment allocation.", "The primary endpoint was development of colorectal cancer.", "Analysis was by intention to treat and per protocol.", "This trial is registered, ISRCTN59521990.   \n", "RESULTS 861 participants were randomly assigned to aspirin or aspirin placebo.", "At a mean follow-up of 55\u00b77 months, 48 participants had developed 53 primary colorectal cancers (18 of 427 randomly assigned to aspirin, 30 of 434 to aspirin placebo).", "Intention-to-treat analysis of time to first colorectal cancer showed a hazard ratio (HR) of 0\u00b763 (95% CI 0\u00b735-1\u00b713, p=0\u00b712).", "Poisson regression taking account of multiple primary events gave an incidence rate ratio (IRR) of 0\u00b756 (95% CI 0\u00b732-0\u00b799, p=0\u00b705).", "For participants completing 2 years of intervention (258 aspirin, 250 aspirin placebo), per-protocol analysis yielded an HR of 0\u00b741 (0\u00b719-0\u00b786, p=0\u00b702) and an IRR of 0\u00b737 (0\u00b718-0\u00b778, p=0\u00b7008).", "No data for adverse events were available postintervention; during the intervention, adverse events did not differ between aspirin and placebo groups.   \n", "INTERPRETATION 600 mg aspirin per day for a mean of 25 months substantially reduced cancer incidence after 55\u00b77 months in carriers of hereditary colorectal cancer.", "Further studies are needed to establish the optimum dose and duration of aspirin treatment.   \n", "FUNDING European Union; Cancer Research UK; Bayer Corporation; National Starch and Chemical Co; UK Medical Research Council; Newcastle Hospitals trustees; Cancer Council of Victoria Australia; THRIPP South Africa; The Finnish Cancer Foundation; SIAK Switzerland; Bayer Pharma."], "structured": true}
{"doc_id": 15655418, "title": "Drosophila CPEB Orb2A Mediates Memory Independent of Its RNA-Binding Domain", "abstract": ["Long-term memory and synaptic plasticity are thought to require the synthesis of new proteins at activated synapses.", "The CPEB family of RNA binding proteins, including Drosophila Orb2, has been implicated in this process.", "The precise mechanism by which these molecules regulate memory formation is however poorly understood.", "We used gene targeting and site-specific transgenesis to specifically modify the endogenous orb2 gene in order to investigate its role in long-term memory formation.", "We show that the Orb2A and Orb2B isoforms, while both essential, have distinct functions in memory formation.", "These two isoforms have common glutamine-rich and RNA-binding domains, yet Orb2A uniquely requires the former and Orb2B the latter.", "We further show that Orb2A induces Orb2 complexes in a manner dependent upon both its glutamine-rich region and neuronal activity.", "We propose that Orb2B acts as a conventional CPEB to regulate transport and/or translation of specific mRNAs, whereas Orb2A acts in an unconventional manner to form stable Orb2 complexes that are essential for memory to persist."], "structured": false}
{"doc_id": 15657779, "title": "Functional hemichannels in astrocytes: a novel mechanism of glutamate release.", "abstract": ["Little is known about the expression and possible functions of unopposed gap junction hemichannels in the brain.", "Emerging evidence suggests that gap junction hemichannels can act as stand-alone functional channels in astrocytes.", "With immunocytochemistry, dye uptake, and HPLC measurements, we show that astrocytes in vitro express functional hemichannels that can mediate robust efflux of glutamate and aspartate.", "Functional hemichannels were confirmed by passage of extracellular lucifer yellow (LY) into astrocytes in nominal divalent cation-free solution (DCFS) and the ability to block this passage with gap junction blocking agents.", "Glutamate/aspartate release (or LY loading) in DCFS was blocked by multivalent cations (Ca2+, Ba2+, Sr2+, Mg2+, and La3+) and by gap junction blocking agents (carbenoxolone, octanol, heptanol, flufenamic acid, and 18alpha-glycyrrhetinic acid) with affinities close to those reported for blockade of gap junction intercellular communication.", "Glutamate efflux via hemichannels was also accompanied by greatly reduced glutamate uptake.", "Glutamate release in DCFS, however, was not significantly mediated by reversal of the glutamate transporter: release did not saturate and was not blocked by glutamate transporter blockers.", "Control experiments in DCFS precluded glutamate release by volume-sensitive anion channels, P2X7 purinergic receptor pores, or general purinergic receptor activation.", "Blocking intracellular Ca2+ mobilization by BAPTA-AM or thapsigargin did not inhibit glutamate release in DCFS.", "Divalent cation removal also induced glutamate release from intact CNS white matter (acutely isolated optic nerve) that was blocked by carbenoxolone, suggesting the existence of functional hemichannels in situ.", "Our results indicated that astrocyte hemichannels could influence CNS levels of extracellular glutamate with implications for normal and pathological brain function."], "structured": false}
{"doc_id": 15659108, "title": "Human Rad52 binds and wraps single-stranded DNA and mediates annealing via two hRad52\u2013ssDNA complexes", "abstract": ["Rad52 promotes the annealing of complementary strands of DNA bound by replication protein A (RPA) during discrete repair pathways.", "Here, we used a fluorescence resonance energy transfer (FRET) between two fluorescent dyes incorporated into DNA substrates to probe the mechanism by which human Rad52 (hRad52) interacts with and mediates annealing of ssDNA-hRPA complexes.", "Human Rad52 bound ssDNA or ssDNA-hRPA complex in two, concentration-dependent modes.", "At low hRad52 concentrations, ssDNA was wrapped around the circumference of the protein ring, while at higher protein concentrations, ssDNA was stretched between multiple hRad52 rings.", "Annealing by hRad52 occurred most efficiently when each complementary DNA strand or each ssDNA-hRPA complex was bound by hRad52 in a wrapped configuration, suggesting homology search and annealing occur via two hRad52-ssDNA complexes.", "In contrast to the wild type protein, hRad52(RQK/AAA) and hRad52(1-212) mutants with impaired ability to bind hRPA protein competed with hRPA for binding to ssDNA and failed to counteract hRPA-mediated duplex destabilization highlighting the importance of hRad52-hRPA interactions in promoting efficient DNA annealing."], "structured": false}
{"doc_id": 15663829, "title": "Mendelian Randomization Study of B-Type Natriuretic Peptide and Type 2 Diabetes: Evidence of Causal Association from Population Studies", "abstract": ["BACKGROUND Genetic and epidemiological evidence suggests an inverse association between B-type natriuretic peptide (BNP) levels in blood and risk of type 2 diabetes (T2D), but the prospective association of BNP with T2D is uncertain, and it is unclear whether the association is confounded.   \n", "METHODS AND FINDINGS We analysed the association between levels of the N-terminal fragment of pro-BNP (NT-pro-BNP) in blood and risk of incident T2D in a prospective case-cohort study and genotyped the variant rs198389 within the BNP locus in three T2D case-control studies.", "We combined our results with existing data in a meta-analysis of 11 case-control studies.", "Using a Mendelian randomization approach, we compared the observed association between rs198389 and T2D to that expected from the NT-pro-BNP level to T2D association and the NT-pro-BNP difference per C allele of rs198389.", "In participants of our case-cohort study who were free of T2D and cardiovascular disease at baseline, we observed a 21% (95% CI 3%-36%) decreased risk of incident T2D per one standard deviation (SD) higher log-transformed NT-pro-BNP levels in analysis adjusted for age, sex, body mass index, systolic blood pressure, smoking, family history of T2D, history of hypertension, and levels of triglycerides, high-density lipoprotein cholesterol, and low-density lipoprotein cholesterol.", "The association between rs198389 and T2D observed in case-control studies (odds ratio = 0.94 per C allele, 95% CI 0.91-0.97) was similar to that expected (0.96, 0.93-0.98) based on the pooled estimate for the log-NT-pro-BNP level to T2D association derived from a meta-analysis of our study and published data (hazard ratio = 0.82 per SD, 0.74-0.90) and the difference in NT-pro-BNP levels (0.22 SD, 0.15-0.29) per C allele of rs198389.", "No significant associations were observed between the rs198389 genotype and potential confounders.   \n", "CONCLUSIONS Our results provide evidence for a potential causal role of the BNP system in the aetiology of T2D.", "Further studies are needed to investigate the mechanisms underlying this association and possibilities for preventive interventions.", "Please see later in the article for the Editors' Summary."], "structured": true}
{"doc_id": 15669393, "title": "brain organization", "abstract": ["Transient activation of estrogen receptors (ER) in the developing brain during a limited perinatal \"window of time\" is recognized as a key mechanism of defeminization of neural control of reproductive function and sexual behavior.", "Two major ER isoforms, alpha and beta, are present in neural circuits that govern ovarian cycle and sexual behavior.", "Using highly selective ER agonists, this study provides the first evidence for distinct contribution of individual ER isoforms to the process of estrogen dependent defeminization.", "Neonatal activation of the ERalpha in female rats resulted in abrogation of cyclic ovarian activity and female sexual behavior in adulthood.", "These effects are associated with male-like alterations in the morphology of the anteroventral periventricular (AVPV) and sexually dimorphic nucleus of the preoptic area (SDN-POA), as well as refractoriness to estrogen-mediated induction of sexual receptivity.", "Exposure to an ERbeta-selective agonist induced persistent estrus and had a strong defeminizing effect on the hypothalamic gonadotropin \"surge generator\" AVPV.", "However, neonatal ERbeta activation failed to alter female sexual behavior, responsiveness to estrogens and morphometric features of the behaviorally relevant SDN-POA.", "Thus, although co-present in several brain regions involved in the control of female reproductive function, ER isoforms convey different, and probably not synergistic, chemical signals in the course of neonatal sex-specific brain organization."], "structured": false}
{"doc_id": 15670968, "title": "Thresholds for the cost\u2013effectiveness of interventions: alternative approaches", "abstract": ["Many countries use the cost-effectiveness thresholds recommended by the World Health Organization's Choosing Interventions that are Cost-Effective project (WHO-CHOICE) when evaluating health interventions.", "This project sets the threshold for cost-effectiveness as the cost of the intervention per disability-adjusted life-year (DALY) averted less than three times the country's annual gross domestic product (GDP) per capita.", "Highly cost-effective interventions are defined as meeting a threshold per DALY averted of once the annual GDP per capita.", "We argue that reliance on these thresholds reduces the value of cost-effectiveness analyses and makes such analyses too blunt to be useful for most decision-making in the field of public health.", "Use of these thresholds has little theoretical justification, skirts the difficult but necessary ranking of the relative values of locally-applicable interventions and omits any consideration of what is truly affordable.", "The WHO-CHOICE thresholds set such a low bar for cost-effectiveness that very few interventions with evidence of efficacy can be ruled out.", "The thresholds have little value in assessing the trade-offs that decision-makers must confront.", "We present alternative approaches for applying cost-effectiveness criteria to choices in the allocation of health-care resources."], "structured": false}
{"doc_id": 15678772, "title": "Effect of low doses of ionising radiation in infancy on cognitive function in adulthood: Swedish population based cohort study.", "abstract": ["OBJECTIVE To determine whether exposure to low doses of ionising radiation in infancy affects cognitive function in adulthood.   \n", "DESIGN Population based cohort study.   \n", "SETTING Sweden.   \n", "PARTICIPANTS 3094 men who had received radiation for cutaneous haemangioma before age 18 months during 1930-59.   \n", "MAIN OUTCOME MEASURES Radiation dose to frontal and posterior parts of the brain, and association between dose and intellectual capacity at age 18 or 19 years based on cognitive tests (learning ability, logical reasoning, spatial recognition) and high school attendance.   \n", "RESULTS The proportion of boys who attended high school decreased with increasing doses of radiation to both the frontal and the posterior parts of the brain from about 32% among those not exposed to around 17% in those who received > 250 mGy.", "For the frontal dose, the multivariate odds ratio was 0.47 (95% confidence interval 0.26 to 0.85, P for trend 0.0003) and for the posterior dose it was 0.59 (0.23 to 1.47, 0.0005).", "A negative dose-response relation was also evident for the three cognitive tests for learning ability and logical reasoning but not for the test of spatial recognition.   \n", "CONCLUSIONS Low doses of ionising radiation to the brain in infancy influence cognitive abilities in adulthood."], "structured": true}
{"doc_id": 15685921, "title": "Differential effects of charybdotoxin on the activity of retinal ganglion cells in the dark- and light-adapted mouse retina", "abstract": ["Patch-clamp recordings were made from retinal ganglion cells in the mouse retina.", "Under dark adaptation, blockage of BK(Ca) channels increases the spontaneous excitatory postsynaptic currents (EPSCs) and light-evoked On-EPSCs, while it decreases the light-evoked Off inhibitory postsynaptic currents (IPSCs).", "However, under light adaptation it decreases the light-evoked On-EPSCs, the spontaneous IPSCs and the light-evoked On- and Off-IPSCs.", "Blockage of BK(Ca) channels significantly altered the outputs of RGCs by changing their light-evoked responses into a bursting pattern and increasing the light-evoked depolarization of the membrane potentials, while it did not significantly change the peak firing rates of light-evoked responses."], "structured": false}
{"doc_id": 15692098, "title": "Hutchinson-Gilford progeria syndrome: review of the phenotype", "abstract": ["Hutchinson-Gilford progeria syndrome (HGPS) is a rare but well known entity characterized by extreme short stature, low body weight, early loss of hair, lipodystrophy, scleroderma, decreased joint mobility, osteolysis, and facial features that resemble aged persons.", "Cardiovascular compromise leads to early demise.", "Cognitive development is normal.", "Data on 10 of our own cases and 132 cases from literature are presented.", "The incidence in the last century in the Netherlands was 1:4,000,000.", "Sex ratio was 1.2:1.", "Main first symptoms were failure to thrive (55%), hair loss (40%), skin problems (28%), and lipodystrophy (20%).", "Mean age at diagnosis was 2.9 years.", "Growth in weight was more disturbed than growth in height, and growth delay started already prenatally.", "Mean height > 13 years was 109.0 cm, mean weight was 14.5 kg.", "Osteolysis was wide-spread but not expressed, except in the viscerocranium, and remained limited to membranous formed bone.", "Lipodystrophy is generalized, only intra-abdominal fat depositions remain present.", "Cardiovascular problems are extremely variable, both in age of onset and nature.", "Stroke and coronary dysfunctioning are most frequent.", "Pathologic findings in coronaries and aorta resemble sometimes the findings in elderly persons, but can also be much more limited.", "Loss of smooth muscle cells seems the most important finding.", "Mean age of demise was 12.6 years.", "Patients can be subdivided in patients with classical HGPS, which follows an autosomal dominant pattern of inheritance, (almost) all cases representing spontaneous mutations, and in non-classical progeria, in whom growth can be less retarded, scalp hair remains present for a longer time, lipodystrophy is more slowly progressive, osteolysis is more expressed except in the face, and survival well into adulthood is not uncommon.", "Pattern of inheritance of non-classical progeria is most probably autosomal recessive.", "The cause of HGPS is an abnormally formed Lamin A, either directly by a mutated LMNA gene, or through abnormal posttranslational processing (ZMPSTE24 gene mutations).", "Of 34 LMNA mutations found in progeria patients, there were 26 classical p.", "G608G mutations (76%).", "Pathogenesis is most likely to follow several different pathways.", "Potential therapeutic strategies are developed along these lines and include RNA interference techniques and inhibition of the dominant-negative influence of abnormally formed Lamin A on polymerization with normally formed Lamin A."], "structured": false}
{"doc_id": 15707049, "title": "Identification of an autoantigen demonstrates a link between interstitial lung disease and a defect in central tolerance.", "abstract": ["Interstitial lung disease (ILD) is a common manifestation of systemic autoimmunity characterized by progressive inflammation or scarring of the lungs.", "Patients who develop these complications can exhibit significantly impaired gas exchange that may result in hypoxemia, pulmonary hypertension, and even death.", "Unfortunately, little is understood about how these diseases arise, including the role of specific defects in immune tolerance.", "Another key question is whether autoimmune responses targeting the lung parenchyma are critical to ILD pathogenesis, including that of isolated idiopathic forms.", "We show that a specific defect in central tolerance brought about by mutations in the autoimmune regulator gene (Aire) leads to an autoreactive T cell response to a lung antigen named vomeromodulin and the development of ILD.", "We found that a human patient and mice with defects in Aire develop similar lung pathology, demonstrating that the AIRE-deficient model of autoimmunity is a suitable translational system in which to unravel fundamental mechanisms of ILD pathogenesis."], "structured": false}
{"doc_id": 15716328, "title": "In vivo role of ER-associated peptidase activity in tailoring peptides for presentation by MHC class Ia and class Ib molecules", "abstract": ["Endoplasmic reticulum (ER)-associated aminopeptidase (ERAP)1 has been implicated in the final proteolytic processing of peptides presented by major histocompatibility complex (MHC) class I molecules.", "To evaluate the in vivo role of ERAP1, we have generated ERAP1-deficient mice.", "Cell surface expression of the class Ia molecules H-2Kb and H-2Db and of the class Ib molecule Qa-2 was significantly reduced in these animals.", "Although cells from mutant animals exhibited reduced capacity to present several self- and foreign antigens to Kb-, Db-, or Qa-1b\u2013restricted CD8+ cytotoxic T cells, presentation of some antigens was unaffected or significantly enhanced.", "Consistent with these findings, mice generated defective CD8+ T cell responses against class I\u2013presented antigens.", "These findings reveal an important in vivo role of ER-associated peptidase activity in tailoring peptides for presentation by MHC class Ia and class Ib molecules."], "structured": false}
{"doc_id": 15721252, "title": "PD 0332991, a selective cyclin D kinase 4/6 inhibitor, preferentially inhibits proliferation of luminal estrogen receptor-positive human breast cancer cell lines in vitro", "abstract": ["INTRODUCTION Alterations in cell cycle regulators have been implicated in human malignancies including breast cancer.", "PD 0332991 is an orally active, highly selective inhibitor of the cyclin D kinases (CDK)4 and CDK6 with ability to block retinoblastoma (Rb) phosphorylation in the low nanomolar range.", "To identify predictors of response, we determined the in vitro sensitivity to PD 0332991 across a panel of molecularly characterized human breast cancer cell lines.   \n", "METHODS Forty-seven human breast cancer and immortalized cell lines representing the known molecular subgroups of breast cancer were treated with PD 0332991 to determine IC50 values.", "These data were analyzed against baseline gene expression data to identify genes associated with PD 0332991 response.   \n", "RESULTS Cell lines representing luminal estrogen receptor-positive (ER+) subtype (including those that are HER2 amplified) were most sensitive to growth inhibition by PD 0332991 while nonluminal/basal subtypes were most resistant.", "Analysis of variance identified 450 differentially expressed genes between sensitive and resistant cells.", "pRb and cyclin D1 were elevated and CDKN2A (p16) was decreased in the most sensitive lines.", "Cell cycle analysis showed G0/G1 arrest in sensitive cell lines and Western blot analysis demonstrated that Rb phosphorylation is blocked in sensitive lines but not resistant lines.", "PD 0332991 was synergistic with tamoxifen and trastuzumab in ER+ and HER2-amplified cell lines, respectively.", "PD 0332991 enhanced sensitivity to tamoxifen in cell lines with conditioned resistance to ER blockade.   \n", "CONCLUSIONS These studies suggest a role for CDK4/6 inhibition in some breast cancers and identify criteria for patient selection in clinical studies of PD 0332991"], "structured": true}
{"doc_id": 15727984, "title": "Identification of secreted proteins that mediate cell-cell interactions in an in vitro model of the lung cancer microenvironment.", "abstract": ["Non-small cell lung cancer (NSCLC) cells with somatic mutations in K-ras recruit to the tumor a variety of cell types (hereafter collectively termed \"stromal cells\") that can promote or inhibit tumorigenesis by mechanisms that have not been fully elucidated.", "Here, we postulated that stromal cells in the tumor microenvironment alter the tumor cell secretome, including those proteins required for tumor growth and dissemination, and we developed an in vitro model to test this hypothesis.", "Coculturing a murine K-ras mutant lung adenocarcinoma cell line (LKR-13) with a murine lung stromal cell (macrophage, endothelial cell, or fibroblast) enhanced stromal cell migration, induced endothelial tube formation, increased LKR-13 cell proliferation, and regulated the secretion of proteins involved in angiogenesis, inflammation, cell proliferation, and epithelial-to-mesenchymal transition.", "Among these proteins, CXCL1 has been reported to promote NSCLC development, whereas interleukin-18 (IL-18) has an undefined role.", "Genetic and pharmacologic strategies to inhibit CXCL1 and IL-18 revealed that stromal cell migration, LKR-13 cell proliferation, and LKR-13 cell tumorigenicity required one or both of these proteins.", "We conclude that stromal cells enhanced LKR-13 cell tumorigenicity partly through their effects on the secretome of LKR-13 cells.", "Strategies to inhibit tumor/stromal cell interactions may be useful as therapeutic approaches in NSCLC patients."], "structured": false}
{"doc_id": 15728433, "title": "Tightrope act: autophagy in stem cell renewal, differentiation, proliferation, and aging", "abstract": ["Autophagy is a constitutive lysosomal catabolic pathway that degrades damaged organelles and protein aggregates.", "Stem cells are characterized by self-renewal, pluripotency, and quiescence; their long life span, limited capacity to dilute cellular waste and spent organelles due to quiescence, along with their requirement for remodeling in order to differentiate, all suggest that they require autophagy more than other cell types.", "Here, we review the current literature on the role of autophagy in embryonic and adult stem cells, including hematopoietic, mesenchymal, and neuronal stem cells, highlighting the diverse and contrasting roles autophagy plays in their biology.", "Furthermore, we review the few studies on stem cells, lysosomal activity, and autophagy.", "Novel techniques to detect autophagy in primary cells are required to study autophagy in different stem cell types.", "These will help to elucidate the importance of autophagy in stem cells during transplantation, a promising therapeutic approach for many diseases."], "structured": false}
{"doc_id": 15778034, "title": "Variant Histone H2A.Z Is Globally Localized to the Promoters of Inactive Yeast Genes and Regulates Nucleosome Positioning", "abstract": ["H2A.Z is an evolutionary conserved histone variant involved in transcriptional regulation, antisilencing, silencing, and genome stability.", "The mechanism(s) by which H2A.Z regulates these various biological functions remains poorly defined, in part due to the lack of knowledge regarding its physical location along chromosomes and the bearing it has in regulating chromatin structure.", "Here we mapped H2A.Z across the yeast genome at an approximately 300-bp resolution, using chromatin immunoprecipitation combined with tiling microarrays.", "We have identified 4,862 small regions\u2014typically one or two nucleosomes wide\u2014decorated with H2A.Z. Those \u201cZ loci\u201d are predominantly found within specific nucleosomes in the promoter of inactive genes all across the genome.", "Furthermore, we have shown that H2A.Z can regulate nucleosome positioning at the GAL1 promoter.", "Within HZAD domains, the regions where H2A.Z shows an antisilencing function, H2A.Z is localized in a wider pattern, suggesting that the variant histone regulates a silencing and transcriptional activation via different mechanisms.", "Our data suggest that the incorporation of H2A.Z into specific promoter-bound nucleosomes configures chromatin structure to poise genes for transcriptional activation.", "The relevance of these findings to higher eukaryotes is discussed."], "structured": false}
{"doc_id": 15780826, "title": "Collective trauma in northern Sri Lanka: a qualitative psychosocial-ecological study", "abstract": ["BACKGROUND Complex situations that follow war and natural disasters have a psychosocial impact on not only the individual but also on the family, community and society.", "Just as the mental health effects on the individual psyche can result in non pathological distress as well as a variety of psychiatric disorders; massive and widespread trauma and loss can impact on family and social processes causing changes at the family, community and societal levels.   \n", "METHOD This qualitative, ecological study is a naturalistic, psychosocial ethnography in Northern Sri Lanka, while actively involved in psychosocial and community mental health programmes among the Tamil community.", "Participatory observation, key informant interviews and focus group discussion with community level relief and rehabilitation workers and government and non-governmental officials were used to gather data.", "The effects on the community of the chronic, man-made disaster, war, in Northern Sri Lanka were compared with the contexts found before the war and after the tsunami.   \n", "RESULTS Fundamental changes in the functioning of the family and the community were observed.", "While the changes after the tsunami were not so prominent, the chronic war situation caused more fundamental social transformations.", "At the family level, the dynamics of single parent families, lack of trust among members, and changes in significant relationships, and child rearing practices were seen.", "Communities tended to be more dependent, passive, silent, without leadership, mistrustful, and suspicious.", "Additional adverse effects included the breakdown in traditional structures, institutions and familiar ways of life, and deterioration in social norms and ethics.", "A variety of community level interventions were tried.   \n", "CONCLUSION Exposure to conflict, war and disaster situations impact on fundamental family and community dynamics resulting in changes at a collective level.", "Relief, rehabilitation and development programmes to be effective will need to address the problem of collective trauma, particularly using integrated multi-level approaches."], "structured": true}
{"doc_id": 15790930, "title": "Guidelines for the selection of highly effective siRNA sequences for mammalian and chick RNA interference.", "abstract": ["In the present study, the relationship between short interfering RNA (siRNA) sequence and RNA interference (RNAi) effect was extensively analyzed using 62 targets of four exogenous and two endogenous genes and three mammalian and Drosophila cells.", "We present the rules that may govern siRNA sequence preference and in accordance with which highly effective siRNAs essential for systematic mammalian functional genomics can be readily designed.", "These rules indicate that siRNAs which simultaneously satisfy all four of the following sequence conditions are capable of inducing highly effective gene silencing in mammalian cells: (i) A/U at the 5' end of the antisense strand; (ii) G/C at the 5' end of the sense strand; (iii) at least five A/U residues in the 5' terminal one-third of the antisense strand; and (iv) the absence of any GC stretch of more than 9 nt in length.", "siRNAs opposite in features with respect to the first three conditions give rise to little or no gene silencing in mammalian cells.", "Essentially the same rules for siRNA sequence preference were found applicable to DNA-based RNAi in mammalian cells and in ovo RNAi using chick embryos.", "In contrast to mammalian and chick cells, little siRNA sequence preference could be detected in Drosophila in vivo RNAi."], "structured": false}
{"doc_id": 15795880, "title": "Overview of the CCP4 suite and current developments", "abstract": ["The CCP4 (Collaborative Computational Project, Number 4) software suite is a collection of programs and associated data and software libraries which can be used for macromolecular structure determination by X-ray crystallography.", "The suite is designed to be flexible, allowing users a number of methods of achieving their aims.", "The programs are from a wide variety of sources but are connected by a common infrastructure provided by standard file formats, data objects and graphical interfaces.", "Structure solution by macromolecular crystallography is becoming increasingly automated and the CCP4 suite includes several automation pipelines.", "After giving a brief description of the evolution of CCP4 over the last 30 years, an overview of the current suite is given.", "While detailed descriptions are given in the accompanying articles, here it is shown how the individual programs contribute to a complete software package."], "structured": false}
{"doc_id": 15803282, "title": "Histone Demethylase Expression Enhances Human Somatic Cell Nuclear Transfer Efficiency and Promotes Derivation of Pluripotent Stem Cells.", "abstract": ["The extremely low efficiency of human embryonic stem cell (hESC) derivation using somatic cell nuclear transfer (SCNT) limits its potential application.", "Blastocyst formation from human SCNT embryos occurs at a low rate and with only some oocyte donors.", "We previously showed in mice that reduction of histone H3 lysine 9 trimethylation (H3K9me3) through ectopic expression of the H3K9me3 demethylase Kdm4d greatly improves SCNT embryo development.", "Here we show that overexpression of a related H3K9me3 demethylase KDM4A improves human SCNT, and that, as in mice, H3K9me3 in the human somatic cell genome is an SCNT reprogramming barrier.", "Overexpression of KDM4A significantly improves the blastocyst formation rate in human SCNT embryos by facilitating transcriptional reprogramming, allowing efficient derivation of SCNT-derived ESCs using adult Age-related Macular Degeneration (AMD) patient somatic nuclei donors.", "This conserved mechanistic insight has potential applications for improving SCNT in a variety of contexts, including regenerative medicine."], "structured": false}
{"doc_id": 15816729, "title": "Interface Contractility between Differently Fated Cells Drives Cell Elimination and Cyst Formation", "abstract": ["Although cellular tumor-suppression mechanisms are widely studied, little is known about mechanisms that act at the level of tissues to suppress the occurrence of aberrant cells in epithelia.", "We find that ectopic expression of transcription factors that specify cell fates causes abnormal epithelial cysts in Drosophila imaginal discs.", "Cysts do not form cell autonomously but result from the juxtaposition of two cell populations with divergent fates.", "Juxtaposition of wild-type and aberrantly specified cells induces enrichment of actomyosin at their entire shared interface, both at adherens junctions as well as along basolateral interfaces.", "Experimental validation of 3D vertex model simulations demonstrates that enhanced interface contractility is sufficient to explain many morphogenetic behaviors, which depend on cell cluster size.", "These range from cyst formation by intermediate-sized clusters to segregation of large cell populations by formation of smooth boundaries or apical constriction in small groups of cells.", "In addition, we find that single cells experiencing lateral interface contractility are eliminated from tissues by apoptosis.", "Cysts, which disrupt epithelial continuity, form when elimination of single, aberrantly specified cells fails and cells proliferate to intermediate cell cluster sizes.", "Thus, increased interface contractility functions as error correction mechanism eliminating single aberrant cells from tissues, but failure leads to the formation of large, potentially disease-promoting cysts.", "Our results provide a novel perspective on morphogenetic mechanisms, which arise from cell-fate heterogeneities within tissues and maintain or disrupt epithelial homeostasis."], "structured": false}
{"doc_id": 15830352, "title": "Resonating circadian clocks enhance fitness in cyanobacteria.", "abstract": ["In some organisms longevity, growth, and developmental rate are improved when they are maintained on a light/dark cycle, the period of which \"resonates\" optimally with the period of the endogenous circadian clock.", "However, to our knowledge no studies have demonstrated that reproductive fitness per se is improved by resonance between the endogenous clock and the environmental cycle.", "We tested the adaptive significance of circadian programming by measuring the relative fitness under competition between various strains of cyanobacteria expressing different circadian periods.", "Strains that had a circadian period similar to that of the light/dark cycle were favored under competition in a manner that indicates the action of soft selection."], "structured": false}
{"doc_id": 15832146, "title": "Stromal Fibroblasts Present in Invasive Human Breast Carcinomas Promote Tumor Growth and Angiogenesis through Elevated SDF-1/CXCL12 Secretion", "abstract": ["Fibroblasts often constitute the majority of the stromal cells within a breast carcinoma, yet the functional contributions of these cells to tumorigenesis are poorly understood.", "Using a coimplantation tumor xenograft model, we demonstrate that carcinoma-associated fibroblasts (CAFs) extracted from human breast carcinomas promote the growth of admixed breast carcinoma cells significantly more than do normal mammary fibroblasts derived from the same patients.", "The CAFs, which exhibit the traits of myofibroblasts, play a central role in promoting the growth of tumor cells through their ability to secrete stromal cell-derived factor 1 (SDF-1); CAFs promote angiogenesis by recruiting endothelial progenitor cells (EPCs) into carcinomas, an effect mediated in part by SDF-1.", "CAF-secreted SDF-1 also stimulates tumor growth directly, acting through the cognate receptor, CXCR4, which is expressed by carcinoma cells.", "Our findings indicate that fibroblasts within invasive breast carcinomas contribute to tumor promotion in large part through the secretion of SDF-1."], "structured": false}
{"doc_id": 15833835, "title": "Embryonic Origin of Postnatal Neural Stem Cells", "abstract": ["Adult neural stem/progenitor (B1) cells within the walls of the lateral ventricles generate different types of neurons for the olfactory bulb (OB).", "The location of B1 cells determines the types of OB neurons they generate.", "Here we show that the majority of mouse B1 cell precursors are produced between embryonic days (E) 13.5 and 15.5 and remain largely quiescent until they become reactivated postnatally.", "Using a retroviral library carrying over 100,000 genetic tags, we found that B1 cells share a common progenitor with embryonic cells of the cortex, striatum, and septum, but this lineage relationship is lost before E15.5.", "The regional specification of B1 cells is evident as early as E11.5 and is spatially linked to the production of neurons that populate different areas of the forebrain.", "This study reveals an early embryonic regional specification of postnatal neural stem cells and the lineage relationship between them and embryonic progenitor cells."], "structured": false}
{"doc_id": 15836115, "title": "The Opa1-Dependent Mitochondrial Cristae Remodeling Pathway Controls Atrophic, Apoptotic, and Ischemic Tissue Damage", "abstract": ["Mitochondrial morphological and ultrastructural changes occur during apoptosis and autophagy, but whether they are relevant in vivo for tissue response to damage is unclear.", "Here we investigate the role of the optic atrophy 1 (OPA1)-dependent cristae remodeling pathway in vivo and provide evidence that it regulates the response of multiple tissues to apoptotic, necrotic, and atrophic stimuli.", "Genetic inhibition of the cristae remodeling pathway in vivo does not affect development, but protects mice from denervation-induced muscular atrophy, ischemic heart and brain damage, as well as hepatocellular apoptosis.", "Mechanistically, OPA1-dependent mitochondrial cristae stabilization increases mitochondrial respiratory efficiency and blunts mitochondrial dysfunction, cytochrome c release, and reactive oxygen species production.", "Our results indicate that the OPA1-dependent cristae remodeling pathway is a fundamental, targetable determinant of tissue damage in vivo."], "structured": false}
{"doc_id": 15856466, "title": "First Proposal of Minimum Information About a Cellular Assay for Regenerative Medicine", "abstract": [": Advances in stem cell research have triggered scores of studies in regenerative medicine in a large number of institutions and companies around the world.", "However, reproducibility and data exchange among laboratories or cell banks are constrained by the lack of a standardized format for experiments.", "To enhance information flow in stem cell and derivative cell research, here we propose a minimum information standard to describe cellular assay data to facilitate practical regenerative medicine.", "Based on the existing Minimum Information About a Cellular Assay, we developed Minimum Information About a Cellular Assay for Regenerative Medicine (MIACARM), which allows for the description of advanced cellular experiments with defined taxonomy of human cell types.", "By using controlled terms, such as ontologies, MIACARM will provide a platform for cellular assay data exchange among cell banks or registries that have been established at more than 20 sites in the world.   ", "SIGNIFICANCE Currently, there are more than 20 human cell information storage sites around the world.", "However, reproducibility and data exchange among different laboratories or cell information providers are usually inadequate or nonexistent because of the lack of a standardized format for experiments.", "This study, which is the fruit of collaborative work by scientists at stem cell banks and cellular information registries worldwide, including those in the U.S., the U.K., Europe, and Japan, proposes new minimum information guidelines, Minimum Information About a Cellular Assay for Regenerative Medicine (MIACARM), for cellular assay data deposition.", "MIACARM is intended to promote data exchange and facilitation of practical regenerative medicine."], "structured": false}
{"doc_id": 15868816, "title": "The PAR proteins: fundamental players in animal cell polarization.", "abstract": ["The par genes were discovered in genetic screens for regulators of cytoplasmic partitioning in the early embryo of C. elegans, and encode six different proteins required for asymmetric cell division by the worm zygote.", "Some of the PAR proteins are localized asymmetrically and form physical complexes with one another.", "Strikingly, the PAR proteins have been found to regulate cell polarization in many different contexts in diverse animals, suggesting they form part of an ancient and fundamental mechanism for cell polarization.", "Although the picture of how the PAR proteins function remains incomplete, cell biology and biochemistry are beginning to explain how PAR proteins polarize cells."], "structured": false}
{"doc_id": 15879544, "title": "Prions Adhere to Soil Minerals and Remain Infectious", "abstract": ["An unidentified environmental reservoir of infectivity contributes to the natural transmission of prion diseases (transmissible spongiform encephalopathies [TSEs]) in sheep, deer, and elk.", "Prion infectivity may enter soil environments via shedding from diseased animals and decomposition of infected carcasses.", "Burial of TSE-infected cattle, sheep, and deer as a means of disposal has resulted in unintentional introduction of prions into subsurface environments.", "We examined the potential for soil to serve as a TSE reservoir by studying the interaction of the disease-associated prion protein (PrPSc) with common soil minerals.", "In this study, we demonstrated substantial PrPSc adsorption to two clay minerals, quartz, and four whole soil samples.", "We quantified the PrPSc-binding capacities of each mineral.", "Furthermore, we observed that PrPSc desorbed from montmorillonite clay was cleaved at an N-terminal site and the interaction between PrPSc and Mte was strong, making desorption of the protein difficult.", "Despite cleavage and avid binding, PrPSc bound to Mte remained infectious.", "Results from our study suggest that PrPSc released into soil environments may be preserved in a bioavailable form, perpetuating prion disease epizootics and exposing other species to the infectious agent."], "structured": false}
{"doc_id": 15879931, "title": "Regulated Accumulation of Desmosterol Integrates Macrophage Lipid Metabolism and Inflammatory Responses", "abstract": ["Inflammation and macrophage foam cells are characteristic features of atherosclerotic lesions, but the mechanisms linking cholesterol accumulation to inflammation and LXR-dependent response pathways are poorly understood.", "To investigate this relationship, we utilized lipidomic and transcriptomic methods to evaluate the effect of diet and LDL receptor genotype on macrophage foam cell formation within the peritoneal cavities of mice.", "Foam cell formation was associated with significant changes in hundreds of lipid species and unexpected suppression, rather than activation, of inflammatory gene expression.", "We provide evidence that regulated accumulation of desmosterol underlies many of the homeostatic responses, including activation of LXR target genes, inhibition of SREBP target genes, selective reprogramming of fatty acid metabolism, and suppression of inflammatory-response genes, observed in macrophage foam cells.", "These observations suggest that macrophage activation in atherosclerotic lesions results from extrinsic, proinflammatory signals generated within the artery wall that suppress homeostatic and anti-inflammatory functions of desmosterol."], "structured": false}
{"doc_id": 15889329, "title": "A JOURNAL OF NEUROLOGY", "abstract": ["Brain glial cells, five times more prevalent than neurons, have recently received attention for their potential involvement in epileptic seizures.", "Microglia and astrocytes, associated with inflammatory innate immune responses, are responsible for surveillance of brain damage that frequently results in seizures.", "Thus, an intriguing suggestion has been put forward that seizures may be facilitated and perhaps triggered by brain immune responses.", "Indeed, recent evidence strongly implicates innate immune responses in lowering seizure threshold in experimental models of epilepsy, yet, there is no proof that they can play an independent role in initiating seizures in vivo.", "Here, we show that cortical innate immune responses alone produce profound increases of brain excitability resulting in focal seizures.", "We found that cortical application of lipopolysaccharide, binding to toll-like receptor 4 (TLR4), triples evoked field potential amplitudes and produces focal epileptiform discharges.", "These effects are prevented by pre-application of interleukin-1 receptor antagonist.", "Our results demonstrate how the innate immune response may participate in acute seizures, increasing neuronal excitability through interleukin-1 release in response to TLR4 detection of the danger signals associated with infections of the central nervous system and with brain injury.", "These results suggest an important role of innate immunity in epileptogenesis and focus on glial inhibition, through pharmacological blockade of TLR4 and the pro-inflammatory mediators released by activated glia, in the study and treatment of seizure disorders in humans."], "structured": false}
{"doc_id": 15893330, "title": "Sequential domain assembly of ribosomal protein S3 drives 40S subunit maturation.", "abstract": ["Eukaryotic ribosomes assemble by association of ribosomal RNA with ribosomal proteins into nuclear precursor particles, which undergo a complex maturation pathway coordinated by non-ribosomal assembly factors.", "Here, we provide functional insights into how successive structural re-arrangements in ribosomal protein S3 promote maturation of the 40S ribosomal subunit.", "We show that S3 dimerizes and is imported into the nucleus with its N-domain in a rotated conformation and associated with the chaperone Yar1.", "Initial assembly of S3 with 40S precursors occurs via its C-domain, while the N-domain protrudes from the 40S surface.", "Yar1 is replaced by the assembly factor Ltv1, thereby fixing the S3 N-domain in the rotated orientation and preventing its 40S association.", "Finally, Ltv1 release, triggered by phosphorylation, and flipping of the S3 N-domain into its final position results in the stable integration of S3.", "Such a stepwise assembly may represent a new paradigm for the incorporation of ribosomal proteins."], "structured": false}
{"doc_id": 15907458, "title": "Assaying proliferation and differentiation capacity of stem cells using disaggregated adult mouse epidermis", "abstract": ["In this protocol, we describe how to isolate keratinocytes from adult mouse epidermis, fractionate them into different sub-populations on the basis of cell surface markers and examine their function in an in vivo skin reconstitution assay with disaggregated neonatal dermal cells.", "We also describe how the isolated keratinocytes can be subjected to clonal analysis in vitro and in vivo and how to enrich for hair follicle-inducing dermal papilla cells in the dermal preparation.", "Using these approaches, it is possible to compare the capacity of different populations of adult epidermal stem cells to proliferate and to generate progeny that differentiate along the different epidermal lineages.", "Isolating, fractionating and grafting cells for the skin reconstitution assay is normally spread over 2 d. Clonal growth in culture is assessed after 14 d, while evaluation of the grafts is carried out after 4\u20135 weeks."], "structured": false}
{"doc_id": 15913433, "title": "Telomerase-negative immortalized human cells contain a novel type of promyelocytic leukemia (PML) body.", "abstract": ["Telomerase-negative immortalized human cells maintain their telomeres by a mechanism known as alternative lengthening of telomeres (ALT).", "We report here that ALT cells contain a novel promyelocytic leukemia (PML) body (ALT-associated PML body, APB).", "APBs are large donut-shaped nuclear structures containing PML protein, telomeric DNA, and the telomere binding proteins human telomere repeat binding factors 1 and 2.", "Immunostaining showed that APBs also contain replication factor A, RAD51, and RAD52, proteins involved in DNA synthesis and recombination.", "During immortalization, APBs appeared at exactly the same time as activation of ALT.", "APBs were found in ALT tumors and cell lines but not in mortal cell strains or in telomerase-positive cell lines or tumors."], "structured": false}
{"doc_id": 15925931, "title": "Prediction of coronary artery disease by a systemic atherosclerosis score index derived from whole-body MR angiography", "abstract": ["BACKGROUND Whole-body magnetic resonance angiography (WB-MRA) has shown its potential for the non-invasive assessment of nearly the entire arterial vasculature within one examination.", "Since the presence of extra-cardiac atherosclerosis is associated with an increased risk of coronary events, our goal was to establish the relationship between WB-MRA findings, including a systemic atherosclerosis score index, and the presence of significant coronary artery disease (CAD).   \n", "METHODS WB-MRA was performed on a 1.5T scanner in 50 patients scheduled to undergo elective cardiac catheterization for suspected CAD.", "In each patient, 40 extra-cardiac vessel segments were evaluated and assigned scores according to their luminal narrowing.", "The atherosclerosis score index (ASI) was generated as the ratio of summed scores to analyzable segments.   \n", "RESULTS ASI was higher in patients with significant (> 50% stenosis) CAD (n = 27) vs. patients without CAD (n = 22; 1.56 vs. 1.28, p = 0.004).", "ASI correlated with PROCAM (R = 0.57, p < 0.001) and Framingham (R = 0.36, p = 0.01) risk scores as estimates of the 10-year risk of coronary events.", "A ROC derived ASI of > 1.54 predicted significant CAD with a sensitivity of 59%, specificity of 86% and a positive predictive value of 84%.", "Logistic regression revealed ASI > 1.54 as the strongest independent predictor for CAD with a 11-fold increase in likelihood to suffer from significant coronary disease.", "On the contrary, while 15/27 (55%) of patients with CAD exhibited at least one extra-cardiac stenosis > 50%, only 3/22 (14%) of those patients without CAD did (p = 0.003).", "The likelihood for an extra-cardiac stenosis when CAD is present differed between vascular territories and ranged from 15% for a carotid stenosis to 44% for a stenosis in the lower extremities.   \n", "CONCLUSION This study provides important new evidence for the close association of extra-cardiac and coronary atherosclerosis.", "The novel findings that a WB-MRA derived systemic atherosclerosis score index is not only associated with established cardiovascular risk scores but is also predictive of significant CAD suggest its potential prognostic implications and underline the importance to screen for coronary disease in patients with extra-cardiac manifestations of atherosclerosis."], "structured": true}
{"doc_id": 15926408, "title": "Analysis of re-replication from deregulated origin licensing by DNA fiber spreading", "abstract": ["A major challenge each human cell-division cycle is to ensure that DNA replication origins do not initiate more than once, a phenomenon known as re-replication.", "Acute deregulation of replication control ultimately causes extensive DNA damage, cell-cycle checkpoint activation and cell death whereas moderate deregulation promotes genome instability and tumorigenesis.", "In the absence of detectable increases in cellular DNA content however, it has been difficult to directly demonstrate re-replication or to determine if the ability to re-replicate is restricted to a particular cell-cycle phase.", "Using an adaptation of DNA fiber spreading we report the direct detection of re-replication on single DNA molecules from human chromosomes.", "Using this method we demonstrate substantial re-replication within 1 h of S phase entry in cells overproducing the replication factor, Cdt1.", "Moreover, a comparison of the HeLa cancer cell line to untransformed fibroblasts suggests that HeLa cells produce replication signals consistent with low-level re-replication in otherwise unperturbed cell cycles.", "Re-replication after depletion of the Cdt1 inhibitor, geminin, in an untransformed fibroblast cell line is undetectable by standard assays but readily quantifiable by DNA fiber spreading analysis.", "Direct evaluation of re-replicated DNA molecules will promote increased understanding of events that promote or perturb genome stability."], "structured": false}
{"doc_id": 15928989, "title": "Liver receptor homolog-1 is essential for pregnancy", "abstract": ["Successful pregnancy requires coordination of an array of signals and factors from multiple tissues.", "One such element, liver receptor homolog-1 (Lrh-1), is an orphan nuclear receptor that regulates metabolism and hormone synthesis.", "It is strongly expressed in granulosa cells of ovarian follicles and in the corpus luteum of rodents and humans.", "Germline ablation of Nr5a2 (also called Lrh-1), the gene coding for Lrh-1, in mice is embryonically lethal at gastrulation.", "Depletion of Lrh-1 in the ovarian follicle shows that it regulates genes required for both steroid synthesis and ovulation.", "To study the effects of Lrh-1 on mouse gestation, we genetically disrupted its expression in the corpus luteum, resulting in luteal insufficiency.", "Hormone replacement permitted embryo implantation but was followed by gestational failure with impaired endometrial decidualization, compromised placental formation, fetal growth retardation and fetal death.", "Lrh-1 is also expressed in the mouse and human endometrium, and in a primary culture of human endometrial stromal cells, reduction of NR5A2 transcript abundance by RNA interference abrogated decidualization.", "These findings show that Lrh-1 is necessary for maintenance of the corpus luteum, for promotion of decidualization and for formation of the placenta.", "It therefore has multiple, indispensible roles in establishing and sustaining pregnancy."], "structured": false}
{"doc_id": 15945975, "title": "Transcriptional Signature and Memory Retention of Human-Induced Pluripotent Stem Cells", "abstract": ["Genetic reprogramming of somatic cells to a pluripotent state (induced pluripotent stem cells or iPSCs) by over-expression of specific genes has been accomplished using mouse and human cells.", "However, it is still unclear how similar human iPSCs are to human Embryonic Stem Cells (hESCs).", "Here, we describe the transcriptional profile of human iPSCs generated without viral vectors or genomic insertions, revealing that these cells are in general similar to hESCs but with significant differences.", "For the generation of human iPSCs without viral vectors or genomic insertions, pluripotent factors Oct4 and Nanog were cloned in episomal vectors and transfected into human fetal neural progenitor cells.", "The transient expression of these two factors, or from Oct4 alone, resulted in efficient generation of human iPSCs.", "The reprogramming strategy described here revealed a potential transcriptional signature for human iPSCs yet retaining the gene expression of donor cells in human reprogrammed cells free of viral and transgene interference.", "Moreover, the episomal reprogramming strategy represents a safe way to generate human iPSCs for clinical purposes and basic research."], "structured": false}
{"doc_id": 15946643, "title": "A CXCL1 Paracrine Network Links Cancer Chemoresistance and Metastasis", "abstract": ["Metastasis and chemoresistance in cancer are linked phenomena, but the molecular basis for this link is unknown.", "We uncovered a network of paracrine signals between carcinoma, myeloid, and endothelial cells that drives both processes in breast cancer.", "Cancer cells that overexpress CXCL1 and 2 by transcriptional hyperactivation or 4q21 amplification are primed for survival in metastatic sites.", "CXCL1/2 attract CD11b(+)Gr1(+) myeloid cells into the tumor, which produce chemokines including S100A8/9 that enhance cancer cell survival.", "Although chemotherapeutic agents kill cancer cells, these treatments trigger a parallel stromal reaction leading to TNF-\u03b1 production by endothelial and other stromal cells.", "TNF-\u03b1 via NF-kB heightens the CXCL1/2 expression in cancer cells, thus amplifying the CXCL1/2-S100A8/9 loop and causing chemoresistance.", "CXCR2 blockers break this cycle, augmenting the efficacy of chemotherapy against breast tumors and particularly against metastasis.", "This network of endothelial-carcinoma-myeloid signaling interactions provides a mechanism linking chemoresistance and metastasis, with opportunities for intervention."], "structured": false}
{"doc_id": 15948830, "title": "Prophylaxis of postoperative vomiting in children undergoing tonsillectomy: a systematic review and meta-analysis.", "abstract": ["Postoperative vomiting (POV) remains one of the commonest causes of significant morbidity after tonsillectomy in children.", "A variety of prophylactic anti-emetic interventions have been reported, but there has only been a limited systematic review in this patient group.", "A systematic search was performed by using Cochrane Controlled Trials Register, MEDLINE and EMBASE to identify double-blind, randomized, placebo-controlled trials of prophylactic anti-emetic interventions in children undergoing tonsillectomy, with or without adenoidectomy.", "The outcome of interest was POV in the first 24 h. Summary estimates of the effect of each prophylactic anti-emetic strategy were derived using fixed effect meta-analysis.", "Where appropriate, dose-response effects were estimated using logistic regression and 22 articles were identified.", "Good evidence was found for the prophylactic anti-emetic effect of dexamethasone [odds ratio (OR) 0.23, 95% CI 0.16-0.33], and the serotinergic antagonists ondansetron (OR 0.36, 95% CI 0.29-0.46), granisetron (OR 0.11, 95% CI 0.06-0.19), tropisetron (OR 0.15, 95% CI 0.06-0.35) and dolasetron (OR 0.25, 95% CI 0.1-0.59).", "Metoclopramide was also found to be efficacious (OR 0.51, 95% CI 0.34-0.77).", "There is not sufficient evidence to suggest that dimenhydrinate, perphenazine or droperidol, in the doses studied, are efficacious, nor were gastric aspiration or acupuncture.", "In conclusion, dexamethasone and the anti-serotinergic agents appear to be the most effective agents for the prophylaxis for POV in children undergoing tonsillectomy."], "structured": false}
{"doc_id": 15953181, "title": "A method of comparing the areas under receiver operating characteristic curves derived from the same cases.", "abstract": ["Receiver operating characteristic (ROC) curves are used to describe and compare the performance of diagnostic technology and diagnostic algorithms.", "This paper refines the statistical comparison of the areas under two ROC curves derived from the same set of patients by taking into account the correlation between the areas that is induced by the paired nature of the data.", "The correspondence between the area under an ROC curve and the Wilcoxon statistic is used and underlying Gaussian distributions (binormal) are assumed to provide a table that converts the observed correlations in paired ratings of images into a correlation between the two ROC areas.", "This between-area correlation can be used to reduce the standard error (uncertainty) about the observed difference in areas.", "This correction for pairing, analogous to that used in the paired t-test, can produce a considerable increase in the statistical sensitivity (power) of the comparison.", "For studies involving multiple readers, this method provides a measure of a component of the sampling variation that is otherwise difficult to obtain."], "structured": false}
{"doc_id": 15955172, "title": "Transient inactivation of Rb and ARF yields regenerative cells from postmitotic mammalian muscle.", "abstract": ["An outstanding biological question is why tissue regeneration in mammals is limited, whereas urodele amphibians and teleost fish regenerate major structures, largely by cell cycle reentry.", "Upon inactivation of Rb, proliferation of postmitotic urodele skeletal muscle is induced, whereas in mammalian muscle this mechanism does not exist.", "We postulated that a tumor suppressor present in mammals but absent in regenerative vertebrates, the Ink4a product ARF (alternative reading frame), is a regeneration suppressor.", "Concomitant inactivation of Arf and Rb led to mammalian muscle cell cycle reentry, loss of differentiation properties, and upregulation of cytokinetic machinery.", "Single postmitotic myocytes were isolated by laser micro-dissection-catapulting, and transient suppression of Arf and Rb yielded myoblast colonies that retained the ability to differentiate and fuse into myofibers upon transplantation in vivo.", "These results show that differentiation of mammalian cells is reversed by inactivation of Arf and Rb and support the hypothesis that Arf evolved at the expense of regeneration."], "structured": false}
{"doc_id": 15960670, "title": "CENP-B Controls Centromere Formation Depending on the Chromatin Context", "abstract": ["The centromere is a chromatin region that serves as the spindle attachment point and directs accurate inheritance of eukaryotic chromosomes during cell divisions.", "However, the mechanism by which the centromere assembles and stabilizes at a specific genomic region is not clear.", "The de novo formation of a human/mammalian artificial chromosome (HAC/MAC) with a functional centromere assembly requires the presence of alpha-satellite DNA containing binding motifs for the centromeric CENP-B protein.", "We demonstrate here that de novo centromere assembly on HAC/MAC is dependent on CENP-B. In contrast, centromere formation is suppressed in cells expressing CENP-B when alpha-satellite DNA was integrated into a chromosomal site.", "Remarkably, on those integration sites CENP-B enhances histone H3-K9 trimethylation and DNA methylation, thereby stimulating heterochromatin formation.", "Thus, we propose that CENP-B plays a dual role in centromere formation, ensuring de novo formation on DNA lacking a functional centromere but preventing the formation of excess centromeres on chromosomes."], "structured": false}
{"doc_id": 15966318, "title": "Improved tools for biological sequence comparison.", "abstract": ["We have developed three computer programs for comparisons of protein and DNA sequences.", "They can be used to search sequence data bases, evaluate similarity scores, and identify periodic structures based on local sequence similarity.", "The FASTA program is a more sensitive derivative of the FASTP program, which can be used to search protein or DNA sequence data bases and can compare a protein sequence to a DNA sequence data base by translating the DNA data base as it is searched.", "FASTA includes an additional step in the calculation of the initial pairwise similarity score that allows multiple regions of similarity to be joined to increase the score of related sequences.", "The RDF2 program can be used to evaluate the significance of similarity scores using a shuffling method that preserves local sequence composition.", "The LFASTA program can display all the regions of local similarity between two sequences with scores greater than a threshold, using the same scoring parameters and a similar alignment algorithm; these local similarities can be displayed as a \"graphic matrix\" plot or as individual alignments.", "In addition, these programs have been generalized to allow comparison of DNA or protein sequences based on a variety of alternative scoring matrices."], "structured": false}
{"doc_id": 15968271, "title": "The adverse consequences of unmet need among older persons living in the community: dual-eligible versus Medicare-only beneficiaries.", "abstract": ["OBJECTIVE Our objective is to estimate and compare the prevalence of selected adverse consequences associated with unmet need for assistance among a socioeconomically and medically vulnerable subgroup of the older adult population, those who are dually eligible for Medicare and Medicaid, with those eligible for Medicare only.   \n", "METHOD Using data from the National Health and Aging Trends Study (NHATS), a representative survey of the older Medicare population, we calculated the prevalence of disability-related need for assistance with self-care, household tasks, and mobility activities and the prevalence of adverse consequences of unmet need by dually eligible and Medicare only status.   \n", "RESULTS Over 2 million community-dwelling older persons experienced an adverse consequence due to unmet need for assistance with self-care (e.g., soiled their clothes), over 2 million experienced adverse consequences due to unmet need for assistance with household tasks (e.g., went without groceries), and over 3 million persons experienced at least one adverse consequence of unmet need for assistance with mobility-related activities (e.g., had to stay in bed) in the month prior to the NHATS interview.", "Dually eligible persons experienced higher rates of 6 of the 11 adverse consequences studied and were more likely to have at least one adverse consequence in all 3 domains than others.   ", "DISCUSSION Several care models are emerging with the goal of integrating medical care, behavioral health, and long-term services for the dual eligible population.", "Indicators of adverse consequences of unmet need could be used to monitor the quality and adequacy of such care systems."], "structured": true}
{"doc_id": 15969637, "title": "Supplementary information: \u2018MesoRD User\u2019s Guide \u2019 and other", "abstract": ["UNLABELLED MesoRD is a tool for stochastic simulation of chemical reactions and diffusion.", "In particular, it is an implementation of the next subvolume method, which is an exact method to simulate the Markov process corresponding to the reaction-diffusion master equation.   ", "AVAILABILITY MesoRD is free software, written in C++ and licensed under the GNU general public license (GPL).", "MesoRD runs on Linux, Mac OS X, NetBSD, Solaris and Windows XP.", "It can be downloaded from http://mesord.sourceforge.net.   ", "CONTACT johan.elf@icm.uu.se; johan.hattne@embl-hamburg.de   SUPPLEMENTARY INFORMATION 'MesoRD User's Guide' and other documents are available at http://mesord.sourceforge.net."], "structured": false}
{"doc_id": 15972906, "title": "Functional anatomy of T cell activation and synapse formation.", "abstract": ["T cell activation and function require a structured engagement of antigen-presenting cells.", "These cell contacts are characterized by two distinct dynamics in vivo: transient contacts resulting from promigratory junctions called immunological kinapses or prolonged contacts from stable junctions called immunological synapses.", "Kinapses operate in the steady state to allow referencing to self-peptide-MHC (pMHC) and searching for pathogen-derived pMHC.", "Synapses are induced by T cell receptor (TCR) interactions with agonist pMHC under specific conditions and correlate with robust immune responses that generate effector and memory T cells.", "High-resolution imaging has revealed that the synapse is highly coordinated, integrating cell adhesion, TCR recognition of pMHC complexes, and an array of activating and inhibitory ligands to promote or prevent T cell signaling.", "In this review, we examine the molecular components, geometry, and timing underlying kinapses and synapses.", "We integrate recent molecular and physiological data to provide a synthesis and suggest ways forward."], "structured": false}
{"doc_id": 15975146, "title": "Modulation of Replicative Lifespan in Cryptococcus neoformans: Implications for Virulence", "abstract": ["The fungal pathogen, Cryptococcus neoformans, has been shown to undergo replicative aging.", "Old cells are characterized by advanced generational age and phenotypic changes that appear to mediate enhanced resistance to host and antifungal-based killing.", "As a consequence of this age-associated resilience, old cells accumulate during chronic infection.", "Based on these findings, we hypothesized that shifting the generational age of a pathogenic yeast population would alter its vulnerability to the host and affect its virulence.", "SIR2 is a well-conserved histone deacetylase, and a pivotal target for the development of anti-aging drugs.", "We tested its effect on C. neoformans' replicative lifespan (RLS).", "First, a mutant C. neoformans strain (sir2\u0394) was generated, and confirmed a predicted shortened RLS in sir2\u0394 cells consistent with its known role in aging.", "Next, RLS analysis showed that treatment of C. neoformans with Sir2p-agonists resulted in a significantly prolonged RLS, whereas treatment with a Sir2p-antagonist shortened RLS.", "RLS modulating effects were dependent on SIR2 and not observed in sir2\u0394 cells.", "Because SIR2 loss resulted in a slightly impaired fitness, effects of genetic RLS modulation on virulence could not be compared with wild type cells.", "Instead we chose to chemically modulate RLS, and investigated the effect of Sir2p modulating drugs on C. neoformans cells in a Galleria mellonella infection model.", "Consistent with our hypothesis that shifts in the generational age of the infecting yeast population alters its vulnerability to host cells, we observed decreased virulence of C. neoformans in the Galleria host when RLS was prolonged by treatment with Sir2p agonists.", "In contrast, treatment with a Sir2p antagonist, which shortens RLS enhanced virulence in Galleria.", "In addition, combination of Sir2p agonists with antifungal therapy enhanced the antifungal's effect.", "Importantly, no difference in virulence was observed with drug treatment when sir2\u0394 cells were used for infection, which confirmed target specificity and ruled out non-specific effects of the drugs on the Galleria host.", "Thus, this study suggests that RLS modulating drugs, such as Sir2p agonists, shift lifespan and vulnerability of the fungal population, and should be further investigated as a potential class of novel antifungal drug targets that can enhance antifungal efficacy."], "structured": false}
{"doc_id": 15981174, "title": "Pf4-Cre transgenic mice allow the generation of lineage-restricted gene knockouts for studying megakaryocyte and platelet function in vivo.", "abstract": ["To generate transgenic mice that express Cre-recombinase exclusively in the megakaryocytic lineage, we modified a mouse bacterial artificial chromosome (BAC) clone by homologous recombination and replaced the first exon of the platelet factor 4 (Pf4), also called CXCL4, with a codon-improved Cre cDNA.", "Several strains expressing the transgene were obtained and one strain, Q3, was studied in detail.", "Crossing Q3 mice with the ROSA26-lacZ reporter strain showed that Cre-recombinase activity was confined to megakaryocytes.", "These results were further verified by crossing the Q3 mice with a strain containing loxP-flanked integrin beta1.", "Excision of this conditional allele in megakaryocytes was complete at the DNA level, and platelets were virtually devoid of the integrin beta1 protein.", "The Pf4-Cre transgenic strain will be a valuable tool to study megakaryopoiesis, platelet formation, and platelet function."], "structured": false}
{"doc_id": 15983148, "title": "LIN-44/Wnt Directs Dendrite Outgrowth through LIN-17/Frizzled in C. elegans Neurons", "abstract": ["Nervous system function requires proper development of two functional and morphological domains of neurons, axons and dendrites.", "Although both these domains are equally important for signal transmission, our understanding of dendrite development remains relatively poor.", "Here, we show that in C. elegans the Wnt ligand, LIN-44, and its Frizzled receptor, LIN-17, regulate dendrite development of the PQR oxygen sensory neuron.", "In lin-44 and lin-17 mutants, PQR dendrites fail to form, display stunted growth, or are misrouted.", "Manipulation of temporal and spatial expression of LIN-44, combined with cell-ablation experiments, indicates that this molecule is patterned during embryogenesis and acts as an attractive cue to define the site from which the dendrite emerges.", "Genetic interaction between lin-44 and lin-17 suggests that the LIN-44 signal is transmitted through the LIN-17 receptor, which acts cell autonomously in PQR.", "Furthermore, we provide evidence that LIN-17 interacts with another Wnt molecule, EGL-20, and functions in parallel to MIG-1/Frizzled in this process.", "Taken together, our results reveal a crucial role for Wnt and Frizzled molecules in regulating dendrite development in vivo."], "structured": false}
{"doc_id": 15983982, "title": "Why do general practitioners prescribe antibiotics for upper respiratory tract infections to meet patient expectations: a mixed methods study", "abstract": ["OBJECTIVES To describe the role patient expectations play in general practitioners (GPs) antibiotic prescribing for upper respiratory tract infections (URTI).   \n", "METHODS Concurrent explanatory mixed methods approach using a cross-sectional survey and semistructured interviews.   \n", "SETTINGS Primary care GPs in Australia.   \n", "PARTICIPANTS 584 GPs (response rate of 23.6%) completed the cross-sectional survey.", "32 GPs were interviewed individually.   \n", "OUTCOME MEASURE Prescribing of antibiotics for URTI.   \n", "RESULTS More than half the GP respondents to the survey in Australia self-reported that they would prescribe antibiotics for an URTI to meet patient expectations.", "Our qualitative findings suggest that 'patient expectations' may be the main reason given for inappropriate prescribing, but it is an all-encompassing phrase that includes other reasons.", "These include limited time, poor doctor-patient communication and diagnostic uncertainty.", "We have identified three role archetypes to explain the behaviour of GPs in reference to antibiotic prescribing for URTIs.", "The main themes emerging from the qualitative component was that many GPs did not think that antibiotic prescribing in primary care was responsible for the development of antibiotic resistance nor that their individual prescribing would make any difference in light of other bigger issues like hospital prescribing or veterinary use.", "For them, there were negligible negative consequences from their inappropriate prescribing.   \n", "CONCLUSIONS There is a need to increase awareness of the scope and magnitude of antibiotic resistance and the role primary care prescribing plays, and of the contribution of individual prescribing decisions to the problem of antibiotic resistance."], "structured": true}
{"doc_id": 15984735, "title": "Migraine and cardiovascular disease: systematic review and meta-analysis.", "abstract": ["OBJECTIVE To evaluate the association between migraine and cardiovascular disease, including stroke, myocardial infarction, and death due to cardiovascular disease.   \n", "DESIGN Systematic review and meta-analysis.   \n", "DATA SOURCES Electronic databases (PubMed, Embase, Cochrane Library) and reference lists of included studies and reviews published until January 2009.", "Selection criteria Case-control and cohort studies investigating the association between any migraine or specific migraine subtypes and cardiovascular disease.", "Review methods Two investigators independently assessed eligibility of identified studies in a two step approach.", "Disagreements were resolved by consensus.", "Studies were grouped according to a priori categories on migraine and cardiovascular disease.   \n", "DATA EXTRACTION Two investigators extracted data.", "Pooled relative risks and 95% confidence intervals were calculated.   \n", "RESULTS Studies were heterogeneous for participant characteristics and definition of cardiovascular disease.", "Nine studies investigated the association between any migraine and ischaemic stroke (pooled relative risk 1.73, 95% confidence interval 1.31 to 2.29).", "Additional analyses indicated a significantly higher risk among people who had migraine with aura (2.16, 1.53 to 3.03) compared with people who had migraine without aura (1.23, 0.90 to 1.69; meta-regression for aura status P=0.02).", "Furthermore, results suggested a greater risk among women (2.08, 1.13 to 3.84) compared with men (1.37, 0.89 to 2.11).", "Age less than 45 years, smoking, and oral contraceptive use further increased the risk.", "Eight studies investigated the association between migraine and myocardial infarction (1.12, 0.95 to 1.32) and five between migraine and death due to cardiovascular disease (1.03, 0.79 to 1.34).", "Only one study investigated the association between women who had migraine with aura and myocardial infarction and death due to cardiovascular disease, showing a twofold increased risk.   \n", "CONCLUSION Migraine is associated with a twofold increased risk of ischaemic stroke, which is only apparent among people who have migraine with aura.", "Our results also suggest a higher risk among women and risk was further magnified for people with migraine who were aged less than 45, smokers, and women who used oral contraceptives.", "We did not find an overall association between any migraine and myocardial infarction or death due to cardiovascular disease.", "Too few studies are available to reliably evaluate the impact of modifying factors, such as migraine aura, on these associations."], "structured": true}
{"doc_id": 15997009, "title": "Effect of Duration and Intermittency of Rifampin on Tuberculosis Treatment Outcomes: A Systematic Review and Meta-Analysis", "abstract": ["BACKGROUND Treatment regimens for active tuberculosis (TB) that are intermittent, or use rifampin during only the initial phase, offer practical advantages, but their efficacy has been questioned.", "We conducted a systematic review of treatment regimens for active TB, to assess the effect of duration and intermittency of rifampin use on TB treatment outcomes.   \n", "METHODS AND FINDINGS PubMed, Embase, and the Cochrane CENTRAL database for clinical trials were searched for randomized controlled trials, published in English, French, or Spanish, between 1965 and June 2008.", "Selected studies utilized standardized treatment with rifampin-containing regimens.", "Studies reported bacteriologically confirmed failure and/or relapse in previously untreated patients with bacteriologically confirmed pulmonary TB.", "Pooled cumulative incidences of treatment outcomes and association with risk factors were computed with stratified random effects meta-analyses.", "Meta-regression was performed using a negative binomial regression model.", "A total of 57 trials with 312 arms and 21,472 participants were included in the analysis.", "Regimens utilizing rifampin only for the first 1-2 mo had significantly higher rates of failure, relapse, and acquired drug resistance, as compared to regimens that used rifampin for 6 mo.", "This was particularly evident when there was initial drug resistance to isoniazid, streptomycin, or both.", "On the other hand, there was little evidence of difference in failure or relapse with daily or intermittent schedules of treatment administration, although there was insufficient published evidence of the efficacy of twice-weekly rifampin administration throughout therapy.   \n", "CONCLUSIONS TB treatment outcomes were significantly worse with shorter duration of rifampin, or with initial drug resistance to isoniazid and/or streptomycin.", "Treatment outcomes were similar with all intermittent schedules evaluated, but there is insufficient evidence to support administration of treatment twice weekly throughout therapy."], "structured": true}
{"doc_id": 16016673, "title": "A novel set of DNA methylation markers in urine sediments for sensitive/specific detection of bladder cancer.", "abstract": ["PURPOSE This study aims to provide a better set of DNA methylation markers in urine sediments for sensitive and specific detection of bladder cancer.   ", "EXPERIMENTAL DESIGN Fifty-nine tumor-associated genes were profiled in three bladder cancer cell lines, a small cohort of cancer biopsies and urine sediments by methylation-specific PCR.", "Twenty-one candidate genes were then profiled in urine sediments from 132 bladder cancer patients (8 cases for stage 0a; 68 cases for stage I; 50 cases for stage II; 4 cases for stages III; and 2 cases for stage IV), 23 age-matched patients with noncancerous urinary lesions, 6 neurologic diseases, and 7 healthy volunteers.   \n", "RESULTS Despite six incidences of four genes reported in 3 of 23 noncancerous urinary lesion patients analyzed, cancer-specific hypermethylation in urine sediments were reported for 15 genes (P < 0.05).", "Methylation assessment of an 11-gene set (SALL3, CFTR, ABCC6, HPR1, RASSF1A, MT1A, RUNX3, ITGA4, BCL2, ALX4, MYOD1, DRM, CDH13, BMP3B, CCNA1, RPRM, MINT1, and BRCA1) confirmed the existing diagnosis of 121 among 132 bladder cancer cases (sensitivity, 91.7%) with 87% accuracy.", "Significantly, more than 75% of stage 0a and 88% of stage I disease were detected, indicating its value in the early diagnosis of bladder cancer.", "Interestingly, the cluster of reported methylation markers used in the U.S. bladder cancers is distinctly different from that identified in this study, suggesting a possible epigenetic disparity between the American and Chinese cases.   \n", "CONCLUSIONS Methylation profiling of an 11-gene set in urine sediments provides a sensitive and specific detection of bladder cancer."], "structured": true}
{"doc_id": 16056410, "title": "Posttranslational Acetylation of \u03b1-Tubulin Constrains Protofilament Number in Native Microtubules", "abstract": ["BACKGROUND Microtubules are built from linear polymers of \u03b1-\u03b2 tubulin dimers (protofilaments) that form a tubular quinary structure.", "Microtubules assembled from purified tubulin in vitro contain between 10 and 16 protofilaments; however, such structural polymorphisms are not found in cells.", "This discrepancy implies that factors other than tubulin constrain microtubule protofilament number, but the nature of these constraints is unknown.   \n", "RESULTS Here, we show that acetylation of MEC-12 \u03b1-tubulin constrains protofilament number in C. elegans touch receptor neurons (TRNs).", "Whereas the sensory dendrite of wild-type TRNs is packed with a cross-linked bundle of long, 15-protofilament microtubules, mec-17;atat-2 mutants lacking \u03b1-tubulin acetyltransferase activity have short microtubules, rampant lattice defects, and variable protofilament number both between and within microtubules.", "All-atom molecular dynamics simulations suggest a model in which acetylation of lysine 40 promotes the formation of interprotofilament salt bridges, stabilizing lateral interactions between protofilaments and constraining quinary structure to produce stable, structurally uniform microtubules in vivo.   \n", "CONCLUSIONS Acetylation of \u03b1-tubulin is an essential constraint on protofilament number in vivo.", "We propose a structural model in which this posttranslational modification promotes the formation of lateral salt bridges that fine-tune the association between adjacent protofilaments and enable the formation of uniform microtubule populations in vivo."], "structured": true}
{"doc_id": 16056514, "title": "A KEY ROLE FOR OREXIN IN PANIC ANXIETY", "abstract": ["Panic disorder is a severe anxiety disorder with recurrent, debilitating panic attacks.", "In individuals with panic disorder there is evidence of decreased central gamma-aminobutyric acid (GABA) activity as well as marked increases in autonomic and respiratory responses after intravenous infusions of hypertonic sodium lactate.", "In a rat model of panic disorder, chronic inhibition of GABA synthesis in the dorsomedial-perifornical hypothalamus of rats produces anxiety-like states and a similar vulnerability to sodium lactate-induced cardioexcitatory responses.", "The dorsomedial-perifornical hypothalamus is enriched in neurons containing orexin (ORX, also known as hypocretin), which have a crucial role in arousal, vigilance and central autonomic mobilization, all of which are key components of panic.", "Here we show that activation of ORX-synthesizing neurons is necessary for developing a panic-prone state in the rat panic model, and either silencing of the hypothalamic gene encoding ORX (Hcrt) with RNAi or systemic ORX-1 receptor antagonists blocks the panic responses.", "Moreover, we show that human subjects with panic anxiety have elevated levels of ORX in the cerebrospinal fluid compared to subjects without panic anxiety.", "Taken together, our results suggest that the ORX system may be involved in the pathophysiology of panic anxiety and that ORX antagonists constitute a potential new treatment strategy for panic disorder."], "structured": false}
{"doc_id": 16057926, "title": "Local Increases in Mechanical Tension Shape Compartment Boundaries by Biasing Cell Intercalations", "abstract": ["Mechanical forces play important roles during tissue organization in developing animals.", "Many tissues are organized into adjacent, nonmixing groups of cells termed compartments.", "Boundaries between compartments display a straight morphology and are associated with signaling centers that are important for tissue growth and patterning.", "Local increases in mechanical tension at cell junctions along compartment boundaries have recently been shown to prevent cell mixing and to maintain straight boundaries.", "The cellular mechanisms by which local increases in mechanical tension prevent cell mixing at compartment boundaries, however, remain poorly understood.", "Here, we have used live imaging and quantitative image analysis to determine cellular dynamics at and near the anteroposterior compartment boundaries of the Drosophila pupal abdominal epidermis.", "We show that cell mixing within compartments involves multiple cell intercalations.", "Frequency and orientation of cell intercalations are unchanged along the compartment boundaries; rather, an asymmetry in the shrinkage of junctions during intercalation is biased, resulting in cell rearrangements that suppress cell mixing.", "Simulations of tissue growth show that local increases in mechanical tension can account for this bias in junctional shrinkage.", "We conclude that local increases in mechanical tension maintain cell populations separate by influencing junctional rearrangements during cell intercalation."], "structured": false}
{"doc_id": 16058322, "title": "MDA5 and PTPN2, two candidate genes for type 1 diabetes, modify pancreatic \u03b2-cell responses to the viral by-product double-stranded RNA", "abstract": ["beta-Cell destruction in type 1 diabetes (T1D) is at least in part consequence of a 'dialog' between beta-cells and immune system.", "This dialog may be affected by the individual's genetic background.", "We presently evaluated whether modulation of MDA5 and PTPN2, two candidate genes for T1D, affects beta-cell responses to double-stranded RNA (dsRNA), a by-product of viral replication.", "These genes were selected following comparison between known candidate genes for T1D and genes expressed in pancreatic beta-cells, as identified in previous array analysis.", "INS-1E cells and primary fluorescence-activated cell sorting-purified rat beta-cells were transfected with small interference RNAs (siRNAs) targeting MDA5 or PTPN2 and subsequently exposed to intracellular synthetic dsRNA (polyinosinic-polycitidilic acid-PIC).", "Real-time RT-PCR, western blot and viability assays were performed to characterize gene/protein expression and viability.", "PIC increased MDA5 and PTPN2 mRNA expression, which was inhibited by the specific siRNAs.", "PIC triggered apoptosis in INS-1E and primary beta-cells and this was augmented by PTPN2 knockdown (KD), although inhibition of MDA5 did not modify PIC-induced apoptosis.", "In contrast, MDA5 silencing decreased PIC-induced cytokine and chemokine expression, although inhibition of PTPN2 induced minor or no changes in these inflammatory mediators.", "These findings indicate that changes in MDA5 and PTPN2 expression modify beta-cell responses to dsRNA.", "MDA5 regulates inflammatory signals, whereas PTPN2 may function as a defence mechanism against pro-apoptotic signals generated by dsRNA.", "These two candidate genes for T1D may thus modulate beta-cell apoptosis and/or local release of inflammatory mediators in the course of a viral infection by acting, at least in part, at the pancreatic beta-cell level."], "structured": false}
{"doc_id": 16066726, "title": "Tumor necrosis factor signaling mediates resistance to mycobacteria by inhibiting bacterial growth and macrophage death.", "abstract": ["Tumor necrosis factor (TNF), a key effector in controlling tuberculosis, is thought to exert protection by directing formation of granulomas, organized aggregates of macrophages and other immune cells.", "Loss of TNF signaling causes progression of tuberculosis in humans, and the increased mortality of Mycobacterium tuberculosis-infected mice is associated with disorganized necrotic granulomas, although the precise roles of TNF signaling preceding this endpoint remain undefined.", "We monitored transparent Mycobacterium marinum-infected zebrafish live to conduct a stepwise dissection of how TNF signaling operates in mycobacterial pathogenesis.", "We found that loss of TNF signaling caused increased mortality even when only innate immunity was operant.", "In the absence of TNF, intracellular bacterial growth and granuloma formation were accelerated and was followed by necrotic death of overladen macrophages and granuloma breakdown.", "Thus, TNF is not required for tuberculous granuloma formation, but maintains granuloma integrity indirectly by restricting mycobacterial growth within macrophages and preventing their necrosis."], "structured": false}
{"doc_id": 16086778, "title": "Loss of negative regulation by Numb over Notch is relevant to human breast carcinogenesis", "abstract": ["The biological antagonism between Notch and Numb controls the proliferative/differentiative balance in development and homeostasis.", "Although altered Notch signaling has been linked to human diseases, including cancer, evidence for a substantial involvement of Notch in human tumors has remained elusive.", "Here, we show that Numb-mediated control on Notch signaling is lost in \u223c50% of human mammary carcinomas, due to specific Numb ubiquitination and proteasomal degradation.", "Mechanistically, Numb operates as an oncosuppressor, as its ectopic expression in Numb-negative, but not in Numb-positive, tumor cells inhibits proliferation.", "Increased Notch signaling is observed in Numb-negative tumors, but reverts to basal levels after enforced expression of Numb.", "Conversely, Numb silencing increases Notch signaling in normal breast cells and in Numb-positive breast tumors.", "Finally, growth suppression of Numb-negative, but not Numb-positive, breast tumors can be achieved by pharmacological inhibition of Notch.", "Thus, the Numb/Notch biological antagonism is relevant to the homeostasis of the normal mammary parenchyma and its subversion contributes to human mammary carcinogenesis."], "structured": false}
{"doc_id": 16090672, "title": "Cortical Dynein Controls Microtubule Dynamics to Generate Pulling Forces that Position Microtubule Asters", "abstract": ["Dynein at the cortex contributes to microtubule-based positioning processes such as spindle positioning during embryonic cell division and centrosome positioning during fibroblast migration.", "To investigate how cortical dynein interacts with microtubule ends to generate force and how this functional association impacts positioning, we have reconstituted the 'cortical' interaction between dynein and dynamic microtubule ends in an in vitro system using microfabricated barriers.", "We show that barrier-attached dynein captures microtubule ends, inhibits growth, and triggers microtubule catastrophes, thereby controlling microtubule length.", "The subsequent interaction with shrinking microtubule ends generates pulling forces up to several pN. By combining experiments in microchambers with a theoretical description of aster mechanics, we show that dynein-mediated pulling forces lead to the reliable centering of microtubule asters in simple confining geometries.", "Our results demonstrate the intrinsic ability of cortical microtubule-dynein interactions to regulate microtubule dynamics and drive positioning processes in living cells."], "structured": false}
{"doc_id": 16098747, "title": "Breast cancer risk factors in relation to breast density (United States)", "abstract": ["Evaluate known breast cancer risk factors in relation to breast density.", "We examined factors in relation to breast density in 144,018 New Hampshire (NH) women with at least one mammogram recorded in a statewide mammography registry.", "Mammographic breast density was measured by radiologists using the BI-RADS classification; risk factors of interest were obtained from patient intake forms and questionnaires.", "Initial analyses showed a strong inverse influence of age and body mass index (BMI) on breast density.", "In addition, women with late age at menarche, late age at first birth, premenopausal women, and those currently using hormone therapy (HT) tended to have higher breast density, while those with greater parity tended to have less dense breasts.", "Analyses stratified on age and BMI suggested interactions, which were formally assessed in a multivariable model.", "The impact of current HT use, relative to nonuse, differed across age groups, with an inverse association in younger women, and a positive association in older women (p < 0.0001 for the interaction).", "The positive effects of age at menarche and age at first birth, and the inverse influence of parity were less apparent in women with low BMI than in those with high BMI (p = 0.04, p < 0.0001 and p = 0.01, respectively, for the interactions).", "We also noted stronger positive effects for age at first birth in postmenopausal women (p = 0.004 for the interaction).", "The multivariable model indicated a slight positive influence of family history of breast cancer.", "The influence of age at menarche and reproductive factors on breast density is less evident in women with high BMI.", "Density is reduced in young women using HT, but increased in HT users of age 50 or more."], "structured": false}
{"doc_id": 16108876, "title": "Perspective: repression of competition and the evolution of cooperation.", "abstract": ["Repression of competition within groups joins kin selection as the second major force in the history of life shaping the evolution of cooperation.", "When opportunities for competition against neighbors are limited within groups, individuals can increase their own success only by enhancing the efficiency and productivity of their group.", "Thus, characters that repress competition within groups promote cooperation and enhance group success.", "Leigh first expressed this idea in the context of fair meiosis, in which each chromosome has an equal chance of transmission via gametes.", "Randomized success means that each part of the genome can increase its own success only by enhancing the total number of progeny and thus increasing the success of the group.", "Alexander used this insight about repression of competition in fair meiosis to develop his theories for the evolution of human sociality.", "Alexander argued that human social structures spread when they repress competition within groups and promote successful group-against-group competition.", "Buss introduced a new example with his suggestion that metazoan success depended on repression of competition between cellular lineages.", "Maynard Smith synthesized different lines of thought on repression of competition.", "In this paper, I develop simple mathematical models to illustrate the main processes by which repression of competition evolves.", "With the concepts made clear, I then explain the history of the idea.", "I finish by summarizing many new developments in this subject and the most promising lines for future study."], "structured": false}
{"doc_id": 16119973, "title": "Article", "abstract": ["IBD is characterized by uncontrolled immune responses in inflamed mucosa, with dominance of IL-17-producing cells and deficiency of Treg cells.", "The aim of this study was to explore the effect and mechanisms of RA, the ligand of RARalpha, on immune responses in human and murine colitis.", "Colonic biopsies from patients with UC were cultured and treated with RA as the agonist of RARalpha or LE135 as the antagonist of RARalpha.", "Expressions of IL-17 and FOXP3 were detected by immunohistochemistry.", "Murine colitis was induced by intrarectal administration with TNBS at Day 1.", "Mice were then i.p.-treated with RA or LE135 daily for 7 days.", "Cytokine levels in the cultures of mouse LPMCs were measured.", "Expressions of FOXP3 and IL-17 in colon tissues or MLN were detected by immunohistological analysis.", "Body weight and colon inflammation were evaluated.", "RA treatment up-regulated FOXP3 expression and down-regulated IL-17 expression in colon biopsies of patients and in colon tissues and MLN of mice with colitis compared with controls.", "LPMCs from RA-treated mice produced lower levels of proinflammatory cytokines (TNF-alpha, IL-1beta, IL-17) but more regulatory cytokines (IL-10, TGF-beta) compared with that of untreated mice.", "LE135 showed the opposite effect of RA.", "Furthermore, RA ameliorated TNBS-induced colitis in a dose-dependent manner, as seen by improved body weight and colon inflammation.", "RA down-regulates colon inflammatory responses in patients with IBD in vitro and in murine colitis in vivo, representing a potential therapeutic approach in IBD treatment."], "structured": false}
{"doc_id": 16120395, "title": "Multiple RNA surveillance pathways limit aberrant expression of iron uptake mRNAs and prevent iron toxicity in S. cerevisiae.", "abstract": ["Tight regulation of the expression of mRNAs encoding iron uptake proteins is essential to control iron homeostasis and avoid intracellular iron toxicity.", "We show that many mRNAs encoding iron uptake or iron mobilization proteins are expressed in iron-replete conditions in the absence of the S. cerevisiae RNase III ortholog Rnt1p or of the nuclear exosome component Rrp6p.", "Extended forms of these mRNAs accumulate in the absence of Rnt1p or of the 5'-->3' exonucleases Xrn1p and Rat1p, showing that multiple degradative pathways contribute to the surveillance of aberrant forms of these transcripts.", "RNase III-deficient cells are hypersensitive to high iron concentrations, suggesting that Rnt1p-mediated RNA surveillance is required to prevent iron toxicity.", "These results show that RNA surveillance through multiple ribonucleolytic pathways plays a role in iron homeostasis in yeast to avoid the potentially toxic effects of the expression of the iron starvation response in iron-replete conditions."], "structured": false}
{"doc_id": 16128711, "title": "Differential regulation of adherens junction dynamics during apical-basal polarization.", "abstract": ["Adherens junctions (AJs) in epithelial cells are constantly turning over to modulate adhesion properties under various physiological and developmental contexts, but how such AJ dynamics are regulated during the apical-basal polarization of primary epithelia remains unclear.", "Here, we used new and genetically validated GFP markers of Drosophila E-cadherin (DE-cadherin, hereafter referred to as DE-Cad) and \u03b2-catenin (Armadillo, Arm) to quantitatively assay the in vivo dynamics of biosynthetic turnover and membrane redistribution by fluorescence recovery after photobleaching (FRAP) assays.", "Our data showed that membrane DE-Cad and Arm in AJs of polarizing epithelial cells had much faster biosynthetic turnover than in polarized cells.", "Fast biosynthetic turnover of membrane DE-Cad is independent of actin- and dynamin-based trafficking, but is microtubule-dependent.", "Furthermore, Arm in AJs of polarizing cells showed a faster and diffusion-based membrane redistribution that was both quantitatively and qualitatively different from the slower and exchange-based DE-Cad membrane distribution, indicating that the association of Arm with DE-Cad is more dynamic in polarizing cells, and only becomes stable in polarized epithelial cells.", "Consistently, biochemical assays showed that the binding of Arm to DE-Cad is weaker in polarizing cells than in polarized cells.", "Our data revealed that the molecular interaction between DE-Cad and Arm is modulated during apical-basal polarization, suggesting a new mechanism that might be crucial for establishing apical-basal polarity through regulating the AJ dynamics."], "structured": false}
{"doc_id": 16167746, "title": "Phylogenetic analysis of mRNA polyadenylation sites reveals a role of transposable elements in evolution of the 3\u2032-end of genes", "abstract": ["mRNA polyadenylation is an essential step for the maturation of almost all eukaryotic mRNAs, and is tightly coupled with termination of transcription in defining the 3'-end of genes.", "Large numbers of human and mouse genes harbor alternative polyadenylation sites [poly(A) sites] that lead to mRNA variants containing different 3'-untranslated regions (UTRs) and/or encoding distinct protein sequences.", "Here, we examined the conservation and divergence of different types of alternative poly(A) sites across human, mouse, rat and chicken.", "We found that the 3'-most poly(A) sites tend to be more conserved than upstream ones, whereas poly(A) sites located upstream of the 3'-most exon, also termed intronic poly(A) sites, tend to be much less conserved.", "Genes with longer evolutionary history are more likely to have alternative polyadenylation, suggesting gain of poly(A) sites through evolution.", "We also found that nonconserved poly(A) sites are associated with transposable elements (TEs) to a much greater extent than conserved ones, albeit less frequently utilized.", "Different classes of TEs have different characteristics in their association with poly(A) sites via exaptation of TE sequences into polyadenylation elements.", "Our results establish a conservation pattern for alternative poly(A) sites in several vertebrate species, and indicate that the 3'-end of genes can be dynamically modified by TEs through evolution."], "structured": false}
{"doc_id": 16172576, "title": "Inter- and Intra-Host Viral Diversity in a Large Seasonal DENV2 Outbreak", "abstract": ["BACKGROUND High genetic diversity at both inter- and intra-host level are hallmarks of RNA viruses due to the error-prone nature of their genome replication.", "Several groups have evaluated the extent of viral variability using different RNA virus deep sequencing methods.", "Although much of this effort has been dedicated to pathogens that cause chronic infections in humans, few studies investigated arthropod-borne, acute viral infections.   \n", "METHODS AND PRINCIPAL FINDINGS We deep sequenced the complete genome of ten DENV2 isolates from representative classical and severe cases sampled in a large outbreak in Brazil using two different approaches.", "Analysis of the consensus genomes confirmed the larger extent of the 2010 epidemic in comparison to a previous epidemic caused by the same viruses in another city two years before (genetic distance = 0.002 and 0.0008 respectively).", "Analysis of viral populations within the host revealed a high level of conservation.", "After excluding homopolymer regions of 454/Roche generated sequences, we found 10 to 44 variable sites per genome population at a frequency of >1%, resulting in very low intra-host genetic diversity.", "While up to 60% of all variable sites at intra-host level were non-synonymous changes, only 10% of inter-host variability resulted from non-synonymous mutations, indicative of purifying selection at the population level.   \n", "CONCLUSIONS AND SIGNIFICANCE Despite the error-prone nature of RNA-dependent RNA-polymerase, dengue viruses maintain low levels of intra-host variability."], "structured": true}
{"doc_id": 16180601, "title": "Serum Soluble Corin Deficiency Predicts Major Disability within 3 Months after Acute Stroke", "abstract": ["OBJECTIVE Serum soluble corin has been associated with stroke.", "However, whether it is associated with stroke prognosis has not yet been studied.", "Therefore, we aimed to study the association of serum soluble corin with risk of poor outcomes within 3 months after stroke.   \n", "METHODS We followed 522 stroke patients for 3 months to identify major disability, death and vascular events.", "Serum soluble corin was measured at baseline for all participants.", "Logistic regression was used to examine the associations of baseline serum soluble corin with outcomes of stroke, adjusting for age, sex, baseline NIHSS score, hours from onset to hospitalization, smoking, drinking, hypertension, diabetes, coronary heart disease, atrial fibrillation, family history of stroke, and stroke subtype.   \n", "RESULTS Patients with high corin had a significantly lower crude risk for the composite outcome of major disability or death (OR = 0.64, 95%CI: 0.43-0.96) than patients with low corin (the lowest tertile).", "After adjustment for age and baseline NIHSS score, patients with high corin still had a significantly lower risk for the composite outcome of major disability or death (OR = 0.60, 95%CI: 0.36-0.99).", "This association became bottom line significant after additionally adjusting for other conventional factors (OR = 0.61, P = 0.058).", "No association was found between serum soluble corin and other composite outcomes.   \n", "CONCLUSION Serum soluble corin deficiency predicted risk for major disability within 3 months after stroke, independent of baseline neurological deficient.", "Our results may indicate a probable role of corin in stroke prognosis."], "structured": true}
{"doc_id": 16201748, "title": "Altered PTEN expression; a diagnostic marker for differentiating normal, hyperplastic and neoplastic endometrium", "abstract": ["BACKGROUND Different molecular alterations have been described in endometrioid endometrial carcinoma (EECA).", "Among them the most frequently altered is loss of the PTEN protein, a tumor suppressor gene.", "The purpose of this study was to evaluate the expression pattern of PTEN gene in normal, hyperplastic and neoplastic endometrium.   \n", "METHODS In a study in a referral gynecologic hospital in Tehran, Iran, immunohistochemical (IHC) evaluation of PTEN was performed on 87 consecutive specimens to the following three groups; group A- normal proliferative endometrium(n = 29); group B- hyperplastic endometrium [including simple hyperplasia without atypia(n = 21) and complex hyperplasia with atypia (n = 8)] and group C- EECA(n = 29).", "Immunostaining of cells was analyzed by arbitrary quantitative methods according to both slide's area staining and intensity of color reaction.   \n", "RESULTS PTEN immunoreactivity was present in all normal proliferative endometrium, all simple hyperplasia, 75% of atypical complex hyperplasia and in 48% of EECA (P < 0.001).", "The intensity of PTEN reaction was significantly higher in group with proliferative endometrium than hyperplastic endometrium and EECA (P < 0.001).   \n", "CONCLUSION PTEN expression was significantly higher in cyclical endometrium than in atypical hyperplasia and endometrioid carcinoma."], "structured": true}
{"doc_id": 16204011, "title": "Care Seeking for Neonatal Illness in Low- and Middle-Income Countries: A Systematic Review", "abstract": ["BACKGROUND Despite recent achievements to reduce child mortality, neonatal deaths continue to remain high, accounting for 41% of all deaths in children under five years of age worldwide, of which over 90% occur in low- and middle-income countries (LMICs).", "Infections are a leading cause of death and limitations in care seeking for ill neonates contribute to high mortality rates.", "As estimates for care-seeking behaviors in LMICs have not been studied, this review describes care seeking for neonatal illnesses in LMICs, with particular attention to type of care sought.   \n", "METHODS AND FINDINGS We conducted a systematic literature review of studies that reported the proportion of caregivers that sought care for ill or suspected ill neonates in LMICs.", "The initial search yielded 784 studies, of which 22 studies described relevant data from community household surveys, facility-based surveys, and intervention trials.", "The majority of studies were from South Asia (n = 17/22), set in rural areas (n = 17/22), and published within the last 4 years (n = 18/22).", "Of the 9,098 neonates who were ill or suspected to be ill, 4,320 caregivers sought some type of care, including care from a health facility (n = 370) or provider (n = 1,813).", "Care seeking ranged between 10% and 100% among caregivers with a median of 59%.", "Care seeking from a health care provider yielded a similar range and median, while care seeking at a health care facility ranged between 1% and 100%, with a median of 20%.", "Care-seeking estimates were limited by the few studies conducted in urban settings and regions other than South Asia.", "There was a lack of consistency regarding illness, care-seeking, and care provider definitions.   \n", "CONCLUSIONS There is a paucity of data regarding newborn care-seeking behaviors; in South Asia, care seeking is low for newborn illness, especially in terms of care sought from health care facilities and medically trained providers.", "There is a need for representative data to describe care-seeking patterns in different geographic regions and better understand mechanisms to enhance care seeking during this vulnerable time period."], "structured": true}
{"doc_id": 16208091, "title": "Synaptic Incorporation of AMPA Receptors during LTP Is Controlled by a PKC Phosphorylation Site on GluR1", "abstract": ["Incorporation of GluR1-containing AMPA receptors into synapses is essential to several forms of neural plasticity, including long-term potentiation (LTP).", "Numerous signaling pathways that trigger this process have been identified, but the direct modifications of GluR1 that control its incorporation into synapses are unclear.", "Here, we show that phosphorylation of GluR1 by PKC at a highly conserved serine 818 residue is increased during LTP and critical for LTP expression.", "GluR1 is phosphorylated by PKC at this site in vitro and in vivo.", "In addition, acute phosphorylation at GluR1 S818 by PKC, as well as a phosphomimetic mutation, promotes GluR1 synaptic incorporation.", "Conversely, preventing GluR1 S818 phosphorylation reduces LTP and blocks PKC-driven synaptic incorporation of GluR1.", "We conclude that the phosphorylation of GluR1 S818 by PKC is a critical event in the plasticity-driven synaptic incorporation of AMPA receptors."], "structured": false}
{"doc_id": 16217855, "title": "The Bloom's syndrome helicase promotes the annealing of complementary single-stranded DNA", "abstract": ["The product of the gene mutated in Bloom's syndrome, BLM, is a 3\u2032\u20135\u2032 DNA helicase belonging to the highly conserved RecQ family.", "In addition to a conventional DNA strand separation activity, BLM catalyzes both the disruption of non-B-form DNA, such as G-quadruplexes, and the branch migration of Holliday junctions.", "Here, we have characterized a new activity for BLM: the promotion of single-stranded DNA (ssDNA) annealing.", "This activity does not require Mg2+, is inhibited by ssDNA binding proteins and ATP, and is dependent on DNA length.", "Through analysis of various truncation mutants of BLM, we show that the C-terminal domain is essential for strand annealing and identify a 60 amino acid stretch of this domain as being important for both ssDNA binding and strand annealing.", "We present a model in which the ssDNA annealing activity of BLM facilitates its role in the processing of DNA intermediates that arise during repair of damaged replication forks."], "structured": false}
{"doc_id": 16232581, "title": "Bayesian selection of continuous-time Markov chain evolutionary models.", "abstract": ["We develop a reversible jump Markov chain Monte Carlo approach to estimating the posterior distribution of phylogenies based on aligned DNA/RNA sequences under several hierarchical evolutionary models.", "Using a proper, yet nontruncated and uninformative prior, we demonstrate the advantages of the Bayesian approach to hypothesis testing and estimation in phylogenetics by comparing different models for the infinitesimal rates of change among nucleotides, for the number of rate classes, and for the relationships among branch lengths.", "We compare the relative probabilities of these models and the appropriateness of a molecular clock using Bayes factors.", "Our most general model, first proposed by Tamura and Nei, parameterizes the infinitesimal change probabilities among nucleotides (A, G, C, T/U) into six parameters, consisting of three parameters for the nucleotide stationary distribution, two rate parameters for nucleotide transitions, and another parameter for nucleotide transversions.", "Nested models include the Hasegawa, Kishino, and Yano model with equal transition rates and the Kimura model with a uniform stationary distribution and equal transition rates.", "To illustrate our methods, we examine simulated data, 16S rRNA sequences from 15 contemporary eubacteria, halobacteria, eocytes, and eukaryotes, 9 primates, and the entire HIV genome of 11 isolates.", "We find that the Kimura model is too restrictive, that the Hasegawa, Kishino, and Yano model can be rejected for some data sets, that there is evidence for more than one rate class and a molecular clock among similar taxa, and that a molecular clock can be rejected for more distantly related taxa."], "structured": false}
{"doc_id": 16233471, "title": "The intersection between aging and cardiovascular disease.", "abstract": ["The average lifespan of humans is increasing, and with it the percentage of people entering the 65 and older age group is growing rapidly and will continue to do so in the next 20 years.", "Within this age group, cardiovascular disease will remain the leading cause of death, and the cost associated with treatment will continue to increase.", "Aging is an inevitable part of life and unfortunately poses the largest risk factor for cardiovascular disease.", "Although numerous studies in the cardiovascular field have considered both young and aged humans, there are still many unanswered questions as to how the genetic pathways that regulate aging in model organisms influence cardiovascular aging.", "Likewise, in the molecular biology of aging field, few studies fully assess the role of these aging pathways in cardiovascular health.", "Fortunately, this gap is beginning to close, and these two fields are merging together.", "We provide an overview of some of the key genes involved in regulating lifespan and health span, including sirtuins, AMP-activated protein kinase, mammalian target of rapamycin, and insulin-like growth factor 1 and their roles regulating cardiovascular health.", "We then discuss a series of review articles that will appear in succession and provide a more comprehensive analysis of studies carried out linking genes of aging and cardiovascular health, and perspectives of future directions of these two intimately linked fields."], "structured": false}
{"doc_id": 16237005, "title": "Single-RNA counting reveals alternative modes of gene expression in yeast", "abstract": ["Proper execution of transcriptional programs is a key requirement of gene expression regulation, demanding accurate control of timing and amplitude.", "How precisely the transcription machinery fulfills this task is not known.", "Using an in situ hybridization approach that detects single mRNA molecules, we measured mRNA abundance and transcriptional activity within single Saccharomyces cerevisiae cells.", "We found that expression levels for particular genes are higher than initially reported and can vary substantially among cells.", "However, variability for most constitutively expressed genes is unexpectedly small.", "Combining single-transcript measurements with computational modeling indicates that low expression variation is achieved by transcribing genes using single transcription-initiation events that are clearly separated in time, rather than by transcriptional bursts.", "In contrast, PDR5, a gene regulated by the transcription coactivator complex SAGA, is expressed using transcription bursts, resulting in larger variation.", "These data directly demonstrate the existence of multiple expression modes used to modulate the transcriptome."], "structured": false}
{"doc_id": 16242975, "title": "A complete landscape of post-transcriptional modifications in mammalian mitochondrial tRNAs", "abstract": ["In mammalian mitochondria, 22 species of tRNAs encoded in mitochondrial DNA play crucial roles in the translation of 13 essential subunits of the respiratory chain complexes involved in oxidative phosphorylation.", "Following transcription, mitochondrial tRNAs are modified by nuclear-encoded tRNA-modifying enzymes.", "These modifications are required for the proper functioning of mitochondrial tRNAs (mt tRNAs), and the absence of these modifications can cause pathological consequences.", "To date, however, the information available about these modifications has been incomplete.", "To address this issue, we isolated all 22 species of mt tRNAs from bovine liver and comprehensively determined the post-transcriptional modifications in each tRNA by mass spectrometry.", "Here, we describe the primary structures with post-transcriptional modifications of seven species of mt tRNAs which were previously uncharacterized, and provide revised information regarding base modifications in five other mt tRNAs.", "In the complete set of bovine mt tRNAs, we found 15 species of modified nucleosides at 118 positions (7.48% of total bases).", "This result provides insight into the molecular mechanisms underlying the decoding system in mammalian mitochondria and enables prediction of candidate tRNA-modifying enzymes responsible for each modification of mt tRNAs."], "structured": false}
{"doc_id": 16252863, "title": "Preventing coronary heart disease: B vitamins and homocysteine.", "abstract": ["The list of preventable and reversible risk factors for atherosclerotic cardiovascular disease continues to grow.", "Cigarette smoking, high blood pressure, physical inactivity, elevated cholesterol, underlying lipoprotein abnormalities, lipoprotein(a), diabetes, overweight, male gender, and age are well-established risk factors.", "During the 1990s, there have been many reports associating elevated plasma homocysteine levels with arteriosclerotic cardiovascular disease and consistent evidence that dietary and supplemental folic acid can reduce homocysteine levels.1 2   The article by Robinson and colleagues3 in this issue of Circulation presents further evidence of the importance of homocysteine and suggestive evidence that plasma folate and plasma pyrixodal-l-phosphate (vitamin B6) are protective factors.", "Their study is part of the European Concerted Action Project,4 which examined 750 patients younger than age 60 with diagnoses within the previous 12 months of coronary, cerebrovascular, or peripheral vascular disease and 800 healthy control subjects.", "The patient groups were young (47 years for cases and 44 years for control subjects) and heterogeneous, with nonfatal clinical events or symptoms of arteriosclerotic cardiovascular disease supported by ECG, angiographic, or Doppler evidence; the study involved 19 centers in nine European countries.", "Men in the highest quintile for fasting total homocysteine (tHcy), compared with the remainder of the population, had an estimated relative risk of 2.2 (95% confidence interval [CI], 1.6 to 2.9), with a striking dose-response relationship and a more-than-multiplicative interaction with cigarette smoking and high blood pressure on vascular disease risk4 ; the corresponding estimated relative risk for coronary heart disease was similar (2.0; 95% CI 1.6 to 2.8).", "(tHcy is the sum of homocysteine and homocysteinyl moieties of oxidized disulfides, homocystine, and cysteine- homocysteine.", ")  ", "Robinson and colleagues3 examined three B vitamins in detail to determine their effects on fasting and post\u2013methionine-loading tHcy levels and any independent effects on cardiovascular disease \u2026"], "structured": false}
{"doc_id": 16256507, "title": "Relationship between serum parathyroid hormone levels, vitamin D sufficiency, and calcium intake.", "abstract": ["CONTEXT Adequate vitamin D status for optimum bone health has received increased recognition in recent years; however, the ideal intake is not known.", "Serum 25-hydroxyvitamin D is the generally accepted indicator of vitamin D status, but no universal reference level has been reached.   \n", "OBJECTIVE To investigate the relative importance of high calcium intake and serum 25-hydroxyvitamin D for calcium homeostasis, as determined by serum intact parathyroid hormone (PTH).   \n", "DESIGN, SETTING, AND PARTICIPANTS Cross-sectional study of 2310 healthy Icelandic adults who were divided equally into 3 age groups (30-45 years, 50-65 years, or 70-85 years) and recruited from February 2001 to January 2003.", "They were administered a semi-quantitative food frequency questionnaire, which assessed vitamin D and calcium intake.", "Participants were further divided into groups according to calcium intake (<800 mg/d, 800-1200 mg/d, and >1200 mg/d) and serum 25-hydroxyvitamin D level (<10 ng/mL, 10-18 ng/mL, and >18 ng/mL).   \n", "MAIN OUTCOME MEASURE Serum intact PTH as determined by calcium intake and vitamin D.   RESULTS A total of 944 healthy participants completed all parts of the study.", "After adjusting for relevant factors, serum PTH was lowest in the group with a serum 25-hydroxyvitamin D level of more than 18 ng/mL but highest in the group with a serum 25-hydroxyvitamin D level of less than 10 ng/mL. At the low serum 25-hydroxyvitamin D level (<10 ng/mL), calcium intake of less than 800 mg/d vs more than 1200 mg/d was significantly associated with higher serum PTH (P = .04); and at a calcium intake of more than 1200 mg/d, there was a significant difference between the lowest and highest vitamin D groups (P = .04).   \n", "CONCLUSIONS As long as vitamin D status is ensured, calcium intake levels of more than 800 mg/d may be unnecessary for maintaining calcium metabolism.", "Vitamin D supplements are necessary for adequate vitamin D status in northern climates."], "structured": true}
{"doc_id": 16267205, "title": "Sex-specific effects of the DAF-12 steroid receptor on aging in Caenorhabditis elegans.", "abstract": ["Sex differences in longevity and aging are seen throughout the animal kingdom.", "These are likely to result, in part, from sex differences in endocrinology.", "In the nematode Caenorhabditis elegans, males are the longer-lived sex.", "Here we explore the possibility that sex differences in insulin/insulin-like growth factor 1 (IGF-1) and steroid endocrinology contribute to this sex difference in aging by studying C. elegans populations in liquid culture.", "We report that in hermaphrodite populations, mutational loss of the DAF-12 steroid receptor affected life span as in previous plate-culture studies: mutant longevity is suppressed in a weak daf-2 insulin/IGF-1 receptor mutant but enhanced in a stronger daf-2 mutant.", "However, in males, mutation of daf-12 had little effect on aging in either weak or strong daf-2 mutants.", "Moreover, while mutation of daf-12 marginally reduced life span in daf-2(+) hermaphrodites, as in plate-cultured populations, it did not in daf-2(+) males.", "These results could imply that in C. elegans, as in mammals, sex differences in steroid endocrinology contribute to sex differences in aging."], "structured": false}
{"doc_id": 16270577, "title": "Nonclassical binding of formylated peptide in crystal structure of the MHC class lb molecule H2-M3", "abstract": ["H2-M3 is a class Ib MHC molecule of the mouse with a 10(4)-fold preference for binding N-formylated peptides.", "To elucidate the basis of this unusual specificity, we expressed and crystallized a soluble form of M3 with a formylated nonamer peptide, fMYFINILTL, and determined the structure by X-ray crystallography.", "M3, refined at 2.1 A resolution, resembles class la MHC molecules in its overall structure, but differs in the peptide-binding groove.", "The A pocket, which usually accommodates the free N-terminus of a bound peptide, is closed, and the peptide is shifted one residue, such that the P1 side chain is lodged in the B pocket.", "The formyl group is coordinated by His-9 and a bound water on the floor of the groove."], "structured": false}
{"doc_id": 16280642, "title": "Sequential signals toward podosome formation in NIH-src cells", "abstract": ["Podosomes (also termed invadopodia in cancer cells) are actin-rich adhesion structures with matrix degradation activity that develop in various cell types.", "Despite their significant physiological importance, the molecular mechanism of podosome formation is largely unknown.", "In this study, we investigated the molecular mechanisms of podosome formation.", "The expression of various phosphoinositide-binding domains revealed that the podosomes in Src-transformed NIH3T3 (NIH-src) cells are enriched with PtdIns(3,4)P2, suggesting an important role of this phosphoinositide in podosome formation.", "Live-cell imaging analysis revealed that Src-expression stimulated podosome formation at focal adhesions of NIH3T3 cells after PtdIns(3,4)P2 accumulation.", "The adaptor protein Tks5/FISH, which is essential for podosome formation, was found to form a complex with Grb2 at adhesion sites in an Src-dependent manner.", "Further, it was found that N-WASP bound all SH3 domains of Tks5/FISH, which facilitated circular podosome formation.", "These results indicate that augmentation of the N-WASP-Arp2/3 signal was accomplished on the platform of Tks5/FISH-Grb2 complex at focal adhesions, which is stabilized by PtdIns(3,4)P2."], "structured": false}
{"doc_id": 16284655, "title": "Forebrain engraftment by human glial progenitor cells enhances synaptic plasticity and learning in adult mice.", "abstract": ["Human astrocytes are larger and more complex than those of infraprimate mammals, suggesting that their role in neural processing has expanded with evolution.", "To assess the cell-autonomous and species-selective properties of human glia, we engrafted human glial progenitor cells (GPCs) into neonatal immunodeficient mice.", "Upon maturation, the recipient brains exhibited large numbers and high proportions of both human glial progenitors and astrocytes.", "The engrafted human glia were gap-junction-coupled to host astroglia, yet retained the size and pleomorphism of hominid astroglia, and propagated Ca2+ signals 3-fold faster than their hosts.", "Long-term potentiation (LTP) was sharply enhanced in the human glial chimeric mice, as was their learning, as assessed by Barnes maze navigation, object-location memory, and both contextual and tone fear conditioning.", "Mice allografted with murine GPCs showed no enhancement of either LTP or learning.", "These findings indicate that human glia differentially enhance both activity-dependent plasticity and learning in mice."], "structured": false}
{"doc_id": 16287725, "title": "Reprogramming of human fibroblasts to pluripotency with lineage specifiers.", "abstract": ["Since the initial discovery that OCT4, SOX2, KLF4, and c-MYC overexpression sufficed for the induction of pluripotency in somatic cells, methodologies replacing the original factors have enhanced our understanding of the reprogramming process.", "However, unlike in mouse, OCT4 has not been replaced successfully during reprogramming of human cells.", "Here we report on a strategy to accomplish this replacement.", "Through a combination of transcriptome and bioinformatic analysis we have identified factors previously characterized as being lineage specifiers that are able to replace OCT4 and SOX2 in the reprogramming of human fibroblasts.", "Our results show that it is possible to replace OCT4 and SOX2 simultaneously with alternative lineage specifiers in the reprogramming of human cells.", "At a broader level, they also support a model in which counteracting lineage specification networks underlies the induction of pluripotency."], "structured": false}
{"doc_id": 16319097, "title": "Mechanisms of endocytosis.", "abstract": ["Endocytic mechanisms control the lipid and protein composition of the plasma membrane, thereby regulating how cells interact with their environments.", "Here, we review what is known about mammalian endocytic mechanisms, with focus on the cellular proteins that control these events.", "We discuss the well-studied clathrin-mediated endocytic mechanisms and dissect endocytic pathways that proceed independently of clathrin.", "These clathrin-independent pathways include the CLIC/GEEC endocytic pathway, arf6-dependent endocytosis, flotillin-dependent endocytosis, macropinocytosis, circular doral ruffles, phagocytosis, and trans-endocytosis.", "We also critically review the role of caveolae and caveolin1 in endocytosis.", "We highlight the roles of lipids, membrane curvature-modulating proteins, small G proteins, actin, and dynamin in endocytic pathways.", "We discuss the functional relevance of distinct endocytic pathways and emphasize the importance of studying these pathways to understand human disease processes."], "structured": false}
{"doc_id": 16322674, "title": "Birth Size and Breast Cancer Risk: Re-analysis of Individual Participant Data from 32 Studies", "abstract": ["BACKGROUND Birth size, perhaps a proxy for prenatal environment, might be a correlate of subsequent breast cancer risk, but findings from epidemiological studies have been inconsistent.", "We re-analysed individual participant data from published and unpublished studies to obtain more precise estimates of the magnitude and shape of the birth size-breast cancer association.   \n", "METHODS AND FINDINGS Studies were identified through computer-assisted and manual searches, and personal communication with investigators.", "Individual participant data from 32 studies, comprising 22,058 breast cancer cases, were obtained.", "Random effect models were used, if appropriate, to combine study-specific estimates of effect.", "Birth weight was positively associated with breast cancer risk in studies based on birth records (pooled relative risk [RR] per one standard deviation [SD] [= 0.5 kg] increment in birth weight: 1.06; 95% confidence interval [CI] 1.02-1.09) and parental recall when the participants were children (1.02; 95% CI 0.99-1.05), but not in those based on adult self-reports, or maternal recall during the woman's adulthood (0.98; 95% CI 0.95-1.01) (p for heterogeneity between data sources = 0.003).", "Relative to women who weighed 3.000-3.499 kg, the risk was 0.96 (CI 0.80-1.16) in those who weighed < 2.500 kg, and 1.12 (95% CI 1.00-1.25) in those who weighed > or = 4.000 kg (p for linear trend = 0.001) in birth record data.", "Birth length and head circumference from birth records were also positively associated with breast cancer risk (pooled RR per one SD increment: 1.06 [95% CI 1.03-1.10] and 1.09 [95% CI 1.03-1.15], respectively).", "Simultaneous adjustment for these three birth size variables showed that length was the strongest independent predictor of risk.", "The birth size effects did not appear to be confounded or mediated by established breast cancer risk factors and were not modified by age or menopausal status.", "The cumulative incidence of breast cancer per 100 women by age 80 y in the study populations was estimated to be 10.0, 10.0, 10.4, and 11.5 in those who were, respectively, in the bottom, second, third, and top fourths of the birth length distribution.   \n", "CONCLUSIONS This pooled analysis of individual participant data is consistent with birth size, and in particular birth length, being an independent correlate of breast cancer risk in adulthood."], "structured": true}
{"doc_id": 16346504, "title": "LncRNA-GAS5 induces PTEN expression through inhibiting miR-103 in endometrial cancer cells", "abstract": ["BACKGROUND Growth arrest-specific 5 (GAS5) was reported to be implicated and aberrantly express in multiple cancers.", "However, the expression and mechanism of action of GAS5 were largely poor understood in endometrial carcinoma.   \n", "RESULTS According to the result of real-time reverse-transcriptase polymerase chain reaction (RT-PCR) and flow cytometry analysis, we identified that GAS5 was down-regulated in endometrial cancer cells and stimulated the apoptosis of endometrial cancer cells.", "To investigate the expression of GAS5, PTEN and miR-103, RT-PCR was performed.", "And we found that the expression of PTEN was up-regulated when endometrial cancer cells overexpressed GAS5.", "The prediction of bioinformatics online revealed that GAS5 could bind to miR-103, which was further found to be regulated by GAS5.", "Finally, we found that miR-103 mimic could decrease the mRNA and protein levels of PTEN through luciferase reporter assay and western blotting, and GAS5 plasmid may reverse this regulation effect in endometrial cancer cells.   \n", "CONCLUSION In summary, we demonstrate that GAS5 acts as an tumor suppressor lncRNA in endometrial cancer.", "Through inhibiting the expression of miR-103, GAS5 significantly enhanced the expression of PTEN to promote cancer cell apoptosis, and, thus, could be an important mediator in the pathogenesis of endometrial cancer."], "structured": true}
{"doc_id": 16355392, "title": "Modification of kidney barrier function by the urokinase receptor", "abstract": ["Podocyte dysfunction, represented by foot process effacement and proteinuria, is often the starting point for progressive kidney disease.", "Therapies aimed at the cellular level of the disease are currently not available.", "Here we show that induction of urokinase receptor (uPAR) signaling in podocytes leads to foot process effacement and urinary protein loss via a mechanism that includes lipid-dependent activation of \u03b1v\u03b23 integrin.", "Mice lacking uPAR (Plaur\u2212/\u2212) are protected from lipopolysaccharide (LPS)-mediated proteinuria but develop disease after expression of a constitutively active \u03b23 integrin.", "Gene transfer studies reveal a prerequisite for uPAR expression in podocytes, but not in endothelial cells, for the development of LPS-mediated proteinuria.", "Mechanistically, uPAR is required to activate \u03b1v\u03b23 integrin in podocytes, promoting cell motility and activation of the small GTPases Cdc42 and Rac1.", "Blockade of \u03b1v\u03b23 integrin reduces podocyte motility in vitro and lowers proteinuria in mice.", "Our findings show a physiological role for uPAR signaling in the regulation of kidney permeability."], "structured": false}
{"doc_id": 16361581, "title": "Jagged1-induced Notch signaling drives proliferation of multiple myeloma cells.", "abstract": ["Notch receptors expressed on hematopoietic stem cells interact with their ligands on bone marrow stromal cells and thereby control cell fate decisions and survival.", "We recently demonstrated that Notch signaling is involved in proliferation and survival of B cell-derived tumor cells of classic Hodgkin disease and described a novel mechanism for the oncogenic capacity of Notch.", "In this study we investigated whether Notch signaling is involved in the tight interactions between neoplastic plasma cells and their bone marrow microenvironment, which are essential for tumor cell growth in multiple myeloma (MM).", "Here we demonstrate that Notch receptors and their ligand Jagged1 are highly expressed in cultured and primary MM cells, whereas nonneoplastic counterparts show low to undetectable levels of Notch.", "Functional data indicate that ligand-induced Notch signaling is a growth factor for MM cells and suggest that these interactions contribute to myelomagenesis in vivo."], "structured": false}
{"doc_id": 16364639, "title": "An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma", "abstract": ["By analyzing gene expression data in glioblastoma in combination with matched microRNA profiles, we have uncovered a posttranscriptional regulation layer of surprising magnitude, comprising more than 248,000 microRNA (miR)-mediated interactions.", "These include \u223c7,000 genes whose transcripts act as miR \"sponges\" and 148 genes that act through alternative, nonsponge interactions.", "Biochemical analyses in cell lines confirmed that this network regulates established drivers of tumor initiation and subtype implementation, including PTEN, PDGFRA, RB1, VEGFA, STAT3, and RUNX1, suggesting that these interactions mediate crosstalk between canonical oncogenic pathways.", "siRNA silencing of 13 miR-mediated PTEN regulators, whose locus deletions are predictive of PTEN expression variability, was sufficient to downregulate PTEN in a 3'UTR-dependent manner and to increase tumor cell growth rates.", "Thus, miR-mediated interactions provide a mechanistic, experimentally validated rationale for the loss of PTEN expression in a large number of glioma samples with an intact PTEN locus."], "structured": false}
{"doc_id": 16375102, "title": "Direct reprogramming of mouse fibroblasts to neural progenitors.", "abstract": ["The simple yet powerful technique of induced pluripotency may eventually supply a wide range of differentiated cells for cell therapy and drug development.", "However, making the appropriate cells via induced pluripotent stem cells (iPSCs) requires reprogramming of somatic cells and subsequent redifferentiation.", "Given how arduous and lengthy this process can be, we sought to determine whether it might be possible to convert somatic cells into lineage-specific stem/progenitor cells of another germ layer in one step, bypassing the intermediate pluripotent stage.", "Here we show that transient induction of the four reprogramming factors (Oct4, Sox2, Klf4, and c-Myc) can efficiently transdifferentiate fibroblasts into functional neural stem/progenitor cells (NPCs) with appropriate signaling inputs.", "Compared with induced neurons (or iN cells, which are directly converted from fibroblasts), transdifferentiated NPCs have the distinct advantage of being expandable in vitro and retaining the ability to give rise to multiple neuronal subtypes and glial cells.", "Our results provide a unique paradigm for iPSC-factor-based reprogramming by demonstrating that it can be readily modified to serve as a general platform for transdifferentiation."], "structured": false}
{"doc_id": 16389141, "title": "Tissue-Specific Knockout of the Insulin Receptor in Pancreatic \u03b2 Cells Creates an Insulin Secretory Defect Similar to that in Type 2 Diabetes", "abstract": ["Dysfunction of the pancreatic beta cell is an important defect in the pathogenesis of type 2 diabetes, although its exact relationship to the insulin resistance is unclear.", "To determine whether insulin signaling has a functional role in the beta cell we have used the Cre-loxP system to specifically inactivate the insulin receptor gene in the beta cells.", "The resultant mice exhibit a selective loss of insulin secretion in response to glucose and a progressive impairment of glucose tolerance.", "These data indicate an important functional role for the insulin receptor in glucose sensing by the pancreatic beta cell and suggest that defects in insulin signaling at the level of the beta cell may contribute to the observed alterations in insulin secretion in type 2 diabetes."], "structured": false}
{"doc_id": 16390264, "title": "Social variations in access to hospital care for patients with colorectal, breast, and lung cancer between 1999 and 2006: retrospective analysis of hospital episode statistics", "abstract": ["OBJECTIVES To determine the extent to which type of hospital admission (emergency compared with elective) and surgical procedure varied by socioeconomic circumstances, age, sex, and year of admission for colorectal, breast, and lung cancer.   \n", "DESIGN Repeated cross sectional study with data from individual patients, 1 April 1999 to 31 March 2006.   \n", "SETTING Hospital episode statistics (HES) dataset.   \n", "PARTICIPANTS 564 821 patients aged 50 and over admitted with a diagnosis of colorectal, breast, or lung cancer.   \n", "MAIN OUTCOME MEASURES Proportion of patients admitted as emergencies, and the proportion receiving the recommended surgical treatment.   \n", "RESULTS Patients from deprived areas, older people, and women were more likely to be admitted as emergencies.", "For example, the adjusted odds ratio for patients with breast cancer in the least compared with most deprived fifth of deprivation was 0.63 (95% confidence interval 0.60 to 0.66) and the adjusted odds ratio for patients with lung cancer aged 80-89 compared with those aged 50-59 was 3.13 (2.93 to 3.34).", "There were some improvements in disparities between age groups but not for patients living in deprived areas over time.", "Patients from deprived areas were less likely to receive preferred procedures for rectal, breast, and lung cancer.", "These findings did not improve with time.", "For example, 67.4% (3529/5237) of patients in the most deprived fifth of deprivation had anterior resection for rectal cancer compared with 75.5% (4497/5959) of patients in the least deprived fifth (1.34, 1.22 to 1.47).", "Over half (54.0%, 11 256/20 849) of patients in the most deprived fifth of deprivation had breast conserving surgery compared with 63.7% (18 445/28 960) of patients in the least deprived fifth (1.21, 1.16 to 1.26).", "Men were less likely than women to undergo anterior resection and lung cancer resection and older people were less likely to receive breast conserving surgery and lung cancer resection.", "For example, the adjusted odds ratio for lung cancer patients aged 80-89 compared with those aged 50-59 was 0.52 (0.46 to 0.59).", "Conclusions Despite the implementation of the NHS Cancer Plan, social factors still strongly influence access to and the provision of care."], "structured": true}
{"doc_id": 16398049, "title": "Identification of Gene Positioning Factors Using High-Throughput Imaging Mapping", "abstract": ["Genomes are arranged non-randomly in the 3D space of the cell nucleus.", "Here, we have developed HIPMap, a high-precision, high-throughput, automated fluorescent in situ hybridization imaging pipeline, for mapping of the spatial location of genome regions at large scale.", "High-throughput imaging position mapping (HIPMap) enabled an unbiased siRNA screen for factors involved in genome organization in human cells.", "We identify 50 cellular factors required for proper positioning of a set of functionally diverse genomic loci.", "Positioning factors include chromatin remodelers, histone modifiers, and nuclear envelope and pore proteins.", "Components of the replication and post-replication chromatin re-assembly machinery are prominently represented among positioning factors, and timely progression of cells through replication, but not mitosis, is required for correct gene positioning.", "Our results establish a method for the large-scale mapping of genome locations and have led to the identification of a compendium of cellular factors involved in spatial genome organization."], "structured": false}
{"doc_id": 16398827, "title": "Astrocyte-Mediated Distributed Plasticity at Hypothalamic Glutamate Synapses", "abstract": ["Afferent activity can induce fast, feed-forward changes in synaptic efficacy that are synapse specific.", "Using combined electrophysiology, caged molecule photolysis, and Ca(2+) imaging, we describe a plasticity in which the recruitment of astrocytes in response to afferent activity causes a fast and feed-forward, yet distributed increase in the amplitude of quantal synaptic currents at multiple glutamate synapses on magnocellular neurosecretory cells in the hypothalamic paraventricular nucleus.", "The plasticity is largely multiplicative, consistent with a proportional increase or \"scaling\" in the strength of all synapses on the neuron.", "This effect requires a metabotropic glutamate receptor-mediated rise in Ca(2+) in the astrocyte processes surrounding the neuron and the release of the gliotransmitter ATP, which acts on postsynaptic purinergic receptors.", "These data provide evidence for a form of distributed synaptic plasticity that is feed-forward, expressed quickly, and mediated by the synaptic activation of neighboring astrocytes."], "structured": false}
{"doc_id": 16422880, "title": "Effect of smoking reduction on lung cancer risk.", "abstract": ["CONTEXT Many smokers are unable or unwilling to completely quit smoking.", "A proposed means of harm reduction is to reduce the number of cigarettes smoked per day.", "However, it is not clear whether this strategy decreases the risk for tobacco-related diseases.   \n", "OBJECTIVE To assess the effects of smoking reduction on lung cancer incidence.   \n", "DESIGN, SETTING, AND PARTICIPANTS Observational population-based cohort study with up to 31 years of follow-up from the Copenhagen Centre for Prospective Population Studies, which administrates data from 3 longitudinal studies conducted in Copenhagen and suburbs, the Copenhagen City Heart Study, the Copenhagen Male Study, and the Glostrup Population Studies, Denmark.", "Participants were 11,151 men and 8563 women (N = 19,714) aged 20 to 93 years, who attended 2 consecutive examinations with a 5- to 10-year interval between 1964 and 1988.", "Participants underwent a physical examination and completed self-filled questionnaires about lifestyle habits.", "The study population was divided into 6 groups according to smoking habits: continued heavy smokers (> or =15 cigarettes/d), reducers (reduced from > or =15 cigarettes/d by minimum of 50% without quitting), continued light smokers (1-14 cigarettes/d), quitters (stopped between first and second examination), stable ex-smokers, and never smokers.   \n", "MAIN OUTCOME MEASURE Incident primary lung cancer cases assessed by record linkage with the National Cancer Registry until December 31, 2003.   \n", "RESULTS There were 864 incident lung cancers during follow-up.", "Using Cox regression, the adjusted hazard ratio (HR) for lung cancer in reducers was 0.73 (95% confidence interval [CI], 0.54-0.98) compared with persistent heavy smokers.", "The HR for light smokers was 0.44 (95% CI, 0.35-0.56); for quitters, HR 0.50 (95% CI, 0.36-0.69), for stable ex-smokers, HR 0.17 (95% CI, 0.13-0.23), and for never smokers, HR 0.09 (95% CI, 0.06-0.13).   \n", "CONCLUSION Among individuals who smoke 15 or more cigarettes per day, smoking reduction by 50% significantly reduces the risk of lung cancer."], "structured": true}
{"doc_id": 16427454, "title": "Facilities for macromolecular crystallography at the Helmholtz-Zentrum Berlin", "abstract": ["Three macromolecular crystallography (MX) beamlines at the Helmholtz-Zentrum Berlin (HZB) are available for the regional, national and international structural biology user community.", "The state-of-the-art synchrotron beamlines for MX BL14.1, BL14.2 and BL14.3 are located within the low-\u03b2 section of the BESSY II electron storage ring.", "All beamlines are fed from a superconducting 7 T wavelength-shifter insertion device.", "BL14.1 and BL14.2 are energy tunable in the range 5-16 keV, while BL14.3 is a fixed-energy side station operated at 13.8 keV. All three beamlines are equipped with CCD detectors.", "BL14.1 and BL14.2 are in regular user operation providing about 200 beam days per year and about 600 user shifts to approximately 50 research groups across Europe.", "BL14.3 has initially been used as a test facility and was brought into regular user mode operation during the year 2010.", "BL14.1 has recently been upgraded with a microdiffractometer including a mini-\u03ba goniometer and an automated sample changer.", "Additional user facilities include office space adjacent to the beamlines, a sample preparation laboratory, a biology laboratory (safety level 1) and high-end computing resources.", "In this article the instrumentation of the beamlines is described, and a summary of the experimental possibilities of the beamlines and the provided ancillary equipment for the user community is given."], "structured": false}
{"doc_id": 16461149, "title": "                PHENIX: a comprehensive Python-based system for macromolecular structure solution", "abstract": ["Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level.", "However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics.", "PHENIX has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on the automation of all procedures.", "This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms."], "structured": false}
{"doc_id": 16465895, "title": "Telomeric 3\u2032 Overhangs Derive from Resection by Exo1 and Apollo and Fill-In by POT1b-Associated CST", "abstract": ["A 3' overhang is critical for the protection and maintenance of mammalian telomeres, but its synthesis must be regulated to avoid excessive resection of the 5' end, which could cause telomere shortening.", "How this balance is achieved in mammals has not been resolved.", "Here, we determine the mechanism for 3' overhang synthesis in mouse cells by evaluating changes in telomeric overhangs throughout the cell cycle and at leading- and lagging-end telomeres.", "Apollo, a nuclease bound to the shelterin subunit TRF2, initiates formation of the 3' overhang at leading-, but not lagging-end telomeres.", "Hyperresection by Apollo is blocked at both ends by the shelterin protein POT1b.", "Exo1 extensively resects both telomere ends, generating transient long 3' overhangs in S/G2.", "CST/AAF, a DNA pol\u03b1.primase accessory factor, binds POT1b and shortens the extended overhangs produced by Exo1, likely through fill-in synthesis.", "3' overhang formation is thus a multistep, shelterin-controlled process, ensuring functional telomeric overhangs at chromosome ends."], "structured": false}
{"doc_id": 16472469, "title": "Targeting BRCA1 and BRCA2 Deficiencies with G-Quadruplex-Interacting Compounds", "abstract": ["G-quadruplex (G4)-forming genomic sequences, including telomeres, represent natural replication fork barriers.", "Stalled replication forks can be stabilized and restarted by homologous recombination (HR), which also repairs DNA double-strand breaks (DSBs) arising at collapsed forks.", "We have previously shown that HR facilitates telomere replication.", "Here, we demonstrate that the replication efficiency of guanine-rich (G-rich) telomeric repeats is decreased significantly in cells lacking HR.", "Treatment with the G4-stabilizing compound pyridostatin (PDS) increases telomere fragility in BRCA2-deficient cells, suggesting that G4 formation drives telomere instability.", "Remarkably, PDS reduces proliferation of HR-defective cells by inducing DSB accumulation, checkpoint activation, and deregulated G2/M progression and by enhancing the replication defect intrinsic to HR deficiency.", "PDS toxicity extends to HR-defective cells that have acquired olaparib resistance through loss of 53BP1 or REV7.", "Altogether, these results highlight the therapeutic potential of G4-stabilizing drugs to selectively eliminate HR-compromised cells and tumors, including those resistant to PARP inhibition."], "structured": false}
{"doc_id": 16488405, "title": "Downloaded from", "abstract": ["Physical activity induces a subclinical inflammatory response, mediated in part by leukocytes, and manifested by elevated concentrations of circulating proinflammatory cytokines, including interleukin (IL)-1\u03b2, IL-6, and tumor necrosis factor-\u03b1 (TNF-\u03b1).", "However, the source of the cytokines that appear during exercise remains unknown.", "In this study, we examined exercise-induced changes in plasma cytokine concentrations and their corresponding mRNA expression in peripheral blood mononuclear cells.", "Ten healthy [peak oxygen uptake = 48.8 \u00b1 6.5 (SD) ml \u00b7 kg\u22121 \u00b7 min\u22121] but untrained men [age = 25 \u00b1 5 (SD) yr] undertook 3 h of exercise (cycling and inclined walking) at 60\u201365% peak oxygen uptake.", "Circulating leukocyte subset counts were elevated during and 2 h postexercise but returned to normal within 24 h. Plasma concentrations of IL-1\u03b2, IL-6, and TNF-\u03b1 peaked at the end of exercise and remained elevated at 2 h (IL-6) and up to 24 h (IL-1\u03b2 and TNF-\u03b1) postexercise.", "Cytokine gene expression in circulating mononucl..."], "structured": false}
{"doc_id": 16494316, "title": "Receptor tyrosine kinases endocytosis in endothelium: biology and signaling.", "abstract": ["Receptor tyrosine kinases are involved in regulation of key processes in endothelial biology, including proliferation, migration, and angiogenesis.", "It is now generally accepted that receptor tyrosine kinase signaling occurs intracellularly and on the plasma membrane, although many important details remain to be worked out.", "Endocytosis and subsequent intracellular trafficking spatiotemporally regulate receptor tyrosine kinase signaling, whereas signaling endosomes provide a platform for the compartmentalization of signaling events.", "This review summarizes recent advances in our understanding of endothelial receptor tyrosine kinase endocytosis and signaling using vascular endothelial growth factor receptor-2 as a paradigm."], "structured": false}
{"doc_id": 16495649, "title": "Ethnographic study of incidence and severity of intravenous drug errors.", "abstract": ["OBJECTIVES To determine the incidence and clinical importance of errors in the preparation and administration of intravenous drugs and the stages of the process in which errors occur.   \n", "DESIGN Prospective ethnographic study using disguised observation.   \n", "PARTICIPANTS Nurses who prepared and administered intravenous drugs.   \n", "SETTING 10 wards in a teaching and non-teaching hospital in the United Kingdom.   \n", "MAIN OUTCOME MEASURES Number, type, and clinical importance of errors.   \n", "RESULTS 249 errors were identified.", "At least one error occurred in 212 out of 430 intravenous drug doses (49%, 95% confidence interval 45% to 54%).", "Three doses (1%) had potentially severe errors, 126 (29%) potentially moderate errors, and 83 (19%) potentially minor errors.", "Most errors occurred when giving bolus doses or making up drugs that required multiple step preparation.   \n", "CONCLUSIONS The rate of intravenous drug errors was high.", "Although most errors would cause only short term adverse effects, a few could have been serious.", "A combination of reducing the amount of preparation on the ward, training, and technology to administer slow bolus doses would probably have the greatest effect on error rates."], "structured": true}
{"doc_id": 16510361, "title": "Feature Selection with the Boruta Package", "abstract": ["This article describes a R package Boruta, implementing a novel feature selection algorithm for finding emph{all relevant variables}. The algorithm is designed as a wrapper around a Random Forest classification algorithm.", "It iteratively removes the features which are proved by a statistical test to be less relevant than random probes.", "The Boruta package provides a convenient interface to the algorithm.", "The short description of the algorithm and examples of its application are presented."], "structured": false}
{"doc_id": 16511863, "title": "Integrin-linked kinase expression is elevated in human cardiac hypertrophy and induces hypertrophy in transgenic mice.", "abstract": ["BACKGROUND Although numerous signaling pathways are known to be activated in experimental cardiac hypertrophy, the molecular basis of the hypertrophic response inherent in human heart diseases remains largely unknown.", "Integrin-linked kinase (ILK) is a multifunctional protein kinase that physically links beta-integrins with the actin cytoskeleton, suggesting a potential mechanoreceptor role.   \n", "METHODS AND RESULTS Here, we show a marked increase in ILK protein levels in hypertrophic ventricles of patients with congenital and acquired outflow tract obstruction.", "This increase in ILK was associated with activation of the Rho family guanine triphosphatases, Rac1 and Cdc42, and known hypertrophic signaling kinases, including extracellular signal-related kinases (ERK1/2) and p70 S6 kinase.", "Transgenic mice with cardiac-specific expression of a constitutively active ILK (ILK(S343D)) or wild-type ILK (ILK(WT)) exhibited a compensated ventricular hypertrophic phenotype and displayed an activation profile of guanine triphosphatases and downstream protein kinases concordant with that seen in human hypertrophy.", "In contrast, transgenic mice with cardiomyocyte-restricted expression of a kinase-inactive ILK (ILK(R211A)) were unable to mount a compensatory hypertrophic response to angiotensin II in vivo.   \n", "CONCLUSIONS Taken together, these results identify ILK-regulated signaling as a broadly adaptive hypertrophic response mechanism relevant to a wide range of clinical heart disease."], "structured": true}
{"doc_id": 16527698, "title": "Functional and molecular defects of pancreatic islets in human type 2 diabetes.", "abstract": ["To shed further light on the primary alterations of insulin secretion in type 2 diabetes and the possible mechanisms involved, we studied several functional and molecular properties of islets isolated from the pancreata of 13 type 2 diabetic and 13 matched nondiabetic cadaveric organ donors.", "Glucose-stimulated insulin secretion from type 2 diabetic islets was significantly lower than from control islets, whereas arginine- and glibenclamide-stimulated insulin release was less markedly affected.", "The defects were accompanied by reduced mRNA expression of GLUT1 and -2 and glucokinase and by diminished glucose oxidation.", "In addition, AMP-activated protein kinase activation was reduced.", "Furthermore, the expression of insulin was decreased, and that of pancreatic duodenal homeobox-1 (PDX-1) and forkhead box O1 (Foxo-1) was increased.", "Nitrotyrosine and 8-hydroxy-2'-deoxyguanosine concentrations, markers of oxidative stress, were significantly higher in type 2 diabetic than control islets, and they were correlated with the degree of glucose-stimulated insulin release impairment.", "Accordingly, 24-h exposure to glutathione significantly improved glucose-stimulated insulin release and decreased nitrotyrosine concentration, with partial recovery of insulin mRNA expression.", "These results provide direct evidence that the defects of insulin secretion in type 2 diabetic islets are associated with multiple islet cell alterations.", "Most importantly, the current study shows that the functional impairment of type 2 diabetic islets can be, at least in part, reversible.", "In this regard, it is suggested that reducing islet cell oxidative stress is a potential target of human type 2 diabetes therapy."], "structured": false}
{"doc_id": 16532419, "title": "Induction of stem-like cells with malignant properties by chronic exposure of human lung epithelial cells to single-walled carbon nanotubes", "abstract": ["BACKGROUND Carbon nanotubes (CNT) hold great promise to create new and better products for commercial and biomedical applications, but their long-term adverse health effects are a major concern.", "The objective of this study was to address human lung cancer risks associated with chronic pulmonary exposure to single-walled (SW) CNT through the fundamental understanding of cellular and molecular processes leading to carcinogenesis.", "We hypothesized that the acquisition of cancer stem cells (CSC), a subpopulation that drive tumor initiation and progression, may contribute to CNT carcinogenesis.   \n", "METHODS Non-tumorigenic human lung epithelial cells were chronically exposed to well-dispersed SWCNT for a period of 6 months at the physiologically relevant concentration of 0.02 \u03bcg/cm2 surface area dose.", "Chronic SWCNT-exposed cells were evaluated for the presence of CSC-like cells under CSC-selective conditions of tumor spheres and side population (SP).", "CSC-like cells were isolated using fluorescence-activated cell sorting and were assessed for aggressive behaviors, including acquired apoptosis resistance and increased cell migration and invasion in vitro, and tumor-initiating capability in vivo.", "Non-small cell lung cancer cells served as a positive control.   \n", "RESULTS We demonstrated for the first time the existence of CSC-like cells in all clones of chronic SWCNT-exposed lung epithelial cells.", "These CSC-like cells, in contrary to their non-CSC counterpart, possessed all biological features of lung CSC that are central to irreversible malignant transformation, self-renewal, aggressive cancer behaviors, and in vivo tumorigenesis.", "These cells also displayed aberrant stem cell markers, notably Nanog, SOX-2, SOX-17 and E-cadherin.", "Restored expression of tumor suppressor p53 abrogated CSC properties of CSC-like cells.", "Furthermore, we identified specific stem cell surface markers CD24low and CD133high that are associated with SWCNT-induced CSC formation and tumorigenesis.   \n", "CONCLUSIONS Our findings provide new and compelling evidence for the acquisition of CSC-like cells induced by chronic SWCNT exposure, which are likely to be a major driving force for SWCNT tumorigenesis.", "Thus, our study supports prudent adoption of prevention strategies and implementation of exposure control for SWCNT.", "We also suggest that the detection of CSC and associated surface markers may provide an effective screening tool for prediction of the carcinogenic potential of SWCNT and related nanoparticles."], "structured": true}
{"doc_id": 16541762, "title": "Reprogramming factor stoichiometry influences the epigenetic state and biological properties of induced pluripotent stem cells.", "abstract": ["We compared two genetically highly defined transgenic systems to identify parameters affecting reprogramming of somatic cells to a pluripotent state.", "Our results demonstrate that the level and stoichiometry of reprogramming factors during the reprogramming process strongly influence the resulting pluripotency of iPS cells.", "High expression of Oct4 and Klf4 combined with lower expression of c-Myc and Sox2 produced iPS cells that efficiently generated \"all-iPSC mice\" by tetraploid (4n) complementation, maintained normal imprinting at the Dlk1-Dio3 locus, and did not create mice with tumors.", "Loss of imprinting (LOI) at the Dlk1-Dio3 locus did not strictly correlate with reduced pluripotency though the efficiency of generating \"all-iPSC mice\" was diminished.", "Our data indicate that stoichiometry of reprogramming factors can influence epigenetic and biological properties of iPS cells.", "This concept complicates efforts to define a \"generic\" epigenetic state of iPSCs and ESCs and should be considered when comparing different iPS and ES cell lines."], "structured": false}
{"doc_id": 16546131, "title": "Activator protein-1 (AP-1) DNA binding activity is induced by hydroxyurea in organogenesis stage mouse embryos", "abstract": ["Hydroxyurea is a potent teratogen; free radical scavengers or antioxidants reduce its teratogenicity.", "Activator Protein-1 (AP-1) and NF-kappaB are redox-sensitive transcription factors with important roles in normal development and the stress response.", "This study was designed to determine if exposure to teratogenic doses of hydroxyurea induces oxidative stress and alters gene expression by activating these transcription factors.", "Pregnant mice were treated with saline or hydroxyurea (400, 500, or 600 mg/kg) on gestation day 9 (GD 9) and killed either on GD 9, 0.5, 3, or 6 h after treatment, to assess oxidative stress and transcription factor activities, or on GD 18, to assess fetal development.", "Exposure to 400 mg/kg hydroxyurea did not affect the progeny, whereas exposure to 500 or 600 mg/kg resulted in dose-dependent increases in fetal resorptions and malformations, including curly tails, abnormal limbs (oligodactyly, hemimelia, and amelia), and short ribs.", "Hydroxyurea did not induce oxidative stress, as assessed by the ratio of oxidized to reduced glutathione, nor did it alter NF-kappaB DNA binding activity in the GD 9 conceptus.", "In contrast, exposure to hydroxyurea at any dose increased AP-1 DNA binding activity in embryos and yolk sacs 0.5 or 3 h after treatment.", "Hydroxyurea-induced c-Fos heterodimer activity in the embryo peaked 3-4-fold above control at 3 h and remained elevated by 6 h; in contrast, the activity of c-Jun dimers was not altered by drug exposure.", "A dramatic and region-specific increase in c-Fos immunoreactivity was found in hydroxyurea-treated embryos.", "The induction of AP-1 DNA binding activity by hydroxyurea represents an early, sensitive marker of the embryonic response to insult."], "structured": false}
{"doc_id": 16550075, "title": "BCL-6 represses genes that function in lymphocyte differentiation, inflammation, and cell cycle control.", "abstract": ["BCL-6, a transcriptional repressor frequently translocated in lymphomas, regulates germinal center B cell differentiation and inflammation.", "DNA microarray screening identified genes repressed by BCL-6, including many lymphocyte activation genes, suggesting that BCL-6 modulates B cell receptor signals.", "BCL-6 repression of two chemokine genes, MIP-1alpha and IP-10, may also attenuate inflammatory responses.", "Blimp-1, another BCL-6 target, is important for plasmacytic differentiation.", "Since BCL-6 expression is silenced in plasma cells, repression of blimp-1 by BCL-6 may control plasmacytic differentiation.", "Indeed, inhibition of BCL-6 function initiated changes indicative of plasmacytic differentiation, including decreased expression of c-Myc and increased expression of the cell cycle inhibitor p27kip1.", "These data suggest that malignant transformation by BCL-6 involves inhibition of differentiation and enhanced proliferation."], "structured": false}
{"doc_id": 16557565, "title": "Local, Efflux-Dependent Auxin Gradients as a Common Module for Plant Organ Formation", "abstract": ["Plants, compared to animals, exhibit an amazing adaptability and plasticity in their development.", "This is largely dependent on the ability of plants to form new organs, such as lateral roots, leaves, and flowers during postembryonic development.", "Organ primordia develop from founder cell populations into organs by coordinated cell division and differentiation.", "Here, we show that organ formation in Arabidopsis involves dynamic gradients of the signaling molecule auxin with maxima at the primordia tips.", "These gradients are mediated by cellular efflux requiring asymmetrically localized PIN proteins, which represent a functionally redundant network for auxin distribution in both aerial and underground organs.", "PIN1 polar localization undergoes a dynamic rearrangement, which correlates with establishment of auxin gradients and primordium development.", "Our results suggest that PIN-dependent, local auxin gradients represent a common module for formation of all plant organs, regardless of their mature morphology or developmental origin."], "structured": false}
{"doc_id": 16562534, "title": "Drosophila MICAL regulates myofilament organization and synaptic structure", "abstract": ["The overall size and structure of a synaptic terminal is an important determinant of its function.", "In a large-scale mutagenesis screen, designed to identify Drosophila mutants with abnormally structured neuromuscular junctions (NMJs), we discovered mutations in Drosophila mical, a conserved gene encoding a multi-domain protein with a N-terminal monooxygenase domain.", "In mical mutants, synaptic boutons do not sprout normally over the muscle surface and tend to form clusters along synaptic branches and at nerve entry sites.", "Consistent with high expression of MICAL in somatic muscles, immunohistochemical stainings reveal that the subcellular localization and architecture of contractile muscle filaments are dramatically disturbed in mical mutants.", "Instead of being integrated into a regular sarcomeric pattern, actin and myosin filaments are disorganized and accumulate beneath the plasmamembrane.", "Whereas contractile elements are strongly deranged, the proposed organizer of sarcomeric structure, D-Titin, is much less affected.", "Transgenic expression of interfering RNA molecules demonstrates that MICAL is required in muscles for the higher order arrangement of myofilaments.", "Ultrastructural analysis confirms that myosin-rich thick filaments enter submembranous regions and interfere with synaptic development, indicating that the disorganized myofilaments may cause the synaptic growth phenotype.", "As a model, we suggest that the filamentous network around synaptic boutons restrains the spreading of synaptic branches."], "structured": false}
{"doc_id": 16572581, "title": "Viral Infection of Engrafted Human Islets Leads to Diabetes", "abstract": ["Type 1 diabetes (T1D) is characterized by the destruction of the insulin-producing \u03b2-cells of pancreatic islets.", "Genetic and environmental factors both contribute to T1D development.", "Viral infection with enteroviruses is a suspected trigger for T1D, but a causal role remains unproven and controversial.", "Studies in animals are problematic because of species-specific differences in host cell susceptibility and immune responses to candidate viral pathogens such as coxsackievirus B (CVB).", "In order to resolve the controversial role of viruses in human T1D, we developed a viral infection model in immunodeficient mice bearing human islet grafts.", "Hyperglycemia was induced in mice by specific ablation of native \u03b2-cells.", "Human islets, which are naturally susceptible to CVB infection, were transplanted to restore normoglycemia.", "Transplanted mice were infected with CVB4 and monitored for hyperglycemia.", "Forty-seven percent of CVB4-infected mice developed hyperglycemia.", "Human islet grafts from infected mice contained viral RNA, expressed viral protein, and had reduced insulin levels compared with grafts from uninfected mice.", "Human-specific gene expression profiles in grafts from infected mice revealed the induction of multiple interferon-stimulated genes.", "Thus, human islets can become severely dysfunctional with diminished insulin production after CVB infection of \u03b2-cells, resulting in diabetes."], "structured": false}
{"doc_id": 16605494, "title": "MicroRNA-22 (miR-22) Overexpression Is Neuroprotective via General Anti-Apoptotic Effects and May also Target Specific Huntington\u2019s Disease-Related Mechanisms", "abstract": ["BACKGROUND Whereas many causes and mechanisms of neurodegenerative diseases have been identified, very few therapeutic strategies have emerged in parallel.", "One possible explanation is that successful treatment strategy may require simultaneous targeting of more than one molecule of pathway.", "A new therapeutic approach to have emerged recently is the engagement of microRNAs (miRNAs), which affords the opportunity to target multiple cellular pathways simultaneously using a single sequence.   \n", "METHODOLOGY/PRINCIPAL FINDINGS We identified miR-22 as a potentially neuroprotective miRNA based on its predicted regulation of several targets implicated in Huntington's disease (histone deacetylase 4 (HDAC4), REST corepresor 1 (Rcor1) and regulator of G-protein signaling 2 (Rgs2)) and its diminished expression in Huntington's and Alzheimer's disease brains.", "We then tested the hypothesis that increasing cellular levels of miRNA-22 would achieve neuroprotection in in vitro models of neurodegeneration.", "As predicted, overexpression of miR-22 inhibited neurodegeneration in primary striatal and cortical cultures exposed to a mutated human huntingtin fragment (Htt171-82Q).", "Overexpression of miR-22 also decreased neurodegeneration in primary neuronal cultures exposed to 3-nitropropionic acid (3-NP), a mitochondrial complex II/III inhibitor.", "In addition, miR-22 improved neuronal viability in an in vitro model of brain aging.", "The mechanisms underlying the effects of miR-22 included a reduction in caspase activation, consistent with miR-22's targeting the pro-apoptotic activities of mitogen-activated protein kinase 14/p38 (MAPK14/p38) and tumor protein p53-inducible nuclear protein 1 (Tp53inp1).", "Moreover, HD-specific effects comprised not only targeting HDAC4, Rcor1 and Rgs2 mRNAs, but also decreasing focal accumulation of mutant Htt-positive foci, which occurred via an unknown mechanism.   \n", "CONCLUSIONS These data show that miR-22 has multipartite anti-neurodegenerative activities including the inhibition of apoptosis and the targeting of mRNAs implicated in the etiology of HD.", "These results motivate additional studies to evaluate the feasibility and therapeutic efficacy of manipulating miR-22 in vivo."], "structured": true}
{"doc_id": 16625620, "title": "Research in cardiovascular care: a position statement of the Council on Cardiovascular Nursing and Allied Professionals of the European Society of Cardiology.", "abstract": ["To deliver optimal patient care, evidence-based care is advocated and research is needed to support health care staff of all disciplines in deciding which options to use in their daily practice.", "Due to the increasing complexity of cardiac care across the life span of patients combined with the increasing opportunities and challenges in multidisciplinary research, the Science Committee of the Council on Cardiovascular Nursing and Allied Professionals (CCNAP) recognised the need for a position statement to guide researchers, policymakers and funding bodies to contribute to the advancement of the body of knowledge that is needed to further improve cardiovascular care.", "In this paper, knowledge gaps in current research related to cardiovascular patient care are identified, upcoming challenges are explored and recommendations for future research are given."], "structured": false}
{"doc_id": 16626264, "title": "Genome-Wide Dynamics of Htz1, a Histone H2A Variant that Poises Repressed/Basal Promoters for Activation through Histone Loss", "abstract": ["Histone variants help specialize chromatin regions; however, their impact on transcriptional regulation is largely unknown.", "Here, we determined the genome-wide localization and dynamics of Htz1, the yeast histone H2A variant.", "Htz1 localizes to hundreds of repressed/basal Pol II promoters and prefers TATA-less promoters.", "Specific Htz1 deposition requires the SWR1 complex, which largely colocalizes with Htz1.", "Htz1 occupancy correlates with particular histone modifications, and Htz1 deposition is partially reliant on Gcn5 (a histone acetyltransferase) and Bdf1, an SWR1 complex member that binds acetylated histones.", "Changes in growth conditions cause a striking redistribution of Htz1 from activated to repressed/basal promoters.", "Furthermore, Htz1 promotes full gene activation but does not generally impact repression.", "Importantly, Htz1 releases from purified chromatin in vitro under conditions where H2A and H3 remain associated.", "We suggest that Htz1-bearing nucleosomes are deposited at repressed/basal promoters but facilitate activation through their susceptibility to loss, thereby helping to expose promoter DNA."], "structured": false}
{"doc_id": 16626846, "title": "Metagenomic analysis of microbial consortium from natural crude oil that seeps into the marine ecosystem offshore Southern California", "abstract": ["Crude oils can be major contaminants of the marine ecosystem and microorganisms play a significant role in the degradation of its main constituents.", "To increase our understanding of the microbial hydrocarbon degradation process in the marine ecosystem, we collected crude oil from an active seep area located in the Santa Barbara Channel (SBC) and generated a total of about 52 Gb of raw metagenomic sequence data.", "The assembled data comprised ~500 Mb, representing ~1.1 million genes derived primarily from chemolithoautotrophic bacteria.", "Members of Oceanospirillales, a bacterial order belonging to the Deltaproteobacteria, recruited less than 2% of the assembled genes within the SBC metagenome.", "In contrast, the microbial community associated with the oil plume that developed in the aftermath of the Deepwater Horizon (DWH) blowout in 2010, was dominated by Oceanospirillales, which comprised more than 60% of the metagenomic data generated from the DWH oil plume.", "This suggests that Oceanospirillales might play a less significant role in the microbially mediated hydrocarbon conversion within the SBC seep oil compared to the DWH plume oil.", "We hypothesize that this difference results from the SBC oil seep being mostly anaerobic, while the DWH oil plume is aerobic.", "Within the Archaea, the phylum Euryarchaeota, recruited more than 95% of the assembled archaeal sequences from the SBC oil seep metagenome, with more than 50% of the sequences assigned to members of the orders Methanomicrobiales and Methanosarcinales.", "These orders contain organisms capable of anaerobic methanogenesis and methane oxidation (AOM) and we hypothesize that these orders - and their metabolic capabilities - may be fundamental to the ecology of the SBC oil seep."], "structured": false}
{"doc_id": 16627684, "title": "Hmga2 Promotes Neural Stem Cell Self-Renewal in Young but Not Old Mice by Reducing p16Ink4a and p19Arf Expression", "abstract": ["Stem cells persist throughout life in diverse tissues by undergoing self-renewing divisions.", "Self-renewal capacity declines with age, partly because of increasing expression of the tumor suppressor p16(Ink4a).", "We discovered that the Hmga2 transcriptional regulator is highly expressed in fetal neural stem cells but that expression declines with age.", "This decrease is partly caused by the increasing expression of let-7b microRNA, which is known to target HMGA2.", "Hmga2-deficient mice show reduced stem cell numbers and self-renewal throughout the central and peripheral nervous systems of fetal and young-adult mice but not old-adult mice.", "Furthermore, p16(Ink4a) and p19(Arf) expression were increased in Hmga2-deficient fetal and young-adult stem cells, and deletion of p16(Ink4a) and/or p19(Arf) partially restored self-renewal capacity.", "let-7b overexpression reduced Hmga2 and increased p16(Ink4a)/p19(Arf) expression.", "Hmga2 thus promotes fetal and young-adult stem cell self-renewal by decreasing p16(Ink4a)/p19(Arf) expression.", "Changes in let-7 and Hmga2 expression during aging contribute to the decline in neural stem cell function."], "structured": false}
{"doc_id": 16630060, "title": "Genotoxic Stress Abrogates Renewal of Melanocyte Stem Cells by Triggering Their Differentiation", "abstract": ["Somatic stem cell depletion due to the accumulation of DNA damage has been implicated in the appearance of aging-related phenotypes.", "Hair graying, a typical sign of aging in mammals, is caused by the incomplete maintenance of melanocyte stem cells (MSCs) with age.", "Here, we report that irreparable DNA damage, as caused by ionizing radiation, abrogates renewal of MSCs in mice.", "Surprisingly, the DNA-damage response triggers MSC differentiation into mature melanocytes in the niche, rather than inducing their apoptosis or senescence.", "The resulting MSC depletion leads to irreversible hair graying.", "Furthermore, deficiency of Ataxia-telangiectasia mutated (ATM), a central transducer kinase of the DNA-damage response, sensitizes MSCs to ectopic differentiation, demonstrating that the kinase protects MSCs from their premature differentiation by functioning as a \"stemness checkpoint\" to maintain the stem cell quality and quantity."], "structured": false}
{"doc_id": 16630996, "title": "Gemcitabine chemoresistance and molecular markers associated with gemcitabine transport and metabolism in human pancreatic cancer cells", "abstract": ["To identify predictive molecular markers for gemcitabine resistance, we investigated changes in the expression of four genes associated with gemcitabine transport and metabolism during the development of acquired gemcitabine resistance of pancreatic cancer cell lines.", "The expression levels of human equilibrative nucleoside transporter-1 (hENT1), deoxycytidine kinase (dCK), RRM1, and RRM2 mRNA were analysed by real-time light cycler-PCR in various subclones during the development of acquired resistance to gemcitabine.", "Real-time light cycler-PCR demonstrated that the expression levels of either RRM1 or RRM2 progressively increased during the development of gemcitabine resistance.", "Expression of dCK was slightly increased in cells resistant to lower concentrations of gemcitabine, but was decreased below the undetectable level in higher concentration-resistant subclones.", "Expression of hENT1 was increased in the development of gemcitabine resistance.", "As acquired resistance to gemcitabine seems to correlate with the balance of these four factors, we calculated the ratio of hENT1 \u00d7 dCK/RRM1 \u00d7 RRM2 gene expression in gemcitabine-resistant subclones.", "The ratio of gene expression decreased progressively with development of acquired resistance in gemcitabine-resistant subclones.", "Furthermore, the expression ratio significantly correlated with gemcitabine sensitivity in eight pancreatic cancer cell lines, whereas no single gene expression level correlated with the sensitivity.", "These results suggest that the sensitivity of pancreatic cancer cells to gemcitabine is determined by the ratio of four factors involved in gemcitabine transport and metabolism.", "The ratio of the four gene expression levels correlates with acquired gemcitabine-resistance in pancreatic cancer cells, and may be useful as a predictive marker for the efficacy of gemcitabine therapy in pancreatic cancer patients."], "structured": false}
{"doc_id": 16644043, "title": "The DNA Damage Machinery and Homologous Recombination Pathway Act Consecutively to Protect Human Telomeres", "abstract": ["Telomeres protect chromosome ends from being detected as lesions and from triggering DNA damage checkpoints.", "Paradoxically, telomere function depends on checkpoint proteins such as ATM and ATR, but a molecular model explaining this seemingly contradictory relationship has been missing so far.", "Here we show that the DNA damage machinery acts on telomeres in at least two independent steps.", "First, the ATR-dependent machinery is recruited to telomeres before telomere replication is completed, likely in response to single-stranded DNA resulting from replication fork stalling.", "Second, after replication, telomeres attract ATM and the homologous recombination (HR) machinery.", "In vivo and in vitro results suggest that the HR machinery is required for formation of a telomere-specific structure at chromosome ends after replication.", "Our results suggest that telomere ends need to be recognized as DNA damage to complete end replication and to acquire a structure that is essential for function."], "structured": false}
{"doc_id": 16660256, "title": "Sprouty1 Regulates Reversible Quiescence of a Self-Renewing Adult Muscle Stem Cell Pool during Regeneration", "abstract": ["Satellite cells are skeletal muscle stem cells capable of self-renewal and differentiation after transplantation, but whether they contribute to endogenous muscle fiber repair has been unclear.", "The transcription factor Pax7 marks satellite cells and is critical for establishing the adult satellite cell pool.", "By using a lineage tracing approach, we show that after injury, quiescent adult Pax7(+) cells enter the cell cycle; a subpopulation returns to quiescence to replenish the satellite cell compartment, while others contribute to muscle fiber formation.", "We demonstrate that Sprouty1 (Spry1), a receptor tyrosine kinase signaling inhibitor, is expressed in quiescent Pax7(+) satellite cells in uninjured muscle, downregulated in proliferating myogenic cells after injury, and reinduced as Pax7(+) cells re-enter quiescence.", "We show that Spry1 is required for the return to quiescence and homeostasis of the satellite cell pool during repair.", "Our results therefore define a role for Spry1 in adult muscle stem cell biology and tissue repair."], "structured": false}
{"doc_id": 16669757, "title": "Mechanosensitivity in the enteric nervous system", "abstract": ["The enteric nervous system (ENS) autonomously controls gut muscle activity.", "Mechanosensitive enteric neurons (MEN) initiate reflex activity by responding to mechanical deformation of the gastrointestinal wall.", "MEN throughout the gut primarily respond to compression or stretch rather than to shear force.", "Some MEN are multimodal as they respond to compression and stretch.", "Depending on the region up to 60% of the entire ENS population responds to mechanical stress.", "MEN fire action potentials after mechanical stimulation of processes or soma although they are more sensitive to process deformation.", "There are at least two populations of MEN based on their sensitivity to different modalities of mechanical stress and on their firing pattern.", "(1) Rapidly, slowly and ultra-slowly adapting neurons which encode compressive forces.", "(2) Ultra-slowly adapting stretch-sensitive neurons encoding tensile forces.", "Rapid adaptation of firing is typically observed after compressive force while slow adaptation or ongoing spike discharge occurs often during tensile stress (stretch).", "All MEN have some common properties: they receive synaptic input, are low fidelity mechanoreceptors and are multifunctional in that some serve interneuronal others even motor functions.", "Consequently, MEN possess processes with mechanosensitive as well as efferent functions.", "This raises the intriguing hypothesis that MEN sense and control muscle activity at the same time as servo-feedback loop.", "The mechanosensitive channel(s) or receptor(s) expressed by the different MEN populations are unknown.", "Future concepts have to incorporate compressive and tensile-sensitive MEN into neural circuits that controls muscle activity.", "They may interact to control various forms of a particular motor pattern or regulate different motor patterns independently from each other."], "structured": false}
{"doc_id": 16686383, "title": "Phosphorylation of centromeric histone H3 variant regulates chromosome segregation in Saccharomyces cerevisiae", "abstract": ["The centromeric histone H3 variant (CenH3) is essential for chromosome segregation in eukaryotes.", "We identify posttranslational modifications of Saccharomyces cerevisiae CenH3, Cse4.", "Functional characterization of cse4 phosphorylation mutants shows growth and chromosome segregation defects when combined with kinetochore mutants okp1 and ame1.", "Using a phosphoserine-specific antibody, we show that the association of phosphorylated Cse4 with centromeres increases in response to defective microtubule attachment or reduced cohesion.", "We determine that evolutionarily conserved Ipl1/Aurora B contributes to phosphorylation of Cse4, as levels of phosphorylated Cse4 are reduced at centromeres in ipl1 strains in vivo, and in vitro assays show phosphorylation of Cse4 by Ipl1.", "Consistent with these results, we observe that a phosphomimetic cse4-4SD mutant suppresses the temperature-sensitive growth of ipl1-2 and Ipl1 substrate mutants dam1 spc34 and ndc80, which are defective for chromosome biorientation.", "Furthermore, cell biology approaches using a green fluorescent protein-labeled chromosome show that cse4-4SD suppresses chromosome segregation defects in dam1 spc34 strains.", "On the basis of these results, we propose that phosphorylation of Cse4 destabilizes defective kinetochores to promote biorientation and ensure faithful chromosome segregation.", "Taken together, our results provide a detailed analysis, in vivo and in vitro, of Cse4 phosphorylation and its role in promoting faithful chromosome segregation."], "structured": false}
{"doc_id": 16691520, "title": "Genome-wide analysis of estrogen receptor binding sites", "abstract": ["The estrogen receptor is the master transcriptional regulator of breast cancer phenotype and the archetype of a molecular therapeutic target.", "We mapped all estrogen receptor and RNA polymerase II binding sites on a genome-wide scale, identifying the authentic cis binding sites and target genes, in breast cancer cells.", "Combining this unique resource with gene expression data demonstrates distinct temporal mechanisms of estrogen-mediated gene regulation, particularly in the case of estrogen-suppressed genes.", "Furthermore, this resource has allowed the identification of cis-regulatory sites in previously unexplored regions of the genome and the cooperating transcription factors underlying estrogen signaling in breast cancer."], "structured": false}
{"doc_id": 16693950, "title": "Replicative aging in yeast: the means to the end.", "abstract": ["Progress in aging research is now rapid, and surprisingly, studies in a single-celled eukaryote are a driving force.", "The genetic modulators of replicative life span in yeast are being identified, the molecular events that accompany aging are being discovered, and the extent to which longevity pathways are conserved between yeast and multicellular eukaryotes is being tested.", "In this review, we provide a brief retrospective view on the development of yeast as a model for aging and then turn to recent discoveries that have pushed aging research into novel directions and also linked aging in yeast to well-developed hypotheses in mammals.", "Although the question of what causes aging still cannot be answered definitively, that day may be rapidly approaching."], "structured": false}
{"doc_id": 16701509, "title": "Serum high-density lipoprotein cholesterol, metabolic profile, and breast cancer risk.", "abstract": ["BACKGROUND The prevalence of metabolic syndrome (obesity, glucose intolerance, low serum high-density lipoprotein cholesterol [HDL-C], high serum triglycerides, hypertension) is high and increasing in parallel with an increasing breast cancer incidence worldwide.", "HDL-C represents an important aspect of the syndrome, yet its role in breast cancer is still undefined.   \n", "METHODS In two population-based screening surveys during 1977-1983 and 1985-1987, serum HDL-C was assayed enzymatically among 38,823 Norwegian women aged 17-54 years at entry.", "Height, weight, blood pressure, serum lipids, fat and energy intake, physical activity, parity, oral contraceptive use, hormone therapy use, alcohol intake, and tobacco use were also assessed.", "We used Cox proportional hazards modeling to estimate the relative risk (RR) of breast cancer associated with serum HDL-C levels and to adjust for potential confounding variables.", "We performed stratified analyses to evaluate effect modification by body mass index (BMI) and menopausal status.", "All statistical tests were two-sided.   \n", "RESULTS During a median follow-up of 17.2 years, we identified 708 cases of invasive breast cancer.", "In multivariable analysis, the risk of postmenopausal breast cancer was inversely related to quartile of HDL-C (P(trend) =.02).", "Among women with HDL-C above 1.64 mmol/L (highest quartile) versus below 1.20 mmol/L (lowest quartile), the relative risk was 0.75 (95% confidence interval [CI] = 0.58 to 0.97).", "The HDL-C association was confined to women in the heavier subgroup (BMI > or =25 kg/m2), for whom the relative risk of postmenopausal breast cancer in those with HDL-C above 1.64 mmol/L versus below 1.20 mmol/L was 0.43 (95% CI = 0.28 to 0.67; P(trend)<.001; P(interaction) =.001).   \n", "CONCLUSION Low HDL-C, as part of the metabolic syndrome, is associated with increased postmenopausal breast cancer risk."], "structured": true}
{"doc_id": 16705338, "title": "Prediction of Chemical-Protein Interactions Network with Weighted Network-Based Inference Method", "abstract": ["Chemical-protein interaction (CPI) is the central topic of target identification and drug discovery.", "However, large scale determination of CPI is a big challenge for in vitro or in vivo experiments, while in silico prediction shows great advantages due to low cost and high accuracy.", "On the basis of our previous drug-target interaction prediction via network-based inference (NBI) method, we further developed node- and edge-weighted NBI methods for CPI prediction here.", "Two comprehensive CPI bipartite networks extracted from ChEMBL database were used to evaluate the methods, one containing 17,111 CPI pairs between 4,741 compounds and 97 G protein-coupled receptors, the other including 13,648 CPI pairs between 2,827 compounds and 206 kinases.", "The range of the area under receiver operating characteristic curves was 0.73 to 0.83 for the external validation sets, which confirmed the reliability of the prediction.", "The weak-interaction hypothesis in CPI network was identified by the edge-weighted NBI method.", "Moreover, to validate the methods, several candidate targets were predicted for five approved drugs, namely imatinib, dasatinib, sertindole, olanzapine and ziprasidone.", "The molecular hypotheses and experimental evidence for these predictions were further provided.", "These results confirmed that our methods have potential values in understanding molecular basis of drug polypharmacology and would be helpful for drug repositioning."], "structured": false}
{"doc_id": 16712164, "title": "Exploiting the yeast stress-activated signaling network to inform on stress biology and disease signaling", "abstract": ["Healthy cells utilize intricate systems to monitor their environment and mount robust responses in the event of cellular stress.", "Whether stress arises from external insults or defects due to mutation and disease, cells must be able to respond precisely to mount the appropriate defenses.", "Multi-faceted stress responses are generally coupled with arrest of growth and cell-cycle progression, which both limits the transmission of damaged materials and serves to reallocate limited cellular resources toward defense.", "Therefore, stress defense versus rapid growth represent competing interests in the cell.", "How eukaryotic cells set the balance between defense versus proliferation, and in particular knowledge of the regulatory networks that control this decision, are poorly understood.", "In this perspective, we expand upon our recent work inferring the stress-activated signaling network in budding yeast, which captures pathways controlling stress defense and regulators of growth and cell-cycle progression.", "We highlight similarities between the yeast and mammalian stress responses and explore how stress-activated signaling networks in yeast can inform on signaling defects in human cancers."], "structured": false}
{"doc_id": 16728949, "title": "Cell Stem Cell Review FoxO Transcription Factors and Stem Cell Homeostasis: Insights from the Hematopoietic System", "abstract": ["The forkhead O (FoxO) family of transcription factors participates in diverse physiologic processes, including induction of cell-cycle arrest, stress resistance, differentiation, apoptosis, and metabolism.", "Several recent studies indicate that FoxO-dependent signaling is required for long-term regenerative potential of the hematopoietic stem cell (HSC) compartment through regulation of HSC response to physiologic oxidative stress, quiescence, and survival.", "These observations link FoxO function in mammalian systems with the evolutionarily conserved role of FoxO in promotion of stress resistance and longevity in lower phylogenetic systems.", "Furthermore, these findings have implications for aging in higher organisms and in malignant stem cell biology, and suggest that FoxOs may play an important role in the maintenance and integrity of stem cell compartments in a broad spectrum of tissues."], "structured": false}
{"doc_id": 16732790, "title": "A Teratocarcinoma-Like Human Embryonic Stem Cell (hESC) Line and Four hESC Lines Reveal Potentially Oncogenic Genomic Changes", "abstract": ["The first Swiss human embryonic stem cell (hESC) line, CH-ES1, has shown features of a malignant cell line.", "It originated from the only single blastomere that survived cryopreservation of an embryo, and it more closely resembles teratocarcinoma lines than other hESC lines with respect to its abnormal karyotype and its formation of invasive tumors when injected into SCID mice.", "The aim of this study was to characterize the molecular basis of the oncogenicity of CH-ES1 cells, we looked for abnormal chromosomal copy number (by array Comparative Genomic Hybridization, aCGH) and single nucleotide polymorphisms (SNPs).", "To see how unique these changes were, we compared these results to data collected from the 2102Ep teratocarcinoma line and four hESC lines (H1, HS293, HS401 and SIVF-02) which displayed normal G-banding result.", "We identified genomic gains and losses in CH-ES1, including gains in areas containing several oncogenes.", "These features are similar to those observed in teratocarcinomas, and this explains the high malignancy.", "The CH-ES1 line was trisomic for chromosomes 1, 9, 12, 17, 19, 20 and X. Also the karyotypically (based on G-banding) normal hESC lines were also found to have several genomic changes that involved genes with known roles in cancer.", "The largest changes were found in the H1 line at passage number 56, when large 5 Mb duplications in chromosomes 1q32.2 and 22q12.2 were detected, but the losses and gains were seen already at passage 22.", "These changes found in the other lines highlight the importance of assessing the acquisition of genetic changes by hESCs before their use in regenerative medicine applications.", "They also point to the possibility that the acquisition of genetic changes by ESCs in culture may be used to explore certain aspects of the mechanisms regulating oncogenesis."], "structured": false}
{"doc_id": 16734530, "title": "The Association between Single-Nucleotide Polymorphisms of ORAI1 Gene and Breast Cancer in a Taiwanese Population", "abstract": ["BACKGROUND Breast cancer is the most common malignancy in women.", "There is increasing evidence suggesting that ORAI1, components of store-operated calcium channel, play a pivotal role in breast cancer progression and metastasis.   \n", "METHODS A total of 384 female patients with breast cancer were included in this study.", "We selected five representative tagging ORAI1 SNPs from HapMap database with minimum allele frequency (MAF) >10%.", "Genotyping was performed using TaqMan allelic discrimination assay.", "Chi-square (\u03c7\u00b2) test was used to analyze statistical differences among control and patient groups in genotype and allelic frequencies.   \n", "RESULTS Two of the ORAI1 SNPs (rs12320939 and rs12313273) were associated with estrogen receptors positive in breast cancer patients under the recessive model.", "When the Bonferroni correction was performed, the significance still existed.", "In addition, rs12320939 also associated with the lymph nodal involvement.   \n", "CONCLUSION We showed that genetic polymorphisms of ORAI1 associated strongly with lymph nodal involvement and estrogen receptors (ERs) positive breast cancer patients in a Taiwanese population."], "structured": true}
{"doc_id": 16736872, "title": "Noninvasive Imaging beyond the Diffraction Limit of 3D Dynamics in Thickly Fluorescent Specimens", "abstract": ["Optical imaging of the dynamics of living specimens involves tradeoffs between spatial resolution, temporal resolution, and phototoxicity, made more difficult in three dimensions.", "Here, however, we report that rapid three-dimensional (3D) dynamics can be studied beyond the diffraction limit in thick or densely fluorescent living specimens over many time points by combining ultrathin planar illumination produced by scanned Bessel beams with super-resolution structured illumination microscopy.", "We demonstrate in vivo karyotyping of chromosomes during mitosis and identify different dynamics for the actin cytoskeleton at the dorsal and ventral surfaces of fibroblasts.", "Compared to spinning disk confocal microscopy, we demonstrate substantially reduced photodamage when imaging rapid morphological changes in D. discoideum cells, as well as improved contrast and resolution at depth within developing C. elegans embryos.", "Bessel beam structured plane illumination thus promises new insights into complex biological phenomena that require 4D subcellular spatiotemporal detail in either a single or multicellular context."], "structured": false}
{"doc_id": 16736883, "title": "The Ndc80 Kinetochore Complex Forms Load-Bearing Attachments to Dynamic Microtubule Tips via Biased Diffusion", "abstract": ["Kinetochores couple chromosomes to the assembling and disassembling tips of microtubules, a dynamic behavior that is fundamental to mitosis in all eukaryotes but poorly understood.", "Genetic, biochemical, and structural studies implicate the Ndc80 complex as a direct point of contact between kinetochores and microtubules, but these approaches provide only a static view.", "Here, using techniques for manipulating and tracking individual molecules in vitro, we demonstrate that the Ndc80 complex is capable of forming the dynamic, load-bearing attachments to assembling and disassembling tips required for coupling in vivo.", "We also establish that Ndc80-based coupling likely occurs through a biased diffusion mechanism and that this activity is conserved from yeast to humans.", "Our findings demonstrate how an ensemble of Ndc80 complexes may provide the combination of plasticity and strength that allows kinetochores to maintain load-bearing tip attachments during both microtubule assembly and disassembly."], "structured": false}
{"doc_id": 16737163, "title": "Myelin oligodendrocyte glycoprotein antibodies are associated with a non-MS course in children", "abstract": ["OBJECTIVE To determine whether myelin oligodendrocyte glycoprotein antibodies (MOG-Abs) were predictive of a demyelination phenotype in children presenting with acquired demyelinating syndrome (ADS).   \n", "METHOD Sixty-five children with a first episode of ADS (12 acute disseminated encephalomyelitis, 24 optic neuritis, 18 transverse myelitis, 11 other clinically isolated syndrome) were identified from 2 national demyelination programs in the United Kingdom and France.", "Acute serum samples were tested for MOG-Abs by cell-based assay.", "Antibodies were used to predict diagnosis of multiple sclerosis (MS) at 1 year.   \n", "RESULTS Twenty-three of 65 (35%) children had MOG-Abs.", "Antibody-positive and antibody-negative patients were not clinically different at presentation, but identification of MOG-Abs predicted a non-MS course at 1-year follow-up: only 2/23 (9%) MOG-Ab-positive patients were diagnosed with MS compared to 16/42 (38%) MOG-Ab-negative patients (p = 0.019, Fisher exact test).", "Antibody positivity at outset was a useful predictor for a non-MS disease course, with a positive predictive value of 91% (95% confidence interval [CI] 72-99), negative predictive value of 38% (95% CI 24-54), positive likelihood ratio of 4.02 (CI 1.0-15.4), and odds ratio of 6.5 (CI 1.3-31.3).   \n", "CONCLUSIONS MOG-Abs are found at presentation in 35% of patients with childhood ADS, across a range of demyelinating disorders.", "Antibody positivity can be useful in predicting a non-MS disease course at onset."], "structured": true}
{"doc_id": 16737210, "title": "Kidney paired donation and optimizing the use of live donor organs.", "abstract": ["CONTEXT Blood type and crossmatch incompatibility will exclude at least one third of patients in need from receiving a live donor kidney transplant.", "Kidney paired donation (KPD) offers incompatible donor/recipient pairs the opportunity to match for compatible transplants.", "Despite its increasing popularity, very few transplants have resulted from KPD.   \n", "OBJECTIVE To determine the potential impact of improved matching schemes on the number and quality of transplants achievable with KPD.   \n", "DESIGN, SETTING, AND POPULATION We developed a model that simulates pools of incompatible donor/recipient pairs.", "We designed a mathematically verifiable optimized matching algorithm and compared it with the scheme currently used in some centers and regions.", "Simulated patients from the general community with characteristics drawn from distributions describing end-stage renal disease patients eligible for renal transplantation and their willing and eligible live donors.   \n", "MAIN OUTCOME MEASURES Number of kidneys matched, HLA mismatch of matched kidneys, and number of grafts surviving 5 years after transplantation.   \n", "RESULTS A national optimized matching algorithm would result in more transplants (47.7% vs 42.0%, P<.001), better HLA concordance (3.0 vs 4.5 mismatched antigens; P<.001), more grafts surviving at 5 years (34.9% vs 28.7%; P<.001), and a reduction in the number of pairs required to travel (2.9% vs 18.4%; P<.001) when compared with an extension of the currently used first-accept scheme to a national level.", "Furthermore, highly sensitized patients would benefit 6-fold from a national optimized scheme (2.3% vs 14.1% successfully matched; P<.001).", "Even if only 7% of patients awaiting kidney transplantation participated in an optimized national KPD program, the health care system could save as much as $750 million.   \n", "CONCLUSIONS The combination of a national KPD program and a mathematically optimized matching algorithm yields more matches with lower HLA disparity.", "Optimized matching affords patients the flexibility of customizing their matching priorities and the security of knowing that the greatest number of high-quality matches will be found and distributed equitably."], "structured": true}
{"doc_id": 16745747, "title": "Genetic Interaction between Mutations in c-Myb and the KIX Domains of CBP and p300 Affects Multiple Blood Cell Lineages and Influences Both Gene Activation and Repression", "abstract": ["Adult blood cell production or definitive hematopoiesis requires the transcription factor c-Myb.", "The closely related KAT3 histone acetyltransferases CBP (CREBBP) and p300 (EP300) bind c-Myb through their KIX domains and mice homozygous for a p300 KIX domain mutation exhibit multiple blood defects.", "Perplexingly, mice homozygous for the same KIX domain mutation in CBP have normal blood.", "Here we test the hypothesis that the CBP KIX domain contributes subordinately to hematopoiesis via a genetic interaction with c-Myb.", "We assessed hematopoiesis in mice bearing compound mutations of c-Myb and/or the KIX domains of CBP and p300, and measured the effect of KIX domain mutations on c-Myb-dependent gene expression.", "We found that in the context of a p300 KIX mutation, the CBP KIX domain mutation affects platelets, B cells, T cells, and red cells.", "Gene interaction (epistasis) analysis provides mechanistic evidence that blood defects in KIX mutant mice are consistent with reduced c-Myb and KIX interaction.", "Lastly, we demonstrated that the CBP and p300 KIX domains contribute to both c-Myb-dependent gene activation and repression.", "Together these results suggest that the KIX domains of CBP, and especially p300, are principal mediators of c-Myb-dependent gene activation and repression that is required for definitive hematopoiesis."], "structured": false}
{"doc_id": 16760369, "title": "Comparative determinants of 4-year cardiovascular event rates in stable outpatients at risk of or with atherothrombosis.", "abstract": ["CONTEXT Clinicians and trialists have difficulty with identifying which patients are highest risk for cardiovascular events.", "Prior ischemic events, polyvascular disease, and diabetes mellitus have all been identified as predictors of ischemic events, but their comparative contributions to future risk remain unclear.   \n", "OBJECTIVE To categorize the risk of cardiovascular events in stable outpatients with various initial manifestations of atherothrombosis using simple clinical descriptors.   \n", "DESIGN, SETTING, AND PATIENTS Outpatients with coronary artery disease, cerebrovascular disease, or peripheral arterial disease or with multiple risk factors for atherothrombosis were enrolled in the global Reduction of Atherothrombosis for Continued Health (REACH) Registry and were followed up for as long as 4 years.", "Patients from 3647 centers in 29 countries were enrolled between 2003 and 2004 and followed up until 2008.", "Final database lock was in April 2009.   \n", "MAIN OUTCOME MEASURES Rates of cardiovascular death, myocardial infarction, and stroke.   \n", "RESULTS A total of 45,227 patients with baseline data were included in this 4-year analysis.", "During the follow-up period, a total of 5481 patients experienced at least 1 event, including 2315 with cardiovascular death, 1228 with myocardial infarction, 1898 with stroke, and 40 with both a myocardial infarction and stroke on the same day.", "Among patients with atherothrombosis, those with a prior history of ischemic events at baseline (n = 21,890) had the highest rate of subsequent ischemic events (18.3%; 95% confidence interval [CI], 17.4%-19.1%); patients with stable coronary, cerebrovascular, or peripheral artery disease (n = 15,264) had a lower risk (12.2%; 95% CI, 11.4%-12.9%); and patients without established atherothrombosis but with risk factors only (n = 8073) had the lowest risk (9.1%; 95% CI, 8.3%-9.9%) (P < .001 for all comparisons).", "In addition, in multivariable modeling, the presence of diabetes (hazard ratio [HR], 1.44; 95% CI, 1.36-1.53; P < .001), an ischemic event in the previous year (HR, 1.71; 95% CI, 1.57-1.85; P < .001), and polyvascular disease (HR, 1.99; 95% CI, 1.78-2.24; P < .001) each were associated with a significantly higher risk of the primary end point.   \n", "CONCLUSION Clinical descriptors can assist clinicians in identifying high-risk patients within the broad range of risk for outpatients with atherothrombosis."], "structured": true}
{"doc_id": 16787954, "title": "The association between sterilizing activity and drug distribution into tuberculosis lesions", "abstract": ["Finding new treatment-shortening antibiotics to improve cure rates and curb the alarming emergence of drug resistance is the major objective of tuberculosis (TB) drug development.", "Using a matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging suite in a biosafety containment facility, we show that the key sterilizing drugs rifampicin and pyrazinamide efficiently penetrate the sites of TB infection in lung lesions.", "Rifampicin even accumulates in necrotic caseum, a critical lesion site where persisting tubercle bacilli reside.", "In contrast, moxifloxacin, which is active in vitro against a subpopulation of Mycobacterium tuberculosis that persists in specific niches under drug pressure and has achieved treatment shortening in mice, does not diffuse well in caseum, concordant with its failure to shorten therapy in recent clinical trials.", "We suggest that such differential spatial distribution and kinetics of accumulation in lesions may create temporal and spatial windows of monotherapy in specific niches, allowing the gradual development of multidrug-resistant TB.", "We propose an alternative working model to prioritize new antibiotic regimens based on quantitative and spatial distribution of TB drugs in the major lesion types found in human lungs.", "The finding that lesion penetration may contribute to treatment outcome has wide implications for TB."], "structured": false}
{"doc_id": 16790253, "title": "Notch signaling: cell fate control and signal integration in development.", "abstract": ["Notch signaling defines an evolutionarily ancient cell interaction mechanism, which plays a fundamental role in metazoan development.", "Signals exchanged between neighboring cells through the Notch receptor can amplify and consolidate molecular differences, which eventually dictate cell fates.", "Thus, Notch signals control how cells respond to intrinsic or extrinsic developmental cues that are necessary to unfold specific developmental programs.", "Notch activity affects the implementation of differentiation, proliferation, and apoptotic programs, providing a general developmental tool to influence organ formation and morphogenesis."], "structured": false}
{"doc_id": 16806763, "title": "A long non-coding RNA signature to improve prognosis prediction of colorectal cancer", "abstract": ["Increasing evidence suggests long non-coding RNAs (lncRNAs) are frequently aberrantly expressed in cancers, however, few related lncRNA signatures have been established for prediction of cancer prognosis.", "We aimed to develop a lncRNA signature to improve prognosis prediction of colorectal cancer (CRC).", "Using a lncRNA-mining approach, we performed lncRNA expression profiling in large CRC cohorts from Gene Expression Ominus (GEO), including GSE39582 test series(N=436), internal validation series (N=117); and two independent validation series GSE14333 (N=197) and GSE17536(N=145).", "We established a set of six lncRNAs that were significantly correlated with the disease free survival (DFS) in the test series.", "Based on this six-lncRNA signature, the test series patients could be classified into high-risk and low-risk subgroups with significantly different DFS (HR=2.670; P<0.0001).", "The prognostic value of this six-lncRNA signature was confirmed in the internal validation series and another two independent CRC sets.", "Gene set enrichment analysis (GSEA) analysis suggested that risk score positively correlated with several cancer metastasis related pathways.", "Functional experiments demonstrated three dysregulated lncRNAs, AK123657, BX648207 and BX649059 were required for efficient invasion and proliferation suppression in CRC cell lines.", "Our results might provide an efficient classification tool for clinical prognosis evaluation of CRC."], "structured": false}
{"doc_id": 16812091, "title": "Clinical use of bone densitometry: scientific review.", "abstract": ["CONTEXT Osteoporosis causes substantial morbidity and costs $13.8 billion annually in the United States.", "Measurement of bone mass by densitometry is a primary part of diagnosing osteoporosis and deciding a preventive treatment course.", "Bone mineral densitometry has become more widely available and commonly used in practice.   \n", "OBJECTIVE To review evidence about the value of various clinical applications of bone densitometry.   \n", "DATA SOURCES A MEDLINE search was performed to update previous meta-analyses of the relationship between various measurements of bone density and risk of vertebral and hip fracture.", "We used data from the prospective Study of Osteoporotic Fractures to estimate risk of fracture from bone density and age in postmenopausal women.   ", "STUDY SELECTION AND DATA EXTRACTION When available, meta-analyses and systematic reviews are emphasized in the review.   \n", "DATA SYNTHESIS Bone mineral density (BMD) predicts fracture and can be used in combination with age to estimate absolute risk of fractures in postmenopausal white women.", "Hip BMD predicts hip fracture more strongly than other measurements of BMD.", "There are insufficient data to translate BMD results into risk of fracture for men and nonwhite women.", "The benefits of treatments to prevent fractures depend on BMD: women with osteoporosis have a greater risk of fractures and greater benefit from treatments than women without osteoporosis.   \n", "CONCLUSIONS Guidelines based on systematic reviews and a cost-effectiveness analysis have suggested that it is worthwhile to measure BMD in white women older than 65 years and perhaps to use risk factors to select younger postmenopausal women for densitometry.", "Other potential clinical applications of BMD that have not yet been adequately studied include screening men or nonwhite women, monitoring BMD in patients receiving treatment, and using BMD to identify patients who should be evaluated for secondary causes of osteoporosis."], "structured": true}
{"doc_id": 16826810, "title": "Vascular Calcifying Progenitor Cells Possess Bidirectional Differentiation Potentials", "abstract": ["Vascular calcification is an advanced feature of atherosclerosis for which no effective therapy is available.", "To investigate the modulation or reversal of calcification, we identified calcifying progenitor cells and investigated their calcifying/decalcifying potentials.", "Cells from the aortas of mice were sorted into four groups using Sca-1 and PDGFR\u03b1 markers.", "Sca-1(+) (Sca-1(+)/PDGFR\u03b1(+) and Sca-1(+)/PDGFR\u03b1(-)) progenitor cells exhibited greater osteoblastic differentiation potentials than Sca-1(-) (Sca-1(-)/PDGFR\u03b1(+) and Sca-1(-)/PDGFR\u03b1(-)) progenitor cells.", "Among Sca-1(+) progenitor populations, Sca-1(+)/PDGFR\u03b1(-) cells possessed bidirectional differentiation potentials towards both osteoblastic and osteoclastic lineages, whereas Sca-1(+)/PDGFR\u03b1(+) cells differentiated into an osteoblastic lineage unidirectionally.", "When treated with a peroxisome proliferator activated receptor \u03b3 (PPAR\u03b3) agonist, Sca-1(+)/PDGFR\u03b1(-) cells preferentially differentiated into osteoclast-like cells.", "Sca-1(+) progenitor cells in the artery originated from the bone marrow (BM) and could be clonally expanded.", "Vessel-resident BM-derived Sca-1(+) calcifying progenitor cells displayed nonhematopoietic, mesenchymal characteristics.", "To evaluate the modulation of in vivo calcification, we established models of ectopic and atherosclerotic calcification.", "Computed tomography indicated that Sca-1(+) progenitor cells increased the volume and calcium scores of ectopic calcification.", "However, Sca-1(+)/PDGFR\u03b1(-) cells treated with a PPAR\u03b3 agonist decreased bone formation 2-fold compared with untreated cells.", "Systemic infusion of Sca-1(+)/PDGFR\u03b1(-) cells into Apoe(-/-) mice increased the severity of calcified atherosclerotic plaques.", "However, Sca-1(+)/PDGFR\u03b1(-) cells in which PPAR\u03b3 was activated displayed markedly decreased plaque severity.", "Immunofluorescent staining indicated that Sca-1(+)/PDGFR\u03b1(-) cells mainly expressed osteocalcin; however, activation of PPAR\u03b3 triggered receptor activator for nuclear factor-\u03baB (RANK) expression, indicating their bidirectional fate in vivo.", "These findings suggest that a subtype of BM-derived and vessel-resident progenitor cells offer a therapeutic target for the prevention of vascular calcification and that PPAR\u03b3 activation may be an option to reverse calcification."], "structured": false}
{"doc_id": 16839245, "title": "Physiological relevance of cell cycle kinases.", "abstract": ["The basic biology of the cell division cycle and its control by protein kinases was originally studied through genetic and biochemical studies in yeast and other model organisms.", "The major regulatory mechanisms identified in this pioneer work are conserved in mammals.", "However, recent studies in different cell types or genetic models are now providing a new perspective on the function of these major cell cycle regulators in different tissues.", "Here, we review the physiological relevance of mammalian cell cycle kinases such as cyclin-dependent kinases (Cdks), Aurora and Polo-like kinases, and mitotic checkpoint regulators (Bub1, BubR1, and Mps1) as well as other less-studied enzymes such as Cdc7, Nek proteins, or Mastl and their implications in development, tissue homeostasis, and human disease.", "Among these functions, the control of self-renewal or asymmetric cell division in stem/progenitor cells and the ability to regenerate injured tissues is a central issue in current research.", "In addition, many of these proteins play previously unexpected roles in metabolism, cardiovascular function, or neuron biology.", "The modulation of their enzymatic activity may therefore have multiple therapeutic benefits in human disease."], "structured": false}
{"doc_id": 16853734, "title": "Matrix Metalloproteinase 1 Is Necessary for the Migration of Human Bone Marrow-Derived Mesenchymal Stem Cells Toward Human Glioma", "abstract": ["Human mesenchymal stem cells (MSCs) have increasingly been used as cellular vectors for the delivery of therapeutic genes to tumors.", "However, the precise mechanism of mobilization remains poorly defined.", "In this study, MSCs that expressed similar cell surface markers and exhibited multilineage differentiation potentials were isolated from various donors.", "Interestingly, different MSC isolates displayed differential migration ability toward human glioma cells.", "We hypothesized that distinct molecular signals may be involved in the varied tumor tropisms exhibited by different MSC isolates.", "To test this hypothesis, gene expression profiles of tumor-trophic MSCs were compared with those of non-tumor-trophic MSCs.", "Among the various differentially regulated genes, matrix metalloproteinase one (MMP1) gene expression and its protein activities were enhanced by 27-fold and 21-fold, respectively, in highly migrating MSCs compared with poorly migrating MSCs.", "By contrast, there was no change in the transcriptional levels of other MMPs.", "Functional inactivation of MMP1 abrogated the migratory potential of MSCs toward glioma-conditioned medium.", "Conversely, the nonmigratory phenotype of poorly migrating MSC could be rescued in the presence of either recombinant MMP1 or conditioned medium from the highly migrating MSCs.", "Ectopic expression of MMP1 in these poorly migrating cells also rendered the cells responsive to the signaling cues from the glioma cells in vivo.", "However, blocking the interaction of MMP1 and its cognate receptor PAR1 effectively diminished the migratory ability of MSCs.", "Taken together, this study provides, for the first time, supporting evidence that MMP1 is critically involved in the migration capacity of MSCs, acting through the MMP1/PAR1 axis."], "structured": false}
{"doc_id": 16855829, "title": "Bullying in school: are short pupils at risk? Questionnaire study in a cohort.", "abstract": ["Bullying is still prevalent in schools and is clearly stressful for victims.", "1 2 It may also have undesirable consequences for bullies, with antisocial behaviour persisting into adulthood.", "Victims are generally reported to be weaker than the bullies.", "2 3 This would suggest that very short pupils are more likely to be victims and less likely to be the aggressors.", "The Wessex growth study allowed us to examine the prevalence of bullying, as experienced or perpetrated by pupils of different heights.  ", "Ninety two short normal adolescents who had been below the third centile for height at school entry4 and 117 controls matched for age and sex completed a bullying questionnaire, derived from work by Whitney and Smith.5 There were no refusals or any significant differences in sex or social class between the groups.", "Mean age (range) was 14.7 (13.4-15.7) years.", "Mean height SD scores were: short pupils \u22121.90 (\u22123.53 to \u22120.01), controls 0.31 (\u22121.41 \u2026"], "structured": false}
{"doc_id": 16863359, "title": "Inflammasome-induced IL-1\u03b2 secretion in microglia is characterized by delayed kinetics and is only partially dependent on inflammatory caspases.", "abstract": ["Inflammasomes are multiprotein complexes that link pathogen recognition and cellular stress to the processing of the proinflammatory cytokine interleukin-1\u03b2 (IL-1\u03b2).", "Whereas inflammasome-mediated activation is heavily studied in hematopoietic macrophages and dendritic cells, much less is known about microglia, resident tissue macrophages of the brain that originate from a distinct progenitor.", "To directly compare inflammasome-mediated activation in different types of macrophages, we isolated primary microglia and hematopoietic macrophages from adult, healthy rhesus macaques.", "We analyzed the expression profile of NOD (nucleotide-binding oligomerization domain)-like receptors, adaptor proteins, and caspases and characterized inflammasome activation and regulation in detail.", "We here demonstrate that primary microglia can respond to the same innate stimuli as hematopoietic macrophages.", "However, microglial responses are more persistent due to lack of negative regulation on pro-IL-1\u03b2 expression.", "In addition, we show that while caspase 1, 4, and 5 activation is pivotal for inflammasome-induced IL-1\u03b2 secretion by hematopoietic macrophages, microglial secretion of IL-1\u03b2 is only partially dependent on these inflammatory caspases.", "These results identify key cell type-specific differences that may aid the development of strategies to modulate innate immune responses in the brain."], "structured": false}
{"doc_id": 16882895, "title": "microRNA-29a suppresses cell proliferation by targeting SPARC in hepatocellular carcinoma.", "abstract": ["In the present study, we constructed a lentivirus vector encoding the miR-29a             precursor and established two stably infected cell lines, PLC-29a and 97L-29a.             ", "The overexpression of miR-29a was confirmed by TaqMan RT-PCR and significantly             suppressed the growth of the hepatocellular carcinoma cell lines MHCC-97L and             PLC.", "Dual-luciferase reporter assays indicated that the SPARC mRNA 3'UTR was directly             targeted by miR-29a since the mutated 3'UTR was not affected.", "Silencing SPARC             expression by RNAi knockdown resulted in a similar effect as miR-29a overexpression             on hepatocellular carcinoma (HCC) cell growth regulation.", "Anti-miR-29a oligonucleotides             (AMOs) upregulated the levels of SPARC in the HCC cells.", "The phosphorylation of             AKT/mTOR downstream of SPARC was inhibited in miR-29a-overexpressing HCC cells.             ", "We further examined and compared the expression levels of miR-29a in HCC tissues             and the corresponding nearby non-cancerous liver tissues of 110 patients with             HCC by qRT-PCR, and significantly lower expression of miR-29a was observed in             the tissues affected by HCC.", "Our findings demonstrate that the expression of miR-29a             is important in the regulation of the SPARC-AKT pathway and HCC growth."], "structured": false}
{"doc_id": 16905344, "title": "Another Barrier to Regeneration in the CNS: Activated Macrophages Induce Extensive Retraction of Dystrophic Axons through Direct Physical Interactions", "abstract": ["Injured axons of the adult CNS undergo lengthy retraction from the initial site of axotomy after spinal cord injury.", "Macrophage infiltration correlates spatiotemporally with this deleterious phenomenon, but the direct involvement of these inflammatory cells has not been demonstrated.", "In the present study, we examined the role of macrophages in axonal retraction within the dorsal columns after spinal cord injury in vivo and found that retraction occurred between days 2 and 28 after lesion and that the ends of injured axons were associated with ED-1+ cells.", "Clodronate liposome-mediated depletion of infiltrating macrophages resulted in a significant reduction in axonal retraction; however, we saw no evidence of regeneration.", "We used time-lapse imaging of adult dorsal root ganglion neurons in an in vitro model of the glial scar to examine macrophage-axon interactions and observed that adhesive contacts and considerable physical interplay between macrophages and dystrophic axons led to extensive axonal retraction.", "The induction of retraction was dependent on both the growth state of the axon and the activation state of the macrophage.", "Only dystrophic adult axons were susceptible to macrophage \"attack.", "\"", "Unlike intrinsically active cell line macrophages, both primary macrophages and microglia required activation to induce axonal retraction.", "Contact with astrocytes had no deleterious effect on adult dystrophic axons, suggesting that the induction of extensive retraction was specific to phagocytic cells.", "Our data are the first to indicate a direct role of activated macrophages in axonal retraction by physical cell-cell interactions with injured axons."], "structured": false}
{"doc_id": 16927286, "title": "Large-Scale Movements of IF3 and tRNA during Bacterial Translation Initiation", "abstract": ["In bacterial translational initiation, three initiation factors (IFs 1-3) enable the selection of initiator tRNA and the start codon in the P site of the 30S ribosomal subunit.", "Here, we report 11 single-particle cryo-electron microscopy (cryoEM) reconstructions of the complex of bacterial 30S subunit with initiator tRNA, mRNA, and IFs 1-3, representing different steps along the initiation pathway.", "IF1 provides key anchoring points for IF2 and IF3, thereby enhancing their activities.", "IF2 positions a domain in an extended conformation appropriate for capturing the formylmethionyl moiety charged on tRNA.", "IF3 and tRNA undergo large conformational changes to facilitate the accommodation of the formylmethionyl-tRNA (fMet-tRNA(fMet)) into the P site for start codon recognition."], "structured": false}
{"doc_id": 16929739, "title": "Corresponding Author:", "abstract": ["In higher eukaryotes, introns are spliced out of protein-coding mRNAs by the spliceosome, a massive complex comprising five non-coding RNAs (ncRNAs) and about 200 proteins.", "By comparing the differences between spliceosomal proteins from many basal eukaryotic lineages, it is possible to infer properties of the splicing system in the last common ancestor of extant eukaryotes, the eukaryotic ancestor.", "We begin with the hypothesis that, similar to intron length (that appears to have increased in multicellular eukaryotes), the spliceosome has increased in complexity throughout eukaryotic evolution.", "However, examination of the distribution of spliceosomal components indicates that not only was a spliceosome present in the eukaryotic ancestor but it also contained most of the key components found in today's eukaryotes.", "All the small nuclear ribonucleoproteins (snRNPs) protein components are likely to have been present, as well as many splicing-related proteins.", "Both major and trans-splicing are likely to have been present, and the spliceosome had already formed links with other cellular processes such as transcription and capping.", "However, there is no evidence as yet to suggest that minor (U12-dependent) splicing was present in the eukaryotic ancestor.", "Although the last common ancestor of extant eukaryotes appears to show much of the molecular complexity seen today, we do not, from this work, infer anything of the properties of the earlier \"first eukaryote.", "\""], "structured": false}
{"doc_id": 16939583, "title": "2D and 3D Stem Cell Models of Primate Cortical Development Identify Species-Specific Differences in Progenitor Behavior Contributing to Brain Size.", "abstract": ["Variation in cerebral cortex size and complexity is thought to contribute to differences in cognitive ability between humans and other animals.", "Here we compare cortical progenitor cell output in humans and three nonhuman primates using directed differentiation of pluripotent stem cells (PSCs) in adherent two-dimensional (2D) and organoid three-dimensional (3D) culture systems.", "Clonal lineage analysis showed that primate cortical progenitors proliferate for a protracted period of time, during which they generate early-born neurons, in contrast to rodents, where this expansion phase largely ceases before neurogenesis begins.", "The extent of this additional cortical progenitor expansion differs among primates, leading to differences in the number of neurons generated by each progenitor cell.", "We found that this mechanism for controlling cortical size is regulated cell autonomously in culture, suggesting that primate cerebral cortex size is regulated at least in part at the level of individual cortical progenitor cell clonal output."], "structured": false}
{"doc_id": 16962732, "title": "Multicolor \u201cDiOlistic\u201d Labeling of the Nervous System Using Lipophilic Dye Combinations", "abstract": ["We describe a technique for rapid labeling of a large number of cells in the nervous system with many different colors.", "By delivering lipophilic dye-coated particles to neuronal preparations with a \"gene gun,\" individual neurons and glia whose membranes are contacted by the particles are quickly labeled.", "Using particles that are each coated with different combinations of various lipophilic dyes, many cells within a complex neuronal network can be simultaneously labeled with a wide variety of colors.", "This approach is most effective in living material but also labels previously fixed material.", "In living material, labeled neurons continue to show normal synaptic responses and undergo dendritic remodeling.", "This technique is thus useful for studying structural plasticity of neuronal circuits in living preparations.", "In addition, the Golgi-like labeling of neurons with many different colors provides a novel way to study neuronal connectivity."], "structured": false}
{"doc_id": 16963081, "title": "A DNA test to sex most birds.", "abstract": ["Birds are difficult to sex.", "Nestlings rarely show sex-linked morphology and we estimate that adult females appear identical to males in over 50% of the world's bird species.", "This problem can hinder both evolutionary studies and human-assisted breeding of birds.", "DNA-based sex identification provides a solution.", "We describe a test based on two conserved CHD (chromo-helicase-DNA-binding) genes that are located on the avian sex chromosomes of all birds, with the possible exception of the ratites (ostriches, etc.; Struthioniformes).", "The CHD-W gene is located on the W chromosome; therefore it is unique to females.", "The other gene, CHD-Z, is found on the Z chromosome and therefore occurs in both sexes (female, ZW; male, ZZ).", "The test employs PCR with a single set of primers.", "It amplifies homologous sections of both genes and incorporates introns whose lengths usually differ.", "When examined on a gel there is a single CHD-Z band in males but females have a second, distinctive CHD-W band."], "structured": false}
{"doc_id": 16964262, "title": "Evidence that Embryonic Neurons Regulate the Onset of Cortical Gliogenesis via Cardiotrophin-1", "abstract": ["Precursor cells of the embryonic cortex sequentially generate neurons and then glial cells, but the mechanisms regulating this neurogenic-to-gliogenic transition are unclear.", "Using cortical precursor cultures, which temporally mimic this in vivo differentiation pattern, we demonstrate that cortical neurons synthesize and secrete the neurotrophic cytokine cardiotrophin-1, which activates the gp130-JAK-STAT pathway and is essential for the timed genesis of astrocytes in vitro.", "Our data indicate that a similar phenomenon also occurs in vivo.", "In utero electroporation of neurotrophic cytokines in the environment of embryonic cortical precursors causes premature gliogenesis, while acute perturbation of gp130 in cortical precursors delays the normal timed appearance of astrocytes.", "Moreover, the neonatal cardiotrophin-1-/- cortex contains fewer astrocytes.", "Together, these results describe a neural feedback mechanism; newly born neurons produce cardiotrophin-1, which instructs multipotent cortical precursors to generate astrocytes, thereby ensuring that gliogenesis does not occur until neurogenesis is largely complete."], "structured": false}
{"doc_id": 16966326, "title": "The Inhibition of TDP-43 Mitochondrial Localization Blocks Its Neuronal Toxicity", "abstract": ["Genetic mutations in TAR DNA-binding protein 43 (TARDBP, also known as TDP-43) cause amyotrophic lateral sclerosis (ALS), and an increase in the presence of TDP-43 (encoded by TARDBP) in the cytoplasm is a prominent histopathological feature of degenerating neurons in various neurodegenerative diseases.", "However, the molecular mechanisms by which TDP-43 contributes to ALS pathophysiology remain elusive.", "Here we have found that TDP-43 accumulates in the mitochondria of neurons in subjects with ALS or frontotemporal dementia (FTD).", "Disease-associated mutations increase TDP-43 mitochondrial localization.", "In mitochondria, wild-type (WT) and mutant TDP-43 preferentially bind mitochondria-transcribed messenger RNAs (mRNAs) encoding respiratory complex I subunits ND3 and ND6, impair their expression and specifically cause complex I disassembly.", "The suppression of TDP-43 mitochondrial localization abolishes WT and mutant TDP-43-induced mitochondrial dysfunction and neuronal loss, and improves phenotypes of transgenic mutant TDP-43 mice.", "Thus, our studies link TDP-43 toxicity directly to mitochondrial bioenergetics and propose the targeting of TDP-43 mitochondrial localization as a promising therapeutic approach for neurodegeneration."], "structured": false}
{"doc_id": 16979690, "title": "Effect on the quality of peer review of blinding reviewers and asking them to sign their reports: a randomized controlled trial.", "abstract": ["CONTEXT Anxiety about bias, lack of accountability, and poor quality of peer review has led to questions about the imbalance in anonymity between reviewers and authors.   \n", "OBJECTIVE To evaluate the effect on the quality of peer review of blinding reviewers to the authors' identities and requiring reviewers to sign their reports.   \n", "DESIGN Randomized controlled trial.   \n", "SETTING A general medical journal.   \n", "PARTICIPANTS A total of 420 reviewers from the journal's database.   \n", "INTERVENTION We modified a paper accepted for publication introducing 8 areas of weakness.", "Reviewers were randomly allocated to 5 groups.", "Groups 1 and 2 received manuscripts from which the authors' names and affiliations had been removed, while groups 3 and 4 were aware of the authors' identities.", "Groups 1 and 3 were asked to sign their reports, while groups 2 and 4 were asked to return their reports unsigned.", "The fifth group was sent the paper in the usual manner of the journal, with authors' identities revealed and a request to comment anonymously.", "Group 5 differed from group 4 only in that its members were unaware that they were taking part in a study.   \n", "MAIN OUTCOME MEASURE The number of weaknesses in the paper that were commented on by the reviewers.   \n", "RESULTS Reports were received from 221 reviewers (53%).", "The mean number of weaknesses commented on was 2 (1.7, 2.1, 1.8, and 1.9 for groups 1, 2, 3, and 4 and 5 combined, respectively).", "There were no statistically significant differences between groups in their performance.", "Reviewers who were blinded to authors' dentities were less likely to recommend rejection than those who were aware of the authors' identities (odds ratio, 0.5; 95% confidence interval, 0.3-1.0).   \n", "CONCLUSIONS Neither blinding reviewers to the authors and origin of the paper nor requiring them to sign their reports had any effect on rate of detection of errors.", "Such measures are unlikely to improve the quality of peer review reports."], "structured": true}
{"doc_id": 16980892, "title": "2001. Comparison of three management strategies for patients with atypical squamous cells of undetermined significance. Baseline results from a randomized trial", "abstract": ["BACKGROUND More than 2 million U.S. women receive an equivocal cervical cytologic diagnosis (atypical squamous cells of undetermined significance [ASCUS]) each year.", "Effective colposcopy triage strategies are needed to identify the minority of women who have clinically significant disease while avoiding excessive follow-up evaluation for others.   \n", "METHODS The ASCUS/LSIL (i.e., low-grade squamous intraepithelial lesion) Triage Study (ALTS) is a multicenter, randomized trial comparing the sensitivity and specificity of the following three management strategies to detect cervical intraepithelial neoplasia grade 3 (CIN3): 1) immediate colposcopy (considered to be the reference standard), 2) triage to colposcopy based on human papillomavirus (HPV) results from Hybrid Capture 2(TM) (HC 2) and thin-layer cytology results, or 3) triage based on cytology results alone.", "This article summarizes the cross-sectional enrollment results for 3488 women with a referral diagnosis of ASCUS.", "All statistical tests are two-sided.   \n", "RESULTS Among participants with ASCUS, the underlying prevalence of histologically confirmed CIN3 was 5.1%.", "Sensitivity to detect CIN3 or above by testing for cancer-associated HPV DNA was 96.3% (95% confidence interval [CI] = 91.6% to 98.8%), with 56.1% of women referred to colposcopy.", "Sensitivity of a single repeat cytology specimen with a triage threshold of HSIL or above was 44.1% (95% CI = 35.6% to 52.9%), with 6.9% referred.", "Sensitivity of a lower cytology triage threshold of ASCUS or above was 85.3% (95% CI = 78.2% to 90.8%), with 58.6% referred.   \n", "CONCLUSIONS HC 2 testing for cancer-associated HPV DNA is a viable option in the management of women with ASCUS.", "It has greater sensitivity to detect CIN3 or above and specificity comparable to a single additional cytologic test indicating ASCUS or above."], "structured": true}
{"doc_id": 16999023, "title": "Cell Stem Cell Article In Vivo Fate Analysis Reveals the Multipotent and Self-Renewal Capacities of Sox2 + Neural Stem Cells in the Adult Hippocampus", "abstract": ["To characterize the properties of adult neural stem cells (NSCs), we generated and analyzed Sox2-GFP transgenic mice.", "Sox2-GFP cells in the subgranular zone (SGZ) express markers specific for progenitors, but they represent two morphologically distinct populations that differ in proliferation levels.", "Lentivirus- and retrovirus-mediated fate-tracing studies showed that Sox2+ cells in the SGZ have potential to give rise to neurons and astrocytes, revealing their multipotency at the population as well as at a single-cell level.", "A subpopulation of Sox2+ cells gives rise to cells that retain Sox2, highlighting Sox2+ cells as a primary source for adult NSCs.", "In response to mitotic signals, increased proliferation of Sox2+ cells is coupled with the generation of Sox2+ NSCs as well as neuronal precursors.", "An asymmetric contribution of Sox2+ NSCs may play an important role in maintaining the constant size of the NSC pool and producing newly born neurons during adult neurogenesis."], "structured": false}
{"doc_id": 17000834, "title": "Past exposure to sun, skin phenotype, and risk of multiple sclerosis: case-control study.", "abstract": ["OBJECTIVE To examine whether past high sun exposure is associated with a reduced risk of multiple sclerosis.   \n", "DESIGN Population based case-control study.   \n", "SETTING Tasmania, latitudes 41-3 degrees S.   PARTICIPANTS 136 cases with multiple sclerosis and 272 controls randomly drawn from the community and matched on sex and year of birth.   \n", "MAIN OUTCOME MEASURE Multiple sclerosis defined by both clinical and magnetic resonance imaging criteria.   \n", "RESULTS Higher sun exposure when aged 6-15 years (average 2-3 hours or more a day in summer during weekends and holidays) was associated with a decreased risk of multiple sclerosis (adjusted odds ratio 0.31, 95% confidence interval 0.16 to 0.59).", "Higher exposure in winter seemed more important than higher exposure in summer.", "Greater actinic damage was also independently associated with a decreased risk of multiple sclerosis (0.32, 0.11 to 0.88 for grades 4-6 disease).", "A dose-response relation was observed between multiple sclerosis and decreasing sun exposure when aged 6-15 years and with actinic damage.   \n", "CONCLUSION Higher sun exposure during childhood and early adolescence is associated with a reduced risk of multiple sclerosis.", "Insufficient ultraviolet radiation may therefore influence the development of multiple sclerosis."], "structured": true}
{"doc_id": 17017465, "title": "Endocytic Trafficking of Rac Is Required for the Spatial Restriction of Signaling in Cell Migration", "abstract": ["The small GTPases, Rab5 and Rac, are essential for endocytosis and actin remodeling, respectively.", "Coordination of these processes is critical to achieve spatial restriction of intracellular signaling, which is essential for a variety of polarized functions.", "Here, we show that clathrin- and Rab5-mediated endocytosis are required for the activation of Rac induced by motogenic stimuli.", "Rac activation occurs on early endosomes, where the RacGEF Tiam1 is also recruited.", "Subsequent recycling of Rac to the plasma membrane ensures localized signaling, leading to the formation of actin-based migratory protrusions.", "Thus, membrane trafficking of Rac is required for the spatial resolution of Rac-dependent motogenic signals.", "We further demonstrate that a Rab5-to-Rac circuitry controls the morphology of motile mammalian tumor cells and primordial germinal cells during zebrafish development, suggesting that this circuitry is relevant for the regulation of migratory programs in various cells, in both in vitro settings and whole organisms."], "structured": false}
{"doc_id": 17021845, "title": "Significance of stem cell marker Nanog gene in the diagnosis and prognosis of lung cancer", "abstract": ["The aim of the present study was to analyze the stem cell marker, Nanog gene, for the diagnosis and prognosis of lung cancer cases, and to study its application in the diagnosis of lung cancer.", "In total, 100 patients diagnosed with lung cancer between April, 2013 and May, 2015 were included in the present study.", "The patients were randomly divided into group A (lung cancer) and group B (squamous cell lung carcinoma).", "RT-PCR was used to detect the cancer and adjacent tissues, and Nanog gene expression was detected in groups A and B in cells.", "The results showed that, analysis of Nanog gene expression in the two groups of patients varied to different degrees.", "There was no significant difference between the two groups with regard to age, gender, disease stage and lymph node metastasis.", "Nanog gene expression in patients with carcinoma were significantly higher than that in the adjacent tissues (p<0.05).", "By contrast, differentiated and well-differentiated carcinoma tissue showed a significantly higher Nanog gene expression than poorly differentiated and undifferentiated carcinoma (p<0.05).", "The expression of Nanog in normal cells was significantly higher than that in normal lung tissues and benign lesions in lung cancer stem cells.", "Nanog was highly expressed in CD44+ cells, and Nanog expression in lung cancer stem cells was significantly higher (p<0.05).", "In conclusion, for groups A (lung cancer) and B (squamous cell lung carcinoma) the Nanog gene expression was significantly higher.", "The data of the present study show that the patients with stage III and IV lung cancer had a higher Nanog gene expression.", "In addition, there was a higher expression of Nanog in lung cancer patients.", "By contrast, a lower degree of cell differentiation was associated with strong Nanog gene expression in lung cancer."], "structured": false}
{"doc_id": 17023584, "title": "Current knowledge and future directions of TLR and NOD signaling in sepsis", "abstract": ["The incidence of sepsis is increasing over time, along with an increased risk of dying from the condition.", "Sepsis care costs billions annually in the United States.", "Death from sepsis is understood to be a complex process, driven by a lack of normal immune homeostatic functions and excessive production of proinflammatory cytokines, which leads to multi-organ failure.", "The Toll-like receptor (TLR) family, one of whose members was initially discovered in Drosophila, performs an important role in the recognition of microbial pathogens.", "These pattern recognition receptors (PRRs), upon sensing invading microorganisms, activate intracellular signal transduction pathways.", "NOD signaling is also involved in the recognition of bacteria and acts synergistically with the TLR family in initiating an efficient immune response for the eradication of invading microbial pathogens.", "TLRs and NOD1/NOD2 respond to different pathogen-associated molecular patterns (PAMPs).", "Modulation of both TLR and NOD signaling is an area of research that has prompted much excitement and debate as a therapeutic strategy in the management of sepsis.", "Molecules targeting TLR and NOD signaling pathways exist but regrettably thus far none have proven efficacy from clinical trials."], "structured": false}
{"doc_id": 17049436, "title": "Concentration Sensing by the Moving Nucleus in Cell Fate Determination: A Computational Analysis", "abstract": ["During development of the vertebrate neuroepithelium, the nucleus in neural progenitor cells (NPCs) moves from the apex toward the base and returns to the apex (called interkinetic nuclear migration) at which point the cell divides.", "The fate of the resulting daughter cells is thought to depend on the sampling by the moving nucleus of a spatial concentration profile of the cytoplasmic Notch intracellular domain (NICD).", "However, the nucleus executes complex stochastic motions including random waiting and back and forth motions, which can expose the nucleus to randomly varying levels of cytoplasmic NICD.", "How nuclear position can determine daughter cell fate despite the stochastic nature of nuclear migration is not clear.", "Here we derived a mathematical model for reaction, diffusion, and nuclear accumulation of NICD in NPCs during interkinetic nuclear migration (INM).", "Using experimentally measured trajectory-dependent probabilities of nuclear turning, nuclear waiting times and average nuclear speeds in NPCs in the developing zebrafish retina, we performed stochastic simulations to compute the nuclear trajectory-dependent probabilities of NPC differentiation.", "Comparison with experimentally measured nuclear NICD concentrations and trajectory-dependent probabilities of differentiation allowed estimation of the NICD cytoplasmic gradient.", "Spatially polarized production of NICD, rapid NICD cytoplasmic consumption and the time-averaging effect of nuclear import/export kinetics are sufficient to explain the experimentally observed differentiation probabilities.", "Our computational studies lend quantitative support to the feasibility of the nuclear concentration-sensing mechanism for NPC fate determination in zebrafish retina."], "structured": false}
{"doc_id": 17050065, "title": "Odorant-specific adaptation pathways generate olfactory plasticity in C. elegans", "abstract": ["Following prolonged exposure to an odorant, C. elegans exhibits a diminished response to the odorant for several hours.", "This olfactory adaptation is odorant selective; animals can adapt independently to different odorants sensed by a single pair of olfactory neurons, the AWC neurons.", "The mechanism of olfactory adaptation is genetically complex, with different genes required for adaptation to different odorants.", "Animals mutant for the gene adp-1 fail to adapt to a subset of AWC-sensed odorants; adp-1 affects a calcium-dependent process required for adaptation.", "Mutations in another gene, osm-9, affect adaptation to a different but overlapping subset of AWC-sensed odorants.", "Mutations in adp-1 and osm-9 do not diminish the ability of unadapted animals to respond to odorants, indicating that odorant sensation and odorant adaptation are distinct processes."], "structured": false}
{"doc_id": 17055665, "title": "Genome-wide dFOXO targets and topology of the transcriptomic response to stress and insulin signalling", "abstract": ["FoxO transcription factors, inhibited by insulin/insulin-like growth factor signalling (IIS), are crucial players in numerous organismal processes including lifespan.", "Using genomic tools, we uncover over 700 direct dFOXO targets in adult female Drosophila.", "dFOXO is directly required for transcription of several IIS components and interacting pathways, such as TOR, in the wild-type fly.", "The genomic locations occupied by dFOXO in adults are different from those observed in larvae or cultured cells.", "These locations remain unchanged upon activation by stresses or reduced IIS, but the binding is increased and additional targets activated upon genetic reduction in IIS.", "We identify the part of the IIS transcriptional response directly controlled by dFOXO and the indirect effects and show that parts of the transcriptional response to IIS reduction do not require dfoxo.", "Promoter analyses revealed GATA and other forkhead factors as candidate mediators of the indirect and dfoxo-independent effects.", "We demonstrate genome-wide evolutionary conservation of dFOXO targets between the fly and the worm Caenorhabditis elegans, enriched for a second tier of regulators including the dHR96/daf-12 nuclear hormone receptor."], "structured": false}
{"doc_id": 17077004, "title": "Stable partnership and progression to AIDS or death in HIV infected patients receiving highly active antiretroviral therapy: Swiss HIV cohort study.", "abstract": ["OBJECTIVES To explore the association between a stable partnership and clinical outcome in HIV infected patients receiving highly active antiretroviral therapy (HAART).   \n", "DESIGN Prospective cohort study of adults with HIV (Swiss HIV cohort study).   \n", "SETTING Seven outpatient clinics throughout Switzerland.   \n", "PARTICIPANTS The 3736 patients in the cohort who started HAART before 2002 (median age 36 years, 29% female, median follow up 3.6 years).   \n", "MAIN OUTCOME MEASURES Time to AIDS or death (primary endpoint), death alone, increases in CD4 cell count of at least 50 and 100 above baseline, optimal viral suppression (a viral load below 400 copies/ml), and viral rebound.   \n", "RESULTS During follow up 2985 (80%) participants reported a stable partnership on at least one occasion.", "When starting HAART, 52% (545/1042) of participants reported a stable partnership; after five years of follow up 46% (190/412) of participants reported a stable partnership.", "In an analysis stratified by previous antiretroviral therapy and clinical stage when starting HAART (US Centers for Disease Control and Prevention group A, B, or C), the adjusted hazard ratio for progression to AIDS or death was 0.79 (95% confidence interval 0.63 to 0.98) for participants with a stable partnership compared with those without.", "Adjusted hazards ratios for other endpoints were 0.59 (0.44 to 0.79) for progression to death, 1.15 (1.06 to 1.24) for an increase in CD4 cells of 100 counts/microl or more, and 1.06 (0.98 to 1.14) for optimal viral suppression.   \n", "CONCLUSIONS A stable partnership is associated with a slower rate of progression to AIDS or death in HIV infected patients receiving HAART."], "structured": true}
{"doc_id": 17081238, "title": "Specific deficit of the ON response in visual transmission by targeted disruption of the mGIuR6 gene", "abstract": ["Taking advantage of the restricted expression of metabotropic glutamate receptor subtype 6 (mGluR6) in retinal ON bipolar cells, we generated knockout mice lacking mGluR6 expression.", "The homozygous mutant mice showed a loss of ON responses but unchanged OFF responses to light.", "The mutant mice displayed no obvious changes in retinal cell organization nor in the projection of optic fibers to the brain.", "Furthermore, the mGluR6-deficient mice showed visual behavioral responses to light stimulation as examined by shuttle box avoidance behavior experiments using light exposure as a conditioned stimulus.", "The results demonstrate that mGluR6 is essential in synaptic transmission to the ON bipolar cell and that the OFF response provides an important means for transmitting visual information."], "structured": false}
{"doc_id": 17088791, "title": "Common BRCA1 variants and susceptibility to breast and ovarian cancer in the general population.", "abstract": ["Most multiple case families of young onset breast cancer and ovarian cancer are thought to be due to highly penetrant mutations in the predisposing genes BRCA1 and BRCA2.", "However, these mutations are uncommon in the population and they probably account for only a few percent of all breast cancer incidence.", "A much larger fraction of breast cancer might, in principle, be due to common variants which confer more modest individual risks.", "There are several common polymorphisms in the BRCA1 gene which generate amino acid substitutions.", "We have examined the frequency of four of these polymorphisms: Gln356Arg, Pro871Leu, Glu1038Gly and Ser1613Gly in large series of breast and ovarian cancer cases and matched controls.", "Due to strong linkage disequilibrium, these four sites generate only three haplotypes with a frequency > 1.3%.", "The most common haplotypes, defined by the alleles Gln356Pro871Glu1038Ser1613 and Gln356Leu871Gly1038Gly1613, have frequencies of 0.57 and 0.32 respectively, and these frequencies do not differ significantly between patient and control groups.", "Thus the most common polymorphisms of the BRCA1 gene do not make a significant contribution to breast or ovarian cancer risk.", "However, our data suggest that the Arg356 allele may have a different genotype distribution in breast cancer patients from that in controls (Arg356 homozygotes are more frequent in the control groups, P = 0.01), indicating that it may be protective against breast cancer.", "If this finding can be confirmed, it may provide an insight into the structural features of the BRCA1 protein that are important for its function."], "structured": false}
{"doc_id": 17097974, "title": "Exercise causes a tissue-specific change of NO production in the kidney and lung.", "abstract": ["Nitric oxide (NO) is produced in the vascular endothelium and is a potent vasodilator substance that participates in the regulation of local vascular tone.", "Exercise causes peculiar changes in systemic and regional blood flow, i.e., an increase of systemic blood flow and a redistribution of local tissue blood flow, by which the blood flow is greatly increased in the working muscles, whereas it is decreased in some organs such as the kidney and intestine.", "Thus we hypothesized that exercise causes a tissue-specific change of NO production in some internal organs.", "We studied whether exercise affects expression of NO synthase (NOS) mRNA and protein, NOS activity, and tissue level of nitrite/nitrate (stable end products of NO) in the kidneys (in which blood flow during exercise is decreased) and lungs (in which blood flow during exercise is increased with the increase of cardiac output) of rat.", "Rats ran on a treadmill for 45 min at a speed of 25 m/min.", "Immediately after this exercise, kidneys and lungs were quickly removed.", "Control rats remained at rest during this 45-min period.", "Expression of endothelial NOS (eNOS) mRNA in the kidneys was markedly lower in exercise rats than in control rats, whereas that in the lungs was significantly higher in exercise rats than in control rats.", "Western blot analysis confirmed down- and upregulation of eNOS protein in the kidney and lung, respectively, after exercise.", "On the other hand, neither expression of neuronal NOS (nNOS) mRNA and nNOS protein nor inducible NOS (iNOS) mRNA and iNOS protein in the kidneys and lungs differed between exercise and control rats.", "NOS activity in the kidney was significantly lower in exercise rats than in control rats, whereas that in the lung was significantly higher in exercise rats than in control rats.", "On the other hand, the iNOS activity in the kidneys and lungs did not differ between exercise rats and control rats.", "Tissue nitrite/nitrate level in the kidneys was markedly lower in exercise rats, whereas that in the lungs was significantly higher in exercise rats.", "The present results show that production of NO is markedly and tissue-specifically changed in the kidney and lung by exercise."], "structured": false}
{"doc_id": 17101262, "title": "Ballistic labeling and dynamic imaging of astrocytes in organotypic hippocampal slice cultures", "abstract": ["Protoplasmic astrocytes in mammalian CNS tissues in vivo have a highly complex 3D morphology, but in dissociated cell cultures they often assume a flattened, fibroblast-like morphology bearing only a few, simple processes.", "By fluorescent labeling and confocal reconstruction we show that many astrocytes in organotypic hippocampal slice cultures exhibit a more native complex cytoarchitecture.", "Although astrocytes at the surface of slice cultures show a reactive form with several thick glial fibrillary acidic protein (GFAP)-positive processes, astrocytes situated in deeper portions of tissue slices retain a highly complex 3D morphology with many fine spine- or veil-like protrusions.", "Dozens of astrocytes can be labeled in single slice cultures by gene gun-mediated ballistic delivery of gold or tungsten particles carrying cDNAs (Biolistics), lipophilic dyes (DiOlistics), or fluorescent intracellular calcium indicators (Calistics).", "Expression of a membrane-targeted form of eGFP (Lck-GFP) is superior to soluble eGFP for resolving fine astrocytic processes.", "Time-lapse confocal imaging of Lck-GFP transfected astrocytes or \"calistically\" labeled astrocytes show structural remodeling and calcium transients, respectively.", "This approach provides an in vitro system for investigating the functional architecture, development and dynamic remodeling of astrocytes and their relationships to neurons and glia in live mammalian brain tissues."], "structured": false}
{"doc_id": 17119869, "title": "A bipotential precursor population for pancreas and liver within the embryonic endoderm.", "abstract": ["The pancreas emerges independently from dorsal and ventral domains of embryonic gut endoderm.", "Gene inactivation experiments in mice have identified factors required for dorsal pancreas development, but factors that initiate the ventral pancreas have remained elusive.", "In this study, we investigated the hypothesis that the emergence of the ventral pancreas is related to the emergence of the liver.", "We find that the liver and ventral pancreas are specified at the same time and in the same general domain of cells.", "Using embryo tissue explantation experiments, we find that the default fate of the ventral foregut endoderm is to activate the pancreas gene program.", "FGF signalling from the cardiac mesoderm diverts this endoderm to express genes for liver instead of those for pancreas.", "No evidence was found to indicate that the cell type choice for pancreas or liver involves a selection for growth or viability.", "Cardiac mesoderm or FGF induces the local expression of sonic hedgehog, which in turn is inhibitory to pancreas but not to liver.", "The bipotential precursor cell population for pancreas and liver in embryonic development and its fate selection by FGF has features that appear to be recapitulated in the adult pancreas and are reflected in the evolution of these organs."], "structured": false}
{"doc_id": 17123316, "title": "ErbB4-neuregulin signaling modulates synapse development and dendritic arborization through distinct mechanisms.", "abstract": ["Perturbations in neuregulin-1 (NRG1)/ErbB4 function have been associated with schizophrenia.", "Affected patients exhibit altered levels of these proteins and display hypofunction of glutamatergic synapses as well as altered neuronal circuitry.", "However, the role of NRG1/ErbB4 in regulating synapse maturation and neuronal process formation has not been extensively examined.", "Here we demonstrate that ErbB4 is expressed in inhibitory interneurons at both excitatory and inhibitory postsynaptic sites.", "Overexpression of ErbB4 postsynaptically enhances size but not number of presynaptic inputs.", "Conversely, knockdown of ErbB4 using shRNA decreases the size of presynaptic inputs, demonstrating a specific role for endogenous ErbB4 in synapse maturation.", "Using ErbB4 mutant constructs, we demonstrate that ErbB4-mediated synapse maturation requires its extracellular domain, whereas its tyrosine kinase activity is dispensable for this process.", "We also demonstrate that depletion of ErbB4 decreases the number of primary neurites and that stimulation of ErbB4 using a soluble form of NRG1 results in exuberant dendritic arborization through activation of the tyrosine kinase domain of ErbB4 and the phosphoinositide 3-kinase pathway.", "These findings demonstrate that NRG1/ErbB4 signaling differentially regulates synapse maturation and dendritic morphology via two distinct mechanisms involving trans-synaptic signaling and tyrosine kinase activity, respectively."], "structured": false}
{"doc_id": 17123657, "title": "Dynamic Helix Interactions in Transmembrane Signaling", "abstract": ["Studying how protein transmembrane domains transmit signals across membranes is beset by unique challenges.", "Here, we discuss the circumstances that have led to success and reflect on what has been learned from these examples.", "Such efforts suggest that some of the most interesting properties of transmembrane helix interactions may be the least amenable to study by current techniques."], "structured": false}
{"doc_id": 17124832, "title": "Association between smoking and risk of bladder cancer among men and women.", "abstract": ["CONTEXT Previous studies indicate that the population attributable risk (PAR) of bladder cancer for tobacco smoking is 50% to 65% in men and 20% to 30% in women and that current cigarette smoking triples bladder cancer risk relative to never smoking.", "During the last 30 years, incidence rates have remained stable in the United States in men (123.8 per 100,000 person-years to 142.2 per 100,000 person-years) and women (32.5 per 100,000 person-years to 33.2 per 100,000 person-years); however, changing smoking prevalence and cigarette composition warrant revisiting risk estimates for smoking and bladder cancer.   \n", "OBJECTIVE To evaluate the association between tobacco smoking and bladder cancer.   \n", "DESIGN, SETTING, AND PARTICIPANTS Men (n = 281,394) and women (n = 186,134) of the National Institutes of Health-AARP (NIH-AARP) Diet and Health Study cohort completed a lifestyle questionnaire and were followed up between October 25, 1995, and December 31, 2006.", "Previous prospective cohort studies of smoking and incident bladder cancer were identified by systematic review and relative risks were estimated from fixed-effects models with heterogeneity assessed by the I(2) statistic.   \n", "MAIN OUTCOME MEASURES Hazard ratios (HRs), PARs, and number needed to harm (NNH).   \n", "RESULTS During 4,518,941 person-years of follow-up, incident bladder cancer occurred in 3896 men (144.0 per 100,000 person-years) and 627 women (34.5 per 100,000 person-years).", "Former smokers (119.8 per 100,000 person-years; HR, 2.22; 95% confidence interval [CI], 2.03-2.44; NNH, 1250) and current smokers (177.3 per 100,000 person-years; HR, 4.06; 95% CI, 3.66-4.50; NNH, 727) had higher risks of bladder cancer than never smokers (39.8 per 100,000 person-years).", "In contrast, the summary risk estimate for current smoking in 7 previous studies (initiated between 1963 and 1987) was 2.94 (95% CI, 2.45-3.54; I(2) = 0.0%).", "The PAR for ever smoking in our study was 0.50 (95% CI, 0.45-0.54) in men and 0.52 (95% CI, 0.45-0.59) in women.   \n", "CONCLUSION Compared with a pooled estimate of US data from cohorts initiated between 1963 and 1987, relative risks for smoking in the more recent NIH-AARP Diet and Health Study cohort were higher, with PARs for women comparable with those for men."], "structured": true}
{"doc_id": 17150648, "title": "Leptin regulates glutamate and glucose transporters in hypothalamic astrocytes.", "abstract": ["Glial cells perform critical functions that alter the metabolism and activity of neurons, and there is increasing interest in their role in appetite and energy balance.", "Leptin, a key regulator of appetite and metabolism, has previously been reported to influence glial structural proteins and morphology.", "Here, we demonstrate that metabolic status and leptin also modify astrocyte-specific glutamate and glucose transporters, indicating that metabolic signals influence synaptic efficacy and glucose uptake and, ultimately, neuronal function.", "We found that basal and glucose-stimulated electrical activity of hypothalamic proopiomelanocortin (POMC) neurons in mice were altered in the offspring of mothers fed a high-fat diet.", "In adulthood, increased body weight and fasting also altered the expression of glucose and glutamate transporters.", "These results demonstrate that whole-organism metabolism alters hypothalamic glial cell activity and suggest that these cells play an important role in the pathology of obesity."], "structured": false}
{"doc_id": 17163294, "title": "Metabolic phenotyping of human blood plasma: a powerful tool to discriminate between cancer types?", "abstract": ["BACKGROUND Accumulating evidence has shown that cancer cell metabolism differs from that of normal cells.", "However, up to now it is not clear whether different cancer types are characterized by a specific metabolite profile.", "Therefore, this study aims to evaluate whether the plasma metabolic phenotype allows to discriminate between lung and breast cancer.   \n", "PATIENTS AND METHODS The proton nuclear magnetic resonance spectrum of plasma is divided into 110 integration regions, representing the metabolic phenotype.", "These integration regions reflect the relative metabolite concentrations and were used to train a classification model in discriminating between 80 female breast cancer patients and 54 female lung cancer patients, all with an adenocarcinoma.", "The validity of the model was examined by permutation testing and by classifying an independent validation cohort of 60 female breast cancer patients and 81 male lung cancer patients, all with an adenocarcinoma.   \n", "RESULTS The model allows to classify 99% of the breast cancer patients and 93% of the lung cancer patients correctly with an area under the curve (AUC) of 0.96 and can be validated in the independent cohort with a sensitivity of 89%, a specificity of 82% and an AUC of 0.94.", "Decreased levels of sphingomyelin and phosphatidylcholine (phospholipids with choline head group) and phospholipids with short, unsaturated fatty acid chains next to increased levels of phospholipids with long, saturated fatty acid chains seem to indicate that cell membranes of lung tumors are more rigid and less sensitive to lipid peroxidation.", "The other discriminating metabolites are pointing to a more pronounced response of the body to the Warburg effect for lung cancer.   \n", "CONCLUSION Metabolic phenotyping of plasma allows to discriminate between lung and breast cancer, indicating that the metabolite profile reflects more than a general cancer marker.   ", "CLINICAL TRIAL REGISTRATION NUMBER NCT02362776."], "structured": true}
{"doc_id": 17168045, "title": "Direct in vivo assessment of microcirculatory dysfunction in severe falciparum malaria.", "abstract": ["BACKGROUND This study sought to describe and quantify microcirculatory changes in the mucosal surfaces of patients with severe malaria, by direct in vivo observation using orthogonal polarization spectral (OPS) imaging.   \n", "METHODS The microcirculation in the rectal mucosa of adult patients with severe malaria was assessed by use of OPS imaging, at admission and then daily.", "Comparison groups comprised patients with uncomplicated falciparum malaria, patients with bacterial sepsis, and healthy individuals.   \n", "RESULTS Erythrocyte velocities were measured directly in 43 adult patients with severe falciparum malaria, of whom 20 died.", "Microcirculatory blood flow was markedly disturbed, with heterogeneous obstruction that was proportional to severity of disease.", "Blocked capillaries were found in 29 patients (67%) and were associated with concurrent hyperdynamic blood flow (erythrocyte velocity, >750 mm/s) in adjacent vessels in 27 patients (93%).", "The proportion of blocked capillaries correlated with the base deficit in plasma and with the concentration of lactate.", "Abnormalities disappeared when the patients recovered.", "In healthy individuals and in patients with uncomplicated malaria or sepsis, no stagnant erythrocytes were detected, and, in patients with sepsis, hyperdynamic blood flow was prominent.   \n", "CONCLUSION Patients with severe falciparum malaria show extensive microvascular obstruction that is proportional to the severity of the disease.", "This finding underscores the prominent role that microvascular obstruction plays in the pathophysiology of severe malaria and illustrates the fundamental difference between the microvascular pathophysiology of malaria and that of bacterial sepsis."], "structured": true}
{"doc_id": 17173492, "title": "Multiple archaeal groups mediate methane oxidation in anoxic cold seep sediments.", "abstract": ["No microorganism capable of anaerobic growth on methane as the sole carbon source has yet been cultivated.", "Consequently, information about these microbes has been inferred from geochemical and microbiological observations of field samples.", "Stable isotope analysis of lipid biomarkers and rRNA gene surveys have implicated specific microbes in the anaerobic oxidation of methane (AOM).", "Here we use combined fluorescent in situ hybridization and secondary ion mass spectrometry analyses, to identify anaerobic methanotrophs in marine methane-seep sediments.", "The results provide direct evidence for the involvement of at least two distinct archaeal groups (ANME-1 and ANME-2) in AOM at methane seeps.", "Although both archaeal groups often occurred in direct physical association with bacteria, they also were observed as monospecific aggregations and as single cells.", "The ANME-1 archaeal group more frequently existed in monospecific aggregations or as single filaments, apparently without a bacterial partner.", "Bacteria associated with both archaeal groups included, but were not limited to, close relatives of Desulfosarcina species.", "Isotopic analyses suggest that monospecific archaeal cells and cell aggregates were active in anaerobic methanotrophy, as were multispecies consortia.", "In total, the data indicate that the microbial species and biotic interactions mediating anaerobic methanotrophy are diverse and complex.", "The data also clearly show that highly structured ANME-2/Desulfosarcina consortia are not the sole entities responsible for AOM at marine methane seeps.", "Other microbial groups, including ANME-1 archaea, are capable of anaerobic methane consumption either as single cells, in monospecific aggregates, or in multispecies consortia."], "structured": false}
{"doc_id": 17188921, "title": "N-cadherin in the spotlight of cell-cell adhesion, differentiation, embryogenesis, invasion and signalling.", "abstract": ["Cell migration is a process which is essential during embryonic development, throughout adult life and in some pathological conditions.", "Cadherins, and more specifically the neural cell adhesion molecule N-cadherin, play an important role in migration.", "In embryogenesis, N-cadherin is the key molecule during gastrulation and neural crest development.", "N-cadherin mediated contacts activate several pathways like Rho GTPases and function in tyrosine kinase signalling (for example via the fibroblast growth factor receptor).", "In cancer, cadherins control the balance between suppression and promotion of invasion.", "E-cadherin functions as an invasion suppressor and is downregulated in most carcinomas, while N-cadherin, as an invasion promoter, is frequently upregulated.", "Expression of N-cadherin in epithelial cells induces changes in morphology to a fibroblastic phenotype, rendering the cells more motile and invasive.", "However in some cancers, like osteosarcoma, N-cadherin may behave as a tumour suppressor.", "N-cadherin can have multiple functions: promoting adhesion or induction of migration dependent on the cellular context."], "structured": false}
{"doc_id": 17194716, "title": "Role of fascin in filopodial protrusion", "abstract": ["In this study, the mechanisms of actin-bundling in filopodia were examined.", "Analysis of cellular localization of known actin cross-linking proteins in mouse melanoma B16F1 cells revealed that fascin was specifically localized along the entire length of all filopodia, whereas other actin cross-linkers were not.", "RNA interference of fascin reduced the number of filopodia, and remaining filopodia had abnormal morphology with wavy and loosely bundled actin organization.", "Dephosphorylation of serine 39 likely determined cellular filopodia frequency.", "The constitutively active fascin mutant S39A increased the number and length of filopodia, whereas the inactive fascin mutant S39E reduced filopodia frequency.", "Fluorescence recovery after photobleaching of GFP-tagged wild-type and S39A fascin showed that dephosphorylated fascin underwent rapid cycles of association to and dissociation from actin filaments in filopodia, with t1/2 < 10 s. We propose that fascin is a key specific actin cross-linker, providing stiffness for filopodial bundles, and that its dynamic behavior allows for efficient coordination between elongation and bundling of filopodial actin filaments."], "structured": false}
{"doc_id": 17195001, "title": "TOR Signaling in Growth and Metabolism", "abstract": ["The target of rapamycin (TOR) is a conserved Ser/Thr kinase that regulates cell growth and metabolism in response to environmental cues.", "Here, highlighting contributions from studies in model organisms, we review mammalian TOR complexes and the signaling branches they mediate.", "TOR is part of two distinct multiprotein complexes, TOR complex 1 (TORC1), which is sensitive to rapamycin, and TORC2, which is not.", "The physiological consequences of mammalian TORC1 dysregulation suggest that inhibitors of mammalian TOR may be useful in the treatment of cancer, cardiovascular disease, autoimmunity, and metabolic disorders."], "structured": false}
{"doc_id": 17208742, "title": "Self-Organization of the Escherichia coli Chemotaxis Network Imaged with Super-Resolution Light Microscopy", "abstract": ["The Escherichia coli chemotaxis network is a model system for biological signal processing.", "In E. coli, transmembrane receptors responsible for signal transduction assemble into large clusters containing several thousand proteins.", "These sensory clusters have been observed at cell poles and future division sites.", "Despite extensive study, it remains unclear how chemotaxis clusters form, what controls cluster size and density, and how the cellular location of clusters is robustly maintained in growing and dividing cells.", "Here, we use photoactivated localization microscopy (PALM) to map the cellular locations of three proteins central to bacterial chemotaxis (the Tar receptor, CheY, and CheW) with a precision of 15 nm.", "We find that cluster sizes are approximately exponentially distributed, with no characteristic cluster size.", "One-third of Tar receptors are part of smaller lateral clusters and not of the large polar clusters.", "Analysis of the relative cellular locations of 1.1 million individual proteins (from 326 cells) suggests that clusters form via stochastic self-assembly.", "The super-resolution PALM maps of E. coli receptors support the notion that stochastic self-assembly can create and maintain approximately periodic structures in biological membranes, without direct cytoskeletal involvement or active transport."], "structured": false}
{"doc_id": 17209919, "title": "Ciliary Extracellular Vesicles: Txt Msg Organelles", "abstract": ["Cilia are sensory organelles that protrude from cell surfaces to monitor the surrounding environment.", "In addition to its role as sensory receiver, the cilium also releases extracellular vesicles (EVs).", "The release of sub-micron sized EVs is a conserved form of intercellular communication used by all three kingdoms of life.", "These extracellular organelles play important roles in both short and long range signaling between donor and target cells and may coordinate systemic responses within an organism in normal and diseased states.", "EV shedding from ciliated cells and EV\u2013cilia interactions are evolutionarily conserved phenomena, yet remarkably little is known about the relationship between the cilia and EVs and the fundamental biology of EVs.", "Studies in the model organisms Chlamydomonas and Caenorhabditis elegans have begun to shed light on ciliary EVs.", "Chlamydomonas EVs are shed from tips of flagella and are bioactive.", "Caenorhabditis elegans EVs are shed and released by ciliated sensory neurons in an intraflagellar transport-dependent manner.", "Caenorhabditis elegans EVs play a role in modulating animal-to-animal communication, and this EV bioactivity is dependent on EV cargo content.", "Some ciliary pathologies, or ciliopathies, are associated with abnormal EV shedding or with abnormal cilia\u2013EV interactions.", "Until the 21st century, both cilia and EVs were ignored as vestigial or cellular junk.", "As research interest in these two organelles continues to gain momentum, we envision a new field of cell biology emerging.", "Here, we propose that the cilium is a dedicated organelle for EV biogenesis and EV reception.", "We will also discuss possible mechanisms by which EVs exert bioactivity and explain how what is learned in model organisms regarding EV biogenesis and function may provide insight to human ciliopathies."], "structured": false}
{"doc_id": 17223891, "title": "The NOD-like receptor NLRP12 attenuates colon inflammation and tumorigenesis.", "abstract": ["NLRP12 is a member of the intracellular Nod-like receptor (NLR) family that has been suggested to downregulate the production of inflammatory cytokines, but its physiological role in regulating inflammation has not been characterized.", "We analyzed mice deficient in Nlrp12 to study its role in inflammatory diseases such as colitis and colorectal tumorigenesis.", "We show that Nlrp12-deficient mice are highly susceptible to colon inflammation and tumorigenesis, which is associated with increased production of inflammatory cytokines, chemokines, and tumorigenic factors.", "Enhanced colon inflammation and colorectal tumor development in Nlrp12-deficient mice are due to a failure to dampen NF-\u03baB and ERK activation in macrophages.", "These results reveal a critical role for NLRP12 in maintaining intestinal homeostasis and providing protection against colorectal tumorigenesis."], "structured": false}
{"doc_id": 17231273, "title": "Ionic mechanism of ouabain-induced concurrent apoptosis and necrosis in individual cultured cortical neurons", "abstract": ["Energy deficiency and dysfunction of the Na+, K+-ATPase are common consequences of many pathological insults.", "The nature and mechanism of cell injury induced by impaired Na+, K+-ATPase, however, are not well defined.", "We used cultured cortical neurons to examine the hypothesis that blocking the Na+, K+-ATPase induces apoptosis by depleting cellular K+ and, concurrently, induces necrotic injury in the same cells by increasing intracellular Ca2+ and Na+.", "The Na+, K+-ATPase inhibitor ouabain induced concentration-dependent neuronal death.", "Ouabain triggered transient neuronal cell swelling followed by cell shrinkage, accompanied by intracellular Ca2+ and Na+ increase, K+ decrease, cytochrome c release, caspase-3 activation, and DNA laddering.", "Electron microscopy revealed the coexistence of ultrastructural features of both apoptosis and necrosis in individual cells.", "The caspase inhibitor Z-Val-Ala-Asp(OMe)-fluoromethyl ketone (Z-VAD-FMK) blocked >50% of ouabain-induced neuronal death.", "Potassium channel blockers or high K+ medium, but not Ca2+ channel blockade, prevented cytochrome c release, caspase activation, and DNA damage.", "Blocking of K+, Ca2+, or Na+ channels or high K+ medium each attenuated the ouabain-induced cell death; combined inhibition of K+ channels and Ca2+ or Na+ channels resulted in additional protection.", "Moreover, coapplication of Z-VAD-FMK and nifedipine produced virtually complete neuroprotection.", "These results suggest that the neuronal death associated with Na+, K+-pump failure consists of concurrent apoptotic and necrotic components, mediated by intracellular depletion of K+ and accumulation of Ca2+ and Na+, respectively.", "The ouabain-induced hybrid death may represent a distinct form of cell death related to the brain injury of inadequate energy supply and disrupted ion homeostasis."], "structured": false}
{"doc_id": 17236106, "title": "Potential consequences of replacing a retail alcohol monopoly with a private licence system: results from Sweden.", "abstract": ["AIM To examine the potential effects of replacing the Swedish alcohol retail system with a private licensing system on alcohol consumption and alcohol-related harm.   \n", "DESIGN Two possible scenarios were analysed: (1) replacing the current alcohol retail monopoly with private licensed stores that specialize in alcohol sales or (2) making all alcohol available in grocery stores.", "We utilized a multiplicative model that projected effects of changes in a set of key factors including hours of sale, retail prices, promotion and advertising and outlet density.", "Next, we estimated the effect of the projected consumption increase on a set of harm indicators.", "Values for the model parameters were obtained from the research literature.   \n", "MEASUREMENTS Measures of alcohol-related harm included explicitly alcohol-related mortality, accident mortality, suicide, homicide, assaults, drinking driving and sickness absence.   \n", "FINDINGS According to the projections, scenario 1 yields a consumption increase of 17% (1.4 litres/capita), which in turn would cause an additional 770 deaths, 8500 assaults, 2700 drinking driving offences and 4.5 million sick days per year.", "The corresponding figures for scenario 2 are a consumption increase of 37.4% (3.1 litres/capita) leading to an additional annual toll of 2000 deaths, 20 000 assaults, 6600 drinking driving offences and 11.1 million days of sick leave.   \n", "CONCLUSIONS Projections based on the research literature suggest that privatization of the Swedish alcohol retail market would significantly increase alcohol consumption and alcohol-related harm."], "structured": true}
{"doc_id": 17240457, "title": "A comprehensive genomic binding map of gene and chromatin regulatory proteins in Saccharomyces.", "abstract": ["Hundreds of different proteins regulate and implement transcription in Saccharomyces.", "Yet their interrelationships have not been investigated on a comprehensive scale.", "Here we determined the genome-wide binding locations of 200 transcription-related proteins, under normal and acute heat-shock conditions.", "This study distinguishes binding between distal versus proximal promoter regions as well as the 3' ends of genes for nearly all mRNA and tRNA genes.", "This study reveals (1) a greater diversity and specialization of regulation associated with the SAGA transcription pathway compared to the TFIID pathway, (2) new regulators enriched at tRNA genes, (3) a global co-occupancy network of >20,000 unique regulator combinations that show a high degree of regulatory interconnections among lowly expressed genes, (4) regulators of the SAGA pathway located largely distal to the core promoter and regulators of the TFIID pathway located proximally, and (5) distinct mobilization of SAGA- versus TFIID-linked regulators during acute heat shock."], "structured": false}
{"doc_id": 17271462, "title": "Tie2/Angiopoietin-1 Signaling Regulates Hematopoietic Stem Cell Quiescence in the Bone Marrow Niche", "abstract": ["The quiescent state is thought to be an indispensable property for the maintenance of hematopoietic stem cells (HSCs).", "Interaction of HSCs with their particular microenvironments, known as the stem cell niches, is critical for adult hematopoiesis in the bone marrow (BM).", "Here, we demonstrate that HSCs expressing the receptor tyrosine kinase Tie2 are quiescent and antiapoptotic, and comprise a side-population (SP) of HSCs, which adhere to osteoblasts (OBs) in the BM niche.", "The interaction of Tie2 with its ligand Angiopoietin-1 (Ang-1) induced cobblestone formation of HSCs in vitro and maintained in vivo long-term repopulating activity of HSCs.", "Furthermore, Ang-1 enhanced the ability of HSCs to become quiescent and induced adhesion to bone, resulting in protection of the HSC compartment from myelosuppressive stress.", "These data suggest that the Tie2/Ang-1 signaling pathway plays a critical role in the maintenance of HSCs in a quiescent state in the BM niche."], "structured": false}
{"doc_id": 17324544, "title": "Thirty-One Novel Biomarkers as Predictors for Clinically Incident Diabetes", "abstract": ["BACKGROUND The prevalence of diabetes is increasing in all industrialized countries and its prevention has become a public health priority.", "However, the predictors of diabetes risk are insufficiently understood.", "We evaluated, whether 31 novel biomarkers could help to predict the risk of incident diabetes.   \n", "METHODS AND FINDINGS The biomarkers were evaluated primarily in the FINRISK97 cohort (n = 7,827; 417 cases of clinically incident diabetes during the follow-up).", "The findings were replicated in the Health 2000 cohort (n = 4,977; 179 cases of clinically incident diabetes during the follow-up).", "We used Cox proportional hazards models to calculate the relative risk of diabetes, after adjusting for the classic risk factors, separately for each biomarker.", "Next, we assessed the discriminatory ability of single biomarkers using receiver operating characteristic curves and C-statistics, integrated discrimination improvement (IDI) and net reclassification improvement (NRI).", "Finally, we derived a biomarker score in the FINRISK97 cohort and validated it in the Health 2000 cohort.", "A score consisting of adiponectin, apolipoprotein B, C-reactive protein and ferritin almost doubled the relative risk of diabetes in the validation cohort (HR per one standard deviation increase 1.88, p = 2.8 e-5).", "It also improved discrimination of the model (IDI = 0.0149, p<0.0001) and reclassification of diabetes risk (NRI = 11.8%, p = 0.006).", "Gender-specific analyses suggested that the best score differed between men and women.", "Among men, the best results were obtained with the score of four biomarkers: adiponectin, apolipoprotein B, ferritin and interleukin-1 receptor antagonist, which gave an NRI of 25.4% (p<0.0001).", "Among women, the best score included adiponectin, apolipoprotein B, C-reactive protein and insulin.", "It gave an NRI of 13.6% (p = 0.041).   \n", "CONCLUSIONS We identified novel biomarkers that were associated with the risk of clinically incident diabetes over and above the classic risk factors.", "This gives new insights into the pathogenesis of diabetes and may help with targeting prevention and treatment."], "structured": true}
{"doc_id": 17327939, "title": "Exploiting lymphatic transport and complement activation in nanoparticle vaccines", "abstract": ["Antigen targeting and adjuvancy schemes that respectively facilitate delivery of antigen to dendritic cells and elicit their activation have been explored in vaccine development.", "Here we investigate whether nanoparticles can be used as a vaccine platform by targeting lymph node\u2013residing dendritic cells via interstitial flow and activating these cells by in situ complement activation.", "After intradermal injection, interstitial flow transported ultra-small nanoparticles (25 nm) highly efficiently into lymphatic capillaries and their draining lymph nodes, targeting half of the lymph node\u2013residing dendritic cells, whereas 100-nm nanoparticles were only 10% as efficient.", "The surface chemistry of these nanoparticles activated the complement cascade, generating a danger signal in situ and potently activating dendritic cells.", "Using nanoparticles conjugated to the model antigen ovalbumin, we demonstrate generation of humoral and cellular immunity in mice in a size- and complement-dependent manner."], "structured": false}
{"doc_id": 17333231, "title": "The sheddase ADAM10 is a potent modulator of prion disease", "abstract": ["The prion protein (PrP(C)) is highly expressed in the nervous system and critically involved in prion diseases where it misfolds into pathogenic PrP(Sc).", "Moreover, it has been suggested as a receptor mediating neurotoxicity in common neurodegenerative proteinopathies such as Alzheimer's disease.", "PrP(C) is shed at the plasma membrane by the metalloprotease ADAM10, yet the impact of this on prion disease remains enigmatic.", "Employing conditional knockout mice, we show that depletion of ADAM10 in forebrain neurons leads to posttranslational increase of PrP(C) levels.", "Upon prion infection of these mice, clinical, biochemical, and morphological data reveal that lack of ADAM10 significantly reduces incubation times and increases PrP(Sc) formation.", "In contrast, spatiotemporal analysis indicates that absence of shedding impairs spread of prion pathology.", "Our data support a dual role for ADAM10-mediated shedding and highlight the role of proteolytic processing in prion disease."], "structured": false}
{"doc_id": 17338543, "title": "High-affinity zinc inhibition of NMDA NR1-NR2A receptors", "abstract": ["Micromolar concentrations of extracellular Zn2+ are known to antagonize native NMDA receptors via a dual mechanism involving both a voltage-independent and a voltage-dependent inhibition.", "We have tried to evaluate the relative importance of these two effects and their subunit specificity on recombinant NMDA receptors expressed in HEK 293 cells and Xenopus oocytes.", "The comparison of NR1a-NR2A and NR1a-NR2B receptors shows that the voltage-dependent inhibition is similar in both types of receptors but that the voltage-independent inhibition occurs at much lower Zn2+ concentrations in NR1a-NR2A receptors (IC50 in the nanomolar range) than in NR1a-NR2B receptors (IC50 in the micromolar range).", "The high affinity of the effect observed with NR1a-NR2A receptors was found to be attributable mostly to the slow dissociation of Zn2+ from its binding site.", "By analyzing the effects of Zn2+ on varied combinations of NR1 (NR1a or NR1b) and NR2 (NR2A, NR2B, NR2C), we show that both the NR1 and the NR2 subunits contribute to the voltage-independent Zn2+ inhibition.", "We have observed further that under control conditions, i.e., in zero nominal Zn2+ solutions, the addition of low concentrations of heavy metal chelators markedly potentiates the responses of NR1a-NR2A receptors, but not of NR1a-NR2B receptors.", "This result suggests that traces of a heavy metal (probably Zn2+) contaminate standard solutions and tonically inhibit NR1a-NR2A receptors.", "Chelation of a contaminant metal also could account for the rapid NR2A subunit-specific potentiations produced by reducing compounds like DTT or glutathione."], "structured": false}
{"doc_id": 17368516, "title": "PrimPol, an Archaic Primase/Polymerase Operating in Human Cells", "abstract": ["We describe a second primase in human cells, PrimPol, which has the ability to start DNA chains with deoxynucleotides unlike regular primases, which use exclusively ribonucleotides.", "Moreover, PrimPol is also a DNA polymerase tailored to bypass the most common oxidative lesions in DNA, such as abasic sites and 8-oxoguanine.", "Subcellular fractionation and immunodetection studies indicated that PrimPol is present in both nuclear and mitochondrial DNA compartments.", "PrimPol activity is detectable in mitochondrial lysates from human and mouse cells but is absent from mitochondria derived from PRIMPOL knockout mice.", "PRIMPOL gene silencing or ablation in human and mouse cells impaired mitochondrial DNA replication.", "On the basis of the synergy observed with replicative DNA polymerases Pol\u03b3 and Pol\u03b5, PrimPol is proposed to facilitate replication fork progression by acting as a translesion DNA polymerase or as a specific DNA primase reinitiating downstream of lesions that block synthesis during both mitochondrial and nuclear DNA replication."], "structured": false}
{"doc_id": 17374970, "title": "Predictors of Attrition and Academic Success of Medical Students: A 30-Year Retrospective Study", "abstract": ["AIM To determine attrition and predictors of academic success among medical students at University of Split, Croatia.   \n", "METHODS We analysed academic records of 2054 students enrolled during 1979-2008 period.   \n", "RESULTS We found that 26% (533/2054) of enrolled students did not graduate.", "The most common reasons for attrition were 'personal' (36.4%), transfer to another medical school (35.6%), and dismissal due to unsatisfactory academic record (21.2%).", "Grade point average (GPA) and study duration of attrition students were significantly associated with parental education.", "There were 1126 graduates, 395 men and 731 women.", "Their average graduation GPA was 3.67\u00b10.53 and study duration 7.6\u00b12.44 years.", "During 5-year curriculum only 6.4% (42/654) of students graduated in time, and 55% (240/472) of students graduated in time after curriculum was extended to 6 years.", "Variables predicting whether a student will graduate or not were high school grades, entrance exam score and year of enrollment.", "Significant predictors of graduation grades were high school grades and entrance exam score.", "Entrance exam score predicted length of studying.   \n", "CONCLUSION Preadmission academic qualifications and year of enrollment predict academic success in medical school.", "More attention should be devoted to high attrition."], "structured": true}
{"doc_id": 17388232, "title": "Mechanical regulation of cell function with geometrically modulated elastomeric substrates", "abstract": ["We report the establishment of a library of micromolded elastomeric micropost arrays to modulate substrate rigidity independently of effects on adhesive and other material surface properties.", "We demonstrated that micropost rigidity impacts cell morphology, focal adhesions, cytoskeletal contractility and stem cell differentiation.", "Furthermore, early changes in cytoskeletal contractility predicted later stem cell fate decisions in single cells."], "structured": false}
{"doc_id": 17402386, "title": "THE EMBO JOURNAL", "abstract": ["Glutamate-gated ion channels (ionotropic glutamate receptors, iGluRs) sense the extracellular milieu via an extensive extracellular portion, comprised of two clamshell-shaped segments.", "The distal, N-terminal domain (NTD) has allosteric potential in NMDA-type iGluRs, which has not been ascribed to the analogous domain in AMPA receptors (AMPARs).", "In this study, we present new structural data uncovering dynamic properties of the GluA2 and GluA3 AMPAR NTDs.", "GluA3 features a zipped-open dimer interface with unconstrained lower clamshell lobes, reminiscent of metabotropic GluRs (mGluRs).", "The resulting labile interface supports interprotomer rotations, which can be transmitted to downstream receptor segments.", "Normal mode analysis reveals two dominant mechanisms of AMPAR NTD motion: intraprotomer clamshell motions and interprotomer counter-rotations, as well as accessible interconversion between AMPAR and mGluR conformations.", "In addition, we detect electron density for a potential ligand in the GluA2 interlobe cleft, which may trigger lobe motions.", "Together, these data support a dynamic role for the AMPAR NTDs, which widens the allosteric landscape of the receptor and could provide a novel target for ligand development."], "structured": false}
{"doc_id": 17412260, "title": "A complex secretory program orchestrated by the inflammasome controls paracrine senescence", "abstract": ["Oncogene-induced senescence (OIS) is crucial for tumour suppression.", "Senescent cells implement a complex pro-inflammatory response termed the senescence-associated secretory phenotype (SASP).", "The SASP reinforces senescence, activates immune surveillance and paradoxically also has pro-tumorigenic properties.", "Here, we present evidence that the SASP can also induce paracrine senescence in normal cells both in culture and in human and mouse models of OIS in vivo.", "Coupling quantitative proteomics with small-molecule screens, we identified multiple SASP components mediating paracrine senescence, including TGF-\u03b2 family ligands, VEGF, CCL2 and CCL20.", "Amongst them, TGF-\u03b2 ligands play a major role by regulating p15(INK4b) and p21(CIP1).", "Expression of the SASP is controlled by inflammasome-mediated IL-1 signalling.", "The inflammasome and IL-1 signalling are activated in senescent cells and IL-1\u03b1 expression can reproduce SASP activation, resulting in senescence.", "Our results demonstrate that the SASP can cause paracrine senescence and impact on tumour suppression and senescence in vivo."], "structured": false}
{"doc_id": 17415081, "title": "Prospective Study of One Million Deaths in India: Rationale, Design, and Validation Results", "abstract": ["Over 75% of the annual estimated 9.5 million deaths in India occur in the home, and the large majority of these do not have a certified cause.", "India and other developing countries urgently need reliable quantification of the causes of death.", "They also need better epidemiological evidence about the relevance of physical (such as blood pressure and obesity), behavioral (such as smoking, alcohol, HIV-1 risk taking, and immunization history), and biological (such as blood lipids and gene polymorphisms) measurements to the development of disease in individuals or disease rates in populations.", "This report here is on the rationale, design, and implementation of the world\u00e2\u20ac\u2122s largest prospective study of the causes and correlates of mortality.", "Nearly 14 million people in 2.4 million nationally representative Indian households will be monitored (for vital status and, if dead, the causes of death through a well-validated verbal autopsy (VA) instrument.", "be addressed.", "This study will reliably document not only the underlying cause of child and adult deaths but also key risk factors (behavioral, physical, environmental, and eventually, genetic).", "It offers a globally replicable model for reliably estimating cause-specific mortality using VA and strengthens India\u00e2\u20ac\u2122s flagship mortality monitoring system.", "Despite the misclassification that is still expected, the new cause-of-death data will be substantially better than that available previously.[PLoS Medicine, February 2006.]"], "structured": false}
{"doc_id": 17416520, "title": "Genome-wide identification of genes directly regulated by the pleiotropic transcription factor Spx in Bacillus subtilis", "abstract": ["The transcriptional regulator Spx plays a key role in maintaining the redox homeostasis of Bacillus subtilis cells exposed to disulfide stress.", "Defects in Spx were previously shown to lead to differential expression of numerous genes but direct and indirect regulatory effects could not be distinguished.", "Here we identified 283 discrete chromosomal sites potentially bound by the Spx-RNA polymerase (Spx-RNAP) complex using chromatin immunoprecipitation of Spx.", "Three quarters of these sites were located near Sigma(A)-dependent promoters, and upon diamide treatment, the fraction of the Spx-RNAP complex increased in parallel with the number and occupancy of DNA sites.", "Correlation of Spx-RNAP-binding sites with gene differential expression in wild-type and \u0394spx strains exposed or not to diamide revealed that 144 transcription units comprising 275 genes were potentially under direct Spx regulation.", "Spx-controlled promoters exhibited an extended -35 box in which nucleotide composition at the -43/-44 positions strongly correlated with observed activation.", "In vitro transcription confirmed activation by oxidized Spx of seven newly identified promoters, of which one was also activated by reduced Spx.", "Our study globally characterized the Spx regulatory network, revealing its role in the basal expression of some genes and its complex interplay with other stress responses."], "structured": false}
{"doc_id": 17421851, "title": "Expression of interleukin-18 in human atherosclerotic plaques and relation to plaque instability.", "abstract": ["BACKGROUND Interleukin (IL)-18 is a potent proinflammatory cytokine with potential atherogenic properties.", "Its expression and role in atherosclerosis, however, are unknown.   \n", "METHODS AND RESULTS In the present study, we examined stable and unstable human carotid atherosclerotic plaques retrieved by endarterectomy for the presence of IL-18 using reverse transcription-polymerase chain reaction (PCR), Western blot, and immunohistochemical techniques.", "IL-18 was highly expressed in the atherosclerotic plaques compared with control normal arteries and was localized mainly in plaque macrophages.", "IL-18 receptor was also upregulated in plaque macrophages and endothelial cells, suggesting potential biological effects.", "To examine the role of IL-18 in atherosclerosis, we determined the relation between IL-18 mRNA expression and signs of plaque instability using real-time quantitative PCR.", "Interestingly, significantly higher levels of IL-18 mRNA were found in symptomatic (unstable) plaques than asymptomatic (stable) plaques (P<0.01).   \n", "CONCLUSIONS These results suggest, for the first time, a major role for IL-18 in atherosclerotic plaque destabilization leading to acute ischemic syndromes."], "structured": true}
{"doc_id": 17422777, "title": " US-SOMO HPLC-SAXS module: dealing with capillary fouling and extraction of pure component patterns from poorly resolved SEC-SAXS data", "abstract": ["Size-exclusion chromatography coupled with SAXS (small-angle X-ray scattering), often performed using a flow-through capillary, should allow direct collection of monodisperse sample data.", "However, capillary fouling issues and non-baseline-resolved peaks can hamper its efficacy.", "The UltraScan solution modeler (US-SOMO) HPLC-SAXS (high-performance liquid chromatography coupled with SAXS) module provides a comprehensive framework to analyze such data, starting with a simple linear baseline correction and symmetrical Gaussian decomposition tools [Brookes, P\u00e9rez, Cardinali, Profumo, Vachette & Rocco (2013 \u25b8).", "J. Appl.", "Cryst.46, 1823-1833].", "In addition to several new features, substantial improvements to both routines have now been implemented, comprising the evaluation of outcomes by advanced statistical tools.", "The novel integral baseline-correction procedure is based on the more sound assumption that the effect of capillary fouling on scattering increases monotonically with the intensity scattered by the material within the X-ray beam.", "Overlapping peaks, often skewed because of sample interaction with the column matrix, can now be accurately decomposed using non-symmetrical modified Gaussian functions.", "As an example, the case of a polydisperse solution of aldolase is analyzed: from heavily convoluted peaks, individual SAXS profiles of tetramers, octamers and dodecamers are extracted and reliably modeled."], "structured": false}
{"doc_id": 17433284, "title": "Determination of Malaria Epidemiological Status in Iran\u2019s Malarious Areas as Baseline Information for Implementation of Malaria Elimination Program in Iran", "abstract": ["BACKGROUND According to willingness of the Ministry of Health, Iran and presence of appropriate conditions for disease elimination, national malaria control program decided to conduct a research to clarify malaria status in 2007 and to provide required information to perform the elimination program.", "This review is comprised of the basis of national malaria elimination program in vision of 2025, which was started in 2010.   \n", "METHODS In this descriptive study, data were analyzed by applications of different variables at district level.", "All districts in the three south eastern provinces, in which malaria has local transmission, were considered.", "Malaria cases has been determined and studied based on the national malaria surveillance system.   \n", "RESULTS Since vivax malaria is predominant in Sistan & Baluchestan Province, number of vivax cases is equal to malaria positive cases approximately.", "The important point is that Nikshahr contains the maximum number of local vivax cases in this province and the maximum number of falciparum cases is reported from Sarbaz district.", "Among all districts of Hormozgan Province, no case of autochthonous falciparum was detected except in Bandar Jask and one case in Minab.", "There was no case of autochthonous falciparum in Kerman Province, except in Kahnoj and Ghale Ganj that each of them had one case in 2007.   \n", "CONCLUSION It appears that the report of locally transmitted cases in Iran is increasing over the past few years, before starting malaria elimination plan.", "Since the Afghan refugees started to return to their own country so the main source of reporting of imported malaria cases reduced and local cases would be demonstrated more clearly."], "structured": true}
{"doc_id": 17438862, "title": "Local neuroinflammation and the progression of Alzheimer\u2019s disease", "abstract": ["Postmortem immunohistochemical studies have revealed a state of chronic inflammation limited to lesioned areas of brain in Alzheimer\u2019s disease.", "Some key actors in this inflammation are activated microglia (brain macrophages), proteins of the classical complement cascade, the pentraxins, cytokines, and chemokines.", "The inflammation does not involve the adaptive immune system or peripheral organs, but is rather due to the phylogenetically much older innate immune system, which appears to operate in most tissues of the body.", "Chronic inflammation can damage host tissue and the brain may be particularly vulnerable because of the postmitotic nature of neurons.", "Many of the inflammatory mediators have been shown to be locally produced and selectively elevated in affected regions of Alzheimer\u2019s brain.", "Moreover, studies of tissue in such degenerative processes as atherosclerosis and infarcted heart suggest a similar local innate immune reaction may be important in such conditions.", "Much epidemiological and limited clinical evidence suggests that nonsteroidal anti-inflammatory drugs may impede the onset and slow the progression of Alzheimer\u2019s disease.", "But these drugs strike at the periphery of the inflammatory reaction.", "Much better results might be obtained if drugs were found that could inhibit the activation of microglia or the complement system in brain, and combinations of drugs aimed at different inflammatory targets might be much more effective than single agents."], "structured": false}
{"doc_id": 17447653, "title": "BLAST+: architecture and applications", "abstract": ["BACKGROUND Sequence similarity searching is a very important bioinformatics task.", "While Basic Local Alignment Search Tool (BLAST) outperforms exact methods through its use of heuristics, the speed of the current BLAST software is suboptimal for very long queries or database sequences.", "There are also some shortcomings in the user-interface of the current command-line applications.   \n", "RESULTS We describe features and improvements of rewritten BLAST software and introduce new command-line applications.", "Long query sequences are broken into chunks for processing, in some cases leading to dramatically shorter run times.", "For long database sequences, it is possible to retrieve only the relevant parts of the sequence, reducing CPU time and memory usage for searches of short queries against databases of contigs or chromosomes.", "The program can now retrieve masking information for database sequences from the BLAST databases.", "A new modular software library can now access subject sequence data from arbitrary data sources.", "We introduce several new features, including strategy files that allow a user to save and reuse their favorite set of options.", "The strategy files can be uploaded to and downloaded from the NCBI BLAST web site.   \n", "CONCLUSION The new BLAST command-line applications, compared to the current BLAST tools, demonstrate substantial speed improvements for long queries as well as chromosome length database sequences.", "We have also improved the user interface of the command-line applications."], "structured": true}
{"doc_id": 17450673, "title": "Intrauterine environments and breast cancer risk: meta-analysis and systematic review", "abstract": ["INTRODUCTION Various perinatal factors, including birth weight, birth order, maternal age, gestational age, twin status, and parental smoking, have been postulated to affect breast cancer risk in daughters by altering the hormonal environment of the developing fetal mammary glands.", "Despite ample biologic plausibility, epidemiologic studies to date have yielded conflicting results.", "We investigated the associations between perinatal factors and subsequent breast cancer risk through meta-analyses.   \n", "METHODS We reviewed breast cancer studies published from January 1966 to February 2007 that included data on birth weight, birth order, maternal age, gestational age, twin status, and maternal or paternal smoking.", "Meta-analyses using random effect models were employed to summarize the results.   \n", "RESULTS We found that heavier birth weights were associated with increased breast cancer risk, with studies involving five categories of birth weight identifying odds ratios (ORs) of 1.24 (95% confidence interval [CI] 1.04 to 1.48) for 4,000 g or more and 1.15 (95% CI 1.04 to 1.26) for 3,500 g to 3,999 g, relative to a birth weight of 2,500 to 2,599 g. These studies provided no support for a J-shaped relationship of birthweight to risk.", "Support for an association with birthweight was also derived from studies based on three birth weight categories (OR 1.15 [95% CI 1.01 to 1.31] for > or =4,000 g relative to <3,000 g) and two birth weight categories (OR 1.09 [95% CI 1.02 to 1.18] for > or =3,000 g relative to <3,000 g).", "Women born to older mothers and twins were also at some increased risk, but the results were heterogeneous across studies and publication years.", "Birth order, prematurity, and maternal smoking were unrelated to breast cancer risk.   \n", "CONCLUSION Our findings provide some support for the hypothesis that in utero exposures reflective of higher endogenous hormone levels could affect risk for development of breast cancer in adulthood."], "structured": true}
{"doc_id": 17454301, "title": "Epidemiologic studies on Dengue in Santiago de Cuba, 1997.", "abstract": ["A small, isolated outbreak of dengue hemorrhagic fever/dengue shock syndrome (DHF/DSS) due to dengue virus type 2 (DEN-2) was documented in Santiago de Cuba on the island of Cuba beginning in January 1997.", "There were 205 DHF/DSS cases, all in persons older than age 15 years.", "All but three had evidence of a prior dengue infection, with the only known opportunity being the islandwide dengue virus type 1 (DEN-1) epidemic of 1977-1979.", "Virtually complete clinical and laboratory surveillance of overt disease was achieved.", "From December 1997 to January 1998, a random, age-stratified serum sample was obtained from 1,151 persons in 40 residential clusters in Santiago.", "Sera were tested for DEN-1 and DEN-2 neutralizing antibodies.", "The prevalence of DEN-2 antibodies in children age 15 years and under, born after the 1981 DEN-2 epidemic, was taken as the 1997 DEN-2 infection rate.", "This was adjusted slightly to accommodate observed cases, resulting in an estimated infection rate of 4.3%.", "Dengue fever and DHF/DSS attack rates were calculated from estimated total primary and secondary DEN-2 infections.", "Only 3% of 13,116 primary infections were overt.", "The DHF/DSS attack rate for adults of all ages was 420 per 10,000 secondary DEN-2 infections."], "structured": false}
{"doc_id": 17462437, "title": "Prognostic and Predictive Value of KRAS Mutations in Advanced Non-Small Cell Lung Cancer", "abstract": ["Clinical implications of KRAS mutations in advanced non-small cell lung cancer remain unclear.", "We retrospectively evaluated the prognostic and predictive value of KRAS mutations in patients with advanced NSCLC.", "Among 484 patients with available results for both KRAS and EGFR mutations, 39 (8%) had KRAS and 182 (38%) EGFR mutations, with two cases having both mutations.", "The median overall survivals for patients with KRAS mutations, EGFR mutations, or both wild types were 7.7, 38.0, and 15.0 months, respectively (P<0.001).", "The KRAS mutation was an independent poor prognostic factor in the multivariate analysis (hazard ratio = 2.6, 95% CI: 1.8-3.7).", "Response rates and progression-free survival (PFS) for the pemetrexed-based regimen in the KRAS mutation group were 14% and 2.1 months, inferior to those (28% and 3.9 months) in the KRAS wild type group.", "KRAS mutation tended to be associated with inferior treatment outcomes after gemcitabine-based chemotherapy, while there was no difference regarding taxane-based regimen.", "Although the clinical outcomes to EGFR tyrosine kinase inhibitors (TKIs) seemed to be better in patients with KRAS wild type than those with KRAS mutations, there was no statistical difference in response rates and PFS according to KRAS mutation status when EGFR mutation status was considered.", "Two patients with both KRAS and EGFR mutations showed partial response to EGFR TKIs.", "Although G12D mutation appeared more frequently in never smokers, there was no difference in clinical outcomes according to KRAS genotypes.", "These results suggested KRAS mutations have an independent prognostic value but a limited predictive role for EGFR TKIs or cytotoxic chemotherapy in advanced NSCLC."], "structured": false}
{"doc_id": 17463469, "title": "A Heteroskedasticity-Consistent Covariance Matrix Estimator And A Direct Test For Heteroskedasticity", "abstract": ["This paper presents a parameter covariance matrix estimator which is consistent even when the disturbances of a linear regression model are heteroskedastic.", "This estimator does not depend on a formal model of the structure of the heteroskedasticity.", "By comparing the elements of the new estimator to those of the usual covariance estimator, one obtains a direct test for heteroskedasticity, since in the absence of heteroskedasticity, the two estimators will be approximately equal, but will generally diverge otherwise.", "The test has an appealing least squares interpretation."], "structured": false}
{"doc_id": 17463549, "title": "Two Subsets of Naive T Helper Cells with Distinct T Cell Receptor Excision Circle Content in Human Adult Peripheral Blood", "abstract": ["During ageing thymic function declines and is unable to meet the demand for peripheral T helper (Th) cell replenishment.", "Therefore, population maintenance of naive Th cells must be at least partly peripherally based.", "Such peripheral postthymic expansion of recent thymic emigrants (RTEs) during ageing consequently should lead to loss or dilution of T cell receptor excision circles (TRECs) from a subset of naive T cells.", "We have identified two subsets of naive Th cells in human adult peripheral blood characterized by a striking unequal content of TRECs, indicating different peripheral proliferative histories.", "TRECs are highly enriched in peripheral naive CD45RA+ Th cells coexpressing CD31 compared with peripheral naive CD45RA+ Th cells lacking CD31 expression, in which TRECs can hardly be detected.", "Furthermore we show that CD31\u2212CD45RA+ Th cells account for increasing percentages of the naive peripheral Th cell pool during ageing but retain phenotypic and functional features of naive Th cells.", "As CD31 is lost upon T cell receptor (TCR) engagement in vitro, we hypothesize that TCR triggering is a prerequisite for homeostatically driven peripheral postthymic expansion of human naive RTEs.", "We describe here the identification of peripherally expanded naive Th cells in human adult blood characterized by the loss of CD31 expression and a highly reduced TREC content."], "structured": false}
{"doc_id": 17464771, "title": "A Role for the Vacuolating Cytotoxin, VacA, in Colonization and Helicobacter pylori\u2013Induced Metaplasia in the Stomach", "abstract": ["Carriage of Helicobacter pylori strains producing more active (s1/i1) forms of VacA is strongly associated with gastric adenocarcinoma.", "To our knowledge, we are the first to determine effects of different polymorphic forms of VacA on inflammation and metaplasia in the mouse stomach.", "Bacteria producing the less active s2/i2 form of VacA colonized mice more efficiently than mutants null for VacA or producing more active forms of it, providing the first evidence of a positive role for the minimally active s2/i2 toxin.", "Strains producing more active toxin forms induced more severe and extensive metaplasia and inflammation in the mouse stomach than strains producing weakly active (s2/i2) toxin.", "We also examined the association in humans, controlling for cagPAI status.", "In human gastric biopsy specimens, the vacA i1 allele was strongly associated with precancerous intestinal metaplasia, with almost complete absence of intestinal metaplasia in subjects infected with i2-type strains, even in a vacA s1, cagA(+) background."], "structured": false}
{"doc_id": 17482507, "title": "Systematic review of role of bisphosphonates on skeletal morbidity in metastatic cancer.", "abstract": ["OBJECTIVE To review the evidence for the use of bisphosphonates to reduce skeletal morbidity in cancer patients with bone metastases.   \n", "DATA SOURCES Electronic databases, scanning reference lists, and consultation with experts and pharmaceutical companies.", "Foreign language papers were included.   ", "STUDY SELECTION Included trials were randomised controlled trials of patients with malignant disease and bone metastases who were treated with oral or intravenous bisphosphonate compared with another bisphosphonate, placebo, or standard care.", "All trials measured at least one outcome of skeletal morbidity.   \n", "RESULTS 95 articles were identified; 30 studies fulfilled inclusion criteria.", "In studies that lasted > or = 6 months, compared with placebo bisphosphonates significantly reduced the odds ratio for fractures (vertebral 0.69, 95% confidence interval 0.57 to 0.84, P < 0.0001; non-vertebral 0.65, 0.54 to 0.79, P < 0.0001; combined 0.65, 0.55 to 0.78, P < 0.0001), radiotherapy (0.67, 0.57 to 0.79, P < 0.0001), and hypercalcaemia (0.54, 0.36 to 0.81, P = 0.003) but not for orthopaedic surgery (0.70, 0.46 to 1.05, P = 0.086) or spinal cord compression (0.71, 0.47 to 1.08, P = 0.113).", "The reduction in orthopaedic surgery was significant in studies that lasted over a year (0.59, 0.39 to 0.88, P = 0.009).", "Use of bisphosphonates significantly increased time to first skeletal related event but did not increase survival.", "Subanalyses showed that most evidence supports use of intravenous aminobisphosphonates.   \n", "CONCLUSIONS In people with metastatic bone disease bisphosphonates significantly decrease skeletal morbidity, except for spinal cord compression and increased time to first skeletal related event.", "Treatment should start when bone metastases are diagnosed and continue until it is no longer clinically relevant."], "structured": true}
{"doc_id": 17506075, "title": "Rodent Models of Depression: Neurotrophic and Neuroinflammatory Biomarkers", "abstract": ["Rodent models are an indispensable tool for studying etiology and progress of depression.", "Since interrelated systems of neurotrophic factors and cytokines comprise major regulatory mechanisms controlling normal brain plasticity, impairments of these systems form the basis for development of cerebral pathologies, including mental diseases.", "The present review focuses on the numerous experimental rodent models of depression induced by different stress factors (exteroceptive and interoceptive) during early life (including prenatal period) or adulthood, giving emphasis to the data on the changes of neurotrophic factors and neuroinflammatory indices in the brain.", "These parameters are closely related to behavioral depression-like symptoms and impairments of neuronal plasticity and are both gender- and genotype-dependent.", "Stress-related changes in expression of neurotrophins and cytokines in rodent brain are region-specific.", "Some contradictory data reported by different groups may be a consequence of differences of stress paradigms or their realization in different laboratories.", "Like all experimental models, stress-induced depression-like conditions are experimental simplification of clinical depression states; however, they are suitable for understanding the involvement of neurotrophic factors and cytokines in the pathogenesis of the disease-a goal unachievable in the clinical reality.", "These major regulatory systems may be important targets for therapeutic measures as well as for development of drugs for treatment of depression states."], "structured": false}
{"doc_id": 17518195, "title": "The docking domain of histone H2A is required for H1 binding and RSC-mediated nucleosome remodeling", "abstract": ["Histone variants within the H2A family show high divergences in their C-terminal regions.", "In this work, we have studied how these divergences and in particular, how a part of the H2A COOH-terminus, the docking domain, is implicated in both structural and functional properties of the nucleosome.", "Using biochemical methods in combination with Atomic Force Microscopy and Electron Cryo-Microscopy, we show that the H2A-docking domain is a key structural feature within the nucleosome.", "Deletion of this domain or replacement with the incomplete docking domain from the variant H2A.Bbd results in significant structural alterations in the nucleosome, including an increase in overall accessibility to nucleases, un-wrapping of \u223c10 bp of DNA from each end of the nucleosome and associated changes in the entry/exit angle of DNA ends.", "These structural alterations are associated with a reduced ability of the chromatin remodeler RSC to both remodel and mobilize the nucleosomes.", "Linker histone H1 binding is also abrogated in nucleosomes containing the incomplete docking domain of H2A.Bbd.", "Our data illustrate the unique role of the H2A-docking domain in coordinating the structural-functional aspects of the nucleosome properties.", "Moreover, our data suggest that incorporation of a 'defective' docking domain may be a primary structural role of H2A.Bbd in chromatin."], "structured": false}
{"doc_id": 17539488, "title": "Regulation of poly(A) site choice of several yeast mRNAs", "abstract": ["Several yeast genes produce multiple transcripts with different 3'-ends.", "Of these, four genes are known to produce truncated transcripts that end within the coding sequence of longer transcripts: CBP1 , AEP2 / ATP13 , RNA14 and SIR1 .", "It has been shown that the level of the truncated CBP1 transcript increases during the switch to respiratory growth while that of the full-length transcript decreases.", "To determine whether this phenomenon is unique to CBP1 , northern analysis was used to determine whether the levels of other truncated transcripts are regulated similarly by carbon source.", "The levels of the shortest transcripts of AEP2 / ATP13 and RNA14 increased during respiration while the shortest SIR1 transcript remained constant.", "However, two longer SIR1 transcripts were regulated reciprocally by carbon source.", "Mapping the 3'-ends of each transcript by sequencing partial cDNA clones revealed multiple 3'-ends for each transcript.", "Examination of the sequences surrounding the 3'-ends of the induced transcripts failed to identify a consensus sequence but did reveal weak putative 3'-end formation signals in all of the transcripts.", "Similarly, no consensus sequence was found when the sequences surrounding the 3'-ends of the longest transcripts were compared, but again weak putative 3'-end formation signals were identified.", "These data are suggestive of carbon source regulation of alternative poly(A) site choice in yeast."], "structured": false}
{"doc_id": 17544977, "title": "Circular RNA and miR-7 in cancer.", "abstract": ["MicroRNAs (miRNA) play important roles in fine-tuning gene expression and are often deregulated in cancer.", "The identification of competing endogenous RNA and circular RNA (circRNA) as important regulators of miRNA activity underscores the increasing complexity of ncRNA-mediated regulatory networks.", "Particularly, the recently identified circular RNA, ciRS-7, which acts as a designated miR-7 inhibitor/sponge, has conceptually changed the mechanistic understanding of miRNA networks.", "As miR-7 modulates the expression of several oncogenes, disclosing the regulation of miR-7 activity will likely advance the understanding of various cancer etiologies.", "Here, we review the current knowledge about the ciRS-7/miR-7 axis in cancer-related pathways and discuss possible models explaining the relevance of coexpressing miR-7 along with a circRNA inhibitor."], "structured": false}
{"doc_id": 17546486, "title": "Angiotensin II Evokes Angiogenic Signals within Skeletal Muscle through Co-ordinated Effects on Skeletal Myocytes and Endothelial Cells", "abstract": ["Skeletal muscle overload induces the expression of angiogenic factors such as vascular endothelial growth factor (VEGF) and matrix metalloproteinase (MMP)-2, leading to new capillary growth.", "We found that the overload-induced increase in angiogenesis, as well as increases in VEGF, MMP-2 and MT1-MMP transcripts were abrogated in muscle VEGF KO mice, highlighting the critical role of myocyte-derived VEGF in controlling this process.", "The upstream mediators that contribute to overload-induced expression of VEGF have yet to be ascertained.", "We found that muscle overload increased angiotensinogen expression, a precursor of angiotensin (Ang) II, and that Ang II signaling played an important role in basal VEGF production in C2C12 cells.", "Furthermore, matrix-bound VEGF released from myoblasts induced the activation of endothelial cells, as evidenced by elevated endothelial cell phospho-p38 levels.", "We also found that exogenous Ang II elevates VEGF expression, as well as MMP-2 transcript levels in C2C12 myotubes.", "Interestingly, these responses also were observed in skeletal muscle endothelial cells in response to Ang II treatment, indicating that these cells also can respond directly to the stimulus.", "The involvement of Ang II in muscle overload-induced angiogenesis was assessed.", "We found that blockade of AT1R-dependent Ang II signaling using losartan did not attenuate capillary growth.", "Surprisingly, increased levels of VEGF protein were detected in overloaded muscle from losartan-treated rats.", "Similarly, we observed elevated VEGF production in cultured endothelial cells treated with losartan alone or in combination with Ang II.", "These studies conclusively establish the requirement for muscle derived VEGF in overload-induced angiogenesis and highlight a role for Ang II in basal VEGF production in skeletal muscle.", "However, while Ang II signaling is activated following overload and plays a role in muscle VEGF production, inhibition of this pathway is not sufficient to halt overload-induced angiogenesis, indicating that AT1-independent signals maintain VEGF production in losartan-treated muscle."], "structured": false}
{"doc_id": 17553026, "title": "A specific loop in human DNA polymerase mu allows switching between creative and DNA-instructed synthesis", "abstract": ["Human DNA polymerase mu (Pol\u03bc) is a family X member that has terminal transferase activity but, in spite of a non-orthodox selection of the template information, displays its maximal catalytic efficiency in DNA-templated reactions.", "As terminal deoxynucleotidyl transferase (TdT), Pol\u03bc has a specific loop (loop1) that could provide this enzyme with its terminal transferase activity.", "When loop1 was deleted, human Pol\u03bc lacked TdT activity but improved DNA-binding and DNA template-dependent polymerization.", "Interestingly, when loop1 from TdT was inserted in Pol\u03bc (substituting its cognate loop1), the resulting chimaera displayed TdT activity, preferentially inserting dGTP residues, but had a strongly reduced template-dependent polymerization activity.", "Therefore, a specialized loop in Pol\u03bc, that could adopt alternative conformations, appears to provide this enzyme with a dual capacity: (i) template independency to create new DNA information, in which loop1 would have an active role by acting as a \u2018pseudotemplate\u2019; (ii) template-dependent polymerization, in which loop1 must allow binding of the template strand.", "Recent in vivo and in vitro data suggest that such a dual capacity could be advantageous to resolve microhomology-mediated end-joining reactions."], "structured": false}
{"doc_id": 17587795, "title": "Dnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes", "abstract": ["Dnmt1 epigenetically propagates symmetrical CG methylation in many eukaryotes.", "Their genomes are typically depleted of CG dinucleotides because of imperfect repair of deaminated methylcytosines.", "Here, we extensively survey diverse species lacking Dnmt1 and show that, surprisingly, symmetrical CG methylation is nonetheless frequently present and catalyzed by a different DNA methyltransferase family, Dnmt5.", "Numerous Dnmt5-containing organisms that diverged more than a billion years ago exhibit clustered methylation, specifically in nucleosome linkers.", "Clustered methylation occurs at unprecedented densities and directly disfavors nucleosomes, contributing to nucleosome positioning between clusters.", "Dense methylation is enabled by a regime of genomic sequence evolution that enriches CG dinucleotides and drives the highest CG frequencies known.", "Species with linker methylation have small, transcriptionally active nuclei that approach the physical limits of chromatin compaction.", "These features constitute a previously unappreciated genome architecture, in which dense methylation influences nucleosome positions, likely facilitating nuclear processes under extreme spatial constraints."], "structured": false}
{"doc_id": 17591478, "title": "The Immunogenicity and Safety of the Live-attenuated SA 14-14-2 Japanese Encephalitis Vaccine Given with a Two-dose Primary Schedule in Children", "abstract": ["Effective and tolerable vaccination is an essential strategy to prevent Japanese encephalitis (JE) in endemic areas.", "Although the live attenuated SA 14-14-2 JE vaccine (LAJEV) has been widely used since its introduction, the systemic data of LAJEV was very rarely available in Korea.", "We conducted the open-label, prospective cohort study to assess the immunogenicity and safety of this vaccine.", "Ninety subjects were enrolled, and LAJEV in a 2-dose primary series was given with a 12-month interval.", "Neutralizing antibody titers were measured before and after each vaccination, and active monitoring for adverse events was performed.", "After the first dose, 91.1% of subjects had seroprotection with a geometric mean titer (GMT) of 40.9.", "Seroprotection rate after the second dose was 97%, and GMT showed an increase of 6.5-fold.", "Most adverse events following immunization were self-limited, and no serious adverse events were reported until 42 days after each dose.", "The 2-dose administration of LAJEV in the primary immunization schedule appeared to be highly immunogenic and safe."], "structured": false}
{"doc_id": 17601006, "title": "Centrosome-dependent asymmetric inheritance of the midbody ring in Drosophila germline stem cell division", "abstract": ["Many stem cells, including Drosophila germline stem cells (GSCs), divide asymmetrically, producing one stem cell and one differentiating daughter.", "Cytokinesis is often asymmetric, in that only one daughter cell inherits the midbody ring (MR) upon completion of abscission even in apparently symmetrically dividing cells.", "However, whether the asymmetry in cytokinesis correlates with cell fate or has functional relevance has been poorly explored.", "Here we show that the MR is asymmetrically segregated during GSC divisions in a centrosome age-dependent manner: male GSCs, which inherit the mother centrosome, exclude the MR, whereas female GSCs, which we here show inherit the daughter centrosome, inherit the MR.", "We further show that stem cell identity correlates with the mode of MR inheritance.", "Together our data suggest that the MR does not inherently dictate stem cell identity, although its stereotypical inheritance is under the control of stemness and potentially provides a platform for asymmetric segregation of certain factors."], "structured": false}
{"doc_id": 17625068, "title": "Penile Curvature Incidence in Hypospadias: Can It Be Determined?", "abstract": ["The aim was to retrospectively determine the real incidence of congenital penile curvature in various forms of hypospadias, in order to indicate intraoperative assessment and correction of curvature.", "We analyzed 842 patients with hypospadias who underwent surgery from 2003 to 2010, classified into two groups.", "First group was intraoperatively checked for curvature as a routine procedure, while a curvature in the second group was assessed mostly in severe hypospadias.", "Results are analyzed using Fisher's and chi-square tests.", "In total, 238 cases (28.3%) of associated curvature were confirmed.", "Curvature was significantly more frequent in the first group, regarding hypospadias in general (P < 0.01), as well as distal (P < 0.05) and midshaft forms (P < 0.01).", "Penile curvature is common figure in hypospadias, including distal types.", "Intraoperative testing for associated curvature should be considered as a routine procedure in hypospadias repair."], "structured": false}
{"doc_id": 17626822, "title": "Home birth and barriers to referring women with obstetric complications to hospitals: a mixed-methods study in Zahedan, southeastern Iran", "abstract": ["BACKGROUND One factor that contributes to high maternal mortality in developing countries is the delayed use of Emergency Obstetric-Care (EmOC) facilities.", "The objective of this study was to determine the factors that hinder midwives and parturient women from using hospitals when complications occur during home birth in Sistan and Baluchestan province, Iran, where 23% of all deliveries take place in non- hospital settings.   \n", "METHODS In the study and data management, a mixed-methods approach was used.", "In the quantitative phase, we compared the existing health-sector data with World Health Organization (WHO) standards for the availability and use of EmOC services.", "The qualitative phase included collection and analysis of interviews with midwives and traditional birth attendants and twenty-one in-depth interviews with mothers.", "The data collected in this phase were managed according to the principles of qualitative data analysis.   \n", "RESULTS The findings demonstrate that three distinct factors lead to indecisiveness and delay in the use of EmOC by the midwives and mothers studied.", "Socio-cultural and familial reasons compel some women to choose to give birth at home and to hesitate seeking professional emergency care for delivery complications.", "Apprehension about being insulted by physicians, the necessity of protecting their professional integrity in front of patients and an inability to persuade their patients lead to an over-insistence by midwives on completing deliveries at the mothers' homes and a reluctance to refer their patients to hospitals.", "The low quality and expense of EmOC and the mothers' lack of health insurance also contribute to delays in referral.   \n", "CONCLUSIONS Women who choose to give birth at home accept the risk that complications may arise.", "Training midwives and persuading mothers and significant others who make decisions about the value of referring women to hospitals at the onset of life-threatening complications are central factors to increasing the use of available hospitals.", "The hospitals must be safe, comfortable and attractive environments for parturition and should give appropriate consideration to the ethical and cultural concerns of the women.", "Appropriate management of financial and insurance-related issues can help midwives and mothers make a rational decision when complications arise."], "structured": true}
{"doc_id": 17628888, "title": "ATPase-Dependent Control of the Mms21 SUMO Ligase during DNA Repair", "abstract": ["Modification of proteins by SUMO is essential for the maintenance of genome integrity.", "During DNA replication, the Mms21-branch of the SUMO pathway counteracts recombination intermediates at damaged replication forks, thus facilitating sister chromatid disjunction.", "The Mms21 SUMO ligase docks to the arm region of the Smc5 protein in the Smc5/6 complex; together, they cooperate during recombinational DNA repair.", "Yet how the activity of the SUMO ligase is controlled remains unknown.", "Here we show that the SUMO ligase and the chromosome disjunction functions of Mms21 depend on its docking to an intact and active Smc5/6 complex, indicating that the Smc5/6-Mms21 complex operates as a large SUMO ligase in vivo.", "In spite of the physical distance separating the E3 and the nucleotide-binding domains in Smc5/6, Mms21-dependent sumoylation requires binding of ATP to Smc5, a step that is part of the ligase mechanism that assists Ubc9 function.", "The communication is enabled by the presence of a conserved disruption in the coiled coil domain of Smc5, pointing to potential conformational changes for SUMO ligase activation.", "In accordance, scanning force microscopy of the Smc5-Mms21 heterodimer shows that the molecule is physically remodeled in an ATP-dependent manner.", "Our results demonstrate that the ATP-binding activity of the Smc5/6 complex is coordinated with its SUMO ligase, through the coiled coil domain of Smc5 and the physical remodeling of the molecule, to promote sumoylation and chromosome disjunction during DNA repair."], "structured": false}
{"doc_id": 17631671, "title": "Cadherins in brain morphogenesis and wiring.", "abstract": ["Cadherins are Ca(2+)-dependent cell-cell adhesion molecules that play critical roles in animal morphogenesis.", "Various cadherin-related molecules have also been identified, which show diverse functions, not only for the regulation of cell adhesion but also for that of cell proliferation and planar cell polarity.", "During the past decade, understanding of the roles of these molecules in the nervous system has significantly progressed.", "They are important not only for the development of the nervous system but also for its functions and, in turn, for neural disorders.", "In this review, we discuss the roles of cadherins and related molecules in neural development and function in the vertebrate brain."], "structured": false}
{"doc_id": 17648235, "title": "Autocrine WNT signaling contributes to breast cancer cell proliferation via the canonical WNT pathway and EGFR transactivation", "abstract": ["De-regulation of the wingless and integration site growth factor (WNT) signaling pathway via mutations in APC and Axin, proteins that target \u03b2-catenin for destruction, have been linked to various types of human cancer.", "These genetic alterations rarely, if ever, are observed in breast tumors.", "However, various lines of evidence suggest that WNT signaling may also be de-regulated in breast cancer.", "Most breast tumors show hypermethylation of the promoter region of secreted Frizzled-related protein 1 (sFRP1), a negative WNT pathway regulator, leading to downregulation of its expression.", "As a consequence, WNT signaling is enhanced and may contribute to proliferation of human breast tumor cells.", "We previously demonstrated that, in addition to the canonical WNT/\u03b2-catenin pathway, WNT signaling activates the extracellular signal-regulated kinase 1/2 (ERK1/2) pathway in mouse mammary epithelial cells via epidermal growth factor receptor (EGFR) transactivation.", "Using the WNT modulator sFRP1 and short interfering RNA-mediated Dishevelled (DVL) knockdown, we interfered with autocrine WNT signaling at the ligand-receptor level.", "The impact on proliferation was measured by cell counting, YOPRO, and the MTT (3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyl-tetrazolium bromide) assay; \u03b2-catenin, EGFR, ERK1/2 activation, and PARP (poly [ADP-ribose]polymerase) cleavages were assessed by Western blotting after treatment of human breast cancer cell lines with conditioned media, purified proteins, small-molecule inhibitors, or blocking antibodies.", "Phospho-DVL and stabilized \u03b2-catenin are present in many breast tumor cell lines, indicating autocrine WNT signaling activity.", "Interfering with this loop decreases active \u03b2-catenin levels, lowers ERK1/2 activity, blocks proliferation, and induces apoptosis in MDA-MB-231, BT474, SkBr3, JIMT-1, and MCF-7 cells.", "The effects of WNT signaling are mediated partly by EGFR transactivation in human breast cancer cells in a metalloprotease- and Src-dependent manner.", "Furthermore, Wnt1 rescues estrogen receptor-positive (ER+) breast cancer cells from the anti-proliferative effects of 4-hydroxytamoxifen (4-HT) and this activity can be blocked by an EGFR tyrosine kinase inhibitor.", "Our data show that interference with autocrine WNT signaling in human breast cancer reduces proliferation and survival of human breast cancer cells and rescues ER+ tumor cells from 4-HT by activation of the canonical WNT pathway and EGFR transactivation.", "These findings suggest that interference with WNT signaling at the ligand-receptor level in combination with other targeted therapies may improve the efficiency of breast cancer treatments."], "structured": false}
{"doc_id": 17656445, "title": "Alternative Markers of Hyperglycemia and Risk of Diabetes", "abstract": ["OBJECTIVE Fructosamine, glycated albumin, and 1,5-anhydroglucitol (1,5-AG) are of interest for monitoring short-term glycemic control in patients with diabetes; however, their associations with diabetes risk are uncharacterized.   ", "RESEARCH DESIGN AND METHODS", "We used Cox proportional hazards models to examine the associations of fructosamine, glycated albumin, and 1,5-AG with incident diabetes in 1,299 participants, from the Atherosclerosis Risk in Communities (ARIC) Study (2005-2006), who had no history of diagnosed diabetes at baseline.", "Incident diabetes was self-reported during annual telephone calls.   \n", "RESULTS There were 119 new cases of diabetes during a median follow-up of 3.3 years.", "When compared with the lowest quartile, the fourth quartiles of fructosamine and glycated albumin were significantly associated with diabetes risk (hazard ratio [HR] 3.99 [95% CI 1.93-8.28] and 5.22 [2.49-10.94], respectively).", "The fourth quartile of 1,5-AG was associated with a significantly lower diabetes risk (0.27 [0.14-0.55]).", "Associations were attenuated but still significant after adjustment for hemoglobin A(1c) (A1C) or fasting glucose.   \n", "CONCLUSIONS Fructosamine, glycated albumin, and 1,5-AG were associated with the subsequent development of diabetes independently of baseline A1C and fasting glucose.", "Our results suggest these alternative biomarkers may be useful in identifying persons at risk for diabetes."], "structured": true}
{"doc_id": 17671145, "title": "ROR-\u03b3 drives androgen receptor expression and represents a therapeutic target in castration-resistant prostate cancer", "abstract": ["The androgen receptor (AR) is overexpressed and hyperactivated in human castration-resistant prostate cancer (CRPC).", "However, the determinants of AR overexpression in CRPC are poorly defined.", "Here we show that retinoic acid receptor-related orphan receptor \u03b3 (ROR-\u03b3) is overexpressed and amplified in metastatic CRPC tumors, and that ROR-\u03b3 drives AR expression in the tumors.", "ROR-\u03b3 recruits nuclear receptor coactivator 1 and 3 (NCOA1 and NCOA3, also known as SRC-1 and SRC-3) to an AR-ROR response element (RORE) to stimulate AR gene transcription.", "ROR-\u03b3 antagonists suppress the expression of both AR and its variant AR-V7 in prostate cancer (PCa) cell lines and tumors.", "ROR-\u03b3 antagonists also markedly diminish genome-wide AR binding, H3K27ac abundance and expression of the AR target gene network.", "Finally, ROR-\u03b3 antagonists suppressed tumor growth in multiple AR-expressing, but not AR-negative, xenograft PCa models, and they effectively sensitized CRPC tumors to enzalutamide, without overt toxicity, in mice.", "Taken together, these results establish ROR-\u03b3 as a key player in CRPC by acting upstream of AR and as a potential therapeutic target for advanced PCa."], "structured": false}
{"doc_id": 17676273, "title": "affy--analysis of Affymetrix GeneChip data at the probe level.", "abstract": ["MOTIVATION The processing of the Affymetrix GeneChip data has been a recent focus for data analysts.", "Alternatives to the original procedure have been proposed and some of these new methods are widely used.   \n", "RESULTS The affy package is an R package of functions and classes for the analysis of oligonucleotide arrays manufactured by Affymetrix.", "The package is currently in its second release, affy provides the user with extreme flexibility when carrying out an analysis and make it possible to access and manipulate probe intensity data.", "In this paper, we present the main classes and functions in the package and demonstrate how they can be used to process probe-level data.", "We also demonstrate the importance of probe-level analysis when using the Affymetrix GeneChip platform."], "structured": true}
{"doc_id": 17682477, "title": "Inducible caspase-9 suicide gene controls adverse effects from alloreplete T cells after haploidentical stem cell transplantation.", "abstract": ["To test the feasibility of a single T-cell manipulation to eliminate alloreactivity while sparing antiviral and antitumor T cells, we infused 12 haploidentical hematopoietic stem cell transplant patients with increasing numbers of alloreplete haploidentical T cells expressing the inducible caspase 9 suicide gene (iC9-T cells).", "We determined whether the iC9-T cells produced immune reconstitution and if any resultant graft-versus-host disease (GVHD) could be controlled by administration of a chemical inducer of dimerization (CID; AP1903/Rimiducid).", "All patients receiving >10(4) alloreplete iC9-T lymphocytes per kilogram achieved rapid reconstitution of immune responses toward 5 major pathogenic viruses and concomitant control of active infections.", "Four patients received a single AP1903 dose.", "CID infusion eliminated 85% to 95% of circulating CD3(+)CD19(+) T cells within 30 minutes, with no recurrence of GVHD within 90 days.", "In one patient, symptoms and signs of GVHD-associated cytokine release syndrome (CRS-hyperpyrexia, high levels of proinflammatory cytokines, and rash) resolved within 2 hours of AP1903 infusion.", "One patient with varicella zoster virus meningitis and acute GVHD had iC9-T cells present in the cerebrospinal fluid, which were reduced by >90% after CID.", "Notably, virus-specific T cells recovered even after AP1903 administration and continued to protect against infection.", "Hence, alloreplete iC9-T cells can reconstitute immunity posttransplant and administration of CID can eliminate them from both peripheral blood and the central nervous system (CNS), leading to rapid resolution of GVHD and CRS.", "The approach may therefore be useful for the rapid and effective treatment of toxicities associated with infusion of engineered T lymphocytes.", "This trial was registered at www.clinicaltrials.gov as #NCT01494103."], "structured": false}
{"doc_id": 17685207, "title": "Clonal analysis of epiblast fate during germ layer formation in the mouse embryo.", "abstract": ["The fate of cells in the epiblast at prestreak and early primitive streak stages has been studied by injecting horseradish peroxidase (HRP) into single cells in situ of 6.7-day mouse embryos and identifying the labelled descendants at midstreak to neural plate stages after one day of culture.", "Ectoderm was composed of descendants of epiblast progenitors that had been located in the embryonic axis anterior to the primitive streak.", "Embryonic mesoderm was derived from all areas of the epiblast except the distal tip and the adjacent region anterior to it: the most anterior mesoderm cells originated posteriorly, traversing the primitive streak early; labelled cells in the posterior part of the streak at the neural plate stage were derived from extreme anterior axial and paraxial epiblast progenitors; head process cells were derived from epiblast at or near the anterior end of the primitive streak.", "Endoderm descendants were most frequently derived from a region that included, but extended beyond, the region producing the head process: descendants of epiblast were present in endoderm by the midstreak stage, as well as at later stages.", "Yolk sac and amnion mesoderm developed from posterolateral and posterior epiblast.", "The resulting fate map is essentially the same as those of the chick and urodele and indicates that, despite geometrical differences, topological fate relationships are conserved among these vertebrates.", "Clonal descendants were not necessarily confined to a single germ layer or to extraembryonic mesoderm, indicating that these lineages are not separated at the beginning of gastrulation.", "The embryonic axis lengthened up to the neural plate stage by (1) elongation of the primitive streak through progressive incorporation of the expanding lateral and initially more anterior regions of epiblast and, (2) expansion of the region of epiblast immediately cranial to the anterior end of the primitive streak.", "The population doubling time of labelled cells was 7.5 h; a calculated 43% were in, or had completed, a 4th cell cycle, and no statistically significant regional differences in the number of descendants were found.", "This clonal analysis also showed that (1) growth in the epiblast was noncoherent and in most regions anisotropic and directed towards the primitive streak and (2) the midline did not act as a barrier to clonal spread, either in the epiblast in the anterior half of the axis or in the primitive streak.", "These results taken together with the fate map indicate that, while individual cells in the epiblast sheet behave independently with respect to their neighbours, morphogenetic movement during germ layer formation is coordinated in the population as a whole."], "structured": false}
{"doc_id": 17691617, "title": "Effects of a High-Intensity Functional Exercise Program on Dependence in Activities of Daily Living and Balance in Older Adults with Dementia", "abstract": ["OBJECTIVES To investigate the effects of a high-intensity functional exercise program on independence in activities of daily living (ADLs) and balance in older people with dementia and whether exercise effects differed between dementia types.   \n", "DESIGN Cluster-randomized controlled trial: Ume\u00e5 Dementia and Exercise (UMDEX) study.   \n", "SETTING Residential care facilities, Ume\u00e5, Sweden.   \n", "PARTICIPANTS Individuals aged 65 and older with a dementia diagnosis, a Mini-Mental State Examination score of 10 or greater, and dependence in ADLs (N=186).   \n", "INTERVENTION Ninety-three participants each were allocated to the high-intensity functional exercise program, comprising lower limb strength and balance exercises, and 93 to a seated control activity.   \n", "MEASUREMENTS Blinded assessors measured ADL independence using the Functional Independence Measure (FIM) and Barthel Index (BI) and balance using the Berg Balance Scale (BBS) at baseline and 4 (directly after intervention completion) and 7 months.   \n", "RESULTS Linear mixed models showed no between-group effect on ADL independence at 4 (FIM=1.3, 95% confidence interval (CI)=-1.6-4.3; BI=0.6, 95% CI=-0.2-1.4) or 7 (FIM=0.8, 95% CI=-2.2-3.8; BI=0.6, 95% CI=-0.3-1.4) months.", "A significant between-group effect on balance favoring exercise was observed at 4 months (BBS=4.2, 95% CI=1.8-6.6).", "In interaction analyses, exercise effects differed significantly between dementia types.", "Positive between-group exercise effects were found in participants with non-Alzheimer's dementia according to the FIM at 7 months and BI and BBS at 4 and 7 months.   \n", "CONCLUSION In older people with mild to moderate dementia living in residential care facilities, a 4-month high-intensity functional exercise program appears to slow decline in ADL independence and improve balance, albeit only in participants with non-Alzheimer's dementia."], "structured": true}
{"doc_id": 17693849, "title": "Effect of Health Literacy on Quality of Life amongst Patients with Ischaemic Heart Disease in Australian General Practice", "abstract": ["BACKGROUND Appropriate understanding of health information by patients with cardiovascular disease (CVD) is fundamental for better management of risk factors and improved morbidity, which can also benefit their quality of life.   \n", "OBJECTIVES To assess the relationship between health literacy and health-related quality of life (HRQoL) in patients with ischaemic heart disease (IHD), and to investigate the role of sociodemographic and clinical variables as possible confounders.   \n", "METHODS Cross-sectional study of patients with IHD recruited from a stratified sample of general practices in two Australian states (Queensland and South Australia) between 2007 and 2009.", "Health literacy was measured using a validated questionnaire and classified as inadequate, marginal, or adequate.", "Physical and mental components of HRQoL were assessed using the Medical Outcomes Study Short Form (SF12) questionnaire.", "Analyses were adjusted for confounders (sociodemographic variables, clinical history of IHD, number of CVD comorbidities, and CVD risk factors) using multiple linear regression.   \n", "RESULTS A total sample of 587 patients with IHD (mean age 72.0\u00b18.4 years) was evaluated: 76.8% males, 84.2% retired or pensioner, and 51.4% with up to secondary educational level.", "Health literacy showed a mean of 39.6\u00b16.7 points, with 14.3% (95%CI 11.8-17.3) classified as inadequate.", "Scores of the physical component of HRQoL were 39.6 (95%CI 37.1-42.1), 42.1 (95%CI 40.8-43.3) and 44.8 (95%CI 43.3-46.2) for inadequate, marginal, and adequate health literacy, respectively (p-value for trend = 0.001).", "This association persisted after adjustment for confounders.", "Health literacy was not associated with the mental component of HRQoL (p-value = 0.482).", "Advanced age, lower educational level, disadvantaged socioeconomic position, and a larger number of CVD comorbidities adversely affected both, health literacy and HRQoL.   CONCLUSION Inadequate health literacy is a contributing factor to poor physical functioning in patients with IHD.", "Increasing health literacy may improve HRQoL and reduce the impact of IHD among patients with this chronic CVD."], "structured": true}
{"doc_id": 17695748, "title": "in", "abstract": ["Transglutaminase 2 (TGase 2) is a Ca+2-dependent enzyme that catalyzes both intracellular and extracellular cross-linking reactions by transamidation of specific glutamine residues.", "TGase 2 is known to be involved in the membrane-mediated events required for glucose-stimulated insulin release from the pancreatic beta cells.", "Here we show that targeted disruption of TGase 2 impairs glucose-stimulated insulin secretion.", "TGase 2-/- mice show glucose intolerance after intraperitoneal glucose loading.", "TGase 2-/- mice manifest a tendency to develop hypoglycemia after administration of exogenous insulin as a consequence of enhanced insulin receptor substrate 2 (IRS-2) phosphorylation.", "We suggest that the increased peripheral sensitivity to insulin partially compensates for the defective secretion in this animal model.", "TGase 2-/- mouse phenotype resembles that of the maturity-onset diabetes of young (MODY) patients.", "In the course of screening for human TGase 2 gene in Italian subjects with the clinical features of MODY, we detected a missense mutation (N333S) in the active site of the enzyme.", "Collectively, these results identify TGase 2 as a potential candidate gene in type 2 diabetes."], "structured": false}
{"doc_id": 17702490, "title": "Chromatin structure and gene expression programs of human embryonic and induced pluripotent stem cells.", "abstract": ["Knowledge of both the global chromatin structure and the gene expression programs of human embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) should provide a robust means to assess whether the genomes of these cells have similar pluripotent states.", "Recent studies have suggested that ESCs and iPSCs represent different pluripotent states with substantially different gene expression profiles.", "We describe here a comparison of global chromatin structure and gene expression data for a panel of human ESCs and iPSCs.", "Genome-wide maps of nucleosomes with histone H3K4me3 and H3K27me3 modifications indicate that there is little difference between ESCs and iPSCs with respect to these marks.", "Gene expression profiles confirm that the transcriptional programs of ESCs and iPSCs show very few consistent differences.", "Although some variation in chromatin structure and gene expression was observed in these cell lines, these variations did not serve to distinguish ESCs from iPSCs."], "structured": false}
{"doc_id": 17708753, "title": "Myeloid Cells Expressing VEGF and Arginase-1 Following Uptake of Damaged Retinal Pigment Epithelium Suggests Potential Mechanism That Drives the Onset of Choroidal Angiogenesis in Mice", "abstract": ["Whilst data recognise both myeloid cell accumulation during choroidal neovascularisation (CNV) as well as complement activation, none of the data has presented a clear explanation for the angiogenic drive that promotes pathological angiogenesis.", "One possibility that is a pre-eminent drive is a specific and early conditioning and activation of the myeloid cell infiltrate.", "Using a laser-induced CNV murine model, we have identified that disruption of retinal pigment epithelium (RPE) and Bruch's membrane resulted in an early recruitment of macrophages derived from monocytes and microglia, prior to angiogenesis and contemporaneous with lesional complement activation.", "Early recruited CD11b(+) cells expressed a definitive gene signature of selective inflammatory mediators particularly a pronounced Arg-1 expression.", "Accumulating macrophages from retina and peripheral blood were activated at the site of injury, displaying enhanced VEGF expression, and notably prior to exaggerated VEGF expression from RPE, or earliest stages of angiogenesis.", "All of these initial events, including distinct VEGF (+) Arg-1(+) myeloid cells, subsided when CNV was established and at the time RPE-VEGF expression was maximal.", "Depletion of inflammatory CCR2-positive monocytes confirmed origin of infiltrating monocyte Arg-1 expression, as following depletion Arg-1 signal was lost and CNV suppressed.", "Furthermore, our in vitro data supported a myeloid cell uptake of damaged RPE or its derivatives as a mechanism generating VEGF (+) Arg-1(+) phenotype in vivo.", "Our results reveal a potential early driver initiating angiogenesis via myeloid-derived VEGF drive following uptake of damaged RPE and deliver an explanation of why CNV develops during any of the stages of macular degeneration and can be explored further for therapeutic gain."], "structured": false}
{"doc_id": 17717391, "title": "Monitoring Tumorigenesis and Senescence In Vivo with a p16INK4a-Luciferase Model", "abstract": ["Monitoring cancer and aging in vivo remains experimentally challenging.", "Here, we describe a luciferase knockin mouse (p16(LUC)), which faithfully reports expression of p16(INK4a), a tumor suppressor and aging biomarker.", "Lifelong assessment of luminescence in p16(+/LUC) mice revealed an exponential increase with aging, which was highly variable in a cohort of contemporaneously housed, syngeneic mice.", "Expression of p16(INK4a) with aging did not predict cancer development, suggesting that the accumulation of senescent cells is not a principal determinant of cancer-related death.", "In 14 of 14 tested tumor models, expression of p16(LUC) was focally activated by early neoplastic events, enabling visualization of tumors with sensitivity exceeding other imaging modalities.", "Activation of p16(INK4a) was noted in the emerging neoplasm and surrounding stromal cells.", "This work suggests that p16(INK4a) activation is a characteristic of all emerging cancers, making the p16(LUC) allele a sensitive, unbiased reporter of neoplastic transformation."], "structured": false}
{"doc_id": 17731780, "title": "The Bacteroides sp. 3_1_23 Pif1 protein is a multifunctional helicase", "abstract": ["ScPif1 DNA helicase is the prototypical member of a 5'-to-3' helicase superfamily conserved from bacteria to human and plays various roles in the maintenance of genomic homeostasis.", "While many studies have been performed with eukaryotic Pif1 helicases, including yeast and human Pif1 proteins, the potential functions and biochemical properties of prokaryotic Pif1 helicases remain largely unknown.", "Here, we report the expression, purification and biochemical analysis of Pif1 helicase from Bacteroides sp. 3_1_23 (BsPif1).", "BsPif1 binds to a large panel of DNA substrates and, in particular, efficiently unwinds partial duplex DNAs with 5'-overhang, fork-like substrates, D-loop and flap-like substrates, suggesting that BsPif1 may act at stalled DNA replication forks and enhance Okazaki fragment maturation.", "Like its eukaryotic homologues, BsPif1 resolves R-loop structures and unwinds DNA-RNA hybrids.", "Furthermore, BsPif1 efficiently unfolds G-quadruplexes and disrupts nucleoprotein complexes.", "Altogether, these results highlight that prokaryotic Pif1 helicases may resolve common issues that arise during DNA transactions.", "Interestingly, we found that BsPif1 is different from yeast Pif1, but resembles more human Pif1 with regard to substrate specificity, helicase activity and mode of action.", "These findings are discussed in the context of the possible functions of prokaryotic Pif1 helicases in vivo."], "structured": false}
{"doc_id": 17741440, "title": "Netting neutrophils in autoimmune small-vessel vasculitis", "abstract": ["Small-vessel vasculitis (SVV) is a chronic autoinflammatory condition linked to antineutrophil cytoplasm autoantibodies (ANCAs).", "Here we show that chromatin fibers, so-called neutrophil extracellular traps (NETs), are released by ANCA-stimulated neutrophils and contain the targeted autoantigens proteinase-3 (PR3) and myeloperoxidase (MPO).", "Deposition of NETs in inflamed kidneys and circulating MPO-DNA complexes suggest that NET formation triggers vasculitis and promotes the autoimmune response against neutrophil components in individuals with SVV."], "structured": false}
{"doc_id": 17755060, "title": "Control of Nutrient Stress-Induced Metabolic Reprogramming by PKC\u03b6 in Tumorigenesis", "abstract": ["Tumor cells have high-energetic and anabolic needs and are known to adapt their metabolism to be able to survive and keep proliferating under conditions of nutrient stress.", "We show that PKC\u03b6 deficiency promotes the plasticity necessary for cancer cells to reprogram their metabolism to utilize glutamine through the serine biosynthetic pathway in the absence of glucose.", "PKC\u03b6 represses the expression of two key enzymes of the pathway, PHGDH and PSAT1, and phosphorylates PHGDH at key residues to inhibit its enzymatic activity.", "Interestingly, the loss of PKC\u03b6 in mice results in enhanced intestinal tumorigenesis and increased levels of these two metabolic enzymes, whereas patients with low levels of PKC\u03b6 have a poor prognosis.", "Furthermore, PKC\u03b6 and caspase-3 activities are correlated with PHGDH levels in human intestinal tumors.", "Taken together, this demonstrates that PKC\u03b6 is a critical metabolic tumor suppressor in mouse and human cancer."], "structured": false}
{"doc_id": 17768946, "title": "XRCC4's interaction with XLF is required for coding (but not signal) end joining", "abstract": ["XRCC4 and XLF are structurally related proteins important for DNA Ligase IV function.", "XRCC4 forms a tight complex with DNA Ligase IV while XLF interacts directly with XRCC4.", "Both XRCC4 and XLF form homodimers that can polymerize as heterotypic filaments independently of DNA Ligase IV.", "Emerging structural and in vitro biochemical data suggest that XRCC4 and XLF together generate a filamentous structure that promotes bridging between DNA molecules.", "Here, we show that ablating XRCC4's affinity for XLF results in DNA repair deficits including a surprising deficit in VDJ coding, but not signal end joining.", "These data are consistent with a model whereby XRCC4/XLF complexes hold DNA ends together--stringently required for coding end joining, but dispensable for signal end joining.", "Finally, DNA-PK phosphorylation of XRCC4/XLF complexes disrupt DNA bridging in vitro, suggesting a regulatory role for DNA-PK's phosphorylation of XRCC4/XLF complexes."], "structured": false}
{"doc_id": 17775228, "title": "Loss of imprinting in colorectal cancer linked to hypomethylation of H19 and IGF2.", "abstract": ["Epigenetic alterations in human cancers include global DNA hypomethylation,gene hypomethylation and promoter hypermethylation, and loss of imprinting (LOI) of the insulin-like growth factor-II gene (IGF2).", "A mechanism for LOI described previously is hypermethylation of a differentially methylated region (DMR) upstream of the H19 gene, allowing activation of the normally silent maternal allele of IGF2.", "Here we show that this mechanism does not apply to colorectal cancers, which show hypomethylation of the H19 DMR as well as a DMR upstream of exon 3 of IGF2.", "This hypomethylation is found in both colorectal cancers and normal mucosa from the same patients, and in cell lines with somatic cell knockout of DNA methyltransferases DNMT1 and DNMT3B.", "These data suggest that hypomethylation is a mechanism for LOI, that the popular IGF2-H19 enhancer competition model for IGF2 imprinting does not apply to the human colon, and that an alternative model for LOI would involve a transcriptional repressor acting on the normally silent maternal allele of IGF2."], "structured": false}
{"doc_id": 17779800, "title": "Management of patients with sore throats in relation to guidelines: An interview study in Sweden", "abstract": ["OBJECTIVE To explore how a group of Swedish general practitioners (GPs) manage patients with a sore throat in relation to current guidelines as expressed in interviews.   \n", "DESIGN Qualitative content analysis was used to analyse semi-structured interviews.   \n", "SETTING Swedish primary care.   ", "SUBJECTS A strategic sample of 25 GPs.   \n", "MAIN OUTCOME MEASURES Perceived management of sore throat patients.   \n", "RESULTS It was found that nine of the interviewed GPs were adherent to current guidelines for sore throat and 16 were non-adherent.", "The two groups differed in terms of guideline knowledge, which was shared within the team for adherent GPs while idiosyncratic knowledge dominated for the non-adherent GPs.", "Adherent GPs had no or low concerns for bacterial infections and differential diagnosis whilst non-adherent GPs believed that in patients with a sore throat any bacterial infection should be identified and treated with antibiotics.", "Patient history and examination was mainly targeted by adherent GPs whilst for non-adherent GPs it was often redundant.", "Non-adherent GPs reported problems getting patients to abstain from antibiotics, whilst no such problems were reported in adherent GPs.   \n", "CONCLUSION This interview study of sore throat management in a strategically sampled group of Swedish GPs showed that while two-thirds were non-adherent and had a liberal attitude to antibiotics one-third were guideline adherent with a restricted view on antibiotics.", "Non-adherent GPs revealed significant knowledge gaps.", "Adherent GPs had discussed guidelines within the primary care team while non-adherent GPs had not.", "Guideline implementation thus seemed to be promoted by knowledge shared in team discussions."], "structured": true}
{"doc_id": 17805221, "title": "Catch and release: how do kinetochores hook the right microtubules during mitosis?", "abstract": ["Sport fishermen keep tension on their lines to prevent hooked fish from releasing.", "A molecular version of this angler's trick, operating at kinetochores, ensures accuracy during mitosis: the mitotic spindle attaches randomly to chromosomes and then correctly bioriented attachments are stabilized due to the tension exerted on them by opposing microtubules.", "Incorrect attachments, which lack tension, are unstable and release quickly, allowing another chance for biorientation.", "Stabilization of molecular interactions by tension also occurs in other physiological contexts, such as cell adhesion, motility, hemostasis, and tissue morphogenesis.", "Here, we review models for the stabilization of kinetochore attachments with an eye toward emerging models for other force-activated systems.", "Although attention in the mitosis field has focused mainly on one kinase-based mechanism, multiple mechanisms may act together to stabilize properly bioriented kinetochores and some principles governing other tension-sensitive systems may also apply to kinetochores."], "structured": false}
{"doc_id": 17814815, "title": "Label-free in vivo imaging of myelinated axons in health and disease with spectral confocal reflectance microscopy", "abstract": ["We report a newly developed technique for high-resolution in vivo imaging of myelinated axons in the brain, spinal cord and peripheral nerve that requires no fluorescent labeling.", "This method, based on spectral confocal reflectance microscopy (SCoRe), uses a conventional laser-scanning confocal system to generate images by merging the simultaneously reflected signals from multiple lasers of different wavelengths.", "Striking color patterns unique to individual myelinated fibers are generated that facilitate their tracing in dense axonal areas.", "These patterns highlight nodes of Ranvier and Schmidt-Lanterman incisures and can be used to detect various myelin pathologies.", "Using SCoRe we carried out chronic brain imaging up to 400 \u03bcm deep, capturing de novo myelination of mouse cortical axons in vivo.", "We also established the feasibility of imaging myelinated axons in the human cerebral cortex.", "SCoRe adds a powerful component to the evolving toolbox for imaging myelination in living animals and potentially in humans."], "structured": false}
{"doc_id": 17821387, "title": "Applicability of current staging/categorization of \u03b1-synuclein pathology and their clinical relevance", "abstract": ["In Parkinson's disease (PD) and dementia with Lewy bodies (DLB) alpha-synuclein (alphaS) pathology is seen that displays a predictable topographic distribution.", "There are two staging/categorization systems,", "i.e. Braak's and McKeith's, currently in use for the assessment of alphaS pathology.", "The aim of these diagnostic strategies in pathology is, in addition to assess the stage/severity of pathology, to assess the probabilities of the related clinical symptomatology i.e. dementia and extrapyramidal symptoms (EPS).", "Herein, we assessed the applicability of these two staging/categorization systems and the frequency of dementia and EPS in a cohort of 226 alphaS-positive-subjects.", "These subject were selected from a large autopsy sample (n = 1,720), irrespective of the clinical presentation, based on the detection of alphaS-immunoreactivity (IR) in one of the most vulnerable nuclei; in the dorsal motor nucleus of vagus, substantia nigra and basal forebrain.", "The frequency of alphaS-IR lesions in this large cohort was 14% (248 out of 1,720).", "If applicable, each of the 226 subjects with all required material available was assigned a neuropathological stage/category of PD/DLB and finally the neuropathological data was analyzed in relation to dementia and EPS.", "83% of subjects showed a distribution pattern of alphaS-IR that was compatible with the current staging/categorization systems.", "Around 55% of subjects with widespread alphaS pathology (Braak's PD stages 5-6) lacked clinical signs of dementia or EPS.", "Similarly, in respect to those subjects that fulfilled the McKeith criteria for diffuse neocortical category and displaying only mild concomitant Alzheimer's disease-related pathology, only 48% were demented and 54% displayed EPS.", "It is noteworthy that some subjects (17%) deviated from the suggested caudo-rostral propagation suggesting alternative routes of progression, perhaps due to concomitant diseases and genetic predisposition.", "In conclusion, our results do indeed confirm that current staging/categorization systems can readily be applied to most of the subjects with alphaS pathology.", "However, finding that around half of the subjects with abundant alphaS pathology remain neurologically intact is intriguing and raises the question whether we do assess the actual disease process."], "structured": false}
{"doc_id": 17829012, "title": "Batf is important for IL-4 expression in T follicular helper cells", "abstract": ["Apart from T helper (Th)-2 cells, T follicular helper (Tfh) cells are a major class of IL-4-producing T cells, required for regulation of type 2 humoral immunity; however, transcriptional control of IL-4 production in Tfh cells remains mainly unknown.", "Here, we show that the basic leucine zipper transcription factor ATF-like, Batf is important for IL-4 expression in Tfh cells rather than in canonical Th2 cells.", "Functionally, Batf in cooperation with interferon regulatory factor (IRF) 4 along with Stat3 and Stat6 trigger IL-4 production in Tfh cells by directly binding to and activation of the CNS2 region in the IL-4 locus.", "In addition, Batf-to-c-Maf signalling is an important determinant of IL-4 expression in Tfh cells.", "Batf deficiency impairs the generation of IL-4-producing Tfh cells that results in protection against allergic asthma.", "Our results thus indicate a positive role of Batf in promoting the generation of pro-allergic IL-4-producing Tfh cells."], "structured": false}
{"doc_id": 17844478, "title": "Autocrine VEGF Signaling Synergizes with EGFR in Tumor Cells to Promote Epithelial Cancer Development", "abstract": ["It is established that tumor cell-derived VEGF acts on endothelial cells to promote angiogenesis and tumor growth.", "Here, we demonstrate that in K5-SOS-dependent mouse skin tumors, autocrine VEGF is required for tumor cell proliferation in a cell-autonomous and angiogenesis-independent manner.", "VEGF is upregulated in SOS-expressing tumors, and its deletion in epidermal cells delays tumorigenesis by suppressing angiogenesis and tumor cell proliferation.", "Epidermis-specific Flt1 deletion also impairs tumorigenesis and proliferation.", "Surprisingly, complete tumor inhibition occurs in the absence of VEGF in EGFR mutant mice, demonstrating that VEGFR and EGFR synergize in neoplastic cells to promote tumor growth.", "Mechanistically, K5-SOS upregulates VEGF, Flt1, and Neuropilin-1 in an Erk-dependent manner, thereby activating an autocrine proliferation loop, whereas EGFR prevents tumor cells from apoptosis.", "Moreover, Flt1 is upregulated in human SCC, and its inhibition in SCC cells impairs proliferation.", "Thus, in addition to regulating angiogenesis, VEGF has to be considered as a potent growth factor for epidermal tumors."], "structured": false}
{"doc_id": 17876040, "title": "Discovery and development of the Polo-like kinase inhibitor volasertib in cancer therapy", "abstract": ["Owing to their integral involvement in cell cycle regulation, the Polo-like kinase (Plk) family, particularly Plk1, has emerged as an attractive therapeutic target in oncology.", "In recent years, several Plk1 inhibitors have been developed, with some agents showing encouraging results in early-phase clinical trials.", "This review focuses on volasertib (BI 6727; an investigational agent), a potent and selective Plk inhibitor.", "Volasertib has shown promising activity in various cancer cell lines and xenograft models of human cancer.", "Trials performed to date suggest that volasertib has clinical efficacy in a range of malignancies, with the most promising results seen in patients with acute myeloid leukemia (AML).", "Encouragingly, recent phase II data have demonstrated that volasertib combined with low-dose cytarabine (LDAC) was associated with higher response rates and improved event-free survival than LDAC alone in patients with previously untreated AML.", "Based on these observations, and its presumably manageable safety profile, volasertib is currently in phase III development as a potential treatment for patients with AML who are ineligible for intensive remission induction therapy.", "Given that many patients with AML are of an older age and frail, this constitutes an area of major unmet need.", "In this review, we discuss the biologic rationale for Plk1 inhibitors in cancer, the clinical development of volasertib to date in solid tumors and AML, and the future identification of biomarkers that might predict response to volasertib and help determine the role of this agent in the clinic."], "structured": false}
{"doc_id": 17877537, "title": "Babies driving robots: self-generated mobility in very young infants", "abstract": ["Self-generated mobility via locomotion is a key for the cognitive, social and motor development of young infants.", "For certain children with special needs, self-generated mobility is only attained via assistive technology such as a power wheelchair.", "Up until recently, infants under 24 months of age were not considered candidates for training in power mobility.", "Recent work in our labs and others suggest that younger infants can utilize their reaching and grasping ability to learn power mobility.", "This interdisciplinary study combines our previous work in motor development and learning in infants with special needs, and the application of robot technology for rehabilitation to determine whether young infants without structured training, would drive a mobile robot, and if so, to determine how their driving would change over multiple sessions.", "The two infants that were seen for the most sessions were the focus of this pilot study.", "Both infants increased their total session time, percentage of session time spent driving, and total path length.", "These results suggest that, without training, young infants will independently move themselves using a mobile robot.", "These results provide the foundation for training studies to advance the self-generated mobility in young infants with special needs.", "Our future studies will explore the multiple training and technology combinations to reduce the barriers to exploration via self-generated mobility, and advance the general development of infants with special needs."], "structured": false}
{"doc_id": 17897801, "title": "Effects of Abciximab on the architecture of platelet-rich clots in patients with acute myocardial infarction undergoing primary coronary intervention.", "abstract": ["BACKGROUND Abciximab plus aspirin improves the TIMI 3 flow rate of the infarct-related artery in patients treated with either percutaneous coronary intervention or thrombolysis.", "The present study investigated whether the reperfusion efficacy of abciximab relates to modifications of clot architecture in patients admitted for acute myocardial infarction (AMI).   \n", "METHODS AND RESULTS A total of 23 AMI patients in the Abciximab before Direct angioplasty and stenting in Myocardial Infarction Regarding Acute and Long term follow-up (ADMIRAL) trial received, in a double-blind fashion, either abciximab (n=13) or placebo (n=10) before primary stenting.", "Viscoelastic (G' in dyne/cm(2)) and morphological (mean platelet aggregate surface area [SAG] in micrometer(2)) indexes of ex vivo platelet-rich clots (PRC) were assessed in a double-blind fashion before and after the bolus administration of abciximab or placebo.", "G' and SAG reflect the mechanical and morphological impact of activated platelets on the PRC fibrin network, respectively.", "Abciximab administration reduced G' by 63% (P=0.0001) and SAG by 65% (P=0.0007), and no effect was seen in the placebo group.", "These abciximab-related changes increased fibrin exposure as a consequence of the platelet-aggregate surface reduction and may have improved endogenous fibrinolysis.", "These effects were identified in all patients, independent of previous heparin administration.   \n", "CONCLUSIONS Abciximab dramatically reduces platelet aggregate size and increases the fibrin accessibility of ex vivo PRC in AMI patients.", "These modifications could participate in the better coronary artery patency observed with abciximab."], "structured": true}
{"doc_id": 17911973, "title": "Natural Mutagenesis of Human Genomes by Endogenous Retrotransposons", "abstract": ["Two abundant classes of mobile elements, namely Alu and L1 elements, continue to generate new retrotransposon insertions in human genomes.", "Estimates suggest that these elements have generated millions of new germline insertions in individual human genomes worldwide.", "Unfortunately, current technologies are not capable of detecting most of these young insertions, and the true extent of germline mutagenesis by endogenous human retrotransposons has been difficult to examine.", "Here, we describe technologies for detecting these young retrotransposon insertions and demonstrate that such insertions indeed are abundant in human populations.", "We also found that new somatic L1 insertions occur at high frequencies in human lung cancer genomes.", "Genome-wide analysis suggests that altered DNA methylation may be responsible for the high levels of L1 mobilization observed in these tumors.", "Our data indicate that transposon-mediated mutagenesis is extensive in human genomes and is likely to have a major impact on human biology and diseases."], "structured": false}
{"doc_id": 17914395, "title": "Knowledge of young African American adults about heart disease: a cross-sectional survey", "abstract": ["BACKGROUND African Americans have higher rates of cardiovascular disease (CVD) mortality than other ethnic groups.", "Young adults are prime targets for intervention strategies to prevent and reduce disease risk.", "The study purpose was to determine the level of knowledge of lifestyle risk factors for CVD among young African American adults in Phoenix.", "The results will be used to guide the development of CVD outreach programs targeted to this population.", "The Health Belief Model was used as a conceptual framework.   \n", "METHODS A convenience sample of 172 African American men and women aged 18-26 years completed a questionnaire adapted from the American Heart Association national surveys.", "Descriptive statistics were compared by age, gender, education level, and health status variables including BMI, smoking status, and physical activity.   \n", "RESULTS Some aspects of heart-disease were well known among young adult African Americans.", "Knowledge of certain other important risk factors (menopause) and preventive behaviors (eating fewer animal products), however, was more variable and inconsistent among the respondents.", "Differences in knowledge of individual variables was greater by education level than by gender overall.", "Predictors of a summary CVD knowledge score included higher education, female gender, and high self-efficacy (adjusted R2 = 0.158, p < .001).", "Predictors of self-efficacy in changing CVD risk were higher education and perceived low risk of CVD (adjusted R2 = 0.064, p < .001), but these characteristics explained only 6% of the variance.   \n", "CONCLUSIONS Evaluation of baseline knowledge of CVD is essential before designing and implementing health promotion programs.", "Existing strengths and weaknesses in knowledge can guide tailoring of programs to be more effective.", "Further research would help to identify the range of other characteristics that determine knowledge and risk perception."], "structured": true}
{"doc_id": 17917408, "title": "Recent insights into the role of Notch signaling in tumorigenesis", "abstract": ["Members of the Notch family of transmembrane receptors play an important role in cell fate determination.", "Over the past decade, a role for Notch in the pathogenesis of hematologic and solid malignancies has become apparent.", "Numerous cellular functions and microenvironmental cues associated with tumorigenesis are modulated by Notch signaling, including proliferation, apoptosis, adhesion, epithelial-to-mesenchymal transition, and angiogenesis.", "It is becoming increasingly evident that Notch signaling can be both oncogenic and tumor suppressive.", "This review highlights recent findings regarding the molecular and functional aspects of Notch-mediated neoplastic transformation.", "In addition, cellular mechanisms that potentially explain the complex role of Notch in tumorigenesis are discussed."], "structured": false}
{"doc_id": 17919731, "title": "BRIEFINGS IN FUNCTIONAL GENOMICS AND PROTEOMICS. VOL 5. NO 3. 209^221 doi:10.1093/bfgp/ell028 Histone acetylation in gene regulation", "abstract": ["Genetic information is packaged in the highly dynamic nucleoprotein structure called chromatin.", "Many biological processes are regulated via post-translational modifications of key proteins.", "Acetylation of lysine residues at the N-terminal histone tails is one of the most studied covalent modifications influencing gene regulation in eukaryotic cells.", "This review focuses on the role of enzymes involved in controlling both histone and non-histone proteins acetylation levels in the cell, with particular emphasis on their effects on cancer."], "structured": false}
{"doc_id": 17925632, "title": "Efficacy of monthly tafenoquine for prophylaxis of Plasmodium vivax and multidrug-resistant P. falciparum malaria.", "abstract": ["We assessed monthly doses of tafenoquine for preventing Plasmodium vivax and multidrug-resistant P. falciparum malaria.", "In a randomized, double-blind, placebo-controlled study, 205 Thai soldiers received either a loading dose of tafenoquine 400 mg (base) daily for 3 days, followed by single monthly 400-mg doses (n = 104), or placebo (n = 101), for up to 5 consecutive months.", "In volunteers completing follow-up (96 tafenoquine and 91 placebo recipients), there were 22 P. vivax, 8 P. falciparum, and 1 mixed infection.", "All infections except 1 P. vivax occurred in placebo recipients, giving tafenoquine a protective efficacy of 97% for all malaria (95% confidence interval [CI], 82%-99%), 96% for P. vivax malaria (95% CI, 76%-99%), and 100% for P. falciparum malaria (95% CI, 60%-100%).", "Monthly tafenoquine was safe, well tolerated, and highly effective in preventing P. vivax and multidrug-resistant P. falciparum malaria in Thai soldiers during 6 months of prophylaxis."], "structured": false}
{"doc_id": 17930286, "title": "Headache, migraine, and structural brain lesions and function: population based Epidemiology of Vascular Ageing-MRI study", "abstract": ["OBJECTIVE To evaluate the association of overall and specific headaches with volume of white matter hyperintensities, brain infarcts, and cognition.   \n", "DESIGN Population based, cross sectional study.   \n", "SETTING Epidemiology of Vascular Ageing study, Nantes, France.   \n", "PARTICIPANTS 780 participants (mean age 69, 58.5% women) with detailed headache assessment.   \n", "MAIN OUTCOME MEASURES Brain scans were evaluated for volume of white matter hyperintensities (by fully automated imaging processing) and for classification of infarcts (by visual reading with a standardised assessment grid).", "Cognitive function was assessed by a battery of tests including the mini-mental state examination.   \n", "RESULTS 163 (20.9%) participants reported a history of severe headache and 116 had migraine, of whom 17 (14.7%) reported aura symptoms.", "An association was found between any history of severe headache and increasing volume of white matter hyperintensities.", "The adjusted odds ratio of being in the highest third for total volume of white matter hyperintensities was 2.0 (95% confidence interval 1.3 to 3.1, P for trend 0.002) for participants with any history of severe headache when compared with participants without severe headache being in the lowest third.", "The association pattern was similar for all headache types.", "Migraine with aura was the only headache type strongly associated with volume of deep white matter hyperintensities (highest third odds ratio 12.4, 1.6 to 99.4, P for trend 0.005) and with brain infarcts (3.4, 1.2 to 9.3).", "The location of infarcts was predominantly outside the cerebellum and brain stem.", "Evidence was lacking for cognitive impairment for any headache type with or without brain lesions.   \n", "CONCLUSIONS In this population based study, any history of severe headache was associated with an increased volume of white matter hyperintensities.", "Migraine with aura was the only headache type associated with brain infarcts.", "Evidence that headache of any type by itself or in combination with brain lesions was associated with cognitive impairment was lacking."], "structured": true}
{"doc_id": 17933691, "title": "Characterization of adipocytes derived from fibro/adipogenic progenitors resident in human skeletal muscle", "abstract": ["A population of fibro/adipogenic but non-myogenic progenitors located between skeletal muscle fibers was recently discovered.", "The aim of this study was to determine the extent to which these progenitors differentiate into fully functional adipocytes.", "The characterization of muscle progenitor-derived adipocytes is a central issue in understanding muscle homeostasis.", "They are considered as being the cellular origin of intermuscular adipose tissue that develops in several pathophysiological situations.", "Here fibro/adipogenic progenitors were isolated from a panel of 15 human muscle biopsies on the basis of the specific cell-surface immunophenotype CD15+/PDGFR\u03b1+CD56-.", "This allowed investigations of their differentiation into adipocytes and the cellular functions of terminally differentiated adipocytes.", "Adipogenic differentiation was found to be regulated by the same effectors as those regulating differentiation of progenitors derived from white subcutaneous adipose tissue.", "Similarly, basic adipocyte functions, such as triglyceride synthesis and lipolysis occurred at levels similar to those observed with subcutaneous adipose tissue progenitor-derived adipocytes.", "However, muscle progenitor-derived adipocytes were found to be insensitive to insulin-induced glucose uptake, in association with the impairment of phosphorylation of key insulin-signaling effectors.", "Our findings indicate that muscle adipogenic progenitors give rise to bona fide white adipocytes that have the unexpected feature of being insulin-resistant."], "structured": false}
{"doc_id": 17934082, "title": "Membrane lipids in invadopodia and podosomes: Key structures for cancer invasion and metastasis", "abstract": ["Invadopodia are extracellular matrix (ECM)-degrading protrusions formed by invasive cancer cells.", "Podosomes are structures functionally similar to invadopodia that are found in oncogene-transformed fibroblasts and monocyte-derived cells, including macrophages and osteoclasts.", "These structures are thought to play important roles in the pericellular remodeling of ECM during cancer invasion and metastasis.", "Much effort has been directed toward identification of the molecular components and regulators of invadopodia/podosomes, which could be therapeutic targets in the treatment of malignant cancers.", "However, it remains largely unknown how these components are assembled into invadopodia/podosomes and how the assembly process is spatially and temporally regulated.", "This review will summarize recent progress on the molecular mechanisms of invadopodia/podosome formation, with strong emphasis on the roles of lipid rafts and phosphoinositides."], "structured": false}
{"doc_id": 17934603, "title": "CCR2 and CXCR4 regulate peripheral blood monocyte pharmacodynamics and link to efficacy in experimental autoimmune encephalomyelitis", "abstract": ["BACKGROUND CCR2 plays a key role in regulating monocyte trafficking to sites of inflammation and therefore has been the focus of much interest as a target for inflammatory disease.   \n", "METHODS Here we examined the effects of CCR2 blockade with a potent small molecule antagonist to determine the pharmacodynamic consequences on the peripheral blood monocyte compartment in the context of acute and chronic inflammatory processes.   \n", "RESULTS We demonstrate that CCR2 antagonism in vivo led to a rapid decrease in the number of circulating Ly6Chi monocytes and that this decrease was largely due to the CXCR4-dependent sequestration of these cells in the bone marrow, providing pharmacological evidence for a mechanism by which monocyte dynamics are regulated in vivo.", "CCR2 antagonism led to an accumulation of circulating CCL2 and CCL7 levels in the blood, indicating a role for CCR2 in regulating the levels of its ligands under homeostatic conditions.", "Finally, we show that the pharmacodynamic changes due to CCR2 antagonism were apparent after chronic dosing in mouse experimental autoimmune encephalomyelitis, a model in which CCR2 blockade demonstrated a dramatic reduction in disease severity, manifest in a reduced accumulation of monocytes and other cells in the CNS.   \n", "CONCLUSION CCR2 antagonism in vivo has tractable pharmacodynamic effects that can be used to align target engagement with biologic effects on disease activity."], "structured": true}
{"doc_id": 17939443, "title": "Displacement of a DNA binding protein by Dda helicase", "abstract": ["Bacteriophage T4 Dda helicase has recently been shown to be active as a monomer for unwinding of short duplex oligonucleotides and for displacing streptavidin from 3\u2032-biotinylated oligonucleotides.", "However, its activity for streptavidin displacement and DNA unwinding has been shown to increase as the number of Dda molecules bound to the substrate molecule increases.", "A substrate was designed to address the ability of Dda to displace DNA binding proteins.", "A DNA binding site for the Escherichia coli trp repressor was introduced into an oligonucleotide substrate for Dda helicase containing single-stranded overhang.", "Here we show that a Dda monomer is insufficient to displace the E.coli trp repressor from dsDNA under single turnover conditions, although the substrate is unwound and the repressor displaced when the single-stranded overhang is long enough to accommodate two Dda molecules.", "The quantity of product formed increases when the substrate is able to accommodate more than two Dda molecules.", "These results indicate that multiple Dda molecules act to displace DNA binding proteins in a manner that correlates with the DNA unwinding activity and streptavidin displacement activity.", "We suggest a cooperative inchworm model to describe the activities of Dda helicase."], "structured": false}
{"doc_id": 17945638, "title": "Control of Developmental Regulators by Polycomb in Human Embryonic Stem Cells", "abstract": ["Polycomb group proteins are essential for early development in metazoans, but their contributions to human development are not well understood.", "We have mapped the Polycomb Repressive Complex 2 (PRC2) subunit SUZ12 across the entire nonrepeat portion of the genome in human embryonic stem (ES) cells.", "We found that SUZ12 is distributed across large portions of over two hundred genes encoding key developmental regulators.", "These genes are occupied by nucleosomes trimethylated at histone H3K27, are transcriptionally repressed, and contain some of the most highly conserved noncoding elements in the genome.", "We found that PRC2 target genes are preferentially activated during ES cell differentiation and that the ES cell regulators OCT4, SOX2, and NANOG cooccupy a significant subset of these genes.", "These results indicate that PRC2 occupies a special set of developmental genes in ES cells that must be repressed to maintain pluripotency and that are poised for activation during ES cell differentiation."], "structured": false}
{"doc_id": 17967608, "title": "PAD4 is essential for antibacterial innate immunity mediated by neutrophil extracellular traps", "abstract": ["Neutrophils trap and kill bacteria by forming highly decondensed chromatin structures, termed neutrophil extracellular traps (NETs).", "We previously reported that histone hypercitrullination catalyzed by peptidylarginine deiminase 4 (PAD4) correlates with chromatin decondensation during NET formation.", "However, the role of PAD4 in NET-mediated bacterial trapping and killing has not been tested.", "Here, we use PAD4 knockout mice to show that PAD4 is essential for NET-mediated antibacterial function.", "Unlike PAD4(+/+) neutrophils, PAD4(-/-) neutrophils cannot form NETs after stimulation with chemokines or incubation with bacteria, and are deficient in bacterial killing by NETs.", "In a mouse infectious disease model of necrotizing fasciitis, PAD4(-/-) mice are more susceptible to bacterial infection than PAD4(+/+) mice due to a lack of NET formation.", "Moreover, we found that citrullination decreased the bacterial killing activity of histones and nucleosomes, which suggests that PAD4 mainly plays a role in chromatin decondensation to form NETs instead of increasing histone-mediated bacterial killing.", "Our results define a role for histone hypercitrullination in innate immunity during bacterial infection."], "structured": false}
{"doc_id": 17973161, "title": "Human \u2018brite / beige\u2019 adipocytes develop from capillary networks and their implantation improves metabolic homeostasis in mice", "abstract": ["Uncoupling protein 1 (UCP1) is highly expressed in brown adipose tissue, where it generates heat by uncoupling electron transport from ATP production.", "UCP1 is also found outside classical brown adipose tissue depots, in adipocytes that are termed 'brite' (brown-in-white) or 'beige'.", "In humans, the presence of brite or beige (brite/beige) adipocytes is correlated with a lean, metabolically healthy phenotype, but whether a causal relationship exists is not clear.", "Here we report that human brite/beige adipocyte progenitors proliferate in response to pro-angiogenic factors, in association with expanding capillary networks.", "Adipocytes formed from these progenitors transform in response to adenylate cyclase activation from being UCP1 negative to being UCP1 positive, which is a defining feature of the beige/brite phenotype, while displaying uncoupled respiration.", "When implanted into normal chow-fed, or into high-fat diet (HFD)-fed, glucose-intolerant NOD-scid IL2rg(null) (NSG) mice, brite/beige adipocytes activated in vitro enhance systemic glucose tolerance.", "These adipocytes express neuroendocrine and secreted factors, including the pro-protein convertase PCSK1, which is strongly associated with human obesity.", "Pro-angiogenic conditions therefore drive the proliferation of human beige/brite adipocyte progenitors, and activated beige/brite adipocytes can affect systemic glucose homeostasis, potentially through a neuroendocrine mechanism."], "structured": false}
{"doc_id": 17973630, "title": "Mindfulness meditation and improvement in sleep quality and daytime impairment among older adults with sleep disturbances: a randomized clinical trial.", "abstract": ["IMPORTANCE Sleep disturbances are most prevalent among older adults and often go untreated.", "Treatment options for sleep disturbances remain limited, and there is a need for community-accessible programs that can improve sleep.   \n", "OBJECTIVE To determine the efficacy of a mind-body medicine intervention, called mindfulness meditation, to promote sleep quality in older adults with moderate sleep disturbances.   \n", "DESIGN, SETTING, AND PARTICIPANTS Randomized clinical trial with 2 parallel groups conducted from January 1 to December 31, 2012, at a medical research center among an older adult sample (mean [SD] age, 66.3 [7.4] years) with moderate sleep disturbances (Pittsburgh Sleep Quality Index [PSQI] >5).   \n", "INTERVENTIONS A standardized mindful awareness practices (MAPs) intervention (n = 24) or a sleep hygiene education (SHE) intervention (n = 25) was randomized to participants, who received a 6-week intervention (2 hours per week) with assigned homework.   \n", "MAIN OUTCOMES AND MEASURES The study was powered to detect between-group differences in moderate sleep disturbance measured via the PSQI at postintervention.", "Secondary outcomes pertained to sleep-related daytime impairment and included validated measures of insomnia symptoms, depression, anxiety, stress, and fatigue, as well as inflammatory signaling via nuclear factor (NF)-\u03baB.   RESULTS Using an intent-to-treat analysis, participants in the MAPs group showed significant improvement relative to those in the SHE group on the PSQI.", "With the MAPs intervention, the mean (SD) PSQIs were 10.2 (1.7) at baseline and 7.4 (1.9) at postintervention.", "With the SHE intervention, the mean (SD) PSQIs were 10.2 (1.8) at baseline and 9.1 (2.0) at postintervention.", "The between-group mean difference was 1.8 (95% CI, 0.6-2.9), with an effect size of 0.89.", "The MAPs group showed significant improvement relative to the SHE group on secondary health outcomes of insomnia symptoms, depression symptoms, fatigue interference, and fatigue severity (P < .05 for all).", "Between-group differences were not observed for anxiety, stress, or NF-\u03baB, although NF-\u03baB concentrations significantly declined over time in both groups (P < .05).   \n", "CONCLUSIONS AND RELEVANCE The use of a community-accessible MAPs intervention resulted in improvements in sleep quality at immediate postintervention, which was superior to a highly structured SHE intervention.", "Formalized mindfulness-based interventions have clinical importance by possibly serving to remediate sleep problems among older adults in the short term, and this effect appears to carry over into reducing sleep-related daytime impairment that has implications for quality of life.   \n", "TRIAL REGISTRATION clinicaltrials.gov Identifier: NCT01534338."], "structured": true}
{"doc_id": 17991818, "title": "THE ORIGIN AND DIFFERENTIATION OF MICROGLIAL CELLS DURING DEVELOPMENT", "abstract": ["Some authors claim that microglia originate from the neuroepithelium, although most now believe that microglial cells are of mesodermal origin, and probably belong to the monocyte/macrophage cell line.", "These cells must enter the developing central nervous system (CNS) from the blood stream, the ventricular space or the meninges.", "Afterward microglial cells are distributed more or less homogeneously through the entire nervous parenchyma.", "Stereotyped patterns of migration have been recognized during development, in which long-distance tangential migration precedes radial migration of individual cells.", "Microglial cells moving through the nervous parenchyma are ameboid microglia, which apparently differentiate into ramified microglia after reaching their definitive location.", "This is supported by the presence of cells showing intermediate features between those of ameboid and ramified microglia.", "The factors that control the invasion of the nervous parenchyma, migration within the developing CNS and differentiation of microglial cells are not well known.", "These phenomena apparently depend on environmental factors such as soluble or cell-surface bound molecules and components of the extracellular matrix.", "Microglial cells within the developing CNS are involved in clearing cell debris and withdrawing misdirected or transitory axons, and presumably support cell survival and neurite growth."], "structured": false}
{"doc_id": 17997584, "title": "Integrin \u03b1v\u03b28-Mediated TGF-\u03b2 Activation by Effector Regulatory T Cells Is Essential for Suppression of T-Cell-Mediated Inflammation", "abstract": ["Regulatory T (Treg) cells play a pivotal role in suppressing self-harmful T cell responses, but how Treg cells mediate suppression to maintain immune homeostasis and limit responses during inflammation is unclear.", "Here we show that effector Treg cells express high amounts of the integrin \u03b1v\u03b28, which enables them to activate latent transforming growth factor-\u03b2 (TGF-\u03b2).", "Treg-cell-specific deletion of integrin \u03b1v\u03b28 did not result in a spontaneous inflammatory phenotype, suggesting that this pathway is not important in Treg-cell-mediated maintenance of immune homeostasis.", "However, Treg cells lacking expression of integrin \u03b1v\u03b28 were unable to suppress pathogenic T cell responses during active inflammation.", "Thus, our results identify a mechanism by which Treg cells suppress exuberant immune responses, highlighting a key role for effector Treg-cell-mediated activation of latent TGF-\u03b2 in suppression of self-harmful T cell responses during active inflammation."], "structured": false}
{"doc_id": 18025240, "title": "Effects of treatment for intestinal helminth infection on growth and cognitive performance in children: systematic review of randomised trials.", "abstract": ["OBJECTIVE To summarise the effects of anthelmintic drug treatment on growth and cognitive performance in children.   \n", "DATA SOURCES Electronic databases: Cochrane Infectious Diseases Group controlled trial register, Cochrane controlled trials register, Embase, and Medline.", "Citations of all identified trials.", "Contact with the World Health Organization and field researchers.   ", "REVIEW METHODS Systematic review of randomised controlled trials in children aged 1-16 that compared anthelmintic treatment with placebo or no treatment.", "Assessment of validity and data abstraction conducted independently by two reviewers.   \n", "MAIN OUTCOME MEASURES Growth and cognitive performance.   \n", "RESULTS Thirty randomised controlled trials in more than 15 000 children were identified.", "Effects on mean weight were unremarkable, and heterogeneity was evident in the results.", "There were some positive effects on mean weight change in the trials reporting this outcome: after a single dose (any anthelmintic) the pooled estimates were 0.24 kg (95% confidence interval 0.15 kg to 0.", "32 kg; fixed effects model assumed) and 0.38 kg (0.01 kg to 0.77 kg; random effects model assumed).", "Results from trials of multiple doses showed mean weight change in up to one year of follow up of 0.10 kg (0.04 kg to 0.17 kg; fixed effects) or 0.15 kg (0.00 to 0.30; random effects).", "At more than one year of follow up, mean weight change was 0.12 kg (-0.02 kg to 0.26 kg; fixed effects) and 0.43 (-0.61 to 1. 47; random effects).", "Results from studies of cognitive performance were inconclusive.   \n", "CONCLUSIONS There is some limited evidence that routine treatment of children in areas where helminths are common has effects on weight gain, but this is not consistent between trials.", "There is insufficient evidence as to whether this intervention improves cognitive performance."], "structured": true}
{"doc_id": 18027063, "title": "Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences.", "abstract": ["Although phylogenetic inference of protein-coding sequences continues to dominate the literature, few analyses incorporate evolutionary models that consider the genetic code.", "This problem is exacerbated by the exclusion of codon-based models from commonly employed model selection techniques, presumably due to the computational cost associated with codon models.", "We investigated an efficient alternative to standard nucleotide substitution models, in which codon position (CP) is incorporated into the model.", "We determined the most appropriate model for alignments of 177 RNA virus genes and 106 yeast genes, using 11 substitution models including one codon model and four CP models.", "The majority of analyzed gene alignments are best described by CP substitution models, rather than by standard nucleotide models, and without the computational cost of full codon models.", "These results have significant implications for phylogenetic inference of coding sequences as they make it clear that substitution models incorporating CPs not only are a computationally realistic alternative to standard models but may also frequently be statistically superior."], "structured": false}
{"doc_id": 18037805, "title": "Polycomb Proteins Remain Bound to Chromatin and DNA during DNA Replication In Vitro", "abstract": ["The transcriptional status of a gene can be maintained through multiple rounds of cell division during development.", "This epigenetic effect is believed to reflect heritable changes in chromatin folding and histone modifications or variants at target genes, but little is known about how these chromatin features are inherited through cell division.", "A particular challenge for maintaining transcription states is DNA replication, which disrupts or dilutes chromatin-associated proteins and histone modifications.", "PRC1-class Polycomb group protein complexes are essential for development and are thought to heritably silence transcription by altering chromatin folding and histone modifications.", "It is not known whether these complexes and their effects are maintained during DNA replication or subsequently re-established.", "We find that when PRC1-class Polycomb complex-bound chromatin or DNA is replicated in vitro, Polycomb complexes remain bound to replicated templates.", "Retention of Polycomb proteins through DNA replication may contribute to maintenance of transcriptional silencing through cell division."], "structured": false}
{"doc_id": 18038250, "title": "Control of CNS Cell-Fate Decisions by SHP-2 and Its Dysregulation in Noonan Syndrome", "abstract": ["Within the developing mammalian CNS, growth factors direct multipotent precursors to generate neurons versus glia, a process that if perturbed might lead to neural dysfunction.", "In this regard, genetic mutations resulting in constitutive activation of the protein tyrosine phosphatase SHP-2 cause Noonan Syndrome (NS), which is associated with learning disabilities and mental retardation.", "Here, we demonstrate that genetic knockdown of SHP-2 in cultured cortical precursors or in the embryonic cortex inhibited basal neurogenesis and caused enhanced and precocious astrocyte formation.", "Conversely, expression of an NS SHP-2 mutant promoted neurogenesis and inhibited astrogenesis.", "Neural cell-fate decisions were similarly perturbed in a mouse knockin model that phenocopies human NS.", "Thus, SHP-2 instructs precursors to make neurons and not astrocytes during the neurogenic period, and perturbations in the relative ratios of these two cell types upon constitutive SHP-2 activation may contribute to the cognitive impairments in NS patients."], "structured": false}
{"doc_id": 18038955, "title": "Global Regulation of H2A.Z Localization by the INO80 Chromatin-Remodeling Enzyme Is Essential for Genome Integrity", "abstract": ["INO80 is an evolutionarily conserved, ATP-dependent chromatin-remodeling enzyme that plays roles in transcription, DNA repair, and replication.", "Here, we show that yeast INO80 facilitates these diverse processes at least in part by controlling genome-wide distribution of the histone variant H2A.Z. In the absence of INO80, H2A.Z nucleosomes are mislocalized, and H2A.Z levels at promoters show reduced responsiveness to transcriptional changes, suggesting that INO80 controls H2A.Z dynamics.", "Additionally, we demonstrate that INO80 has a histone-exchange activity in which the enzyme can replace nucleosomal H2A.Z/H2B with free H2A/H2B dimers.", "Genetic interactions between ino80 and htz1 support a model in which INO80 catalyzes the removal of unacetylated H2A.Z from chromatin as a mechanism to promote genome stability."], "structured": false}
{"doc_id": 18041692, "title": "Rho GTPase signalling in cell migration", "abstract": ["Cells migrate in multiple different ways depending on their environment, which includes the extracellular matrix composition, interactions with other cells, and chemical stimuli.", "For all types of cell migration, Rho GTPases play a central role, although the relative contribution of each Rho GTPase depends on the environment and cell type.", "Here, I review recent advances in our understanding of how Rho GTPases contribute to different types of migration, comparing lamellipodium-driven versus bleb-driven migration modes.", "I also describe how cells migrate across the endothelium.", "In addition to Rho, Rac and Cdc42, which are well known to regulate migration, I discuss the roles of other less-well characterized members of the Rho family."], "structured": false}
{"doc_id": 18042803, "title": "A Novel Adaptor Protein Orchestrates Receptor Patterning and Cytoskeletal Polarity in T-Cell Contacts", "abstract": ["Recognition of antigen by T cells requires the formation of a specialized junction between the T cell and the antigen-presenting cell.", "This junction is generated by the recruitment and the exclusion of specific proteins from the contact area.", "The mechanisms that regulate these events are unknown.", "Here we demonstrate that ligand engagement of the adhesion molecule, CD2, initiates a process of protein segregation, CD2 clustering, and cytoskeletal polarization.", "Although protein segregation was not dependent on the cytoplasmic domain of CD2, CD2 clustering and cytoskeletal polarization required an interaction of the CD2 cytoplasmic domain with a novel SH3-containing protein.", "This novel protein, called CD2AP, is likely to facilitate receptor patterning in the contact area by linking specific adhesion receptors to the cytoskeleton."], "structured": false}
{"doc_id": 18062308, "title": "Operable non-small cell lung cancer diagnosed by transpleural techniques : do they affect relapse and prognosis?", "abstract": ["STUDY OBJECTIVE We assessed whether transpleural methods for diagnosing peripheral lung cancer, such as needle aspiration or tumor excision, affect relapse and prognosis, because these techniques have potential to spread malignant cells from the tumor.   \n", "DESIGN A retrospective study.   \n", "SETTING National referral hospital.   \n", "PATIENTS We reviewed 239 patients who underwent surgery between 1990 and 1998 and for whom non-small cell lung cancer (NSCLC) of < 3 cm in maximum diameter was completely resected.", "The duration of postoperative follow-up ranged from 12 to 105 months, with a median period of 45 months.   \n", "INTERVENTIONS We defined the transbronchial method as using a bronchoscope, and the transpleural method as using needle aspiration cytology or tumor excision.", "Dichotomous variables included gender, histologic type of squamous cell carcinoma or other type of carcinoma, pathologic stage, and whether the diagnostic method was the transbronchial type only (first-line method) or the transpleural type (second-line method).   \n", "RESULTS NSCLC was diagnosed in 45 patients by the transpleural technique and in 194 patients by the transbronchial technique.", "There were no significant statistical differences in age of patients, gender, histologic type, pathologic stage, and tumor size.", "There were 42 relapses, 7 in the transpleural technique group and 35 in the transbronchial technique group (p = 0.90).", "Of the 7 patients in the transpleural group, there were 4 distant metastasis and 3 local relapses; of the 35 patients in the transbronchial group, there were 20 distant metastasis and 15 local relapses (p = 0.99).", "Pleural carcinomatosis occurred in none of the 45 patients in the transpleural group and in 1 case (0.5%) in the 194 patients in the transbronchial group (p = 0.99).", "Patients in the transpleural group had a statistically better 5-year survival rate than patients in the transbronchial group (79.4% vs 60.3%, p = 0.04).", "This is also confirmed as an independent prognostic factor in a multivariate analysis.   \n", "CONCLUSIONS Transpleural methods seem to be an advisable way to diagnose operable lung cancer that is difficult to diagnose using bronchoscopy, because these methods did not affect relapse and prognosis in the patients in our study."], "structured": true}
{"doc_id": 18064113, "title": "Characterization of the adipocyte cellular lineage in vivo", "abstract": ["Mature adipocytes are generated through the proliferation and differentiation of precursor cells.", "Our previous studies identified adipocyte progenitors in white adipose tissue (WAT) as Lin(-):CD29(+):CD34(+):Sca-1(+):CD24(+) (CD24(+)) cells that are capable of generating functional WAT (ref.  ).", "Here, we employ several Cre recombinase mouse models to identify the adipocyte cellular lineage in vivo.", "Although it has been proposed that white adipocytes are derived from endothelial and haematopoietic lineages, we find that neither of these lineages label white adipocytes.", "However, platelet-derived growth factor receptor \u03b1 (PdgfR\u03b1)-Cre trace labels all white adipocytes.", "Analysis of WAT from PdgfR\u03b1-Cre reporter mice identifies CD24(+) and Lin(-):CD29(+):CD34(+):Sca-1(+): CD24(-) (CD24(-)) cells as adipocyte precursors.", "We show that CD24(+) cells generate the CD24(-) population in vivo and the CD24(-) cells express late markers of adipogenesis.", "From these data we propose a model where the CD24(+) adipocyte progenitors become further committed to the adipocyte lineage as CD24 expression is lost, generating CD24(-) preadipocytes.", "This characterization of the adipocyte cellular lineage will facilitate the study of the mechanisms that regulate WAT formation in vivo and WAT mass expansion in obesity."], "structured": false}
{"doc_id": 18074797, "title": "Reducing Plasmodium falciparum Malaria Transmission in Africa: A Model-Based Evaluation of Intervention Strategies", "abstract": ["BACKGROUND Over the past decade malaria intervention coverage has been scaled up across Africa.", "However, it remains unclear what overall reduction in transmission is achievable using currently available tools.   \n", "METHODS AND FINDINGS We developed an individual-based simulation model for Plasmodium falciparum transmission in an African context incorporating the three major vector species (Anopheles gambiae s.s., An.", "arabiensis, and An.", "funestus) with parameters obtained by fitting to parasite prevalence data from 34 transmission settings across Africa.", "We incorporated the effect of the switch to artemisinin-combination therapy (ACT) and increasing coverage of long-lasting insecticide treated nets (LLINs) from the year 2000 onwards.", "We then explored the impact on transmission of continued roll-out of LLINs, additional rounds of indoor residual spraying (IRS), mass screening and treatment (MSAT), and a future RTS,S/AS01 vaccine in six representative settings with varying transmission intensity (as summarized by the annual entomological inoculation rate, EIR: 1 setting with low, 3 with moderate, and 2 with high EIRs), vector-species combinations, and patterns of seasonality.", "In all settings we considered a realistic target of 80% coverage of interventions.", "In the low-transmission setting (EIR approximately 3 ibppy [infectious bites per person per year]), LLINs have the potential to reduce malaria transmission to low levels (<1% parasite prevalence in all age-groups) provided usage levels are high and sustained.", "In two of the moderate-transmission settings (EIR approximately 43 and 81 ibppy), additional rounds of IRS with DDT coupled with MSAT could drive parasite prevalence below a 1% threshold.", "However, in the third (EIR = 46) with An.", "arabiensis prevailing, these interventions are insufficient to reach this threshold.", "In both high-transmission settings (EIR approximately 586 and 675 ibppy), either unrealistically high coverage levels (>90%) or novel tools and/or substantial social improvements will be required, although considerable reductions in prevalence can be achieved with existing tools and realistic coverage levels.   \n", "CONCLUSIONS Interventions using current tools can result in major reductions in P. falciparum malaria transmission and the associated disease burden in Africa.", "Reduction to the 1% parasite prevalence threshold is possible in low- to moderate-transmission settings when vectors are primarily endophilic (indoor-resting), provided a comprehensive and sustained intervention program is achieved through roll-out of interventions.", "In high-transmission settings and those in which vectors are mainly exophilic (outdoor-resting), additional new tools that target exophagic (outdoor-biting), exophilic, and partly zoophagic mosquitoes will be required."], "structured": true}
{"doc_id": 18078750, "title": "Golgi Export of the Kir2.1 Channel Is Driven by a Trafficking Signal Located within Its Tertiary Structure", "abstract": ["Mechanisms that are responsible for sorting newly synthesized proteins for traffic to the cell surface from the Golgi are poorly understood.", "Here, we show that the potassium channel Kir2.1, mutations in which are associated with Andersen-Tawil syndrome, is selected as cargo into Golgi export carriers in an unusual signal-dependent manner.", "Unlike conventional trafficking signals, which are typically comprised of short linear peptide sequences, Golgi exit of Kir2.1 is dictated by residues that are embedded within the confluence of two separate domains.", "This signal patch forms a recognition site for interaction with the AP1 adaptor complex, thereby marking Kir2.1 for incorporation into clathrin-coated vesicles at the trans-Golgi.", "The identification of a trafficking signal in the tertiary structure of Kir2.1 reveals a quality control step that couples protein conformation to Golgi export and provides molecular insight into how mutations in Kir2.1 arrest the channels at the Golgi."], "structured": false}
{"doc_id": 18084826, "title": "Characteristics of Body Fat, Body Fat Percentage and Other Body Composition for Koreans from KNHANES IV", "abstract": ["Accurate measurement of fat mass has become increasingly important with the increasing incidence of obesity.", "We assessed fat and muscle mass of Koreans with the Korea National Health and Nutrition Examination Survey IV (KNHANES IV).", "We studied 10,456 subjects (aged 20 to 85 yr; 4,476 men, 5,980 women).", "Fat and muscle mass were measured by dual-energy x-ray absorptiometry.", "Reference values of body compositions were obtained using the LMS method.", "The fat mass index (FMI, body fat mass/height(2); kg/m(2)) of Korean men did not correlate with age (P = 0.452), but those of Korean women (P < 0.001) did.", "The ratio of percentage of fat in the trunk and legs was positively related with age in both the genders.", "The appendicular lean mass/height(2) (kg/m(2)) of Korean men was negatively related to age (P < 0.001).", "In women, this ratio increased with age (P < 0.001).", "When we defined obesity according to the FMI classification, the rates of obesity were 6.1% (FMI > 9 kg/m(2)) in men and 2.7% (FMI > 13 kg/m(2)) in women.", "It is concluded that the muscle mass decreases and obesity increases with aging in Korean men, whereas both fat mass and obesity increase with aging in Korean women."], "structured": false}
{"doc_id": 18098290, "title": "The Evolution of Dominance in Sporophytic Self-Incompatibility Systems. II. Mate Availability and Recombination", "abstract": ["Sporophytic self-incompatibility (SSI) is a self-pollen recognition system that enforces outcrossing in plants.", "Recognition in SSI systems is typically controlled by a complex locus (5-locus) with separate genes that determine pollen and stigma specificity.", "Experimental studies show that S-alleles can be dominant, recessive, or codominant, and that the dominance level of a given S-allele can depend upon whether pollen or stigma specificity is examined.", "Here and in the companion paper by Llaurens and colleagues, the evolution of dominance in single-locus SSI is explored using numerical models and simulation.", "Particular attention is directed at factors that can cause S-allele dominance to differ in pollen versus stigma.", "The effect of recombination between the S-locus and modifier locus is also examined.", "The models predict that limitation in the number of compatible mates is required for the evolution of S-allele dominance in the stigma but not in the pollen.", "Tight linkage between the S-locus and modifier promotes the evolution of S-allele dominance hierarchies.", "Model results are interpreted with respect to published information on the molecular basis of dominance in SSI systems, and reported S-allele dominance relationships in a variety of species.", "These studies show that dominant S-alleles are more common in the pollen than in the stigma, a pattern that when interpreted in light of model predictions, suggests that mate limitation may be relatively infrequent in natural populations with SSI."], "structured": false}
{"doc_id": 18104691, "title": "Neurological outcomes of animal models of uterine artery ligation and relevance to human intrauterine growth restriction: a systematic review", "abstract": ["AIM This review explores the molecular, neurological, and behavioural outcomes in animal models of uterine artery ligation.", "We analyse the relevance of this type of model to the pathological and functional phenotypes that are consistent with cerebral palsy and its developmental comorbidities in humans.   \n", "METHOD A literature search of the PubMed database was conducted for research using the uterine artery ligation model published between 1990 and 2013.", "From the studies included, any relevant neuroanatomical and behavioural deficits were then summarized from each document and used for further analysis.   \n", "RESULTS There were 25 papers that met the criteria included for review, and several outcomes were summarized from the results of these papers.", "Fetuses with growth restriction demonstrated a gradient of reduced body weight with a relative sparing of brain mass.", "There was a significant reduction in the size of the somatosensory cortex, hippocampus, and corpus callosum.", "The motor cortex appeared to be spared of identifiable deficits.", "Apoptotic proteins were upregulated, while those important to neuronal survival, growth, and differentiation were downregulated.", "Neuronal apoptosis and astrogliosis occurred diffusely throughout the brain regions.", "White matter injury involved oligodendrocyte precursor maturation arrest, hypomyelination, and an aberrant organization of existing myelin.", "Animals with growth restriction demonstrated deficits in gait, memory, object recognition, and spatial processing.   \n", "INTERPRETATION This review concludes that neuronal death, white matter injury, motor abnormalities, and cognitive deficits are important outcomes of uterine artery ligation in animal models.", "Therefore, this is a clinically relevant type of model, as these findings resemble deficits in human cerebral palsy."], "structured": true}
{"doc_id": 18111172, "title": "The fidelity of the ligation step determines how ends are resolved during Nonhomologous end joining", "abstract": ["Nonhomologous end joining (NHEJ) can effectively resolve chromosome breaks despite diverse end structures; however, it is unclear how the steps employed for resolution are determined.", "We sought to address this question by analysing cellular NHEJ of ends with systematically mispaired and damaged termini.", "We show NHEJ is uniquely proficient at bypassing subtle terminal mispairs and radiomimetic damage by direct ligation.", "Nevertheless, bypass ability varies widely, with increases in mispair severity gradually reducing bypass products from 85 to 6%.", "End-processing by nucleases and polymerases is increased to compensate, although paths with the fewest number of steps to generate a substrate suitable for ligation are favoured.", "Thus, both the frequency and nature of end processing are tailored to meet the needs of the ligation step.", "We propose a model where the ligase organizes all steps during NHEJ within the stable paired-end complex to limit end processing and associated errors."], "structured": false}
{"doc_id": 18126445, "title": "Laminin-based cell adhesion anchors microtubule plus ends to the epithelial cell basal cortex through LL5\u03b1/\u03b2", "abstract": ["LL5beta has been identified as a microtubule-anchoring factor that attaches EB1/CLIP-associating protein (CLASP)-bound microtubule plus ends to the cell cortex.", "In this study, we show that LL5beta and its homologue LL5alpha (LL5s) colocalize with autocrine laminin-5 and its receptors, integrins alpha3beta1 and alpha6beta4, at the basal side of fully polarized epithelial sheets.", "Depletion of both laminin receptor integrins abolishes the cortical localization of LL5s, whereas LL5 depletion reduces the amount of integrin alpha3 at the basal cell cortex.", "Activation of integrin alpha3 is sufficient to initiate LL5 accumulation at the cell cortex.", "LL5s form a complex with the cytoplasmic tails of these integrins, but their interaction might be indirect.", "Analysis of the three-dimensional distribution of microtubule growth by visualizing EB1-GFP in epithelial sheets in combination with RNA interference reveals that LL5s are required to maintain the density of growing microtubules selectively at the basal cortex.", "These findings reveal that signaling from laminin-integrin associations attaches microtubule plus ends to the epithelial basal cell cortex."], "structured": false}
{"doc_id": 18144189, "title": "DNA topoisomerases: structure, function, and mechanism.", "abstract": ["DNA topoisomerases solve the topological problems associated with DNA replication, transcription, recombination, and chromatin remodeling by introducing temporary single- or double-strand breaks in the DNA.", "In addition, these enzymes fine-tune the steady-state level of DNA supercoiling both to facilitate protein interactions with the DNA and to prevent excessive supercoiling that is deleterious.", "In recent years, the crystal structures of a number of topoisomerase fragments, representing nearly all the known classes of enzymes, have been solved.", "These structures provide remarkable insights into the mechanisms of these enzymes and complement previous conclusions based on biochemical analyses.", "Surprisingly, despite little or no sequence homology, both type IA and type IIA topoisomerases from prokaryotes and the type IIA enzymes from eukaryotes share structural folds that appear to reflect functional motifs within critical regions of the enzymes.", "The type IB enzymes are structurally distinct from all other known topoisomerases but are similar to a class of enzymes referred to as tyrosine recombinases.", "The structural themes common to all topoisomerases include hinged clamps that open and close to bind DNA, the presence of DNA binding cavities for temporary storage of DNA segments, and the coupling of protein conformational changes to DNA rotation or DNA movement.", "For the type II topoisomerases, the binding and hydrolysis of ATP further modulate conformational changes in the enzymes to effect changes in DNA topology."], "structured": false}
{"doc_id": 18153456, "title": "Pilot testing of dipsticks as point-of-care assays for rapid diagnosis of poor-quality artemisinin drugs in endemic settings", "abstract": ["BACKGROUND Good-quality artemisinin drugs are essential for malaria treatment, but increasing prevalence of poor-quality artemisinin drugs in many endemic countries hinders effective management of malaria cases.   \n", "METHODS To develop a point-of-care assay for rapid identification of counterfeit and substandard artemisinin drugs for resource-limited areas, we used specific monoclonal antibodies against artesunate and artemether, and developed prototypes of lateral flow dipstick assays.", "In this pilot test, we evaluated the feasibility of these dipsticks under different endemic settings and their performance in the hands of untrained personnel.   \n", "RESULTS The results showed that the dipstick tests can be successfully performed by different investigators with the included instruction sheet.", "None of the artemether and artesunate drugs collected from public pharmacies in different endemic countries failed the test.   \n", "CONCLUSION It is possible that the simple dipstick assays, with future optimization of test conditions and sensitivity, can be used as a qualitative and semi-quantitative assay for rapid screening of counterfeit artemisinin drugs in endemic settings."], "structured": true}
{"doc_id": 18174210, "title": "Increased Microerythrocyte Count in Homozygous \u03b1+-Thalassaemia Contributes to Protection against Severe Malarial Anaemia", "abstract": ["BACKGROUND The heritable haemoglobinopathy alpha(+)-thalassaemia is caused by the reduced synthesis of alpha-globin chains that form part of normal adult haemoglobin (Hb).", "Individuals homozygous for alpha(+)-thalassaemia have microcytosis and an increased erythrocyte count.", "Alpha(+)-thalassaemia homozygosity confers considerable protection against severe malaria, including severe malarial anaemia (SMA) (Hb concentration < 50 g/l), but does not influence parasite count.", "We tested the hypothesis that the erythrocyte indices associated with alpha(+)-thalassaemia homozygosity provide a haematological benefit during acute malaria.   \n", "METHODS AND FINDINGS Data from children living on the north coast of Papua New Guinea who had participated in a case-control study of the protection afforded by alpha(+)-thalassaemia against severe malaria were reanalysed to assess the genotype-specific reduction in erythrocyte count and Hb levels associated with acute malarial disease.", "We observed a reduction in median erythrocyte count of approximately 1.5 x 10(12)/l in all children with acute falciparum malaria relative to values in community children (p < 0.001).", "We developed a simple mathematical model of the linear relationship between Hb concentration and erythrocyte count.", "This model predicted that children homozygous for alpha(+)-thalassaemia lose less Hb than children of normal genotype for a reduction in erythrocyte count of >1.1 x 10(12)/l as a result of the reduced mean cell Hb in homozygous alpha(+)-thalassaemia.", "In addition, children homozygous for alpha(+)-thalassaemia require a 10% greater reduction in erythrocyte count than children of normal genotype (p = 0.02) for Hb concentration to fall to 50 g/l, the cutoff for SMA.", "We estimated that the haematological profile in children homozygous for alpha(+)-thalassaemia reduces the risk of SMA during acute malaria compared to children of normal genotype (relative risk 0.52; 95% confidence interval [CI] 0.24-1.12, p = 0.09).   \n", "CONCLUSIONS The increased erythrocyte count and microcytosis in children homozygous for alpha(+)-thalassaemia may contribute substantially to their protection against SMA.", "A lower concentration of Hb per erythrocyte and a larger population of erythrocytes may be a biologically advantageous strategy against the significant reduction in erythrocyte count that occurs during acute infection with the malaria parasite Plasmodium falciparum.", "This haematological profile may reduce the risk of anaemia by other Plasmodium species, as well as other causes of anaemia.", "Other host polymorphisms that induce an increased erythrocyte count and microcytosis may confer a similar advantage."], "structured": true}
{"doc_id": 18188022, "title": "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection", "abstract": ["We have systematically made a set of precisely defined, single\u2010gene deletions of all nonessential genes in Escherichia coli K\u201012.", "Open\u2010reading frame coding regions were replaced with a kanamycin cassette flanked by FLP recognition target sites by using a one\u2010step method for inactivation of chromosomal genes and primers designed to create in\u2010frame deletions upon excision of the resistance cassette.", "Of 4288 genes targeted, mutants were obtained for 3985.", "To alleviate problems encountered in high\u2010throughput studies, two independent mutants were saved for every deleted gene.", "These mutants\u2014the \u2018Keio collection\u2019\u2014provide a new resource not only for systematic analyses of unknown gene functions and gene regulatory networks but also for genome\u2010wide testing of mutational effects in a common strain background, E .", "coli K\u201012 BW25113.", "We were unable to disrupt 303 genes, including 37 of unknown function, which are candidates for essential genes.", "Distribution is being handled via GenoBase (http://ecoli.aist\u2010nara.ac.jp/)."], "structured": false}
{"doc_id": 18190552, "title": "Validated RealTime reverse transcriptase PCR methods for the diagnosis and pathotyping of Eurasian H7 avian influenza viruses", "abstract": ["BACKGROUND Avian influenza (AI) caused by H7 AI viruses (AIVs) of both low pathogenicity (LP) and high pathogenicity (HP) are notifiable poultry diseases.   \n", "OBJECTIVES Design and validate two RealTime reverse transcriptase polymerase chain reactions (RRT PCRs) for Eurasian H7 AIV detection and pathotyping.   \n", "METHODS The H7 RRT PCRs amplified within the (i) HA2 and (ii) cleavage site CS regions of the haemagglutinin gene.", "Both were validated against 65 H7 AIVs, 57 non-H7 AIVs and 259 poultry swabs in comparison to M gene (AI generic) RRT PCR and virus isolation (VI).", "An additional 38 swabs and 20 tissue specimens extended validation against M gene RRT PCR.   \n", "RESULTS Both H7 RRT PCRs amplified all 61 Eurasian lineage H7 AIVs and none of 57 non-H7 AIVs.", "A total of 297 poultry swabs were used to determine diagnostic sensitivity and specificity relative to M gene RRT PCR, sensitivity was 95.4% and 64.6% for the HA2 and CS RRT PCRs respectively, and specificity 97.9% and 99.6% respectively.", "The H7 HA2 RRT PCR was more sensitive than VI.", "This was emphasized by analysis of 37 swabs from turkeys infected experimentally with HPAI H7N1 virus sampled at 24 hours post-inoculation and LPAI H7N1 chicken infections sampled at 40-64 hours.", "Although less sensitive, usefulness of the H7 CS RRT PCR was confirmed by the correct molecular pathotyping for all 61 Eurasian lineage H7 AIVs tested.   \n", "CONCLUSIONS The high sensitivity of H7 HA2 RRT PCR confirms its suitability for use in poultry surveillance and disease diagnosis.", "H7 CS RRT PCR provides an opportunity for rapid pathotyping of H7 AIVs."], "structured": true}
{"doc_id": 18199839, "title": "Interleukin-6 receptor pathways in coronary heart disease: a collaborative meta-analysis of 82 studies", "abstract": ["BACKGROUND Persistent inflammation has been proposed to contribute to various stages in the pathogenesis of cardiovascular disease.", "Interleukin-6 receptor (IL6R) signalling propagates downstream inflammation cascades.", "To assess whether this pathway is causally relevant to coronary heart disease, we studied a functional genetic variant known to affect IL6R signalling.   \n", "METHODS In a collaborative meta-analysis, we studied Asp358Ala (rs2228145) in IL6R in relation to a panel of conventional risk factors and inflammation biomarkers in 125,222 participants.", "We also compared the frequency of Asp358Ala in 51,441 patients with coronary heart disease and in 136,226 controls.", "To gain insight into possible mechanisms, we assessed Asp358Ala in relation to localised gene expression and to postlipopolysaccharide stimulation of interleukin 6.   \n", "FINDINGS The minor allele frequency of Asp358Ala was 39%.", "Asp358Ala was not associated with lipid concentrations, blood pressure, adiposity, dysglycaemia, or smoking (p value for association per minor allele \u22650\u00b704 for each).", "By contrast, for every copy of 358Ala inherited, mean concentration of IL6R increased by 34\u00b73% (95% CI 30\u00b74-38\u00b72) and of interleukin 6 by 14\u00b76% (10\u00b77-18\u00b74), and mean concentration of C-reactive protein was reduced by 7\u00b75% (5\u00b79-9\u00b71) and of fibrinogen by 1\u00b70% (0\u00b77-1\u00b73).", "For every copy of 358Ala inherited, risk of coronary heart disease was reduced by 3\u00b74% (1\u00b78-5\u00b70).", "Asp358Ala was not related to IL6R mRNA levels or interleukin-6 production in monocytes.   \n", "INTERPRETATION Large-scale human genetic and biomarker data are consistent with a causal association between IL6R-related pathways and coronary heart disease.   \n", "FUNDING British Heart Foundation; UK Medical Research Council; UK National Institute of Health Research, Cambridge Biomedical Research Centre; BUPA Foundation."], "structured": true}
{"doc_id": 18207615, "title": "Plasma exosomes can deliver exogenous short interfering RNA to monocytes and lymphocytes", "abstract": ["Despite the promise of RNA interference (RNAi) and its potential, e.g. for use in cancer therapy, several technical obstacles must first be overcome.", "The major hurdle of RNAi-based therapeutics is to deliver nucleic acids across the cell's plasma membrane.", "This study demonstrates that exosome vesicles derived from humans can deliver short interfering RNA (siRNA) to human mononuclear blood cells.", "Exosomes are nano-sized vesicles of endocytic origin that are involved in cell-to-cell communication, i.e. antigen presentation, tolerance development and shuttle RNA (mainly mRNA and microRNA).", "Having tested different strategies, an optimized method (electroporation) was used to introduce siRNA into human exosomes of various origins.", "Plasma exosomes (exosomes from peripheral blood) were used as gene delivery vector (GDV) to transport exogenous siRNA to human blood cells.", "The vesicles effectively delivered the administered siRNA into monocytes and lymphocytes, causing selective gene silencing of mitogen-activated protein kinase 1.", "These data suggest that human exosomes can be used as a GDV to provide cells with heterologous nucleic acids such as therapeutic siRNAs."], "structured": false}
{"doc_id": 18218379, "title": "Quantitative analysis of tumor-derived methylated p16INK4a sequences in plasma, serum, and blood cells of hepatocellular carcinoma patients.", "abstract": ["PURPOSE AND EXPERIMENTAL DESIGN Using real-time quantitative methylation-specific PCR (RTQ-MSP), we quantified methylated p16INK4a sequences and determined the fractional concentrations of circulating tumor DNA in plasma, serum, and peripheral blood cells collected preoperatively, intraoperatively, and postoperatively from 49 patients with hepatocellular carcinoma (HCC).   \n", "RESULTS RTQ-MSP was sufficiently sensitive to detect down to 10 genome-equivalents of methylated p16INK4a sequences.", "Quantitative MSP data were expressed in terms of the methylation index, which was the percentage of bisulfite converted unmethylated and methylated p16INK4a sequences that consisted of methylated p16INK4a sequences.", "Quantities of methylated p16INK4a sequences were detected in peripheral circulation of 80% (23 of 29) of HCC patients.", "No significant difference was seen in the detectability and concentrations of methylated p16INK4a sequences (range: 10-4046 genome-equivalents/ml) between preoperative plasma and serum samples from HCC patients.", "Preoperatively, the p16INK4a methylation indices ranged from 0.2 to 100% and from 0.012 to 0.075% in the patients' plasma and buffy coat samples, respectively.", "After surgical resection, the median p16INK4a methylation indices in plasma and buffy coat concordantly decreased 12- and 15-fold, respectively.", "These results demonstrated the clinical usefulness and effectiveness of peripheral blood RTQ-MSP for detecting and monitoring HCC after treatment.", "Furthermore, none of the intraoperative plasma samples and only two of the intraoperative buffy coat samples were p16INK4a methylation positive.   \n", "CONCLUSIONS Quantification of epigenetic changes in peripheral blood by RTQ-MSP is useful for the detection and monitoring of HCC."], "structured": true}
{"doc_id": 18231257, "title": "Dynamic control of excitatory synapse development by a Rac1 GEF/GAP regulatory complex.", "abstract": ["The small GTPase Rac1 orchestrates actin-dependent remodeling essential for numerous cellular processes including synapse development.", "While precise spatiotemporal regulation of Rac1 is necessary for its function, little is known about the mechanisms that enable Rac1 activators (GEFs) and inhibitors (GAPs) to act in concert to regulate Rac1 signaling.", "Here, we identify a regulatory complex composed of a Rac-GEF (Tiam1) and a Rac-GAP (Bcr) that cooperate to control excitatory synapse development.", "Disruption of Bcr function within this complex increases Rac1 activity and dendritic spine remodeling, resulting in excessive synaptic growth that is rescued by Tiam1 inhibition.", "Notably, EphB receptors utilize the Tiam1-Bcr complex to control synaptogenesis.", "Following EphB activation, Tiam1 induces Rac1-dependent spine formation, whereas Bcr prevents Rac1-mediated receptor internalization, promoting spine growth over retraction.", "The finding that a Rac-specific GEF/GAP complex is required to maintain optimal levels of Rac1 signaling provides an important insight into the regulation of small GTPases."], "structured": false}
{"doc_id": 18231807, "title": "4-1BB Costimulation Ameliorates T Cell Exhaustion Induced by Tonic Signaling of Chimeric Antigen Receptors", "abstract": ["Chimeric antigen receptors (CARs) targeting CD19 have mediated dramatic antitumor responses in hematologic malignancies, but tumor regression has rarely occurred using CARs targeting other antigens.", "It remains unknown whether the impressive effects of CD19 CARs relate to greater susceptibility of hematologic malignancies to CAR therapies, or superior functionality of the CD19 CAR itself.", "We show that tonic CAR CD3-\u03b6 phosphorylation, triggered by antigen-independent clustering of CAR single-chain variable fragments, can induce early exhaustion of CAR T cells that limits antitumor efficacy.", "Such activation is present to varying degrees in all CARs studied, except the highly effective CD19 CAR.", "We further determine that CD28 costimulation augments, whereas 4-1BB costimulation reduces, exhaustion induced by persistent CAR signaling.", "Our results provide biological explanations for the antitumor effects of CD19 CARs and for the observations that CD19 CAR T cells incorporating the 4-1BB costimulatory domain are more persistent than those incorporating CD28 in clinical trials."], "structured": false}
{"doc_id": 18236313, "title": "Ultrafast Evolution and Loss of CRISPRs Following a Host Shift in a Novel Wildlife Pathogen, Mycoplasma gallisepticum", "abstract": ["Measureable rates of genome evolution are well documented in human pathogens but are less well understood in bacterial pathogens in the wild, particularly during and after host switches.", "Mycoplasma gallisepticum (MG) is a pathogenic bacterium that has evolved predominantly in poultry and recently jumped to wild house finches (Carpodacus mexicanus), a common North American songbird.", "For the first time we characterize the genome and measure rates of genome evolution in House Finch isolates of MG, as well as in poultry outgroups.", "Using whole-genome sequences of 12 House Finch isolates across a 13-year serial sample and an additional four newly sequenced poultry strains, we estimate a nucleotide diversity in House Finch isolates of only \u223c2% of ancestral poultry strains and a nucleotide substitution rate of 0.8-1.2\u00d710(-5) per site per year both in poultry and in House Finches, an exceptionally fast rate rivaling some of the highest estimates reported thus far for bacteria.", "We also found high diversity and complete turnover of CRISPR arrays in poultry MG strains prior to the switch to the House Finch host, but after the invasion of House Finches there is progressive loss of CRISPR repeat diversity, and recruitment of novel CRISPR repeats ceases.", "Recent (2007) House Finch MG strains retain only \u223c50% of the CRISPR repertoire founding (1994-95) strains and have lost the CRISPR-associated genes required for CRISPR function.", "Our results suggest that genome evolution in bacterial pathogens of wild birds can be extremely rapid and in this case is accompanied by apparent functional loss of CRISPRs."], "structured": false}
{"doc_id": 18237384, "title": "Inducing Tumor Immunity through the Selective Engagement of Activating Fc\u03b3 Receptors on Dendritic Cells", "abstract": ["Induction of tumor-specific immunity requires that dendritic cells (DCs) efficiently capture and present tumor antigens to result in the expansion and activation of tumor-specific cytotoxic T cells.", "The transition from antigen capture to T cell stimulation requires a maturation signal; in its absence tolerance, rather than immunity may develop.", "While immune complexes (ICs) are able to enhance antigen capture, they can be poor at inducing DC maturation, naive T cell activation and protective immunity.", "We now demonstrate that interfering with the inhibitory signal delivered by Fc\u03b3RIIB on DCs converts ICs to potent maturation agents and results in T cell activation.", "Applying this approach to immunization with DCs pulsed ex-vivo with ICs, we have generated antigen-specific CD8+ T cells in vivo and achieved efficient protective immunity in a murine melanoma model.", "These data imply that ICs may normally function to maintain tolerance through the binding to inhibitory Fc\u03b3Rs on DCs, but they can be converted to potent immunogenic stimuli by selective engagement of activating Fc\u03b3Rs.", "This mechanism suggests a novel approach to the development of tumor vaccines."], "structured": false}
{"doc_id": 18256197, "title": "Homocysteine and the risk of ischemic stroke in a triethnic cohort: the NOrthern MAnhattan Study.", "abstract": ["BACKGROUND AND PURPOSE The level of total homocysteine (tHcy) that confers a risk of ischemic stroke is unsettled, and no prospective cohort studies have included sufficient elderly minority subjects.", "We investigated the association between mild to moderate fasting tHcy level and the incidence of ischemic stroke, myocardial infarction, and vascular death in a multiethnic prospective study.   \n", "METHODS A population-based cohort was followed for vascular events (stroke, myocardial infarction, and vascular death).", "Baseline values of tHcy and methylmalonic acid were measured among 2939 subjects (mean age, 69+/-10; 61% women, 53% Hispanics, 24% blacks, and 20% whites).", "Cox proportional models were used to calculate hazard ratios (HRs) and 95% CIs in tHcy categories after adjusting for age, race, education, renal insufficiency, B12 deficiency, and other risk factors.   \n", "RESULTS The adjusted HR for a tHcy level > or =15 micromol/L compared with <10 micromol/L was greatest for vascular death (HR=6.04; 95% CI, 3.44 to 10.60), followed by combined vascular events (HR=2.27; 95% CI, 1.51 to 3.43), ischemic stroke (HR=2.01; 95% CI, 1.00 to 4.05), and nonvascular death (HR=2.02; 95% CI, 1.31 to 3.14).", "Mild to moderate elevations of tHcy of 10 to 15 micromol/L were not significantly predictive of ischemic stroke, but increased the risk of vascular death (2.27; 95% CI, 1.44 to 3.60) and combined vascular events (1.42; 95% CI, 1.06 to 1.88).", "The effect of tHcy was stronger among whites and Hispanics, but not a significant risk factor for blacks.   \n", "CONCLUSIONS Total Hcy elevations above 15 micromol/L are an independent risk factor for ischemic stroke, whereas mild elevations of tHcy of 10 to 15 micromol/L are less predictive.", "The vascular effects of tHcy are greatest among whites and Hispanics, and less among blacks."], "structured": true}
{"doc_id": 18261004, "title": "Expression and purification of recombinant methylated HBHA in Mycobacterium smegmatis.", "abstract": ["The Heparin-Binding Haemagglutinin (HBHA) is a mycobacterial adhesin involved in the dissemination of Mycobacterium tuberculosis from the site of primary infection and a potential candidate for the development of a new vaccine against tuberculosis.", "Methylation of HBHA is a novel post-translational event that imparts important immunological properties to the protein.", "Since recombinant HBHA expressed in Escherichia coli is not methylated, we investigated the possibility of producing recombinant methylated HBHA in fast growing mycobacteria for use in immunological and biochemical studies.", "The complete coding sequence of HBHA was cloned in the plasmid pMV206, under the control of a strong promoter (hsp60) or its own promoter.", "The constructs generated were electroporated into Mycobacterium smegmatis and the recombinant strains obtained were analyzed for the presence of the HBHA protein using the anti-HBHA monoclonal antibodies D2 and E4.", "Our results indicate that expression of high amounts of intact protein can be toxic for the mycobacteria, that methylated HBHA can be obtained in M. smegmatis only when using a promoter sequence weaker than hsp60 and that the expression of the complete structural gene is required in order to obtain methylated HBHA.", "We constructed a recombinant M. smegmatis strain (pMV3-38) that expresses a histidine-tagged methylated HBHA that can be easily purified.", "The use of fast-growing strains of M. smegmatis to obtain significant amounts of purified HBHA protein within a short timeframe, should be an effective strategy for the evaluation of a new HBHA-based vaccine candidate for tuberculosis."], "structured": false}
{"doc_id": 18263406, "title": "Detection of alternative lengthening of telomeres by telomere quantitative PCR", "abstract": ["Alternative lengthening of telomeres (ALT) is one of the two known telomere length maintenance mechanisms that are essential for the unlimited proliferation potential of cancer cells.", "Existing methods for detecting ALT in tumors require substantial amounts of tumor material and are labor intensive, making it difficult to study prevalence and prognostic significance of ALT in large tumor cohorts.", "Here, we present a novel strategy utilizing telomere quantitative PCR to diagnose ALT.", "The protocol is more rapid than conventional methods and scrutinizes two distinct characteristics of ALT cells concurrently: long telomeres and the presence of C-circles (partially double-stranded circles of telomeric C-strand DNA).", "Requiring only 30 ng of genomic DNA, this protocol will facilitate large-scale studies of ALT in tumors and can be readily adopted by clinical laboratories."], "structured": false}
{"doc_id": 18264714, "title": "Noise and interlocking signaling pathways promote distinct transcription factor dynamics in response to different stresses", "abstract": ["All cells perceive and respond to environmental stresses through elaborate stress-sensing networks.", "Yeast cells sense stress through diverse signaling pathways that converge on the transcription factors Msn2 and Msn4, which respond by initiating rapid, idiosyncratic cycles into and out of the nucleus.", "To understand the role of Msn2/4 nuclear localization dynamics, we combined time-lapse studies of Msn2-GFP localization in living cells with computational modeling of stress-sensing signaling networks.", "We find that several signaling pathways, including Ras/protein kinase A, AMP-activated kinase, the high-osmolarity response mitogen-activated protein kinase pathway, and protein phosphatase 1, regulate activation of Msn2 in distinct ways in response to different stresses.", "Moreover, we find that bursts of nuclear localization elicit a more robust transcriptional response than does sustained nuclear localization.", "Using stochastic modeling, we reproduce in silico the responses of Msn2 to different stresses, and demonstrate that bursts of localization arise from noise in the signaling pathways amplified by the small number of Msn2 molecules in the cell.", "This noise imparts diverse behaviors to genetically identical cells, allowing cell populations to \"hedge their bets\" in responding to an uncertain future, and to balance growth and survival in an unpredictable environment."], "structured": false}
{"doc_id": 18268012, "title": "Long-term financing needs for HIV control in sub-Saharan Africa in 2015-2050: a modelling study.", "abstract": ["OBJECTIVES To estimate the present value of current and future funding needed for HIV treatment and prevention in 9 sub-Saharan African (SSA) countries that account for 70% of HIV burden in Africa under different scenarios of intervention scale-up.", "To analyse the gaps between current expenditures and funding obligation, and discuss the policy implications of future financing needs.   \n", "DESIGN We used the Goals module from Spectrum, and applied the most up-to-date cost and coverage data to provide a range of estimates for future financing obligations.", "The four different scale-up scenarios vary by treatment initiation threshold and service coverage level.", "We compared the model projections to current domestic and international financial sources available in selected SSA countries.   \n", "RESULTS In the 9 SSA countries, the estimated resources required for HIV prevention and treatment in 2015-2050 range from US$98 billion to maintain current coverage levels for treatment and prevention with eligibility for treatment initiation at CD4 count of <500/mm(3) to US$261 billion if treatment were to be extended to all HIV-positive individuals and prevention scaled up.", "With the addition of new funding obligations for HIV--which arise implicitly through commitment to achieve higher than current treatment coverage levels--overall financial obligations (sum of debt levels and the present value of the stock of future HIV funding obligations) would rise substantially.   \n", "CONCLUSIONS Investing upfront in scale-up of HIV services to achieve high coverage levels will reduce HIV incidence, prevention and future treatment expenditures by realising long-term preventive effects of ART to reduce HIV transmission.", "Future obligations are too substantial for most SSA countries to be met from domestic sources alone.", "New sources of funding, in addition to domestic sources, include innovative financing.", "Debt sustainability for sustained HIV response is an urgent imperative for affected countries and donors."], "structured": true}
{"doc_id": 18275697, "title": "Cell-mediated immunity and antibody responses elicited by attenuated Salmonella enterica Serovar Typhi strains used as live oral vaccines in humans.", "abstract": ["The development of improved typhoid vaccines is a high global public health priority.", "However, their development has been hampered by a lack of information regarding the specific determinants of protective immunity to Salmonella enterica serovar Typhi (S. Typhi) infection in humans.", "Although antibodies to S. Typhi O, H, and Vi appear to be involved in protection against S. Typhi infection, it is unknown whether such antibodies mediate protection, act in conjunction with other adaptive responses, or serve as a surrogate for the presence of other, more dominant protective immune responses (e.g., cell-mediated immunity [CMI]).", "CMI responses elicited by immunization of subjects with attenuated S. Typhi oral vaccines include lymphoproliferation; production of type 1 cytokines (e.g., interferon- gamma and tumor necrosis factor- alpha ); and classical major histocompatibility complex (MHC) class Ia-restricted and novel, nonclassical MHC class Ib (human leukocyte antigen [HLA]-E)-restricted CD8(+) cytotoxic T cell responses.", "In sum, human immunity to S. Typhi elicited by immunization is unexpectedly broad and complex.", "However, the immunologic correlates of protection remain largely undefined."], "structured": false}
{"doc_id": 18276599, "title": "Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation", "abstract": ["Higher-order chromosomal organization for transcription regulation is poorly understood in eukaryotes.", "Using genome-wide Chromatin Interaction Analysis with Paired-End-Tag sequencing (ChIA-PET), we mapped long-range chromatin interactions associated with RNA polymerase II in human cells and uncovered widespread promoter-centered intragenic, extragenic, and intergenic interactions.", "These interactions further aggregated into higher-order clusters, wherein proximal and distal genes were engaged through promoter-promoter interactions.", "Most genes with promoter-promoter interactions were active and transcribed cooperatively, and some interacting promoters could influence each other implying combinatorial complexity of transcriptional controls.", "Comparative analyses of different cell lines showed that cell-specific chromatin interactions could provide structural frameworks for cell-specific transcription, and suggested significant enrichment of enhancer-promoter interactions for cell-specific functions.", "Furthermore, genetically-identified disease-associated noncoding elements were found to be spatially engaged with corresponding genes through long-range interactions.", "Overall, our study provides insights into transcription regulation by three-dimensional chromatin interactions for both housekeeping and cell-specific genes in human cells."], "structured": false}
{"doc_id": 18321590, "title": "Resazurin microtiter assay plate: simple and inexpensive method for detection of drug resistance in Mycobacterium tuberculosis.", "abstract": ["A method for detecting multidrug-resistant Mycobacterium tuberculosis by using a reduction of resazurin is described.", "Eighty clinical isolates were evaluated against isoniazid and rifampin; results at 7 days were compared with those of the proportion method.", "Specificity and sensitivity were excellent.", "The method is simple, inexpensive, and rapid and might be used with other antituberculosis drugs."], "structured": false}
{"doc_id": 18333304, "title": "The pervasiveness and plasticity of circadian oscillations: the coupled circadian-oscillators framework.", "abstract": ["MOTIVATION Circadian oscillations have been observed in animals, plants, fungi and cyanobacteria and play a fundamental role in coordinating the homeostasis and behavior of biological systems.", "Genetically encoded molecular clocks found in nearly every cell, based on negative transcription/translation feedback loops and involving only a dozen genes, play a central role in maintaining these oscillations.", "However, high-throughput gene expression experiments reveal that in a typical tissue, a much larger fraction ([Formula: see text]) of all transcripts oscillate with the day-night cycle and the oscillating species vary with tissue type suggesting that perhaps a much larger fraction of all transcripts, and perhaps also other molecular species, may bear the potential for circadian oscillations.   \n", "RESULTS To better quantify the pervasiveness and plasticity of circadian oscillations, we conduct the first large-scale analysis aggregating the results of 18 circadian transcriptomic studies and 10 circadian metabolomic studies conducted in mice using different tissues and under different conditions.", "We find that over half of protein coding genes in the cell can produce transcripts that are circadian in at least one set of conditions and similarly for measured metabolites.", "Genetic or environmental perturbations can disrupt existing oscillations by changing their amplitudes and phases, suppressing them or giving rise to novel circadian oscillations.", "The oscillating species and their oscillations provide a characteristic signature of the physiological state of the corresponding cell/tissue.", "Molecular networks comprise many oscillator loops that have been sculpted by evolution over two trillion day-night cycles to have intrinsic circadian frequency.", "These oscillating loops are coupled by shared nodes in a large network of coupled circadian oscillators where the clock genes form a major hub.", "Cells can program and re-program their circadian repertoire through epigenetic and other mechanisms.   ", "AVAILABILITY AND IMPLEMENTATION High-resolution and tissue/condition specific circadian data and networks available at http://circadiomics.igb.uci.edu.   ", "CONTACT pfbaldi@ics.uci.edu   SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online."], "structured": true}
{"doc_id": 18340282, "title": "Gene\u2013environment interactions in 7610 women with breast cancer: prospective evidence from the Million Women Study", "abstract": ["BACKGROUND Information is scarce about the combined effects on breast cancer incidence of low-penetrance genetic susceptibility polymorphisms and environmental factors (reproductive, behavioural, and anthropometric risk factors for breast cancer).", "To test for evidence of gene-environment interactions, we compared genotypic relative risks for breast cancer across the other risk factors in a large UK prospective study.   \n", "METHODS We tested gene-environment interactions in 7610 women who developed breast cancer and 10 196 controls without the disease, studying the effects of 12 polymorphisms (FGFR2-rs2981582, TNRC9-rs3803662, 2q35-rs13387042, MAP3K1-rs889312, 8q24-rs13281615, 2p-rs4666451, 5p12-rs981782, CASP8-rs1045485, LSP1-rs3817198, 5q-rs30099, TGFB1-rs1982073, and ATM-rs1800054) in relation to prospectively collected information about ten established environmental risk factors (age at menarche, parity, age at first birth, breastfeeding, menopausal status, age at menopause, use of hormone replacement therapy, body-mass index, height, and alcohol consumption).   \n", "FINDINGS After allowance for multiple testing none of the 120 comparisons yielded significant evidence of a gene-environment interaction.", "By contrast with previous suggestions, there was little evidence that the genotypic relative risks were affected by use of hormone replacement therapy, either overall or for oestrogen-receptor-positive disease.", "Only one of the 12 polymorphisms was correlated with any of the ten other risk factors: carriers of the high-risk C allele of MAP3K1-rs889312 were significantly shorter than non-carriers (mean height 162.4 cm [95% CI 162.1-162.7] vs 163.1 cm [162.9-163.2]; p=0.01 after allowance for multiple testing).   \n", "INTERPRETATION Risks of breast cancer associated with low-penetrance susceptibility polymorphisms do not vary significantly with these ten established environmental risk factors.   \n", "FUNDING Cancer Research UK and the UK Medical Research Council."], "structured": true}
{"doc_id": 18344910, "title": "Thrombocytopenia as an Indicator of Malaria in Adult Population", "abstract": ["Objectives.", "To evaluate the predictive value of thrombocytopenia in malaria.", "Patients and Methods.", "It was a prospective observational study on all febrile patients with thrombocytopenia presenting to the Medical Unit of Hayat Abad Medical Complex during November 2008 to November 2010.", "Results.", "Of the total of 228 patients with fever and thrombocytopenia, 121 patients (53%) proved to be suffering from malaria.", "Of them 82 patients (68%) had falciparum malaria while 39 patients (32%) had vivax infection.", "Of these 121 patients, platelet counts ranged between 25,000 and 150,000/dL with a mean value of 101,000/dL (SD \u00b1 47, 500) and a median of 75,000/dL. Of the 107 patients who were not suffering from malaria, the counts ranged between 10,000 and 150,000/dL with a mean value of 58,000/dL (SD \u00b1 54, 000) and median of 50,000/dL. Conclusions.", "The presence of thrombocytopenia may be a predictor of malaria in adult population."], "structured": false}
{"doc_id": 18346333, "title": "AMPA receptor ligand binding domain mobility revealed by functional cross linking.", "abstract": ["Glutamate receptors mediate the majority of excitatory synaptic transmission in the CNS.", "The AMPA-subtype has rapid kinetics, with activation, deactivation and desensitization proceeding on the millisecond timescale or faster.", "Crystallographic, biochemical, and functional studies suggest that GluR2 Cys mutants which form intermolecular disulfide cross-links between the lower D2 lobes of the ligand binding cores can be trapped in a conformation that represents the desensitized state.", "We used multi-channel rapid perfusion techniques to examine the state dependence of cross-linking in these mutants.", "Under reducing conditions, both wild-type GluR2 and the G725C and S729C mutants have normal activation and desensitization kinetics, but the Cys mutants can be efficiently trapped in nonconducting states when oxidized.", "In contrast the I664C mutant is only partially inactivated under oxidizing conditions.", "For S729C, disulfide cross-links form rapidly when receptors are desensitized in the presence of glutamate, but receptors also become trapped at rest, in the absence of agonist.", "We assessed such spontaneous trapping in various conditions, including CNQX, a competitive antagonist; kainate, a weak partial agonist; or when desensitization was blocked by the L483Y mutation that stabilizes the D1 dimer interface.", "These experiments suggest that trapping in the absence of glutamate is due to two motions: Spontaneous breaking of the D1 dimer interface and hyperextension of the lower lobes of the ligand binding core.", "These data show that the glutamate binding domains are surprisingly mobile in the absence of ligand, which could influence receptor activity in the brain."], "structured": false}
{"doc_id": 18348376, "title": "Ncf1 (p47phox) Is Essential for Direct Regulatory T Cell Mediated Suppression of CD4+ Effector T Cells", "abstract": ["BACKGROUND Multiple mechanisms have been advanced to account for CD4+FOXP3+ regulatory T cell (Treg)-mediated suppression of CD4+ effector T cells (Teffs) but none appear to completely explain suppression.", "Previous data indicates that Tregs may affect the microenvironment redox state.", "Given the inherent redox sensitivity of T cells, we tested the hypothesis that oxidants may mediate the direct suppression of Teffs by Tregs.   \n", "METHODOLOGY/PRINCIPAL FINDINGS Tregs and Teffs were isolated from the spleens of wild type (WT) C57BL/6 mice or Ncf1(p47phox)-deficient C57BL/6 mice which lack NADPH oxidase function.", "Teffs were labeled with CFSE and co-cultured with unlabeled Tregs at varying Treg:Teff ratios in the presence of anti-CD3/CD28 coated beads for 3 days in suppression assays.", "Treg-mediated suppression was quantified by flow cytometric analysis of CFSE dilution in Teffs.", "The presence of the antioxidants n-acetylcysteine (NAC) or 2-mercaptoethanol or inhibitors of NADPH oxidase (diphenyleneiodonium and VAS-2870) resulted in reduced WT Treg-mediated suppression.", "The observed suppression was in part dependent upon TGF\u03b2 as it was partially blocked with neutralizing antibodies.", "The suppression of Teff proliferation induced by exogenous TGF\u03b2 treatment could be overcome with NAC.", "Ncf1-deficient Teff were slightly but significantly less sensitive than WT Teff to suppression by exogenous TGF\u03b2.", "Ncf1-deficient Tregs suppressed Ncf1-deficient Teff very poorly compared to wild type controls.", "There was partial but incomplete reconstitution of suppression in assays with WT Tregs and Ncf1-deficient Teff.   \n", "CONCLUSIONS/SIGNIFICANCE We present evidence that NADPH oxidase derived ROS plays a role in the direct Treg mediated suppression of CD4+ effector T cells in a process that is blocked by thiol-containing antioxidants, NADPH oxidase inhibitors or a lack of Ncf1 expression in Tregs and Teffs.", "Oxidants may represent a potential new target for therapeutic modulation of Treg function."], "structured": true}
{"doc_id": 18358026, "title": "Oxidative damage targets complexes containing DNA methyltransferases, SIRT1, and polycomb members to promoter CpG Islands.", "abstract": ["Cancer cells simultaneously harbor global losses and gains in DNA methylation.", "We demonstrate that inducing cellular oxidative stress by hydrogen peroxide treatment recruits DNA methyltransferase 1 (DNMT1) to damaged chromatin.", "DNMT1 becomes part of a complex(es) containing DNMT3B and members of the polycomb repressive complex 4.", "Hydrogen peroxide treatment causes relocalization of these proteins from non-GC-rich to GC-rich areas.", "Key components are similarly enriched at gene promoters in an in vivo colitis model.", "Although high-expression genes enriched for members of the complex have histone mark and nascent transcription changes, CpG island-containing low-expression genes gain promoter DNA methylation.", "Thus, oxidative damage induces formation and relocalization of a silencing complex that may explain cancer-specific aberrant DNA methylation and transcriptional silencing."], "structured": false}
{"doc_id": 18361917, "title": "Expression profiles during dedifferentiation in newt lens regeneration revealed by expressed sequence tags", "abstract": ["PURPOSE The adult newt can regenerate lens from pigmented epithelial cells (PECs) of the dorsal iris via dedifferentiation.", "The purpose of this research is to obtain sequence resources for a newt lens regeneration study and to obtain insights of dedifferentiation at the molecular level.   \n", "METHODS mRNA was purified from iris during dedifferentiation and its cDNA library was constructed.", "From the cDNA library 10,449 clones were sequenced and analyzed.   \n", "RESULTS From 10,449 reads, 780 contigs and 1,666 singlets were annotated.", "The presence of several cancer- and apoptosis-related genes during newt dedifferentiation was revealed.", "Moreover, several candidate genes, which might participate in reprogramming during dedifferentiation, were also found.   \n", "CONCLUSIONS The expression of cancer- and apoptosis-related genes could be hallmarks during dedifferentiation.", "The expression sequence tag (EST) resource is useful for the future study of newt dedifferentiation, and the sequence information is available in GenBank (accession numbers; FS290155-FS300559)."], "structured": true}
{"doc_id": 18374364, "title": "In vivo proliferation and cell cycle kinetics of long-term self-renewing hematopoietic stem cells.", "abstract": ["A rare set of hematopoietic stem cells (HSC) must undergo a massive expansion to produce mature blood cells.", "The phenotypic isolation of HSC from mice offers the opportunity to determine directly their proliferation kinetics.", "We analyzed the proliferation and cell cycle kinetics of long-term self-renewing HSC (LT-HSC) in normal adult mice.", "At any one time, approximately 5% of LT-HSC were in S/G2/M phases of the cell cycle and another 20% were in G1 phase.", "BrdUrd incorporation was used to determine the rate at which different cohorts of HSC entered the cell cycle over time.", "About 50% of LT-HSC incorporated BrdUrd by 6 days and >90% incorporated BrdUrd by 30 days.", "By 6 months, 99% of LT-HSC had incorporated BrdUrd.", "We calculated that approximately 8% of LT-HSC asynchronously entered the cell cycle per day.", "Nested reverse transcription-PCR analysis revealed cyclin D2 expression in a high proportion of LT-HSC.", "Although approximately 75% of LT-HSC are quiescent in G0 at any one time, all HSC are recruited into cycle regularly such that 99% of LT-HSC divide on average every 57 days."], "structured": false}
{"doc_id": 18375089, "title": "The role of the tissue omega-6/omega-3 fatty acid ratio in regulating tumor angiogenesis", "abstract": ["Angiogenesis is a necessary step in tumor growth and metastasis.", "It is well established that the metabolites of omega-6 and omega-3 fatty acids, which must be obtained through the diet and cannot be synthesized de novo in mammals, have differential effects on cellular processes.", "Omega-6 fatty acid (n\u22126 FA)-derived metabolites promote angiogenesis by increasing growth factor expression whereas omega-3 fatty acids (n\u22123 FA) have anti-angiogenic and antitumor properties.", "However, most studies thus far have failed to account for the role of the n\u22126 FA/n\u22123 FA ratio in angiogenesis and instead examined the absolute levels of n\u22126 and n\u22123 FA.", "This review highlights the biochemical interactions between n\u22126 and n\u22123 FA and focuses on how the n\u22126/n\u22123 FA ratio in tissues modulates tumor angiogenesis.", "We suggest that future work should consider the n\u22126/n\u22123 FA ratio to be a key element in experimental design and analysis.", "Furthermore, we recommend that clinical interventions should aim to both reduce n\u22126 metabolites and simultaneously increase n\u22123 FA intake."], "structured": false}
{"doc_id": 18379855, "title": "The Natural Statistics of Audiovisual Speech", "abstract": ["Humans, like other animals, are exposed to a continuous stream of signals, which are dynamic, multimodal, extended, and time varying in nature.", "This complex input space must be transduced and sampled by our sensory systems and transmitted to the brain where it can guide the selection of appropriate actions.", "To simplify this process, it's been suggested that the brain exploits statistical regularities in the stimulus space.", "Tests of this idea have largely been confined to unimodal signals and natural scenes.", "One important class of multisensory signals for which a quantitative input space characterization is unavailable is human speech.", "We do not understand what signals our brain has to actively piece together from an audiovisual speech stream to arrive at a percept versus what is already embedded in the signal structure of the stream itself.", "In essence, we do not have a clear understanding of the natural statistics of audiovisual speech.", "In the present study, we identified the following major statistical features of audiovisual speech.", "First, we observed robust correlations and close temporal correspondence between the area of the mouth opening and the acoustic envelope.", "Second, we found the strongest correlation between the area of the mouth opening and vocal tract resonances.", "Third, we observed that both area of the mouth opening and the voice envelope are temporally modulated in the 2-7 Hz frequency range.", "Finally, we show that the timing of mouth movements relative to the onset of the voice is consistently between 100 and 300 ms.", "We interpret these data in the context of recent neural theories of speech which suggest that speech communication is a reciprocally coupled, multisensory event, whereby the outputs of the signaler are matched to the neural processes of the receiver."], "structured": false}
{"doc_id": 18399038, "title": "Establishment of human iPSC-based models for the study and targeting of glioma initiating cells", "abstract": ["Glioma tumour-initiating cells (GTICs) can originate upon the transformation of neural progenitor cells (NPCs).", "Studies on GTICs have focused on primary tumours from which GTICs could be isolated and the use of human embryonic material.", "Recently, the somatic genomic landscape of human gliomas has been reported.", "RTK (receptor tyrosine kinase) and p53 signalling were found dysregulated in \u223c90% and 86% of all primary tumours analysed, respectively.", "Here we report on the use of human-induced pluripotent stem cells (hiPSCs) for modelling gliomagenesis.", "Dysregulation of RTK and p53 signalling in hiPSC-derived NPCs (iNPCs) recapitulates GTIC properties in vitro.", "In vivo transplantation of transformed iNPCs leads to highly aggressive tumours containing undifferentiated stem cells and their differentiated derivatives.", "Metabolic modulation compromises GTIC viability.", "Last, screening of 101 anti-cancer compounds identifies three molecules specifically targeting transformed iNPCs and primary GTICs.", "Together, our results highlight the potential of hiPSCs for studying human tumourigenesis."], "structured": false}
{"doc_id": 18414462, "title": "Thyroid Hormone Receptor Repression Linked to Type I Pneumocyte Associated Respiratory Distress Syndrome", "abstract": ["Although the lung is a defining feature of air-breathing animals, the pathway controlling the formation of type I pneumocytes, the cells that mediate gas exchange, is poorly understood.", "In contrast, the glucocorticoid receptor and its cognate ligand have long been known to promote type II pneumocyte maturation; prenatal administration of glucocorticoids is commonly used to attenuate the severity of infant respiratory distress syndrome (RDS).", "Here we show that knock-in mutations of the nuclear co-repressor SMRT (silencing mediator of retinoid and thyroid hormone receptors) in C57BL/6 mice (SMRTmRID) produces a previously unidentified respiratory distress syndrome caused by prematurity of the type I pneumocyte.", "Though unresponsive to glucocorticoids, treatment with anti-thyroid hormone drugs (propylthiouracil or methimazole) completely rescues SMRT-induced RDS, suggesting an unrecognized and essential role for the thyroid hormone receptor (TR) in lung development.", "We show that TR and SMRT control type I pneumocyte differentiation through Klf2, which, in turn, seems to directly activate the type I pneumocyte gene program.", "Conversely, mice without lung Klf2 lack mature type I pneumocytes and die shortly after birth, closely recapitulating the SMRTmRID phenotype.", "These results identify TR as a second nuclear receptor involved in lung development, specifically type I pneumocyte differentiation, and suggest a possible new type of therapeutic option in the treatment of RDS that is unresponsive to glucocorticoids."], "structured": false}
{"doc_id": 18421962, "title": "Assessing the ceRNA hypothesis with quantitative measurements of miRNA and target abundance.", "abstract": ["Recent studies have reported that competitive endogenous RNAs (ceRNAs) can act as sponges for a microRNA (miRNA) through their binding sites and that changes in ceRNA abundances from individual genes can modulate the activity of miRNAs.", "Consideration of this hypothesis would benefit from knowing the quantitative relationship between a miRNA and its endogenous target sites.", "Here, we altered intracellular target site abundance through expression of an miR-122 target in hepatocytes and livers and analyzed the effects on miR-122 target genes.", "Target repression was released in a threshold-like manner at high target site abundance (\u22651.5 \u00d7 10(5) added target sites per cell), and this threshold was insensitive to the effective levels of the miRNA.", "Furthermore, in response to extreme metabolic liver disease models, global target site abundance of hepatocytes did not change sufficiently to affect miRNA-mediated repression.", "Thus, modulation of miRNA target abundance is unlikely to cause significant effects on gene expression and metabolism through a ceRNA effect."], "structured": false}
{"doc_id": 18429416, "title": "Immunological mechanisms for desensitization and tolerance in food allergy", "abstract": ["Food allergy is a major public health concern in westernized countries, estimated to affect 5 % of children and 3\u20134 % of adults.", "Allergen-specific immunotherapy for food allergy is currently being actively evaluated, but is still experimental.", "The optimal protocol, in terms of the route of administration of the food, target maintenance dose, and duration of maintenance therapy, and the optimal patient for these procedures are still being worked out.", "The mechanisms underlying successful food desensitization are also unclear, in part, because there is no standard immunotherapy protocol.", "The mechanisms involved, however, may include mast cell and basophil suppression, development of food-specific IgG4 antibodies, reduction in the food-specific IgE/IgG4 ratio, up-regulation and expansion of natural or inducible regulatory T cells, a skewing from a Th2 to a Th1 profile, and the development of anergy and/or deletion in antigen-specific cells.", "Additional studies are required to elucidate and understand these mechanisms by which desensitization and tolerance are achieved, which may reveal valuable biomarkers for evaluating and following food allergic patients on immunotherapy."], "structured": false}
{"doc_id": 18446525, "title": "Prodromal non-motor symptoms of Parkinson\u2019s disease", "abstract": ["The motor symptoms of Parkinson\u2019s disease (PD), bradykinesia, muscular rigidity, and tremor depend upon degeneration of the dopaminergic neurons in the substantia nigra pars compacta.", "Recent neuropathological studies show that the Lewy bodies, the intraneuronal landmark of PD, accumulate in several neuronal cell types in the brain.", "An ascending gradient of pathological involvement, from the medulla oblongata to neocortical areas has been reported.", "Thus the original view of PD as a disease characterized by selective damage of the dopaminergic neurons in the mesencephalon should be updated into the concept of a severe multisystemic neurodegenerative disorder.", "Additionally, the neuropathological alterations outside the substantia nigra are soundly correlated with the non-motor symptoms of PD.", "As a result of these findings, interest is growing in the identification of prodromal non-motor symptoms of PD.", "Indeed, data from the literature suggest that autonomic disturbances, olfactory dysfunctions, depression and sleep disorders (in particular REM-sleep behavior disorder) may represent prodromal non-motor symptoms of PD.", "Several tests are available to detect most of these symptoms.", "Thus, the identification of prodromal non-motor symptoms may contribute to the precocious diagnosis of PD, and might be useful in the future to test the efficacy of neuroprotective agents."], "structured": false}
{"doc_id": 18447487, "title": "Erythroid Kr\u00fcppel-Like Factor Directly Activates the Basic Kr\u00fcppel-Like Factor Gene in Erythroid Cells \ufffd", "abstract": ["The Sp/Kr\u00fcppel-like factor (Sp/Klf) family is comprised of around 25 zinc finger transcription factors that recognize CACCC boxes and GC-rich elements.", "We have investigated basic Kr\u00fcppel-like factor (Bklf/Klf3) and show that in erythroid tissues its expression is highly dependent on another family member, erythroid Kr\u00fcppel-like factor (Eklf/Klf1).", "We observe that Bklf mRNA is significantly reduced in erythroid tissues from Eklf-null murine embryos.", "We find that Bklf is driven primarily by two promoters, a ubiquitously active GC-rich upstream promoter, 1a, and an erythroid downstream promoter, 1b.", "Transcripts from the two promoters encode identical proteins.", "Interestingly, both the ubiquitous and the erythroid promoter are dependent on Eklf in erythroid cells.", "Eklf also activates both promoters in transient assays.", "Experiments utilizing an inducible form of Eklf demonstrate activation of the endogenous Bklf gene in the presence of an inhibitor of protein synthesis.", "The kinetics of activation are also consistent with Bklf being a direct Eklf target.", "Chromatin immunoprecipitation assays confirm that Eklf associates with both Bklf promoters.", "Eklf is typically an activator of transcription, whereas Bklf is noted as a repressor.", "Our results support the hypothesis that feedback cross-regulation occurs within the Sp/Klf family in vivo."], "structured": false}
{"doc_id": 18450716, "title": "Noncanonical Wnt Signaling Promotes Obesity-Induced Adipose Tissue Inflammation and Metabolic Dysfunction Independent of Adipose Tissue Expansion", "abstract": ["Adipose tissue dysfunction plays a pivotal role in the development of insulin resistance in obese individuals.", "Cell culture studies and gain-of-function mouse models suggest that canonical Wnt proteins modulate adipose tissue expansion.", "However, no genetic evidence supports a role for endogenous Wnt proteins in adipose tissue dysfunction, and the role of noncanonical Wnt signaling remains largely unexplored.", "Here we provide evidence from human, mouse, and cell culture studies showing that Wnt5a-mediated, noncanonical Wnt signaling contributes to obesity-associated metabolic dysfunction by increasing adipose tissue inflammation.", "Wnt5a expression is significantly upregulated in human visceral fat compared with subcutaneous fat in obese individuals.", "In obese mice, Wnt5a ablation ameliorates insulin resistance, in parallel with reductions in adipose tissue inflammation.", "Conversely, Wnt5a overexpression in myeloid cells augments adipose tissue inflammation and leads to greater impairments in glucose homeostasis.", "Wnt5a ablation or overexpression did not affect fat mass or adipocyte size.", "Mechanistically, Wnt5a promotes the expression of proinflammatory cytokines by macrophages in a Jun NH2-terminal kinase-dependent manner, leading to defective insulin signaling in adipocytes.", "Exogenous interleukin-6 administration restores insulin resistance in obese Wnt5a-deficient mice, suggesting a central role for this cytokine in Wnt5a-mediated metabolic dysfunction.", "Taken together, these results demonstrate that noncanonical Wnt signaling contributes to obesity-induced insulin resistance independent of adipose tissue expansion."], "structured": false}
{"doc_id": 18467982, "title": "A cluster of ribosome synthesis factors regulate pre-rRNA folding and 5.8S rRNA maturation by the Rat1 exonuclease", "abstract": ["The 5'-exonuclease Rat1 degrades pre-rRNA spacer fragments and processes the 5'-ends of the 5.8S and 25S rRNAs.", "UV crosslinking revealed multiple Rat1-binding sites across the pre-rRNA, consistent with its known functions.", "The major 5.8S 5'-end is generated by Rat1 digestion of the internal transcribed spacer 1 (ITS1) spacer from cleavage site A(3).", "Processing from A(3) requires the 'A(3)-cluster' proteins, including Cic1, Erb1, Nop7, Nop12 and Nop15, which show interdependent pre-rRNA binding.", "Surprisingly, A(3)-cluster factors were not crosslinked close to site A(3), but bound sites around the 5.8S 3'- and 25S 5'-regions, which are base paired in mature ribosomes, and in the ITS2 spacer that separates these rRNAs.", "In contrast, Nop4, a protein required for endonucleolytic cleavage in ITS1, binds the pre-rRNA near the 5'-end of 5.8S.", "ITS2 was reported to undergo structural remodelling.", "In vivo chemical probing indicates that A(3)-cluster binding is required for this reorganization, potentially regulating the timing of processing.", "We predict that Nop4 and the A(3) cluster establish long-range interactions between the 5.8S and 25S rRNAs, which are subsequently maintained by ribosomal protein binding."], "structured": false}
{"doc_id": 18473550, "title": "Synergistic activity of the histone deacetylase inhibitor suberoylanilide hydroxamic acid and the bisphosphonate zoledronic acid against prostate cancer cells in vitro.", "abstract": ["Bisphosphonates are widely used agents for the treatment of malignant bone disease.", "They inhibit osteoclast-mediated bone resorption and can have direct effects on cancer cells.", "In this study, we investigated whether the anticancer activity of the third-generation bisphosphonate zoledronic acid (ZOL) could be enhanced by combination with the histone deacetylase inhibitor suberoylanilide hydroxamic acid (SAHA).", "We found that ZOL and SAHA cooperated to induce cell death in the prostate cancer cell lines LNCaP and PC-3.", "The effect was synergistic, as evidenced by combination index isobologram analysis.", "ZOL and SAHA synergized to induce dissipation of the mitochondrial transmembrane potential, to activate caspase-3, and to trigger DNA fragmentation, showing that the combination of ZOL and SAHA resulted in the initiation of apoptosis.", "Because ZOL acts by inhibiting the mevalonate pathway, thereby preventing protein prenylation, we explored whether the mevalonate pathway was also the target of the cooperative action of ZOL and SAHA.", "We found that geranylgeraniol, but not farnesol, significantly reduced ZOL/SAHA-induced cell death, indicating that the synergistic action of the agents was due to the inhibition of geranylgeranylation.", "Consistently, a direct inhibitor of geranylgeranylation, GGTI-298, synergized with SAHA to induce cell death, whereas an inhibitor of farnesylation, FTI-277, had no effect.", "In addition, SAHA synergized with mevastatin, an inhibitor of the proximal enzyme in the mevalonate pathway.", "These in vitro findings provide a rationale for an in vivo exploration into the potential of combining SAHA and ZOL, or other inhibitors of the mevalonate pathway, as an effective strategy for anticancer therapy."], "structured": false}
{"doc_id": 18488986, "title": "The Immune Response to Melanoma Is Limited by Thymic Selection of Self-Antigens", "abstract": ["The expression of melanoma-associated antigens (MAA) being limited to normal melanocytes and melanomas, MAAs are ideal targets for immunotherapy and melanoma vaccines.", "As MAAs are derived from self, immune responses to these may be limited by thymic tolerance.", "The extent to which self-tolerance prevents efficient immune responses to MAAs remains unknown.", "The autoimmune regulator (AIRE) controls the expression of tissue-specific self-antigens in thymic epithelial cells (TECs).", "The level of antigens expressed in the TECs determines the fate of auto-reactive thymocytes.", "Deficiency in AIRE leads in both humans (APECED patients) and mice to enlarged autoreactive immune repertoires.", "Here we show increased IgG levels to melanoma cells in APECED patients correlating with autoimmune skin features.", "Similarly, the enlarged T cell repertoire in AIRE(-/-) mice enables them to mount anti-MAA and anti-melanoma responses as shown by increased anti-melanoma antibodies, and enhanced CD4(+) and MAA-specific CD8(+) T cell responses after melanoma challenge.", "We show that thymic expression of gp100 is under the control of AIRE, leading to increased gp100-specific CD8(+) T cell frequencies in AIRE(-/-) mice.", "TRP-2 (tyrosinase-related protein), on the other hand, is absent from TECs and consequently TRP-2 specific CD8(+) T cells were found in both AIRE(-/-) and AIRE(+/+) mice.", "This study emphasizes the importance of investigating thymic expression of self-antigens prior to their inclusion in vaccination and immunotherapy strategies."], "structured": false}
{"doc_id": 18489989, "title": "Murine embryonic stem cell differentiation is promoted by SOCS-3 and inhibited by the zinc finger transcription factor Klf4.", "abstract": ["Embryonic stem (ES) cells homozygous for a Shp-2 mutation (Shp-2(Delta46-110)) demonstrate leukemia inhibitory factor (LIF) hypersensitivity and increased LIF-stimulated phosphorylation of signal transducer and activator of transcription (STAT3).", "We hypothesized that LIF-responsive genes in Shp-2(Delta46-110) cells would represent potential candidates for molecules vital for ES cell self-renewal.", "Using microarray analysis, we detected 41 genes whose expression was modified by LIF in Shp-2(Delta46-110) ES cells.", "Induction of 2 significantly up-regulated genes, suppressor of cytokine signaling-3 (SOCS-3) and Kruppel-like factor 4 (Klf4), was verified using Northern blotting.", "ES cells overexpressing SOCS-3 had an increased capacity to differentiate to hematopoietic progenitors, rather than to self-renew.", "In contrast, ES cells overexpressing Klf4 had a greater capacity to self-renew based on secondary embryoid body (EB) formation.", "Klf4-transduced d6 EBs expressed higher levels of Oct-4, consistent with the notion that Klf4 promotes ES cell self-renewal.", "These findings verify the negative role of SOCS-3 on LIF signaling and provide a novel role for Klf4 in ES cell function."], "structured": false}
{"doc_id": 18494847, "title": "MicroScope\u2014an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data", "abstract": ["MicroScope is an integrated platform dedicated to both the methodical updating of microbial genome annotation and to comparative analysis.", "The resource provides data from completed and ongoing genome projects (automatic and expert annotations), together with data sources from post-genomic experiments (i.e. transcriptomics, mutant collections) allowing users to perfect and improve the understanding of gene functions.", "MicroScope (http://www.genoscope.cns.fr/agc/microscope) combines tools and graphical interfaces to analyse genomes and to perform the manual curation of gene annotations in a comparative context.", "Since its first publication in January 2006, the system (previously named MaGe for Magnifying Genomes) has been continuously extended both in terms of data content and analysis tools.", "The last update of MicroScope was published in 2009 in the Database journal.", "Today, the resource contains data for >1600 microbial genomes, of which \u223c300 are manually curated and maintained by biologists (1200 personal accounts today).", "Expert annotations are continuously gathered in the MicroScope database (\u223c50 000 a year), contributing to the improvement of the quality of microbial genomes annotations.", "Improved data browsing and searching tools have been added, original tools useful in the context of expert annotation have been developed and integrated and the website has been significantly redesigned to be more user-friendly.", "Furthermore, in the context of the European project Microme (Framework Program 7 Collaborative Project), MicroScope is becoming a resource providing for the curation and analysis of both genomic and metabolic data.", "An increasing number of projects are related to the study of environmental bacterial (meta)genomes that are able to metabolize a large variety of chemical compounds that may be of high industrial interest."], "structured": false}
{"doc_id": 18537148, "title": "Comparison of Maximal Oxygen Consumption Between Black and White Prepubertal and Pubertal Children", "abstract": ["The purpose of this investigation was to determine whether maximal oxygen consumption (VO2max) differed between two selected groups of black and white children and whether a difference existed to determine whether it was related to hematologic profiles, body composition, and/or physical activity/inactivity level.", "Forty-five prepubertal and 42 pubertal, clinically normal black and white children participated.", "Dual-energy x-ray absorptiometry was used to determine body composition.", "A computed tomography scan of the abdomen was used to determine visceral adipose tissue and s.c.", "adipose tissue.", "Daily physical activity/inactivity was assessed by questionnaire.", "Black prepubertal and pubertal children had lower VO2max values when compared with white children (28.8 \u00b1 7.8 versus 35.0 \u00b1 6.5 mL \u00b7 kg\u22121 \u00b7 min\u22121, p < 0.01; 33.7 \u00b1 6.4 versus 40.4 \u00b1 10.2 mL \u00b7 kg\u22121 \u00b7 min\u22121, p < 0.05; respectively).", "Black prepubertal and pubertal children had lower Hb concentrations ([Hb]) and hematocrits than white children (prepubertal: 12.1 \u00b1 0.5 versus 12.8 \u00b1 0.9 g/dL, p < 0.001; 35.6 \u00b1 1.4 versus 37.4 \u00b1 2.3%, p < 0.01, respectively; pubertal: 13.0 \u00b1 0.9 versus 13.6 \u00b1 0.7 g/dL, p < 0.05; 37.7 \u00b1 2.5 versus 39.5 \u00b1 2.1%, p < 0.05, respectively).", "In conclusion, these findings indicate that black prepubertal and pubertal children had lower VO2max when compared with their white peers matched for age, pubertal stage, and body mass index.", "This difference in VO2max could be attributed at least in part to comparatively lower [Hb] and more sedentary lifestyle in the black children.", "Further investigations should study Hb flow rate (a function of [Hb] \u00d7 maximal cardiac output) in black and white children as it relates to VO2max."], "structured": false}
{"doc_id": 18546584, "title": "Retinoic acid inhibits Th17 polarization and enhances FoxP3 expression through a Stat-3/Stat-5 independent signaling pathway.", "abstract": ["CD4(+) helper T (Th) cells play a crucial role in the delicate balance between host defense and autoimmune disease.", "Two important populations of helper T cells are the proinflammatory, interleukin-17 (IL-17)-producing (Th17) cells and the anti-inflammatory forkhead box P3-positive (FoxP3(+)) T regulatory (Treg) cells.", "Here we show that all-trans retinoic acid (ATRA) and other agonists of the retinoic acid receptor alpha (RARalpha) inhibit the formation of Th17 cells and promote FoxP3 expression.", "Conversely, inhibition of retinoic acid signaling constrains transforming growth factor beta (TGF-beta1) induction of FoxP3.", "The effect of ATRA is mediated independently of IL-2, signal transducer and activator of transcription 5 (Stat5) and Stat3, representing a novel mechanism for the induction of FoxP3 in CD4 T cells.", "As previous studies have shown that vitamin A derivatives are protective in animal models of autoimmune disease, the current data suggest a previously unrecognized role for RARalpha in the regulation of CD4(+) T-cell differentiation and provide a mechanism for the anti-inflammatory effects of retinoic acid."], "structured": false}
{"doc_id": 18557974, "title": "British Journal of Nutrition (2003), 89, 295\u2013301 q The Authors 2003 DOI: 10.1079/BJN2002776 Plasma homocysteine concentration is decreased by dietary intervention*", "abstract": ["High plasma total homocysteine (tHcy) concentration is reported to be a risk factor for vascular diseases.", "We investigated the extent to which serum folate and plasma tHcy respond to a high intake of natural folate from food.", "Thirty-seven healthy females volunteered t o participate in a crossover dietary intervention.", "The study included a baseline period and two 5-week diet periods (low- and high-folate diets) with a 3-week washout in between.", "The low-folate diet contained one serving of both vegetables and fruit/d, while during the high-folate diet the subjects ate at least seven servings of vegetables, berries, and citrus fruit/d.", "Serum and erythrocyte (RBC) folate, serum vitamin B (12), and plasma tHcy concentrations were measured at the base-line and at the end of each diet period.", "The mean concentrations of serum and RBC folate were 11.0 (SD 3.0) nmol/l and 412 (SD 120) nmol/l at the end of the low-folate diet and 78 (95 % CI 62, 94) % and 14 (95 % CI 8, 20) % higher in response to the high-folate diet (P< 0.001).", "The serum concentration of vitamin B12 remained unchanged during the intervention.", "The mean plasma tHcy concentration was 8.0 pmol/ at the end of the low-folate diet and decreased by 13 (95% CI 9, 18) % in response to the high-folate diet (P<0.001).", "In conclusion, a diet high in fresh berries, citrus fruit, and vegetables effectively increases serum and RBC folate and decreases plasma homocysteine."], "structured": false}
{"doc_id": 18568804, "title": "Achieving increased resolution and more pixels with Superresolution Optical Fluctuation Imaging (SOFI)", "abstract": ["Superresolution Optical Fluctuation Imaging (SOFI) as initially demonstrated allows for a resolution enhancement in imaging by a factor of square-root of two.", "Here, we demonstrate how to increase the resolution of SOFI images by re-weighting the Optical Transfer Function (OTF).", "Furthermore, we demonstrate how cross-cumulants can be exploited to obtain a fair approximation of the underlying Point-Spread Function.", "We show a two-fold increase of resolution (over the diffraction limit) of near-infrared quantum dot labeled tubulin-network of 3T3 fibroblasts."], "structured": false}
{"doc_id": 18574146, "title": "Evaluation of reagent strips in detecting asymptomatic bacteriuria in early pregnancy: prospective case series.", "abstract": ["OBJECTIVE To evaluate the performance of reagent test strips in screening pregnant women for asymptomatic bacteriuria at their first visit to an antenatal clinic.   \n", "DESIGN Prospective case series.   \n", "SETTING Antenatal clinic of a large inner city maternity hospital.   ", "SUBJECTS All women attending for their first antenatal clinic.", "Patients taking antibiotics for any reason and those with urinary tract symptoms were excluded.   \n", "INTERVENTION A midstream urine specimen was divided; half was sent for microscopy and formal bacteriological culture and the other half was tested with a commercial reagent strip test for the presence of blood, protein, nitrite, and leucocyte esterase.   \n", "MAIN OUTCOME MEASURES Sensitivity, specificity, and positive and negative predictive values of the reagent strips in diagnosing asymptomatic bacteriuria (defined as 10(5) colony forming units/ml urine).   \n", "RESULTS Sensitivity was low, with a maximum of 33% when all four tests were used in combination.", "Specificity was high, with typical values of 99% or more.", "Positive predictive value reached a maximum of 69% and negative predictive value was typically 95% or more.   \n", "CONCLUSION Urine reagent strips are not sufficiently sensitive to be of use in the screening for asymptomatic bacteriuria and therefore many patients would be missed.", "In view of the potentially serious sequelae of this condition in pregnant women we recommend that formal bacteriological investigation remain the investigation of choice in this group of patients."], "structured": true}
{"doc_id": 18575183, "title": "Wnt5a functions in planar cell polarity regulation in mice.", "abstract": ["Planar cell polarity (PCP) refers to the polarization of cells within the plane of a cell sheet.", "A distinctive epithelial PCP in vertebrates is the uniform orientation of stereociliary bundles of the sensory hair cells in the mammalian cochlea.", "In addition to establishing epithelial PCP, planar polarization is also required for convergent extension (CE); a polarized cellular movement that occurs during neural tube closure and cochlear extension.", "Studies in Drosophila and vertebrates have revealed a conserved PCP pathway, including Frizzled (Fz) receptors.", "Here we use the cochlea as a model system to explore the involvement of known ligands of Fz, Wnt morphogens, in PCP regulation.", "We show that Wnt5a forms a reciprocal expression pattern with a Wnt antagonist, the secreted frizzled-related protein 3 (Sfrp3 or Frzb), along the axis of planar polarization in the cochlear epithelium.", "We further demonstrate that Wnt5a antagonizes Frzb in regulating cochlear extension and stereociliary bundle orientation in vitro, and that Wnt5a(-/-) animals have a shortened and widened cochlea.", "Finally, we show that Wnt5a is required for proper subcellular distribution of a PCP protein, Ltap/Vangl2, and that Wnt5a interacts genetically with Ltap/Vangl2 for uniform orientation of stereocilia, cochlear extension, and neural tube closure.", "Together, these findings demonstrate that Wnt5a functions in PCP regulation in mice."], "structured": false}
{"doc_id": 18576103, "title": "The RNA Polymerase \u201cSwitch Region\u201d Is a Target for Inhibitors", "abstract": ["The alpha-pyrone antibiotic myxopyronin (Myx) inhibits bacterial RNA polymerase (RNAP).", "Here, through a combination of genetic, biochemical, and structural approaches, we show that Myx interacts with the RNAP \"switch region\"--the hinge that mediates opening and closing of the RNAP active center cleft--to prevent interaction of RNAP with promoter DNA.", "We define the contacts between Myx and RNAP and the effects of Myx on RNAP conformation and propose that Myx functions by interfering with opening of the RNAP active-center cleft during transcription initiation.", "We further show that the structurally related alpha-pyrone antibiotic corallopyronin (Cor) and the structurally unrelated macrocyclic-lactone antibiotic ripostatin (Rip) function analogously to Myx.", "The RNAP switch region is distant from targets of previously characterized RNAP inhibitors, and, correspondingly, Myx, Cor, and Rip do not exhibit crossresistance with previously characterized RNAP inhibitors.", "The RNAP switch region is an attractive target for identification of new broad-spectrum antibacterial therapeutic agents."], "structured": false}
{"doc_id": 18592108, "title": "How reliable are light traps in estimating biting rates of adult Anopheles gambiae s.l. (Diptera: Culicidae) in the presence of treated bed nets?", "abstract": ["The sampling efficiency of light trap catches relative to human bait catches in estimating biting rates of the mosquito Anopheles gambiae Giles was investigated in two types of community in southern Sierra Leone: (i) where most of the inhabitants slept under treated bed nets; and (ii) where most of the inhabitants slept without bed nets.", "The number of female A. gambiae mosquitoes caught in these communities by light trap was strongly correlated (r > or = 0.72) with those from corresponding human biting catches performed either on the same or adjacent nights.", "It was found that the relative sampling efficiency of light traps varied slightly but significantly with mosquito abundance in villages with treated bed nets, but not in those without them.", "Nevertheless, the relationship between relative sampling efficiency and mosquito abundance did not differ significantly between the two types of village.", "Overall, there was insufficient evidence to show that the presence of treated nets altered the relative efficiency of light traps and any bias was only slight, and unlikely to be of any practical importance.", "Hence, it was concluded that light traps can be used as a surrogate for human bait catches in estimating biting rates of A. gambiae mosquitoes in the two communities."], "structured": false}
{"doc_id": 18600579, "title": "Development of a novel mouse glioma model using lentiviral vectors", "abstract": ["We report the development of a new method to induce glioblastoma multiforme in adult immunocompetent mice by injecting Cre-loxP\u2013controlled lentiviral vectors expressing oncogenes.", "Cell type- or region-specific expression of activated forms of the oncoproteins Harvey-Ras and AKT in fewer than 60 glial fibrillary acidic protein\u2013positive cells in the hippocampus, subventricular zone or cortex of mice heterozygous for the gene encoding the tumor suppressor Tp53 were tested.", "Mice developed glioblastoma multiforme when transduced either in the subventricular zone or the hippocampus.", "However, tumors were rarely detected when the mice were transduced in the cortex.", "Transplantation of brain tumor cells into naive recipient mouse brain resulted in the formation of glioblastoma multiforme\u2013like tumors, which contained CD133+ cells, formed tumorspheres and could differentiate into neurons and astrocytes.", "We suggest that the use of Cre-loxP\u2013controlled lentiviral vectors is a novel way to generate a mouse glioblastoma multiforme model in a region- and cell type-specific manner in adult mice."], "structured": false}
{"doc_id": 18617259, "title": "Research Letters", "abstract": ["We report a case of preclinical variant Creutzfeldt-Jakob disease (vCJD) in a patient who died from a non-neurological disorder 5 years after receiving a blood transfusion from a donor who subsequently developed vCJD.", "Protease-resistant prion protein (PrP(res)) was detected by western blot, paraffin-embedded tissue blot, and immunohistochemistry in the spleen, but not in the brain.", "Immunohistochemistry for prion protein was also positive in a cervical lymph node.", "The patient was a heterozygote at codon 129 of PRNP, suggesting that susceptibility to vCJD infection is not confined to the methionine homozygous PRNP genotype.", "These findings have major implications for future estimates and surveillance of vCJD in the UK."], "structured": false}
{"doc_id": 18639989, "title": "Swi1Timeless Prevents Repeat Instability at Fission Yeast Telomeres", "abstract": ["Genomic instability associated with DNA replication stress is linked to cancer and genetic pathologies in humans.", "If not properly regulated, replication stress, such as fork stalling and collapse, can be induced at natural replication impediments present throughout the genome.", "The fork protection complex (FPC) is thought to play a critical role in stabilizing stalled replication forks at several known replication barriers including eukaryotic rDNA genes and the fission yeast mating-type locus.", "However, little is known about the role of the FPC at other natural impediments including telomeres.", "Telomeres are considered to be difficult to replicate due to the presence of repetitive GT-rich sequences and telomere-binding proteins.", "However, the regulatory mechanism that ensures telomere replication is not fully understood.", "Here, we report the role of the fission yeast Swi1(Timeless), a subunit of the FPC, in telomere replication.", "Loss of Swi1 causes telomere shortening in a telomerase-independent manner.", "Our epistasis analyses suggest that heterochromatin and telomere-binding proteins are not major impediments for telomere replication in the absence of Swi1.", "Instead, repetitive DNA sequences impair telomere integrity in swi1\u0394 mutant cells, leading to the loss of repeat DNA.", "In the absence of Swi1, telomere shortening is accompanied with an increased recruitment of Rad52 recombinase and more frequent amplification of telomere/subtelomeres, reminiscent of tumor cells that utilize the alternative lengthening of telomeres pathway (ALT) to maintain telomeres.", "These results suggest that Swi1 ensures telomere replication by suppressing recombination and repeat instability at telomeres.", "Our studies may also be relevant in understanding the potential role of Swi1(Timeless) in regulation of telomere stability in cancer cells."], "structured": false}
{"doc_id": 18654430, "title": "Prediction of guide strand of microRNAs from its sequence and secondary structure", "abstract": ["BACKGROUND MicroRNAs (miRNAs) are produced by the sequential processing of a long hairpin RNA transcript by Drosha and Dicer, an RNase III enzymes, and form transitory small RNA duplexes.", "One strand of the duplex, which incorporates into RNA-induced silencing complex (RISC) and silences the gene expression is called guide strand, or miRNA; while the other strand of duplex is degraded and called the passenger strand, or miRNA*. Predicting the guide strand of miRNA is important for better understanding the RNA interference pathways.   \n", "RESULTS This paper describes support vector machine (SVM) models developed for predicting the guide strands of miRNAs.", "All models were trained and tested on a dataset consisting of 329 miRNA and 329 miRNA* pairs using five fold cross validation technique.", "Firstly, models were developed using mono-, di-, and tri-nucleotide composition of miRNA strands and achieved the highest accuracies of 0.588, 0.638 and 0.596 respectively.", "Secondly, models were developed using split nucleotide composition and achieved maximum accuracies of 0.553, 0.641 and 0.602 for mono-, di-, and tri-nucleotide respectively.", "Thirdly, models were developed using binary pattern and achieved the highest accuracy of 0.708.", "Furthermore, when integrating the secondary structure features with binary pattern, an accuracy of 0.719 was seen.", "Finally, hybrid models were developed by combining various features and achieved maximum accuracy of 0.799 with sensitivity 0.781 and specificity 0.818.", "Moreover, the performance of this model was tested on an independent dataset that achieved an accuracy of 0.80.", "In addition, we also compared the performance of our method with various siRNA-designing methods on miRNA and siRNA datasets.   \n", "CONCLUSION In this study, first time a method has been developed to predict guide miRNA strands, of miRNA duplex.", "This study demonstrates that guide and passenger strand of miRNA precursors can be distinguished using their nucleotide sequence and secondary structure.", "This method will be useful in understanding microRNA processing and can be implemented in RNA silencing technology to improve the biological and clinical research.", "A web server has been developed based on SVM models described in this study (http://crdd.osdd.net:8081/RISCbinder/)."], "structured": true}
{"doc_id": 18662787, "title": "NIPBL, encoding a homolog of fungal Scc2-type sister chromatid cohesion proteins and fly Nipped-B, is mutated in Cornelia de Lange syndrome", "abstract": ["Cornelia de Lange syndrome (CdLS) is a multiple malformation disorder characterized by dysmorphic facial features, mental retardation, growth delay and limb reduction defects.", "We indentified and characterized a new gene, NIPBL, that is mutated in individuals with CdLS and determined its structure and the structures of mouse, rat and zebrafish homologs.", "We named its protein product delangin.", "Vertebrate delangins have substantial homology to orthologs in flies, worms, plants and fungi, including Scc2-type sister chromatid cohesion proteins, and D. melanogaster Nipped-B. We propose that perturbed delangin function may inappropriately activate DLX genes, thereby contributing to the proximodistal limb patterning defects in CdLS.", "Genome analyses typically identify individual delangin or Nipped-B-like orthologs in diploid animal and plant genomes.", "The evolution of an ancestral sister chromatid cohesion protein to acquire an additional role in developmental gene regulation suggests that there are parallels between CdLS and Roberts syndrome."], "structured": false}
{"doc_id": 18676539, "title": "Impaired FANCD2 monoubiquitination and hypersensitivity to camptothecin uniquely characterize Fanconi anemia complementation group M.", "abstract": ["FANCM is a component of the Fanconi anemia (FA) core complex and one FA patient (EUFA867) with biallelic mutations in FANCM has been described.", "Strikingly, we found that EUFA867 also carries biallelic mutations in FANCA.", "After correcting the FANCA defect in EUFA867 lymphoblasts, a \"clean\" FA-M cell line was generated.", "These cells were hypersensitive to mitomycin C, but unlike cells defective in other core complex members, FANCM(-/-) cells were proficient in monoubiquitinating FANCD2 and were sensitive to the topoisomerase inhibitor camptothecin, a feature shared only with the FA subtype D1 and N. In addition, FANCM(-/-) cells were sensitive to UV light.", "FANCM and a C-terminal deletion mutant rescued the cross-linker sensitivity of FANCM(-/-) cells, whereas a FANCM ATPase mutant did not.", "Because both mutants restored the formation of FANCD2 foci, we conclude that FANCM functions in an FA core complex-dependent and -independent manner."], "structured": false}
{"doc_id": 18678095, "title": "Vesicular Glycolysis Provides On-Board Energy for Fast Axonal Transport", "abstract": ["Fast axonal transport (FAT) requires consistent energy over long distances to fuel the molecular motors that transport vesicles.", "We demonstrate that glycolysis provides ATP for the FAT of vesicles.", "Although inhibiting ATP production from mitochondria did not affect vesicles motility, pharmacological or genetic inhibition of the glycolytic enzyme GAPDH reduced transport in cultured neurons and in Drosophila larvae.", "GAPDH localizes on vesicles via a huntingtin-dependent mechanism and is transported on fast-moving vesicles within axons.", "Purified motile vesicles showed GAPDH enzymatic activity and produced ATP.", "Finally, we show that vesicular GAPDH is necessary and sufficient to provide on-board energy for fast vesicular transport.", "Although detaching GAPDH from vesicles reduced transport, targeting GAPDH to vesicles was sufficient to promote FAT in GAPDH deficient neurons.", "This specifically localized glycolytic machinery may supply constant energy, independent of mitochondria, for the processive movement of vesicles over long distances in axons."], "structured": false}
{"doc_id": 18682109, "title": "RB loss in resistant EGFR mutant lung adenocarcinomas that transform to small-cell lung cancer", "abstract": ["Tyrosine kinase inhibitors are effective treatments for non-small-cell lung cancers (NSCLCs) with epidermal growth factor receptor (EGFR) mutations.", "However, relapse typically occurs after an average of 1 year of continuous treatment.", "A fundamental histological transformation from NSCLC to small-cell lung cancer (SCLC) is observed in a subset of the resistant cancers, but the molecular changes associated with this transformation remain unknown.", "Analysis of tumour samples and cell lines derived from resistant EGFR mutant patients revealed that Retinoblastoma (RB) is lost in 100% of these SCLC transformed cases, but rarely in those that remain NSCLC.", "Further, increased neuroendocrine marker and decreased EGFR expression as well as greater sensitivity to BCL2 family inhibition are observed in resistant SCLC transformed cancers compared with resistant NSCLCs.", "Together, these findings suggest that this subset of resistant cancers ultimately adopt many of the molecular and phenotypic characteristics of classical SCLC."], "structured": false}
{"doc_id": 18691097, "title": "Periostin Deficiency Increases Bone Damage and Impairs Injury Response to Fatigue Loading in Adult Mice", "abstract": ["Bone damage removal and callus formation in response to fatigue loading are essential to prevent fractures.", "Periostin (Postn) is a matricellular protein that mediates adaptive response of cortical bone to loading.", "Whether and how periostin influences damage and the injury response to fatigue remains unknown.", "We investigated the skeletal response of Postn(-/-) and Postn(+/+) mice after fatigue stimulus by axial compression of their tibia.", "In Postn(+/+) mice, cracks number and surface (CsNb, CsS) increased 1h after fatigue, with a decrease in strength compared to non-fatigued tibia.", "At 15 days, CsNb had started to decline, while CtTV and CtBV increased in fatigued vs non-fatigued tibia, reflecting a woven bone response that was present in 75% of the fatigued bones.", "Cortical porosity and remodelling also prominently increased in the fatigued tibia of Postn(+/+) mice.", "At 30 days, paralleling a continuous removal of cortical damage, strength of the fatigued tibia was similar to the non-fatigue tibia.", "In Postn(-/-) mice, cracks were detectable even in the absence of fatigue, while the amount of collagen crosslinks and tissue hardness was decreased compared to Postn(+/+).", "Fatigue significantly increased CsNb and CsS in Postn(-/-), but was not associated with changes in CtTV and CtBV, as only 16% of the fatigued bones formed some woven bone.", "Cortical porosity and remodelling did not increase either after fatigue in Postn(-/-), and the level of damage remained high even after 30 days.", "As a result, strength remained compromised in Postn(-/-) mice.", "Contrary to Postn(+/+), which osteocytic lacunae showed a change in the degree of anisotropy (DA) after fatigue, Postn(-/-) showed no DA change.", "Hence periostin appears to influence bone materials properties, damage accumulation and repair, including local modeling/remodeling processes in response to fatigue.", "These observations suggest that the level of periostin expression could influence the propensity to fatigue fractures."], "structured": false}
{"doc_id": 18694784, "title": "Preferential occupancy of histone variant H2AZ at inactive promoters influences local histone modifications and chromatin remodeling.", "abstract": ["The yeast histone variant H2AZ (Htz1) is implicated in transcription activation, prevention of the ectopic spread of heterochromatin, and genome integrity.", "Our genome-wide localization analysis revealed that Htz1 is widely, but nonrandomly, distributed throughout the genome in an SWR1-dependent manner.", "We found that Htz1 is enriched in intergenic regions compared with coding regions.", "Its occupancy is inversely proportional to transcription rates and the enrichment of the RNA polymerase II under different growth conditions.", "However, Htz1 does not seem to directly regulate transcription repression genome-wide; instead, the presence of Htz1 under the inactivated condition is essential for optimal activation of a subset of genes.", "In addition, Htz1 is not generally responsible for nucleosome positioning, even at those promoters where Htz1 is highly enriched.", "Finally, using a biochemical approach, we demonstrate that incorporation of Htz1 into nucleosomes inhibits activities of histone modifiers associated with transcription, Dot1, Set2, and NuA4 and reduces the nucleosome mobilization driven by chromatin remodeling complexes.", "These lines of evidence collectively suggest that Htz1 may serve to mark quiescent promoters for proper activation."], "structured": false}
{"doc_id": 18695970, "title": "Genomic organisation and transcription characterisation of the gene encoding Leishmania (Leishmania) amazonensis arginase and its protein structure prediction.", "abstract": ["The genomic organisation of the gene encoding Leishmania (Leishmania) amazonensis arginase as well as its flanking regions were characterised.", "The size of the transcribed RNA was determined, allowing us to map the genomic sites signalling for RNA trans-splicing and putative polyadenylation regions.", "The general organisation was compared with genes encoding other proteins already described in organisms of the Trypanosomatid family.", "The complete nucleotide sequence of the arginase open reading frame was obtained and the three-dimensional structure of the enzyme was inferred by a computational analysis of the deduced amino acid sequence, based on the established crystal structure described for Rattus norvergicus arginase.", "The human liver arginase sequence was analysed in the same way and the comparison of the presumed structure of both the Leishmania and human enzymes identified some differences that may be exploited in chemotherapeutic studies."], "structured": false}
{"doc_id": 18734652, "title": "Endometrial carcinoma risk among women diagnosed with endometrial hyperplasia: the 34-year experience in a large health plan", "abstract": ["Classifying endometrial hyperplasia (EH) according to the severity of glandular crowding (simple hyperplasia (SH) vs complex hyperplasia (CH)) and nuclear atypia (simple atypical hyperplasia (SAH) vs complex atypical hyperplasia (CAH)) should predict subsequent endometrial carcinoma risk, but data on progression are lacking.", "Our nested case\u2013control study of EH progression included 138 cases, who were diagnosed with EH and then with carcinoma (1970\u20132003) at least 1 year (median, 6.5 years) later, and 241 controls, who were individually matched on age, date, and follow-up duration and counter-matched on EH classification.", "After centralised pathology panel and medical record review, we generated rate ratios (RRs) and 95% confidence intervals (CIs), adjusted for treatment and repeat biopsies.", "With disordered proliferative endometrium (DPEM) as the referent, AH significantly increased carcinoma risk (RR=14, 95% CI, 5\u201338).", "Risk was highest 1\u20135 years after AH (RR=48, 95% CI, 8\u2013294), but remained elevated 5 or more years after AH (RR=3.5, 95% CI, 1.0\u20139.6).", "Progression risks for SH (RR=2.0, 95% CI, 0.9\u20134.5) and CH (RR=2.8, 95% CI, 1.0\u20137.9) were substantially lower and only slightly higher than the progression risk for DPEM.", "The higher progression risks for AH could foster management guidelines based on markedly different progression risks for atypical vs non-atypical EH."], "structured": false}
{"doc_id": 18747744, "title": "Redefining the Genetic Hierarchies Controlling Skeletal Myogenesis: Pax-3 and Myf-5 Act Upstream of MyoD", "abstract": ["We analyzed Pax-3 (splotch), Myf-5 (targeted with nlacZ), and splotch/Myf-5 homozygous mutant mice to investigate the roles that these genes play in programming skeletal myogenesis.", "In splotch and Myf-5 homozygous embryos, myogenic progenitor cell perturbations and early muscle defects are distinct.", "Remarkably, splotch/Myf-5 double homozygotes have a dramatic phenotype not seen in the individual mutants: body muscles are absent.", "MyoD does not rescue this double mutant phenotype since activation of this gene proves to be dependent on either Pax-3 or Myf-5.", "Therefore, Pax-3 and Myf-5 define two distinct myogenic pathways, and MyoD acts genetically downstream of these genes for myogenesis in the body.", "This genetic hierarchy does not appear to operate for head muscle formation."], "structured": false}
{"doc_id": 18750453, "title": "Assessment of Volume Depletion in Children with Malaria", "abstract": ["Background The degree of volume depletion in severe malaria is currently unknown, although knowledge of fluid compartment volumes can guide therapy.", "To assist management of severely ill children, and to test the hypothesis that volume changes in fluid compartments reflect disease severity, we measured body compartment volumes in Gabonese children with malaria.", "Methods and Findings Total body water volume (TBW) and extracellular water volume (ECW) were estimated in children with severe or moderate malaria and in convalescence by tracer dilution with heavy water and bromide, respectively.", "Intracellular water volume (ICW) was derived from these parameters.", "Bioelectrical impedance analysis estimates of TBW and ECW were calibrated against dilution methods, and bioelectrical impedance analysis measurements were taken daily until discharge.", "Sixteen children had severe and 19 moderate malaria.", "Severe childhood malaria was associated with depletion of TBW (mean [SD] of 37 [33] ml/kg, or 6.7% [6.0%]) relative to measurement at discharge.", "This is defined as mild dehydration in other conditions.", "ECW measurements were normal on admission in children with severe malaria and did not rise in the first few days of admission.", "Volumes in different compartments (TBW, ECW, and ICW) were not related to hyperlactataemia or other clinical and laboratory markers of disease severity.", "Moderate malaria was not associated with a depletion of TBW."], "structured": false}
{"doc_id": 18758057, "title": "NSOM/QD-Based Direct Visualization of CD3-Induced and CD28-Enhanced Nanospatial Coclustering of TCR and Coreceptor in Nanodomains in T Cell Activation", "abstract": ["Direct molecular imaging of nano-spatial relationship between T cell receptor (TCR)/CD3 and CD4 or CD8 co-receptor before and after activation of a primary T cell has not been reported.", "We have recently innovated application of near-field scanning optical microscopy (NSOM) and immune-labeling quantum dots (QD) to image Ag-specific TCR response during in vivo clonal expansion, and now up-graded the NSOM/QD-based nanotechnology through dipole-polarization and dual-color imaging.", "Using this imaging system scanning cell-membrane molecules at a best-optical lateral resolution, we demonstrated that CD3, CD4 or CD8 molecules were distinctly distributed as single QD-bound molecules or nano-clusters equivalent to 2-4 QD fluorescence-intensity/size on cell-membrane of un-stimulated primary T cells, and approximately 6-10% of CD3 were co-clustering with CD4 or CD8 as 70-110 nm nano-clusters without forming nano-domains.", "The ligation of TCR/CD3 on CD4 or CD8 T cells led to CD3 nanoscale co-clustering or interaction with CD4 or CD8 co-receptors forming 200-500 nm nano-domains or >500 nm micro-domains.", "Such nano-spatial co-clustering of CD3 and CD4 or CD3 and CD8 appeared to be an intrinsic event of TCR/CD3 ligation, not purely limited to MHC engagement, and be driven by Lck phosphorylation.", "Importantly, CD28 co-stimulation remarkably enhanced TCR/CD3 nanoscale co-clustering or interaction with CD4 co-receptor within nano- or micro-domains on the membrane.", "In contrast, CD28 co-stimulation did not enhance CD8 clustering or CD3-CD8 co-clustering in nano-domains although it increased molecular number and density of CD3 clustering in the enlarged nano-domains.", "These nanoscale findings provide new insights into TCR/CD3 interaction with CD4 or CD8 co-receptor in T-cell activation."], "structured": false}
{"doc_id": 18806488, "title": "Hoxa9 transforms primary bone marrow cells through specific collaboration with Meis1a but not Pbx1b.", "abstract": ["Hoxa9, Meis1 and Pbx1 encode homeodomaincontaining proteins implicated in leukemic transformation in both mice and humans.", "Hoxa9, Meis1 and Pbx1 proteins have been shown to physically interact with each other, as Hoxa9 cooperatively binds consensus DNA sequences with Meis1 and with Pbx1, while Meis1 and Pbx1 form heterodimers in both the presence and absence of DNA.", "In this study, we sought to determine if Hoxa9 could transform hemopoietic cells in collaboration with either Pbx1 or Meis1.", "Primary bone marrow cells, retrovirally engineered to overexpress Hoxa9 and Meis1a simultaneously, induced growth factor-dependent oligoclonal acute myeloid leukemia in <3 months when transplanted into syngenic mice.", "In contrast, overexpression of Hoxa9, Meis1a or Pbx1b alone, or the combination of Hoxa9 and Pbx1b failed to transform these cells acutely within 6 months post-transplantation.", "Similar results were obtained when FDC-P1 cells, engineered to overexpress these genes, were transplanted to syngenic recipients.", "Thus, these studies demonstrate a selective collaboration between a member of the Hox family and one of its DNA-binding partners in transformation of hemopoietic cells."], "structured": false}
{"doc_id": 18810195, "title": "Tyr26 phosphorylation of PGAM1 provides a metabolic advantage to tumours by stabilizing the active conformation", "abstract": ["How oncogenic signalling coordinates glycolysis and anabolic biosynthesis in cancer cells remains unclear.", "We recently reported that the glycolytic enzyme phosphoglycerate mutase 1 (PGAM1) regulates anabolic biosynthesis by controlling intracellular levels of its substrate 3-phosphoglycerate and product 2-phosphoglycerate.", "Here we report a novel mechanism in which Y26 phosphorylation enhances PGAM1 activation through release of inhibitory E19 that blocks the active site, stabilising cofactor 2,3-bisphosphoglycerate binding and H11 phosphorylation.", "We also report the crystal structure of H11-phosphorylated PGAM1 and find that phospho-H11 activates PGAM1 at least in part by promoting substrate 3-phosphoglycerate binding.", "Moreover, Y26 phosphorylation of PGAM1 is common in human cancer cells and contributes to regulation of 3-phosphoglycerate and 2-phosphoglycerate levels, promoting cancer cell proliferation and tumour growth.", "As PGAM1 is a negative transcriptional target of TP53, and is therefore commonly upregulated in human cancers, these findings suggest that Y26 phosphorylation represents an additional acute mechanism underlying phosphoglycerate mutase 1 upregulation."], "structured": false}
{"doc_id": 18816720, "title": "Spatial and Temporal Clustering of Dengue Virus Transmission in Thai Villages", "abstract": ["BACKGROUND Transmission of dengue viruses (DENV), the leading cause of arboviral disease worldwide, is known to vary through time and space, likely owing to a combination of factors related to the human host, virus, mosquito vector, and environment.", "An improved understanding of variation in transmission patterns is fundamental to conducting surveillance and implementing disease prevention strategies.", "To test the hypothesis that DENV transmission is spatially and temporally focal, we compared geographic and temporal characteristics within Thai villages where DENV are and are not being actively transmitted.   \n", "METHODS AND FINDINGS Cluster investigations were conducted within 100 m of homes where febrile index children with (positive clusters) and without (negative clusters) acute dengue lived during two seasons of peak DENV transmission.", "Data on human infection and mosquito infection/density were examined to precisely (1) define the spatial and temporal dimensions of DENV transmission, (2) correlate these factors with variation in DENV transmission, and (3) determine the burden of inapparent and symptomatic infections.", "Among 556 village children enrolled as neighbors of 12 dengue-positive and 22 dengue-negative index cases, all 27 DENV infections (4.9% of enrollees) occurred in positive clusters (p < 0.01; attributable risk [AR] = 10.4 per 100; 95% confidence interval 1-19.8 per 100].", "In positive clusters, 12.4% of enrollees became infected in a 15-d period and DENV infections were aggregated centrally near homes of index cases.", "As only 1 of 217 pairs of serologic specimens tested in positive clusters revealed a recent DENV infection that occurred prior to cluster initiation, we attribute the observed DENV transmission subsequent to cluster investigation to recent DENV transmission activity.", "Of the 1,022 female adult Ae.", "aegypti collected, all eight (0.8%) dengue-infected mosquitoes came from houses in positive clusters; none from control clusters or schools.", "Distinguishing features between positive and negative clusters were greater availability of piped water in negative clusters (p < 0.01) and greater number of Ae.", "aegypti pupae per person in positive clusters (p = 0.04).", "During primarily DENV-4 transmission seasons, the ratio of inapparent to symptomatic infections was nearly 1:1 among child enrollees.", "Study limitations included inability to sample all children and mosquitoes within each cluster and our reliance on serologic rather than virologic evidence of interval infections in enrollees given restrictions on the frequency of blood collections in children.   \n", "CONCLUSIONS Our data reveal the remarkably focal nature of DENV transmission within a hyperendemic rural area of Thailand.", "These data suggest that active school-based dengue case detection prompting local spraying could contain recent virus introductions and reduce the longitudinal risk of virus spread within rural areas.", "Our results should prompt future cluster studies to explore how host immune and behavioral aspects may impact DENV transmission and prevention strategies.", "Cluster methodology could serve as a useful research tool for investigation of other temporally and spatially clustered infectious diseases."], "structured": true}
{"doc_id": 18834078, "title": "Secondary T cell\u2013T cell synaptic interactions drive the differentiation of protective CD8+ T cells", "abstract": ["Immunization results in the differentiation of CD8+ T cells, such that they acquire effector abilities and convert into a memory pool.", "Priming of T cells takes place via an immunological synapse formed with an antigen-presenting cell (APC).", "By disrupting synaptic stability at different times, we found that the differentiation of CD8+ T cells required cell interactions beyond those made with APCs.", "We identified a critical differentiation period that required interactions between primed T cells.", "We found that T cell\u2013T cell synapses had a major role in the generation of protective CD8+ T cell memory.", "T cell\u2013T cell synapses allowed T cells to polarize critical secretion of interferon-\u03b3 (IFN-\u03b3) toward each other.", "Collective activation and homotypic clustering drove cytokine sharing and acted as regulatory stimuli for T cell differentiation."], "structured": false}
{"doc_id": 18841257, "title": "The Histone H3 Lysine-27 Demethylase Jmjd3 Links Inflammation to Inhibition of Polycomb-Mediated Gene Silencing", "abstract": ["Epigenetic chromatin marks restrict the ability of differentiated cells to change gene expression programs in response to environmental cues and to transdifferentiate.", "Polycomb group (PcG) proteins mediate gene silencing and repress transdifferentiation in a manner dependent on histone H3 lysine 27 trimethylation (H3K27me3).", "However, macrophages migrated into inflamed tissues can transdifferentiate, but it is unknown whether inflammation alters PcG-dependent silencing.", "Here we show that the JmjC-domain protein Jmjd3 is a H3K27me demethylase expressed in macrophages in response to bacterial products and inflammatory cytokines.", "Jmjd3 binds PcG target genes and regulates their H3K27me3 levels and transcriptional activity.", "The discovery of an inducible enzyme that erases a histone mark controlling differentiation and cell identity provides a link between inflammation and reprogramming of the epigenome, which could be the basis for macrophage plasticity and might explain the differentiation abnormalities in chronic inflammation."], "structured": false}
{"doc_id": 18852643, "title": "Apolipoprotein E and atherosclerosis: beyond lipid effect.", "abstract": ["In humans, apolipoprotein E (apoE) is a polymorphic multifunctional protein.1 It is coded by three alleles (e2, e3, e4) of a modulator gene (level, variability, and susceptibility gene) at the apoE locus on chromosome 19, determining six apoE genotypes and plasma phenotypes.", "Its pleiotropic effects are exerted on plasma lipoprotein metabolism, coagulation, oxidative processes, macrophage, glial cell and neuronal cell homeostasis, adrenal function, central nervous system physiology, inflammation, and cell proliferation.2,3 ApoE polymorphism modulates susceptibility to many diseases.", "It is, however, particularly notorious for its role in neurodegenerative disorders4 and atherosclerotic arterial disease.5,6 The e4 allele (phenotypes E4/4 and E4/3) that is associated with higher low density lipoprotein cholesterol (LDL-C) is considered proatherogenic, whereas the presence of the e2 allele (E3/2, E2/2), being associated with lower LDL-C levels, is deemed to have the opposite effect (although it may be associated with increased plasma triglycerides and lipoprotein remnants).", "This simple equation, however, is an oversimplification because these properties are subject to many environmental and genetic influences.", "ApoE has allele- and gender-dependent effects on reverse cholesterol transport, platelet aggregation, and oxidative processes that are likely to affect the overall atherogenic potential ascribed to modulation of lipoprotein metabolism.2,3,6 Notwithstanding the context dependency, a recent meta-analysis fully supports the presence of the e4 allele as a significant risk factor for coronary artery disease.7 Several mechanisms have been evoked to link apoE with atherosclerosis, but the relationship is not fully unraveled in humans.", "Nevertheless, some apoE mimetic peptides that promote LDL clearance are currently tested in animals for potential clinical applications.8,9  See page 436   The situation is relatively simpler in animals.", "The mouse model has been prominently useful to test mechanisms \u2026"], "structured": false}
{"doc_id": 18855191, "title": "Exploitative and Hierarchical Antagonism in a Cooperative Bacterium", "abstract": ["Social organisms that cooperate with some members of their own species, such as close relatives, may fail to cooperate with other genotypes of the same species.", "Such noncooperation may take the form of outright antagonism or social exploitation.", "Myxococcus xanthus is a highly social prokaryote that cooperatively develops into spore-bearing, multicellular fruiting bodies in response to starvation.", "Here we have characterized the nature of social interactions among nine developmentally proficient strains of M. xanthus isolated from spatially distant locations.", "Strains were competed against one another in all possible pairwise combinations during starvation-induced development.", "In most pairings, at least one competitor exhibited strong antagonism toward its partner and a majority of mixes showed bidirectional antagonism that decreased total spore production, even to the point of driving whole populations to extinction.", "Differential response to mixing was the primary determinant of competitive superiority rather than the sporulation efficiencies of unmixed populations.", "In some competitive pairings, the dominant partner sporulated more efficiently in mixed populations than in clonal isolation.", "This finding represents a novel form of exploitation in bacteria carried out by socially competent genotypes and is the first documentation of social exploitation among natural bacterial isolates.", "Patterns of antagonistic superiority among these strains form a highly linear dominance hierarchy.", "At least some competition pairs construct chimeric, rather than segregated, fruiting bodies.", "The cooperative prokaryote M. xanthus has diverged into a large number of distinct social types that cooperate with clone-mates but exhibit intense antagonism toward distinct social types of the same species.", "Most lengthy migration events in nature may thus result in strong antagonism between migratory and resident populations, and this antagonism may have large effects on local population sizes and dynamics.", "Intense mutual antagonism appears to be more prevalent in this prokaryotic social species than has been observed in the eukaryotic social slime mold Dictyostelium discoideum, which also exhibits multicellular development.", "The finding of several cases of facultative social exploitation among these natural isolates suggests that such exploitation may occur frequently in nature in many prokaryotes with cooperative traits."], "structured": false}
{"doc_id": 18872233, "title": "Mental Health Conditions Among Patients Seeking and Undergoing Bariatric Surgery: A Meta-analysis.", "abstract": ["IMPORTANCE Bariatric surgery is associated with sustained weight loss and improved physical health status for severely obese individuals.", "Mental health conditions may be common among patients seeking bariatric surgery; however, the prevalence of these conditions and whether they are associated with postoperative outcomes remains unknown.   \n", "OBJECTIVE To determine the prevalence of mental health conditions among bariatric surgery candidates and recipients, to evaluate the association between preoperative mental health conditions and health outcomes following bariatric surgery, and to evaluate the association between surgery and the clinical course of mental health conditions.   \n", "DATA SOURCES We searched PubMed, MEDLINE on OVID, and PsycINFO for studies published between January 1988 and November 2015.", "Study quality was assessed using an adapted tool for risk of bias; quality of evidence was rated based on GRADE (Grading of Recommendations Assessment, Development and Evaluation) criteria.   \n", "FINDINGS We identified 68 publications meeting inclusion criteria: 59 reporting the prevalence of preoperative mental health conditions (65,363 patients) and 27 reporting associations between preoperative mental health conditions and postoperative outcomes (50,182 patients).", "Among patients seeking and undergoing bariatric surgery, the most common mental health conditions, based on random-effects estimates of prevalence, were depression (19% [95% CI, 14%-25%]) and binge eating disorder (17% [95% CI, 13%-21%]).", "There was conflicting evidence regarding the association between preoperative mental health conditions and postoperative weight loss.", "Neither depression nor binge eating disorder was consistently associated with differences in weight outcomes.", "Bariatric surgery was, however, consistently associated with postoperative decreases in the prevalence of depression (7 studies; 8%-74% decrease) and the severity of depressive symptoms (6 studies; 40%-70% decrease).   \n", "CONCLUSIONS AND RELEVANCE Mental health conditions are common among bariatric surgery patients-in particular, depression and binge eating disorder.", "There is inconsistent evidence regarding the association between preoperative mental health conditions and postoperative weight loss.", "Moderate-quality evidence supports an association between bariatric surgery and lower rates of depression postoperatively."], "structured": true}
{"doc_id": 18882947, "title": "The Nuclear Effector of Wnt-Signaling, Tcf1, Functions as a T-Cell\u2013Specific Tumor Suppressor for Development of Lymphomas", "abstract": ["The HMG-box factor Tcf1 is required during T-cell development in the thymus and mediates the nuclear response to Wnt signals.", "Tcf1(-/-) mice have previously been characterized and show developmental blocks at the CD4-CD8- double negative (DN) to CD4+CD8+ double positive transition.", "Due to the blocks in T-cell development, Tcf1(-/-) mice normally have a very small thymus.", "Unexpectedly, a large proportion of Tcf1(-/-) mice spontaneously develop thymic lymphomas with 50% of mice developing a thymic lymphoma/leukemia at the age of 16 wk.", "These lymphomas are clonal, highly metastatic, and paradoxically show high Wnt signaling when crossed with Wnt reporter mice and have high expression of Wnt target genes Lef1 and Axin2.", "In wild-type thymocytes, Tcf1 is higher expressed than Lef1, with a predominance of Wnt inhibitory isoforms.", "Loss of Tcf1 as repressor of Lef1 leads to high Wnt activity and is the initiating event in lymphoma development, which is exacerbated by activating Notch1 mutations.", "Thus, Notch1 and loss of Tcf1 functionally act as collaborating oncogenic events.", "Tcf1 deficiency predisposes to the development of thymic lymphomas by ectopic up-regulation of Lef1 due to lack of Tcf1 repressive isoforms and frequently by cooperating activating mutations in Notch1.", "Tcf1 therefore functions as a T-cell-specific tumor suppressor gene, besides its established role as a Wnt responsive transcription factor.", "Thus, Tcf1 acts as a molecular switch between proliferative and repressive signals during T-lymphocyte development in the thymus."], "structured": false}
{"doc_id": 18895793, "title": "Activator Control of Nucleosome Occupancy in Activation and Repression of Transcription", "abstract": ["The relationship between chromatin structure and gene expression is a subject of intense study.", "The universal transcriptional activator Gal4 removes promoter nucleosomes as it triggers transcription, but how it does so has remained obscure.", "The reverse process, repression of transcription, has often been correlated with the presence of nucleosomes.", "But it is not known whether nucleosomes are required for that effect.", "A new quantitative assay describes, for any given location, the fraction of DNA molecules in the population that bears a nucleosome at any given instant.", "This allows us to follow the time courses of nucleosome removal and reformation, in wild-type and mutant cells, upon activation (by galactose) and repression (by glucose) of the GAL genes of yeast.", "We show that upon being freed of its inhibitor Gal80 by the action of galactose, Gal4 quickly recruits SWI/SNF to the genes, and that nucleosome \"remodeler\" rapidly removes promoter nucleosomes.", "In the absence of SWI/SNF, Gal4's action also results in nucleosome removal and the activation of transcription, but both processes are significantly delayed.", "Addition of glucose to cells growing in galactose represses transcription.", "But if galactose remains present, Gal4 continues to work, recruiting SWI/SNF and maintaining the promoter nucleosome-free despite it being repressed.", "This requirement for galactose is obviated in a mutant in which Gal4 works constitutively.", "These results show how an activator's recruiting function can control chromatin structure both during gene activation and repression.", "Thus, both under activating and repressing conditions, the activator can recruit an enzymatic machine that removes promoter nucleosomes.", "Our results show that whereas promoter nucleosome removal invariably accompanies activation, reformation of nucleosomes is not required for repression.", "The finding that there are two routes to nucleosome removal and activation of transcription-one that requires the action of SWI/SNF recruited by the activator, and a slower one that does not-clarifies our understanding of the early events of gene activation, and in particular corrects earlier reports that SWI/SNF plays no role in GAL gene induction.", "Our finding that chromatin structure is irrelevant for repression as studied here-that is, repression sets in as efficiently whether or not promoter nucleosomes are allowed to reform-contradicts the widely held, but little tested, idea that nucleosomes are required for repression.", "These findings were made possible by our nucleosome occupancy assay.", "The assay, we believe, will prove useful in studying other outstanding issues in the field."], "structured": false}
{"doc_id": 18909530, "title": "Contractile forces sustain and polarize hematopoiesis from stem and progenitor cells.", "abstract": ["Self-renewal and differentiation of stem cells depend on asymmetric division and polarized motility processes that in other cell types are modulated by nonmuscle myosin-II (MII) forces and matrix mechanics.", "Here, mass spectrometry-calibrated intracellular flow cytometry of human hematopoiesis reveals MIIB to be a major isoform that is strongly polarized in hematopoietic stem cells and progenitors (HSC/Ps) and thereby downregulated in differentiated cells via asymmetric division.", "MIIA is constitutive and activated by dephosphorylation during cytokine-triggered differentiation of cells grown on stiff, endosteum-like matrix, but not soft, marrow-like matrix.", "In vivo, MIIB is required for generation of blood, while MIIA is required for sustained HSC/P engraftment.", "Reversible inhibition of both isoforms in culture with blebbistatin enriches for long-term hematopoietic multilineage reconstituting cells by 5-fold or more as assessed in vivo.", "Megakaryocytes also become more polyploid, producing 4-fold more platelets.", "MII is thus a multifunctional node in polarized division and niche sensing."], "structured": false}
{"doc_id": 18914652, "title": "Critical Role of the Virus-Encoded MicroRNA-155 Ortholog in the Induction of Marek's Disease Lymphomas", "abstract": ["Notwithstanding the well-characterised roles of a number of oncogenes in neoplastic transformation, microRNAs (miRNAs) are increasingly implicated in several human cancers.", "Discovery of miRNAs in several oncogenic herpesviruses such as KSHV has further highlighted the potential of virus-encoded miRNAs to contribute to their oncogenic capabilities.", "Nevertheless, despite the identification of several possible cancer-related genes as their targets, the direct in vivo role of virus-encoded miRNAs in neoplastic diseases such as those induced by KSHV is difficult to demonstrate in the absence of suitable models.", "However, excellent natural disease models of rapid-onset Marek's disease (MD) lymphomas in chickens allow examination of the oncogenic potential of virus-encoded miRNAs.", "Using viruses modified by reverse genetics of the infectious BAC clone of the oncogenic RB-1B strain of MDV, we show that the deletion of the six-miRNA cluster 1 from the viral genome abolished the oncogenicity of the virus.", "This loss of oncogenicity appeared to be primarily due to the single miRNA within the cluster, miR-M4, the ortholog of cellular miR-155, since its deletion or a 2-nucleotide mutation within its seed region was sufficient to inhibit the induction of lymphomas.", "The definitive role of this miR-155 ortholog in oncogenicity was further confirmed by the rescue of oncogenic phenotype by revertant viruses that expressed either the miR-M4 or the cellular homolog gga-miR-155.", "This is the first demonstration of the direct in vivo role of a virus-encoded miRNA in inducing tumors in a natural infection model.", "Furthermore, the use of viruses deleted in miRNAs as effective vaccines against virulent MDV challenge, enables the prospects of generating genetically defined attenuated vaccines."], "structured": false}
{"doc_id": 18924534, "title": "Functional insights into the role of nuclear-retained long noncoding RNAs in gene expression control in mammalian cells", "abstract": ["The mammalian genome harbors thousands of long noncoding RNA (lncRNA) genes.", "Recent studies have indicated the involvement of several of these lncRNAs in the regulation of gene expression.", "lncRNAs play crucial roles in various biological processes ranging from epigenetic gene regulation, transcriptional control, to post-transcriptional regulation.", "lncRNAs are localized in various subcellular compartments, and major proportion of these are retained in the cell nucleus and could be broadly classified as nuclear-retained lncRNAs (nrRNAs).", "Based on the identified functions, members of the nrRNAs execute diverse roles, including providing architectural support to the hierarchical subnuclear organization and influencing the recruitment of chromatin modifier factors to specific chromatin sites.", "In this review, we will summarize the recently described roles of mammalian nrRNAs in controlling gene expression by influencing chromatin organization, transcription, pre-mRNA processing, nuclear organization, and their involvement in disease."], "structured": false}
{"doc_id": 18938992, "title": "Downregulation of TAP1 in B lymphocytes by cellular and Epstein-Barr virus-encoded interleukin-10.", "abstract": ["Virally infected cells degrade intracellular viral proteins proteolytically and present the resulting peptides in association with major histocompatibility complex (MHC) class I molecules to CD8+ cytotoxic T lymphocytes (CTLs).", "These cells are normally prone to CTL-mediated elimination.", "However, several viruses have evolved strategies to avoid detection by the immune system that interfere with the pathway of antigen presentation.", "Epstein-Barr virus (EBV) expresses a predominantly late protein, the BCRF1 gene product vIL-10, that is similar in sequence to the human interleukin-10 (hIL-10).", "We show here that vIL-10 affects the expression of one of the two transporter proteins (TAPs) associated with antigen presentation.", "Similarly, hIL-10 showed the same activity.", "Expression of the LMP2 and TAP1 genes but not expression of TAP2 or LMP7 is efficiently downregulated, indicating a specific IL-10 effect on the two divergently transcribed TAP1 and LMP2 genes.", "Downregulation of TAP1 by IL-10 hampers the transport of peptide antigens into the endoplasmatic reticulum, as shown in the TAP-specific peptide transporter assay, their loading onto empty MHC I molecules, and the subsequent translocation to the cell surface.", "As a consequence, IL-10 causes a general reduction of surface MHC I molecules on B lymphocytes that might also affect the recognition of EBV-infected cells by cytotoxic T cells."], "structured": false}
{"doc_id": 18949516, "title": "TGF-\u03b2 and Insulin Signaling Regulate Reproductive Aging via Oocyte and Germline Quality Maintenance", "abstract": ["Reproductive cessation is perhaps the earliest aging phenotype that humans experience.", "Similarly, reproduction of Caenorhabditis elegans ceases in mid-adulthood.", "Although somatic aging has been studied in both worms and humans, mechanisms regulating reproductive aging are not yet understood.", "Here, we show that TGF-\u03b2 Sma/Mab and Insulin/IGF-1 signaling regulate C. elegans reproductive aging by modulating multiple aspects of the reproductive process, including embryo integrity, oocyte fertilizability, chromosome segregation fidelity, DNA damage resistance, and oocyte and germline morphology.", "TGF-\u03b2 activity regulates reproductive span and germline/oocyte quality noncell-autonomously and is temporally and transcriptionally separable from its regulation of growth.", "Chromosome segregation, cell cycle, and DNA damage response genes are upregulated in TGF-\u03b2 mutant oocytes, decline in aged mammalian oocytes, and are critical for oocyte quality maintenance.", "Our data suggest that C. elegans and humans share many aspects of reproductive aging, including the correlation between reproductive aging and declining oocyte quality and mechanisms determining oocyte quality."], "structured": false}
{"doc_id": 18953920, "title": "The Epithelial-Mesenchymal Transition Generates Cells with Properties of Stem Cells", "abstract": ["The epithelial-mesenchymal transition (EMT) is a key developmental program that is often activated during cancer invasion and metastasis.", "We here report that the induction of an EMT in immortalized human mammary epithelial cells (HMLEs) results in the acquisition of mesenchymal traits and in the expression of stem-cell markers.", "Furthermore, we show that those cells have an increased ability to form mammospheres, a property associated with mammary epithelial stem cells.", "Independent of this, stem cell-like cells isolated from HMLE cultures form mammospheres and express markers similar to those of HMLEs that have undergone an EMT.", "Moreover, stem-like cells isolated either from mouse or human mammary glands or mammary carcinomas express EMT markers.", "Finally, transformed human mammary epithelial cells that have undergone an EMT form mammospheres, soft agar colonies, and tumors more efficiently.", "These findings illustrate a direct link between the EMT and the gain of epithelial stem cell properties."], "structured": false}
{"doc_id": 18956141, "title": "NEMO Prevents RIP Kinase 1-Mediated Epithelial Cell Death and Chronic Intestinal Inflammation by NF-\u03baB-Dependent and -Independent Functions", "abstract": ["Intestinal epithelial cells (IECs) regulate gut immune homeostasis, and impaired epithelial responses are implicated in the pathogenesis of inflammatory bowel diseases (IBD).", "IEC-specific ablation of nuclear factor \u03baB (NF-\u03baB) essential modulator (NEMO) caused Paneth cell apoptosis and impaired antimicrobial factor expression in the ileum, as well as colonocyte apoptosis and microbiota-driven chronic inflammation in the colon.", "Combined RelA, c-Rel, and RelB deficiency in IECs caused Paneth cell apoptosis but not colitis, suggesting that NEMO prevents colon inflammation by NF-\u03baB-independent functions.", "Inhibition of receptor-interacting protein kinase 1 (RIPK1) kinase activity or combined deficiency of Fas-associated via death domain protein (FADD) and RIPK3 prevented epithelial cell death, Paneth cell loss, and colitis development in mice with epithelial NEMO deficiency.", "Therefore, NEMO prevents intestinal inflammation by inhibiting RIPK1 kinase activity-mediated IEC death, suggesting that RIPK1 inhibitors could be effective in the treatment of colitis in patients with NEMO mutations and possibly in IBD."], "structured": false}
{"doc_id": 18987782, "title": "Suppression of Myc oncogenic activity by ribosomal protein haploinsufficiency", "abstract": ["The Myc oncogene regulates the expression of several components of the protein synthetic machinery, including ribosomal proteins, initiation factors of translation, RNA polymerase III and ribosomal DNA.", "Whether and how increasing the cellular protein synthesis capacity affects the multistep process leading to cancer remains to be addressed.", "Here we use ribosomal protein heterozygote mice as a genetic tool to restore increased protein synthesis in Emu-Myc/+ transgenic mice to normal levels, and show that the oncogenic potential of Myc in this context is suppressed.", "Our findings demonstrate that the ability of Myc to increase protein synthesis directly augments cell size and is sufficient to accelerate cell cycle progression independently of known cell cycle targets transcriptionally regulated by Myc.", "In addition, when protein synthesis is restored to normal levels, Myc-overexpressing precancerous cells are more efficiently eliminated by programmed cell death.", "Our findings reveal a new mechanism that links increases in general protein synthesis rates downstream of an oncogenic signal to a specific molecular impairment in the modality of translation initiation used to regulate the expression of selective messenger RNAs.", "We show that an aberrant increase in cap-dependent translation downstream of Myc hyperactivation specifically impairs the translational switch to internal ribosomal entry site (IRES)-dependent translation that is required for accurate mitotic progression.", "Failure of this translational switch results in reduced mitotic-specific expression of the endogenous IRES-dependent form of Cdk11 (also known as Cdc2l and PITSLRE), which leads to cytokinesis defects and is associated with increased centrosome numbers and genome instability in Emu-Myc/+ mice.", "When accurate translational control is re-established in Emu-Myc/+ mice, genome instability is suppressed.", "Our findings demonstrate how perturbations in translational control provide a highly specific outcome for gene expression, genome stability and cancer initiation that have important implications for understanding the molecular mechanism of cancer formation at the post-genomic level."], "structured": false}
{"doc_id": 18988265, "title": "Susceptibility to exacerbation in chronic obstructive pulmonary disease.", "abstract": ["BACKGROUND Although we know that exacerbations are key events in chronic obstructive pulmonary disease (COPD), our understanding of their frequency, determinants, and effects is incomplete.", "In a large observational cohort, we tested the hypothesis that there is a frequent-exacerbation phenotype of COPD that is independent of disease severity.   \n", "METHODS We analyzed the frequency and associations of exacerbation in 2138 patients enrolled in the Evaluation of COPD Longitudinally to Identify Predictive Surrogate Endpoints (ECLIPSE) study.", "Exacerbations were defined as events that led a care provider to prescribe antibiotics or corticosteroids (or both) or that led to hospitalization (severe exacerbations).", "Exacerbation frequency was observed over a period of 3 years.   \n", "RESULTS Exacerbations became more frequent (and more severe) as the severity of COPD increased; exacerbation rates in the first year of follow-up were 0.85 per person for patients with stage 2 COPD (with stage defined in accordance with Global Initiative for Chronic Obstructive Lung Disease [GOLD] stages), 1.34 for patients with stage 3, and 2.00 for patients with stage 4.", "Overall, 22% of patients with stage 2 disease, 33% with stage 3, and 47% with stage 4 had frequent exacerbations (two or more in the first year of follow-up).", "The single best predictor of exacerbations, across all GOLD stages, was a history of exacerbations.", "The frequent-exacerbation phenotype appeared to be relatively stable over a period of 3 years and could be predicted on the basis of the patient's recall of previous treated events.", "In addition to its association with more severe disease and prior exacerbations, the phenotype was independently associated with a history of gastroesophageal reflux or heartburn, poorer quality of life, and elevated white-cell count.   \n", "CONCLUSIONS Although exacerbations become more frequent and more severe as COPD progresses, the rate at which they occur appears to reflect an independent susceptibility phenotype.", "This has implications for the targeting of exacerbation-prevention strategies across the spectrum of disease severity.", "(Funded by GlaxoSmithKline; ClinicalTrials.gov number, NCT00292552.)"], "structured": true}
{"doc_id": 18997216, "title": "Sympathetic baroreflex gain in normotensive pregnant women.", "abstract": ["Muscle sympathetic nerve activity is increased during normotensive pregnancy while mean arterial pressure is maintained or reduced, suggesting baroreflex resetting.", "We hypothesized spontaneous sympathetic baroreflex gain would be reduced in normotensive pregnant women relative to nonpregnant matched controls.", "Integrated muscle sympathetic burst incidence and total sympathetic activity (microneurography), blood pressure (Finometer), and R-R interval (ECG) were assessed at rest in 11 pregnant women (33 \u00b1 1 wk gestation, 31 \u00b1 1 yr, prepregnancy BMI: 23.5 \u00b1 0.9 kg/m(2)) and 11 nonpregnant controls (29 \u00b1 1 yr; BMI: 25.2 \u00b1 1.7 kg/m(2)).", "Pregnant women had elevated baseline sympathetic burst incidence (43 \u00b1 2 vs. 33 \u00b1 2 bursts/100 heart beats, P = 0.01) and total sympathetic activity (1,811 \u00b1 148 vs. 1,140 \u00b1 55 au, P < 0.01) relative to controls.", "Both mean (88 \u00b1 3 vs. 91 \u00b1 2 mmHg, P = 0.4) and diastolic (DBP) (72 \u00b1 3 vs. 73 \u00b1 2 mmHg, P = 0.7) pressures were similar between pregnant and nonpregnant women, respectively, indicating an upward resetting of the baroreflex set point with pregnancy.", "Baroreflex gain, calculated as the linear relationship between sympathetic burst incidence and DBP, was reduced in pregnant women relative to controls (-3.7 \u00b1 0.5 vs. -5.4 \u00b1 0.5 bursts\u00b7100 heart beats(-1)\u00b7mmHg(-1), P = 0.03), as was baroreflex gain calculated with total sympathetic activity (-294 \u00b1 24 vs. -210 \u00b1 24 au\u00b7100 heart beats(-1)\u00b7mmHg(-1); P = 0.03).", "Cardiovagal baroreflex gain (sequence method) was not different between nonpregnant controls and pregnant women (49 \u00b1 8 vs. 36 \u00b1 8 ms/mmHg; P = 0.2).", "However, sympathetic (burst incidence) and cardiovagal gains were negatively correlated in pregnant women (R = -0.7; P = 0.02).", "Together, these data indicate that the influence of the sympathetic nervous system over arterial blood pressure is reduced in normotensive pregnancy, in terms of both long-term and beat-to-beat regulation of arterial pressure, likely through a baroreceptor-dependent mechanism."], "structured": false}
{"doc_id": 18998807, "title": "Facilitators and Impediments of the Pluripotency Reprogramming Factors' Initial Engagement with the Genome", "abstract": ["The ectopic expression of transcription factors can reprogram cell fate, yet it is unknown how the initial binding of factors to the genome relates functionally to the binding seen in the minority of cells that become reprogrammed.", "We report a map of Oct4, Sox2, Klf4, and c-Myc (O, S, K, and M) on the human genome during the first 48 hr of reprogramming fibroblasts to pluripotency.", "Three striking aspects of the initial chromatin binding events include an unexpected role for c-Myc in facilitating OSK chromatin engagement, the primacy of O, S, and K as pioneer factors at enhancers of genes that promote reprogramming, and megabase-scale chromatin domains spanned by H3K9me3, including many genes required for pluripotency, that prevent initial OSKM binding and impede the efficiency of reprogramming.", "We find diverse aspects of initial factor binding that must be overcome in the minority of cells that become reprogrammed."], "structured": false}
{"doc_id": 19004126, "title": "Fibrillar Collagen Inhibits Arterial Smooth Muscle Proliferation through Regulation of Cdk2 Inhibitors", "abstract": ["Arterial smooth muscle cells (SMCs) are arrested in the G1 phase of the cell cycle on polymerized type I collagen fibrils, while monomer collagen supports SMC proliferation.", "Cyclin E-associated kinase and cyclin-dependent kinase 2 (cdk2) phosphorylation are inhibited on polymerized collagen, and levels of the cdk2 inhibitors p27Kip1 and p21Cip1/Waf1 are increased compared with SMCs on monomer collagen.", "p27Kip1 associates with the cyclin E-cdk2-p21Cip1/Waf1 complex in SMCs on polymerized collagen.", "Monovalent blocking antibodies to alpha2 integrins, integrins that mediate adhesion to both forms of collagen, mimic these effects on monomer collagen.", "Furthermore, polymerized collagen rapidly suppresses p70 S6 kinase, a possible regulator of p27Kip1.", "Thus, fibrillar collagen specifically regulates early integrin signaling that may lead to up-regulation of cdk2 inhibitors and inhibition of SMC proliferation."], "structured": false}
{"doc_id": 19005293, "title": "Memory CD4+ T cells induce innate responses independently of pathogen", "abstract": ["Inflammation induced by recognition of pathogen-associated molecular patterns markedly affects subsequent adaptive responses.", "We asked whether the adaptive immune system can also affect the character and magnitude of innate inflammatory responses.", "We found that the response of memory, but not naive, CD4+ T cells enhances production of multiple innate inflammatory cytokines and chemokines (IICs) in the lung and that, during influenza infection, this leads to early control of virus.", "Memory CD4+ T cell\u2013induced IICs and viral control require cognate antigen recognition and are optimal when memory cells are either T helper type 1 (TH1) or TH17 polarized but are independent of interferon-\u03b3 (IFN-\u03b3) and tumor necrosis factor-\u03b1 (TNF-\u03b1) production and do not require activation of conserved pathogen recognition pathways.", "This represents a previously undescribed mechanism by which memory CD4+ T cells induce an early innate response that enhances immune protection against pathogens."], "structured": false}
{"doc_id": 19047331, "title": "Direct Upregulation of STAT3 by MicroRNA-551b-3p Deregulates Growth and Metastasis of Ovarian Cancer.", "abstract": ["3q26.2 amplification in high-grade serous ovarian cancer leads to increased expression of mature microRNA miR551b-3p, which is associated with poor clinical outcome.", "Importantly, miR551b-3p contributes to resistance to apoptosis and increased survival and proliferation of cancer cells in vitro and in vivo.", "miR551b-3p upregulates STAT3 protein levels, and STAT3 is required for the effects of miR551b-3p on cell proliferation.", "Rather than decreasing levels of target mRNA as expected, we demonstrate that miR551b-3p binds a complementary sequence on the STAT3 promoter, recruiting RNA polymerase II and the TWIST1 transcription factor to activate STAT3 transcription, and thus directly upregulates STAT3 expression.", "Furthermore, anti-miR551b reduced STAT3 expression in ovarian cancer cells in vitro and in vivo and reduced ovarian cancer growth in vivo.", "Together, our data demonstrate a role for miR551b-3p in transcriptional activation.", "Thus, miR551b-3p represents a promising candidate biomarker and therapeutic target in ovarian cancer."], "structured": false}
{"doc_id": 19052713, "title": "Human albumin administration in critically ill patients: systematic review of randomised controlled trials.", "abstract": ["OBJECTIVE To quantify effect on mortality of administering human albumin or plasma protein fraction during management of critically ill patients.   \n", "DESIGN Systematic review of randomised controlled trials comparing administration of albumin or plasma protein fraction with no administration or with administration of crystalloid solution in critically ill patients with hypovolaemia, burns, or hypoalbuminaemia.   ", "SUBJECTS 30 randomised controlled trials including 1419 randomised patients.   \n", "MAIN OUTCOME MEASURE Mortality from all causes at end of follow up for each trial.   \n", "RESULTS For each patient category the risk of death in the albumin treated group was higher than in the comparison group.", "For hypovolaemia the relative risk of death after albumin administration was 1.46 (95% confidence interval 0.97 to 2.22), for burns the relative risk was 2.40 (1.11 to 5.19), and for hypoalbuminaemia", "it was 1.69 (1.07 to 2.67).", "Pooled relative risk of death with albumin administration was 1.68 (1.26 to 2.23).", "Pooled difference in the risk of death with albumin was 6% (95% confidence interval 3% to 9%) with a fixed effects model.", "These data suggest that for every 17 critically ill patients treated with albumin there is one additional death.   \n", "CONCLUSIONS There is no evidence that albumin administration reduces mortality in critically ill patients with hypovolaemia, burns, or hypoalbuminaemia and a strong suggestion that it may increase mortality.", "These data suggest that use of human albumin in critically ill patients should be urgently reviewed and that it should not be used outside the context of rigorously conducted, randomised controlled trials."], "structured": true}
{"doc_id": 19058822, "title": "A fine-scale map of recombination rates and hotspots across the human genome.", "abstract": ["Genetic maps, which document the way in which recombination rates vary over a genome, are an essential tool for many genetic analyses.", "We present a high-resolution genetic map of the human genome, based on statistical analyses of genetic variation data, and identify more than 25,000 recombination hotspots, together with motifs and sequence contexts that play a role in hotspot activity.", "Differences between the behavior of recombination rates over large (megabase) and small (kilobase) scales lead us to suggest a two-stage model for recombination in which hotspots are stochastic features, within a framework in which large-scale rates are constrained."], "structured": false}
{"doc_id": 19071857, "title": "Mental Health Support Provided Throughout the Bariatric Surgery Clinical Pathway in French Specialized Care Centers for Obesity", "abstract": ["Pre-operative psychological assessment is recommended by international guidelines for bariatric surgery candidates.", "Thereby, service teams caring for bariatric patients should include at least one mental health provider (e.g., a psychologist or psychiatrist).", "The objective of this study was to evaluate the psychology and psychiatry resources and practices in the 37 specialized obesity centers (CSOs) created by the French Ministry of Health.", "CSO coordinators were contacted by e-mail to collect general information on the centers (e.g., number of bariatric operations).", "Secondly, psychologists and psychiatrists of each center completed an anonymous questionnaire assessing their professional practices and their organization of care pathways.", "The vast majority of CSO coordinators (81%, n = 26/32) answered our survey.", "These results show significant differences and shortages in terms of the psychology/psychiatry resources available.", "Most of the psychologists (n = 26/31) and psychiatrists (n = 10/10) stated that they systematically meet new patients only before surgery (56%) or both before and after the operation (30%); however, some psychologists and psychiatrists (14%) do not systematically meet all the patients (before and/or after surgery).", "Nevertheless, all the professionals provide psychology assessments, and about 75% of them offer a psychological follow-up, indicating a similarity regarding the practices of psychologists and psychiatrists.", "Our results highlight the place of psychological/psychiatric evaluations in French CSOs and emphasize the absence of mental health providers in several of these services.", "Post-operative psychological follow-up is not usually provided.", "It would be appropriate to create clear recommendations for post-operative psychological or psychiatric long-term follow-up."], "structured": false}
{"doc_id": 19079491, "title": "Calcium: Regulation of cell death: the calcium\u2013apoptosis link", "abstract": ["To live or to die?", "This crucial question eloquently reflects the dual role of Ca2+ in living organisms \u2013 survival factor or ruthless killer.", "It has long been known that Ca2+ signals govern a host of vital cell functions and so are necessary for cell survival.", "However, more recently it has become clear that cellular Ca2+ overload, or perturbation of intracellular Ca2+ compartmentalization, can cause cytotoxicity and trigger either apoptotic or necrotic cell death."], "structured": false}
{"doc_id": 19099739, "title": "Breaking the code of DNA binding specificity of TAL-type III effectors.", "abstract": ["The pathogenicity of many bacteria depends on the injection of effector proteins via type III secretion into eukaryotic cells in order to manipulate cellular processes.", "TAL (transcription activator-like) effectors from plant pathogenic Xanthomonas are important virulence factors that act as transcriptional activators in the plant cell nucleus, where they directly bind to DNA via a central domain of tandem repeats.", "Here, we show how target DNA specificity of TAL effectors is encoded.", "Two hypervariable amino acid residues in each repeat recognize one base pair in the target DNA.", "Recognition sequences of TAL effectors were predicted and experimentally confirmed.", "The modular protein architecture enabled the construction of artificial effectors with new specificities.", "Our study describes the functionality of a distinct type of DNA binding domain and allows the design of DNA binding domains for biotechnology."], "structured": false}
{"doc_id": 19130782, "title": "Interferon-Gamma at the Crossroads of Tumor Immune Surveillance or Evasion", "abstract": ["Interferon-gamma (IFN-\u03b3) is a pleiotropic molecule with associated antiproliferative, pro-apoptotic and antitumor mechanisms.", "This effector cytokine, often considered as a major effector of immunity, has been used in the treatment of several diseases, despite its adverse effects.", "Although broad evidence implicating IFN-\u03b3 in tumor immune surveillance, IFN-\u03b3-based therapies undergoing clinical trials have been of limited success.", "In fact, recent reports suggested that it may also play a protumorigenic role, namely, through IFN-\u03b3 signaling insensitivity, downregulation of major histocompatibility complexes, and upregulation of indoleamine 2,3-dioxygenase and of checkpoint inhibitors, as programmed cell-death ligand 1.", "However, the IFN-\u03b3-mediated responses are still positively associated with patient's survival in several cancers.", "Consequently, major research efforts are required to understand the immune contexture in which IFN-\u03b3 induces its intricate and highly regulated effects in the tumor microenvironment.", "This review discusses the current knowledge on the pro- and antitumorigenic effects of IFN-\u03b3 as part of the complex immune response to cancer, highlighting the relevance to identify IFN-\u03b3 responsive patients for the improvement of therapies that exploit associated signaling pathways."], "structured": false}
{"doc_id": 19132741, "title": "Role of antioxidants in paraquat toxicity.", "abstract": ["Paraquat, a quarternary nitrogen herbicide, is a highly toxic compound for humans and animals and many cases of acute poisoning and death have been reported over the past few decades.", "The mechanisms of paraquat toxicity involve: the generation of the superoxide anion, which can lead to the formation of more toxic reactive oxygen species, such as hydrogen peroxide and hydroxyl radical; and the oxidation of the cellular NADPH, the major source of reducing equivalents for the intracellular reduction of paraquat, which results in the disruption of important NADPH-requiring biochemical processes.", "The major cause of death in paraquat poisoning is respiratory failure due to an oxidative insult to the alveolar epithelium with subsequent obliterating fibrosis.", "Management of paraquat poisoning has remained mostly supportive and has been directed towards the modification of the toxicokinetics of the poison.", "Currently, there are no true pharmacological antagonists for paraquat and there are no chelating agents capable of binding the poison in the blood or other tissues.", "Recognizing the fact that paraquat induces its toxic effects via oxidative stress-mediated mechanisms, innovations in the management of paraquat poisoning are directed towards the use of antioxidants.", "In this review, the status of antioxidants in ameliorating or treating the toxic effects produced by paraquat is presented."], "structured": false}
{"doc_id": 19138874, "title": "Nucleation of nuclear bodies by RNA", "abstract": ["The biogenesis of the many functional compartments contained in the mammalian cell nucleus is poorly understood.", "More specifically, little is known regarding the initial nucleation step required for nuclear body formation.", "Here we show that RNA can function as a structural element and a nucleator of nuclear bodies.", "We find that several types of coding and noncoding RNAs are sufficient to de novo assemble, and are physiologically enriched in, histone locus bodies (with associated Cajal bodies), nuclear speckles, paraspeckles and nuclear stress bodies.", "Formation of nuclear bodies occurs through recruitment and accumulation of proteins resident in the nuclear bodies by nucleating RNA.", "These results demonstrate that transcription is a driving force in nuclear body formation and RNA transcripts can function as a scaffold in the formation of major nuclear bodies.", "Together, these data suggest that RNA-primed biogenesis of nuclear bodies is a general principle of nuclear organization."], "structured": false}
{"doc_id": 19140422, "title": "Evaluation of human papillomavirus testing in primary screening for cervical abnormalities: comparison of sensitivity, specificity, and frequency of referral.", "abstract": ["CONTEXT Human papillomavirus (HPV) DNA testing of women having Papanicolaou (Pap) smears showing atypical squamous cells of undetermined significance (ASCUS) has clinical usefulness.", "Whether HPV DNA testing alone is useful in primary screening remains to be determined.   \n", "OBJECTIVE To determine the accuracy of HPV DNA testing for detecting cervical intraepithelial neoplasia (CIN) grade 3 or cancer (the criterion standard).   \n", "DESIGN, SETTING, AND PARTICIPANTS Between December 1997 and October 2000, 4075 women who attended Planned Parenthood clinics in Washington State were screened simultaneously using thin-layer Pap and HPV DNA testing by a polymerase chain reaction (PCR)-based method and by a liquid-based RNA-DNA hybridization capture with signal amplification assay (signal amplification).", "Women who were positive for high-risk HPV types, or had Pap results of ASCUS or higher, were considered to have positive screening test results and were referred for colposcopy and biopsy.", "Additionally, a random sample of women with negative screening test results was referred for colposcopy.", "Based on individual and combined thin-layer Pap, HPV PCR, and HPV signal amplification test results from the screening and the colposcopy visits, 7 colposcopy triage strategies were defined and evaluated.   \n", "MAIN OUTCOME MEASURE Sensitivity and specificity for detecting cervical lesions graded CIN 3 or higher for each of the 7 triage strategies.   \n", "RESULTS The estimated prevalence of CIN 3 or higher was 3.2%.", "The sensitivity (95% confidence interval) of thin-layer Pap (with a result of > or = ASCUS) for identifying women with CIN 3 or higher was only 61.3% (48.5%-70.9%) compared with 88.2% (78.9%-93.8%) for HPV testing by PCR and 90.8% (83.1%-95.8%) by signal amplification.", "Differences in specificities were also observed: 82.4% (81.8%-83.1%) for thin-layer Pap (with a result of > or = ASCUS), 78.8% (77.9%-79.7%) for PCR, and 72.6% (69.4%-75.0%) for signal amplification.", "Compared with referral for colposcopy of all women with ASCUS or higher, signal amplification testing of women with ASCUS and referral of those with a positive result was about as sensitive (61.3% vs 60.3%, respectively) and significantly more specific (82.4% vs 88.9%, respectively).", "The strategy requiring repeat positive PCR tests on 2 visits had a sensitivity of 84.2% (75.3%-91.0%) and a specificity of 86.2% (85.1%-87.3%).", "All tests were more specific and less sensitive in older (> or = 30 years) vs younger women.   \n", "CONCLUSIONS Testing for HPV has higher sensitivity but lower specificity than thin-layer Pap screening.", "In some settings, particularly where screening intervals are long or haphazard, screening for HPV DNA may be a reasonable alternative to cytology-based screening of reproductive-age women."], "structured": true}
{"doc_id": 19149247, "title": "Breaking the chains: structure and function of the deubiquitinases", "abstract": ["Ubiquitylation is a reversible protein modification that is implicated in many cellular functions.", "Recently, much progress has been made in the characterization of a superfamily of isopeptidases that remove ubiquitin: the deubiquitinases (DUBs; also known as deubiquitylating or deubiquitinating enzymes).", "Far from being uniform in structure and function, these enzymes display a myriad of distinct mechanistic features.", "The small number (<100) of DUBs might at first suggest a low degree of selectivity; however, DUBs are subject to multiple layers of regulation that modulate both their activity and their specificity.", "Due to their wide-ranging involvement in key regulatory processes, these enzymes might provide new therapeutic targets."], "structured": false}
{"doc_id": 19165076, "title": "Replication protein A: a heterotrimeric, single-stranded DNA-binding protein required for eukaryotic DNA metabolism.", "abstract": ["Replication protein A [RPA; also known as replication factor A (RFA) and human single-stranded DNA-binding protein] is a single-stranded DNA-binding protein that is required for multiple processes in eukaryotic DNA metabolism, including DNA replication, DNA repair, and recombination.", "RPA homologues have been identified in all eukaryotic organisms examined and are all abundant heterotrimeric proteins composed of subunits of approximately 70, 30, and 14 kDa.", "Members of this family bind nonspecifically to single-stranded DNA and interact with and/or modify the activities of multiple proteins.", "In cells, RPA is phosphorylated by DNA-dependent protein kinase when RPA is bound to single-stranded DNA (during S phase and after DNA damage).", "Phosphorylation of RPA may play a role in coordinating DNA metabolism in the cell.", "RPA may also have a role in modulating gene expression."], "structured": false}
{"doc_id": 19182166, "title": "Internal fixation versus nonoperative treatment of displaced 3-part proximal humeral fractures in elderly patients: a randomized controlled trial.", "abstract": ["BACKGROUND The aim of the study was to report the 2-year outcome after a displaced 3-part fracture of the proximal humerus in elderly patients randomized to treatment with a locking plate or nonoperative treatment.   \n", "PATIENTS AND METHODS We included 60 patients, mean age 74 years (range, 56-92), 81% being women.", "The main outcome measures were the Constant and Disabilities of the Arm, Shoulder and Hand (DASH) scores and the health-related quality of life (HRQoL) according to the EQ-5D.   \n", "RESULTS At the final 2-year follow-up, the results for range of motion (ROM), function and HRQoL were all in favor of the locking plate group.", "The mean flexion in the locking plate group was 120\u00b0 compared to 111\u00b0 in the nonoperative group (P = .36) and the mean abduction was 114\u00b0 compared to 106\u00b0 (P = .28).", "The corresponding values for the Constant score were 61 versus 58 (P = .64), for DASH 26 versus 35 (P = .19), and the mean EQ-5D (index) score was 0.70 compared to 0.59 (P = .26).", "In spite of good primary reduction in 86% of the fractures in the locking plate group, 13% of the patients had a fracture complication requiring a major reoperation and 17% had a minor reoperation.   \n", "CONCLUSION The results of our study indicate an advantage in functional outcome and HRQoL in favor of the locking plate compared to nonoperative treatment in elderly patients with a displaced 3-part fracture of the proximal humerus, but at the cost of additional surgery in 30% of the patients."], "structured": true}
{"doc_id": 19185192, "title": "Good and bad consequences of altered fatty acid metabolism in heart failure: evidence from mouse models.", "abstract": ["The shift in substrate preference away from fatty acid oxidation (FAO) towards increased glucose utilization in heart failure has long been interpreted as an oxygen-sparing mechanism.", "Inhibition of FAO has therefore evolved as an accepted approach to treat heart failure.", "However, recent data indicate that increased reliance on glucose might be detrimental rather than beneficial for the failing heart.", "This review discusses new insights into metabolic adaptations in heart failure.", "A particular focus lies on data obtained from mouse models with modulations of cardiac FA metabolism at different levels of the FA metabolic pathway and how these differently affect cardiac function.", "Based on studies in which these mouse models were exposed to ischaemic and non-ischaemic heart failure, we discuss whether and when modulations in FA metabolism are protective against heart failure."], "structured": false}
{"doc_id": 19204979, "title": "Pericytes of human skeletal muscle are myogenic precursors distinct from satellite cells", "abstract": ["Cells derived from blood vessels of human skeletal muscle can regenerate skeletal muscle, similarly to embryonic mesoangioblasts.", "However, adult cells do not express endothelial markers, but instead express markers of pericytes, such as NG2 proteoglycan and alkaline phosphatase (ALP), and can be prospectively isolated from freshly dissociated ALP+ cells.", "Unlike canonical myogenic precursors (satellite cells), pericyte-derived cells express myogenic markers only in differentiated myotubes, which they form spontaneously with high efficiency.", "When transplanted into severe combined immune deficient\u2013X-linked, mouse muscular dystrophy (scid\u2013mdx) mice, pericyte-derived cells colonize host muscle and generate numerous fibres expressing human dystrophin.", "Similar cells isolated from Duchenne patients, and engineered to express human mini-dystrophin, also give rise to many dystrophin-positive fibres in vivo.", "These data show that myogenic precursors, distinct from satellite cells, are associated with microvascular walls in the human skeletal muscle, may represent a correlate of embryonic 'mesoangioblasts' present after birth and may be a promising candidate for future cell-therapy protocols in patients."], "structured": false}
{"doc_id": 19205326, "title": "Ten years' experience with alendronate for osteoporosis in postmenopausal women.", "abstract": ["BACKGROUND Antiresorptive agents are widely used to treat osteoporosis.", "We report the results of a multinational randomized, double-blind study, in which postmenopausal women with osteoporosis were treated with alendronate for up to 10 years.   \n", "METHODS The initial three-year phase of the study compared three daily doses of alendronate with placebo.", "Women in the original placebo group received alendronate in years 4 and 5 and then were discharged.", "Women in the original active-treatment groups continued to receive alendronate during the initial extension (years 4 and 5).", "In two further extensions (years 6 and 7, and 8 through 10), women who had received 5 mg or 10 mg of alendronate daily continued on the same treatment.", "Women in the discontinuation group received 20 mg of alendronate daily for two years and 5 mg daily in years 3, 4, and 5, followed by five years of placebo.", "Randomized group assignments and blinding were maintained throughout the 10 years.", "We report results for the 247 women who participated in all four phases of the study.   \n", "RESULTS Treatment with 10 mg of alendronate daily for 10 years produced mean increases in bone mineral density of 13.7 percent at the lumbar spine (95 percent confidence interval, 12.0 to 15.5 percent), 10.3 percent at the trochanter (95 percent confidence interval, 8.1 to 12.4 percent), 5.4 percent at the femoral neck (95 percent confidence interval, 3.5 to 7.4 percent), and 6.7 percent at the total proximal femur (95 percent confidence interval, 4.4 to 9.1 percent) as compared with base-line values; smaller gains occurred in the group given 5 mg daily.", "The discontinuation of alendronate resulted in a gradual loss of effect, as measured by bone density and biochemical markers of bone remodeling.", "Safety data, including fractures and stature, did not suggest that prolonged treatment resulted in any loss of benefit.   \n", "CONCLUSIONS The therapeutic effects of alendronate were sustained, and the drug was well tolerated over a 10-year period.", "The discontinuation of alendronate resulted in the gradual loss of its effects."], "structured": true}
{"doc_id": 19205437, "title": "UCP1-independent signaling involving SERCA2b-mediated calcium cycling regulates beige fat thermogenesis and systemic glucose homeostasis", "abstract": ["Uncoupling protein 1 (UCP1) plays a central role in nonshivering thermogenesis in brown fat; however, its role in beige fat remains unclear.", "Here we report a robust UCP1-independent thermogenic mechanism in beige fat that involves enhanced ATP-dependent Ca2+ cycling by sarco/endoplasmic reticulum Ca2+-ATPase 2b (SERCA2b) and ryanodine receptor 2 (RyR2).", "Inhibition of SERCA2b impairs UCP1-independent beige fat thermogenesis in humans and mice as well as in pigs, a species that lacks a functional UCP1 protein.", "Conversely, enhanced Ca2+ cycling by activation of \u03b11- and/or \u03b23-adrenergic receptors or the SERCA2b-RyR2 pathway stimulates UCP1-independent thermogenesis in beige adipocytes.", "In the absence of UCP1, beige fat dynamically expends glucose through enhanced glycolysis, tricarboxylic acid metabolism and pyruvate dehydrogenase activity for ATP-dependent thermogenesis through the SERCA2b pathway; beige fat thereby functions as a 'glucose sink' and improves glucose tolerance independently of body weight loss.", "Our study uncovers a noncanonical thermogenic mechanism through which beige fat controls whole-body energy homeostasis via Ca2+ cycling."], "structured": false}
{"doc_id": 19255949, "title": "Poly(A)-specific ribonuclease (PARN) mediates 3\u2032-end maturation of the telomerase RNA component", "abstract": ["Mutations in the PARN gene (encoding poly(A)-specific ribonuclease) cause telomere diseases including familial idiopathic pulmonary fibrosis (IPF) and dyskeratosis congenita, but how PARN deficiency impairs telomere maintenance is unclear.", "Here, using somatic cells and induced pluripotent stem cells (iPSCs) from patients with dyskeratosis congenita with PARN mutations, we show that PARN is required for the 3\u2032-end maturation of the telomerase RNA component (TERC).", "Patient-derived cells as well as immortalized cells in which PARN is disrupted show decreased levels of TERC.", "Deep sequencing of TERC RNA 3\u2032 termini shows that PARN is required for removal of post-transcriptionally acquired oligo(A) tails that target nuclear RNAs for degradation.", "Diminished TERC levels and the increased proportion of oligo(A) forms of TERC are normalized by restoring PARN, which is limiting for TERC maturation in cells.", "Our results demonstrate a new role for PARN in the biogenesis of TERC and provide a mechanism linking PARN mutations to telomere diseases."], "structured": false}
{"doc_id": 19278208, "title": "Folic acid supplementation and dietary folate intake, and risk of preeclampsia", "abstract": ["Background/Objectives:Folic acid supplementation has been suggested to reduce the risk of preeclampsia.", "However, results from few epidemiologic studies have been inconclusive.", "We investigated the hypothesis that folic acid supplementation and dietary folate intake before conception and during pregnancy reduce the risk of preeclampsia.", "Subjects/Methods:A birth cohort study was conducted in 2010\u20132012 at the Gansu Provincial Maternity & Child Care Hospital in Lanzhou, China.", "A total of 10 041 pregnant women without chronic hypertension or gestational hypertension were enrolled.", "Results:Compared with nonusers, folic acid supplement users had a reduced risk of preeclampsia (OR=0.61, 95% CI: 0.43\u20130.87).", "A significant dose\u2013response of duration of use was observed among women who used folic acid supplemention during pregnancy only (P-trend=0.007).", "The reduced risk associated with folic acid supplement was similar for mild or severe preeclampsia and for early- or late-onset preeclampsia, although the statistical significant associations were only observed for mild (OR=0.50, 95% CI: 0.30\u20130.81) and late-onset (OR=0.60, 95% CI: 0.42\u20130.86) preeclampsia.", "The reduced risk associated with dietary folate intake during pregnancy was only seen for severe preeclampsia (OR=0.52, 95% CI: 0.31\u20130.87, for the highest quartile of dietary folate intake compared with the lowest).Conclusions:Our study results suggest that folic acid supplementation and higher dietary folate intake during pregnancy reduce the risk of preeclampsia.", "Future studies are needed to confirm the associations."], "structured": false}
{"doc_id": 19293654, "title": "Model-based Analysis of ChIP-Seq (MACS)", "abstract": ["We present Model-based Analysis of ChIP-Seq data, MACS, which analyzes data generated by short read sequencers such as Solexa's Genome Analyzer.", "MACS empirically models the shift size of ChIP-Seq tags, and uses it to improve the spatial resolution of predicted binding sites.", "MACS also uses a dynamic Poisson distribution to effectively capture local biases in the genome, allowing for more robust predictions.", "MACS compares favorably to existing ChIP-Seq peak-finding algorithms, and is freely available."], "structured": false}
{"doc_id": 19307912, "title": "Familial obesity and leanness.", "abstract": ["Using the Princeton School District Family Study cohort, our specific aim was to estimate the prevalence of suspected familial ponderosity and leanness, to provide empirical risk estimates for the proportion of probands' first-degree relatives who were similarly affected, and to estimate the contributions of diseases, drugs and caloric intake to relative obesity and leanness.", "We studied 379 probands, 125 whites and 52 blacks from a random recall group, 147 whites and 55 blacks from a hyperlipidemic recall group.", "Suspected familial obesity and leanness were arbitrarily identified in those kindreds with at least two first-degree relatives in the same Quetelet index decile as the proband, top or bottom respectively.", "Suspected familial obesity was observed in 2.4 percent and 6 percent respectively of random and hyperlipidemic recall group whites.", "Suspected familial leanness was identified in 2.4 percent and 1.4 percent of random and hyperlipidemic recall whites and in 3.8 percent of randomly recalled blacks.", "Approximately twice as many as expected white first-degree relatives of top Quetelet index decile probands themselves had top decile Quetelet indices; approximately three times as many as expected first-degree relatives of bottom decile Quetelet index probands themselves had bottom decile Quetelet indices.", "Nineteen percent and 31 percent of top decile Quetelet index white probands from random and hyperlipidemic recall groups came from families where at least two other first-degree relatives were similarly obese; 18 percent and 20 percent of white random and hyperlipidemic recall group probands with bottom decile Quetelet indices had suspected familial leanness.", "Nearly all subjects with familial obesity or leanness had no overt metabolic or pharmacological explanations for their body habitus.", "Within-family clustering of hypertension was common in kindreds with suspected familial obesity and was absent in kindreds with suspected familial leanness.", "Marked within-family clustering of both obesity and leanness is useful diagnostically; therapeutic intervention to reduce obesity, to be most effective, should be family-wide in the many kindreds which share familial obesity."], "structured": false}
{"doc_id": 19308127, "title": "In-hospital switching of oral P2Y12 inhibitor treatment in patients with acute coronary syndrome undergoing percutaneous coronary intervention: prevalence, predictors and short-term outcome.", "abstract": ["BACKGROUND P2Y12 inhibitor switching has appeared in clinical practice as a consequence of prasugrel and ticagrelor availability, apart from clopidogrel, for use in patients with acute coronary syndrome (ACS) undergoing percutaneous coronary intervention (PCI).   \n", "METHODS In the context of the GReek AntiPlatelet REgistry (GRAPE) we assessed the prevalence, predictive factors and short-term outcome of in-hospital P2Y12 inhibitor switching in 1794 ACS patients undergoing PCI.   \n", "RESULTS Switching occurred in 636 (35.5%) patients of which in the form of clopidogrel to a novel agent, novel agent to clopidogrel and between prasugrel and ticagrelor in 574 (90.4%), 34 (5.3%) and 27 (4.3%) patients, respectively.", "Presentation to non PCI-capable hospital, bivalirudin use, age \u226575 years (inverse predictor), and regional trends emerged as predictive factors of switching to a novel agent.", "At combined in-hospital and one-month follow-up, propensity matched pairs analysis showed no differences in major adverse cardiovascular (MACE) or bleeding events between switching from clopidogrel to a novel agent vs novel agent constant administration.", "More Bleeding Academic Research Consortium type 1, type 2 and any type events and fewer MACE were seen when switching from clopidogrel to a novel agent vs only clopidogrel administration (23.7%, 3.8%, 30.6%, 1.2% vs 8.9%, 1.2%, 12.0%, 3.8% with P < .001, P = .03, P < .001 and P = .03 respectively).   \n", "CONCLUSIONS In a real-life experience with contemporary antiplatelet treatment in ACS patients undergoing PCI, in-hospital switching represents common clinical practice.", "Clinical factors and regional practice differences seem to affect this strategy's choice, while switching to a novel agent may be associated with higher risk of bleeding."], "structured": true}
{"doc_id": 19313533, "title": "Structural basis of allosteric and synergistic activation of AMPK by furan-2-phosphonic derivative C2 binding.", "abstract": ["The metabolic stress-sensing enzyme AMP-activated protein kinase (AMPK) is responsible for regulating metabolism in response to energy supply and demand.", "Drugs that activate AMPK may be useful in the treatment of metabolic diseases including type 2 diabetes.", "We have determined the crystal structure of AMPK in complex with its activator 5-(5-hydroxyl-isoxazol-3-yl)-furan-2-phosphonic acid (C2), revealing two C2-binding sites in the \u03b3-subunit distinct from nucleotide sites.", "C2 acts synergistically with the drug A769662 to activate AMPK \u03b11-containing complexes independent of upstream kinases.", "Our results show that dual drug therapies could be effective AMPK-targeting strategies to treat metabolic diseases."], "structured": false}
{"doc_id": 19315511, "title": "Validity of age at menarche self-reported in adulthood.", "abstract": ["OBJECTIVE To test the validity of age at menarche self-reported in adulthood and examine whether socioeconomic position, education, experience of gynaecological events and psychological symptoms influence the accuracy of recall.   \n", "DESIGN Prospective birth cohort study.   \n", "SETTING England, Scotland and Wales.   \n", "PARTICIPANTS 1050 women from the Medical Research Council National Survey of Health and Development, with two measures of age at menarche, one recorded in adolescence and the other self-reported at age 48 years.   \n", "RESULTS By calculating the limits of agreement, kappa statistic and Pearson's correlation coefficients (r), we found that the validity of age at menarche self-reported in middle age compared with that recorded in adolescence was moderate (kappa = 0.35, r = 0.66, n = 1050).", "Validity was improved by categorising age at menarche into three groups: early, normal and late (kappa = 0.43).", "Agreement was influenced by educational level and having had a stillbirth or miscarriage.   \n", "CONCLUSIONS The level of validity shown in this study throws some doubt on whether it is justifiable to use age at menarche self-reported in middle age.", "It is likely to introduce error and bias, and researchers should be aware of these limitations and use such measures with caution."], "structured": true}
{"doc_id": 19327364, "title": "Seroepidemiologic survey of captive Old-World primates for antibodies to human and simian retroviruses, and isolation of a lentivirus from sooty mangabeys (Cercocebus atys).", "abstract": ["Sera from 526 Old-World monkeys and apes, representing 50 species and 20 genera and living in US zoos and vivaria, were screened for antibodies to HTLV-I, HTLV-III/LAV, and simian-AIDS retrovirus, type I (SRV-I).", "Sera were screened initially by ELISA, and ELISA-positive sera, as well as ELISA-negative sera from cage contacts, were further tested by Western blotting.", "A large number of false-positive and a small number of false-negative ELISA sera were identified.", "Although most true positive reactions were directed to a single retrovirus, a number of individuals from 4 species were positive for more than one retrovirus.", "Specific seroreactivity to HTLV-I was found in 39/526 (7%) animals of 15 species.", "True positive reactions to SRV-I were found in 21/516 (4%) animals, including talapoins and 2 species of macaques.", "Specific serologic reactions to HTLV-III/LAV were detected in 23/526 (4%) monkeys.", "Many of the HTLV-III/LAV seropositive animals were from one mixed-species zoo exhibit, containing sooty mangabeys, mandrills, Kolb's guenons, and talapoins.", "A type D virus was isolated from the blood of 3/10 SRV-I antibody-positive Tonkeana macaques, but from none of 11 seropositive talapoins.", "A lentivirus was isolated from the blood of 4/7 HTLV-III/LAV seropositive sooty mangabeys, but not from seropositive talapoins in the same exhibit or from 2 seropositive colobus from another zoo.", "The sooty mangabey lentivirus produced generalized lymphadenopathy, leukopenia, and decreased levels of T4 lymphocytes in 2 experimentally infected rhesus macaques."], "structured": false}
{"doc_id": 19332616, "title": "Coronary plaque disruption.", "abstract": ["Coronary atherosclerosis is by far the most frequent cause of ischemic heart disease, and plaque disruption with superimposed thrombosis is the main cause of the acute coronary syndromes of unstable angina, myocardial infarction, and sudden death.1 2 3 4 5 Therefore, for event-free survival, the vital question is not why atherosclerosis develops but rather why, after years of indolent growth, it suddenly becomes complicated by life-threatening thrombosis.", "The composition and vulnerability of plaque rather than its volume or the consequent severity of stenosis produced have emerged as being the most important determinants for the development of the thrombus-mediated acute coronary syndromes; lipid-rich and soft plaques are more dangerous than collagen-rich and hard plaques because they are more unstable and rupture-prone and highly thrombogenic after disruption.6 This review will explore potential mechanisms responsible for the sudden conversion of a stable atherosclerotic plaque to an unstable and life-threatening atherothrombotic lesion\u2014an event known as plaque fissuring, rupture, or disruption.7 8   Atherosclerosis is the result of a complex interaction between blood elements, disturbed flow, and vessel wall abnormality, involving several pathological processes: inflammation, with increased endothelial permeability, endothelial activation, and monocyte recruitment9 10 11 12 13 14 ; growth, with smooth muscle cell (SMC) proliferation, migration, and matrix synthesis15 16 ; degeneration, with lipid accumulation17 18 ; necrosis, possibly related to the cytotoxic effect of oxidized lipid19 ; calcification/ossification, which may represent an active rather than a dystrophic process20 21 ; and thrombosis, with platelet recruitment and fibrin formation.1 22 23 Thrombotic factors may play a role early during atherogenesis, but a flow-limiting thrombus does not develop until mature plaques are present, which is why thrombosis often is classified as a complication rather than a genuine component of atherosclerosis.   ", "### Mature Plaques: Atherosis and Sclerosis   As the name atherosclerosis implies, mature \u2026"], "structured": false}
{"doc_id": 19343151, "title": "p16INK4A is a robust in vivo biomarker of cellular aging in human skin.", "abstract": ["The cell-cycle regulating gene, p16INK4A, encoding an inhibitor of cyclin-dependent kinases 4 and 6, is considered to play an important role in cellular aging and in premature senescence.", "Although there is an age-dependent increase of p16INK4A expression in human fibroblast senescence in vitro, no data are available regarding the age dependency of p16INK4A in vivo.", "To determine whether p16INK4A expression in human skin correlates with donor age, p16INK4A expression was analyzed by immunohistochemistry as well as the expression of the p16INK4A repressor BMI1.", "Samples from the age groups 0-20, 21-70, and 71-95 years were selected from a bank of healthy human skin.", "We show that the number of p16INK4A positive cells is significantly higher in elderly individuals compared to the younger age groups.", "The number of p16INK4A positive cells was found to be increased in both epidermis and dermis, compartments with strictly different proliferative activities.", "BMI1 gene expression was significantly down-regulated with increasing donor age, whereas no striking age differences were observed for Ki67.", "In immunofluorescence co-expression studies, Ki67-positive cells were negative for p16INK4A and BMI1-expressing cells also stained negatively for Ki67.", "In conclusion, we provide for the first time evidence that p16INK4A expression directly correlates with chronological aging of human skin in vivo.", "p16INK4A therefore is a biomarker for human aging in vivo.", "The data reported here suggest a model for changes in regulatory gene expression that drive aging in human skin."], "structured": false}
{"doc_id": 19356271, "title": "hPrimpol1/CCDC111 is a human DNA primase-polymerase required for the maintenance of genome integrity.", "abstract": ["Prim-pol is a recently identified DNA primase-polymerase belonging to the archaeao-eukaryotic primase (AEP) superfamily.", "Here, we characterize a previously unrecognized prim-pol in human cells, which we designate hPrimpol1 (human primase-polymerase 1).", "hPrimpol1 possesses primase and DNA polymerase activities in vitro, interacts directly with RPA1 and is recruited to sites of DNA damage and stalled replication forks in an RPA1-dependent manner.", "Cells depleted of hPrimpol1 display increased spontaneous DNA damage and defects in the restart of stalled replication forks.", "Both RPA1 binding and the primase activity of hPrimpol1 are required for its cellular function during DNA replication.", "Our results indicate that hPrimpol1 is a novel factor involved in the response to DNA replication stress."], "structured": false}
{"doc_id": 19358586, "title": "Functional proteomics identifies miRNAs to target a p27/Myc/phospho-Rb signature in breast and ovarian cancer", "abstract": ["The myc oncogene is overexpressed in almost half of all breast and ovarian cancers, but attempts at therapeutic interventions against myc have proven to be challenging.", "Myc regulates multiple biological processes, including the cell cycle, and as such is associated with cell proliferation and tumor progression.", "We identified a protein signature of high myc, low p27 and high phospho-Rb significantly correlated with poor patient survival in breast and ovarian cancers.", "Screening of a miRNA library by functional proteomics in multiple cell lines and integration of data from patient tumors revealed a panel of five microRNAs (miRNAs) (miR-124, miR-365, miR-34b*, miR-18a and miR-506) as potential tumor suppressors capable of reversing the p27/myc/phospho-Rb protein signature.", "Mechanistic studies revealed an RNA-activation function of miR-124 resulting in direct induction of p27 protein levels by binding to and inducing transcription on the p27 promoter region leading to a subsequent G1 arrest.", "Additionally, in vivo studies utilizing a xenograft model demonstrated that nanoparticle-mediated delivery of miR-124 could reduce tumor growth and sensitize cells to etoposide, suggesting a clinical application of miRNAs as therapeutics to target the functional effect of myc on tumor growth."], "structured": false}
{"doc_id": 19368793, "title": "The potential role of miRNAs 21 and 199-a in early diagnosis of hepatocellular carcinoma.", "abstract": ["BACKGROUND Hepatocellular carcinoma (HCC) is regarded as one of the most common malignancies and among the leading causes of cancer death among the whole world.", "The most urgent needs are to find sensitive markers for early diagnosis for HCC.", "MicroRNAs (miRNAs) are reported as a group of small non-coding RNAs that can function as endogenous RNA interference to regulate expression of the targeted genes.", "This study was conducted to detect the serum and tissue expression of miR 21 and miR 199-a to be applied as early detectors for HCC.   \n", "METHODS A total of 40 serum and tissue samples (17 samples from chronic hepatitis and 23 samples from HCC patients) were collected.", "The levels of the two mature miRNAs (miR-21 and miR-199-a) were detected by real time quantitative reverse-transcriptase PCR (RT-qPCR) in sera and tissues of chronic hepatitis and HCC patients.", "Besides, miR-21 and miR-199-a levels in relation to clinical and pathological factors were explored.   \n", "RESULTS We found that the expression of serum miR-21 was distinctly increased in HCC compared with chronic hepatitis (P<0.001).", "miR 199-a was distinctly decreased in HCC compared with chronic hepatitis (P<0.001).", "In addition, median of miR 21 was increased in malignant when compared to adjacent non-malignant tissues without significant differences (P=0.191) while miR 199-a was significantly decreased in malignant when compared to adjacent nonmalignant tissues (P<0.001).", "ROC analysis showed that miR-21 and miR-199-a might be potential biomarkers for HCC.   \n", "CONCLUSIONS In conclusion, the expression of miR-21 was significantly up-regulated and miR-199-a was significantly down regulated in serum of patients with HCC.", "Due to their reasonable sensitivity and specificity for disease progression, miR-21 and miR-199-a could be used as potential circulating biomarkers for HCC."], "structured": true}
{"doc_id": 19384430, "title": "Tex10 Coordinates Epigenetic Control of Super-Enhancer Activity in Pluripotency and Reprogramming.", "abstract": ["Super-enhancers (SEs) are large clusters of transcriptional enhancers that are co-occupied by multiple lineage-specific transcription factors driving expression of genes that define cell identity.", "In embryonic stem cells (ESCs), SEs are highly enriched for the core pluripotency factors Oct4, Sox2, and Nanog.", "In this study, we sought to dissect the molecular control mechanism of SE activity in pluripotency and reprogramming.", "Starting from a protein interaction network surrounding Sox2, we identified Tex10 as a key pluripotency factor that plays a functionally significant role in ESC self-renewal, early embryo development, and reprogramming.", "Tex10 is enriched at SEs in a Sox2-dependent manner and coordinates histone acetylation and DNA demethylation at SEs.", "Tex10 activity is also important for pluripotency and reprogramming in human cells.", "Our study therefore highlights Tex10 as a core component of the pluripotency network and sheds light on its role in epigenetic control of SE activity for cell fate determination."], "structured": false}
{"doc_id": 19408393, "title": "Value of whole brain re-irradiation for brain metastases--single centre experience.", "abstract": ["AIMS There is controversy in published studies regarding the role of repeat whole brain radiation (WBRT) for previously irradiated brain metastases.", "The aim of our retrospective study was to document the practice at Princess Margaret Hospital with respect to the re-irradiation of patients with progressive or recurrent brain metastatic disease after initial WBRT.   ", "MATERIALS AND METHODS A comprehensive computerised database was used to identify patients treated for brain metastases with more than one course of WBRT between 1997 and 2003.", "Seventy-two patients were treated with WBRT for brain metastases and retreated with WBRT at a later date.", "The records of these patients were reviewed.   \n", "RESULTS The median age was 56.5 years.", "The most common primary sites were lung (51 patients) and breast (17 patients).", "The most frequent dose used for the initial radiotherapy was 20 Gy/5 fractions (62 patients).", "The most common doses of re-irradiation were 25 Gy/10 fractions (22 patients), 20 Gy/10 fractions (12 patients), 15 Gy/5 fractions (11 patients) and 20 Gy/8 fractions (10 patients).", "Thirty-one per cent of patients experienced a partial clinical response after re-irradiation, as judged by follow-up clinical notes; 27% remained stable; 32% deteriorated after re-irradiation.", "Patients who had Eastern Cooperative Oncology Group performance status 0-1 at the time of retreatment lived longer.", "In responders, the mean duration of response was 5.1 months.", "The median survival after re-irradiation was 4.1 months.", "One patient was reported as having memory impairment and pituitary insufficiency after 5 months of progression-free survival.   \n", "CONCLUSION Repeat radiotherapy may be a useful treatment in carefully selected patients.", "With increased survival and better systemic options for patients with metastatic disease, more patients may be candidates for consideration of repeat WBRT for recurrent brain metastases, but prospective studies are needed to more clearly document their outcomes."], "structured": true}
{"doc_id": 19419439, "title": "Bisphosphonates in oncology: rising stars or fallen heroes.", "abstract": ["The introduction of bisphosphonates in oncology has dramatically changed the management of patients with metastatic bone disease.", "In this manuscript, we thoroughly scrutinize the available body of clinical trials supporting the use of bisphosphonates in this setting and review new and ongoing research.", "Additionally, we summarize the data showing the benefits of bisphosphonate use in the prevention of treatment-induced bone loss and the intriguing emerging evidence on the antitumor potential of some of these agents when used in the adjuvant setting.", "Finally, we address the need for a careful consideration of potential benefits of bisphosphonate therapy and the risk for osteonecrosis of the jaw, a recently recognized late-toxicity of their use."], "structured": false}
{"doc_id": 19427410, "title": "IL-33, a recently identified interleukin-1 gene family member, is expressed in human adipocytes.", "abstract": ["Inflammation occurs in adipose tissue in obesity.", "We have examined whether IL-33, a recently identified IL-1 gene family member, and its associated receptors are expressed in human adipocytes.", "IL-33, IL-1RL1 and IL-1RAP gene expression was observed in human visceral white fat, in preadipocytes and in adipocytes (SGBS cells).", "Treatment with TNFalpha for 24h induced a 6-fold increase in IL-33 mRNA level in preadipocytes and adipocytes.", "Time-course studies with adipocytes showed that the increase in IL-33 mRNA with TNFalpha was maximal (>55-fold) at 12h.", "This response was markedly different to IL-1beta (peak mRNA increase at 2h; 5.4-fold) and 1L-18 (peak mRNA increase at 6h; >1500-fold).", "Exposure of adipocytes to hypoxia (1% O(2), 24h) did not alter IL-33 mRNA level; in preadipocytes, however, there was a 3-fold increase.", "Human adipocytes and preadipocytes express IL-33, but the various IL-1 family members exhibit major differences in responsiveness to TNFalpha."], "structured": false}
{"doc_id": 19450341, "title": "Imaging techniques for assaying lymphocyte activation in action", "abstract": ["Imaging techniques have greatly improved our understanding of lymphocyte activation.", "Technical advances in spatial and temporal resolution and new labelling tools have enabled researchers to directly observe the activation process.", "Consequently, research using imaging approaches to study lymphocyte activation has expanded, providing an unprecedented level of cellular and molecular detail in the field.", "As a result, certain models of lymphocyte activation have been verified, others have been revised and yet others have been replaced with new concepts.", "In this article, we review the current imaging techniques that are used to assess lymphocyte activation in different contexts, from whole animals to single molecules, and discuss the advantages and potential limitations of these methods."], "structured": false}
{"doc_id": 19460822, "title": "Extending healthy life span--from yeast to humans.", "abstract": ["When the food intake of organisms such as yeast and rodents is reduced (dietary restriction), they live longer than organisms fed a normal diet.", "A similar effect is seen when the activity of nutrient-sensing pathways is reduced by mutations or chemical inhibitors.", "In rodents, both dietary restriction and decreased nutrient-sensing pathway activity can lower the incidence of age-related loss of function and disease, including tumors and neurodegeneration.", "Dietary restriction also increases life span and protects against diabetes, cancer, and cardiovascular disease in rhesus monkeys, and in humans it causes changes that protect against these age-related pathologies.", "Tumors and diabetes are also uncommon in humans with mutations in the growth hormone receptor, and natural genetic variants in nutrient-sensing pathways are associated with increased human life span.", "Dietary restriction and reduced activity of nutrient-sensing pathways may thus slow aging by similar mechanisms, which have been conserved during evolution.", "We discuss these findings and their potential application to prevention of age-related disease and promotion of healthy aging in humans, and the challenge of possible negative side effects."], "structured": false}
{"doc_id": 19464037, "title": "Hospital and 1-year survival of patients admitted to intensive care units with acute exacerbation of chronic obstructive pulmonary disease.", "abstract": ["OBJECTIVE To describe outcomes and identify variables associated with hospital and 1-year survival for patients admitted to an intensive care unit (ICU) with an acute exacerbation of chronic obstructive pulmonary disease (COPD).   \n", "DESIGN Prospective, multicenter, inception cohort study.   \n", "SETTING Forty-two ICUs at 40 US hospitals.   \n", "PATIENTS A total of 362 admissions for COPD exacerbation selected from the Acute Physiology and Chronic Health Evaluation (APACHE) III database of 17,440 ICU admissions.   \n", "MEASUREMENTS AND RESULTS Hospital mortality for the 362 admissions was 24%.", "For the 167 patients aged 65 years or older, mortality was 30% at hospital discharge, 41% at 90 days, 47% at 180 days, and 59% at 1 year.", "Median survival for all patients was 224 days, and median survival for the patients who died within 1 year was 30.5 days.", "On multiple regression analysis, variables associated with hospital mortality included age, severity of respiratory and nonrespiratory organ system dysfunction, and hospital length of stay before ICU admission.", "Development of nonrespiratory organ system dysfunction was the major predictor of hospital mortality (60% of total explanatory power) and 180-day outcomes (54% of explanatory power).", "Respiratory physiological variables (respiratory rate, serum pH, PaCO2, PaO2, and alveolar-arterial difference in partial pressure of oxygen [PAO2-PaO2]) indicative of advanced dysfunction were more strongly associated with 180-day mortality rates (22% of explanatory power) than hospital death rates (4% of explanatory power).", "After controlling for severity of illness, mechanical ventilation at ICU admission was not associated with either hospital mortality or subsequent survival.   \n", "CONCLUSIONS Patients with COPD admitted to an ICU for an acute exacerbation have a substantial hospital mortality (24%).", "For patients aged 65 years or older, mortality doubles in 1 year from 30% to 59%.", "Hospital and longer-term mortality is closely associated with development of nonrespiratory organ system dysfunction; severity of the underlying respiratory function substantially influences mortality following hospital discharge.", "The need for mechanical ventilation at ICU admission did not influence either short- or long-term outcomes.", "Physicians should be aware of these relationships when making treatment decisions or evaluating new therapies."], "structured": true}
{"doc_id": 19482914, "title": "Kindlin-3 is essential for integrin activation and platelet aggregation", "abstract": ["Integrin-mediated platelet adhesion and aggregation are essential for sealing injured blood vessels and preventing blood loss, and excessive platelet aggregation can initiate arterial thrombosis, causing heart attacks and stroke.", "To ensure that platelets aggregate only at injury sites, integrins on circulating platelets exist in a low-affinity state and shift to a high-affinity state (in a process known as integrin activation or priming) after contacting a wounded vessel.", "The shift is mediated through binding of the cytoskeletal protein Talin to the \u03b2 subunit cytoplasmic tail.", "Here we show that platelets lacking the adhesion plaque protein Kindlin-3 cannot activate integrins despite normal Talin expression.", "As a direct consequence, Kindlin-3 deficiency results in severe bleeding and resistance to arterial thrombosis.", "Mechanistically, Kindlin-3 can directly bind to regions of \u03b2-integrin tails distinct from those of Talin and trigger integrin activation.", "We have therefore identified Kindlin-3 as a novel and essential element for platelet integrin activation in hemostasis and thrombosis."], "structured": false}
{"doc_id": 19485243, "title": "Opening of compacted chromatin by early developmental transcription factors HNF3 (FoxA) and GATA-4.", "abstract": ["The transcription factors HNF3 (FoxA) and GATA-4 are the earliest known to bind the albumin gene enhancer in liver precursor cells in embryos.", "To understand how they access sites in silent chromatin, we assembled nucleosome arrays containing albumin enhancer sequences and compacted them with linker histone.", "HNF3 and GATA-4, but not NF-1, C/EBP, and GAL4-AH, bound their sites in compacted chromatin and opened the local nucleosomal domain in the absence of ATP-dependent enzymes.", "The ability of HNF3 to open chromatin is mediated by a high affinity DNA binding site and by the C-terminal domain of the protein, which binds histones H3 and H4.", "Thus, factors that potentiate transcription in development are inherently capable of initiating chromatin opening events."], "structured": false}
{"doc_id": 19485649, "title": "N- and E-cadherins in Xenopus are specifically required in the neural and non-neural ectoderm, respectively, for F-actin assembly and morphogenetic movements.", "abstract": ["Transmembrane cadherins are calcium-dependent intercellular adhesion molecules.", "Recently, they have also been shown to be sites of actin assembly during adhesive contact formation.", "However, the roles of actin assembly on transmembrane cadherins during development are not fully understood.", "We show here, using the developing ectoderm of the Xenopus embryo as a model, that F-actin assembly is a primary function of both N-cadherin in the neural ectoderm and E-cadherin in the non-neural (epidermal) ectoderm, and that each cadherin is essential for the characteristic morphogenetic movements of these two tissues.", "However, depletion of N-cadherin and E-cadherin did not cause dissociation in these tissues at the neurula stage, probably owing to the expression of C-cadherin in each tissue.", "Depletion of each of these cadherins is not rescued by the other, nor by the expression of C-cadherin, which is expressed in both tissues.", "One possible reason for this is that each cadherin is expressed in a different domain of the cell membrane.", "These data indicate the combinatorial nature of cadherin function, the fact that N- and E-cadherin play primary roles in F-actin assembly in addition to roles in cell adhesion, and that this function is specific to individual cadherins.", "They also show how cell adhesion and motility can be combined in morphogenetic tissue movements that generate the form and shape of the embryonic organs."], "structured": false}
{"doc_id": 19487477, "title": "Mutation of the fumarase gene in two siblings with progressive encephalopathy and fumarase deficiency.", "abstract": ["We report an inborn error of the tricarboxylic acid cycle, fumarase deficiency, in two siblings born to first cousin parents.", "They presented with progressive encephalopathy, dystonia, leucopenia, and neutropenia.", "Elevation of lactate in the cerebrospinal fluid and high fumarate excretion in the urine led us to investigate the activities of the respiratory chain and of the Krebs cycle, and to finally identify fumarase deficiency in these two children.", "The deficiency was profound and present in all tissues investigated, affecting the cytosolic and the mitochondrial fumarase isoenzymes to the same degree.", "Analysis of fumarase cDNA demonstrated that both patients were homozygous for a missense mutation, a G-955-->C transversion, predicting a Glu-319-->Gln substitution.", "This substitution occurred in a highly conserved region of the fumarase cDNA.", "Both parents exhibited half the expected fumarase activity in their lymphocytes and were found to be heterozygous for this substitution.", "The present study is to our knowledge the first molecular characterization of tricarboxylic acid deficiency, a rare inherited inborn error of metabolism in childhood."], "structured": false}
{"doc_id": 19489351, "title": "Adult Neurogenesis Is Sustained by Symmetric Self-Renewal and Differentiation.", "abstract": ["Somatic stem cells have been identified in multiple adult tissues.", "Whether self-renewal occurs symmetrically or asymmetrically is key to understanding long-term stem cell maintenance and generation of progeny for cell replacement.", "In the adult mouse brain, neural stem cells (NSCs) (B1 cells) are retained in the walls of the lateral ventricles (ventricular-subventricular zone [V-SVZ]).", "The mechanism of B1 cell retention into adulthood for lifelong neurogenesis is unknown.", "Using multiple clonal labeling techniques, we show that the vast majority of B1 cells divide symmetrically.", "Whereas 20%-30% symmetrically self-renew and can remain in the niche for several months before generating neurons, 70%-80% undergo consuming divisions generating progeny, resulting in the depletion of B1 cells over time.", "This cellular mechanism decouples self-renewal from the generation of progeny.", "Limited rounds of symmetric self-renewal and consuming symmetric differentiation divisions can explain the levels of neurogenesis observed throughout life."], "structured": false}
{"doc_id": 19497526, "title": "A common missense variant in NUDT15 confers susceptibility to thiopurine-induced leukopenia", "abstract": ["Thiopurine therapy, commonly used in autoimmune conditions, can be complicated by life-threatening leukopenia.", "This leukopenia is associated with genetic variation in TPMT (encoding thiopurine S-methyltransferase).", "Despite a lower frequency of TPMT mutations in Asians, the incidence of thiopurine-induced leukopenia is higher in Asians than in individuals of European descent.", "Here we performed an Immunochip-based 2-stage association study in 978 Korean subjects with Crohn's disease treated with thiopurines.", "We identified a nonsynonymous SNP in NUDT15 (encoding p.", "Arg139Cys) that was strongly associated with thiopurine-induced early leukopenia (odds ratio (OR) = 35.6; Pcombined = 4.88 \u00d7 10\u221294).", "In Koreans, this variant demonstrated sensitivity and specificity of 89.4% and 93.2%, respectively, for thiopurine-induced early leukopenia (in comparison to 12.1% and 97.6% for TPMT variants).", "Although rare, this SNP was also strongly associated with thiopurine-induced leukopenia in subjects with inflammatory bowel disease of European descent (OR = 9.50; P = 4.64 \u00d7 10\u22124).", "Thus, NUDT15 is a pharmacogenetic determinant for thiopurine-induced leukopenia in diverse populations."], "structured": false}
{"doc_id": 19510470, "title": "Induction of cell cycle entry eliminates human leukemia stem cells in a mouse model of AML", "abstract": ["Cancer stem cells have been proposed to be important for initiation, maintenance and recurrence of various malignancies, including acute myeloid leukemia (AML).", "We have previously reported that CD34+CD38\u2212 human primary AML stem cells residing in the endosteal region of the bone marrow are relatively chemotherapy resistant.", "Using a NOD/SCID/IL2r\u03b3null mouse model of human AML, we now show that the AML stem cells in the endosteal region are cell cycle quiescent and that these stem cells can be induced to enter the cell cycle by treatment with granulocyte colony-stimulating factor (G-CSF).", "In combination with cell cycle-dependent chemotherapy, G-CSF treatment significantly enhances induction of apoptosis and elimination of human primary AML stem cells in vivo.", "The combination therapy leads to significantly increased survival of secondary recipients after transplantation of leukemia cells compared with chemotherapy alone."], "structured": false}
{"doc_id": 19511011, "title": "Reconstitution of the immune system after hematopoietic stem cell transplantation in humans", "abstract": ["Hematopoietic stem cell transplantation is associated with a severe immune deficiency.", "As a result, the patient is at high risk of infections.", "Innate immunity, including epithelial barriers, monocytes, granulocytes, and NK cells recovers within weeks after transplantation.", "By contrast, adaptive immunity recovers much slower.", "B- and T-cell counts normalize during the first months after transplantation, but in particular, T-cell immunity may remain impaired for years.", "During the last decade, much of the underlying mechanisms have been identified.", "These insights may provide new therapies to accelerate recovery."], "structured": false}
{"doc_id": 19521501, "title": "Vision tests in the mouse: Functional phenotyping with electroretinography.", "abstract": ["Electroretinography (ERG) is an established diagnostic technique in clinical ophthalmology and provides objective information about retinal function.", "This technique is also applied in basic research, where animal models of hereditary retinopathies have significantly contributed to our understanding of the composition of ERG responses in general and how retinal degenerative pathologies alter retinal function specifically.", "Indeed, electrophysiologic assessment of transgenic mice, which are genetically engineered to mimic human mutations that lead to retinal diseases, can be well compared with clinical data.", "Furthermore, limitations on examinations (e.g. length of measurement, range of light intensity) are much less of a concern when assessing mice compared to human patients.", "In order to measure and analyze retinal responses properly, several important aspects have to be considered.", "This paper focuses on these aspects, and shows exemplary ERG data which were obtained from normal wild-type mice and from transgenic mice with specific functional properties, namely Rho-/- (rod opsin knockout, cone function only), and Cnga3-/- (cone CNG channel deficient, rod function only) to illustrate rod and cone system contributions to ERG responses."], "structured": false}
{"doc_id": 19522248, "title": "Cyclin-dependent kinase 2 is essential for meiosis but not for mitotic cell division in mice", "abstract": ["We targeted the locus encoding the cyclin-dependent kinase 2 (CDK2) by homologous recombination in mouse embryonic stem (ES) cells.", "Embryonic fibroblasts lacking CDK2 proliferate normally and become immortal after continuous passage in culture.", "Elimination of a conditional Cdk2 allele in immortal cells does not have a significant effect on proliferation.", "Cdk2\u2212/\u2212 mice are viable and survive for up to two years, indicating that CDK2 is also dispensable for proliferation and survival of most cell types.", "But CDK2 is essential for completion of prophase I during meiotic cell division in male and female germ cells, an unforeseen role for this cell cycle kinase."], "structured": false}
{"doc_id": 19529370, "title": "Capsaicin-sensitive sensory nerve fibers contribute to the generation and maintenance of skeletal fracture pain.", "abstract": ["Although skeletal pain can have a marked impact on a patient's functional status and quality of life, relatively little is known about the specific populations of peripheral nerve fibers that drive non-malignant bone pain.", "In the present report, neonatal male Sprague-Dawley rats were treated with capsaicin or vehicle and femoral fracture was produced when the animals were young adults (15-16 weeks old).", "Capsaicin treatment, but not vehicle, resulted in a significant (>70%) depletion in the density of calcitonin-gene related peptide positive (CGRP(+)) sensory nerve fibers, but not 200 kDa neurofilament H positive (NF200(+)) sensory nerve fibers in the periosteum.", "The periosteum is a thin, cellular and fibrous tissue that tightly adheres to the outer surface of all but the articulated surface of bone and appears to play a pivotal role in driving fracture pain.", "In animals treated with capsaicin, but not vehicle, there was a 50% reduction in the severity, but no change in the time course, of fracture-induced skeletal pain-related behaviors as measured by spontaneous flinching, guarding and weight bearing.", "These results suggest that both capsaicin-sensitive (primarily CGRP(+) C-fibers) and capsaicin-insensitive (primarily NF200(+) A-delta fibers) sensory nerve fibers participate in driving skeletal fracture pain.", "Skeletal pain can be a significant impediment to functional recovery following trauma-induced fracture, osteoporosis-induced fracture and orthopedic surgery procedures such as knee and hip replacement.", "Understanding the specific populations of sensory nerve fibers that need to be targeted to inhibit the generation and maintenance of skeletal pain may allow the development of more specific mechanism-based therapies that can effectively attenuate acute and chronic skeletal pain."], "structured": false}
{"doc_id": 19532163, "title": "Surgical therapy for dystonia.", "abstract": ["Surgical treatments for dystonia have been available since the early 20th century, but have improved in their efficacy to adversity ratio through a combination of technologic advances and better understanding of the role of the basal ganglia in dystonia.", "The word \"dystonia\" describes a phenotype of involuntary movement that may manifest from a variety of conditions.", "Dystonia may affect only certain regions of the body or may be generalized.", "It appears to be critical to determine whether the etiology underlying the dystonia is \"primary\" (ie, occurring from a genetic or idiopathic origin) or \"secondary\" (ie, occurring as a result of structural, metabolic, or neurodegenerative disorders).", "Secondary dystonias are far more common than primary dystonias.", "Primary dystonias respond well to pallidotomy or deep brain stimulation of the internal segment of the globus pallidum, whereas secondary dystonias appear to respond partially at best.", "Limited historic and current data suggest that the thalamus may be a promising target for the treatment of secondary dystonias, but more careful, prospective, randomized studies are needed.", "Combinations of bilateral targets are possible with the current technology of DBS, but not widely used due to surgical morbidity and expense.", "This article reviews the surgical treatment of dystonia from past to present, with a focus on separating the outcomes for primary versus secondary and generalized versus cervical dystonia."], "structured": false}
{"doc_id": 19541444, "title": "MEG3 imprinted gene contribution in tumorigenesis.", "abstract": ["Maternally expressed gene 3 (MEG3) is a maternally expressed imprinted gene representing a large noncoding RNA in which microRNAs (miRNAs) and small nucleolar RNAs are also hosted.", "It is capable of interacting with cyclic AMP, p53, murine double minute 2 (MDM2) and growth differentiation factor 15 (GDF15) playing a role in cell proliferation control.", "MEG3 expression is under epigenetic control, and aberrant CpG methylation has been observed in several types of cancer.", "Moreover, gene copy number loss has been reported as additional mechanism associated with tumorigenesis.", "MEG3 deletion seems to upregulate the paternally expressed genes and on the other hand downregulate the expression of downstream maternally expressed genes and tumor suppressor miRNAs, although there are conflicting data on the topic.", "MEG3 could represent a tumor suppressor gene located in chromosome 14q32 and its association with tumorigenesis is growing every day."], "structured": false}
{"doc_id": 19546104, "title": "Uptake of rosuvastatin by isolated rat hepatocytes: comparison with pravastatin.", "abstract": ["1.", "The liver is the target organ for the lipid-regulating effect of rosuvastatin, a new 3-hydroxy-3-methylglutaryl coenzyme A reductase inhibitor, and liver-selective uptake of this drug is therefore a desirable property.", "The uptake kinetics of rosuvastatin were investigated and compared with those of pravastatin using isolated rat hepatocytes.", "2.", "Uptake for both drugs involved both active transport and passive diffusion processes.", "The Michaelis constant (K(m)) of uptake rate for rosuvastatin (9.17 micro M) was approximately half that for pravastatin (16.5 micro M).", "However, the maximum uptake rate (V(max)) and carrier-mediated uptake clearance (V(max)/K(m)) of rosuvastatin were significantly (p < 0.01) greater than those of pravastatin, and a larger contribution of carrier-mediated uptake clearance to total uptake clearance was shown for rosuvastatin (contribution ratio 0.903 versus pravastatin 0.654).", "3.", "Sodium and chloride ions did not play a significant role in the uptake of rosuvastatin and pravastatin, but the uptake of both drugs was inhibited both by depletion of cellular ATP and by organic anions such as bromosulfophthalein.", "4.", "Rosuvastatin competitively inhibited the uptake of pravastatin, with an inhibition constant (K(i)) (2.75 micro M) relatively similar to its K(m).", "5.", "The results suggest that an organic anion transport protein is the main mediator of the hepatic uptake of rosuvastatin and pravastatin, which occurs in an ATP-dependent manner.", "Our results indicated that rosuvastatin was taken up by the hepatocytes via the same transport systems as pravastatin, but with a greater affinity and efficiency than pravastatin."], "structured": false}
{"doc_id": 19561411, "title": "Junctophilin-4, a component of the endoplasmic reticulum-plasma membrane junctions, regulates Ca2+ dynamics in T cells.", "abstract": ["Orai1 and stromal interaction molecule 1 (STIM1) mediate store-operated Ca(2+) entry (SOCE) in immune cells.", "STIM1, an endoplasmic reticulum (ER) Ca(2+) sensor, detects store depletion and interacts with plasma membrane (PM)-resident Orai1 channels at the ER-PM junctions.", "However, the molecular composition of these junctions in T cells remains poorly understood.", "Here, we show that junctophilin-4 (JP4), a member of junctional proteins in excitable cells, is expressed in T cells and localized at the ER-PM junctions to regulate Ca(2+) signaling.", "Silencing or genetic manipulation of JP4 decreased ER Ca(2+) content and SOCE in T cells, impaired activation of the nuclear factor of activated T cells (NFAT) and extracellular signaling-related kinase (ERK) signaling pathways, and diminished expression of activation markers and cytokines.", "Mechanistically, JP4 directly interacted with STIM1 via its cytoplasmic domain and facilitated its recruitment into the junctions.", "Accordingly, expression of this cytoplasmic fragment of JP4 inhibited SOCE.", "Furthermore, JP4 also formed a complex with junctate, a Ca(2+)-sensing ER-resident protein, previously shown to mediate STIM1 recruitment into the junctions.", "We propose that the junctate-JP4 complex located at the junctions cooperatively interacts with STIM1 to maintain ER Ca(2+) homeostasis and mediate SOCE in T cells."], "structured": false}
{"doc_id": 19565018, "title": "The PI3K inhibitor arsenal: choose your weapon!", "abstract": ["Owing to its widespread activation in inflammation and cancer, a growing appreciation of the therapeutic potential of inhibitors of the phosphoinositide 3-kinase (PI3K) pathway has stimulated intense interest in compounds with suitable pharmacological profiles.", "These are primarily directed toward PI3K itself.", "However, as class I PI3Ks are also essential for a range of normal physiological processes, broad spectrum PI3K inhibition could be poorly tolerated.", "In recent years, patents describing a new generation of PI3K inhibitors have started to appear, with a particular focus on the development of compounds with enhanced isoform selectivity for use as anti-cancer and anti-inflammatory therapies.", "However, challenges remain for the efforts to pharmacologically target this enzyme family in a successful manner."], "structured": false}
{"doc_id": 19571273, "title": "Infralimbic BDNF/TrkB enhancement of GluN2B currents facilitates extinction of a cocaine-conditioned place preference.", "abstract": ["Brain-derived neurotrophic factor (BDNF) regulates synaptic activity and behavioral flexibility, and reduction of BDNF strongly predicts psychiatric disorders and cognitive dysfunction.", "Restoration of BDNF-dependent activity could alleviate these impairments, but BDNF has limited clinical utility due to its pharmacokinetics.", "Here we demonstrate that activation of a primary BDNF target, the tropomyosin-related kinase B (TrkB) receptor, enhances the amplitude and prolongs the decay kinetics of N-methyl-d-aspartate receptor (NMDAR) currents in male rat infralimbic prefrontal pyramidal neurons.", "Moreover, these effects were prevented and reversed by blockade of NMDARs containing the GluN2B subunit.", "Our results show that this signaling cascade bidirectionally regulates extinction of a cocaine-induced conditioned place preference (CPP), a task that requires behavioral flexibility.", "Blockade of infralimbic TrkB receptors or GluN2B-containing NMDARs disrupted consolidation of extinction of the CPP.", "In contrast, extinction was strengthened by potentiation of TrkB receptor activity with infralimbic infusions of BDNF or systemic injections of 7,8 dihydroxyflavone (7,8DHF), the newly synthesized TrkB receptor agonist.", "The 7,8DHF-induced enhancement of extinction was prevented by infralimbic infusions of a GluN2B-specific receptor antagonist, demonstrating that TrkB receptor activation enhances extinction of cocaine-CPP via GluN2B-containing NMDARs.", "Together, infralimbic TrkB receptor activation strengthens GluN2B-containing NMDAR currents to support extinction learning.", "TrkB receptor agonists would therefore be useful as pharmacological adjuncts for extinction-based therapies for treatment of psychiatric disorders associated with reduced BDNF activity."], "structured": false}
{"doc_id": 19572798, "title": "Compaction of chromatin by diverse Polycomb group proteins requires localized regions of high charge.", "abstract": ["Polycomb group (PcG) proteins are required for the epigenetic maintenance of developmental genes in a silent state.", "Proteins in the Polycomb-repressive complex 1 (PRC1) class of the PcG are conserved from flies to humans and inhibit transcription.", "One hypothesis for PRC1 mechanism is that it compacts chromatin, based in part on electron microscopy experiments demonstrating that Drosophila PRC1 compacts nucleosomal arrays.", "We show that this function is conserved between Drosophila and mouse PRC1 complexes and requires a region with an overrepresentation of basic amino acids.", "While the active region is found in the Posterior Sex Combs (PSC) subunit in Drosophila, it is unexpectedly found in a different PRC1 subunit, a Polycomb homolog called M33, in mice.", "We provide experimental support for the general importance of a charged region by predicting the compacting capability of PcG proteins from species other than Drosophila and mice and by testing several of these proteins using solution assays and microscopy.", "We infer that the ability of PcG proteins to compact chromatin in vitro can be predicted by the presence of domains of high positive charge and that PRC1 components from a variety of species conserve this highly charged region.", "This supports the hypothesis that compaction is a key aspect of PcG function."], "structured": false}
{"doc_id": 19583924, "title": "Angiopoietin-like proteins stimulate ex vivo expansion of hematopoietic stem cells", "abstract": ["Successful ex vivo expansion of hematopoietic stem cells (HSCs) would greatly benefit the treatment of disease and the understanding of crucial questions of stem cell biology.", "Here we show, using microarray studies, that the HSC-supportive mouse fetal liver CD3+ cells specifically express the proteins angiopoietin-like 2 (Angptl2) and angiopoietin-like 3 (Angptl3).", "We observed a 24- or 30-fold net expansion of long-term HSCs by reconstitution analysis when we cultured highly enriched HSCs for 10 days in the presence of Angptl2 or Angptl3 together with saturating levels of other growth factors.", "The coiled-coil domain of Angptl2 was capable of stimulating expansion of HSCs.", "Furthermore, angiopoietin-like 5, angiopoietin-like 7 and microfibril-associated glycoprotein 4 also supported expansion of HSCs in culture."], "structured": false}
{"doc_id": 19603353, "title": "Balancing co-stimulation and inhibition with BTLA and HVEM", "abstract": ["The interaction between B- and T-lymphocyte attenuator (BTLA), an inhibitory receptor whose extracellular domain belongs to the immunoglobulin superfamily, and herpesvirus-entry mediator (HVEM), a co-stimulatory tumour-necrosis factor receptor, is unique in that it is the only receptor\u2013ligand interaction that directly bridges these two families of receptors.", "This interaction has raised many questions about how receptors from two different families could interact and what downstream signalling events might occur as a result of receptor ligation.", "As we discuss, recent studies show that engagement of HVEM with its endogenous ligand (LIGHT) from the tumour-necrosis factor family induces a powerful immune response, whereas HVEM interactions with BTLA negatively regulate T-cell responses."], "structured": false}
{"doc_id": 19644821, "title": "Lin28b is sufficient to drive liver cancer and necessary for its maintenance in murine models.", "abstract": ["Lin28a/b are RNA-binding proteins that influence stem cell maintenance, metabolism, and oncogenesis.", "Poorly differentiated, aggressive cancers often overexpress Lin28, but its role in tumor initiation or maintenance has not been definitively addressed.", "We report that LIN28B overexpression is sufficient to initiate hepatoblastoma and hepatocellular carcinoma in murine models.", "We also detected Lin28b overexpression in MYC-driven hepatoblastomas, and liver-specific deletion of Lin28a/b reduced tumor burden, extended latency, and prolonged survival.", "Both intravenous siRNA against Lin28b and conditional Lin28b deletion reduced tumor burden and prolonged survival.", "Igf2bp proteins are upregulated, and Igf2bp3 is required in the context of LIN28B overexpression to promote growth.", "Therefore, multiple murine models demonstrate that Lin28b is both sufficient to initiate liver cancer and necessary for its maintenance."], "structured": false}
{"doc_id": 19651306, "title": "Nanoenzymology of the 20S proteasome: proteasomal actions are controlled by the allosteric transition.", "abstract": ["The proteasome is a major cytosolic proteolytic assembly, essential for the physiology of eukaryotic cells.", "Both the architecture and enzymatic properties of the 20S proteasome are relatively well understood.", "However, despite longstanding interest, the integration of structural and functional properties of the proteasome into a coherent model explaining the mechanism of its enzymatic actions has been difficult.", "Recently, we used tapping mode atomic force microscopy (AFM) in liquid to demonstrate that the alpha-rings of the proteasome imaged in a top-view position repeatedly switched between their open and closed conformations, apparently to control access to the central channel.", "Here, we show with AFM that the molecules in a side-view position acquired two stable conformations.", "The overall shapes of the 20S particles were classified as either barrel-like or cylinder-like.", "The relative abundance of the two conformers depended on the nature of their interactions with ligands.", "Similarly to the closed molecules in top view, the barrels predominated in control or inhibited molecules.", "The cylinders and open molecules prevailed when the proteasome was observed in the presence of peptide substrates.", "Based on these data, we developed the two-state model of allosteric transitions to explain the dynamics of proteasomal structure.", "This model helps to better understand the observed properties of the 20S molecule, and sets foundations for further studies of the structural dynamics of the proteasome."], "structured": false}
{"doc_id": 19658917, "title": "Changes in plasma copeptin, the c-terminal portion of arginine vasopressin during water deprivation and excess in healthy subjects.", "abstract": ["CONTEXT The measurement of arginine vasopressin (AVP) is often cumbersome because it is unstable with a short half-life time.", "AVP is derived from a larger precursor peptide along with the more stable peptide copeptin.", "Copeptin is the C-terminal part of provasopressin and has been shown to be a useful tool to indicate AVP concentration in critically ill patients.   \n", "OBJECTIVE The objective of the study was to evaluate the clinical usefulness of copeptin as a new marker in disordered states of blood volume and plasma osmolality.   \n", "DESIGN AND SETTING This was a prospective observational study in a university hospital.   \n", "PARTICIPANTS AND MAIN OUTCOME MEASURES Three techniques with respective control studies were used in 24 healthy adults to produce changes in plasma osmolality and/or volume: 1) a 28-h water deprivation, 2) a 17-h hypertonic saline infusion combined with thirsting, and 3) a hypotonic saline infusion with iv desmopressin administration during free water intake.   \n", "RESULTS Water deprivation produced a weight loss of 1.7 kg, an increase in plasma osmolality to 294.8 +/-", "4.3 mosmol/kg, and an increase of copeptin from 4.6 +/-", "1.7 pmol/liter to 9.2 +/-", "5.2 pmol/liter (P < 0.0001).", "During hypertonic saline infusion and thirsting with a raise of plasma osmolality to 296.1 +/-", "3.4 mosmol/kg, copeptin increased from 4.9 +/-", "3.0 pmol/liter to 19.9 +/-", "4.8 pmol/liter (P < 0.0001).", "Conversely, during hypotonic saline infusion, plasma osmolality decreased to 271.3 +/-", "4.1 mosmol/kg, and copeptin decreased from 6.2 +/-", "2.4 pmol/liter to 2.4 +/-", "2.1 pmol/liter (P < 0.01).   \n", "CONCLUSION Copeptin shows identical changes during disordered water states as previously shown for AVP.", "It might be a reliable marker of AVP secretion and substitute for the measurement of circulating AVP levels in clinical routine."], "structured": true}
{"doc_id": 19661996, "title": "Propagation and recovery of intact, infectious Epstein-Barr virus from prokaryotic to human cells.", "abstract": ["With current techniques, genetic alterations of herpesviruses are difficult to perform, mostly because of the large size of their genomes.", "To solve this problem, we have designed a system that allows the cloning of any gamma-herpesvirus in Escherichia coli onto an F factor-derived plasmid.", "Immortalized B cell lines were readily established with recombinant Epstein-Barr virus (EBV), demonstrating that the F factor-cloned EBV genome has all the characteristics of wild-type EBV.", "Because any genetic modification is possible in E. coli, this experimental approach opens the way to the genetic analysis of all EBV functions.", "Moreover, it is now feasible to generate attenuated EBV strains in vitro such that vaccine strains can be designed.", "Because we incorporated the genes for hygromycin resistance and green fluorescent protein onto the E. coli cloned EBV genome, the still open question of the EBV target cells other than B lymphocytes will be addressed."], "structured": false}
{"doc_id": 19673227, "title": "Chemosensitivity profile assay of circulating cancer cells: prognostic and predictive value in epithelial tumors.", "abstract": ["The prognostic value associated with the detection of circulating tumor cells (CTCs) in metastatic breast cancer by the CellSearch technology raise additional issues regarding the biological value of this information.", "We postulated that a drug-resistance profile of CTCs may predict response to chemotherapy in cancer patients and therefore could be used for patient selection.", "One hundred 5 patients with diagnosis of carcinoma were enrolled in a prospective trial.", "CTCs were isolated from peripheral blood, and positive samples were evaluated for the expression of a panel of genes involved in anticancer drugs resistance.", "The drug-resistance profile was correlated with disease-free survival (DFS; patients in adjuvant setting) and time to progression (TTP; metastatic patients) in a 24-months follow-up.", "Objective response correlation was a secondary end point.", "Fifty-one percent of patients were found positive for CTCs while all blood samples from healthy donors were negative.", "The drug-resistance profile correlates with DFS and TTP (p < 0.001 in both).", "Sensitivity of the test: able to predict treatment response in 98% of patients.", "Specificity of the test: 100%; no sample from healthy subject was positive for the presence of CTCs.", "Positive and negative predictive values were found to be 96.5 and 100%, respectively.", "We identified a drug-resistance profile of CTCs, which is predictive of response to chemotherapy, independent of tumor type and stage of disease.", "This approach may represent a first step toward the individualization of chemotherapy in cancer patients."], "structured": false}
{"doc_id": 19675911, "title": "Trends in heart failure incidence and survival in a community-based population.", "abstract": ["CONTEXT The epidemic of heart failure has yet to be fully investigated, and data on incidence, survival, and sex-specific temporal trends in community-based populations are limited.   \n", "OBJECTIVE To test the hypothesis that the incidence of heart failure has declined and survival after heart failure diagnosis has improved over time but that secular trends have diverged by sex.   \n", "DESIGN, SETTING, AND PARTICIPANTS Population-based cohort study using the resources of the Rochester Epidemiology Project conducted in Olmsted County, Minnesota.", "Patients were 4537 Olmsted County residents (57% women; mean [SD] age, 74 [14] years) with a diagnosis of heart failure between 1979 and 2000.", "Framingham criteria and clinical criteria were used to validate the diagnosis   MAIN OUTCOME MEASURES Incidence of heart failure and survival after heart failure diagnosis.   \n", "RESULTS The incidence of heart failure was higher among men (378/100 000 persons; 95% confidence interval [CI], 361-395 for men; 289/100 000 persons; 95% CI, 277-300 for women) and did not change over time among men or women.", "After a mean follow-up of 4.2 years (range, 0-23.8 years), 3347 deaths occurred, including 1930 among women and 1417 among men.", "Survival after heart failure diagnosis was worse among men than women (relative risk, 1.33; 95% CI, 1.24-1.43) but overall improved over time (5-year age-adjusted survival, 43% in 1979-1984 vs 52% in 1996-2000, P<.001).", "However, men and younger persons experienced larger survival gains, contrasting with less or no improvement for women and elderly persons.   \n", "CONCLUSION In this community-based cohort, the incidence of heart failure has not declined during 2 decades, but survival after onset of heart failure has increased overall, with less improvement among women and elderly persons."], "structured": true}
{"doc_id": 19683625, "title": "Doxycycline induces apoptosis in PANC-1 pancreatic cancer cells.", "abstract": ["BACKGROUND Tetracyclines such as doxycycline are reported to possess cytotoxic activity against mammalian tumor cells, but the mechanism of their effects on cell proliferation remains unclear.   ", "MATERIALS AND METHODS The antitumor effect of doxycycline was investigated in human pancreatic cancer cell line, PANC-1.", "We also investigated the effect of doxycycline on expression of a potent proangiogenic factor, interleukin (IL)-8.   \n", "RESULTS In excess of 20 microg/ml, cytotoxic effects of doxycycline were accompanied by G(1)-S cell cycle arrest and DNA fragmentation in PANC-1 cells.", "Doxycycline consistently activated transcription of p53, p21 and Fas/FasL-cascade-related genes, while reducing the expression of Bcl-xL and Mcl-1.", "Doxycycline (5 microg/ml) below the cytotoxic level suppressed endogenous and paclitaxel-induced IL-8 expression.", "In the mouse xenograft model, doxycycline treatment was shown to suppress tumor growth by 80%.   \n", "CONCLUSION These data suggest that doxycycline exerts its antitumor effect by activating proapoptotic genes, inhibiting IL-8 expression, and suppressing antiapoptotic genes."], "structured": true}
{"doc_id": 19685306, "title": "Orientationally invariant indices of axon diameter and density from diffusion MRI.", "abstract": ["This paper proposes and tests a technique for imaging orientationally invariant indices of axon diameter and density in white matter using diffusion magnetic resonance imaging.", "Such indices potentially provide more specific markers of white matter microstructure than standard indices from diffusion tensor imaging.", "Orientational invariance allows for combination with tractography and presents new opportunities for mapping brain connectivity and quantifying disease processes.", "The technique uses a four-compartment tissue model combined with an optimized multishell high-angular-resolution pulsed-gradient-spin-echo acquisition.", "We test the method in simulation, on fixed monkey brains using a preclinical scanner and on live human brains using a clinical 3T scanner.", "The human data take about one hour to acquire.", "The simulation experiments show that both monkey and human protocols distinguish distributions of axon diameters that occur naturally in white matter.", "We compare the axon diameter index with the mean axon diameter weighted by axon volume.", "The index differs from this mean and is protocol dependent, but correlation is good for the monkey protocol and weaker, but discernible, for the human protocol where greater diffusivity and lower gradient strength limit sensitivity to only the largest axons.", "Maps of axon diameter and density indices from the monkey and human data in the corpus callosum and corticospinal tract reflect known trends from histology.", "The results show orientationally invariant sensitivity to natural axon diameter distributions for the first time with both specialist and clinical hardware.", "This demonstration motivates further refinement, validation, and evaluation of the precise nature of the indices and the influence of potential confounds."], "structured": false}
{"doc_id": 19688024, "title": "IFI16 and cGAS cooperate in the activation of STING during DNA sensing in human keratinocytes", "abstract": ["Many human cells can sense the presence of exogenous DNA during infection though the cytosolic DNA receptor cyclic GMP-AMP synthase (cGAS), which produces the second messenger cyclic GMP-AMP (cGAMP).", "Other putative DNA receptors have been described, but whether their functions are redundant, tissue-specific or integrated in the cGAS-cGAMP pathway is unclear.", "Here we show that interferon-\u03b3 inducible protein 16 (IFI16) cooperates with cGAS during DNA sensing in human keratinocytes, as both cGAS and IFI16 are required for the full activation of an innate immune response to exogenous DNA and DNA viruses.", "IFI16 is also required for the cGAMP-induced activation of STING, and interacts with STING to promote STING phosphorylation and translocation.", "We propose that the two DNA sensors IFI16 and cGAS cooperate to prevent the spurious activation of the type I interferon response."], "structured": false}
{"doc_id": 19701340, "title": "Oncostatic effects of the indole melatonin and expression of its cytosolic and nuclear receptors in cultured human melanoma cell lines.", "abstract": ["Melatonin has been shown to have oncostatic effects on malignant melanoma in vitro and in vivo.", "We studied the growth suppressive effects of melatonin over a wide range of concentrations in four melanoma cell lines (SBCE2, WM-98, WM-164 and SKMEL-188) representative for different growth stages and phenotype.", "Melanoma cells were incubated with melatonin 10(-12)-10(-3) M, and proliferation and clonogenicity was assessed at 12 h and 14 days, respectively.", "We also determined the expression of cytosolic quinone oxidoreductases NQO1, NQO2 (known as MT3 receptor) and nuclear receptor RORalpha by RT-PCR.", "Melatonin at pharmacological concentrations (10(-3)-10(-7) M) suppressed proliferation in all melanoma cell lines.", "In SKMEL-188 cells cultured in serum-free media, melatonin at low concentrations (10(-12)-10(-10) M) also slightly attenuated the proliferation.", "The effects of pharmacological doses of melatonin were confirmed in the clonogenic assay.", "Expression of NQO1 was detected in all cell lines, whereas NQO2 and nuclear receptor RORalpha including its isoform RORalpha4 were present only in SBCE2, WM-164 and WM-98.", "Thus, melatonin differentially suppressed proliferation in melanoma cell lines of different behaviour.", "The intensity of the oncostatic response to melatonin could be related to the cell-line specific pattern of melatonin cellular receptors and cytosolic binding protein expression."], "structured": false}
{"doc_id": 19708993, "title": "Lysosomal localization of TRPML3 depends on TRPML2 and the mucolipidosis-associated protein TRPML1.", "abstract": ["Mucolipidosis type IV is an autosomal recessive lysosomal storage disorder characterized by severe neurodegeneration, achlorhydria, and visual impairments such as corneal opacity and strabismus.", "The disease arises due to mutations in a group 2 transient receptor potential (TRP)-related cation channel, TRPML1.", "Mammals encode two additional TRPML proteins named TRPML2 and TRPML3.", "Information regarding the propensity of these proteins to multimerize, their subcellular distribution and mechanisms that regulate their trafficking are limited.", "Here we demonstrate that TRPMLs interact to form homo- and heteromultimers.", "Moreover, the presence of either TRPML1 or TRPML2 specifically influences the spatial distribution of TRPML3.", "TRPML1 and TRPML2 homomultimers are lysosomal proteins, whereas TRPML3 homomultimers are in the endoplasmic reticulum.", "However, TRPML3 localizes to lysosomes when coexpressed with either TRPML1 or TRPML2 and is comparably mislocalized when lysosomal targeting of TRPML1 and TRPML2 is disrupted.", "Conversely, TRPML3 does not cause retention of TRPML1 or TRPML2 in the endoplasmic reticulum.", "These data demonstrate that there is a hierarchy controlling the subcellular distributions of the TRPMLs such that TRPML1 and TRPML2 dictate the localization of TRPML3 and not vice versa."], "structured": false}
{"doc_id": 19736671, "title": "Evolution of metastasis revealed by mutational landscapes of chemically induced skin cancers", "abstract": ["Human tumors show a high level of genetic heterogeneity, but the processes that influence the timing and route of metastatic dissemination of the subclones are unknown.", "Here we have used whole-exome sequencing of 103 matched benign, malignant and metastatic skin tumors from genetically heterogeneous mice to demonstrate that most metastases disseminate synchronously from the primary tumor, supporting parallel rather than linear evolution as the predominant model of metastasis.", "Shared mutations between primary carcinomas and their matched metastases have the distinct A-to-T signature of the initiating carcinogen dimethylbenzanthracene, but non-shared mutations are primarily G-to-T, a signature associated with oxidative stress.", "The existence of carcinomas that either did or did not metastasize in the same host animal suggests that there are tumor-intrinsic factors that influence metastatic seeding.", "We also demonstrate the importance of germline polymorphisms in determining allele-specific mutations, and we identify somatic genetic alterations that are specifically related to initiation of carcinogenesis by Hras or Kras mutations.", "Mouse tumors that mimic the genetic heterogeneity of human cancers can aid our understanding of the clonal evolution of metastasis and provide a realistic model for the testing of novel therapies."], "structured": false}
{"doc_id": 19752008, "title": "A specific inhibitor of phosphatidylinositol 3-kinase, 2-(4-morpholinyl)-8-phenyl-4H-1-benzopyran-4-one (LY294002).", "abstract": ["Phosphatidylinositol (PtdIns) 3-kinase is an enzyme implicated in growth factor signal transduction by associating with receptor and nonreceptor tyrosine kinases, including the platelet-derived growth factor receptor.", "Inhibitors of PtdIns 3-kinase could potentially give a better understanding of the function and regulatory mechanisms of the enzyme.", "Quercetin, a naturally occurring bioflavinoid, was previously shown to inhibit PtdIns 3-kinase with an IC50 of 1.3 microgram/ml (3.8 microM); inhibition appeared to be directed at the ATP-binding site of the kinase.", "Analogs of quercetin were investigated as PtdIns 3-kinase inhibitors, with the most potent ones exhibiting IC50 values in the range of 1.7-8.4 micrograms/ml.", "In contrast, genistein, a potent tyrosine kinase inhibitor of the isoflavone class, did not inhibit PtdIns 3-kinase significantly (IC50 > 30 micrograms/ml).", "Since quercetin has also been shown to inhibit other PtdIns and protein kinases, other chromones were evaluated as inhibitors of PtdIns 3-kinase without affecting PtdIns 4-kinase or selected protein kinases.", "One such compound, 2-(4-morpholinyl)-8-phenyl-4H-1-benzopyran-4-one (also known as 2-(4-morpholinyl)-8-phenylchromone, LY294002), completely and specifically abolished PtdIns 3-kinase activity (IC50 = 0.43 microgram/ml; 1.40 microM) but did not inhibit PtdIns 4-kinase or tested protein and lipid kinases.", "Analogs of LY294002 demonstrated a very selective structure-activity relationship, with slight changes in structure causing marked decreases in inhibition.", "LY294002 was shown to completely abolish PtdIns 3-kinase activity in fMet-Leu-Phe-stimulated human neutrophils, as well as inhibit proliferation of smooth muscle cells in cultured rabbit aortic segments.", "Since PtdIns 3-kinase appears to be centrally involved with growth factor signal transduction, the development of specific inhibitors against the kinase may be beneficial in the treatment of proliferative diseases as well as in elucidating the biological role of the kinase in cellular proliferation and growth factor response."], "structured": false}
{"doc_id": 19756935, "title": "A simple two-step protocol for the purification of human pancreatic beta cells", "abstract": ["Isolated pure human beta cells would be helpful for a number of research purposes.", "However, lack of beta cell-specific surface antigens has been a major problem.", "We aimed to develop a simple method for human beta cell isolation based on the initial elimination of ductal cells by their expression of carbohydrate antigen 19-9 (CA19-9), followed by positive selection of beta cells by their expression of polysialic acid\u2013neural cell adhesion molecule (PSA-NCAM).", "Cell type-specific expression of CA19-9, NCAM and PSA-NCAM was studied in sections of adult human pancreas and in cultured primary endocrine and exocrine cells.", "Dispersed human islet cells were purified in two steps, after 4 days of suspension culture, by binding to magnetic microbeads coupled to antibodies against CA19-9 and PSA-NCAM.", "NCAM expression was detected in ducts and islets in the human pancreas.", "In contrast, PSA-NCAM immunoreactivity was detected only in islets.", "PSA-NCAM staining in dispersed cells revealed that the marker is expressed in all endocrine cell types, but not in duct cells.", "Purification of dispersed islet cells using PSA-NCAM microbeads alone did not completely eliminate contaminating duct cells.", "However, elimination of the duct cells by CA19-9 microbeads followed by positive sorting of the PSA-NCAM-positive cells in five consecutive islet preparations resulted in 90 to 98% pure endocrine cells, of which 89 to 97% were beta cells.", "We describe a simple and reproducible method for purification of viable human pancreatic beta cells devoid of exocrine acini and ducts."], "structured": false}
{"doc_id": 19770974, "title": "Prev | Table of Contents Reports Embryonic Stem Cell Lines Derived from Human", "abstract": ["Human blastocyst-derived, pluripotent cell lines are described that have normal karyotypes, express high levels of telomerase activity, and express cell surface markers that characterize primate embryonic stem cells but do not characterize other early lineages.", "After undifferentiated proliferation in vitro for 4 to 5 months, these cells still maintained the developmental potential to form trophoblast and derivatives of all three embryonic germ layers, including gut epithelium (endoderm); cartilage, bone, smooth muscle, and striated muscle (mesoderm); and neural epithelium, embryonic ganglia, and stratified squamous epithelium (ectoderm).", "These cell lines should be useful in human developmental biology, drug discovery, and transplantation medicine."], "structured": false}
{"doc_id": 19799455, "title": "Ascorbic-acid transporter Slc23a1 is essential for vitamin C transport into the brain and for perinatal survival", "abstract": ["The only proven requirement for ascorbic acid (vitamin C) is in preventing scurvy, presumably because it is a cofactor for hydroxylases required for post-translational modifications that stabilize collagen.", "We have created mice deficient in the mouse ortholog (solute carrier family 23 member 1 or Slc23a1) of a rat ascorbic-acid transporter, Svct2 (ref.", "4).", "Cultured embryonic fibroblasts from homozygous Slc23a1\u2212/\u2212 mice had less than 5% of normal ascorbic-acid uptake.", "Ascorbic-acid levels were undetectable or markedly reduced in the blood and tissues of Slc23a1\u2212/\u2212 mice.", "Prenatal supplementation of pregnant females did not elevate blood ascorbic acid in Slc23a1\u2212/\u2212 fetuses, suggesting Slc23a1 is important in placental ascorbic-acid transport.", "Slc23a1\u2212/\u2212 mice died within a few minutes of birth with respiratory failure and intraparenchymal brain hemorrhage.", "Lungs showed no postnatal expansion but had normal surfactant protein B levels.", "Brain hemorrhage was unlikely to be simply a form of scurvy since Slc23a1\u2212/\u2212 mice showed no hemorrhage in any other tissues and their skin had normal skin 4-hydroxyproline levels despite low ascorbic-acid content.", "We conclude that Slc23a1 is required for transport of ascorbic acid into many tissues and across the placenta.", "Deficiency of the transporter is lethal in newborn mice, thereby revealing a previously unrecognized requirement for ascorbic acid in the perinatal period."], "structured": false}
{"doc_id": 19800147, "title": "MVP-mediated exosomal sorting of miR-193a promotes colon cancer progression", "abstract": ["Exosomes are emerging mediators of intercellular communication; whether the release of exosomes has an effect on the exosome donor cells in addition to the recipient cells has not been investigated to any extent.", "Here, we examine different exosomal miRNA expression profiles in primary mouse colon tumour, liver metastasis of colon cancer and naive colon tissues.", "In more advanced disease, higher levels of tumour suppressor miRNAs are encapsulated in the exosomes.", "miR-193a interacts with major vault protein (MVP).", "Knockout of MVP leads to miR-193a accumulation in the exosomal donor cells instead of exosomes, inhibiting tumour progression.", "Furthermore, miR-193a causes cell cycle G1 arrest and cell proliferation repression through targeting of Caprin1, which upregulates Ccnd2 and c-Myc.", "Human colon cancer patients with more advanced disease show higher levels of circulating exosomal miR-193a.", "In summary, our data demonstrate that MVP-mediated selective sorting of tumour suppressor miRNA into exosomes promotes tumour progression."], "structured": false}
{"doc_id": 19804204, "title": "Casual blood pressure and neurocognitive function in children with chronic kidney disease: a report of the children with chronic kidney disease cohort study.", "abstract": ["BACKGROUND AND OBJECTIVES Children with chronic kidney disease (CKD) are at risk for cognitive dysfunction, and over half have hypertension.", "Data on the potential contribution of hypertension to CKD-associated neurocognitive deficits in children are limited.", "Our objective was to determine whether children with CKD and elevated BP (EBP) had decreased performance on neurocognitive testing compared with children with CKD and normal BP.   \n", "DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS This was a cross-sectional analysis of the relation between auscultatory BP and neurocognitive test performance in children 6 to 17 years enrolled in the Chronic Kidney Disease in Children (CKiD) project.   \n", "RESULTS Of 383 subjects, 132 (34%) had EBP (systolic BP and/or diastolic BP \u226590(th) percentile).", "Subjects with EBP had lower mean (SD) scores on Wechsler Abbreviated Scales of Intelligence (WASI) Performance IQ than those with normal BP (normal BP versus EBP, 96.1 (16.7) versus 92.4 (14.9), P = 0.03) and WASI Full Scale IQ (97.0 (16.2) versus 93.4 (16.5), P = 0.04).", "BP index (subject's BP/95(th) percentile BP) correlated inversely with Performance IQ score (systolic, r = -0.13, P = 0.01; diastolic, r = -0.19, P < 0.001).", "On multivariate analysis, the association between lower Performance IQ score and increased BP remained significant after controlling for demographic and disease-related variables (EBP, \u03b2 = -3.7, 95% confidence interval [CI]: -7.3 to -0.06; systolic BP index, \u03b2 = -1.16 to 95% CI: -2.1, -0.21; diastolic BP index, \u03b2 = -1.17, 95% CI: -1.8 to -0.55).   \n", "CONCLUSIONS Higher BP was independently associated with decreased WASI Performance IQ scores in children with mild-to-moderate CKD."], "structured": true}
{"doc_id": 19822046, "title": "Bone marrow failure and developmental delay caused by mutations in poly(A)-specific ribonuclease (PARN).", "abstract": ["BACKGROUND Deadenylation regulates RNA function and fate.", "Poly(A)-specific ribonuclease (PARN) is a deadenylase that processes mRNAs and non-coding RNA.", "Little is known about the biological significance of germline mutations in PARN.   \n", "METHODS We identified mutations in PARN in patients with haematological and neurological manifestations.", "Genomic, biochemical and knockdown experiments in human marrow cells and in zebrafish have been performed to clarify the role of PARN in the human disease.   \n", "RESULTS We identified large monoallelic deletions in PARN in four patients with developmental delay or mental illness.", "One patient in particular had a severe neurological phenotype, central hypomyelination and bone marrow failure.", "This patient had an additional missense mutation on the non-deleted allele and severely reduced PARN protein and deadenylation activity.", "Cells from this patient had impaired oligoadenylation of specific H/ACA box small nucleolar RNAs.", "Importantly, PARN-deficient patient cells manifested short telomeres and an aberrant ribosome profile similar to those described in some variants of dyskeratosis congenita.", "Knocking down PARN in human marrow cells and zebrafish impaired haematopoiesis, providing further evidence for a causal link with the human disease.   \n", "CONCLUSIONS Large monoallelic mutations of PARN can cause developmental/mental illness.", "Biallelic PARN mutations cause severe bone marrow failure and central hypomyelination."], "structured": true}
{"doc_id": 19824183, "title": "The changing epidemiology of malaria in Ifakara Town, southern Tanzania.", "abstract": ["Between 1995 and 2000 there were marked changes in the epidemiology of malaria in Ifakara, southern Tanzania.", "We documented these changes using parasitological and clinical data from a series of community- and hospital-based studies involving children up to the age of 5 years.", "There was a right shift and lowering in the age-specific parasite prevalence in the community-based cohort studies.", "The incidence of clinical malaria in placebo-receiving infants in additional study cohorts dropped from 0.8 in 1995 to 0.43 episodes per infant per year in 2000, an incidence rate ratio of 0.53 (95% confidence interval: 0.404, 0.70, P<0.0001).", "At the same time, there was an increase in the total number of malaria admissions and a marked right shift in the age pattern of these admissions (median age in 1995 1.55 years vs. 2.33 in 2000, P<0.0001).", "However, the burden of malaria deaths remained in infants.", "We discuss how these dramatic changes in the epidemiology of malaria may have arisen from the use of currently available malaria control tools.", "Caution is required in the interpretation of hospital-based data as it is likely to underestimate the impact of anaemia on mortality in the community, where most paediatric deaths occur.", "Even in low/moderate malaria transmission settings, where older children suffer most malaria episodes, targeting effective malaria control at infants may produce important reductions in infant mortality caused by malaria."], "structured": false}
{"doc_id": 19828689, "title": "MicroRNA-192 in diabetic kidney glomeruli and its function in TGF-beta-induced collagen expression via inhibition of E-box repressors.", "abstract": ["Key features of diabetic nephropathy (DN) include the accumulation of extracellular matrix proteins such as collagen 1-alpha 1 and -2 (Col1a1 and -2).", "Transforming growth factor beta1 (TGF-beta), a key regulator of these extracellular matrix genes, is increased in mesangial cells (MC) in DN.", "By microarray profiling, we noted that TGF-beta increased Col1a2 mRNA in mouse MC (MMC) but also decreased mRNA levels of an E-box repressor, deltaEF1.", "TGF-beta treatment or short hairpin RNAs targeting deltaEF1 increased enhancer activity of upstream E-box elements in the Col1a2 gene.", "TGF-beta also decreased the expression of Smad-interacting protein 1 (SIP1), another E-box repressor similar to deltaEF1.", "Interestingly, we noted that SIP1 is a target of microRNA-192 (miR-192), a key miR highly expressed in the kidney.", "miR-192 levels also were increased by TGF-beta in MMC.", "TGF-beta treatment or transfection with miR-192 decreased endogenous SIP1 expression as well as reporter activity of a SIP1 3' UTR-containing luciferase construct in MMC.", "Conversely, a miR-192 inhibitor enhanced the luciferase activity, confirming SIP1 to be a miR-192 target.", "Furthermore, miR-192 synergized with deltaEF1 short hairpin RNAs to increase Col1a2 E-box-luc activity.", "Importantly, the in vivo relevance was noted by the observation that miR-192 levels were enhanced significantly in glomeruli isolated from streptozotocin-injected diabetic mice as well as diabetic db/db mice relative to corresponding nondiabetic controls, in parallel with increased TGF-beta and Col1a2 levels.", "These results uncover a role for miRs in the kidney and DN in controlling TGF-beta-induced Col1a2 expression by down-regulating E-box repressors."], "structured": false}
{"doc_id": 19843244, "title": "Activation of PAR(2) receptors sensitizes primary afferents and causes leukocyte rolling and adherence in the rat knee joint.", "abstract": ["BACKGROUND AND PURPOSE The PAR(2) receptors are involved in chronic arthritis by mechanisms that are as yet unclear.", "Here, we examined PAR(2) activation in the rat knee joint.   ", "EXPERIMENTAL APPROACH PAR(2) in rat knee joint dorsal root ganglia (DRG) cells at L3-L5, retrogradely labelled with Fluoro-gold (FG) were demonstrated immunohistochemically.", "Electrophysiological recordings from knee joint nerve fibres in urethane anaesthetized Wistar rats assessed the effects of stimulating joint PAR(2) with its activating peptide, 2-furoyl-LIGRLO-NH(2) (1-100 nmol\u00b7100 \u03bcL(-1) , via close intra-arterial injection).", "Fibre firing rate was recorded during joint rotations before and 15 min after administration of PAR(2) activating peptide or control peptide.", "Leukocyte kinetics in the synovial vasculature upon PAR(2) activation were followed by intravital microscopy for 60 min after perfusion of 2-furoyl-LIGRLO-NH(2) or control peptide.", "Roles for transient receptor potential vanilloid-1 (TRPV1) or neurokinin-1 (NK(1) ) receptors in the PAR(2) responses were assessed using the selective antagonists, SB366791 and RP67580 respectively.   ", "KEY RESULTS PAR(2) were expressed in 59 \u00b1 5% of FG-positive DRG cells; 100 nmol 2-furoyl-LIGRLO-NH(2) increased joint fibre firing rate during normal and noxious rotation, maximal at 3 min (normal; 110 \u00b1 43%, noxious; 90 \u00b1 31%).", "2-Furoyl-LIGRLO-NH(2) also significantly increased leukocyte rolling and adhesion over 60 min.", "All these effects were blocked by pre-treatment with SB366791 and RP67580 (P < 0.05 compared with 2-furoyl-LIGRLO-NH(2) alone).   \n", "CONCLUSIONS AND IMPLICATIONS PAR(2) receptors play an acute inflammatory role in the knee joint via TRPV1- and NK(1) -dependent mechanisms involving both PAR(2) -mediated neuronal sensitization and leukocyte trafficking."], "structured": true}
{"doc_id": 19851614, "title": "Polyphosphate kinase 1, a central node in the stress response network of Mycobacterium tuberculosis, connects the two-component systems MprAB and SenX3-RegX3 and the extracytoplasmic function sigma factor, sigma E.", "abstract": ["Polyphosphate (poly P) metabolism regulates the stress response in mycobacteria.", "Here we describe the regulatory architecture of a signal transduction system involving the two-component system (TCS) SenX3-RegX3, the extracytoplasmic function sigma factor sigma E (SigE) and the poly P-synthesizing enzyme polyphosphate kinase 1 (PPK1).", "The ppk1 promoter of Mycobacterium tuberculosis is activated under phosphate starvation.", "This is attenuated upon deletion of an imperfect palindrome likely representing a binding site for the response regulator RegX3, a component of the two-component system SenX3-RegX3 that responds to phosphate starvation.", "Binding of phosphorylated RegX3 to this site was confirmed by electrophoretic mobility shift assay.", "The activity of the ppk1 promoter was abrogated upon deletion of a putative SigE binding site.", "Pull-down of SigE from M. tuberculosis lysates of phosphate-starved cells with a biotinylated DNA harbouring the SigE binding site confirmed the likely binding of SigE to the ppk1 promoter.", "In vitro transcription corroborated the involvement of SigE in ppk1 transcription.", "Finally, the overexpression of RseA (anti-SigE) attenuated ppk1 expression under phosphate starvation, supporting the role of SigE in ppk1 transcription.", "The regulatory elements identified in ppk1 transcription in this study, combined with our earlier observation that PPK1 is itself capable of regulating sigE expression via the MprAB TCS, suggest the presence of multiple positive-feedback loops in this signalling circuit.", "In combination with the sequestering effect of RseA, we hypothesize that this architecture could be linked to bistability in the system that, in turn, could be a key element of persistence in M. tuberculosis."], "structured": false}
{"doc_id": 19854543, "title": "Natural history of asymptomatic unruptured cerebral aneurysms evaluated at CT angiography: growth and rupture incidence and correlation with epidemiologic risk factors.", "abstract": ["PURPOSE To characterize the relationship between aneurysm size and epidemiologic risk factors with growth and rupture by using computed tomographic (CT) angiography.   ", "MATERIALS AND METHODS In this HIPAA-compliant, institutional review board approved study, patients with known asymptomatic unruptured intracerebral aneurysms were followed up longitudinally with CT angiographic examinations.", "Growth was defined as an increase in one or more dimensions above the measurement error, and at least 5% volume by using the ABC/2 method.", "Associations of epidemiologic factors with aneurysm growth and rupture were analyzed by using logistic regression analysis.", "Intra- and interobserver agreement coefficients for dimension, volume, and growth were evaluated by using the Pearson correlation coefficient and difference of means with 95% confidence intervals, the agreement statistic, and the McNemar \u03c7(2).   \n", "RESULTS Patients (n = 165) with aneurysms (n = 258) had a mean follow-up time of 2.24 years from time of diagnosis.", "Forty-six of 258 (18%) aneurysms in 38 patients grew larger.", "Spontaneous rupture occurred in four of 228 (1.8%) intradural aneurysms of average size (6.2 mm).", "Risk of aneurysm rupture per patient-year was 2.4% (95% CI: 0.5%, 7.12%) with growth and 0.2% (95% CI: 0.006%, 1.22%) without growth (P = .034).", "There was a 12-fold higher risk of rupture for growing aneurysms (P < .002), with high intra- and interobserver correlation coefficients for size, volume, and growth.", "Tobacco smoking (3.806, one degree of freedom; P < .015,) and initial size (5.895, two degrees of freedom; P < .051) were independent covariates, predicting 78.4% of growing aneurysms.   \n", "CONCLUSION These results support imaging follow-up of all patients with aneurysms, including those whose aneurysms are smaller than the current 7-mm treatment threshold.", "Aneurysm growth, size, and smoking were associated with increased rupture risk."], "structured": true}
{"doc_id": 19854744, "title": "A search for the presence of the enteroviral capsid protein VP1 in pancreases of patients with Type 1 (insulin-dependent) diabetes and pancreases and hearts of infants who died of coxsackieviral myocarditis", "abstract": ["Using an antiserum raised to a recombinant coxsackie virus B3 capsid protein, VP1, an immunocytochemical technique was developed which was capable of detecting the presence of all coxsackie B viruses in formalin fixed paraffin embedded infected tissue culture cells.", "This technique was tested on autopsy heart and pancreas from 21 patients who were thought to have died of acute coxsackievirus B myocarditis.", "Cardiac myocytes were positive for the VP1 protein in 12 of 20 cases where the heart was available for study.", "Insulitis was present in the pancreas in seven of these cases and in all seven islet endocrine cells containing VP1 were found.", "VP1 was only rarely found in exocrine pancreas.", "In heart and pancreas, cells shown to contain VP1 usually showed signs of necrosis.", "Autopsy pancreases from 88 patients who had died at clinical presentation of Type 1 (insulin-dependent) diabetes mellitus showed no evidence of the presence of VP1.", "The continuing destruction of insulin-secreting B cells seen at the time of death in the diabetic pancreas is unlikely to be due to a direct cytopathic effect of a coxsackie B virus.", "However, this study does not exclude the possibility that a persistent infection of B cells by a defective enterovirus may result in their destruction by an autoimmune mechanism."], "structured": false}
{"doc_id": 19855358, "title": "Direct reprogramming of mouse fibroblasts to cardiomyocyte-like cells using Yamanaka factors on engineered poly(ethylene glycol) (PEG) hydrogels.", "abstract": ["Direct reprogramming strategies enable rapid conversion of somatic cells to cardiomyocytes or cardiomyocyte-like cells without going through the pluripotent state.", "A recently described protocol couples Yamanaka factor induction with pluripotency inhibition followed by BMP4 treatment to achieve rapid reprogramming of mouse fibroblasts to beating cardiomyocyte-like cells.", "The original study was performed using Matrigel-coated tissue culture polystyrene (TCPS), a stiff material that also non-specifically adsorbs serum proteins.", "Protein adsorption-resistant poly(ethylene glycol) (PEG) materials can be covalently modified to present precise concentrations of adhesion proteins or peptides without the unintended effects of non-specifically adsorbed proteins.", "Here, we describe an improved protocol that incorporates custom-engineered materials.", "We first reproduced the Efe et al. protocol on Matrigel-coated TCPS (the original material), reprogramming adult mouse tail-tip mouse fibroblasts (TTF) and mouse embryonic fibroblasts (MEF) to cardiomyocyte-like cells that demonstrated striated sarcomeric \u03b1-actinin staining, spontaneous calcium transients, and visible beating.", "We then designed poly(ethylene glycol) culture substrates to promote MEF adhesion via laminin and RGD-binding integrins.", "PEG hydrogels improved proliferation and reprogramming efficiency (evidenced by beating patch number and area, gene expression, and flow cytometry), yielding almost twice the number of sarcomeric \u03b1-actinin positive cardiomyocyte-like cells as the originally described substrate.", "These results illustrate that cellular reprogramming may be enhanced using custom-engineered materials."], "structured": false}
{"doc_id": 19878070, "title": "Effects of risedronate treatment on vertebral and nonvertebral fractures in women with postmenopausal osteoporosis: a randomized controlled trial. Vertebral Efficacy With Risedronate Therapy (VERT) Study Group.", "abstract": ["CONTEXT Risedronate, a potent bisphosphonate, has been shown to be effective in the treatment of Paget disease of bone and other metabolic bone diseases but, to our knowledge, it has not been evaluated in the treatment of established postmenopausal osteoporosis.   \n", "OBJECTIVE To test the efficacy and safety of daily treatment with risedronate to reduce the risk of vertebral and other fractures in postmenopausal women with established osteoporosis.   \n", "DESIGN, SETTING, AND PARTICIPANTS Randomized, double-blind, placebo-controlled trial of 2458 ambulatory postmenopausal women younger than 85 years with at least 1 vertebral fracture at baseline who were enrolled at 1 of 110 centers in North America conducted between December 1993 and January 1998.   \n", "INTERVENTIONS Subjects were randomly assigned to receive oral treatment for 3 years with risedronate (2.5 or 5 mg/d) or placebo.", "All subjects received calcium, 1000 mg/d.", "Vitamin D (cholecalciferol, up to 500 IU/d) was provided if baseline levels of 25-hydroxyvitamin D were low.   \n", "MAIN OUTCOME MEASURES Incidence of new vertebral fractures as detected by quantitative and semiquantitative assessments of radiographs; incidence of radiographically confirmed nonvertebral fractures and change from baseline in bone mineral density as determined by dual x-ray absorptiometry.   \n", "RESULTS The 2.5 mg/d of risedronate arm was discontinued after 1 year; in the placebo and 5 mg/d of risedronate arms, 450 and 489 subjects, respectively, completed all 3 years of the trial.", "Treatment with 5 mg/d of risedronate, compared with placebo, decreased the cumulative incidence of new vertebral fractures by 41 % (95% confidence interval [CI], 18%-58%) over 3 years (11.3 % vs 16.3%; P= .003).", "A fracture reduction of 65% (95% CI, 38%-81 %) was observed after the first year (2.4% vs 6.4%; P<.001).", "The cumulative incidence of nonvertebral fractures over 3 years was reduced by 39% (95% CI, 6%-61 %) (5.2 % vs 8.4%; P = .02).", "Bone mineral density increased significantly compared with placebo at the lumbar spine (5.4% vs 1.1 %), femoral neck (1.6% vs -1.2%), femoral trochanter (3.3% vs -0.7%), and midshaft of the radius (0.2% vs -1.4%).", "Bone formed during risedronate treatment was histologically normal.", "The overall safety profile of risedronate, including gastrointestinal safety, was similar to that of placebo.   \n", "CONCLUSIONS These data suggest that risedronate therapy is effective and well tolerated in the treatment of women with established postmenopausal osteoporosis."], "structured": true}
{"doc_id": 19882228, "title": "Hypoxia \u2014 a key regulatory factor in tumour growth", "abstract": ["Cells undergo a variety of biological responses when placed in hypoxic conditions, including activation of signalling pathways that regulate proliferation, angiogenesis and death.", "Cancer cells have adapted these pathways, allowing tumours to survive and even grow under hypoxic conditions, and tumour hypoxia is associated with poor prognosis and resistance to radiation therapy.", "Many elements of the hypoxia-response pathway are therefore good candidates for therapeutic targeting."], "structured": false}
{"doc_id": 19912367, "title": "Loss of fibronectin from the aged stem cell niche affects the regenerative capacity of skeletal muscle in mice", "abstract": ["Age-related changes in the niche have long been postulated to impair the function of somatic stem cells.", "Here we demonstrate that the aged stem cell niche in skeletal muscle contains substantially reduced levels of fibronectin (FN), leading to detrimental consequences for the function and maintenance of muscle stem cells (MuSCs).", "Deletion of the gene encoding FN from young regenerating muscles replicates the aging phenotype and leads to a loss of MuSC numbers.", "By using an extracellular matrix (ECM) library screen and pathway profiling, we characterize FN as a preferred adhesion substrate for MuSCs and demonstrate that integrin-mediated signaling through focal adhesion kinase and the p38 mitogen-activated protein kinase pathway is strongly de-regulated in MuSCs from aged mice because of insufficient attachment to the niche.", "Reconstitution of FN levels in the aged niche remobilizes stem cells and restores youth-like muscle regeneration.", "Taken together, we identify the loss of stem cell adhesion to FN in the niche ECM as a previously unknown aging mechanism."], "structured": false}
{"doc_id": 19922508, "title": "Monitoring starvation-induced reactive oxygen species formation.", "abstract": ["Reactive oxygen species (ROS) are potentially harmful to cells because of their ability to oxidize cell constituents such as DNA, proteins, and lipids.", "However, at low levels, and under tight control, this feature makes them excellent modifiers in a variety of signal transduction pathways, including autophagy.", "Autophagy was traditionally associated with oxidative stress, acting in the degradation of oxidized proteins and organelles.", "Recently, a signaling role was suggested for ROS in the regulation of autophagy, leading, under different circumstances, either to survival or to death.", "To study the effects of ROS on this pathway, one must determine the localization, intensity, kinetics, and essentiality of the oxidative signal in autophagy.", "Moreover, once characterized, detection and manipulation of ROS formation could be used to monitor and control autophagic activity.", "In this chapter we discuss methods to examine ROS in the context of autophagy."], "structured": false}
{"doc_id": 19945096, "title": "Why do patients with multimorbidity in England report worse experiences in primary care? Evidence from the General Practice Patient Survey", "abstract": ["OBJECTIVES To describe and explain the primary care experiences of people with multiple long-term conditions in England.   \n", "DESIGN AND METHODS Using questionnaire data from 906,578 responders to the English 2012 General Practice Patient Survey, we describe the primary care experiences of patients with long-term conditions, including 583,143 patients who reported one or more long-term conditions.", "We employed mixed effect logistic regressions to analyse data on six items covering three care domains (access, continuity and communication) and a single item on overall primary care experience.", "We controlled for sociodemographic characteristics, and for general practice using a random effect, and further, controlled for, and explored the importance of, health-related quality of life measured using the EuroQoL (EQ-5D) scale.   \n", "RESULTS Most patients with long-term conditions report a positive experience of care at their general practice (after adjusting for sociodemographic characteristics and general practice, range 74.0-93.1% reporting positive experience of care across seven questions) with only modest variation by type of condition.", "For all three domains of patient experience, an increasing number of comorbid conditions is associated with a reducing percentage of patients reporting a positive experience of care.", "For example, compared with respondents with no long-term condition, the OR for reporting a positive experience is 0.83 (95% CI 0.80 to 0.87) for respondents with four or more long-term conditions.", "However, this relationship is no longer observed after adjusting for health-related quality of life (OR (95% CI) single condition=1.23 (1.21 to 1.26); four or more conditions=1.31 (1.25 to 1.37)), with pain making the greatest difference among five quality of life variables included in the analysis.   \n", "CONCLUSIONS Patients with multiple long-term conditions more frequently report worse experiences in primary care.", "However, patient-centred measures of health-related quality of life, especially pain, are more important than the number of conditions in explaining why patients with multiple long-term conditions report worse experiences of care."], "structured": true}
{"doc_id": 19950357, "title": "The rice FISH BONE gene encodes a tryptophan aminotransferase, which affects pleiotropic auxin-related processes.", "abstract": ["Auxin is a fundamental plant hormone and its localization within organs plays pivotal roles in plant growth and development.", "Analysis of many Arabidopsis mutants that were defective in auxin biosynthesis revealed that the indole-3-pyruvic acid (IPA) pathway, catalyzed by the TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS (TAA) and YUCCA (YUC) families, is the major biosynthetic pathway of indole-3-acetic acid (IAA).", "In contrast, little information is known about the molecular mechanisms of auxin biosynthesis in rice.", "In this study, we identified a auxin-related rice mutant, fish bone (fib).", "FIB encodes an orthologue of TAA genes and loss of FIB function resulted in pleiotropic abnormal phenotypes, such as small leaves with large lamina joint angles, abnormal vascular development, small panicles, abnormal organ identity and defects in root development, together with a reduction in internal IAA levels.", "Moreover, we found that auxin sensitivity and polar transport activity were altered in the fib mutant.", "From these results, we suggest that FIB plays a pivotal role in IAA biosynthesis in rice and that auxin biosynthesis, transport and sensitivity are closely interrelated."], "structured": false}
{"doc_id": 19951373, "title": "Successful mouse cloning of an outbred strain by trichostatin A treatment after somatic nuclear transfer.", "abstract": ["Although the somatic cloning technique has been used for numerous applications and basic research of reprogramming in various species, extremely low success rates have plagued this technique for a decade.", "Further in mice, the \"clonable\" strains have been limited to mainly hybrid F1 strains such as B6D2F1.", "Recently, we established a new efficient cloning technique using trichostatin A (TSA) which leads to a 2-5 fold increase in success rates for mouse cloning of B6D2F1 cumulus cells.", "To further test the validity of this TSA cloning technique, we tried to clone the adult ICR mouse, an outbred strain, which has never been directly cloned before.", "Only when TSA was used did we obtain both male and female cloned mice from cumulus and fibroblast cells of adult ICR mice with 4-5% success rates, which is comparable to 5-7% of B6D2F1.", "Thus, the TSA treatment is the first cloning technique to allow us to successfully clone outbred mice, demonstrating that this technique not only improves the success rates of cloning from hybrid strains, but also enables mouse cloning from normally \"unclonable\" strains."], "structured": false}
{"doc_id": 19957813, "title": "A Genome-wide CRISPR Death Screen Identifies Genes Essential for Oxidative Phosphorylation.", "abstract": ["Oxidative phosphorylation (OXPHOS) is the major pathway for ATP production in humans.", "Deficiencies in OXPHOS can arise from mutations in either mitochondrial or nuclear genomes and comprise the largest collection of inborn errors of metabolism.", "At present we lack a complete catalog of human genes and pathways essential for OXPHOS.", "Here we introduce a genome-wide CRISPR \"death screen\" that actively selects dying cells to reveal human genes required for OXPHOS, inspired by the classic observation that human cells deficient in OXPHOS survive in glucose but die in galactose.", "We report 191 high-confidence hits essential for OXPHOS, including 72 underlying known OXPHOS diseases.", "Our screen reveals a functional module consisting of NGRN, WBSCR16, RPUSD3, RPUSD4, TRUB2, and FASTKD2 that regulates the mitochondrial 16S rRNA and intra-mitochondrial translation.", "Our work yields a rich catalog of genes required for OXPHOS and, more generally, demonstrates the power of death screening for functional genomic analysis."], "structured": false}
{"doc_id": 19958277, "title": "RecQ helicases: caretakers of the genome", "abstract": ["RecQ helicases are highly conserved from bacteria to man.", "Germline mutations in three of the five known family members in humans give rise to debilitating disorders that are characterized by, amongst other things, a predisposition to the development of cancer.", "One of these disorders \u2014 Bloom's syndrome \u2014 is uniquely associated with a predisposition to cancers of all types.", "So how do RecQ helicases protect against cancer?", "They seem to maintain genomic stability by functioning at the interface between DNA replication and DNA repair."], "structured": false}
{"doc_id": 19961177, "title": "Mortality from causes amenable and non-amenable to medical care: the experience of eastern Europe.", "abstract": ["OBJECTIVE To investigate comparative national trends in mortality from conditions amenable to timely, appropriate medical care and from those considered not to be amenable to such care.   \n", "DESIGN Analysis of trends in direct age standardised mortality from the 1950s to 1987.   \n", "SETTING Four eastern European nations (Hungary, Czechoslovakia, Poland, the German Democratic Republic) and two western European (the Federal Republic of Germany and England and Wales) and two North American nations (United States and Canada).   ", "SUBJECTS The total populations of the relevant countries during the period examined.   \n", "MAIN OUTCOME MEASURES Proportional changes over time in age standardised mortality.", "Mortality from amenable and non-amenable causes was restricted to the age group 0-64.   \n", "RESULTS A divergence in the trends for all cause mortality between eastern Europe and the western nations occurred in about 1970, when the rates in western countries steadily declined but those in eastern Europe remained fairly static.", "In the age group 0-64 mortality from causes considered amenable to medical care fell less quickly in eastern Europe than in the West, particularly after 1970.", "In the same age group, mortality from non-amenable causes rose in eastern European countries from the late 1960s compared with substantial declines in such mortality in the West.   \n", "CONCLUSIONS Non-amenable causes of death seem to be the principal, but not exclusive, reason for lack of improvement in trends in all cause mortality in eastern Europe from 1970.", "The agenda for action in eastern Europe should give priority to a healthier lifestyle and improvement of the environment though not neglect enhancements in the quality and efficiency of direct health services."], "structured": true}
{"doc_id": 19966976, "title": "Dynamic regulation of heterochromatin function via phosphorylation of HP1-family proteins.", "abstract": ["Heterochromatin is characterized by methylation of histone H3 at lysine 9, which is recognized by well-conserved HP1-family proteins.", "Heterochromatin participates in various chromosome functions, which include transcriptional gene silencing and sister-chromatid cohesion.", "These heterochromatic functions are carried out by various effector proteins that associate with HP1-family proteins; however, the regulation of this association with the effectors is not well understood.", "Recently, we showed that phosphorylation of the fission-yeast HP1 homolog Swi6 regulates the association of the transcriptional regulators differentially and changes the transcriptional activity of heterochromatin, without affecting sister-chromatid cohesion.", "This study, together with another study performed using other systems, indicates that phosphorylation of HP1/Swi6 provides a dynamic pathway for the differential regulation of heterochromatin in response to inter- and intracellular signals."], "structured": false}
{"doc_id": 19970015, "title": "Modeling neurogenesis impairment in Down syndrome with induced pluripotent stem cells from Trisomy 21 amniotic fluid cells.", "abstract": ["Down syndrome (DS), or Trisomy 21 (T21) syndrome, one of the most common chromosomal abnormalities, is caused by an extra duplication of chromosome 21.", "In studies of neuron development, experimental models based on human cells are considered to be the most desired and accurate for basic research.", "The generation of diseased induced pluripotetn stem (iPS) cell is a critical step in understanding the developmental stages of complex neuronal diseases.", "Here, we generated human DS iPS cell lines from second trimester amniotic fluid (AF) cells with T21 by co-expressing Yamanaka factors through lentiviral delivery and subsequently differentiated them into neuronal progenitor cells (NPCs) for further analyses.", "T21 AF-iPS cells were characterized for the expression of pluripotent markers and for their ability to differentiate into all three germ layers by forming embryoid bodies in vitro and teratomas in vivo.", "The T21 AF-iPS cells maintained their unique pattern of chromosomal karyotypes: three pairs of chromosome 21.", "The level of amyloid precursor protein was significantly increased in NPCs derived from T21 AF-iPS cells compared with NPCs from normal AF-iPS cells.", "The expression levels of miR-155 and miR-802 in T21 AF-iPS-NPCs were highly elevated in the presence of low expression of MeCP2.", "We observed that T21 iPS-NPCs generated fewer neurons compared with controls.", "T21 iPS-NPCs exhibit developmental defects during neurogenesis.", "Our findings suggest that T21 AF-iPS cells serve as a good source to further elucidate the impairment neurogenesis of DS and the onset of Alzheimer's disease."], "structured": false}
{"doc_id": 19974105, "title": "Control over DNA replication in time and space.", "abstract": ["DNA replication is precisely regulated in time and space, thereby safeguarding genomic integrity.", "In eukaryotes, replication initiates from multiple sites along the genome, termed origins of replication, and propagates bidirectionally.", "Dynamic origin bound complexes dictate where and when replication should initiate.", "During late mitosis and G1 phase, putative origins are recognized and become \"licensed\" through the assembly of pre-replicative complexes (pre-RCs) that include the MCM2-7 helicases.", "Subsequently, at the G1/S phase transition, a fraction of pre-RCs are activated giving rise to the establishment of replication forks.", "Origin location is influenced by chromatin and nuclear organization and origin selection exhibits stochastic features.", "The regulatory mechanisms that govern these cell cycle events rely on the periodic fluctuation of cyclin dependent kinase (CDK) activity through the cell cycle."], "structured": false}
{"doc_id": 19979816, "title": "MYC/MIZ1-dependent gene repression inversely coordinates the circadian clock with cell cycle and proliferation", "abstract": ["The circadian clock and the cell cycle are major cellular systems that organize global physiology in temporal fashion.", "It seems conceivable that the potentially conflicting programs are coordinated.", "We show here that overexpression of MYC in U2OS cells attenuates the clock and conversely promotes cell proliferation while downregulation of MYC strengthens the clock and reduces proliferation.", "Inhibition of the circadian clock is crucially dependent on the formation of repressive complexes of MYC with MIZ1 and subsequent downregulation of the core clock genes BMAL1 (ARNTL), CLOCK and NPAS2.", "We show furthermore that BMAL1 expression levels correlate inversely with MYC levels in 102 human lymphomas.", "Our data suggest that MYC acts as a master coordinator that inversely modulates the impact of cell cycle and circadian clock on gene expression."], "structured": false}
{"doc_id": 19994006, "title": "Relevance of asystole during head-up tilt testing.", "abstract": ["The prognosis of patients manifesting prolonged asystole during head-up tilt testing is unclear.", "In 209 consecutive patients with a history of syncope and positive head-up tilt tests, 19 had asystole lasting > 5 seconds (mean duration 15 +/-", "10) (group 1a).", "When compared with patients without asystole (group 1b), group 1a patients were younger (32 +/-", "12 vs 47 +/-", "21 years, p < 0.005), but clinical manifestations were not any more dramatic (the number of episodes of syncope [7 +/- 5 vs 8 +/-", "6 episodes, p = NS] and injury during syncope [2 vs 13 patients, p = NS] were similar).", "During follow-up (mean 2 +/-", "1 year), with the patient taking pharmacologic therapy such as beta blockers, ephedrine, theophylline, or disopyramide, the recurrence rate was 11% and 8% in groups 1a and 1b (p = NS).", "No patient in the asystole group underwent pacemaker implantation.", "Additionally, of 75 normal volunteers (group 2) with no history of syncope undergoing tilt tests to define its specificity, 3 had asystole (mean duration 10 seconds).", "During > 1 year of follow-up, despite no treatment, all 3 are symptom free.", "Thus, asystole during head-up tilt testing does not predict either a more malignant outcome or a poor response to pharmacologic therapy.", "Moreover, an asystolic response does not enhance the specificity of the head-up tilt test because it may be present in asymptomatic \"normal\" volunteers."], "structured": false}
{"doc_id": 20008796, "title": "Increasing informed uptake and non-uptake of screening: evidence from a systematic review.", "abstract": ["OBJECTIVE To report data relating to the informed uptake of screening tests.   ", "SEARCH STRATEGY Electronic databases, bibliographies and experts were used to identify relevant published and unpublished studies up until August 2000.   ", "INCLUSION CRITERIA RCTs, quasi-RCTs and controlled trials of interventions aimed at increasing the informed uptake of screening.", "All participants were eligible as defined by the entry criteria of individual programmes.", "Studies had to report actual uptake and meet three out of four criteria used to define informed uptake.   \n", "DATA EXTRACTION AND SYNTHESIS Relevant studies were identified, data extracted and their validity assessed by two reviewers independently.", "Outcome data included screening uptake, knowledge, informed decision-making and attitudes to screening.", "A random-effects model was used to calculate individual relative risks and 95% confidence intervals.   \n", "MAIN RESULTS Six controlled trials (five RCTs and one quasi-RCT), focusing on antenatal and prostate specific antigen screening, were included.", "All reported risks/benefits of screening and assessed knowledge.", "Two also assessed decision-making.", "Two reported risks/benefits to all randomized groups and evaluated different ways of presenting information.", "Neither found that interventions such as videos, information leaflets with decision trees, or touch screen computers conveyed any additional benefits over well-prepared leaflets.   \n", "CONCLUSIONS There is some evidence to suggest that changing the format of informed choice interventions in screening does not alter knowledge, satisfaction or decisions about screening.", "It is not clear whether informed choice in screening affects uptake.", "More well-designed RCTs are required and further research should also be directed towards the development of a valid instrument for measuring all components of informed choice in screening."], "structured": true}
{"doc_id": 20018321, "title": "Mitochondrial RNA Granules Are Centers for Posttranscriptional RNA Processing and Ribosome Biogenesis.", "abstract": ["Cytoplasmic RNA granules play a central role in mRNA metabolism, but the importance of mitochondrial RNA granules remains relatively unexplored.", "We characterized their proteome and found that they contain a large toolbox of proteins dedicated to RNA metabolism.", "Investigation of four uncharacterized putative RNA-binding proteins-two RNA helicases, DHX30 and DDX28, and two proteins of the Fas-activated serine-threonine kinase (FASTKD) family, FASTKD2 and FASTKD5-demonstrated that both helicases and FASTKD2 are required for mitochondrial ribosome biogenesis.", "RNA-sequencing (RNA-seq) analysis showed that DDX28 and FASTKD2 bound the 16S rRNA.", "FASTKD5 is required for maturing precursor mRNAs that are not flanked by tRNAs and that therefore cannot be processed by the canonical mRNA maturation pathway.", "Silencing FASTKD5 rendered mature COX I mRNA almost undetectable, which severely reduced the synthesis of COX I, resulting in a complex IV assembly defect.", "These data demonstrate that mitochondrial RNA granules are centers for posttranscriptional RNA processing and the biogenesis of mitochondrial ribosomes."], "structured": false}
{"doc_id": 20028729, "title": "Controlling nuclear receptors: the circular logic of cofactor cycles", "abstract": ["Nuclear receptors regulate many biologically important processes in development and homeostasis by their bimodal function as repressors and activators of gene transcription.", "A finely tuned modulation of the transcriptional activities of nuclear receptors is crucial for determining highly specific and diversified programmes of gene expression.", "Recent studies have provided insights into the molecular mechanisms that are required to switch between repression and activation functions, the combinatorial roles of the multiple cofactor complexes that are required for mediating transcriptional regulation, and the central question of how several different signalling pathways can be integrated at the nuclear level to achieve specific profiles of gene expression."], "structured": false}
{"doc_id": 20033112, "title": "Reprogramming fibroblasts into bipotential hepatic stem cells by defined factors.", "abstract": ["Recent studies have demonstrated direct reprogramming of fibroblasts into a range of somatic cell types, but to date stem or progenitor cells have only been reprogrammed for the blood and neuronal lineages.", "We previously reported generation of induced hepatocyte-like (iHep) cells by transduction of Gata4, Hnf1\u03b1, and Foxa3 in p19 Arf null mouse embryonic fibroblasts (MEFs).", "Here, we show that Hnf1\u03b2 and Foxa3, liver organogenesis transcription factors, are sufficient to reprogram MEFs into induced hepatic stem cells (iHepSCs).", "iHepSCs can be stably expanded in vitro and possess the potential of bidirectional differentiation into both hepatocytic and cholangiocytic lineages.", "In the injured liver of fumarylacetoacetate hydrolase (Fah)-deficient mice, repopulating iHepSCs become hepatocyte-like cells.", "They also engraft as cholangiocytes into bile ducts of mice with DDC-induced bile ductular injury.", "Lineage conversion into bipotential expandable iHepSCs provides a strategy to enable efficient derivation of both hepatocytes and cholangiocytes for use in disease modeling and tissue engineering."], "structured": false}
{"doc_id": 20045514, "title": "Spatial genome organization: contrasting views from chromosome conformation capture and fluorescence in situ hybridization.", "abstract": ["Although important for gene regulation, most studies of genome organization use either fluorescence in situ hybridization (FISH) or chromosome conformation capture (3C) methods.", "FISH directly visualizes the spatial relationship of sequences but is usually applied to a few loci at a time.", "The frequency at which sequences are ligated together by formaldehyde cross-linking can be measured genome-wide by 3C methods, with higher frequencies thought to reflect shorter distances.", "FISH and 3C should therefore give the same views of genome organization, but this has not been tested extensively.", "We investigated the murine HoxD locus with 3C carbon copy (5C) and FISH in different developmental and activity states and in the presence or absence of epigenetic regulators.", "We identified situations in which the two data sets are concordant but found other conditions under which chromatin topographies extrapolated from 5C or FISH data are not compatible.", "We suggest that products captured by 3C do not always reflect spatial proximity, with ligation occurring between sequences located hundreds of nanometers apart, influenced by nuclear environment and chromatin composition.", "We conclude that results obtained at high resolution with either 3C methods or FISH alone must be interpreted with caution and that views about genome organization should be validated by independent methods."], "structured": false}
{"doc_id": 20048431, "title": "Development and evaluation of a self-administered computerized 24-h dietary recall method for adolescents in Europe", "abstract": ["Objective:To describe the development of a European computerized 24-h dietary recall method for adolescents, and to investigate the feasibility of self-administration (self report) by comparison with administration by a dietician (interview).Methods:Two hundred and thirty-six adolescents (mean age 14.6 years (s.d.=1.7)) of eight European cities completed the 24-h recall (Young Adolescents Nutrition Assessment on Computer (YANA-C)) twice (once by self-report and once by interview).Results:A small but significant underestimate in energy (61 (s.e.=31) kcal) and fat (4.2 (s.e.=1.7) g) intake was found in the self-reports in comparison with the interviews; no significant differences were found for the intake of carbohydrates, proteins, fibre, calcium, iron and ascorbic acid.", "Spearman's correlations were highly significant for all nutrients and energy ranging between 0.86 and 0.91.", "Agreement in categorizing the respondents as consumers and non-consumers for the 29 food groups was high (kappa statistics \u2a7e0.73).", "Percentage omissions were on average 3.7%; percentage intrusions: 2.0%.", "Spearman's correlations between both modes were high for all food groups, for the total sample (\u2a7e0.76) as well as for the consumers only (\u2a7e0.72).", "Analysing the consumer only, on an average 54% of the consumed amounts were exactly the same; nevertheless, only for one group \u2018rice and pasta\u2019 a significant difference in consumption was found.", "Conclusion:Adaptation, translation and standardization of YANA-C make it possible to assess the dietary intake of adolescents in a broad international context.", "In general, good agreement between the administration modes was found, the latter offering significant potential for large-scale surveys where the amount of resources to gather data is limited."], "structured": false}
{"doc_id": 20052986, "title": "JTK_CYCLE: an efficient nonparametric algorithm for detecting rhythmic components in genome-scale data sets.", "abstract": ["Circadian rhythms are oscillations of physiology, behavior, and metabolism that have period lengths near 24 hours.", "In several model organisms and humans, circadian clock genes have been characterized and found to be transcription factors.", "Because of this, researchers have used microarrays to characterize global regulation of gene expression and algorithmic approaches to detect cycling.", "This article presents a new algorithm, JTK_CYCLE, designed to efficiently identify and characterize cycling variables in large data sets.", "Compared with COSOPT and the Fisher's G test, two commonly used methods for detecting cycling transcripts, JTK_CYCLE distinguishes between rhythmic and nonrhythmic transcripts more reliably and efficiently.", "JTK_CYCLE's increased resistance to outliers results in considerably greater sensitivity and specificity.", "Moreover, JTK_CYCLE accurately measures the period, phase, and amplitude of cycling transcripts, facilitating downstream analyses.", "Finally, JTK_CYCLE is several orders of magnitude faster than COSOPT, making it ideal for large-scale data sets.", "JTK_CYCLE was used to analyze legacy data sets including NIH3T3 cells, which have comparatively low amplitude oscillations.", "JTK_CYCLE's improved power led to the identification of a novel cluster of RNA-interacting genes whose abundance is under clear circadian regulation.", "These data suggest that JTK_CYCLE is an ideal tool for identifying and characterizing oscillations in genome-scale data sets."], "structured": false}
{"doc_id": 20054396, "title": "Polo-like kinase 1 regulates Nlp, a centrosome protein involved in microtubule nucleation.", "abstract": ["In animal cells, most microtubules are nucleated at centrosomes.", "At the onset of mitosis, centrosomes undergo a structural reorganization, termed maturation, which leads to increased microtubule nucleation activity.", "Centrosome maturation is regulated by several kinases, including Polo-like kinase 1 (Plk1).", "Here, we identify a centrosomal Plk1 substrate, termed Nlp (ninein-like protein), whose properties suggest an important role in microtubule organization.", "Nlp interacts with two components of the gamma-tubulin ring complex and stimulates microtubule nucleation.", "Plk1 phosphorylates Nlp and disrupts both its centrosome association and its gamma-tubulin interaction.", "Overexpression of an Nlp mutant lacking Plk1 phosphorylation sites severely disturbs mitotic spindle formation.", "We propose that Nlp plays an important role in microtubule organization during interphase, and that the activation of Plk1 at the onset of mitosis triggers the displacement of Nlp from the centrosome, allowing the establishment of a mitotic scaffold with enhanced microtubule nucleation activity."], "structured": false}
{"doc_id": 20083834, "title": "Consumption of isoflavone-rich soy protein does not alter homocysteine or markers of inflammation in postmenopausal women", "abstract": ["Background/Objective:To investigate the effect of soy protein containing isoflavones on homocysteine (Hcy), C-reactive protein (CRP), soluble E-selectin (sE-selectin), soluble vascular adhesion molecule-1 (sVCAM-1) and soluble intercellular adhesion molecule-1 (sICAM-1).Subject/Methods:In a randomized crossover design, 34 postmenopausal women consumed soy protein isolate (26\u00b15 g protein containing 44\u00b18 mg isoflavones per day) or milk protein isolate (26\u00b15 g protein per day) for 6 weeks each.", "Fasting blood samples were collected at the end of each diet period and end points analyzed by enzyme-linked immunosorbent assay.", "Results:Concentrations of Hcy, CRP, sE-selectin, sVCAM-1 and sICAM-1 were not different between soy and milk diet treatments.", "Results did not differ by equol production status or by baseline lipid concentration.", "Adjustment for intake of folate and methionine did not alter the Hcy results.", "Conclusions:These data suggest that decreasing vascular inflammation and Hcy concentration are not likely mechanisms by which soy consumption reduces coronary heart disease risk."], "structured": false}
{"doc_id": 20101846, "title": "Homogeneously dispersed multimetal oxygen-evolving catalysts", "abstract": ["Earth-abundant first-row (3d) transition metal\u2013based catalysts have been developed for the oxygen-evolution reaction (OER); however, they operate at overpotentials substantially above thermodynamic requirements.", "Density functional theory suggested that non-3d high-valency metals such as tungsten can modulate 3d metal oxides, providing near-optimal adsorption energies for OER intermediates.", "We developed a room-temperature synthesis to produce gelled oxyhydroxides materials with an atomically homogeneous metal distribution.", "These gelled FeCoW oxyhydroxides exhibit the lowest overpotential (191 millivolts) reported at 10 milliamperes per square centimeter in alkaline electrolyte.", "The catalyst shows no evidence of degradation after more than 500 hours of operation.", "X-ray absorption and computational studies reveal a synergistic interplay between tungsten, iron, and cobalt in producing a favorable local coordination environment and electronic structure that enhance the energetics for OER."], "structured": false}
{"doc_id": 20109325, "title": "Global strategy for the diagnosis, management, and prevention of chronic obstructive pulmonary disease: GOLD executive summary.", "abstract": ["Chronic obstructive pulmonary disease (COPD) is a global health problem, and since 2001, the Global Initiative for Chronic Obstructive Lung Disease (GOLD) has published its strategy document for the diagnosis and management of COPD.", "This executive summary presents the main contents of the second 5-year revision of the GOLD document that has implemented some of the vast knowledge about COPD accumulated over the last years.", "Today, GOLD recommends that spirometry is required for the clinical diagnosis of COPD to avoid misdiagnosis and to ensure proper evaluation of severity of airflow limitation.", "The document highlights that the assessment of the patient with COPD should always include assessment of (1) symptoms, (2) severity of airflow limitation, (3) history of exacerbations, and (4) comorbidities.", "The first three points can be used to evaluate level of symptoms and risk of future exacerbations, and this is done in a way that splits patients with COPD into four categories-A, B, C, and D. Nonpharmacologic and pharmacologic management of COPD match this assessment in an evidence-based attempt to relieve symptoms and reduce risk of exacerbations.", "Identification and treatment of comorbidities must have high priority, and a separate section in the document addresses management of comorbidities as well as COPD in the presence of comorbidities.", "The revised document also contains a new section on exacerbations of COPD.", "The GOLD initiative will continue to bring COPD to the attention of all relevant shareholders and will hopefully inspire future national and local guidelines on the management of COPD."], "structured": false}
{"doc_id": 20127522, "title": "Circulating tumor cells: a useful predictor of treatment efficacy in metastatic breast cancer.", "abstract": ["PURPOSE Five or more circulating tumor cells (CTCs) per 7.5 mL of blood predicts for poorer progression-free survival (PFS) in patients with metastatic breast cancer (MBC).", "We conducted a prospective study to demonstrate that CTC results correlate strongly with radiographic disease progression at the time of and in advance of imaging.   \n", "PATIENTS AND METHODS Serial CTC levels were obtained in patients starting a new treatment regimen for progressive, radiographically measurable MBC.", "Peripheral blood was collected for CTC enumeration at baseline and at 3- to 4-week intervals.", "Clinical outcomes were based on radiographic studies performed in 9- to 12-week intervals.   \n", "RESULTS Sixty-eight patients were evaluable for the CTC-imaging correlations, and 74 patients were evaluable for the PFS analysis.", "Median follow-up was 13.3 months.", "A statistically significant correlation was demonstrated between CTC levels and radiographic disease progression in patients receiving chemotherapy or endocrine therapy.", "This correlation applied to CTC results obtained at the time of imaging (odds ratio [OR], 6.3), 3 to 5 weeks before imaging (OR, 3.1), and 7 to 9 weeks before imaging (OR, 4.9).", "Results from analyses stratified by type of therapy remained statistically significant.", "Shorter PFS was observed for patients with five or more CTCs at 3 to 5 weeks and at 7 to 9 weeks after the start of treatment.   \n", "CONCLUSION We provide, to our knowledge, the first evidence of a strong correlation between CTC results and radiographic disease progression in patients receiving chemotherapy or endocrine therapy for MBC.", "These findings support the role of CTC enumeration as an adjunct to standard methods of monitoring disease status in MBC."], "structured": true}
{"doc_id": 20128547, "title": "Recovery of supraspinal control of stepping via indirect propriospinal relay connections after spinal cord injury", "abstract": ["Spinal cord injuries (SCIs) in humans and experimental animals are often associated with varying degrees of spontaneous functional recovery during the first months after injury.", "Such recovery is widely attributed to axons spared from injury that descend from the brain and bypass incomplete lesions, but its mechanisms are uncertain.", "To investigate the neural basis of spontaneous recovery, we used kinematic, physiological and anatomical analyses to evaluate mice with various combinations of spatially and temporally separated lateral hemisections with or without the excitotoxic ablation of intrinsic spinal cord neurons.", "We show that propriospinal relay connections that bypass one or more injury sites are able to mediate spontaneous functional recovery and supraspinal control of stepping, even when there has been essentially total and irreversible interruption of long descending supraspinal pathways in mice.", "Our findings show that pronounced functional recovery can occur after severe SCI without the maintenance or regeneration of direct projections from the brain past the lesion and can be mediated by the reorganization of descending and propriospinal connections.", "Targeting interventions toward augmenting the remodeling of relay connections may provide new therapeutic strategies to bypass lesions and restore function after SCI and in other conditions such as stroke and multiple sclerosis."], "structured": false}
{"doc_id": 20130904, "title": "\"Grazing\": a high-risk behavior.", "abstract": ["BACKGROUND Gastric bypass patients with a range of disturbed eating patterns before surgery may be at risk of returning to old patterns postoperatively.", "Recent research has shown that binge eating is common among the obese before surgery as well as in the postoperative maintenance phase and appears to be linked to poorer outcome.", "Although \"grazing\" behavior has not been specifically studied, it is also a high-risk pattern.", "This paper is a descriptive investigation summarizing postoperative eating patterns in a group of patients.   \n", "METHODS Patients completed self-report questionnaires before surgery and were seen for a preoperative mental health evaluation with particular focus on assessing eating patterns.", "Patients with high-risk eating patterns, both binge eating and \"grazing\", were identified, invited to attend a post-surgery therapy group, and were given additional follow-up questionnaires regarding postoperative eating patterns.   \n", "RESULTS Consistent with recent studies, many high-risk patients reported recurrent loss of control over eating and, in some cases, subsequent weight gain.", "Although no longer able to eat large amounts, \"grazing\" became a more common pattern, appearing >or=6 months following surgery.   \n", "CONCLUSION Different forms of overeating need to be assessed in this population, focusing on the subjective loss of control rather than on the quantity consumed.", "Although many patients do not meet strict criteria for binge eating disorder before surgery, these \"grazers\" are also high-risk.", "Former binge eaters often turn into \"grazers\" following surgery.", "Interventions are needed for at-risk patients."], "structured": true}
{"doc_id": 20132778, "title": "Molecular strategies in biological evolution of antimicrobial peptides.", "abstract": ["Gene-encoded antimicrobial peptides that protect the skin of hylid and ranin frogs against noxious microorganisms are processed from a unique family of precursor polypeptides with a unique pattern of conserved and variable regions opposite to that of conventional secreted peptides.", "Precursors belonging to this family, designated the preprodermaseptin, have a common N-terminal preproregion that is remarkably well conserved both within and between species, but a hypervariable C-terminal domain corresponding to antimicrobial peptides with very different lengths, sequences, charges and antimicrobial spectra.", "Each frog species has its own distinct panoply of 10-20 antimicrobial peptides so that the 5000 species of ranids and hylids may produce approximately 100,000 different peptide antibiotics.", "The strategy that these frogs have evolved to generate this enormous array of peptides includes repeated duplications of a 150 million years old ancestral gene, focal hypermutation of the antimicrobial peptide domain maybe involving a mutagenic DNA polymerase similar to Escherichia coli Pol V, and subsequent actions of positive (diversifying) selection.", "The hyperdivergence of skin antimicrobial peptides can be viewed as the successful evolution of a multi-drug defense system that provides frogs with maximum protection against rapidly changing microbial biota and minimizes the chance of microorganisms developing resistance to individual peptides.", "The impressive variations in the expression of frog skin antimicrobial peptides may be exploited for discovering new molecules and structural motifs targeting specific microorganisms for which the therapeutic armamentarium is scarce."], "structured": false}
{"doc_id": 20148808, "title": "Microbiome-driven allergic lung inflammation is ameliorated by short-chain fatty acids", "abstract": ["The mammalian gastrointestinal tract harbors a microbial community with metabolic activity critical for host health, including metabolites that can modulate effector functions of immune cells.", "Mice treated with vancomycin have an altered microbiome and metabolite profile, exhibit exacerbated T helper type 2 cell (Th2) responses, and are more susceptible to allergic lung inflammation.", "Here we show that dietary supplementation with short-chain fatty acids (SCFAs) ameliorates this enhanced asthma susceptibility by modulating the activity of T cells and dendritic cells (DCs).", "Dysbiotic mice treated with SCFAs have fewer interleukin-4 (IL4)-producing CD4+ T cells and decreased levels of circulating immunoglobulin E (IgE).", "In addition, DCs exposed to SCFAs activate T cells less robustly, are less motile in response to CCL19 in vitro, and exhibit a dampened ability to transport inhaled allergens to lung draining nodes.", "Our data thus demonstrate that gut dysbiosis can exacerbate allergic lung inflammation through both T cell- and DC-dependent mechanisms that are inhibited by SCFAs."], "structured": false}
{"doc_id": 20155713, "title": "Promiscuous gene expression in medullary thymic epithelial cells mirrors the peripheral self", "abstract": ["Expression of peripheral antigens in the thymus has been implicated in T cell tolerance and autoimmunity.", "Here we identified medullary thymic epithelial cells as being a unique cell type that expresses a diverse range of tissue-specific antigens.", "We found that this promiscuous gene expression was a cell-autonomous property of medullary epithelial cells and was maintained during the entire period of thymic T cell output.", "It may facilitate tolerance induction to self-antigens that would otherwise be temporally or spatially secluded from the immune system.", "However, the array of promiscuously expressed self-antigens appeared random rather than selected and was not confined to secluded self-antigens."], "structured": false}
{"doc_id": 20179918, "title": "Signal transducer and activator of transcription 3 is a transcriptional factor regulating the gene expression of SALL4.", "abstract": ["Both signal transducer and activator of transcription 3 (STAT3) and SALL4 are important in maintaining the pluripotent and self-renewal state of embryonic stem cells.", "We hypothesized that STAT3, a latent transcriptional factor, may regulate the gene expression of SALL4.", "In support of this hypothesis, DNA sequence analysis of the SALL4 gene promoter revealed four putative STAT3-binding sites.", "Using a SALL4-luciferase reporter gene assay, we found that modulation of the STAT3 activity significantly up-regulated the luciferase activity.", "By chromatin immunoprecipitation, the segment of the SALL4 promoter showing the highest affinity to STAT3 was localized to -366 to -163, in which there was only one putative STAT3 binding site starting at -199.", "Site-directed mutagenesis of all four putative STAT3-binding sites in the SALL4 promoter significantly reduced its responsiveness to STAT3, although the most dramatic effect was seen at the binding site starting at -199.", "We further tested the functional relationship between STAT3 and SALL4 using MDA-MB-231, a breast cell line carrying constitutive SALL4 expression and STAT3 activity.", "Down-regulation of the STAT3 activity using a dominant-negative construct resulted in a significant decrease in the expression of SALL4.", "To conclude, our data suggest that STAT3 and SALL4 probably cooperate in both physiological and pathological states."], "structured": false}
{"doc_id": 20183360, "title": "GATA3 transcription factor abrogates Smad4 transcription factor-mediated fascin overexpression, invadopodium formation, and breast cancer cell invasion.", "abstract": ["Transforming growth factor \u03b2 (TGF\u03b2) is a potent and context-dependent regulator of tumor progression.", "TGF\u03b2 promotes the lung metastasis of basal-like (but not the luminal-like) breast cancer.", "Here, we demonstrated that fascin, a pro-metastasis actin bundling protein, was a direct target of the canonical TGF\u03b2-Smad4 signaling pathway in basal-like breast cancer cells.", "TGF\u03b2 and Smad4 induced fascin overexpression by directly binding to a Smad binding element on the fascin promoter.", "We identified GATA3, a transcription factor crucial for mammary gland morphogenesis and luminal differentiation, as a negative regulator of TGF\u03b2- and Smad4-induced fascin overexpression.", "When ectopically expressed in basal-like breast cancer cells, GATA-3 abrogated TGF\u03b2- and Smad4-mediated overexpression of fascin and other TGF\u03b2 response genes, invadopodium formation, cell migration, and invasion, suggesting suppression of the canonical TGF\u03b2-Smad signaling axis.", "Mechanistically, GATA3 abrogated the canonical TGF\u03b2-Smad signaling by abolishing interactions between Smad4 and its DNA binding elements, potentially through physical interactions between the N-terminal of GATA3 and Smad3/4 proteins.", "Our findings provide mechanistic insight into how TGF\u03b2-mediated cell motility and invasiveness are differentially regulated in breast cancer."], "structured": false}
{"doc_id": 20186513, "title": "The American Rheumatism Association 1987 revised criteria for the classification of rheumatoid arthritis.", "abstract": ["The revised criteria for the classification of rheumatoid arthritis (RA) were formulated from a computerized analysis of 262 contemporary, consecutively studied patients with RA and 262 control subjects with rheumatic diseases other than RA (non-RA).", "The new criteria are as follows: 1) morning stiffness in and around joints lasting at least 1 hour before maximal improvement; 2) soft tissue swelling (arthritis) of 3 or more joint areas observed by a physician; 3) swelling (arthritis) of the proximal interphalangeal, metacarpophalangeal, or wrist joints; 4) symmetric swelling (arthritis); 5) rheumatoid nodules; 6) the presence of rheumatoid factor; and 7) radiographic erosions and/or periarticular osteopenia in hand and/or wrist joints.", "Criteria 1 through 4 must have been present for at least 6 weeks.", "Rheumatoid arthritis is defined by the presence of 4 or more criteria, and no further qualifications (classic, definite, or probable) or list of exclusions are required.", "In addition, a \"classification tree\" schema is presented which performs equally as well as the traditional (4 of 7) format.", "The new criteria demonstrated 91-94% sensitivity and 89% specificity for RA when compared with non-RA rheumatic disease control subjects."], "structured": false}
{"doc_id": 20186814, "title": "A new look at the origin, function, and \"stem-cell\" status of muscle satellite cells.", "abstract": ["Muscle satellite cells have long been considered a distinct myogenic lineage responsible for postnatal growth, repair, and maintenance of skeletal muscle.", "Recent studies in mice, however, have revealed the potential for highly purified hematopoietic stem cells from bone marrow to participate in muscle regeneration.", "Perhaps more significantly, a population of putative stem cells isolated directly from skeletal muscle efficiently reconstitutes the hematopoietic compartment and participates in muscle regeneration following intravenous injection in mice.", "The plasticity of muscle stem cells has raised important questions regarding the relationship between the muscle-derived stem cells and the skeletal muscle satellite cells.", "Furthermore, the ability of hematopoietic cells to undergo myogenesis has prompted new investigations into the embryonic origin of satellite cells.", "Recent developmental studies suggest that a population of satellite cells is derived from progenitors in the embryonic vasculature.", "Taken together, these studies provide the first evidence that pluripotential stem cells are present within adult skeletal muscle.", "Tissue-specific stem cells, including satellite cells, may share a common embryonic origin and possess the capacity to activate diverse genetic programs in response to environmental stimuli.", "Manipulation of such tissue-specific stem cells may eventually revolutionize therapies for degenerative diseases, including muscular dystrophy."], "structured": false}
{"doc_id": 20187433, "title": "Involving family members in cancer care: focus group considerations of patients and oncological providers.", "abstract": ["Family members are an integral part of a patient's cancer care from the moment the diagnosis is delivered to the conclusion of treatment.", "Family members bring with them a range of emotional reactions, interpersonal dynamics and expectations for the care the patient receives.", "This study is part of a multi-institutional project to continue to improve the process of cancer care.", "In this study, 19 focus groups (11 patient and 8 provider) were conducted concerning issues related to doctor-patient communication in eight cancer centers in the United States.", "The content of the conversations was analyzed and thematic categories emerged that highlight the various strengths and difficulties associated with family involvement.", "The focus groups' comments support the need for explicit conversations between professional caregivers, patients and their loved ones, in order to negotiate the expectations and needs of each team member.", "Implications for clinical practice and strategies for working with family members are offered."], "structured": false}
{"doc_id": 20188586, "title": "Improving Adherence to Antiretroviral Therapy With Triggered Real-time Text Message Reminders: The China Adherence Through Technology Study.", "abstract": ["BACKGROUND Real-time adherence monitoring is now possible through medication storage devices equipped with cellular technology.", "We assessed the effect of triggered cell phone reminders and counseling using objective adherence data on antiretroviral therapy (ART) adherence among Chinese HIV-infected patients.   \n", "METHODS We provided ART patients in Nanning, China, with a medication device (Wisepill) to monitor their ART adherence electronically.", "After 3 months, we randomized subjects within optimal (\u226595%) and suboptimal (<95%) adherence strata to intervention vs. control arms.", "In months 4-9, intervention subjects received individualized reminders triggered by late dose taking (no device opening by 30 minutes past dose time) and counseling using device-generated data.", "Controls received no reminders or data-informed counseling.", "We compared postintervention proportions achieving optimal adherence, mean adherence, and clinical outcomes.   \n", "RESULTS Of 120 subjects enrolled, 116 (96.7%) completed the trial.", "Preintervention optimal adherence was similar in intervention vs. control arms (63.5% vs. 58.9%, respectively; P = 0.60).", "In the last intervention month, 87.3% vs. 51.8% achieved optimal adherence [risk ratio (RR): 1.7, 95% confidence interval (CI): 1.3 to 2.2] and mean adherence was 96.2% vs. 89.1% (P = 0.003).", "Among preintervention suboptimal adherers, 78.3% vs. 33.3% (RR: 2.4, CI: 1.2 to 4.5) achieved optimal adherence and mean adherence was 93.3% vs. 84.7% (P = 0.039).", "Proportions were 92.5% and 62.9% among optimal adherers, respectively (RR: 1.5, CI: 1.1 to 1.9) and mean adherence was 97.8% vs. 91.7% (P = 0.028).", "Postintervention clinical outcomes were not significant.   \n", "CONCLUSIONS Real-time reminders significantly improved ART adherence in this population.", "This approach seems promising for managing HIV and other chronic diseases and warrants further investigation and adaptation in other settings."], "structured": true}
{"doc_id": 20220731, "title": "Origin and T cell receptor diversity of Foxp3+CD4+CD25+ T cells.", "abstract": ["Foxp3(+)CD4(+)CD25(+) regulatory T cells can differentiate from Foxp3(-)CD4(+) medullary thymocytes and Foxp3(-)CD4(+) naive T cells.", "However, the impact of these two processes on size and composition of the peripheral repertoire of regulatory T cells is unclear.", "Here we followed the fate of individual Foxp3(+)CD4(+)CD25(+) thymocytes and T cells in vivo in T cell receptor (TCR) transgenic mice that express a restricted but polyclonal repertoire of TCRs.", "By utilizing high-throughput single-cell analysis, we showed that Foxp3(+)CD4(+) peripheral T cells were derived from thymic precursors that expressed a different TCRs than Foxp3(-)CD4(+) medullary thymocytes and Foxp3(-)CD4(+) T cells.", "Furthermore, the diversity of TCRs on Foxp3(+)CD4(+) regulatory T cells exceeded the diversity of TCRs on Foxp3(-)CD4(+) naive T cells, even in mice that lack expression of tissue-specific antigens.", "Our results imply that higher TCR diversity on Foxp3(+) regulatory T cells helps these cells to match the specificities of autoreactive and naive T cells."], "structured": false}
{"doc_id": 20221907, "title": "Reproducibility of the diagnosis of atypical endometrial hyperplasia: a Gynecologic Oncology Group study.", "abstract": ["BACKGROUND Most gynecologists determine therapy based on current International Society of Gynecologic Pathologists (ISGP)/World Health Organization classification of endometrial hyperplasia, the reproducibility of which has been questioned.", "The Gynecologic Oncology Group (GOG) initiated a protocol to assess the efficacy of hormonal therapy of atypical endometrial hyperplasia (AEH).", "Primary goals of the first phase (Part A) were to prospectively determine reproducibility of referring institution's pathologist's diagnosis of AEH by a panel of 3 gynecologic pathologists and to determine reproducibility of diagnoses by panel members.   \n", "METHODS Three hundred six women were entered on this protocol with a referring institution's pathologist diagnosis of AEH based on biopsy or curettage.", "Available slides were assessed independently and interpreted by each of a panel of 3 gynecologic pathologists who used International Society of Gynecologic Pathologists (ISGP)/World Health Organization criteria.", "The majority diagnosis was based on diagnostic concordance by at least 2 of the 3 panelists.   \n", "RESULTS The referring institution's pathologist's diagnosis of AEH was supported by the majority of the panel in only 38% of cases.", "Overall kappa value for the panel diagnosis of AEH was 0.28.", "The majority diagnosis was adenocarcinoma in 29%, cycling endometrium in 7%, and nonatypical hyperplasia in 18% of cases.", "Unanimous agreement for any diagnosis was reached among all 3 of the panel in 40% of cases.", "For the panel, paired kappa values for any diagnosis ranged 0.34-0.43, with an overall kappa value of 0.40.   \n", "CONCLUSION Reproducibility of referring institution's pathologists' diagnosis of AEH by a panel of gynecologic pathologists is poor.", "Both underestimation and overestimation of the severity of the lesion are very common.", "The level of reproducibility among subspecialist panel members for diagnosis of AEH in these specimens also is poor.", "Better criteria and better sampling are needed to improve reproducibility of this diagnosis, particularly if it is to be used for clinical decisions."], "structured": true}
{"doc_id": 20231138, "title": "Replication Fork Slowing and Reversal upon DNA Damage Require PCNA Polyubiquitination and ZRANB3 DNA Translocase Activity", "abstract": ["DNA damage tolerance during eukaryotic replication is orchestrated by PCNA ubiquitination.", "While monoubiquitination activates mutagenic translesion synthesis, polyubiquitination activates an error-free pathway, elusive in mammals, enabling damage bypass by template switching.", "Fork reversal is driven in vitro by multiple enzymes, including the DNA translocase ZRANB3, shown to bind polyubiquitinated PCNA.", "However, whether this interaction promotes fork remodeling and template switching in vivo was unknown.", "Here we show that damage-induced fork reversal in mammalian cells requires PCNA ubiquitination, UBC13, and K63-linked polyubiquitin chains, previously involved in error-free damage tolerance.", "Fork reversal in vivo also requires ZRANB3 translocase activity and its interaction with polyubiquitinated PCNA, pinpointing ZRANB3 as a key effector of error-free DNA damage tolerance.", "Mutations affecting fork reversal also induced unrestrained fork progression and chromosomal breakage, suggesting fork remodeling as a global fork slowing and protection mechanism.", "Targeting these fork protection systems represents a promising strategy to potentiate cancer chemotherapy."], "structured": false}
{"doc_id": 20240998, "title": "Bed sharing when parents do not smoke: is there a risk of SIDS? An individual level analysis of five major case\u2013control studies", "abstract": ["OBJECTIVE To resolve uncertainty as to the risk of Sudden Infant Death Syndrome (SIDS) associated with sleeping in bed with your baby if neither parent smokes and the baby is breastfed.   \n", "DESIGN Bed sharing was defined as sleeping with a baby in the parents' bed; room sharing as baby sleeping in the parents' room.", "Frequency of bed sharing during last sleep was compared between babies who died of SIDS and living control infants.", "Five large SIDS case-control datasets were combined.", "Missing data were imputed.", "Random effects logistic regression controlled for confounding factors.   \n", "SETTING Home sleeping arrangements of infants in 19 studies across the UK, Europe and Australasia.   \n", "PARTICIPANTS 1472 SIDS cases, and 4679 controls.", "Each study effectively included all cases, by standard criteria.", "Controls were randomly selected normal infants of similar age, time and place.   \n", "RESULTS In the combined dataset, 22.2% of cases and 9.6% of controls were bed sharing, adjusted OR (AOR) for all ages 2.7; 95% CI (1.4 to 5.3).", "Bed sharing risk decreased with increasing infant age.", "When neither parent smoked, and the baby was less than 3 months, breastfed and had no other risk factors, the AOR for bed sharing versus room sharing was 5.1 (2.3 to 11.4) and estimated absolute risk for these room sharing infants was very low (0.08 (0.05 to 0.14)/1000 live-births).", "This increased to 0.23 (0.11 to 0.43)/1000 when bed sharing.", "Smoking and alcohol use greatly increased bed sharing risk.   \n", "CONCLUSIONS Bed sharing for sleep when the parents do not smoke or take alcohol or drugs increases the risk of SIDS.", "Risks associated with bed sharing are greatly increased when combined with parental smoking, maternal alcohol consumption and/or drug use.", "A substantial reduction of SIDS rates could be achieved if parents avoided bed sharing."], "structured": true}
{"doc_id": 20261352, "title": "Decoupling activation and exhaustion of B cells in spontaneous controllers of HIV infection.", "abstract": ["OBJECTIVE To define the impact of chronic viremia and associated immune activation on B-cell exhaustion in HIV infection.   \n", "DESIGN Progressive HIV infection is marked by B-cell anergy and exhaustion coupled with dramatic hypergammaglobulinemia.", "Although both upregulation of CD95 and loss of CD21 have been used as markers of infection-associated B-cell dysfunction, little is known regarding the specific profiles of dysfunctional B cells and whether persistent viral replication and its associated immune activation play a central role in driving B-cell dysfunction.   \n", "METHODS Multiparameter flow cytometry was used to define the profile of dysfunctional B cells.", "The changes in the expression of CD21 and CD95 were tracked on B-cell subpopulations in patients with differential control of viral replication.   \n", "RESULTS : Although the emergence of exhausted, CD21 tissue-like memory B cells followed similar patterns in both progressors and controllers, the frequency of CD21 activated memory B cells was lower in spontaneous controllers.   \n", "CONCLUSION Our results suggest that the loss of CD21 and the upregulation of CD95 occur as separate events during the development of B-cell dysfunction.", "The loss of CD21 is a marker of B-cell exhaustion induced in the absence of appreciable viral replication, whereas the upregulation of CD95 is tightly linked to persistent viral replication and its associated immune activation.", "Thus, these dysfunctional profiles potentially represent two functionally distinct states within the B-cell compartment."], "structured": true}
{"doc_id": 20279166, "title": "Label-free DNA imaging in vivo with stimulated Raman scattering microscopy.", "abstract": ["Label-free DNA imaging is highly desirable in biology and medicine to perform live imaging without affecting cell function and to obtain instant histological tissue examination during surgical procedures.", "Here we show a label-free DNA imaging method with stimulated Raman scattering (SRS) microscopy for visualization of the cell nuclei in live animals and intact fresh human tissues with subcellular resolution.", "Relying on the distinct Raman spectral features of the carbon-hydrogen bonds in DNA, the distribution of DNA is retrieved from the strong background of proteins and lipids by linear decomposition of SRS images at three optimally selected Raman shifts.", "Based on changes on DNA condensation in the nucleus, we were able to capture chromosome dynamics during cell division both in vitro and in vivo.", "We tracked mouse skin cell proliferation, induced by drug treatment, through in vivo counting of the mitotic rate.", "Furthermore, we demonstrated a label-free histology method for human skin cancer diagnosis that provides comparable results to other conventional tissue staining methods such as H&E. Our approach exhibits higher sensitivity than SRS imaging of DNA in the fingerprint spectral region.", "Compared with spontaneous Raman imaging of DNA, our approach is three orders of magnitude faster, allowing both chromatin dynamic studies and label-free optical histology in real time."], "structured": false}
{"doc_id": 20280410, "title": "A common variant in BRCA2 is associated with both breast cancer risk and prenatal viability", "abstract": ["Inherited mutations in the gene BRCA2 predispose carriers to early onset breast cancer, but such mutations account for fewer than 2% of all cases in East Anglia.", "It is likely that low penetrance alleles explain the greater part of inherited susceptibility to breast cancer; polymorphic variants in strongly predisposing genes, such as BRCA2, are candidates for this role.", "BRCA2 is thought to be involved in DNA double strand break-repair.", "Few mice in which Brca2 is truncated survive to birth; of those that do, most are male, smaller than their normal littermates and have high cancer incidence.", "Here we show that a common human polymorphism (N372H) in exon 10 of BRCA2 confers an increased risk of breast cancer: the HH homozygotes have a 1.31-fold (95% CI, 1.07\u20131.61) greater risk than the NN group.", "Moreover, in normal female controls of all ages there is a significant deficiency of homozygotes compared with that expected from Hardy-Weinberg equilibrium, whereas in males there is an excess of homozygotes: the HH group has an estimated fitness of 0.82 in females and 1.38 in males.", "Therefore, this variant of BRCA2 appears also to affect fetal survival in a sex-dependent manner."], "structured": false}
{"doc_id": 20287253, "title": "Pathophysiology of obstructive nephropathy in the newborn.", "abstract": ["Congenital obstructive nephropathy is a consequence abnormal urinary tract development resulting in renal growth failure and injury manifested by progressive tubular atrophy and interstitial fibrosis.", "We have studied the renal cellular and physiological response to unilateral ureteral obstruction (UUO) in the neonatal rodent (guinea pig, rat, and mouse).", "Whereas in the adult, UUO stimulates renal cellular proliferation, UUO in the neonate reduces nephrogenesis, glomerular maturation, and tubular cellular proliferation.", "This is accompanied by a proportionately greater compensatory growth of the intact opposite kidney in the neonate.", "Impaired renal growth and tubular atrophy are likely owing at least in part to stimulation of renal tubular apoptosis.", "This, in turn, may result from a combination of factors, including loss of epithelial cell polarity, a reduction in the oncoprotein bcl-2 and epidermal growth factor (EGF), and increased expression of the fibrogenic cytokine, transforming growth factor-beta1 (TGF-beta1).", "Infusion of EGF stimulates cellular proliferation, suppresses apoptosis, and reduces tubular atrophy and interstitial fibrosis.", "TGF-beta1 is regulated by the renin-angiotensin system, which is markedly activated by UUO in the neonate.", "The functional consequences of obstructive nephropathy in early development are hyperfiltration by remaining nephrons, followed by progressive decrease in glomerular filtration rate that may only develop in later life.", "Improved management of congenital urinary tract obstruction will depend on a better understanding of the cellular mechanisms, which may lead to specific treatment using gene therapy or modulators of renal growth and development."], "structured": false}
{"doc_id": 20288322, "title": "Lipid homeostasis, lipotoxicity and the metabolic syndrome.", "abstract": ["In the 20th century industrialized nations have become afflicted with an unprecedented pandemic of increased adiposity.", "In the United States, the epicenter of the epidemic, over 2/3 of the population, is overweight and 1 of every 6 Americans carries the diagnosis of metabolic syndrome.", "Although genes determine susceptibility to environmental factors, the epidemic is clearly due to increased consumption of calorie-dense, highly lipogenic foods, coupled with a marked decrease in physical exertion resulting from modern technologies.", "If this lifestyle continues, morbid consequences are virtually inevitable.", "They include type II diabetes and a cluster of disorders known as \"the metabolic syndrome\" usually appearing in middle age.", "The morbid consequences of the chronic caloric surplus are buffered before middle age by the partitioning of these calories as fat in the adipocyte compartment which is specifically designed to store triglycerides.", "Leptin has been proposed as the major hormonal regulator of the partitioning of surplus calories.", "However, multiple factors can determine the storage capacity of the fat tissue and when it is exceeded ectopic lipid deposition begins.", "The organs affected in metabolic syndrome include skeletal muscle, liver, heart and pancreas, which are now known to contain abnormal levels of triglycerides.", "While neutral fat is probably harmless, it is an index of ectopic lipid overload.", "Fatty acid derivatives can interfere with the function of the cell and ultimately lead to its demise through lipoapoptosis, the consequences of which are gradual organ failure."], "structured": false}
{"doc_id": 20302714, "title": "A twin-study of genetic contributions to morningness-eveningness and depression.", "abstract": ["Circadian rhythms are associated with the preference for sleep-wake timing, also known as morningness-eveningness (ME).", "Both circadian rhythms and ME are influenced by genetic factors.", "Studies show an association between eveningness and depression.", "This study investigates the heritability of ME and whether ME and depression share common genetic influences.", "Study participants (n = 1237) were from the Vietnam Era Twin Study of Aging, a longitudinal study of aging with a baseline in midlife.", "Participants received the Morningness-Eveningness Questionnaire (MEQ) and the Center for Epidemiologic Studies Depression (CES-D) Scale as part of an extensive neurocognitive and psychosocial assessment.", "MEQ correlations between members of twin pairs were 0.41 (95% CI 0.31-0.49) for monozygotic (MZ) twins and 0.28 for dizygotic (DZ) twins (95% CI 0.19-0.41).", "CES-D correlations were 0.38 (95% CI 0.28-0.46) for MZ twins and 0.24 (95% CI 0.14-0.36) for DZ twins.", "Greater eveningness (i.e. lower MEQ scores) was significantly related to more depression symptoms (phenotypic correlation = -0.15 (95% CI -0.21 to -0.09).", "In the best fitting model, the heritability estimates are 0.42 for the MEQ and 0.37 for the CES-D. A significant genetic correlation of -0.21 indicated that ME and depression share a significant amount of their underlying genetic variance.", "The genetic covariance between ME and depression accounted for 59.1% of the phenotypic correlation.", "Of the CES-D sub-scales, Depressed Mood and Interpersonal Difficulties were significantly heritable, while only Well-Being had a significant genetic correlation with ME.", "ME and depression are both heritable (ME 0.42, depression 0.37) and share common genetic factors, suggesting an overlap in etiology and the relevance of circadian rhythms to depression.", "Further study of this relationship may help elucidate etiological factors in depression and targets for treatment."], "structured": false}
{"doc_id": 20310709, "title": "The Transcription Factor T-bet Regulates Intestinal Inflammation Mediated by Interleukin-7 Receptor+ Innate Lymphoid Cells", "abstract": ["Mice lacking the transcription factor T-bet in the innate immune system develop microbiota-dependent colitis.", "Here, we show that interleukin-17A (IL-17A)-producing IL-7R\u03b1(+) innate lymphoid cells (ILCs) were potent promoters of disease in Tbx21(-/-)Rag2(-/-) ulcerative colitis (TRUC) mice.", "TNF-\u03b1 produced by CD103(-)CD11b(+) dendritic cells synergized with IL-23 to drive IL-17A production by ILCs, demonstrating a previously unrecognized layer of cellular crosstalk between dendritic cells and ILCs.", "We have identified Helicobacter typhlonius as a key disease trigger driving excess TNF-\u03b1 production and promoting colitis in TRUC mice.", "Crucially, T-bet also suppressed the expression of IL-7R, a key molecule involved in controlling intestinal ILC homeostasis.", "The importance of IL-7R signaling in TRUC disease was highlighted by the dramatic reduction in intestinal ILCs and attenuated colitis following IL-7R blockade.", "Taken together, these data demonstrate the mechanism by which T-bet regulates the complex interplay between mucosal dendritic cells, ILCs, and the intestinal microbiota."], "structured": false}
{"doc_id": 20311968, "title": "Chimeric Antigen Receptor-Redirected Regulatory T Cells Suppress Experimental Allergic Airway Inflammation, a Model of Asthma", "abstract": ["Cellular therapy with chimeric antigen receptor (CAR)-redirected cytotoxic T cells has shown impressive efficacy in the treatment of hematologic malignancies.", "We explored a regulatory T cell (Treg)-based therapy in the treatment of allergic airway inflammation, a model for asthma, which is characterized by an airway hyper-reactivity (AHR) and a chronic, T helper-2 (Th2) cell-dominated immune response to allergen.", "To restore the immune balance in the lung, we redirected Tregs by a CAR toward lung epithelia in mice upon experimentally induced allergic asthma, closely mimicking the clinical situation.", "Adoptively transferred CAR Tregs accumulated in the lung and in tracheobronchial lymph nodes, reduced AHR and diminished eosinophilic airway inflammation, indicated by lower cell numbers in the bronchoalveolar lavage fluid and decreased cell infiltrates in the lung.", "CAR Treg cells furthermore prevented excessive pulmonary mucus production as well as increase in allergen-specific IgE and Th2 cytokine levels in exposed animals.", "CAR Tregs were more efficient in controlling asthma than non-modified Tregs, indicating the pivotal role of specific Treg cell activation in the affected organ.", "Data demonstrate that lung targeting CAR Treg cells ameliorate key features of experimental airway inflammation, paving the way for cell therapy of severe allergic asthma."], "structured": false}
{"doc_id": 20313748, "title": "\u03b1-Catenin as a tension transducer that induces adherens junction development", "abstract": ["Adherens junctions (AJs), which are organized by adhesion proteins and the underlying actin cytoskeleton, probably sense pulling forces from adjacent cells and modulate opposing forces to maintain tissue integrity, but the regulatory mechanism remains unknown at the molecular level.", "Although the possibility that \u03b1-catenin acts as a direct linker between the membrane and the actin cytoskeleton for AJ formation and function has been minimized, here we show that \u03b1-catenin recruits vinculin, another main actin-binding protein of AJs, through force-dependent changes in \u03b1-catenin conformation.", "We identified regions in the \u03b1-catenin molecule that are required for its force-dependent binding of vinculin by introducing mutant \u03b1-catenin into cells and using in vitro binding assays.", "Fluorescence recovery after photobleaching analysis for \u03b1-catenin mobility and the existence of an antibody recognizing \u03b1-catenin in a force-dependent manner further supported the notion that \u03b1-catenin is a tension transducer that translates mechanical stimuli into a chemical response, resulting in AJ development."], "structured": false}
{"doc_id": 20321154, "title": "A population-based cohort study to elucidate temporal relationship between schizophrenia and metabolic syndrome (KCIS no. PSY3).", "abstract": ["BACKGROUND The bidirectional relationships between metabolic syndrome (MetS) and schizophrenia (SCZ) play a crucial role in clinical treatment of both diseases but such bidirectional causal effects have not been comprehensively elucidated.   ", "AIMS To investigate the influence of MetS on incident SCZ and the opposite direction as well as their predictors for each direction with a population-based cohort sample.   \n", "METHOD We enrolled 76,545 subjects who had participated in a community-based health screening program during 1999-2004.", "After excluding those with the existing MetS or SCZ at baseline, the two normal prospective cohorts corresponding to each independent variable of MetS or SCZ, respectively, were followed over time to ascertain incident outcome of SCZ and MetS. The crude and adjusted hazard ratios for the effect of the predictor on each incident outcome were estimated after controlling for the possible confounding factors.   \n", "RESULTS The overall incidence rate (per 10(5)person-years) of SCZ was 61.15.", "The incidence rate in patients with MetS was lower than those without (44.24 versus 64.20), indicating the presence of MetS failed to find an increased risk of developing incident SCZ.", "However, participants with abnormal waist circumference (WC) were two times (95% CI: 1.37 to 2.93) more likely to yield incident SCZ compared to those with normal WC.", "In the opposite direction, the incidence of MetS was statistically higher in patients with SCZ than those without SCZ (11.25% vs 7.94%, respectively), suggesting SCZ conferred a higher risk for yielding incident MetS (adjusted hazard ratio=1.89, 95% CI: 1.36, 2.63).   \n", "CONCLUSIONS After examining the bidirectional causal relationships between SCZ and MetS with the theoretically sound and large population-based prospective cohort study, central obesity, one of the individual components of MetS, was corroborated as an independent predictor for incident SCZ.", "Patients diagnosed with SCZ were at greater risk of having incident cases of MetS. Such significant temporal bidirectional relationships between SCZ and central obesity suggest a reciprocal interaction exits between SCZ and central obesity."], "structured": true}
{"doc_id": 20326526, "title": "DEVELOPMENT AND VALIDATION OF A MEASURE OF EMOTIONAL INTELLIGENCE", "abstract": ["This series of studies describes the development of a measure of emotional intelligence based on the model of emotional intelligence developed by Salovey and Mayer [Salovey, P. & Mayer, J. D. (1990).", "Emotional intelligence.", "Imagination, Cognition and Personality, 9, 185\u2013211.].", "A pool of 62 items represented the different dimensions of the model.", "A factor analysis of the responses of 346 participants suggested the creation of a 33-item scale.", "Additional studies showed the 33-item measure to have good internal consistency and testretest reliability.", "Validation studies showed that scores on the 33-item measure  1.  ", "(a) correlated with eight of nine theoretically related constructs, including alexithymia, attention to feelings, clarity of feelings, mood repair, optimism and impulse control;    2.  (b) predicted first-year college grades;    3.  ", "(c) were significantly higher for therapists than for therapy clients or for prisoners;    4.  (d) were significantly higher for females than males, consistent with prior findings in studies of emotional skills;    5.  ", "(e) were not related to cognitive ability and    6.  ", "(f) were associated with the openness to experience trait of the big five personality dimensions."], "structured": false}
{"doc_id": 20330519, "title": "Cholesterol glucosylation promotes immune evasion by Helicobacter pylori", "abstract": ["Helicobacter pylori infection causes gastric pathology such as ulcer and carcinoma.", "Because H. pylori is auxotrophic for cholesterol, we have explored the assimilation of cholesterol by H. pylori in infection.", "Here we show that H. pylori follows a cholesterol gradient and extracts the lipid from plasma membranes of epithelial cells for subsequent glucosylation.", "Excessive cholesterol promotes phagocytosis of H. pylori by antigen-presenting cells, such as macrophages and dendritic cells, and enhances antigen-specific T cell responses.", "A cholesterol-rich diet during bacterial challenge leads to T cell\u2013dependent reduction of the H. pylori burden in the stomach.", "Intrinsic \u03b1-glucosylation of cholesterol abrogates phagocytosis of H. pylori and subsequent T cell activation.", "We identify the gene hp0421 as encoding the enzyme cholesterol-\u03b1-glucosyltransferase responsible for cholesterol glucosylation.", "Generation of knockout mutants lacking hp0421 corroborates the importance of cholesteryl glucosides for escaping phagocytosis, T cell activation and bacterial clearance in vivo.", "Thus, we propose a mechanism regulating the host\u2013pathogen interaction whereby glucosylation of a lipid tips the scales towards immune evasion or response."], "structured": false}
{"doc_id": 20333864, "title": "Regulation of in situ to invasive breast carcinoma transition.", "abstract": ["The transition of ductal carcinoma in situ (DCIS) to invasive carcinoma is a poorly understood key event in breast tumor progression.", "Here, we analyzed the role of myoepithelial cells and fibroblasts in the progression of in situ carcinomas using a model of human DCIS and primary breast tumors.", "Progression to invasion was promoted by fibroblasts and inhibited by normal myoepithelial cells.", "Molecular profiles of isolated luminal epithelial and myoepithelial cells identified an intricate interaction network involving TGFbeta, Hedgehog, cell adhesion, and p63 required for myoepithelial cell differentiation, the elimination of which resulted in loss of myoepithelial cells and progression to invasion."], "structured": false}
{"doc_id": 20334484, "title": "Health and access to care: perspectives of homeless youth in Baltimore City, U.S.A.", "abstract": ["Homeless youth suffer from high rates of health problems, yet little is known about their perceptions of or context for their own health issues.", "In this study, a combination of qualitative techniques from participatory rural appraisal and rapid assessment procedures was used to investigate the perceptions of health needs of shelter-based youth in Baltimore, MD in the U.S.A. The most common youth-identified health problems included STDs, HIV/AIDS, pregnancy, depression, drug use and injuries.", "These correlate well with more objective health status data for the same youth.", "The youth spoke of environmental safety threats of violence and victimization by adults, as well as racism and sexism in their lives.", "Youth reported that trusted adult figures such as grandmothers are important sources of health advice.", "Many homeless youth from less than ideal family situations remain in contact with and continue to seek advice from parents and other family members.", "Health interventions with urban street youth need to acknowledge the primacy of the social context for these youth, as well as the reality of violence as a daily health threat."], "structured": false}
{"doc_id": 20344442, "title": "Differential requirement for CARMA1 in agonist-selected T-cell development.", "abstract": ["Caspase recruitment domain-containing membrane-associated guanylate kinase protein-1 (CARMA1) is a critical component of the NF-kappaB signaling cascade mediated by TCR engagement.", "In addition to activation of na\u00efve T cells, TCR signaling is important for the development of agonist-selected T-cell subsets such as Treg, NKT cells, and CD8-alpha alpha T cells.", "However, little is known about the role of CARMA1 in the development of these lineages.", "Here we show that CARMA1-deficient mice (CARMA1(-/-)) have altered populations of specific subsets of agonist-selected T cells.", "Specifically, CARMA1(-/-) mice have impaired natural and adaptive Treg development, whereas NKT cell numbers are normal compared with wild-type mice.", "Interestingly, CD8-alpha alpha T cells, which may also be able to develop through an extrathymic selection pathway, are enriched in the gut of CARMA1(-/-) mice, whereas memory-phenotype CD4(+) T cells (CD62L(low)/CD44(high)) are present at reduced numbers in the periphery.", "These results indicate that CARMA1 is essential for Treg development, but is not necessary for the development of other agonist-selected T-cell subsets.", "Overall, these data reveal an important but differential role for CARMA1-mediated TCR signaling in T-cell development."], "structured": false}
{"doc_id": 20357868, "title": "Simian immunodeficiency viruses of diverse origin can use CXCR4 as a coreceptor for entry into human cells.", "abstract": ["Primary simian immunodeficiency virus (SIV) isolated from sooty mangabey (SIVsm [n = 6]), stumptail (SIVstm [n = 1]), mandrill (SIVmnd [n = 1]), and African green (SIVagm [n = 1]) primates were examined for their ability to infect human cells and for their coreceptor requirements.", "All isolates infected human peripheral blood mononuclear cells (PBMCs) from a CCR5(+/+) donor, and seven of eight isolates tested also infected CCR5(-/-) PBMCs.", "Analysis of coreceptor utilization using GHOST and U87 cell lines revealed that all of the isolates tested used CCR5 and the orphan receptors STRL33 and GPR15.", "Coreceptors such as CCR2b, CCR3, CCR8, and CX3CR1 were also utilized by some primary SIV isolates.", "More importantly, we found that CXCR4 was used as a coreceptor by the SIVstm, the SIVagm, and four of the SIVsm isolates in GHOST and U87 cells.", "These data suggest that primary SIV isolates from diverse primate species can utilize CXCR4 for viral entry, similar to what has been described for human immunodeficiency viruses."], "structured": false}
{"doc_id": 20363389, "title": "Cloning of rat uncoupling protein-3 and uncoupling protein-2 cDNAs: their gene expression in rats fed high-fat diet.", "abstract": ["In order to elucidate energy balance in the skeletal muscle, we cloned cDNA of a homologue of uncoupling protein (UCP) from rat skeletal muscle.", "We also cloned rat UCP-2 cDNA from rat brown adipose tissue (BAT).", "The UCP cloned from rat skeletal muscle showed 57% and 72% identity with rat UCP-1 and UCP-2.", "The mRNA was expressed abundantly in the skeletal muscle, moderately in the BAT, and slightly in the white adipose tissue (WAT) with a major band at 2.5 kb and a minor band at 2.8 kb, while the UCP-2 gene expression was widely detected in the whole body with substantial levels in the WAT and with slight levels in the skeletal muscle and BAT.", "The rat UCP cloned in the present study showed 86% identity with the recently cloned human UCP-3, which was also expressed abundantly in the skeletal muscle with a signal of 2.4 kb.", "Therefore, the rat UCP was considered to be rat UCP-3.", "In rats fed high-fat diet the UCP-3 gene expression was augmented 2-fold in the skeletal muscle while UCP-2 mRNA levels were increased significantly (1.6-fold) in the epididymal WAT.", "Augmented expression of UCPs may provide defense against high-fat induced obesity and impairment of glucose metabolism."], "structured": false}
{"doc_id": 20368353, "title": "A two-step mechanism for epigenetic specification of centromere identity and function", "abstract": ["The basic determinant of chromosome inheritance, the centromere, is specified in many eukaryotes by an epigenetic mark.", "Using gene targeting in human cells and fission yeast, chromatin containing the centromere-specific histone H3 variant CENP-A is demonstrated to be the epigenetic mark that acts through a two-step mechanism to identify, maintain and propagate centromere function indefinitely.", "Initially, centromere position is replicated and maintained by chromatin assembled with the centromere-targeting domain (CATD) of CENP-A substituted into H3.", "Subsequently, nucleation of kinetochore assembly onto CATD-containing chromatin is shown to require either the amino- or carboxy-terminal tail of CENP-A for recruitment of inner kinetochore proteins, including stabilizing CENP-B binding to human centromeres or direct recruitment of CENP-C, respectively."], "structured": false}
{"doc_id": 20372201, "title": "Cancer stem cell theory in gastrointestinal malignancies: recent progress and upcoming challenges", "abstract": ["A growing body of evidence supports the notion that malignant tumors are heterogeneous and contain diverse subpopulations of cells with unique characteristics including the ability to initiate a tumor and metastasize.", "This phenomenon might be explained by the so-called cancer stem cell (CSC) theory.", "Recent technological developments have allowed a deeper understanding and characterization of CSCs.", "Even though the application of this theory to hematopoietic malignancies and solid tumors holds promise for new ways to treat cancer, it also brings some skepticism.", "Efficacious therapeutic approaches targeting the CSC population should be explored to overcome therapeutic failure and improve patient outcomes.", "This review will focus on the intrinsic and extrinsic regulation of CSCs, as well as the development of therapeutic approaches against CSCs, predominantly focusing on gastrointestinal malignancies."], "structured": false}
{"doc_id": 20374609, "title": "In vitro splicing pathways of pre-mRNAs containing multiple intervening sequences?", "abstract": ["We analyzed the in vitro splicing pathways of three multi-intervening-sequence (IVS) pre-mRNAs: human beta-globin, which contains two IVSs (K. M. Lang, V. L. van Santen, and R. A. Spritz, EMBO J. 4:1991-1996, 1985); rat alpha-lactalbumin, which contains three IVSs; and murine interleukin-3, which contains four IVSs.", "We found that there are highly preferred pathways of IVS removal from these multi-IVS pre-mRNAs in vitro.", "The three IVSs of rat alpha-lactalbumin pre-mRNA were excised sequentially from 5' to 3'; in most molecules, IVS1 was removed first, followed by IVS2 and finally by IVS3.", "The splicing pathway of interleukin-3 pre-mRNA in vitro was more complex.", "The four IVSs were excised in a highly preferred temporal order, but the order was not strictly sequential or directional.", "In most molecules, IVS1 and IVS4 were removed first, either simultaneously or in rapid succession.", "Subsequently, IVS2 was excised, followed by IVS3.", "The observed splicing pathways apparently resulted from differences in lag times and maximum excision rates of the different IVSs.", "We detected no exon skipping during splicing of these transcripts in vitro.", "These observations have implication for proposed models of splice site selection."], "structured": false}
{"doc_id": 20375264, "title": "Automated genome sequence analysis and annotation.", "abstract": ["MOTIVATION Large-scale genome projects generate a rapidly increasing number of sequences, most of them biochemically uncharacterized.", "Research in bioinformatics contributes to the development of methods for the computational characterization of these sequences.", "However, the installation and application of these methods require experience and are time consuming.   \n", "RESULTS We present here an automatic system for preliminary functional annotation of protein sequences that has been applied to the analysis of sets of sequences from complete genomes, both to refine overall performance and to make new discoveries comparable to those made by human experts.", "The GeneQuiz system includes a Web-based browser that allows examination of the evidence leading to an automatic annotation and offers additional information, views of the results, and links to biological databases that complement the automatic analysis.", "System structure and operating principles concerning the use of multiple sequence databases, underlying sequence analysis tools, lexical analyses of database annotations and decision criteria for functional assignments are detailed.", "The system makes automatic quality assessments of results based on prior experience with the underlying sequence analysis tools; overall error rates in functional assignment are estimated at 2.5-5% for cases annotated with highest reliability ('clear' cases).", "Sources of over-interpretation of results are discussed with proposals for improvement.", "A conservative definition for reporting 'new findings' that takes account of database maturity is presented along with examples of possible kinds of discoveries (new function, family and superfamily) made by the system.", "System performance in relation to sequence database coverage, database dynamics and database search methods is analysed, demonstrating the inherent advantages of an integrated automatic approach using multiple databases and search methods applied in an objective and repeatable manner.   ", "AVAILABILITY The GeneQuiz system is publicly available for analysis of protein sequences through a Web server at http://www.sander.ebi.ac.", "uk/gqsrv/submit"], "structured": true}
{"doc_id": 20381484, "title": "GAPDH Mediates Nitrosylation of Nuclear Proteins", "abstract": ["S-nitrosylation of proteins by nitric oxide is a major mode of signalling in cells.", "S-nitrosylation can mediate the regulation of a range of proteins, including prominent nuclear proteins, such as HDAC2 (ref.", "2) and PARP1 (ref.", "3).", "The high reactivity of the nitric oxide group with protein thiols, but the selective nature of nitrosylation within the cell, implies the existence of targeting mechanisms.", "Specificity of nitric oxide signalling is often achieved by the binding of nitric oxide synthase (NOS) to target proteins, either directly or through scaffolding proteins such as PSD-95 (ref.", "5) and CAPON.", "As the three principal isoforms of NOS--neuronal NOS (nNOS), endothelial NOS (eNOS) and inducible NOS (iNOS)--are primarily non-nuclear, the mechanisms by which nuclear proteins are selectively nitrosylated have been elusive.", "Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is physiologically nitrosylated at its Cys 150 residue.", "Nitrosylated GAPDH (SNO-GAPDH) binds to Siah1, which possesses a nuclear localization signal, and is transported to the nucleus.", "Here, we show that SNO-GAPDH physiologically transnitrosylates nuclear proteins, including the deacetylating enzyme sirtuin-1 (SIRT1), histone deacetylase-2 (HDAC2) and DNA-activated protein kinase (DNA-PK).", "Our findings reveal a novel mechanism for targeted nitrosylation of nuclear proteins and suggest that protein-protein transfer of nitric oxide groups may be a general mechanism in cellular signal transduction."], "structured": false}
{"doc_id": 20388894, "title": "The transcription factor c-Maf controls the production of interleukin-4 but not other Th2 cytokines.", "abstract": ["IL-4 promotes the differentiation of naive CD4+ T cells into IL-4-producing T helper 2 (Th2) cells.", "Previous work provided suggestive but not conclusive evidence that the transcription factor c-Maf directed the tissue-specific expression of IL-4.", "It was not known whether c-Maf controlled the transcription of other Th2 cytokine genes.", "To elucidate the role of c-Maf in vivo, we examined cytokine production in mice lacking c-Maf (c-maf(-/-)).", "CD4+ T cells and NK T cells from c-maf(-/-) mice were markedly deficient in IL-4 production.", "However, the mice produced normal levels of IL-13 and IgE, and, when differentiated in the presence of exogenous IL-4, c-maf(-/-) T cells produced approximately normal levels of other Th2 cytokines.", "We conclude that c-Maf has a critical and selective function in IL-4 gene transcription in vivo."], "structured": false}
{"doc_id": 20399078, "title": "Genome-wide association of IL28B with response to pegylated interferon-\u03b1 and ribavirin therapy for chronic hepatitis C", "abstract": ["The recommended treatment for patients with chronic hepatitis C, pegylated interferon-\u03b1 (PEG-IFN-\u03b1) plus ribavirin (RBV), does not provide sustained virologic response (SVR) in all patients.", "We report a genome-wide association study (GWAS) to null virological response (NVR) in the treatment of patients with hepatitis C virus (HCV) genotype 1 within a Japanese population.", "We found two SNPs near the gene IL28B on chromosome 19 to be strongly associated with NVR (rs12980275, P = 1.93 \u00d7 10\u221213, and rs8099917, 3.11 \u00d7 10\u221215).", "We replicated these associations in an independent cohort (combined P values, 2.84 \u00d7 10\u221227 (OR = 17.7; 95% CI = 10.0\u201331.3) and 2.68 \u00d7 10\u221232 (OR = 27.1; 95% CI = 14.6\u201350.3), respectively).", "Compared to NVR, these SNPs were also associated with SVR (rs12980275, P = 3.99 \u00d7 10\u221224, and rs8099917, P = 1.11 \u00d7 10\u221227).", "In further fine mapping of the region, seven SNPs (rs8105790, rs11881222, rs8103142, rs28416813, rs4803219, rs8099917 and rs7248668) located in the IL28B region showed the most significant associations (P = 5.52 \u00d7 10\u221228\u20132.68 \u00d7 10\u221232; OR = 22.3\u201327.1).", "Real-time quantitative PCR assays in peripheral blood mononuclear cells showed lower IL28B expression levels in individuals carrying the minor alleles (P = 0.015)."], "structured": false}
{"doc_id": 20402596, "title": "The WUSCHEL-related homeobox gene WOX11 is required to activate shoot-borne crown root development in rice.", "abstract": ["In rice (Oryza sativa), the shoot-borne crown roots are the major root type and are initiated at lower stem nodes as part of normal plant development.", "However, the regulatory mechanism of crown root development is poorly understood.", "In this work, we show that a WUSCHEL-related Homeobox (WOX) gene, WOX11, is involved in the activation of crown root emergence and growth.", "WOX11 was found to be expressed in emerging crown roots and later in cell division regions of the root meristem.", "The expression could be induced by exogenous auxin or cytokinin.", "Loss-of-function mutation or downregulation of the gene reduced the number and the growth rate of crown roots, whereas overexpression of the gene induced precocious crown root growth and dramatically increased the root biomass by producing crown roots at the upper stem nodes and the base of florets.", "The expressions of auxin- and cytokinin-responsive genes were affected in WOX11 overexpression and RNA interference transgenic plants.", "Further analysis showed that WOX11 directly repressed RR2, a type-A cytokinin-responsive regulator gene that was found to be expressed in crown root primordia.", "The results suggest that WOX11 may be an integrator of auxin and cytokinin signaling that feeds into RR2 to regulate cell proliferation during crown root development."], "structured": false}
{"doc_id": 20418809, "title": "Inducible depletion of satellite cells in adult, sedentary mice impairs muscle regenerative capacity without affecting sarcopenia", "abstract": ["A key determinant of geriatric frailty is sarcopenia, the age-associated loss of skeletal muscle mass and strength.", "Although the etiology of sarcopenia is unknown, the correlation during aging between the loss of activity of satellite cells, which are endogenous muscle stem cells, and impaired muscle regenerative capacity has led to the hypothesis that the loss of satellite cell activity is also a cause of sarcopenia.", "We tested this hypothesis in male sedentary mice by experimentally depleting satellite cells in young adult animals to a degree sufficient to impair regeneration throughout the rest of their lives.", "A detailed analysis of multiple muscles harvested at various time points during aging in different cohorts of these mice showed that the muscles were of normal size, despite low regenerative capacity, but did have increased fibrosis.", "These results suggest that lifelong reduction of satellite cells neither accelerated nor exacerbated sarcopenia and that satellite cells did not contribute to the maintenance of muscle size or fiber type composition during aging, but that their loss may contribute to age-related muscle fibrosis."], "structured": false}
{"doc_id": 20419913, "title": "Reproductive clonality in protozoan pathogens--truth or artefact?", "abstract": ["The debate around the frequency and importance of genetic exchange in parasitic protozoa is now several decades old.", "Recently, fresh assertions have been made that predominant clonal evolution explains the population structures of several key protozoan pathogens.", "Here, we present an alternative perspective.", "On the assumption that much apparent clonality may be an artefact of inadequate sampling and study design, we review current research to define why sex might be so difficult to detect in protozoan parasite populations.", "In doing so, we contrast laboratory models of genetic exchange in parasitic protozoa with natural patterns of genetic diversity and consider the fitness advantage of sex at different evolutionary scales.", "We discuss approaches to improve the accuracy of efforts to characterize genetic exchange in the field.", "We also examine the implications of the first population genomic studies for the debate around sex and clonality in parasitic protozoa and discuss caveats for the future."], "structured": false}
{"doc_id": 20420780, "title": "The ACF1 complex is required for DNA double-strand break repair in human cells.", "abstract": ["DNA double-strand breaks (DSBs) are repaired via nonhomologous end-joining (NHEJ) or homologous recombination (HR), but cellular repair processes remain elusive.", "We show here that the ATP-dependent chromatin-remodeling factors, ACF1 and SNF2H, accumulate rapidly at DSBs and are required for DSB repair in human cells.", "If the expression of ACF1 or SNF2H is suppressed, cells become extremely sensitive to X-rays and chemical treatments producing DSBs, and DSBs remain unrepaired.", "ACF1 interacts directly with KU70 and is required for the accumulation of KU proteins at DSBs.", "The KU70/80 complex becomes physically more associated with the chromatin-remodeling factors of the CHRAC complex, which includes ACF1, SNF2H, CHRAC15, and CHRAC17, after treatments producing DSBs.", "Furthermore, the frequency of NHEJ as well as HR induced by DSBs in chromosomal DNA is significantly decreased in cells depleted of either of these factors.", "Thus, ACF1 and its complexes play important roles in DSBs repair."], "structured": false}
{"doc_id": 20422174, "title": "Findings to date from the ASCUS-LSIL Triage Study (ALTS).", "abstract": ["Controversy exists in the United States regarding the proper evaluation and management of low-grade squamous intraepithelial lesion (LSIL) and equivocal (atypical squamous cells of undetermined significance [ASCUS, now ASC-US]) cervical cytologic interpretations.", "To address this issue, the National Cancer Institute initiated the ASCUS-LSIL Triage Study (ALTS).", "ALTS is a multicenter, randomized clinical trial designed to evaluate 3 alternative methods of management, namely, immediate colposcopy, cytologic follow-up, and triage by human papillomavirus (HPV) DNA testing.", "This article summarizes the major findings of ALTS that have been published to date.", "Patients with ASCUS (n = 3488) or LSIL (n = 1572) were randomly assigned to research arms between November 1996 and December 1998, and were monitored for 2 years.", "The disease outcome was histologic cervical intraepithelial neoplasia (CIN) 3/cancer.", "The prevalence of oncogenic HPV was too high to permit effective triage of LSIL using HPV DNA testing by Hybrid Capture 2.", "However, for the women referred with a cytologic interpretation of ASCUS, HPV triage proved useful, with sensitivity equivalent to immediate colposcopy and a halving of colposcopic referrals.", "Among older women with ASCUS, HPV testing remained sensitive for detecting CIN 3 and cancer, but the referral percentage was dramatically lower compared to younger women.", "ALTS yielded insight into the performance of cytology and histopathology; experienced pathologists differed significantly in their interpretations of cervical abnormalities, especially histologic CIN 1 and cytologic ASCUS.", "Nonetheless, it was possible to distinguish a relatively uncommon type of ASCUS, equivocal for high-grade squamous intraepithelial lesion, that has a high positive predictive value for identifying women with underlying high-grade CIN.", "Many additional analyses are underway."], "structured": false}
{"doc_id": 20428155, "title": "Marine organisms as a source of new anticancer agents.", "abstract": ["Various active anticancer agents are derived from plants and terrestrial microorganisms.", "The isolation of C-nucleosides from the Caribbean sponge, Cryptotheca crypta, four decades ago, provided the basis for the synthesis of cytarabine, the first marine-derived anticancer agent to be developed for clinical use.", "Cytarabine is currently used in the routine treatment of patients with leukaemia and lymphoma.", "Gemcitabine, one of its fluorinated derivatives, has also been approved for use in patients with pancreatic, breast, bladder, and non-small-cell lung cancer.", "Over the past decade, several new experimental anticancer agents derived from marine sources have entered preclinical and clinical trials.", "This field has expanded significantly as a result of improvements in the technology of deep-sea collection, extraction, and large-scale production through aquaculture and synthesis.", "In this paper, examples of marine-derived experimental agents that are currently undergoing preclinical and early clinical evaluation are briefly discussed.", "A summary of the available information on the results of phase I and II trials of agents such as aplidine, ecteinascidin-734 (ET-734), dolastatin 10 and bryostatin 1 is also presented."], "structured": false}
{"doc_id": 20454006, "title": "A randomized, placebo-controlled trial of diindolylmethane for breast cancer biomarker modulation in patients taking tamoxifen", "abstract": ["Diindolylmethane (DIM), a bioactive metabolite of indole-3-carbinol found in cruciferous vegetables, has proposed cancer chemoprevention activity in the breast.", "There is limited evidence of clinically relevant activity of DIM or long-term safety data of its regular use.", "A randomized, double-blind, placebo-controlled trial was conducted to determine the activity and safety of combined use of BioResponse DIM\u00ae (BR-DIM) with tamoxifen.", "Women prescribed tamoxifen (n = 130) were randomly assigned oral BR-DIM at 150 mg twice daily or placebo, for 12 months.", "The primary study endpoint was change in urinary 2/16\u03b1-hydroxyestrone (2/16\u03b1-OHE1) ratio.", "Changes in 4-hydroxyestrone (4-OHE1), serum estrogens, sex hormone-binding globulin (SHBG), breast density, and tamoxifen metabolites were assessed.", "Ninety-eight women (51 placebo, 47 DIM) completed intervention; compliance with treatment was >91%.", "BR-DIM increased the 2/16\u03b1-OHE1 ratio (+3.2 [0.8, 8.4]) compared to placebo (\u22120.7 [\u22121.7, 0.8], P < 0.001).", "Serum SHBG increased with BR-DIM compared to placebo (+25 \u00b1 22 and +1.1 \u00b1 19 nmol/L, respectively).", "No change in breast density measured by mammography or by MRI was observed.", "Plasma tamoxifen metabolites (endoxifen, 4-OH tamoxifen, and N-desmethyl-tamoxifen) were reduced in women receiving BR-DIM versus placebo (P < 0.001).", "Minimal adverse events were reported and did not differ by treatment arm.", "In patients taking tamoxifen for breast cancer, daily BR-DIM promoted favorable changes in estrogen metabolism and circulating levels of SHBG.", "Further research is warranted to determine whether BR-DIM associated decreases in tamoxifen metabolites, including effects on endoxifen levels, attenuates the clinical benefit of tamoxifen.", "Trial Registration: ClinicalTrials.gov NCT01391689."], "structured": false}
{"doc_id": 20456030, "title": "Intracellular coenzymes as natural biomarkers for metabolic activities and mitochondrial anomalies.", "abstract": ["Mitochondria play a pivotal role in energy metabolism, programmed cell death and oxidative stress.", "Mutated mitochondrial DNA in diseased cells compromises the structure of key enzyme complexes and, therefore, mitochondrial function, which leads to a myriad of health-related conditions such as cancer, neurodegenerative diseases, diabetes and aging.", "Early detection of mitochondrial and metabolic anomalies is an essential step towards effective diagnoses and therapeutic intervention.", "Reduced nicotinamide adenine dinucleotide (NADH) and flavin adenine dinucleotide (FAD) play important roles in a wide range of cellular oxidation-reduction reactions.", "Importantly, NADH and FAD are naturally fluorescent, which allows noninvasive imaging of metabolic activities of living cells and tissues.", "Furthermore, NADH and FAD autofluorescence, which can be excited using distinct wavelengths for complementary imaging methods and is sensitive to protein binding and local environment.", "This article highlights recent developments concerning intracellular NADH and FAD as potential biomarkers for metabolic and mitochondrial activities."], "structured": false}
{"doc_id": 20457190, "title": "Biochemical differences in the alphabeta T cell receptor.CD3 surface complex between CD8+ and CD4+ human mature T lymphocytes.", "abstract": ["We have reported the existence of biochemical and conformational differences in the alphabeta T cell receptor (TCR) complex between CD4(+) and CD8(+) CD3gamma-deficient (gamma(-)) mature T cells.", "In the present study, we have furthered our understanding and extended the observations to primary T lymphocytes from normal (gamma(+)) individuals.", "Surface TCR.CD3 components from CD4(+) gamma(-) T cells, other than CD3gamma, were detectable and similar in size to CD4(+) gamma(+) controls.", "Their native TCR.CD3 complex was also similar to CD4(+) gamma(+) controls, except for an alphabeta(deltaepsilon)(2)zeta(2) instead of an alphabetagammaepsilondeltaepsilonzeta(2) stoichiometry.", "In contrast, the surface TCRalpha, TCRbeta, and CD3delta chains of CD8(+) gamma(-) T cells did not possess their usual sizes.", "Using confocal immunofluorescence, TCRalpha was hardly detectable in CD8(+) gamma(-) T cells.", "Blue native gels (BN-PAGE) demonstrated the existence of a heterogeneous population of TCR.CD3 in these cells.", "Using primary peripheral blood T lymphocytes from normal (gamma(+)) donors, we performed a broad epitopic scan.", "In contrast to all other TCR.CD3-specific monoclonal antibodies, RW2-8C8 stained CD8(+) better than it did CD4(+) T cells, and the difference was dependent on glycosylation of the TCR.CD3 complex but independent of T cell activation or differentiation.", "RW2-8C8 staining of CD8(+) T cells was shown to be more dependent on lipid raft integrity than that of CD4(+) T cells.", "Finally, immunoprecipitation studies on purified primary CD4(+) and CD8(+) T cells revealed the existence of TCR glycosylation differences between the two.", "Collectively, these results are consistent with the existence of conformational or topological lineage-specific differences in the TCR.CD3 from CD4(+) and CD8(+) wild type T cells.", "The differences may be relevant for cis interactions during antigen recognition and signal transduction."], "structured": false}
{"doc_id": 20459964, "title": "Circulating mitochondrial DNA in serum of patients with granulomatosis with polyangiitis.", "abstract": ["Neutrophil is a key cell in pathophysiology of granulomatosis with polyangiitis.", "Recently, neutrophil extracellular traps were described in this disease.", "Mitochondrial DNA is also released during traps formation.", "We measured circulating cell-free mitochondrial and genomic DNA in serum of patients with granulomatosis with polyangiitis.", "Subjects with the disease (14 active and 11 in remission stage) and 10 healthy controls were enrolled.", "Quantitative real-time polymerase chain reaction (PCR) was used to measure 79 base pairs (bp) and 230 bp mtDNA fragments.", "Alu repeats were quantified to evaluate abundance of nuclear DNA in serum at the presence of plasmid control.", "Both fragments of mtDNA (79 bp and 230 bp) and genomic DNA were elevated significantly in granulomatosis with polyangiitis compared to controls.", "Only the shorter 79 bp mtDNA correlated with active stage of granulomatosis with polyangiitis and clinical symptoms.", "A mechanism of extracellular release of mitochondrial DNA accompanies the active stage of the disease.", "Circulating mtDNA is extremely high in untreated patients.", "This suggests that biomarker properties of mtDNA are useful for monitoring of treatment."], "structured": false}
{"doc_id": 20460020, "title": "Estrogen receptor-alpha promotes alternative macrophage activation during cutaneous repair.", "abstract": ["Efficient local monocyte/macrophage recruitment is critical for tissue repair.", "Recruited macrophages are polarized toward classical (proinflammatory) or alternative (prohealing) activation in response to cytokines, with tight temporal regulation crucial for efficient wound repair.", "Estrogen acts as a potent anti-inflammatory regulator of cutaneous healing.", "However, an understanding of estrogen/estrogen receptor (ER) contribution to macrophage polarization and subsequent local effects on wound healing is lacking.", "Here we identify, to our knowledge previously unreported, a role whereby estrogen receptor \u03b1 (ER\u03b1) signaling preferentially polarizes macrophages from a range of sources to an alternative phenotype.", "Cell-specific ER ablation studies confirm an in vivo role for inflammatory cell ER\u03b1, but not ER\u03b2, in poor healing associated with an altered cytokine profile and fewer alternatively activated macrophages.", "Furthermore, we reveal intrinsic changes in ER\u03b1-deficient macrophages, which are unable to respond to alternative activation signals in vitro.", "Collectively, our data reveal that inflammatory cell-expressed ER\u03b1 promotes alternative macrophage polarization, which is beneficial for timely healing.", "Given the diverse physiological roles of ERs, these findings will likely be of relevance to many pathologies involving excessive inflammation."], "structured": false}
{"doc_id": 20471181, "title": "Disturbance in cerebral spinal fluid sphingolipid content is associated with memory impairment in subjects infected with the human immunodeficiency virus", "abstract": ["Despite widespread use of antiretroviral therapies to control replication of the human immunodeficiency virus (HIV), dysfunctions of cognition that are collectively termed HIV-associated neurocognitive disorders (HAND) still occur in approximately 50% of those infected by the virus.", "Currently there is not a biomarker that can identify HIV-infected people who are at risk for the development of HAND.", "Previous studies have identified particular sphingolipid species that are dysregulated in HAND, but the neurocognitive correlates of these biochemical findings are not currently understood.", "To address this question, we compared cerebrospinal fluid (CSF) levels of sphingomyelin, ceramide, and sterol species with performance on standard neurological tests designed to assess the function of multiple cognitive and motor domains in HIV-infected subjects.", "We found that sphingomyelin:ceramide ratios for acyl chain lengths of C16\u22360, C18\u22360, C22\u22360, and C24\u22360 were associated with worse performance on several indices of memory.", "The most striking finding was for the acyl chain of C18\u22360 that consistently associatedwith performance onmultiple tests of memory.", "These findings suggest that the sphingomyelin:ceramide ratio for C18\u22360 may be a reasonable surrogate marker for memory dysfunction in HIV-infected subjects."], "structured": false}
{"doc_id": 20473074, "title": "An observational study fluid balance and patient outcomes in the Randomized Evaluation of Normal vs. Augmented Level of Replacement Therapy trial.", "abstract": ["OBJECTIVE To examine associations between mean daily fluid balance during intensive care unit study enrollment and clinical outcomes in patients enrolled in the Randomized Evaluation of Normal vs. Augmented Level (RENAL) replacement therapy study.   \n", "DESIGN Statistical analysis of data from multicenter, randomized, controlled trials.   \n", "SETTING Thirty-five intensive care units in Australia and New Zealand.   \n", "PATIENTS Cohort of 1453 patients enrolled in the RENAL study.   \n", "INTERVENTIONS We analyzed the association between daily fluid balance on clinical outcomes using multivariable logistic regression, Cox proportional hazards, time-dependent analysis, and repeated measure analysis models.   \n", "MEASUREMENTS AND MAIN RESULTS During intensive care unit stay, mean daily fluid balance among survivors was -234 mL/day compared with +560 mL/day among nonsurvivors (p < .0001).", "Mean cumulative fluid balance over the same period was -1941 vs. +1755 mL (p = .0003).", "A negative mean daily fluid balance during study treatment was independently associated with a decreased risk of death at 90 days (odds ratio 0.318; 95% confidence interval 0.24-0.43; p < .000.1) and with increased survival time (p < .0001).", "In addition, a negative mean daily fluid balance was associated with significantly increased renal replacement-free days (p = .0017), intensive care unit-free days (p < .0001), and hospital-free days (p = .01).", "These findings were unaltered after the application of different statistical models.   \n", "CONCLUSIONS In the RENAL study, a negative mean daily fluid balance was consistently associated with improved clinical outcomes.", "Fluid balance may be a target for specific manipulation in future interventional trials of critically ill patients receiving renal replacement therapy."], "structured": true}
{"doc_id": 20491205, "title": "Prison health care: a review of the literature.", "abstract": ["The prison population is increasing and the health problems of prisoners are considerable.", "Prison is designed with punishment, correction and rehabilitation to the community in mind and these goals may conflict with the aims of health care.", "A literature review showed that the main issues in prison health care are mental health, substance abuse and communicable diseases.", "Women prisoners and older prisoners have needs which are distinct from other prisoners.", "Health promotion and the health of the community outside prisons are desirable aims of prison health care.", "The delivery of effective health care to prisoners is dependent upon partnership between health and prison services and telemedicine is one possible mode of delivery."], "structured": false}
{"doc_id": 20492020, "title": "A Brief History of Long-Term Potentiation", "abstract": ["Since the discovery of long-term potentiation (LTP) in 1973, thousands of papers have been published on this intriguing phenomenon, which provides a compelling cellular model for learning and memory.", "Although LTP has suffered considerable growing pains over the years, LTP has finally come of age.", "Here the rich history of LTP is reviewed.", "These are exciting times and the pace of discovery is remarkable."], "structured": false}
{"doc_id": 20501163, "title": "Tumor-Induced IL-6 Reprograms Host Metabolism to Suppress Anti-tumor Immunity", "abstract": ["In patients with cancer, the wasting syndrome, cachexia, is associated with caloric deficiency.", "Here, we describe tumor-induced alterations of the host metabolic response to caloric deficiency that cause intratumoral immune suppression.", "In pre-cachectic mice with transplanted colorectal cancer or autochthonous pancreatic ductal adenocarcinoma (PDA), we find that IL-6 reduces the hepatic ketogenic potential through suppression of PPARalpha, the transcriptional master regulator of ketogenesis.", "When these mice are challenged with caloric deficiency, the resulting relative hypoketonemia triggers a marked rise in glucocorticoid levels.", "Multiple intratumoral immune pathways are suppressed by this hormonal stress response.", "Moreover, administering corticosterone to elevate plasma corticosterone to a level that is lower than that occurring in cachectic mice abolishes the response of mouse PDA to an immunotherapy that has advanced to clinical trials.", "Therefore, tumor-induced IL-6 impairs the ketogenic response to reduced caloric intake, resulting in a systemic metabolic stress response that blocks anti-cancer immunotherapy."], "structured": false}
{"doc_id": 20524091, "title": "Chaperoning stem cells: a role for heat shock proteins in the modulation of stem cell self-renewal and differentiation?", "abstract": ["Self-renewal and differentiation of stem cells are tightly regulated processes subject to intrinsic and extrinsic signals.", "Molecular chaperones and co-chaperones, especially heat shock proteins (Hsp), are ubiquitous molecules involved in the modulation of protein conformational and complexation states.", "The function of Hsp, which are typically associated with stress response and tolerance, is well characterized in differentiated cells, while their role in stem cells remains unclear.", "It appears that embryonic stem cells exhibit increased stress tolerance and concomitant high levels of chaperone expression.", "This review critically evaluates stem cell research from a molecular chaperone perspective.", "Furthermore, we propose a model of chaperone-modulated self-renewal in mouse embryonic stem cells."], "structured": false}
{"doc_id": 20526907, "title": "How much alcohol and how often? Population based case-control study of alcohol consumption and risk of a major coronary event.", "abstract": ["OBJECTIVE To quantify the effects of quantity and frequency of alcohol consumption on risk of acute myocardial infarction and coronary death.   \n", "DESIGN Case-control study.   \n", "SETTING Lower Hunter region of New South Wales, Australia, 1983-94.   ", "SUBJECTS Men and women aged 35-69 years.   \n", "MAIN OUTCOME MEASURE Acute myocardial infarction or coronary death.   \n", "RESULTS Alcohol consumption patterns were compared between 11,511 cases of acute myocardial infarction or coronary death and 6077 controls randomly selected from the same study population.", "After adjusting for the effects of age, smoking, and medical history, men and women who consumed one or two drinks of alcohol on five or six days a week had a reduction in risk of a major coronary event compared with men and women who were non-drinkers (odds ratios: men 0.31 (95% confidence interval 0.22 to 0.45); women 0.33 (0.18 to 0.59)).", "A similar reduction in risk was found after excluding non-drinkers who were formerly moderate to heavy drinkers.", "An acute protective effect of alcohol consumption was also found for regular drinkers who consumed one or two drinks in the 24 hours preceding the onset of symptoms (odds ratios: men 0.74 (0.51 to 1.09); women 0.43 (0.20 to 0.95)).   \n", "CONCLUSIONS Frequency and quantity of alcohol consumption are important in assessing the risk of a major coronary event.", "Risk is lowest among men who report one to four drinks daily on five or six days a week and among women who report one or two drinks daily on five or six days a week."], "structured": true}
{"doc_id": 20532591, "title": "Tracking adipogenesis during white adipose tissue development, expansion and regeneration", "abstract": ["White adipose tissue displays high plasticity.", "We developed a system for the inducible, permanent labeling of mature adipocytes that we called the AdipoChaser mouse.", "We monitored adipogenesis during development, high-fat diet (HFD) feeding and cold exposure.", "During cold-induced 'browning' of subcutaneous fat, most 'beige' adipocytes stem from de novo\u2013differentiated adipocytes.", "During HFD feeding, epididymal fat initiates adipogenesis after 4 weeks, whereas subcutaneous fat undergoes hypertrophy for a period of up to 12 weeks.", "Gonadal fat develops postnatally, whereas subcutaneous fat develops between embryonic days 14 and 18.", "Our results highlight the extensive differences in adipogenic potential in various fat depots."], "structured": false}
{"doc_id": 20544428, "title": "Blockade of adrenoreceptors inhibits the splenic response to stroke.", "abstract": ["Recent studies have highlighted the involvement of the peripheral immune system in delayed cellular degeneration after stroke.", "In the permanent middle cerebral artery occlusion (MCAO) model of stroke, the spleen decreases in size.", "This reduction occurs through the release of splenic immune cells.", "Systemic treatment with human umbilical cord blood cells (HUCBC) 24 h post-stroke blocks the reduction in spleen size while significantly reducing infarct volume.", "Splenectomy 2 weeks prior to MCAO also reduces infarct volume, further demonstrating the detrimental role of this organ in stroke-induced neurodegeneration.", "Activation of the sympathetic nervous system after MCAO results in elevated catecholamine levels both at the level of the spleen, through direct splenic innervation, and throughout the systemic circulation upon release from the adrenal medulla.", "These catecholamines bind to splenic alpha and beta adrenoreceptors.", "This study examines whether catecholamines regulate the splenic response to stroke.", "Male Sprague-Dawley rats either underwent splenic denervation 2 weeks prior to MCAO or received injections of carvedilol, a pan adrenergic receptor blocker, prazosin, an alpha1 receptor blocker, or propranolol, a beta receptor blocker.", "Denervation was confirmed by reduced splenic expression of tyrosine hydroxylase.", "Denervation prior to MCAO did not alter infarct volume or spleen size.", "Propranolol treatment also had no effects on these outcomes.", "Treatment with either prazosin or carvedilol prevented the reduction in spleen size, yet only carvedilol significantly reduced infarct volume (p < 0.05).", "These results demonstrate that circulating blood borne catecholamines regulate the splenic response to stroke through the activation of both alpha and beta adrenergic receptors."], "structured": false}
{"doc_id": 20554003, "title": "Effects of Thiazolidinediones on Stroke Recovery: A Case-Matched Controlled Study", "abstract": ["Anti-inflammatory therapy decreases infarct size and enhances stroke recovery.", "Thiazolidinedione peroxisome proliferator-activated receptor (PPAR)gamma agonists have potent anti-inflammatory and insulin-sensitizing anti-diabetic actions.", "Thirty stroke patients with type 2 diabetes admitted for acute inpatient stroke rehabilitation receiving pioglitazone or rosiglitazone were matched for age, sex, initial FIMTM score and interval post-stroke with 30 stroke patients with type 2 diabetes not receiving thiazolidinediones.", "Relevant outcome variables were compared for both groups.", "The thiazolidinedione treated group showed significantly greater mean improvement in FIMTM score compared to control group (25.6 \u00b1 10.2 SD vs. 19.8 \u00b1 10.5, respectively, P = 0.015).", "There was no significant difference in length of rehabilitation hospital stay (24.2 \u00b1 7.6 vs. 25.1 \u00b1 7.4 days, P = 0.657) or final discharge destination (home/institution, 19/11 versus 17/13, P = 0.792).", "Use of thiazolidinediones was associated with enhanced functional recovery in stroke patients with type 2 diabetes."], "structured": false}
{"doc_id": 20568364, "title": "Crosstalk between tumor and endothelial cells promotes tumor angiogenesis by MAPK activation of Notch signaling.", "abstract": ["While significant progress has been made in understanding the induction of tumor vasculature by secreted angiogenic factors, little is known regarding contact-dependent signals that promote tumor angiogenesis.", "Here, we report that the Notch ligand Jagged1 induced by growth factors via mitogen-activating protein kinase (MAPK) in head and neck squamous cell carcinoma (HNSCC) cells triggered Notch activation in neighboring endothelial cells (ECs) and promoted capillary-like sprout formation.", "Jagged1-expressing HNSCC cells significantly enhanced neovascularization and tumor growth in vivo.", "Moreover, the level of Jagged1 was significantly correlated with tumor blood vessel content and associated with HNSCC development.", "Our results elucidate a novel mechanism by which the direct interplay between tumor cells and ECs promotes angiogenesis through MAPK and Notch signaling pathways."], "structured": false}
{"doc_id": 20585600, "title": "A Sequential splicing mechanism promotes selection of an optimal exon by repositioning a downstream 5' splice site in preprotachykinin pre-mRNA.", "abstract": ["To explore the structural basis of alternative splicing, we have analyzed the splicing of pre-mRNAs containing an optional exon, E4, from the preprotachykinin gene.", "This gene encodes substance P and related tachykinin peptides by alternative splicing of a common pre-mRNA.", "We have shown that alternative splicing of preprotachykinin pre-mRNA occurs by preferential skipping of optional E4.", "The competing mechanism that incorporates E4 into the final spliced RNA is constrained by an initial block to splicing of the immediate upstream intervening sequence (IVS), IVS3.", "This block is relieved by sequential splicing, in which the immediate downstream IVS4 is removed first.", "The structural change resulting from the first splicing event is directly responsible for activation of IVS3 splicing.", "This structural rearrangement replaces IVS4 sequences with E5 and its adjacent IVS5 sequences.", "To determine how this structural change promoted IVS3 splicing, we asked what structural change(s) would restore activity of IVS3 splicing-defective mutants.", "The most significant effect was observed by a 2-nucleotide substitution that converted the 5' splice site of E4 to an exact consensus match, GUAAGU.", "Exon 5 sequences alone were found not to promote splicing when present in one or multiple copies.", "However, when a 15-nucleotide segment of IVS5 containing GUAAGU was inserted into a splicing-defective mutant just downstream of the hybrid exon segment E4E5, splicing activity was recovered.", "Curiously, the 72-nucleotide L2 exon of adenovirus, without its associated 5' splice site, activates splicing when juxtaposed to E4.", "Models for the activation of splicing by an RNA structural change are discussed."], "structured": false}
{"doc_id": 20602517, "title": "Melatonin and the circadian regulation of sleep initiation, consolidation, structure, and the sleep EEG.", "abstract": ["The endogenous circadian rhythm of melatonin, driven by the suprachiasmatic nucleus, exhibits a close association with the endogenous circadian component of the sleep propensity rhythm and the endogenous circadian component of the variation in electroencephalogram (EEG) oscillations such as sleep spindles and slow waves.", "This association is maintained even when the sleep-wake cycle is desynchronized from the endogenous circadian rhythm of melatonin.", "Administration of melatonin during the day increases daytime sleep propensity as indexed by both the latency to sleep onset and sleep consolidation.", "The EEG during daytime sleep after melatonin administration exhibits characteristics reminiscent of the nocturnal sleep EEG, that is, increased sleep spindle activity and reduced slow-wave sleep and slow-wave activity, as detected by quantitative EEG analysis.", "Administration of higher doses of melatonin (5 mg or more) prior to nocturnal sleep results in an increase in rapid eye movement (REM) sleep.", "These data demonstrate that melatonin exerts effects on the main characteristics of human sleep, that is, latency to sleep onset, sleep consolidation, slow waves, sleep spindles, and REM sleep.", "There is a need for further studies using physiological doses and delivery systems that generate physiological plasma melatonin profiles to firmly establish the role of the endogenous circadian rhythm of melatonin in the circadian regulation of sleep."], "structured": false}
{"doc_id": 20606520, "title": "Long-term survival, quality of life, and quality-adjusted life-years among critically ill elderly patients.", "abstract": ["OBJECTIVES To assess mortality, quality of life (QOL), and quality-adjusted life-years (QALYs) for critically ill elderly patients.   \n", "DESIGN Cross-sectional survey.   \n", "SETTING A ten-bed medical-surgical intensive care unit (ICU) in a tertiary care university hospital.   \n", "PATIENTS The study group included 882 elderly patients (> or =65 yrs of age) and 1,827 controls (<65 yrs of age) treated during the period of 1995 to 2000.   \n", "INTERVENTION None.   \n", "MEASUREMENTS AND MAIN RESULTS Mortality was assessed during the ICU and hospital stays, and 12, 24, and 36 months after ICU discharge.", "The cumulative 3-yr mortality rate among the elderly (57%) was higher (p < .05) than that among the controls (40%).", "The majority (66%) of the elderly nonsurvivors died within 1 month after intensive care discharge.", "All elderly patients with day-1 Sequential Organ Failure (SOFA) scores >15 died during the ICU stay.", "QOL was assessed with EQ-5D and RAND-36 measures from 10 months to 7 yrs after discharge.", "The majority (88%) of the elderly survivors assessed their present health state as good or satisfactory; 66% found it to be similar or better than 12 months earlier, and 48% similar or better than their preadmission state.", "QOL measures by RAND-36 revealed that aging decreased their competencies most in physical functioning, physical role limitations, and vitality, but the elderly had better values in mental health than the controls.", "However, QALYs of the elderly respondents were 21% to 35% lower than the mean QALY minus 2 sd units of the age- and gender-adjusted general population.   \n", "CONCLUSIONS High age alone is not a valid reason to refuse intensive care, but the benefits perceived by intensive care seem to decrease with aging, if reflected as QALYs.", "However, 97% of the elderly survivors lived at home and 88% of them considered their QOL satisfactory or good after hospital discharge.", "Therefore, more reliable information on the outcome for the elderly is clearly needed."], "structured": true}
{"doc_id": 20608982, "title": "Recent developments and complexities in neutrophil transmigration.", "abstract": ["PURPOSE OF REVIEW As the migration of neutrophils from blood to inflamed tissues is an essential component of innate immunity and a key contributing factor to the pathogenesis of inflammatory disorders, this aspect of leukocyte biology continues to be a highly dynamic field of research.", "This review summarizes recent findings in this area, focusing on the mechanisms that mediate neutrophil transmigration, an area where significant progress has been made.   ", "RECENT FINDINGS The topics to be covered will include responses that are prerequisite to neutrophil migration through venular walls, such as leukocyte luminal crawling and cellular and molecular changes in leukocytes and endothelial cells (e.g. formation of protrusions) that collectively support leukocyte transendothelial cell migration.", "Advances in both paracellular and transcellular neutrophil migration through endothelial cells will be discussed, addressing the associated roles and regulation of expression of endothelial cell luminal and junctional adhesion molecules.", "Beyond the endothelium, migration through the vascular pericyte coverage and basement membrane will be reviewed.   ", "SUMMARY The unquestionable role of neutrophils in the development and progression of inflammatory conditions suggests that a better understanding of the tissue-specific and stimulus-specific mechanisms that mediate this response may identify novel pathways that could be exploited for the development of more specific anti-inflammatory interventions."], "structured": true}
{"doc_id": 20610390, "title": "Exploring the epidemiological characteristics of cancers of unknown primary site in an Australian population: implications for research and clinical care.", "abstract": ["OBJECTIVES To investigate incidence, mortality and case survival trends for cancer of unknown primary site (CUP) and consider clinical implications.   \n", "METHOD South Australian Cancer Registry data were used to calculate age-standardised incidence and mortality rates from 1977 to 2004.", "Disease-specific survivals, socio-demographic, histological and secular predictors of CUP, compared with cancers of known primary site, and of CUP histological types, using multivariable logistic regression were investigated.   \n", "RESULTS Incidence and mortality rates increased approximately 60% between 1977--80 and 1981--84.", "Rates peaked in 1993--96.", "Male to female incidence and mortality rate ratios approximated 1.3:1.", "Incidence and mortality rates increased with age.", "The odds of unspecified histological type, compared with the more common adenocarcinomas, were higher for males than females, non-metropolitan residents, low socio-economic areas, and for 1977--88 than subsequent diagnostic periods.", "CUP represented a higher proportion of cancers in Indigenous patients.", "Case survival was 7% at 10 years from diagnosis.", "Factors predictive of lower case survival included older age, male sex, Indigenous status, lower socio-economic status, and unspecified histology type.   \n", "CONCLUSION Results point to poor CUP outcomes, but with a modest improvement in survival.", "The study identifies socio-demographic groups at elevated risk of CUP and of worse treatment outcomes where increased research and clinical attention are required."], "structured": true}
{"doc_id": 20610557, "title": "Alkylating agent melphalan augments the efficacy of adoptive immunotherapy using tumor-specific CD4+ T cells.", "abstract": ["In recent years, the immune-potentiating effects of some widely used chemotherapeutic agents have been increasingly appreciated.", "This provides a rationale for combining conventional chemotherapy with immunotherapy strategies to achieve durable therapeutic benefits.", "Previous studies have implicated the immunomodulatory effects of melphalan, an alkylating agent commonly used to treat multiple myeloma, but the underlying mechanisms remain obscure.", "In the present study, we investigated the impact of melphalan on endogenous immune cells as well as adoptively transferred tumor-specific CD4(+) T cells in tumor-bearing mice.", "We showed that melphalan treatment resulted in a rapid burst of inflammatory cytokines and chemokines during the cellular recovery phase after melphalan-induced myelodepletion and leukodepletion.", "After melphalan treatment, tumor cells exhibited characteristics of immunogenic cell death, including membrane translocation of the endoplasmic reticulum-resident calreticulin and extracellular release of high-mobility group box 1.", "Additionally, there was enhanced tumor Ag uptake by dendritic cells in the tumor-draining lymph node.", "Consistent with these immunomodulatory effects, melphalan treatment of tumor-bearing mice led to the activation of the endogenous CD8(+) T cells and, more importantly, effectively drove the clonal expansion and effector differentiation of adoptively transferred tumor-specific CD4(+) T cells.", "Notably, the combination of melphalan and CD4(+) T cell adoptive cell therapy was more efficacious than either treatment alone in prolonging the survival of mice with advanced B cell lymphomas or colorectal tumors.", "These findings provide mechanistic insights into melphalan's immunostimulatory effects and demonstrate the therapeutic potential of combining melphalan with adoptive cell therapy utilizing antitumor CD4(+) T cells."], "structured": false}
{"doc_id": 20611846, "title": "Influence of cigarette smoking on inhaled corticosteroid treatment in mild asthma.", "abstract": ["BACKGROUND Although inhaled corticosteroids have an established role in the treatment of asthma, studies have tended to concentrate on non-smokers and little is known about the possible effect of cigarette smoking on the efficacy of treatment with inhaled steroids in asthma.", "A study was undertaken to investigate the effect of active cigarette smoking on responses to treatment with inhaled corticosteroids in patients with mild asthma.   \n", "METHODS The effect of treatment with inhaled fluticasone propionate (1000 microg daily) or placebo for 3 weeks was studied in a double blind, prospective, randomised, placebo controlled study of 38 steroid na\u00efve adult asthmatic patients (21 non-smokers).", "Efficacy was assessed using morning and evening peak expiratory flow (PEF) readings, spirometric parameters, bronchial hyperreactivity, and sputum eosinophil counts.", "Comparison was made between responses to treatment in non-smoking and smoking asthmatic patients.   \n", "RESULTS There was a significantly greater increase in mean morning PEF in non-smokers than in smokers following inhaled fluticasone (27 l/min v -5 l/min).", "Non-smokers had a statistically significant increase in mean morning PEF (27 l/min), mean forced expiratory volume in 1 second (0.17 l), and geometric mean PC20 (2.6 doubling doses), and a significant decrease in the proportion of sputum eosinophils (-1.75%) after fluticasone compared with placebo.", "No significant changes were observed in the smoking asthmatic patients for any of these parameters.   \n", "CONCLUSIONS Active cigarette smoking impairs the efficacy of short term inhaled corticosteroid treatment in mild asthma.", "This finding has important implications for the management of patients with mild asthma who smoke."], "structured": true}
{"doc_id": 20620012, "title": "Hitting the target: emerging technologies in the search for kinase substrates.", "abstract": ["Through phosphorylation, protein kinases can alter the activity, localization, protein association, and stability of their targets.", "Despite the importance to our understanding of all aspects of cell biology, progress toward identifying bona fide substrates of specific protein kinases has been slow.", "Traditionally used techniques to identify true kinase substrates, such as genetics, yeast two-hybrid screens, and biochemical purification, are often laborious and unreliable.", "However, several new approaches have recently been developed and used successfully to identify genuine in vivo substrates of certain protein kinases.", "These methods include screening for phosphorylation of proteins from phage expression libraries, peptide library screens to determine optimal motifs favored by specific kinases, the use of phospho-motif antibodies, and an approach that uses structurally altered kinases and allele-specific adenosine triphosphate analogs and kinase inhibitors.", "We describe these approaches and discuss their utility and inherent caveats."], "structured": false}
{"doc_id": 20630805, "title": "Histone phosphorylation: a chromatin modification involved in diverse nuclear events.", "abstract": ["Histone posttranslational modifications are key components of diverse processes that modulate chromatin structure.", "These marks function as signals during various chromatin-based events, and act as platforms for recruitment, assembly or retention of chromatin-associated factors.", "The best-known function of histone phosphorylation takes place during cellular response to DNA damage, when phosphorylated histone H2A(X) demarcates large chromatin domains around the site of DNA breakage.", "However, multiple studies have also shown that histone phosphorylation plays crucial roles in chromatin remodeling linked to other nuclear processes.", "In this review, we summarize the current knowledge of histone phosphorylation and describe the many kinases and phosphatases that regulate it.", "We discuss the key roles played by this histone mark in DNA repair, transcription and chromatin compaction during cell division and apoptosis.", "Additionally, we describe the intricate crosstalk that occurs between phosphorylation and other histone modifications and allows for sophisticated control over the chromatin remodeling processes."], "structured": false}
{"doc_id": 20645335, "title": "Neurodevelopmental Outcome After a Single Course of Antenatal Steroids in Children Born Preterm: A Systematic Review and Meta-analysis.", "abstract": ["OBJECTIVE To systematically review and integrate data on the neurodevelopmental outcome of children after administration of a single course of antenatal corticosteroids for threatened preterm labor.   \n", "DATA SOURCES MEDLINE, Scopus, CENTRAL, and www.clinicaltrials.gov (inception to August 2014) using combinations of the terms \"prenatal,\" \"antenatal,\" \"cortico*,\" \"*steroid*,\" \"betamethasone,\" \"dexamethasone,\" \"neurodevelopment*,\" \"*development*,\" and \"follow-up.", "\"", "We perused the references of the retrieved articles.   \n", "METHODS OF STUDY SELECTION We included randomized and nonrandomized trials reporting on the neurodevelopmental outcomes of children whose mothers were administered a single course of betamethasone or dexamethasone antenatally for threatened preterm birth as opposed to placebo or no treatment.   ", "TABULATION, INTEGRATION, AND RESULTS Summary risk ratio (RR) was calculated for dichotomous data; standardized mean difference was calculated for trials that measured the same outcome but used different methods.", "Heterogeneity was assessed using the I statistic.", "Sensitivity and subgroup analyses were planned according to study design, specific steroid, and mean gestational age at birth.", "A single course of antenatal corticosteroids was associated with reduced risk for cerebral palsy (seven studies; treated: 390 of 5,199, untreated: 146 of 1,379; RR 0.678, 95% confidence interval [CI] 0.564-0.815), psychomotor development index less than 70 (two studies; treated: 783 of 3,049, untreated: 258 of 969; RR 0.829, 95% CI 0.737-0.933), and severe disability (five studies; treated: 1,567 of 4,840, untreated: 475 of 1,211; RR 0.787, 95% CI 0.729-0.850).", "Steroid treatment increased the rates of intact survival (six studies; treated: 1,082 of 2,013, untreated: 273 of 561; RR 1.186, 95% CI 1.056-1.332).", "Betamethasone was found to significantly decrease the risk for severe disability and increase the rate of intact survival.", "Dexamethasone increased the rate of intact survival; however, data for dexametasone and the other planned subgroup analyses were limited (fewer than 1,000 children at most).", "The major limitations involved inclusion of nonrandomized studies and scarcity of data on finer neurodevelopmental outcomes.   \n", "CONCLUSION A single course of antenatal corticosteroids in women at high risk for preterm birth appears to improve most neurodevelopmental outcomes in offspring born before 34 weeks of gestation."], "structured": true}
{"doc_id": 20645538, "title": "Prognostic impact of minimal pleural effusion in non-small-cell lung cancer.", "abstract": ["PURPOSE Minimal (< 10 mm thick) pleural effusion (PE) may represent an early phase of malignant PE, but its clinical relevance has rarely been studied.", "Therefore, we examined the proportion of minimal PE in patients with non-small-cell lung cancer (NSCLC) and its impact on survival.", "We also considered possible accumulation mechanisms in our data set.   \n", "PATIENTS AND METHODS On the basis of PE status from chest computed tomography scans at diagnosis, 2,061 patients were classified into three groups: no PE, minimal PE, and malignant PE.", "Twenty-one variables associated with four factors-patient, stage migration, tumor, and treatment-were investigated for correlation with survival.   \n", "RESULTS Minimal PE presented in 272 patients (13.2%).", "Of 2,061 patients, the proportion of each stage was the following: 5.2% stage I, 10.9% stage II, 13.2% stage IIIA, 23.8% stage IIIB, and 13.9% stage IV.", "Minimal PE correlated significantly with shorter survival time than did no PE (median survival time, 7.7 v 17.7 months; log-rank P < .001), even after full adjustment with all variables (adjusted hazard ratio, 1.40; 95% CI, 1.21 to 1.62).", "Prognostic impact of minimal PE was higher in early versus advanced stages (Pinteraction = .001).", "In 237 patients (87.8%) with minimal PE, pleural invasion or attachment as a direct mechanism was observed, and it was an independent factor predicting worse survival (P = .03).   \n", "CONCLUSION Minimal PE is a commonly encountered clinical concern in staging NSCLCs.", "Its presence is an important prognostic factor of worse survival, especially in early-stage disease."], "structured": true}
{"doc_id": 20646904, "title": "Fusion proteins for versatile antigen targeting to cell surface receptors reveal differential capacity to prime immune responses.", "abstract": ["Targeting of proteins to APCs is an attractive strategy for eliciting adaptive immune responses.", "However, the relationship between the choice of the targeted receptor and the quality and quantity of responses remains poorly understood.", "We describe a strategy for expression of Ags including hydrophobic proteins as soluble fusion proteins that are optimized for proteasome-dependent MHC class I-restricted cross-presentation and form stable complexes with a wide variety of targeting Abs.", "Upon s.c.", "immunization, these complexes were initially taken up by CD169+ lymph node subcapsular sinus macrophages.", "In the OVA model system, receptor-targeted antigenic complexes primed specific T and B cell responses in vitro and in vivo at least 100-fold more efficiently than Ag alone.", "Comparison of 10 targeting receptors allowed us to establish a ranking with respect to priming of CD8+ T cell responses and demonstrated striking differences with respect to the relative efficacy of CD8+ and CD4+ T cell subset and B cell priming.", "The described fusion proteins should help in developing optimized strategies for targeted delivery of protein Ags in the context of tolerization or vaccination."], "structured": false}
{"doc_id": 20649327, "title": "A sequential model for peptide binding and transport by the transporters associated with antigen processing.", "abstract": ["The TAP proteins translocate antigenic peptides into the endoplasmic reticulum.", "Investigation of the specificity of this process has been complicated by TAP-independent factors that influence the amount of peptide that accumulates in the ER in transport assays.", "We have developed an overexpression system in which binding of peptides to the TAP substrate-binding site and peptide transport by TAP can be quantified separately.", "Efficiency of peptide accumulation in the ER parallels affinity for the TAP substrate-binding site, but can be modified by interaction with the glycosylation system within the ER and, probably, peptide efflux.", "Random peptide mixtures of 9-16 aa display significantly higher affinity for the binding site than mixtures of shorter or longer peptides.", "Peptide binds to TAP heteromers in the absence of ATP and is released by the binding of ATP, suggesting a model for TAP function."], "structured": false}
{"doc_id": 20649735, "title": "Outcome of repeated radiosurgery for recurrent metastatic brain tumors.", "abstract": ["OBJECTIVE We investigated the outcome of repeated gamma knife radiosurgery (GKS) for local or remote recurrence after initial radiosurgery.   ", "MATERIAL AND METHODS We retrospectively reviewed 204 patients who were treated with GKS.", "Among them 43 patients (21%) underwent GKS more than once.", "The second GKS was given for recurrence at the previously treated sites in 16 patients, new lesions at remote sites in 13, and both local recurrence and new lesions in 14.   \n", "RESULTS The median survival from the first GKS was 36 (7-190) weeks in all patients and 68 (16-156) weeks in 43 patients with repeated GKS.", "The median time from the first GKS to the second was 37 weeks.", "The median survival from the second radiosurgical intervention was 32 (7-132) weeks.", "Local control rate at 6 months after salvage GKS was 90.7%.", "RPA class was the commonly dominant prognostic factor in both initial and salvage GKS.   \n", "CONCLUSION Recurrence is common for patients with metastatic brain tumors after initial radiosurgery.", "Local control and survival time after salvage treatment are comparable with those after initial radiosurgery.", "GKS as a salvage treatment may provide additional survival benefit in selected patients."], "structured": true}
{"doc_id": 20659283, "title": "Human CYP3A4 and murine Cyp3A11 are regulated by equol and genistein via the pregnane X receptor in a species-specific manner.", "abstract": ["Pregnane X receptor (PXR) is an important component of the body's adaptive defense system responsible for the elimination of various toxic xenobiotics.", "PXR activation by endogenous and exogenous chemicals, including steroids, antibiotics, bile acids, and herbal compounds, results in induction of drug metabolism.", "We investigated the ability of the isoflavones genistein, daidzein, and the daidzein metabolite equol to activate human and mouse PXR in vitro using cell-based transient transfection studies and primary hepatocytes and in vivo in a mouse model.", "In transient transfection assays, the isoflavones genistein and daidzein activate full-length, wild-type mouse PXR, but not a mutant form, with genistein being the most potent.", "In contrast, equol was a more potent activator of human PXR than genistein or daidzein.", "In a mammalian 2-hybrid assay, isoflavones induced recruitment of the coactivator steroid receptor coactivator 1 to PXR.", "When tested against the native human Cytochrome P450 3A4 (CYP3A4) promoter, equol was the more potent activator and treatment of human hepatocytes with equol increased CYP3A4 mRNA and immunoreactive protein expression.", "Treatment of wild-type, but not PXR(-/-), mouse hepatocytes showed that genistein and daidzein induced the expression of Cytochrome P450 3A11 (Cyp3A11) mRNA, whereas equol had no effect.", "Cyp3A11 mRNA was also induced in vivo in mice fed a soy protein-containing diet.", "The results presented herein demonstrate that there is a species-specific difference in the activation of PXR by isoflavones and equol."], "structured": false}
{"doc_id": 20672596, "title": "Metabolism of glucose, glutamine, long-chain fatty acids and ketone bodies by murine macrophages.", "abstract": ["Maximum activities of some key enzymes of metabolism were studied in elicited (inflammatory) macrophages of the mouse and lymph-node lymphocytes of the rat.", "The activity of hexokinase in the macrophage is very high, as high as that in any other major tissue of the body, and higher than that of phosphorylase or 6-phosphofructokinase, suggesting that glucose is a more important fuel than glycogen and that the pentose phosphate pathway is also important in these cells.", "The latter suggestion is supported by the high activities of both glucose-6-phosphate dehydrogenase and 6-phosphogluconate dehydrogenase.", "However, the rate of glucose utilization by 'resting' macrophages incubated in vitro is less than the 10% of the activity of 6-phosphofructokinase: this suggests that the rate of glycolysis is increased dramatically during phagocytosis or increased secretory activity.", "The macrophages possess higher activities of citrate synthase and oxoglutarate dehydrogenase than do lymphocytes, suggesting that the tricarboxylic acid cycle may be important in energy generation in these cells.", "The activity of 3-oxoacid CoA-transferase is higher in the macrophage, but that of 3-hydroxybutyrate dehydrogenase is very much lower than those in the lymphocytes.", "The activity of carnitine palmitoyltransferase is higher in macrophages, suggesting that fatty acids as well as acetoacetate could provide acetyl-CoA as substrate for the tricarboxylic acid cycle.", "No detectable rate of acetoacetate or 3-hydroxybutyrate utilization was observed during incubation of resting macrophages, but that of oleate was 1.0 nmol/h per mg of protein or about 2.2% of the activity of palmitoyltransferase.", "The activity of glutaminase is about 4-fold higher in macrophages than in lymphocytes, which suggests that the rate of glutamine utilization could be very high.", "The rate of utilization of glutamine by resting incubated macrophages was similar to that reported for rat lymphocytes, but was considerably lower than the activity of glutaminase."], "structured": false}
{"doc_id": 20675284, "title": "TGF-beta inhibition of endothelial cell proliferation: alteration of EGF binding and EGF-induced growth-regulatory (competence) gene expression.", "abstract": ["Transforming growth factor-beta (TGF-beta) inhibits the growth of endothelial cells derived from various sources, including human umbilical vein, bovine aorta, and rat heart.", "Long-term exposure of rat heart endothelial cells to TGF-beta also induces dramatic changes in morphology that are characteristic of senescent cells.", "These changes are accompanied by a decrease in the number of high-affinity receptors for epidermal growth factor (EGF), with almost no change in total receptor number.", "Additionally, the EGF-induced expression of specific competence genes (c-myc, JE, KC) is decreased, whereas the induction of c-fos gene expression by EGF is unaltered by TGF-beta treatment.", "These data suggest that growth inhibitors such as TGF-beta may act by altering the cell's response to growth-stimulatory factors."], "structured": false}
{"doc_id": 20690388, "title": "Human NK cells in acute myeloid leukaemia patients: analysis of NK cell-activating receptors and their ligands", "abstract": ["Natural killer (NK) cell activation is strictly regulated to ensure that healthy cells are preserved, but tumour-transformed or virus-infected cells are recognized and eliminated.", "To carry out this selective killing, NK cells have an ample repertoire of receptors on their surface.", "Signalling by inhibitory and activating receptors by interaction with their ligands will determine whether the NK cell becomes activated and kills the target cell.", "Here, we show reduced expression of NKp46, NKp30, DNAM-1, CD244 and CD94/NKG2C activating receptors on NK cells from acute myeloid leukaemia patients.", "This reduction may be induced by chronic exposure to their ligands on leukaemic blasts.", "The analysis of ligands for NK cell-activating receptors showed that leukaemic blasts from the majority of patients express ligands for NK cell-activating receptors.", "DNAM-1 ligands are frequently expressed on blasts, whereas the expression of the NKG2D ligand MICA/B is found in half of the patients and CD48, a ligand for CD244, in only one-fourth of the patients.", "The decreased expression of NK cell-activating receptors and/or the heterogeneous expression of ligands for major receptors on leukaemic blasts can lead to an inadequate tumour immunosurveillance by NK cells.", "A better knowledge of the activating receptor repertoire on NK cells and their putative ligands on blasts together with the possibility to modulate their expression will open new possibilities for the use of NK cells in immunotherapy against leukaemia."], "structured": false}
{"doc_id": 20696397, "title": "Production of interleukin-6 in contracting human skeletal muscles can account for the exercise-induced increase in plasma interleukin-6.", "abstract": ["1.", "Plasma interleukin (IL)-6 concentration is increased with exercise and it has been demonstrated that contracting muscles can produce IL-The question addressed in the present study was whether the IL-6 production by contracting skeletal muscle is of such a magnitude that it can account for the IL-6 accumulating in the blood.", "2.", "This was studied in six healthy males, who performed one-legged dynamic knee extensor exercise for 5 h at 25 W, which represented 40% of peak power output (Wmax).", "Arterial-femoral venous (a-fv) differences over the exercising and the resting leg were obtained before and every hour during the exercise.", "Leg blood flow was measured in parallel by the ultrasound Doppler technique.", "IL-6 was measured by enzyme-linked immunosorbent assay (ELISA).", "3.", "Arterial plasma concentrations for IL-6 increased 19-fold compared to rest.", "The a-fv difference for IL-6 over the exercising leg followed the same pattern as did the net IL-6 release.", "Over the resting leg, there was no significant a-fv difference or net IL-6 release.", "The work was produced by 2.5 kg of active muscle, which means that during the last 2 h of exercise, the median IL-6 production was 6.8 ng min-1 (kg active muscle)-1 (range, 3.96-9.69 ng min-1 kg-1).", "4.", "The net IL-6 release from the muscle over the last 2 h of exercise was 17-fold higher than the elevation in arterial IL-6 concentration and at 5 h of exercise the net release during 1 min was half of the IL-6 content in the plasma.", "This indicates a very high turnover of IL-6 during muscular exercise.", "We suggest that IL-6 produced by skeletal contracting muscle contributes to the maintenance of glucose homeostasis during prolonged exercise."], "structured": false}
{"doc_id": 20697217, "title": "Symptoms of hypoglycemia in children with IDDM.", "abstract": ["OBJECTIVE To examine the symptoms of hypoglycemia in children with insulin-dependent diabetes, from the perspective both of the child and of the child's parents, and to compare the symptom reporting of the diabetic children with that of adult diabetic patients.   ", "RESEARCH DESIGN AND METHODS Interviews were conducted with 100 parents and 43 of their children.", "The frequency and intensity of symptoms of hypoglycemia were documented using a structured interview and classified into groups using Principal Components Analysis (PCA).   \n", "RESULTS Diabetic children and their parents showed close agreement concerning the relative frequency and the intensity of symptoms reported.", "PCA of the symptom reports showed that diabetic children and their parents identified the same distinct subgroups of hypoglycemia-related symptoms: behavioral disturbance and autonomic-neuroglycopenic subgroups.   \n", "CONCLUSIONS Hypoglycemic symptoms in children with diabetes clearly differ from those experienced by insulin-treated adults and, in particular, include behavioral changes as primary features of a low blood glucose.", "These observations have important implications for parental education on hypoglycemia."], "structured": true}
{"doc_id": 20707861, "title": "Comparative Protein Structure Modeling Using MODELLER.", "abstract": ["Comparative protein structure modeling predicts the three-dimensional structure of a given protein sequence (target) based primarily on its alignment to one or more proteins of known structure (templates).", "The prediction process consists of fold assignment, target-template alignment, model building, and model evaluation.", "This unit describes how to calculate comparative models using the program MODELLER and how to use the ModBase database of such models, and discusses all four steps of comparative modeling, frequently observed errors, and some applications.", "Modeling lactate dehydrogenase from Trichomonas vaginalis (TvLDH) is described as an example.", "The download and installation of the MODELLER software is also described.", "\u00a9 2016 by John Wiley & Sons, Inc."], "structured": false}
{"doc_id": 20722510, "title": "IL-6 as a keystone cytokine in health and disease", "abstract": ["Interleukin 6 (IL-6) has a broad effect on cells of the immune system and those not of the immune system and often displays hormone-like characteristics that affect homeostatic processes.", "IL-6 has context-dependent pro- and anti-inflammatory properties and is now regarded as a prominent target for clinical intervention.", "However, the signaling cassette that controls the activity of IL-6 is complicated, and distinct intervention strategies can inhibit this pathway.", "Clinical experience with antagonists of IL-6 has raised new questions about how and when to block this cytokine to improve disease outcome and patient wellbeing.", "Here we discuss the effect of IL-6 on innate and adaptive immunity and the possible advantages of various antagonists of IL-6 and consider how the immunobiology of IL-6 may inform clinical decisions."], "structured": false}
{"doc_id": 20725212, "title": "Chaperoning 5S RNA assembly.", "abstract": ["In eukaryotes, three of the four ribosomal RNAs (rRNAs)\u2014the 5.8S, 18S, and 25S/28S rRNAs\u2014are processed from a single pre-rRNA transcript and assembled into ribosomes.", "The fourth rRNA, the 5S rRNA, is transcribed by RNA polymerase III and is assembled into the 5S ribonucleoprotein particle (RNP), containing ribosomal proteins Rpl5/uL18 and Rpl11/uL5, prior to its incorporation into preribosomes.", "In mammals, the 5S RNP is also a central regulator of the homeostasis of the tumor suppressor p53.", "The nucleolar localization of the 5S RNP and its assembly into preribosomes are performed by a specialized complex composed of Rpf2 and Rrs1 in yeast or Bxdc1 and hRrs1 in humans.", "Here we report the structural and functional characterization of the Rpf2-Rrs1 complex alone, in complex with the 5S RNA, and within pre-60S ribosomes.", "We show that the Rpf2-Rrs1 complex contains a specialized 5S RNA E-loop-binding module, contacts the Rpl5 protein, and also contacts the ribosome assembly factor Rsa4 and the 25S RNA.", "We propose that the Rpf2-Rrs1 complex establishes a network of interactions that guide the incorporation of the 5S RNP in preribosomes in the initial conformation prior to its rotation to form the central protuberance found in the mature large ribosomal subunit."], "structured": false}
{"doc_id": 20732789, "title": "Chronic obstructive pulmonary disease and neutrophil infiltration: role of cigarette smoke and cyclooxygenase products.", "abstract": ["Cigarette smoke is the main cause of chronic obstructive pulmonary disease (COPD), where it can contribute to the observed airway inflammation.", "PGE(2) is produced within human airways, and both pro- and anti-inflammatory activities have been reported.", "We quantitated PGE(2) concentrations in induced sputum supernatants from different groups of subjects and correlated the obtained values to neutrophil infiltration as well as to the expression of cyclooxygenase-2 (COX-2).", "Cigarette smoke extract (CSE) was used to evaluate the effect of smoking on COX-2 and PGE(2) receptor expression as well as on PGE(2) release in neutrophils and alveolar macrophages (AM) obtained from normal donors.", "The effects of PGE(2) and of PGE receptor agonists and antagonists were evaluated on the adhesion of neutrophil to a human bronchial epithelial cell line (16HBE).", "PGE(2) levels, COX-2 expression, and neutrophil infiltration were significantly higher in normal smokers and COPD smokers (P < 0.0001) compared with controls and COPD former smokers.", "Induced sputum supernatant caused neutrophil adhesion to 16HBE that was significantly reduced, in COPD smokers only, by PGE(2) immunoprecipitation.", "In vitro experiments confirmed that CSE increased PGE(2) release and COX-2 and PGE(2) receptor expression in neutrophils and AM; PGE(2) enhanced the adhesion of neutrophils to 16HBE, and a specific E-prostanoid 4 (EP(4)) receptor antagonist blunted its effect.", "These results suggest that CSE promote the induction of COX-2 and contributes to the proinflammatory effects of PGE(2) in the airways of COPD subjects."], "structured": false}
{"doc_id": 20738970, "title": "Non-receptor tyrosine kinase Etk is involved in the apoptosis of small cell lung cancer cells.", "abstract": ["Epithelial and endothelial tyrosine kinase (Etk), also known as Bmx (bone marrow X kinase) plays an important role in apoptosis of epithelial cells.", "The goal of this study was to investigate whether Etk is involved in apoptosis of small cell lung cancer (SCLC) cells and correlated with the expression levels of apoptosis-associated proteins such as Bcl-2, Bcl-X(L) and p53.", "One hundred and seventy-one cases of lung cancer specimens including seventy-one SCLCs and one hundred NSCLCs were immunostained for Etk, Bcl-2, Bcl-X(L) and p53.", "Parental SCLC H446 cell line, and its subline (H446-Etk) that overexpresses Etk, were used to study the role of Etk in apoptosis induced by doxorubicin.", "It was found that high expression of Etk occurs in 74.6% of SCLC cases, but only in 40% of NSCLC cases, and there is marked difference in the expression levels of Bcl-2, Bcl-X(L) and p53 between Etk-positive and Etk-negative SCLC cases.", "Furthermore, the levels of Bcl-2 and Bcl-X(L) significantly increased in H446-Etk cells than that in H446 cells after doxorubicin treatment, and were positively associated with Etk expression.", "However, p53 did not correspond with Etk expression although its expression decreased greatly with apoptosis both in H446-Etk and H446 cells.", "After doxorubicin treatment, the cell viability was significantly higher in H446-Etk cells than in parental H446 cells.", "Downregulation of Etk by Etk siRNA sensitized H446 cells to doxorubicin.", "Our results indicate that upregulation of tyrosine kinase Etk may be a new mechanism involved in protection of SCLC cells from apoptosis.", "Bcl-2 and Bcl-X(L) but not p53 may contribute to doxorubicin-induced apoptosis through Etk pathway."], "structured": false}
{"doc_id": 20743803, "title": "No Pasaran! Role of the axon initial segment in the regulation of protein transport and the maintenance of axonal identity.", "abstract": ["The transmission of information in the brain depends on the highly polarized architecture of neurons.", "A number of cellular transport processes support this organization, including active targeting of proteins and passive corralling between compartments.", "The axon initial segment (AIS), which separates the somatodendritic and axonal compartments, has a key role in neuronal physiology, as both the initiation site of action potentials and the gatekeeper of the axonal arborization.", "Over the years, the AIS main components and their interactions have been progressively unraveled, as well as their role in the AIS assembly and maintenance.", "Two mechanisms have been shown to contribute to the regulation of protein transport at the AIS: a surface diffusion barrier and an intracellular traffic filter.", "However, a molecular understanding of these processes is still lacking.", "In the view of recent results on the AIS cytoskeleton structure, we will discuss how a better knowledge of the AIS architecture can help understanding its role in the regulation of protein transport and the maintenance of axonal identity."], "structured": false}
{"doc_id": 20746604, "title": "The effectiveness of right heart catheterization in the initial care of critically ill patients. SUPPORT Investigators.", "abstract": ["OBJECTIVE To examine the association between the use of right heart catheterization (RHC) during the first 24 hours of care in the intensive care unit (ICU) and subsequent survival, length of stay, intensity of care, and cost of care.   \n", "DESIGN Prospective cohort study.   \n", "SETTING Five US teaching hospitals between 1989 and 1994.   ", "SUBJECTS A total of 5735 critically ill adult patients receiving care in an ICU for 1 of 9 prespecified disease categories.   \n", "MAIN OUTCOME MEASURES Survival time, cost of care, intensity of care, and length of stay in the ICU and hospital, determined from the clinical record and from the National Death Index.", "A propensity score for RHC was constructed using multivariable logistic regression.", "Case-matching and multivariable regression modeling techniques were used to estimate the association of RHC with specific outcomes after adjusting for treatment selection using the propensity score.", "Sensitivity analysis was used to estimate the potential effect of an unidentified or missing covariate on the results.   \n", "RESULTS By case-matching analysis, patients with RHC had an increased 30-day mortality (odds ratio, 1.24; 95% confidence interval, 1.03-1.49).", "The mean cost (25th, 50th, 75th percentiles) per hospital stay was $49 300 ($17 000, $30 500, $56 600) with RHC and $35 700 ($11 300, $20 600, $39 200) without RHC.", "Mean length of stay in the ICU was 14.8 (5, 9, 17) days with RHC and 13.0 (4, 7, 14) days without RHC.", "These findings were all confirmed by multivariable modeling techniques.", "Subgroup analysis did not reveal any patient group or site for which RHC was associated with improved outcomes.", "Patients with higher baseline probability of surviving 2 months had the highest relative risk of death following RHC.", "Sensitivity analysis suggested that a missing covariate would have to increase the risk of death 6-fold and the risk of RHC 6-fold for a true beneficial effect of RHC to be misrepresented as harmful.   \n", "CONCLUSION In this observational study of critically ill patients, after adjustment for treatment selection bias, RHC was associated with increased mortality and increased utilization of resources.", "The cause of this apparent lack of benefit is unclear.", "The results of this analysis should be confirmed in other observational studies.", "These findings justify reconsideration of a randomized controlled trial of RHC and may guide patient selection for such a study."], "structured": true}
{"doc_id": 20754359, "title": "Natural history of adult T-cell leukemia/lymphoma and approaches to therapy", "abstract": ["After cell-to-cell transmission, HTLV-I increases its viral genome by de novo infection and proliferation of infected cells.", "Proliferation of infected cells is clonal and persistent in vivo.", "During the carrier state, infected cells are selected in vivo by the host's immune system, the genetic and epigenetic environment of proviral integration sites, and other factors.", "In leukemic cells, tax gene expression is frequently impaired by genetic and epigenetic mechanisms.", "Such loss of Tax expression enables ATL cells to escape the host immune system.", "On the other hand, ATL cells acquire the ability to proliferate without Tax by intracellular genetic and epigenetic changes.", "Despite advances in support and the development of novel treatment agents, the prognosis for ATLL remains poor.", "A number of therapies, however, do appear to improve prognosis compared to CHOP (VEPA).", "These include interferon-\u03b1 plus zidovudine (probably after 1\u20132 cycles of CHOP), intensive chemotherapy as in LSG-15 with G-CSF support and Allo-SCT (which includes the potential for cure).", "Emerging novel approaches include HDAC inhibitors, monoclonal antibodies, and proteasome inhibitors.", "Comparison between different therapeutic approaches is complicated by the range of natural history of ATLL, different recruitments of na\u00efve-to-therapy, refractory or relapsed patients, and variations in the reporting of outcome that frequently excludes difficult-to-evaluate patients.", "Moreover, results from relatively small proof-of-principle studies have not been extended with randomized, controlled trials.", "As a result, currently, there is no clear evidence to support the value of any particular treatment approach over others.", "To avoid further unnecessary patient suffering and to identify optimal therapy as rapidly as possible, large randomized, controlled trials encompassing multicenter, international collaborations will be necessary."], "structured": false}
{"doc_id": 20758340, "title": "Hierarchical organization of the plasma membrane: investigations by single-molecule tracking vs. fluorescence correlation spectroscopy.", "abstract": ["Single-molecule tracking and fluorescence correlation spectroscopy (FCS) applied to the plasma membrane in living cells have allowed a number of unprecedented observations, thus fostering a new basic understanding of molecular diffusion, interaction, and signal transduction in the plasma membrane.", "It is becoming clear that the plasma membrane is a heterogeneous entity, containing diverse structures on nano-meso-scales (2-200 nm) with a variety of lifetimes, where certain membrane molecules stay together for limited durations.", "Molecular interactions occur in the time-dependent inhomogeneous two-dimensional liquid of the plasma membrane, which might be a key for plasma membrane functions."], "structured": false}
{"doc_id": 20761364, "title": "Stability of the antimalarial drug dihydroartemisinin under physiologically relevant conditions: implications for clinical treatment and pharmacokinetic and in vitro assays.", "abstract": ["Artemisinins are peroxidic antimalarial drugs known to be very potent but highly chemically unstable; they degrade in the presence of ferrous iron, Fe(II)-heme, or biological reductants.", "Less documented is how this translates into chemical stability and antimalarial activity across a range of conditions applying to in vitro testing and clinical situations.", "Dihydroartemisinin (DHA) is studied here because it is an antimalarial drug on its own and the main metabolite of other artemisinins.", "The behaviors of DHA in phosphate-buffered saline, plasma, or erythrocyte lysate at different temperatures and pH ranges were examined.", "The antimalarial activity of the residual drug was evaluated using the chemosensitivity assay on Plasmodium falciparum, and the extent of decomposition of DHA was established through use of high-performance liquid chromatography with electrochemical detection analysis.", "The role of the Fe(II)-heme was investigated by blocking its reactivity using carbon monoxide (CO).", "A significant reduction in the antimalarial activity of DHA was seen after incubation in plasma and to a lesser extent in erythrocyte lysate.", "Activity was reduced by half after 3 h and almost completely abolished after 24 h. Serum-enriched media also affected DHA activity.", "Effects were temperature and pH dependent and paralleled the increased rate of decomposition of DHA from pH 7 upwards and in plasma.", "These results suggest that particular care should be taken in conducting and interpreting in vitro studies, prone as their results are to experimental and drug storage conditions.", "Disorders such as fever, hemolysis, or acidosis associated with malaria severity may contribute to artemisinin instability and reduce their clinical efficacy."], "structured": false}
{"doc_id": 20764484, "title": "Modulation of anxiety through blockade of anandamide hydrolysis", "abstract": ["The psychoactive constituent of cannabis, \u03949-tetrahydrocannabinol, produces in humans subjective responses mediated by CB1 cannabinoid receptors, indicating that endogenous cannabinoids may contribute to the control of emotion.", "But the variable effects of \u03949-tetrahydrocannabinol obscure the interpretation of these results and limit the therapeutic potential of direct cannabinoid agonists.", "An alternative approach may be to develop drugs that amplify the effects of endogenous cannabinoids by preventing their inactivation.", "Here we describe a class of potent, selective and systemically active inhibitors of fatty acid amide hydrolase, the enzyme responsible for the degradation of the endogenous cannabinoid anandamide.", "Like clinically used anti-anxiety drugs, in rats the inhibitors exhibit benzodiazepine-like properties in the elevated zero-maze test and suppress isolation-induced vocalizations.", "These effects are accompanied by augmented brain levels of anandamide and are prevented by CB1 receptor blockade.", "Our results indicate that anandamide participates in the modulation of emotional states and point to fatty acid amide hydrolase inhibition as an innovative approach to anti-anxiety therapy."], "structured": false}
{"doc_id": 20767776, "title": "Familial clustering of reflux symptoms", "abstract": ["Objective:A number of case reports describe multiple family members with gastroesophageal reflux disease and Barrett's esophagus.", "The wider importance of familial factors in gastroesophageal reflux disease has not been established.", "Therefore, we have studied the prevalence of reflux symptoms and medication use among relatives of patients with documented gastroesophageal reflux disease.", "Methods:A postal questionnaire study of the first degree relatives of six groups of matched patients.", "The groups comprised patients with 1) no dyspeptic symptoms; 2) reflux symptoms and a normal pH study; 3) reflux symptoms, an abnormal pH study, and a lower esophageal sphincter (LOS) pressure more than 10 mm Hg; 4) reflux symptoms, an abnormal pH study, and a LOS pressure less than 10 mm Hg; 5) Barrett's esophagus; and 6) peptic stricture.", "Results:Four hundred eighteen subjects replied (78% response).", "Infrequent reflux symptoms were equally common in all groups of relatives.", "Frequent reflux symptoms, however, were more common among relatives of patients with an abnormal pH study and normal (26%, p= 0.007) or low LOS pressure (27%, p= 0.01) or Barrett's esophagus (30%, p= 0.003), compared with relatives of nondyspeptic patients (9%).", "Frequent reflux symptoms were no more common among relatives of patients with a normal pH study (16%) or peptic stricture (18%).", "Reflux medication use showed a similar pattern.", "Conclusions:Familial clustering of reflux symptoms is seen in relatives of patients with reflux symptoms and increased esophageal acid exposure and in relatives of patients with Barrett's esophagus."], "structured": false}
{"doc_id": 20781656, "title": "Histone chaperones: 30 years from isolation to elucidation of the mechanisms of nucleosome assembly and disassembly", "abstract": ["Some three decades have passed since the discovery of nucleosomes in 1974 and the first isolation of a histone chaperone in 1978.", "While various types of histone chaperones have been isolated and functionally analyzed, the elementary processes of nucleosome assembly and disassembly have been less well characterized.", "Recently, the tertiary structure of a hetero-trimeric complex composed of the histone chaperone CIA/ASF1 and the histone H3-H4 dimer was determined, and this complex was proposed to be an intermediate in nucleosome assembly and disassembly reactions.", "In addition, CIA alone was biochemically shown to dissociate the histone (H3-H4)2 tetramer into two histone H3-H4 dimers.", "This activity suggested that CIA regulates the semi-conservative replication of nucleosomes.", "Here, we provide an overview of prominent histone chaperones with the goal of elucidating the mechanisms that preserve and modify epigenetic information.", "We also discuss the reactions involved in nucleosome assembly and disassembly."], "structured": false}
{"doc_id": 20821402, "title": "Specificity of the dRP/AP lyase of Ku promotes nonhomologous end joining (NHEJ) fidelity at damaged ends.", "abstract": ["Nonhomologous end joining (NHEJ) is essential for efficient repair of chromosome breaks.", "However, the NHEJ ligation step is often obstructed by break-associated nucleotide damage, including base loss (abasic site or 5'-dRP/AP sites).", "Ku, a 5'-dRP/AP lyase, can excise such damage at ends in preparation for the ligation step.", "We show here that this activity is greatest if the abasic site is within a short 5' overhang, when this activity is necessary and sufficient to prepare such termini for ligation.", "In contrast, Ku is less active near 3' strand termini, where excision would leave a ligation-blocking \u03b1,\u03b2-unsaturated aldehyde.", "The Ku AP lyase activity is also strongly suppressed by as little as two paired bases 5' of the abasic site.", "Importantly, in vitro end joining experiments show that abasic sites significantly embedded in double-stranded DNA do not block the NHEJ ligation step.", "Suppression of the excision activity of Ku in this context therefore is not essential for ligation and further helps NHEJ retain terminal sequence in junctions.", "We show that the DNA between the 5' terminus and the abasic site can also be retained in junctions formed by cellular NHEJ, indicating that these sites are at least partly resistant to other abasic site-cleaving activities as well.", "High levels of the 5'-dRP/AP lyase activity of Ku are thus restricted to substrates where excision of an abasic site is required for ligation, a degree of specificity that promotes more accurate joining."], "structured": false}
{"doc_id": 20829129, "title": "Gut-expressed gustducin and taste receptors regulate secretion of glucagon-like peptide-1.", "abstract": ["Glucagon-like peptide-1 (GLP-1), released from gut endocrine L cells in response to glucose, regulates appetite, insulin secretion, and gut motility.", "How glucose given orally, but not systemically, induces GLP-1 secretion is unknown.", "We show that human duodenal L cells express sweet taste receptors, the taste G protein gustducin, and several other taste transduction elements.", "Mouse intestinal L cells also express alpha-gustducin.", "Ingestion of glucose by alpha-gustducin null mice revealed deficiencies in secretion of GLP-1 and the regulation of plasma insulin and glucose.", "Isolated small bowel and intestinal villi from alpha-gustducin null mice showed markedly defective GLP-1 secretion in response to glucose.", "The human L cell line NCI-H716 expresses alpha-gustducin, taste receptors, and several other taste signaling elements.", "GLP-1 release from NCI-H716 cells was promoted by sugars and the noncaloric sweetener sucralose, and blocked by the sweet receptor antagonist lactisole or siRNA for alpha-gustducin.", "We conclude that L cells of the gut \"taste\" glucose through the same mechanisms used by taste cells of the tongue.", "Modulating GLP-1 secretion in gut \"taste cells\" may provide an important treatment for obesity, diabetes and abnormal gut motility."], "structured": false}
{"doc_id": 20839751, "title": "Apoptosis in breast cancer: relationship with other pathological parameters.", "abstract": ["Apoptosis is a frequent phenomenon in breast cancer and it can be detected by light microscopy in conventional histopathological sections or by special staining techniques.", "The number of apoptotic cells as a percentage of cells present, or the number of apoptotic cells per square millimetre of neoplastic tissue, is usually described as the apoptotic index (AI).", "In breast cancer, the AI is not related to tumour size, axillary lymph node metastasis or distant metastasis at diagnosis.", "It is greater in invasive ductal carcinomas than in other histological types.", "High AI is also related to high histological grade, high nuclear grade, comedo-type necrosis, lack of tubule formation, and dense infiltration of the tumour by lymphocytes.", "Sex steroid receptor-negative tumours have greater AIs than the sex steroid receptor-positive ones.", "Aneuploid breast cancers with high S-phase fractions (SPFs) also have high AI values compared with diploid tumours with low SPFs.", "p53-Positive breast cancers have high AIs, whereas tumours that are Bcl-2 positive have low AIs.", "The AI shows a strong positive correlation to all direct or indirect indicators of cell proliferation, such as mitotic index and Ki67 immunolabelling.", "Univariate survival analyses show that a high AI is linked with unfavourable disease outcome in axillary lymph node-negative and -positive breast cancer, but multivariate analyses indicate that AI is not an independent prognostic factor.", "In conclusion, a high AI is related to malignant cellular features and indicators of invasiveness and cell proliferation in breast cancer."], "structured": false}
{"doc_id": 20851402, "title": "Dietary flavonoids: bioavailability, metabolic effects, and safety.", "abstract": ["Flavonoids comprise the most common group of plant polyphenols and provide much of the flavor and color to fruits and vegetables.", "More than 5000 different flavonoids have been described.", "The six major subclasses of flavonoids include the flavones (e.g., apigenin, luteolin), flavonols (e.g., quercetin, myricetin), flavanones (e.g., naringenin, hesperidin), catechins or flavanols (e.g., epicatechin, gallocatechin), anthocyanidins (e.g., cyanidin, pelargonidin), and isoflavones (e.g., genistein, daidzein).", "Most of the flavonoids present in plants are attached to sugars (glycosides), although occasionally they are found as aglycones.", "Interest in the possible health benefits of flavonoids has increased owing to their potent antioxidant and free-radical scavenging activities observed in vitro.", "There is growing evidence from human feeding studies that the absorption and bioavailability of specific flavonoids is much higher than originally believed.", "However, epidemiologic studies exploring the role of flavonoids in human health have been inconclusive.", "Some studies support a protective effect of flavonoid consumption in cardiovascular disease and cancer, other studies demonstrate no effect, and a few studies suggest potential harm.", "Because there are many biological activities attributed to the flavonoids, some of which could be beneficial or detrimental depending on specific circumstances, further studies in both the laboratory and with populations are warranted."], "structured": false}
{"doc_id": 20864487, "title": "Virus-specific cytotoxic T-lymphocyte responses select for amino-acid variation in simian immunodeficiency virus Env and Nef", "abstract": ["Cytotoxic T-lymphocyte (CTL) responses to human immunodeficiency virus arise early after infection, but ultimately fail to prevent progression to AIDS.", "Human immunodeficiency virus may evade the CTL response by accumulating amino-acid replacements within CTL epitopes.", "We studied 10 CTL epitopes during the course of simian immunodeficiency virus disease progression in three related macaques.", "All 10 of these CTL epitopes accumulated amino-acid replacements and showed evidence of positive selection by the time the macaques died.", "Many of the amino-acid replacements in these epitopes reduced or eliminated major histocompatibility complex class I binding and/or CTL recognition.", "These findings strongly support the CTL 'escape' hypothesis."], "structured": false}
{"doc_id": 20868160, "title": "TRICHOME BIREFRINGENCE and its homolog AT5G01360 encode plant-specific DUF231 proteins required for cellulose biosynthesis in Arabidopsis.", "abstract": ["The Arabidopsis (Arabidopsis thaliana) trichome birefringence (tbr) mutant has severely reduced crystalline cellulose in trichomes, but the molecular nature of TBR was unknown.", "We determined TBR to belong to the plant-specific DUF231 domain gene family comprising 46 members of unknown function in Arabidopsis.", "The genes harbor another plant-specific domain, called the TBL domain, which contains a conserved GDSL motif known from some esterases/lipases.", "TBR and TBR-like3 (TBL3) are transcriptionally coordinated with primary and secondary CELLULOSE SYNTHASE (CESA) genes, respectively.", "The tbr and tbl3 mutants hold lower levels of crystalline cellulose and have altered pectin composition in trichomes and stems, respectively, tissues generally thought to contain mainly secondary wall crystalline cellulose.", "In contrast, primary wall cellulose levels remain unchanged in both mutants as measured in etiolated tbr and tbl3 hypocotyls, while the amount of esterified pectins is reduced and pectin methylesterase activity is increased in this tissue.", "Furthermore, etiolated tbr hypocotyls have reduced length with swollen epidermal cells, a phenotype characteristic for primary cesa mutants or the wild type treated with cellulose synthesis inhibitors.", "Taken together, we show that two TBL genes contribute to the synthesis and deposition of secondary wall cellulose, presumably by influencing the esterification state of pectic polymers."], "structured": false}
{"doc_id": 20886584, "title": "Genetic predictors of taxane-induced neurotoxicity in a SWOG phase III intergroup adjuvant breast cancer treatment trial (S0221)", "abstract": ["Taxanes have resulted in improved survival for breast cancer patients, but often cause neurological toxicities.", "Identification of biomarkers related to toxicities could be important for dictating treatment regimen.", "We evaluated single nucleotide polymorphisms (SNPs) in the Fanconi Anemia (FA)/BRCA pathway in relation to grade 3/4 neurotoxicities in patients (n = 888) from SWOG0221, a phase III adjuvant trial for breast cancer of 4 dose/schedules of cyclophosphamide (C), doxorubicin (A), and paclitaxel (T).", "In a separate cohort, we measured the correlation of significant FANCD2 SNPs with corresponding gene expression.", "For FANCD2, permutation testing revealed that 4 (out of 20) SNPs were significantly associated with an almost two-fold increased risk of toxicity.", "Two FANCD2 haplotypes were also associated with neurological toxicity, with odds ratios (OR) in the overall population of 1.8 (95% confidence interval (CI) 1.3, 2.5) and 1.7 (95% CI, 1.2, 2.4).", "Although numbers were small, an African-American-specific haplotype was associated with an almost 3-fold increase in risk of neurologic toxicity (OR = 2.84, 95% CI = 1.2, 6.9).", "Expression analyses revealed that significant FANCD2 SNPs were associated with FANCD2 expression levels (P = 0.03).", "There were no associations between SNPs in BRCA1 and neurotoxicities.", "In this trial of CA+T for breast cancer, SNPs in FANCD2, but not in BRCA1, were associated with a 70\u201380% increase in the odds of grade 3/4 neurological toxicities and increased expression of the gene.", "If replicated, women with these genotypes should be closely monitored for toxicities and could be targeted for preventive measures or alternative therapeutic approaches."], "structured": false}
{"doc_id": 20887554, "title": "Preoperative C-reactive protein predicts mid-term outcome after cardiac surgery.", "abstract": ["BACKGROUND C-reactive protein (CRP) is a known risk factor for cardiovascular events in the healthy population and in patients with coronary artery disease.", "High CRP levels before cardiac surgery are associated with worse short-term outcome, but its role after discharge home remains unknown.", "The study objective was to evaluate the effect of CRP on short-term and mid-term outcome after cardiac surgery.   \n", "METHODS From August 2000 to May 2004, values for preoperative CRP were available for 597 unselected patients undergoing cardiac operations.", "CRP was used to divide this cohort in two groups: a low inflammatory status (LHS) group of 354 patients with CRP of less than 0.5 mg/dL, and a high inflammatory status (HIS) group of 243 patients with a CRP of 0.5 mg/dL or more.", "Follow-up lasted a maximum of 3 years (median, 1.8 +/-", "1.5 years) and was 92.6% complete.   \n", "RESULTS In-hospital mortality was 8.2% in the HIS group and 3.4% in the LIS group (odds ratio [OR], 2.61; p = 0.02).", "Incidence of postoperative infections was 16.5% in the HIS group and 5.1% in the LIS group (OR, 3.25; p = 0.0001).", "Sternal wound infections were also more frequent in the HIS group (10.7% versus 2.8%; OR, 3.43; p = 0.002).", "During follow-up, the HIS group had worse survival (88.5% +/-", "2.9% versus 91.9% +/-", "2.5%; OR, 1.93; p = 0.05) and a higher need of hospitalization for cardiac-related causes (73.6% +/-", "6% versus 86.5% +/-", "3.2%; OR, 1.82; p = 0.05).   \n", "CONCLUSIONS Patients undergoing cardiac surgery with a CRP level of 0.5 mg/dL or more are exposed to a higher risk of in-hospital mortality and postoperative infections.", "Despite surgical correction of cardiac disease, a high preoperative CRP value is an independent risk factor for mid-term survival and hospitalization for cardiac causes."], "structured": true}
{"doc_id": 20888849, "title": "Inhibition of Hedgehog signaling enhances delivery of chemotherapy in a mouse model of pancreatic cancer.", "abstract": ["Pancreatic ductal adenocarcinoma (PDA) is among the most lethal human cancers in part because it is insensitive to many chemotherapeutic drugs.", "Studying a mouse model of PDA that is refractory to the clinically used drug gemcitabine, we found that the tumors in this model were poorly perfused and poorly vascularized, properties that are shared with human PDA.", "We tested whether the delivery and efficacy of gemcitabine in the mice could be improved by coadministration of IPI-926, a drug that depletes tumor-associated stromal tissue by inhibition of the Hedgehog cellular signaling pathway.", "The combination therapy produced a transient increase in intratumoral vascular density and intratumoral concentration of gemcitabine, leading to transient stabilization of disease.", "Thus, inefficient drug delivery may be an important contributor to chemoresistance in pancreatic cancer."], "structured": false}
{"doc_id": 20904154, "title": "Mutant SOD1 inhibits ER-Golgi transport in amyotrophic lateral sclerosis.", "abstract": ["Cu/Zn-superoxide dismutase is misfolded in familial and sporadic amyotrophic lateral sclerosis, but it is not clear how this triggers endoplasmic reticulum (ER) stress or other pathogenic processes.", "Here, we demonstrate that mutant SOD1 (mSOD1) is predominantly found in the cytoplasm in neuronal cells.", "Furthermore, we show that mSOD1 inhibits secretory protein transport from the ER to Golgi apparatus.", "ER-Golgi transport is linked to ER stress, Golgi fragmentation and axonal transport and we also show that inhibition of ER-Golgi trafficking preceded ER stress, Golgi fragmentation, protein aggregation and apoptosis in cells expressing mSOD1.", "Restoration of ER-Golgi transport by over-expression of coatomer coat protein II subunit Sar1 protected against inclusion formation and apoptosis, thus linking dysfunction in ER-Golgi transport to cellular pathology.", "These findings thus link several cellular events in amyotrophic lateral sclerosis into a single mechanism occurring early in mSOD1 expressing cells."], "structured": false}
{"doc_id": 20931483, "title": "High spatial resolution mapping of malaria transmission risk in the Gambia, west Africa, using LANDSAT TM satellite imagery.", "abstract": ["Understanding local variability in malaria transmission risk is critically important when designing intervention or vaccine trials.", "Using a combination of field data, satellite image analysis, and GIS modeling, we developed a high-resolution map of malaria entomological inoculation rates (EIR) in The Gambia, West Africa.", "The analyses are based on the variation in exposure to malaria parasites experienced in 48 villages in 1996 and 21 villages in 1997.", "The entomological inoculation rate (EIR) varied from 0 to 166 infective bites per person per rainy season.", "Detailed field surveys identified the major Anopheles gambiae s.l.", "breeding habitats.", "These habitats were mapped by classification of a LANDSAT TM satellite image with an overall accuracy of 85%.", "Village EIRs decreased as a power function based on the breeding areas size and proximity.", "We use this relationship and the breeding habitats to map the variation in EIR over the entire 2500-km(2) study area."], "structured": false}
{"doc_id": 20935673, "title": "Functional analysis of repressor binding sites in the iab-2 regulatory region of the abdominal-A homeotic gene.", "abstract": ["Spatial boundaries of homeotic gene expression are initiated and maintained by two sets of transcriptional repressors: the gap gene products and the Polycomb group proteins.", "Previously, the Hunchback (HB) protein has been implicated in setting the anterior expression limit of the UBX homeotic protein in parasegment 6.", "Here we investigate DNA elements and trans-acting repressors that control spatial expression of the Abdominal-A (ABD-A) homeotic protein.", "Analysis of a 1.7-kb enhancer element [iab-2(1.7)] from the iab-2 regulatory region shows that in contrast to Ubx enhancer elements, both HB and Kr\u00fcppel (KR) are required to set the ABD-A anterior boundary in parasegment 7.", "DNase I footprinting and site-directed mutagenesis show that HB and KR are direct regulators of this iab-2 enhancer.", "The single KR site can be moved to a new location 100 bp away and still maintain repressive activity, whereas relocation by 300 bp abolishes activity.", "These results suggest that KR repression occurs through a local quenching mechanism.", "We also show that the gap repressor Giant (GT) initially establishes a posterior expression limit at PS9, which shifts posteriorly after the blastoderm stage.", "Finally, we show that this iab-2 enhancer contains multiple binding sites for the Polycomb group protein Pleiohomeotic (PHO).", "These iab-2 PHO sites are required in vivo for chromosome pairing-dependent repression of a mini-white reporter.", "However, the PHO sites are not sufficient to maintain repression of a homeotic reporter gene anterior to PS7.", "Full maintenance at late embryonic stages requires additional sequences adjacent to the iab-2(1.7) enhancer."], "structured": false}
{"doc_id": 20937018, "title": "Apolipoprotein E: high-avidity binding to beta-amyloid and increased frequency of type 4 allele in late-onset familial Alzheimer disease.", "abstract": ["Apolipoprotein E is immunochemically localized to the senile plaques, vascular amyloid, and neurofibrillary tangles of Alzheimer disease.", "In vitro, apolipoprotein E in cerebrospinal fluid binds to synthetic beta A4 peptide (the primary constituent of the senile plaque) with high avidity.", "Amino acids 12-28 of the beta A4 peptide are required.", "The gene for apolipoprotein E is located on chromosome 19q13.2, within the region previously associated with linkage of late-onset familial Alzheimer disease.", "Analysis of apolipoprotein E alleles in Alzheimer disease and controls demonstrated that there was a highly significant association of apolipoprotein E type 4 allele (APOE-epsilon 4) and late-onset familial Alzheimer disease.", "The allele frequency of the APOE-epsilon 4 in 30 random affected patients, each from a different Alzheimer disease family, was 0.50 +/-", "0.06; the allele frequency of APOE-epsilon 4 in 91 age-matched unrelated controls was 0.16 +/-", "0.03 (Z = 2.44, P = 0.014).", "A functional role of the apolipoprotein E-E4 isoform in the pathogenesis of late-onset familial Alzheimer disease is suggested."], "structured": false}
{"doc_id": 20942644, "title": "Unmarked gene deletion and host\u2013vector system for the hyperthermophilic crenarchaeon Sulfolobus islandicus", "abstract": ["Sulfolobus islandicus is being used as a model for studying archaeal biology, geo-biology and evolution.", "However, no genetic system is available for this organism.", "To produce an S. islandicus mutant suitable for genetic analyses, we screened for colonies with a spontaneous pyrEF mutation.", "One mutant was obtained containing only 233 bp of the original pyrE sequence in the mutant allele and it was used as a host to delete the \u03b2-glycosidase (lacS) gene.", "Two unmarked gene deletion methods were employed, namely plasmid integration and segregation, and marker replacement and looping out, and unmarked lacS mutants were obtained by each method.", "A new alternative recombination mechanism, i.e., marker circularization and integration, was shown to operate in the latter method, which did not yield the designed deletion mutation.", "Subsequently, Sulfolobus\u2013E. coli plasmid shuttle vectors were constructed, which genetically complemented \u0394pyrEF\u0394lacS mutation after transformation.", "Thus, a complete set of genetic tools was established for S. islandicus with pyrEF and lacS as genetic markers."], "structured": false}
{"doc_id": 20943272, "title": "ADAM13 disintegrin and cysteine-rich domains bind to the second heparin-binding domain of fibronectin.", "abstract": ["ADAM13 is a member of the disintegrin and metalloprotease protein family that is expressed on cranial neural crest cells surface and is essential for their migration.", "ADAM13 is an active protease that can cleave fibronectin in vitro and remodel a fibronectin substrate in vivo.", "Using a recombinant secreted protein containing both disintegrin and cysteine-rich domains of ADAM13, we show that this \"adhesive\" region of the protein binds directly to fibronectin.", "Fibronectin fusion proteins corresponding to the various functional domains were used to define the second heparin-binding domain as the ADAM13 binding site.", "Mutation of the syndecan-binding site (PPRR --> PPTM) within this domain abolishes binding of the recombinant disintegrin and cysteine-rich domains of ADAM13.", "We further show that the adhesive disintegrin and cysteine-rich domain of ADAM13 can promote cell adhesion via beta(1) integrins.", "This adhesion requires integrin activation and can be prevented by antibodies to the cysteine-rich domain of ADAM13 and beta(1) integrin.", "Finally, wild type, but not the E/A mutant of ADAM13 metalloprotease domain, can be shed from the cell surface, releasing the metalloprotease domain associated with the disintegrin and cysteine-rich domains.", "This suggests that ADAM13 shedding may involve its own metalloprotease activity and that the released protease may interact with both integrins and extracellular matrix proteins."], "structured": false}
{"doc_id": 20945963, "title": "Clinical epidemiology of heart failure.", "abstract": ["The aim of this paper is to review the clinical epidemiology of heart failure.", "The last paper comprehensively addressing the epidemiology of heart failure in Heart appeared in 2000.", "Despite an increase in manuscripts describing epidemiological aspects of heart failure since the 1990s, additional information is still needed, as indicated by various editorials."], "structured": false}
{"doc_id": 20960682, "title": "Toll-like receptor 7 agonist GS-9620 induces prolonged inhibition of HBV via a type I interferon-dependent mechanism.", "abstract": ["BACKGROUND & AIMS GS-9620, an oral agonist of toll-like receptor 7 (TLR7), is in clinical development for the treatment of chronic hepatitis B (CHB).", "GS-9620 was previously shown to induce prolonged suppression of serum viral DNA and antigens in the woodchuck and chimpanzee models of CHB.", "Herein, we investigated the molecular mechanisms that contribute to the antiviral response to GS-9620 using in vitro models of hepatitis B virus (HBV) infection.   \n", "METHODS Cryopreserved primary human hepatocytes (PHH) and differentiated HepaRG (dHepaRG) cells were infected with HBV and treated with GS-9620, conditioned media from human peripheral blood mononuclear cells treated with GS-9620 (GS-9620 conditioned media [GS-9620-CM]), or other innate immune stimuli.", "The antiviral and transcriptional response to these agents was determined.   \n", "RESULTS GS-9620 had no antiviral activity in HBV-infected PHH, consistent with low level TLR7 mRNA expression in human hepatocytes.", "In contrast, GS-9620-CM induced prolonged reduction of HBV DNA, RNA, and antigen levels in PHH and dHepaRG cells via a type I interferon (IFN)-dependent mechanism.", "GS-9620-CM did not reduce covalently closed circular DNA (cccDNA) levels in either cell type.", "Transcriptional profiling demonstrated that GS-9620-CM strongly induced various HBV restriction factors - although not APOBEC3A or the Smc5/6 complex - and indicated that established HBV infection does not modulate innate immune sensing or signaling in cryopreserved PHH.", "GS-9620-CM also induced expression of immunoproteasome subunits and enhanced presentation of an immunodominant viral peptide in HBV-infected PHH.   \n", "CONCLUSIONS Type I IFN induced by GS-9620 durably suppressed HBV in human hepatocytes without reducing cccDNA levels.", "Moreover, HBV antigen presentation was enhanced, suggesting additional components of the TLR7-induced immune response played a role in the antiviral response to GS-9620 in animal models of CHB.   ", "LAY SUMMARY GS-9620 is a drug currently being tested in clinical trials for the treatment of chronic hepatitis B virus (HBV) infection.", "GS-9620 has previously been shown to suppress HBV in various animal models, but the underlying antiviral mechanisms were not completely understood.", "In this study, we determined that GS-9620 does not directly activate antiviral pathways in human liver cells, but can induce prolonged suppression of HBV via induction of an antiviral cytokine called interferon.", "However, interferon did not destroy the HBV genome, suggesting that other parts of the immune response (e.g. activation of immune cells that kill infected cells) also play an important role in the antiviral response to GS-9620."], "structured": true}
{"doc_id": 20977638, "title": "Depletion of glutathione induces 4-hydroxynonenal protein adducts and hydroxyurea teratogenicity in the organogenesis stage mouse embryo.", "abstract": ["Glutathione (GSH) homeostasis is important during organogenesis.", "To elucidate the impact of GSH depletion in organogenesis stage embryos on oxidative stress and drug teratogenicity, l-buthionine-S,R-sulfoximine (BSO) was given to timed pregnant CD-1 mice 4 h before exposure to a model teratogen, hydroxyurea (HU) [400 mg/kg (HU-400) or 600 mg/kg (HU-600)].", "Treatment with BSO or HU alone or with BSO plus HU-400 did not alter the ratios of glutathione disulfide/GSH in the embryo; in contrast, the combination of BSO plus HU-600 did increase this ratio at both 0.5 and 3 h post-HU, indicating the induction of oxidative stress in the embryos.", "Immunoreactivity to a product of lipid peroxidation, 4-hydroxynonenal (4-HNE) protein adducts, was detected in saline-treated embryos; the intensity and nuclear localization of 4-HNE protein adduct immunoreactivity in specific regions in the embryo was significantly increased by exposure to BSO alone or BSO and either dose of HU.", "BSO pretreatment increased the spectrum and incidence of external and skeletal malformations (curly tail, hind limb malformations, hydrocephaly, exencephaly, open eye, spina bifida, and gastroschisis) induced by HU-400 and HU-600; BSO exposure did not alter the effects of HU on fetal mortality or fetal weights or HU induction of c-Fos heterodimer-dependent activator protein 1 DNA binding activity.", "The formation of 4-HNE protein adducts in teratogen-exposed embryos was localized to regions of the embryo that were highly susceptible to insult, namely the somites and caudal neural tube, correlating the presence of 4-HNE adducts with the disruption of pattern formation during organogenesis."], "structured": false}
{"doc_id": 20996244, "title": "Nonproductive human immunodeficiency virus type 1 infection in nucleoside-treated G0 lymphocytes.", "abstract": ["Productive infection by human immunodeficiency virus type 1 (HIV-1) requires the activation of target cells.", "Infection of quiescent peripheral CD4 lymphocytes by HIV-1 results in incomplete, labile, reverse transcripts.", "We have previously identified G1b as the cell cycle stage required for the optimal completion of the reverse transcription process in T lymphocytes.", "However, the mechanism(s) involved in the blockage of reverse transcription remains undefined.", "In this study we investigated whether nucleotide levels influence viral reverse transcription in G0 cells.", "For this purpose the role of the enzyme ribonucleotide reductase was bypassed, by adding exogenous deoxyribonucleosides to highly purified T cells in the G0 or the G1a phase of the cell cycle.", "Our data showed a significant increase in the efficiency of the reverse transcription process following the addition of the deoxyribonucleosides.", "To define the stability and functionality of these full reverse transcripts, we used an HIV-1 reporter virus that expresses the murine heat-stable antigen on the surfaces of infected cells.", "Following activation of infected quiescent cells treated with exogenous nucleosides, no increased rescue of productive infection was seen.", "Thus, in addition to failure to complete reverse transcription, there was an additional nonreversible blockage of productive infection in quiescent T cells.", "These experiments have important relevance in the gene therapy arena, in terms of improving the ability of lentivirus vectors to enter metabolically inactive cells, such as hematopoietic stem cells."], "structured": false}
{"doc_id": 20999249, "title": "Imported malaria in children: a national surveillance in the Netherlands and a review of European studies.", "abstract": ["BACKGROUND Falciparum malaria or malaria tropica is one of the leading causes of childhood mortality worldwide.", "Malaria-related deaths occur mainly in sub-Saharan Africa, where an estimated 365 million clinical cases of Plasmodium falciparum malaria occur each year.", "In Europe, imported malaria cases occur due to returning travellers or immigration mostly from African countries.", "Children are more at risk than adults.", "The objective of this study was to identify high risk groups for imported childhood malaria in Europe in order to guide development of strategies for prevention, early recognition and management.   \n", "METHODS In the period May 2003-January 2005 we reviewed all cases of paediatric malaria in the Netherlands notified by the Dutch Paediatric Surveillance System (Nederland Signalerings Centrum Kindergeneeskunde, NSCK) and the literature on imported malaria in children in Europe published between 1996 and 2006.   \n", "RESULTS Malaria occurred mainly in children of long-term (n = 15, 47%) and new (n = 8, 25%) immigrants and was mostly acquired in sub-Saharan Africa.", "The dominant species was P. falciparum.", "Only one quarter of children had used adequate malaria chemoprophylaxis.", "Complicated disease occurred in 10 (31%) of cases.", "We also reviewed the literature and found 6082 reported cases of imported malaria among children in Europe; among these, four died and only one was reported to develop neurological sequelae.   \n", "CONCLUSION Imported malaria in children remains an important problem and is unlikely to decrease unless the reasons for inadequate prophylaxis are addressed."], "structured": true}
{"doc_id": 21003930, "title": "Respiratory and cardiovascular responses to walking down a traffic-polluted road compared with walking in a traffic-free area in participants aged 60 years and older with chronic lung or heart disease and age-matched healthy controls: a randomised, crossover study", "abstract": ["BACKGROUND Long-term exposure to pollution can lead to an increase in the rate of decline of lung function, especially in older individuals and in those with chronic obstructive pulmonary disease (COPD), whereas shorter-term exposure at higher pollution levels has been implicated in causing excess deaths from ischaemic heart disease and exacerbations of COPD.", "We aimed to assess the effects on respiratory and cardiovascular responses of walking down a busy street with high levels of pollution compared with walking in a traffic-free area with lower pollution levels in older adults.   \n", "METHODS In this randomised, crossover study, we recruited men and women aged 60 years and older with angiographically proven stable ischaemic heart disease or stage 2 Global initiative for Obstructive Lung Disease (GOLD) COPD who had been clinically stable for 6 months, and age-matched healthy volunteers.", "Individuals with ischaemic heart disease or COPD were recruited from existing databases or outpatient respiratory and cardiology clinics at the Royal Brompton & Harefield NHS Foundation Trust and age-matched healthy volunteers using advertising and existing databases.", "All participants had abstained from smoking for at least 12 months and medications were taken as recommended by participants' doctors during the study.", "Participants were randomly assigned by drawing numbered disks at random from a bag to do a 2 h walk either along a commercial street in London (Oxford Street) or in an urban park (Hyde Park).", "Baseline measurements of participants were taken before the walk in the hospital laboratory.", "During each walk session, black carbon, particulate matter (PM) concentrations, ultrafine particles, and nitrogen dioxide (NO2) concentrations were measured.   \n", "FINDINGS Between October, 2012, and June, 2014, we screened 135 participants, of whom 40 healthy volunteers, 40 individuals with COPD, and 39 with ischaemic heart disease were recruited.", "Concentrations of black carbon, NO2, PM10, PM2.5, and ultrafine particles were higher on Oxford Street than in Hyde Park.", "Participants with COPD reported more cough (odds ratio [OR] 1\u00b795, 95% CI 0\u00b796-3\u00b795; p<0\u00b71), sputum (3\u00b715, 1\u00b739-7\u00b713; p<0\u00b705), shortness of breath (1\u00b786, 0\u00b797-3\u00b757; p<0\u00b71), and wheeze (4\u00b700, 1\u00b752-10\u00b750; p<0\u00b705) after walking down Oxford Street compared with Hyde Park.", "In all participants, irrespective of their disease status, walking in Hyde Park led to an increase in lung function (forced expiratory volume in the first second [FEV1] and forced vital capacity [FVC]) and a decrease in pulse wave velocity (PWV) and augmentation index up to 26 h after the walk.", "By contrast, these beneficial responses were attenuated after walking on Oxford Street.", "In participants with COPD, a reduction in FEV1 and FVC, and an increase in R5-20 were associated with an increase in during-walk exposure to NO2, ultrafine particles and PM2.5, and an increase in PWV and augmentation index with NO2 and ultrafine particles.", "In healthy volunteers, PWV and augmentation index were associated both with black carbon and ultrafine particles.   \n", "INTERPRETATION Short-term exposure to traffic pollution prevents the beneficial cardiopulmonary effects of walking in people with COPD, ischaemic heart disease, and those free from chronic cardiopulmonary diseases.", "Medication use might reduce the adverse effects of air pollution in individuals with ischaemic heart disease.", "Policies should aim to control ambient levels of air pollution along busy streets in view of these negative health effects.   \n", "FUNDING British Heart Foundation."], "structured": true}
{"doc_id": 21009874, "title": "Overall and cancer related mortality among patients with ocular inflammation treated with immunosuppressive drugs: retrospective cohort study.", "abstract": ["CONTEXT Whether immunosuppressive treatment adversely affects survival is unclear.   \n", "OBJECTIVE To assess whether immunosuppressive drugs increase mortality.   \n", "DESIGN Retrospective cohort study evaluating overall and cancer mortality in relation to immunosuppressive drug exposure among patients with ocular inflammatory diseases.", "Demographic, clinical, and treatment data derived from medical records, and mortality results from United States National Death Index linkage.", "The cohort's mortality risk was compared with US vital statistics using standardised mortality ratios.", "Overall and cancer mortality in relation to use or non-use of immunosuppressive drugs within the cohort was studied with survival analysis.   \n", "SETTING Five tertiary ocular inflammation clinics.", "Patients 7957 US residents with non-infectious ocular inflammation, 2340 of whom received immunosuppressive drugs during follow up.", "Exposures Use of antimetabolites, T cell inhibitors, alkylating agents, and tumour necrosis factor inhibitors.   \n", "MAIN OUTCOME MEASURES Overall mortality, cancer mortality.   \n", "RESULTS Over 66 802 person years (17 316 after exposure to immunosuppressive drugs), 936 patients died (1.4/100 person years), 230 (24.6%) from cancer.", "For patients unexposed to immunosuppressive treatment, risks of death overall (standardised mortality ratio 1.02, 95% confidence interval [CI] 0.94 to 1.11) and from cancer (1.10, 0.93 to 1.29) were similar to those of the US population.", "Patients who used azathioprine, methotrexate, mycophenolate mofetil, ciclosporin, systemic corticosteroids, or dapsone had overall and cancer mortality similar to that of patients who never took immunosuppressive drugs.", "In patients who used cyclophosphamide, overall mortality was not increased and cancer mortality was non-significantly increased.", "Tumour necrosis factor inhibitors were associated with increased overall (adjusted hazard ratio [HR] 1.99, 95% CI 1.00 to 3.98) and cancer mortality (adjusted HR 3.83, 1.13 to 13.01).   \n", "CONCLUSIONS Most commonly used immunosuppressive drugs do not seem to increase overall or cancer mortality.", "Our results suggesting that tumour necrosis factor inhibitors might increase mortality are less robust than the other findings; additional evidence is needed."], "structured": true}
{"doc_id": 21012916, "title": "Ephrin B1\u2013mediated repulsion and signaling control germinal center T cell territoriality and function", "abstract": ["Follicular T helper (TFH) cells orchestrate the germinal center (GC) reaction locally.", "Local mechanisms regulating their dynamics and helper functions are not well defined.", "Here we found that GC-expressed ephrin B1 (EFNB1) repulsively inhibited T cell to B cell adhesion and GC TFH retention by signaling through TFH-expressed EPHB6 receptor.", "At the same time, EFNB1 promoted interleukin-21 production from GC TFH cells by signaling predominantly through EPHB4.", "Consequently, EFNB1-null GCs were associated with defective production of plasma cells despite harboring excessive TFH cells.", "In a competitive GC reaction, EFNB1-deficient B cells more efficiently interacted with TFH cells and produced more bone-marrow plasma cells, likely as a result of gaining more contact-dependent help.", "Our results reveal a contact-dependent repulsive guidance system that controls GC TFH dynamics and effector functions locally."], "structured": false}
{"doc_id": 21033230, "title": "Molecular profiling and predictive value of circulating tumor cells in patients with metastatic breast cancer: an option for monitoring response to breast cancer related therapies", "abstract": ["Purpose We analyzed circulating tumor cells (CTC) in blood of metastatic breast cancer patients (n = 42) and determined the ability of this method to predict therapy response.", "Methods CTC from blood were analyzed before and during therapy for EpCAM, MUC1 and HER2 transcripts with the AdnaTest BreastCancer.", "The estrogen (ER) and progesterone (PR) receptor expression was assessed by RT-PCR.", "Results The overall detection rate for CTC was 52% (thereof 86% EpCAM; 86% MUC1; 32% HER2; 35% ER; 12% PR).", "CTC were ER, PR and HER2 negative in 45% (ER), 78% (PR) and 60% (HER-2) of patients with steroid receptor-positive tumors.", "29% of patients with HER2-negative tumors had HER2-positive CTC.", "The test predicted therapy response in 78% of all cases.", "Persistence of CTC significantly correlated with shorter overall survival (P = 0.005).", "Conclusions Molecular profiling of CTC may offer superior prognostic information with regard to risk assessment for recurrence and predictive judgement of therapeutical regimens."], "structured": false}
{"doc_id": 21046889, "title": "Alternate-day wheel access: effects on feeding, body weight, and running.", "abstract": ["For rats access to a running wheel results in a pronounced but temporary suppression of feeding.", "The reasons for the feeding suppression and its temporary nature are unclear.", "The effects of alternate-day wheel access were explored by comparing feeding and running in 25 male Sprague-Dawley rats given either no wheel access, continuous wheel access, or alternate-day wheel access.", "With alternate-day wheel access food intake was suppressed on wheel days and elevated on non-wheel days for the full 32 days of the experiment.", "Body weight decreased on wheel days and showed a large increase on non-wheel days.", "Acquisition of running over days was similar in both wheel groups and plateaued at the same level, but running was elevated, compared to continuous-access rats, for the first few hours when alternate-day rats were returned to the wheel.", "These results suggest that wheel-induced feeding suppression is not due to the novelty of the wheel and that this suppression can be extended by providing periods with no wheel access.", "The temporary nature of feeding suppression in chronic access conditions may be due to secondary longer term motivational changes."], "structured": false}
{"doc_id": 21048969, "title": "Evaluation of the association between the first observation and the longitudinal change in C-reactive protein, and all-cause mortality.", "abstract": ["OBJECTIVE To evaluate the association between vascular inflammation as measured by subacute C-reactive protein (CRP; 1-10 mg/l) and all-cause mortality and the association between change in CRP status (normal <or=3 mg/l and elevated >3 mg/l) and all-cause mortality.   \n", "METHODS Probabilistic record linkage was used to match hospital episode data, laboratory reports and mortality statistics in a large urban population.", "Survival was evaluated using Cox proportional hazards regression models.   \n", "RESULTS 22 962 patients had their first CRP measurement in the subacute range (1-10 mg/l).", "Analysis grouped by each additional unit increase in CRP across the subacute range was associated with a 7.3% (95% CI 5.4% to 9.2%) increase in the hazard ratio (HR) of death over 4 years, after controlling for confounding factors (p<0.001).", "Repeated CRP observations around 1 year apart were recorded in 5811 subjects.", "After controlling for confounding factors, in patients whose CRP changed from normal (<or=3 mg/l) to elevated (>3 mg/l), the HR increased 6.7-fold (p<0.001) relative to cases whose CRP remained normal.", "By comparison, among those subjects whose CRP was reduced from elevated to normal, the hazard ratio halved to 3.5 (p = 0.018).", "In an underpowered analysis of time to cardiovascular events, an identical pattern of risk emerged.   \n", "CONCLUSIONS CRP level predicted all-cause mortality, and additional inclusion of prior change in CRP level and current CRP level more so.", "Increasing vascular inflammation, as measured by CRP, increases the likelihood of death."], "structured": true}
{"doc_id": 21050357, "title": "Research Priorities in Sudden Unexpected Infant Death: An International Consensus.", "abstract": ["Despite the success of safe sleep campaigns and the progress in understanding risk factors, the rate of reduction in the cases of sudden infant death syndrome has now slowed and it remains a leading cause of postneonatal mortality in many developed countries.", "Strategic action is needed to tackle this problem and it is now vital to identify how the sudden infant death research community may best target its efforts.", "The Global Action and Prioritization of Sudden Infant Death Project was an international consensus process that aimed to define and direct future research by investigating the priorities of expert and lay members of the sudden unexpected infant death (SUID) community across countries.", "The aim was to identify which areas of research should be prioritized to reduce the number of SUID deaths globally.", "Scientific researchers, clinicians, counselors, educators, and SUID parents from 25 countries took part across 2 online surveys to identify potential research priorities.", "Workshops subsequently took place in the United Kingdom, United States, and Australia to reach consensus and 10 priority areas for research were established.", "Three main themes among the priorities emerged: (1) a better understanding of mechanisms underlying SUID, (2) ensuring best practice in data collection, management and sharing, and (3) a better understanding of target populations and more effective communication of risk.", "SUID is a global problem and this project provides the international SUID community with a list of shared research priorities to more effectively work toward explaining and reducing the number of sudden infant deaths."], "structured": false}
{"doc_id": 21053753, "title": "Modification of the Constant-Murley shoulder score-introduction of the individual relative Constant score Individual shoulder assessment.", "abstract": ["The Constant-Murley shoulder assessment score has proven to be a valuable diagnostic instrument.", "Thus, in the literature it has been mentioned that the clinical accuracy of this score varies especially when comparing patients in larger, inhomogeneous patient groups.", "The \"relative Constant score\" (CS(rel)) tries to minimize these problems by using reference parameters out of healthy age and gender related control groups.", "The authors of this study tried to show that it is even more accurate to use the functional performance of the uninjured collateral shoulder of the same individual as reference, introducing the \"individual relative Constant score\" (CS(indiv)).", "The CS(indiv) and the CS(rel) were compared for 125 consecutive patients with shoulder disorders, and a group of 125 healthy volunteers as a control group.", "In a non-parametric comparison of the reciever operating characteristics the CS(indiv) shows the higher ability to discriminate between patients and healthy volunteers (p=0.004).", "This indicates that the individual relative Constant score gives a more accurate view about the functional result for shoulder disorders.", "It is expected to be more reliable for larger and incoherent patient populations, because specific interindividual differences, regarding the patient's age, gender and constitution are eliminated as well as other individual physiological parameters."], "structured": false}
{"doc_id": 21060008, "title": "Celiac disease screening by immunochromatographic visual assays: results of a multicenter study.", "abstract": ["OBJECTIVE To assay the efficiency for celiac disease (CD) screening of 2 immunochromatographic visual stick assays based on human recombinant tissue transglutaminase (tTG).", "One was the antitissue transglutaminase antibodies (AtTGA) stick for IgA/G antibodies to tTG detection, the other was the AtTGA/antigliadin antibodies (AGA) stick for IgA antibodies for tTG and/or gliadins.   \n", "PATIENTS AND METHODS In a prospective multicenter study, 4 pediatric gastroenterology units from Spain and 2 from Latin America enrolled 72 control children with a normal small bowel mucosa and 113 untreated patients with CD with Marsh type 3 lesions.   \n", "RESULTS Evaluation of results by the gastroenterologists and by 2 independent observers at the coordination center showed a remarkably low interobserver variability.", "For the AtTGA stick, sensitivity was 96.5% and specificity was 98.6%.", "The AtTGA/AGA stick displayed a sensitivity of 94.5% and a specificity of 98.6% for AtTGA and a sensitivity of 63.1% and a specificity of 95.2% for AGA.", "The highest efficiency and positive likelihood ratio was obtained for the AtTGA stick, higher than for IgA AtTGA by enzyme-linked immunosorbent assay.", "One additional advantage was that previous investigation of total serum IgA levels could be eluded.", "The IgA AtTGA/AGA stick, with an efficiency of 95.1%, compared with 89.2% when the combined results of the 2 enzyme-linked immunosorbent assays were considered, turned out to be an excellent diagnostic tool for infants with no IgA deficiency.   \n", "CONCLUSION These 2 assays are extremely efficient for CD screening, by combining a high diagnostic accuracy with the simplicity and rapidity of visual methods."], "structured": true}
{"doc_id": 21063817, "title": "Down-regulation of keratin 4 and keratin 13 expression in oral squamous cell carcinoma and epithelial dysplasia: a clue for histopathogenesis.", "abstract": ["AIMS This study aimed to identify relevant keratin subtypes that may associate with the pathogenesis of oral epithelial neoplasms.   \n", "METHODS AND RESULTS Expression of all the keratin subtypes was examined by cDNA microarray analysis of 43 oral squamous cell carcinoma (OSCC) cases.", "Immunohistochemical expression of the major keratins was examined in 100 OSCC and oral epithelial dysplasia (OED) cases.", "Many changes in keratin expression were observed and, significantly, consistent down-regulation of keratin 4 (K4) and K13 expression was observed.", "Aberrant expression of K4 and K13 was associated with morphological changes in the affected oral epithelium.", "Experiments with cell cultures transfected with various keratin subtypes suggested that alterations in keratin subtype expression can cause changes in cell shape and movement.   \n", "CONCLUSIONS Aberrant expression of K4 and K13, which are the dominant pair of differentiation-related keratins in oral keratinocytes, indicates dysregulation of epithelial differentiation in OSCC and OED.", "These keratins, especially K4, may be useful for pathological diagnosis.", "We propose that the aberrant expression of K4 and K13 and concomitant up-regulation of the other keratins may be one of the causative factors for morphological alterations in the affected epithelium."], "structured": true}
{"doc_id": 21093407, "title": "Identification of short-lived long non-coding RNAs as surrogate indicators for chemical stress response.", "abstract": ["Abiotic and biotic stressors in human cells are often a result of sudden and/or frequent changes in environmental factors.", "The molecular response to stress involves elaborate modulation of gene expression and is of homeostatic, ecological, and evolutionary importance.", "Although attention has primarily focused on signaling pathways and protein networks, long non-coding RNAs (ncRNAs) are increasingly involved in the molecular mechanisms associated with responses to cellular stresses.", "We identified six novel short-lived long ncRNAs (MIR22HG, GABPB-AS1, LINC00152, IDI2-AS1, SNHG15, and FLJ33630) that responded to chemical stressors (cisplatin, cycloheximide, and mercury (II) oxide) in HeLa Tet-off cells.", "Our results indicate that short-lived long ncRNAs respond to general and specific chemical stressors.", "The expression levels of the short-lived long ncRNAs were elevated because of prolonged decay rates in response to chemical stressors and interruption of RNA degradation pathways.", "We propose that these long ncRNAs have the potential to be surrogate indicators of cellular stress responses."], "structured": false}
{"doc_id": 21108759, "title": "Isolation of a gene encoding a functional zinc finger protein homologous to erythroid Kr\u00fcppel-like factor: identification of a new multigene family.", "abstract": ["We have identified and characterized the gene for a novel zinc finger transcription factor which we have termed lung Kr\u00fcppel-like factor (LKLF).", "LKLF was isolated through the use of the zinc finger domain of erythroid Kr\u00fcppel-like factor (ELKF) as a hybridization probe and is closely related to this erythroid cell-specific gene.", "LKLF is expressed in a limited number of tissues, with the predominant expression seen in the lungs and spleen.", "The gene is developmentally controlled, with expression noted in the 7-day embryo followed by a down-regulation at 11 days and subsequent reactivation.", "A high degree of similarity is noted in the zinc finger regions of LKLF and EKLF.", "Beyond this domain, the sequences diverge significantly, although the putative transactivation domains for both LKLF and EKLF are proline-rich regions.", "In the DNA-binding domain, the three zinc finger motifs are so closely conserved that the predicted DNA contact sites are identical, suggesting that both proteins may bind to the same core sequence.", "This was further suggested by transactivation assays in which mouse fibroblasts were transiently transfected with a human beta-globin reporter gene in the absence and presence of an LKLF cDNA construct.", "Expression of the LKLF gene activates this human beta-globin promoter containing the CACCC sequence previously shown to be a binding site for EKLF.", "Mutation of this potential binding site results in a significant reduction in the reporter gene expression.", "LKLF and EKLF can thus be grouped as members of a unique family of transcription factors which have discrete patterns of expression in different tissues and which appear to recognize the same DNA-binding site."], "structured": false}
{"doc_id": 21114100, "title": "A small molecule restores function to TRPML1 mutant isoforms responsible for mucolipidosis type IV.", "abstract": ["Mucolipidosis type IV (MLIV) is an autosomal recessive lysosomal storage disorder often characterized by severe neurodevelopmental abnormalities and neuro-retinal degeneration.", "Mutations in the TRPML1 gene are causative for MLIV.", "We used lead optimization strategies to identify--and MLIV patient fibroblasts to test--small-molecule activators for their potential to restore TRPML1 mutant channel function.", "Using the whole-lysosome planar patch-clamp technique, we found that activation of MLIV mutant isoforms by the endogenous ligand PI(3,5)P2 is strongly reduced, while activity can be increased using synthetic ligands.", "We also found that the F465L mutation renders TRPML1 pH insensitive, while F408\u0394 impacts synthetic ligand binding.", "Trafficking defects and accumulation of zinc in lysosomes of MLIV mutant fibroblasts can be rescued by the small molecule treatment.", "Collectively, our data demonstrate that small molecules can be used to restore channel function and rescue disease associated abnormalities in patient cells expressing specific MLIV point mutations."], "structured": false}
{"doc_id": 21141798, "title": "Characterization of a murine monoclonal antibody to Cryptococcus neoformans polysaccharide that is a candidate for human therapeutic studies.", "abstract": ["The murine monoclonal antibody (MAb) 18B7 [immunoglobulin G1(kappa)] is in preclinical development for treatment of Cryptococcus neoformans infections.", "In anticipation of its use in humans, we defined the serological and biological properties of MAb 18B7 in detail.", "Structural comparison to the related protective MAb 2H1 revealed conservation of the antigen binding site despite several amino acid differences.", "MAb 18B7 was shown by immunofluorescence and agglutination studies to bind to all four serotypes of C. neoformans, opsonize C. neoformans serotypes A and D, enhance human and mouse effector cell antifungal activity, and activate the complement pathway leading to deposition of complement component 3 (C3) on the cryptococcal capsule.", "Administration of MAb 18B7 to mice led to rapid clearance of serum cryptococcal antigen and deposition in the liver and spleen.", "Immunohistochemical studies revealed that MAb 18B7 bound to capsular glucuronoxylomannan in infected mouse tissues.", "No reactivity of MAb 18B7 with normal human, rat, or mouse tissues was detected.", "The results show that both the variable and constant regions of MAb 18B7 are biologically functional and support the use of this MAb in human therapeutic trials."], "structured": false}
{"doc_id": 21150010, "title": "Treatment with cyclooxygenase-2 inhibitors enables repeated administration of vaccinia virus for control of ovarian cancer.", "abstract": ["Metastatic ovarian cancer is the leading cause of death among women with gynecologic malignancies in the United States.", "The lack of effective treatment for patients with advanced ovarian cancer warrants development of innovative therapies.", "Cancer therapy using oncolytic viruses represents a promising new approach for controlling tumors.", "Vaccinia virus has been shown to preferentially infect tumor cells but not normal tissue.", "However, oncolytic therapy using recombinant viruses faces the limitation of viral clearance due to generation of neutralizing antibodies.", "In the current study, we found that cyclooxygenase-2 (Cox-2) inhibitors circumvented this limitation, enabling repeated administration of vaccinia virus without losing infectivity.", "We quantified the antivaccinia antibody response using enzyme-linked immunosorbent assay (ELISA) and neutralization assays to show that treatment of Cox-2 inhibitors inhibited the generation of neutralizing antibodies.", "Furthermore, we showed that combination treatment of Cox-2 inhibitors with vaccinia virus was more effective that either treatment alone in treating MOSEC/luc tumor-bearing mice.", "Thus, the combination of Cox-2 inhibitors and vaccinia virus represents a potential innovative approach to controlling ovarian tumors."], "structured": false}
{"doc_id": 21164071, "title": "Ser-752-->Pro mutation in the cytoplasmic domain of integrin beta 3 subunit and defective activation of platelet integrin alpha IIb beta 3 (glycoprotein IIb-IIIa) in a variant of Glanzmann thrombasthenia.", "abstract": ["Integrins are membrane receptors which mediate cell-cell or cell-matrix adhesion.", "Integrin alpha IIb beta 3 (glycoprotein IIb-IIIa) acts as a fibrinogen receptor of platelets and mediates platelet aggregation.", "Platelet activation is required for alpha IIb beta 3 to shift from noncompetent to competent for binding soluble fibrinogen.", "The steps involved in this transition are poorly understood.", "We have studied a variant of Glanzmann thrombasthenia, a congenital bleeding disorder characterized by absence of platelet aggregation and fibrinogen binding.", "The patient's platelets did not bind fibrinogen after platelet activation by ADP or thrombin, though his platelets contained alpha IIb beta 3.", "However, isolated alpha IIb beta 3 was able to bind to an Arg-Gly-Asp-Ser affinity column, and binding of soluble fibrinogen to the patient's platelets could be triggered by modulators of alpha IIb beta 3 conformation such as the Arg-Gly-Asp-Ser peptide and alpha-chymotrypsin.", "These data suggested that a functional Arg-Gly-Asp binding site was present within alpha IIb beta 3 and that the patient's defect was not secondary to a blockade of alpha IIb beta 3 in a noncompetent conformational state.", "This was evocative of a defect in the coupling between platelet activation and alpha IIb beta 3 up-regulation.", "We therefore sequenced the cytoplasmic domain of beta 3, following polymerase chain reaction (PCR) on platelet RNA, and found a T-->C mutation at nucleotide 2259, corresponding to a Ser-752-->Pro substitution.", "This mutation is likely to be responsible for the uncoupling of alpha IIb beta 3 from cellular activation because (i) it is not a polymorphism, (ii) it is the only mutation in the entire alpha IIb beta 3 sequence, and (iii) genetic analysis of the family showed that absence of the Pro-752 beta 3 allele was associated with the normal phenotype.", "Our data thus identify the C-terminal portion of the cytoplasmic domain of beta 3 as an intrinsic element in the coupling between alpha IIb beta 3 and platelet activation."], "structured": false}
{"doc_id": 21170174, "title": "Crossover and noncrossover pathways in mouse meiosis.", "abstract": ["During meiosis, recombination between homologous chromosomes generates crossover (CR) and noncrossover (NCR) products.", "CRs establish connections between homologs, whereas intermediates leading to NCRs have been proposed to participate in homologous pairing.", "How these events are differentiated and regulated remains to be determined.", "We have developed a strategy to detect, quantify, and map NCRs in parallel to CRs, at the Psmb9 meiotic recombination hot spot, in male and female mouse germ lines.", "Our results report direct molecular evidence for distinct CR and NCR pathways of DNA double-strand break (DSB) repair in mouse meiosis based on three observations: both CRs and NCRs require Spo11, NCR products have shorter conversion tracts than CRs, and only CRs require the MutL homolog Mlh1.", "We show that both products are formed from middle to late pachytene of meiotic prophase and provide evidence for an Mlh1-independent CR pathway, where mismatch repair does not require Mlh1."], "structured": false}
{"doc_id": 21179714, "title": "IAP regulation of metastasis.", "abstract": ["Inhibitor-of-Apoptosis (IAP) proteins contribute to tumor progression, but the requirements of this pathway are not understood.", "Here, we show that intermolecular cooperation between XIAP and survivin stimulates tumor cell invasion and promotes metastasis.", "This pathway is independent of IAP inhibition of cell death.", "Instead, a survivin-XIAP complex activates NF-kappaB, which in turn leads to increased fibronectin gene expression, signaling by beta1 integrins, and activation of cell motility kinases FAK and Src.", "Therefore, IAPs are direct metastasis genes, and their antagonists could provide antimetastatic therapies in patients with cancer."], "structured": false}
{"doc_id": 21181273, "title": "15-Hydroxyprostaglandin dehydrogenase is down-regulated in colorectal cancer.", "abstract": ["Prostaglandin E2 (PGE2) can stimulate tumor progression by modulating several proneoplastic pathways, including proliferation, angiogenesis, cell migration, invasion, and apoptosis.", "Although steady-state tissue levels of PGE2 stem from relative rates of biosynthesis and breakdown, most reports examining PGE2 have focused solely on the cyclooxygenase-dependent formation of this bioactive lipid.", "Enzymatic degradation of PGE2 involves the NAD+-dependent 15-hydroxyprostaglandin dehydrogenase (15-PGDH).", "The present study examined a range of normal tissues in the human and mouse and found high levels of 15-PGDH in the large intestine.", "By contrast, the expression of 15-PGDH is decreased in several colorectal carcinoma cell lines and in other human malignancies such as breast and lung carcinomas.", "Consistent with these findings, we observe diminished 15-Pgdh expression in ApcMin+/- mouse adenomas.", "Enzymatic activity of 15-PGDH correlates with expression levels and the genetic disruption of 15-Pgdh completely blocks production of the urinary PGE2 metabolite.", "Finally, 15-PGDH expression and activity are significantly down-regulated in human colorectal carcinomas relative to matched normal tissue.", "In summary, these results suggest a novel tumor suppressive role for 15-PGDH due to loss of expression during colorectal tumor progression."], "structured": false}
{"doc_id": 21185923, "title": "Stimulation of CD25+CD4+ regulatory T cells through GITR breaks immunological self-tolerance", "abstract": ["CD25+CD4+ regulatory T cells in normal animals are engaged in the maintenance of immunological self-tolerance.", "We show here that glucocorticoid-induced tumor necrosis factor receptor family\u2013related gene (GITR, also known as TNFRSF18)\u2014a member of the tumor necrosis factor\u2013nerve growth factor (TNF-NGF) receptor gene superfamily\u2014is predominantly expressed on CD25+CD4+ T cells and on CD25+CD4+CD8\u2212 thymocytes in normal na\u00efve mice.", "We found that stimulation of GITR abrogated CD25+CD4+ T cell\u2013mediated suppression.", "In addition, removal of GITR-expressing T cells or administration of a monoclonal antibody to GITR produced organ-specific autoimmune disease in otherwise normal mice.", "Thus, GITR plays a key role in dominant immunological self-tolerance maintained by CD25+CD4+ regulatory T cells and could be a suitable molecular target for preventing or treating autoimmune disease."], "structured": false}
{"doc_id": 21186109, "title": "The missing cases of tuberculosis in Malawi: the contribution from cross-border registrations.", "abstract": ["Low case detection rates of new smear-positive pulmonary tuberculosis (PTB) patients globally are a cause for concern.", "The aim of this study was to determine for patients registered for TB in Malawi the number and percentage who lived in a neighbouring country and the registration, recording and reporting practices for these 'foreign' patients.", "All 44 non-private hospitals, which register and treat all TB patients in the public health sector in Malawi, were visited.", "Ten (23%) hospitals in 2001 and 14 (32%) in 2002 maintained a separate register for cross-border TB cases.", "Patients recorded in these registers were not formally reported to the Malawi National TB Programme (NTP), the neighbouring country's NTP, nor to WHO.", "They therefore constitute missing cases.", "In Malawi, the number of cross-border new smear-positive PTB cases was 77 in 2001 and 91 in 2002, constituting about 3% of missing smear-positive cases in those hospitals that maintain cross-border registers and about 1% of missing cases nationally."], "structured": false}
{"doc_id": 21199527, "title": "Parathyroid hormone induces E4bp4 messenger ribonucleic acid expression primarily through cyclic adenosine 3',5'-monophosphate signaling in osteoblasts.", "abstract": ["PTH binding to its receptor activates protein kinase A (PKA), protein kinase C (PKC), and calcium signaling to induce transcription of primary response genes in osteoblasts.", "Adenovirus E4 promoter-binding protein/nuclear factor regulated by IL-3 (E4BP4/NFIL3), a transcriptional repressor, is a PTH-induced primary response gene in primary mouse osteoblasts (MOBs).", "Here we investigate the signaling pathway(s) that lead to PTH induction of E4bp4 mRNA expression.", "Ten and 100 nm PTH induced maximum E4bp4 expression in MOBs.", "Forskolin (FSK), an adenylate cyclase inducer, 8-bromo-cAMP, a cAMP analog, and phorbol myristate acetate, a PKC activator, increased E4bp4 mRNA levels, whereas ionomycin, a calcium ionophore, had no effect.", "Pretreatment of cells with 30 microm H89, a PKA inhibitor, strongly inhibited PTH- and FSK-induced E4bp4 expression.", "In contrast, overnight pretreatment with 1 microm phorbol myristate acetate to down-regulate PKC signaling did not alter PTH and FSK effects.", "Moreover, PTH (3-34) that does not activate cAMP signaling did not increase E4bp4 expression.", "Prostaglandin E(2), which signals through cAMP, increased E4bp4 mRNA at all doses, whereas prostaglandin F(2alpha) that primarily activates PKC and calcium signaling, induced E4bp4 only at high doses and fluprostenol that only activates PKC and calcium signaling, had no effect.", "Finally, 80 microg/kg PTH (1-34) ip injection induced E4bp4 mRNA expression at 1 h in mice.", "In contrast, 80 microg/kg PTH (3-34) had no effect.", "Our data suggest that PTH-induced E4bp4 mRNA expression is mediated primarily through cAMP-PKA signaling in vitro and in vivo.", "In conjunction with our previous report, we hypothesize that E4bp4 attenuates transcription of osteoblastic genes possessing E4bp4 promoter binding sites."], "structured": false}
{"doc_id": 21203899, "title": "Managing finances of shipping living donor kidneys for donor exchanges.", "abstract": ["Kidney donor exchanges enable recipients with immunologically incompatible donors to receive compatible living donor grafts; however, the financial management of these exchanges, especially when an organ is shipped, is complex and thus has the potential to impede the broader implementation of donor exchange programs.", "Representatives from transplant centers that utilize the National Kidney Registry database to facilitate donor exchange transplants developed a financial model applicable to paired donor exchanges and donor chain transplants.", "The first tenet of the model is to eliminate financial liability to the donor.", "Thereafter, it accounts for the donor evaluation, donor nephrectomy hospital costs, donor nephrectomy physician fees, organ transport, donor complications and recipient inpatient services.", "Billing between hospitals is based on Medicare cost report defined costs rather than charges.", "We believe that this model complies with current federal regulations and effectively captures costs of the donor and recipient services.", "It could be considered as a financial paradigm for the United Network for Organ Sharing managed donor exchange program."], "structured": false}
{"doc_id": 21216726, "title": "Human herpesvirus 8 infection and Kaposi's sarcoma among human immunodeficiency virus-infected and -uninfected women.", "abstract": ["Little is known about the epidemiology of human herpesvirus 8 (HHV-8) infections among women.", "A cross-sectional study was conducted of HHV-8 infection among human immunodeficiency virus (HIV)-infected and high-risk HIV-uninfected women.", "Serological tests with noninduced (latent) and induced (lytic) HHV-8 antigens were used to detect infection among 2483 participants of a multisite cohort.", "Reactivity to latent antigen was present in 4.1% and to induced antigens in 12.0% of women.", "Seven of 8 women who reported Kaposi's sarcoma had HHV-8 antibodies.", "Among HIV-positive women, HHV-8 infection was associated with use of crack, cocaine, or heroin (76% vs. 65%; P<.001), past syphilis (29% vs. 20%; P<.001), an injection drug-using male sex partner (61% vs. 53%; P=.014), black race (P=.010), and enrollment site (P=.015).", "In multivariate analysis, HIV infection, older age, past syphilis, black race, and enrollment site were independently associated with HHV-8 infection.", "In this cohort of North American women, HHV-8 infection was associated with HIV infection, drug use, and risky sexual behavior."], "structured": false}
{"doc_id": 21219071, "title": "Cloning of three novel neuronal Cdk5 activator binding proteins.", "abstract": ["Neuronal Cdc2-like kinase (Nclk) is involved in the regulation of neuronal differentiation and neuro-cytoskeleton dynamics.", "The active kinase consists of a catalytic subunit, Cdk5, and a 25 kDa activator protein (p25nck5a) derived from a 35 kDa neuronal-specific protein (p35nck5a).", "As an extension of our previous study (Qi, Z., Tang, D., Zhu, X., Fujita, D.J., Wang, J.H., 1998.", "Association of neurofilament proteins with neuronal Cdk5 activator.", "J. Biol.", "Chem.", "270, 2329-2335), which showed that neurofilament is one of the p35nck5a-associated proteins, we now report the isolation of three other novel p35nck5a-associated proteins using the yeast two-hybrid screen.", "The full-length forms of these three novel proteins, designated C42, C48 and C53, have a molecular mass of 66, 24, and 57 kDa, respectively.", "Northern analysis indicates that these novel proteins are widely expressed in human tissues, including the heart, brain, skeletal muscle, placenta, lung, liver, kidney and pancreas.", "The bacterially expressed glutathione S-transferase (GST)-fusion forms of these three proteins were able to co-precipitate p35nck5a complexed with Cdk5 from insect cell lysate.", "Among these three proteins, only C48 and C53 can be phosphorylated by Nclk, suggesting that they may be the substrates of Nclk.", "Sequence homology searches have suggested that the C48 protein is marginally related to restin protein, whereas the C42 protein has homologues of unknown function in Caenorhabditis elegans and Arabidopsis thaliana."], "structured": false}
{"doc_id": 21221346, "title": "The Artemis:DNA-PKcs endonuclease cleaves DNA loops, flaps, and gaps.", "abstract": ["In eukaryotic cells, nonhomologous DNA end joining (NHEJ) is a major pathway for repair of double-strand DNA breaks (DSBs).", "Artemis and the 469kDa DNA-dependent protein kinase (DNA-PKcs) together form a key nuclease for NHEJ in vertebrate organisms.", "The structure-specific endonucleolytic activity of Artemis is activated by binding to and phosphorylation by DNA-PKcs.", "We tested various DNA structures in order to understand the range of structural features that are recognized by the Artemis:DNA-PKcs complex.", "We find that all tested substrates that contain single-to-double-strand transitions can be cleaved by the Artemis:DNA-PKcs complex near the transition region.", "The cleaved substrates include heterologous loops, stem-loops, flaps, and gapped substrates.", "Such versatile activity on single-/double-strand transition regions is important in understanding how reconstituted NHEJ systems that lack DNA polymerases can join incompatible DNA ends and yet preserve 3' overhangs.", "Additionally, the flexibility of the Artemis:DNA-PKcs nuclease may be important in removing secondary structures that hinder processing of DNA ends during NHEJ."], "structured": false}
{"doc_id": 21230110, "title": "A promoter derived from taro bacilliform badnavirus drives strong expression in transgenic banana and tobacco plants", "abstract": ["Taro bacilliform virus (TaBV) is a pararetrovirus of the genus Badnavirus which infects the monocotyledonous plant, taro (Colocasia esculenta).", "A region of the TaBV genome spanning nucleotides 6,281 to 12 (T1200), including the 3\u2032 end of open reading frame 3 (ORF 3) and the intergenic region to the end of the tRNAmet-binding site, was tested for promoter activity along with four different 5\u2032 deletion fragments (T600, T500, T250 and T100).", "In transient assays, only the T1200, T600, T500 fragments were shown to have promoter activity in taro leaf, banana suspension cells and tobacco callus.", "When these three promoters were evaluated in stably transformed, in vitro-grown transgenic banana and tobacco plants, all were found to drive near-constitutive expression of either the green fluorescent protein or \u03b2-glucuronidase (GUS) reporter gene in the stem (or pseudostem), leaves and roots, with strongest expression observed in the vascular tissue.", "In transgenic banana leaves, the T600 promoter directed four-fold greater GUS activity than that of the T1200, T500 and the maize polyubiquitin-1 promoters.", "In transgenic tobacco leaves, the levels of GUS expression directed by the three promoters was between four- and ten-fold lower than that of the double Cauliflower mosaic virus 35S promoter.", "These results indicate that the TaBV-derived promoters may be useful for the high-level constitutive expression of transgenes in either monocotyledonous or dicotyledonous species."], "structured": false}
{"doc_id": 21232018, "title": "Age of ovary determines remaining life expectancy in old ovariectomized mice.", "abstract": ["We investigated the capacity of young ovaries, transplanted into old ovariectomized CBA mice, to improve remaining life expectancy of the hosts.", "Donor females were sexually mature 2-month-olds; recipients were prepubertally ovariectomized at 3 weeks and received transplants at 5, 8 or 11 months of age.", "Relative to ovariectomized control females, life expectancy at 11 months was increased by 60% in 11-month recipient females and by 40% relative to intact control females.", "Only 20% of the 11-month transplant females died in the 300-day period following ovarian transplantation, whereas nearly 65% of the ovariectomized control females died during this same period.", "The 11-month-old recipient females resumed oestrus and continued to cycle up to several months beyond the age of control female reproductive senescence.", "Across the three recipient age groups, transplantation of young ovaries increased life expectancy in proportion to the relative youth of the ovary.", "Our results relate to recent findings on the gonadal input upon aging in Caenorhabditis elegans and may suggest how the mammalian gonad, including that of humans, could regulate aging and determine longevity."], "structured": false}
{"doc_id": 21239672, "title": "Use of macrolides in mother and child and risk of infantile hypertrophic pyloric stenosis: nationwide cohort study", "abstract": ["OBJECTIVE To assess the association between use of macrolide antibiotics in mothers and infants from pregnancy onset until 120 days after birth and infantile hypertrophic pyloric stenosis (IHPS).   \n", "DESIGN Nationwide register based cohort study.   \n", "SETTING Denmark, 1996-2011.   \n", "PARTICIPANTS 999,378 liveborn singletons and linked individual level information on macrolide prescriptions (maternal use during pregnancy, n=30,091; maternal use after birth, n=21,557; use in infants, n=6591), surgery for IHPS, and potential confounders.   \n", "MAIN OUTCOME MEASURES Surgery for IHPS by three categories of macrolide use: in mothers during pregnancy, in mothers after birth, and in infants after birth.   \n", "RESULTS 880 infants developed IHPS (0.9 cases per 1000 births).", "Compared with infants with no use of macrolides, the adjusted rate ratio for IHPS in infants with use of macrolides during days 0 to 13 after birth was 29.8 (95% confidence interval 16.4 to 54.1) and during days 14 to 120 was 3.24 (1.20 to 8.74); the corresponding absolute risk differences were 24.4 (95% confidence interval 13.0 to 44.1) and 0.65 (0.06 to 2.21) cases per 1000 infants exposed to macrolides, respectively.", "The rate ratio for maternal use of macrolides for days 0 to 13 after birth was 3.49 (1.92 to 6.34) and for days 14 to 120 was 0.70 (0.26 to 1.90); the corresponding absolute risk differences were 2.15 (0.82 to 4.64) and -0.11 (-0.26 to 0.31).", "The rate ratios for maternal use of macrolides during pregnancy were 1.02 (0.65 to 1.59) for weeks 0 to 27 and 1.77 (0.95 to 3.31) for weeks 28 to birth; the corresponding absolute risk differences were 0.01 (-0.31 to 0.50) and 0.67 (-0.06 to 2.02).   \n", "CONCLUSIONS Treatment of young infants with macrolide antibiotics was strongly associated with IHPS and should therefore only be administered if potential treatment benefits outweigh the risk.", "Maternal use of macrolides during the first two weeks after birth was also associated with an increased risk of IHPS.", "A possible association was also found with use during late pregnancy."], "structured": true}
{"doc_id": 21246752, "title": "The psychiatric manifestations of mitochondrial disorders: a case and review of the literature.", "abstract": ["OBJECTIVE Mitochondrial disorders are caused by gene mutations in mitochondrial or nuclear DNA and affect energy-dependent organs such as the brain.", "Patients with psychiatric illness, particularly those with medical comorbidities, may have primary mitochondrial disorders.", "To date, this issue has received little attention in the literature, and mitochondrial disorders are likely underdiagnosed in psychiatric patients.   \n", "DATA SOURCES This article describes a patient who presented with borderline personality disorder and treatment-resistant depression and was ultimately diagnosed with mitochondrial encephalomyopathy with lactic acidosis and stroke-like episodes (MELAS) 3271.", "We also searched the literature for all case reports of patients with mitochondrial disorders who initially present with prominent psychiatric symptoms by using MEDLINE (from 1948-February 2011), Embase (from 1980-February 2011), PsycINFO (from 1806-February 2011), and the search terms mitochondrial disorder, mitochondria, psychiatry, mental disorders, major depression, anxiety, schizophrenia, and psychosis.   ", "STUDY SELECTION Fifty cases of mitochondrial disorders with prominent psychiatric symptomatology were identified.   \n", "DATA EXTRACTION Information about the psychiatric presentation of the cases was extracted.", "This information was combined with our case, the most common psychiatric manifestations of mitochondrial disorders were identified, and the important diagnostic and treatment implications for patients with psychiatric illness were reviewed.   \n", "RESULTS The most common psychiatric presentations in the cases of mitochondrial disorders included mood disorder, cognitive deterioration, psychosis, and anxiety.", "The most common diagnosis (52% of cases) was a MELAS mutation.", "Other genetic mitochondrial diagnoses included polymerase gamma mutations, Kearns-Sayre syndrome, mitochondrial DNA deletions, point mutations, twinkle mutations, and novel mutations.   \n", "CONCLUSIONS Patients with mitochondrial disorders can present with primary psychiatric symptomatology, including mood disorder, cognitive impairment, psychosis, and anxiety.", "Psychiatrists need to be aware of the clinical features that are indicative of a mitochondrial disorder, investigate patients with suggestive presentations, and be knowledgeable about the treatment implications of the diagnosis."], "structured": true}
{"doc_id": 21250322, "title": "Polo kinase and Asp are needed to promote the mitotic organizing activity of centrosomes", "abstract": ["Interfering with the activity of polo-like kinases can lead to the formation of monopolar spindles.", "Polo-like kinases also regulate mitotic entry, activation of the anaphase-promoting complex and the necessary preconditions for cytokinesis.", "Similarities between the phenotypes of the Drosophila mutants asp and polo point towards a common role in spindle pole function.", "The abnormal spindles of asp mutants are bipolar but have disorganized broad poles at which \u03b3-tubulin has an abnormal distribution.", "Moreover, the synergism or of polo1 aspE3 double mutants indicates a possible involvement of these genes in a common process.", "Asp is a microtubule-associated protein of relative molecular mass 220,000 (Mr 220K) found at the face of the centrosome that contacts spindle microtubules.", "In partially purified centrosomes, it is required with \u03b3-tubulin to organize microtubule asters.", "Here, we show that Asp is the previously identified Mr 220K substrate of Polo kinase.", "Polo phosphorylates Asp in vitro, converting it into an MPM2 epitope.", "Polo and Asp proteins immunoprecipitate together and exist as part of a 25\u201338S complex.", "Extracts of polo-derived embryos are unable to restore the ability of salt-stripped centrosomes to nucleate microtubule asters.", "This can be rescued by addition of phosphorylated Asp or active Polo kinase."], "structured": false}
{"doc_id": 21257564, "title": "How long will long-term potentiation last?", "abstract": ["The paramount feature of long-term potentiation (LTP) as a memory mechanism is its characteristic persistence over time.", "Although the basic phenomenology of LTP persistence was established 30 years ago, new insights have emerged recently about the extent of LTP persistence and its regulation by activity and experience.", "Thus, it is now evident that LTP, at least in the dentate gyrus, can either be decremental, lasting from hours to weeks, or stable, lasting months or longer.", "Although mechanisms engaged during the induction of LTP regulate its subsequent persistence, the maintenance of LTP is also governed by activity patterns post-induction, whether induced experimentally or generated by experience.", "These new findings establish dentate gyrus LTP as a useful model system for studying the mechanisms governing the induction, maintenance and interference with long-term memory, including very long-term memory lasting months or longer.", "The challenge is to study LTP persistence in other brain areas, and to relate, if possible, the properties and regulation of LTP maintenance to these same properties of the information that is actually stored in those regions."], "structured": false}
{"doc_id": 21258863, "title": "An IL-13 inhibitor blocks the development of hepatic fibrosis during a T-helper type 2-dominated inflammatory response.", "abstract": ["In schistosomiasis, chronic parasite egg-induced granuloma formation can lead to tissue destruction and fibrosis, which causes much of the morbidity and mortality associated with this disease.", "Here we show the importance of IL-13 in the pathogenesis of schistosomiasis, and demonstrate, perhaps for the first time, the therapeutic efficacy of an IL-13 inhibitor, sIL-13Ralpha2-Fc, in the control of hepatic fibrosis.", "T-helper type 2 (Th2) cytokines dominate the immune response in mice infected with Schistosoma mansoni, yet the specific contributions of IL-13 and IL-4 to the development of fibrosis were not previously investigated.", "Our studies demonstrate that both cytokines play redundant roles in granuloma formation, which explains the ability of IL-4-deficient mice to form granulomas around eggs.", "More importantly, however, these studies demonstrate that IL-13 is the dominant Th2-type cytokine regulating fibrosis.", "IL-13 stimulated collagen production in fibroblasts, and procollagen I and procollagen III mRNA expression was decreased in sIL-13Ralpha2-Fc-treated mice.", "Moreover, the reduction in fibrosis observed in IL-4-deficient mice was much less pronounced than that in sIL-13Ralpha2-Fc-treated animals.", "Fibrosis is a major pathological manifestation of a number of allergic, autoimmune, and infectious diseases.", "Thus, our findings provide evidence that IL-13 inhibitors may be of general therapeutic benefit in preventing damaging tissue fibrosis resulting from Th2-dominated inflammatory responses."], "structured": false}
{"doc_id": 21260231, "title": "Validity and reliability of observational methods for studying medication administration errors.", "abstract": ["The validity and reliability of observational methods for studying medication administration errors (MAEs) were studied.", "Between January and June 1998, two pharmacists observed consecutive drug administration rounds by nurses on two wards in a U.K. hospital and recorded all MAEs identified.", "The observers intervened in cases of potentially harmful errors.", "MAE records were audited to determine the percentage of omitted doses for which a corresponding reason was documented for the observation periods and for nonobservation periods.", "Error rates for each drug administration round were analyzed according to whether they were for the nurse's first, second, third (and so on) observed round.", "Error rates were calculated before and after the first intervention with nurses for whom an intervention was made.", "Observer reliability was calculated by comparing the rates of errors identified by the two observers.", "There was no difference between the observation and nonobservation periods in the percentage of omitted doses for which a reason was documented, and there was no change in the error rate with repeated observations.", "There was no difference in error rates before and after the first intervention for each nurse.", "There was also no difference in error detection between the two observers and no change with increasing duration of observation.", "Observation of nurses during drug administration at a U.K. hospital did not significantly affect the MAE rate; nor did tactful interventions by the observers.", "Observer reliability was high.", "Concerns about the validity and reliability of observational methods for identifying MAEs may be unfounded."], "structured": false}
{"doc_id": 21271817, "title": "Directly reprogrammed fibroblasts show global epigenetic remodeling and widespread tissue contribution.", "abstract": ["Ectopic expression of the four transcription factors Oct4, Sox2, c-Myc, and Klf4 is sufficient to confer a pluripotent state upon the fibroblast genome, generating induced pluripotent stem (iPS) cells.", "It remains unknown if nuclear reprogramming induced by these four factors globally resets epigenetic differences between differentiated and pluripotent cells.", "Here, using novel selection approaches, we have generated iPS cells from fibroblasts to characterize their epigenetic state.", "Female iPS cells showed reactivation of a somatically silenced X chromosome and underwent random X inactivation upon differentiation.", "Genome-wide analysis of two key histone modifications indicated that iPS cells are highly similar to ES cells.", "Consistent with these observations, iPS cells gave rise to viable high-degree chimeras with contribution to the germline.", "These data show that transcription factor-induced reprogramming leads to the global reversion of the somatic epigenome into an ES-like state.", "Our results provide a paradigm for studying the epigenetic modifications that accompany nuclear reprogramming and suggest that abnormal epigenetic reprogramming does not pose a problem for the potential therapeutic applications of iPS cells."], "structured": false}
{"doc_id": 21272977, "title": "Exocrine ontogenies: on the development of pancreatic acinar, ductal and centroacinar cells.", "abstract": ["This review summarizes our current understanding of exocrine pancreas development, including the formation of acinar, ductal and centroacinar cells.", "We discuss the transcription factors associated with various stages of exocrine differentiation, from multipotent progenitor cells to fully differentiated acinar and ductal cells.", "Within the branching epithelial tree of the embryonic pancreas, this involves the progressive restriction of multipotent pancreatic progenitor cells to either a central \"trunk\" domain giving rise to the islet and ductal lineages, or a peripheral \"tip\" domain giving rise to acinar cells.", "This review also discusses the soluble morphogens and other signaling pathways that influence these events.", "Finally, we examine centroacinar cells as an enigmatic pancreatic cell type whose lineage remains uncertain, and whose possible progenitor capacities continue to be explored."], "structured": false}
{"doc_id": 21274496, "title": "The history of SIVS and AIDS: epidemiology, phylogeny and biology of isolates from naturally SIV infected non-human primates (NHP) in Africa.", "abstract": ["Simian immunodeficiency virus (SIV) naturally infects non-human primates in Africa.", "To date, 40 SIVs have been described both in natural hosts and in heterologous species.", "These viruses are highly diverse and the majority cluster in 6 relatively equidistant phylogenetic lineages.", "At least 8 SIVs are currently considered as recombinant viruses, based on different clustering patterns in different genomic regions.", "Only three types of genomes are known, based on the number of accessory genes: vpr-containing genomes, vpr-vpx containing genomes and vpr-vpu-containing genomes.", "vpx resulted by a duplication of the vpr gene following non-homologous recombination and is characteristic of SIVs infecting the Papionini tribe of monkeys and HIV-2 in humans.", "vpu is characteristic of SIVcpz and HIV-1 and may have originated from a recombination involving SIVs from cercopitecini monkeys.", "SIV seems to be non-pathogenic in the vast majority of natural hosts in spite of a high levels of viral replication.", "This is probably a consequence of virus-host adaptation, in which the incubation period of the disease generally exceeds the life span of the African primate host.", "SIVs also have a high propensity for cross-species transmission.", "In the new host, the outcome may vary from inapparent infection to highly pathogenic, the former being reported for African monkeys, whereas the latter being observed in macaques and humans.", "The high diversity of SIVs was generated by a high mutation rate due to a low fidelity of the reverse-transcriptase and active viral and host cell turnover, host-dependent evolution and recombination.", "Cross-species transmission is not rare, however preferential host switching may drive the majority of cross-species transmissions.", "Numerous SIVs tested so far are able to grow in vitro on human PBMC, therefore it has been postulated that SIV represents a threat for infection of humans in Central Africa and that AIDS is a zoonosis.", "However, although the simian origin of the two HIV types is broadly acknowledged, there are no data that AIDS is acquired like a zoonosis.", "SIV may undergo adaptation in the new human host in order to emerge in the general population.", "The study of SIV in their natural hosts should provide important clues to the real threat to human populations and also elucidate the mechanisms associated with a long-term persistent viral infection without clinical consequences for the host."], "structured": false}
{"doc_id": 21274919, "title": "The association between common physical impairments and dementia in low and middle income countries, and, among people with dementia, their association with cognitive function and disability. A 10/66 Dementia Research Group population-based study.", "abstract": ["OBJECTIVE Chronic physical comorbidity is common in dementia.", "However, there is an absence of evidence to support good practice guidelines for attention to these problems.", "We aimed to study the extent of this comorbidity and its impact on cognitive function and disability in population-based studies in low and middle income countries, where chronic diseases and impairments are likely to be both common and undertreated.   \n", "METHODS A multicentre cross-sectional survey of all over 65 year old residents (n = 15 022) in 11 catchment areas in China, India, Cuba, Dominican Republic, Venezuela, Mexico and Peru.", "We estimated the prevalence of pain, incontinence, hearing and visual impairments, mobility impairment and undernutrition according to the presence of dementia and its severity, and, among those with dementia, the independent contribution of these impairments to cognitive function and disability, adjusting for age, gender, education and dementia severity.   \n", "RESULTS Incontinence, hearing impairment, mobility impairment and undernutrition were consistently linearly associated with the presence of dementia and its severity across regions.", "Among people with dementia, incontinence, hearing impairment and mobility impairment were independently associated with disability in all regions while the contributions of pain, visual impairment and undernutrition were inconsistent.", "Only hearing impairment made a notable independent contribution to cognitive impairment.   \n", "CONCLUSIONS There is an urgent need for clinical trials of the feasibility, efficacy and cost-effectiveness of regular physical health checks and remediation of identified pathologies, given the considerable comorbidity identified in our population based studies, and the strong evidence for independent impact upon functioning."], "structured": true}
{"doc_id": 21287352, "title": "Serum biomarkers as predictors of lung function decline in chronic obstructive pulmonary disease.", "abstract": ["BACKGROUND Recent studies show that COPD patients exhibit low-grade systemic inflammation, and that plasma fibrinogen and high neutrophil counts are related to faster declines in lung function.", "We examined correlations between serum biomarkers and the decline of lung function in COPD patients.   \n", "METHOD Baseline levels of 9 serum biomarkers (TIMP-1, alpha1-antitrypsin, MMP-9, TNF-alpha, TGF-beta, IL-6, IL-8, neutrophil elastase and CRP), fibrinogen and white blood cell counts (WCC) were measured in 96 COPD patients.", "Lung function was measured at the time of blood sampling and every 3-6 months during the observation period (median 25.0 months).   \n", "RESULTS Twenty patients were rapid decliners of lung function and 53 patients were non-decliners.", "Neutrophil counts, serum CRP and MMP-9 were significantly higher in the rapid decliners (p<0.05).", "The annual change of % predicted FEV(1) was inversely correlated with MMP-9 (r=-0.288; p<0.01) and CRP (r=-0.354; p<0.005) (partial correlation coefficients adjusted for age, sex, cardiovascular disease, smoking history, and baseline % predicted FEV(1)).", "The remaining biomarkers were not correlated with the annual change of % predicted FEV(1).   \n", "CONCLUSION Serum CRP and MMP-9 levels were related to FEV(1) decline.", "These markers are good candidates as predictors for rapid decline of FEV(1) in COPD patients.", "Additional long-term and larger size studies of COPD patients could help determine the exact roles for these biomarkers."], "structured": true}
{"doc_id": 21295300, "title": "Phosphorylation of ATM by Cdk5 mediates DNA damage signaling and regulates neuronal death", "abstract": ["The phosphatidylinositol-3-kinase-like kinase ATM (ataxia-telangiectasia mutated) has a central role in coordinating DNA damage responses, including cell-cycle checkpoint control, DNA repair and apoptosis.", "Mutations of ATM cause a spectrum of defects ranging from neurodegeneration to cancer predisposition.", "However, the mechanism by which DNA damage activates ATM is poorly understood.", "Here we show that Cdk5 (cyclin-dependent kinase 5), activated by DNA damage, directly phosphorylates ATM at Ser 794 in post-mitotic neurons.", "Phosphorylation at Ser 794 precedes, and is required for, ATM autophosphorylation at Ser 1981, and activates ATM kinase activity.", "The Cdk5-ATM signal regulates phosphorylation and function of the ATM targets p53 and H2AX.", "Interruption of the Cdk5-ATM pathway attenuates DNA-damage-induced neuronal cell cycle re-entry and expression of the p53 targets PUMA and Bax, protecting neurons from death.", "Thus, activation of Cdk5 by DNA damage serves as a critical signal to initiate the ATM response and regulate ATM-dependent cellular processes."], "structured": false}
{"doc_id": 21297708, "title": "Nerve-induced release of nitric oxide in the rabbit gastrointestinal tract as measured by in vivo microdialysis.", "abstract": ["1.", "Nitric oxide (NO) has been suggested as a gastrointestinal neurotransmitter, mediating the gastric receptive relaxation and the relaxation in the peristaltic reflex.", "The aim of the present study was to measure nerve-induced NO formation in vivo in the gastrointestinal tract.", "2.", "Formation of the nitric oxide oxidation products nitrite and nitrate during vagal nerve stimulation were measured in the anaesthetized rabbit.", "Microdialysis probes were inserted into the wall of the stomach and proximal colon, and nitrite and nitrate in dialysate measured by capillary electrophoresis.", "3.", "During bilateral vagal nerve stimulation there was an increase in nitrite and nitrate formation at the level of the stomach and in nitrite formation at the level of the colon.", "This increase was inhibited by intravenous administration of the NO synthase inhibitor N omega-nitro-L-arginine methyl ester (L-NAME 30 mg kg-1).", "Furthermore, L-NAME significantly increased nerve-induced gastric and colonic contractions, as well as spontaneous colonic contractions.", "4.", "In summary, we present a new methodological procedure for quantification of small changes in nitric oxide formation in vivo.", "This study provides evidence that nitric oxide is released in the stomach and colonic wall during vagal nerve activity, at concentrations able to cause inhibition of smooth muscle contractions in vivo."], "structured": false}
{"doc_id": 21301090, "title": "Screening for concomitant diseases in peripheral vascular patients. Results of a systematic approach.", "abstract": ["BACKGROUND Patients considered for arterial surgery, have been shown to have a high incidence of coexistent cardiac, vascular and other diseases, affecting operative risk and survival.", "We developed a systematic workup strategy for detecting these coexistent diseases in our vascular surgical patients, mainly based on non-invasive diagnostic techniques.   \n", "METHODS We evaluated 200 consecutive patients, admitted to the department of vascular surgery in an academic teaching hospital, in order to establish the total incidence of relevant concomitant disorders, the extent to which this screening yielded previously unknown diagnostic information, and the impact on short-term (one year) survival.   \n", "RESULTS Coronary artery disease was present in 46% of the patients; 22% had active ischaemia, newly diagnosed in 5.5%.", "Impaired cardiac function was found in 37%: severely impaired in 12%, newly diagnosed in 27%.", "Carotid artery disease was present in 32%: critical stenoses were found in 9%; new diagnoses in 29.9%.", "Aortic aneurysms were present in 7%, newly diagnosed in 5%.", "Severe renal artery stenosis was present in 5%, newly diagnosed in 3.5%.", "Sixteen % of the patients had chronic obstructive pulmonary disease, newly diagnosed in 3.5%, and 4.5% had unexpected disorders, which were all new diagnoses.", "Overall, new diagnoses were reached in 64.5% of the population, affecting therapeutic strategy immediately in 21% of the patients.", "The presence of coronary artery disease and of cardiac failure were clearly related to one year survival.   \n", "CONCLUSIONS We conclude that a systematic screening strategy, mainly based on noninvasive techniques, can detect the presence of concomitant diseases in the vascular surgical patient.", "Most important seem the newly diagnosed diseases altering surgical management in one out of every five patients; they also have important implications for patient prognosis."], "structured": true}
{"doc_id": 21302115, "title": "Archetypal trajectories of social, psychological, and spiritual wellbeing and distress in family care givers of patients with lung cancer: secondary analysis of serial qualitative interviews", "abstract": ["OBJECTIVE To assess if family care givers of patients with lung cancer experience the patterns of social, psychological, and spiritual wellbeing and distress typical of the patient, from diagnosis to death.   \n", "DESIGN Secondary analysis of serial qualitative interviews carried out every three months for up to a year or to bereavement.   \n", "SETTING South east Scotland.   \n", "PARTICIPANTS 19 patients with lung cancer and their 19 family carers, totalling 88 interviews (42 with patients and 46 with carers).   \n", "RESULTS Carers followed clear patterns of social, psychological, and spiritual wellbeing and distress that mirrored the experiences of those for whom they were caring, with some carers also experiencing deterioration in physical health that impacted on their ability to care.", "Psychological and spiritual distress were particularly dynamic and commonly experienced.", "In addition to the \"Why us?\" response, witnessing suffering triggered personal reflections in carers on the meaning and purpose of life.", "Certain key time points in the illness tended to be particularly problematic for both carers and patients: at diagnosis, at home after initial treatment, at recurrence, and during the terminal stage.   \n", "CONCLUSIONS Family carers witness and share much of the illness experience of the dying patient.", "The multidimensional experience of distress suffered by patients with lung cancer was reflected in the suffering of their carers in the social, psychological, and spiritual domains, with psychological and spiritual distress being most pronounced.", "Carers may need to be supported throughout the period of illness not just in the terminal phase and during bereavement, as currently tends to be the case."], "structured": true}
{"doc_id": 21307488, "title": "HER-2/neu induces p53 ubiquitination via Akt-mediated MDM2 phosphorylation", "abstract": ["HER-2/neu amplification or overexpression can make cancer cells resistant to apoptosis and promotes their growth.", "p53 is crucial in regulating cell growth and apoptosis, and is often mutated or deleted in many types of tumour.", "Moreover, many tumours with a wild-type gene for p53 do not have normal p53 function, suggesting that some oncogenic signals suppress the function of p53.", "In this study, we show that HER-2/neu-mediated resistance to DNA-damaging agents requires the activation of Akt, which enhances MDM2-mediated ubiquitination and degradation of p53.", "Akt physically associates with MDM2 and phosphorylates it at Ser166 and Ser186.", "Phosphorylation of MDM2 enhances its nuclear localization and its interaction with p300, and inhibits its interaction with p19ARF, thus increasing p53 degradation.", "Our study indicates that blocking the Akt pathway mediated by HER-2/neu would increase the cytotoxic effect of DNA-damaging drugs in tumour cells with wild-type p53."], "structured": false}
{"doc_id": 21320417, "title": "T cell memory.", "abstract": ["T cell memory induced by prior infection or vaccination provides enhanced protection against subsequent microbial infections.", "The processes involved in generating and maintaining T cell memory are becoming better understood due to recent technological advances in identifying memory T cells and monitoring their behavior and function in vivo.", "Memory T cells develop in response to a progressive set of cues-starting with signals from antigen-loaded, activated antigen-presenting cells (APCs) and inflammatory mediators induced by the innate immune response, to the poorly defined subsequent signals triggered as the immune response wanes toward homeostasis.", "The persistence of the resting memory T cells that eventually develop is regulated by cytokines.", "This chapter discusses recent findings on how memory T cells develop to confer long-term protective immunity."], "structured": false}
{"doc_id": 21323587, "title": "The impact of organisational change on outcome in an intensive care unit in the United Kingdom", "abstract": ["Objectives: To study the change in outcome for patients admitted to an intensive care unit following the establishment of a team of resident medical staff and a change from an \"open\" to a \"closed\" organisational format.", "Design: Database review of prospectively collected data.", "Setting: Intensive care unit of a postgraduate teaching hospital.", "Subjects: 1134 admissions to the intensive care unit over a 3-year period, of whom 476 (42%) followed elective surgery.", "Main outcome measure: Hospital mortality corrected for illness severity by using the APACHE II scoring system.", "Results: Crude hospital mortality fell from 28% before the changes to 20% afterwards (P=0.01).", "With correction for case-mix factors, the probability of death after the changes was reduced by almost half (OR 0.51; CI 0.32, 0.82, P=0.005).", "Conclusion: A \"closed\" format of organisation of the delivery of care may result in improved outcomes for patients admitted to intensive care units."], "structured": false}
{"doc_id": 21323758, "title": "Monitoring effectiveness and safety of Tafamidis in transthyretin amyloidosis in Italy: a longitudinal multicenter study in a non-endemic area", "abstract": ["Tafamidis is a transthyretin (TTR) stabilizer able to prevent TTR tetramer dissociation.", "There have been a few encouraging studies on Tafamidis efficacy in early-onset inherited transthyretin amyloidosis (ATTR) due to Val30Met mutation.", "However, less is known about its efficacy in later disease stages and in non-Val30Met mutations.", "We performed a multi-center observational study on symptomatic ATTR patients prescribed to receive Tafamidis.", "We followed up patients according to a standardized protocol including general medical, cardiological and neurological assessments at baseline and every 6 months up to 3 years.", "Sixty-one (42 males) patients were recruited.", "Only 28 % of enrolled subjects had the common Val30Met mutation, mean age of onset was remarkably late (59 years) and 18 % was in advanced disease stage at study entry.", "Tafamidis proved safe and well-tolerated.", "One-third of patients did not show significant progression along 36 months, independently from mutation type and disease stage.", "Neurological function worsened particularly in the first 6 months but progression slowed significantly thereafter.", "Autonomic function remained stable in 33 %, worsened in 56 % and improved in 10 %.", "Fifteen percent of patients showed cardiac disease progression and 30 % new onset of cardiomyopathy.", "Overall, Tafamidis was not able to prevent functional progression of the disease in 23 (43 %) subjects, including 16 patients who worsened in their walking ability and 12 patients who reached a higher NYHA score during the follow-up period.", "A higher mBMI at baseline was associated with better preservation of neurological function.", "In conclusion, neuropathy and cardiomyopathy progressed in a significant proportion of patients despite treatment.", "However, worsening of neurological function slowed after the first 6 months and also subjects with more advanced neuropathy, as well as patients with non-Val30Met mutation, benefited from treatment.", "Body weight preservation is an important favorable prognostic factor."], "structured": false}
{"doc_id": 21330280, "title": "The Spliceosome: Design Principles of a Dynamic RNP Machine", "abstract": ["Ribonucleoproteins (RNPs) mediate key cellular functions such as gene expression and its regulation.", "Whereas most RNP enzymes are stable in composition and harbor preformed active sites, the spliceosome, which removes noncoding introns from precursor messenger RNAs (pre-mRNAs), follows fundamentally different strategies.", "In order to provide both accuracy to the recognition of reactive splice sites in the pre-mRNA and flexibility to the choice of splice sites during alternative splicing, the spliceosome exhibits exceptional compositional and structural dynamics that are exploited during substrate-dependent complex assembly, catalytic activation, and active site remodeling."], "structured": false}
{"doc_id": 21363424, "title": "Blimp-1 attenuates Th1 differentiation by repression of ifng, tbx21, and bcl6 gene expression.", "abstract": ["T cell-specific deletion of Blimp-1 causes abnormal T cell homeostasis and function, leading to spontaneous, fatal colitis in mice.", "Herein we explore the role of Blimp-1 in Th1/Th2 differentiation.", "Blimp-1 mRNA and protein are more highly expressed in Th2 cells compared with Th1 cells, and Blimp-1 attenuates IFN-gamma production in CD4 cells activated under nonpolarizing conditions.", "Although Blimp-1-deficient T cells differentiate normally to Th2 cytokines in vitro, Blimp-1 is required in vivo for normal Th2 humoral responses to NP-KLH (4-hydroxy-3-nitrophenylacetyl/keyhole lymphocyte hemocyanin) immunization.", "Lack of Blimp-1 in CD4 T cells causes increased IFN-gamma, T-bet, and Bcl-6 mRNA.", "By chromatin immunoprecipitation we show that Blimp-1 binds directly to a distal regulatory region in the ifng gene and at multiple sites in tbx21 and bcl6 genes.", "Our data provide evidence that Blimp-1 functions in Th2 cells to reinforce Th2 differentiation by repressing critical Th1 genes."], "structured": false}
{"doc_id": 21366394, "title": "CX3CR1 is required for airway inflammation by promoting T helper cell survival and maintenance in inflamed lung", "abstract": ["Allergic asthma is a T helper type 2 (T(H)2)-dominated disease of the lung.", "In people with asthma, a fraction of CD4(+) T cells express the CX3CL1 receptor, CX3CR1, and CX3CL1 expression is increased in airway smooth muscle, lung endothelium and epithelium upon allergen challenge.", "Here we found that untreated CX3CR1-deficient mice or wild-type (WT) mice treated with CX3CR1-blocking reagents show reduced lung disease upon allergen sensitization and challenge.", "Transfer of WT CD4(+) T cells into CX3CR1-deficient mice restored the cardinal features of asthma, and CX3CR1-blocking reagents prevented airway inflammation in CX3CR1-deficient recipients injected with WT T(H)2 cells.", "We found that CX3CR1 signaling promoted T(H)2 survival in the inflamed lungs, and injection of B cell leukemia/lymphoma-2 protein (BCl-2)-transduced CX3CR1-deficient T(H)2 cells into CX3CR1-deficient mice restored asthma.", "CX3CR1-induced survival was also observed for T(H)1 cells upon airway inflammation but not under homeostatic conditions or upon peripheral inflammation.", "Therefore, CX3CR1 and CX3CL1 may represent attractive therapeutic targets in asthma."], "structured": false}
{"doc_id": 21369472, "title": "TRPC6 is a glomerular slit diaphragm-associated channel required for normal renal function", "abstract": ["Progressive kidney failure is a genetically and clinically heterogeneous group of disorders.", "Podocyte foot processes and the interposed glomerular slit diaphragm are essential components of the permeability barrier in the kidney.", "Mutations in genes encoding structural proteins of the podocyte lead to the development of proteinuria, resulting in progressive kidney failure and focal segmental glomerulosclerosis.", "Here, we show that the canonical transient receptor potential 6 (TRPC6) ion channel is expressed in podocytes and is a component of the glomerular slit diaphragm.", "We identified five families with autosomal dominant focal segmental glomerulosclerosis in which disease segregated with mutations in the gene TRPC6 on chromosome 11q.", "Two of the TRPC6 mutants had increased current amplitudes.", "These data show that TRPC6 channel activity at the slit diaphragm is essential for proper regulation of podocyte structure and function."], "structured": false}
{"doc_id": 21372171, "title": "Usefulness of high mobility group box 1 protein as a plasma biomarker in patient with peripheral artery disease.", "abstract": ["Atherosclerosis is often associated with chronic vascular inflammation.", "High-mobility group box 1 protein (HMGB1) plays various roles, not only as a transcriptional regulatory factor in the nucleus, but also as an inflammatory mediator.", "A previous study suggested that fibrinogen is an important factor associated with atherosclerosis progression.", "The present study was performed to examine the levels of plasma HMGB1 protein in atherosclerosis patients.", "We studied 24 patients with peripheral artery disease (PAD) with atherosclerosis, and 10 healthy controls.", "We found that the concentrations of HMGB1 were increased in the plasma of the patients with atherosclerosis, and there were significant correlations between the plasma HMGB1 and fibrinogen levels.", "Plasma HMGB1 may play a key role in the pathogenesis of clinical and experimental atherosclerosis."], "structured": false}
{"doc_id": 21373240, "title": "Functional specialization of Piwi proteins in Paramecium tetraurelia from post-transcriptional gene silencing to genome remodelling", "abstract": ["Proteins of the Argonaute family are small RNA carriers that guide regulatory complexes to their targets.", "The family comprises two major subclades.", "Members of the Ago subclade, which are present in most eukaryotic phyla, bind different classes of small RNAs and regulate gene expression at both transcriptional and post-transcriptional levels.", "Piwi subclade members appear to have been lost in plants and fungi and were mostly studied in metazoa, where they bind piRNAs and have essential roles in sexual reproduction.", "Their presence in ciliates, unicellular organisms harbouring both germline micronuclei and somatic macronuclei, offers an interesting perspective on the evolution of their functions.", "Here, we report phylogenetic and functional analyses of the 15 Piwi genes from Paramecium tetraurelia.", "We show that four constitutively expressed proteins are involved in siRNA pathways that mediate gene silencing throughout the life cycle.", "Two other proteins, specifically expressed during meiosis, are required for accumulation of scnRNAs during sexual reproduction and for programmed genome rearrangements during development of the somatic macronucleus.", "Our results indicate that Paramecium Piwi proteins have evolved to perform both vegetative and sexual functions through mechanisms ranging from post-transcriptional mRNA cleavage to epigenetic regulation of genome rearrangements."], "structured": false}
{"doc_id": 21373821, "title": "A parasomnia overlap disorder involving sleepwalking, sleep terrors, and REM sleep behavior disorder in 33 polysomnographically confirmed cases.", "abstract": ["A series of 33 patients with combined (injurious) sleepwalking, sleep terrors, and rapid eye movement (REM) sleep behavior disorder (viz.", "\"parasomnia overlap disorder\") was gathered over an 8-year period.", "Patients underwent clinical and polysomnographic evaluations.", "Mean age was 34 +/-", "14 (SD) years; mean age of parasomnia onset was 15 +/-", "16 years (range 1-66); 70% (n = 23) were males.", "An idiopathic subgroup (n = 22) had a significantly earlier mean age of parasomnia onset (9 +/-", "7 years) than a symptomatic subgroup (n = 11) (27 +/-", "23 years, p = 0.002), whose parasomnia began with either of the following: neurologic disorders, n = 6 [congenital Mobius syndrome, narcolepsy, multiple sclerosis, brain tumor (and treatment), brain trauma, indeterminate disorder (exaggerated startle response/atypical cataplexy)]; nocturnal paroxysmal atrial fibrillation, n = 1; posttraumatic stress disorder/major depression, n = 1; chronic ethanol/amphetamine abuse and withdrawal, n = 1; or mixed disorders (schizophrenia, brain trauma, substance abuse), n = 2.", "The rate of DSM-III-R (Diagnostic and Statistical Manual, 3rd edition, revised)", "Axis 1 psychiatric disorders was not elevated; group scores on various psychometric tests were not elevated.", "Forty-five percent (n = 15) had previously received psychologic or psychiatric therapy for their parasomnia, without benefit.", "Treatment outcome was available for n = 20 patients; 90% (n = 18) had substantial parasomnia control with bedtime clonazepam (n = 13), alprazolam and/or carbamazepine (n = 4), or self-hypnosis (n = 1).", "Thus, \"parasomnia overlap disorder\" is a treatable condition that emerges in various clinical settings and can be understood within the context of current knowledge on parasomnias and motor control/dyscontrol during sleep."], "structured": false}
{"doc_id": 21377587, "title": "How can health care organizations be reliably compared?: Lessons from a national survey of patient experience.", "abstract": ["BACKGROUND Patient experience is increasingly used to assess organizational performance, for example in public reporting or pay-for-performance schemes.", "Conventional approaches using 95% confidence intervals are commonly used to determine required survey samples or to report performance but these may result in unreliable organizational comparisons.   \n", "METHODS We analyzed data from 2.2 million patients who responded to the English 2009 General Practice Patient Survey, which included 45 patient experience questions nested within 6 different care domains (access, continuity of care, communication, anticipatory care planning, out-of-hours care, and overall care satisfaction).", "For each question, unadjusted and case-mix adjusted (for age, sex, and ethnicity) organization-level reliability, and intraclass correlation coefficients were calculated.   \n", "RESULTS Mean responses per organization ranged from 23 to 256 for questions evaluating primary care practices, and from 1454 to 2758 for questions evaluating out-of-hours care organizations.", "Adjusted and unadjusted reliability values were similar.", "Twenty-six questions had excellent reliability (\u22650.90).", "Seven nurse communication questions had very good reliability (\u22650.85), but 3 anticipatory care planning questions had lower reliability (<0.70).", "Reliability was typically <0.70 for questions with <100 mean responses per practice, usually indicating questions which only a subset of patients were eligible to answer.", "Nine questions had both excellent reliability and high intraclass correlation coefficients (\u22650.10) indicating both reliable measurement and substantial performance variability.   \n", "CONCLUSIONS High reliability is a necessary property of indicators used to compare health care organizations.", "Using the English General Practice Patient Survey as a case study, we show how reliability and intraclass correlation coefficients can be used to select measures to support robust organizational comparisons, and to design surveys that will both provide high-quality measurement and optimize survey costs."], "structured": true}
{"doc_id": 21380232, "title": "Conservation of methylation reprogramming in mammalian development: aberrant reprogramming in cloned embryos.", "abstract": ["Mouse embryos undergo genome-wide methylation reprogramming by demethylation in early preimplantation development, followed by remethylation thereafter.", "Here we show that genome-wide reprogramming is conserved in several mammalian species and ask whether it also occurs in embryos cloned with the use of highly methylated somatic donor nuclei.", "Normal bovine, rat, and pig zygotes showed a demethylated paternal genome, suggesting active demethylation.", "In bovine embryos methylation was further reduced during cleavage up to the eight-cell stage, and this reduction in methylation was followed by de novo methylation by the 16-cell stage.", "In cloned one-cell embryos there was a reduction in methylation consistent with active demethylation, but no further demethylation occurred subsequently.", "Instead, de novo methylation and nuclear reorganization of methylation patterns resembling those of differentiated cells occurred precociously in many cloned embryos.", "Cloned, but not normal, morulae had highly methylated nuclei in all blastomeres that resembled those of the fibroblast donor cells.", "Our study shows that epigenetic reprogramming occurs aberrantly in most cloned embryos; incomplete reprogramming may contribute to the low efficiency of cloning."], "structured": false}
{"doc_id": 21380348, "title": "Intracellular transport of fat-soluble vitamins A and E.", "abstract": ["Vitamins are compounds that are essential for the normal growth, reproduction and functioning of the human body.", "Of the 13 known vitamins, vitamins A, D, E and K are lipophilic compounds and are therefore called fat-soluble vitamins.", "Because of their lipophilicity, fat-soluble vitamins are solubilized and transported by intracellular carrier proteins to exert their actions and to be metabolized properly.", "Vitamin A and its derivatives, collectively called retinoids, are solubilized by intracellular retinoid-binding proteins such as cellular retinol-binding protein (CRBP), cellular retinoic acid-binding protein (CRABP) and cellular retinal-binding protein (CRALBP).", "These proteins act as chaperones that regulate the metabolism, signaling and transport of retinoids.", "CRALBP-mediated intracellular retinoid transport is essential for vision in human.", "\u03b1-Tocopherol, the main form of vitamin E found in the body, is transported by \u03b1-tocopherol transfer protein (\u03b1-TTP) in hepatic cells.", "Defects of \u03b1-TTP cause vitamin E deficiency and neurological disorders in humans.", "Recently, it has been shown that the interaction of \u03b1-TTP with phosphoinositides plays a critical role in the intracellular transport of \u03b1-tocopherol and is associated with familial vitamin E deficiency.", "In this review, we summarize the mechanisms and biological significance of the intracellular transport of vitamins A and E."], "structured": false}
{"doc_id": 21382907, "title": "Reduced Cytokine Release in Ex Vivo Response to Cilengitide and Cetuximab Is a Marker for Improved Survival of Head and Neck Cancer Patients", "abstract": ["Targeting of \u03b1V\u03b23 and \u03b1V\u03b25 integrins by cilengitide may reduce growth of solid tumors including head and neck squamous cell carcinoma (HNSCC).", "Preclinical investigations suggest increased activity of cilengitide in combination with other treatment modalities.", "The only published trial in HNSCC (ADVANTAGE) investigated cisplatin, 5-fluorouracil, and cetuximab (PFE) without or with once (PFE+CIL1W) or twice weekly cilengitide (PFE+CIL2W) in recurrent/metastatic HNSCC.", "ADVANTAGE showed good tolerability of the cilengitide arms and even lower adverse events (AEs) compared to PFE but not the benefit in overall survival expected based on preclinical data.", "As we found in the FLAVINO assay, a short-time ex vivo assay for prediction of chemosensitivity, only a subgroup of HNSCC had an increased suppressive effect of cilengitide containing combination therapies on colony formation of epithelial cells (CFec) and release of pro-angiogenetic and pro-inflammatory cytokines, whereas other HNSCC failed to respond.", "Response to \u03b1V\u03b23 and \u03b1V\u03b25 integrin targeting by cilengitide classifies HNSCC regarding outcome.", "We present FLAVINO data arguing for further development of cilengitide plus cetuximab in treatment of a subgroup of HNSCC potentially identified by the FLAVINO assay using a set of biomarkers for response evaluation."], "structured": false}
{"doc_id": 21383026, "title": "Genes required for mycobacterial growth defined by high density mutagenesis.", "abstract": ["Despite over a century of research, tuberculosis remains a leading cause of infectious death worldwide.", "Faced with increasing rates of drug resistance, the identification of genes that are required for the growth of this organism should provide new targets for the design of antimycobacterial agents.", "Here, we describe the use of transposon site hybridization (TraSH) to comprehensively identify the genes required by the causative agent, Mycobacterium tuberculosis, for optimal growth.", "These genes include those that can be assigned to essential pathways as well as many of unknown function.", "The genes important for the growth of M. tuberculosis are largely conserved in the degenerate genome of the leprosy bacillus, Mycobacterium leprae, indicating that non-essential functions have been selectively lost since this bacterium diverged from other mycobacteria.", "In contrast, a surprisingly high proportion of these genes lack identifiable orthologues in other bacteria, suggesting that the minimal gene set required for survival varies greatly between organisms with different evolutionary histories."], "structured": false}
{"doc_id": 21387297, "title": "Production of de novo cardiomyocytes: human pluripotent stem cell differentiation and direct reprogramming.", "abstract": ["Cardiovascular disease is a leading cause of death worldwide.", "The limited capability of heart tissue to regenerate has prompted methodological developments for creating de novo cardiomyocytes, both in vitro and in vivo.", "Beyond uses in cell replacement therapy, patient-specific cardiomyocytes may find applications in drug testing, drug discovery, and disease modeling.", "Recently, approaches for generating cardiomyocytes have expanded to encompass three major sources of starting cells: human pluripotent stem cells (hPSCs), adult heart-derived cardiac progenitor cells (CPCs), and reprogrammed fibroblasts.", "We discuss state-of-the-art methods for generating de novo cardiomyocytes from hPSCs and reprogrammed fibroblasts, highlighting potential applications and future challenges."], "structured": false}
{"doc_id": 21392223, "title": "Within the hemopoietic system, LAR phosphatase is a T cell lineage-specific adhesion receptor-like protein whose phosphatase activity appears dispensable for T cell development, repertoire selection and function.", "abstract": ["Expression of the receptor-type tyrosine phosphatase LAR was studied in cells of the murine hemopoietic system.", "The gene is expressed in all cells of the T cell lineage but not in cells of any other hemopoietic lineage and the level of expression in T cells is developmentally regulated.", "The CD4(-)8(-)44(+) early thymic immigrants and mature (CD4(+)8(-)/CD4(-)8(+)) thymocytes and T cells express low levels, whereas immature (CD4(-)8(-)44(-) and CD4(+)8(+)) thymocytes express high levels of LAR.", "Among bone marrow cells only uncommitted c-kit(+)B220(+)CD19(-) precursors, but not B cell lineage committed c-kit(+)B220(+)CD19(+) precursors, express low levels of LAR.", "In contrast to the c-kit(+)B220(+)CD19(+) pre-BI cells from normal mice, counterparts of pre-BI cells from PAX-5-deficient mice express LAR, indicating that PAX-5-mediated commitment to the B cell lineage results in suppression of LAR.", "During differentiation of PAX-5-deficient pre-BI cell line into non-T cell lineages, expression of LAR is switched off, but it is up-regulated during differentiation into thymocytes.", "Thus, within the hemopoietic system, LAR appears to be a T cell lineage-specific receptor-type phosphatase.", "However, surprisingly, truncation of its phosphatase domains has no obvious effect on T cell development, repertoire selection or function."], "structured": false}
{"doc_id": 21392703, "title": "Competition and the evolution of reproductive restraint in malaria parasites.", "abstract": ["All organisms must trade off resource allocation between different life processes that determine their survival and reproduction.", "Malaria parasites replicate asexually in the host but must produce sexual stages to transmit between hosts.", "Because different specialized stages are required for these functions, the division of resources between these life-history components is a key problem for natural selection to solve.", "Despite the medical and economic importance of these parasites, their reproductive strategies remain poorly understood and often seem counterintuitive.", "Here, we tested recent theory predicting that in-host competition shapes how parasites trade off investment in in-host replication relative to between-host transmission.", "We demonstrate, across several genotypes, that Plasmodium chabaudi parasites detect the presence of competing genotypes and facultatively respond by reducing their investment in sexual stages in the manner predicted to maximize their competitive ability.", "Furthermore, we show that genotypes adjust their allocation to sexual stages in line with the availability of exploitable red blood cell resources.", "Our findings are predicted by evolutionary theory developed to explain life-history trade-offs in more traditionally studied multicellular taxa and suggest that the answer to the long-standing question of why so few transmission stages are produced is that in most natural infections heavy investment in reproduction may compromise in-host survival."], "structured": false}
{"doc_id": 21395936, "title": "[Neutrophils and macrophages related to the pathogenesis and disease development of chronic obstructive pulmonary disease by the inflammatory reaction].", "abstract": ["Chronic obstructive pulmonary disease (COPD) is a chronic airway disorder characterized by obstructive airflow limitation which is not completely reversible with treatment.", "Inflammatory changes in the peripheral airways, especially those with the diameter less than 2mm (so-called small airway disease) have been speculated to be initial steps of COPD.", "And so it must be quite clear that neutrophils and macrophages play an essential role in the pathogenesis of these lesions.", "Studies with bronchoalveolar lavage demonstrated an increase in neutrophil numbers and the neutrophil chemoattractant interleukin-8.", "Recent studies demonstrated that neutrophils and macrophages are increased and contain a variety of proteases, which are involved in cell infiltration and activation.", "Studies with gene-engineered animals and anti-cytokine treatment will facilitate better understanding the role of neutrophils and macrophages, and eventual novel therapy."], "structured": false}
{"doc_id": 21414718, "title": "Piezo1 Is as a Novel Trefoil Factor Family 1 Binding Protein that Promotes Gastric Cancer Cell Mobility In Vitro", "abstract": ["Trefoil factor family 1 (TFF1) is a member of the TFF-domain peptide family involved in epithelial restitution and cell motility.", "Recently, we screened Piezo1 as a candidate TFF1-binding protein.", "We aimed to confirm Piezo1 as a novel TFF1 binding protein and to assess the role of this interaction in mediating gastric cancer cell mobility.", "This interaction was confirmed by co-immunoprecipitation and co-localisation of TFF1 and Piezo1 in GES-1 cells.", "We used stable RNA interference to knockdown Piezo1 protein expression and restored the expression of TFF1 in the gastric cancer cell lines SGC-7901 and BGC-823.", "Cell motility was evaluated using invasion assay and migration assay in vitro.", "The expression levels of the integrin subunits \u03b21, \u03b25, \u03b11 as well as the expression of \u03b2-catenin and E-cadherin were detected by Western blot.", "We demonstrate that TFF1, but not TFF2 or TFF3, bind to and co-localize with Piezo1 in the cytoplasm in vitro.", "TFF1 interacts with the C-terminal portion of the Piezo1 protein.", "Wound healing and trans-well assays demonstrated that the restored expression of TFF1 promoted cell mobility in gastric cancer cells, and this effect was attenuated by the knockdown of Piezo1.", "Western blots demonstrated the decreased expression of integrin \u03b21 in Piezo1-knockdown cells.", "Our data demonstrate that Piezo1 is a novel TFF1 binding protein that is important for TFF1-mediated cell migration and suggest that this interaction may be a therapeutic target in the invasion and metastasis of gastric cancer."], "structured": false}
{"doc_id": 21425864, "title": "A conditionally lethal yeast mutant blocked at the first step in glycosyl phosphatidylinositol anchor synthesis.", "abstract": ["Glycosyl phosphatidylinositols (GPIs) anchor many proteins to the surface of eukaryotic cells and may also serve as sorting signals on proteins and participate in signal transduction.", "We have isolated a Saccharomyces cerevisiae GPI anchoring mutant, gpi1, using a colony screen for cells blocked in [3H]inositol incorporation into protein.", "The gpi1 mutant is defective in vitro in the synthesis of N-acetylglucosaminyl phosphatidylinositol, the first intermediate in GPI synthesis, and is also temperature-sensitive for growth.", "Completion of the first step in GPI assembly is therefore required for growth of the unicellular eukaryote S. cerevisiae.", "GPI synthesis could therefore be exploited as a target for antifungal or antiparasitic agents."], "structured": false}
{"doc_id": 21439293, "title": "Beyond pattern recognition: five immune checkpoints for scaling the microbial threat", "abstract": ["Pattern recognition by the innate immune system enables the detection of microorganisms, but how the level of microbial threat is evaluated \u2014 a process that is crucial for eliciting measured antimicrobial responses with minimal inflammatory tissue damage \u2014 is less well understood.", "New evidence has shown that features of microbial viability can be detected by the immune system and thereby induce robust responses that are not warranted for dead microorganisms.", "Here, we propose five immune checkpoints that, as defined here, collectively determine the gravity of microbial encounters."], "structured": false}
{"doc_id": 21439640, "title": "Macrophages induce COX-2 expression in breast cancer cells: role of IL-1\u03b2 autoamplification.", "abstract": ["Tumor-associated macrophages and high levels of cyclooxygenase-2 (COX-2) are associated with poor prognosis in breast cancer patients, but their potential interdependence has not been evaluated.", "The objective of this study was to determine whether macrophages regulate COX-2 expression in breast cancer cells.", "For this purpose, THP-1 cells were cocultured with HCC1954 breast cancer cells.", "Coculture led to increased COX-2 expression in the HCC1954 cells and elevated prostaglandin E(2) levels in conditioned media.", "Similar results were observed when THP-1 cells were incubated with HCC1937 breast cancer cells or when human monocyte-derived macrophages were cocultured with HCC1954 cells.", "Coculture triggered production of reactive oxygen species (ROS) in HCC1954 cells.", "COX-2 induction was blocked in cells preincubated with an reduced nicotinamide adenine dinucleotide phosphate (NADPH) oxidase inhibitor or by silencing p67PHOX, a subunit of NADPH oxidase.", "ROS production triggered activation of Src and mitogen-activated protein kinases (MAPKs).", "Blocking Src or MAPK activities or antagonizing the activator protein-1 (AP-1) transcription factor attenuated COX-2 induction in HCC1954 cells.", "Coculture caused rapid induction of interleukin-1\u03b2 (IL-1\u03b2) in both breast cancer cells and macrophages.", "Increased IL-1\u03b2 expression was blocked by an interleukin-1 receptor antagonist (IL-1Ra), suggesting autocrine and paracrine effects.", "Importantly, macrophage-induced COX-2 expression was blocked in HCC1954 cells preincubated with IL-1Ra or anti-IL-1\u03b2 IgG. Together, these results indicate that macrophage-mediated induction of COX-2 in breast cancer cells is a consequence of IL-1\u03b2-mediated stimulation of ROS\u2192Src\u2192MAPK\u2192AP-1 signaling.", "IL-1\u03b2-dependent induction of COX-2 in breast cancer cells provides a mechanism whereby macrophages contribute to tumor progression and potential therapeutic targets in breast cancer."], "structured": false}
{"doc_id": 21456232, "title": "A graphene-based platform for induced pluripotent stem cells culture and differentiation.", "abstract": ["Induced pluripotent stem cells (iPSCs) hold great promise as a cell source for regenerative medicine yet its culture, maintenance of pluripotency and induction of differentiation remain challenging.", "Conversely, graphene (G) and graphene oxide (GO) have captured tremendous interests in the fields of materials science, physics, chemistry and nanotechnology.", "Here we report on that G and GO can support the mouse iPSCs culture and allow for spontaneous differentiation.", "Intriguingly, G and GO surfaces led to distinct cell proliferation and differentiation characteristics.", "In comparison with the glass surface, iPSCs cultured on the G surface exhibited similar degrees of cell adhesion and proliferation while iPSCs on the GO surface adhered and proliferated at a faster rate.", "Moreover, G favorably maintained the iPSCs in the undifferentiated state while GO expedited the differentiation.", "The iPSCs cultured on both G and GO surfaces spontaneously differentiated into ectodermal and mesodermal lineages without significant disparity, but G suppressed the iPSCs differentiation towards the endodermal lineage whereas GO augmented the endodermal differentiation.", "These data collectively demonstrated that the different surface properties of G and GO governed the iPSCs behavior and implicate the potentials of graphene-based materials as a platform for iPSCs culture and diverse applications."], "structured": false}
{"doc_id": 21459247, "title": "Aerobic capacity in black adolescent girls.", "abstract": ["Our purpose was to determine the aerobic capacities (VO2max) of a group of black female adolescents (age = 11.4-15.8 years) randomly chosen from a single urban school.", "Of 91 girls selected, 64 performed an incremental treadmill running test to volitional exhaustion and achieved VO2max as determined from expired gas measures.", "Other measures included height (m), weight (kg), and calf and triceps skinfolds (for % fat estimates).", "Girls were also asked whether they had achieved menarche.", "VO2max averaged 37.3 +/-", "6.2 ml.kg-1 x min-1 and was significantly correlated (r[62]) with height (-.32, p < .01), body mass index (-.63, p < .001), and % fat (-.65, p < .001) but not with age (-.16, p > .10).", "Postmenarchal girls were significantly taller and older than premenarchal girls.", "Contrary to previous studies, the girls' VO2max values were not related to biological age.", "Our subjects' aerobic capacity values averaged 14% less than those of nonblack U.S. female adolescents previously reported in the literature.", "This difference in VO2max was primarily a function of body weight.", "Study implications support the possibility that overweight in adult black women may originate prior to or during early adolescence.", "Future longitudinal studies should be designed to investigate the effects of aerobic fitness on cardiovascular risk factor reduction in black adolescent girls."], "structured": false}
{"doc_id": 21465696, "title": "Acetylation controls Notch3 stability and function in T-cell leukemia", "abstract": ["Post-translational modifications of Notch3 and their functional role with respect to Notch3 overexpression in T-cell leukemia are still poorly understood.", "We identify here a specific novel property of Notch3 that is acetylated and deacetylated at lysines 1692 and 1731 by p300 and HDAC1, respectively, a balance impaired by HDAC inhibitors (HDACi) that favor hyperacetylation.", "By using HDACi and a non-acetylatable Notch3 mutant carrying K/R1692\u22121731 mutations in the intracellular domain, we show that Notch3 acetylation primes ubiquitination and proteasomal-mediated degradation of the protein.", "As a consequence, Notch3 protein expression and its transcriptional activity are decreased both in vitro and in vivo in Notch3 transgenic (tg) mice, thus impairing downstream signaling upon target genes.", "Consistently, Notch3-induced T-cell proliferation is inhibited by HDACi, whereas it is enhanced by the non-acetylatable Notch3-K/R1692\u22121731 mutant.", "Finally, HDACi-induced Notch3 hyperacetylation prevents in vivo growth of T-cell leukemia/lymphoma in Notch3 tg mice.", "Together, our findings suggest a novel level of Notch signaling control in which Notch3 acetylation/deacetylation process represents a key regulatory switch, thus representing a suitable druggable target for Notch3-sustained T-cell acute lymphoblastic leukemia therapy."], "structured": false}
{"doc_id": 21472388, "title": "Hypoglycemia: incidence and clinical predictors in a large population-based sample of children and adolescents with IDDM.", "abstract": ["OBJECTIVE To determine the frequency of moderate and severe hypoglycemia and to identify clinical predictors associated with its occurrence in a large population-based sample of children and adolescents with IDDM.   ", "RESEARCH DESIGN AND METHODS A total of 657 patients (age: 12.1 +/-", "4.4 years, mean +/-", "SD) were included in the study, yielding 1,449 patient-years of data.", "A prospective assessment of severe hypoglycemia (an event resulting in a seizure or coma) and moderate hypoglycemia (an event requiring assistance of another, excluding severe episodes) was made over a 3-year period.", "Patients and caregivers detailed episodes of significant hypoglycemia (moderate and severe events) and these were recorded at each 3-month clinic visit along with HbA1c.", "Data were analyzed using generalized estimating equation models fitted with the exchange correlation structure.   \n", "RESULTS The overall incidence of severe events was 4.8/100 patient-years and of moderate events was 13.1/100 patient-years.", "Over 3 years, severe events occurred in 8.5% of children and moderate events occurred in 26.9%.", "Significant hypoglycemia was rare in the first 12 months after diagnosis.", "Rates of hypoglycemia were increased in children < 6 years of age versus > 6 years of age (40.9 vs. 16.6/100 patient-years, age < or = 6 years vs. age > 6 years, P < 0.001).", "Rates of hypoglycemia doubled when HbA1c fell below 8%, and children with HbA1c < 7% had a threefold increase in both moderate and severe hypoglycemia (e.g., severe episodes 14.9 vs. 4.1/100 patient-years, HbA1c < or = 7% vs. HbA1c > 7%, P < 0.001).", "Most severe events were seizures, and 75% of them occurred at night.", "The majority of events were related to missed meals or increased activity.", "However, in 38% no predisposing factor was evident.   \n", "CONCLUSIONS Newly diagnosed children appear to be protected from severe hypoglycemia.", "Rates increase with lower glycated hemoglobin, especially when mean HbA1c is < 8.0%.", "Younger children, who may be more susceptible to the adverse effects of neuroglycopenia, are at a particular risk of significant hypoglycemia."], "structured": true}
{"doc_id": 21479231, "title": "Efficacy of a 6-month versus 9-month intermittent treatment regimen in HIV-infected patients with tuberculosis: a randomized clinical trial.", "abstract": ["RATIONALE The outcome of fully intermittent thrice-weekly antituberculosis treatment of various durations in HIV-associated tuberculosis is unclear.   \n", "OBJECTIVES To compare the efficacy of an intermittent 6-month regimen (Reg6M: 2EHRZ(3)/4HR(3) [ethambutol, 1,200 mg; isoniazid, 600 mg; rifampicin, 450 or 600 mg depending on body weight <60 or > or =60 kg; and pyrazinamide, 1,500 mg for 2 mo; followed by 4 mo of isoniazid and rifampicin at the same doses]) versus a 9-month regimen (Reg9M: 2EHRZ(3)/7HR(3)) in HIV/tuberculosis (TB).   \n", "METHODS HIV-infected patients with newly diagnosed pulmonary or extrapulmonary TB were randomly assigned to Reg6M (n = 167) or Reg9M (n = 160) and monitored by determination of clinical, immunological, and bacteriological parameters for 36 months.", "Primary outcomes included favorable responses at the end of treatment and recurrences during follow-up, whereas the secondary outcome was death.", "Intent-to-treat and on-treatment analyses were performed.", "All patients were antiretroviral treatment-naive during treatment.   \n", "MEASUREMENTS AND MAIN RESULTS Of the patients, 70% had culture-positive pulmonary TB; the median viral load was 155,000 copies/ml and the CD4(+) cell count was 160 cells/mm(3).", "Favorable response to antituberculosis treatment was similar by intent to treat (Reg6M, 83% and Reg9M, 76%; P = not significant).", "Bacteriological recurrences occurred significantly more often in Reg6M than in Reg9M (15 vs. 7%; P < 0.05) although overall recurrences were not significantly different (Reg6M, 19% vs. Reg9M, 13%).", "By 36 months, 36% of patients undergoing Reg6M and 35% undergoing Reg9M had died, with no significant difference between regimens.", "All 19 patients who failed treatment developed acquired rifamycin resistance (ARR), the main risk factor being baseline isoniazid resistance.   \n", "CONCLUSIONS Among antiretroviral treatment-naive HIV-infected patients with TB, a 9-month regimen resulted in a similar outcome at the end of treatment but a significantly lower bacteriological recurrence rate compared with a 6-month thrice-weekly regimen.", "ARR was high with these intermittent regimens and neither mortality nor ARR was altered by lengthening TB treatment.", "Clinical Trials Registry Information: ID# NCT00376012 registered at www.clinicaltrials.gov."], "structured": true}
{"doc_id": 21479575, "title": "High prevalence of evolutionarily conserved and species-specific genomic aberrations in mouse pluripotent stem cells.", "abstract": ["Mouse pluripotent stem cells (PSCs) are the best studied pluripotent system and are regarded as the \"gold standard\" to which human PSCs are compared.", "However, while the genomic integrity of human PSCs has recently drawn much attention, mouse PSCs have not been systematically evaluated in this regard.", "The genomic stability of PSCs is a matter of profound significance, as it affects their pluripotency, differentiation, and tumorigenicity.", "We thus performed a thorough analysis of the genomic integrity of 325 samples of mouse PSCs, including 127 induced pluripotent stem cell (iPSC) samples.", "We found that genomic aberrations occur frequently in mouse embryonic stem cells of various mouse strains, add in mouse iPSCs of various cell origins and derivation techniques.", "Four hotspots of chromosomal aberrations were detected: full trisomy 11 (with a minimally recurrent gain in 11qE2), full trisomy 8, and deletions in chromosomes 10qB and 14qC-14qE. The most recurrent aberration in mouse PSCs, gain 11qE2, turned out to be fully syntenic to the common aberration 17q25 in human PSCs, while other recurrent aberrations were found to be species specific.", "Analysis of chromosomal aberrations in 74 samples of rhesus macaque PSCs revealed a gain in chromosome 16q, syntenic to the hotspot in human 17q.", "Importantly, these common aberrations jeopardize the interpretation of published comparisons of PSCs, which were unintentionally conducted between normal and aberrant cells.", "Therefore, this work emphasizes the need to carefully monitor genomic integrity of PSCs from all species, for their proper use in biomedical research."], "structured": false}
{"doc_id": 21487212, "title": "Inhibition of cell proliferation and induction of apoptosis by ExFABP gene targeting.", "abstract": ["Ex-FABP, an extracellular fatty acid binding lipocalin, is physiologically expressed by differentiating chicken chondrocytes and myoblasts.", "Its expression is enhanced after cell treatment with inflammatory stimuli and repressed by anti-inflammatory agents, behaving as an acute phase protein.", "Chicken liver fragments in culture show enhanced protein expression after bacterial endotoxin treatment.", "To investigate the biological role of Ex-FABP, we stably transfected proliferating chondrocytes with an expression vector carrying antisense oriented Ex-FABP cDNA.", "We observed a dramatic loss of cell viability and a strong inhibition of cell proliferation and differentiation.", "When chondrocytes were transfected with the antisense oriented Ex-FABP cDNA we observed that Ex-FABP down-modulation increased apoptotic cell number.", "Myoblasts transfected with the same expression vector showed extensive cell death and impaired myotube formation.", "We suggest that Ex-FABP acts as a constitutive survival protein and that its expression and activation are fundamental to protect chondrocytes from cell death."], "structured": false}
{"doc_id": 21489324, "title": "Profile of the Navrongo Health and Demographic Surveillance System.", "abstract": ["Located in the Kassena-Nankana districts of northern Ghana, the Navrongo health and demographic surveillance system (NHDSS) was established in 1992 by the Navrongo health research centre (NHRC).", "The NHRC is one of three research centres of the Ghana health service.", "The activities and potential of the NHDSS for collaborative research are described.", "The NHDSS monitors health and demographic dynamics of the two Kassena-Nankana districts of northern Ghana and facilitates evaluation of the morbidity and mortality impact of health and social interventions.", "The total population currently under surveillance is 152 000 residing in 32 000 households.", "Events monitored routinely include pregnancies, births, morbidity, deaths, migration, marriages and vaccination coverage.", "Data updates are done every 4 months by trained fieldworkers.", "The NHRC also undertakes biomedical and socio-economic studies.", "Additional features of the NHDSS include the community key informant system where trained volunteers routinely report key events, such as births and deaths as they occur in their locality and the verbal autopsy (VA) system for determining the probable causes of deaths that occur at the community level.", "Data from the NHDSS are shared with funders and collaborators and partners in the INDEPTH Network.", "The Director of the NHDSS is the contact person for potential collaboration with the NHDSS and the use of its data."], "structured": false}
{"doc_id": 21495419, "title": "The impact of COPD on lung health worldwide: epidemiology and incidence.", "abstract": ["Information on the prevalence of COPD was obtained from vital statistics, health interview surveys, hospital charge records, national publications, and the World Health Organization (WHO).", "These data indicate that COPD is a common disease with implications for global health.", "In the United States, morbidity caused by COPD is 4%, making COPD the fourth leading cause of death, exceeded only by heart attacks, cancer, and stroke.", "Internationally, there is substantial variation in death rates possibly reflecting smoking behavior, type and processing of tobacco, pollution, climate, respiratory management, and genetic factors.", "The Global Obstructive Lung Disease Initiative, initiated by the National Heart, Lung, and Blood Institute and the WHO, aims to raise awareness of the increasing burden of COPD, decrease morbidity and mortality, promote further study of the condition, and implement programs to prevent COPD."], "structured": false}
{"doc_id": 21498497, "title": "TLR activation triggers the rapid differentiation of monocytes into macrophages and dendritic cells", "abstract": ["Leprosy enables investigation of mechanisms by which the innate immune system contributes to host defense against infection, because in one form, the disease progresses, and in the other, the infection is limited.", "We report that Toll-like receptor (TLR) activation of human monocytes induces rapid differentiation into two distinct subsets: DC-SIGN+ CD16+ macrophages and CD1b+ DC-SIGN\u2212 dendritic cells.", "DC-SIGN+ phagocytic macrophages were expanded by TLR-mediated upregulation of interleukin (IL)-15 and IL-15 receptor.", "CD1b+ dendritic cells were expanded by TLR-mediated upregulation of granulocyte-macrophage colony-stimulating factor (GM-CSF) and its receptor, promoted T cell activation and secreted proinflammatory cytokines.", "Whereas DC-SIGN+ macrophages were detected in lesions and after TLR activation in all leprosy patients, CD1b+ dendritic cells were not detected in lesions or after TLR activation of peripheral monocytes in individuals with the progressive lepromatous form, except during reversal reactions in which bacilli were cleared by T helper type 1 (TH1) responses.", "In tuberculoid lepromatous lesions, DC-SIGN+ cells were positive for macrophage markers, but negative for dendritic cell markers.", "Thus, TLR-induced differentiation of monocytes into either macrophages or dendritic cells seems to crucially influence effective host defenses in human infectious disease."], "structured": false}
{"doc_id": 21502234, "title": "Mismatch repair status and clinical outcome in endometrial cancer: a systematic review and meta-analysis.", "abstract": ["BACKGROUND The association between the deficiency in mismatch repair (MMR) genes and prognosis in women with endometrial cancer is unclear.", "Here we report a systematic review and meta-analysis exploring this association.   \n", "METHODS We searched literature databases (MEDLINE, EMBASE, and Cochrane) from 1980 until December 2011 to identify studies evaluating the association between MMR status and clinical outcome in endometrial cancer.", "The main outcome measures were overall survival (OS) and disease-free survival (DFS).   \n", "RESULTS Twenty-three studies met the inclusion criteria.", "The median sample size of studies was 112, 74% were retrospective case-series and 70% performed microsatellite instability (MSI) analysis to evaluate the status of MMR.", "Only 22% of studies used the panel of five microsatellite markers recommended by the National Cancer Institute.", "Seven studies used immunohistochemistry to define MMR deficiency, but only two of them determined the expression of all four MMR proteins.", "Overall, significant associations between MMR and outcome were observed in 32% of studies.", "There was marked inter-study heterogeneity for estimates of OS and DFS.", "Pooled analysis did not show any significant association between deficiency in MMR and worse OS (6 studies, hazard ratio [HR] 2.0, p=0.11) or DFS (4 studies, HR ratio 1.31, p=0.66).   \n", "CONCLUSION There is no definitive evidence of a significant association between MMR status and detrimental survival in endometrial cancer."], "structured": true}
{"doc_id": 21521236, "title": "p53 induces formation of NEAT1 lncRNA-containing paraspeckles that modulate replication stress response and chemosensitivity", "abstract": ["In a search for mediators of the p53 tumor suppressor pathway, which induces pleiotropic and often antagonistic cellular responses, we identified the long noncoding RNA (lncRNA) NEAT1.", "NEAT1 is an essential architectural component of paraspeckle nuclear bodies, whose pathophysiological relevance remains unclear.", "Activation of p53, pharmacologically or by oncogene-induced replication stress, stimulated the formation of paraspeckles in mouse and human cells.", "Silencing Neat1 expression in mice, which prevents paraspeckle formation, sensitized preneoplastic cells to DNA-damage-induced cell death and impaired skin tumorigenesis.", "We provide mechanistic evidence that NEAT1 promotes ATR signaling in response to replication stress and is thereby engaged in a negative feedback loop that attenuates oncogene-dependent activation of p53.", "NEAT1 targeting in established human cancer cell lines induced synthetic lethality with genotoxic chemotherapeutics, including PARP inhibitors, and nongenotoxic activation of p53.", "This study establishes a key genetic link between NEAT1 paraspeckles, p53 biology and tumorigenesis and identifies NEAT1 as a promising target to enhance sensitivity of cancer cells to both chemotherapy and p53 reactivation therapy."], "structured": false}
{"doc_id": 21535641, "title": "Regulation of innate immunity by NADPH oxidase.", "abstract": ["NADPH oxidase is a critical regulator of both antimicrobial host defense and inflammation.", "Activated in nature by microbes and microbial-derived products, the phagocyte NADPH oxidase is rapidly assembled, and generates reactive oxidant intermediates (ROIs) in response to infectious threat.", "Chronic granulomatous disease (CGD) is an inherited disorder of the NADPH oxidase characterized by recurrent and severe bacterial and fungal infections, and pathology related to excessive inflammation.", "Studies in CGD patients and CGD mouse models indicate that NADPH oxidase plays a key role in modulating inflammation and injury that is distinct from its antimicrobial function.", "The mechanisms by which NADPH oxidase mediates killing of pathogens and regulation of inflammation have broad relevance to our understanding of normal physiological immune responses and pathological states, such as acute lung injury and bacterial or fungal infections."], "structured": false}
{"doc_id": 21547032, "title": "Protection from olanzapine-induced metabolic toxicity in mice by acetaminophen and tetrahydroindenoindole", "abstract": ["Objective:In mice and in humans, treatment with the second-generation antipsychotic drug olanzapine (OLZ) produces excessive weight gain, adiposity and secondary metabolic complications, including loss of glucose and insulin homeostasis.", "In mice consuming a high-fat (HF) diet, a similar phenotype develops, which is inhibited by the analgesic acetaminophen (APAP) and by the antioxidant tetrahydroindenoindole (THII).", "Therefore, we examined the ability of APAP and THII to prevent metabolic changes in mice receiving OLZ.Design and Measurement:C57BL/6J mice received either a normal diet or a HF diet, and were administered daily dosages of OLZ (3 mg kg\u22121 body weight), alone or with APAP (30 mg kg\u22121 body weight) or THII (4.5 mg kg\u22121 body weight), for 10 weeks.", "Parameters of body composition and metabolism, including glucose and insulin homeostasis and oxidative stress, were examined.", "Results:OLZ treatment doubled the HF diet-induced increases in body weight and percent body fat.", "These increases were partially prevented by both APAP and THII, although food consumption was constant in all groups.", "The THII protection was associated with an increase in whole body and mitochondrial respiration.", "OLZ also exacerbated, and both APAP and THII prevented, HF diet-induced loss of glucose tolerance and insulin resistance.", "As increased body fat promotes insulin resistance by a pathway involving oxidative stress, we evaluated production of reactive oxygen and lipid peroxidation in white adipose tissue (WAT).", "HF diet caused an increase in lipid peroxidation, NADPH-dependent O2 uptake and H2O2 production, which were further exacerbated by OLZ.", "APAP, THII and the NADPH oxidase inhibitor, diphenyleneiodonium chloride, each abolished oxidative stress in WAT.Conclusions:We conclude that both APAP and THII intervene in the development of obesity and metabolic complications associated with OLZ treatment."], "structured": false}
{"doc_id": 21550246, "title": "Detection of prions in blood", "abstract": ["Prion diseases are caused by an unconventional infectious agent termed prion, composed mainly of the misfolded prion protein (PrPSc).", "The development of highly sensitive assays for biochemical detection of PrPSc in blood is a top priority for minimizing the spread of the disease.", "Here we show that the protein misfolding cyclic amplification (PMCA) technology can be automated and optimized for high-efficiency amplification of PrPSc.", "We show that 140 PMCA cycles leads to a 6,600-fold increase in sensitivity over standard detection methods.", "Two successive rounds of PMCA cycles resulted in a 10 million\u2013fold increase in sensitivity and a capability to detect as little as 8,000 equivalent molecules of PrPSc.", "Notably, serial PMCA enables detection of PrPSc in blood samples of scrapie-afflicted hamsters with 89% sensitivity and 100% specificity.", "These findings represent the first time that PrPSc has been detected biochemically in blood, offering promise for developing a noninvasive method for early diagnosis of prion diseases."], "structured": false}
{"doc_id": 21551568, "title": "Genetic alterations and their relationship in the phosphatidylinositol 3-kinase/Akt pathway in thyroid cancer.", "abstract": ["PURPOSE To investigate the overall occurrence and relationship of genetic alterations in the phosphatidylinositol 3-kinase (PI3K)/Akt pathway in thyroid tumors and explore the scope of this pathway as a therapeutic target for thyroid cancer.   ", "EXPERIMENTAL DESIGN We examined collectively the major genetic alterations and their relationship in this pathway, including PIK3CA copy number gain and mutation, Ras mutation, and PTEN mutation, in a large series of primary thyroid tumors.   \n", "RESULTS Occurrence of any of these genetic alterations was found in 25 of 81 (31%) benign thyroid adenoma (BTA), 47 of 86 (55%) follicular thyroid cancer (FTC), 21 of 86 (24%) papillary thyroid cancer (PTC), and 29 of 50 (58%) anaplastic thyroid cancer (ATC), with FTC and ATC most frequently harboring these genetic alterations.", "PIK3CA copy gain was associated with increased PIK3CA protein expression.", "A mutual exclusivity among these genetic alterations was seen in BTA, FTC, and PTC, suggesting an independent role of each of them through the PI3K/Akt pathway in the tumorigenesis of the differentiated thyroid tumors.", "However, coexistence of these genetic alterations was increasingly seen with progression from differentiated tumor to undifferentiated ATC.", "Their coexistence with BRAF mutation was also frequent in PTC and ATC.   \n", "CONCLUSIONS The data provide strong genetic implication that aberrant activation of PI3K/Akt pathway plays an extensive role in thyroid tumorigenesis, particularly in FTC and ATC, and promotes progression of BTA to FTC and to ATC as the genetic alterations of this pathway accumulate.", "Progression of PTC to ATC may be facilitated by coexistence of PI3K/Akt pathway-related genetic alterations and BRAF mutation.", "The PI3K/Akt pathway may thus be a major therapeutic target in thyroid cancers."], "structured": true}
{"doc_id": 21553394, "title": "Vitamin D and obesity: current perspectives and future directions.", "abstract": ["In recent years, new functional roles of vitamin D beyond its traditional role in calcium homoeostasis and bone metabolism have emerged linking the fat-soluble vitamin to various non-communicable diseases.", "Vitamin D deficiency (25-hydroxyvitamin D (25(OH)D) < 25-30 nmol/l) and sub-optimal status (25(OH)D < 50-100 nmol/l) are increasingly associated with unfavourable metabolic phenotypes, including insulin resistance, type 2 diabetes and CVD; conditions also commonly linked with overweight and obesity.", "Early studies reported poor vitamin D status in the morbidly obese.", "More recently, it has been observed that a graded relationship between vitamin D status and BMI, or specifically adiposity, exists in the general population.", "A number of hypotheses have been proposed to explain the potential mechanisms whereby alterations in the vitamin D endocrine system occur in the obese state.", "Plausible explanations include sequestration in adipose tissue, volumetric dilution or negative feedback mechanisms from increased circulating 1,25-dihydroxyvitamin D3.", "Others hypothesise that heavier individuals may partake in less outdoor activity, may also cover-up and wear more clothing than leaner individuals, thus decreasing sun exposure and limiting endogenous production of cholecalciferol in the skin.", "Moreover, in some but not all studies, BMI and adiposity have been negatively associated with the change in vitamin D status following vitamin D supplementation.", "It therefore remains unclear if body size and/or adiposity should be taken into account when determining the dietary requirements for vitamin D. This review will evaluate the current evidence linking vitamin D status and supplementation to overweight and obesity, and discuss the implications for setting dietary requirements."], "structured": false}
{"doc_id": 21557055, "title": "Transcriptional regulation by p53 through intrinsic DNA/chromatin binding and site-directed cofactor recruitment.", "abstract": ["The tumor suppressor protein, p53, plays a critical role in mediating cellular response to stress signals by regulating genes involved in cell cycle arrest and apoptosis.", "p53 is believed to be inactive for DNA binding unless its C terminus is modified or structurally altered.", "We show that unmodified p53 actively binds to two sites at -1.4 and -2.3 kb within the chromatin-assembled p21 promoter and requires the C terminus and the histone acetyltransferase, p300, for transcription.", "Acetylation of the C terminus by p300 is not necessary for binding or promoter activation.", "Instead, p300 acetylates p53-bound nucleosomes in the p21 promoter with spreading to the TATA box.", "Thus, p53 is an active DNA and chromatin binding protein that may selectively regulate its target genes by recruitment of specific cofactors to structurally distinct binding sites."], "structured": false}
{"doc_id": 21557614, "title": "Pleiotropic effects of statins.", "abstract": ["Statins are potent inhibitors of cholesterol biosynthesis.", "In clinical trials, statins are beneficial in the primary and secondary prevention of coronary heart disease.", "However, the overall benefits observed with statins appear to be greater than what might be expected from changes in lipid levels alone, suggesting effects beyond cholesterol lowering.", "Indeed, recent studies indicate that some of the cholesterol-independent or \"pleiotropic\" effects of statins involve improving endothelial function, enhancing the stability of atherosclerotic plaques, decreasing oxidative stress and inflammation, and inhibiting the thrombogenic response.", "Furthermore, statins have beneficial extrahepatic effects on the immune system, CNS, and bone.", "Many of these pleiotropic effects are mediated by inhibition of isoprenoids, which serve as lipid attachments for intracellular signaling molecules.", "In particular, inhibition of small GTP-binding proteins, Rho, Ras, and Rac, whose proper membrane localization and function are dependent on isoprenylation, may play an important role in mediating the pleiotropic effects of statins."], "structured": false}
{"doc_id": 21561474, "title": "Increasing the efficiency of precise genome editing with CRISPR-Cas9 by inhibition of nonhomologous end joining", "abstract": ["Methods to introduce targeted double-strand breaks (DSBs) into DNA enable precise genome editing by increasing the rate at which externally supplied DNA fragments are incorporated into the genome through homologous recombination.", "The efficiency of these methods is limited by nonhomologous end joining (NHEJ), an alternative DNA repair pathway that competes with homology-directed repair (HDR).", "To promote HDR at the expense of NHEJ, we targeted DNA ligase IV, a key enzyme in the NHEJ pathway, using the inhibitor Scr7.", "Scr7 treatment increased the efficiency of HDR-mediated genome editing, using Cas9 in mammalian cell lines and in mice for all four genes examined, up to 19-fold.", "This approach should be applicable to other customizable endonucleases, such as zinc finger nucleases and transcription activator\u2013like effector nucleases, and to nonmammalian cells with sufficiently conserved mechanisms of NHEJ and HDR."], "structured": false}
{"doc_id": 21562657, "title": "Molecular mechanism of BST2/tetherin downregulation by K5/MIR2 of Kaposi's sarcoma-associated herpesvirus.", "abstract": ["K3/MIR1 and K5/MIR2 of Kaposi's sarcoma-associated herpesvirus (KSHV) are viral members of the membrane-associated RING-CH (MARCH) ubiquitin ligase family and contribute to viral immune evasion by directing the conjugation of ubiquitin to immunostimulatory transmembrane proteins.", "In a quantitative proteomic screen for novel host cell proteins downregulated by viral immunomodulators, we previously observed that K5, as well as the human immunodeficiency virus type 1 (HIV-1) immunomodulator VPU, reduced steady-state levels of bone marrow stromal cell antigen 2 (BST2; also called CD317 or tetherin), suggesting that BST2 might be a novel substrate of K5 and VPU.", "Recent work revealed that in the absence of VPU, HIV-1 virions are tethered to the plasma membrane in BST2-expressing HeLa cells.", "By targeting BST2, K5 might thus similarly overcome an innate antiviral host defense mechanism.", "Here we establish that despite its type II transmembrane topology and carboxy-terminal glycosylphosphatidylinositol (GPI) anchor, BST2 represents a bona fide target of K5 that is downregulated during primary infection by and reactivation of KSHV.", "Upon exit of the protein from the endoplasmic reticulum, lysines in the short amino-terminal domain of BST2 are ubiquitinated by K5, resulting in rapid degradation of BST2.", "Ubiquitination of BST2 is required for degradation, since BST2 lacking cytosolic lysines was K5 resistant and ubiquitin depletion by proteasome inhibitors restored BST2 surface expression.", "Thus, BST2 represents the first type II transmembrane protein targeted by K5 and the first example of a protein that is both ubiquitinated and GPI linked.", "We further demonstrate that KSHV release is decreased in the absence of K5 in a BST2-dependent manner, suggesting that K5 contributes to the evasion of intracellular antiviral defense programs."], "structured": false}
{"doc_id": 21564598, "title": "Regulation of beta catenin signaling and parathyroid hormone anabolic effects in bone by the matricellular protein periostin.", "abstract": ["Periostin (Postn) is a matricellular protein preferentially expressed by osteocytes and periosteal osteoblasts in response to mechanical stimulation and parathyroid hormone (PTH).", "Whether and how periostin expression influences bone anabolism, however, remains unknown.", "We investigated the skeletal response of adult Postn(-/-) and Postn(+/+) mice to intermittent PTH.", "Compared with Postn(+/+), Postn(-/-) mice had a lower bone mass, cortical bone volume, and strength response to PTH.", "PTH-stimulated bone-forming indices were all significantly lower in Postn(-/-) mice, particularly at the periosteum.", "Furthermore, in vivo stimulation of Wnt-\u03b2-catenin signaling by PTH, as evaluated in TOPGAL reporter mice, was inhibited in the absence of periostin (TOPGAL;Postn(-/-) mice).", "PTH stimulated periostin and inhibited MEF2C and sclerostin (Sost) expression in bone and osteoblasts in vitro.", "Recombinant periostin also suppressed Sost expression, which was mediated through the integrin \u03b1V\u03b23 receptor, whereas periostin-blocking antibody prevented inhibition of MEF2C and Sost by PTH.", "In turn, administration of a Sost-blocking antiboby partially restored the PTH-mediated increase in bone mass in Postn(-/-) mice.", "In addition, primary osteoblasts from Postn(-/-) mice showed a lower proliferation, mineralization, and migration, both spontaneously and in response to PTH.", "Osteoblastic gene expression levels confirmed a defect of Postn(-/-) osteoblast differentiation with and without PTH, as well as an increased osteoblast apoptosis in the absence of periostin.", "These data elucidate the complex role of periostin on bone anabolism, through the regulation of Sost, Wnt-\u03b2-catenin signaling, and osteoblast differentiation."], "structured": false}
{"doc_id": 21571708, "title": "Lipoprotein(a) concentration and the risk of coronary heart disease, stroke, and nonvascular mortality.", "abstract": ["CONTEXT Circulating concentration of lipoprotein(a) (Lp[a]), a large glycoprotein attached to a low-density lipoprotein-like particle, may be associated with risk of coronary heart disease (CHD) and stroke.   \n", "OBJECTIVE To assess the relationship of Lp(a) concentration with risk of major vascular and nonvascular outcomes.   ", "STUDY SELECTION Long-term prospective studies that recorded Lp(a) concentration and subsequent major vascular morbidity and/or cause-specific mortality published between January 1970 and March 2009 were identified through electronic searches of MEDLINE and other databases, manual searches of reference lists, and discussion with collaborators.   \n", "DATA EXTRACTION Individual records were provided for each of 126,634 participants in 36 prospective studies.", "During 1.3 million person-years of follow-up, 22,076 first-ever fatal or nonfatal vascular disease outcomes or nonvascular deaths were recorded, including 9336 CHD outcomes, 1903 ischemic strokes, 338 hemorrhagic strokes, 751 unclassified strokes, 1091 other vascular deaths, 8114 nonvascular deaths, and 242 deaths of unknown cause.", "Within-study regression analyses were adjusted for within-person variation and combined using meta-analysis.", "Analyses excluded participants with known preexisting CHD or stroke at baseline.   \n", "DATA SYNTHESIS Lipoprotein(a) concentration was weakly correlated with several conventional vascular risk factors and it was highly consistent within individuals over several years.", "Associations of Lp(a) with CHD risk were broadly continuous in shape.", "In the 24 cohort studies, the rates of CHD in the top and bottom thirds of baseline Lp(a) distributions, respectively, were 5.6 (95% confidence interval [CI], 5.4-5.9) per 1000 person-years and 4.4 (95% CI, 4.2-4.6) per 1000 person-years.", "The risk ratio for CHD, adjusted for age and sex only, was 1.16 (95% CI, 1.11-1.22) per 3.5-fold higher usual Lp(a) concentration (ie, per 1 SD), and it was 1.13 (95% CI, 1.09-1.18) following further adjustment for lipids and other conventional risk factors.", "The corresponding adjusted risk ratios were 1.10 (95% CI, 1.02-1.18) for ischemic stroke, 1.01 (95% CI, 0.98-1.05) for the aggregate of nonvascular mortality, 1.00 (95% CI, 0.97-1.04) for cancer deaths, and 1.00 (95% CI, 0.95-1.06) for nonvascular deaths other than cancer.   \n", "CONCLUSION Under a wide range of circumstances, there are continuous, independent, and modest associations of Lp(a) concentration with risk of CHD and stroke that appear exclusive to vascular outcomes."], "structured": true}
{"doc_id": 21578627, "title": "The biphasic behavior of incoherent feed-forward loops in biomolecular regulatory networks.", "abstract": ["An incoherent feed-forward loop (FFL) is one of the most-frequently observed motifs in biomolecular regulatory networks.", "It has been thought that the incoherent FFL is designed simply to induce a transient response shaped by a 'fast activation and delayed inhibition'.", "We find that the dynamics of various incoherent FFLs can be further classified into two types: time-dependent biphasic responses and dose-dependent biphasic responses.", "Why do the structurally identical incoherent FFLs play such different dynamical roles?", "Through computational studies, we show that the dynamics of the two types of incoherent FFLs are mutually exclusive.", "Following from further computational results and experimental observations, we hypothesize that incoherent FFLs have been optimally designed to achieve distinct biological function arising from different cellular contexts.", "Additional Supporting Information may be found in the online version of the article."], "structured": false}
{"doc_id": 21590125, "title": "Antipsychotic prescribing patterns in Germany: a retrospective analysis using a large outpatient prescription database.", "abstract": ["Data of prescribing practices for antipsychotics are of great interest with respect to quality of care.", "Consequently, we analysed all prescriptions under the statutory health insurance redeemed at pharmacies in Southern Germany between July 1999 and December 2001.", "The database covers prescriptions for approximately 25 million people.", "Up to 6% of the population were prescribed an antipsychotic at least once during the study period.", "Most prescriptions were for conventional antipsychotics and written by non-specialists.", "Patients receiving second generation antipsychotics were more likely to receive continuous antipsychotic therapy.", "For a large proportion of patients, antipsychotic polypharmacy, as well as comedication for somatic illnesses, were observed.", "In particular, drugs for the treatment of cardiovascular and metabolic disorders were frequently co-prescribed.", "Physicians should consider patients' cardiovascular and metabolic risk profile when making treatment choices.", "The data suggest that the majority of antipsychotics are used for the treatment of disorders other than schizophrenia.", "It is important to raise awareness among non-specialists about the indications, efficacy and side-effects of the antipsychotics because these physicians account for the majority of antipsychotic prescriptions."], "structured": false}
{"doc_id": 21598000, "title": "Structural basis for the activation of microtubule assembly by the EB1 and p150Glued complex.", "abstract": ["Plus-end tracking proteins, such as EB1 and the dynein/dynactin complex, regulate microtubule dynamics.", "These proteins are thought to stabilize microtubules by forming a plus-end complex at microtubule growing ends with ill-defined mechanisms.", "Here we report the crystal structure of two plus-end complex components, the carboxy-terminal dimerization domain of EB1 and the microtubule binding (CAP-Gly) domain of the dynactin subunit p150Glued.", "Each molecule of the EB1 dimer contains two helices forming a conserved four-helix bundle, while also providing p150Glued binding sites in its flexible tail region.", "Combining crystallography, NMR, and mutational analyses, our studies reveal the critical interacting elements of both EB1 and p150Glued, whose mutation alters microtubule polymerization activity.", "Moreover, removal of the key flexible tail from EB1 activates microtubule assembly by EB1 alone, suggesting that the flexible tail negatively regulates EB1 activity.", "We, therefore, propose that EB1 possesses an auto-inhibited conformation, which is relieved by p150Glued as an allosteric activator."], "structured": false}
{"doc_id": 21601459, "title": "Epigenetic regulation of NANOG by miR-302 cluster-MBD2 completes induced pluripotent stem cell reprogramming.", "abstract": ["While most somatic cells undergoing induced pluripotent stem (iPS) cell reprogramming with Yamanaka factors accumulate at stable partially reprogrammed stages, the molecular mechanisms required to achieve full reprogramming are unknown.", "MicroRNAs (miRNAs) fine-tune mRNA translation and are implicated in reprogramming, but miRNA functional targets critical for complete iPS cell reprogramming remain elusive.", "We identified methyl-DNA binding domain protein 2 (MBD2) as an epigenetic suppressor, blocking full reprogramming of somatic to iPS cells through direct binding to NANOG promoter elements preventing transcriptional activation.", "When we overexpressed miR-302 cluster we observed a significant increase in conversion of partial to fully reprogrammed iPS cells by suppressing MBD2 expression, thereby increasing NANOG expression.", "Thus, expression of exogenous miR-302 cluster (without miR-367) is efficient in attaining a fully reprogrammed iPS state in partially reprogrammed cells by relieving MBD2-mediated inhibition of NANOG expression.", "Our studies provide a direct molecular mechanism involved in generating complete human iPS cell reprogramming to study disease pathogenesis, drug screening, and for potential cell-based therapies."], "structured": false}
{"doc_id": 21602220, "title": "Complex physiology and compound stress responses during fermentation of alkali-pretreated corn stover hydrolysate by an Escherichia coli ethanologen.", "abstract": ["The physiology of ethanologenic Escherichia coli grown anaerobically in alkali-pretreated plant hydrolysates is complex and not well studied.", "To gain insight into how E. coli responds to such hydrolysates, we studied an E. coli K-12 ethanologen fermenting a hydrolysate prepared from corn stover pretreated by ammonia fiber expansion.", "Despite the high sugar content (\u223c6% glucose, 3% xylose) and relatively low toxicity of this hydrolysate, E. coli ceased growth long before glucose was depleted.", "Nevertheless, the cells remained metabolically active and continued conversion of glucose to ethanol until all glucose was consumed.", "Gene expression profiling revealed complex and changing patterns of metabolic physiology and cellular stress responses during an exponential growth phase, a transition phase, and the glycolytically active stationary phase.", "During the exponential and transition phases, high cell maintenance and stress response costs were mitigated, in part, by free amino acids available in the hydrolysate.", "However, after the majority of amino acids were depleted, the cells entered stationary phase, and ATP derived from glucose fermentation was consumed entirely by the demands of cell maintenance in the hydrolysate.", "Comparative gene expression profiling and metabolic modeling of the ethanologen suggested that the high energetic cost of mitigating osmotic, lignotoxin, and ethanol stress collectively limits growth, sugar utilization rates, and ethanol yields in alkali-pretreated lignocellulosic hydrolysates."], "structured": false}
{"doc_id": 21616324, "title": "Systemic arterial hypertension in children following renal transplantation: prevalence and risk factors.", "abstract": ["BACKGROUND Control of blood pressure (BP) following renal transplantation may improve allograft and patient survival.", "Our aims were (i) to describe the distribution of BP and the prevalence of systolic and/or diastolic hypertension in children over the first 5 years following renal transplantation and (ii) to evaluate clinical risk factors and centre-specific factors associated with hypertension in this population.   \n", "METHODS We conducted a retrospective case note review of all current paediatric kidney transplant patients in the UK, with data collected at 6 months, 1, 2 and 5 years following transplantation in subjects with hypertension (systolic and/or diastolic BP > 95th > ) and non-hypertensive subjects BP \u2264 95th > .   \n", "RESULTS In total, 27.3% (117/428), 27.6% (118/428), 26.0% (95/365) and 25.6% (50/195) of the patients were hypertensive (systolic and/or diastolic BP > 95th > ) at 6 months, 1, 2 and 5 years following transplantation, respectively.", "A total of 58.4% of the patients at 6 months, 52.8% at 1 year, 48.2% at 2 years and 48.2% at 5 years were receiving anti-hypertensive therapy, of whom 31.6-36.6% remained hypertensive.", "When subjects were identified as being hypertensive, on anti-hypertensive medication or had untreated hypertension (systolic and/or diastolic BP > 95th > ), 66.4, 61.0, 56.4 and 55.9% of patients were hypertensive at 6 months, 1, 2 and 5 years, respectively.", "In a multivariate model, odds ratios for systolic hypertension were 4.16 (deceased versus living donor), 2.65 (lowest versus highest quartile of height z-score) and 2.07 (if on anti-hypertensive;", "yes versus no).", "There was significant variation in prevalent rates of hypertension between centres (P < 0.0001) that remained significant (P = 0.003) after adjustment for all the factors in the multivariate model.   \n", "CONCLUSIONS Control of BP after kidney transplantation remains sub-optimal in paediatric centres in the UK.", "Just over 25% of patients remain hypertensive 5 years following transplantation.", "Significant differences between centres remain unexplained and may reflect differences in assessment and management of hypertension."], "structured": true}
{"doc_id": 21622715, "title": "Coupling cAMP signaling to transcription in the liver: pivotal role of CREB and CREM.", "abstract": ["Transcriptional factors binding to cAMP-responsive elements (CREs) in the promoters of various genes belong to the basic domain-leucine zipper superfamily and are composed of three genes in mammals, CREB, CREM, and ATF-1.", "A large number of CREB, CREM, and ATF-1 proteins are generated by posttranscriptional events, mostly alternative splicing, and regulate gene expression by acting as activators or repressors.", "Activation is classically brought about by signaling-dependent phosphorylation of a key acceptor site (Ser133 in CREB) by a number of possible kinases, including PKA, CamKIV, and Rsk-2.", "Phosphorylation is the prerequisite for the interaction of CBP (CREB-binding protein), a co-activator that has also histone acetyltransferase activity.", "Repression may involve dynamic dephosphorylation of the activators and thus decreased association with CBP.", "Another pathway of transcriptional repression on CRE sites implicates the inducible repressor ICER (inducible cAMP early repressor), a product of the CREM gene.", "Being an inducible repressor, ICER is involved in autoregulatory feedback loops of transcription that govern the down-regulation of early response genes, such as the proto-oncogene c-fos.", "The liver represents a remarkable physiological setting where cAMP-responsive signaling plays a major role.", "Indeed, a finely tuned program of gene expression is triggered by partial hepatectomy, so that through specific checkpoints a coordinated regeneration of the tissue is obtained.", "Temporal kinetics of transcriptional activation after hepatectomy reveals a pattern of early induction for several genes, some of them controlled by the CREB/CREM transcription factors.", "An important role of CREM in liver physiology was suggested by the robust induction of ICER after partial hepatectomy.", "The delay in tissue regeneration in CREM-deficient mice confirmed the important function of this factor in regulating hepatocyte proliferation.", "As gene induction is accompanied by critical changes in chromatin organization, the deciphering of the specific modification codes that histones display during liver regeneration and physiology will provide exciting new insights into the dynamics of chromatin architecture."], "structured": false}
{"doc_id": 21623140, "title": "Comparison of dietary assessment methods in a Southern French population: use of weighed records, estimated-diet records and a food-frequency questionnaire", "abstract": ["Objective: The main objective of the study was to develop appropriate dietary assessment instruments for the French Mediterranean region and to validate the measurements they provide.", "Subjects and Methods: Three different assessment methods were submitted to a sample of 150 male and female volunteers.", "98 completed the protocol, which consisted of a 4 d weighed dietary record (PETRA) and a 7 d estimated-diet record (S7) based on a check list and a set of photographs, both these records being completed once in each season of the year, and a semi-quantitative (standard portion) food-frequency questionnaire (FFQ) including questions eliciting socio-demographic and anthropometric data, which was completed once only.", "The days when PETRA was used to evaluate food consumption coincided with the first 4 d of S7 (S4).Results: Validation was based on nutrients and foods.", "Energy-adjusted Pearson correlation coefficients between S4 and PETRA ranged from 0.32 for vitamin E to 0.81 for vitamin C (mean: 0.65 for 21 nutrients).", "There was practically no misclassification in opposite extreme quartiles.", "Spearman correlation coefficients ranged from 0.63 for fish and sea-food to 0.90 for wine (mean: 0.76 for 16 food groups).", "There was practically no misclassification in opposite extreme quartiles.", "De-attenuated energy-adjusted Pearson correlation coefficients between FFQ and S7 ranged from 0.22 for proteins and monounsaturated fatty acids to 0.80 for iron (mean: 0.45).", "10% or less of subjects were misclassified in opposite extreme quartiles (except for vitamin C, 12%).", "Spearman correlation coefficients ranged from 0.25 for green-yellow-red raw vegetables to 0.76 for wine (mean: 0.42).", "8% or less of subjects were misclassified in opposite extreme quartiles (except for citrus fruit, 11%).Conclusions: Portion estimation using the set of photographs was validated by the correlation between S4 and PETRA for both nutrients and foods.", "The FFQ provides a reasonably reliable measure of macronutrient intake and a good measure of micronutrient intake when compared with the data in the literature.", "It performs less well for food intake.", "Better results can be achieved for FFQ: (i) by using the set of photographs instead of standard portions and (ii) by adding further questions on foods which are insufficiently covered.", "Sponsorship: This work has been financially supported by INSERM contract 91-1006 and the Ard\u00e8che and H\u00e9rault Committees of the \u2018Ligue contre le cancer\u2019."], "structured": false}
{"doc_id": 21626639, "title": "Substrate fate in activated macrophages: a comparison between innate, classic, and alternative activation.", "abstract": ["Macrophages play a relevant role in innate and adaptive immunity depending on the balance of the stimuli received.", "From an analytical and functional point of view, macrophage stimulation can be segregated into three main modes, as follows: innate, classic, and alternative pathways.", "These differential activations result in the expression of specific sets of genes involved in the release of pro- or anti-inflammatory stimuli.", "In the present work, we have analyzed whether specific metabolic patterns depend on the signaling pathway activated.", "A [1,2-(13)C(2)]glucose tracer-based metabolomics approach has been used to characterize the metabolic flux distributions in macrophages stimulated through the classic, innate, and alternative pathways.", "Using this methodology combined with mass isotopomer distribution analysis of the new formed metabolites, the data show that activated macrophages are essentially glycolytic cells, and a clear cutoff between the classic/innate activation and the alternative pathway exists.", "Interestingly, macrophage activation through LPS/IFN-gamma or TLR-2, -3, -4, and -9 results in similar flux distribution patterns regardless of the pathway activated.", "However, stimulation through the alternative pathway has minor metabolic effects.", "The molecular basis of the differences between these two types of behavior involves a switch in the expression of 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase (PFK2) from the liver type-PFK2 to the more active ubiquitous PFK2 isoenzyme, which responds to Hif-1alpha activation and increases fructose-2,6-bisphosphate concentration and the glycolytic flux.", "However, using macrophages targeted for Hif-1alpha, the switch of PFK2 isoenzymes still occurs in LPS/IFN-gamma-activated macrophages, suggesting that this pathway regulates ubiquitous PFK2 expression through Hif-1alpha-independent mechanisms."], "structured": false}
{"doc_id": 21636085, "title": "The effect of folic acid supplementation on plasma homocysteine in an elderly population.", "abstract": ["BACKGROUND Increased plasma homocysteine is associated with coronary artery disease, peripheral vascular disease and venous thrombosis.", "Folic acid is the most effective therapy for reducing homocysteine levels.", "The lowest effective supplement of folic acid is not known, particularly for the elderly who have the highest prevalence of these conditions.   ", "AIM To explore the effects of daily supplements of 0, 50, 100, 200, 400 and 600 microg folic acid on plasma homocysteine in an elderly population.   \n", "DESIGN Randomized double-blind placebo-controlled trial.   \n", "METHODS Participants (n=368) aged 65-75 years were randomly allocated to receive one of the treatments for 6 weeks.", "Plasma homocysteine was recorded after 3 weeks and 6 weeks of supplementation.   \n", "RESULTS Only the 400 microg and 600 microg groups had significantly lower homocysteine levels compared to placebo (p=0.038 and p<0.001, respectively).", "Using multiple linear regression and each individual's total folic acid intake (diet plus supplement), a total daily folic acid intake of 926 microg per day would be required to ensure that 95% of the elderly population would be without cardiovascular risk from folate deficiency.   ", "DISCUSSION A daily folic acid intake of 926 microg is unlikely to be achieved by diet alone.", "Individual supplementation or fortification of food with folic acid will be required to reach this target."], "structured": true}
{"doc_id": 21641088, "title": "Central obesity and hyperinsulinaemia in women are associated with polymorphism in the 5' flanking region of the human insulin gene.", "abstract": ["Obesity is a multifactorial disease with a marked genetic component.", "The situation is further complicated by the heterogeneity of obesity demonstrated by the topographical distribution of body fat, e.g. upper body (central) and lower body (gluteal) obesity.", "Furthermore, the distribution of fat shows a stronger heritable tendency compared with total body fat.", "Central obesity is characterized by hyperinsulinaemia and insulin resistance, a feature in common with non-insulin dependent diabetes mellitus, hypertension and atherosclerosis.", "In order to study the molecular genetics of central obesity we have examined 56 severely obese (mean body mass index 40), unrelated British Caucasoid young non-diabetic women for associations of restriction fragment length polymorphism of candidate genes with anthropometric measurements and indices of insulin secretion and resistance.", "The candidate genes examined were insulin receptor, insulin sensitive glucose transporter and insulin.", "An association of the class 3 allele of the hypervariable region in the 5' flanking region of the insulin gene was found with upper segment obesity (P = 0.005).", "Furthermore, the class 3 allele was also associated with fasting hyperinsulinaemia (P = 0.01), stimulated insulin secretion (P = 0.01) and insulin resistance as calculated from the homeostatic model of assessment (HOMA; P = 0.008).", "No such associations were found with the other candidate genes studied.", "This data suggests that polymorphisms in the 5' flanking region of the insulin gene may affect expression of the gene and thereby modulate insulin production in severely obese female subjects."], "structured": false}
{"doc_id": 21644993, "title": "Population density profiles of nasopharyngeal carriage of 5 bacterial species in pre-school children measured using quantitative PCR offer potential insights into the dynamics of transmission.", "abstract": ["Bacterial vaccines can reduce carriage rates.", "Colonization is usually a binary endpoint.", "Real time quantitative PCR (qPCR) can quantify bacterial DNA in mucosal samples over a wide range.", "Using culture and single-gene species-specific qPCRs for Streptococcus pneumoniae (lytA), Streptococcus pyogenes (ntpC), Moraxella catarrhalis (ompJ), Haemophilus influenzae (hdp) and Staphylococcus aureus (nuc) and standard curves against log-phase reference strain broth cultures we described frequency and peak density distributions of carriage in nasopharyngeal swabs from 161 healthy 2-4 y old children collected into STGG broth.", "In general, detection by qPCR and culture was consistent.", "Discordance mostly occurred at lower detection thresholds of both methods, although PCR assays for S. pyogenes and S. aureus were less sensitive.", "Density varied across 5-7 orders of magnitude for the 5 species with the abundant species skewed toward high values (modes: S. pneumoniae log3-4, M. catarrhalis & H. influenzae log4-5 CFU/ml broth).", "Wide ranges of bacterial DNA concentrations in healthy children carrying these bacteria could mean that different individuals at different times vary greatly in infectiousness.", "Understanding the host, microbial and environmental determinants of colonization density will permit more accurate prediction of vaccine effectiveness."], "structured": false}
{"doc_id": 21645205, "title": "Circadian mechanisms in murine and human bone marrow mesenchymal stem cells following dexamethasone exposure.", "abstract": ["A core group of regulatory factors control circadian rhythms in mammalian cells.", "While the suprachiasmatic nucleus in the brain serves as the central core circadian oscillator, circadian clocks also exist within peripheral tissues and cells.", "A growing body of evidence has demonstrated that >20% of expressed mRNAs in bone and adipose tissues oscillate in a circadian manner.", "The current manuscript reports evidence of the core circadian transcriptional apparatus within primary cultures of murine and human bone marrow-derived mesenchymal stem cells (BMSCs).", "Exposure of confluent, quiescent BMSCs to dexamethasone synchronized the oscillating expression of the mRNAs encoding the albumin D binding protein (dbp), brain-muscle arnt-like 1 (bmal1), period 3 (per3), rev-erb alpha (Rev A), and rev-erb beta (Rev B).", "The genes displayed a mean oscillatory period of 22.2 to 24.3 h. The acrophase or peak expression of mRNAs encoding \"positive\" (bmal1) and \"negative\" (per3) components of the circadian regulatory apparatus were out of phase with each other by approximately 8-12 h, consistent with in vivo observations.", "In vivo, phosphyrylation by glycogen synthase kinase 3beta (GSK3beta) is known to regulate the turnover of per3 and components of the core circadian regulatory apparatus.", "In vitro addition of lithium chloride, a GSK3beta inhibitor, significantly shifted the acrophase of all genes by 4.2-4.7 h oscillation in BMSCs; however, only the male murine BMSCs displayed a significant increase in the length of the period of oscillation.", "We conclude that human and murine BMSCs represent a valid in vitro model for the analysis of circadian mechanisms in bone metabolism and stem cell biology."], "structured": false}
{"doc_id": 21651116, "title": "Herpesvirus-encoded GPCRs: neglected players in inflammatory and proliferative diseases?", "abstract": ["Herpesviruses encode membrane-associated G protein-coupled receptors (GPCRs) in their viral genomes that are structurally similar to chemokine receptors.", "These GPCRs hijack GPCR-mediated cellular signalling networks of the host for survival, replication and pathogenesis.", "In particular the herpesvirus-encoded chemokine receptors ORF74, BILF1 and US28, which are present at inflammatory sites and tumour cells, provide important virus-specific targets for directed therapies.", "Given the high druggability of GPCRs in general, these viral GPCRs can be considered promising antiviral drug targets."], "structured": false}
{"doc_id": 21676556, "title": "Midbody accumulation through evasion of autophagy contributes to cellular reprogramming and tumorigenicity", "abstract": ["The midbody is a singular organelle formed between daughter cells during cytokinesis and required for their final separation.", "Midbodies persist in cells long after division as midbody derivatives (MBds), but their fate is unclear.", "Here we show that MBds are inherited asymmetrically by the daughter cell with the older centrosome.", "They selectively accumulate in stem cells, induced pluripotent stem cells and potential cancer \u2018stem cells\u2019 in vivo and in vitro.", "MBd loss accompanies stem-cell differentiation, and involves autophagic degradation mediated by binding of the autophagic receptor NBR1 to the midbody protein CEP55.", "Differentiating cells and normal dividing cells do not accumulate MBds and possess high autophagic activity.", "Stem cells and cancer cells accumulate MBds by evading autophagosome encapsulation and exhibit low autophagic activity.", "MBd enrichment enhances reprogramming to induced pluripotent stem cells and increases the in vitro tumorigenicity of cancer cells.", "These results indicate unexpected roles for MBds in stem cells and cancer \u2018stem cells\u2019."], "structured": false}
{"doc_id": 21692235, "title": "Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1.", "abstract": ["The Cancer Genome Atlas Network recently cataloged recurrent genomic abnormalities in glioblastoma multiforme (GBM).", "We describe a robust gene expression-based molecular classification of GBM into Proneural, Neural, Classical, and Mesenchymal subtypes and integrate multidimensional genomic data to establish patterns of somatic mutations and DNA copy number.", "Aberrations and gene expression of EGFR, NF1, and PDGFRA/IDH1 each define the Classical, Mesenchymal, and Proneural subtypes, respectively.", "Gene signatures of normal brain cell types show a strong relationship between subtypes and different neural lineages.", "Additionally, response to aggressive therapy differs by subtype, with the greatest benefit in the Classical subtype and no benefit in the Proneural subtype.", "We provide a framework that unifies transcriptomic and genomic dimensions for GBM molecular stratification with important implications for future studies."], "structured": false}
{"doc_id": 21700295, "title": "Chronic Hepatitis B Infection: A Review", "abstract": ["Importance More than 240 million individuals worldwide are infected with chronic hepatitis B virus (HBV).", "Among individuals with chronic HBV infection who are untreated, 15% to 40% progress to cirrhosis, which may lead to liver failure and liver cancer.", "Observations Pegylated interferon and nucleos(t)ide analogues (lamivudine, adefovir, entecavir, tenofovir disoproxil, and tenofovir alafenamide) suppress HBV DNA replication and improve liver inflammation and fibrosis.", "Long-term viral suppression is associated with regression of liver fibrosis and reduced risk of hepatocellular carcinoma in cohort studies.", "The cure (defined as hepatitis B surface antigen loss with undetectable HBV DNA) rates after treatment remain low (3%-7% with pegylated interferon and 1%-12% with nucleos[t]ide analogue therapy).", "Pegylated interferon therapy can be completed in 48 weeks and is not associated with the development of resistance; however, its use is limited by poor tolerability and adverse effects such as bone marrow suppression and exacerbation of existing neuropsychiatric symptoms such as depression.", "Newer agents (entecavir, tenofovir disoproxil, and tenofovir alafenamide) may be associated with a significantly reduced risk of drug resistance compared with older agents (lamivudine and adefovir) and should be considered as the first-line treatment.", "Conclusions and Relevance Antiviral treatment with either pegylated interferon or a nucleos(t)ide analogue (lamivudine, adefovir, entecavir, tenofovir disoproxil, or tenofovir alafenamide) should be offered to patients with chronic HBV infection and liver inflammation in an effort to reduce progression of liver disease.", "Nucleos(t)ide analogues should be considered as first-line therapy.", "Because cure rates are low, most patients will require therapy indefinitely."], "structured": false}
{"doc_id": 21719289, "title": "CD64 expression distinguishes monocyte-derived and conventional dendritic cells and reveals their distinct role during intramuscular immunization.", "abstract": ["Although most vaccines are administered i.m., little is known about the dendritic cells (DCs) that are present within skeletal muscles.", "In this article, we show that expression of CD64, the high-affinity IgG receptor Fc\u03b3RI, distinguishes conventional DCs from monocyte-derived DCs (Mo-DCs).", "By using such a discriminatory marker, we defined the distinct DC subsets that reside in skeletal muscles and identified their migratory counterparts in draining lymph nodes (LNs).", "We further used this capability to analyze the functional specialization that exists among muscle DCs.", "After i.m.", "administration of Ag adsorbed to alum, we showed that alum-injected muscles contained large numbers of conventional DCs that belong to the CD8\u03b1(+)- and CD11b(+)-type DCs.", "Both conventional DC types were capable of capturing Ag and of migrating to draining LNs, where they efficiently activated naive T cells.", "In alum-injected muscles, Mo-DCs were as numerous as conventional DCs, but only a small fraction migrated to draining LNs.", "Therefore, alum by itself poorly induces Mo-DCs to migrate to draining LNs.", "We showed that addition of small amounts of LPS to alum enhanced Mo-DC migration.", "Considering that migratory Mo-DCs had, on a per cell basis, a higher capacity to induce IFN-\u03b3-producing T cells than conventional DCs, the addition of LPS to alum enhanced the overall immunogenicity of Ags presented by muscle-derived DCs.", "Therefore, a full understanding of the role of adjuvants during i.m.", "vaccination needs to take into account the heterogeneous migratory and functional behavior of muscle DCs and Mo-DCs revealed in this study."], "structured": false}
{"doc_id": 21746539, "title": "T-cell-antigen recognition and the immunological synapse", "abstract": ["Much excitement of the past five years in the area of T-cell-antigen recognition has centred around the immunological synapse \u2014 a complex cellular structure that forms at the interface of a T cell and a cell that expresses the appropriate peptide\u2013MHC complexes.", "Thanks to new imaging technologies, we are now beginning to understand the role of cell-surface molecules and some of their attendant signalling modules in the context of cell-to-cell communication.", "Progress has been so rapid that T-cell-antigen recognition might be the first system in which the molecular basis of cell\u2013cell recognition is understood."], "structured": false}
{"doc_id": 21754541, "title": "Key interactions by conserved polar amino acids located at the transmembrane helical boundaries in Class B GPCRs modulate activation, effector specificity and biased signalling in the glucagon-like peptide-1 receptor.", "abstract": ["Class B GPCRs can activate multiple signalling effectors with the potential to exhibit biased agonism in response to ligand stimulation.", "Previously, we highlighted key TM domain polar amino acids that were crucial for the function of the GLP-1 receptor, a key therapeutic target for diabetes and obesity.", "Using a combination of mutagenesis, pharmacological characterisation, mathematical and computational molecular modelling, this study identifies additional highly conserved polar residues located towards the TM helical boundaries of Class B GPCRs that are important for GLP-1 receptor stability and/or controlling signalling specificity and biased agonism.", "This includes (i) three positively charged residues (R3.30227, K4.64288, R5.40310) located at the extracellular boundaries of TMs 3, 4 and 5 that are predicted in molecular models to stabilise extracellular loop 2, a crucial domain for ligand affinity and receptor activation; (ii) a predicted hydrogen bond network between residues located in TMs 2 (R2.46176), 6 (R6.37348) and 7 (N7.61406 and E7.63408) at the cytoplasmic face of the receptor that is important for stabilising the inactive receptor and directing signalling specificity, (iii) residues at the bottom of TM 5 (R5.56326) and TM6 (K6.35346 and K6.40351) that are crucial for receptor activation and downstream signalling; (iv) residues predicted to be involved in stabilisation of TM4 (N2.52182 and Y3.52250) that also influence cell signalling.", "Collectively, this work expands our understanding of peptide-mediated signalling by the GLP-1 receptor."], "structured": false}
{"doc_id": 21767325, "title": "Influence of lifestyle modification on arterial stiffness and wave reflections.", "abstract": ["Arterial stiffness and wave reflections exert a number of adverse effects on cardiovascular function and disease risk and are associated with a greater rate of mortality in patients with end-stage renal failure and essential hypertension.", "Accordingly, the prevention and treatment of arterial stiffness are of paramount importance.", "Because arterial stiffening is being recognized as a critical precursor of cardiovascular disease (CVD), it is essential to understand the role of lifestyle modifications on preventing and reversing arterial stiffening.", "Available evidence indicates that lifestyle modifications, in particular aerobic exercise and sodium restriction, appear to be clinically efficacious therapeutic interventions for preventing and treating arterial stiffening.", "Thus, sufficient evidence is available to recommend lifestyle modifications as part of a first-line therapeutic approach for arterial stiffening.", "However, more information is needed for a full understanding and optimal use of lifestyle modifications in the management of arterial stiffening."], "structured": false}
{"doc_id": 21789744, "title": "Effect of exercise-induced ischemia on QT interval dispersion.", "abstract": ["An increased spatial dispersion of ventricular repolarization duration (QT dispersion) is associated with an increased vulnerability to arrhythmias.", "This study was designed to examine the effect of exercise on QT dispersion in ischemic heart disease (IHD).", "QT dispersion, corrected QT dispersion, and percentage change in uncorrected and corrected QT dispersion between rest and peak exercise were examined in 14 members of a control group, 17 patients with IHD, and 14 patients with IHD who were receiving beta-blockers (IHD-B).", "All subjects had undergone a standard Bruce protocol exercise test, and QT intervals were measured at rest and peak exercise with a digitizing tablet interfaced to a personal computer.", "QT dispersion at rest was markedly increased in the IHD group compared with that in the control and IHD-B groups, respectively (corrected QT dispersion in milliseconds), 74 +/-", "7, 40 +/- 4, 49 +/-", "5, p < 0.03).", "The corrected QT dispersion at peak exercise was greater in the IHD group compared with that in the control group (57 +/- 5 vs 26 +/-", "3 msec, p < 0.03).", "The percentage change in QT dispersion with exercise was significantly higher in the IHD group (52% +/-", "5%) compared with that in both the control group (28% +/-", "4%, p < 0.002) and the IHD-B group (30% +/-", "3%, p < 0.01).", "A larger mean QT dispersion at peak exercise and an increased percentage change in QT dispersion with exercise may help explain the increased susceptibility of the IHD group for arrhythmias.", "The cardioprotective action of beta-blockers may be explained by their blunting effect on exercise-related changes in QT dispersion."], "structured": false}
{"doc_id": 21790313, "title": "Effects of powered mobility on self-initiated behaviors of very young children with locomotor disability.", "abstract": ["This study reports the effects of powered mobility on the self-initiated behavior of six children with various disabilities who, between 23 and 38 months of age, learnt to use motorized wheelchairs in less than three weeks.", "Using a multiple baseline design, two-hour observation periods were video-recorded at 10-day intervals before and after they achieved independent mobility.", "Frequency of self-initiated interaction with objects, spatial exploration and communication with care-giver were analyzed.", "Three children increased all three types of behavior; one increased in two types but decreased in interaction with objects; and two increased in spatial exploration only."], "structured": false}
{"doc_id": 21793890, "title": "BCR/ABL modifies the kinetics and fidelity of DNA double-strand breaks repair in hematopoietic cells.", "abstract": ["The oncogenic BCR/ABL tyrosine kinase facilitates the repair of DNA double-strand breaks (DSBs).", "We find that after gamma-irradiation BCR/ABL-positive leukemia cells accumulate more DSBs in comparison to normal cells.", "These lesions are efficiently repaired in a time-dependent fashion by BCR/ABL-stimulated non-homologous end-joining (NHEJ) followed by homologous recombination repair (HRR) mechanisms.", "However, mutations and large deletions were detected in HRR and NHEJ products, respectively, in BCR/ABL-positive leukemia cells.", "We propose that unfaithful repair of DSBs may contribute to genomic instability in the Philadelphia chromosome-positive leukemias."], "structured": false}
{"doc_id": 21804115, "title": "Bone morphogenetic protein signaling in nephron progenitor cells", "abstract": ["Bone morphogenetic protein (BMP) signaling plays an essential role in many aspects of kidney development, and is a major determinant of outcome in kidney injury.", "BMP treatment is also an essential component of protocols for differentiation of nephron progenitors from pluripotent stem cells.", "This review discusses the role of BMP signaling to nephron progenitor cells in each of these contexts."], "structured": false}
{"doc_id": 21853444, "title": "Computational analysis of 3'-ends of ESTs shows four classes of alternative polyadenylation in human, mouse, and rat.", "abstract": ["Alternative initiation, splicing, and polyadenylation are key mechanisms used by many organisms to generate diversity among mature mRNA transcripts originating from the same transcription unit.", "While previous computational analyses of alternative polyadenylation have focused on polyadenylation activities within or downstream of the normal 3'-terminal exons, we present the results of the first genome-wide analysis of patterns of alternative polyadenylation in the human, mouse, and rat genomes occurring over the entire transcribed regions of mRNAs using 3'-ESTs with poly(A) tails aligned to genomic sequences.", "Four distinct classes of patterns of alternative polyadenylation result from this analysis: tandem poly(A) sites, composite exons, hidden exons, and truncated exons.", "We estimate that at least 49% (human), 31% (mouse), and 28% (rat) of polyadenylated transcription units have alternative polyadenylation.", "A portion of these alternative polyadenylation events result in new protein isoforms."], "structured": false}
{"doc_id": 21855837, "title": "Epigenetic instability in ES cells and cloned mice.", "abstract": ["Cloning by nuclear transfer (NT) is an inefficient process in which most clones die before birth and survivors often display growth abnormalities.", "In an effort to correlate gene expression with survival and fetal overgrowth, we have examined imprinted gene expression in both mice cloned by nuclear transfer and in the embryonic stem (ES) cell donor populations from which they were derived.", "The epigenetic state of the ES cell genome was found to be extremely unstable.", "Similarly, variation in imprinted gene expression was observed in most cloned mice, even in those derived from ES cells of the same subclone.", "Many of the animals survived to adulthood despite widespread gene dysregulation, indicating that mammalian development may be rather tolerant to epigenetic aberrations of the genome.", "These data imply that even apparently normal cloned animals may have subtle abnormalities in gene expression."], "structured": false}
{"doc_id": 21859699, "title": "Successful three-way kidney paired donation with cross-country live donor allograft transport.", "abstract": ["Providing transplantation opportunities for patients with incompatible live donors through kidney paired donation (KPD) is seen as one of the important strategies for easing the crisis in organ availability.", "It has been estimated that an additional 1000-2000 transplants per year could be accomplished if a national KPD program were implemented in the United States.", "While most of these transplants could be arranged within the participants' local or regional area, patients with hard-to-match blood types or broad HLA sensitization would benefit from matching across larger geographic areas.", "In this case, either patients or organs would need to travel in order to obtain maximum benefit from a national program.", "In this study, we describe how a triple KPD enabled a highly sensitized patient (PRA 96%) to receive a well-matched kidney from a live donor on the opposite coast.", "The kidney was removed in San Francisco and transported to Baltimore where it was reperfused 8 h later.", "The patient had prompt function and 1 year later has a serum creatinine of 1.1 mg/dl.", "This case provides a blueprint for solving some of the complexities that are inherent in the implementation of a national KPD program in a large country like the United States."], "structured": false}
{"doc_id": 21866916, "title": "Role of PACAP and VIP in astroglial functions.", "abstract": ["Astrocytes represent at least 50% of the volume of the human brain.", "Besides their roles in various supportive functions, astrocytes are involved in the regulation of stem cell proliferation, synaptic plasticity and neuroprotection.", "Astrocytes also influence neuronal physiology by responding to neurotransmitters and neuropeptides and by releasing regulatory factors termed gliotransmitters.", "In particular, astrocytes express the PACAP-specific receptor PAC1-R and the PACAP/VIP mutual receptors VPAC1-R and VPAC2-R during development and/or in the adult.", "There is now clear evidence that PACAP and VIP modulate a number of astrocyte activities such as proliferation, plasticity, glycogen production, and biosynthesis of neurotrophic factors and gliotransmitters."], "structured": false}
{"doc_id": 21868715, "title": "A subset of 26S proteasomes is activated at critically low ATP concentrations and contributes to myocardial injury during cold ischemia.", "abstract": ["Molecular mechanisms leading to myocardial injury during warm or cold ischemia are insufficiently understood.", "Although proteasomes are thought to contribute to myocardial ischemia-reperfusion injury, their roles during the ischemic period remain elusive.", "Because donor hearts are commonly exposed to prolonged global cold ischemia prior to cardiac transplantation, we evaluated the role and regulation of the proteasome during cold ischemic storage of rat hearts in context of the myocardial ATP content.", "When measured at the actual tissue ATP concentration, cardiac proteasome peptidase activity increased by 225% as ATP declined during cold ischemic storage of hearts in University of Wisconsin (UW) solution for up to 48h.", "Addition of the specific proteasome inhibitor epoxomicin to the UW solution inhibited proteasome activity in the cardiac extracts, significantly reduced edema formation and preserved the ultrastructural integrity of the cardiomyocyte.", "Utilizing purified 20S/26S proteasome enzyme preparations, we demonstrate that this activation can be attributed to a subset of 26S proteasomes which are stable at ATP concentrations far below physiological levels, that ATP negatively regulates its activity and that maximal activation occurs at ATP concentrations in the low mumol/L range.", "These data suggest that proteasome activation is a pathophysiologically relevant mechanism of cold ischemic myocardial injury.", "A subset of 26S proteasomes appears to be a cell-destructive protease that is activated as ATP levels decline.", "Proteasome inhibition during cold ischemia preserves the ultrastructural integrity of the cardiomyocyte."], "structured": false}
{"doc_id": 21870716, "title": "Coping and satisfaction with growth hormone treatment among short-stature children.", "abstract": ["The ability of children to cope with a chronic medical problem requiring prolonged treatment has an effect on the quality of life of these children and of their parents and serves as an index of the quality of treatment.", "This study deals with coping ability and satisfaction with treatment of children whose stature was two or more SD below the average for age and gender.", "The study population included 96 patients, 53 of whom were male, who were on growth hormone (GH) treatment for at least 1 year.", "65 patients were without any underlying disease, 15 had classical GH deficiency and 16 had Turner syndrome or renal disease.", "All patients were treated with daily injections at home from 12 to 66 months.", "Using a self-administered questionnaire, the ability to cope and the degree of satisfaction and compliance with treatment were assessed.", "No significant differences were found with respect to gender, the presence of an underlying disease, age at which treatment commenced or duration of treatment.", "Despite the fact that the outcome of GH treatment on final height has yet to be established, satisfaction and compliance were high."], "structured": false}
{"doc_id": 21874312, "title": "Risk for breast cancer development determined by mammographic parenchymal pattern.", "abstract": ["A classification of risk for developing breast cancer has been devised based solely on the appearance of the breast parenchyma by mammography.", "Four groups of patients were isolated.", "The study encompassed a five-year period and was done by reviewing the mammograms of all women over the age of 30 who had been examined at Hutzel Hospital, Detroit.", "The average time of followup would be approximately 2 1/2 years.", "Four groups had an incidence of developing breast cancer of 0.1, 0.4, 1.7, and 2.2.", "These parenchymal patterns are described and criteria for their identification are given."], "structured": false}
{"doc_id": 21874414, "title": "Accurate coarse-grained modeling of red blood cells.", "abstract": ["We develop a systematic coarse-graining procedure for modeling red blood cells (RBCs) using arguments based on mean-field theory.", "The three-dimensional RBC membrane model takes into account the bending energy, in-plane shear energy, and constraints of fixed surface area and fixed enclosed volume.", "The coarse-graining procedure is general, it can be used for arbitrary level of coarse-graining and does not employ any fitting parameters.", "The sensitivity of the coarse-grained model is investigated and its behavior is validated against available experimental data and in dissipative particle dynamics (DPD) simulations of RBCs in capillary and shear flows."], "structured": false}
{"doc_id": 21878751, "title": "Mice deficient in CD4 T cells have only transiently diminished levels of IFN-gamma, yet succumb to tuberculosis.", "abstract": ["CD4 T cells are important in the protective immune response against tuberculosis.", "Two mouse models deficient in CD4 T cells were used to examine the mechanism by which these cells participate in protection against Mycobacterium tuberculosis challenge.", "Transgenic mice deficient in either MHC class II or CD4 molecules demonstrated increased susceptibility to M. tuberculosis, compared with wild-type mice.", "MHC class II-/- mice were more susceptible than CD4-/- mice, as measured by survival following M. tuberculosis challenge, but the relative resistance of CD4-/- mice did not appear to be due to increased numbers of CD4-8- (double-negative) T cells.", "Analysis of in vivo IFN-gamma production in the lungs of infected mice revealed that both mutant mouse strains were only transiently impaired in their ability to produce IFN-gamma following infection.", "At 2 wk postinfection, IFN-gamma production, assessed by RT-PCR and intracellular cytokine staining, in the mutant mice was reduced by >50% compared with that in wild-type mice.", "However, by 4 wk postinfection, both mutant and wild-type mice had similar levels of IFN-gamma mRNA and protein production.", "In CD4 T cell-deficient mice, IFN-gamma production was due to CD8 T cells.", "Thus, the importance of IFN-gamma production by CD4 T cells appears to be early in infection, lending support to the hypothesis that early events in M. tuberculosis infection are crucial determinants of the course of infection."], "structured": false}
{"doc_id": 21884059, "title": "Treatment and management of graft-versus-host disease: improving response and survival.", "abstract": ["Graft-versus-host disease (GVHD) is a significant cause of morbidity and mortality following allogenic haematopoietic stem-cell transplantation and thus the focus of much ongoing research.", "Despite considerable advances in our understanding of the pathophysiology, diagnosis and predisposing factors for both acute and chronic forms of the disease, a standardised therapeutic strategy is still lacking.", "There is good evidence for initial treatment of both acute and chronic forms of the disease with corticosteroid therapy.", "However, the most effective approach to steroid-refractory disease remains controversial, with current practice based mainly on smaller studies and varying considerably between local institutions.", "Timely diagnosis, multidisciplinary working and good supportive care, including infection prophylaxis, are clearly important in optimizing response and survival in such patients.", "It is hoped that in the future systematic research strategies and the identification of novel therapeutic targets may improve outcome further.", "The following review aims to outline some of the existing options for the treatment and management of acute and chronic GVHD."], "structured": false}
{"doc_id": 21884449, "title": "The value of self-report assessment of adherence, rhinitis and smoking in relation to asthma control.", "abstract": ["AIMS To explore the utility of self-report measures of inhaled corticosteroid (ICS) adherence, degree of rhinitis and smoking status and their association with asthma control.   \n", "METHODS Patients prescribed ICS for asthma at 85 UK practices were sent validated questionnaire measures of control (Asthma Control Questionnaire; ACQ) and adherence (Medication Adherence Report Scale), a two-item measure of smoking status, and a single-item measure of rhinitis.   \n", "RESULTS Complete anonymised questionnaires were available for 3916 participants.", "Poor asthma control (ACQ >1.5) was associated with reported rhinitis (OR = 4.62; 95% CI: 3.71-5.77), smoking (OR = 4.33; 95% CI: 3.58-5.23) and low adherence to ICS (OR = 1.35; 95% CI: 1.18-1.55).", "The degree of rhinitis was important, with those reporting severe rhinitis exhibiting the worst asthma control, followed by those reporting mild rhinitis and then those reporting no rhinitis symptoms (F(2, 3913)=128.7, p<.001).", "There was a relationship between the number of cigarettes smoked each day and asthma control (F(5,655)=6.08, p<.001).   \n", "CONCLUSIONS Poor asthma control is associated with self-reported rhinitis, smoking and low medication adherence.", "These potentially modifiable predictors of poor asthma control can be identified through a brief self-report questionnaire, used routinely as part of an asthma review."], "structured": true}
{"doc_id": 21891856, "title": "Development of a syngeneic mouse model for events related to ovarian cancer.", "abstract": ["Mouse ovarian surface epithelial cells (MOSEC) were obtained from virgin, mature mice by mild trypsinization and were repeatedly passaged in vitro.", "Early passage cells (<20 passages) exhibited a cobblestone morphology and contact inhibition of growth.", "After approximately 20 passages in vitro, cobblestone morphology and contact inhibition of growth was lost.", "Tumor forming potential was determined by s.c.", "and i.p.", "injection of early and late passage cells into athymic and syngeneic C57BL6 mice.", "Subcutaneous tumors formed in approximately 4 months and were present only at the injection site.", "Intraperitoneal injection of late passage MOSEC into athymic and syngeneic mice resulted in growth of tumor implants throughout the abdominal cavity, and production of hemorrhagic ascitic fluid.", "Early passage MOSEC did not form tumors in vivo.", "Histopathologic analysis of tumors revealed a highly malignant neoplasm containing both carcinomatous and sarcomatous components.", "Late passage MOSEC expressed cytokeratin and did not produce ovarian steroids in response to gonadotropin stimulation in vitro.", "Ten clonal lines were established from late passage MOSEC.", "Each clone formed multiple peritoneal tumors and ascitic fluid after i.p.", "injection into C57BL6 mice.", "Three cell lines examined cytogenetically were polyploid with near-tetraploid modal chromosome numbers.", "Common clonal chromosome gains and losses included +5, +15, +19 and -X, -3, -4.", "One cell line had a clonal translocation between chromosomes 15 and 18 and another had a small marker chromosome; common structural abnormalities were not observed.", "These data describe the development of a mouse model for the study of events related to ovarian cancer in humans.", "The ability of the MOSEC to form extensive tumors within the peritoneal cavity, similar to those seen in women with Stage III and IV cancer, and the ability of the MOSEC to produce tumors in mice with intact immune systems, makes this model unique for investigations of molecular and immune interactions in ovarian cancer development."], "structured": false}
{"doc_id": 21902400, "title": "Hypoxia in cancer: significance and impact on clinical outcome", "abstract": ["Hypoxia, a characteristic feature of locally advanced solid tumors, has emerged as a pivotal factor of the tumor (patho-)physiome since it can promote tumor progression and resistance to therapy.", "Hypoxia represents a \u201cJanus face\u201d in tumor biology because (a) it is associated with restrained proliferation, differentiation, necrosis or apoptosis, and (b) it can also lead to the development of an aggressive phenotype.", "Independent of standard prognostic factors, such as tumor stage and nodal status, hypoxia has been suggested as an adverse prognostic factor for patient outcome.", "Studies of tumor hypoxia involving the direct assessment of the oxygenation status have suggested worse disease-free survival for patients with hypoxic cervical cancers or soft tissue sarcomas.", "In head & neck cancers the studies suggest that hypoxia is prognostic for survival and local control.", "Technical limitations of the direct O2 sensing technique have prompted the use of surrogate markers for tumor hypoxia, such as hypoxia-related endogenous proteins (e.g., HIF-1\u03b1, GLUT-1, CA IX) or exogenous bioreductive drugs.", "In many\u2014albeit not in all\u2014studies endogenous markers showed prognostic significance for patient outcome.", "The prognostic relevance of exogenous markers, however, appears to be limited.", "Noninvasive assessment of hypoxia using imaging techniques can be achieved with PET or SPECT detection of radiolabeled tracers or with MRI techniques (e.g., BOLD).", "Clinical experience with these methods regarding patient prognosis is so far only limited.", "In the clinical studies performed up until now, the lack of standardized treatment protocols, inconsistencies of the endpoints characterizing the oxygenation status and methodological differences (e.g., different immunohistochemical staining procedures) may compromise the power of the prognostic parameter used."], "structured": false}
{"doc_id": 21902910, "title": "Knowledge and Practice of Standard Precautions and Awareness Regarding Post-Exposure Prophylaxis for HIV among Interns of a Medical College in West Bengal, India.", "abstract": ["OBJECTIVES To assess the knowledge of interns on standard precautions and post-exposure prophylaxis for HIV, and identify the gap between knowledge and practice relating to standard precautions, as well as determining the perceived barriers against adherence to standard precautions.   \n", "METHODS The study was conducted on 130 interns of 2010-11 batch from a government-run medical college in Kolkata, India.", "All participants completed a self-administered questionnaire with items relating to basic components of standard precautions and post-exposure prophylaxis for HIV.", "The questionnaire also included open ended questions relating to reasons for non-adherence to the practice of standard precautions along with additional space for specific comments, if any.   \n", "RESULTS Poor adherence in the use of personal protective equipment, hand washing, safe handling and disposal of needles and sharp objects were found to be among the practices for which the interns expressed correct knowledge.", "While the main reasons for non-adherence were found to be clumsiness in handling needles, wearing gloves, feeling uncomfortable when wearing aprons, impracticality of regular hand-washing and non-availability of equipment.", "Although the majority of the respondents (84.6%) expressed awareness of washing sites of injured with soap and water, approximately 32.3% did not know that antiseptics could cause more damage.", "Also, only 63.8% expressed awareness of reporting any incidence of occupational exposure, while knowledge on post-exposure prophylaxis regimens was generally found to be poor.   \n", "CONCLUSION The considerable gap between knowledge and practice of standard precautions and inadequate knowledge of post-exposure prophylaxis emphasizes the need for continuous onsite training of interns with supportive supervision and monitoring of their activities."], "structured": true}
{"doc_id": 21909315, "title": "Viruses and microRNAs", "abstract": ["The discovery of RNA interference and cellular microRNAs (miRNAs) has not only affected how biological research is conducted but also revealed an entirely new level of post-transcriptional gene regulation.", "Here, I discuss the potential functions of the virally encoded miRNAs recently identified in several pathogenic human viruses and propose that cellular miRNAs may have had a substantial effect on viral evolution and may continue to influence the in vivo tissue tropism of viruses.", "Our increasing knowledge of the role and importance of virally encoded miRNAs will probably offer new insights into how viruses that establish latent infections, such as herpesviruses, avoid elimination by the host innate or adaptive immune system.", "Research into viral miRNA function might also suggest new approaches for treating some virally induced diseases."], "structured": false}
{"doc_id": 21914176, "title": "Economic impact of primary open-angle glaucoma in Australia.", "abstract": ["BACKGROUND Glaucoma is the World's leading cause of irreversible blindness, and poses serious public health and economic concerns.   \n", "DESIGN   Review.   ", "SAMPLES Published randomized trials and population-based studies since 1985.   \n", "METHODS We report the economic impact of primary open-angle glaucoma and model the effect of changes in detection rates and management strategies.   \n", "MAIN OUTCOME MEASURES The cost-effectiveness of different interventions to prevent vision loss from primary open-angle glaucoma was measured in terms of financial cost (Australian dollars) and disability-adjusted life years.   \n", "RESULTS The prevalence of glaucoma in Australia is expected to increase from 208 000 in 2005 to 379 000 in 2025 because of the aging population.", "Health system costs over the same time period are estimated to increase from $AU355 million to $AU784 million.", "Total costs (health system costs, indirect costs and costs of loss of well-being) will increase from $AU1.9 billion to $AU4.3 billion in Australia.   \n", "CONCLUSION Primary open-angle glaucoma poses a significant economic burden, which will increase substantially by 2025.", "This dynamic model provides a valuable tool for ongoing policy formulation and determining the economic impact of interventions to better prevent visual impairment and blindness from glaucoma."], "structured": true}
{"doc_id": 21922424, "title": "The LIM domain-containing homeo box gene Xlim-1 is expressed specifically in the organizer region of Xenopus gastrula embryos.", "abstract": ["A novel cysteine-rich motif, named LIM, has been identified in the homeo box genes lin-11, Isl-1, and mec-3; the mec-3 and lin-11 genes determine cell lineages in Caenorhabditis elegans.", "We isolated LIM class homeo box genes from Xenopus laevis that are closely related to lin-11 and mec-3 in the LIM and homeo domains.", "This paper deals with one of these genes, Xlim-1.", "Xlim-1 mRNA is found at low abundance in the unfertilized egg, has a major expression phase at the gastrula stage, decreases, and rises again during the tadpole stage.", "In adult tissues the brain shows the highest abundance, by far, of Xlim-1 mRNA.", "The maternal and late expression phases of the Xlim-1 gene suggest that it has multiple functions at different stages of the Xenopus life cycle.", "In the gastrula embryo, Xlim-1 mRNA is localized in the dorsal lip and the dorsal mesoderm, that is, in the region of Spemann's organizer.", "Explant experiments showed that Xlim-1 mRNA is induced by the mesoderm-inducer activin A and by retinoic acid, which is not a mesoderm inducer but affects patterning during Xenopus embryogenesis; application of activin A and retinoic acid together results in synergistic induction.", "The structure, inducibility, and localized expression in the organizer of the Xlim-1 gene suggest that it has a role in establishing body pattern during gastrulation."], "structured": false}
{"doc_id": 21931005, "title": "Signal transduction proteins that associate with the platelet-derived growth factor (PDGF) receptor mediate the PDGF-induced release of glucose-6-phosphate dehydrogenase from permeabilized cells.", "abstract": ["Permeabilized rat kidney cells rapidly released glucose 6-phosphate dehydrogenase (G6PD) following stimulation with peptide growth factors (Stanton, R.C., Seifter, J.L., Boxer, D.C., Zimmerman, E., and Cantley, L. C. (1991) J. Biol.", "Chem.", "266, 12442-12448).", "To evaluate the signal transduction pathways mediating release of G6PD, two cell lines transfected with wild type or mutant platelet-derived growth factor (PDGF) receptors (PDGFR) were studied using two permeabilization protocols.", "G6PD release was evaluated by enzyme activity and Western blot analysis.", "PDGF caused a significant increase in G6PD release in 1 min in cells transfected with wild type PDGFR.", "PDGF did not stimulate G6PD release in cells transfected with tyrosine kinase-deficient PDGFR.", "PDGF did not stimulate G6PD release in cells transfected with partially autophosphorylation-deficient PDGFR in which four known signaling proteins do not associate with the PDGFR.", "The PDGF-stimulated release of G6PD was partially restored in PDGFR mutants in which either phosphatidylinositol-3-kinase or phospholipase C gamma 1 could associate with the PDGFR.", "Lastly, there was no basal or PDGF-stimulated phosphorylation of G6PD.", "We conclude that release of G6PD: 1) requires intrinsic PDGFR tyrosine kinase activity; 2) requires PDGFR autophosphorylation; 3) is mediated by signaling proteins that associate with the PDGFR; 4) is not mediated by direct phosphorylation of G6PD."], "structured": false}
{"doc_id": 21932050, "title": "Microarrays for the study of viral gene expression during human cytomegalovirus latent infection.", "abstract": ["Human cytomegalovirus (HCMV) is one of the largest known DNA viruses.", "It is ubiquitous, and following resolution of primary productive infection, it persists in the human host by establishing a lifelong latent infection in myeloid lineage cells such as monocytes and their progenitors.", "Most adults with HCMV infection are healthy but it can cause neurologic deficits in infants, and remains an important cause of morbidity and mortality in the immunosuppressed patient.", "Microarray-based studies of HCMV have provided useful information about genes that are transcriptionally active during both productive and latent phases of infection.", "This chapter describes how to study genes in HCMV using microarrays and two cell types (productively infected human foreskin fibroblasts, and latently infected primary human myeloid progenitor cells)."], "structured": false}
{"doc_id": 21932297, "title": "Physiological implications of hydrogen sulfide: a whiff exploration that blossomed.", "abstract": ["The important life-supporting role of hydrogen sulfide (H(2)S) has evolved from bacteria to plants, invertebrates, vertebrates, and finally to mammals.", "Over the centuries, however, H(2)S had only been known for its toxicity and environmental hazard.", "Physiological importance of H(2)S has been appreciated for about a decade.", "It started by the discovery of endogenous H(2)S production in mammalian cells and gained momentum by typifying this gasotransmitter with a variety of physiological functions.", "The H(2)S-catalyzing enzymes are differentially expressed in cardiovascular, neuronal, immune, renal, respiratory, gastrointestinal, reproductive, liver, and endocrine systems and affect the functions of these systems through the production of H(2)S. The physiological functions of H(2)S are mediated by different molecular targets, such as different ion channels and signaling proteins.", "Alternations of H(2)S metabolism lead to an array of pathological disturbances in the form of hypertension, atherosclerosis, heart failure, diabetes, cirrhosis, inflammation, sepsis, neurodegenerative disease, erectile dysfunction, and asthma, to name a few.", "Many new technologies have been developed to detect endogenous H(2)S production, and novel H(2)S-delivery compounds have been invented to aid therapeutic intervention of diseases related to abnormal H(2)S metabolism.", "While acknowledging the challenges ahead, research on H(2)S physiology and medicine is entering an exponential exploration era."], "structured": false}
{"doc_id": 21943141, "title": "TatC is a specificity determinant for protein secretion via the twin-arginine translocation pathway.", "abstract": ["The recent discovery of a ubiquitous translocation pathway, specifically required for proteins with a twin-arginine motif in their signal peptide, has focused interest on its membrane-bound components, one of which is known as TatC. Unlike most organisms of which the genome has been sequenced completely, the Gram-positive eubacterium Bacillus subtilis contains two tatC-like genes denoted tatCd and tatCy.", "The corresponding TatCd and TatCy proteins have the potential to be involved in the translocation of 27 proteins with putative twin-arginine signal peptides of which approximately 6-14 are likely to be secreted into the growth medium.", "Using a proteomic approach, we show that PhoD of B. subtilis, a phosphodiesterase belonging to a novel protein family of which all known members are synthesized with typical twin-arginine signal peptides, is secreted via the twin-arginine translocation pathway.", "Strikingly, TatCd is of major importance for the secretion of PhoD, whereas TatCy is not required for this process.", "Thus, TatC appears to be a specificity determinant for protein secretion via the Tat pathway.", "Based on our observations, we hypothesize that the TatC-determined pathway specificity is based on specific interactions between TatC-like proteins and other pathway components, such as TatA, of which three paralogues are present in B. subtilis."], "structured": false}
{"doc_id": 21948782, "title": "Function and regulation of SUMO proteases", "abstract": ["Covalent attachment of small ubiquitin-like modifier (SUMO) to proteins is highly dynamic, and both SUMO\u2013protein conjugation and cleavage can be regulated.", "Protein desumoylation is carried out by SUMO proteases, which control cellular mechanisms ranging from transcription and cell division to ribosome biogenesis.", "Recent advances include the discovery of two novel classes of SUMO proteases, insights regarding SUMO protease specificity, and revelations of previously unappreciated SUMO protease functions in several key cellular pathways.", "These developments, together with new connections between SUMO proteases and the recently discovered SUMO-targeted ubiquitin ligases (STUbLs), make this an exciting period to study these enzymes."], "structured": false}
{"doc_id": 21956124, "title": "Review article: prebiotics in the gastrointestinal tract.", "abstract": ["BACKGROUND Prebiotics are short-chain carbohydrates that alter the composition, or metabolism, of the gut microbiota in a beneficial manner.", "It is therefore expected that prebiotics will improve health in a way similar to probiotics, whilst at the same time being cheaper, and carrying less risk and being easier to incorporate into the diet than probiotics.   ", "AIM To review published evidence for prebiotic effects on gut function and human health.   \n", "METHODS We searched the Science Citation Index with the terms prebiotic, microbiota, gut bacteria, large intestine, mucosa, bowel habit, constipation, diarrhoea, inflammatory bowel disease, Crohn's disease, ulcerative colitis, pouchitis, calcium and cancer, focussing principally on studies in humans and reports in the English language.", "Search of the Cochrane Library did not identify any clinical study or meta-analysis on this topic.   \n", "RESULTS Three prebiotics, oligofructose, galacto-oligosaccharides and lactulose, clearly alter the balance of the large bowel microbiota by increasing bifidobacteria and Lactobacillus numbers.", "These carbohydrates are fermented and give rise to short-chain fatty acid and intestinal gas; however, effects on bowel habit are relatively small.", "Randomized-controlled trials of their effect in a clinical context are few, although animal studies show anti-inflammatory effects in inflammatory bowel disease, while calcium absorption is increased.   \n", "CONCLUSIONS", "It is still early days for prebiotics, but they offer the potential to modify the gut microbial balance in such a way as to bring direct health benefits cheaply and safely."], "structured": true}
{"doc_id": 21957231, "title": "Pain catastrophizing and general health status in a large Dutch community sample.", "abstract": ["The aim of the present study was to examine the association between pain catastrophizing and general health status in a Dutch adult community sample, including various subgroups of people with musculoskeletal pain in the analyses.", "For exploratory reasons this study partly replicated previous studies of the factor structure, reliability, and validity of the Pain Catastrophizing Scale (PCS).", "Results demonstrated that across different pain subgroups, catastrophizing uniquely contributed variance to the prediction of the various aspects of general health status beyond the variance explained by pain intensity, age, gender, and chronicity.", "Across subgroups strongest associations were found between catastrophizing and mental health, general health perception, social functioning, and vitality.", "Furthermore, the association between catastrophizing and the various aspects of general health status was not moderated by the chronicity of the pain.", "Results of the confirmatory factor analysis statistically confirmed a three-factor model of the PCS, which was invariant across different subgroups of people with musculoskeletal pain.", "Inter-factor correlations were high, and the incremental explanatory power of the three-factor model over that of a one-factor model was only marginal.", "This implies that a one-factor model might be justifiable as well, at least in the general community.", "Across various pain subgroups the reliability of the PCS total and subscales was adequate.", "Additional evidence for the concurrent validity of the PCS was found as well."], "structured": false}
{"doc_id": 21958900, "title": "Variability in risk of gastrointestinal complications with individual non-steroidal anti-inflammatory drugs: results of a collaborative meta-analysis.", "abstract": ["OBJECTIVE To compare the relative risks of serious gastrointestinal complications reported with individual non-steroidal anti-inflammatory drugs.   \n", "DESIGN Systematic review of controlled epidemiological studies that found a relation between use of the drugs and admission to hospital for haemorrhage or perforation.   \n", "SETTING Hospital and community based case-control and cohort studies.   \n", "MAIN OUTCOME MEASURES (a) Estimated relative risks of gastrointestinal complications with use of individual drugs, exposure to ibuprofen being used as reference; (b) a ranking that best summarised the sequence of relative risks observed in the studies.   \n", "RESULTS 12 studies met the inclusion criteria.", "11 provided comparative data on ibuprofen and other drugs.", "Ibuprofen ranked lowest or equal lowest for risk in 10 of the 11 studies.", "Pooled relative risks calculated with exposure to ibuprofen used as reference were all significantly greater than 1.0 (interval of point estimates 1.6 to 9.2).", "Overall, ibuprofen was associated with the lowest relative risk, followed by diclofenac.", "Azapropazone, tolmetin, ketoprofen, and piroxicam ranked highest for risk and indomethacin, naproxen, sulindac, and aspirin occupied intermediate positions.", "Higher doses of ibuprofen were associated with relative risks similar to those with naproxen and indomethacin.   \n", "CONCLUSIONS The low risk of serious gastrointestinal complications with ibuprofen seems to be attributable mainly to the low doses of the drug used in clinical practice.", "In higher doses ibuprofen is associated with a similar risk to other non-steroidal anti-inflammatory drugs.", "Use of low risk drugs in low dosage as first line treatment would substantially reduce the morbidity and mortality due to serious gastrointestinal toxicity from these drugs."], "structured": true}
{"doc_id": 21993510, "title": "Accuracy of weighed dietary records in studies of diet and health.", "abstract": ["OBJECTIVE To provide an independent evaluation of seven day weighed dietary records, which are currently accepted as the most accurate technique for assessing habitual dietary intake in studies investigating the links between diet and health.   \n", "DESIGN Subjects who had previously participated in the Northern Ireland diet and health study were reselected by stratified random sampling to represent the range of energy intakes in the study as assessed by the seven day weighed dietary record.   \n", "SETTING Northern Ireland.   ", "SUBJECTS 31 Free living adults (16 men and 15 women).   \n", "MAIN OUTCOME MEASURES Energy intake as measured by the seven day weighed dietary record and total energy expenditure estimated concurrently by the doubly labelled water technique.   \n", "RESULTS Average recorded energy intakes were significantly lower than measured expenditure in the group overall (9.66 MJ/day v 12.15 MJ/day, 95% confidence interval 1.45 to 3.53 MJ/day).", "Among those in the upper third of energy intakes the mean (SE) ratio of intake to expenditure was close to 1.0, indicating accurate records (men 1.01 (0.11), women 0.96 (0.08].", "In the middle and lower thirds the ratios for men were only 0.74 (0.05) and 0.70 (0.07) respectively and for women 0.89 (0.07) and 0.61 (0.07).   \n", "CONCLUSIONS These results show a serious bias in reporting habitual energy intake.", "If substantiated they may have wide implications for the interpretation of many nutritional studies."], "structured": true}
{"doc_id": 22003328, "title": "A novel family of sequence-specific endoribonucleases associated with the clustered regularly interspaced short palindromic repeats.", "abstract": ["Clustered regularly interspaced short palindromic repeats (CRISPRs) together with the associated CAS proteins protect microbial cells from invasion by foreign genetic elements using presently unknown molecular mechanisms.", "All CRISPR systems contain proteins of the CAS2 family, suggesting that these uncharacterized proteins play a central role in this process.", "Here we show that the CAS2 proteins represent a novel family of endoribonucleases.", "Six purified CAS2 proteins from diverse organisms cleaved single-stranded RNAs preferentially within U-rich regions.", "A representative CAS2 enzyme, SSO1404 from Sulfolobus solfataricus, cleaved the phosphodiester linkage on the 3'-side and generated 5'-phosphate- and 3'-hydroxyl-terminated oligonucleotides.", "The crystal structure of SSO1404 was solved at 1.6A resolution revealing the first ribonuclease with a ferredoxin-like fold.", "Mutagenesis of SSO1404 identified six residues (Tyr-9, Asp-10, Arg-17, Arg-19, Arg-31, and Phe-37) that are important for enzymatic activity and suggested that Asp-10 might be the principal catalytic residue.", "Thus, CAS2 proteins are sequence-specific endoribonucleases, and we propose that their role in the CRISPR-mediated anti-phage defense might involve degradation of phage or cellular mRNAs."], "structured": false}
{"doc_id": 22007333, "title": "Menstrual and reproductive factors in relation to mammographic density: the Study of Women\u2019s Health Across the Nation (SWAN)", "abstract": ["Menstrual and reproductive factors may increase breast cancer risk through a pathway that includes increased mammographic density.", "We assessed whether known or suspected menstrual and reproductive breast cancer risk factors were cross-sectionally associated with mammographic density, by measuring area of radiographic density and total breast area on mammograms from 801 participants in the Study of Women\u2019s Health Across the Nation (SWAN), a multi-ethnic cohort of pre- and early perimenopausal women.", "From multivariable linear regression, the following menstrual or reproductive factors were independently associated with percent mammographic density (area of dense breast/breast area): older age at menarche (\u03b2 = 10.3, P < 0.01, for >13 vs. <12 years), premenstrual cravings and bloating (\u03b2 = \u22123.36, P = 0.02), younger age at first full-term birth (\u03b2 = \u22128.12, P < 0.01 for \u226423 years versus no births), greater number of births (\u03b2 = \u22126.80, P < 0.01 for \u22653 births versus no births), and premenopausal status (\u03b2 = 3.78, P < 0.01 versus early perimenopausal).", "Only number of births remained associated with percent density after adjustment for age, race/ethnicity, study site, body mass index (BMI), and smoking.", "In addition, stratified analyses revealed that the association with number of births was confined to women within the lowest BMI tertile (\u03b2 = \u221212.2, P < 0.01 for \u22653 births versus no births).", "Our data support a mechanism for parity and breast cancer that involves mammographic density among pre- and early perimenopausal women that may be modified by body size."], "structured": false}
{"doc_id": 22023404, "title": "Genetic and environmental determinants of 25-hydroxyvitamin D and 1,25-dihydroxyvitamin D levels in Hispanic and African Americans.", "abstract": ["CONTEXT Vitamin D deficiency is associated with many adverse health outcomes, yet little is known about the genetic epidemiology of vitamin D or its metabolites.   \n", "OBJECTIVE Our objective was to examine the relationship among three vitamin D-related genes and levels of 25-hydroxyvitamin D [25(OH)D] and 1,25-dihydroxyvitamin D [1,25(OH)2D] in Hispanics (HAs) and African Americans (AAs).   \n", "DESIGN AND SETTING The cross-sectional Insulin Resistance Atherosclerosis Family Study recruited and examined subjects in: Los Angeles, California (AAs; 513 individuals from 42 families); San Luis Valley (SLV), Colorado (HAs; 513 individuals from 30 families); and San Antonio (SA), Texas (HAs; 504 individuals from 58 families).   \n", "MAIN OUTCOME MEASURES Plasma levels of 25(OH)D and 1,25(OH)2D were measured.   \n", "RESULTS Levels of 25(OH)D were highest in SLV-HAs [18.3 +/-", "7.7 ng/ml (45.7 +/-", "19.2 nmol/liter)], lower in SA-HAs [14.6 +/-", "6.4 ng/ml (36.4 +/-", "16.0 nmol/liter)], and lowest in AAs [11.0 +/-", "5.4 ng/ml (27.5 +/-", "13.5 nmol/liter)].", "Levels of 1,25(OH)2D were similar in AAs [43.5 +/-", "13.9 pg/ml (113.1 +/-", "36.1 pmol/liter)] and SLV-HAs [43.2 +/-", "13.3 pg/ml (112.3 +/-", "34.6 pmol/liter)], but higher in SA-HAs [48.6 +/-", "17.0 pg/ml (126.4 +/-", "44.2 pmol/liter)].", "After adjusting for gender and age within the site, two single nucleotide polymorphisms (SNPs) in the vitamin D binding protein gene (DBP), rs4588 and rs7041, were associated with 25(OH)D, and one SNP in the DBP, rs4588, was associated with 1,25(OH)2D at all three study centers.   \n", "CONCLUSIONS SNPs in the DBP are associated with levels of 25(OH)D and 1,25(OH)2D in HA and AA participants in the Insulin Resistance Atherosclerosis Family Study."], "structured": true}
{"doc_id": 22025252, "title": "Changes in the levels of inositol phosphates after agonist-dependent hydrolysis of membrane phosphoinositides.", "abstract": ["The formation of inositol phosphates in response to agonists was studied in brain slices, parotid gland fragments and in the insect salivary gland.", "The tissues were first incubated with [3H]inositol, which was incorporated into the phosphoinositides.", "All the tissues were found to contain glycerophosphoinositol, inositol 1-phosphate, inositol 1,4-bisphosphate and inositol 1,4,5-trisphosphate, which were identified by using anion-exchange and high-resolution anion-exchange chromatography, high-voltage paper ionophoresis and paper chromatography.", "There was no evidence for the existence of inositol 1:2-cyclic phosphate.", "A simple anion-exchange chromatographic method was developed for separating these inositol phosphates for quantitative analysis.", "Stimulation caused no change in the levels of glycerophosphoinositol in any of the tissues.", "The most prominent change concerned inositol 1,4-bisphosphate, which increased enormously in the insect salivary gland and parotid gland after stimulation with 5-hydroxytryptamine and carbachol respectively.", "Carbachol also induced a large increase in the level of inositol 1,4,5-trisphosphate in the parotid.", "Stimulation of brain slices with carbachol induced modest increase in the bis- and tris-phosphate.", "In all the tissues studied, there was a significant agonist-dependent increase in the level of inositol 1-phosphate.", "The latter may be derived from inositol 1,4-bisphosphate, because homogenates of the insect salivary gland contain a bisphosphatase in addition to a trisphosphatase.", "These results suggest that the earliest event in the stimulus-response pathway is the hydrolysis of polyphosphoinositides by a phosphodiesterase to yield inositol 1,4,5-trisphosphate and inositol 1,4-bisphosphate, which are subsequently hydrolysed to inositol 1-phosphate and inositol.", "The absence of inositol 1:2-cyclic phosphate could indicate that, at very short times after stimulation, phosphatidylinositol is not catabolized by its specific phosphodiesterase, or that any cyclic derivative liberated is rapidly hydrolysed by inositol 1:2-cyclic phosphate 2-phosphohydrolase."], "structured": false}
{"doc_id": 22029384, "title": "RNA editing in brain controls a determinant of ion flow in glutamate-gated channels.", "abstract": ["L-glutamate, the principal excitatory transmitter in the brain, gates ion channels mediating fast neurotransmission.", "Subunit components of two related classes of glutamate receptor channels have been characterized by cDNA cloning and shown to carry either an arginine or a glutamine residue in a defined position of their putative channel-forming segment.", "The arginine residue in this segment profoundly alters, and dominates, the properties of ion flow, as demonstrated for one channel class.", "We now show that the genomic DNA sequences encoding the particular channel segment of all subunits harbor a glutamine codon (CAG), even though an arginine codon (CGG) is found in mRNAs of three subunits.", "Multiple genes and alternative exons were excluded as sources for the arginine codon; hence, we propose that transcripts for three subunits are altered by RNA editing.", "This process apparently edits subunit transcripts of the two glutamate receptor classes with different efficiency and selectivity."], "structured": false}
{"doc_id": 22036571, "title": "Post-translational modifications of the beta-1 subunit of AMP-activated protein kinase affect enzyme activity and cellular localization.", "abstract": ["The AMP-activated protein kinase (AMPK) is a ubiquitous mammalian protein kinase important in the adaptation of cells to metabolic stress.", "The enzyme is a heterotrimer, consisting of a catalytic alpha subunit and regulatory beta and gamma subunits, each of which is a member of a larger isoform family.", "The enzyme is allosterically regulated by AMP and by phosphorylation of the alpha subunit.", "The beta subunit is post-translationally modified by myristoylation and multi-site phosphorylation.", "In the present study, we have examined the impact of post-translational modification of the beta-1 subunit on enzyme activity, heterotrimer assembly and subcellular localization, using site-directed mutagenesis and expression of subunits in mammalian cells.", "Removal of the myristoylation site (G2A mutant) results in a 4-fold activation of the enzyme and relocalization of the beta subunit from a particulate extranuclear distribution to a more homogenous cell distribution.", "Mutation of the serine-108 phosphorylation site to alanine is associated with enzyme inhibition, but no change in cell localization.", "In contrast, the phosphorylation site mutations, SS24, 25AA and S182A, while having no effects on enzyme activity, are associated with nuclear redistribution of the subunit.", "Taken together, these results indicate that both myristoylation and phosphorylation of the beta subunit of AMPK modulate enzyme activity and subunit cellular localization, increasing the complexity of AMPK regulation."], "structured": false}
{"doc_id": 22038539, "title": "Caloric restriction delays age-related methylation drift", "abstract": ["In mammals, caloric restriction consistently results in extended lifespan.", "Epigenetic information encoded by DNA methylation is tightly regulated, but shows a striking drift associated with age that includes both gains and losses of DNA methylation at various sites.", "Here, we report that epigenetic drift is conserved across species and the rate of drift correlates with lifespan when comparing mice, rhesus monkeys, and humans.", "Twenty-two to 30-year-old rhesus monkeys exposed to 30% caloric restriction since 7-14 years of age showed attenuation of age-related methylation drift compared to ad libitum-fed controls such that their blood methylation age appeared 7 years younger than their chronologic age.", "Even more pronounced effects were seen in 2.7-3.2-year-old mice exposed to 40% caloric restriction starting at 0.3 years of age.", "The effects of caloric restriction on DNA methylation were detectable across different tissues and correlated with gene expression.", "We propose that epigenetic drift is a determinant of lifespan in mammals.", "Caloric restriction has been shown to increase lifespan in mammals.", "Here, the authors provide evidence that age-related methylation drift correlates with lifespan and that caloric restriction in mice and rhesus monkeys results in attenuation of age-related methylation drift."], "structured": false}
{"doc_id": 22042345, "title": "Structural analysis of multiprotein complexes by cross-linking, mass spectrometry, and database searching.", "abstract": ["Most protein complexes are inaccessible to high resolution structural analysis.", "We report the results of a combined approach of cross-linking, mass spectrometry, and bioinformatics to two human complexes containing large coiled-coil segments, the NDEL1 homodimer and the NDC80 heterotetramer.", "An important limitation of the cross-linking approach, so far, was the identification of cross-linked peptides from fragmentation spectra.", "Our novel approach overcomes the data analysis bottleneck of cross-linking and mass spectrometry.", "We constructed a purpose-built database to match spectra with cross-linked peptides, define a score that expresses the quality of our identification, and estimate false positive rates.", "We show that our analysis sheds light on critical structural parameters such as the directionality of the homodimeric coiled coil of NDEL1, the register of the heterodimeric coiled coils of the NDC80 complex, and the organization of a tetramerization region in the NDC80 complex.", "Our approach is especially useful to address complexes that are difficult in addressing by standard structural methods."], "structured": false}
{"doc_id": 22049489, "title": "The long non-coding RNA H19-derived miR-675 modulates human gastric cancer cell proliferation by targeting tumor suppressor RUNX1.", "abstract": ["The lncRNA H19 has been recently shown to be upregulated and play important roles in gastric cancer tumorigenesis.", "However, the precise molecular mechanism of H19 and its mature product miR-675 in the carcinogenesis of gastric cancer remains unclear.", "In this study, we found that miR-675 was positively expressed with H19 and was a pivotal mediator in H19-induced gastric cancer cell growth promotion.", "Subsequently, the tumor suppressor Runt Domain Transcription Factor1 (RUNX1) was confirmed to be a direct target of miR-675 using a luciferase reporter assay and Western blotting analyses.", "A series of rescue assays indicated that RUNX1 mediated H19/miR-67-induced gastric cancer cell phenotypic changes.", "Moreover, the inverse relationship between the expression of RUNX1 and H19/miR-675 was also revealed in gastric cancer tissues and gastric cancer cell lines.", "Taken together, our study demonstrated that the novel pathway H19/miR-675/RUNX1 regulates gastric cancer development and may serve as a potential target for gastric cancer therapy."], "structured": false}
{"doc_id": 22057077, "title": "Methylphenidate-induced erections in a prepubertal child.", "abstract": ["Methylphenidate is a medication used routinely in the management of attention deficit hyperactivity disorder.", "We report a case of a prepubertal child who developed unwanted erections after commencing a response-adjusted dosing regimen of sustained release methylphenidate.", "Despite priapism being a rare adverse reaction associated with methylphenidate, physicians and parents need to be aware as it can have significant long-term complications."], "structured": false}
{"doc_id": 22059387, "title": "Mechanism of NO-mediated oxidative and nitrative DNA damage in hamsters infected with Opisthorchis viverrini: a model of inflammation-mediated carcinogenesis.", "abstract": ["Inflammation mediated by infection is an important factor causing carcinogenesis.", "Opisthorchis viverrini (OV) infection is a risk factor of cholangiocarcinoma (CHCA), probably through chronic inflammation.", "Formation of 8-nitroguanine and 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG), and expression of inducible nitric oxide synthase (iNOS) and heme oxygenase-1 (HO-1) were assessed in the liver of hamsters infected with OV.", "We newly produced specific anti-8-nitroguanine antibody without cross-reaction.", "Double immunofluorescence staining revealed that 8-oxodG and 8-nitroguanine were formed mainly in the same inflammatory cells and epithelium of bile ducts from day 7 and showed the strongest immunoreactivity on days 21 and 30, respectively.", "It is noteworthy that 8-oxodG and 8-nitroguanine still remained in epithelium of bile ducts on day 180, although amount of alanine aminotransferase activity returned to normal level.", "A time course of 8-nitroguanine was associated with iNOS expression.", "Furthermore, this study demonstrated that HO-1 expression and subsequent iron accumulation may be involved in enhancement of oxidative DNA damage in epithelium of small bile ducts.", "In conclusion, nitrative and oxidative DNA damage via iNOS expression in hamsters infected with OV may participate in CHCA carcinogenesis."], "structured": false}
{"doc_id": 22067786, "title": "Monte Carlo tests for associations between disease and alleles at highly polymorphic loci.", "abstract": ["In an association analysis comparing cases and controls with respect to allele frequencies at a highly polymorphic locus, a potential problem is that the conventional chi-squared test may not be valid for a large, sparse contingency table.", "However, reliance on statistics with known asymptotic distribution is now unnecessary, as Monte Carlo simulations can be performed to estimate the significance level of any test statistic.", "We have implemented a Monte Carlo method for four 'chi-squared' test statistics, three of which involved combination of alleles, and evaluated their performance on a real data set.", "Combining rare alleles to avoid small expected cell counts, and considering each allele in turn against the rest, reduced the power to detect a genuine association when the number of alleles was very large.", "We should either not combine alleles at all, or combine them in such a way that preserves the evidence for an association."], "structured": false}
{"doc_id": 22080671, "title": "KLF4-dependent phenotypic modulation of smooth muscle cells has a key role in atherosclerotic plaque pathogenesis", "abstract": ["Previous studies investigating the role of smooth muscle cells (SMCs) and macrophages in the pathogenesis of atherosclerosis have provided controversial results owing to the use of unreliable methods for clearly identifying each of these cell types.", "Here, using Myh11-CreERT2 ROSA floxed STOP eYFP Apoe\u2212/\u2212 mice to perform SMC lineage tracing, we find that traditional methods for detecting SMCs based on immunostaining for SMC markers fail to detect >80% of SMC-derived cells within advanced atherosclerotic lesions.", "These unidentified SMC-derived cells exhibit phenotypes of other cell lineages, including macrophages and mesenchymal stem cells (MSCs).", "SMC-specific conditional knockout of Kr\u00fcppel-like factor 4 (Klf4) resulted in reduced numbers of SMC-derived MSC- and macrophage-like cells, a marked reduction in lesion size, and increases in multiple indices of plaque stability, including an increase in fibrous cap thickness as compared to wild-type controls.", "On the basis of in vivo KLF4 chromatin immunoprecipitation\u2013sequencing (ChIP-seq) analyses and studies of cholesterol-treated cultured SMCs, we identified >800 KLF4 target genes, including many that regulate pro-inflammatory responses of SMCs.", "Our findings indicate that the contribution of SMCs to atherosclerotic plaques has been greatly underestimated, and that KLF4-dependent transitions in SMC phenotype are critical in lesion pathogenesis."], "structured": false}
{"doc_id": 22107641, "title": "Late-life depression and microstructural abnormalities in dorsolateral prefrontal cortex white matter.", "abstract": ["OBJECTIVE The purpose of this study was to determine whether microstructural abnormalities in the white matter of the dorsolateral prefrontal cortex are associated with late-life depression.   \n", "METHOD Seventeen elderly depressed subjects were compared with 16 elderly subjects who were not depressed.", "Diffusion tensor imaging was used to measure the fractional anisotropy of the white matter in the dorsolateral prefrontal cortex's superior and middle frontal gyri bilaterally and in the left occipital lobe as a control region.", "The authors compared results between groups while controlling for age, sex, and comorbid medical disorders.   \n", "RESULTS Even after controlling for age, sex, hypertension, and heart disease, the authors found significantly lower fractional anisotropy values in the right superior frontal gyrus white matter of depressed patients than comparison subjects.   \n", "CONCLUSIONS Microstructural changes in the white matter of the right superior frontal gyrus are associated with late-life depression.", "Further work is needed to determine how these changes contribute to depression outcomes."], "structured": true}
{"doc_id": 22116439, "title": "Pioglitazone prevents tau oligomerization.", "abstract": ["Tau aggregation and amyloid \u03b2 protein (A\u03b2) deposition are the main causes of Alzheimer's disease (AD).", "Peroxisome proliferator-activated receptor \u03b3 (PPAR\u03b3) activation modulates A\u03b2 production.", "To test whether the PPAR\u03b3 agonist pioglitazone (PIO) is also effective in preventing tau aggregation in AD, we used a cellular model in which wild-type tau protein (4R0N) is overexpressed (M1C cells) (Hamano et al., 2012) as well as primary neuronal cultures.", "PIO reduced both phosphorylated and total tau levels, and inactivated glycogen synthase kinase 3\u03b2, a major tau kinase, associated with activation of Akt.", "In addition, PIO decreased cleaved caspase3 and C-terminal truncated tau species by caspase, which is expected to decrease tau aggregation.", "A fractionation study showed that PIO reduced high molecular-weight (120 kDa), oligomeric tau species in Tris Insoluble, sarkosyl-soluble fractions.", "Tau decrease was reversed by adding GW9662, a PPAR\u03b3 antagonist.", "Together, our current results support the idea that PPAR\u03b3 agonists may be useful therapeutic agents for AD."], "structured": false}
{"doc_id": 22123421, "title": "Prognostic impact of the mean platelet volume/platelet count ratio in terms of survival in advanced non-small cell lung cancer.", "abstract": ["BACKGROUND Mean platelet volume (MPV) is a platelet volume index.", "Classically, MPV was recognized as a hallmark of platelet activation.", "Recent studies have revealed that the MPV and MPV/platelet count (PC) ratio can predict long-term mortality in patients with ischemic cardio-vascular disease.", "In addition, these indices were correlated with the pathophysiological characteristics of patients with various disorders, including malignant tumors.   \n", "PATIENTS AND METHODS We retrospectively analyzed various hematological indices of patients with advanced non-small cell lung cancer (NSCLC).", "The aim of this study was to evaluate the contribution of platelet volume indices to survival in these patients.   \n", "RESULTS A total of 268 patients were enrolled in the study.", "The median age of the patients was 68 years (range: 31-87 years).", "We compared various hematological indices between the NSCLC group and an age- and sex-matched comparator group.", "MPV was significantly decreased in the NSCLC group compared to the comparator group.", "In contrast, the PC was significantly increased in the NSCLC group.", "Consequently, the MPV/PC ratio was also decreased in the NSCLC group (0.397 vs. 0.501).", "In receiver operating characteristics (ROC) curve analysis, the MPV/PC ratio was associated with a sensitivity of 62.3% and a specificity of 74.6% at a cutoff value of 0.408730 (area under the curve [AUC], 0.72492)].", "Univariate analysis revealed that overall survival (OS) was significantly shorter in the group with a low MPV/PC ratio than in the other group (median survival time [MST]: 10.3 months vs. 14.5 months, log-rank, P=0.0245).", "Multivariate analysis confirmed that a low MPV/PC ratio was an independent unfavorable predictive factor for OS (hazard ratio [HR]: 1.668, 95% confidence interval [CI]: 1.235-2.271, P=0.0008).   \n", "CONCLUSION These data clearly demonstrate that the MPV/PC ratio was closely associated with survival in patients with advanced NSCLC."], "structured": true}
{"doc_id": 22130056, "title": "Traceability of biologicals: present challenges in pharmacovigilance.", "abstract": ["INTRODUCTION Traceability is important in the postmarketing surveillance of biologicals, since changes in the manufacturing process may give rise to product- or batch-specific risks.", "With the expected expansion of the biosimilar market, there have been concerns about the ability to trace individual products within pharmacovigilance databases.   ", "AREAS COVERED The authors discuss the present challenges in the traceability of biologicals in relation to pharmacovigilance, by exploring the processes involved in ensuring traceability.", "They explore both the existing systems that are in place for the recording of exposure information in clinical practice, as well as the critical steps involved in the transfer of exposure data to various pharmacovigilance databases.   ", "EXPERT OPINION The existing systems ensure the traceability of biologicals down to the manufacturer within pharmacy records, but do not support the routine recording of batch information.", "Expected changes in supply chain standards provide opportunities to systematically record detailed exposure information.", "Spontaneous reporting systems are the most vulnerable link in ensuring traceability, due to the manual nature of data transfer.", "Efforts to improve the traceability should, in the short term, be focused toward encouraging health professionals and patients to systematically record and report detailed exposure information.", "Long-term solutions lie in expanding the accessibility to, and increasing the electronic exchange of exposure data."], "structured": false}
{"doc_id": 22134353, "title": "Regulation of self-ligands for activating natural killer cell receptors.", "abstract": ["Natural killer (NK) cells are able to lyse infected and tumor cells while sparing healthy cells.", "Recognition of diseased cells by NK cells is governed by several activating and inhibitory receptors.", "We review numerous pathways that have been implicated in the regulation of self-ligands for activating receptors, including NKG2D, DNAM-1, LFA-1, NKp30, NKp44, NKp46, NKp65, and NKp80 found on NK cells and some T cells.", "Understanding how the regulation of self-encoded ligand expression is regulated may provide novel avenues for future therapeutic approaches to infections and cancer."], "structured": false}
{"doc_id": 22150633, "title": "A core Klf circuitry regulates self-renewal of embryonic stem cells", "abstract": ["Embryonic stem (ES) cells are unique in their ability to self-renew indefinitely and maintain pluripotency.", "These properties require transcription factors that specify the gene expression programme of ES cells.", "It has been possible to reverse the highly differentiated state of somatic cells back to a pluripotent state with a combination of four transcription factors: Klf4 is one of the reprogramming factors required, in conjunction with Oct4, Sox2 and c-Myc.", "Maintenance of self-renewal and pluripotency of ES cells requires Oct4, Sox2 and c-Myc, but Klf4 is dispensable.", "Here, we show that Kr\u00fcppel-like factors are required for the self-renewal of ES cells.", "Simultaneous depletion of Klf2, Klf4 and Klf5 lead to ES cell differentiation.", "Chromatin immunoprecipitation coupled to microarray assay reveals that these Klf proteins share many common targets of Nanog, suggesting a close functional relationship between these factors.", "Expression analysis after triple RNA interference (RNAi) of the Klfs shows that they regulate key pluripotency genes, such as Nanog.", "Taken together, our study provides new insight into how the core Klf circuitry integrates into the Nanog transcriptional network to specify gene expression that is unique to ES cells."], "structured": false}
{"doc_id": 22153455, "title": "A myeloid hypoxia-inducible factor 1\u03b1-Kr\u00fcppel-like factor 2 pathway regulates gram-positive endotoxin-mediated sepsis.", "abstract": ["Although gram-positive infections account for the majority of cases of sepsis, the molecular mechanisms underlying their effects remains poorly understood.", "We investigated how cell wall components of gram-positive bacteria contribute to the development of sepsis.", "Experimental observations derived from cultured primary macrophages and the cell line indicate that gram-positive bacterial endotoxins induce hypoxia-inducible factor 1\u03b1 (HIF-1\u03b1) mRNA and protein expression.", "Inoculation of live or heat-inactivated gram-positive bacteria with macrophages induced HIF-1 transcriptional activity in macrophages.", "Concordant with these results, myeloid deficiency of HIF-1\u03b1 attenuated gram-positive bacterial endotoxin-induced cellular motility and proinflammatory gene expression in macrophages.", "Conversely, gram-positive bacteria and their endotoxins reduced expression of the myeloid anti-inflammatory transcription factor Kr\u00fcppel-like transcription factor 2 (KLF2).", "Sustained expression of KLF2 reduced and deficiency of KLF2 enhanced gram-positive endotoxins induced HIF-1\u03b1 mRNA and protein expression in macrophages.", "More importantly, KLF2 attenuated gram-positive endotoxins induced cellular motility and proinflammatory gene expression in myeloid cells.", "Consistent with these results, mice deficient in myeloid HIF-1\u03b1 were protected from gram-positive endotoxin-induced sepsis mortality and clinical symptomatology.", "By contrast, myeloid KLF2-deficient mice were susceptible to gram-positive sepsis induced mortality and clinical symptoms.", "Collectively, these observations identify HIF-1\u03b1 and KLF2 as critical regulators of gram-positive endotoxin-mediated sepsis."], "structured": false}
{"doc_id": 22159299, "title": "Autophagy controls Salmonella infection in response to damage to the Salmonella-containing vacuole.", "abstract": ["Salmonella enterica serovar Typhimurium (S. Typhimurium) is a facultative intracellular pathogen that causes disease in a variety of hosts.", "S. Typhimurium actively invade host cells and typically reside within a membrane-bound compartment called the Salmonella-containing vacuole (SCV).", "The bacteria modify the fate of the SCV using two independent type III secretion systems (TTSS).", "TTSS are known to damage eukaryotic cell membranes and S. Typhimurium has been suggested to damage the SCV using its Salmonella pathogenicity island (SPI)-1 encoded TTSS.", "Here we show that this damage gives rise to an intracellular bacterial population targeted by the autophagy system during in vitro infection.", "Approximately 20% of intracellular S. Typhimurium colocalized with the autophagy marker GFP-LC3 at 1 h postinfection.", "Autophagy of S. Typhimurium was dependent upon the SPI-1 TTSS and bacterial protein synthesis.", "Bacteria targeted by the autophagy system were often associated with ubiquitinated proteins, indicating their exposure to the cytosol.", "Surprisingly, these bacteria also colocalized with SCV markers.", "Autophagy-deficient (atg5-/-) cells were more permissive for intracellular growth by S. Typhimurium than normal cells, allowing increased bacterial growth in the cytosol.", "We propose a model in which the host autophagy system targets bacteria in SCVs damaged by the SPI-1 TTSS.", "This serves to retain intracellular S. Typhimurium within vacuoles early after infection to protect the cytosol from bacterial colonization.", "Our findings support a role for autophagy in innate immunity and demonstrate that Salmonella infection is a powerful model to study the autophagy process."], "structured": false}
{"doc_id": 22174015, "title": "PI3K-Akt-mTORC1-S6K1/2 axis controls Th17 differentiation by regulating Gfi1 expression and nuclear translocation of ROR\u03b3.", "abstract": ["The PI3K-Akt-mTORC1 axis contributes to the activation, survival, and proliferation of CD4(+) T cells upon stimulation through TCR and CD28.", "Here, we demonstrate that the suppression of this axis by deletion of p85\u03b1 or PI3K/mTORC1 inhibitors as well as T cell-specific deletion of raptor, an essential component of mTORC1, impairs Th17 differentiation in vitro and in vivo in a S6K1/2-dependent fashion.", "Inhibition of PI3K-Akt-mTORC1-S6K1 axis impairs the downregulation of Gfi1, a negative regulator of Th17 differentiation.", "Furthermore, we demonstrate that S6K2, a nuclear counterpart of S6K1, is induced by the PI3K-Akt-mTORC1 axis, binds ROR\u03b3, and carries ROR\u03b3 to the nucleus.", "These results point toward a pivotal role of PI3K-Akt-mTORC1-S6K1/2 axis in Th17 differentiation."], "structured": false}
{"doc_id": 22178316, "title": "Disrupted-in-schizophrenia 1 and neuregulin 1 are required for the specification of oligodendrocytes and neurones in the zebrafish brain.", "abstract": ["Schizophrenia may arise from subtle abnormalities in brain development due to alterations in the functions of candidate susceptibility genes such as Disrupted-in-schizophrenia 1 (DISC1) and Neuregulin 1 (NRG1).", "To provide novel insights into the functions of DISC1 in brain development, we mapped the expression of zebrafish disc1 and set out to characterize its role in early embryonic development using morpholino antisense methods.", "These studies revealed a critical requirement for disc1 in oligodendrocyte development by promoting specification of olig2-positive cells in the hindbrain and other brain regions.", "Since NRG1 has well-documented roles in myelination, we also analyzed the roles of nrg1 and ErbB signalling in zebrafish brain development and we observed strikingly similar defects to those seen in disc1 morphant embryos.", "In addition to their effects on oligodendrocyte development, knock-down of disc1 or nrg1 caused near total loss of olig2-positive cerebellar neurones, but caused no apparent loss of spinal motor neurones.", "These findings suggest that disc1 and nrg1 function in common or related pathways controlling development of oligodendrocytes and neurones from olig2-expressing precursor cells.", "Like DISC1 and NRG1, OLIG2 and ERBB4 are promising candidate susceptibility genes for schizophrenia.", "Hence our findings in the zebrafish embryo suggest that hitherto unappreciated neurodevelopmental connections may exist between key human schizophrenia susceptibility genes.", "These connections could be investigated in Disc1 and Nrg1 mouse models and in genetically defined groups of patients in order to determine whether they are relevant to the pathobiology of schizophrenia.", "GenBank accession number for Danio rerio disc1: EU273350."], "structured": false}
{"doc_id": 22180793, "title": "Monoclonal antibody targeting of N-cadherin inhibits prostate cancer growth, metastasis and castration resistance", "abstract": ["The transition from androgen-dependent to castration-resistant prostate cancer (CRPC) is a lethal event of uncertain molecular etiology.", "Comparing gene expression in isogenic androgen-dependent and CRPC xenografts, we found a reproducible increase in N-cadherin expression, which was also elevated in primary and metastatic tumors of individuals with CRPC.", "Ectopic expression of N-cadherin in nonmetastatic, androgen-dependent prostate cancer models caused castration resistance, invasion and metastasis.", "Monoclonal antibodies against the ectodomain of N-cadherin reduced proliferation, adhesion and invasion of prostate cancer cells in vitro.", "In vivo, these antibodies slowed the growth of multiple established CRPC xenografts, blocked local invasion and metastasis and, at higher doses, led to complete regression.", "N-cadherin\u2013specific antibodies markedly delayed the time to emergence of castration resistance, markedly affected tumor histology and angiogenesis, and reduced both AKT serine-threonine kinase activity and serum interleukin-8 (IL-8) secretion.", "These data indicate that N-cadherin is a major cause of both prostate cancer metastasis and castration resistance.", "Therapeutic targeting of this factor with monoclonal antibodies may have considerable clinical benefit."], "structured": false}
{"doc_id": 22185730, "title": "PP2A regulates tau phosphorylation directly and also indirectly via activating GSK-3beta.", "abstract": ["Abnormal hyperphosphorylation of tau appears to be crucial in neurofibrillary degeneration in Alzheimer's disease (AD).", "Previous studies suggest that a down-regulation of protein phosphatase 2A (PP2A), the major tau phosphatase in human brain, contributes to tau hyperphosphorylation in AD.", "However, the effects of PP2A down-regulation on site-specific tau hyperphosphorylation is not well understood.", "In the present study, we showed that PP2A dephosphorylated tau at several phosphorylation sites with different efficiencies.", "Among the sites studied, Thr205, Thr212, Ser214, and Ser262 were the most favorable sites, and Ser199 and Ser404 were the least favorable sites for PP2A in vitro.", "Inhibition of PP2A with okadaic acid in metabolically active rat brain slices caused inhibition of glycogen synthase kinase-3beta (GSK-3beta) via an increase in its phosphorylation at Ser9.", "GSK-3beta phosphorylated tau at many sites, with Ser199, Thr205, and Ser396 being the most favorable sites in cells.", "The overall alterations in tau phosphorylation induced by PP2A inhibition were the result of the combined effects of both reduced tau dephosphorylation due to PP2A inhibition directly and reduced phosphorylation by GSK-3beta due to its inhibition.", "Because the impacts of tau phosphorylation on its biological activity and on neurofibrillary degeneration are site-specific, this study provides a new insight into the role of PP2A down-regulation in neurofibrillary degeneration in AD."], "structured": false}
{"doc_id": 22186938, "title": "Human artificial chromosomes containing chromosome 17 alphoid DNA maintain an active centromere in murine cells but are not stable.", "abstract": ["Human artificial chromosomes (HACs) are autonomous molecules that can function and segregate as normal chromosomes in human cells.", "De novo HACs have successfully been used as gene expression vectors to complement genetic deficiencies in human cultured cells.", "HACs now offer the possibility of studying the regulation and expression of large genes in a variety of cell types from different tissues and correcting gene deficiencies caused by human inherited diseases.", "Complementary gene expression studies in mice, especially in mouse models of human genetic diseases, are also important in determining if large human transgenes can be expressed appropriately from artificial chromosomes.", "Toward this aim we are establishing artificial chromosomes in murine cells as novel gene expression vectors.", "Initially we transferred HAC vectors into murine cells, but were unable to generate de novo HACs at a reasonable frequency.", "We then transferred HACs previously established in human HT1080 cells to three different murine cell types by microcell fusion, followed by positive selection.", "We observed that the HACs in murine cells bound centromere protein C (CENP-C), a marker of active centromeres, and were detected under selection but rapidly lost when selection was removed.", "These results suggest that the HACs maintain at least a partially functional centromere complex in murine cells, but other factors are required for stability and segregation.", "Artificial chromosomes containing mouse centromeric sequences may be required for better stability and maintenance in murine cells."], "structured": false}
{"doc_id": 22190276, "title": "How nascent phagosomes mature to become phagolysosomes.", "abstract": ["Phagocytosis mediates the clearance of apoptotic bodies and also the elimination of microbial pathogens.", "The nascent phagocytic vacuole formed upon particle engulfment lacks microbicidal and degradative activity.", "These capabilities are acquired as the phagosome undergoes maturation; a progressive remodeling of its membrane and contents that culminates in the formation of phagolysosomes.", "Maturation entails orderly sequential fusion of the phagosomal vacuole with specialized endocytic and secretory compartments.", "Concomitantly, the phagosomal membrane undergoes both inward and outward vesiculation and tubulation followed by fission, thereby recycling components and maintaining its overall size.", "Here, we summarize what is known about the molecular machinery that governs this complex metamorphosis of phagosome maturation."], "structured": false}
{"doc_id": 22191759, "title": "Purification and structural characterization of bovine cathelicidins, precursors of antimicrobial peptides.", "abstract": ["Cathelicidins are a novel family of antimicrobial peptide precursors from mammalian myeloid cells.", "They are characterized by a conserved N-terminal region while the C-terminal antimicrobial domain can vary considerably in both primary sequence and length.", "Four cathelicidins, proBac5, proBac7, prododecapeptide and proBMAP-28, have been concurrently purified from bovine neutrophils, using simple and rapid methodologies.", "The correlation of ES-MS data from the purified proteins with their cDNA-deduced sequences has revealed several common features of their primary sequence, such as the presence of N-terminal 5-oxoproline (pyroglutamate) residues and two disulfide bridges in a 1-2, 3-4 arrangement.", "The N-terminal domains of the cathelicidins present one or two Asp-Pro bonds, which are particularly acid-labile in proBac5 and proBac7, but stable in prododecapeptide.", "This suggests that the spatial organization around these bonds may vary in different cathelicidins, and favour hydrolysis in some cases.", "An unexpected feature of the prododecapeptide is that it exists as dimers formed by three possible combinations of its two isoforms.", "The isolation of a truncated, monomeric form of this protein, lacking the cysteine-containing antimicrobial dodecapeptide, indicates that dimerization occurs via disulfide bridge formation at the level of the C-terminal domain and that the dodecapeptide is likely released as a dimer from its precursor.", "Sequence-based secondary structure predictions and CD results indicate for cathelicidins a 30-50% content of extended conformation and <20% content of alpha-helical conformation, with the alpha-helical segment placed near the N-terminus.", "Finally, similarity searching and topology-based structure prediction underline a significant sequential and structural similarity between the conserved N-terminal domain of cathelicidins and cystatin-like domains, placing this family within the cystatin superfamily.", "When assayed against cathepsin L, unlike the potent cystatin inhibitors, three of the four cathelicidins show only a poor inhibitory activity (Ki = 0.6-3 microM)."], "structured": false}
{"doc_id": 22194407, "title": "Tuberculosis mortality in England and Wales during 1982-1992: its association with poverty, ethnicity and AIDS.", "abstract": ["This paper seeks to establish the strength of association between contemporary tuberculosis (TB) in England and Wales and several potential aetiological factors.", "It presents an ecological analysis of standardised annual TB mortality rates for the 403 local authority districts between 1982 and 1992, disaggregated by age and sex.", "Social, demographic and ethnicity measures from the 1981 and 1991 censuses and standardised annual AIDS-related mortality rates for young men are used to calculate Poisson regression models.", "A strong association was found between all TB mortality groups and overcrowding at the household level.", "For women, no other measures improved the explanatory power of the models.", "In multiple regressions, both poverty and AIDS-related mortality explained additional variation in the model for younger men.", "The link between ethnicity and tuberculosis notifications was not reflected in this analysis of mortality.", "For all groups no evidence of a positive relationship with ethnicity was found, once overcrowding had been accounted for.", "The significance of household as opposed to district level crowding suggests that prolonged contact is required for disease transmission.", "Regression analysis indicates that it is the overcrowding and poverty among ethnic populations that is significant for their tuberculosis mortality.", "The fact that the relationship between AIDS and TB is confined to the group most typical of AIDS patients provides evidence that AIDS has little influence on the level of tuberculosis mortality in the wider population.", "Explanations for the observed relationship include preferential certification, migration for treatment and shortcomings in health care provision."], "structured": false}
{"doc_id": 22198971, "title": "Noncognate interaction with MHC class II molecules is essential for maintenance of T cell metabolism to establish optimal memory CD4 T cell function.", "abstract": ["CD4 memory T cells surviving in the absence of MHC class II contact lose their characteristic memory function.", "To investigate the mechanisms underlying the impaired function of memory T cells in the absence of MHC class II molecules, we analyzed gene expression profiles of resting memory T cells isolated from MHC class II-competent or -deficient hosts.", "The analysis focused on five transcripts related to T cell activation, metabolism, and survival that are underexpressed in resting memory T cells from MHC class II-deficient hosts compared with MHC class II-competent hosts.", "CD4 memory cells isolated from MHC class II-deficient hosts display alterations in their degree of differentiation as well as metabolic activity, and these changes are already manifest in the effector phase despite the presence of Ag-expressing dendritic cells.", "Our data suggest that the absence of interactions with noncognate MHC class II molecules compromises the progressive accumulation of signals that ensure optimal survival and fitness to sustain the metabolic activity of activated T cells and shape the functional capacity of the future memory compartment.", "Signals via AKT coordinate survival and metabolic pathways and may be one of the crucial events linking interaction with MHC class II molecules to the successful generation of a long-lived functional memory CD4 T cell population."], "structured": false}
{"doc_id": 22210434, "title": "The kinase TAK1 integrates antigen and cytokine receptor signaling for T cell development, survival and function", "abstract": ["The kinase TAK1 is critical for innate and B cell immunity.", "The function of TAK1 in T cells is unclear, however.", "We show here that T cell\u2013specific deletion of the gene encoding TAK1 resulted in reduced development of thymocytes, especially of regulatory T cells expressing the transcription factor Foxp3.", "In mature thymocytes, TAK1 was required for interleukin 7\u2013mediated survival and T cell receptor\u2013dependent activation of transcription factor NF-\u03baB and the kinase Jnk.", "In effector T cells, TAK1 was dispensable for T cell receptor\u2013dependent NF-\u03baB activation and cytokine production, but was important for proliferation and activation of the kinase p38 in response to interleukins 2, 7 and 15.", "Thus, TAK1 is essential for the integration of T cell receptor and cytokine signals to regulate the development, survival and function of T cells."], "structured": false}
{"doc_id": 22227889, "title": "Caregiver burden in HIV-positive and HIV-negative partners of men with AIDS.", "abstract": ["This study examines factors associated with caregiver burden in 82 HIV-positive (HIV+) and 162 HIV-negative (HIV-) partners of men with AIDS.", "We expected HIV+ caregivers to report more burden than HIV- caregivers because of the toll of their disease on their resources.", "HIV+ caregivers did report more burden and, compared with the HIV- caregivers, they were more religious or spiritual, had less income, and coped by using more positive reappraisal and cognitive escape-avoidance and by seeking social support.", "Comparisons of HIV+ caregivers with 61 HIV+ partners of healthy men indicated that most differences between HIV+ and HIV- caregivers were associated with HIV seropositivity rather than caregiving.", "However, of the variables associated with HIV seropositivity, only religiosity or spirituality contributed independently to burden in HIV+ caregivers, suggesting a relatively weak link between HIV seropositivity and caregiver burden.", "The model explained 62% of the variance in burden in HIV+ caregivers and 36% of the variance in HIV- caregivers."], "structured": false}
{"doc_id": 22236223, "title": "Renal Disease and Pregnancy", "abstract": ["Pregnancy in women with different renal diseases has important consequences for the developing fetus and maternal health.", "Kidneys and the urinary tract have to adapt to the pregnancy status and therefore suffer significant anatomical, hemodynamic and endocrine changes.", "Failure to adapt can aggravate the preexisting maternal disease and can also create suboptimal environment for fetal development and increase the risk of obstetric complications.", "Knowledge and correct interpretation of the renal functional tests is necessary for the modern obstetrician, avoiding an incorrect diagnosis for renal disease where only specific renal changes during pregnancy are present, but meanwhile a correct evaluation of the renal function and changes can detect a pathology that can aggravate both the mother\u2019s and the baby\u2019s condition.", "Improvement and better understanding of the renal pathophysiology in pregnancy made possible that pregnant woman look forward for a good outcome, including here also the women with renal transplant.", "Nowadays is underlined the concept of multidisciplinary teamwork, a very important concept of modern medicine.", "The obstetrician should consider nephrologists as key players in the team and in our opinion should refer to them the pregnant women for a routine check-up of the renal status in the 2nd or beginning of 3rd trimester by ultrasound, beside the usual blood and urine analysis.", "The nephrologists and urologists should be involved in the management of severe medical conditions, such as preeclampsia, acute and chronic renal failure and never the less in the complex management of dialysis or renal transplant patients.", "In pregnancy it can be encountered several renal diseases, some of them preexisting the pregnancy and other developed or being direct influenced by pregnancy.", "This chapter will discuss briefly the basic evaluation of renal status in order to present and better understand the acute and chronic renal disorders in pregnancy.", "The chapter will focus on the most common preexisting diseases in pregnancy such as: chronic glomerulonephritis, secondary glomerular nephropathies, interstitial nephropathies (chronic pyelonephritis, renal tuberculosis), diabetes nephropathy, unique surgical kidney, chronic renal failure.", "From the renal diseases directly influenced by pregnancy it will be discussed: asymptomatic bacteriuria, symptomatic urinary infection, urolithiasis and acute renal failure in pregnancy.", "It will be presented also the management of dialysis in pregnancy and pregnant women with renal transplant."], "structured": false}
{"doc_id": 22241778, "title": "Integrin beta1-mediated matrix assembly and signaling are critical for the normal development and function of the kidney glomerulus.", "abstract": ["The human kidneys filter 180 l of blood every day via about 2.5 million glomeruli.", "The three layers of the glomerular filtration apparatus consist of fenestrated endothelium, specialized extracellular matrix known as the glomerular basement membrane (GBM) and the podocyte foot processes with their modified adherens junctions known as the slit diaphragm (SD).", "In this study we explored the contribution of podocyte beta1 integrin signaling for normal glomerular function.", "Mice with podocyte specific deletion of integrin beta1 (podocin-Cre beta1-fl/fl mice) are born normal but cannot complete postnatal renal development.", "They exhibit detectable proteinuria on day 1 and die within a week.", "The kidneys of podocin-Cre beta1-fl/fl mice exhibit normal glomerular endothelium but show severe GBM defects with multilaminations and splitting including podocyte foot process effacement.", "The integrin linked kinase (ILK) is a downstream mediator of integrin beta1 activity in epithelial cells.", "To further explore whether integrin beta1-mediated signaling facilitates proper glomerular filtration, we generated mice deficient of ILK in the podocytes (podocin-Cre ILK-fl/fl mice).", "These mice develop normally but exhibit postnatal proteinuria at birth and die within 15 weeks of age due to renal failure.", "Collectively, our studies demonstrate that podocyte beta1 integrin and ILK signaling is critical for postnatal development and function of the glomerular filtration apparatus."], "structured": false}
{"doc_id": 22264117, "title": "The Aging Epigenome.", "abstract": ["During aging, the mechanisms that normally maintain health and stress resistance strikingly decline, resulting in decrepitude, frailty, and ultimately death.", "Exactly when and how this decline occurs is unknown.", "Changes in transcriptional networks and chromatin state lie at the heart of age-dependent decline.", "These epigenomic changes are not only observed during aging but also profoundly affect cellular function and stress resistance, thereby contributing to the progression of aging.", "We propose that the dysregulation of transcriptional and chromatin networks is a crucial component of aging.", "Understanding age-dependent epigenomic changes will yield key insights into how aging begins and progresses and should lead to the development of new therapeutics that delay or even reverse aging and age-related diseases."], "structured": false}
{"doc_id": 22267225, "title": "Cancer chemoprevention: Much has been done, but there is still much to do. State of the art and possible new approaches.", "abstract": ["Over the past three decades great efforts have been made in search of cancer chemoprevention strategies.", "The increase in knowledge of the long process from normal to cancer cell has enabled interventions in terms of lifestyle modifications, natural compounds or drugs to block or reverse the process.", "Great successes have been achieved, especially for breast and colorectal cancer.", "However, these strategies have yet to find clinical application on a large scale.", "In this article we identify the achievements, the pitfalls and the next steps to be taken to improve the efficacy and applicability of chemoprevention strategies.", "Among the crucial key points to be implemented are educational activities for physicians to appropriately disseminate the aim and indeed the culture of chemoprevention.", "It is essential to improve the risk-benefit balance, seeking the minimal active doses, intermittent schedules, a better characterization of the risk categories via a more personalized intervention based on individual characteristics, and ensure the containment of costs of public and private health prevention programs."], "structured": false}
{"doc_id": 22281684, "title": "Secreted Frizzled-related Protein 5 Diminishes Cardiac Inflammation and Protects the Heart from Ischemia/Reperfusion Injury.", "abstract": ["Wnt signaling has diverse actions in cardiovascular development and disease processes.", "Secreted frizzled-related protein 5 (Sfrp5) has been shown to function as an extracellular inhibitor of non-canonical Wnt signaling that is expressed at relatively high levels in white adipose tissue.", "The aim of this study was to investigate the role of Sfrp5 in the heart under ischemic stress.", "Sfrp5 KO and WT mice were subjected to ischemia/reperfusion (I/R).", "Although Sfrp5-KO mice exhibited no detectable phenotype when compared with WT control at baseline, they displayed larger infarct sizes, enhanced cardiac myocyte apoptosis, and diminished cardiac function following I/R. The ischemic lesions of Sfrp5-KO mice had greater infiltration of Wnt5a-positive macrophages and greater inflammatory cytokine and chemokine gene expression when compared with WT mice.", "In bone marrow-derived macrophages, Wnt5a promoted JNK activation and increased inflammatory gene expression, whereas treatment with Sfrp5 blocked these effects.", "These results indicate that Sfrp5 functions to antagonize inflammatory responses after I/R in the heart, possibly through a mechanism involving non-canonical Wnt5a/JNK signaling."], "structured": false}
{"doc_id": 22309946, "title": "Asymptomatic spinal cord lesions predict disease progression in radiologically isolated syndrome.", "abstract": ["BACKGROUND Technological advancements in neuroimaging and the increased use of these diagnostic modalities are responsible for the discovery of incidentally identified anomalies within the CNS.", "In addition to the identification of unanticipated brain MRI abnormalities suggestive of demyelinating disease in patients undergoing neuroimaging for a medical reason other than evaluation for multiple sclerosis (MS), asymptomatic spinal cord lesions are periodically identified.   \n", "OBJECTIVE To determine if asymptomatic spinal cord lesions are associated with clinical progression in subjects with radiologically isolated syndrome (RIS).   \n", "METHODS A retrospective review of RIS cases at the University of California, San Francisco Multiple Sclerosis Center was performed.", "The presence of asymptomatic cervical spinal cord MRI lesions was analyzed as a potential predictor for clinical progression.   \n", "RESULTS Twenty-five of 71 subjects with RIS possessed findings within the cervical spine that were highly suggestive of demyelinating disease.", "Of these subjects, 21 (84%) progressed clinically to clinically isolated syndrome (n = 19) or primary progressive multiple sclerosis (n = 2) over a median time of 1.6 years from the date of RIS identification (interquartile range 0.8-3.8).", "The sensitivity, specificity, and positive predictive value of an asymptomatic spinal cord lesion for subsequent development of either a first demyelinating attack or primary progressive MS were 87.5%, 91.5%, and 84%, respectively.", "The odds ratio of clinical progression was 75.3 (95% confidence interval 16.1-350.0, p < 0.0001).", "This association remained significant after adjusting for potential confounders.   \n", "CONCLUSION These findings suggest that the presence of asymptomatic spinal cord lesions place subjects with RIS at substantial risk for clinical conversion to either an acute or progressive event, a risk that is independent of brain lesions on MRI."], "structured": true}
{"doc_id": 22312627, "title": "YqhC regulates transcription of the adjacent Escherichia coli genes yqhD and dkgA that are involved in furfural tolerance", "abstract": ["Previous results have demonstrated that the silencing of adjacent genes encoding NADPH-dependent furfural oxidoreductases (yqhD dkgA) is responsible for increased furfural tolerance in an E. coli strain EMFR9 [Miller et al., Appl Environ Microbiol 75:4315\u20134323, 2009].", "This gene silencing is now reported to result from the spontaneous insertion of an IS10 into the coding region of yqhC, an upstream gene.", "YqhC shares homology with transcriptional regulators belonging to the AraC/XylS family and was shown to act as a positive regulator of the adjacent operon encoding YqhD and DkgA. Regulation was demonstrated by constructing a chromosomal deletion of yqhC, a firefly luciferase reporter plasmid for yqhC, and by a direct comparison of furfural resistance and NADPH-dependent furfural reductase activity.", "Closely related bacteria contain yqhC, yqhD, and dkgA orthologs in the same arrangement as in E. coli LY180.", "Orthologs of yqhC are also present in more distantly related Gram-negative bacteria.", "Disruption of yqhC offers a useful approach to increase furfural tolerance in bacteria."], "structured": false}
{"doc_id": 22317868, "title": "A direct role for Met endocytosis in tumorigenesis", "abstract": ["Compartmentalization of signals generated by receptor tyrosine kinase (RTK) endocytosis has emerged as a major determinant of various cell functions.", "Here, using tumour-associated Met-activating mutations, we demonstrate a direct link between endocytosis and tumorigenicity.", "Met mutants exhibit increased endocytosis/recycling activity and decreased levels of degradation, leading to accumulation on endosomes, activation of the GTPase Rac1, loss of actin stress fibres and increased levels of cell migration.", "Blocking endocytosis inhibited mutants\u2019 anchorage-independent growth, in vivo tumorigenesis and metastasis while maintaining their activation.", "One mutant resistant to inhibition by a Met-specific tyrosine kinase inhibitor was sensitive to endocytosis inhibition.", "Thus, oncogenicity of Met mutants results not only from activation but also from their altered endocytic trafficking, indicating that endosomal signalling may be a crucial mechanism regulating RTK-dependent tumorigenesis."], "structured": false}
{"doc_id": 22328290, "title": "Immediate effects of droperidol", "abstract": ["The subjective and behavioural responses of 20 healthy volunteers taking droperidol 5 mg as part of a cognitive challenge programme were catalogued.", "Some form of akathisia was universally experienced.", "Half of the subjects were dysphoric, but there appeared to be a number of different inputs to their dysphoria and a range of other effects were noted, including sedation, dissociative experiences, alterations in sensation and subtle changes in physiognomy.", "The duration of these effects varied from a few hours to over a week.", "In the acute phase, insight as to the origin of what was happening was mixed.", "The results have implications for the interpretation of cognitive challenge tests, the nature of akathisia, clinical therapeutics and drug development.", "\u00a9 1998 John Wiley & Sons, Ltd."], "structured": false}
{"doc_id": 22334300, "title": "Toxicity of Nerium oleander in the monkey (Cebus apella).", "abstract": ["The toxic effects of Nerium oleander were evaluated in capuchin monkeys (Cebus apella) by examination of clinical signs, hematologic and serum chemical values, and gross and microscopic lesions.", "Dried and ground oleander leaves were given at intervals of 48 h in doses of 30, 7.5, and 3 mg/kg body weight.", "The cumulative lethal dose ranged from 30 to 60 mg/kg body weight in monkeys that were given doses of 30 and 7.5 mg/kg body weight.", "Monkeys that received doses of 3 mg/kg body weight (total cumulative dose: 60 mg/kg) survived.", "Clinical signs were vomiting, salivation, polyuria, bradycardia, vaginal hemorrhage, abortion, anorexia, constipation, loss of body weight, narcosis, restlessness, weakness, and shallow and rapid respirations.", "Changes in blood values were leukocytosis; neutrophilia; increased potassium, glutamic-oxalacetic transaminase, glutamic-pyruvic transaminase, blood urea nitrogen and \u03b1-globulins; reticulo-cytopenia; and decreased calcium, glucose, total serum protein, albumin, \u03b3-globulin leve..."], "structured": false}
{"doc_id": 22358449, "title": "Plzf regulates limb and axial skeletal patterning", "abstract": ["The promyelocytic leukaemia zinc finger (Plzf) protein (encoded by the gene Zfp145) belongs to the POZ/zinc-finger family of transcription factors.", "Here we generate Zfp145\u2212/\u2212 mice and show that Plzf is essential for patterning of the limb and axial skeleton.", "Plzf inactivation results in patterning defects affecting all skeletal structures of the limb, including homeotic transformations of anterior skeletal elements into posterior structures.", "We demonstrate that Plzf acts as a growth-inhibitory and pro-apoptotic factor in the limb bud.", "The expression of members of the abdominal b (Abdb) Hox gene complex, as well as genes encoding bone morphogenetic proteins (Bmps), is altered in the developing limb of Zfp145\u2212/\u2212 mice.", "Plzf regulates the expression of these genes in the absence of aberrant polarizing activity and independently of known patterning genes.", "Zfp145\u2212/\u2212 mice also exhibit anterior-directed homeotic transformation throughout the axial skeleton with associated alterations in Hox gene expression.", "Plzf is therefore a mediator of anterior-to-posterior (AP) patterning in both the axial and appendicular skeleton and acts as a regulator of Hox gene expression."], "structured": false}
{"doc_id": 22362025, "title": "Requirement for the ERI/DICER complex in endogenous RNA interference and sperm development in Caenorhabditis elegans.", "abstract": ["Small regulatory RNAs are key regulators of gene expression.", "One class of small regulatory RNAs, termed the endogenous small interfering RNAs (endo siRNAs), is thought to negatively regulate cellular transcripts via an RNA interference (RNAi)-like mechanism termed endogenous RNAi (endo RNAi).", "A complex of proteins composed of ERI-1/3/5, RRF-3, and DICER (the ERI/DICER complex) mediates endo RNAi processes in Caenorhabditis elegans.", "We conducted a genetic screen to identify additional components of the endo RNAi machinery.", "Our screen recovered alleles of eri-9, which encodes a novel DICER-interacting protein, and a missense mutation within the helicase domain of DICER [DCR-1(G492R)].", "ERI-9(-) and DCR-1(G492) animals exhibit defects in endo siRNA expression and a concomitant failure to regulate mRNAs that exhibit sequence homology to these endo siRNAs, indicating that ERI-9 and the DCR-1 helicase domain function in the C. elegans endo RNAi pathway.", "We define a subset of Eri mutant animals (including eri-1, rrf-3, eri-3, and dcr-1, but not eri-9 or ergo-1) that exhibit temperature-sensitive, sperm-specific sterility and defects in X chromosome segregation.", "Among these mutants we find multiple aberrations in sperm development beginning with cytokinesis and extending through terminal differentiation.", "These results identify novel components of the endo RNAi machinery, demonstrate differential requirements for the Eri factors in the sperm-producing germline, and begin to delineate the functional requirement for the ERI/DICER complex in sperm development."], "structured": false}
{"doc_id": 22371455, "title": "Drug-induced thrombocytopenia: pathogenesis, evaluation, and management.", "abstract": ["Although drugs are a common cause of acute immune-mediated thrombocytopenia in adults, the drug etiology is often initially unrecognized.", "Most cases of drug-induced thrombocytopenia (DITP) are caused by drug-dependent antibodies that are specific for the drug structure and bind tightly to platelets by their Fab regions but only in the presence of the drug.", "A comprehensive database of 1301 published reports describing 317 drugs, available at www.ouhsc.edu/platelets, provides information on the level of evidence for a causal relation to thrombocytopenia.", "Typically, DITP occurs 1 to 2 weeks after beginning a new drug or suddenly after a single dose when a drug has previously been taken intermittently.", "However, severe thrombocytopenia can occur immediately after the first administration of antithrombotic agents that block fibrinogen binding to platelet GP IIb-IIIa, such as abciximab, tirofiban, and eptifibatide.", "Recovery from DITP usually begins within 1 to 2 days of stopping the drug and is typically complete within a week.", "Drug-dependent antibodies can persist for many years; therefore, it is important that the drug etiology be confirmed and the drug be avoided thereafter."], "structured": false}
{"doc_id": 22401061, "title": "Costs and financial feasibility of malaria elimination", "abstract": ["The marginal costs and benefits of converting malaria programmes from a control to an elimination goal are central to strategic decisions, but empirical evidence is scarce.", "We present a conceptual framework to assess the economics of elimination and analyse a central component of that framework-potential short-term to medium-term financial savings.", "After a review that showed a dearth of existing evidence, the net present value of elimination in five sites was calculated and compared with effective control.", "The probability that elimination would be cost-saving over 50 years ranged from 0% to 42%, with only one site achieving cost-savings in the base case.", "These findings show that financial savings should not be a primary rationale for elimination, but that elimination might still be a worthy investment if total benefits are sufficient to outweigh marginal costs.", "Robust research into these elimination benefits is urgently needed."], "structured": false}
{"doc_id": 22401720, "title": "Expression of the angiogenic factors vascular endothelial cell growth factor, acidic and basic fibroblast growth factor, tumor growth factor beta-1, platelet-derived endothelial cell growth factor, placenta growth factor, and pleiotrophin in human primary breast cancer and its relation to angiogenes", "abstract": ["Angiogenesis is a significant prognostic factor in breast cancer, but the factors that control angiogenesis in vivo are not well defined.", "Multiple angiogenic polypeptides are known, and we have determined the expression of seven of these in primary human breast cancers; the relationship of expression to estrogen receptor and vascular density was also examined.", "Vascular endothelial growth factor (VEGF) and its four isoforms (121, 165, 189, and 206 amino acids), transforming growth factor (TGF)-beta1, pleiotrophin, acidic and basic fibroblast growth factor (FGF), placental growth factor, and thymidine phosphorylase (platelet-derived endothelial cell growth factor) were quantitated by RNase protection analysis.", "beta-FGF was also measured by ELISA.", "The estrogen receptor (ER), epidermal growth factor receptor, and vascular density were analyzed in 64 primary breast cancers.", "All tumors expressed at least six different vascular growth factors.", "VEGF was most abundant, and the transcript for the 121-amino acid form predominated.", "Other angiogenic factors expressed at high levels were thymidine phosphorylase and TGF-beta1.", "Expression of most of the angiogenic factors did not correlate with that of ER or vascular density.", "However, thymidine phosphorylase did, with a correlation coefficient of 0.3 (P = 0.03).", "There were significant associations of pleiotrophin with acidic FGF expression (P = 0.001) and TGF-beta with platelet-derived endothelial cell growth factor expression (P = 0.001).", "Thus, angiogenesis may involve a coordinate regulation of some vascular growth factors.", "High VEGF expression correlated with poor prognosis in univariate analysis (P = 0.03), as did ER and epidermal growth factor receptor expression.", "Basic FGF was also assessed by ELISA and was more highly expressed in tumors than normal breast tissues (median, 346 microg/ml cytosol; range, 54-1323 versus median, 149; range, 32-509; P = 0.01).", "Implications for therapy are that broad spectrum agents that block features common to these factors may be useful (e.g., antagonism of heparin-binding activity agents), because so many angiogenic factors are expressed.", "Inhibiting endothelial migration or agents directly toxic to endothelium would be of value in a combined approach to therapy."], "structured": false}
{"doc_id": 22405338, "title": "Cnn1 inhibits the interactions between the KMN complexes of the yeast kinetochore", "abstract": ["Kinetochores attach the replicated chromosomes to the mitotic spindle and orchestrate their transmission to the daughter cells.", "Kinetochore\u2013spindle binding and chromosome segregation are mediated by the multi-copy KNL1Spc105, MIS12Mtw1 and NDC80Ndc80 complexes that form the so-called KMN network.", "KMN\u2013spindle attachment is regulated by the Aurora BIpl1 and MPS1Mps1 kinases.", "It is unclear whether other mechanisms exist that support KMN activity during the cell cycle.", "Using budding yeast, we show that kinetochore protein Cnn1 localizes to the base of the Ndc80 complex and promotes a functionally competent configuration of the KMN network.", "Cnn1 regulates KMN activity in a spatiotemporal manner by inhibiting the interaction between its complexes.", "Cnn1 activity peaks in anaphase and is driven by the Cdc28, Mps1 and Ipl1 kinases."], "structured": false}
{"doc_id": 22406695, "title": "Origin and functions of tissue macrophages.", "abstract": ["Macrophages are distributed in tissues throughout the body and contribute to both homeostasis and disease.", "Recently, it has become evident that most adult tissue macrophages originate during embryonic development and not from circulating monocytes.", "Each tissue has its own composition of embryonically derived and adult-derived macrophages, but it is unclear whether macrophages of distinct origins are functionally interchangeable or have unique roles at steady state.", "This new understanding also prompts reconsideration of the function of circulating monocytes.", "Classical Ly6c(hi) monocytes patrol the extravascular space in resting organs, and Ly6c(lo) nonclassical monocytes patrol the vasculature.", "Inflammation triggers monocytes to differentiate into macrophages, but whether resident and newly recruited macrophages possess similar functions during inflammation is unclear.", "Here, we define the tools used for identifying the complex origin of tissue macrophages and discuss the relative contributions of tissue niche versus ontological origin to the regulation of macrophage functions during steady state and inflammation."], "structured": false}
{"doc_id": 22414304, "title": "Treatment outcome of an unselected cohort of tuberculosis patients in relation to human immunodeficiency virus serostatus in Zomba Hospital, Malawi.", "abstract": ["There is little information about treatment outcome in patients with smear-negative pulmonary tuberculosis (PTB) or extrapulmonary tuberculosis (EPTB) treated under routine programme conditions in subsaharan Africa.", "A prospective study was carried out to determine treatment outcome in an unselected cohort of TB patients admitted to Zomba General Hospital, Malawi.", "Eight hundred and twenty-seven adult TB patients (451 men and 376 women) were registered between 1 July and 31 December 1995.", "Standardized treatment outcomes of treatment completion, death, default, and transfer to another district were assessed in relation to type of TB, human immunodeficiency virus (HIV) serostatus, age and gender.", "Two hundred and fifty-four patients (31%) died by the end of treatment, half of the deaths occurring in the first month.", "Death rates were 19% among 386 patients with smear-positive PTB, 46% among 211 patients with smear-negative PTB, and 37% among 230 patients with EPTB; 77% of the patients were HIV seropositive.", "Among new patients, HIV-positive patients had higher death rates than HIV-negative patients (hazard ratio [HR] 2.5; 95% confidence interval [95% CI] 1.6-3.8).", "Smear-negative patients had the highest death rates (HR 3.9; 95% CI 2.7-5.5 compared to smear-positive patients), followed by EPTB patients (HR 2.6, 95% CI 1.8-3.7 compared to smear-positive patients).", "Death rates increased with age but were similar in men and women.", "Adult patients in Malawi with smear-negative PTB and EPTB have low treatment completion and high death rates, related to high levels of HIV infection.", "National TB control programmes in areas of high HIV prevalence should no longer ignore treatment outcomes in patients with smear-negative PTB or EPTB."], "structured": false}
{"doc_id": 22420524, "title": "Statin use and risk of gallstone disease followed by cholecystectomy.", "abstract": ["CONTEXT Gallstone disease is a leading cause of morbidity in western countries and carries a high economic burden.", "Statins decrease hepatic cholesterol biosynthesis and may therefore lower the risk of cholesterol gallstones by reducing the cholesterol concentration in the bile.", "Data on this association in humans are scarce.   \n", "OBJECTIVE To study the association between the use of statins, fibrates, or other lipid-lowering agents and the risk of incident gallstone disease followed by cholecystectomy.   \n", "DESIGN, SETTING, AND PARTICIPANTS Case-control analysis using the UK-based General Practice Research Database.", "Incident patients between 1994 and 2008 and 4 controls per each patient were identified and matched on age, sex, general practice, calendar time, and years of history in the database.", "The study population was 76% women and the mean (SD) age was 53.4 (15.0) years at the index date.", "Conditional logistic regression was used to estimate the odds ratio (OR) of developing gallstones followed by cholecystectomy in relation to exposure to lipid-lowering agents, stratified by exposure timing and duration.", "The ORs and 95% confidence intervals (CIs) were adjusted for smoking, body mass index, ischemic heart disease, stroke, and estrogen use.   \n", "MAIN OUTCOME MEASURE The adjusted OR (AOR) for developing gallstone disease followed by cholecystectomy in relation to exposure to lipid-lowering agents.   \n", "RESULTS A total of 27,035 patients with cholecystectomy and 106,531 matched controls were identified, including 2396 patients and 8868 controls who had statin use.", "Compared with nonuse, current statin use (last prescription recorded within 90 days before the first-time diagnosis of the disease) was 1.0% for patients and 0.8% for controls (AOR, 1.10; 95% CI, 0.95-1.27) for 1 to 4 prescriptions; 2.6% vs 2.4% (AOR, 0.85; 95% CI, 0.77-0.93) for 5 to 19 prescriptions, and 3.2% vs 3.7% (AOR, 0.64; 95% CI, 0.59-0.70) for 20 or more prescriptions.", "The AORs for current use of statins defined as 20 or more prescriptions were similar (around 0.6) across age, sex, and body mass index categories, and across the statin class.   \n", "CONCLUSION Long-term use of statins was associated with a decreased risk of gallstones followed by cholecystectomy."], "structured": true}
{"doc_id": 22428640, "title": "Chromatin remodeling in embryonic stem cells: regulating the balance between pluripotency and differentiation.", "abstract": ["Embryonic stem cells have an unlimited potential for self-renewal yet are pluripotent, capable of differentiating into three different germ layers and ultimately into multiple cell lineages.", "Key pluripotency specific factors maintain an undifferentiated ES cell phenotype while lineage specific factors work in opposition to promote cell specialization.", "In addition to these important transcriptional regulators, epigenetic modifiers play a defining role in regulating the balance between pluripotency and differentiation by promoting changes in chromatin structure."], "structured": false}
{"doc_id": 22431418, "title": "The National Advisory Group on Immunization (NAGI) of the Republic of South Africa.", "abstract": ["The National Immunization Technical Advisory Group (NITAG) in South Africa, known as the National Advisory Group on Immunization (NAGI), was established in 1993 to advise the National Department of Health (DoH) on issues related to vaccination.", "Meetings are held as needed but at least twice a year.", "The scope includes vaccines and immunization and other relevant infectious disease issues.", "NAGI also makes recommendations on vaccine schedules and formulations.", "Agendas are set by DoH and the Chairman of NAGI.", "NAGI brings together experts from a range of different fields relevant to vaccines and vaccinations and has been an important resource for guiding the Expanded Program of Immunization (EPI) in South Africa."], "structured": false}
{"doc_id": 22442133, "title": "Effect of n-3 long chain polyunsaturated fatty acid supplementation in pregnancy on infants\u2019 allergies in first year of life: randomised controlled trial", "abstract": ["OBJECTIVE To determine whether dietary n-3 long chain polyunsaturated fatty acid (LCPUFA) supplementation of pregnant women with a fetus at high risk of allergic disease reduces immunoglobulin E associated eczema or food allergy at 1 year of age.   \n", "DESIGN Follow-up of infants at high hereditary risk of allergic disease in the Docosahexaenoic Acid to Optimise Mother Infant Outcome (DOMInO) randomised controlled trial.   \n", "SETTING Adelaide, South Australia.   \n", "PARTICIPANTS 706 infants at high hereditary risk of developing allergic disease whose mothers were participating in the DOMInO trial.   \n", "INTERVENTIONS The intervention group (n=368) was randomly allocated to receive fish oil capsules (providing 900 mg of n-3 LCPUFA daily) from 21 weeks' gestation until birth; the control group (n=338) received matched vegetable oil capsules without n-3 LCPUFA.   \n", "MAIN OUTCOME MEASURE Immunoglobulin E associated allergic disease (eczema or food allergy with sensitisation) at 1 year of age.   \n", "RESULTS No differences were seen in the overall percentage of infants with immunoglobulin E associated allergic disease between the n-3 LCPUFA and control groups (32/368 (9%) v 43/338 (13%); unadjusted relative risk 0.68, 95% confidence interval 0.43 to 1.05, P=0.08; adjusted relative risk 0.70, 0.45 to 1.09, P=0.12), although the percentage of infants diagnosed as having atopic eczema (that is, eczema with associated sensitisation) was lower in the n-3 LCPUFA group (26/368 (7%) v 39/338 (12%); unadjusted relative risk 0.61, 0.38 to 0.98, P=0.04; adjusted relative risk 0.64, 0.40 to 1.02, P=0.06).", "Fewer infants were sensitised to egg in the n-3 LCPUFA group (34/368 (9%) v 52/338 (15%); unadjusted relative risk 0.61, 0.40 to 0.91, P=0.02; adjusted relative risk 0.62, 0.41 to 0.93, P=0.02), but no difference between groups in immunoglobulin E associated food allergy was seen.   \n", "CONCLUSION n-3 LCPUFA supplementation in pregnancy did not reduce the overall incidence of immunoglobulin E associated allergies in the first year of life, although atopic eczema and egg sensitisation were lower.", "Longer term follow-up is needed to determine if supplementation has an effect on respiratory allergic diseases and aeroallergen sensitisation in childhood.   \n", "TRIAL REGISTRATION Australian New Zealand Clinical Trials Registry ACTRN12610000735055 (DOMInO trial: ACTRN12605000569606)."], "structured": true}
{"doc_id": 22444939, "title": "ModLoop: automated modeling of loops in protein structures.", "abstract": ["SUMMARY ModLoop is a web server for automated modeling of loops in protein structures.", "The input is the atomic coordinates of the protein structure in the Protein Data Bank format, and the specification of the starting and ending residues of one or more segments to be modeled, containing no more than 20 residues in total.", "The output is the coordinates of the non-hydrogen atoms in the modeled segments.", "A user provides the input to the server via a simple web interface, and receives the output by e-mail.", "The server relies on the loop modeling routine in MODELLER that predicts the loop conformations by satisfaction of spatial restraints, without relying on a database of known protein structures.", "For a rapid response, ModLoop runs on a cluster of Linux PC computers.   ", "AVAILABILITY The server is freely accessible to academic users at http://salilab.org/modloop"], "structured": false}
{"doc_id": 22446093, "title": "What is the best way to help caregivers in cancer and palliative care? A systematic literature review of interventions and their effectiveness.", "abstract": ["Informal carers in cancer and palliative care are known to have high needs and psychological morbidity, yet a literature review identified few targeted interventions.", "This systematic review of interventions for carers of patients using home cancer and palliative care services searched Medline, CancerLit, Psycinfo and Cinahl databases.", "The terms used were carer(s), caregiver(s), palliative and cancer.", "Papers that reported interventions for adults actively providing informal care for noninstitutionalized cancer and palliative care patients were reviewed.", "Twenty-two interventions were identified, comprising home nursing care (four), respite services (three), social networks and activity enhancement (two), problem solving and education (three) and group work (10).", "Of these, nine were delivered solely to carers (i.e., were targeted services).", "Only six of the carers' interventions had been evaluated, two of these had used a randomized control trial (RCT; grades IB), three employed a single group methodology (two prospective grades IIIC and one retrospective grade IIIC) and one was evaluated using facilitator feedback.", "There was a lack of outcome evaluation designs, small sample sizes and a reliance on intervention descriptions and formative evaluations.", "Methodological challenges may mean alternatives to 'pure' RCTs should be considered.", "The current evidence contributes more to understanding feasibility and acceptability than to effectiveness.", "Practitioners and evaluators must prioritize the further development of intervention studies."], "structured": false}
{"doc_id": 22467585, "title": "Brief Internet-Based Intervention Reduces Posttraumatic Stress and Prolonged Grief in Parents after the Loss of a Child during Pregnancy: A Randomized Controlled Trial", "abstract": ["Background: The loss of a child during pregnancy causes significant psychological distress for many women and their partners, and may lead to long-lasting psychiatric disorders.", "Internet-based interventions using exposure techniques and cognitive restructuring have proved effective for posttraumatic stress disorder (PTSD) and prolonged grief.", "This study compared the effects of an Internet-based intervention for parents after prenatal loss with a waiting list condition (WLC).", "Methods: The Impact of Event Scale - Revised assessed symptoms of PTSD; the Inventory of Complicated Grief and the Brief Symptom Inventory assessed depression, anxiety, and general mental health.", "The 228 participants (92% female) were randomly allocated to a treatment group (TG; n = 115) or a WLC group (n = 113).", "The TG received a 5-week cognitive behavioral intervention including (1) self-confrontation, (2) cognitive restructuring, and (3) social sharing.", "Results: The TG showed significantly reduced symptoms of posttraumatic stress, prolonged grief, depression, and anxiety relative to the WLC control group.", "Intention-to-treat analysis revealed treatment effects of between d = 0.84 and d = 1.02 for posttraumatic stress and prolonged grief from pre- to posttreatment time points.", "Further significant improvement in all symptoms of PTSD and prolonged grief was found from the posttreatment evaluation to the 12-month follow-up.", "The attrition rate of 14% was relatively low.", "Conclusions: The Internet-based intervention proved to be a feasible and cost-effective treatment, reducing symptoms of posttraumatic stress, grief, depression, anxiety, and general mental health after pregnancy loss.", "Low-threshold e-health interventions should be further evaluated and implemented routinely to improve psychological support after pregnancy loss."], "structured": false}
{"doc_id": 22478394, "title": "Up-regulation of PPAR-gamma mRNA expression in the liver of obese patients: an additional reinforcing lipogenic mechanism to SREBP-1c induction.", "abstract": ["INTRODUCTION Triglyceride accumulation in the liver is an early feature in the development of nonalcoholic fatty liver disease (NAFLD) associated with human obesity, which is a multifactorial syndrome and whose underlying mechanisms are beginning to be understood.   \n", "OBJECTIVES Liver peroxisome proliferator-activated receptor-\u03b3 (PPAR-\u03b3) mRNA expression was measured as a signaling mechanism related to steatosis in obese patients with NAFLD.   \n", "METHODS Liver PPAR-\u03b3 and sterol receptor element-binding protein 1c (SREBP-1c) mRNA (real-time RT-PCR), serum total adiponectin (RIA), and high molecular weight (HMW)-adiponectin (ELISA) levels, and insulin resistance (IR) evolution (homeostasis model assessment-IR) were determined in 22 obese NAFLD patients (16 with steatosis and six with steatohepatitis) who underwent subtotal gastrectomy with gastrojejunal anastomosis in Roux-en-Y and 16 nonobese subjects who underwent laparoscopic cholecystectomy (controls).   \n", "RESULTS Liver PPAR-\u03b3 mRNA levels were 112 and 188% higher (P < 0.05) than control values in obese patients with steatosis and steatohepatitis, respectively, who also exhibited 70 and 62% increases in those of SREBP-1c, concomitantly with IR and lower levels of serum total adiponectin and HMW-adiponectin (P < 0.05).", "Liver PPAR-\u03b3 expression showed positive associations with SREBP-1c mRNA levels (r = 0.86; P < 0.0001), serum insulin levels (r = 0.39; P < 0.01), and homeostasis model assessment-IR (r = 0.60; P < 0.0001), and negative correlations with total adiponectin (r = -0.37; P < 0.01) and HMW-adiponectin (r = -0.51; P < 0.001) levels in serum.   \n", "CONCLUSIONS PPAR-\u03b3 is up-regulated in the liver of obese patients with NAFLD, representing an additional reinforcing lipogenic mechanism to SREBP-1c induction in the development of hepatic steatosis."], "structured": true}
{"doc_id": 22482024, "title": "Ribosomal protein S17 gene (RPS17) is mutated in Diamond-Blackfan anemia.", "abstract": ["Diamond-Blackfan anemia (DBA) is a congenital erythroid aplasia characterized as a normochromic macrocytic anemia with a selective deficiency in red blood cell precursors in otherwise normocellular bone marrow.", "In 40% of DBA patients, various physical anomalies are also present.", "Currently two genes are associated with the DBA phenotype--the ribosomal protein (RP) S19 mutated in 25% of DBA patients and RPS24 mutated in approximately 1.4% of DBA patients.", "Here we report the identification of a mutation in yet another ribosomal protein, RPS17.", "The mutation affects the translation initiation start codon, changing T to G (c.2T>G), thus eliminating the natural start of RPS17 protein biosynthesis.", "RNA analysis revealed that the mutated allele was expressed, and the next downstream start codon located at position +158 should give rise to a short peptide of only four amino acids (Met-Ser-Arg-Ile).", "The mutation arose de novo, since all healthy family members carry the wild-type alleles.", "The identification of a mutation in the third RP of the small ribosomal subunit in DBA patients further supports the theory that impaired translation may be the main cause of DBA pathogenesis."], "structured": false}
{"doc_id": 22482820, "title": "An overview of the effective combination therapies for the treatment of breast cancer.", "abstract": ["Breast cancer (BC) is generally classified based on the receptors overexpressed on the cell nucleus, which include hormone receptors such as progesterone (PR) and estrogen (ER), and HER2.", "Triple-negative breast cancer (TNBC) is a type of cancer that lacks any of these three types of receptor proteins (ER/PR/HER2).", "Tumor cells exhibit drug resistant phenotypes that decrease the efficacy of chemotherapeutic treatments.", "Generally, drug resistance has a genetic basis that is caused by an abnormal gene expression, nevertheless, there are several types of drug resistance: efflux pumps reducing the cellular concentration of the drug, alterations in membrane lipids that reduce cellular uptake, increased or altered drug targets, metabolic alteration of the drug, inhibition of apoptosis, repair of the damaged DNA, and alteration of the cell cycle checkpoints.", "The use of \"combination therapy\" is recognized as an efficient solution to treat human diseases, in particular, breast cancer.", "In this review, we give examples of different nanocarriers used to co-deliver multiple therapeutics (chemotherapeutic agent and nucleic acid) to drug-resistant tumor cells, and lastly, we give our recommendations for the future directions for the co-delivery treatments."], "structured": false}
{"doc_id": 22483580, "title": "Disturbed sleep in bipolar disorder is related to an elevation of IL-6 in peripheral monocytes.", "abstract": ["Bipolar disorder is a severe psychiatric disorder that is associated with persistent changes in the quality, duration and architecture of sleep.", "Currently there is no unifying hypothesis explaining the alterations in sleep observable in patients with bipolar disorder and management is often difficult though vital.", "Sleep is modified by various cytokines including IL-6.", "Elevated levels of IL-6 are associated with a poorer quality of sleep and changes in the architecture of sleep similar to those observed in bipolar disorder.", "Therapeutic administration of Interferon causes elevations of intrathecal IL-6 concentrations and appears to provoke a deteriorating quality of sleep.", "The blockade of IL-6 with tocilizumab in rheumatoid arthritis is associated with improvements in the quality of sleep.", "Bipolar disorder is associated with elevated levels of IL-6 and in particular elevated levels of mRNA coding for IL-6 in peripheral monocytes.", "We propose that the changes observed in the sleep of patients with bipolar disorder are related to the elevation of IL-6 and that this correlates with an elevated expression of mRNA coding for IL-6 expression in peripheral monocytes."], "structured": false}
{"doc_id": 22488511, "title": "Targeted blockade of TGF-\u03b2 and IL-6/JAK2/STAT3 pathways inhibits lung cancer growth promoted by bone marrow-derived myofibroblasts", "abstract": ["To investigate the role of TGF-\u03b2 and IL-6 in myofibroblasts (MFs) - lung cancer cell interactions, lung cancer cells (Lewis and CTM-167 cell lines) were stimulated by IL-6, MF-conditioned medium (MF-CM) or MFs, with or without TGF-\u03b2 signaling inhibitor - SB431542 and/or JAK2/STAT3 inhibitor - JSI-124.", "MFs were stimulated by TGF-\u03b2, cancer cell-CM or cancer cells, with or without SB431542 and JSI-124.", "Cell proliferation, the levels of cytokines, expression of mRNA and protein were determined.", "Mice bearing xenograft tumors were intraperitoneally treated with SB431542 or JSI-124 and monitored for up to 45 days.", "In co-culture systems, MFs secreted high levels of IL-6, while cancer cells produced high levels of TGF-\u03b2.", "Recombinant IL-6 and MF-CM activated STAT3 and upregulated TGF-\u03b2 in cancer cells.", "In contrast, cancer cell-CM or TGF-\u03b2 stimulated MFs to produce IL-6.", "Blockade of JAK2/STAT3 and TGF-\u03b2 signaling by specific inhibitors significantly inhibited cell proliferation in vitro and tumor growth in vivo of lung cancer cells.", "Our study demontrated that the TGF-\u03b2 and IL-6/JAK2/STAT3 signaling pathways form a positive feedback signaling loop that mediated the interactions between MFs and lung cancer cells.", "Targeted inhibiton of this signaling loop could be a new approach for lung cancer prevention and therapy."], "structured": false}
{"doc_id": 22490293, "title": "Production of cloned mice and ES cells from adult somatic cells by nuclear transfer: how to improve cloning efficiency?", "abstract": ["Although it has now been 10 years since the first cloned mammals were generated from somatic cells using nuclear transfer (NT), most cloned embryos usually undergo developmental arrest prior to or soon after implantation, and the success rate for producing live offspring by cloning remains below 5%.", "The low success rate is believed to be associated with epigenetic errors, including abnormal DNA hypermethylation, but the mechanism of \"reprogramming\" is unclear.", "We have been able to develop a stable NT method in the mouse in which donor nuclei are directly injected into the oocyte using a piezo-actuated micromanipulator.", "Especially in the mouse, only a few laboratories can make clones from adult somatic cells, and cloned mice are never successfully produced from most mouse strains.", "However, this technique promises to be an important tool for future research in basic biology.", "For example, NT can be used to generate embryonic stem (NT-ES) cell lines from a patient's own somatic cells.", "We have shown that NT-ES cells are equivalent to ES cells derived from fertilized embryos and that they can be generated relatively easily from a variety of mouse genotypes and cell types of both sexes, even though it may be more difficult to generate clones directly.", "In general, NT-ES cell techniques are expected to be applied to regenerative medicine; however, this technique can also be applied to the preservation of genetic resources of mouse strain instead of embryos, oocytes and spermatozoa.", "This review describes how to improve cloning efficiency and NT-ES cell establishment and further applications."], "structured": false}
{"doc_id": 22495397, "title": "Recruitment of Tat to heterochromatin protein HP1 via interaction with CTIP2 inhibits human immunodeficiency virus type 1 replication in microglial cells.", "abstract": ["The Tat protein of human immunodeficiency virus type 1 (HIV-1) plays a key role as inducer of viral gene expression.", "We report that Tat function can be potently inhibited in human microglial cells by the recently described nuclear receptor cofactor chicken ovalbumin upstream promoter transcription factor-interacting protein 2 (CTIP2).", "Overexpression of CTIP2 leads to repression of HIV-1 replication, as a result of inhibition of Tat-mediated transactivation.", "In contrast, the related CTIP1 was unable to affect Tat function and viral replication.", "Using confocal microscopy to visualize Tat subcellular distribution in the presence of the CTIPs, we found that overexpression of CTIP2, and not of CTIP1, leads to disruption of Tat nuclear localization and recruitment of Tat within CTIP2-induced nuclear ball-like structures.", "In addition, our studies demonstrate that CTIP2 colocalizes and associates with the heterochromatin-associated protein HP1alpha.", "The CTIP2 protein harbors two Tat and HP1 interaction interfaces, the 145-434 and the 717-813 domains.", "CTIP2 and HP1alpha associate with Tat to form a three-protein complex in which the 145-434 CTIP2 domain interacts with the N-terminal region of Tat, while the 717-813 domain binds to HP1.", "The importance of this Tat binding interface and of Tat subnuclear relocation was confirmed by analysis of CTIP2 deletion mutants.", "Our findings suggest that inhibition of HIV-1 expression by CTIP2 correlates with recruitment of Tat within CTIP2-induced structures and relocalization within inactive regions of the chromatin via formation of the Tat-CTIP2-HP1alpha complex.", "These data highlight a new mechanism of Tat inactivation through subnuclear relocalization that may ultimately lead to inhibition of viral pathogenesis."], "structured": false}
{"doc_id": 22500262, "title": "Cryptochrome Mediates Circadian Regulation of cAMP Signaling and Hepatic Gluconeogenesis", "abstract": ["During fasting, mammals maintain normal glucose homeostasis by stimulating hepatic gluconeogenesis.", "Elevations in circulating glucagon and epinephrine, two hormones that activate hepatic gluconeogenesis, trigger the cAMP-mediated phosphorylation of cAMP response element-binding protein (Creb) and dephosphorylation of the Creb-regulated transcription coactivator-2 (Crtc2)--two key transcriptional regulators of this process.", "Although the underlying mechanism is unclear, hepatic gluconeogenesis is also regulated by the circadian clock, which coordinates glucose metabolism with changes in the external environment.", "Circadian control of gene expression is achieved by two transcriptional activators, Clock and Bmal1, which stimulate cryptochrome (Cry1 and Cry2) and Period (Per1, Per2 and Per3) repressors that feed back on Clock-Bmal1 activity.", "Here we show that Creb activity during fasting is modulated by Cry1 and Cry2, which are rhythmically expressed in the liver.", "Cry1 expression was elevated during the night-day transition, when it reduced fasting gluconeogenic gene expression by blocking glucagon-mediated increases in intracellular cAMP concentrations and in the protein kinase A-mediated phosphorylation of Creb.", "In biochemical reconstitution studies, we found that Cry1 inhibited accumulation of cAMP in response to G protein-coupled receptor (GPCR) activation but not to forskolin, a direct activator of adenyl cyclase.", "Cry proteins seemed to modulate GPCR activity directly through interaction with G(s)\u03b1.", "As hepatic overexpression of Cry1 lowered blood glucose concentrations and improved insulin sensitivity in insulin-resistant db/db mice, our results suggest that compounds that enhance cryptochrome activity may provide therapeutic benefit to individuals with type 2 diabetes."], "structured": false}
{"doc_id": 22505190, "title": "Toll-like receptor 4 gene Asp299Gly polymorphism in myocardial infarction: a meta-analysis of 15,148 subjects.", "abstract": ["It remains controversial regarding the association between toll-like receptor 4 (TLR4) gene Asp299Gly (+896 A/G) polymorphism and myocardial infarction (MI) risk.", "Thus, a large-scale meta-analysis evaluating the potential association between this gene variant and MI risk is required.", "PubMed, Embase, Web of Science, CBMdisc, CNKI, and Google Scholar were searched until February 6, 2013.", "All the statistical tests were performed using Stata 11.0.", "Nine articles involving 10 studies were included in the final meta-analysis, covering a total of 8299 MI cases and 6849 controls.", "Overall, no significant association was found between the TLR4 gene Asp299Gly polymorphism and MI risk (G allele vs. A allele: OR=0.95, 95% CI=0.74-1.22, p=0.71; G/G vs. A/A: OR=1.03, 95% CI=0.54-1.98, p=0.93; G/G vs. A/G+A/A: OR=1.05, 95% CI=0.55-2.03, p=0.87; G/G+A/G vs. A/A: OR=0.92, 95% CI=0.75-1.13, p=0.42).", "In the subgroup analysis based on source of controls, there was also lack of evidence for significant association between the TLR4 gene Asp299Gly polymorphism and MI risk.", "In summary, the present meta-analysis indicated that the TLR4 gene Asp299Gly polymorphism was not associated with MI risk."], "structured": false}
{"doc_id": 22505710, "title": "Matrix metalloproteinase and proinflammatory cytokine production by chondrocytes of human osteoarthritic cartilage: associations with degenerative changes.", "abstract": ["OBJECTIVE To examine by immunohistochemistry the relative distributions of 6 matrix metalloproteinases (MMPs 1, 2, 3, 8, 9, and 13) and the 2 proinflammatory cytokines interleukin-1beta (IL-1beta) and tumor necrosis factor alpha (TNFalpha) in osteoarthritic (OA) cartilage compared with normal, age-matched articular cartilage.   \n", "METHODS Articular cartilage samples were obtained from the tibial plateau of OA knees removed at arthroplasty and from normal, nonarthritic, knees obtained at autopsy.", "Specimens were promptly fixed in Carnoy's fixative, processed, embedded in paraffin, sectioned, and examined by immunohistochemistry for MMP and cytokine production.", "In addition, human articular chondrocytes (HAC) were treated in vitro with either IL-1beta, TNFalpha, or phorbol myristate acetate (PMA) to assess their potential to produce each of the MMPs, as determined by Western blotting and gelatin zymography.   \n", "RESULTS Immunodetection of the collagenases (MMPs 1, 8, and 13) and stromelysin 1 (MMP-3) was demonstrated in a proportion of chondrocytes in the superficial zone of almost all of the OA specimens that had degenerative matrix changes.", "The gelatinases (MMPs 2 and 9) were also demonstrated by immunohistochemistry but were not so prominent.", "IL-1beta- and TNFalpha-positive chondrocytes were also observed in a proportion of cells in the superficial zones of OA specimens.", "Much less immunostaining for MMPs and cytokines was observed in the deep zone of all OA specimens, where the cartilage matrix and chondrocyte morphology appeared normal.", "In contrast, full-thickness normal cartilage specimens showed virtually no immunostaining for these MMPs or cytokines.", "Confirmation that chondrocytes can produce these 6 MMPs was obtained from HAC cultures treated with either IL-1beta, TNFalpha, or PMA; conditioned medium from activated HAC contained all the MMPs demonstrated by immunohistochemistry.", "Dual immunolocalization studies of OA cartilage specimens demonstrated the coexpression of IL-1 with MMP-8 by individual chondrocytes in situ.   \n", "CONCLUSION These results indicate that the superficial zone of OA cartilage specimens, which is characterized by fibrillations, chondrocyte clusters, and degenerative matrix changes, contains a variable proportion of cells that immunostain for IL-1beta, TNFalpha, and 6 different MMPs.", "These observations support the concept that cytokine-MMP associations reflect a modified chondrocyte phenotype and an intrinsic process of cartilage degradation in OA."], "structured": true}
{"doc_id": 22509015, "title": "\u03b2-catenin-independent WNT signaling in basal-like breast cancer and brain metastasis.", "abstract": ["A role of WNT signaling for primary breast cancers of the basal-like subtype and as a predictor of brain metastasis has been described.", "However, a responsible WNT ligand has not been identified.", "To further clarify this question, we comparatively investigated 22 human breast cancer brain metastases as well as the highly invasive human breast cancer cell line MDA-MB-231 and the weakly motile MCF-7 as models for the basal-like and the luminal A subtype.", "WNT5A and B were found overexpressed in MDA-MB-231 cells as compared with MCF-7.", "This corresponded to reduction of MDA-MB-231 invasiveness by WNT inhibitors, whereas MCF-7 invasion was enhanced by recombinant WNT5B and abolished by WNT and Jun-N-terminal kinase antagonists.", "Expression and subcellular distribution of \u03b2-catenin remained uninfluenced.", "Consistently, \u03b2-catenin was not localized in the nuclei of brain metastases while there was strong nuclear c-Jun staining.", "Similar to MDA-MB-231, metastases showed expression of WNT5A/B and the alternative WNT receptors ROR1 and 2.", "These findings were validated using external gene expression datasets (Gene Expression Omnibus) of different breast cancer subtypes and brain metastases.", "Hierarchical cluster analysis yielded a close relation between basal-like cancers and brain metastases.", "Gene set enrichment analyses confirmed WNT pathway enrichment not only in basal-like primaries but also in cerebral metastases of all subtypes.", "In conclusion, WNT signaling seems highly relevant for basal-like and other subtypes of breast cancers metastasizing into the brain.", "\u03b2-catenin-independent WNT signaling, presumably via ROR1-2, plays a major role in this context."], "structured": false}
{"doc_id": 22517564, "title": "Retinal attenuates inflammatory arthritis by reciprocal regulation of IL-17-producing T cells and Foxp3(+) regulatory T cells and the inhibition of osteoclastogenesis.", "abstract": ["Retinoids (e.g., vitamin A and its derivatives) can regulate immune responses.", "The aim of this study was to determine whether all-trans retinaldehyde (retinal), a vitamin A derivative, can inhibit inflammatory responses and joint destruction in DBA/1J mice with collagen-induced arthritis (CIA).", "The arthritis score and incidence of arthritis were lower in mice treated with retinal compared to those treated with cottonseed oil.", "Histopathologic evidence of joint damage was lower in mice treated with retinal, corresponding with a reduction in the infiltration of immune cells in mice treated with retinal type II collagen (CII)-stimulated spleen cells.", "In addition, the expression of proinflammatory cytokines, oxidative stress proteins, and osteoclast markers were significantly reduced in mice treated with retinal.", "In vitro, retinal induced increased Foxp3 expression and inhibited Th17 development.", "The proportion of Foxp3(+) Treg cells was increased in the spleens of mice treated with retinal, whereas the proportion of Th17 cells was reduced.", "In both mice and a human culture system, tartrate-resistant acid phosphatase (TRAP) positive mononuclear cells and multinucleated cells were significantly reduced after treatment with retinal.", "The expression of osteoclast differentiation markers was dramatically decreased upon addition of retinal.", "This is the first study to demonstrate the therapeutic effect of retinal on an autoimmune arthritis model in mice through reciprocal regulation of Th17 and regulatory T cells and protection of differentiation and activation of osteoclasts.", "Taken together, our findings indicate that retinal has profound immunoregulatory functions and potential value for the treatment of autoimmune inflammatory disorders."], "structured": false}
{"doc_id": 22521091, "title": "NRAGE promotes the malignant phenotype of hepatocellular carcinoma.", "abstract": ["Hepatocellular carcinoma (HCC) is a fatal disease, primarily due to the limited effective therapies available for patients with advanced or recurrent stages of the disease.", "Therefore, in order to improve patient prognosis, it is important to identify an informative biomarker for HCC progression, as well as a molecular target for therapy.", "Neurotrophin receptor-interacting melanoma antigen-encoding protein (NRAGE), a member of the type II melanoma-associated antigen family, mediates apoptosis and cell death through interactions with a wide range of proteins, and is implicated as a tumor suppressor or oncoprotein depending on cell type.", "However, the role of NRAGE in HCC is currently unknown, therefore, the present study aimed to identify the underlying function of NRAGE in HCC tumorigenesis.", "Resected tumor and non-cancerous liver tissues from 151 patients with HCC, alongside HCC cell lines, were analyzed by polymerase chain reaction and immunohistochemical techniques to determine NRAGE expression levels, as well as the expression levels of potential genes encoding interacting proteins.", "It was demonstrated that the expression levels of NRAGE mRNA correlated significantly with those of apoptosis-antagonizing transcription factor (AATF), and were not affected by cirrhosis in non-cancerous liver tissues when compared to elevated levels in HCC tissues.", "The expression patterns of NRAGE protein and mRNA were consistent among 30 representative specimen pairs.", "Furthermore, increased NRAGE expression in patients with HCC correlated significantly with a shorter disease-specific survival time, and was identified as an independent prognostic factor via multivariate analysis (hazard ratio, 2.23; 95% confidence interval, 1.06-3.83; P=0.020).", "Therefore, the results of the present study indicated that increased NRAGE expression affects HCC progression via its interaction with AATF, and may represent a novel biomarker and molecular target for the treatment of HCC."], "structured": false}
{"doc_id": 22522432, "title": "Regulation of ISW2 by concerted action of histone H4 tail and extranucleosomal DNA.", "abstract": ["The stable contact of ISW2 with nucleosomal DNA approximately 20 bp from the dyad was shown by DNA footprinting and photoaffinity labeling using recombinant histone octamers to require the histone H4 N-terminal tail.", "Efficient ISW2 remodeling also required the H4 N-terminal tail, although the lack of the H4 tail can be mostly compensated for by increasing the incubation time or concentration of ISW2.", "Similarly, the length of extranucleosomal DNA affected the stable contact of ISW2 with this same internal nucleosomal site, with the optimal length being 70 to 85 bp.", "These data indicate the histone H4 tail, in concert with a favorable length of extranucleosomal DNA, recruits and properly orients ISW2 onto the nucleosome for efficient nucleosome remodeling.", "One consequence of this property of ISW2 is likely its previously observed nucleosome spacing activity."], "structured": false}
{"doc_id": 22530842, "title": "Embryonic Stem Cells for Severe Heart Failure: Why and How?", "abstract": ["The experience accumulated in cardiac cell therapy suggests that regeneration of extensively necrotic myocardial areas is unlikely to be achieved by the sole paracrine effects of the grafted cells but rather requires the conversion of these cells into cardiomyocytes featuring the capacity to substitute for those which have been irreversibly lost.", "In this setting, the use of human pluripotent embryonic stem cells has a strong rationale.", "The experimental results obtained in animal models of myocardial infarction are encouraging.", "However, the switch to clinical applications still requires to address some critical issues, among which the optimization of the cardiac specification of the embryonic stem cells, the purification of the resulting progenitor cells so as to graft a purified population devoid from any contamination by residual pluripotent cells which carry the risk of tumorigenesis, and the control of the expected allogeneic rejection by clinically acceptable methods.", "If the solution to these problems is a prerequisite, the therapeutic success of this approach will also depend on the capacity to efficiently transfer the cells to the target tissue, to keep them alive once engrafted, and to allow them to spatially organize in such a way that they can contribute to the contractile function of the heart."], "structured": false}
{"doc_id": 22534357, "title": "A comparison of letrozole to gonadotropins for ovulation induction, in subjects who failed to conceive with clomiphene citrate.", "abstract": ["OBJECTIVE To compare pregnancy rates (PR) for letrozole and gonadotropins in individuals who failed to conceive with clomiphene citrate (CC).   \n", "DESIGN Retrospective cohort study.   \n", "SETTING University reproductive center.   \n", "PATIENT(S) Individuals treated with letrozole or gonadotropins who failed to conceive with CC.   \n", "INTERVENTION(S) Controlled ovarian hyperstimulation (COH), transvaginal ultrasound, ovulation induction, IUI.   \n", "MAIN OUTCOME MEASURE(S)", "Pregnancy rates per cycle.   \n", "RESULT(S) Among patients who failed to conceive with at least three cycles of CC, gonadotropins had a higher PR per cycle than letrozole.", "Among individuals who failed to conceive with less than three cycles of CC and whose medications were changed because of thin uterine lining or intolerable side effects, average PR per cycle for letrozole and gonadotropin treatments were equivalent.", "All patients conceived within three stimulation cycles with either gonadotropins or letrozole.   \n", "CONCLUSION(S) In patients who failed to conceive with CC, gonadotropins have higher PR for ovulation induction than letrozole.", "However, PR were high enough with letrozole to justify its use in this population of patients.", "Letrozole and gonadotropins should not be used for more than three cycles without a conception."], "structured": true}
{"doc_id": 22543403, "title": "Epigenetic mechanisms in neurological disease", "abstract": ["The exploration of brain epigenomes, which consist of various types of DNA methylation and covalent histone modifications, is providing new and unprecedented insights into the mechanisms of neural development, neurological disease and aging.", "Traditionally, chromatin defects in the brain were considered static lesions of early development that occurred in the context of rare genetic syndromes, but it is now clear that mutations and maladaptations of the epigenetic machinery cover a much wider continuum that includes adult-onset neurodegenerative disease.", "Here, we describe how recent advances in neuroepigenetics have contributed to an improved mechanistic understanding of developmental and degenerative brain disorders, and we discuss how they could influence the development of future therapies for these conditions."], "structured": false}
{"doc_id": 22544171, "title": "Reversal of the cellular phenotype in the premature aging disease Hutchinson-Gilford progeria syndrome", "abstract": ["Hutchinson-Gilford progeria syndrome (HGPS) is a childhood premature aging disease caused by a spontaneous point mutation in lamin A (encoded by LMNA), one of the major architectural elements of the mammalian cell nucleus.", "The HGPS mutation activates an aberrant cryptic splice site in LMNA pre-mRNA, leading to synthesis of a truncated lamin A protein and concomitant reduction in wild-type lamin A. Fibroblasts from individuals with HGPS have severe morphological abnormalities in nuclear envelope structure.", "Here we show that the cellular disease phenotype is reversible in cells from individuals with HGPS.", "Introduction of wild-type lamin A protein does not rescue the cellular disease symptoms.", "The mutant LMNA mRNA and lamin A protein can be efficiently eliminated by correction of the aberrant splicing event using a modified oligonucleotide targeted to the activated cryptic splice site.", "Upon splicing correction, HGPS fibroblasts assume normal nuclear morphology, the aberrant nuclear distribution and cellular levels of lamina-associated proteins are rescued, defects in heterochromatin-specific histone modifications are corrected and proper expression of several misregulated genes is reestablished.", "Our results establish proof of principle for the correction of the premature aging phenotype in individuals with HGPS."], "structured": false}
{"doc_id": 22545779, "title": "Agouti-related peptide\u2013expressing neurons are mandatory for feeding", "abstract": ["Multiple hormones controlling energy homeostasis regulate the expression of neuropeptide Y (NPY) and agouti-related peptide (AgRP) in the arcuate nucleus of the hypothalamus.", "Nevertheless, inactivation of the genes encoding NPY and/or AgRP has no impact on food intake in mice.", "Here we demonstrate that induced selective ablation of AgRP-expressing neurons in adult mice results in acute reduction of feeding, demonstrating direct evidence for a critical role of these neurons in the regulation of energy homeostasis."], "structured": false}
{"doc_id": 22547508, "title": "Predictors of survival after acute paraquat poisoning.", "abstract": ["Acute paraquat poisoning is often fatal.", "Many studies have investigated successful treatment modalities, but no standard treatment yet exists.", "The purpose of this study was to determine the predictors of survival after acute paraquat poisoning in 602 patients.", "The paraquat exposure was assessed based on the amount of ingested paraquat and a semiquantitative measure of the urine level of paraquat.", "Initial clinical parameters including vital signs, hemoglobin, white-blood-cell count, pH, PaCO2, PaO2, blood urea nitrogen, creatinine, aspartate aminotransferase, alanine aminotransferase, total bilirubin, amylase, and glucose were obtained at the time of arrival at the emergency room.", "Outcomes after acute paraquat poisoning were categorized as survivors and nonsurvivors.", "Multiple logistic regression analysis was applied to assess the predictors of survival after acute paraquat poisoning.", "Some patients (55.5%) survived after oral ingestion of paraquat, whereas all those exposed to paraquat percutaneous or inhalational route survived.", "The amount of paraquat (24.5% concentrate of 1,1'-dimethyl-4,4'-bipyridium dichloride) ingested was 45.6 +/-", "74.1 mL (mean +/-", "SD).", "In addition to degree of paraquat exposure, survival after acute paraquat poisoning was associated with age, respiratory rate, pH, PaCO2, hemoglobin, white-blood-cell count, blood urea nitrogen, amylase, and the number of failed organs in multiple logistic regression analysis.", "In conclusion, young age, percutaneous or inhalational route, exposure to less paraquat, and lesser degrees of leukocytosis, acidosis, and renal, hepatic, and pancreatic failures on admission are good prognostic factors of survival after acute paraquat poisoning."], "structured": false}
{"doc_id": 22549449, "title": "Decreased neurogenesis after cholinergic forebrain lesion in the adult rat.", "abstract": ["Adult neurogenesis has been shown to be regulated by a multitude of extracellular cues, including hormones, growth factors, and neurotransmitters.", "The cholinergic system of the basal forebrain is one of the key transmitter systems for learning and memory.", "Because adult neurogenesis has been implicated in cognitive performance, the present work aims at defining the role of cholinergic input for adult neurogenesis by using an immunotoxic lesion approach.", "The immunotoxin 192IgG-saporin was infused into the lateral ventricle of adult rats to selectively lesion cholinergic neurons of the cholinergic basal forebrain (CBF), which project to the two main regions of adult neurogenesis: the dentate gyrus and the olfactory bulb.", "Five weeks after lesioning, neurogenesis, defined by the number of cells colocalized for bromodeoxyuridine (BrdU) and the neuronal nuclei marker NeuN, declined significantly in the granule cell layers of the dentate gyrus and olfactory bulb.", "Furthermore, immunotoxic lesions to the CBF led to increased numbers of apoptotic cells specifically in the subgranular zone, the progenitor region of the dentate gyrus, and within the periglomerular layer of the olfactory bulb.", "We propose that the cholinergic system plays a survival-promoting role for neuronal progenitors and immature neurons within regions of adult neurogenesis, similar to effects observed previously during brain development.", "As a working hypothesis, neuronal loss within the CBF system leads not only to cognitive deficits but may also alter on a cellular level the functionality of the dentate gyrus, which in turn may aggravate cognitive deficits."], "structured": false}
{"doc_id": 22551259, "title": "DNA Methylation in Major Depressive Disorder.", "abstract": ["Epigenetic mechanisms regulate gene expression, influencing protein levels and ultimately shaping phenotypes during life.", "However, both stochastic epigenetic variations and environmental reprogramming of the epigenome might influence neurodevelopment and ageing, and this may contribute to the origins of mental ill-health.", "Studying the role of epigenetic mechanisms is challenging, as genotype-, tissue- and cell type-dependent epigenetic changes have to be taken into account, while the nature of mental disorders also poses significant challenges for linking them with biological profiles.", "In this chapter, we summarise the current evidence suggesting the role of DNA methylation as a key epigenetic mechanism in major depressive disorder."], "structured": false}
{"doc_id": 22561064, "title": "Consensus structural features of purified bacterial TatABC complexes.", "abstract": ["The twin-arginine translocation (Tat) system transports folded proteins across bacterial plasma membranes and the chloroplast thylakoid membrane.", "Here, we investigate the composition and structural organization of three different purified Tat complexes from Escherichia coli, Salmonella typhimurium and Agrobacterium tumefaciens.", "First, we demonstrate the functional activity of these Tat systems in vivo, since expression of the tatABC operons from S.typhimurium or A.tumefaciens in an E.coli tat null mutant strain resulted in efficient Tat-dependent export of an E.coli cofactor-containing substrate, TMAO reductase.", "The three isolated, affinity-tagged Tat complexes comprised TatA, TatB and TatC in each case, demonstrating a strong interaction between these three subunits.", "Single-particle electron microscopy studies of all three complexes revealed approximately oval-shaped, asymmetric particles with maximal dimensions up to 13 nm.", "A common feature is a number of stain-excluding densities surrounding more or less central pools of stain, suggesting protein-lined pores or cavities.", "The characteristics of size variation among the particles suggest a modular form of assembly and/or the recruitment of varying numbers of TatBC/TatA units.", "Despite low levels of sequence homology, the combined data indicate structural and functional conservation in the Tat systems of these three bacterial species."], "structured": false}
{"doc_id": 22613657, "title": "Advances in graft-versus-host disease biology and therapy", "abstract": ["Allogeneic haematopoietic stem cell transplantation is used to treat a variety of disorders, but its efficacy is limited by the occurrence of graft-versus-host disease (GVHD).", "The past decade has brought impressive advances in our understanding of the role of stimulatory and suppressive elements of the adaptive and innate immune systems from both the donor and the host in GVHD pathogenesis.", "New insights from basic immunology, preclinical models and clinical studies have led to novel approaches for prevention and treatment.", "This Review highlights the recent advances in understanding the pathophysiology of GVHD and its treatment, with a focus on manipulations of the immune system that are amenable to clinical application."], "structured": false}
{"doc_id": 22621251, "title": "Ly6Chi monocytes direct alternatively activated profibrotic macrophage regulation of lung fibrosis.", "abstract": ["RATIONALE Idiopathic pulmonary fibrosis (IPF) is a devastating disease.", "Antiinflammatory therapies, including corticosteroids, are of no benefit.", "The role of monocytes and macrophages is therefore controversial.   \n", "OBJECTIVES To define the role of monocytes and macrophages during lung fibrogenesis and resolution, and explore the phenotype of the cells involved.   \n", "METHODS We used multiple in vivo depletional strategies, backed up by adoptive transfer techniques.", "Further studies were performed on samples from patients with IPF.   \n", "MEASUREMENTS AND MAIN RESULTS Depletion of lung macrophages during fibrogenesis reduced pulmonary fibrosis as measured by lung collagen (P = 0.0079); fibrosis score (P = 0.0051); and quantitative polymerase chain reaction for surrogate markers of fibrosis Col1 (P = 0.0083) and a-smooth muscle actin (P = 0.0349).", "There was an associated reduction in markers of the profibrotic alternative macrophage activation phenotype, Ym1 (P = 0.0179), and Arginase 1.", "The alternative macrophage marker CD163 was expressed on lung macrophages from patients with IPF.", "Depletion of Ly6Chi circulating monocytes reduced pulmonary fibrosis (P = 0.0052) and the number of Ym1- positive alternatively activated lung macrophages (P = 0.0310).", "Their adoptive transfer during fibrogenesis exacerbated fibrosis (P = 0.0304); however, adoptively transferred CD45.1 Ly6Chi cells were not found in the lungs of recipient CD45.2 mice.   \n", "CONCLUSIONS We demonstrate the importance of circulating monocytes and lung macrophages during pulmonary fibrosis, and emphasize the importance of the alternatively activated macrophage phenotype.", "We show that Ly6Chi monocytes facilitate the progression of pulmonary fibrosis, but are not obviously engrafted into lungs thereafter.", "Finally, we provide empirical data to suggest that macrophages may have a resolution-promoting role during the reversible phase of bleomycin-induced pulmonary fibrosis."], "structured": true}
{"doc_id": 22623275, "title": "A single RNA-dependent RNA polymerase assembles with mutually exclusive nucleotidyl transferase subunits to direct different pathways of small RNA biogenesis.", "abstract": ["Members of the conserved family of eukaryotic RNA-dependent RNA polymerases (Rdrs) synthesize double-stranded RNA (dsRNA) intermediates in diverse pathways of small RNA (sRNA) biogenesis and RNA-mediated silencing.", "Rdr-dependent pathways of sRNA production are poorly characterized relative to Rdr-independent pathways, and the Rdr enzymes themselves are poorly characterized relative to their viral RNA-dependent RNA polymerase counterparts.", "We previously described a physical and functional coupling of the Tetrahymena thermophila Rdr, Rdr1, and a Dicer enzyme, Dcr2, in the production of approximately 24-nucleotide (nt) sRNA in vitro.", "Here we characterize the endogenous complexes that harbor Rdr1, termed RDRCs.", "Distinct RDRCs assemble to contain Rdr1 and subsets of the total of four tightly Rdr1-associated proteins.", "Of particular interest are two RDRC subunits, Rdn1 and Rdn2, which possess noncanonical ribonucleotidyl transferase motifs.", "We show that the two Rdn proteins are uridine-specific polymerases of separate RDRCs.", "Two additional RDRC subunits, Rdf1 and Rdf2, are present only in RDRCs containing Rdn1.", "Rdr1 catalytic activity is retained in RDRCs purified from cell extracts lacking any of the nonessential RDRC subunits (Rdn2, Rdf1, Rdf2) or if the RDRC harbors a catalytically inactive Rdn.", "However, specific disruption of each RDRC imposes distinct loss-of-function consequences at the cellular level and has a differential impact on the accumulation of specific 23-24-nt sRNA sequences in vivo.", "The biochemical and biological phenotypes of RDRC subunit disruption reveal a previously unanticipated complexity of Rdr-dependent sRNA biogenesis in vivo."], "structured": false}
{"doc_id": 22632303, "title": "Identification of T6SS-dependent effector and immunity proteins by Tn-seq in Vibrio cholerae.", "abstract": ["Type VI protein secretion system (T6SS) is important for bacterial competition through contact-dependent killing of competitors.", "T6SS delivers effectors to neighboring cells and corresponding antagonistic proteins confer immunity against effectors that are delivered by sister cells.", "Although T6SS has been found in more than 100 gram-negative bacteria including many important human pathogens, few T6SS-dependent effector and immunity proteins have been experimentally determined.", "Here we report a high-throughput approach using transposon mutagenesis and deep sequencing (Tn-seq) to identify T6SS immunity proteins in Vibrio cholerae.", "Saturating transposon mutagenesis was performed in wild type and a T6SS null mutant.", "Genes encoding immunity proteins were predicted to be essential in the wild type but dispensable in the T6SS mutant.", "By comparing the relative abundance of each transposon mutant in the mutant library using deep sequencing, we identified three immunity proteins that render protection against killing by T6SS predatory cells.", "We also identified their three cognate T6SS-secreted effectors and show these are important for not only antibacterial and antieukaryotic activities but also assembly of T6SS apparatus.", "The lipase and muramidase T6SS effectors identified in this study underscore the diversity of T6SS-secreted substrates and the distinctly different mechanisms that target these for secretion by the dynamic T6SS organelle."], "structured": false}
{"doc_id": 22635278, "title": "Immunotherapy of metastatic kidney cancer.", "abstract": ["From April 1986 to September 2000, 122 MRCC patients were treated by monthly intralymphatic injections (containing a mean of 573 IL-2 U and 26 x 10(6) LAK cells) and i.m.", "administration of IFN and TF; 71 patients also received a 3-day cycle of monthly IL-2 inhalations with a mean of 998 daily U. MRCC cases not treated by immunotherapy (n = 89) represent our historical controls.", "Adverse clinical side effects related to treatment were negligible.", "CR (n = 11) and PR (n = 13) were noticed in 24/122 patients.", "Of 24 responding patients, 17 resumed progression, whereas 7 remain in remission 11-69 months later.", "The overall median survival of treated patients (28 months) was 3.5-fold higher than the median survival of historical controls (7.5 months), and a Kaplan-Meier curve showed 25% survival 11 years after the beginning of immunotherapy.", "Apparently, the addition of IL-2 by inhalation improved survival.", "The present immunotherapy protocol appears to be efficacious, safe, devoid of adverse side effects, far less costly than others and able to offer a good quality of life to MRCC patients; if confirmed in a multicenter trial, it could set the basis for developing low-dose immunomodulatory treatments."], "structured": false}
{"doc_id": 22647695, "title": "Autoimmune T cell responses in the central nervous system", "abstract": ["Autoreactive T cell responses have a crucial role in central nervous system (CNS) diseases such as multiple sclerosis.", "Recent data indicate that CNS autoimmunity can be mediated by two distinct lineages of CD4+ T cells that are defined by the production of either interferon-\u03b3 or interleukin-17.", "The activity of these CD4+ T cell subsets within the CNS influences the pathology and clinical course of disease.", "New animal models show that myelin-specific CD8+ T cells can also mediate CNS autoimmunity.", "This Review focuses on recent progress in delineating the pathogenic mechanisms, regulation and interplay between these different T cell subsets in CNS autoimmunity."], "structured": false}
{"doc_id": 22674621, "title": "Effects of FXR in foam-cell formation and atherosclerosis development.", "abstract": ["Farnesoid X receptor (FXR), a bile-acid-activated member of the nuclear receptor superfamily, is essential in regulating bile-acid, cholesterol, and triglyceride homeostasis.", "Disruption of the FXR gene in mice results in a proatherosclerotic lipid profile with increased serum cholesterols and triglycerides.", "However, the role of FXR in foam-cell formation and atherosclerosis development remains unclear.", "The current study showed that the peritoneal macrophages isolated from FXR-null mice took up less oxidized LDL-cholesterol (oxLDL-C), which was accompanied by a marked reduction in CD36 expression in these cells.", "This result appears to be FXR-independent, as FXR was not detected in the peritoneal macrophages.", "To assess to what extent FXR modulates atherosclerosis development, FXR/ApoE double-null mice were generated.", "Female mice were used for atherosclerosis analysis.", "Compared to ApoE-null mice, the FXR/ApoE double-null mice were found to have less atherosclerotic lesion area in the aorta, despite a further increase in the serum cholesterols and triglycerides.", "Our results indicate that disruption of the FXR gene could attenuate atherosclerosis development, most likely resulting from reduced oxLDL-C uptake by macrophages.", "Our study cautions the use of serum lipid levels as a surrogate marker to determine the efficiency of FXR modulators in treating hyperlipidemia."], "structured": false}
{"doc_id": 22682497, "title": "Purkinje cell compartments in the reeler mutant mouse as revealed by Zebrin II and 90-acetylated glycolipid antigen expression", "abstract": ["The cerebellum is organized into a series of parasagittally aligned bands that may be revealed histologically in the adult mouse by largely complementary immunostaining of Purkinje cell sets with the monoclonal antibodies Zebrin II (ZII; antigen:aldolase C) and P-path (PP; antigen:90-acetyl glycolipids).", "We compared the normal staining pattern using these markers and an antibody to calbindin with that found in the reeler mutants (rl/rl), in which most Purkinje cell migration is halted beneath the cerebellar white matter.", "The results revealed that Purkinje cells in reeler mutants, despite their ectopic location in large subcortical masses, show a clear tendency to distribute into alternating zones that either stain for Zebrin II or for P-path, with variable transition zones of mixed labeling.", "However, the estimated number of zones was fewer than in the normal adult cortex: roughly 7\u20139 zones are revealed per side in the mutant compared with 14 major divisions in wild type mice.", "These results raise the possibility that neurons destined to express these markers are segregated during their migration and that the final phase of migration into the cortex might involve further splitting or interdigitation between cell sets expressing the two antigens."], "structured": false}
{"doc_id": 22688699, "title": "Awake craniotomy with brain mapping as the routine surgical approach to treating patients with supratentorial intraaxial tumors: a prospective trial of 200 cases.", "abstract": ["OBJECT Awake craniotomy was performed as the standard surgical approach to supratentorial intraaxial tumors, regardless of the involvement of eloquent cortex, in a prospective trial of 200 patients surgically treated by the same surgeon at a single institution.   \n", "METHODS Patient presentations, comorbid conditions, tumor locations, and the histological characteristics of lesions were recorded.", "Brain mapping was possible in 195 (97.5%) of 200 patients.", "The total number of patients sustaining complications was 33 for an overall complication rate of 16.5%.", "There were two deaths in this series, for a mortality rate of 1%.", "New postoperative neurological deficits were seen in 13% of the patients, but these were permanent in only 4.5% of them.", "Complication rates were higher in patients who had gliomas or preoperative neurological deficits and in those who had undergone prior radiation therapy or surgery.", "No patient who entered the operating room neurologically intact sustained a permanent neurological deficit postoperatively.", "Of the most recent 50 patients treated, three (6%) required a stay in the intensive care unit, and the median total hospital stay was 1 day.   \n", "CONCLUSIONS Use of awake craniotomy can result in a considerable reduction in resource utilization without compromising patient care by minimizing intensive care time and total hospital stay.", "Awake craniotomy is a practical and effective standard surgical approach to supratentorial tumors with a low complication rate, and provides an excellent alternative to craniotomy performed with the patient in the state of general anesthesia because it allows the opportunity for brain mapping and avoids general anesthesia."], "structured": true}
{"doc_id": 22696649, "title": "Reactive Oxygen Species Localization Programs Inflammation to Clear Microbes of Different Size", "abstract": ["How the number of immune cells recruited to sites of infection is determined and adjusted to differences in the cellular stoichiometry between host and pathogen is unknown.", "Here, we have uncovered a role for reactive oxygen species (ROS) as sensors of microbe size.", "By sensing the differential localization of ROS generated in response to microbes of different size, neutrophils tuned their interleukin (IL)-1\u03b2 expression via the selective oxidation of NF-\u03baB, in order to implement distinct inflammatory programs.", "Small microbes triggered ROS intracellularly, suppressing IL-1\u03b2 expression to limit neutrophil recruitment as each phagocyte eliminated numerous pathogens.", "In contrast, large microbes triggered ROS extracellularly, amplifying IL-1\u03b2 expression to recruit numerous neutrophils forming cooperative clusters.", "Defects in ROS-mediated microbe size sensing resulted in large neutrophil infiltrates and clusters in response to small microbes that contribute to inflammatory disease.", "These findings highlight the impact of ROS localization on signal transduction."], "structured": false}
{"doc_id": 22703082, "title": "Helicobacter pylori infection triggers aberrant expression of activation-induced cytidine deaminase in gastric epithelium", "abstract": ["Infection with Helicobacter pylori (H. pylori) is a risk factor for the development of gastric cancer.", "Here we show that infection of gastric epithelial cells with 'cag' pathogenicity island (cagPAI)-positive H. pylori induced aberrant expression of activation-induced cytidine deaminase (AID), a member of the cytidine-deaminase family that acts as a DNA- and RNA-editing enzyme, via the I\u03baB kinase\u2013dependent nuclear factor-\u03baB activation pathway.", "H. pylori\u2013mediated upregulation of AID resulted in the accumulation of nucleotide alterations in the TP53 tumor suppressor gene in gastric cells in vitro.", "Our findings provide evidence that aberrant AID expression caused by H. pylori infection might be a mechanism of mutation accumulation in the gastric mucosa during H. pylori\u2013associated gastric carcinogenesis."], "structured": false}
{"doc_id": 22705234, "title": "The role of the immune response during SIVagm infection of the African green monkey natural host.", "abstract": ["The African green monkey (AGM) is one of many African species endemically infected with simian immunodeficiency virus (SIV).", "Like the other natural hosts, AGMs do not succumb to AIDS and understanding the basis for this resistance to disease progression would be of enormous theoretical and practical importance.", "Early efforts by our group that concentrated on identifying immune mechanisms presumed to keep the virus under control failed to find any obvious candidates.", "The presumption of virus control was invalidated by the finding that SIVagm replicates in AGMs with the same vigor as HIV-1 does in humans.", "Focus therefore shifted to identifying possible immunopathologic features present in disease susceptible hosts but absent in the AGM natural host.", "The apparent immunologic tolerance of AGMs to the SIVagm core protein led to the development of a hypothesis implicating anti-Gag antibodies in the formation of immune complexes, virus trapping in the lymph nodes and immune dysfunction.", "The idea proved difficult to test in vivo and present work focuses on the possibility that Gag tolerance at the T-cell level plays an important role in preventing the catastrophic demise of the immune system characteristic of immunodeficiency virus infection of the heterologous primate host."], "structured": false}
{"doc_id": 22707413, "title": "The S-LANSS score for identifying pain of predominantly neuropathic origin: validation for use in clinical and postal research.", "abstract": ["This article describes the development and validation of the S-LANSS score, a self-report version of the Leeds Assessment of Neuropathic Symptoms and Signs pain scale.", "The S-LANSS aims to identify pain of predominantly neuropathic origin, as distinct from nociceptive pain, without the need for clinical examination.", "Two hundred patients with chronic pain were asked to complete the S-LANSS unaided.", "A researcher then administered the S-LANSS scale and the Neuropathic Pain Scale (NPS) in interview format.", "An independent clinician determined the pain type (neuropathic versus nociceptive) and rated his or her certainty about diagnosis.", "The S-LANSS scale was also incorporated into a chronic pain questionnaire that was sent to 160 community patients and 150 newly referred patients waiting for pain clinic assessment.", "The S-LANSS scale correctly identified 75% of pain types when self-completed and 80% when used in interview format.", "Sensitivity for self-completed S-LANSS scores ranged from 74% to 78%, depending on the cutoff score.", "There were significant associations between NPS items and total score with S-LANSS score.", "In the postal survey, completed questionnaires were returned by 57% of patients (n = 174).", "Internal consistency and convergent validity of the survey S-LANSS scores were confirmed.", "The findings support the S-LANSS scale as a valid and reliable self-report instrument for identifying neuropathic pain and it is also acceptable for use in postal survey research.", "Establishing valid measures of symptoms and signs in neuropathic pain will allow standardized comparisons with other investigational measures.", "This might lead to new insights into the relationship between pathophysiologic mechanisms and clinical manifestations of pain."], "structured": false}
{"doc_id": 22711954, "title": "Bias in meta-analysis detected by a simple, graphical test.", "abstract": ["OBJECTIVE Funnel plots (plots of effect estimates against sample size) may be useful to detect bias in meta-analyses that were later contradicted by large trials.", "We examined whether a simple test of asymmetry of funnel plots predicts discordance of results when meta-analyses are compared to large trials, and we assessed the prevalence of bias in published meta-analyses.   \n", "DESIGN Medline search to identify pairs consisting of a meta-analysis and a single large trial (concordance of results was assumed if effects were in the same direction and the meta-analytic estimate was within 30% of the trial); analysis of funnel plots from 37 meta-analyses identified from a hand search of four leading general medicine journals 1993-6 and 38 meta-analyses from the second 1996 issue of the Cochrane Database of Systematic Reviews.   \n", "MAIN OUTCOME MEASURE Degree of funnel plot asymmetry as measured by the intercept from regression of standard normal deviates against precision.   \n", "RESULTS In the eight pairs of meta-analysis and large trial that were identified (five from cardiovascular medicine, one from diabetic medicine, one from geriatric medicine, one from perinatal medicine) there were four concordant and four discordant pairs.", "In all cases discordance was due to meta-analyses showing larger effects.", "Funnel plot asymmetry was present in three out of four discordant pairs but in none of concordant pairs.", "In 14 (38%) journal meta-analyses and 5 (13%) Cochrane reviews, funnel plot asymmetry indicated that there was bias.   \n", "CONCLUSIONS A simple analysis of funnel plots provides a useful test for the likely presence of bias in meta-analyses, but as the capacity to detect bias will be limited when meta-analyses are based on a limited number of small trials the results from such analyses should be treated with considerable caution."], "structured": true}
{"doc_id": 22712546, "title": "Exploring Metabolic Configurations of Single Cells within Complex Tissue Microenvironments.", "abstract": ["Over the past years, plenty of evidence has emerged illustrating how metabolism supports many aspects of cellular function and how metabolic reprogramming can drive cell differentiation and fate.", "Here, we present a method to assess the metabolic configuration of single cells within their native tissue microenvironment via the visualization and quantification of multiple enzymatic activities measured at saturating substrate conditions combined with subsequent cell type identification.", "After careful validation of the approach and to demonstrate its potential, we assessed the intracellular metabolic configuration of different human immune cell populations in healthy and tumor colon tissue.", "Additionally, we analyzed the intercellular metabolic relationship between cancer cells and cancer-associated fibroblasts in a breast cancer tissue array.", "This study demonstrates that the determination of metabolic configurations in single cells could be a powerful complementary tool for every researcher interested to study metabolic networks in situ."], "structured": false}
{"doc_id": 22730024, "title": "Twenty-four hour and early morning blood pressure control of olmesartan vs. ramipril in elderly hypertensive patients: pooled individual data analysis of two randomized, double-blind, parallel-group studies.", "abstract": ["OBJECTIVE To assess the antihypertensive efficacy of olmesartan medoxomil and ramipril on 24-h ambulatory blood pressure (ABP) in elderly hypertensive patients by pooled data analysis of two studies with identical designs (one Italian, one European).   \n", "METHODS After a 2-week placebo wash-out 1453 elderly hypertensive patients (65-89 years; sitting office DBP 90-109 mmHg and/or sitting office SBP 140-179 mmHg) were randomized to a 12-week double-blind treatment with olmesartan medoxomil 10 mg or ramipril 2.5 mg once-daily, up-titrated (20 and 40 mg olmesartan medoxomil; 5 and 10 mg ramipril) after 2 and 6 weeks in patients without normalized office BP.", "24-h ABP was recorded at randomization and after 12 weeks.   \n", "RESULTS In 715 patients with valid baseline and end-of-treatment recordings baseline-adjusted 24-h SBP and DBP reductions were greater with olmesartan medoxomil (n = 356) than with ramipril (n = 359) [between-treatment differences and 95% confidence interval (CI), SBP: 2.2 (3.8, 0.6), P = 0.006; DBP: 1.3 (2.2, 0.3), P = 0.009].", "Olmesartan medoxomil showed larger BP reductions in the last 6 h from the dosing interval and higher smoothness indices than ramipril.", "Olmesartan medoxomil reduced the SBP morning rise [-2.8 (-4.9, -0.8) mmHg], whereas ramipril did not [+1.5 (-0.6, +3.6) mmHg; P = 0.004 between-treatments].", "Five hundred and eighty-two patients with sustained hypertension (office and 24-h ambulatory hypertension) showed the largest antihypertensive effect, with between-treatment differences still in favor of olmesartan medoxomil [SBP: 2.1 (3.9, 0.4), P = 0.019; DBP: 1.2 (2.3, 0.1), P = 0.032].   \n", "CONCLUSIONS Olmesartan medoxomil provides a more effective and sustained 24-h BP control than ramipril in elderly hypertensive patients, particularly in the hours farthest from last intake."], "structured": true}
{"doc_id": 22767022, "title": "Abi1 is essential for the formation and activation of a WAVE2 signalling complex", "abstract": ["WAVE2 belongs to a family of proteins that mediates actin reorganization by relaying signals from Rac to the Arp2/3 complex, resulting in lamellipodia protrusion.", "WAVE2 displays Arp2/3-dependent actin nucleation activity in vitro, and does not bind directly to Rac.", "Instead, it forms macromolecular complexes that have been reported to exert both positive and negative modes of regulation.", "How these complexes are assembled, localized and activated in vivo remains to be established.", "Here we use tandem mass spectrometry to identify an Abi1-based complex containing WAVE2, Nap1 (Nck-associated protein) and PIR121.", "Abi1 interacts directly with the WHD domain of WAVE2, increases WAVE2 actin polymerization activity and mediates the assembly of a WAVE2\u2013Abi1\u2013Nap1\u2013PIR121 complex.", "The WAVE2\u2013Abi1\u2013Nap1\u2013PIR121 complex is as active as the WAVE2\u2013Abi1 sub-complex in stimulating Arp2/3, and after Rac activation it is re-localized to the leading edge of ruffles in vivo.", "Consistently, inhibition of Abi1 by RNA interference (RNAi) abrogates Rac-dependent lamellipodia protrusion.", "Thus, Abi1 orchestrates the proper assembly of the WAVE2 complex and mediates its activation at the leading edge in vivo."], "structured": false}
{"doc_id": 22791348, "title": "The dendritic cell lineage: ontogeny and function of dendritic cells and their subsets in the steady state and the inflamed setting.", "abstract": ["Dendritic cells (DCs) form a remarkable cellular network that shapes adaptive immune responses according to peripheral cues.", "After four decades of research, we now know that DCs arise from a hematopoietic lineage distinct from other leukocytes, establishing the DC system as a unique hematopoietic branch.", "Recent work has also established that tissue DCs consist of developmentally and functionally distinct subsets that differentially regulate T lymphocyte function.", "This review discusses major advances in our understanding of the regulation of DC lineage commitment, differentiation, diversification, and function in situ."], "structured": false}
{"doc_id": 22800314, "title": "IL-15 Receptor Deletion Results in Circadian Changes of Locomotor and Metabolic Activity", "abstract": ["Interleukin-15 (IL-15) is a cytokine produced in the normal brain that acts on its specific receptor IL-15R\u03b1 and co-receptors IL-2R\u03b2 and IL-2R\u03b3 in neuronal cells.", "The functions of the cerebral IL-15 system, however, are not yet clear.", "To test the hypothesis that IL-15R\u03b1 regulates metabolic activity and body temperature, we quantified the specific metabolic phenotype of IL-15R\u03b1 knockout mice.", "These normal-appearing mice were leaner with lower fat composition.", "During the entire circadian cycle, the knockout mice had a significantly higher acrophase in locomotor activity and heat dissipation.", "During the light phase, there was significantly greater food intake, oxygen consumption, and carbon dioxide production.", "The difference in the dark and light phases suggests that IL-15R\u03b1 participates in circadian rhythm regulation.", "The higher oxygen consumption in the light phase indicates adaptive thermogenesis in the knockout mice.", "The body temperature of the receptor knockout mice was significantly higher than the control in the light phase, and this was mainly caused by a large difference occurring between 0600 and 0900 h. In addition to the metabolic chamber studies and circadian rhythm analyses, qPCR of hypothalamic homogenates indicated higher mRNA expression of orexin and transient receptor potential vanilloid 4 cation channels.", "Consistent with a direct role of IL-15R\u03b1 in the hypothalamus, IL-15 treatment of the wild-type mice induced c-Fos expression in the preoptic area.", "We conclude that activation of hypothalamic neurons by IL-15 in mice contributes to thermoregulation and modifies the metabolic phenotype."], "structured": false}
{"doc_id": 22815457, "title": "Vaginal progesterone, cerclage or cervical pessary for preventing preterm birth in asymptomatic singleton pregnant women with a history of preterm birth and a sonographic short cervix.", "abstract": ["OBJECTIVE To compare the outcome of pregnancy in cohorts of women with singleton pregnancy and history of preterm birth and sonographic short cervix managed with different treatment protocols, namely cerclage, vaginal progesterone or cervical pessary.   \n", "METHODS This was a comparison of three management protocols for women with singleton pregnancy and a high risk of preterm birth because of a prior spontaneous preterm birth before 34 weeks and a shortened cervical length detected by transvaginal ultrasound.", "The study included 142 women who were initially treated with cerclage (USA), 59 with vaginal progesterone (UK) and 42 with cervical pessary (Spain).", "Perinatal outcomes were compared between the three cohorts.   \n", "RESULTS", "There were no statistically significant differences in perinatal losses, neonatal morbidity and preterm births among the three groups, apart from a higher rate of preterm birth before 34 weeks' gestation after treatment with vaginal progesterone in comparison with treatment with cervical pessary (32% vs 12%; relative risk (RR) = 2.70; 95% CI, 1.10-6.67).", "When only the subgroups of women with cervical length < 25 mm, irrespective of gestational age, were compared, the difference between these two cohorts was not statistically significant (RR = 2.21; 95% CI, 0.83-5.89).   \n", "CONCLUSION Cerclage, vaginal progesterone and pessary appear to have similar effectiveness as management strategies in women with singleton pregnancy, previous spontaneous preterm birth and short cervix.", "Direct randomized comparisons of these strategies, or combinations thereof, are needed to determine optimal management."], "structured": true}
{"doc_id": 22820637, "title": "The oxytocinase subfamily of M1 aminopeptidases.", "abstract": ["The placental leucine aminopeptidase (P-LAP), adipocyte-derived leucine aminopeptidase (A-LAP) and leukocyte-derived aminopeptidase (L-RAP) belong to one distinct group of the M1 family of amimopeptidases, which we term the \"Oxytocinase subfamily\".", "They share HEXXH(X)18E Zn-binding and GAMEN motifs essential for the enzymatic activities.", "Intracellular localization is the characteristic feature of the subfamily members.", "While P-LAP is translocated from intracellular vesicles to plasma membrane in a stimulus-dependent manner, both A-LAP and L-RAP are retained in the endoplasmic reticulum.", "They contain sequences necessary for the specific localization in the cell.", "It is getting evident that the subfamily members play important roles in the maintenance of homeostasis including maintenance of normal pregnancy, memory retention, blood pressure regulation and antigen presentation.", "In this review, current situation of this newly identified subfamily is summarized."], "structured": false}
{"doc_id": 22843616, "title": "Myc represses primitive endoderm differentiation in pluripotent stem cells.", "abstract": ["The generation of induced pluripotent stem cells (iPSCs) provides a novel method to facilitate investigations into the mechanisms that control stem cell pluripotency and self-renewal.", "Myc has previously been shown to be critical for murine embryonic stem cell (mESC) maintenance, while also enhancing directed reprogramming of fibroblasts by effecting widespread changes in gene expression.", "Despite several studies identifying in vivo target genes, the precise mechanism by which Myc regulates pluripotency remains unknown.", "Here we report that codeletion of c- and N-MYC in iPSCs and ESCs results in their spontaneous differentiation to primitive endoderm.", "We show that Myc sustains pluripotency through repression of the primitive endoderm master regulator GATA6, while also contributing to cell cycle control by regulation of the mir-17-92 miRNA cluster.", "Our findings demonstrate the indispensable requirement for c- or N-myc in pluripotency beyond proliferative and metabolic control."], "structured": false}
{"doc_id": 22843838, "title": "[Vitamin D and latitude as environmental factors in multiple sclerosis].", "abstract": ["Multiple sclerosis (MS) shows a multifold increase in prevalence with an increase in latitudes, both north and south of the equator.", "One of the potential factors related to the difference of the prevalence is vitamin D, because the strength of ambient ultraviolet light, which is essential for vitamin D production, decreases with increasing latitude.", "It is known that vitamin D has immunomodulatory functions and suppresses an animal model of MS.", "It is also considered that vitamin D-related genes are critical susceptible genes for MS.", "An approach from environmental and genetic aspects is needed to investigate the association between vitamin D and MS."], "structured": false}
{"doc_id": 22852120, "title": "Type 2 cytokines: mechanisms and therapeutic strategies", "abstract": ["Type 2 immune responses are defined by the cytokines interleukin-4 (IL-4), IL-5, IL-9 and IL-13, which can either be host protective or have pathogenic activity.", "Type 2 immunity promotes antihelminth immunity, suppresses type 1-driven autoimmune disease, neutralizes toxins, maintains metabolic homeostasis, and regulates wound repair and tissue regeneration pathways following infection or injury.", "Nevertheless, when type 2 responses are dysregulated, they can become important drivers of disease.", "Type 2 immunity induces a complex inflammatory response characterized by eosinophils, mast cells, basophils, type 2 innate lymphoid cells, IL-4-and/or IL-13-conditioned macrophages and T helper 2 (TH2) cells, which are crucial to the pathogenesis of many allergic and fibrotic disorders.", "As chronic type 2 immune responses promote disease, the mechanisms that regulate their maintenance are thought to function as crucial disease modifiers.", "This Review discusses the many endogenous negative regulatory mechanisms that antagonize type 2 immunity and highlights how therapies that target some of these pathways are being developed to treat type 2-mediated disease."], "structured": false}
{"doc_id": 22867765, "title": "Implanted microvessels progress through distinct neovascularization phenotypes.", "abstract": ["We have previously demonstrated that implanted microvessels form a new microcirculation with minimal host-derived vessel investment.", "Our objective was to define the vascular phenotypes present during neovascularization in these implants and identify post-angiogenesis events.", "Morphological, functional and transcriptional assessments identified three distinct vascular phenotypes in the implants: sprouting angiogenesis, neovascular remodeling, and network maturation.", "A sprouting angiogenic phenotype appeared first, characterized by high proliferation and low mural cell coverage.", "This was followed by a neovascular remodeling phenotype characterized by a perfused, poorly organized neovascular network, reduced proliferation, and re-associated mural cells.", "The last phenotype included a vascular network organized into a stereotypical tree structure containing vessels with normal perivascular cell associations.", "In addition, proliferation was low and was restricted to the walls of larger microvessels.", "The transition from angiogenesis to neovascular remodeling coincided with the appearance of blood flow in the implant neovasculature.", "Analysis of vascular-specific and global gene expression indicates that the intermediate, neovascular remodeling phenotype is transcriptionally distinct from the other two phenotypes.", "Therefore, this vascular phenotype likely is not simply a transitional phenotype but a distinct vascular phenotype involving unique cellular and vascular processes.", "Furthermore, this neovascular remodeling phase may be a normal aspect of the general neovascularization process.", "Given that this phenotype is arguably dysfunctional, many of the microvasculatures present within compromised or diseased tissues may not represent a failure to progress appropriately through a normally occurring neovascularization phenotype."], "structured": false}
{"doc_id": 22871664, "title": "Characterization of a highly variable eutherian microRNA gene.", "abstract": ["Mouse microRNAs (miRNAs) miR-290-miR295 are encoded by a cluster of partially homologous pre-miRNA hairpins and are likely to be functionally important in embryonic stem (ES) cells and preimplantation embryos.", "We present evidence that a spliced, capped, and polyadenylated primary transcript spans this entire Early Embryonic microRNA Cluster (EEmiRC).", "Partial Drosha processing yields additional large nuclear RNA intermediates.", "A conserved promoter element containing a TATA-box directs EEmiRC transcription.", "Sequence analysis shows that the EEmiRC transcription unit is remarkably variable and can only be identified bioinformatically in placental (eutherian) mammals.", "Consistent with eutherian-specific function, EEmiRC is expressed in trophoblastic stem (TS) cells.", "When analyzing evolutionary and functional relationships, the organization of the entire miRNA loci should be considered in addition to the mature miRNA sequences.", "Application of this concept suggests that EEmiRC is a recently acquired rapidly evolving gene important for eutherian development."], "structured": false}
{"doc_id": 22874817, "title": "The function of follicular helper T cells is regulated by the strength of T cell antigen receptor binding", "abstract": ["How follicular helper T cells (TFH cells) differentiate to regulate B cell immunity is critical for effective protein vaccination.", "Here we define three transcription factor T-bet\u2013expressing antigen-specific effector helper T cell subsets with distinguishable function, migratory properties and developmental programming in vivo.", "Expression of the transcriptional repressor Blimp-1 distinguished T zone 'lymphoid' effector helper T cells (CD62LhiCCR7hi) from CXCR5lo 'emigrant' effector helper T cells and CXCR5hi 'resident' TFH cells expressing the transcriptional repressor Bcl-6 (CD62LloCCR7lo).", "We then show by adoptive transfer and intact polyclonal responses that helper T cells with the highest specific binding of peptide\u2013major histocompatibility complex class II and the most restricted T cell antigen receptor junctional diversity 'preferentially' developed into the antigen-specific effector TFH compartment.", "Our studies demonstrate a central function for differences in the binding strength of the T cell antigen receptor in the antigen-specific mechanisms that 'program' specialized effector TFH function in vivo."], "structured": false}
{"doc_id": 22889972, "title": "Disruption of tumor necrosis factor-alpha gene diminishes the development of atherosclerosis in ApoE-deficient mice.", "abstract": ["Inflammatory cytokines, including tumor necrosis factor-alpha (TNF-alpha) have been implicated in atherogenesis.", "However, the precise role of TNF-alpha in atherogenesis is still unclear.", "To examine the effect of TNF-alpha on atherogenesis, we generated compound-deficient mice in apolipoprotein E (apoE) and TNF-alpha (apoE-/-/TNF-alpha-/-) and compared them with apoE-/- mice.", "Although serum total cholesterol levels were markedly elevated in both apoE-/-/TNF-alpha-/- and apoE-/- mice compared to wild-type mice, no differences were observed between apoE-/-/TNF-alpha-/- and apoE-/- mice.", "The atherosclerotic plaque area in the aortic luminal surface of apoE-/-/TNF-alpha-/- mice (n=8, 3.1+/-0.4%) was significantly smaller than that of apoE-/- mice (n=7, 4.7+/-0.4%, p<0.001) despite the lack of difference in serum cholesterol levels.", "The atherosclerotic lesion size in the aortic sinus of apoE-/-/TNF-alpha-/- mice (n=10, 5.1+/-0.3 x 10(5)microm(2)) was also significantly smaller than that of apoE-/- mice (n=11, 7.0+/-0.3 x 10(5)microm(2), p<0.0001).", "RT-PCR analysis indicated that the expression levels of intercellular adhesion molecule-1 (ICAM-1), vascular cell adhesion molecule-1 (VCAM-1) and monocyte chemoattractant protein-1 (MCP-1) were significantly higher in apoE-/- than apoE-/-/TNF-alpha-/- mice.", "Macrophages from apoE(-/-) mice showed higher uptake level of oxidized LDL and increased expression level of scavenger receptor class A (SRA) compared to those from apoE-/-/TNF-alpha-/- mice.", "These results indicate that TNF-alpha plays an atherogenic role by upregulating the expressions of ICAM-1, VCAM-1 and MCP-1 in the vascular wall, and by inducing SRA expression and oxidized LDL uptake in macrophages."], "structured": false}
{"doc_id": 22890091, "title": "Differential expression of bcl-2 and susceptibility to anti-Fas-mediated cell death in peripheral blood lymphocytes, monocytes, and neutrophils.", "abstract": ["The recently identified Fas antigen (Ag) is a cell surface molecule that can mediate apoptosis.", "The cytoplasmic product of proto-oncogene bcl-2 has been shown to prolong the cellular survival by inhibiting apoptosis.", "To elucidate the physiologic significance of expression of both molecules, we examined the expression of Fas Ag and bcl-2 on blood leukocyte populations and evaluated their sensitivity to the cytolytic action of anti-Fas antibody.", "Although Fas Ag was expressed on a fraction of lymphocytes, both neutrophils and monocytes expressed Fas Ag constitutively.", "In contrast, there was marked difference among these leukocytes regarding bcl-2 expression.", "Lymphocytes expressed bcl-2 intensely, but monocytes showed weaker bcl-2 expression, and neutrophils were essentially absent for bcl-2 expression.", "Seemingly reflecting this lack of bcl-2-expression, neutrophils more easily underwent apoptotic cell death in vitro as compared with monocytes and lymphocytes.", "We showed that anti-Fas antibody affectively accelerated apoptotic cell death in neutrophils.", "However, the apoptosis-inducing effect of anti-Fas antibody was minimal on monocytes, and lymphocytes were resistant to this antibody.", "These results suggest that anti-Fas-mediated cell death may, in part, be determined by bcl-2 expression status in Fas+ lymphoid and hematopoietic cells."], "structured": false}
{"doc_id": 22896384, "title": "Foxp2 and Foxp1 cooperatively regulate lung and esophagus development.", "abstract": ["The airways of the lung develop through a reiterative process of branching morphogenesis that gives rise to the intricate and extensive surface area required for postnatal respiration.", "The forkhead transcription factors Foxp2 and Foxp1 are expressed in multiple foregut-derived tissues including the lung and intestine.", "In this report, we show that loss of Foxp2 in mouse leads to defective postnatal lung alveolarization, contributing to postnatal lethality.", "Using in vitro and in vivo assays, we show that T1alpha, a lung alveolar epithelial type 1 cell-restricted gene crucial for lung development and function, is a direct target of Foxp2 and Foxp1.", "Remarkably, loss of a single Foxp1 allele in addition to complete loss of Foxp2 results in increased severity of morphological defects in mutant lungs and leads to perinatal loss of all Foxp2(-/-);Foxp1(+/-) mice.", "Expression of N-myc and Hop, crucial regulators of lung development, is compromised in Foxp2(-/-);Foxp1(+/-) mutants.", "In addition to the defects in lung development, esophageal muscle development is disrupted in Foxp2(-/-);Foxp1(+/-) embryos, a tissue where Foxp2 and Foxp1 are co-expressed.", "These data identify Foxp2 and Foxp1 as crucial regulators of lung and esophageal development, underscoring the necessity of these transcription factors in the development of anterior foregut-derived tissues and demonstrating functional cooperativity between members of the Foxp1/2/4 family in tissues where they are co-expressed."], "structured": false}
{"doc_id": 22896970, "title": "Crystal structure of the eukaryotic 60S ribosomal subunit in complex with initiation factor 6.", "abstract": ["Protein synthesis in all organisms is catalyzed by ribosomes.", "In comparison to their prokaryotic counterparts, eukaryotic ribosomes are considerably larger and are subject to more complex regulation.", "The large ribosomal subunit (60S) catalyzes peptide bond formation and contains the nascent polypeptide exit tunnel.", "We present the structure of the 60S ribosomal subunit from Tetrahymena thermophila in complex with eukaryotic initiation factor 6 (eIF6), cocrystallized with the antibiotic cycloheximide (a eukaryotic-specific inhibitor of protein synthesis), at a resolution of 3.5 angstroms.", "The structure illustrates the complex functional architecture of the eukaryotic 60S subunit, which comprises an intricate network of interactions between eukaryotic-specific ribosomal protein features and RNA expansion segments.", "It reveals the roles of eukaryotic ribosomal protein elements in the stabilization of the active site and the extent of eukaryotic-specific differences in other functional regions of the subunit.", "Furthermore, it elucidates the molecular basis of the interaction with eIF6 and provides a structural framework for further studies of ribosome-associated diseases and the role of the 60S subunit in the initiation of protein synthesis."], "structured": false}
{"doc_id": 22901758, "title": "Hedgehog signaling regulates brain tumor-initiating cell proliferation and portends shorter survival for patients with PTEN-coexpressing glioblastomas.", "abstract": ["The identification of brain tumor stem-like cells (BTSCs) has implicated a role of biological self-renewal mechanisms in clinical brain tumor initiation and propagation.", "The molecular mechanisms underlying the tumor-forming capacity of BTSCs, however, remain unknown.", "Here, we have generated molecular signatures of glioblastoma multiforme (GBM) using gene expression profiles of BTSCs and have identified both Sonic Hedgehog (SHH) signaling-dependent and -independent BTSCs and their respective glioblastoma surgical specimens.", "BTSC proliferation could be abrogated in a pathway-dependent fashion in vitro and in an intracranial tumor model in athymic mice.", "Both SHH-dependent and -independent brain tumor growth required phosphoinositide 3-kinase-mammalian target of rapamycin signaling.", "In human GBMs, the levels of SHH and PTCH1 expression were significantly higher in PTEN-expressing tumors than in PTEN-deficient tumors.", "In addition, we show that hyperactive SHH-GLI signaling in PTEN-coexpressing human GBM is associated with reduced survival time.", "Thus, distinct proliferation signaling dependence may underpin glioblastoma propagation by BTSCs.", "Modeling these BTSC proliferation mechanisms may provide a rationale for individualized glioblastoma treatment."], "structured": false}
{"doc_id": 22908536, "title": "Stress and host immunity amplify Mycobacterium tuberculosis phenotypic heterogeneity and induce nongrowing metabolically active forms.", "abstract": ["Nonreplicating and metabolically quiescent bacteria are implicated in latent tuberculosis infections and relapses following \"sterilizing\" chemotherapy.", "However, evidence linking bacterial dormancy and persistence in vivo is largely inconclusive.", "Here we measure the single-cell dynamics of Mycobacterium tuberculosis replication and ribosomal activity using quantitative time-lapse microscopy and a reporter of ribosomal RNA gene expression.", "Single-cell dynamics exhibit heterogeneity under standard growth conditions, which is amplified by stressful conditions such as nutrient limitation, stationary phase, intracellular replication, and growth in mouse lungs.", "Additionally, the lungs of chronically infected mice harbor a subpopulation of nongrowing but metabolically active bacteria, which are absent in mice lacking interferon-\u03b3, a cytokine essential for antituberculosis immunity.", "These cryptic bacterial forms are prominent in mice treated with the antituberculosis drug isoniazid, suggesting a role in postchemotherapeutic relapses.", "Thus, amplification of bacterial phenotypic heterogeneity in response to host immunity and drug pressure may contribute to tuberculosis persistence."], "structured": false}
{"doc_id": 22914228, "title": "Proteomic analysis reveals Warburg effect and anomalous metabolism of glutamine in pancreatic cancer cells.", "abstract": ["In this present work, we characterized the proteomes of pancreatic ductal adenocarcinoma (PDAC) cell line PANC-1 and normal pancreatic duct cells by mass spectrometry using LTQ-Orbitrap and identified more than 1700 proteins from each sample.", "On the basis of the spectra count label-free quantification approach, we identified a large number of differentially expressed metabolic enzymes and proteins involved in cytoskeleton, cell adhesion, transport, transcription, translation, and cell proliferation as well.", "The data demonstrated that metabolic pathways were altered in PANC-1, consistent with the Warburg effect.", "In addition, the comparative MS analysis unveiled anomalous metabolism of glutamine, suggesting that glutamine was largely consumed as a nitrogen donor in nucleotide and amino acid biosynthesis in PANC-1.", "Our analysis provides a potentially comprehensive picture of metabolism in PANC-1, which may serve as the basis of new diagnostics and treatment of PDAC."], "structured": false}
{"doc_id": 22922353, "title": "Prevalence of attempting weight loss and strategies for controlling weight.", "abstract": ["CONTEXT Overweight and obesity are increasing in the United States.", "Changes in diet and physical activity are important for weight control.   \n", "OBJECTIVES To examine the prevalence of attempting to lose or to maintain weight and to describe weight control strategies among US adults.   \n", "DESIGN", "The Behavioral Risk Factor Surveillance System, a random-digit telephone survey conducted in 1996 by state health departments.", "Setting The 49 states (and the District of Columbia) that participated in the survey.   \n", "PARTICIPANTS Adults aged 18 years and older (N = 107 804).   \n", "MAIN OUTCOME MEASURES Reported current weights and goal weights, prevalence of weight loss or maintenance attempts, and strategies used to control weight (eating fewer calories, eating less fat, or using physical activity) by population subgroup.   \n", "RESULTS The prevalence of attempting to lose and maintain weight was 28.8% and 35.1 % among men and 43.6% and 34.4% among women, respectively.", "Among those attempting to lose weight, a common strategy was to consume less fat but not fewer calories (34.9% of men and 40.0% of women); only 21.5% of men and 19.4% of women reported using the recommended combination of eating fewer calories and engaging in at least 150 minutes of leisure-time physical activity per week.", "Among men trying to lose weight, the median weight was 90.4 kg with a goal weight of 81.4 kg.", "Among women, the median weight was 70.3 kg with a goal weight of 59.0 kg.   \n", "CONCLUSIONS Weight loss and weight maintenance are common concerns for US men and women.", "Most persons trying to lose weight are not using the recommended combination of reducing calorie intake and engaging in leisure-time physical activity 150 minutes or more per week."], "structured": true}
{"doc_id": 22937651, "title": "Antibodies specific for Epstein-Barr virus nuclear antigen-1 cross-react with human heterogeneous nuclear ribonucleoprotein L.", "abstract": ["Epstein-Barr virus (EBV) is associated with multiple sclerosis (MS), and antibodies to the EBV nuclear antigen-1 (EBNA-1) are consistently increased in MS patients.", "The hypothesis of this study is that anti-EBNA-1 antibodies cross-react with a self antigen in MS patients.", "We affinity purified anti-EBNA-1 antibodies from human plasma, used the anti-EBNA-1 to immunoprecipitate antigens from human brain, and identified bound antigens with mass spectrometry.", "Anti-EBNA-1 consistently bound heterogeneous nuclear ribonucleoprotein L (HNRNPL).", "We expressed both the long and short isoforms of this protein, and verified with Western blots and ELISA that the long isoform cross-reacts with EBNA-1.", "Immunohistochemistry demonstrated that anti-EBNA-1 bound to an antigen in the nucleus of cultured rat central nervous system cells.", "ELISA demonstrated the presence of antibodies to HNRNPL in the plasma of both healthy controls and MS patients, but anti-HNRNPL was not increased in MS patients.", "We conclude that HNRNPL is an autoantigen which cross-reacts with EBNA-1.", "The relevance of this autoantigen to MS and other autoimmune diseases remains to be investigated."], "structured": false}
{"doc_id": 22937815, "title": "Roles of chromatin remodellers in DNA double strand break repair.", "abstract": ["Now that we have a good understanding of the DNA double strand break (DSB) repair mechanisms and DSB-induced damage signalling, attention is focusing on the changes to the chromatin environment needed for efficient DSB repair.", "Mutations in chromatin remodelling complexes have been identified in cancers, making it important to evaluate how they impact upon genomic stability.", "Our current understanding of the DSB repair pathways suggests that each one has distinct requirements for chromatin remodelling.", "Moreover, restricting the extent of chromatin modifications could be a significant factor regulating the decision of pathway usage.", "In this review, we evaluate the distinct DSB repair pathways for their potential need for chromatin remodelling and review the roles of ATP-driven chromatin remodellers in the pathways."], "structured": false}
{"doc_id": 22938539, "title": "Epstein-Barr virus and virus human protein interaction maps.", "abstract": ["A comprehensive mapping of interactions among Epstein-Barr virus (EBV) proteins and interactions of EBV proteins with human proteins should provide specific hypotheses and a broad perspective on EBV strategies for replication and persistence.", "Interactions of EBV proteins with each other and with human proteins were assessed by using a stringent high-throughput yeast two-hybrid system.", "Overall, 43 interactions between EBV proteins and 173 interactions between EBV and human proteins were identified.", "EBV-EBV and EBV-human protein interaction, or \"interactome\" maps provided a framework for hypotheses of protein function.", "For example, LF2, an EBV protein of unknown function interacted with the EBV immediate early R transactivator (Rta) and was found to inhibit Rta transactivation.", "From a broader perspective, EBV genes can be divided into two evolutionary classes, \"core\" genes, which are conserved across all herpesviruses and subfamily specific, or \"noncore\" genes.", "Our EBV-EBV interactome map is enriched for interactions among proteins in the same evolutionary class.", "Furthermore, human proteins targeted by EBV proteins were enriched for highly connected or \"hub\" proteins and for proteins with relatively short paths to all other proteins in the human interactome network.", "Targeting of hubs might be an efficient mechanism for EBV reorganization of cellular processes."], "structured": false}
{"doc_id": 22942787, "title": "Relation between Medicare screening reimbursement and stage at diagnosis for older patients with colon cancer.", "abstract": ["CONTEXT Medicare's reimbursement policy was changed in 1998 to provide coverage for screening colonoscopies for patients with increased colon cancer risk, and expanded further in 2001 to cover screening colonoscopies for all individuals.   \n", "OBJECTIVE To determine whether the Medicare reimbursement policy changes were associated with an increase in either colonoscopy use or early stage colon cancer diagnosis.   \n", "DESIGN, SETTING, AND PARTICIPANTS Patients in the Surveillance, Epidemiology, and End Results Medicare linked database who were 67 years of age and older and had a primary diagnosis of colon cancer during 1992-2002, as well as a group of Medicare beneficiaries who resided in Surveillance, Epidemiology, and End Results areas but who were not diagnosed with cancer.   \n", "MAIN OUTCOME MEASURES Trends in colonoscopy and sigmoidoscopy use among Medicare beneficiaries without cancer were assessed using multivariate Poisson regression.", "Among the patients with cancer, stage was classified as early (stage I) vs all other (stages II-IV).", "Time was categorized as period 1 (no screening coverage, 1992-1997), period 2 (limited coverage, January 1998-June 2001), and period 3 (universal coverage, July 2001-December 2002).", "A multivariate logistic regression (outcome = early stage) was used to assess temporal trends in stage at diagnosis; an interaction term between tumor site and time was included.   \n", "RESULTS Colonoscopy use increased from an average rate of 285/100,000 per quarter in period 1 to 889 and 1919/100,000 per quarter in periods 2 (P<.001) and 3 (P vs 2<.001), respectively.", "During the study period, 44,924 eligible patients were diagnosed with colorectal cancer.", "The proportion of patients diagnosed at an early stage increased from 22.5% in period 1 to 25.5% in period 2 and 26.3% in period 3 (P<.001 for each pairwise comparison).", "The changes in Medicare coverage were strongly associated with early stage at diagnosis for patients with proximal colon lesions (adjusted relative risk period 2 vs 1, 1.19; 95% confidence interval, 1.13-1.26; adjusted relative risk period 3 vs 2, 1.10; 95% confidence interval, 1.02-1.17) but weakly associated, if at all, for patients with distal colon lesions (adjusted relative risk period 2 vs 1, 1.07; 95% confidence interval, 1.01-1.13; adjusted relative risk period 3 vs 2, 0.97; 95% confidence interval, 0.90-1.05).   \n", "CONCLUSIONS Expansion of Medicare reimbursement to cover colon cancer screening was associated with an increased use of colonoscopy for Medicare beneficiaries, and for those who were diagnosed with colon cancer, an increased probability of being diagnosed at an early stage.", "The selective effect of the coverage change on proximal colon lesions suggests that increased use of whole-colon screening modalities such as colonoscopy may have played a pivotal role."], "structured": true}
{"doc_id": 22948960, "title": "Direct visualization of the endomitotic cell cycle in living megakaryocytes: differential patterns in low and high ploidy cells.", "abstract": ["Endomitosis in megakaryocytes (MKs) involves repeated DNA replication in the absence of cytokinesis and is a crucial part of MK development.", "However, chromosomal dynamics have never been observed in living MKs.", "We developed a new transgenic mouse model in which the expression of human histone H2B fused in-frame to green fluorescent protein is targeted to MKs.", "Ex vivo time-lapse microscopy analysis indicated that chromosomal condensation occurs at early mitosis in all MKs.", "In high ploidy MKs (>or=8N), late anaphase was marked by a ring-type alignment of chromosomes with multiple territories formed between them.", "By contrast, in low ploidy MKs mitotic chromosomes segregated to form two groups separated by a clear space before re-joining to one cluster.", "This is the first study to document chromosomal segregation patterns during endomitosis ex vivo and to indicate their potential differential regulation in low and high ploidy cells."], "structured": false}
{"doc_id": 22963769, "title": "Aberrant expression and altered cellular localization of desmosomal and hemidesmosomal proteins are associated with aggressive clinicopathological features of oral squamous cell carcinoma", "abstract": ["Disruption of cell adhesion plays a central role in dedifferentiation, invasion, and metastasis of various cancers.", "The desmosome and hemidesmosome are anchoring junctions that control cell-cell and cell-matrix adhesion, respectively.", "To clarify their contributions in mediating the biological properties of oral cancer, we immunohistochemically examined the expression of desmoglein 1 (DSG1), DSG2, DSG3, desmocollin 2 (DSC2), integrin beta 4 (ITGB4), laminin gamma chain 2 (LAMC2), and collagen type 17 alpha 1 (COL17A1) in 51 cases of oral squamous cell carcinoma.", "On normal oral epithelial cells, DSG1, DSG3, DSC2, and COL17A1 were expressed on the plasma membrane, while ITGB4 and mature LAMC2 were present at the basement membrane.", "In cancer, the expression of DSG1, DSG3, DSC2, and COL17A1 decreased and internalized to the cytoplasm.", "Cytoplasmic expression of DSG2, ITGB4, and LAMC2 was induced in the cancer cells facing to the stroma.", "We scored immunohistochemical expression and correlated this to clinicopathological parameters including histologic differentiation, pattern of invasion, and presence of lymph node metastasis.", "Decrease of DSG3 and DSC2 expression correlated with a more aggressive cancer phenotype: less differentiated and more invasive histologic features and a higher incidence of nodal metastasis.", "Lower COL17A1 and higher LAMC2 expression were also associated with a more aggressive phenotype.", "The present study demonstrates that aberrant expression and altered cellular localization of desmosomal and hemidesmosomal proteins are associated with aggressive clinicopathological features of oral cancer.", "This reinforces the notion that disturbance of the keratin-associated anchoring junctions confers aggressive features to cancer cells."], "structured": false}
{"doc_id": 22968257, "title": "Histone/protein deacetylase inhibitors increase suppressive functions of human FOXP3+ Tregs.", "abstract": ["Histone/protein deacetylases (HDACs) decrease histone and protein acetylation, typically leading to suppression of gene transcription and modulation of various protein functions.", "We found significant differences in expression of HDAC before and after stimulation of human T regulatory (Treg) and T effector cells, suggesting the potential for future selective targeting of Tregs with HDAC inhibitors (HDACi).", "Use of various HDACi small molecules enhanced, by up to 4.5-fold (average 2-fold), the suppressive functions of both freshly isolated and expanded human Tregs, consistent with our previous murine data.", "HDACi use increased Treg expression of CTLA-4, a key negative regulator of immune response, and we found a direct and significant correlation between CTLA-4 expression and Treg suppression.", "Hence, HDACi compounds are promising pharmacologic tools to increase Treg suppressive functions, and this action may potentially be of use in patients with autoimmunity or post-transplantation."], "structured": false}
{"doc_id": 22972632, "title": "Enhanced pathological angiogenesis in mice lacking \u03b23 integrin or \u03b23 and \u03b25 integrins", "abstract": ["Inhibition of \u03b1v\u03b23 or \u03b1v\u03b25 integrin function has been reported to suppress neovascularization and tumor growth, suggesting that these integrins are critical modulators of angiogenesis.", "Here we report that mice lacking \u03b23 integrins or both \u03b23 and \u03b25 integrins not only support tumorigenesis, but have enhanced tumor growth as well.", "Moreover, the tumors in these integrin-deficient mice display enhanced angiogenesis, strongly suggesting that neither \u03b23 nor \u03b25 integrins are essential for neovascularization.", "We also observed that angiogenic responses to hypoxia and vascular endothelial growth factor (VEGF) are augmented significantly in the absence of \u03b23 integrins.", "We found no evidence that the expression or functions of other integrins were altered as a consequence of the \u03b23 deficiency, but we did observe elevated levels of VEGF receptor-2 (also called Flk-1) in \u03b23-null endothelial cells.", "These data indicate that \u03b1v\u03b23 and \u03b1v\u03b25 integrins are not essential for vascular development or pathological angiogenesis and highlight the need for further evaluation of the mechanisms of action of \u03b1v-integrin antagonists in anti-angiogenic therapeutics."], "structured": false}
{"doc_id": 22973574, "title": "A lineage of myeloid cells independent of Myb and hematopoietic stem cells.", "abstract": ["Macrophages and dendritic cells (DCs) are key components of cellular immunity and are thought to originate and renew from hematopoietic stem cells (HSCs).", "However, some macrophages develop in the embryo before the appearance of definitive HSCs.", "We thus reinvestigated macrophage development.", "We found that the transcription factor Myb was required for development of HSCs and all CD11b(high) monocytes and macrophages, but was dispensable for yolk sac (YS) macrophages and for the development of YS-derived F4/80(bright) macrophages in several tissues, such as liver Kupffer cells, epidermal Langerhans cells, and microglia--cell populations that all can persist in adult mice independently of HSCs.", "These results define a lineage of tissue macrophages that derive from the YS and are genetically distinct from HSC progeny."], "structured": false}
{"doc_id": 22975806, "title": "Heterogenic Loss of the Wild-Type BRCA Allele in Human Breast Tumorigenesis", "abstract": ["For individuals genetically predisposed to breast and ovarian cancer through inheritance of a mutant BRCA allele, somatic loss of heterozygosity affecting the wild-type allele is considered obligatory for cancer initiation and/or progression.", "However, several lines of evidence suggest that phenotypic effects may result from BRCA haploinsufficiency.", "Archival fixed and embedded tissue specimens from women with germ line deleterious mutations in BRCA1 or BRCA2 were identified.", "After pathologic review, focal areas of normal breast epithelium, atypical ductal hyperplasia, ductal carcinoma-in-situ, and invasive ductal carcinoma were identified from 14 BRCA1-linked and 9 BRCA2-linked breast cancers.", "Ten BRCA-linked prophylactic mastectomy specimens and 12 BRCA-linked invasive ovarian carcinomas were also studied.", "Laser catapult microdissection was used to isolate cells from the various pathologic lesions and corresponding normal tissues.", "After DNA isolation, real-time polymerase chain reaction assays were used to quantitate the proportion of wild-type to mutant BRCA alleles in each tissue sample.", "Quantitative allelotyping of microdissected cells revealed a high level of heterogeneity in loss of heterozygosity within and between preinvasive lesions and invasive cancers from BRCA1 and BRCA2 heterozygotes with breast cancer.", "In contrast, all BRCA-associated ovarian cancers displayed complete loss of the wild-type BRCA allele.", "These data suggest that loss of the wild-type BRCA allele is not required for BRCA-linked breast tumorigenesis, which would have important implications for the genetic mechanism of BRCA tumor suppression and for the clinical management of this patient population."], "structured": false}
{"doc_id": 22980205, "title": "Targeted therapies in urothelial carcinoma.", "abstract": ["PURPOSE OF REVIEW Greater understanding of the biology and genetics of urothelial carcinoma is helping to identify and define the role of molecules and pathways appropriate for novel-targeted therapies.", "Here, we review the targeted therapies that have been reported or are in ongoing urothelial carcinoma clinical trials, and highlight molecular targets characterized in preclinical and clinical studies.   ", "RECENT FINDINGS Trials in nonmuscle-invasive bladder cancer are evaluating the role of immunotherapy and agents targeting vascular endothelial growth factor (VEGF) or fibroblast growth factor receptor-3.", "In muscle-invasive bladder cancer, neoadjuvant studies have focused on combining VEGF agents with chemotherapy; adjuvant studies are testing vaccines and agents targeting the human epidermal growth factor receptor 2, p53, and Hsp27.", "In the first-line treatment of metastatic urothelial carcinoma, tubulin, cytotoxic T-lymphocyte antigen 4, Hsp27, and p53 are novel targets in clinical trials.", "The majority of targeted agents studied in urothelial carcinoma are in the second-line setting; new targets include CD105, polo-like kinase-1, phosphatidylinositide 3-kinases (PI3K), transforming growth factor \u03b2 receptor/activin receptor-like kinase \u03b2, estrogen receptor, and the hepatocyte growth factor receptor (HGFR or MET).   ", "SUMMARY Development of targeted therapies for urothelial carcinoma is still in early stages, consequently there have been no major therapeutic advances to date.", "However, greater understanding of urothelial carcinoma and solid tumor biology has resulted in a proliferation of clinical trials that could lead to significant advances in treatment strategies."], "structured": true}
{"doc_id": 22995164, "title": "H2S and HS\u2212 donor NaHS releases nitric oxide from nitrosothiols, metal nitrosyl complex, brain homogenate and murine L1210 leukaemia cells", "abstract": ["Nitrosoglutathione [(GSNO), 500 nmol/l] relaxed the norepinephrine precontracted rat aortic rings.", "The relaxation effect was pronouncedly enhanced by H2S- and HS\u2212-donor NaHS (30 \u03bcmol/l) at 7.5 pH but not at 6.3 pH. To study molecular mechanism of this effect, we investigated whether NaHS can release NO from NO donors.", "Using an electron paramagnetic resonance spectroscopy method of spin trap and by measuring the NO oxidation product, which is nitrite, by the Griess reaction, we report that NaHS released NO from nitrosothiols, namely from GSNO, S-nitroso-N-acetyl-dl-penicillamine (SNAP), from metal nitrosyl complex nitroprusside (SNP) and from rat brain homogenate and murine L1210 leukaemia cells.", "From the observation that the releasing effect was more pronounced at 8.0 pH than 6.0 pH, we suppose that HS\u2212, rather than H2S, is responsible for the NO-releasing effect.", "Since in mammals, H2S and HS\u2212 are produced endogenously, we assume that their effect to release NO from nitrosothiols and from metal nitrosyl complexes are responsible for some of their biological activities and that this mechanism may be involved in S-nitrosothiol-signalling reactions."], "structured": false}
{"doc_id": 22995579, "title": "Amitriptyline is effective in chronic but not in episodic tension-type headache: pathogenetic implications.", "abstract": ["The tricyclic antidepressant, amitriptyline, is an effective drug for the treatment of chronic tension-type headache and for other chronic pain syndromes, but it is also effective in the prophylaxis of an episodic type of headache such as migraine.", "However, its efficacy in episodic tension-type headache has not yet been clarified.", "We compared the efficacy of amitriptyline (25 mg/day) in 82 nondepressed patients with either chronic or episodic tension-type headache in an open-label study.", "Amitriptyline significantly reduced (P < 0.05) frequency and duration of headache as well as analgesic consumption in chronic, but not in episodic, tension-type headache.", "Further placebo-controlled trials, possibly with higher doses of amitriptyline, might confirm if the different pattern of response to amitriptyline can be explained in terms of different involvement of central nociception and of peripheral myofascial factors in the chronic and in the episodic forms of tension-type headache."], "structured": false}
{"doc_id": 22997657, "title": "Kruppel-like factor 2 is required for trafficking but not quiescence in postactivated T cells.", "abstract": ["The transcription factor Kruppel-like factor 2 (KLF2) was proposed to regulate genes involved in cell cycle entry and T cell trafficking; however, the physiological role of its expression in postactivated T cells is not well defined.", "Previous studies suggested that the cytokines IL-2 and IL-15 differentially regulate KLF2 re-expression in postactivation T cells and that these cytokines also influence effector versus memory T cell differentiation.", "Using conditional and inducible KLF2-knockout model systems, we tested the specific role of KLF2 expression in activated CD8(+) T cells cultured with these cytokines.", "KLF2 was required for effective transcription of sphingosine-1-phosphate receptor-1 (S1P(1)) and CD62L in postactivation T cells.", "However, although different cytokines dramatically altered the expression of cell-cycle-related genes, endogenous KLF2 had a minimal impact.", "Correspondingly, KLF2-deficient T cells showed dysregulated trafficking but not altered proliferative characteristics following in vivo responses to Ag.", "Thus, our data help to define KLF2-dependent and -independent aspects of activated CD8(+) T cell differentiation and argue against a physiological role in cell cycle regulation."], "structured": false}
{"doc_id": 23013317, "title": "Hypoalbuminemia in acute illness: is there a rationale for intervention? A meta-analysis of cohort studies and controlled trials.", "abstract": ["OBJECTIVE To determine whether hypoalbuminemia is an independent risk factor for poor outcome in the acutely ill, and to assess the potential of exogenous albumin administration for improving outcomes in hypoalbuminemic patients.   ", "SUMMARY BACKGROUND DATA Hypoalbuminemia is associated with poor outcomes in acutely ill patients, but whether this association is causal has remained unclear.", "Trials investigating albumin therapy to correct hypoalbuminemia have proven inconclusive.   \n", "METHODS A meta-analysis was conducted of 90 cohort studies with 291,433 total patients evaluating hypoalbuminemia as an outcome predictor by multivariate analysis and, separately, of nine prospective controlled trials with 535 total patients on correcting hypoalbuminemia.   \n", "RESULTS Hypoalbuminemia was a potent, dose-dependent independent predictor of poor outcome.", "Each 10-g/L decline in serum albumin concentration significantly raised the odds of mortality by 137%, morbidity by 89%, prolonged intensive care unit and hospital stay respectively by 28% and 71%, and increased resource utilization by 66%.", "The association between hypoalbuminemia and poor outcome appeared to be independent of both nutritional status and inflammation.", "Analysis of dose-dependency in controlled trials of albumin therapy suggested that complication rates may be reduced when the serum albumin level attained during albumin administration exceeds 30 g/L.   CONCLUSIONS Hypoalbuminemia is strongly associated with poor clinical outcomes.", "Further well-designed trials are needed to characterize the effects of albumin therapy in hypoalbuminemic patients.", "In the interim, there is no compelling basis to withhold albumin therapy if it is judged clinically appropriate."], "structured": true}
{"doc_id": 23017040, "title": "Methionine restriction decreases visceral fat mass and preserves insulin action in aging male Fischer 344 rats independent of energy restriction.", "abstract": ["Reduced dietary methionine intake (0.17% methionine, MR) and calorie restriction (CR) prolong lifespan in male Fischer 344 rats.", "Although the mechanisms are unclear, both regimens feature lower body weight and reductions in adiposity.", "Reduced fat deposition in CR is linked to preservation of insulin responsiveness in older animals.", "These studies examine the relationship between insulin responsiveness and visceral fat in MR and test whether, despite lower food intake observed in MR animals, decreased visceral fat accretion and preservation of insulin sensitivity is not secondary to CR.", "Accordingly, rats pair fed (pf) control diet (0.86% methinone, CF) to match the food intake of MR for 80 weeks exhibit insulin, glucose, and leptin levels similar to control-fed animals and comparable amounts of visceral fat.", "Conversely, MR rats show significantly reduced visceral fat compared to CF and PF with concomitant decreases in basal insulin, glucose, and leptin, and increased adiponectin and triiodothyronine.", "Daily energy expenditure in MR animals significantly exceeds that of both PF and CF.", "In a separate cohort, insulin responses of older MR animals as measured by oral glucose challenge are similar to young animals.", "Longitudinal assessments of MR and CF through 112 weeks of age reveal that MR prevents age-associated increases in serum lipids.", "By 16 weeks, MR animals show a 40% reduction in insulin-like growth factor-1 (IGF-1) that is sustained throughout life; CF IGF-1 levels decline much later, beginning at 112 weeks.", "Collectively, the results indicate that MR reduces visceral fat and preserves insulin activity in aging rats independent of energy restriction."], "structured": false}
{"doc_id": 23032247, "title": "Generation of T cell receptor\u2013retrogenic mice: improved retroviral-mediated stem cell gene transfer", "abstract": ["The use of retrogenic mice offers a rapid and flexible approach to T cell receptor (TCR)-transgenic mice.", "By transducing bone marrow progenitor cells with a retrovirus that encodes a given TCR-\u03b1/\u03b2 subunit, TCR-retrogenic mice can be generated in as few as 4\u20136 weeks, whereas conventional TCR transgenics can take 6 months or longer.", "In this updated protocol, we have increased the efficiency of the bone marrow transduction and bone marrow reconstitution compared with our previously published protocol.", "The main departure from the previous protocol is the implementation of spin transduction with the viral supernatant instead of coculture with the viral producer cell line.", "The changes in this protocol improve bone marrow viability, increase consistency of the bone marrow transduction and bone marrow engraftment, and they reduce the ratio of bone marrow donor mice to bone marrow recipients."], "structured": false}
{"doc_id": 23036207, "title": "Transient delivery of modified mRNA encoding TERT rapidly extends telomeres in human cells.", "abstract": ["Telomere extension has been proposed as a means to improve cell culture and tissue engineering and to treat disease.", "However, telomere extension by nonviral, nonintegrating methods remains inefficient.", "Here we report that delivery of modified mRNA encoding TERT to human fibroblasts and myoblasts increases telomerase activity transiently (24-48 h) and rapidly extends telomeres, after which telomeres resume shortening.", "Three successive transfections over a 4 d period extended telomeres up to 0.9 kb in a cell type-specific manner in fibroblasts and myoblasts and conferred an additional 28 \u00b1 1.5 and 3.4 \u00b1 0.4 population doublings (PDs), respectively.", "Proliferative capacity increased in a dose-dependent manner.", "The second and third transfections had less effect on proliferative capacity than the first, revealing a refractory period.", "However, the refractory period was transient as a later fourth transfection increased fibroblast proliferative capacity by an additional 15.2 \u00b1 1.1 PDs, similar to the first transfection.", "Overall, these treatments led to an increase in absolute cell number of more than 10(12)-fold.", "Notably, unlike immortalized cells, all treated cell populations eventually stopped increasing in number and expressed senescence markers to the same extent as untreated cells.", "This rapid method of extending telomeres and increasing cell proliferative capacity without risk of insertional mutagenesis should have broad utility in disease modeling, drug screening, and regenerative medicine."], "structured": false}
{"doc_id": 23052989, "title": "The death receptor CD95 activates adult neural stem cells for working memory formation and brain repair.", "abstract": ["Adult neurogenesis persists in the subventricular zone and the dentate gyrus and can be induced upon central nervous system injury.", "However, the final contribution of newborn neurons to neuronal networks is limited.", "Here we show that in neural stem cells, stimulation of the \"death receptor\" CD95 does not trigger apoptosis but unexpectedly leads to increased stem cell survival and neuronal specification.", "These effects are mediated via activation of the Src/PI3K/AKT/mTOR signaling pathway, ultimately leading to a global increase in protein translation.", "Induction of neurogenesis by CD95 was further confirmed in the ischemic CA1 region, in the naive dentate gyrus, and after forced expression of CD95L in the adult subventricular zone.", "Lack of hippocampal CD95 resulted in a reduction in neurogenesis and working memory deficits.", "Following global ischemia, CD95-mediated brain repair rescued behavioral impairment.", "Thus, we identify the CD95/CD95L system as an instructive signal for ongoing and injury-induced neurogenesis."], "structured": false}
{"doc_id": 23073816, "title": "Umbilical Cord Blood Therapy Potentiated with Erythropoietin for Children with Cerebral Palsy: A Double-blind, Randomized, Placebo-Controlled Trial", "abstract": ["Allogeneic umbilical cord blood (UCB) has therapeutic potential for cerebral palsy (CP).", "Concomitant administration of recombinant human erythropoietin (rhEPO) may boost the efficacy of UCB, as it has neurotrophic effects.", "The objectives of this study were to assess the safety and efficacy of allogeneic UCB potentiated with rhEPO in children with CP.", "Children with CP were randomly assigned to one of three parallel groups: the pUCB group, which received allogeneic UCB potentiated with rhEPO; the EPO group, which received rhEPO and placebo UCB; and the Control group, which received placebo UCB and placebo rhEPO.", "All participants received rehabilitation therapy.", "The main outcomes were changes in scores on the following measures during the 6 months treatment period: the gross motor performance measure (GMPM), gross motor function measure, and Bayley scales of infant development-II (BSID-II) Mental and Motor scales (18).", "F-fluorodeoxyglucose positron emission tomography (18F-FDG-PET/CT) and diffusion tensor images (DTI) were acquired at baseline and followed up to detect changes in the brain.", "In total, 96 subjects completed the study.", "Compared with the EPO (n = 33) and Control (n = 32) groups, the pUCB (n = 31) group had significantly higher scores on the GMPM and BSID-II Mental and Motor scales at 6 months.", "DTI revealed significant correlations between the GMPM increment and changes in fractional anisotropy in the pUCB group.", "18F-FDG-PET/CT showed differential activation and deactivation patterns between the three groups.", "The incidence of serious adverse events did not differ between groups.", "In conclusion, UCB treatment ameliorated motor and cognitive dysfunction in children with CP undergoing active rehabilitation, accompanied by structural and metabolic changes in the brain."], "structured": false}
{"doc_id": 23076291, "title": "Pituitary adenylate cyclase-activating polypeptide (PACAP(1-38)) enhances N-methyl-D-aspartate receptor function and brain-derived neurotrophic factor expression via RACK1.", "abstract": ["We recently identified a novel mechanism for modulation of the phosphorylation state and function of the N-methyl-d-aspartate (NMDA) receptor via the scaffolding protein RACK1.", "We found that RACK1 binds both the NR2B subunit of the NMDA receptor and the nonreceptor protein-tyrosine kinase, Fyn.", "RACK1 inhibits Fyn phosphorylation of NR2B and decreases NMDA receptor-mediated currents in CA1 hippocampal slices (Yaka, R., Thornton, C., Vagts, A. J., Phamluong, K., Bonci, A., and Ron, D. (2002) Proc.", "Natl.", "Acad.", "Sci.", "U. S. A. 99, 5710-5715).", "Here, we identified the signaling cascade by which RACK1 is released from the NMDA receptor complex and identified the consequences of the dissociation.", "We found that activation of the cAMP/protein kinase A pathway in hippocampal slices induced the release of RACK1 from NR2B and Fyn.", "This resulted in the induction of NR2B phosphorylation and the enhancement of NMDA receptor-mediated activity via Fyn.", "We identified the neuropeptide, pituitary adenylate cyclase activating polypeptide (PACAP(1-38)), as a ligand that induced phosphorylation of NR2B and enhanced NMDA receptor potentials.", "Finally, we found that activation of the cAMP/protein kinase A pathway induced the movement of RACK1 to the nuclear compartment in dissociated hippocampal neurons.", "Nuclear RACK1 in turn was found to regulate the expression of brain-derived neurotrophic factor induced by PACAP(1-38).", "Taken together our results suggest that activation of adenylate cyclase by PACAP(1-38) results in the release of RACK1 from the NMDA receptor and Fyn.", "This in turn leads to NMDA receptor phosphorylation, enhanced activity mediated by Fyn, and to the induction of brain-derived neurotrophic factor expression by RACK1."], "structured": false}
{"doc_id": 23078022, "title": "MUC1 oncoprotein activates the I\u03baB kinase \u03b2 complex and constitutive NF-\u03baB signalling", "abstract": ["Nuclear factor-\u03baB (NF-\u03baB) is constitutively activated in diverse human malignancies by mechanisms that are not understood.", "The MUC1 oncoprotein is aberrantly overexpressed by most human carcinomas and, similarly to NF-\u03baB, blocks apoptosis and induces transformation.", "This study demonstrates that overexpression of MUC1 in human carcinoma cells is associated with constitutive activation of NF-\u03baB p65.", "We show that MUC1 interacts with the high-molecular-weight I\u03baB kinase (IKK) complex in vivo and that the MUC1 cytoplasmic domain binds directly to IKK\u03b2 and IKK\u03b3.", "Interaction of MUC1 with both IKK\u03b2 and IKK\u03b3 is necessary for IKK\u03b2 activation, resulting in phosphorylation and degradation of I\u03baB\u03b1.", "Studies in non-malignant epithelial cells show that MUC1 is recruited to the TNF-R1 complex and interacts with IKK\u03b2\u2013IKK\u03b3 in response to TNF\u03b1 stimulation.", "TNF\u03b1-induced recruitment of MUC1 is dependent on TRADD and TRAF2, but not the death-domain kinase RIP1.", "In addition, MUC1-mediated activation of IKK\u03b2 is dependent on TAK1 and TAB2.", "These findings indicate that MUC1 is important for physiological activation of IKK\u03b2 and that overexpression of MUC1, as found in human cancers, confers sustained induction of the IKK\u03b2\u2013NF-\u03baB p65 pathway."], "structured": false}
{"doc_id": 23100220, "title": "Lipoxins: novel series of biologically active compounds formed from arachidonic acid in human leukocytes.", "abstract": ["Trihydroxytetraenes, a novel series of oxygenated derivatives formed from arachidonic acid in human leukocytes, were recently isolated [Serhan, C. N., Hamberg, M. & Samuelsson, B. (1984) Biochem.", "Biophys.", "Res.", "Commun.", "118, 943-949].", "The structure of the major compound was established--i.e., 5,6,15L-trihydroxy-7,9,11,13-icosatetraenoic acid.", "The present study reports the structure of a second member of the trihydroxytetraene series of compounds--i.e., 5D,14,15L-trihydroxy-6,8,10,12-icosatetraenoic acid.", "When added to human neutrophils, 5,6,15L-trihydroxy-7,9,11,13-icosatetraenoic acid stimulated superoxide anion generation and degranulation at submicromolar concentrations without provoking a substantial aggregation response.", "With respect to superoxide anion generation, 5,6,15L-trihydroxy-7,9,11,13-icosatetraenoic acid proved to be as potent as leukotriene B4.", "In contrast, the compound was approximately 2 orders of magnitude less potent than either leukotriene B4 or fMet-Leu-Phe at provoking degranulation.", "The results indicate that interaction(s) between the 5- and 15-lipoxygenase pathways of human leukocytes leads to formation of a new series of oxygenated derivatives of arachidonic acid that may be involved in regulating specific cellular responses.", "The trivial names lipoxin A (5,6,15L-trihydroxy-7,9,11,13-icosatetraenoic acid) and lipoxin B (5D,14,15L-trihydroxy-6,8,10,12-icosatetraenoic acid) are proposed for the new compounds."], "structured": false}
{"doc_id": 23100962, "title": "Nitric oxide synthase generates superoxide and nitric oxide in arginine-depleted cells leading to peroxynitrite-mediated cellular injury.", "abstract": ["Besides synthesizing nitric oxide (NO), purified neuronal NO synthase (nNOS) can produce superoxide (.O2-) at lower L-Arg concentrations.", "By using electron paramagnetic resonance spin-trapping techniques, we monitored NO and .O2- formation in nNOS-transfected human kidney 293 cells.", "In control transfected cells, the Ca2+ ionophore A23187 triggered NO generation but no .O2- was seen.", "With cells in L-Arg-free medium, we observed .O2- formation that increased as the cytosolic L-Arg levels decreased, while NO generation declined.", ".O2- formation was virtually abolished by the specific NOS blocker, N-nitro-L-arginine methyl ester (L-NAME).", "Nitrotyrosine, a specific nitration product of peroxynitrite, accumulated in L-Arg-depleted cells but not in control cells.", "Activation by A23187 was cytotoxic to L-Arg-depleted, but not to control cells, with marked lactate dehydrogenase release.", "The cytotoxicity was largely prevented by either superoxide dismutase or L-NAME.", "Thus, with reduced L-Arg availability NOS elicits cytotoxicity by generating .O2- and NO that interact to form the potent oxidant peroxynitrite.", "Regulating arginine levels may provide a therapeutic approach to disorders involving .O2-/NO-mediated cellular injury."], "structured": false}
{"doc_id": 23117378, "title": "Sudden infant death syndrome and unclassified sudden infant deaths: a definitional and diagnostic approach.", "abstract": ["The definition of sudden infant death syndrome (SIDS) originally appeared in 1969 and was modified 2 decades later.", "During the following 15 years, an enormous amount of additional information has emerged, justifying additional refinement of the definition of SIDS to incorporate epidemiologic features, risk factors, pathologic features, and ancillary test findings.", "An expert panel of pediatric and forensic pathologists and pediatricians considered these issues and developed a new general definition of SIDS for administrative and vital statistics purposes.", "The new definition was then stratified to facilitate research into sudden infant death.", "Another category, defined as unclassified sudden infant deaths, was introduced for cases that do not meet the criteria for a diagnosis of SIDS and for which alternative diagnoses of natural or unnatural conditions were equivocal.", "It is anticipated that these new definitions will be modified in the future to accommodate new understanding of SIDS and sudden infant death."], "structured": false}
{"doc_id": 23117928, "title": "Inter-viral conflicts that exploit host CRISPR immune systems of Sulfolobus.", "abstract": ["Infection of Sulfolobus islandicus REY15A with mixtures of different Sulfolobus viruses, including STSV2, did not induce spacer acquisition by the host CRISPR immune system.", "However, coinfection with the tailed fusiform viruses SMV1 and STSV2 generated hyperactive spacer acquisition in both CRISPR loci, exclusively from STSV2, with the resultant loss of STSV2 but not SMV1.", "SMV1 was shown to activate adaptation while itself being resistant to CRISPR-mediated adaptation and DNA interference.", "Exceptionally, a single clone S-1 isolated from an SMV1 + STSV2-infected culture, that carried STSV2-specific spacers and had lost STSV2 but not SMV1, acquired spacers from SMV1.", "This effect was also reproducible on reinfecting wild-type host cells with a variant SMV1 isolated from the S-1 culture.", "The SMV1 variant lacked a virion protein ORF114 that was shown to bind DNA.", "This study also provided evidence for: (i) limits on the maximum sizes of CRISPR loci; (ii) spacer uptake strongly retarding growth of infected cultures; (iii) protospacer selection being essentially random and non-directional, and (iv) the reversible uptake of spacers from STSV2 and SMV1.", "A hypothesis is presented to explain the interactive conflicts between SMV1 and the host CRISPR immune system."], "structured": false}
{"doc_id": 23122306, "title": "Lung Carcinogenesis by Diesel Exhaust Particles and the Carcinogenic Mechanism Via Active Oxygens.", "abstract": ["In an experiment to clarify the involvement of oxygen radicals in lung carcinogenesis induced by diesel exhaust particles (DEP), we found that there is a strong relation between lung tumor response and formation of 8-hydroxydeoxyguanosine (8-OHdG) in lung DNA of mice administered DEP by repeated intratracheal instillation.", "Repeated intratracheal instillation of DEP also induced the activity of cytochrome P-450 reductase in the lungs as a representative enzyme of superoxide generation, and two types of nitric oxide (NO) synthase, cNOS and iNOS, in the lungs.", "On the other hand, activities of CuZn-superoxide dismutase (SOD) and Mn-SOD antioxidant enzymes were depressed by the instillation of DEP.", "These results suggest that generation of superoxide, hydroxyI radical, and nitric oxide are increased in epithelial cells in airways, and that the increased superoxide and nitric oxide react very easily to produce peroxynitrite (ONOO(-)).", "The peroxynitrite also produce hydroxyI radical.", "The hydroxyl radical may play an important role in carcinogenesis by DEP."], "structured": false}
{"doc_id": 23124332, "title": "Prion-induced amyloid heart disease with high blood infectivity in transgenic mice.", "abstract": ["We investigated extraneural manifestations in scrapie-infected transgenic mice expressing prion protein lacking the glycophosphatydylinositol membrane anchor.", "In the brain, blood, and heart, both abnormal protease-resistant prion protein (PrPres) and prion infectivity were readily detected by immunoblot and by inoculation into nontransgenic recipients.", "The titer of infectious scrapie in blood plasma exceeded 10(7) 50% infectious doses per milliliter.", "The hearts of these transgenic mice contained PrPres-positive amyloid deposits that led to myocardial stiffness and cardiac disease."], "structured": false}
{"doc_id": 23126677, "title": "Circulating plasma microRNAs as a screening method for detection of colorectal adenomas.", "abstract": ["BACKGROUND MicroRNAs (miRNAs) are small non-coding RNA molecules.", "Reduced or increased levels of specific miRNAs are observed in colon and other cancers, supporting their role in carcinogenesis.", "Detection of colorectal polyps is the cornerstone of the Bowel Cancer Screening Programme in the UK.", "However, uptake of screening nationally remains under 60%.", "We aimed to see whether circulating plasma miRNAs can be used to screen for patients with colorectal polyps, adenomas, or both.   \n", "METHODS Blood samples were taken from patients from the Bowel Cancer Screening Programme (asymptomatic but faecal occult blood testing [FOBt] positive).", "Plasma RNA was extracted, target miRNAs (19a, 98, 146b, 186, 191, 222*, 331-5p, 452, 625, 664, 1247) were identified on pooled case miRNA assay cards, and miRNA fraction was quantified by quantitative RT-PCR assay.", "Results were compared with endoscopy reports and with histology of any polyps identified and removed.", "Analysis was done with Excel (2011) and SPSS (version 20) software.   \n", "FINDINGS 210 patients were included (117 with polyps, 12 with cancer, 81 healthy controls [FOBt positive]).", "The miRNA panel showed significant differences in expression (on t testing) for patients compared with controls for those with polyps, cancer, or both (miR-19a, p=0\u00b70184; miR-98, p=0\u00b70206; miR-146b, p=0\u00b70029; miR-186, p=0\u00b70006; miR-62,5 p=0\u00b70008), polyps (miR-19a, p=0\u00b70233; miR-98, p=0\u00b70224; miR-146b, p=0\u00b7003; miR-186, p=0\u00b70004; miR-625, p=0\u00b7001), adenomas (miR-19a, p=0\u00b70339; miR-98, p=0\u00b70266; miR-146b, p=0\u00b70045; miR-186, p=0\u00b70008; miR-625, p=0\u00b70049), multiple adenomas (both sides of colon; miR-146b, p=0\u00b70194; miR-186, p=0\u00b70226; miR-625, p=0\u00b70013), and right-sided adenomas (miR-98, p=0\u00b7031; miR-146b, p=0\u00b70076; miR-186, p=0\u00b70041; miR-331-5p, p=0\u00b70142; miR-625, p=0\u00b70049).", "Receiver operating characteristic analysis showed sensitivity of 60% or more, and specificity of 86% or more for men with polyps, men with adenomas, all patients with haemorrhoids or diverticulosis and polyps, and all patients with haemorrhoids or diverticulosis and adenomas.   \n", "INTERPRETATION The target miRNAs that we identified showed significant differences in expression levels for patients with polyps and patients with adenomas from controls.", "Use of this panel has potential as a screening test.   \n", "FUNDING Bowel Disease Research Foundation."], "structured": true}
{"doc_id": 23136735, "title": "Short term persistence of human papillomavirus and risk of cervical precancer and cancer: population based cohort study", "abstract": ["OBJECTIVE To evaluate the cumulative incidence of cervical intraepithelial neoplasia II or worse (grade II+) or cervical intraepithelial neoplasia grade III+ after short term persistence of prevalently detected carcinogenic human papillomavirus (HPV).   \n", "DESIGN Population based cohort study.   \n", "SETTING Guanacaste, Costa Rica.   \n", "PARTICIPANTS 2282 sexually active women actively followed after enrolment.   \n", "MAIN OUTCOME MEASURES Primary end points: three year and five year cumulative incidence of histologically confirmed cervical intraepithelial neoplasia grade II+ (n=70).", "Cervical specimens collected at each visit tested for more than 40 HPV genotypes.", "HPV 16, 18, 26, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66, 68, 73, and 82 were considered the primary carcinogenic genotypes.   \n", "RESULTS Women who tested positive for a carcinogenic HPV at enrolment and after about one year (9-21 months) (positive/positive) had a three year cumulative incidence of cervical intraepithelial neoplasia grade II+ of 17.0% (95% confidence interval 12.1% to 22.0%).", "Those who tested negative/positive (3.4%, 0.1% to 6.8%), positive/negative (1.2%, -0.2% to 2.5%), and negative/negative (0.5%, 0.1% to 0.9%) were at a significantly lower risk.", "There was little difference in the cumulative incidence of cervical intraepithelial neoplasia grade II+ between testing positive twice for any carcinogenic HPV genotype (same genotype or different genotypes) v testing positive twice for the same carcinogenic genotype (17.0% v 21.3%, respectively).", "Short term persistence of HPV 16 strongly predicted cervical intraepithelial neoplasia grade II+, with a three year cumulative incidence of 40.8% (26.4% to 55.1%).", "Similar patterns were observed for the five year cumulative incidence of grade II+ and for three year and five year cumulative incidence of grade III+.   \n", "CONCLUSIONS Short term persistence of a prevalently detected carcinogenic HPV infection, especially HPV 16, strongly predicts a subsequent diagnosis of cervical intraepithelial neoplasia II+ over the next few years."], "structured": true}
{"doc_id": 23141360, "title": "Nature and anisotropy of cortical forces orienting Drosophila tissue morphogenesis", "abstract": ["The morphogenesis of developing embryos and organs relies on the ability of cells to remodel their contacts with neighbouring cells.", "Using quantitative modelling and laser nano-dissection, we probed the mechanics of a morphogenetic process, the elongation of Drosophila melanogaster embryos, which results from polarized cell neighbour exchanges.", "We show that anisotropy of cortical tension at apical cell junctions is sufficient to drive tissue elongation.", "We estimated its value through comparisons between in silico and in vivo data using various tissue descriptors.", "Nano-dissection of the actomyosin network indicates that tension is anisotropically distributed and depends on myosin II accumulation.", "Junction relaxation after nano-dissection also suggests that cortical elastic forces are dominant in this process.", "Interestingly, fluctuations in vertex position (points where three or more cells meet) facilitate neighbour exchanges.", "We delineate the contribution of subcellular tensile activity polarizing junction remodelling, and the permissive role of vertex fluctuations during tissue elongation."], "structured": false}
{"doc_id": 23148978, "title": "The influence of some metabolic inhibitors on phagocytic activity of mouse macrophages in vitro.", "abstract": ["The action of different metabolic inhibitors on phagocytosis by macrophages from mouse peritoneal exudate cultured in vitro was studied.", "The following metabolic inhibitors were tested: sodium iodoacetate, sodium fluoride, sodium fluoroacetate, sodium malonate, 2-4-dinitrophenol, sodium azide, ouabain and cycloheximide, all at the concentration of 10(-3) M. Iodoacetate caused a strong inhibitory effect on phagocytosis; this observation confirms that glycolysis is the main source of energy for the phagocytic process.", "On the contrary, fluoride, although it is an effective inhibitor of glycolysis, did not exert any effect.", "This difference may be explained by the fact that sodium fluoride blocks anaerobic glycolysis only in vitro at an unphysiological temperature (0 degrees C).", "Fluoroacetate and malonate, two compounds which interfere with the Krebs cycle, did not inhibit phagocytosis, but it is known that the Krebs cycle activity is poorly developed in the macrophagic cells.", "Sodium azide and 2-4-dinitrophenol, two inhibitors of oxidative phosphorylation, showed an effect on phagocytosis only after 3 h of contact with the cell cultures.", "Ouabain blocks Na+ and K+ transport across the plasma membrane and, probably, it inhibited phagocytosis by interfering with the movements of the cell membrane.", "Finally, the mode of action of cycloheximide on phagocytosis is uncertain.", "This compound inhibits the protein synthesis and, perhaps, it can act by preventing the renewal of the cell membrane."], "structured": false}
{"doc_id": 23160444, "title": "Two-tiered coupling between flowing actin and immobilized N-cadherin/catenin complexes in neuronal growth cones.", "abstract": ["Neuronal growth cones move forward by dynamically connecting actin-based motility to substrate adhesion, but the mechanisms at the individual molecular level remain unclear.", "We cultured primary neurons on N-cadherin-coated micropatterned substrates, and imaged adhesion and cytoskeletal proteins at the ventral surface of growth cones using single particle tracking combined to photoactivated localization microscopy (sptPALM).", "We demonstrate transient interactions in the second time scale between flowing actin filaments and immobilized N-cadherin/catenin complexes, translating into a local reduction of the actin retrograde flow.", "Normal actin flow on micropatterns was rescued by expression of a dominant negative N-cadherin construct competing for the coupling between actin and endogenous N-cadherin.", "Fluorescence recovery after photobleaching (FRAP) experiments confirmed the differential kinetics of actin and N-cadherin, and further revealed a 20% actin population confined at N-cadherin micropatterns, contributing to local actin accumulation.", "Computer simulations with relevant kinetic parameters modeled N-cadherin and actin turnover well, validating this mechanism.", "Such a combination of short- and long-lived interactions between the motile actin network and spatially restricted adhesive complexes represents a two-tiered clutch mechanism likely to sustain dynamic environment sensing and provide the force necessary for growth cone migration."], "structured": false}
{"doc_id": 23180075, "title": "Cloning of factors related to HIV-inducible LBP proteins that regulate steroidogenic factor-1-independent human placental transcription of the cholesterol side-chain cleavage enzyme, P450scc.", "abstract": ["The cholesterol side-chain cleavage enzyme, cytochrome P450scc, initiates the biosynthesis of all steroid hormones.", "Adrenal and gonadal strategies for P450scc gene transcription are essentially identical and depend on the orphan nuclear receptor steroidogenic factor-1, but the placental strategy for transcription of P450scc employs cis-acting elements different from those used in the adrenal strategy and is independent of steroidogenic factor-1.", "Because placental expression of P450scc is required for human pregnancy, we sought factors that bind to the -155/-131 region of the human P450scc promoter, which participates in its placental but not adrenal or gonadal transcription.", "A yeast one-hybrid screen of 2.4 x 10(6) cDNA clones from human placental JEG-3 cells yielded two unique clones; one is the previously described transcription factor LBP-1b, which is induced by HIV, type I infection of lymphocytes, and the other is a new factor, termed LBP-9, that shares 83% amino acid sequence identity with LBP-1b.", "When expressed in transfected yeast, both factors bound specifically to the -155/-131 DNA; antisera to LBP proteins supershifted the LBP-9.DNA complex and inhibited formation of the LBP-1b.", "DNA complex.", "Reverse transcriptase-polymerase chain reaction detected LBP-1b in human placental JEG-3, adrenal NCI-H295A, liver HepG2, cervical HeLa, and monkey kidney COS-1 cells, but LBP-9 was detected only in JEG-3 cells.", "When the -155/-131 fragment was linked to a minimal promoter, co-expression of LBP-1b increased transcription 21-fold in a dose-dependent fashion, but addition of LBP-9 suppressed the stimulatory effect of LBP-1b.", "The roles of LBP transcription factors in normal human physiology have been unclear.", "Their modulation of placental but not adrenal P450scc transcription underscores the distinctiveness of placental strategies for steroidogenic enzyme gene transcription."], "structured": false}
{"doc_id": 23190392, "title": "Functional reprogramming of polyploidization in megakaryocytes.", "abstract": ["Polyploidization is a natural process that frequently accompanies differentiation; its deregulation is linked to genomic instability and cancer.", "Despite its relevance, why cells select different polyploidization mechanisms is unknown.", "Here we report a systematic genetic analysis of endomitosis, a process in which megakaryocytes become polyploid by entering mitosis but aborting anaphase.", "Whereas ablation of the APC/C cofactor Cdc20 results in mitotic arrest and severe thrombocytopenia, lack of the kinases Aurora-B, Cdk1, or Cdk2 does not affect megakaryocyte polyploidization or platelet levels.", "Ablation of Cdk1 forces a switch to endocycles without mitosis, whereas polyploidization in the absence of Cdk1 and Cdk2 occurs in the presence of aberrant re-replication events.", "Importantly, ablation of these kinases rescues the defects in Cdc20 null megakaryocytes.", "These findings suggest that endomitosis can be functionally replaced by alternative polyploidization mechanisms in vivo and provide the cellular basis for therapeutic approaches aimed to discriminate mitotic and polyploid cells."], "structured": false}
{"doc_id": 23195302, "title": "Histone methyltransferase activity associated with a human multiprotein complex containing the Enhancer of Zeste protein.", "abstract": ["Enhancer of Zeste [E(z)] is a Polycomb-group transcriptional repressor and one of the founding members of the family of SET domain-containing proteins.", "Several SET-domain proteins possess intrinsic histone methyltransferase (HMT) activity.", "However, recombinant E(z) protein was found to be inactive in a HMT assay.", "Here we report the isolation of a multiprotein E(z) complex that contains extra sex combs, suppressor of zeste-12 [Su(z)12], and the histone binding proteins RbAp46/RbAp48.", "This complex, which we termed Polycomb repressive complex (PRC) 2, possesses HMT activity with specificity for Lys 9 (K9) and Lys 27 (K27) of histone H3.", "The HMT activity of PRC2 is dependent on an intact SET domain in the E(z) protein.", "We hypothesize that transcriptional repression by the E(z) protein involves methylation-dependent recruitment of PRC1.", "The presence of Su(z)12, a strong suppressor of position effect variegation, in PRC2 suggests that PRC2 may play a widespread role in heterochromatin-mediated silencing."], "structured": false}
{"doc_id": 23195674, "title": "Simvastatin reduces platelet-endocardium adhesion in atrial fibrillation.", "abstract": ["OBJECTIVES To evaluate the relationship between CD40/CD40L system and increased thrombogenesis in AF, and to test the effects of simvastatin treatment.   \n", "METHODS In vitro study using human tissue, University Hospital (tertiary referral center).", "Experiments on right atrial segments obtained before the onset of cardiopulmonary bypass were done in either presence or absence of 5 microM simvastatin.", "Two groups of patients in either chronic atrial fibrillation or sinus rhythm at the time of cardiac surgery.", "The endocardial expression of CD40, the release of CD40L, and adhesion of platelets to endocardium.", "Additionally, the thickness of platelet aggregates and the platelet distribution on the endocardium were also evaluated.   \n", "RESULTS Atrial fibrillation was associated with a significant increase of endocardial CD40 expression (293.1+/-55.1 pg/ml vs. 230.9+/-53.3 pg/ml, p<0.01), and platelet-endocardial adhesion compared with sinus rhythm atria (10.8+/-2.2 vs. 5.2+/-1.3 platelet CD41 AU p<0.01).", "At immunofluorescence about 62% of fibrillating endocardium was covered by platelets, compared with 12% of not sinus rhythm atria.", "Addition of simvastatin significantly reduced CD40 expression as well as platelet adhesion to fibrillating atria; its efficacy was not reversed by the addition of mevalonic acid.   \n", "CONCLUSIONS Chronic atrial fibrillation acutely upregulates CD40 expression as well as platelet adhesion to the endocardium.", "Simvastatin is effective in modulating this expression, thus it may potentially contribute to reduce the risk of intra-atrial thrombus formation."], "structured": true}
{"doc_id": 23203102, "title": "Transmission of sporadic Creutzfeldt-Jakob disease by blood transfusion: risk factor or possible biases.", "abstract": ["BACKGROUND The occurrence of transfusion transmissions of variant Creutzfeldt-Jakob disease (CJD) cases has reawakened attention to the possible similar risk posed by other forms of CJD.   ", "STUDY DESIGN AND METHODS CJD with a definite or probable diagnosis (sporadic CJD, n = 741; genetic CJD, n = 175) and no-CJD patients with definite alternative diagnosis (n = 482) with available blood transfusion history were included in the study.", "The risk of exposure to blood transfusion occurring more than 10 years before disease onset and for some possible confounding factors was evaluated by calculating crude odds ratios (ORs).", "Variables with significant ORs in univariate analyses were included in multivariate logistic regression analyses.   \n", "RESULTS In the univariate model, blood transfusion occurring more than 10 years before clinical onset is 4.1-fold more frequent in sporadic CJD than in other neurologic disorders.", "This significance is lost when the 10-year lag time was not considered.", "Multivariate analyses show that the risk of developing sporadic CJD after transfusion increases (OR, 5.05) after adjusting for possible confounding factors.", "Analysis conducted on patients with genetic CJD did not reveal any significant risk factor associated with transfusion.   \n", "CONCLUSION This is the first case-control study showing a significant risk of transfusion occurring more than 10 years before clinical onset in sporadic CJD patients.", "It remains questionable whether the significance of these data is biologically plausible or the consequence of biases in the design of the study, but they counterbalance previous epidemiologic negative reports that might have overestimated the assessment of blood safety in sporadic CJD."], "structured": true}
{"doc_id": 23206239, "title": "Advantages and pitfalls of fructosamine and glycated albumin in the diagnosis and treatment of diabetes.", "abstract": ["The efficient diagnosis and accurate monitoring of diabetic patients are cornerstones for reducing the risk of diabetic complications.", "The current diagnostic and prognostic strategies in diabetes are mainly based on two tests, plasma (or capillary) glucose and glycated hemoglobin (HbA1c).", "Nevertheless, these measures are not foolproof, and their clinical usefulness is biased by a number of clinical and analytical factors.", "The introduction of other indices of glucose homeostasis in clinical practice such as fructosamine and glycated albumin (GA) may be regarded as an attractive alternative, especially in patients in whom the measurement of HbA1c may be biased or even unreliable.", "These include patients with rapid changes of glucose homeostasis and larger glycemic excursions, and patients with red blood cell disorders and renal disease.", "According to available evidence, the overall diagnostic efficiency of GA seems superior to that of fructosamine throughout a broad range of clinical settings.", "The current method for measuring GA is also better standardized and less vulnerable to preanalytical variables than those used for assessing fructosamine.", "Additional advantages of GA over HbA1c are represented by lower reagent cost and being able to automate the GA analysis on many conventional laboratory instruments.", "Although further studies are needed to definitely establish that GA can complement or even replace conventional measures of glycemic control such as HbA1c, GA may help the clinical management of patients with diabetes in whom HbA1c values might be unreliable."], "structured": false}
{"doc_id": 23208167, "title": "Catalytic-Independent Functions of PARP-1 Determine Sox2 Pioneer Activity at Intractable Genomic Loci.", "abstract": ["Pioneer transcription factors (TFs) function as genomic first responders, binding to inaccessible regions of chromatin to promote enhancer formation.", "The mechanism by which pioneer TFs gain access to chromatin remains an important unanswered question.", "Here we show that PARP-1, a nucleosome-binding protein, cooperates with intrinsic properties of the pioneer TF Sox2 to facilitate its binding to intractable genomic loci in embryonic stem cells.", "These actions of PARP-1 occur independently of its poly(ADP-ribosyl) transferase activity.", "PARP-1-dependent Sox2-binding sites reside in euchromatic regions of the genome with relatively high nucleosome occupancy and low co-occupancy by other transcription factors.", "PARP-1 stabilizes Sox2 binding to nucleosomes at suboptimal sites through cooperative interactions on DNA.", "Our results define intrinsic and extrinsic features that determine Sox2 pioneer activity.", "The conditional pioneer activity observed with Sox2 at a subset of binding sites may be a key feature of other pioneer TFs operating at intractable genomic loci."], "structured": false}
{"doc_id": 23237995, "title": "Steroid regulation of C. elegans diapause, developmental timing, and longevity.", "abstract": ["Hormones play a critical role in driving major stage transitions and developmental timing events in many species.", "In the nematode C. elegans the steroid hormone receptor, DAF-12, works at the confluence of pathways regulating developmental timing, stage specification, and longevity.", "DAF-12 couples environmental and physiologic signals to life history regulation, and it is embedded in a rich architecture governing diverse processes.", "Here, we highlight the molecular insights, extraordinary circuitry, and signaling pathways governing life stage transitions in the worm and how they have yielded fundamental insights into steroid regulation of biological time."], "structured": false}
{"doc_id": 23244529, "title": "A core subunit of Polycomb repressive complex 1 is broadly conserved in function but not primary sequence.", "abstract": ["Polycomb Group (PcG) proteins mediate heritable gene silencing by modifying chromatin structure.", "An essential PcG complex, PRC1, compacts chromatin and inhibits chromatin remodeling.", "In Drosophila melanogaster, the intrinsically disordered C-terminal region of PSC (PSC-CTR) mediates these noncovalent effects on chromatin, and is essential for viability.", "Because the PSC-CTR sequence is poorly conserved, the significance of its effects on chromatin outside of Drosophila was unclear.", "The absence of folded domains also made it difficult to understand how the sequence of PSC-CTR encodes its function.", "To determine the mechanistic basis and extent of conservation of PSC-CTR activity, we identified 17 metazoan PSC-CTRs spanning chordates to arthropods, and examined their sequence features and biochemical properties.", "PSC-CTR sequences are poorly conserved, but are all highly charged and structurally disordered.", "We show that active PSC-CTRs--which bind DNA tightly and inhibit chromatin remodeling efficiently--are distinguished from less active ones by the absence of extended negatively charged stretches.", "PSC-CTR activity can be increased by dispersing its contiguous negative charge, confirming the importance of this property.", "Using the sequence properties defined as important for PSC-CTR activity, we predicted the presence of active PSC-CTRs in additional diverse genomes.", "Our analysis reveals broad conservation of PSC-CTR activity across metazoans.", "This conclusion could not have been determined from sequence alignments.", "We further find that plants that lack active PSC-CTRs instead possess a functionally analogous PcG protein, EMF1.", "Thus, our study suggests that a disordered domain with dispersed negative charges underlies PRC1 activity, and is conserved across metazoans and plants."], "structured": false}
{"doc_id": 23245050, "title": "Dietary status of trained female cyclists.", "abstract": ["Dietary status was evaluated in eight highly trained female cyclists.", "Each cyclist kept a 3-day weighed food record.", "Diets were analyzed for nutrient content using a computerized software package.", "Blood was also obtained and evaluated for hemoglobin, hematocrit, and albumin.", "For an athletic group, the cyclists' diets were found to be low in energy (85% RDA) and carbohydrate (4.4 gm/kg body weight per day).", "Mean daily dietary intakes were well below the RDAs for folacin (76% RDA), magnesium (81%), iron (59%), and zinc (48%).", "In addition, more than one-third of the cyclists failed to consume 67% of the RDA for the following micronutrients: pyridoxine, folacin, cobalamin, vitamin E, magnesium, iron, and zinc.", "Hemoglobin (135 gm/L), hematocrit (0.39), and albumin (45 gm/L) values were all normal, although most hemoglobin values were in the lower 50% of normal range.", "Foods such as meats, poultry, fish, beans, peas, and nuts were low or absent from the diets of most athletes.", "Dietary quality in this group of female cyclists could have been greatly improved with the addition of more of those foods.", "These athletes could benefit from nutrition education and diet counseling."], "structured": false}
{"doc_id": 23253955, "title": "Regulation of Pax-3 expression in the dermomyotome and its role in muscle development.", "abstract": ["The segmented mesoderm in vertebrates gives rise to a variety of cell types in the embryo including the axial skeleton and muscle.", "A number of transcription factors containing a paired domain (Pax proteins) are expressed in the segmented mesoderm during embryogenesis.", "These include Pax-3 and a closely related gene, Pax-7, both of which are expressed in the segmental plate and in the dermomyotome.", "In this paper, we show that signals from the notochord pattern the expression of Pax-3, Pax-7 and Pax-9 in somites and the subsequent differentiation of cell types that arise from the somitic mesoderm.", "We directly assess the role of the Pax-3 gene in the differentiation of cell types derived from the dermomyotome by analyzing the development of muscle in splotch mouse embryos which lack a functional Pax-3 gene.", "A population of Pax-3-expressing cells derived from the dermomyotome that normally migrate into the limb are absent in homozygous splotch embryos and, as a result, limb muscles are lost.", "No abnormalities were detected in the trunk musculature of splotch embryos indicating that Pax-3 is necessary for the development of the limb but not trunk muscle."], "structured": false}
{"doc_id": 23260700, "title": "Angiopoietin 2 is a partial agonist/antagonist of Tie2 signaling in the endothelium.", "abstract": ["Angiopoietin 2 (Ang2) was originally shown to be a competitive antagonist for Ang1 of the receptor tyrosine kinase Tie2 in endothelial cells (ECs).", "Since then, reports have conflicted on whether Ang2 is an agonist or antagonist of Tie2.", "Here we show that Ang2 functions as an agonist when Ang1 is absent but as a dose-dependent antagonist when Ang1 is present.", "Exogenous Ang2 activates Tie2 and the promigratory, prosurvival PI3K/Akt pathway in ECs but with less potency and lower affinity than exogenous Ang1.", "ECs produce Ang2 but not Ang1.", "This endogenous Ang2 maintains Tie2, phosphatidylinositol 3-kinase, and Akt activities, and it promotes EC survival, migration, and tube formation.", "However, when ECs are stimulated with Ang1 and Ang2, Ang2 dose-dependently inhibits Ang1-induced Tie2 phosphorylation, Akt activation, and EC survival.", "We conclude that Ang2 is both an agonist and an antagonist of Tie2.", "Although Ang2 is a weaker agonist than Ang1, endogenous Ang2 maintains a level of Tie2 activation that is critical to a spectrum of EC functions.", "These findings may reconcile disparate reports of Ang2's effect on Tie2, impact our understanding of endogenous receptor tyrosine kinase signal transduction mechanisms, and affect how Ang2 and Tie2 are targeted under conditions such as sepsis and cancer."], "structured": false}
{"doc_id": 23262027, "title": "Bacteremia caused by a strain of Desulfovibrio related to the provisionally named Desulfovibrio fairfieldensis.", "abstract": ["Eight isolates of Desulfovibrio spp. have been obtained over 5 years from abdominal or brain abscesses or blood.", "Seven isolates were part of a mixed flora [corrected].", "One strain was isolated in pure culture from the blood of a patient with peritonitis of appendicular origin.", "According to the 16S rRNA gene sequences, this strain was close to Desulfovibrio fairfieldensis.", "The present report describes the fourth isolate of this recently described species to be isolated in pure culture or as a predominant part of the flora and to be associated with infectious processes.", "Thus, D. fairfieldensis may possess a higher pathogenic potential than other Desulfovibrio species."], "structured": false}
{"doc_id": 23267371, "title": "Vitamin D: The \"sunshine\" vitamin.", "abstract": ["Vitamin D insufficiency affects almost 50% of the population worldwide.", "An estimated 1 billion people worldwide, across all ethnicities and age groups, have a vitamin D deficiency (VDD).", "This pandemic of hypovitaminosis D can mainly be attributed to lifestyle (for example, reduced outdoor activities) and environmental (for example, air pollution) factors that reduce exposure to sunlight, which is required for ultraviolet-B (UVB)-induced vitamin D production in the skin.", "High prevalence of vitamin D insufficiency is a particularly important public health issue because hypovitaminosis D is an independent risk factor for total mortality in the general population.", "Current studies suggest that we may need more vitamin D than presently recommended to prevent chronic disease.", "As the number of people with VDD continues to increase, the importance of this hormone in overall health and the prevention of chronic diseases are at the forefront of research.", "VDD is very common in all age groups.", "As few foods contain vitamin D, guidelines recommended supplementation at suggested daily intake and tolerable upper limit levels.", "It is also suggested to measure the serum 25-hydroxyvitamin D level as the initial diagnostic test in patients at risk for deficiency.", "Treatment with either vitamin D2 or vitamin D3 is recommended for deficient patients.", "A meta-analysis published in 2007 showed that vitamin D supplementation was associated with significantly reduced mortality.", "In this review, we will summarize the mechanisms that are presumed to underlie the relationship between vitamin D and understand its biology and clinical implications."], "structured": false}
{"doc_id": 23269537, "title": "Cyclin D1 activation in B-cell malignancy: association with changes in histone acetylation, DNA methylation, and RNA polymerase II binding to both promoter and distal sequences.", "abstract": ["Cyclin D1 expression is deregulated by chromosome translocation in mantle cell lymphoma and a subset of multiple myeloma.", "The molecular mechanisms involved in long-distance gene deregulation remain obscure, although changes in acetylated histones and methylated CpG dinucleotides may be important.", "The patterns of DNA methylation and histone acetylation were determined at the cyclin D1 locus on chromosome 11q13 in B-cell malignancies.", "The cyclin D1 promoter was hypomethylated and hyperacetylated in expressing cell lines and patient samples, and methylated and hypoacetylated in nonexpressing cell lines.", "Domains of hyperacetylated histones and hypomethylated DNA extended over 120 kb upstream of the cyclin D1 gene.", "Interestingly, hypomethylated DNA and hyperacetylated histones were also located at the cyclin D1 promoter but not the upstream major translocation cluster region in cyclin D1-nonexpressing, nontumorigenic B and T cells.", "RNA polymerase II binding was demonstrated both at the cyclin D1 promoter and 3' immunoglobulin heavy-chain regulatory regions only in malignant B-cell lines with deregulated cyclin D1 expression.", "Our results suggest a model where RNA polymerase II bound at IgH regulatory sequences can activate the cyclin D1 promoter by either long-range polymerase transfer or tracking."], "structured": false}
{"doc_id": 23273454, "title": "The physiological regulation of toll-like receptor expression and function in humans.", "abstract": ["Eleven mammalian toll-like receptors (TLRs 1-11) have been identified to date and are known to play a crucial role in the regulation of immune responses; however, the factors that regulate TLR expression and function in vivo are poorly understood.", "Therefore, in the present study, we investigated the physiological regulation of TLR expression and function in humans.", "To examine the influence of diurnal rhythmicity on TLR expression and function, peripheral venous blood samples were collected from healthy volunteers (n = 8) at time points coinciding with the peak and nadir in the endogenous circulating cortisol concentration.", "While no diurnal rhythmicity in the expression of TLRs 1, 2, 4 or 9 was observed, the upregulation of costimulatory (CD80 and CD86) and antigen-presenting (MHC class II) molecules on CD14(+) monocytes following activation with specific TLR ligands was greater (P < 0.05) in samples obtained in the evening compared with the morning.", "To examine the influence of physical stress on TLR expression and function, peripheral venous blood samples were collected from healthy volunteers (n = 11) at rest and following 1.5 h of strenuous exercise in the heat (34 degrees C).", "Strenuous exercise resulted in a decrease (P < 0.005) in the expression of TLRs 1, 2 and 4 on CD14(+) monocytes.", "Furthermore, the upregulation of CD80, CD86, MHC class II and interleukin-6 by CD14(+) monocytes following activation with specific TLR ligands was decreased (P < 0.05) in samples obtained following exercise compared with at rest.", "These results demonstrate that TLR function is subject to modulation under physiological conditions in vivo and provide evidence for the role of immunomodulatory hormones in the regulation of TLR function."], "structured": false}
{"doc_id": 23284774, "title": "A review of psychosocial needs of breast-cancer patients and their relatives.", "abstract": ["AIM To identify the psychosocial needs of breast-cancer patients and their relatives along with factors affecting these needs and to develop a tentative model to guide further research and need assessments in clinical practice.   \n", "BACKGROUND Women experiencing breast cancer must deal with the diagnosis of a life-threatening illness.", "Treatment and the recovery process can be demanding for patients and their relatives.", "Need assessment may help clinicians focus on providing appropriate help.   \n", "DESIGN Literature review.   \n", "METHOD Undertaken using electronic databases and specific research terms; 20 articles were identified and analysed.   \n", "RESULTS The needs identified by patients involve (1) treatment-related physical and social impairment like fatigue, menopausal symptoms and a changed body image and (2) emotional distress like fear of recurrence, anxiety and depression.", "Partners need help to protect themselves and the patient from different threats.", "Women need information to maintain control and manage their illness.", "Partners want information concerning the patient's condition and both of them about the prognosis and perspectives.", "There is a lack of knowledge of relatives' needs.", "Mutual familial support, women's and partners' health and emotional distress may affect the interaction between the patients and their partners.   \n", "CONCLUSIONS A tentative family-based model to guide further research and clinical support is proposed.", "Further research is needed to determine precisely which psychosocial factors may influence fulfilment of the patients' and relatives' needs.   ", "RELEVANCE TO CLINICAL PRACTICE The proposed model may provide a framework for healthcare professionals to evaluate the patients' and relatives' met and unmet needs and the real demand for help, to guide care planning, counselling and education."], "structured": true}
{"doc_id": 23286603, "title": "Poly(ADP-ribose) Polymerase 1 Represses Liver X Receptor-mediated ABCA1 Expression and Cholesterol Efflux in Macrophages.", "abstract": ["Liver X receptors (LXR) are oxysterol-activated nuclear receptors that play a central role in reverse cholesterol transport through up-regulation of ATP-binding cassette transporters (ABCA1 and ABCG1) that mediate cellular cholesterol efflux.", "Mouse models of atherosclerosis exhibit reduced atherosclerosis and enhanced regression of established plaques upon LXR activation.", "However, the coregulatory factors that affect LXR-dependent gene activation in macrophages remain to be elucidated.", "To identify novel regulators of LXR that modulate its activity, we used affinity purification and mass spectrometry to analyze nuclear LXR\u03b1 complexes and identified poly(ADP-ribose) polymerase-1 (PARP-1) as an LXR-associated factor.", "In fact, PARP-1 interacted with both LXR\u03b1 and LXR\u03b2.", "Both depletion of PARP-1 and inhibition of PARP-1 activity augmented LXR ligand-induced ABCA1 expression in the RAW 264.7 macrophage line and primary bone marrow-derived macrophages but did not affect LXR-dependent expression of other target genes, ABCG1 and SREBP-1c.", "Chromatin immunoprecipitation experiments confirmed PARP-1 recruitment at the LXR response element in the promoter of the ABCA1 gene.", "Further, we demonstrated that LXR is poly(ADP-ribosyl)ated by PARP-1, a potential mechanism by which PARP-1 influences LXR function.", "Importantly, the PARP inhibitor 3-aminobenzamide enhanced macrophage ABCA1-mediated cholesterol efflux to the lipid-poor apolipoprotein AI.", "These findings shed light on the important role of PARP-1 on LXR-regulated lipid homeostasis.", "Understanding the interplay between PARP-1 and LXR may provide insights into developing novel therapeutics for treating atherosclerosis."], "structured": false}
{"doc_id": 23294314, "title": "Emergency contraception: advance provision in a young, high-risk clinic population.", "abstract": ["OBJECTIVE To assess whether advance provision of emergency contraception increases its use and whether it has secondary effects on regular contraceptive use.   \n", "METHODS We conducted a controlled trial of female clients, aged 16-24 years, who attended a publicly funded family planning clinic.", "Women were systematically assigned to receive an advance provision of emergency contraception and education (treatment) or education only (control).", "Among 263 participants enrolled (133 treatment, 130 control), follow-up was completed in 213 (111 treatment, 102 control).", "The main outcome measures were emergency contraception knowledge and use, frequency of unprotected sex, and pattern of contraceptive use in the past 4 months.   \n", "RESULTS Participants were aware of emergency contraception at follow-up, but the treatment group was three times as likely to use it (P =.006).", "Although the treatment group did not report higher frequencies of unprotected sex than the control group, women in the treatment group (28%) were more likely than those in the control group (17%) to report using less effective contraception at follow-up compared with enrollment (P =.05).", "The proportion of women in both groups who reported consistent pill use increased from enrollment to follow-up (34% versus 45%); however, the control group (58%) was more likely than the treatment group (32%) to report consistent pill use at follow-up (P =.03).   \n", "CONCLUSION Use of emergency contraception was increased by providing it in advance, but not by education alone.", "Changes to less effective contraceptive methods and patterns of pill use were potentially negative effects that need to be explored in relation to observed benefits."], "structured": true}
{"doc_id": 23304931, "title": "Immunophenotypic analysis of AIDS-related diffuse large B-cell lymphoma and clinical implications in patients from AIDS malignancies consortium clinical trials 010 and 034", "abstract": ["PURPOSE Diffuse large B-cell lymphoma (DLBCL) represents a clinically heterogeneous disease.", "Models based on immunohistochemistry predict clinical outcome.", "These include subdivision into germinal center (GC) versus non-GC subtypes; proliferation index (measured by expression of Ki-67), and expression of BCL-2, FOXP1, or B-lymphocyte-induced maturation protein (Blimp-1)/PRDM1.", "We sought to determine whether immunohistochemical analyses of biopsies from patients with DLBCL having HIV infection are similarly relevant for prognosis.   \n", "PATIENTS AND METHODS We examined 81 DLBCLs from patients with AIDS in AMC010 (cyclophosphamide, doxorubicin, vincristine, and prednisone [CHOP] v CHOP-rituximab) and AMC034 (etoposide, doxorubicin, vincristine, prednisone, and dose-adjusted cyclophosphamide plus rituximab concurrent v sequential) clinical trials and compared the immunophenotype with survival data, Epstein-Barr virus (EBV) positivity, and CD4 counts.   \n", "RESULTS The GC and non-GC subtypes of DLBCL did not differ significantly with respect to overall survival or CD4 count at cancer presentation.", "EBV could be found in both subtypes of DLBCL, although less frequently in the GC subtype, and did not affect survival.", "Expression of FOXP1, Blimp-1/PRDM1, or BCL-2 was not correlated with the outcome in patients with AIDS-related DLBCL.   \n", "CONCLUSION These data indicate that with current treatment strategies for lymphoma and control of HIV infection, commonly used immunohistochemical markers may not be clinically relevant in HIV-infected patients with DLBCL.", "The only predictive immunohistochemical marker was found to be Ki-67, where a higher proliferation index was associated with better survival, suggesting a better response to therapy in patients whose tumors had higher proliferation rates."], "structured": true}
{"doc_id": 23305547, "title": "Prion-like activity of Cu/Zn superoxide dismutase: implications for amyotrophic lateral sclerosis.", "abstract": ["Neurodegenerative diseases belong to a larger group of protein misfolding disorders, known as proteinopathies.", "There is increasing experimental evidence implicating prion-like mechanisms in many common neurodegenerative disorders, including Alzheimer disease, Parkinson disease, the tauopathies, and amyotrophic lateral sclerosis (ALS), all of which feature the aberrant misfolding and aggregation of specific proteins.", "The prion paradigm provides a mechanism by which a mutant or wild-type protein can dominate pathogenesis through the initiation of self-propagating protein misfolding.", "ALS, a lethal disease characterized by progressive degeneration of motor neurons is understood as a classical proteinopathy; the disease is typified by the formation of inclusions consisting of aggregated protein within and around motor neurons that can contribute to neurotoxicity.", "It is well established that misfolded/oxidized SOD1 protein is highly toxic to motor neurons and plays a prominent role in the pathology of ALS.", "Recent work has identified propagated protein misfolding properties in both mutant and wild-type SOD1, which may provide the molecular basis for the clinically observed contiguous spread of the disease through the neuroaxis.", "In this review we examine the current state of knowledge regarding the prion-like properties of SOD1 and comment on its proposed mechanisms of intercellular transmission."], "structured": false}
{"doc_id": 23305884, "title": "Analysis of Epstein-Barr virus-regulated host gene expression changes through primary B-cell outgrowth reveals delayed kinetics of latent membrane protein 1-mediated NF-\u03baB activation.", "abstract": ["Epstein-Barr virus (EBV) is an oncogenic human herpesvirus that dramatically reorganizes host gene expression to immortalize primary B cells.", "In this study, we analyzed EBV-regulated host gene expression changes following primary B-cell infection, both during initial proliferation and through transformation into lymphoblastoid cell lines (LCLs).", "While most EBV-regulated mRNAs were changed during the transition from resting, uninfected B cells through initial B-cell proliferation, a substantial number of mRNAs changed uniquely from early proliferation through LCL outgrowth.", "We identified constitutively and dynamically EBV-regulated biological processes, protein classes, and targets of specific transcription factors.", "Early after infection, genes associated with proliferation, stress responses, and the p53 pathway were highly enriched.", "However, the transition from early to long-term outgrowth was characterized by genes involved in the inhibition of apoptosis, the actin cytoskeleton, and NF-\u03baB activity.", "It was previously thought that the major viral protein responsible for NF-\u03baB activation, latent membrane protein 1 (LMP1), is expressed within 2 days after infection.", "Our data indicate that while this is true, LCL-level LMP1 expression and NF-\u03baB activity are not evident until 3 weeks after primary B-cell infection.", "Furthermore, heterologous NF-\u03baB activation during the first week after infection increased the transformation efficiency, while early NF-\u03baB inhibition had no effect on transformation.", "Rather, inhibition of NF-\u03baB was not toxic to EBV-infected cells until LMP1 levels and NF-\u03baB activity were high.", "These data collectively highlight the dynamic nature of EBV-regulated host gene expression and support the notion that early EBV-infected proliferating B cells have a fundamentally distinct growth and survival phenotype from that of LCLs."], "structured": false}
{"doc_id": 23326722, "title": "Clinical and laboratory features of adult T-cell leukaemia lymphoma in Barbados.", "abstract": ["We describe the clinical and pathological features of 23 Afro-Caribbean patients with adult T-cell leukaemia/lymphoma admitted to the Queen Elizabeth Hospital, Barbados over a 5 year period.", "There were 9 males and 14 females, with a median age of 38 years (range 14-84).", "Twelve had acute leukaemia, 10 lymphoma (including 4 with solitary extra nodal lesions) and 1 smouldering subtype.", "Two patients had a past history of tropical spastic paraparesis/HTLV I associated myelopathy (TSP/HAM).", "The prognosis was poor, with only 3 complete responses to chemotherapy (CHOP) lasting from 9 to 36 months.", "We conclude that ATLL in Barbados is similar to the disease in the other Caribbean islands and Japan, except that in Barbados the age of onset is over a decade younger than in Japan."], "structured": false}
{"doc_id": 23331269, "title": "Acoustic landmarks drive delta-theta oscillations to enable speech comprehension by facilitating perceptual parsing.", "abstract": ["A growing body of research suggests that intrinsic neuronal slow (<10 Hz) oscillations in auditory cortex appear to track incoming speech and other spectro-temporally complex auditory signals.", "Within this framework, several recent studies have identified critical-band temporal envelopes as the specific acoustic feature being reflected by the phase of these oscillations.", "However, how this alignment between speech acoustics and neural oscillations might underpin intelligibility is unclear.", "Here we test the hypothesis that the 'sharpness' of temporal fluctuations in the critical band envelope acts as a temporal cue to speech syllabic rate, driving delta-theta rhythms to track the stimulus and facilitate intelligibility.", "We interpret our findings as evidence that sharp events in the stimulus cause cortical rhythms to re-align and parse the stimulus into syllable-sized chunks for further decoding.", "Using magnetoencephalographic recordings, we show that by removing temporal fluctuations that occur at the syllabic rate, envelope-tracking activity is reduced.", "By artificially reinstating these temporal fluctuations, envelope-tracking activity is regained.", "These changes in tracking correlate with intelligibility of the stimulus.", "Together, the results suggest that the sharpness of fluctuations in the stimulus, as reflected in the cochlear output, drive oscillatory activity to track and entrain to the stimulus, at its syllabic rate.", "This process likely facilitates parsing of the stimulus into meaningful chunks appropriate for subsequent decoding, enhancing perception and intelligibility."], "structured": false}
{"doc_id": 23342686, "title": "Crystal structures of complexes of the small ribosomal subunit with tetracycline, edeine and IF3.", "abstract": ["The small ribosomal subunit is responsible for the decoding of genetic information and plays a key role in the initiation of protein synthesis.", "We analyzed by X-ray crystallography the structures of three different complexes of the small ribosomal subunit of Thermus thermophilus with the A-site inhibitor tetracycline, the universal initiation inhibitor edeine and the C-terminal domain of the translation initiation factor IF3.", "The crystal structure analysis of the complex with tetracycline revealed the functionally important site responsible for the blockage of the A-site.", "Five additional tetracycline sites resolve most of the controversial biochemical data on the location of tetracycline.", "The interaction of edeine with the small subunit indicates its role in inhibiting initiation and shows its involvement with P-site tRNA.", "The location of the C-terminal domain of IF3, at the solvent side of the platform, sheds light on the formation of the initiation complex, and implies that the anti-association activity of IF3 is due to its influence on the conformational dynamics of the small ribosomal subunit."], "structured": false}
{"doc_id": 23342845, "title": "Plasmid-encoded proinsulin preserves C-peptide while specifically reducing proinsulin-specific CD8\u207a T cells in type 1 diabetes.", "abstract": ["In type 1 diabetes (T1D), there is an intense inflammatory response that destroys the \u03b2 cells in the pancreatic islets of Langerhans, the site where insulin is produced and released.", "A therapy for T1D that targets the specific autoimmune response in this disease while leaving the remainder of the immune system intact, has long been sought.", "Proinsulin is a major target of the adaptive immune response in T1D.", "We hypothesized that an engineered DNA plasmid encoding proinsulin (BHT-3021) would preserve \u03b2 cell function in T1D patients through reduction of insulin-specific CD8\u207a T cells.", "We studied 80 subjects over 18 years of age who were diagnosed with T1D within the past 5 years.", "Subjects were randomized 2:1 to receive intramuscular injections of BHT-3021 or BHT-placebo, weekly for 12 weeks, and then monitored for safety and immune responses in a blinded fashion.", "Four dose levels of BHT-3021 were evaluated: 0.3, 1.0, 3.0, and 6.0 mg.", "C-peptide was used both as an exploratory efficacy measure and as a safety measure.", "Islet-specific CD8\u207a T cell frequencies were assessed with multimers of monomeric human leukocyte antigen class I molecules loaded with peptides from pancreatic and unrelated antigens.", "No serious adverse events related to BHT-3021 were observed.", "C-peptide levels improved relative to placebo at all doses, at 1 mg at the 15-week time point (+19.5% BHT-3021 versus -8.8% BHT-placebo, P < 0.026).", "Proinsulin-reactive CD8\u207a T cells, but not T cells against unrelated islet or foreign molecules, declined in the BHT-3021 arm (P < 0.006).", "No significant changes were noted in interferon-\u03b3, interleukin-4 (IL-4), or IL-10 production in CD4 T cells.", "Thus, we demonstrate that a plasmid encoding proinsulin reduces the frequency of CD8\u207a T cells reactive to proinsulin while preserving C-peptide over the course of dosing."], "structured": false}
{"doc_id": 23349986, "title": "Dexamethasone and risk of nausea and vomiting and postoperative bleeding after tonsillectomy in children: a randomized trial.", "abstract": ["CONTEXT Dexamethasone is widely used to prevent postoperative nausea and vomiting (PONV) in pediatric tonsillectomy.   \n", "OBJECTIVE To assess whether dexamethasone dose-dependently reduces the risk of PONV at 24 hours after tonsillectomy.   \n", "DESIGN, SETTING, AND PATIENTS Randomized placebo-controlled trial conducted among 215 children undergoing elective tonsillectomy at a major public teaching hospital in Switzerland from February 2005 to December 2007.   \n", "INTERVENTIONS Children were randomly assigned to receive dexamethasone (0.05, 0.15, or 0.5 mg/kg) or placebo intravenously after induction of anesthesia.", "Acetaminophen-codeine and ibuprofen were given as postoperative analgesia.", "Follow-up continued until the 10th postoperative day.   \n", "MAIN OUTCOME MEASURES The primary end point was prevention of PONV at 24 hours; secondary end points were decrease in the need for ibuprofen at 24 hours and evaluation of adverse effects.   \n", "RESULTS At 24 hours, 24 of 54 participants who received placebo (44%; 95% confidence interval [CI], 31%-59%) had experienced PONV compared with 20 of 53 (38%; 95% CI, 25%-52%), 13 of 54 (24%; 95% CI, 13%-38%), and 6 of 52 (12%; 95% CI, 4%-23%) who received dexamethasone at 0.05, 0.15, and 0.5 mg/kg, respectively (P<.001 for linear trend).", "Children who received dexamethasone received significantly less ibuprofen.", "There were 26 postoperative bleeding episodes in 22 children.", "Two of 53 (4%; 95% CI, 0.5%-13%)", "children who received placebo had bleeding compared with 6 of 53 (11%; 95% CI, 4%-23%), 2 of 51 (4%; 95% CI, 0.5%-13%), and 12 of 50 (24%; 95% CI, 13%-38%) who received dexamethasone at 0.05, 0.15, and 0.5 mg/kg, respectively (P = .003).", "Dexamethasone, 0.5 mg/kg, was associated with the highest bleeding risk (adjusted relative risk, 6.80; 95% CI, 1.77-16.5).", "Eight children had to undergo emergency reoperation because of bleeding, all of whom had received dexamethasone.", "The trial was stopped early for safety reasons.   \n", "CONCLUSION In this study of children undergoing tonsillectomy, dexamethasone decreased the risk of PONV dose dependently but was associated with an increased risk of postoperative bleeding.   \n", "TRIAL REGISTRATION clinicaltrials.gov Identifier: NCT00403806."], "structured": true}
{"doc_id": 23351136, "title": "Detection of sweet and umami taste in the absence of taste receptor T1r3.", "abstract": ["The tastes of sugars (sweet) and glutamate (umami) are thought to be detected by T1r receptors expressed in taste cells.", "Molecular genetics and heterologous expression implicate T1r2 plus T1r3 as a sweet-responsive receptor,and T1r1 plus T1r3,as well as a truncated form of the type 4 metabotropic glutamate receptor (taste-mGluR4),as umami-responsive receptors.", "Here,we show that mice lacking T1r3 showed no preference for artificial sweeteners and had diminished but not abolished behavioral and nerve responses to sugars and umami compounds.", "These results indicate that T1r3-independent sweet- and umami-responsive receptors and/or pathways exist in taste cells."], "structured": false}
{"doc_id": 23356816, "title": "Cyclin A1 is required for meiosis in the male mouse", "abstract": ["The mammalian A-type cyclin family consists of two members, cyclin A1 (encoded by Ccna1) and cyclin A2 (encoded by Ccna2).", "Cyclin A2 promotes both G1/S and G2/M transitions, and targeted deletion of Ccna2 in mouse is embryonic lethal.", "Cyclin A1 is expressed in mice exclusively in the germ cell lineage and is expressed in humans at highest levels in the testis and certain myeloid leukaemia cells.", "To investigate the role of cyclin A1 and possible redundancy among the cyclins in vivo, we generated mice bearing a null mutation of Ccna1.", "Ccna1-/- males were sterile due to a block of spermatogenesis before the first meiotic division, whereas females were normal.", "Meiosis arrest in Ccna1\u2013/\u2013 males was associated with increased germ cell apoptosis, desynapsis abnormalities and reduction of Cdc2 kinase activation at the end of meiotic prophase.", "Cyclin A1 is therefore essential for spermatocyte passage into the first meiotic division in male mice, a function that cannot be complemented by the concurrently expressed B-type cyclins."], "structured": false}
{"doc_id": 23369842, "title": "Metabolic effects of isoenergetic nutrient exchange over 24 hours in relation to obesity in women.", "abstract": ["Twenty-four hour whole body indirect calorimetry has been used to study the effects of feeding, during a sedentary test day, isoenergetic diets which varied in fat (3 or 40 per cent of total energy) and carbohydrate (82 or 45 per cent) content.", "Three groups of women were studied: lean, obese and 'post-obese' after slimming.", "Energy expenditure was greater in absolute terms in the obese women.", "Twenty-four hour energy expenditure was lower by only 3-7 per cent when fasting compared to that when fed to achieve energy balance.", "There were no large differences in energy expenditure between the two diets or between the groups but the thermogenic effect of the high carbohydrate diet was significantly greater than that of the high fat diet (5.8 vs 3.5 per cent of energy expenditure: P less than 0.01).", "The post-obese tended to have lower energy expenditure per kg FFM than controls when fasting and when high-fat fed, but this pattern was not shown by the obese.", "Sleeping energy expenditure was particularly low in the post-obese group when high-fat fed.", "Dirunal variations in RQ appear to show more marked rise in morning RQ from the nocturnal minimum in the obese and post-obese, which might be evidence for an energy-saving mechanism through greater availability of stored dietary carbohydrate."], "structured": false}
{"doc_id": 23377475, "title": "Acute kidney injury and chronic kidney disease: an integrated clinical syndrome.", "abstract": ["The previous conventional wisdom that survivors of acute kidney injury (AKI) tend to do well and fully recover renal function appears to be flawed.", "AKI can cause end-stage renal disease (ESRD) directly, and increase the risk of developing incident chronic kidney disease (CKD) and worsening of underlying CKD.", "In addition, severity, duration, and frequency of AKI appear to be important predictors of poor patient outcomes.", "CKD is an important risk factor for the development and ascertainment of AKI.", "Experimental data support the clinical observations and the bidirectional nature of the relationships between AKI and CKD.", "Reductions in renal mass and nephron number, vascular insufficiency, cell cycle disruption, and maladaptive repair mechanisms appear to be important modulators of progression in patients with and without coexistent CKD.", "Distinction between AKI and CKD may be artificial.", "Consideration should be given to the integrated clinical syndrome of diminished GFR, with acute and chronic stages, where spectrum of disease state and outcome is determined by host factors, including the balance of adaptive and maladaptive repair mechanisms over time.", "Physicians must provide long-term follow-up to patients with first episodes of AKI, even if they presented with normal renal function."], "structured": false}
{"doc_id": 23388442, "title": "Fatty acids as modulators of the immune response.", "abstract": ["Research describing fatty acids as modulators of inflammation and immune responses abounds.", "Many of these studies have focused on one particular group of fatty acids, omega-3.", "The data from animal studies have shown that these fatty acids can have powerful anti-inflammatory and immunomodulatory activities in a wide array of diseases (e.g., autoimmunity, arthritis, and infection).", "However, the evidence from human trials is more equivocal.", "In this review, a historical framework for understanding how and why fatty acids may affect the immune system is provided.", "Second, highlights of two recent landmark reports from the Agency for Healthcare Research and Quality are presented.", "These reports critically evaluate the evidence from human clinical trials of omega-3 fatty acids and rheumatoid arthritis, asthma, and a few other immune-mediated diseases.", "Third, the data from human clinical trials investigating the impact of various bioactive fatty acids on ex vivo and in vivo immune response are reviewed.", "Limitations in experimental design and immune assays commonly used are discussed.", "The discordance between expectation and evidence in this field has been a disappointment.", "Recommendations for improving both animal-based and human studies are provided."], "structured": false}
{"doc_id": 23389795, "title": "Common and rare variants in multifactorial susceptibility to common diseases", "abstract": ["Here, we give a historical overview of the search for genetic variants that influence the susceptibility of an individual to a chronic disease, from RA Fisher's seminal work to the current excitement of whole-genome association studies (WGAS).", "We then discuss the concepts behind the identification of common variants as disease causal factors and contrast them to the basic ideas that underlie the rare variant hypothesis.", "The identification of rare variants involves the careful selection of candidate genes to examine, the availability of highly efficient resequencing techniques and the appropriate assessment of the functional consequences of the implicated variant.", "We believe that this strategy can be successfully applied at present in order to unravel the contribution of rare variants to the multifactorial inheritance of common diseases, which could lead to the implementation of much needed preventative screening schemes."], "structured": false}
{"doc_id": 23393712, "title": "Cell-cell adhesion and signalling.", "abstract": ["Signalling pathways activated by Rho small GTPases have recently been identified that coordinate junction assembly, stability and function, as well as interactions of adhesive complexes with the underlying cortical cytoskeleton.", "Particularly exciting is the interplay between adherens junctions, activation of Rho proteins and the dynamics of microtubule, actin and intermediate filaments.", "This interplay has important implications for functional regulation of cell-cell adhesion, and points to a more integrated view of signalling processes."], "structured": false}
{"doc_id": 23397658, "title": "Fibroblast growth factor 21 as an emerging metabolic regulator: clinical perspectives.", "abstract": ["Fibroblast growth factor 21 (FGF21), a metabolic hormone predominantly produced by the liver, is also expressed in adipocytes and the pancreas.", "It regulates glucose and lipid metabolism through pleiotropic actions in these tissues and the brain.", "In mice, fasting leads to increased PPAR-\u03b1 mediated expression of FGF21 in the liver where it stimulates gluconeogenesis, fatty acid oxidation, and ketogenesis, as an adaptive response to fasting and starvation.", "In the fed state, FGF21 acts as an autocrine factor in adipocytes, regulating the activity of PPAR-\u03b3 through a feed-forward loop mechanism.", "Administration of recombinant FGF21 has been shown to confer multiple metabolic benefits on insulin sensitivity, blood glucose, lipid profile and body weight in obese mice and diabetic monkeys, without mitogenic or other side effects.", "Such findings highlight the potential role of FGF21 as a therapeutic agent for obesity-related medical conditions.", "However, in human studies, high circulating FGF21 levels are found in obesity and its related cardiometabolic disorders including the metabolic syndrome, type 2 diabetes, non-alcoholic fatty liver disease and coronary artery disease.", "These findings may indicate the presence of FGF21 resistance or compensatory responses to the underlying metabolic stress, and imply the need for supraphysiological doses of FGF21 to achieve therapeutic efficacy.", "On the other hand, serum FGF21 has been implicated as a potential biomarker for the early detection of these cardiometabolic disorders.", "This review summarizes recent developments in the understanding of FGF21, from physiological and clinical perspectives."], "structured": false}
{"doc_id": 23400191, "title": "Assessment of the cerebral circulation in adults with coarctation of the aorta.", "abstract": ["AIMS There is a fivefold increase in the frequency of intracranial aneurysm (IA) in adults with coarctation of the aorta (CoA).", "Current guidelines for management of adults with CoA recommend computed tomography angiography (CTA) or magnetic resonance imaging of the intracranial vessels.", "However, this recommendation has not been universally accepted.", "The purpose of our study was to prospectively perform CTA of the intracranial vessels in adults with CoA to evaluate the prevalence and identify high-risk features of this complication.   \n", "METHODS AND RESULTS From January 2008 to February 2011, adults \u226518 years of age with CoA were prospectively enrolled in a screening program with CTA of the intracranial vessels.", "Analyses of prognostic variables were performed with both Fisher's exact and two sample t-test.", "Forty-three patients (58% female, 33.55 \u00b1 10.21 years) with CoA completed CTA of the intracranial vessels.", "Five patients (11%) were found to have IA.", "Patients with IA were older than those without (45.6 \u00b1 8.17 vs. 30.89 \u00b1 7.89, P = 0.0003).", "There were no statistically significant differences detected between measurements of fasting lipid profiles, C-reactive protein, brain natriuretic peptide, and homocysteine levels among CoA patients with and without IA (P = not significant).   \n", "CONCLUSION Prospective screening of adults with CoA confirmed the increased prevalence of IA but also identified increased age as the sole risk factor.", "These data suggested that screening is justified particularly in the fourth and fifth decades of life.", "Further studies are required that focus on the development, natural history, and treatment of IA."], "structured": true}
{"doc_id": 23403754, "title": "Bioenergetic aspects of apoptosis, necrosis and mitoptosis", "abstract": ["In this review I summarize interrelations between bioenergetic processes and such programmed death phenomena as cell suicide (apoptosis and necrosis) and mitochondrial suicide (mitoptosis).", "The following conclusions are made.", "(I) ATP and rather often mitochondrial hyperpolarization (i.e. an increase in membrane potential, \u0394\u03a8) are required for certain steps of apoptosis and necrosis.", "(II) Apoptosis, even if it is accompanied by \u0394\u03a8 and [ATP] increases at its early stage, finally results in a \u0394\u03a8 collapse and ATP decrease.", "(III) Moderate (about three-fold) lowering of [ATP] for short and long periods of time induces apoptosis and necrosis, respectively.", "In some types of apoptosis and necrosis, the cell death is mediated by a \u0394\u03a8-dependent overproduction of ROS by the initial (Complex I) and the middle (Complex III) spans of the respiratory chain.", "ROS initiate mitoptosis which is postulated to rid the intracellular population of mitochondria from those that are ROS overproducing.", "Massive mitoptosis can result in cell death due to release to cytosol of the cell death proteins normally hidden in the mitochondrial intermembrane space."], "structured": false}
{"doc_id": 23418635, "title": "Embryonic stem cells require Wnt proteins to prevent differentiation to epiblast stem cells", "abstract": ["Pluripotent stem cells exist in naive and primed states, epitomized by mouse embryonic stem cells (ESCs) and the developmentally more advanced epiblast stem cells (EpiSCs; ref. ).", "In the naive state of ESCs, the genome has an unusual open conformation and possesses a minimum of repressive epigenetic marks.", "In contrast, EpiSCs have activated the epigenetic machinery that supports differentiation towards the embryonic cell types.", "The transition from naive to primed pluripotency therefore represents a pivotal event in cellular differentiation.", "But the signals that control this fundamental differentiation step remain unclear.", "We show here that paracrine and autocrine Wnt signals are essential self-renewal factors for ESCs, and are required to inhibit their differentiation into EpiSCs.", "Moreover, we find that Wnt proteins in combination with the cytokine LIF are sufficient to support ESC self-renewal in the absence of any undefined factors, and support the derivation of new ESC lines, including ones from non-permissive mouse strains.", "Our results not only demonstrate that Wnt signals regulate the naive-to-primed pluripotency transition, but also identify Wnt as an essential and limiting ESC self-renewal factor."], "structured": false}
{"doc_id": 23420615, "title": "CLIP identifies Nova-regulated RNA networks in the brain.", "abstract": ["Nova proteins are neuron-specific antigens targeted in paraneoplastic opsoclonus myoclonus ataxia (POMA), an autoimmune neurologic disease characterized by abnormal motor inhibition.", "Nova proteins regulate neuronal pre-messenger RNA splicing by directly binding to RNA.", "To identify Nova RNA targets, we developed a method to purify protein-RNA complexes from mouse brain with the use of ultraviolet cross-linking and immunoprecipitation (CLIP).Thirty-four transcripts were identified multiple times by Nova CLIP.Three-quarters of these encode proteins that function at the neuronal synapse, and one-third are involved in neuronal inhibition.", "Splicing targets confirmed in Nova-/- mice include c-Jun N-terminal kinase 2, neogenin, and gephyrin; the latter encodes a protein that clusters inhibitory gamma-aminobutyric acid and glycine receptors, two previously identified Nova splicing targets.", "Thus, CLIP reveals that Nova coordinately regulates a biologically coherent set of RNAs encoding multiple components of the inhibitory synapse, an observation that may relate to the cause of abnormal motor inhibition in POMA."], "structured": false}
{"doc_id": 23420807, "title": "Anti-Angiogenic Activity of Selected Receptor Tyrosine Kinase Inhibitors, PD166285 and PD173074: Implications for Combination Treatment with Photodynamic Therapy", "abstract": ["Angiogenesis, the formation of new blood vessels from an existing vasculature, is requisite for tumor growth.", "It entails intercellular coordination of endothelial and tumor cells through angiogenic growth factor signaling.", "Interruption of these events has implications in the suppression of tumor growth.", "PD166285, a broad-spectrum receptor tyrosine kinase (RTK) inhibitor, and PD173074, a selective FGFR1TK inhibitor, were evaluated for their anti-angiogenic activity and anti-tumor efficacy in combination with photodynamic therapy (PDT).", "To evaluate the anti-angiogenic and anti-tumor activities of these compounds, RTK assays, in vitro tumor cell growth and microcapillary formation assays, in vivo murine angiogenesis and anti-tumor efficacy studies utilizing RTK inhibitors in combination with photodynamic therapy were performed.", "PD166285 inhibited PDGFR-\u03b2-, EGFR-, and FGFR1TKs and c-src TK by 50% (IC50) at concentrations between 7\u221285nM. PD173074 displayed selective inhibitory activity towards FGFR1TK at 26nM. PD173074 demonstrated (>100 fold) selective growth inhibitory action towards human umbilical vein endothelial cells compared with a panel of tumor cell lines.", "Both PD166285 and PD173074 (at 10nM) inhibited the formation of microcapillaries on Matrigel-coated plastic.", "In vivo anti-angiogenesis studies in mice revealed that oral administration (p.o.) of either PD166285 (1\u221225 mg/kg) or PD173074 (25\u2212100 mg/kg) generated dose dependent inhibition of angiogenesis.", "Against a murine mammary 16c tumor, significantly prolonged tumor regressions were achieved with daily p.o.", "doses of PD166285 (5\u221210 mg/kg) or PD173074 (30\u221260 mg/kg) following PDT compared with PDT alone (p<0.001).", "Many long-term survivors were also noted in combination treatment groups.", "PD166285 and PD173074 displayed potent anti-angiogenic and anti-tumor activity and prolonged the duration of anti-tumor response to PDT.", "Interference in membrane signal transduction by inhibitors of specific RTKs (e.g. FGFR1TK) should result in new chemotherapeutic agents having the ability to limit tumor angiogenesis and regrowth following cytoreductive treatments such as PDT."], "structured": false}
{"doc_id": 23423230, "title": "The VirB type IV secretion system of Bartonella henselae mediates invasion, proinflammatory activation and antiapoptotic protection of endothelial cells.", "abstract": ["Bartonella henselae is an arthropod-borne zoonotic pathogen causing intraerythrocytic bacteraemia in the feline reservoir host and a broad range of clinical manifestations in incidentally infected humans.", "Remarkably, B. henselae can specifically colonize the human vascular endothelium, resulting in inflammation and the formation of vasoproliferative lesions known as bacillary angiomatosis and bacillary peliosis.", "Cultured human endothelial cells provide an in vitro system to study this intimate interaction of B. henselae with the vascular endothelium.", "However, little is known about the bacterial virulence factors required for this pathogenic process.", "Recently, we identified the type IV secretion system (T4SS) VirB as an essential pathogenicity factor in Bartonella, required to establish intraerythrocytic infection in the mammalian reservoir.", "Here, we demonstrate that the VirB T4SS also mediates most of the virulence attributes associated with the interaction of B. henselae during the interaction with human endothelial cells.", "These include: (i) massive rearrangements of the actin cytoskeleton, resulting in the formation of bacterial aggregates and their internalization by the invasome structure; (ii) nuclear factor kappaB-dependent proinflammatory activation, leading to cell adhesion molecule expression and chemokine secretion, and (iii) inhibition of apoptotic cell death, resulting in enhanced endothelial cell survival.", "Moreover, we show that the VirB system mediates cytostatic and cytotoxic effects at high bacterial titres, which interfere with a potent VirB-independent mitogenic activity.", "We conclude that the VirB T4SS is a major virulence determinant of B. henselae, required for targeting multiple endothelial cell functions exploited by this vasculotropic pathogen."], "structured": false}
{"doc_id": 23439808, "title": "Serum Cystatin C Is Related to Pulse Wave Velocity Even in Subjects with Normal Serum Creatinine", "abstract": ["We hypothesized that serum cystatin C can be a more predictable marker of arterial stiffness than serum creatinine and creatinine-based glomerular filtration rate (GFR).", "The aim of this study is to evaluate whether serum cystatin C is related to arterial stiffness independently of serum creatinine in subjects for whom serum creatinine is normal.", "A total of 2,018 individuals (1,120 males, 898 females) were enrolled.", "Mean brachial-ankle pulse wave velocity (baPWV) was used as a marker of arterial stiffness and sex-specific analysis was performed.", "A positive relationship between baPWV and serum cystatin C (Y=1109.0548+329.9102X, r2=0.056, p<0.001) was found in males.", "Stepwise multivariate regression analysis in males showed that age, waist circumference, heart rate, cystatin C level, triglyceride level, and fasting glucose were independent contributors to baPWV.", "In females, a positive relationship between baPWV and serum cystatin C (Y=1035.7828+402.2970X, r2=0.090, p<0.001) was found.", "Stepwise multivariate regression analysis showed that age, heart rate, cystatin C level, fasting glucose and insulin level were independent contributors to baPWV.", "Age, heart rate, fasting glucose and serum cystatin C were the significant variables in both genders that contributed to baPWV.", "In conclusion, this study confirmed that serum cystatin C was related to pulse wave velocity even in subjects with normal serum creatinine.", "This finding suggested that cystatin C could be a more predictable marker of arterial stiffness than serum creatinine and creatinine-based GFR."], "structured": false}
{"doc_id": 23440856, "title": "Screening for inhibition of Vibrio cholerae VipA-VipB interaction identifies small-molecule compounds active against type VI secretion.", "abstract": ["The type VI secretion system (T6SS) is the most prevalent bacterial secretion system and an important virulence mechanism utilized by Gram-negative bacteria, either to target eukaryotic cells or to combat other microbes.", "The components show much variability, but some appear essential for the function, and two homologues, denoted VipA and VipB in Vibrio cholerae, have been identified in all T6SSs described so far.", "Secretion is dependent on binding of an \u03b1-helical region of VipA to VipB, and in the absence of this binding, both components are degraded within minutes and secretion is ceased.", "The aim of the study was to investigate if this interaction could be blocked, and we hypothesized that such inhibition would lead to abrogation of T6S.", "A library of 9,600 small-molecule compounds was screened for their ability to block the binding of VipA-VipB in a bacterial two-hybrid system (B2H).", "After excluding compounds that showed cytotoxicity toward eukaryotic cells, that inhibited growth of Vibrio, or that inhibited an unrelated B2H interaction, 34 compounds were further investigated for effects on the T6SS-dependent secretion of hemolysin-coregulated protein (Hcp) or of phospholipase A1 activity.", "Two compounds, KS100 and KS200, showed intermediate or strong effects in both assays.", "Analogues were obtained, and compounds with potent inhibitory effects in the assays and desirable physicochemical properties as predicted by in silico analysis were identified.", "Since the compounds specifically target a virulence mechanism without affecting bacterial replication, they have the potential to mitigate the virulence with minimal risk for development of resistance."], "structured": false}
{"doc_id": 23460562, "title": "Early life compartmentalization of human T cell differentiation and regulatory function in mucosal and lymphoid tissues", "abstract": ["It is unclear how the immune response in early life becomes appropriately stimulated to provide protection while also avoiding excessive activation as a result of diverse new antigens.", "T cells are integral to adaptive immunity; mouse studies indicate that tissue localization of T cell subsets is important for both protective immunity and immunoregulation.", "In humans, however, the early development and function of T cells in tissues remain unexplored.", "We present here an analysis of lymphoid and mucosal tissue T cells derived from pediatric organ donors in the first two years of life, as compared to adult organ donors, revealing early compartmentalization of T cell differentiation and regulation.", "Whereas adult tissues contain a predominance of memory T cells, in pediatric blood and tissues the main subset consists of naive recent thymic emigrants, with effector memory T cells (T(EM)) found only in the lungs and small intestine.", "Additionally, regulatory T (T(reg)) cells comprise a high proportion (30-40%) of CD4(+) T cells in pediatric tissues but are present at much lower frequencies (1-10%) in adult tissues.", "Pediatric tissue T(reg) cells suppress endogenous T cell activation, and early T cell functionality is confined to the mucosal sites that have the lowest T(reg):T(EM) cell ratios, which suggests control in situ of immune responses in early life."], "structured": false}
{"doc_id": 23471400, "title": "Circulating microRNAs as biomarkers for hepatocellular carcinoma.", "abstract": ["GOALS We investigated whether measurement of serum levels of the microRNAs (miRNAs) miR-16, miR-195, and miR-199a, alone or in combination with conventional serum markers, can help to differentiate hepatocellular carcinoma (HCC) from chronic liver diseases (CLDs).   \n", "BACKGROUND Recent reports suggest a link between aberrant expression of miRNA, and HCC.   ", "STUDY This retrospective analysis was conducted using sera from 105 HCC patients, 107 CLD patients, and 71 normal control subjects.", "The miRNAs were measured using real-time reverse transcription-polymerase chain reaction.", "The conventional HCC markers \u03b1-fetoprotein (AFP), lens culinaris agglutinin-reactive AFP (AFP-L3%), and des-\u03b3-carboxyprothrombin (DCP) were measured with commercial kits.   \n", "RESULTS Serum levels of miR-16 and miR-199a were significantly lower in HCC than in CLD patients or control subjects (P<0.01).", "As a single marker, miR-16 had the highest sensitivity for HCC, followed by miR-199a, AFP, DCP, AFP-L3%, and miR-195.", "The combination of miR-16, AFP, AFP-L3%, and DCP yielded the optimal combination of sensitivity (92.4%) and specificity (78.5%) for HCC, overall and when analysis was restricted to patients with tumors size smaller than 3 cm.", "As a second-line HCC marker, miR-16 yielded positive HCC predictions in 18 of the 26 (69.2%) HCC patients with negative results on all 3 conventional markers, most of whom had tumors size smaller than 3 cm; miR-16 was falsely positive in only 12 of 96 (12.5%) CLD patients.   \n", "CONCLUSIONS The addition of miR-16 to conventional serum markers improved sensitivity and specificity for HCC.", "Use of miR-16 for second-line testing in cases considered negative on the basis of conventional HCC markers should be explored in larger, prospective studies."], "structured": true}
{"doc_id": 23495058, "title": "Mitochondrial haplogroups and hypervariable region polymorphisms in schizophrenia: a case-control study.", "abstract": ["Previous studies have detected associations between mitochondrial haplogroups and schizophrenia (SZ).", "However, no study has examined the relationship between major mitochondrial DNA (mtDNA) haplogroups and SZ in the Chinese population.", "The aim of this study was to assess the association between mtDNA haplogroups and SZ genesis in the Chinese Han population.", "We used a case-control study and sequenced the mtDNA hypervariable regions (HVR1, HVR2, and HVR3) in the Han population.", "We analyzed mtDNA haplogroups and HVR polymorphisms in 298 SZ patients and 298 controls.", "The haplotypes were classified into 10 major haplogroups: A, B, CZ, D, F, G, M, N, N9a, and R. Statistical analysis revealed that only N9a showed a nominally significant association with protection from SZ [1.68% vs. 6.38%, p=0.004, OR=0.251 (0.092-0.680); after adjustment for age and sex: p=0.006, OR=0.246 (0.090-0.669)].", "Three HVR polymorphisms were found to be nominally significantly different between subjects with SZ and controls, and all except one (m.204T>C) are linked to the N9a haplogroup.", "Our results indicate that mtDNA haplogroup N9a might be a protective factor for SZ."], "structured": false}
{"doc_id": 23509113, "title": "Resolution of acute inflammation in the lung.", "abstract": ["Acute inflammation in the lung is essential to health.", "So too is its resolution.", "In response to invading microbes, noxious stimuli, or tissue injury, an acute inflammatory response is mounted to protect the host.", "To limit inflammation and prevent collateral injury of healthy, uninvolved tissue, the lung orchestrates the formation of specialized proresolving mediators, specifically lipoxins, resolvins, protectins, and maresins.", "These immunoresolvents are agonists for resolution that interact with specific receptors on leukocytes and structural cells to blunt further inflammation and promote catabasis.", "This process appears to be defective in several common lung diseases that are characterized by excess or chronic inflammation.", "Here, we review the molecular and cellular effectors of resolution of acute inflammation in the lung."], "structured": false}
{"doc_id": 23509593, "title": "The calcium sensor STIM1 is regulated by androgens in prostate stromal cells.", "abstract": ["BACKGROUND Prostate development and maintenance in the adult results from an interaction of stromal and glandular components.", "Androgens can drive this process by direct action on the stroma.", "We investigated whether there was a direct link between androgens and another key regulator of stromal cells, intracellular Ca2+ ([Ca2+ ]i ).   \n", "METHODS Prostate stromal cells were freshly obtained and cultures derived from patients with benign prostatic hyperplasia.", "Gene expression in dihydrotestosterone treated and untreated cells was compared using Affymetrix gene expression arrays and Ca2+ regulated features were identified by Gene Ontology (GO).", "Changes in [Ca2+]i were determined in Fluo-4 loaded cells.", "Androgen regulation was confirmed by chromatin immunoprecipitaion.   \n", "RESULTS Stromal cell cultures were sorted for expression of integrin \u03b11 \u03b21 , which enriched for cells expressing the androgen receptor (AR).", "We identified key functional categories, within the androgen-induced gene expression signature, focusing on genes involved in calcium signaling.", "From this analysis, stromal interaction molecule-1 (STIM1) was identified as a significantly differentially expressed gene with four relevant associated GO terms.", "DNA sequence analysis showed that the promoter region of STIM1 contained putative androgen response element sequences in which AR binding ability of STIM1 was confirmed.", "Androgens directly regulated STIM1 expression and STIM1 effects on store-operated calcium entry were inhibited by STIM1 knock-down.", "Reduced STIM1 expression in prostate stromal cells led to a reduction in basal Ca2+ levels, the amount of Ca2+ released by thapsigargin and a reduction in store filling following TG-induced store depletion.   \n", "CONCLUSIONS These results indicate that androgens modulate [Ca2+]i through the direct regulation of the STIM1 gene by AR binding to the STIM1 promoter."], "structured": true}
{"doc_id": 23513718, "title": "Role of soluble guanylate cyclase in dilator responses of the cerebral microcirculation.", "abstract": ["Responses of cerebral blood vessels to nitric oxide (NO) are mediated by soluble guanylate cyclase (sGC)-dependent and potentially by sGC-independent mechanisms.", "One sGC-independent mechanism by which NO may produce vasodilatation is inhibition of formation of a vasoconstrictor metabolite produced through the cytochrome P450 pathway.", "In these experiments, we examined the hypothesis that dilatation of cerebral microvessels in response to NO is dependent on activation of sGC.", "Diameters of cerebral arterioles (baseline diameter=94+/-5 micrometers, mean+/-S.E.) were measured using a closed cranial window in anesthetized rabbits.", "Under control conditions, YC-1 [3-(5'-hydroxymethyl-2'-furyl)-1-benzyl indazole], an NO-independent activator of sGC, produced vasodilation that was blocked by ODQ (1H-[1,2,4]oxadiazolo[4,3,-a]quinoxalin-1-one)(10 microM), an inhibitor of sGC.", "These findings indicate that sGC is functionally important in cerebral arterioles.", "In addition, acetylcholine (which stimulates endogenous production of NO by endothelium) produced dilatation of cerebral arterioles that was inhibited by ODQ.", "For example, 1 microM acetylcholine dilated cerebral arterioles by 34+/-7 and 5+/-1% in the absence and presence of ODQ (10 microM), respectively.", "Increases in arteriolar diameter in response to sodium nitroprusside (1 microM, an NO donor) were inhibited by approximately 80% by ODQ, but were not affected by 17-ODYA (10 microM) or clotrimazole (10 microM), inhibitors of the cytochrome P450 pathway.", "Thus, dilatation of the cerebral microcirculation in response to exogenously applied and endogenously produced NO is dependent, in large part, on activation of sGC."], "structured": false}
{"doc_id": 23513818, "title": "Noxa controls Mule-dependent Mcl-1 ubiquitination through the regulation of the Mcl-1/USP9X interaction.", "abstract": ["The level of the Mcl-1 pro-survival protein is highly regulated, and the down-regulation of Mcl-1 expression favors the apoptotic process.", "Mcl-1 physically interacts with different BH3-only proteins; particularly, Noxa is involved in the modulation of Mcl-1 expression.", "In this study, we demonstrated that Noxa triggers the degradation of Mcl-1 at the mitochondria according to the exclusive location of Noxa at this compartment.", "The Noxa-induced degradation of Mcl-1 required the E3 ligase Mule, which is responsible for the polyubiquitination of Mcl-1.", "Because the USP9X deubiquitinase was recently demonstrated to be involved in Mcl-1 protein turnover by preventing its degradation through the removal of conjugated ubiquitin, we investigated whether Noxa affected the deubiquitination process.", "Interestingly, Noxa over-expression caused a decrease in the USP9X/Mcl-1 interaction associated with an increase in the Mcl-1 polyubiquitinated forms.", "Additionally, Noxa over-expression triggered an increase in the Mule/Mcl-1 interaction in parallel with the decrease in Mule/USP9X complex formation.", "Taken together, these modifications result in the degradation of Mcl-1 by the proteasome machinery.", "The implication of Noxa in the regulation of Mcl-1 proteasomal degradation adds complexity to this process, which is governed by multiple interactions."], "structured": false}
{"doc_id": 23531592, "title": "Paediatric HIV infection.", "abstract": ["By the year 2000 there will be six million pregnant women and five to ten million children infected with HIV-1.", "Intervention strategies have been planned and in some instances already started.", "A timely and cost-effective strategy needs to take into account that most HIV-1 infected individuals reside in developing countries.", "Further studies are needed on immunological and virological factors affecting HIV-1 transmission from mother to child, on differential disease progression in affected children, and on transient infection."], "structured": false}
{"doc_id": 23535770, "title": "Potential role of NF-kappaB in adult neural stem cells: the underrated steersman?", "abstract": ["Neural stem cells are precursors of neurons and glial cells.", "During brain development, these cells proliferate, migrate and differentiate into specific lineages.", "Recently neural stem cells within the adult central nervous system were identified.", "Informations are now emerging about regulation of stem cell proliferation, migration and differentiation by numerous soluble factors such as chemokines and cytokines.", "However, the signal transduction mechanisms downstream of these factors are less clear.", "Here, we review potential evidences for a novel central role of the transcription factor nuclear factor kappa B (NF-kappaB) in these crucial signal transduction processes.", "NF-kappaB is an inducible transcription factor detected in neurons, glia and neural stem cells.", "NF-kappaB was discovered by David Baltimore's laboratory as a transcription factor in lymphocytes.", "NF-kappaB is involved in many biological processes such as inflammation and innate immunity, development, apoptosis and anti-apoptosis.", "It has been recently shown that members of the NF-kappaB family are widely expressed by neurons, glia and neural stem cells.", "In the nervous system, NF-kappaB plays a crucial role in neuronal plasticity, learning, memory consolidation, neuroprotection and neurodegeneration.", "Recent data suggest an important role of NF-kappaB on proliferation, migration and differentiation of neural stem cells.", "NF-kappaB is composed of three subunits: two DNA-binding and one inhibitory subunit.", "Activation of NF-kappaB takes place in the cytoplasm and results in degradation of the inhibitory subunit, thus enabling the nuclear import of the DNA-binding subunits.", "Within the nucleus, several target genes could be activated.", "In this review, we suggest a model explaining the multiple action of NF-kappaB on neural stem cells.", "Furthermore, we discuss the potential role of NF-kappaB within the so-called brain cancer stem cells."], "structured": false}
{"doc_id": 23557241, "title": "Intrauterine factors and risk of breast cancer: a systematic review and meta-analysis of current evidence.", "abstract": ["BACKGROUND Emerging evidence suggests an association between female prenatal experience and her subsequent risk of developing breast cancer.", "Potential underlying mechanisms include variation in amounts of maternal endogenous sex hormones and growth hormones, germ-cell mutations, formation of cancer stem-cells, and other genetic or epigenetic events.", "We reviewed and summarised quantitatively the available data on intrauterine exposures and risk of breast cancer.   \n", "METHODS We systematically searched for studies that assessed association between perinatal factors and risk of breast cancer.", "We reviewed separately each of the perinatal factors, including birthweight, birth length, parental age at delivery, gestational age, intrauterine exposure to diethylstilbestrol, twin membership, maternal pre-eclampsia or eclampsia, and other factors.   \n", "FINDINGS We identified 57 studies published between Oct 1, 1980, and June 21, 2007.", "Increased risk of breast cancer was noted with increased birthweight (relative risk [RR] 1.15 [95% CI 1.09-1.21]), birth length (1.28 [1.11-1.48]), higher maternal age (1.13 [1.02-1.25]), and paternal age (1.12 [1.05-1.19]).", "Decreased risk of breast cancer was noted for maternal pre-eclampsia and eclampsia (0.48 [0.30-0.78]) and twin membership (0.93 [0.87-1.00]).", "No association was noted between risk of breast cancer and gestational age at birth (0.95 [0.71-1.26]) or maternal diethylstilbestrol treatment (1.40 [0.86-2.28]).   \n", "INTERPRETATION The intrauterine environment contributes to the predisposition of women to breast cancer in adulthood.", "The in-utero mechanisms responsible for such predisposition need to be elucidated."], "structured": true}
{"doc_id": 23573229, "title": "Helicobacter hepaticus does not induce or potentiate colitis in interleukin-10-deficient mice.", "abstract": ["Helicobacter hepaticus has been reported to induce colitis, hepatitis, and hepatocellular carcinoma in several different murine models.", "The aim of this study was to determine if H. hepaticus will cause colitis in monoassociated mice lacking the interleukin-10 gene (IL-10(-/-) mice) and potentiate colitis in specific-pathogen-free (SPF) IL-10(-/-) mice.", "Germfree IL-10(-/-) mice on either a mixed (C57BL/6 x 129/Ola) or inbred (129/SvEv) genetic background were monoassociated with H. hepaticus ATCC 51448 by oral feeding and rectal enemas.", "In a second experiment, germfree IL-10(-/-) mice were colonized with stool from SPF mice that harbored or did not harbor endogenous H. hepaticus.", "After 7 to 9 weeks of colonization, weight loss and mortality were assessed, the colon was isolated for histology and IL-12 secretion, and mesenteric lymph node cells were assessed for T-cell activation markers.", "It was found that IL-10(-/-) mice monoassociated with H. hepaticus for up to 16 weeks showed almost no histologic colitis or increased IL-12 production.", "SPF IL-10-knockout mice had no significant difference in weight loss, mortality rate, histologic scores, colonic IL-12 secretion, or T-cell activation with or without H. hepaticus.", "We conclude that H. hepaticus does not induce or potentiate disease in our IL-10(-/-) mice and therefore is not required to induce colitis in genetically susceptible hosts."], "structured": false}
{"doc_id": 23576165, "title": "Metabolic interplay between glycolysis and mitochondrial oxidation: The reverse Warburg effect and its therapeutic implication.", "abstract": ["Aerobic glycolysis, i.e., the Warburg effect, may contribute to the aggressive phenotype of hepatocellular carcinoma.", "However, increasing evidence highlights the limitations of the Warburg effect, such as high mitochondrial respiration and low glycolysis rates in cancer cells.", "To explain such contradictory phenomena with regard to the Warburg effect, a metabolic interplay between glycolytic and oxidative cells was proposed, i.e., the \"reverse Warburg effect\".", "Aerobic glycolysis may also occur in the stromal compartment that surrounds the tumor; thus, the stromal cells feed the cancer cells with lactate and this interaction prevents the creation of an acidic condition in the tumor microenvironment.", "This concept provides great heterogeneity in tumors, which makes the disease difficult to cure using a single agent.", "Understanding metabolic flexibility by lactate shuttles offers new perspectives to develop treatments that target the hypoxic tumor microenvironment and overcome the limitations of glycolytic inhibitors."], "structured": false}
{"doc_id": 23576726, "title": "Enhanced waterlogging tolerance in barley by manipulation of expression of the N\u2010end rule pathway E3 ligase PROTEOLYSIS6 ", "abstract": ["Increased tolerance of crops to low oxygen (hypoxia) during flooding is a key target for food security.", "In Arabidopsis thaliana (L.) Heynh., the N-end rule pathway of targeted proteolysis controls plant responses to hypoxia by regulating the stability of group VII ethylene response factor (ERFVII) transcription factors, controlled by the oxidation status of amino terminal (Nt)-cysteine (Cys).", "Here, we show that the barley (Hordeum vulgare L.) ERFVII BERF1 is a substrate of the N-end rule pathway in vitro.", "Furthermore, we show that Nt-Cys acts as a sensor for hypoxia in vivo, as the stability of the oxygen-sensor reporter protein MCGGAIL-GUS increased in waterlogged transgenic plants.", "Transgenic RNAi barley plants, with reduced expression of the N-end rule pathway N-recognin E3 ligase PROTEOLYSIS6 (HvPRT6), showed increased expression of hypoxia-associated genes and altered seed germination phenotypes.", "In addition, in response to waterlogging, transgenic plants showed sustained biomass, enhanced yield, retention of chlorophyll, and enhanced induction of hypoxia-related genes.", "HvPRT6 RNAi plants also showed reduced chlorophyll degradation in response to continued darkness, often associated with waterlogged conditions.", "Barley Targeting Induced Local Lesions IN Genomes (TILLING) lines, containing mutant alleles of HvPRT6, also showed increased expression of hypoxia-related genes and phenotypes similar to RNAi lines.", "We conclude that the N-end rule pathway represents an important target for plant breeding to enhance tolerance to waterlogging in barley and other cereals."], "structured": false}
{"doc_id": 23577014, "title": "A SUMO-Dependent Protein Network Regulates Chromosome Congression during Oocyte Meiosis", "abstract": ["During Caenorhabditis elegans oocyte meiosis, a multi-protein ring complex (RC) localized between homologous chromosomes, promotes chromosome congression through the action of the chromokinesin KLP-19.", "While some RC components are known, the mechanism of RC assembly has remained obscure.", "We show that SUMO E3 ligase GEI-17/PIAS is required for KLP-19 recruitment to the RC, and proteomic analysis identified KLP-19 as a SUMO substrate in vivo.", "In vitro analysis revealed that KLP-19 is efficiently sumoylated in a GEI-17-dependent manner, while GEI-17 undergoes extensive auto-sumoylation.", "GEI-17 and another RC component, the kinase BUB-1, contain functional SUMO interaction motifs (SIMs), allowing them to recruit SUMO modified proteins, including KLP-19, into the RC.", "Thus, dynamic SUMO modification and the presence of SIMs in RC components generate a SUMO-SIM network that facilitates assembly of the RC.", "Our results highlight the importance of SUMO-SIM networks in regulating the assembly of dynamic protein complexes."], "structured": false}
{"doc_id": 23577867, "title": "Prediagnostic levels of C-peptide, IGF-I, IGFBP -1, -2 and -3 and risk of endometrial cancer.", "abstract": ["Conditions related to chronic hyperinsulinemia, such as obesity, noninsulin dependent diabetes mellitus and polycystic ovary syndrome, are associated with an increased risk of endometrial cancer.", "Elevated plasma IGF-I and decreased levels of IGF-binding proteins have been shown to be associated with increased risk of several cancer types that are frequent in affluent societies.", "We investigated for the first time in a prospective study the association of pre-diagnostic blood concentrations of C-peptide (a marker of pancreatic insulin production), IGF-I, IGFBP-1, -2 and -3 with endometrial cancer risk.", "A case-control study was nested within 3 cohorts in New York (USA), Ume\u00e5 (Sweden) and Milan (Italy).", "It included 166 women with primary invasive endometrial cancer and 315 matched controls, of which 44 case and 78 control subjects were premenopausal at recruitment.", "Endometrial cancer risk increased with increasing levels of C-peptide (ptrend = 0.0002), up to an odds ratio (OR) of 4.76 [95% confidence interval (CI) = 1.91-11.8] for the highest quintile.", "This association remained after adjustment for BMI and other confounders [OR for the top quintile = 4.40 (1.65-11.7)].", "IGFBP-1 levels were inversely related to endometrial cancer [ptrend = 0.002; OR in the upper quintile = 0.30 (0.15-0.62)], but the association was weakened and lost statistical significance after adjustment for confounders [ptrend = 0.06; OR in the upper quintile = 0.49 (0.22-1.07)].", "Risk was unrelated to levels of IGF-I, IGFBP-2 and IGFBP-3.", "Chronic hyperinsulinemia, as reflected by increased circulating C-peptide, is associated with increased endometrial cancer risk.", "Decrease in the prevalence of chronic hyperinsulinemia, through changes in lifestyle or medication, is expected to prevent endometrial cancer."], "structured": false}
{"doc_id": 23581096, "title": "Interactions between SRY and SOX genes in mammalian sex determination.", "abstract": ["The SRY gene on the mammalian Y chromosome undoubtedly acts to determine testis, but it is still quite unclear how.", "It was originally supposed that SRY acts directly to activate other genes in the testis-determining pathway.", "This paper presents an alternative hypothesis that SRY functions indirectly, by interacting with related genes SOX3 (from which SRY evolved) and SOX9 (which appears to be intimately involved in vertebrate gonad differentiation).", "Specifically, I propose that in females SOX3 inhibits SOX9 function, but in males, SRY inhibits SOX3 and permits SOX9 to enact its testis-determining role.", "This hypothesis makes testable predictions of the phenotypes of XX and XY individuals with deficiencies or overproduction of any of the three genes, and is able to account for the difficult cases of XX(SRY-) males and transdifferentiation in the absence of SRY.", "The hypothesis also suggests a way that the dominant SRY sex-determining system of present-day mammals may have evolved from an ancient system relying on SOX3 dosage."], "structured": false}
{"doc_id": 23586085, "title": "Chromatin immunoprecipitation and microarray-based analysis of protein location", "abstract": ["Genome-wide location analysis, also known as ChIP-Chip, combines chromatin immunoprecipitation and DNA microarray analysis to identify protein-DNA interactions that occur in living cells.", "Protein-DNA interactions are captured in vivo by chemical crosslinking.", "Cell lysis, DNA fragmentation and immunoaffinity purification of the desired protein will co-purify DNA fragments that are associated with that protein.", "The enriched DNA population is then labeled, combined with a differentially labeled reference sample and applied to DNA microarrays to detect enriched signals.", "Various computational and bioinformatic approaches are then applied to normalize the enriched and reference channels, to connect signals to the portions of the genome that are represented on the DNA microarrays, to provide confidence metrics and to generate maps of protein-genome occupancy.", "Here, we describe the experimental protocols that we use from crosslinking of cells to hybridization of labeled material, together with insights into the aspects of these protocols that influence the results.", "These protocols require approximately 1 week to complete once sufficient numbers of cells have been obtained, and have been used to produce robust, high-quality ChIP-chip results in many different cell and tissue types."], "structured": false}
{"doc_id": 23594156, "title": "Spatial and temporal clusters of Barmah Forest virus disease in Queensland, Australia.", "abstract": ["OBJECTIVE To identify the spatial and temporal clusters of Barmah Forest virus (BFV) disease in Queensland in Australia, using geographical information systems and spatial scan statistic (SaTScan).   \n", "METHODS We obtained BFV disease cases, population and statistical local areas (SLAs) boundary data from Queensland Health and Australian Bureau of Statistics, respectively, during 1992-2008 for Queensland.", "A retrospective Poisson-based analysis using SaTScan software and method was conducted to identify both purely spatial and space-time BFV disease high-rate clusters.", "A spatial cluster size of a proportion of the population and a 200 km radius and varying time windows from 1 to 12 months were chosen (for the space-time analysis).   \n", "RESULTS The spatial scan statistic detected a most likely significant purely spatial cluster (including 23 SLAs) and a most likely significant space-time cluster (including 24 SLAs) in approximately the same location.", "Significant secondary clusters were also identified from both the analyses in several locations.   \n", "CONCLUSIONS This study provides evidence of the existence of statistically significant BFV disease clusters in Queensland, Australia.", "The study also demonstrated the relevance and applicability of SaTScan in analysing ongoing surveillance data to identify clusters to facilitate the development of effective BFV disease prevention and control strategies in Queensland, Australia."], "structured": true}
{"doc_id": 23599024, "title": "Surfactant Protein B Suppresses Lung Cancer Progression by Inhibiting Secretory Phospholipase A2 Activity and Arachidonic Acid Production", "abstract": ["Background/Aims: Radiotherapy is applied to patients with inoperable cancer types including advanced stage non-small cell lung cancer (NSCLC) and radioresistance functions as a critical obstacle in radiotherapy.", "This study was aimed to investigate the mechanism of radioresistance regulated by surfactant protein B (SP-B).", "Methods: To investigate the role of SP-B in radioresistance, \u0394SFTPB A549 cell line was established and SP-B expression was analyzed.", "In response to ionizing radiation (IR), the change of SP-B expression was analyzed in A549 and NCI-H441 cell lines.", "Conditioned media (CM) from NSCLC cells were utilized to evaluate the downstream signaling pathway.", "The in vivo effects of SP-B were assessed through mouse xenograft model with intratumoral injection of CM.", "Results: In response to IR, NSCLC cell lines showed decreased SP-B regulated by the TGF-\u03b2 signaling and decreased SP-B stimulated cell survival and epithelial-mesenchymal transition.", "Treatment with CM from irradiated cells activated sPLA2, enhanced protein kinase C\u03b4-MAPKs signaling pathway, and increased arachidonic acid production.", "We confirmed the in vivo roles of SP-B through mouse xenograft model.", "Conclusion: Our results revealed that down-regulation of SP-B was involved in the radiation-induced metastatic conversion of NSCLC and provided evidence that SP-B acted as a suppressor of NSCLC progression."], "structured": false}
{"doc_id": 23601616, "title": "Liraglutide improves hippocampal synaptic plasticity associated with increased expression of Mash1 in ob/ob mice", "abstract": ["Objective:Consumption of high-fat diet exerts adverse effects on learning and memory formation, which is linked to impaired hippocampal function.", "Activation of glucagon-like peptide-1 (GLP-1) signalling ameliorates detrimental effects of obesity-diabetes on cognitive function; however, mechanisms underlying these beneficial actions remain unclear.", "This study examined effects of daily subcutaneous treatment with GLP-1 mimetic, Liraglutide, on synaptic plasticity, hippocampal gene expression and metabolic control in adult obese diabetic (ob/ob) mice.", "Results:Long-term potentiation (LTP) induced by area CA1 was completely abolished in ob/ob mice compared with lean controls.", "Deleterious effects on LTP were rescued (P<0.001) with Liraglutide.", "Indeed, Liraglutide-treated mice exhibited superior LTP profile compared with lean controls (P<0.01).", "Expression of hippocampal brain-derived neurotropic factor and neurotrophic tyrosine kinase receptor-type 2 were not significantly different, but synaptophysin and Mash1 were decreased in ob/ob mice.", "Treatment with Liraglutide over 21 days increased expression of Mash1 in ob/ob mice (2.0-fold; P<0.01).", "These changes were associated with significantly reduced plasma glucose (21% reduction; P<0.05) and markedly improved plasma insulin concentrations (2.1- to 3.3-fold; P<0.05 to P<0.01).", "Liraglutide also significantly reduced the glycaemic excursion following an intraperitonal glucose load (area under curve (AUC) values: 22%; P<0.05) and markedly enhanced the insulin response to glucose (AUC values: 1.6-fold; P<0.05).", "O2 consumption, CO2 production, respiratory exchange ratio and energy expenditure were not altered by Liraglutide therapy.", "On day 21, accumulated food intake (32% reduction; P<0.05) and number of feeding bouts (32% reduction; P<0.05) were significantly reduced but simple energy restriction was not responsible for the beneficial actions of Liraglutide.", "Conclusion:Liraglutide elicits beneficial effects on metabolic control and synaptic plasticity in mice with severe obesity and insulin resistance mediated in part through increased expression of Mash1 believed to improve hippocampal neurogenesis and cell survival."], "structured": false}
{"doc_id": 23604601, "title": "Post-transcriptional regulation of IME1 determines initiation of meiosis in Saccharomyces cerevisiae.", "abstract": ["The IME1 gene of Saccharomyces cerevisiae is required for initiation of meiosis.", "Transcription of IME1 is detected under conditions which are known to induce initiation of meiosis, namely starvation for nitrogen and glucose, and the presence of MATa1 and MAT alpha 2 gene products.", "In this paper we show that IME1 is also subject to translational regulation.", "Translation of IME1 mRNA is achieved either upon nitrogen starvation, or upon G1 arrest.", "In the presence of nutrients, constitutively elevated transcription of IME1 is also sufficient for the translation of IME1 RNA.", "Four different conditions were found to cause expression of Ime1 protein in vegetative cultures: elevated transcription levels due to the presence of IME1 on a multicopy plasmid; elevated transcription provided by a Gal-IME1 construct; G1 arrest due to alpha-factor treatment; G1 arrest following mild heat-shock treatment of cdc28 diploids.", "Using these conditions, we obtained evidence that starvation is required not only for transcription and efficient translation of IME1, but also for either the activation of Ime1 protein or for the induction/activation of another factor that, either alone or in combination with Ime1, induces meiosis."], "structured": false}
{"doc_id": 23618826, "title": "Targeted proteomics reveals compositional dynamics of 60S pre-ribosomes after nuclear export", "abstract": ["Construction and intracellular targeting of eukaryotic pre-ribosomal particles involve a multitude of diverse transiently associating trans-acting assembly factors, energy-consuming enzymes, and transport factors.", "The ability to rapidly and reliably measure co-enrichment of multiple factors with maturing pre-ribosomal particles presents a major biochemical bottleneck towards revealing their function and the precise contribution of >50 energy-consuming steps that drive ribosome assembly.", "Here, we devised a workflow that combines genetic trapping, affinity-capture, and selected reaction monitoring mass spectrometry (SRM-MS), to overcome this deficiency.", "We exploited this approach to interrogate the dynamic proteome of pre-60S particles after nuclear export.", "We uncovered assembly factors that travel with pre-60S particles to the cytoplasm, where they are released before initiating translation.", "Notably, we identified a novel shuttling factor that facilitates nuclear export of pre-60S particles.", "Capturing and quantitating protein interaction networks of trapped intermediates of macromolecular complexes by our workflow is a reliable discovery tool to unveil dynamic processes that contribute to their in vivo assembly and transport."], "structured": false}
{"doc_id": 23627419, "title": "Obstructive sleep apnea-hypopnea and incident stroke: the sleep heart health study.", "abstract": ["RATIONALE Although obstructive sleep apnea is associated with physiological perturbations that increase risk of hypertension and are proatherogenic, it is uncertain whether sleep apnea is associated with increased stroke risk in the general population.   \n", "OBJECTIVES To quantify the incidence of ischemic stroke with sleep apnea in a community-based sample of men and women across a wide range of sleep apnea.   \n", "METHODS Baseline polysomnography was performed between 1995 and 1998 in a longitudinal cohort study.", "The primary exposure was the obstructive apnea-hypopnea index (OAHI) and outcome was incident ischemic stroke.   \n", "MEASUREMENTS AND MAIN RESULTS A total of 5,422 participants without a history of stroke at the baseline examination and untreated for sleep apnea were followed for a median of 8.7 years.", "One hundred ninety-three ischemic strokes were observed.", "In covariate-adjusted Cox proportional hazard models, a significant positive association between ischemic stroke and OAHI was observed in men (P value for linear trend: P = 0.016).", "Men in the highest OAHI quartile (>19) had an adjusted hazard ratio of 2.86 (95% confidence interval, 1.1-7.4).", "In the mild to moderate range (OAHI, 5-25), each one-unit increase in OAHI in men was estimated to increase stroke risk by 6% (95% confidence interval, 2-10%).", "In women, stroke was not significantly associated with OAHI quartiles, but increased risk was observed at an OAHI greater than 25.   \n", "CONCLUSIONS The strong adjusted association between ischemic stroke and OAHI in community-dwelling men with mild to moderate sleep apnea suggests that this is an appropriate target for future stroke prevention trials."], "structured": true}
{"doc_id": 23633726, "title": "Reproducibility of 31P cardiac magnetic resonance spectroscopy at 3 T.", "abstract": ["The purpose of this work was to take advantage of the new clinical field strength of 3 T to implement and optimize a chemical shift imaging (CSI) acquisition protocol to produce spectra of high quality with high specificity to the myocardium within a clinically feasible scan time.", "Further, an analysis method was implemented dependent purely on anatomical location of spectra, and as such free from any potential user bias caused by inference from spectral information.", "Twenty healthy male subjects were scanned on two separate occasions using the optimized CSI protocol at 3 T. Data were analyzed for intra- and inter-subject variability, as well as intra- and inter-observer variability.", "The average phosphocreatine (PCr)/adenosine triphosphate (ATP) value for scan 1 was 2.07 +/-", "0.38 and for scan 2 was 2.14 +/-", "0.46, showing no significant difference between scans.", "Intra-subject variability was 0.43 +/-", "0.35 (percentage difference 20%) and the inter-subject coefficient of variation was 18%.", "The intra-observer variability, assessed as the absolute difference between analyses of the data by a single observer, was 0.14 +/-", "0.24 with no significant difference between analyses.", "The inter-observer variability showed no significant differences between the PCr/ATP value measured by four different observers as demonstrated by an intra-class correlation coefficient of 0.763.", "The increased signal available at 3 T has improved spatial resolution and thereby increased myocardial specificity without any significant decrease in reproducibility over previous studies at 1.5 T. We present an acquisition protocol that routinely provides high quality spectra and a robust analysis method that is free from potential user bias."], "structured": false}
{"doc_id": 23634484, "title": "Nuclear HuR accumulation through phosphorylation by Cdk1.", "abstract": ["A predominantly nuclear RNA-binding protein, HuR translocates to the cytoplasm in response to stress and proliferative signals, where it stabilizes or modulates the translation of target mRNAs.", "Here, we present evidence that HuR phosphorylation at S202 by the G2-phase kinase Cdk1 influences its subcellular distribution.", "HuR was specifically phosphorylated in synchronous G2-phase cultures; its cytoplasmic levels increased by Cdk1-inhibitory interventions and declined in response to Cdk1-activating interventions.", "In keeping with the prominently cytoplasmic location of the nonphosphorylatable point mutant HuR(S202A), phospho-HuR(S202) was shown to be predominantly nuclear using a novel anti-phospho-HuR(S202) antibody.", "The enhanced cytoplasmic presence of unphosphorylated HuR was linked to its decreased association with 14-3-3 and to its heightened binding to target mRNAs.", "Our findings suggest that Cdk1 phosphorylates HuR during G2, thereby helping to retain it in the nucleus in association with 14-3-3 and hindering its post-transcriptional function and anti-apoptotic influence."], "structured": false}
{"doc_id": 23639838, "title": "Surgical Resection for Patients with Solid Brain Metastases: Current Status", "abstract": ["Brain metastases occur in up to 40% of patients with cancer.", "Their management has been revolutionized in the last decade by three developments: improved imaging and detection of metastases, better treatment of systemic disease with the result that metastases occur more often; and improved surgical techniques including image-guided surgery to treat metastatic lesions.", "Class 1 data suggest that surgery is a better treatment for metastases than whole brain radiation.", "Other data suggest that metastases even in eloquent cortex can be removed safely.", "The complication rate is low and the recurrence rate is less than 10%.", "In general, indications for surgery include a mass with an unknown primary; a symptomatic mass including one in eloquent areas; a mass with considerable edema requiring high dose steroids; a mass greater than 3 cm; or patient preference when radiosurgery may also be an option.", "The question of radiosurgery or whole brain radiation as adjunct to surgical removal requires further evaluation."], "structured": false}
{"doc_id": 23649163, "title": "Clinical features and treatment of peristomal pyoderma gangrenosum.", "abstract": ["CONTEXT Peristomal pyoderma gangrenosum (PPG), an unusual variant of pyoderma gangrenosum, has been reported almost exclusively in patients with inflammatory bowel disease (IBD) and is frequently misdiagnosed.   \n", "OBJECTIVE To better characterize the clinical manifestations, diagnosis, and management of PPG.   \n", "DESIGN, SETTING, AND PATIENTS Retrospective analysis of 7 patients with PPG observed in a university-affiliated community setting between 1988 and December 1999.   \n", "MAIN OUTCOME MEASURES Clinical and histopathologic features, associated disorders, and microbiologic findings.   \n", "RESULTS Two patients had Crohn disease, 2 had ulcerative colitis, and 3 had abdominal cancer.", "Five patients had at least 1 relapse of PPG after initial healing.", "Although 3 of 4 patients with IBD had active bowel disease, a parallel course with PPG occurred in only 1 patient.", "Both patients whose stoma was relocated developed an ulcer at the new site.", "Effective therapies included topical superpotent corticosteroids; intralesional injection of triamcinolone acetonide at the ulcer margin; topical cromolyn sodium; oral dapsone, prednisone, cyclosporine, mycophenolate mofetil; and intravenous infliximab.   \n", "CONCLUSION Our experiences demonstrate that although PPG has been most often reported in patients with IBD, it may occur in the absence of IBD.", "Biopsy of the skin lesion is not diagnostic but excludes other causes.", "Relocation of the stoma may be associated with a new ulceration and should be avoided.", "Trauma to the skin of a predisposed patient may elicit the pustules or ulcerations associated with pathergy.", "JAMA.", "2000;284:1546-1548."], "structured": true}
{"doc_id": 23664875, "title": "The Tof1p-Csm3p protein complex counteracts the Rrm3p helicase to control replication termination of Saccharomyces cerevisiae.", "abstract": ["Termination of replication forks at the natural termini of the rDNA of Saccharomyces cerevisiae is controlled in a sequence-specific and polar mode by the interaction of the Fob1p replication terminator protein with the tandem Ter sites located in the nontranscribed spacers.", "Here we show, by both 2D gel analyses and chromatin immunoprecipitations (ChIP), that there exists a second level of global control mediated by the intra-S-phase checkpoint protein complex of Tof1p and Csm3p that protect stalled forks at Ter sites against the activity of the Rrm3p helicase (\"sweepase\").", "The sweepase tends to release arrested forks presumably by the transient displacement of the Ter-bound Fob1p.", "Consistent with this mechanism, very few replication forks were arrested at the natural replication termini in the absence of the two checkpoint proteins.", "In the absence of the Rrm3p helicase, there was a slight enhancement of fork arrest at the Ter sites.", "Simultaneous deletions of the TOF1 (or CSM3), and the RRM3 genes restored fork arrest by removing both the fork-releasing and fork-protection activities.", "Other genes such as MRC1, WSS1, and PSY2 that are also involved in the MRC1 checkpoint pathway were not involved in this global control.", "This observation suggests that Tof1p-Csm3p function differently from MRC1 and the other above-mentioned genes.", "This mechanism is not restricted to the natural Ter sites but was also observed at fork arrest caused by the meeting of a replication fork with transcription approaching from the opposite direction."], "structured": false}
{"doc_id": 23665162, "title": "Association of hypomethylation of LINE-1 repetitive element in blood leukocyte DNA with an increased risk of hepatocellular carcinoma", "abstract": ["Global DNA hypomethylation has been associated with increased risk for cancers of the colorectum, bladder, breast, head and neck, and testicular germ cells.", "The aim of this study was to examine whether global hypomethylation in blood leukocyte DNA is associated with the risk of hepatocellular carcinoma (HCC).", "A total of 315 HCC cases and 356 age-, sex- and HBsAg status-matched controls were included.", "Global methylation in blood leukocyte DNA was estimated by analyzing long interspersed element-1 (LINE-1) repeats using bisulfite-polymerase chain reaction (PCR) and pyrosequencing.", "We observed that the median methylation level in HCC cases (percentage of 5-methylcytosine (5mC)=77.7%) was significantly lower than that in controls (79.5% 5mC) (P=0.004, Wilcoxon rank-sum test).", "The odds ratios (ORs) of HCC for individuals in the third, second, and first (lowest) quartiles of LINE-1 methylation were 1.1 (95% confidence interval (CI) 0.7\u20131.8), 1.4 (95% CI 0.8\u20132.2), and 2.6 (95% CI 1.7\u20134.1) (P for trend <0.001), respectively, compared to individuals in the fourth (highest) quartile.", "A 1.9-fold (95% CI 1.4\u20132.6) increased risk of HCC was observed among individuals with LINE-1 methylation below the median compared to individuals with higher (>median) LINE-1 methylation.", "Our results demonstrate for the first time that individuals with global hypomethylation measured in LINE-1 repeats in blood leukocyte DNA have an increased risk for HCC.", "Our data provide the evidence that global hypomethylation detected in the easily obtainable DNA source of blood leukocytes may help identify individuals at risk of HCC."], "structured": false}
{"doc_id": 23670644, "title": "The ketogenic diet for the treatment of childhood epilepsy: a randomised controlled trial.", "abstract": ["BACKGROUND The ketogenic diet has been widely and successfully used to treat children with drug-resistant epilepsy since the 1920s.", "The aim of this study was to test the efficacy of the ketogenic diet in a randomised controlled trial.   \n", "METHODS 145 children aged between 2 and 16 years who had at least daily seizures (or more than seven seizures per week), had failed to respond to at least two antiepileptic drugs, and had not been treated previously with the ketogenic diet participated in a randomised controlled trial of its efficacy to control seizures.", "Enrolment for the trial ran between December, 2001, and July, 2006.", "Children were seen at one of two hospital centres or a residential centre for young people with epilepsy.", "Children were randomly assigned to receive a ketogenic diet, either immediately or after a 3-month delay, with no other changes to treatment (control group).", "Neither the family nor investigators were blinded to the group assignment.", "Early withdrawals were recorded, and seizure frequency on the diet was assessed after 3 months and compared with that of the controls.", "The primary endpoint was a reduction in seizures; analysis was intention to treat.", "Tolerability of the diet was assessed by questionnaire at 3 months.", "The trial is registered with ClinicalTrials.gov, number NCT00564915.   \n", "FINDINGS 73 children were assigned to the ketogenic diet and 72 children to the control group.", "Data from 103 children were available for analysis: 54 on the ketogenic diet and 49 controls.", "Of those who did not complete the trial, 16 children did not receive their intervention, 16 did not provide adequate data, and ten withdrew from the treatment before the 3-month review, six because of intolerance.", "After 3 months, the mean percentage of baseline seizures was significantly lower in the diet group than in the controls (62.0%vs 136.9%, 75% decrease, 95% CI 42.4-107.4%; p<0.0001).", "28 children (38%) in the diet group had greater than 50% seizure reduction compared with four (6%) controls (p<0.0001), and five children (7%) in the diet group had greater than 90% seizure reduction compared with no controls (p=0.0582).", "There was no significant difference in the efficacy of the treatment between symptomatic generalised or symptomatic focal syndromes.", "The most frequent side-effects reported at 3-month review were constipation, vomiting, lack of energy, and hunger.   \n", "INTERPRETATION The results from this trial of the ketogenic diet support its use in children with treatment-intractable epilepsy.   \n", "FUNDING HSA Charitable Trust; Smiths Charity; Scientific Hospital Supplies; Milk Development Council."], "structured": true}
{"doc_id": 23686039, "title": "Building-in biosafety for synthetic biology.", "abstract": ["As the field of synthetic biology develops, real-world applications are moving from the realms of ideas and laboratory-confined research towards implementation.", "A pressing concern, particularly with microbial systems, is that self-replicating re-engineered cells may produce undesired consequences if they escape or overwhelm their intended environment.", "To address this biosafety issue, multiple mechanisms for constraining microbial replication and horizontal gene transfer have been proposed.", "These include the use of host-construct dependencies such as toxin-antitoxin pairs, conditional plasmid replication or the requirement for a specific metabolite to be present for cellular function.", "While refactoring of the existing genetic code or tailoring of orthogonal systems, e.g. xeno nucleic acids, offers future promise of more stringent 'firewalls' between natural and synthetic cells, here we focus on what can be achieved using existing technology.", "The state-of-the-art in designing for biosafety is summarized and general recommendations are made (e.g. short environmental retention times) for current synthetic biology projects to better isolate themselves against potentially negative impacts."], "structured": false}
{"doc_id": 23698769, "title": "Sustained active site rigidity during synthesis by human DNA polymerase \u03bc", "abstract": ["DNA polymerase \u03bc (Pol \u03bc) is the only template-dependent human DNA polymerase capable of repairing double-strand DNA breaks (DSBs) with unpaired 3\u2032 ends in nonhomologous end joining (NHEJ).", "To probe this function, we structurally characterized Pol \u03bc's catalytic cycle for single-nucleotide incorporation.", "These structures indicate that, unlike other template-dependent DNA polymerases, Pol \u03bc shows no large-scale conformational changes in protein subdomains, amino acid side chains or DNA upon dNTP binding or catalysis.", "Instead, the only major conformational change is seen earlier in the catalytic cycle, when the flexible loop 1 region repositions upon DNA binding.", "Pol \u03bc variants with changes in loop 1 have altered catalytic properties and are partially defective in NHEJ.", "The results indicate that specific loop 1 residues contribute to Pol \u03bc's unique ability to catalyze template-dependent NHEJ of DSBs with unpaired 3\u2032 ends."], "structured": false}
{"doc_id": 23700330, "title": "Angiopoietin-1 requires p190 RhoGAP to protect against vascular leakage in vivo.", "abstract": ["Angiopoietin-1 (Ang-1), a ligand of the endothelium-specific receptor Tie-2, inhibits permeability in the mature vasculature, but the mechanism remains unknown.", "Here we show that Ang-1 signals Rho family GTPases to organize the cytoskeleton into a junction-fortifying arrangement that enhances the permeability barrier function of the endothelium.", "Ang-1 phosphorylates Tie-2 and its downstream effector phosphatidylinositol 3-kinase.", "This induces activation of one endogenous GTPase, Rac1, and inhibition of another, RhoA. Loss of either part of this dual effect abrogates the cytoskeletal and anti-permeability actions of Ang-1, suggesting that coordinated GTPase regulation is necessary for the vessel-sealing effects of Ang-1.", "p190 RhoGAP, a GTPase regulatory protein, provides this coordinating function as it is phosphorylated by Ang-1 treatment, requires Rac1 activation, and is necessary for RhoA inhibition.", "Ang-1 prevents the cytoskeletal and pro-permeability effects of endotoxin but requires p190 RhoGAP to do so.", "Treatment with p190 RhoGAP small interfering RNA completely abolishes the ability of Ang-1 to rescue endotoxemia-induced pulmonary vascular leak and inflammation in mice.", "We conclude that Ang-1 prevents vascular permeability by regulating the endothelial cytoskeleton through coordinated and opposite effects on the Rho GTPases Rac1 and RhoA. By linking Rac1 activation and RhoA inhibition, p190 RhoGAP is critical to the protective effects of Ang-1 against endotoxin.", "These results provide mechanistic evidence that targeting the endothelium through Tie-2 may offer specific therapeutic strategies in life-threatening endotoxemic conditions such as sepsis and acute respiratory distress syndrome."], "structured": false}
{"doc_id": 23702805, "title": "Vesicular trafficking of semaphorin 3A is activity-dependent and differs between axons and dendrites.", "abstract": ["Secreted semaphorins act as guidance cues in the developing nervous system and may have additional functions in mature neurons.", "How semaphorins are transported and secreted by neurons is poorly understood.", "We find that endogenous semaphorin 3A (Sema3A) displays a punctate distribution in axons and dendrites of cultured cortical neurons.", "GFP-Sema3A shows a similar distribution and co-localizes with secretory vesicle cargo proteins.", "Live-cell imaging reveals highly dynamic trafficking of GFP-Sema3A vesicles with distinct properties in axons and dendrites regarding directionality, velocity, mobility and pausing time.", "In axons, most GFP-Sema3A vesicles move fast without interruption, almost exclusively in the anterograde direction, while in dendrites many GFP-Sema3A vesicles are stationary and move equally frequent in both directions.", "Disruption of microtubules, but not of actin filaments, significantly impairs GFP-Sema3A transport.", "Interestingly, depolarization induces a reversible arrest of axonal transport of GFP-Sema3A vesicles but has little effect on dendritic transport.", "Conversely, action potential blockade using tetrodotoxin (TTX) accelerates axonal transport, but not dendritic transport.", "These data indicate that axons and dendrites regulate trafficking of Sema3A and probably other secretory vesicles in distinct ways, with axons specializing in fast, uninterrupted, anterograde transport.", "Furthermore, neuronal activity regulates secretory vesicle trafficking in axons by a depolarization-evoked trafficking arrest."], "structured": false}
{"doc_id": 23704559, "title": "Frequency of Intracranial Aneurysms Determined by Magnetic Resonance Angiography in Children (Mean Age 16) Having Operative or Endovascular Treatment of Coarctation of the Aorta (Mean Age 3).", "abstract": ["Coarctation of the aorta (CofA) has been associated with an increased risk of intracranial aneurysm (IA).", "This magnetic resonance angiography (MRA) study investigates the prevalence of IAs in 80 children treated in early life for CofA. MRA was performed at mean age of 15.7 \u00b1 7.1 years, and surgical or endovascular treatment for CofA occurred at a mean age of 2.6 \u00b1 4.4 years.", "No IA was found.", "In contrast with earlier findings in adult patients with late treatment for CofA, this first systematic study of very early treated patients for CofA failed to confirm the association between CofA and IAs.", "Our results call the abnormal developmental relation between CofA and IAs into question and suggest that modifiable risk factors like hypertension may be responsible for IA development in patients with CofA with adult diagnosis and treatment.", "In conclusion, our data suggest that early treatment of CofA can reduce the formation of IAs in children so as to make MRA screening less valuable in this young population."], "structured": false}
{"doc_id": 23716150, "title": "Transcriptional profiling of the heart reveals chamber-specific gene expression patterns.", "abstract": ["Cardiac chamber-specific gene expression is critical for the normal development and function of the heart.", "To investigate the genetic basis of cardiac anatomical specialization, we have undertaken a nearly genome-wide transcriptional profiling of the four heart chambers and the interventricular septum.", "Rigorous statistical analysis has allowed the identification of known and novel members of gene families that are felt to be important in cardiac development and function, including LIM proteins, homeobox proteins, wnt and T-box pathway proteins, as well as structural proteins like actins and myosins.", "In addition, these studies have allowed the identification of thousands of additional differentially expressed genes, for which there is little structural or functional information.", "Clustering of genes with known and unknown functions provides insights into signaling pathways that are essential for development and maintenance of chamber-specific features.", "To facilitate future research in this area, a searchable internet database has been constructed that allows study of the chamber-specific expression of any gene represented on this comprehensive microarray.", "It is anticipated that further study of genes identified through this effort will provide insights into the specialization of heart chamber tissues, and their specific roles in cardiac development, aging, and disease."], "structured": false}
{"doc_id": 23727313, "title": "CD34+ hematopoietic stem-progenitor cell microRNA expression and function: a circuit diagram of differentiation control.", "abstract": ["MicroRNAs (miRNAs) are a recently identified class of epigenetic elements consisting of small noncoding RNAs that bind to the 3' untranslated region of mRNAs and down-regulate their translation to protein.", "miRNAs play critical roles in many different cellular processes including metabolism, apoptosis, differentiation, and development.", "We found 33 miRNAs expressed in CD34+ hematopoietic stem-progenitor cells (HSPCs) from normal human bone marrow and mobilized human peripheral blood stem cell harvests.", "We then combined these data with human HSPC mRNA expression data and with miRNA-mRNA target predictions, into a previously undescribed miRNA:mRNA interaction database called the Transcriptome Interaction Database.", "The in silico predictions from the Transcriptome Interaction Database pointed to miRNA control of hematopoietic differentiation through translational control of mRNAs critical to hematopoiesis.", "From these predictions, we formulated a model for miRNA control of stages of hematopoiesis in which many of the genes specifying hematopoietic differentiation are expressed by HSPCs, but are held in check by miRNAs until differentiation occurs.", "We validated miRNA control of several of these target mRNAs by demonstrating that their translation in fact is decreased by miRNAs.", "Finally, we chose miRNA-155 for functional characterization in hematopoiesis, because we predicted that it would control both myelopoiesis and erythropoiesis.", "As predicted, miRNA-155 transduction greatly reduced both myeloid and erythroid colony formation of normal human HSPCs."], "structured": false}
{"doc_id": 23737024, "title": "Acute exercise activates nuclear factor (NF)-kappaB signaling pathway in rat skeletal muscle.", "abstract": ["Two studies were performed to investigate the effects of an acute bout of physical exercise on the nuclear protein kappaB (NF-kappaB) signaling pathway in rat skeletal muscle.", "In Study 1, a group of rats (n=6) was run on the treadmill at 25 m/min, 5% grade, for 1 h or until exhaustion (Ex), and compared with a second group (n=6) injected with two doses of pyrrolidine dithiocarbamate (PDTC, 100 mg/kg, i.p.) 24 and 1 h prior to the acute exercise bout.", "Three additional groups of rats (n=6) were injected with either 8 mg/kg (i.p.) of lipopolysaccharide (LPS), 1 mmol/kg (i.p.) t-butylhydroperoxide (tBHP), or saline (C) and killed at resting condition.", "Ex rats showed higher levels of NF-kappaB binding and P50 protein content in muscle nuclear extracts compared with C rats.", "Cytosolic IkappaBalpha and IkappaB kinase (IKK) contents were decreased, whereas phospho-IkappaBalpha and phospho-IKK contents were increased, comparing Ex vs. C. The exercise-induced activation of NF-kappaB signaling cascade was partially abolished by PDTC treatment.", "LPS, but not tBHP, treatment mimicked and exaggerated the effects observed in Ex rats.", "In Study 2, the time course of exercise-induced NF-kappaB activation was examined.", "Highest levels of NF-kappaB binding were observed at 2 h postexercise.", "Decreased cytosolic IkappaBalpha and increased phosphor-IkappaBalpha content were found 0-1 h postexercise whereas P65 reached peak levels at 2-4 h. These data suggest that the NF-kappaB signaling pathway can be activated in a redox-sensitive manner during muscular contraction, presumably due to increased oxidant production.", "The cascade of intracellular events may be the overture to elevated gene expression of manganese superoxide dismutase reported earlier (Pfluegers Arch.", "442, 426-434, 2001)."], "structured": false}
{"doc_id": 23746313, "title": "Staphylococcus aureus RNAIII and the endoribonuclease III coordinately regulate spa gene expression.", "abstract": ["Staphylococcus aureus RNAIII is one of the largest regulatory RNAs, which controls several virulence genes encoding exoproteins and cell-wall-associated proteins.", "One of the RNAIII effects is the repression of spa gene (coding for the surface protein A) expression.", "Here, we show that spa repression occurs not only at the transcriptional level but also by RNAIII-mediated inhibition of translation and degradation of the stable spa mRNA by the double-strand-specific endoribonuclease III (RNase III).", "The 3' end domain of RNAIII, partially complementary to the 5' part of spa mRNA, efficiently anneals to spa mRNA through an initial loop-loop interaction.", "Although this annealing is sufficient to inhibit in vitro the formation of the translation initiation complex, the coordinated action of RNase III is essential in vivo to degrade the mRNA and irreversibly arrest translation.", "Our results further suggest that RNase III is recruited for targeting the paired RNAs.", "These findings add further complexity to the expression of the S. aureus virulon."], "structured": false}
{"doc_id": 23746332, "title": "Fast calcium and voltage-sensitive dye imaging in enteric neurones reveal calcium peaks associated with single action potential discharge.", "abstract": ["Slow changes in [Ca(2+)](i) reflect increased neuronal activity.", "Our study demonstrates that single-trial fast [Ca(2+)](i) imaging (\u2265200 Hz sampling rate) revealed peaks each of which are associated with single spike discharge recorded by consecutive voltage-sensitive dye (VSD) imaging in enteric neurones and nerve fibres.", "Fast [Ca(2+)](i) imaging also revealed subthreshold fast excitatory postsynaptic potentials.", "Nicotine-evoked [Ca(2+)](i) peaks were reduced by -conotoxin and blocked by ruthenium red or tetrodotoxin.", "Fast [Ca(2+)](i) imaging can be used to directly record single action potentials in enteric neurones.", "[Ca(2+)](i) peaks required opening of voltage-gated sodium and calcium channels as well as Ca(2+) release from intracellular stores."], "structured": false}
{"doc_id": 23763738, "title": "New colorimetric cytotoxicity assay for anticancer-drug screening.", "abstract": ["We have developed a rapid, sensitive, and inexpensive method for measuring the cellular protein content of adherent and suspension cultures in 96-well microtiter plates.", "The method is suitable for ordinary laboratory purposes and for very large-scale applications, such as the National Cancer Institute's disease-oriented in vitro anticancer-drug discovery screen, which requires the use of several million culture wells per year.", "Cultures fixed with trichloroacetic acid were stained for 30 minutes with 0.4% (wt/vol) sulforhodamine B (SRB) dissolved in 1% acetic acid.", "Unbound dye was removed by four washes with 1% acetic acid, and protein-bound dye was extracted with 10 mM unbuffered Tris base [tris (hydroxymethyl)aminomethane] for determination of optical density in a computer-interfaced, 96-well microtiter plate reader.", "The SRB assay results were linear with the number of cells and with values for cellular protein measured by both the Lowry and Bradford assays at densities ranging from sparse subconfluence to multilayered supraconfluence.", "The signal-to-noise ratio at 564 nm was approximately 1.5 with 1,000 cells per well.", "The sensitivity of the SRB assay compared favorably with sensitivities of several fluorescence assays and was superior to those of both the Lowry and Bradford assays and to those of 20 other visible dyes.", "The SRB assay provides a colorimetric end point that is nondestructive, indefinitely stable, and visible to the naked eye.", "It provides a sensitive measure of drug-induced cytotoxicity, is useful in quantitating clonogenicity, and is well suited to high-volume, automated drug screening.", "SRB fluoresces strongly with laser excitation at 488 nm and can be measured quantitatively at the single-cell level by static fluorescence cytometry."], "structured": false}
{"doc_id": 23777820, "title": "A murine model of human myeloma bone disease.", "abstract": ["Myeloma causes a devastating and unique form of osteolytic bone disease.", "Although osteoclast activation is responsible for bone destruction, the precise mechanisms by which myeloma cells increase osteoclast activity have not been defined.", "An animal model of human myeloma bone disease would help in clarification of these mechanisms.", "Multiple myeloma occurs spontaneously in aging C57 BL/KaLwRij mice and has all of the features of the disease in humans, including the characteristic bone lesions.", "The disease can be induced in normal C57 BL/KaLwRij mice by inoculation of fresh marrow-derived cells from mice with myeloma, but this model is difficult to study because of variability in the number of myeloma cells in marrow-derived preparations.", "To develop a better animal model of human myeloma bone disease, we have established and subcloned a cell line from this murine myeloma and found that it causes osteolytic bone lesions in mice characteristic of human myeloma bone disease.", "The cell line produces interleukin-6, but grows independent of exogenous interleukin-6.", "Mice inoculated intravenously with the cultured cells predictably develop an identical disease to the mice injected intravenously with fresh bone-marrow-derived myeloma cells, including monoclonal gammopathy and radiologic bone lesions.", "We found that some of the mice became hypercalcemic, and the bone lesions are characterized by increased osteoclast activity.", "We found identical results when we inoculated Nu/Bg/XID mice with cultured murine myeloma cells.", "Because we can inoculate mice with precise numbers of cells and predict accurately when the mice will develop bone lesions, become hypercalcemic, and die, this should be a convenient model for determining the mechanisms by which the myeloma cells cause osteoclast activation in this model of human myeloma bone disease."], "structured": false}
{"doc_id": 23783727, "title": "Ticagrelor vs. clopidogrel in patients with acute coronary syndromes and diabetes: a substudy from the PLATelet inhibition and patient Outcomes (PLATO) trial", "abstract": ["AIMS patients with diabetes mellitus (DM) have high platelet reactivity and are at increased risk of ischaemic events and bleeding post-acute coronary syndromes (ACS).", "In the PLATelet inhibition and patient Outcomes (PLATO) trial, ticagrelor reduced the primary composite endpoint of cardiovascular death, myocardial infarction, or stroke, but with similar rates of major bleeding compared with clopidogrel.", "We aimed to investigate the outcome with ticagrelor vs. clopidogrel in patients with DM or poor glycaemic control.   \n", "METHODS AND RESULTS we analysed patients with pre-existing DM (n = 4662), including 1036 patients on insulin, those without DM (n = 13 951), and subgroups based on admission levels of haemoglobin A1c (HbA1c; n = 15 150).", "In patients with DM, the reduction in the primary composite endpoint (HR: 0.88, 95% CI: 0.76-1.03), all-cause mortality (HR: 0.82, 95% CI: 0.66-1.01), and stent thrombosis (HR: 0.65, 95% CI: 0.36-1.17) with no increase in major bleeding (HR: 0.95, 95% CI: 0.81-1.12) with ticagrelor was consistent with the overall cohort and without significant diabetes status-by-treatment interactions.", "There was no heterogeneity between patients with or without ongoing insulin treatment.", "ticagrelor reduced the primary endpoint, all-cause mortality, and stent thrombosis in patients with HbA1c above the median (HR: 0.80, 95% CI: 0.70-0.91; HR: 0.78, 95% CI: 0.65-0.93; and HR: 0.62, 95% CI: 0.39-1.00, respectively) with similar bleeding rates (HR: 0.98, 95% CI: 0.86-1.12).   \n", "CONCLUSION ticagrelor, when compared with clopidogrel, reduced ischaemic events in ACS patients irrespective of diabetic status and glycaemic control, without an increase in major bleeding events."], "structured": true}
{"doc_id": 23785605, "title": "Cardiovascular risk factors and migraine: the GEM population-based study.", "abstract": ["BACKGROUND Migraine, particularly with aura, is a risk factor for early-onset ischemic stroke.", "The underlying mechanisms are unknown, but may in part be due to migraineurs having an increased risk profile for cardiovascular disease.", "In this study, the authors compare the cardiovascular risk profile of adult migraineurs to that of nonmigraineurs.   \n", "METHODS Participants (n = 5,755, 48% men, age 20 to 65 years) are from the Genetic Epidemiology of Migraine (GEM) study, a population-based study in the Netherlands.", "A total of 620 current migraineurs were identified: 31% with aura (MA), 64% without aura (MO), and 5% unclassified.", "Controls were 5,135 individuals without lifetime migraine.", "Measured cardiovascular risk factors included blood pressure (BP), serum total and high-density lipoprotein cholesterol (TC, HDL), smoking, oral contraceptive use, and the Framingham risk score for myocardial infarction or coronary heart disease (CHD) death.   \n", "RESULTS Compared to controls, migraineurs were more likely to smoke (OR = 1.43 [1.1 to 1.8]), less likely to consume alcohol (OR = 0.58 [0.5 to 0.7]), and more likely to report a parental history of early myocardial infarction.", "Migraineurs with aura were more likely to have an unfavorable cholesterol profile (TC > or = 240 mg/dL [OR = 1.43 (0.97 to 2.1)], TC:HDL ratio > 5.0 [OR = 1.64 (1.1 to 2.4)]), have elevated BP (systolic BP > 140 mm Hg or diastolic BP > 90 mm Hg [OR = 1.76 (1.04 to 3.0)]), and report a history of early onset CHD or stroke (OR = 3.96 [1.1 to 14.3]); female migraineurs with aura were more likely to be using oral contraceptives (OR = 2.06 [1.05 to 4.0]).", "The odds of having an elevated Framingham risk score for CHD were approximately doubled for the migraineurs with aura.   \n", "CONCLUSIONS Migraineurs, particularly with aura, have a higher cardiovascular risk profile than individuals without migraine."], "structured": true}
{"doc_id": 23801039, "title": "Th2-mediated host protective immunity to intestinal nematode infections.", "abstract": ["Despite many years of study, relatively little is known about the effector mechanisms that operate against intestine-dwelling nematodes.", "Most of the current understanding comes from studies of laboratory model systems in rodents.", "It is clear that when an intestinal helminth infection takes place the immune system generates a strong Th2-mediated response, which regulates a variety of responses characteristic of helminth infections such as eosinophilia, intestinal mastocytosis and elevated IgE production.", "The ability to modulate the host's immune response in vivo with cytokine-specific monoclonal antibodies and recombinant cytokines, together with the use of animals with disruption of key genes involved in the immune response, have provided powerful tools with which to dissect the potential effector mechanisms operating.", "In the absence of a T-cell compartment the host is unable to expel the parasite.", "If a Th1-dominated response is generated, protective immunity is almost universally compromised.", "Thus, it it would appear that some aspect of a Th2-mediated response controls effector mechanisms.", "Although it is clear that for some infections the mast cell appears to be involved in protection, probably through the generation of a non-specific inflammatory response, how these cells become activated remains unclear.", "Data from infections in transgenic animals suggest that activation is not through the high-affinity receptor for IgE. Such studies also call into doubt the importance of conventional interactions between effector leucocytes and antibody.", "There is little evidence to support a protective role for eosinophilia in any system.", "New data also imply that, although interleukin 4 (IL-4) is generally important (and can exert effects independent of an adaptive immune response), it is not always sufficient to mediate protection; other Th2 cytokines (e.g. IL-13) may warrant closer investigation.", "It is apparent that a number of potential Th2-controlled effector mechanisms (some of which may be particularly important at mucosal surfaces) remain to be explored.", "Overall, it is likely that worm expulsion is the result of a combination of multiple mechanisms, some of which are more critical to some species of parasite than to others."], "structured": false}
{"doc_id": 23804187, "title": "Wnt/\u03b2-catenin signaling defines organizing centers that orchestrate growth and differentiation of the regenerating zebrafish caudal fin.", "abstract": ["Zebrafish regenerate their fins via the formation of a population of progenitor cells, the blastema.", "Wnt/\u03b2-catenin signaling is essential for blastemal cell proliferation and patterning of the overlying epidermis.", "Yet, we find that \u03b2-catenin signaling is neither active in the epidermis nor the majority of the proliferative blastemal cells.", "Rather, tissue-specific pathway interference indicates that Wnt signaling in the nonproliferative distal blastema is required for cell proliferation in the proximal blastema, and signaling in cells lining the osteoblasts directs osteoblast differentiation.", "Thus, Wnt signaling regulates epidermal patterning, blastemal cell proliferation, and osteoblast maturation indirectly via secondary signals.", "Gene expression profiling, chromatin immunoprecipitation, and functional rescue experiments suggest that Wnt/\u03b2-catenin signaling acts through Fgf and Bmp signaling to control epidermal patterning, whereas retinoic acid and Hedgehog signals mediate its effects on blastemal cell proliferation.", "We propose that Wnt signaling orchestrates fin regeneration by defining organizing centers that instruct cellular behaviors of adjacent tissues."], "structured": false}
{"doc_id": 23816832, "title": "The utility of cerebrospinal fluid analysis in patients with multiple sclerosis", "abstract": ["Diagnosis of multiple sclerosis (MS) requires the exclusion of other possible diagnoses.", "For this reason, the cerebrospinal fluid (CSF) should be routinely analysed in patients with a first clinical event suggestive of MS.", "CSF analysis is no longer mandatory for diagnosis of relapsing\u2013remitting MS, as long as MRI diagnostic criteria are fulfilled.", "However, caution is required in diagnosing MS in patients with negative MRI findings or in the absence of CSF analysis, as CSF investigation is useful to eliminate other causes of disease.", "The detection of oligoclonal IgG bands in CSF has potential prognostic value and is helpful for clinical decision-making.", "In addition, CSF analysis is important for research into the pathogenesis of MS.", "Pathophysiological and neurodegenerative findings of inflammation in MS have been derived from CSF investigations.", "Novel CSF biomarkers, though not yet validated, have been identified for diagnosis of MS and for ascertaining disease activity, prognosis and response to treatment, and are likely to increase in number with modern detection techniques.", "In this Review, we summarize CSF findings that shed light on the differential diagnosis of MS, and highlight the potential of novel biomarkers for this disease that could advance understanding of its pathophysiology."], "structured": false}
{"doc_id": 23830488, "title": "Expression of circadian genes correlates with liver metastasis and outcomes in colorectal cancer.", "abstract": ["Circadian rhythms are daily oscillations in various biological processes, generated by the feedback loops of eight core circadian genes: Period1 (Per1), Period2 (Per2), Period3 (Per3), Cryptochrome1 (Cry1), Cryptochrome2 (Cry2), Clock, Bmal1 and Casein Kinase I \u03b5 (CKI\u03b5).", "Recent studies have suggested that circadian genes participate in the growth and development of various cancers.", "This study examined the relations of circadian gene expression to clinicopathological factors and outcomes in patients with colorectal cancer.", "We studied surgical specimens of cancer tissue and adjacent normal mucosa obtained from 202 patients with untreated colorectal cancer.", "The relative expression levels of the circadian genes in the specimens were measured by quantitative real-time, reverse-transcription polymerase chain reaction.", "Expression of the Clock gene and the CKI\u03b5 gene in cancer tissue were significantly higher compared to that in adjacent normal mucosa.", "Expression of the Per1 and Per3 genes in cancer tissue was significantly lower compared to that in adjacent normal mucosa.", "Analysis of the relations between clinicopathological features and expression of the eight circadian genes in cancer tissue showed that high expression of the Bmal1 gene and low expression of the Per1 gene correlated with liver metastasis.", "On analysis of the relations between outcomes and gene expression, high expression of the Per2 gene was associated with significantly better outcomes than low expression of the Per2 gene.", "Overexpression of the Bmal1 gene and reduced expression of the Per1 gene may thus be useful predictors of liver metastasis.", "Moreover, reduced expression of the Per2 gene may be a predictor of outcomes in patients with colorectal cancer."], "structured": false}
{"doc_id": 23841828, "title": "The Danish prescription registries.", "abstract": ["The extensive computerisation of Danish pharmacies has permitted the establishment of two large prescription registries: The Odense University Pharmacoepidemiological Database (OPED) and the Pharmacoepidemiological Prescription Database of North Jutland (PDNJ).", "The Danish prescription registries content, coverage, completeness and the quality of the data are discussed in this article.", "Furthermore, conditions for access to the data are presented.", "The two prescription registries cover a background population of approximately one million or 18% of the Danish population.", "The populations covered by the registries are stable and representative of the Danish population in general.", "The registries cover all reimbursed medicine at the level of the individual user.", "Registration of a unique and permanent personal identifier enables the compilation of longitudinal drug histories and allows the linking of prescription data to other population-based Danish registries.", "The degree of completeness of the Danish prescription registries is excellent for reimbursed prescription drugs.", "A small number of comparison studies also indicate high validity of the register information.", "The Danish prescription registries represent a useful new data source for pharmacoepidemiological studies."], "structured": false}
{"doc_id": 23848916, "title": "Oridonin, a diterpenoid purified from Rabdosia rubescens, inhibits the proliferation of cells from lymphoid malignancies in association with blockade of the NF-kappa B signal pathways.", "abstract": ["This study found that oridonin, a natural diterpenoid purified from Rabdosia rubescens, inhibited growth of multiple myeloma (MM; U266, RPMI8226), acute lymphoblastic T-cell leukemia (Jurkat), and adult T-cell leukemia (MT-1) cells with an effective dose that inhibited 50% of target cells (ED50) ranging from 0.75 to 2.7 microg/mL. Terminal deoxynucleotidyltransferase-mediated dUTP nick end labeling staining showed that oridonin caused apoptosis of MT-1 cells in a time-dependent manner.", "We explored effects of oridonin on antiapoptotic Bcl-2 family members and found that it down-regulated levels of Mcl-1 and BCL-x(L), but not Bcl-2 protein, in both MT-1 and RPMI8226 cells.", "Further studies found that oridonin inhibited nuclear factor-kappa B (NF-kappa B) DNA-binding activity in these cells as measured by luciferase reporter gene, ELISA-based, and electrophoretic mobility shift assays.", "Oridonin also blocked tumor necrosis factor-alpha- and lipopolysaccharide-stimulated NF-kappa B activity in Jurkat cells as well as RAW264.7 murine macrophages.", "Of note, oridonin decreased survival of freshly isolated adult T-cell leukemia (three samples), acute lymphoblastic leukemia (one sample), chronic lymphocytic leukemia (one sample), non-Hodgkin's lymphoma (three samples), and MM (four samples) cells from patients in association with inhibition of NF-kappa B DNA-binding activity.", "On the other hand, oridonin did not affect survival of normal lymphoid cells from healthy volunteers.", "Taken together, oridonin might be useful as adjunctive therapy for individuals with lymphoid malignancies, including the lethal disease adult T-cell leukemia."], "structured": false}
{"doc_id": 23851261, "title": "Uncertainty in integrative structural modeling.", "abstract": ["Integrative structural modeling uses multiple types of input information and proceeds in four stages: (i) gathering information, (ii) designing model representation and converting information into a scoring function, (iii) sampling good-scoring models, and (iv) analyzing models and information.", "In the first stage, uncertainty originates from data that are sparse, noisy, ambiguous, or derived from heterogeneous samples.", "In the second stage, uncertainty can originate from a representation that is too coarse for the available information or a scoring function that does not accurately capture the information.", "In the third stage, the major source of uncertainty is insufficient sampling.", "In the fourth stage, clustering, cross-validation, and other methods are used to estimate the precision and accuracy of the models and information."], "structured": false}
{"doc_id": 23862975, "title": "Moist occlusive dressing (Aquacel(\u00ae) Ag) versus moist open dressing (MEBO(\u00ae)) in the management of partial-thickness facial burns: a comparative study in Ain Shams University.", "abstract": ["INTRODUCTION The face is the central point of the physical features; it transmits expressions and emotions, communicates feelings and allows for individual identity.", "Facial burns are very common and are devastating to the affected patient and results into numerous physical, emotional and psychosocial sequels.", "Partial thickness facial burns are very common especially among children.", "This study compares the effect of standard moist open technique management and a moist closed technique for partial thickness burns of the face.   \n", "PATIENTS AND METHODS Patients with partial-thickness facial burns admitted in the burn unit, Ain Shams University, Cairo, Egypt in the period from April 2009 to December 2009 were included in this study.", "They were divided into two groups to receive either open treatment with MEBO(\u00ae) (n=20) or coverage with Aquacel(\u00ae) Ag (n=20).", "Demographics (age, gender, ethnicity, TBSA, burn areas), length of hospital stay (LOS), rate of infections, time to total healing, frequency of dressing changes, pain, cost benefit and patient discomfort were compared between the two groups.", "The long-term outcome (incidence of hypertrophic scarring) was assessed for up to 6 months follow-up period.   \n", "RESULTS There were no significant differences in demographics between the two groups.", "In the group treated with the Aquacel(\u00ae) Ag, the mean time for re-epithelialization was 10.5 days, while it was 12.4 days in the MEBO(\u00ae) group (p<0.05).", "Frequency of changes, pain and patient discomfort were less with Aquacel(\u00ae) Ag.", "Cost was of no significant difference between the two groups.", "Scar quality improved in the Aquacel(\u00ae) Ag treatment group.", "Three and 6 months follow-up was done and long-term outcomes were recorded in both groups.   \n", "CONCLUSION Moist occlusive dressing (Aquacel(\u00ae) Ag) significantly improves the management and healing rate of partial thickness facial burns with better long-term outcome compared to moist open dressing (MEBO(\u00ae))."], "structured": true}
{"doc_id": 23863551, "title": "Feedback upregulation of HER3 (ErbB3) expression and activity attenuates antitumor effect of PI3K inhibitors.", "abstract": ["We examined the effects of an inhibitor of PI3K, XL147, against human breast cancer cell lines with constitutive PI3K activation.", "Treatment with XL147 resulted in dose-dependent inhibition of cell growth and levels of pAKT and pS6, signal transducers in the PI3K/AKT/TOR pathway.", "In HER2-overexpressing cells, inhibition of PI3K was followed by up-regulation of expression and phosphorylation of multiple receptor tyrosine kinases, including HER3.", "Knockdown of FoxO1 and FoxO3a transcription factors suppressed the induction of HER3, InsR, IGF1R, and FGFR2 mRNAs upon inhibition of PI3K.", "In HER2(+) cells, knockdown of HER3 with siRNA or cotreatment with the HER2 inhibitors trastuzumab or lapatinib enhanced XL147-induced cell death and inhibition of pAKT and pS6.", "Trastuzumab and lapatinib each synergized with XL147 for inhibition of pAKT and growth of established BT474 xenografts.", "These data suggest that PI3K antagonists will inhibit AKT and relieve suppression of receptor tyrosine kinase expression and their activity.", "Relief of this feedback limits the sustained inhibition of the PI3K/AKT pathway and attenuates the response to these agents.", "As a result, PI3K pathway inhibitors may have limited clinical activity overall if used as single agents.", "In patients with HER2-overexpressing breast cancer, PI3K inhibitors should be used in combination with HER2/HER3 antagonists."], "structured": false}
{"doc_id": 23863576, "title": "Developmental RacGAP \u03b12-Chimaerin Signaling Is a Determinant of the Morphological Features of Dendritic Spines in Adulthood.", "abstract": ["UNLABELLED Morphological characteristics of dendritic spines form the basis of cognitive ability.", "However, molecular mechanisms involved in fine-tuning of spine morphology during development are not fully understood.", "Moreover, it is unclear whether, and to what extent, these developmental mechanisms determine the normal adult spine morphological features.", "Here, we provide evidence that \u03b12-isoform of Rac-specific GTPase-activating protein \u03b1-chimaerin (\u03b12-chimaerin) is involved in spine morphological refinement during late postnatal period, and furthermore show that this developmental \u03b12-chimaerin function affects adult spine morphologies.", "We used a series of mice with global and conditional knock-out of \u03b1-chimaerin isoforms (\u03b11-chimaerin and \u03b12-chimaerin).", "\u03b12-Chimaerin disruption, but not \u03b11-chimaerin disruption, in the mouse results in an increased size (and density) of spines in the hippocampus.", "In contrast, overexpression of \u03b12-chimaerin in developing hippocampal neurons induces a decrease of spine size.", "Disruption of \u03b12-chimaerin suppressed EphA-mediated spine morphogenesis in cultured developing hippocampal neurons.", "\u03b12-Chimaerin disruption that begins during the juvenile stage results in an increased size of spines in the hippocampus.", "Meanwhile, spine morphologies are unaltered when \u03b12-chimaerin is deleted only in adulthood.", "Consistent with these spine morphological results, disruption of \u03b12-chimaerin beginning in the juvenile stage led to an increase in contextual fear learning in adulthood; whereas contextual learning was recently shown to be unaffected when \u03b12-chimaerin was deleted only in adulthood.", "Together, these results suggest that \u03b12-chimaerin signaling in developmental stages contributes to determination of the morphological features of adult spines and establishment of normal cognitive ability.   ", "SIGNIFICANCE STATEMENT Recent studies of neurodevelopmental disorders in humans and their animal models have led to an attractive hypothesis that spine morphogenesis during development forms the basis of adult cognition.", "In particular, the roles of Rac and its regulators, such as Rac-specific GTPase-activating proteins (RacGAPs) and Rac guanine nucleotide exchange factors, are a topic of focus in spine morphogenesis and cognitive ability.", "Using a series of mice with global and conditional knock-out (KO) of RacGAP \u03b1-chimaerin isoforms (\u03b11-chimaerin and \u03b12-chimaerin), we provide compelling evidence demonstrating that \u03b12-chimaerin is involved in spine morphological refinement during late postnatal development and that this developmental \u03b12-chimaerin function affects adult spine morphologies.", "Furthermore, our results clearly showed that \u03b12-chimaerin signaling during late postnatal development contributes to normal cognitive ability in adult mice."], "structured": false}
{"doc_id": 23865182, "title": "Efficacy and tolerability of amitriptylinoxide in the treatment of chronic tension-type headache: a multi-centre controlled study.", "abstract": ["Amitriptyline is the medication of first choice in the treatment of chronic tension-type headache.", "In 197 patients with chronic tension-type headache (87M and 110F with a mean age of 38 +/-", "13 (18-68)) efficacy and tolerability of 60-90 mg amitriptylinoxide (AO) were compared with 50-75 mg amitriptyline (AM) and placebo (PL) in a double-blind, parallel-group trial consisting of a four weeks' baseline phase and 12 weeks of treatment.", "The primary study endpoint was a reduction of at least 50% of the product of headache duration and frequency and a reduction of at least 50% in headache intensity.", "Statistics used were Fisher's exact test and analysis of variance.", "No significant difference emerged between AO, AM and PL with respect to the primary study endpoint.", "Treatment response occurred in 30.3% of the AO, 22.4% of the AM and 21.9% of the PL group.", "A reduction in headache duration and frequency of at least 50% was found in 39.4% on AO, in 25.4% on AM and in 26.6% on PL (PAO-PL = .1384, PAM-PL = 1.000, PAO-AM = .0973).", "A reduction in headache intensity of at least 50% was found in 31.8% on AO, in 26.9% on AM and in 26.6% on PL (PAO-PL = .5657, PAM-PL = 1.000, PAO-AM = .5715).", "Trend analysis with respect to a significant reduction of headache intensity (p < 0.05) and the product of headache duration and frequency revealed a superior effect of AO.(ABSTRACT TRUNCATED AT 250 WORDS)"], "structured": false}
{"doc_id": 23868856, "title": "Downregulation of Superoxide Dismutase Activity and Gene Expression in Cultured Rat Brain Astrocytes after Incubation with Vitamin C", "abstract": ["Reactive oxygen species have been linked with neuropathological changes in the central nervous system.", "Epidemiological studies supported the beneficial effect of supplementation of antioxidants.", "Superoxide dismutase (SOD) is an endogenous enzyme which can scavenge reactive oxygen species.", "This study investigated the effect of supplementation with ascorbic acid (vitamin C) on the changes of SOD in cultured neurological cells.", "Rat brain astrocytes (RBA-1 cells) were incubated with vitamin C and divided into four groups: a control group (without vitamin C) and three treatment groups with vitamin C at 40, 80, and 160 \u00b5mol/l.", "After short-term (2 days) and long-term (7 days) incubation, SOD activity, SOD mRNA level by Northern blotting, and SOD protein amounts by Western blotting were measured.", "After 2 days of incubation, vitamin C resulted in a decrease in the activity of SOD in a concentration-dependent manner (Mn-SOD from 14.8 \u00b1 1.2 to 13.2 \u00b1 0.5 U/mg protein and Cu/Zn-SOD from 64.8 \u00b1 1.2 to 51.7 \u00b1 0.9 U/mg protein; p < 0.05), and vitamin C also attenuated the Cu/Zn-SOD mRNA level from 100 to 86.3 \u00b1 6.7%; p < 0.01), whereas the protein amounts of these two SODs remained unchanged.", "After 7 days of incubation with vitamin C, the SOD activity of RBA-1 cells decreased significantly (Mn-SOD from 14.9 \u00b1 0.3 to 11.8 \u00b1 0.3 U/mg protein and Cu/Zn SOD from 61.8 \u00b1 1.8 to 54.6 \u00b1 0.9 U/mg protein; p < 0.01), and the mRNA level was also attenuated (Mn-SOD from 100 to 86.8 \u00b1 8.7% and Cu/Zn-SOD from 100 to 84.7 \u00b1 4.8%; p < 0.01).", "These results suggest that 2 and 7 days of incubation with relatively high concentrations of vitamin C may downregulate activity and gene expression of SOD in cultured RBA-1 cells."], "structured": false}
{"doc_id": 23869951, "title": "Lateral Hypothalamic Area Glutamatergic Neurons and Their Projections to the Lateral Habenula Regulate Feeding and Reward.", "abstract": ["UNLABELLED The overconsumption of calorically dense, highly palatable foods is thought to be a major contributor to the worldwide obesity epidemic; however, the precise neural circuits that directly regulate hedonic feeding remain elusive.", "Here, we show that lateral hypothalamic area (LHA) glutamatergic neurons, and their projections to the lateral habenula (LHb), negatively regulate the consumption of palatable food.", "Genetic ablation of LHA glutamatergic neurons increased daily caloric intake and produced weight gain in mice that had access to a high-fat diet, while not altering general locomotor activity.", "Anterior LHA glutamatergic neurons send a functional glutamatergic projection to the LHb, a brain region involved in processing aversive stimuli and negative reward prediction outcomes.", "Pathway-specific, optogenetic stimulation of glutamatergic LHA-LHb circuit resulted in detectable glutamate-mediated EPSCs as well as GABA-mediated IPSCs, although the net effect of neurotransmitter release was to increase the firing of most LHb neurons.", "In vivo optogenetic inhibition of LHA-LHb glutamatergic fibers produced a real-time place preference, whereas optogenetic stimulation of LHA-LHb glutamatergic fibers had the opposite effect.", "Furthermore, optogenetic inhibition of LHA-LHb glutamatergic fibers acutely increased the consumption of a palatable liquid caloric reward.", "Collectively, these results demonstrate that LHA glutamatergic neurons are well situated to bidirectionally regulate feeding and potentially other behavioral states via their functional circuit connectivity with the LHb and potentially other brain regions.   ", "SIGNIFICANCE STATEMENT In this study, we show that the genetic ablation of LHA glutamatergic neurons enhances caloric intake.", "Some of these LHA glutamatergic neurons project to the lateral habenula, a brain area important for generating behavioral avoidance.", "Optogenetic stimulation of this circuit has net excitatory effects on postsynaptic LHb neurons.", "This is the first study to characterize the functional connectivity and behavioral relevance of this circuit within the context of feeding and reward-related behavior."], "structured": false}
{"doc_id": 23887844, "title": "Glucose Metabolism Inhibits Apoptosis in Neurons and Cancer Cells by Redox Inactivation of Cytochrome c", "abstract": ["Neurons and cancer cells use glucose extensively, yet the precise advantage of this adaptation remains unclear.", "These two seemingly disparate cell types also show an increased regulation of the apoptotic pathway, which allows for their long-term survival.", "Here we show that both neurons and cancer cells strictly inhibit cytochrome c-mediated apoptosis by a mechanism dependent on glucose metabolism.", "We report that the pro-apoptotic activity of cytochrome c is influenced by its redox state and that increases in reactive oxygen species (ROS) following an apoptotic insult lead to the oxidation and activation of cytochrome c. In healthy neurons and cancer cells, however, cytochrome c is reduced and held inactive by intracellular glutathione (GSH), generated as a result of glucose metabolism by the pentose phosphate pathway.", "These results uncover a striking similarity in apoptosis regulation between neurons and cancer cells and provide insight into an adaptive advantage offered by the Warburg effect for cancer cell evasion of apoptosis and for long-term neuronal survival."], "structured": false}
{"doc_id": 23895668, "title": "mTORC2 Regulates Amino Acid Metabolism in Cancer by Phosphorylation of the Cystine-Glutamate Antiporter xCT.", "abstract": ["Mutations in cancer reprogram amino acid metabolism to drive tumor growth, but the molecular mechanisms are not well understood.", "Using an unbiased proteomic screen, we identified mTORC2 as a critical regulator of amino acid metabolism in cancer via phosphorylation of the cystine-glutamate antiporter xCT.", "mTORC2 phosphorylates serine 26 at the cytosolic N terminus of xCT, inhibiting its activity.", "Genetic inhibition of mTORC2, or pharmacologic inhibition of the mammalian target of rapamycin (mTOR) kinase, promotes glutamate secretion, cystine uptake, and incorporation into glutathione, linking growth factor receptor signaling with amino acid uptake and utilization.", "These results identify an unanticipated mechanism regulating amino acid metabolism in cancer, enabling tumor cells to adapt to changing environmental conditions."], "structured": false}
{"doc_id": 23897346, "title": "Bayesian models leveraging bioactivity and cytotoxicity information for drug discovery.", "abstract": ["Identification of unique leads represents a significant challenge in drug discovery.", "This hurdle is magnified in neglected diseases such as tuberculosis.", "We have leveraged public high-throughput screening (HTS) data to experimentally validate a virtual screening approach employing Bayesian models built with bioactivity information (single-event model) as well as bioactivity and cytotoxicity information (dual-event model).", "We virtually screened a commercial library and experimentally confirmed actives with hit rates exceeding typical HTS results by one to two orders of magnitude.", "This initial dual-event Bayesian model identified compounds with antitubercular whole-cell activity and low mammalian cell cytotoxicity from a published set of antimalarials.", "The most potent hit exhibits the in vitro activity and in vitro/in vivo safety profile of a drug lead.", "These Bayesian models offer significant economies in time and cost to drug discovery."], "structured": false}
{"doc_id": 23901235, "title": "A role for interleukin-1\u03b2 in determining the lineage fate of embryonic rat hippocampal neural precursor cells.", "abstract": ["Neurogenesis occurs in the hippocampus of the developing and adult brain due to the presence of multipotent stem cells and restricted precursor cells at different stages of differentiation.", "It has been proposed that they may be of potential benefit for use in cell transplantation approaches for neurodegenerative disorders and trauma.", "Prolonged release of interleukin-1\u03b2 (IL-1\u03b2) from activated microglia has a deleterious effect on hippocampal neurons and is implicated in the impaired neurogenesis and cognitive dysfunction associated with aging, Alzheimer's disease and depression.", "This study assessed the effect of IL-1\u03b2 on the proliferation and differentiation of embryonic rat hippocampal NPCs in vitro.", "We show that IL-1R1 is expressed on proliferating NPCs and that IL-1\u03b2 treatment decreases cell proliferation and neurosphere growth.", "When NPCs were differentiated in the presence of IL-1\u03b2, a significant reduction in the percentages of newly-born neurons and post-mitotic neurons and a significant increase in the percentage of astrocytes was observed in these cultures.", "These effects were attenuated by IL-1 receptor antagonist.", "These data reveal that IL-1\u03b2 exerts an anti-proliferative, anti-neurogenic and pro-gliogenic effect on embryonic hippocampal NPCs, which is mediated by IL-1R1.", "The present results emphasise the consequences of an inflammatory environment during NPC development, and indicate that strategies to inhibit IL-1\u03b2 signalling may be necessary to facilitate effective cell transplantation approaches or in conditions where endogenous hippocampal neurogenesis is impaired."], "structured": false}
{"doc_id": 23908217, "title": "Bone disease in pediatric patients undergoing dialysis with CAPD or CCPD.", "abstract": ["The histologic features of renal osteodystrophy and the prevalence of bone aluminum deposition in children receiving regular dialysis have not been described.", "Forty-four pediatric patients undergoing continuous ambulatory (CAPD) or cycling (CCPD) peritoneal dialysis had bone biopsies and deferoxamine (DFO) infusion tests; all were receiving oral calcitriol.", "Osteitis fibrosa (OF) was found in 39%, mild lesions (M) in 25%, normal histology (NH) in 16%, aplastic lesions (AP) in 11%, and osteomalacia (OM) in 9%.", "Bone surface aluminum (SA) was present by histochemical staining in 10 out of 20 given aluminum-containing phosphate-binding agents and in 0 of 24 treated with calcium carbonate; chi 2 = 15.5, P less than 0.0001.", "Serum biochemistries and DFO infusion tests failed to predict bone histology, but plasma aluminum levels were markedly elevated and bone aluminum content was highest in patients with OM.", "Bone formation rate (BFR) correlated with serum parathyroid hormone (PTH), r = 0.55, P less than 0.001; BFR was inversely related to bone aluminum content (r = -0.42, P less than 0.01), even in patients with OF (r = -0.66, P less than 0.05).", "All patients with SA greater than 30% had normal or reduced BFR when compared to those with SA less than 30%; chi 2 = 12.2, P less than 0.005.", "Based on SA greater than 30%, six patients were classified as aluminum-related bone disease: three OM, one AP, and two NH.", "Two-thirds of pediatric patients undergoing CAPD/CCPD have persistent hyperparathyroidism despite treatment with calcitriol, but aluminum can adversely affect BFR when SA exceeds 30% regardless of histologic lesion or serum PTH level."], "structured": false}
{"doc_id": 23912923, "title": "Disruption of the immune-checkpoint VISTA gene imparts a proinflammatory phenotype with predisposition to the development of autoimmunity.", "abstract": ["V domain-containing Ig suppressor of T-cell activation (VISTA) is a negative checkpoint regulator that suppresses T cell-mediated immune responses.", "Previous studies using a VISTA-neutralizing monoclonal antibody show that VISTA blockade enhances T-cell activation.", "The current study describes a comprehensive characterization of mice in which the gene for VISTA has been deleted.", "Despite the apparent normal hematopoietic development in young mice, VISTA genetic deficiency leads to a gradual accumulation of spontaneously activated T cells, accompanied by the production of a spectrum of inflammatory cytokines and chemokines.", "Enhanced T-cell responsiveness was also observed upon immunization with neoantigen.", "Despite the presence of multiorgan chronic inflammation, aged VISTA-deficient mice did not develop systemic or organ-specific autoimmune disease.", "Interbreeding of the VISTA-deficient mice with 2D2 T-cell receptor transgenic mice, which are predisposed to the development of experimental autoimmune encephalomyelitis, drastically enhanced disease incidence and intensity.", "Disease development is correlated with the increase in the activation of encephalitogenic T cells in the periphery and enhanced infiltration into the CNS.", "Taken together, our data suggest that VISTA is a negative checkpoint regulator whose loss of function lowers the threshold for T-cell activation, allowing for an enhanced proinflammatory phenotype and an increase in the frequency and intensity of autoimmunity under susceptible conditions."], "structured": false}
{"doc_id": 23913146, "title": "Molecular mechanisms that funnel RNA precursors into endogenous small-interfering RNA and microRNA biogenesis pathways in Drosophila.", "abstract": ["In Drosophila, three types of endogenous small RNAs-microRNAs (miRNAs), PIWI-interacting RNAs (piRNAs), and endogenous small-interfering RNAs (endo-siRNAs or esiRNAs)-function as triggers in RNA silencing.", "Although piRNAs are produced independently of Dicer, miRNA and esiRNA biogenesis pathways require Dicer1 and Dicer2, respectively.", "Recent studies have shown that among the four isoforms of Loquacious (Loqs), Loqs-PB and Loqs-PD are involved in miRNA and esiRNA processing pathways, respectively.", "However, how these Loqs isoforms function in their respective small RNA biogenesis pathways remains elusive.", "Here, we show that Loqs-PD associates specifically with Dicer2 through its C-terminal domain.", "The Dicer2-Loqs-PD complex contains R2D2, another known Dicer2 partner, and excises both exogenous siRNAs and esiRNAs from their corresponding precursors in vitro.", "However, Loqs-PD, but not R2D2, enhanced Dicer2 activity.", "The Dicer2-Loqs-PD complex processes esiRNA precursor hairpins with long stems, which results in the production of AGO2-associated small RNAs.", "Interestingly, however, small RNAs derived from terminal hairpins of esiRNA precursors are loaded onto AGO1; thus, they are classified as a new subset of miRNAs.", "These results suggest that the precursor RNA structure determines the biogenesis mechanism of esiRNAs and miRNAs, thereby implicating hairpin structures with long stems as intermediates in the evolution of Drosophila miRNA."], "structured": false}
{"doc_id": 23915841, "title": "Neutralizing antibody responses in acute human immunodeficiency virus type 1 subtype C infection.", "abstract": ["The study of the evolution and specificities of neutralizing antibodies during the course of human immunodeficiency virus type 1 (HIV-1) infection may be important in the discovery of possible targets for vaccine design.", "In this study, we assessed the autologous and heterologous neutralization responses of 14 HIV-1 subtype C-infected individuals, using envelope clones obtained within the first 2 months postinfection.", "Our data show that potent but relatively strain-specific neutralizing antibodies develop within 3 to 12 months of HIV-1 infection.", "The magnitude of this response was associated with shorter V1-to-V5 envelope lengths and fewer glycosylation sites, particularly in the V1-V2 region.", "Anti-MPER antibodies were detected in 4 of 14 individuals within a year of infection, while antibodies to CD4-induced (CD4i) epitopes developed to high titers in 12 participants, in most cases before the development of autologous neutralizing antibodies.", "However, neither anti-MPER nor anti-CD4i antibody specificity conferred neutralization breadth.", "These data provide insights into the kinetics, potency, breadth, and epitope specificity of neutralizing antibody responses in acute HIV-1 subtype C infection."], "structured": false}
{"doc_id": 23918031, "title": "The cell cycle in polyploid megakaryocytes is associated with reduced activity of cyclin B1-dependent cdc2 kinase.", "abstract": ["The platelet precursor, the megakaryocyte, matures to a polyploid cell as a result of DNA replication in the absence of mitosis (endomitosis).", "The factors controlling endomitosis are accessible to analysis in our megakaryocytic cell line, MegT, generated by targeted expression of temperature-sensitive simian virus 40 large T antigen to megakaryocytes of transgenic mice.", "We aimed to define whether endomitosis consists of a continuous phase of DNA synthesis (S) or of S phases interrupted by gaps.", "Analysis of the cell cycle in MegT cells revealed that, upon inactivation of large T antigen, the cells shifted from a mitotic cell cycle to an endomitotic cell cycle consisting of S/Gap phases.", "The level of the G1/S cyclin, cyclin A, as well as of the G1 phase cyclin, cyclin D3, were elevated at the onset of DNA synthesis, either in MegT cells undergoing a mitotic cell cycle or during endomitosis.", "In contrast, the level of the mitotic cyclin, cyclin B1, cycled in cells displaying a mitotic cell cycle while not detectable during endomitosis.", "Comparable levels of the mitotic kinase protein, Cdc2, were detected during the mitotic cell cycle or during endomitosis; however, cyclin B1-dependent Cdc2 kinase activity was largely abolished in the polyploid cells.", "Fibroblasts immortalized with the same heat-labile oncogene do not display reduced levels of cyclin B1 upon shifting to high temperature nor do they become polyploid, indicating that reduced levels of cyclin B1 is a property of megakaryocytes and not of the T-antigen mutant.", "We conclude that cellular programming during endoreduplication in megakaryocytes is associated with reduced levels of cyclin B1."], "structured": false}
{"doc_id": 23929297, "title": "Ghrelin secretion stimulated by {beta}1-adrenergic receptors in cultured ghrelinoma cells and in fasted mice.", "abstract": ["Ghrelin, an octanoylated peptide hormone produced in the stomach, rises dramatically in mouse plasma during chronic severe calorie deprivation, an event that is essential to maintain life.", "The mechanism for this increase is not understood.", "Here, we study the control of ghrelin secretion in tissue culture cells derived from mice bearing ghrelinomas induced by a tissue-specific SV40 T-antigen transgene.", "We found that the ghrelin-secreting cells express high levels of mRNA encoding beta(1)-adrenergic receptors.", "Addition of norepinephrine or epinephrine to the culture medium stimulated ghrelin secretion, and this effect was blocked by atenolol, a selective beta(1)-adrenergic antagonist.", "When WT mice were treated with reserpine to deplete adrenergic neurotransmitters from sympathetic neurons, the fasting-induced increase in plasma ghrelin was blocked.", "Inhibition was also seen following atenolol administration.", "We conclude that ghrelin secretion during fasting is induced by adrenergic agents released by sympathetic neurons and acting directly on beta(1) receptors on the ghrelin-secreting cells of the stomach."], "structured": false}
{"doc_id": 23932173, "title": "Dominance relationships between S-alleles in self-incompatible Brassica campestris L.", "abstract": ["Dominance relationships were studied for 249 out of 276 possible pair-wise combinations between 24 S-alleles of Brassica campestris that had been isolated from two natural populations from Turkey and Japan.", "Each F1 hybrid was test-crossed reciprocally against its respective parental S-homozygotes to determine the dominance relationships between the pair of S-alleles it contained.", "The 24 S-alleles were classified into two groups on the stigma side and three groups on the pollen side.", "In the stigma, codominance occurred frequently, and dominance or recessiveness seemed to appear according to the combination of S-alleles.", "In the pollen, codominance was less frequent, and there seemed to be a certain hierarchy of the dominance relationships as a whole, although dominance appeared with certain specific combinations of S-alleles.", "Interactions among 24 S-alleles were different in the stigma and in the pollen.", "Independent weakening of S-alleles was found between 20 pairs in the pollen, but only two in the stigma.", "This interaction seems to be correlated with recessiveness of S-alleles."], "structured": false}
{"doc_id": 23934390, "title": "MicroRNA-203 inhibits cellular proliferation and invasion by targeting Bmi1 in non-small cell lung cancer.", "abstract": ["MicroRNAs are proposed to serve vital functions in the regulation of tumor progression and invasion.", "However, the expression levels of miR-203 in non-small cell lung cancer (NSCLC) and its clinical significance remain unknown.", "In the present study, the association between B-cell-specific moloney murine leukemia virus insertion site 1 (Bmi1) and miR-203 was investigated.", "miR-203 was demonstrated to act as a tumor suppressor by regulating the expression of Bmi1.", "miR-203 expression levels were downregulated in NSCLC tissues while Bmi1 expression was upregulated in NSCLC tissues and cell lines.", "Furthermore, downregulated Bmi1 or enhanced miR-203 expression inhibited NSCLC cell proliferation and invasion in vitro.", "In addition, a dual-luciferase reporter assay was performed, which identified Bmi1 as a novel target of miR-203.", "In conclusion, the present study demonstrated that miR-203 functions as a tumor suppressor and is important in inhibiting the proliferation of NSCLC cells through targeting Bmi1.", "These findings indicate that miR-203 may be useful as a novel potential therapeutic target for NSCLC."], "structured": false}
{"doc_id": 23938319, "title": "Characterization of the interaction between retinoic acid receptor/retinoid X receptor (RAR/RXR) heterodimers and transcriptional coactivators through structural and fluorescence anisotropy studies.", "abstract": ["Retinoid receptors (RARs and RXRs) are ligand-activated transcription factors that regulate the transcription of target genes by recruiting coregulator complexes at cognate promoters.", "To understand the effects of heterodimerization and ligand binding on coactivator recruitment, we solved the crystal structure of the complex between the RARbeta/RXRalpha ligand-binding domain heterodimer, its 9-cis retinoic acid ligand, and an LXXLL-containing peptide (termed NR box 2) derived from the nuclear receptor interaction domain (NID) of the TRAP220 coactivator.", "In parallel, we measured the binding affinities of the isolated NR box 2 peptide or the full-length NID of the coactivator SRC-1 for retinoid receptors in the presence of various types of ligands.", "Our correlative analysis of three-dimensional structures and fluorescence data reveals that heterodimerization does not significantly alter the structure of individual subunits or their intrinsic capacity to interact with NR box 2.", "Similarly, we show that the ability of a protomer to recruit NR box 2 does not vary as a function of the ligand binding status of the partner receptor.", "In contrast, the strength of the overall association between the heterodimer and the full-length SRC-1 NID is dictated by the combinatorial action of RAR and RXR ligands, the simultaneous presence of the two receptor agonists being required for highest binding affinity.", "We identified an LXXLL peptide-driven mechanism by which the concerted reorientation of three phenylalanine side chains generates an \"aromatic clamp\" that locks the RXR activation helix H12 in the transcriptionally active conformation.", "Finally, we show how variations of helix H11-ligand interactions can alter the communication pathway linking helices H11, H12, and the connecting loop L11-12 to the coactivator-binding site.", "Together, our results reveal molecular and structural features that impact on the ligand-dependent interaction of the RAR/RXR heterodimer with nuclear receptor coactivators."], "structured": false}
{"doc_id": 23959496, "title": "PRC2 complexes with JARID2, MTF2, and esPRC2p48 in ES cells to modulate ES cell pluripotency and somatic cell reprogramming.", "abstract": ["Polycomb repressive complex two (PRC2) has been implicated in embryonic stem (ES) cell pluripotency; however, the mechanistic roles of this complex are unclear.", "It was assumed that ES cells contain PRC2 with the same subunit composition as that identified in HeLa cells and Drosophila embryos.", "Here, we report that PRC2 in mouse ES cells contains at least three additional subunits: JARID2, MTF2, and a novel protein denoted esPRC2p48.", "JARID2, MTF2, and esPRC2p48 are highly expressed in mouse ES cells compared to differentiated cells.", "Importantly, knockdowns of JARID2, MTF2, or esPRC2p48 alter the level of PRC2-mediated H3K27 methylation and result in the expression of differentiation-associated genes in ES cells.", "Interestingly, expression of JARID2, MTF2, and esPRC2p48 together, but not individually, enhances Oct4/Sox2/Klf4-mediated reprogramming of mouse embryonic fibroblasts (MEFs) into induced pluripotent stem cells, whereas knockdown or knockout of JARID2, MTF2, or esPRC2p48 significantly inhibits reprogramming.", "JARID2, MTF2, and esPRC2p48 modulate H3K27 methylation and facilitate repression of lineage-associated gene expression when transduced into MEFs, and synergistically stimulate the histone methyltransferase activity of PRC2 in vitro.", "Therefore, these studies identify JARID2, MTF2, and esPRC2p48 as important regulatory subunits of PRC2 in ES cells and reveal critical functions of these subunits in modulating PRC2's activity and gene expression both in ES cells and during somatic cell reprogramming."], "structured": false}
{"doc_id": 23967973, "title": "General and abdominal adiposity and risk of death in Europe.", "abstract": ["BACKGROUND Previous studies have relied predominantly on the body-mass index (BMI, the weight in kilograms divided by the square of the height in meters) to assess the association of adiposity with the risk of death, but few have examined whether the distribution of body fat contributes to the prediction of death.   \n", "METHODS We examined the association of BMI, waist circumference, and waist-to-hip ratio with the risk of death among 359,387 participants from nine countries in the European Prospective Investigation into Cancer and Nutrition (EPIC).", "We used a Cox regression analysis, with age as the time variable, and stratified the models according to study center and age at recruitment, with further adjustment for educational level, smoking status, alcohol consumption, physical activity, and height.   \n", "RESULTS During a mean follow-up of 9.7 years, 14,723 participants died.", "The lowest risks of death related to BMI were observed at a BMI of 25.3 for men and 24.3 for women.", "After adjustment for BMI, waist circumference and waist-to-hip ratio were strongly associated with the risk of death.", "Relative risks among men and women in the highest quintile of waist circumference were 2.05 (95% confidence interval [CI], 1.80 to 2.33) and 1.78 (95% CI, 1.56 to 2.04), respectively, and in the highest quintile of waist-to-hip ratio, the relative risks were 1.68 (95% CI, 1.53 to 1.84) and 1.51 (95% CI, 1.37 to 1.66), respectively.", "BMI remained significantly associated with the risk of death in models that included waist circumference or waist-to-hip ratio (P<0.001).   \n", "CONCLUSIONS These data suggest that both general adiposity and abdominal adiposity are associated with the risk of death and support the use of waist circumference or waist-to-hip ratio in addition to BMI in assessing the risk of death."], "structured": true}
{"doc_id": 23972114, "title": "Phosphorylation of the autophagy receptor optineurin restricts Salmonella growth.", "abstract": ["Selective autophagy can be mediated via receptor molecules that link specific cargoes to the autophagosomal membranes decorated by ubiquitin-like microtubule-associated protein light chain 3 (LC3) modifiers.", "Although several autophagy receptors have been identified, little is known about mechanisms controlling their functions in vivo.", "In this work, we found that phosphorylation of an autophagy receptor, optineurin, promoted selective autophagy of ubiquitin-coated cytosolic Salmonella enterica.", "The protein kinase TANK binding kinase 1 (TBK1) phosphorylated optineurin on serine-177, enhancing LC3 binding affinity and autophagic clearance of cytosolic Salmonella.", "Conversely, ubiquitin- or LC3-binding optineurin mutants and silencing of optineurin or TBK1 impaired Salmonella autophagy, resulting in increased intracellular bacterial proliferation.", "We propose that phosphorylation of autophagy receptors might be a general mechanism for regulation of cargo-selective autophagy."], "structured": false}
{"doc_id": 23974474, "title": "PKD1 Inhibits AMPK\u03b12 through Phosphorylation of Serine 491 and Impairs Insulin Signaling in Skeletal Muscle Cells.", "abstract": ["AMP-activated protein kinase (AMPK) is an energy-sensing enzyme whose activity is inhibited in settings of insulin resistance.", "Exposure to a high glucose concentration has recently been shown to increase phosphorylation of AMPK at Ser(485/491) of its \u03b11/\u03b12 subunit; however, the mechanism by which it does so is not known.", "Diacylglycerol (DAG), which is also increased in muscle exposed to high glucose, activates a number of signaling molecules including protein kinase (PK)C and PKD1.", "We sought to determine whether PKC or PKD1 is involved in inhibition of AMPK by causing Ser(485/491) phosphorylation in skeletal muscle cells.", "C2C12 myotubes were treated with the PKC/D1 activator phorbol 12-myristate 13-acetate (PMA), which acts as a DAG mimetic.", "This caused dose- and time-dependent increases in AMPK Ser(485/491) phosphorylation, which was associated with a \u223c60% decrease in AMPK\u03b12 activity.", "Expression of a phosphodefective AMPK\u03b12 mutant (S491A) prevented the PMA-induced reduction in AMPK activity.", "Serine phosphorylation and inhibition of AMPK activity were partially prevented by the broad PKC inhibitor G\u00f66983 and fully prevented by the specific PKD1 inhibitor CRT0066101.", "Genetic knockdown of PKD1 also prevented Ser(485/491) phosphorylation of AMPK.", "Inhibition of previously identified kinases that phosphorylate AMPK at this site (Akt, S6K, and ERK) did not prevent these events.", "PMA treatment also caused impairments in insulin-signaling through Akt, which were prevented by PKD1 inhibition.", "Finally, recombinant PKD1 phosphorylated AMPK\u03b12 at Ser(491) in cell-free conditions.", "These results identify PKD1 as a novel upstream kinase of AMPK\u03b12 Ser(491) that plays a negative role in insulin signaling in muscle cells."], "structured": false}
{"doc_id": 23983289, "title": "Accuracy of ICD-9-CM codes for identifying cardiovascular and stroke risk factors.", "abstract": ["OBJECTIVES We sought to determine which ICD-9-CM codes in Medicare Part A data identify cardiovascular and stroke risk factors.   \n", "DESIGN AND PARTICIPANTS This was a cross-sectional study comparing ICD-9-CM data to structured medical record review from 23,657 Medicare beneficiaries aged 20 to 105 years who had atrial fibrillation.   \n", "MEASUREMENTS Quality improvement organizations used standardized abstraction instruments to determine the presence of 9 cardiovascular and stroke risk factors.", "Using the chart abstractions as the gold standard, we assessed the accuracy of ICD-9-CM codes to identify these risk factors.   \n", "MAIN RESULTS ICD-9-CM codes for all risk factors had high specificity (>0.95) and low sensitivity (< or =0.76).", "The positive predictive values were greater than 0.95 for 5 common, chronic risk factors-coronary artery disease, stroke/transient ischemic attack, heart failure, diabetes, and hypertension.", "The sixth common risk factor, valvular heart disease, had a positive predictive value of 0.93.", "For all 6 common risk factors, negative predictive values ranged from 0.52 to 0.91.", "The rare risk factors-arterial peripheral embolus, intracranial hemorrhage, and deep venous thrombosis-had high negative predictive value (> or =0.98) but moderate positive predictive values (range, 0.54-0.77) in this population.   \n", "CONCLUSIONS Using ICD-9-CM codes alone, heart failure, coronary artery disease, diabetes, hypertension, and stroke can be ruled in but not necessarily ruled out.", "Where feasible, review of additional data (eg, physician notes or imaging studies) should be used to confirm the diagnosis of valvular disease, arterial peripheral embolus, intracranial hemorrhage, and deep venous thrombosis."], "structured": true}
{"doc_id": 23985464, "title": "Modulation of cellular and viral promoters by mutant human p53 proteins found in tumor cells.", "abstract": ["Wild-type p53 has recently been shown to repress transcription from several cellular and viral promoters.", "Since p53 mutations are the most frequently reported genetic defects in human cancers, it becomes important to study the effects of mutations of p53 on promoter functions.", "We, therefore, have studied the effects of wild-type and mutant human p53 on the human proliferating-cell nuclear antigen (PCNA) promoter and on several viral promoters, including the herpes simplex virus type 1 UL9 promoter, the human cytomegalovirus major immediate-early promoter-enhancer, and the long terminal repeat promoters of Rous sarcoma virus and human T-cell lymphotropic virus type I. HeLa cells were cotransfected with a wild-type or mutant p53 expression vector and a plasmid containing a chloramphenicol acetyltransferase reporter gene under viral (or cellular) promoter control.", "As expected, expression of the wild-type p53 inhibited promoter function.", "Expression of a p53 with a mutation at any one of the four amino acid positions 175, 248, 273, or 281, however, correlated with a significant increase of the PCNA promoter activity (2- to 11-fold).", "The viral promoters were also activated, although to a somewhat lesser extent.", "We also showed that activation by a mutant p53 requires a minimal promoter containing a lone TATA box.", "A more significant increase (25-fold) in activation occurs when the promoter contains a binding site for the activating transcription factor or cyclic AMP response element-binding protein.", "Using Saos-2 cells that do not express p53, we showed that activation by a mutant p53 was a direct enhancement.", "The mutant forms of p53 used in this study are found in various cancer cells.", "The activation of PCNA by mutant p53s may indicate a way to increase cell proliferation by the mutant p53s.", "Thus, our data indicate a possible functional role for the mutants of p53 found in cancer cells in activating several important loci, including PCNA."], "structured": false}
{"doc_id": 24003461, "title": "Valvular interstitial cells suppress calcification of valvular endothelial cells.", "abstract": ["BACKGROUND Calcific aortic valve disease (CAVD) is the most common heart valve disease in the Western world.", "We previously proposed that valvular endothelial cells (VECs) replenish injured adult valve leaflets via endothelial-to-mesenchymal transformation (EndMT); however, whether EndMT contributes to valvular calcification is unknown.", "We hypothesized that aortic VECs undergo osteogenic differentiation via an EndMT process that can be inhibited by valvular interstitial cells (VICs).   ", "APPROACH AND RESULTS VEC clones underwent TGF-\u03b21-mediated EndMT, shown by significantly increased mRNA expression of the EndMT markers \u03b1-SMA (5.3 \u00b1 1.2), MMP-2 (13.5 \u00b1 0.6) and Slug (12 \u00b1 2.1) (p < 0.05), (compared to unstimulated controls).", "To study the effects of VIC on VEC EndMT, clonal populations of VICs were derived from the same valve leaflets, placed in co-culture with VECs, and grown in control/TGF-\u03b21 supplemented media.", "In the presence of VICs, EndMT was inhibited, shown by decreased mRNA expression of \u03b1-SMA (0.1 \u00b1 0.5), MMP-2 (0.1 \u00b1 0.1), and Slug (0.2 \u00b1 0.2) (p < 0.05).", "When cultured in osteogenic media, VECs demonstrated osteogenic changes confirmed by increase in mRNA expression of osteocalcin (8.6 \u00b1 1.3), osteopontin (3.7 \u00b1 0.3), and Runx2 (5.5 \u00b1 1.5).", "The VIC presence inhibited VEC osteogenesis, demonstrated by decreased expression of osteocalcin (0.4 \u00b1 0.1) and osteopontin (0.2 \u00b1 0.1) (p < 0.05).", "Time course analysis suggested that EndMT precedes osteogenesis, shown by an initial increase of \u03b1-SMA and MMP-2 (day 7), followed by an increase of osteopontin and osteocalcin (day 14).   \n", "CONCLUSIONS The data indicate that EndMT may precede VEC osteogenesis.", "This study shows that VICs inhibit VEC EndMT and osteogenesis, indicating the importance of VEC-VIC interactions in valve homeostasis."], "structured": true}
{"doc_id": 24005548, "title": "The HMG-CoA reductase inhibitor simvastatin activates the protein kinase Akt and promotes angiogenesis in normocholesterolemic animals.", "abstract": ["Recent studies suggest that statins can function to protect the vasculature in a manner that is independent of their lipid-lowering activity.", "We show here that statins rapidly activate the protein kinase Akt/PKB in endothelial cells.", "Accordingly, simvastatin enhanced phosphorylation of the endogenous Akt substrate endothelial nitric oxide synthase (eNOS), inhibited apoptosis and accelerated vascular structure formation in vitro in an Akt-dependent manner.", "Similar to vascular endothelial growth factor (VEGF) treatment, both simvastatin administration and enhanced Akt signaling in the endothelium promoted angiogenesis in ischemic limbs of normocholesterolemic rabbits.", "Therefore, activation of Akt represents a mechanism that can account for some of the beneficial side effects of statins, including the promotion of new blood vessel growth."], "structured": false}
{"doc_id": 24019260, "title": "Varenicline, an alpha4beta2 nicotinic acetylcholine receptor partial agonist, selectively decreases ethanol consumption and seeking.", "abstract": ["Alcohol dependence is a disease that impacts millions of individuals worldwide.", "There has been some progress with pharmacotherapy for alcohol-dependent individuals; however, there remains a critical need for the development of novel and additional therapeutic approaches.", "Alcohol and nicotine are commonly abused together, and there is evidence that neuronal nicotinic acetylcholine receptors (nAChRs) play a role in both alcohol and nicotine dependence.", "Varenicline, a partial agonist at the alpha4beta2 nAChRs, reduces nicotine intake and was recently approved as a smoking cessation aid.", "We have investigated the role of varenicline in the modulation of ethanol consumption and seeking using three different animal models of drinking.", "We show that acute administration of varenicline, in doses reported to reduce nicotine reward, selectively reduced ethanol but not sucrose seeking using an operant self-administration drinking paradigm and also decreased voluntary ethanol but not water consumption in animals chronically exposed to ethanol for 2 months before varenicline treatment.", "Furthermore, chronic varenicline administration decreased ethanol consumption, which did not result in a rebound increase in ethanol intake when the varenicline was no longer administered.", "The data suggest that the alpha4beta2 nAChRs may play a role in ethanol-seeking behaviors in animals chronically exposed to ethanol.", "The selectivity of varenicline in decreasing ethanol consumption combined with its reported safety profile and mild side effects in humans suggest that varenicline may prove to be a treatment for alcohol dependence."], "structured": false}
{"doc_id": 24042363, "title": "Targeting TLR4 signaling by TLR4 Toll/IL-1 receptor domain-derived decoy peptides: identification of the TLR4 Toll/IL-1 receptor domain dimerization interface.", "abstract": ["Agonist-induced dimerization of TLR4 Toll/IL-1R (TIR) domains initiates intracellular signaling.", "Therefore, identification of the TLR4-TIR dimerization interface is one key to the rational design of therapeutics that block TLR4 signaling.", "A library of cell-permeating decoy peptides, each of which represents a nonfragmented patch of the TLR4 TIR surface, was designed such that the peptides entirely encompass the TLR4 TIR surface.", "Each peptide was synthesized in tandem with a cell-permeating Antennapedia homeodomain sequence and tested for the ability to inhibit early cytokine mRNA expression and MAPK activation in LPS-stimulated primary murine macrophages.", "Five peptides--4R1, 4R3, 4BB, 4R9, and 4\u03b1E--potently inhibited all manifestations of TLR4, but not TLR2 signaling.", "When tested for their ability to bind directly to TLR4 TIR by F\u00f6rster resonance energy transfer using time-resolved fluorescence spectroscopy, Bodipy-TMR-X-labeled 4R1, 4BB, and 4\u03b1E quenched fluorescence of TLR4-Cerulean expressed in HeLa or HEK293T cells, whereas 4R3 was partially active, and 4R9 was least active.", "These findings suggest that the area between the BB loop of TLR4 and its fifth helical region mediates TLR4 TIR dimerization.", "Moreover, our data provide direct evidence for the utility of the decoy peptide approach, in which peptides representing various surface-exposed segments of a protein are initially probed for the ability to inhibit protein function, and then their specific targets are identified by F\u00f6rster resonance energy transfer to define recognition sites in signaling proteins that may be targeted therapeutically to disrupt functional transient protein interactions."], "structured": false}
{"doc_id": 24042919, "title": "A paediatric case of sideroblastic anaemia. Ultrastructural studies of erythroblasts cultured from marrow BFU-E in a methylcellulose micromethod.", "abstract": ["We examined the morphological and functional characteristics of erythroblasts derived from marrow erythroid progenitor cells grown in a methylcellulose microculture, which were taken from a female child with rare atypical sideroblastic anaemia (SA) partially responsive to pyridoxine.", "Colony formation was within the normal range in three successive cultures (median values: 82.25 CFU-E and 16.4 BFU-E derived colonies/6.6 X 10(4) cells) compared to growth by normal cells (65-315 CFU-E and 9-40 BFU-E).", "We evaluated in vitro differentiation by biochemical microassay of a cytosol enzyme involved in the haem pathway: uroporphyrinogen I synthase (UROS).", "The UROS values in the erythroid colonies from SA marrow were at the lowere end of the normal range (median values: 6.7 +/- 0.3 and 14.4 +/-", "3.8 pmol uroporphyrinogen/h in CFU-E and BFU-E-derived colonies respectively versus 17.4 +/- 7.3 and 25 +/-", "7.2 pmol/h in CFU-E and BFU-E colonies from normal subjects.", "Ultrastructural examination of the SA erythroblasts from non-cultured bone marrow or derived from cultured BFU-E revealed the characteristic deposition of iron in mitochondria around the nucleus of most cells (ringed sideroblasts).", "However, the majority of cultured cells had marked dyserythropoietic features, with a large number of bilobulated or trilobulated erythroblasts, multiple cytoplasmic vacuoles, numerous abnormalities of the nucleus, and excessive membrane material beneath the plasma membrane, all features difficult to observe in non-cultured marrows."], "structured": false}
{"doc_id": 24044977, "title": "Innate lymphoid cells: emerging insights in development, lineage relationships, and function.", "abstract": ["Innate lymphoid cells (ILCs) are immune cells that lack a specific antigen receptor yet can produce an array of effector cytokines that in variety match that of T helper cell subsets.", "ILCs function in lymphoid organogenesis, tissue remodeling, antimicrobial immunity, and inflammation, particularly at barrier surfaces.", "Their ability to promptly respond to insults inflicted by stress-causing microbes strongly suggests that ILCs are critical in first-line immunological defenses.", "Here, we review current data on developmental requirements, lineage relationships, and effector functions of two families of ILCs: (a) Ror\u03b3t-expressing cells involved in lymphoid tissue formation, mucosal immunity, and inflammation and (b) type 2 ILCs that are important for helminth immunity.", "We also discuss the potential roles of ILCs in the pathology of immune-mediated inflammatory and infectious diseases including allergy."], "structured": false}
{"doc_id": 24049225, "title": "No net renal extraction of homocysteine in fasting humans.", "abstract": ["BACKGROUND The pathophysiological mechanism of hyperhomocysteinemia in chronic renal failure in humans is unknown.", "The loss of a putative renal homocysteine extraction in chronic renal failure has been hypothesized as significant homocysteine uptake has been demonstrated in the normal rat kidney.", "We studied homocysteine extraction in the normal human kidney.   \n", "METHODS We measured plasma total (free and protein-bound) and free homocysteine (tHcy and fHcy, respectively) in arterial and renal venous blood sampled from the aorta and right-side renal vein during cardiac catheterization in 20 fasting patients with normal renal function.", "Renal homocysteine extraction was calculated as the arteriovenous difference divided by the arterial levels times 100%.   \n", "RESULTS No significant renal extraction was demonstrated either for tHcy: 0.9% (SD 5.8; 95% CI -1.8 to +3.6) or for fHcy: -0.2% (11.0; -5.4 to +4.9).   \n", "CONCLUSIONS We conclude that no significant net renal uptake of homocysteine occurs in fasting humans with normal renal function.", "The loss of such uptake, therefore, cannot cause hyperhomocysteinemia in patients with renal failure."], "structured": true}
{"doc_id": 24055603, "title": "Traditional Chinese acupuncture in tension-type headache: a controlled study.", "abstract": ["Thirty patients with tension-type headache were randomly chosen to undergo a trial of traditional Chinese acupuncture and sham acupuncture.", "Five measures were used to assess symptom severity and treatment response: intensity, duration and frequency of headache pain episodes, headache index and analgesic intake.", "The five measures were assessed during a 4 week baseline period, after 4 and 8 weeks of treatment, and 1, 6 and 12 months thereafter.", "Before the start of the study, each patient was administered the MMPI.", "Split-plot ANOVAs showed that, compared to baseline, at 1 month after the end of treatment and for the 12 month follow-up, the frequency of headache episodes, analgesic consumption and the headache index (but not the duration or intensity of headache episodes) significantly decreased over time; however, no difference between acupuncture and placebo treatment was found.", "No single MMPI scale predicted the response to treatment, but the mean MMPI profile of acupuncture non-responders showed the presence of 'Conversion V'."], "structured": false}
{"doc_id": 24069089, "title": "TCR stimulation with modified anti-CD3 mAb expands CD8+ T cell population and induces CD8+CD25+ Tregs.", "abstract": ["Modified anti-CD3 mAbs are emerging as a possible means of inducing immunologic tolerance in settings including transplantation and autoimmunity such as in type 1 diabetes.", "In a trial of a modified anti-CD3 mAb [hOKT3gamma1(Ala-Ala)] in patients with type 1 diabetes, we identified clinical responders by an increase in the number of peripheral blood CD8+ cells following treatment with the mAb.", "Here we show that the anti-CD3 mAb caused activation of CD8+ T cells that was similar in vitro and in vivo and induced regulatory CD8+CD25+ T cells.", "These cells inhibited the responses of CD4+ cells to the mAb itself and to antigen.", "The regulatory CD8+CD25+ cells were CTLA4 and Foxp3 and required contact for inhibition.", "Foxp3 was also induced on CD8+ T cells in patients during mAb treatment, which suggests a potential mechanism of the anti-CD3 mAb immune modulatory effects involving induction of a subset of regulatory CD8+ T cells."], "structured": false}
{"doc_id": 24077493, "title": "Interactions between Non-Physician Clinicians and Industry: A Systematic Review", "abstract": ["BACKGROUND With increasing restrictions placed on physician-industry interactions, industry marketing may target other health professionals.", "Recent health policy developments confer even greater importance on the decision making of non-physician clinicians.", "The purpose of this systematic review is to examine the types and implications of non-physician clinician-industry interactions in clinical practice.   \n", "METHODS AND FINDINGS We searched MEDLINE and Web of Science from January 1, 1946, through June 24, 2013, according to PRISMA guidelines.", "Non-physician clinicians eligible for inclusion were: Registered Nurses, nurse prescribers, Physician Assistants, pharmacists, dieticians, and physical or occupational therapists; trainee samples were excluded.", "Fifteen studies met inclusion criteria.", "Data were synthesized qualitatively into eight outcome domains: nature and frequency of industry interactions; attitudes toward industry; perceived ethical acceptability of interactions; perceived marketing influence; perceived reliability of industry information; preparation for industry interactions; reactions to industry relations policy; and management of industry interactions.", "Non-physician clinicians reported interacting with the pharmaceutical and infant formula industries.", "Clinicians across disciplines met with pharmaceutical representatives regularly and relied on them for practice information.", "Clinicians frequently received industry \"information,\" attended sponsored \"education,\" and acted as distributors for similar materials targeted at patients.", "Clinicians generally regarded this as an ethical use of industry resources, and felt they could detect \"promotion\" while benefiting from industry \"information.", "\"", "Free samples were among the most approved and common ways that clinicians interacted with industry.", "Included studies were observational and of varying methodological rigor; thus, these findings may not be generalizable.", "This review is, however, the first to our knowledge to provide a descriptive analysis of this literature.   \n", "CONCLUSIONS Non-physician clinicians' generally positive attitudes toward industry interactions, despite their recognition of issues related to bias, suggest that industry interactions are normalized in clinical practice across non-physician disciplines.", "Industry relations policy should address all disciplines and be implemented consistently in order to mitigate conflicts of interest and address such interactions' potential to affect patient care.", "Please see later in the article for the Editors' Summary."], "structured": true}
{"doc_id": 24082820, "title": "Emtricitabine-tenofovir concentrations and pre-exposure prophylaxis efficacy in men who have sex with men.", "abstract": ["Drug concentrations associated with protection from HIV-1 acquisition have not been determined.", "We evaluated drug concentrations among men who have sex with men in a substudy of the iPrEx trial (1).", "In this randomized placebo-controlled trial, daily oral doses of emtricitabine/tenofovir disoproxil fumarate were used as pre-exposure prophylaxis (PrEP) in men who have sex with men.", "Drug was detected less frequently in blood plasma and in viable cryopreserved peripheral blood mononuclear cells (PBMCs) in HIV-infected cases at the visit when HIV was first discovered compared with controls at the matched time point of the study (8% versus 44%; P < 0.001) and in the 90 days before that visit (11% versus 51%; P < 0.001).", "An intracellular concentration of the active form of tenofovir, tenofovir-diphosphate (TFV-DP), of 16 fmol per million PBMCs was associated with a 90% reduction in HIV acquisition relative to the placebo arm.", "Directly observed dosing in a separate study, the STRAND trial, yielded TFV-DP concentrations that, when analyzed according to the iPrEx model, corresponded to an HIV-1 risk reduction of 76% for two doses per week, 96% for four doses per week, and 99% for seven doses per week.", "Prophylactic benefits were observed over a range of doses and drug concentrations, suggesting ways to optimize PrEP regimens for this population."], "structured": false}
{"doc_id": 24088502, "title": "Clinical outcomes following institution of the Canadian universal leukoreduction program for red blood cell transfusions.", "abstract": ["CONTEXT A number of countries have implemented a policy of universal leukoreduction of their blood supply, but the potential role of leukoreduction in decreasing postoperative mortality and infection is unclear.   \n", "OBJECTIVE To evaluate clinical outcomes following adoption of a national universal prestorage leukoreduction program for blood transfusions.   \n", "DESIGN, SETTING, AND POPULATION Retrospective before-and-after cohort study conducted from August 1998 to August 2000 in 23 academic and community hospitals throughout Canada, enrolling 14 786 patients who received red blood cell transfusions following cardiac surgery or repair of hip fracture, or who required intensive care following a surgical intervention or multiple trauma.   \n", "INTERVENTION Universal prestorage leukoreduction program introduced by 2 Canadian blood agencies.", "A total of 6982 patients were enrolled during the control period and 7804 patients were enrolled following prestorage leukoreduction.   \n", "MAIN OUTCOME MEASURES All-cause in-hospital mortality and serious nosocomial infections (pneumonia, bacteremia, septic shock, all surgical site infections) occurring after first transfusion and at least 2 days after index procedure or intensive care unit admission.", "Secondary outcomes included rates of posttransfusion fever and antibiotic use.   \n", "RESULTS Unadjusted in-hospital mortality rates were significantly lower following the introduction of leukoreduction compared with the control period (6.19% vs 7.03%, respectively; P =.04).", "Compared with the control period, the adjusted odds of death following leukoreduction were reduced (odds ratio [OR], 0.87; 95% confidence interval [CI], 0.75-0.99), but serious nosocomial infections did not decrease (adjusted OR, 0.97; 95% CI, 0.87-1.09).", "The frequency of posttransfusion fevers decreased significantly following leukoreduction (adjusted OR, 0.86; 95% CI, 0.79-0.94), as did antibiotic use (adjusted OR, 0.90; 95% CI, 0.82-0.99).   \n", "CONCLUSION A national universal leukoreduction program is potentially associated with decreased mortality as well as decreased fever episodes and antibiotic use after red blood cell transfusion in high-risk patients."], "structured": true}
{"doc_id": 24097933, "title": "Failure of continuous venovenous hemofiltration to prevent death in paraquat poisoning.", "abstract": ["Paraquat poisoning is characterized by multiorgan failure and pulmonary fibrosis with respiratory failure.", "Multiorgan failure with circulatory collapse is a major cause of early death within 3 days of paraquat ingestion.", "Recent studies suggested that continuous venovenous hemofiltration (CVVH) had a role in the treatment of multiorgan failure by promoting hemodynamic stability.", "We therefore evaluated the effect of prophylactic CVVH in 80 patients with paraquat poisoning (August 1996 to February 1999).", "The amount ingested was 2.1 +/-", "1.0 mouthfuls (as 20% concentrate).", "All patients were treated with hemoperfusion (HP; duration, 6.4 +/-", "3.0 hours) within 24 hours of ingestion and then randomly assigned to the HP-alone or HP-CVVH group.", "Forty-four patients underwent HP only, and 36 patients underwent CVVH (duration, 57.4 +/-", "31.3 hours; ultrafiltration volume, 40.2 +/-", "4.8 L/d) after HP.", "Although time to death after ingestion was significantly longer in the HP-CVVH than HP group (5.0 +/- 5.0 versus 2.5 +/-", "2.1 days; P < 0.05), there was no difference in mortality rates between the two groups (66.7% versus 63.6%; P = 0.82).", "In the HP group, early circulatory collapse was a major cause of death compared with the HP-CVVH group, in which late respiratory failure was a major cause of death.", "In conclusion, prophylactic CVVH after HP prevented early death caused by circulatory collapse and prolonged survival time.", "However, it could not prevent late death caused by respiratory failure and did not provide a survival benefit in acute paraquat poisoning."], "structured": false}
{"doc_id": 24101431, "title": "The antidiabetic effect of mesenchymal stem cells is unrelated to their transdifferentiation potential but to their capability to restore Th1/Th2 balance and to modify the pancreatic microenvironment.", "abstract": ["Type 1 diabetes mellitus (T1DM) is a chronic metabolic disease that results from cell-mediated autoimmune destruction of insulin-producing cells.", "In T1DM animal models, it has been shown that the systemic administration of multipotent mesenchymal stromal cells, also referred as to mesenchymal stem cells (MSCs), results in the regeneration of pancreatic islets.", "Mechanisms underlying this effect are still poorly understood.", "Our aims were to assess whether donor MSCs (a) differentiate into pancreatic \u03b2-cells and (b) modify systemic and pancreatic pathophysiologic markers of T1DM.", "After the intravenous administration of 5 \u00d7 10(5) syngeneic MSCs, we observed that mice with T1DM reverted their hyperglycemia and presented no donor-derived insulin-producing cells.", "In contrast, 7 and 65 days post-transplantation, MSCs were engrafted into secondary lymphoid organs.", "This correlated with a systemic and local reduction in the abundance of autoaggressive T cells together with an increase in regulatory T cells.", "Additionally, in the pancreas of mice with T1DM treated with MSCs, we observed a cytokine profile shift from proinflammatory to antinflammatory.", "MSC transplantation did not reduce pancreatic cell apoptosis but recovered local expression and increased the circulating levels of epidermal growth factor, a pancreatic trophic factor.", "Therefore, the antidiabetic effect of MSCs intravenously administered is unrelated to their transdifferentiation potential but to their capability to restore the balance between Th1 and Th2 immunological responses along with the modification of the pancreatic microenvironment.", "Our data should be taken into account when designing clinical trials aimed to evaluate MSC transplantation in patients with T1DM since the presence of endogenous precursors seems to be critical in order to restore glycemic control."], "structured": false}
{"doc_id": 24142891, "title": "Tmem27: a cleaved and shed plasma membrane protein that stimulates pancreatic beta cell proliferation.", "abstract": ["The signals and molecular mechanisms that regulate the replication of terminally differentiated beta cells are unknown.", "Here, we report the identification and characterization of transmembrane protein 27 (Tmem27, collectrin) in pancreatic beta cells.", "Expression of Tmem27 is reduced in Tcf1(-/-) mice and is increased in islets of mouse models with hypertrophy of the endocrine pancreas.", "Tmem27 forms dimers and its extracellular domain is glycosylated, cleaved and shed from the plasma membrane of beta cells.", "This cleavage process is beta cell specific and does not occur in other cell types.", "Overexpression of full-length Tmem27, but not the truncated or soluble protein, leads to increased thymidine incorporation, whereas silencing of Tmem27 using RNAi results in a reduction of cell replication.", "Furthermore, transgenic mice with increased expression of Tmem27 in pancreatic beta cells exhibit increased beta cell mass.", "Our results identify a pancreatic beta cell transmembrane protein that regulates cell growth of pancreatic islets."], "structured": false}
{"doc_id": 24144677, "title": "The ATM missense mutation p.Ser49Cys (c.146C>G) and the risk of breast cancer.", "abstract": ["Homozygous mutation in the ATM gene causes ataxia telangiectasia and heterozygous mutation carriers may be at increased risk of breast cancer.", "We studied a total of 22 ATM variants; 18 variants were analyzed in one of two large population-based studies from the U.S. and Poland, and four variants were analyzed in all 2,856 breast cancer cases and 3,344 controls from the two studies.", "The missense mutation Ser49Cys (c.146C>G, p.", "S49C), carried by approximately 2% of subjects, was more common in cases than controls in both study populations, combined odds ratio (OR) 1.69 (95% CI, 1.19-2.40; P=0.004).", "Another missense mutation at approximately 2% frequency, Phe858Leu (c.2572T>C, p.", "F858L), was associated with a significant increased risk in the U.S. study but not in Poland, and had a combined OR of 1.44 (95% CI, 0.98-2.11; P=0.06).", "These analyses provide the most convincing evidence thus far that missense mutations in ATM, particularly p.", "S49C, may be breast cancer susceptibility alleles.", "Because of their low frequency, even larger sample sizes are required to more firmly establish these associations."], "structured": false}
{"doc_id": 24148722, "title": "A diffusion tensor magnetic resonance imaging study of corpus callosum from adult patients with migraine complicated with depressive/anxious disorder.", "abstract": ["OBJECTIVE The aim of this study was to investigate the possible microstructural abnormalities of the corpus callosum (CC) in adult patients with migraine without aura complicated with depressive/anxious disorder.   \n", "BACKGROUND Emotional disorders, especially depression and anxiety, are with relatively higher incidence in migraine population.", "However, the mechanism of migraine complicated with depressive/anxious disorder remains unclear.   \n", "METHODS Diffusion tensor magnetic resonance imaging was carried out in 12 adult patients with simple migraine (without aura and without depressive/anxious disorder) (S-M group), 12 adult patients with complicated migraine (without aura but complicated with depressive/anxious disorder) (Co-M group), and 12 age- and sex-matched healthy subjects (Control group).", "Fractional anisotropy (FA) and apparent diffusion coefficient were measured at genu, body, and splenium of the CC, respectively.   \n", "RESULTS There were significant differences in FA values at all locations of the CC among the 3 groups.", "The FA values from both the SM and Co-M groups were significantly lower than the control (P < .05 and P < .01, respectively).", "The FA values from Co-M group were significantly lower than the SM group (P < .01).", "The apparent diffusion coefficient values of the above regions had no significant differences among these groups (P > .05).", "There were negative correlations between FA value of genu of the CC and disease course as well as FA value of genu and body of the CC and headache frequency (P < .05).", "Negative correlations were also found between FA values at all locations of the CC and Hamilton anxiety and Hamilton depression scores (both P < .05).   \n", "CONCLUSIONS There might be an integrity change of neurofibrotic microstructures existing as a possible neuroanatomical basis in the CC of migraine patients complicated with depressive/anxious disorder."], "structured": true}
{"doc_id": 24150328, "title": "Peroxisome proliferator-activated receptor gamma agonists for the Prevention of Adverse events following percutaneous coronary Revascularization--results of the PPAR study.", "abstract": ["BACKGROUND Patients with metabolic syndrome are at increased risk for cardiovascular complications.", "We sought to determine whether peroxisome proliferator-activated receptor gamma agonists had any beneficial effect on patients with metabolic syndrome undergoing percutaneous coronary intervention (PCI).   \n", "METHODS A total of 200 patients with metabolic syndrome undergoing PCI were randomized to rosiglitazone or placebo and followed for 1 year.", "Carotid intima-medial thickness (CIMT), inflammatory markers, lipid levels, brain natriuretic peptide, and clinical events were measured at baseline, 6 months, and 12 months.   \n", "RESULTS There was no significant difference in CIMT between the 2 groups.", "There was no difference in the 12-month composite end point of death, myocardial infarction (MI), stroke, or any recurrent ischemia (31.4% vs 30.2%, P = .99).", "The rate of death, MI, or stroke at 12 months was numerically lower in the rosiglitazone group (11.9% vs 6.4%, P = .19).", "There was a trend toward a greater decrease over time in high-sensitivity C-reactive protein values compared with baseline in the group randomized to rosiglitazone versus placebo both at 6 months (-35.4% vs -15.8%, P = .059) and 12 months (-40.0% vs -20.9%, P = .089) and higher change in high-density lipoprotein (+15.5% vs +4.1%, P = .05) and lower triglycerides (-13.9% vs +14.9%, P = .004) in the rosiglitazone arm.", "There was a trend toward less new onset diabetes in the rosiglitazone group (0% vs 3.3%, P = .081) and no episodes of symptomatic hypoglycemia.", "There was no excess of new onset of clinical heart failure in the rosiglitazone group, nor was there a significant change in brain natriuretic peptide levels.   \n", "CONCLUSIONS Patients with metabolic syndrome presenting for PCI are at increased risk for subsequent cardiovascular events.", "Rosiglitazone for 12 months did not appear to affect CIMT in this population, although it did have beneficial effects on high-sensitivity C-reactive protein, high-density lipoprotein, and triglycerides.", "Further study of peroxisome proliferator-activated receptor agonism in patients with metabolic syndrome undergoing PCI may be warranted."], "structured": true}
{"doc_id": 24155601, "title": "Accumulation of hydroxyethyl starch in human and animal tissues: a systematic review", "abstract": ["To systematically review clinical and preclinical data on hydroxyethyl starch (HES) tissue storage.", "MEDLINE (PubMed) was searched and abstracts were screened using defined criteria to identify articles containing original data on HES tissue accumulation.", "Forty-eight studies were included: 37 human studies with a total of 635 patients and 11 animal studies.", "The most frequent indication for fluid infusion was surgery accounting for 282 patients (45.9 %).", "HES localization in skin was shown by 17 studies, in kidney by 12, in liver by 8, and in bone marrow by 5.", "Additional sites of HES deposition were lymph nodes, spleen, lung, pancreas, intestine, muscle, trophoblast, and placental stroma.", "Among major organs the highest measured tissue concentration of HES was in the kidney.", "HES uptake into intracellular vacuoles was observed by 30 min after infusion.", "Storage was cumulative, increasing in proportion to dose, although in 15 % of patients storage and associated symptoms were demonstrated at the lowest cumulative doses (0.4 g kg\u22121).", "Some HES deposits were extremely long-lasting, persisting for 8 years or more in skin and 10 years in kidney.", "Pruritus associated with HES storage was described in 17 studies and renal dysfunction in ten studies.", "In one included randomized trial, HES infusion produced osmotic nephrosis-like lesions indicative of HES storage (p = 0.01) and also increased the need for renal replacement therapy (odds ratio, 9.50; 95 % confidence interval, 1.09\u201382.7; p = 0.02).", "The tissue distribution of HES was generally similar in animals and humans.", "Tissue storage of HES is widespread, rapid, cumulative, frequently long-lasting, and potentially harmful."], "structured": false}
{"doc_id": 24157077, "title": "Cationic host defense (antimicrobial) peptides.", "abstract": ["Members of the cationic host defense (antimicrobial) peptide family are widely distributed in nature, existing in organisms from insects to plants to mammals and non-mammalian vertebrates.", "Although many demonstrate direct antimicrobial activity against bacteria, fungi, eukaryotic parasites and/or viruses, it has been established that cationic peptides have a key modulatory role in the innate immune response.", "More recent evidence suggests that host defense peptides are effective adjuvants, are synergistic with other immune effectors, polarize the adaptive response, and support wound healing.", "In addition, the mechanisms of action are being unraveled, which support more effective implementation of derivatives of these endogenous peptides as therapeutic agents."], "structured": false}
{"doc_id": 24159217, "title": "A mental health intervention for schoolchildren exposed to violence: a randomized controlled trial.", "abstract": ["CONTEXT No randomized controlled studies have been conducted to date on the effectiveness of psychological interventions for children with symptoms of posttraumatic stress disorder (PTSD) that has resulted from personally witnessing or being personally exposed to violence.   \n", "OBJECTIVE To evaluate the effectiveness of a collaboratively designed school-based intervention for reducing children's symptoms of PTSD and depression that has resulted from exposure to violence.   \n", "DESIGN A randomized controlled trial conducted during the 2001-2002 academic year.   \n", "SETTING AND PARTICIPANTS Sixth-grade students at 2 large middle schools in Los Angeles who reported exposure to violence and had clinical levels of symptoms of PTSD.   \n", "INTERVENTION Students were randomly assigned to a 10-session standardized cognitive-behavioral therapy (the Cognitive-Behavioral Intervention for Trauma in Schools) early intervention group (n = 61) or to a wait-list delayed intervention comparison group (n = 65) conducted by trained school mental health clinicians.   \n", "MAIN OUTCOME MEASURES Students were assessed before the intervention and 3 months after the intervention on measures assessing child-reported symptoms of PTSD (Child PTSD Symptom Scale; range, 0-51 points) and depression (Child Depression Inventory; range, 0-52 points), parent-reported psychosocial dysfunction (Pediatric Symptom Checklist; range, 0-70 points), and teacher-reported classroom problems using the Teacher-Child Rating Scale (acting out, shyness/anxiousness, and learning problems; range of subscales, 6-30 points).   \n", "RESULTS Compared with the wait-list delayed intervention group (no intervention), after 3 months of intervention students who were randomly assigned to the early intervention group had significantly lower scores on symptoms of PTSD (8.9 vs 15.5, adjusted mean difference, - 7.0; 95% confidence interval [CI], - 10.8 to - 3.2), depression (9.4 vs 12.7, adjusted mean difference, - 3.4; 95% CI, - 6.5 to - 0.4), and psychosocial dysfunction (12.5 vs 16.5, adjusted mean difference, - 6.4; 95% CI, -10.4 to -2.3).", "Adjusted mean differences between the 2 groups at 3 months did not show significant differences for teacher-reported classroom problems in acting out (-1.0; 95% CI, -2.5 to 0.5), shyness/anxiousness (0.1; 95% CI, -1.5 to 1.7), and learning (-1.1, 95% CI, -2.9 to 0.8).", "At 6 months, after both groups had received the intervention, the differences between the 2 groups were not significantly different for symptoms of PTSD and depression; showed similar ratings for psychosocial function; and teachers did not report significant differences in classroom behaviors.   \n", "CONCLUSION A standardized 10-session cognitive-behavioral group intervention can significantly decrease symptoms of PTSD and depression in students who are exposed to violence and can be effectively delivered on school campuses by trained school-based mental health clinicians."], "structured": true}
{"doc_id": 24163770, "title": "Knowledge gaps and misconceptions about coronary heart disease among U.S. South Asians.", "abstract": ["BACKGROUND Although South Asians are at higher risk for coronary heart disease (CHD) than most other U.S. racial/ethnic groups, very little research has addressed this disparity.   ", "PURPOSE As a first step in developing culturally targeted CHD prevention messages for this rapidly growing community, this study examined South Asians' knowledge and beliefs about CHD.   \n", "METHODS Analyses, conducted in 2009, were based on data collected from January to July 2008 in a cross-sectional study population of 270 South Asian adults in Illinois.", "Interviews were conducted in English, Hindi, or Urdu using a standardized questionnaire.", "Multivariate regression models were used to examine the associations between sociodemographics and CHD knowledge and attitudes about preventability.   \n", "RESULTS Eighty-one percent of respondents had one or more CHD risk factors.", "Most participants (89%) said they knew little or nothing about CHD.", "Stress was the most frequently mentioned risk factor (44%).", "Few mentioned controlling blood pressure (11%); cholesterol (10%); and diabetes (5%) for prevention.", "Fifty-three percent said that heart attacks are not preventable.", "Low education level, being interviewed in Urdu or Hindi, and low level of acculturation were associated with less knowledge and believing that CHD is not preventable.   \n", "CONCLUSIONS A majority of South Asians in this study believed that CHD is not preventable and had low awareness of modifiable risk factors.", "As a first step, CHD education should target the knowledge gaps that may affect risk factor control and behavior change.", "Educational messages may need to be somewhat different for subgroups (e.g., by education and language) to be maximally effective."], "structured": true}
{"doc_id": 24177706, "title": "Innate host defense requires TFEB-mediated transcription of cytoprotective and antimicrobial genes.", "abstract": ["Animal host defense against infection requires the expression of defense genes at the right place and the right time.", "Understanding such tight control of host defense requires the elucidation of the transcription factors involved.", "By using an unbiased approach in the model Caenorhabditis elegans, we discovered that HLH-30 (known as TFEB in mammals) is a key transcription factor for host defense.", "HLH-30 was activated shortly after Staphylococcus aureus infection, and drove the expression of close to 80% of the host response, including antimicrobial and autophagy genes that were essential for host tolerance of infection.", "TFEB was also rapidly activated in murine macrophages upon S. aureus infection and was required for proper transcriptional induction of several proinflammatory cytokines and chemokines.", "Thus, our data suggest that TFEB is a previously unappreciated, evolutionarily ancient transcription factor in the host response to infection."], "structured": false}
{"doc_id": 24185667, "title": "DAP kinase regulates JNK signaling by binding and activating protein kinase D under oxidative stress", "abstract": ["The stress-activated kinase JNK mediates key cellular responses to oxidative stress.", "Here we show that DAP kinase (DAPk), a cell death promoting Ser/Thr protein kinase, plays a main role in oxidative stress-induced JNK signaling.", "We identify protein kinase D (PKD) as a novel substrate of DAPk and demonstrate that DAPk physically interacts with PKD in response to oxidative stress.", "We further show that DAPk activates PKD in cells and that induction of JNK phosphorylation by ectopically expressed DAPk can be attenuated by knocking down PKD expression or by inhibiting its catalytic activity.", "Moreover, knockdown of DAPk expression caused a marked reduction in JNK activation under oxidative stress, indicating that DAPk is indispensable for the activation of JNK signaling under these conditions.", "Finally, DAPk is shown to be required for cell death under oxidative stress in a process that displays the characteristics of caspase-independent necrotic cell death.", "Taken together, these findings establish a major role for DAPk and its specific interaction with PKD in regulating the JNK signaling network under oxidative stress."], "structured": false}
{"doc_id": 24186125, "title": "The changes of antioxidant defense system caused by quercetin administration do not lead to DNA damage and apoptosis in the spleen and bone marrow cells of rats.", "abstract": ["Quercetin may have the opposite effect, namely anti- as well as pro-oxidant.", "The aim of this study was to assess the results of quercetin anti- and/or pro-oxidant activity in the bone marrow and spleen cells of rats.", "The experimental rats were treated daily, with quercetin in a dose of 8 or 80mg/kg b.w.", "by gavage for 40 days.", "The intracellular redox state in cells were assessed by measuring the ferric ion reducing antioxidant power (FRAP) level and malonodialdehyde concentration.", "HO-1 mRNA expression was examined with real-time PCR.", "The extent of DNA damage was determined by the alkaline-labile comet assay.", "A potential pro-apoptotic quercetin action was determined using the FITC-Annexin V kit.", "The quercetin and isorhamnetin concentrations in serum were analyzed by HPLC-ECD.", "MDA concentration and FRAP values, were significantly decreased in the spleen and bone marrow cells of rats treated with quercetin, in a dose of 80mg/kg b.w.", "in comparison with the control rats; no significant changes were observed after quercetin was administered in a dose ten times as low.", "Treatment with quercetin dose-dependently upregulated the expression of HO-1 mRNA in the bone marrow cells.", "Quercetin administration to the rats did not induce either DNA damage or apoptosis in the examined cells.", "The results of our study prove that changes in the antioxidant state, caused by quercetin, do not lead to DNA damage or exert any pro-apoptotic activity in vivo."], "structured": false}
{"doc_id": 24190159, "title": "Mutated KRAS results in overexpression of DUSP4, a MAP-kinase phosphatase, and SMYD3, a histone methyltransferase, in rectal carcinomas.", "abstract": ["Mutations of the KRAS oncogene are predictive for resistance to treatment with antibodies against the epithelial growth factor receptor in patients with colorectal cancer.", "Overcoming this therapeutic dilemma could potentially be achieved by the introduction of drugs that inhibit signaling pathways that are activated by KRAS mutations.", "To identify comprehensively such signaling pathways, we profiled pretreatment biopsies and normal mucosa from 65 patients with locally advanced rectal cancer-30 of which carried mutated KRAS-using global gene expression microarrays.", "By comparing all tumor tissues exclusively to matched normal mucosa, we could improve assay sensitivity, and identified a total of 22,297 features that were differentially expressed (adjusted P-value <0.05) between normal mucosa and cancer, including several novel potential rectal cancer genes.", "We then used this comprehensive description of the rectal cancer transcriptome as the baseline for identifying KRAS-dependent alterations.", "The presence of activating KRAS mutations is significantly correlated to an upregulation of 13 genes (adjusted P-value <0.05), among them DUSP4, a MAP-kinase phosphatase, and SMYD3, a histone methyltransferase.", "Inhibition of the expression of both genes has previously been shown using the MEK1-inhibitor PD98059 and the antibacterial compound Novobiocin, respectively.", "These findings suggest a potential approach to overcome resistance to treatment with antibodies against the epithelial growth factor receptor in patients with KRAS-mutant rectal carcinomas."], "structured": false}
{"doc_id": 24205118, "title": "Clinicopathological and prognostic significance of Bmi-1 expression in human cervical cancer.", "abstract": ["OBJECTIVE To investigate the clinical significance of Bmi-1 expression as a prognostic marker for cervical cancer.", "Design.", "Retrospectively collected data from a population-based cohort.   \n", "SETTING Jiangsu Province Hospital.", "Population.", "Eighty-eight women diagnosed with cervical carcinoma between 2000 and 2003.   \n", "METHODS RT-PCR assay was performed to determine Bmi-1 mRNA expression in 18 cervical cancer and noncancerous tissue samples and immunohistochemistry to detect Bmi-1 protein expression in 88 cervical cancer samples.", "The correlation between Bmi-1 expression and clinicopathological factors was analyzed.", "Additionally, statistical analyses were applied to test for prognostic associations.", "RNA interference was used to downregulate Bmi-1 expression in a cervical cancer cell line (HeLa).", "In vitro cytotoxicity was measured by the methylthiazoletetrazolium and colony formation assays.", "Effects of Bmi-1 inhibition on in vivo growth of cancer cells was detected by the tumorigenicity assay.", "Cell cycle distribution and cell apoptosis were measured by flow cytometry.   \n", "MAIN OUTCOME MEASURES The levels of Bmi-1 mRNA and protein expression in tissues were evaluated by RT-PCR and Western Blot assays.   \n", "RESULTS The level of Bmi-1 mRNA expression in cervical cancer tissues was significantly higher than that in corresponding noncancerous tissues.", "High Bmi-1 expression was significantly correlated with poor tumor differentiation, advanced International Federation of Gynecology and Obstetrics stage and positive lymph node metastasis.", "Patients with high Bmi-1 expression showed shorter overall survival than those with low expression.", "Univariate and multivariate analyses showed that high Bmi-1 expression was an independent prognostic factor.   \n", "CONCLUSIONS RNA interference-mediated Bmi-1 inhibition could inhibit in vitro and in vivo growth, enhance apoptosis and induce cell cycle arrest of cervical cancer cells.", "Bmi-1 might be an independent prognostic marker for cervical cancer patients."], "structured": true}
{"doc_id": 24211561, "title": "Dexamethasone decreases vomiting by children after tonsillectomy.", "abstract": ["We evaluated the effect of dexamethasone on vomiting after elective tonsillectomy in 133 healthy children aged 2-12 yr in a randomized, stratified, blocked, double-blind, placebo-controlled study.", "General anesthesia was induced by inhalation of N2O and halothane or intravenously (IV) with propofol.", "Anesthesia was maintained with N2O and halothane.", "Dexamethasone 150 micrograms/kg up to a maximum dose of 8 mg, or placebo, was administered IV before surgery.", "All patients received 1.5 mg/kg codeine intramuscularly (IM) intraoperatively.", "Perioperative IV fluids, management of emesis, postoperative pain and hospital discharge criteria were all standardized.", "The groups were similar with respect to number, age, weight, length of surgery, and estimated intraoperative blood loss.", "Dexamethasone reduced the overall incidence of vomiting from 72% (placebo) to 40% (P < 0.001).", "Vomiting, both in-hospital and postdischarge, was decreased by the prophylactic administration of dexamethasone.", "Each episode of in-hospital vomiting prolonged discharge by 13 +/-", "2 min, mean +/-", "SD (P < 0.001).", "In conclusion, dexamethasone markedly decreased vomiting by healthy children after elective tonsillectomy in an ambulatory hospital setting."], "structured": false}
{"doc_id": 24221369, "title": "A Conserved Histidine in the RNA Sensor RIG-I Controls Immune Tolerance to N1-2'O-Methylated Self RNA.", "abstract": ["The cytosolic helicase retinoic acid-inducible gene-I (RIG-I) initiates immune responses to most RNA viruses by detecting viral 5'-triphosphorylated RNA (pppRNA).", "Although endogenous mRNA is also 5'-triphosphorylated, backbone modifications and the 5'-ppp-linked methylguanosine ((m7)G) cap prevent immunorecognition.", "Here we show that the methylation status of endogenous capped mRNA at the 5'-terminal nucleotide (N1) was crucial to prevent RIG-I activation.", "Moreover, we identified a single conserved amino acid (H830) in the RIG-I RNA binding pocket as the mediator of steric exclusion of N1-2'O-methylated RNA.", "H830A alteration (RIG-I(H830A)) restored binding of N1-2'O-methylated pppRNA.", "Consequently, endogenous mRNA activated the RIG-I(H830A) mutant but not wild-type RIG-I. Similarly, knockdown of the endogenous N1-2'O-methyltransferase led to considerable RIG-I stimulation in the absence of exogenous stimuli.", "Studies involving yellow-fever-virus-encoded 2'O-methyltransferase and RIG-I(H830A) revealed that viruses exploit this mechanism to escape RIG-I. Our data reveal a new role for cap N1-2'O-methylation in RIG-I tolerance of self-RNA."], "structured": false}
{"doc_id": 24234341, "title": "lumi: a pipeline for processing Illumina microarray.", "abstract": ["UNLABELLED Illumina microarray is becoming a popular microarray platform.", "The BeadArray technology from Illumina makes its preprocessing and quality control different from other microarray technologies.", "Unfortunately, most other analyses have not taken advantage of the unique properties of the BeadArray system, and have just incorporated preprocessing methods originally designed for Affymetrix microarrays.", "lumi is a Bioconductor package especially designed to process the Illumina microarray data.", "It includes data input, quality control, variance stabilization, normalization and gene annotation portions.", "In specific, the lumi package includes a variance-stabilizing transformation (VST) algorithm that takes advantage of the technical replicates available on every Illumina microarray.", "Different normalization method options and multiple quality control plots are provided in the package.", "To better annotate the Illumina data, a vendor independent nucleotide universal identifier (nuID) was devised to identify the probes of Illumina microarray.", "The nuID annotation packages and output of lumi processed results can be easily integrated with other Bioconductor packages to construct a statistical data analysis pipeline for Illumina data.   ", "AVAILABILITY The lumi Bioconductor package, www.bioconductor.org"], "structured": false}
{"doc_id": 24237492, "title": "Large scale replication and meta-analysis of variants on chromosome 4q25 associated with atrial fibrillation.", "abstract": ["AIMS A recent genome-wide association study identified a haplotype block on chromosome 4q25 associated with atrial fibrillation (AF).", "We sought to replicate this association in four independent cohorts.   \n", "METHODS AND RESULTS The Framingham Heart Study and Rotterdam Study are community-based longitudinal studies.", "The Vanderbilt AF Registry and German AF Network (AFNet) are case-control studies.", "Participants with AF (n = 3508) were more likely to be male and were older than referent participants (n = 12 173; Framingham 82 +/- 10 vs. 71 +/-", "13 years; Rotterdam 73 +/-", "8 vs. 69 +/-", "9 years; Vanderbilt 54 +/- 14 vs. 57 +/-", "14 years; AFNet 62 +/- 12 vs. 49 +/-", "14 years).", "Single nucleotide polymorphism (SNP) rs2200733 was associated with AF in all four cohorts, with odds ratios (ORs) ranging from 1.37 in Rotterdam [95% confidence interval (CI) 1.18-1.59; P = 3.1 x 10(-5)] to 2.52 in AFNet (95% CI 2.22-2.8; P = 1.8 x 10(-49)).", "There also was a significant association between AF and rs10033464 in Framingham (OR 1.34; 95% CI 1.03-1.75; P = 0.031) and AFNet (OR 1.30; 95% CI 1.13-1.51; P = 0.0002), but not Vanderbilt (OR 1.16; 95% CI 0.86-1.56; P = 0.33).", "A meta-analysis of the current and prior AF studies revealed an OR of 1.90 (95% CI 1.60-2.26; P = 3.3 x 10(-13)) for rs2200733 and of 1.36 (95% CI 1.26-1.47; P = 6.7 x 10(-15)) for rs10033464.   \n", "CONCLUSION The non-coding SNPs rs2200733 and rs10033464 are strongly associated with AF in four cohorts of European descent.", "These results confirm the significant relations between AF and intergenic variants on chromosome 4."], "structured": true}
{"doc_id": 24241932, "title": "Ecological analysis of ethnic differences in relation between tuberculosis and poverty.", "abstract": ["OBJECTIVE To examine the effect of ethnicity on the relation between tuberculosis and deprivation.   \n", "DESIGN Retrospective ecological study comparing incidence of tuberculosis in white and south Asian residents of the 39 electoral wards in Birmingham with ethnic specific indices of deprivation.   \n", "SETTING Birmingham, 1989-93.   ", "SUBJECTS 1516 notified cases of tuberculosis.   \n", "MAIN OUTCOME MEASURES Rates of tuberculosis and measures of deprivation.   \n", "RESULTS Univariate analysis showed significant associations of tuberculosis rates for the whole population with several indices of deprivation (P<0.01) and with the proportion of the population of south Asian origin (P<0.01).", "All deprivation covariates were positively associated with each other but on multiple regression, higher level of overcrowding was independently associated with tuberculosis rates.", "For the white population, overcrowding was associated with tuberculosis rates independently of other variables (P=0.0036).", "No relation with deprivation was found for the south Asian population in either single or multivariable analyses.   \n", "CONCLUSIONS Poverty is significantly associated with tuberculosis in the white population, but no such relation exists for those of Asian ethnicity.", "These findings suggest that causal factors, and therefore potential interventions, will also differ by ethnic group."], "structured": true}
{"doc_id": 24249915, "title": "Reduced expression of oestrogen receptor beta in invasive breast cancer and its re-expression using DNA methyl transferase inhibitors in a cell line model.", "abstract": ["To gain insights into the possible role of oestrogen receptor (ER) beta in breast carcinogenesis, immunohistochemical analysis of ER beta was performed on 512 breast specimens encompassing normal (n = 138), pure ductal carcinoma in situ (n = 16), invasive cancers (n = 319), lymph node metastases (n = 31), and recurrences (n = 8).", "Real-time polymerase chain reaction (PCR) was used to investigate the methylation status of the ER beta gene in the ER beta negative breast cancer cell lines SkBr3 and MDA-MB-435.", "A gradual reduction in, but not a complete loss of, ER beta expression was observed during the transition from normal and pre-invasive lesions to invasive cancers, where ER beta was lost in 21% of cases.", "This was more pronounced in invasive ductal than in lobular carcinomas, a significantly higher proportion of which were ER beta-positive (74% compared with 91%, respectively, p = 0.0004).", "Examination of paired primary cancers with their axillary lymph node metastases showed that if ER beta was present in the primary tumour, it persisted in the metastasis.", "Treatment of ER beta-negative cell lines with DNA methyl transferase inhibitors restored ER beta expression, providing experimental evidence that silencing of ER beta in breast carcinomas could be due to promoter hypermethylation.", "These results suggest that loss of ER beta expression is one of the hallmarks of breast carcinogenesis and that it may be a reversible process involving methylation."], "structured": false}
{"doc_id": 24269361, "title": "Atopy risk in infants and children in relation to early exposure to fish, oily fish, or long-chain omega-3 fatty acids: a systematic review.", "abstract": ["There are two main families of polyunsaturated fatty acids (PUFAs), the n-6 and the n-3 families.", "It has been suggested that there is a causal relationship between n-6 PUFA intake and allergic disease, and there are biologically plausible mechanisms, involving eicosanoid mediators of the n-6 PUFA arachidonic acid, that could explain this.", "Fish and fish oils are sources of long-chain n-3 PUFAs and these fatty acids act to oppose the actions of n-6 PUFAs.", "Thus, it is considered that n-3 PUFAs will protect against atopic sensitization and against the clinical manifestations of atopy.", "Evidence to examine this has been acquired from epidemiologic studies investigating associations between fish intake in pregnancy, lactation, infancy, and childhood, and atopic outcomes in infants and children and from intervention studies with fish oil supplements in pregnancy, lactation, infancy, and childhood, and atopic outcomes in infants and children.", "All five epidemiological studies investigating the effect of maternal fish intake during pregnancy on atopic or allergic outcomes in infants/children of those pregnancies concluded protective associations.", "One study investigating the effects of maternal fish intake during lactation did not observe any significant associations.", "The evidence from epidemiological studies investigating the effects of fish intake during infancy and childhood on atopic outcomes in those infants or children is inconsistent, although the majority of the studies (nine of 14) showed a protective effect of fish intake during infancy or childhood on atopic outcomes in those infants/children.", "Fish oil supplementation during pregnancy and lactation or during infancy or childhood results in a higher n-3 PUFA status in the infants or children.", "Fish oil provision to pregnant women is associated with immunologic changes in cord blood and such changes may persist.", "Studies performed to date indicate that provision of fish oil during pregnancy may reduce sensitization to common food allergens and reduce prevalence and severity of atopic dermatitis in the first year of life, with a possible persistence until adolescence with a reduction in eczema, hay fever, and asthma.", "Fish oil provision to infants or children may be associated with immunologic changes in the blood but it is not clear if these are of clinical significance and whether they persist.", "Fish oil supplementation in infancy may decrease the risk of developing some manifestations of allergic disease, but this benefit may not persist as other factors come into play.", "It is not clear whether fish oil can be used to treat children with asthma as the two studies conducted to date give divergent results.", "Further studies of increased long-chain n-3 PUFA provision in during pregnancy, lactation, and infancy are needed to more clearly identify the immunologic and clinical effects in infants and children and to identify protective and therapeutic effects and their persistence."], "structured": false}
{"doc_id": 24273592, "title": "Dietary quality among men and women in 187 countries in 1990 and 2010: a systematic assessment", "abstract": ["BACKGROUND Healthy dietary patterns are a global priority to reduce non-communicable diseases.", "Yet neither worldwide patterns of diets nor their trends with time are well established.", "We aimed to characterise global changes (or trends) in dietary patterns nationally and regionally and to assess heterogeneity by age, sex, national income, and type of dietary pattern.   \n", "METHODS In this systematic assessment, we evaluated global consumption of key dietary items (foods and nutrients) by region, nation, age, and sex in 1990 and 2010.", "Consumption data were evaluated from 325 surveys (71\u00b77% nationally representative) covering 88\u00b77% of the global adult population.", "Two types of dietary pattern were assessed: one reflecting greater consumption of ten healthy dietary items and the other based on lesser consumption of seven unhealthy dietary items.", "The mean intakes of each dietary factor were divided into quintiles, and each quintile was assigned an ordinal score, with higher scores being equivalent to healthier diets (range 0-100).", "The dietary patterns were assessed by hierarchical linear regression including country, age, sex, national income, and time as exploratory variables.   \n", "FINDINGS From 1990 to 2010, diets based on healthy items improved globally (by 2\u00b72 points, 95% uncertainty interval (UI) 0\u00b79 to 3\u00b75), whereas diets based on unhealthy items worsened (-2\u00b75, -3\u00b73 to -1\u00b77).", "In 2010, the global mean scores were 44\u00b70 (SD 10\u00b75) for the healthy pattern and 52\u00b71 (18\u00b76) for the unhealthy pattern, with weak intercorrelation (r=-0\u00b708) between countries.", "On average, better diets were seen in older adults compared with younger adults, and in women compared with men (p<0\u00b70001 each).", "Compared with low-income nations, high-income nations had better diets based on healthy items (+2\u00b75 points, 95% UI 0\u00b73 to 4\u00b71), but substantially poorer diets based on unhealthy items (-33\u00b70, -37\u00b78 to -28\u00b73).", "Diets and their trends were very heterogeneous across the world regions.", "For example, both types of dietary patterns improved in high-income countries, but worsened in some low-income countries in Africa and Asia.", "Middle-income countries showed the largest improvement in dietary patterns based on healthy items, but the largest deterioration in dietary patterns based on unhealthy items.   \n", "INTERPRETATION Consumption of healthy items improved, while consumption of unhealthy items worsened across the world, with heterogeneity across regions and countries.", "These global data provide the best estimates to date of nutrition transitions across the world and inform policies and priorities for reducing the health and economic burdens of poor diet quality.   \n", "FUNDING The Bill & Melinda Gates Foundation and Medical Research Council."], "structured": true}
{"doc_id": 24276304, "title": "The epidemiology of major depressive disorder: results from the National Comorbidity Survey Replication (NCS-R).", "abstract": ["CONTEXT Uncertainties exist about prevalence and correlates of major depressive disorder (MDD).   \n", "OBJECTIVE To present nationally representative data on prevalence and correlates of MDD by Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition (DSM-IV) criteria, and on study patterns and correlates of treatment and treatment adequacy from the recently completed National Comorbidity Survey Replication (NCS-R).   \n", "DESIGN Face-to-face household survey conducted from February 2001 to December 2002.   \n", "SETTING The 48 contiguous United States.   \n", "PARTICIPANTS Household residents ages 18 years or older (N = 9090) who responded to the NCS-R survey.   \n", "MAIN OUTCOME MEASURES Prevalence and correlates of MDD using the World Health Organization's (WHO) Composite International Diagnostic Interview (CIDI), 12-month severity with the Quick Inventory of Depressive Symptomatology Self-Report (QIDS-SR), the Sheehan Disability Scale (SDS), and the WHO disability assessment scale (WHO-DAS).", "Clinical reinterviews used the Structured Clinical Interview for DSM-IV.   \n", "RESULTS The prevalence of CIDI MDD for lifetime was 16.2% (95% confidence interval [CI], 15.1-17.3) (32.6-35.1 million US adults) and for 12-month was 6.6% (95% CI, 5.9-7.3) (13.1-14.2 million US adults).", "Virtually all CIDI 12-month cases were independently classified as clinically significant using the QIDS-SR, with 10.4% mild, 38.6% moderate, 38.0% severe, and 12.9% very severe.", "Mean episode duration was 16 weeks (95% CI, 15.1-17.3).", "Role impairment as measured by SDS was substantial as indicated by 59.3% of 12-month cases with severe or very severe role impairment.", "Most lifetime (72.1%) and 12-month (78.5%) cases had comorbid CIDI/DSM-IV disorders, with MDD only rarely primary.", "Although 51.6% (95% CI, 46.1-57.2) of 12-month cases received health care treatment for MDD, treatment was adequate in only 41.9% (95% CI, 35.9-47.9) of these cases, resulting in 21.7% (95% CI, 18.1-25.2) of 12-month MDD being adequately treated.", "Sociodemographic correlates of treatment were far less numerous than those of prevalence.   \n", "CONCLUSIONS Major depressive disorder is a common disorder, widely distributed in the population, and usually associated with substantial symptom severity and role impairment.", "While the recent increase in treatment is encouraging, inadequate treatment is a serious concern.", "Emphasis on screening and expansion of treatment needs to be accompanied by a parallel emphasis on treatment quality improvement."], "structured": true}
{"doc_id": 24276902, "title": "The Pain Catastrophizing Scale: Further Psychometric Evaluation with Adult Samples", "abstract": ["Previous studies with undergraduates have provided support for the reliability and oblique three-factor structure of a new scale, the Pain Catastrophizing Scale (PCS).", "We examined the reliability and validity of the PCS in adult community and pain outpatient samples.", "The PCS showed a high internal consistency in both groups.", "Using data from the community sample, confirmatory factor analyses showed that the PCS taps a single construct characterized by three related dimensions.", "Gender differences were obtained on the PCS total score in the community and the outpatient samples.", "The analyses also showed significant differences between the community and the outpatient samples on the PCS total and subscales.", "Overall, the results showed strong evidence of criterion-related, concurrent, and discriminant validity for the PCS in the community sample.", "Limitations of the present study are discussed."], "structured": false}
{"doc_id": 24278870, "title": "Temsirolimus, interferon alfa, or both for advanced renal-cell carcinoma.", "abstract": ["BACKGROUND Interferon alfa is widely used for metastatic renal-cell carcinoma but has limited efficacy and tolerability.", "Temsirolimus, a specific inhibitor of the mammalian target of rapamycin kinase, may benefit patients with this disease.   \n", "METHODS In this multicenter, phase 3 trial, we randomly assigned 626 patients with previously untreated, poor-prognosis metastatic renal-cell carcinoma to receive 25 mg of intravenous temsirolimus weekly, 3 million U of interferon alfa (with an increase to 18 million U) subcutaneously three times weekly, or combination therapy with 15 mg of temsirolimus weekly plus 6 million U of interferon alfa three times weekly.", "The primary end point was overall survival in comparisons of the temsirolimus group and the combination-therapy group with the interferon group.   \n", "RESULTS Patients who received temsirolimus alone had longer overall survival (hazard ratio for death, 0.73; 95% confidence interval [CI], 0.58 to 0.92; P=0.008) and progression-free survival (P<0.001) than did patients who received interferon alone.", "Overall survival in the combination-therapy group did not differ significantly from that in the interferon group (hazard ratio, 0.96; 95% CI, 0.76 to 1.20; P=0.70).", "Median overall survival times in the interferon group, the temsirolimus group, and the combination-therapy group were 7.3, 10.9, and 8.4 months, respectively.", "Rash, peripheral edema, hyperglycemia, and hyperlipidemia were more common in the temsirolimus group, whereas asthenia was more common in the interferon group.", "There were fewer patients with serious adverse events in the temsirolimus group than in the interferon group (P=0.02).   \n", "CONCLUSIONS As compared with interferon alfa, temsirolimus improved overall survival among patients with metastatic renal-cell carcinoma and a poor prognosis.", "The addition of temsirolimus to interferon did not improve survival.", "(ClinicalTrials.gov number, NCT00065468 [ClinicalTrials.gov].)."], "structured": true}
{"doc_id": 24282306, "title": "Macrophage Diversity Enhances Tumor Progression and Metastasis", "abstract": ["There is persuasive clinical and experimental evidence that macrophages promote cancer initiation and malignant progression.", "During tumor initiation, they create an inflammatory environment that is mutagenic and promotes growth.", "As tumors progress to malignancy, macrophages stimulate angiogenesis, enhance tumor cell migration and invasion, and suppress antitumor immunity.", "At metastatic sites, macrophages prepare the target tissue for arrival of tumor cells, and then a different subpopulation of macrophages promotes tumor cell extravasation, survival, and subsequent growth.", "Specialized subpopulations of macrophages may represent important new therapeutic targets."], "structured": false}
{"doc_id": 24285403, "title": "Ankle brachial index as a predictor of cognitive impairment in the general population: ten-year follow-up of the Edinburgh Artery Study.", "abstract": ["OBJECTIVES To determine whether the ankle brachial index (ABI, a marker of generalized atherosclerosis) is associated with cognitive impairment after 10 years in older people.   \n", "DESIGN Cohort study (Edinburgh Artery Study).   \n", "SETTING Eleven general practices in Edinburgh, Scotland.   \n", "PARTICIPANTS Seven hundred seventeen men and women aged 55 to 74 from the general population, followed for 10 years.   \n", "MEASUREMENTS ABI measured at baseline and major cognitive functions (including premorbid function using the National Adult Reading Test, NART) tested after 10 years.   \n", "RESULTS After adjustment for age and sex, a low ABI was associated with lower scoring (bottom tertile vs top tertile) on Raven's Matrices (odds ratio (OR)=1.6, 95% confidence interval (CI) =1.0-2.6), Verbal Fluency (OR =1.8, 95% CI =1.1-3.0), and Digit Symbol Test (OR =2.3, 95% CI =1.3-4.2), suggesting that the ABI is predictive of poorer performance in nonverbal reasoning, verbal fluency, and information processing speed.", "The association between ABI and the Digit Symbol Test remained significant after further adjustment for premorbid cognitive function (tested using the NART), suggesting that the ABI is also predictive of decline in information processing speed (from premorbid ability to that measured here in older age).   \n", "CONCLUSION The ABI may be useful in identifying older individuals at higher risk of cognitive impairment.", "In the future, preventive measures developed to target individuals with a low ABI should consider measures to reduce vascular-related cognitive decline as well as cardiovascular events, in an effort to reduce the incidence and consequences of subsequent cognitive impairment and dementia."], "structured": true}
{"doc_id": 24294572, "title": "PTEN Regulates PI(3,4)P2 Signaling Downstream of Class I PI3K", "abstract": ["The PI3K signaling pathway regulates cell growth and movement and is heavily mutated in cancer.", "Class I PI3Ks synthesize the lipid messenger PI(3,4,5)P3.", "PI(3,4,5)P3 can be dephosphorylated by 3- or 5-phosphatases, the latter producing PI(3,4)P2.", "The PTEN tumor suppressor is thought to function primarily as a PI(3,4,5)P3 3-phosphatase, limiting activation of this pathway.", "Here we show that PTEN also functions as a PI(3,4)P2 3-phosphatase, both in vitro and in vivo.", "PTEN is a major PI(3,4)P2 phosphatase in Mcf10a cytosol, and loss of PTEN and INPP4B, a known PI(3,4)P2 4-phosphatase, leads to synergistic accumulation of PI(3,4)P2, which correlated with increased invadopodia in epidermal growth factor (EGF)-stimulated cells.", "PTEN deletion increased PI(3,4)P2 levels in a mouse model of prostate cancer, and it inversely correlated with PI(3,4)P2 levels across several EGF-stimulated prostate and breast cancer lines.", "These results point to a role for PI(3,4)P2 in the phenotype caused by loss-of-function mutations or deletions in PTEN."], "structured": false}
{"doc_id": 24307695, "title": "Genetic analysis of an ARS element from the fission yeast Schizosaccharomyces pombe.", "abstract": ["ARS (autonomously replicating sequence) elements are DNA fragments that can function as origins of DNA replication in yeast.", "We report the first fine-structure analysis of ars1, an ARS element of the fission yeast Schizosaccharomyces pombe.", "Characterization of a series of nested deletion mutations indicated that the minimal fragment of DNA encompassing ars1 is surprisingly large.", "No fragment < 650 bp retained significant ARS activity.", "Analysis of deletion and substitution mutations scanning the entire minimal ars1 identified a single essential 50 bp fragment (segment 1).", "Only one other 50 bp mutation reduced activity as much as 5-fold and most deletions were without effect.", "Thus, the minimal ars1 is composed of two general types of genetic elements, a small segment that is absolutely required for efficient ARS activity and a much larger region that is tolerant of internal structural alterations.", "Higher resolution analysis of segment 1 defined a critical 30 bp A/T-rich segment which appears to contain redundant genetic elements.", "Schizosaccharomyces pombe ars1 promoted high frequency transformation in the budding yeast S.cerevisiae but this heterologous activity was not dependent on segment 1.", "Our analysis indicates that the functional elements required for ARS function in S.pombe and S.cerevisiae are clearly different."], "structured": false}
{"doc_id": 24311787, "title": "N terminus of Swr1 binds to histone H2AZ and provides a platform for subunit assembly in the chromatin remodeling complex.", "abstract": ["Variant histone H2AZ-containing nucleosomes are involved in the regulation of gene expression.", "In Saccharomyces cerevisiae, chromatin deposition of histone H2AZ is mediated by the fourteen-subunit SWR1 complex, which catalyzes ATP-dependent exchange of nucleosomal histone H2A for H2AZ.", "Previous work defined the role of seven SWR1 subunits (Swr1 ATPase, Swc2, Swc3, Arp6, Swc5, Yaf9, and Swc6) in maintaining complex integrity and H2AZ histone replacement activity.", "Here we examined the function of three additional SWR1 subunits, bromodomain containing Bdf1, actin-related protein Arp4 and Swc7, by analyzing affinity-purified mutant SWR1 complexes.", "We observed that depletion of Arp4 (arp4-td) substantially impaired the association of Bdf1, Yaf9, and Swc4.", "In contrast, loss of either Bdf1 or Swc7 had minimal effects on overall complex integrity.", "Furthermore, the basic H2AZ histone replacement activity of SWR1 in vitro required Arp4, but not Bdf1 or Swc7.", "Thus, three out of fourteen SWR1 subunits, Bdf1, Swc7, and previously noted Swc3, appear to have roles auxiliary to the basic histone replacement activity.", "The N-terminal region of the Swr1 ATPase subunit is necessary and sufficient to direct association of Bdf1 and Swc7, as well as Arp4, Act1, Yaf9 and Swc4.", "This same region contains an additional H2AZ-H2B specific binding site, distinct from the previously identified Swc2 subunit.", "These findings suggest that one SWR1 enzyme might be capable of binding two H2AZ-H2B dimers, and provide further insight on the hierarchy and interdependency of molecular interactions within the SWR1 complex."], "structured": false}
{"doc_id": 24315156, "title": "Role of the cytoskeleton during leukocyte responses", "abstract": ["The cytoskeleton is a cellular network of structural, adaptor and signalling molecules that regulates most cellular functions that are related to the immune response, including migration, extravasation, antigen recognition, activation and phagocytosis by different subsets of leukocytes.", "Recently, a large number of regulatory elements and structural constituents of the leukocyte cytoskeleton have been identified.", "In this review, we discuss the composition and regulation of the different cytoskeletal elements and their role in immune responses."], "structured": false}
{"doc_id": 24318630, "title": "Integration of mental health into primary healthcare in low-income countries: avoiding medicalization.", "abstract": ["Since 2008 the World Health Organization (WHO), through its mental health Gap Action Programme, has attempted to revitalize efforts to integrate mental health into non-specialized (e.g. primary) healthcare.", "While this has led to renewed interest in this potential method of mental health service delivery, it has also prompted criticism.", "Some concerns raised are that it would contribute to the medicalization of social and psychological problems, and narrowly focus on primary care without sufficient attention given to strengthening other levels of the healthcare system, notably community-based care and care on district levels.", "This paper discusses seven elements that may be critical to preventing inadvertently contributing to increasing a narrow biomedical approach to mental healthcare when integrating mental health into non-specialized healthcare: (1) using task shifting approaches within a system of stepped care, (2) ensuring primary mental healthcare also includes brief psychotherapeutic interventions, (3) promote community-based recovery-oriented interventions for people with disabling chronic mental disorders, (4) conceptualizing training as a continuous process of strengthening clinical competencies through supervision, (5) engaging communities as partners in psychosocial interventions, (6) embedding shifts to primary mental healthcare within wider health policy reforms, and (7) promoting inter-sectoral approaches to address social determinants of mental health."], "structured": false}
{"doc_id": 24323369, "title": "Comparison of clomiphene citrate, metformin, or the combination of both for first-line ovulation induction and achievement of pregnancy in 154 women with polycystic ovary syndrome.", "abstract": ["OBJECTIVE To determine which first-line medication is more effective in polycystic ovary syndrome (PCOS) patients for ovulation induction and pregnancy achievement and to verify whether any patient characteristic is associated with a better response to therapy.   \n", "DESIGN Observational comparative study.   \n", "SETTING Fertility clinic.   \n", "PATIENT(S) One hundred fifty-four infertile women with oligomenorrhea and hyperandrogenism.   \n", "INTERVENTION(S) Group 1 (56 patients) received clomiphene citrate (CC) 50 mg from days 5-9 of the cycle.", "Group 2 (57 patients) received 500 mg of metformin 3 times a day.", "Group 3 (41 patients) received both medications.   \n", "MAIN OUTCOME MEASURE(S) Ovulation and pregnancy.   \n", "RESULT(S) Patients receiving metformin alone had an increased ovulation rate compared with those receiving CC alone (75.4% vs. 50%).", "Patients on metformin had similar ovulation rates compared with those in the combination group (75.4% vs. 63.4%).", "Pregnancy rates were equivalent in the 3 groups.", "Response to metformin was independent of body weight and dose.", "Finally, nonsmoking predicted better ovulatory response overall as well as lower fasting glucose for CC and lower androgens for metformin.   \n", "CONCLUSION(S)", "Metformin is better for ovulation induction than CC alone and equivalent for pregnancy achievement.", "We suggest that metformin can be used first for ovulation induction in patients with PCOS regardless of their weight and insulin levels because of its efficacy and known safety profile."], "structured": true}
{"doc_id": 24323695, "title": "Pulmonologist involvement, stage-specific treatment, and survival in adults with non-small cell lung cancer and chronic obstructive pulmonary disease.", "abstract": ["RATIONALE Up to 80% of patients with lung cancer have comorbid chronic obstructive pulmonary disease (COPD).", "Many of them are poor candidates for stage-specific lung cancer treatment due to diminished lung function and poor functional status, and many forego treatment.", "The negative effect of COPD may be moderated by pulmonologist-guided management.   \n", "OBJECTIVES This study examined the association between pulmonologist management and the probability of receiving the recommended stage-specific treatment modality and overall survival among patients with non-small cell lung cancer (NSCLC) with preexisting COPD.   \n", "METHODS Early- and advanced-stage NSCLC cases diagnosed between 2002 and 2005 with a prior COPD diagnosis (3-24 months before NSCLC diagnosis) were identified in Surveillance, Epidemiology, and End Results tumor registry data linked to Medicare claims.", "Study outcomes included receipt of recommended stage-specific treatment (surgical resection for early-stage NSCLC and chemotherapy for advanced-stage NSCLC [advNSCLC]) and overall survival.", "Pulmonologist management was considered present if one or more Evaluation and Management visit claims with pulmonologist specialty were observed within 6 months after NSCLC diagnosis.", "Stage-specific multivariate logistic regression tested association between pulmonologist management and treatment received.", "Cox proportional hazard models examined the independent association between pulmonologist care and mortality.", "Two-stage residual inclusion instrumental variable (2SRI-IV) analyses tested and adjusted for potential confounding based on unobserved factors or measurement error.   \n", "MEASUREMENTS AND MAIN RESULTS The cohorts included 5,488 patients with early-stage NSCLC and 6,426 patients with advNSCLC disease with preexisting COPD.", "Pulmonologist management was recorded for 54.9% of patients with early stage NSCLC and 35.7% of patients with advNSCLC.", "Of those patients with pulmonologist involvement, 58.5% of patients with early NSCLC received surgical resection, and 43.6% of patients with advNSCLC received chemotherapy.", "Pulmonologist management post NSCLC diagnosis was associated with increased surgical resection rates (odds ratio, 1.26; 95% confidence interval, 1.11-1.45) for early NSCLC and increased chemotherapy rates (odds ratio, 1.88; 95% confidence interval, 1.67-2.10) for advNSCLC.", "Pulmonologist management was also associated with reduced mortality risk for patients with early-stage NSCLC but not AdvNSCLC.   \n", "CONCLUSIONS Pulmonologist management had a positive association with rates of stage-specific treatment in both groups and overall survival in early-stage NSCLC.", "These results provide preliminary support for the recently published guidelines emphasizing the role of pulmonologists in lung cancer management."], "structured": true}
{"doc_id": 24335068, "title": "Divalent cations differentially regulate integrin alphaIIb cytoplasmic tail binding to beta3 and to calcium- and integrin-binding protein.", "abstract": ["We have used recombinant or synthetic alphaIIb and beta3 integrin cytoplasmic peptides to study their in vitro complexation and ligand binding capacity by surface plasmon resonance.", "alpha.beta heterodimerization occurred in a 1:1 stoichiometry with a weak KD in the micromolar range.", "Divalent cations were not required for this association but stabilized the alpha.beta complex by decreasing the dissociation rate.", "alpha.beta complexation was impaired by the R995A substitution or the KVGFFKR deletion in alphaIIb but not by the beta3 S752P mutation.", "Recombinant calcium- and integrin-binding protein (CIB), an alphaIIb-specific ligand, bound to the alphaIIb cytoplasmic peptide in a Ca2+- or Mn2+-independent, one-to-one reaction with a KD value of 12 microM. In contrast, in vitro liquid phase binding of CIB to intact alphaIIbbeta3 occurred preferentially with Mn2+-activated alphaIIbbeta3 conformers, as demonstrated by enhanced coimmunoprecipitation of CIB with PAC-1-captured Mn2+-activated alphaIIbbeta3, suggesting that Mn2+ activation of intact alphaIIbbeta3 induces the exposure of a CIB-binding site, spontaneously exposed by the free alphaIIb peptide.", "Since CIB did not stimulate PAC-1 binding to inactive alphaIIbbeta3 nor prevented activated alphaIIbbeta3 occupancy by PAC-1, we conclude that CIB does not regulate alphaIIbbeta3 inside-out signaling, but rather is involved in an alphaIIbbeta3 post-receptor occupancy event."], "structured": false}
{"doc_id": 24338780, "title": "Lethal autoimmune myocarditis in interferon-gamma receptor-deficient mice: enhanced disease severity by impaired inducible nitric oxide synthase induction.", "abstract": ["BACKGROUND Interferon-gamma (IFN-gamma) is an essential cytokine in the regulation of inflammatory responses in autoimmune diseases.", "Little is known about its role in inflammatory heart disease.   \n", "METHODS AND RESULTS We showed that IFN-gamma receptor-deficient mice (IFN-gammaR(-/-)) on a BALB/c background immunized with a peptide derived from cardiac alpha-myosin heavy chain develop severe myocarditis with high mortality.", "Although myocarditis subsided in wild-type mice after 3 weeks, IFN-gammaR(-/-) mice showed persistent disease.", "The persistent inflammation was accompanied by vigorous in vitro CD4 T-cell responses and impaired inducible nitric oxide synthase expression, together with evidence of impaired nitric oxide production in IFN-gammaR(-/-) hearts.", "Treatment of wild-type mice with the nitric oxide synthetase inhibitor N:-nitro-l-arginine-methyl-ester enhanced in vitro CD4 T-cell proliferation and prevented healing of myocarditis.   \n", "CONCLUSIONS Our data provide evidence that IFN-gamma protects mice from lethal autoimmune myocarditis by inducing the expression of inducible nitric oxide synthase followed by the downregulation of T-cell responses."], "structured": true}
{"doc_id": 24341590, "title": "Association between CYP2D6 polymorphisms and outcomes among women with early stage breast cancer treated with tamoxifen.", "abstract": ["CONTEXT The growth inhibitory effect of tamoxifen, which is used for the treatment of hormone receptor-positive breast cancer, is mediated by its metabolites, 4-hydroxytamoxifen and endoxifen.", "The formation of active metabolites is catalyzed by the polymorphic cytochrome P450 2D6 (CYP2D6) enzyme.   \n", "OBJECTIVE To determine whether CYP2D6 variation is associated with clinical outcomes in women receiving adjuvant tamoxifen.   \n", "DESIGN, SETTING, AND PATIENTS Retrospective analysis of German and US cohorts of patients treated with adjuvant tamoxifen for early stage breast cancer.", "The 1325 patients had diagnoses between 1986 and 2005 of stage I through III breast cancer and were mainly postmenopausal (95.4%).", "Last follow-up was in December 2008; inclusion criteria were hormone receptor positivity, no metastatic disease at diagnosis, adjuvant tamoxifen therapy, and no chemotherapy.", "DNA from tumor tissue or blood was genotyped for CYP2D6 variants associated with reduced (*10, *41) or absent (*3, *4, *5) enzyme activity.", "Women were classified as having an extensive (n=609), heterozygous extensive/intermediate (n=637), or poor (n=79) CYP2D6 metabolism.   \n", "MAIN OUTCOME MEASURES Time to recurrence, event-free survival, disease-free survival, and overall survival.   \n", "RESULTS Median follow-up was 6.3 years.", "At 9 years of follow-up, the recurrence rates were 14.9% for extensive metabolizers, 20.9% for heterozygous extensive/intermediate metabolizers, and 29.0% for poor metabolizers, and all-cause mortality rates were 16.7%, 18.0%, and 22.8%, respectively.", "Compared with extensive metabolizers, there was a significantly increased risk of recurrence for heterozygous extensive/intermediate metabolizers (time to recurrence adjusted hazard ratio [HR], 1.40; 95% confidence interval [CI], 1.04-1.90) and for poor metabolizers (time to recurrence HR, 1.90; 95% CI, 1.10-3.28).", "Compared with extensive metabolizers, those with decreased CYP2D6 activity (heterozygous extensive/intermediate and poor metabolism) had worse event-free survival (HR, 1.33; 95% CI, 1.06-1.68) and disease-free survival (HR, 1.29; 95% CI, 1.03-1.61), but there was no significant difference in overall survival (HR, 1.15; 95% CI, 0.88-1.51).   \n", "CONCLUSION Among women with breast cancer treated with tamoxifen, there was an association between CYP2D6 variation and clinical outcomes, such that the presence of 2 functional CYP2D6 alleles was associated with better clinical outcomes and the presence of nonfunctional or reduced-function alleles with worse outcomes."], "structured": true}
{"doc_id": 24346598, "title": "Long-term, nightly benzodiazepine treatment of injurious parasomnias and other disorders of disrupted nocturnal sleep in 170 adults.", "abstract": ["PURPOSE To assess the efficacy, dose stability, safety, and abuse potential of long-term, nightly benzodiazepine treatment of chronic disorders of disrupted nocturnal sleep.   \n", "PATIENTS AND METHODS During a 12-year period, one author evaluated and treated 170 adult referrals for > or = 6 months with nightly benzodiazepine therapy for longstanding, sleep-disruptive disorders: injurious sleepwalking and sleep terrors (69); rapid eye movement sleep behavior disorder (52); chronic, severe insomnia (25); and restless legs syndrome/periodic limb movement disorder (24).   \n", "RESULTS Complete/substantial control of the sleep disorders was achieved by 146 patients (86%); 8% had adverse effects requiring medication changes; 2% had relapses of alcohol or chemical abuse requiring hospitalization; another 2% at times misused their medications.", "A total of 136 patients received clonazepam nightly for a mean 3.5 (+/-", "2.4) years, with no significant difference in inital versus final mean dose: 0.77 mg (+/- 0.46) versus 1.10 mg (+/- 0.96).", "Similar results were obtained with chronic alprazolam treatment and with other benzodiazepine treatments.   \n", "CONCLUSION Long-term, nightly benzodiazepine treatment of injurious parasomnias and other disorders of disrupted nocturnal sleep resulted in sustained efficacy in most cases, with low risk of dosage tolerance, adverse effects, or abuse.", "Data from this study on the treatment of chronic, severe insomnia (a small subset of all insomnia) are not generalizable to the typical insomnia patient."], "structured": true}
{"doc_id": 24347647, "title": "Decreased proteasomal activity causes age-related phenotypes and promotes the development of metabolic abnormalities.", "abstract": ["The proteasome is a multicatalytic enzyme complex responsible for the degradation of both normal and damaged proteins.", "An age-related decline in proteasomal activity has been implicated in various age-related pathologies.", "The relevance of decreased proteasomal activity to aging and age-related diseases remains unclear, however, because suitable animal models are not available.", "In the present study, we established a transgenic (Tg) mouse model with decreased proteasomal chymotrypsin-like activity.", "Tg mice exhibited a shortened life span and developed age-related phenotypes.", "In Tg mice, polyubiquitinated and oxidized proteins accumulated, and the expression levels of cellular proteins such as Bcl-xL and RNase L were altered.", "When Tg mice were fed a high-fat diet, they developed more pronounced obesity and hepatic steatosis than did wild-type mice.", "Consistent with its role in lipid droplet formation, the expression of adipose differentiation-related protein (ADRP) was elevated in the livers of Tg mice.", "Of note, obesity and hepatic steatosis induced by a high-fat diet were more pronounced in aged than in young wild-type mice, and aged wild-type mice had elevated levels of ADRP, suggesting that the metabolic abnormalities present in Tg mice mimic those in aged mice.", "Our results provide the first in vivo evidence that decreased proteasomal chymotrypsin-like activity affects longevity and aggravates age-related metabolic disorders, such as obesity and hepatic steatosis."], "structured": false}
{"doc_id": 24349430, "title": "Orai1/CRACM1 overexpression suppresses cell proliferation via attenuation of the store-operated calcium influx-mediated signalling pathway in A549 lung cancer cells.", "abstract": ["BACKGROUND Orai1/CRACM1 is a principal component of the store-operated calcium channels.", "Store-operated calcium influx is highly correlated with inflammatory reactions, immunological regulation, and cell proliferation.", "Epidermal growth factor (EGF), which plays an important role in the regulation of cell proliferation, can activate store-operated calcium channels.", "However, the consequences of Orai1/CRACM1 overexpression in EGF-mediated lung cancer cells growth are not known.   \n", "METHODS To investigate the role of Orai1/CRACM1 in EGF-mediated lung cancer cell proliferation, Orai1/CRACM1 plasmids were transfected into cells by lipofection.", "A cell proliferation assay, immunofluorescence staining, flow cytometry, and real-time polymerase chain reaction were employed to monitor cell proliferation.", "The calcium influx signals were investigated using a fluorescent-based calcium assay.   \n", "RESULTS Transfection of Orai1/CRACM1 plasmids resulted in the inhibition of EGF-mediated cell proliferation.", "ERK1/2 and Akt phosphorylation were inhibited by Orai1/CRACM1 overexpression.", "Expression of the cell cycle modulator p21 was induced in the Orai1/CRACM1-overexpressing cells, whereas the expression of cyclin D3 was reduced.", "Flow cytometry revealed that overexpression of Orai1/CRACM1 resulted in G0/G1 cell cycle arrest.", "Importantly, Orai1/CRACM1 overexpression significantly attenuated EGF-mediated store-operated calcium influx.", "In addition, application of 2-APB, a store-operated calcium channel inhibitor, resulted in the inhibition of EGF-mediated cancer cell proliferation.   \n", "CONCLUSIONS We conclude that Orai1/CRACM1 overexpression attenuates store-operated Ca(2+) influx that in turn blocks EGF-mediated proliferative signaling and drives cell cycle arrest."], "structured": true}
{"doc_id": 24349992, "title": "Oxidative stress in cancer associated fibroblasts drives tumor-stroma co-evolution: A new paradigm for understanding tumor metabolism, the field effect and genomic instability in cancer cells.", "abstract": ["Loss of stromal fibroblast caveolin-1 (Cav-1) is a powerful single independent predictor of poor prognosis in human breast cancer patients, and is associated with early tumor recurrence, lymph node metastasis and tamoxifen-resistance.", "We developed a novel co-culture system to understand the mechanism(s) by which a loss of stromal fibroblast Cav-1 induces a \"lethal tumor micro-environment.", "\"", "Here, we propose a new paradigm to explain the powerful prognostic value of stromal Cav-1.", "In this model, cancer cells induce oxidative stress in cancer-associated fibroblasts, which then acts as a \"metabolic\" and \"mutagenic\" motor to drive tumor-stroma co-evolution, DNA damage and aneuploidy in cancer cells.", "More specifically, we show that an acute loss of Cav-1 expression leads to mitochondrial dysfunction, oxidative stress and aerobic glycolysis in cancer associated fibroblasts.", "Also, we propose that defective mitochondria are removed from cancer-associated fibroblasts by autophagy/mitophagy that is induced by oxidative stress.", "As a consequence, cancer associated fibroblasts provide nutrients (such as lactate) to stimulate mitochondrial biogenesis and oxidative metabolism in adjacent cancer cells (the \"Reverse Warburg Effect\").", "We provide evidence that oxidative stress in cancer-associated fibroblasts is sufficient to induce genomic instability in adjacent cancer cells, via a bystander effect, potentially increasing their aggressive behavior.", "Finally, we directly demonstrate that nitric oxide (NO) over-production, secondary to Cav-1 loss, is the root cause for mitochondrial dysfunction in cancer associated fibroblasts.", "In support of this notion, treatment with anti-oxidants (such as N-acetyl-cysteine, metformin and quercetin) or NO inhibitors (L-NAME) was sufficient to reverse many of the cancer-associated fibroblast phenotypes that we describe.", "Thus, cancer cells use \"oxidative stress\" in adjacent fibroblasts (i) as an \"engine\" to fuel their own survival via the stromal production of nutrients and (ii) to drive their own mutagenic evolution towards a more aggressive phenotype, by promoting genomic instability.", "We also present evidence that the \"field effect\" in cancer biology could also be related to the stromal production of ROS and NO species.", "eNOS-expressing fibroblasts have the ability to downregulate Cav-1 and induce mitochondrial dysfunction in adjacent fibroblasts that do not express eNOS.", "As such, the effects of stromal oxidative stress can be laterally propagated, amplified and are effectively \"contagious\"--spread from cell-to-cell like a virus--creating an \"oncogenic/mutagenic\" field promoting widespread DNA damage."], "structured": false}
{"doc_id": 24351680, "title": "Telomeres and telomerase: more than the end of the line", "abstract": ["Early studies of telomerase suggested that telomeres are maintained by an elegant but relatively simple and highly conserved mechanism of telomerase-mediated replication.", "As we learn more, it has become clear that the mechanism is elegant but not as simple as first thought.", "It is also evident that, although many species use similar, sometimes identical, DNA sequences for telomeres, these species express their own individuality in the way they regulate these sequences and, perhaps, in the additional tasks that they have imposed on their telomeric DNA.", "The striking similarities between telomeres in different species have revealed much about chromosome ends; the differences are proving to be equally informative.", "In addition to the differences between species that use telomerase, there are also a few exceptional organisms with atypical telomeres for which no telomerase activity has been detected.", "This review addresses recent studies, the insights they offer, and, perhaps more importantly, the questions they raise."], "structured": false}
{"doc_id": 24356383, "title": "Reduced osteoblastic population and defective mineralization in osteopetrotic (op/op) mice.", "abstract": ["Osteopetrotic (op/op) mice fail to exhibit bone remodeling because of a defective osteoclast formation due to a lack of macrophage colony-stimulating factor.", "In this study, we investigated the femora of op/op mice to clarify whether the osteoblastic population and bone mineralization are involved in osteoclasts or their bone resorption.", "The op/op mice extended the meshwork of trabecular bones from the chondro-osseous junction to the diaphyseal region.", "In the femoral metaphyses of op/op mice, intense alkaline phosphatase (ALPase)-positive osteoblasts were observed on the metaphyseal bone in close proximity to the erosion zone of the growth plates.", "Von Kossa's staining revealed scattered mineralized nodules and a fine meshwork of mineralized bone matrices while the wild-type littermates developed well-mineralized trabeculae parallel to the longitudinal axis.", "In contrast to the metaphysis, some op/op diaphyses showed flattened osteoblasts with weak ALPase-positivity, and the other diaphyses displayed bone surfaces without a covering by osteoblasts.", "It is likely, therefore, that the osteoblastic population and activity were lessened in the op/op diaphyses.", "Despite the osteopetrotic model, von Kossa's staining demonstrated patchy unmineralized areas in the op/op diaphyses, indicating that a lower population and/or the activity of osteoblasts resulted in defective mineralization in the bone.", "Transmission electron microscopy disclosed few osteoblasts on the diaphyseal bones, and instead, bone marrow cells and vascular endothelial cells were often attached to the unmineralized bone.", "Osteocytes were embedded in the unmineralized bone matrix.", "Thus, osteoclasts appear to be involved in the osteoblastic population and activity as well as subsequent bone mineralization."], "structured": false}
{"doc_id": 24384587, "title": "Interleukin 18 function in atherosclerosis is mediated by the interleukin 18 receptor and the Na-Cl co-transporter", "abstract": ["Interleukin-18 (IL18) participates in atherogenesis through several putative mechanisms.", "Interruption of IL18 action reduces atherosclerosis in mice.", "Here, we show that absence of the IL18 receptor (IL18r) does not affect atherosclerosis in apolipoprotein E\u2013deficient (Apoe\u2212/\u2212) mice, nor does it affect IL18 cell surface binding to or signaling in endothelial cells.", "As identified initially by co-immunoprecipitation with IL18, we found that IL18 interacts with the Na-Cl co-transporter (NCC; also known as SLC12A3), a 12-transmembrane-domain ion transporter protein preferentially expressed in the kidney.", "NCC is expressed in atherosclerotic lesions, where it colocalizes with IL18r.", "In Apoe\u2212/\u2212 mice, combined deficiency of IL18r and NCC, but not single deficiency of either protein, protects mice from atherosclerosis.", "Peritoneal macrophages from Apoe\u2212/\u2212 mice or from Apoe\u2212/\u2212 mice lacking IL18r or NCC show IL18 binding and induction of cell signaling and cytokine and chemokine expression, but macrophages from Apoe\u2212/\u2212 mice with combined deficiency of IL18r and NCC have a blunted response.", "An interaction between NCC and IL18r on macrophages was detected by co-immunoprecipitation.", "IL18 binds to the cell surface of NCC-transfected COS-7 cells, which do not express IL18r, and induces cell signaling and cytokine expression.", "This study identifies NCC as an IL18-binding protein that collaborates with IL18r in cell signaling, inflammatory molecule expression, and experimental atherogenesis."], "structured": false}
{"doc_id": 24387017, "title": "Notch promotes survival of pre\u2013T cells at the \u03b2-selection checkpoint by regulating cellular metabolism", "abstract": ["Notch signals are necessary for the functional outcomes of T cell receptor \u03b2-selection, including differentiation, proliferation and rescue from apoptosis.", "The mechanism underlying this requirement for T cell development is unknown.", "Here we show that Notch receptor and Delta-like 1 ligand interactions promoted the survival of CD4\u2212CD8\u2212 pre\u2013T cells through the maintenance of cell size, glucose uptake and metabolism.", "Furthermore, the trophic effects of Notch signaling were mediated by the pathway of phosphatidylinositol-3-OH kinase and the kinase Akt, such that expression of active Atk overcame the requirement for Notch in \u03b2-selection.", "Collectively, our results demonstrate involvement of Notch receptor\u2013ligand interactions in the regulation of cellular metabolism, thus enabling the autonomous signaling capacity of the pre\u2013T cell receptor complex.*Note:", "In the version of this article initially published online, in the fourth sentence of the abstract, the term \"Atk\" was a misspelling; this should be \"Akt.", "\"", "In the fourth sentence of the second paragraph of the introduction, the name of the second kinase mentioned, \"PI(3)K-dependent kinase 1,\" was incorrect; this should read \"phosphoinositide-dependent kinase 1.", "\"", "These errors have been corrected for the HTML and print versions of the article."], "structured": false}
{"doc_id": 24396137, "title": "Blood pressure, salivary cortisol, and inflammatory cytokine outcomes in senior female cancer survivors enrolled in a tai chi chih randomized controlled trial", "abstract": ["Older cancer survivors are a vulnerable population due to an increased risk for chronic diseases (e.g., cardiovascular disease) compounded with treatment late-effects and declines in physical functioning.", "Therefore, interventions that reduce chronic disease risk factors (i.e., blood pressure, chronic inflammation, and cortisol) are important in this population.", "Tai chi chih (TCC) is a mind-body exercise associated with reductions in chronic disease risk factors, but has not been examined with older cancer survivors.", "In a feasibility randomized controlled trial of TCC, we examined secondary outcomes of blood pressure, salivary cortisol, and inflammatory cytokines (interleukin (IL)-6, IL-12, tumor necrosis factor-\u03b1, IL-10, IL-4) due to their implications in chronic diseases.", "Sixty-three senior female cancer survivors (M age = 67 years, SD = 7.15) with physical functioning limitations (SF-12 physical functioning \u226480 or role-physical \u226472) were randomized to 12-weeks (60-min, three times a week) of TCC or Health Education control (HEC) classes.", "Resting blood pressure, 1-day salivary cortisol samples, and fasting plasma samples for cytokine multiplex assays were collected at baseline and 1-week post-intervention.", "Controlling for baseline values, the TCC group had significantly lower systolic blood pressure (SBP, p = 0.002) and cortisol area-under-curve (AUC, p = 0.02) at post-intervention than the HEC group.", "There was no intervention effect on inflammatory cytokines (p\u2019s > 0.05).", "This TCC feasibility trial was associated with significant reductions in SBP and cortisol AUC in senior female cancer survivors.", "Larger, definitive trials are needed to confirm these findings.", "Senior survivors\u2019 have an increased risk for chronic diseases; however, TCC interventions may help reduce associated risk factors."], "structured": false}
{"doc_id": 24408040, "title": "Heart failure admissions in adults with congenital heart disease; risk factors and prognosis.", "abstract": ["BACKGROUND Heart failure (HF) is a serious complication and often the cause of death in adults with congenital heart disease (CHD).", "Therefore, our aims were to determine the frequency of HF-admissions, and to assess risk factors of first HF-admission and of mortality after first HF-admission in adults with CHD.   \n", "METHODS The Dutch CONCOR registry was linked to the Hospital Discharge Registry and National Mortality Registry to obtain data on HF-admissions and mortality.", "Risk factors for both HF-admission and mortality were assessed using Cox regression models.   \n", "RESULTS Of 10,808 adult patients (49% male), 274 (2.5%) were admitted for HF during a median follow-up period of 21 years.", "The incidence of first HF-admission was 1.2 per 1000 patient-years, but the incidence of HF itself will be higher.", "Main defect, multiple defects, and surgical interventions in childhood were identified as independent risk factors of HF-admission.", "Patients admitted for HF had a five-fold higher risk of mortality than patients not admitted (hazard ratio (HR)=5.3; 95% confidence interval 4.2-6.9).", "One- and three-year mortality after first HF-admission were 24% and 35% respectively.", "Independent risk factors for three-year mortality after first HF-admission were male gender, pacemaker implantation, admission duration, non-cardiac medication use and high serum creatinine.   \n", "CONCLUSIONS The incidence of HF-admission in adults with CHD is 1.2 per 1000 patient-years.", "Mortality risk is substantially increased after HF-admission, which emphasises the importance to identify patients at high risk of HF-admission.", "These patients might benefit from closer follow-up and earlier medical interventions.", "The presented risk factors may facilitate surveillance."], "structured": true}
{"doc_id": 24414345, "title": "New pathologic classification of lung cancer: relevance for clinical practice and clinical trials.", "abstract": ["We summarize significant changes in pathologic classification of lung cancer resulting from the 2011 International Association for the Study of Lung Cancer/American Thoracic Society/European Respiratory Society (IASLC/ATS/ERS) lung adenocarcinoma classification.", "The classification was developed by an international core panel of experts representing IASLC, ATS, and ERS with oncologists/pulmonologists, pathologists, radiologists, molecular biologists, and thoracic surgeons.", "Because 70% of patients with lung cancer present with advanced stages, a new approach to small biopsies and cytology with specific terminology and criteria focused on the need for distinguishing squamous cell carcinoma from adenocarcinoma and on molecular testing for EGFR mutations and ALK rearrangement.", "Tumors previously classified as non-small-cell carcinoma, not otherwise specified, because of the lack of clear squamous or adenocarcinoma morphology should be classified further by using a limited immunohistochemical workup to preserve tissue for molecular testing.", "The terms \"bronchioloalveolar carcinoma\" and \"mixed subtype adenocarcinoma\" have been discontinued.", "For resected adenocarcinomas, new concepts of adenocarcinoma in situ and minimally invasive adenocarcinoma define patients who, if they undergo complete resection, will have 100% disease-free survival.", "Invasive adenocarcinomas are now classified by predominant pattern after using comprehensive histologic subtyping with lepidic, acinar, papillary, and solid patterns; micropapillary is added as a new histologic subtype with poor prognosis.", "Former mucinous bronchioloalveolar carcinomas are now called \"invasive mucinous adenocarcinoma.", "\"", "Because the lung cancer field is now rapidly evolving with new advances occurring on a frequent basis, particularly in the molecular arena, this classification provides a much needed standard for pathologic diagnosis not only for patient care but also for clinical trials and TNM classification."], "structured": false}
{"doc_id": 24423427, "title": "Polymorphisms in EGFR and IL28B are associated with spontaneous clearance in an HCV-infected iranian population", "abstract": ["Although most hepatitis C virus (HCV)-infected individuals develop chronic infection, about 25% of them are able to clear the virus spontaneously without any therapeutic intervention.", "The aim of the present study was to identify genes associated with spontaneous HCV clearance in a population of Iranian patients.", "We genotyped 110 single-nucleotide polymorphisms (SNPs) in 59 selected\u2014candidate\u2014genes in a cohort of 107 HCV-infected participants who spontaneously cleared the infection and 176 participants whose infection persisted.", "Three out of the 110 SNPs were found to be associated with HCV outcome (P-values<0.03).", "rs11506105 in EGFR (epidermal growth factor receptor gene), and rs11881222 and rs12979860 in IL28B (interferon-\u03bb3 gene).", "Multivariate logistic regression of the three markers showed that the A/A genotypes in both rs11506105 (EFGR) and rs11881222 (IL28B), and the C/C genotype in rs12979860 (IL28B) are associated with HCV clearance (recessive model: odds ratio (OR)=2.06, 95% confidence interval (95% CI)=1.09\u20133.88, P=0.025; OR=2.09, 95% CI=1.23\u20133.60, P=0.007; and OR=1.95, 95% CI=1.15\u20133.35, P=0.014 for rs11506105, rs12979860 and rs11881222, respectively).", "In conclusion, EGFR and IL28B SNPs are strong independent predictive markers of spontaneous viral clearance."], "structured": false}
{"doc_id": 24443043, "title": "Cardiopulmonary exercise testing variables reflect the degree of diastolic dysfunction in patients with heart failure-normal ejection fraction.", "abstract": ["PURPOSE Previous investigations have reported a relationship between variables obtained from echocardiography with tissue Doppler imaging (TDI) and cardiopulmonary exercise testing (CPX) in systolic heart failure (HF) cohorts.", "The purpose of the present investigation was to perform a comparative analysis between echocardiography with TDI and CPX in patients with HF and normal ejection fraction (NEF).   \n", "METHODS Patients with HF-NEF (N = 32) underwent echocardiography with TDI and CPX to determine the following variables: (1) the ratio between mitral early velocity (E) and mitral annular velocity (E'), (2) ejection fraction, (3) left ventricular (LV) mass, (4) left ventricular end systolic volume, (5) peak oxygen uptake (.VO2), (6) ventilatory efficiency, (7) the partial pressure of end-tidal carbon dioxide (P(ET)CO2) at rest and peak exercise, and (8) heart rate recovery at 1 minute (HRR1).   \n", "RESULTS Pearson correlation revealed that E/E' was significantly correlated with peak oxygen uptake (r = -0.55, P = .001), the ventilatory efficiency slope (r = 0.60, P < .001), resting P(ET)CO2 (r = -0.39, P = .03), peak P(ET)CO2 (r = -0.50, P = .004), and HRR1 (r = -0.63, P < .001).", "Left ventricular mass and left ventricular end systolic volume were not correlated with any CPX variable.", "Ejection fraction was correlated with HRR1 (r = -0.55, P = .001).", "An HRR1 threshold of less than 16 and/or 16 or more beats per minute (higher value positive) effectively identified subjects with an E/E' > 10 (positive likelihood ratio: 13:2).   ", "DISCUSSION E/E' provides an accurate reflection of LV filling pressure and thus, insight into diastolic function.", "The results of the present investigation indicate CPX provides insight into cardiac dysfunction in patients with HF-NEF and thus, may eventually prove to be a valuable and accepted clinical assessment."], "structured": true}
{"doc_id": 24450344, "title": "Radical prostatectomy for pathological Gleason 8 or greater prostate cancer: influence of concomitant pathological variables.", "abstract": ["PURPOSE We evaluated the long-term outcome of radical prostatectomy for pathological Gleason score 8 or greater prostate cancer and characterized the prognostic significance of other pathological variables.   ", "MATERIALS AND METHODS A total of 6,419 patients underwent radical prostatectomy between 1987 and 1996.", "There were 407 patients classified as having pathological Gleason 8 or greater, including 8 in 48%, 9 in 49% and 10 in 3%.", "Adjuvant treatment was used in 45% of patients and adjuvant hormonal therapy was administered to 155 (38%).", "Progression-free, including local or systemic, and/or prostate specific antigen (PSA) 0.4 ng./ml. or greater, and cancer specific survival were determined by the Kaplan-Meier method.", "The effect of pathological grade and stage, preoperative PSA, DNA ploidy, margin status, tumor dimension, seminal vesicle invasion, and adjuvant treatment was assessed with the univariate and multivariate analyses.   \n", "RESULTS Pathological stage distribution was pT2 in 26% of patients, pT3 48% and pTxN+ 27%.", "Overall and progression-free survival at 10 years was 67% and 36%, respectively, compared to cancer specific survival 85%.", "Adjuvant treatment, pathological stage, preoperative PSA and pathological grade were significant (less than 0.05) univariate predictors of progression-free survival.", "Pathological stage, margin status and ploidy were univariately associated with cancer specific survival.", "Progression-free survival at 10 years of those patients who did and did not receive adjuvant treatment was 52% and 23%, respectively.", "In the multivariate analysis pathological grade (p=0.02), preoperative PSA (p <0.0001), adjuvant therapy (p <0.0001) and pathological stage (p=0.036) were significant independent predictors of progression-free survival.   \n", "CONCLUSIONS High grade prostate cancer can be controlled with radical prostatectomy in some patients with disease confined pathologically, and 10-year cause specific survival is 96%.", "Predictors of outcome in patients with Gleason 8 disease or greater are similar to established predictors derived by using all grades.", "Although adjuvant hormonal therapy appears to improve disease progression rates after radical prostatectomy on the basis of this nonrandomized study, it may not affect prostate cancer death rates within 10 years in patients with high grade cancer."], "structured": true}
{"doc_id": 24466904, "title": "Successful establishment of long-term bone marrow cultures in 103 patients with myelodysplastic syndromes.", "abstract": ["We used bone marrow biopsies instead of mononuclear cells to maintain long-term cultures from 103 patients belonging to all five sub-categories of myelodysplastic syndromes (MDS), as well as 12 normal controls.", "By week 4, 30-50% confluency was reached and could be maintained for up to 12 weeks with 100% confluency.", "The four prominent cells were fibroblasts, macrophages, endothelial cells and adipocytes.", "Immunohistochemical and electron microscopic studies provided lineage confirmation.", "Normal hematopoiesis was well supported by MDS stroma.", "Neither the FAB nor cytogenetics was co-related with the potency of growth.", "MDS stroma appears to be both morphologically and functionally normal."], "structured": false}
{"doc_id": 24494539, "title": "[Acupuncture combined with auricular point sticking therapy for post stroke depression:a randomized controlled trial].", "abstract": ["OBJECTIVE To observe the clinical effects of acupuncture combined with auricular point sticking based on the western medication for post stroke depression (PSD).   \n", "METHODS Sixty patients with PSD were randomly assigned into an acupuncture plus auricular application group (a combination group) and a medication group, 30 cases in each one.", "20 mg paroxetine hydrochloride was prescribed orally in the medication group, once a day for continuous 8 weeks.", "Based on the above treatment, 30-minute acupuncture was used in the combination group for 8 weeks at Baihui (GV 20), Sishencong (EX-HN 1), Shenting (GV 24), Yintang (GV 29), Shenmen (HT 7), Neiguan (PC 6), Taichong (LR 3), Hegu (LI 4), Zusanli (ST 36), Sanyinjiao (SP 6) and Fenglong (ST 40), once the other day and three times a week.", "Auricular point sticking therapy for 8 weeks was applied at shenmen (TF4), pizhixia (AT4), xin (CO15), and gan (CO12), with pressing 3 times a day and once 3-5 days.", "The total score and each factor scores of Hamilton's depression scale (HAMD) were observed in the two groups before and after treatment, and Asberg's antidepressant side-effect rating scale (SERS) and clinical effect were evaluated.   \n", "RESULTS After treatment, the total HAMD scores of the two groups decreased compared with those before treatment (both P<0.05), with better effect in the combination group (P<0.05).", "The scores of the combination group after treatment were lower than those in the medication group, including the anxiety/somatization factor, sleep disturbance factor, hopelessness factor (all P<0.05).", "The total effective rate of the combination group was 86.7% (26/30), which was better than 66.7% (20/30) of the medication group (P<0.05).", "The SERS score of the combination group was lower than that of the medication group (P<0.05).   \n", "CONCLUSIONS Acupuncture combined with auricular point sticking can improve the clinical symptoms and are effective and safe for PSD."], "structured": true}
{"doc_id": 24496245, "title": "Selective enhancement of endothelial BMPR-II with BMP9 reverses pulmonary arterial hypertension", "abstract": ["Genetic evidence implicates the loss of bone morphogenetic protein type II receptor (BMPR-II) signaling in the endothelium as an initiating factor in pulmonary arterial hypertension (PAH).", "However, selective targeting of this signaling pathway using BMP ligands has not yet been explored as a therapeutic strategy.", "Here, we identify BMP9 as the preferred ligand for preventing apoptosis and enhancing monolayer integrity in both pulmonary arterial endothelial cells and blood outgrowth endothelial cells from subjects with PAH who bear mutations in the gene encoding BMPR-II, BMPR2.", "Mice bearing a heterozygous knock-in allele of a human BMPR2 mutation, R899X, which we generated as an animal model of PAH caused by BMPR-II deficiency, spontaneously developed PAH.", "Administration of BMP9 reversed established PAH in these mice, as well as in two other experimental PAH models, in which PAH develops in response to either monocrotaline or VEGF receptor inhibition combined with chronic hypoxia.", "These results demonstrate the promise of direct enhancement of endothelial BMP signaling as a new therapeutic strategy for PAH."], "structured": false}
{"doc_id": 24498673, "title": "Coordinated actions of SLX1-SLX4 and MUS81-EME1 for Holliday junction resolution in human cells.", "abstract": ["Holliday junctions (HJs) are four-way DNA intermediates that form during homologous recombination, and their efficient resolution is essential for chromosome segregation.", "Here, we show that three structure-selective endonucleases, namely SLX1-SLX4, MUS81-EME1, and GEN1, define two pathways of HJ resolution in human cells.", "One pathway is mediated by GEN1, whereas SLX1-SLX4 and MUS81-EME1 provide a second and genetically distinct pathway (SLX-MUS).", "Cells depleted for SLX-MUS or GEN1 pathway proteins exhibit severe defects in chromosome segregation and reduced survival.", "In response to CDK-mediated phosphorylation, SLX1-SLX4 and MUS81-EME1 associate at the G2/M transition to form a stable SLX-MUS holoenzyme, which can be reconstituted in vitro.", "Biochemical studies show that SLX-MUS is a HJ resolvase that coordinates the active sites of two distinct endonucleases during HJ resolution.", "This cleavage reaction is more efficient and orchestrated than that mediated by SLX1-SLX4 alone, which exhibits a potent nickase activity that acts promiscuously upon DNA secondary structures."], "structured": false}
{"doc_id": 24510595, "title": "Prevalence of frequent headache in a population sample.", "abstract": ["PURPOSE Patients with daily or near-daily headaches are commonly seen in neurology practices and in headache subspecialty centers, but there is little information on the prevalence of this condition in the general population.", "We present the first US-based study describing the prevalence and characteristics of frequent headache in the general population.   \n", "METHODS In Baltimore County, Maryland, 13 343 individuals 18 to 65 years of age were selected by random-digit dialing and interviewed by telephone about their headaches.", "Subjects reporting 180 or more headaches per year were classified as having frequent headache.", "Three mutually exclusive subtypes of frequent headache were identified: frequent headache with migrainous features, chronic tension-type headache, and unclassified frequent headache.   \n", "RESULTS The overall prevalence of frequent headache was 4.1% (5.0% female, 2.8% male; 1.8:1 female to male ratio).", "Frequent headache was 33% more common in Caucasians (4.4%) than in African Americans (3.3%).", "In both males and females, prevalence was highest in the lowest educational category.", "Among frequent headache sufferers, more than half (52% female, 56% male) met criteria for chronic tension-type headache, almost one third (33% female, 25% male) met criteria for frequent headache with migrainous features, and the remainder (15% female, 19% male) were unclassified.", "Overall, 30% of female and 25% of male frequent headache sufferers met International Headache Society (IHS) criteria for migraine (with or without aura).   \n", "CONCLUSIONS Frequent headache is common in the general population and is more prevalent in Caucasians and in those with less than a high school education.", "Chronic tension-type headache is more common than frequent headache with migrainous features, though the latter is more disabling.", "Although more common in females than males, the female preponderance of frequent headache is less marked than in migraine.", "The sex ratio varies by frequent headache subtype."], "structured": true}
{"doc_id": 24512064, "title": "HTLV-I/II associated disease in England and Wales, 1993-7: retrospective review of serology requests.", "abstract": ["Apart from HIV two exogenous retroviruses (human T cell leukaemia viruses type I (HTLV-I) and type II (HTLV-II)) infect humans.", "HTLV-I infection is endemic in Japan, the Caribbean, Africa, and Melanesia and is found among immigrants from these regions in Europe.", "HTLV-I infection is associated with a 1-5% lifetime risk of adult T cell leukaemia/lymphoma, 1 a 0.25% lifetime risk of HTLV-I associated myelopathy, 2 and other inflammatory conditions (uveitis, alveolitis, and arthritis).1 HTLV-II infection is endemic in some native American and African peoples and among injecting drug users and has been associated with neurological disease.1 Between 1986 and 1992, 100 cases of HTLV-I associated myelopathy and 44 cases of adult T cell leukaemia/lymphoma were diagnosed in the United Kingdom.3 Adult T cell leukaemia/lymphoma was first described in 1977 and patients with it have a mean life expectancy of only six months, so most of the 44 cases were probably incident cases.", "\u2026"], "structured": false}
{"doc_id": 24512417, "title": "Lentiviral vector design and imaging approaches to visualize the early stages of cellular reprogramming.", "abstract": ["Induced pluripotent stem cells (iPSCs) can be derived from somatic cells by gene transfer of reprogramming transcription factors.", "Expression levels of these factors strongly influence the overall efficacy to form iPSC colonies, but additional contribution of stochastic cell-intrinsic factors has been proposed.", "Here, we present engineered color-coded lentiviral vectors in which codon-optimized reprogramming factors are co-expressed by a strong retroviral promoter that is rapidly silenced in iPSC, and imaged the conversion of fibroblasts to iPSC.", "We combined fluorescence microscopy with long-term single cell tracking, and used live-cell imaging to analyze the emergence and composition of early iPSC clusters.", "Applying our engineered lentiviral vectors, we demonstrate that vector silencing typically occurs prior to or simultaneously with the induction of an Oct4-EGFP pluripotency marker.", "Around 7 days post-transduction (pt), a subfraction of cells in clonal colonies expressed Oct4-EGFP and rapidly expanded.", "Cell tracking of single cell-derived iPSC colonies supported the concept that stochastic epigenetic changes are necessary for reprogramming.", "We also found that iPSC colonies may emerge as a genetic mosaic originating from different clusters.", "Improved vector design with continuous cell tracking thus creates a powerful system to explore the subtle dynamics of biological processes such as early reprogramming events."], "structured": false}
{"doc_id": 24521894, "title": "EIF2AK3, encoding translation initiation factor 2-\u03b1 kinase 3, is mutated in patients with Wolcott-Rallison syndrome", "abstract": ["Wolcott-Rallison syndrome (WRS) is a rare, autosomal recessive disorder characterized by permanent neonatal or early infancy insulin-dependent diabetes.", "Epiphyseal dysplasia, osteoporosis and growth retardation occur at a later age.", "Other frequent multisystemic manifestations include hepatic and renal dysfunction, mental retardation and cardiovascular abnormalities.", "On the basis of two consanguineous families, we mapped WRS to a region of less than 3 cM on chromosome 2p12, with maximal evidence of linkage and homozygosity at 4 microsatellite markers within an interval of approximately 1 cM. The gene encoding the eukaryotic translation initiation factor 2-\u03b1 kinase 3 (EIF2AK3) resides in this interval; thus we explored it as a candidate.", "We identified distinct mutations of EIF2AK3 that segregated with the disorder in each of the families.", "The first mutation produces a truncated protein in which the entire catalytic domain is missing.", "The other changes an amino acid, located in the catalytic domain of the protein, that is highly conserved among kinases from the same subfamily.", "Our results provide evidence for the role of EIF2AK3 in WRS.", "The identification of this gene may provide insight into the understanding of the more common forms of diabetes and other pathologic manifestations of WRS."], "structured": false}
{"doc_id": 24523573, "title": "Beta oscillations in a large-scale sensorimotor cortical network: directional influences revealed by Granger causality.", "abstract": ["Previous studies have shown that synchronized beta frequency (14-30 Hz) oscillations in the primary motor cortex are involved in maintaining steady contractions of contralateral arm and hand muscles.", "However, little is known about the role of postcentral cortical areas in motor maintenance and their patterns of interaction with motor cortex.", "We investigated the functional relations of beta-synchronized neuronal assemblies in pre- and postcentral areas of two monkeys as they pressed a hand lever during the wait period of a visual discrimination task.", "By using power and coherence spectral analysis, we identified a beta-synchronized large-scale network linking pre- and postcentral areas.", "We then used Granger causality spectra to measure directional influences among recording sites.", "In both monkeys, strong Granger causal influences were observed from primary somatosensory cortex to both motor cortex and inferior posterior parietal cortex, with the latter area also exerting Granger causal influences on motor cortex.", "Granger causal influences from motor cortex to postcentral sites, however, were weak in one monkey and not observed in the other.", "These results are the first, to our knowledge, to demonstrate in awake monkeys that synchronized beta oscillations bind multiple sensorimotor areas into a large-scale network during motor maintenance behavior and carry Granger causal influences from primary somatosensory and inferior posterior parietal cortices to motor cortex."], "structured": false}
{"doc_id": 24524403, "title": "Aging, frailty and age-related diseases", "abstract": ["The concept of frailty as a medically distinct syndrome has evolved based on the clinical experience of geriatricians and is clinically well recognizable.", "Frailty is a nonspecific state of vulnerability, which reflects multisystem physiological change.", "These changes underlying frailty do not always achieve disease status, so some people, usually very elderly, are frail without a specific life threatening illness.", "Current thinking is that not only physical but also psychological, cognitive and social factors contribute to this syndrome and need to be taken into account in its definition and treatment.", "Together, these signs and symptoms seem to reflect a reduced functional reserve and consequent decrease in adaptation (resilience) to any sort of stressor and perhaps even in the absence of extrinsic stressors.", "The overall consequence is that frail elderly are at higher risk for accelerated physical and cognitive decline, disability and death.", "All these characteristics associated with frailty can easily be applied to the definition and characterization of the aging process per se and there is little consensus in the literature concerning the physiological/biological pathways associated with or determining frailty.", "It is probably true to say that a consensus view would implicate heightened chronic systemic inflammation as a major contributor to frailty.", "This review will focus on the relationship between aging, frailty and age-related diseases, and will highlight possible interventions to reduce the occurrence and effects of frailty in elderly people."], "structured": false}
{"doc_id": 24525112, "title": "A case of paraquat intoxication caused by intravenous injection.", "abstract": ["Paraquat intoxication is a fatal problem.", "Most paraquat intoxications happen through oral administration.", "We report a case of death after intravenous paraquat injection.", "There is little clinical data on parenteral paraquat exposure, and we describe this case and fatal progression.", "Toxic symptoms and severe organ function impairment developed soon after injection.", "Treatment with repeated activated charcoal hemoperfusion with pulse steroids, cyclophosphamide, and antioxidants was attempted.", "The patient died from multiple organ failure 3 days after intoxication.", "This case indicates that paraquat intoxication via intravenous injection, even in very small amounts, has an extremely poor prognosis."], "structured": false}
{"doc_id": 24530130, "title": "Genome-wide association study identifies variants at CLU and CR1 associated with Alzheimer's disease", "abstract": ["The gene encoding apolipoprotein E (APOE) on chromosome 19 is the only confirmed susceptibility locus for late-onset Alzheimer's disease.", "To identify other risk loci, we conducted a large genome-wide association study of 2,032 individuals from France with Alzheimer's disease (cases) and 5,328 controls.", "Markers outside APOE with suggestive evidence of association (P < 10\u22125) were examined in collections from Belgium, Finland, Italy and Spain totaling 3,978 Alzheimer's disease cases and 3,297 controls.", "Two loci gave replicated evidence of association: one within CLU (also called APOJ), encoding clusterin or apolipoprotein J, on chromosome 8 (rs11136000, OR = 0.86, 95% CI 0.81\u20130.90, P = 7.5 \u00d7 10\u22129 for combined data) and the other within CR1, encoding the complement component (3b/4b) receptor 1, on chromosome 1 (rs6656401, OR = 1.21, 95% CI 1.14\u20131.29, P = 3.7 \u00d7 10\u22129 for combined data).", "Previous biological studies support roles of CLU and CR1 in the clearance of \u03b2 amyloid (A\u03b2) peptide, the principal constituent of amyloid plaques, which are one of the major brain lesions of individuals with Alzheimer's disease."], "structured": false}
{"doc_id": 24530633, "title": "Identification and characterization of subpopulations in undifferentiated ES cell culture.", "abstract": ["Embryonic stem (ES) cells are pluripotent cells derived from the inner cell mass (ICM) and the epiblast, and have been suggested to be a homogeneous population with characteristics intermediate between them.", "These cells express Oct3/4 and Rex1 genes, which have been used as markers to indicate the undifferentiated state of ES cells.", "Whereas Oct3/4 is expressed in totipotent and pluripotent cells in the mouse life cycle, Rex1 expression is restricted to the ICM, and is downregulated in pluripotent cell populations in the later stages, i.e. the epiblast and primitive ectoderm (PrE).", "To address whether ES cells comprise a homogeneous population equivalent to a certain developmental stage of pluripotent cells or a heterogeneous population composed of cells corresponding to various stages of differentiation, we established knock-in ES cell lines in which genes for fluorescent proteins were inserted into the Rex1 and Oct3/4 gene loci to visualize the expression of these genes.", "We found that undifferentiated ES cells included at least two different populations, Rex1(+)/Oct3/4(+) cells and Rex1(-)/Oct3/4(+) cells.", "The Rex1(-)/Oct3/4(+) and Rex1(+)/Oct3/4(+) populations could convert into each other in the presence of LIF.", "In accordance with our assumption that Rex1(+)/Oct3/4(+) cells and Rex1(-)/Oct3/4(+) cells have characteristics similar to those of ICM and early-PrE cells, Rex1(+)/Oct3/4(+) cells predominantly differentiated into primitive ectoderm and contributed to chimera formation, whereas Rex1(-)/Oct3/4(+) cells differentiated into cells of the somatic lineage more efficiently than non-fractionated ES cells in vitro and showed poor ability to contribute to chimera formation.", "These results confirmed that undifferentiated ES cell culture contains subpopulations corresponding to ICM, epiblast and PrE."], "structured": false}
{"doc_id": 24541180, "title": "Isolation of intact nuclei of high purity from mouse liver.", "abstract": ["Current methods of nuclear isolation from liver disrupt the plasmalemmae via homogenization and separation of the nuclei by high centrifugal force (HCF) through gradients of sucrose or other substances for up to 80 min.", "The use of HCF for such a long time increases the potential for nuclear damage and degradation by endogenous proteases.", "We compared four combinations of alterations to classical nuclear isolation methods as follows.", "Mouse liver was gently crushed through a fine mesh with and without in vivo perfusion with collagenase.", "The cell suspension was centrifuged at 600 g to remove gross debris and then at moderate centrifugal force (MCF, 16,000 g) or high centrifugal force (HCF, 70,000 g) through sucrose gradients for 30 min.", "The purity of the isolated nuclei was assessed biologically and morphologically, including analyses of representative marker proteins for nuclei and cytoplasm.", "The results indicate that MCF and no collagenase provided the highest nuclear integrity and purity, whereas MCF with collagenase is a viable option if priority is given to yield.", "The method is especially suited for small samples and so should facilitate studies with human liver biopsies and livers from mice, the most widely used species for gene targeting."], "structured": false}
{"doc_id": 24550453, "title": "Two structurally independent domains of E. coli NusG create regulatory plasticity via distinct interactions with RNA polymerase and regulators.", "abstract": ["NusG is a conserved regulatory protein that interacts with elongation complexes (ECs) of RNA polymerase, DNA, and RNA to modulate transcription in multiple and sometimes opposite ways.", "In Escherichia coli, NusG suppresses pausing and increases elongation rate, enhances termination by E. coli rho and phage HK022 Nun protein, and promotes antitermination by lambdaN and in ribosomal RNA operons.", "We report NMR studies that suggest that E. coli NusG consists of two largely independent N- and C-terminal structural domains, NTD and CTD, respectively.", "Based on tests of the functions of the NTD and CTD and variants of NusG in vivo and in vitro, we find that NTD alone is sufficient to suppress pausing and enhance transcript elongation in vitro.", "However, neither domain alone can enhance rho-dependent termination or support antitermination, indicating that interactions of both domains with ECs are required for these processes.", "We propose that the two domains of NusG mediate distinct interactions with ECs: the NTD interacts with RNA polymerase and the CTD interacts with rho and other regulators, providing NusG with different combinations of interactions to effect different regulatory outcomes."], "structured": false}
{"doc_id": 24552097, "title": "Cytochemistry and C-values: the less-well-known world of nuclear DNA amounts.", "abstract": ["BACKGROUND In the plant sciences there are two widely applied technologies for measuring nuclear DNA content: Feulgen absorbance cytophotometry and flow cytometry (FCM).", "While FCM is, with good reasons, increasingly popular among plant scientists, absorbance-cytophotometric techniques lose ground.", "This results in a narrowing of the methodological repertoire, which is neither desirable nor beneficial.", "Both approaches have their advantages, but static cytophotometry seems to pose more instrumental difficulties and material-based problems than FCM, so that Feulgen-based data in the literature are often less reliable than one would expect.   ", "SCOPE The purpose of this article is to present a selective overview of the field of nuclear DNA content measurement, and C-values in particular, with a focus on the technical difficulties imposed by the characteristics of the biological material and with some comments on the photometrical aspects of the work.", "For over 20 years it has been known that plant polyphenols cause problems in Feulgen DNA cytophotometry, since they act as major staining inhibitors leading to unreliable results.", "However, little information is available about the chemical classes of plant metabolites capable of DNA staining interference and the mechanisms of their inhibition.", "Plant slimes are another source of concern.   \n", "CONCLUSIONS In FCM research to uncover the effects of secondary metabolites on measurement results has begun only recently.", "In particular, the analysis of intraspecific genome size variation demands a stringent methodology which accounts for inhibitors.", "FCM tests for inhibitory effects of endogenous metabolites should become obligatory.", "The use of dry seeds for harvesting embryo and endosperm nuclei for FCM and Feulgen densitometry may often provide a means of circumventing staining inhibitors.", "The importance of internal standardization is highlighted.", "Our goal is a better understanding of phytochemical/cytochemical interactions in plant DNA photometry for the benefit of an ever-growing list of plant genome sizes."], "structured": true}
{"doc_id": 24554740, "title": "Integrins and cell proliferation: regulation of cyclin-dependent kinases via cytoplasmic signaling pathways.", "abstract": ["Cell cycle progression in mammalian cells is strictly regulated by both integrin-mediated adhesion to the extracellular matrix and by binding of growth factors to their receptors.", "This regulation is mediated by G1 phase cyclin-dependent kinases (CDKs), which are downstream of signaling pathways under the integrated control of both integrins and growth factor receptors.", "Recent advances demonstrate a surprisingly diverse array of integrin-dependent signals that are channeled into the regulation of the G1 phase CDKs.", "Regulation of cyclin D1 by the ERK pathway may provide a paradigm for understanding how cell adhesion can determine cell cycle progression."], "structured": false}
{"doc_id": 24555417, "title": "Interplay between microtubule bundling and sorting factors ensures acentriolar spindle stability during C. elegans oocyte meiosis", "abstract": ["In many species, oocyte meiosis is carried out in the absence of centrioles.", "As a result, microtubule organization, spindle assembly, and chromosome segregation proceed by unique mechanisms.", "Here, we report insights into the principles underlying this specialized form of cell division, through studies of C. elegans KLP-15 and KLP-16, two highly homologous members of the kinesin-14 family of minus-end-directed kinesins.", "These proteins localize to the acentriolar oocyte spindle and promote microtubule bundling during spindle assembly; following KLP-15/16 depletion, microtubule bundles form but then collapse into a disorganized array.", "Surprisingly, despite this defect we found that during anaphase, microtubules are able to reorganize into a bundled array that facilitates chromosome segregation.", "This phenotype therefore enabled us to identify factors promoting microtubule organization during anaphase, whose contributions are normally undetectable in wild-type worms; we found that SPD-1 (PRC1) bundles microtubules and KLP-18 (kinesin-12) likely sorts those bundles into a functional orientation capable of mediating chromosome segregation.", "Therefore, our studies have revealed an interplay between distinct mechanisms that together promote spindle formation and chromosome segregation in the absence of structural cues such as centrioles."], "structured": false}
{"doc_id": 24555878, "title": "Development of a questionnaire to measure heart disease risk knowledge in people with diabetes: the Heart Disease Fact Questionnaire.", "abstract": ["This paper describes a paper and pencil questionnaire that measures heart disease risk knowledge in people with diabetes.", "The Heart Disease Fact Questionnaire (HDFQ) is a 25-item questionnaire that was developed to tap into respondents' knowledge of major risk factors for the development of CHD.", "Approximately half of these items specifically address diabetes-related CHD risk factors.", "Based on extensive pilot data, the current study analyzed responses from 524 people with diabetes to assess the psychometric properties.", "The HDFQ is readable to an average 13-year old and imposes little burden.", "It shows good content and face validity.", "It demonstrates adequate internal consistency, with Kuder-Richardson-20 formula = 0.77 and good item-total correlations.", "Item analysis showed a desirable range in P-values.", "In discriminant function analyses, HDFQ scores differentiated respondents by knowledge of their own cardiovascular health, use of lipid lowering medications, health insurance status, and educational attainment, thus indicating good criterion related validity.", "This measure of heart disease risk knowledge is brief, understandable to respondents, and easy to administer and score.", "Its potential for use in research and practice is discussed.", "Future research should establish norms as well as investigate its test-retest reliability and predictive validity."], "structured": false}
{"doc_id": 24557631, "title": "Prevalence of Multiple Sclerosis in Isfahan, Iran", "abstract": ["Background: The prevalence of multiple sclerosis (MS) shows considerable variability all over the world.", "According to Kurtzke, Iran is considered to have a low prevalence.", "Objective: To estimate the period prevalence and risk factors of MS in Isfahan, central part of Iran.", "Methods: A cross-sectional case register study conducted between 2004 and 2005.", "In the province of Isfahan, Iran, all patients known to have definite MS during 2004 and 2005, being alive and resident within Isfahan as well as being a member of the Isfahan MS Association were included in the study.", "Demographic and case-related information was recorded.", "1,391 definite MS patients (308 men and 1,083 women) from the Isfahan MS Association, Iran, have been identified.", "The disease was confirmed using clinical information and MRI findings by a neurologist and radiologist.", "The patients were evaluated by interview and a questionnaire.", "Population data were obtained from the year 1999 Iran Census.", "The mean (SD) age of the participants was 32.5 (9.3) years with a mean (SD) duration of the disease of 6.4 (5.1) years for men and 6.9 (5.3) years for women.", "Results: The period prevalence of MS was 35.5 per 100,000 [95% confidence interval (CI) 33.6\u201337.3] in a population of 3,923,255, with a higher rate in women than men [54.5 (95% CI: 51.1\u201357.8) for women and 14.9 (95% CI: 13.3\u201316.6) for men].", "The female/male ratio was 3.6 (95% CI: 3.2\u20134.1).", "The direct age-adjusted period prevalence was 59.5 per 100,000 (95% CI: 44.8\u201375.2) for women and 17.0 per 100,000 (95% CI: 8.9\u201325.1) for men.", "MS rates were highest among 30- to 39-year-olds and decreased with increasing age.", "Sensory and visual disturbances were the most common initial presentations with a prevalence of 51.1% (95% CI: 48.4\u201353.7) and 47.0% (95% CI: 44.4\u201349.7), respectively.", "Conclusion: Isfahan could be considered as an area with a medium to high risk of MS.", "This is in sharp contrast with the gradient hypothesis."], "structured": false}
{"doc_id": 24558930, "title": "A kinetochore-independent mechanism drives anaphase chromosome separation during acentrosomal meiosis", "abstract": ["Although assembly of acentrosomal meiotic spindles has been extensively studied, little is known about the segregation of chromosomes on these spindles.", "Here, we show in Caenorhabditis elegans oocytes that the kinetochore protein, KNL-1, directs assembly of meiotic kinetochores that orient chromosomes.", "However, in contrast to mitosis, chromosome separation during meiotic anaphase is kinetochore-independent.", "Before anaphase, meiotic kinetochores and spindle poles disassemble along with the microtubules on the poleward side of chromosomes.", "During anaphase, microtubules then form between the separating chromosomes.", "Functional analysis implicated a set of proteins that localize to a ring-shaped domain between kinetochores during pre-anaphase spindle assembly and anaphase separation.", "These proteins are localized by the chromosomal passenger complex, which regulates the loss of meiotic chromosome cohesion.", "Thus, meiotic segregation in C. elegans is a two-stage process, where kinetochores orient chromosomes, but are then dispensable for their separation.", "We suggest that separation is controlled by a meiosis-specific chromosomal domain to coordinate cohesin removal and chromosome segregation."], "structured": false}
{"doc_id": 24575065, "title": "Association between the Medicare Modernization Act of 2003 and patient wait times and travel distance for chemotherapy.", "abstract": ["CONTEXT The Medicare Prescription Drug, Improvement, and Modernization Act of 2003 (MMA) altered reimbursements for outpatient chemotherapy drugs and drug administration services.", "Anecdotal reports suggest that these adjustments may have negatively affected access to chemotherapy for Medicare beneficiaries.   \n", "OBJECTIVE To compare patient wait times and travel distances for chemotherapy before and after the enactment of the MMA.   \n", "DESIGN, SETTING, AND PATIENTS Analysis of a nationally representative 5% sample of claims from the Centers for Medicare & Medicaid Services for the period 2003 through 2006.", "Patients were Medicare beneficiaries with incident breast cancer, colorectal cancer, leukemia, lung cancer, or lymphoma who received chemotherapy in inpatient hospital, institutional outpatient, or physician office settings.   \n", "MAIN OUTCOME MEASURES Days from incident diagnosis to first chemotherapy visit and distance traveled for treatment, controlling for age, sex, race/ethnicity, cancer type, geographic region, comorbid conditions, and year of diagnosis and treatment.   \n", "RESULTS There were 5082 incident cases of breast cancer, colorectal cancer, leukemia, lung cancer, or lymphoma in 2003; 5379 cases in 2004; 5116 cases in 2005; and 5288 cases in 2006.", "Approximately 70% of patients received treatment in physician office settings in each year.", "Although the distribution of treatment settings in 2004 and 2005 was not significantly different from 2003 (P = .24 and P = .72, respectively), there was a small but significant change from 2003 to 2006 (P = .02).", "The proportion of patients receiving chemotherapy in inpatient settings decreased from 10.2% in 2003 to 8.8% in 2006 (P = .03), and the proportion in institutional outpatient settings increased from 21.1% to 22.5% (P = .004).", "The proportion in physician offices remained at 68.7% (P = .29).", "The median time from diagnosis to initial chemotherapy visit was 28 days in 2003, 27 days in 2004, 29 days in 2005, and 28 days in 2006.", "In multivariate analyses, average wait times for chemotherapy were 1.96 days longer in 2005 than in 2003 (95% confidence interval [CI], 0.11-3.80 days; P = .04) but not significantly different in 2006 (0.88 days; 95% CI, -0.96 to 2.71 days; P = .35).", "Median travel distance was 7 miles (11.2 km) in 2003 and 8 miles (12.8 km) in 2004 through 2006.", "After adjustment, average travel distance remained slightly longer in 2004 (1.47 miles [2.35 km]; 95% CI, 0.87-2.07 miles [1.39-3.31 km]; P < .001), 2005 (1.19 miles [1.90 km]; 95% CI, 0.58-1.80 miles [0.93-2.88 km]; P < .001), and 2006 (1.30 miles [2.08 km]; 95% CI, 0.69-1.90 miles [1.10-3.04 km]; P < .001) compared with 2003.   \n", "CONCLUSION There have not been major changes in travel distance and patient wait times for chemotherapy in the Medicare population since 2003, the year before MMA-related changes in reimbursement."], "structured": true}
{"doc_id": 24581365, "title": "20-year outcomes following conservative management of clinically localized prostate cancer.", "abstract": ["CONTEXT The appropriate therapy for men with clinically localized prostate cancer is uncertain.", "A recent study suggested an increasing prostate cancer mortality rate for men who are alive more than 15 years following diagnosis.   \n", "OBJECTIVE To estimate 20-year survival based on a competing risk analysis of men who were diagnosed with clinically localized prostate cancer and treated with observation or androgen withdrawal therapy alone, stratified by age at diagnosis and histological findings.   \n", "DESIGN, SETTING, AND PATIENTS A retrospective population-based cohort study using Connecticut Tumor Registry data supplemented by hospital record and histology review of 767 men aged 55 to 74 years with clinically localized prostate cancer diagnosed between January 1, 1971, and December 31, 1984.", "Patients were treated with either observation or immediate or delayed androgen withdrawal therapy, with a median observation of 24 years.   \n", "MAIN OUTCOME MEASURES Probability of mortality from prostate cancer or other competing medical conditions, given a patient's age at diagnosis and tumor grade.   \n", "RESULTS The prostate cancer mortality rate was 33 per 1000 person-years during the first 15 years of follow-up (95% confidence interval [CI], 28-38) and 18 per 1000 person-years after 15 years of follow-up (95% CI, 10-29).", "The mortality rates for these 2 follow-up periods were not statistically different, after adjusting for differences in tumor histology (rate ratio, 1.1; 95% CI, 0.6-1.9).", "Men with low-grade prostate cancers have a minimal risk of dying from prostate cancer during 20 years of follow-up (Gleason score of 2-4, 6 deaths per 1000 person-years; 95% CI, 2-11).", "Men with high-grade prostate cancers have a high probability of dying from prostate cancer within 10 years of diagnosis (Gleason score of 8-10, 121 deaths per 1000 person-years; 95% CI, 90-156).", "Men with Gleason score of 5 or 6 tumors have an intermediate risk of prostate cancer death.   \n", "CONCLUSION The annual mortality rate from prostate cancer appears to remain stable after 15 years from diagnosis, which does not support aggressive treatment for localized low-grade prostate cancer."], "structured": true}
{"doc_id": 24586989, "title": "Role of beta adrenergic receptor polymorphisms in heart failure: systematic review and meta-analysis.", "abstract": ["Heart Failure (HF) is a common disorder associated with substantial morbidity and mortality.", "beta adrenergic receptors (betaAR) are the primary pathway through which cardiac function is influenced.", "Chronic beta(1)AR activation is implicated in the pathogenesis of HF and betaAR blockade improves survival in left ventricular systolic dysfunction.", "Common functional polymorphisms in beta adrenergic receptor genes (ADRB) have been associated with HF phenotypes, and with pharmacogenetic interaction with beta adrenergic receptor blockers (beta blockers).", "However, these associations have not been consistently replicated.", "The evidence for ADRB variant involvement in pathogenesis, progression and response to beta blockers in HF is reviewed.", "In addition, a meta-analysis of three studies analysing the effect of ADRB1 Arg389Gly polymorphism on left ventricular remodelling with the use of beta blockers, demonstrating a 5% improvement in left ventricular ejection fraction in Arg389 homozygotes, is presented.", "There is now accumulating molecular evidence for a different functional response to beta blockers associated with this polymorphism.", "In the future, confirmed genotypic associations may enable patients to be identified who are either at greater risk of developing HF, whose HF may rapidly progress, or who are unlikely to benefit from beta blockers, and such patients may benefit from targeted aggressive therapy."], "structured": false}
{"doc_id": 24594624, "title": "New development of the yolk sac theory in diabetic embryopathy: molecular mechanism and link to structural birth defects.", "abstract": ["Maternal diabetes mellitus is a significant risk factor for structural birth defects, including congenital heart defects and neural tube defects.", "With the rising prevalence of type 2 diabetes mellitus and obesity in women of childbearing age, diabetes mellitus-induced birth defects have become an increasingly significant public health problem.", "Maternal diabetes mellitus in vivo and high glucose in vitro induce yolk sac injuries by damaging the morphologic condition of cells and altering the dynamics of organelles.", "The yolk sac vascular system is the first system to develop during embryogenesis; therefore, it is the most sensitive to hyperglycemia.", "The consequences of yolk sac injuries include impairment of nutrient transportation because of vasculopathy.", "Although the functional relationship between yolk sac vasculopathy and structural birth defects has not yet been established, a recent study reveals that the quality of yolk sac vasculature is related inversely to embryonic malformation rates.", "Studies in animal models have uncovered key molecular intermediates of diabetic yolk sac vasculopathy, which include hypoxia-inducible factor-1\u03b1, apoptosis signal-regulating kinase 1, and its inhibitor thioredoxin-1, c-Jun-N-terminal kinases, nitric oxide, and nitric oxide synthase.", "Yolk sac vasculopathy is also associated with abnormalities in arachidonic acid and myo-inositol.", "Dietary supplementation with fatty acids that restore lipid levels in the yolk sac lead to a reduction in diabetes mellitus-induced malformations.", "Although the role of the human yolk in embryogenesis is less extensive than in rodents, nevertheless, human embryonic vasculogenesis is affected negatively by maternal diabetes mellitus.", "Mechanistic studies have identified potential therapeutic targets for future intervention against yolk sac vasculopathy, birth defects, and other complications associated with diabetic pregnancies."], "structured": false}
{"doc_id": 24596228, "title": "Hepatitis B and C in HIV-infected patients. Prevalence and prognostic value.", "abstract": ["BACKGROUND/AIMS There is only limited information on the prevalence and influence of coinfection with either hepatitis B or C on the clinical course in patients infected with the human immunodeficiency virus (HIV).   \n", "METHODS Follow-up was available in 232 HIV-infected patients (age 37+/-8 years, CD4 count 167+/-167 microl; 46% had AIDS).", "Samples were investigated for markers of HBV and HCV infection (HBsAg, HBeAg, HBV-DNA, Anti-HBs, anti-HBc, anti-HCV, HCV-RNA).   \n", "RESULTS 60/232 patients (23%) were anti-HCV positive.", "78% of these sera were positive for HCV-RNA.", "22/232 patients (9%) suffered from chronic HBV infection (HBsAg positive), 18/22 (82%) of these sera had detectable HBeAg and 19/22 (86%) HBV-DNA.", "Presence of HCV-RNA, HBeAg and amount of HBV-DNA were related to the degree of immunodeficiency.", "In contrast to the control group without HBV or HCV infection, patients infected with HIV and either HBV or HCV showed a direct correlation between a reduction in CD4 counts and decreased cholinesterase activity.", "In patients with AIDS, coinfection with HBV or HCV was associated with a reduced survival compared to controls (HBV: 212 days, 95%CI, 106-317; HCV: 267, 95%CI, 112-396; controls: 439 days, 95%CI, 364-513).   \n", "CONCLUSIONS Coinfection of HIV and HBV or HCV is frequently observed.", "Our results suggest that with prolonged survival of HIV-infected patients, coinfection with either HBV or HCV correlates with a reduced survival rate."], "structured": true}
{"doc_id": 24612804, "title": "Requirement of endogenous stem cell factor and granulocyte-colony-stimulating factor for IL-17-mediated granulopoiesis.", "abstract": ["IL-17 is a novel, CD4+ T cell-restricted cytokine.", "In vivo, it stimulates hematopoiesis and causes neutrophilia consisting of mature granulocytes.", "In this study, we show that IL-17-mediated granulopoiesis requires G-CSF release and the presence or induction of the transmembrane form of stem cell factor (SCF) for optimal granulopoiesis.", "However, IL-17 also protects mice from G-CSF neutralization-induced neutropenia.", "G-CSF neutralization completely reversed IL-17-induced BM progenitor expansion, whereas splenic CFU-GM/CFU-granulocyte-erythrocyte-megakaryocyte-monocyte was only reduced by 50% in both Sl/Sld and littermate control mice.", "Thus, there remained a significant SCF/G-CSF-independent effect of IL-17 on splenic granulopoiesis, resulting in a preservation of mature circulating granulocytes.", "IL-17 is a cytokine that potentially interconnects lymphocytic and myeloid host defense and may have potential for therapeutic development."], "structured": false}
{"doc_id": 24624992, "title": "The expression of immediate early gene X-1 (IEX-1) is differentially induced by retinoic acids in NB4 and KG1 cells: possible implication in the distinct phenotype of retinoic acid-responsive and -resistant leukemic cells", "abstract": ["In a cell-type- and stimulus-dependent fashion, the early response gene immediate early gene X-1 (IEX-1) is involved in growth control and modulation of apoptosis.", "The present study demonstrates that, in the two acute promyelocytic leukemia (APL) cell lines NB4 and KG1, exhibiting distinct responsiveness to retinoic acids (RAs), IEX-1 expression is rapidly (30\u201360 min) induced by all-trans- or cis-RA and independently of other signal transduction mediators, such as TNF\u03b1, NF-\u03baB or MAP kinases.", "In NB4 cells (expressing PML\u2013RAR\u03b1), this increase is transient and completely reversible, along with a cell cycle arrest, ongoing differentiation and lower sensitivity to anti-cancer-drug-induced apoptosis.", "In contrast, the RA-induced IEX-1 expression in KG1 cells (expressing PLZF\u2013RAR\u03b1) persists over days, along with continued cell cycle progression and increased apoptotic sensitivity.", "Furthermore, two functional RA-response elements in the IEX-1 promoter were identified by gel shift and luciferase reporter gene assays.", "IEX-1 might be a rather unique transcriptional target of the two X\u2013RAR\u03b1 fusion receptors exhibiting distinct responsiveness to RAs.", "Following a different time course of direct transcriptional induction by PML\u2013RAR\u03b1 and PLZF\u2013RAR\u03b1 in NB4 and KG1 cells, respectively, IEX-1 expression may be involved in the modified actions of these receptors and the distinct phenotypes of APL cells."], "structured": false}
{"doc_id": 24625323, "title": "Comorbidity between ADHD and obesity: exploring shared mechanisms and clinical implications.", "abstract": ["Recent studies suggest an association between attention-deficit/hyperactivity disorder (ADHD) and obesity.", "In this article, we systematically review and critically discuss evidence on the prevalence of ADHD in obese patients as well as the weight status of individuals with ADHD.", "Relevant articles were searched in PubMed, PsychInfo, and ISI Web of Science (January 1980 to June 2010).", "We found that current evidence indicates a high prevalence of ADHD in clinical samples of patients seeking treatment for their obesity.", "Moreover, available studies show that individuals with ADHD have higher-than-average body mass index z scores and/or a significantly higher prevalence of obesity compared with subjects without ADHD.", "Three mechanisms underlying the association between ADHD and obesity have been proposed: 1) it is possible that obesity and/or factors associated with it (such as sleep-disordered breathing) manifest as ADHD-like symptoms; 2) ADHD and obesity share common biological dysfunctions; and 3) ADHD contributes to obesity.", "With regards to the possible clinical implications, our findings suggest that it is noteworthy to screen for ADHD in patients with obesity and to look for abnormal eating behaviors as possible contributing factors of obesity in patients with ADHD.", "Based on preliminary findings, appropriate treatment of ADHD may improve the weight status of individuals with both obesity and ADHD."], "structured": false}
{"doc_id": 24632480, "title": "Rapamycin treatment augments motor neuron degeneration in SOD1(G93A) mouse model of amyotrophic lateral sclerosis.", "abstract": ["Aberrant protein misfolding may contribute to the pathogenesis of amyotrophic lateral sclerosis (ALS) but the detailed mechanisms are largely unknown.", "Our previous study has shown that autophagy is altered in the mouse model of ALS.", "In the present study, we systematically investigated the correlation of the autophagic alteration with the motor neurons (MNs) degeneration in the ALS mice.", "We have demonstrated that the autophagic protein marker LC3-II is markedly and specifically increased in the spinal cord MNs of the ALS mice.", "Electron microscopy and immunochemistry studies have shown that autophagic vacuoles are significantly accumulated in the dystrophic axons of spinal cord MNs of the ALS mice.", "All these changes in the ALS mice appear at the age of 90 d when the ALS mice display modest clinical symptoms; and they become prominent at the age of 120 d. The clinical symptoms are correlated with the progression of MNs degeneration.", "Moreover, we have found that p62/SQSTM1 is accumulated progressively in the spinal cord, indicating that the possibility of impaired autophagic flux in the SOD1(G93A) mice.", "Furthermore, to our surprise, we have found that treatment with autophagy enhancer rapamycin accelerates the MNs degeneration, shortens the life span of the ALS mice, and has no obvious effects on the accumulation of SOD1 aggregates.", "In addition, we have demonstrated that rapamycin treatment in the ALS mice causes more severe mitochondrial impairment, higher Bax levels and greater caspase-3 activation.", "These findings suggest that selective degeneration of MNs is associated with the impairment of the autophagy pathway and that rapamycin treatment may exacerbate the pathological processing through apoptosis and other mechanisms in the ALS mice."], "structured": false}
{"doc_id": 24634621, "title": "Improvements in survival and clinical benefit with gemcitabine as first-line therapy for patients with advanced pancreas cancer: a randomized trial.", "abstract": ["PURPOSE Most patients with advanced pancreas cancer experience pain and must limit their daily activities because of tumor-related symptoms.", "To date, no treatment has had a significant impact on the disease.", "In early studies with gemcitabine, patients with pancreas cancer experienced an improvement in disease-related symptoms.", "Based on those findings, a definitive trial was performed to assess the effectiveness of gemcitabine in patients with newly diagnosed advanced pancreas cancer.   \n", "PATIENTS AND METHODS One hundred twenty-six patients with advanced symptomatic pancreas cancer completed a lead-in period to characterize and stabilize pain and were randomized to receive either gemcitabine 1,000 mg/m2 weekly x 7 followed by 1 week of rest, then weekly x 3 every 4 weeks thereafter (63 patients), or to fluorouracil (5-FU) 600 mg/m2 once weekly (63 patients).", "The primary efficacy measure was clinical benefit response, which was a composite of measurements of pain (analgesic consumption and pain intensity), Karnofsky performance status, and weight.", "Clinical benefit required a sustained (> or = 4 weeks) improvement in at least one parameter without worsening in any others.", "Other measures of efficacy included response rate, time to progressive disease, and survival.   \n", "RESULTS Clinical benefit response was experienced by 23.8% of gemcitabine-treated patients compared with 4.8% of 5-FU-treated patients (P = .0022).", "The median survival durations were 5.65 and 4.41 months for gemcitabine-treated and 5-FU-treated patients, respectively (P = .0025).", "The survival rate at 12 months was 18% for gemcitabine patients and 2% for 5-FU patients.", "Treatment was well tolerated.   \n", "CONCLUSION This study demonstrates that gemcitabine is more effective than 5-FU in alleviation of some disease-related symptoms in patients with advanced, symptomatic pancreas cancer.", "Gemcitabine also confers a modest survival advantage over treatment with 5-FU."], "structured": true}
{"doc_id": 24640046, "title": "Endothelial-myofibroblast transition contributes to the early development of diabetic renal interstitial fibrosis in streptozotocin-induced diabetic mice.", "abstract": ["Diabetic nephropathy is the leading cause of chronic renal failure.", "Myofibroblasts play a major role in the synthesis and secretion of extracellular matrix in diabetic renal fibrosis.", "Increasing evidence suggests that endothelial cells may undergo endothelial-myofibroblast transition under physiological and pathophysiological circumstances.", "Therefore, this study investigates whether endothelial-myofibroblast transition occurs and contributes to the development of diabetic renal interstitial fibrosis.", "Diabetes was induced by administration of streptozotocin to Tie2-Cre;LoxP-EGFP mice, an endothelial lineage-traceable mouse line generated by crossbreeding B6.Cg-Tg(Tek-cre)12F1v/J mice with B6.Cg-Tg(ACTB-Bgeo/GFP)21Lbe/J mice.", "The endothelial-myofibroblast transition was also studied in MMECs (a mouse pancreatic microvascular endothelial cell line) and primary cultures of CD31+/EYFP- (enhanced yellow fluorescent protein) endothelial cells isolated from adult normal alpha-smooth muscle actin promoter-driven-EYFP (alpha-SMA/EYFP) mouse kidneys.", "Confocal microscopy demonstrated that 10.4 +/- 4.2 and 23.5 +/-", "7.4% of renal interstitial myofibroblasts (alpha-SMA+) in 1- and 6-month streptozotocin-induced diabetic kidneys were of endothelial origin (EGFP+/alpha-SMA+ cells), compared with just 0.2 +/-", "0.1% of myofibroblasts in vehicle-treated Tie2-Cre;LoxP-EGFP mice (P < 0.01).", "Confocal microscopy and real-time PCR showed that transforming growth factor (TGF)-beta1 induced de novo expression of alpha-SMA and loss of expression of VE-cadherin and CD31 in MMECs and primary cultures of renal endothelial cells in a time- and dose-dependent fashion.", "These findings demonstrate that the endothelial-myofibroblast transition occurs and contributes to the early development and progression of diabetic renal interstitial fibrosis and suggest that the endothelial-myofibroblast transition may be a therapeutic target."], "structured": false}
{"doc_id": 24645237, "title": "Effect of phosducin silencing on the photokinetic motile response of Blepharisma japonicum.", "abstract": ["The coloured ciliate Blepharisma japonicum changes swimming velocity (positive photokinesis) and elongates its body in response to a prolonged illumination.", "We have recently proposed that alterations in the phosphorylation level of the ciliate phosducin (Pdc) may be involved in light-induced cell elongation, which in turn affects the interaction of \u03b2\u03b3-dimer of G-proteins (G\u03b2\u03b3) with \u03b2-tubulin and subsequent cytoskeletal remodelling.", "The cellular mechanism that governs the photokinetic effect in this ciliate has not been elucidated.", "In the present study, we utilise real-time PCR to demonstrate that the levels of ciliate Pdc mRNA are significantly reduced in Pdc-RNAi-treated cells compared to cells fed with bacteria carrying the empty vector (control cells).", "Using western immunoblotting, we confirmed that these cells treated with Pdc-RNAi expressed a substantially lower level of the Pdc protein.", "The assay also revealed that in ciliates treated with Pdc-RNAi and exposed to light, the cytosolic level of G\u03b2 (~36 kDa) was reduced, whereas the level of G\u03b2 localized to the membrane (~32 kDa) was increased compared to control cells.", "In addition, behavioural analysis of the cells indicated a substantial reduction of photokinesis.", "The findings in this study provide additional characterization of the functional properties of the ciliate Pdc protein and we discuss a likely role for this phosphoprotein in the photokinetic phenomenon of the ciliate protist Blepharisma."], "structured": false}
{"doc_id": 24652030, "title": "Alzheimer\u2019s disease and NGF signaling", "abstract": ["Age-related degeneration of basal forebrain cholinergic neurons (BFCNs) occurs early and contributes significantly to cognitive decline in Alzheimer\u2019s disease (AD).", "Proper function and morphology of BFCNs depends on the supply of nerve growth factor (NGF) from the cortex and the hippocampus.", "A large number of experiments have shown that decreased supply of NGF at the level of BFCN cell bodies leads to loss of neuronal markers and shrinkage, mimicking what is observed in AD.", "The delivery of sufficient amounts of NGF signal to BFCN cell bodies depends on the effective participation of several factors including sufficient synthesis and release of NGF, adequate synthesis and expression of NGF receptors by BFCNs, normal signaling and retrograde transport of NGF-receptor complex, and finally effective induction of gene expression by NGF.", "In the past few years it has become clear that decreased amounts of NGF at the level of BFCN cell bodies is largely due to failed retrograde transport rather than decreased synthesis, binding or expression of NGF receptors in the BFCN terminals.", "We will discuss in vivo evidence supporting decreased retrograde transport of NGF in a mouse model with BFCN degeneration, and will attempt to match these findings with our studies in postmortem human AD brain.", "We will speculate about the possible mechanisms of failed NGF retrograde transport and its relationship to AD pathology."], "structured": false}
{"doc_id": 24660385, "title": "Echocardiographic assessment of left ventricular hypertrophy: comparison to necropsy findings.", "abstract": ["To determine the accuracy of echocardiographic left ventricular (LV) dimension and mass measurements for detection and quantification of LV hypertrophy, results of blindly read antemortem echocardiograms were compared with LV mass measurements made at necropsy in 55 patients.", "LV mass was calculated using M-mode LV measurements by Penn and American Society of Echocardiography (ASE) conventions and cube function and volume correction formulas in 52 patients.", "Penn-cube LV mass correlated closely with necropsy LV mass (r = 0.92, p less than 0.001) and overestimated it by only 6%; sensitivity in 18 patients with LV hypertrophy (necropsy LV mass more than 215 g) was 100% (18 of 18 patients) and specificity was 86% (29 of 34 patients).", "ASE-cube LV mass correlated similarly to necropsy LV mass (r = 0.90, p less than 0.001), but systematically overestimated it (by a mean of 25%); the overestimation could be corrected by the equation: LV mass = 0.80 (ASE-cube LV mass) + 0.6 g. Use of ASE measurements in the volume correction formula systematically underestimated necropsy LV mass (by a mean of 30%).", "In a subset of 9 patients, 3 of whom had technically inadequate M-mode echocardiograms, 2-dimensional echocardiographic (echo) LV mass by 2 methods was also significantly related to necropsy LV mass (r = 0.68, p less than 0.05 and r = 0.82, p less than 0.01).", "Among other indexes of LV anatomy, only measurement of myocardial cross-sectional area was acceptably accurate for quantitation of LV mass (r = 0.80, p less than 0.001) or diagnosis of LV hypertrophy (sensitivity = 72%, specificity = 94%).(ABSTRACT TRUNCATED AT 250 WORDS)"], "structured": false}
{"doc_id": 24670522, "title": "R93W mutation in Orai1 causes impaired calcium influx in platelets.", "abstract": ["The intracellular Ca(2+) concentration of many nonexcitable cells is regulated by calcium store release and store-operated calcium entry (SOCE).", "In platelets, STIM1 was recently identified as the main calcium sensor expressed in the endoplasmic reticulum.", "To evaluate the role of the SOC channel moiety, Orai1, in platelet SOCE, we generated mice expressing a mutated, inactive form of Orai1 in blood cells only (Orai1(R93W)).", "Platelets expressing Orai1(R93W) were characterized by markedly reduced SOCE and impaired agonist-induced increases in [Ca(2+)](i).", "Orai1(R93W) platelets showed reduced integrin activation and impaired degranulation when stimulated with low agonist concentrations under static conditions.", "This defect, however, did not significantly affect the ability of Orai1(R93W) platelets to aggregate or to adhere to collagen under arterial flow conditions ex vivo.", "In contrast, these adherent Orai1(R93W) platelets were defective in surface phosphatidylserine exposure, suggesting that Orai1 is crucial for the platelets' procoagulant response rather than for other Ca(2+)-dependent cellular responses."], "structured": false}
{"doc_id": 24697979, "title": "[Efficacy on post-stroke depression treated with acupuncture at the acupoints based on ziwuliuzhu and prozac].", "abstract": ["OBJECTIVE To observe the effects on post-stroke depression treated with acupuncture at the acu points based on ziwuliuzhu (the midnight-noon ebb-flow theory).   \n", "METHODS Ninety-three patients were randomized into a comprehensive group, a ziwuliuzhu group and a prozac group, 31 cases in each group.", "In the ziwuliuzhu group, acupuncture was applied to the acupoints based on ziwuliuzhu, once a day, 5 times in a week.", "In the prozac group, fluoxertine hydrochloride (prozac) was prescribed for oral administration, once a day, 20 mg each time.", "In the comprehensive group, acupuncture based on ziwuliuzhu combined with the oral administration of prozac were adopted and the treatment frequency was the same as the ziwuliuzhu group and the prozac group.", "The 4-week treatment was taken as one session in the three groups and 6 sessions were required totally.", "The clinical efficacy and the Hamilton depression rating scale (HAMD) score and the adverse reaction were compared among the 3 groups.   \n", "RESULTS The total effective rate was 96.8% (30/31) in the comprehensive group, better than 83.9% (26/31) in the ziwuliuzhu group and 80.", "6% (25/31) in the prozac group (both P<0.05).", "In 4, 12 and 24 weeks of treatment, HAMD score was lower significantly than that before the treatment in the three groups (all P<0.05), and the score in the comprehensive group at each time point after treatment was lower than the other two groups (all P<0.05).", "In 4 and 12 weeks of treatment, there were not different significantly between the ziwuliuzhu group and the prozac group (both P>0.05).", "In 24 weeks of treatment, HAMD score in the ziwuliuzhu group was lower than that in the prozac group (P<0.05).", "For the adverse reaction, there were 2 cases in the comprehensive group, 6 cases in the prozac group and 0 case in the ziwzuliuzhu group.   \n", "CONCLUSION The comprehensive therapy of acupuncture at the acupoints based on ziwuliuzhu and oral administration of prozac is superior to either the simple oral administration of prozac or the ziwuliuzhu acu-puncture in terms of clinical efficacy and the improvements in depressive state.", "Regarding the clinical efficacy, the impact of simple ziwuliuzhu acupuncture is not different significantly as compared with the simple oral administration of prozac, but it is better than the simple oral administration of prozac in terms of the long-term HAMD score and safety."], "structured": true}
{"doc_id": 24700152, "title": "Linkage with methadone treatment upon release from incarceration: a promising opportunity.", "abstract": ["Injection drug users (IDUs) are at increased risk for HIV, viral hepatitis, and tuberculosis, and making up more than a quarter of the incarcerated population in the United States.", "Methadone maintenance treatment of opiate addiction is highly effective at reducing drug use, drug-related criminal activity, and risk of HIV transmission.", "Recently released inmates are at particularly high risk for overdose and disease transmission.", "Linkage to methadone treatment immediately upon release from incarceration is a promising opportunity to combat disease transmission, facilitate reentry into the community, and reduce recidivism."], "structured": false}
{"doc_id": 24704139, "title": "The Diabetes Prevention Program: baseline characteristics of the randomized cohort. The Diabetes Prevention Program Research Group.", "abstract": ["OBJECTIVE The Diabetes Prevention Program (DPP) is a 27-center randomized clinical trial designed to evaluate the safety and efficacy of interventions that may delay or prevent development of diabetes in people at increased risk for type 2 diabetes.   ", "RESEARCH DESIGN AND METHODS Eligibility requirements were age > or = 25 years, BMI > or = 24 kg/m2 (> or = 22 kg/m2 for Asian-Americans), and impaired glucose tolerance plus a fasting plasma glucose of 5.3-6.9 mmol/l (or < or = 6.9 mmol for American Indians).", "Randomization of participants into the DPP over 2.7 years ended in June 1999.", "Baseline data for the three treatment groups--intensive lifestyle modification, standard care plus metformin, and standard care plus placebo--are presented for the 3,234 participants who have been randomized.   \n", "RESULTS Of all participants", ", 55% were Caucasian, 20% were African-American, 16% were Hispanic, 5% were American Indian, and 4% were Asian-American.", "Their average age at entry was 51 +/-", "10.7 years (mean +/-", "SD), and 67.7% were women.", "Moreover, 16% were < 40 years of age, and 20% were > or = 60 years of age.", "Of the women, 48% were postmenopausal.", "Men and women had similar frequencies of history of hypercholesterolemia (37 and 33%, respectively) or hypertension (29 and 26%, respectively).", "On the basis of fasting lipid determinations, 54% of men and 40% of women fit National Cholesterol Education Program criteria for abnormal lipid profiles.", "More men than women were current or former cigarette smokers or had a history of coronary heart disease.", "Furthermore, 66% of men and 71% of women had a first-degree relative with diabetes.", "Overall, BMI averaged 34.0 +/-", "6.7 kg/m2 at baseline with 57% of the men and 73% of women having a BMI > or = 30 kg/m2.", "Average fasting plasma glucose (6.0 +/-", "0.5 mmol/l) and HbA1c (5.9 +/-", "0.5%) in men were comparable with values in women (5.9 +/- 0.4 mmol/l and 5.9 +/-", "0.5%, respectively).   \n", "CONCLUSIONS The DPP has successfully randomized a large cohort of participants with a wide distribution of age, obesity, and ethnic and racial backgrounds who are at high risk for developing type 2 diabetes.", "The study will examine the effects of interventions on the development of diabetes."], "structured": true}
{"doc_id": 24705390, "title": "Chronic Helicobacter pylori infections induce gastric mutations in mice.", "abstract": ["BACKGROUND & AIMS Helicobacter pylori is an important etiologic factor in the development of gastric cancer.", "The aim of this study was to analyze the role of H. pylori infections in the induction of mutagenic events in gastric epithelial cells.", "The effect of a high-salt diet as a genotoxic risk factor was also investigated.   \n", "METHODS Big Blue transgenic male mice (C57Bl/6) were inoculated with H. pylori (strain SS1) or Helicobacter felis (strain CS1) for 6 and 12 months.", "The frequency and spectrum of mutations at the stomach level were assessed.", "Inflammatory host response and inducible nitric oxide synthase (iNOS) expression by reverse-transcription polymerase chain reaction and immunohistochemistry analysis were also performed.   \n", "RESULTS After 6 months, the gastric mutant frequency was 4-fold and 1.7-fold higher in mice infected with H. pylori and H. felis, respectively, than in uninfected mice.", "It was associated with a high frequency of transversions (AT --> CG and GC --> TA) known to result from oxidative damages.", "The Helicobacter-infected mice exhibited severe gastritis and a high level of iNOS messenger RNA expression.", "Hyperplasia developed 12 months after inoculation, and both the mutagenic effects and iNOS expression decreased in H. pylori- and H. felis-infected mice.", "No synergistic effects of a high-salt diet and Helicobacter infection were observed regarding the frequency of gastric mutation.   \n", "CONCLUSIONS A direct gastric mutagenic effect due to H. pylori infection in the Big Blue transgenic mouse model has been shown 6 months after inoculation.", "This genotoxicity can be attributable to oxidative DNA damage involving the inflammatory host response."], "structured": true}
{"doc_id": 24706198, "title": "A minimal Tat system from a gram-positive organism: a bifunctional TatA subunit participates in discrete TatAC and TatA complexes.", "abstract": ["The Tat system transports folded proteins across bacterial and thylakoid membranes.", "In Gram-negative organisms, a TatABC substrate-binding complex and separate TatA complex are believed to coalesce to form an active translocon, with all three subunits essential for translocation.", "Most Gram-positive organisms lack a tatB gene, indicating major differences in organization and possible differences in mode of action.", "Here, we have studied Tat complexes encoded by the tatAdCd genes of Bacillus subtilis.", "Expression of tatAdCd in an Escherichia coli tat null mutant results in efficient export of a large, cofactor-containing E. coli Tat substrate, TorA. We show that the tatAd gene complements E. coli mutants lacking either tatAE or tatB, indicating a bifunctional role for this subunit in B. subtilis.", "Second, we have identified and characterized two distinct Tat complexes that are novel in key respects: a TatAdCd complex of approximately 230 kDa that is significantly smaller than the analogous E. coli TatABC complex (approximately 370 kDa on BN gels) and a separate TatAd complex.", "The latter is a discrete entity of approximately 270 kDa as judged by gel filtration chromatography, very different from the highly heterogeneous E. coli TatA complex that ranges in size from approximately 50 kDa to over 600 kDa.", "TatA heterogeneity has been linked to the varying size of Tat substrates being translocated, but the singular nature of the B. subtilis TatAd complex suggests that discrete TatAC and TatA complexes may form a single form of translocon."], "structured": false}
{"doc_id": 24707550, "title": "A systemic granulomatous response to Schistosoma mansoni eggs alters responsiveness of bone-marrow-derived macrophages to Toll-like receptor agonists.", "abstract": ["Macrophages play a pivotal role in innate and acquired immune responses to Schistosoma mansoni.", "Classical (M1) or alternative (M2) activation states of these cells further delineate their roles in tissue damage through innate immunity or fibrotic remodeling, respectively.", "In the present study, we addressed the following question: Does systemic Th2-type cytokine polarization evoked by S. mansoni affect macrophage differentiation and activation?", "To this end, we analyzed bone marrow-derived macrophages from mice with S. mansoni egg-induced pulmonary granulomas and unchallenged (or na\u00efve) mice to determine their activation state and their response to specific TLR agonists, including S. mansoni egg antigens.", "Unlike na\u00efve macrophages, macrophages from Th2-polarized mice constitutively expressed significantly higher \"found in inflammatory zone-1\" (FIZZ1) and ST2 (M2 markers) and significantly lower NO synthase 2, CCL3, MIP-2, TNF-alpha, and IL-12 (M1 markers).", "Also, compared with na\u00efve macrophages, Th2-polarized macrophages exhibited enhanced responses to the presence of specific TLR agonists, which consistently induced significantly higher levels of gene and protein levels for M2 and M1 markers in these cells.", "Together, these data show that signals received by bone marrow precursors during S. mansoni egg-induced granuloma responses dynamically alter the development of macrophages and enhance the TLR responsiveness of these cells, which may ultimately have a significant effect on the pulmonary granulomatous response."], "structured": false}
{"doc_id": 24712186, "title": "Orai1 and STIM reconstitute store-operated calcium channel function.", "abstract": ["The two membrane proteins, STIM1 and Orai1, have each been shown to be essential for the activation of store-operated channels (SOC).", "Yet, how these proteins functionally interact is not known.", "Here, we reveal that STIM1 and Orai1 expressed together reconstitute functional SOCs.", "Expressed alone, Orai1 strongly reduces store-operated Ca(2+) entry (SOCE) in human embryonic kidney 293 cells and the Ca(2+) release-activated Ca(2+) current (I(CRAC)) in rat basophilic leukemia cells.", "However, expressed along with the store-sensing STIM1 protein, Orai1 causes a massive increase in SOCE, enhancing the rate of Ca(2+)entry by up to 103-fold.", "This entry is entirely store-dependent since the same coexpression causes no measurable store-independent Ca(2+) entry.", "The entry is completely blocked by the SOC blocker, 2-aminoethoxydiphenylborate.", "Orai1 and STIM1 coexpression also caused a large gain in CRAC channel function in rat basophilic leukemia cells.", "The close STIM1 homologue, STIM2, inhibited SOCE when expressed alone but coexpressed with Orai1 caused substantial constitutive (store-independent) Ca(2+) entry.", "STIM proteins are known to mediate Ca(2+) store-sensing and endoplasmic reticulum-plasma membrane coupling with no intrinsic channel properties.", "Our results revealing a powerful gain in SOC function dependent on the presence of both Orai1 and STIM1 strongly suggest that Orai1 contributes the PM channel component responsible for Ca(2+) entry.", "The suppression of SOC function by Orai1 overexpression likely reflects a required stoichiometry between STIM1 and Orai1."], "structured": false}
{"doc_id": 24713020, "title": "Tet and TDG mediate DNA demethylation essential for mesenchymal-to-epithelial transition in somatic cell reprogramming.", "abstract": ["Tet-mediated DNA oxidation is a recently identified mammalian epigenetic modification, and its functional role in cell-fate transitions remains poorly understood.", "Here, we derive mouse embryonic fibroblasts (MEFs) deleted in all three Tet genes and examine their capacity for reprogramming into induced pluripotent stem cells (iPSCs).", "We show that Tet-deficient MEFs cannot be reprogrammed because of a block in the mesenchymal-to-epithelial transition (MET) step.", "Reprogramming of MEFs deficient in TDG is similarly impaired.", "The block in reprogramming is caused at least in part by defective activation of key miRNAs, which depends on oxidative demethylation promoted by Tet and TDG.", "Reintroduction of either the affected miRNAs or catalytically active Tet and TDG restores reprogramming in the knockout MEFs.", "Thus, oxidative demethylation to promote gene activation appears to be functionally required for reprogramming of fibroblasts to pluripotency.", "These findings provide mechanistic insight into the role of epigenetic barriers in cell-lineage conversion."], "structured": false}
{"doc_id": 24721347, "title": "The last and the next hundred years of malariology.", "abstract": ["The founding fathers of malariology combined scientific originality, perseverance in research, strong characters, breadth of interest and social concern.", "A hundred years later research and understanding has made immense progress but the world still bears a huge burden of malaria.", "For the next century research requires both more specialism and a holistic range if it is to be used in control, requiring multidisciplinary team work.", "Environmental changes and interventions produce a dynamic and changing pattern of malaria, not the static one of the past.", "From the original parasite life cycle, research has analysed a series of other cycles at electron microscope, biochemical and genome levels on decreasing size scales and quantitative epidemiological cycles for control.", "Recent additions to these concepts have been stage-specific antigens, cycles of disease rather than parasites alone, considering populations of parasites rather than just cases, and also genetic variation in each component of the parasite-human host-vector triad.", "In this volume there emerges for the first time a coherent overall picture of the biomedical aspects of basic malariology as the interacting population genetics of malaria parasites, anophelines and people.", "This provides a coherent model for the new century dealing with the great biological malaria problems of drug resistance, vaccine development, insecticidal and net control and can feed, with socio-economic work, into the gathering renewal of control efforts.", "New work on large-scale changes of malaria in space and time enables us to be precise about effects of local and global environmental changes to predict epidemics.", "Future research will be as much about linking these different scales of understanding as control will be about linking different levels of the health system.", "The grim situation in poor holoendemic countries also requires practical support of the type that the founders of malariology were involved in.", "A coherent understanding needs to feed into the new control efforts, from Roll Back Malaria onwards, for the next century."], "structured": false}
{"doc_id": 24721866, "title": "Activation of AMP-activated protein kinase suppresses oxidized low-density lipoprotein-induced macrophage proliferation.", "abstract": ["Macrophage-derived foam cells play important roles in the progression of atherosclerosis.", "We reported previously that ERK1/2-dependent granulocyte/macrophage colony-stimulating factor (GM-CSF) expression, leading to p38 MAPK/ Akt signaling, is important for oxidized low density lipoprotein (Ox-LDL)-induced macrophage proliferation.", "Here, we investigated whether activation of AMP-activated protein kinase (AMPK) could suppress macrophage proliferation.", "Ox-LDL-induced proliferation of mouse peritoneal macrophages was assessed by [(3)H]thymidine incorporation and cell counting assays.", "The proliferation was significantly inhibited by the AMPK activator 5-aminoimidazole-4-carboxamide ribonucleoside (AICAR) and restored by dominant-negative AMPKalpha1, suggesting that AMPK activation suppressed macrophage proliferation.", "AICAR partially suppressed Ox-LDL-induced ERK1/2 phosphorylation and GM-CSF expression, suggesting that another mechanism is also involved in the AICAR-mediated suppression of macrophage proliferation.", "AICAR suppressed GM-CSF-induced macrophage proliferation without suppressing p38 MAPK/Akt signaling.", "GM-CSF suppressed p53 phosphorylation and expression and induced Rb phosphorylation.", "Overexpression of p53 or p27(kip) suppressed GM-CSF-induced macrophage proliferation.", "AICAR induced cell cycle arrest, increased p53 phosphorylation and expression, and suppressed GM-CSF-induced Rb phosphorylation via AMPK activation.", "Moreover, AICAR induced p21(cip) and p27(kip) expression via AMPK activation, and small interfering RNA (siRNA) of p21(cip) and p27(kip) restored AICAR-mediated suppression of macrophage proliferation.", "In conclusion, AMPK activation suppressed Ox-LDL-induced macrophage proliferation by suppressing GM-CSF expression and inducing cell cycle arrest.", "These effects of AMPK activation may represent therapeutic targets for atherosclerosis."], "structured": false}
{"doc_id": 24724242, "title": "Evaluation of cortical bone by peripheral quantitative computed tomography in renal transplant recipients.", "abstract": ["BACKGROUND The absolute risk of fractures in renal transplant patients is 3 times that of matched controls.", "Most of the symptomatic fractures are peripheral, suggesting a greater compromise of cortical bone.", "Peripheral quantitative computed tomography (pQCT) is a new imaging technique that allows separate noninvasive evaluations of cortical and trabecular bones.", "We investigated cortical bone by pQCT in 12 renal transplant patients (seven men and five women) for comparison with 27 normal controls.   \n", "METHODS pQCT (XCT 960, Stratec, Pforheim, Germany) was performed upon the distal radius of the nondominant forearm (15% the length of the ulna, proximal from the radius end plate).", "We evaluated total and cortical bone mineral density (TBMD, cBMD), total (cross-sectional) and cortical area (TA, cA), cortical thickness (cThk), endosteal and periosteal circumferences, and the buckling ratio (r/cThK).   \n", "RESULTS Compared with normal controls transplant patients as a whole showed a significant increase in TA, in endosteal circumference (P < .001), and in the buckling ratio (P < .001) with a significant reduction in cThK (P < .001).", "Female patients had a marked decrease in cA (51.4 vs 69.3 [pixel n]; P < .0001) and cThK (2.08 vs 2.78 mm; P < .0001).", "Male patients also had a decrease in cThK (2.54 vs 3.30 mm; P = .0001) and an increase in endosteal perimeter (31.2 vs 26.4 mm; P < .0001).", "Total time on dialysis prior to renal graft correlated negatively with cortical thickness (r = .62; P < .01).   \n", "CONCLUSIONS Our results suggest that a marked thinning of cortical bone may explain the increased incidence of peripheral fractures among renal transplant patients."], "structured": true}
{"doc_id": 24725136, "title": "Ataxia, dementia, and hypogonadotropism caused by disordered ubiquitination.", "abstract": ["BACKGROUND The combination of ataxia and hypogonadism was first described more than a century ago, but its genetic basis has remained elusive.   \n", "METHODS We performed whole-exome sequencing in a patient with ataxia and hypogonadotropic hypogonadism, followed by targeted sequencing of candidate genes in similarly affected patients.", "Neurologic and reproductive endocrine phenotypes were characterized in detail.", "The effects of sequence variants and the presence of an epistatic interaction were tested in a zebrafish model.   \n", "RESULTS Digenic homozygous mutations in RNF216 and OTUD4, which encode a ubiquitin E3 ligase and a deubiquitinase, respectively, were found in three affected siblings in a consanguineous family.", "Additional screening identified compound heterozygous truncating mutations in RNF216 in an unrelated patient and single heterozygous deleterious mutations in four other patients.", "Knockdown of rnf216 or otud4 in zebrafish embryos induced defects in the eye, optic tectum, and cerebellum; combinatorial suppression of both genes exacerbated these phenotypes, which were rescued by nonmutant, but not mutant, human RNF216 or OTUD4 messenger RNA.", "All patients had progressive ataxia and dementia.", "Neuronal loss was observed in cerebellar pathways and the hippocampus; surviving hippocampal neurons contained ubiquitin-immunoreactive intranuclear inclusions.", "Defects were detected at the hypothalamic and pituitary levels of the reproductive endocrine axis.   \n", "CONCLUSIONS The syndrome of hypogonadotropic hypogonadism, ataxia, and dementia can be caused by inactivating mutations in RNF216 or by the combination of mutations in RNF216 and OTUD4.", "These findings link disordered ubiquitination to neurodegeneration and reproductive dysfunction and highlight the power of whole-exome sequencing in combination with functional studies to unveil genetic interactions that cause disease.", "(Funded by the National Institutes of Health and others.)."], "structured": true}
{"doc_id": 24726600, "title": "Combination cancer immunotherapies tailored to the tumour microenvironment", "abstract": ["Evidence suggests that cancer immunotherapy will be a major part of the combination treatment plan for many patients with many cancer types in the near future.", "There are many types of immune processes involving different antitumour and tumour-promoting leucocytes, and tumour cells use many strategies to evade the immune response.", "The tumour microenvironment can help determine which immune suppressive pathways become activated to restrain antitumour immunity.", "This includes immune checkpoint receptors on effector T-cells and myeloid cells, and release of inhibitory cytokines and metabolites.", "Therapeutic approaches that target these pathways, particularly immune-checkpoint receptors, can induce durable antitumour responses in patients with advanced-stage cancers, including melanoma.", "Nevertheless, many patients do not have a good response to monotherapy approaches and alternative strategies are required to achieve optimal therapeutic benefit.", "These strategies include eliminating the bulk of tumour cells to provoke tumour-antigen release and antigen-presenting cell (APC) function, using adjuvants to enhance APC function, and using agents that enhance effector-cell activity.", "In this Review, we discuss the stratification of the tumour microenvironment according to tumour-infiltrating lymphocytes and PD-L1 expression in the tumour, and how this stratification enables the design of optimal combination cancer therapies tailored to target different tumour microenvironments."], "structured": false}
{"doc_id": 24730100, "title": "Cyclic AMP-dependent phosphorylation of thromboxane A(2) receptor-associated Galpha(13).", "abstract": ["Although it is well established that cAMP inhibits platelet activation induced by all agonists, the thromboxane A(2) signal transduction pathway was found to be particularly sensitive to such inhibition.", "Therefore, we examined whether cAMP-dependent kinase mediates phosphorylation of the thromboxane A(2) receptor-G-protein complex.", "It was found that cAMP induces protein kinase A-dependent [gamma-(32)P]ATP labeling of solubilized membrane proteins in the region of Galpha subunits, i.e. 38-45 kDa.", "Moreover, ligand affinity chromatography purification of thromboxane A(2) receptor-G-protein complexes from these membranes revealed that 38-45-kDa phosphoproteins co-purify with thromboxane A(2) receptors.", "Immunoprecipitation of the affinity column eluate with a Galpha(13) antibody demonstrated that 8-Br-cAMP increased phosphorylation of thromboxane A(2) receptor-associated Galpha(13) by 87 +/-", "27%.", "In separate experiments, immunopurification of Galpha(13) on microtiter wells coated with a different Galpha(13) antibody revealed that 8-Br-cAMP increased Galpha(13) phosphorylation by 53 +/-", "19%.", "Finally, treatment of (32)P-labeled whole platelets with prostacyclin resulted in a 90 +/-", "14% increase in phosphorylated Galpha(13) that was abolished by pretreatment with the adenylate cyclase inhibitor MDL-12.", "These results provide the first evidence that protein kinase A mediates phosphorylation of Galpha(13) both in vitro and in vivo and provides a basis for the preferential inhibition of thromboxane A(2)-mediated signaling in platelets by cAMP."], "structured": false}
{"doc_id": 24731248, "title": "Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine.", "abstract": ["5-methylcytosine (5mC) in DNA plays an important role in gene expression, genomic imprinting, and suppression of transposable elements.", "5mC can be converted to 5-hydroxymethylcytosine (5hmC) by the Tet (ten eleven translocation) proteins.", "Here, we show that, in addition to 5hmC, the Tet proteins can generate 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) from 5mC in an enzymatic activity-dependent manner.", "Furthermore, we reveal the presence of 5fC and 5caC in genomic DNA of mouse embryonic stem cells and mouse organs.", "The genomic content of 5hmC, 5fC, and 5caC can be increased or reduced through overexpression or depletion of Tet proteins.", "Thus, we identify two previously unknown cytosine derivatives in genomic DNA as the products of Tet proteins.", "Our study raises the possibility that DNA demethylation may occur through Tet-catalyzed oxidation followed by decarboxylation."], "structured": false}
{"doc_id": 24735908, "title": "Long-term use of aspirin and age-related macular degeneration.", "abstract": ["CONTEXT Aspirin is widely used for relief of pain and for cardioprotective effects.", "Its use is of concern to ophthalmologists when ocular surgery is being considered and also in the presence of age-related macular degeneration (AMD).   \n", "OBJECTIVE To examine the association of regular aspirin use with incidence of AMD.   \n", "DESIGN, SETTING, AND PARTICIPANTS The Beaver Dam Eye Study, a longitudinal population-based study of age-related eye diseases conducted in Wisconsin.", "Examinations were performed every 5 years over a 20-year period (1988-1990 through 2008-2010).", "Study participants (N = 4926) were aged 43 to 86 years at the baseline examination.", "At subsequent examinations, participants were asked if they had regularly used aspirin at least twice a week for more than 3 months.   \n", "MAIN OUTCOME MEASURE Incidence of early AMD, late AMD, and 2 subtypes of late AMD (neovascular AMD and pure geographic atrophy), assessed in retinal photographs according to the Wisconsin Age-Related Maculopathy Grading System.   \n", "RESULTS The mean duration of follow-up was 14.8 years.", "There were 512 incident cases of early AMD (of 6243 person-visits at risk) and 117 incident cases of late AMD (of 8621 person-visits at risk) over the course of the study.", "Regular aspirin use 10 years prior to retinal examination was associated with late AMD (hazard ratio [HR], 1.63 [95% CI, 1.01-2.63]; P = .05), with estimated incidence of 1.76% (95% CI, 1.17%-2.64%) in regular users and 1.03% (95% CI, 0.70%-1.51%) in nonusers.", "For subtypes of late AMD, regular aspirin use 10 years prior to retinal examination was significantly associated with neovascular AMD (HR, 2.20 [95% CI, 1.20-4.15]; P = .01) but not pure geographic atrophy (HR, 0.66 [95% CI, 0.25-1.95]; P = .45).", "Aspirin use 5 years (HR, 0.86 [95% CI, 0.71-1.05]; P = .13) or 10 years (HR, 0.86 [95% CI, 0.65-1.13]; P = .28) prior to retinal examination was not associated with incident early AMD.   \n", "CONCLUSIONS Among an adult cohort, aspirin use 5 years prior to observed incidence was not associated with incident early or late AMD.", "However, regular aspirin use 10 years prior was associated with a small but statistically significant increase in the risk of incident late and neovascular AMD."], "structured": true}
{"doc_id": 24737389, "title": "Growth control and ribosomopathies.", "abstract": ["Ribosome biogenesis and protein synthesis are two of the most energy consuming processes in a growing cell.", "Moreover, defects in their molecular components can alter the pattern of gene expression.", "Thus it is understandable that cells have developed a surveillance system to monitor the status of the translational machinery.", "Recent discoveries of causative mutations and deletions in genes linked to ribosome biogenesis have defined a group of similar pathologies termed ribosomopathies.", "Over the past decade, much has been learned regarding the relationship between growth control and ribosome biogenesis.", "The discovery of extra-ribosomal functions of several ribosome proteins and their regulation of p53 levels has provided a link from ribosome impairment to cell cycle regulation.", "Yet, evidence suggesting p53 and/or Hdm2 independent pathways also exists.", "In this review, we summarize recent advances in understanding the mechanisms underlying the pathologies of ribosomopathies and discuss the relationship between ribosome production and tumorigenesis."], "structured": false}
{"doc_id": 24742375, "title": "Tunable signal processing through modular control of transcription factor translocation.", "abstract": ["Signaling pathways can induce different dynamics of transcription factor (TF) activation.", "We explored how TFs process signaling inputs to generate diverse dynamic responses.", "The budding yeast general stress-responsive TF Msn2 acted as a tunable signal processor that could track, filter, or integrate signals in an input-dependent manner.", "This tunable signal processing appears to originate from dual regulation of both nuclear import and export by phosphorylation, as mutants with one form of regulation sustained only one signal-processing function.", "Versatile signal processing by Msn2 is crucial for generating distinct dynamic responses to different natural stresses.", "Our findings reveal how complex signal-processing functions are integrated into a single molecule and provide a guide for the design of TFs with \"programmable\" signal-processing functions."], "structured": false}
{"doc_id": 24746892, "title": "Killing by bactericidal antibiotics does not depend on reactive oxygen species.", "abstract": ["Bactericidal antibiotics kill by modulating their respective targets.", "This traditional view has been challenged by studies that propose an alternative, unified mechanism of killing, whereby toxic reactive oxygen species (ROS) are produced in the presence of antibiotics.", "We found no correlation between an individual cell's probability of survival in the presence of antibiotic and its level of ROS.", "An ROS quencher, thiourea, protected cells from antibiotics present at low concentrations, but the effect was observed under anaerobic conditions as well.", "There was essentially no difference in survival of bacteria treated with various antibiotics under aerobic or anaerobic conditions.", "This suggests that ROS do not play a role in killing of bacterial pathogens by antibiotics."], "structured": false}
{"doc_id": 24760136, "title": "A naturally occurring mouse model of X-linked congenital stationary night blindness.", "abstract": ["PURPOSE To describe a naturally occurring X-linked recessive mutation, no b-wave (nob), that compromises visual transmission between photoreceptors and second-order neurons in mice.   \n", "METHODS Affected mice were identified by recording the light-evoked response of the retina, the electroretinogram (ERG).", "To evaluate visual transmission, cortical potentials were recorded with a scalp electrode.", "The inheritance pattern for nob was defined by breeding nob animals with normal mice.", "Retinal histologic analysis was performed by light microscopy.   \n", "RESULTS Although the photoreceptor-mediated ERG component (a-wave) was normal in nob mice, the major response component reflecting postreceptoral neuronal activity (b-wave) was missing.", "Visually-driven cortical activity was also abnormal in nob animals.", "At the light microscopic level, the nob retina appeared to have a normal cytoarchitecture.   \n", "CONCLUSIONS These findings suggest that the nob defect interferes with the transmission of visual information through the retina and that these mice are a useful model for the study of outer retinal synaptic function.", "In addition, this mutant mouse seems to provide an animal model for the complete form of congenital stationary night blindness, a human disorder in which patients have a profound loss of rod-mediated visual sensitivity."], "structured": true}
{"doc_id": 24766509, "title": "Differentiation of mesenchymal stem cells and embryonic stem cells into steroidogenic cells using steroidogenic factor-1 and liver receptor homolog-1.", "abstract": ["Previously, we have demonstrated that mesenchymal stem cells could be differentiated into steroidogenic cells through steroidogenic factor-1 and 8bromo-cAMP treatment.", "Use of liver receptor homolog-1, another of the nuclear receptor 5A family nuclear receptors, with 8bromo-cAMP also resulted in the differentiation of human mesenchymal stem cells into steroid hormone-producing cells.", "The same approaches could not be applied to other undifferentiated cells such as embryonic stem cells or embryonal carcinoma cells, because the over-expression of the nuclear receptor 5A family is cytotoxic to these cells.", "We established embryonic stem cells carrying tetracycline-regulated steroidogenic factor-1 gene at the ROSA26 locus.", "The embryonic stem cells were first differentiated into a mesenchymal cell lineage by culturing on collagen IV-coated dishes and treating with pulse exposures of retinoic acid before expression of steroidogenic factor-1.", "Although the untreated embryonic stem cells could not be converted into steroidogenic cells by expression of steroidogenic factor-1 in the absence of leukemia inhibitory factor due to inability of the cells to survive, the differentiated cells could be successfully converted into steroidogenic cells when expression of steroidogenic factor-1 was induced.", "They exhibited characteristics of adrenocortical-like cells and produced a large amount of corticosterone.", "These results indicated that pluripotent stem cells could be differentiated into steroidogenic cells by the nuclear receptor 5A family of protein via the mesenchymal cell lineage.", "This approach may provide a source of cells for future gene therapy for diseases caused by steroidogenesis deficiencies."], "structured": false}
{"doc_id": 24770122, "title": "Chronic daily headache. A clinical and psychological profile before and after treatment.", "abstract": ["To assess the clinical and personality characteristics of patients with chronic daily headache before and after treatment, 20 patients were examined and the Minnesota Multiphasic Personality Inventory (MMPI [Italian 356-item abbreviated version]) and the Strait and Trait Anxiety Index 1,2 (STAI) administered.", "There were two groups: group 1 (n = 6), with a \"conversion V\" configuration (with elevation of hypochondria and hysteria scales, the depression scale being somewhat lower); and group 2 (n = 13) with elevation of depression and of other MMPI scales.", "One patient had no scale elevation.", "STAI 1,2 scores were high in both groups.", "Several psychosomatic symptoms and some migraine features were present in almost all patients.", "Occurrence, severity, and duration of headache were recorded regularly and the MMPI and the STAI administered again after treatment.", "Improvement of headaches and a decrease of several MMPI and STAI 2 scores were observed.", "However, 12 of 20 patients showed a conversion V configuration after treatment.", "It is concluded that chronic daily headache was transformed migraine in most cases and was accompanied by anxiety levels in all patients and hysteric traits in some.", "With time, these patients may develop a depressive disorder.", "After treatment, hysterical traits are still present at a lower level in those showing these traits before treatment and may be unmasked in those that had depression."], "structured": false}
{"doc_id": 24770913, "title": "Potassium channel structure and function as reported by a single glycosylation sequon.", "abstract": ["Inwardly rectifying K+ channels (IRKs) are highly K(+)-selective, integral membrane proteins that help maintain resting the membrane potential and cell volume.", "Integral membrane proteins as a class are frequently N-glycosylated with the attached carbohydrate being extracellular and perhaps modulating function.", "However, dynamic effects of glycosylation have yet to be demonstrated at the molecular level.", "ROMK1, a member of the IRK family is particularly suited to the study of glycosylation because it has a single N-glycosylation consensus sequence (Ho, K., Nichols, C. G., Lederer, W. J., Lytton, J., Vassilev, P. M., Kanazirska, M. V., and Herbert, S. C. (1993) Nature 362, 31-38).", "We show that ROMK1 is expressed in a functional state in the plasmalemma of an insect cell line (Spodoptera frugiperda, Sf9) and has two structures, glycosylated and unglycosylated.", "To test functionality, glycosylation was abolished by an N117Q mutation or by treatment with tunicamycin.", "Whole cell currents were greatly reduced in both of the unglycosylated forms compared to wild-type.", "Single channel currents revealed a dramatic decrease in opening probability, po, as the causative factor.", "Thus we have shown biochemically that the N-glycosylation sequon is extracellular, a result consistent with present topological models of IRKs, and we conclude that sequon occupancy by carbohydrate stabilizes the open state of ROMK1."], "structured": false}
{"doc_id": 24783597, "title": "Role of the novel Th17 cytokine IL-17F in inflammatory bowel disease (IBD): upregulated colonic IL-17F expression in active Crohn's disease and analysis of the IL17F p.His161Arg polymorphism in IBD.", "abstract": ["BACKGROUND Interleukin (IL)-17F, produced in IL-23R-expressing Th17 cells, is a novel member of the IL-17 cytokine family.", "Given the association of IL23R with inflammatory bowel disease (IBD), we characterized the role of IL-17F in IBD including its intestinal gene expression and the effect of the IL17F p.", "His161Arg polymorphism on disease susceptibility and phenotype of Crohn's disease (CD) and ulcerative colitis (UC).", "In addition, we analyzed the IL17F p.", "His161Arg polymorphism for potential epistasis with IL23R and NOD2/CARD15 variants.   \n", "METHODS Intestinal IL-17F mRNA expression was measured by quantitative polymerase chain reaction (PCR).", "Genomic DNA from 1682 individuals (CD: n = 499; UC: n = 216; controls: n = 967) was analyzed for the presence of the IL17F p.", "His161Arg polymorphism, the 3 NOD2 variants, p.", "Arg702Trp, p.", "Gly908Arg, and p.", "Leu1007fsX1008, and 10 CD-associated IL23R variants.   \n", "RESULTS Intestinal IL-17F mRNA expression was 4.4-fold increased in inflamed colonic lesions compared to uninflamed biopsies in CD (P = 0.016) but not in UC.", "However, the mean intestinal IL-17F mRNA expression was higher in UC than in CD (P < 0.0001).", "The IL17F p.", "His161Arg substitution was observed with similar frequencies in IBD patients and controls and was not associated with a certain disease phenotype, but weakly associated with a low body mass index (BMI; P = 0.009) and an earlier age of disease onset (P = 0.039) in UC.", "There was no evidence for epistasis between the IL17F p.", "His161Arg polymorphism and IBD-associated single nucleotide polymorphisms within the IL23R gene.   \n", "CONCLUSIONS Intestinal IL17F gene expression is increased in active CD.", "The IL17F p.", "His161Arg polymorphism is not associated with IBD susceptibility and has no epistatic interaction with CD-associated IL23R variants."], "structured": true}
{"doc_id": 24790460, "title": "Targeting brain cancer: advances in the molecular pathology of malignant glioma and medulloblastoma", "abstract": ["Malignant brain tumours continue to be the cause of a disproportionate level of morbidity and mortality across a wide range of individuals.", "The most common variants in the adult and paediatric populations \u2014 malignant glioma and medulloblastoma, respectively \u2014 have been the subject of increasingly intensive research over the past two decades that has led to considerable advances in the understanding of their basic biology and pathogenesis.", "This Review summarizes these developments in the context of the evolving notion of molecular pathology and discusses the implications that this work has on the design of new treatment regimens."], "structured": false}
{"doc_id": 24795767, "title": "Rapid helper T-cell recovery above 200 \u00d7 106/l at 3 months correlates to successful transplant outcomes after allogeneic stem cell transplantation", "abstract": ["The current study evaluates the role of quantitative measurement of peripheral lymphocyte subsets, especially CD4+ helper T-cell recovery, in predicting transplant outcomes including overall survival (OS) and non-relapse mortality (NRM) after allogeneic stem cell transplantation.", "A total of 69 allogeneic recipients were included with following diagnoses: acute myeloid leukemia 42, acute lymphoblastic leukemia 5, chronic myeloid leukemia 15, non-Hodgkin's lymphoma 5 and high-risk myelodysplastic syndrome 2.", "The peripheral lymphocyte subset counts (CD3+ T cells, CD3+4+ helper T cells, CD3+8+ cytotoxic T cells, CD19+ B cells, and CD56+ natural killer cells) were measured at 3, 6 and 12 months.", "The CD4+ helper T-cell reconstitution at 3 months was strongly correlated with OS (P<0.0001), NRM (P=0.0007), and opportunistic infections (P=0.0108) at the cutoff value of 200 \u00d7 106/l CD4+ helper T cells.", "Rapid CD4+ helper T-cell recovery was also associated with a higher CD4+ helper T-cell transplant dose (P=0.006) and donor type (P<0.001).", "An early CD4+ helper T-cell recovery at 3 months correlated with a subsequent faster helper T-cell recovery until 12 months, yet not with B-cell recovery.", "In a multivariate analysis, rapid recovery of CD4+ helper T cells at 3 months was a favorable prognostic factor together with higher CD34+ cell transplant dose in terms of OS (P=0.001) and NRM (P=0.005)."], "structured": false}
{"doc_id": 24825841, "title": "Generating an iPSC bank for HLA-matched tissue transplantation based on known donor and recipient HLA types.", "abstract": ["The likelihood for immunological rejection of Human Leukocyte Antigens (HLA)-mismatched induced pluripotent stem cells (iPSCs) limits their therapeutic potential.", "Here we show how a tissue bank from 150 selected homozygous HLA-typed volunteers could match 93% of the UK population with a minimal requirement for immunosuppression.", "Our model provides a practical approach for using existing HLA-typed samples to generate an iPSC stem cell bank that circumvents prospective typing of a large number of individuals."], "structured": false}
{"doc_id": 24828165, "title": "Promiscuous gene expression and the developmental dynamics of medullary thymic epithelial cells.", "abstract": ["Thymic epithelial cells (TEC) form the structural and functional microenvironment necessary for the establishment and quality control of the T cell repertoire.", "In addition, they provide an ectopic source of numerous tissue-restricted antigens (TRA), a feature called promiscuous gene expression (pGE).", "How the regulation of pGE is related to the cell biology of TEC subset(s), e.g. their turnover and developmental interrelationship is still poorly understood.", "The observation that pGE is foremost a property of phenotypically and functionally mature medullary TEC (mTEC) implies that the full implementation of pGE is contingent on mTEC differentiation.", "Here, we show that the emergence of TEC subsets and pGE is tightly correlated during ontogeny and we provide evidence that mature CD80pos mTEC develop from an immature CD80neg subset.", "This differentiation step proceeds continuously in the postnatal thymus.", "While mature mTEC turnover in 2 to 3 weeks, immature mTEC encompass a smaller cycling and a larger non-cycling pool.", "The latter might serve as a reservoir of committed precursors, which sustain this renewal process.", "Our data document that mTEC represent a highly dynamic cell population, and they imply that the availability and display of TRA in the thymus undergoes a perpetual temporal and spatial reorganization."], "structured": false}
{"doc_id": 24834968, "title": "Evaluation of HER-2/neu amplification and other biological markers as predictors of response to neoadjuvant anthracycline-based chemotherapy in primary breast cancer: the role of anthracycline dose intensity.", "abstract": ["OBJECTIVES The value of HER-2/neu status as a predictor of response to anthracycline-based chemotherapy is still a matter of debate.", "We evaluated the contribution of HER-2/neu gene amplification and other biologic markers in predicting response to different doses of neoadjuvant anthracycline-based chemotherapy.   \n", "METHODS Clinical and pathologic records of 115 primary breast cancer patients were reviewed.", "Forty-eight and 67 patients received high (doxorubicin > or =20 mg/m2/wk; epirubicin > or =30 mg/m2/wk) and moderate-low anthracycline dose intensity regimens, respectively.", "Pathologic diagnosis, hormonal receptor status (HR), Ki67, and HER-2/neu status were assessed on tumor samples before neoadjuvant chemotherapy.", "HER-2/neu was determined by fluorescence in situ hybridization (FISH).   \n", "RESULTS HER-2/neu amplification was observed in 29/115 (25%) tumors, 18 from moderate-low-dose and 11 from high-dose group.", "In the univariate analysis, a high Ki67 index (> or =20%) and positive clinical axillary nodes were predictive of an objective tumor response (P = 0.033 and 0.001, respectively).", "In the multivariate analysis, Ki67 was the only factor predictive of response (OR = 3.08, 95% CI = 1.1-8.5, P = 0.03).", "HER-2/neu status was not a factor in predicting objective response to different anthracycline dose intensities.", "The same finding was observed with regards to HR and Ki67.   \n", "CONCLUSIONS In our series, no significant dose-response relationship was found according to HER-2/neu status."], "structured": true}
{"doc_id": 24863571, "title": "Radioactive labeling of mitochondrial translation products in cultured cells.", "abstract": ["The mammalian mitochondrial genome contains 37 genes, 13 of which encode polypeptide subunits in the enzyme complexes of the oxidative phosphorylation system.", "The other genes encode the rRNAs and tRNAs necessary for their translation.", "The mitochondrial translation machinery is located in the mitochondrial matrix, and is exclusively dedicated to the synthesis of these 13 enzyme subunits.", "Mitochondrial disease in humans is often associated with defects in mitochondrial translation.", "This can manifest as a global decrease in the rate of mitochondrial protein synthesis, a decrease in the synthesis of specific polypeptides, the synthesis of abnormal polypeptides, or in altered stability of specific translation products.", "All of these changes in the normal pattern of mitochondrial translation can be assessed by a straightforward technique that takes advantage of the insensitivity of the mitochondrial translation machinery to antibiotics that completely inhibit cytoplasmic translation.", "Thus, specific radioactive labeling of the mitochondrial translation products can be achieved in cultured cells, and the results can be visualized on gradient gels.", "The analysis of mitochondrial translation in cells cultured from patient biopsies is useful in the study of disease-causing mutations in both the mitochondrial and the nuclear genomes."], "structured": false}
{"doc_id": 24864273, "title": "Caenorhabditis elegans cyclin A- and B-type genes: a cyclin A multigene family, an ancestral cyclin B3 and differential germline expression.", "abstract": ["We have cloned cDNAs for Caenorhabditis elegans cyclins A1, B and B3.", "While cyclins A1 and B are most closely related to either A- or B-type cyclins of other species, cyclin B3 is less related to these cyclins.", "However, this cyclin is most similar to the recently identified chicken cyclin B3.", "Our identification of a Caenorhabditis homolog demonstrates that cyclin B3 has been conserved in evolution.", "Cyclin A1 is a member of an A-type multigene family; however the cyclin A1 cDNA only recognizes a single band on northern blots.", "A single-sized RNA is also observed for the cyclin B3 cDNA.", "In contrast, three different transcripts are observed for the cyclin B cDNA.", "Based on our analyses using RNAs from germline-defective mutants and from populations enriched for males, one cyclin B transcript is specific to the paternal germline.", "The two other cyclin B transcripts, as well as the cyclin A1 and cyclin B3 transcripts, are most abundant in the maternal germline and are only present at low levels in other tissues.", "Moreover, the 3' untranslated regions of each Caenorhabditis cyclin cDNA possess several copies of potential translational control elements shown in Xenopus and Drosophila maternal cyclin mRNAs to function during oogenesis and early embryogenesis."], "structured": false}
{"doc_id": 24865781, "title": "A comparison of pharmacological (amitriptyline HCL) and nonpharmacological (cognitive-behavioral) therapies for chronic tension headaches.", "abstract": ["Forty-one recurrent tension headache sufferers were randomly assigned to either cognitive-behavioral therapy (administered in a primarily home-based treatment protocol) or to amitriptyline therapy (with dosage individualized at 25, 50, or 75 mg/day).", "Cognitive-behavioral therapy and amitriptyline each yielded clinically significant improvements in headache activity, both when improvement was assessed with patient daily recordings (56% and 27% reduction in headache index, respectively), and when improvement was assessed with neurologist ratings of clinical improvement (94% and 69% of patients rated at least moderately improved, respectively).", "In instances where differences in treatment effectiveness were observed (headache index, somatic complaints, perceptions of control of headache activity), cognitive-behavioral therapy yielded somewhat more positive outcomes than did amitriptyline.", "Neither treatment, however, eliminated headache problems."], "structured": false}
{"doc_id": 24872571, "title": "Homeostasis model assessment: insulin resistance and \u03b2-cell function from fasting plasma glucose and insulin concentrations in man", "abstract": ["The steady-state basal plasma glucose and insulin concentrations are determined by their interaction in a feedback loop.", "A computer-solved model has been used to predict the homeostatic concentrations which arise from varying degrees of \u03b2-cell deficiency and insulin resistance.", "Comparison of a patient's fasting values with the model's predictions allows a quantitative assessment of the contributions of insulin resistance and deficient \u03b2-cell function to the fasting hyperglycaemia (homeostasis model assessment, HOMA).", "The accuracy and precision of the estimate have been determined by comparison with independent measures of insulin resistance and \u03b2-cell function using hyperglycaemic and euglycaemic clamps and an intravenous glucose tolerance test.", "The estimate of insulin resistance obtained by homeostasis model assessment correlated with estimates obtained by use of the euglycaemic clamp (Rs = 0.88, p < 0.0001), the fasting insulin concentration (Rs = 0.81, p < 0.0001), and the hyperglycaemic clamp, (Rs = 0.69, p < 0.01).", "There was no correlation with any aspect of insulin-receptor binding.", "The estimate of deficient \u03b2-cell function obtained by homeostasis model assessment correlated with that derived using the hyperglycaemic clamp (Rs = 0.61, p < 0.01) and with the estimate from the intravenous glucose tolerance test (Rs = 0.64, p < 0.05).", "The low precision of the estimates from the model (coefficients of variation: 31% for insulin resistance and 32% for \u03b2-cell deficit) limits its use, but the correlation of the model's estimates with patient data accords with the hypothesis that basal glucose and insulin interactions are largely determined by a simple feed back loop."], "structured": false}
{"doc_id": 24873253, "title": "Clinical benefits and considerations of bisphosphonate treatment in metastatic bone disease.", "abstract": ["Patients with metastatic bone disease are at risk for developing skeletal-related events that can negatively influence quality of life, contributing to loss of autonomy and functional capabilities.", "Bisphosphonates have become an important component in the treatment of patients with bone metastases as they delay the onset and reduce the risk of skeletal-related events and also palliate or control bone pain in multiple cancer types, thus preserving quality of life.", "Zoledronic acid has proven efficacy and safety in patients with bone lesions from breast cancer, prostate cancer, lung cancer, and other solid tumors, as well as in patients with multiple myeloma.", "Current data suggest that early treatment with zoledronic acid (before the onset of bone pain) may provide additional clinical benefits and also positive effects on survival in subsets of patients who have elevated levels of N-telopeptide of type I collagen (NTX), a biochemical marker of bone resorption.", "Studies have shown that in patients with breast cancer, prostate cancer, lung cancer, or other solid tumors, normalization of elevated levels of NTX was observed in the majority of patients who received zoledronic acid.", "Furthermore, normalization of NTX values correlated with extended survival."], "structured": false}
{"doc_id": 24879055, "title": "Distinct memory CD4+ T cells with commitment to T follicular helper- and T helper 1-cell lineages are generated after acute viral infection.", "abstract": ["CD4(+) T follicular helper (Tfh) cells provide the required signals to B cells for germinal center reactions that are necessary for long-lived antibody responses.", "However, it remains unclear whether there are CD4(+) memory T cells committed to the Tfh cell lineage after antigen clearance.", "By using adoptive transfer of antigen-specific memory CD4(+) T cell subpopulations in the lymphocytic choriomeningitis virus infection model, we found that there are distinct memory CD4(+) T cell populations with commitment to either Tfh- or Th1-cell lineages.", "Our conclusions are based on gene expression profiles, epigenetic studies, and phenotypic and functional analyses.", "Our findings indicate that CD4(+) memory T cells \"remember\" their previous effector lineage after antigen clearance, being poised to reacquire their lineage-specific effector functions upon antigen reencounter.", "These findings have important implications for rational vaccine design, where improving the generation and engagement of memory Tfh cells could be used to enhance vaccine-induced protective immunity."], "structured": false}
{"doc_id": 24881307, "title": "Control of synapse development and plasticity by Rho GTPase regulatory proteins", "abstract": ["Synapses are specialized cell-cell contacts that mediate communication between neurons.", "Most excitatory synapses in the brain are housed on dendritic spines, small actin-rich protrusions extending from dendrites.", "During development and in response to environmental stimuli, spines undergo marked changes in shape and number thought to underlie processes like learning and memory.", "Improper spine development, in contrast, likely impedes information processing in the brain, since spine abnormalities are associated with numerous brain disorders.", "Elucidating the mechanisms that regulate the formation and plasticity of spines and their resident synapses is therefore crucial to our understanding of cognition and disease.", "Rho-family GTPases, key regulators of the actin cytoskeleton, play essential roles in orchestrating the development and remodeling of spines and synapses.", "Precise spatio-temporal regulation of Rho GTPase activity is critical for their function, since aberrant Rho GTPase signaling can cause spine and synapse defects as well as cognitive impairments.", "Rho GTPases are activated by guanine nucleotide exchange factors (GEFs) and inhibited by GTPase-activating proteins (GAPs).", "We propose that Rho-family GEFs and GAPs provide the spatiotemporal regulation and signaling specificity necessary for proper Rho GTPase function based on the following features they possess: (i) existence of multiple GEFs and GAPs per Rho GTPase, (ii) developmentally regulated expression, (iii) discrete localization, (iv) ability to bind to and organize specific signaling networks, and (v) tightly regulated activity, perhaps involving GEF/GAP interactions.", "Recent studies describe several Rho-family GEFs and GAPs that uniquely contribute to spinogenesis and synaptogenesis.", "Here, we highlight several of these proteins and discuss how they occupy distinct biochemical niches critical for synaptic development."], "structured": false}
{"doc_id": 24896957, "title": "Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing.", "abstract": ["Knowledge of the rate and nature of spontaneous mutation is fundamental to understanding evolutionary and molecular processes.", "In this report, we analyze spontaneous mutations accumulated over thousands of generations by wild-type Escherichia coli and a derivative defective in mismatch repair (MMR), the primary pathway for correcting replication errors.", "The major conclusions are (i) the mutation rate of a wild-type E. coli strain is ~1 \u00d7 10(-3) per genome per generation; (ii) mutations in the wild-type strain have the expected mutational bias for G:C > A:T mutations, but the bias changes to A:T > G:C mutations in the absence of MMR; (iii) during replication, A:T > G:C transitions preferentially occur with A templating the lagging strand and T templating the leading strand, whereas G:C > A:T transitions preferentially occur with C templating the lagging strand and G templating the leading strand; (iv) there is a strong bias for transition mutations to occur at 5'ApC3'/3'TpG5' sites (where bases 5'A and 3'T are mutated) and, to a lesser extent, at 5'GpC3'/3'CpG5' sites (where bases 5'G and 3'C are mutated); (v) although the rate of small (\u22644 nt) insertions and deletions is high at repeat sequences, these events occur at only 1/10th the genomic rate of base-pair substitutions.", "MMR activity is genetically regulated, and bacteria isolated from nature often lack MMR capacity, suggesting that modulation of MMR can be adaptive.", "Thus, comparing results from the wild-type and MMR-defective strains may lead to a deeper understanding of factors that determine mutation rates and spectra, how these factors may differ among organisms, and how they may be shaped by environmental conditions."], "structured": false}
{"doc_id": 24906548, "title": "Apolipoprotein E4 as a predictor of outcomes in pediatric mild traumatic brain injury.", "abstract": ["The epsilon4 allele of the apolipoprotein E (APOE) gene has been linked to negative outcomes among adults with traumatic brain injury (TBI) across the spectrum of severity, with preliminary evidence suggesting a similar pattern among children.", "This study investigated the relationship of the APOE epsilon4 allele to outcomes in children with mild TBI.", "Participants in this prospective, longitudinal study included 99 children with mild TBI between the ages of 8 and 15 recruited from consecutive admissions to Emergency Departments at two large children's hospitals.", "Outcomes were assessed acutely in the Emergency Department and at follow-ups at 2 weeks, 3 months, and 12 months post-injury.", "Among the 99 participants, 28 had at least one epsilon4 allele.", "Children with and without an epsilon4 allele did not differ demographically.", "Children with an epsilon4 allele were significantly more likely than those without an epsilon4 allele to have a Glasgow Coma Scale score of less than 15, but the groups did not differ on any other measures of injury severity.", "Those with an epsilon4 allele exhibited better performance than children without an epsilon4 allele on a test of constructional skill, but the groups did not differ on any other neuropsychological tests.", "Children with and without an epsilon4 allele also did not differ on measures of post-concussive symptoms.", "Overall, the findings suggest that the APOE epsilon4 allele is not consistently related to the outcomes of mild TBI in children."], "structured": false}
{"doc_id": 24916604, "title": "Do physicians follow systemic treatment and funding policy guidelines?", "abstract": ["BACKGROUND The use of bisphosphonates for the prevention of skeletal related events in women with bone metastases from breast cancer is well established.", "We undertook an evaluation of bisphosphonate use in clinical practice in three Canadian cancer centres.", "In addition we assessed whether or not physicians at these centres are following their local treatment guidelines and funding policies.   \n", "METHODS Charts and electronic files of patients who had received either clodronate or pamidronate at any time between January 2000 and December 2001 at three Canadian cancer centres were retrospectively reviewed.   \n", "RESULTS There has been a marked improvement in the time between the diagnosis of bone metastases and the commencement of bisphosphonates from a median of 155 days in 1998 to 24 days in 2001.", "However, despite a local funding policy requiring that oral clodronate be the first bisphosphonate used, this was the case in only 67% of patients.", "In addition, despite one centre's guidelines recommending that bisphosphonates be stopped once the patient was progressing, 90% of their patients remained on bisphosphonates until they died.   \n", "CONCLUSIONS A considerable amount of effort is spent on the creation of \"evidence based\" treatment guidelines.", "Funding agencies develop policies based on these treatment guidelines, but often funding is more restrictive than the treatment guideline would suggest.", "It is clear from this review that physicians still appear to manage a substantial proportion of patients outside of funding policies, but within evidence based recommendations.", "Therefore, a need exists for either the creation of guidelines and policies that physicians will follow or the implementation of methods to ensure that restrictive policies are actually followed."], "structured": true}
{"doc_id": 24917562, "title": "Increased resting energy expenditure and weight loss are related to a systemic inflammatory response in lung cancer patients.", "abstract": ["PURPOSE To determine whether an increased resting energy expenditure (REE) and weight loss in lung cancer patients are related to a systemic inflammatory response.   ", "MATERIALS AND METHODS REE was measured by indirect calorimetry using a ventilated hood system.", "Soluble tumor necrosis factor receptor 55 (sTNF-R55) and sTNF-R75, soluble intercellular adhesion molecule (sICAM)-1, soluble E (sE)-selectin, lipopolysaccharide (LPS)-binding protein (LBP), interleukin (IL)-6, and TNF-alpha were measured using sandwich enzyme-linked immunosorbent assay (ELISA), and C-reactive protein (CRP) was measured by turbidimetry.", "A cross-sectional study was performed to compare inflammatory mediators between hypermetabolic (REE/Harris Benedict [HB] equation > or = 110%) versus normometabolic (REE/HB < 110%) patients and between patients who lost weight (more than 10% loss of preillness weight) versus those whose weight remained stable.   \n", "RESULTS Eighty-seven patients with primary non-small-cell lung cancer were consecutively entered onto the study.", "Mean REE expressed as a percentage of the HB reference values was 118% +/-", "12%; 67 patients were considered hypermetabolic.", "Twenty-six patients had a substantial loss of more than 10% of their preillness weight.", "Hypermetabolic patients were found to have significantly increased levels of sTNF-R55, sE-selectin, LBP, and CRP compared with normometabolic patients.", "Weight loss was related with increased levels of the sTNF-Rs, sICAM-1, IL-6, LBP, and CRP.   \n", "CONCLUSION Hypermetabolism and weight loss are related to the presence of a systemic inflammatory response as reflected by enhanced levels of inflammatory mediators and acute phase proteins in patients with primary non-small-cell lung cancer."], "structured": true}
{"doc_id": 24918110, "title": "Exercise capacity and body mass as predictors of mortality among male veterans with type 2 diabetes.", "abstract": ["OBJECTIVE To demonstrate the relation of exercise capacity and BMI to mortality in a population of male veterans with type 2 diabetes.   ", "RESEARCH DESIGN AND METHODS After excluding two underweight patients (BMI <18.5 kg/m2), the study population comprised 831 consecutive patients with type 2 diabetes (mean age 61 +/-", "9 years) referred for exercise testing for clinical reasons between 1995 and 2006.", "Exercise capacity was determined from a maximal exercise test and measured in metabolic equivalents (METs).", "Patients were classified both according to BMI category (18.5-24.9, 25.0-29.9, and > or =30 kg/m2) and by exercise capacity (<5.0 or > or =5.0 maximal METs).", "The association among exercise capacity, BMI, other clinical variables, and all-cause mortality was assessed by Cox proportional hazards.", "Study participants were followed for mortality up to 30 June 2006.   \n", "RESULTS During a mean follow-up of 4.8 +/-", "3.0 years, 112 patients died, for an average annual mortality rate of 2.2%.", "Each 1-MET increase in exercise capacity conferred a 10% survival benefit (hazard ratio 0.90 [95% CI 0.82-0.98]; P = 0.01), but BMI was not significantly associated with mortality.", "After adjustment for age, ethnicity, examination year, BMI, presence of cardiovascular disease (CVD), and CVD risk factors, diabetic patients achieving <5 maximal METs were 70% more likely to die (1.70 [1.13-2.54]) than those achieving > or =5 maximal METs.   \n", "CONCLUSIONS There was a strong inverse association between exercise capacity and mortality in this cohort of men with documented diabetes, and this relationship was independent of BMI."], "structured": true}
{"doc_id": 24921368, "title": "Impaired awareness of hypoglycaemia: a review.", "abstract": ["Impaired awareness of hypoglycaemia (IAH) is an acquired complication of insulin therapy, which affects people with type 1 and insulin-treated type 2 diabetes mellitus, whereby the ability to perceive the onset of hypoglycaemia becomes diminished or absent.", "Deficiencies of the counter-regulatory hormonal responses to hypoglycaemia usually co-exist.", "The development of IAH and counter-regulatory failure greatly increases the risk of severe hypoglycaemia.", "Scoring systems have been developed that can be used in the clinical setting and assist with identification of this group of individuals at risk of severe hypoglycaemia.", "The mainstay of treatment of IAH is the scrupulous avoidance of hypoglycaemia."], "structured": false}
{"doc_id": 24922825, "title": "A chikungunya fever vaccine utilizing an insect-specific virus platform", "abstract": ["Traditionally, vaccine development involves tradeoffs between immunogenicity and safety.", "Live-attenuated vaccines typically offer rapid and durable immunity but have reduced safety when compared to inactivated vaccines.", "In contrast, the inability of inactivated vaccines to replicate enhances safety at the expense of immunogenicity, often necessitating multiple doses and boosters.", "To overcome these tradeoffs, we developed the insect-specific alphavirus, Eilat virus (EILV), as a vaccine platform.", "To address the chikungunya fever (CHIKF) pandemic, we used an EILV cDNA clone to design a chimeric virus containing the chikungunya virus (CHIKV) structural proteins.", "The recombinant EILV/CHIKV was structurally identical at 10 \u00c5 to wild-type CHIKV, as determined by single-particle cryo-electron microscopy, and it mimicked the early stages of CHIKV replication in vertebrate cells from attachment and entry to viral RNA delivery.", "Yet the recombinant virus remained completely defective for productive replication, providing a high degree of safety.", "A single dose of EILV/CHIKV produced in mosquito cells elicited rapid (within 4 d) and long-lasting (>290 d) neutralizing antibodies that provided complete protection in two different mouse models.", "In nonhuman primates, EILV/CHIKV elicited rapid and robust immunity that protected against viremia and telemetrically monitored fever.", "Our EILV platform represents the first structurally native application of an insect-specific virus in preclinical vaccine development and highlights the potential application of such viruses in vaccinology."], "structured": false}
{"doc_id": 24923605, "title": "Molecular elements of low-oxygen signaling in plants.", "abstract": ["Oxygen and its limitation are emerging as a crucial factor in plant fitness, growth and development.", "Recent studies revealed the mechanisms by which oxygen is perceived by plant cells.", "This sensory system partly relies on an oxygen-mediated branch of the N-end rule pathway for protein degradation acting on a specific clade of ethylene responsive transcription factors (ERF-VII).", "A complementary regulative step is provided by aerobic sequestration of an ERF-VII protein at the plasma membrane and its timely release when hypoxia occurs.", "Complete absence of oxygen triggers the transient accumulation of reactive hydrogen peroxide and induces an additional set of reactive oxygen species-related genes involved in both signaling and attenuation of oxidative stress.", "Moreover, temporary hypoxic environments that are built up as consequence of dense cell packing have been demonstrated to trigger cell-fate determination in maize anthers.", "Similarly, limited oxygen delivery in bulky fruit or tuber tissues growing in aerobic conditions were shown to stimulate anaerobic-like responses.", "These advances in low-oxygen signaling and its effect on cell development highlight the importance of taking hypoxia into account in agronomical practices as well as in breeding programs."], "structured": false}
{"doc_id": 24928817, "title": "Purification, characterization, and sequence analysis of a potential virulence factor from Porphyromonas gingivalis, peptidylarginine deiminase.", "abstract": ["The initiation and progression of adult-onset periodontitis has been associated with infection of the gingival sulcus by Porphyromonas gingivalis.", "This organism utilizes a multitude of virulence factors to evade host defenses as it establishes itself as one of the predominant pathogens in periodontal pockets.", "A feature common to many other oral pathogens is the production of ammonia due to its protective effect during acidic cleansing cycles in the mouth.", "Additionally, ammonia production by P. gingivalis has been proposed as a virulence factor due to its negative effects on neutrophil function.", "In this study, we describe the first purification of a peptidylarginine deiminase (PAD) from a prokaryote.", "PAD exhibits biochemical characteristics and properties that suggest that it may be a virulence agent.", "PAD deiminates the guanidino group of carboxyl-terminal arginine residues on a variety of peptides, including the vasoregulatory peptide-hormone bradykinin, to yield ammonia and a citrulline residue.", "The soluble protein has an apparent mass of 46 kDa, while the DNA sequence predicts a full-length protein of 61.7 kDa.", "PAD is optimally active at 55 degrees C, stable at low pH, and shows the greatest activity above pH 9.0.", "Interestingly, in the presence of stabilizing factors, PAD is resistant to limited proteolysis and retains significant activity after short-term boiling.", "We propose that PAD, acting in concert with arginine-specific proteinases from P. gingivalis, promotes the growth of the pathogen in the periodontal pocket, initially by enhancing its survivability and then by assisting the organism in its circumvention of host humoral defenses."], "structured": false}
{"doc_id": 24942840, "title": "Traumatic encephalopathy: review and provisional research diagnostic criteria.", "abstract": ["OBJECTIVES To determine the frequency of neurobehavioral signs and symptoms reported in every published case of traumatic encephalopathy with a view toward the development of clinical diagnostic criteria with predictive validity.   ", "INTRODUCTION Cases of persistent or progressive neurological or neurobehavioral change following exposure to one or more head injuries have been reported since 1928.", "This condition is often referred to as traumatic encephalopathy (TE).", "To date, however, no diagnostic criteria have been advanced or accepted for the clinical diagnosis of TE.", "Provisional research diagnostic criteria are required not only for meaningful diagnosis but also to facilitate research to determine the epidemiology, etiology, course, prognosis, imaging and biomarkers, neuropathological features and potentially effective treatments of TE.   \n", "METHODS All 436 published cases of TE in all languages were reviewed.", "All symptoms and signs reported in these cases were classified and enumerated.   \n", "RESULTS Ninety-seven cases met inclusion criteria based on sufficient documentation of the history and neurobehavioral examination.", "Provisional research diagnostic criteria for clinically probable and clinically possible TE were developed based on the most frequently reported clinical features.   \n", "CONCLUSION The provisional diagnostic criteria for TE presented here are the first published criteria for this condition based upon a systematic analysis of its clinical characteristics.", "This is the first a step toward scientifically derived consensus criteria, which are essential to accelerate progress in the investigation of this important condition."], "structured": true}
{"doc_id": 24943534, "title": "Hepatitis C and human immunodeficiency virus infection.", "abstract": ["In the United States, an estimated 200,000 persons are infected with both hepatitis C virus (HCV) and human immunodeficiency virus (HIV).", "As the lives of HIV-infected persons have been prolonged by use of highly active antiretroviral therapy, liver disease has emerged as an important, and in some settings, the leading cause of morbidity and mortality.", "Human immunodeficiency virus infection appears to adversely affect all stages of hepatitis C infection, leading to increased viral persistence and accelerated progression of HCV-related liver disease.", "In turn, hepatitis C may affect the management of HIV infection, increasing the incidence of liver toxicity caused by antiretroviral medications.", "The medical management of hepatitis C in HIV-infected persons remains controversial, in part because of the complexity of both infections and potential drug interactions, but chiefly because there is so little published information.", "Nonetheless, the burden of liver disease is too high to delay management of HIV/HCV-coinfected persons while awaiting better data.", "Instead, the management of hepatitis C today must be based on data generated on persons without HIV and an understanding of both infections.", "Properly designed studies of therapy in HIV/HCV-coinfected persons are needed to help guide management of these patients in the future."], "structured": false}
{"doc_id": 24974080, "title": "Role of the vascular endothelial growth factor pathway in tumor growth and angiogenesis.", "abstract": ["New blood vessel formation (angiogenesis) is a fundamental event in the process of tumor growth and metastatic dissemination.", "Hence, the molecular basis of tumor angiogenesis has been of keen interest in the field of cancer research.", "The vascular endothelial growth factor (VEGF) pathway is well established as one of the key regulators of this process.", "The VEGF/VEGF-receptor axis is composed of multiple ligands and receptors with overlapping and distinct ligand-receptor binding specificities, cell-type expression, and function.", "Activation of the VEGF-receptor pathway triggers a network of signaling processes that promote endothelial cell growth, migration, and survival from pre-existing vasculature.", "In addition, VEGF mediates vessel permeability, and has been associated with malignant effusions.", "More recently, an important role for VEGF has emerged in mobilization of endothelial progenitor cells from the bone marrow to distant sites of neovascularization.", "The well-established role of VEGF in promoting tumor angiogenesis and the pathogenesis of human cancers has led to the rational design and development of agents that selectively target this pathway.", "Studies with various anti-VEGF/VEGF-receptor therapies have shown that these agents can potently inhibit angiogenesis and tumor growth in preclinical models.", "Recently, an anti-VEGF antibody (bevacizumab), when used in combination with chemotherapy, was shown to significantly improve survival and response rates in patients with metastatic colorectal cancer and thus, validate VEGF pathway inhibitors as an important new treatment modality in cancer therapy."], "structured": false}
{"doc_id": 24979644, "title": "Frozen robust multiarray analysis (fRMA).", "abstract": ["Robust multiarray analysis (RMA) is the most widely used preprocessing algorithm for Affymetrix and Nimblegen gene expression microarrays.", "RMA performs background correction, normalization, and summarization in a modular way.", "The last 2 steps require multiple arrays to be analyzed simultaneously.", "The ability to borrow information across samples provides RMA various advantages.", "For example, the summarization step fits a parametric model that accounts for probe effects, assumed to be fixed across arrays, and improves outlier detection.", "Residuals, obtained from the fitted model, permit the creation of useful quality metrics.", "However, the dependence on multiple arrays has 2 drawbacks: (1) RMA cannot be used in clinical settings where samples must be processed individually or in small batches and (2) data sets preprocessed separately are not comparable.", "We propose a preprocessing algorithm, frozen RMA (fRMA), which allows one to analyze microarrays individually or in small batches and then combine the data for analysis.", "This is accomplished by utilizing information from the large publicly available microarray databases.", "In particular, estimates of probe-specific effects and variances are precomputed and frozen.", "Then, with new data sets, these are used in concert with information from the new arrays to normalize and summarize the data.", "We find that fRMA is comparable to RMA when the data are analyzed as a single batch and outperforms RMA when analyzing multiple batches.", "The methods described here are implemented in the R package fRMA and are currently available for download from the software section of http://rafalab.jhsph.edu."], "structured": false}
{"doc_id": 24980622, "title": "Hypoxia in relation to vasculature and proliferation in liver metastases in patients with colorectal cancer.", "abstract": ["PURPOSE To investigate hypoxia measured by pimonidazole binding, glucose transporter 1 (GLUT1) and carbonic anhydrase IX (CA-IX) expression, proliferation, and vascularity in liver metastases of colorectal cancer and to compare GLUT1 and CA-IX expression in corresponding primary tumors.   \n", "METHODS AND MATERIALS Twenty-five patients with liver metastases of colorectal cancer, planned for metastasectomy, were included.", "The hypoxia marker pimonidazole and proliferation marker iododeoxyuridine were administered before surgery.", "After immunofluorescent staining of the frozen metastases, pimonidazole binding, vascularity, and proliferation were analyzed quantitatively.", "Thirteen paraffin-embedded primary tumors were stained immunohistochemically for GLUT1 and CA-IX expression, which was analyzed semiquantitatively in primary tumors and corresponding liver metastases.   \n", "RESULTS In liver metastases, pimonidazole binding showed a pattern consistent with diffusion-limited hypoxia.", "The mean pimonidazole-positive fraction was 0.146; the mean distance from vessels to pimonidazole-positive areas was 80 microm.", "When expressed, often co-localization was observed between pimonidazole binding and GLUT1 or CA-IX expression, but microregional areas of mismatch were also observed.", "No correlation between the level of pimonidazole binding and GLUT1 or CA-IX expression was observed.", "In some patients, a large fraction (up to 30%) of proliferating cells was present in pimonidazole-stained areas.", "Expression of CA-IX in primary tumors and metastases showed a significant correlation, which was absent for GLUT1 expression.   \n", "CONCLUSIONS Compared with other tumor types, liver metastases of colorectal cancer contain large amounts of hypoxic cells.", "The lack of correlation with pimonidazole binding brings into question the value of GLUT1 and CA-IX as endogenous markers of hypoxia."], "structured": true}
{"doc_id": 24988745, "title": "Unmet needs mediate the relationship between symptoms and quality of life in breast cancer survivors", "abstract": ["This study aimed to compare the symptoms, unmet needs, and QoL reported by women at 6 months to <2 years and 2 to 5 years following surgery and adjuvant treatment for breast cancer.", "It also evaluated the relationships among symptoms, unmet needs, and QoL using structural equation modeling.", "In this study, 113 and 137 survivors following breast cancer treatment 6 months to <2 years and 2 to 5 years, respectively, completed the Memorial Symptom Assessment Scale, the Supportive Care Needs Survey-34, and the Medical Outcomes Study 12-item Short Form Health Survey version 2.0 during their medical follow-up.", "The mean numbers of symptoms and unmet needs were 5.43 and 3.0, respectively, for survivors at <2 years, and 5.24 and 2.42, respectively, for survivors at 2 to 5 years following treatment.", "The most common reported symptoms were related primarily to physical domains.", "No significant differences were found between the two survivor groups on the MSAS scores.", "Survivors at <2 years reported significantly higher scores in Psychological and Health Care System/Information needs (p < 0.01), and lower composite scores in physical and mental QoL (p < 0.05) than those at 2 to 5 years post-treatment.", "Significant direct and indirect effects were found of symptom burden through unmet needs on survivors\u2019 physical and mental QoL after adjustment for survival time, and the models showed a good fit.", "Results suggest that breast cancer survivors continue to endure many symptoms independent of the survivorship period.", "The unmet needs mediate the relationship between symptom burden and survivors\u2019 QoL."], "structured": false}
{"doc_id": 24989194, "title": "Phagocytosis and deposition of vascular beta-amyloid in rat brains injected with Alzheimer beta-amyloid.", "abstract": ["The presence of extracellular deposits of beta-amyloid protein in the brain is a hallmark of Alzheimer's disease (AD).", "In an effort to determine the effect of amyloid in an animal model, the authors injected amyloid cores isolated from AD brains into the cortex and hippocampus of rats.", "Lipofuscin, a major contaminant of the plaque core preparation, was injected on the contralateral side and used as a control to induce an analogous phagocytic cell response.", "Rats were sacrificed 2 days, 7 days, and 1 month after injection and amyloid located by four histochemical techniques.", "Amyloid and lipofuscin move from the site of injection into otherwise undamaged neuropil, persist for at least 1 month and are both associated with increases in glial fibrillary acidic protein and microglia (OX-42) staining.", "By 1 week, many of the amyloid cores are ingested by phagocytes.", "Some of the beta-amyloid-containing phagocytes migrate to the vessels and to the ventricles, and by 1 month, a significant amount of the amyloid is directly associated with the vessels.", "This suggests that phagocytic cells can internalize exogenous amyloid and attempt to clear it from the central nervous system (CNS).", "Therefore, the observed distribution of amyloid is not necessarily the initial site of deposition."], "structured": false}
{"doc_id": 24995939, "title": "Specific sites in the C terminus of CTCF interact with the SA2 subunit of the cohesin complex and are required for cohesin-dependent insulation activity.", "abstract": ["Recent studies have shown that the protein CTCF, which plays an important role in insulation and in large-scale organization of chromatin within the eukaryotic nucleus, depends for both activities on recruitment of the cohesin complex.", "We show here that the interaction of CTCF with the cohesin complex involves direct contacts between the cohesin subunit SA2 and specific regions of the C-terminal tail of CTCF.", "All other cohesin components are recruited through their interaction with SA2.", "Expression in vivo of CTCF mutants lacking the C-terminal domain, or with mutations at sites within it required for SA2 binding, disrupts the normal expression profile of the imprinted genes IGF2-H19 and also results in a loss of insulation activity.", "Taken together, our results demonstrate that specific sites on the C terminus of CTCF are essential for cohesin binding and insulator function.", "The only direct interaction between CTCF and cohesin involves contact with SA2, which is external to the cohesin ring.", "This suggests that in recruiting cohesin to CTCF, SA2 could bind first and the ring could assemble subsequently."], "structured": false}
{"doc_id": 24998637, "title": "Interleukin 6 plays a key role in the development of antigen-induced arthritis.", "abstract": ["To investigate the direct role of interleukin (IL) 6 in the development of rheumatoid arthritis, IL-6-deficient (IL-6 -/-) mice were backcrossed for eight generations into C57BL/6 mice, a strain of mice with a genetic background of susceptibility for antigen-induced arthritis (AIA).", "Both histological and immunological comparisons were made between IL-6-deficient (IL-6 -/-) mice and wild-type (IL-6 +/+) littermates after the induction of AIA.", "Although all IL-6 +/+ mice developed severe arthritis, only mild arthritis was observed in IL-6 -/- mice.", "Safranin O staining demonstrated that articular cartilage was well preserved in IL-6 -/- mice, whereas it was destroyed completely in IL-6 +/+ mice.", "In addition, comparable mRNA expression for both IL-1beta and tumor necrosis factor alpha, but not for IL-6, was detected in the inflamed joints of IL-6 -/- mice, suggesting that IL-6 may play a more crucial role in cartilage destruction than either IL-1beta or tumor necrosis factor alpha.", "In immunological comparisons, both antigen-specific in vitro proliferative response in lymph node cells and in vivo antibody production were elicited in IL-6 -/- mice, but they were reduced to less than half of that found in IL-6 +/+ mice.", "Lymph node cells of IL-6 -/- mice produced many more Th2 cytokines than did IL-6 +/+ mice with either antigen-specific or nonspecific stimulation in in vitro culture.", "Taken together, these results indicate that IL-6 may play a key role in the development of AIA at the inductive as well as the effector phase, and the blockade of IL-6 is possibly beneficial in the treatment of rheumatoid arthritis."], "structured": false}
{"doc_id": 24998764, "title": "Relation between renal function within the normal range and central and peripheral arterial stiffness in hypertension.", "abstract": ["Chronic kidney disease is accompanied by increased large-artery stiffness, but the relation between glomerular filtration rate within the reference range and central or peripheral arterial stiffness has been understudied.", "The link between renal function and arterial stiffness was assessed in 305 patients with never-treated essential hypertension (men: 58%; age: 48+/-11 years, blood pressure: 151/95+/-20/11 mm Hg), free from overt cardiovascular disease and with serum creatinine values <1.4 mg/dL (men) and <1.2 mg/dL (women), who underwent noninvasive aortic and upper-limb pulse wave velocity (PWV) determination.", "Aortic PWV was strongly related to age (r=0.55; P<0.001), whereas upper-limb PWV had a weaker nonlinear relation with age (beta=1.392; P<0.001 for age; beta=-1.312; P<0.001 for age squared) and a weak relation with aortic PWV (r=0.22; P<0.001).", "Glomerular filtration rate (GFR), estimated according to the Mayo clinic equation for healthy subjects, was inversely correlated with large-artery stiffness, as assessed by aortic PWV (r=-0.34; P<0.001), and with peripheral artery stiffness, as assessed by upper-limb PWV (r=-0.25; P<0.001).", "In a multivariate linear regression, aortic PWV was independently predicted by age (beta=0.48; P<0.001), mean arterial pressure (beta=0.14; P=0.013), and GFR (beta=-0.13, P=0.029).", "Upper-limb PWV was predicted by GFR (beta=-0.24; P<0.001) and mean arterial pressure (beta=0.20; P<0.001).", "We conclude that, in hypertensive patients with normal renal function, an inverse relationship exists between GFR and stiffness of both central elastic and peripheral muscular arteries.", "These relations are in part independent from the effect of several confounders, including age, sex, and blood pressure values."], "structured": false}
{"doc_id": 25001628, "title": "Comparative gene expression profiling of in vitro differentiated megakaryocytes and erythroblasts identifies novel activatory and inhibitory platelet membrane proteins.", "abstract": ["To identify previously unknown platelet receptors we compared the transcriptomes of in vitro differentiated megakaryocytes (MKs) and erythroblasts (EBs).", "RNA was obtained from purified, biologically paired MK and EB cultures and compared using cDNA microarrays.", "Bioinformatical analysis of MK-up-regulated genes identified 151 transcripts encoding transmembrane domain-containing proteins.", "Although many of these were known platelet genes, a number of previously unidentified or poorly characterized transcripts were also detected.", "Many of these transcripts, including G6b, G6f, LRRC32, LAT2, and the G protein-coupled receptor SUCNR1, encode proteins with structural features or functions that suggest they may be involved in the modulation of platelet function.", "Immunoblotting on platelets confirmed the presence of the encoded proteins, and flow cytometric analysis confirmed the expression of G6b, G6f, and LRRC32 on the surface of platelets.", "Through comparative analysis of expression in platelets and other blood cells we demonstrated that G6b, G6f, and LRRC32 are restricted to the platelet lineage, whereas LAT2 and SUCNR1 were also detected in other blood cells.", "The identification of the succinate receptor SUCNR1 in platelets is of particular interest, because physiologically relevant concentrations of succinate were shown to potentiate the effect of low doses of a variety of platelet agonists."], "structured": false}
{"doc_id": 25007443, "title": "Topographic mapping of VMH \u2192 arcuate nucleus microcircuits and their reorganization by fasting", "abstract": ["In the hypothalamic arcuate nucleus (ARC), pro-opiomelanocortin (POMC) neurons inhibit feeding and neuropeptide-Y (NPY) neurons stimulate feeding.", "We tested whether neurons in the ventromedial hypothalamic nucleus (VMH), a known satiety center, activate anorexigenic neuronal pathways in the ARC by projecting either excitatory synaptic inputs to POMC neurons and/or inhibitory inputs to NPY neurons.", "Using laser scanning photostimulation in brain slices from transgenic mice, we found that POMC and NPY neurons, which are interspersed in the ARC, are nevertheless regulated by anatomically distinct synaptic inputs.", "POMC neurons received strong excitatory input from the medial VMH (mVMH), whereas NPY neurons did not and, instead, received weak inhibitory input only from within the ARC.", "The strength of the excitatory input from the mVMH to POMC neurons was diminished by fasting.", "These data identify a new molecularly defined circuit that is dynamically regulated by nutritional state in a manner consistent with the known role of the VMH as a satiety center."], "structured": false}
{"doc_id": 25014337, "title": "The human immunodeficiency virus type 1 nonnucleoside reverse transcriptase inhibitor resistance mutation I132M confers hypersensitivity to nucleoside analogs.", "abstract": ["We previously identified a rare mutation in human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT), I132M, which confers high-level resistance to the nonnucleoside RT inhibitors (NNRTIs) nevirapine and delavirdine.", "In this study, we have further characterized the role of this mutation in viral replication capacity and in resistance to other RT inhibitors.", "Surprisingly, our data show that I132M confers marked hypersusceptibility to the nucleoside analogs lamivudine (3TC) and tenofovir at both the virus and enzyme levels.", "Subunit-selective mutagenesis studies revealed that the mutation in the p51 subunit of RT was responsible for the increased sensitivity to the drugs, and transient kinetic analyses showed that this hypersusceptibility was due to I132M decreasing the enzyme's affinity for the natural dCTP substrate but increasing its affinity for 3TC-triphosphate.", "Furthermore, the replication capacity of HIV-1 containing I132M is severely impaired.", "This decrease in viral replication capacity could be partially or completely compensated for by the A62V or L214I mutation, respectively.", "Taken together, these results help to explain the infrequent selection of I132M in patients for whom NNRTI regimens are failing and furthermore demonstrate that a single mutation outside of the polymerase active site and inside of the p51 subunit of RT can significantly influence nucleotide selectivity."], "structured": false}
{"doc_id": 25022826, "title": "AFF1 and AFF4 differentially regulate the osteogenic differentiation of human MSCs", "abstract": ["AFF1 and AFF4 belong to the AFF (AF4/FMR2) family of proteins, which function as scaffolding proteins linking two different transcription elongation factors, positive elongation factor b (P-TEFb) and ELL1/2, in super elongation complexes (SECs).", "Both AFF1 and AFF4 regulate gene transcription through elongation and chromatin remodeling.", "However, their function in the osteogenic differentiation of mesenchymal stem cells (MSCs) is unknown.", "In this study, we show that small interfering RNA (siRNA)-mediated depletion of AFF1 in human MSCs leads to increased alkaline phosphatase (ALP) activity, enhanced mineralization and upregulated expression of osteogenic-related genes.", "On the contrary, depletion of AFF4 significantly inhibits the osteogenic potential of MSCs.", "In addition, we confirm that overexpression of AFF1 and AFF4 differentially affects osteogenic differentiation in vitro and MSC-mediated bone formation in vivo.", "Mechanistically, we find that AFF1 regulates the expression of DKK1 via binding to its promoter region.", "Depletion of DKK1 in HA-AFF1-overexpressing MSCs abrogates the impairment of osteogenic differentiation.", "Moreover, we detect that AFF4 is enriched in the promoter region of ID1.", "AFF4 knockdown blunts the BRE luciferase activity, SP7 expression and ALP activity induced by BMP2 treatment.", "In conclusion, our data indicate that AFF1 and AFF4 differentially regulate the osteogenic differentiation of human MSCs."], "structured": false}
{"doc_id": 25028913, "title": "Markers of myocardial damage and inflammation in relation to long-term mortality in unstable coronary artery disease. FRISC Study Group. Fragmin during Instability in Coronary Artery Disease.", "abstract": ["BACKGROUND In patients with unstable coronary artery disease, there is a relation between the short-term risk of death and blood levels of troponin T (a marker of myocardial damage) and C-reactive protein and fibrinogen (markers of inflammation).", "Using information obtained during an extension of the follow-up period in the Fragmin during Instability in Coronary Artery Disease trial, we evaluated the usefulness of troponin T, C-reactive protein, and fibrinogen levels and other indicators of risk as predictors of the long-term risk of death from cardiac causes.   \n", "METHODS Levels of C-reactive protein and fibrinogen at enrollment and the maximal level of troponin T during the first 24 hours after enrollment were analyzed in 917 patients included in a clinical trial of low-molecular-weight heparin in unstable coronary artery disease.", "The patients were followed for a mean of 37.0 months (range, 1.6 to 50.6).   \n", "RESULTS During follow-up, 1.2 percent of the 173 patients with maximal blood troponin T levels of less than 0.06 microg per liter died of cardiac causes, as compared with 8.7 percent of the 367 patients with levels of 0.06 to 0.59 microg per liter and 15.4 percent of the 377 patients with levels of at least 0.60 microg per liter (P=0.007 and P=0.001, respectively).", "The rates of death from cardiac causes were 5.7 percent among the 314 patients with blood C-reactive protein levels of less than 2 mg per liter, 7.8 percent among the 294 with levels of 2 to 10 mg per liter, and 16.5 percent among the 309 with levels of more than 10 mg per liter (P=0.29 and P=0.001, respectively).", "The rates of death from cardiac causes were 5.4 percent among the 314 patients with blood fibrinogen levels of less than 3.4 g per liter, 12.0 percent among the 300 with levels of 3.4 to 3.9 g per liter, and 12.9 percent among the 303 with levels of at least 4.0 g per liter (P=0.004 and P=0.69, respectively).", "In a multivariate analysis, levels of troponin T and C-reactive protein were independent predictors of the risk of death from cardiac causes.   \n", "CONCLUSIONS In unstable coronary artery disease, elevated levels of troponin T and C-reactive protein are strongly related to the long-term risk of death from cardiac causes.", "These markers are independent risk factors, and their effects are additive with respect to each other and other clinical indicators of risk."], "structured": true}
{"doc_id": 25036988, "title": "Loss of lamin B1 results in prolongation of S phase and decondensation of chromosome territories.", "abstract": ["Nuclear lamin B1 (LMNB1) constitutes one of the major structural proteins in the lamina mesh.", "We silenced the expression of LMNB1 by RNA interference in the colon cancer cell line DLD-1 and showed a dramatic redistribution of H3K27me3 from the periphery to a more homogeneous nuclear dispersion.", "In addition, we observed telomere attrition and an increased frequency of micronuclei and nuclear blebs.", "By 3D-FISH analyses, we demonstrated that the volume and surface of chromosome territories were significantly larger in LMNB1-depleted cells, suggesting that LMNB1 is required to maintain chromatin condensation in interphase nuclei.", "These changes led to a prolonged S phase due to activation of Chk1.", "Finally, silencing of LMNB1 resulted in extensive changes in alternative splicing of multiple genes and in a higher number of enlarged nuclear speckles.", "Taken together, our results suggest a mechanistic role of the nuclear lamina in the organization of chromosome territories, maintenance of genome integrity and proper gene splicing."], "structured": false}
{"doc_id": 25041967, "title": "Human artificial chromosomes with alpha satellite-based de novo centromeres show increased frequency of nondisjunction and anaphase lag.", "abstract": ["Human artificial chromosomes have been used to model requirements for human chromosome segregation and to explore the nature of sequences competent for centromere function.", "Normal human centromeres require specialized chromatin that consists of alpha satellite DNA complexed with epigenetically modified histones and centromere-specific proteins.", "While several types of alpha satellite DNA have been used to assemble de novo centromeres in artificial chromosome assays, the extent to which they fully recapitulate normal centromere function has not been explored.", "Here, we have used two kinds of alpha satellite DNA, DXZ1 (from the X chromosome) and D17Z1 (from chromosome 17), to generate human artificial chromosomes.", "Although artificial chromosomes are mitotically stable over many months in culture, when we examined their segregation in individual cell divisions using an anaphase assay, artificial chromosomes exhibited more segregation errors than natural human chromosomes (P < 0.001).", "Naturally occurring, but abnormal small ring chromosomes derived from chromosome 17 and the X chromosome also missegregate more than normal chromosomes, implicating overall chromosome size and/or structure in the fidelity of chromosome segregation.", "As different artificial chromosomes missegregate over a fivefold range, the data suggest that variable centromeric DNA content and/or epigenetic assembly can influence the mitotic behavior of artificial chromosomes."], "structured": false}
{"doc_id": 25045244, "title": "Identification of a human HLA-E-restricted CD8+ T cell subset in volunteers immunized with Salmonella enterica serovar Typhi strain Ty21a typhoid vaccine.", "abstract": ["Our previous studies in volunteers immunized with Salmonella enterica serovar Typhi (S. Typhi) have suggested an important role for CD8+ T cells in host defense.", "In this study we describe a novel subset of nonclassical human HLA-E-restricted S. Typhi-specific CD8+ T cells derived from PBMC of Ty21a typhoid vaccinees.", "CD3+CD8+CD4-CD56- T cells effectively killed S. Typhi-infected targets regardless of whether they share classical HLA class I molecules with them, by a FAS-independent, granule-dependent mechanism, as evidenced by induction of granzyme B release and the blocking effects of concanamycin and strontium ions.", "The expression of HLA-E Ags, but not CD1-a, -b, or -c, on the membrane of S. Typhi-infected targets rendered them susceptible to lysis.", "Moreover, anti-HLA-E Abs partially blocked these responses.", "We also demonstrated that presentation of S. Typhi Ags via HLA-E could stimulate IFN-gamma production.", "Increases in the net frequency of IFN-gamma spot-forming cells were observed in the presence of targets coated with peptides that contain S. Typhi GroEL HLA-E binding motifs.", "These results demonstrate that HLA-E binds nonamer peptides derived from bacterial proteins and trigger CD8+-mediated lysis and IFN-gamma production when exposed to infected targets, raising the possibility that this novel effector mechanism might contribute to host defense against intracellular bacterial infections."], "structured": false}
{"doc_id": 25049067, "title": "Costs and cost-effectiveness of alternative tuberculosis management strategies in South Africa--implications for policy.", "abstract": ["OBJECTIVE To conduct an economic analysis of the Hlabisa community-based directly observed therapy management strategy for tuberculosis and to project costs of three alternative strategies.   \n", "SETTING Hlabisa health district, KwaZulu-Natal, South Africa.   \n", "METHODS An economic analysis comparing the current tuberculosis management strategy in Hlabisa with three alternative strategies (the Hlabisa strategy prior to 1991 based on hospitalisation, the national strategy and sanatorium care) in terms of costs to both health service and patient and of cost-effectiveness.   \n", "RESULTS The current Hlabisa strategy was the most cost-effective (R3799 per patient cured), compared with R98307 for the strategy used prior to 1991, R9940 for the national strategy, and R11145 for sanatorium care.", "Between 71% and 88% of treatment costs lie with the health service, and hospitalisation (R119 per day) is the most expensive item.", "Prolonged hospitalisation is extremely expensive, but community care is cheaper (community clinic visit, R28; community health worker visit, R7).", "The total cost of supervising a patient in the community under the current Hlabisa strategy was R503, equivalent to 4.2 days in hospital.", "Drug costs (R157) are equivalent to just 1.3 days in hospital.   \n", "CONCLUSION Cost to both health service and patient can be substantially reduced by using community-based directly observed therapy for tuberculosis, a strategy that is cheap and cost-effective in Hlabisa.", "These findings have important national implications, supporting the goals of the new tuberculosis control programme."], "structured": true}
{"doc_id": 25050364, "title": "Interleukin-18 null mutation increases weight and food intake and reduces energy expenditure and lipid substrate utilization in high-fat diet fed mice", "abstract": ["OBJECTIVE The proinflammatory cytokine interleukin-18 (IL-18) putatively modulates food intake and energy metabolism, but the effects of IL-18 in high-fat diet fed animals are unknown.", "Whether IL-18 alters basal metabolic rate or metabolic processes of living is unknown.", "Here, we tested the hypothesis that IL-18 modulates weight gain, energy intake, whole-body energy expenditure, and utilization of lipid as a fuel substrate in high-fat diet fed mice.   \n", "METHODS Food intake, whole-body metabolism, and motor activity of IL-18 knockout mice were compared to those of wildtype littermates; anorectic effects of intracerebroventricular IL-18 administration were compared between IL-18 receptor knockout, IL-18/IL-18R knockout and wildtype mice.   \n", "RESULTS Chow-reared IL-18 knockout mice were overweight at 6 months of age and then gained excess weight on both low-fat and high-fat diets, ate more high-fat diet, and showed reduced whole-body energy expenditure and increased respiratory exchange ratios.", "Reductions in energy expenditure of IL-18 knockout mice were seen across fasting vs. feeding conditions, low- vs. high-fat diets, high vs. low levels of physical activity and times of day, suggesting actions on basal metabolic rate.", "The circadian amplitude of energy expenditure, but not respiratory exchange ratio, food intake, or motor activity, also was blunted in IL-18 knockout mice.", "Central IL-18 administration reduced high-fat diet intake in wildtype mice, but not in mice lacking the IL-18 receptor.   \n", "CONCLUSION The loss-of-function results support the hypothesis that endogenous IL-18 suppresses appetite and promote energy expenditure and lipid fuel substrate utilization not only during sickness, but also in healthy adults consuming high-fat diets."], "structured": true}
{"doc_id": 25050969, "title": "Notch activation promotes cell proliferation and the formation of neural stem cell-like colonies in human glioma cells", "abstract": ["Since Notch signaling plays a critical role in stem cells and oncogenesis, we hypothesized that Notch signaling might play roles in cancer stem cells and cancer cells with a stem cell phenotype.", "In this study, we accessed potential functions of the Notch pathway in the formation of cancer stem cells using human glioma.", "Using RT-PCR, we found that most human astrogliomas of different grades expressed moderate to high level of Notch receptors and ligands.", "mRNA of Hes5 but not Hes1, both of which are major downstream molecules of the Notch pathway, was also detected.", "In human glioma cell lines BT325, U251, SHG-44, and U87, mRNA encoding different types of Notch receptors were detected, but active form of Notch1 (NIC) was only detected in SHG-44 and U87 by Western blot.", "Interestingly, proliferation of these two glioma cell lines appeared faster than that of the other two lines in which NIC was not detected.", "We have over-expressed NIC of Notch1 in SHG-44 cells by constitutive transfection to evaluate the effects of Notch signaling on glioma cells.", "Our results showed that over-expression of NIC in SHG-44 cells promoted the growth and the colony-forming activity of SHG-44 cells.", "Interestingly, over-expression of NIC increased the formation neurosphere-like colonies in the presence of growth factors.", "These colonies expressed nestin, and could be induced to cells expressing neuron-, astrocyte-, or oligodendrocyte-specific markers, consistent with phenotypes of neural stem cells.", "These data suggest that Notch signaling promote the formation of cancer stem cell-like cells in human glioma."], "structured": false}
{"doc_id": 25052749, "title": "Rodent models in bone-related research: the relevance of calvarial defects in the assessment of bone regeneration strategies.", "abstract": ["In vivo research with animal models has been a preferred experimental system in bone-related biomedical research since, by approximation, it allows relevant data gathering regarding physiological and pathological conditions that could be of use to establish more effective clinical interventions.", "Animal models, and more specifically rodent models, have been extensively used and have contributed greatly to the development and establishment of a wide range of translational approaches aiming to regenerate the bone tissue.", "In this regard, the calvarial defect model has found great application in basic and applied research, nonetheless the controversial rationalization for the use of critical size defects - defects that are unable to report spontaneous healing - or subcritical size defects in the proposed applications.", "Accordingly, this work aims to review the advantages and limitations of the use of rodent models in biomedical bone-related research, emphasizing the problematic issues of the use of calvarial critical and subcritical size defects.", "Additionally, surgical protocols for the establishment of both defects in rat calvarial bone, as well as the description and exemplification of the most frequently used techniques to access the bone tissue repair, are portrayed."], "structured": false}
{"doc_id": 25062868, "title": "The transcriptional responses of Mycobacterium tuberculosis to inhibitors of metabolism: novel insights into drug mechanisms of action.", "abstract": ["The differential transcriptional response of Mycobacterium tuberculosis to drugs and growth-inhibitory conditions was monitored to generate a data set of 430 microarray profiles.", "Unbiased grouping of these profiles independently clustered agents of known mechanism of action accurately and was successful at predicting the mechanism of action of several unknown agents.", "These predictions were validated biochemically for two agents of previously uncategorized mechanism, pyridoacridones and phenothiazines.", "Analysis of this data set further revealed 150 underlying clusters of coordinately regulated genes offering the first glimpse at the full metabolic potential of this organism.", "A signature subset of these gene clusters was sufficient to classify all known agents as to mechanism of action.", "Transcriptional profiling of both crude and purified natural products can provide critical information on both mechanism and detoxification prior to purification that can be used to guide the drug discovery process.", "Thus, the transcriptional profile generated by a crude marine natural product recapitulated the mechanistic prediction from the pure active component.", "The underlying gene clusters further provide fundamental insights into the metabolic response of bacteria to drug-induced stress and provide a rational basis for the selection of critical metabolic targets for screening for new agents with improved activity against this important human pathogen."], "structured": false}
{"doc_id": 25068298, "title": "Electron microscopic studies of macrophages in early human yolk sacs.", "abstract": ["Distribution and fine structure of macrophages were studied in 10 human embryos in the 6th and 7th week of gestation, 5.5 to 12 mm in crown-rump length.", "The yolk sac macrophages were found in the extravascular mesenchymal tissues and intravascular spaces long before the first appearance of bone marrow and lymphatic tissues in the embryos.", "In addition to the macrophages, the fibroblastic cells and the cells of erythropoietic series were also present in the extravascular space.", "The macrophages showed a variety of cellular structures suggesting transition from immature cell type with no heterophagolysosomes to mature cell type in phagocytosis.", "The mature macrophages avidly phagocytized the primitive erythroblasts and occasionally platelets.", "They were positively stained for lysosomal enzymes and were characterized by numerous pleomorphic heterophagolysosomes which exhibited various stages of digestion of phagocytized blood cells.", "The origin of intravascular macrophages may be in either migrated extravascular macrophages or phagocytic endothelial cells.", "The phagocytosis and degradation of erythroblasts appear to be one of the main functions of yolk sac macrophages.", "The presence of the macrophages in mitosis indicates their proliferation in situ."], "structured": false}
{"doc_id": 25069745, "title": "Urban malaria and anaemia in children: a cross-sectional survey in two cities of Ghana.", "abstract": ["OBJECTIVE To describe the epidemiology of urban malaria, an emerging problem in sub-Saharan Africa.   \n", "METHOD Cross-sectional surveys of communities in Accra and Kumasi, Ghana, determining risk factors for malaria infection and anaemia in children aged 6-60 months.   \n", "RESULTS Malaria prevalence rates ranged from 2% to 33% between urban communities.", "47.1% of children were anaemic (Hb<11.0 g/dl).", "Factors associated with malaria prevalence were low socio-economic status, age and anaemia.", "The attributable risks of anaemia and severe anaemia (Hb<8.0 g/dl) caused by malaria were 5% and 23% respectively.   \n", "CONCLUSIONS Malaria in urban areas displayed a heterogeneity and complexity that differed from the rural environment, which has important implications for malaria control.", "Marked intra-city variation indicates the importance of targeting specific areas or districts.", "The most vulnerable group, the urban poor, should be prioritized when designing control measures.", "This would require careful assessment of the malaria risk pattern in any city to guide an integrated control program."], "structured": true}
{"doc_id": 25079962, "title": "Nitrite infusions to prevent delayed cerebral vasospasm in a primate model of subarachnoid hemorrhage.", "abstract": ["CONTEXT Delayed cerebral vasospasm causes permanent neurological deficits or death in at least 15% of patients following otherwise successful treatment for ruptured intracranial aneurysm.", "Decreased bioavailability of nitric oxide has been associated with the development of cerebral vasospasm.   \n", "OBJECTIVE To determine whether infusions of nitrite will prevent delayed cerebral vasospasm.   \n", "DESIGN, SETTING, AND SUBJECTS A total of 14 anesthetized cynomolgus monkeys had an autologous blood clot placed around the right middle cerebral artery.", "Cerebral arteriography was performed before clot placement and on days 7 and 14 to assess vasospasm.", "The study was conducted from August 2003 to February 2004.   \n", "INTERVENTIONS A 90-mg sodium nitrite intravenous solution infused over 24 hours plus a 45-mg sodium nitrite bolus daily (n = 3); a 180-mg sodium nitrite intravenous solution infused over 24 hours (n = 3); or a control saline solution infusion (n = 8).", "Each was infused continuously for 14 days.   \n", "MAIN OUTCOME MEASURES Nitrite, S-nitrosothiol, and methemoglobin levels in blood and cerebrospinal fluid and degree of arteriographic vasospasm.   \n", "RESULTS In control monkeys, mean (SD) cerebrospinal fluid nitrite levels decreased from 3.1 (1.5) micromol/L to 0.4 (0.1) micromol/L at day 7 and to 0.4 (0.4) micromol/L at day 14 (P = .03).", "All 8 control monkeys developed significant vasospasm of the right middle cerebral artery, which was complicated by stroke and death in 1 animal.", "Sodium nitrite infusions increased the nitrite and methemoglobin levels (<2.1% of total hemoglobin) in the blood and cerebrospinal fluid without evoking systemic hypotension.", "Nitrite infusion prevented development of vasospasm (no animals developed significant vasospasm; mean [SD] reduction in right middle cerebral artery area on day 7 after subarachnoid hemorrhage of 8% [9%] in nitrite-treated monkeys vs 47% [5%] in saline-treated controls; P<.001).", "There was a negative correlation between the concentration of nitrite in cerebrospinal fluid and the degree of cerebral vasospasm (P<.001).", "Pharmacological effects of nitrite infusion were also associated with the formation of S-nitrosothiol in cerebrospinal fluid.", "There was no clinical or pathological evidence of nitrite toxicity.   \n", "CONCLUSION Subacute sodium nitrite infusions prevented delayed cerebral vasospasm in a primate model of subarachnoid hemorrhage."], "structured": true}
{"doc_id": 25085979, "title": "Developmental gene networks: a triathlon on the course to T cell identity", "abstract": ["Cells acquire their ultimate identities by activating combinations of transcription factors that initiate and sustain expression of the appropriate cell type-specific genes.", "T cell development depends on the progression of progenitor cells through three major phases, each of which is associated with distinct transcription factor ensembles that control the recruitment of these cells to the thymus, their proliferation, lineage commitment and responsiveness to T cell receptor signals, all before the allocation of cells to particular effector programmes.", "All three phases are essential for proper T cell development, as are the mechanisms that determine the boundaries between each phase.", "Cells that fail to shut off one set of regulators before the next gene network phase is activated are predisposed to leukaemic transformation."], "structured": false}
{"doc_id": 25089501, "title": "A tumor necrosis factor-\u03b1\u2013mediated pathway promoting autosomal dominant polycystic kidney disease", "abstract": ["Autosomal dominant polycystic kidney disease (ADPKD) is caused by heterozygous mutations in either PKD1 or PKD2, genes that encode polycystin-1 and polycystin-2, respectively.", "We show here that tumor necrosis factor-\u03b1 (TNF-\u03b1), an inflammatory cytokine present in the cystic fluid of humans with ADPKD, disrupts the localization of polycystin-2 to the plasma membrane and primary cilia through a scaffold protein, FIP2, which is induced by TNF-\u03b1.", "Treatment of mouse embryonic kidney organ cultures with TNF-\u03b1 resulted in formation of cysts, and this effect was exacerbated in the Pkd2+/\u2212 kidneys.", "TNF-\u03b1 also stimulated cyst formation in vivo in Pkd2+/\u2212 mice.", "In contrast, treatment of Pkd2+/\u2212 mice with the TNF-\u03b1 inhibitor etanercept prevented cyst formation.", "These data reveal a pathway connecting TNF-\u03b1 signaling, polycystins and cystogenesis, the activation of which may reduce functional polycystin-2 below a critical threshold, precipitating the ADPKD cellular phenotype."], "structured": false}
{"doc_id": 25098790, "title": "Inappropriate inhaler use: assessment of use and patient preference of seven inhalation devices. EDICI.", "abstract": ["Inefficient inhaler technique is a common problem resulting in poor drug delivery, decreased disease control and increased inhaler use.", "The aim of this study was to assess patients' use of different inhaler devices and to ascertain whether patient preference is indicative of ease of use and whether current inhaler use has any influence on either technique or preference.", "We also wished to define the most appropriate method of selecting an inhaler for a patient, taking into account observed technique and device cost.", "One hundred patients received instruction, in randomized order, in the use of seven different inhaler devices.", "After instruction they were graded (using predetermined criteria) in their inhaler technique.", "After assessment patients were asked which three inhalers they most preferred and which, if any, they currently used.", "Technique was best using the breath-actuated inhalers; the Easi-Breathe and Autohaler, with 91% seen to have good technique.", "The pressurized metered dose inhaler (pMDI) fared poorly, in last position with only 79% of patients showing good technique, despite being the most commonly prescribed.", "The Easi-Breathe was by far the most popular device with the patients.", "The Autohaler came in second position closely followed by the Clickhaler and Accuhaler.", "The majority of patients (55%) currently used the pMDI but the pMDI did not score highly for preference or achieve better grades than the other devices.", "Only 79% of patients tested could use the pMDI effectively even after expert instruction yet it continues to be commonly prescribed.", "This has important repercussions for drug delivery and hence disease control.", "Prescribing a patient's preferred device increases cost but can improve efficiency and therefore be cost effective in the long term.", "Using an inexpensive device (pMDI) when technique is good and the patient's preferred inhaler device when not is one way to optimize delivery and may even reduce cost."], "structured": false}
{"doc_id": 25104843, "title": "Hemoperfusion-hemodialysis ineffective for paraquat removal in life-threatening poisoning?", "abstract": ["We report on a patient treated with hemoperfusion-hemodialysis (HP-HD) for severe paraquat poisoning.", "This procedure was adopted since the combination of adsorption and dialysis may improve overall drug removal.", "On admission blood paraquat was 15.8 micrograms/ml.", "He received conventional treatment and combined HP-HD which started within 3 hours after ingestion of the chemical and lasted 5 hours.", "Blood samples were obtained during and after HP-HD.", "The samples during HP-HD were taken before the charcoal column, between the charcoal column and the artificial kidney and after the artificial kidney.", "Blood clearances of paraquat were 116 +/-", "32 ml/min (n=6) for the charcoal column (HP), 90 +/-", "54 ml/min (n=6) for the artificial kidney (HD) and 151 +/-", "37 ml/min (n=6) for the combined systems (HP-HD).", "After HP-HD a limited rebound of blood paraquat level was seen.", "One day after admission renal and hepatic failure had developed, and the patient died after 5 days.", "Tissue paraquat levels (microgram/g wet tissue) were: skeletal muscle 9.4, pancreas 6.0, prostate 5.6, thyroid 4.2, lungs 4.0, bone marrow 4.0, kidney 3.1, spleen 2.9, adrenal 2.9, heart 2.8, liver 2.3, stomach and testis below 1.0.", "Measurements of blood levels demonstrated the efficient clearances of paraquat with HP-HD from the central (plasma) compartment.", "However, the present results confirmed those previously reported which suggest that the efficiency of short HP-HD in treating severe paraquat poisoning is questionable since paraquat levels in the peripheral (tissue) compartment remain elevated."], "structured": false}
{"doc_id": 25121903, "title": "Cancer treatment and survivorship statistics, 2014.", "abstract": ["The number of cancer survivors continues to increase due to the aging and growth of the population and improvements in early detection and treatment.", "In order for the public health community to better serve these survivors, the American Cancer Society and the National Cancer Institute collaborated to estimate the number of current and future cancer survivors using data from the Surveillance, Epidemiology, and End Results (SEER) program registries.", "In addition, current treatment patterns for the most common cancer types are described based on information in the National Cancer Data Base and the SEER and SEER-Medicare linked databases; treatment-related side effects are also briefly described.", "Nearly 14.5 million Americans with a history of cancer were alive on January 1, 2014; by January 1, 2024, that number will increase to nearly 19 million.", "The 3 most common prevalent cancers among males are prostate cancer (43%), colorectal cancer (9%), and melanoma (8%), and those among females are cancers of the breast (41%), uterine corpus (8%), and colon and rectum (8%).", "The age distribution of survivors varies substantially by cancer type.", "For example, the majority of prostate cancer survivors (62%) are aged 70 years or older, whereas less than one-third (32%) of melanoma survivors are in this older age group.", "It is important for clinicians to understand the unique medical and psychosocial needs of cancer survivors and to proactively assess and manage these issues.", "There are a growing number of resources that can assist patients, caregivers, and health care providers in navigating the various phases of cancer survivorship."], "structured": false}
{"doc_id": 25124117, "title": "Massive activation of archaeal defense genes during viral infection.", "abstract": ["Archaeal viruses display unusually high genetic and morphological diversity.", "Studies of these viruses proved to be instrumental for the expansion of knowledge on viral diversity and evolution.", "The Sulfolobus islandicus rod-shaped virus 2 (SIRV2) is a model to study virus-host interactions in Archaea.", "It is a lytic virus that exploits a unique egress mechanism based on the formation of remarkable pyramidal structures on the host cell envelope.", "Using whole-transcriptome sequencing, we present here a global map defining host and viral gene expression during the infection cycle of SIRV2 in its hyperthermophilic host S. islandicus LAL14/1.", "This information was used, in combination with a yeast two-hybrid analysis of SIRV2 protein interactions, to advance current understanding of viral gene functions.", "As a consequence of SIRV2 infection, transcription of more than one-third of S. islandicus genes was differentially regulated.", "While expression of genes involved in cell division decreased, those genes playing a role in antiviral defense were activated on a large scale.", "Expression of genes belonging to toxin-antitoxin and clustered regularly interspaced short palindromic repeat (CRISPR)-Cas systems was specifically pronounced.", "The observed different degree of activation of various CRISPR-Cas systems highlights the specialized functions they perform.", "The information on individual gene expression and activation of antiviral defense systems is expected to aid future studies aimed at detailed understanding of the functions and interplay of these systems in vivo."], "structured": false}
{"doc_id": 25134146, "title": "Impact of human immunodeficiency virus infection on the histological features of chronic hepatitis C: a case-control study. The MULTIVIRC group.", "abstract": ["Hepatitis C virus (HCV) is frequently encountered in human immunodeficiency virus (HIV)-infected patients because of common routes of transmission.", "Previous studies suggested that HIV infection impaired the natural course of chronic hepatitis C, with a more rapid progression to cirrhosis.", "However, these studies did not assess the HIV infection impact on chronic hepatitis C by taking into account the risk factors for liver fibrosis progression: alcohol, sex, age at the contamination, and duration of HCV infection.", "We studied liver biopsy specimens of 2 groups of 58 patients that were infected by both HCV and HIV or by HCV alone.", "The 2 groups were matched according those risk factors, and liver biopsy responses were evaluated with the METAVIR items.", "The METAVIR activity was higher in HIV-positive than HIV-negative patients.", "Cirrhosis was more frequent: (1) in HIV-positive patients with CD4 < or = 200 cells/microL (45%) than in HIV-negative patients (10%) (P = .003), (2) in HIV-positive patients with CD4 < or = 200 cells/microL (45%) than in HIV-positive patients with CD4 > 200 cells/microL (17%) (P = .04).", "These differences, which were linked to HIV status, might be related to the enhanced HCV replication during HIV infection or other immune mechanisms that need further studies."], "structured": false}
{"doc_id": 25135304, "title": "Relation of plasma leptin concentrations to sex, body fat, dietary intake, and peak oxygen uptake in young adult women and men.", "abstract": ["The purpose of this study was to examine the relation of leptin to metabolic and dietary factors in college-age adults.", "Young adult women and men (n = 32) were recruited and underwent testing for measurement of body mass index, body composition, peak oxygen consumption (VO2peak), dietary intake, and plasma levels of leptin and insulin.", "Ln leptin was significantly greater for women than for men (2.1 versus 1.2 ng/mL, respectively).", "This difference remained significant even after adjusting ln leptin for fat mass and fat-free mass as covariates in separate analyses.", "VO2peak was higher for men than for women and this remained significant after adjustment for differences in fat-free mass and total body mass.", "Significant correlations were found between ln leptin and indicators of fat mass in women and men, with higher correlations for similar variables observed in men (r = 0.548, 0.674, and 0.732 for body mass index, percentage of body fat, and fat mass [kg] for women, respectively, and r = 0.740, 0.888, 0.858 for body mass index, percentage of body fat, and fat mass [kg] for men, respectively).", "Ln leptin showed a significant inverse relationship with VO2peak (r = -0.751) in men only.", "After adjusting ln leptin for body fat mass using partial correlations, ln leptin was not significantly associated with any of the measured variables.", "Alternatively, after normalization of ln leptin using fat mass as the divisor, a less adequate statistical analysis method, men showed statistical significant correlations between ln leptin and dietary intake and VO2peak.", "Although plasma leptin values were higher in women, stronger associations were evident for men than for women between leptin and metabolic and dietary factors."], "structured": false}
{"doc_id": 25141908, "title": "Expression of a human cytomegalovirus latency-associated homolog of interleukin-10 during the productive phase of infection.", "abstract": ["The human cytomegalovirus UL111A region is active during both productive and latent phases of infection.", "During productive infection, the virus expresses ORF79, a protein with oncogenic properties, and cmvIL-10, a functional homolog of human IL-10.", "During latent infection of myeloid progenitor cells, an alternately spliced variant of cmvIL-10, termed latency-associated (LA) cmvIL-10 has previously been identified.", "To determine whether LAcmvIL-10 transcription occurs during productive infection, we performed 5' and 3' RACE to map UL111A-region transcripts in productively infected human foreskin fibroblasts (HFFs).", "This analysis revealed the presence of a singly spliced UL111A-region transcript predicted to encode LAcmvIL-10.", "This transcript was expressed in HFFs with early (beta) kinetics, a temporal class that differs from that of ORF79 (alpha kinetics) and cmvIL-10 (gamma kinetics).", "These data identify and map a transcript encoding a latency-associated homolog of IL-10 which is expressed by the virus during the productive phase of infection."], "structured": false}
{"doc_id": 25148216, "title": "Kruppel-like factor 4 is essential for inflammatory monocyte differentiation in vivo.", "abstract": ["Several members of the Kruppel-like factor (KLF) family of transcription factors play important roles in differentiation, survival, and trafficking of blood and immune cell types.", "We demonstrate in this study that hematopoietic cells from KLF4(-/-) fetal livers (FL) contained normal numbers of functional hematopoietic progenitor cells, were radioprotective, and performed as well as KLF4(+/+) cells in competitive repopulation assays.", "However, hematopoietic \"KLF4(-/-) chimeras\" generated by transplantation of KLF4(-/-) fetal livers cells into lethally irradiated wild-type mice completely lacked circulating inflammatory (CD115(+)Gr1(+)) monocytes, and had reduced numbers of resident (CD115(+)Gr1(-)) monocytes.", "Although the numbers and function of peritoneal macrophages were normal in KLF4(-/-) chimeras, bone marrow monocytic cells from KLF4(-/-) chimeras expressed lower levels of key trafficking molecules and were more apoptotic.", "Thus, our in vivo loss-of-function studies demonstrate that KLF4, previously shown to mediate proinflammatory signaling in human macrophages in vitro, is essential for differentiation of mouse inflammatory monocytes, and is involved in the differentiation of resident monocytes.", "In addition, inducible expression of KLF4 in the HL60 human acute myeloid leukemia cell line stimulated monocytic differentiation and enhanced 12-O-tetradecanoylphorbol 13-acetate induced macrophage differentiation, but blocked all-trans-retinoic acid induced granulocytic differentiation of HL60 cells.", "The inflammation-selective effects of loss-of-KLF4 and the gain-of-KLF4-induced monocytic differentiation in HL60 cells identify KLF4 as a key regulator of monocytic differentiation and a potential target for translational immune modulation."], "structured": false}
{"doc_id": 25157790, "title": "A population-based, case\u2013control study of green tea consumption and leukemia risk in southwestern Taiwan", "abstract": ["This study investigated the association between green tea consumption and leukemia.", "A total of 252 cases (90.3% response) and 637 controls (53.4% response) were enrolled.", "Controls were matched for cases on age and gender.", "Information was collected on participants\u2019 living habits, including tea consumption.", "Green tea was used as a standard to estimate the total amount of individual catechin consumption.", "We stratified individual consumption of catechins into four levels.", "Conditional logistic regression models were fit to subjects aged 0\u201315 and 16\u201329 years to evaluate separate associations between leukemia and catechin consumption.", "A significant inverse association between green tea consumption and leukemia risk was found in individuals aged 16\u201329 years, whereas no significant association was found in the younger age groups.", "For the older group with higher amounts of tea consumption (>550 units of catechins), the adjusted odds ratio (OR) compared with the group without tea consumption was 0.47 [95% confidence interval (CI) = 0.23\u20130.97].", "After we adjusted for smoking status and medical irradiation exposure, the overall OR for all participants was 0.49 (95% CI = 0.27\u20130.91), indicating an inverse relation between large amounts of catechins and leukemia.", "Drinking sufficient amounts of tea, especially green tea, which contains more catechins than oolong tea and black tea, may reduce the risk of leukemia."], "structured": false}
{"doc_id": 25175223, "title": "Specific HDV RNA-templated transcription by pol II in vitro.", "abstract": ["RNA polymerase II is implicated in the RNA-templated RNA synthesis during replication of viroids and Hepatitis Delta Virus (HDV); however, neither the RNA template nor protein factor requirements for this process are well defined.", "We have developed an in vitro transcription system based on HeLa cell nuclear extract (NE), in which a segment of antigenomic RNA corresponding to the left-hand tip region of the HDV rod-like structure serves as a template for efficient and highly specific RNA synthesis.", "Accumulation of the unique RNA product is highly sensitive to alpha-amanitin in HeLa NE and only partially sensitive to this drug in NE from PMG cells that contain an allele of the alpha-amanitin-resistant subunit of pol II, strongly suggesting pol II involvement in this reaction.", "Detailed analysis of the RNA product revealed that it represents a chimeric molecule composed of a newly synthesized transcript covalently attached to the 5' half of the RNA template.", "Selection of the start site for transcription is remarkably specific and depends on the secondary structure of the RNA template, rather than on its primary sequence.", "Some features of this reaction resemble the RNA cleavage-extension process observed for pol II-arrested complexes in vitro.", "A possible involvement of the described reaction in HDV replication is discussed."], "structured": false}
{"doc_id": 25175997, "title": "Pulmonary vascular lesions in end-stage idiopathic pulmonary fibrosis: Histopathologic study on lung explant specimens and correlations with pulmonary hemodynamics.", "abstract": ["In patients presenting with idiopathic pulmonary fibrosis (IPF), modifications of pulmonary vessels are well defined in fibrotic areas but have not been accurately assessed in the intervening patches of preserved lung.", "Moreover, the relation between pulmonary vessel lesions and pulmonary hemodynamics is not well known.", "We therefore designed a retrospective study on lung explant specimens from 26 patients with a firm diagnosis of IPF who had undergone lung transplantation.", "Our aim was to (1) describe the vascular lesions, especially in preserved lung areas, and (2) correlate them with pulmonary hemodynamics.", "In dense fibrotic zones, thickening of the arterial and venous wall with severe luminal narrowing was present in each patient.", "In architecturally preserved lung zones, occlusion of venules and small pulmonary veins was observed in 65% of the patients, although there were only mild changes of muscular pulmonary arteries.", "We found a significant positive correlation between the macroscopic extent of lung fibrosis and mean pulmonary artery pressure, but we failed to find a relation between mean pulmonary artery pressure and venous/venular lesions in nonfibrotic areas.", "Our study points out that in many patients with IPF, nonfibrotic lung areas demonstrate an occlusive venopathy, the signification of which remains undetermined."], "structured": false}
{"doc_id": 25182647, "title": "Maternal and perinatal outcome in severe pregnancy-related liver disease.", "abstract": ["Acute fatty liver of pregnancy (AFLP) and the syndrome of hemolysis, elevated liver enzyme levels, and low platelet count (HELLP) are rare but major disorders of the third trimester of pregnancy.", "Over a 10-year period, 46 women (median age, 30 years; range, 17-41 years) developed hepatic dysfunction severe enough to require transfer to our Liver Failure Unit.", "Three quarters of the women were nulliparous, and 5 had twin pregnancies; the median gestational age was 35 weeks (range, 24-40 weeks).", "At admission, 32 patients (70%) were preeclamptic and 21 (46%) were encephalopathic and/or ventilated.", "Thirty-two patients (70%) had clinical features and laboratory values consistent with AFLP, and 7 (15%) had HELLP syndrome.", "One patient had preeclamptic liver rupture requiring liver transplantation.", "In 6 other patients, causes of severe liver dysfunction unrelated to pregnancy were found.", "Infectious complications occurred in 17 of the patients with AFLP (53%) and in 2 of those with HELLP syndrome (29%).", "Major intra-abdominal bleeding occurred in 12 women (10 with AFLP), 9 of whom required laparotomies for clot evacuation.", "Four patients with AFLP (12.5%) had a fatal outcome, with a corresponding perinatal mortality rate of 9%.", "There were no maternal or perinatal deaths associated with HELLP syndrome.", "In contrast to results of many previous studies, the results of this large series suggest a relatively favorable maternal and perinatal outcome in severe AFLP and HELLP syndrome.", "Further improvements in outcome are likely to be achieved through the prevention of the bleeding and infectious complications associated with these disorders."], "structured": false}
{"doc_id": 25183830, "title": "Circadian rhythms and the regulation of metabolic tissue function and energy homeostasis.", "abstract": ["Circadian oscillators play an indispensable role in the coordination of physiological processes with the cyclic changes in the physical environment.", "A significant number of recent clinical and molecular studies suggest that circadian biology may play an important role in the regulation of adipose and other metabolic tissue functions.", "In this discussion, we present the hypothesis that circadian dysfunction may be involved in the pathogenesis of obesity, type 2 diabetes, and the metabolic syndrome."], "structured": false}
{"doc_id": 25186412, "title": "Large-scale gene function analysis with the PANTHER classification system", "abstract": ["The PANTHER (protein annotation through evolutionary relationship) classification system (http://www.pantherdb.org/) is a comprehensive system that combines gene function, ontology, pathways and statistical analysis tools that enable biologists to analyze large-scale, genome-wide data from sequencing, proteomics or gene expression experiments.", "The system is built with 82 complete genomes organized into gene families and subfamilies, and their evolutionary relationships are captured in phylogenetic trees, multiple sequence alignments and statistical models (hidden Markov models or HMMs).", "Genes are classified according to their function in several different ways: families and subfamilies are annotated with ontology terms (Gene Ontology (GO) and PANTHER protein class), and sequences are assigned to PANTHER pathways.", "The PANTHER website includes a suite of tools that enable users to browse and query gene functions, and to analyze large-scale experimental data with a number of statistical tests.", "It is widely used by bench scientists, bioinformaticians, computer scientists and systems biologists.", "In the 2013 release of PANTHER (v.8.0), in addition to an update of the data content, we redesigned the website interface to improve both user experience and the system's analytical capability.", "This protocol provides a detailed description of how to analyze genome-wide experimental data with the PANTHER classification system."], "structured": false}
{"doc_id": 25191216, "title": "Periostin, a novel marker of intramembranous ossification, is expressed in fibrous dysplasia and in c-Fos-overexpressing bone lesions.", "abstract": ["Fibrous dysplasia is a benign bone disease caused by a mutation in the gene for the stimulatory guanine nucleotide-binding protein Gs alpha, leading to high cyclic adenosine monophosphate levels.", "Histologically, fibrous dysplasia is characterized by the production of fibrous tissue accompanied by the deposition of ectopic type I collagen and other bone-associated extracellular matrix proteins, as well as by irregular woven intramembranous bone onto which type I collagen-containing Sharpey fibers are often attached.", "Fibrous dysplasia is also characterized by high expression of c-Fos/c-Jun, known targets for cyclic adenosine monophosphate signaling.", "In this study, we examined the expression of the bone-related extracellular matrix protein, periostin, and its known receptor, integrin alpha v beta 3 (CD51/61), in normal bones as well as in fibrous dysplasia.", "Immunohistochemistry and in situ hybridization studies revealed that periostin was expressed in the extracellular matrix during intramembranous but not endochondral ossification, as well as in the fibrous component of fibrous dysplasia; and all cells adjacent to periostin-positive regions expressed CD51/61.", "Importantly, periostin was abundantly localized to Sharpey fibers.", "To investigate the contribution of c-Fos, we examined transgenic mice overexpressing c-fos, which develop sclerotic lesions closely resembling those found in fibrous dysplasia.", "In all lesions, transformed osteoblasts expressed high levels of periostin, whereas normal osteoblasts did not.", "Our results show that periostin is a novel marker for intramembranous ossification, and is a good candidate as a diagnostic tool and/or a therapeutic target in fibrous dysplasia.", "Moreover, the Gs alpha-cyclic adenosine monophosphate-c-Fos pathway might represent one mechanism of periostin up-regulation in fibrous dysplasia, resulting in altered collagen fibrillogenesis characteristic of this disease."], "structured": false}
{"doc_id": 25238950, "title": "FGF-2 enhances intestinal stem cell survival and its expression is induced after radiation injury.", "abstract": ["Fibroblast growth factors (FGFs) have mitogenic activity toward a wide variety of cells of mesenchymal, neuronal, and epithelial origin and regulate events in normal embryonic development, angiogenesis, wound repair, and neoplasia.", "FGF-2 is expressed in many normal adult tissues and can regulate migration and replication of intestinal epithelial cells in culture.", "However, little is known about the effects of FGF-2 on intestinal epithelial stem cells during either normal epithelial renewal or regeneration of a functional epithelium after injury.", "In this study, we investigated the expression of FGF-2 in the mouse small intestine after irradiation and determined the effect of exogenous FGF-2 on crypt stem cell survival after radiation injury.", "Expression of FGF-2 mRNA and protein began to increase at 12 h after gamma-irradiation, and peak levels were observed from 48 to 120 h after irradiation.", "At all times after irradiation, the higher molecular mass isoform ( approximately 24 kDa) of FGF-2 was the predominant form expressed in the small intestine.", "Immunohistochemical analysis of FGF-2 expression after radiation injury demonstrated that FGF-2 was predominantly found in the mesenchyme surrounding regenerating crypts.", "Exogenous recombinant human FGF-2 (rhFGF-2) markedly enhanced crypt stem cell survival when given before irradiation.", "We conclude that expression of FGF-2 is induced by radiation injury and that rhFGF-2 can enhance crypt stem cell survival after subsequent injury."], "structured": false}
{"doc_id": 25251625, "title": "Caspase inhibitors promote alternative cell death pathways.", "abstract": ["The use of caspase inhibitors has revealed the existence of alternative backup cell death programs for apoptosis.", "The broad-spectrum caspase inhibitor zVAD-fmk modulates the three major types of cell death.", "Addition of zVAD-fmk blocks apoptotic cell death, sensitizes cells to necrotic cell death, and induces autophagic cell death.", "Several studies have shown a crucial role for the kinase RIP1 and the adenosine nucleotide translocator (ANT)-cyclophilin D (CypD) complex in necrotic cell death.", "The underlying mechanism of zVAD-fmk-mediated sensitization to necrotic cell death involves the inhibition of caspase-8-mediated proteolysis of RIP1 and disturbance of the ANT-CypD interaction.", "RIP1 is also involved in autophagic cell death.", "Caspase inhibitors and knockdown studies have revealed negative roles for catalase and caspase-8 in autophagic cell death.", "The positive role of RIP1 and the negative role of caspase-8 in both necrotic and autophagic cell death suggest that the pathways of these two types of cell death are interconnected.", "Necrotic cell death represents a rapid cellular response involving mitochondrial reactive oxygen species (ROS) production, decreased adenosine triphosphate concentration, and other cellular insults, whereas autophagic cell death first starts as a survival attempt by cleaning up ROS-damaged mitochondria.", "However, when this process occurs in excess, autophagy itself becomes cytotoxic and eventually leads to autophagic cell death.", "A better understanding of the molecular mechanisms of these alternative cell death pathways may provide therapeutic tools to combat cell death associated with neurodegenerative diseases, ischemia-reperfusion pathologies, and infectious diseases, and may also facilitate the development of alternative cytotoxic strategies in cancer treatment."], "structured": false}
{"doc_id": 25254425, "title": "Nucleosome stability mediated by histone variants H3.3 and H2A.Z.", "abstract": ["Nucleosomes containing the histone variant H3.3 tend to be clustered in vivo in the neighborhood of transcriptionally active genes and over regulatory elements.", "It has not been clear, however, whether H3.3-containing nucleosomes possess unique properties that would affect transcription.", "We report here that H3.3 nucleosomes isolated from vertebrates, regardless of whether they are partnered with H2A or H2A.Z, are unusually sensitive to salt-dependent disruption, losing H2A/H2B or H2A.Z/H2B dimers.", "Immunoprecipitation studies of nucleosome core particles (NCPs) show that NCPs that contain both H3.3 and H2A.Z are even less stable than NCPs containing H3.3 and H2A.", "Intriguingly, NCPs containing H3 and H2A.Z are at least as stable as H3/H2A NCPs.", "These results establish an hierarchy of stabilities for native nucleosomes carrying different complements of variants, and suggest how H2A.Z could play different roles depending on its partners within the NCP.", "They also are consistent with the idea that H3.3 plays an active role in maintaining accessible chromatin structures in enhancer regions and transcribed regions.", "Consistent with this idea, promoters and enhancers at transcriptionally active genes and coding regions at highly expressed genes have nucleosomes that simultaneously carry both H3.3 and H2A.Z, and should therefore be extremely sensitive to disruption."], "structured": false}
{"doc_id": 25259746, "title": "Increased growth after long-term oral 1alpha,25-vitamin D3 in childhood renal osteodystrophy.", "abstract": ["We evaluated oral 1,25-vitamin D3 for as long as 26 months in six prepubescent children with renal osteodystrophy previously treated with vitamin D2.", "Therapy was given at 14 to 41 ng per kilogram per day to correct hypocalcemia and reverse bone disease.", "Serum levels of 1,25-vitamin D3 were initially reduced at 15 +/-", "5 pg per milliliter (mean +/-", "S.E.M.) and after treatment rose to 54 +/-", "13.", "Serum calcium rose from 7.5 +/-", "1.6 mg per deciliter (mean +/-", "S.D.) to 9.8 +/- 0.6 after one month (P less than 0.02).", "Alkaline phosphatase activity fell from 536 +/-", "298 to 208 +/-", "91 IU per liter after 12 months (P less than 0.05).", "Serum immunoreactive parathyroid levels fell from 900 +/-", "562 microliter eq per milliliter 411 +/-", "377.", "Healing of rickets and subperiosteal erosions was found.", "Remineralization of bone was demonstrated by the photon absorption technic.", "In four patients growth velocity, evaluated for 12 months before and after therapy, increased from 2.6 +/-", "0.8 to 8.0 +/-", "3.2 cm per year.", "Growth velocity per year increased from less than third percentile in each to the 10th to 97th percentile after therapy.", "Height increment ranged from 27 to 113 per cent of that expected for change in chronologic age and 40 to 114 per cent expected for change in bone age after therapy.", "This trial demonstrates that oral 1,25-vitamin D3 can reverse renal bone disease and increase growth in uremic children."], "structured": false}
{"doc_id": 25261168, "title": "Rapid progression of familial amyloidotic polyneuropathy: a multinational natural history study.", "abstract": ["OBJECTIVES To assess the association between severity of neuropathy and disease stage, and estimate the rate of neuropathy progression in a retrospective cross-sectional analysis of a multinational population of patients with familial amyloidotic polyneuropathy (FAP).   \n", "METHODS We characterize neuropathy severity and rate of progression in available patients with FAP in France, the United States, Portugal, and Italy.", "Neuropathy Impairment Scores (NIS), time from symptom onset to NIS measurement, polyneuropathy disability (PND) scores, FAP disease stage, and manual grip strength data were collected.", "We estimated neuropathy progression using Loess Fit and Gompertz Fit models.   \n", "RESULTS For the 283 patients studied (mean age, 56.4 years), intercountry genotypic variation in the transthyretin (TTR) mutation was observed, with the majority of patients in Portugal (92%) having early-onset Val30Met-FAP.", "There was also marked intercountry variation in PND score, FAP stage, and TTR stabilizer use.", "NIS was associated with PND score (NIS 10 and 99 for scores I and IV, respectively; p < 0.0001) and FAP stage (NIS 14 and 99 for stages 1 and 3, respectively; p < 0.0001).", "In addition, there was an association between NIS and TTR genotype.", "The estimated rate of NIS progression for a population with a median NIS of 32 was 14.3 points/year; the corresponding estimated rate for the modified NIS+7 is 17.8 points/year.   \n", "CONCLUSIONS In a multinational population of patients with FAP, rapid neuropathic progression is observed and the severity of neuropathy is associated with functional scales of locomotion."], "structured": true}
{"doc_id": 25263810, "title": "The BRRF1 early gene of Epstein-Barr virus encodes a transcription factor that enhances induction of lytic infection by BRLF1.", "abstract": ["The switch from the latent to the lytic form of Epstein-Barr virus (EBV) infection is mediated by expression of the viral immediate-early (IE) proteins, BZLF1 (Z) and BRLF1 (R).", "An EBV early protein, BRRF1 (Na), is encoded by the opposite strand of the BRLF1 intron, but the function of this nuclear protein in the viral life cycle is unknown.", "Here we demonstrate that Na enhances the R-mediated induction of lytic EBV infection in 293 cells latently infected with a recombinant EBV (R-KO) defective for the expression of both R and Na.", "Na also enhances R-induced lytic infections in a gastric carcinoma line (AGS) carrying the R-KO virus, although it has no effect in a Burkitt lymphoma line (BL-30) stably infected with the same mutant virus.", "We show that Na is a transcription factor that increases the ability of R to activate Z expression from the R-KO viral genome in 293 cells and that Na by itself activates the Z promoter (Zp) in EBV-negative cells.", "Na activation of Zp requires a CRE motif (ZII), and a consensus CRE motif is sufficient to transfer Na responsiveness to the heterologous E1b promoter.", "Furthermore, we show that Na enhances the transactivator function of a Gal4-c-Jun fusion protein but does not increase the transactivator function of other transcription factors (including ATF-1, ATF-2, and CREB) known to bind CRE motifs.", "Na expression in cells results in increased levels of a hyperphosphorylated form of c-Jun, suggesting a mechanism by which Na activates c-Jun.", "Our results indicate that Na is a transcription factor that activates the EBV Zp IE promoter through its effects on c-Jun and suggest that Na cooperates with BRLF1 to induce the lytic form of EBV infection in certain cell types."], "structured": false}
{"doc_id": 25263942, "title": "Stromal p16 expression differentiates endometrial polyp from endometrial hyperplasia", "abstract": ["Endometrial polyps are very common benign endometrial lesions, but their pathogenesis is poorly understood, except for a few studies indicating the possibility of benign stromal neoplasm.", "Although the histopathological diagnosis of endometrial polyp on a surgical specimen is straightforward, it is often difficult to differentiate endometrial polyp from endometrial hyperplasia on a biopsy or curettage specimen.", "Presently, there is no immunohistochemical marker helpful in this differential diagnosis.", "In this study, we examined p16 expression in 35 endometrial polyps and 33 cases of endometrial hyperplasia that included 16 simple hyperplasias, 14 complex atypical hyperplasias, and 3 complex hyperplasias without atypia.", "Stromal p16 expression differed significantly between the two groups; it was seen in 31 (89 %) endometrial polyps, but in only 1 (3 %) endometrial hyperplasia.", "The percentage of p16-positive stromal cells ranged from 10 to 90 % (mean, 47 %) and the positive cells tended to be distributed around glands.", "Six cases of endometrial hyperplasia within an endometrial polyp were also examined and all cases showed stromal p16 expression.", "There was no difference in glandular p16 expression between endometrial polyps 33 (94 %) and hyperplasia 27 (82 %).", "The p16-immunoreactivity was mostly confined to metaplastic epithelial cells in both groups.", "Stromal p16 expression might be a peculiar characteristic of endometrial polyp and constitute a useful marker for the diagnosis, especially in fragmented specimens from biopsy or curettage.", "Stromal p16 expression might be a reflection of p16-induced cellular senescence, which has been documented in several benign mesenchymal neoplasms."], "structured": false}
{"doc_id": 25293616, "title": "A systematic review of mortality in schizophrenia: is the differential mortality gap worsening over time?", "abstract": ["CONTEXT Despite improvements in mental health services in recent decades, it is unclear whether the risk of mortality in schizophrenia has changed over time.   \n", "OBJECTIVE To explore the distribution of standardized mortality ratios (SMRs) for people with schizophrenia.   \n", "DATA SOURCES Broad search terms were used in MEDLINE, PsychINFO, Web of Science, and Google Scholar to identify all studies that investigated mortality in schizophrenia, published between January 1, 1980, and January 31, 2006.", "References were also identified from review articles, reference lists, and communication with authors.   ", "STUDY SELECTION Population-based studies that reported primary data on deaths in people with schizophrenia.   \n", "DATA EXTRACTION Operationalized criteria were used to extract key study features and mortality data.   \n", "DATA SYNTHESIS We examined the distribution of SMRs and pooled selected estimates using random-effects meta-analysis.", "We identified 37 articles drawn from 25 different nations.", "The median SMR for all persons for all-cause mortality was 2.58 (10%-90% quantile, 1.18-5.76), with a corresponding random-effects pooled SMR of 2.50 (95% confidence interval, 2.18-2.43).", "No sex difference was detected.", "Suicide was associated with the highest SMR (12.86); however, most of the major causes-of-death categories were found to be elevated in people with schizophrenia.", "The SMRs for all-cause mortality have increased during recent decades (P = .03).   \n", "CONCLUSIONS With respect to mortality, a substantial gap exists between the health of people with schizophrenia and the general community.", "This differential mortality gap has worsened in recent decades.", "In light of the potential for second-generation antipsychotic medications to further adversely influence mortality rates in the decades to come, optimizing the general health of people with schizophrenia warrants urgent attention."], "structured": true}
{"doc_id": 25293721, "title": "Antioxidant Defenses in the Rat Placenta in Late Gestation: Increased Labyrinthine Expression of Superoxide Dismutases, Glutathione Peroxidase 3, and Uncoupling Protein 21", "abstract": ["Placental oxidative stress plays a key role in the pathophysiology of placenta-related disorders, most notably preeclampsia (PE) and intrauterine growth restriction (IUGR).", "Oxidative stress occurs when accumulation of reactive oxygen species (ROS) damages DNA, proteins and lipids, an outcome that is limited by antioxidant enzymes; mitochondrial uncoupling protein 2 (UCP2) may also limit oxidative stress by reducing ROS production.", "Here we characterized placental antioxidant defenses during normal gestation and following glucocorticoid-induced IUGR.", "Placentas were collected on Days 16 and 22 of normal rat pregnancy (term = Day 23) and at Day 22 after dexamethasone treatment from Day 13.", "Expression of several genes encoding antioxidant enzymes (Sod1, Sod2, Sod3, Cat, Gpx3, Txn1, Txnrd1, Txnrd2, and Txnrd3) and Ucp2 was measured by quantitative RT-PCR in the labyrinth (LZ) and junctional zones (JZ) of the placenta.", "Expression of Sod1 and Ucp2 mRNAs and the activity of xanthine oxidase, a source of ROS, all increased from Days 16 to 22 in both placental zones, whereas Sod2 and Gpx3 increased only in the rapidly growing LZ.", "In contrast, Sod3 and Txnrd1 expression fell in the LZ over this period, whereas total superoxide dismutase activity remained stable.", "Dexamethasone treatment reduced fetal-placental growth and LZ expression of Ucp2 but increased JZ expression of Txn1.", "Indices of placental oxidative damage (TBARS, F2-isoprostanes, and 8-OHdG) did not change with gestational age or dexamethasone, indicative of adequate antioxidant protection.", "Overall, our data suggest that the rat placenta is protected from oxidative stress by the dynamic zone- and stage-dependent expression of antioxidant defense genes."], "structured": false}
{"doc_id": 25298276, "title": "Emerging role of bisphosphonates in the clinic--antitumor activity and prevention of metastasis to bone.", "abstract": ["Bisphosphonates are currently used for the treatment of bone metastases, and emerging data suggest that they may also have antitumor properties.", "Preclinical studies have demonstrated that zoledronic acid can inhibit angiogenesis, invasion and adhesion of tumor cells, and overall tumor progression, and emerging evidence suggests that the use of these agents may impede the development of skeletal metastases.", "In a recent clinical study in patients with metastatic bone disease, basal levels of vascular endothelial growth factor, a factor essential for angiogenesis, were significantly reduced in patients receiving zoledronic acid, suggesting that zoledronic acid may have clinically relevant antiangiogenic properties.", "Early clinical data on prevention of bone metastases by the early-generation bisphosphonate clodronate have yielded promising results in patients with breast cancer, and trials are currently ongoing to assess the efficacy of clodronate in this setting.", "Similarly, the new-generation bisphosphonate zoledronic acid has demonstrated activity in the prevention of bone metastases in small, 18-month pilot studies in patients with high-risk solid tumors (N=40; P=0.0002).", "Similarly, in a separate 5-year trial, the overall survival of patients with multiple myeloma was greater in patients whose standard treatment regimens included zoledronic acid compared with standard treatment alone (P<0.01).", "These encouraging early clinical results supported the initiation of larger randomized trials that are currently ongoing."], "structured": false}
{"doc_id": 25300426, "title": "LIF/STAT3 controls ES cell self-renewal and pluripotency by a Myc-dependent mechanism.", "abstract": ["Murine ES cells can be maintained as a pluripotent, self-renewing population by LIF/STAT3-dependent signaling.", "The downstream effectors of this pathway have not been previously defined.", "In this report, we identify a key target of the LIF self-renewal pathway by showing that STAT3 directly regulates the expression of the Myc transcription factor.", "Murine ES cells express elevated levels of Myc and following LIF withdrawal, Myc mRNA levels collapse and Myc protein becomes phosphorylated on threonine 58 (T58), triggering its GSK3beta dependent degradation.", "Maintained expression of stable Myc (T58A) renders self-renewal and maintenance of pluripotency independent of LIF.", "By contrast, expression of a dominant negative form of Myc antagonizes self-renewal and promotes differentiation.", "Transcriptional control by STAT3 and suppression of T58 phosphorylation are crucial for regulation of Myc activity in ES cells and therefore in promoting self-renewal.", "Together, our results establish a mechanism for how LIF and STAT3 regulate ES cell self-renewal and pluripotency."], "structured": false}
{"doc_id": 25300664, "title": "Chronic renal failure accelerates atherogenesis in apolipoprotein E-deficient mice.", "abstract": ["Cardiovascular mortality is 10 to 20 times increased in patients with chronic renal failure (CRF).", "Risk factors for atherosclerosis are abundant in patients with CRF.", "However, the pathogenesis of cardiovascular disease in CRF remains to be elucidated.", "The effect of CRF on the development of atherosclerosis in apolipoprotein E-deficient male mice was examined.", "Seven-week-old mice underwent 5/6 nephrectomy (CRF, n = 28), unilateral nephrectomy (UNX, n = 24), or no surgery (n = 23).", "Twenty-two weeks later, CRF mice showed increased aortic plaque area fraction (0.266 +/- 0.033 versus 0.045 +/-", "0.006; P < 0.001), aortic cholesterol content (535 +/- 62 versus 100 +/-", "9 nmol/cm(2) intimal surface area; P < 0.001), and aortic root plaque area (205,296 +/-", "22,098 versus 143,662 +/-", "13,302 micro m(2); P < 0.05) as compared with no-surgery mice; UNX mice showed intermediate values.", "The plaques from uremic mice contained CD11b-positive macrophages and showed strong staining for nitrotyrosine.", "Systolic BP and plasma homocysteine concentrations were similar in uremic and nonuremic mice.", "Plasma urea and cholesterol concentrations were elevated 2.6-fold (P < 0.001) and 1.5-fold (P < 0.001) in CRF compared with no-surgery mice.", "Both variables correlated with aortic plaque area fraction (r(2) = 0.5, P < 0.001 and r(2) = 0.3, P < 0.001, respectively) and with each other (r(2) = 0.5, P < 0.001).", "On multiple linear regression analysis, only plasma urea was a significant predictor of aortic plaque area fraction.", "In conclusion, the present findings suggest that uremia markedly accelerates atherogenesis in apolipoprotein E-deficient mice.", "This effect could not be fully explained by changes in BP, plasma homocysteine levels, or total plasma cholesterol concentrations.", "Thus, the CRF apolipoprotein E-deficient mouse is a new model for studying the pathogenesis of accelerated atherosclerosis in uremia."], "structured": false}
{"doc_id": 25301182, "title": "Left ventricular function and exercise capacity.", "abstract": ["CONTEXT Limited information exists regarding the role of left ventricular function in predicting exercise capacity and impact on age- and sex-related differences.   \n", "OBJECTIVES To determine the impact of measures of cardiac function assessed by echocardiography on exercise capacity and to determine if these associations are modified by sex or advancing age.   \n", "DESIGN Cross-sectional study of patients undergoing exercise echocardiography with routine measurements of left ventricular systolic and diastolic function by 2-dimensional and Doppler techniques.", "Analyses were conducted to determine the strongest correlates of exercise capacity and the age and sex interactions of these variables with exercise capacity.   \n", "SETTING Large tertiary referral center in Rochester, Minnesota, in 2006.   \n", "PARTICIPANTS Patients undergoing exercise echocardiography using the Bruce protocol (N = 2867).", "Patients with echocardiographic evidence of exercise-induced ischemia, ejection fractions lower than 50%, or significant valvular heart disease were excluded.   \n", "MAIN OUTCOME MEASURE Exercise capacity in metabolic equivalents (METs).   \n", "RESULTS Diastolic dysfunction was strongly and inversely associated with exercise capacity.", "Compared with normal function, after multivariate adjustment, those with moderate/severe resting diastolic dysfunction (-1.30 METs; 95% confidence interval [CI], -1.52 to -0.99; P < .001) and mild resting diastolic dysfunction (-0.70 METs; 95% CI, -0.88 to -0.46; P < .001) had substantially lower exercise capacity.", "Variation of left ventricular systolic function within the normal range was not associated with exercise capacity.", "Left ventricular filling pressures measured by resting E/e' of 15 or greater (-0.41 METs; 95% CI, -0.70 to -0.11; P = .007) or postexercise E/e' of 15 or greater (-0.41 METs; 95% CI, -0.71 to -0.11; P = .007) were similarly associated with a reduction in exercise capacity, each in separate multivariate analyses.", "Individuals with impaired relaxation (mild dysfunction) or resting E/e' of 15 or greater had a progressive increase in the magnitude of reduction in exercise capacity with advancing age (P < .001 and P = .02, respectively).", "Other independent correlates of exercise capacity were age (unstandardized beta coefficient, -0.85 METs; 95% CI, -0.92 to -0.77, per 10-year increment; P < .001), female sex (-1.98 METs; 95% CI, -2.15 to -1.84; P < .001), and body mass index greater than 30 (-1.24 METs; 95% CI, -1.41 to -1.10; P < .001).   \n", "CONCLUSION In this large cross-sectional study of those referred for exercise echocardiography and not limited by ischemia, abnormalities of left ventricular diastolic function were independently associated with exercise capacity."], "structured": true}
{"doc_id": 25308734, "title": "A dynamic population model to investigate effects of climate on geographic range and seasonality of the tick Ixodes scapularis.", "abstract": ["A dynamic population model of Ixodes scapularis, the vector of a number of tick-borne zoonoses in North America, was developed to simulate effects of temperature on tick survival and seasonality.", "Tick development rates were modelled as temperature-dependent time delays, calculated using mean monthly normal temperature data from specific meteorological stations.", "Temperature also influenced host-finding success in the model.", "Using data from stations near endemic populations of I. scapularis, the model reached repeatable, stable, cyclical equilibria with seasonal activity of different instars being very close to that observed in the field.", "In simulations run using data from meteorological stations in central and eastern Canada, the maximum equilibrium numbers of ticks declined the further north was the station location, and simulated populations died out at more northerly stations.", "Tick die-out at northern latitudes was due to a steady increase in mortality of all life stages with decreasing temperature rather than a specific threshold event in phenology of one life stage.", "By linear regression we investigated mean annual numbers of degree-days >0 degrees C (DD>0 degrees C) as a readily mapped index of the temperature conditions at the meteorological stations providing temperature data for the model.", "Maximum numbers of ticks at equilibrium were strongly associated with the mean DD>0 degrees C (r2>0.96, P<0.001), when the Province of origin of the meteorological station was accounted for (Quebec>Ontario, beta=103, P<0.001).", "The intercepts of the regression models provided theoretical limits for the establishment of I. scapularis in Canada.", "Maps of these limits suggested that the range of southeast Canada where temperature conditions are currently suitable for the tick, is much wider than the existing distribution of I. scapularis, implying that there is potential for spread.", "Future applications of the model in investigating climate change effects on I. scapularis are discussed."], "structured": false}
{"doc_id": 25315295, "title": "Inflammatory cytokines in depression: neurobiological mechanisms and therapeutic implications.", "abstract": ["Mounting evidence indicates that inflammatory cytokines contribute to the development of depression in both medically ill and medically healthy individuals.", "Cytokines are important for development and normal brain function, and have the ability to influence neurocircuitry and neurotransmitter systems to produce behavioral alterations.", "Acutely, inflammatory cytokine administration or activation of the innate immune system produces adaptive behavioral responses that promote conservation of energy to combat infection or recovery from injury.", "However, chronic exposure to elevated inflammatory cytokines and persistent alterations in neurotransmitter systems can lead to neuropsychiatric disorders and depression.", "Mechanisms of cytokine behavioral effects involve activation of inflammatory signaling pathways in the brain that results in changes in monoamine, glutamate, and neuropeptide systems, and decreases in growth factors, such as brain-derived neurotrophic factor.", "Furthermore, inflammatory cytokines may serve as mediators of both environmental (e.g. childhood trauma, obesity, stress, and poor sleep) and genetic (functional gene polymorphisms) factors that contribute to depression's development.", "This review explores the idea that specific gene polymorphisms and neurotransmitter systems can confer protection from or vulnerability to specific symptom dimensions of cytokine-related depression.", "Additionally, potential therapeutic strategies that target inflammatory cytokine signaling or the consequences of cytokines on neurotransmitter systems in the brain to prevent or reverse cytokine effects on behavior are discussed."], "structured": false}
{"doc_id": 25319221, "title": "Sputum inflammation predicts exacerbations after cessation of inhaled corticosteroids in COPD.", "abstract": ["INTRODUCTION The GOLD guidelines advocate not to institute inhaled corticosteroids (ICS) in patients with mild-to-moderate COPD.", "However, many patients do use ICS and in some patients, withdrawal is associated with deteriorating lung function and increased exacerbation rates.", "Unfortunately, physicians do not know in which patients they can stop ICS treatment safely.   ", "AIM To identify predictors of COPD exacerbations after ICS withdrawal.   \n", "METHODS During ICS treatment, post-bronchodilator spirometry, body plethysmography, and health status assessment were performed in 68 COPD patients using ICS.", "Additionally, sputum cell differentials, supernatant leukotriene B(4), eosinophilic cationic protein, and myeloperoxidase, serum C-reactive protein and soluble intracellular adhesion molecule, and urinary desmosine were assessed.", "Sputum was also analysed for mRNA levels of haemoxygenase-1, tumour necrosis factor-\u03b1, RANTES, interleukin 5(IL-5), IL-10, IL-12, IL-13, transforming growth factor-\u03b2, and interferon-\u03b3.   ", "STATISTICS Cox regression analyses were performed using time to exacerbation as outcome variable to identify significant hazards for a COPD exacerbation after ICS withdrawal.   \n", "RESULTS Higher sputum % eosinophils, higher sputum MPO/neutrophil level, longer duration of COPD symptoms, <40 packyears smoking, and ICS withdrawal in November, December or January were significant hazards (all p<0.05) for experiencing a COPD exacerbation after ICS withdrawal in a monovariate model.", "In a multivariate model, all factors proved independent predictors except for sputum MPO/neutrophil level.   \n", "CONCLUSIONS Decisions on whether or not inhaled corticosteroids can be safely withdrawn in mild-to-moderate COPD can be facilitated by assessment of sputum inflammation, particularly eosinophil numbers, next to packyears smoking, season, and duration of COPD symptoms."], "structured": true}
{"doc_id": 25328476, "title": "Peroxisome proliferator-activated receptor alpha activation decreases metastatic potential of melanoma cells in vitro via down-regulation of Akt.", "abstract": ["PURPOSE Peroxisome proliferator-activated receptors (PPAR) regulate lipid and glucose metabolism but their anticancer properties have been recently studied as well.", "We previously reported the antimetastatic activity of the PPARalpha ligand, fenofibrate, against melanoma tumors in vivo.", "Here we investigated possible molecular mechanisms of fenofibrate anti metastatic action.   ", "EXPERIMENTAL DESIGN Monolayer cultures of mouse (B16F10) and human (SkMell88) melanoma cell lines, soft agar assay, and cell migration assay were used in this study.", "In addition, we analyzed PPARalpha expression and its transcriptional activity in response to fenotibrate by using Western blots and liciferase-based reporter system.   \n", "RESULTS Fenofibrate inhibited migration of B16F10 and SkMel188 cells in Transwell chambers and colony formation in soft agar.", "These effects were reversed by PPAR inhibitor, GW9662.", "Western blot analysis revealed time-dependent down-regulation of Akt and extracellular signal-regulated kinase l/2 phosphorylation in fenofibrate-treated cells.", "A B16F10 cell line stably expressing constitutively active Akt mutant was resistant to fenofibrate.", "In contrast, Akt gene silencing with siRNA mimicked the fenofibrate action and reduced the migratory ability of B16F1O cells.", "In addition, fenofibrate strongly sensitized BI6FIO cells to the proapoptotic drug staurosporine, further supporting the possibility that fenofibrate-induced down-regulation of Akt function contributes to fenofibrate-mediated inhibition of metastatic potential in this experimental model.   \n", "CONCLUSIONS Our results show that the PPAR-dependent antimetastatic activity of fenofibrate involves down-regulation of Akt phosphorylation and suggest that supplementation with this drug may improve the effectiveness of melanoma chemotherapy."], "structured": true}
{"doc_id": 25344732, "title": "PHC3, a component of the hPRC-H complex, associates with E2F6 during G0 and is lost in osteosarcoma tumors", "abstract": ["Polyhomeotic-like 3 (PHC3) is a ubiquitously expressed member of the polycomb gene family and part of the human polycomb complex hPRC-H. We found that in normal cells PHC3 associated with both hPRC-H complex components and with the transcription factor E2F6.", "In differentiating and confluent cells, PHC3 and E2F6 showed nuclear colocalization in a punctate pattern that resembled the binding of polycomb bodies to heterochromatin.", "This punctate pattern was not seen in proliferating cells suggesting that PHC3 may be part of an E2F6-polycomb complex that has been shown to occupy and silence target promoters in G0.", "Previous loss of heterozygosity (LoH) analyses had shown that the region containing PHC3 underwent frequent LoH in primary human osteosarcoma tumors.", "When we examined normal bone and human osteosarcoma tumors, we found loss of PHC3 expression in 36 of 56 osteosarcoma tumors.", "Sequence analysis revealed that PHC3 was mutated in nine of 15 primary osteosarcoma tumors.", "These findings suggest that loss of PHC3 may favor tumorigenesis by potentially disrupting the ability of cells to remain in G0."], "structured": false}
{"doc_id": 25353658, "title": "Germinal center T follicular helper cell IL-4 production is dependent on signaling lymphocytic activation molecule receptor (CD150).", "abstract": ["CD4 T cell help is critical for the generation and maintenance of germinal centers (GCs), and T follicular helper (T(FH)) cells are the CD4 T cell subset required for this process.", "Signaling lymphocytic activation molecule (SLAM)-associated protein (SAP [SH2D1A]) expression in CD4 T cells is essential for GC development.", "However, SAP-deficient mice have only a moderate defect in T(FH) differentiation, as defined by common T(FH) surface markers.", "CXCR5(+) T(FH) cells are found within the GC, as well as along the boundary regions of T/B cell zones.", "In this study, we show that GC-associated T follicular helper (GC T(FH)) cells can be identified by their coexpression of CXCR5 and the GL7 epitope, allowing for phenotypic and functional analysis of T(FH) and GC T(FH) populations.", "GC T(FH) cells are a functionally discrete subset of further polarized T(FH) cells, with enhanced B cell help capacity and a specialized ability to produce IL-4 in a T(H)2-independent manner.", "Strikingly, SAP-deficient mice have an absence of the GC T(FH) cell subset and SAP(-) T(FH) cells are defective in IL-4 and IL-21 production.", "We further demonstrate that SLAM (Slamf1, CD150), a surface receptor that uses SAP signaling, is specifically required for IL-4 production by GC T(FH) cells.", "GC T(FH) cells require IL-4 and -21 production for optimal help to B cells.", "These data illustrate complexities of SAP-dependent SLAM family receptor signaling, revealing a prominent role for SLAM receptor ligation in IL-4 production by GC CD4 T cells but not in T(FH) cell and GC T(FH) cell differentiation."], "structured": false}
{"doc_id": 25355575, "title": "High cardiovascular mortality in Russia cannot be explained by the classical risk factors. The Arkhangelsk study 2000", "abstract": ["Since the beginning of the 1990s the public health situation in Russia has been characterized by an extremely high mortality and a significant reduction in life expectancy.", "Cardiovascular diseases remained the major cause of death.", "Only a few large population studies were conducted in Russia during this period.", "A total of 1968 men and 1737 women aged 18\u201375 years participated in a health survey in Arkhangelsk, Russia, over the period 1999\u20132000.", "Investigation included assessment of classic cardiovascular risk factors (family history, smoking, blood pressure, and blood lipids) along with general health variables.", "The paper presents sex specific data on risk factors for coronary heart disease.", "Though the cardiovascular mortality is high in Russia, the calculated risk for coronary heart disease (the Framingham risk score and the Norwegian risk score) was lower in all age groups of men and women in Arkhangelsk compared with studies from the Western Europe and USA.", "Our data suggest that high cardiovascular mortality in Russia may be driven not only by the classic risk factors for coronary heart disease."], "structured": false}
{"doc_id": 25365522, "title": "Wnt7a/Fzd7 Signalling Directly Activates the Akt/mTOR Anabolic Growth Pathway in Skeletal Muscle", "abstract": ["Wnt7a signals through its receptor Fzd7 to activate the planar-cell-polarity pathway and drive the symmetric expansion of satellite stem cells resulting in enhanced repair of skeletal muscle.", "In differentiated myofibres, we observed that Wnt7a binding to Fzd7 directly activates the Akt/mTOR growth pathway, thereby inducing myofibre hypertrophy.", "Notably, the Fzd7 receptor complex was associated with G\u03b1(s) and PI(3)K and these components were required for Wnt7a to activate the Akt/mTOR growth pathway in myotubes.", "Wnt7a-Fzd7 activation of this pathway was completely independent of IGF-receptor activation.", "Together, these experiments demonstrate that Wnt7a-Fzd7 activates distinct pathways at different developmental stages during myogenic lineage progression, and identify a non-canonical anabolic signalling pathway for Wnt7a and its receptor Fzd7 in skeletal muscle."], "structured": false}
{"doc_id": 25373397, "title": "Four newly located pseudouridylate residues in Escherichia coli 23S ribosomal RNA are all at the peptidyltransferase center: analysis by the application of a new sequencing technique.", "abstract": ["A new technique has been developed for the facile location of pseudouridylate (psi) residues in any RNA molecule.", "The method uses two known modification procedures which in combination uniquely identify U residues which have been converted into psi.", "The first procedure involves reaction of all U-like and G-like residues with N-cyclohexyl-N'-beta-(4-methylmorpholinium)ethylcarbodiimide p-tosylate (CMC), followed by alkaline removal of all CMC groups except those linked to the N3 of psi.", "This stops reverse transcription, resulting in a gel band which identifies the U residue.", "The second procedure is uridine-specific hydrazinolysis which cleaves the RNA chain at all U residues and produces a gel band upon reverse transcription.", "psi residues, being resistant to hydrazinolysis, are not cleaved and do not stop reverse transcription.", "This leads to the absence of a band at psi residues.", "The combined method can also distinguish psi from 5-methyluridine, 4-thiouridine, uridine-5-oxyacetic acid, and 2-thio-5-methylaminomethyluridine as shown by treating rRNA and tRNA species known to contain these modified bases at defined sites.", "By this procedure, four new sites for psi in Escherichia coli 23S RNA were discovered, and one was disproven.", "The four new sites are at positions 2457, 2504, 2580, and 2605.", "The erroneous site is at position 2555.", "These four new psi residues, which are all in or within 2-3 residues of the peptidyltransferase ring, are thus in a position to play a functional and/or structural role at the peptidyltransferase center.(ABSTRACT TRUNCATED AT 250 WORDS)"], "structured": false}
{"doc_id": 25388309, "title": "Pharmacological characterization of 1-(5-chloro-6-(trifluoromethoxy)-1H-benzoimidazol-2-yl)-1H-pyrazole-4-carboxylic acid (JNJ-42041935), a potent and selective hypoxia-inducible factor prolyl hydroxylase inhibitor.", "abstract": ["The hypoxia-inducible factor (HIF) prolyl hydroxylase (PHD) enzymes represent novel targets for the treatment of anemia, ulcerative colitis, and ischemic and metabolic disease inter alia.", "We have identified a novel small-molecule inhibitor of PHD, 1-(5-chloro-6-(trifluoromethoxy)-1H-benzoimidazol-2-yl)-1H-pyrazole-4-carboxylic acid (JNJ-42041935), through structure-based drug design methods.", "The pharmacology of JNJ-42041935 was investigated in enzyme, cellular, and whole-animal systems and was compared with other compounds described in the literature as PHD inhibitors.", "JNJ-42041935, was a potent (pK(I) = 7.3-7.9), 2-oxoglutarate competitive, reversible, and selective inhibitor of PHD enzymes.", "In addition, JNJ-42041935 was used to compare the effect of selective inhibition of PHD to intermittent, high doses (50 \u03bcg/kg i.p.) of an exogenous erythropoietin receptor agonist in an inflammation-induced anemia model in rats.", "JNJ-42041935 (100 \u03bcmol/kg, once a day for 14 days) was effective in reversing inflammation-induced anemia, whereas erythropoietin had no effect.", "The results demonstrate that JNJ-42041935 is a new pharmacological tool, which can be used to investigate PHD inhibition and demonstrate that PHD inhibitors offer great promise for the treatment of inflammation-induced anemia."], "structured": false}
{"doc_id": 25404036, "title": "Three-Dimensional Modeling and Quantitative Analysis of Gap Junction Distributions in Cardiac Tissue", "abstract": ["Gap junctions play a fundamental role in intercellular communication in cardiac tissue.", "Various types of heart disease including hypertrophy and ischemia are associated with alterations of the spatial arrangement of gap junctions.", "Previous studies applied two-dimensional optical and electron-microscopy to visualize gap junction arrangements.", "In normal cardiomyocytes, gap junctions were primarily found at cell ends, but can be found also in more central regions.", "In this study, we extended these approaches toward three-dimensional reconstruction of gap junction distributions based on high-resolution scanning confocal microscopy and image processing.", "We developed methods for quantitative characterization of gap junction distributions based on analysis of intensity profiles along the principal axes of myocytes.", "The analyses characterized gap junction polarization at cell ends and higher-order statistical image moments of intensity profiles.", "The methodology was tested in rat ventricular myocardium.", "Our analysis yielded novel quantitative data on gap junction distributions.", "In particular, the analysis demonstrated that the distributions exhibit significant variability with respect to polarization, skewness, and kurtosis.", "We suggest that this methodology provides a quantitative alternative to current approaches based on visual inspection, with applications in particular in characterization of engineered and diseased myocardium.", "Furthermore, we propose that these data provide improved input for computational modeling of cardiac conduction."], "structured": false}
{"doc_id": 25413327, "title": "Clonally derived human embryonic stem cell lines maintain pluripotency and proliferative potential for prolonged periods of culture.", "abstract": ["Embryonic stem (ES) cell lines derived from human blastocysts have the developmental potential to form derivatives of all three embryonic germ layers even after prolonged culture.", "Here we describe the clonal derivation of two human ES cell lines, H9.1 and H9.2.", "At the time of the clonal derivation of the H9.1 and H9.2 ES cell lines, the parental ES cell line, H9, had already been continuously cultured for 6 months.", "After an additional 8 months of culture, H9.1 and H9.2 ES cell lines continued to: (1) actively proliferate, (2) express high levels of telomerase, and (3) retain normal karyotypes.", "Telomere lengths, while somewhat variable, were maintained between 8 and 12 kb in high-passage H9.1 and H9.2 cells.", "High-passage H9.1 and H9.2 cells both formed teratomas in SCID-beige mice that included differentiated derivatives of all three embryonic germ layers.", "These results demonstrate the pluripotency of single human ES cells, the maintenance of pluripotency during an extended period of culture, and the long-term self-renewing properties of cultured human ES cells.", "The remarkable developmental potential, proliferative capacity, and karyotypic stability of human ES cells distinguish them from adult cells."], "structured": false}
{"doc_id": 25416944, "title": "Autosomal dominant lateral temporal epilepsy: two families with novel mutations in the LGI1 gene.", "abstract": ["PURPOSE Mutations in the leucine rich, glioma inactivated gene (LGI1) were recently described in a small number of families with autosomal dominant lateral temporal epilepsy (ADLTE).", "ADLTE is characterized by partial seizures with symptoms suggestive of a lateral temporal onset, including frequent auditory aura.", "Here we report the results of clinical and genetic analyses of two newly identified families with ADTLE.   \n", "METHODS We identified two families whose seizure semiology was suggestive of ADLTE.", "Evaluation included a detailed history and neurologic examination, as well as collection of DNA.", "The coding sequence of the LGI1 gene from affected subjects from both families was analyzed for evidence of mutation.   \n", "RESULTS Each patient had a history of partial seizures, often with secondary generalization earlier in the course.", "Auditory aura was reported by approximately two thirds of affected patients in each pedigree.", "Novel mutations in LGI1 were detected in both families.", "A heterozygous single-nucleotide deletion at position 329 (del 329C) was detected in affected individuals from one family, whereas patients from the second family had a nonsynonymous variation, corresponding to C435G.   \n", "CONCLUSIONS We identified two novel mutations in the LGI1 gene.", "The phenotype of these two families was similar to that of other kindreds with ADLTE, as auditory aura was absent in one third of affected individuals.", "Our results further support that LGI1 mutations should be considered in patients with a history of partial seizures if the semiology of seizures is consistent with the onset in the lateral temporal lobe."], "structured": true}
{"doc_id": 25419778, "title": "Identification of Senescent Cells in the Bone Microenvironment.", "abstract": ["Cellular senescence is a fundamental mechanism by which cells remain metabolically active yet cease dividing and undergo distinct phenotypic alterations, including upregulation of p16Ink4a , profound secretome changes, telomere shortening, and decondensation of pericentromeric satellite DNA.", "Because senescent cells accumulate in multiple tissues with aging, these cells and the dysfunctional factors they secrete, termed the senescence-associated secretory phenotype (SASP), are increasingly recognized as promising therapeutic targets to prevent age-related degenerative pathologies, including osteoporosis.", "However, the cell type(s) within the bone microenvironment that undergoes senescence with aging in vivo has remained poorly understood, largely because previous studies have focused on senescence in cultured cells.", "Thus in young (age 6 months) and old (age 24 months) mice, we measured senescence and SASP markers in vivo in highly enriched cell populations, all rapidly isolated from bone/marrow without in vitro culture.", "In both females and males, p16Ink4a expression by real-time quantitative polymerase chain reaction (rt-qPCR) was significantly higher with aging in B cells, T cells, myeloid cells, osteoblast progenitors, osteoblasts, and osteocytes.", "Further, in vivo quantification of senescence-associated distension of satellites (SADS), ie, large-scale unraveling of pericentromeric satellite DNA, revealed significantly more senescent osteocytes in old compared with young bone cortices (11% versus 2%, p < 0.001).", "In addition, primary osteocytes from old mice had sixfold more (p < 0.001) telomere dysfunction-induced foci (TIFs) than osteocytes from young mice.", "Corresponding with the age-associated accumulation of senescent osteocytes was significantly higher expression of multiple SASP markers in osteocytes from old versus young mice, several of which also showed dramatic age-associated upregulation in myeloid cells.", "These data show that with aging, a subset of cells of various lineages within the bone microenvironment become senescent, although senescent myeloid cells and senescent osteocytes predominantly develop the SASP.", "Given the critical roles of osteocytes in orchestrating bone remodeling, our findings suggest that senescent osteocytes and their SASP may contribute to age-related bone loss.", "\u00a9 2016 American Society for Bone and Mineral Research."], "structured": false}
{"doc_id": 25420421, "title": "Changes in white blood cells and platelets in children with falciparum malaria: relationship to disease outcome.", "abstract": ["Little is known about the changes in white blood cells and platelets in children with falciparum malaria in endemic areas.", "We measured the white cell count (WCC) and platelets of 230 healthy children from the community, 1369 children admitted to hospital with symptomatic malaria, and 1461 children with other medical conditions.", "Children with malaria had a higher WCC compared with community controls, and leucocytosis was strongly associated with younger age, deep breathing, severe anaemia, thrombocytopenia and death.", "The WCC was not associated with a positive blood culture.", "In children with malaria, high lymphocyte and low monocyte counts were independently associated with mortality.", "A platelet count of less than 150 x 109/l was found in 56.7% of children with malaria, and was associated with age, prostration and parasite density, but not with bleeding problems or mortality.", "The mean platelet volume was also higher in children with malaria compared with other medical conditions.", "This may reflect early release from the bone marrow in response to peripheral platelet destruction.", "Thus, leucocytosis was associated with both severity and mortality in children with falciparum malaria, irrespective of bacteraemia, whereas thrombocytopenia, although very common, was not associated with adverse outcome."], "structured": false}
{"doc_id": 25435456, "title": "Microenvironmental regulation of biomacromolecular therapies", "abstract": ["There is currently great interest in molecular therapies to treat various diseases, and this has prompted extensive efforts to achieve target-specific and controlled delivery of bioactive macromolecules (for example, proteins, antibodies, DNA and small interfering RNA) through the design of smart drug carriers.", "By contrast, the influence of the microenvironment in which the target cell resides and the effect it might have on the success of biomacromolecular therapies has been under-appreciated.", "The extracellular matrix (ECM) component of the cellular niche may be particularly important, as many diseases and injury disrupt the normal ECM architecture, the cell adhesion to ECM, and the subsequent cellular activities.", "This Review will discuss the importance of the ECM and the ECM\u2013cell interactions on the cell response to bioactive macromolecules, and suggest how this information could lead to new criteria for the design of novel drug delivery systems."], "structured": false}
{"doc_id": 25439264, "title": "Homocysteine Induces Trophoblast Cell Death with Apoptotic Features1", "abstract": ["Abstract Hyperhomocysteinemia has been suggested as a possible risk factor in women suffering from habitual abortions, placental abruption or infarcts, preeclampsia, and/or intrauterine growth retardation.", "However, little is known about the pathogenic mechanisms underlying the action of homocysteine.", "The present study investigated the in vitro ability of homocysteine to affect trophoblast gonadotropin secretion and to induce cell death.", "In primary human trophoblast cells, homocysteine treatment (20 \u03bcmol/L) resulted in cellular flattening and enlargement, extension of pseudopodia, and cellular vacuolization.", "Cellular detachment, apoptosis, and necrosis were favored.", "With in situ nick end labeling, we investigated DNA degradation, and we used M30 CytoDEATH to selectively stain the cytoplasm of apoptotic cells.", "Cytochrome c release from mitochondria to the cytosol and DNA cleavage in agarose gel have been investigated.", "Homocysteine, but not cysteine, induced trophoblast apoptosis and significantly reduced human chorionic gonadotropin secretion.", "These findings suggest that trophoblast cell death might represent a pathogenic mechanism by which homocysteine may cause pregnancy complications related to placental diseases."], "structured": false}
{"doc_id": 25440070, "title": "Intrahippocampal administration of an androgen receptor antagonist, flutamide, can increase anxiety-like behavior in intact and DHT-replaced male rats.", "abstract": ["Testosterone (T) and its 5alpha-reduced metabolite, dihydrotestosterone (DHT), can decrease anxiety-like behavior; however, the mechanisms underlying these effects have not been established.", "First, we hypothesized that if T reduces anxiety-like behavior through actions of its 5alpha-reduced metabolite, DHT, then gonadectomy (GDX) would increase anxiety-like behavior, an effect which would be reversed by systemic administration of DHT.", "Second, we hypothesized that if T and DHT reduce anxiety-like behavior in part through actions at intracellular androgen receptors in the hippocampus, then administration of an androgen receptor antagonist, flutamide, directly to the hippocampus should increase anxiety-like behavior of intact and DHT-replaced, but not GDX, male rats.", "Inserts that were empty or contained flutamide were applied directly to the dorsal hippocampus of intact, GDX, or GDX and DHT-replaced rats 2 h prior to testing in the open field, elevated plus maze, or defensive freezing tasks.", "GDX rats exhibited significantly more anxiety-like behaviors than intact or DHT-replaced rats.", "Intact and DHT-replaced rats administered flutamide to the hippocampus showed significantly more anxiety-like behavior than did intact and DHT-replaced controls.", "However, flutamide alone did not increase anxiety-like behavior of GDX rats.", "Together, these findings suggest that androgens can decrease anxiety-like behavior of male rats in part through DHT's actions at androgen receptors in the hippocampus."], "structured": false}
{"doc_id": 25451374, "title": "Cardiovascular risk and events in 17 low-, middle-, and high-income countries.", "abstract": ["BACKGROUND More than 80% of deaths from cardiovascular disease are estimated to occur in low-income and middle-income countries, but the reasons are unknown.   \n", "METHODS We enrolled 156,424 persons from 628 urban and rural communities in 17 countries (3 high-income, 10 middle-income, and 4 low-income countries) and assessed their cardiovascular risk using the INTERHEART Risk Score, a validated score for quantifying risk-factor burden without the use of laboratory testing (with higher scores indicating greater risk-factor burden).", "Participants were followed for incident cardiovascular disease and death for a mean of 4.1 years.   \n", "RESULTS The mean", "INTERHEART Risk Score was highest in high-income countries, intermediate in middle-income countries, and lowest in low-income countries (P<0.001).", "However, the rates of major cardiovascular events (death from cardiovascular causes, myocardial infarction, stroke, or heart failure) were lower in high-income countries than in middle- and low-income countries (3.99 events per 1000 person-years vs. 5.38 and 6.43 events per 1000 person-years, respectively; P<0.001).", "Case fatality rates were also lowest in high-income countries (6.5%, 15.9%, and 17.3% in high-, middle-, and low-income countries, respectively; P=0.01).", "Urban communities had a higher risk-factor burden than rural communities but lower rates of cardiovascular events (4.83 vs. 6.25 events per 1000 person-years, P<0.001) and case fatality rates (13.52% vs. 17.25%, P<0.001).", "The use of preventive medications and revascularization procedures was significantly more common in high-income countries than in middle- or low-income countries (P<0.001).   \n", "CONCLUSIONS Although the risk-factor burden was lowest in low-income countries, the rates of major cardiovascular disease and death were substantially higher in low-income countries than in high-income countries.", "The high burden of risk factors in high-income countries may have been mitigated by better control of risk factors and more frequent use of proven pharmacologic therapies and revascularization.", "(Funded by the Population Health Research Institute and others.)."], "structured": true}
{"doc_id": 25452937, "title": "Increased density of tumor-associated macrophages is associated with decreased survival in advanced thyroid cancer.", "abstract": ["Thyroid cancers are infiltrated with tumor-associated macrophages (TAMs), yet their role in cancer progression is not known.", "The objectives of this study were to characterize the density of TAMs in well-differentiated (WDTC), poorly differentiated (PDTC), and anaplastic thyroid cancers (ATC) and to correlate TAM density with clinicopathologic parameters.", "Immunohistochemistry was performed on tissue microarray sections from WDTC (n=33), PDTC (n=37), and ATC (n=20) using macrophage-specific markers.", "Electronic medical records were used to gather clinical and pathologic data.", "Follow-up information of PDTC patients was available for 0-12 years.", "In total, 9 out of 33 WDTC (27%), 20 out of 37 PDTC (54%), and 19 out of 20 ATC (95%) had an increased density of CD68(+) TAMs (> or = 10 per 0.28 mm(2); WDTC versus PDTC, P=0.03; WDTC versus ATC, P<0.0001; PDTC versus ATC, P<0.002).", "Increased TAMs in PDTC was associated with capsular invasion (P=0.034), extrathyroidal extension (P=0.009), and decreased cancer-related survival (P=0.009) compared with PDTC with a low density of TAMs.", "In conclusion, the density of TAMs is increased in advanced thyroid cancers.", "The presence of a high density of TAMs in PDTC correlates with invasion and decreased cancer-related survival.", "These results suggest that TAMs may facilitate tumor progression.", "As novel therapies directed against thyroid tumor cell-specific targets are being tested, the potential role of TAMs as potential modulators of the thyroid cancer behavior will need to be considered."], "structured": false}
{"doc_id": 25453683, "title": "Blockade of Tim-1 and Tim-4 Enhances Atherosclerosis in Low-Density Lipoprotein Receptor-Deficient Mice.", "abstract": ["OBJECTIVE T cell immunoglobulin and mucin domain (Tim) proteins are expressed by numerous immune cells, recognize phosphatidylserine on apoptotic cells, and function as costimulators or coinhibitors.", "Tim-1 is expressed by activated T cells but is also found on dendritic cells and B cells.", "Tim-4, present on macrophages and dendritic cells, plays a critical role in apoptotic cell clearance, regulates the number of phosphatidylserine-expressing activated T cells, and is genetically associated with low low-density lipoprotein and triglyceride levels.", "Because these functions of Tim-1 and Tim-4 could affect atherosclerosis, their modulation has potential therapeutic value in cardiovascular disease.   ", "APPROACH AND RESULTS ldlr(-/-) mice were fed a high-fat diet for 4 weeks while being treated with control (rat immunoglobulin G1) or anti-Tim-1 (3D10) or -Tim-4 (21H12) monoclonal antibodies that block phosphatidylserine recognition and phagocytosis.", "Both anti-Tim-1 and anti-Tim-4 treatments enhanced atherosclerosis by 45% compared with controls by impairment of efferocytosis and increasing aortic CD4(+)T cells.", "Consistently, anti-Tim-4-treated mice showed increased percentages of activated T cells and late apoptotic cells in the circulation.", "Moreover, in vitro blockade of Tim-4 inhibited efferocytosis of oxidized low-density lipoprotein-induced apoptotic macrophages.", "Although anti-Tim-4 treatment increased T helper cell (Th)1 and Th2 responses, anti-Tim-1 induced Th2 responses but dramatically reduced the percentage of regulatory T cells.", "Finally, combined blockade of Tim-1 and Tim-4 increased atherosclerotic lesion size by 59%.   \n", "CONCLUSIONS Blockade of Tim-4 aggravates atherosclerosis likely by prevention of phagocytosis of phosphatidylserine-expressing apoptotic cells and activated T cells by Tim-4-expressing cells, whereas Tim-1-associated effects on atherosclerosis are related to changes in Th1/Th2 balance and reduced circulating regulatory T cells."], "structured": true}
{"doc_id": 25462689, "title": "Genetic and physical analysis of double-strand break repair and recombination in Saccharomyces cerevisiae.", "abstract": ["We have investigated HO endonuclease-induced double-strand break (DSB) recombination and repair in a LACZ duplication plasmid in yeast.", "A 117-bp MATa fragment, embedded in one copy of LACZ, served as a site for initiation of a DSB when HO endonuclease was expressed.", "The DSB could be repaired using wild-type sequences located on a second, promoterless, copy of LACZ on the same plasmid.", "In contrast to normal mating-type switching, crossing-over associated with gene conversion occurred at least 50% of the time.", "The proportion of conversion events accompanied by exchange was greater when the two copies of LACZ were in direct orientation (80%), than when inverted (50%).", "In addition, the fraction of plasmids lost was significantly greater in the inverted orientation.", "The kinetics of appearance of intermediates and final products were also monitored.", "The repair of the DSB is slow, requiring at least an hour from the detection of the HO-cut fragments to completion of repair.", "Surprisingly, the appearance of the two reciprocal products of crossing over did not occur with the same kinetics.", "For example, when the two LACZ sequences were in the direct orientation, the HO-induced formation of a large circular deletion product was not accompanied by the appearance of a small circular reciprocal product.", "We suggest that these differences may reflect two kinetically separable processes, one involving only one cut end and the other resulting from the concerted participation of both ends of the DSB."], "structured": false}
{"doc_id": 25475802, "title": "Nitroxergic nerves mediate vagally induced relaxation in the isolated stomach of the guinea pig.", "abstract": ["Here we show that the relaxation induced by stimulation of the vagus nerve in the presence of cholinergic (muscarinic) and adrenergic blockade in the isolated stomach of the guinea pig is mediated by nitric oxide (NO).", "This is substantiated by inhibition of vagal relaxation by NG-monomethyl-L-arginine, an inhibitor of NO synthesis.", "The effect of NG-monomethyl-L-arginine was partially reversed by coincubation with L-arginine but not with D-arginine.", "NO activates soluble guanylate cyclase, and relaxation of the stomach induced by vagal stimulation was prevented by an inhibitor of soluble guanylate cyclase, methylene blue, further supporting our conclusions.", "The relaxant effect of vagal stimulation was also ablated by hexamethonium, an inhibitor of ganglionic nicotinic receptors, thereby showing that ganglionic transmission did not rely on NO, through its release from preganglionic neurons.", "However, hexamethonium did not inhibit the gastric relaxation brought about by increasing the intragastric pressure, which is also mediated by NO as previously described by us.", "The selective inhibition by hexamethonium of only the vagally mediated relaxation but not of the pressure-induced relaxation of the stomach indicates the existence of at least two separate neuronal pathways able to generate NO and bring about gastric accommodation of food or fluid."], "structured": false}
{"doc_id": 25479072, "title": "Efficient T cell activation requires an optimal dwell-time of interaction between the TCR and the pMHC complex", "abstract": ["Cytotoxic T cell (CTL) activation by antigen requires the specific detection of peptide\u2013major histo-compatibility class I (pMHC) molecules on the target-cell surface by the T cell receptor (TCR).", "We examined the effect of mutations in the antigen-binding site of a Kb-restricted TCR on T cell activation, antigen binding and dissociation from antigen.", "These parameters were also examined for variants derived from a Kd-restricted peptide that was recognized by a CTL clone.", "Using these two independent systems, we show that T cell activation can be impaired by mutations that either decrease or increase the binding half-life of the TCR-pMHC interaction.", "Our data indicate that efficient T cell activation occurs within an optimal dwell-time range of TCR-pMHC interaction.", "This restricted dwell-time range is consistent with the exclusion of either extremely low or high affinity T cells from the expanded population during immune responses."], "structured": false}
{"doc_id": 25483562, "title": "Crystal structure of human insulin-regulated aminopeptidase with specificity for cyclic peptides.", "abstract": ["Insulin-regulated aminopeptidase (IRAP or oxytocinase) is a membrane-bound zinc-metallopeptidase that cleaves neuroactive peptides in the brain and produces memory enhancing effects when inhibited.", "We have determined the crystal structure of human IRAP revealing a closed, four domain arrangement with a large, mostly buried cavity abutting the active site.", "The structure reveals that the GAMEN exopeptidase loop adopts a very different conformation from other aminopeptidases, thus explaining IRAP's unique specificity for cyclic peptides such as oxytocin and vasopressin.", "Computational docking of a series of IRAP-specific cognitive enhancers into the crystal structure provides a molecular basis for their structure-activity relationships and demonstrates that the structure will be a powerful tool in the development of new classes of cognitive enhancers for treating a variety of memory disorders such as Alzheimer's disease."], "structured": false}
{"doc_id": 25488034, "title": "Glutathione and glutathione-dependent enzymes represent a co-ordinately regulated defence against oxidative stress.", "abstract": ["Increases in the intracellular levels of reactive oxygen species (ROS), frequently referred to as oxidative stress, represents a potentially toxic insult which if not counteracted will lead to membrane dysfunction, DNA damage and inactivation of proteins.", "Chronic oxidative stress has numerous pathological consequences including cancer, arthritis and neurodegenerative disease.", "Glutathione-associated metabolism is a major mechanism for cellular protection against agents which generate oxidative stress.", "It is becoming increasingly apparent that the glutathione tripeptide is central to a complex multifaceted detoxification system, where there is substantial inter-dependence between separate component members.", "Glutathione participates in detoxification at several different levels, and may scavenge free radicals, reduce peroxides or be conjugated with electrophilic compounds.", "Thus, glutathione provides the cell with multiple defences not only against ROS but also against their toxic products.", "This article discusses how glutathione biosynthesis, glutathione peroxidases, glutathione S-transferases and glutathione S-conjugate efflux pumps function in an integrated fashion to allow cellular adaption to oxidative stress.", "Co-ordination of this response is achieved, at least in part, through the antioxidant responsive element (ARE) which is found in the promoters of many of the genes that are inducible by oxidative and chemical stress.", "Transcriptional activation through this enhancer appears to be mediated by basic leucine zipper transcription factors such as Nrf and small Maf proteins.", "The nature of the intracellular sensor(s) for ROS and thiol-active chemicals which induce genes through the ARE is described.", "Gene activation through the ARE appears to account for the enhanced antioxidant and detoxification capacity of normal cells effected by many cancer chemopreventive agents.", "In certain instances it may also account for acquired resistance of tumours to cancer chemotherapeutic drugs.", "It is therefore clear that determining the mechanisms involved in regulation of ARE-driven gene expression has enormous medical implications."], "structured": false}
{"doc_id": 25493293, "title": "Does socioeconomic status matter? A meta-analysis on parent training effectiveness for disruptive child behavior.", "abstract": ["Disadvantaged family socioeconomic status (SES) is often assumed to diminish parent training program effectiveness.", "In examining effects of SES, influences of initial problem severity have been largely ignored.", "In the present meta-analysis, we examined (a) whether there is a differential influence of SES on parent training effectiveness at immediate posttreatment and at 1-year follow-up-controlling for levels of initial problem severity--and (b) whether SES interacts with initial problem severity in its effect on program effectiveness.", "Seventy-five studies on parent training program effectiveness to reduce disruptive child behavior were included.", "Separate analyses were conducted for immediate posttreatment and approximately 1-year follow-up assessments.", "Immediately posttreatment, disadvantaged samples benefited less from parent training, but only when they had low levels of initial problem severity.", "At follow-up, disadvantaged samples benefited less from parent training regardless of initial problem severity.", "Initial problem severity was a strong predictor of effect sizes both immediately posttreatment and at follow-up.", "Parent training programs are equally effective for disadvantaged and nondisadvantaged families immediately posttreatment, at least when initial problems are severe.", "Maintenance of treatment gain, however, seems harder for disadvantaged families, suggesting that more sustained family support may be needed."], "structured": false}
{"doc_id": 25499612, "title": "Infectiousness of malaria-endemic human populations to vectors.", "abstract": ["Despite its key role in determining the stability and intensity of malaria transmission, the infectiousness of human populations to mosquitoes has rarely been estimated.", "Field-based analyses of malaria transmission have frequently relied on the prevalence of asexual parasites or gametocytes as proxies for infectiousness.", "We now summarize empirical data on human infectiousness from Africa and Papua New Guinea.", "Over a wide range of transmission intensities there is little relationship between the infectiousness of human populations to vector mosquitoes and mosquito-to-human transmission intensity.", "We compare these data with the predictions of a stochastic simulation model of Plasmodium falciparum epidemiology.", "This model predicted little variation in the infectiousness of the human population for entomologic inoculation rates (EIRs) greater than approximately 10 infectious bites per year, demonstrating that the lack of relationship between the EIR and the infectious reservoir can be explained without invoking any effects of acquired transmission-blocking immunity.", "The near absence of field data from areas with an EIR < 10 per year precluded validation of the model predictions for low EIR values.", "These results suggest that interventions reducing mosquito-to-human transmission will have little or no effect on human infectiousness at the levels of transmission found in most rural areas of sub-Saharan Africa.", "Unless very large reductions in transmission can be achieved, measures to prevent mosquito-to-human transmission need to be complemented with interventions that reduce the density or infectiousness of blood stage parasites."], "structured": false}
{"doc_id": 25504006, "title": "Molecular analysis of circulating tumour cells\u2014biology and biomarkers", "abstract": ["Growing evidence for intratumour heterogeneity informs us that single-site biopsies fall short of revealing the complete genomic landscape of a tumour.", "With an expanding repertoire of targeted agents entering the clinic, screening tumours for genomic aberrations is increasingly important, as is interrogating the tumours for resistance mechanisms upon disease progression.", "Multiple biopsies separated spatially and temporally are impractical, uncomfortable for the patient and not without risk.", "Here, we describe how circulating tumour cells (CTCs), captured from a minimally invasive blood test\u2014and readily amenable to serial sampling\u2014have the potential to inform intratumour heterogeneity and tumour evolution, although it remains to be determined how useful this will be in the clinic.", "Technologies for detecting and isolating CTCs include the validated CellSearch\u00ae system, but other technologies are gaining prominence.", "We also discuss how recent CTC discoveries map to mechanisms of haematological spread, previously described in preclinical models, including evidence for epithelial\u2013mesenchymal transition, collective cell migration and cells with tumour-initiating capacity within the circulation.", "Advances in single-cell molecular analysis are enhancing our ability to explore mechanisms of metastasis, and the combination of CTC and cell-free DNA assays are anticipated to provide invaluable blood-borne biomarkers for real-time patient monitoring and treatment stratification."], "structured": false}
{"doc_id": 25510546, "title": "Endoplasmic reticulum stress contributes to beta cell apoptosis in type 2 diabetes", "abstract": ["Increased lipid supply causes beta cell death, which may contribute to reduced beta cell mass in type 2 diabetes.", "We investigated whether endoplasmic reticulum (ER) stress is necessary for lipid-induced apoptosis in beta cells and also whether ER stress is present in islets of an animal model of diabetes and of humans with type 2 diabetes.", "Expression of genes involved in ER stress was evaluated in insulin-secreting MIN6 cells exposed to elevated lipids, in islets isolated from db/db mice and in pancreas sections of humans with type 2 diabetes.", "Overproduction of the ER chaperone heat shock 70 kDa protein 5 (HSPA5, previously known as immunoglobulin heavy chain binding protein [BIP]) was performed to assess whether attenuation of ER stress affected lipid-induced apoptosis.", "We demonstrated that the pro-apoptotic fatty acid palmitate triggers a comprehensive ER stress response in MIN6 cells, which was virtually absent using non-apoptotic fatty acid oleate.", "Time-dependent increases in mRNA levels for activating transcription factor 4 (Atf4), DNA-damage inducible transcript 3 (Ddit3, previously known as C/EBP homologous protein [Chop]) and DnaJ homologue (HSP40) C3 (Dnajc3, previously known as p58) correlated with increased apoptosis in palmitate- but not in oleate-treated MIN6 cells.", "Attenuation of ER stress by overproduction of HSPA5 in MIN6 cells significantly protected against lipid-induced apoptosis.", "In islets of db/db mice, a variety of marker genes of ER stress were also upregulated.", "Increased processing (activation) of X-box binding protein 1 (Xbp1) mRNA was also observed, confirming the existence of ER stress.", "Finally, we observed increased islet protein production of HSPA5, DDIT3, DNAJC3 and BCL2-associated X protein in human pancreas sections of type 2 diabetes subjects.", "Our results provide evidence that ER stress occurs in type 2 diabetes and is required for aspects of the underlying beta cell failure."], "structured": false}
{"doc_id": 25513319, "title": "Coactivator SRC-2-dependent metabolic reprogramming mediates prostate cancer survival and metastasis.", "abstract": ["Metabolic pathway reprogramming is a hallmark of cancer cell growth and survival and supports the anabolic and energetic demands of these rapidly dividing cells.", "The underlying regulators of the tumor metabolic program are not completely understood; however, these factors have potential as cancer therapy targets.", "Here, we determined that upregulation of the oncogenic transcriptional coregulator steroid receptor coactivator 2 (SRC-2), also known as NCOA2, drives glutamine-dependent de novo lipogenesis, which supports tumor cell survival and eventual metastasis.", "SRC-2 was highly elevated in a variety of tumors, especially in prostate cancer, in which SRC-2 was amplified and overexpressed in 37% of the metastatic tumors evaluated.", "In prostate cancer cells, SRC-2 stimulated reductive carboxylation of \u03b1-ketoglutarate to generate citrate via retrograde TCA cycling, promoting lipogenesis and reprogramming of glutamine metabolism.", "Glutamine-mediated nutrient signaling activated SRC-2 via mTORC1-dependent phosphorylation, which then triggered downstream transcriptional responses by coactivating SREBP-1, which subsequently enhanced lipogenic enzyme expression.", "Metabolic profiling of human prostate tumors identified a massive increase in the SRC-2-driven metabolic signature in metastatic tumors compared with that seen in localized tumors, further implicating SRC-2 as a prominent metabolic coordinator of cancer metastasis.", "Moreover, SRC-2 inhibition in murine models severely attenuated the survival, growth, and metastasis of prostate cancer.", "Together, these results suggest that the SRC-2 pathway has potential as a therapeutic target for prostate cancer."], "structured": false}
{"doc_id": 25515662, "title": "In vitro substrate specificity of protein tyrosine kinases", "abstract": ["Synthetic peptides such as P60stc autophosphorylation site peptides and angiotensin are indiscriminately phosphorylated by protein tyrosine kinases.", "The observation has led to the general belief that protein tyrosine kinases are highly promiscuous, displaying littlein vitro site specificity.", "In recent years, evidence has been accumulating to indicate that such a belief requires close examination.", "Synthetic peptides showing high substrate activity for specific groups of protein tyrosine kinases have been obtained.", "Systematic modification of certain substrate peptides suggests that kinase substrate determinants reside with specific amino acid residues proximal to the target tyrosine.", "A number of protein kinases have been shown to be regulated by tyrosine phosphorylation at specific sites by highly specific protein tyrosine kinases.", "These and other selected biochemical studies that contribute to the evolving view ofin vitro substrate specificity of protein tyrosine kinases are reviewed."], "structured": false}
{"doc_id": 25515907, "title": "Relative effectiveness of clinic and home blood pressure monitoring compared with ambulatory blood pressure monitoring in diagnosis of hypertension: systematic review", "abstract": ["OBJECTIVE To determine the relative accuracy of clinic measurements and home blood pressure monitoring compared with ambulatory blood pressure monitoring as a reference standard for the diagnosis of hypertension.   \n", "DESIGN Systematic review with meta-analysis with hierarchical summary receiver operating characteristic models.", "Methodological quality was appraised, including evidence of validation of blood pressure measurement equipment.   \n", "DATA SOURCES Medline (from 1966), Embase (from 1980), Cochrane Database of Systematic Reviews, DARE, Medion, ARIF, and TRIP up to May 2010.", "Eligibility criteria for selecting studies Eligible studies examined diagnosis of hypertension in adults of all ages using home and/or clinic blood pressure measurement compared with those made using ambulatory monitoring that clearly defined thresholds to diagnose hypertension.   \n", "RESULTS The 20 eligible studies used various thresholds for the diagnosis of hypertension, and only seven studies (clinic) and three studies (home) could be directly compared with ambulatory monitoring.", "Compared with ambulatory monitoring thresholds of 135/85 mm Hg, clinic measurements over 140/90 mm Hg had mean sensitivity and specificity of 74.6% (95% confidence interval 60.7% to 84.8%) and 74.6% (47.9% to 90.4%), respectively, whereas home measurements over 135/85 mm Hg had mean sensitivity and specificity of 85.7% (78.0% to 91.0%) and 62.4% (48.0% to 75.0%).   \n", "CONCLUSIONS Neither clinic nor home measurement had sufficient sensitivity or specificity to be recommended as a single diagnostic test.", "If ambulatory monitoring is taken as the reference standard, then treatment decisions based on clinic or home blood pressure alone might result in substantial overdiagnosis.", "Ambulatory monitoring before the start of lifelong drug treatment might lead to more appropriate targeting of treatment, particularly around the diagnostic threshold."], "structured": true}
{"doc_id": 25516011, "title": "Purification and characterization of mouse hematopoietic stem cells.", "abstract": ["Mouse bone marrow hematopoietic stem cells were isolated with the use of a variety of phenotypic markers.", "These cells can proliferate and differentiate with approximately unit efficiency into myelomonocytic cells, B cells, or T cells.", "Thirty of these cells are sufficient to save 50 percent of lethally irradiated mice, and to reconstitute all blood cell types in the survivors."], "structured": false}
{"doc_id": 25519138, "title": "Regulation of arabinose and xylose metabolism in Escherichia coli.", "abstract": ["Bacteria such as Escherichia coli will often consume one sugar at a time when fed multiple sugars, in a process known as carbon catabolite repression.", "The classic example involves glucose and lactose, where E. coli will first consume glucose, and only when it has consumed all of the glucose will it begin to consume lactose.", "In addition to that of lactose, glucose also represses the consumption of many other sugars, including arabinose and xylose.", "In this work, we characterized a second hierarchy in E. coli, that between arabinose and xylose.", "We show that, when grown in a mixture of the two pentoses, E. coli will consume arabinose before it consumes xylose.", "Consistent with a mechanism involving catabolite repression, the expression of the xylose metabolic genes is repressed in the presence of arabinose.", "We found that this repression is AraC dependent and involves a mechanism where arabinose-bound AraC binds to the xylose promoters and represses gene expression.", "Collectively, these results demonstrate that sugar utilization in E. coli involves multiple layers of regulation, where cells will consume first glucose, then arabinose, and finally xylose.", "These results may be pertinent in the metabolic engineering of E. coli strains capable of producing chemical and biofuels from mixtures of hexose and pentose sugars derived from plant biomass."], "structured": false}
{"doc_id": 25523969, "title": "MicroRNA expression profiling of human metastatic cancers identifies cancer gene targets.", "abstract": ["Small non-coding microRNAs (miRNAs) contribute to cancer development and progression, and are differentially expressed in normal tissues and cancers.", "However, the specific role of miRNAs in the metastatic process is still unknown.", "To seek a specific miRNA expression signature characterizing the metastatic phenotype of solid tumours, we performed a miRNA microarray analysis on 43 paired primary tumours (ten colon, ten bladder, 13 breast, and ten lung cancers) and one of their related metastatic lymph nodes.", "We identified a metastatic cancer miRNA signature comprising 15 overexpressed and 17 underexpressed miRNAs.", "Our results were confirmed by qRT-PCR analysis.", "Among the miRNAs identified, some have a well-characterized association with cancer progression, eg miR-10b, miR-21, miR-30a, miR-30e, miR-125b, miR-141, miR-200b, miR-200c, and miR-205.", "To further support our data, we performed an immunohistochemical analysis for three well-defined miRNA gene targets (PDCD4, DHFR, and HOXD10 genes) on a small series of paired colon, breast, and bladder cancers, and one of their metastatic lymph nodes.", "We found that the immunohistochemical expression of these targets significantly follows the corresponding miRNA deregulation.", "Our results suggest that specific miRNAs may be directly involved in cancer metastasis and that they may represent a novel diagnostic tool in the characterization of metastatic cancer gene targets."], "structured": false}
{"doc_id": 25536577, "title": "Circos: an information aesthetic for comparative genomics.", "abstract": ["We created a visualization tool called Circos to facilitate the identification and analysis of similarities and differences arising from comparisons of genomes.", "Our tool is effective in displaying variation in genome structure and, generally, any other kind of positional relationships between genomic intervals.", "Such data are routinely produced by sequence alignments, hybridization arrays, genome mapping, and genotyping studies.", "Circos uses a circular ideogram layout to facilitate the display of relationships between pairs of positions by the use of ribbons, which encode the position, size, and orientation of related genomic elements.", "Circos is capable of displaying data as scatter, line, and histogram plots, heat maps, tiles, connectors, and text.", "Bitmap or vector images can be created from GFF-style data inputs and hierarchical configuration files, which can be easily generated by automated tools, making Circos suitable for rapid deployment in data analysis and reporting pipelines."], "structured": false}
{"doc_id": 25543207, "title": "Pharmacokinetic, pharmacodynamic and clinical profile of novel antiplatelet drugs targeting vascular diseases.", "abstract": ["Platelet inhibitors are the mainstay treatment for patients with vascular diseases.", "The current 'gold standard' antiplatelet agent clopidogrel has several pharmacological and clinical limitations that have prompted the search for more effective platelet antagonists.", "The candidates include various blockers of the purinergic P2Y12 receptor such as prasugrel, an oral irreversible thienopyridine; two adenosine triphosphate analogues that bind reversibly to the P2Y12 receptor: ticagrelor (oral) and cangrelor (intravenous); elinogrel, a direct-acting reversible P2Y12 receptor inhibitor (the only antiplatelet compound that can be administered both intravenously and orally); BX 667, an orally active and reversible small-molecule P2Y12 receptor antagonist; SCH 530348, SCH 205831, SCH 602539 and E5555, highly selective and orally active antagonists on the protease-activated receptor 1.", "A number of drugs also hit new targets: terutroban, an oral, selective and specific inhibitor of the thromboxane receptor; ARC1779, a second-generation, nuclease resistant aptamer which inhibits von Willebrand factor-dependent platelet aggregation; ALX-0081, a bivalent humanized nanobody targeting the GPIb binding site of von Willebrand factor and AJW200, an IgG4 monoclonal antibody of von Willebrand factor.", "The pharmacology and clinical profiles of new platelet antagonists indicate that they provide more consistent, more rapid and more potent platelet inhibition than agents currently used.", "Whether these potential advantages will translate into clinical advantages will require additional comparisons in properly powered, randomized, controlled trials."], "structured": false}
{"doc_id": 25550665, "title": "BLM is required for faithful chromosome segregation and its localization defines a class of ultrafine anaphase bridges.", "abstract": ["Mutations in BLM cause Bloom's syndrome, a disorder associated with cancer predisposition and chromosomal instability.", "We investigated whether BLM plays a role in ensuring the faithful chromosome segregation in human cells.", "We show that BLM-defective cells display a higher frequency of anaphase bridges and lagging chromatin than do isogenic corrected derivatives that eptopically express the BLM protein.", "In normal cells undergoing mitosis, BLM protein localizes to anaphase bridges, where it colocalizes with its cellular partners, topoisomerase IIIalpha and hRMI1 (BLAP75).", "Using BLM staining as a marker, we have identified a class of ultrafine DNA bridges in anaphase that are surprisingly prevalent in the anaphase population of normal human cells.", "These so-called BLM-DNA bridges, which also stain for the PICH protein, frequently link centromeric loci, and are present at an elevated frequency in cells lacking BLM.", "On the basis of these results, we propose that sister-chromatid disjunction is often incomplete in human cells even after the onset of anaphase.", "We present a model for the action of BLM in ensuring complete sister chromatid decatenation in anaphase."], "structured": false}
{"doc_id": 25562234, "title": "Association Between High Serum Soluble Corin and Hypertension: A Cross-Sectional Study in a General Population of China.", "abstract": ["BACKGROUND Corin has been suggested to be associated with hypertension by cell- and animal-based studies.", "However, the association still lacks population-based evidence which critically promotes translation from basic research to clinical and preventive practice.", "Here, we aimed to explore the association in a general population of China.   \n", "METHODS From January to May 2010, we conducted a cross-sectional study in 2,498 participants aged above 30 years, residing in Gusu district of Suzhou.", "Serum soluble corin and blood pressure were measured.   \n", "RESULTS Hypertensive participants had a higher level of serum corin than nonhypertensive participants (median (interquartile range): 1,836.83 (1,497.85-2,327.87) pg/ml vs. 1,579.14 (1,322.18-1,956.82) pg/ml, P < 0.001).", "Higher serum corin was positively associated with prevalent hypertension (odds ratio (OR) = 2.01, P < 0.001).", "In the multiple analysis, participants in the third (OR = 1.43, P = 0.007) and fourth (OR = 1.96, P < 0.001) quartiles had significantly increased odds of hypertension compared to those in the lowest quartile of serum corin.", "ORs of hypertension positively and significantly increased with serum corin levels (P for trend <0.001).", "Further subgroup analysis showed that ORs of hypertension associated with high corin (over the median level of serum corin: 1,689.20 pg/ml) were still significant in subgroups by age, body mass index, total cholesterol, low-density lipoprotein cholesterol, and fasting plasma glucose (all P < 0.05).   \n", "CONCLUSIONS Our study showed that hypertensive participants had an increased serum corin level compared to those without hypertension.", "This \ufb01nding suggests that corin may play a role in the pathology of hypertension."], "structured": true}
{"doc_id": 25571386, "title": "Shared and distinct genetic variants in type 1 diabetes and celiac disease.", "abstract": ["BACKGROUND Two inflammatory disorders, type 1 diabetes and celiac disease, cosegregate in populations, suggesting a common genetic origin.", "Since both diseases are associated with the HLA class II genes on chromosome 6p21, we tested whether non-HLA loci are shared.   \n", "METHODS We evaluated the association between type 1 diabetes and eight loci related to the risk of celiac disease by genotyping and statistical analyses of DNA samples from 8064 patients with type 1 diabetes, 9339 control subjects, and 2828 families providing 3064 parent-child trios (consisting of an affected child and both biologic parents).", "We also investigated 18 loci associated with type 1 diabetes in 2560 patients with celiac disease and 9339 control subjects.   \n", "RESULTS Three celiac disease loci--RGS1 on chromosome 1q31, IL18RAP on chromosome 2q12, and TAGAP on chromosome 6q25--were associated with type 1 diabetes (P<1.00x10(-4)).", "The 32-bp insertion-deletion variant on chromosome 3p21 was newly identified as a type 1 diabetes locus (P=1.81x10(-8)) and was also associated with celiac disease, along with PTPN2 on chromosome 18p11 and CTLA4 on chromosome 2q33, bringing the total number of loci with evidence of a shared association to seven, including SH2B3 on chromosome 12q24.", "The effects of the IL18RAP and TAGAP alleles confer protection in type 1 diabetes and susceptibility in celiac disease.", "Loci with distinct effects in the two diseases included INS on chromosome 11p15, IL2RA on chromosome 10p15, and PTPN22 on chromosome 1p13 in type 1 diabetes and IL12A on 3q25 and LPP on 3q28 in celiac disease.   \n", "CONCLUSIONS A genetic susceptibility to both type 1 diabetes and celiac disease shares common alleles.", "These data suggest that common biologic mechanisms, such as autoimmunity-related tissue damage and intolerance to dietary antigens, may be etiologic features of both diseases."], "structured": true}
{"doc_id": 25576204, "title": "Promotion of tumorigenesis by heterozygous disruption of the beclin 1 autophagy gene.", "abstract": ["Malignant cells often display defects in autophagy, an evolutionarily conserved pathway for degrading long-lived proteins and cytoplasmic organelles.", "However, as yet, there is no genetic evidence for a role of autophagy genes in tumor suppression.", "The beclin 1 autophagy gene is monoallelically deleted in 40-75% of cases of human sporadic breast, ovarian, and prostate cancer.", "Therefore, we used a targeted mutant mouse model to test the hypothesis that monoallelic deletion of beclin 1 promotes tumorigenesis.", "Here we show that heterozygous disruption of beclin 1 increases the frequency of spontaneous malignancies and accelerates the development of hepatitis B virus-induced premalignant lesions.", "Molecular analyses of tumors in beclin 1 heterozygous mice show that the remaining wild-type allele is neither mutated nor silenced.", "Furthermore, beclin 1 heterozygous disruption results in increased cellular proliferation and reduced autophagy in vivo.", "These findings demonstrate that beclin 1 is a haplo-insufficient tumor-suppressor gene and provide genetic evidence that autophagy is a novel mechanism of cell-growth control and tumor suppression.", "Thus, mutation of beclin 1 or other autophagy genes may contribute to the pathogenesis of human cancers."], "structured": false}
{"doc_id": 25589047, "title": "Treatment-related mortality with bevacizumab in cancer patients: a meta-analysis.", "abstract": ["CONTEXT Fatal adverse events (FAEs) have been reported in cancer patients treated with the widely used angiogenesis inhibitor bevacizumab in combination with chemotherapy.", "Currently, the role of bevacizumab in treatment-related mortality is not clear.   \n", "OBJECTIVE To perform a systematic review and meta-analysis of published randomized controlled trials (RCTs) to determine the overall risk of FAEs associated with bevacizumab.   \n", "DATA SOURCES PubMed, EMBASE, and Web of Science databases as well as abstracts presented at American Society of Clinical Oncology conferences from January 1966 to October 2010 were searched to identify relevant studies.   ", "STUDY SELECTION AND DATA EXTRACTION Eligible studies included prospective RCTs in which bevacizumab in combination with chemotherapy or biological therapy was compared with chemotherapy or biological therapy alone.", "Summary incidence rates, relative risks (RRs), and 95% confidence intervals (CIs) were calculated using fixed- or random-effects models.   \n", "DATA SYNTHESIS A total of 10,217 patients with a variety of advanced solid tumors from 16 RCTs were included in the analysis.", "The overall incidence of FAEs with bevacizumab was 2.5% (95% CI, 1.7%-3.9%).", "Compared with chemotherapy alone, the addition of bevacizumab was associated with an increased risk of FAEs, with an RR of 1.46 (95% CI, 1.09-1.94; P = .01; incidence, 2.5% vs 1.7%).", "This association varied significantly with chemotherapeutic agents (P = .045) but not with tumor types (P = .13) or bevacizumab doses (P = .16).", "Bevacizumab was associated with an increased risk of FAEs in patients receiving taxanes or platinum agents (RR, 3.49; 95% CI, 1.82-6.66; incidence, 3.3% vs 1.0%) but was not associated with increased risk of FAEs when used in conjunction with other agents (RR, 0.85; 95% CI, 0.25-2.88; incidence, 0.8% vs 0.9%).", "The most common causes of FAEs were hemorrhage (23.5%), neutropenia (12.2%), and gastrointestinal tract perforation (7.1%).   \n", "CONCLUSION In a meta-analysis of RCTs, bevacizumab in combination with chemotherapy or biological therapy, compared with chemotherapy alone, was associated with increased treatment-related mortality."], "structured": true}
{"doc_id": 25597580, "title": "Quiescent and active hippocampal neural stem cells with distinct morphologies respond selectively to physiological and pathological stimuli and aging.", "abstract": ["New neurons are generated in the adult hippocampus throughout life by neural stem/progenitor cells (NSCs), and neurogenesis is a plastic process responsive to external stimuli.", "We show that canonical Notch signaling through RBP-J is required for hippocampal neurogenesis.", "Notch signaling distinguishes morphologically distinct Sox2(+) NSCs, and within these pools subpopulations can shuttle between mitotically active or quiescent.", "Radial and horizontal NSCs respond selectively to neurogenic stimuli.", "Physical exercise activates the quiescent radial population whereas epileptic seizures induce expansion of the horizontal NSC pool.", "Surprisingly, reduced neurogenesis correlates with a loss of active horizontal NSCs in aged mice rather than a total loss of stem cells, and the transition to a quiescent state is reversible to rejuvenate neurogenesis in the brain.", "The discovery of multiple NSC populations with Notch dependence but selective responses to stimuli and reversible quiescence has important implications for the mechanisms of adaptive learning and also for regenerative therapy."], "structured": false}
{"doc_id": 25599283, "title": "Low serum vitamin D is associated with high risk of diabetes in Korean adults.", "abstract": ["Vitamin D may play a role in glucose metabolism.", "A low vitamin D level has been associated with increased risk of diabetes mellitus, but the association has not been confirmed in Asians.", "Our objective was to examine the association of serum 25-hydroxyvitamin D [25(OH)D] levels with insulin resistance and diabetes mellitus in Korean adults based on a large population-based survey.", "Cross-sectional analyses were carried out on 5787 Korean adults (2453 men and 3334 women) who were 20 y or older and participated in the Fourth Korea NHANES conducted in 2008.", "Diabetes mellitus was defined as fasting plasma glucose \u22657 mmol/L or current use of oral hypoglycemic agents or insulin.", "Insulin resistance was estimated by homeostatic model assessment for insulin resistance (HOMA-IR) and quantitative insulin sensitivity check index (QUICKI).", "Compared to individuals with a sufficient serum 25(OH)D concentration \u226575 nmol/L, the OR (95% CI) for diabetes mellitus were 1.73 (1.09-2.74), 1.30 (0.91-1.84), and 1.40 (0.99-1.98) for serum 25(OH)D concentrations <25, 25 to <50, and 50 to <75 nmol/L, respectively, after multiple adjustments (P-trend < 0.0001).", "Furthermore, the serum 25(OH)D level was inversely associated with HOMA-IR (\u03b2 = -0.061; P = 0.001) and positively associated with QUICKI (\u03b2 = 0.059; P = 0.001) in overweight or obese participants.", "In conclusion, a low serum vitamin D concentration is associated with a high risk of diabetes mellitus in Korean adults and the concentration is inversely associated with insulin resistance in those who are overweight or obese."], "structured": false}
{"doc_id": 25602549, "title": "When NK cells overcome their lack of education.", "abstract": ["Cells of the immune system have evolved various molecular mechanisms to sense their environment and react to alterations of self.", "NK cells are lymphocytes with effector and regulatory functions, which are remarkably adaptable to changes in self.", "In a study published in this issue of the JCI, Tarek and colleagues report the clinical benefits of manipulating NK cell adaptation to self in an innovative mAb-based therapy against neuroblastoma (NB).", "This novel therapeutic strategy should stimulate further research on NK cell therapies."], "structured": false}
{"doc_id": 25606339, "title": "Toll-like receptor-3 mediates HIV-1 transactivation via NF\u03baB and JNK pathways and histone acetylation, but prolonged activation suppresses Tat and HIV-1 replication.", "abstract": ["TLR3 has been implicated in the pathogenesis of several viral infections, including SIV- and HIV-1-induced inflammation and AIDS.", "However the molecular mechanisms of these TLR3-mediated effects are not known, and it is not known whether HIV interacts with cellular TLR3 to affect disease process.", "Here we investigate the effects of TLR3 ligands on HIV-1 transactivation using both primary human macrophages and cells containing integrated copies of the HIV-1 promoter.", "We demonstrate that TLR3 activation induced upregulation of transcription factors such as c-Jun, CCAAT/enhancer-binding protein alpha (CEBPA), signal transducer and activator of transcription (STAT)-1, STAT-2, RELB, and nuclear factor kappa-B1 (NF\u03baB1), most of which are known to regulate the HIV promoter activity.", "We also demonstrate that TLR3 activation increased HIV-1 transactivation via the c-Jun N-terminal kinase (JNK) and NF\u03baB pathways.", "This was associated with epigenetic modifications, including decreased histone deacetylase activity, increased histone acetyl transferase (HAT) activity, and increased acetylation of histones H3 and H4 at lysine residues in the nucleosome-0 and nucleosome-1 of the HIV-1 promoter.", "However, prolonged TLR3 activation decreased HIV-1 transactivation, decreased HAT activity and Tat transcription, and suppressed viral replication.", "Overall, data suggests that TLR3 can act as viral sensor to mediate viral transactivation, cellular signaling, innate immune response, and inflammation in HIV-infected humans.", "Our study provides novel insights into the molecular basis for these TLR3-mediated effects."], "structured": false}
{"doc_id": 25612629, "title": "Patent ductus arteriosus: are current neonatal treatment options better or worse than no treatment at all?", "abstract": ["Although a moderate-sized patent ductus arteriosus (PDA) needs to be closed by the time a child is 1-2 years old, there is great uncertainty about whether it needs to be closed during the neonatal period.", "Although 95% of neonatologists believe that a moderate-sized PDA should be closed if it persists in infants (born before 28 weeks) who still require mechanical ventilation, the number of neonatologists who treat a PDA when it occurs in infants who do not require mechanical ventilation varies widely.", "Both the high likelihood of spontaneous ductus closure and the absence of randomized controlled trials, specifically addressing the risks and benefits of neonatal ductus closure, add to the current uncertainty.", "New information suggests that early pharmacologic treatment has several important short-term benefits for the preterm newborn.", "By contrast, ductus ligation, while eliminating the detrimental effects of a PDA on lung development, may create its own set of morbidities that counteract many of the benefits derived from ductus closure."], "structured": false}
{"doc_id": 25623469, "title": "A conserved phosphatase cascade that regulates nuclear membrane biogenesis.", "abstract": ["A newly emerging family of phosphatases that are members of the haloacid dehalogenase superfamily contains the catalytic motif DXDX(T/V).", "A member of this DXDX(T/V) phosphatase family known as Dullard was recently shown to be a potential regulator of neural tube development in Xenopus [Satow R, Chan TC, Asashima M (2002) Biochem Biophys Res Commun 295:85-91].", "Herein, we demonstrate that human Dullard and the yeast protein Nem1p perform similar functions in mammalian cells and yeast cells, respectively.", "In addition to similarity in primary sequence, Dullard and Nem1p possess similar domains and show similar substrate preferences, and both localize to the nuclear envelope.", "Additionally, we show that human Dullard can rescue the aberrant nuclear envelope morphology of nem1Delta yeast cells, functionally replacing Nem1p.", "Finally, Nem1p, has been shown to deposphorylate the yeast phosphatidic acid phosphatase Smp2p [Santos-Rosa H, Leung J, Grimsey N, Peak-Chew S, Siniossoglou S (2005) EMBO J 24:1931-1941], and we show that Dullard dephosphorylates the mammalian phospatidic acid phosphatase, lipin.", "Therefore, we propose that Dullard participates in a unique phosphatase cascade regulating nuclear membrane biogenesis, and that this cascade is conserved from yeast to mammals."], "structured": false}
{"doc_id": 25628793, "title": "Increased expression of CYP1A1 and CYP1B1 in ovarian/peritoneal endometriotic lesions.", "abstract": ["Endometriosis is an estrogen-dependent disease affecting up to 10% of all premenopausal women.", "There is evidence that different endometriosis sites show distinct local estrogen concentration, which, in turn, might be due to a unique local estrogen metabolism.", "We aimed to investigate whether there was a site-specific regulation of selected enzymes responsible for the oxidative metabolism of estrogens in biopsy samples and endometrial and endometriotic stromal cells.", "Cytochrome P450 (CYP) 1A1 and CYP1B1 mRNA and protein expressions in deep-infiltrating (rectal, retossigmoidal, and uterossacral) lesions, superficial (ovarian and peritoneal) lesions, and eutopic and healthy (control) endometrium were evaluated by real-time PCR and western blot.", "Using a cross-sectional study design with 58 premenopausal women who were not under hormonal treatment, we were able to identify an overall increased CYP1A1 and CYP1B1 mRNA expression in superficial lesions compared with the healthy endometrium.", "CYP1A1 mRNA expression in superficial lesions was also greater than in the eutopic endometrium.", "Interestingly, we found a similar pattern of CYP1A1 and CYP1B1 expression in in vitro stromal cells isolated from ovarian lesions (n=3) when compared with stromal cells isolated from either rectum lesions or eutopic endometrium.", "In contradiction, there was an increased half-life of estradiol (measured by HPLC-MS-MS) in ovarian endometriotic stromal cells compared with paired eutopic stromal endometrial cells.", "Our results indicate that there is a site-dependent regulation of CYP1A1 and CYP1B1 in ovarian/peritoneal lesions and ovarian endometriotic stromal cells, whereas a slower metabolism is taking place in these cells."], "structured": false}
{"doc_id": 25629722, "title": "Eset partners with Oct4 to restrict extraembryonic trophoblast lineage potential in embryonic stem cells.", "abstract": ["The histone H3 Lys 9 (H3K9) methyltransferase Eset is an epigenetic regulator critical for the development of the inner cell mass (ICM).", "Although ICM-derived embryonic stem (ES) cells are normally unable to contribute to the trophectoderm (TE) in blastocysts, we find that depletion of Eset by shRNAs leads to differentiation with the formation of trophoblast-like cells and induction of trophoblast-associated gene expression.", "Using chromatin immmunoprecipitation (ChIP) and sequencing (ChIP-seq) analyses, we identified Eset target genes with Eset-dependent H3K9 trimethylation.", "We confirmed that genes that are preferentially expressed in the TE (Tcfap2a and Cdx2) are bound and repressed by Eset.", "Single-cell PCR analysis shows that the expression of Cdx2 and Tcfap2a is also induced in Eset-depleted morula cells.", "Importantly, Eset-depleted cells can incorporate into the TE of a blastocyst and, subsequently, placental tissues.", "Coimmunoprecipitation and ChIP assays further demonstrate that Eset interacts with Oct4, which in turn recruits Eset to silence these trophoblast-associated genes.", "Our results suggest that Eset restricts the extraembryonic trophoblast lineage potential of pluripotent cells and links an epigenetic regulator to key cell fate decision through a pluripotency factor."], "structured": false}
{"doc_id": 25641414, "title": "Suicides after pregnancy in Finland, 1987-94: register linkage study.", "abstract": ["OBJECTIVE To determine rates of suicide associated with pregnancy by the type of pregnancy.   \n", "DESIGN Register linkage study.", "Information on suicides in women of reproductive age was linked with the Finnish birth, abortion, and hospital discharge registers to find out how many women who committed suicide had had a completed pregnancy during her last year of life.   \n", "SETTING Nationwide data from Finland.   ", "SUBJECTS Women who committed suicide in 1987-94.   \n", "RESULTS There were 73 suicides associated with pregnancy, representing 5.4% of all suicides in women in this age group.", "The mean annual suicide rate was 11.3 per 100,000.", "The suicide rate associated with birth was significantly lower (5.9) and the rates associated with miscarriage (18.1) and induced abortion (34.7) were significantly higher than in the population.", "The risk associated with birth was higher among teenagers and that associated with abortion was increased in all age groups.", "Women who had committed a suicide tended to come from lower social classes and were more likely to be unmarried than other women who had had a completed pregnancy.   \n", "CONCLUSIONS The increased risk of suicide after an induced abortion indicates either common risk factors for both or harmful effects of induced abortion on mental health."], "structured": true}
{"doc_id": 25643818, "title": "Metformin-associated lactic acidosis: a rare or very rare clinical entity?", "abstract": ["AIMS Lactic acidosis is a well recognized complication of biguanide therapy which is potentially serious.", "Although the prevalence of metformin-associated lactic acidosis (MALA) is much lower than that associated with phenformin, it is still being reported sporadically which raises concerns for the practising clinicians.", "We review the currently available world-wide data of the prevalence of MALA, the risk factors for its development and the current practical guidelines on the use of metformin to minimize the risk of this potential hazard.   \n", "METHODS An extensive literature search was conducted from both Medline and Ovid (1965-98) using the following keywords: 'Type 2 diabetes mellitus', 'oral hypoglycaemic drugs', 'biguanides', 'metformin-associated lactic acidosis' and 'renal impairment'.   \n", "RESULTS MALA was found to be a very rare clinical entity, being 20 times less common than phenformin-associated lactic acidosis.", "Amongst all the risk factors, renal impairment appears to be the major precipitating factor for the development of MALA in metformin-treated patients.", "We also found cases of MALA where no precipitating factors were identified and the underlying mechanism in these cases remains unclear.", "Practical recommendations of metformin use to minimize the risk of MALA have been listed based on previous reports.   \n", "CONCLUSIONS The low prevalence of MALA is comparable to the prevalence of sulphonylurea-induced hypoglycaemia.", "Metformin has many beneficial metabolic effects in the management of Type 2 diabetes mellitus.", "Provided that the recommended guidelines for metformin use are strictly adhered to, its widespread use would be safe and the incidence of MALA will be further reduced."], "structured": true}
{"doc_id": 25649545, "title": "Inborn errors of human JAKs and STATs.", "abstract": ["Inborn errors of the genes encoding two of the four human JAKs (JAK3 and TYK2) and three of the six human STATs (STAT1, STAT3, and STAT5B) have been described.", "We review the disorders arising from mutations in these five genes, highlighting the way in which the molecular and cellular pathogenesis of these conditions has been clarified by the discovery of inborn errors of cytokines, hormones, and their receptors, including those interacting with JAKs and STATs.", "The phenotypic similarities between mice and humans lacking individual JAK-STAT components suggest that the functions of JAKs and STATs are largely conserved in mammals.", "However, a wide array of phenotypic differences has emerged between mice and humans carrying biallelic null alleles of JAK3, TYK2, STAT1, or STAT5B.", "Moreover, the high degree of allelic heterogeneity at the human JAK3, TYK2, STAT1, and STAT3 loci has revealed highly diverse immunological and clinical phenotypes, which had not been anticipated."], "structured": false}
{"doc_id": 25649714, "title": "Mental health problems of homeless children and families: longitudinal study.", "abstract": ["OBJECTIVE To establish the mental health needs of homeless children and families before and after rehousing.   \n", "DESIGN Cross sectional, longitudinal study.   \n", "SETTING City of Birmingham.   ", "SUBJECTS 58 rehoused families with 103 children aged 2-16 years and 21 comparison families of low socioeconomic status in stable housing, with 54 children.   \n", "MAIN OUTCOME MEASURES Children's mental health problems and level of communication; mothers' mental health problems and social support one year after rehousing.   \n", "RESULTS Mental health problems remained significantly higher in rehoused mothers and their children than in the comparison group (mothers 26% v 5%, P = 0.04; children 39% v 11%, P = 0.0003).", "Homeless mothers continued to have significantly less social support at follow up.", "Mothers with a history of abuse and poor social integration were more likely to have children with persistent mental health problems.   \n", "CONCLUSIONS Homeless families have a high level of complex needs that cannot be met by conventional health services and arrangements.", "Local strategies for rapid rehousing into permanent accommodation, effective social support and health care for parents and children, and protection from violence and intimidation should be developed and implemented."], "structured": true}
{"doc_id": 25653703, "title": "The flip side of perception-action coupling: locomotor experience and the ontogeny of visual-postural coupling.", "abstract": ["The possible role of motor development on psychological function is once again a topic of great theoretical and practical importance.", "The revival of this issue has stemmed from a different approach to the topic, away from Gesell's interest in the long-term prediction of psychological functions from early motoric assessments, toward an attempt to understand how the acquisition of motor skills orchestrates psychological changes.", "This paper describes how the acquisition of one motor skill, prone locomotion, has been linked to developmental changes in an infant's ability to regulate posture based on information available in patterns of optic flow.", "It is argued that the onset of prone locomotion presses the infant to differentiate spatially delimited regions of optic flow to effectively and efficiently control the important subtasks nested within the larger task of locomotion, namely, steering, attending to the surface of support, and maintaining postural control.", "Following this argument, a research program is described that aims to determine if locomotor experience is causally linked to improvements in the ability to functionalize peripheral optic flow for postural control or whether locomotor experience is merely a maturational forecaster of such improvements.", "Finally, a hypothesis is put forward that links the emergence of wariness of heights to infants' ability to regulate posture on the basis of peripheral optic flow.", "The paper's overarching theoretical point is the principle of probabilistic epigenesis, which states that one developmental acquisition produces experiences that bring about a host of new developmental changes in the same and different domains."], "structured": false}
{"doc_id": 25657127, "title": "Crystal structure of the first plant urease from jack bean: 83 years of journey from its first crystal to molecular structure.", "abstract": ["Urease, a nickel-dependent metalloenzyme, is synthesized by plants, some bacteria, and fungi.", "It catalyzes the hydrolysis of urea into ammonia and carbon dioxide.", "Although the amino acid sequences of plant and bacterial ureases are closely related, some biological activities differ significantly.", "Plant ureases but not bacterial ureases possess insecticidal properties independent of its ureolytic activity.", "To date, the structural information is available only for bacterial ureases although the jack bean urease (Canavalia ensiformis; JBU), the best-studied plant urease, was the first enzyme to be crystallized in 1926.", "To better understand the biological properties of plant ureases including the mechanism of insecticidal activity, we initiated the structural studies on some of them.", "Here, we report the crystal structure of JBU, the first plant urease structure, at 2.05 A resolution.", "The active-site architecture of JBU is similar to that of bacterial ureases containing a bi-nickel center.", "JBU has a bound phosphate and covalently modified residue (Cys592) by beta-mercaptoethanol at its active site, and the concomitant binding of multiple inhibitors (phosphate and beta-mercaptoethanol) is not observed so far in bacterial ureases.", "By correlating the structural information of JBU with the available biophysical and biochemical data on insecticidal properties of plant ureases, we hypothesize that the amphipathic beta-hairpin located in the entomotoxic peptide region of plant ureases might form a membrane insertion beta-barrel as found in beta-pore-forming toxins."], "structured": false}
{"doc_id": 25670099, "title": "Studies of nuclear and cytoplasmic behaviour during the five mitotic cycles that precede gastrulation in Drosophila embryogenesis.", "abstract": ["Using differential interference contrast optics, combined with cinematography, we have studied the morphological changes that the living, syncytial embryo undergoes from stage 10 through 14 of Drosophila embryogenesis, that is just prior to and during formation of the cellular blastoderm.", "We have supplemented these studies with data collected from fixed, stained, whole embryos.", "The following information has been obtained.", "The average duration of nuclear cycles 10, 11, 12 and 13 is about 9, 10, 12 and 21 min, respectively (25 degrees C).", "In these four cycles, the duration of that portion of the mitotic period that lacks a discrete nuclear envelope is 3, 3, 3 and 5 min, respectively.", "The length of nuclear cycle 14 varies in a position-specific manner throughout the embryo, the shortest cycles being of 65 min duration.", "During nuclear cycles 10 through 13, it is commonly observed in living embryos that the syncytial blastoderm nuclei enter (and leave) mitosis in one of two waves that originate nearly simultaneously from the opposite anterior and posterior poles of the embryo, and terminate in its midregion.", "From our preparations of quick-frozen embryos, we estimate that these mitotic waves take on average about half a minute to travel over the embryonic surface from pole to equator.", "The yolk nuclei, which remain in the core of the embryo when the rest of the nuclei migrate to the periphery, divide in synchrony with the migrating nuclei at nuclear cycles 8 and 9, and just after the now peripherally located nuclei at nuclear cycle 10.", "After cycle 10, these yolk nuclei cease dividing and become polyploid.", "The syncytial embryo has at least three distinct levels of cytoskeletal organization: structured domains of cytoplasm are organized around each blastoderm nucleus; radially directed tracks orient colchicine-sensitive saltatory transport throughout the peripheral cytoplasm; and a long-range organization of the core of the embryo makes possible coherent movements of the large inner yolk mass in concert with each nuclear cycle.", "This highly organized cytoplasm may be involved in providing positional information for the important process of nuclear determination that is known to occur during these stages."], "structured": false}
{"doc_id": 25677651, "title": "Activation of liver X receptors and retinoid X receptors prevents bacterial-induced macrophage apoptosis.", "abstract": ["Microbe-macrophage interactions play a central role in the pathogenesis of many infections.", "The ability of some bacterial pathogens to induce macrophage apoptosis has been suggested to contribute to their ability to elude innate immune responses and successfully colonize the host.", "Here, we provide evidence that activation of liver X receptors (LXRs) and retinoid X receptors (RXRs) inhibits apoptotic responses of macrophages to macrophage colony-stimulating factor (M-CSF) withdrawal and several inducers of apoptosis.", "In addition, combined activation of LXR and RXR protected macrophages from apoptosis caused by infection with Bacillus anthracis, Escherichia coli, and Salmonella typhimurium.", "Expression-profiling studies demonstrated that LXR and RXR agonists induced the expression of antiapoptotic regulators, including AIM/CT2, Bcl-X(L), and Birc1a.", "Conversely, LXR and RXR agonists inhibited expression of proapoptotic regulators and effectors, including caspases 1, 4/11, 7, and 12; Fas ligand; and Dnase1l3.", "The combination of LXR and RXR agonists was more effective than either agonist alone at inhibiting apoptosis in response to various inducers of apoptosis, and it acted synergistically to induce expression of AIM/CT2.", "Inhibition of AIM/CT2 expression in response to LXR/RXR agonists partially reversed their antiapoptotic effects.", "These findings reveal unexpected roles of LXRs and RXRs in the control of macrophage survival and raise the possibility that LXR/RXR agonists may be exploited to enhance innate immunity to bacterial pathogens that induce apoptotic programs as a strategy for evading host responses."], "structured": false}
{"doc_id": 25682129, "title": "p53 binding to nucleosomal DNA depends on the rotational positioning of DNA response element.", "abstract": ["The sequence-specific binding to DNA is crucial for the p53 tumor suppressor function.", "To investigate the constraints imposed on p53-DNA recognition by nucleosomal organization, we studied binding of the p53 DNA binding domain (p53DBD) and full-length wild-type p53 protein to a single p53 response element (p53RE) placed near the nucleosomal dyad in six rotational settings.", "We demonstrate that the strongest p53 binding occurs when the p53RE in the nucleosome is bent in the same direction as observed for the p53-DNA complexes in solution and in co-crystals.", "The p53RE becomes inaccessible, however, if its orientation in the core particle is changed by approximately 180 degrees.", "Our observations indicate that the orientation of the binding sites on a nucleosome may play a significant role in the initial p53-DNA recognition and subsequent cofactor recruitment."], "structured": false}
{"doc_id": 25687558, "title": "Diminished sympathetic nervous system activity in genetically obese (ob/ob) mouse.", "abstract": ["The genetically obese (ob/ob) mouse exhibits defective thermoregulatory responses to cold exposure.", "Pathophysiological explanations for this phenomenon have focused on abnormalities in intracellular metabolism or insensitivity of peripheral tissues to the thermogenic effects of catecholamines.", "Because the sympathetic nervous system (SNS) is subject to feedback regulation, a peripheral impairment in thermogenesis should be associated with a compensatory increase in SNS activity.", "To examine SNS activity in the ob/ob mouse, norepinephrine (NE) turnover was measured in heart and interscapular brown adipose tissue (IBAT) of ob/ob and lean mice.", "The results from studies utilizing radiolabeled NE or inhibition of NE biosynthesis with alpha-methyl-p-tyrosine to measure NE turnover demonstrated reductions in SNS activity of 33-56% in heart and of 45-73% in IBAT in ob/ob mice at ambient temperature (22 degrees C) compared with measurements in lean controls.", "During cold exposure (4 degrees C) NE turnover increased in heart and IBAT to a similar extent in both ob/ob and lean mice, but NE turnover rates in heart, and probably in IBAT as well, remained lower in the obese mice than in the lean despite the gradual development of hypothermia in the ob/ob mice during this period.", "Administration of naltrexone, a long-acting opiate antagonist, failed to reverse the suppression of SNS activity observed in the ob/ob mice.", "These data indicate that diminished SNS activity in ob/ob mice may be an additional factor contributing to the defective thermogenesis characteristic of these animals."], "structured": false}
{"doc_id": 25690516, "title": "Quality of life of young adults with idiopathic short stature: effect of growth hormone treatment. Dutch Growth Hormone Working Group.", "abstract": ["The aim of the study was to evaluate whether treatment with recombinant human growth hormone (rhGH) affects the quality of life of young adults who were diagnosed as idiopathic short stature (ISS) during childhood, and whether their quality of life and aspects of the personality are different from normal.", "Experiences and expectations concerning rhGH treatment of the subjects and their parents were also investigated.", "Eighty-nine subjects were included into the study: 24 subjects (16M, 8F) were treated with rhGH from childhood, whereas 65 subjects (40M, 25F) were never treated.", "At the time of the interview all subjects had attained final height [mean (SD) -2.3 (0.9) SDS for Dutch references], and the age of the treated subjects was 20.5 (1.0) y, and 25.7 (3.5) y of the control subjects (p < 0.001).", "The level of education was similar, but the treated subjects had less often a partner compared to the control subjects (adjusted for age and gender, p < 0.001).", "The Nottingham Health Profile and Short Form 36 Health Survey showed no difference in general health state between treated and control subjects, and the healthy Dutch age-specific references (norm group).", "Although 74% of the subjects reported one or more negative events related to their height, and 61% would like to be taller, only 22% and 11% were willing to trade-off at Time Trade-Off and Standard Gamble, respectively.", "The personality of the subjects, which was measured by the Minnesota Multiphasic Personality Inventory, was not different from the norm group.", "The satisfaction with the rhGH treatment was high, as it had caused 12 (8) cm and 13 (7) cm gain in final height according to the subjects and parents, respectively.", "Based on initial predicted adult height (Bayley & Pinneau), this gain was only 3.3 (5.6) cm.", "We concluded that although the treated subjects had a partner less often when compared to the control subjects, the quality of life of subjects with ISS at adult age is normal and appears not to be affected by rhGH therapy, The treated subjects were very satisfied with the treatment, probably by overestimation of the final height gain."], "structured": false}
{"doc_id": 25690564, "title": "Neighborhood Racial/Ethnic Concentration, Social Disadvantage, and Homicide Risk: An Ecological Analysis of 10 U.S. Cities", "abstract": ["Homicide is one of the leading causes of death among African-American and Hispanic men.", "We investigated how neighborhood characteristics associated with social disadvantage explain racial/ethnic homicide gaps in 10 U.S. cities.", "The test hypotheses were that (1) higher concentrations of African-Americans and Hispanics would be associated with higher homicide rates and (2) the relationship between racial/ethnic concentration and homicide would be attenuated after adjusting for neighborhood characteristics (e.g., unemployment, median household income, low educational attainment, and female headship).", "The test hypotheses were examined using separate Poisson regression models, which adjusted for spatial autocorrelation.", "Homicide rates were greater in neighborhoods with higher concentrations of African-Americans and Hispanics than in other groups, and the association of neighborhood racial/ethnic concentration with homicide was reduced after adjusting for neighborhood social disadvantage variables, especially percent female head of household and percent persons with less than a high school education.", "We also found that the relationship between neighborhood racial/ethnic concentration and homicide was explained more by social disadvantage variables in some cities than in others.", "Based on our findings, policy makers may wish to consider implementation of policies that (1) expand early childhood education programs and higher education opportunities and (2) encourage economic and community development initiatives in socially disadvantaged neighborhoods."], "structured": false}
{"doc_id": 25691541, "title": "Preterm patent ductus arteriosus: A continuing conundrum for the neonatologist?", "abstract": ["How to manage the preterm patent ductus arteriosus (PDA) remains a conundrum.", "On the one hand, physiology and statistical association with adverse outcomes suggest that it is pathological.", "On the other hand, clinical trials of treatment strategies have failed to show any long-term benefit.", "Ultrasound studies of PDA have suggested that the haemodynamic impact may be much earlier after birth than previously thought (in the first hours); however, we still do not know when to treat PDA.", "Studies that have tested symptomatic or pre-symptomatic treatment are mainly historical and have not tested the effect of no treatment.", "Prophylactic treatment is the best-studied regimen but improvements in some short-term outcomes do not translate to any difference in longer-term outcomes.", "Neonatologists have been reluctant to engage in trials that test treatment against almost never treating.", "Observations of very early postnatal haemodynamic significance suggest that targeting treatment on the basis of the early postnatal constrictive response of the duct may optimize benefits.", "A pilot trial of this strategy showed reduction in the incidence of pulmonary haemorrhage but more trials of this strategy are needed."], "structured": false}
{"doc_id": 25691878, "title": "Political and economic aspects of the transition to universal health coverage.", "abstract": ["Countries have reached universal health coverage by different paths and with varying health systems.", "Nonetheless, the trajectory toward universal health coverage regularly has three common features.", "The first is a political process driven by a variety of social forces to create public programmes or regulations that expand access to care, improve equity, and pool financial risks.", "The second is a growth in incomes and a concomitant rise in health spending, which buys more health services for more people.", "The third is an increase in the share of health spending that is pooled rather than paid out-of-pocket by households.", "This pooled share is sometimes mobilised as taxes and channelled through governments that provide or subsidise care--in other cases it is mobilised in the form of contributions to mandatory insurance schemes.", "The predominance of pooled spending is a necessary condition (but not sufficient) for achieving universal health coverage.", "This paper describes common patterns in countries that have successfully provided universal access to health care and considers how economic growth, demographics, technology, politics, and health spending have intersected to bring about this major development in public health."], "structured": false}
{"doc_id": 25725663, "title": "Wedelolactone protects human bronchial epithelial cell injury against cigarette smoke extract-induced oxidant stress and inflammation responses through Nrf2 pathway.", "abstract": ["Cigarette smoke is the leading cause of the development of various lung diseases including lung cancer through triggering oxidant stress and inflammatory responses which contributed to the lesions of normal human bronchial epithelial (NHBE) cell.", "Wedelolactone (WEL), a natural compound from Eclipta prostrata L., has been found to possess the inhibitive effects on the proliferation and growth of cancers.", "In the present study, we investigated the effects of WEL on NHBE cell injury induced by cigarette smoke extract (CSE) in vitro.", "It showed that the pretreatment WEL (2.5-20\u03bcM) resulted in a significant protective effect on 10% CSE-induced cell death in NHBE cells.", "The pretreatment with WEL dose-dependently and significantly reversed the activities of SOD, CAT, GSH and the level of MDA to normal level.", "We also found that the protein expression levels of COX-2 and ICAM-1 which are related to inflammatory response were remarkably reduced by WEL compared with 10% CSE treatment.", "Additionally, WEL also reduced the expressions of antioxidases including NAD(P)H dehydrogenase:Quinone 1 (NQO1) and heme oxygenase-1 (HO-1).", "Moreover, Nrf2 inhibitor all-trans-retinoic acid (ATRA) decreased remarkably their expressions.", "These results suggest that WEL protects NHBE cell against CSE-induced injury through modulating Nrf2 pathway.", "Our study indicates that WEL may be a new potential protective agent against CSE-induced lung injury."], "structured": false}
{"doc_id": 25726838, "title": "IL-17 promotes tumor development through the induction of tumor promoting microenvironments at tumor sites and myeloid-derived suppressor cells.", "abstract": ["The role of immune responses in tumor development is a central issue for tumor biology and immunology.", "IL-17 is an important cytokine for inflammatory and autoimmune diseases.", "Although IL-17-producing cells are detected in cancer patients and tumor-bearing mice, the role of IL-17 in tumor development is controversial, and mechanisms remain to be fully elucidated.", "In the current study, we found that the development of tumors was inhibited in IL-17R-deficient mice.", "A defect in IFN-gammaR increased tumor growth, whereas tumor growth was inhibited in mice that were deficient in both IL-17R and IFN-gammaR compared with wild-type animals.", "Further experiments showed that neutralization of IL-17 by Abs inhibited tumor growth in wild-type mice, whereas systemic administration of IL-17 promoted tumor growth.", "The IL-17R deficiency increased CD8 T cell infiltration, whereas it reduced the infiltration of myeloid-derived suppressor cells (MDSCs) in tumors.", "In contrast, administration of IL-17 inhibited CD8 T cell infiltration and increased MDSCs in tumors.", "Further analysis indicated that IL-17 was required for the development and tumor-promoting activity of MDSCs in tumor-bearing mice.", "These data demonstrate that IL-17-mediated responses promote tumor development through the induction of tumor-promoting microenvironments at tumor sites.", "IL-17-mediated regulation of MDSCs is a primary mechanism for its tumor-promoting effects.", "The study provides novel insights into the role of IL-17 in tumor development and has major implications for targeting IL-17 in treatment of tumors."], "structured": false}
{"doc_id": 25732836, "title": "Circulating tumor cells and [18F]fluorodeoxyglucose positron emission tomography/computed tomography for outcome prediction in metastatic breast cancer.", "abstract": ["PURPOSE Circulating tumor cells (CTCs) and [(18)F]fluorodeoxyglucose (FDG) positron emission tomography (PET)/computed tomography (CT) are two new promising tools for therapeutic monitoring.", "In this study, we compared the prognostic value of CTC and FDG-PET/CT monitoring during systemic therapy for metastatic breast cancer (MBC).   \n", "PATIENTS AND METHODS A retrospective analyses of 115 MBC patients who started a new line of therapy and who had CTC counts and FDG-PET/CT scans performed at baseline and at 9 to 12 weeks during therapy (midtherapy) was performed.", "Patients were categorized according to midtherapy CTC counts as favorable (ie, < five CTCs/7.5 mL blood) or unfavorable (> or = five CTCs/7.5 mL blood) outcomes.", "CTC counts and FDG-PET/CT response at midtherapy were compared, and univariate and multivariate analyses were performed to identify factors associated with survival.   \n", "RESULTS In 102 evaluable patients, the median overall survival time was 14 months (range, 1 to > 41 months).", "Midtherapy CTC levels correlated with FDG-PET/CT response in 68 (67%) of 102 evaluable patients.", "In univariate analysis, midtherapy CTC counts and FDG-PET/CT response predicted overall survival (P < .001 and P = .001, respectively).", "FDG-PET/CT predicted overall survival (P = .0086) in 31 (91%) of 34 discordant patients who had fewer than five CTCs at midtherapy.", "Only midtherapy CTC levels remained significant in a multivariate analysis (P = .004).   \n", "CONCLUSION Detection of five or more CTCs during therapeutic monitoring can accurately predict prognosis in MBC beyond metabolic response.", "FDG-PET/CT deserves a role in patients who have fewer than five CTCs at midtherapy.", "Prospective trials should evaluate the most sensitive and cost-effective modality for therapeutic monitoring in MBC."], "structured": true}
{"doc_id": 25737507, "title": "Phylogenetic analysis of Portuguese Feline Immunodeficiency Virus sequences reveals high genetic diversity.", "abstract": ["Feline Immunodeficiency Virus (FIV) is a Lentivirus responsible for an immunodeficiency like disease in domestic cats.", "Based on the genetic diversity of the V3-V5 region of env gene FIV is divided in five phylogenetic subtypes (A, B, C, D and E) with a world-wide distribution.", "To understand the subtype diversity of FIV in Portugal a serological survey was conducted during 1 year in the Veterinary Faculty Hospital, Lisbon, Portugal to identify seropositive animals.", "Two viral genomic regions were amplified by a nested PCR, sequenced and the phylogenetic relationships between 24 new Portuguese FIV sequences and other previously published FIV isolates were assessed.", "The introduction of these sequences induced a subclustering in subtype B including most of the new Portuguese sequences.", "Moreover, a new cluster emerged, with two highly divergent new sequences that might represent a new subtype.", "The study of these new FIV isolates showed the presence in Portugal of a unique viral population subclustering within subtype B and of sequences clearly divergent from the five known subtypes, providing a contribution for the understanding of FIV's genetic diversity."], "structured": false}
{"doc_id": 25738896, "title": "Aire deficiency promotes TRP-1-specific immune rejection of melanoma.", "abstract": ["The thymic transcription factor autoimmune regulator (Aire) prevents autoimmunity in part by promoting expression of tissue-specific self-antigens, which include many cancer antigens.", "For example, AIRE-deficient patients are predisposed to vitiligo, an autoimmune disease of melanocytes that is often triggered by efficacious immunotherapies against melanoma.", "Therefore, we hypothesized that Aire deficiency in mice may elevate immune responses to cancer and provide insights into how such responses might be triggered.", "In this study, we show that Aire deficiency decreases thymic expression of TRP-1 (TYRP1), which is a self-antigen in melanocytes and a cancer antigen in melanomas.", "Aire deficiency resulted in defective negative selection of TRP-1-specific T cells without affecting thymic numbers of regulatory T cells.", "Aire-deficient mice displayed elevated T-cell immune responses that were associated with suppression of melanoma outgrowth.", "Furthermore, transplantation of Aire-deficient thymic stroma was sufficient to confer more effective immune rejection of melanoma in an otherwise Aire wild-type host.", "Together, our work showed how Aire deficiency can enhance immune responses against melanoma and how manipulating TRP-1-specific T-cell negative selection may offer a logical strategy to enhance immune rejection of melanoma."], "structured": false}
{"doc_id": 25742130, "title": "Mass screening programmes and trends in cervical cancer in Finland and the Netherlands.", "abstract": ["With respect to cervical cancer management, Finland and the Netherlands are comparable in relevant characteristics, e.g., fertility rate, age-of-mother at first birth and a national screening programme for several years.", "The aim of this study is to compare trends in incidence of and mortality from cervical cancer in Finland and the Netherlands in relation to the introduction and intensity of the screening programmes.", "Therefore, incidence and mortality rates were calculated using the Cancer Registries of Finland and the Netherlands.", "Data on screening intensity were obtained from the Finnish Cancer Registry and the Dutch evaluation centre at ErasmusMC-Rotterdam.", "Women aged 30-60 have been screened every 5 years, in Finland since 1992 and in the Netherlands since 1996.", "Screening protocols for smear taking and referral to the gynaecologist are comparable.", "Incidence and mortality rates have declined more in Finland.", "In 2003, age-adjusted incidence and mortality in Finland were 4.0 and 0.9 and in the Netherlands 4.9 and 1.4 per 100,000 woman-years, respectively.", "Excess smear use in the Netherlands was estimated to be 24 per 1,000 women during a 5-year interval compared to 121 in Finland.", "The decline in mortality in Finland seems to be almost completely related to the screening programme whereas in the Netherlands it was initially considered to be a natural decline.", "Differences in risk factors might also play a role: the Netherlands has higher population density and higher percentages of immigrants and (female) smokers.", "The greater excess smear use in Finland might also have affected incidence."], "structured": false}
{"doc_id": 25742205, "title": "Biochemical characterization of the Ran-RanBP1-RanGAP system: are RanBP proteins and the acidic tail of RanGAP required for the Ran-RanGAP GTPase reaction?", "abstract": ["RanBP type proteins have been reported to increase the catalytic efficiency of the RanGAP-mediated GTPase reaction on Ran.", "Since the structure of the Ran-RanBP1-RanGAP complex showed RanBP1 to be located away from the active site, we reinvestigated the reaction using fluorescence spectroscopy under pre-steady-state conditions.", "We can show that RanBP1 indeed does not influence the rate-limiting step of the reaction, which is the cleavage of GTP and/or the release of product P(i).", "It does, however, influence the dynamics of the Ran-RanGAP interaction, its most dramatic effect being the 20-fold stimulation of the already very fast association reaction such that it is under diffusion control (4.5 x 10(8) M(-1) s(-1)).", "Having established a valuable kinetic system for the interaction analysis, we also found, in contrast to previous findings, that the highly conserved acidic C-terminal end of RanGAP is not required for the switch-off reaction.", "Rather, genetic experiments in Saccharomyces cerevisiae demonstrate a profound effect of the acidic tail on microtubule organization during mitosis.", "We propose that the acidic tail of RanGAP is required for a process during mitosis."], "structured": false}
{"doc_id": 25747721, "title": "Concomitant induction of CD4+ and CD8+ T cell responses in volunteers immunized with Salmonella enterica serovar typhi strain CVD 908-htrA.", "abstract": ["Type 1 cell-mediated immunity might play an important role in protection from typhoid fever.", "We evaluated whether immunization with Salmonella enterica serovar Typhi (S. Typhi) strain CVD 908-htrA (a Delta aroC Delta aroD Delta htrA mutant), a leading live oral typhoid vaccine candidate, elicits specific CD4(+) and CD8(+) S. Typhi immune responses.", "Potent CTL responses and IFN-gamma secretion by CD8(+) T cells were detected following immunization with CVD 908-htrA in high (4.5 x 10(8) CFU) and low (5 x 10(7) CFU) dosages.", "S. Typhi-specific CTL were observed in six of eight vaccinees (four high and two low dose) after immunization.", "Mean increases in the frequency of IFN-gamma spot-forming cells (SFC) in the presence of S. Typhi-infected targets were 221 +/-", "41 SFC/10(6) PBMC and 233 +/-", "87 SFC/10(6) PBMC, in the high and low dose groups, respectively.", "Strong CD4(+) T cell responses were also observed.", "Increases in the IFN-gamma production to soluble S. Typhi flagella (STF) occurred in 82 and 38% of the volunteers who received the high and low doses, respectively.", "Robust correlations were observed between volunteers that responded with IFN-gamma SFC to stimulation with S. Typhi-infected cells and IFN-gamma released in response to stimulation with STF Ags (r = 0.822, p < 0.001) and between CTL and IFN-gamma production to STF (r = 0.818, p = 0.013).", "These data demonstrating the concomitant induction of both CD4- and CD8-mediated CMI are consistent with a significant role for type 1 immunity in controlling typhoid infection and support the continuing evaluation of CVD 908-htrA as a typhoid vaccine candidate."], "structured": false}
{"doc_id": 25748308, "title": "The diverse functions of GAPDH: views from different subcellular compartments.", "abstract": ["Multiple roles for glyceraldehyde-3-phosphate dehydrogenase (GAPDH) have been recently appreciated.", "In addition to the cytoplasm where the majority of GAPDH is located under the basal condition, GAPDH is also found in the particulate fractions, such as the nucleus, the mitochondria, and the small vesicular fractions.", "When cells are exposed to various stressors, dynamic subcellular re-distribution of GAPDH occurs.", "Here we review these multifunctional properties of GAPDH, especially linking them to its oligomerization, posttranslational modification, and subcellular localization.", "This includes mechanistic descriptions of how S-nitrosylation of GAPDH under oxidative stress may lead to cell death/dysfunction via nuclear translocation of GAPDH, which is counteracted by a cytosolic GOSPEL.", "GAPDH is also involved in various diseases, especially neurodegenerative disorders and cancers.", "Therapeutic strategies to these conditions based on molecular understanding of GAPDH are discussed."], "structured": false}
{"doc_id": 25761154, "title": "Exercise-induced asthma: a practical guide to definitions, diagnosis, prevalence, and treatment.", "abstract": ["Exercise-induced asthma is defined as an intermittent narrowing of the airways, demonstrated by a decrease in some measure of flow, that the patient experiences as wheezing, chest tightness, coughing, and difficulty breathing that is triggered by exercise.", "Exercise will trigger asthma in most individuals who have chronic asthma, as well as in some who do not otherwise have asthma.", "Definitive diagnosis requires demonstration of a drop in flow rate, typically > or = 13-15% for forced expiratory volume in one second (FEV1) and > or = 15-20% for peak expiratory flow rate (PEFR), after exercise, associated with symptoms.", "Prevalence data indicate that this disorder is very common in those who participate in recreational sports as well as in highly competitive athletes, with at least 12-15% of unselected athletes having positive exercise challenges.", "Treatment of exercise induced asthma involves use of nonpharmacological measures (such as the use of the refractory period after exercise and prewarming air) as well as use of medications (beta-agonists, cromolyn, and nedocromil).", "With treatment, those who suffer from exercise-induced asthma may be able to participate and compete at the highest levels of performance."], "structured": false}
{"doc_id": 25786167, "title": "Effect of sample quality on the sensitivity of endoscopic biopsy for detecting gastric and duodenal lesions in dogs and cats.", "abstract": ["BACKGROUND The quality of histopathology slides of endoscopic biopsies from different laboratories varies, but the effect of biopsy quality on outcome is unknown.   ", "HYPOTHESIS The ability to demonstrate a histologic lesion in the stomach or duodenum of a dog or cat is affected by the quality of endoscopic biopsy samples submitted.", "More endoscopic samples are needed to find a lesion in poor-quality tissue specimens.   ", "ANIMALS Tissues from 99 dogs and 51 cats were examined as clinical cases at 8 veterinary institutions or practices in 5 countries.   \n", "METHODS Histopathology slides from sequential cases that underwent endoscopic biopsy were submitted by participating institutions.", "Quality of the histologic section of tissue (inadequate, marginal, adequate), type of lesion (lymphangiectasia, crypt lesion, villus blunting, cellular infiltrate), and severity of lesion (normal, mild, moderate, severe) were determined.", "Sensitivity of different quality tissue samples for finding different lesions was determined.   \n", "RESULTS Fewer samples were required from dogs for diagnosis as the quality of the sample improved from inadequate to marginal to adequate.", "Duodenal lesions in cats displayed the same trend except for moderate duodenal infiltrates for which quality of tissue sample made no difference.", "Gastric lesions in dogs and mild gastric lesions in cats had the same trend, whereas the number of tissue samples needed to diagnose moderately severe gastric lesions in cats was not affected by the quality of tissue sample.   \n", "CONCLUSIONS AND CLINICAL IMPORTANCE The quality of endoscopically obtained tissue samples has a profound effect on their sensitivity for identifying certain lesions, and there are differences between biopsies of canine and feline tissues."], "structured": true}
{"doc_id": 25787749, "title": "G-quadruplexes significantly stimulate Pif1 helicase-catalyzed duplex DNA unwinding.", "abstract": ["The evolutionarily conserved G-quadruplexes (G4s) are faithfully inherited and serve a variety of cellular functions such as telomere maintenance, gene regulation, DNA replication initiation, and epigenetic regulation.", "Different from the Watson-Crick base-pairing found in duplex DNA, G4s are formed via Hoogsteen base pairing and are very stable and compact DNA structures.", "Failure of untangling them in the cell impedes DNA-based transactions and leads to genome instability.", "Cells have evolved highly specific helicases to resolve G4 structures.", "We used a recombinant nuclear form of Saccharomyces cerevisiae Pif1 to characterize Pif1-mediated DNA unwinding with a substrate mimicking an ongoing lagging strand synthesis stalled by G4s, which resembles a replication origin and a G4-structured flap in Okazaki fragment maturation.", "We find that the presence of G4 may greatly stimulate the Pif1 helicase to unwind duplex DNA.", "Further studies reveal that this stimulation results from G4-enhanced Pif1 dimerization, which is required for duplex DNA unwinding.", "This finding provides new insights into the properties and functions of G4s.", "We discuss the observed activation phenomenon in relation to the possible regulatory role of G4s in the rapid rescue of the stalled lagging strand synthesis by helping the replicator recognize and activate the replication origin as well as by quickly removing the G4-structured flap during Okazaki fragment maturation."], "structured": false}
{"doc_id": 25789730, "title": "Diffusion tensor imaging detects and differentiates axon and myelin degeneration in mouse optic nerve after retinal ischemia.", "abstract": ["Both axon and myelin degeneration have significant impact on the long-term disability of patients with white matter disorder.", "However, the clinical manifestations of the neurological dysfunction caused by white matter disorders are not sufficient to determine the origin of neurological deficits.", "A noninvasive biological marker capable of detecting and differentiating axon and myelin degeneration would be a significant addition to currently available tools.", "Directional diffusivities derived from diffusion tensor imaging (DTI) have been previously proposed by this group as potential biological markers to detect and differentiate axon and myelin degeneration.", "To further test the hypothesis that axial (lambdaparallel) and radial (lambdaperpendicular) diffusivities reflect axon and myelin pathologies, respectively, the optic nerve was examined serially using DTI in a mouse model of retinal ischemia.", "A significant decrease of lambdaparallel, the putative DTI axonal marker, was observed 3 days after ischemia without concurrently detectable changes in lambdaperpendicular, the putative myelin marker.", "This result is consistent with histological findings of significant axonal degeneration with no detectable demyelination at 3 days after ischemia.", "The elevation of lambdaperpendicular observed 5 days after ischemia is consistent with histological findings of myelin degeneration at this time.", "These results support the hypothesis that lambdaparallel and lambdaperpendicular hold promise as specific markers of axonal and myelin injury, respectively, and, further, that the coexistence of axonal and myelin degeneration does not confound this utility."], "structured": false}
{"doc_id": 25799020, "title": "Direct isolation and identification of promoters in the human genome.", "abstract": ["Transcriptional regulatory elements play essential roles in gene expression during animal development and cellular response to environmental signals, but our knowledge of these regions in the human genome is limited despite the availability of the complete genome sequence.", "Promoters mark the start of every transcript and are an important class of regulatory elements.", "A large, complex protein structure known as the pre-initiation complex (PIC) is assembled on all active promoters, and the presence of these proteins distinguishes promoters from other sequences in the genome.", "Using components of the PIC as tags, we isolated promoters directly from human cells as protein-DNA complexes and identified the resulting DNA sequences using genomic tiling microarrays.", "Our experiments in four human cell lines uncovered 252 PIC-binding sites in 44 semirandomly selected human genomic regions comprising 1% (30 megabase pairs) of the human genome.", "Nearly 72% of the identified fragments overlap or immediately flank 5' ends of known cDNA sequences, while the remainder is found in other genomic regions that likely harbor putative promoters of unannotated transcripts.", "Indeed, molecular analysis of the RNA isolated from one cell line uncovered transcripts initiated from over half of the putative promoter fragments, and transient transfection assays revealed promoter activity for a significant proportion of fragments when they were fused to a luciferase reporter gene.", "These results demonstrate the specificity of a genome-wide analysis method for mapping transcriptional regulatory elements and also indicate that a small, yet significant number of human genes remains to be discovered."], "structured": false}
{"doc_id": 25806385, "title": "Attempted suicide in Europe: rates, trends and sociodemographic characteristics of suicide attempters during the period 1989-1992. Results of the WHO/EURO Multicentre Study on Parasuicide.", "abstract": ["The World Health Organization/EURO Multicentre Project on Parasuicide is part of the action to implement target 12 of the WHO programme, \"Health for All by the Year 2000', for the European region.", "Sixteen centres in 13 European countries are participating in the monitoring aspect of the project, in which trends in the epidemiology of suicide attempts are assessed.", "The highest average male age-standardized rate of suicide attempts was found for Helsinki, Finland (314/100,000), and the lowest rate (45/100,000) was for Guipuzcoa, Spain, representing a sevenfold difference.", "The highest average female age-standardized rate was found for Cergy-Pontoise, France (462/100,000), and the lowest (69/100,000) again for Guipuzcoa, Spain.", "With only one exception (Helsinki), the person-based suicide attempt rates were higher among women than among men.", "In the majority of centres, the highest person-based rates were found in the younger age groups.", "The rates among people aged 55 years or over were generally the lowest.", "For the majority of the centres, the rates for individuals aged 15 years or over decreased between 1989 and 1992.", "The methods used were primarily \"soft' (poisoning) or cutting.", "More than 50% of the suicide attempters made more than one attempt, and nearly 20% of the second attempts were made within 12 months after the first attempt.", "Compared with the general population, suicide attempters more often belong to the social categories associated with social destabilization and poverty."], "structured": false}
{"doc_id": 25811797, "title": "Recurrent outbreaks of Salmonella Enteritidis infections in a Texas restaurant: phage type 4 arrives in the United States.", "abstract": ["In recent years infection caused by Salmonella serotype Enteritidis (SE) phage type 4 has spread through Europe but has been uncommon in the USA.", "The first recognized outbreak of this strain in the USA occurred in a Chinese restaurant in EI Paso, Texas, in April 1993; no source was identified.", "In September 1993, a second outbreak caused by SE phage type 4 was associated with the same restaurant.", "To determine the cause of the second outbreak, we compared food exposures of the 19 patients with that of two control groups.", "Egg rolls were the only item significantly associated with illness in both analyses (first control group: odds ratio [OR] 8.2, 95% confidence interval [CI] 2.3-31.6; second control group: OR 13.1, 95% CI 2.1-97.0).", "Retrospective analysis of the April outbreak also implicated egg rolls (OR 32.4, 95% CI 9.1-126.6).", "Egg roll batter was made from pooled shell eggs and was left at room temperature throughout the day.", "These two outbreaks of SE phage type 4 likely could have been prevented by using pasteurized eggs and safe food preparation practices."], "structured": false}
{"doc_id": 25813706, "title": "Strand-specific mismatch correction in nuclear extracts of human and Drosophila melanogaster cell lines.", "abstract": ["Nuclear extracts derived from HeLa and Drosophila melanogaster KC cell lines have been found to correct single base-base mispairs within open circular DNA heteroduplexes containing a strand-specific, site-specific incision located 808 base pairs from the mismatch.", "Correction in both extract systems is strand specific, being highly biased to the incised DNA strand.", "Different mispairs within a homologous set of heteroduplexes were processed with different efficiencies (G.T greater than G.G approximately equal to A.C greater than C.C), and correction was accompanied by mismatch-dependent DNA synthesis localized to the region spanning the mispair and the strand break, thus demonstrating that mismatch recognition is associated with the repair reaction.", "Correction of each of these heteroduplexes was abolished by aphidicolin but was relatively insensitive to the presence of high concentrations of ddTTP, indicating probable involvement of alpha and/or delta class DNA polymerase(s).", "These findings suggest that higher eukaryotic cells possess a general, strand-specific mismatch repair system analogous to the Escherichia coli mutHLS and the Streptococcus pneumoniae hexAB pathways, systems that contribute in a major way to the genetic stability of these bacterial species."], "structured": false}
{"doc_id": 25816994, "title": "Renal outcomes with telmisartan, ramipril, or both, in people at high vascular risk (the ONTARGET study): a multicentre, randomised, double-blind, controlled trial.", "abstract": ["BACKGROUND Angiotensin receptor blockers (ARB) and angiotensin converting enzyme (ACE) inhibitors are known to reduce proteinuria.", "Their combination might be more effective than either treatment alone, but long-term data for comparative changes in renal function are not available.", "We investigated the renal effects of ramipril (an ACE inhibitor), telmisartan (an ARB), and their combination in patients aged 55 years or older with established atherosclerotic vascular disease or with diabetes with end-organ damage.   \n", "METHODS The trial ran from 2001 to 2007.", "After a 3-week run-in period, 25 620 participants were randomly assigned to ramipril 10 mg a day (n=8576), telmisartan 80 mg a day (n=8542), or to a combination of both drugs (n=8502; median follow-up was 56 months), and renal function and proteinuria were measured.", "The primary renal outcome was a composite of dialysis, doubling of serum creatinine, and death.", "Analysis was by intention to treat.", "This study is registered with ClinicalTrials.gov, number NCT00153101.   \n", "FINDINGS 784 patients permanently discontinued randomised therapy during the trial because of hypotensive symptoms (406 on combination therapy, 149 on ramipril, and 229 on telmisartan).", "The number of events for the composite primary outcome was similar for telmisartan (n=1147 [13.4%]) and ramipril (1150 [13.5%]; hazard ratio [HR] 1.00, 95% CI 0.92-1.09), but was increased with combination therapy (1233 [14.5%]; HR 1.09, 1.01-1.18, p=0.037).", "The secondary renal outcome, dialysis or doubling of serum creatinine, was similar with telmisartan (189 [2.21%]) and ramipril (174 [2.03%]; HR 1.09, 0.89-1.34) and more frequent with combination therapy (212 [2.49%]: HR 1.24, 1.01-1.51, p=0.038).", "Estimated glomerular filtration rate (eGFR) declined least with ramipril compared with telmisartan (-2.82 [SD 17.2] mL/min/1.73 m(2)vs -4.12 [17.4], p<0.0001) or combination therapy (-6.11 [17.9], p<0.0001).", "The increase in urinary albumin excretion was less with telmisartan (p=0.004) or with combination therapy (p=0.001) than with ramipril.   \n", "INTERPRETATION In people at high vascular risk, telmisartan's effects on major renal outcomes are similar to ramipril.", "Although combination therapy reduces proteinuria to a greater extent than monotherapy, overall it worsens major renal outcomes."], "structured": true}
{"doc_id": 25817686, "title": "Hypothermic preservation up-regulates calpain expression and increases ubiquitination in cultured vascular endothelial cells: influence of dopamine pretreatment.", "abstract": ["BACKGROUND Prolonged hypothermia, as occurs during solid organ transplantation, negatively influences transplantation outcome.", "Proteolysis is one of the deleterious events implicated in preservation injury of organ allografts.", "This strongly affects graft quality and hence immediate organ function.", "Since donor catecholamine treatment improves transplantation outcome after renal transplantation, the present study was conducted to examine the influence of dopamine (DA) pretreatment on hypothermia induced proteolysis in endothelial cells subjected to prolonged cold storage.   ", "MATERIALS AND METHODS Lactate dehydrogenase (LDH) assay, two-dimensional electrophoresis, ubiquitination analysis, intracellular calcium measurement, and Western blot analysis were performed on human umbilical vein endothelial cells (HUVEC) subjected to hypothermic preservation or not.   \n", "RESULTS HUVEC were highly susceptible to cold storage, which was reflected by morphological changes, loss of viability, and by significant changes in cellular proteome.", "DA pretreatment prevented cell death during cold storage.", "Western blot analysis demonstrated a time dependent up-regulation of calpain 1 and 2 during cold storage, which could be prevented by addition of EDTA.", "DA pretreatment abolished autoproteolysis of calpain 1.", "Analysis of ubiquitination revealed a significant increase in ubiquitinated conjugates after cold storage.", "This was not prevented by DA pretreatment.", "Neither proteasome nor calpain inhibitors prevented cell death during cold storage.   \n", "CONCLUSION In endothelial cells subjected to cold preservation, activation of the calpain pathway and the ubiquitin proteasome system occur.", "Although DA pretreatment inhibits the former, calpain inhibition did not protect endothelial cells during cold storage.", "DA pretreatment might influence proteolysis, but proteolysis is not the major cause of endothelial cell death."], "structured": true}
{"doc_id": 25821556, "title": "The three 'C' s of chromosome conformation capture: controls, controls, controls", "abstract": ["Transcription regulation in higher eukaryotes is controlled by regulatory elements such as enhancers that are recognized by transcription factors.", "In many cases regulatory elements can be located at distances up to several megabases from their target genes.", "Recent evidence shows that long-range control of gene expression can be mediated through direct physical interactions between genes and these regulatory elements.", "Such looping interactions can be detected using the chromosome conformation capture (3C) methodology.", "Although 3C is experimentally straightforward, to draw meaningful conclusions one must carefully design 3C experiments and implement the conscientious use of controls.", "The general guidelines presented here should help experimental design and minimize misinterpretation of 3C experiments."], "structured": false}
{"doc_id": 25822299, "title": "Effects of exercise training of 8 weeks and detraining on plasma levels of endothelium-derived factors, endothelin-1 and nitric oxide, in healthy young humans.", "abstract": ["Vascular endothelial cells produce nitric oxide (NO), which is a potent vasodilator substance and has been proposed as having antiatherosclerotic property.", "Vascular endothelial cells also produce endothelin-1 (ET-1), which is a potent vasoconstrictor peptide and has potent proliferating activity on vascular smooth muscle cells.", "Therefore, ET-1 has been implicated in the progression of atheromatous vascular disease.", "Because exercise training has been reported to produce an alteration in the function of vascular endothelial cells in animals, we hypothesized that exercise training influences the production of NO and ET-1 in humans.", "The purpose of the present study was to examine whether chronic exercise could influence the plasma levels of NO (measured as the stable end product of NO, i.e., nitrite/nitrate [NOx]) and ET-1 in humans.", "Eight healthy young subjects (20.3 +/-", "0.5 yr old) participated in the study and exercised by cycling on a leg ergometer (70% VO2max for 1 hour, 3-4 days/week) for 8 weeks.", "Venous plasma concentrations of NOx and ET-1 were measured before and after (immediately before the end of 8-week exercise training) the exercise training, and also after the 4th and 8th week after the cessation of training.", "The VO2max significantly increased after exercise training.", "After the exercise training, the plasma concentration of NOx significantly increased (30.69 +/-", "3.20 vs. 48.64 +/-", "8.16 micromol/L, p < 0.05), and the plasma concentration of ET-1 significantly decreased (1.65 +/- 0.14 vs. 1.23 +/-", "0.12 pg/mL, p < 0.05).", "The increase in NOx level and the decrease in ET-1 level lasted to the 4th week after the cessation of exercise training and these levels (levels of NOx and ET-1) returned to the basal levels (the levels before the exercise training) in the 8th week after the cessation of exercise training.", "There was a significant negative correlation between plasma NOx concentration and plasma ET-1 concentration.", "The present study suggests that chronic exercise causes an increase in production of NO and a decrease in production of ET-1 in humans, which may produce beneficial effects (i.e., vasodilative and antiatherosclerotic) on the cardiovascular system."], "structured": false}
{"doc_id": 25827024, "title": "Neuron-specific expression of CuZnSOD prevents the loss of muscle mass and function that occurs in homozygous CuZnSOD-knockout mice.", "abstract": ["Deletion of copper-zinc superoxide dismutase (CuZnSOD) in Sod1(-/-) mice leads to accelerated loss of muscle mass and force during aging, but the losses do not occur with muscle-specific deletion of CuZnSOD.", "To determine the role of motor neurons in the muscle decline, we generated transgenic Sod1(-/-) mice in which CuZnSOD was expressed under control of the synapsin 1 promoter (SynTgSod1(-/-) mice).", "SynTgSod1(-/-) mice expressed CuZnSOD in brain, spinal cord, and peripheral nerve, but not in other tissues.", "Sciatic nerve CuZnSOD content in SynTgSod1(-/-) mice was ~20% that of control mice, but no reduction in muscle mass or isometric force was observed in SynTgSod1(-/-) mice compared with control animals, whereas muscles of age-matched Sod1(-/-) mice displayed 30-40% reductions in mass and force.", "In addition, increased oxidative damage and adaptations in stress responses observed in muscles of Sod1(-/-) mice were absent in SynTgSod1(-/-) mice, and degeneration of neuromuscular junction (NMJ) structure and function occurred in Sod1(-/-) mice but not in SynTgSod1(-/-) mice.", "Our data demonstrate that specific CuZnSOD expression in neurons is sufficient to preserve NMJ and skeletal muscle structure and function in Sod1(-/-) mice and suggest that redox homeostasis in motor neurons plays a key role in initiating sarcopenia during aging."], "structured": false}
{"doc_id": 25830701, "title": "A developmental transition in definitive erythropoiesis: erythropoietin expression is sequentially regulated by retinoic acid receptors and HNF4.", "abstract": ["The cytokine erythropoietin (Epo) promotes erythropoietic progenitor cell proliferation and is required for erythropoietic differentiation.", "We have found that the Epo gene is a direct transcriptional target gene of retinoic acid signaling during early erythropoiesis (prior to embryonic day E12.5) in the fetal liver.", "Mouse embryos lacking the retinoic acid receptor gene RXR alpha have a morphological and histological phenotype that is comparable with embryos in which the Epo gene itself has been mutated, and flow cytometric analysis indicates that RXR alpha-deficient embryos are deficient in erythroid differentiation.", "Epo mRNA levels are reduced substantially in the fetal livers of RXR alpha(-/-) embryos at E10.25 and E11.25, and genetic analysis shows that the RXR alpha and Epo genes are coupled in the same pathway.", "We furthermore show that the Epo gene is retinoic acid inducible in embryos, and that the Epo gene enhancer contains a DR2 sequence that represents a retinoic acid receptor-binding site and a retinoic acid receptor transcriptional response element.", "However, unlike Epo-deficient embryos that die from anemia, the erythropoietic deficiency in RXR alpha(-/-) embryos is transient; Epo mRNA is expressed at normal levels by E12.5, and erythropoiesis and liver morphology are normal by E14.5.", "We show that HNF4, like RXR alpha a member of the nuclear receptor family, is abundantly expressed in fetal liver hepatocytes, and is competitive with retinoic acid receptors for occupancy of the Epo gene enhancer DR2 element.", "We propose that Epo expression is regulated during the E9.5--E11.5 phase of fetal liver erythropoiesis by RXR alpha and retinoic acid, and that expression then becomes dominated by HNF4 activity from E11.5 onward.", "This transition may be responsible for switching regulation of Epo expression from retinoic acid control to hypoxic control, as is found throughout the remainder of life."], "structured": false}
{"doc_id": 25832301, "title": "Tetraspanin 7 (TSPAN7) expression is upregulated in multiple myeloma patients and inhibits myeloma tumour development in vivo.", "abstract": ["BACKGROUND Increased expression of the tetraspanin TSPAN7 has been observed in a number of cancers; however, it is unclear how TSPAN7 plays a role in cancer progression.   \n", "METHODS We investigated the expression of TSPAN7 in the haematological malignancy multiple myleoma (MM) and assessed the consequences of TSPAN7 expression in the adhesion, migration and growth of MM plasma cells (PC) in vitro and in bone marrow (BM) homing and tumour growth in vivo.", "Finally, we characterised the association of TSPAN7 with cell surface partner molecules in vitro.   \n", "RESULTS TSPAN7 was found to be highly expressed at the RNA and protein level in CD138(+) MM PC from approximately 50% of MM patients.", "TSPAN7 overexpression in the murine myeloma cell line 5TGM1 significantly reduced tumour burden in 5TGM1/KaLwRij mice 4 weeks after intravenous adminstration of 5TGM1 cells.", "While TSPAN7 overexpression did not affect cell proliferation in vitro, TSPAN7 increased 5TGM1 cell adhesion to BM stromal cells and transendothelial migration.", "In addition, TSPAN7 was found to associate with the molecular chaperone calnexin on the cell surface.   \n", "CONCLUSION These results suggest that elevated TSPAN7 may be associated with better outcomes for up to 50% of MM patients."], "structured": true}
{"doc_id": 25837950, "title": "Association of body mass index with outcomes in patients with CKD.", "abstract": ["Obesity is associated with higher mortality in the general population, but this association is reversed in patients on dialysis.", "The nature of the relationship of obesity with adverse clinical outcomes in nondialysis-dependent CKD and the putative interaction of the severity of disease with this association are unclear.", "We analyzed data from a nationally representative cohort of 453,946 United States veterans with eGFR<60 ml/min per 1.73 m(2).", "The associations of body mass index categories (<20, 20 to <25, 25 to <30, 30 to <35, 35 to <40, 40 to <45, 45 to <50, and \u226550 kg/m(2)) with all-cause mortality and disease progression (using multiple definitions, including incidence of ESRD, doubling of serum creatinine, and the slopes of eGFR) were examined in Cox proportional hazards models and logistic regression models.", "Multivariable adjustments were made for age, race, comorbidities and medications, and baseline eGFR.", "Body mass index showed a relatively consistent U-shaped association with clinical outcomes, with the best outcomes observed in overweight and mildly obese patients.", "Body mass index levels <25 kg/m(2) were associated with worse outcomes in all patients, independent of severity of CKD.", "Body mass index levels \u226535 kg/m(2) were associated with worse outcomes in patients with earlier stages of CKD, but this association was attenuated in those patients with eGFR<30 ml/min per 1.73 m(2).", "Thus, until clinical trials establish the ideal body mass index, a cautious approach to weight management is warranted in this patient population."], "structured": false}
{"doc_id": 25838286, "title": "WRN, the protein deficient in Werner syndrome, plays a critical structural role in optimizing DNA repair.", "abstract": ["Werner syndrome (WS) predisposes patients to cancer and premature aging, owing to mutations in WRN.", "The WRN protein is a RECQ-like helicase and is thought to participate in DNA double-strand break (DSB) repair by non-homologous end joining (NHEJ) or homologous recombination (HR).", "It has been previously shown that non-homologous DNA ends develop extensive deletions during repair in WS cells, and that this WS phenotype was complemented by wild-type (wt) WRN.", "WRN possesses both 3' --> 5' exonuclease and 3' --> 5' helicase activities.", "To determine the relative contributions of each of these distinct enzymatic activities to DSB repair, we examined NHEJ and HR in WS cells (WRN-/-) complemented with either wtWRN, exonuclease-defective WRN (E-), helicase-defective WRN (H-) or exonuclease/helicase-defective WRN (E-H-).", "The single E-and H- mutants each partially complemented the NHEJ abnormality of WRN-/- cells.", "Strikingly, the E-H- double mutant complemented the WS deficiency nearly as efficiently as did wtWRN.", "Similarly, the double mutant complemented the moderate HR deficiency of WS cells nearly as well as did wtWRN, whereas the E- and H- single mutants increased HR to levels higher than those restored by either E-H- or wtWRN.", "These results suggest that balanced exonuclease and helicase activities of WRN are required for optimal HR.", "Moreover, WRN appears to play a structural role, independent of its enzymatic activities, in optimizing HR and efficient NHEJ repair.", "Another human RECQ helicase, BLM, suppressed HR but had little or no effect on NHEJ, suggesting that mammalian RECQ helicases have distinct functions that can finely regulate recombination events."], "structured": false}
{"doc_id": 25842866, "title": "In vitro generated antibodies specific for telomeric guanine-quadruplex DNA react with Stylonychia lemnae macronuclei.", "abstract": ["Most eukaryotic telomeres contain a repeating motif with stretches of guanine residues that form a 3'-terminal overhang extending beyond the telomeric duplex region.", "The telomeric repeat of hypotrichous ciliates, d(T(4)G(4)), forms a 16-nucleotide 3'-overhang.", "Such sequences can adopt parallel-stranded as well as antiparallel-stranded quadruplex conformations in vitro.", "Although it has been proposed that guanine-quadruplex conformations may have important cellular roles including telomere function, recombination, and transcription, evidence for the existence of this DNA structure in vivo has been elusive to date.", "We have generated high-affinity single-chain antibody fragment (scFv) probes for the guanine-quadruplex formed by the Stylonychia telomeric repeat, by ribosome display from the Human Combinatorial Antibody Library.", "Of the scFvs selected, one (Sty3) had an affinity of K(d) = 125 pM for the parallel-stranded guanine-quadruplex and could discriminate with at least 1,000-fold specificity between parallel or antiparallel quadruplex conformations formed by the same sequence motif.", "A second scFv (Sty49) bound both the parallel and antiparallel quadruplex with similar (K(d) = 3--5 nM) affinity.", "Indirect immunofluorescence studies show that Sty49 reacts specifically with the macronucleus but not the micronucleus of Stylonychia lemnae.", "The replication band, the region where replication and telomere elongation take place, was also not stained, suggesting that the guanine-quadruplex is resolved during replication.", "Our results provide experimental evidence that the telomeres of Stylonychia macronuclei adopt in vivo a guanine-quadruplex structure, indicating that this structure may have an important role for telomere functioning."], "structured": false}
{"doc_id": 25853741, "title": "Incidence of skin cancer after renal transplantation in The Netherlands.", "abstract": ["The incidence of squamous cell carcinoma (SCC) and basal cell carcinoma (BCC) was analyzed separately in all 764 patients who received a renal allograft between 1966 and 1988 at the Leiden University Hospital.", "The mean follow-up period was 8.7 posttransplant years (range 1-21 years).", "During this time period 176 skin cancers were diagnosed in 47 patients.", "The overall risk to develop a first tumor increased from 10% after 10 years to 40% after 20 years of graft survival.", "The overall incidence of SCC was 250 times higher and that of BCC 10 times higher when compared with the general Dutch population.", "Moreover the localization of SCCs and BCCs differed considerably.", "Solar radiation is thought to be an important risk factor for the development of skin cancer.", "However, the occurrence of skin cancer in long-term graft survivors forms also a major problem in a country with a higher geographical latitude and a moderate amount of sun-exposure, such as the Netherlands."], "structured": false}
{"doc_id": 25858295, "title": "Myogenic and morphogenetic defects in the heart tubes of murine embryos lacking the homeo box gene Nkx2-5.", "abstract": ["The murine homeo box gene Nkx2-5 is expressed in precardiac mesoderm and in the myocardium of embryonic and fetal hearts.", "Targeted interruption of Nkx2-5 resulted in abnormal heart morphogenesis, growth retardation and embryonic lethality at approximately 9-10 days postcoitum (p.c.).", "Heart tube formation occurred normally in mutant embryos, but looping morphogenesis, a critical determinant of heart form, was not initiated at the linear heart tube stage (8.25-8.5 days p.c.).", "Commitment to the cardiac muscle lineage, expression of most myofilament genes and myofibrillogenesis were not compromised.", "However, the myosin light-chain 2V gene (MLC2V) was not expressed in mutant hearts nor in mutant ES cell-derived cardiocytes.", "MLC2V expression normally occurs only in ventricular cells and is the earliest known molecular marker of ventricular differentiation.", "The regional expression in mutant hearts of two other ventricular markers, myosin heavy-chain beta and cyclin D2, indicated that not all ventricle-specific gene expression is dependent on Nkx2-5.", "The data demonstrate that Nkx2-5 is essential for normal heart morphogenesis, myogenesis, and function.", "Furthermore, this gene is a component of a genetic pathway required for myogenic specialization of the ventricles."], "structured": false}
{"doc_id": 25878014, "title": "Hygiene hypothesis in inflammatory bowel disease: a critical review of the literature.", "abstract": ["The hygiene hypothesis is thought to be a significant contributor to the growing incidence of inflammatory bowel disease (IBD) around the world, although the evidence for specific factors that underlie the hygiene hypothesis in IBD is unclear.", "We aimed to systematically review the literature to determine which hygiene-related factors are associated with the development of IBD.", "Publications identified from a broad based MEDLINE and Current Contents search between 1966 and 2007 on key terms relevant to the 'hygiene hypothesis' and IBD including H pylori exposure, helminths, cold chain hypothesis, measles infection and vaccination, antibiotic use, breastfeeding, family size, sibship, urban upbringing, day care attendance and domestic hygiene were reviewed.", "The literature suggests that the hygiene hypothesis and its association with decreased microbial exposure in childhood probably plays an important role in the development of IBD, although the strength of the supporting data for each of the factors varies considerably.", "The most promising factors that may potentially be associated with development of IBD include H pylori exposure, helminths, breastfeeding and sibship.", "However, the vast majority of studies in this area are plagued by serious methodological shortcomings, particularly the reliance on retrospective recall of information making it difficult to truly ascertain the importance of a 'hygiene hypothesis' in IBD.", "The 'hygiene hypothesis' in IBD is an important area of research that may give clues to the aetiology of this disease.", "Directions for future research are recommended."], "structured": false}
{"doc_id": 25886725, "title": "Are dual eligibles admitted to poorer quality skilled nursing facilities?", "abstract": ["BACKGROUND Dual eligibles, persons who qualify for both Medicare and Medicaid coverage, often receive poorer quality care relative to other Medicare beneficiaries.   \n", "OBJECTIVES To determine whether dual eligibles are discharged to lower quality post-acute skilled nursing facilities (SNFs) compared with Medicare-only beneficiaries.   ", "RESEARCH DESIGN Following the random utility maximization model, we specified a discharge function using a conditional logit model and tested how this discharge rule varied by dual-eligibility status.   ", "SUBJECTS A total of 692,875 Medicare fee-for-service patients (22% duals) who were discharged for Medicare paid SNF care between July 2004 and June 2005.   \n", "MEASURES Medicare enrollment and the Medicaid Analytic Extract files were used to determine dual eligibility.", "The proportion of Medicaid patients and nursing staff characteristics provided measures of SNF quality.   \n", "RESULTS Duals are more likely to be discharged to SNFs with a higher share of Medicaid patients and fewer nurses.", "These results are robust to estimation with an alternative subsample of patients based on primary diagnoses, propensity of being dual eligible, and likelihood of remaining in the nursing home.   \n", "CONCLUSIONS Disparities exist in access to quality SNF care for duals.", "Strategies to improve discharge planning processes are required to redirect patients to higher quality providers, regardless of Medicaid eligibility."], "structured": true}
{"doc_id": 25895285, "title": "Quantitative phosphoproteomic analysis of acquired cancer drug resistance to pazopanib and dasatinib", "abstract": ["Acquired drug resistance impacts the majority of patients being treated with tyrosine kinase inhibitors (TKIs) and remains a key challenge in modern anti-cancer therapy.", "The lack of clinically effective therapies to overcome resistance represents an unmet need.", "Understanding the signalling that drives drug resistance will facilitate the development of new salvage therapies to treat patients with secondary TKI resistance.", "In this study, we utilise mass spectrometry to characterise the global phosphoproteomic alterations that accompany the acquisition of resistance to two FDA-approved TKIs, pazopanib and dasatinib, in the A204 rhabdoid tumour cell line.", "Our analysis finds that only 6% and 9.7% of the quantified phosphoproteome is altered upon the acquisition of pazopanib and dasatinib resistance, respectively.", "Pazopanib resistant cells display elevated phosphorylation in cytoskeletal regulatory pathways while dasatinib resistant cells show an upregulation of the insulin receptor/IGF-1R signalling pathway.", "Drug response profiling rediscovers several previously reported vulnerabilities associated with pazopanib and dasatinib resistance and identifies a new dependency to the second generation HSP90 inhibitor NVP-AUY-922.", "This study provides a useful resource detailing the candidate signalling determinants of acquired TKI resistance; and reveals a therapeutic approach of inhibiting HSP90 function as a means of salvage therapy to overcome pazopanib and dasatinib resistance.   ", "SIGNIFICANCE Pazopanib and dasatinib are tyrosine kinase inhibitors (TKIs) approved for the treatment of multiple cancer types.", "Patients who are treated with these drugs are prone to the development of drug resistance and consequently tumour relapse.", "Here we use quantitative phosphoproteomics to characterise the signalling pathways which are enriched in cells that have acquired resistance to these two drugs.", "Furthermore, targeted drug screens were used to identify salvage therapies capable of overcoming pazopanib and dasatinib resistance.", "This data advances our understanding of the mechanisms of TKI resistance and highlights candidate targets for cancer therapy."], "structured": false}
{"doc_id": 25897733, "title": "Pandemic H1N12009 influenza and HIV: a review of natural history, management and vaccine immunogenicity.", "abstract": ["PURPOSE OF REVIEW The 2009 pandemic HIN1 influenza strain (H1N12009) produced more severe disease and increased risk for mortality.", "As an at-risk population for more severe influenza illness, particular concern regarding HIV patients triggered a focused effort to evaluate disease burden and vaccine efficacy in these populations.   ", "RECENT FINDINGS As with other immune-compromised individuals, most HIV-infected individuals recovered without major consequence.", "Although HIV infection was assumed to be a risk factor for more severe disease and death, the published literature does not indicate this to be so.", "Neuraminadase inhibitors were well tolerated by this population and there was no evidence of clinically significant pharmacokinetic interactions with antiretroviral therapy.", "Immunogenicity was increased with H1N12009 vaccine compared to the historical results of nonpandemic vaccines and optimized by the use of adjuvants.", "Booster dosing was also of benefit.", "H1N12009 vaccine was generally well tolerated without evidence of detrimental effect on HIV status.   ", "SUMMARY The worse case scenario was not realized for H1N12009 in the general population or in those with HIV.", "Immunization with adjuvant represents a key measure to protect this population from H1N12009 and other future novel influenza strains."], "structured": true}
{"doc_id": 25900857, "title": "Population genomics of the honey bee reveals strong signatures of positive selection on worker traits.", "abstract": ["Most theories used to explain the evolution of eusociality rest upon two key assumptions: mutations affecting the phenotype of sterile workers evolve by positive selection if the resulting traits benefit fertile kin, and that worker traits provide the primary mechanism allowing social insects to adapt to their environment.", "Despite the common view that positive selection drives phenotypic evolution of workers, we know very little about the prevalence of positive selection acting on the genomes of eusocial insects.", "We mapped the footprints of positive selection in Apis mellifera through analysis of 40 individual genomes, allowing us to identify thousands of genes and regulatory sequences with signatures of adaptive evolution over multiple timescales.", "We found Apoidea- and Apis-specific genes to be enriched for signatures of positive selection, indicating that novel genes play a disproportionately large role in adaptive evolution of eusocial insects.", "Worker-biased proteins have higher signatures of adaptive evolution relative to queen-biased proteins, supporting the view that worker traits are key to adaptation.", "We also found genes regulating worker division of labor to be enriched for signs of positive selection.", "Finally, genes associated with worker behavior based on analysis of brain gene expression were highly enriched for adaptive protein and cis-regulatory evolution.", "Our study highlights the significant contribution of worker phenotypes to adaptive evolution in social insects, and provides a wealth of knowledge on the loci that influence fitness in honey bees."], "structured": false}
{"doc_id": 25901598, "title": "An acetylation switch in p53 mediates holo-TFIID recruitment.", "abstract": ["Posttranslational modifications mediate important regulatory functions in biology.", "The acetylation of the p53 transcription factor, for example, promotes transcriptional activation of target genes including p21.", "Here we show that the acetylation of two lysine residues in p53 promotes recruitment of the TFIID subunit TAF1 to the p21 promoter through its bromodomains.", "UV irradiation of cells diacetylates p53 at lysines 373 and 382, which in turn recruits TAF1 to a distal p53-binding site on the p21 promoter prior to looping to the core promoter.", "Disruption of acetyl-p53/bromodomain interaction inhibits TAF1 recruitment to both the distal p53-binding site and the core promoter.", "Further, the TFIID subunits TAF4, TAF5, and TBP are detected on the core promoter prior to TAF1, suggesting that, upon DNA damage, distinct subunits of TFIID may be recruited separately to the p21 promoter and that the transcriptional activation depends on posttranslational modification of the p53 transcription factor."], "structured": false}
{"doc_id": 25915873, "title": "Dasatinib inhibits both osteoclast activation and prostate cancer PC-3-cell-induced osteoclast formation.", "abstract": ["PURPOSE Therapies to target prostate cancer bone metastases have only limited effects.", "New treatments are focused on the interaction between cancer cells, bone marrow cells and the bone matrix.", "Osteoclasts play an important role in the development of bone tumors caused by prostate cancer.", "Since Src kinase has been shown to be necessary for osteoclast function, we hypothesized that dasatinib, a Src family kinase inhibitor, would reduce osteoclast activity and prostate cancer (PC-3) cell-induced osteoclast formation.   \n", "RESULTS Dasatinib inhibited RANKL-induced osteoclast differentiation of bone marrow-derived monocytes with an EC(50) of 7.5 nM. PC-3 cells, a human prostate cancer cell line, were able to differentiate RAW 264.7 cells, a murine monocytic cell line, into osteoclasts, and dasatinib inhibited this differentiation.", "In addition, conditioned medium from PC-3 cell cultures was able to differentiate RAW 264.7 cells into osteoclasts and this too, was inhibited by dasatinib.", "Even the lowest concentration of dasatinib, 1.25 nmol, inhibited osteoclast differentiation by 29%.", "Moreover, dasatinib inhibited osteoclast activity by 58% as measured by collagen 1 release.   ", "EXPERIMENTAL DESIGN We performed in vitro experiments utilizing the Src family kinase inhibitor dasatinib to target osteoclast activation as a means of inhibiting prostate cancer bone metastases.   \n", "CONCLUSION Dasatinib inhibits osteoclast differentiation of mouse primary bone marrow-derived monocytes and PC-3 cell-induced osteoclast differentiation.", "Dasatinib also inhibits osteoclast degradation activity.", "Inhibiting osteoclast differentiation and activity may be an effective targeted therapy in patients with prostate cancer bone metastases."], "structured": true}
{"doc_id": 25928548, "title": "BMP receptor ALK3 controls collecting system development.", "abstract": ["The molecular signals that regulate growth and branching of the ureteric bud during formation of the renal collecting system are largely undefined.", "Members of the bone morphogenetic protein (BMP) family signal through the type I BMP receptor ALK3 to inhibit ureteric bud and collecting duct cell morphogenesis in vitro.", "We investigated the function of the BMP signaling pathway in vivo by generating a murine model of ALK3 deficiency restricted to the ureteric bud lineage (Alk3(UB-/-) mice).", "At the onset of branching morphogenesis, Alk3(UB-/-) kidneys are characterized by an abnormal primary (1 degrees ) ureteric bud branch pattern and an increased number of ureteric bud branches.", "However, during later stages of renal development, Alk3(UB-/-) kidneys have fewer ureteric bud branches and collecting ducts than wild-type kidneys.", "Postnatal Alk3(UB-/-) mice exhibit a dysplastic renal phenotype characterized by hypoplasia of the renal medulla, a decreased number of medullary collecting ducts, and abnormal expression of beta-catenin and c-MYC in medullary tubules.", "In summary, normal kidney development requires ALK3-dependent BMP signaling, which controls ureteric bud branching."], "structured": false}
{"doc_id": 25937484, "title": "Increased release of ferritin and iron by iron-loaded alveolar macrophages in cigarette smokers.", "abstract": ["The lower respiratory tract of cigarette smokers contains an increased amount of iron that is predominantly sequestered within alveolar macrophages (AM), but is also present in alveolar epithelial fluid.", "Extracellular ferritin-bound iron could potentially be released by reductants present in cigarette smoke and catalyze generation of highly reactive hydroxyl radicals capable of causing oxidant injury.", "To determine whether AM are a source of alveolar extracellular ferritin and iron, we assessed in vitro release of iron, ferritin, and transferrin by AM recovered by bronchoalveolar lavage (BAL) of 27 healthy subjects including nine nonsmokers (NS), nine light smokers (LS), and nine heavy smokers (HS).", "Release of iron in vitro over 20 h was increased in AM recovered from LS (2.24 +/-", "0.21 nmol/10(6) AM/20 h, p < 0.001) and HS (3.11 +/-", "0.32 nmol/10(6) AM, p < 0.001) compared with NS (1.28 +/-", "0.08 nmol/10(6) AM).", "Release of ferritin in vitro over 20 h was also increased in AM recovered from LS (71 +/-", "24 ng/10(6) AM, p < 0.05) and HS (176 +/-", "35 ng/10(6), p < 0.001) compared with NS (18 +/-", "3 ng/10(6) AM).", "AM recovered from 12 smokers (8 HS, 4 LS) contained greater than 10 nmol of iron per 10(6) cells.", "These iron-loaded AM released a greater percentage of cell ferritin stores in vitro over 4 h (8.4% +/-", "1.1, p < 0.01) than did AM from NS (3.2% +/- 0.6).", "Release of lactate dehydrogenase (LDH) over 4 h was substantially less (2.9% +/-", "0.3, p < 0.001) than ferritin release.(ABSTRACT TRUNCATED AT 250 WORDS)"], "structured": false}
{"doc_id": 25938221, "title": "The spectrum of retinopathy in adults with Plasmodium falciparum malaria", "abstract": ["A specific retinopathy has been described in African children with cerebral malaria, but in adults this has not been extensively studied.", "Since the structure and function of the retinal vasculature greatly resembles the cerebral vasculature, study of retinal changes can reveal insights into the pathophysiology of cerebral malaria.", "A detailed observational study of malarial retinopathy in Bangladeshi adults was performed using high-definition portable retinal photography.", "Retinopathy was present in 17/27 adults (63%) with severe malaria and 14/20 adults (70%) with cerebral malaria.", "Moderate or severe retinopathy was more frequent in cerebral malaria (11/20, 55%) than in uncomplicated malaria (3/15, 20%; P=0.039), bacterial sepsis (0/5, 0%; P=0.038) or healthy controls (0/18, 0%; P<0.001).", "The spectrum of malarial retinopathy was similar to that previously described in African children, but no vessel discolouration was observed.", "The severity of retinal whitening correlated with admission venous plasma lactate (P=0.046), suggesting that retinal ischaemia represents systemic ischaemia.", "In conclusion, retinal changes related to microvascular obstruction were common in adults with severe falciparum malaria and correlated with disease severity and coma, suggesting that a compromised microcirculation has important pathophysiological significance in severe and cerebral malaria.", "Portable retinal photography has potential as a valuable tool to study malarial retinopathy."], "structured": false}
{"doc_id": 25938251, "title": "Prospective randomized open blinded end-point (PROBE) study. A novel design for intervention trials. Prospective Randomized Open Blinded End-Point.", "abstract": ["A novel design for intervention studies is presented, the so called PROBE study (Prospective Randomized Open, Blinded End-point).", "This design is compared to the classical double-blind design.", "Among the advantages of the PROBE design are lower cost and greater similarity to standard clinical practice, which should make the results more easily applicable in routine medical care.", "Since end-points are evaluated by a blinded end-point committee it is obvious that there should be no difference between the two types of trials in this regard."], "structured": false}
{"doc_id": 25942757, "title": "PSGL-1 function in immunity and steady state homeostasis.", "abstract": ["The substantial importance of P-selectin glycoprotein ligand 1 (PSGL-1) in leukocyte trafficking has continued to emerge beyond its initial identification as a selectin ligand.", "PSGL-1 seemed to be a relatively simple molecule with an extracellular mucin domain extended as a flexible rod, teleologically consistent with its primary role in tethering leukocytes to endothelial selectins.", "The rolling interaction between leukocyte and endothelium mediated by this selectin-PSGL-1 interaction requires branched O-glycan extensions on specific PSGL-1 amino acid residues.", "In some cells, such as neutrophils, the glycosyltransferases involved in formation of the O-glycans are constitutively expressed, while in other cells, such as T cells, they are expressed only after appropriate activation.", "Thus, PSGL-1 supports leukocyte recruitment in both innate and adaptive arms of the immune response.", "A complex array of amino acids within the selectins engage multiple sugar residues of the branched O-glycans on PSGL-1 and provide the molecular interactions responsible for the velcro-like catch bonds that support leukocyte rolling.", "Such binding of PSGL-1 can also induce signaling events that influence cell phenotype and function.", "Scrutiny of PSGL-1 has revealed a better understanding of how it performs as a selectin ligand and yielded unexpected insights that extend its scope from supporting leukocyte rolling in inflammatory settings to homeostasis including stem cell homing to the thymus and mature T-cell homing to secondary lymphoid organs.", "PSGL-1 has been found to bind homeostatic chemokines CCL19 and CCL21 and to support the chemotactic response to these chemokines.", "Surprisingly, the O-glycan modifications of PSGL-1 that support rolling mediated by selectins in inflammatory conditions interfere with PSGL-1 binding to homeostatic chemokines and thereby limit responsiveness to the chemotactic cues used in steady state T-cell traffic.", "The multi-level influence of PSGL-1 on cell traffic in both inflammatory and steady state settings is therefore substantially determined by the orchestrated addition of O-glycans.", "However, central as specific O-glycosylation is to PSGL-1 function, in vivo regulation of PSGL-1 glycosylation in T cells remains poorly understood.", "It is our purpose herein to review what is known, and not known, of PSGL-1 glycosylation and to update understanding of PSGL-1 functional scope."], "structured": false}
{"doc_id": 25946292, "title": "Ligand binding determines whether CD46 is internalized by clathrin-coated pits or macropinocytosis.", "abstract": ["CD46 is a ubiquitous human cell surface receptor for the complement components C3b and C4b and for various pathogens, including the measles virus and human herpes virus 6.", "Ligand binding to CD46 affects (i) protection of autologous cells from complement attack by breakdown of complement components, (ii) intracellular signals that affect the regulation of immune cell function, (iii) antigen presentation, and (iv) down-regulation of cell surface CD46.", "Recent evidence indicates that CD46 signaling can link innate and acquired immune function.", "The molecular mechanisms for these processes and the importance of intracellular trafficking of the receptor have not yet been elucidated.", "We demonstrate here that, in nonlymphoid cells, CD46 is constitutively internalized via clathrin-coated pits, traffics to multivesicular bodies, and is recycled to the cell surface.", "However, cross-linking of CD46 at the cell surface, by either multivalent antibody or by measles virus, induces pseudopodia that engulf the ligand in a process similar to macropinocytosis, and leads to the degradation of cell surface CD46.", "Thus, we have elucidated two pathways for CD46 internalization, which are regulated by the valence of cross-linking of CD46 and which utilize either clathrin-coated pits or pseudopodial extension.", "This has important implications for CD46 signaling, antigen presentation, CD46 down-regulation, and engulfment of pathogens."], "structured": false}
{"doc_id": 25950264, "title": "A three-dimensional cell biology model of human hepatocellular carcinoma in vitro", "abstract": ["We established an in vitro 3-D model of metastatic hepatocellular carcinoma (HCC) by culturing MHCC97H cells on molecular scaffolds within a rotating wall vessel bioreactor.", "Morphological and biochemical analyses revealed that the 3-D HCC model mirrored many clinical pathological features of HCC in vivo, including cancer cell morphology, tissue ultrastructure, protein production and secretion, glucose metabolism, tissue-specific gene expression, and apoptosis.", "Xenografts into livers of nude mice resulted in tumorigenesis and distant metastasis.", "This 3-D HCC spheroid is a promising model for HCC tumor biology, anticancer drug screening, and for the establishment of HCC animal models."], "structured": false}
{"doc_id": 25953438, "title": "Patterns of age-specific mortality in children in endemic areas of sub-Saharan Africa.", "abstract": ["Understanding of the age- and season- dependence of malaria mortality is an important prerequisite for epidemiologic models of malaria immunity.", "However, most studies of malaria mortality have aggregated their results into broad age groups and across seasons, making it hard to predict the likely impact of interventions targeted at specific age groups of children.", "We present age-specific mortality rates for children aged < 15 years for the period of 2001-2005 in 7 demographic surveillance sites in areas of sub-Saharan Africa with stable endemic Plasmodium falciparum malaria.", "We use verbal autopsies (VAs) to estimate the proportion of deaths by age group due to malaria, and thus calculate malaria-specific mortality rates for each site, age-group, and month of the year.", "In all sites a substantial proportion of deaths (ranging from 20.1% in a Mozambican site to 46.2% in a site in Burkina Faso) were attributed to malaria.", "The overall age patterns of malaria mortality were similar in the different sites.", "Deaths in the youngest children (< 3 months old) were only rarely attributed to malaria, but in children over 1 year of age the proportion of deaths attributed to malaria was only weakly age-dependent.", "In most of the sites all-cause mortality rates peaked during the rainy season, but the strong seasonality in malaria transmission in these sites was not reflected in strong seasonality in the proportion of deaths attributed to malaria, except in the two sites in Burkina Faso.", "Improvement in the specificity of malaria verbal autopsies would make it easier to interpret the age and season patterns in such data."], "structured": false}
{"doc_id": 25969485, "title": "Obesity due to melanocortin 4 receptor (MC4R) deficiency is associated with increased linear growth and final height, fasting hyperinsulinemia, and incompletely suppressed growth hormone secretion.", "abstract": ["CONTEXT Melanocortin receptor 4 (MC4R) deficiency is characterized by increased linear growth greater than expected for the degree of obesity.   \n", "OBJECTIVE The objective of the investigation was to study the somatotroph axis in obese MC4R-deficient patients and equally obese controls.   \n", "PATIENTS AND METHODS We obtained anthropometric measurements and insulin concentrations in 153 MC4R-deficient subjects and 1392 controls matched for age and severity of obesity.", "We measured fasting IGF-I, IGF-II, IGF binding protein (IGFBP)-1, IGFBP-3, and acid-labile subunit levels in a subset of 33 MC4R-deficient patients and 36 control subjects.", "We examined pulsatile GH secretion in six adult MC4R-deficient subjects and six obese controls.   \n", "RESULTS Height sd score was significantly greater in MC4R-deficient children under 5 yr of age compared with controls (mean \u00b1 SEM: 2.3 \u00b1 0.06 vs. 1.8 \u00b1 0.04, P < 0.001), an effect that persisted throughout childhood.", "Final height (cm) was greater in MC4R-deficient men (mean \u00b1 SEM 173 \u00b1 2.5 vs. 168 \u00b1 2.1, P < 0.001) and women (mean 165 \u00b1 2.1 vs. 158 \u00b1 1.9, P < 0.001).", "Fasting IGF-I, IGF-II, acid-labile subunit, and IGFBP-3 concentrations were similar in the two groups.", "GH levels were markedly suppressed in obese controls, but pulsatile GH secretion was retained in MC4R deficiency.", "The mean maximal GH secretion rate per burst (P < 0.05) and mass per burst (P < 0.05) were increased in MC4R deficiency, consistent with increased pulsatile and total GH secretion.", "Fasting insulin levels were markedly elevated in MC4R-deficient children.   \n", "CONCLUSIONS In MC4R deficiency, increased linear growth in childhood leads to increased adult final height, greater than predicted by obesity alone.", "GH pulsatility is maintained in MC4R deficiency, a finding consistent with animal studies, suggesting a role for MC4R in controlling hypothalamic somatostatinergic tone.", "Fasting insulin levels are significantly higher in children carrying MC4R mutations.", "Both of these factors may contribute to the accelerated growth phenotype characteristic of MC4R deficiency."], "structured": true}
{"doc_id": 25970224, "title": "The selectivity of beta-adrenoceptor antagonists on isoprenaline-induced changes in heart rate, blood pressure, soleus muscle contractility and airways function in anaesthetized cats.", "abstract": ["The beta-adrenoceptor antagonist of propranolol, metoprolol, atenolol and butoxamine in anaesthetized cats has been measured and compared with the activity of four synthetic phenylethanolamine derivatives.", "The effects of isoprenaline on four parameters in the anaesthetized cat: heart rate, blood pressure, soleus muscle contractility and airway reactance, were measured and the modification of the isoprenaline dose-response relation by each of the antagonist drugs assessed.", "Parallel shifts in log dose-response curves for isoprenaline were caused by propranolol for all parameters, by metoprolol and atenolol for each parameter except blood pressure, and butoxamine for each except soleus muscle and heart rate.", "Selectivity of action of the antagonists between different organs was measured by comparing DR10 values, computed from isoprenaline dose-ratios.", "Propranolol was the most potent antagonist and showed slight selectivity of action on soleus muscle compared with heart.", "Atenolol and metoprolol were approximately equipotent and were cardioselective at low doses only.", "Butoxamine was the least potent antagonist and possessed non-beta-adrenoceptor effects on the parameters measured.", "Each of the new compounds, 4'-bromo-2'-methoxy-N-isopropyl phenylethanolamine, the 4'-chloro- and 4'-methyl analogues, and 4'-methoxy-N-t-butyl phenylethanolamine, was a potent antagonist but did not exhibit any selectivity of action.", "The results suggest no clear separation of beta-adrenoceptors into beta 1- and beta 2-subclasses in organs of the cat.", "There is no apparent separation of beta-adrenoceptor-mediated effects on skeletal muscle and airways."], "structured": false}
{"doc_id": 25973484, "title": "Breast cancer and obesity: an update.", "abstract": ["Obesity has a complicated relationship to both breast cancer risk and the clinical behavior of the established disease.", "In postmenopausal women, particularly the elderly, various measures of obesity have been positively associated with risk.", "However, before menopause increased body weight is inversely related to breast cancer risk.", "In both premenopausal and postmenopausal breast cancer, the mechanisms by which body weight and obesity affect risk have been related to estrogenic activity.", "Obesity has also been related to advanced disease at diagnosis and with a poor prognosis in both premenopausal and postmenopausal breast cancer.", "Breast cancer in African-American women, considering its relationship to obesity, exhibits some important differences from those described in white women, although the high prevalence of obesity in African-American women may contribute to the relatively poor prognosis compared with white American women.", "Despite the emphasis on estrogens to explain the effects of obesity on breast cancer, other factors may prove to be equally or more important, particularly as they relate to expression of an aggressive tumor phenotype.", "Among these, this review serves to stress insulin, insulin-like growth factor-I, and leptin, and their relationship to angiogenesis, and transcriptional factors."], "structured": false}
{"doc_id": 25974070, "title": "Dietary saturated and unsaturated fats as determinants of blood pressure and vascular function.", "abstract": ["The amount and type of dietary fat have long been associated with the risk of CVD.", "Arterial stiffness and endothelial dysfunction are important risk factors in the aetiology of CHD.", "A range of methods exists to assess vascular function that may be used in nutritional science, including clinic and ambulatory blood pressure monitoring, pulse wave analysis, pulse wave velocity, flow-mediated dilatation and venous occlusion plethysmography.", "The present review focuses on the quantity and type of dietary fat and effects on blood pressure, arterial compliance and endothelial function.", "Concerning fat quantity, the amount of dietary fat consumed habitually appears to have little influence on vascular function independent of fatty acid composition, although single high-fat meals postprandially impair endothelial function compared with low-fat meals.", "The mechanism is related to increased circulating lipoproteins and NEFA which may induce pro-inflammatory pathways and increase oxidative stress.", "Regarding the type of fat, cross-sectional data suggest that saturated fat adversely affects vascular function whereas polyunsaturated fat (mainly linoleic acid (18 : 2n-6) and n-3 PUFA) are beneficial.", "EPA (20 : 5n-3) and DHA (22 : 6n-3) can reduce blood pressure, improve arterial compliance in type 2 diabetics and dyslipidaemics, and augment endothelium-dependent vasodilation.", "The mechanisms for this vascular protection, and the nature of the separate physiological effects induced by EPA and DHA, are priorities for future research.", "Since good-quality observational or interventional data on dietary fatty acid composition and vascular function are scarce, no further recommendations can be suggested in addition to current guidelines at the present time."], "structured": false}
{"doc_id": 25985964, "title": "Very small embryonic-like stem cells with maximum regenerative potential get discarded during cord blood banking and bone marrow processing for autologous stem cell therapy.", "abstract": ["Very small embryonic-like stem cells (VSELs) are possibly lost during cord blood banking and bone marrow (BM) processing for autologus stem cell therapy mainly because of their small size.", "The present study was conducted on human umbilical cord blood (UCB, n=6) and discarded red blood cells (RBC) fraction obtained after separation of mononuclear cells from human BM (n=6), to test this hypothesis.", "The results show that VSELs, which are pluripotent stem cells with maximum regenerative potential, settle along with the RBCs during Ficoll-Hypaque density separation.", "These cells are very small in size (3-5 \u03bcm), have high nucleo-cytoplasmic ratio, and express nuclear Oct-4, cell surface protein SSEA-4, and other pluripotent markers such as Nanog, Sox-2, Rex-1, and Tert as indicated by immunolocalization and quantitative polymerase chain reaction (Q-PCR) studies.", "Interestingly, a distinct population of slightly larger, round hematopoietic stem cells (HSCs) with cytoplasmic Oct-4 were detected in the \"buffy\" coat, which usually gets banked or used during autologus stem cell therapy.", "Immunohistochemical studies on the umbilical cord tissue (UCT) sections (n=3) showed the presence of nuclear Oct-4-positive VSELs and many fibroblast-like mesenchymal stem cells (MSCs) with cytoplasmic Oct-4.", "These VSELs with nuclear Oct-4, detected in UCB, UCT, and discarded RBC fraction obtained after BM processing, may persist throughout life, maintain tissue homeostasis, and undergo asymmetric cell division to self-renew as well as produce larger progenitor stem cells, viz.", "HSCs or MSCs, which follow differentiation trajectories depending on the somatic niche.", "Hence, it can be concluded that the true stem cells in adult body tissues are the VSELs, whereas the HSCs and MSCs are actually progenitor stem cells that arise by asymmetric cell division of VSELs.", "The results of the present study may help explain low efficacy reported during adult autologous stem cell trials, wherein unknowingly progenitor stem cells are injected rather than the pluripotent stem cells with maximum regenerative potential."], "structured": false}
{"doc_id": 25988622, "title": "CNS repair requires both effector and regulatory T cells with distinct temporal and spatial profiles.", "abstract": ["Monocyte-derived macrophages (mo-M\u03a6s) and T cells have been shown to contribute to spinal cord repair.", "Recently, the remote brain choroid plexus epithelium (CP) was identified as a portal for monocyte recruitment, and its activation for leukocyte trafficking was found to be IFN-\u03b3-dependent.", "Here, we addressed how the need for effector T cells can be reconciled with the role of inflammation-resolving immune cells in the repair process.", "Using an acute spinal cord injury model, we show that in mice deficient in IFN-\u03b3-producing T cells, the CP was not activated, and recruitment of inflammation-resolving mo-M\u03a6 to the spinal cord parenchyma was limited.", "We further demonstrate that mo-M\u03a6 locally regulated recruitment of thymic-derived Foxp3(+) regulatory T (Treg) cells to the injured spinal cord parenchyma at the subacute/chronic phase.", "Importantly, an ablation protocol that resulted in reduced Tregs at this stage interfered with tissue remodeling, in contrast to Treg transient ablation, restricted to the 4 d period before the injury, which favored repair.", "The enhanced functional recovery observed following such a controlled decrease of Tregs suggests that reduced systemic immunosuppression at the time of the insult can enhance CNS repair.", "Overall, our data highlight a dynamic immune cell network needed for repair, acting in discrete compartments and stages, and involving effector and regulatory T cells, interconnected by mo-M\u03a6.", "Any of these populations may be detrimental to the repair process if their level or activity become dysregulated.", "Accordingly, therapeutic interventions must be both temporally and spatially controlled."], "structured": false}
{"doc_id": 25993718, "title": "Sperm function tests and fertility.", "abstract": ["Traditionally, the diagnosis of male infertility has depended upon a descriptive evaluation of human semen with emphasis on the number of spermatozoa that are present in the ejaculate, their motility and their morphology.", "The fundamental tenet underlying this approach is that male fertility can be defined by reference to a threshold concentration of motile, morphologically normal spermatozoa that must be exceeded in order to achieve conception.", "Many independent studies have demonstrated that this fundamental concept is flawed and, in reality, it is not so much the absolute number of spermatozoa that determines fertility, but their functional competence.", "In the light of this conclusion, a range of in vitro tests have been developed to monitor various aspects of sperm function including their potential for movement, cervical mucus penetration, capacitation, zona recognition, the acrosome reaction and sperm-oocyte fusion.", "Such functional assays have been found to predict the fertilizing capacity of human spermatozoa in vitro and in vivo with some accuracy.", "Recent developments in this field include the introduction of tests to assess the degree to which human spermatozoa have suffered oxidative stress as well as the integrity of their nuclear and mitochondrial DNA.", "Such assessments not only yield information on the fertilizing capacity of human spermatozoa but also their ability to support normal embryonic development."], "structured": false}
{"doc_id": 25994317, "title": "Isolation and characterization of the cDNA encoding BKLF/TEF-2, a major CACCC-box-binding protein in erythroid cells and selected other cells.", "abstract": ["CACCC boxes are among the critical sequences present in regulatory elements of genes expressed in erythroid cells, as well as in selected other cell types.", "While an erythroid cell-specific CACCC-box-binding protein, EKLF, has been shown to be required in vivo for proper expression of the adult beta-globin gene, it is dispensable for the regulation of several other globin and nonglobin erythroid cell-expressed genes.", "In the work described here, we searched for additional CACCC-box transcription factors that might be active in murine erythroid cells.", "We identified a major gel shift activity (termed BKLF), present in yolk sac and fetal liver erythroid cells, that could be distinguished from EKLF by specific antisera.", "Through relaxed-stringency hybridization, we obtained the cDNA encoding BKLF, a highly basic, novel zinc finger protein that is related to EKLF and other Kr\u00fcppel-like members in its DNA-binding domain but unrelated elsewhere.", "BKLF, which is widely but not ubiquitously expressed in cell lines, is highly expressed in the midbrain region of embryonic mice and appears to correspond to the gel shift activity TEF-2, a transcriptional activator implicated in regulation of the simian virus 40 enhancer and other CACCC-box-containing regulatory elements.", "Because BKLF binds with high affinity and preferentially over Sp1 to many CACCC sequences of erythroid cell expressed genes, it is likely to participate in the control of many genes whose expression appears independent of the action of EKLF."], "structured": false}
{"doc_id": 26000593, "title": "Effect of osteoporosis treatments on risk of non-vertebral fractures: review and meta-analysis of intention-to-treat studies", "abstract": ["Most osteoporosis treatments have proven efficacy in reducing the risk of vertebral fractures, whereas evidence is less straightforward for prevention of non-vertebral fractures.", "Conclusions as to the efficacy of a treatment should be based primarily on analyses of the intention to treat (ITT) population rather than on exploratory subgroup analyses; however, non-vertebral anti-fracture efficacy has been largely derived by post-hoc subgroup analyses.", "This review and meta-analysis was performed to assess non-vertebral anti-fracture efficacy of several osteoporosis therapies, including a more stringent assessment of the ITT populations.", "Data on non-vertebral anti-fracture efficacy, a defined endpoint of the ITT analyses and confirmed by radiographs, were obtained from randomized, placebo-controlled, phase III clinical trials of at least 3-year duration.", "Meta-analyses were performed for the two bisphosphonates, alendronate and risedronate.", "Relative risks (RR), 95% confidence intervals (CI) and statistical significance for active treatment compared with placebo were calculated.", "Eleven clinical trials met the criteria for review, three of which showed statistically significant ( P \u22640.05) non-vertebral anti-fracture efficacy in the ITT population: two trials with risedronate and one trial with strontium.", "A meta-analysis showed significant reductions in the relative risk of non-vertebral fracture for both alendronate (RR=0.86; 95% CI: 0.76\u20130.97, P =0.012) and risedronate (RR=0.81; 95% CI: 0.71\u20130.92, P =0.001).", "Risedronate and strontium ranelate were the only treatments to show non-vertebral anti-fracture efficacy in this robust assessment of anti-fracture efficacy of osteoporosis therapy using ITT populations in trials of 3 years or more in duration.", "Risedronate was the only agent shown to demonstrate efficacy in more than one trial.", "Meta-analysis showed that both alendronate and risedronate provide non-vertebral anti-fracture efficacy."], "structured": false}
{"doc_id": 26008063, "title": "Islet1 deletion causes kidney agenesis and hydroureter resembling CAKUT.", "abstract": ["Islet1 (Isl1) is a transcription factor transiently expressed in a subset of heart and limb progenitors.", "During studies of limb development, conditional Isl1 deletion produced unexpected kidney abnormalities.", "Here, we studied the renal expression of Isl1 and whether it has a role in kidney development.", "In situ hybridization revealed Isl1 expression in the mesenchymal cells surrounding the base of the ureteric bud in mice.", "Conditional deletion of Isl1 caused kidney agenesis or hypoplasia and hydroureter, a phenotype resembling human congenital anomalies of the kidney and urinary tract (CAKUT).", "The absence of Isl1 led to ectopic branching of the ureteric bud out from the nephric duct or to the formation of accessory buds, both of which could lead to obstruction of the ureter-bladder junction and consequent hydroureter.", "The abnormal elongation and poor branching of the ureteric buds were the likely causes of the kidney agenesis or hypoplasia.", "Furthermore, the lack of Isl1 reduced the expression of Bmp4, a gene implicated in the CAKUT-like phenotype, in the metanephric region before ureteric budding.", "In conclusion, Isl1 is essential for proper development of the kidney and ureter by repressing the aberrant formation of the ureteric bud.", "These observations call for further studies to investigate whether Isl1 may be a causative gene for human CAKUT."], "structured": false}
{"doc_id": 26008462, "title": "Tissue transglutaminase (TG2)--a wound response enzyme.", "abstract": ["Repair of tissue after injury depends on a series of concerted but overlapping events including, inflammation, re-epithelialization, neovascularization and synthesis and stabilization of a fibrous extracellular matrix (ECM) that is remodeled to emulate normal tissue over time.", "Particular members of the transglutaminase (TG) family are upregulated during wound healing and act as a novel class of wound-healing mediators during the repair process.", "This group of enzymes which crosslink proteins via epsilon(gamma-glutamyl) lysine bridges are involved in wound healing through their ability to stabilize proteins and also by regulating the behavior of a wide variety of cell types that are recruited to the damaged area in order to carry out tissue repair.", "In this article we discuss the function of the most widely expressed member of the TG family \"tissue transglutaminase\" (TG2) in wound repair.", "Using both early and recent evidence from the literature we demonstrate how the multifunctional TG2 affects the stability of the ECM, cell-ECM interactions and as a consequence cell behavior within the different phases of wound healing, and highlight how TG2 itself might be exploited for therapeutic use."], "structured": false}
{"doc_id": 26011884, "title": "Crystal structures of the glutamate receptor ion channel GluK3 and GluK5 amino-terminal domains.", "abstract": ["Ionotropic glutamate receptors (iGluRs) mediate the majority of fast excitatory synaptic neurotransmission in the central nervous system.", "The selective assembly of iGluRs into AMPA, kainate, and N-methyl-d-aspartic acid (NMDA) receptor subtypes is regulated by their extracellular amino-terminal domains (ATDs).", "Kainate receptors are further classified into low-affinity receptor families (GluK1-GluK3) and high-affinity receptor families (GluK4-GluK5) based on their affinity for the neurotoxin kainic acid.", "These two families share a 42% sequence identity for the intact receptor but only a 27% sequence identity at the level of ATD.", "We have determined for the first time the high-resolution crystal structures of GluK3 and GluK5 ATDs, both of which crystallize as dimers but with a strikingly different dimer assembly at the R1 interface.", "By contrast, for both GluK3 and GluK5, the R2 domain dimer assembly is similar to those reported previously for other non-NMDA iGluRs.", "This observation is consistent with the reports that GluK4-GluK5 cannot form functional homomeric ion channels and require obligate coassembly with GluK1-GluK3.", "Our analysis also reveals that the relative orientation of domains R1 and R2 in individual non-NMDA receptor ATDs varies by up to 10\u00b0, in contrast to the 50\u00b0 difference reported for the NMDA receptor GluN2B subunit.", "This restricted domain movement in non-NMDA receptor ATDs seems to result both from extensive intramolecular contacts between domain R1 and domain R2 and from their assembly as dimers, which interact at both R1 and R2 domains.", "Our results provide the first insights into the structure and function of GluK4-GluK5, the least understood family of iGluRs."], "structured": false}
{"doc_id": 26016929, "title": "Effectiveness of screening older people for impaired vision in community setting: systematic review of evidence from randomised controlled trials.", "abstract": ["OBJECTIVE To assess whether population screening for impaired vision among older people in the community leads to improvements in vision.   \n", "DESIGN Systematic review of randomised controlled trials of population screening in the community that included any assessment of vision or visual function with at least 6 months' follow up.   ", "SUBJECTS Adults aged 65 or over.   \n", "MAIN OUTCOME MEASURE Proportions with visual impairment in intervention and control groups with any method of assessing visual impairment.   \n", "RESULTS There were no trials that primarily assessed visual screening.", "Outcome data on vision were available for 3494 people in five trials of multiphasic assessment.", "All the trials used self reported measures for vision impairment, both as screening tools and as outcome measures.", "The inclusion of a visual screening component in the assessment did not result in improvements in self reported visual problems (pooled odds ratio 1.04:95% confidence interval 0.89 to 1.22).", "A small reduction (11%) in the number of older people with self reported visual problems cannot be excluded.   \n", "CONCLUSIONS Screening of asymptomatic older people in the community is not justified on present evidence.", "Visual impairment in this age group can usually be reduced with treatment.", "It is unclear why no benefit was seen.", "Further work is needed to clarify what interventions are appropriate for older people with unreported impairment of vision."], "structured": true}
{"doc_id": 26019505, "title": "Protein interaction network of the mammalian Hippo pathway reveals mechanisms of kinase-phosphatase interactions.", "abstract": ["The Hippo pathway regulates organ size and tissue homeostasis in response to multiple stimuli, including cell density and mechanotransduction.", "Pharmacological inhibition of phosphatases can also stimulate Hippo signaling in cell culture.", "We defined the Hippo protein-protein interaction network with and without inhibition of serine and threonine phosphatases by okadaic acid.", "We identified 749 protein interactions, including 599 previously unrecognized interactions, and demonstrated that several interactions with serine and threonine phosphatases were phosphorylation-dependent.", "Mutation of the T-loop of MST2 (mammalian STE20-like protein kinase 2), which prevented autophosphorylation, disrupted its association with STRIPAK (striatin-interacting phosphatase and kinase complex).", "Deletion of the amino-terminal forkhead-associated domain of SLMAP (sarcolemmal membrane-associated protein), a component of the STRIPAK complex, prevented its association with MST1 and MST2.", "Phosphatase inhibition produced temporally distinct changes in proteins that interacted with MOB1A and MOB1B (Mps one binder kinase activator-like 1A and 1B) and promoted interactions with upstream Hippo pathway proteins, such as MST1 and MST2, and with the trimeric protein phosphatase 6 complex (PP6).", "Mutation of three basic amino acids that are part of a phospho-serine- and phospho-threonine-binding domain in human MOB1B prevented its interaction with MST1 and PP6 in cells treated with okadaic acid.", "Collectively, our results indicated that changes in phosphorylation orchestrate interactions between kinases and phosphatases in Hippo signaling, providing a putative mechanism for pathway regulation."], "structured": false}
{"doc_id": 26025370, "title": "Differential Effects of N-Acetylcysteine, Theophylline or Bicarbonate on Contrast-Induced Rat Renal Vasoconstriction", "abstract": ["Background: Vasoconstriction and reactive oxygen species (ROS) accumulation following contrast media (CM) injection are the key factors triggering CM-induced nephropathy.", "We compared the effects of N-acetylcysteine (NAC), theophylline or sodium bicarbonate on intrarenal vasoconstriction and ROS generation in a rat model of CM-induced nephropathy.", "Methods: Following a 3-day dehydration, Sprague-Dawley rats received CM (Telebrix) or sham \u2018CM\u2019 injection of 0.9% saline.", "Part of them received NAC, theophylline or bicarbonate prior to CM.", "Medullar renal blood flow was estimated by laser Doppler.", "The animals were sacrificed 1, 15 or 30 min after the respective treatments, their kidneys allocated and intrarenal STAT-8 isoprostane, PGE2 and NO assessed.", "Results: Vasoconstriction was significantly attenuated by NAC.", "Theophylline only mildly attenuated the perfusion drop at 15 min, and was ineffective following 30 min.", "Unlike theophylline or bicarbonate, NAC significantly augmented intrarenal PGE2.", "NAC, theophylline but not bicarbonate, gradually increased intrarenal NO.", "In all experimental variables, CM-induced ROS accumulation, represented by STAT-8 isoprostane estimation, progressed undisturbed.", "Conclusions: (1) CM-induced intrarenal vasoconstriction was efficiently prohibited by NAC but not bicarbonate or theophylline; (2) the vasodilatory effect of NAC was mediated via increased PGE2 synthesis, and (3) ROS accumulation was a primary renal response to CM-induced injury, not affected by any pharmacologic manipulations."], "structured": false}
{"doc_id": 26025820, "title": "Induction of AMPK activity corrects early pathophysiological alterations in the subtotal nephrectomy model of chronic kidney disease.", "abstract": ["The rat kidney ablation and infarction (A/I) model of subtotal or 5/6th nephrectomy is the most commonly studied model of nondiabetic chronic kidney disease (CKD).", "The A/I kidney at 1 wk exhibits reductions in kidney function, as determined by glomerular filtration rate, and diminished metabolic efficiency as determined by oxygen consumption per sodium transport (QO2/TNa).", "As renoprotective AMPK activity is affected by metabolic changes and cellular stress, we evaluated AMPK activity in this model system.", "We show that these early pathophysiological changes are accompanied by a paradoxical decrease in AMPK activity.", "Over time, these kidney parameters progressively worsen with extensive kidney structural, functional, metabolic, and fibrotic changes observed at 4 wk after A/I. We show that induction of AMPK activity with either metformin or 5-aminoimidazole-4-carboxamide ribonucleotide increases AMPK activity in this model and also corrects kidney metabolic inefficiency, improves kidney function, and ameliorates kidney fibrosis and structural alterations.", "We conclude that AMPK activity is reduced in the subtotal nephrectomy model of nondiabetic CKD, that altered regulation of AMPK is coincident with the progression of disease parameters, and that restoration of AMPK activity can suppress the progressive loss of function characteristic of this model.", "We propose that induction of AMPK activity may prove an effective therapeutic target for the treatment of nondiabetic CKD."], "structured": false}
{"doc_id": 26026009, "title": "Magnetic resonance imaging for volume estimation of large multinodular goitres: a comparison with scintigraphy.", "abstract": ["As a result of increasing interest in non-surgical treatment for the reduction of goitre size the use of magnetic resonance (MR) imaging for volume estimation of large multinodular goitres was evaluated in 20 patients (three males and 17 females; age 61 +/-", "21 years) with a multinodular goitre larger than 100 ml.", "In addition, MR measurements were compared with scintigraphic (SC) volume estimations.", "Intraobserver coefficient of variation (CV) of MR measurements was 2.2 +/-", "2.0% (Observer 1) and interobserver CV 4.1 +/-", "2.2% (Observers 1 and 2).", "In all 20 patients signs of mechanical complications were shown on MR images.", "For SC measurements intraobserver CV was 7.5 +/-", "5.7% (Observer 3) and 5.4 +/-", "5.1% (Observer 4).", "Interobserver CV was 10.1 +/-", "6.1%.", "The correlation between measurements with both methods was not strong (r = 0.665) and the resulting CV was 17.3 +/-", "14.2%.", "Underestimation of SC volumes could not be explained by the presence of cysts on the surface of the thyroid.", "It is concluded that MR imaging can be used for in vivo thyroid volume estimation in large multinodular goitres.", "The high precision of MR measurements makes this technique potentially useful for the evaluation of thyroid growth and non-surgical treatment for reducing goitre size.", "Scintigraphic volume measurements do not suffice for this purpose.", "An additional advantage of MR imaging is the detailed anatomical information it provides with regard to mechanical complications of large goitres."], "structured": false}
{"doc_id": 26030079, "title": "Differential role of CbpA and PspA in modulation of in vitro CXC chemokine responses of respiratory epithelial cells to infection with Streptococcus pneumoniae.", "abstract": ["Respiratory epithelial cells play an active part in the host response to respiratory pathogens, such as Streptococcus pneumoniae, by releasing chemokines responsible for neutrophil recruitment.", "In order to investigate the role of specific pneumococcal virulence factors in eliciting CXC chemokine responses, type II pneumocytes (A549) and nasopharyngeal cells (Detroit-562) were infected with S. pneumoniae D39 or mutants lacking choline-binding protein A (CbpA), pneumococcal surface protein A (PspA), or specific domains thereof.", "In response to wild-type D39, both A549 and Detroit-562 cells showed a significant increase in CXC chemokine mRNA and interleukin-8 protein.", "This response was increased twofold when a cbpA deletion mutant (DeltaCbpA) was used, suggesting that CbpA inhibits CXC chemokine induction.", "All three N-terminal domains of CbpA are required for this effect, as in-frame deletion of the respective region of cbpA had the same effect on the CXC chemokine response as deletion of cbpA altogether.", "Infection with a pspA deletion mutant (DeltaPspA) led to a twofold decrease in the CXC chemokine response of A549 but not Detroit-562 cells, compared to infection with D39 at 2 h. Thus, PspA appears to have the ability to stimulate early CXC chemokine release from A549 cells.", "Deletion of the region of pspA encoding the first N-terminal alpha-helical domain reduced the ability of S. pneumoniae to elicit a chemokine response to the same degree as deletion of pspA altogether.", "Thus, the N termini of CbpA and PspA exert differential effects on CXC chemokine induction in epithelial cells infected with S. pneumoniae."], "structured": false}
{"doc_id": 26038789, "title": "HIV-1 therapy with monoclonal antibody 3BNC117 elicits host immune responses against HIV-1", "abstract": ["3BNC117 is a broad and potent neutralizing antibody to HIV-1 that targets the CD4 binding site on the viral envelope spike.", "When administered passively, this antibody can prevent infection in animal models and suppress viremia in HIV-1\u2013infected individuals.", "Here we report that HIV-1 immunotherapy with a single injection of 3BNC117 affects host antibody responses in viremic individuals.", "In comparison to untreated controls that showed little change in their neutralizing activity over a 6-month period, 3BNC117 infusion significantly improved neutralizing responses to heterologous tier 2 viruses in nearly all study participants.", "We conclude that 3BNC117-mediated immunotherapy enhances host humoral immunity to HIV-1."], "structured": false}
{"doc_id": 26045237, "title": "Safety and efficacy of RNAi therapy for transthyretin amyloidosis.", "abstract": ["BACKGROUND Transthyretin amyloidosis is caused by the deposition of hepatocyte-derived transthyretin amyloid in peripheral nerves and the heart.", "A therapeutic approach mediated by RNA interference (RNAi) could reduce the production of transthyretin.   \n", "METHODS We identified a potent antitransthyretin small interfering RNA, which was encapsulated in two distinct first- and second-generation formulations of lipid nanoparticles, generating ALN-TTR01 and ALN-TTR02, respectively.", "Each formulation was studied in a single-dose, placebo-controlled phase 1 trial to assess safety and effect on transthyretin levels.", "We first evaluated ALN-TTR01 (at doses of 0.01 to 1.0 mg per kilogram of body weight) in 32 patients with transthyretin amyloidosis and then evaluated ALN-TTR02 (at doses of 0.01 to 0.5 mg per kilogram) in 17 healthy volunteers.   \n", "RESULTS Rapid, dose-dependent, and durable lowering of transthyretin levels was observed in the two trials.", "At a dose of 1.0 mg per kilogram, ALN-TTR01 suppressed transthyretin, with a mean reduction at day 7 of 38%, as compared with placebo (P=0.01); levels of mutant and nonmutant forms of transthyretin were lowered to a similar extent.", "For ALN-TTR02, the mean reductions in transthyretin levels at doses of 0.15 to 0.3 mg per kilogram ranged from 82.3 to 86.8%, with reductions of 56.6 to 67.1% at 28 days (P<0.001 for all comparisons).", "These reductions were shown to be RNAi-mediated.", "Mild-to-moderate infusion-related reactions occurred in 20.8% and 7.7% of participants receiving ALN-TTR01 and ALN-TTR02, respectively.   \n", "CONCLUSIONS ALN-TTR01 and ALN-TTR02 suppressed the production of both mutant and nonmutant forms of transthyretin, establishing proof of concept for RNAi therapy targeting messenger RNA transcribed from a disease-causing gene.", "(Funded by Alnylam Pharmaceuticals; ClinicalTrials.gov numbers, NCT01148953 and NCT01559077.)."], "structured": true}
{"doc_id": 26047921, "title": "The mechanosensitive ion channel Piezo1 is inhibited by the peptide GsMTx4.", "abstract": ["Cells can respond to mechanical stress by gating mechanosensitive ion channels (MSCs).", "The cloning of Piezo1, a eukaryotic cation selective MSC, defines a new system for studying mechanical transduction at the cellular level.", "Because Piezo1 has electrophysiological properties similar to those of endogenous cationic MSCs that are selectively inhibited by the peptide GsMTx4, we tested whether the peptide targets Piezo1 activity.", "Extracellular GsMTx4 at micromolar concentrations reversibly inhibited \u223c80% of the mechanically induced current of outside-out patches from transfected HEK293 cells.", "The inhibition was voltage insensitive, and as seen with endogenous MSCs, the mirror image d enantiomer inhibited like the l. The rate constants for binding and unbinding based on Piezo1 current kinetics provided association and dissociation rates of 7.0 \u00d7 10(5) M(-1) s(-1) and 0.11 s(-1), respectively, and a K(D) of \u223c155 nM, similar to values previously reported for endogenous MSCs.", "Consistent with predicted gating modifier behavior, GsMTx4 produced an \u223c30 mmHg rightward shift in the pressure-gating curve and was active on closed channels.", "In contrast, streptomycin, a nonspecific inhibitor of cationic MSCs, showed the use-dependent inhibition characteristic of open channel block.", "The peptide did not block currents of the mechanical channel TREK-1 on outside-out patches.", "Whole-cell Piezo1 currents were also reversibly inhibited by GsMTx4, and although the off rate was nearly identical to that of outside-out patches, differences were observed for the on rate.", "The ability of GsMTx4 to target the mechanosensitivity of Piezo1 supports the use of this channel in high-throughput screens for pharmacological agents and diagnostic assays."], "structured": false}
{"doc_id": 26058927, "title": "Thiazolidinediones improve beta-cell function in type 2 diabetic patients.", "abstract": ["Thiazolidinediones (TZDs) improve glycemic control and insulin sensitivity in patients with type 2 diabetes mellitus (T2DM).", "There is growing evidence from in vivo and in vitro studies that TZDs improve pancreatic beta-cell function.", "The aim of this study was to determine whether TZD-induced improvement in glycemic control is associated with improved beta-cell function.", "We studied 11 normal glucose-tolerant and 53 T2DM subjects [age 53+/-2 yr; BMI 29.4+/-0.8 kg/m2; fasting plasma glucose (FPG) 10.3+/-0.4 mM; Hb A1c 8.2+/-0.3%].", "Diabetic patients were randomized to receive placebo or TZD for 4 mo.", "Subjects received 1) 2-h OGTT with determination of plasma glucose, insulin, and C-peptide concentrations and 2) two-step euglycemic insulin (40 and 160 mU.m-2.min-1) clamp with [3-(3)H]glucose.", "T2DM patients were then randomized to receive 4 mo of treatment with pioglitazone (45 mg/day), rosiglitazone (8 mg/day), or placebo.", "Pioglitazone and rosiglitazone similarly improved FPG, mean plasma glucose during OGTT, Hb A1c, and insulin-mediated total body glucose disposal (Rd) and decreased mean plasma FFA during OGTT (all P<0.01, ANOVA).", "The insulin secretion/insulin resistance (disposition) index [DeltaISR(AUC)/Deltaglucose(AUC)/IR] was significantly improved in all TZD-treated groups: +1.8+/-0.7 (PIO+drug-na\u00efve diabetics), +0.7+/-0.3 (PIO+sulfonylurea-treated diabetics), and 0.7+/-0.2 (ROSI+sulfonylurea-withdrawn diabetics) vs. -0.2+/-0.3 in the two placebo groups (P<0.01, all TZDs vs. placebo, ANOVA).", "Improved insulin secretion correlated positively with increased body weight, fat mass, and Rd and inversely with decreased plasma glucose and FFA during the OGTT.", "In T2DM patients, TZD treatment leads to improved beta-cell function, which correlates strongly with improved glycemic control."], "structured": false}
{"doc_id": 26059876, "title": "A novel Ku70 function in colorectal homeostasis separate from nonhomologous end joining", "abstract": ["Ku70, a known nonhomologous end-joining (NHEJ) factor, also functions in tumor suppression, although this molecular mechanism remains uncharacterized.", "Previously, we showed that mice deficient for DNA ligase IV (Lig4), another key NHEJ factor, succumbed to aggressive lymphoma in the absence of tumor suppressor p53.", "However, the tumor phenotype is abrogated by the introduction of a hypomorphic mutant p53R172P, which impaired p53-mediated apoptosis but not cell-cycle arrest.", "However, Lig4\u2212/\u2212p53R172P mice succumbed to severe diabetes.", "To further elucidate the role of NHEJ and p53-mediated apoptosis in vivo, we bred Ku70\u2212/\u2212 p53R172P mice.", "Unexpectedly, these mice were free of diabetes, although 80% of the mutant mice had abnormally enlarged colons with pronounced inflammation.", "Remarkably, most of these mutant mice progressed to dysplasia, adenoma and adenocarcinoma; this is in contrast to the Lig4\u2212/\u2212p53R172P phenotype, strongly suggesting an NHEJ-independent function of Ku70.", "Significantly, our analyses of Ku70\u2212/\u2212p53R172P colonic epithelial cells show nuclear stabilization of \u03b2-catenin accompanied by higher expression of cyclin D1 and c-Myc in affected colon sections than in control samples.", "This is not due to the p53 mutation, as Ku70\u2212/\u2212 mice share this phenotype.", "Our results not only unravel a novel function of Ku70 essential for colon homeostasis, but also establish an excellent in vivo model in which to study how chronic inflammation and abnormal cellular proliferation underlie tumorigenesis and tumor progression in the colon."], "structured": false}
{"doc_id": 26064662, "title": "Association of Sickle Cell Trait With Hemoglobin A1c in African Americans", "abstract": ["Importance Hemoglobin A1c (HbA1c) reflects past glucose concentrations, but this relationship may differ between those with sickle cell trait (SCT) and those without it.", "Objective To evaluate the association between SCT and HbA1c for given levels of fasting or 2-hour glucose levels among African Americans.", "Design, Setting, and Participants Retrospective cohort study using data collected from 7938 participants in 2 community-based cohorts, the Coronary Artery Risk Development in Young Adults (CARDIA) study and the Jackson Heart Study (JHS).", "From the CARDIA study, 2637 patients contributed a maximum of 2 visits (2005-2011); from the JHS, 5301 participants contributed a maximum of 3 visits (2000-2013).", "All visits were scheduled at approximately 5-year intervals.", "Participants without SCT data, those without any concurrent HbA1c and glucose measurements, and those with hemoglobin variants HbSS, HbCC, or HbAC were excluded.", "Analysis of the primary outcome was conducted using generalized estimating equations (GEE) to examine the association of SCT with HbA1c levels, controlling for fasting or 2-hour glucose measures.", "Exposures Presence of SCT.", "Main Outcomes and Measures Hemoglobin A1c stratified by the presence or absence of SCT was the primary outcome measure.", "Results The analytic sample included 4620 participants (mean age, 52.3 [SD, 11.8] years; 2835 women [61.3%]; 367 [7.9%] with SCT) with 9062 concurrent measures of fasting glucose and HbA1c levels.", "In unadjusted GEE analyses, for a given fasting glucose, HbA1c values were statistically significantly lower in those with (5.72%) vs those without (6.01%) SCT (mean HbA1c difference, \u22120.29%; 95% CI, \u22120.35% to \u22120.23%).", "Findings were similar in models adjusted for key risk factors and in analyses using 2001 concurrent measures of 2-hour glucose and HbA1c concentration for those with SCT (mean, 5.35%) vs those without SCT (mean, 5.65%) for a mean HbA1c difference of \u22120.30% (95% CI, \u22120.39% to \u22120.21%).", "The HbA1c difference by SCT was greater at higher fasting (P = .02 for interaction) and 2-hour (P = .03) glucose concentrations.", "The prevalence of prediabetes and diabetes was statistically significantly lower among participants with SCT when defined using HbA1c values (29.2% vs 48.6% for prediabetes and 3.8% vs 7.3% for diabetes in 572 observations from participants with SCT and 6877 observations from participants without SCT; P<.001 for both comparisons).", "Conclusions and Relevance Among African Americans from 2 large, well-established cohorts, participants with SCT had lower levels of HbA1c at any given concentration of fasting or 2-hour glucose compared with participants without SCT.", "These findings suggest that HbA1c may systematically underestimate past glycemia in black patients with SCT and may require further evaluation."], "structured": false}
{"doc_id": 26064942, "title": "PGAP2 mutations, affecting the GPI-anchor-synthesis pathway, cause hyperphosphatasia with mental retardation syndrome.", "abstract": ["Recently, mutations in genes involved in the biosynthesis of the glycosylphosphatidylinositol (GPI) anchor have been identified in a new subclass of congenital disorders of glycosylation (CDGs) with a distinct spectrum of clinical features.", "To date, mutations have been identified in six genes (PIGA, PIGL, PIGM, PIGN, PIGO, and PIGV) encoding proteins in the GPI-anchor-synthesis pathway in individuals with severe neurological features, including seizures, muscular hypotonia, and intellectual disability.", "We developed a diagnostic gene panel for targeting all known genes encoding proteins in the GPI-anchor-synthesis pathway to screen individuals matching these features, and we detected three missense mutations in PGAP2, c.46C>T, c.380T>C, and c.479C>T, in two unrelated individuals with hyperphosphatasia with mental retardation syndrome (HPMRS).", "The mutations cosegregated in the investigated families.", "PGAP2 is involved in fatty-acid GPI-anchor remodeling, which occurs in the Golgi apparatus and is required for stable association between GPI-anchored proteins and the cell-surface membrane rafts.", "Transfection of the altered protein constructs, p.", "Arg16Trp (NP_001243169.1), p.", "Leu127Ser, and p.", "Thr160Ile, into PGAP2-null cells showed only partial restoration of GPI-anchored marker proteins, CD55 and CD59, on the cell surface.", "In this work, we show that an impairment of GPI-anchor remodeling also causes HPMRS and conclude that targeted sequencing of the genes encoding proteins in the GPI-anchor-synthesis pathway is an effective diagnostic approach for this subclass of CDGs."], "structured": false}
{"doc_id": 26067999, "title": "Screening for Lung Cancer: U.S. Preventive Services Task Force Recommendation Statement", "abstract": ["The U.S. Preventive Services Task Force (USPSTF) makes recommendations about the effectiveness of specific preventive care services for patients without related signs or symptoms.", "It bases its recommendations on the evidence of both the benefits and harms of the service and an assessment of the balance.", "The USPSTF does not consider the costs of providing a service in this assessment.", "The USPSTF recognizes that clinical decisions involve more considerations than evidence alone.", "Clinicians should understand the evidence but individualize decision making to the specific patient or situation.", "Similarly, the USPSTF notes that policy and coverage decisions involve considerations in addition to the evidence of clinical benefits and harms.", "Summary of Recommendation and Evidence The USPSTF recommends annual screening for lung cancer with low-dose computed tomography (LDCT) in adults aged 55 to 80 years who have a 30 pack-year smoking history and currently smoke or have quit within the past 15 years.", "Screening should be discontinued once a person has not smoked for 15 years or develops a health problem that substantially limits life expectancy or the ability or willingness to have curative lung surgery.", "(B recommendation)", "See the Clinical Considerations section for suggestions for implementation in practice.", "See the Figure for a summary of the recommendation and suggestions for clinical practice.", "Figure.", "Screening for lung cancer: clinical summary of U.S. Preventive Services Task Force recommendation.", "Appendix Table 1 describes the USPSTF grades, and Appendix Table 2 describes the USPSTF classification of levels of certainty about net benefit.", "Appendix Table 1.", "What the USPSTF Grades Mean and Suggestions for Practice Appendix Table 2.", "USPSTF Levels of Certainty Regarding Net Benefit Supplement.", "Consumer Fact Sheet.", "Rationale Importance Lung cancer is the third most common cancer and the leading cause of cancer-related death in the United States (1).", "The most important risk factor for lung cancer is smoking, which results in approximately 85% of all U.S. lung cancer cases (2).", "Although the prevalence of smoking has decreased, approximately 37% of U.S. adults are current or former smokers (2).", "The incidence of lung cancer increases with age and occurs most commonly in persons aged 55 years or older.", "Increasing age and cumulative exposure to tobacco smoke are the 2 most common risk factors for lung cancer.", "Lung cancer has a poor prognosis, and nearly 90% of persons with lung cancer die of the disease.", "However, early-stage nonsmall cell lung cancer (NSCLC) has a better prognosis and can be treated with surgical resection.", "Detection Most lung cancer cases are NSCLC, and most screening programs focus on the detection and treatment of early-stage NSCLC.", "Although chest radiography and sputum cytologic evaluation have been used to screen for lung cancer, LDCT has greater sensitivity for detecting early-stage cancer (3).", "Benefits of Detection and Early Treatment Although lung cancer screening is not an alternative to smoking cessation, the USPSTF found adequate evidence that annual screening for lung cancer with LDCT in a defined population of high-risk persons can prevent a substantial number of lung cancerrelated deaths.", "Direct evidence from a large, well-conducted, randomized, controlled trial (RCT) provides moderate certainty of the benefit of lung cancer screening with LDCT in this population (4).", "The magnitude of benefit to the person depends on that person's risk for lung cancer because those who are at highest risk are most likely to benefit.", "Screening cannot prevent most lung cancerrelated deaths, and smoking cessation remains essential.", "Harms of Detection and Early Intervention and Treatment The harms associated with LDCT screening include false-negative and false-positive results, incidental findings, overdiagnosis, and radiation exposure.", "False-positive LDCT results occur in a substantial proportion of screened persons; 95% of all positive results do not lead to a diagnosis of cancer.", "In a high-quality screening program, further imaging can resolve most false-positive results; however, some patients may require invasive procedures.", "The USPSTF found insufficient evidence on the harms associated with incidental findings.", "Overdiagnosis of lung cancer occurs, but its precise magnitude is uncertain.", "A modeling study performed for the USPSTF estimated that 10% to 12% of screen-detected cancer cases are overdiagnosedthat is, they would not have been detected in the patient's lifetime without screening.", "Radiation harms, including cancer resulting from cumulative exposure to radiation, vary depending on the age at the start of screening; the number of scans received; and the person's exposure to other sources of radiation, particularly other medical imaging.", "USPSTF Assessment The USPSTF concludes with moderate certainty that annual screening for lung cancer with LDCT is of moderate net benefit in asymptomatic persons who are at high risk for lung cancer based on age, total cumulative exposure to tobacco smoke, and years since quitting smoking.", "The moderate net benefit of screening depends on limiting screening to persons who are at high risk, the accuracy of image interpretation being similar to that found in the NLST (National Lung Screening Trial), and the resolution of most false-positive results without invasive procedures (4).", "Clinical Considerations Patient Population Under Consideration The risk for lung cancer increases with age and cumulative exposure to tobacco smoke and decreases with time since quitting smoking.", "The best evidence for the benefit of screening comes from the NLST, which enrolled adults aged 55 to 74 years who had at least a 30 pack-year smoking history and were current smokers or had quit within the past 15 years.", "As with all screening trials, the NLST tested a specific intervention over a finite period.", "Because initial eligibility extended through age 74 years and participants received 3 annual screening computed tomographic scans, the oldest participants in the trial were aged 77 years.", "The USPSTF used modeling studies to predict the benefits and harms of screening programs that use different screening intervals, age ranges, smoking histories, and times since quitting.", "A program that annually screens adults aged 55 to 80 years who have a 30 pack-year smoking history and currently smoke or have quit within the past 15 years is projected to have a reasonable balance of benefits and harms.", "The model assumes that persons who achieve 15 years of smoking cessation during the screening program discontinue screening.", "This model predicts the outcomes of continuing the screening program used in the NLST through age 80 years.", "Screening may not be appropriate for patients with substantial comorbid conditions, particularly those at the upper end of the screening age range.", "The NLST excluded persons who were unlikely to complete curative lung cancer surgery and those with medical conditions that posed a substantial risk for death during the 8-year trial.", "The baseline characteristics of the NLST showed a relatively healthy sample, and fewer than 10% of enrolled participants were older than 70 years (5).", "Persons with serious comorbid conditions may experience net harm, no net benefit, or at least substantially less net benefit.", "Similarly, persons who are unwilling to have curative lung surgery are unlikely to benefit from a screening program.", "Assessment of Risk Age, total exposure to tobacco smoke, and years since quitting smoking are important risk factors for lung cancer and were used to determine eligibility in the NLST.", "Other risk factors include specific occupational exposures, radon exposure, family history, and history of pulmonary fibrosis or chronic obstructive lung disease.", "The incidence of lung cancer is relatively low in persons younger than 50 years but increases with age, especially after age 60 years.", "In current and former smokers, age-specific incidence rates increase with age and cumulative exposure to tobacco smoke.", "Smoking cessation substantially reduces a person's risk for developing and dying of lung cancer.", "Among persons enrolled in the NLST, those who were at highest risk because of additional risk factors or a greater cumulative exposure to tobacco smoke experienced most of the benefit (6).", "A validated multivariate model showed that persons in the highest 60% of risk accounted for 88% of all deaths preventable by screening.", "Screening Tests Low-dose computed tomography has shown high sensitivity and acceptable specificity for the detection of lung cancer in high-risk persons.", "Chest radiography and sputum cytologic evaluation have not shown adequate sensitivity or specificity as screening tests.", "Therefore, LDCT is currently the only recommended screening test for lung cancer.", "Treatment Surgical resection is the current standard of care for localized NSCLC.", "This type of cancer is treated with surgical resection when possible and also with radiation and chemotherapy.", "Annual LDCT screening may not be useful for patients with life-limiting comorbid conditions or poor functional status who may not be candidates for surgery.", "Other Approaches to Prevention Smoking cessation is the most important intervention to prevent NSCLC.", "Advising smokers to stop smoking and preventing nonsmokers from being exposed to tobacco smoke are the most effective ways to decrease the morbidity and mortality associated with lung cancer.", "Current smokers should be informed of their continuing risk for lung cancer and offered cessation treatments.", "Screening with LDCT should be viewed as an adjunct to tobacco cessation interventions.", "Useful Resources Clinicians have many resources to help patients stop smoking.", "The Centers for Disease Control and Prevention has developed a Web site with many such resources, including information on tobacco quit lines, available in several languages (www.cdc.gov/tobacco/campaign/tips).", "Quit l"], "structured": false}
{"doc_id": 26068103, "title": "Dual role of interleukin-10 in the regulation of respiratory syncitial virus (RSV)-induced lung inflammation.", "abstract": ["RSV lower respiratory tract infections (LRTI) are among the most common diseases necessitating hospital admission in children.", "In addition to causing acute respiratory failure, RSV infections are associated with sequelae such as secondary bacterial infections and reactive airway disease.", "One characteristic host response observed in severe RSV-induced LRTI and/or subsequent development of asthma is increased expression of interleukin (IL)-10.", "However, contradictory results have been reported regarding whether IL-10 inhibits asthmatic responses or intensifies the disease.", "We aimed to reconcile these discordant observations by elucidating the role of IL-10 in regulating the host response to RSV LRTI.", "In this study, we used a lung-specific, inducible IL-10 over-expression (OE) transgenic mouse model to address this question.", "Our results showed that the presence of IL-10 at the time of RSV infection not only attenuated acute inflammatory process (i.e. 24 h post-infection), but also late inflammatory changes [characterized by T helper type 2 (Th2) cytokine and chemokine expression].", "While this result appears contradictory to some clinical observations where elevated IL-10 levels are observed in asthmatic patients, we also found that delaying IL-10 OE until the late immune response to RSV infection, additive effects rather than inhibitory effects were observed.", "Importantly, in non-infected, IL-10 OE mice, IL-10 OE alone induced up-regulation of Th2 cytokine (IL-13 and IL-5) and Th2-related chemokine [monocyte chemoattractant protein 1 (MCP-1), chemokine (C-C motif) ligand 3 (CCL3) and regulated upon activation normal T cell expressed and secreted (RANTES)] expression.", "We identified a subset of CD11b(+)CD11c(+)CD49b(+)F4/80(-)Gr-1(-) myeloid cells as a prinicipal source of IL-10-induced IL-13 production.", "Therefore, the augmented pathological responses observed in our 'delayed' IL-10 over-expression model could be attributed to IL-10 OE alone.", "Taken together, our study indicated dual roles of IL-10 on RSV-induced lung inflammation which appear to depend upon the timing of when elevated IL-10 is expressed in the lung."], "structured": false}
{"doc_id": 26071782, "title": "Latent membrane protein 1 of Epstein\u2013Barr virus coordinately regulates proliferation with control of apoptosis", "abstract": ["Latent membrane protein 1 (LMP1), an oncoprotein encoded by Epstein\u2013Barr virus (EBV), is an integral membrane protein, which acts like a constitutively active receptor.", "LMP1 is critical for some facet of EBV's induction and maintenance of proliferation of infected B cells.", "It, in part, mimics signaling by the CD40 receptor and has been implicated in regulating proliferation, survival, or both properties of EBV-infected cells.", "We established a conditional LMP1 allele in the context of the intact EBV genome to define the immediate-early cellular target genes regulated by LMP1 in order to assess its contributions to infected human B cells.", "The functional analysis of this conditional system indicated that LMP1 specifically induces mitogenic B-cell activation through c-myc and Jun/AP1 family members and confirms its direct role in upregulating expression of multiple genes with opposing activities involved in cell survival.", "LMP1's signals were found to be essential for the G1/S transition in human B cells; cells lacking LMP1's signals are cell cycle arrested and survive quiescently.", "LMP1's activities are therefore not required to maintain survival in nonproliferating cells.", "LMP1 does induce both pro- and antiapoptotic genes whose balance seems to permit survival during LMP1's induction and maintenance of proliferation."], "structured": false}
{"doc_id": 26079071, "title": "Crizotinib in ROS1-rearranged non-small-cell lung cancer.", "abstract": ["BACKGROUND Chromosomal rearrangements of the gene encoding ROS1 proto-oncogene receptor tyrosine kinase (ROS1) define a distinct molecular subgroup of non-small-cell lung cancers (NSCLCs) that may be susceptible to therapeutic ROS1 kinase inhibition.", "Crizotinib is a small-molecule tyrosine kinase inhibitor of anaplastic lymphoma kinase (ALK), ROS1, and another proto-oncogene receptor tyrosine kinase, MET.   \n", "METHODS We enrolled 50 patients with advanced NSCLC who tested positive for ROS1 rearrangement in an expansion cohort of the phase 1 study of crizotinib.", "Patients were treated with crizotinib at the standard oral dose of 250 mg twice daily and assessed for safety, pharmacokinetics, and response to therapy.", "ROS1 fusion partners were identified with the use of next-generation sequencing or reverse-transcriptase-polymerase-chain-reaction assays.   \n", "RESULTS The objective response rate was 72% (95% confidence interval [CI], 58 to 84), with 3 complete responses and 33 partial responses.", "The median duration of response was 17.6 months (95% CI, 14.5 to not reached).", "Median progression-free survival was 19.2 months (95% CI, 14.4 to not reached), with 25 patients (50%) still in follow-up for progression.", "Among 30 tumors that were tested, we identified 7 ROS1 fusion partners: 5 known and 2 novel partner genes.", "No correlation was observed between the type of ROS1 rearrangement and the clinical response to crizotinib.", "The safety profile of crizotinib was similar to that seen in patients with ALK-rearranged NSCLC.   \n", "CONCLUSIONS In this study, crizotinib showed marked antitumor activity in patients with advanced ROS1-rearranged NSCLC.", "ROS1 rearrangement defines a second molecular subgroup of NSCLC for which crizotinib is highly active.", "(Funded by Pfizer and others; ClinicalTrials.gov number, NCT00585195.)."], "structured": true}
{"doc_id": 26083387, "title": "The S. cerevisiae Rrm3p DNA helicase moves with the replication fork and affects replication of all yeast chromosomes.", "abstract": ["The Saccharomyces cerevisiae DNA helicase Rrm3p is needed for normal fork progression through >1000 discrete sites scattered throughout the genome.", "Here we show that replication of all yeast chromosomes was markedly delayed in rrm3 cells.", "Delayed replication was seen even in a region that lacks any predicted Rrm3p-dependent sites.", "Based on the pattern of replication intermediates in two-dimensional gels, the rate of fork movement in rrm3 cells appeared similar to wild-type except at known Rrm3p-dependent sites.", "These data suggest that although Rrm3p has a global role in DNA replication, its activity is needed only or primarily at specific, difficult-to-replicate sites.", "By the criterion of chromatin immunoprecipitation, Rrm3p was associated with both Rrm3p-dependent and -independent sites, and moved with the replication fork through both.", "In addition, Rrm3p interacted with Pol2p, the catalytic subunit of DNA polymerase epsilon, in vivo.", "Thus, rather than being recruited to its sites of action when replication forks stall at these sites, Rrm3p is likely a component of the replication fork apparatus."], "structured": false}
{"doc_id": 26089649, "title": "The pathophysiology of protein-overload proteinuria.", "abstract": ["Alterations in glomerular function and structure were studied in protein-overload nephrosis in the rat induced by intraperitoneal administration of bovine serum albumin (BSA).", "Fractional clearance (C/GFR) studies using inulin and tracer proteins of different molecular size and charge revealed in proteinuric rats 1) unchanged glomerular filtration rate and renal plasma flow; 2) a 34-fold increase in C/GFR of rat serum albumin, reaching values similar to BSA; 3) a 2-fold increase in C/GFR for anionic horse radish peroxidase (HRP), but normal values for neutral and cationic HRP, and 4) an 11- and 3-fold increase for heterologous IgG and IgM, respectively.", "Glomerular epithelial cells showed degenerative changes, but the distribution of anionic sites in the glomerular basement membrane was found to be unaltered, as determined by polyethyleneimine binding studies.", "In summary, an elevation of serum albumin concentration resulted in an increased transcapillary albumin transport.", "This was found to lead to degenerative changes of glomerular epithelial cells with development of large pore defects, which were completely reversible."], "structured": false}
{"doc_id": 26099680, "title": "Effects of aging on central and peripheral mammalian clocks.", "abstract": ["Circadian organization changes with age, but we do not know the extent to which age-related changes are the result of alterations in the central pacemakers, the peripheral oscillators, or the coupling mechanisms that hold the system together.", "By using transgenic rats with a luciferase (luc) reporter, we assessed the effects of aging on the rhythm of expression of the Period 1 (Per1) gene in the suprachiasmatic nucleus (SCN) and in peripheral tissues.", "Young (2 months) and aged (24-26 months) Per1-luc transgenic rats, entrained to light-dark cycles, were killed, and tissues were removed and cultured.", "Per1-luc expression was measured from 10 tissues.", "In the SCN, the central mammalian pacemaker, Per1-luc expression was robustly rhythmic for more than 7 weeks in culture.", "The only difference between SCN rhythmicity in young and old rats was a small but significant age-related shortening of the free-running period.", "Circadian rhythmicity in some peripheral tissues was unaffected by aging, whereas rhythmicity in other tissues was either phase advanced relative to the light cycle or absent.", "Those tissues that were arrhythmic could be induced to oscillate by application of forskolin, suggesting that they retained the capacity to oscillate but were not being appropriately driven in vivo.", "Overall, the results provide new insights into the effects of aging on the mammalian circadian system.", "Aging seems to affect rhythms in some but not in all tissues and may act primarily on interactions among circadian oscillators, perhaps attenuating the ability of the SCN to drive damped oscillators in the periphery."], "structured": false}
{"doc_id": 26104554, "title": "CtBP3/BARS drives membrane fission in dynamin-independent transport pathways", "abstract": ["Membrane fission is a fundamental step in membrane transport.", "So far, the only fission protein machinery that has been implicated in in vivo transport involves dynamin, and functions in several, but not all, transport pathways.", "Thus, other fission machineries may exist.", "Here, we report that carboxy-terminal binding protein 3/brefeldin A-ribosylated substrate (CtBP3/BARS) controls fission in basolateral transport from the Golgi to the plasma membrane and in fluid-phase endocytosis, whereas dynamin is not involved in these steps.", "Conversely, CtBP3/BARS protein is inactive in apical transport to the plasma membrane and in receptor-mediated endocytosis, both steps being controlled by dynamin.", "This indicates that CtBP3/BARS controls membrane fission in endocytic and exocytic transport pathways, distinct from those that require dynamin."], "structured": false}
{"doc_id": 26105746, "title": "Influenza A myocarditis developing in an adult liver transplant recipient despite vaccination: a case report and review of the literature.", "abstract": ["Solid organ transplant recipients receiving chronic immunosuppressive agents are at increased risk to acquire influenza virus despite vaccination.", "Myocarditis is a known but rare complication of influenza infection.", "We present the first adult liver transplant recipient who received prophylactic vaccination but developed influenza A myocarditis.", "This may occur in solid organ transplant recipients, because they have reduced response to protein vaccines, which may leave them vulnerable to infections.", "Studies are needed to evaluate if antiviral chemoprophylaxis in solid organ transplant recipients during influenza season would be an effective preventive therapy against influenza in this high-risk population."], "structured": false}
{"doc_id": 26107000, "title": "Extrapulmonary effects of chronic obstructive pulmonary disease on physical activity: a cross-sectional study.", "abstract": ["RATIONALE Physical activity is reduced in patients with chronic obstructive pulmonary disease (COPD).", "COPD has a systemic component that includes significant extrapulmonary effects that may contribute to its severity in individual patients.   \n", "OBJECTIVES To investigate the association of extrapulmonary effects of the disease and its comorbidities with reduced physical activity in patients with COPD.   \n", "METHODS In a cross-sectional study, 170 outpatients with COPD (GOLD [Global Initiative for Chronic Obstructive Lung Disease] stages I-IV; BODE [body mass index, airway obstruction, dyspnea, and exercise capacity] score 0-10) underwent a series of tests.", "Physical activity was assessed over 5 to 6 consecutive days by using a multisensor accelerometer armband that records steps per day and the physical activity level (total daily energy expenditure divided by whole-night sleeping energy expenditure).", "Cardiovascular status was assessed by echocardiography, vascular Doppler sonography, and levels of N-terminal pro-B-type natriuretic peptide.", "Mental status, metabolic/muscular status, systemic inflammation, and anemia were assessed by Beck Depression Inventory, bioelectrical impedance analysis, handgrip strength, high-sensitivity C-reactive protein/fibrinogen, and hemoglobin, respectively.   \n", "MEASUREMENTS AND MAIN RESULTS In a multivariate linear regression analysis using either steps per day or physical activity level as a dependent variable, the extrapulmonary parameters that were associated with reduced physical activity in patients with COPD independently of GOLD stages or BODE score were N-terminal pro-B-type natriuretic peptide levels, echocardiographically measured left ventricular diastolic function, and systemic inflammation.   \n", "CONCLUSIONS Higher values of systemic inflammation and left cardiac dysfunction are associated with reduced physical activity in patients with COPD."], "structured": true}
{"doc_id": 26108767, "title": "Cleavage efficient 2A peptides for high level monoclonal antibody expression in CHO cells.", "abstract": ["Linking the heavy chain (HC) and light chain (LC) genes required for monoclonal antibodies (mAb) production on a single cassette using 2A peptides allows control of LC and HC ratio and reduces non-expressing cells.", "Four 2A peptides derived from the foot-and-mouth disease virus (F2A), equine rhinitis A virus (E2A), porcine teschovirus-1 (P2A) and Thosea asigna virus (T2A), respectively, were compared for expression of 3 biosimilar IgG1 mAbs in Chinese hamster ovary (CHO) cell lines.", "HC and LC were linked by different 2A peptides both in the absence and presence of GSG linkers.", "Insertion of a furin recognition site upstream of 2A allowed removal of 2A residues that would otherwise be attached to the HC.", "Different 2A peptides exhibited different cleavage efficiencies that correlated to the mAb expression level.", "The relative cleavage efficiency of each 2A peptide remains similar for expression of different IgG1 mAbs in different CHO cells.", "While complete cleavage was not observed for any of the 2A peptides, GSG linkers did enhance the cleavage efficiency and thus the mAb expression level.", "T2A with the GSG linker (GT2A) exhibited the highest cleavage efficiency and mAb expression level.", "Stably amplified CHO DG44 pools generated using GT2A had titers 357, 416 and 600 mg/L for the 3 mAbs in shake flask batch cultures.", "Incomplete cleavage likely resulted in incorrectly processed mAb species and aggregates, which were removed with a chromatin-directed clarification method and protein A purification.", "The vector and methods presented provide an easy process beneficial for both mAb development and manufacturing."], "structured": false}
{"doc_id": 26112624, "title": "The complexity of human ribosome biogenesis revealed by systematic nucleolar screening of Pre-rRNA processing factors.", "abstract": ["Mature ribosomal RNAs (rRNAs) are produced from polycistronic precursors following complex processing.", "Precursor (pre)-rRNA processing has been extensively characterized in yeast and was assumed to be conserved in humans.", "We functionally characterized 625 nucleolar proteins in HeLa cells and identified 286 required for processing, including 74 without a yeast homolog.", "For selected candidates, we demonstrated that pre-rRNA processing defects are conserved in different cell types (including primary cells), defects are not due to activation of a p53-dependent nucleolar tumor surveillance pathway, and they precede cell-cycle arrest and apoptosis.", "We also investigated the exosome's role in processing internal transcribed spacers (ITSs) and report that 3' end maturation of 18S rRNA involves EXOSC10/Rrp6, a yeast ITS2 processing factor.", "We conclude that human cells adopt unique strategies and recruit distinct trans-acting factors to carry out essential processing steps, posing fundamental implications for understanding ribosomopathies at the molecular level and developing effective therapeutic agents."], "structured": false}
{"doc_id": 26112696, "title": "Maximal aerobic capacity in African-American and Caucasian prepubertal children.", "abstract": ["The purpose of this study was to examine differences in resting, submaximal, and maximal (VO2max) oxygen consumption (VO2) in African-American (n = 44) and Caucasian (n = 31) prepubertal children aged 5-10 yr.", "Resting VO2 was measured via indirect calorimetry in the fasted state.", "Submaximal VO2 and VO2max were determined during an all out, progressive treadmill exercise test appropriate for children.", "Dual-energy X-ray absorptiometry was used to determine total fat mass (FM), soft lean tissue mass (LTM), and leg soft LTM.", "Doubly labeled water was used to determine total energy expenditure (TEE) and activity energy expenditure (AEE).", "A significant effect of ethnicity (P < 0.01) was found for VO2max but not resting or submaximal VO2, with African-American children having absolute VO2max approximately 15% lower than Caucasian children (1.21 +/- 0.032 vs. 1.43 +/-", "0.031 l/min, respectively).", "The lower VO2max persisted in African-American children after adjustment for soft LTM (1.23 +/- 0.025 vs. 1.39 +/-", "0.031 l/min; P < 0.01), leg soft LTM (1.20 +/-", "0.031 vs. 1.43 +/-", "0.042 l/min; P < 0.01), and soft LTM and FM (1.23 +/-", "0.025 vs. 1.39 +/-", "0.031 l/min; P < 0.01).", "The lower VO2max persisted also after adjustment for TEE (1.20 +/-", "0.02 vs. 1.38 +/-", "0.0028 l/min P < 0.001) and AEE (1.20 +/- 0.024 vs. 1.38 +/-", "0.028 l/min; P < 0.001).", "In conclusion, our data indicate that African-American and Caucasian children have similar rates of VO2 at rest and during submaximal exercise, but VO2max is approximately 15% lower in African-American children, independent of soft LTM, FM, leg LTM, TEE, and AEE."], "structured": false}
{"doc_id": 26117607, "title": "Penaeus monodon Dscam (PmDscam) has a highly diverse cytoplasmic tail and is the first membrane-bound shrimp Dscam to be reported.", "abstract": ["Down syndrome cell adhesion molecule (Dscam) seems likely to play a key role in the \"alternative adaptive immunity\" that has been reported in invertebrates.", "Dscam consists of a cytoplasmic tail that is involved in signal transduction and a hypervariable extracellular region that might use a pathogen recognition mechanism similar to that used by the vertebrate antibodies.", "In our previous paper, we isolated a unique tail-less form of Dscam from Litopenaeus vannamei.", "In this study, we report the first membrane-bound form of shrimp Dscam: PmDscam was isolated from Penaeus monodon, and it occurred in both membrane-bound and tail-less forms.", "Phylogenetic analysis showed that while the crustacean Dscams from shrimp and water flea did not share a single subclade, they were distinct from the invertebrate Dscam-like molecules and from the insecta Dscams.", "In the extracellular region, the variable regions of PmDscam were located in N-terminal Ig2, N-terminal Ig3 and the entire Ig7 domain.", "The PmDscam extracellular variants and transmembrane domain variants were produced by mutually exclusive alternative splicing events.", "The cytoplasmic tail variants were produced by exon inclusion/exclusion.", "Based on the genomic organization of Daphnia Dscam's cytoplasmic tail, we propose a model of how the shrimp Dscam genomic locus might use Type III polyadenylation to generate both the tail-less and membrane-bound forms."], "structured": false}
{"doc_id": 26118532, "title": "The different biological effects of telomestatin and TMPyP4 can be attributed to their selectivity for interaction with intramolecular or intermolecular G-quadruplex structures.", "abstract": ["Demonstration of the existence of G-quadruplex structures in telomeres of Stylonychia macronuclei and in the promoter of c-myc in human cells has validated these secondary DNA structures as potential targets for drug design.", "The next important issue is the selectivity of G-quadruplex-interactive agents for the different types of G-quadruplex structures.", "In this study, we have taken an important step in associating specific biological effects of these drugs with selective interaction with either intermolecular or intramolecular G-quadruplex structures formed in telomeres.", "Telomestatin is a natural product isolated from Streptomyces anulatus 3533-SV4 and has been shown to be a very potent telomerase inhibitor through its G-quadruplex interaction.", "We have demonstrated that telomestatin interacts preferentially with intramolecular versus intermolecular G-quadruplex structures and also has a 70-fold selectivity for intramolecular G-quadruplex structures over duplex DNA.", "Telomestatin is able to stabilize G-quadruplex structures that are formed from duplex human telomeric DNA as well as from single-stranded DNA.", "Importantly, telomestatin stabilizes these G-quadruplex structures in the absence of monovalent cations, which is a unique characteristic among G-quadruplex-interactive compounds.", "At noncytotoxic concentrations, telomestatin suppresses the proliferation of telomerase-positive cells within several weeks.", "In contrast, TMPyP4, a compound that preferentially facilitates the formation of intermolecular G-quadruplex structures, suppresses the proliferation of alternative lengthening of telomeres (ALT)-positive cells as well as telomerase-positive cells.", "We have also demonstrated that TMPyP4 induces anaphase bridges in sea urchin embryos, whereas telomestatin did not have this effect, leading us to conclude that the selectivity of telomestatin for intramolecular G-quadruplex structures and TMPyP4 for intermolecular G-quadruplex structures is important in mediating different biological effects: stabilization of intramolecular G-quadruplex structures produces telomerase inhibition and accelerated telomere shortening, whereas facilitation of the formation of intermolecular G-quadruplex structures induces the formation of anaphase bridges."], "structured": false}
{"doc_id": 26121646, "title": "Targeting oxidative stress to treat endometriosis.", "abstract": ["INTRODUCTION Endometriosis affects 10% of women of reproductive age.", "It is defined as the presence of implanted active endometrial tissue outside the uterine cavity.", "The exact pathophysiology of endometriosis is still uncertain, although several optional etiological theories have been suggested.", "Being so common, a novel treatment for endometriosis is widely quested.", "Recent studies addressing the pathological characteristics of endometriosis have revealed a vicious cycle in which oxidative stress (OS) is generated, which in turn facilitates the implantation of the ectopic endometrium.", "At the same time, the generation of high amounts of reactive oxygen species further triggers a state of OS.   ", "AREAS COVERED The author examined the evidence associating OS and endometriosis.", "After establishing an association, a search for antioxidant agents that were investigated specifically on endometriosis patients are described including Vitamins C and E, melatonin, resveratrol, xanthohumol and epigallocatechin-3-gallate.", "A significant effect of all the reviewed antioxidants on endometriosis is reported.   ", "EXPERT OPINION Aiming for the reduction of OS as the treatment goal for endometriosis looks promising.", "However, since most of the studies are either in vitro or are animal based, further studies on human subjects are deemed necessary to elucidate the impact of OS reduction on patients with endometriosis."], "structured": false}
{"doc_id": 26124606, "title": "Interferon alpha for the treatment of chronic hepatitis C in patients infected with human immunodeficiency virus. Hepatitis-HIV Spanish Study Group.", "abstract": ["Liver disease secondary to hepatitis C virus (HCV) infection is a rising cause of morbidity and mortality among individuals who have been infected parenterally with human immunodeficiency virus (HIV) such as injection drug users, hemophiliacs, and transfused patients.", "We analyzed both the efficacy of interferon (IFN) alpha therapy in these patients and the predictors of response to this agent.", "A total of 119 patients with chronic hepatitis C (90 of whom were infected with HIV and 29 of whom were not) were included in a multicenter, prospective, open, nonrandomized observational study.", "IFN-alpha was given subcutaneously in a dosage of 5 million units three times a week during a 3-month period; those patients who responded received a dose of 3 million units given subcutaneously three times a week for an additional 9 months.", "One hundred seven patients completed the study; the level of aminotransferases returned to normal and sera became negative (complete response) for HCV RNA in 26 (32.5%) of 80 HIV-infected patients and 10 (37.0%) of 27 non-HIV-infected patients (P = .666) after completion of the treatment.", "Two variables were independently associated with a response in HIV-infected patients: a CD4+ T lymphocyte count of > 500 x 10(6)/L and a baseline HCV viremia level of < 10(7) copies/mL. In the 12 months following treatment, relapses occurred in 30.8% of the HIV-infected patients and 12.5% of non-HIV-infected patients (P = .403)."], "structured": false}
{"doc_id": 26132041, "title": "Vanishing cerebellar infarcts in a migraine patient.", "abstract": ["Recent population-based studies have suggested that migraine is a risk factor for the development of infarct-like lesions in the territory of the posterior circulation.", "These lesions are thought to be true vascular infarcts based on their size, location and magnetic resonance imaging (MRI) characteristics.", "However, as there are no postmortem studies identifying the pathology of these MRI findings, their true aetiology is unknown.", "A case patient with migraine is presented, who developed what appeared to be cerebellar infarcts on MRI, but these lesions vanished on repeat imaging 16 days later, questioning their aetiology as vascular ischaemic based infarcts."], "structured": false}
{"doc_id": 26133404, "title": "A novel viral transcript with homology to human interleukin-10 is expressed during latent human cytomegalovirus infection.", "abstract": ["Human cytomegalovirus (CMV) establishes latent infections in hematopoietic cells such as granulocyte-macrophage progenitors (GM-Ps).", "During latency the virus is sequestered in a nonreplicating state, although limited transcriptional activity has been previously reported.", "In this study we sought to further examine viral gene expression during the latent phase of infection.", "Using an experimental model of latency, primary human GM-Ps were latently infected with CMV strain Toledo and extracted RNA subjected to reverse transcription-PCR by using CMV gene-specific primers.", "Using this approach, we detected transcription from the UL111.5A region of the viral genome.", "This transcription was also detected in GM-Ps latently infected with AD169 and Towne strains, indicating that expression was CMV strain independent.", "Significantly, we detected UL111.5A-region transcripts in mononuclear cells from healthy bone marrow and mobilized peripheral blood allograft donors, demonstrating expression during natural latent infection.", "Mapping experiments with RNA extracted from latently infected GM-Ps revealed the expression of a novel UL111.5A region transcript with a splicing pattern that differed from that reported during productive infection of permissive cells.", "This UL111.5A region transcript expressed during latent infection is predicted to encode a 139-amino-acid protein with homology to the potent immunosuppressor interleukin-10 (IL-10) and to the viral IL-10 homolog that is expressed during productive CMV infection.", "Expression of a latency-associated cmvIL-10 may confer upon the virus an ability to avoid immune recognition and clearance during the latent phase of infection."], "structured": false}
{"doc_id": 26150367, "title": "Treatments for somnambulism in adults: assessing the evidence.", "abstract": ["Somnambulism, or sleepwalking, is a parasomnia of non-rapid eye movement (NREM) sleep where movement behaviours usually confined to wakefulness are displayed during sleep.", "Generally, if sleepwalking is causing distress or danger in spite of safety measures, medical or psychological treatment is indicated.", "Clinicians will need to assess the evidence for treatment options.", "MEDLINE, EMBASE, PsycINFO and the Ovid Evidence-Based Medicine Reviews (EBM) multifile databases were searched.", "No properly powered rigorous controlled trials were found for treatment of sleepwalking in adults.", "Seven reports described small trials with some kind of control arm, or retrospective case series which included 30 or more patients.", "With no high quality evidence to underpin recommendations for treatments of somnambulism, full discussion with patients is advised.", "Adequately powered, well-designed clinical trials are now needed, and multi-centre collaborations may be required to obtain the sample sizes required."], "structured": false}
{"doc_id": 26182390, "title": "Premature chromosome condensation: evidence for in vivo cell fusion in human malignant tumours.", "abstract": ["Premature chromosome condensation (PCC) was studied in direct preparations of tissues from patients with haematological diseases and carcinomas of various histological types.", "PCC was found in 6 out of 166 malignancies (128 haematological cases, 35 carcinomas and 3 malignant effusions) analysed with the GTG-technique.", "Chromosome analysis revealed S-phase and G1-phase PCC in each case; the frequency of PCC varied between 1, 4 and 8.6% of the metaphases analysed.", "It is suggested that PCC chromosomes, which represent cell fusion in vivo, are not very rare in naturally-occurring human malignancies, and that cell fusion may affect the malignant phenotype.", "In conjunction with other factors they may also explain the heterogeneity of tumour cell populations."], "structured": false}
{"doc_id": 26199970, "title": "Blockade of the angiotensin system improves mental health domain of quality of life: A meta-analysis of randomized clinical trials", "abstract": ["Objective: It is unclear whether blockade of the angiotensin system has effects on mental health.", "Our objective was to determine the impact of angiotensin converting enzyme inhibitors and angiotensin II type 1 receptor (AT1R) blockers on mental health domain of quality of life.", "Study design: Meta-analysis of published literature.", "Data sources: PubMed and clinicaltrials.gov databases.", "The last search was conducted in January 2017.", "Study selection: Randomized controlled trials comparing any angiotensin converting enzyme inhibitor or AT1R blocker versus placebo or non-angiotensin converting enzyme inhibitor or non-AT1R blocker were selected.", "Study participants were adults without any major physical symptoms.", "We adhered to meta-analysis reporting methods as per PRISMA and the Cochrane Collaboration.", "Data synthesis: Eleven studies were included in the analysis.", "When compared with placebo or other antihypertensive medications, AT1R blockers and angiotensin converting enzyme inhibitors were associated with improved overall quality of life (standard mean difference = 0.11, 95% confidence interval = [0.08, 0.14], p < 0.0001), positive wellbeing (standard mean difference = 0.11, 95% confidence interval = [0.05, 0.17], p < 0.0001), mental (standard mean difference = 0.15, 95% confidence interval = [0.06, 0.25], p < 0.0001), and anxiety (standard mean difference = 0.08, 95% confidence interval = [0.01, 0.16], p < 0.0001) domains of QoL. No significant difference was found for the depression domain (standard mean difference = 0.05, 95% confidence interval = [0.02, 0.12], p = 0.15).", "Conclusions: Use of angiotensin blockers and inhibitors for the treatment of hypertension in otherwise healthy adults is associated with improved mental health domains of quality of life.", "Mental health quality of life was a secondary outcome in the included studies.", "Research specifically designed to analyse the usefulness of drugs that block the angiotensin system is necessary to properly evaluate this novel psychiatric target."], "structured": false}
{"doc_id": 26230669, "title": "The role of epigenetics in aging and autoimmunity.", "abstract": ["The decline in immunocompetence with age is accompanied by the increase in the incidence of autoimmune diseases.", "Aging of the immune system, or immunosenescence, is characterized by a decline of both T and B cell function, and paradoxically the presence of low-grade chronic inflammation.", "There is growing evidence that epigenetics, the study of inherited changes in gene expression that are not encoded by the DNA sequence itself, changes with aging.", "Interestingly, emerging evidence suggests a key role for epigenetics in human pathologies, including inflammatory and neoplastic disorders.", "Here, we will review the potential mechanisms that contribute to the increase in autoimmune responses in aging.", "In particular, we will discuss how epigenetic alterations, especially DNA methylation and histone acetylation, are accumulated during aging and how these events contribute to autoimmunity risk."], "structured": false}
{"doc_id": 26231129, "title": "A framework for understanding and targeting residual disease in oncogene-driven solid cancers", "abstract": ["Molecular targeted therapy has the potential to dramatically improve survival in patients with cancer.", "However, complete and durable responses to targeted therapy are rare in individuals with advanced-stage solid cancers.", "Even the most effective targeted therapies generally do not induce a complete tumor response, resulting in residual disease and tumor progression that limits patient survival.", "We discuss the emerging need to more fully understand the molecular basis of residual disease as a prelude to designing therapeutic strategies to minimize or eliminate residual disease so that we can move from temporary to chronic control of disease, or a cure, for patients with advanced-stage solid cancers.", "Ultimately, we propose a shift from the current reactive paradigm of analyzing and treating acquired drug resistance to a pre-emptive paradigm of defining the mechanisms that result in residual disease, to target and limit this disease reservoir."], "structured": false}
{"doc_id": 26244918, "title": "Long-term inhibition of dipeptidyl peptidase-4 in Alzheimer's prone mice.", "abstract": ["We tested here the impact of a long-term inhibition of dipeptidyl peptidase-4 (DPP-4) with sitagliptin on the deposition of amyloid-beta within the brain and deficits in memory-related behavioral paradigms in a model of Alzheimer's disease (AD): double transgenic mice B6*Cg-Tg(APPswe,PSEN1dE9)85Dbo/J. Mice began to receive sitagliptin at 7 months of age.", "Three different dose of sitagliptin (5, 10 and 20 mg/kg), were administered daily for 12 weeks by gastric gavage.", "The treatments counteracted: (i) the memory impairment in the contextual fear conditioning test; (ii) increased the brain levels of GLP-1; (iii) produced significant reductions of nitrosative stress and inflammation hallmarks within the brain, as well as (iv) a significant diminution in the ultimate number and total area of betaAPP and Abeta deposits.", "All these effects much more evident for the dose of 20 mg/kg sitagliptin.", "The long-term inhibition of the endogenous DPP-4 enzymes with sitagliptin can significantly delay some forms of AD pathology, including amyloid deposition, when administered early in the disease course of a transgenic mouse model of AD."], "structured": false}
{"doc_id": 26283293, "title": "Structural and mechanistic insights into phospholipid transfer by Ups1\u2013Mdm35 in mitochondria", "abstract": ["Eukaryotic cells are compartmentalized into membrane-bounded organelles whose functions rely on lipid trafficking to achieve membrane-specific compositions of lipids.", "Here we focused on the Ups1-Mdm35 system, which mediates phosphatidic acid (PA) transfer between the outer and inner mitochondrial membranes, and determined the X-ray structures of Mdm35 and Ups1-Mdm35 with and without PA.", "The Ups1-Mdm35 complex constitutes a single domain that has a deep pocket and flexible \u03a9-loop lid.", "Structure-based mutational analyses revealed that a basic residue at the pocket bottom and the \u03a9-loop lid are important for PA extraction from the membrane following Ups1 binding.", "Ups1 binding to the membrane is enhanced by the dissociation of Mdm35.", "We also show that basic residues around the pocket entrance are important for Ups1 binding to the membrane and PA extraction.", "These results provide a structural basis for understanding the mechanism of PA transfer between mitochondrial membranes."], "structured": false}
{"doc_id": 26297042, "title": "Redox regulation of cell migration and adhesion.", "abstract": ["Reactive oxygen species (ROS), particularly hydrogen peroxide, and the proteins that regulate them play important roles in the migration and adhesion of cells.", "Stimulation of cell surface receptors with growth factors and chemoattractants generates ROS, which relay signals from the cell surface to key signaling proteins inside the cell.", "ROS act within cells to promote migration and also in nonmigrating cells to influence the behavior of migrating cells.", "Hydrogen peroxide has also been suggested to act as a chemoattractant in its own right, drawing immune cells to wounds.", "We discuss recent progress made towards understanding how organisms use ROS, and to what degree they depend on them, during the related processes of cell migration and adhesion."], "structured": false}
{"doc_id": 26314743, "title": "Systemic Inflammatory Response Syndrome, Quick Sequential Organ Function Assessment, and Organ Dysfunction: Insights From a Prospective Database of ED Patients With Infection", "abstract": ["BACKGROUND: A proposed revision of sepsis definitions has abandoned the systemic inflammatory response syndrome (SIRS), defined organ dysfunction as an increase in total Sequential Organ Function Assessment (SOFA) score of \u2265 2, and conceived \u201cqSOFA\u201d (quick SOFA) as a bedside indicator of organ dysfunction.", "We aimed to (1) determine the prognostic impact of SIRS, (2) compare the diagnostic accuracy of SIRS and qSOFA for organ dysfunction, and (3) compare standard (Sepsis\u20102) and revised (Sepsis\u20103) definitions for organ dysfunction in ED patients with infection.\n", "METHODS: Consecutive ED patients admitted with presumed infection were prospectively enrolled over 3 years.", "Sufficient observational data were collected to calculate SIRS, qSOFA, SOFA, comorbidity, and mortality.\n", "RESULTS: We enrolled 8,871 patients, with SIRS present in 4,176 (47.1%).", "SIRS was associated with increased risk of organ dysfunction (relative risk [RR] 3.5) and mortality in patients without organ dysfunction (OR 3.2).", "SIRS and qSOFA showed similar discrimination for organ dysfunction (area under the receiver operating characteristic curve, 0.72 vs 0.73).", "qSOFA was specific but poorly sensitive for organ dysfunction (96.1% and 29.7%, respectively).", "Mortality for patients with organ dysfunction was similar for Sepsis\u20102 and Sepsis\u20103 (12.5% and 11.4%, respectively), although 29% of patients with Sepsis\u20103 organ dysfunction did not meet Sepsis\u20102 criteria.", "Increasing numbers of Sepsis\u20102 organ system dysfunctions were associated with greater mortality.\n", "CONCLUSIONS: SIRS was associated with organ dysfunction and mortality, and abandoning the concept appears premature.", "A qSOFA score \u2265 2 showed high specificity, but poor sensitivity may limit utility as a bedside screening method.", "Although mortality for organ dysfunction was comparable between Sepsis\u20102 and Sepsis\u20103, more prognostic and clinical information is conveyed using Sepsis\u20102 regarding number and type of organ dysfunctions.", "The SOFA score may require recalibration."], "structured": true}
{"doc_id": 26330861, "title": "Requirement of NAD and SIR2 for life-span extension by calorie restriction in Saccharomyces cerevisiae.", "abstract": ["Calorie restriction extends life-span in a wide variety of organisms.", "Although it has been suggested that calorie restriction may work by reducing the levels of reactive oxygen species produced during respiration, the mechanism by which this regimen slows aging is uncertain.", "Here, we mimicked calorie restriction in yeast by physiological or genetic means and showed a substantial extension in life-span.", "This extension was not observed in strains mutant for SIR2 (which encodes the silencing protein Sir2p) or NPT1 (a gene in a pathway in the synthesis of NAD, the oxidized form of nicotinamide adenine dinucleotide).", "These findings suggest that the increased longevity induced by calorie restriction requires the activation of Sir2p by NAD."], "structured": false}
{"doc_id": 26336593, "title": "Pathways disrupted in human ALS motor neurons identified through genetic correction of mutant SOD1.", "abstract": ["Although many distinct mutations in a variety of genes are known to cause Amyotrophic Lateral Sclerosis (ALS), it remains poorly understood how they selectively impact motor neuron biology and whether they converge on common pathways to cause neuronal degeneration.", "Here, we have combined reprogramming and stem cell differentiation approaches with genome engineering and RNA sequencing to define the transcriptional and functional changes that are induced in human motor neurons by mutant SOD1.", "Mutant SOD1 protein induced a transcriptional signature indicative of increased oxidative stress, reduced mitochondrial function, altered subcellular transport, and activation of the ER stress and unfolded protein response pathways.", "Functional studies demonstrated that these pathways were perturbed in a manner dependent on the SOD1 mutation.", "Finally, interrogation of stem-cell-derived motor neurons produced from ALS patients harboring a repeat expansion in C9orf72 indicates that at least a subset of these changes are more broadly conserved in ALS."], "structured": false}
{"doc_id": 26341063, "title": "Effect of enalapril on 12-year survival and life expectancy in patients with left ventricular systolic dysfunction: a follow-up study.", "abstract": ["BACKGROUND In the studies of left ventricular dysfunction (SOLVD), enalapril reduced mortality in patients with symptomatic but not asymptomatic left ventricular systolic dysfunction during the trial.", "We did a 12-year follow-up of SOLVD to establish if the mortality reduction with enalapril among patients with heart failure was sustained, and whether a subsequent reduction in mortality would emerge among those with asymptomatic ventricular dysfunction.   \n", "METHODS Of the 6797 patients previously enrolled in the SOLVD prevention and treatment trials, we ascertained the subsequent vital status of 5165 individuals who were alive when the trials had been completed.", "Follow-up was done through direct contacts in Belgium and linkages with national death registries and federal beneficiary or historic tax summary files in the USA and Canada.   \n", "FINDINGS Follow-up was 99.8% (6784/6797) complete.", "In the prevention trial, 50.9% (1074/2111) of the enalapril group had died compared with 56.4% (1195/2117) of the placebo group (generalised Wilcoxon p=0.001).", "In the treatment trial, 79.8% (1025/1285) of the enalapril group had died compared with 80.8% (1038/1284) of the placebo group (generalised Wilcoxon p=0.01).", "The reductions in cardiac deaths were significant and similar in both trials.", "When data for the prevention and treatment trials were combined, the hazard ratio for death was 0.90 for the enalapril group compared with the placebo group (95% CI 0.84-0.95, generalised Wilcoxon p=0.0003).", "Enalapril extended median survival by 9.4 months in the combined trials (95% CI 2.8-16.5, p=0.004).   \n", "INTERPRETATION Treatment with enalapril for 3-4 years led to a sustained improvement in survival beyond the original trial period in patients with left ventricular systolic dysfunction, with an important increase in life expectancy."], "structured": true}
{"doc_id": 26374799, "title": "TGFbeta/activin/nodal signaling is necessary for the maintenance of pluripotency in human embryonic stem cells.", "abstract": ["Human embryonic stem cells (hESCs) self-renew indefinitely and give rise to derivatives of all three primary germ layers, yet little is known about the signaling cascades that govern their pluripotent character.", "Because it plays a prominent role in the early cell fate decisions of embryonic development, we have examined the role of TGFbeta superfamily signaling in hESCs.", "We found that, in undifferentiated cells, the TGFbeta/activin/nodal branch is activated (through the signal transducer SMAD2/3) while the BMP/GDF branch (SMAD1/5) is only active in isolated mitotic cells.", "Upon early differentiation, SMAD2/3 signaling is decreased while SMAD1/5 signaling is activated.", "We next tested the functional role of TGFbeta/activin/nodal signaling in hESCs and found that it is required for the maintenance of markers of the undifferentiated state.", "We extend these findings to show that SMAD2/3 activation is required downstream of WNT signaling, which we have previously shown to be sufficient to maintain the undifferentiated state of hESCs.", "Strikingly, we show that in ex vivo mouse blastocyst cultures, SMAD2/3 signaling is also required to maintain the inner cell mass (from which stem cells are derived).", "These data reveal a crucial role for TGFbeta signaling in the earliest stages of cell fate determination and demonstrate an interconnection between TGFbeta and WNT signaling in these contexts."], "structured": false}
{"doc_id": 26378103, "title": "The structure and expression of a novel gene activated in early mouse embryogenesis.", "abstract": ["We report the cloning and sequence determination of the mouse H19 gene.", "This gene is under the genetic control of two trans-acting loci in the mouse, termed raf and Rif.", "These loci determine the adult basal and inducible levels, respectively, of H19 mRNA, as well as the mRNA for alpha-fetoprotein.", "By elucidating the sequence and structure of the H19 gene we show that it is unrelated to the alpha-fetoprotein gene, and therefore must have acquired its regulation by raf and Rif independently.", "The sequence also indicates that the H19 gene has a very unusual structure.", "It is composed of five exons, 1307, 135, 119, 127 and 560 bp in size, along with four very small introns whose combined lengths are 270 bases.", "The largest open reading frame of the gene, sufficient to encode a protein of approximately 14 kd, is contained entirely within the first large exon, 680 bases downstream of the cap site of the mRNA.", "Preceding the translation initiation codon are four ATG codons, each of which is followed shortly thereafter by translation terminator codons.", "The rest of the gene, which encompasses all five exons, is presumed to be untranslated.", "That the long 5' untranslated region may be used to regulate the translation of the mRNA is suggested from in vitro translation studies.", "Experiments which utilized tissue culture cell lines of the mesodermal lineage suggest that the gene is activated very early during muscle cell differentiation."], "structured": false}
{"doc_id": 26409363, "title": "Diminished linear growth during intermittent calcitriol therapy in children undergoing CCPD.", "abstract": ["Daily calcitriol therapy has been reported to improve linear growth in children with renal bone disease, and 1,25-dihydroxyvitamin D is a key regultor of chondrocyte proliferation and differentiation.", "Whereas large intermittent doses of calcitriol can lower serum parathyroid hormone (PTH) levels and reverse the skeletal changes of secondary hyperparathyroidism, the impact of intermittent calcitriol therapy on linear growth in children is not known.", "Thus, we studied 16 pre-pubertal patients with bone biopsy-proven secondary hyperparathyroidism who completed a 12-month prospective clinical trial of intermittent calcitriol therapy.", "Biochemical results and growth data obtained during intermittent calcitriol therapy were compared to values determined during the preceding 12 months of daily calcitriol therapy in each study subject; changes in bone histology were assessed after one year of intermittent calcitriol therapy.", "Z-scores for height did not change during 12 months of daily calcitriol therapy.", "Although the skeletal lesions of secondary hyperparathyroidism improved in most patients, Z-scores for height decreased from -1.8 +/-", "0.32 to -2.0 +/-", "0.33, P < 0.01, during intermittent calcitriol therapy.", "The largest reductions were seen in patients who developed adynamic bone lesions after 12 months of treatment.", "Delta Z-scores for height correlated with serum PTH, r = 0.71, P < 0.01, and alkaline phosphatase levels, r = 0.67, P < 0.01, during intermittent calcitriol therapy but not during daily calcitriol therapy.", "The data suggest that high dose intermittent calcitriol therapy adversely affects linear growth, particularly in patients with the adynamic lesion.", "The higher doses of calcitriol or the intermittent schedule of calcitriol administration may directly inhibit chondrocyte activity within growth plate cartilage of children with end-stage renal disease."], "structured": false}
{"doc_id": 26445118, "title": "Comparison of pain syndromes associated with nervous or somatic lesions and development of a new neuropathic pain diagnostic questionnaire (DN4)", "abstract": ["Few studies have directly compared the clinical features of neuropathic and non-neuropathic pains.", "For this purpose, the French Neuropathic Pain Group developed a clinician-administered questionnaire named DN4 consisting of both sensory descriptors and signs related to bedside sensory examination.", "This questionnaire was used in a prospective study of 160 patients presenting with pain associated with a definite neurological or somatic lesion.", "The most common aetiologies of nervous lesions (n=89) were traumatic nerve injury, post herpetic neuralgia and post stroke pain.", "Non-neurological lesions (n=71) were represented by osteoarthritis, inflammatory arthropathies and mechanical low back pain.", "Each patient was seen independently by two experts in order to confirm the diagnosis of neuropathic or non-neuropathic pain.", "The prevalence of pain descriptors and sensory dysfunctions were systematically compared in the two groups of patients.", "The analysis of the psychometric properties of the DN4 questionnaire included: face validity, inter-rater reliability, factor analysis and logistic regression to identify the discriminant properties of items or combinations of items for the diagnosis of neuropathic pain.", "We found that a relatively small number of items are sufficient to discriminate neuropathic pain.", "The 10-item questionnaire developed in the present study constitutes a new diagnostic instrument, which might be helpful both in clinical research and daily practice."], "structured": false}
{"doc_id": 26456326, "title": "Changing the density of alcohol outlets to reduce alcohol-related problems.", "abstract": ["Increasingly, it seems, legal and political debates regarding the granting of new liquor licences are turning to the issue of whether the number and density of alcohol outlets makes a difference in rates of alcohol consumption and alcohol-related harm.", "But what is the state of the evidence on this question?", "In this Harm Reduction Digest Livingston, Chikritzhs and Room review the research literature on the effects of density of alcohol sales outlets on alcohol consumption and alcohol-related problems; suggest a new way of conceptualising the relationships; and discuss the implications for reducing alcohol-related harm."], "structured": false}
{"doc_id": 26461066, "title": "[Pharmacokinetics and biotransformation of the antimycotic drug ciclopiroxolamine in animals and man after topical and systemic administration].", "abstract": ["1.", "Following the dermal application of the carbon-14 labelled broad spectrum antimycotic 6-cyclohexyl-1-hydroxy-4-methyl-2(1H)-pyridone, 2-aminoethanol salt (ciclopiroxolamine, Hoe 296, Batrafen) in the form of a 1% aqueous cream to healthy human dorsal skin (penetration time: 6 h; occlusive dressing for 5 h), percutaneous absorption accounted on average for 1.3% of the dose applied.", "Excretion occurred via the kidney, with biological half-lives of 1.7 h. As can be seen from penetration studies of cadaverous skin, the horny layer contained the highest concentrations, with values of 2300-4500 microgram/cm3.", "The levels determined in the corium were still above the minimum inhibitory concentrations.", "These concentrations were already obtained at the first test stage (1.5 h after application) and did not change virtually at all over the longer penetration period.", "According to studies using histoautoradiography, ciclopirox can penetrate the skin via the epidermis and the hair follicles.", "When ciclopirox-14C-olamine aqueous cream was spread on the surface of fingernails, the radioactive-labelled compound penetrated right through the nail.", "The percutaneous absorption in dogs was higher, at 5-15% of the dose, than it was in humans.", "2.", "After vaginal application (1 mg/kg) of ciclopirox-14C-olamine in the form of a 1% aqueous cream to bitches, between 42 and 97% of the dose (depending on the animal) was recovered in the urine and faeces, the remainder having penetrated into the tampon used to close the vagina.", "3.", "Ciclopirox is excreted by dogs and man in the urine, primarily as a glucuronide.", "In humans another glucuronide with properties similar to those of the original substance was detected.", "Two conjugated, relatively non-polar metabolites were also present in small amounts.", "The metabolite patterns after oral and dermal application were similar.", "The binding of ciclopirox to serum proteins in humans was 96 +/-", "2% in a concentration range of 0.01-11.0 microgram/ml.", "4.", "Placental transfer was low in the rats studied.", "Though there was good absorption by the mother animal, the radioactivity in the foetal tissues was always lower than that of the maternal blood."], "structured": false}
{"doc_id": 26462632, "title": "Maximizing the diagnostic utility of endoscopic biopsy in dogs and cats with gastrointestinal disease.", "abstract": ["Flexible endoscopy has become a valuable tool for the diagnosis of many small animal gastrointestinal (GI) diseases, but the techniques must be performed carefully so that the results are meaningful.", "This article reviews the current diagnostic utility of flexible endoscopy, including practical/technical considerations for endoscopic biopsy, optimal instrumentation for mucosal specimen collection, the correlation of endoscopic indices to clinical activity and to histopathologic findings, and new developments in the endoscopic diagnosis of GI disease.", "Recent studies have defined endoscopic biopsy guidelines for the optimal number and quality of diagnostic specimens from different regions of the gut.", "They also have shown the value of ileal biopsy in the diagnosis of canine and feline chronic enteropathies, and have demonstrated the utility of endoscopic biopsy specimens beyond routine hematoxylin and eosin histopathological analysis, including their use in immunohistochemical, microbiological, and molecular studies."], "structured": false}
{"doc_id": 26474812, "title": "Age-structured red blood cell susceptibility and the dynamics of malaria infections.", "abstract": ["Malaria parasites and immune responses in an infected human interact on a dynamic landscape, in which a population of replicating parasites depletes a population of replenishing red blood cells (RBCs).", "These underlying dynamics receive relatively little attention, but they offer unique insights into the processes that control most malaria infections.", "Here, we focus on the observation that three of the four malaria-parasite species that infect humans are restricted to particular age classes of RBC.", "We explicitly incorporate this observation in models of infection dynamics to distinguish common from species-specific pressures on host immune responses, and we find that age structuring has profound effects on the course of infection.", "For all four species conditions exist under which the parasites may persist at low densities, or may clear, even in the absence of an immune response.", "Catastrophic anemia can occur even with the two species that attack only the youngest RBCs, although only a small fraction of cells are parasitized at any point.", "Furthermore, with these two, compensatory erythropoetic responses in the host accelerate parasite population growth.", "A \"basic reproduction rate\" characterizes these differences in outcomes."], "structured": false}
{"doc_id": 26488879, "title": "Helicobacter pylori AlpA and AlpB bind host laminin and influence gastric inflammation in gerbils.", "abstract": ["Helicobacter pylori persistently colonizes humans, causing gastritis, ulcers, and gastric cancer.", "Adherence to the gastric epithelium has been shown to enhance inflammation, yet only a few H. pylori adhesins have been paired with targets in host tissue.", "The alpAB locus has been reported to encode adhesins involved in adherence to human gastric tissue.", "We report that abrogation of H. pylori AlpA and AlpB reduces binding of H. pylori to laminin while expression of plasmid-borne alpA or alpB confers laminin-binding ability to Escherichia coli.", "An H. pylori strain lacking only AlpB is also deficient in laminin binding.", "Thus, we conclude that both AlpA and AlpB contribute to H. pylori laminin binding.", "Contrary to expectations, the H. pylori SS1 mutant deficient in AlpA and AlpB causes more severe inflammation than the isogenic wild-type strain in gerbils.", "Identification of laminin as the target of AlpA and AlpB will facilitate future investigations of host-pathogen interactions occurring during H. pylori infection."], "structured": false}
{"doc_id": 26491450, "title": "A quantitative analysis of kinase inhibitor selectivity", "abstract": ["Kinase inhibitors are a new class of therapeutics with a propensity to inhibit multiple targets.", "The biological consequences of multi-kinase activity are poorly defined, and an important step toward understanding the relationship between selectivity, efficacy and safety is the exploration of how inhibitors interact with the human kinome.", "We present interaction maps for 38 kinase inhibitors across a panel of 317 kinases representing >50% of the predicted human protein kinome.", "The data constitute the most comprehensive study of kinase inhibitor selectivity to date and reveal a wide diversity of interaction patterns.", "To enable a global analysis of the results, we introduce the concept of a selectivity score as a general tool to quantify and differentiate the observed interaction patterns.", "We further investigate the impact of panel size and find that small assay panels do not provide a robust measure of selectivity."], "structured": false}
{"doc_id": 26495128, "title": "Ribosomal protein S9 is a novel B23/NPM-binding protein required for normal cell proliferation.", "abstract": ["B23 (NPM/nucleophosmin) is a multifunctional nucleolar protein and a member of the nucleoplasmin superfamily of acidic histone chaperones.", "B23 is essential for normal embryonic development and plays an important role in genomic stability, ribosome biogenesis, and anti-apoptotic signaling.", "Altered protein expression or genomic mutation of B23 is encountered in many different forms of cancer.", "Although described as multifunctional, a genuine molecular function of B23 is not fully understood.", "Here we show that B23 is associated with a protein complex consisting of ribosomal proteins and ribosome-associated RNA helicases.", "A novel, RNA-independent interaction between ribosomal protein S9 (RPS9) and B23 was further investigated.", "We found that S9 binding requires an intact B23 oligomerization domain.", "Depletion of S9 by small interfering RNA resulted in decreased protein synthesis and G(1) cell cycle arrest, in association with induction of p53 target genes.", "We determined that S9 is a short-lived protein in the absence of ribosome biogenesis, and proteasomal inhibition significantly increased S9 protein level.", "Overexpression of B23 facilitated nucleolar storage of S9, whereas knockdown of B23 led to diminished levels of nucleolar S9.", "Our results suggest that B23 selectively stores, and protects ribosomal protein S9 in nucleoli and therefore could facilitate ribosome biogenesis."], "structured": false}
{"doc_id": 26501027, "title": "Vasculature-associated cells expressing nestin in developing bones encompass early cells in the osteoblast and endothelial lineage.", "abstract": ["Nestin-positive (Nes(+)) cells are important hematopoiesis-supporting constituents in adult bone marrow.", "However, how these cells originate during endochondral bone development is unknown.", "Studies using mice expressing GFP under the direction of nestin promoter/enhancer (Nes-GFP) revealed distinct endothelial and nonendothelial Nes(+) cells in the embryonic perichondrium; the latter were early cells of the osteoblast lineage immediately descended from their progenitors upon Indian hedgehog action and Runx2 expression.", "During vascular invasion and formation of ossification centers, these Nes(+) cells were closely associated with each other and increased in number progressively.", "Interestingly, cells targeted by tamoxifen-inducible cre recombinase driven by nestin enhancer (Nes-creER) in developing bone marrow were predominantly endothelial cells.", "Furthermore, Nes(+) cells in postnatal bones were heterogeneous populations, including a range of cells in the osteoblast and endothelial lineage.", "These findings reveal an emerging complexity of stromal populations, accommodating Nes(+) cells as vasculature-associated early cells in the osteoblast and endothelial lineage."], "structured": false}
{"doc_id": 26532518, "title": "Public health, academic medicine, and the alcohol industry's corporate social responsibility activities.", "abstract": ["We explored the emerging relationships among the alcohol industry, academic medicine, and the public health community in the context of public health theory dealing with corporate social responsibility.", "We reviewed sponsorship of scientific research, efforts to influence public perceptions of research, dissemination of scientific information, and industry-funded policy initiatives.", "To the extent that the scientific evidence supports the reduction of alcohol consumption through regulatory and legal measures, the academic community has come into increasing conflict with the views of the alcohol industry.", "We concluded that the alcohol industry has intensified its scientific and policy-related activities under the general framework of corporate social responsibility initiatives, most of which can be described as instrumental to the industry's economic interests."], "structured": false}
{"doc_id": 26561572, "title": "RET, ROS1 and ALK fusions in lung cancer", "abstract": ["Through an integrated molecular- and histopathology-based screening system, we performed a screening for fusions of anaplastic lymphoma kinase (ALK) and c-ros oncogene 1, receptor tyrosine kinase (ROS1) in 1,529 lung cancers and identified 44 ALK-fusion\u2013positive and 13 ROS1-fusion\u2013positive adenocarcinomas, including for unidentified fusion partners for ROS1.", "In addition, we discovered previously unidentified kinase fusions that may be promising for molecular-targeted therapy, kinesin family member 5B (KIF5B)-ret proto-oncogene (RET) and coiled-coil domain containing 6 (CCDC6)-RET, in 14 adenocarcinomas.", "A multivariate analysis of 1,116 adenocarcinomas containing these 71 kinase-fusion\u2013positive adenocarcinomas identified four independent factors that are indicators of poor prognosis: age \u226550 years, male sex, high pathological stage and negative kinase-fusion status."], "structured": false}
{"doc_id": 26596106, "title": "Genetic and biochemical interactions among Yar1, Ltv1 and Rps3 define novel links between environmental stress and ribosome biogenesis in Saccharomyces cerevisiae.", "abstract": ["In the yeast S. cerevisiae, ribosome assembly is linked to environmental conditions by the coordinate transcriptional regulation of genes required for ribosome biogenesis.", "In this study we show that two nonessential stress-responsive genes, YAR1 and LTV1, function in 40S subunit production.", "We provide genetic and biochemical evidence that Yar1, a small ankyrin-repeat protein, physically interacts with RpS3, a component of the 40S subunit, and with Ltv1, a protein recently identified as a substoichiometric component of a 43S preribosomal particle.", "We demonstrate that cells lacking YAR1 or LTV1 are hypersensitive to particular protein synthesis inhibitors and exhibit aberrant polysome profiles, with a reduced absolute number of 40S subunits and an excess of free 60S subunits.", "Surprisingly, both mutants are also hypersensitive to a variety of environmental stress conditions.", "Overexpression of RPS3 suppresses both the stress sensitivity and the ribosome biogenesis defect of Deltayar1 mutants, but does not suppress either defect in Deltaltv1 mutants.", "We propose that YAR1 and LTV1 play distinct, nonessential roles in 40S subunit production.", "The stress-sensitive phenotypes of strains lacking these genes reveal a hitherto unknown link between ribosome biogenesis factors and environmental stress sensitivity."], "structured": false}
{"doc_id": 26607366, "title": "Rational design of acridine-based ligands with selectivity for human telomeric quadruplexes.", "abstract": ["Structure-based modeling methods have been used to design a series of disubstituted triazole-linked acridine compounds with selectivity for human telomeric quadruplex DNAs.", "A focused library of these compounds was prepared using click chemistry and the selectivity concept was validated against two promoter quadruplexes from the c-kit gene with known molecular structures, as well as with duplex DNA using a FRET-based melting method.", "Lead compounds were found to have reduced effects on the thermal stability of the c-kit quadruplexes and duplex DNA structures.", "These effects were further explored with a series of competition experiments, which confirmed that binding to duplex DNA is very low even at high duplex:telomeric quadruplex ratios.", "Selectivity to the c-kit quadruplexes is more complex, with some evidence of their stabilization at increasing excess over human telomeric quadruplex DNA.", "Selectivity is a result of the dimensions of the triazole-acridine compounds, and in particular the separation of the two alkyl-amino terminal groups.", "Both lead compounds also have selective inhibitory effects on the proliferation of cancer cell lines compared to a normal cell line, and one has been shown to inhibit the activity of the telomerase enzyme, which is selectively expressed in tumor cells, where it plays a role in maintaining telomere integrity and cellular immortalization."], "structured": false}
{"doc_id": 26611094, "title": "Hospital volume and the outcomes of mechanical ventilation.", "abstract": ["BACKGROUND An increased volume of patients is associated with improved survival in numerous high-risk medical and surgical conditions.", "The relationship between the number of patients admitted (hospital volume) and outcome among patients with critical illnesses is unknown.   \n", "METHODS We analyzed data from 20,241 nonsurgical patients receiving mechanical ventilation at 37 acute care hospitals in the Acute Physiology and Chronic Health Evaluation clinical information system from 2002 through 2003.", "Multivariate analyses were performed to adjust for the severity of illness and other differences in the case mix.   \n", "RESULTS An increase in hospital volume was associated with improved survival among patients receiving mechanical ventilation in the intensive care unit (ICU) and in the hospital.", "Admission to a hospital in the highest quartile according to volume (i.e., >400 patients receiving mechanical ventilation per year) was associated with a 37 percent reduction in the adjusted odds of death in the ICU as compared with admission to hospitals in the lowest quartile (< or =150 patients receiving mechanical ventilation per year, P<0.001).", "In-hospital mortality was similarly reduced (adjusted odds ratio, 0.66; 95 percent confidence interval, 0.52 to 0.83; P<0.001).", "A typical patient in a hospital in a low-volume quartile would have an adjusted in-hospital mortality of 34.2 percent as compared with 25.5 percent in a hospital in a high-volume quartile.", "Among survivors, there were no significant trends in the length of stay in the ICU or the hospital.   \n", "CONCLUSIONS Mechanical ventilation of patients in a hospital with a high case volume is associated with reduced mortality.", "Further research is needed to determine the mechanism of the relationship between volume and outcome among patients with a critical illness."], "structured": true}
{"doc_id": 26611834, "title": "A meta-analysis of depression during pregnancy and the risk of preterm birth, low birth weight, and intrauterine growth restriction.", "abstract": ["CONTEXT Maternal depressive symptoms during pregnancy have been reported in some, but not all, studies to be associated with an increased risk of preterm birth (PTB), low birth weight (LBW), and intrauterine growth restriction (IUGR).   \n", "OBJECTIVE To estimate the risk of PTB, LBW, and IUGR associated with antenatal depression.   \n", "DATA SOURCES AND STUDY SELECTION", "We searched for English-language and non-English-language articles via the MEDLINE, PsycINFO, CINAHL, Social Work Abstracts, Social Services Abstracts, and Dissertation Abstracts International databases (January 1980 through December 2009).", "We aimed to include prospective studies reporting data on antenatal depression and at least 1 adverse birth outcome: PTB (<37 weeks' gestation), LBW (<2500 g), or IUGR (<10th percentile for gestational age).", "Of 862 reviewed studies, 29 US-published and non-US-published studies met the selection criteria.   \n", "DATA EXTRACTION Information was extracted on study characteristics, antenatal depression measurement, and other biopsychosocial risk factors and was reviewed twice to minimize error.   \n", "DATA SYNTHESIS Pooled relative risks (RRs) for the effect of antenatal depression on each birth outcome were calculated using random-effects methods.", "In studies of PTB, LBW, and IUGR that used a categorical depression measure, pooled effect sizes were significantly larger (pooled RR [95% confidence interval] = 1.39 [1.19-1.61], 1.49 [1.25-1.77], and 1.45 [1.05-2.02], respectively) compared with studies that used a continuous depression measure (1.03 [1.00-1.06], 1.04 [0.99-1.09], and 1.02 [1.00-1.04], respectively).", "The estimates of risk for categorically defined antenatal depression and PTB and LBW remained significant when the trim-and-fill procedure was used to correct for publication bias.", "The risk of LBW associated with antenatal depression was significantly larger in developing countries (RR = 2.05; 95% confidence interval, 1.43-2.93) compared with the United States (RR = 1.10; 95% confidence interval, 1.01-1.21) or European social democracies (RR = 1.16; 95% confidence interval, 0.92-1.47).", "Categorically defined antenatal depression tended to be associated with an increased risk of PTB among women of lower socioeconomic status in the United States.   \n", "CONCLUSIONS Women with depression during pregnancy are at increased risk for PTB and LBW, although the magnitude of the effect varies as a function of depression measurement, country location, and US socioeconomic status.", "An important implication of these findings is that antenatal depression should be identified through universal screening and treated."], "structured": true}
{"doc_id": 26612216, "title": "ES cell pluripotency and germ-layer formation require the SWI/SNF chromatin remodeling component BAF250a.", "abstract": ["ATP-dependent chromatin remodeling complexes are a notable group of epigenetic modifiers that use the energy of ATP hydrolysis to change the structure of chromatin, thereby altering its accessibility to nuclear factors.", "BAF250a (ARID1a) is a unique and defining subunit of the BAF chromatin remodeling complex with the potential to facilitate chromosome alterations critical during development.", "Our studies show that ablation of BAF250a in early mouse embryos results in developmental arrest (about embryonic day 6.5) and absence of the mesodermal layer, indicating its critical role in early germ-layer formation.", "Moreover, BAF250a deficiency compromises ES cell pluripotency, severely inhibits self-renewal, and promotes differentiation into primitive endoderm-like cells under normal feeder-free culture conditions.", "Interestingly, this phenotype can be partially rescued by the presence of embryonic fibroblast cells.", "DNA microarray, immunostaining, and RNA analyses revealed that BAF250a-mediated chromatin remodeling contributes to the proper expression of numerous genes involved in ES cell self-renewal, including Sox2, Utf1, and Oct4.", "Furthermore, the pluripotency defects in BAF250a mutant ES cells appear to be cell lineage-specific.", "For example, embryoid body-based analyses demonstrated that BAF250a-ablated stem cells are defective in differentiating into fully functional mesoderm-derived cardiomyocytes and adipocytes but are capable of differentiating into ectoderm-derived neurons.", "Our results suggest that BAF250a is a key component of the gene regulatory machinery in ES cells controlling self-renewal, differentiation, and cell lineage decisions."], "structured": false}
{"doc_id": 26625002, "title": "Metabolic shutdown in Escherichia coli cells lacking the outer membrane channel TolC.", "abstract": ["The outer membrane channel TolC is a key component of multidrug efflux and type I secretion transporters in Escherichia coli.", "Mutational inactivation of TolC renders cells highly susceptible to antibiotics and leads to defects in secretion of protein toxins.", "Despite impairment of various transport functions, no growth defects were reported in cells lacking TolC. Unexpectedly, we found that the loss of TolC notably impairs cell division and growth in minimal glucose medium.", "The TolC-dependent phenotype was further exacerbated by the loss of ygiB and ygiC genes expressed in the same operon as tolC and their homologues yjfM and yjfC located elsewhere on the chromosome.", "Our results show that this growth deficiency is caused by depletion of the critical metabolite NAD(+) and high NADH/NAD(+) ratios.", "The increased amounts of PspA and decreased rates of NADH oxidation in Delta tolC membranes indicated stress on the membrane and dissipation of a proton motive force.", "We conclude that inactivation of TolC triggers metabolic shutdown in E. coli cells grown in minimal glucose medium.", "The Delta tolC phenotype is partially rescued by YgiBC and YjfMC, which have parallel functions independent from TolC."], "structured": false}
{"doc_id": 26652147, "title": "Acyl and total ghrelin are suppressed strongly by ingested proteins, weakly by lipids, and biphasically by carbohydrates.", "abstract": ["CONTEXT Ghrelin is an orexigenic hormone that can increase body weight.", "Its circulating levels increase before meals and are suppressed after food ingestion.", "Understanding the effects of specific types of ingested macronutrients on ghrelin regulation could facilitate the design of weight-reducing diets.   \n", "OBJECTIVE We sought to understand how ingestion of carbohydrates, proteins, or lipids affect acyl (bioactive) and total ghrelin levels among human subjects, hypothesizing that lipids might suppress ghrelin levels less effectively than do either carbohydrates or proteins.   \n", "DESIGN This was a randomized, within-subjects cross-over study.   \n", "SETTING The study was conducted at a University Clinical Research Center.   \n", "PARTICIPANTS", "There were 16 healthy human subjects included in the study.   \n", "INTERVENTIONS Isocaloric, isovolemic beverages composed primarily of carbohydrates, proteins, or lipids were provided.   \n", "MAIN OUTCOME MEASURES The magnitude of postprandial suppression of total and acyl ghrelin levels (measured with a novel acyl-selective, two-site ELISA) was determined.   \n", "RESULTS All beverages suppressed plasma acyl and total ghrelin levels.", "A significant effect of macronutrient class on decremental area under the curve for both acyl and total ghrelin was observed; the rank order for magnitude of suppression was protein more than carbohydrate more than lipid.", "Total ghrelin nadir levels were significantly lower after both carbohydrate and protein, compared with lipid beverages.", "In the first 3 postprandial hours, the rank order for acyl and total ghrelin suppression was carbohydrate more than protein more than lipid.", "In the subsequent 3 h, there was a marked rebound above preprandial values of acyl and total ghrelin after carbohydrate ingestion alone.   \n", "CONCLUSIONS These findings suggest possible mechanisms contributing to the effects of high-protein/low-carbohydrate diets to promote weight loss, and high-fat diets to promote weight gain."], "structured": true}
{"doc_id": 26658659, "title": "Hydrogen sulfide increases nitric oxide production with calcium-dependent activation of endothelial nitric oxide synthase in endothelial cells.", "abstract": ["Hydrogen sulfide (H(2)S) was recently discovered to be synthesized in mammalian tissues by several different enzymes.", "Numerous studies have shown that H(2)S has vasodilator and antihypertensive effects in the cardiovascular system.", "However, intracellular mechanisms of the H(2)S-induced vasodilation and its interactions with other endothelium-derived relaxing factors, such as nitric oxide (NO), remain unclear.", "We investigated whether H(2)S directly regulates endothelial NO synthase (eNOS) activity and NO production in endothelial cells.", "NaHS, a H(2)S donor, dose-dependently increased NO production in cultured endothelial cells.", "This effect was abolished by a calcium chelator (BAPTA-AM), but not by the absence of extracellular calcium.", "The NaHS-induced NO production was partially blocked by inhibitors of ryanodine receptor (dantrolene) or inositol 1,4,5-triphosphate receptor (xestospongin C).", "NaHS significantly increased intracellular calcium concentrations, and this effect was attenuated by dantrolene or xestospongin C. NaHS induced phosphorylation of eNOS at the activating phosphoserine residue 1179.", "The NaHS-induced eNOS phosphorylation and NO production were not affected by a PI3K/Akt inhibitor (wortmannin).", "The data of this study suggest that H(2)S directly acts on endothelial cells to induce eNOS activation and NO production by releasing calcium from the intracellular store in endoplasmic reticulum, which may explain one of mechanisms of its vasodilator function."], "structured": false}
{"doc_id": 26668245, "title": "Fear of falling and visual field loss from glaucoma.", "abstract": ["OBJECTIVE To determine if visual field (VF) loss resulting from glaucoma is associated with greater fear of falling.   \n", "DESIGN Prospective, observational study.   \n", "PARTICIPANTS Fear of falling was compared between 83 glaucoma subjects with bilateral VF loss and 60 control subjects with good visual acuity and without significant VF loss recruited from patients followed up for suspicion of glaucoma.   \n", "METHODS Participants completed the University of Illinois at Chicago Fear of Falling Questionnaire.", "The extent of fear of falling was assessed using Rasch analysis.   \n", "MAIN OUTCOME MEASURES Subject ability to perform tasks without fear of falling was expressed in logits, with lower scores implying less ability and greater fear of falling.   \n", "RESULTS Glaucoma subjects had greater VF loss than control subjects (median better-eye mean deviation [MD] of -8.0 decibels [dB] vs. +0.2 dB; P<0.001), but did not differ with regard to age, race, gender, employment status, the presence of other adults in the home, body mass index (BMI), grip strength, cognitive ability, mood, or comorbid illness (P \u2265 0.1 for all).", "In multivariate models, glaucoma subjects reported greater fear of falling as compared with controls (\u03b2 = -1.20 logits; 95% confidence interval [CI], -1.87 to -0.53; P = 0.001), and fear of falling increased with greater VF loss severity (\u03b2 = -0.52 logits per 5-dB decrement in the better eye VF MD; 95% CI, -0.72 to -0.33; P<0.001).", "Other variables predicting greater fear of falling included female gender (\u03b2 = -0.55 logits; 95% CI, -1.03 to -0.06; P = 0.03), higher BMI (\u03b2 = -0.07 logits per 1-unit increase in BMI; 95% CI, -0.13 to -0.01; P = 0.02), living with another adult (\u03b2 = -1.16 logits; 95% CI, -0.34 to -1.99 logits; P = 0.006), and greater comorbid illness (\u03b2 = -0.53 logits/1 additional illness; 95% CI, -0.74 to -0.32; P<0.001).   \n", "CONCLUSIONS Bilateral VF loss resulting from glaucoma is associated with greater fear of falling, with an impact that exceeds numerous other risk factors.", "Given the physical and psychological repercussions associated with fear of falling, significant quality-of-life improvements may be achievable in patients with VF loss by screening for, and developing interventions to minimize, fear of falling."], "structured": true}
{"doc_id": 26672703, "title": "Repeat instability: mechanisms of dynamic mutations", "abstract": ["Disease-causing repeat instability is an important and unique form of mutation that is linked to more than 40 neurological, neurodegenerative and neuromuscular disorders.", "DNA repeat expansion mutations are dynamic and ongoing within tissues and across generations.", "The patterns of inherited and tissue-specific instability are determined by both gene-specific cis-elements and trans-acting DNA metabolic proteins.", "Repeat instability probably involves the formation of unusual DNA structures during DNA replication, repair and recombination.", "Experimental advances towards explaining the mechanisms of repeat instability have broadened our understanding of this mutational process.", "They have revealed surprising ways in which metabolic pathways can drive or protect from repeat instability."], "structured": false}
{"doc_id": 26673492, "title": "Demographic Risk Factors for Alcohol-Related Aggression In and Around Licensed Venues.", "abstract": ["AIMS Few studies have examined the role of gender and both area-level and individual socio-economic status (SES) as independent predictors of alcohol-related aggression (ARA) in and around licensed venues.   \n", "METHODS The aim of the present study was to investigate the relationship between gender, area-level SES and individual SES (operationalised as occupational category) and ARA in and around licensed venues.", "The sample comprised 697 men and 649 women aged 16-47, who completed a patron intercept survey as part of a larger study assessing trends in harm and stakeholders' views surrounding local community level interventions in dealing with alcohol-related problems in the night-time economy.   \n", "RESULTS Binary logistic regression analyses showed that age, gender, occupational category, area-level SES and level of intoxication at time of interview were all significant predictors of involvement in ARA.", "Being male doubled the odds of involvement in ARA, while age was a protective factor.", "Blue collar workers had more than double the odds of ARA involvement of professionals, while those living in the most socio-economically disadvantaged areas were over twice as likely to report experiencing ARA compared to those living in the most advantaged areas.", "However, assessment of the predictive model by gender revealed that effects of age, occupational category and area-level SES were restricted to male participants, with greater intoxication no longer predictive.   \n", "CONCLUSIONS ARA among patrons was significantly more likely to occur among men, those in blue collar occupations, and individuals living in low SES areas, suggesting both individual and area-level disadvantage may play a role in ARA."], "structured": true}
{"doc_id": 26688294, "title": "Schizophrenia susceptibility pathway neuregulin 1\u2013ErbB4 suppresses Src upregulation of NMDA receptors", "abstract": ["Hypofunction of the N-methyl D-aspartate subtype of glutamate receptor (NMDAR) is hypothesized to be a mechanism underlying cognitive dysfunction in individuals with schizophrenia.", "For the schizophrenia-linked genes NRG1 and ERBB4, NMDAR hypofunction is thus considered a key detrimental consequence of the excessive NRG1-ErbB4 signaling found in people with schizophrenia.", "However, we show here that neuregulin 1\u03b2\u2013ErbB4 (NRG1\u03b2-ErbB4) signaling does not cause general hypofunction of NMDARs.", "Rather, we find that, in the hippocampus and prefrontal cortex, NRG1\u03b2-ErbB4 signaling suppresses the enhancement of synaptic NMDAR currents by the nonreceptor tyrosine kinase Src.", "NRG1\u03b2-ErbB4 signaling prevented induction of long-term potentiation at hippocampal Schaffer collateral\u2013CA1 synapses and suppressed Src-dependent enhancement of NMDAR responses during theta-burst stimulation.", "Moreover, NRG1\u03b2-ErbB4 signaling prevented theta burst\u2013induced phosphorylation of GluN2B by inhibiting Src kinase activity.", "We propose that NRG1-ErbB4 signaling participates in cognitive dysfunction in schizophrenia by aberrantly suppressing Src-mediated enhancement of synaptic NMDAR function."], "structured": false}
{"doc_id": 26702468, "title": "Intestinal bacteria and the regulation of immune cell homeostasis.", "abstract": ["The human intestine is colonized by an estimated 100 trillion bacteria.", "Some of these bacteria are essential for normal physiology, whereas others have been implicated in the pathogenesis of multiple inflammatory diseases including IBD and asthma.", "This review examines the influence of signals from intestinal bacteria on the homeostasis of the mammalian immune system in the context of health and disease.", "We review the bacterial composition of the mammalian intestine, known bacterial-derived immunoregulatory molecules, and the mammalian innate immune receptors that recognize them.", "We discuss the influence of bacterial-derived signals on immune cell function and the mechanisms by which these signals modulate the development and progression of inflammatory disease.", "We conclude with an examination of successes and future challenges in using bacterial communities or their products in the prevention or treatment of human disease."], "structured": false}
{"doc_id": 26710772, "title": "Sympathetic activation during early pregnancy in humans.", "abstract": ["Sympathetic activity has been reported to increase in normotensive pregnant women, and to be even greater in women with gestational hypertension and preeclampsia at term.", "Whether sympathetic overactivity develops early during pregnancy, remaining high throughout gestation, or whether it only occurs at term providing the substrate for hypertensive disorders is unknown.", "We tested the hypothesis that sympathetic activation occurs early during pregnancy in humans.", "Eleven healthy women (29 \u00b1 3 (SD) years) without prior hypertensive pregnancies were tested during the mid-luteal phase (PRE) and early pregnancy (EARLY; 6.2 \u00b1 1.2 weeks of gestation).", "Muscle sympathetic nerve activity (MSNA) and haemodynamics were measured supine, at 30 deg and 60 deg upright tilt for 5 min each.", "Blood samples were drawn for catecholamines, direct renin, and aldosterone.", "MSNA was significantly greater during EARLY than PRE (supine: 25 \u00b1 8 vs. 14 \u00b1 8 bursts min(-1), 60 deg tilt: 49 \u00b1 14 vs. 40 \u00b1 10 bursts min(-1); main effect, P < 0.05).", "Resting diastolic pressure trended lower (P = 0.09), heart rate was similar, total peripheral resistance decreased (2172 \u00b1 364 vs. 2543 \u00b1 352 dyne s cm(-5); P < 0.05), sympathetic vascular transduction was blunted (0.10 \u00b1 0.05 vs. 0.36 \u00b1 0.47 units a.u.(-1) min(-1); P < 0.01), and both renin (supine: 27.9 \u00b1 6.2 vs. 14.2 \u00b1 8.7 pg ml(-1), P < 0.01) and aldosterone (supine: 16.7 \u00b1 14.1 vs. 7.7 \u00b1 6.8 ng ml(-1), P = 0.05) were higher during EARLY than PRE.", "These results suggest that sympathetic activation is a common characteristic of early pregnancy in humans despite reduced diastolic pressure and total peripheral resistance.", "These observations challenge conventional thinking about blood pressure regulation during pregnancy, showing marked sympathetic activation occurring within the first few weeks of conception, and may provide the substrate for pregnancy induced cardiovascular complications."], "structured": false}
{"doc_id": 26720366, "title": "Psychological adaptation in children with idiopathic short stature treated with growth hormone or placebo.", "abstract": ["The influence of short stature on psychological adaptation in childhood and adolescence is controversial.", "GH is currently used to treat children with idiopathic short stature (ISS, also known as non-GH-deficient short stature).", "This study represents the first double-blind, placebo-controlled trial of the effects of GH on the psychological adaptation of children and adolescents with ISS, treated with GH until adult height was attained.", "Sixty-eight children (53 males, 15 females), 9-16 yr old, with marked ISS (measured height or predicted adult height -2.5 sd or less) received either GH 0.074 mg/kg or placebo sc three times per week until height velocity decreased to less than 1.5 cm/yr.", "Parents completed the Child Behavior Checklist (CBCL) and children the Self-Perception Profile (SPP) and Silhouette Apperception Technique at baseline and annually thereafter.", "Baseline behavioral/emotional adjustment (CBCL) and self-concept (SPP) scores for children with ISS were within the normative range.", "The two study groups exhibited similar behavioral and self-concept profiles (CBCL) during the first 2 yr of the study.", "However, CBCL behavior problems (internalizing, externalizing, and total problems) appeared to decline, in yr 3 and 4, in the GH-treated group relative to the placebo-treated group.", "Group differences in CBCL competency domains and the SPP were not observed at any point during the study.", "Short stature among children with ISS enrolled in this long-term, placebo-controlled study was not associated with problems in psychological adaptation or self-concept with the psychological instruments employed.", "GH treatment was associated with a trend toward improvement in problem behaviors, as measured by questionnaires (CBCL) completed by study participants' parents.", "It remains to be determined whether GH treatment significantly impacts adaptation, psychosocial function, or quality of life in children with ISS."], "structured": false}
{"doc_id": 26731863, "title": "Distinct and essential roles of transcription factors IRF-3 and IRF-7 in response to viruses for IFN-alpha/beta gene induction.", "abstract": ["Induction of the interferon (IFN)-alpha/beta gene transcription in virus-infected cells is an event central to innate immunity.", "Mice lacking the transcription factor IRF-3 are more vulnerable to virus infection.", "In embryonic fibroblasts, virus-induced IFN-alpha/beta gene expression levels are reduced and the spectrum of the IFN-alpha mRNA subspecies altered.", "Furthermore, cells additionally defective in IRF-7 expression totally fail to induce these genes in response to infections by any of the virus types tested.", "In these cells, a normal profile of IFN-alpha/beta mRNA induction can be achieved by coexpressing both IRF-3 and IRF-7.", "These results demonstrate the essential and distinct roles of thetwo factors, which together ensure the transcriptional efficiency and diversity of IFN-alpha/beta genes for the antiviral response."], "structured": false}
{"doc_id": 26735018, "title": "Interleukin-2- and interferon-gamma-secreting T cells in normal and diseased human intestinal mucosa.", "abstract": ["A sensitive reverse haemolytic plaque assay to detect lymphokine-secreting T cells, and Northern blot analysis to detect expression of lymphokine messenger RNA (mRNA) were used to study interferon-gamma (IFN-gamma) and interleukin-2 (IL-2) production in the mucosa of children with Crohn's disease or ulcerative colitis (UC), and in histologically normal mucosa from patients without inflammatory bowel disease.", "In the mucosa of most patients with UC and control patients, IL-2- and IFN-gamma-secreting cells were absent or were present at only low levels.", "In contrast, in mucosa from patients with Crohn's disease, lymphokine-secreting cells were readily detectable (3-18%).", "IFN-gamma mRNA was detected by Northern blot analysis in 5/6 Crohn's tissues, but only in 1/5 UC samples and none of nine samples of control mucosa.", "These studies reveal an ongoing cell-mediated immune response in the mucosa in Crohn's disease."], "structured": false}
{"doc_id": 26735905, "title": "Metabolic reprogramming of stromal fibroblasts through p62-mTORC1 signaling promotes inflammation and tumorigenesis.", "abstract": ["The tumor microenvironment plays a critical role in cancer progression, but the precise mechanisms by which stromal cells influence the epithelium are poorly understood.", "Here we show that p62 levels were reduced in the stroma of several tumors and that its loss in the tumor microenvironment or stromal fibroblasts resulted in increased tumorigenesis of epithelial prostate cancer cells.", "The mechanism involves the regulation of cellular redox through an mTORC1/c-Myc pathway of stromal glucose and amino acid metabolism, resulting in increased stromal IL-6 production, which is required for tumor promotion in the epithelial compartment.", "Thus, p62 is an anti-inflammatory tumor suppressor that acts through the modulation of metabolism in the tumor stroma."], "structured": false}
{"doc_id": 26751583, "title": "Drosophila RNAi screen reveals CD36 family member required for mycobacterial infection.", "abstract": ["Certain pathogens, such as Mycobacterium tuberculosis, survive within the hostile intracellular environment of a macrophage.", "To identify host factors required for mycobacterial entry and survival within macrophages, we performed a genomewide RNA interference screen in Drosophila macrophage-like cells, using Mycobacterium fortuitum.", "We identified factors required for general phagocytosis, as well as those needed specifically for mycobacterial infection.", "One specific factor, Peste (Pes), is a CD36 family member required for uptake of mycobacteria, but not Escherichia coli or Staphylococcus aureus.", "Moreover, mammalian class B scavenger receptors (SRs) conferred uptake of bacteria into nonphagocytic cells, with SR-BI and SR-BII uniquely mediating uptake of M. fortuitum, which suggests a conserved role for class B SRs in pattern recognition and innate immunity."], "structured": false}
{"doc_id": 26798867, "title": "Knowledge, attitudes, and practice on second primary cancer screening among cancer survivors: a qualitative study.", "abstract": ["OBJECTIVE The goal of this study was to examine the knowledge, attitude, and practice on second cancer screening among cancer survivors.   \n", "METHODS Three focus group interviews were conducted with thirteen disease-free stomach, colorectal, breast and thyroid cancer survivors.", "Recurrent issues were identified and then placed into thematic categories.   \n", "RESULTS None of the study participants had heard SPC, and they could not differentiate SPC from 'recurrence' or 'metastasis.'", "Survivors believed that they had been cured, and they were not aware of their increased risk of SPC.", "Although they had high awareness of cancer screening, they could not make a distinction between 'cancer screening' and 'routine surveillance test' after cancer treatment.", "Survivors said that they would have had the screening for SPC if they had known about it.", "They preferred physicians as the most reliable source for screening information.   \n", "CONCLUSION Cancer survivors had limited knowledge about SPC, and lack of information was the main barrier for SPC screening.   ", "PRACTICE IMPLICATIONS An educational intervention would help cancer survivors to understand their risk of SPC and the needs of screening after the first cancer."], "structured": true}
{"doc_id": 26848994, "title": "LncRNA HANR Promotes Tumorigenesis and Increase of Chemoresistance in Hepatocellular Carcinoma", "abstract": ["Background/Aims: Hepatocellular carcinoma (HCC) is the fifth most common cancer in the world and the third leading cause of cancer-related death.", "Critical roles for long non-coding RNAs (lncRNAs) have recently been demonstrated for a variety of cancers, including hepatocellular carcinoma.", "However, the effect and mechanism of lncRNAs in HCC tumorigenesis and chemoresistance have not been extensively characterized.", "Methods: In the current study, we have identified a HCC-expressed lncRNA termed as HANR (HCC associated long non-coding RNA).", "We identified HANR by microarray analysis and validated its up-regulated expression by quantitative PCR.", "RNA pull-down and pathway analyses were conducted to evaluate physical and functional interactions with HANR.", "In vivo experiments were performed to assess tumorigenesis and increase of chemoresistance.", "In addition, the HANR expression in HCC specimens was detected by FISH.", "Xenograft and orthotopic mice model was constructed to observe the effect of HANR on tumorigenesis and chemoresistance in vivo.", "Results: HANR was demonstrated to be up-regulated in HCC patients and HCC cell lines.", "Increased HANR expression in HCC predicted short survival of patients.", "Knock-down of HANR markedly retarded cell proliferation, suppressed HCC xenograft/orthotopic tumor growth, induced apoptosis and enhanced chemosensitivity to doxorubicin, while over-expression of HANR showed the opposite effects.", "It was found that HANR bind to GSKIP for regulating the phosphorylation of GSK3\u03b2 in HCC.", "Conclusion: Our results demonstrate that HANR contributes to the development of HCC and is a promising therapeutic target for chemosensitization of HCC cells to doxorubicin, which may represent a promising therapeutic target in the future."], "structured": false}
{"doc_id": 26851674, "title": "Dissection of signaling cascades through gp130 in vivo: reciprocal roles for STAT3- and SHP2-mediated signals in immune responses.", "abstract": ["We generated a series of knockin mouse lines, in which the cytokine receptor gp130-dependent STAT3 and/or SHP2 signals were disrupted, by replacing the mouse gp130 gene with human gp130 mutant cDNAs.", "The SHP2 signal-deficient mice (gp130F759/F759 were born normal but displayed splenomegaly and lymphadenopathy and an enhanced acute phase reaction.", "In contrast, the STAT3 signal-deficient mice (gp130FXQ/FXXQ) died perinatally, like the gp130-deficient mice (gp130D/D).", "The gp130F759/F759 mice showed prolonged gp130-induced STAT3 activation, indicating a negative regulatory role for SHP2.", "Th1-type cytokine production and IgG2a and IgG2b production were increased in the gp130F759/F759 mice, while they were decreased in the gp130FXXQ/FXXQ immune system.", "These results indicate that the balance of positive and negative signals generated through gp130 regulates the immune responses."], "structured": false}
{"doc_id": 26873988, "title": "Viral interleukin-10 expressed by human cytomegalovirus during the latent phase of infection modulates latently infected myeloid cell differentiation.", "abstract": ["The human cytomegalovirus UL111A gene is expressed during latent and productive infections, and it codes for homologs of interleukin-10 (IL-10).", "We examined whether viral IL-10 expressed during latency altered differentiation of latently infected myeloid progenitors.", "In comparison to infection with parental virus or mock infection, latent infection with a virus in which the gene encoding viral IL-10 has been deleted upregulated cytokines associated with dendritic cell (DC) formation and increased the proportion of myeloid DCs.", "These data demonstrate that viral IL-10 restricts the ability of latently infected myeloid progenitors to differentiate into DCs and identifies an immunomodulatory role for viral IL-10 which may limit the host's ability to clear latent virus."], "structured": false}
{"doc_id": 26886351, "title": "Bortezomib enhances dendritic cell (DC)-mediated induction of immunity to human myeloma via exposure of cell surface heat shock protein 90 on dying tumor cells: therapeutic implications.", "abstract": ["Most anticancer chemotherapies are immunosuppressive and induce nonimmunogenic tumor cell death.", "Bortezomib, a specific inhibitor of 26S proteasome, has shown clinical activity in several human tumors, including myeloma.", "Here we show that the uptake of human myeloma cells by dendritic cells (DCs) after tumor cell death by bortezomib, but not gamma irradiation or steroids, leads to the induction of antitumor immunity, including against primary tumor cells, without the need for any additional adjuvants.", "The delivery of activating signal from bortezomib-killed tumor cells to DCs depends on cell-cell contact between DCs and dying tumor cells and is mediated by bortezomib-induced exposure of heat shock protein 90 (hsp90) on the surface of dying cells.", "The combination of bortezomib and geldanamycin (an hsp90 inhibitor) leads to greater apoptosis of tumor cells but abrogates their immunogenicity.", "These data identify drug-induced exposure of endogenous heat shock proteins on the surface of dying cells as a mechanism of immunogenic death of human tumors.", "Specific targeting of bortezomib to tumors may enhance their immunogenicity and the induction of antitumor immunity."], "structured": false}
{"doc_id": 26887439, "title": "Survivin depletion preferentially reduces the survival of activated K-Ras-transformed cells.", "abstract": ["To identify cancer-specific targets, we have conducted a synthetic lethal screen using a small interfering RNA (siRNA) library targeting approximately 4,000 individual genes for enhanced killing in the DLD-1 colon carcinoma cell line that expresses an activated copy of the K-Ras oncogene.", "We found that siRNAs targeting baculoviral inhibitor of apoptosis repeat-containing 5 (survivin) significantly reduced the survival of activated K-Ras-transformed cells compared with its normal isogenic counterpart in which the mutant K-Ras gene had been disrupted (DKS-8).", "In addition, survivin siRNA induced a transient G(2)-M arrest and marked polyploidy that was associated with increased caspase-3 activation in the activated K-Ras cells.", "These results indicate that tumors expressing the activated K-Ras oncogene may be particularly sensitive to inhibitors of the survivin protein."], "structured": false}
{"doc_id": 26899920, "title": "Small molecules enable cardiac reprogramming of mouse fibroblasts with a single factor, Oct4.", "abstract": ["It was recently shown that mouse fibroblasts could be reprogrammed into cells of a cardiac fate by forced expression of multiple transcription factors and microRNAs.", "For ultimate application of such a reprogramming strategy for cell-based therapy or in vivo cardiac regeneration, reducing or eliminating the genetic manipulations by small molecules would be highly desirable.", "Here, we report the identification of a defined small-molecule cocktail that enables the highly efficient conversion of mouse fibroblasts into cardiac cells with only one transcription factor, Oct4, without any evidence of entrance into the pluripotent state.", "Small-molecule-induced cardiomyocytes spontaneously contract and exhibit a ventricular phenotype.", "Furthermore, these induced cardiomyocytes pass through a cardiac progenitor stage.", "This study lays the foundation for future pharmacological reprogramming approaches and provides a small-molecule condition for investigation of the mechanisms underlying the cardiac reprogramming process."], "structured": false}
{"doc_id": 26902591, "title": "A switch from white to brown fat increases energy expenditure in cancer-associated cachexia.", "abstract": ["Cancer-associated cachexia (CAC) is a wasting syndrome characterized by systemic inflammation, body weight loss, atrophy of white adipose tissue (WAT) and skeletal muscle.", "Limited therapeutic options are available and the underlying mechanisms are poorly defined.", "Here we show that a phenotypic switch from WAT to brown fat, a phenomenon termed WAT browning, takes place in the initial stages of CAC, before skeletal muscle atrophy.", "WAT browning is associated with increased expression of uncoupling protein 1 (UCP1), which uncouples mitochondrial respiration toward thermogenesis instead of ATP synthesis, leading to increased lipid mobilization and energy expenditure in cachectic mice.", "Chronic inflammation and the cytokine interleukin-6 increase UCP1 expression in WAT, and treatments that reduce inflammation or \u03b2-adrenergic blockade reduce WAT browning and ameliorate the severity of cachexia.", "Importantly, UCP1 staining is observed in WAT from CAC patients.", "Thus, inhibition of WAT browning represents a promising approach to ameliorate cachexia in cancer patients."], "structured": false}
{"doc_id": 26907074, "title": "Potential Mechanisms of Action of Lithium in Bipolar Disorder", "abstract": ["Lithium has been used for over half a century for the treatment of bipolar disorder as the archetypal mood stabilizer, and has a wealth of empirical evidence supporting its efficacy in this role.", "Despite this, the specific mechanisms by which lithium exerts its mood-stabilizing effects are not well understood.", "Given the inherently complex nature of the pathophysiology of bipolar disorder, this paper aims to capture what is known about the actions of lithium ranging from macroscopic changes in mood, cognition and brain structure, to its effects at the microscopic level on neurotransmission and intracellular and molecular pathways.", "A comprehensive literature search of databases including MEDLINE, EMBASE and PsycINFO was conducted using relevant keywords and the findings from the literature were then reviewed and synthesized.", "Numerous studies report that lithium is effective in the treatment of acute mania and for the long-term maintenance of mood and prophylaxis; in comparison, evidence for its efficacy in depression is modest.", "However, lithium possesses unique anti-suicidal properties that set it apart from other agents.", "With respect to cognition, studies suggest that lithium may reduce cognitive decline in patients; however, these findings require further investigation using both neuropsychological and functional neuroimaging probes.", "Interestingly, lithium appears to preserve or increase the volume of brain structures involved in emotional regulation such as the prefrontal cortex, hippocampus and amygdala, possibly reflecting its neuroprotective effects.", "At a neuronal level, lithium reduces excitatory (dopamine and glutamate) but increases inhibitory (GABA) neurotransmission; however, these broad effects are underpinned by complex neurotransmitter systems that strive to achieve homeostasis by way of compensatory changes.", "For example, at an intracellular and molecular level, lithium targets second-messenger systems that further modulate neurotransmission.", "For instance, the effects of lithium on the adenyl cyclase and phospho-inositide pathways, as well as protein kinase C, may serve to dampen excessive excitatory neurotransmission.", "In addition to these many putative mechanisms, it has also been proposed that the neuroprotective effects of lithium are key to its therapeutic actions.", "In this regard, lithium has been shown to reduce the oxidative stress that occurs with multiple episodes of mania and depression.", "Further, it increases protective proteins such as brain-derived neurotrophic factor and B-cell lymphoma 2, and reduces apoptotic processes through inhibition of glycogen synthase kinase 3 and autophagy.", "Overall, it is clear that the processes which underpin the therapeutic actions of lithium are sophisticated and most likely inter-related."], "structured": false}
{"doc_id": 26952804, "title": "The role of autophagy in cancer development and response to therapy", "abstract": ["Autophagy is a process in which subcellular membranes undergo dynamic morphological changes that lead to the degradation of cellular proteins and cytoplasmic organelles.", "This process is an important cellular response to stress or starvation.", "Many studies have shed light on the importance of autophagy in cancer, but it is still unclear whether autophagy suppresses tumorigenesis or provides cancer cells with a rescue mechanism under unfavourable conditions.", "What is the present state of our knowledge about the role of autophagy in cancer development, and in response to therapy?", "And how can the autophagic process be manipulated to improve anticancer therapeutics?"], "structured": false}
{"doc_id": 26973393, "title": "The quest to overcome resistance to EGFR-targeted therapies in cancer", "abstract": ["All patients with metastatic lung, colorectal, pancreatic or head and neck cancers who initially benefit from epidermal growth factor receptor (EGFR)-targeted therapies eventually develop resistance.", "An increasing understanding of the number and complexity of resistance mechanisms highlights the Herculean challenge of killing tumors that are resistant to EGFR inhibitors.", "Our growing knowledge of resistance pathways provides an opportunity to develop new mechanism-based inhibitors and combination therapies to prevent or overcome therapeutic resistance in tumors.", "We present a comprehensive review of resistance pathways to EGFR-targeted therapies in lung, colorectal and head and neck cancers and discuss therapeutic strategies that are designed to circumvent resistance."], "structured": false}
{"doc_id": 26990001, "title": "An organ culture model for the study of metanephric development.", "abstract": ["A murine whole organ metanephric culture system was designed to study the developmental aspects of mammalian nephrogenesis.", "Metanephros and ureteric bud were removed from CFI albino mouse embryos at 13.5 +/-", "0.4 days gestation, and grown in Dulbecco's modified Eagle's Minimal Essential Medium supplemented with 20 per cent donor bovine serum at 37C in a mixed air--5 per cent CO2 environment.", "Under the experimental conditions employed, the metanephric explants showed organotypic tubular and glomerular epithelial development.", "A well-developed proximal tubule with microvilli, and characteristic intracellular organelles and intercellular junctions developed by 72 hours of culture.", "By 120 hours of culture, unique devascularized glomeruli consisting of parietal and visceral epithelial layers formed.", "The glomerular visceral epithelial cells formed foot processes and slit pore diaphragms, and produced islands of basement membrane.", "No endothelial or mesangial elements were present at any stage in organ culture development, indicating that advanced nephrogenesis can occur following initial epithelial-mesenchymal induction despite the absence of vascularization.", "The whole organ culture model system isolates renal structural development from the influences of perfusion and urine formation.", "The system thus affords the opportunity to study normal, as well as abnormal mammalian renal development under highly controlled experimental conditions."], "structured": false}
{"doc_id": 26993601, "title": "Molecular layers underlying cytoskeletal remodelling during cortical development", "abstract": ["During neural development, the cytoskeleton of newborn neurons undergoes extensive and dynamic remodelling to facilitate the sequential steps of neurogenesis, cell migration and terminal differentiation.", "It is clear from studying the mechanisms that precipitate these functions that different configurations of the cytoskeleton prefigure the correct execution of each step and define cohorts of proteins the functions of which are indispensable for the control of neuronal migration but not terminal differentiation.", "These combinatorial protein functions are also predetermined by regulated gene expression and the precise subcellular localisation of their protein products.", "Here, we expand on this view in the context of recent data on how the cytoskeleton is regulated during the maturation of cortical neurons within the developing brain."], "structured": false}
{"doc_id": 26996935, "title": "Strong bias in the bacterial CRISPR elements that confer immunity to phage.", "abstract": ["Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems provide adaptive immunity against phage via spacer-encoded CRISPR RNAs that are complementary to invasive nucleic acids.", "Here, we challenge Streptococcus thermophilus with a bacteriophage, and used PCR-based metagenomics to monitor phage-derived spacers daily for 15 days in two experiments.", "Spacers that target the host chromosome are infrequent and strongly selected against, suggesting autoimmunity is lethal.", "In experiments that recover over half a million spacers, we observe early dominance by a few spacer sub-populations and rapid oscillations in sub-population abundances.", "In two CRISPR systems and in replicate experiments, a few spacers account for the majority of spacer sequences.", "Nearly all phage locations targeted by the acquired spacers have a proto-spacer adjacent motif (PAM), indicating PAMs are involved in spacer acquisition.", "We detect a strong and reproducible bias in the phage genome locations from which spacers derive.", "This may reflect selection for specific spacers based on location and effectiveness."], "structured": false}
{"doc_id": 27022864, "title": "Chronic hypoxia induces modification of the N-methyl-D-aspartate receptor in rat brain.", "abstract": ["This study examined [3H]MK-801 binding to the N-methyl-D-aspartate (NMDA) receptor in membranes prepared from cerebral cortex, hippocampus and corpus striatum of 3 week old rats exposed to 10 weeks of intermittent hypobaric hypoxia (4300 m; 450 Torr) and compared results with those of normoxic controls.", "The cortex, hippocampus and striatum of hypoxic animals had a 36, 35 and 31% reduction in binding sites (Bmax) and a 29, 32 and 17% decrease (reflecting increased affinity) in the dissociation constant (Kd) when compared to controls.", "In the cerebral cortex, both glutamate (100 microM) and glycine (10 microM) enhanced 3[H]MK-801 binding by two to 3-fold.", "Coagonist glutamate, however, had a higher EC50 (0.44 microM) in the hypoxic cortical membranes when compared to controls (0.28 microM).", "No significant differences were found in the EC50 of glycine.", "The results show that the NMDA receptor is altered in several brain regions of rats developing in a hypoxic environment."], "structured": false}
{"doc_id": 27024392, "title": "Cannabinoids in Clinical Practice", "abstract": ["Cannabis has a potential for clinical use often obscured by unreliable and purely anecdotal reports.", "The most important natural cannabinoid is the psychoactive tetrahydrocannabinol (\u03949-THC); others include cannabidiol (CBD) and cannabigerol (CBG).", "Not all the observed effects can be ascribed to THC, and the other constituents may also modulate its action; for example CBD reduces anxiety induced by THC.", "A standardised extract of the herb may be therefore be more beneficial in practice and clinical trial protocols have been drawn up to assess this.", "The mechanism of action is still not fully understood, although cannabinoid receptors have been cloned and natural ligands identified.", "Cannabis is frequently used by patients with multiple sclerosis (MS) for muscle spasm and pain, and in an experimental model of MS low doses of cannabinoids alleviated tremor.", "Most of the controlled studies have been carried out with THC rather than cannabis herb and so do not mimic the usual clincal situation.", "Small clinical studies have confirmed the usefulness of THC as an analgesic; CBD and CBG also have analgesic and antiinflammatory effects, indicating that there is scope for developing drugs which do not have the psychoactive properties ofTHC.", "Patients taking the synthetic derivative nabilone for neurogenic pain actually preferred cannabis herb and reported that it relieved not only pain but the associated depression and anxiety.", "Cannabinoids are effective in chemotherapy-induced emesis and nabilone has been licensed for this use for several years.", "Currently, the synthetic cannabinoid HU211 is undergoing trials as a protective agent after brain trauma.", "Anecdotal reports of cannabis use include case studies in migraine and Tourette\u2019s syndrome, and as a treatment for asthma and glaucoma.", "Apart from the smoking aspect, the safety profile of cannabis is fairly good.", "However, adverse reactions include panic or anxiety attacks, which are worse in the elderly and in women, and less likely in children.", "Although psychosis has been cited as a consequence of cannabis use, an examination of psychiatric hospital admissions found no evidence of this, however, it may exacerbate existing symptoms.", "The relatively slow elimination from the body of the cannabinoids has safety implications for cognitive tasks, especially driving and operating machinery; although driving impairment with cannabis is only moderate, there is a significant interaction with alcohol.", "Natural materials are highly variable and multiple components need to be standardised to ensure reproducible effects.", "Pure natural and synthetic compounds do not have these disadvantages but may not have the overall therapeutic effect of the herb."], "structured": false}
{"doc_id": 27049238, "title": "Large deformation of red blood cell ghosts in a simple shear flow.", "abstract": ["Red blood cells are known to change shape in response to local flow conditions.", "Deformability affects red blood cell physiological function and the hydrodynamic properties of blood.", "The immersed boundary method is used to simulate three-dimensional membrane-fluid flow interactions for cells with the same internal and external fluid viscosities.", "The method has been validated for small deformations of an initially spherical capsule in simple shear flow for both neo-Hookean and the Evans-Skalak membrane models.", "Initially oblate spheroidal capsules are simulated and it is shown that the red blood cell membrane exhibits asymptotic behavior as the ratio of the dilation modulus to the extensional modulus is increased and a good approximation of local area conservation is obtained.", "Tank treading behavior is observed and its period calculated."], "structured": false}
{"doc_id": 27054878, "title": "Preoperative C-reactive protein predicts long-term mortality and hospital length of stay after primary, nonemergent coronary artery bypass grafting.", "abstract": ["BACKGROUND Preoperative C-reactive protein (CRP) levels more than 10 mg/l have been shown to be associated with increased morbidity and mortality after cardiac surgery.", "We examine the value of preoperative CRP levels less than 10 mg/l for predicting long-term, all-cause mortality and hospital length of stay in surgical patients undergoing primary, nonemergent coronary artery bypass graft-only surgery.   \n", "METHODS We examined the association between preoperative CRP levels stratified into four categories (< 1, 1-3, 3-10, and > 10 mg/l), and 7-yr all-cause mortality and hospital length of stay in 914 prospectively enrolled primary, nonemergent coronary artery bypass graft-only surgical patients using a proportional hazards regression model.   \n", "RESULTS Eighty-seven patients (9.5%) died during a mean follow-up period of 4.8 +/-", "1.5 yr.", "After proportional hazards adjustment, the 3-10 and > 10 mg/l preoperative CRP groups were associated with long-term, all-cause mortality (hazards ratios [95% CI]: 2.50 [1.22-5.16], P = 0.01 and 2.66 [1.21-5.80], P = 0.02, respectively) and extended hospital length of stay (1.32 [1.07-1.63], P < 0.001 and 1.27 [1.02-1.62], P = 0.001, respectively).   \n", "CONCLUSION We demonstrate that preoperative CRP levels as low as 3 mg/l are associated with increased long-term mortality and extended hospital length of stay in relatively lower-acuity patients undergoing primary, nonemergent coronary artery bypass graft-only surgery.", "These important findings may allow for more objective risk stratification of patients who present for uncomplicated surgical coronary revascularization."], "structured": true}
{"doc_id": 27061085, "title": "Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation.", "abstract": ["High-throughput mRNA sequencing (RNA-Seq) promises simultaneous transcript discovery and abundance estimation.", "However, this would require algorithms that are not restricted by prior gene annotations and that account for alternative transcription and splicing.", "Here we introduce such algorithms in an open-source software program called Cufflinks.", "To test Cufflinks, we sequenced and analyzed >430 million paired 75-bp RNA-Seq reads from a mouse myoblast cell line over a differentiation time series.", "We detected 13,692 known transcripts and 3,724 previously unannotated ones, 62% of which are supported by independent expression data or by homologous genes in other species.", "Over the time series, 330 genes showed complete switches in the dominant transcription start site (TSS) or splice isoform, and we observed more subtle shifts in 1,304 other genes.", "These results suggest that Cufflinks can illuminate the substantial regulatory flexibility and complexity in even this well-studied model of muscle development and that it can improve transcriptome-based genome annotation."], "structured": false}
{"doc_id": 27063470, "title": "Sporadic Creutzfeldt-Jakob disease in the United Kingdom: analysis of epidemiological surveillance data for 1970-96.", "abstract": ["OBJECTIVE To identify changes in the occurrence of Creutzfeldt-Jakob disease that might be related to the epidemic of bovine spongiform encephalopathy.   \n", "DESIGN Epidemiological surveillance of the United Kingdom population for Creutzfeldt-Jakob disease based on (a) referral of suspected cases by neurologists, neuropathologists, and neurophysiologists and (b) death certificates.   \n", "SETTING England and Wales during 1970-84, and whole of the United Kingdom during 1985-96.   ", "SUBJECTS All 662 patients identified as sporadic cases of Creutzfeldt-Jakob disease.   \n", "MAIN OUTCOME MEASURES Age distribution of patients, age specific time trends of disease, occupational exposure to cattle, potential exposure to causative agent of bovine spongiform encephalopathy.   \n", "RESULTS During 1970-96 there was an increase in the number of sporadic cases of Creutzfeldt-Jakob disease recorded yearly in England and Wales.", "The greatest increase was among people aged over 70.", "There was a statistically significant excess of cases among dairy farm workers and their spouses and among people at increased risk of contact with live cattle infected with bovine spongiform encephalopathy.", "During 1994-6 there were six deaths from sporadic Creutzfeldt-Jakob disease in the United Kingdom in patients aged under 30.   \n", "CONCLUSIONS The increase in the incidence of sporadic Creutzfeldt-Jakob disease and the high incidence in dairy farmers in the United Kingdom may be unrelated to bovine spongiform encephalopathy.", "The most striking change in the pattern of Creutzfeldt-Jakob disease in the United Kingdom after the epidemic of bovine spongiform encephalopathy is provided by the incidence in a group of exceptionally young patients with a consistent and unusual neuropathological profile.", "The outcome of mouse transmission studies and the future incidence of the disease in the United Kingdom and elsewhere, will be important in judging whether the agent causing bovine spongiform encephalopathy has infected humans."], "structured": true}
{"doc_id": 27076725, "title": "Documented head injury in early adulthood and risk of Alzheimer's disease and other dementias.", "abstract": ["BACKGROUND The association between antecedent head injury and AD is inconsistent.   \n", "OBJECTIVE To examine the association between early adult head injury, as documented by military hospital records, and dementia in late life; and to evaluate the interaction between head injury and APOE epsilon4 as risk factors for dementia.   \n", "METHODS The study had a population-based prospective historical cohort design.", "It included men who were World War II Navy and Marine veterans, and were hospitalized during their military service with a diagnosis of either a nonpenetrating head injury or another unrelated condition.", "In 1996 to 1997, military medical records were abstracted to document the occurrence and details of closed head injury.", "The entire sample was then evaluated for dementia and AD using a multistage procedure.", "There were 548 veterans with head injury and 1228 without head injury who completed all assigned stages of the study.", "The authors estimated risk of dementia, specifically AD, using proportional hazards models.   \n", "RESULTS Both moderate head injury (hazard ratio [HR] = 2.32; CI = 1.04 to 5.17) and severe head injury (HR = 4.51; CI = 1.77 to 11.47) were associated with increased risk of AD.", "Results were similar for dementia in general.", "The results for mild head injury were inconclusive.", "When the authors stratified by the number of APOE epsilon4 alleles, they observed a nonsignificant trend toward a stronger association between AD and head injury in men with more epsilon4 alleles.   \n", "CONCLUSIONS Moderate and severe head injuries in young men may be associated with increased risk of AD and other dementias in late life.", "However, the authors cannot exclude the possibility that other unmeasured factors may be influencing this association."], "structured": true}
{"doc_id": 27077180, "title": "Transient receptor potential channels as drug targets: from the science of basic research to the art of medicine.", "abstract": ["The large Trp gene family encodes transient receptor potential (TRP) proteins that form novel cation-selective ion channels.", "In mammals, 28 Trp channel genes have been identified.", "TRP proteins exhibit diverse permeation and gating properties and are involved in a plethora of physiologic functions with a strong impact on cellular sensing and signaling pathways.", "Indeed, mutations in human genes encoding TRP channels, the so-called \"TRP channelopathies,\" are responsible for a number of hereditary diseases that affect the musculoskeletal, cardiovascular, genitourinary, and nervous systems.", "This review gives an overview of the functional properties of mammalian TRP channels, describes their roles in acquired and hereditary diseases, and discusses their potential as drug targets for therapeutic intervention."], "structured": false}
{"doc_id": 27078065, "title": "Identification of genes associated with the astrocyte-specific gene Gfap during astrocyte differentiation.", "abstract": ["Chromosomes and genes are non-randomly arranged within the mammalian cell nucleus, and gene clustering is of great significance in transcriptional regulation.", "However, the relevance of gene clustering and their expression during the differentiation of neural precursor cells (NPCs) into astrocytes remains unclear.", "We performed a genome-wide enhanced circular chromosomal conformation capture (e4C) to screen for genes associated with the astrocyte-specific gene glial fibrillary acidic protein (Gfap) during astrocyte differentiation.", "We identified 18 genes that were specifically associated with Gfap and expressed in NPC-derived astrocytes.", "Our results provide additional evidence for the functional significance of gene clustering in transcriptional regulation during NPC differentiation."], "structured": false}
{"doc_id": 27093166, "title": "Ketamine reduces LPS-induced HMGB1 via activation of the Nrf2/HO-1 pathway and NF-\u03baB suppression.", "abstract": ["BACKGROUND Ketamine, as an anesthetic agent, has an anti-inflammatory effect.", "In the present study, we investigated whether ketamine inhibits release of high mobility group box 1 (HMGB1), a late-phase cytokine of sepsis, in lipopolysaccharide (LPS)-stimulated macrophages through heme oxygenase-1 (HO-1) induction.   \n", "METHODS Macrophages were preincubated with various concentrations of ketamine and then treated with LPS (1 \u03bcg/mL).", "The cell culture supernatants were collected to measure inflammatory mediators (HMGB1, nitric oxide, tumor necrosis factor-\u03b1, and interleukin 1\u03b2) by enzyme-linked immunosorbent assay.", "Moreover, HO-1 protein expression, the phosphorylation and degradation of I\u03baB-\u03b1, and the nuclear translocation of nuclear factor E2-related factor 2 and nuclear factor \u03baB (NF-\u03baB) p65 were tested by Western blot analysis.", "In addition, to further identify the role of HO-1 in this process, tin protoporphyrin (SnPP), an HO-1 inhibitor, was used.   \n", "RESULTS Ketamine treatment dose-dependently attenuated the increased levels of proinflammatory mediators (HMGB1, nitric oxide, tumor necrosis factor \u03b1, and interleukin 1\u03b2) and increased the HO-1 protein expression in LPS-activated macrophages.", "Furthermore, ketamine suppressed the phosphorylation and degradation of I\u03baB-\u03b1 as well as the LPS-stimulated nuclear translocation of NF-\u03baB p65 in macrophages.", "In addition, the present study also demonstrated that ketamine induced HO-1 expression through the nuclear translocation of nuclear factor E2-related factor 2 in macrophages.", "The effects of ketamine on LPS-induced proinflammatory cytokines production were partially reversed by the HO inhibitor tin protoporphyrin (SnPP).   \n", "CONCLUSION Ketamine inhibits the release of HMGB1 in LPS-stimulated macrophages, and this effect is at least partly mediated by the activation of the Nrf2/HO-1 pathway and NF-\u03baB suppression."], "structured": true}
{"doc_id": 27099731, "title": "Association Between Early Screening for Patent Ductus Arteriosus and In-Hospital Mortality Among Extremely Preterm Infants.", "abstract": ["IMPORTANCE There is currently no consensus for the screening and treatment of patent ductus arteriosus (PDA) in extremely preterm infants.", "Less pharmacological closure and more supportive management have been observed without evidence to support these changes.   \n", "OBJECTIVE To evaluate the association between early screening echocardiography for PDA and in-hospital mortality.   \n", "DESIGN, SETTING, AND PARTICIPANTS Comparison of screened and not screened preterm infants enrolled in the EPIPAGE 2 national prospective population-based cohort study that included all preterm infants born at less than 29 weeks of gestation and hospitalized in 68 neonatal intensive care units in France from April through December 2011.", "Two main analyses were performed to adjust for potential selection bias, one using propensity score matching and one using neonatal unit preference for early screening echocardiography as an instrumental variable.   ", "EXPOSURES Early screening echocardiography before day 3 of life.   \n", "MAIN OUTCOMES AND MEASURES The primary outcome was death between day 3 and discharge.", "The secondary outcomes were major neonatal morbidities (pulmonary hemorrhage, severe bronchopulmonary dysplasia, severe cerebral lesions, and necrotizing enterocolitis).   \n", "RESULTS Among the 1513 preterm infants with data available to determine exposure, 847 were screened for PDA and 666 were not; 605 infants from each group could be paired.", "Exposed infants were treated for PDA more frequently during their hospitalization than nonexposed infants (55.1% vs 43.1%; odds ratio [OR], 1.62 [95% CI, 1.31 to 2.00]; absolute risk reduction [ARR] in events per 100 infants, -12.0 [95% CI, -17.3 to -6.7).", "Exposed infants had a lower hospital death rate (14.2% vs 18.5% ; OR, 0.73 [95% CI, 0.54 to 0.98]; ARR, 4.3 [95% CI, 0.3 to 8.3]) and a lower rate of pulmonary hemorrhage (5.6% vs 8.9%; OR, 0.60 [95% CI, 0.38 to 0.95]; ARR, 3.3 [95% CI, 0.4 to 6.3]).", "No differences in rates of necrotizing enterocolitis, severe bronchopulmonary dysplasia, or severe cerebral lesions were observed.", "In the overall cohort, instrumental variable analysis yielded an adjusted OR for in-hospital mortality of 0.62 [95% CI, 0.37 to 1.04].   \n", "CONCLUSIONS AND RELEVANCE In this national population-based cohort of extremely preterm infants, screening echocardiography before day 3 of life was associated with lower in-hospital mortality and likelihood of pulmonary hemorrhage but not with differences in necrotizing enterocolitis, severe bronchopulmonary dysplasia, or severe cerebral lesions.", "However, results of the instrumental variable analysis leave some ambiguity in the interpretation, and longer-term evaluation is needed to provide clarity."], "structured": true}
{"doc_id": 27123743, "title": "Role of birthweight in the etiology of breast cancer.", "abstract": ["Breast cancer may originate in utero.", "We reviewed the available evidence on the association between birthweight and the risk of breast cancer.", "To date, 26 research papers addressing this issue have been published.", "The majority of studies identified a positive link between birthweight and premenopausal, but not postmenopausal, breast cancer.", "The relative risk estimate for breast cancer comparing women with high birthweight to women with low birthweight combining all studies including both pre- and postmenopausal breast cancer was 1.23 (95% confidence interval 1.13-1.34).", "The mechanisms underlying this association likely include elevated levels of growth factors that may increase the number of susceptible stem cells in the mammary gland or initiate tumors through DNA mutations.", "Loss of imprinting (LOI) of growth hormone genes relevant for intrauterine growth, such as insulin-like growth factor 2 (IGF2), leads to abnormally high levels of these hormones evidenced by high birthweight.", "LOI of IGF2 has also been found in mammary tumor tissue.", "The role of environmental factors that stimulate such epigenetic regulation of gene expression remains to be elucidated."], "structured": false}
{"doc_id": 27127885, "title": "An activator of the cAMP/PKA/CREB pathway promotes osteogenesis from human mesenchymal stem cells.", "abstract": ["Mesenchymal stem cells (MSCs) are multipotent adult stem cells capable of differentiating along the osteoblast, adipocyte, and chondrocyte lineages.", "Regulation of MSCs differentiation may be a useful tool for regenerative medicine and cell-based therapy.", "The discovery of small molecule that activates the osteogenic differentiation of MSCs could aid in the development of a new anabolic drug for osteoporosis treatment.", "We identified CW008, a derivative of pyrazole-pyridine, that stimulates osteoblast differentiation of human MSCs and increases bone formation in ovariectomized mice.", "CW008 promotes osteogenesis by activating cAMP/PKA/CREB signaling pathway and inhibiting leptin secretion.", "These results suggest that CW008 is an agonist of cAMP/PKA/CREB pathway in osteogenic differentiation and that application of CW008 may be useful for the treatment of bone-related diseases and for the study of bone biology."], "structured": false}
{"doc_id": 27129115, "title": "Magnesium sulphate for women at risk of preterm birth for neuroprotection of the fetus.", "abstract": ["BACKGROUND Epidemiological and basic science evidence suggests that magnesium sulphate before birth may be neuroprotective for the fetus.   \n", "OBJECTIVES To assess the effects of magnesium sulphate as a neuroprotective agent when given to women considered at risk of preterm birth.   ", "SEARCH STRATEGY We searched the Cochrane Pregnancy and Childbirth Group's Trials Register (31 August 2008).   ", "SELECTION CRITERIA Randomised controlled trials of antenatal magnesium sulphate therapy in women threatening or likely to give birth at less than 37 weeks' gestational age.", "For one subgroup analysis, studies were broadly categorised by the primary intent of the study into \"neuroprotective intent\", or \"other intent (maternal neuroprotective - pre-eclampsia)\", or \"other intent (tocolytic)\".   \n", "DATA COLLECTION AND ANALYSIS At least two authors assessed trial eligibility and quality, and extracted data.   \n", "MAIN RESULTS Five trials (6145 babies) were eligible for this review.", "Antenatal magnesium sulphate therapy given to women at risk of preterm birth substantially reduced the risk of cerebral palsy in their child (Relative Risk (RR) 0.68; 95% Confidence interval (CI) 0.54 to 0.87; five trials; 6145 infants).", "There was also a significant reduction in the rate of substantial gross motor dysfunction (RR 0.61; 95% CI 0.44 to 0.85; four trials; 5980 infants).", "No statistically significant effect of antenatal magnesium sulphate therapy was detected on paediatric mortality (RR 1.04; 95% CI 0.92 to 1.17; five trials; 6145 infants), or on other neurological impairments or disabilities in the first few years of life.", "Overall there were no significant effects of antenatal magnesium therapy on combined rates of mortality with cerebral palsy, although there were significant reductions for the neuroprotective groups RR 0.85; 95% CI 0.74 to 0.98; four trials; 4446 infants, but not for the other intent subgroups.", "There were higher rates of minor maternal side effects in the magnesium groups, but no significant effects on major maternal complications.   ", "AUTHORS' CONCLUSIONS The neuroprotective role for antenatal magnesium sulphate therapy given to women at risk of preterm birth for the preterm fetus is now established.", "The number of women needed to be treated to benefit one baby by avoiding cerebral palsy is 63 (95% confidence interval 43 to 87).", "Given the beneficial effects of magnesium sulphate on substantial gross motor function in early childhood, outcomes later in childhood should be evaluated to determine the presence or absence of later potentially important neurological effects, particularly on motor or cognitive function."], "structured": true}
{"doc_id": 27134527, "title": "The growing landscape of lysine acetylation links metabolism and cell signalling", "abstract": ["Lysine acetylation is a conserved protein post-translational modification that links acetyl-coenzyme A metabolism and cellular signalling.", "Recent advances in the identification and quantification of lysine acetylation by mass spectrometry have increased our understanding of lysine acetylation, implicating it in many biological processes through the regulation of protein interactions, activity and localization.", "In addition, proteins are frequently modified by other types of acylations, such as formylation, butyrylation, propionylation, succinylation, malonylation, myristoylation, glutarylation and crotonylation.", "The intricate link between lysine acylation and cellular metabolism has been clarified by the occurrence of several such metabolite-sensitive acylations and their selective removal by sirtuin deacylases.", "These emerging findings point to new functions for different lysine acylations and deacylating enzymes and also highlight the mechanisms by which acetylation regulates various cellular processes."], "structured": false}
{"doc_id": 27134931, "title": "COMPASS, a histone H3 (Lysine 4) methyltransferase required for telomeric silencing of gene expression.", "abstract": ["The trithorax (Trx) family of proteins is required for maintaining a specific pattern of gene expression in some organisms.", "Recently we reported the isolation and characterization of COMPASS, a multiprotein complex that includes the Trx-related protein Set1 of the yeast Saccharomyces cerevisiae.", "Here we report that COMPASS catalyzes methylation of the fourth lysine of histone H3 in vitro.", "Set1 and several other components of COMPASS are also required for histone H3 methylation in vivo and for transcriptional silencing of a gene located near a chromosome telomere."], "structured": false}
{"doc_id": 27138601, "title": "Free water elimination diffusion tractography: A comparison with conventional and fluid-attenuated inversion recovery, diffusion tensor imaging acquisitions.", "abstract": ["PURPOSE White matter tractography reconstructions using conventional diffusion tensor imaging (DTI) near cerebrospinal fluid (CSF) spaces are often adversely affected by CSF partial volume effects (PVEs).", "This study evaluates the ability of free water elimination (FWE) DTI methods to minimize the PVE of CSF for deterministic tractography applications.   ", "MATERIALS AND METHODS Ten healthy individuals were scanned with \"traditional,\" FLAIR (fluid-attenuated inversion recovery), and FWE DTI scans.", "The fornix, corpus callosum, and cingulum bundles were reconstructed using deterministic tractography.", "The FWE DTI scan was performed twice to separately match total acquisition time (long FWE) and number of measurements (encoding directions, short FWE) to the FLAIR and \"traditional\" DTI scans.", "PVE resolution was determined based on reconstructed tract volume.", "All reconstructions underwent blinded review for anatomical correctness, symmetry, and completeness.   \n", "RESULTS Reconstructions of the fornix demonstrated that the FWE and FLAIR scans produce more complete, anatomically plausible reconstructions than \"traditional\" DTI.", "Additionally, the tract reconstructions using FWE-DTI were significantly larger than when FLAIR was used with DTI (P < 0.0005).", "FLAIR and the FWE methods led to signal-to-noise ratio (SNR) reductions of 33% and 11%, respectively, compared with conventional DTI.", "The long and short FWE acquisitions did not significantly (P \u2265 0.31) differ from one another for any of the reconstructed tracts.   \n", "CONCLUSION The FWE diffusion model overcomes CSF PVE without the time, SNR, and volumetric coverage penalties inherent to FLAIR DTI."], "structured": true}
{"doc_id": 27150276, "title": "A systematic review of randomized controlled trials of acupuncture in the treatment of depression.", "abstract": ["BACKGROUND Acupuncture has become a popular complementary and alternative treatment approach.", "This review examined the randomized controlled trials (RCTs) examining the effects of acupuncture treatment of depression.   \n", "METHODS RCTs of the treatment of depression with acupuncture were located using MEDLINE, Allied and Complementary Medicine and the Cochrane Central Register of Controlled Trials.", "The methodology of RCTs was assessed using the Jadad criteria, and elements of research design, i.e., randomization, blinding, assessment of attrition rates, were quantified for systematic comparisons among studies.   \n", "RESULTS Among the 9 RCTs examined, five were deemed to be of low quality based upon Jadad criteria.", "The odds ratios derived from comparing acupuncture with control conditions within the RCTs suggests some evidence for the utility of acupuncture in depression.", "General trends suggest that acupuncture modalities were as effective as antidepressants employed for treatment of depression in the limited studies available for comparison.", "However, placebo acupuncture treatment was often no different from intended verum acupuncture.   ", "LIMITATIONS The RCTs extracted were limited by small sample sizes, imprecise enrollment criteria, problems with randomization, blinding, brief duration of study and lack of longitudinal follow-up.   \n", "CONCLUSIONS Despite the findings that the odds ratios of existing literature suggest a role for acupuncture in the treatment of depression, the evidence thus far is inconclusive.", "However, efforts are being made to standardize complementary approaches to treat depression, and further systematized research into their use is warranted."], "structured": true}
{"doc_id": 27158570, "title": "Genome-Wide Gene-Sodium Interaction Analyses on Blood Pressure: The Genetic Epidemiology Network of Salt-Sensitivity Study.", "abstract": ["We performed genome-wide analyses to identify genomic loci that interact with sodium to influence blood pressure (BP) using single-marker-based (1 and 2 df joint tests) and gene-based tests among 1876 Chinese participants of the Genetic Epidemiology Network of Salt-Sensitivity (GenSalt) study.", "Among GenSalt participants, the average of 3 urine samples was used to estimate sodium excretion.", "Nine BP measurements were taken using a random zero sphygmomanometer.", "A total of 2.05 million single-nucleotide polymorphisms were imputed using Affymetrix 6.0 genotype data and the Chinese Han of Beijing and Japanese of Tokyo HapMap reference panel.", "Promising findings (P<1.00\u00d710(-4)) from GenSalt were evaluated for replication among 775 Chinese participants of the Multi-Ethnic Study of Atherosclerosis (MESA).", "Single-nucleotide polymorphism and gene-based results were meta-analyzed across the GenSalt and MESA studies to determine genome-wide significance.", "The 1 df tests identified interactions for UST rs13211840 on diastolic BP (P=3.13\u00d710(-9)).", "The 2 df tests additionally identified associations for CLGN rs2567241 (P=3.90\u00d710(-12)) and LOC105369882 rs11104632 (P=4.51\u00d710(-8)) with systolic BP.", "The CLGN variant rs2567241 was also associated with diastolic BP (P=3.11\u00d710(-22)) and mean arterial pressure (P=2.86\u00d710(-15)).", "Genome-wide gene-based analysis identified MKNK1 (P=6.70\u00d710(-7)), C2orf80 (P<1.00\u00d710(-12)), EPHA6 (P=2.88\u00d710(-7)), SCOC-AS1 (P=4.35\u00d710(-14)), SCOC (P=6.46\u00d710(-11)), CLGN (P=3.68\u00d710(-13)), MGAT4D (P=4.73\u00d710(-11)), ARHGAP42 (P\u22641.00\u00d710(-12)), CASP4 (P=1.31\u00d710(-8)), and LINC01478 (P=6.75\u00d710(-10)) that were associated with at least 1 BP phenotype.", "In summary, we identified 8 novel and 1 previously reported BP loci through the examination of single-nucleotide polymorphism and gene-based interactions with sodium."], "structured": false}
{"doc_id": 27162821, "title": "Percentile curves for hemoglobin and red cell volume in infancy and childhood.", "abstract": ["Percentile curves were calculated for hemoglobin and mean corpuscular volume in children between 0.5 and 16 years of age.", "The curves were derived from several populations of non-indigent white children who lived near sea level.", "Subjects were excluded from the reference population if they had laboratory evidence of iron deficiency, thalassemia minor, and/or hemoglobinopathy.", "The final reference populations included 9,946 children for the derivation of the hemoglobin curves and 2,314 for the MCV curves.", "The percentile curves should be particularly applicable to the diagnosis and screening of iron deficiency and thalassemia minor."], "structured": false}
{"doc_id": 27166444, "title": "Preservation of pancreatic beta-cell function and prevention of type 2 diabetes by pharmacological treatment of insulin resistance in high-risk hispanic women.", "abstract": ["Type 2 diabetes frequently results from progressive failure of pancreatic beta-cell function in the presence of chronic insulin resistance.", "We tested whether chronic amelioration of insulin resistance would preserve pancreatic beta-cell function and delay or prevent the onset of type 2 diabetes in high-risk Hispanic women.", "Women with previous gestational diabetes were randomized to placebo (n = 133) or the insulin-sensitizing drug troglitazone (400 mg/day; n = 133) administered in double-blind fashion.", "Fasting plasma glucose was measured every 3 months, and oral glucose tolerance tests (OGTTs) were performed annually to detect diabetes.", "Intravenous glucose tolerance tests (IVGTTs) were performed at baseline and 3 months later to identify early metabolic changes associated with any protection from diabetes.", "Women who did not develop diabetes during the trial returned for OGTTs and IVGTTs 8 months after study medications were stopped.", "During a median follow-up of 30 months on blinded medication, average annual diabetes incidence rates in the 236 women who returned for at least one follow-up visit were 12.1 and 5.4% in women assigned to placebo and troglitazone, respectively (P < 0.01).", "Protection from diabetes in the troglitazone group 1) was closely related to the degree of reduction in endogenous insulin requirements 3 months after randomization, 2) persisted 8 months after study medications were stopped, and 3) was associated with preservation of beta-cell compensation for insulin resistance.", "Treatment with troglitazone delayed or prevented the onset of type 2 diabetes in high-risk Hispanic women.", "The protective effect was associated with the preservation of pancreatic beta-cell function and appeared to be mediated by a reduction in the secretory demands placed on beta-cells by chronic insulin resistance."], "structured": false}
{"doc_id": 27167110, "title": "Androgen regulation of micro-RNAs in prostate cancer.", "abstract": ["BACKGROUND Androgens play a critical role in the growth of both androgen dependent and castration-resistant prostate cancer (CRPC).", "Only a few micro-RNAs (miRNAs) have been suggested to be androgen regulated.", "We aim to identify androgen regulated miRNAs.   \n", "METHODS We utilized LNCaP derived model, we have established, and which overexpresses the androgen receptor (AR), the VCaP cell line, and 13 intact-castrated prostate cancer (PC) xenograft pairs, as well as clinical specimens of untreated (PC) and CRPC.", "The expression of miRNAs was analyzed by microarrays and quantitative RT-PCR (Q-RT-PCR).", "Transfection of pre-miR-141 and anti-miR-141 was also used.   \n", "RESULTS Seventeen miRNAs were > 1.5-fold up- or downregulated upon dihydrotestosterone (DHT) treatment in the cell lines, and 42 after castration in the AR-positive xenografts.", "Only four miRNAs (miR-10a, miR-141, miR-150*, and miR-1225-5p) showed similar androgen regulation in both cell lines and xenografts.", "Of those, miR-141 was found to be expressed more in PC and CRPC compared to benign prostate hyperplasia.", "Additionally, the overexpression of miR-141 enhanced growth of parental LNCaP cells while inhibition of miR-141 by anti-miR-141 suppressed the growth of the LNCaP subline overexpressing AR.   \n", "CONCLUSIONS Only a few miRNAs were found to be androgen-regulated in both cell lines and xenografts models.", "Of those, the expression of miR-141 was upregulated in cancer.", "The ectopic overexpression of miR-141 increased growth of LNCaP cell suggesting it may contribute to the progression of PC."], "structured": true}
{"doc_id": 27188320, "title": "Relationship between drug treatment services, retention, and outcomes.", "abstract": ["OBJECTIVE This longitudinal study conducted path analyses to examine the relationships between treatment processes and outcomes among patients in community-based drug treatment programs.   \n", "METHODS A total of 1,939 patients from 36 outpatient drug-free and residential treatment programs in 13 California counties were assessed at intake, discharge, three months after admission, and nine months after admission.", "Path analyses were conducted to relate the quantity and quality of services that were received in the first three months of treatment to treatment retention and outcomes at the nine-month follow-up.", "Patients were determined to have a favorable outcome if for at least 30 days before the follow-up assessment they did not use drugs, were not involved in criminal activity, and lived in the community.", "The path analyses controlled for patients' baseline characteristics.   \n", "RESULTS Greater service intensity and satisfaction were positively related to either treatment completion or longer treatment retention, which in turn was related to favorable treatment outcomes.", "Patients with greater problem severity received more services and were more likely to be satisfied with treatment.", "These patterns were similar for patients regardless of whether they were treated in outpatient drug-free programs or residential programs.   \n", "CONCLUSIONS The positive association between process measures-that is, greater levels of service intensity, satisfaction, and either treatment completion or retention-and treatment outcome strongly suggests that improvements in these key elements of the treatment process will improve treatment outcomes."], "structured": true}
{"doc_id": 27240667, "title": "Breast cancer mortality trends in the United States according to estrogen receptor status and age at diagnosis.", "abstract": ["PURPOSE Since 1990, overall breast cancer mortality rates in the United States decreased 24%.", "This decline has been attributed to mammography screening and adjuvant systemic therapy.", "However, the efficacy of these modalities may depend on estrogen receptor (ER) expression and age.", "We therefore examined breast cancer mortality trends in the United States according to ER status and age.   \n", "METHODS Using the Surveillance, Epidemiology, and End Results (SEER) program (1990-2003), we calculated trends in incidence-based mortality (IBM), annual hazard rates for breast cancer deaths after diagnosis, and relative hazard rates for women with ER-positive and ER-negative tumors.", "Relative hazard rates were assessed with Cox proportional hazards models, adjusted for stage and grade, and stratified by age at diagnosis.   \n", "RESULTS During the study period, IBM and annual hazard rates for breast cancer deaths decreased among women with ER-positive and ER-negative tumors, although declines were greater for those with ER-positive tumors.", "Among women younger than 70 years, relative hazard rates declined 38% for those with ER-positive tumors versus 19% for those with ER-negative tumors.", "Among women 70 years or older, relative hazard rates declined 14% for those with ER-positive tumors versus no significant decline for those with ER-negative tumors.   \n", "CONCLUSION In the United States, breast cancer mortality rates have declined among women with ER-positive and ER-negative tumors, with greater declines among younger women and those with ER-positive tumors.", "Although mortality in all groups remains unacceptably high, additional emphasis should be placed on improving outcomes of breast cancer patients older than 70 years and those of all ages with ER-negative tumors."], "structured": true}
{"doc_id": 27240699, "title": "An adenovirus mutant that replicates selectively in p53-deficient human tumor cells.", "abstract": ["The human adenovirus E1B gene encodes a 55-kilodalton protein that inactivates the cellular tumor suppressor protein p53.", "Here it is shown that a mutant adenovirus that does not express this viral protein can replicate in and lyse p53-deficient human tumor cells but not cells with functional p53.", "Ectopic expression of the 55-kilodalton EIB protein in the latter cells rendered them sensitive to infection with the mutant virus.", "Injection of the mutant virus into p53-deficient human cervical carcinomas grown in nude mice caused a significant reduction in tumor size and caused complete regression of 60 percent of the tumors.", "These data raise the possibility that mutant adenoviruses can be used to treat certain human tumors."], "structured": false}
{"doc_id": 27243019, "title": "Immune reconstitution after cord blood transplantation: peculiarities, clinical implications and management strategies.", "abstract": ["Umbilical cord blood (UCB) is now widely used as an alternative hematopoietic stem cell source for patients lacking closely matched related or unrelated adult donors.", "UCB transplantation has traditionally been associated with delayed engraftment, poor immune reconstitution and consequent increased risk of infection.", "More recent clinical studies, however, suggest that conditioning regimens and in particular the omission of in vivo T-cell depletion may play a crucial role in post-transplant T-cell expansion, facilitating a uniquely rapid immune recovery after UCB transplantation.", "The peculiar characteristics of UCB cells, the importance of thymic function and the role of conditioning regimens and graft-versus-host disease influencing immune reconstitution are described.", "The last part of the review reports available data on UCB, as well as third-party peripheral blood derived anti-viral cell therapy, which provides a novel approach to rescue UCB recipients with viral complications in the post-transplant period."], "structured": false}
{"doc_id": 27247460, "title": "OVEREXPRESSION OF BOTH CLOCK AND BMAL1 INHIBITS ENTRY TO S PHASE IN HUMAN COLON CANCER CELLS.", "abstract": ["Many physiological, biochemical and behavioral processes operate under the circadian rhythm, which is generated by an internal time-keeping mechanism commonly referred to as the biological clock, in almost all organisms from bacteria to mammals.", "The core circadian oscillator is composed of an autoregulatory transcription-translation feedback loop, in which CLOCK and BMAL1 are positive regulators.", "A cell has two mechanisms, \"cell cycle\" and \"cell rhythm\", the relationship between which remains controversial.", "Therefore, the aim of this study was to explore the effect of Clock and Bmal1 on cell cycle, especially on the G1 phase, using vectors with the tetracycline operator-repressor system.", "The present study revealed that simultaneous induction of Bmal1 and Clock had an influential effect on the cell cycle in SW480/T-REx/Clock/Bmal1 cells, in which both Clock and Bmal1 could be induced by tetracycline.", "The observation that induction of both Clock and Bmal1 inhibited cell growth and the significant increase of the G1 phase proportion of in SW480/T-REx/Clock/Bmal1 cells indicated that entry from the G1 to S phase was inhibited by the induction of Clock and Bmal1.", "Furthermore, overexpression of Clock and Bmal1 prevented the cells from entering into the G2/M phase induced by Paclitaxel, and made the cells more resistant to the agent.", "In conclusion, we found that overexpression of both Clock and Bmal1 suppressed cell growth.", "In addition, the present study raised the possibility that Clock and Bmal1 may in part play a role in preventing the cells from entering G1 to S phase of cell cycle via suppression of CyclinD1 expression, and thus acquiring resistance to Paclitaxel."], "structured": false}
{"doc_id": 27260630, "title": "Composition of gall bladder stones associated with octreotide: response to oral ursodeoxycholic acid.", "abstract": ["Octreotide, an effective treatment for acromegaly, induces gall bladder stones in 13-60% of patients.", "Because knowledge of stone composition is essential for studies of their pathogenesis, treatment, and prevention, this was investigated by direct and indirect methods in 14 octreotide treated acromegalic patients with gall stones.", "Chemical analysis of gall stones retrieved at cholecystectomy from two patients, showed that they contained 71% and 87% cholesterol by weight.", "In the remaining 12 patients, localised computed tomography of the gall bladder showed that eight had stones with maximum attenuation scores of < 100 Hounsfield units (values of < 100 HU predict cholesterol rich, dissolvable stones).", "Gall bladder bile was obtained by ultrasound guided, fine needle puncture from six patients.", "All six patients had supersaturated bile (mean (SEM) cholesterol saturation index of 1.19 (0.08) (range 1.01-1.53)) and all had abnormally rapid cholesterol microcrystal nucleation times (< 4 days (range 1-4)), whilst in four, the bile contained cholesterol microcrystals immediately after sampling.", "Of the 12 patients considered for oral ursodeoxycholic acid (UDCA) treatment, two had a blocked cystic duct and were not started on UDCA while one was lost to follow up.", "After one year of treatment, five of the remaining nine patients showed either partial (n = 3) or complete (n = 2) gall stone dissolution, suggesting that their stones were cholesterol rich.", "This corresponds, by actuarial (life table) analysis, to a combined gall stone dissolution rate of 58.3 (15.9%).", "In conclusion, octreotide induced gall stones are generally small, multiple, and cholesterol rich although, in common with spontaneous gall stone disease, at presentation some patients will have a blocked cystic duct and some gall stones containing calcium."], "structured": false}
{"doc_id": 27264454, "title": "Imiquimod 5% cream for the treatment of superficial basal cell carcinoma: results from a randomized vehicle-controlled phase III study in Europe.", "abstract": ["BACKGROUND Imiquimod is an immune response modifier that acts through toll-like receptor 7 to induce cytokine production and a subsequent innate and adaptive cell-mediated immune response.", "Clinical studies have demonstrated clinical and histological clearance of superficial basal cell carcinoma (sBCC) after treatment with imiquimod 5% cream.   \n", "OBJECTIVES To evaluate the safety and clinical efficacy of imiquimod (Aldaratrade mark; 3M Pharmaceuticals, St Paul, MN, U.S.A.) 5% cream for the treatment of sBCC in a multicentre, randomized, parallel, vehicle-controlled, double-blind, phase III clinical study conducted at 26 centres in Europe.   \n", "METHODS Subjects who had at least one histologically confirmed sBCC tumour were randomized to apply imiquimod or vehicle cream to the target tumour once daily, seven times per week (7 x/week) for 6 weeks.", "The target tumour location was identified with an indelible ink mark before treatment initiation.", "The treated tumour site was clinically assessed for treatment response at 12 weeks post-treatment and was then excised for histological evaluation.", "Efficacy assessments included the composite response rates (proportion of subjects with clinical and histological clearance) and response rates solely based on histology (proportion of subjects with histological clearance).", "Safety assessments, which included adverse events and scoring of local skin reactions (LSRs), were carried out throughout the study.   \n", "RESULTS In total, 166 subjects were enrolled in this study.", "For the intent-to-treat dataset, there was a statistically significant difference between imiquimod and vehicle groups for both composite clearance rates (clinical and histological assessments) and histological clearance rates.", "Composite clearance was demonstrated in 77% and 6% of subjects treated with imiquimod and vehicle cream, respectively.", "Histological clearance was demonstrated in 80% and 6% of subjects treated with imiquimod and vehicle cream, respectively.", "The most frequently reported safety findings were investigator-assessed LSRs and spontaneous reports by subjects of application site reactions, which occurred more frequently in the imiquimod group than in the vehicle group.   \n", "CONCLUSIONS Imiquimod 5% cream administered 7 x/week for 6 weeks is a safe and effective treatment for sBCC when compared with vehicle cream."], "structured": true}
{"doc_id": 27270151, "title": "Changing the course of pancreatic cancer--Focus on recent translational advances.", "abstract": ["In the past decade, insightful preclinical research has led to important breakthroughs in our understanding of pancreatic cancer.", "Even though the vast majority of pancreatic cancers are KRAS mutated, not all pancreatic cancer tumors are \"KRAS equal\"; there seems to be varying dependencies on the KRAS pathway.", "While KRAS-targeting therapies have been disappointing in the clinic, 'synthetic lethal' approaches hold promise in this setting.", "The pancreatic cancer stromal microenvironment appears to have contradictory roles.", "While there is evidence to suggest that stromal barrier prevents drug delivery, in other circumstances, stroma can play a protective role and its disruption enhances tumor dissemination.", "Clinical trials aimed at manipulating the various stromal components are in progress.", "BRCA mutation-related pancreatic tumors illustrate a unique subtype with enhanced susceptibility to DNA damaging agents and PARP-inhibition.", "DNA repair defects in cancer extend beyond germ line BRCA mutation and may extend the indications for DNA repair-targeting agents.", "Immune strategies are an area of active investigation in pancreatic cancer.", "Although the initial trials of single-agent checkpoint inhibitors have been negative, combinational approaches using immune-modifying agents and vaccines appear promising and goal is to identify an 'immune-therapy responsive' profile in pancreatic cancer."], "structured": false}
{"doc_id": 27274441, "title": "Swc2 is a widely conserved H2AZ-binding module essential for ATP-dependent histone exchange", "abstract": ["The histone variant H2AZ is incorporated preferentially at specific locations in chromatin to modulate chromosome functions.", "In Saccharomyces cerevisiae, deposition of histone H2AZ is mediated by the multiprotein SWR1 complex, which catalyzes ATP-dependent exchange of nucleosomal histone H2A for H2AZ.", "Here, we define interactions between SWR1 components and H2AZ, revealing a link between the ATPase domain of Swr1 and three subunits required for the binding of H2AZ.", "We discovered that Swc2 binds directly to and is essential for transfer of H2AZ.", "Swc6 and Arp6 are necessary for the association of Swc2 and for nucleosome binding, whereas other subunits, Swc5 and Yaf9, are required for H2AZ transfer but neither H2AZ nor nucleosome binding.", "Finally, the C-terminal \u03b1-helix of H2AZ is crucial for its recognition by SWR1.", "These findings provide insight on the initial events of histone exchange."], "structured": false}
{"doc_id": 27279525, "title": "Detection, characterization, and spontaneous differentiation in vitro of very small embryonic-like putative stem cells in adult mammalian ovary.", "abstract": ["The present study was undertaken to detect, characterize, and study differentiation potential of stem cells in adult rabbit, sheep, monkey, and menopausal human ovarian surface epithelium (OSE).", "Two distinct populations of putative stem cells (PSCs) of variable size were detected in scraped OSE, one being smaller and other similar in size to the surrounding red blood cells in the scraped OSE.", "The smaller 1-3 \u03bcm very small embryonic-like PSCs were pluripotent in nature with nuclear Oct-4 and cell surface SSEA-4, whereas the bigger 4-7 \u03bcm cells with cytoplasmic localization of Oct-4 and minimal expression of SSEA-4 were possibly the tissue committed progenitor stem cells.", "Pluripotent gene transcripts of Oct-4, Oct-4A, Nanog, Sox-2, TERT, and Stat-3 in human and sheep OSE were detected by reverse transcriptase-polymerase chain reaction.", "The PSCs underwent spontaneous differentiation into oocyte-like structures, parthenote-like structures, embryoid body-like structures, cells with neuronal-like phenotype, and embryonic stem cell-like colonies, whereas the epithelial cells transformed into mesenchymal phenotype by epithelial-mesenchymal transition in 3 weeks of OSE culture.", "Germ cell markers like c-Kit, DAZL, GDF-9, VASA, and ZP4 were immuno-localized in oocyte-like structures.", "In conclusion, as opposed to the existing view of OSE being a bipotent source of oocytes and granulosa cells, mammalian ovaries harbor distinct very small embryonic-like PSCs and tissue committed progenitor stem cells population that have the potential to develop into oocyte-like structures in vitro, whereas mesenchymal fibroblasts appear to form supporting granulosa-like somatic cells.", "Research at the single-cell level, including complete gene expression profiling, is required to further confirm whether postnatal oogenesis is a conserved phenomenon in adult mammals."], "structured": false}
{"doc_id": 27306942, "title": "Rearrangement of CRLF2 is associated with mutation of JAK kinases, alteration of IKZF1, Hispanic/Latino ethnicity, and a poor outcome in pediatric B-progenitor acute lymphoblastic leukemia.", "abstract": ["Gene expression profiling of 207 uniformly treated children with high-risk B-progenitor acute lymphoblastic leukemia revealed 29 of 207 cases (14%) with markedly elevated expression of CRLF2 (cytokine receptor-like factor 2).", "Each of the 29 cases harbored a genomic rearrangement of CRLF2: 18 of 29 (62%) had a translocation of the immunoglobulin heavy chain gene IGH@ on 14q32 to CRLF2 in the pseudoautosomal region 1 of Xp22.3/Yp11.3, whereas 10 (34%) cases had a 320-kb interstitial deletion centromeric of CRLF2, resulting in a P2RY8-CRLF2 fusion.", "One case had both IGH@-CRLF2 and P2RY8-CRLF2, and another had a novel CRLF2 rearrangement.", "Only 2 of 29 cases were Down syndrome.", "CRLF2 rearrangements were significantly associated with activating mutations of JAK1 or JAK2, deletion or mutation of IKZF1, and Hispanic/Latino ethnicity (Fisher exact test, P < .001 for each).", "Within this cohort, patients with CRLF2 rearrangements had extremely poor treatment outcomes compared with those without CRLF2 rearrangements (35.3% vs 71.3% relapse-free survival at 4 years; P < .001).", "Together, these observations suggest that activation of CRLF2 expression, mutation of JAK kinases, and alterations of IKZF1 cooperate to promote B-cell leukemogenesis and identify these pathways as important therapeutic targets in this disease."], "structured": false}
{"doc_id": 27373088, "title": "Substrate requirements for ErmC' methyltransferase activity.", "abstract": ["ErmC' is a methyltransferase that confers resistance to the macrolide-lincosamide-streptogramin B group of antibiotics by catalyzing the methylation of 23S rRNA at a specific adenine residue (A-2085 in Bacillus subtilis; A-2058 in Escherichia coli).", "The gene for ErmC' was cloned and expressed to a high level in E. coli, and the protein was purified to virtual homogeneity.", "Studies of substrate requirements of ErmC' have shown that a 262-nucleotide RNA fragment within domain V of B. subtilis 23S rRNA can be utilized efficiently as a substrate for methylation at A-2085.", "Kinetic studies of the monomethylation reaction showed that the apparent Km of this 262-nucleotide RNA oligonucleotide was 26-fold greater than the value determined for full-size and domain V 23S rRNA.", "In addition, the Vmax for this fragment also rose sevenfold.", "A model of RNA-ErmC' interaction involving multiple binding sites is proposed from the kinetic data presented."], "structured": false}
{"doc_id": 27391365, "title": "Validity of the World Health Organization Adult ADHD Self-Report Scale (ASRS) Screener in a representative sample of health plan members.", "abstract": ["The validity of the six-question World Health Organization Adult ADHD Self-Report Scale (ASRS) Screener was assessed in a sample of subscribers to a large health plan in the US.", "A convenience subsample of 668 subscribers was administered the ASRS Screener twice to assess test-retest reliability and then a third time in conjunction with a clinical interviewer for DSM-IV adult ADHD.", "The data were weighted to adjust for discrepancies between the sample and the population on socio-demographics and past medical claims.", "Internal consistency reliability of the continuous ASRS Screener was in the range 0.63-0.72 and test-retest reliability (Pearson correlations) in the range 0.58-0.77.", "A four-category version The ASRS Screener had strong concordance with clinician diagnoses, with an area under the receiver operating characteristic curve (AUC) of 0.90.", "The brevity and ability to discriminate DSM-IV cases from non-cases make the six-question ASRS Screener attractive for use both in community epidemiological surveys and in clinical outreach and case-finding initiatives."], "structured": false}
{"doc_id": 27393799, "title": "The body-mass index of twins who have been reared apart.", "abstract": ["To assess the relative importance of genetic and environmental effects on the body-mass index (weight in kilograms divided by the square of the height in meters), we studied samples of identical and fraternal twins, reared apart or reared together.", "The samples consisted of 93 pairs of identical twins reared apart, 154 pairs of identical twins reared together, 218 pairs of fraternal twins reared apart, and 208 pairs of fraternal twins reared together.", "The intrapair correlation coefficients of the values for body-mass index of identical twins reared apart were 0.70 for men and 0.66 for women.", "These are the most direct estimates of the relative importance of genetic influences (heritability) on the body-mass index, and they were only slightly lower than those for twins reared together in this and earlier studies.", "Similar estimates were derived from maximum-likelihood model-fitting analyses--0.74 for men and 0.69 for women.", "Nonadditive genetic variance made a significant contribution to the estimates of heritability, particularly among men.", "Of the potential environmental influences, only those unique to the individual and not those shared by family members were important, contributing about 30 percent of the variance.", "Sharing the same childhood environment did not contribute to the similarity of the body-mass index of twins later in life.", "We conclude that genetic influences on body-mass index are substantial, whereas the childhood environment has little or no influence.", "These findings corroborate and extend the results of earlier studies of twins and adoptees."], "structured": false}
{"doc_id": 27396415, "title": "A study of high cell density cultivation process of recombinant Helicobacter pylori multi-epitope vaccine engineering bacteria.", "abstract": ["OBJECTIVE To establish high cell density cultivation process of recombinant Helicobacter pylori multi-epitope vaccine engineering bacteria BIB.   \n", "METHODS Based on the results of shake flask fermentation, the process was magnified into volume of a 50 L fermenter to optimize and verify the factors affecting the yield of the target protein, such as the fermentation medium, working seed inoculation amount, inducer concentration, induction starting time, induction duration, inducer adding mode and feeding strategy.   \n", "RESULTS After activated in modified TB medium at 37\u00b0C for 8 h, the BIB working seed was inoculated at 5% (v/v) and was induced for expression for another 11 h by the final concentration of 5 mmol/L lactose.", "In growth phase, glucose at rate of 80 ml/h was used as carbon source, and in induction phase, glycerol at rate of 40 ml/h was used as carbon source; ammonia water was added dropwise to control pH at about 7.0, and revolution speed is adjusted to control the dissolved oxygen at above 30%; ultimately the output of bacterial body was 70 g/L and protein expression amount was about 32%.   \n", "CONCLUSION After high cell density cultivation of the recombinant engineering bacteria, expression and yield of the target protein rBIB significantly increased."], "structured": true}
{"doc_id": 27403802, "title": "Phorbol esters and cytokines regulate the expression of the NEMO-related protein, a molecule involved in a NF-kappa B-independent pathway.", "abstract": ["The NF-kappaB signaling pathway plays a crucial role in the immune, inflammatory, and apoptotic responses.", "Recently, we identified the NF-kappaB Essential Modulator (NEMO) as an essential component of this pathway.", "NEMO is a structural and regulatory subunit of the high molecular kinase complex (IKK) responsible for the phosphorylation of NF-kappaB inhibitors.", "Data base searching led to the isolation of a cDNA encoding a protein we called NRP (NEMO-related protein), which shows a strong homology to NEMO.", "Here we show that NRP is present in a novel high molecular weight complex, that contains none of the known members of the IKK complex.", "Consistently, we could not observe any effect of NRP on NF-kappaB signaling.", "Nonetheless, we could demonstrate that treatment with phorbol esters induces NRP phosphorylation and decreases its half-life.", "This phosphorylation event could only be inhibited by K-252a and stauroporin.", "We also show that de novo expression of NRP can be induced by interferon and tumor necrosis factor alpha and that these two stimuli have a synergistic effect on NRP expression.", "In addition, we observed that endogenous NRP is associated with the Golgi apparatus.", "Analogous to NEMO, we find that NRP is associated in a complex with two kinases, suggesting that NRP could play a similar role in another signaling pathway."], "structured": false}
{"doc_id": 27408104, "title": "Tailoring Nutritional Advice for Mexicans Based on Prevalence Profiles of Diet-Related Adaptive Gene Polymorphisms", "abstract": ["Diet-related adaptive gene (DRAG) polymorphisms identified in specific populations are associated with chronic disorders in carriers of the adaptive alleles due to changes in dietary and lifestyle patterns in recent times.", "Mexico's population is comprised of Amerindians (AM) and Mestizos who have variable AM, European (EUR) and African genetic ancestry and an increased risk of nutrition-related chronic diseases.", "Nutritional advice based on the Mexican genome and the traditional food culture is needed to develop preventive and therapeutic strategies.", "Therefore, we aimed to provide a prevalence profile of several DRAG polymorphisms in the Mexican population, including Central West (CW) Mexico subpopulations.", "Geographic heat maps were built using ArcGIS10 (Esri, Redlands, CA, USA) software, based on the published data of the MTHFR C677T (rs1801133), ABCA1 Arg230Cys (rs9282541), APOE T388C (rs429358)/C526T (rs7412), LCT C-13910T (rs4988235) polymorphisms and AMY1 copy number variation (CNV).", "Also, new data obtained by allelic discrimination-real-time polymerase chain reaction (RT-PCR) assays for the MTHFR, ABCA1, and APOE polymorphisms as well as the AMY1 CNV in the CW Mexico subpopulations with different proportions of AM and EUR ancestry were included.", "In the CW region, the highest frequency of the MTHFR 677T, ABCA1 230C and APOE \u03b54 adaptive alleles was observed in the AM groups, followed by Mestizos with intermediate AM ancestry.", "The LCT-13910T allele frequency was highest in Mestizos-EUR but extremely low in AM, while the AMY1 diploid copy number was 6.82 \u00b1 3.3 copies.", "Overall, the heat maps showed a heterogeneous distribution of the DRAG polymorphisms, in which the AM groups revealed the highest frequencies of the adaptive alleles followed by Mestizos.", "Given these genetic differences, genome-based nutritional advice should be tailored in a regionalized and individualized manner according to the available foods and Mexican traditional food culture that may lead to a healthier dietary pattern."], "structured": false}
{"doc_id": 27428509, "title": "Prevention of Type 2 Diabetes Mellitus Through Inhibition of the Renin-Angiotensin System", "abstract": ["Type 2 diabetes mellitus is becoming a major health problem associated with excess morbidity and mortality.", "As the prevalence of type 2 diabetes is rapidly increasing, prevention of the disease should be considered as a key objective in the near future.", "Besides lifestyle changes, various pharmacological treatments have proven their efficacy in placebo-controlled clinical trials, including antidiabetic drugs such as metformin, acarbose and troglitazone, or antiobesity agents such as orlistat.", "Arterial hypertension, a clinical entity in which insulin resistance is common, is strongly associated with type 2 diabetes and may precede the disease by several years.", "While antihypertensive agents such as diuretics or \u03b2-adrenoceptor antagonists may worsen insulin resistance and impair glucose tolerance, newer antihypertensive agents exert neutral or even slightly positive metabolic effects.", "Numerous clinical trials have investigated the effects of ACE inhibitors or angiotensin II receptor antagonists (ARAs) on insulin sensitivity in hypertensive patients, with or without diabetes, with no consistent results.", "Almost half of the studies with ACE inhibitors in hypertensive nondiabetic individuals demonstrated a slight but significant increase in insulin sensitivity as assessed by insulin-stimulated glucose disposal during a euglycaemic hyperinsulinaemic clamp, while the other half failed to reveal any significant change.", "The effects of ARAs on insulin sensitivity are neutral in most studies.", "Mechanisms of improvement of glucose tolerance and insulin sensitivity through the inhibition of the renin-angiotensin system (RAS) are complex.", "They may include improvement of blood flow and microcirculation in skeletal muscles and, thereby, enhancement of insulin and glucose delivery to the insulin-sensitive tissues, facilitating insulin signalling at the cellular level and improvement of insulin secretion by the \u03b2 cells.", "Six recent large-scale clinical studies reported a remarkably consistent reduction in the incidence of type 2 diabetes in hypertensive patients treated with either ACE inhibitors or ARAs for 3\u20136 years, compared with a thiazide diuretic, \u03b2-adrenoceptor antagonist, the calcium channel antagonist amlodipine or even placebo.", "The relative risk reduction averaged 14% (p = 0.034) in the CAPPP (Captopril Prevention Project) with captopril compared with a thiazide or \u03b21-adrenoceptor antagonist, 34% (p < 0.001) in the HOPE (Heart Outcomes Prevention Evaluation) study with ramipril compared with placebo, 30% (p < 0.001) in the ALLHAT (Antihypertensive and Lipid-Lowering Treatment to Prevent Heart Attack Trial) with lisinopril compared with chlortalidone, 25% (p < 0.001) in the LIFE (Losartan Intervention For Endpoint reduction in hypertension study) with losartan compared with atenolol, and 25% (p = 0.09) in the SCOPE (Study on Cognition and Prognosis in the Elderly) with candesartan cilexetil compared with placebo, and 23% (p < 0.0001) in the VALUE (Valsartan Antihypertensive Long-term Use Evaluation) trial with valsartan compared with amlodipine.", "All these studies considered the development of diabetes as a secondary endpoint, except the HOPE trial where it was a post hoc analysis.", "These encouraging observations led to the initiation of two large, prospective, placebo-controlled randomised clinical trials whose primary outcome is the prevention of type 2 diabetes: the DREAM (Diabetes REduction Approaches with ramipril and rosiglitazone Medications) trial with the ACE inhibitor ramipril and the NAVIGATOR (Nateglinide And Valsartan in Impaired Glucose Tolerance Outcomes Research) trial with the ARA valsartan.", "Finally, ONTARGET (ONgoing Telmisartan Alone and in combination with Ramipril Global Endpoint Trial) will also investigate as a secondary endpoint whether it is possible to prevent the development of type 2 diabetes by blocking the RAS with either an ACE inhibitor or an ARA or a combination of both.", "Thus, the recent consistent observations of a 14\u201334% reduction of the development of diabetes in hypertensive patients receiving ACE inhibitors or ARAs are exciting.", "From a theoretical point of view, they emphasise that there are many aspects of the pathogenesis, prevention and treatment of type 2 diabetes that still need to be uncovered.", "From a practical point of view, they may offer a new strategy to reduce the ongoing epidemic and burden of type 2 diabetes."], "structured": false}
{"doc_id": 27437459, "title": "Randomized dose-finding clinical trial of oncolytic immunotherapeutic vaccinia JX-594 in liver cancer", "abstract": ["Oncolytic viruses and active immunotherapeutics have complementary mechanisms of action (MOA) that are both self amplifying in tumors, yet the impact of dose on subject outcome is unclear.", "JX-594 (Pexa-Vec) is an oncolytic and immunotherapeutic vaccinia virus.", "To determine the optimal JX-594 dose in subjects with advanced hepatocellular carcinoma (HCC), we conducted a randomized phase 2 dose-finding trial (n = 30).", "Radiologists infused low- or high-dose JX-594 into liver tumors (days 1, 15 and 29); infusions resulted in acute detectable intravascular JX-594 genomes.", "Objective intrahepatic Modified Response Evaluation Criteria in Solid Tumors (mRECIST) (15%) and Choi (62%) response rates and intrahepatic disease control (50%) were equivalent in injected and distant noninjected tumors at both doses.", "JX-594 replication and granulocyte-macrophage colony-stimulating factor (GM-CSF) expression preceded the induction of anticancer immunity.", "In contrast to tumor response rate and immune endpoints, subject survival duration was significantly related to dose (median survival of 14.1 months compared to 6.7 months on the high and low dose, respectively; hazard ratio 0.39; P = 0.020).", "JX-594 demonstrated oncolytic and immunotherapy MOA, tumor responses and dose-related survival in individuals with HCC."], "structured": false}
{"doc_id": 27438378, "title": "Misread protein creates membrane channels: an essential step in the bactericidal action of aminoglycosides.", "abstract": ["Among the pleiotropic effects of aminoglycosides, their irreversible uptake and their blockade of initiating ribosomes have appeared to explain their bactericidal action, while the contributions of translational misreading and membrane damage and the mechanism of that damage have remained uncertain.", "We now present evidence that incorporation of misread proteins into the membrane can account for the membrane damage.", "The bactericidal action thus appears to result from the following sequence, in which each step is essential: slight initial entry of the antibiotic; interaction with chain-elongating ribosomes, resulting in misreading; incorporation of misread protein into the membrane, creating abnormal channels; increased (and irreversible) entry through these channels, and hence increased misreading and formation of channels; and, finally, blockade of initiating ribosomes.", "This mechanism can account for several previously unexplained observations: that streptomycin uptake requires protein synthesis during, but not after, the lag before the membrane damage; that streptomycin-resistant cells, which fail to take up streptomycin, can do so after treatment by another aminoglycoside; and that puromycin at moderate concentrations accelerates streptomycin uptake, while high concentrations (which release shorter chains) prevent it.", "In addition, puromycin, prematurely releasing polypeptides of normal sequence, also evidently creates channels, since it is reported to promote streptomycin uptake even in streptomycin-resistant cells.", "These findings imply that normal membrane proteins must be selected not only for a hydrophobic anchoring surface, but also for a tight fit in the membrane."], "structured": false}
{"doc_id": 27446873, "title": "Rate of cervical cancer, severe intraepithelial neoplasia, and adenocarcinoma in situ in primary HPV DNA screening with cytology triage: randomised study within organised screening programme.", "abstract": ["OBJECTIVE To assess the performance and impact of primary human papillomavirus (HPV) DNA screening with cytology triage compared with conventional cytology on cervical cancer and severe pre-cancerous lesions.   \n", "DESIGN Randomised trial.   \n", "SETTING Population based screening programme for cervical cancer in southern Finland in 2003-5.   \n", "PARTICIPANTS 58 076 women, aged 30-60, invited to the routine population based screening programme for cervical cancer.   \n", "INTERVENTIONS Primary HPV DNA test (hybrid capture II) with cytology triage if the result was positive or conventional cytological screening (reference).   \n", "MAIN OUTCOME MEASURES Rate of cervical cancer, cervical intraepithelial neoplasia (CIN) grade III, and adenocarcinoma in situ (as a composite outcome referred to as CIN III+) during 2003-7 through record linkage between files from the screening registry and the national cancer registry.   \n", "RESULTS In the HPV and conventional arms there were 95 600 and 95 700 woman years of follow-up and 76 and 53 cases of CIN III+, respectively (of which six and eight were cervical cancers).", "The relative rate of CIN III+ in the HPV arm versus the conventional arm was 1.44 (95% confidence interval 1.01 to 2.05) among all women invited for screening and 1.77 (1.16 to 2.74) among those who attended.", "Among women with a normal or negative test result, the relative rate of subsequent CIN III+ was 0.28 (0.04 to 1.17).", "The rate of cervical cancer between arms was 0.75 (0.25 to 2.16) among women invited for screening and 1.98 (0.52 to 9.38) among those who attended.   \n", "CONCLUSIONS When incorporated into a well established organised screening programme, primary HPV screening with cytology triage was more sensitive than conventional cytology in detecting CIN III+ lesions.", "The number of cases of cervical cancer was small, but considering the high probability of progression of CIN III the findings are of importance regarding cancer prevention.   \n", "TRIAL REGISTRATION Current Controlled Trials ISRCTN23885553."], "structured": true}
{"doc_id": 27449472, "title": "Metabolic syndrome as a risk factor for diabetes.", "abstract": ["The metabolic syndrome was initially described as an insulin-resistance syndrome characterized by the clustering of metabolic traits such as high triglycerides, low high-density lipoprotein cholesterol, high blood pressure, abdominal obesity and different degrees of impaired glucose regulation.", "Although different definitions have been developed by various consensus groups, epidemiological studies demonstrate that they all associate the metabolic syndrome with a similar cardiometabolic risk, which is high for diabetes (ranging between three- and 20-fold), depending on the number of components and the inclusion of impaired fasting glucose, impaired glucose tolerance or both.", "The latter appear to indicate the failure of the beta cell to produce enough insulin to compensate for the increased demand due to insulin resistance.", "There is a hyperbolic relationship between insulin production and insulin sensitivity, which can be calculated by the disposition index.", "When this is altered there is a higher risk of developing Type 2 diabetes.", "There have been no clinical trials in subjects selected by the diagnosis of metabolic syndrome, but structured lifestyle changes have been tested in people with impaired fasting glucose/impaired glucose tolerance and have been able to reduce incident Type 2 diabetes by almost 50%, as long as a weight loss of at least 5% is achieved.", "Oral antidiabetic and anti-obesity drugs have also been successful to a lesser degree.", "Some fibrates have reduced or delayed incident diabetes.", "Extended-release niacin has a neutral effect and statins are controversial.", "ACE inhibitors and ARBs are the antihypertensive agents least associated with incident diabetes."], "structured": false}
{"doc_id": 27453479, "title": "The fallacy of the ecological fallacy: the potential misuse of a concept and the consequences.", "abstract": ["Ecological studies have been evaluated in epidemiological contexts in terms of the \"ecological fallacy.", "\"", "Although the empirical evidence for a lack of comparability between correlations derived from ecological- and individual-level analyses is compelling, the conceptual meaning of the ecological fallacy remains problematic.", "This paper argues that issues in cross-level inference can be usefully conceptualized as validity problems, problems not peculiar to ecological-level analyses.", "Such an approach increases the recognition of both potential inference problems in individual-level studies and the unique contributions of ecological variables.", "This, in turn, expands the terrain for the location of causes for disease and interventions to improve the public's health."], "structured": false}
{"doc_id": 27460509, "title": "Blocking caspase-activated apoptosis improves contractility in failing myocardium.", "abstract": ["Cardiac myocyte apoptosis has been demonstrated in end-stage failing human hearts.", "The therapeutic utility of blocking apoptosis in congestive heart failure (CHF) has not been elucidated.", "This study investigated the role of caspase activation in cardiac contractility and sarcomere organization in the development of CHF.", "In a rabbit model of heart failure obtained by rapid ventricular pacing, we demonstrate, using in vivo transcoronary adenovirus-mediated gene delivery of the potent caspase inhibitor p35, that caspase activation is associated with a reduction in contractile force of failing myocytes by destroying sarcomeric structure.", "In this animal model gene transfer of p35 prevented the rise in caspase 3 activity and DNA-histone formation.", "Genetically manipulated hearts expressing p35 had a significant improvement in left ventricular pressure rise (+dp/dt), decreased end-diastolic chamber pressure (LVEDP), and the development of heart failure was delayed.", "To better understand this benefit, we examined the effects of caspase 3 on cardiomyocyte dysfunction in vitro.", "Microinjection of activated caspase 3 into the cytoplasm of intact myocytes induced sarcomeric disorganization and reduced contractility of the cells.", "These results demonstrate a direct impact of caspases on cardiac function and may lead to novel therapeutic strategies via antiapoptotic regimens."], "structured": false}
{"doc_id": 27466734, "title": "Development and validation of QRISK3 risk prediction algorithms to estimate future risk of cardiovascular disease: prospective cohort study", "abstract": ["Objectives To develop and validate updated QRISK3 prediction algorithms to estimate the 10 year risk of cardiovascular disease in women and men accounting for potential new risk factors.", "Design Prospective open cohort study.", "Setting General practices in England providing data for the QResearch database.", "Participants 1309 QResearch general practices in England: 981 practices were used to develop the scores and a separate set of 328 practices were used to validate the scores.", "7.89 million patients aged 25-84 years were in the derivation cohort and 2.67 million patients in the validation cohort.", "Patients were free of cardiovascular disease and not prescribed statins at baseline.", "Methods Cox proportional hazards models in the derivation cohort to derive separate risk equations in men and women for evaluation at 10 years.", "Risk factors considered included those already in QRISK2 (age, ethnicity, deprivation, systolic blood pressure, body mass index, total cholesterol: high density lipoprotein cholesterol ratio, smoking, family history of coronary heart disease in a first degree relative aged less than 60 years, type 1 diabetes, type 2 diabetes, treated hypertension, rheumatoid arthritis, atrial fibrillation, chronic kidney disease (stage 4 or 5)) and new risk factors (chronic kidney disease (stage 3, 4, or 5), a measure of systolic blood pressure variability (standard deviation of repeated measures), migraine, corticosteroids, systemic lupus erythematosus (SLE), atypical antipsychotics, severe mental illness, and HIV/AIDs).", "We also considered erectile dysfunction diagnosis or treatment in men.", "Measures of calibration and discrimination were determined in the validation cohort for men and women separately and for individual subgroups by age group, ethnicity, and baseline disease status.", "Main outcome measures Incident cardiovascular disease recorded on any of the following three linked data sources: general practice, mortality, or hospital admission records.", "Results 363 565 incident cases of cardiovascular disease were identified in the derivation cohort during follow-up arising from 50.8 million person years of observation.", "All new risk factors considered met the model inclusion criteria except for HIV/AIDS, which was not statistically significant.", "The models had good calibration and high levels of explained variation and discrimination.", "In women, the algorithm explained 59.6% of the variation in time to diagnosis of cardiovascular disease (R2, with higher values indicating more variation), and the D statistic was 2.48 and Harrell's C statistic was 0.88 (both measures of discrimination, with higher values indicating better discrimination).", "The corresponding values for men were 54.8%, 2.26, and 0.86.", "Overall performance of the updated QRISK3 algorithms was similar to the QRISK2 algorithms.", "Conclusion Updated QRISK3 risk prediction models were developed and validated.", "The inclusion of additional clinical variables in QRISK3 (chronic kidney disease, a measure of systolic blood pressure variability (standard deviation of repeated measures), migraine, corticosteroids, SLE, atypical antipsychotics, severe mental illness, and erectile dysfunction) can help enable doctors to identify those at most risk of heart disease and stroke."], "structured": false}
{"doc_id": 27527854, "title": "The importance of engaging policy-makers at the outset to guide research on and introduction of vaccines: the use of policy-maker surveys.", "abstract": ["Face-to-face surveys of policy-makers and other influential leaders are a useful tool to identify, at an early stage, (a) major issues regarding the introduction of a new vaccine, (b) persons and groups in a country who play a major decision-making or influential role in the introduction of vaccines, (c) potential obstacles to the introduction of vaccines, and (d) data-needs of policy-makers to overcome these obstacles.", "By surveying the opinions and beliefs of those who will make or influence decisions on whether to introduce a new vaccine, these studies can help ensure that research activities respond to the needs of policy-makers in countries endemic for the target diseases.", "These surveys can also inform vaccine-introduction strategies by identifying financially and politically feasible means of distributing, targeting, and financing the vaccines.", "This paper describes the methodology used in conducting such surveys and discusses methodological issues.", "It also presents lessons learnt from two policy-maker surveys carried out in several Asian countries in regard to new-generation vaccines against cholera, typhoid fever, and shigellosis; and future vaccines against dengue fever/dengue haemorrhagic fever."], "structured": false}
{"doc_id": 27545868, "title": "Histone acetyltransferase PCAF regulates inflammatory molecules in the development of renal injury.", "abstract": ["Kidney diseases, including chronic kidney disease (CKD) and acute kidney injury (AKI), are associated with inflammation.", "The mechanism that regulates inflammation in these renal injuries remains unclear.", "Here, we demonstrated that p300/CBP-associated factor (PCAF), a histone acetyltransferase, was overexpressed in the kidneys of db/db mice and lipopolysaccharide (LPS)-injected mice.", "Moreover, elevated histone acetylation, such as H3K18ac, and up-regulation of some inflammatory genes, such as ICAM-1, VCAM-1, and MCP-1, were found upon these renal injuries.", "Furthermore, increased H3K18ac was recruited to the promoters of ICAM-1, VCAM-1, and MCP-1 in the kidneys of LPS-injected mice.", "In vitro studies demonstrated that PCAF knockdown in human renal proximal tubule epithelial cells (HK-2) led to downregulation of inflammatory molecules, including VCAM-1, ICAM-1, p50 subunit of NF-\u03baB (p50), and MCP-1 mRNA and protein levels, together with significantly decreased H3K18ac level.", "Consistent with these, overexpression of PCAF enhanced the expression of inflammatory molecules.", "Furthermore, PCAF deficiency reduced palmitate-induced recruitment of H3K18ac on the promoters of ICAM-1 and MCP-1, as well as inhibited palmitate-induced upregulation of these inflammatory molecules.", "In summary, the present work demonstrates that PCAF plays an essential role in the regulation of inflammatory molecules through H3K18ac, which provides a potential therapeutic target for inflammation-related renal diseases."], "structured": false}
{"doc_id": 27550580, "title": "T1 mapping for myocardial extracellular volume measurement by CMR: bolus only versus primed infusion technique.", "abstract": ["OBJECTIVES The aim of this study was to determine the accuracy of the contrast \"bolus only\" T1 mapping cardiac magnetic resonance (CMR) technique for measuring myocardial extracellular volume fraction (ECV).   \n", "BACKGROUND Myocardial ECV can be measured with T1 mapping before and after contrast agent if the contrast agent distribution between blood/myocardium is at equilibrium.", "Equilibrium distribution can be achieved with a primed contrast infusion (equilibrium contrast-CMR [EQ-CMR]) or might be approximated by the dynamic equilibration achieved by delayed post-bolus measurement.", "This bolus only approach is highly attractive, but currently limited data support its use.", "We compared the bolus only technique with 2 independent standards: collagen volume fraction (CVF) from myocardial biopsy in aortic stenosis (AS); and the infusion technique in 5 representative conditions.   \n", "METHODS One hundred forty-seven subjects were studied: healthy volunteers (n = 50); hypertrophic cardiomyopathy (n = 25); severe AS (n = 22); amyloid (n = 20); and chronic myocardial infarction (n = 30).", "Bolus only (at 15 min) and infusion ECV measurements were performed and compared.", "In 18 subjects with severe AS the results were compared with histological CVF.   \n", "RESULTS The ECV by both techniques correlated with histological CVF (n = 18, r\u00b2 = 0.69, p < 0.01 vs. r\u00b2 = 0.71, p < 0.01, p = 0.42 for comparison).", "Across health and disease, there was strong correlation between the techniques (r\u00b2 = 0.97).", "However, in diseases of high ECV (amyloid, hypertrophic cardiomyopathy late gadolinium enhancement, and infarction), Bland-Altman analysis indicates the bolus only technique has a consistent and increasing offset, giving a higher value for ECVs above 0.4 (mean difference \u00b1 limit of agreement for ECV <0.4 = -0.004 \u00b1 0.037 vs. ECV >0.4 = 0.040 \u00b1 0.075, p < 0.001).   \n", "CONCLUSIONS Bolus only, T1 mapping-derived ECV measurement is sufficient for ECV measurement across a range of cardiac diseases, and this approach is histologically validated in AS.", "However, when ECV is >0.4, the bolus only technique consistently measures ECV higher compared with infusion."], "structured": true}
{"doc_id": 27555165, "title": "Cytomegalovirus US2 destroys two components of the MHC class II pathway, preventing recognition by CD4+ T cells", "abstract": ["Human cytomegalovirus (HCMV) is a ubiquitous herpesvirus that causes life-threatening disease in patients who are immunosuppressed for bone marrow or tissue transplantation or who have AIDS (ref.", "1).", "HCMV establishes lifelong latent infections and, after periodic reactivation from latency, uses a panel of immune evasion proteins to survive and replicate in the face of robust, fully primed host immunity.", "Monocyte/macrophages are important host cells for HCMV, serving as a latent reservoir and as a means of dissemination throughout the body.", "Macrophages and other HCMV-permissive cells, such as endothelial and glial cells, can express MHC class II proteins and present antigens to CD4+ T lymphocytes.", "Here, we show that the HCMV protein US2 causes degradation of two essential proteins in the MHC class II antigen presentation pathway: HLA-DR-\u03b1 and DM-\u03b1.", "This was unexpected, as US2 has been shown to cause degradation of MHC class I (refs.", "5,6), which has only limited homology with class II proteins.", "Expression of US2 in cells reduced or abolished their ability to present antigen to CD4+ T lymphocytes.", "Thus, US2 may allow HCMV-infected macrophages to remain relatively 'invisible' to CD4+ T cells, a property that would be important after virus reactivation."], "structured": false}
{"doc_id": 27567994, "title": "CD169-positive macrophages dominate antitumor immunity by crosspresenting dead cell-associated antigens.", "abstract": ["The generation of tumor-directed cytotoxic T lymphocytes is considered crucial for the induction of antitumor immunity.", "To activate these CD8(+) T cells, antigen-presenting cells (APCs) must initially acquire tumor cell-associated antigens.", "The major source of tumor antigens is dead tumor cells, but little is known about how APCs in draining lymph nodes acquire and crosspresent these antigens.", "Here we show that CD169(+) macrophages phagocytose dead tumor cells transported via lymphatic flow and subsequently crosspresent tumor antigens to CD8(+) T cells.", "Subcutaneous immunization with irradiated tumor cells protects mice from syngenic tumor.", "However, tumor antigen-specific CD8(+) T cell activation and subsequent antitumor immunity are severely impaired in mice depleted with CD169(+) macrophages.", "Neither migratory dendritic cells (DCs) nor lymph node-resident conventional DCs are essential for the crosspresentation of tumor antigens.", "Thus, we have identified CD169(+) macrophages as lymph node-resident APCs dominating early activation of tumor antigen-specific CD8(+) T cells."], "structured": false}
{"doc_id": 27569370, "title": "Emerging mechanisms in morphogen-mediated axon guidance.", "abstract": ["Early in animal development, gradients of secreted morphogenic molecules, such as Sonic hedgehog (Shh), Wnt and TGFbeta/Bmp family members, regulate cell proliferation and determine the fate and phenotype of the target cells by activating well-characterized signalling pathways, which ultimately control gene transcription.", "Shh, Wnt and TGFbeta/Bmp signalling also play an important and evolutionary conserved role in neural circuit assembly.", "They regulate neuronal polarization, axon and dendrite development and synaptogenesis, processes that require rapid and local changes in cytoskeletal organization and plasma membrane components.", "A key question then is whether morphogen signalling at the growth cone uses similar mechanisms and intracellular pathway components to those described for morphogen-mediated cell specification.", "This review discusses recent advances towards the understanding of this problem, showing how Shh, Wnt and TGFbeta/Bmp have adapted their 'classical' signalling pathways or adopted alternative and novel molecular mechanisms to influence different aspects of neuronal circuit formation."], "structured": false}
{"doc_id": 27580223, "title": "Lessons learnt from malaria epidemics in the Islamic Republic of Iran.", "abstract": ["The Islamic Republic of Iran is in the pre-elimination phase of malaria control, but malaria epidemics are still a concern in the south of the country.", "This retrospective study presents the epidemiological characteristics and predisposing factors of 60 of the malaria epidemics reported in Sistan va Baluchestan province during 2005-09.", "A zero-truncated negative binomial model was used to investigate the relation between predictor variables and the total number of malaria cases.", "Malaria epidemics occurred mainly in the southern part of the province, mostly between July and October, peaking in August.", "Most malaria epidemics were small-scale (68.3% were < 100 cases) and short (51.7% lasted < 1 month).", "Plasmodium falciparum was present in 46.7% of the epidemics.", "An increase in the rainfall rate as well as population movements were the most significant predisposing factors.", "The results may help inform an epidemic investigation and reporting system as the country approaches the malaria elimination phase."], "structured": false}
{"doc_id": 27587267, "title": "Autoradiography of chromosomal DNA fibers from Chinese hamster cells.", "abstract": ["Ignorance of the true length of the DNA molecules in the chromosomes of higher organisms has always been a major obstacle to understanding chromosome structure.", "Consequently, attempts have been made, usually with the aid of electron microscopy, to estimate the size of DNA in higher organisms.", "Solari (1) has reported the longest such DNA measured before now-a DNA fiber from a sea urchin sperm at least 93 \u03bc, long."], "structured": false}
{"doc_id": 27588420, "title": "Epigenetic memory and preferential lineage-specific differentiation in induced pluripotent stem cells derived from human pancreatic islet beta cells.", "abstract": ["Human induced pluripotent stem cells (HiPSCs) appear to be highly similar to human embryonic stem cells (HESCs).", "Using two genetic lineage-tracing systems, we demonstrate the generation of iPSC lines from human pancreatic islet beta cells.", "These reprogrammed cells acquired markers of pluripotent cells and differentiated into the three embryonic germ layers.", "However, the beta cell-derived iPSCs (BiPSCs) maintained open chromatin structure at key beta-cell genes, together with a unique DNA methylation signature that distinguishes them from other PSCs.", "BiPSCs also demonstrated an increased ability to differentiate into insulin-producing cells both in vitro and in vivo, compared with ESCs and isogenic non-beta iPSCs.", "Our results suggest that the epigenetic memory may predispose BiPSCs to differentiate more readily into insulin producing cells.", "These findings demonstrate that HiPSC phenotype may be influenced by their cells of origin, and suggest that their skewed differentiation potential may be advantageous for cell replacement therapy."], "structured": false}
{"doc_id": 27602752, "title": "CCL2/monocyte chemoattractant protein-1 mediates enhanced transmigration of human immunodeficiency virus (HIV)-infected leukocytes across the blood-brain barrier: a potential mechanism of HIV-CNS invasion and NeuroAIDS.", "abstract": ["Encephalitis and dementia associated with acquired immunodeficiency syndrome (AIDS) are characterized by leukocyte infiltration into the CNS, microglia activation, aberrant chemokine expression, blood-brain barrier (BBB) disruption, and eventual loss of neurons.", "Little is known about whether human immunodeficiency virus 1 (HIV-1) infection of leukocytes affects their ability to transmigrate in response to chemokines and to alter BBB integrity.", "We now demonstrate that HIV infection of human leukocytes results in their increased transmigration across our tissue culture model of the human BBB in response to the chemokine CCL2, as well as in disruption of the BBB, as evidenced by enhanced permeability, reduction of tight junction proteins, and expression of matrix metalloproteinases (MMP)-2 and MMP-9.", "HIV-infected cells added to our model did not transmigrate in the absence of CCL2, nor did this condition alter BBB integrity.", "The chemokines CXCL10/interferon-gamma-inducible protein of 10 kDa, CCL3/macrophage inflammatory protein-1alpha, or CCL5/RANTES (regulated on activation normal T-cell expressed and secreted) did not enhance HIV-infected leukocyte transmigration or BBB permeability.", "The increased capacity of HIV-infected leukocytes to transmigrate in response to CCL2 correlated with their increased expression of CCR2, the chemokine receptor for CCL2.", "These data suggest that CCL2, but not other chemokines, plays a key role in infiltration of HIV-infected leukocytes into the CNS and the subsequent pathology characteristic of NeuroAIDS."], "structured": false}
{"doc_id": 27615329, "title": "Prostaglandin E2 as an inhibitory modulator of fibrogenesis in human lung allografts.", "abstract": ["RATIONALE Donor mesenchymal stromal/stem cell (MSC) expansion and fibrotic differentiation is associated with development of bronchiolitis obliterans syndrome (BOS) in human lung allografts.", "However, the regulators of fibrotic differentiation of these resident mesenchymal cells are not well understood.   \n", "OBJECTIVES This study examines the role of endogenous and exogenous prostaglandin (PG)E2 as a modulator of fibrotic differentiation of human lung allograft-derived MSCs.   \n", "METHODS Effect of PGE2 on proliferation, collagen secretion, and \u03b1-smooth muscle actin (\u03b1-SMA) expression was assessed in lung-resident MSCs (LR-MSCs) derived from patients with and without BOS.", "The response pathway involved was elucidated by use of specific agonists and antagonists.   \n", "MEASUREMENT AND MAIN RESULTS PGE2 treatment of LR-MSCs derived from normal lung allografts significantly inhibited their proliferation, collagen secretion, and \u03b1-SMA expression.", "On the basis of pharmacologic and small-interfering RNA approaches, a PGE2/E prostanoid (EP)2/adenylate cyclase pathway was implicated in these suppressive effects.", "Stimulation of endogenous PGE2 secretion by IL-1\u03b2 was associated with amelioration of their myofibroblast differentiation in vitro, whereas its inhibition by indomethacin augmented \u03b1-SMA expression.", "LR-MSCs from patients with BOS secreted significantly less PGE2 than non-BOS LR-MSCs.", "Furthermore, BOS LR-MSCs were found to be defective in their ability to induce cyclooxygenase-2, and therefore unable to up-regulate PGE2 synthesis in response to IL-1\u03b2.", "BOS LR-MSCs also demonstrated resistance to the inhibitory actions of PGE2 in association with a reduction in the EP2/EP1 ratio.   \n", "CONCLUSIONS These data identify the PGE2 axis as an important autocrine-paracrine brake on fibrotic differentiation of LR-MSCs, a failure of which is associated with BOS."], "structured": true}
{"doc_id": 27635177, "title": "Association of DNA polymerase mu (pol mu) with Ku and ligase IV: role for pol mu in end-joining double-strand break repair.", "abstract": ["Mammalian DNA polymerase mu (pol mu) is related to terminal deoxynucleotidyl transferase, but its biological role is not yet clear.", "We show here that after exposure of cells to ionizing radiation (IR), levels of pol mu protein increase.", "pol mu also forms discrete nuclear foci after IR, and these foci are largely coincident with IR-induced foci of gammaH2AX, a previously characterized marker of sites of DNA double-strand breaks.", "pol mu is thus part of the cellular response to DNA double-strand breaks.", "pol mu also associates in cell extracts with the nonhomologous end-joining repair factor Ku and requires both Ku and another end-joining factor, XRCC4-ligase IV, to form a stable complex on DNA in vitro.", "pol mu in turn facilitates both stable recruitment of XRCC4-ligase IV to Ku-bound DNA and ligase IV-dependent end joining.", "In contrast, the related mammalian DNA polymerase beta does not form a complex with Ku and XRCC4-ligase IV and is less effective than pol mu in facilitating joining mediated by these factors.", "Our data thus support an important role for pol mu in the end-joining pathway for repair of double-strand breaks."], "structured": false}
{"doc_id": 27647593, "title": "Stromal-epithelial metabolic coupling in cancer: integrating autophagy and metabolism in the tumor microenvironment.", "abstract": ["Cancer cells do not exist as pure homogeneous populations in vivo.", "Instead they are embedded in \"cancer cell nests\" that are surrounded by stromal cells, especially cancer associated fibroblasts.", "Thus, it is not unreasonable to suspect that stromal fibroblasts could influence the metabolism of adjacent cancer cells, and visa versa.", "In accordance with this idea, we have recently proposed that the Warburg effect in cancer cells may be due to culturing cancer cells by themselves, out of their normal stromal context or tumor microenvironment.", "In fact, when cancer cells are co-cultured with fibroblasts, then cancer cells increase their mitochondrial mass, while fibroblasts lose their mitochondria.", "An in depth analysis of this phenomenon reveals that aggressive cancer cells are \"parasites\" that use oxidative stress as a \"weapon\" to extract nutrients from surrounding stromal cells.", "Oxidative stress in fibroblasts induces the autophagic destruction of mitochondria, by mitophagy.", "Then, stromal cells are forced to undergo aerobic glycolysis, and produce energy-rich nutrients (such as lactate and ketones) to \"feed\" cancer cells.", "This mechanism would allow cancer cells to seed anywhere, without blood vessels as a food source, as they could simply induce oxidative stress wherever they go, explaining how cancer cells survive during metastasis.", "We suggest that stromal catabolism, via autophagy and mitophagy, fuels the anabolic growth of tumor cells, promoting tumor progression and metastasis.", "We have previously termed this new paradigm \"The Autophagic Tumor Stroma Model of Cancer Metabolism\", or the \"Reverse Warburg Effect\".", "We also discuss how glutamine addiction (glutaminolysis) in cancer cells fits well with this new model, by promoting oxidative mitochondrial metabolism in aggressive cancer cells."], "structured": false}
{"doc_id": 27665523, "title": "Oxidative stress in renal dysfunction: mechanisms, clinical sequelae and therapeutic options", "abstract": ["Oxidative stress has been increasingly linked to the high incidence of cardiovascular events in patients with chronic kidney disease (CKD), especially as traditional cardiovascular risk factors seem to not be able to account for the huge cardiovascular morbidity and mortality in this population group.", "Oxidative stress is increased in patients with renal impairment as a result of increased oxidant activity and reduced antioxidant capacity, and this is increased in a graded manner with increasing renal dysfunction.", "Inflammation, which is also present in CKD, further amplifies the oxidant generation process.", "The two clinical sequelae of oxidative stress are endothelial dysfunction and left ventricular hypertrophy, which have adverse cardiovascular consequences.", "With our new understanding of oxidative stress, it is now important to assess treatment options that reduce it in the hope that they reverse endothelial dysfunction and left ventricular hypertrophy and the clinical sequelae of these abnormalities."], "structured": false}
{"doc_id": 27686445, "title": "Effect of age, sex, and sites on the cellularity of the adipose tissue in mice and rats rendered obese by a high-fat diet.", "abstract": ["Cell size and number of parametrial fat pads were determined in Swiss mice made obese by means of a high-fat diet (40% lard w/w) given ad lib.", "This diet and a control were introduced to two groups of mothers during gestation and lactation, and sucklings were given the same diets as their mothers at weaning and throughout life.2-wk old mice suckled by mothers fed a high-fat diet have fatter parametrial pads.", "This difference is due solely to an increase in fat cell size.", "After weaning, until the 18th wk, the two groups differed with a striking fat cell enlargement seen in the obese group.", "Later on, whereas cell numbers did not change in the control group, a constant and uninterrupted increase in number is shown in those of obese mice until the 52nd wk.", "Hyperplasia was observed only in adults.", "When the high-fat diet was introduced to adult rats it also triggered an increase in fat cell number.", "Three sites of fat pads were compared in both sexes at 32 wk of age.", "All sites increased in weight in the high-fat fed group.", "This was due to: hyperplasia in perirenal site, hypertrophy in epididymal and subcutaneous sites, and hyperplasia plus hypertrophy in the parametrial one.", "So, in each sex, adipose sites in the obese mice reacted to the diet in a site-specific way.", "It was concluded that the level of fat in a diet is involved in both formation and maturation of new fat cells and in the regulation of fat cell lipid content.", "The two processes may be separated or may act together according to the adipose tissue site."], "structured": false}
{"doc_id": 27693891, "title": "Transcriptional integration of mitochondrial biogenesis.", "abstract": ["Gene regulatory factors encoded by the nuclear genome are essential for mitochondrial biogenesis and function.", "Some of these factors act exclusively within the mitochondria to regulate the control of mitochondrial transcription, translation, and other functions.", "Others govern the expression of nuclear genes required for mitochondrial metabolism and organelle biogenesis.", "The peroxisome proliferator-activated receptor \u03b3 coactivator-1 (PGC-1) family of transcriptional coactivators play a major role in transducing and integrating physiological signals governing metabolism, differentiation, and cell growth to the transcriptional machinery controlling mitochondrial functional capacity.", "Thus, the PGC-1 coactivators serve as a central component of the transcriptional regulatory circuitry that coordinately controls the energy-generating functions of mitochondria in accordance with the metabolic demands imposed by changing physiological conditions, senescence, and disease."], "structured": false}
{"doc_id": 27709445, "title": "RFID system evaluation against radiated transient noise", "abstract": ["In this paper a radiofrequency identification system according to standard ISO/IEC 14443 type-B is evaluated in  presence of transient noise.", "This real time communication system working at 13.56 MHz is interfered in a controlled environment by different transient bursts varying their level, frequency and duration.", "The transient burst interference is applied in an AC main wire close to the system and the effect over the digital communication system is evaluated using two different methods.  ", "The first one is observing directly an RFID equipment in presence of transient signals, and the second one is capturing the  interference in time domain an evaluating its effect by means of simulation.", "The RFID system is affected by these transient noises  causing different types of errors.", "It is shown that it is essential to measure and evaluate in time domain the transient phenomena to ensure that the RFID system do not have susceptibility problems."], "structured": false}
{"doc_id": 27711043, "title": "Musculoskeletal pain in Europe: its impact and a comparison of population and medical perceptions of treatment in eight European countries.", "abstract": ["OBJECTIVES To describe the impact of musculoskeletal pain (MP); to compare management of MP by the population and by primary care physicians; and to identify misconceptions about treatment.   \n", "METHODS 5803 people with MP and 1483 primary care physicians, randomly selected, in eight European countries were interviewed by telephone.", "A structured questionnaire was used to ask about usual management of MP and perceived benefits and risks of treatment.", "Current health status (SF-12) was also assessed.   \n", "RESULTS From primary care physicians' perceptions, MP appears to be well managed.", "All presenting patients are offered some form of treatment, 90% or more doctors are trying to improve patients' quality of life, and most are aware and concerned about the risks of treatment with NSAIDs.", "From a population perspective, up to 27% of people with pain do not seek medical help and of those who do, several wait months/years before seeing a doctor.", "55% or fewer patients who have seen a doctor are currently receiving prescription treatment for their pain.", "Communication between doctors and patients is poor; few patients are given information about their condition; and many have misconceptions about treatment.   \n", "CONCLUSIONS Management of MP is similar across eight European countries, but there is discordance between physician and patient perspectives of care.", "Some people with pain have never sought medical help despite being in constant/daily pain.", "Those who do seek help receive little written information or explanation and many have misperceptions about the benefits and risks of treatment that limit their ability to actively participate in decisions about their care."], "structured": true}
{"doc_id": 27712433, "title": "[Palliative care in Germany].", "abstract": ["The delivery of palliative care in Germany is still characterized by a wide-spread undersupply both for inpatients and outpatients.", "Nevertheless over the last 15 years progress has also been made in Germany, which is pleasing and which has directed professional and public attention increasingly to the situation of the incurably ill and dying.", "In the course of this development the first structures for specialized palliative care have been established.", "In particular the situation for inpatients in hospitals and hospices is pleasing, even if a satisfaction for total coverage is not yet reached.", "More seriously however is the demand for the outpatients.", "Financial means, which are steered so far only rudimentarily for palliative care, must be made sufficiently available, in order to be able to meet the demand with the help of appropriate structural offers.", "It is important to realize the needs of the incurably ill and dying and of their relatives and friends.", "Our society has to call attention to this subject and it should be placed on the healthpolitical agenda as a topic of the highest priority level.", "The current developments in the federation and in the federal states are encouraging and allowing hope that the delivery of palliative care for all who need it (and not only the ill) will improve further in the coming years."], "structured": false}
{"doc_id": 27731651, "title": "A view to a kill: the bacterial type VI secretion system.", "abstract": ["The bacterial type VI secretion system (T6SS) is an organelle that is structurally and mechanistically analogous to an intracellular membrane-attached contractile phage tail.", "Recent studies determined that a rapid conformational change in the structure of a sheath protein complex propels T6SS spike and tube components along with antibacterial and antieukaryotic effectors out of predatory T6SS(+) cells and into prey cells.", "The contracted organelle is then recycled in an ATP-dependent process.", "T6SS is regulated at transcriptional and posttranslational levels, the latter involving detection of membrane perturbation in some species.", "In addition to directly targeting eukaryotic cells, the T6SS can also target other bacteria coinfecting a mammalian host, highlighting the importance of the T6SS not only for bacterial survival in environmental ecosystems, but also in the context of infection and disease.", "This review highlights these and other advances in our understanding of the structure, mechanical function, assembly, and regulation of the T6SS."], "structured": false}
{"doc_id": 27768226, "title": "Open Access Increases Citation Rate", "abstract": ["PLoS Biology publishes today a research article by Gunther Eysenbach that is not about biology.", "It is about citations.", "It provides robust evidence that open-access articles (OA articles) are more immediately recognized and cited than non-OA articles.", "As such, it adds objective support to the belief we have always held that open-access publication speeds up scientific dialog between researchers and, consequently, should be extended to the whole scientific literature as quickly as possible.", "It is therefore fitting that we publish such a paper.    ", "We have long argued that papers freely available in a journal will be more often read and cited than those behind a subscription barrier.", "However, solid evidence to support or refute such a claim has been surprisingly hard to find.", "Since most open-access journals are new, comparisons of the effects of open access with established subscription-based journals are easily confounded by age and reputation.", "In the current study, Eysenbach compared citations compiled by Thomson Scientific (formerly Thomson ISI) to individual articles published between June 2004 and December 2004 in the same journal\u2014namely, Proceedings of the National Academy of Sciences (PNAS), which announced its open-access option for authors on June 8 of that year, with an associated publication charge of US$1,000.", "Non-OA articles in PNAS are subject to a six-month \u201ctoll-access\u201d delay before the article becomes publicly available.", "The results of this natural experiment are clear: in the 4 to 16 months following publication, OA articles gained a significant citation advantage over non-OA articles during the same period.", "They are twice as likely to be cited 4 to 10 months after publication and almost three times as likely between 10 and 16 months.", "Given that PNAS delays open access for only six months, the disparity between OA and non-OA articles in journals where the delay is longer or where articles remain \u201ctoll-access\u201d is likely to be even greater.    ", "Eysenbach also looked at the impact of self-archiving non-OA articles.", "One route to open access, it is argued, is for authors to archive their published articles on their own Web sites or in institutional repositories, although this does not include an explicit business model to cover the cost of peer-review and publishing.", "The analysis revealed that self-archived articles are also cited less often than OA articles from the same journal.    ", "Yes, you're right; we do have a strong and vested interest in publishing results that so obviously endorse our existence.", "Moreover, the author of the article is also an editor of an open-access journal.", "But sometimes a potential conflict of interest can actually help to ensure rigor.", "In this case, we have an acute interest in ensuring that the article meets the same, if not higher, standards as any other research article we publish.", "Not only must the conclusions provide a significant advance for the field, but the study must be technically sound, with appropriate evidence to support those conclusions.", "As with all our research articles, we consulted throughout the evaluation process with an academic editor with appropriate expertise\u2014in this case, Carol Tenopir, professor of information sciences at the University of Tennessee (Knoxville, Tennessee, United States).", "The article was reviewed by two experts in bibliometric analyses and information science, and an experienced research biologist with expertise in statistics.", "They all enthusiastically supported publication, although one understandably questioned the suitability of PLoS Biology as the publication venue.    ", "We have no intention of making PLoS Biology a regular home for bibliometric studies (even when about open access).", "What makes this study worth publishing in PLoS Biology is not only the relative strength of evidence supporting the claim but also the extent to which many (especially other publishers) have anticipated such an analysis.", "As far as we are aware, no other study has compared OA and non-OA articles from the same journal and controlled for so many potentially confounding factors.", "Eysenbach's multivariate analysis took into account the number of days since publication, number of authors, article type, country of the corresponding author, funding type, subject area, submission track ( PNAS has three different ways that authors can submit a paper), and the previous citation record of the first and last authors.", "He even administered a supplementary questionnaire to assess whether authors choosing the OA option in PNAS chose to do so for only their most important research (they didn't).", "As Ian Rowlands from the Centre for Publishing at University College London\u2014and one of the reviewers who agreed to be identified in this article\u2014said at the start of his review:          \u201cMany (most) of the papers and presentations I have read/seen on this topic have completely failed to address the kinds of confounding issues that are so convincingly tackled here.", "For that reason alone, this paper deserves to be published and alerted to the widest possible audience.", "\u201d          In addition to providing evidence for the immediate advantage of open access, Eysenbach's analysis also highlights several potential challenges to its long-term future.", "Although a limited dataset, the citation history of the first and last authors differed between those who chose the open-access option and those who did not.", "In the group that chose open access, last authors tended to have a \u201cstronger\u201d previous citation record, whereas this situation was reversed among the group that declined the open-access option\u2014here, it was the first authors who tended to be stronger.", "This may reflect varying attitudes of authors at different stages of their career, a stronger influence from the leader of a particular group, or an age- or career-related difference in the ability to pay the publication charge (e.g., [ 1]).", "Indeed, access to appropriate funds may also be a reason why a lower proportion of authors from European countries tended to choose the open-access option.", "In many of these countries, funds for page charges\u2014and, by extension, open-access publication fees\u2014are often not included within research grants.    ", "PNAS was one of the first journals to offer an open-access option to its authors.", "However, such hybrid journals are increasing: Blackwell, Springer, and Oxford University Press now provide this option as well.", "This means that similar experiments can be replicated.", "Moreover, although the evidence from the current analysis argues most strongly for a time advantage in citation for OA articles, a study over longer periods will reveal whether this translates into a sustained increase in the number of citations.", "In the meantime, open-access advocates should be emboldened by tangible evidence for what has seemed obvious all along."], "structured": false}
{"doc_id": 27772649, "title": "Serum immunoglobulin A from patients with celiac disease inhibits human T84 intestinal crypt epithelial cell differentiation.", "abstract": ["BACKGROUND & AIMS Celiac disease is characterized by disturbed jejunal crypt-villus axis biology with immunoglobulin (Ig) A deposits underlining the epithelium.", "The aim of this study was to test whether celiac disease serum IgA (reticulin/endomysial autoantibodies) interferes with the mesenchymal-epithelial cell cross-talk.   \n", "METHODS Differentiation of T84 epithelial cells was induced with IMR-90 fibroblasts or transforming growth factor beta in three-dimensional collagen gel cultures.", "The effects of purified celiac IgA and monoclonal tissue transglutaminase antibodies (CUB7402) were studied by adding the antibodies to the cocultures.   \n", "RESULTS Active celiac disease IgA, reactive for tissue transglutaminase, significantly inhibited T84 epithelial cell differentiation (P < 0.001) and increased epithelial cell proliferation (P = 0.024).", "Similar effects were obtained with antibodies against tissue transglutaminase.   \n", "CONCLUSIONS Celiac disease-associated IgA class antibodies disturb transforming growth factor beta-mediated fibroblast-epithelial cell cross-talk in this in vitro crypt-villus axis model.", "This primary finding indicates that celiac disease-specific autoantibodies may also contribute to the formation of the gluten-triggered jejunal mucosal lesion in celiac disease."], "structured": true}
{"doc_id": 27789588, "title": "Pathogenesis of diseases associated with antineutrophil cytoplasm autoantibodies.", "abstract": ["Little is known about the etiologies of diseases associated with circulating antineutrophil cytoplasm autoantibodies (ANCA), such as primary vasculitides and inflammatory bowel diseases.", "However, the understanding of immune mechanisms supposedly involved in the pathogenesis of these diseases is still growing.", "In the present review, we first focus on the mechanisms triggering the development of ANCA, including the potential role of microbial superantigens and the possible defect(s) in the progression of apoptosis or in the removal of apoptotic cells.", "We next concentrate on the contribution of ANCA to the clinical symptoms and on the pathogenic role of ANCA, including the accessibility of ANCA antigens as targets for circulating antibodies and the mode of action of ANCA.", "Mechanisms of neutrophil activation by ANCA include the engagement of Fcgamma receptors, the possible mechanisms of neutrophil-mediated tissue damage, and the neutrophil-endothelial interaction."], "structured": false}
{"doc_id": 27815697, "title": "The common marmoset as a novel animal model system for biomedical and neuroscience research applications.", "abstract": ["The common marmoset (Callithrix jacchus), a small New World primate, has been attracting much attention in the research field of biomedical science and neuroscience, based on its (i) cross-reactivity with human cytokines or hormones, (ii) comparative ease in handling due to its small size, (iii) high reproductive efficiency, (iv) establishment of basic research tools, and (v) advantages of its unique behavioral and cognitive characters.", "Various neurological disease models have been developed in the common marmoset, including Parkinson's disease, Huntington's disease, Alzheimer's disease, stroke, multiple sclerosis and spinal cord injury.", "We recently developed transgenic common marmoset with germline transmission, which is expected to provide a new animal model for the study of human diseases.", "In this review, we summarize the recent progress of biomedical research and neuroscience using common marmoset as an excellent model system."], "structured": false}
{"doc_id": 27822315, "title": "Liver receptor homolog-1 regulates the transcription of steroidogenic enzymes and induces the differentiation of mesenchymal stem cells into steroidogenic cells.", "abstract": ["Steroidogenic factor-1 (SF-1, also known as Ad4BP) has been demonstrated to be a primary transcriptional regulator of steroidogenic-related genes.", "However, mRNA for liver receptor homolog-1 (LRH-1), which together with SF-1, belongs to the NR5A nuclear receptor family, is expressed at much higher levels than SF-1 mRNA in the human gonad.", "In our previous studies, we demonstrated that SF-1 induced the differentiation of bone marrow-derived mesenchymal stem cells (MSCs) into steroidogenic cells such as Leydig or adrenocortical cells.", "The introduction of LRH-1 into human MSCs (hMSCs) with the aid of cAMP also induced the expression of steroidogenic enzymes, including CYP17, and their differentiation into steroid hormone-producing cells.", "Promoter analysis, EMSA, and chromatin immunoprecipitation assay using LRH-1-transduced hMSCs indicated that three LRH-1 binding sites were responsible for CYP17 transactivation.", "Immunohistochemical studies showed that LRH-1 protein was expressed in human Leydig cells.", "The CYP17 promoter region was highly methylated in hMSCs, whereas it was demethylated by the introduction of LRH-1 and cAMP treatment.", "These results indicate that LRH-1 could represent another key regulator of the steroidogenic lineage in MSCs and play a vital role in steroid hormone production in human Leydig cells."], "structured": false}
{"doc_id": 27840664, "title": "Checkpoint responses to replication fork barriers.", "abstract": ["The fidelity of DNA replication is of paramount importance to the maintenance of genome integrity.", "When an active replication fork is perturbed, multiple cellular pathways are recruited to stabilize the replication apparatus and to help to bypass or correct the causative problem.", "However, if the problem is not corrected, the fork may collapse, exposing free DNA ends to potentially inappropriate processing.", "In prokaryotes, replication fork collapse promotes the activity of recombination proteins to restore a replication fork.", "Recent work has demonstrated that recombination is also intimately linked to replication in eukaryotic cells, and that recombination proteins are recruited to collapsed, but not stalled, replication forks.", "In this review we discuss the different types of potential replication fork barriers (RFB) and how these distinct RFBs can result in different DNA structures at the stalled replication fork.", "The DNA structure checkpoints which act within S phase respond to different RFBs in different ways and we thus discuss the processes that are controlled by the DNA replication checkpoints, paying particular attention to the function of the intra-S phase checkpoint that stabilises the stalled fork."], "structured": false}
{"doc_id": 27841037, "title": "Ecology, economics and political will: the vicissitudes of malaria strategies in Asia.", "abstract": ["The documented history of malaria in parts of Asia goes back more than 2,000 years, during which the disease has been a major player on the socioeconomic stage in many nation states as they waxed and waned in power and prosperity.", "On a much shorter time scale, the last half century has seen in microcosm a history of large fluctuations in endemicity and impact of malaria across the spectrum of rice fields and rain forests, mountains and plains that reflect the vast ecological diversity inhabited by this majority aggregation of mankind.", "That period has seen some of the most dramatic changes in social and economic structure, in population size, density and mobility, and in political structure in history: all have played a part in the changing face of malaria in this extensive region of the world.", "While the majority of global malaria cases currently reside in Africa, greater numbers inhabited Asia earlier this century before malaria programs savored significant success, and now Asia harbors a global threat in the form of the epicenter of multidrug resistant Plasmodium falciparum which is gradually encompassing the tropical world.", "The latter reflects directly the vicissitudes of economic change over recent decades, particularly the mobility of populations in search of commerce, trade and personal fortunes, or caught in the misfortunes of physical conflicts.", "The period from the 1950s to the 1990s has witnessed near \"eradication\" followed by resurgence of malaria in Sri Lanka, control and resurgence in India, the influence of war and postwar instability on drug resistance in Cambodia, increase in severe and cerebral malaria in Myanmar during prolonged political turmoil, the essential disappearance of the disease from all but forested border areas of Thailand where it remains for the moment intractable, the basic elimination of vivax malaria from many provinces of central China.", "Both positive and negative experiences have lessons to teach in the debate between eradication and control as alternative strategies.", "China has for years held high the goal of \"basic elimination\", eradication by another name, in sensible semi-defiance of WHO dictates.", "The Chinese experience makes it clear that, given community organization, exhaustive attention to case detection, management and focus elimination, plus the political will at all levels of society, it is possible both to eliminate malaria from large areas of an expansive nation and to implement surveillance necessary to maintain something approaching eradication status in those areas.", "But China has not succeeded in the international border regions of the tropical south where unfettered population movement confounds the program.", "Thailand, Malaysia and to an extent Vietnam have also reached essential elimination in their rice field plains by vigorous vertical programs but fall short at their forested borders.", "Economics is central to the history of the rise and fall of nations, and to the history of disease in the people who constitute nations.", "The current love affair with free market economics as the main driving force for advance of national wealth puts severe limitations on the essential involvement of communities in malaria management.", "The task of malaria control or elimination needs to be clearly related to the basic macroeconomic process that preoccupies governments, not cloistered away in the health sector Historically malaria has had a severe, measurable, negative impact on the productivity of nations.", "Economic models need rehoning with political aplomb and integrating with technical and demographic strategies.", "Recent decades in Chinese malaria history carry some lessons that may be relevant in this context."], "structured": false}
{"doc_id": 27866735, "title": "Global and regional risk of disabling sequelae from bacterial meningitis: a systematic review and meta-analysis.", "abstract": ["Few data sources are available to assess the global and regional risk of sequelae from bacterial meningitis.", "We aimed to estimate the risks of major and minor sequelae caused by bacterial meningitis, estimate the distribution of the different types of sequelae, and compare risk by region and income.", "We systematically reviewed published papers from 1980 to 2008.", "Standard global burden of disease categories (cognitive deficit, bilateral hearing loss, motor deficit, seizures, visual impairment, hydrocephalus) were labelled as major sequelae.", "Less severe, minor sequelae (behavioural problems, learning difficulties, unilateral hearing loss, hypotonia, diplopia), and multiple impairments were also included.", "132 papers were selected for inclusion.", "The median (IQR) risk of at least one major or minor sequela after hospital discharge was 19.9% (12.3-35.3%).", "The risk of at least one major sequela was 12.8% (7.2-21.1%) and of at least one minor sequela was 8.6% (4.4-15.3%).", "The median (IQR) risk of at least one major sequela was 24.7% (16.2-35.3%) in pneumococcal meningitis; 9.5% (7.1-15.3%) in Haemophilus influenzae type b (Hib), and 7.2% (4.3-11.2%) in meningococcal meningitis.", "The most common major sequela was hearing loss (33.9%), and 19.7% had multiple impairments.", "In the random-effects meta-analysis, all-cause risk of a major sequela was twice as high in the African (pooled risk estimate 25.1% [95% CI 18.9-32.0%]) and southeast Asian regions (21.6% [95% CI 13.1-31.5%]) as in the European region (9.4% [95% CI 7.0-12.3%]; overall I(2)=89.5%, p<0.0001).", "Risks of long-term disabling sequelae were highest in low-income countries, where the burden of bacterial meningitis is greatest.", "Most reported sequelae could have been averted by vaccination with Hib, pneumococcal, and meningococcal vaccines."], "structured": false}
{"doc_id": 27873158, "title": "Efficacy of human papillomavirus testing for the detection of invasive cervical cancers and cervical intraepithelial neoplasia: a randomised controlled trial.", "abstract": ["BACKGROUND Human papillomavirus (HPV) testing is known to be more sensitive, but less specific than cytology for detecting cervical intraepithelial neoplasia (CIN).", "We assessed the efficacy of cervical-cancer screening policies that are based on HPV testing.   \n", "METHODS Between March, 2004, and December, 2004, in two separate recruitment phases, women aged 25-60 years were randomly assigned to conventional cytology or to HPV testing in combination with liquid-based cytology (first phase) or alone (second phase).", "Randomisation was done by computer in two screening centres and by sequential opening of numbered sealed envelopes in the remaining seven centres.", "During phase one, women who were HPV-positive and aged 35-60 years were referred to colposcopy, whereas women aged 25-34 years were referred to colposcopy only if cytology was also abnormal or HPV testing was persistently positive.", "During phase two, women in the HPV group were referred for colposcopy if the HPV test was positive.", "Two rounds of screening occurred in each phase, and all women had cytology testing only at the second round.", "The primary endpoint was the detection of grade 2 and 3 CIN, and of invasive cervical cancers during the first and second screening rounds.", "Analysis was done by intention to screen.", "This trial is registered, number ISRCTN81678807.   \n", "FINDINGS In total for both phases, 47,001 women were randomly assigned to the cytology group and 47,369 to HPV testing.", "33,851 women from the cytology group and 32,998 from the HPV-testing group had a second round of screening.", "We also retrieved the histological diagnoses from screening done elsewhere.", "The detection of invasive cervical cancers was similar for the two groups in the first round of screening (nine in the cytology group vs seven in the HPV group, p=0.62); no cases were detected in the HPV group during round two, compared with nine in the cytology group (p=0.004).", "Overall, in the two rounds of screening, 18 invasive cancers were detected in the cytology group versus seven in the HPV group (p=0.028).", "Among women aged 35-60 years, at round one the relative detection (HPV vs cytology) was 2.00 (95% CI 1.44-2.77) for CIN2, 2.08 (1.47-2.95) for CIN3, and 2.03 (1.60-2.57) for CIN2 and 3 together.", "At round two the relative detection was 0.54 (0.23-1.28) for CIN2, 0.48 (0.21-1.11) for CIN3, and 0.51 (0.28-0.93) for CIN2 and 3 together.", "Among women aged 25-34 years, there was significant heterogeneity between phases in the relative detection of CIN3.", "At round one the relative detection was 0.93 (0.52-1.64) in phase one and 3.91 (2.02-7.57) in phase two.", "At round two the relative detection was 1.34 (0.46-3.84) in phase one and 0.20 (0.04-0.93) in phase two.", "Pooling both phases, the detection ratio of CIN2 for women aged 25-34 years was 4.09 (2.24-7.48) at round one and 0.64 (0.23-1.27) at round two.   \n", "INTERPRETATION HPV-based screening is more effective than cytology in preventing invasive cervical cancer, by detecting persistent high-grade lesions earlier and providing a longer low-risk period.", "However, in younger women, HPV screening leads to over-diagnosis of regressive CIN2.   \n", "FUNDING European Union, Italian Ministry of Health, Regional Health Administrations of Piemonte, Tuscany, Veneto and Emilia-Romagna, and Public Health Agency of Lazio."], "structured": true}
{"doc_id": 27889071, "title": "Microcytosis, iron deficiency and thalassaemia in a multi-ethnic community: a pilot study.", "abstract": ["The high prevalence of microcytosis (defined here as mean cell haemoglobin<27 pg) with no other abnormality is a principal cause of confusion in screening for haemoglobin disorders.", "Here we report the results of a small pilot study aiming to resolve this confusion by routinely proceeding to plasma ferritin and HPLC assay, using the original sequestrene blood sample, when microcytosis is detected.", "Participants comprised a random sample of 1,302 people referred for a full blood count by their General Practitioner (GP) to the laboratory of a North London district general hospital serving a multi-ethnic inner-city population.", "Ethnicity was established by questionnaire.", "In North Europeans, microcytosis was present in 3% of males (half were iron-deficient) and 11% of females (most were iron-deficient).", "Among ethnic minorities, microcytosis was present in 35% of males (one tenth were iron-deficient), and 45% of females (less than half were iron-deficient): an exclusion diagnosis of \"probable alpha thalassaemia\" could be made in the remainder.", "We conclude that when microcytosis is present, routine further analysis of the original sequestrene sample by plasma ferritin assay and haemoglobinopathy screening could lead to a more efficient and cost-effective laboratory service for primary care and maternity services."], "structured": false}
{"doc_id": 27900414, "title": "Crystal structure of the human AAA+ protein RuvBL1.", "abstract": ["RuvBL1 is an evolutionarily highly conserved eukaryotic protein belonging to the AAA(+)-family of ATPases (ATPase associated with diverse cellular activities).", "It plays important roles in essential signaling pathways such as the c-Myc and Wnt pathways in chromatin remodeling, transcriptional and developmental regulation, and DNA repair and apoptosis.", "Herein we present the three-dimensional structure of the selenomethionine variant of human RuvBL1 refined using diffraction data to 2.2A of resolution.", "The crystal structure of the hexamer is formed of ADP-bound RuvBL1 monomers.", "The monomers contain three domains, of which the first and the third are involved in ATP binding and hydrolysis.", "Although it has been shown that ATPase activity of RuvBL1 is needed for several in vivo functions, we could only detect a marginal activity with the purified protein.", "Structural homology and DNA binding studies demonstrate that the second domain, which is unique among AAA(+) proteins and not present in the bacterial homolog RuvB, is a novel DNA/RNA-binding domain.", "We were able to demonstrate that RuvBL1 interacted with single-stranded DNA/RNA and double-stranded DNA.", "The structure of the RuvBL1.ADP complex, combined with our biochemical results, suggest that although RuvBL1 has all the structural characteristics of a molecular motor, even of an ATP-driven helicase, one or more as yet undetermined cofactors are needed for its enzymatic activity."], "structured": false}
{"doc_id": 27907205, "title": "Characteristics of a monoclonal antibody (RM124) against acute myelocytic leukemia cells.", "abstract": ["A monoclonal antibody was raised against cells from an experimental rat myelocytic leukemia (BNML).", "The major characteristics of the rat leukemia model resemble those of human acute myelocytic leukemia.", "The monoclonal antibody (MCA) RM124 was characterized with respect to its labeling pattern of BNML leukemia cells, normal rat bone marrow cells, and the hemopoietic stem cell (HSC), by flow cytometric methods and complement-dependent cytotoxicity assays.", "Flow cytometry revealed a much higher labeling of the leukemic cells by the MCA-RM124 compared with normal bone marrow cells, including CFU-S and CFU-C. Only a subpopulation of the normal granulocytes showed cross reactivity, however, at a lower labeling density.", "On using the cytotoxicity assays, it was evident that there was a selective killing of leukemic cells as compared with the activity towards the normal hemopoietic stem cells (CFU-S)."], "structured": false}
{"doc_id": 27910499, "title": "Quantitative assessment of T-cell repertoire recovery after hematopoietic stem cell transplantation", "abstract": ["Delayed T cell recovery and restricted T cell receptor (TCR) diversity after allogeneic hematopoietic stem cell transplantation (allo-HSCT) are associated with increased risks of infection and cancer relapse.", "Technical challenges have limited faithful measurement of TCR diversity after allo-HSCT.", "Here we combined 5' rapid amplification of complementary DNA ends PCR with deep sequencing to quantify TCR diversity in 28 recipients of allo-HSCT using a single oligonucleotide pair.", "Analysis of duplicate blood samples confirmed that we accurately determined the frequency of individual TCRs.", "After 6 months, cord blood-graft recipients approximated the TCR diversity of healthy individuals, whereas recipients of T cell-depleted peripheral-blood stem cell grafts had 28-fold and 14-fold lower CD4(+) and CD8(+) T cell diversities, respectively.", "After 12 months, these deficiencies had improved for the CD4(+) but not the CD8(+) T cell compartment.", "Overall, this method provides unprecedented views of T cell repertoire recovery after allo-HSCT and may identify patients at high risk of infection or relapse."], "structured": false}
{"doc_id": 27944135, "title": "Silver sulfadiazine for the treatment of partial-thickness burns and venous stasis ulcers.", "abstract": ["BACKGROUND For decades silver-containing antibiotics such as silver sulfadiazine (SSD) have been applied as standard topical therapy for patients with partial-thickness burns and venous stasis ulcers.", "This evidence-based review intends to answer the following research question: in ambulatory patients with partial-thickness burns or stasis dermatitis ulcers, does the use of topical SSD compared with nonantibiotic dressings improve mortality, wound healing, re-epithelialization, or infection rates?   \n", "METHODS MEDLINE, EMBASE, Cochrane Library, and other databases were searched.", "We considered trials that enrolled patients of any age with partial-thickness burns or venous stasis ulcers and randomized them to either topical SSD or placebo, saline-soaked gauze, paraffin gauze, sterile dry dressing, or nonantibiotic moist dressing.", "Outcomes included mortality, wound healing, speed of re-epithelialization, and infection rates.   \n", "RESULTS For burns, our search revealed 400 potential articles.", "No human studies met the inclusion criteria.", "Only 7 animal studies (1 mouse, 4 rat, and 2 pig) were relevant to the proposed question.", "These animal studies provided conflicting results.", "Whereas some support the use of SSD for treatment of partial-thickness burns, others question its effectiveness.", "For stasis dermatitis ulcer, the search identified 50 articles for review, of which 20 abstracts were reviewed, and one article met the inclusion criteria.", "This study did not show any significant improvement in the rate of complete healing in SSD group compared with placebo either at 4 weeks (relative risk 6.2, 95% confidence interval 0.8-48) or at 1 year (relative risk 5.2, 95% confidence interval 0.6-41.6) of follow-up.   \n", "CONCLUSION There is insufficient evidence to either support or refute the routine use of SSD for ambulatory patients with either partial-thickness burns or stasis dermatitis ulcers to decrease mortality, prevent infection, or augment wound healing in human beings."], "structured": true}
{"doc_id": 27949347, "title": "Putting p53 in Context", "abstract": ["TP53 is the most frequently mutated gene in human cancer.", "Functionally, p53 is activated by a host of stress stimuli and, in turn, governs an exquisitely complex anti-proliferative transcriptional program that touches upon a bewildering array of biological responses.", "Despite the many unveiled facets of the p53 network, a clear appreciation of how and in what contexts p53 exerts its diverse effects remains unclear.", "How can we interpret p53's disparate activities and the consequences of its dysfunction to understand how cell type, mutation profile, and epigenetic cell state dictate outcomes, and how might we restore its tumor-suppressive activities in cancer?"], "structured": false}
{"doc_id": 27995781, "title": "Modeling the evolution of culture-adapted human embryonic stem cells.", "abstract": ["The long-term culture of human embryonic stem (ES) cells is inevitably subject to evolution, since any mutant that arises with a growth advantage will be selectively amplified.", "However, the evolutionary influences of population size, mutation rate, and selection pressure are frequently overlooked.", "We have constructed a Monte Carlo simulation model to predict how changes in these factors can influence the appearance and spread of mutant ES cells, and verified its applicability by comparison with in vitro data.", "This simulation provides an estimate for the expected rate of generation of culture-adapted ES cells under different assumptions for the key parameters.", "In particular, it highlights the effect of population size, suggesting that the maintenance of cells in small populations reduces the likelihood that abnormal cultures will develop."], "structured": false}
{"doc_id": 28006126, "title": "CD28 delivers a unique signal leading to the selective recruitment of RelA and p52 NF-kappaB subunits on IL-8 and Bcl-xL gene promoters.", "abstract": ["CD28 is one of the most important costimulatory receptors necessary for full T lymphocyte activation.", "The CD28 receptor can enhance T cell antigen receptor (TCR) signals, as well as deliver independent signals.", "Indeed, CD28 engagement by B7 can generate TCR-independent signals leading to IkappaB kinase and NF-kappaB activation.", "Here we demonstrate that the TCR-independent CD28 signal leads to the selective transcription of survival (Bcl-xL) and inflammatory (IL-8 and B cell activation factor, but not proliferative (IL-2), genes, in a NF-kappaB-dependent manner.", "CD28-stimulated T cells actively secrete IL-8, and Bcl-xL up-regulation protects T cells from radiation-induced apoptosis.", "The transcription of CD28-induced genes is mediated by the specific recruitment of RelA and p52 NF-kappaB subunits to target promoters.", "In contrast, p50 and c-Rel, which preferentially bind NF-kappaB sites on the IL-2 gene promoter after anti-CD3 stimulation, are not involved.", "Thus, we identify CD28 as a key regulator of genes important for both survival and inflammation."], "structured": false}
{"doc_id": 28015516, "title": "Netting neutrophils are major inducers of type I IFN production in pediatric systemic lupus erythematosus.", "abstract": ["Systemic lupus erythematosus (SLE) is a systemic autoimmune disease characterized by a breakdown of tolerance to nuclear antigens and the development of immune complexes.", "Genomic approaches have shown that human SLE leukocytes homogeneously express type I interferon (IFN)-induced and neutrophil-related transcripts.", "Increased production and/or bioavailability of IFN-\u03b1 and associated alterations in dendritic cell (DC) homeostasis have been linked to lupus pathogenesis.", "Although neutrophils have long been shown to be associated with lupus, their potential role in disease pathogenesis remains elusive.", "Here, we show that mature SLE neutrophils are primed in vivo by type I IFN and die upon exposure to SLE-derived anti-ribonucleoprotein antibodies, releasing neutrophil extracellular traps (NETs).", "SLE NETs contain DNA as well as large amounts of LL37 and HMGB1, neutrophil proteins that facilitate the uptake and recognition of mammalian DNA by plasmacytoid DCs (pDCs).", "Indeed, SLE NETs activate pDCs to produce high levels of IFN-\u03b1 in a DNA- and TLR9 (Toll-like receptor 9)-dependent manner.", "Our results reveal an unsuspected role for neutrophils in SLE pathogenesis and identify a novel link between nucleic acid-recognizing antibodies and type I IFN production in this disease."], "structured": false}
{"doc_id": 28017005, "title": "Assessment for selection for the health care professions and specialty training: consensus statement and recommendations from the Ottawa 2010 Conference.", "abstract": ["Assessment for selection in medicine and the health professions should follow the same quality assurance processes as in-course assessment.", "The literature on selection is limited and is not strongly theoretical or conceptual.", "For written testing, there is evidence of the predictive validity of Medical College Admission Test (MCAT) for medical school and licensing examination performance.", "There is also evidence for the predictive validity of grade point average, particularly in combination with MCAT for graduate entry but little evidence about the predictive validity of school leaver scores.", "Interviews have not been shown to be robust selection measures.", "Studies of multiple mini-interviews have indicated good predictive validity and reliability.", "Of other measures used in selection, only the growing interest in personality testing appears to warrant future work.", "Widening access to medical and health professional programmes is an increasing priority and relates to the social accountability mandate of medical and health professional schools.", "While traditional selection measures do discriminate against various population groups, there is little evidence on the effect of non-traditional measures in widening access.", "Preparation and outreach programmes show most promise.", "In summary, the areas of consensus for assessment for selection are small in number.", "Recommendations for future action focus on the adoption of principles of good assessment and curriculum alignment, use of multi-method programmatic approaches, development of interdisciplinary frameworks and utilisation of sophisticated measurement models.", "The social accountability mandate of medical and health professional schools demands that social inclusion, workforce issues and widening of access are embedded in the principles of good assessment for selection."], "structured": false}
{"doc_id": 28025754, "title": "THE GLYOXAL BIS(2-HYDROXYANIL) METHOD MODIFIED FOR LOCALIZING INSOLUBLE CALCIUM SALTS.", "abstract": ["TO enable staining of insoluble calcium salts with glyoxal bis(2-hydroxyanil) (GBHA), the original solution containing 2 ml of 0.4% GBHA in absolute ethanol, and 0.3 ml of aqueous 5% NaOH, and limited to staining only soluble calcium salts, was modified as follows: 1, 2 ml of 0.4% GBHA in absolute ethanol in 0.6 ml of 10% aqueous NaOH; 11, 0.1 gm GBHA in 2 ml of 3.4% NaOH in 75% ethanol.", "To prevent diffusion and loss of calcium, the tissues were processed by the freeze-substitution or freeze-dry method and sections stained without removing the paraffin.", "Modification I is effective only when 1 or 2 drops placed on the section are evaporated gradually to dryness, concentrating the GBHA and NaOH on the insoluble calcium salts.", "Modification II is effective when dried or poured on the the section and allowed to stain for 5 min.", "The stained slides are immersed for 15 min in 90% ethanol saturated with KCN and Na2CO3 for specificity to calcium; rinsed and counterstained in 95% ethanol containing 0.1% each of fast..."], "structured": false}
{"doc_id": 28069701, "title": "Detecting selective sweeps: a new approach based on hidden markov models.", "abstract": ["Detecting and localizing selective sweeps on the basis of SNP data has recently received considerable attention.", "Here we introduce the use of hidden Markov models (HMMs) for the detection of selective sweeps in DNA sequences.", "Like previously published methods, our HMMs use the site frequency spectrum, and the spatial pattern of diversity along the sequence, to identify selection.", "In contrast to earlier approaches, our HMMs explicitly model the correlation structure between linked sites.", "The detection power of our methods, and their accuracy for estimating the selected site location, is similar to that of competing methods for constant size populations.", "In the case of population bottlenecks, however, our methods frequently showed fewer false positives."], "structured": false}
{"doc_id": 28071965, "title": "A Balance between Secreted Inhibitors and Edge Sensing Controls Gastruloid Self-Organization.", "abstract": ["The earliest aspects of human embryogenesis remain mysterious.", "To model patterning events in the human embryo, we used colonies of human embryonic stem cells (hESCs) grown on micropatterned substrate and differentiated with BMP4.", "These gastruloids recapitulate the embryonic arrangement of the mammalian germ layers and provide an assay to assess the structural and signaling mechanisms patterning the human gastrula.", "Structurally, high-density hESCs localize their receptors to transforming growth factor \u03b2 at their lateral side in the center of the colony while maintaining apical localization of receptors at the edge.", "This relocalization insulates cells at the center from apically applied ligands while maintaining response to basally presented ones.", "In addition, BMP4 directly induces the expression of its own inhibitor, NOGGIN, generating a reaction-diffusion mechanism that underlies patterning.", "We develop a quantitative model that integrates edge sensing and inhibitors to predict human fate positioning in gastruloids and, potentially, the human embryo."], "structured": false}
{"doc_id": 28086354, "title": "Tenectin is a novel alphaPS2betaPS integrin ligand required for wing morphogenesis and male genital looping in Drosophila.", "abstract": ["Morphogenesis of the adult structures of holometabolous insects is regulated by ecdysteroids and juvenile hormones and involves cell-cell interactions mediated in part by the cell surface integrin receptors and their extracellular matrix (ECM) ligands.", "These adhesion molecules and their regulation by hormones are not well characterized.", "We describe the gene structure of a newly described ECM molecule, tenectin, and demonstrate that it is a hormonally regulated ECM protein required for proper morphogenesis of the adult wing and male genitalia.", "Tenectin's function as a new ligand of the PS2 integrins is demonstrated by both genetic interactions in the fly and by cell spreading and cell adhesion assays in cultured cells.", "Its interaction with the PS2 integrins is dependent on RGD and RGD-like motifs.", "Tenectin's function in looping morphogenesis in the development of the male genitalia led to experiments that demonstrate a role for PS integrins in the execution of left-right asymmetry."], "structured": false}
{"doc_id": 28107602, "title": "Schedule-dependent interaction between anticancer treatments", "abstract": ["The oncogene MDMX is overexpressed in many cancers, leading to suppression of the tumor suppressor p53.", "Inhibitors of the oncogene product MDMX therefore might help reactivate p53 and enhance the efficacy of DNA-damaging drugs.", "However, we currently lack a quantitative understanding of how MDMX inhibition affects the p53 signaling pathway and cell sensitivity to DNA damage.", "Live cell imaging showed that MDMX depletion triggered two distinct phases of p53 accumulation in single cells: an initial postmitotic pulse, followed by low-amplitude oscillations.", "The response to DNA damage was sharply different in these two phases; in the first phase, MDMX depletion was synergistic with DNA damage in causing cell death, whereas in the second phase, depletion of MDMX inhibited cell death.", "Thus a quantitative understanding of signal dynamics and cellular states is important for designing an optimal schedule of dual-drug administration."], "structured": false}
{"doc_id": 28138927, "title": "Potent, Selective, and Orally Bioavailable Inhibitors of VPS34 Provide Chemical Tools to Modulate Autophagy in Vivo.", "abstract": ["Autophagy is a dynamic process that regulates lysosomal-dependent degradation of cellular components.", "Until recently the study of autophagy has been hampered by the lack of reliable pharmacological tools, but selective inhibitors are now available to modulate the PI 3-kinase VPS34, which is required for autophagy.", "Here we describe the discovery of potent and selective VPS34 inhibitors, their pharmacokinetic (PK) properties, and ability to inhibit autophagy in cellular and mouse models."], "structured": false}
{"doc_id": 28149602, "title": "The role of neutrophils in the pathogenesis of systemic lupus erythematosus.", "abstract": ["PURPOSE OF REVIEW Recent discoveries implicate neutrophils as important regulators of innate and adaptive immunity and in the development of organ damage in systemic autoimmune diseases, including systemic lupus erythematosus (SLE).   ", "RECENT FINDINGS Various putative SLE biomarkers are neutrophil-related, including neutrophil granular proteins and histones undergoing post-translational modifications during neutrophil extracellular trap (NET) formation.", "In the bone marrow, lupus neutrophils can drive B and T cell abnormalities, at least in part, by their enhanced production of type-I interferons, tumor necrosis factor-alpha (TNF\u03b1) and the B-cell stimulating factors B-cell activating factor (BAFF) and a proliferation-inducing ligand (APRIL).", "Lupus neutrophils and, in particular, lupus low-density granulocytes (a distinct pathogenic subset) display epigenetic modifications and genomic alterations that may be relevant to their deleterious roles in SLE.", "Proteins and enzymes externalized by lupus NETs can affect vascular health by inducing endothelial apoptosis and oxidizing lipoproteins.", "Hampering NET formation through peptidylarginine deiminase inhibitors abrogates lupus phenotype and atherosclerosis in murine studies.   ", "SUMMARY Recent discoveries support the notion that neutrophils, low-density granulocytes and aberrant NET formation and clearance play important roles in lupus pathogenesis.", "Future studies should focus on how to selectively target these immunostimulatory pathways in this disease."], "structured": true}
{"doc_id": 28164534, "title": "Enhancement of proteasome function by PA28\u03b1 overexpression protects against oxidative stress.", "abstract": ["The principal function of the proteasome is targeted degradation of intracellular proteins.", "Proteasome dysfunction has been observed in experimental cardiomyopathies and implicated in human congestive heart failure.", "Measures to enhance proteasome proteolytic function are currently lacking but would be beneficial in testing the pathogenic role of proteasome dysfunction and could have significant therapeutic potential.", "The association of proteasome activator 28 (PA28) with the 20S proteasome may play a role in antigen processing.", "It is unclear, however, whether the PA28 plays any important role outside of antigen presentation, although up-regulation of PA28 has been observed in certain types of cardiomyopathy.", "Here, we show that PA28\u03b1 overexpression (PA28\u03b1OE) stabilized PA28\u03b2, increased 11S proteasomes, and enhanced the degradation of a previously validated proteasome surrogate substrate (GFPu) in cultured neonatal rat cardiomyocytes.", "PA28\u03b1OE significantly attenuated H(2)O(2)-induced increases in the protein carbonyls and markedly suppressed apoptosis in cultured cardiomyocytes under basal conditions or when stressed by H(2)O(2).", "We conclude that PA28\u03b1OE is sufficient to up-regulate 11S proteasomes, enhance proteasome-mediated removal of misfolded and oxidized proteins, and protect against oxidative stress in cardiomyocytes, providing a highly sought means to increase proteasomal degradation of abnormal cellular proteins."], "structured": false}
{"doc_id": 28193026, "title": "A unified concept of species and its consequences for the future of taxonomy", "abstract": ["Contemporary species concepts are diverse.", "Nonetheless, all share the fundamental idea that species are segments of lineages at the population level of biological organization.", "They differ in the secondary properties (e.g., intrinsic reproductive isolation, monophyly, diagnosability) that are treated as necessary for considering lineages to be species.", "A unified species concept can be achieved by interpreting the common fundamental idea of being a separately evolving lineage segment as the only necessary property of species and viewing the various secondary properties either as lines of evidence relevant to assessing lineage separation or as properties that define different subcategories of the species category (e.g., reproductively isolated species, monophyletic species, diagnosable species).", "This unified species concept has a number of consequences for taxonomy, including the need to acknowledge that undifferentiated and undiagnosable lineages are species, that species can fuse, that species can be nested within other species, that the species category is not a taxonomic rank, and that new taxonomic practices and conventions are needed to accommodate these conclusions.", "Although acceptance of a unified species concept has some radical consequences for taxonomy, it also reflects a change in the general conceptualization of the species category that has been underway for more than a half-century \u2014 a shift from viewing the species category as one member of the hierarchy of taxonomic ranks to viewing it as a natural kind whose members are the units at one of the levels of biological organization.", "This change is related to a more general shift in the primary concern of the discipline of systematics (including taxonomy), from the utilitarian activity of classifying organisms to the scientific activity of testing hypotheses about lineage boundaries and phylogenetic relationships.", "The unified species concept is a natural outcome of this conceptual shift and represents the more complete acceptance of the idea that species are one of the fundamental units of biology.", "As such, the unified species concept is central to the future of taxonomy."], "structured": false}
{"doc_id": 28195565, "title": "Regulation of the small GTP-binding protein Rho by cell adhesion and the cytoskeleton.", "abstract": ["Soluble factors from serum such as lysophosphatidic acid (LPA) are thought to activate the small GTP-binding protein Rho based on their ability to induce actin stress fibers and focal adhesions in a Rho-dependent manner.", "Cell adhesion to extracellular matrices (ECM) has also been proposed to activate Rho, but this point has been controversial due to the difficulty of distinguishing changes in Rho activity from the structural contributions of ECM to the formation of focal adhesions.", "To address these questions, we established an assay for GTP-bound cellular Rho.", "Plating Swiss 3T3 cells on fibronectin-coated dishes elicited a transient inhibition of Rho, followed by a phase of Rho activation.", "The activation phase was greatly enhanced by serum.", "In serum-starved adherent cells, LPA induced transient Rho activation, whereas in suspended cells Rho activation was sustained.", "Furthermore, suspended cells showed higher Rho activity than adherent cells in the presence of serum.", "These data indicate the existence of an adhesion-dependent negative-feedback loop.", "We also observed that both cytochalasin D and colchicine trigger Rho activation despite their opposite effects on stress fibers and focal adhesions.", "Our results show that ECM, cytoskeletal structures and soluble factors all contribute to regulation of Rho activity."], "structured": false}
{"doc_id": 28206748, "title": "Core binding factors are necessary for natural killer cell development and cooperate with Notch signaling during T-cell specification.", "abstract": ["CBFbeta is the non-DNA binding subunit of the core binding factors (CBFs).", "Mice with reduced CBFbeta levels display profound, early defects in T-cell but not B-cell development.", "Here we show that CBFbeta is also required at very early stages of natural killer (NK)-cell development.", "We also demonstrate that T-cell development aborts during specification, as the expression of Gata3 and Tcf7, which encode key regulators of T lineage specification, is substantially reduced, as are functional thymic progenitors.", "Constitutively active Notch or IL-7 signaling cannot restore T-cell expansion or differentiation of CBFbeta insufficient cells, nor can overexpression of Runx1 or CBFbeta overcome a lack of Notch signaling.", "Therefore, the ability of the prethymic cell to respond appropriately to Notch is dependent on CBFbeta, and both signals converge to activate the T-cell developmental program."], "structured": false}
{"doc_id": 28207326, "title": "VEGF and podocytes in diabetic nephropathy.", "abstract": ["Vascular endothelial growth factor-A (VEGF-A) is a protein secreted by podocytes that is necessary for survival of endothelial cells, podocytes, and mesangial cells.", "VEGF-A regulates slit-diaphragm signaling and podocyte shape via VEGF-receptor 2-nephrin-nck-actin interactions.", "Chronic hyperglycemia-induced excess podocyte VEGF-A and low endothelial nitric oxide drive the development and the progression of diabetic nephropathy.", "The abnormal cross-talk between VEGF-A and nitric oxide pathways is fueled by the diabetic milieu, resulting in increased oxidative stress.", "Recent findings on these pathogenic molecular mechanisms provide new potential targets for therapy for diabetic renal disease."], "structured": false}
{"doc_id": 28230867, "title": "Detection and distribution patterns of telomerase activity in insects.", "abstract": ["Telomeres of most insects consist of pentanucleotide (TTAGG)n repeats, although the repeats are absent in Diptera and some other insect species, where the telomere regions are perhaps maintained without telomerase.", "To understand various and unusual telomere formation in insects, we have studied the characteristic features of a putative insect telomerase that has not been previously described.", "Using a modified telomeric repeat amplification protocol (TRAP), we first detected the telomerase activity in crickets, cockroaches and two Lepidopteran insects.", "The telomerase from crickets and cockroaches required dATP, dGTP and dTTP but not dCTP as a substrate and sequence analyses of the products of TRAP revealed that the (TTAGG)n repeats are synthesized by telomerase.", "The cockroach telomerase was detected both in somatic (fat body, muscle and neural tissues) and germ line (testis) cells, suggesting that expression of this enzyme is not regulated in a tissue-specific manner at an adult stage.", "While we detected high levels of telomerase activity in crickets and cockroaches, we could not detect activity in all tissues and cell cultures of the silkworm, Bombyx mori and in two Drosophila and one Sarcophaga cell lines.", "This supports the theory that Dipteran insects maintain their telomeres without telomerase."], "structured": false}
{"doc_id": 28243325, "title": "Conversion of the lac repressor into an allosterically regulated transcriptional activator for mammalian cells.", "abstract": ["A novel mammalian regulatory system was created by using the Escherichia coli lac repressor.", "The lac repressor was converted into a mammalian transcriptional activator by modifying the lac repressor coding region to include a nuclear localization signal from the simian virus 40 (SV40) large tumor antigen and the transcription activation domain from the herpes simplex virus type 1 virion protein 16.", "The lac activator protein (LAP) fusions were potent activators of several promoters containing lac operator sequences positioned either upstream or downstream of the transcription unit.", "A single lac operator allowed for transactivation, whereas multiple operators acted synergistically when separated by a small distance.", "Promoters containing 14 or 21 operator sequences were induced at least 1,000-fold in response to LAP, reaching levels of activity 20 to 30 times greater than that of the SV40 early promoter in HeLa cells.", "Activation was strongly inhibited by isopropyl-beta-D-thiogalactoside (IPTG), indicating that LAP retained the functions needed for allosteric regulation.", "LAP was bifunctional, also acting as a repressor of expression of an SV40 promoter containing an operator immediately downstream of the TATA box.", "Finally, genetic selection schemes were developed such that LAP-expressing cell lines can be generated at high frequency from either established or primary cells in culture."], "structured": false}
{"doc_id": 28247027, "title": "Antigen availability determines CD8\u207a T cell-dendritic cell interaction kinetics and memory fate decisions.", "abstract": ["T cells are activated by antigen (Ag)-bearing dendritic cells (DCs) in lymph nodes in three phases.", "The duration of the initial phase of transient, serial DC-T cell interactions is inversely correlated with Ag dose.", "The second phase, characterized by stable DC-T cell contacts, is believed to be necessary for full-fledged T cell activation.", "Here we have shown that this is not the case.", "CD8\u207a T cells interacting with DCs presenting low-dose, short-lived Ag did not transition to phase 2, whereas higher Ag dose yielded phase 2 transition.", "Both antigenic constellations promoted T cell proliferation and effector differentiation but yielded different transcriptome signatures at 12 hr and 24 hr.", "T cells that experienced phase 2 developed long-lived memory, whereas conditions without stable contacts yielded immunological amnesia.", "Thus, T cells make fate decisions within hours after Ag exposure, resulting in long-term memory or abortive effector responses, correlating with T cell-DCs interaction kinetics."], "structured": false}
{"doc_id": 28249680, "title": "BAX/BAK-independent mitoptosis during cell death induced by proteasome inhibition?", "abstract": ["Proteasome inhibitors induce rapid death of cancer cells.", "We show that in epithelial cancer cells, such death is associated with dramatic and simultaneous up-regulation of several BH3-only proteins, including BIK, BIM, MCL-1S, NOXA, and PUMA, as well as p53.", "Elevated levels of these proteins seem to be the result of direct inhibition of their proteasomal degradation, induction of transcription, and active translation.", "Subsequent cell death is independent of BAX, and probably BAK, and proceeds through the intrinsic mitochondrial apoptosis pathway.", "We identify the cascade of molecular events responsible for cell death induced by a prototypical proteasome inhibitor, MG132, starting with rapid accumulation of BH3-only proteins in the mitochondria, proceeding through mitochondrial membrane permeabilization and subsequent loss of DeltaPsi(m), and leading to irreversible changes of mitochondrial ultrastructure, degradation of mitochondrial network, and detrimental impairment of crucial mitochondrial functions.", "Our results also establish a rationale for the broader use of proteasome inhibitors to kill apoptosis-resistant tumor cells that lack functional BAX/BAK proteins."], "structured": false}
{"doc_id": 28264919, "title": "Site of action of a ribosomal RNA methylase responsible for resistance to erythromycin and other antibiotics.", "abstract": ["The enzyme which confers resistance to erythromycin in the producing organism Streptomyces erythraeus dimethylates a single adenine residue in Bacillus stearothermophilus 23 S rRNA.", "This corresponds to residue Ade 2058 in Escherichia coli 23 S RNA.", "The methylase responsible for resistance to macrolides, lincomycin, and streptogramin B-related antibiotics in Staphylococcus aureus also acts at this site."], "structured": false}
{"doc_id": 28271439, "title": "53BP1 nuclear bodies form around DNA lesions generated by mitotic transmission of chromosomes under replication stress", "abstract": ["Completion of genome duplication is challenged by structural and topological barriers that impede progression of replication forks.", "Although this can seriously undermine genome integrity, the fate of DNA with unresolved replication intermediates is not known.", "Here, we show that mild replication stress increases the frequency of chromosomal lesions that are transmitted to daughter cells.", "Throughout G1, these lesions are sequestered in nuclear compartments marked by p53-binding protein 1 (53BP1) and other chromatin-associated genome caretakers.", "We show that the number of such 53BP1 nuclear bodies increases after genetic ablation of BLM, a DNA helicase associated with dissolution of entangled DNA.", "Conversely, 53BP1 nuclear bodies are partially suppressed by knocking down SMC2, a condensin subunit required for mechanical stability of mitotic chromosomes.", "Finally, we provide evidence that 53BP1 nuclear bodies shield chromosomal fragile sites sequestered in these compartments against erosion.", "Together, these data indicate that restoration of DNA or chromatin integrity at loci prone to replication problems requires mitotic transmission to the next cell generations."], "structured": false}
{"doc_id": 28334217, "title": "Targeted inhibition of tumor-specific glutaminase diminishes cell-autonomous tumorigenesis.", "abstract": ["Glutaminase (GLS), which converts glutamine to glutamate, plays a key role in cancer cell metabolism, growth, and proliferation.", "GLS is being explored as a cancer therapeutic target, but whether GLS inhibitors affect cancer cell-autonomous growth or the host microenvironment or have off-target effects is unknown.", "Here, we report that loss of one copy of Gls blunted tumor progression in an immune-competent MYC-mediated mouse model of hepatocellular carcinoma.", "Compared with results in untreated animals with MYC-induced hepatocellular carcinoma, administration of the GLS-specific inhibitor bis-2-(5-phenylacetamido-1,3,4-thiadiazol-2-yl)ethyl sulfide (BPTES) prolonged survival without any apparent toxicities.", "BPTES also inhibited growth of a MYC-dependent human B cell lymphoma cell line (P493) by blocking DNA replication, leading to cell death and fragmentation.", "In mice harboring P493 tumor xenografts, BPTES treatment inhibited tumor cell growth; however, P493 xenografts expressing a BPTES-resistant GLS mutant (GLS-K325A) or overexpressing GLS were not affected by BPTES treatment.", "Moreover, a customized Vivo-Morpholino that targets human GLS mRNA markedly inhibited P493 xenograft growth without affecting mouse Gls expression.", "Conversely, a Vivo-Morpholino directed at mouse Gls had no antitumor activity in vivo.", "Collectively, our studies demonstrate that GLS is required for tumorigenesis and support small molecule and genetic inhibition of GLS as potential approaches for targeting the tumor cell-autonomous dependence on GLS for cancer therapy."], "structured": false}
{"doc_id": 28338268, "title": "Dominant optic atrophy, deafness, ptosis, ophthalmoplegia, dystaxia, and myopathy. A new syndrome.", "abstract": ["Twenty-three members of a 96-member family exhibited an autosomal dominant disorder which has not previously been described.", "This disorder involves progressive optic atrophy, abnormal electroretinography without retinal pigment changes, and progressive sensorineural hearing loss usually evident in the first or second decade of life.", "In midlife, ptosis, ophthalmoplegia, dystaxia, and a nonspecific myopathy occur."], "structured": false}
{"doc_id": 28369117, "title": "Dynein is required for polarized dendritic transport and uniform microtubule orientation in axons", "abstract": ["Axons and dendrites differ in both microtubule organization and in the organelles and proteins they contain.", "Here we show that the microtubule motor dynein has a crucial role in polarized transport and in controlling the orientation of axonal microtubules in Drosophila melanogaster dendritic arborization (da) neurons.", "Changes in organelle distribution within the dendritic arbors of dynein mutant neurons correlate with a proximal shift in dendritic branch position.", "Dynein is also necessary for the dendrite-specific localization of Golgi outposts and the ion channel Pickpocket.", "Axonal microtubules are normally oriented uniformly plus-end-distal; however, without dynein, axons contain both plus- and minus-end distal microtubules.", "These data suggest that dynein is required for the distinguishing properties of the axon and dendrites: without dynein, dendritic organelles and proteins enter the axon and the axonal microtubules are no longer uniform in polarity."], "structured": false}
{"doc_id": 28386343, "title": "Small molecule screening in human induced pluripotent stem cell-derived terminal cell types.", "abstract": ["A need for better clinical outcomes has heightened interest in the use of physiologically relevant human cells in the drug discovery process.", "Patient-specific human induced pluripotent stem cells may offer a relevant, robust, scalable, and cost-effective model of human disease physiology.", "Small molecule high throughput screening in human induced pluripotent stem cell-derived cells with the intent of identifying novel therapeutic compounds is starting to influence the drug discovery process; however, the use of these cells presents many high throughput screening development challenges.", "This technology has the potential to transform the way drug discovery is performed."], "structured": false}
{"doc_id": 28390999, "title": "Gene expression during gonadogenesis in the chicken embryo.", "abstract": ["Genes implicated in vertebrate sex determination and differentiation were studied in embryonic chicken gonads using reverse transcription and the polymerase chain reaction (RT-PCR).", "Expression profiles were obtained during gonadal sex differentiation for AMH, SOX9, SOX3, the Wilm's Tumour gene, WT1, and the orphan nuclear receptor genes, SF1 and DAX1.", "Some of these genes showed sexually dimorphic expression profiles during gonadal development, whereas others were expressed at similar levels in both sexes.", "The gene encoding Anti-M\u00fcllerian hormone (AMH) was expressed in both sexes prior to and during sexual differentiation of the gonads, with levels of expression consistently higher in males than in females.", "SOX9 expression was male-specific, and was up-regulated after the detection of AMH transcripts.", "SOX3 expression was observed prior to clear SOX9 expression and was up-regulated in both sexes at the onset of gonadal sex differentiation (but declined later in development).", "The WT1 gene was highly expressed in both sexes, whereas SF1 expression was clearly higher in developing ovaries compared to testes.", "DAX1 transcripts were observed in both sexes at all stages examined, but expression appeared somewhat higher in developing ovaries.", "These expression profiles are analysed in terms of current theories of vertebrate sex determination."], "structured": false}
{"doc_id": 28392393, "title": "Organ-resident, nonlymphoid cells suppress proliferation of autoimmune T-helper lymphocytes.", "abstract": ["Local presentation of autoantigen by organ-resident cells inappropriately expressing Ia determinants has been implicated in organ-specific autoimmunity.", "Experimental autoimmune uveoretinitis, induced in rats by immunization with retinal soluble antigen, is used as a model of organ-specific autoimmunity.", "In an in vitro system derived from this model, uveitogenic rat T-helper lymphocytes specific to the retinal soluble antigen, or control T-helper lymphocytes reactive to the purified protein derivative of tuberculin, were cocultured with Ia-expressing syngeneic retinal glial cells (M\u00fcller cells) in the presence of specific antigen.", "Antigen presentation was not apparent under ordinary culture conditions, and the M\u00fcller cells profoundly suppressed the proliferative response of primed T-helper lymphocytes to antigen presented on conventional antigen-presenting cells, as well as their subsequent interleukin-2 (IL-2)-dependent expansion.", "Suppression of proliferation was accompanied by inhibition of IL-2 production in response to antigen, as well as by reduction in high-affinity IL-2 receptor expression, and proceeded via a contact-dependent mechanism.", "These results suggest a role for locally acting suppression mechanisms in immune regulation and maintenance of tissue homeostasis."], "structured": false}
{"doc_id": 28419824, "title": "Drug induced refractory headache--clinical features and management.", "abstract": ["Two hundred patients who were taking daily symptomatic or immediate relief medications, often in excessive quantities, yet suffering from daily or near daily severe headaches were studied.", "One hundred and sixteen (58%) of them were also taking concomitant prophylactic medications and they were ineffective.", "Low tyramine, low caffeine dietary instructions and biofeedback training were given to all patients.", "The effect of continuing symptomatic medications, discontinuing symptomatic medications, and adding or changing prophylactic medications were studied in the various treatment groups.", "It is concluded that; 1.)", "Daily use of symptomatic or immediate relief medications result in chronic daily headache.", "2.) Discontinuing daily symptomatic medications itself result in improvement of headache.", "3.)", "Concomitant use of symptomatic medications nullifies the effect of prophylactic medications.", "4.) Discontinuing daily symptomatic medications enhances the beneficial effect of prophylactic medications."], "structured": false}
{"doc_id": 28436879, "title": "Neuromodulation of neurons and synapses.", "abstract": ["Neuromodulation underlies the flexibility of neural circuit operation and behavior.", "Individual neuromodulators can have divergent actions in a neuron by targeting multiple physiological mechanisms.", "Conversely, multiple neuromodulators may have convergent actions through overlapping targets.", "The divergent and convergent neuromodulator actions can be unambiguously synergistic or antagonistic, but neuromodulation often entails balanced adjustment of nonlinear membrane and synaptic properties by targeting ion channel and synaptic dynamics rather than just excitability or synaptic strength.", "In addition, neuromodulators can exert effects at multiple timescales, from short-term adjustments of neuron and synapse function to persistent long-term regulation.", "This short review summarizes some highlights of the diverse actions of neuromodulators on ion channel and synaptic properties."], "structured": false}
{"doc_id": 28441310, "title": "Mutation frequency and specificity with age in liver, bladder and brain of lacI transgenic mice.", "abstract": ["Mutation frequency and specificity were determined as a function of age in nuclear DNA from liver, bladder, and brain of Big Blue lacI transgenic mice aged 1.5-25 months.", "Mutations accumulated with age in liver and accumulated more rapidly in bladder.", "In the brain a small initial increase in mutation frequency was observed in young animals; however, no further increase was observed in adult mice.", "To investigate the origin of mutations, the mutational spectra for each tissue and age were determined.", "DNA sequence analysis of mutant lacI transgenes revealed no significant changes in mutational specificity in any tissue at any age.", "The spectra of mutations found in aging animals were identical to those in younger animals, suggesting that they originated from a common set of DNA lesions manifested during DNA replication.", "The data also indicated that there were no significant age-related mutational changes due to oxidative damage, or errors resulting from either changes in the fidelity of DNA polymerase or the efficiency of DNA repair.", "Hence, no evidence was found to support hypotheses that predict that oxidative damage or accumulation of errors in nuclear DNA contributes significantly to the aging process, at least in these three somatic tissues."], "structured": false}
{"doc_id": 28468276, "title": "Breaching the basement membrane: who, when and how?", "abstract": ["The basement membrane (BM), a specialized network of extracellular matrix macromolecules, surrounds epithelial, endothelial, muscle, fat and nerve cells.", "During development, immune surveillance and disease states ranging from cancer to fibrosis, host cells penetrate the BM by engaging tissue-invasive programs, the identity of which remain largely undefined.", "Although it is commonly assumed that all cells employ similar mechanisms to cross BM barriers, accumulating evidence indicates that cells might selectively mobilize protease-dependent or -independent invasion programs.", "New data indicate that protease-dependent transmigration is largely reliant on a group of membrane-anchored metalloenzymes, termed the membrane-type matrix metalloproteinases, which irreversibly remodel BM structure.", "By contrast, mechanisms that enable protease-independent transmigration remain undefined and potentially involve the reversible disassembly of the BM network.", "Further characterization of the molecular mechanisms underlying BM transmigration should provide important insights into pathophysiologic tissue remodeling events and also enable the development of novel therapeutics."], "structured": false}
{"doc_id": 28517384, "title": "Soluble MD-2 is an acute-phase protein and an opsonin for Gram-negative bacteria.", "abstract": ["Myeloid differentiation factor-2 (MD-2) is a lipopolysaccharide (LPS)-binding protein usually coexpressed with and binding to Toll-like receptor 4 (TLR4), conferring LPS responsiveness of immune cells.", "MD-2 is also found as a soluble protein.", "Soluble MD-2 (sMD-2) levels are markedly elevated in plasma from patients with severe infections, and in other fluids from inflamed tissues.", "We show that sMD-2 is a type II acute-phase protein.", "Soluble MD-2 mRNA and protein levels are up-regulated in mouse liver after the induction of an acute-phase response.", "It is secreted by human hepatocytic cells and up-regulated by interleukin-6.", "Soluble MD-2 binds to Gram-negative but not Gram-positive bacteria, and sMD-2 secreted by hepatocytic cells is an essential cofactor for the activation of TLR4-expressing cells by Gram-negative bacteria.", "Soluble MD-2 opsonization of Gram-negative bacteria accelerates and enhances phagocytosis, principally by polymorphonuclear neutrophils.", "In summary, our results demonstrate that sMD-2 is a newly recognized type II acute-phase reactant, an opsonin for Gram-negative bacteria, and a cofactor essential for the activation of TLR4-expressing cells.", "This suggests that sMD-2 plays a key role in the host innate immune response to Gram-negative infections."], "structured": false}
{"doc_id": 28530299, "title": "Division-coupled astrocytic differentiation and age-related depletion of neural stem cells in the adult hippocampus.", "abstract": ["Production of new neurons in the adult hippocampus decreases with age; this decline may underlie age-related cognitive impairment.", "Here we show that continuous depletion of the neural stem cell pool, as a consequence of their division, may contribute to the age-related decrease in hippocampal neurogenesis.", "Our results indicate that adult hippocampal stem cells, upon exiting their quiescent state, rapidly undergo a series of asymmetric divisions to produce dividing progeny destined to become neurons and subsequently convert into mature astrocytes.", "Thus, the decrease in the number of neural stem cells is a division-coupled process and is directly related to their production of new neurons.", "We present a scheme of the neurogenesis cascade in the adult hippocampus that includes a proposed \"disposable stem cell\" model and accounts for the disappearance of hippocampal neural stem cells, the appearance of new astrocytes, and the age-related decline in the production of new neurons."], "structured": false}
{"doc_id": 28542402, "title": "P19 embryonal carcinoma cells.", "abstract": ["P19 cells are a line of pluripotent embryonal carcinoma able to grow continuously in serum-supplemented media.", "The differentiation of these cells can be controlled by nontoxic drugs.", "Retinoic acid effectively induces the development of neurons, astroglia and microglia--cell types normally derived from the neuroectoderm.", "Aggregates of P19 cells exposed to dimethyl sulfoxide differentiate into endodermal and mesodermal derivatives including cardiac and skeletal muscle.", "P19 cells can be effectively transfected with DNA encoding recombinant genes and stable lines expressing these genes can be readily isolated.", "These manipulations make P19 cells suitable material for investigating the molecular mechanisms governing developmental decision made by differentiating pluripotent cells."], "structured": false}
{"doc_id": 28562710, "title": "Iguanas and Salmonella marina infection in children: a reflection of the increasing incidence of reptile-associated salmonellosis in the United States.", "abstract": ["OBJECTIVE To investigate clinical aspects and risk factors for Salmonella serotype Marina infection in the United States.   \n", "METHODS We identified all isolates of S Marina reported in 1994 to the National Salmonella Surveillance System.", "Patients were interviewed about demographic information, clinical course, diet, travel history, and contact with reptiles before illness.   \n", "RESULTS Twenty-six (81%) of 32 patients were infants (<1 year of age) and 24 (75%) were male.", "This differs from other Salmonella isolates reported to the Centers for Disease Control and Prevention in 1994, of which 14% were from infants and 49% from male patients.", "Eleven patients (34%) were hospitalized for a median of 3.5 days (range: 2 to 21 days), and 1 died.", "Of 28 patients (88%) with reported iguana exposure, only 4 (14%) touched the reptile, and only 12 respondents (43%) realized that it might have been the source of infection.", "Seven (32%) of 22 families who owned an iguana at the time of illness continued to own an iguana when contacted a median of 28 weeks later.", "Persons who thought that the iguana was the source of infection were more likely to have given away or sold the pet than those who did not.", "Four isolates (13%) were from blood.", "Bacteremia was associated with taking antibiotics during the 30 days before S Marina infection (odds ratio: 24; 95% confidence interval: 1.2-1309).   \n", "CONCLUSION S Marina infection is a potentially serious illness associated with iguana exposure, and it reflects the larger problem of reptile-associated salmonellosis.", "Many parents do not know that owning an iguana puts their children at risk for Salmonella infection.", "Pediatricians, veterinarians, and pet store owners should inform their patients and customers of the potential risks of owning reptiles and provide appropriate preventive education."], "structured": true}
{"doc_id": 28592273, "title": "Siblings with opposite chromosome constitutions, dup(2q)/del(7q) and del(2q)/dup(7q).", "abstract": ["Chromosome 7q36 microdeletion syndrome is a rare genomic disorder characterized by underdevelopment of the brain, microcephaly, anomalies of the sex organs, and language problems.", "Developmental delay, intellectual disability, autistic spectrum disorders, BDMR syndrome, and unusual facial morphology are the key features of the chromosome 2q37 microdeletion syndrome.", "A genetic screening for two brothers with global developmental delay using high-resolution chromosomal analysis and subtelomeric multiplex ligation-dependent probe amplification revealed subtelomeric rearrangements on the same sites of 2q37.2 and 7q35, with reversed deletion and duplication.", "Both of them showed dysmorphic facial features, severe disability of physical and intellectual development, and abnormal genitalia with differential abnormalities in their phenotypes.", "The family did not have abnormal genetic phenotypes.", "According to the genetic analysis of their parents, adjacent-1 segregation from their mother's was suggested as a mechanism of their gene mutation.", "By comparing the phenotypes of our patients with previous reports on similar patients, we tried to obtain the information of related genes and their chromosomal locations."], "structured": false}
{"doc_id": 28598374, "title": "Methods for quantifying follicular numbers within the mouse ovary.", "abstract": ["Accurate estimation of the number of ovarian follicles at various stages of development is an important indicator of the process of folliculogenesis in relation to the endocrine signals and paracrine/autocrine mechanisms that control the growth and maturation of the oocytes and their supporting follicular cells.", "There are 10-fold or greater differences in follicular numbers per ovary at similar ages and/or strains reported in earlier studies using various methods, leading to difficulties with interpretation of ovarian function in control vs experimental conditions.", "This study describes unbiased, assumption-free stereological methods for quantification of early and growing follicular numbers in the mouse ovary.", "A fractionator approach was used to sample a defined fraction of histological sections of adult wild-type ovaries.", "Primordial and primary follicles were counted independently with the optical and physical disector methods.", "The fractionator/disector methods, which are independent of follicular size or shape, gave estimations of 1930 +/-", "286 (S.E.M.) and 2227 +/-", "101 primordial follicles, and 137 +/-", "25 and 265 +/-", "32 primary follicles per ovary at 70 and 100 days of age respectively.", "From exact counts on serial sections, secondary and later follicular numbers at 100 days of age were estimated at 135 per ovary.", "Remnants of zona pellucidae (a marker of previous follicular atresia) were estimated using a fractionator/physical disector approach and were approximately 500 per ovary.", "The application of the quantitative methods described will facilitate an improved understanding of follicular dynamics and the factors that mediate their growth and maturation and allow for a better comparison between different studies."], "structured": false}
{"doc_id": 28614776, "title": "Identification of functional cooperative mutations of SETD2 in human acute leukemia", "abstract": ["Acute leukemia characterized by chromosomal rearrangements requires additional molecular disruptions to develop into full-blown malignancy, yet the cooperative mechanisms remain elusive.", "Using whole-genome sequencing of a pair of monozygotic twins discordant for MLL (also called KMT2A) gene\u2013rearranged leukemia, we identified a transforming MLL-NRIP3 fusion gene and biallelic mutations in SETD2 (encoding a histone H3K36 methyltransferase).", "Moreover, loss-of-function point mutations in SETD2 were recurrent (6.2%) in 241 patients with acute leukemia and were associated with multiple major chromosomal aberrations.", "We observed a global loss of H3K36 trimethylation (H3K36me3) in leukemic blasts with mutations in SETD2.", "In the presence of a genetic lesion, downregulation of SETD2 contributed to both initiation and progression during leukemia development by promoting the self-renewal potential of leukemia stem cells.", "Therefore, our study provides compelling evidence for SETD2 as a new tumor suppressor.", "Disruption of the SETD2-H3K36me3 pathway is a distinct epigenetic mechanism for leukemia development."], "structured": false}
{"doc_id": 28617573, "title": "Evidence regarding human papillomavirus testing in secondary prevention of cervical cancer.", "abstract": ["More than ever, clinicians need regularly updated reviews given the continuously increasing amount of new information regarding innovative cervical cancer prevention methods.", "A summary is given from recent meta-analyses and systematic reviews on 3 possible clinical applications of human papillomavirus (HPV) testing: triage of women with equivocal or low-grade cytologic abnormalities; prediction of the therapeutic outcome after treatment of cervical intraepithelial neoplasia (CIN) lesions, and last not but not least, primary screening for cervical cancer and pre-cancer.", "Consistent evidence is available indicating that HPV-triage with the Hybrid Capture(\u00ae) 2 assay (Qiagen Gaithersburg, Inc., MD, USA [previously Digene Corp.] (HC2) is more accurate (higher sensitivity, similar specificity) than repeat cytology to triage women with equivocal Pap smear results.", "Several other tests show at least similar accuracy but mRNA testing with the APTIMA(\u00ae) (Gen-Probe Inc., San Diego, CA, USA) test is similarly sensitive but more specific compared to HC2.", "In triage of low-grade squamous intraepithelial lesions (LSIL), HC2 is more sensitive but its specificity is substantially lower compared to repeat cytology.", "The APTIMA(\u00ae) test is more specific than HC2 without showing a loss in sensitivity.", "Identification of DNA of HPV types 16 and/or 18, or RNA from the five most carcinogenic HPV types allow selecting women at highest risk for CIN3+ but the sensitivity and negative predictive value of these markers are lower than full-range high-risk HPV (hrHPV) testing.", "After conservative treatment of cervical pre-cancer, HPV testing picks up more quickly, with higher sensitivity and not lower specificity, residual or recurrent high-grade CIN than follow-up cytology.", "Primary screening for hrHPV generally detects more CIN2, CIN3 or cancer compared to cytology at cut-off atypical squamous cells of undetermined significance (ASC-US) or LSIL, but is less specific.", "Combined HPV and cytology screening provides a further small gain in sensitivity at the expense of a considerable loss in specificity if positive by either test is referred to colposcopy, in comparison with HPV testing only.", "Randomised trials and follow-up of cohort studies consistently demonstrate a significantly lower cumulative incidence of CIN3+ and even of cancer, in women aged 30 years or older, who were at enrollment hrHPV DNA negative compared to those who were cytologically negative.", "The difference in cumulative risk of CIN3+ or cancer for double negative (cytology & HPV) versus only HPV-negative women is small.", "HC2, GP5+/6+ PCR (polymerase chain reaction), cobas(\u00ae) 4800 PCR (Roche Molecular Systems Inc., Alameda, CA, USA) and Real Time PCR (Abbott Molecular, Des Plaines, IL, USA) can be considered as clinically validated for use in primary screening.", "The loss in specificity associated with primary HPV-based screening can be compensated by appropriate algorithms involving reflex cytology and/or HPV genotyping for HPV16 or 18.", "There exists a substantial evidence base to support that HPV testing is advantageous both in triage of women with equivocal abnormal cytology, in surveillance after treatment of CIN lesions and in primary screening of women aged 30 years or older.", "However, the possible advantages offered by HPV-based screening require a well organised program with good compliance with screening and triage policies.", "This article forms part of a special supplement entitled \"Comprehensive Control of HPV Infections and Related Diseases\" Vaccine Volume 30, Supplement 5, 2012."], "structured": false}
{"doc_id": 28633594, "title": "International standards for fetal growth based on serial ultrasound measurements: the Fetal Growth Longitudinal Study of the INTERGROWTH-21st Project.", "abstract": ["BACKGROUND In 2006, WHO produced international growth standards for infants and children up to age 5 years on the basis of recommendations from a WHO expert committee.", "Using the same methods and conceptual approach, the Fetal Growth Longitudinal Study (FGLS), part of the INTERGROWTH-21(st) Project, aimed to develop international growth and size standards for fetuses.   \n", "METHODS The multicentre, population-based FGLS assessed fetal growth in geographically defined urban populations in eight countries, in which most of the health and nutritional needs of mothers were met and adequate antenatal care was provided.", "We used ultrasound to take fetal anthropometric measurements prospectively from 14 weeks and 0 days of gestation until birth in a cohort of women with adequate health and nutritional status who were at low risk of intrauterine growth restriction.", "All women had a reliable estimate of gestational age confirmed by ultrasound measurement of fetal crown-rump length in the first trimester.", "The five primary ultrasound measures of fetal growth--head circumference, biparietal diameter, occipitofrontal diameter, abdominal circumference, and femur length--were obtained every 5 weeks (within 1 week either side) from 14 weeks to 42 weeks of gestation.", "The best fitting curves for the five measures were selected using second-degree fractional polynomials and further modelled in a multilevel framework to account for the longitudinal design of the study.   \n", "FINDINGS We screened 13,108 women commencing antenatal care at less than 14 weeks and 0 days of gestation, of whom 4607 (35%) were eligible.", "4321 (94%) eligible women had pregnancies without major complications and delivered live singletons without congenital malformations (the analysis population).", "We documented very low maternal and perinatal mortality and morbidity, confirming that the participants were at low risk of adverse outcomes.", "For each of the five fetal growth measures, the mean differences between the observed and smoothed centiles for the 3rd, 50th, and 97th centiles, respectively, were small: 2\u00b725 mm (SD 3\u00b70), 0\u00b702 mm (3\u00b70), and -2\u00b769 mm (3\u00b72) for head circumference; 0\u00b783 mm (0\u00b79), -0\u00b705 mm (0\u00b78), and -0\u00b784 mm (1\u00b70) for biparietal diameter; 0\u00b763 mm (1\u00b72), 0\u00b704 mm (1\u00b71), and -1\u00b705 mm (1\u00b73) for occipitofrontal diameter; 2\u00b799 mm (3\u00b71), 0\u00b725 mm (3\u00b72), and -4\u00b722 mm (3\u00b77) for abdominal circumference; and 0\u00b762 mm (0\u00b78), 0\u00b703 mm (0\u00b78), and -0\u00b765 mm (0\u00b78) for femur length.", "We calculated the 3rd, 5th 10th, 50th, 90th, 95th and 97th centile curves according to gestational age for these ultrasound measures, representing the international standards for fetal growth.   \n", "INTERPRETATION We recommend these international fetal growth standards for the clinical interpretation of routinely taken ultrasound measurements and for comparisons across populations.   \n", "FUNDING Bill & Melinda Gates Foundation."], "structured": true}
{"doc_id": 28644298, "title": "Role of NF-kappa B in cell survival and transcription of latent membrane protein 1-expressing or Epstein-Barr virus latency III-infected cells.", "abstract": ["Epstein-Barr virus (EBV) latency III infection converts B lymphocytes into lymphoblastoid cell lines (LCLs) by expressing EBV nuclear and membrane proteins, EBNAs, and latent membrane proteins (LMPs), which regulate transcription through Notch and tumor necrosis factor receptor pathways.", "The role of NF-kappa B in LMP1 and overall EBV latency III transcriptional effects was investigated by treating LCLs with BAY11-7082 (BAY11).", "BAY11 rapidly and irreversibly inhibited NF-kappa B, decreased mitochondrial membrane potential, induced apoptosis, and altered LCL gene expression.", "BAY11 effects were similar to those of an NF-kappa B inhibitor, Delta N-I kappa B alpha, in effecting decreased JNK1 expression and in microarray analyses.", "More than 80% of array elements that decreased with Delta N-I kappa B alpha expression decreased with BAY11 treatment.", "Newly identified NF-kappa B-induced, LMP1-induced, and EBV-induced genes included pleckstrin, Jun-B, c-FLIP, CIP4, and I kappa B epsilon.", "Of 776 significantly changed array elements, 134 were fourfold upregulated in EBV latency III, and 74 were fourfold upregulated with LMP1 expression alone, whereas only 28 were more than fourfold downregulated by EBV latency III.", "EBV latency III-regulated gene products mediate cell migration (EBI2, CCR7, RGS1, RANTES, MIP1 alpha, MIP1 beta, CXCR5, and RGS13), antigen presentation (major histocompatibility complex proteins and JAW1), mitogen-activated protein kinase pathway (DUSP5 and p62Dok), and interferon (IFN) signaling (IFN-gamma R alpha, IRF-4, and STAT1).", "Comparison of EBV latency III LCL gene expression to immunoglobulin M (IgM)-stimulated B cells, germinal-center B cells, and germinal-center-derived lymphomas clustered LCLs with IgM-stimulated B cells separately from germinal-center cells or germinal-center lymphoma cells.", "Expression of IRF-2, AIM1, ASK1, SNF2L2, and components of IFN signaling pathways further distinguished EBV latency III-infected B cells from IgM-stimulated or germinal-center B cells."], "structured": false}
{"doc_id": 28647122, "title": "Endotoxin tolerance: new mechanisms, molecules and clinical significance.", "abstract": ["Prior exposure of innate immune cells like monocytes/macrophages to minute amounts of endotoxin cause them to become refractory to subsequent endotoxin challenge, a phenomenon called \"endotoxin tolerance\".", "Clinically, this state is associated with monocytes/macrophages in sepsis patients where they contribute to \"immunosuppression\" and mortality.", "The molecular mechanisms underlying endotoxin tolerance remain elusive.", "The recent appreciation of inflammation as a self-regulating process, the relative contribution of MyD88 versus TRIF signaling pathways in inducing activation or tolerance, plasticity of NF-kappaB function and the role of chromatin modification and microRNAs in LPS-induced gene reprogramming urges a re-evaluation of endotoxin tolerance.", "This review integrates these new findings into an up-to-date account of endotoxin tolerance, its molecular basis and clinical implications in different pathologies."], "structured": false}
{"doc_id": 28651643, "title": "Pancreatic tumor cells with mutant K-ras suppress ERK activity by MEK-dependent induction of MAP kinase phosphatase-2.", "abstract": ["Activating mutations within the K-ras gene occur in a high percentage of human pancreatic carcinomas.", "We reported previously that the presence of oncogenic, activated K-ras in human pancreatic carcinoma cell lines did not result in constitutive activation of the extracellular signal-regulated kinases (ERK1 and ERK2).", "In the present study, we further characterized the ERK signaling pathway in pancreatic tumor cell lines in order to determine whether the ERK pathway is subject to a compensatory downregulation.", "We found that the attenuation of serum-induced ERK activation was not due to a delay in the kinetics of ERK phosphorylation.", "Treatment with the tyrosine phosphatase inhibitor orthovanadate increased the level of ERK phosphorylation, implicating a vanadate-sensitive tyrosine phosphatase in the negative regulation of ERK.", "Furthermore, expression of a dual specificity phosphatase capable of inactivating ERK known as mitogen-activated protein (MAP) kinase phosphatase-2 (MKP-2) was elevated in most of the pancreatic tumor cell lines and correlated with the presence of active MAP kinase kinase (MEK).", "Taken together, these results suggest that pancreatic tumor cells expressing oncogenic K-ras compensate, in part, by upregulating the expression of MKP-2 to repress the ERK signaling pathway."], "structured": false}
{"doc_id": 28697248, "title": "E2F3 is a mediator of DNA damage-induced apoptosis.", "abstract": ["The E2F transcription factors have emerged as critical apoptotic effectors.", "Herein we report that the E2F family member E2F3a can be induced by DNA damage through transcriptional and posttranslational mechanisms.", "We demonstrate that the posttranslational induction of human E2F3a is dependent on the checkpoint kinases.", "Moreover, we show that human E2F3a is a substrate for the checkpoint kinases (chk kinases) and that mutation of the chk phosphorylation site eliminates the DNA damage inducibility of the protein.", "Furthermore, we demonstrate that E2F1 and E2F2 are transcriptionally induced by DNA damage in an E2f3-dependent manner.", "Finally, using both in vitro and in vivo approaches, we establish that E2f3 is required for DNA damage-induced apoptosis.", "Thus, our data reveal the novel ability of E2f3 to function as a master regulator of the DNA damage response."], "structured": false}
{"doc_id": 28704738, "title": "miR-294/miR-302 promotes proliferation, suppresses G1-S restriction point, and inhibits ESC differentiation through separable mechanisms.", "abstract": ["The miR-294 and miR-302 microRNAs promote the abbreviated G1 phase of the embryonic stem cell (ESC) cell cycle and suppress differentiation induced by let-7.", "Here, we evaluated the role of the retinoblastoma (Rb) family proteins in these settings.", "Under normal growth conditions, miR-294 promoted the rapid G1-S transition independent of the Rb family.", "In contrast, miR-294 suppressed the further accumulation of cells in G1 in response to nutrient deprivation and cell-cell contact in an Rb-dependent fashion.", "We uncovered five additional miRNAs (miR-26a, miR-99b, miR-193, miR-199a-5p, and miR-218) that silenced ESC self-renewal in the absence of other miRNAs, all of which were antagonized by miR-294 and miR-302.", "Four of the six differentiation-inducing miRNAs induced an Rb-dependent G1 accumulation.", "However, all six still silenced self-renewal in the absence of the Rb proteins.", "These results show that the miR-294/miR-302 family acts through Rb-dependent and -independent pathways to regulate the G1 restriction point and the silencing of self-renewal, respectively."], "structured": false}
{"doc_id": 28707489, "title": "Bacteriophage latent-period evolution as a response to resource availability.", "abstract": ["Bacteriophages (phages) modify microbial communities by lysing hosts, transferring genetic material, and effecting lysogenic conversion.", "To understand how natural communities are affected it is important to develop predictive models.", "Here we consider how variation between models--in eclipse period, latent period, adsorption constant, burst size, the handling of differences in host quantity and host quality, and in modeling strategy--can affect predictions.", "First we compare two published models of phage growth, which differ primarily in terms of how they model the kinetics of phage adsorption; one is a computer simulation and the other is an explicit calculation.", "At higher host quantities (approximately 10(8) cells/ml), both models closely predict experimentally determined phage population growth rates.", "At lower host quantities (10(7) cells/ml), the computer simulation continues to closely predict phage growth rates, but the explicit model does not.", "Next we concentrate on predictions of latent-period optima.", "A latent-period optimum is the latent period that maximizes the population growth of a specific phage growing in the presence of a specific quantity and quality of host cells.", "Both models predict similar latent-period optima at higher host densities (e.g., 17 min at 10(8) cells/ml).", "At lower host densities, however, the computer simulation predicts latent-period optima that are much shorter than those suggested by explicit calculations (e.g., 90 versus 1,250 min at 10(5) cells/ml).", "Finally, we consider the impact of host quality on phage latent-period evolution.", "By taking care to differentiate latent-period phenotypic plasticity from latent-period evolution, we argue that the impact of host quality on phage latent-period evolution may be relatively small."], "structured": false}
{"doc_id": 28712203, "title": "Neutrophil elastase-mediated lung disease.", "abstract": ["Elastases of both the neutrophil and macrophage have been implicated in lung disease initiation and progression.", "Although it is unlikely that these proteases evolved for the purpose of injuring lung tissue, the elastin-rich connective tissue framework of the lungs appears to be particularly susceptible to the action of elastolytic proteases.", "Assuming that neutrophil elastase most likely plays a role in the migration of neutrophils toward a site of inflammation and degradation of proteins from invading organisms or other products of the inflammatory response, it is the role of inhibitors of this protease to protect normal tissues from its effects.", "In alpha-1 antitrypsin deficiency we find an experiment of nature that disrupts this protease-anti-protease balance, resulting in an increased risk of destructive lung disease."], "structured": false}
{"doc_id": 28724565, "title": "Role of TRPML and two-pore channels in endolysosomal cation homeostasis.", "abstract": ["The transient receptor potential (TRP) channels TRPML1, TRPML2, and TRPML3 (also called mucolipins 1-3 or MCOLN1-3) are nonselective cation channels.", "Mutations in the Trpml1 gene cause mucolipidosis type IV in humans with clinical features including psychomotor retardation, corneal clouding, and retinal degeneration, whereas mutations in the Trpml3 gene cause deafness, circling behavior, and coat color dilution in mice.", "No disease-causing mutations are reported for the Trpml2 gene.", "Like TRPML channels, which are expressed in the endolysosomal pathway, two-pore channels (TPCs), namely TPC1, TPC2, and TPC3, are found in intracellular organelles, in particular in endosomes and lysosomes.", "Both TRPML channels and TPCs may function as calcium/cation release channels in endosomes, lysosomes, and lysosome-related organelles with TRPMLs being activated by phosphatidylinositol 3,5-bisphosphate and regulated by pH and TPCs being activated by nicotinic acid adenine dinucleotide phosphate in a calcium- and pH-dependent manner.", "They may also be involved in endolysosomal transport and fusion processes, e.g., as intracellular calcium sources.", "Currently, however, the exact physiological roles of TRPML channels and TPCs remain quite elusive, and whether TRPML channels are purely endolysosomal ion channels or whether they may also be functionally active at the plasma membrane in vivo remains to be determined."], "structured": false}
{"doc_id": 28738741, "title": "Adult T-cell leukemia/lymphoma in London: clinical experience of 21 cases.", "abstract": ["Adult T-cell leukemia/lymphoma (ATLL) is uncommon in the United Kingdom and has so far been restricted to people of Afro-Caribbean extraction.", "Between 1981 and 1995, 21 cases presented to 2 inner London teaching hospitals where 17% of the population are of Afro-Caribbean origin.", "Clinical presentations were similar to those of the disease in HTLV-I-endemic areas.", "Major responses (CR + PR) were obtained in 10/16 assessable patients (63%) treated with combination chemotherapy.", "However, median survival was only 5.5 months.", "Disease progression and opportunistic infection were the major causes of treatment failure and death.", "Three patients (14%) relapsed in the central nervous system (CNS).", "Our cases confirm the profound immunosuppression in ATLL.", "The poor prognosis of acute and lymphoma types of ATLL highlight the need for new approaches to treatment such as zidovudine and alpha-interferon, incorporating prophylaxis against CNS disease and opportunistic infections."], "structured": false}
{"doc_id": 28783084, "title": "Regeneration, tissue injury and the immune response.", "abstract": ["The involvement of the immune system in the response to tissue injury has raised the possibility that it might influence tissue, organ or appendage regeneration following injury.", "One hypothesis that has been discussed is that inflammatory aspects may preclude the occurrence of regeneration, but there is also evidence for more positive roles of immune components.", "The vertebrate eye is an immunoprivileged site where inflammatory aspects are inhibited by several immunomodulatory mechanisms.", "In various newt species the ocular tissues such as the lens are regenerative and it has recently been shown that the response to local injury of the lens involves activation of antigen-presenting cells which traffic to the spleen and return to displace and engulf the lens, thereby inducing regeneration from the dorsal iris.", "The activation of thrombin from prothrombin in the dorsal iris is one aspect of the injury response that is important in the initiation of regeneration.", "The possible relationships between the immune response and the regenerative response are considered with respect to phylogenetic variation of regeneration in general, and lens regeneration in particular."], "structured": false}
{"doc_id": 28806780, "title": "Poverty, Hunger, Education, and Residential Status Impact Survival in HIV", "abstract": ["Despite combination antiretroviral therapy (ART), HIV infected people have higher mortality than non-infected.", "Lower socioeconomic status (SES) predicts higher mortality in many chronic illnesses but data in people with HIV is limited.", "We evaluated 878 HIV infected individuals followed from 1995 to 2005.", "Cox proportional hazards for all-cause mortality were estimated for SES measures and other factors.", "Mixed effects analyses examined how SES impacts factors predicting death.", "The 200 who died were older, had lower CD4 counts, and higher viral loads (VL).", "Age, transmission category, education, albumin, CD4 counts, VL, hunger, and poverty predicted death in univariate analyses; age, CD4 counts, albumin, VL, and poverty in the multivariable model.", "Mixed models showed associations between (1) CD4 counts with education and hunger; (2) albumin with education, homelessness, and poverty; and (3) VL with education and hunger.", "SES contributes to mortality in HIV infected persons directly and indirectly, and should be a target of health policy in this population."], "structured": false}
{"doc_id": 28809022, "title": "The INO80 ATP-dependent chromatin remodeling complex is a nucleosome spacing factor.", "abstract": ["The mobilization of nucleosomes by the ATP-dependent remodeler INO80 is quite different from another remodeler (SWI/SNF) that is also involved in gene activation.", "Unlike that recently shown for SWI/SNF, INO80 is unable to disassemble nucleosomes when remodeling short nucleosomal arrays.", "Instead, INO80 more closely resembles, although with notable exceptions, the nucleosome spacing activity of ISW2 and ISW1a, which are generally involved in transcription repression.", "INO80 required a minimum of 33 to 43 bp of extranucleosomal DNA for mobilizing nucleosomes, with 70 bp being optimal.", "INO80 prefers to move mononucleosomes to the center of DNA, like ISW2 and ISW1a, but does so with higher precision.", "Unlike ISW2/1a, INO80 does not require the H4 tail for nucleosome mobilization; instead, the H2A histone tail negatively regulates nucleosome movement by INO80.", "INO80 moved arrays of two or three nucleosomes with 50 or 79 bp of linker DNA closer together, with a final length of \u223c30 bp of linker DNA or a repeat length of \u223c177 bp.", "A minimum length of >30 bp of linker DNA was required for nucleosome movement and spacing by INO80 in arrays."], "structured": false}
{"doc_id": 28821565, "title": "Concentrations of tenofovir and emtricitabine in saliva: implications for preexposure prophylaxis of oral HIV acquisition.", "abstract": ["To prevent acquisition of HIV through oral sex, drugs used for preexposure prophylaxis (Prep) need to diffuse in saliva.", "We measured tenofovir (TFV) and emtricitabine (FTC) concentrations simultaneously in the plasma and saliva of 41 HIV-infected patients under stable antiretroviral treatment.", "Mean ratios of saliva/plasma concentration were 3% (\u00b14%) and 86.9% (\u00b1124%) for TFV and FTC, respectively.", "Tenofovir disoproxil fumarate (TDF) should be used in combination with FTC to prevent oral acquisition of HIV."], "structured": false}
{"doc_id": 28845338, "title": "Increased lean body mass as an early indicator of olanzapine-induced weight gain in healthy men.", "abstract": ["One of the primary limitations of many psychiatric medications is weight gain, the mechanism of which remains to be fully elucidated.", "We conducted a 2-week double-blind placebo-controlled study on weight gain with olanzapine, which is frequently but unpredictably associated with this side effect, to address the possible mechanisms of weight gain independent of changes in the psychiatric condition for which it is prescribed.", "Healthy male volunteers were randomly assigned to olanzapine (5 mg/day for 7 days, then 10 mg/day for 7 days) or a matching placebo.", "Of the 24 participants, 19 completed the study (olanzapine, n=13; placebo, n=6).", "Body weight, glucose, triglyceride, total cholesterol, lipid, leptin, insulin, and aldosterone levels, resting metabolic rate, body composition, physical activity, and 24-h dietary intake were assessed.", "A significant increase in weight as well as triglyceride, insulin, and leptin levels were found in the olanzapine group as a whole.", "In participants receiving olanzapine who actually gained weight (n=8), lean but not fat mass increased, as did insulin, fasting glucose, total cholesterol, low-density lipoprotein, and non-high-density lipoprotein levels, whereas aldosterone levels decreased.", "There were no significant metabolic or endocrine changes in participants receiving placebo or in those receiving olanzapine who did not gain weight.", "Early metabolic changes appear to be independent of accumulation of fat."], "structured": false}
{"doc_id": 28894097, "title": "QTc interval length and QT dispersion as predictors of mortality in patients with non-insulin-dependent diabetes.", "abstract": ["Patients with non-insulin-dependent diabetes (NIDDM) are at independent risk of cardiovascular death.", "The reason is only partially understood.", "The aim of our study was therefore to evaluate the impact of corrected QT interval length (QTc) and QT dispersion (QT-disp) on mortality in a cohort of 324 Caucasian NIDDM patients.", "A resting 12-lead ECG was recorded at baseline.", "Maximum (QT-max) and minimum QT (QT-min) intervals were measured, and QT-max was corrected for heart rate (QTc-max).", "QT-disp was defined as the difference between QT-max and QT-min.", "QTc-max was 454 (376-671) ms(1/2) (median (range)) and QT-disp 61 (0-240) ms.", "Prolonged QTc interval (PQTc), defined as QTc-max > 440 ms(1/2), was present in 67% of the patients and prolonged QT-disp (PQT-disp), defined as QT-disp > 50 ms, was present in 51%.", "During the 9-year follow-up period, 100 patients died (52 from cardiovascular diseases).", "Thirty-seven percent of the patients with PQTc died compared with 17% with normal QTc interval (p<0.001).", "The Cox proportional hazard model, including putative risk factors at baseline, revealed the following independent predictors of all cause mortality; QTc-max (p<0.05), age (p<0.0001), albuminuria (p<0.01), retinopathy (p<0.01), HbA1c (p<0.05), insulin treatment (p<0.01), total cholesterol (p<0.01), serum creatinine (p<0.05) and presence of cardiac heart disease based on Minnesota coded ECG (p<0.001).", "Whereas QT-disp was not a predictor, QTc-max interval was an independent predictor of cardiovascular mortality.", "Our study showed a high prevalence of QTc and QT-disp abnormalities and indicated that QTc-max but not QT-disp is an independent predictor of all cause and cardiovascular mortality in NIDDM patients."], "structured": false}
{"doc_id": 28904104, "title": "Repriming of DNA synthesis at stalled replication forks by human PrimPol", "abstract": ["DNA replication forks that collapse during the process of genomic duplication lead to double-strand breaks and constitute a threat to genomic stability.", "The risk of fork collapse is higher in the presence of replication inhibitors or after UV irradiation, which introduces specific modifications in the structure of DNA.", "In these cases, fork progression may be facilitated by error-prone translesion synthesis (TLS) DNA polymerases.", "Alternatively, the replisome may skip the damaged DNA, leaving an unreplicated gap to be repaired after replication.", "This mechanism strictly requires a priming event downstream of the lesion.", "Here we show that PrimPol, a new human primase and TLS polymerase, uses its primase activity to mediate uninterrupted fork progression after UV irradiation and to reinitiate DNA synthesis after dNTP depletion.", "As an enzyme involved in tolerance to DNA damage, PrimPol might become a target for cancer therapy."], "structured": false}
{"doc_id": 28910120, "title": "Recombinant human tumor necrosis factor administered as a five-day continuous infusion in cancer patients: phase I toxicity and effects on lipid metabolism.", "abstract": ["Recombinant human tumor necrosis factor (rH-TNF) is a cytotoxic monokine with pleiotropic effects.", "A phase I trial of rH-TNF was initiated using a five-day continuous intravenous (IV) infusion repeated every 28 days.", "Thirty-eight courses of therapy were administered to 19 patients.", "The starting dose was 5 X 10(4) U/m2/d, with escalations to 1.0 X 10(5), 2.0 X 10(5), 2.4 X 10(5), and 3.0 X 10(5) U/m2/d.", "Systemic side effects, including fever, chills, hypotension, fatigue, anorexia, and headaches, were mild and self-limiting.", "At the maximum tolerated dose of 3.0 X 10(5) U/m2/d, dose-limiting hematologic toxicity was manifested by transient thrombocytopenia and leukopenia.", "Elevated bilirubin levels were also seen at the higher dose levels.", "Lipoprotein analysis demonstrated that the five-day treatment with rH-TNF was associated with decreases in high-density lipoproteins, as well as increases in triglycerides and very-low-density lipoproteins.", "Pharmacokinetic studies using an enzyme-linked immunosorbent assay (ELISA) test indicated plasma rH-TNF levels less than 0.2 U/mL. The recommended phase II dose of rH-TNF administered as a five-day continuous infusion is 2.4 X 10(5) U/m2/d."], "structured": false}
{"doc_id": 28928964, "title": "Tissue-specific expression and regulation of sexually dimorphic genes in mice.", "abstract": ["We report a comprehensive analysis of gene expression differences between sexes in multiple somatic tissues of 334 mice derived from an intercross between inbred mouse strains C57BL/6J and C3H/HeJ. The analysis of a large number of individuals provided the power to detect relatively small differences in expression between sexes, and the use of an intercross allowed analysis of the genetic control of sexually dimorphic gene expression.", "Microarray analysis of 23,574 transcripts revealed that the extent of sexual dimorphism in gene expression was much greater than previously recognized.", "Thus, thousands of genes showed sexual dimorphism in liver, adipose, and muscle, and hundreds of genes were sexually dimorphic in brain.", "These genes exhibited highly tissue-specific patterns of expression and were enriched for distinct pathways represented in the Gene Ontology database.", "They also showed evidence of chromosomal enrichment, not only on the sex chromosomes, but also on several autosomes.", "Genetic analyses provided evidence of the global regulation of subsets of the sexually dimorphic genes, as the transcript levels of a large number of these genes were controlled by several expression quantitative trait loci (eQTL) hotspots that exhibited tissue-specific control.", "Moreover, many tissue-specific transcription factor binding sites were found to be enriched in the sexually dimorphic genes."], "structured": false}
{"doc_id": 28931537, "title": "The role of prevention in oncology practice: results from a 2004 survey of American Society of Clinical Oncology members.", "abstract": ["PURPOSE In 2004, the American Society of Clinical Oncology (ASCO) Cancer Prevention Committee surveyed the members to describe involvement in clinical prevention activities.   \n", "METHODS A previously administered survey, with updated items on genetics, chemoprevention, and survivorship, was mailed to a stratified random sample of 2,000 domestic members and a convenience sample of 3,144 international members.   \n", "RESULTS A total of 49.7% of domestic members contacted and survey eligible responded (n = 851).", "Nonresponders were younger (50.5 v 51.7 years; P < .01); 465 international members responded.", "Overall, 35% had received formal instruction in cancer prevention and control, and most respondents expected increased use of prevention, screening/early detection, and risk reduction/genetic counseling in their practices in the next 5 years.", "Most reported caring for cancer survivors, including providing general medical care.", "They also either directly provide or refer patients for cancer prevention and control services (eg, cancer screening, tobacco and nutrition counseling, risk reduction, and chemoprevention).", "Multivariable modeling found fewer perceived barriers to inclusion of cancer prevention activities in clinical practice among those practicing in an academic setting, seeing a higher proportion of patients without a cancer diagnosis, having formal training in prevention and control, expecting an increase in prevention activities in the next 5 years, and providing community advice on prevention.   \n", "CONCLUSION Barriers to the inclusion of cancer prevention and control activities in oncology clinical practice exist.", "Nevertheless, a substantial proportion of both domestic and international ASCO members report an interest in cancer prevention and control activities, with a desire for more specific educational programs in this emerging area of oncology practice."], "structured": true}
{"doc_id": 28937856, "title": "Stress-dependent regulation of FOXO transcription factors by the SIRT1 deacetylase.", "abstract": ["The Sir2 deacetylase modulates organismal life-span in various species.", "However, the molecular mechanisms by which Sir2 increases longevity are largely unknown.", "We show that in mammalian cells, the Sir2 homolog SIRT1 appears to control the cellular response to stress by regulating the FOXO family of Forkhead transcription factors, a family of proteins that function as sensors of the insulin signaling pathway and as regulators of organismal longevity.", "SIRT1 and the FOXO transcription factor FOXO3 formed a complex in cells in response to oxidative stress, and SIRT1 deacetylated FOXO3 in vitro and within cells.", "SIRT1 had a dual effect on FOXO3 function: SIRT1 increased FOXO3's ability to induce cell cycle arrest and resistance to oxidative stress but inhibited FOXO3's ability to induce cell death.", "Thus, one way in which members of the Sir2 family of proteins may increase organismal longevity is by tipping FOXO-dependent responses away from apoptosis and toward stress resistance."], "structured": false}
{"doc_id": 29015485, "title": "TLR-Mediated Innate Production of IFN-\u03b3 by CD8+ T Cells Is Independent of Glycolysis.", "abstract": ["CD8(+) T cells can respond to unrelated infections in an Ag-independent manner.", "This rapid innate-like immune response allows Ag-experienced T cells to alert other immune cell types to pathogenic intruders.", "In this study, we show that murine CD8(+) T cells can sense TLR2 and TLR7 ligands, resulting in rapid production of IFN-\u03b3 but not of TNF-\u03b1 and IL-2.", "Importantly, Ag-experienced T cells activated by TLR ligands produce sufficient IFN-\u03b3 to augment the activation of macrophages.", "In contrast to Ag-specific reactivation, TLR-dependent production of IFN-\u03b3 by CD8(+) T cells relies exclusively on newly synthesized transcripts without inducing mRNA stability.", "Furthermore, transcription of IFN-\u03b3 upon TLR triggering depends on the activation of PI3K and serine-threonine kinase Akt, and protein synthesis relies on the activation of the mechanistic target of rapamycin.", "We next investigated which energy source drives the TLR-induced production of IFN-\u03b3.", "Although Ag-specific cytokine production requires a glycolytic switch for optimal cytokine release, glucose availability does not alter the rate of IFN-\u03b3 production upon TLR-mediated activation.", "Rather, mitochondrial respiration provides sufficient energy for TLR-induced IFN-\u03b3 production.", "To our knowledge, this is the first report describing that TLR-mediated bystander activation elicits a helper phenotype of CD8(+) T cells.", "It induces a short boost of IFN-\u03b3 production that leads to a significant but limited activation of Ag-experienced CD8(+) T cells.", "This activation suffices to prime macrophages but keeps T cell responses limited to unrelated infections."], "structured": false}
{"doc_id": 29022271, "title": "Recommendations for the presurgical psychosocial evaluation of bariatric surgery patients.", "abstract": ["Psychosocial factors have significant potential to affect long-term outcomes of bariatric surgery, including emotional adjustment, adherence to the recommended postoperative lifestyle regimen, weight loss outcomes, and co-morbidity improvement and or resolution.", "Thus, it is recommended that bariatric behavioral health clinicians with specialized knowledge and experience be involved in the evaluation and care of patients both before and after surgery.", "The evaluating clinician plays a number of important roles in the multidisciplinary treatment of the bariatric patient.", "Central among these is the role of identifying factors that may pose challenges to optimal surgical outcome and providing recommendations to the patient and bariatric team on how to address these issues.", "This document outlines recommendations for the psychosocial evaluation of bariatric surgery patients, appropriate qualifications of those conducting these evaluations, communication of evaluation results and suggested treatment plan, and the extension of behavioral healthcare of the bariatric patient to the entire span of the surgical and postsurgical process."], "structured": false}
{"doc_id": 29023309, "title": "Simian immunodeficiency virus\u2013induced mucosal interleukin-17 deficiency promotes Salmonella dissemination from the gut", "abstract": ["Salmonella typhimurium causes a localized enteric infection in immunocompetent individuals, whereas HIV-infected individuals develop a life-threatening bacteremia.", "Here we show that simian immunodeficiency virus (SIV) infection results in depletion of T helper type 17 (TH17) cells in the ileal mucosa of rhesus macaques, thereby impairing mucosal barrier functions to S. typhimurium dissemination.", "In SIV-negative macaques, the gene expression profile induced by S. typhimurium in ligated ileal loops was dominated by TH17 responses, including the expression of interleukin-17 (IL-17) and IL-22.", "TH17 cells were markedly depleted in SIV-infected rhesus macaques, resulting in blunted TH17 responses to S. typhimurium infection and increased bacterial dissemination.", "IL-17 receptor\u2013deficient mice showed increased systemic dissemination of S. typhimurium from the gut, suggesting that IL-17 deficiency causes defects in mucosal barrier function.", "We conclude that SIV infection impairs the IL-17 axis, an arm of the mucosal immune response preventing systemic microbial dissemination from the gastrointestinal tract."], "structured": false}
{"doc_id": 29025270, "title": "An adoption study of human obesity.", "abstract": ["We examined the contributions of genetic factors and the family environment to human fatness in a sample of 540 adult Danish adoptees who were selected from a population of 3580 and divided into four weight classes: thin, median weight, overweight, and obese.", "There was a strong relation between the weight class of the adoptees and the body-mass index of their biologic parents - for the mothers, P less than 0.0001; for the fathers, P less than 0.02.", "There was no relation between the weight class of the adoptees and the body-mass index of their adoptive parents.", "Cumulative distributions of the body-mass index of parents showed similar results; there was a strong relation between the body-mass index of biologic parents and adoptee weight class and no relation between the index of adoptive parents and adoptee weight class.", "Furthermore, the relation between biologic parents and adoptees was not confined to the obesity weight class, but was present across the whole range of body fatness - from very thin to very fat.", "We conclude that genetic influences have an important role in determining human fatness in adults, whereas the family environment alone has no apparent effect."], "structured": false}
{"doc_id": 29073751, "title": "Redox-dependent downregulation of Rho by Rac", "abstract": ["Rac and Rho GTPases function as critical regulators of actin cytoskeleton remodelling during cell spreading and migration.", "Here we demonstrate that Rac-mediated reactive oxygen species (ROS) production results in the downregulation of Rho activity.", "The redox-dependent decrease in Rho activity is required for Rac-induced formation of membrane ruffles and integrin-mediated cell spreading.", "The pathway linking generation of ROS to downregulation of Rho involves inhibition of the low-molecular-weight protein tyrosine phosphatase (LMW-PTP) and then an increase in the tyrosine phosphorylation and activation of its target, p190Rho-GAP.", "Our findings define a novel mechanism for the coupling of changes in cellular redox state to the control of actin cytoskeleton rearrangements by Rho GTPases."], "structured": false}
{"doc_id": 29090823, "title": "The epidemiology of trachoma in Eastern Equatoria and Upper Nile States, southern Sudan.", "abstract": ["OBJECTIVE Limited surveys and anecdotal data indicate that trachoma is endemic in the states of Eastern Equatoria and Upper Nile in southern Sudan.", "However, its magnitude and geographical distribution are largely unknown.", "We conducted surveys to ascertain the prevalence and geographical distribution of trachoma, and to identify targets for control interventions.   \n", "METHODS Population-based cross-sectional surveys were conducted in nine sites in southern Sudan between September 2001 and June 2004.", "Two-stage random cluster sampling with probability proportional to size was used to select the sample.", "Trachoma grading was done using the WHO simplified grading system.   \n", "FINDINGS A total of 17 016 persons were examined, a response rate of 86.1% of the enumerated population.", "Prevalence of signs of active trachoma in children aged 1-9 years was: TF=53.7% (95% confidence interval (CI)=52.1-55.3); TI=42.7% (95% CI=41.2-44.2); TF and/or TI=64.1% (95% CI=62.5-65.5).", "Prevalence of trichiasis (TT) in children aged less than 15 years was 1.2% (95% CI=0.9-1.4), while TT prevalence in persons aged 15 years and above was 9.2% (95% CI=8.6-9.9).", "Women were more likely to have trichiasis compared to men (odds ratio (OR)=1.57; 95% CI=1.34-1.84).", "Tentative extrapolation to the states of Eastern Equatoria and Upper Nile estimates that there is a backlog of 178,250 (lower and upper bounds=156,027-205,995) persons requiring surgery and the entire population, estimated to be over 3.9 million, is in need of the SAFE strategy to control blinding trachoma.   \n", "CONCLUSION Trachoma is a public health problem in all nine of the study sites surveyed.", "The unusually high prevalence of active trachoma and TT in children points to the severity of the problem.", "There is urgent need to implement trachoma control interventions in trachoma endemic regions of southern Sudan."], "structured": true}
{"doc_id": 29098525, "title": "A single residue determines the cooperative binding property of a primosomal DNA replication protein, PriB, to single-stranded DNA.", "abstract": ["PriB is a primosomal protein required for re-initiation of replication in bacteria.", "We characterized and compared the DNA-binding properties of PriB from Salmonella enterica serovar Typhimurium LT2 (StPriB) and Escherichia coli (EcPriB).", "Only one residue of EcPriB, V6, was different in StPriB (replaced by A6).", "Previous structural information revealed that this residue is located on the putative dimer-dimer interface of PriB and is not involved in single-stranded DNA (ssDNA) binding.", "The cooperative binding mechanism of StPriB to DNA is, however, very different from that of EcPriB. Unlike EcPriB, which forms a single complex with ssDNAs of various lengths, StPriB forms two or more distinct complexes.", "Based on these results, as well as information on structure, binding modes for forming a stable complex of PriB with ssDNA of 25 nucleotides (nt), (EcPriB)25, and (StPriB)25 are proposed."], "structured": false}
{"doc_id": 29107180, "title": "Genomic organization and chromosomal location of the human dsRNA adenosine deaminase gene: the enzyme for glutamate-activated ion channel RNA editing.", "abstract": ["The structure of the human gene encoding the double-stranded RNA (dsRNA) adenosine deaminase (DRADA) was characterized.", "This nuclear localized enzyme is involved in the RNA editing required for the expression of certain subtypes of glutamate-gated ion channel subunits.", "The DRADA gene span 30 kb pairs and harbors 15 exons.", "The transcription of the DRADA gene driven by the putative promoter region, which contains no typical TATA or CCAAT box-like sequences, is initiated at multiple sites, 164 to 216 nucleotides upstream of the translation initiation codon.", "The three dsRNA binding motifs (DRBM), 70 amino acid residues long, are each encoded by two exons plus an intervening sequence that interrupts the motif at the identical amino acid position.", "This finding is consistent with the notion that the dsRNA binding domains may be composed of two separate functional subdomains.", "Fluorescent in situ hybridization localized the DRADA gene on the long arm chromosome 1, region q21.", "The gene structure and sequence information reported in this study will facilitate the investigation of involvement of DRADA in hereditary diseases that may be the result of malfunction of glutamate-gated ion channels."], "structured": false}
{"doc_id": 29107210, "title": "\"We charge them; otherwise we cannot run the hospital\" front line workers, clients and health financing policy implementation gaps in Ghana.", "abstract": ["OBJECTIVES This paper examines policy implementation gaps of user fees plus exemptions and health insurance in providing financial access to primary clinical care for children under five in Ghana.   \n", "METHODS Methods included analysis of routine data, focus group discussions, in-depth interviews, and administration of a structured questionnaire.   \n", "RESULTS Providers modified exemptions policy implementation arrangements, sometimes giving partial or no exemptions.", "Clients who knew or suspected exemption entitlements failed to request them because of fear of negative reactions from providers.", "Providers attributed their modification of implementation arrangements and negative reactions to the threat posed to the financial viability of their institutions by reimbursement uncertainty and delays.", "At the time of the study insurance coverage was low and frontline workers were not noticeably modifying implementation arrangements.", "However, the underlying goal conflicts, resource scarcity, conditions of work and relationships between frontline workers and clients that fueled the exemptions policy implementation gaps were unchanged.", "The potential for the health insurance policy to stumble over implementation gaps as happened with the exemptions policy therefore remained.   \n", "CONCLUSIONS Policies that do not take into account the incentives for frontline worker adherence and align them better with policy objectives may experience implementation gaps."], "structured": true}
{"doc_id": 29124963, "title": "EML4-ALK translocation predicts better outcome in lung adenocarcinoma patients with wild-type EGFR.", "abstract": ["INTRODUCTION The echinoderm microtubule-associated protein like 4-anaplastic lymphoma kinase (EML4-ALK) fusion represents a novel target in a subset of non-small cell lung cancer, especially adenocarcinoma.", "EML4-ALK fusion is mutually exclusive with epidermal growth factor receptor (EGFR) mutations.", "To understand the impact of EML4-ALK on the prognosis of non-small cell lung cancer, we examined EML4-ALK fusion in lung adenocarcinoma from patients with wild-type EGFR and analyzed their clinical treatment outcomes.   \n", "METHODS Lung adenocarcinoma patients with malignant pleural effusions having wild-type EGFR and measurable target lesions were enrolled for EML4-ALK analysis by reverse transcription-polymerase chain reaction and direct sequencing.", "Demographic data, EML4-ALK status, and survival data were analyzed.", "We also performed fluorescence in situ hybridization on some available tumor samples to validate the PCR result.", "In addition, K-ras mutation was analyzed for patients without EML4-ALK fusion genes.   \n", "RESULTS A total of 116 patients with wild-type EGFR sequencing results had complete clinical data for analysis.", "No patients received ALK inhibitor therapy.", "There were 39 patients (34%) with the EML4-ALK fusion gene.", "The concordance rate between reverse transcription-polymerase chain reaction and fluorescence in situ hybridization was 85%.", "The K-ras mutation rate for patients without EML4-ALK fusion gene was 6.5%.", "By multivariate analysis, patients who had better performance status (p < 0.001) and EML4-ALK translocation (p = 0.017) had longer overall survival.", "Comparing patients with tumors harboring variant 1 with those harboring nonvariant 1 EML4-ALK fusion genes, there were no significant differences in clinical factors and survival outcome.   \n", "CONCLUSION For lung adenocarcinoma patients with wild-type EGFR, EML4-ALK translocation is associated with longer overall survival."], "structured": true}
{"doc_id": 29125354, "title": "Transcriptional Repression of Gata3 Is Essential for Early B Cell Commitment", "abstract": ["The mechanisms underlying the silencing of alternative fate potentials in very early B cell precursors remain unclear.", "Using gain- and loss-of-function approaches together with a synthetic Zinc-finger polypeptide (6ZFP) engineered to prevent transcription factor binding to a defined cis element, we show that the transcription factor EBF1 promotes B cell lineage commitment by directly repressing expression of the T-cell-lineage-requisite Gata3 gene.", "Ebf1-deficient lymphoid progenitors exhibited increased T cell lineage potential and elevated Gata3 transcript expression, whereas enforced EBF1 expression inhibited T cell differentiation and caused rapid loss of Gata3 mRNA.", "Notably, 6ZFP-mediated perturbation of EBF1 binding to a Gata3 regulatory region restored Gata3 expression, abrogated EBF1-driven suppression of T cell differentiation, and prevented B cell differentiation via a GATA3-dependent mechanism.", "Furthermore, EBF1 binding to Gata3 regulatory sites induced repressive histone modifications across this region.", "These data identify a transcriptional circuit critical for B cell lineage commitment."], "structured": false}
{"doc_id": 29134911, "title": "Isolation and partial characterization of an unusual human immunodeficiency retrovirus from two persons of west-central African origin.", "abstract": ["An unusual human retrovirus was isolated from two patients with persistent generalized lymphadenopathy who originate from West-Central Africa and are currently residing in Belgium.", "Although the virus shared a number of the same biological and morphological properties as human immunodeficiency retrovirus type 1 (HIV-1) and HIV-2, significant antigenic differences could be demonstrated.", "Several of the viral proteins also differed in molecular weight from the corresponding HIV-1 and HIV-2 proteins.", "Partial chemical cleavage of the most highly conserved viral proteins resulted in patterns which differed from those of HIV-1 and HIV-2.", "Furthermore, nucleic acid hybridization experiments were capable of discriminating between the virus types.", "Sequence analysis of the viral U3 region revealed a unique enhancer organization not found in other immunodeficiency viruses.", "The data indicated that the new isolate is more closely related to HIV-1 than to HIV-2 but clearly differs in a number of important respects."], "structured": false}
{"doc_id": 29148743, "title": "Role of circulating nitrite and S-nitrosohemoglobin in the regulation of regional blood flow in humans.", "abstract": ["To determine the relative contributions of endothelial-derived nitric oxide (NO) vs. intravascular nitrogen oxide species in the regulation of human blood flow, we simultaneously measured forearm blood flow and arterial and venous levels of plasma nitrite, LMW-SNOs and HMW-SNOs, and red cell S-nitrosohemoglobin (SNO-Hb).", "Measurements were made at rest and during regional inhibition of NO synthesis, followed by forearm exercise.", "Surprisingly, we found significant circulating arterial-venous plasma nitrite gradients, providing a novel delivery source for intravascular NO.", "Further supporting the notion that circulating nitrite is bioactive, the consumption of nitrite increased significantly with exercise during the inhibition of regional endothelial synthesis of NO.", "The role of circulating S-nitrosothiols and SNO-Hb in the regulation of basal vascular tone is less certain.", "We found that low-molecular-weight S-nitrosothiols were undetectable and S-nitroso-albumin levels were two logs lower than previously reported.", "In fact, S-nitroso-albumin primarily formed in the venous circulation, even during NO synthase inhibition.", "Whereas SNO-Hb was measurable in the human circulation (brachial artery levels of 170 nM in whole blood), arterial-venous gradients were not significant, and delivery of NO from SNO-Hb was minimal.", "In conclusion, we present data that suggest (i) circulating nitrite is bioactive and provides a delivery gradient of intravascular NO, (ii) S-nitroso-albumin does not deliver NO from the lungs to the tissue but forms in the peripheral circulation, and (iii) SNO-Hb and S-nitrosothiols play a minimal role in the regulation of basal vascular tone, even during exercise stress."], "structured": false}
{"doc_id": 29183629, "title": "Extra centrosomes and/or chromosomes prolong mitosis in human cells", "abstract": ["Using laser microsurgery and cell fusion we have explored how additional centrosomes and/or chromosomes influence the duration of mitosis in human cells.", "We found that doubling the chromosome number added approximately 10 min to a 20 min division, whereas doubling the number of centrosomes added approximately 30 min more.", "Extra centrosomes and/or chromosomes prolong mitosis by delaying satisfaction of the spindle assembly checkpoint.", "Thus mitosis can be prolonged by non-genetic means and extra chromosomes and centrosomes probably contribute to the elevated mitotic index seen in many tumours."], "structured": false}
{"doc_id": 29185044, "title": "Familial recurrence-pattern analysis of nonsyndromic isolated cleft palate--a Danish Registry study.", "abstract": ["The finding of an association between genetic variation at the transforming growth-factor alpha (TGFA) locus and nonsyndromic isolated cleft palate (CP) represents a potentially important breakthrough in our understanding of this condition.", "The present study was undertaken to assess the feasibility of detecting linkage to putative CP-susceptibility loci, such as TGFA.", "To this end, the familial recurrence pattern for CP was evaluated to determine the most likely mode of inheritance for this condition.", "The study took advantage of the high ascertainment and uniform registration of CP in Denmark.", "In addition, the study utilized estimates of familial recurrence that were obtained by register linkage and, hence, were not subject to either recall bias or the potentially biasing influence of nonresponders.", "The recurrence risks for first-, second-, and third-degree relatives of 1,364 nonsyndromic CP probands were estimated to be 2.74% (72/2,628), 0.28% (3/1,068), and 0.00% (0/360), respectively.", "These estimates are close to published estimates based on questionnaire and interview data.", "The population prevalence for nonsyndromic CP was, however, found to be considerable higher than usually reported (0.058% [1,456/2,523,023]).", "Analyses of these and previously published data, using the method presented by Risch, indicated that major-locus or additive multilocus inheritance of CP is unlikely.", "The familial recurrence pattern was, however, consistent with CP being determined by several interacting loci.", "Under such a model, a single locus accounting for more than a sixfold increase in the risk to first-degree relatives of CP probands is unlikely, whereas a single locus accounting for a threefold increase provided a good fit to the data.", "Such a locus could be detected in a realistic sample of affected sib pairs."], "structured": false}
{"doc_id": 29190724, "title": "Gene methylation in gastric cancer.", "abstract": ["Gastric cancer is one of the most common malignancies and remains the second leading cause of cancer-related death worldwide.", "Over 70% of new cases and deaths occur in developing countries.", "In the early years of the molecular biology revolution, cancer research mainly focuses on genetic alterations, including gastric cancer.", "Epigenetic mechanisms are essential for normal development and maintenance of tissue-specific gene expression patterns in mammals.", "Disruption of epigenetic processes can lead to altered gene function and malignant cellular transformation.", "Recent advancements in the rapidly evolving field of cancer epigenetics have shown extensive reprogramming of every component of the epigenetic machinery in cancer, including DNA methylation, histone modifications, nucleosome positioning, noncoding RNAs, and microRNAs.", "Aberrant DNA methylation in the promoter regions of gene, which leads to inactivation of tumor suppressor and other cancer-related genes in cancer cells, is the most well-defined epigenetic hallmark in gastric cancer.", "The advantages of gene methylation as a target for detection and diagnosis of cancer in biopsy specimens and non-invasive body fluids such as serum and gastric washes have led to many studies of application in gastric cancer.", "This review focuses on the most common and important phenomenon of epigenetics, DNA methylation, in gastric cancer and illustrates the impact epigenetics has had on this field."], "structured": false}
{"doc_id": 29214508, "title": "Klebsiella aerogenes urease gene cluster: sequence of ureD and demonstration that four accessory genes (ureD, ureE, ureF, and ureG) are involved in nickel metallocenter biosynthesis.", "abstract": ["The region located immediately upstream from the Klebsiella aerogenes urease structural genes was sequenced and shown to possess an open reading frame capable of encoding a 29.8-kDa peptide.", "Deletions were generated in this gene, denoted ureD, and in each of the genes (ureE, ureF, and ureG) located immediately downstream of the three structural genes.", "Transformation of the mutated plasmids into Escherichia coli resulted in high levels of urease expression, but the enzyme was inactive (deletions in ureD, ureF, or ureG) or only partially active (deletions in ureE).", "Ureases were purified from the recombinant cells and shown to be identical to control enzyme when analyzed by gel filtration chromatography and sodium dodecyl sulfate-polyacrylamide gel electrophoresis; however, in every case the activity levels correlated to nickel contents as analyzed by atomic absorption analysis.", "UreD, UreE, UreF, and UreG peptides were tentatively identified by gel electrophoretic comparison of mutant and control cell extracts, by in vivo expression of separately cloned genes, or by in vitro transcription-translation analyses; the assignments were confirmed for UreE and UreG by amino-terminal sequencing.", "The latter peptides (apparent M(r)s, 23,900 and 28,500) were present at high levels comparable to those of the urease subunits, whereas the amounts of UreF (apparent M(r), 27,000) and UreD (apparent M(r), 29,300) were greatly reduced, perhaps because of the lack of good ribosome binding sites in the regions upstream of these open reading frames.", "These results demonstrate that all four accessory genes are necessary for the functional incorporation of the urease metallocenter."], "structured": false}
{"doc_id": 29224825, "title": "Hepatic polyploidy and liver growth control.", "abstract": ["The onset of cellular polyploidy is recognized in all differentiated mammalian tissues.", "Polyploidy has been noted frequently in the normal liver, as well as in pathophysiological states of the liver.", "As insights into the significance of polyploidy accumulate gradually, it is becoming clear that cells belonging to high ploidy classes exhibit advancement toward terminal differentiation and cellular senescence with greater probabilities of apoptosis.", "Involvement of specific genetic abnormalities, such as impaired DNA repair, may lead to hepatocellular polyploidy.", "Working models indicate that extensive polyploidy could lead to organ failure, as well as to oncogenesis with activation of precancerous cell clones."], "structured": false}
{"doc_id": 29231620, "title": "Disturbances in the positioning, proliferation and apoptosis of neural progenitors contribute to subcortical band heterotopia formation.", "abstract": ["Cortical malformations are commonly associated with intractable epilepsy and other developmental disorders.", "Our studies utilize the tish rat, a spontaneously occurring genetic model of subcortical band heterotopia (SBH) associated with epilepsy, to evaluate the developmental events underlying SBH formation in the neocortex.", "Our results demonstrate that Pax6(+) and Tbr2(+) progenitors are mislocalized in tish(+/-) and tish(-/-)- neocortex throughout neurogenesis.", "In addition, mislocalized tish(-/-) progenitors possess a longer cell cycle than wild type or normally-positioned tish(-/-) progenitors, owing to a lengthened G(2)+M+G(1) time.", "This mislocalization is not associated with adherens junction breakdown or loss of radial glial polarity in the ventricular zone (VZ), as assessed by immunohistochemistry against phalloidin (to identify F-actin), aPKC-\u03bb and Par3.", "However, vimentin immunohistochemistry indicates that the radial glial scaffold is disrupted in the region of the tish(-/-) heterotopia.", "Moreover, lineage tracing experiments using in utero electroporation in tish(-/-) neocortex demonstrate that mislocalized progenitors do not retain contact with the ventricular surface and that ventricular/subventricular zone (SVZ) progenitors produce neurons that migrate into both the heterotopia and cortical plate (CP).", "Taken together, these findings define a series of developmental errors contributing to SBH formation that differs fundamentally from a primary error in neuronal migration."], "structured": false}
{"doc_id": 29253460, "title": "Sex-related differences in the presentation, treatment and outcomes among patients with acute coronary syndromes: the Global Registry of Acute Coronary Events.", "abstract": ["OBJECTIVE To assess whether sex differences exist in the angiographic severity, management and outcomes of acute coronary syndromes (ACS).   \n", "METHODS The study comprised 7638 women and 19 117 men with ACS who underwent coronary angiography and were included in GRACE (Global Registry of Acute Coronary Events) from 1999-2006.", "Normal vessels/mild disease was defined as <50% stenosis in all epicardial vessels; advanced disease was defined as >or=one vessel with >or=50% stenosis.   \n", "RESULTS Women were older than men and had higher rates of cardiovascular risk factors.", "Men and women presented equally with chest pain; however, jaw pain and nausea were more frequent among women.", "Women were more likely to have normal/mild disease (12% vs 6%, p<0.001) and less likely to have left-main and three-vessel disease (27% vs 32%, p<0.001) or undergo percutaneous coronary intervention (65% vs 68%, p<0.001).", "Women and men with normal and mild disease were treated less aggressively than those with advanced disease.", "Women with advanced disease had a higher risk of death (4% vs 3%, p<0.01).", "After adjustment for age and extent of disease, women were more likely to have adverse outcomes (death, myocardial infarction, stroke and rehospitalisation) at six months compared to men (odds ratio 1.24, 95% confidence interval 1.14 to 1.34); however, sex differences in mortality were no longer statistically significant.   \n", "CONCLUSIONS Women with ACS were more likely to have cardiovascular disease risk factors and atypical symptoms such as nausea compared with men, but were more likely to have normal/mild angiographic coronary artery disease.", "Further study regarding sex differences related to disease severity is warranted."], "structured": true}
{"doc_id": 29288582, "title": "GITR, a member of the TNF receptor superfamily, is costimulatory to mouse T lymphocyte subpopulations.", "abstract": ["GITR (glucocorticoid-induced TNFR family related gene) is a member of the TNFR superfamily (TNFRSF) that is expressed in different cell types, including T lymphocytes.", "Because of a high homology in its cytoplasmic region with other known costimulatory members of the TNFRSF, we investigated whether GITR played a costimulatory role in T lymphocyte subpopulations.", "Our results show that the proliferation response of CD8+ and CD4+ peripheral T cell subpopulations was potentiated when a GITR costimulus was added to an anti-CD3 stimulus.", "Furthermore, expression of the main activation-induced receptor (IL-2Ralpha) and production of IL-2 and IFN-gamma were increased more with a GITR costimulus than with anti-CD3 alone.", "GITR stimulation also enhanced anti-CD3-induced ERK phosphorylation, suggesting that GITR is involved in MAPK-pathway activation.", "Interestingly, CD4+CD25+ regulatory T cell (Treg cell) proliferation was triggered by the GITR costimulus; Treg cell proliferation was paralleled by the loss of the anergic phenotype and suppressor activity.", "Nevertheless, unstimulated GITR(-/-) CD4+CD25+ and GITR(+/+) CD4+CD25+ cells were equally able to exert suppressor activity on CD4+CD25- responder cells.", "These results indicate a novel function for GITR as costimulatory molecule of T cell subsets."], "structured": false}
{"doc_id": 29321530, "title": "PI3K and cancer: lessons, challenges and opportunities", "abstract": ["The central role of phosphoinositide 3-kinase (PI3K) activation in tumour cell biology has prompted a sizeable effort to target PI3K and/or downstream kinases such as AKT and mammalian target of rapamycin (mTOR) in cancer.", "However, emerging clinical data show limited single-agent activity of inhibitors targeting PI3K, AKT or mTOR at tolerated doses.", "One exception is the response to PI3K\u03b4 inhibitors in chronic lymphocytic leukaemia, where a combination of cell-intrinsic and -extrinsic activities drive efficacy.", "Here, we review key challenges and opportunities for the clinical development of inhibitors targeting the PI3K\u2013AKT\u2013mTOR pathway.", "Through a greater focus on patient selection, increased understanding of immune modulation and strategic application of rational combinations, it should be possible to realize the potential of this promising class of targeted anticancer agents."], "structured": false}
{"doc_id": 29334259, "title": "Sequence-based species delimitation for the DNA taxonomy of undescribed insects.", "abstract": ["Cataloging the very large number of undescribed species of insects could be greatly accelerated by automated DNA based approaches, but procedures for large-scale species discovery from sequence data are currently lacking.", "Here, we use mitochondrial DNA variation to delimit species in a poorly known beetle radiation in the genus Rivacindela from arid Australia.", "Among 468 individuals sampled from 65 sites and multiple morphologically distinguishable types, sequence variation in three mtDNA genes (cytochrome oxidase subunit 1, cytochrome b, 16S ribosomal RNA) was strongly partitioned between 46 or 47 putative species identified with quantitative methods of species recognition based on fixed unique (\"diagnostic\") characters.", "The boundaries between groups were also recognizable from a striking increase in branching rate in clock-constrained calibrated trees.", "Models of stochastic lineage growth (Yule models) were combined with coalescence theory to develop a new likelihood method that determines the point of transition from species-level (speciation and extinction) to population-level (coalescence) evolutionary processes.", "Fitting the location of the switches from speciation to coalescent nodes on the ultrametric tree of Rivacindela produced a transition in branching rate occurring at 0.43 Mya, leading to an estimate of 48 putative species (confidence interval for the threshold ranging from 47 to 51 clusters within 2 logL units).", "Entities delimited in this way exhibited biological properties of traditionally defined species, showing coherence of geographic ranges, broad congruence with morphologically recognized species, and levels of sequence divergence typical for closely related species of insects.", "The finding of discontinuous evolutionary groupings that are readily apparent in patterns of sequence variation permits largely automated species delineation from DNA surveys of local communities as a scaffold for taxonomy in this poorly known insect group."], "structured": false}
{"doc_id": 29347970, "title": "CCR6 regulates the migration of inflammatory and regulatory T cells.", "abstract": ["Th17 and regulatory T (Treg) cells play opposite roles in autoimmune diseases.", "However, the mechanisms underlying their proper migration to inflammatory tissues are unclear.", "In this study, we report that these two T cell subsets both express CCR6.", "CCR6 expression in Th17 cells is regulated by TGF-beta and requires two nuclear receptors, RORalpha and RORgamma.", "Th17 cells also express the CCR6 ligand CCL20, which is induced synergistically by TGF-beta and IL-6, which requires STAT3, RORgamma and IL-21.", "Th17 cells, by producing CCL20, promote migration of Th17 and Treg cells in vitro in a CCR6-dependent manner.", "Lack of CCR6 in Th17 cells reduces the severity of experimental autoimmune encephalomyelitis and Th17 and Treg recruitment into inflammatory tissues.", "Similarly, CCR6 on Treg cells is also important for their recruitment into inflammatory tissues.", "Our data indicate an important role of CCR6 in Treg and Th17 cell migration."], "structured": false}
{"doc_id": 29362104, "title": "Inhibition of receptor-mediated calcium influx in T cells by unsaturated non-esterified fatty acids.", "abstract": ["The effect of omega-3, omega-6 and omega-9 unsaturated fatty acids (UFAs) on receptor-mediated Ca2+ entry was investigated in a T-cell line (JURKAT) by using anti-CD3 antibodies (OKT3) to induce intracellular Ca2+ [( Ca2+]i) increase and Ca2+ influx.", "All the UFAs, as well as Ni2+ ions and 12-O-tetradecanoylphorbol 13-acetate, decreased the OKT3-induced sustained [Ca2+]i increase to basal levels.", "Although non-esterified fatty acids activate protein kinase C (PKC) [McPhail, Clayton & Snyderman (1984) Science 224, 622-624; Murakami, Chan & Routtenberg (1986) J. Biol.", "Chem.", "261, 15424-15429], studies using H-7 and analysis of the PKC-dependent phosphorylation of 19 and 80 kDa marker substrates ruled out the involvement of PKC in UFA-induced inhibition of Ca2+ entry.", "Flow-cytometry analysis showed that UFAs do not interfere with antibody-receptor binding.", "BSA (0.2%, w/v) reversed the effect of UFAs after these fatty acids have decreased the OKT3-induced [Ca2+]i increase to basal levels.", "The relevance of these findings and possible mechanisms for inhibition by UFAs of receptor-mediated Ca2+ influx were discussed."], "structured": false}
{"doc_id": 29366489, "title": "Deleted in liver cancer-1 (DLC-1): a tumor suppressor not just for liver.", "abstract": ["Deleted in liver cancer 1 (DLC-1), as its name implied, was originally isolated as a potential tumor suppressor gene often deleted in hepatocellular carcinoma.", "Further studies have indicated that down-expression of DLC-1 either by genomic deletion or DNA methylation is associated with a variety of cancer types including lung, breast, prostate, kidney, colon, uterus, ovary, and stomach.", "Re-expression of DLC-1 in cancer cells regulates the structure of actin cytoskeleton and focal adhesions and significantly inhibits cell growth, supporting its role as a tumor suppressor.", "This tumor suppressive function relies on DLC-1's RhoGTPase activating protein (RhoGAP) activity and steroidogenic acute regulatory (StAR)-related lipid transfer (START) domain, as well as its focal adhesion localization, which is recruited by the Src Homology 2 (SH2) domains of tensins in a phosphotyrosine-independent fashion.", "Therefore, the expression and subcellular localization of DLC-1 could be a useful molecular marker for cancer prognosis, whereas DLC-1 and its downstream signaling molecules might be therapeutic targets for the treatment of cancer."], "structured": false}
{"doc_id": 29367554, "title": "Interaction of Helicobacter pylori with gastric epithelial cells is mediated by the p53 protein family.", "abstract": ["BACKGROUND & AIMS Although the p53 tumor suppressor has been extensively studied, many critical questions remain unanswered about the biological functions of p53 homologs, p73 and p63.", "Accumulating evidence suggests that both p73 and p63 play important roles in regulation of apoptosis, cell differentiation, and therapeutic drug sensitivity.   \n", "METHODS Gastric epithelial cells were cocultured with Helicobacter pylori, and the roles of p63 and p73 proteins were assessed by luciferase reporter, real-time polymerase chain reaction, immunoblotting, and cell survival assays.", "Short hairpin RNA and dominant-negative mutants were used to inhibit activity of p73 and p63 isoforms.", "Human and murine gastric tissues were analyzed by immunohistochemistry with p73 and p63 antibodies and modified Steiner's silver method.   \n", "RESULTS Interaction of H pylori with gastric epithelial cells leads to robust up-regulation of p73 protein in vitro and in vivo in human gastritis specimens and H pylori-infected mice.", "The p73 increase resulted in up-regulation of pro-apoptotic genes, NOXA, PUMA, and FAS receptor in gastric epithelial cells.", "Down-regulation of p73 activity suppressed cell death and Fas receptor induced by H pylori.", "Bacterial virulence factors within the cag pathogenicity island, c-Abl tyrosine kinase, and interaction with p63 isoforms control the activity of p73.   \n", "CONCLUSION Our findings implicate p73 in H pylori-induced apoptosis and more generally suggest that the p53 family may play a role in the epithelial cell response to H pylori infection."], "structured": true}
{"doc_id": 29381091, "title": "Brown and white adipose tissues: intrinsic differences in gene expression and response to cold exposure in mice", "abstract": ["Brown adipocytes dissipate energy, whereas white adipocytes are an energy storage site.", "We explored the plasticity of different white adipose tissue depots in acquiring a brown phenotype by cold exposure.", "By comparing cold-induced genes in white fat to those enriched in brown compared with white fat, at thermoneutrality we defined a \"brite\" transcription signature.", "We identified the genes, pathways, and promoter regulatory motifs associated with \"browning,\" as these represent novel targets for understanding this process.", "For example, neuregulin 4 was more highly expressed in brown adipose tissue and upregulated in white fat upon cold exposure, and cell studies showed that it is a neurite outgrowth-promoting adipokine, indicative of a role in increasing adipose tissue innervation in response to cold.", "A cell culture system that allows us to reproduce the differential properties of the discrete adipose depots was developed to study depot-specific differences at an in vitro level.", "The key transcriptional events underpinning white adipose tissue to brown transition are important, as they represent an attractive proposition to overcome the detrimental effects associated with metabolic disorders, including obesity and type 2 diabetes."], "structured": false}
{"doc_id": 29387024, "title": "Continuous glucose monitoring in pregnant women with type 1 diabetes (CONCEPTT): a multicentre international randomised controlled trial", "abstract": ["BACKGROUND Pregnant women with type 1 diabetes are a high-risk population who are recommended to strive for optimal glucose control, but neonatal outcomes attributed to maternal hyperglycaemia remain suboptimal.", "Our aim was to examine the effectiveness of continuous glucose monitoring (CGM) on maternal glucose control and obstetric and neonatal health outcomes.   \n", "METHODS In this multicentre, open-label, randomised controlled trial, we recruited women aged 18-40 years with type 1 diabetes for a minimum of 12 months who were receiving intensive insulin therapy.", "Participants were pregnant (\u226413 weeks and 6 days' gestation) or planning pregnancy from 31 hospitals in Canada, England, Scotland, Spain, Italy, Ireland, and the USA.", "We ran two trials in parallel for pregnant participants and for participants planning pregnancy.", "In both trials, participants were randomly assigned to either CGM in addition to capillary glucose monitoring or capillary glucose monitoring alone.", "Randomisation was stratified by insulin delivery (pump or injections) and baseline glycated haemoglobin (HbA1c).", "The primary outcome was change in HbA1c from randomisation to 34 weeks' gestation in pregnant women and to 24 weeks or conception in women planning pregnancy, and was assessed in all randomised participants with baseline assessments.", "Secondary outcomes included obstetric and neonatal health outcomes, assessed with all available data without imputation.", "This trial is registered with ClinicalTrials.gov, number NCT01788527.   \n", "FINDINGS Between March 25, 2013, and March 22, 2016, we randomly assigned 325 women (215 pregnant, 110 planning pregnancy) to capillary glucose monitoring with CGM (108 pregnant and 53 planning pregnancy) or without (107 pregnant and 57 planning pregnancy).", "We found a small difference in HbA1c in pregnant women using CGM (mean difference -0\u00b719%; 95% CI -0\u00b734 to -0\u00b703; p=0\u00b70207).", "Pregnant CGM users spent more time in target (68% vs 61%; p=0\u00b70034) and less time hyperglycaemic (27% vs 32%; p=0\u00b70279) than did pregnant control participants, with comparable severe hypoglycaemia episodes (18 CGM and 21 control) and time spent hypoglycaemic (3% vs 4%; p=0\u00b710).", "Neonatal health outcomes were significantly improved, with lower incidence of large for gestational age (odds ratio 0\u00b751, 95% CI 0\u00b728 to 0\u00b790; p=0\u00b70210), fewer neonatal intensive care admissions lasting more than 24 h (0\u00b748; 0\u00b726 to 0\u00b786; p=0\u00b70157), fewer incidences of neonatal hypoglycaemia (0\u00b745; 0\u00b722 to 0\u00b789; p=0\u00b70250), and 1-day shorter length of hospital stay (p=0\u00b70091).", "We found no apparent benefit of CGM in women planning pregnancy.", "Adverse events occurred in 51 (48%) of CGM participants and 43 (40%) of control participants in the pregnancy trial, and in 12 (27%) of CGM participants and 21 (37%) of control participants in the planning pregnancy trial.", "Serious adverse events occurred in 13 (6%) participants in the pregnancy trial (eight [7%] CGM, five [5%] control) and in three (3%) participants in the planning pregnancy trial (two [4%] CGM and one [2%] control).", "The most common adverse events were skin reactions occurring in 49 (48%) of 103 CGM participants and eight (8%) of 104 control participants during pregnancy and in 23 (44%) of 52 CGM participants and five (9%) of 57 control participants in the planning pregnancy trial.", "The most common serious adverse events were gastrointestinal (nausea and vomiting in four participants during pregnancy and three participants planning pregnancy).   \n", "INTERPRETATION Use of CGM during pregnancy in patients with type 1 diabetes is associated with improved neonatal outcomes, which are likely to be attributed to reduced exposure to maternal hyperglycaemia.", "CGM should be offered to all pregnant women with type 1 diabetes using intensive insulin therapy.", "This study is the first to indicate potential for improvements in non-glycaemic health outcomes from CGM use.   \n", "FUNDING Juvenile Diabetes Research Foundation, Canadian Clinical Trials Network, and National Institute for Health Research."], "structured": true}
{"doc_id": 29399239, "title": "Neutrophil extracellular traps: Is immunity the second function of chromatin?", "abstract": ["Neutrophil extracellular traps (NETs) are made of processed chromatin bound to granular and selected cytoplasmic proteins.", "NETs are released by white blood cells called neutrophils, maybe as a last resort, to control microbial infections.", "This release of chromatin is the result of a unique form of cell death, dubbed \"NETosis.", "\"", "Here we review our understanding of how NETs are made, their function in infections and as danger signals, and their emerging importance in autoimmunity and coagulation."], "structured": false}
{"doc_id": 29422484, "title": "Phosphorylation of p35 and p39 by Cdk5 determines the subcellular location of the holokinase in a phosphorylation-site-specific manner.", "abstract": ["Cdk5 is a member of the cyclin-dependent kinase (Cdk) family, which is activated by neuronal activators p35 or p39.", "Cdk5 regulates a variety of neuronal activities including migration, synaptic activity and neuronal death.", "p35 and p39 impart cytoplasmic membrane association of p35-Cdk5 and p39-Cdk5, respectively, through their myristoylation, but it is not clearly understood how the cellular localization is related to different functions.", "We investigated the role of Cdk5 activity in the subcellular localization of p35-Cdk5 and p39-Cdk5.", "Cdk5 activity affected the localization of p35-Cdk5 and p39-Cdk5 through phosphorylation of p35 or p39.", "Using unphosphorylated or phosphomimetic mutants of p35 and p39, we found that phosphorylation at Ser8, common to p35 and p39, by Cdk5 regulated the cytoplasmic localization and perinuclear accumulation of unphosphorylated S8A mutants, and whole cytoplasmic distribution of phosphomimetic S8E mutants.", "Cdk5 activity was necessary to retain Cdk5-activator complexes in the cytoplasm.", "Nevertheless, small but distinct amounts of p35 and p39 were detected in the nucleus.", "In particular, nuclear p35 and p39 were increased when the Cdk5 activity was inhibited.", "p39 had a greater propensity to accumulate in the nucleus than p35, and phosphorylation at Thr84, specific to p39, regulated the potential nuclear localization activity of the Lys cluster in p39.", "These results suggest that the subcellular localization of the Cdk5-activator complexes is determined by its kinase activity, and also implicate a role for p39-Cdk5 in the nucleus."], "structured": false}
{"doc_id": 29423324, "title": "Interleukin-12 and -23 Control Plasticity of CD127(+) Group 1 and Group 3 Innate Lymphoid Cells in the Intestinal Lamina Propria.", "abstract": ["Human group 1 ILCs consist of at least three phenotypically distinct subsets, including NK cells, CD127(+) ILC1, and intraepithelial CD103(+) ILC1.", "In inflamed intestinal tissues from Crohn's disease patients, numbers of CD127(+) ILC1 increased at the cost of ILC3.", "Here we found that differentiation of ILC3 to CD127(+) ILC1 is reversible in vitro and in vivo.", "CD127(+) ILC1 differentiated to ILC3 in the presence of interleukin-2 (IL-2), IL-23, and IL-1\u03b2 dependent on the transcription factor ROR\u03b3t, and this process was enhanced in the presence of retinoic acid.", "Furthermore, we observed in resection specimen from Crohn's disease patients a higher proportion of CD14(+) dendritic cells (DC), which in vitro promoted polarization from ILC3 to CD127(+) ILC1.", "In contrast, CD14(-) DCs promoted differentiation from CD127(+) ILC1 toward ILC3.", "These observations suggest that environmental cues determine the composition, function, and phenotype of CD127(+) ILC1 and ILC3 in the gut."], "structured": false}
{"doc_id": 29429111, "title": "Transcriptional regulation of neuronal genes and its effect on neural functions: expression and function of forkhead transcription factors in neurons.", "abstract": ["Forkhead box transcription factor, class O (FOXO) is a mammalian homologue of DAF-16, which is known to regulate the lifespan of Caenorhabditis elegans and includes subfamilies of forkhead transcription factors such as AFX, FKHRL1, and FKHR.", "FKHR is phosphorylated on three sites (Thr-24, Ser-256, and Ser-319) in a phosphatidylinositol 3-kinase (PI3K)/Akt-dependent manner, thereby inhibiting death signals.", "We here documented dephosphorylation of FKHR following transient forebrain ischemia with its concomitant translocation into the nucleus in neurons in gerbil and mouse brains.", "The activation of FKHR preceded delayed neuronal death in the vulnerable hippocampal regions following ischemic brain injury.", "The FKHR activation was accompanied by an increase in DNA binding activity for FKHR-responsive element on the Fas ligand promoter.", "We also defined FKHR-induced downstream targets such as Fas ligand and Bim in brain ischemia.", "Therefore, we propose a new strategy to rescue neurons from delayed neuronal death by promoting the survival signaling.", "Sodium orthovanadate, a protein tyrosine phosphatase inhibitor, up-regulated Akt activity in the brain and in turn rescue neurons from delayed neuronal death by inhibiting FKHR-dependent or -independent death signals in neurons."], "structured": false}
{"doc_id": 29459383, "title": "ERAAP synergizes with MHC class I molecules to make the final cut in the antigenic peptide precursors in the endoplasmic reticulum.", "abstract": ["The major histocompatibility complex class I molecules display peptides (pMHC I) on the cell surface for immune surveillance by CD8(+) T cells.", "These peptides are generated by proteolysis of intracellular polypeptides by the proteasome in the cytoplasm and then in the endoplasmic reticulum (ER) by the ER aminopeptidase associated with antigen processing (ERAAP).", "To define the unknown mechanism of ERAAP function in vivo, we analyzed naturally processed peptides in cells with or without appropriate MHC I and ERAAP.", "In the absence of MHC I, ERAAP degraded the antigenic precursors in the ER.", "However, MHC I molecules could bind proteolytic intermediates and were essential for generation of the final peptide by ERAAP.", "Thus, ERAAP synergizes with MHC I to generate the final pMHC I repertoire."], "structured": false}
{"doc_id": 29460384, "title": "Estimates of animal and plant protein intake in US adults: results from the Third National Health and Nutrition Examination Survey, 1988-1991.", "abstract": ["OBJECTIVE To describe the sources of protein intake in a sample of the US adult population and among subgroups defined by race-ethnicity, age, and gender.   \n", "DESIGN", "The Third National Health and Nutrition Examination Survey, 1988-1991, is a stratified random sample of the total civilian noninstitutionalized population, drawn from the 50 United States and the District of Columbia.", "For all foods consumed by the participants, based on a 24-hour dietary recall, protein sources and the contribution of each protein type to the total protein intake were determined.   ", "SUBJECTS Adult participants in the third National Health and Nutrition Examination Survey (n = 7,924).   ", "STATISTICAL ANALYSES Weighted total, age-specific, and age-adjusted mean protein intakes were calculated using SAS and WesVarPC.", "Statistical differences were determined by 2-tailed t tests.   \n", "RESULTS The main protein source in the American diet is animal protein (69%).", "Meat, fish, and poultry protein combined contributed the most to animal protein (42%), followed by dairy protein (20%).", "Grains (18%) contributed the most to plant protein consumption.", "Women consumed a lower percentage of beef (14%) and pork (7%) protein than did men (18% and 9%, respectively).", "Women also consumed a higher percentage of poultry (13%), dairy (22%), and fruit and vegetable (11%) protein than did men (11%, 19%, and 9%, respectively).", "Blacks reported eating a higher percentage of poultry (18%) and pork (11%) protein and a lower percent of dairy protein (14%) than did whites (12%, 7%, and 22%, respectively) and Mexican-Americans (11%, 8%, and 17%, respectively).", "Mexican-Americans consumed a higher percentage of legume (7%) and egg (7%) protein than did whites (4% and 4%, respectively) and blacks (4% and 5%, respectively).", "Whites consumed a higher percentage of grain protein (19%) than did blacks (16%) and Mexican-Americans (15%).   \n", "CONCLUSIONS These results show that, although the percentage of total energy from protein may be similar among race-ethnicities and between men and women, their sources of protein are different.", "These differences should be taken into account when providing nutrition education for specific populations."], "structured": true}
{"doc_id": 29467201, "title": "CYP18A1, a key enzyme of Drosophila steroid hormone inactivation, is essential for metamorphosis.", "abstract": ["Ecdysteroids are steroid hormones, which coordinate major developmental transitions in insects.", "Both the rises and falls in circulating levels of active hormones are important for coordinating molting and metamorphosis, making both ecdysteroid biosynthesis and inactivation of physiological relevance.", "We demonstrate that Drosophila melanogaster Cyp18a1 encodes a cytochrome P450 enzyme (CYP) with 26-hydroxylase activity, a prominent step in ecdysteroid catabolism.", "A clear ortholog of Cyp18a1 exists in most insects and crustaceans.", "When Cyp18a1 is transfected in Drosophila S2 cells, extensive conversion of 20-hydroxyecdysone (20E) into 20-hydroxyecdysonoic acid is observed.", "This is a multi-step process, which involves the formation of 20,26-dihydroxyecdysone as an intermediate.", "In Drosophila larvae, Cyp18a1 is expressed in many target tissues of 20E.", "We examined the consequences of Cyp18a1 inactivation on Drosophila development.", "Null alleles generated by excision of a P element and RNAi knockdown of Cyp18a1 both result in pupal lethality, possibly as a consequence of impaired ecdysteroid degradation.", "Our data suggest that the inactivation of 20E is essential for proper development and that CYP18A1 is a key enzyme in this process."], "structured": false}
{"doc_id": 29473081, "title": "The sialyltransferase ST3GAL6 influences homing and survival in multiple myeloma.", "abstract": ["Glycosylation is a stepwise procedure of covalent attachment of oligosaccharide chains to proteins or lipids, and alterations in this process, especially increased sialylation, have been associated with malignant transformation and metastasis.", "The role of altered sialylation in multiple myeloma (MM) cell trafficking has not been previously investigated.", "In the present study we identified high expression of \u03b2-galactoside \u03b1-2,3-sialyltransferase, ST3GAL6, in MM cell lines and patients.", "This gene plays a key role in selectin ligand synthesis in humans through the generation of functional sialyl Lewis X. In MRC IX patients, high expression of this gene is associated with inferior overall survival.", "In this study we demonstrate that knockdown of ST3GAL6 results in a significant reduction in levels of \u03b1-2,3-linked sialic acid on the surface of MM cells with an associated significant reduction in adhesion to MM bone marrow stromal cells and fibronectin along with reduced transendothelial migration in vitro.", "In support of our in vitro findings, we demonstrate significantly reduced homing and engraftment of ST3GAL6 knockdown MM cells to the bone marrow niche in vivo, along with decreased tumor burden and prolonged survival.", "This study points to the importance of altered glycosylation, particularly sialylation, in MM cell adhesion and migration."], "structured": false}
{"doc_id": 29495185, "title": "New developments in the epidemiology of cancer prognosis: traditional and molecular predictors of treatment response and survival.", "abstract": ["There have been numerous epidemiologic investigations to determine factors that may affect cancer risk.", "There is also a rich tradition of evaluating potential somatic changes in the cancer itself to predict recurrence and/or mortality after diagnosis.", "However, there has been relatively little"], "structured": false}
{"doc_id": 29504413, "title": "Behavioral effects of estrogen receptor gene disruption in male mice.", "abstract": ["Gonadal steroid hormones regulate sexually dimorphic development of brain functions and behaviors.", "Their nuclear receptors offer the opportunity to relate molecular events in neurons to simple instinctive mammalian behaviors.", "We have determined the role of estrogen receptor (ER) activation by endogenous estrogen in the development of male-typical behaviors by the use of transgenic estrogen-receptor-deficient (ERKO) mice.", "Surprisingly, in spite of the fact that they are infertile, ERKO mice showed normal motivation to mount females but they achieved less intromissions and virtually no ejaculations.", "Aggressive behaviors were dramatically reduced and male-typical offensive attacks were rarely displayed by ERKO males.", "Moreover, ER gene disruption demasculinized open-field behaviors.", "In the brain, despite the evident loss of functional ER protein, the androgen-dependent system appears to be normally present in ERKO mice.", "Together, these findings indicate that ER gene expression during development plays a major role in the organization of male-typical aggressive and emotional behaviors in addition to simple sexual behaviors."], "structured": false}
{"doc_id": 29509926, "title": "High-Density Lipoproteins Exert Pro-inflammatory Effects on Macrophages via Passive Cholesterol Depletion and PKC-NF-\u03baB/STAT1-IRF1 Signaling.", "abstract": ["Membrane cholesterol modulates a variety of cell signaling pathways and functions.", "While cholesterol depletion by high-density lipoproteins (HDLs) has potent anti-inflammatory effects in various cell types, its effects on inflammatory responses in macrophages remain elusive.", "Here we show overt pro-inflammatory effects of HDL-mediated passive cholesterol depletion and lipid raft disruption in murine and human primary macrophages in vitro.", "These pro-inflammatory effects were confirmed in vivo in peritoneal macrophages from apoA-I transgenic mice, which have elevated HDL levels.", "In line with these findings, the innate immune responses required for clearance of P. aeruginosa bacterial infection in lung were compromised in mice with low HDL levels.", "Expression analysis, ChIP-PCR, and combinatorial pharmacological and genetic intervention studies unveiled that both native and reconstituted HDL enhance Toll-like-receptor-induced signaling by activating a PKC-NF-\u03baB/STAT1-IRF1 axis, leading to increased inflammatory cytokine expression.", "HDL's pro-inflammatory activity supports proper functioning of macrophage immune responses."], "structured": false}
{"doc_id": 29518440, "title": "Hypoxia of the renal medulla--its implications for disease.", "abstract": ["In land mammals, a major task of the kidney is to reabsorb water to allow survival in a dry environment.", "Water conservation is enhanced by the renal medulla, which concentrates the urine to a level up to four times the osmolality of plasma.", "To produce this unique gradient of osmolality, the medulla has a countercurrent system of vessels and tubules that dictates active reabsorption of sodium in a milieu poor in oxygen (Figure 1).1 In this review, we describe how hypoxia of the medulla may relate to susceptibility to acute and chronic renal injury.", "The Renal Medullary Concentrating Mechanism as . .", "."], "structured": false}
{"doc_id": 29526125, "title": "Troponin concentrations for stratification of patients with acute coronary syndromes in relation to therapeutic efficacy of tirofiban. PRISM Study Investigators. Platelet Receptor Inhibition in Ischemic Syndrome Management.", "abstract": ["BACKGROUND A major challenge for physicians is to identify patients with acute coronary syndromes who may benefit from treatment with glycoprotein-IIb/IIIa-receptor antagonists.", "We investigated whether troponin concentrations can be used to stratify patients for benefit from treatment with tirofiban.   \n", "METHODS We enrolled 2222 patients of the Platelet Receptor Inhibition in Ischemic Syndrome Management study with coronary artery disease and who had had chest pain in the previous 24 h. All patients received aspirin and were randomly assigned treatment with tirofiban or heparin.", "We took baseline measurements of troponin I and troponin T. We recorded death, myocardial infarction, or recurrent ischaemia after 48 h infusion treatment and at 7 days and 30 days.   \n", "FINDINGS 629 (28.3%) patients had troponin I concentrations higher than the diagnostic threshold of 1.0 microg/L and 644 (29.0%) troponin T concentrations higher than 0.1 microg/L. 30-day event rates (death, myocardial infarction) were 13.0% for troponin-I-positive patients compared with 4.9% for troponin-I-negative patients (p<0.0001), and 13.7% compared wth 3.5% for troponin T (p<0.001).", "At 30 days, in troponin-I-positive patients, tirofiban had lowered the risk of death (adjusted hazard ratio 0.25 [95% CI 0.09-0.68], p=0.004) and myocardial infarction (0.37 [0.16-0.84], p=0.01).", "This benefit was seen in medically managed patients (0.30 [0.10-0.84], p=0.004) and those undergoing revascularisation (0.37 [0.15-0.93] p=0.02) after 48 h infusion treatment.", "By contrast, no treatment effect was seen for troponin-I-negative patients.", "Similar benefits were seen for troponin-T-positive patients.   \n", "INTERPRETATION Troponin I and troponin T reliably identified high-risk patients with acute coronary syndromes, managed medically and by revascularisation, who would benefit from tirofiban."], "structured": true}
{"doc_id": 29557235, "title": "Evolution and function of ubiquitin-like protein-conjugation systems", "abstract": ["Ubiquitin functions by covalently modifying other proteins.", "In the past few years, a surprising number of other proteins have been identified that, despite often being only slightly similar to ubiquitin, can also be attached to proteins.", "Newly discovered parallels between the activation of ubiquitin and the biosynthesis of certain enzyme cofactors now hint at the possible evolutionary origins of the ubiquitin system."], "structured": false}
{"doc_id": 29564505, "title": "Inflammatory biomarkers and exacerbations in chronic obstructive pulmonary disease.", "abstract": ["IMPORTANCE Exacerbations of respiratory symptoms in chronic obstructive pulmonary disease (COPD) have profound and long-lasting adverse effects on patients.   \n", "OBJECTIVE To test the hypothesis that elevated levels of inflammatory biomarkers in individuals with stable COPD are associated with an increased risk of having exacerbations.   \n", "DESIGN, SETTING, AND PARTICIPANTS Prospective cohort study examining 61,650 participants with spirometry measurements from the Copenhagen City Heart Study (2001-2003) and the Copenhagen General Population Study (2003-2008).", "Of these, 6574 had COPD, defined as a ratio between forced expiratory volume in 1 second (FEV1) and forced vital capacity below 0.7.   \n", "MAIN OUTCOMES AND MEASURES Baseline levels of C-reactive protein (CRP) and fibrinogen and leukocyte count were measured in participants at a time when they were not experiencing symptoms of exacerbations.", "Exacerbations were recorded and defined as short-course treatment with oral corticosteroids alone or in combination with an antibiotic or as a hospital admission due to COPD.", "Levels of CRP and fibrinogen and leukocyte count were defined as high or low according to cut points of 3 mg/L, 14 \u03bcmol/L, and 9 \u00d710(9)/L, respectively.   \n", "RESULTS During follow-up, 3083 exacerbations were recorded (mean, 0.5/participant).", "In the first year of follow-up, multivariable-adjusted odds ratios for having frequent exacerbations were 1.2 (95% CI, 0.7-2.2; 17 events/1000 person-years) for individuals with 1 high biomarker, 1.7 (95% CI, 0.9-3.2; 32 events/1000 person-years) for individuals with 2 high biomarkers, and 3.7 (95% CI, 1.9-7.4; 81 events/1000 person-years) for individuals with 3 high biomarkers compared with individuals who had no elevated biomarkers (9 events/1000 person-years; trend: P = 2 \u00d7 10(-5)).", "Corresponding hazard ratios using maximum follow-up time were 1.4 (95% CI, 1.1-1.8), 1.6 (95% CI, 1.3-2.2), and 2.5 (95% CI, 1.8-3.4), respectively (trend: P = 1 \u00d7 10(-8)).", "The addition of inflammatory biomarkers to a basic model including age, sex, FEV1 percent predicted, smoking, use of any inhaled medication, body mass index, history of previous exacerbations, and time since most recent prior exacerbation improved the C statistics from 0.71 to 0.73 (comparison: P = 9 \u00d7 10(-5)).", "Relative risks were consistent in those with milder COPD, in those with no history of frequent exacerbations, and in the 2 studies separately.", "The highest 5-year absolute risks of having frequent exacerbations in those with 3 high biomarkers (vs no high biomarkers) were 62% (vs 24%) for those with Global Initiative for Chronic Obstructive Lung Disease (GOLD) grades C-D (n = 558), 98% (vs 64%) in those with a history of frequent exacerbations (n = 127), and 52% (vs 15%) for those with GOLD grades 3-4 (n = 465).   \n", "CONCLUSIONS AND RELEVANCE Simultaneously elevated levels of CRP and fibrinogen and leukocyte count in individuals with COPD were associated with increased risk of having exacerbations, even in those with milder COPD and in those without previous exacerbations.", "Further investigation is needed to determine the clinical value of these biomarkers for risk stratification."], "structured": true}
{"doc_id": 29634262, "title": "Gene supplementation therapy for recessive forms of inherited retinal dystrophies", "abstract": ["Over the last decade, gene supplementation therapy for inherited retinal degeneration has come of age.", "Early proof-of-concept studies in animal models of disease showed modest, but genuine improvements in retinal function and/or survival.", "Further development of the vectors used for gene transfer to the retina has led to better treatment efficacy in a wide variety of animal models, leading in 2008 to the initiation of three clinical trials for Leber congenital amaurosis caused by retinal pigment epithelium 65 deficiency.", "The results from these trials suggest that the treatment of inherited retinal dystrophy by gene therapy can be safe and effective.", "Here, we examine the progress of gene supplementation therapy in the retina, and discuss the potential for using gene therapy to treat different forms of inherited retinal degeneration."], "structured": false}
{"doc_id": 29638116, "title": "Complex Tissue and Disease Modeling using hiPSCs.", "abstract": ["Defined genetic models based on human pluripotent stem cells have opened new avenues for understanding disease mechanisms and drug screening.", "Many of these models assume cell-autonomous mechanisms of disease but it is possible that disease phenotypes or drug responses will only be evident if all cellular and extracellular components of a tissue are present and functionally mature.", "To derive optimal benefit from such models, complex multicellular structures with vascular components that mimic tissue niches will thus likely be necessary.", "Here we consider emerging research creating human tissue mimics and provide some recommendations for moving the field forward."], "structured": false}
{"doc_id": 29641682, "title": "Reprogramming somatic cells towards pluripotency by cellular fusion.", "abstract": ["Pluripotent cells arise within the inner cell mass (ICM) of mammals and have the potential to generate all cell types of the adult organism through a process of commitment and ordered differentiation.", "Despite many decades of investigation, the mechanisms that guide and stabilise cell fate choice as well as those that can be engineered to promote its reversal, remain only partially resolved.", "Reprogramming of somatic cells towards a pluripotent-like state can be achieved by several different experimental routes including nuclear transfer, the supply of a defined cocktail of transcription factors, or by fusing somatic cells with a pluripotent stem cell partner.", "These approaches have been used to demonstrate the remarkable intrinsic epigenetic plasticity of many terminally differentiated cell types, as well as to define the factors that are required for pluripotent conversion.", "In this review we summarise some recent advances using cell fusion-based studies to better understand the basis of pluripotency and the epigenetic mechanisms that promote cell type inter-conversion."], "structured": false}
{"doc_id": 29657303, "title": "Anorectic drugs and pulmonary hypertension from the bedside to the bench.", "abstract": ["Anorectic drugs have been used for more than 30 years as an aid in weight reduction for obese persons.", "The use of aminorex, an amphetamine analog that increases norepinephrine levels in the central nervous system, led to an epidemic of primary pulmonary hypertension (PPH) in Europe in the late 1960s and early 1970s.", "The use of fenfluramine and later dexfenfluramine [drugs that inhibit 5-hydroxytryptamine (5-HT) release and reuptake and increases 5-HT and thus 5-HT secretion in the brain] was associated with a second epidemic of PPH.", "All of these drugs have been voluntarily withdrawn from the market.", "The pathogenesis of PPH in patients treated with these agents is uncertain, but recent evidence suggests that potassium channel abnormalities and vasoactive and proliferative properties of 5-HT may play a role.", "There is increasing experimental evidence suggesting that aminorex, fenfluramine and dexfenfluramine inhibit 4-aminopyridine-sensitive currents in potassium channels resulting in vasoconstriction in pulmonary resistance vessels and perhaps smooth muscle cell proliferation.", "5-HT causes pulmonary artery vasoconstriction and smooth muscle cell proliferation.", "Its levels are known to be high in those with fenfluramine-induced PPH.", "However, a firm cause-and-effect relationship has not yet been established.", "One potentially beneficial effect of the epidemics of anorectic-related PPH is that it may have provided important insights into the causes of PPH unrelated to anorectic agents."], "structured": false}
{"doc_id": 29689140, "title": "B-catenin deficiency, but not Myc deletion, suppresses the immediate phenotypes of APC loss in the liver.", "abstract": ["Dysregulated Wnt signaling is seen in approximately 30% of hepatocellular carcinomas; thus, finding pathways downstream of the activation of Wnt signaling is key.", "Here, using cre-lox technology, we deleted the Apc gene in the adult mouse liver and observed a rapid increase in nuclear beta-catenin and c-Myc, which is associated with an induction of proliferation that led to hepatomegaly within 4 days of gene deletion.", "To investigate the downstream pathways responsible for these phenotypes, we analyzed the impact of inactivating APC in the context of deficiency of the potentially key effectors beta-catenin and c-Myc.", "beta-catenin loss rescues both the proliferation and hepatomegaly phenotypes after APC loss.", "However, c-Myc deletion, which rescues the phenotypes of APC loss in the intestine, had no effect on the phenotypes of APC loss in the liver.", "The consequences of the deregulation of the Wnt pathway within the liver are therefore strikingly different from those observed within the intestine, with the vast majority of Wnt targets being beta-catenin-dependent but c-Myc-independent in the liver."], "structured": false}
{"doc_id": 29691654, "title": "Uncoupling Mitochondrial Respiration for Diabesity.", "abstract": ["Until recently, the mechanism of adaptive thermogenesis was ascribed to the expression of uncoupling protein 1 (UCP1) in brown and beige adipocytes.", "UCP1 is known to catalyze a proton leak of the inner mitochondrial membrane, resulting in uncoupled oxidative metabolism with no production of adenosine triphosphate and increased energy expenditure.", "Thus increasing brown and beige adipose tissue with augmented UCP1 expression is a viable target for obesity-related disorders.", "Recent work demonstrates an UCP1-independent pathway to uncouple mitochondrial respiration.", "A secreted enzyme, PM20D1, enriched in UCP1+ adipocytes, exhibits catalytic and hydrolytic activity to reversibly form N-acyl amino acids.", "N-acyl amino acids act as endogenous uncouplers of mitochondrial respiration at physiological concentrations.", "Administration of PM20D1 or its products, N-acyl amino acids, to diet-induced obese mice improves glucose tolerance by increasing energy expenditure.", "In short-term studies, treated animals exhibit no toxicity while experiencing 10% weight loss primarily of adipose tissue.", "Further study of this metabolic pathway may identify novel therapies for diabesity, the disease state associated with diabetes and obesity."], "structured": false}
{"doc_id": 29723642, "title": "A functional polymorphism in the prodynorphin gene promotor is associated with temporal lobe epilepsy.", "abstract": ["The prodynorphin gene (PDYN) encoding the anticonvulsant peptide dynorphin is a strong candidate for a seizure suppressor gene and thus a possible modulator of susceptibility to temporal lobe epilepsy.", "We performed a case control association study in 155 patients with nonlesional temporal lobe epilepsy and 202 controls and found that PDYN promotor low-expression L-alleles confer an increased risk for temporal lobe epilepsy in patients with a family history for seizures.", "Irrespective of the familial background, L-homozygotes display a higher risk for secondarily generalized seizures and status epilepticus."], "structured": false}
{"doc_id": 29735200, "title": "Cardiovascular and renal benefits of dry bean and soybean intake.", "abstract": ["Dry beans and soybeans are nutrient-dense, fiber-rich, and are high-quality sources of protein.", "Protective and therapeutic effects of both dry bean and soybean intake have been documented.", "Studies show that dry bean intake has the potential to decrease serum cholesterol concentrations, improve many aspects of the diabetic state, and provide metabolic benefits that aid in weight control.", "Soybeans are a unique source of the isoflavones genistein and diadzein, which have numerous biological functions.", "Soybeans and soyfoods potentially have multifaceted health-promoting effects, including cholesterol reduction, improved vascular health, preserved bone mineral density, and reduction of menopausal symptoms.", "Soy appears to have salutary effects on renal function, although these effects are not well understood.", "Whereas populations consuming high intakes of soy have lower prevalences of certain cancers, definitive experimental data are insufficient to clarify a protective role of soy.", "The availability of legume products and resources is increasing, incorporating dry beans and soyfoods into the diet can be practical and enjoyable.", "With the shift toward a more plant-based diet, dry beans and soy will be potent tools in the treatment and prevention of chronic disease."], "structured": false}
{"doc_id": 29745822, "title": "Nonuniform probability of glutamate release at a hippocampal synapse.", "abstract": ["A change in the probability of neurotransmitter release (Pr) is an important mechanism underlying synaptic plasticity.", "Although Pr is often assumed to be the same for all terminals at a single synapse, this assumption is difficult to reconcile with the nonuniform size and structure of synaptic terminals in the central nervous system.", "Release probability was measured at excitatory synapses on cultured hippocampal neurons by analysis of the progressive block of N-methyl-D-aspartate receptor-mediated synaptic currents by the irreversible open channel blocker MK-801.", "Release probability was nonuniform (range of 0.09 to 0.54) for terminals arising from a single axon, the majority of which had a low Pr.", "However, terminals with high Pr are more likely to be affected by the activity-dependent modulation that occurs in long-term potentiation."], "structured": false}
{"doc_id": 29785642, "title": "An autoimmune disease, APECED, caused by mutations in a novel gene featuring two PHD-type zinc-finger domains", "abstract": ["Autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED) is the only described systemic autoimmune disease with established monogenic background, and the first autoimmune disorder localized outside the major histocompatibility complex (MHC) region.", "The primary biochemical defect in APECED is unknown.", "We have isolated a novel gene, AIRE, encoding for a putative nuclear protein featuring two PHD-type zinc-finger motifs, suggesting its involvement in transcriptional regulation.", "Five mutations in AIRE are reported in individuals with this disorder.", "This is the first report of a single-gene defect causing a systemic human autoimmune disease, providing a tool for exploring the molecular basis of autoimmunity."], "structured": false}
{"doc_id": 29788648, "title": "NuA4 lysine acetyltransferase Esa1 is targeted to coding regions and stimulates transcription elongation with Gcn5.", "abstract": ["NuA4, the major H4 lysine acetyltransferase (KAT) complex in Saccharomyces cerevisiae, is recruited to promoters and stimulates transcription initiation.", "NuA4 subunits contain domains that bind methylated histones, suggesting that histone methylation should target NuA4 to coding sequences during transcription elongation.", "We show that NuA4 is cotranscriptionally recruited, dependent on its physical association with elongating polymerase II (Pol II) phosphorylated on the C-terminal domain by cyclin-dependent kinase 7/Kin28, but independently of subunits (Eaf1 and Tra1) required for NuA4 recruitment to promoters.", "Whereas histone methylation by Set1 and Set2 is dispensable for NuA4's interaction with Pol II and targeting to some coding regions, it stimulates NuA4-histone interaction and H4 acetylation in vivo.", "The NuA4 KAT, Esa1, mediates increased H4 acetylation and enhanced RSC occupancy and histone eviction in coding sequences and stimulates the rate of transcription elongation.", "Esa1 cooperates with the H3 KAT in SAGA, Gcn5, to enhance these functions.", "Our findings delineate a pathway for acetylation-mediated nucleosome remodeling and eviction in coding sequences that stimulates transcription elongation by Pol II in vivo."], "structured": false}
{"doc_id": 29806339, "title": "Targeting mitotic exit leads to tumor regression in vivo: Modulation by Cdk1, Mastl, and the PP2A/B55\u03b1,\u03b4 phosphatase.", "abstract": ["Targeting mitotic exit has been recently proposed as a relevant therapeutic approach against cancer.", "By using genetically engineered mice, we show that the APC/C cofactor Cdc20 is essential for anaphase onset in vivo in embryonic or adult cells, including progenitor/stem cells.", "Ablation of Cdc20 results in efficient regression of aggressive tumors, whereas current mitotic drugs display limited effects.", "Yet, Cdc20 null cells can exit from mitosis upon inactivation of Cdk1 and the kinase Mastl (Greatwall).", "This mitotic exit depends on the activity of PP2A phosphatase complexes containing B55\u03b1 or B55\u03b4 regulatory subunits.", "These data illustrate the relevance of critical players of mitotic exit in mammals and their implications in the balance between cell death and mitotic exit in tumor cells."], "structured": false}
{"doc_id": 29807737, "title": "DrugBank 5.0: a major update to the DrugBank database for 2018", "abstract": ["DrugBank (www.drugbank.ca) is a web-enabled database containing comprehensive molecular information about drugs, their mechanisms, their interactions and their targets.", "First described in 2006, DrugBank has continued to evolve over the past 12 years in response to marked improvements to web standards and changing needs for drug research and development.", "This year's update, DrugBank 5.0, represents the most significant upgrade to the database in more than 10 years.", "In many cases, existing data content has grown by 100% or more over the last update.", "For instance, the total number of investigational drugs in the database has grown by almost 300%, the number of drug-drug interactions has grown by nearly 600% and the number of SNP-associated drug effects has grown more than 3000%.", "Significant improvements have been made to the quantity, quality and consistency of drug indications, drug binding data as well as drug-drug and drug-food interactions.", "A great deal of brand new data have also been added to DrugBank 5.0.", "This includes information on the influence of hundreds of drugs on metabolite levels (pharmacometabolomics), gene expression levels (pharmacotranscriptomics) and protein expression levels (pharmacoprotoemics).", "New data have also been added on the status of hundreds of new drug clinical trials and existing drug repurposing trials.", "Many other important improvements in the content, interface and performance of the DrugBank website have been made and these should greatly enhance its ease of use, utility and potential applications in many areas of pharmacological research, pharmaceutical science and drug education."], "structured": false}
{"doc_id": 29828242, "title": "Analyzing mechanisms of alternative pre-mRNA splicing using in vitro splicing assays.", "abstract": ["The development of in vitro assays to analyze pre-mRNA splicing resulted in the discovery of many fundamental features characterizing splicing signals and the machinery that completes this process.", "Because in vitro assays can be manipulated by various biochemical approaches, the versatility of investigating alternative pre-mRNA splicing in the test tube appears endless.", "Importantly, modifications in reaction conditions can lead to the accumulation, isolation, and characterization of reaction intermediates, a prerequisite for gaining mechanistic insights into how the spliceosome carries out intron removal, and how regulatory elements assist the general splicing machinery in defining splice sites and alternative exons.", "These considerable experimental advantages have made the in vitro splicing system a standard assay, even though this approach is independent from RNA transcription and other RNA processing events, and in some respects deviates from the natural process of mRNA biogenesis.", "Here, we describe the tools and techniques necessary to carry out in vitro splicing assays.", "Analyses of various experimental designs are presented to highlight the approaches taken to gain insights into the mechanisms by which splice site recognition and activation are communicated with the general splicing machinery.", "Methods to measure the kinetics of splicing, to observe the formation of the pre-spliceosomal complexes, and to manipulate and modify the in vitro system to resolve the regulatory influences in alternative splicing are presented."], "structured": false}
{"doc_id": 29845974, "title": "New Roles for Pharmacists in Community Mental Health Care: A Narrative Review", "abstract": ["Medicines are a major treatment modality for many mental illnesses, and with the growing burden of mental disorders worldwide pharmacists are ideally positioned to play a greater role in supporting people with a mental illness.", "This narrative review aims to describe the evidence for pharmacist-delivered services in mental health care and address the barriers and facilitators to increasing the uptake of pharmacist services as part of the broader mental health care team.", "This narrative review is divided into three main sections: (1) the role of the pharmacist in mental health care in multidisciplinary teams and in supporting early detection of mental illness; (2) the pharmacists' role in supporting quality use of medicines in medication review, strategies to improve medication adherence and antipsychotic polypharmacy, and shared decision making; and (3) barriers and facilitators to the implementation of mental health pharmacy services with a focus on organizational culture and mental health stigma.", "In the first section, the review presents new roles for pharmacists within multidisciplinary teams, such as in case conferencing or collaborative drug therapy management; and new roles that would benefit from increased pharmacist involvement, such as the early detection of mental health conditions, development of care plans and follow up of people with mental health problems.", "The second section describes the impact of medication review services and other pharmacist-led interventions designed to reduce inappropriate use of psychotropic medicines and improve medication adherence.", "Other new potential roles discussed include the management of antipsychotic polypharmacy and involvement in patient-centered care.", "Finally, barriers related to pharmacists' attitudes, stigma and skills in the care of patients with mental health problems and barriers affecting pharmacist-physician collaboration are described, along with strategies to reduce mental health stigma."], "structured": false}
{"doc_id": 29851836, "title": "UV light-induced DNA synthesis arrest in HeLa cells is associated with changes in phosphorylation of human single-stranded DNA-binding protein.", "abstract": ["We show that DNA replication activity in extracts of human HeLa cells decreases following UV irradiation.", "Alterations in replication activity in vitro parallel the UV-induced block in cell cycle progression of these cells in culture.", "UV irradiation also induces specific changes in the pattern of phosphorylation of the 34 kDa subunit of a DNA replication protein, human single-stranded DNA-binding protein (hSSB).", "The appearance of a hyperphosphorylated form of hSSB correlates with reduced in vitro DNA replication activity in extracts of UV-irradiated cells.", "Replication activity can be restored to these extracts in vitro by addition of purified hSSB.", "These results suggest that UV-induced DNA synthesis arrest may be mediated in part through phosphorylation-related alterations in the activity of hSSB, an essential component of the DNA replication apparatus."], "structured": false}
{"doc_id": 29863668, "title": "P446L-importin-beta inhibits nuclear envelope assembly by sequestering nuclear envelope assembly factors to the microtubules.", "abstract": ["The P446L mutant Drosophila importin-beta (P446L-imp-beta) has been reported to prohibit--in dominant negative fashion--nuclear envelope (NE) assembly.", "Along elucidating the mode of action of P446L-imp-beta we studied in vitro NE assembly on Sepharose beads.", "While Drosophila embryo extracts support NE assembly over Sepharose beads coated with Ran, NE assembly does not take place in extracts supplied with exogenous P446L-imp-beta.", "A NE also forms over importin-beta-coated beads.", "Surprisingly, when immobilized to Sepharose beads P446L-imp-beta as efficiently recruits NE vesicles as normal importin-beta.", "The discrepancy in behavior of cytoplasmic and bead-bound P446L-imp-beta appears to be related to icreased--as compared to normal importin-beta--microtubule (MT) binding ability of P446L-imp-beta.", "While wild-type importin-beta is able to bind MTs and the binding decreases upon RanGTP interaction, P446L-imp-beta cannot be removed from the MTs by RanGTP.", "P446L-imp-beta, like normal importin-beta, binds some types of the nucleoporins that have been known to be required for NE assembly at the end of mitosis.", "It appears that the inhibitory effect of P446L-imp-beta on NE assembly is caused by sequestering some of the nucleoporins required for NE assembly to the MTs."], "structured": false}
{"doc_id": 29877890, "title": "Histone chaperones and nucleosome assembly.", "abstract": ["Recent structures of the nucleosome core particle reveal details of histone-histone and histone-DNA interactions.", "These structures have now set the stage for understanding chromatin assembly and dynamics during replication and transcription.", "Histone chaperones and chromatin remodeling complexes are important in both of these processes.", "The nucleosome and its protein core, the histone octamer, have twofold symmetry, which histone chaperones may use to bind core histones.", "Recent studies suggest that the nucleoplasmin pentamer may mediate histone storage, sperm chromatin decondensation and nucleosome assembly, by dimerizing to form a decamer.", "In this model, histone binding on the lateral surface of the chaperone involves stereospecific interactions and a shared twofold axis."], "structured": false}
{"doc_id": 29947146, "title": "Intestinal methane production in obese individuals is associated with a higher body mass index.", "abstract": ["BACKGROUND Obesity is an epidemic that affects 1 in 3 individuals in the United States, and recent evidence suggests that enteric microbiota may play a significant role in the development of obesity.", "This study evaluated the association between methanogenic archaea and obesity in human subjects.   \n", "METHODS Subjects with a body mass index (BMI) of 30 kg/m\u00b2 or higher were prospectively recruited from the weight loss program of a tertiary care medical center.", "Subjects who met the study's inclusion criteria were asked to complete a questionnaire that included a series of visual analogue scores for bowel symptom severities.", "Subjects then provided a single end-expiratory breath sample to quantitate methane levels.", "Bivariate and multivariate analyses were used to determine associations with BMI.   \n", "RESULTS A total of 58 patients qualified for enrollment.", "Twenty percent of patients (n = 12) had breath test results that were positive for methane (>3 parts per million [ppm]), with a mean breath methane concentration of 12.2\u00b13.1 ppm.", "BMI was significantly higher in methane-positive subjects (45.2\u00b12.3 kg/m\u00b2) than in methane-negative subjects (38.5\u00b10.8 kg/m\u00b2; P=.001).", "Methane-positive subjects also had a greater severity of constipation than methane-negative subjects (21.3\u00b16.4 vs 9.5\u00b12.4; P=.043).", "Multiple regression analysis illustrated a significant association between BMI and methane, constipation, and antidepressant use.", "However, methane remained an independent predictor of elevated BMI when controlling for antidepressant use (P<.001) and when controlling for both constipation and antidepressant use (6.55 kg/m\u00b2 greater BMI; P=.003).   \n", "CONCLUSION This is the first human study to demonstrate that a higher concentration of methane detected by breath testing is a predictor of significantly greater obesity in overweight subjects."], "structured": true}
{"doc_id": 29955650, "title": "Study of infectious intestinal disease in England: rates in the community, presenting to general practice, and reported to national surveillance. The Infectious Intestinal Disease Study Executive.", "abstract": ["OBJECTIVE To establish the incidence and aetiology of infectious intestinal disease in the community and presenting to general practitioners.", "Comparison with incidence and aetiology of cases reaching national laboratory based surveillance.   \n", "DESIGN Population based community cohort incidence study, general practice based incidence studies, and case linkage to national laboratory surveillance.   \n", "SETTING 70 general practices throughout England.   \n", "PARTICIPANTS 459 975 patients served by the practices.", "Community surveillance of 9776 randomly selected patients.   \n", "MAIN OUTCOME MEASURES Incidence of infectious intestinal disease in community and reported to general practice.   \n", "RESULTS 781 cases were identified in the community cohort, giving an incidence of 19.4/100 person years (95% confidence interval 18.1 to 20.8).", "8770 cases presented to general practice (3.3/100 person years (2.94 to 3.75)).", "One case was reported to national surveillance for every 1.4 laboratory identifications, 6.2 stools sent for laboratory investigation, 23 cases presenting to general practice, and 136 community cases.", "The ratio of cases in the community to cases reaching national surveillance was lower for bacterial pathogens (salmonella 3.2:1, campylobacter 7.6:1) than for viruses (rotavirus 35:1, small round structured viruses 1562:1).", "There were many cases for which no organism was identified.   \n", "CONCLUSIONS Infectious intestinal disease occurs in 1 in 5 people each year, of whom 1 in 6 presents to a general practitioner.", "The proportion of cases not recorded by national laboratory surveillance is large and varies widely by microorganism.", "Ways of supplementing the national laboratory surveillance system for infectious intestinal diseases should be considered."], "structured": true}
{"doc_id": 29981186, "title": "Venous thrombosis in cancer patients: insights from the FRONTLINE survey.", "abstract": ["BACKGROUND Venous thromboembolism (VTE) is a common complication in cancer patients and a significant cause of morbidity and mortality.", "However, little information is available on oncologists' perceptions of the risk of VTE and its management.", "The Fundamental Research in Oncology and Thrombosis (FRONTLINE) study is the first comprehensive global survey of thrombosis and cancer.", "The study was designed to collect data on the perceived risk and patterns of practice with regard to VTE in cancer patients undergoing surgical and medical management of their malignancy and to provide information on international and regional practice patterns, allowing for the design of research studies to answer the concerns of practicing clinicians.   \n", "METHODS Literature reviews were performed to provide a current evidence base against which to compare the findings, and a survey was developed under the guidance of an advisory board.", "A paper-based reply-paid questionnaire was distributed globally between July and November 2001 to clinicians involved in cancer care and was made available on a dedicated website.   \n", "FINDINGS A total of 3,891 completed responses were available for analysis.", "Brain and pancreatic tumors were considered to carry a high risk for VTE, and 80% of respondents considered the use of central venous lines to be associated with a high risk of VTE.", "Marked differences were seen in the use of thromboprophylaxis for surgical and medical cancer patients, with over 50% of surgeons reporting that they initiated thromboprophylaxis routinely, while most medical oncologists reported using thromboprophylaxis in less than 5% of medical patients.", "Low molecular weight heparin (LMWH) was the most popular method of thromboprophylaxis employed in both surgical and medical patients and was more favored by European than U.S. clinicians.", "Some 20% of respondents reported using aspirin for prophylaxis, despite there being no reliable evidence for this agent as effective in prevention in this population.", "For the treatment of VTE, LMWH was again the most common initial treatment, although, for the long-term, oral anticoagulation therapy was widely adopted.", "Many patients were treated for VTE on an outpatient basis, and secondary prevention of VTE was typically continued for 3 to 6 months after an episode of deep vein thrombosis or for longer in the case of pulmonary embolism.   \n", "INTERPRETATION The results of the FRONTLINE survey demonstrate a need for guidelines to direct clinical practice in line with evidence-based data concerning cancer and VTE.", "Oncologists need to be educated regarding the true risks of VTE associated with certain cancers and on strategies for prevention and treatment to reduce the morbidity and mortality associated with VTE in all cancer patients.", "The study has also helped identify areas for future research."], "structured": true}
{"doc_id": 30034334, "title": "A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair.", "abstract": ["Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) and the associated proteins (Cas) comprise a system of adaptive immunity against viruses and plasmids in prokaryotes.", "Cas1 is a CRISPR-associated protein that is common to all CRISPR-containing prokaryotes but its function remains obscure.", "Here we show that the purified Cas1 protein of Escherichia coli (YgbT) exhibits nuclease activity against single-stranded and branched DNAs including Holliday junctions, replication forks and 5'-flaps.", "The crystal structure of YgbT and site-directed mutagenesis have revealed the potential active site.", "Genome-wide screens show that YgbT physically and genetically interacts with key components of DNA repair systems, including recB, recC and ruvB. Consistent with these findings, the ygbT deletion strain showed increased sensitivity to DNA damage and impaired chromosomal segregation.", "Similar phenotypes were observed in strains with deletion of CRISPR clusters, suggesting that the function of YgbT in repair involves interaction with the CRISPRs.", "These results show that YgbT belongs to a novel, structurally distinct family of nucleases acting on branched DNAs and suggest that, in addition to antiviral immunity, at least some components of the CRISPR-Cas system have a function in DNA repair."], "structured": false}
{"doc_id": 30041340, "title": "Antibodies from patients with rheumatoid arthritis target citrullinated histone 4 contained in neutrophils extracellular traps.", "abstract": ["BACKGROUND Histone deimination regulates gene function and contributes to antimicrobial response, allowing the formation of neutrophil extracellular traps (NETs).", "Deiminated proteins are target of anti-citrullinated peptides antibodies (ACPA) in rheumatoid arthritis (RA).   \n", "OBJECTIVE The objective of this paper is to test the hypothesis that RA sera react with deiminated histones contained in NETs.   \n", "METHODS Neutrophils from peripheral blood were stimulated with A23187 and acid treated; NETosis was induced by phorbol myristate acetate, and NET proteins were isolated.", "Sera were tested by immunoblot on acid extracted proteins from neutrophils and from NETs, and by ELISA on deiminated histone H4 or H4-derived peptides.", "Bands reactive with RA sera were excised from gels, digested with trypsin and subjected to matrix-assisted laser desorption/ionisation time of flight (MALDI-TOF) analysis, before and after derivatisation to detect citrullinated peptides.   \n", "RESULTS RA sera reacted with a deiminated antigen of 11 KDa from activated neutrophils, recognised also by anti-H4 and antideiminated H4 antibodies.", "A similar reactivity was observed with NET proteins.", "The antigen from neutrophils or NETs was identified as citrullinated H4 by MALDI-TOF analysis.", "By ELISA, RA sera bound in vitro citrullinated H4.", "Citrullinated H4 14-34 and 31-50 peptides detected antibodies in 67% and 63% of RA sera and in less than 5% of controls; antibody titre was correlated with anti-CCP2.   \n", "CONCLUSIONS Citrullinated H4 from activated neutrophils and NETs is a target of antibodies in RA, and synthetic citrullinated H4-derived peptides are a new substrate for ACPA detection.", "As NETosis can generate antigens for ACPA, these data suggest a novel connection between innate and adaptive immunity in RA."], "structured": true}
{"doc_id": 30041895, "title": "Mechanosensitive ion channel Piezo2 is important for enterochromaffin cell response to mechanical forces", "abstract": ["KEY POINTS The gastrointestinal epithelial enterochromaffin (EC) cell synthesizes the vast majority of the body's serotonin.", "As a specialized mechanosensor, the EC cell releases this serotonin in response to mechanical forces.", "However, the molecular mechanism of EC cell mechanotransduction is unknown.", "In the present study, we show, for the first time, that the mechanosensitive ion channel Piezo2 is specifically expressed by the human and mouse EC cells.", "Activation of Piezo2 by mechanical forces results in a characteristic ionic current, the release of serotonin and stimulation of gastrointestinal secretion.", "Piezo2 inhibition by drugs or molecular knockdown decreases mechanosensitive currents, serotonin release and downstream physiological effects.", "The results of the present study suggest that the mechanosensitive ion channel Piezo2 is specifically expressed by the EC cells of the human and mouse small bowel and that it is important for EC cell mechanotransduction.   ", "ABSTRACT The enterochromaffin (EC) cell in the gastrointestinal (GI) epithelium is the source of nearly all systemic serotonin (5-hydroxytryptamine; 5-HT), which is an important neurotransmitter and endocrine, autocrine and paracrine hormone.", "The EC cell is a specialized mechanosensor, and it is well known that it releases 5-HT in response to mechanical forces.", "However, the EC cell mechanotransduction mechanism is unknown.", "The present study aimed to determine whether Piezo2 is involved in EC cell mechanosensation.", "Piezo2 mRNA was expressed in human jejunum and mouse mucosa from all segments of the small bowel.", "Piezo2 immunoreactivity localized specifically within EC cells of human and mouse small bowel epithelium.", "The EC cell model released 5-HT in response to stretch, and had Piezo2 mRNA and protein, as well as a mechanically-sensitive inward non-selective cation current characteristic of Piezo2.", "Both inward currents and 5-HT release were inhibited by Piezo2 small interfering RNA and antagonists (Gd3+ and D-GsMTx4).", "Jejunum mucosal pressure increased 5-HT release and short-circuit current via submucosal 5-HT3 and 5-HT4 receptors.", "Pressure-induced secretion was inhibited by the mechanosensitive ion channel antagonists gadolinium, ruthenium red and D-GsMTx4.", "We conclude that the EC cells in the human and mouse small bowel GI epithelium selectively express the mechanosensitive ion channel Piezo2, and also that activation of Piezo2 by force leads to inward currents, 5-HT release and an increase in mucosal secretion.", "Therefore, Piezo2 is critical to EC cell mechanosensitivity and downstream physiological effects."], "structured": false}
{"doc_id": 30058568, "title": "Improved prognosis of thoracic aortic aneurysms: a population-based study.", "abstract": ["CONTEXT Managing thoracic aortic aneurysms identified incidentally by increased use of computed tomography, echocardiography, and magnetic resonance imaging is problematic, especially in the elderly.   \n", "OBJECTIVE To ascertain whether the previously reported poor prognosis for individuals with thoracic aortic aneurysms has changed with better medical therapies and improved surgical techniques that can now be applied to aneurysm management.   \n", "DESIGN Population-based cohort study.   \n", "SETTING AND PATIENTS All 133 patients with the diagnosis of degenerative thoracic aortic aneurysms among Olmsted County, Minnesota, residents between 1980 and 1994 compared with a previously reported cohort of similar patients between 1951 and 1980.   \n", "MAIN OUTCOME MEASURES The primary clinical end points were incidence, cumulative rupture risk, rupture risk as a function of aneurysm size, and survival.   \n", "RESULTS In contrast to abdominal aortic aneurysms, for which men are affected predominately, 51% of thoracic aortic aneurysms were identified in women who were considerably older at recognition than men (mean age, 75.9 vs 62.8 years, respectively; P= .01).", "The overall incidence rate of 10.4 per 100000 person-years (95% confidence interval [CI], 8.6-12.2) between 1980 and 1994 was more than 3-fold higher than the rate from 1951 to 1980.", "The cumulative risk of rupture was 20% after 5 years.", "Seventy-nine percent of ruptures occurred in women (P= .01).", "The 5-year risk of rupture as a function of aneurysm size at recognition was 0% for aneurysms less than 4 cm in diameter, 16% (95% CI, 4%-28%) for those 4 to 5.9 cm, and 31% (95% CI, 5%-56%) for aneurysms 6 cm or more.", "Overall 5-year survival improved to 56% (95% CI, 48%-66%) between 1980 and 1994 compared with only 19% between 1951 and 1980 (P<.01).   \n", "CONCLUSIONS In this population, elderly women represent an increasing portion of all patients with clinically recognized thoracic aortic aneurysms and constitute the majority of patients whose aneurysm eventually ruptures.", "Overall survival for thoracic aortic aneurysms has improved significantly in the past 15 years."], "structured": true}
{"doc_id": 30101891, "title": "Intravenous valproate is well tolerated in unstable patients with status epilepticus.", "abstract": ["The authors reviewed hospital records of 13 patients with status epilepticus and hypotension who received IV valproate therapy.", "Most patients were elderly (74.4 +/-", "12.5 [SD] years) and received a loading dose of valproate of 25.1 +/-", "5.0 mg/kg (range 14.7 to 32.7), at a rate of 36.6 +/-", "25.1 mg/min (range 6.3 to 100).", "There were no significant changes in blood pressure, pulse, or use of vasopressors.", "The data suggest that valproate loading is well tolerated, even in patients with cardiovascular instability."], "structured": false}
{"doc_id": 30122260, "title": "Interplays between ATM/Tel1 and ATR/Mec1 in sensing and signaling DNA double-strand breaks.", "abstract": ["DNA double-strand breaks (DSBs) are highly hazardous for genome integrity because they have the potential to cause mutations, chromosomal rearrangements and genomic instability.", "The cellular response to DSBs is orchestrated by signal transduction pathways, known as DNA damage checkpoints, which are conserved from yeasts to humans.", "These pathways can sense DNA damage and transduce this information to specific cellular targets, which in turn regulate cell cycle transitions and DNA repair.", "The mammalian protein kinases ATM and ATR, as well as their budding yeast corresponding orthologs Tel1 and Mec1, act as master regulators of the checkpoint response to DSBs.", "Here, we review the early steps of DSB processing and the role of DNA-end structures in activating ATM/Tel1 and ATR/Mec1 in an orderly and reciprocal manner."], "structured": false}
{"doc_id": 30152134, "title": "The \u2018definitive\u2019 (and \u2018primitive\u2019) guide to zebrafish hematopoiesis", "abstract": ["Progressive advances using zebrafish as a model organism have provided hematologists with an additional genetic system to study blood cell formation and hematological malignancies.", "Despite extensive evolutionary divergence between bony fish (teleosts) and mammals, the molecular pathways governing hematopoiesis have been highly conserved.", "As a result, most (if not all) of the critical hematopoietic transcription factor genes identified in mammals have orthologues in zebrafish.", "As in other vertebrates, all of the teleost blood lineages are believed to originate from a pool of pluripotent, self-renewing hematopoietic stem cells.", "Here, we provide a detailed review of the timing, anatomical location, and transcriptional regulation of zebrafish \u2018primitive\u2019 and \u2018definitive\u2019 hematopoiesis as well as discuss a model of T-cell leukemia and recent advances in blood cell transplantation.", "Given that many of the regulatory genes that control embryonic hematopoiesis have been implicated in oncogenic pathways in adults, an understanding of blood cell ontogeny is likely to provide insights into the pathophysiology of human leukemias."], "structured": false}
{"doc_id": 30184745, "title": "Steroid receptor interactions with heat shock protein and immunophilin chaperones.", "abstract": ["We have provided a historical perspective on a body of steroid receptor research dealing with the structure and physiological significance of the untransformed 9S receptor that has often confused both novice and expert investigators.", "The frequent controversies and equivocations of earlier studies were due to the fact that the native, hormone-free state of these receptors is a large multiprotein complex that resisted description for many years because of its unstable and dynamic nature.", "The untransformed 9S state of the steroid and dioxin receptors has provided a unique system for studying the function of the ubiquitous, abundant, and conserved heat shock protein, hsp90.", "The hormonal control of receptor association with hsp90 provided a method of manipulating the receptor heterocomplex in a manner that was physiologically meaningful.", "For several steroid receptors, binding to hsp90 was required for the receptor to be in a native hormone-binding state, and for all of the receptors, hormone binding promoted dissociation of the receptor from hsp90 and conversion of the receptor to the DNA-binding state.", "Although the complexes between tyrosine kinases and hsp90 were discovered earlier, the hormonal regulation or steroid receptor association with hsp90 permitted much more rapid and facile study of hsp90 function.", "The observations that hsp90 binds to the receptors through their HBDs and that these domains can be fused to structurally different proteins bringing their function under hormonal control provided a powerful linkage between the hormonal regulation of receptor binding to hsp90 and the initial step in steroid hormone action.", "Because the 9S receptor hsp90 heterocomplexes could be physically stabilized by molybdate, their protein composition could be readily studied, and it became clear that these complexes are multiprotein structures containing a number of unique proteins, such as FKBP51, FKBP52, CyP-40, and p23, that were discovered because of their presence in these structures.", "Further analysis showed that hsp90 itself exists in a variety of native multiprotein heterocomplexes independent of steroid receptors and other 'substrate' proteins.", "Cell-free systems can now be used to study the formation of receptor heterocomplexes.", "As we outlined in the scheme of Fig. 1, the multicomponent receptor-hsp90 heterocomplex assembly system is being reconstituted, and the importance of individual proteins, such as hsp70, p60, and p23, in the assembly process is becoming recognized.", "It should be noted that our understanding of the mechanism and purpose of steroid receptor heterocomplex assembly is still at an early stage.", "We can now speculate on the roles of receptor-associated proteins in receptor action, both as individuals and as a group, but their actual functions are still vague or unknown.", "We can make realistic models about the chaperoning and trafficking of steroid receptors, but we don't yet know how these processes occur, we don't know where chaperoning occurs in the cell", "(e.g. Is it limited to the cytoplasm?", "Is it a diffuse process or does chaperoning occur in association with structural elements?), and, with the exception of the requirement for hormone binding, we don't know the extent to which the hsp90-based chaperone system impacts on steroid hormone action.", "It is not yet clear how far the discovery of this hsp90 heterocomplex assembly system will be extended to the development of a general understanding of protein processing in the cell.", "Because this assembly system is apparently present in all eukaryotic cells, it probably performs an essential function for many proteins.", "The bacterial homolog of hsp90 is not an essential protein, but hsp90 is essential in eukaryotes, and recent studies indicate that the development of the cell nucleus from prokaryotic progenitors was accompanied by the duplication of genes for hsp90 and hsp70 (698).", "(ABSTRACT TRUNCATED)"], "structured": false}
{"doc_id": 30208015, "title": "Molecular Characterization of Oxysterol Binding to the Epstein-Barr Virus-induced Gene 2 (GPR183)* ", "abstract": ["Oxysterols are oxygenated cholesterol derivates that are emerging as a physiologically important group of molecules.", "Although they regulate a range of cellular processes, only few oxysterol-binding effector proteins have been identified, and the knowledge of their binding mode is limited.", "Recently, the family of G protein-coupled seven transmembrane-spanning receptors (7TM receptors) was added to this group.", "Specifically, the Epstein-Barr virus-induced gene 2 (EBI2 or GPR183) was shown to be activated by several oxysterols, most potently by 7\u03b1,25-dihydroxycholesterol (7\u03b1,25-OHC).", "Nothing is known about the binding mode, however.", "Using mutational analysis, we identify here four key residues for 7\u03b1,25-OHC binding: Arg-87 in TM-II (position II:20/2.60), Tyr-112 and Tyr-116 (positions III:09/3.33 and III:13/3.37) in TM-III, and Tyr-260 in TM-VI (position VI:16/6.51).", "Substituting these residues with Ala and/or Phe results in a severe decrease in agonist binding and receptor activation.", "Docking simulations suggest that Tyr-116 interacts with the 3\u03b2-OH group in the agonist, Tyr-260 with the 7\u03b1-OH group, and Arg-87, either directly or indirectly, with the 25-OH group, although nearby residues likely also contribute.", "In addition, Tyr-112 is involved in 7\u03b1,25-OHC binding but via hydrophobic interactions.", "Finally, we show that II:20/2.60 constitutes an important residue for ligand binding in receptors carrying a positively charged residue at this position.", "This group is dominated by lipid- and nucleotide-activated receptors, here exemplified by the CysLTs, P2Y12, and P2Y14.", "In conclusion, we present the first molecular characterization of oxysterol binding to a 7TM receptor and identify position II:20/2.60 as a generally important residue for ligand binding in certain 7TM receptors."], "structured": false}
{"doc_id": 30221601, "title": "Up-regulation of neuronal calcium sensor-1 (NCS-1) in the prefrontal cortex of schizophrenic and bipolar patients.", "abstract": ["The delineation of dopamine dysfunction in the mentally ill has been a long-standing quest of biological psychiatry.", "The present study focuses on a recently recognized group of dopamine receptor-interacting proteins as possible novel sites of dysfunction in schizophrenic and bipolar patients.", "We demonstrate that the dorsolateral prefrontal cortex in schizophrenia and bipolar cases from the Stanley Foundation Neuropathology Consortium display significantly elevated levels of the D2 dopamine receptor desensitization regulatory protein, neuronal calcium sensor-1.", "These levels of neuronal calcium sensor-1 were not influenced by age, gender, hemisphere, cause of death, postmortem period, alcohol consumption, or antipsychotic and mood stabilizing medications.", "The present study supports the hypothesis that schizophrenia and bipolar disorder may be associated with abnormalities in dopamine receptor-interacting proteins."], "structured": false}
{"doc_id": 30224907, "title": "c-Abl: activation and nuclear targets", "abstract": ["The c-Abl tyrosine kinase and its transforming variants have been implicated in tumorigenesis and in many important cellular processes.", "c-Abl is localized in the nucleus and the cytoplasm, where it plays distinct roles.", "The effects of c-Abl are mediated by multiple protein-protein and protein-DNA interactions and its tyrosine kinase domain.", "At the biochemical level, the mechanism of c-Abl kinase activation and the identification of its target proteins and cellular machineries have in part been solved.", "However, the phenotypic outcomes of these molecular events remained in large elusive.", "c-Abl has been shown to regulate the cell cycle and to induce under certain conditions cell growth arrest and apoptosis.", "In this respect the interaction of c-Abl with p53 and p73 has attracted particular attention.", "Recent findings have implicated c-Abl in an ionizing irradiation signaling pathway that elicits apoptosis.", "In this pathway p73 is an important immediate downstream effector.", "Here I review the current knowledge about these nuclear processes in which c-Abl is engaged and discuss some of their possible implications on cell physiology."], "structured": false}
{"doc_id": 30226988, "title": "Cancer survival increases in Europe, but international differences remain wide.", "abstract": ["The EUROCARE project analysed cancer survival data from 45 population-based cancer registries in 17 European countries, revealing wide international differences in cancer survival.", "We calculated 5-year relative survival for 1836287 patients diagnosed with one of 13 cancers during the period 1978-1989.", "The data, from 20 cancer registries in 13 countries, were grouped into four regions: Finland, Sweden, Iceland (Northern Europe); Denmark, England and Scotland (UK and Denmark); France, The Netherlands, Germany, Italy and Switzerland (Western Europe); Estonia and Poland (Eastern Europe), and broken down into four periods (1978-1980, 1981-1983, 1984-1986, 1987-1989).", "For each cancer, mean European and regional survival was estimated as the weighted mean of 5-year relative survival in each country.", "Survival increased with time for all tumours, particularly for cancers of testis (12% increase, i.e. from 79.9 to 91.9%), breast, large bowel, skin melanoma (approximately 9-10%), and lymphomas (approximately 7%).", "For most solid tumours, survival was highest in Northern Europe and lowest in Eastern Europe, and also low in the UK and Denmark.", "Regional variation was less marked for the lymphomas.", "Survival improved more in Western than Northern Europe, and the differences between these regions fell for bowel cancer (from 8.0% for those diagnosed in 1978-1980 to 2% for those diagnosed in 1987-1989), breast cancer (from 7.4% to 3.9%), skin melanoma (from 13.4% to 11.0%) and Hodgkin's disease (from 7.2 to 0.6%).", "For potentially curable malignancies such as Hodgkin's disease, large bowel, breast and testicular cancers, there were substantial increases in survival, suggesting an earlier diagnosis and more effective treatment.", "The persisting regional differences suggest there are corresponding differences in the availability of diagnostic and therapeutic facilities, and in the effectiveness of healthcare systems."], "structured": false}
{"doc_id": 30261663, "title": "A nuclear translation-like factor eIF4AIII is recruited to the mRNA during splicing and functions in nonsense-mediated decay.", "abstract": ["In eukaryotes, a surveillance mechanism known as nonsense-mediated decay (NMD) degrades the mRNA when a premature-termination codon (PTC) is present.", "NMD requires translation to read the frame of the mRNA and detect the PTC.", "During pre-mRNA splicing, the exon-exon junction complex (EJC) is recruited to a region 20-24 nt upstream of the exon junction on the mature mRNA.", "The presence of a PTC upstream from the EJC elicits NMD.", "Eukaryotic initiation factor 4A (eIF4A) III is a nuclear protein that interacts physically or functionally with translation initiation factors eIF4G and eIF4B, respectively, and shares strikingly high identity with the initiation factors eIF4AI/II.", "Here we show that siRNA against eIF4AIII, but not against eIF4AI/II, inhibits NMD.", "Moreover, eIF4AIII, but not eIF4AI, is specifically recruited to the EJC during splicing.", "The observations that eIF4AIII is loaded onto the mRNA during splicing in the nucleus, has properties related to a translation initiation factor, and functions in NMD raises the possibility that eIF4AIII substitutes for eIF4AI/II during NMD."], "structured": false}
{"doc_id": 30292811, "title": "Swaddling: a systematic review.", "abstract": ["Swaddling was an almost universal child-care practice before the 18th century.", "It is still tradition in certain parts of the Middle East and is gaining popularity in the United Kingdom, the United States, and The Netherlands to curb excessive crying.", "We have systematically reviewed all articles on swaddling to evaluate its possible benefits and disadvantages.", "In general, swaddled infants arouse less and sleep longer.", "Preterm infants have shown improved neuromuscular development, less physiologic distress, better motor organization, and more self-regulatory ability when they are swaddled.", "When compared with massage, excessively crying infants cried less when swaddled, and swaddling can soothe pain in infants.", "It is supportive in cases of neonatal abstinence syndrome and infants with neonatal cerebral lesions.", "It can be helpful in regulating temperature but can also cause hyperthermia when misapplied.", "Another possible adverse effect is an increased risk of the development of hip dysplasia, which is related to swaddling with the legs in extension and adduction.", "Although swaddling promotes the favorable supine position, the combination of swaddling with prone position increases the risk of sudden infant death syndrome, which makes it necessary to warn parents to stop swaddling if infants attempt to turn.", "There is some evidence that there is a higher risk of respiratory infections related to the tightness of swaddling.", "Furthermore, swaddling does not influence rickets onset or bone properties.", "Swaddling immediately after birth can cause delayed postnatal weight gain under certain conditions, but does not seem to influence breastfeeding parameters."], "structured": false}
{"doc_id": 30297355, "title": "Expression of the Norrie disease gene (Ndp) in developing and adult mouse eye, ear, and brain.", "abstract": ["The Norrie disease gene (Ndp) codes for a secreted protein, Norrin, that activates canonical Wnt signaling by binding to its receptor, Frizzled-4.", "This signaling system is required for normal vascular development in the retina and for vascular survival in the cochlea.", "In mammals, the pattern of Ndp expression beyond the retina is poorly defined due to the low abundance of Norrin mRNA and protein.", "Here, we characterize Ndp expression during mouse development by studying a knock-in mouse that carries the coding sequence of human placental alkaline phosphatase (AP) inserted at the Ndp locus (Ndp(AP)).", "In the CNS, Ndp(AP) expression is apparent by E10.5 and is dynamic and complex.", "The anatomically delimited regions of Ndp(AP) expression observed prenatally in the CNS are replaced postnatally by widespread expression in astrocytes in the forebrain and midbrain, Bergman glia in the cerebellum, and M\u00fcller glia in the retina.", "In the developing and adult cochlea, Ndp(AP) expression is closely associated with two densely vascularized regions, the stria vascularis and a capillary plexus between the organ of Corti and the spiral ganglion.", "These observations suggest the possibility that Norrin may have developmental and/or homeostatic functions beyond the retina and cochlea."], "structured": false}
{"doc_id": 30303335, "title": "Control of NFAT Isoform Activation and NFAT-Dependent Gene Expression through Two Coincident and Spatially Segregated Intracellular Ca2+ Signals", "abstract": ["Excitation-transcription coupling, linking stimulation at the cell surface to changes in nuclear gene expression, is conserved throughout eukaryotes.", "How closely related coexpressed transcription factors are differentially activated remains unclear.", "Here, we show that two Ca2+-dependent transcription factor isoforms, NFAT1 and NFAT4, require distinct sub-cellular InsP3 and Ca2+ signals for physiologically sustained activation.", "NFAT1 is stimulated by sub-plasmalemmal Ca2+ microdomains, whereas NFAT4 additionally requires Ca2+ mobilization from the inner nuclear envelope by nuclear InsP3 receptors.", "NFAT1 is rephosphorylated (deactivated) more slowly than NFAT4 in both cytoplasm and nucleus, enabling a more prolonged activation phase.", "Oscillations in cytoplasmic Ca2+, long considered the physiological form of Ca2+ signaling, play no role in activating either NFAT protein.", "Instead, effective sustained physiological activation of NFAT4 is tightly linked to oscillations in nuclear Ca2+.", "Our results show how gene expression can be controlled by coincident yet geographically distinct Ca2+ signals, generated by a freely diffusible InsP3 message."], "structured": false}
{"doc_id": 30351165, "title": "Brain region-specific up-regulation of mouse apolipoprotein E by pharmacological estrogen treatments.", "abstract": ["Cerebral apolipoprotein E (apoE) has been implicated in neuronal protection and repair.", "Due to the variable levels and types of estrogen receptors within different brain regions, the effect of estrogen on apoE and the mechanism of this effect may vary within different regions.", "Ovariectomized female C57BL/6 mice were treated with pharmacological levels of 17 beta-estradiol or placebo for 5 days, resulting in supraphysiological plasma levels of estradiol in the treated mice.", "ApoE and glial fibrillary acidic protein (GFAP) levels were measured in the cortex, hippocampus and diencephalon.", "17 beta-Estradiol up-regulated apoE but not GFAP in the cortex and diencephalon, whereas in the hippocampus, GFAP and apoE were equally up-regulated.", "Treatment of estrogen receptor (ER) alpha knockout mice with 17 beta-estradiol or treatment of C57BL/6 mice with 17 alpha-estradiol, a poor estrogen receptor agonist, specifically induced apoE in the cortex, but not in the diencephalon.", "These results indicate that 17 beta-estradiol effects on apoE are either directly or indirectly mediated by ER alpha in the diencephalon, while the effects in the cortex may be mediated by a non-classical mechanism or by ER beta.", "Measurement of mRNA levels in estrogen versus placebo-treated wild-type mice indicated that the effect of 17 beta-estradiol on apoE was not associated with changes in apoE mRNA levels."], "structured": false}
{"doc_id": 30353437, "title": "ATM and ataxia telangiectasia.", "abstract": ["Ataxia telangiectasia (AT) has long intrigued the biomedical research community owing to the spectrum of defects that are characteristic of the disease, including neurodegeneration, immune dysfunction, radiosensitivity and cancer predisposition.", "Following the identification of mutations in ATM (ataxia telangiectasia, mutated) as the underlying cause of the disease, biochemical analysis of this protein kinase has shown that it is a crucial nexus for the cellular response to DNA double-stranded breaks.", "Many ATM kinase substrates are important players in the cellular responses that prevent cancer.", "Accordingly, AT is a disease that results from defects in the response to specific types of DNA damage.", "Thus, although it is a rare neurodegenerative disease, understanding the biology of AT will lead to a greater understanding of the fundamental processes that underpin cancer and neurodegeneration."], "structured": false}
{"doc_id": 30369606, "title": "A novel immortalized human endometrial stromal cell line with normal progestational response.", "abstract": ["Obtaining primary human endometrial stromal cells (HESCs) for in vitro studies is limited by the scarcity of adequate human material and the inability to passage these cells in culture for long periods.", "Immortalization of these cells would greatly facilitate studies; however, the process of immortalization often results in abnormal karyotypes and aberrant functional characteristics.", "To meet this need, we have introduced telomerase into cultured HESCs to prevent the normal shortening of telomeres observed in adult somatic cells during mitosis.", "We have now developed and analyzed a newly immortalized HESC line that contains no clonal chromosomal structural or numerical abnormalities.", "In addition, when compared with the primary unpassaged parent cells, the new cell line displayed similar biochemical endpoints after treatment with ovarian steroids.", "Classical decidualization response to estradiol plus medroxyprogesterone acetate were seen in both morphologically, and progestin was seen to induce or regulate the expression of IGF binding protein-1, fibronectin, prolactin, tissue factor, plasminogen activator inhibitor-1, and Fas/Fas ligand.", "In summary, an immortalized HESC line has been developed that is karyotypically, morphologically, and phenotypically similar to the primary parent cells, and it is a powerful and consistent resource for in vitro work."], "structured": false}
{"doc_id": 30379039, "title": "Comparison of the intrinsic kinase activity and substrate specificity of c-Abl and Bcr-Abl.", "abstract": ["We studied the intrinsic tyrosine kinase activity and substrate specificity of c-Abl and Bcr-Abl protein tyrosine kinases (PTKs) using the peptide substrates discovered from a synthetic combinatorial peptide library.", "Our data indicate that the phosphorylation of these peptides by Bcr-Abl was consistently stronger than that by c-Abl.", "Bcr-Abl also showed substrate preference towards those peptides with one or more positive charges."], "structured": false}
{"doc_id": 30398773, "title": "Strong association between respiratory viral infection early after hematopoietic stem cell transplantation and the development of life-threatening acute and chronic alloimmune lung syndromes.", "abstract": ["Alloimmune lung syndromes (allo-LS), including idiopathic pneumonia syndrome, bronchiolitis obliterans syndrome, and bronchiolitis obliterans organizing pneumonia, are severe complications after hematopoietic stem cell transplantation (HSCT).", "In our cohort of 110 pediatric patients, 30 had allo-LS (27.3%), 18 with idiopathic pneumonia syndrome and 12 with bronchiolitis obliterans syndrome.", "Multivariate analysis showed that respiratory viral infection early after HSCT is an important predictor for the development of allo-LS (P <.0001).", "This was true for all viruses tested.", "In multivariate analysis, allo-LS was the only predictor for higher mortality (P = .04).", "Paradoxically, prolonged administration of immunosuppressive agents because of acute graft-versus-host disease had a protective effect on the development of allo-LS (P = .004).", "We hypothesize that early infection of the respiratory tract with a common cold virus makes the lungs a target for alloimmunity."], "structured": false}
{"doc_id": 30437264, "title": "Hepatitis C virus blocks interferon effector function by inducing protein kinase R phosphorylation.", "abstract": ["Hepatitis C virus (HCV) is a single-stranded RNA virus encoding a single polyprotein whose translation is driven by an internal ribosome entry site (IRES).", "HCV infection strongly induces antiviral interferon-stimulated gene (ISG) expression in the liver, yet it persists, suggesting that HCV can block ISG effector function.", "We now show that HCV infection triggers phosphorylation and activation of the RNA-dependent protein kinase PKR, which inhibits eukaryotic translation initiation factor eIF2 alpha and attenuates ISG protein expression despite normal ISG mRNA induction.", "ISG protein induction is restored and the antiviral effects of interferon are enhanced when PKR expression is suppressed in interferon-treated infected cells.", "Whereas host protein translation, including antiviral ISGs, is suppressed by activated PKR, HCV IRES-dependent translation is not.", "These results suggest that the ability of HCV to activate PKR may, paradoxically, be advantageous for the virus during an IFN response by preferentially suppressing the translation of ISGs."], "structured": false}
{"doc_id": 30464859, "title": "The influence of denervation on grafted hindlimb regeneration of larval Xenopus laevis.", "abstract": ["The aim of the present research is to ascertain whether in larval Xenopus laevis nerve-independence for the regeneration of early stage limbs and nerve-dependence of late stage limbs observed in a previous work (Filoni and Paglialunga, '90) is related to extrinsic (systemic) factors or to intrinsic changes taking place in the limb cells themselves during development.", "In this paper the regenerative capacity of early and late stage hindlimbs under the same extrinsic conditions, insofar as both are grafted onto the denervated hindlimbs of host larvae at the same developmental stage, is studied.", "All the grafted limbs are amputated after the host larvae have reached stage 57-58 (according to Nieuwkoop and Faber, '56).", "In experiment I, the grafted limb is amputated at stage 52, at the thigh level; in experiment II, the grafted limb is amputated at stage 54-55, at the tarsalia level; in experiment III the grafted limb is amputated at stage 57, at the tarsalia level.", "In all three experiments, together with the grafted limb, also the host limb is amputated at the tarsalia level.", "The results show that while grafted limbs amputated at stages 52 and 54-55 regenerate in the absence of nerves, grafted limbs amputated at stage 57 cannot.", "The failure of late stage grafted limbs to regenerate cannot be explained in terms of an immune-type inhibiting reaction since it has been observed also in denervated autografted limbs and in the host limbs.", "Since all the grafted limbs are in the same environmental conditions, the results show that in larval Xenopus laevis nerve-independence for regeneration of early stage limbs and nerve-dependence of late stage limbs are not related to factors extrinsic to the limb but to intrinsic changes taking place in the limb cells themselves during development."], "structured": false}
{"doc_id": 30468386, "title": "Adult c-Kit(+) progenitor cells are necessary for maintenance and regeneration of olfactory neurons.", "abstract": ["The olfactory epithelium houses chemosensory neurons, which transmit odor information from the nose to the brain.", "In adult mammals, the olfactory epithelium is a uniquely robust neuroproliferative zone, with the ability to replenish its neuronal and non-neuronal populations due to the presence of germinal basal cells.", "The stem and progenitor cells of these germinal layers, and their regulatory mechanisms, remain incompletely defined.", "Here we show that progenitor cells expressing c-Kit, a receptor tyrosine kinase marking stem cells in a variety of embryonic tissues, are required for maintenance of the adult neuroepithelium.", "Mouse genetic fate-mapping analyses show that embryonically, a c-Kit(+) population contributes to olfactory neurogenesis.", "In adults under conditions of normal turnover, there is relatively sparse c-Kit(+) progenitor cell (ckPC) activity.", "However, after experimentally induced neuroepithelial injury, ckPCs are activated such that they reconstitute the neuronal population.", "There are also occasional non-neuronal cells found to arise from ckPCs.", "Moreover, the selective depletion of the ckPC population, utilizing temporally controlled targeted diphtheria toxin A expression, results in failure of neurogenesis after experimental injury.", "Analysis of this model indicates that most ckPCs reside among the globose basal cell populations and act downstream of horizontal basal cells, which can serve as stem cells.", "Identification of the requirement for olfactory c-Kit-expressing progenitors in olfactory maintenance provides new insight into the mechanisms involved in adult olfactory neurogenesis.", "Additionally, we define an important and previously unrecognized site of adult c-Kit activity."], "structured": false}
{"doc_id": 30471052, "title": "Neurogenin3: a master regulator of pancreatic islet differentiation and regeneration.", "abstract": ["The basic helix-loop-helix transcription factor neurogenin-3 (Ngn3, Neurog3) is critical for the development of the endocrine cells of the islets.", "Either disrupted or forced expression of Ngn3 early in mouse pancreas development abrogates the formation of islets.", "The successive waves of Ngn3 expression that occur during the primary and secondary transitions of endocrine cell development temporally determine the four distinct endocrine cell lineages, \u03b1, \u03b2, PP, and \u03b4 cells that express glucagon, insulin, pancreatic polypeptide, and somatostatin, respectively.", "During islet regeneration after injury of the adult mouse pancreas, such as by duct ligation or streptozotocin, Ngn3 is activated in duct-associated stem/progenitor cells that transform into alpha and/or beta cells (Xu et al, Collombat et al).", "The important role of Ngn3 as a master regulator of endocrine pancreas development directs attention to finding therapeutic approaches to enhance Ngn3 expression in diabetes as a means to increase beta cell mass and functions."], "structured": false}
{"doc_id": 30492966, "title": "Detection of Mycoplasmas in Patients with Amyotrophic Lateral Sclerosis", "abstract": ["Amyotrophic Lateral Sclerosis (ALS) is a progressive degenerative  disease of the motor neurons and the cause is unknown.", "Diverse factors such as  genetic defects, nutritional deficiencies, head trauma, environmental toxin,  autoimmune responses and viral and bacterial infections are involved.", "Mycoplasmas  have been implicated as causal agents of different illnesses in human.", "The  purpose of this study was to investigate the presence of mycoplasmas in  the bloodstream of patients with ALS.", "Patients with ALS and healthy individuals  were included in the study.", "A blood sample was taken in tubes with or without  anticoagulant.", "Mycoplasmas were detected by culture or direct PCR, and the  presence of antibodies IgM and IgG against LAMPs of these microorganisms by  Western blot.", "Cultures for aerobic facultative bacteria were also done.", "Blood samples  from 13 patients and 44 healthy individuals were screened.", "All blood cultures  for non-fermentative mycoplasmas and aerobic facultative bacteria were  negative.", "Cultures for fermentative mycoplasmas were considered positive after  identification of mycoplasmal DNA by PCR.", "Mycoplasma sp. was detected by culture or  direct PCR in 6/13 (46%) patients and in 4/44 (9%) of healthy individuals.", "M. fermentans was detected by PCR using  specific primers in six patients and in two healthy individuals.", "IgM against  LAMPs of M. fermentans were detected  in 6/13 (46%) blood samples from patients and in 13/44 (30%) from healthy  individuals, while.", "IgG was detected in 4/13 (31%) patients and in 3/44 (7%)  healthy individuals.", "The results of this study show that mycoplasmas cause a  systemic infection and could play a role in the origin or progression of the  ALS."], "structured": false}
{"doc_id": 30500829, "title": "Correlation and variable importance in random forests", "abstract": ["This paper is about variable selection with the random forests algorithm in presence of correlated predictors.", "In high-dimensional regression or classification frameworks, variable selection is a difficult task, that becomes even more challenging in the presence of highly correlated predictors.", "Firstly we provide a theoretical study of the permutation importance measure for an additive regression model.", "This allows us to describe how the correlation between predictors impacts the permutation importance.", "Our results motivate the use of the Recursive Feature Elimination (RFE) algorithm for variable selection in this context.", "This algorithm recursively eliminates the variables using permutation importance measure as a ranking criterion.", "Next various simulation experiments illustrate the efficiency of the RFE algorithm for selecting a small number of variables together with a good prediction error.", "Finally, this selection algorithm is tested on the Landsat Satellite data from the UCI Machine Learning Repository."], "structured": false}
{"doc_id": 30507607, "title": "An Oct4-Centered Protein Interaction Network in Embryonic Stem Cells", "abstract": ["Transcription factors, such as Oct4, are critical for establishing and maintaining pluripotent cell identity.", "Whereas the genomic locations of several pluripotency transcription factors have been reported, the spectrum of their interaction partners is underexplored.", "Here, we use an improved affinity protocol to purify Oct4-interacting proteins from mouse embryonic stem cells (ESCs).", "Subsequent purification of Oct4 partners Sall4, Tcfcp2l1, Dax1, and Esrrb resulted in an Oct4 interactome of 166 proteins, including transcription factors and chromatin-modifying complexes with documented roles in self-renewal, but also many factors not previously associated with the ESC network.", "We find that Esrrb associated with the basal transcription machinery and also detect interactions between transcription factors and components of the TGF-beta, Notch, and Wnt signaling pathways.", "Acute depletion of Oct4 reduced binding of Tcfcp2l1, Dax1, and Esrrb to several target genes.", "In conclusion, our purification protocol allowed us to bring greater definition to the circuitry controlling pluripotent cell identity."], "structured": false}
{"doc_id": 30534237, "title": "GABA(B) receptor 1 polymorphism (G1465A) is associated with temporal lobe epilepsy.", "abstract": ["BACKGROUND Dysfunction of gamma-aminobutyric acid (GABA) (B) receptors has been implicated in the pathogenesis of temporal lobe epilepsy (TLE).   \n", "OBJECTIVE To evaluate the genetic contribution of cloned human GABA(B) receptors to TLE.   \n", "METHODS The authors genotyped 141 patients (78 women and 63 men; mean age = 49.1 +/-", "18.0 years) with nonlesional TLE and 372 age- and sex-matched normal individuals for the known polymorphism G1465A in the human GABA(B) receptor 1 [GABA(B[1])] gene.   \n", "RESULTS There was a highly significant overrepresentation of the G1465A heterozygote in patients with TLE compared with controls.", "The A/G genotype was found in 17% of the 141 patients with TLE and in only 0.5% of the 372 controls (p < 0.0001).", "The authors also found that patients carrying the A allele had a significantly higher risk (p = 0.003, OR = 6.47, 95% CI = 2.02 to 20.76) of developing drug-resistant TLE.", "Furthermore, the age at onset of seizures tended to be lower in patients with A/G genotype, but the difference was not significant.   \n", "CONCLUSIONS The results of this study indicate that the GABA(B[1]) polymorphism (G1465A) confers a highly increased susceptibility to TLE.", "Moreover, it seems to influence the severity of this common epileptic disorder."], "structured": true}
{"doc_id": 30543439, "title": "Crystal structure, biochemical and cellular activities demonstrate separate functions of MTH1 and MTH2", "abstract": ["Deregulated redox metabolism in cancer leads to oxidative damage to cellular components including deoxyribonucleoside triphosphates (dNTPs).", "Targeting dNTP pool sanitizing enzymes, such as MTH1, is a highly promising anticancer strategy.", "The MTH2 protein, known as NUDT15, is described as the second human homologue of bacterial MutT with 8-oxo-dGTPase activity.", "We present the first NUDT15 crystal structure and demonstrate that NUDT15 prefers other nucleotide substrates over 8-oxo-dGTP.", "Key structural features are identified that explain different substrate preferences for NUDT15 and MTH1.", "We find that depletion of NUDT15 has no effect on incorporation of 8-oxo-dGTP into DNA and does not impact cancer cell survival in cell lines tested.", "NUDT17 and NUDT18 were also profiled and found to have far less activity than MTH1 against oxidized nucleotides.", "We show that NUDT15 is not a biologically relevant 8-oxo-dGTPase, and that MTH1 is the most prominent sanitizer of the cellular dNTP pool known to date."], "structured": false}
{"doc_id": 30553457, "title": "De novo expression of Trpm4 initiates secondary hemorrhage in spinal cord injury", "abstract": ["The role of transient receptor potential M4 (Trpm4), an unusual member of the Trp family of ion channels, is poorly understood.", "Using rodent models of spinal cord injury, we studied involvement of Trpm4 in the progressive expansion of secondary hemorrhage associated with capillary fragmentation, the most destructive mechanism of secondary injury in the central nervous system.", "Trpm4 mRNA and protein were abundantly upregulated in capillaries preceding their fragmentation and formation of petechial hemorrhages.", "Trpm4 expression in vitro rendered COS-7 cells highly susceptible to oncotic swelling and oncotic death following ATP depletion.", "After spinal cord injury, in vivo gene suppression in rats treated with Trpm4 antisense or in Trpm4\u2212/\u2212 mice preserved capillary structural integrity, eliminated secondary hemorrhage, yielded a threefold to fivefold reduction in lesion volume and produced a substantial improvement in neurological function.", "To our knowledge, this is the first example of a Trp channel that must undergo de novo expression for manifestation of central nervous system pathology."], "structured": false}
{"doc_id": 30580263, "title": "Differential expression of bcl-2 in intestinal epithelia. Correlation with attenuation of apoptosis in colonic crypts and the incidence of colonic neoplasia.", "abstract": ["The cell-positional incidence of both spontaneous and damage-induced apoptosis of epithelial cells was assessed in longitudinal sections of the crypts of small intestine and colon of BDF1 mice.", "This was compared, using immunohistochemistry, with the pattern of expression of bcl-2, a suppressor of apoptosis.", "In the small intestine, apoptosis was maximal around cell position 4 from the base of the crypt; this closely corresponds to the position considered to contain the stem cells.", "In the colon, however, apoptosis was not confined to the area considered to harbour the stem cells (position 1 and 2).", "Instead, apoptosis was attenuated and distributed along the length of the crypt.", "Some cells at the base of murine colonic crypts expressed bcl-2 protein, whereas bcl-2 was absent in the crypts of the small intestine.", "Most pertinently, bcl-2 was absent from small intestinal crypt cells at positions 4-5 (the stem cell region).", "The importance of the expression of bcl-2 to the attenuation of apoptosis in stem cells was confirmed by analysis of the levels of both spontaneous and induced apoptosis in homozygously bcl-2 null C57BL/6 mice: in colonic crypts the level of spontaneous apoptosis rose significantly, and selectively at the base of the crypt, in comparison with crypts from wild-type animals.", "In contrast, there was no rise in spontaneous apoptosis in the small intestinal crypts from the bcl-2 null animals.", "Analysis of sections of human colon and small intestine also showed that expression of bcl-2 was confined to the base of the colonic crypt.", "The attenuation of apoptosis by bcl-2 in the region of the stem cells of the colonic crypts may dispose these to neoplastic transformation.", "Indeed, analysis of human carcinomas revealed expression of bcl-2, which in some samples was reciprocal with the expression of p53."], "structured": false}
{"doc_id": 30639847, "title": "Aortic stiffness, blood pressure progression, and incident hypertension.", "abstract": ["CONTEXT Vascular stiffness increases with advancing age and is a major risk factor for age-related morbidity and mortality.", "Vascular stiffness and blood pressure pulsatility are related; however, temporal relationships between vascular stiffening and blood pressure elevation have not been fully delineated.   \n", "OBJECTIVE To examine temporal relationships among vascular stiffness, central hemodynamics, microvascular function, and blood pressure progression.   \n", "DESIGN, SETTING, AND PARTICIPANTS Longitudinal community-based cohort study conducted in Framingham, Massachusetts.", "The present investigation is based on the 2 latest examination cycles (cycle 7: 1998-2001; cycle 8: 2005-2008 [last visit: January 25, 2008]) of the Framingham Offspring study (recruited: 1971-1975).", "Temporal relationships among blood pressure and 3 measures of vascular stiffness and pressure pulsatility derived from arterial tonometry (carotid-femoral pulse wave velocity [CFPWV], forward wave amplitude [FWA], and augmentation index) were examined over a 7-year period in 1759 participants (mean [SD] age: 60 [9] years; 974 women).   \n", "MAIN OUTCOME MEASURES The primary outcomes were blood pressure and incident hypertension during examination cycle 8.", "The secondary outcomes were CFPWV, FWA, and augmentation index during examination cycle 8.   \n", "RESULTS In a multivariable-adjusted regression model, higher FWA (\u03b2, 1.3 [95% CI, 0.5-2.1] mm Hg per 1 SD; P = .002) and higher CFPWV (\u03b2, 1.5 [95% CI, 0.5-2.6] mm Hg per 1 SD; P = .006) during examination cycle 7 were jointly associated with systolic blood pressure during examination cycle 8.", "Similarly, in a model that included systolic and diastolic blood pressure and additional risk factors during examination cycle 7, higher FWA (odds ratio [OR], 1.6 [95% CI, 1.3-2.0] per 1 SD; P < .001), augmentation index (OR, 1.7 [95% CI, 1.4-2.0] per 1 SD; P < .001), and CFPWV (OR, 1.3 [95% CI, 1.0-1.6] per 1 SD; P = .04) were associated with incident hypertension during examination cycle 8 (338 cases [32%] in 1048 participants without hypertension during examination cycle 7).", "Conversely, blood pressure during examination cycle 7 was not associated with CFPWV during examination cycle 8.", "Higher resting brachial artery flow (OR, 1.23 [95% CI, 1.04-1.46]) and lower flow-mediated dilation (OR, 0.80 [95% CI, 0.67-0.96]) during examination cycle 7 were associated with incident hypertension (in models that included blood pressure and tonometry measures collected during examination cycle 7).   \n", "CONCLUSION In this cohort, higher aortic stiffness, FWA, and augmentation index were associated with higher risk of incident hypertension; however, initial blood pressure was not independently associated with risk of progressive aortic stiffening."], "structured": true}
{"doc_id": 30655442, "title": "The EMBL nucleotide sequence database.", "abstract": ["The EMBL Nucleotide Sequence Database (http://www.ebi.ac.uk/embl. html ) constitutes Europe's primary nucleotide sequence resource.", "DNA and RNA sequences are directly submitted from researchers and genome sequencing groups and collected from the scientific literature and patent applications (Fig. 1).", "In collaboration with DDBJ and GenBank the database is produced, maintained and distributed at the European Bioinformatics Institute.", "Database releases are produced quarterly and are distributed on CD-ROM.", "EBI's network services allow access to the most up-to-date data collection via Internet and World Wide Web interface, providing database searching and sequence similarity facilities plus access to a large number of additional databases."], "structured": false}
{"doc_id": 30658796, "title": "Anaphase catastrophe is a target for cancer therapy.", "abstract": ["Neoplastic cells are genetically unstable.", "Strategies that target pathways affecting genome instability can be exploited to disrupt tumor cell growth, potentially with limited consequences to normal cells.", "Chromosomal instability (CIN) is one type of genome instability characterized by mitotic defects that increase the rate of chromosome mis-segregation.", "CIN is frequently caused by extra centrosomes that transiently disrupt normal bipolar spindle geometry needed for accurate chromosome segregation.", "Tumor cells survive with extra centrosomes because of biochemical pathways that cluster centrosomes and promote chromosome segregation on bipolar spindles.", "Recent work shows that targeted inhibition of these pathways prevents centrosome clustering and forces chromosomes to segregate to multiple daughter cells, an event triggering apoptosis that we refer to as anaphase catastrophe.", "Anaphase catastrophe specifically kills tumor cells with more than 2 centrosomes.", "This death program can occur after genetic or pharmacologic inhibition of cyclin dependent kinase 2 (Cdk2) and is augmented by combined treatment with a microtubule inhibitor.", "This proapoptotic effect occurs despite the presence of ras mutations in cancer cells.", "Anaphase catastrophe is a previously unrecognized mechanism that can be pharmacologically induced for apoptotic death of cancer cells and is, therefore, appealing to engage for cancer therapy and prevention."], "structured": false}
{"doc_id": 30675656, "title": "Dishevelled Activates JNK and Discriminates between JNK Pathways in Planar Polarity and wingless Signaling", "abstract": ["Frizzled family proteins have been described as receptors of Wnt signaling molecules.", "In Drosophila, the two known Frizzled proteins are associated with distinct developmental processes.", "Genesis of epithelial planar polarity requires Frizzled, whereas Dfz2 affects morphogenesis by wingless-mediated signaling.", "Dishevelled is required in both signaling pathways.", "Here, we use genetic and overexpression assays to show that Dishevelled activates JNK cascades.", "Rescue analysis reveals different protein domain requirements in Dishevelled for the two pathways; the C-terminal DEP domain is essential to rescue planar polarity defects and induce JNK signaling.", "Furthermore, the planar polarity-specific dsh1 allele is mutated in the DEP domain.", "Our results indicate that different Wnt/Fz signals activate distinct intracellular pathways, and Dishevelled discriminates among them by distinct domain interactions."], "structured": false}
{"doc_id": 30714190, "title": "Genome-wide lineage-specific transcriptional networks underscore Ikaros-dependent lymphoid priming in hematopoietic stem cells.", "abstract": ["The mechanisms regulating lineage potential during early hematopoiesis were investigated.", "First, a cascade of lineage-affiliated gene expression signatures, primed in hematopoietic stem cells (HSCs) and differentially propagated in lineage-restricted progenitors, was identified.", "Lymphoid transcripts were primed as early as the HSC, together with myeloid and erythroid transcripts.", "Although this multilineage priming was resolved upon subsequent lineage restrictions, an unexpected cosegregation of lymphoid and myeloid gene expression and potential past a nominal myeloid restriction point was identified.", "Finally, we demonstrated that whereas the zinc finger DNA-binding factor Ikaros was required for induction of lymphoid lineage priming in the HSC, it was also necessary for repression of genetic programs compatible with self-renewal and multipotency downstream of the HSC.", "Taken together, our studies provide new insight into the priming and restriction of lineage potentials during early hematopoiesis and identify Ikaros as a key bivalent regulator of this process."], "structured": false}
{"doc_id": 30720103, "title": "Vitamin D status: measurement, interpretation, and clinical application.", "abstract": ["Vitamin D, the sunshine vitamin, is now recognized not only for its importance in promoting bone health in children and adults but also for other health benefits, including reducing the risk of chronic diseases such as autoimmune diseases, common cancer, and cardiovascular disease.", "Vitamin D made in the skin or ingested in the diet is biologically inert and requires 2 successive hydroxylations first in the liver on carbon 25 to form 25-hydroxyvitamin D [25(OH)D], and then in the kidney for a hydroxylation on carbon 1 to form the biologically active form of vitamin D, 1,25-dihydroxyvitamin D [1,25(OH)(2)D].", "With the identification of 25(OH)D and 1,25(OH)(2)D, methods were developed to measure these metabolites in the circulation.", "Serum 25(OH)D is the barometer for vitamin D status.", "Serum 1,25(OH)(2)D provides no information about vitamin D status and is often normal or even increased as the result of secondary hyperparathyroidism associated with vitamin D deficiency.", "Most experts agree that 25(OH)D of <20 ng/mL is considered to be vitamin D deficiency, whereas a 25(OH)D of 21-29 ng/mL is considered to be insufficient.", "The goal should be to maintain both children and adults at a level >30 ng/mL to take full advantage of all the health benefits that vitamin D provides."], "structured": false}
{"doc_id": 30741007, "title": "Lessons from the past: managing insecticide resistance in malaria control and eradication programmes.", "abstract": ["The distribution of insecticide-treated bednets to help combat the burden of malaria in sub-Saharan Africa has accelerated in the past 5 years.", "Additionally, many countries are also considering, or have already begun, indoor residual spraying campaigns.", "These are positive developments, since vector control has repeatedly proven to be an effective means of reducing malaria transmission.", "However, the sustainability of these insecticide-based interventions relies on the continuing susceptibility of the anopheles vectors to the limited number of available insecticides.", "Continual monitoring for early signs of insecticide resistance and the adoption of carefully considered resistance management strategies are therefore required.", "Regrettably, this essential monitoring component is frequently given a low priority in the push to meet ambitious coverage targets.", "We outline the key requirements for establishing an insecticide resistance surveillance system and urge all those involved in malaria vector control, either directly or as facilitators, to ensure that these measures are incorporated into control programmes.", "Failure to act now will inevitably lead to a future breakdown in disease control and jeopardise hopes of eradicating this major public-health problem."], "structured": false}
{"doc_id": 30774694, "title": "T helper 2 cytokines inhibit autophagic control of intracellular Mycobacterium tuberculosis.", "abstract": ["Autophagy is a recently recognized immune effector mechanism against intracellular pathogens.", "The role of autophagy in innate immunity has been well established, but the extent of its regulation by the adaptive immune response is less well understood.", "The T helper 1 (Th1) cell cytokine IFN-gamma induces autophagy in macrophages to eliminate Mycobacterium tuberculosis.", "Here, we report that Th2 cytokines affect autophagy in macrophages and their ability to control intracellular M. tuberculosis.", "IL-4 and IL-13 abrogated autophagy and autophagy-mediated killing of intracellular mycobacteria in murine and human macrophages.", "Inhibition of starvation-induced autophagy by IL-4 and IL-13 was dependent on Akt signaling, whereas the inhibition of IFN-gamma-induced autophagy was Akt independent and signal transducer and activator of transcription 6 (STAT6) dependent.", "These findings establish a mechanism through which Th1-Th2 polarization differentially affects the immune control of intracellular pathogens."], "structured": false}
{"doc_id": 30786800, "title": "Lipid-based nutrient supplement increases the birth size of infants of primiparous women in Ghana.", "abstract": ["BACKGROUND The International Lipid-Based Nutrient Supplements Project developed a small-quantity (20 g/d) lipid-based nutrient supplement (LNS) for pregnant and lactating women.   \n", "OBJECTIVE We evaluated the effects of prenatal LNS supplementation on fetal growth.   \n", "DESIGN In a community-based, partially double-blind, individually randomized controlled trial, 1320 women \u226420 wk pregnant received 60 mg Fe/400 \u03bcg folic acid (IFA), or 1-2 Recommended Dietary Allowances of 18 micronutrients, including 20 mg Fe (MMN), or LNS with the same micronutrients as the MMN group, plus 4 minerals and macronutrients contributing 118 kcal (LNS) daily until delivery.", "Fetal growth was compared across groups by using intention-to-treat analysis.", "The primary outcome was birth length.   \n", "RESULTS This analysis included 1057 women (IFA = 349, MMN = 354, LNS = 354).", "Groups did not differ significantly in mean birth length, length-for-age z score (LAZ), head circumference, or percentage low birth length but differed in mean birth weight (P = 0.044), weight-for-age z score (WAZ; P = 0.046), and BMI-for-age z score (BMIZ; P = 0.040), with a trend toward differences in low birth weight (P = 0.069).", "In pairwise comparisons, the LNS group had greater mean birth weight (+85 g; P = 0.040), WAZ (+0.19; P = 0.045), and BMIZ (+0.21; P = 0.035) and a lower risk of low birth weight (RR: 0.61, 95% CI: 0.39, 0.96; P = 0.032) than did the IFA group.", "The other group differences were not significant.", "The effect of intervention was modified by mother's parity, age, height, baseline hemoglobin, household food insecurity, and child sex, with parity being the most consistent modifier.", "Among primiparous women (IFA = 131; MMN = 110; LNS = 128), the LNS group had greater mean birth length (+0.91 cm; P = 0.001), LAZ (+0.47; P = 0.001), weight (+237 g; P < 0.001), WAZ (+0.56; P < 0.001), BMIZ (+0.52; P < 0.001), head circumference (0.50 cm; P = 0.017), and head circumference-for-age z score (+0.40; P = 0.022) than did the IFA group; similar differences were found when comparing the LNS and MMN groups among primiparous women, and no group differences were found among multiparous women.   \n", "CONCLUSION Prenatal LNS supplementation can improve fetal growth among vulnerable women in Ghana, particularly primiparous women.", "This trial was registered at clinicaltrials.gov as NCT00970866."], "structured": true}
{"doc_id": 30805636, "title": "Peroxisome proliferator-activated receptor ligand bezafibrate for prevention of type 2 diabetes mellitus in patients with coronary artery disease.", "abstract": ["BACKGROUND Recent studies have shown that type 2 diabetes is preventable by both lifestyle interventions and medications that influence primary glucose metabolism.", "Whether pharmacological interventions that influence primary lipid metabolism can also delay development of type 2 diabetes is unknown.", "The goal of this study was to evaluate the effect of the peroxisome proliferator-activated receptor ligand bezafibrate on the progression of impaired fasting glucose phase to type 2 diabetes in patients with coronary artery disease over a 6.2-year follow-up period.   \n", "METHODS AND RESULTS The study sample comprised 303 nondiabetic patients 42 to 74 years of age with a fasting blood glucose level of 110 to 125 mg/dL (6.1 to 6.9 mmol/L).", "The patients received either 400 mg bezafibrate retard (156 patients) or placebo (147 patients) once a day.", "No patients were using statins, and use of ACE inhibitors, which also reduce diabetes incidence, was relatively low.", "During follow-up, development of new-onset diabetes was recorded in 146 patients: in 80 (54.4%) from the placebo group and 66 (42.3%) from the bezafibrate group (P=0.04).", "The mean time until onset of new diabetes was significantly delayed in patients on bezafibrate compared with patients on placebo: 4.6+/-2.3 versus 3.8+/-2.6 years (P=0.004).", "Multivariate analysis identified bezafibrate treatment as an independent predictor of reduced risk of new diabetes development (hazard ratio, 0.70; 95% CI, 0.49 to 0.99).", "Other significant variables associated with future overt type 2 diabetes in patients with impaired fasting glucose were total cholesterol level (hazard ratio, 1.22; 95% CI 1.0 to 1.51) and body mass index (hazard ratio, 1.10; 95% CI, 1.05 to 1.16).   \n", "CONCLUSIONS Bezafibrate reduces the incidence and delays the onset of type 2 diabetes in patients with impaired fasting glucose.", "Whether the combination of bezafibrate with other recommended drugs for secondary prevention (statins and ACE inhibitors) would be as efficacious as suggested by our results remains to be determined."], "structured": true}
{"doc_id": 30813140, "title": "Familial occurrence of chronic tension-type headache.", "abstract": ["Chronic tension-type headache (CTTH) assessed by proband report was evaluated in a family study of CTTH.", "A clinical interview of first-degree relatives by a physician was used as index of validity.", "Familial occurrence of CTTH in first-degree relatives was also investigated.", "Patterns of familial aggregation of CTTH were assessed by calculating the population relative risk.", "A neurological resident carried out all the interviews of probands and their first-degree relatives.", "The operational diagnostic criteria of the International Headache Society were used.", "The 122 probands had 377 first-degree relatives.", "Sensitivity, specificity, predictive values, and chance-corrected agreement rate for the diagnosis CTTH were 68%, 86%, 53% (PVpos), 92% (PVneg), and 0.48, respectively.", "The low sensitivity of CTTH assessed by proband report indicates that a clinical interview by a physician is necessary in family studies of CTTH.", "Clinically interviewed parents, siblings, and children had a 2.1 to 3.9-fold significantly increased risk of CTTH compared with the general population.", "The gender of the probands did not influence the risk of CTTH among first-degree relatives.", "The significantly increased familial risk of CTTH and no increased risk of CTTH in spouses suggest that a genetic factor is involved in CTTH."], "structured": false}
{"doc_id": 30835854, "title": "Complex formation of SMAP/KAP3, a KIF3A/B ATPase motor-associated protein, with a human chromosome-associated polypeptide.", "abstract": ["We have recently isolated SMAP (Smg GDS-associated protein; Smg GDS: small G protein GDP dissociation stimulator) as a novel Smg GDS-associated protein, which has Armadillo repeats and is phosphorylated by Src tyrosine kinase.", "SMAP is a human counterpart of mouse KAP3 (kinesin superfamily-associated protein) that is associated with mouse KIF3A/B (a kinesin superfamily protein), which functions as a microtubule-based ATPase motor for organelle transport.", "We isolated here a SMAP-interacting protein from a human brain cDNA library, identified it to be a human homolog of Xenopus XCAP-E (Xenopus chromosome-associated polypeptide), a subunit of condensins that regulate the assembly and structural maintenance of mitotic chromosomes, and named it HCAP (Human chromosome-associated polypeptide).", "Tissue and subcellular distribution analyses indicated that HCAP was ubiquitously expressed and highly concentrated in the nuclear fraction, where SMAP and KIF3B were also present.", "SMAP was extracted as a ternary complex with HCAP and KIF3B from the nuclear fraction in the presence of Mg-ATP.", "The results suggest that SMAP/KAP3 serves as a linker between HCAP and KIF3A/B in the nucleus, and that SMAP/KAP3 plays a role in the interaction of chromosomes with an ATPase motor protein."], "structured": false}
{"doc_id": 30844602, "title": "Surveillance for foodborne-disease outbreaks--United States, 1993-1997.", "abstract": ["PROBLEM/CONDITION Since 1973, CDC has maintained a collaborative surveillance program for collection and periodic reporting of data on the occurrence and causes of foodborne-disease outbreaks (FBDOs) in the United States.   ", "REPORTING PERIOD COVERED This summary reviews data from January 1993 through December 1997.   ", "DESCRIPTION OF SYSTEM The Foodborne-Disease Outbreak Surveillance System reviews data concerning FBDOs, defined as the occurrence of two or more cases of a similar illness resulting from the ingestion of a common food.", "State and local public health departments have primary responsibility for identifying and investigating FBDOs.", "State, local, and territorial health departments use a standard form to report these outbreaks to CDC.   \n", "RESULTS During 1993-1997, a total of 2,751 outbreaks of foodborne disease were reported (489 in 1993, 653 in 1994, 628 in 1995, 477 in 1996, and 504 in 1997).", "These outbreaks caused a reported 86,058 persons to become ill.", "Among outbreaks for which the etiology was determined, bacterial pathogens caused the largest percentage of outbreaks (75%) and the largest percentage of cases (86%).", "Salmonella serotype Enteritidis accounted for the largest number of outbreaks, cases, and deaths; most of these outbreaks were attributed to eating eggs.", "Chemical agents caused 17% of outbreaks and 1% of cases; viruses, 6% of outbreaks and 8% of cases; and parasites, 2% of outbreaks and 5% of cases.   \n", "INTERPRETATION The annual number of FBDOs reported to CDC did not change substantially during this period or from previous years.", "During this reporting period, S. Enteritidis continued to be a major cause of illness and death.", "In addition, multistate outbreaks caused by contaminated produce and outbreaks caused by Escherichia coli O157:H7 remained prominent.   ", "ACTIONS TAKEN Current methods to detect FBDOs are improving, and several changes to improve the ease and timeliness of reporting FBDO data are occurring (e.g., a revised form to simplify FBDO reporting by state health departments and electronic reporting methods).", "State and local health departments continue to investigate and report FBDOs as part of efforts to better understand and define the epidemiology of foodborne disease in the United States.", "At the regional and national levels, surveillance data provide an indication of the etiologic agents, vehicles of transmission, and contributing factors associated with FBDOs and help direct public health actions to reduce illness and death caused by FBDOs."], "structured": true}
{"doc_id": 30861948, "title": "Nuclear-cytoplasmic shuttling of C-ABL tyrosine kinase.", "abstract": ["The ubiquitously expressed nonreceptor tyrosine kinase c-Abl contains three nuclear localization signals, however, it is found in both the nucleus and the cytoplasm of proliferating fibroblasts.", "A rapid and transient loss of c-Abl from the nucleus is observed upon the initial adhesion of fibroblasts onto a fibronectin matrix, suggesting the possibility of nuclear export [Lewis, J., Baskaran, R. , Taagepera, S., Schwartz, M. & Wang, J. (1996) Proc.", "Natl.", "Acad.", "Sci.", "USA 93, 15174-15179].", "Here we show that the C terminus of c-Abl does indeed contain a functional nuclear export signal (NES) with the characteristic leucine-rich motif.", "The c-Abl NES can functionally complement an NES-defective HIV Rev protein (RevDelta3NI) and can mediate the nuclear export of glutathione-S-transferase.", "The c-Abl NES function is sensitive to the nuclear export inhibitor leptomycin B. Mutation of a single leucine (L1064A) in the c-Abl NES abrogates export function.", "The NES-mutated c-Abl, termed c-Abl NES(-), is localized exclusively to the nucleus.", "Treatment of cells with leptomycin B also leads to the nuclear accumulation of wild-type c-Abl protein.", "The c-Abl NES(-) is not lost from the nucleus when detached fibroblasts are replated onto fibronectin matrix.", "Taken together, these results demonstrate that c-Abl shuttles continuously between the nucleus and the cytoplasm and that the rate of nuclear import and export can be modulated by the adherence status of fibroblastic cells."], "structured": false}
{"doc_id": 30884033, "title": "Regulation of embryonic stem cell pluripotency by heat shock protein 90.", "abstract": ["Deciphering the molecular basis of stem cell pluripotency is fundamental to the understanding of stem cell biology, early embryonic development, and to the clinical application of regenerative medicine.", "We report here that the molecular chaperone heat shock protein 90 (Hsp90) is essential for mouse embryonic stem cell (ESC) pluripotency through regulating multiple pluripotency factors, including Oct4, Nanog, and signal transducer and activator of transcription 3.", "Inhibition of Hsp90 by either 17-N-Allylamino-17-demethoxygeldanamycin or miRNA led to ESC differentiation.", "Overexpression of Hsp90\u03b2 partially rescued the phenotype; in particular, the levels of Oct4 and Nanog were restored.", "Notably, Hsp90 associated with Oct4 and Nanog in the same cellular complex and protected them from degradation by the ubiquitin proteasome pathway, suggesting that Oct4 and Nanog are potential novel Hsp90 client proteins.", "In addition, Hsp90 inhibition reduced the mRNA level of Oct4, but not that of Nanog, indicating that Hsp90 participates in Oct4 mRNA processing or maturation.", "Hsp90 inhibition also increased expression of some protein markers for mesodermal lineages, implying that Hsp90 suppresses mesodermal differentiation from ESCs.", "These findings support a new role for Hsp90 in maintaining ESC pluripotency by sustaining the level of multiple pluripotency factors, particularly Oct4 and Nanog."], "structured": false}
{"doc_id": 30908508, "title": "CD4+CD25+Foxp3+Regulatory T Cells Protect Endothelial Function Impaired by Oxidized Low Density Lipoprotein via the KLF-2 Transcription Factor", "abstract": ["Objective: To investigate the regulation of CD4+CD25+ Regulatory T cells (Tregs) on pro-inflammatory adhesion molecules, Kr\u00fcppel-Like Factor-2 (KLF-2) and its downstream transcriptional targets in human umbilical vein endothelial cells (HUVECs) impaired by ox-LDL and the mechanisms of it.", "Methods and results: HUVECs were cultured in the continuous presence of ox-LDL(0 mg/L,25 mg/L,50 mg/L,100 mg/L) for 4, 6, 12 and 24 hours to allow identification of early-and late-induced genes, respectively, whereas non-stimulated controls were taken at 0 hours.", "The expression of pro-inflammatory adhesion molecules such as vascular cell adhesion molecule-1 (VCAM-1), intracellular adhesion molecule-1 (ICAM-1), E-selectin, KLF-2 and its target genes eNOS, PAI-1 were determined by real time RT-PCR and/or western-blot analysis.", "Expression of pro-inflammatory adhesion molecules, KLF-2, eNOS and PAI-1 in HUVEC cultured alone or with anti-CD3 mAbs activated Tregs, followed by addition of ox-LDL (50 mg/L) for 6 hours, are compared to expression levels in control cultures.", "Ox-LDL treated HUVECs increased pro-inflammatory adhesion molecules expression, as well as increased PAI-1 but decreased eNOS expression accompanied with significant downregulating of KLF-2 at a dose and time dependent manner.", "Furthermore, ox-LDL increased pro-inflammatory adhesion molecules but inhibited KLF2 expression was reversed by addition of Tregs.", "Small interfering RNA reduced endogenous KLF-2 expression and partly reversed the suppressive effect of Tregs on HUVECs activation, which strongly implicate KLF-2 as a transcriptional regulator of the Tregs-mediated effects in endothelial cells.", "Mechanism studies reveal that Treg-mediated KLF2 expression in HUVECs impaired by ox-LDL requires cell contact as well as soluble factors.", "Conclusions: Tregs could protect endothelial function that is largely dependent on KLF2 and its downstream transcriptional targets regulation involving cell-to-cell contact and soluble factors."], "structured": false}
{"doc_id": 30915421, "title": "Metformin Normalizes Type 2 Diabetes-Induced Decrease in Cell Proliferation and Neuroblast Differentiation in the Rat Dentate Gyrus", "abstract": ["In this study, we observed the effects of metformin, one of the most widely prescribed drugs for the treatment of type 2 diabetes, on cell proliferation and neuroblast differentiation in the subgranular zone of the hippocampal dentate gyrus (SZDG) in Zucker diabetic fatty (ZDF) rats, which are a model for type 2 diabetes.", "For this, metformin was administered orally once a day to 14-week-old ZDF rats for 2 weeks and the animals were sacrificed at 16 weeks of age.", "During this period, blood glucose levels were higher in the vehicle-treated ZDF rats than in the Zucker lean control (ZLC) rats.", "Metformin treatment significantly decreased the blood glucose levels from 15.5 weeks of age.", "In the SZDG, Ki67 (a marker for cell proliferation)- and doublecortin (DCX, a marker for differentiated neuroblasts)-immunoreactive cells were much lower in the vehicle-treated ZDF rats than in the ZLC rats.", "In the metformin-treated ZDF group, Ki67- and DCX-immunoreactive cells were significantly increased in the SZDG compared to those in the vehicle-treated ZDF group.", "These results suggest that diabetes significantly reduces cell proliferation and neuroblast differentiation in the SZDG and that metformin treatment normalizes the reduction of cell proliferation and neuroblast differentiation in the SZDG in diabetic rats."], "structured": false}
{"doc_id": 30919024, "title": "Molecular mechanisms underlying tumor dormancy.", "abstract": ["Evidence suggests that dormant, microscopic tumors are not only common, but are highly prevalent in otherwise healthy individuals.", "Due to their small size and non-invasive nature, these dormant tumors remain asymptomatic and, in most cases, undetected.", "With advances in diagnostic imaging and molecular biology, it is now becoming clear that such neoplasms can remain in an asymptomatic, dormant stage for considerable periods of time without expanding in size.", "Although a number of processes may play a role in thwarting the expansion of microscopic tumors, one critical mechanism behind tumor dormancy is the ability of the tumor population to induce angiogenesis.", "Although cancer can arise through multiple pathways, it is assumed that essentially most tumors begin as microscopic, non-angiogenic neoplasms which cannot expand in size until vasculature is established.", "It is now becoming clear that cancer does not progress through a continuous exponential growth and mass expansion.", "Clinical cancer is usually manifested only in late, unavoidably symptomatic stages of the disease when tumors are sufficiently large to be readily detected.", "While dormancy in primary tumors is best defined as the time between the carcinogenic transformation event and the onset of inexorable progressive growth, it can also occur as minimal residual or occult disease from treated tumors or as micro-metastases.", "The existence of dormant tumors has important implications for the early detection and treatment of cancer.", "Elucidating the regulatory machinery of these processes will be instrumental in identifying novel early cancer biomarkers and could provide a rationale for the development of dormancy-promoting tumor therapies.", "Despite the high prevalence of microscopic, dormant tumors in humans and the significant clinical implications of their early detection, this area in cancer research has, to date, been under-investigated.", "In this mini review observations, models and experimental approaches to study tumor dormancy are summarized.", "Additionally, analogies and distinctions between the concepts of \"tumor dormancy\" and that of the \"cellular dormancy\" of tumor cells, as well as between the \"exit from tumor dormancy\" and the \"onset of the angiogenic switch\" are discussed."], "structured": false}
{"doc_id": 30933307, "title": "The myeloid transcription factor GATA-2 regulates the viral UL144 gene during human cytomegalovirus latency in an isolate-specific manner.", "abstract": ["It is generally accepted that, following primary infection, human cytomegalovirus (HCMV) establishes lifelong latency in CD34(+) progenitor cells and other derivative cells of the myeloid lineage.", "In this study, we show that the viral UL144 gene is expressed during latent infection in two cell types of the myeloid lineage, CD34(+) and CD14(+) monocytes, and that the UL144 protein is functional in latently infected monocytes.", "However, this latency-associated expression of UL144 occurs only in certain isolates of HCMV and depends on the presence of functional GATA-2 transcription factor binding sites in the UL144 promoter, in contrast to the viral latency-associated gene LUNA, which we also show is regulated by GATA-2 but expressed uniformly during latent infection independent of the virus isolate.", "Taken together, these data suggest that the HCMV latency-associated transcriptome may be virus isolate specific and dependent on the repertoire of transcription factor binding sites in the promoters of latency-associated genes."], "structured": false}
{"doc_id": 30981192, "title": "How to control residual cardiovascular risk despite statin treatment: focusing on HDL-cholesterol.", "abstract": ["Lowering low-density lipoprotein-cholesterol (LDL-C) is the primary target in the management of dyslipidemia in patients at high risk of cardiovascular disease.", "However, patients who have achieved LDL-C levels below the currently recommended targets may still experience cardiovascular events.", "This may result, in part, from elevated triglyceride (TG) levels and low levels of high-density lipoprotein-cholesterol (HDL-C).", "Low HDL-C and high TG levels are common and are recognized as independent risk factors for cardiovascular morbidity and mortality.", "Furthermore, atherogenic dyslipidemia, characterized by low levels of HDL-C, high TG, and small, dense LDL particles, is a typical phenotype of dyslipidemia in subjects with insulin resistance and metabolic syndrome.", "Therefore, to reduce further the risk of coronary heart disease (CHD), raising HDL-C and lowering TG may be the secondary therapeutic target for patients who achieve LDL-C levels below the currently recommended targets but are still at risk of CHD.", "However, whether increasing HDL-C levels alone reduces CHD has not yet been confirmed in large randomized clinical trials, and whether functional HDL is more important than HDL-C in reducing CHD remains controversial.", "Large CHD endpoint trials that include many patients with diabetes are underway to compare combination treatments with statin and niacin, fibrates, or cholesteryl ester transfer protein inhibitors with statin alone treatments.", "In this review, we discuss the rationale and importance of increasing HDL-C levels with and without lowering TG levels in the treatment and prevention of cardiovascular events."], "structured": false}
{"doc_id": 30983338, "title": "The prevalence of congenital malformations is still higher in pregnant women with pregestational diabetes despite near-normal HbA1c: a literature review.", "abstract": ["AIMS/HYPOTHESIS We assessed the association between congenital malformations and maternal hyperglycemia in pregnant women with pregestational (type 1 or type 2) diabetes and investigated if the rate of congenital malformations was similar in women with near-normal glycemic control compared to the background population.", "We also assessed the association between congenital malformations and maternal hyperglycemia in pregnant women with pregestational diabetes with special focus on women with near-normal HbA1c in early pregnancy.   ", "MATERIALS AND METHODS This is a literature review based on an electronic literature search of the databases PubMed, Cochrane, Embase and Web of Science conducted in July 2017 using the search terms diabetes, pregnancy, HbA1c or glycemic control and congenital anomaly or congenital anomaly.", "We included original papers in English published after 1997 with data on congenital malformations and HbA1c in at least 250 women with pregestational diabetes.   \n", "RESULTS Nine papers with in total 6225 women with type 1 diabetes and 2334 women with type 2 diabetes were included.", "The prevalence of congenital malformations was 6.4% in women with type 1 diabetes and 4.3% in women with type 2 diabetes and for the combined group of women with pregestational diabetes, the relative risk compared to the background population was 3.2.", "In women with HbA1c < 53 mmol/mol (7.0%) in early pregnancy or HbA1c 53-64 mmol/mol (7.0-8.0%) the prevalence of congenital malformations was 4.3 and 3.7%, respectively, with a relative risk of 2.2 and 1.9, respectively.   \n", "CONCLUSIONS In pregnant women with pregestational diabetes the prevalence of congenital abnormalities was threefold higher in women with pregestational diabetes compared to the background population.", "However, HbA1c below 53 mmol/mol (7.0%) in early pregnancy was also associated with a two times increased risk of congenital malformations compared to the background population."], "structured": true}
{"doc_id": 31001322, "title": "Local and systemic insulin resistance resulting from hepatic activation of IKK-beta and NF-kappaB.", "abstract": ["We show that NF-kappaB and transcriptional targets are activated in liver by obesity and high-fat diet (HFD).", "We have matched this state of chronic, subacute 'inflammation' by low-level activation of NF-kappaB in the liver of transgenic mice, designated LIKK, by selectively expressing constitutively active IKK-b in hepatocytes.", "These mice exhibit a type 2 diabetes phenotype, characterized by hyperglycemia, profound hepatic insulin resistance, and moderate systemic insulin resistance, including effects in muscle.", "The hepatic production of proinflammatory cytokines, including IL-6, IL-1beta and TNF-alpha, was increased in LIKK mice to a similar extent as induced by HFD in in wild-type mice.", "Parallel increases were observed in cytokine signaling in liver and mucscle of LIKK mice.", "Insulin resistance was improved by systemic neutralization of IL-6 or salicylate inhibition of IKK-beta.", "Hepatic expression of the IkappaBalpha superrepressor (LISR) reversed the phenotype of both LIKK mice and wild-type mice fed an HFD.", "These findings indicate that lipid accumulation in the liver leads to subacute hepatic 'inflammation' through NF-kappaB activation and downstream cytokine production.", "This causes insulin resistance both locally in liver and systemically."], "structured": false}
{"doc_id": 31019903, "title": "Homelessness and health.", "abstract": ["Homelessness affects tens of thousands of canadians and has important health implications.", "Homeless people are at increased risk of dying prematurely and suffer from a wide range of health problems, including seizures, chronic obstructive pulmonary disease, musculoskeletal disorders, tuberculosis, and skin and foot problems.", "Homeless people also face significant barriers that impair their access to health care.", "More research is needed to identify better ways to deliver care to this population."], "structured": false}
{"doc_id": 31070360, "title": "Serum metabolomics in animal models and human disease.", "abstract": ["PURPOSE OF REVIEW The aim of this study is to highlight some recent uses of serum metabolomics in human and animal studies.", "The main themes are the importance of understanding the underlying variation in human metabolism and the use of serum metabolomics in disease profiling.   ", "RECENT FINDINGS Several studies have attempted to use serum metabolomics to develop noninvasive biomarkers of disease and/or track the consequences of nutritional and genetic interventions.", "Many advances have been made with common changes being identified in ageing, the menopause and cancer but several problems of interpretation have emerged from these studies.", "These include the small sample sizes in most human studies and the differences between human and rodent metabolomes.", "However, a metabolic screen of over 1000 'healthy' humans (the Humsermet project) has highlighted many variables that may be used to refine the interpretation and design of previous and future human studies alike, in addition to data mining.   ", "SUMMARY Some common serum metabolome alterations have been identified but many inconsistencies remain.", "The construction of a human serum metabolome database should be informative in the design of future human and animal model studies."], "structured": true}
{"doc_id": 31107919, "title": "Differential Requirement of the Extracellular Domain in Activation of Class B G Protein-coupled Receptors.", "abstract": ["G protein-coupled receptors (GPCRs) from the secretin-like (class B) family are key players in hormonal homeostasis and are important drug targets for the treatment of metabolic disorders and neuronal diseases.", "They consist of a large N-terminal extracellular domain (ECD) and a transmembrane domain (TMD) with the GPCR signature of seven transmembrane helices.", "Class B GPCRs are activated by peptide hormones with their C termini bound to the receptor ECD and their N termini bound to the TMD.", "It is thought that the ECD functions as an affinity trap to bind and localize the hormone to the receptor.", "This in turn would allow the hormone N terminus to insert into the TMD and induce conformational changes of the TMD to activate downstream signaling.", "In contrast to this prevailing model, we demonstrate that human class B GPCRs vary widely in their requirement of the ECD for activation.", "In one group, represented by corticotrophin-releasing factor receptor 1 (CRF1R), parathyroid hormone receptor (PTH1R), and pituitary adenylate cyclase activating polypeptide type 1 receptor (PAC1R), the ECD requirement for high affinity hormone binding can be bypassed by induced proximity and mass action effects, whereas in the other group, represented by glucagon receptor (GCGR) and glucagon-like peptide-1 receptor (GLP-1R), the ECD is required for signaling even when the hormone is covalently linked to the TMD.", "Furthermore, the activation of GLP-1R by small molecules that interact with the intracellular side of the receptor is dependent on the presence of its ECD, suggesting a direct role of the ECD in GLP-1R activation."], "structured": false}
{"doc_id": 31141365, "title": "Genome-wide maps of histone modifications unwind in vivo chromatin states of the hair follicle lineage.", "abstract": ["Using mouse skin, where bountiful reservoirs of synchronized hair follicle stem cells (HF-SCs) fuel cycles of regeneration, we explore how adult SCs remodel chromatin in response to activating cues.", "By profiling global mRNA and chromatin changes in quiescent and activated HF-SCs and their committed, transit-amplifying (TA) progeny, we show that polycomb-group (PcG)-mediated H3K27-trimethylation features prominently in HF-lineage progression by mechanisms distinct from embryonic-SCs.", "In HF-SCs, PcG represses nonskin lineages and HF differentiation.", "In TA progeny, nonskin regulators remain PcG-repressed, HF-SC regulators acquire H3K27me3-marks, and HF-lineage regulators lose them.", "Interestingly, genes poised in embryonic stem cells, active in HF-SCs, and PcG-repressed in TA progeny encode not only key transcription factors, but also signaling regulators.", "We document their importance in balancing HF-SC quiescence, underscoring the power of chromatin mapping in dissecting SC behavior.", "Our findings explain how HF-SCs cycle through quiescent and activated states without losing stemness and define roles for PcG-mediated repression in governing a fate switch irreversibly."], "structured": false}
{"doc_id": 31148090, "title": "Two classes of endogenous small RNAs in Tetrahymena thermophila.", "abstract": ["Endogenous small RNAs function in RNA interference (RNAi) pathways to guide RNA cleavage, translational repression, or methylation of DNA or chromatin.", "In Tetrahymena thermophila, developmentally regulated DNA elimination is governed by an RNAi mechanism involving approximately 27-30-nucleotide (nt) RNAs.", "Here we characterize the sequence features of the approximately 27-30-nt RNAs and a approximately 23-24-nt RNA class representing a second RNAi pathway.", "The approximately 23-24-nt RNAs accumulate strain-specifically manner and map to the genome in clusters that are antisense to predicted genes.", "These findings reveal the existence of distinct endogenous RNAi pathways in the unicellular T. thermophila, a complexity previously demonstrated only in multicellular organisms."], "structured": false}
{"doc_id": 31154082, "title": "The binding of maize DHN1 to lipid vesicles. Gain of structure and lipid specificity.", "abstract": ["Dehydrins (DHNs; late embryogenesis abundant D-11) are a family of plant proteins induced in response to abiotic stresses such as drought, low temperature, and salinity or during the late stages of embryogenesis.", "Spectral and thermal properties of these proteins in purified form suggest that they are \"intrinsically unstructured.", "\"", "However, DHNs contain at least one copy of a consensus 15-amino acid sequence, the \"K segment,\" which resembles a class A2 amphipathic alpha-helical, lipid-binding domain found in other proteins such as apolipoproteins and alpha-synuclein.", "The presence of the K segment raises the question of whether DHNs bind lipids, bilayers, or phospholipid vesicles.", "Here, we show that maize (Zea mays) DHN DHN1 can bind to lipid vesicles that contain acidic phospholipids.", "We also observe that DHN1 binds more favorably to vesicles of smaller diameter than to larger vesicles, and that the association of DHN1 with vesicles results in an apparent increase of alpha-helicity of the protein.", "Therefore, DHNs, and presumably somewhat similar plant stress proteins in the late embryogenesis abundant and cold-regulated classes may undergo function-related conformational changes at the water/membrane interface, perhaps related to the stabilization of vesicles or other endomembrane structures under stress conditions."], "structured": false}
{"doc_id": 31166180, "title": "Requirement of heterochromatin for cohesion at centromeres.", "abstract": ["Centromeres are heterochromatic in many organisms, but the mitotic function of this silent chromatin remains unknown.", "During cell division, newly replicated sister chromatids must cohere until anaphase when Scc1/Rad21-mediated cohesion is destroyed.", "In metazoans, chromosome arm cohesins dissociate during prophase, leaving centromeres as the only linkage before anaphase.", "It is not known what distinguishes centromere cohesion from arm cohesion.", "Fission yeast Swi6 (a Heterochromatin protein 1 counterpart) is a component of silent heterochromatin.", "Here we show that this heterochromatin is specifically required for cohesion between sister centromeres.", "Swi6 is required for association of Rad21-cohesin with centromeres but not along chromosome arms and, thus, acts to distinguish centromere from arm cohesion.", "Therefore, one function of centromeric heterochromatin is to attract cohesin, thereby ensuring sister centromere cohesion and proper chromosome segregation."], "structured": false}
{"doc_id": 31200375, "title": "Gene expression in human skeletal muscle: alternative normalization method and effect of repeated biopsies", "abstract": ["The reverse transcriptase-polymerase chain reaction (RT-PCR) method has lately become widely used to determine transcription and mRNA content in rodent and human muscle samples.", "However, the common use of endogenous controls for correcting for variance in cDNA between samples is not optimal.", "Specifically, we investigated (1) a new normalization method based on determining the cDNA content by the flourophores PicoGreen and OliGreen, (2) effect of repeated muscle biopsies on mRNA gene expression, and (3) the spatial heterogeneity in mRNA expression across the muscle.", "Standard curves using oligo standards revealed a high degree of sensitivity and linearity (2.5\u201345 ng; R 2>0.99) with OliGreen reagent, as was the case for OliGreen analyses with standard curves constructed from serial dilutions of representative RT samples (R 2 >0.99 for a ten times dilution range of a representative reversed transcribed (RT) sample).", "Likewise, PicoGreen reagent detected the RNA:DNA hybrid content in RT samples with great sensitivity.", "Standard curves constructed from both double-stranded lambda DNA (1\u201310 ng) and from serial dilutions of representative RT samples consistently resulted in linearity with R 2 >0.99.", "The present determination of cDNA content in reversed transcribed human skeletal muscle RNA samples by both PicoGreen and OliGreen analyses suggests that these fluorophores provide a potential alternative normalization procedure for human gene expression studies.", "In addition, the present study shows that multiple muscle biopsies obtained from the same muscle do not influence the mRNA response induced by an acute exercise bout for any of the genes examined."], "structured": false}
{"doc_id": 31208367, "title": "The Impact of Location of Progressive Visual Field Loss on Longitudinal Changes in Quality of Life of Patients with Glaucoma.", "abstract": ["PURPOSE To evaluate the association between rates of progressive loss in different regions of the visual field and longitudinal changes in quality of life (QoL).   \n", "DESIGN Prospective, observational cohort study.   \n", "PARTICIPANTS The study included 236 patients with glaucomatous visual field loss followed for an average of 4.3\u00b11.5 years.   \n", "METHODS All subjects had the 25-item National Eye Institute Visual Functioning Questionnaire (NEI VFQ-25) performed annually and standard automated perimetry (SAP) at 6-month intervals.", "Subjects were included if they had a minimum of 2 NEI VFQ-25 and 5 SAP tests during follow-up.", "Evaluation of rates of visual field change was performed using 4 different regions (central inferior, central superior, peripheral inferior, and peripheral superior) of the integrated binocular visual field.", "The association between change in NEI VFQ-25 Rasch-calibrated scores and change in different regions of the visual field was investigated with a joint multivariable longitudinal linear mixed model.   \n", "MAIN OUTCOME MEASURES The relationship between change in QoL scores and change of mean sensitivity in different regions of the visual field.   \n", "RESULTS There was a significant correlation between change in the NEI VFQ-25 Rasch scores during follow-up and change in different regions of the visual field.", "Each 1 decibel (dB)/year change in binocular mean sensitivity of the central inferior area was associated with a decline of 2.6 units/year in the NEI VFQ-25 scores (R(2) = 35%; P < 0.001).", "Corresponding associations with change in QoL scores for the peripheral inferior, central superior, and peripheral superior areas of the visual field had R(2) values of 30%, 24%, and 19%, respectively.", "The association for the central inferior visual field area was statistically significantly stronger than those of the central superior area (P = 0.011) and peripheral superior area (P = 0.001), but not the peripheral inferior area (P = 0.171).", "Greater declines in NEI VFQ-25 scores were also seen in patients who had worse visual field sensitivity at baseline.   \n", "CONCLUSIONS Progressive decline in sensitivity in the central inferior area of the visual field had the strongest association with longitudinal decline in QoL of patients with glaucoma."], "structured": true}
{"doc_id": 31229233, "title": "Use of thiazolidinediones and the risk of bladder cancer among people with type 2 diabetes: a meta-analysis.", "abstract": ["BACKGROUND Patients with type 2 diabetes have a 40% increased risk of bladder cancer.", "Thiazolidinediones, especially pioglitazone, may increase the risk.", "We conducted a systematic review and meta-analysis to evaluate the risk of bladder cancer among adults with type 2 diabetes taking thiazolidinediones.   \n", "METHODS We searched key biomedical databases (including MEDLINE, Embase and Scopus) and sources of grey literature from inception through March 2012 for published and unpublished studies, without language restrictions.", "We included randomized controlled trials (RCTs), cohort studies and case-control studies that reported incident bladder cancer among people with type 2 diabetes who ever (v. never) were exposed to pioglitazone (main outcome), rosiglitazone or any thiazolidinedione.   \n", "RESULTS Of the 1787 studies identified, we selected 4 RCTs, 5 cohort studies and 1 case-control study.", "The total number of patients was 2,657,365, of whom 3643 had newly diagnosed bladder cancer, for an overall incidence of 53.1 per 100,000 person-years.", "The one RCT that reported on pioglitazone use found no significant association with bladder cancer (risk ratio [RR] 2.36, 95% confidence interval [CI] 0.91-6.13).", "The cohort studies of thiazolidinediones (pooled RR 1.15, 95% CI 1.04-1.26; I(2) = 0%) and of pioglitazone specifically (pooled RR 1.22, 95% CI 1.07-1.39; I(2) = 0%) showed significant associations with bladder cancer.", "No significant association with bladder cancer was observed in the two RCTs that evaluated rosiglitazone use (pooled RR 0.87, 95% CI 0.34-2.23; I(2) = 0%).   \n", "INTERPRETATION The limited evidence available supports the hypothesis that thiazolidinediones, particularly pioglitazone, are associated with an increased risk of bladder cancer among adults with type 2 diabetes."], "structured": true}
{"doc_id": 31272411, "title": "Immune signaling by RIG-I-like receptors.", "abstract": ["The RIG-I-like receptors (RLRs) RIG-I, MDA5, and LGP2 play a major role in pathogen sensing of RNA virus infection to initiate and modulate antiviral immunity.", "The RLRs detect viral RNA ligands or processed self RNA in the cytoplasm to trigger innate immunity and inflammation and to impart gene expression that serves to control infection.", "Importantly, RLRs cooperate in signaling crosstalk networks with Toll-like receptors and other factors to impart innate immunity and to modulate the adaptive immune response.", "RLR regulation occurs at a variety of levels ranging from autoregulation to ligand and cofactor interactions and posttranslational modifications.", "Abberant RLR signaling or dysregulation of RLR expression is now implicated in the development of autoimmune diseases.", "Understanding the processes of RLR signaling and response will provide insights to guide RLR-targeted therapeutics for antiviral and immune-modifying applications."], "structured": false}
{"doc_id": 31293581, "title": "Ionizing radiation-induced long-term expression of senescence markers in mice is independent of p53 and immune status.", "abstract": ["Exposure to IR has been shown to induce the formation of senescence markers, a phenotype that coincides with lifelong delayed repair and regeneration of irradiated tissues.", "We hypothesized that IR-induced senescence markers could persist long-term in vivo, possibly contributing to the permanent reduction in tissue functionality.", "Here, we show that mouse tissues exposed to a sublethal dose of IR display persistent (up to 45 weeks, the maximum time analyzed) DNA damage foci and increased p16(INK4a) expression, two hallmarks of cellular senescence and aging.", "BrdU-labeling experiments revealed that IR-induced damaged cells are preferentially eliminated, at least partially, in a tissue-dependent manner.", "Unexpectedly, the accumulation of damaged cells was found to occur independent from the DNA damage response modulator p53, and from an intact immune system, as their levels were similar in wild-type and Rag2(-/-) gammaC(-/-) mice, the latter being deficient in T, B, and NK cells.", "Together, our results provide compelling evidence that exposure to IR induces long-term expression of senescence markers in vivo, an effect that may contribute to the reduced tissue functionality observed in cancer survivors."], "structured": false}
{"doc_id": 31304956, "title": "Cranial neural crest and the building of the vertebrate head", "abstract": ["Head development in vertebrates involves a complex series of molecular and morphogenetic events that generate a coordinated pattern of cartilages, bones and nerves, and result in species-specific craniofacial morphologies.", "A specialized cell type of neural origin, the neural crest, is central to this process, as it provides the main source of craniofacial mesenchyme.", "The degree of patterning information that is intrinsic to the neural crest has been recently debated, and new advances have underscored the influence of environmental signalling on the transcriptional readout that coordinates craniofacial morphogenesis in space and time."], "structured": false}
{"doc_id": 31311495, "title": "Tamoxifen resistance in MCF7 cells promotes EMT-like behaviour and involves modulation of beta-catenin phosphorylation.", "abstract": ["We have previously demonstrated that, following acquisition of endocrine resistance, breast cancer cells display an altered growth rate together with increased aggressive behaviour in vitro.", "Since dysfunctional cell-cell adhesive interactions can promote an aggressive phenotype, we investigated the integrity of this protein complex in our breast cancer model of tamoxifen resistance.", "In culture, tamoxifen-resistant MCF7 (TamR) cells grew as loosely packed colonies with loss of cell-cell junctions and demonstrated altered morphology characteristic of cells undergoing epithelial-to-mesenchymal transition (EMT).", "Neutralising E-cadherin function promoted the invasion and inhibited the aggregation of endocrine-sensitive MCF7 cells, whilst having little effect on the behaviour of TamR cells.", "Additionally, TamR cells had increased levels of tyrosine-phosphorylated beta-catenin, whilst serine/threonine-phosphorylated beta-catenin was decreased.", "These cells also displayed loss of association between beta-catenin and E-cadherin, increased cytoplasmic and nuclear beta-catenin and elevated transcription of beta-catenin target genes known to be involved in tumour progression and EMT.", "Inhibition of EGFR kinase activity in TamR cells reduced beta-catenin tyrosine phosphorylation, increased beta-catenin-E-cadherin association and promoted cell-cell adhesion.", "In such treated cells, the association of beta-catenin with Lef-1 and the transcription of c-myc, cyclin-D1, CD44 and COX-2 were also reduced.", "These results suggest that homotypic adhesion in tamoxifen-resistant breast cancer cells is dysfunctional due to EGFR-driven modulation of the phosphorylation status of beta-catenin and may contribute to an enhanced aggressive phenotype and transition towards a mesenchymal phenotype in vitro."], "structured": false}
{"doc_id": 31313782, "title": "Expression profiles of Toll-like receptors in non-small cell lung cancer and idiopathic pulmonary fibrosis.", "abstract": ["Patients with idiopathic pulmonary fibrosis (IPF) have a higher incidence             of lung cancer.", "The role of Toll-like receptors (TLRs), a key component of the             innate immunity, in interstitial lung diseases (ILDs) and lung cancer pathogenesis             is not clarified.", "TLR2, TLR3, TLR4, TLR7, TLR8 and TLR9 mRNA expression was quantitatively             measured by real-time reverse transcriptase polymerase chain reaction (RT-PCR)             in bronchoalveolar lavage fluid (BALF) of 16 IPF patients, 16 non-small cell lung             cancer (NSCLC) patients and 9 control subjects.", "TLR2, TLR3, TLR4 and TLR9 protein             expression was assessed on BALF T-lymphocytes using flow cytometry.", "TLR3 mRNA             expression was significantly higher in NSCLC compared to IPF (p=0.023) and controls             (p=0.001).", "TLR7 mRNA expression levels were significantly higher in both NSCLC             and IPF groups compared to controls (p=0.029, p=0.009).", "TLR9 expression at the             mRNA level was significantly higher in both NSCLC and IPF groups compared to controls             (p=0.01, p=0.001).", "Finally, TLR2 mRNA expression was significantly higher in IPF             patients compared to controls (p=0.042).", "Flow cytometry revealed decreased TLR3             and TLR9 expression in IPF patients compared to the NSCLC group (p=0.02, p=0.014)             and decreased TLR9 expression in IPF compared with the controls (p=0.04).", "TLR2             protein expression was significantly higher in IPF patients compared to NSCLC             (p=0.04).", "Increased expression of endosomal TLRs in NSCLC patients and elevated             expression of TLR2 in pulmonary fibrosis are the main results of this study.", "These             results do not provide support for a common TLR pathway hypothesis between NSCLC             and IPF."], "structured": false}
{"doc_id": 31324978, "title": "A protein farnesyltransferase inhibitor ameliorates disease in a mouse model of progeria.", "abstract": ["Progerias are rare genetic diseases characterized by premature aging.", "Several progeroid disorders are caused by mutations that lead to the accumulation of a lipid-modified (farnesylated) form of prelamin A, a protein that contributes to the structural scaffolding for the cell nucleus.", "In progeria, the accumulation of farnesyl-prelamin A disrupts this scaffolding, leading to misshapen nuclei.", "Previous studies have shown that farnesyltransferase inhibitors (FTIs) reverse this cellular abnormality.", "We tested the efficacy of an FTI (ABT-100) in Zmpste24-deficient mice, a mouse model of progeria.", "The FTI-treated mice exhibited improved body weight, grip strength, bone integrity, and percent survival at 20 weeks of age.", "These results suggest that FTIs may have beneficial effects in humans with progeria."], "structured": false}
{"doc_id": 31347396, "title": "A rare mutation in UNC5C predisposes to late-onset Alzheimer's disease and increases neuronal cell death", "abstract": ["We have identified a rare coding mutation, T835M (rs137875858), in the UNC5C netrin receptor gene that segregated with disease in an autosomal dominant pattern in two families enriched for late-onset Alzheimer's disease and that was associated with disease across four large case-control cohorts (odds ratio = 2.15, Pmeta = 0.0095).", "T835M alters a conserved residue in the hinge region of UNC5C, and in vitro studies demonstrate that this mutation leads to increased cell death in human HEK293T cells and in rodent neurons.", "Furthermore, neurons expressing T835M UNC5C are more susceptible to cell death from multiple neurotoxic stimuli, including \u03b2-amyloid (A\u03b2), glutamate and staurosporine.", "On the basis of these data and the enriched hippocampal expression of UNC5C in the adult nervous system, we propose that one possible mechanism in which T835M UNC5C contributes to the risk of Alzheimer's disease is by increasing susceptibility to neuronal cell death, particularly in vulnerable regions of the Alzheimer's disease brain."], "structured": false}
{"doc_id": 31363207, "title": "Treatment of active tuberculosis in HIV-coinfected patients: a systematic review and meta-analysis.", "abstract": ["BACKGROUND Patients with human immunodeficiency virus (HIV) infection and tuberculosis have an increased risk of death, treatment failure, and relapse.   \n", "METHODS A systematic review and meta-analysis of randomized, controlled trials and cohort studies was conducted to evaluate the impact of duration and dosing schedule of rifamycin and use of antiretroviral therapy in the treatment of active tuberculosis in HIV-positive patients.", "In included studies, the initial tuberculosis diagnosis, failure, and/or relapse were microbiologically confirmed, and patients received standardized rifampin- or rifabutin-containing regimens.", "Pooled cumulative incidence of treatment failure, death during treatment, and relapse were calculated using random-effects models.", "Multivariable meta-regression was performed using negative binomial regression.   \n", "RESULTS After screening 5158 citations, 6 randomized trials and 21 cohort studies were included.", "Relapse was more common with regimens using 2 months rifamycin (adjusted risk ratio, 3.6; 95% confidence interval, 1.1-11.7) than with regimens using rifamycin for at least 8 months.", "Compared with daily therapy in the initial phase (n=3352 patients from 35 study arms), thrice-weekly therapy (n=211 patients from 5 study arms) was associated with higher rates of failure (adjusted risk ratio, 4.0; 95% confidence interval, 1.5-10.4) and relapse [adjusted risk ratio, 4.8; 95% confidence interval, 1.8-12.8).", "There were trends toward higher relapse rates if rifamycins were used for only 6 months, compared with > or =8 months, or if antiretroviral therapy was not used.   \n", "CONCLUSIONS This review raises serious concerns regarding current recommendations for treatment of HIV-tuberculosis coinfection.", "The data suggest that at least 8 months duration of rifamycin therapy, initial daily dosing, and concurrent antiretroviral therapy might be associated with better outcomes, but adequately powered randomized trials are urgently needed to confirm this."], "structured": true}
{"doc_id": 31387717, "title": "Crystal structure and association behaviour of the GluR2 amino-terminal domain.", "abstract": ["Fast excitatory neurotransmission is mediated largely by ionotropic glutamate receptors (iGluRs), tetrameric, ligand-gated ion channel proteins comprised of three subfamilies, AMPA, kainate and NMDA receptors, with each subfamily sharing a common, modular-domain architecture.", "For all receptor subfamilies, active channels are exclusively formed by assemblages of subunits within the same subfamily, a molecular process principally encoded by the amino-terminal domain (ATD).", "However, the molecular basis by which the ATD guides subfamily-specific receptor assembly is not known.", "Here we show that AMPA receptor GluR1- and GluR2-ATDs form tightly associated dimers and, by the analysis of crystal structures of the GluR2-ATD, propose mechanisms by which the ATD guides subfamily-specific receptor assembly."], "structured": false}
{"doc_id": 31407112, "title": "Deficiency in l-serine deaminase results in abnormal growth and cell division of Escherichia coli K-12.", "abstract": ["The loss of the ability to deaminate l-serine severely impairs growth and cell division in Escherichia coli K-12.", "A strain from which the three genes (sdaA, sdaB, tdcG) coding for this organism's three l-serine deaminases had been deleted grows well in glucose minimal medium but, on subculture into minimal medium with glucose and casamino acids, it makes very large, abnormally shaped cells, many of which lyse.", "When inoculated into Luria-Bertani (LB) broth with or without glucose, it makes very long filaments.", "Provision of S-adenosylmethionine restores cell division in LB broth with glucose, and repairs much of the difficulty in growth in medium with casamino acids.", "We suggest that replication of E. coli is regulated by methylation, that an unusually high intracellular l-serine concentration, in the presence of other amino acids, starves the cell for S-adenosylmethionine and that it is the absence of S-adenosylmethionine and/or of C1-tetrahydrofolate derivatives that prevents normal cell division."], "structured": false}
{"doc_id": 31439189, "title": "Stem cell characteristics in prostate cancer cell lines.", "abstract": ["BACKGROUND Recent studies indicate the presence of a small, stem-like cell population in several human cancers that is crucial for the tumour (re)population.   \n", "OBJECTIVE Six established prostate cancer (PCa) cell lines-DU145, DuCaP, LAPC-4, 22Rv1, LNCaP, and PC-3-were examined for their stem cell properties in vitro.   \n", "DESIGN, SETTINGS, AND PARTICIPANTS The colony-forming efficiency and self-renewal ability of morphologically distinguishable holoclones and paraclones were tested with low-density plating and serial passaging.", "Expression of the putative stem cell marker CD133 and breast cancer resistance protein (BCRP) was examined with flow cytometry, and immunohistochemical stainings were made for CD133, alpha2-integrin, nestin, BCRP, cytokeratin 5 (CK5), and cytokeratin 18 (CK18).   \n", "RESULTS AND LIMITATIONS Five out of six cell lines formed clear holo-, mero-, and paraclones.", "Unlike paraclones, we can maintain DU145 holoclones in culture for several passages, which is indicative of self-renewal ability.", "Using fluorescence-activated cell sorting (FACS) analysis only in DU145 cells, a small fraction (0.01%) of CD133(+) cells was detected.", "CD133(+) cells; however, like DU145 BCRP(+) (0.15%) cells, they were not more clonogenic, and they did not show more holoclone formation than the marker-negative cells or unselected cells.", "Immunohistochemistry revealed alpha2-integrin and BCRP as potential stem cell markers and CK5 with the combination of CK18 to distinguish transient amplifying cells.   \n", "CONCLUSIONS These results indicate the possible presence of stem-like cells in several established PCa cell lines.", "CD133 selection does not enrich for stem-like cells in PCa cell lines."], "structured": true}
{"doc_id": 31460499, "title": "Resistance to antimicrobials in humans and animals.", "abstract": ["Overusing antibiotics is not the only cause and reducing use is not the only solution   W arning signs of antimicrobial resistance, chinks in the antimicrobial armour, began to appear in the middle of the last century, and by the 1990s various reports had signalled the dangers of excessive or inappropriate use of antibiotics in clinical medicine and of the use of antibiotics in animal feed as growth promoters.1\u20133 Overuse of antimicrobials emerged as the main culprit, and reducing their use was seen as the answer.", "But it may not be that simple.  ", "The idea that reducing antibiotic use would redress the problem formed part of a positive response on the part of the United Kingdom government to the House of Lords report,1 including a public information campaign, surveillance of resistance along the food chain, targets with respect to hospital acquired infections, and setting up of an overarching advisory body on all aspects of antibiotic use.", "However, the concept of overuse has proved too simplistic, for, although the evidence of overprescribing as the \u2026"], "structured": false}
{"doc_id": 31495049, "title": "Unmet needs and depressive symptoms among low--income older adults.", "abstract": ["Previous studies have found that declining health, decreased social interaction, and inadequate financial resources were significant risk factors for late-life depression, and social support from families and friends and religiosity were significant protective factors.", "In this study, we examined if low-income older adults' perceived unmet need for home- and community-based services for many aging-associated problems would be independently associated with their depressive symptoms, controlling for these known risk and protective factors.", "We interviewed a total of 213 community-residing older adults to assess their depressive symptoms, using the Geriatric Depression Scale (GDS), and unmet needs in the areas of personal assistance, instrumental and environmental support, emotional support, and other facilitative/enabling services.", "We found that the number of unmet needs was significantly positively associated with these older adults' depressive symptoms, although it explained only a small proportion of the variance of the GDS scores.", "Future research and practice implications are discussed."], "structured": false}
{"doc_id": 31514338, "title": "A key role for Ctf4 in coupling the MCM2-7 helicase to DNA polymerase alpha within the eukaryotic replisome.", "abstract": ["The eukaryotic replisome is a crucial determinant of genome stability, but its structure is still poorly understood.", "We found previously that many regulatory proteins assemble around the MCM2-7 helicase at yeast replication forks to form the replisome progression complex (RPC), which might link MCM2-7 to other replisome components.", "Here, we show that the RPC associates with DNA polymerase alpha that primes each Okazaki fragment during lagging strand synthesis.", "Our data indicate that a complex of the GINS and Ctf4 components of the RPC is crucial to couple MCM2-7 to DNA polymerase alpha.", "Others have found recently that the Mrc1 subunit of RPCs binds DNA polymerase epsilon, which synthesises the leading strand at DNA replication forks.", "We show that cells lacking both Ctf4 and Mrc1 experience chronic activation of the DNA damage checkpoint during chromosome replication and do not complete the cell cycle.", "These findings indicate that coupling MCM2-7 to replicative polymerases is an important feature of the regulation of chromosome replication in eukaryotes, and highlight a key role for Ctf4 in this process."], "structured": false}
{"doc_id": 31543713, "title": "Data analysis methods for detection of differential protein expression in two-dimensional gel electrophoresis.", "abstract": ["The recent development of microarray technology has led statisticians and bioinformaticians to develop new statistical methodologies for comparing different biological samples.", "The objective is to identify a small number of differentially expressed genes from among thousands.", "In quantitative proteomics, analysis of protein expression using two-dimensional gel electrophoresis shows some similarities with transcriptomic studies.", "Thus, the goal of this study was to evaluate different data analysis methodologies widely used in array analysis using different proteomic data sets of hundreds of proteins.", "Even with few replications, the significance analysis of microarrays method appeared to be more powerful than the Student's t test in truly declaring differentially expressed proteins.", "This procedure will avoid wasting time due to false positives and losing information with false negatives."], "structured": false}
{"doc_id": 31554917, "title": "A clinical approach to circadian rhythm sleep disorders.", "abstract": ["Circadian rhythm sleep disorders are characterized by complaints of insomnia and excessive sleepiness that are primarily due to alterations in the internal circadian timing system or a misalignment between the timing of sleep and the 24-h social and physical environment.", "In addition to physiological and environmental factors, maladaptive behaviors often play an important role in the development of many of the circadian rhythm sleep disorders.", "This review will focus on the clinical approach to the diagnosis and management of the various circadian rhythm sleep disorders, including delayed sleep phase disorder, advanced sleep phase disorder, non-entrained type, irregular sleep-wake rhythm, shift work sleep disorder and jet lag disorder.", "Diagnostic tools such as sleep diaries and wrist activity monitoring are often useful in confirming the diagnosis.", "Because behavioral and environmental factors often are involved in the development of these conditions, a multimodal approach is usually necessary.", "Interventions include sleep hygiene education, timed exposure to bright light as well as avoidance of bright light at the wrong time of the day and pharmacologic approaches, such as melatonin.", "However, it should be noted that the use of melatonin is not an FDA-approved indication for the treatment of circadian rhythm sleep disorders."], "structured": false}
{"doc_id": 31560225, "title": "SIVrcm infection of macaques.", "abstract": ["In a prior report, we described the isolation and characterization of SIVrcm, a distinct primate lentivirus found in a household pet Red-Capped Mangabey (RCM) in Gabon.", "SIVrcm is divergent from HIV-1 and HIV-2/SIV families of primate lentiviruses.", "In this report, additional in vitro replication studies and the results of SIVrcm infection in macaques are presented.", "SIVrcm causes little cytopathic effedct in Molt 4 Clone 8 cells and in rhesus and human PBMCs.", "In vivo, SIVrcm is non-pathogenic after 200 days in rhesus macaques and after one year in cynomolgous macaques, but does cause a chronic infection in both macaques."], "structured": false}
{"doc_id": 31562330, "title": "Integrating nutrition security with treatment of people living with HIV: lessons from Kenya.", "abstract": ["BACKGROUND The increased caloric requirements of HIV-positive individuals, undesirable side effects of treatment that may be worsened by malnutrition (but alleviated by nutritional support), and associated declines in adherence and possible increased drug resistance are all justifications for developing better interventions to strengthen the nutrition security of individuals receiving antiretroviral treatment.   \n", "OBJECTIVE To highlight key benefits and challenges relating to interventions aimed at strengthening the nutrition security of people living with HIV who are receiving antiretroviral treatment.   \n", "METHODS Qualitative research was undertaken on a short-term nutrition intervention linked to the provision of free antiretroviral treatment for people living with HIV in western Kenya in late 2005 and early 2006.   \n", "RESULTS Patients enrolled in the food program while on treatment regimens self-reported greater adherence to their medication, fewer side effects, and a greater ability to satisfy increased appetite.", "Most clients self-reported weight gain, recovery of physical strength, and the resumption of labor activities while enrolled in dual (food supplementation and treatment) programs.", "Such improvements were seen to catalyze increased support from family and community.   \n", "CONCLUSIONS These findings provide further empirical support to calls for a more holistic and comprehensive response to the coexistence of AIDS epidemics with chronic nutrition insecurity.", "Future work is needed to clarify ways of bridging the gap between short-term nutritional support to individuals and longer-term livelihood security programming for communities affected by AIDS.", "Such interdisciplinary research will need to be matched by intersectoral action on the part of the agriculture and health sectors in such environments."], "structured": true}
{"doc_id": 31564409, "title": "Acylated and desacyl ghrelin stimulate lipid accumulation in human visceral adipocytes", "abstract": ["Objectives:The orexigenic hormone ghrelin circulates mainly in two forms, acylated and desacyl ghrelin.", "We evaluated the impact of obesity and obesity-associated type 2 diabetes (T2D) on ghrelin forms and the potential role of acylated and desacyl ghrelin in the control of adipogenesis in humans.", "Methods:Plasma concentrations of the different ghrelin forms were measured in 80 subjects.", "The expression of the ghrelin receptor (growth hormone secretagogue receptor, GHS-R) was analyzed in omental adipose tissue using western blot and immunohistochemistry, and the effect of acylated ghrelin and desacyl ghrelin (0.1\u20131000 pmol l\u22121) on adipogenesis was determined in vitro in omental adipocytes.", "Results:Circulating concentrations of acylated ghrelin were increased, whereas desacyl ghrelin levels were decreased, in obesity and obesity-associated T2D.", "Body mass index, waist circumference, insulin and HOMA (homeostasis model assessment) index were positively correlated with acylated ghrelin levels.", "Obese individuals showed a lower protein expression of GHS-R in omental adipose tissue.", "In differentiating omental adipocytes, incubation with both acylated and desacyl ghrelin significantly increased PPAR\u03b3 (peroxisome proliferator-activated receptor \u03b3) and SREBP1 (sterol-regulatory element binding protein-1) mRNA levels, as well as several fat storage-related proteins, including acetyl-CoA carboxylase, fatty acid synthase, lipoprotein lipase and perilipin.", "Consequently, both the ghrelin forms stimulated intracytoplasmatic lipid accumulation.", "Conclusions:Both acylated and desacyl ghrelin stimulate lipid accumulation in human visceral adipocytes.", "Given the lipogenic effect of acylated ghrelin on visceral adipocytes, the herein-reported elevation of its circulating concentrations in obese individuals may play a role in excessive fat accumulation in obesity."], "structured": false}
{"doc_id": 31591262, "title": "Significant correlation between LKB1 and LGR5 gene expression and the association with poor recurrence-free survival in rectal cancer after preoperative chemoradiotherapy", "abstract": ["The aim of the present study was to investigate whether the gene expression levels of LKB1 and LGR5 correlated with clinical outcome in patients with locally advanced rectal cancer treated with preoperative chemoradiotherapy (CRT).", "Residual cancer cells were obtained from 52 patients with locally advanced rectal cancer treated with preoperative CRT.", "Total RNA was then isolated from formalin-fixed, paraffin-embedded specimens using microdissection.", "The expression levels of LKB1 and LGR5 genes were measured using real-time reverse-transcription polymerase chain reaction and by immunohistochemistry.", "In addition, in vitro studies were performed using colon cancer cell lines to study the serial changes of LKB1, LGR5 and PRKAA1 (AMPK) gene expression levels after irradiation.", "Our data demonstrate that specimens obtained from patients with poor pathological response and tumor recurrence had significantly higher gene expression levels of LKB1 and LGR5 than those without them (P < 0.05), and there was a significant positive correlation between LKB1 and LGR5 gene expression after CRT (Spearman\u2019s \u03c1: 0.429, P = 0.0023).", "The patients with high expression levels of both LKB1 and LGR5 had a significantly lower recurrence-free survival compared with the other group (P = 0.0055, 95 % confidence interval: 1.39\u201311.08).", "Lastly, in vitro studies demonstrated a similar pattern of serial gene expression among LKB1, LGR5 and PRKAA1 after irradiation.", "Our results suggest that LKB1 and LGR5 expression may be implicated in resistance to CRT, therefore contributing to tumor relapse in patients with locally advanced rectal cancer treated with preoperative CRT."], "structured": false}
{"doc_id": 31612088, "title": "Evaluating the impact of pharmacists in mental health: a systematic review.", "abstract": ["Efforts to improve the outcomes of patients with mental illness often have involved incorporating the skills of a variety of health care professionals into collaborative care models.", "For over 30 years, clinical pharmacists have contributed to these care models in capacities ranging from educator to consultant to provider.", "This systematic review evaluates the quantity and quality of medical literature examining the impact of pharmacists in mental health from 1972-2003.", "Although we identified approximately 35 publications describing the roles of clinical pharmacists in this regard, only 16 were of sufficient scientific rigor to permit evaluation and comparison.", "The 16 studies were divided equally between inpatient and outpatient settings and were conducted in a variety of health care organizations (e.g., Veterans Administration, health maintenance organizations, community mental health clinics, and nursing homes).", "Nine of the studies examined the role of pharmacists in providing treatment recommendations and patient education, five featured pharmacists as providers (with prescriptive authority), and the remaining two described the impact pharmacists have in delivering education to the psychiatric staff.", "Six of the 16 studies were prospective, but only three of these incorporated a randomization procedure for patients or facilities.", "Collectively, the results of the 16 studies were positive, demonstrating improvements in outcomes, prescribing practices, patient satisfaction, and resource use.", "Unfortunately, most of the investigations were small, and significant limitations in study design limited further comparison.", "Given the long history and anecdotal success of pharmacists in mental health care settings, additional multicenter cost-effectiveness trials are warranted to further support the role of the psychiatric pharmacist."], "structured": false}
{"doc_id": 31616203, "title": "Multicenter phase II study of lapatinib in patients with brain metastases from HER2-positive breast cancer.", "abstract": ["PURPOSE Brain metastases develop in one third of patients with advanced HER2+ breast cancer.", "Effective therapy for patients with central nervous system (CNS) progression after cranial radiation is extremely limited and represents a major clinical challenge.", "Lapatinib, an epidermal growth factor receptor/HER2 inhibitor, was associated with regressions of CNS lesions in a small phase 2 trial.", "The current study was done to further evaluate the CNS activity of lapatinib.", "The study was later amended to allow patients who progressed on lapatinib the option of receiving lapatinib plus capecitabine.   ", "EXPERIMENTAL DESIGN Eligible patients had HER2+ breast cancer, progressive brain metastases, prior trastuzumab, and cranial radiotherapy.", "The primary end point was CNS objective response, defined as >or=50% volumetric reduction of CNS lesion(s) in the absence of increasing steroid use, progressive neurologic signs and symptoms, or progressive extra-CNS disease.   \n", "RESULTS Two-hundred and forty-two patients entered the study.", "CNS objective responses to lapatinib were observed in 6% of patients.", "In an exploratory analysis, 21% of patients experienced a >or=20% volumetric reduction in their CNS lesions.", "An association was observed between volumetric reduction and improvement in progression-free survival and neurologic signs and symptoms.", "Of the 50 evaluable patients who entered the lapatinib plus capecitabine extension, 20% experienced a CNS objective response and 40% experienced a >or=20% volumetric reduction in their CNS lesions.   \n", "CONCLUSIONS This study confirms the modest CNS antitumor activity of lapatinib.", "Additional responses were observed with the combination of lapatinib and capecitabine.", "Further studies of lapatinib-based regimens for CNS metastases from HER2+ breast cancer are warranted."], "structured": true}
{"doc_id": 31624828, "title": "Control of signaling-mediated clearance of apoptotic cells by the tumor suppressor p53", "abstract": ["The inefficient clearance of dying cells can lead to abnormal immune responses, such as unresolved inflammation and autoimmune conditions.", "We show that tumor suppressor p53 controls signaling-mediated phagocytosis of apoptotic cells through its target, Death Domain1\u03b1 (DD1\u03b1), which suggests that p53 promotes both the proapoptotic pathway and postapoptotic events.", "DD1\u03b1 appears to function as an engulfment ligand or receptor that engages in homophilic intermolecular interaction at intercellular junctions of apoptotic cells and macrophages, unlike other typical scavenger receptors that recognize phosphatidylserine on the surface of dead cells.", "DD1\u03b1-deficient mice showed in vivo defects in clearing dying cells, which led to multiple organ damage indicative of immune dysfunction.", "p53-induced expression of DD1\u03b1 thus prevents persistence of cell corpses and ensures efficient generation of precise immune responses."], "structured": false}
{"doc_id": 31634628, "title": "Circulating tumor DNA as a non-invasive substitute to metastasis biopsy for tumor genotyping and personalized medicine in a prospective trial across all tumor types.", "abstract": ["Cell-free tumor DNA (ctDNA) has the potential to enable non-invasive diagnostic tests for personalized medicine in providing similar molecular information as that derived from invasive tumor biopsies.", "The histology-independent phase II SHIVA trial matches patients with targeted therapeutics based on previous screening of multiple somatic mutations using metastatic biopsies.", "To evaluate the utility of ctDNA in this trial, as an ancillary study we performed de novo detection of somatic mutations using plasma DNA compared to metastasis biopsies in 34 patients covering 18 different tumor types, scanning 46 genes and more than 6800 COSMIC mutations with a multiplexed next-generation sequencing panel.", "In 27 patients, 28 of 29 mutations identified in metastasis biopsies (97%) were detected in matched ctDNA.", "Among these 27 patients, one additional mutation was found in ctDNA only.", "In the seven other patients, mutation detection from metastasis biopsy failed due to inadequate biopsy material, but was successful in all plasma DNA samples providing three more potential actionable mutations.", "These results suggest that ctDNA analysis is a potential alternative and/or replacement to analyses using costly, harmful and lengthy tissue biopsies of metastasis, irrespective of cancer type and metastatic site, for multiplexed mutation detection in selecting personalized therapies based on the patient's tumor genetic content."], "structured": false}
{"doc_id": 31682248, "title": "TGF-beta suppresses tumor progression in colon cancer by inhibition of IL-6 trans-signaling.", "abstract": ["Alterations of TGF-beta signaling have been described in colorectal cancer, although the molecular consequences are largely unknown.", "By using transgenic mice overexpressing TGF-beta or a dominant-negative TGF-betaRII, we demonstrate that TGF-beta signaling in tumor infiltrating T lymphocytes controls the growth of dysplastic epithelial cells in experimental colorectal cancer, as determined by histology and a novel system for high-resolution chromoendoscopy.", "At the molecular level, TGF-beta signaling in T cells regulated STAT-3 activation in tumor cells via IL-6.", "IL-6 signaling required tumor cell-derived soluble IL-6R rather than membrane bound IL-6R and suppression of such TGF-beta-dependent IL-6 trans-signaling prevented tumor progression in vivo.", "Taken together, our data provide novel insights into TGF-beta signaling in colorectal cancer and suggest novel therapeutic approaches for colorectal cancer based on inhibition of TGF-beta-dependent IL-6 trans-signaling."], "structured": false}
{"doc_id": 31715818, "title": "New opportunities: the use of nanotechnologies to manipulate and track stem cells.", "abstract": ["Nanotechnologies are emerging platforms that could be useful in measuring, understanding, and manipulating stem cells.", "Examples include magnetic nanoparticles and quantum dots for stem cell labeling and in vivo tracking; nanoparticles, carbon nanotubes, and polyplexes for the intracellular delivery of genes/oligonucleotides and protein/peptides; and engineered nanometer-scale scaffolds for stem cell differentiation and transplantation.", "This review examines the use of nanotechnologies for stem cell tracking, differentiation, and transplantation.", "We further discuss their utility and the potential concerns regarding their cytotoxicity."], "structured": false}
{"doc_id": 31761981, "title": "The emergence of order in the Drosophila pupal retina.", "abstract": ["During pupation, long-range order is imposed on the autonomously developing ommatidia which compose the Drosophila eye.", "To accomplish this, eight additional cell types arise: the primary, secondary, and tertiary pigment cells, and the four cells that form the bristle.", "These cells form an interweaving lattice between ommatidia.", "The lattice is refined when excess cells are removed to bring neighboring ommatidia into register.", "Recent evidence suggests that in larval development, local contacts direct cell fate.", "The same appears to be true during pupal development: the contacts a cell makes predict the cell type it will become.", "Cells which contact the anterior or posterior cone cells in an ommatidium invariably become primary pigment cells.", "Cells which contact primary pigment cells from different ommatidia become secondary and tertiary pigment cells.", "Bristle development is in several ways distinct from ommatidial development.", "The four cells of each bristle group appear to be immediate descendents of a single founder cell.", "During their early differentiation, they do not make stereotyped contacts with surrounding ommatidial cells, but do make particular contacts within the bristle group.", "And unlike the surrounding ommatidia, differentiation of the bristles radiates from the center of the eye to the edges.", "As cells are removed during two stages of programmed cell death, the bristles are brought into their final position.", "When all cells in the lattice have achieved their final position, a second stage of retinal development begins as structures specific to each cell type are produced.", "This paper follows these various stages of pupal development, and suggests how local cell-cell contacts may produce the cells needed for a functional retina."], "structured": false}
{"doc_id": 31803596, "title": "Gene expression analysis by cDNA microarray in oral squamous cell carcinoma.", "abstract": ["BACKGROUND Oral squamous cell carcinoma (OSCC) is common type of human cancer, but little is known about the molecular mechanisms deciding on this malignancy.", "Comprehensive gene expression profiling is essential for understanding OSCC.   \n", "METHODS cDNA microarray was used to analyze expression patterns of 16 617 genes in nine OSCC patients.   \n", "RESULTS Forty-seven genes with altered expression among all cases were extracted.", "The ontology of these 47 genes was classified into 10 categories.", "To validate the microarray data, the expression of genes, including TGFBI, FADD and DUSP1 was analyzed by reverse transcriptase-polymerase chain reaction (RT-PCR).", "By hierarchical clustering analysis, the nine cases were divided into two clusters.   \n", "CONCLUSIONS The 47 genes are suggested as having a functional significance in oral squamous cell carcinogenesis.", "It is also suggested that the gene expression patterns by hierarchical clustering analysis can represent degrees of differentiation.", "The postoperative recovery was uneventful and patients free from tumor after surgery.", "In the future, on the occasion when the time comes that the number of cases accumulated for microarray increases and each case is observed more over a long-term, these data of 5-year survival rate will be added.", "Thereby, it will become possible to represent the malignancy of OSCC by these gene expression patterns."], "structured": true}
{"doc_id": 31834381, "title": "Risk factors associated with symptoms of gastroesophageal reflux.", "abstract": ["BACKGROUND Although patients with gastroesophageal reflux are often instructed to change their lifestyle, population-based data on the risk factors for reflux in the United States are lacking.   \n", "METHODS We performed a cross-sectional study in an age- and gender-stratified random sample of the population of Olmsted County, Minnesota.", "Residents aged 25 to 74 years were mailed a valid self-report questionnaire that measured reflux symptoms and potential risk factors.", "Logistic regression was used to estimate the odds ratios (OR) with 95% confidence intervals (CI) for reflux symptoms (heartburn or acid regurgitation) associated with potential risk factors.   \n", "RESULTS Overall, 1,524 (72%) of 2,118 eligible subjects responded.", "A body mass index >30 kg/m2 (OR = 2.8; CI, 1.7 to 4.5), reporting an immediate family member with heartburn or disease of the esophagus or stomach (OR = 2.6; CI, 1.8 to 3.7), a past history of smoking (OR = 1.6; CI, 1.1 to 2.3), consuming more than seven drinks per week (OR = 1.9; Cl, 1.1 to 3.3), and a higher psychosomatic symptom checklist score (OR per 5 units = 1.4; CI, 1.3 to 1.6) were independently associated with frequent (at least weekly) reflux symptoms.   \n", "CONCLUSION Obesity is a strong risk factor for gastroesophageal reflux, although the value of weight reduction remains to be proven.", "That family history was also a risk factor suggests that there may be a genetic component to the disorder."], "structured": true}
{"doc_id": 31844040, "title": "A mathematical investigation of the effects of inhibitor therapy on three putative phosphorylation cascades governing the two-component system of the agr operon.", "abstract": ["Two-component systems (TCSs) are widely employed by bacteria to sense specific external signals and conduct an appropriate response via a phosphorylation cascade within the cell.", "The TCS of the agr operon in the bacterium Staphylococcus aureus forms part of a regulatory process termed quorum sensing, a cell-to-cell communication mechanism used to assess population density.", "Since S. aureus manipulates this \"knowledge\" in order to co-ordinate production of its armoury of exotoxin virulence factors required to promote infection, it is important to understand fully how this process works.", "We present three models of the agr operon, each incorporating a different phosphorylation cascade for the TCS since the precise nature of the cascade is not fully understood.", "Using numerical and asymptotic techniques we examine the effects of inhibitor therapy, a novel approach to controlling bacterial infection through the attenuation of virulence, on each of these three cascades.", "We present results which, if evaluated against appropriate experimental data, provide insights into the potential effectiveness of such therapy.", "Moreover, the TCS models presented here are of broad relevance given that TCSs are widely conserved throughout the bacterial kingdom."], "structured": false}
{"doc_id": 31851367, "title": "Coregulators in nuclear estrogen receptor action: from concept to therapeutic targeting.", "abstract": ["Estrogens are key regulators of growth, differentiation, and the physiological functions of a wide range of target tissues, including the male and female reproductive tracts, breast, and skeletal, nervous, cardiovascular, digestive and immune systems.", "The majority of these biological activities of estrogens are mediated through two genetically distinct receptors, ERalpha and ERbeta, which function as hormone-inducible transcription factors.", "Over the past decade, it has become increasingly clear that the recruitment of coregulatory proteins to ERs is required for ER-mediated transcriptional and biological activities.", "These \"coactivator\" complexes enable the ERs to respond appropriately: 1) to hormones or pharmacological ligands, 2) interpret extra- and intra-cellular signals, 3) catalyze the process of chromatin condensation and 4) to communicate with the general transcription apparatus at target gene promoters.", "In addition to activating proteins, the existence of corepressors, proteins that function as negative regulators of ER activity in either physiological or pharmacological contexts, provides an additional level of complexity in ER action.", "This review also describes current efforts aimed at developing pharmaceutical agents that target ER-cofactor interactions as therapeutics for estrogen-associated pathologies."], "structured": false}
{"doc_id": 31882215, "title": "Autophagy and mTORC1 regulate the stochastic phase of somatic cell reprogramming", "abstract": ["We describe robust induction of autophagy during the reprogramming of mouse fibroblasts to induced pluripotent stem cells by four reprogramming factors (Sox2, Oct4, Klf4 and c-Myc), henceforth 4F.", "This process occurs independently of p53 activation, and is mediated by the synergistic downregulation of mechanistic target of rapamycin complex 1 (mTORC1) and the induction of autophagy-related genes.", "The 4F coordinately repress mTORC1, but bifurcate in their regulation of autophagy-related genes, with Klf4 and c-Myc inducing them but Sox2 and Oct4 inhibiting them.", "On one hand, inhibition of mTORC1 facilitates reprogramming by promoting cell reshaping (mitochondrial remodelling and cell size reduction).", "On the other hand, mTORC1 paradoxically impairs reprogramming by triggering autophagy.", "Autophagy does not participate in cell reshaping in reprogramming but instead degrades p62, whose accumulation in autophagy-deficient cells facilitates reprogramming.", "Our results thus reveal a complex signalling network involving mTORC1 inhibition and autophagy induction in the early phase of reprogramming, whose delicate balance ultimately determines reprogramming efficiency."], "structured": false}
{"doc_id": 31884697, "title": "Lithium Therapy Improves Neurological Function and Hippocampal Dendritic Arborization in a Spinocerebellar Ataxia Type 1 Mouse Model", "abstract": ["Background  Spinocerebellar ataxia type 1 (SCA1) is a dominantly inherited neurodegenerative disorder characterized by progressive motor and cognitive dysfunction.", "Caused by an expanded polyglutamine tract in ataxin 1 (ATXN1), SCA1 pathogenesis involves a multifactorial process that likely begins with misfolding of ATXN1, which has functional consequences on its interactions, leading to transcriptional dysregulation.", "Because lithium has been shown to exert neuroprotective effects in a variety of conditions, possibly by affecting gene expression, we tested the efficacy of lithium treatment in a knock-in mouse model of SCA1 (Sca1154Q/2Q mice) that replicates many features of the human disease.  ", "Methods and Findings  Sca1154Q/2Q mice and their wild-type littermates were fed either regular chow or chow that contained 0.2% lithium carbonate.", "Dietary lithium carbonate supplementation resulted in improvement of motor coordination, learning, and memory in Sca1154Q/2Q mice.", "Importantly, motor improvement was seen when treatment was initiated both presymptomatically and after symptom onset.", "Neuropathologically, lithium treatment attenuated the reduction of dendritic branching in mutant hippocampal pyramidal neurons.", "We also report that lithium treatment restored the levels of isoprenylcysteine carboxyl methyltransferase (Icmt; alternatively, Pccmt), down-regulation of which is an early marker of mutant ATXN1 toxicity.  ", "Conclusions  The effect of lithium on a marker altered early in the course of SCA1 pathogenesis, coupled with its positive effect on multiple behavioral measures and hippocampal neuropathology in an authentic disease model, make it an excellent candidate treatment for human SCA1 patients."], "structured": false}
{"doc_id": 31889025, "title": "The progression from hypertension to congestive heart failure.", "abstract": ["OBJECTIVES - To study the relative and population-attributable risks of hypertension for the development of congestive heart failure (CHF), to assess the time course of progression from hypertension to CHF, and to identify risk factors that contribute to the development of overt heart failure in hypertensive subjects.   \n", "DESIGN - Inception cohort study.   \n", "SETTING - General community.   \n", "PARTICIPANTS - Original Framingham Heart Study and Framingham Offspring Study participants aged 40 to 89 years and free of CHF.", "To reflect more contemporary experience, the starting point of this study was January 1, 1970.   ", "EXPOSURE MEASURES - Hypertension (blood pressure of at least 140 mm Hg systolic or 90 mm Hg diastolic or current use of medications for treatment of high blood pressure) and other potential CHF risk factors were assessed at periodic clinic examinations.   \n", "OUTCOME MEASURE - The development of CHF.   \n", "RESULTS - A total of 5143 eligible subjects contributed 72422 person-years of observation.", "During up to 20.1 years of follow-up (mean, 14.1 years), there were 392 new cases of heart failure; in 91% (357/392), hypertension antedated the development of heart failure.", "Adjusting for age and heart failure risk factors in proportional hazards regression models, the hazard for developing heart failure in hypertensive compared with normotensive subjects was about 2-fold in men and 3-fold in women.", "Multivariable analyses revealed that hypertension had a high population-attributable risk for CHF, accounting for 39% of cases in men and 59% in women.", "Among hypertensive subjects, myocardial infarction, diabetes, left ventricular hypertrophy, and valvular heart disease were predictive of increased risk for CHF in both sexes.", "Survival following the onset of hypertensive CHF was bleak; only 24% of men and 31% of women survived 5 years.   \n", "CONCLUSIONS - Hypertension was the most common risk factor for CHF, and it contributed a large proportion of heart failure cases in this population-based sample.", "Preventive strategies directed toward earlier and more aggressive blood pressure control are likely to offer the greatest promise for reducing the incidence of CHF and its associated mortality."], "structured": true}
{"doc_id": 31890716, "title": "Association of plasma resistin with glomerular filtration rate and albuminuria in hypertensive adults.", "abstract": ["Resistin, a recently discovered proinflammatory cytokine, has been variably associated with insulin resistance, inflammation, and renal dysfunction.", "We investigated the association of plasma resistin with estimated glomerular filtration rate and albuminuria in 1575 hypertensive adults without known coronary heart disease or stroke (857 blacks and 718 non-Hispanic whites).", "Resistin was measured by a solid phase sandwich immunoassay, estimated glomerular filtration rate was estimated from serum creatinine, and albuminuria was expressed as urine albumin:creatinine ratio.", "After adjustment for coronary heart disease risk factors (age, sex, body mass index, smoking history, systolic blood pressure, diabetes, and total and high-density lipoprotein cholesterol) and use of renin-angiotensin blockers and statins, higher plasma resistin levels were associated with lower estimated glomerular filtration rate in both ethnic groups (each P<0.0001); the association remained significant after further adjustment for a marker of insulin resistance (homeostasis model assessment for insulin resistance) and a marker of inflammation (plasma C-reactive protein) and was seen in subjects with and without diabetes (each P<0.0001) in both ethnic groups.", "Higher plasma resistin levels were associated with a higher urine albumin:creatinine ratio in black subjects with diabetes (P<0.0001) and non-Hispanic white subjects with diabetes (P=0.032), independent of coronary heart disease risk factors, hypertension medication use, and statin use; the association remained significant after additional adjustment for homeostasis model assessment for insulin resistance and C-reactive protein.", "In adults with hypertension, higher circulating resistin levels were associated with a lower estimated glomerular filtration rate and with increased urine albumin:creatinine ratio in the presence of concomitant diabetes.", "This association was independent of coronary heart disease risk factors and markers of insulin resistance and inflammation."], "structured": false}
{"doc_id": 31902059, "title": "Large-scale candidate gene scan reveals the role of chemoreceptor genes in host plant specialization and speciation in the pea aphid.", "abstract": ["Understanding the drivers of speciation is critical to interpreting patterns of biodiversity.", "The identification of the genetic changes underlying adaptation and reproductive isolation is necessary to link barriers to gene flow to the causal origins of divergence.", "Here, we present a novel approach to the genetics of speciation, which should complement the commonly used approaches of quantitative trait locus mapping and genome-wide scans for selection.", "We present a large-scale candidate gene approach by means of sequence capture, applied to identifying the genetic changes underlying reproductive isolation in the pea aphid, a model system for the study of ecological speciation.", "Targeted resequencing enabled us to scale up the candidate gene approach, specifically testing for the role of chemosensory gene families in host plant specialization.", "Screening for the signature of divergence under selection at 172 candidate and noncandidate loci, we revealed a handful of loci that show high levels of differentiation among host races, which almost all correspond to odorant and gustatory receptor genes.", "This study offers the first indication that some chemoreceptor genes, often tightly linked together in the genome, could play a key role in local adaptation and reproductive isolation in the pea aphid and potentially other phytophagous insects.", "Our approach opens a new route toward the functional genomics of ecological speciation."], "structured": false}
{"doc_id": 31902335, "title": "The cancer stem cell hypothesis: a guide to potential molecular targets.", "abstract": ["Common cancer theories hold that tumor is an uncontrolled somatic cell proliferation caused by the progressive addition of random mutations in critical genes that control cell growth.", "Nevertheless, various contradictions related to the mutation theory have been reported previously.", "These events may be elucidated by the persistence of residual tumor cells, called Cancer Stem Cells (CSCs) responsible for tumorigenesis, tumor maintenance, tumor spread, and tumor relapse.", "Herein, we summarize the current understanding of CSCs, with a focus on the possibility to identify specific markers of CSCs, and discuss the clinical application of targeting CSCs for cancer treatment."], "structured": false}
{"doc_id": 31933981, "title": "Serum amyloid A: An acute-phase protein involved in tumour pathogenesis", "abstract": ["The synthesis of acute-phase protein serum amyloid A (SAA) is largely regulated by inflammation- associated cytokines and a high concentration of circulating SAA may represent an ideal marker for acute and chronic inflammatory diseases.", "However, SAA is also synthesized in extrahepatic tissues, e.g. human carcinoma metastases and cancer cell lines.", "An increasing body of in vitro data supports the concept of involvement of SAA in carcinogenesis and neoplastic diseases.", "Accumulating evidence suggests that SAA might be included in a group of biomarkers to detect a pattern of physiological events that reflect the growth of malignancy and host response.", "This review is meant to provide a broad overview of the many ways that SAA could contribute to tumour development, and accelerate tumour progression and metastasis, and to gain a better understanding of this acute-phase reactant as a possible link between chronic inflammation and neoplasia."], "structured": false}
{"doc_id": 31942055, "title": "Body size and outcomes on peritoneal dialysis in the United States.", "abstract": ["BACKGROUND Being overweight is often cited as a relative contraindication to peritoneal dialysis.", "Our primary objective was to determine whether actual mortality rates support this opinion.   \n", "METHODS Retrospective cohort study of United States Medicare patients initiating dialysis between 1995 and 2000 (N = 418,021; 11% peritoneal dialysis).   \n", "RESULTS Seven percent were underweight [body mass index (BMI) < 18.5 kg/m2], 27% were overweight (BMI 25.0 to 29.9 kg/m2), and 23% were obese (BMI> 29.9 kg/m2) at dialysis initiation.", "Compared to those with normal BMI, the adjusted odds of initiating peritoneal dialysis were 0.70 (P < 0.05) in underweight, 1.12 (P < 0.05) in overweight, and 0.87 (P < 0.05) in obese subjects.", "Among peritoneal dialysis patients, adjusted mortality hazard ratios in the first, second, and third year were 1.45 (P < 0.05), 1.28 (P < 0.05), and 1.17 for the underweight, respectively; 0.84 (P < 0.05), 0.89 (P < 0.05), and 0.98 for the overweight, respectively; and 0.89 (P < 0.05), 0.99, and 1.00 for the obese, respectively.", "Apart from higher third-year mortality in the obese, associations were similar after censoring at a switch to hemodialysis.", "For transplantation, the corresponding results were 0.76 (P < 0.05), 0.90 (P < 0.05), and 0.88 for the underweight, respectively; 0.95, 1.06, and 0.93 for the overweight, respectively; and 0.62 (P < 0.05), 0.68, and 0.71 for the obese, respectively.", "For switching to hemodialysis, hazards ratios were 0.92, 0.97, and 0.80 for the underweight, respectively; 1.07, 1.11 (P < 0.05), and 1.03 for the overweight, respectively; and 1.28 (P < 0.05), 1.29 (P < 0.05), and 1.36 (P < 0.05) for the obese, respectively.   \n", "CONCLUSION Although less likely to initiate peritoneal dialysis, overweight and obese peritoneal dialysis patients have longer survival than those with lower BMI, not adequately explained by lower transplantation and technique survival rates."], "structured": true}
{"doc_id": 31962403, "title": "The anaphase promoting complex/cyclosome: a machine designed to destroy", "abstract": ["The anaphase promoting complex/cyclosome (APC/C) is a ubiquitin ligase that has essential functions in and outside the eukaryotic cell cycle.", "It is the most complex molecular machine that is known to catalyse ubiquitylation reactions, and it contains more than a dozen subunits that assemble into a large 1.5-MDa complex.", "Recent discoveries have revealed an unexpected multitude of mechanisms that control APC/C activity, and have provided a first insight into how this unusual ubiquitin ligase recognizes its substrates."], "structured": false}
{"doc_id": 32001951, "title": "Regulation of the expression of alkaline phosphatase in a human breast-cancer cell line.", "abstract": ["Treatment of the cultured human breast-cancer cells BC-M1 with dexamethasone induced a placental-type alkaline phosphatase (ALP).", "Both the ALP activity and the mRNA level in the cells were increased.", "The induction of ALP activity by dexamethasone was time- and dose-dependent.", "The accumulation of ALP mRNA was inhibited by both actinomycin D and cycloheximide, indicating that its induction is a complex event and may involve other regulatory proteins.", "Retinoic acid showed opposing effects with dexamethasone on the expression of alkaline phosphatase.", "Retinoic acid (RA) and phorbol 12-myristate 13-acetate also substantially reduced the dexamethasone-induced expression of ALP.", "Studies on thermostability and sensitivity to various amino acid inhibitors indicated that the BC-M1 ALP is most similar to the placental form.", "Northern hybridization analysis also revealed that ALP mRNA transcripts in BC-M1 and term placenta are similar in size and are distinct from that of the placental-like mRNA transcript in choriocarcinoma cells.", "Analysis of the degradation of BC-M1 ALP mRNA showed a similar half-life of 27 h in the untreated and in dexamethasone- or RA-treated cells.", "These findings demonstrated that the induction of ALP in BC-M1 cells by dexamethasone is mainly due to the increase in the transcription of the ALP gene."], "structured": false}
{"doc_id": 32012666, "title": "Declining tuberculosis notification trend associated with strengthened TB and expanded HIV care in Swaziland.", "abstract": ["This retrospective observational review documents the efforts of the Swaziland National Tuberculosis (TB) Control Programme between 2004 and 2014.", "The objective is to describe the disparity between actual declines in case notification and increases in estimated incidence.", "The review of policies and practices shows the most influential factors associated with the decrease in TB case notification to be an increase in access to antiretroviral therapy for co-infected TB patients, the general success of TB and human immunodeficiency virus service integration in the country and improvements in implementation of all components of directly observed treatment, active case finding, and rapid diagnosis using new technologies."], "structured": false}
{"doc_id": 32023005, "title": "Advances in techniques of testing mycobacterial drug sensitivity, and the use of sensitivity tests in tuberculosis control programmes.", "abstract": ["In a paper arising out of an informal international consultation of specialists in the bacteriology of tuberculosis held in 1961, an attempt was made to formulate criteria, and specify technical procedures, for reliable tests of sensitivity (the absolute-concentration method, the resistance-ratio method and the proportion method) to the 3 main antituberculosis drugs (isoniazid, streptomycin and p-aminosalicylic acid).", "Seven years later, a further consultation was held to review the latest developments in the field and to suggest how sensitivity tests might be put to practical use in tuberculosis control programmes.", "The participants reached agreement on how to define drug sensitivity and resistance, and stressed the importance of using a discrimination approach to the calibration of sensitivity tests.", "Their views are contained in the present paper, which also includes descriptions of the sensitivity tests used by the Medical Research Council of Great Britain for first- and second-line drugs (minimal inhibitory concentration and resistance-ratio methods), the two main variants of the proportion method developed by the Institut Pasteur, Paris, and a method for calibrating sensitivity tests."], "structured": false}
{"doc_id": 32084655, "title": "Time from finding abnormality on mass-screening to final diagnosis of lung cancer.", "abstract": ["Mass-screening for lung cancer is rather a unique system in Japan.", "This study illustrates time from finding abnormality on mass-screening to final diagnosis of lung cancer.", "Among the 517 patients with lung cancer who were admitted to our hospital over a 10-year period up to December 2001, 83 (16.1%) were detected by mass-screening.", "We reviewed medical records of the 83 patients and determined the intervals from the mass-screening to the pathological diagnosis with clinical staging.", "Time from the mass-screening to the date of hospital visit was <2 months in 62 (74.7%) cases.", "Five (6.0%) patients visited hospital more than 6 months after the mass-screening.", "With respect to the interval, there was no statistical difference in gender (p=0.0680) and age (p=0.1532).", "Among 60 patients who were referred from outside, on average, patients visited our hospital 0.5 month after they first sought medical attention at nearby clinic, and at our hospital 0.5 month was required to make a pathological diagnosis of lung cancer with TNM staging.", "There was a statistical difference in survival between the patients who were diagnosed <4 months and the patients who were diagnosed >4 months from the screening (p=0.0487).", "The interval in most cases was acceptable.", "However, further improvements are still needed to minimize the delay and to maximize the benefits of early cancer detection."], "structured": false}
{"doc_id": 32101982, "title": "Kr\u00fcppel-like factor 2 (KLF2) regulates B-cell reactivity, subset differentiation, and trafficking molecule expression.", "abstract": ["The transcription factor Kr\u00fcppel-like factor 2 (KLF2) is critical for normal trafficking of T lymphocytes, but its role in B cells is unclear.", "We report that B cell-specific KLF2 deficiency leads to decreased expression of the trafficking molecules CD62L and \u03b27-integrin, yet expression of sphingosine-1 phosphate receptor 1 (which is a critical target of KLF2 in T cells) was, unexpectedly, minimally altered.", "Unexpectedly, Klf2 deletion led to a drastic reduction in the B1 B-cell pool and a substantial increase in transitional and marginal zone B-cell numbers.", "In addition, we observed that KLF2-deficient B cells showed increased apoptosis and impaired proliferation after B-cell receptor cross-linking.", "Gene expression analysis indicated that KLF2-deficient follicular B cells display numerous characteristics shared by normal marginal zone B cells, including reduced expression of several signaling molecules that may contribute to defective activation of these cells.", "Hence, our data indicate that KLF2 plays a critical role in dictating normal subset differentiation and functional reactivity of mature B cells."], "structured": false}
{"doc_id": 32159283, "title": "Antibiotics and risk of subsequent first-time acute myocardial infarction.", "abstract": ["CONTEXT Increasing evidence supports the hypothesis of a causal association between certain bacterial infections and increased risk of developing acute myocardial infarction.", "If such a causal association exists, subjects who used antibiotics active against the bacteria, regardless of indication, might be at lower risk of developing acute myocardial infarction than nonusers.   \n", "OBJECTIVE To determine whether previous use of antibiotics decreases the risk of developing a first-time acute myocardial infarction.   \n", "DESIGN Population-based case-control analysis.   \n", "SETTING The United Kingdom-based General Practice Research Database comprising 350 general practices.   \n", "PATIENTS A total of 3315 case patients aged 75 years or younger with a diagnosis of first-time acute myocardial infarction between 1992 and 1997 and 13139 controls without myocardial infarction matched to cases for age, sex, general practice attended, and calendar time.   \n", "MAIN OUTCOME MEASURES Use of antibiotics among those who did or did not have a first-time acute myocardial infarction.   \n", "RESULTS Cases were significantly less likely to have used tetracycline antibiotics (adjusted odds ratio [OR], 0.70; 95% confidence interval [CI], 0.55-0.90) or quinolones (adjusted OR, 0.45; 95% CI, 0.21-0.95).", "No effect was found for previous use of macrolides (primarily erythromycin), sulfonamides, penicillins, or cephalosporins.   \n", "CONCLUSIONS The findings from this large case-control analysis provide further, albeit indirect, evidence for an association between bacterial infections with organisms susceptible to tetracycline or quinolone antibiotics and the risk of acute myocardial infarction.", "These results of preliminary nature should stimulate more research to further explore the role of infections in the etiology of acute myocardial infarction."], "structured": true}
{"doc_id": 32170702, "title": "Thrombopoietin/MPL signaling regulates hematopoietic stem cell quiescence and interaction with the osteoblastic niche.", "abstract": ["Maintenance of hematopoietic stem cells (HSCs) depends on interaction with their niche.", "Here we show that the long-term (LT)-HSCs expressing the thrombopoietin (THPO) receptor, MPL, are a quiescent population in adult bone marrow (BM) and are closely associated with THPO-producing osteoblastic cells.", "THPO/MPL signaling upregulated beta1-integrin and cyclin-dependent kinase inhibitors in HSCs.", "Furthermore, inhibition and stimulation of THPO/MPL pathway by treatments with anti-MPL neutralizing antibody, AMM2, and with THPO showed reciprocal regulation of quiescence of LT-HSC.", "AMM2 treatment reduced the number of quiescent LT-HSCs and allowed exogenous HSC engraftment without irradiation.", "By contrast, exogenous THPO transiently increased quiescent HSC population and subsequently induced HSC proliferation in vivo.", "Altogether, these observations suggest that THPO/MPL signaling plays a critical role of LT-HSC regulation in the osteoblastic niche."], "structured": false}
{"doc_id": 32177659, "title": "Interlaboratory reproducibility and proficiency testing within the human papillomavirus cervical cancer screening program in Catalonia, Spain.", "abstract": ["In Catalonia, a screening protocol for cervical cancer, including human papillomavirus (HPV) DNA testing using the Digene Hybrid Capture 2 (HC2) assay, was implemented in 2006.", "In order to monitor interlaboratory reproducibility, a proficiency testing (PT) survey of the HPV samples was launched in 2008.", "The aim of this study was to explore the repeatability of the HC2 assay's performance.", "Participating laboratories provided 20 samples annually, 5 randomly chosen samples from each of the following relative light unit (RLU) intervals: <0.5, 0.5 to 0.99, 1 to 9.99, and \u226510.", "Kappa statistics were used to determine the agreement levels between the original and the PT readings.", "The nature and origin of the discrepant results were calculated by bootstrapping.", "A total of 946 specimens were retested.", "The kappa values were 0.91 for positive/negative categorical classification and 0.79 for the four RLU intervals studied.", "Sample retesting yielded systematically lower RLU values than the original test (P<0.005), independently of the time elapsed between the two determinations (median, 53 days), possibly due to freeze-thaw cycles.", "The probability for a sample to show clinically discrepant results upon retesting was a function of the RLU value; samples with RLU values in the 0.5 to 5 interval showed 10.80% probability to yield discrepant results (95% confidence interval [CI], 7.86 to 14.33) compared to 0.85% probability for samples outside this interval (95% CI, 0.17 to 1.69).", "Globally, the HC2 assay shows high interlaboratory concordance.", "We have identified differential confidence thresholds and suggested the guidelines for interlaboratory PT in the future, as analytical quality assessment of HPV DNA detection remains a central component of the screening program for cervical cancer prevention."], "structured": false}
{"doc_id": 32181055, "title": "The role of regulatory variation in complex traits and disease", "abstract": ["We are in a phase of unprecedented progress in identifying genetic loci that cause variation in traits ranging from growth and fitness in simple organisms to disease in humans.", "However, a mechanistic understanding of how these loci influence traits is lacking for the majority of loci.", "Studies of the genetics of gene expression have emerged as a key tool for linking DNA sequence variation to phenotypes.", "Here, we review recent insights into the molecular nature of regulatory variants and describe their influence on the transcriptome and the proteome.", "We discuss conceptual advances from studies in model organisms and present examples of complete chains of causality that link individual polymorphisms to changes in gene expression, which in turn result in physiological changes and, ultimately, disease risk."], "structured": false}
{"doc_id": 32194449, "title": "Adhesion disengagement uncouples intrinsic and extrinsic forces to drive cytokinesis in epithelial tissues.", "abstract": ["Cytokinesis entails cell invagination by a contractile actomyosin ring.", "In epithelia, E-cadherin-mediated adhesion connects the cortices of contacting cells; thus, it is unclear how invagination occurs, how the new junction forms, and how tissue integrity is preserved.", "Investigations in Drosophila embryos first show that apicobasal cleavage is polarized: invagination is faster from the basal than from the apical side.", "Ring contraction but not its polarized constriction is controlled by septin filaments and Anillin.", "Polarized cleavage is due instead to mechanical anchorage of the ring to E-cadherin complexes.", "Formation of the new junction requires local adhesion disengagement in the cleavage furrow, followed by new E-cadherin complex formation at the new interface.", "E-cadherin disengagement depends on the tension exerted by the cytokinetic ring and by neighboring cells.", "We uncover intrinsic and extrinsic forces necessary for cytokinesis and present a framework for understanding how tissue cohesion is preserved during epithelial division."], "structured": false}
{"doc_id": 32250572, "title": "The epithelial inward rectifier channel Kir7.1 displays unusual K+ permeation properties.", "abstract": ["Rat and human cDNAs were isolated that both encoded a 360 amino acid polypeptide with a tertiary structure typical of inwardly rectifying K+ channel (Kir) subunits.", "The new proteins, termed Kir7.1, were <37% identical to other Kir subunits and showed various unique residues at conserved sites, particularly near the pore region.", "High levels of Kir7.1 transcripts were detected in rat brain, lung, kidney, and testis.", "In situ hybridization of rat brain sections demonstrated that Kir7.1 mRNA was absent from neurons and glia but strongly expressed in the secretory epithelial cells of the choroid plexus (as confirmed by in situ patch-clamp measurements).", "In cRNA-injected Xenopus oocytes Kir7.1 generated macroscopic Kir currents that showed a very shallow dependence on external K+ ([K+]e), which is in marked contrast to all other Kir channels.", "At a holding potential of -100 mV, the inward current through Kir7.1 averaged -3.8 +/-", "1.04 microA with 2 mM [K+]e and -4.82 +/-", "1.87 microA with 96 mM [K+]e.", "Kir7.1 has a methionine at position 125 in the pore region where other Kir channels have an arginine.", "When this residue was replaced by the conserved arginine in mutant Kir7.1 channels, the pronounced dependence of K+ permeability on [K+]e, characteristic for other Kir channels, was restored and the Ba2+ sensitivity was increased by a factor of approximately 25 (Ki = 27 microM).", "These findings support the important role of this site in the regulation of K+ permeability in Kir channels by extracellular cations."], "structured": false}
{"doc_id": 32263707, "title": "Oral fingolimod (FTY720) for relapsing multiple sclerosis.", "abstract": ["BACKGROUND Fingolimod (FTY720) is a new oral immunomodulating agent under evaluation for the treatment of relapsing multiple sclerosis.   \n", "METHODS We randomly assigned 281 patients to receive oral fingolimod, at a dose of 1.25 mg or 5.0 mg, or a placebo once daily, and we followed these patients for 6 months with magnetic resonance imaging (MRI) and clinical evaluations (core study, months 0 to 6).", "The primary end point was the total number of gadolinium-enhanced lesions recorded on T(1)-weighted MRI at monthly intervals for 6 months.", "In an extension study in which the investigators and patients remained unaware of the dose assignments (months 7 to 12), patients who received placebo underwent randomization again to one of the fingolimod doses.   \n", "RESULTS A total of 255 patients completed the core study.", "The median total number of gadolinium-enhanced lesions on MRI was lower with 1.25 mg of fingolimod (1 lesion, P<0.001) and 5.0 mg of fingolimod (3 lesions, P=0.006) than with placebo (5 lesions).", "The annualized relapse rate was 0.77 in the placebo group, as compared with 0.35 in the group given 1.25 mg of fingolimod (P=0.009) and 0.36 in the group given 5.0 mg of fingolimod (P=0.01).", "For the 227 patients who completed the extension study, the number of gadolinium-enhanced lesions and relapse rates remained low in the groups that received continuous fingolimod, and both measures decreased in patients who switched from placebo to fingolimod.", "Adverse events included nasopharyngitis, dyspnea, headache, diarrhea, and nausea.", "Clinically asymptomatic elevations of alanine aminotransferase levels were more frequent with fingolimod (10 to 12%, vs. 1% in the placebo group).", "One case of the posterior reversible encephalopathy syndrome occurred in the 5.0-mg group.", "Fingolimod was also associated with an initial reduction in the heart rate and a modest decrease in the forced expiratory volume in 1 second.   \n", "CONCLUSIONS In this proof-of-concept study, fingolimod reduced the number of lesions detected on MRI and clinical disease activity in patients with multiple sclerosis.", "Evaluation in larger, longer-term studies is warranted.", "(Clinicaltrials.gov numbers, NCT00333138 [core study] and NCT00235430 [ClinicalTrials.gov] [extension].)."], "structured": true}
{"doc_id": 32275758, "title": "Nonoverlapping functions of DNA polymerases mu, lambda, and terminal deoxynucleotidyltransferase during immunoglobulin V(D)J recombination in vivo.", "abstract": ["DNA polymerases mu (pol mu), lambda (pol lambda), and terminal deoxynucleotidyltransferase (TdT) are enzymes of the pol X family that share homology in sequence and functional domain organization.", "We showed previously that pol mu participates in light chain but surprisingly not heavy chain gene rearrangement.", "We show here that immunoglobulin heavy chain junctions from pol lambda-deficient animals have shorter length with normal N-additions, thus indicating that pol lambda is recruited during heavy chain rearrangement at a step that precedes the action of TdT. In contrast to previous in vitro studies, analysis of animals with combined inactivation of these enzymes revealed no overlapping or compensatory activities for V(D)J recombination between pol mu, pol lambda, and TdT. This complex usage of polymerases with distinct catalytic specificities may correspond to the specific function that the third hypervariable region assumes for each immunoglobulin chain, with pol lambda maintaining a large heavy chain junctional heterogeneity and pol mu ensuring a restricted light chain junctional variability."], "structured": false}
{"doc_id": 32322418, "title": "Moderate regular exercise increases basal production of nitric oxide in elderly women.", "abstract": ["Vascular endothelial cells produce nitric oxide (NO), which is a potent vasodilator substance and is thought to have antiatherosclerotic properties.", "Therefore, it has also been proposed that NO may be useful to regulate vascular tonus and prevent progression of atherosclerosis.", "On the other hand, NO activity reduces with aging.", "We previously reported that the plasma nitrite/nitrate (NOx: the stable end product of NO) concentration was significantly increased by intense aerobic exercise training in healthy young humans.", "We hypothesized that lifestyle modification (e.g., even mild regular exercise training) can increase NO production in previously sedentary older humans.", "We measured the plasma NOx concentration before and after a mild aerobic exercise training regimen (cycling on a leg ergometer at 80% ventilatory threshold for 30 min, 5 days/week) for 3 months in elderly women.", "In addition, we assessed the plasma concentration of cyclic guanosine monophosphate (cGMP), a second messenger of NO, in the same samples.", "The individual ventilatory threshold increased significantly after the 3-month exercise training.", "The blood pressure at rest significantly decreased after exercise training.", "These results suggest that the 3-month exercise training in the older women produced favorable physiological effects.", "The plasma concentration of NOx significantly increased by the exercise training, and the plasma concentration of cGMP also increased by the exercise training.", "The present study suggests that even a mild regular aerobic-endurance exercise increases NO production in previously sedentary older humans, which may have beneficial effects (i.e., antihypertensive and antiatherosclerotic effects by endogenous NO) on the cardiovascular system."], "structured": false}
{"doc_id": 32324430, "title": "Competition between target sites of regulators shapes post-transcriptional gene regulation", "abstract": ["Post-transcriptional gene regulation (PTGR) of mRNA turnover, localization and translation is mediated by microRNAs (miRNAs) and RNA-binding proteins (RBPs).", "These regulators exert their effects by binding to specific sequences within their target mRNAs.", "Increasing evidence suggests that competition for binding is a fundamental principle of PTGR.", "Not only can miRNAs be sequestered and neutralized by the targets with which they interact through a process termed 'sponging', but competition between binding sites on different RNAs may also lead to regulatory crosstalk between transcripts.", "Here, we quantitatively model competition effects under physiological conditions and review the role of endogenous sponges for PTGR in light of the key features that emerge."], "structured": false}
{"doc_id": 32328114, "title": "Primary prevention of ischemic stroke: A statement for healthcare professionals from the Stroke Council of the American Heart Association.", "abstract": ["Stroke ranks as the third leading cause of death in the United States.", "It is now estimated that there are more than 700 000 incident strokes annually and 4.4 million stroke survivors.1 2 The economic burden of stroke was estimated by the American Heart Association to be $51 billion (direct and indirect costs) in 1999.3 Despite the advent of treatment of selected patients with acute ischemic stroke with tissue plasminogen activator and the promise of other experimental therapies, the best approach to reducing the burden of stroke remains prevention.4 5 High-risk or stroke-prone individuals can be identified and targeted for specific interventions.6 This is important because epidemiological data suggest a substantial leveling off of prior declines in stroke-related mortality and a possible increase in stroke incidence.7 8   The Stroke Council of the American Heart Association formed an ad hoc writing group to provide a clear and concise overview of the evidence regarding various established and potential stroke risk factors.", "The writing group was chosen based on expertise in specific subject areas, and it used literature review, reference to previously published guidelines, and expert opinion to summarize existing evidence and formulate recommendations (Table 1\u21d3).  ", "View this table:   Table 1.  ", "Levels of Evidence and Grading of Recommendations    As given in Tables 2 through 4\u21d3\u21d3\u21d3, risk factors or risk markers for a first stroke were classified according to potential for modification (nonmodifiable, modifiable, or potentially modifiable) and strength of evidence (well documented, less well documented).5 The tables give the estimated prevalence, population attributable risk, relative risk, and risk reduction with treatment for each factor when known.", "Population attributable risk reflects the proportion of ischemic strokes in the population that can be attributed to a particular risk factor and is given by the formula 100\u00d7[prevalence(relative risk\u22121)/prevalence(relative risk\u22121)+1]).", "\u2026"], "structured": false}
{"doc_id": 32353339, "title": "Chimeric live, attenuated vaccine against Japanese encephalitis (ChimeriVax-JE): phase 2 clinical trials for safety and immunogenicity, effect of vaccine dose and schedule, and memory response to challenge with inactivated Japanese encephalitis antigen.", "abstract": ["ChimeriVax-JE is a live, attenuated vaccine against Japanese encephalitis, using yellow fever (YF) 17D vaccine as a vector.", "In a double-blind phase 2 trial, 99 adults received vaccine, placebo, or YF 17D vaccine (YF-VAX).", "ChimeriVax-JE was well tolerated, with no differences in adverse events between treatment groups.", "Viremias resulting from administration of ChimeriVax-JE and YF-VAX were of short duration and low titer; 82 (94%) of 87 subjects administered graded doses (1.8-5.8 log(10)) of ChimeriVax-JE developed neutralizing antibodies.", "A second dose, administered 30 days later, had no booster effect.", "Previous inoculation with YF did not interfere with ChimeriVax-JE, but there was a suggestion (not statistically significant) that ChimeriVax-JE interfered with YF-VAX administered 30 days later.", "A separate study explored immunological memory both in subjects who had received ChimeriVax-JE 9 months before and in ChimeriVax-JE-naive subjects challenged with inactivated mouse-brain vaccine (JE-VAX).", "Anamnestic responses were observed in preimmune individuals.", "ChimeriVax-JE appears to be a safe vaccine that provides protective levels of neutralizing antibody after a single dose."], "structured": false}
{"doc_id": 32357890, "title": "Global prevalence of anxiety disorders: a systematic review and meta-regression.", "abstract": ["BACKGROUND The literature describing the global prevalence of anxiety disorders is highly variable.", "A systematic review and meta-regression were undertaken to estimate the prevalence of anxiety disorders and to identify factors that may influence these estimates.", "The findings will inform the new Global Burden of Disease study.", "Method A systematic review identified prevalence studies of anxiety disorders published between 1980 and 2009.", "Electronic databases, reference lists, review articles and monographs were searched and experts then contacted to identify missing studies.", "Substantive and methodological factors associated with inter-study variability were identified through meta-regression analyses and the global prevalence of anxiety disorders was calculated adjusting for study methodology.   \n", "RESULTS The prevalence of anxiety disorders was obtained from 87 studies across 44 countries.", "Estimates of current prevalence ranged between 0.9% and 28.3% and past-year prevalence between 2.4% and 29.8%.", "Substantive factors including gender, age, culture, conflict and economic status, and urbanicity accounted for the greatest proportion of variability.", "Methodological factors in the final multivariate model (prevalence period, number of disorders and diagnostic instrument) explained an additional 13% of variance between studies.", "The global current prevalence of anxiety disorders adjusted for methodological differences was 7.3% (4.8-10.9%) and ranged from 5.3% (3.5-8.1%) in African cultures to 10.4% (7.0-15.5%) in Euro/Anglo cultures.   \n", "CONCLUSIONS Anxiety disorders are common and the substantive and methodological factors identified here explain much of the variability in prevalence estimates.", "Specific attention should be paid to cultural differences in responses to survey instruments for anxiety disorders."], "structured": true}
{"doc_id": 32372280, "title": "Expression of optineurin, a glaucoma-linked gene, is influenced by elevated intraocular pressure.", "abstract": ["Optineurin (optic neuropathy inducing protein; OPTN) was recently linked to 16.7% of families with primary open-angle glaucoma.", "The function of OPTN in the eye is not known, but is present in the trabecular meshwork, which is responsible for maintenance of intraocular pressure (IOP).", "To gain insight into the role of OPTN in the development of glaucoma we studied its expression in response to factors known to be associated with the disease: elevated IOP, tumor necrosis factor-alpha (TNFalpha), and dexamethasone (DEX).", "We performed the treatments in human organ cultures under conditions mimicking physiological pressure.", "We find OPTN significantly upregulated after 2, 4, and 7 days of sustained elevated IOP.", "OPTN expression is also induced 2.3-fold by TNFalpha and 2.6-fold by prolonged DEX treatment.", "These results demonstrate that OPTN is part of the transcriptome responding to glaucomatous insults and support the protective role of this protein in the trabecular meshwork."], "structured": false}
{"doc_id": 32390525, "title": "Prevention of malaria in long-term travelers.", "abstract": ["CONTEXT Long-term travelers, defined here as those traveling for periods of 6 months or longer, face particular challenges regarding malaria prevention.", "Current guidelines for malaria prevention primarily address prevention of Plasmodium falciparum infections in short-term travelers.   \n", "OBJECTIVES To examine the risk of malaria in long-term travelers, recent developments in personal protective measures, and the safety and tolerability of malaria chemoprophylaxis during long-term use and to consider prevention strategies including continuous chemoprophylaxis, stand-by emergency self-treatment, seasonal prophylaxis, and strategies to prevent primary infection and relapses from P vivax malaria.   ", "EVIDENCE ACQUISITION Comprehensive search of scientific publications including MEDLINE via both OVID and PubMED for relevant studies and articles with a cutoff date of July 2006, using the search terms long-term travel and malaria prevention, long-term malaria chemoprophylaxis, and insect repellent and malaria.", "Additional references were obtained from searching the bibliographies of the selected articles, from dissertations, and from the proceedings of relevant conferences on travel medicine.", "There were no language restrictions.   ", "EVIDENCE SYNTHESIS Long-term travelers have a higher risk of malaria than short-term travelers.", "Long-term travelers underuse personal protective measures and adhere poorly to continuous chemoprophylaxis regimens.", "A number of strategies are used during long-term stays: discontinuation of chemoprophylaxis after the initial period, sequential regimens with different medications for chemoprophylaxis, stand-by emergency self-treatment, and seasonal chemoprophylaxis targeting high-incidence periods or locations.", "All strategies have advantages and drawbacks.", "Counterfeit drugs sold in countries endemic for malaria pose serious concern for long-term travelers who purchase their medications overseas.", "Vivax malaria causes significant illness in travelers, but relapses of vivax malaria are not prevented with the current first-line chemoprophylaxis regimens.", "Consensus guidelines are needed for prevention of malaria in long-term travelers.   \n", "CONCLUSIONS Prevention of malaria in long-term travelers is a complex issue and requires expert advice from travel medicine specialists.", "Recommendations for prevention of malaria in long-term travelers must be individualized."], "structured": true}
{"doc_id": 32408470, "title": "Activation of AMPK\u03b12 in adipocytes is essential for nicotine-induced insulin resistance in vivo", "abstract": ["Cigarette smoking promotes body weight reduction in humans while paradoxically also promoting insulin resistance (IR) and hyperinsulinemia.", "However, the mechanisms behind these effects are unclear.", "Here we show that nicotine, a major constituent of cigarette smoke, selectively activates AMP-activated protein kinase \u03b12 (AMPK\u03b12) in adipocytes, which in turn phosphorylates MAP kinase phosphatase-1 (MKP1) at serine 334, initiating its proteasome-dependent degradation.", "The nicotine-dependent reduction of MKP1 induces the aberrant activation of both p38 mitogen-activated protein kinase and c-Jun N-terminal kinase, leading to increased phosphorylation of insulin receptor substrate 1 (IRS1) at serine 307.", "Phosphorylation of IRS1 leads to its degradation, protein kinase B inhibition, and the loss of insulin-mediated inhibition of lipolysis.", "Consequently, nicotine increases lipolysis, which results in body weight reduction, but this increase also elevates the levels of circulating free fatty acids and thus causes IR in insulin-sensitive tissues.", "These results establish AMPK\u03b12 as an essential mediator of nicotine-induced whole-body IR in spite of reductions in adiposity."], "structured": false}
{"doc_id": 32421068, "title": "Availability of evidence of benefits on overall survival and quality of life of cancer drugs approved by European Medicines Agency: retrospective cohort study of drug approvals 2009-13", "abstract": ["Objective To determine the availability of data on overall survival and quality of life benefits of cancer drugs approved in Europe.", "Design Retrospective cohort study.", "Setting Publicly accessible regulatory and scientific reports on cancer approvals by the European Medicines Agency (EMA) from 2009 to 2013.Main outcome measures Pivotal and postmarketing trials of cancer drugs according to their design features (randomisation, crossover, blinding), comparators, and endpoints.", "Availability and magnitude of benefit on overall survival or quality of life determined at time of approval and after market entry.", "Validated European Society for Medical Oncology Magnitude of Clinical Benefit Scale (ESMO-MCBS) used to assess the clinical value of the reported gains in published studies of cancer drugs.", "Results From 2009 to 2013, the EMA approved the use of 48 cancer drugs for 68 indications.", "Of these, eight indications (12%) were approved on the basis of a single arm study.", "At the time of market approval, there was significant prolongation of survival in 24 of the 68 (35%).", "The magnitude of the benefit on overall survival ranged from 1.0 to 5.8 months (median 2.7 months).", "At the time of market approval, there was an improvement in quality of life in seven of 68 indications (10%).", "Out of 44 indications for which there was no evidence of a survival gain at the time of market authorisation,", "in the subsequent postmarketing period there was evidence for extension of life in three (7%) and reported benefit on quality of life in five (11%).", "Of the 68 cancer indications with EMA approval, and with a median of 5.4 years' follow-up (minimum 3.3 years, maximum 8.1 years), only 35 (51%) had shown a significant improvement in survival or quality of life, while 33 (49%) remained uncertain.", "Of 23 indications associated with a survival benefit that could be scored with the ESMO-MCBS tool, the benefit was judged to be clinically meaningful in less than half (11/23, 48%).Conclusions This systematic evaluation of oncology approvals by the EMA in 2009-13 shows that most drugs entered the market without evidence of benefit on survival or quality of life.", "At a minimum of 3.3 years after market entry, there was still no conclusive evidence that these drugs either extended or improved life for most cancer indications.", "When there were survival gains over existing treatment options or placebo, they were often marginal."], "structured": false}
{"doc_id": 32423829, "title": "A cluster randomized, controlled trial of breast and cervix cancer screening in Mumbai, India: methodology and interim results after three rounds of screening.", "abstract": ["Cervix and Breast cancers are the most common cancers among women worldwide and extract a large toll in developing countries.", "In May 1998, supported by a grant from the NCI (US), the Tata Memorial Hospital, Mumbai, India, started a cluster-randomized, controlled, screening-trial for cervix and breast cancer using trained primary health workers to provide health-education, visual-inspection of cervix (with 4% acetic acid-VIA) and clinical breast examination (CBE) in the screening arm, and only health education in the control arm.", "Four rounds of screening at 2-year intervals will be followed by 8 years of monitoring for incidence and mortality from cervix and breast cancers.", "The methodology and interim results after three rounds of screening are presented here.", "Good randomization was achieved between the screening (n = 75360) and control arms (n = 76178).", "In the screening arm we see: High screening participation rates; Low attrition; Good compliance to diagnostic confirmation; Significant downstaging; Excellent treatment completion rate; Improving case fatality ratios.", "The ever-screened and never-screened participants in the screening arm show significant differences with reference to the variables religion, language, age, education, occupation, income and health-seeking behavior for gynecological and breast-related complaints.", "During the same period, in the control arm we see excellent participation rate for health education; Low attrition and a good number of symptomatic referrals for both cervix and breast."], "structured": false}
{"doc_id": 32450297, "title": "Evidence for energy-dependent accumulation of paraquat into rat lung", "abstract": ["THE herbicide paraquat (N,N\u2032-dimethyl 4,4\u2032-bipyridilium) can produce widespread oedema and fibrosis in the human lung after accidental ingestion1\u20133.", "In those cases where death occurs after several weeks, there are no apparent pulmonary changes during the first few days following ingestion.", "Animal experiments in a variety of species have shown the lung to be the major target organ4\u20136.", "After administration of paraquat to animals, the lung has a high initial concentration and retains paraquat7\u20139.", "This retention appears to be related to the development of lung damage7 (L. L. Smith and M. S. Rose, unpublished work).", "The mechanism of retention of paraquat by the lung is at present not understood."], "structured": false}
{"doc_id": 32454714, "title": "Role of gut commensal microflora in the development of experimental autoimmune encephalomyelitis.", "abstract": ["Mucosal tolerance has been considered a potentially important pathway for the treatment of autoimmune disease, including human multiple sclerosis and experimental conditions such as experimental autoimmune encephalomyelitis (EAE).", "There is limited information on the capacity of commensal gut bacteria to induce and maintain peripheral immune tolerance.", "Inbred SJL and C57BL/6 mice were treated orally with a broad spectrum of antibiotics to reduce gut microflora.", "Reduction of gut commensal bacteria impaired the development of EAE.", "Intraperitoneal antibiotic-treated mice showed no significant decline in the gut microflora and developed EAE similar to untreated mice, suggesting that reduction in disease activity was related to alterations in the gut bacterial population.", "Protection was associated with a reduction of proinflammatory cytokines and increases in IL-10 and IL-13.", "Adoptive transfer of low numbers of IL-10-producing CD25(+)CD4(+) T cells (>75% FoxP3(+)) purified from cervical lymph nodes of commensal bacteria reduced mice and in vivo neutralization of CD25(+) cells suggested the role of regulatory T cells maintaining peripheral immune homeostasis.", "Our data demonstrate that antibiotic modification of gut commensal bacteria can modulate peripheral immune tolerance that can protect against EAE.", "This approach may offer a new therapeutic paradigm in the treatment of multiple sclerosis and perhaps other autoimmune conditions."], "structured": false}
{"doc_id": 32462603, "title": "Epidemiology of surgically managed pelvic organ prolapse and urinary incontinence.", "abstract": ["OBJECTIVE To determine the incidence of surgically managed pelvic organ prolapse and urinary incontinence in a population-based cohort, and to describe their clinical characteristics.   \n", "METHODS Our retrospective cohort study included all patients undergoing surgical treatment for prolapse and incontinence during 1995; all were members of Kaiser Permanente Northwest, which included 149,554 women age 20 or older.", "A standardized data-collection form was used to review all inpatient and outpatient charts of the 395 women identified.", "Variables examined included age, ethnicity, height, weight, vaginal parity, smoking history, medical history, and surgical history, including the preoperative evaluation, procedure performed, and details of all prior procedures.", "Analysis included calculation of age-specific and cumulative incidences and determination of the number of primary operations compared with repeat operations performed for prolapse or incontinence.   \n", "RESULTS The age-specific incidence increased with advancing age.", "The lifetime risk of undergoing a single operation for prolapse or incontinence by age 80 was 11.1%.", "Most patients were older, postmenopausal, parous, and overweight.", "Nearly half were current or former smokers and one-fifth had chronic lung disease.", "Reoperation was common (29.2% of cases), and the time intervals between repeat procedures decreased with each successive repair.   \n", "CONCLUSION Pelvic floor dysfunction is a major health issue for older women, as shown by the 11.1% lifetime risk of undergoing a single operation for pelvic organ prolapse and urinary incontinence, as well as the large proportion of reoperations.", "Our results warrant further epidemiologic research in order to determine the etiology, natural history, and long-term treatment outcomes of these conditions."], "structured": true}
{"doc_id": 32463364, "title": "Antihypertensive classes, cognitive decline and incidence of dementia: a network meta-analysis.", "abstract": ["OBJECTIVES Prevention of cognitive decline and dementia with blood pressure lowering treatments has shown inconsistent results.", "We compared the effects of different classes of antihypertensive drugs on the incidence of dementia, and on cognitive function.   \n", "METHODS We conducted a systematic review and included 19 randomized trials (18 515 individuals) and 11 studies (831 674 individuals) analysing the effects of antihypertensive treatment on cognition and on the incidence of dementia, respectively, in hypertensive patients without prior cerebrovascular disorders.", "Network meta-analysis was used for the comparison of antihypertensive classes.   \n", "RESULTS Antihypertensive treatment, regardless of the drug class, had benefits on overall cognition [effect size 0.05, 95% confidence interval (CI) 0.02-0.07] and all cognitive functions except language.", "Antihypertensive treatment reduced the risk of all-cause dementia by 9%, with reference to the control group (hazard ratio 0.91, 95% CI 0.89-0.94), when randomized trials and observationnal studies were combined (n = 15).", "Result was not significant with randomized trials alone (n = 4).", "Angiotensin II receptor blockers (ARBs) had larger benefits than placebo on overall cognition (adjusted effect size 0.60 \u00b1 0.18, P = 0.02).", "ARBs were more effective than \u03b2-blockers (0.67 \u00b1 0.18, P = 0.01), diuretics (0.54 \u00b1 0.19, P = 0.04) and angiotensin-converting enzyme inhibitors (0.47 \u00b1 0.17, P = 0.04) in rank.", "The mean change in blood pressure did not differ significantly between the different antihypertensive drug classes.   \n", "CONCLUSION Our results support the notion that antihypertensive treatment has beneficial effects on cognitive decline and prevention of dementia, and indicate that these effects may differ between drug classes with ARBs possibly being the most effective."], "structured": true}
{"doc_id": 32481310, "title": "Abnormal hemoglobins in a quarter million people.", "abstract": ["Hemolysates of erythrocytes from more than a quarter million people in Alabama were electrophoresed on cellulose acetate, pH 8.4, and those samples exhibiting an abnormality were also electrophoresed in citrate agar, pH 6.0.", "The globin chains of mutants other than Hb S and C were electrophoresed in urea-mercaptoethanol buffers at both pH 8.9 and pH 6.0, and 60 of them were also analyzed structurally.", "Of about 6000 samples from whites, only three contained abnormal hemoglobins--Hb D Los Angeles, Hb J Baltimore, and one unidentified.", "Of 249,000 samples from blacks, about 29,000 contained electrophoretically detectable abnormalities, most of them associated with Hb S or C, present in a frequency of about 9% and 3%, respectively.", "About 1000 samples resolved into patterns of potential clinical significance.", "Twenty other mutant hemoglobins were detected, in various genetic combinations in 164 kindreds; four of these-Hb Alabama, Montgomery, Titusville, and Mobile--were previously unknown.", "The methods used are rapid, economical, and well suited for large scale surveys.", "They provide highly specific characterizations of many mutant hemoglobins, and no discrepancies were found between the presumptive identifications based on these characterizations and the definitive identifications obtained from structural analyses."], "structured": false}
{"doc_id": 32532238, "title": "Cellular adaptation to mechanical stress: role of integrins, Rho, cytoskeletal tension and mechanosensitive ion channels.", "abstract": ["To understand how cells sense and adapt to mechanical stress, we applied tensional forces to magnetic microbeads bound to cell-surface integrin receptors and measured changes in bead displacement with sub-micrometer resolution using optical microscopy.", "Cells exhibited four types of mechanical responses: (1) an immediate viscoelastic response; (2) early adaptive behavior characterized by pulse-to-pulse attenuation in response to oscillatory forces; (3) later adaptive cell stiffening with sustained (>15 second) static stresses; and (4) a large-scale repositioning response with prolonged (>1 minute) stress.", "Importantly, these adaptation responses differed biochemically.", "The immediate and early responses were affected by chemically dissipating cytoskeletal prestress (isometric tension), whereas the later adaptive response was not.", "The repositioning response was prevented by inhibiting tension through interference with Rho signaling, similar to the case of the immediate and early responses, but it was also prevented by blocking mechanosensitive ion channels or by inhibiting Src tyrosine kinases.", "All adaptive responses were suppressed by cooling cells to 4 degrees C to slow biochemical remodeling.", "Thus, cells use multiple mechanisms to sense and respond to static and dynamic changes in the level of mechanical stress applied to integrins."], "structured": false}
{"doc_id": 32533299, "title": "Cutting edge: Candida albicans hyphae formation triggers activation of the Nlrp3 inflammasome.", "abstract": ["The proinflammatory cytokine IL-1beta plays an important role in antifungal immunity; however, the mechanisms by which fungal pathogens trigger IL-1beta secretion are unclear.", "In this study we show that infection with Candida albicans is sensed by the Nlrp3 inflammasome, resulting in the subsequent release of IL-1beta.", "The ability of C. albicans to switch from a unicellular yeast form into a filamentous form is essential for activation of the Nlrp3 inflammasome, as C. albicans mutants incapable of forming hyphae were defective in their ability to induce macrophage IL- 1beta secretion.", "Nlrp3-deficient mice also demonstrated increased susceptibility to infection with C. albicans, which is consistent with a key role for Nlrp3 in innate immune responses to the pathogen C. albicans."], "structured": false}
{"doc_id": 32534305, "title": "Type 2 diabetes and subsequent incidence of breast cancer in the Nurses' Health Study.", "abstract": ["OBJECTIVE Hyperinsulinemia may promote mammary carcinogenesis.", "Insulin resistance has been linked to an increased risk of breast cancer and is also characteristic of type 2 diabetes.", "We prospectively evaluated the association between type 2 diabetes and invasive breast cancer incidence in the Nurses' Health Study.   ", "RESEARCH DESIGN AND METHODS A total of 116,488 female nurses who were 30-55 years old and free of cancer in 1976 were followed through 1996 for the occurrence of type 2 diabetes and through 1998 for incident invasive breast cancer, verified by medical records and pathology reports.   \n", "RESULTS During 2.3 million person-years of follow-up, we identified 6,220 women with type 2 diabetes and 5,189 incident cases of invasive breast cancer.", "Women with type 2 diabetes had a modestly elevated incidence of breast cancer (hazard ratio [HR] = 1.17; 95% CI 1.01-1.35) compared with women without diabetes, independent of age, obesity, family history of breast cancer, history of benign breast disease, reproductive factors, physical activity, and alcohol consumption.", "This association was apparent among postmenopausal women (1.16; 0.98-1.62) but not premenopausal women (0.83; 0.48-1.42).", "The association was predominant among women with estrogen receptor-positive breast cancer (1.22; 1.01-1.47).   \n", "CONCLUSIONS Women with type 2 diabetes may have a slightly increased risk of breast cancer."], "structured": true}
{"doc_id": 32556431, "title": "Virus-encoded microRNAs.", "abstract": ["MicroRNAs (miRNAs) are the subject of enormous interest.", "They are small non-coding RNAs that play a regulatory role in numerous and diverse cellular processes such as immune function, apoptosis and tumorigenesis.", "Several virus families have been shown to encode miRNAs, and an appreciation for their roles in the viral infectious cycle continues to grow.", "Despite the identification of numerous (>225) viral miRNAs, an in depth functional understanding of most virus-encoded miRNAs is lacking.", "Here we focus on a few viral miRNAs with well-defined functions.", "We use these examples to extrapolate general themes of viral miRNA activities including autoregulation of viral gene expression, avoidance of host defenses, and a likely important role in maintaining latent and persistent infections.", "We hypothesize that although the molecular mechanisms and machinery are similar, the majority of viral miRNAs may utilize a target strategy that differs from host miRNAs.", "That is, many viral miRNAs may have evolved to regulate viral-encoded transcripts or networks of host genes that are unique to viral miRNAs.", "Included in this latter category is a likely abundant class of viral miRNAs that may regulate only one or a few principal host genes.", "Key steps forward for the field are discussed, including the need for additional functional studies that utilize surgical viral miRNA mutants combined with relevant models of infection."], "structured": false}
{"doc_id": 32587939, "title": "Wolfram syndrome 1 and adenylyl cyclase 8 interact at the plasma membrane to regulate insulin production and secretion", "abstract": ["Endoplasmic reticulum (ER) stress causes pancreatic \u03b2-cell dysfunction and contributes to \u03b2-cell loss and the progression of type 2 diabetes.", "Wolfram syndrome 1 (WFS1) has been shown to be an important regulator of the ER stress signalling pathway; however, its role in \u03b2-cell function remains unclear.", "Here we provide evidence that WFS1 is essential for glucose- and glucagon-like peptide 1 (GLP-1)-stimulated cyclic AMP production and regulation of insulin biosynthesis and secretion.", "Stimulation with glucose causes WFS1 translocation from the ER to the plasma membrane, where it forms a complex with adenylyl cyclase 8 (AC8), an essential cAMP-generating enzyme in the \u03b2-cell that integrates glucose and GLP-1 signalling.", "ER stress and mutant WFS1 inhibit complex formation and activation of AC8, reducing cAMP synthesis and insulin secretion.", "These findings reveal that an ER-stress-related protein has a distinct role outside the ER regulating both insulin biosynthesis and secretion.", "The reduction of WFS1 protein on the plasma membrane during ER stress is a contributing factor for \u03b2-cell dysfunction and progression of type 2 diabetes."], "structured": false}
{"doc_id": 32598644, "title": "Two Rice GRAS Family Genes Responsive to N-Acetylchitooligosaccharide Elicitor are Induced by Phytoactive Gibberellins: Evidence for Cross-Talk Between Elicitor and Gibberellin Signaling in Rice Cells", "abstract": ["In this study, we present data showing that two members of the GRAS family of genes from rice, CIGR1 and CIGR2(chitin-inducible gibberellin-responsive), inducible by the potent elicitor N-acetylchitooligosaccharide (GN), are rapidly induced by exogenous gibberellins.", "The pattern of mRNA accumulation was dependent on the dose and biological activity of the gibberellins, suggesting that the induction of the genes by gibberellin is mediated by a biological receptor capable of specific recognition and signal transduction upon perception of the phytoactive compounds.", "Further pharmacological analysis revealed that the CIGR1 and CIGR2 mRNA accumulation by treatment with gibberellin is dependent upon protein phosphorylation/dephosphorylation events.", "In rice calli derived from slender rice 1, a constitutive gibberellin-responsive mutant, or d1, a mutant deficient in the \u03b1-subunit of the heterotrimeric G-protein, CIGR1 and CIGR2 were induced by a GN elicitor, yet not by gibberellin.", "Neither gibberellin nor GN showed related activities in defense or development, respectively.", "These results strongly suggested that the signal transduction cascade from gibberellin is independent of that from GN, and further implied that CIGR1 and CIGR2 have dual, distinct roles in defense and development."], "structured": false}
{"doc_id": 32611468, "title": "Ghrelin's second life: from appetite stimulator to glucose regulator.", "abstract": ["Ghrelin, a 28 amino acid peptide hormone produced by the stomach, was the first orexigenic hormone to be discovered from the periphery.", "The octanoyl modification at Ser\u00b3, mediated by ghrelin O-acyltransferase (GOAT), is essential for ghrelin's biological activity.", "Ghrelin stimulates food intake through binding to its receptor (GRLN-R) on neurons in the arcuate nucleus of the hypothalamus.", "Ghrelin is widely expressed throughout the body; accordingly, it is implicated in several other physiological functions, which include growth hormone release, gastric emptying, and body weight regulation.", "Ghrelin and GRLN-R expression are also found in the pancreas, suggesting a local physiological role.", "Accordingly, several recent studies now point towards an important role for ghrelin and its receptor in the regulation of blood glucose homeostasis, which is the main focus of this review.", "Several mechanisms of this regulation by ghrelin have been proposed, and one possibility is through the regulation of insulin secretion.", "Despite some controversy, most studies suggest that ghrelin exerts an inhibitory effect on insulin secretion, resulting in increased circulating glucose levels.", "Ghrelin may thus be a diabetogenic factor.", "Obesity-related type 2 diabetes has become an increasingly important health problem, almost reaching epidemic proportions in the world; therefore, antagonists of the ghrelin-GOAT signaling pathway, which will tackle both energy- and glucose homeostasis, may be considered as promising new therapies for this disease."], "structured": false}
{"doc_id": 32638085, "title": "Histone acetylation and deacetylation in yeast", "abstract": ["Histone acetylation and deacetylation in the yeast Saccharomyces cerevisiae occur by targeting acetyltransferase and deacetylase enzymes to gene promoters and, in an untargeted and global manner, by affecting most nucleosomes.", "Recently, new roles for histone acetylation have been uncovered, not only in transcription but also in DNA replication, repair and heterochromatin formation.", "Interestingly, specific acetylatable lysines can function as binding sites for regulatory factors.", "Moreover, histone deacetylation is not only repressive but can be required for gene activity."], "structured": false}
{"doc_id": 32665136, "title": "Neuroinflammation in spinal cord injury: therapeutic targets for neuroprotection and regeneration.", "abstract": ["Traumatic spinal cord injury triggers a complex local inflammatory reaction capable of enhancing repair and exacerbating pathology.", "The composition and effector potential of the post-injury cellular and molecular immune cascade changes as a function of time and distance from the lesion.", "Production along this time-space continuum of cytokines, proteases, and growth factors establishes dynamic environments that lead to the death, damage, repair or growth of affected neurons and glia.", "Microenvironmental cues, therefore, generated by the cells therein, may determine these distinct fates of repair versus pathology.", "To harness repair, it is necessary to manipulate the assembly and phenotype of cells that comprise the neuroinflammatory response to injury.", "Here, the potential of the neuroinflammatory response to cause outcomes such as pain, regeneration, and functional recovery is reviewed."], "structured": false}
{"doc_id": 32671519, "title": "Evaluation of systemic amyloidosis by scintigraphy with 123I-labeled serum amyloid P component.", "abstract": ["BACKGROUND In systemic amyloidosis the distribution and progression of disease have been difficult to monitor, because they can be demonstrated only by biopsy.", "Serum amyloid P component (SAP) is a normal circulating plasma protein that is deposited on amyloid fibrils because of its specific binding affinity for them.", "We investigated whether labeled SAP could be used to locate amyloid deposits.   \n", "METHODS Purified human SAP labeled with iodine-123 was given intravenously to 50 patients with biopsy-proved systemic amyloidosis--25 with the AL (primary) type and 25 with the AA (secondary) type--and to 26 control patients with disease and 10 healthy subjects.", "Whole-body images and regional views were obtained after 24 hours and read in a blinded fashion.   \n", "RESULTS In the patients with amyloidosis the 123I-SAP was localized rapidly and specifically in amyloid deposits.", "The scintigraphic images obtained were characteristic and appeared to identify the extent of amyloid deposition in all 50 patients.", "There was no uptake of the 123I-SAP by the control patients and the healthy subjects.", "In all patients with AA amyloidosis the spleen was affected, whereas the scans showed uptake in the heart, skin, carpal region, and bone marrow only in patients with the AL type.", "Positive images were seen in six patients in whom biopsies had been negative or unsuccessful; in all six, amyloid was subsequently found on biopsy or at autopsy.", "Progressive amyloid deposition was observed in 9 of 11 patients studied serially.   \n", "CONCLUSIONS Scintigraphy after the injection of 123I-SAP can be used for diagnosing, locating, and monitoring the extent of systemic amyloidosis."], "structured": true}
{"doc_id": 32697244, "title": "The Neurovascular Unit Coming of Age: A Journey through Neurovascular Coupling in Health and Disease", "abstract": ["The concept of the neurovascular unit (NVU), formalized at the 2001 Stroke Progress Review Group meeting of the National Institute of Neurological Disorders and Stroke, emphasizes the intimate relationship between the brain and its vessels.", "Since then, the NVU has attracted the interest of the neuroscience community, resulting in considerable advances in the field.", "Here the current state of knowledge of the NVU will be assessed, focusing on one of its most vital roles: the coupling between neural activity and blood flow.", "The evidence supports a conceptual shift in the mechanisms of neurovascular coupling, from a unidimensional process involving neuronal-astrocytic signaling to local blood vessels to a multidimensional one in which mediators released from multiple cells engage distinct signaling pathways and effector systems across the entire cerebrovascular network in a highly orchestrated manner.", "The recently appreciated NVU dysfunction in neurodegenerative diseases, although still poorly understood, supports emerging concepts that maintaining neurovascular health promotes brain health."], "structured": false}
{"doc_id": 32712381, "title": "Effects of MAL61 and MAL62 overexpression on maltose fermentation of baker's yeast in lean dough.", "abstract": ["The predominant fermentable sugar in lean dough is maltose.", "To improve the leavening ability of baker's yeast in lean dough, maltose metabolism should be improved.", "Maltase (alpha-glucosidase, encoded by MAL62) and maltose permease (encoded by MAL61) are the major factors involved in maltose metabolism.", "The major rate-limiting factor in maltose metabolism and leavening ability of baker's yeast remains unclear.", "In this work, MAL61 and/or MAL62 overexpression strains were constructed to investigate the decisive factor for maltose metabolism of industrial baker's yeast in lean dough.", "Our results show that elevated maltose permease activity by MAL61 overexpression yielded less improvement in maltose fermentation compared to elevated maltase activity by MAL62 overexpression.", "Significant increase in maltase activity by MAL62 overexpression could result in a 44% increase in leavening ability of industrial baker's yeast in lean dough and a 39% increase in maltose metabolism in a medium containing glucose and maltose.", "Thus, maltase was the rate-limiting factor in maltose fermentation of industrial baker's yeast in lean dough.", "This study lays a foundation for breeding of industrial baker's yeast for quick dough leavening."], "structured": false}
{"doc_id": 32720933, "title": "Human papillomavirus genotype 31 does not express detectable microRNA levels during latent or productive virus replication.", "abstract": ["It has recently become clear that several pathogenic DNA viruses express virally encoded microRNAs in infected cells.", "In particular, numerous microRNAs have been identified in a range of human and animal herpesviruses, and individual microRNAs have also been identified in members of the polyoma- and adenovirus families.", "Although their functions remain largely unknown, it seems likely that these viral microRNAs play an important role in viral replication in vivo.", "Here we present an analysis of the microRNAs expressed in human cells during the latent and productive phases of the human papillomavirus genotype 31 (HPV31) replication cycle.", "Although over 500 cellular microRNAs were cloned and identified, not a single HPV31-specific microRNA was obtained.", "We therefore concluded that HPV31, and possibly human papillomaviruses in general, does not express viral microRNAs."], "structured": false}
{"doc_id": 32721137, "title": "Integrated genomic profiling of endometrial carcinoma associates aggressive tumors with indicators of PI3 kinase activation.", "abstract": ["Although 75% of endometrial cancers are treated at an early stage, 15% to 20% of these recur.", "We performed an integrated analysis of genome-wide expression and copy-number data for primary endometrial carcinomas with extensive clinical and histopathological data to detect features predictive of recurrent disease.", "Unsupervised analysis of the expression data distinguished 2 major clusters with strikingly different phenotypes, including significant differences in disease-free survival.", "To identify possible mechanisms for these differences, we performed a global genomic survey of amplifications, deletions, and loss of heterozygosity, which identified 11 significantly amplified and 13 significantly deleted regions.", "Amplifications of 3q26.32 harboring the oncogene PIK3CA were associated with poor prognosis and segregated with the aggressive transcriptional cluster.", "Moreover, samples with PIK3CA amplification carried signatures associated with in vitro activation of PI3 kinase (PI3K), a signature that was shared by aggressive tumors without PIK3CA amplification.", "Tumors with loss of PTEN expression or PIK3CA overexpression that did not have PIK3CA amplification also shared the PI3K activation signature, high protein expression of the PI3K pathway member STMN1, and an aggressive phenotype in test and validation datasets.", "However, mutations of PTEN or PIK3CA were not associated with the same expression profile or aggressive phenotype.", "STMN1 expression had independent prognostic value.", "The results affirm the utility of systematic characterization of the cancer genome in clinically annotated specimens and suggest the particular importance of the PI3K pathway in patients who have aggressive endometrial cancer."], "structured": false}
{"doc_id": 32742683, "title": "Alteration of the Antitumor Immune Response by Cancer-Associated Fibroblasts", "abstract": ["Among cells present in the tumor microenvironment, activated fibroblasts termed cancer-associated fibroblasts (CAFs), play a critical role in the complex process of tumor-stroma interaction.", "CAFs, one of the prominent stromal cell populations in most types of human carcinomas, have been involved in tumor growth, angiogenesis, cancer stemness, extracellular matrix remodeling, tissue invasion, metastasis, and even chemoresistance.", "During the past decade, these activated tumor-associated fibroblasts have also been involved in the modulation of the anti-tumor immune response on various levels.", "In this review, we describe our current understanding of how CAFs accomplish this task as well as their potential therapeutic implications."], "structured": false}
{"doc_id": 32743723, "title": "Confusion and memory loss from capsular genu infarction: a thalamocortical disconnection syndrome?", "abstract": ["We examined six patients with an abrupt change in behavior after infarction involving the inferior genu of the internal capsule.", "The acute syndrome featured fluctuating alertness, inattention, memory loss, apathy, abulia, and psychomotor retardation, suggesting frontal lobe dysfunction.", "Contralateral hemiparesis and dysarthria were generally mild, except when the infarct extended into the posterior limb.", "Neuropsychological testing in five patients with left-sided infarcts revealed severe verbal memory loss.", "Additional cognitive deficits consistent with dementia occurred in four patients.", "A right-sided infarct caused transient impairment in visuospatial memory.", "Functional brain imaging in three patients showed a focal reduction in hemispheric perfusion most prominent in the ipsilateral inferior and medial frontal cortex.", "We infer that the capsular genu infarct interrupted the inferior and anterior thalamic peduncles, resulting in functional deactivation of the ipsilateral frontal cortex.", "These observations suggest that one mechanism for cognitive deterioration from a lacunar infarct is thalamocortical disconnection of white-matter tracts, in some instances leading to \"strategic-infarct dementia.", "\""], "structured": false}
{"doc_id": 32766786, "title": "Neoadjuvant androgen ablation before radical prostatectomy in cT2bNxMo prostate cancer: 5-year results.", "abstract": ["PURPOSE In the initial report of the Lupron Depot Neoadjuvant Prostate Cancer Study Group patients who received 3 months of androgen deprivation had a significant decrease in the positive margin rate.", "We monitored these patients for 5 years and to our knowledge present the longest followup of any neoadjuvant trial.   ", "MATERIALS AND METHODS A multi-institutional prospective randomized trial was performed between February 1992 and April 1994 involving patients with stage cT2b prostate cancer, including 138 who received 3 months of leuprolide plus flutamide before radical prostatectomy and 144 who underwent radical prostatectomy only.", "Patients were followed every 6 months with serum prostate specific antigen (PSA) testing for 5 years.", "Biochemical recurrence was defined as PSA greater than 0.4 ng./ml.   \n", "RESULTS At 5 years there was no difference in the biochemical recurrence rate.", "PSA was less than 0.4 ng./ml.", "in 64.8% of the patients in the neoadjuvant androgen ablation plus prostatectomy and 67.6% in the prostatectomy only group (p = 0.663).   \n", "CONCLUSIONS Although 3 months of androgen deprivation before radical prostatectomy resulted in an apparently significant decrease in positive surgical margins, a 5-year followup does not indicate any difference in the recurrence rate.", "Until studies document improvement in biochemical or clinical recurrence with longer periods of treatment, induction androgen deprivation before radical prostatectomy is not indicated."], "structured": true}
{"doc_id": 32770503, "title": "Full-length transcriptome assembly from RNA-Seq data without a reference genome.", "abstract": ["Massively parallel sequencing of cDNA has enabled deep and efficient probing of transcriptomes.", "Current approaches for transcript reconstruction from such data often rely on aligning reads to a reference genome, and are thus unsuitable for samples with a partial or missing reference genome.", "Here we present the Trinity method for de novo assembly of full-length transcripts and evaluate it on samples from fission yeast, mouse and whitefly, whose reference genome is not yet available.", "By efficiently constructing and analyzing sets of de Bruijn graphs, Trinity fully reconstructs a large fraction of transcripts, including alternatively spliced isoforms and transcripts from recently duplicated genes.", "Compared with other de novo transcriptome assemblers, Trinity recovers more full-length transcripts across a broad range of expression levels, with a sensitivity similar to methods that rely on genome alignments.", "Our approach provides a unified solution for transcriptome reconstruction in any sample, especially in the absence of a reference genome."], "structured": false}
{"doc_id": 32776084, "title": "Growth restricted in vitro culture conditions alter the imprinted gene expression patterns of mouse embryonic stem cells.", "abstract": ["Embryonic stem (ES) cell-derived clones and chimeras are often associated with growth abnormalities during fetal development, leading to the production of over/under-weight offspring that show elevated neonatal mortality and morbidity.", "Due to the role played by imprinted genes in controlling fetal growth, much of the blame is pointed at improper epigenetic reprogramming of cells used in the procedures.", "We have analyzed the expression pattern of two growth regulatory imprinted genes, namely insulin like growth factor II (Igf2) and H19, in mouse ES cells cultured under growth restricted conditions and after in vitro aging.", "Culture of cells with serum-depleted media (starvation) and at high cell density (confluence) increased the expression of both imprinted genes and led to aberrant methylation profiles of differentially methylated regions in key regulatory sites of Igf2 and H19.", "These findings confirm that growth constrained cultures of ES cells are associated with alterations to methylation of the regulatory domains and the expression patterns of imprinted genes, suggesting a possible role of epigenetic factors in the loss of developmental potential."], "structured": false}
{"doc_id": 32777637, "title": "When is antipsychotic polypharmacy supported by research evidence? Implications for QI.", "abstract": ["BACKGROUND Concurrent use of multiple standing antipsychotics (antipsychotic polypharmacy) is increasingly common among both inpatients and outpatients.", "Although this has often been cited as a potential quality-of-care problem, reviews of research evidence on antipsychotic polypharmacy have not distinguished between appropriate versus inappropriate use.   \n", "METHODS A MEDLINE search from 1966 to December 2007 was completed to identify studies comparing changes in symptoms, functioning, and/or side effects between patients treated with multiple antipsychotics and patients treated with a single antipsychotic.", "The studies were reviewed in two groups on the basis of whether prescribing was concordant with guideline recommendations for multiple-antipsychotic use.   \n", "RESULTS A review of the literature, including three randomized controlled trials, found no support for the use of antipsychotic polypharmacy in patients without an established history of treatment resistance to multiple trials of monotherapy.", "In patients with a history of treatment resistance to multiple monotherapy trials, limited data support antipsychotic polypharmacy, but positive outcomes were primarily found in studies of clozapine augmented with a second-generation antipsychotic.   ", "DISCUSSION Research evidence is consistent with the goal of avoiding antipsychotic polypharmacy in patients who lack guideline-recommended indications for its use.", "The Joint Commission is implementing a core measure set for Hospital-Based Inpatient Psychiatric Services.", "Two of the measures address antipsychotic polypharmacy.", "The first measure assesses the overall rate.", "The second measure determines whether clinically appropriate justification has been documented supporting the use of more than one antipsychotic medication."], "structured": true}
{"doc_id": 32787042, "title": "The Liverpool uveal melanoma liver metastases pathway: outcome following liver resection.", "abstract": ["AIM To determine the outcome of patients that underwent liver resection for metastases from uveal melanoma.   \n", "METHODS Over a 9-year period, patients referred with uveal melanoma metastases were included.", "Following treatment of primary uveal melanoma, high-risk patients were offered to be enrolled into a 6-monthly non-contrast liver magnetic resonance imaging (MRI) surveillance.", "Following detection of liver metastases, patients were staged with a contrast-enhanced (Primovist(\u00ae)) liver MRI, computer tomography (CT) of the thorax and staging laparoscopy.   \n", "RESULTS 155 patients were referred with uveal melanoma liver metastases, of which 17 (11.0%) patients had liver resection and one patient was treated with percutaneous radio-frequency ablation.", "The majority of patients undergoing liver resection were treated with multiple metastectomies (n = 8) and three patients had major liver resections.", "The overall median survival for patients treated with surgery/ablation was 27 (14-90) months, and this was significantly better compared to patients treated palliatively [median = 8(1-30) months, P < 0.001].", "Following surgery, 11 patients had recurrent disease [median = 13(6-36) months].", "Patients who had undergone a major liver resection had a significantly poorer disease-free survival (P = 0.037).   \n", "CONCLUSIONS Patients who can undergo surgical resection for metastatic uveal melanoma have a more favorable survival compared to those who do not."], "structured": true}
{"doc_id": 32797183, "title": "Smooth muscle lineage diversity in the chick embryo. Two types of aortic smooth muscle cell differ in growth and receptor-mediated transcriptional responses to transforming growth factor-beta.", "abstract": ["Lineage analysis studies in the avian embryo have identified two types of smooth muscle cells (SMCs) in the tunica media of large elastic arteries; one that originates within the cardiac neural crest and is ectoderm in origin (Ect) and another that arises from local mesenchyme of mesodermal origin (Mes).", "To determine if differences in primary embryonic lineage can give rise to SMCs with stable differences in growth and differentiation properties, we isolated Ect and Mes SMCs from the Day 14 chick embryo aorta.", "We report that despite different primary embryonic origins, Ect and Mes SMCs express nearly identical levels of seven SMC differentiation markers in vitro, consistent with their common smooth muscle developmental fates in vivo.", "By contrast, Ect SMCs displayed a greater capacity for growth in serum-free medium than Mes SMCs, but only under conditions permitting short-range cell-cell interactions.", "Most of the peptide growth factors tested that might account for serum-independent growth (PDGF-AA, PDGF-BB, basic FGF, EGF, or activin) stimulated DNA synthesis to similar extents in Ect and Mes SMCs.", "However, we found dramatic, lineage-dependent differences in SMC responses to transforming growth factor-beta (TGF-beta).", "Exposure to TGF-beta 1 (0.4 to 400 pmole/liter) consistently increased DNA synthesis in Ect SMCs, whereas in paired cultures of Mes SMCs, TGF-beta 1 was growth inhibitory.", "In SMC cultures transfected with p3TP-lux, a luciferase reporter controlled by the TGF-beta 1-response elements of the human PAI-1 promoter, TGF-beta 1 (120 pM) produced 12 +/-", "2-fold increases in luciferase activity in Ect SMCs and only 3 +/-", "1.5-fold increases in Mes SMCs.", "Analysis of TGF-beta receptor phenotypes by Northern blot, radioligand binding, and crosslinking assays showed that Ect and Mes SMCs expressed similar levels of types I, II, and III TGF-beta receptors.", "However, using a polyclonal antibody specific for the chick type II TGF-beta receptor subunit, we demonstrate that Mes SMCs produce a fully glycosylated form of this protein while Ect SMCs elaborate only an unglycosylated type II TGF-beta receptor.", "These results show that Ect and Mes SMCs exhibit lineage-dependent differences in growth and receptor-mediated transcriptional responses to at least one important class of SMC morphogens and growth modifiers, e.g., the TGF-betas.", "Our findings suggest that different SMC populations within a common vessel wall may respond in lineage-dependent ways to signals that direct formation of the tunica media in the embryo and to factors involved in the progression of vascular disease later in life."], "structured": false}
{"doc_id": 32827351, "title": "THE USE OF LEAD CITRATE AT HIGH pH AS AN ELECTRON-OPAQUE STAIN IN ELECTRON MICROSCOPY", "abstract": ["Aqueous solutions of lead salts (1, 2) and saturated solutions of lead hydroxide (1) have been used as stains to enhance the electron-scattering properties of components of biological materials examined in the electron microscope.", "Saturated solutions of lead hydroxide (1), while staining more intensely than either lead acetate or monobasic lead acetate (l , 2), form insoluble lead carbonate upon exposure to air.", "The avoidance of such precipitates which contaminate surfaces of sections during staining has been the stimulus for the development of elaborate procedures for exclusion of air or carbon dioxide (3, 4).", "Several modifications of Watson's lead hydroxide stain (1) have recently appeared (5-7).", "All utilize relatively high pH (approximately 12) and one contains small amounts of tartrate (6), a relatively weak complexing agent (8), in addition to lead.", "These modified lead stains are less liable to contaminate the surface of the section with precipitated stain products.", "The stain reported here differs from previous alkaline lead stains in that the chelating agent, citrate, is in sufficient excess to sequester all lead present.", "Lead citrate, soluble in high concentrations in basic solutions, is a chelate compound with an apparent association constant (log Ka) between ligand and lead ion of 6.5 (9).", "Tissue binding sites, presumably organophosphates, and other anionic species present in biological components following fixation, dehydration, and plastic embedding apparently have a greater affinity for this cation than lead citrate inasmuch as cellular and extracellular structures in the section sequester lead from the staining solution.", "Alkaline lead citrate solutions are less likely to contaminate sections, as no precipitates form when droplets of fresh staining solution are exposed to air for periods of up to 30 minutes.", "The resultant staining of the sections is of high intensity in sections of Aralditeor Epon-embedded material.", "Cytoplasmic membranes, ribosomes, glycogen, and nuclear material are stained (Figs. 1 to 3).", "STAIN SOLUTION: Lead citrate is prepared by"], "structured": false}
{"doc_id": 32850528, "title": "Amylase, Lipase, and Acute Pancreatitis in People With Type 2 Diabetes Treated With Liraglutide: Results From the LEADER Randomized Trial.", "abstract": ["OBJECTIVE To evaluate serum amylase and lipase levels and the rate of acute pancreatitis in patients with type 2 diabetes and high cardiovascular risk randomized to liraglutide or placebo and observed for 3.5-5.0 years.   ", "RESEARCH DESIGN AND METHODS A total of 9,340 patients with type 2 diabetes were randomized to either liraglutide or placebo (median observation time 3.84 years).", "Fasting serum lipase and amylase were monitored.", "Acute pancreatitis was adjudicated in a blinded manner.   \n", "RESULTS Compared with the placebo group, liraglutide-treated patients had increases in serum lipase and amylase of 28.0% and 7.0%, respectively.", "Levels were increased at 6 months and then remained stable.", "During the study, 18 (0.4% [1.1 events/1,000 patient-years of observation] [PYO]) liraglutide-treated and 23 (0.5% [1.7 events/1,000 PYO]) placebo patients had acute pancreatitis confirmed by adjudication.", "Most acute pancreatitis cases occurred \u226512 months after randomization.", "Liraglutide-treated patients with prior history of pancreatitis (n = 147) were not more likely to develop acute pancreatitis than similar patients in the placebo group (n = 120).", "Elevations of amylase and lipase levels did not predict future risk of acute pancreatitis (positive predictive value <1.0%) in patients treated with liraglutide.   \n", "CONCLUSIONS In a population with type 2 diabetes at high cardiovascular risk, there were numerically fewer events of acute pancreatitis among liraglutide-treated patients (regardless of previous history of pancreatitis) compared with the placebo group.", "Liraglutide was associated with increases in serum lipase and amylase, which were not predictive of an event of subsequent acute pancreatitis."], "structured": true}
{"doc_id": 32852283, "title": "Zoledronic acid is unable to induce apoptosis, but slows tumor growth and prolongs survival for non-small-cell lung cancers.", "abstract": ["BACKGROUND Although zoledronic acid (ZOL), a third-generation nitrogen-containing bisphosphonate, has been identified as an attractive therapeutic agent against breast cancer, prostate cancer, multiple myeloma as well as small-cell lung cancer (SCLC), as best as we are aware, the anti-tumor effect of ZOL upon non-small-cell lung cancer (NSCLC) remains to be effectively investigated.", "This study examined the effects of ZOL upon the line-1 tumor cell, using a murine lung adenocarcinoma cell line similar to the behavior of human lung adenocarcinoma.   \n", "METHODS We investigated the anti-tumor effects of ZOL (3-100 microM) on line-1 tumor cells in vitro, including cellular proliferation, by means of an MTT assay, cell-cycle analysis by flow cytometry and by assessing the level of apoptosis by annexin V/propidium iodide (PI) and 4'-6-diamidino-2-phenylindole (DAPI) staining.", "Further, we evaluated the growth and survival of line-1 tumor cells following ZOL treatment (1 microg/kg/week) using an animal model.", "We also examined the in vivo cell-cycle pattern using lacZ-expressing line-1 cells (line-1/lacZ).   \n", "RESULTS ZOL significantly slowed the line-1 tumor growth in a dose-dependent manner in vitro.", "The treated line-1 tumor cells typically arrested at the S/G2/M-phase of the cell-cycle following ZOL exposure, but no apoptotic cells could be detected by either annexin V/PI or DAPI staining.", "When the ZOL was washed out, the drug-inhibited cells continued to proliferate again and the cell-cycle prolongation elicited earlier by the drug, then disappeared.", "Within 72-96 h following drug removal, the cell-cycle of the treated cells revealed a similar distribution to that of the untreated controls.", "In vivo studies demonstrated that ZOL significantly slowed the line-1 tumor growth.", "Indeed, mice lived significantly longer when they had been ZOL-treated than was the case for untreated mice (p<0.05).", "Using line-1/lacZ cells, the in vivo cell-cycle distribution of line-1 tumor cells subsequent to ZOL exposure revealed S/G2/M-phase arrest that was identical to the in vitro culture.   \n", "CONCLUSIONS ZOL maintains the potential to reduce tumor burden and prolong survival for murine pulmonary adenocarcinoma.", "The flow cytometrical analysis of cell-cycle demonstrated that ZOL induces no apoptosis but is able to arrest line-1 tumor cells at the S/G2/M-phase.", "Although the clinical relevance of these results warrants verification for human lung cancer patients, ZOL combined with chemotherapy and/or radiotherapy appears to be a new therapeutic strategy for the effective treatment of NSCLC."], "structured": true}
{"doc_id": 32906513, "title": "A central role for central tolerance.", "abstract": ["Recent elucidation of the role of central tolerance in preventing organ-specific autoimmunity has changed our concepts of self/nonself discrimination.", "This paradigmatic shift is largely attributable to the discovery of promiscuous expression of tissue-restricted self-antigens (TRAs) by medullary thymic epithelial cells (mTECs).", "TRA expression in mTECs mirrors virtually all tissues of the body, irrespective of developmental or spatio-temporal expression patterns.", "This review summarizes current knowledge on the cellular and molecular regulation of TRA expression in mTECs, outlines relevant mechanisms of antigen presentation and modes of tolerance induction, and discusses implications for the pathogenesis of autoimmune diseases and other biological processes such as fertility, pregnancy, puberty, and tumor defense."], "structured": false}
{"doc_id": 32909242, "title": "Contribution of traditional healers to a rural tuberculosis control programme in Hlabisa, South Africa.", "abstract": ["SETTING The rural health district of Hlabisa, KwaZulu-Natal, South Africa.   OBJECTIVES To assess the acceptability and effectiveness of traditional healers as supervisors of tuberculosis (TB) treatment in an existing directly observed treatment, short-course (DOTS) programme.   \n", "DESIGN An observational study comparing treatment outcomes among new TB patients in the three intervention sub-districts offered the additional option of traditional healers for directly observed treatment (DOT) supervision with those in the remainder of the district offered the standard range of options for DOT supervision (health facility, community health worker and lay persons).", "A comparison was also made of treatment outcomes between different options for DOT supervision.   \n", "RESULTS A total of 3461 TB patients were registered in Hlabisa District from April 1999 to December 2000, of whom 2823 were discharged from hospital to the ambulatory DOT programme.", "Treatment outcomes were known for 1816 patients in Hlabisa District (275 patients in the intervention area and 1541 patients in the control area).", "There was no significant difference (P < 0.5) in treatment outcome in the intervention and control areas (77% vs. 75%).", "Among 275 patients with known outcomes in the intervention area, 48 patients were supervised by traditional healers and 227 patients supervised by people other than traditional healers.", "Treatment completion was not significantly higher among patients supervised by traditional healers than among patients supervised by other categories of DOT supervisor (88% vs. 75%, P = 0.3841).", "Interviews with 41 of 51 traditional healer patients who had completed treatment revealed high levels of satisfaction with the care received.   \n", "CONCLUSIONS Traditional healers make an effective contribution to TB programme performance in this pilot scheme in Hlabisa district.", "Further evaluation will be necessary as this approach is scaled up."], "structured": true}
{"doc_id": 32922179, "title": "Alzheimer's disease: the two-hit hypothesis.", "abstract": ["There are many lines of evidence showing that oxidative stress and aberrant mitogenic changes have important roles in the pathogenesis of Alzheimer's disease (AD).", "However, although both oxidative stress and cell cycle-related abnormalities are early events, occurring before any cytopathology, the relation between these two events, and their role in pathophysiology was, until recently, unclear.", "However, on the basis of studies of mitogenic and oxidative stress signalling pathways in AD, we proposed a \"two-hit hypothesis\" which states that although either oxidative stress or abnormalities in mitotic signalling can independently serve as initiators, both processes are necessary to propagate disease pathogenesis.", "In this paper, we summarise evidence for oxidative stress and abnormal mitotic alterations in AD and explain the two-hit hypothesis by describing how both mechanisms are necessary and invariant features of disease."], "structured": false}
{"doc_id": 32927401, "title": "Toll-like receptor 7 mediates pruritus", "abstract": ["Toll-like receptors are typically expressed in immune cells to regulate innate immunity.", "We found that functional Toll-like receptor 7 (TLR7) was expressed in C-fiber primary sensory neurons and was important for inducing itch (pruritus), but was not necessary for eliciting mechanical, thermal, inflammatory and neuropathic pain in mice.", "Our results indicate that TLR7 mediates itching and is a potential therapeutic target for anti-itch treatment in skin disease conditions."], "structured": false}
{"doc_id": 32927475, "title": "Antigen presentation by major histocompatibility complex class I-B molecules.", "abstract": ["Class I-b genes constitute the majority of MHC class I loci.", "These monomorphic or oligomorphic molecules have been described in many organisms; they are best characterized in the mouse, which contains a substantial number of potentially intact genes.", "Two main characteristics differentiate class I-b from class I-a molecules: limited polymorphism and lower cell surface expression.", "These distinguishing features suggest possible generalizations regarding the evolution and function of this class.", "Additionally, class I-b proteins tend to have shorter cytoplasmic domains or in some cases may be secreted or may substitute a lipid anchor for the transmembrane domain.", "Some are also expressed in a limited distribution of cells or tissues.", "At least six mouse MHC class I-b molecules have been shown to present antigens to alpha beta or gamma delta T cells.", "Recent advances have provided insight into the physiological function of H-2M3a and have defined the natural peptide-binding motif of Qa-2.", "In addition, significant progress has been made toward better understanding of other class I-b molecules, including Qa-1, TL, HLA-E, HLA-G, and the MHC-unlinked class I molecule CD1.", "We begin this review, however, by arguing that the dichotomous categorization of MHC genes as class I-a and I-b is conceptually misleading, despite its historical basis and practical usefulness.", "With these reservations in mind, we then discuss antigen presentation by MHC class I-b molecules with particular attention to their structure, polymorphism, requirements for peptide antigen binding and tissue expression."], "structured": false}
{"doc_id": 32955023, "title": "Pdgfr\u03b2+ Mural Preadipocytes Contribute to Adipocyte Hyperplasia Induced by High-Fat-Diet Feeding and Prolonged Cold Exposure in Adult Mice.", "abstract": ["The expansion of white adipose tissue (WAT) in obesity involves de novo differentiation of new adipocytes; however, the cellular origin of these cells remains unclear.", "Here, we utilize Zfp423(GFP) reporter mice to characterize adipose mural (Pdgfr\u03b2(+)) cells with varying levels of the preadipocyte commitment factor Zfp423.", "We find that adipose tissue contains distinct mural populations, with levels of Zfp423 distinguishing adipogenic from inflammatory-like mural cells.", "Using our \"MuralChaser\" lineage tracking system, we uncover adipose perivascular cells as developmental precursors of adipocytes formed in obesity, with adipogenesis and precursor abundance regulated in a depot-dependent manner.", "Interestingly, Pdgfr\u03b2(+) cells do not significantly contribute to the initial cold-induced recruitment of beige adipocytes in WAT; it is only after prolonged cold exposure that these cells differentiate into beige adipocytes.", "These results provide genetic evidence for a mural cell origin of white adipocytes in obesity and suggest that beige adipogenesis may originate from multiple sources."], "structured": false}
{"doc_id": 32969964, "title": "Effect of clinical guidelines on medical practice: a systematic review of rigorous evaluations.", "abstract": ["Although interest in clinical guidelines has never been greater, uncertainty persists about whether they are effective.", "The debate has been hampered by the lack of a rigorous overview.", "We have identified 59 published evaluations of clinical guidelines that met defined criteria for scientific rigour; 24 investigated guidelines for specific clinical conditions, 27 studied preventive care, and 8 looked at guidelines for prescribing or for support services.", "All but 4 of these studies detected significant improvements in the process of care after the introduction of guidelines and all but 2 of the 11 studies that assessed the outcome of care reported significant improvements.", "We conclude that explicit guidelines do improve clinical practice, when introduced in the context of rigorous evaluations.", "However, the size of the improvements in performance varied considerably."], "structured": false}
{"doc_id": 32975424, "title": "Threonine as a carbon source for Escherichia coli.", "abstract": ["Threonine can be used aerobically as the sole source of carbon and energy by mutants of Escherichia coli K-12.", "The pathway used involves the conversion of threonine via threonine dehydrogenase to aminoketobutyric acid, which is further metabolized by aminoketobutyric acid ligase, forming acetyl coenzyme A and glycine.", "A strain devoid of serine transhydroxymethylase uses this pathway and excretes glycine as a waste product.", "Aminoketobutyric acid ligase activity was demonstrated after passage of crude extracts through Sephadex G100."], "structured": false}
{"doc_id": 32985041, "title": "Protein S-nitrosylation: a physiological signal for neuronal nitric oxide", "abstract": ["Nitric oxide (NO) has been linked to numerous physiological and pathophysiological events that are not readily explained by the well established effects of NO on soluble guanylyl cyclase.", "Exogenous NO S-nitrosylates cysteine residues in proteins, but whether this is an important function of endogenous NO is unclear.", "Here, using a new proteomic approach, we identify a population of proteins that are endogenously S-nitrosylated, and demonstrate the loss of this modification in mice harbouring a genomic deletion of neuronal NO synthase (nNOS).", "Targets of NO include metabolic, structural and signalling proteins that may be effectors for neuronally generated NO.", "These findings establish protein S-nitrosylation as a physiological signalling mechanism for nNOS."], "structured": false}
{"doc_id": 33030946, "title": "Hypoxia\u2010Sensitive COMMD1 Integrates Signaling and Cellular Metabolism in Human Macrophages and Suppresses Osteoclastogenesis", "abstract": ["Summary Hypoxia augments inflammatory responses and osteoclastogenesis by incompletely understood mechanisms.", "We identified COMMD1 as a cell\u2010intrinsic negative regulator of osteoclastogenesis that is suppressed by hypoxia.", "In human macrophages, COMMD1 restrained induction of NF\u2010&kgr;B signaling and a transcription factor E2F1\u2010dependent metabolic pathway by the cytokine RANKL.", "Downregulation of COMMD1 protein expression by hypoxia augmented RANKL\u2010induced expression of inflammatory and E2F1 target genes and downstream osteoclastogenesis.", "E2F1 targets included glycolysis and metabolic genes including CKB that enabled cells to meet metabolic demands in challenging environments, as well as inflammatory cytokine\u2010driven target genes.", "Expression quantitative trait locus analysis linked increased COMMD1 expression with decreased bone erosion in rheumatoid arthritis.", "Myeloid deletion of Commd1 resulted in increased osteoclastogenesis in arthritis and inflammatory osteolysis models.", "These results identify COMMD1 and an E2F\u2010metabolic pathway as key regulators of osteoclastogenic responses under pathological inflammatory conditions and provide a mechanism by which hypoxia augments inflammation and bone destruction.", "Graphical Abstract Figure.", "No Caption available.", "HighlightsCOMMD1 is a negative regulator of osteoclast differentiationCOMMD1 suppresses bone loss in RA and inflammatory arthritis and osteolysis modelsCOMMD1 negatively regulates E2F1\u2010dependent metabolic pathways in macrophagesHypoxia suppresses COMMD1 expression to augment osteoclastogenesis &NA; Pathways that promote osteoclastogenesis are well characterized but less is known about negative regulators that suppress pathological bone loss.", "Murata et al. identify COMMD1 as an inhibitor of osteoclastogenesis that restrains NF\u2010&kgr;B\u2010 and E2F1\u2010CKB\u2010mediated metabolic pathways in macrophages."], "structured": false}
{"doc_id": 33036897, "title": "Production of tyrosol by Candida albicans biofilms and its role in quorum sensing and biofilm development.", "abstract": ["Tyrosol and farnesol are quorum-sensing molecules produced by Candida albicans which accelerate and block, respectively, the morphological transition from yeasts to hyphae.", "In this study, we have investigated the secretion of tyrosol by C. albicans and explored its likely role in biofilm development.", "Both planktonic (suspended) cells and biofilms of four C. albicans strains, including three mutants with defined defects in the Efg 1 and Cph 1 morphogenetic signaling pathways, synthesized extracellular tyrosol during growth at 37 degrees C. There was a correlation between tyrosol production and biomass for both cell types.", "However, biofilm cells secreted at least 50% more tyrosol than did planktonic cells when tyrosol production was related to cell dry weight.", "The addition of exogenous farnesol to a wild-type strain inhibited biofilm formation by up to 33% after 48 h. Exogenous tyrosol appeared to have no effect, but scanning electron microscopy revealed that tyrosol stimulated hypha production during the early stages (1 to 6 h) of biofilm development.", "Experiments involving the simultaneous addition of tyrosol and farnesol at different concentrations suggested that the action of farnesol was dominant, and 48-h biofilms formed in the presence of both compounds consisted almost entirely of yeast cells.", "When biofilm supernatants were tested for their abilities to inhibit or enhance germ tube formation by planktonic cells, the results indicated that tyrosol activity exceeds that of farnesol after 14 h, but not after 24 h, and that farnesol activity increases significantly during the later stages (48 to 72 h) of biofilm development.", "Overall, our results support the conclusion that tyrosol acts as a quorum-sensing molecule for biofilms as well as for planktonic cells and that its action is most significant during the early and intermediate stages of biofilm formation."], "structured": false}
{"doc_id": 33063763, "title": "Regulated nucleo/cytoplasmic exchange of HOG1 MAPK requires the importin beta homologs NMD5 and XPO1.", "abstract": ["MAP kinase signaling modules serve to transduce extracellular signals to the nucleus of eukaryotic cells, but little is known about how signals cross the nuclear envelope.", "Exposure of yeast cells to increases in extracellular osmolarity activates the HOG1 MAP kinase cascade, which is composed of three tiers of protein kinases, namely the SSK2, SSK22 and STE11 MAPKKKs, the PBS2 MAPKK, and the HOG1 MAPK.", "Using green fluorescent protein (GFP) fusions of these kinases, we found that HOG1, PBS2 and STE11 localize to the cytoplasm of unstressed cells.", "Following osmotic stress, HOG1, but neither PBS2 nor STE11, translocates into the nucleus.", "HOG1 translocation occurs very rapidly, is transient, and correlates with the phosphorylation and activation of the MAP kinase by its MAPKK.", "HOG1 phosphorylation is necessary and sufficient for nuclear translocation, because a catalytically inactive kinase when phosphorylated is translocated to the nucleus as efficiently as the wild-type.", "Nuclear import of the MAPK under stress conditions requires the activity of the small GTP binding protein Ran-GSP1, but not the NLS-binding importin alpha/beta heterodimer.", "Rather, HOG1 import requires the activity of a gene, NMD5, that encodes a novel importin beta homolog.", "Similarly, export of dephosphorylated HOG1 from the nucleus requires the activity of the NES receptor XPO1/CRM1.", "Our findings define the requirements for the regulated nuclear transport of a stress-activated MAP kinase."], "structured": false}
{"doc_id": 33068577, "title": "FBW7 regulates endothelial functions by targeting KLF2 for ubiquitination and degradation", "abstract": ["F-box and WD repeat domain-containing 7 (FBW7), the substrate-binding subunit of E3 ubiquitin ligase SCFFBW7 (a complex of SKP1, cullin-1 and FBW7), plays important roles in various physiological and pathological processes.", "Although FBW7 is required for vascular development, its function in the endothelium remains to be investigated.", "In this study, we show that FBW7 is an important regulator of endothelial functions, including angiogenesis, leukocyte adhesion and the endothelial barrier integrity.", "Using RNA interference, we found that the depletion of FBW7 markedly impairs angiogenesis in vitro and in vivo.", "We identified the zinc finger transcription factor Kr\u00fcppel-like factor 2 (KLF2) as a physiological target of FBW7 in endothelial cells.", "Knockdown of FBW7 expression resulted in the accumulation of endogenous KLF2 protein in endothelial cells.", "FBW7-mediated KLF2 destruction was shown to depend on the phosphorylation of KLF2 via glycogen synthase kinase-3 (GSK3) at two conserved phosphodegrons.", "Mutating these phosphodegron motifs abolished the FBW7-mediated degradation and ubiquitination of KLF2.", "The siRNA-mediated knockdown of FBW7 showed that KLF2 is an essential target of FBW7 in the regulation of endothelial functions.", "Moreover, FBW7-mediated KLF2 degradation was shown to be critical for angiogenesis in teratomas and in zebrafish development.", "Taken together, our study suggests a role for FBW7 in the processes of endothelial cell migration, angiogenesis, inflammation and barrier integrity, and provides novel insights into the regulation of KLF2 stability in vivo."], "structured": false}
{"doc_id": 33076846, "title": "Role of RhoA-specific guanine exchange factors in regulation of endomitosis in megakaryocytes.", "abstract": ["Polyploidization can precede the development of aneuploidy in cancer.", "Polyploidization in megakaryocytes (Mks), in contrast, is a highly controlled developmental process critical for efficient platelet production via unknown mechanisms.", "Using primary cells, we demonstrate that the guanine exchange factors GEF-H1 and ECT2, which are often overexpressed in cancer and are essential for RhoA activation during cytokinesis, must be downregulated for Mk polyploidization.", "The first (2N-4N) endomitotic cycle requires GEF-H1 downregulation, whereas subsequent cycles (>4N) require ECT2 downregulation.", "Exogenous expression of both GEF-H1 and ECT2 prevents endomitosis, resulting in proliferation of 2N Mks.", "Furthermore, we have shown that the mechanism by which polyploidization is prevented in Mks lacking Mkl1, which is mutated in megakaryocytic leukemia, is via elevated GEF-H1 expression; shRNA-mediated GEF-H1 knockdown alone rescues this ploidy defect.", "These mechanistic insights enhance our understanding of normal versus malignant megakaryocytopoiesis, as well as aberrant mitosis in aneuploid cancers."], "structured": false}
{"doc_id": 33118292, "title": "Optimal therapy for reduction of lipoprotein(a).", "abstract": ["WHAT IS KNOWN AND OBJECTIVE There is a growing body of experimental and clinical evidence for the atherogenic and pro-thrombotic potential of Lipoprotein(a) [Lp(a)], as well as for its causative role in coronary heart disease and stroke.", "We comment on novel strategies for reducing Lp(a) levels.   ", "COMMENT Irrespective of the underlying biological mechanisms explaining the athero-thrombotic potential of this lipoprotein, most work has focused on the identification of suitable therapies for hyperlipoproteinemia(a).", "These include apheresis techniques, nicotinic acid and statins.", "None of these strategies have been shown to be definitely effective or convenient for the patient and new strategies are being attempted.", "Promising results are emerging with therapeutic interventions targeting the 'inflammatory pathways' by inhibition of Interleukin-6 (IL-6) signalling with natural compounds (e.g., Ginko biloba) or the IL-6 receptor antibody Tocilizumab.", "These may both lower Lp(a) and cardiovascular risk of the patients.", "Besides inhibiting platelet function, antiplatelet therapy with aspirin may also decrease the plasma concentration of Lp(a) and modulate its influence on platelets.   ", "WHAT IS NEW AND CONCLUSION", "We highlight the inadequacy of current approaches for lowering Lp(a) and draw attention to novel insights that may lead to better treatment."], "structured": true}
{"doc_id": 33127778, "title": "Early gastric cancer and dysplasia.", "abstract": ["Since the concept of early gastric cancer was first described in Japan in 1962, its treatment has evolved from curative surgical resection to endoscopic resection, initially with polypectomy to more recently with endoscopic submucosal dissection.", "As worldwide experience with these endoscopic techniques evolve and gain acceptance, studies have confirmed its comparable effectiveness with historical surgical outcomes in carefully selected patients.", "The criteria for endoscopic resection have expanded to offer more patients improved quality of life, avoiding the morbidity and mortality associated with surgery.", "This article summarizes the evolutional role of endoscopic and surgical therapy in early gastric cancer."], "structured": false}
{"doc_id": 33135135, "title": "The impact of homelessness on children.", "abstract": ["This article reviews and critiques community-based research on the effects of homelessness on children.", "Homeless children confront serious threats to their ability to succeed and their future well-being.", "Of particular concern are health problems, hunger, poor nutrition, developmental delays, anxiety, depression, behavioral problems, and educational underachievement.", "Factors that may mediate the observed outcomes include inadequate shelter conditions, instability in residences and shelters, inadequate services, and barriers to accessing services that are available.", "Public policy initiatives are needed to meet the needs of homeless children."], "structured": false}
{"doc_id": 33169058, "title": "Strategies of microbial cheater control.", "abstract": ["The potential benefits of cooperation in microorganisms can be undermined by genetic conflict within social groups, which can take the form of 'cheating'.", "For cooperation to succeed as an evolutionary strategy, the negative effects of such conflict must somehow be either prevented or mitigated.", "To generate an interpretive framework for future research in microbial behavioural ecology, here we outline a wide range of hypothetical mechanisms by which cheaters might be constrained."], "structured": false}
{"doc_id": 33203108, "title": "Golden Hours in Severe Paraquat Poisoning-The Role of Early Haemoperfusion Therapy.", "abstract": ["INTRODUCTION Paraquat is a commonly ingested poison especially in Southern India.", "There is no antidote for paraquat poison and consumption is often fatal.", "The usual cause of death is either acute lung injury or multi-organ failure.   ", "AIM To evaluate the role of early haemoperfusion as a therapy in paraquat poisoned patients.   ", "MATERIALS AND METHODS This study was a retrospective analysis of patients admitted to a Tertiary Medical College Hospital between January 2012 and December 2015 with history of paraquat consumption, comparing outcomes in those who received only gastric lavage and symptomatic treatment with those who received haemoperfusion as a therapy.", "The role of early haemoperfusion (\u2264 6 hours) vs late haemoperfusion (> 6 hours) in paraquat poisoned patients was also compared.", "The data of these patients was extracted and analysed with respect to age, sex, mode of treatment, the outcome in patients who received early and late haemoperfusion.   \n", "RESULTS A total of 101 patients were studied out of which 62 died.", "Deaths were more in those patients who received only gastric lavage with symptomatic treatment as therapy compared to those who received haemoperfusion i.e., 92.1% vs 42.9% respectively.", "We also found that, the survival rate was better in patients who received early haemoperfusion.   \n", "CONCLUSION Early haemoperfusion was helpful in the management of severe paraquat poisoning and improved the survival rate in these patients."], "structured": true}
{"doc_id": 33257464, "title": "Changes in the prevalence of cerebral palsy for children born very prematurely within a population-based program over 30 years.", "abstract": ["CONTEXT Although cerebral palsy (CP) among extremely premature infants has been reported as a major morbidity outcome, there are difficulties comparing published CP rates from many sites over various birth years.   \n", "OBJECTIVE To assess the changes in population-based, gestational age-specific prevalence rates of CP among extremely premature infants over 30 years.   \n", "DESIGN Prospective population-based longitudinal outcome study.   \n", "SETTING AND PARTICIPANTS In Northern Alberta, 2318 infants 20 to 27 weeks' gestational age with birth weights of 500 to 1249 g were liveborn from 1974 through 2003.", "By 2 years of age, 1437 (62%) had died, 23 (1%) were lost to follow-up, and 858 (37%) had received multidisciplinary neurodevelopmental assessment.   \n", "MAIN OUTCOME MEASURE Population-based prevalence rates of CP were determined.", "Logistic regression with linear spline was used to assess changes in CP prevalence over time.   \n", "RESULTS At age 2 years, 122 (14.2%) of 858 survivors had CP.", "This diagnosis was confirmed for each child by age 3 years or older.", "Among those whose gestational age was 20 to 25 weeks, population-based survival increased from 4% to 31% (P<.001), while CP prevalence per 1000 live births increased monotonically from 0 to 110 until the years 1992-1994 (P<.001) and decreased thereafter to 22 in the years 2001-2003 (P<.001).", "Among those whose gestational age was 26 to 27 weeks, population-based survival increased from 23% to between 75% and 80% (P<.001), while CP prevalence per 1000 live births increased monotonically from 15 to 155 until the years 1992-1994 (P<.001) and then decreased to 16 in the years 2001-2003 (P<.001).", "For all survivors born in the years 2001-2003, CP prevalence was 19 per 1000 live births.   \n", "CONCLUSION Population-based CP prevalence rates for children whose gestational age was 20 to 27 weeks and whose birth weight ranged from 500 to 1249 g show steady reductions in the last decade with stable or reducing mortality, reversing trends prior to 1992-1994."], "structured": true}
{"doc_id": 33339202, "title": "Desferrioxamine treatment of porphyria cutanea tarda in a patient with HIV and chronic renal failure.", "abstract": ["Porphyria cutanea tarda (PCT) can occur in HIV patients.", "Current evidence suggests that HIV infection may interfere with the hepatic cytochrome oxidase system, leading to porphyrin metabolism impairment.", "Moreover, chronic hemodialysis in renal failure may be a risk factor for PCT.", "In addition to the contributory factors for PCT associated to HIV infection, it is possible that porphyrin accumulation secondary to renal failure may play a role in the expression of this disease.", "We report a case of PCT in an HIV-1 infected patient under blood dialysis, refractory to antimalarials and controlled with desferrioxamine."], "structured": false}
{"doc_id": 33387953, "title": "Mutations in G protein beta subunits promote transformation and kinase inhibitor resistance", "abstract": ["Activating mutations in genes encoding G protein \u03b1 (G\u03b1) subunits occur in 4-5% of all human cancers, but oncogenic alterations in G\u03b2 subunits have not been defined.", "Here we demonstrate that recurrent mutations in the G\u03b2 proteins GNB1 and GNB2 confer cytokine-independent growth and activate canonical G protein signaling.", "Multiple mutations in GNB1 affect the protein interface that binds G\u03b1 subunits as well as downstream effectors and disrupt G\u03b1 interactions with the G\u03b2\u03b3 dimer.", "Different mutations in G\u03b2 proteins clustered partly on the basis of lineage; for example, all 11 GNB1 K57 mutations were in myeloid neoplasms, and seven of eight GNB1 I80 mutations were in B cell neoplasms.", "Expression of patient-derived GNB1 variants in Cdkn2a-deficient mouse bone marrow followed by transplantation resulted in either myeloid or B cell malignancies.", "In vivo treatment with the dual PI3K-mTOR inhibitor BEZ235 suppressed GNB1-induced signaling and markedly increased survival.", "In several human tumors, mutations in the gene encoding GNB1 co-occurred with oncogenic kinase alterations, including the BCR-ABL fusion protein, the V617F substitution in JAK2 and the V600K substitution in BRAF.", "Coexpression of patient-derived GNB1 variants with these mutant kinases resulted in inhibitor resistance in each context.", "Thus, GNB1 and GNB2 alterations confer transformed and resistance phenotypes across a range of human tumors and may be targetable with inhibitors of G protein signaling."], "structured": false}
{"doc_id": 33390472, "title": "Isolation of major pancreatic cell types and long-term culture-initiating cells using novel human surface markers.", "abstract": ["We have developed a novel panel of cell-surface markers for the isolation and study of all major cell types of the human pancreas.", "Hybridomas were selected after subtractive immunization of Balb/C mice with intact or dissociated human islets and assessed for cell-type specificity and cell-surface reactivity by immunohistochemistry and flow cytometry.", "Antibodies were identified by specific binding of surface antigens on islet (panendocrine or alpha-specific) and nonislet pancreatic cell subsets (exocrine and duct).", "These antibodies were used individually or in combination to isolate populations of alpha, beta, exocrine, or duct cells from primary human pancreas by FACS and to characterize the detailed cell composition of human islet preparations.", "They were also employed to show that human islet expansion cultures originated from nonendocrine cells and that insulin expression levels could be increased to up to 1% of normal islet cells by subpopulation sorting and overexpression of the transcription factors Pdx-1 and ngn3, an improvement over previous results with this culture system.", "These methods permit the analysis and isolation of functionally distinct pancreatic cell populations with potential for cell therapy."], "structured": false}
{"doc_id": 33397197, "title": "Re-engineered CD40 receptor enables potent pharmacological activation of dendritic-cell cancer vaccines in vivo", "abstract": ["Modest clinical outcomes of dendritic-cell (DC) vaccine trials call for the refinement of DC vaccine design.", "Although many potential antigens have been identified, development of methods to enhance antigen presentation by DCs has lagged.", "We have engineered a potent, drug-inducible CD40 (iCD40) receptor that permits temporally controlled, lymphoid-localized, DC-specific activation.", "iCD40 is comprised of a membrane-localized cytoplasmic domain of CD40 fused to drug-binding domains.", "This allows it to respond to a lipid-permeable, high-affinity dimerizer drug while circumventing ectodomain-dependent negative-feedback mechanisms.", "These modifications permit prolonged activation of iCD40-expressing DCs in vivo, resulting in more potent CD8+ T-cell effector responses, including the eradication of previously established solid tumors, relative to activation of DCs ex vivo (P < 0.01), typical of most clinical DC protocols.", "In addition, iCD40-mediated DC activation exceeded that achieved by stimulating the full-length, endogenous CD40 receptor both in vitro and in vivo.", "Because iCD40 is insulated from the extracellular environment and can be activated within the context of an immunological synapse, iCD40-expressing DCs have a prolonged lifespan and should lead to more potent vaccines, perhaps even in immune-compromised patients."], "structured": false}
{"doc_id": 33409100, "title": "Effect of homocysteine lowering on mortality and vascular disease in advanced chronic kidney disease and end-stage renal disease: a randomized controlled trial.", "abstract": ["CONTEXT High plasma homocysteine levels are a risk factor for mortality and vascular disease in observational studies of patients with chronic kidney disease.", "Folic acid and B vitamins decrease homocysteine levels in this population but whether they lower mortality is unknown.   \n", "OBJECTIVE To determine whether high doses of folic acid and B vitamins administered daily reduce mortality in patients with chronic kidney disease.   \n", "DESIGN, SETTING, AND PARTICIPANTS Double-blind randomized controlled trial (2001-2006) in 36 US Department of Veterans Affairs medical centers.", "Median follow-up was 3.2 years for 2056 participants aged 21 years or older with advanced chronic kidney disease (estimated creatinine clearance < or =30 mL/min) (n = 1305) or end-stage renal disease (n = 751) and high homocysteine levels (> or = 15 micromol/L).   \n", "INTERVENTION Participants received a daily capsule containing 40 mg of folic acid, 100 mg of pyridoxine hydrochloride (vitamin B6), and 2 mg of cyanocobalamin (vitamin B12) or a placebo.   \n", "MAIN OUTCOME MEASURES The primary outcome was all-cause mortality.", "Secondary outcomes included myocardial infarction (MI), stroke, amputation of all or part of a lower extremity, a composite of these 3 plus all-cause mortality, time to initiation of dialysis, and time to thrombosis of arteriovenous access in hemodialysis patients.   \n", "RESULTS Mean baseline homocysteine level was 24.0 micromol/L in the vitamin group and 24.2 micromol/L in the placebo group.", "It was lowered 6.3 micromol/L (25.8%; P < .001) in the vitamin group and 0.4 micromol/L (1.7%; P = .14) in the placebo group at 3 months, but there was no significant effect on mortality (448 vitamin group deaths vs 436 placebo group deaths) (hazard ratio [HR], 1.04; 95% CI, 0.91-1.18).", "No significant effects were demonstrated for secondary outcomes or adverse events: there were 129 MIs in the vitamin group vs 150 for placebo (HR, 0.86; 95% CI, 0.67-1.08), 37 strokes in the vitamin group vs 41 for placebo (HR, 0.90; 95% CI, 0.58-1.40), and 60 amputations in the vitamin group vs 53 for placebo (HR, 1.14; 95% CI, 0.79-1.64).", "In addition, the composite of MI, stroke, and amputations plus mortality (P = .85), time to dialysis (P = .38), and time to thrombosis in hemodialysis patients (P = .97) did not differ between the vitamin and placebo groups.   \n", "CONCLUSION Treatment with high doses of folic acid and B vitamins did not improve survival or reduce the incidence of vascular disease in patients with advanced chronic kidney disease or end-stage renal disease.   \n", "TRIAL REGISTRATION clinicaltrials.gov Identifier: NCT00032435."], "structured": true}
{"doc_id": 33417012, "title": "Treated individuals who progress to action or maintenance for one behavior are more likely to make similar progress on another behavior: coaction results of a pooled data analysis of three trials.", "abstract": ["OBJECTIVE This study compared, in treatment and control groups, the phenomena of coaction, which is the probability that taking effective action on one behavior is related to taking effective action on a second behavior.   \n", "METHODS Pooled data from three randomized trials of Transtheoretical Model (TTM) tailored interventions (n=9461), completed in the U.S. in 1999, were analyzed to assess coaction in three behavior pairs (diet and sun protection, diet and smoking, and sun protection and smoking).", "Odds ratios (ORs) compared the likelihood of taking action on a second behavior compared to taking action on only one behavior.   \n", "RESULTS Across behavior pairs, at 12 and 24 months, the ORs for the treatment group were greater on an absolute basis than for the control group, with two being significant.", "The combined ORs at 12 and 24 months, respectively, were 1.63 and 1.85 for treatment and 1.20 and 1.10 for control.   \n", "CONCLUSIONS The results of this study with addictive, energy balance and appearance-related behaviors were consistent with results found in three studies applying TTM tailoring to energy balance behaviors.", "Across studies, there was more coaction within the treatment group.", "Future research should identify predictors of coaction in more multiple behavior change interventions."], "structured": true}
{"doc_id": 33458992, "title": "Trabecular bone score as an indicator for skeletal deterioration in diabetes.", "abstract": ["CONTEXT Trabecular bone score (TBS) is a novel texture index that evaluates the pixel gray-level variations in lumbar spine dual-energy X-ray absorptiometry images and is related to bone microarchitecture independent of bone mineral density (BMD).   \n", "OBJECTIVE We investigated lumbar spine TBS as an indicator for skeletal deterioration in diabetes.   \n", "DESIGN AND SETTING Cross-sectional data were collected from subjects participating in an ongoing prospective, community-based, cohort study from 2009 to 2010.   \n", "PARTICIPANTS We included 1229 men and 1529 postmenopausal women older than 50 years in the Ansung cohort.   \n", "OUTCOME MEASURES Biochemical parameters, lumbar spine TBS, and BMD from dual-energy X-ray absorptiometry images were measured.   \n", "RESULTS Lumbar spine TBS was lower in men with diabetes than in nondiabetic men (1.287 \u00b1 0.005 vs 1.316 \u00b1 0.003, P < .001), whereas lumbar spine BMD was higher in men with diabetes (1.135 \u00b1 0.010 vs 1.088 \u00b1 0.006 g/cm(2)).", "Lumbar spine TBS was lower in women with diabetes than in nondiabetic women only in an unadjusted model (1.333 \u00b1 0.004 vs 1.353 \u00b1 0.003).", "However, women younger than 65 years (n = 707) with diabetes had a lower TBS than those without diabetes, even after adjusted for covariates (P < .001).", "Diabetes was not associated with BMD at femur sites in both genders.", "TBS was negatively correlated with glycated hemoglobin, fasting plasma glucose, fasting insulin, and homeostasis model assessment for insulin resistance but not with homeostasis model assessment for \u03b2-cell function in both genders.   \n", "CONCLUSIONS The inverse association between lumbar spine TBS and insulin resistance may make it an indicator for determining skeletal deterioration in diabetic patients who have high BMD."], "structured": true}
{"doc_id": 33499189, "title": "Full activation of the T cell receptor requires both clustering and conformational changes at CD3.", "abstract": ["T cell receptor (TCR-CD3) triggering involves both receptor clustering and conformational changes at the cytoplasmic tails of the CD3 subunits.", "The mechanism by which TCRalphabeta ligand binding confers conformational changes to CD3 is unknown.", "By using well-defined ligands, we showed that induction of the conformational change requires both multivalent engagement and the mobility restriction of the TCR-CD3 imposed by the plasma membrane.", "The conformational change is elicited by cooperative rearrangements of two TCR-CD3 complexes and does not require accompanying changes in the structure of the TCRalphabeta ectodomains.", "This conformational change at CD3 reverts upon ligand dissociation and is required for T cell activation.", "Thus, our permissive geometry model provides a molecular mechanism that rationalizes how the information of ligand binding to TCRalphabeta is transmitted to the CD3 subunits and to the intracellular signaling machinery."], "structured": false}
{"doc_id": 33507866, "title": "Class III PI3K Vps34 plays an essential role in autophagy and in heart and liver function.", "abstract": ["A critical regulator of autophagy is the Class III PI3K Vps34 (also called PIK3C3).", "Although Vps34 is known to play an essential role in autophagy in yeast, its role in mammals remains elusive.", "To elucidate the physiological function of Vps34 and to determine its precise role in autophagy, we have generated Vps34(f/f) mice, in which expression of Cre recombinase results in a deletion of exon 4 of Vps34 and a frame shift causing a deletion of 755 of the 887 amino acids of Vps34.", "Acute ablation of Vps34 in MEFs upon adenoviral Cre infection results in a diminishment of localized generation of phosphatidylinositol 3-phosphate and blockade of both endocytic and autophagic degradation.", "Starvation-induced autophagosome formation is blocked in both Vps34-null MEFs and liver.", "Liver-specific Albumin-Cre;Vps34(f/f) mice developed hepatomegaly and hepatic steatosis, and impaired protein turnover.", "Ablation of Vps34 in the heart of muscle creatine kinase-Cre;Vps34(f/f) mice led to cardiomegaly and decreased contractility.", "In addition, while amino acid-stimulated mTOR activation was suppressed in the absence of Vps34, the steady-state level of mTOR signaling was not affected in Vps34-null MEFs, liver, or cardiomyocytes.", "Taken together, our results indicate that Vps34 plays an essential role in regulating functional autophagy and is indispensable for normal liver and heart function."], "structured": false}
{"doc_id": 33533307, "title": "Sex-based differences in the effect of digoxin for the treatment of heart failure.", "abstract": ["BACKGROUND The Digitalis Investigation Group trial reported that treatment with digoxin did not decrease overall mortality among patients with heart failure and depressed left ventricular systolic function, although it did reduce hospitalizations slightly.", "Even though the epidemiologic features, causes, and prognosis of heart failure vary between men and women, sex-based differences in the effect of digoxin were not evaluated.   \n", "METHODS We conducted a post hoc subgroup analysis to assess whether there were sex-based differences in the effect of digoxin therapy among the 6800 patients in the Digitalis Investigation Group study.", "The presence of an interaction between sex and digoxin therapy with respect to the primary end point of death from any cause was evaluated with the use of Mantel-Haenszel tests of heterogeneity and a multivariable Cox proportional-hazards model, adjusted for demographic and clinical variables.   \n", "RESULTS There was an absolute difference of 5.8 percent (95 percent confidence interval, 0.5 to 11.1) between men and women in the effect of digoxin on the rate of death from any cause (P=0.034 for the interaction).", "Specifically, women who were randomly assigned to digoxin had a higher rate of death than women who were randomly assigned to placebo (33.1 percent vs. 28.9 percent; absolute difference, 4.2 percent, 95 percent confidence interval, -0.5 to 8.8).", "In contrast, the rate of death was similar among men randomly assigned to digoxin and men randomly assigned to placebo (35.2 percent vs. 36.9 percent; absolute difference, -1.6 percent; 95 percent confidence interval, -4.2 to 1.0).", "In the multivariable analysis, digoxin was associated with a significantly higher risk of death among women (adjusted hazard ratio for the comparison with placebo, 1.23; 95 percent confidence interval, 1.02 to 1.47), but it had no significant effect among men (adjusted hazard ratio, 0.93; 95 percent confidence interval, 0.85 to 1.02; P=0.014 for the interaction).   \n", "CONCLUSIONS The effect of digoxin therapy differs between men and women.", "Digoxin therapy is associated with an increased risk of death from any cause among women, but not men, with heart failure and depressed left ventricular systolic function."], "structured": true}
{"doc_id": 33535222, "title": "Recipient-type specific CD4+CD25+ regulatory T cells favor immune reconstitution and control graft-versus-host disease while maintaining graft-versus-leukemia.", "abstract": ["CD4+CD25+ regulatory T cells (Treg's) play a pivotal role in preventing organ-specific autoimmune diseases and in inducing tolerance to allogeneic organ transplants.", "We and others recently demonstrated that high numbers of Treg's can also modulate graft-versus-host disease (GVHD) if administered in conjunction with allogeneic hematopoietic stem cell transplantation in mice.", "In a clinical setting, it would be impossible to obtain enough freshly purified Treg's from a single donor to have a therapeutic effect.", "Thus, we performed regulatory T cell expansion ex vivo by stimulation with allogeneic APCs, which has the additional effect of producing alloantigen-specific regulatory T cells.", "Here we show that regulatory T cells specific for recipient-type alloantigens control GVHD while favoring immune reconstitution.", "Irrelevant regulatory T cells only mediate a partial protection from GVHD.", "Preferential survival of specific regulatory T cells, but not of irrelevant regulatory T cells, was observed in grafted animals.", "Additionally, the use of specific regulatory T cells was compatible with some form of graft-versus-tumor activity.", "These data suggest that recipient-type specific Treg's could be preferentially used in the control of GVHD in future clinical trials."], "structured": false}
{"doc_id": 33535447, "title": "Expression of the gene encoding the chemorepellent semaphorin III is induced in the fibroblast component of neural scar tissue formed following injuries of adult but not neonatal CNS.", "abstract": ["This study evaluates the expression of the chemorepellent semaphorin III (D)/collapsin-1 (sema III) following lesions to the rat CNS.", "Scar tissue, formed after penetrating injuries to the lateral olfactory tract (LOT), cortex, perforant pathway, and spinal cord, contained numerous spindle-shaped cells expressing high levels of sema III mRNA.", "The properties of these cells were investigated in detail in the lesioned LOT.", "Most sema III mRNA-positive cells were located in the core of the scar and expressed proteins characteristic for fibroblast-like cells.", "Neuropilin-1, a sema III receptor, was expressed in injured neurons with projections to the lesion site, in a subpopulation of scar-associated cells and in blood vessels around the scar.", "In contrast to lesions made in the mature CNS, LOT transection in neonates did not induce sema III mRNA expression within cells in the lesion and was followed by vigorous axonal regeneration.", "The concomitant expression of sema III and its receptor neuropilin-1 in the scar suggests that sema III/neuropilin-1-mediated mechanisms are involved in CNS scar formation.", "The expression of the secreted chemorepellent sema III following CNS injury provides the first evidence that chemorepulsive semaphorins may contribute to the inhibitory effects exerted by scars on the outgrowth of injured CNS neurites.", "The vigorous regrowth of injured axons in the absence of sema III following early neonatal lesions is consistent with this notion.", "The inactivation of sema III in scar tissue by either antibody perturbation or by genetic or pharmacological intervention could be a powerful means to promote long-distance regeneration in the adult CNS."], "structured": false}
{"doc_id": 33554389, "title": "The relationship of the level of cyclic amp to differentiation in primary cultures of chick muscle cells.", "abstract": ["Abstract The effect of increased levels of cAMP upon the differentiation of primary cultures of chick myo blasts has been investigated.", "0.1 mM But 2 cAMP or 1 mM 3-isobutyl-1-methylxanthine was added to the cultures 24 h after plating and maintained throughout the 70 h period of culture examined.", "Both reagents were found to markedly delay the time of fusion of the myoblasts but had no observable effect upon the increase in activity of creatine phosphokinase.", "Morphological examination of the cells revealed no difference in the relative numbers of myoblasts and fibroblasts between the control, But 2 cAMP and 3-isobutyl-1-methylxanthine cultures, but the latter reagent appeared to cause some inhibition of cell proliferation."], "structured": false}
{"doc_id": 33569870, "title": "Intact endothelial autophagy is required to maintain vascular lipid homeostasis.", "abstract": ["The physiological role of autophagic flux within the vascular endothelial layer remains poorly understood.", "Here, we show that in primary endothelial cells, oxidized and native LDL stimulates autophagosome formation.", "Moreover, by both confocal and electron microscopy, excess native or modified LDL appears to be engulfed within autophagic structures.", "Transient knockdown of the essential autophagy gene ATG7 resulted in higher levels of intracellular (125) I-LDL and oxidized LDL (OxLDL) accumulation, suggesting that in endothelial cells, autophagy may represent an important mechanism to regulate excess, exogenous lipids.", "The physiological importance of these observations was assessed using mice containing a conditional deletion of ATG7 within the endothelium.", "Following acute intravenous infusion of fluorescently labeled OxLDL, mice lacking endothelial expression of ATG7 demonstrated prolonged retention of OxLDL within the retinal pigment epithelium (RPE) and choroidal endothelium of the eye.", "In a chronic model of lipid excess, we analyzed atherosclerotic burden in ApoE(-/-) mice with or without endothelial autophagic flux.", "The absence of endothelial autophagy markedly increased atherosclerotic burden.", "Thus, in both an acute and chronic in vivo model, endothelial autophagy appears critically important in limiting lipid accumulation within the vessel wall.", "As such, strategies that stimulate autophagy, or prevent the age-dependent decline in autophagic flux, might be particularly beneficial in treating atherosclerotic vascular disease."], "structured": false}
{"doc_id": 33634749, "title": "Induction of circadian gene expression in human subcutaneous adipose-derived stem cells.", "abstract": ["OBJECTIVE Genes encoding the circadian transcriptional apparatus exhibit robust oscillatory expression in murine adipose tissues.", "This study tests the hypothesis that human subcutaneous adipose-derived stem cells (ASCs) provide an in vitro model in which to monitor the activity of the core circadian transcriptional apparatus.   ", "RESEARCH METHODS AND PROCEDURES Primary cultures of undifferentiated or adipocyte-differentiated ASCs were treated with dexamethasone, rosiglitazone, or 30% fetal bovine serum.", "The response of undifferentiated ASCs to dexamethasone was further evaluated in the presence of lithium chloride.", "Lithium inhibits glycogen synthase kinase 3, a key component of the circadian apparatus.", "Total RNA was harvested at 4-hour intervals over 48 hours and examined by real-time reverse transcription polymerase chain reaction (RT-PCR).   \n", "RESULTS Adipocyte-differentiated cells responded more rapidly to treatments than their donor-matched undifferentiated controls; however, the period of the circadian gene oscillation was longer in the adipocyte-differentiated cells.", "Dexamethasone generated circadian gene expression patterns with mean periods of 25.4 and 26.7 hours in undifferentiated and adipocyte-differentiated ASCs, respectively.", "Both rosiglitazone and serum shock generated a significantly longer period in adipocyte-differentiated ASCs relative to undifferentiated ASCs.", "The Bmal1 profile was phase-shifted by approximately 8 to 12 hours relative to Per1, Per3, and Cry2, consistent with their expression in vivo.", "Lithium chloride inhibited adipogenesis and significantly lengthened the period of Per3 and Rev-erbalpha gene expression profiles by >5 hours in dexamethasone-activated undifferentiated ASCs.   ", "DISCUSSION These results support the initial hypothesis and validate ASCs as an in vitro model for the analysis of circadian biology in human adipose tissue."], "structured": true}
{"doc_id": 33638477, "title": "BCL9 promotes tumor progression by conferring enhanced proliferative, metastatic, and angiogenic properties to cancer cells.", "abstract": ["Several components of the Wnt signaling cascade have been shown to function either as tumor suppressor proteins or as oncogenes in multiple human cancers, underscoring the relevance of this pathway in oncogenesis and the need for further investigation of Wnt signaling components as potential targets for cancer therapy.", "Here, using expression profiling analysis as well as in vitro and in vivo functional studies, we show that the Wnt pathway component BCL9 is a novel oncogene that is aberrantly expressed in human multiple myeloma as well as colon carcinoma.", "We show that BCL9 enhances beta-catenin-mediated transcriptional activity regardless of the mutational status of the Wnt signaling components and increases cell proliferation, migration, invasion, and the metastatic potential of tumor cells by promoting loss of epithelial and gain of mesenchymal-like phenotype.", "Most importantly, BCL9 knockdown significantly increased the survival of xenograft mouse models of cancer by reducing tumor load, metastasis, and host angiogenesis through down-regulation of c-Myc, cyclin D1, CD44, and vascular endothelial growth factor expression by tumor cells.", "Together, these findings suggest that deregulation of BCL9 is an important contributing factor to tumor progression.", "The pleiotropic roles of BCL9 reported in this study underscore its value as a drug target for therapeutic intervention in several malignancies associated with aberrant Wnt signaling."], "structured": false}
{"doc_id": 33667484, "title": "Programmed cell death pathways in cancer: a review of apoptosis, autophagy and programmed necrosis.", "abstract": ["Programmed cell death (PCD), referring to apoptosis, autophagy and programmed necrosis, is proposed to be death of a cell in any pathological format, when mediated by an intracellular program.", "These three forms of PCD may jointly decide the fate of cells of malignant neoplasms; apoptosis and programmed necrosis invariably contribute to cell death, whereas autophagy can play either pro-survival or pro-death roles.", "Recent bulk of accumulating evidence has contributed to a wealth of knowledge facilitating better understanding of cancer initiation and progression with the three distinctive types of cell death.", "To be able to decipher PCD signalling pathways may aid development of new targeted anti-cancer therapeutic strategies.", "Thus in this review, we present a brief outline of apoptosis, autophagy and programmed necrosis pathways and apoptosis-related microRNA regulation, in cancer.", "Taken together, understanding PCD and the complex interplay between apoptosis, autophagy and programmed necrosis may ultimately allow scientists and clinicians to harness the three types of PCD for discovery of further novel drug targets, in the future cancer treatment."], "structured": false}
{"doc_id": 33669399, "title": "Loss of gametophytic self-incompatibility with evolution of inbreeding depression.", "abstract": ["Gametophytic self-incompatibility (SI) in plants is a widespread mechanism preventing self-fertilization and the ensuing inbreeding depression, but it often evolves to self-compatibility.", "We analyze genetic mechanisms for the breakdown of gametophytic SI, incorporating a dynamic model for the evolution of inbreeding depression allowing for partial purging of nearly recessive lethal mutations by selfing, and accounting for pollen limitation and sheltered load linked to the S-locus.", "We consider two mechanisms for the breakdown of gametophytic SI: a nonfunctional S-allele and an unlinked modifier locus that inactivates the S-locus.", "We show that, under a wide range of conditions, self-compatible alleles can invade a self-incompatible population.", "Conditions for invasion are always less stringent for a nonfunctional S-allele than for a modifier locus.", "The spread of self-compatible genotypes is favored by extremely high or low selfing rates, a small number of S-alleles, and pollen limitation.", "Observed parameter values suggest that the maintenance of gametophytic SI is caused by a combination of high inbreeding depression in self-incompatible populations coupled with intermediate selfing rates of the self-compatible genotypes and sheltered load linked to the S-locus."], "structured": false}
{"doc_id": 33677323, "title": "The oncogenic microRNA miR-22 targets the TET2 tumor suppressor to promote hematopoietic stem cell self-renewal and transformation.", "abstract": ["MicroRNAs are frequently deregulated in cancer.", "Here we show that miR-22 is upregulated in myelodysplastic syndrome (MDS) and leukemia and its aberrant expression correlates with poor survival.", "To explore its role in hematopoietic stem cell function and malignancy, we generated transgenic mice conditionally expressing miR-22 in the hematopoietic compartment.", "These mice displayed reduced levels of global 5-hydroxymethylcytosine (5-hmC) and increased hematopoietic stem cell self-renewal accompanied by defective differentiation.", "Conversely, miR-22 inhibition blocked proliferation in both mouse and human leukemic cells.", "Over time, miR-22 transgenic mice developed MDS and hematological malignancies.", "We also identify TET2 as a key target of miR-22 in this context.", "Ectopic expression of TET2 suppressed the miR-22-induced phenotypes.", "Downregulation of TET2 protein also correlated with poor clinical outcomes and miR-22 overexpression in MDS patients.", "Our results therefore identify miR-22 as a potent proto-oncogene and suggest that aberrations in the miR-22/TET2 regulatory network are common in hematopoietic malignancies."], "structured": false}
{"doc_id": 33684572, "title": "Transmission of atherosclerosis susceptibility with gut microbial transplantation.", "abstract": ["Recent studies indicate both clinical and mechanistic links between atherosclerotic heart disease and intestinal microbial metabolism of certain dietary nutrients producing trimethylamine N-oxide (TMAO).", "Here we test the hypothesis that gut microbial transplantation can transmit choline diet-induced TMAO production and atherosclerosis susceptibility.", "First, a strong association was noted between atherosclerotic plaque and plasma TMAO levels in a mouse diversity panel (n = 22 strains, r = 0.38; p = 0.0001).", "An atherosclerosis-prone and high TMAO-producing strain, C57BL/6J, and an atherosclerosis-resistant and low TMAO-producing strain, NZW/LacJ, were selected as donors for cecal microbial transplantation into apolipoprotein e null mice in which resident intestinal microbes were first suppressed with antibiotics.", "Trimethylamine (TMA) and TMAO levels were initially higher in recipients on choline diet that received cecal microbes from C57BL/6J inbred mice; however, durability of choline diet-dependent differences in TMA/TMAO levels was not maintained to the end of the study.", "Mice receiving C57BL/6J cecal microbes demonstrated choline diet-dependent enhancement in atherosclerotic plaque burden as compared with recipients of NZW/LacJ microbes.", "Microbial DNA analyses in feces and cecum revealed transplantation of donor microbial community features into recipients with differences in taxa proportions between donor strains that were transmissible to recipients and that tended to show coincident proportions with TMAO levels.", "Proportions of specific taxa were also identified that correlated with plasma TMAO levels in donors and recipients and with atherosclerotic lesion area in recipients.", "Atherosclerosis susceptibility may be transmitted via transplantation of gut microbiota.", "Gut microbes may thus represent a novel therapeutic target for modulating atherosclerosis susceptibility."], "structured": false}
{"doc_id": 33720691, "title": "The complete primary structure of the spermadhesin AWN, a zona pellucida-binding protein isolated from boar spermatozoa.", "abstract": ["AWN is a boar protein which originates in secretions of the male accessory glands and which becomes sperm surface-associated upon ejaculation.", "It is one of the components thought to mediate sperm adhesion to the egg's zona pellucida through a carbohydrate-recognition mechanism.", "AWN may, thus, participate in the initial events of fertilization in the pig.", "In this report we describe its complete primary structure by combination of protein-chemical and mass spectrometric methods.", "AWN exists as two isoforms, AWN-1 and AWN-2, which differ in that AWN-2 is N-terminally acetylated.", "The amino acid sequence of AWN contains 133 amino acid residues and two disulphide bridges between nearest-neighbour cysteine residues.", "Analysis of the amino acid sequence of the AWN proteins showed significant similarity only to AQN-1 and AQN-3, two other boar spermadhesins."], "structured": false}
{"doc_id": 33723822, "title": "What influences government adoption of vaccines in developing countries? A policy process analysis.", "abstract": ["This paper proposes a framework for examining the process by which government consideration and adoption of new vaccines takes place, with specific reference to developing country settings.", "The cases of early Hepatitis B vaccine adoption in Taiwan and Thailand are used to explore the relevance of explanatory factors identified in the literature as well as the need to go beyond a variable-centric focus by highlighting the role of policy context and process in determining the pace and extent of adoption.", "The cases suggest the feasibility and importance of modeling 'causal diversity'-the complex set of necessary and sufficient conditions leading to particular decisional outcomes-in a broad range of country contexts.", "A better understanding of the lenses through which government decision-makers filter information, and of the arenas in which critical decisions are shaped and taken, may assist both analysts (in predicting institutionalization of new vaccines) and advocates (in crafting targeted strategies to accelerate their diffusion)."], "structured": false}
{"doc_id": 33733520, "title": "Benzodiazepines and injurious falls in community dwelling elders.", "abstract": ["BACKGROUND Benzodiazepines are frequently used medications in the elderly, in whom they are associated with an increased risk of falling, with sometimes dire consequences.   \n", "OBJECTIVE To estimate the impact of benzodiazepine-associated injurious falls in a population of elderly persons.   \n", "METHOD A nested case-control study was conducted using data collected during 10 years of follow-up of the French PAQUID (Personnes Ag\u00e9es QUID) community-based cohort.", "The main outcome measure was the occurrence of an injurious fall, which was defined as a fall resulting in hospitalization, fracture, head trauma or death.", "Controls (3 : 1) were frequency-matched to cases.", "Benzodiazepine exposure was the use of benzodiazepines over the previous 2 weeks reported at the follow-up visit preceding the fall.   \n", "RESULTS Benzodiazepine use was significantly associated with the occurrence of injurious falls, with a significant interaction with age.", "The adjusted odds ratio for injurious falls in subjects exposed to benzodiazepines was 2.2 (95% CI 1.4, 3.4) in subjects aged > or = 80 years and 1.3 (95% CI 0.9, 1.9) in subjects aged <80 years.", "The population attributable risk for injurious falls in subjects exposed to benzodiazepines was 28.1% (95% CI 16.7, 43.2) for subjects aged > or =80 years.", "The incidence of injurious falls in subjects aged > or = 80 years exposed to benzodiazepines in the PAQUID cohort was 2.8/100 person-years.", "Over 9% of these falls were fatal.", "According to these results and to recent population estimates, benzodiazepine use could be held responsible for almost 20 000 injurious falls in subjects aged > or = 80 years every year in France, and for nearly 1800 deaths.   \n", "CONCLUSION Given the considerable morbidity and mortality associated with benzodiazepine use and the fact that existing good practice guidelines on benzodiazepines have not been effective in preventing their misuse (possibly because they have not been applied), new methods for limiting use of benzodiazepines in the elderly need to be found."], "structured": true}
{"doc_id": 33740844, "title": "Effect of women's nutrition before and during early pregnancy on maternal and infant outcomes: a systematic review.", "abstract": ["Current understanding of biologic processes indicates that women's nutritional status before and during early pregnancy may play an important role in determining early developmental processes and ensuring successful pregnancy outcomes.", "We conducted a systematic review of the evidence for the impact of maternal nutrition before and during early pregnancy (<12 weeks gestation) on maternal, neonatal and child health outcomes and included 45 articles (nine intervention trials and 32 observational studies) that were identified through PubMed and EMBASE database searches and examining review articles.", "Intervention trials and observational studies show that periconceptional (<12 weeks gestation) folic acid supplementation significantly reduced the risk of neural tube defects.", "Observational studies suggest that preconceptional and periconceptional intake of vitamin and mineral supplements is associated with a reduced risk of delivering offspring who are low birthweight and/or small-for-gestational age (SGA) and preterm deliveries (PTD).", "Some studies report that indicators of maternal prepregnancy size, low stature, underweight and overweight are associated with increased risks of PTD and SGA.", "The available data indicate the importance of women's nutrition prior to and during the first trimester of pregnancy, but there is a need for well-designed prospective studies and controlled trials in developing country settings that examine relationships with low birthweight, SGA, PTD, stillbirth and maternal and neonatal mortality.", "The knowledge gaps that need to be addressed include the evaluation of periconceptional interventions such as food supplements, multivitamin-mineral supplements and/or specific micronutrients (iron, zinc, iodine, vitamin B-6 and B-12) as well as the relationship between measures of prepregnancy body size and composition and maternal, neonatal and child health outcomes."], "structured": false}
{"doc_id": 33792330, "title": "Kinesin-2 controls development and patterning of the vertebrate skeleton by Hedgehog- and Gli3-dependent mechanisms.", "abstract": ["Hedgehog signaling plays an essential role in patterning of the vertebrate skeleton.", "Here we demonstrate that conditional inactivation of the Kif3a subunit of the kinesin-2 intraflagellar transport motor in mesenchymal skeletal progenitor cells results in severe patterning defects in the craniofacial area, the formation of split sternum and the development of polydactyly.", "These deformities are reminiscent of those previously described in mice with deregulated hedgehog signaling.", "We show that in Kif3a-deficient mesenchymal tissues both the repressor function of Gli3 transcription factor and the activation of the Shh transcriptional targets Ptch and Gli1 are compromised.", "Quantitative analysis of gene expression demonstrates that the Gli1 transcript level is dramatically reduced, whereas Gli3 expression is not significantly affected by kinesin-2 depletion.", "However, the motor appears to be required for the efficient cleavage of the full-length Gli3 transcription factor into a repressor form."], "structured": false}
{"doc_id": 33796570, "title": "Ablation of NF1 function in neurons induces abnormal development of cerebral cortex and reactive gliosis in the brain.", "abstract": ["Neurofibromatosis type 1 (NF1) is a prevalent genetic disorder that affects growth properties of neural-crest-derived cell populations.", "In addition, approximately one-half of NF1 patients exhibit learning disabilities.", "To characterize NF1 function both in vitro and in vivo, we circumvent the embryonic lethality of NF1 null mouse embryos by generating a conditional mutation in the NF1 gene using Cre/loxP technology.", "Introduction of a Synapsin I promoter driven Cre transgenic mouse strain into the conditional NF1 background has ablated NF1 function in most differentiated neuronal populations.", "These mice have abnormal development of the cerebral cortex, which suggests that NF1 has an indispensable role in this aspect of CNS development.", "Furthermore, although they are tumor free, these mice display extensive astrogliosis in the absence of conspicuous neurodegeneration or microgliosis.", "These results indicate that NF1-deficient neurons are capable of inducing reactive astrogliosis via a non-cell autonomous mechanism."], "structured": false}
{"doc_id": 33835579, "title": "Pathology of postprimary tuberculosis in humans and mice: contradiction of long-held beliefs.", "abstract": ["Tuberculosis remains one of the world's leading infectious causes of death.", "Approximately 80% of all disease is due to postprimary (secondary) tuberculosis in the lung.", "Unfortunately, tissues of developing lesions are seldom available and there are no recognized models of postprimary tuberculosis.", "In the preantibiotic era when tissues were more abundant, several investigators described early postprimary tuberculosis as a lipid pneumonia quite different from the caseating granulomas commonly described today.", "We used histopathologic, immunohistochemical and acid fast stains to examine tissues from several people with untreated primary and postprimary tuberculosis and compared the findings with those of mice with reactivation tuberculosis.", "The results confirmed that developing postprimary tuberculosis begins as a lipid pneumonia accompanied by bronchial obstruction in which infection is restricted to foamy alveolar macrophages.", "Cavities result from a combination of caseation of tuberculous pneumonia and microvascular occlusion characteristic of delayed type hypersensitivity (DTH).", "Reactivation tuberculosis in the mouse begins as a similar tuberculous lipid pneumonia with bronchial obstruction and evidence for participation of DTH.", "Developing necrosis in both species is associated with localization of organisms within lipid droplets.", "These results suggest that reactivation tuberculosis in mice is a valuable model of developing human postprimary tuberculosis."], "structured": false}
{"doc_id": 33872649, "title": "Secondary aerosolization of viable Bacillus anthracis spores in a contaminated US Senate Office.", "abstract": ["CONTEXT Bioterrorist attacks involving letters and mail-handling systems in Washington, DC, resulted in Bacillus anthracis (anthrax) spore contamination in the Hart Senate Office Building and other facilities in the US Capitol's vicinity.   \n", "OBJECTIVE To provide information about the nature and extent of indoor secondary aerosolization of B anthracis spores.   \n", "DESIGN Stationary and personal air samples, surface dust, and swab samples were collected under semiquiescent (minimal activities) and then simulated active office conditions to estimate secondary aerosolization of B anthracis spores.", "Nominal size characteristics, airborne concentrations, and surface contamination of B anthracis particles (colony-forming units) were evaluated.   \n", "RESULTS Viable B anthracis spores reaerosolized under semiquiescent conditions, with a marked increase in reaerosolization during simulated active office conditions.", "Increases were observed for B anthracis collected on open sheep blood agar plates (P<.001) and personal air monitors (P =.01) during active office conditions.", "More than 80% of the B anthracis particles collected on stationary monitors were within an alveolar respirable size range of 0.95 to 3.5 micro m.   CONCLUSIONS Bacillus anthracis spores used in a recent terrorist incident reaerosolized under common office activities.", "These findings have important implications for appropriate respiratory protection, remediation, and reoccupancy of contaminated office environments."], "structured": true}
{"doc_id": 33884866, "title": "Fingolimod provides long-term protection in rodent models of cerebral ischemia.", "abstract": ["OBJECTIVE The sphingosine-1-phosphate (S1P) receptor agonist fingolimod (FTY720), that has shown efficacy in advanced multiple sclerosis clinical trials, decreases reperfusion injury in heart, liver, and kidney.", "We therefore tested the therapeutic effects of fingolimod in several rodent models of focal cerebral ischemia.", "To assess the translational significance of these findings, we asked whether fingolimod improved long-term behavioral outcomes, whether delayed treatment was still effective, and whether neuroprotection can be obtained in a second species.   \n", "METHODS We used rodent models of middle cerebral artery occlusion and cell-culture models of neurotoxicity and inflammation to examine the therapeutic potential and mechanisms of neuroprotection by fingolimod.   \n", "RESULTS In a transient mouse model, fingolimod reduced infarct size, neurological deficit, edema, and the number of dying cells in the core and periinfarct area.", "Neuroprotection was accompanied by decreased inflammation, as fingolimod-treated mice had fewer activated neutrophils, microglia/macrophages, and intercellular adhesion molecule-1 (ICAM-1)-positive blood vessels.", "Fingolimod-treated mice showed a smaller infarct and performed better in behavioral tests up to 15 days after ischemia.", "Reduced infarct was observed in a permanent model even when mice were treated 4 hours after ischemic onset.", "Fingolimod also decreased infarct size in a rat model of focal ischemia.", "Fingolimod did not protect primary neurons against glutamate excitotoxicity or hydrogen peroxide, but decreased ICAM-1 expression in brain endothelial cells stimulated by tumor necrosis factor alpha.   \n", "INTERPRETATION These findings suggest that anti-inflammatory mechanisms, and possibly vasculoprotection, rather than direct effects on neurons, underlie the beneficial effects of fingolimod after stroke.", "S1P receptors are a highly promising target in stroke treatment."], "structured": true}
{"doc_id": 33904473, "title": "Induced regeneration\u2014the progress and promise of direct reprogramming for heart repair", "abstract": ["Regeneration of cardiac tissue has the potential to transform cardiovascular medicine.", "Recent advances in stem cell biology and direct reprogramming, or transdifferentiation, have produced powerful new tools to advance this goal.", "In this Review we examine key developments in the generation of new cardiomyocytes in vitro as well as the exciting progress that has been made toward in vivo reprogramming of cardiac tissue.", "We also address controversies and hurdles that challenge the field."], "structured": false}
{"doc_id": 33904789, "title": "\"Sandwich\"-type immunoassay of carcinoembryonic antigen in patients receiving murine monoclonal antibodies for diagnosis and therapy.", "abstract": ["Measurements of carcinoembryonic antigen (CEA) in blood increased dramatically in some patients who were receiving injections of monoclonal antibody.", "CEA titers were measured with a monoclonal antibody-based double-determinant enzyme immunoassay in which untreated plasma specimens were diluted with an equal volume of buffer containing mouse serum.", "Increasing CEA titers were accompanied by the appearance and coincident increase in titers of human antibody against mouse Ig (HAMA).", "Adsorption of these sera with solid-phase anti-human IgG or Protein A restored antigen titers to pretreatment values; evidently the serum factor eliciting false-positive CEA titers was most probably HAMA.", "Neither addition of undiluted mouse serum to the assay mixture nor pretreatment by heating plasma specimens to 70 degrees C effectively abolished HAMA interference.", "By contrast, protein precipitation with polyethylene glycol (130 g/L) or heating plasma samples to 90 degrees C eliminated false-positive titers caused by HAMA, but did not reduce authentic CEA titers."], "structured": false}
{"doc_id": 33911859, "title": "Mutant dynactin in motor neuron disease", "abstract": ["Impaired axonal transport in motor neurons has been proposed as a mechanism for neuronal degeneration in motor neuron disease.", "Here we show linkage of a lower motor neuron disease to a region of 4 Mb at chromosome 2p13.", "Mutation analysis of a gene in this interval that encodes the largest subunit of the axonal transport protein dynactin showed a single base-pair change resulting in an amino-acid substitution that is predicted to distort the folding of dynactin's microtubule-binding domain.", "Binding assays show decreased binding of the mutant protein to microtubules.", "Our results show that dysfunction of dynactin-mediated transport can lead to human motor neuron disease."], "structured": false}
{"doc_id": 33912020, "title": "Thioredoxin mediates oxidation-dependent phosphorylation of CRMP2 and growth cone collapse.", "abstract": ["Semaphorin3A (Sema3A) is a repulsive guidance molecule for axons, which acts by inducing growth cone collapse through phosphorylation of CRMP2 (collapsin response mediator protein 2).", "Here, we show a role for CRMP2 oxidation and thioredoxin (TRX) in the regulation of CRMP2 phosphorylation and growth cone collapse.", "Sema3A stimulation generated hydrogen peroxide (H2O2) through MICAL (molecule interacting with CasL) and oxidized CRMP2, enabling it to form a disulfide-linked homodimer through cysteine-504.", "Oxidized CRMP2 then formed a transient disulfide-linked complex with TRX, which stimulated CRMP2 phosphorylation by glycogen synthase kinase-3, leading to growth cone collapse.", "We also reconstituted oxidation-dependent phosphorylation of CRMP2 in vitro, using a limited set of purified proteins.", "Our results not only clarify the importance of H2O2 and CRMP2 oxidation in Sema3A-induced growth cone collapse but also indicate an unappreciated role for TRX in linking CRMP2 oxidation to phosphorylation."], "structured": false}
{"doc_id": 33912748, "title": "Pathologic indicators of degradation and inflammation in human osteoarthritic cartilage are abrogated by exposure to n-3 fatty acids.", "abstract": ["OBJECTIVE To determine if n-3 polyunsaturated fatty acid (PUFA) supplementation (versus treatment with n-6 polyunsaturated or other fatty acid supplements) affects the metabolism of osteoarthritic (OA) cartilage.   \n", "METHODS The metabolic profile of human OA cartilage was determined at the time of harvest and after 24-hour exposure to n-3 PUFAs or other classes of fatty acids, followed by explant culture for 4 days in the presence or absence of interleukin-1 (IL-1).", "Parameters measured were glycosaminoglycan release, aggrecanase and matrix metalloproteinase (MMP) activity, and the levels of expression of messenger RNA (mRNA) for mediators of inflammation, aggrecanases, MMPs, and their natural tissue inhibitors (tissue inhibitors of metalloproteinases [TIMPs]).   \n", "RESULTS Supplementation with n-3 PUFA (but not other fatty acids) reduced, in a dose-dependent manner, the endogenous and IL-1-induced release of proteoglycan metabolites from articular cartilage explants and specifically abolished endogenous aggrecanase and collagenase proteolytic activity.", "Similarly, expression of mRNA for ADAMTS-4, MMP-13, and MMP-3 (but not TIMP-1, -2, or -3) was also specifically abolished with n-3 PUFA supplementation.", "In addition, n-3 PUFA supplementation abolished the expression of mRNA for mediators of inflammation (cyclooxygenase 2, 5-lipoxygenase, 5-lipoxygenase-activating protein, tumor necrosis factor alpha, IL-1alpha, and IL-1beta) without affecting the expression of message for several other proteins involved in normal tissue homeostasis.   \n", "CONCLUSION These studies show that the pathologic indicators manifested in human OA cartilage can be significantly altered by exposure of the cartilage to n-3 PUFA, but not to other classes of fatty acids."], "structured": true}
{"doc_id": 33918970, "title": "Interactive effects of oligofructose and obesity predisposition on gut hormones and microbiota in diet-induced obese rats.", "abstract": ["OBJECTIVE Oligofructose (OFS) is a prebiotic that reduces energy intake and fat mass via changes in gut satiety hormones and microbiota.", "The effects of OFS may vary depending on predisposition to obesity.", "The aim of this study was to examine the effect of OFS in diet-induced obese (DIO) and diet-resistant (DR) rats.   \n", "METHODS Adult, male DIO, and DR rats were randomized to: high-fat/high-sucrose (HFS) diet or HFS diet + 10% OFS for 6 weeks.", "Body composition, food intake, gut microbiota, plasma gut hormones, and cannabinoid CB(1) receptor expression in the nodose ganglia were measured.   \n", "RESULTS OFS reduced body weight, energy intake, and fat mass in both phenotypes (P < 0.05).", "Select gut microbiota differed in DIO versus DR rats (P < 0.05), the differences being eliminated by OFS.", "OFS did not modify plasma ghrelin or CB(1) expression in nodose ganglia, but plasma levels of GIP were reduced and PYY were elevated (P < 0.05) by OFS.   \n", "CONCLUSIONS OFS was able to reduce body weight and adiposity in both prone and resistant obese phenotypes.", "OFS-induced changes in gut microbiota profiles in DIO and DR rats, along with changes in gut hormone levels, likely contribute to the sustained lower body weights."], "structured": true}
{"doc_id": 33920995, "title": "RKIKK motif in the intracellular domain is critical for spatial and dynamic organization of ICAM-1: functional implication for the leukocyte adhesion and transmigration.", "abstract": ["No direct evidence has been reported whether the spatial organization of ICAM-1 on the cell surface is linked to its physiological function in terms of leukocyte adhesion and transendothelial migration (TEM).", "Here we observed that ICAM-1 by itself directly regulates the de novo elongation of microvilli and is thereby clustered on the microvilli.", "However, truncation of the intracellular domain resulted in uniform cell surface distribution of ICAM-1.", "Mutation analysis revealed that the C-terminal 21 amino acids are dispensable, whereas a segment of 5 amino acids ((507)RKIKK(511)) in the NH-terminal third of intracellular domain, is required for the proper localization and dynamic distribution of ICAM-1 and the association of ICAM-1 with F-actin, ezrin, and moesin.", "Importantly, deletion of the (507)RKIKK(511) significantly delayed the LFA-1-dependent membrane projection and decreased leukocyte adhesion and subsequent TEM.", "Endothelial cells treated with cell-permeant penetratin-ICAM-1 peptides comprising ICAM-1 RKIKK sequences inhibited leukocyte TEM.", "Collectively, these findings demonstrate that (507)RKIKK(511) is an essential motif for the microvillus ICAM-1 presentation and further suggest a novel regulatory role for ICAM-1 topography in leukocyte TEM."], "structured": false}
{"doc_id": 33934971, "title": "Immunology of the tick-host interaction and the control of ticks and tick-borne diseases.", "abstract": ["The first experimental vaccination against ticks was carried out 60 years ago.", "Since then, progress has been slow, although the recent commercial release of a recombinant vaccine against Boophilus microplus is significant.", "The nature of naturally acquired protective immunity against ticks is poorly understood, particularly in the important, domesticated ruminant hosts.", "Characterization of the antigens of naturally acquired immunity remains limited, although more has been achieved with 'concealed' antigens.", "Crucial questions remain about the true impact of tick-induced immunosuppression and the effect of immunity on the transmission of tick-borne diseases, despite some fascinating and important recent results, as discussed here by Peter Willadsen and Frans Jongejan."], "structured": false}
{"doc_id": 33955641, "title": "Rapid method for the isolation of lipoproteins from human serum by precipitation with polyanions.", "abstract": ["Procedures are described for the isolation of lipoproteins from human serum by precipitation with polyanions and divalent cations.", "A mixture of low and very low density lipoproteins can be prepared without ultracentrifugation by precipitation with heparin and either MnCl(2) alone or MgCl(2) plus sucrose.", "In both cases the precipitation is reversible, selective, and complete.", "The highly concentrated isolated lipoproteins are free of other plasma proteins as judged by immunological and electrophoretic methods.", "The low density and very low density lipoproteins can then be separated from each other by ultracentrifugation.", "The advantage of the method is that large amounts of lipoproteins can be prepared with only a single preparative ultracentrifugation.", "Polyanions other than heparin may also be used; when the precipitation of the low and very low density lipoproteins is achieved with dextran sulfate and MnCl(2), or sodium phosphotungstate and MgCl(2), the high density lipoproteins can subsequently be precipitated by increasing the concentrations of the reagents.", "These lipoproteins, containing small amounts of protein contaminants, are further purified by ultracentrifugation at d 1.22.", "With a single preparative ultracentrifugation, immunologically pure high density lipoproteins can be isolated from large volumes of serum."], "structured": false}
{"doc_id": 33960383, "title": "The role of oral antidiabetic agents: why and when to use an early-phase insulin secretion agent in Type II diabetes mellitus", "abstract": ["Abstract Evidence obtained in the 1990's strongly supports the notion that glycaemic control is important not only in Type I (insulin-dependent), but also in Type II (non-insulin-dependent) diabetes mellitus.", "Although measurement of HbA1c is the standard for assessing the effect of glucose control in the occurrence and prevention of diabetic sequelae, more recent evidence indicates that other glucose parameters are also important.", "Postchallenge and postprandial hyperglycaemic peaks seem to be prospective determinants of vascular damage in early Type II diabetes.", "Currently, there is no overall accepted standard approach for the pharmacological management of Type II diabetes.", "The United Kingdom Prospective Diabetes Study has shown that reaching a near-normal glycaemic target is critically important and the pharmacotherapy of this progressive disease is difficult.", "Loss of endogenous insulin secretion has been substantiated to cause the progression of Type II diabetes in the United Kingdom Prospective Diabetes Study.", "Early insulinization, however, was not advantageous over other forms of therapy.", "The advent of polypharmacy in recent years has greatly strengthened the treatment of this disease.", "This synergy has been extended of late with the development of early-phase insulin secretion agents.", "Two such agents, nateglinide and repaglinide, can be used to reduce mealtime glucose excursions and HbA1c as monotherapy, and in combination with metformin; their antidiabetic potential is similar to the combination treatment with glibenclamide and metformin.", "Additional substantiation of their long-term effect on improving life expectancy and reducing diabetic complications in Type II diabetic patients is now required."], "structured": false}
{"doc_id": 33986200, "title": "Layered hydrogels accelerate iPSC-derived neuronal maturation and reveal migration defects caused by MeCP2 dysfunction.", "abstract": ["Probing a wide range of cellular phenotypes in neurodevelopmental disorders using patient-derived neural progenitor cells (NPCs) can be facilitated by 3D assays, as 2D systems cannot entirely recapitulate the arrangement of cells in the brain.", "Here, we developed a previously unidentified 3D migration and differentiation assay in layered hydrogels to examine how these processes are affected in neurodevelopmental disorders, such as Rett syndrome.", "Our soft 3D system mimics the brain environment and accelerates maturation of neurons from human induced pluripotent stem cell (iPSC)-derived NPCs, yielding electrophysiologically active neurons within just 3 wk.", "Using this platform, we revealed a genotype-specific effect of methyl-CpG-binding protein-2 (MeCP2) dysfunction on iPSC-derived neuronal migration and maturation (reduced neurite outgrowth and fewer synapses) in 3D layered hydrogels.", "Thus, this 3D system expands the range of neural phenotypes that can be studied in vitro to include those influenced by physical and mechanical stimuli or requiring specific arrangements of multiple cell types."], "structured": false}
{"doc_id": 33986507, "title": "Inducible gene expression: diverse regulatory mechanisms", "abstract": ["The rapid activation of gene expression in response to stimuli occurs largely through the regulation of RNA polymerase II-dependent transcription.", "In this Review, we discuss events that occur during the transcription cycle in eukaryotes that are important for the rapid and specific activation of gene expression in response to external stimuli.", "In addition to regulated recruitment of the transcription machinery to the promoter, it has now been shown that control steps can include chromatin remodelling and the release of paused polymerase.", "Recent work suggests that some components of signal transduction cascades also play an integral part in activating transcription at target genes."], "structured": false}
{"doc_id": 33989422, "title": "On the origins of ultra-fine anaphase bridges.", "abstract": ["Comment on: Chan KL, Palmai-Pallag T, Ying S, Hickson ID.", "Replication stress induces sister-chromatid bridging at fragile site loci in mitosis.", "Nat Cell Biol 2009; 11:753-60."], "structured": false}
{"doc_id": 34016944, "title": "Resistance to gefitinib in PTEN-null HER-overexpressing tumor cells can be overcome through restoration of PTEN function or pharmacologic modulation of constitutive phosphatidylinositol 3'-kinase/Akt pathway signaling.", "abstract": ["PURPOSE Tyrosine kinase (TK) inhibitors are emerging as a promising new approach to the treatment of HER overexpressing tumors, however optimal use of these agents awaits further definition of the downstream signaling pathways that mediate their effects.", "We reported previously that both EGFR- and Her2-overexpressing tumors are sensitive to the new EGFR-selective TK inhibitor gefitinib (ZD1839, \"Iressa\"), and sensitivity to this agent correlated with its ability to down-regulate Akt.", "However, EGFR-overexpressing MDA-468 cells, which lack PTEN function, are resistant to ZD1839, and ZD1839 is unable to down-regulate Akt activity in these cells.   ", "EXPERIMENTAL DESIGN To study the role of PTEN function, we generated MDA468 cells with tet-inducible PTEN expression.   \n", "RESULTS We show here that the resistance of MDA-468 cells to ZD1839 is attributable to EGFR-independent constitutive Akt activation caused by loss of PTEN function in these cells.", "Reconstitution of PTEN function through tet-inducible expression restores ZD1839 sensitivity to these cells and reestablishes EGFR-stimulated Akt signaling.", "Although restoration of PTEN function to tumors is difficult to implement clinically, much of the effects of PTEN loss are attributable to overactive PI3K/Akt pathway signaling, and this overactivity can be modulated by pharmacologic approaches.", "We show here that pharmacologic down-regulation of constitutive PI3K/Akt pathway signaling using the PI3K inhibitor LY294002 similarly restores EGFR-stimulated Akt signaling and sensitizes MDA-468 cells to ZD1839.   \n", "CONCLUSIONS Sensitivity to ZD1839 requires intact growth factor receptor-stimulated Akt signaling activity.", "PTEN loss leads to uncoupling of this signaling pathway and results in ZD1839 resistance, which can be reversed with reintroduction of PTEN or pharmacologic down-regulation of constitutive PI3K/Akt pathway activity.", "These data have important predictive and therapeutic clinical implications."], "structured": true}
{"doc_id": 34016987, "title": "Transcriptome analysis reveals human cytomegalovirus reprograms monocyte differentiation toward an M1 macrophage.", "abstract": ["Monocytes are primary targets for human CMV (HCMV) infection and are proposed to be responsible for hematogenous dissemination of the virus.", "Monocytes acquire different functional traits during polarization to the classical proinflammatory M1 macrophage or the alternative antiinflammatory M2 macrophage.", "We hypothesized that HCMV induced a proinflammatory M1 macrophage following infection to promote viral dissemination because, biologically, a proinflammatory state provides the tools to drive infected monocytes from the blood into the tissue.", "To test this hypothesis of monocyte conversion from a normal quiescent phenotype to an inflammatory phenotype, we used Affymetrix Microarray to acquire a transcriptional profile of infected monocytes at a time point our data emphasized is a key temporal regulatory point following infection.", "We found that HCMV significantly up-regulated 583 (5.2%) of the total genes and down-regulated 621 (5.5%) of the total genes>or=1.5-fold at 4 h postinfection.", "Further ontology analysis revealed that genes implicated in classical M1 macrophage activation were stimulated by HCMV infection.", "We found that 65% of genes strictly associated with M1 polarization were up-regulated, while only 4% of genes solely associated with M2 polarization were up-regulated.", "Analysis of the monocyte chemokinome at the transcriptional level showed that 44% of M1 and 33% of M2 macrophage chemokines were up-regulated.", "Proteomic analysis using chemokine Ab arrays confirmed the secretion of these chemotactic proteins from HCMV-infected monocytes.", "Overall, the results identify that the HCMV-infected monocyte transcriptome displayed a unique M1/M2 polarization signature that was skewed toward the classical M1 activation phenotype."], "structured": false}
{"doc_id": 34025053, "title": "Antithymocyte globulin treatment for patients with recent-onset type 1 diabetes: 12-month results of a randomised, placebo-controlled, phase 2 trial.", "abstract": ["BACKGROUND Type 1 diabetes results from T-cell-mediated destruction of \u03b2 cells.", "Findings from preclinical studies and pilot clinical trials suggest that antithymocyte globulin (ATG) might be effective for reducing this autoimmune response.", "We assessed the safety and efficacy of rabbit ATG in preserving islet function in participants with recent-onset type 1 diabetes, and report here our 12-month results.   \n", "METHODS For this phase 2, randomised, placebo-controlled, clinical trial, we enrolled patients with recent-onset type 1 diabetes, aged 12-35 years, and with a peak C-peptide of 0.4 nM or greater on mixed meal tolerance test from 11 sites in the USA.", "We used a computer generated randomisation sequence to randomly assign patients (2:1, with permuted-blocks of size three or six and stratified by study site) to receive either 6.5 mg/kg ATG or placebo over a course of four days.", "All participants were masked and initially managed by an unmasked drug management team, which managed all aspects of the study until month 3.", "Thereafter, to maintain masking for diabetes management throughout the remainder of the study, participants received diabetes management from an independent, masked study physician and nurse educator.", "The primary endpoint was the baseline-adjusted change in 2-h area under the curve C-peptide response to mixed meal tolerance test from baseline to 12 months.", "Analyses were by intention to treat.", "This is a planned interim analysis of an on-going trial that will run for 24 months of follow-up.", "This study is registered with ClinicalTrials.gov, number NCT00515099.   \n", "FINDINGS Between Sept 10, 2007, and June 1, 2011, we screened 154 individuals, randomly allocating 38 to ATG and 20 to placebo.", "We recorded no between-group difference in the primary endpoint: participants in the ATG group had a mean change in C-peptide area under the curve of -0.195 pmol/mL (95% CI -0.292 to -0.098) and those in the placebo group had a mean change of -0.239 pmol/mL (-0.361 to -0.118) in the placebo group (p=0.591).", "All except one participant in the ATG group had both cytokine release syndrome and serum sickness, which was associated with a transient rise in interleukin-6 and acute-phase proteins.", "Acute T cell depletion occurred in the ATG group, with slow reconstitution over 12 months.", "However, effector memory T cells were not depleted, and the ratio of regulatory to effector memory T cells declined in the first 6 months and stabilised thereafter.", "ATG-treated patients had 159 grade 3-4 adverse events, many associated with T-cell depletion, compared with 13 in the placebo group, but we detected no between-group difference in incidence of infectious diseases.   \n", "INTERPRETATION Our findings suggest that a brief course of ATG does not result in preservation of \u03b2-cell function 12 months later in patients with new-onset type 1 diabetes.", "Generalised T-cell depletion in the absence of specific depletion of effector memory T cells and preservation of regulatory T cells seems to be an ineffective treatment for type 1 diabetes."], "structured": true}
{"doc_id": 34034749, "title": "The nucleosome family: dynamic and growing.", "abstract": ["Ever since the discovery of the nucleosome in 1974, scientists have stumbled upon discrete particles in which DNA is wrapped around histone complexes of different stoichiometries: octasomes, hexasomes, tetrasomes, \"split\" half-nucleosomes, and, recently, bona fide hemisomes.", "Do all these particles exist in vivo?", "Under what conditions?", "What is their physiological significance in the complex DNA transactions in the eukaryotic nucleus?", "What are their dynamics?", "This review summarizes research spanning more than three decades and provides a new meaning to the term \"nucleosome.", "\"", "The nucleosome can no longer be viewed as a single static entity: rather, it is a family of particles differing in their structural and dynamic properties, leading to different functionalities."], "structured": false}
{"doc_id": 34054472, "title": "Association between serum corin levels and risk of acute myocardial infarction.", "abstract": ["BACKGROUND Accumulating evidence has indicated that corin plays critical roles in regulating salt-water balance, blood pressure and cardiac function by activating natriuretic peptides.", "The present case-control study was designed to evaluate the association of serum soluble corin with acute myocardial infarction (AMI).   \n", "METHODS We enrolled 856 consecutive AMI patients and 856 control subjects and explored the possible relation between serum corin levels and AMI risk using logistic regression model.   \n", "RESULTS Patients with AMI had higher BMI, were less physically active, and were more likely to have histories of hypertension, diabetes, hyperlipidemia and smoking compared with the controls.", "Serum levels of corin were remarkably reduced in AMI patients (825\u00b1263pg/ml) compared with those in healthy controls (1246\u00b1425pg/ml).", "Odds ratios of ST elevation (STEMI) and non-ST elevation myocardial infarction (NSTEMI) were significantly decreased with the increasing levels of serum corin in both men and women (P for trend, <0.001) after adjustment for body mass index, hypertension, diabetes, hyperlipidemia, smoking, and physical activity.   \n", "CONCLUSIONS Our study demonstrates that serum levels of corin are significantly decreased in AMI patients, and it is inversely associated with the incidences of STEMI and NSTEMI in both men and women."], "structured": true}
{"doc_id": 34066665, "title": "Crosstalk between the estrogen receptor and the HER tyrosine kinase receptor family: molecular mechanism and clinical implications for endocrine therapy resistance.", "abstract": ["Breast cancer evolution and tumor progression are governed by the complex interactions between steroid receptor [estrogen receptor (ER) and progesterone receptor] and growth factor receptor signaling.", "In recent years, the field of cancer therapy has witnessed the emergence of multiple strategies targeting these specific cancer pathways and key molecules (ER and growth factor receptors) to arrest tumor growth and achieve tumor eradication; treatment success, however, has varied and both de novo (up front) and acquired resistance have proven a challenge.", "Recent studies of ER biology have revealed new insights into ER action in breast cancer and have highlighted the role of an intimate crosstalk between the ER and HER family signaling pathways as a fundamental contributor to the development of resistance to endocrine therapies against the ER pathway.", "The aim of this review article is to summarize the current knowledge on mechanisms of resistance of breast cancer cells to endocrine therapies due to the crosstalk between the ER and the HER growth factor receptor signaling pathways and to explore new available therapeutic strategies that could prolong duration of response and circumvent endocrine resistant tumor growth."], "structured": false}
{"doc_id": 34071621, "title": "Nuclear PTEN functions as an essential regulator of SRF-dependent transcription to control smooth muscle differentiation", "abstract": ["Vascular disease progression is associated with marked changes in vascular smooth muscle cell (SMC) phenotype and function.", "SMC contractile gene expression and, thus differentiation, is under direct transcriptional control by the transcription factor, serum response factor (SRF); however, the mechanisms dynamically regulating SMC phenotype are not fully defined.", "Here we report that the lipid and protein phosphatase, PTEN, has a novel role in the nucleus by functioning as an indispensible regulator with SRF to maintain the differentiated SM phenotype.", "PTEN interacts with the N-terminal domain of SRF and PTEN-SRF interaction promotes SRF binding to essential promoter elements in SM-specific genes.", "Factors inducing phenotypic switching promote loss of nuclear PTEN through nucleo-cytoplasmic translocation resulting in reduced myogenically active SRF, but enhanced SRF activity on target genes involved in proliferation.", "Overall decreased expression of PTEN was observed in intimal SMCs of human atherosclerotic lesions underlying the potential clinical importance of these findings."], "structured": false}
{"doc_id": 34074902, "title": "SEROSURVEY FOR FELINE LEUKEMIA VIRUS AND LENTIVIRUSES IN CAPTIVE SMALL NEOTROPIC FELIDS IN S\u00c3O PAULO STATE, BRAZIL", "abstract": ["Abstract Feline leukemia virus (FeLV), Gammaretrovirus, and feline immunodeficiency virus, a Lentivirus, are members of the family Retroviridae, and may establish persistent infections in the domestic cat (Felis catus).", "Cytoproliferative and cytosuppressive disorders may result from infection with these viruses.", "Morbidity and mortality rates are high in domestic cats worldwide.", "Infection of endangered neotropic small felids with these viruses could be devastating.", "To investigate the prevalence of FeLV and feline lentiviruses in neotropic small felids kept in captivity in S\u00e3o Paulo state, Brazil, serum samples from 104 animals belonging to the species Leopardus pardalis, Leopardus tigrinus, Leopardus wiedii, Herpailurus yaguarondi, and Oncifelis geoffroyi were tested for FeLV and feline lentiviruses by commercially available immunoassays.", "All results were negative, suggesting that retrovirus infection is not an important clinical problem in these populations.", "Because domestic cats in S\u00e3o Paulo city are naturally infected with these pathogens, and feral cats are commonly found in zoologic facilities in Brazil, preventive measures should be taken to avoid transmission of retroviruses to naive populations of wild and captive neotropic felids in Brazil."], "structured": false}
{"doc_id": 34101101, "title": "Comparing the metabolism of quercetin in rats, mice and gerbils", "abstract": ["Several species of rodents are used to investigate the metabolism of quercetin in vivo.", "However, it is unclear whether they are a proper animal model.", "Thus, we compared the metabolism of quercetin in Wistar rats (rats), Balb/c mice (mice) and Mongolian gerbils (gerbils).", "We determined the levels of quercetin metabolites, quercetin-3-glucuronide (Q3G), quercetin-3\u2032-sulfate (Q3\u2032S) and methyl-quercetin isorhamnetin (IH), in the plasma, lungs and livers of three species of animals by high-performance liquid chromatography after acute and/or chronic quercetin administration.", "The metabolic enzyme activities in the intestinal mucosal membrane and liver were also investigated.", "First, we found that after acute quercetin administration, the Q3\u2032S level was the highest in gerbils.", "However, after long-term supplementation (20 weeks), Q3G was the dominant metabolite in the plasma, lungs and livers followed by IH and Q3\u2032S in all animals, although the gerbils still had a higher Q3\u2032S conversion ratio.", "The average concentrations of total quercetin concentration in the plasma of gerbils were the highest in both short- and long-term studies.", "The activities of uridine 5\u2032-diphosphate-glucuronosyltransferase, phenolsulfotransferase and catechol-O-methyltransferase were induced by quercetin in a dose- and tissue-dependent manner in all animals.", "Taken together, in general, after long-term supplementation the metabolism of quercetin is similar in all animals and is comparable to that of humans.", "However, the accumulation of quercetin and Q3\u2032S conversion ratio in gerbils are higher than those in the other animals."], "structured": false}
{"doc_id": 34103335, "title": "Cytokinesis failure generating tetraploids promotes tumorigenesis in p53-null cells", "abstract": ["A long-standing hypothesis on tumorigenesis is that cell division failure, generating genetically unstable tetraploid cells, facilitates the development of aneuploid malignancies.", "Here we test this idea by transiently blocking cytokinesis in p53-null (p53-/-) mouse mammary epithelial cells (MMECs), enabling the isolation of diploid and tetraploid cultures.", "The tetraploid cells had an increase in the frequency of whole-chromosome mis-segregation and chromosomal rearrangements.", "Only the tetraploid cells were transformed in vitro after exposure to a carcinogen.", "Furthermore, in the absence of carcinogen, only the tetraploid cells gave rise to malignant mammary epithelial cancers when transplanted subcutaneously into nude mice.", "These tumours all contained numerous non-reciprocal translocations and an 8\u201330-fold amplification of a chromosomal region containing a cluster of matrix metalloproteinase (MMP) genes.", "MMP overexpression is linked to mammary tumours in humans and animal models.", "Thus, tetraploidy enhances the frequency of chromosomal alterations and promotes tumour development in p53-/- MMECs."], "structured": false}
{"doc_id": 34105878, "title": "Claspin, a Chk1-regulatory protein, monitors DNA replication on chromatin independently of RPA, ATR, and Rad17.", "abstract": ["Claspin is required for the ATR-dependent activation of Chk1 in Xenopus egg extracts containing incompletely replicated DNA.", "We show here that Claspin associates with chromatin in a regulated manner during S phase.", "Binding of Claspin to chromatin depends on the pre-replication complex (pre-RC) and Cdc45 but not on replication protein A (RPA).", "These dependencies suggest that binding of Claspin occurs around the time of initial DNA unwinding at replication origins.", "By contrast, both ATR and Rad17 require RPA for association with DNA.", "Claspin, ATR, and Rad17 all bind to chromatin independently.", "These findings suggest that Claspin plays a role in monitoring DNA replication during S phase.", "Claspin, ATR, and Rad17 may collaborate in checkpoint regulation by detecting different aspects of a DNA replication fork."], "structured": false}
{"doc_id": 34121231, "title": "Cold-related respiratory symptoms in the general population.", "abstract": ["INTRODUCTION Cold-related respiratory symptoms are common among northern populations, especially among people suffering from respiratory diseases.", "However, the prevalence of such symptoms in the general population and the threshold temperatures at which the symptoms start to emerge are poorly known.   \n", "OBJECTIVES The present study determined the prevalence and threshold temperatures of self-reported respiratory symptoms related to cold, separately for healthy people and those with respiratory disease.   ", "MATERIALS AND METHODS Six thousand five hundred ninety-one men and women aged 25 years-74 years from the national FINRISK study were queried about cold-related respiratory symptoms.", "The results were expressed as age-adjusted prevalence figures and coefficients from multivariate regressions.   \n", "RESULTS Cold-related respiratory symptoms were more often reported by people with asthma (men 69%/women 78%) and by subjects with chronic bronchitis (65%/76%) than the healthy subjects (18%/21%).", "A binomial regression showed an increase of symptom prevalence by age and excesses of 4%, 50% and 21% units because of female sex, asthma and chronic bronchitis, respectively.", "The reported threshold temperature for cold-related symptoms was -14 degrees C for males and -15 degrees C for females, and it showed some increase by age (0 degrees C-5 degrees C), asthma (2 degrees C) and chronic bronchitis (3 degrees C).", "The threshold temperature for mucus production was exceptional as it decreased by age (2 degrees C-5 degrees C) and asthma (2 degrees C).", "The effects of smoking and education were marginal.   \n", "CONCLUSION Cold-related respiratory symptoms are common in patients with chronic respiratory diseases, but they start to emerge at relatively low temperatures.", "In a cold climate, the cold-related symptoms may have an impact on the health-related quality of life."], "structured": true}
{"doc_id": 34139429, "title": "Carvedilol for children and adolescents with heart failure: a randomized controlled trial.", "abstract": ["CONTEXT Although beta-blockers improve symptoms and survival in adults with heart failure, little is known about these medications in children and adolescents.   \n", "OBJECTIVE To prospectively evaluate the effects of carvedilol in children and adolescents with symptomatic systemic ventricular systolic dysfunction.   \n", "DESIGN, SETTING, AND PARTICIPANTS A multicenter, randomized, double-blind, placebo-controlled study of 161 children and adolescents with symptomatic systolic heart failure from 26 US centers.", "In addition to treatment with conventional heart failure medications, patients were assigned to receive placebo or carvedilol.", "Enrollment began in June 2000 and the last dose was given in May 2005 (each patient received medication for 8 months).   \n", "INTERVENTIONS Patients were randomized in a 1:1:1 ratio to twice-daily dosing with placebo, low-dose carvedilol (0.2 mg/kg per dose if weight <62.5 kg or 12.5 mg per dose if weight > or =62.5 kg), or high-dose carvedilol (0.4 mg/kg per dose if weight <62.5 kg or 25 mg per dose if weight > or =62.5 kg) and were stratified according to whether each patient's systemic ventricle was a left ventricle or not.   \n", "MAIN OUTCOME MEASURES The primary outcome was a composite measure of heart failure outcomes in patients receiving carvedilol (low- and high-dose combined) vs placebo.", "Secondary efficacy variables included individual components of this composite, echocardiographic measures, and plasma b-type natriuretic peptide levels.   \n", "RESULTS There was no statistically significant difference between groups for the composite end point based on the percentage of patients who improved, worsened, or were unchanged.", "Among 54 patients assigned to placebo, 30 improved (56%), 16 worsened (30%), and 8 were unchanged (15%); among 103 patients assigned to carvedilol, 58 improved (56%), 25 worsened (24%), and 20 were unchanged (19%).", "The rates of worsening were lower than expected.", "The odds ratio for worsened outcome for patients in the combined carvedilol group vs the placebo group was 0.79 (95% CI, 0.36-1.59; P = .47).", "A prespecified subgroup analysis noted significant interaction between treatment and ventricular morphology (P = .02), indicating a possible differential effect of treatment between patients with a systemic left ventricle (beneficial trend) and those whose systemic ventricle was not a left ventricle (nonbeneficial trend).   \n", "CONCLUSIONS These preliminary results suggest that carvedilol does not significantly improve clinical heart failure outcomes in children and adolescents with symptomatic systolic heart failure.", "However, given the lower than expected event rates, the trial may have been underpowered.", "There may be a differential effect of carvedilol in children and adolescents based on ventricular morphology.   \n", "TRIAL REGISTRATION clinicaltrials.gov Identifier: NCT00052026."], "structured": true}
{"doc_id": 34189936, "title": "The circadian clock gene BMAL1 is a novel therapeutic target for malignant pleural mesothelioma.", "abstract": ["Malignant pleural mesothelioma (MPM) is a highly aggressive neoplasm arising from the mesothelial cells lining the parietal pleura and it exhibits poor prognosis.", "Although there has been significant progress in MPM treatment, development of more efficient therapeutic approaches is needed.", "BMAL1 is a core component of the circadian clock machinery and its constitutive overexpression in MPM has been reported.", "Here, we demonstrate that BMAL1 may serve as a molecular target for MPM.", "The majority of MPM cell lines and a subset of MPM clinical specimens expressed higher levels of BMAL1 compared to a nontumorigenic mesothelial cell line (MeT-5A) and normal parietal pleural specimens, respectively.", "A serum shock induced a rhythmical BMAL1 expression change in MeT-5A but not in ACC-MESO-1, suggesting that the circadian rhythm pathway is deregulated in MPM cells.", "BMAL1 knockdown suppressed proliferation and anchorage-dependent and independent clonal growth in two MPM cell lines (ACC-MESO-1 and H290) but not in MeT-5A.", "Notably, BMAL1 depletion resulted in cell cycle disruption with a substantial increase in apoptotic and polyploidy cell population in association with downregulation of Wee1, cyclin B and p21(WAF1/CIP1) and upregulation of cyclin E expression.", "BMAL1 knockdown induced mitotic catastrophe as denoted by disruption of cell cycle regulators and induction of drastic morphological changes including micronucleation and multiple nuclei in ACC-MESO-1 cells that expressed the highest level of BMAL1.", "Taken together, these findings indicate that BMAL1 has a critical role in MPM and could serve as an attractive therapeutic target for MPM."], "structured": false}
{"doc_id": 34198365, "title": "Mechanism and Regulation of DNA-Protein Crosslink Repair by the DNA-Dependent Metalloprotease SPRTN", "abstract": ["Covalent DNA-protein crosslinks (DPCs) are toxic DNA lesions that interfere with essential chromatin transactions, such as replication and transcription.", "Little was known about DPC-specific repair mechanisms until the recent identification of a DPC-processing protease in yeast.", "The existence of a DPC protease in higher eukaryotes is inferred from data in Xenopus laevis egg extracts, but its identity remains elusive.", "Here we identify the metalloprotease SPRTN as the DPC protease acting in metazoans.", "Loss of SPRTN results in failure to repair DPCs and hypersensitivity to DPC-inducing agents.", "SPRTN accomplishes DPC processing through a unique DNA-induced protease activity, which is controlled by several sophisticated regulatory mechanisms.", "Cellular, biochemical, and structural studies define a DNA switch triggering its protease activity, a ubiquitin switch controlling SPRTN chromatin accessibility, and regulatory autocatalytic cleavage.", "Our data also provide a molecular explanation on how SPRTN deficiency causes the premature aging and cancer predisposition disorder Ruijs-Aalfs syndrome."], "structured": false}
{"doc_id": 34198460, "title": "'Zero is not good for me': implications of infertility in Ghana.", "abstract": ["BACKGROUND Given the high value placed on children in sub-Saharan Africa, previous research suggests that infertility increases the risk of psychological distress and marital conflict, encourages risky sexual behavior and deprives infertile individuals and couples of an important source of economic and social capital.", "This paper explores the implications of infertility for women in Ghana, West Africa.   \n", "METHODS Semi-structured interview data collected from 107 women (aged 21-48 years, mean 33 years) seeking treatment in gynecological and obstetric clinics in Accra, Ghana, are analyzed.", "Based on iterative open coding of the interviews, the focus of the analysis is on mental health, marital instability, social interaction and gendered experiences.   \n", "RESULTS Infertile women report facing severe social stigma, marital strain and a range of mental health difficulties.", "Many women feel that they shoulder a disproportionate share of the blame for infertility and, by extension, face greater social consequences than male partners for difficulties conceiving.", "Women who do not self-identify as infertile corroborate these findings, asserting that the social consequences of infertility are severe, particularly for women.   \n", "CONCLUSIONS Infertility in Ghana has important consequences for social interactions, marital stability and mental health.", "These consequences are not perceived to be shared equally by Ghanaian men."], "structured": true}
{"doc_id": 34208005, "title": "Ethical dilemmas in a randomized trial of asthma treatment: can Bayesian statistical analysis explain the results?", "abstract": ["OBJECTIVES The original objective was to determine whether the use of bilevel positive airway pressure (BiPAP) ventilation would reduce the need for endotracheal intubation, the length of hospital stay, and hospital charges in patients with status asthmaticus.", "The development of physician treatment bias made patient enrollment difficult.", "The article subsequently describes the use of Bayesian statistics to explain study results when this bias occurs.   \n", "METHODS This study was a prospective, randomized controlled clinical trial conducted over a 34.5-month period at an urban university hospital with an emergency department census of 94,000 annual visits.", "Patients remaining in status asthmaticus after initial standard treatment with inhaled beta-agonists and steroids were randomized to receive BiPAP ventilation plus standard treatment versus standard treatment alone (non-BiPAP), with intubation for either group as needed.", "Patients with concurrent cardiac or other pulmonary diseases were excluded.", "The primary outcome measures were endotracheal intubation rate and length of hospital stay.", "Secondary outcome measures included vital signs (respiratory rate, pulse rate, blood pressure), changes in expiratory peak flow, changes in pulse oximetry values, and hospital charges.", "Data were analyzed using Fisher's exact test, Mann-Whitney tests, and Bayesian statistics.", "For patients enrolled in the study more than once, data analysis was performed on the first enrollment only.   \n", "RESULTS Nineteen patients were enrolled in the BiPAP group and 16 patients in the non-BiPAP group.", "Patients were frequently enrolled more than once and the data from the subsequent enrollments were excluded from the analysis.", "A marked decrease in enrollment, due to physician treatment bias, led to a premature termination of the study.", "Demographics showed that the groups were similar in age, sex, initial peak flow rate, and arterial blood gas measurements.", "There was a 7.3% increase (95% CI = -22 to +45) in the intubation rate in the non-BiPAP group (n = 2) compared with that for the BiPAP group (n = 1).", "No significant difference was seen in length of hospital stay or hospital charges, although there was a favorable trend toward the BiPAP group.", "Complications encountered in the BiPAP group included one patient with discomfort associated with the nasal BiPAP mask.", "Bayesian analysis demonstrated that in order for the collected data to be convincing at the 95% confidence level, the prior conviction among treating physicians that BiPAP was a successful treatment modality would have had to be 98.9%.   \n", "CONCLUSIONS In this study, BiPAP appeared to have no deleterious effects in patients with status asthmaticus, with a trend toward decreased endotracheal intubation rate, decreased length of hospital stay, and decreased hospital charges.", "Although further study with more patients is needed to determine the clinical and statistical significance of this intervention, ethical concerns regarding withholding BiPAP treatment from the patients in the control group forced a premature termination of the study in the authors' institution."], "structured": true}
{"doc_id": 34227917, "title": "Mental health in prison populations. A review--with special emphasis on a study of Danish prisoners on remand.", "abstract": ["OBJECTIVE To review the literature on mental health and psychiatric morbidity in prison populations and relate findings to a Danish study on remand prisoners.   \n", "METHOD The literature is reviewed and subdivided in the following section: validity of psychometrics in prison populations, prevalence of psychiatric disorders prior to imprisonment, incidence of psychiatric disorders during imprisonment, psychopathy related to psychiatric comorbidity, dependence syndromes with special emphasis on different administrations of heroin use (smoke vs. injection).", "The results are compared with a longitudinal Danish study on remand prisoners in either solitary confinement (SC) or non-SC.   \n", "RESULTS Many factors must be taken into consideration when dealing with prisoners and mental health, e.g. international differences, the prison setting, demographics and methodological issues.", "The prison populations in general are increasing worldwide.", "Psychometrics may perform differently in prison populations compared with general populations with the General Health Questionnaire-28 having a low validity in remand prisoners.", "Psychiatric morbidity including schizophrenia is higher and perhaps increasing in prison populations compared with general populations with dependence syndromes being the most frequent disorders.", "The early phase of imprisonment is a vulnerable period with a moderately high incidence of adjustment disorders and twice the incidence in SC compared with non-SC.", "Prevalence of psychopathy is lower in European than North American prisons.", "Medium to high scores of psychopathy is related to higher psychiatric comorbidity.", "Opioid dependence is the most frequent drug disorder with subjects using injection representing a more dysfunctional group than subjects using smoke administration.", "Many mentally ill prisoners remain undetected and undertreated.   \n", "CONCLUSION There is a growing population of mentally ill prisoners being insufficiently detected and treated."], "structured": true}
{"doc_id": 34228604, "title": "Why females live longer than males: control of longevity by sex hormones.", "abstract": ["Females live longer than males in many species, including humans.", "We have traced a possible explanation for this phenomenon to the beneficial action of estrogens, which bind to estrogen receptors and increase the expression of longevity-associated genes, including those encoding the antioxidant enzymes superoxide dismutase and glutathione peroxidase.", "As a result, mitochondria from females produce fewer reactive oxygen species than those from males.", "Administering estrogens has serious drawbacks, however--they are feminizing (and thus cannot be administered to males) and may increase the incidence of serious diseases such as uterine cancer in postmenopausal women.", "Phytoestrogens, which are present in soy or wine, may have some of the favorable effects of estrogens without their undesirable effects.", "Study of gender differences in longevity may help us to understand the basic processes of aging and to devise practical strategies to increase the longevity of both females and males."], "structured": false}
{"doc_id": 34254203, "title": "The pre-B-cell receptor: selector of fitting immunoglobulin heavy chains for the B-cell repertoire", "abstract": ["In this Opinion article, I address the role of the pre-B-cell receptor (pre-BCR) in the development of antigen-specific B cells in terms of immunoglobulin heavy chain (IgH) variable-region repertoire selection, precursor B-cell differentiation and proliferation, and IgH allelic exclusion.", "Comparisons with the role of the pre-T-cell receptor (pre-TCR) in T-cell development raise provocative questions.", "Why do B- and T-cell lineages both use a surrogate chain \u2014 the surrogate light chain and the pre-TCR \u03b1-chain, respectively \u2014 as a step to develop their repertoires of antigen-recognizing cells?", "What are the functions of the pre-BCR and pre-TCR in lymphocyte differentiation and antigen-receptor allelic exclusion?", "This article, together with the accompanying article by Harald von Boehmer, hopes to answer some of these questions."], "structured": false}
{"doc_id": 34258065, "title": "Helicobacter species methods and protocols. Introduction.", "abstract": ["Helicobacter infection is a chronic persistent condition which is responsible for the majority of cases of gastric and duodenal ulcers, and gastric cancer.", "The study of the bacteria, the interaction of the bacteria with the host, and the host immune response has greatly benefited from standardization of culture techniques and animal models.", "The following chapters will describe the clinical aspects of infection and touch on the important techniques for optimal investigation of this infection."], "structured": false}
{"doc_id": 34268160, "title": "Effectiveness of statin-eluting stent on early inflammatory response and neointimal thickness in a porcine coronary model.", "abstract": ["BACKGROUND Drug-eluting stent (DES) implantation is routine during coronary revascularization because DES significantly reduce rates of restenosis and target lesion revascularization compared with bare metal stent (BMS).", "However, available DES have limitations, such as late thrombosis because of delayed healing with poorer endothelialization and persistent local inflammation.", "Statins can inhibit cell proliferation, inflammation, and restore endothelial function.", "The present study evaluated the ability of stent-based cerivastatin delivery to reduce stent-induced inflammatory responses and adverse effects on endothelial function, and to inhibit neointimal hyperplasia in a porcine coronary model.   \n", "METHODS AND RESULTS Pigs were randomized into groups in which the coronary arteries (9 pigs, 18 coronaries in each group) had either a cerivastatin-eluting stent (CES) or a BMS.", "All animals survived without any adverse effects.", "Inflammatory cell infiltration evaluated using scanning electron microscopy on day 3 after stenting was significantly decreased in the treated vessels (inflammation score: 1.15+/-0.12 vs 2.43+/-0.34, p<0.0001).", "At day 28, endothelial function with intracoronary infusion of bradykinin was preserved in both the CES and BMS groups.", "Volumetric intravascular ultrasound images revealed decreased intimal volume in the CES group (28.3+/-5.4 vs 75.9+/-4.2 mm3, p<0.0001).", "Histomorphometric analysis showed reduced neointimal area (1.74+/-0.45 vs 3.83+/-0.51 mm2, p<0.0001) in the CES group despite similar injury scores (1.77+/-0.30 vs 1.77+/-0.22, p=0.97).   \n", "CONCLUSION In porcine coronary arteries CES significantly decreased neointimal hyperplasia with a decreased early inflammatory response and without endothelial dysfunction."], "structured": true}
{"doc_id": 34287602, "title": "Genetic variation in West Nile virus from naturally infected mosquitoes and birds suggests quasispecies structure and strong purifying selection.", "abstract": ["Intrahost genetic diversity was analysed in naturally infected mosquitoes and birds to determine whether West Nile virus (WNV) exists in nature as a quasispecies and to quantify selective pressures within and between hosts.", "WNV was sampled from ten infected birds and ten infected mosquito pools collected on Long Island, NY, USA, during the peak of the 2003 WNV transmission season.", "A 1938 nt fragment comprising the 3' 1159 nt of the WNV envelope (E) coding region and the 5' 779 nt of the non-structural protein 1 (NS1) coding region was amplified and cloned and 20 clones per specimen were sequenced.", "Results from this analysis demonstrate that WNV infections are derived from a genetically diverse population of genomes in nature.", "The mean nucleotide diversity was 0.016 % within individual specimens and the mean percentage of clones that differed from the consensus sequence was 19.5 %.", "WNV sequences in mosquitoes were significantly more genetically diverse than WNV in birds.", "No host-dependent bias for particular types of mutations was observed and estimates of genetic diversity did not differ significantly between E and NS1 coding sequences.", "Non-consensus clones obtained from two avian specimens had highly similar genetic signatures, providing preliminary evidence that WNV genetic diversity may be maintained throughout the enzootic transmission cycle, rather than arising independently during each infection.", "Evidence of purifying selection was obtained from both intra- and interhost WNV populations.", "Combined, these data support the observation that WNV populations may be structured as a quasispecies and document strong purifying natural selection in WNV populations."], "structured": false}
{"doc_id": 34316341, "title": "Overlapping patterns of IGF2 and H19 expression during human development: biallelic IGF2 expression correlates with a lack of H19 expression.", "abstract": ["The spatial patterns of IGF2 and H19 gene expression are strikingly similar during parts of human embryonic/fetal and early postnatal development.", "Notable exceptions were found with the ciliary anlage of the embryonic retina and the choroid plexus/leptomeninges, where transcripts from the IGF2 but not the H19 locus could be detected.", "Moreover, in contrast to the other tissue samples examined, the choroid plexus/leptomeninges expressed both parental IGF2 alleles.", "Whilst RNase protection analysis revealed a weak activity of the P1 promoter in the choroid plexus/leptomeninges, the P2, P3 and P4 promoters were all active wherever IGF2 was expressed.", "We discuss these observations with respect to a hypothesized coordinated control of the reciprocally imprinted and closely linked IGF2 and H19 loci."], "structured": false}
{"doc_id": 34328964, "title": "Intimal smooth muscle cell proliferation after balloon catheter injury. The role of basic fibroblast growth factor.", "abstract": ["The localization and synthesis of basic fibroblast growth factor (bFGF) in the rat carotid artery were investigated at times of chronic smooth muscle cell proliferation.", "Immunocytochemical staining showed the presence of bFGF in the uninjured arterial wall, and after balloon injury, this cellular staining was decreased.", "Western and northern blot analyses likewise showed that the amount of bFGF protein and mRNA decreased after injury.", "A neutralizing antibody to bFGF was administered 4 and 5 days after injury and was found to have no effect on intimal smooth muscle cell proliferation.", "These data suggest that an increase in the expression of bFGF is not necessary for chronic smooth muscle cell proliferation observed after balloon catheter injury and that bFGF is not the major mitogen responsible for intimal smooth muscle cell proliferation."], "structured": false}
{"doc_id": 34338075, "title": "Prevention of central venous catheter-associated thrombosis: a meta-analysis.", "abstract": ["PURPOSE Anticoagulant prophylaxis in patients with central venous catheters is controversial.", "We performed a meta-analysis of randomized controlled trials of anticoagulant prophylaxis in patients with central venous catheters.   \n", "METHODS MEDLINE and EMBASE were searched up to May 2006, supplemented by manual searches of conference proceedings and bibliographies.   \n", "RESULTS Fifteen trials were included.", "Unfractionated heparin infusion, oral fixed low-dose vitamin K antagonist, and subcutaneous low-molecular-weight heparin were evaluated.", "For all catheter-associated deep vein thrombosis (symptomatic and asymptomatic combined), the summary relative risks ranged from 0.31 to 0.73 (all achieved statistical significance).", "For symptomatic deep vein thrombosis, the summary relative risks ranged from 0.28 to 0.72, but did not achieve statistical significance for any individual regimen.   \n", "CONCLUSION Anticoagulant prophylaxis is effective for preventing all catheter-associated deep vein thrombosis in patients with central venous catheters.", "The effectiveness for preventing symptomatic venous thromboembolism, including pulmonary embolism, remains uncertain."], "structured": true}
{"doc_id": 34369306, "title": "Long-term efficacy of nicotine replacement therapy for smoking cessation in adolescents: a randomized controlled trial.", "abstract": ["BACKGROUND A double-blind RCT on the short-term efficacy of nicotine patches compared to placebo patches among Dutch adolescents was conducted.", "The findings demonstrated that nicotine patches are efficacious for smoking cessation at end-of-treatment; however, only in highly compliant participants.", "We tested whether the effects of NRT also held in 6- (T7) and 12-month (T8) follow-up assessments.   \n", "METHODS Adolescents aged 12-18 years, who smoked at least seven cigarettes a day and who were motivated to quit smoking were recruited at school yards and randomly assigned to either a nicotine patch (n=182) or a placebo patch (n=180) condition according to a computer generated list.", "Participants (N=257, age: 16.7 \u00b1 1.13 years) attended an information meeting followed by a 6- or 9-week treatment.", "Smoking cessation, compliance, and potential covariates were measured by means of online questionnaires.", "Smoking cessation at T8 was biochemically validated by saliva cotinine.   \n", "RESULTS At T7, 8.1% and 5.7% of participants were abstinent in the nicotine and placebo patch groups, respectively.", "At T8, abstinence was 4.4% and 6.6%, respectively.", "Intention-to-treat analyses showed no significant effects of NRT on abstinence rates at T7 (OR=1.54, 95% CI=0.57, 4.16) and validated abstinence rates at T8 (OR=0.64, 95% CI=0.21, 1.93) neither after considering compliance nor after adjusting for covariates.   \n", "CONCLUSIONS NRT fails in helping adolescents quit smoking at 6- and 12-month follow-ups.", "This finding suggests that a more intensive approach is needed to assist youngsters in their quit attempts."], "structured": true}
{"doc_id": 34378726, "title": "Interferon gamma in autoimmunity: A complicated player on a complex stage.", "abstract": ["Early views of autoimmune disease cast IFN\u03b3 as a prototypic pro-inflammatory factor.", "It is now clear that IFN\u03b3 is capable of both pro- and anti-inflammatory activities with the functional outcome dependent on the physiological and pathological setting examined.", "Here, the major immune modulatory activities of IFN\u03b3 are reviewed and current evidence for the impact of IFN\u03b3 on pathology and regulation of several autoimmune diseases and disease models is summarized."], "structured": false}
{"doc_id": 34386619, "title": "The first gene of the Bacillus subtilis clpC operon, ctsR, encodes a negative regulator of its own operon and other class III heat shock genes.", "abstract": ["The Bacillus subtilis clpC operon is regulated by two stress induction pathways relying on either sigmaB or a class III stress induction mechanism acting at a sigmaA-like promoter.", "When the clpC operon was placed under the control of the isopropyl-beta-D-thiogalactopyranoside (IPTG)-inducible Pspac promoter, dramatic repression of the natural clpC promoters fused to a lacZ reporter gene was noticed after IPTG induction.", "This result strongly indicated negative regulation of the clpC operon by one of its gene products.", "Indeed, the negative regulator could be identified which is encoded by the first gene of the clpC operon, ctsR, containing a predicted helix-turn-helix DNA-binding motif.", "Deletion of ctsR abolished the negative regulation and resulted in high expression of both the clpC operon and the clpP gene under nonstressed conditions.", "Nevertheless, a further increase in clpC and clpP mRNA levels was observed after heat shock, even in the absence of sigmaB, suggesting a second induction mechanism at the vegetative promoter.", "Two-dimensional gel analysis and mRNA studies showed that the expression of other class III stress genes was at least partially influenced by the ctsR deletion.", "Studies with different clpC promoter fragments either fused to the reporter gene bgaB or used in gel mobility shift experiments with the purified CtsR protein revealed a possible target region where the repressor seemed to bind in vivo and in vitro.", "Our data demonstrate that the CtsR protein acts as a global repressor of the clpC operon, as well as other class III heat shock genes, by preventing unstressed transcription from either the sigmaB- or sigmaA-dependent promoter and might be inactivated or dissociate under inducing stress conditions."], "structured": false}
{"doc_id": 34436231, "title": "Role for c-myc in activation-induced apoptotic cell death in T cell hybridomas.", "abstract": ["Immature T cells and some T cell hybridomas undergo apoptotic cell death when activated through the T cell receptor complex, a phenomenon that is probably related to antigen induced negative selection of developing T cells.", "This activation-induced apoptosis depends on active protein and RNA synthesis in the dying cells, although none of the genes required for this process have previously been identified.", "Antisense oligonucleotides corresponding to c-myc block the constitutive expression of c-Myc protein in T cell hybridomas and interfere with all aspects of activation-induced apoptosis without affecting lymphokine production in these cells.", "These data indicate that c-myc expression is a necessary component of activation-induced apoptosis."], "structured": false}
{"doc_id": 34439544, "title": "Examining BCL-2 family function with large unilamellar vesicles.", "abstract": ["The BCL-2 (B cell CLL/Lymphoma) family is comprised of approximately twenty proteins that collaborate to either maintain cell survival or initiate apoptosis(1).", "Following cellular stress (e.g., DNA damage), the pro-apoptotic BCL-2 family effectors BAK (BCL-2 antagonistic killer 1) and/or BAX (BCL-2 associated X protein) become activated and compromise the integrity of the outer mitochondrial membrane (OMM), though the process referred to as mitochondrial outer membrane permeabilization (MOMP)(1).", "After MOMP occurs, pro-apoptotic proteins (e.g., cytochrome c) gain access to the cytoplasm, promote caspase activation, and apoptosis rapidly ensues(2).", "In order for BAK/BAX to induce MOMP, they require transient interactions with members of another pro-apoptotic subset of the BCL-2 family, the BCL-2 homology domain 3 (BH3)-only proteins, such as BID (BH3-interacting domain agonist)(3-6).", "Anti-apoptotic BCL-2 family proteins (e.g., BCL-2 related gene, long isoform, BCL-xL; myeloid cell leukemia 1, MCL-1) regulate cellular survival by tightly controlling the interactions between BAK/BAX and the BH3-only proteins capable of directly inducing BAK/BAX activation(7,8).", "In addition, anti-apoptotic BCL-2 protein availability is also dictated by sensitizer/de-repressor BH3-only proteins, such as BAD (BCL-2 antagonist of cell death) or PUMA (p53 upregulated modulator of apoptosis), which bind and inhibit anti-apoptotic members(7,9).", "As most of the anti-apoptotic BCL-2 repertoire is localized to the OMM, the cellular decision to maintain survival or induce MOMP is dictated by multiple BCL-2 family interactions at this membrane.", "Large unilamellar vesicles (LUVs) are a biochemical model to explore relationships between BCL-2 family interactions and membrane permeabilization(10).", "LUVs are comprised of defined lipids that are assembled in ratios identified in lipid composition studies from solvent extracted Xenopus mitochondria (46.5% phosphatidylcholine, 28.5% phosphatidylethanoloamine, 9% phosphatidylinositol, 9% phosphatidylserine, and 7% cardiolipin)(10).", "This is a convenient model system to directly explore BCL-2 family function because the protein and lipid components are completely defined and tractable, which is not always the case with primary mitochondria.", "While cardiolipin is not usually this high throughout the OMM, this model does faithfully mimic the OMM to promote BCL-2 family function.", "Furthermore, a more recent modification of the above protocol allows for kinetic analyses of protein interactions and real-time measurements of membrane permeabilization, which is based on LUVs containing a polyanionic dye (ANTS: 8-aminonaphthalene-1,3,6-trisulfonic acid) and cationic quencher (DPX: p-xylene-bis-pyridinium bromide)(11).", "As the LUVs permeabilize, ANTS and DPX diffuse apart, and a gain in fluorescence is detected.", "Here, commonly used recombinant BCL-2 family protein combinations and controls using the LUVs containing ANTS/DPX are described."], "structured": false}
{"doc_id": 34445160, "title": "The Hippo pathway effector YAP controls mouse hepatic stellate cell activation.", "abstract": ["BACKGROUND & AIMS Hepatic stellate cell activation is a wound-healing response to liver injury.", "However, continued activation of stellate cells during chronic liver damage causes excessive matrix deposition and the formation of pathological scar tissue leading to fibrosis and ultimately cirrhosis.", "The importance of sustained stellate cell activation for this pathological process is well recognized, and several signalling pathways that can promote stellate cell activation have been identified, such as the TGF\u03b2-, PDGF-, and LPS-dependent pathways.", "However, the mechanisms that trigger and drive the early steps in activation are not well understood.   \n", "METHODS AND RESULTS We identified the Hippo pathway and its effector YAP as a key pathway that controls stellate cell activation.", "YAP is a transcriptional co-activator and we found that it drives the earliest changes in gene expression during stellate cell activation.", "Activation of stellate cells in vivo by CCl4 administration to mice or activation in vitro caused rapid activation of YAP as revealed by its nuclear translocation and by the induction of YAP target genes.", "YAP was also activated in stellate cells of human fibrotic livers as evidenced by its nuclear localization.", "Importantly, knockdown of YAP expression or pharmacological inhibition of YAP prevented hepatic stellate cell activation in vitro and pharmacological inhibition of YAP impeded fibrogenesis in mice.   \n", "CONCLUSIONS YAP activation is a critical driver of hepatic stellate cell activation and inhibition of YAP presents a novel approach for the treatment of liver fibrosis."], "structured": true}
{"doc_id": 34469966, "title": "Human Monocytes Engage an Alternative Inflammasome Pathway.", "abstract": ["Interleukin-1\u03b2 (IL-1\u03b2) is a cytokine whose bioactivity is controlled by activation of the inflammasome.", "However, in response to lipopolysaccharide, human monocytes secrete IL-1\u03b2 independently of classical inflammasome stimuli.", "Here, we report that this constituted a species-specific response that is not observed in the murine system.", "Indeed, in human monocytes, lipopolysaccharide triggered an \"alternative inflammasome\" that relied on NLRP3-ASC-caspase-1 signaling, yet was devoid of any classical inflammasome characteristics including pyroptosome formation, pyroptosis induction, and K(+) efflux dependency.", "Genetic dissection of the underlying signaling pathway in a monocyte transdifferentiation system revealed that alternative inflammasome activation was propagated by TLR4-TRIF-RIPK1-FADD-CASP8 signaling upstream of NLRP3.", "Importantly, involvement of this signaling cascade was limited to alternative inflammasome activation and did not extend to classical NLRP3 activation.", "Because alternative inflammasome activation embraces both sensitivity and promiscuity of TLR4, we propose a pivotal role for this signaling cascade in TLR4-driven, IL-1\u03b2-mediated immune responses and immunopathology in humans."], "structured": false}
{"doc_id": 34481589, "title": "The use of biosimilars in immune-mediated disease: A joint Italian Society of Rheumatology (SIR), Italian Society of Dermatology (SIDeMaST), and Italian Group of Inflammatory Bowel Disease (IG-IBD) position paper.", "abstract": ["Biological agents are widely used in rheumatology, dermatology and inflammatory bowel disease.", "Evidence about their efficacy and safety has been strengthened for all those therapeutic indications over the last decade.", "Biosimilar agents are monoclonal antibodies similar to previously approved biologics.", "In the European Union, they have been approved for all the indications in the management of immune-mediated inflammatory diseases (IMIDs), although data only in rheumatoid arthritis and ankylosing spondylitis are currently available.", "Direct evidence on efficacy, safety, and immunogenicity of biosimilars is mandatory in psoriasis, psoriatic arthritis, and inflammatory bowel disease, as well as in children.", "Based on the current evidence in the literature, we present the joint official position of the Italian Societies of Rheumatology, Dermatology and Inflammatory Bowel Disease on the use of biosimilars in IMIDs."], "structured": false}
{"doc_id": 34498093, "title": "The coordination of cyclic microtubule association/dissociation and tail swing of cytoplasmic dynein.", "abstract": ["The dynein motor domain is composed of a tail, head, and stalk and is thought to generate a force to microtubules by swinging the tail against the head during its ATPase cycle.", "For this \"power stroke,\" dynein has to coordinate the tail swing with microtubule association/dissociation at the tip of the stalk.", "Although a detailed picture of the former process is emerging, the latter process remains to be elucidated.", "By using the single-headed recombinant motor domain of Dictyostelium cytoplasmic dynein, we address the questions of how the interaction of the motor domain with a microtubule is modulated by ATPase steps, how the two mechanical cycles (the microtubule association/dissociation and tail swing) are coordinated, and which ATPase site among the multiple sites in the motor domain regulates the coordination.", "Based on steady-state and pre-steady-state measurements, we demonstrate that the two mechanical cycles proceed synchronously at most of the intermediate states in the ATPase cycle: the motor domain in the poststroke state binds strongly to the microtubule with a K(d) of approximately 0.2 microM, whereas most of the motor domains in the prestroke state bind weakly to the microtubule with a K(d) of >10 microM. However, our results suggest that the timings of the microtubule affinity change and tail swing are staggered at the recovery stroke step in which the tail swings from the poststroke to the prestroke position.", "The ATPase site in the AAA1 module of the motor domain was found to be responsible for the coordination of these two mechanical processes."], "structured": false}
{"doc_id": 34498325, "title": "A conserved modified wobble nucleoside (mcm5s2U) in lysyl-tRNA is required for viability in yeast.", "abstract": ["Transfer RNAs specific for Gln, Lys, and Glu from all organisms (except Mycoplasma) and organelles have a 2-thiouridine derivative (xm(5)s(2)U) as wobble nucleoside.", "These tRNAs read the A- and G-ending codons in the split codon boxes His/Gln, Asn/Lys, and Asp/Glu.", "In eukaryotic cytoplasmic tRNAs the conserved constituent (xm(5)-) in position 5 of uridine is 5-methoxycarbonylmethyl (mcm(5)).", "A protein (Tuc1p) from yeast resembling the bacterial protein TtcA, which is required for the synthesis of 2-thiocytidine in position 32 of the tRNA, was shown instead to be required for the synthesis of 2-thiouridine in the wobble position (position 34).", "Apparently, an ancient member of the TtcA family has evolved to thiolate U34 in tRNAs of organisms from the domains Eukarya and Archaea.", "Deletion of the TUC1 gene together with a deletion of the ELP3 gene, which results in the lack of the mcm(5) side chain, removes all modifications from the wobble uridine derivatives of the cytoplasmic tRNAs specific for Gln, Lys, and Glu, and is lethal to the cell.", "Since excess of the unmodified form of these three tRNAs rescued the double mutant elp3 tuc1, the primary function of mcm(5)s(2)U34 seems to be to improve the efficiency to read the cognate codons rather than to prevent mis-sense errors.", "Surprisingly, overexpression of the mcm(5)s(2)U-lacking tRNA(Lys) alone was sufficient to restore viability of the double mutant."], "structured": false}
{"doc_id": 34537906, "title": "The molecular requirements for cytokinesis.", "abstract": ["After anaphase onset, animal cells build an actomyosin contractile ring that constricts the plasma membrane to generate two daughter cells connected by a cytoplasmic bridge.", "The bridge is ultimately severed to complete cytokinesis.", "Myriad techniques have been used to identify proteins that participate in cytokinesis in vertebrates, insects, and nematodes.", "A conserved core of about 20 proteins are individually involved with cytokinesis in most animal cells.", "These components are found in the contractile ring, on the central spindle, within the RhoA pathway, and on vesicles that expand the membrane and sever the bridge.", "Cytokinesis involves additional proteins, but they, or their requirement in cytokinesis, are not conserved among animal cells."], "structured": false}
{"doc_id": 34544514, "title": "Ibuprofen for the treatment of patent ductus arteriosus in preterm or low birth weight (or both) infants.", "abstract": ["BACKGROUND Indomethacin is used as standard therapy to close a patent ductus arteriosus (PDA) but is associated with reduced blood flow to several organs.", "Ibuprofen, another cyclo-oxygenase inhibitor, may be as effective as indomethacin with fewer adverse effects.   \n", "OBJECTIVES To determine the effectiveness and safety of ibuprofen compared with indomethacin, other cyclo-oxygenase inhibitor, placebo or no intervention for closing a patent ductus arteriosus in preterm, low birth weight, or preterm and low birth weight infants.   ", "SEARCH METHODS We searched The Cochrane Library, MEDLINE, EMBASE, Clincialtrials.gov, Controlled-trials.com, and www.abstracts2view.com/pas in May 2014.   ", "SELECTION CRITERIA Randomised or quasi-randomised controlled trials of ibuprofen for the treatment of a PDA in newborn infants.   \n", "DATA COLLECTION AND ANALYSIS Data collection and analysis conformed to the methods of the Cochrane Neonatal Review Group.   \n", "MAIN RESULTS We included 33 studies enrolling 2190 infants.", "Two studies compared intravenous (iv) ibuprofen versus placebo (270 infants).", "In one study (134 infants) ibuprofen reduced the incidence of failure to close a PDA (risk ratio (RR) 0.71, 95% confidence interval (CI) 0.51 to 0.99; risk difference (RD) -0.18, 95% CI -0.35 to -0.01; number needed to treat for an additional beneficial outcome (NNTB) 6, 95% CI 3 to 100).", "In one study (136 infants), ibuprofen reduced the composite outcome of infant mortality, infants who dropped out, or infants who required rescue treatment (RR 0.58, 95% CI 0.38 to 0.89; RD -0.22, 95% CI -0.38 to -0.06; NNTB 5, 95% CI 3 to 17).", "One study (64 infants) compared oral ibuprofen with placebo and noted a significant reduction in failure to close a PDA (RR 0.26, 95% CI 0.11 to 0.62; RD -0.44, 95% CI -0.65 to -0.23; NNTB 2, 95% CI 2 to 4).Twenty-one studies (1102 infants) reported failure rates for PDA closure with ibuprofen (oral or iv) compared with indomethacin (oral or iv).", "There was no significant difference between the groups (typical RR 1.00, 95% CI 0.84 to 1.20; I(2) = 0%; typical RD 0.00, 95% CI -0.05 to 0.05; I(2) = 0%).", "The risk of developing necrotising enterocolitis (NEC) was reduced for ibuprofen (16 studies, 948 infants; typical RR 0.64, 95% CI 0.45 to 0.93; typical RD -0.05, 95% CI -0.08 to -0.01; NNTB 20, 95% CI 13 to 100; I(2) = 0% for both RR and RD).", "The duration of ventilatory support was reduced with ibuprofen (oral or iv) compared with iv or oral indomethacin (six studies, 471 infants; mean difference (MD) -2.4 days, 95% CI -3.7 to -1.0; I(2) = 19%).Eight studies (272 infants) reported on failure rates for PDA closure in a subgroup of the above studies comparing oral ibuprofen with indomethacin (oral or iv).", "There was no significant difference between the groups (typical RR 0.96, 95% CI 0.73 to 1.27; typical RD -0.01, 95% CI -0.12 to 0.09).", "The risk of NEC was reduced with oral ibuprofen compared with indomethacin (oral or iv) (seven studies, 249 infants; typical RR 0.41, 95% CI 0.23 to 0.73; typical RD -0.13, 95% CI -0.22 to -0.05; NNTB 8, 95% CI 5 to 20; I(2) = 0% for both RR and RD).", "There was a decreased risk of failure to close a PDA with oral ibuprofen compared with iv ibuprofen (four studies, 304 infants; typical RR 0.41, 95% CI 0.27 to 0.64; typical RD -0.21, 95% CI -0.31 to -0.12; NNTB 5, 95% CI 3 to 8).", "Transient renal insufficiency was less common in infants who received ibuprofen compared with indomethacin.", "High dose versus standard dose of iv ibuprofen, early versus expectant administration of iv ibuprofen, echocardiographically guided iv ibuprofen treatment vs. standard iv ibuprofen treatment and continuous infusion of ibuprofen vs. intermittent boluses of ibuprofen and long-term follow-up were studied in too few trials to draw any conclusions.   ", "AUTHORS' CONCLUSIONS Ibuprofen is as effective as indomethacin in closing a PDA and currently appears to be the drug of choice.", "Ibuprofen reduces the risk of NEC and transient renal insufficiency.", "Oro-gastric administration of ibuprofen appears as effective as iv administration.", "To make further recommendations, studies are needed to assess the effectiveness of high-dose versus standard-dose ibuprofen, early versus expectant administration of ibuprofen, echocardiographically guided versus standard iv ibuprofen, and continuous infusion versus intermittent boluses of ibuprofen.", "Studies are lacking evaluating the effect of ibuprofen on longer-term outcomes in infants with PDA."], "structured": true}
{"doc_id": 34559336, "title": "A gradient of template dependence defines distinct biological roles for family X polymerases in nonhomologous end joining.", "abstract": ["Three Pol X family members have been linked to nonhomologous end joining (NHEJ) in mammals.", "Template-independent TdT promotes diversity during NHEJ-dependent repair of V(D)J recombination intermediates, but the roles of the template-dependent polymerases mu and lambda in NHEJ remain unclear.", "We show here that pol mu and pol lambda are similarly recruited by NHEJ factors to fill gaps when ends have partially complementary overhangs, suggesting equivalent roles promoting accuracy in NHEJ.", "However, only pol mu promotes accuracy during immunoglobulin kappa recombination.", "This distinctive in vivo role correlates with the TdT-like ability of pol mu, but not pol lambda, to act when primer termini lack complementary bases in the template strand.", "However, unlike TdT, synthesis by pol mu in this context is primarily instructed by a template from another DNA molecule.", "This apparent gradient of template dependence is largely attributable to a small structural element that is present but different in all three polymerases."], "structured": false}
{"doc_id": 34582256, "title": "Involvement of sympathetic nervous system and brown fat in endotoxin-induced fever in rats.", "abstract": ["The object of this study was to assess the role of brown adipose tissue (BAT) and the sympathetic nervous system in the rise in heat production associated with endotoxin-induced fever.", "Oxygen consumption (VO2) was found to be significantly increased (28%) over a 4-h period after two doses of endotoxin (Escherichia coli lipopolysaccharide, 0.3 mg/100 g body wt) given 24 h apart.", "Injection of a mixed beta-adrenoceptor antagonist (propranolol) reduced VO2 by 14% in endotoxin-treated rats, whereas the selective beta 1- (atenolol) or beta 2- (ICI 118551) antagonists suppressed VO2 by 10%.", "These drugs did not affect VO2 in control animals.", "BAT thermogenic activity assessed from measurements of in vitro mitochondrial guanosine 5'-diphosphate (GDP) binding was elevated by 54% in interscapular BAT and by 171% in other BAT depots.", "Surgical denervation of one lobe of the interscapular depot prevented these responses.", "Endotoxin failed to stimulate GDP binding in rats fed protein-deficient diets.", "This may have been because BAT thermogenic activity was already elevated in control rats fed these diets or because endotoxin caused a marked suppression of food intake in the protein-deficient animals.", "The results indicate that sympathetic activation of BAT is involved in the thermogenic responses to endotoxin and that these can be modified by dietary manipulation."], "structured": false}
{"doc_id": 34603465, "title": "Metabolic, Epigenetic, and Transgenerational Effects of Gut Bacterial Choline Consumption.", "abstract": ["Choline is an essential nutrient and methyl donor required for epigenetic regulation.", "Here, we assessed the impact of gut microbial choline metabolism on bacterial fitness and host biology by engineering a microbial community that lacks a single choline-utilizing enzyme.", "Our results indicate that choline-utilizing bacteria compete with the host for this nutrient, significantly impacting plasma and hepatic levels of methyl-donor metabolites and recapitulating biochemical signatures of choline deficiency.", "Mice harboring high levels of choline-consuming bacteria showed increased susceptibility to metabolic disease in the context of a high-fat diet.", "Furthermore, bacterially induced reduction of methyl-donor availability influenced global DNA methylation patterns in both adult mice and their offspring and engendered behavioral alterations.", "Our results reveal an underappreciated effect of bacterial choline metabolism on host metabolism, epigenetics, and behavior.", "This work suggests that interpersonal differences in microbial metabolism should be considered when determining optimal nutrient intake requirements."], "structured": false}
{"doc_id": 34604584, "title": "Genome-wide analysis reveals SR protein cooperation and competition in regulated splicing.", "abstract": ["SR proteins are well-characterized RNA binding proteins that promote exon inclusion by binding to exonic splicing enhancers (ESEs).", "However, it has been unclear whether regulatory rules deduced on model genes apply generally to activities of SR proteins in the cell.", "Here, we report global analyses of two prototypical SR proteins, SRSF1 (SF2/ASF) and SRSF2 (SC35), using splicing-sensitive arrays and CLIP-seq on mouse embryo fibroblasts (MEFs).", "Unexpectedly, we find that these SR proteins promote both inclusion and skipping of exons in vivo, but their binding patterns do not explain such opposite responses.", "Further analyses reveal that loss of one SR protein is accompanied by coordinated loss or compensatory gain in the interaction of other SR proteins at the affected exons.", "Therefore, specific effects on regulated splicing by one SR protein actually depend on a complex set of relationships with multiple other SR proteins in mammalian genomes."], "structured": false}
{"doc_id": 34615397, "title": "Human tuberculous granulomas induce peripheral lymphoid follicle-like structures to orchestrate local host defence in the lung.", "abstract": ["The human tuberculous granuloma provides the morphological basis for local immune processes central to the outcome of tuberculosis.", "Because of the scarcity of information in human patients, the aim of the present study was to gain insights into the functional and structural properties of infiltrated tissue.", "To this end, the mycobacterial load in lesions and dissemination to different tissue locations were investigated, as well as distribution, biological functions, and interactions of host immune cells.", "Analysis of early granuloma formation in formerly healthy lung tissue revealed a spatio-temporal sequence of cellular infiltration to sites of mycobacterial infection.", "A general structure of the developing granuloma was identified, comprising an inner cell layer with few CD8(+) cells surrounding the necrotic centre and an outer area of lymphocyte infiltration harbouring mycobacteria-containing antigen-presenting cells as well as CD4(+), CD8(+), and B cells in active follicle-like centres resembling secondary lymphoid organs.", "It is concluded that the follicular structures in the peripheral rim of granulomas serve as a morphological substrate for the orchestration of the enduring host response in pulmonary tuberculosis."], "structured": false}
{"doc_id": 34630025, "title": "Eosinophil pathogenicity mechanisms and therapeutics in neuromyelitis optica.", "abstract": ["Eosinophils are abundant in inflammatory demyelinating lesions in neuromyelitis optica (NMO).", "We used cell culture, ex vivo spinal cord slices, and in vivo mouse models of NMO to investigate the role of eosinophils in NMO pathogenesis and the therapeutic potential of eosinophil inhibitors.", "Eosinophils cultured from mouse bone marrow produced antibody-dependent cell-mediated cytotoxicity (ADCC) in cell cultures expressing aquaporin-4 in the presence of NMO autoantibody (NMO-IgG).", "In the presence of complement, eosinophils greatly increased cell killing by a complement-dependent cell-mediated cytotoxicity (CDCC) mechanism.", "NMO pathology was produced in NMO-IgG-treated spinal cord slice cultures by inclusion of eosinophils or their granule toxins.", "The second-generation antihistamines cetirizine and ketotifen, which have eosinophil-stabilizing actions, greatly reduced NMO-IgG/eosinophil-dependent cytotoxicity and NMO pathology.", "In live mice, demyelinating NMO lesions produced by continuous intracerebral injection of NMO-IgG and complement showed marked eosinophil infiltration.", "Lesion severity was increased in transgenic hypereosinophilic mice.", "Lesion severity was reduced in mice made hypoeosinophilic by anti-IL-5 antibody or by gene deletion, and in normal mice receiving cetirizine orally.", "Our results implicate the involvement of eosinophils in NMO pathogenesis by ADCC and CDCC mechanisms and suggest the therapeutic utility of approved eosinophil-stabilizing drugs."], "structured": false}
{"doc_id": 34733465, "title": "Association of cystic fibrosis with abnormalities in fatty acid metabolism.", "abstract": ["BACKGROUND Patients with cystic fibrosis have altered levels of plasma fatty acids.", "We previously demonstrated that arachidonic acid levels are increased and docosahexaenoic acid levels are decreased in affected tissues from cystic fibrosis-knockout mice.", "In this study we determined whether humans with mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene have a similar fatty acid defect in tissues expressing CFTR.   \n", "METHODS Fatty acids from nasal- and rectal-biopsy specimens, nasal epithelial scrapings, and plasma were analyzed from 38 subjects with cystic fibrosis and compared with results in 13 obligate heterozygotes, 24 healthy controls, 11 subjects with inflammatory bowel disease, 9 subjects with upper respiratory tract infection, and 16 subjects with asthma.   \n", "RESULTS The ratio of arachidonic to docosahexaenoic acid was increased in mucosal and submucosal nasal-biopsy specimens (P<0.001) and rectal-biopsy specimens (P=0.009) from subjects with cystic fibrosis and pancreatic sufficiency and subjects with cystic fibrosis and pancreatic insufficiency, as compared with values in healthy control subjects.", "In nasal tissue, this change reflected an increase in arachidonic acid levels and a decrease in docosahexaenoic acid levels.", "In cells from nasal mucosa, the ratio of arachidonic to docosahexaenoic acid was increased in subjects with cystic fibrosis (P<0.001), as compared with healthy controls, with values in obligate heterozygotes intermediate between these two groups (P<0.001).", "The ratio was not increased in subjects with inflammatory bowel disease.", "Subjects with asthma and those with upper respiratory tract infection had values intermediate between those in subjects with cystic fibrosis and those in healthy control subjects.   \n", "CONCLUSIONS These data indicate that alterations in fatty acids similar to those in cystic fibrosis-knockout mice are present in CFTR-expressing tissue from subjects with cystic fibrosis."], "structured": true}
{"doc_id": 34735369, "title": "Actin dynamics and cell-cell adhesion in epithelia.", "abstract": ["Recent advances in the field of intercellular adhesion highlight the importance of adherens junction association with the underlying actin cytoskeleton.", "In skin epithelial cells a dynamic feature of adherens junction formation involves filopodia, which physically project into the membrane of adjacent cells, catalyzing the clustering of adherens junction protein complexes at their tips.", "In turn, actin polymerization is stimulated at the cytoplasmic interface of these complexes.", "Although the mechanism remains unclear, the VASP/Mena family of proteins seems to be involved in organizing actin polymerization at these sites.", "In vivo, adherens junction formation appears to rely upon filopodia in processes where epithelial sheets must be physically moved closer to form stable intercellular connections, for example, in ventral closure in embryonic development or wound healing in the postnatal animal."], "structured": false}
{"doc_id": 34747208, "title": "Lamin A-dependent nuclear defects in human aging.", "abstract": ["Mutations in the nuclear structural protein lamin A cause the premature aging syndrome Hutchinson-Gilford progeria (HGPS).", "Whether lamin A plays any role in normal aging is unknown.", "We show that the same molecular mechanism responsible for HGPS is active in healthy cells.", "Cell nuclei from old individuals acquire defects similar to those of HGPS patient cells, including changes in histone modifications and increased DNA damage.", "Age-related nuclear defects are caused by sporadic use, in healthy individuals, of the same cryptic splice site in lamin A whose constitutive activation causes HGPS.", "Inhibition of this splice site reverses the nuclear defects associated with aging.", "These observations implicate lamin A in physiological aging."], "structured": false}
{"doc_id": 34753204, "title": "Zmpste24 deficiency in mice causes spontaneous bone fractures, muscle weakness, and a prelamin A processing defect.", "abstract": ["Zmpste24 is an integral membrane metalloproteinase of the endoplasmic reticulum.", "Biochemical studies of tissues from Zmpste24-deficient mice (Zmpste24(-/-)) have indicated a role for Zmpste24 in the processing of CAAX-type prenylated proteins.", "Here, we report the pathologic consequences of Zmpste24 deficiency in mice.", "Zmpste24(-/-) mice gain weight slowly, appear malnourished, and exhibit progressive hair loss.", "The most striking pathologic phenotype is multiple spontaneous bone fractures-akin to those occurring in mouse models of osteogenesis imperfecta.", "Cortical and trabecular bone volumes are significantly reduced in Zmpste24(-/-) mice.", "Zmpste24(-/-) mice also manifested muscle weakness in the lower and upper extremities, resembling mice lacking the farnesylated CAAX protein prelamin A. Prelamin A processing was defective both in fibroblasts lacking Zmpste24 and in fibroblasts lacking the CAAX carboxyl methyltransferase Icmt but was normal in fibroblasts lacking the CAAX endoprotease Rce1.", "Muscle weakness in Zmpste24(-/-) mice can be reasonably ascribed to defective processing of prelamin A, but the brittle bone phenotype suggests a broader role for Zmpste24 in mammalian biology."], "structured": false}
{"doc_id": 34760396, "title": "Human and other faeces as breeding media of the trachoma vector Musca sorbens.", "abstract": ["The fly Musca sorbens Wiedemann (Diptera: Muscidae) apparently transmits Chlamydia trachomatis, causing human trachoma.", "The literature indicates that M. sorbens breeds predominantly in isolated human faeces on the soil surface, but not in covered pit latrines.", "We sought to identify breeding media of M. sorbens in a rural Gambian village endemic for trachoma.", "Test breeding media were presented for oviposition on soil-filled buckets and monitored for adult emergence.", "Musca sorbens emerged from human (6/9 trials), calf (3/9), cow (3/9), dog (2/9) and goat (1/9) faeces, but not from horse faeces, composting kitchen scraps or a soil control (0/9 of each).", "After adjusting for mass of medium, the greatest number of flies emerged from human faeces (1426 flies/kg).", "Median time for emergence was 9 (inter quartile range = 8-9.75) days post-oviposition.", "Of all flies emerging from faeces 81% were M. sorbens.", "Male and female flies emerging from human faeces were significantly larger than those from other media, suggesting that they would be more fecund and live longer than smaller flies from other sources.", "Female flies caught from children's eyes were of a similar size to those from human faeces, but significantly larger than those from other media.", "We consider that human faeces are the best larval medium for M. sorbens, although some breeding also occurs in animal faeces.", "Removal of human faeces from the environment, through the provision of basic sanitation, is likely to greatly reduce fly density, eye contact and hence trachoma transmission, but if faeces of other animals are present M. sorbens will persist."], "structured": false}
{"doc_id": 34818263, "title": "Current Health and Environmental Status of the Maasai People in Sub-Saharan Africa", "abstract": ["As time passes, the AIDS pandemic continues to spike, affecting an estimated 38.6 million people worldwide.", "In response, a satellite health clinic is being d esigned by two Cal Poly students to serve the Maasai people living in the Kajiado district in Southern Kenya.", "The Maasai have traditionally lived as pastoralists, surviving off of their cattle with which they share their water, increasing the risk for contamination.", "However, as the population of Kenya increases, the land the Maasai have traditionally used for grazing is shrink\u00ad ing.", "For this reason, some have turned to farming to maintain their liveli\u00ad hood.", "These factors have contributed to the desertification and deforestation of their region.", "As the lifestyle of the Maasai evolves, they rely more on maize than meat and dairy products for their nutrients.", "All of these changes have contributed to the evolution of the Maasai culture.", "We will address these changes in order to better understand the Maasai, as well as highlight pos\u00ad sible further aid needed to support their survival."], "structured": false}
{"doc_id": 34846352, "title": "Identification and characterization of a widely expressed form of adenylyl cyclase.", "abstract": ["A novel mammalian adenylyl cyclase was identified by reverse transcription-polymerase chain reaction amplification using degenerate primers based on a conserved region of previously described adenylyl cyclases (Premont, R. T. (1994) Methods Enzymol. 238, 116-127).", "The full-length cDNA sequence obtained from mouse brain predicts a 1353-amino acid protein possessing a 12-membrane span topology, and containing two regions of high similarity with the catalytic domains of adenylyl cyclases.", "Comparison of this novel adenylyl cyclase with the eight previously described mammalian enzymes indicates that this type 9 adenylyl cyclase sequence is the most divergent, defining a sixth distinct subclass of mammalian adenylyl cyclases.", "The AC9 gene has been localized to human chromosome band 16p13.3-13.2.", "The 8.5-kb mRNA encoding the type 9 adenylyl cyclase is widely distributed, being readily detected in all tissues tested, and is found at very high levels in skeletal muscle and brain.", "AC9 mRNA is found throughout rat brain but is particularly abundant in hippocampus, cerebellum, and neocortex.", "An antiserum directed against the carboxyl terminus of the type 9 adenylyl cyclase detects native and expressed recombinant AC9 protein in tissue and cell membranes.", "Levels of the AC9 protein are highest in mouse brain membranes.", "Characterization of expressed recombinant AC9 reveals that the protein is a functional adenylyl cyclase that is stimulated by Mg2+, forskolin, and mutationally activated Gsalpha.", "AC9 activity is not affected by Ca2+/calmodulin or by G protein betagamma-subunits.", "Thus AC9 represents a functional G protein-regulated adenylyl cyclase found in brain and in most somatic tissues."], "structured": false}
{"doc_id": 34854444, "title": "Expression of Golli mRNA during development in primary immune lymphoid organs of the rat", "abstract": ["The gene-of-the-oligodendrocyte lineage (Golli)-MBP transcription unit contains three Golli-specific exons together with eight exons of the \"classical\" myelin basic protein (MBP) gene, yielding alternatively spliced proteins which share amino acid sequence with MBP.", "Unlike MBP, a late antigen expressed only in the nervous system, Golli gene products are expressed pre- and post-natally at many sites.", "In this study, we determined the sequence of Golli in rat by RT-PCR and 5' RACE and showed that Golli sequences are expressed in primary lymphoid organs as early as e16.5, which could explain the anergic rat T cell response we previously observed in Golli-induced meningitis."], "structured": false}
{"doc_id": 34873974, "title": "Diagnostic accuracy of single baseline measurement of Elecsys Troponin T high-sensitive assay for diagnosis of acute myocardial infarction in emergency department: systematic review and meta-analysis", "abstract": ["OBJECTIVE To obtain summary estimates of the accuracy of a single baseline measurement of the Elecsys Troponin T high-sensitive assay (Roche Diagnostics) for the diagnosis of acute myocardial infarction in patients presenting to the emergency department.   \n", "DESIGN Systematic review and meta-analysis of diagnostic test accuracy studies.   \n", "DATA SOURCES Medline, Embase, and other relevant electronic databases were searched for papers published between January 2006 and December 2013.   ", "STUDY SELECTION Studies were included if they evaluated the diagnostic accuracy of a single baseline measurement of Elecsys Troponin T high-sensitive assay for the diagnosis of acute myocardial infarction in patients presenting to the emergency department with suspected acute coronary syndrome.   ", "STUDY APPRAISAL AND DATA SYNTHESIS The first author screened all titles and abstracts identified through the searches and selected all potentially relevant papers.", "The screening of the full texts, the data extraction, and the methodological quality assessment, using the adapted QUADAS-2 tool, were conducted independently by two reviewers with disagreements being resolved through discussion or arbitration.", "If appropriate, meta-analysis was conducted using the hierarchical bivariate model.   \n", "RESULTS Twenty three studies reported the performance of the evaluated assay at presentation.", "The results for 14 ng/L and 3-5 ng/L cut-off values were pooled separately.", "At 14 ng/L (20 papers), the summary sensitivity was 89.5% (95% confidence interval 86.3% to 92.1%) and the summary specificity was 77.1% (68.7% to 83.7%).", "At 3-5 ng/L (six papers), the summary sensitivity was 97.4% (94.9% to 98.7%) and the summary specificity was 42.4% (31.2% to 54.5%).", "This means that if 21 of 100 consecutive patients have the target condition (21%, the median prevalence across the studies), 2 (95% confidence interval 2 to 3) of 21 patients with acute myocardial infarction will be missed (false negatives) if 14 ng/L is used as a cut-off value and 18 (13 to 25) of 79 patients without acute myocardial infarction will test positive (false positives).", "If the 3-5 ng/L cut-off value is used, <1 (0 to 1) patient with acute myocardial infarction will be missed and 46 (36 to 54) patients without acute myocardial infarction will test positive.   \n", "CONCLUSIONS The results indicate that a single baseline measurement of the Elecsys Troponin T high-sensitive assay could be used to rule out acute myocardial infarction if lower cut-off values such as 3 ng/L or 5 ng/L are used.", "However, this method should be part of a comprehensive triage strategy and may not be appropriate for patients who present less than three hours after symptom onset.", "Care must also be exercised because of the higher imprecision of the evaluated assay and the greater effect of lot-to-lot reagent variation at low troponin concentrations.   ", "SYSTEMATIC REVIEW REGISTRATION PROSPERO registration number CRD42013003926."], "structured": true}
{"doc_id": 34876410, "title": "Pericyte differentiation.", "abstract": ["Pericytes are defined in vivo by their location: They are embedded within the basement membrane of microvessels.", "They form an integral part of the microvascular wall and are believed to participate in angiogenesis, although their precise role is not clear.", "Pericytes derived from the retinal microvasculature have been cultured and identified by a series of phenotypic characteristics that clearly distinguishes them from other stromal cells such as smooth muscle cells.", "Pericytes in vitro form multicellular nodules rich in extracellular matrix.", "This matrix becomes mineralized in the presence of growth medium containing serum, without exogenous beta-glycerophosphate.", "These results indicate that pericytes represent primitive mesenchymal cells able to differentiate into an osteogenic phenotype.", "Pericyte differentiation also is defined by alterations in their response to transforming growth factor beta 1 and changes in the synthesis and/or deposition of various extracellular matrix proteins such as laminin, Type IV collagen, tenascin, Type X collagen osteonectin, and thrombospondin-1.", "Angiogenesis is associated commonly with mineralization.", "These data suggest that pericytes may contribute to mineralization in vivo."], "structured": false}
{"doc_id": 34905328, "title": "Membrane association of the CD3\u03b5 signaling domain is required for optimal T cell development and function.", "abstract": ["The TCR:CD3 complex transduces signals that are critical for optimal T cell development and adaptive immunity.", "In resting T cells, the CD3\u03b5 cytoplasmic tail associates with the plasma membrane via a proximal basic-rich stretch (BRS).", "In this study, we show that mice lacking a functional CD3\u03b5-BRS exhibited substantial reductions in thymic cellularity and limited CD4- CD8- double-negative (DN) 3 to DN4 thymocyte transition, because of enhanced DN4 TCR signaling resulting in increased cell death and TCR downregulation in all subsequent populations.", "Furthermore, positive, but not negative, T cell selection was affected in mice lacking a functional CD3\u03b5-BRS, which led to limited peripheral T cell function and substantially reduced responsiveness to influenza infection.", "Collectively, these results indicate that membrane association of the CD3\u03b5 signaling domain is required for optimal thymocyte development and peripheral T cell function."], "structured": false}
{"doc_id": 34935825, "title": "A new era in ovulation induction.", "abstract": ["OBJECTIVE To evaluate the efficacy of aromatase inhibitors in ovulation induction, superovulation, and IVF.   \n", "DESIGN A literature search was conducted with the key words \"aromatase inhibitor,\" \"letrozole,\" \"anastrazole,\" \"ovulation induction,\" \"ovulation,\" and \"superovulation\" in MEDLINE, EMBASE, and the Cochrane Database of systematic reviews.   \n", "RESULT(S) Ovulation induction with letrozole is associated with an ovulation rate of 70%-84% and a pregnancy rate of 20%-27% per cycle.", "In one study, ovulation and pregnancy rates with letrozole seemed to be higher than those of anastrazole.", "In superovulation, letrozole is associated with few developing follicles and thick endometrium.", "The use of letrozole for superovulation is associated with a pregnancy rate higher than with the use of clomiphene citrate (CC) (16.7% vs. 5.6%).", "The addition of letrozole to FSH treatment leads to a decreased FSH requirement.", "The pregnancy rate for treatment with letrozole and FSH was similar to that for FSH alone.   \n", "CONCLUSION(S) Aromatase inhibitors are as effective as or superior to CC in ovulation induction and in superovulation.", "Unlike CC, they do not carry an antiestrogenic effect on the endometrium.", "Given the advantages of aromatase inhibitors, they can be used to replace CC as ovulation-inducing drugs.", "Their role in IVF remains to be determined."], "structured": true}
{"doc_id": 34982259, "title": "Of lineage and legacy: the development of mammalian hematopoietic stem cells", "abstract": ["The hematopoietic system is one of the first complex tissues to develop in the mammalian conceptus.", "Of particular interest in the field of developmental hematopoiesis is the origin of adult bone marrow hematopoietic stem cells.", "Tracing their origin is complicated because blood is a mobile tissue and because hematopoietic cells emerge from many embryonic sites.", "The origin of the adult mammalian blood system remains a topic of lively discussion and intense research.", "Interest is also focused on developmental signals that induce the adult hematopoietic stem cell program, as these may prove useful for generating and expanding these clinically important cell populations ex vivo.", "This review presents a historical overview of and the most recent data on the developmental origins of hematopoiesis."], "structured": false}
{"doc_id": 35004872, "title": "Long crocidolite asbestos fibers cause polyploidy by sterically blocking cytokinesis.", "abstract": ["Asbestos has been described as a physical carcinogen in that its carcinogenic effects appear to be related primarily to fiber dimensions.", "It has been hypothesized that long asbestos fibers may interfere with chromosome distribution during cell division, causing genomic changes that lead to cell transformation and neoplastic progression.", "Using high-resolution time-lapse light microscopy and serial-section electron microscopy, we have followed individual crocidolite asbestos fibers through the later stages of cell division in LLC-MK2 epithelial cells, and have detailed for the first time their effect on cytokinesis.", "We found that long fibers (15-55 microgram), trapped by the cleavage furrow, sterically blocked cytokinesis, sometimes resulting in the formation of a binucleated cell.", "The ends of blocking fibers were usually found within invaginations of the newly formed nuclei.", "Nuclear envelope-fiber attachment was evident when a chromatin strand ran with the fiber into the intercellular bridge.", "Such strands may break, causing chromosome structural rearrangements.", "Our data are the first to show that individual crocidolite fibers can cause genomic changes by sterically blocking cytokinesis and that fiber length and affinity for the nuclear envelope are important factors.", "Such genomic changes may be among the initial events leading to asbestos-induced cancers."], "structured": false}
{"doc_id": 35008773, "title": "Neural induction and early patterning in vertebrates.", "abstract": ["In vertebrates, the development of the nervous system is triggered by signals from a powerful 'organizing' region of the early embryo during gastrulation.", "This phenomenon--neural induction--was originally discovered and given conceptual definition by experimental embryologists working with amphibian embryos.", "Work on the molecular circuitry underlying neural induction, also in the same model system, demonstrated that elimination of ongoing transforming growth factor-\u03b2 (TGF\u03b2) signaling in the ectoderm is the hallmark of anterior neural-fate acquisition.", "This observation is the basis of the 'default' model of neural induction.", "Endogenous neural inducers are secreted proteins that act to inhibit TGF\u03b2 ligands in the dorsal ectoderm.", "In the ventral ectoderm, where the signaling ligands escape the inhibitors, a non-neural fate is induced.", "Inhibition of the TGF\u03b2 pathway has now been demonstrated to be sufficient to directly induce neural fate in mammalian embryos as well as pluripotent mouse and human embryonic stem cells.", "Hence the molecular process that delineates neural from non-neural ectoderm is conserved across a broad range of organisms in the evolutionary tree.", "The availability of embryonic stem cells from mouse, primates, and humans will facilitate further understanding of the role of signaling pathways and their downstream mediators in neural induction in vertebrate embryos."], "structured": false}
{"doc_id": 35022568, "title": "What's in the 'treatment gap'? Ethnographic perspectives on addiction and global mental health from China, Russia, and the United States.", "abstract": ["Recent years have seen the emergence of a 'global mental health' agenda, focused on providing evidence-based interventions for mental illnesses in low- and middle-income countries.", "Anthropologists and cultural psychiatrists have engaged in vigorous debates about the appropriateness of this agenda.", "In this article, we reflect on these debates, drawing on ethnographic fieldwork on the management of substance use disorders in China, Russia, and the United States.", "We argue that the logic of 'treatment gaps,' which guides much research and intervention under the rubric of global mental health, partially obscures the complex assemblages of institutions, therapeutics, knowledges, and actors framing and managing addiction (as well as other mental health issues) in any particular setting."], "structured": false}
{"doc_id": 35062452, "title": "Generation of mice deficient in both KLF3/BKLF and KLF8 reveals a genetic interaction and a role for these factors in embryonic globin gene silencing.", "abstract": ["Kr\u00fcppel-like factors 3 and 8 (KLF3 and KLF8) are highly related transcriptional regulators that bind to similar sequences of DNA.", "We have previously shown that in erythroid cells there is a regulatory hierarchy within the KLF family, whereby KLF1 drives the expression of both the Klf3 and Klf8 genes and KLF3 in turn represses Klf8 expression.", "While the erythroid roles of KLF1 and KLF3 have been explored, the contribution of KLF8 to this regulatory network has been unknown.", "To investigate this, we have generated a mouse model with disrupted KLF8 expression.", "While these mice are viable, albeit with a reduced life span, mice lacking both KLF3 and KLF8 die at around embryonic day 14.5 (E14.5), indicative of a genetic interaction between these two factors.", "In the fetal liver, Klf3 Klf8 double mutant embryos exhibit greater dysregulation of gene expression than either of the two single mutants.", "In particular, we observe derepression of embryonic, but not adult, globin expression.", "Taken together, these results suggest that KLF3 and KLF8 have overlapping roles in vivo and participate in the silencing of embryonic globin expression during development."], "structured": false}
{"doc_id": 35079452, "title": "Mycobacterium tuberculosis phagosome maturation arrest: selective targeting of PI3P-dependent membrane trafficking.", "abstract": ["The ability of Mycobacterium tuberculosis to enter host macrophages, and reside in a phagosome, which does not mature into a phagolysosome, is central to the spread of tuberculosis and the associated pandemic involving billions of people worldwide.", "Tuberculosis can be viewed as a disease with a significant intracellular trafficking and organellar biogenesis component.", "Current understanding of the block in M. tuberculosis phagosome maturation also sheds light on fundamental aspects of phagolysosome biogenesis.", "The maturation block involves interference with the recruitment and function of rabs, rab effectors (phosphatidylinositol 3-kinases and tethering molecules such as EEA1), SNAREs (Syntaxin 6 and cellubrevin) and Ca2+/calmodulin signaling.", "M. tuberculosis analogs of mammalian phosphatidylinositols interfere with these systems and associated processes."], "structured": false}
{"doc_id": 35085326, "title": "SvpA, a novel surface virulence-associated protein required for intracellular survival of Listeria monocytogenes.", "abstract": ["A previously unknown protein, designated SvpA (surface virulence-associated protein) and implicated in the virulence of the intracellular pathogen Listeria monocytogenes, was identified.", "This 64 kDa protein, encoded by svpA, is both secreted in culture supernatants and surface-exposed, as shown by immunogold labelling of whole bacteria with an anti-SvpA antibody.", "Analysis of the peptide sequence revealed that SvpA contains a leader peptide, a predicted C-terminal transmembrane region and a positively charged tail resembling that of the surface protein ActA, suggesting that SvpA might partially reassociate with the bacterial surface by its C-terminal membrane anchor.", "An allelic mutant was constructed by disrupting svpA in the wild-type strain LO28.", "The virulence of this mutant was strongly attenuated in the mouse, with a 2 log decrease in the LD50 and restricted bacterial growth in organs as compared to the wild-type strain.", "This reduced virulence was not related either to a loss of adherence or to a lower expression of known virulence factors, which remained unaffected in the svpA mutant.", "It was caused by a restriction of intracellular growth of mutant bacteria.", "By following the intracellular behaviour of bacteria within bone-marrow-derived macrophages by confocal and electron microscopy studies, it was found that most svpA mutant bacteria remained confined within phagosomes, in contrast to wild-type bacteria which rapidly escaped to the cytoplasm.", "The regulation of svpA was independent of PrfA, the transcriptional activator of virulence genes in L. monocytogenes.", "In fact, SvpA was down-regulated by MecA, ClpC and ClpP, which are highly homologous to proteins of Bacillus subtilis forming a regulatory complex controlling the competence state of this saprophyte.", "The results indicate that: (i) SvpA is a novel factor involved in the virulence of L. monocytogenes, promoting bacterial escape from phagosomes of macrophages; (ii) SvpA is, at least partially, associated with the surface of bacteria; and (iii) SvpA is PrfA-independent and controlled by a MecA-dependent regulatory network."], "structured": false}
{"doc_id": 35087728, "title": "Measuring adherence to highly active antiretroviral therapy: implications for research and practice.", "abstract": ["Highly active antiretroviral therapy (HAART) has radically changed the course of HIV disease, producing substantial reductions in both HIV-related morbidity and mortality.", "However, the complexity of the typical daily HAART regimen is substantial, and high levels of adherence are essential for complete and long-term viral suppression and the avoidance of drug resistance.", "The complexity of HAART has made the assessment of medication adherence of paramount importance.", "Even though various methods are in use, each measures only a subset of adherence behaviors, and each measure has limited predictive validity.", "Given the individual and public health concerns associated with adherence to HAART, there is a need for the continued development and validation of measures of medication adherence."], "structured": false}
{"doc_id": 35100235, "title": "Survival rates of tropical and temperate passerines: a Trinidadian perspective.", "abstract": ["Mark-recapture data collected using mist nets over a 10-yr period in Trinidad were used to estimate adult survival rates for 17 species of forest passerines.", "Trinidadian survival rates (mean 65%, range 45%-85%) were significantly higher than published estimates for European (mean survival 52%, range 32%-71%) and North American (mean survival 53%, range 29%-63%) passerines of similar body size (equivalent to 45% higher mean life expectancy in Trinidad).", "These findings were confirmed after controlling for phylogeny using a method of independent contrasts.", "Transient and/or young birds were an important feature of the Trinidad data, and studies that fail to allow for the presence of such birds risk underestimating adult survival.", "This study lends support to the hypothesis that avian survival rates are higher in the humid tropics, although the magnitude of the difference may be smaller than previously suggested."], "structured": false}
{"doc_id": 35149431, "title": "P0 glycoprotein peptides 56\u201371 and 180\u2013199 dose-dependently induce acute and chronic experimental autoimmune neuritis in Lewis rats associated with epitope spreading", "abstract": ["Two synthetic peripheral nerve myelin P0 protein peptides, an immunodominant (amino acids 180-199) and a cryptic (amino acids 56-71) one, induced an acute or chronic course of experimental autoimmune neuritis (EAN) in Lewis rats, when given at low dose (50-100 microg/rat) or high dose (250 microg/rat), respectively.", "Corresponding to the different clinical course, pathological changes and immune responses were found: (1) Onset of clinical signs of P0 peptide 56-71 (P0 56-71) induced EAN was 1-3 days later than in P0 peptide 180-199 (P0 180-199) induced EAN at all immunizing doses, whereas the peak of the disease occurred at a similar time point post immunization (p.i.), i.e. at days 14-16 p.i.", "in P0 56-71 induced EAN and at day 16 p.i.", "in P0 180-199 induced EAN.", "(2) Intramolecular epitope spreading as assessed by delayed type hypersensitivity response occurred in P0 56-71 induced EAN at both low and high antigen doses and in P0 180-199 induced EAN at high antigen dose (250 microg/rat) only.", "(3) P0 180-199 stimulated higher levels of interferon-gamma production in P0 180-199 induced EAN than in P0 56-71 induced EAN and vice versa.", "(4) Histopathologic evaluation revealed a similar grade of mononuclear cell infiltration in the sciatic nerves of both types of EAN, but more severe demyelination was found in P0 180-199 induced EAN compared to P0 56-71 induced EAN.", "The results support the hypothesis that high dose autoantigen immunization induces extensive determinant spreading and chronic course of autoimmune diseases."], "structured": false}
{"doc_id": 35186640, "title": "Interaction between broad-spectrum antibiotics and the combined oral contraceptive pill. A literature review.", "abstract": ["There is considerable variation in opinion about the importance of drug interactions between the combined oral contraceptive pill (COCP) and broad-spectrum antibiotics.", "Clinical practice varies widely, especially between doctors in Europe and those in the US.", "Rifampicin and griseofulvin induce hepatic enzymes and do appear to have a genuine interaction with the COCP, leading to reduced efficacy.", "The situation with the broad-spectrum antibiotics is less clear.", "There are relatively few prospective studies of the pharmacokinetics of concurrent COCP and antibiotic use and few, if any, demonstrate a convincing basis for any reduced contraceptive efficacy.", "There is evidence, however, that variable contraceptive steroid handling could make some women, at some times, more susceptible to COCP failure.", "Given the serious consequences of unwanted pregnancy, the cautious approach of using additional or alternative contraception during short courses of broad-spectrum antibiotics and the initial weeks of long-term antibiotic administration may be justified to safeguard the few unidentifiable women who may be at risk.", "Conflicting opinion and advice is potentially confusing to both professionals and patients, and instructions for additional precautions during and after concurrent COCP and antibiotic use are complicated.", "Many women are ignorant of, or confused about, the circumstances that can cause OC to fail.", "Health professionals who prescribe the COCP must continue to strive to educate women about the mode of action and about the times when there is the greatest danger of failure.", "Professionals who feel that concurrent antibiotic use represents a real threat to contraceptive efficacy of the COCP should be prepared to present the advice for additional contraceptive precautions in a simple and consistent way, backed up with written information and reinforced at regular intervals."], "structured": false}
{"doc_id": 35231675, "title": "CLIP-170 interacts with dynactin complex and the APC-binding protein EB1 by different mechanisms.", "abstract": ["CLIP-170 is a \"cytoplasmic linker protein\" implicated in endosome-microtubule interactions and in control of microtubule dynamics.", "CLIP-170 localizes dynamically to growing microtubule plus ends, colocalizing with the dynein activator dynactin and the APC-binding protein EB1.", "This shared \"plus-end tracking\" behavior suggests that CLIP-170 might interact with dynactin and/or EB1.", "We have used site-specific mutagenesis of CLIP-170 and a transfection/colocalization assay to address this question in mammalian tissue culture cells.", "Our results indicate that CLIP-170 interacts, directly or indirectly, with both dynactin and EB1.", "We find that the CLIP-170/dynactin interaction is mediated by the second metal binding motif of the CLIP-170 tail.", "In contrast, the CLIP-170/EB1 interaction requires neither metal binding motif.", "In addition, our experiments suggest that the CLIP-170/dynactin interaction occurs via the shoulder/sidearm subcomplex of dynactin and can occur in the cytosol (i.e., it does not require microtubule binding).", "These results have implications for the targeting of both dynactin and EB1 to microtubule plus ends.", "Our data suggest that the CLIP-170/dynactin interaction can target dynactin complex to microtubule plus ends, although dynactin likely also targets MT plus ends directly via the microtubule binding motif of the p150(Glued) subunit.", "We find that CLIP-170 mutants alter p150(Glued) localization without affecting EB1, indicating that EB1 can target microtubule plus ends independently of dynactin."], "structured": false}
{"doc_id": 35256900, "title": "Subcapsular encounter and complement-dependent transport of immune complexes by lymph node B cells", "abstract": ["The mechanism of B cell\u2013antigen encounter in lymphoid tissues is incompletely understood.", "It is also unclear how immune complexes are transported to follicular dendritic cells.", "Here, using real-time two-photon microscopy we noted rapid delivery of immune complexes through the lymph to macrophages in the lymph node subcapsular sinus.", "B cells captured immune complexes by a complement receptor\u2013dependent mechanism from macrophage processes that penetrated the follicle and transported the complexes to follicular dendritic cells.", "Furthermore, cognate B cells captured antigen-containing immune complexes from macrophage processes and migrated to the T zone.", "Our findings identify macrophages lining the subcapsular sinus as an important site of B cell encounter with immune complexes and show that intrafollicular B cell migration facilitates the transport of immune complexes as well as encounters with cognate antigen."], "structured": false}
{"doc_id": 35271381, "title": "Exercise training-induced adaptations in the coronary circulation.", "abstract": ["Aerobic exercise training induces an increase in coronary blood flow capacity that is associated with altered control of coronary vascular resistance and, therefore, coronary blood flow.", "The relative importance of metabolic, myogenic, endothelium-mediated, and neurohumoral control systems varies throughout the coronary arterial tree, and these control systems contribute in parallel to regulating coronary vascular resistance to differing degrees at each level in the coronary arterial tree.", "In addition to this nonuniformity of the relative importance of vascular control systems in the coronary arterial tree, it appears that exercise training-induced adaptations are also distributed spatially, in a nonuniform manner throughout the coronary tree.", "As a result, it is necessary to examine training-induced adaptations throughout the coronary arterial tree.", "Adaptations in endothelium-mediated control play a role in training-induced changes in control of coronary vascular resistance, and there is evidence that the effects of training may be different in large coronary arteries than in the microcirculation.", "Also, there is evidence that the mode, frequency, and intensity of exercise training bouts and duration of training may influence the adaptive changes in endothelial function.", "Exercise training has also been shown to induce changes in responses of coronary vascular smooth muscle to vasoactive agents and alterations in the cellular-molecular control of intracellular Ca2+ in coronary vascular smooth muscle of conduit coronary arteries and to enhance myogenic reactivity of coronary resistance arteries.", "Exercise training also appears to have different effects on vascular smooth muscle in large coronary arteries than in the microcirculation.", "For example, adenosine sensitivity is increased in conduit coronary arteries and large resistance arteries after training but is not altered in small coronary resistance arteries of trained animals.", "Although much remains to be studied, evidence clearly indicates that chronic exercise alters the phenotype of coronary endothelial and vascular smooth muscle cells and that plasticity of these cells plays a role in adaptation of the cardiovascular system in exercise training."], "structured": false}
{"doc_id": 35301079, "title": "Hepatic intra-arterial versus intravenous fotemustine in patients with liver metastases from uveal melanoma (EORTC 18021): a multicentric randomized trial.", "abstract": ["BACKGROUND In uveal melanoma (UM) with metastatic disease limited to the liver, the effect of an intrahepatic treatment on survival is unknown.", "We investigated prospectively the efficacy and toxicity of hepatic intra-arterial (HIA) versus systemic (IV) fotemustine in patients with liver metastases from UM.   \n", "PATIENTS AND METHODS Patients were randomly assigned to receive either IV or HIA fotemustine at 100 mg/m(2) on days 1, 8, 15 (and 22 in HIA arm only) as induction, and after a 5-week rest period every 3 weeks as maintenance.", "Primary end point was overall survival (OS).", "Response rate (RR), progression-free survival (PFS) and safety were secondary end points.   \n", "RESULTS Accrual was stopped after randomization of 171 patients based on the results of a futility OS analysis.", "A total of 155 patients died and 16 were still alive [median follow-up 1.6 years (range 0.25-6 years)].", "HIA did not improve OS (median 14.6 months) when compared with the IV arm (median 13.8 months), hazard ratio (HR) 1.09; 95% confidence interval (CI) 0.79-1.50, log-rank P = 0.59.", "However, there was a significant benefit on PFS for HIA compared with IV with a median of 4.5 versus 3.5 months, respectively (HR 0.62; 95% CI 0.45-0.84, log-rank P = 0.002).", "The 1-year PFS rate was 24% in the HIA arm versus 8% in the IV arm.", "An improved RR was seen in the HIA (10.5%) compared with IV treatment (2.4%).", "In the IV arm, the most frequent grade \u22653 toxicity was thrombocytopenia (42.1%) and neutropenia (62.6%), compared with 21.2% and 28.7% in the HIA arm.", "The main grade \u22653 toxicity related to HIA was catheter complications (12%) and liver toxicity (4.5%) apart from two toxic deaths.   \n", "CONCLUSION HIA treatment with fotemustine did not translate into an improved OS compared with IV treatment, despite better RR and PFS.", "Intrahepatic treatment should still be considered as experimental.   ", "EUDRACT NUMBER AND CLINICALTRIALSGOV IDENTIFIER 2004-002245-12 and NCT00110123."], "structured": true}
{"doc_id": 35314705, "title": "Comparison of survival between cerebellar and supratentorial glioblastoma patients: surveillance, epidemiology, and end results (SEER) analysis.", "abstract": ["BACKGROUND Cerebellar glioblastoma multiforme (cGBM) is rare, and although there is a general belief that these tumors have a worse prognosis than supratentorial GBM (sGBM), few studies have been published to support this belief.   \n", "OBJECTIVE To investigate the effect of cerebellar location on survival through a case-control design comparing overall survival time of cGBM and sGBM patients.   \n", "METHODS The Surveillance, Epidemiology, and End Results (SEER) registry was used to identify 132 patients with cGBM (1973-2008).", "Each cGBM patient was matched with an sGBM patient from among 20,848 sGBM patients on the basis of age, extent of resection, decade of diagnosis, and radiation therapy using propensity score matching.   \n", "RESULTS Within the cGBM, 37% were older than 65 years of age, 62% were men, and 87% were white.", "Most patients underwent surgery and radiation (74%), whereas only 26% underwent surgical resection only.", "The median survival time for the cGBM and sGBM matched cohort was 8 months; however, the survival distributions differed (log-rank P = .04).", "Survival time for cGBM vs sGBM at 2 years was 21.5% vs 8.0%, and 12.7% vs 5.3% at 3 years.", "Multivariate analysis of survival among cGBM patients showed that younger age (P < .0001) and having radiation therapy (P < .0001) were significantly associated with reduced hazard of mortality.", "Among all patients, multivariate analysis showed that tumor location (P = .03), age (P < .0001), tumor size (P = .009), radiation (P < .0001), and resection (P < .0001) were associated with survival time in the unmatched cohort.   \n", "CONCLUSION Median survival time for cGBM and sGBM patients was 8 months, but cGBM patients had a survival time advantage as the study progressed.", "These findings suggest that cGBM patients should be treated as aggressively as sGBM patients with surgical resection and radiation therapy."], "structured": true}
{"doc_id": 35321950, "title": "Staphylococcus aureus and Candida albicans infection (animal experiments).", "abstract": ["During a certain period of the course of infection in white mice inoculated intraperitoneally with the pure culture of a proteolysing strain of Candida albicans, Staphylococcus aureus and C. albicans both, were isolated simultaneously from the peritoneal abscesses, especially those adhering to the stomach, duodenum, pancreas and the upper part of small intestine.", "This concommitant occurrence of the two pathogens was further corroborated by histopathological examination which revealed large number of staphylococci present in the close neighbourhood of Candida cells, usually in the center of the granulomata caused by the fungus.", "In view of the facts that the proteolytic end-products of C. albicans can offer a good substratum for the growth of S. aureus and the latter may be isolated from the intestinal tract of apparently healthy mice, possibly as a constituent of the transient microflora, the co-existence of these two important aetiologic agents of endogenous infections as encountered during this study appears to be of great clinical interest.", "Furthermore, these observations also demonstrate the importance of controlling the bacterial flora of mice for pure mycological studies."], "structured": false}
{"doc_id": 35329820, "title": "Three common functional polymorphisms in microRNA encoding genes in the susceptibility to hepatocellular carcinoma: a systematic review and meta-analysis.", "abstract": ["Emerging evidences have shown that common genetic polymorphisms in microRNAs may be associated with the development of hepatocellular carcinoma (HCC); but individually published studies and previous meta-analyses revealed inconclusive results.", "The aims of this review and meta-analysis are to assess whether common single-nucleotide polymorphisms (SNPs) in the genes encoding the microRNAs are associated with susceptibility to HCC development and clinicopathologic characteristics of hepatitis B virus (HBV) related HCC.", "A computerized search was performed in PubMed, Embase, Web of Science and China BioMedicine (CBM) databases to identify relevant articles published before January 1st 2013.", "Ten case-control studies were assessed with a total of 3437 cases and 3437 healthy controls.", "Three common functional SNPs in miRNA-encoding genes were found, including miR-146a G>C (rs2910164), miR-196a-2 C>T (rs11614913) and miR-499 T>C (rs3746444).", "This meta-analysis revealed that the miR-146a C variant was associated with a decrease in HCC risk, especially among Asian and male populations; while the miR-196a-2 T variant was associated with susceptibility to HCC among Caucasian populations.", "However, we failed to find any significant correlations between the miR-499 C polymorphism and HCC risks.", "When further stratification on HBV status was conducted, a similar trend of association between the three SNPs and the HBV-related HCC risks was observed, but these results were not statistically significant due to small sample sizes.", "The current meta-analysis demonstrates that SNPs contained in the genes encoding miR-146a and miR-196a-2 may play a major role in genetic susceptibility to HCC."], "structured": false}
{"doc_id": 35345807, "title": "Isonicotinamide enhances Sir2 protein-mediated silencing and longevity in yeast by raising intracellular NAD+ concentration.", "abstract": ["Sirtuins are an evolutionarily conserved family of NAD(+)-dependent protein deacetylases that function in the regulation of gene transcription, cellular metabolism, and aging.", "Their activity requires the maintenance of an adequate intracellular NAD(+) concentration through the combined action of NAD(+) biosynthesis and salvage pathways.", "Nicotinamide (NAM) is a key NAD(+) precursor that is also a byproduct and feedback inhibitor of the deacetylation reaction.", "In Saccharomyces cerevisiae, the nicotinamidase Pnc1 converts NAM to nicotinic acid (NA), which is then used as a substrate by the NAD(+) salvage pathway enzyme NA phosphoribosyltransferase (Npt1).", "Isonicotinamide (INAM) is an isostere of NAM that stimulates yeast Sir2 deacetylase activity in vitro by alleviating the NAM inhibition.", "In this study, we determined that INAM stimulates Sir2 through an additional mechanism in vivo, which involves elevation of the intracellular NAD(+) concentration.", "INAM enhanced normal silencing at the rDNA locus but only partially suppressed the silencing defects of an npt1\u0394 mutant.", "Yeast cells grown in media lacking NA had a short replicative life span, which was extended by INAM in a SIR2-dependent manner and correlated with increased NAD(+).", "The INAM-induced increase in NAD(+) was strongly dependent on Pnc1 and Npt1, suggesting that INAM increases flux through the NAD(+) salvage pathway.", "Part of this effect was mediated by the NR salvage pathways, which generate NAM as a product and require Pnc1 to produce NAD(+).", "We also provide evidence suggesting that INAM influences the expression of multiple NAD(+) biosynthesis and salvage pathways to promote homeostasis during stationary phase."], "structured": false}
{"doc_id": 35395662, "title": "Similar activation of signal transduction pathways by the herpesvirus-encoded chemokine receptors US28 and ORF74.", "abstract": ["The virally encoded chemokine receptors US28 from human cytomegalovirus and ORF74 from human herpesvirus 8 are both constitutively active.", "We show that both receptors constitutively activate the transcription factors nuclear factor of activated T cells (NFAT) and cAMP response element binding protein (CREB) and that both pathways are modulated by their respective endogenous receptor ligands.", "By addition of specific pathway modulators against the G protein subunit Galphai, phospholipase C, protein kinase C, calcineurin, p38 MAP kinase, and MEK1, we find that the constitutive and ligand-dependent inductions are mediated by multiple yet similar pathways in both receptors.", "The NFAT and CREB transcription factors and their upstream activators are known inducers of host and virally encoded genes.", "We propose that the activity of these virally encoded chemokine receptors coordinates host and potentially viral gene expression similarly.", "As ORF74 is a known inducer of neoplasia, these findings may have important implications for cytomegalovirus-associated pathogenicity."], "structured": false}
{"doc_id": 35443524, "title": "The therapeutic promise of the cancer stem cell concept.", "abstract": ["Cancer stem cells (CSCs) are a subpopulation of tumor cells that selectively possess tumor initiation and self-renewal capacity and the ability to give rise to bulk populations of nontumorigenic cancer cell progeny through differentiation.", "As we discuss here, they have been prospectively identified in several human malignancies, and their relative abundance in clinical cancer specimens has been correlated with malignant disease progression in human patients.", "Furthermore, recent findings suggest that clinical cancer progression driven by CSCs may contribute to the failure of existing therapies to consistently eradicate malignant tumors.", "Therefore, CSC-directed therapeutic approaches might represent translationally relevant strategies to improve clinical cancer therapy, in particular for those malignancies that are currently refractory to conventional anticancer agents directed predominantly at tumor bulk populations."], "structured": false}
{"doc_id": 35448676, "title": "3'-End processing of pre-mRNA in eukaryotes.", "abstract": ["3'-Ends of almost all eukaryotic mRNAs are generated by endonucleolytic cleavage and addition of a poly(A) tail.", "In mammalian cells, the reaction depends on the sequence AAUAAA upstream of the cleavage site, a degenerate GU-rich sequence element downstream of the cleavage site and stimulatory sequences upstream of AAUAAA.", "Six factors have been identified that carry out the two reactions.", "With a single exception, they have been purified to homogeneity and cDNAs for 11 subunits have been cloned.", "Some of the cooperative RNA-protein and protein-protein interactions within the processing complex have been analyzed, but many details, including the identity of the endonuclease, remain unknown.", "Several examples of regulated polyadenylation are being analyzed at the molecular level.", "In the yeast Saccharomyces cerevisiae, sequences directing cleavage and polyadenylation are more degenerate than in metazoans, and a downstream element has not been identified.", "The list of processing factors may be complete now with approximately a dozen polypeptides, but their functions in the reaction are largely unknown.", "3'-Processing is known to be coupled to transcription.", "This connection is thought to involve interactions of processing factors with the mRNA cap as well as with RNA polymerase II."], "structured": false}
{"doc_id": 35467590, "title": "Structure and developmental regulation of Golli-mbp, a 105-kilobase gene that encompasses the myelin basic protein gene and is expressed in cells in the oligodendrocyte lineage in the brain.", "abstract": ["We have identified a novel transcription unit of 105 kilobases (called the Golli-mbp gene) that encompasses the mouse myelin basic protein (MBP) gene.", "Three unique exons within this gene are alternatively spliced into MBP exons and introns to produce a family of MBP gene-related mRNAs that are under individual developmental regulation.", "These mRNAs are temporally expressed within cells of the oligodendrocyte lineage at progressive stages of differentiation.", "Thus, the MBP gene is a part of a more complex gene structure, the products of which may play a role in oligodendrocyte differentiation prior to myelination.", "One Golli-mbp mRNA that encodes a protein antigenically related to MBP is also expressed in the spleen and other non-neural tissues."], "structured": false}
{"doc_id": 35495268, "title": "Cardiovascular effects of intensive lifestyle intervention in type 2 diabetes.", "abstract": ["BACKGROUND Weight loss is recommended for overweight or obese patients with type 2 diabetes on the basis of short-term studies, but long-term effects on cardiovascular disease remain unknown.", "We examined whether an intensive lifestyle intervention for weight loss would decrease cardiovascular morbidity and mortality among such patients.   \n", "METHODS In 16 study centers in the United States, we randomly assigned 5145 overweight or obese patients with type 2 diabetes to participate in an intensive lifestyle intervention that promoted weight loss through decreased caloric intake and increased physical activity (intervention group) or to receive diabetes support and education (control group).", "The primary outcome was a composite of death from cardiovascular causes, nonfatal myocardial infarction, nonfatal stroke, or hospitalization for angina during a maximum follow-up of 13.5 years.   \n", "RESULTS The trial was stopped early on the basis of a futility analysis when the median follow-up was 9.6 years.", "Weight loss was greater in the intervention group than in the control group throughout the study (8.6% vs. 0.7% at 1 year; 6.0% vs. 3.5% at study end).", "The intensive lifestyle intervention also produced greater reductions in glycated hemoglobin and greater initial improvements in fitness and all cardiovascular risk factors, except for low-density-lipoprotein cholesterol levels.", "The primary outcome occurred in 403 patients in the intervention group and in 418 in the control group (1.83 and 1.92 events per 100 person-years, respectively; hazard ratio in the intervention group, 0.95; 95% confidence interval, 0.83 to 1.09; P=0.51).   \n", "CONCLUSIONS An intensive lifestyle intervention focusing on weight loss did not reduce the rate of cardiovascular events in overweight or obese adults with type 2 diabetes.", "(Funded by the National Institutes of Health and others; Look AHEAD ClinicalTrials.gov number, NCT00017953.)."], "structured": true}
{"doc_id": 35520219, "title": "Early loss of interneurons and delayed subunit-specific changes in GABA(A)-receptor expression in a mouse model of mesial temporal lobe epilepsy.", "abstract": ["Unilateral injection of kainic acid (KA) into the dorsal hippocampus of adult mice induces spontaneous recurrent partial seizures and replicates histopathological changes observed in human mesial temporal lobe epilepsy (MTLE) (Bouilleret V et al., Neuroscience 1999; 89:717-729).", "Alterations in pre- and postsynaptic components of GABAergic neurotransmission were investigated immunohistochemically at different time points (1-120 days) in this mouse model of MTLE.", "Markers of GABAergic interneurons (parvalbumin, calbindin-D28k, and calretinin), the type-1 GABA transporter (GAT1), and major GABA(A)-receptor subunits expressed in the hippocampal formation were analyzed.", "Acutely, KA injection produced a profound loss of hilar cells but only limited damage to CA1 and CA3 pyramidal cells.", "In addition, parvalbumin and calbindin-D28k staining of interneurons disappeared irreversibly in CA1 and dentate gyrus (DG), whereas calretinin staining was spared.", "The prominent GABA(A)-receptor alpha1 subunit staining of interneurons also disappeared after KA treatment, suggesting acute degeneration of these cells.", "Likewise, GAT1 immunoreactivity revealed degenerating terminals at 24 h post-KA in CA1 and DC and subsided almost completely thereafter.", "Loss of CA1 and, to a lesser extent, CA3 neurons became evident at 7-15 days post-KA.", "It was more accentuated after 1 month, accompanied by a corresponding reduction of GABA(A)-receptor staining.", "In contrast, DC granule cells were markedly enlarged and dispersed in the molecular layer and exhibited a prominent increase in GABA(A)-receptor subunit staining.", "After 4 months, the dorsal CA1 area was lost almost entirely, CA3 was reduced, and the DG represented most of the remaining dorsal hippocampal formation.", "No significant morphological alterations were detected contralaterally.", "These results suggest that loss of hilar cells and GABAergic neurons contributes to epileptogenesis in this model of MTLE.", "In contrast, long-term degeneration of pyramidal cells and granule cell dispersion may reflect distinct responses to recurrent seizures.", "Finally, GABA(A)-receptor upregulation in the DG may represent a compensatory response persisting for several months in epileptic mice."], "structured": false}
{"doc_id": 35521287, "title": "Cardiorespiratory adaptation during sleep in infants and children.", "abstract": ["The cardiorespiratory control system undergoes functional maturation after birth.", "Until this process is completed, the cardiorespiratory system is unstable, placing infants at risk for cardiorespiratory disturbances, especially during sleep.", "The profound influence of states of alertness on respiratory and cardiac control has been the focus of intense scrutiny during the last decade.", "The effects of rapid-eye movement (REM) sleep on various mechanisms involved in cardiorespiratory control are of particular significance during the postnatal period since newborns spend much of their time in this sleep state.", "In fullterm newborns, REM sleep occupies more than 50% of total sleep time, and this percentage is even greater in preterm newborns.", "From term to six months of age, the proportion of REM sleep decreases.", "Since respiratory and cardiac disturbances are known to occur selectively during REM sleep, the predominance of REM sleep may be a risk factor for abnormal sleep-related events during early infancy.", "Awareness of these developmental changes in sleep patterns is important for clinicians dealing with problems such as apparent life-threatening events (ALTE), sudden infant death syndrome (SIDS), and/or cardiorespiratory responses to respiratory disorders.", "Our current understanding of respiratory and cardiac control rests mainly on studies conducted during the first months of life.", "There is a paucity of data on late infancy and early childhood.", "The present paper will review available data on how sleep affects 1) ventilatory mechanics, in particular of the upper airways and the chest wall; ventilation and apnea; gas exchange; chemoreceptor function; and arousal responses; 2) changes in heart rate and heart rate variability, and the occurrence and mechanisms of bradycardia."], "structured": false}
{"doc_id": 35531883, "title": "A Common Signal Patch Drives AP-1 Protein-dependent Golgi Export of Inwardly Rectifying Potassium Channels.", "abstract": ["Nearly all members of the inwardly rectifying potassium (Kir) channel family share a cytoplasmic domain structure that serves as an unusual AP-1 clathrin adaptor-dependent Golgi export signal in one Kir channel, Kir2.1 (KCNJ2), raising the question whether Kir channels share a common Golgi export mechanism.", "Here we explore this idea, focusing on two structurally and functionally divergent Kir family members, Kir2.3 (KCNJ4) and Kir4.1/5.1 (KCNJ10/16), which have \u223c50% amino identity.", "We found that Golgi export of both channels is blocked upon siRNA-mediated knockdown of the AP-1 \u03b3 subunit, as predicted for the common AP-1-dependent trafficking process.", "A comprehensive mutagenic analysis, guided by homology mapping in atomic resolution models of Kir2.1, Kir2.3, and Kir4.1/5.1, identified a common structure that serves as a recognition site for AP-1 binding and governs Golgi export.", "Larger than realized from previous studies with Kir2.1, the signal is created by a patch of residues distributed at the confluence of cytoplasmic N and C termini.", "The signal involves a stretch of hydrophobic residues from the C-terminal region that form a hydrophobic cleft, an adjacent cluster of basic residues within the N terminus, and a potential network of salt bridges that join the N- and C-terminal poles together.", "Because patch formation and AP-1 binding are dependent on proper folding of the cytoplasmic domains, the signal provides a common quality control mechanism at the Golgi for Kir channels.", "These findings identify a new proteostatic mechanism that couples protein folding of channels to forward trafficking in the secretory pathway."], "structured": false}
{"doc_id": 35534019, "title": "Statins in the treatment of polycythaemia vera and allied disorders: an antithrombotic and cytoreductive potential?", "abstract": ["Thrombohaemorrhagic complications are major clinical problems in the classical chronic Ph-negative myeloproliferative disorders (CMPDs), polycytaemia vera (PV), essential thrombocythaemia (ET) and idiopathic myelofibrosis (IMF), contributing significantly to morbidity and mortality.", "Pathophysiologically these disorders are characterized by clonal myeloproliferation, myeloaccumulation and a propensity to develop myelofibrosis and neoangiogenesis in both the bone marrow and spleen.", "Based upon in vitro and in vivo studies of the effects of statins (antithrombotic, antiproliferative, proapoptotic and antiangiogenic), this review focuses on the translation of these effects into potential clinical benefits of statin therapy in patients with CMPDs."], "structured": false}
{"doc_id": 35543846, "title": "Metabolic analysis of senescent human fibroblasts reveals a role for AMP in cellular senescence.", "abstract": ["Cellular senescence is considered a major tumour-suppressor mechanism in mammals, and many oncogenic insults, such as the activation of the ras proto-oncogene, trigger initiation of the senescence programme.", "Although it was shown that activation of the senescence programme involves the up-regulation of cell-cycle regulators such as the inhibitors of cyclin-dependent kinases p16INK4A and p21CIP-1, the mechanisms underlying the senescence response remain to be resolved.", "In the case of stress-induced premature senescence, reactive oxygen species are considered important intermediates contributing to the phenotype.", "Moreover, distinct alterations of the cellular carbohydrate metabolism are known to contribute to oncogenic transformation, as is best documented for the phenomenon of aerobic glycolysis.", "These findings suggest that metabolic alterations are involved in tumourigenesis and tumour suppression; however, little is known about the metabolic pathways that contribute to these processes.", "Using the human fibroblast model of in vitro senescence, we analysed age-dependent changes in the cellular carbohydrate metabolism.", "Here we show that senescent fibroblasts enter into a metabolic imbalance, associated with a strong reduction in the levels of ribonucleotide triphosphates, including ATP, which are required for nucleotide biosynthesis and hence proliferation.", "ATP depletion in senescent fibroblasts is due to dysregulation of glycolytic enzymes, and finally leads to a drastic increase in cellular AMP, which is shown here to induce premature senescence.", "These results suggest that metabolic regulation plays an important role during cellular senescence and hence tumour suppression."], "structured": false}
{"doc_id": 35612665, "title": "Identification of an H2-M3-restricted Listeria epitope: implications for antigen presentation by M3.", "abstract": ["Using expression cloning, we have identified an H2-M3-restricted epitope of the intracellular bacterial pathogen Listeria monocytogenes.", "Picomolar concentrations of an amino-terminal N-formylated hexapeptide, fMIGWII, targeted cells for lysis by CD8+ cytotoxic T cells, while the nonformylated peptide was approximately 100-fold less active.", "The sequence of the 185 aa protein source of this epitope predicts a transmembrane protein that retains its N terminus and assumes an N(out)-C(in) topology.", "This membrane orientation offers an explanation for the protection of the epitope from deformylases present in the bacterial cell and suggests an explanation for the ability of phagocytes to present H2-M3-restricted bacterial epitopes via a vacuolar TAP-independent mechanism."], "structured": false}
{"doc_id": 35621259, "title": "High-resolution peripheral quantitative computed tomographic imaging of cortical and trabecular bone microarchitecture in patients with type 2 diabetes mellitus.", "abstract": ["CONTEXT Cross-sectional epidemiological studies have found that patients with type 2 diabetes mellitus (T2DM) have a higher incidence of certain fragility fractures despite normal or elevated bone mineral density (BMD).   \n", "OBJECTIVE In this study, high-resolution peripheral quantitative computed tomography was applied to characterize cortical and trabecular microarchitecture and biomechanics in the peripheral skeleton of female patients with T2DM.   \n", "DESIGN AND SETTING A cross-sectional study was conducted in patients with T2DM recruited from a diabetic outpatient clinic.   \n", "PARTICIPANTS Elderly female patients (age, 62.9 \u00b1 7.7 yr) with a history of T2DM (n = 19) and age- and height-matched controls (n = 19) were recruited.   \n", "OUTCOME MEASURES Subjects were imaged using high-resolution peripheral quantitative computed tomography at the distal radius and tibia.", "Quantitative measures of volumetric (BMD), cross-sectional geometry, trabecular and cortical microarchitecture were calculated.", "Additionally, compressive mechanical properties were determined by micro-finite element analysis.   \n", "RESULTS Compared to the controls, the T2DM cohort had 10% higher trabecular volumetric BMD (P < 0.05) adjacent to the cortex and higher trabecular thickness in the tibia (13.8%; P < 0.05).", "Cortical porosity differences alone were consistent with impaired bone strength and were significant in the radius (>+50%; P < 0.05), whereas pore volume approached significance in the tibia (+118%; P = 0.1).   \n", "CONCLUSION The results of this pilot investigation provide a potential explanation for the inability of standard BMD measures to explain the elevated fracture incidence in patients with T2DM.", "The findings suggest that T2DM may be associated with impaired resistance to bending loads due to inefficient redistribution of bone mass, characterized by loss of intracortical bone offset by an elevation in trabecular bone density."], "structured": true}
{"doc_id": 35651106, "title": "Critical role of CD28 in protective immunity against Salmonella typhimurium.", "abstract": ["Efficient T cell activation requires both TCR signals and costimulatory signals.", "CD28 is one of the molecules that provide costimulatory signals for T cells.", "We used mice deficient in CD28 expression (CD28-/- mice) to analyze the role of CD28 in the immune response against the intracellular bacterium Salmonella typhimurium, the causative agent of murine typhoid fever.", "CD28-/- mice were highly susceptible to infection with wild-type S. typhimurium and even failed to control infection with attenuated aroA- S. typhimurium.", "More detailed analysis revealed that CD28-/- animals did not mount a T-dependent Ab response and were highly impaired in the production of IFN-gamma.", "Thus, CD28 cosignaling is crucial for immunity against S. typhimurium.", "To our knowledge, this is the first report describing an essential role for CD28 in protective immunity against an intracellular microbial pathogen."], "structured": false}
{"doc_id": 35660758, "title": "D3 phosphoinositides and outside-in integrin signaling by glycoprotein IIb-IIIa mediate platelet actin assembly and filopodial extension induced by phorbol 12-myristate 13-acetate.", "abstract": ["Phorbol 12-myristate 13-acetate (PMA) uncaps a small number of the fast-growing (barbed) ends of actin filaments, thereby eliciting slow actin assembly and extension of filopodia in human blood platelets.", "These reactions, which also occur in response to immunologic perturbation of the integrin glycoprotein (GP) IIb-IIIa, are sensitive to the phosphoinositide 3-kinase inhibitor wortmannin.", "Platelets deficient in GPIIb-IIIa integrins or with GPIIb-IIIa function inhibited by calcium chelation or the peptide RGDS have diminished PMA responsiveness.", "The effects of PMA contrast with thrombin receptor stimulation by >/=5 microM thrombin receptor-activating peptide (TRAP), which causes rapid and massive wortmannin-insensitive actin assembly and lamellar and filopodial extension.", "However, we show here that wortmannin can inhibit filopod formation if the thrombin receptor is ligated using suboptimal doses (<1 microM) of TRAP.", "Phosphatidylinositol 3,4-bisphosphate inhibits actin filament severing and capping by human gelsolin in vitro.", "The findings implicate D3 polyphosphoinositides and integrin signaling in PMA-mediated platelet stimulation and implicate D3 containing phosphoinositides generated in response to protein kinase C activation and GPIIb-IIIa signaling as late-acting intermediates leading to filopodial actin assembly."], "structured": false}
{"doc_id": 35684881, "title": "`Gain of function' phenotype of tumor-derived mutant p53 requires the oligomerization/nonsequence-specific nucleic acid-binding domain", "abstract": ["Tumor-derived p53 mutants can transcriptionally activate a number of promoters of genes involved in cellular proliferation.", "For this transactivation, mutant p53 does not use the wild-type p53 DNA-binding site, suggesting a mechanism of transactivation that is independent of direct DNA binding.", "Here we describe our analysis of the domain requirements for mutant p53 to transactivate promoters of the human epidermal growth factor receptor (EGFR), human multiple drug resistance 1 (MDR-1) and human proliferating cell nuclear antigen (PCNA) genes.", "We also report the identification of a structural domain required for the `gain of function' property of mutant p53-281G.", "`Gain of function' is measured as the tumorigenicity (in nude mice) of 10(3) murine cells expressing mutant p53 constitutively.", "We have generated internal deletion mutants of p53-281G deleting conserved domains I, II, III, IV and V, individually.", "We have also generated one deletion mutant eliminating amino acids 100 through 300 that removes four of the five conserved domains (II\u2013V); another mutant, p53-281G del 393-327, deletes the oligomerization and nonsequence-specific nucleic acid-binding domains of p53.", "For the EGFR and MDR-1 promoters, all these mutants have significantly lower transactivation ability than intact p53-281G.", "These deletion mutants, however, significantly activated the pCNA promoter, suggesting that the mechanism of transactivation of the PCNA promoter is different from that of the EGFR and MDR-1 promoters.", "When expressed constitutively in 10(3) cells, p53-281G del 393-327 was found to be defective in inducing tumor formation in nude mice although intact p53-281G was very efficient.", "Thus, our results suggest that structural domains near the C-terminus are needed for `gain of function'."], "structured": false}
{"doc_id": 35711485, "title": "Banana contains a diverse array of endogenous badnaviruses.", "abstract": ["Banana streak disease is caused by several distinct badnavirus species, one of which is Banana streak Obino l'Ewai virus.", "Banana streak Obino l'Ewai virus has severely hindered international banana (Musa spp.)", "breeding programmes, as new hybrids are frequently infected with this virus, curtailing any further exploitation.", "This infection is thought to arise from viral DNA integrated in the nuclear genome of Musa balbisiana (B genome), one of the wild species contributing to many of the banana cultivars currently grown.", "In order to determine whether the DNA of other badnavirus species is integrated in the Musa genome, PCR-amplified DNA fragments from Musa acuminata, M. balbisiana and Musa schizocarpa, as well as cultivars 'Obino l'Ewai' and 'Klue Tiparot', were cloned.", "In total, 103 clones were sequenced and all had similarity to open reading frame III in the badnavirus genome, although there was remarkable variation, with 36 distinct sequences being recognized with less than 85 % nucleotide identity to each other.", "There was no commonality in the sequences amplified from M. acuminata and M. balbisiana, suggesting that integration occurred following the separation of these species.", "Analysis of rates of non-synonymous and synonymous substitution suggested that the integrated sequences evolved under a high degree of selective constraint as might be expected for a living badnavirus, and that each distinct sequence resulted from an independent integration event."], "structured": false}
{"doc_id": 35714909, "title": "Pregnancy in women with type 1 diabetes: have the goals of St. Vincent declaration been met concerning foetal and neonatal complications?", "abstract": ["OBJECTIVE In 1989 the St. Vincent declaration set a five-year target for approximating outcomes of pregnancies in women with diabetes to those of the background population.", "We investigated and quantified the risk of adverse pregnancy outcomes in pregnant women with type 1 diabetes (T1DM) to evaluate if the goals of the 1989 St. Vincent Declaration have been obtained concerning foetal and neonatal complications.   \n", "METHODS Twelve population-based studies published within the last 10 years with in total 14,099 women with T1DM and 4,035,373 women from the background population were identified.", "The prevalence of four foetal and neonatal complications was compared.   \n", "RESULTS In women with T1DM versus the background population, congenital malformations occurred in 5.0% (2.2-9.0) (weighted mean and range) versus 2.1% (1.5-2.9), relative risk (RR) = 2.4, perinatal mortality in 2.7% (2.0-6.6) versus 0.72% (0.48-0.9), RR = 3.7, preterm delivery in 25.2% (13.0-41.7) versus 6.0% (4.7-7.1), RR = 4.2 and delivery of large for gestational infants in 54.2% (45.1-62.5) versus 10.0%, RR = 4.5.", "Early pregnancy HbA1c was positively associated with adverse pregnancy outcomes.   \n", "CONCLUSION The risk of adverse pregnancy outcomes was two to five times increased in women with T1DM compared with the general population.", "The goals of the St. Vincent declaration have not been achieved."], "structured": true}
{"doc_id": 35724562, "title": "BP control and left ventricular hypertrophy regression in children with CKD.", "abstract": ["In adult patients with CKD, hypertension is linked to the development of left ventricular hypertrophy, but whether this association exists in children with CKD has not been determined conclusively.", "To assess the relationship between BP and left ventricular hypertrophy, we prospectively analyzed data from the Chronic Kidney Disease in Children cohort.", "In total, 478 subjects were enrolled, and 435, 321, and 142 subjects remained enrolled at years 1, 3, and 5, respectively.", "Echocardiograms were obtained 1 year after study entry and then every 2 years; BP was measured annually.", "A linear mixed model was used to assess the effect of BP on left ventricular mass index, which was measured at three different visits, and a mixed logistic model was used to assess left ventricular hypertrophy.", "These models were part of a joint longitudinal and survival model to adjust for informative dropout.", "Predictors of left ventricular mass index included systolic BP, anemia, and use of antihypertensive medications other than angiotensin-converting enzyme inhibitors or angiotensin receptor blockers.", "Predictors of left ventricular hypertrophy included systolic BP, female sex, anemia, and use of other antihypertensive medications.", "Over 4 years, the adjusted prevalence of left ventricular hypertrophy decreased from 15.3% to 12.6% in a systolic BP model and from 15.1% to 12.6% in a diastolic BP model.", "These results indicate that a decline in BP may predict a decline in left ventricular hypertrophy in children with CKD and suggest additional factors that warrant additional investigation as predictors of left ventricular hypertrophy in these patients."], "structured": false}
{"doc_id": 35747505, "title": "Nicotinic Acid Adenine Dinucleotide 2'-Phosphate (NAADP) Binding Proteins in T-Lymphocytes.", "abstract": ["Nicotinic acid adenine dinucleotide phosphate (NAADP) is a messenger that regulates calcium release from intracellular acidic stores.", "Although several channels, including two-pore channels (TPC), ryanodine receptor (RYR) and mucolipin (TRP-ML1) have been implicated in NAADP regulation of calcium signaling, the NAADP receptor has not been identified.", "In this study, the photoaffinity probe, [32P]-5-azido-NAADP ([32P]-5-N3-NAADP), was used to study NAADP binding proteins in extracts from NAADP responsive Jurkat T-lymphocytes.", "[32P]-5-N3-NAADP photolabeling of Jurkat S100 cytosolic fractions resulted in the labeling of at least ten distinct proteins.", "Several of these S100 proteins, including a doublet at 22/23 kDa and small protein at 15 kDa displayed selectivity for NAADP as the labeling was protected by inclusion of unlabeled NAADP, whereas the structurally similar NADP required much higher concentrations for protection.", "Interestingly, the labeling of several S100 proteins (60, 45, 33 and 28 kDa) was stimulated by low concentrations of unlabeled NAADP, but not by NADP.", "The effect of NAADP on the labeling of the 60 kDa protein was biphasic, peaking at 100 nM with a five-fold increase and displaying no change at 1 \u00b5M NAADP.", "Several proteins were also photolabeled when the P100 membrane fraction from Jurkat cells was examined.", "Similar to the results with S100, a 22/23 kDa doublet and a 15 kDa protein appeared to be selectively labeled.", "NAADP did not increase the labeling of any P100 proteins as it did in the S100 fraction.", "The photolabeled S100 and P100 proteins were successfully resolved by two-dimensional gel electrophoresis.", "[32P]-5-N3-NAADP photolabeling and two-dimensional electrophoresis should represent a suitable strategy in which to identify and characterize NAADP binding proteins."], "structured": false}
{"doc_id": 35760786, "title": "Loss of subcellular lipid transport due to ARV1 deficiency disrupts organelle homeostasis and activates the unfolded protein response.", "abstract": ["The ARV1-encoded protein mediates sterol transport from the endoplasmic reticulum (ER) to the plasma membrane.", "Yeast ARV1 mutants accumulate multiple lipids in the ER and are sensitive to pharmacological modulators of both sterol and sphingolipid metabolism.", "Using fluorescent and electron microscopy, we demonstrate sterol accumulation, subcellular membrane expansion, elevated lipid droplet formation, and vacuolar fragmentation in ARV1 mutants.", "Motif-based regression analysis of ARV1 deletion transcription profiles indicates activation of Hac1p, an integral component of the unfolded protein response (UPR).", "Accordingly, we show constitutive splicing of HAC1 transcripts, induction of a UPR reporter, and elevated expression of UPR targets in ARV1 mutants.", "IRE1, encoding the unfolded protein sensor in the ER lumen, exhibits a lethal genetic interaction with ARV1, indicating a viability requirement for the UPR in cells lacking ARV1.", "Surprisingly, ARV1 mutants expressing a variant of Ire1p defective in sensing unfolded proteins are viable.", "Moreover, these strains also exhibit constitutive HAC1 splicing that interacts with DTT-mediated perturbation of protein folding.", "These data suggest that a component of UPR induction in arv1\u0394 strains is distinct from protein misfolding.", "Decreased ARV1 expression in murine macrophages also results in UPR induction, particularly up-regulation of activating transcription factor-4, CHOP (C/EBP homologous protein), and apoptosis.", "Cholesterol loading or inhibition of cholesterol esterification further elevated CHOP expression in ARV1 knockdown cells.", "Thus, loss or down-regulation of ARV1 disturbs membrane and lipid homeostasis, resulting in a disruption of ER integrity, one consequence of which is induction of the UPR."], "structured": false}
{"doc_id": 35764259, "title": "IL-28, IL-29 and their class II cytokine receptor IL-28R", "abstract": ["Cytokines play a critical role in modulating the innate and adaptive immune systems.", "Here, we have identified from the human genomic sequence a family of three cytokines, designated interleukin 28A (IL-28A), IL-28B and IL-29, that are distantly related to type I interferons (IFNs) and the IL-10 family.", "We found that like type I IFNs, IL-28 and IL-29 were induced by viral infection and showed antiviral activity.", "However, IL-28 and IL-29 interacted with a heterodimeric class II cytokine receptor that consisted of IL-10 receptor \u03b2 (IL-10R\u03b2) and an orphan class II receptor chain, designated IL-28R\u03b1.", "This newly described cytokine family may serve as an alternative to type I IFNs in providing immunity to viral infection."], "structured": false}
{"doc_id": 35766603, "title": "High-dose recombinant tumor necrosis factor alpha in combination with interferon gamma and melphalan in isolation perfusion of the limbs for melanoma and sarcoma.", "abstract": ["PURPOSE To determine the toxicity and the therapeutic efficacy of the combination of the recombinant tumor necrosis factor alpha (rTNF alpha), recombinant interferon gamma (rIFN-gamma), and melphalan, we designed a protocol using isolation limb perfusion (ILP) with hyperthermia for in-transit metastases of melanoma and recurrent sarcoma.", "The triple combination was chosen because of the reported synergistic antitumor effect of rTNF alpha with IFN-gamma and of rTNF alpha with alkylating agents.   \n", "PATIENTS AND METHODS Twenty-three patients received a total of 25 ILPs with the triple combination.", "There were 19 females and four males with either multiple progressive in-transit melanoma metastases of the extremities (stage IIIa or IIIab; 19 patients) or recurrent soft tissue sarcoma (five).", "The rTNF alpha was injected as a bolus in the arterial line, and total dose ranged between 2 and 4 mg, under hyperthermic conditions (40 degrees C to 40.5 degrees C) for 90 minutes.", "The rIFN-gamma was given subcutaneously (SC) on days -2 and -1 and in the perfusate, with rTNF alpha at the dose of 0.2 mg.", "Melphalan (Alkeran; Burroughs Wellcome Co, London, England) was administered in the perfusate at 40 micrograms/mL.   RESULTS Toxicity observed during three ILPs in a pilot study with rTNF alpha included only two severe toxicities: one severe hypotension with tachycardia and transient oliguria and one moderate hypotension for 4 hours followed by severe kidney failure with complete recovery on day 29.", "In all 18 ILPs performed in the triple combination protocol, the patients received continuous infusion dopamine at 3 micrograms/kg/min from the start of ILP and for 72 hours and showed only mild hypotension and transient chills and temperature.", "Regional toxicity attributable to rTNF alpha was minimal.", "There have been 11 cases with hematologic toxicity consisting of neutropenia (one grade 4 and one grade 3) and neutropenia with thrombocytopenia (one grade 4 and three grade 2).", "Twelve patients had been previously treated with melphalan in ILP (11) or with cisplatin (one).", "The 23 patients are assessable: there have been 21 complete responses (CRs; range, 4 to 29 months; 89%), two partial responses (PRs; range, 2 to 3 months), and no failures.", "Overall disease-free survival and survival have been 70% and 76%, respectively, at 12 months.", "In all cases, softening of the nodules was obvious within 3 days after ILP and time to definite response ranged between day 5 and 30.   \n", "CONCLUSION This preliminary analysis of a phase II study suggests that high-dose rTNF alpha can be administered with acceptable toxicity by ILP with dopamine and hyperhydration.", "Tumor responses can be evidenced in melanoma and sarcoma.", "Furthermore, combination of rTNF alpha, rIFN-gamma, and melphalan seems to achieve high efficacy with minimal toxicity, even after failure of prior therapy with melphalan alone."], "structured": true}
{"doc_id": 35768199, "title": "Methanosphaera stadtmaniae gen. nov., sp. nov.: a species that forms methane by reducing methanol with hydrogen", "abstract": ["Methanosphaera stadtmaniae is a non-motile, Gram-positive spherical-shaped organism that obtains energy for growth by using hydrogen to reduce methanol to methane.", "It does not produce methane from hydrogen and carbon dioxide, formate, acetate or methylamines and cannot grow with hydrogen and carbon monoxide, nitrate, fumarate, sulfate or choline.", "Its pH optimum is 6.5 to 6.9 and its temperature optimum is 36\u00b0 to 40\u00b0 C. It is not inhibited by bile salts, inhibitors of the synthesis of folic acid coenzymes, cephalothin or clindamycin but is inhibited by metronidazole, bacitracin, monensin, lasalocid, or bromoethanesulfonate.", "It requires acetate, carbon dioxide, isoleucine, ammonium, and thiamin for growth and biotin is stimulatory.", "It does not contain cytochromes and the mol % G+C of its DNA is 25.8.", "The composition of its cell wall and 16 S rRNA and its immunological fingerprint are consistent with characterization of the organism as a member of a new genus of the family Methanobacteriaceae.", "The habitat of the type strain is the human large intestine."], "structured": false}
{"doc_id": 35777860, "title": "Generation of induced pluripotent stem cells from Asian patients with chronic neurodegenerative diseases.", "abstract": ["Induced pluripotent stem (iPS) cells derived from disease patients are an invaluable resource for biomedical research and may provide a source for replacement therapies.", "In this study, we have generated iPS cells from Asian patients with chronic degenerative diseases of the nervous system, including spinal muscular atrophy (SMA), Parkinson disease (PD) and amyotrophic lateral sclerosis (ALS) by transduction with four factors (KLF4, SOX2, OCT4 and c-MYC).", "All of the iPS cells showed pluripotency similar to that of human embryonic stem cells (hESCs) and were able to differentiate into various somatic cell types in vitro and in vivo.", "Furthermore, the iPS cells also can be committed to differentiate into neural cells, the cell type that is affected in chronic degenerative diseases.", "Therefore, the patient-specific iPS cells we generated offer a cellular model in which to investigate disease mechanisms, discover and test novel drugs and develop new therapies for chronic neurodegenerative diseases."], "structured": false}
{"doc_id": 35811036, "title": "Embryonic-like stem cell derived from adult bone marrow: immature morphology, cell surface markers, ultramicrostructure and differentiation into multinucleated fibers in vitro.", "abstract": ["Embryonic-like stem cell (ELSC), expressing part of surface markers of human embryonic stem cells, may be a better candidate for cell therapy of degenerative muscular disease than mesenchymal stem cell (MSC).", "We isolated ELSC and MSC from bone marrow, respectively, and compared their differences in the characteristics and the capacity of myogenic differentiation.", "Results showed that ELSC could be isolated successfully from 3 adult bone marrow samples by using serum-free medium with 10ng/ml basic fibroblast growth factor (bFGF).", "At the same cell density, MSC could also be isolated from the same samples by using DMEM/F12 medium containing 10% new cattle serum.", "However, ELSC appeared as small, morphologically slenderer, upregulated expression of SSEA-4 and ultramicroscopically more immature than MSC derived from the same samples.", "Immunofluorescent staining and RT-PCR analysis showed ELSC weakly expressed Oct-4, Nanog-3 and Sox-2.", "Moreover, ELSC and MSC could be induced into long, multinucleated fibers expressing myogenin and myosin heavy chain (MHC) in myogenic differentiation medium, but by day 10, proportion of multinucleated fibers positive for MHC was respectively 25.0%+/-6.9% and 13.8%+/-7.6% in ELSC and MSC culture.", "These data suggest that bone marrow derived ELSC represent an ideal candidate for cell therapy of degenerative muscular disease."], "structured": false}
{"doc_id": 35828148, "title": "Kinetic evidence for rapid oxidation of (-)-epicatechin by human myeloperoxidase.", "abstract": ["Apocynin has been reported to require dimerization by myeloperoxidase (MPO) to inhibit leukocyte NADPH oxidase.", "(-)-Epicatechin, a dietary flavan-3-ol, has been identified as a 'prodrug' of apocynin-like metabolites that inhibit endothelial NADPH oxidase activity and elevate the cellular level of nitric oxide.", "Since (-)-epicatechin has tentatively been identified as substrate of MPO, we studied the one-electron oxidation of (-)-epicatechin by MPO.", "By using multi-mixing stopped-flow technique, we demonstrate that (-)-epicatechin is one of the most efficient electron donors for heme peroxidases investigated so far.", "Second order rate constants for the (-)-epicatechin-mediated conversion of MPO-compound I to compound II and compound II to resting enzyme were estimated to be 1.9 x 10(7) and 4.5 x 10(6) M(-1)s(-1), respectively (pH 7, 25 degrees C).", "The data indicate that (-)-epicatechin is capable of undergoing fast MPO-mediated one-electron oxidation."], "structured": false}
{"doc_id": 35861290, "title": "Using the yeast gene deletion collection to customize gene expression.", "abstract": ["Substitute Teacher Despite the relative ease of genome manipulation in S. cerevisiae, researchers are always looking to learn still more convenient and rapid methods for substituting yeast promoters.", "Replacing a gene's native promoter with a heterolo-gous promoter of choice allows regulated expression and simplifies the task of discerning functional relevance.", "Although a host of clever chromosomal insertion strategies have been described over the years, the advent of the S. cerevisiae Genome Deletion Project provides an incredible resource for a further streamlined workflow.", "The strategy, explained by Liko et al. on p. 728 is appealingly simple.", "The genome deletion project resulted in a collection of strains in which a single ORF is replaced with a kanamycin resistance module.", "Although the purpose of the collection is to have a comprehensive resource of essentially all possible knockouts, the authors point out that for almost any given yeast promoter of interest there will be a strain in which the ORF imm..."], "structured": false}
{"doc_id": 35884026, "title": "Tyrosine phosphorylation and regulation of the AMPA receptor by SRC family tyrosine kinases.", "abstract": ["Phosphorylation of AMPA receptors is a major mechanism for the regulation of receptor function and underlies several forms of synaptic plasticity in the CNS.", "Although serine and threonine phosphorylation of AMPA receptors has been well studied, the potential role of tyrosine phosphorylation of AMPA receptors has not been investigated.", "Here, we show that the GluR2 subunit of AMPA receptors is tyrosine phosphorylated in vitro and in vivo by Src family tyrosine kinases on tyrosine 876 near its C terminus.", "In addition, GluR agonist treatment of cultured cortical neurons increased phosphorylation of tyrosine 876.", "The association with GluR2-interacting molecules GRIP1/2 was decreased by tyrosine phosphorylation of GluR2, whereas PICK1 interaction was not influenced.", "Moreover, mutation of tyrosine 876 eliminated AMPA- and NMDA-induced internalization of the GluR2 subunit.", "These data indicate that tyrosine phosphorylation of tyrosine 876 on the GluR2 C terminus by Src family tyrosine kinases is important for the regulation of AMPA receptor function and may be important for synaptic plasticity."], "structured": false}
{"doc_id": 35962023, "title": "tBid induces alterations of mitochondrial fatty acid oxidation flux by malonyl-CoA-independent inhibition of carnitine palmitoyltransferase-1", "abstract": ["Recent studies suggest a close relationship between cell metabolism and apoptosis.", "We have evaluated changes in lipid metabolism on permeabilized hepatocytes treated with truncated Bid (tBid) in the presence of caspase inhibitors and exogenous cytochrome c. The measurement of \u03b2-oxidation flux by labeled palmitate demonstrates that tBid inhibits \u03b2-oxidation, thereby resulting in the accumulation of palmitoyl-coenzyme A (CoA) and depletion of acetyl-carnitine and acylcarnitines, which is pathognomonic for inhibition of carnitine palmitoyltransferase-1 (CPT-1).", "We also show that tBid decreases CPT-1 activity by a mechanism independent of both malonyl-CoA, the key inhibitory molecule of CPT-1, and Bak and/or Bax, but dependent on cardiolipin decrease.", "Overexpression of Bcl-2, which is able to interact with CPT-1, counteracts the effects exerted by tBid on \u03b2-oxidation.", "The unexpected role of tBid in the regulation of lipid \u03b2-oxidation suggests a model in which tBid-induced metabolic decline leads to the accumulation of toxic lipid metabolites such as palmitoyl-CoA, which might become participants in the apoptotic pathway."], "structured": false}
{"doc_id": 35987381, "title": "CD8+ T cells are activated in an antigen-independent manner in HIV-infected individuals.", "abstract": ["Hyperactivation of T cells, particularly of CD8(+) T cells, is a hallmark of chronic HIV 1 (HIV-1) infection.", "Little is known about the antigenic specificities and the mechanisms by which HIV-1 causes activation of CD8(+) T cells during chronic infection.", "We report that CD8(+) T cells were activated during in vivo HIV-1 replication irrespective of their Ag specificity.", "Cytokines present during untreated HIV-1 infection, most prominently IL-15, triggered proliferation and expression of activation markers in CD8(+) T cells, but not CD4(+) T cells, in the absence of TCR stimulation.", "Moreover, LPS or HIV-1-activated dendritic cells (DCs) stimulated CD8(+) T cells in an IL-15-dependent but Ag-independent manner, and IL-15 expression was highly increased in DCs isolated from viremic HIV-1 patients, suggesting that CD8(+) T cells are activated by inflammatory cytokines in untreated HIV-1 patients independent of Ag specificity.", "This finding contrasts with CD4(+) T cells whose in vivo activation seems biased toward specificities for persistent Ags.", "These observations explain the higher abundance of activated CD8(+) T cells compared with CD4(+) T cells in untreated HIV-1 infection."], "structured": false}
{"doc_id": 35993767, "title": "Cancer-associated fibroblasts promote hepatocellular carcinoma metastasis through chemokine-activated hedgehog and TGF-\u03b2 pathways.", "abstract": ["Fibroblasts are rich in the surrounding microenvironment of hepatocellular carcinoma (HCC) because most HCCs occur in fibrotic or cirrhotic livers.", "However, the role of cancer-associated fibroblasts (CAFs) in HCC metastasis remains obscure.", "Here, we reported that CAFs promote the migration and invasion of HCC cells in vitro and facilitate the HCC metastasis to the bone, brain and lung in NOD/SCID mice.", "The RayBio human chemokine antibody array revealed that CAFs secret higher levels of CCL2, CCL5, CCL7 and CXCL16 than peri-tumor fibroblasts.", "CCL2 and CCL5 increase the migration but not the invasion of HCC cells, while CCL7 and CXCL16 promote both migration and invasion of HCC cells.", "Moreover, CCL2 and CCL5 stimulate the activation of the hedgehog (Hh) pathway, while CCL7 and CXCL16 enhance the activity of the transforming growth factor-\u03b2 (TGF-\u03b2) pathway in HCC cells.", "The neutralizing antibodies of chemokines notably attenuate the effect of CAFs on HCC metastasis and compromised the activation of Hh and TGF-\u03b2 pathways in HCC cells.", "In summary, CAF-secreted CCL2, CCL5, CCL7 and CXCL16 promote HCC metastasis through the coordinate activation of Hh and TGF-\u03b2 pathways in HCC cells."], "structured": false}
{"doc_id": 36003142, "title": "Mortality risk in patients with dementia treated with antipsychotics versus other psychiatric medications.", "abstract": ["OBJECTIVE Mortality rates in the year following new antipsychotic medication starts for neuropsychiatric symptoms of dementia were compared with rates after starts of other psychiatric medications.   \n", "METHOD The retrospective, cohort study used national data from the Department of Veterans Affairs (fiscal years 2001-2005) on patients older than 65 years who began outpatient treatment with psychiatric medication following a dementia diagnosis (N=10,615).", "Twelve-month mortality rates were compared in patients taking antipsychotics and those taking other psychiatric medications.", "The authors controlled for confounding by using multivariate models and propensity-scoring methods.", "Secondary analyses included a no-medication group and examination of mortality causes.   \n", "RESULTS All groups taking antipsychotics had significantly higher mortality rates (22.6%-29.1%) than patients taking nonantipsychotic medications (14.6%).", "Adjusted mortality risks for atypicals and for combined atypical and conventional antipsychotics were similar to those for conventional antipsychotics.", "The mortality risk was significantly lower for nonantipsychotic medications than conventional antipsychotics.", "Except for anticonvulsants, the adjusted risks for all individual classes of nonantipsychotics were significantly lower than the risk for antipsychotics.", "Mortality risks did not change over 12 months.", "The proportions of patients taking antipsychotics who died from cerebrovascular, cardiovascular, or infectious causes were not higher than rates for those taking nonantipsychotic psychiatric medications.   \n", "CONCLUSIONS Antipsychotic medications taken by patients with dementia were associated with higher mortality rates than were most other medications used for neuropsychiatric symptoms.", "The association between mortality and antipsychotics is not well understood and may be due to a direct medication effect or the pathophysiology underlying neuropsychiatric symptoms that prompt antipsychotic use."], "structured": true}
{"doc_id": 36025357, "title": "Glutathione: overview of its protective roles, measurement, and biosynthesis.", "abstract": ["This review is the introduction to a special issue concerning, glutathione (GSH), the most abundant low molecular weight thiol compound synthesized in cells.", "GSH plays critical roles in protecting cells from oxidative damage and the toxicity of xenobiotic electrophiles, and maintaining redox homeostasis.", "Here, the functions and GSH and the sources of oxidants and electrophiles, the elimination of oxidants by reduction and electrophiles by conjugation with GSH are briefly described.", "Methods of assessing GSH status in the cells are also described.", "GSH synthesis and its regulation are addressed along with therapeutic approaches for manipulating GSH content that have been proposed.", "The purpose here is to provide a brief overview of some of the important aspects of glutathione metabolism as part of this special issue that will provide a more comprehensive review of the state of knowledge regarding this essential molecule."], "structured": false}
{"doc_id": 36033696, "title": "A wellness class for inpatients with psychotic disorders.", "abstract": ["OBJECTIVE The purpose of this project was to educate inpatients with psychotic disorders, many of whom were taking second-generation antipsychotics, about lifestyle changes they can make to combat weight gain.   \n", "METHOD All inpatients on a Veterans Affairs acute inpatient schizophrenia treatment unit were invited to a 30-minute, didactic presentation given by a medical student and a psychology student under the supervision of the primary investigator.", "The topics covered included the health benefits of maintaining an ideal body weight by selecting foods according to the USDA Food Pyramid, determining adequate food portions, choosing healthy meals outside the home, and beginning and adhering to an exercise program.", "Subjects completed a 13-item quiz concerning their knowledge of food and nutrition before and after the presentation to determine its efficacy in teaching patients the material.   \n", "RESULTS Fifty patients completed both the pre- and post-presentation tests.", "The mean percentage of correct answers on the pre-test was 85.6%, which rose to 89.3% on the post-test.", "This difference of 3.7% was statistically significant (t = 2.43, df = 49, p < 0.02), and the mean percent of improvement was 6.1%.   \n", "CONCLUSIONS This study demonstrates that psychotic individuals are able to benefit from educational presentations about nutrition and a healthy lifestyle.", "A statistically significant improvement in test scores suggests that subjects gained an understanding of basic concepts related to food choices and fitness."], "structured": true}
{"doc_id": 36066871, "title": "Heterochromatin integrity affects chromosome reorganization after centromere dysfunction.", "abstract": ["The centromere is essential for the inheritance of genetic information on eukaryotic chromosomes.", "Epigenetic regulation of centromere identity has been implicated in genome stability, karyotype evolution, and speciation.", "However, little is known regarding the manner in which centromere dysfunction affects the chromosomal architectures.", "Here we show that in the fission yeast Schizosaccharomyces pombe, the conditional deletion of the centromere produces survivors that carry either a neocentromere-acquired chromosome at the subtelomeric region or an acentric chromosome rescued by intertelomere fusion with either of the remaining chromosomes.", "The ratio of neocentromere formation to telomere fusion is considerably decreased by the inactivation of genes involved in RNA interference-dependent heterochromatin formation.", "By affecting the modes of chromosomal reorganization, the genomic distribution of heterochromatin may influence the fate of karyotype evolution."], "structured": false}
{"doc_id": 36082224, "title": "Expansion and deletion of CTG repeats from human disease genes are determined by the direction of replication in E. coli", "abstract": ["Several human hereditary neurological and neurodegenerative disease genes are associated with the expansion of CTG repeats.", "Here we show that the frequency of genetic expansions or deletions in Escherichia coli depends on the direction of replication.", "Large expansions occur predominantly when the CTGs are in the leading strand template rather than the lagging strand.", "However, deletions are more prominant when the CTGs are in the opposite orientation.", "Most deletions generated products of defined size classes.", "Strand slippage coupled with non\u2013classical DMA structures may account for these observations and relate to expansion\u2013deletion mechanisms in eukaryotic chromosomes for disease genes."], "structured": false}
{"doc_id": 36089763, "title": "Neutrophil extracellular traps capture and kill Candida albicans yeast and hyphal forms.", "abstract": ["Neutrophils phagocytose and kill microbes upon phagolysosomal fusion.", "Recently we found that activated neutrophils form extracellular fibres that consist of granule proteins and chromatin.", "These neutrophil extracellular traps (NETs) degrade virulence factors and kill Gram positive and negative bacteria.", "Here we show for the first time that Candida albicans, a eukaryotic pathogen, induces NET-formation and is susceptible to NET-mediated killing.", "C. albicans is the predominant aetiologic agent of fungal infections in humans, particularly in immunocompromised hosts.", "One major virulence trait of C. albicans is its ability to reversibly switch from singular budding cells to filamentous hyphae.", "We demonstrate that NETs kill both yeast-form and hyphal cells, and that granule components mediate fungal killing.", "Taken together our data indicate that neutrophils trap and kill ascomycetous yeasts by forming NETs."], "structured": false}
{"doc_id": 36111909, "title": "Katanin p60-like1 promotes microtubule growth and terminal dendrite stability in the larval class IV sensory neurons of Drosophila.", "abstract": ["Dendrite shape is considered a defining component of neuronal function.", "Yet, the mechanisms specifying diverse dendritic morphologies, and the extent to which their function depends on these morphologies, remain unclear.", "Here, we demonstrate a requirement for the microtubule-severing protein katanin p60-like 1 (Kat-60L1) in regulating the elaborate dendrite morphology and nocifensive functions of Drosophila larval class IV dendritic arborization neurons.", "Kat-60L1 mutants exhibit diminished responsiveness to noxious mechanical and thermal stimuli.", "Class IV dendrite branch number and length are also reduced, supporting a correspondence between neuronal function and the full extent of the dendritic arbor.", "These arborization defects occur particularly in late larval development, and live imaging reveals that Kat-60L1 is required for dynamic, filopodia-like nascent branches to stabilize during this stage.", "Mutant dendrites exhibit fewer EB1-GFP-labeled microtubules, suggesting that Kat-60L1 increases polymerizing microtubules to establish terminal branch stability and full arbor complexity.", "Although loss of the related microtubule-severing protein Spastin also reduces the class IV dendrite arbor, microtubule polymerization within dendrites is unaffected.", "Conversely, Spastin overexpression destroys stable microtubules within these neurons, while Kat-60L1 has no effect.", "Kat-60L1 thus sculpts the class IV dendritic arbor through microtubule regulatory mechanisms distinct from Spastin.", "Our data support differential roles of microtubule-severing proteins in regulating neuronal morphology and function, and provide evidence that dendritic arbor development is the product of multiple pathways functioning at distinct developmental stages."], "structured": false}
{"doc_id": 36124058, "title": "Update on technical issues concerning complementary feeding of young children in developing countries and implications for intervention programs.", "abstract": ["This paper provides an update to the 1998 WHO/UNICEF report on complementary feeding.", "New research findings are generally consistent with the guidelines in that report, but the adoption of new energy and micronutrient requirements for infants and young children will result in lower recommendations regarding minimum meal frequency and energy density of complementary foods, and will alter the list of \"problem nutrients.", "\"", "Without fortification, the densities of iron, zinc, and vitamin B6 in complementary foods are often inadequate, and the intake of other nutrients may also be low in some populations.", "Strategies for obtaining the needed amounts of problem nutrients, as well as optimizing breastmilk intake when other foods are added to the diet, are discussed.", "The impact of complementary feeding interventions on child growth has been variable, which calls attention to the need for more comprehensive programs.", "A six-step approach to planning, implementing, and evaluating such programs is recommended."], "structured": false}
{"doc_id": 36178047, "title": "Decrease of learning capacity in offspring with increasing paternal age in the rat.", "abstract": ["The same 15 male Wistar rats at the ages of 2.5, 6, 10, 14, 18, and 22 months were successively randomly mated with 2.5-month-old females.", "In a separate experiment, 15 male Wistar rats at the age of 2.5 months and 15 at the age of 23 months were simultaneously randomly mated with 2.5-month-old females.", "Offspring were evaluated in regard to the mean number per litter, sex ratio, frequency of gross external malformations, growth pattern, and mortality in the first 13 weeks of life and reproductive capacity at 13 weeks of age.", "They were also evaluated for spontaneous activity and emotionality with an open field test and for learning capacity with an avoidance conditioning test, both carried out between 10 and 13 weeks of age.", "Only learning capacity of the offspring, expressed in percentage of success for male or female, decreased consistently and significantly as the father's age increased.", "But females did not seem to be affected in the same way as males.", "The genetic implications are briefly discussed."], "structured": false}
{"doc_id": 36180468, "title": "Processing of the beta-amyloid precursor. Multiple proteases generate and degrade potentially amyloidogenic fragments.", "abstract": ["Proteolytic processing of the beta-amyloid precursor proteins (APP) is required for release of the beta/A4 protein and its deposition into the amyloid plaques characteristic of aging and Alzheimer's disease.", "We have examined the involvement of acidic intracellular compartments in APP processing in cultured human cells.", "The use of acidotropic agents and inhibitors to a specific class of lysosomal protease, coupled with metabolic labeling and immunoprecipitation, revealed that APP is degraded within an acidic compartment to produce at least 12 COOH-terminal fragments.", "Nine likely contain the entire beta/A4 domain and, therefore, are potentially amyloidogenic.", "Treatment with E64 or Z-Phe-Ala-CHN2 irreversibly blocked activities of the lysosomal cysteine proteases cathepsins B and L but did not inhibit the lysosomal aspartic protease cathepsin D and did not alter the production of potentially amyloidogenic fragments.", "Instead, the inhibitors prevented further degradation of the fragments.", "Thus, large numbers of potentially amyloidogenic fragments of APP are routinely generated in an acidic compartment by noncysteine proteases and then are eliminated within lysosomes by cysteine proteases.", "Immunoblot and immunohistochemical analyses confirmed that chronic cysteine protease inhibition leads to accumulation of potentially amyloidogenic APP fragments in lysosomes.", "The results provide further support for the hypothesis that an acidic compartment may be involved in amyloid formation and begin to define the proteolytic events that may be important for amyloidogenesis."], "structured": false}
{"doc_id": 36202354, "title": "Pharmaceutical Public-Private Partnerships in the United States and Europe: Moving from the Bench to the Bedside", "abstract": ["Both to address unmet medical needs and to improve industry competitiveness, regulators in both the United States and the European Union have taken bold steps to translate academic research from the university lab to the patient.", "A pharmaceutical public-private partnership (PPPP), which is a legally binding contract between a private pharmaceutical enterprise and a public research university (or a private university doing research funded with public funds), can be a significant tool to ensure a more efficient payoff in the highly regulated world of pharmaceuticals.", "In particular, a properly framed binding contract, coupled with respect for positive social norms, can move the parties away from an inefficient prisoners\u2019 dilemma Nash Equilibrium to the Pareto Optimal Frontier.", "When coupled with appropriate attention to the difficult task of coordinating the actions of interdependent actors, a PPPP arrangement can enhance the likelihood of successful commercialization by flipping the parties\u2019 incentives as compared with more traditional contracts.", "Because PPPPs are less common in Europe than in the United States, a key purpose of this article is to provide an annotated roadmap that universities, private firms, and EU policy makers can use to create efficient PPPPs to enhance for-profit innovation in the pharmaceutical industry in Europe.", "A secondary purpose is to suggest amendments to the U.S. laws governing the patenting of government-funded technology to prevent undue burdens on the sharing of certain upstream medical discoveries and research tools.", "Our analysis is not only comparative; it also combines, we believe for the first time, a game theory and law and management approach to for-profit PPPPs."], "structured": false}
{"doc_id": 36211049, "title": "Chronic stress and psychological well-being: evidence from Thailand on household crowding.", "abstract": ["This paper examines the effect of one form of chronic stress--household crowding--on psychological well-being, as measured by multiple inverse indicators of psychological well-being.", "We rely on data from a large (n = 2017) random sample of households in Bangkok, Thailand, a context that has a higher level and broader range of crowding than typically found in the United States.", "Objective household crowding is found to be detrimental to psychological well-being, controlling for a number of background characteristics.", "The effect of objective crowding is mediated by subjective crowding, which has strong, consistent and direct detrimental effects on well-being.", "There is no evidence of a gender effect.", "Extended family households are not uncommon in Bangkok, but the effects of objective and subjective crowding are similar in both two- and three-generation households, as well as in one- and multiple-couple households.", "The argument that subjective crowding is an effect, rather than a cause, of psychological well-being is examined and rejected.", "The findings suggest that crowding, as a chronic source of stress, constitutes a major threat to psychological well-being.", "Although the empirical analyses are based on data from one city, we frame the issue of household crowding in a historical and theoretical context in order to suggest in which cultural settings household crowding is most likely to have detrimental effects on psychological well-being."], "structured": false}
{"doc_id": 36212758, "title": "Age- and sex-specific genomic profiles in non-small cell lung cancer.", "abstract": ["CONTEXT Gene expression profiling may be useful in examining differences underlying age- and sex-specific outcomes in non-small cell lung cancer (NSCLC).   \n", "OBJECTIVE To describe clinically relevant differences in the underlying biology of NSCLC based on patient age and sex.   \n", "DESIGN, SETTING, AND PATIENTS Retrospective analysis of 787 patients with predominantly early stage NSCLC performed at Duke University, Durham, North Carolina, from July 2008 to June 2009.", "Lung tumor samples with corresponding microarray and clinical data were used.", "All patients were divided into subgroups based on age (< 70 vs > or = 70 years old) or sex.", "Gene expression signatures representing oncogenic pathway activation and tumor biology/microenvironment status were applied to these samples to obtain patterns of activation/deregulation.   \n", "MAIN OUTCOME MEASURES Patterns of oncogenic and molecular signaling pathway activation that are reproducible and correlate with 5-year recurrence-free patient survival.   \n", "RESULTS Low- and high-risk patient clusters/cohorts were identified with the longest and shortest 5-year recurrence-free survival, respectively, within the age and sex NSCLC subgroups.", "These cohorts of NSCLC demonstrate similar patterns of pathway activation.", "In patients younger than 70 years, high-risk patients, with the shortest recurrence-free survival, demonstrated increased activation of the Src (25% vs 6%; P<.001) and tumor necrosis factor (76% vs 42%; P<.001) pathways compared with low-risk patients.", "High-risk patients aged 70 years or older demonstrated increased activation of the wound healing (40% vs 24%; P = .02) and invasiveness (64% vs 20%; P<.001) pathways compared with low-risk patients.", "In women, high-risk patients demonstrated increased activation of the invasiveness (99% vs 2%; P<.001) and STAT3 (72% vs 35%; P<.001) pathways while high-risk men demonstrated increased activation of the STAT3 (87% vs 18%; P<.001), tumor necrosis factor (90% vs 46%; P<.001), EGFR (13% vs 2%; P = .003), and wound healing (50% vs 22%; P<.001) pathways.", "Multivariate analyses confirmed the independent clinical relevance of the pathway-based subphenotypes in women (hazard ratio [HR], 2.02; 95% confidence interval [CI], 1.34-3.03; P<.001) and patients younger than 70 years (HR, 1.83; 95% CI, 1.24-2.71; P = .003).", "All observations were reproducible in split sample analyses.   \n", "CONCLUSIONS Among a cohort of patients with NSCLC, subgroups defined by oncogenic pathway activation profiles were associated with recurrence-free survival.", "These findings require validation in independent patient data sets."], "structured": true}
{"doc_id": 36216395, "title": "Amelioration of colitis by genetically engineered murine regulatory T cells redirected by antigen-specific chimeric receptor.", "abstract": ["BACKGROUND & AIMS The therapeutic application of regulatory T cells (Tregs) for the treatment of inflammatory diseases is limited by the scarcity of antigen-specific Tregs.", "A preferred approach to endow effector T cells (Teff) with a desired specificity uses chimeric immune receptors with antibody-type specificity.", "Accordingly, employing such chimeric immune receptors to redirect Tregs to sites of inflammation may be a useful therapeutic approach to alleviate a broad scope of diseases in which an uncontrolled inflammatory response plays a major role.   \n", "METHODS To enable application of the approach in clinical setting, which requires the genetic modification of the patient's own Tregs, we describe here a novel protocol that allows the efficient retroviral transduction and 2,4,6-trinitrophenol-specific expansion of murine naturally occurring regulatory T cells (nTregs), with a 2,4,6-trinitrophenol-specific tripartite chimeric receptor.   \n", "RESULTS Transduced Tregs maintained their Foxp3 level, could undergo repeated expansion upon ex vivo encounter with their cognate antigen in a major histocompatibility complex-independent, costimulation-independent, and contact-dependent manner and specifically suppressed Teff cells.", "Adoptive transfer of small numbers of the transduced nTregs was associated with antigen-specific, dose-dependent amelioration of trinitrobenzenesulphonic acid colitis.   \n", "CONCLUSIONS This study demonstrates that nTregs can be efficiently transduced to express functional, antigen-specific chimeric receptors that enable the specific suppression of effector T cells both in vitro and in vivo.", "This approach may enable future cell-based therapeutic application in inflammatory bowel disease, as well as other inflammatory disorders."], "structured": true}
{"doc_id": 36233757, "title": "Purification and activation properties of UreD-UreF-urease apoprotein complexes.", "abstract": ["In vivo assembly of the Klebsiella aerogenes urease nickel metallocenter requires the presence of UreD, UreF, and UreG accessory proteins and is further facilitated by UreE. Prior studies had shown that urease apoprotein exists in an uncomplexed form as well as in a series of UreD-urease (I.-S. Park, M.B. Carr, and R.P. Hausinger, Proc.", "Natl.", "Acad.", "Sci.", "USA 91:3233-3237, 1994) and UreD-UreF-UreG-urease (I.-S. Park and R.P. Hausinger, J. Bacteriol.", "177:1947-1951, 1995) apoprotein complexes.", "This study demonstrates the existence of a distinct series of complexes consisting of UreD, UreF, and urease apoprotein.", "These novel complexes exhibited activation properties that were distinct from urease and UreD-urease apoprotein complexes.", "Unlike the previously described species, the UreD-UreF-urease apoprotein complexes were resistant to inactivation by NiCl2.", "The bicarbonate concentration dependence for UreD-UreF-urease apoenzyme activation was significantly decreased compared with that of the urease and UreD-urease apoproteins.", "Western blot (immunoblot) analyses with polyclonal anti-urease and anti-UreD antibodies indicated that UreD is masked in the UreD-UreF-urease complexes, presumably by UreF. We propose that the binding of UreF modulates the UreD-urease apoprotein activation properties by excluding nickel ions from binding to the active site until after formation of the carbamylated lysine metallocenter ligand."], "structured": false}
{"doc_id": 36242796, "title": "Coordinate regulation of the IL-4, IL-13, and IL-5 cytokine cluster in Th2 clones revealed by allelic expression patterns.", "abstract": ["The cytokines IL-4, IL-13, and IL-5 are markers for the Th2 subset of effector T cells and are often expressed together.", "These cytokine genes are organized within 140 kb of orthologous DNA in both mouse and human.", "Using IL-4-expressing CD4+ T cell clones derived from F1 mice, we identified allelic polymorphisms for each of these cytokines and assessed the parental identity of the cytokine mRNAs.", "Both monoallelic and biallelic expression occurred for each gene and for an additional gene, IL-3, that lies with GM-CSF over 450 kb telomeric on the same chromosome.", "When coexpressed in T cell clones, IL-4 was expressed from the same allele as IL-13 or IL-5 in 81% of instances.", "In contrast, there was only 52% concordance of these three cytokines at the allelic level among clones that expressed IL-3.", "Independent expression of the cytokine alleles occurs commonly in T cells, but the clustered locus encompassing IL-4, IL-13, and IL-5 is subject to coordinate regulation."], "structured": false}
{"doc_id": 36271512, "title": "T-cell activation.", "abstract": ["INTRODUCTION \u2022 \u2022 CELLULAR AND MOLECULAR REQUIREMENTS FOR T-CELL ACTIVATION .", "The T-Cell Antigen Receptor Complex . . .", ".. .", ".", ".", "..... .", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", "...... .", ".", ".", "T-Cell Activation by Antibodies and Leetins . . . . . . . . . .", ".. .", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", "Other Cell Surface Structures (Accessory Molecules) Involved in Antigen Recognition and Activation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .", "Minimal Requirements/or T-Cell Activation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .", "CONSEQUE\ufffdCES o\ufffd, T-CELL AC::IV A TION ; .", "ExpressIOn of ActIVatIOn Anllgens . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .", "Mechanisms of Signal Transmission via the TCR Complex . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .", "The Mode of Control of Gene Expression during T-Cell Activation . . . . . . . . . . . . . . . . . . . . . . . . . .", "The Mechanism of Action of IL-2 . .", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", "Acquisition of Cytolytic Activity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .", ".. .", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", "ANALOGIES WITH IMMATURE T CELLS ."], "structured": false}
{"doc_id": 36288526, "title": "Effect of hydroxyethyl starch on bleeding after cardiopulmonary bypass: a meta-analysis of randomized trials.", "abstract": ["OBJECTIVE The effects of hydroxyethyl starch on bleeding after cardiopulmonary bypass were determined.   \n", "METHODS A meta-analysis was performed of postoperative blood loss in randomized clinical trials of hydroxyethyl starch versus albumin for fluid management in adult cardiopulmonary bypass surgery.", "Impacts of hydroxyethyl starch molecular weight and molar substitution were assessed.", "Randomized trials directly comparing different hydroxyethyl starch solutions were also included.   \n", "RESULTS Eighteen trials with 970 total patients were included.", "Compared with albumin, hydroxyethyl starch increased postoperative blood loss by 33.3% of a pooled SD (95% confidence interval, 18.2%-48.3%; P < .001).", "Risk of reoperation for bleeding was more than doubled by hydroxyethyl starch (relative risk, 2.24; 95% confidence interval, 1.14-4.40; P = .020).", "Hydroxyethyl starch increased transfusion of red blood cells by 28.4% of a pooled SD (95% confidence interval, 12.2%-44.6%; P < .001), of fresh-frozen plasma by 30.6% (95% confidence interval, 8.0%-53.1%; P = .008), and of platelets by 29.8% (95% confidence interval, 3.4%-56.2%; P = .027).", "None of these effects differed significantly between hydroxyethyl starch 450/0.7 and 200/0.5.", "Insufficient data were available for hydroxyethyl starch 130/0.4 versus albumin; however, no significant differences were detected in head-to-head comparisons of hydroxyethyl starch 130/0.4 with 200/0.5.", "Albumin improved hemodynamics.", "There were no differences in fluid balance, ventilator time, intensive care unit stay, or mortality.   \n", "CONCLUSIONS Hydroxyethyl starch increased blood loss, reoperation for bleeding, and blood product transfusion after cardiopulmonary bypass.", "There was no evidence that these risks could be mitigated by lower molecular weight and substitution."], "structured": true}
{"doc_id": 36310858, "title": "Downstream of Mutant KRAS, the Transcription Regulator YAP Is Essential for Neoplastic Progression to Pancreatic Ductal Adenocarcinoma", "abstract": ["Pancreatic ductal adenocarcinoma (PDAC) is an aggressive cancer with poor survival rates and frequently carries oncogenic KRAS mutation.", "However, KRAS has thus far not been a viable therapeutic target.", "We found that the abundance of YAP mRNA, which encodes Yes-associated protein (YAP), a protein regulated by the Hippo pathway during tissue development and homeostasis, was increased in human PDAC tissue compared with that in normal pancreatic epithelia.", "In genetically engineered KrasG12D and KrasG12D:Trp53R172H mouse models, pancreas-specific deletion of Yap halted the progression of early neoplastic lesions to PDAC without affecting normal pancreatic development and endocrine function.", "Although Yap was dispensable for acinar to ductal metaplasia (ADM), an initial step in the progression to PDAC, Yap was critically required for the proliferation of mutant Kras or Kras:Trp53 neoplastic pancreatic ductal cells in culture and for their growth and progression to invasive PDAC in mice.", "Yap functioned as a critical transcriptional switch downstream of the oncogenic KRAS\u2013mitogen-activated protein kinase (MAPK) pathway, promoting the expression of genes encoding secretory factors that cumulatively sustained neoplastic proliferation, a tumorigenic stromal response in the tumor microenvironment, and PDAC progression in Kras and Kras:Trp53 mutant pancreas tissue.", "Together, our findings identified Yap as a critical oncogenic KRAS effector and a promising therapeutic target for PDAC and possibly other types of KRAS-mutant cancers."], "structured": false}
{"doc_id": 36345185, "title": "Rho, Rac and Cdc42 regulate actin organization and cell adhesion in macrophages.", "abstract": ["Rho family proteins are known to regulate actin organization in fibroblasts, but their functions in cells of haematopoietic origin have not been studied in detail.", "Bac1.2F5 cells are a colony-stimulating factor-1 (CSF-1)-dependent murine macrophage cell line; CSF-1 stimulates their proliferation and motility, and acts as a chemoattractant.", "CSF-1 rapidly induced actin reorganization in Bac1 cells: it stimulated the formation of filopodia, lamellipodia and membrane ruffles at the plasma membrane, as well as the appearance of fine actin cables within the cell interior.", "Microinjection of constitutively activated (V12)Rac1 stimulated lamellipodium formation and membrane ruffling.", "The dominant inhibitory Rac mutant, N17Rac1, inhibited CSF-1-induced lamellipodium formation, and also induced cell rounding.", "V12Cdc42 induced the formation of long filopodia, while the dominant inhibitory mutant N17Cdc42 prevented CSF-1-induced formation of filopodia but not lamellipodia.", "V14RhoA stimulated actin cable assembly and cell contraction, while the Rho inhibitor, C3 transferase, induced the loss of actin cables.", "Bac1 cells had cell-to-substratum adhesion sites containing beta1 integrin, pp125FAK, paxillin, vinculin, and tyrosine phosphorylated proteins.", "These 'focal complexes' were present in growing and CSF-1-starved cells, but were disassembled in cells injected with N17Cdc42 or N17Rac1.", "Interestingly, beta1 integrin did not disperse until long after focal phosphotyrosine and vinculin staining had disappeared.", "We conclude that in Bac1 macrophages Cdc42, Rac and Rho regulate the formation of distinct actin filament-based structures, and that Cdc42 and Rac are also required for the assembly of adhesion sites to the extracellular matrix."], "structured": false}
{"doc_id": 36345578, "title": "Visualizing the function and fate of neutrophils in sterile injury and repair", "abstract": ["Neutrophils have been implicated as harmful cells in a variety of inappropriate inflammatory conditions where they injure the host, leading to the death of the neutrophils and their subsequent phagocytosis by monocytes and macrophages.", "Here we show that in a fully repairing sterile thermal hepatic injury, neutrophils also penetrate the injury site and perform the critical tasks of dismantling injured vessels and creating channels for new vascular regrowth.", "Upon completion of these tasks, they neither die at the injury site nor are phagocytosed.", "Instead, many of these neutrophils reenter the vasculature and have a preprogrammed journey that entails a sojourn in the lungs to up-regulate CXCR4 (C-X-C motif chemokine receptor 4) before entering the bone marrow, where they undergo apoptosis."], "structured": false}
{"doc_id": 36355784, "title": "The effect of mass screening on incidence and mortality of squamous and adenocarcinoma of cervix uteri.", "abstract": ["OBJECTIVE To describe the efficacy of the Finnish mass screening program for cervical squamous carcinoma and adenocarcinoma, as reflected by changes of incidence and mortality rate.   \n", "METHODS Cervical cancer incidence and mortality data were obtained from the Finnish Cancer Registry.", "Data were available from the year 1953, when the registry was established.", "The nationwide mass screening program in Finland was started in the mid-1960s.", "A centralized organization administers this program.", "Women age 30-60 years are notified for screening every 5 years.   \n", "RESULTS The mean incidence of cervical carcinoma in the early 1960s was 15.4 per 10(5) woman-years.", "In 1991, it was only 2.7 per 10(5) woman-years.", "The mortality rate has decreased in the same proportion since the mass screening program.", "In the early 1960s, the mortality was 6.6 and in 1991 1.4 per 10(5) woman-years.", "However, the decrease of the incidence is seen almost exclusively in squamous cell carcinomas.", "The mortality caused by adenocarcinoma has decreased in screened birth cohorts, but the incidence rate has remained the same.   \n", "CONCLUSIONS The Finnish mass screening program has been effective and its continuation is of utmost importance.", "In the future more attention should be given to glandular cell atypias in cervical smears.", "Thus, it might be possible to decrease the incidence of cervical adenocarcinoma."], "structured": true}
{"doc_id": 36357627, "title": "Role of 5-HT in the regulation of the brain-pituitary-adrenal axis: effects of 5-HT on adrenocortical cells.", "abstract": ["Serotonin (5-HT) plays a pivotal role in the regulation of the brain-pituitary-adrenal axis.", "In particular, 5-HT has been shown to control the activity of hypothalamic CRF neurons and pituitary corticotrope cells through activation of 5-HT1A and (or) 5-HT(2A/2C) receptor subtypes.", "5-HT, acting through 5-HT2 receptors, can also trigger the renin-angiotensin system by stimulating renin secretion and consequently can enhance aldosterone production.", "At the adrenal level, 5-HT produced locally stimulates the secretory activity of adrenocortical cells through a paracrine mode of communication.", "The presence of 5-HT in the adrenal gland has been demonstrated immunohistochemically and biochemically in various species.", "In the frog, rat, and pig adrenal gland, 5-HT is synthesized by chromaffin cells, while in the mouse adrenal cortex, 5-HT is contained in nerve fibers.", "In man, 5-HT is present in perivascular mast cells.", "In vivo and in vitro studies have shown that 5-HT stimulates corticosteroid secretion in various species (including human).", "The type of receptor involved in the mechanism of action of 5-HT differs between the various species.", "In frogs and humans, the stimulatory effect of 5-HT on adrenocortical cells is mediated through a 5-HT4 receptor subtype positively coupled to adenylyl cyclase and calcium influx.", "In the rat, the effect of 5-HT on aldosterone secretion is mediated via activation of 5-HT7 receptors.", "Clinical studies indicate that 5-HT4 receptor agonists stimulate aldosterone secretion in healthy volunteers and in patients with corticotropic insufficiency and primary hyperaldosteronism.", "Local serotonergic control of corticosteroid production may be involved in the physiological control of the activity of the adrenal cortex as well as in the pathophysiology of cortisol and aldosterone disorders."], "structured": false}
{"doc_id": 36386637, "title": "Effect of interleukin-1 and tumor necrosis factor/cachectin on glucose turnover in the rat.", "abstract": ["We studied the effect of recombinant human interleukin-1 beta (IL-1) and recombinant human tumor necrosis factor alpha/cachectin (TNF) on glucose kinetics in healthy rats by means of a primed constant infusion of D-(6-3H)glucose and D-[U-14C]glucose.", "During the isotope (6-hour) and monokine (4-hour) infusion, plasma levels of glucagon and insulin were determined and correlated with changes in glucose metabolism.", "The rates of glucose appearance (Ra) and disappearance (Rd) were elevated only with IL-1 and were associated with an increase in glucagon and a concomitant decrease in the ratio of insulin to glucagon.", "Plasma glucose concentration was increased early after IL-1 administration and coincided with the peak in the Ra.", "The augmentation of the metabolic clearance rate (MCR) and percent of flux oxidized by IL-1 suggest that this monokine induces the utilization of glucose as a substrate.", "TNF administration failed to modify the Ra or Rd, percent of flux oxidized, or MCR.", "TNF-treated rats increased the percent of glucose recycling, but not the total rate of glucose production.", "The results of this experiment suggest that endogenous macrophage products participate in the diverse alterations of carbohydrate metabolism seen during injury and/or infection."], "structured": false}
{"doc_id": 36398420, "title": "Human and murine very small embryonic-like cells represent multipotent tissue progenitors, in vitro and in vivo.", "abstract": ["The purpose of this study was to determine the lineage progression of human and murine very small embryonic-like (HuVSEL or MuVSEL) cells in vitro and in vivo.", "In vitro, HuVSEL and MuVSEL cells differentiated into cells of all three embryonic germ layers.", "HuVSEL cells produced robust mineralized tissue of human origin compared with controls in calvarial defects.", "Immunohistochemistry demonstrated that the HuVSEL cells gave rise to neurons, adipocytes, chondrocytes, and osteoblasts within the calvarial defects.", "MuVSEL cells were also able to differentiate into similar lineages.", "First round serial transplants of MuVSEL cells into irradiated osseous sites demonstrated that \u223c60% of the cells maintained their VSEL cell phenotype while other cells differentiated into multiple tissues at 3 months.", "Secondary transplants did not identify donor VSEL cells, suggesting limited self renewal but did demonstrate VSEL cell derivatives in situ for up to 1 year.", "At no point were teratomas identified.", "These studies show that VSEL cells produce multiple cellular structures in vivo and in vitro and lay the foundation for future cell-based regenerative therapies for osseous, neural, and connective tissue disorders."], "structured": false}
{"doc_id": 36399107, "title": "High frequency of p16 (CDKN2/MTS-1/INK4A) inactivation in head and neck squamous cell carcinoma.", "abstract": ["The tumor suppressor gene p16 (CDKN2/MTS-1/INK4A) can be inactivated by multiple genetic mechanisms.", "We analyzed 29 invasive primary head and neck squamous cell carcinomas (HNSCC) for p16 inactivation with immunohistochemistry utilizing a new monoclonal antibody (mAb), DCS-50.", "p16 staining of the primary lesions was correlated with genetic analysis including: (a) detailed microsatellite analysis of markers at the p16 locus to detect homozygous deletion; (b) sequence analysis of p16; and (c) Southern blot analysis to determine the methylation status of the 5' CpG island of p16.", "Twenty-four of 29 (83%) head and neck squamous cell carcinoma tumors displayed an absence of p16 nuclear staining using immunohistochemistry.", "Of these 24 tumors, we found that 16 (67%) harbored homozygous deletions, 5 (21%) were methylated, 1 displayed a rearrangement at the p16 locus, and 1 displayed a frameshift mutation in exon 1.", "These data suggest that: (a) inactivation of the p16 tumor suppressor gene is a frequent event in squamous cell carcinomas of the head and neck; (b) p16 is inactivated by several distinct and exclusive events including homozygous deletion, point mutation, and promoter methylation; and (c) immunohistochemical analysis for expression of the p16 gene product is an accurate and relatively simple method for evaluating p16 gene inactivation."], "structured": false}
{"doc_id": 36399109, "title": "Genome-wide RNAi screen of Ca(2+) influx identifies genes that regulate Ca(2+) release-activated Ca(2+) channel activity.", "abstract": ["Recent studies by our group and others demonstrated a required and conserved role of Stim in store-operated Ca(2+) influx and Ca(2+) release-activated Ca(2+) (CRAC) channel activity.", "By using an unbiased genome-wide RNA interference screen in Drosophila S2 cells, we now identify 75 hits that strongly inhibited Ca(2+) influx upon store emptying by thapsigargin.", "Among these hits are 11 predicted transmembrane proteins, including Stim, and one, olf186-F, that upon RNA interference-mediated knockdown exhibited a profound reduction of thapsigargin-evoked Ca(2+) entry and CRAC current, and upon overexpression a 3-fold augmentation of CRAC current.", "CRAC currents were further increased to 8-fold higher than control and developed more rapidly when olf186-F was cotransfected with Stim.", "olf186-F is a member of a highly conserved family of four-transmembrane spanning proteins with homologs from Caenorhabditis elegans to human.", "The endoplasmic reticulum (ER) Ca(2+) pump sarco-/ER calcium ATPase (SERCA) and the single transmembrane-soluble N-ethylmaleimide-sensitive (NSF) attachment receptor (SNARE) protein Syntaxin5 also were required for CRAC channel activity, consistent with a signaling pathway in which Stim senses Ca(2+) depletion within the ER, translocates to the plasma membrane, and interacts with olf186-F to trigger CRAC channel activity."], "structured": false}
{"doc_id": 36432234, "title": "Wedelolactone induces growth of breast cancer cells by stimulation of estrogen receptor signalling.", "abstract": ["Wedelolactone, a plant coumestan, was shown to act as anti-cancer agent for breast and prostate carcinomas in vitro and in vivo targeting multiple cellular proteins including androgen receptors, 5-lipoxygenase and topoisomerase II\u03b1.", "It is cytotoxic to breast, prostate, pituitary and myeloma cancer cell lines in vitro at \u03bcM concentrations.", "In this study, however, a novel biological activity of nM dose of wedelolactone was demonstrated.", "Wedelolactone acts as agonist of estrogen receptors (ER) \u03b1 and \u03b2 as demonstrated by transactivation of estrogen response element (ERE) in cells transiently expressing either ER\u03b1 or ER\u03b2 and by molecular docking of this coumestan into ligand binding pocket of both ER\u03b1 and ER\u03b2.", "In breast cancer cells, wedelolactone stimulates growth of estrogen receptor-positive cells, expression of estrogen-responsive genes and activates rapid non-genomic estrogen signalling.", "All these effects can be inhibited by pretreatment with pure ER antagonist ICI 182,780 and they are not observed in ER-negative breast cancer cells.", "We conclude that wedelolactone acts as phytoestrogen in breast cancer cells by stimulating ER genomic and non-genomic signalling pathways."], "structured": false}
{"doc_id": 36444198, "title": "Subpopulations of mouse blood monocytes differ in maturation stage and inflammatory response.", "abstract": ["Blood monocytes are well-characterized precursors for macrophages and dendritic cells.", "Subsets of human monocytes with differential representation in various disease states are well known.", "In contrast, mouse monocyte subsets have been characterized minimally.", "In this study we identify three subpopulations of mouse monocytes that can be distinguished by differential expression of Ly-6C, CD43, CD11c, MBR, and CD62L.", "The subsets share the characteristics of extensive phagocytosis, similar expression of M-CSF receptor (CD115), and development into macrophages upon M-CSF stimulation.", "By eliminating blood monocytes with dichloromethylene-bisphosphonate-loaded liposomes and monitoring their repopulation, we showed a developmental relationship between the subsets.", "Monocytes were maximally depleted 18 h after liposome application and subsequently reappeared in the circulation.", "These cells were exclusively of the Ly-6C(high) subset, resembling bone marrow monocytes.", "Serial flow cytometric analyses of newly released Ly-6C(high) monocytes showed that Ly-6C expression on these cells was down-regulated while in circulation.", "Under inflammatory conditions elicited either by acute infection with Listeria monocytogenes or chronic infection with Leishmania major, there was a significant increase in immature Ly-6C(high) monocytes, resembling the inflammatory left shift of granulocytes.", "In addition, acute peritoneal inflammation recruited preferentially Ly-6C(med-high) monocytes.", "Taken together, these data identify distinct subpopulations of mouse blood monocytes that differ in maturation stage and capacity to become recruited to inflammatory sites."], "structured": false}
{"doc_id": 36450001, "title": "Proteogenomics to discover the full coding content of genomes: a computational perspective.", "abstract": ["Proteogenomics has emerged as a field at the junction of genomics and proteomics.", "It is a loose collection of technologies that allow the search of tandem mass spectra against genomic databases to identify and characterize protein-coding genes.", "Proteogenomic peptides provide invaluable information for gene annotation, which is difficult or impossible to ascertain using standard annotation methods.", "Examples include confirmation of translation, reading-frame determination, identification of gene and exon boundaries, evidence for post-translational processing, identification of splice-forms including alternative splicing, and also, prediction of completely novel genes.", "For proteogenomics to deliver on its promise, however, it must overcome a number of technological hurdles, including speed and accuracy of peptide identification, construction and search of specialized databases, correction of sampling bias, and others.", "This article reviews the state of the art of the field, focusing on the current successes, and the role of computation in overcoming these challenges.", "We describe how technological and algorithmic advances have already enabled large-scale proteogenomic studies in many model organisms, including arabidopsis, yeast, fly, and human.", "We also provide a preview of the field going forward, describing early efforts in tackling the problems of complex gene structures, searching against genomes of related species, and immunoglobulin gene reconstruction."], "structured": false}
{"doc_id": 36464673, "title": "The in vitro phosphorylation of p53 by calcium-dependent protein kinase C--characterization of a protein-kinase-C-binding site on p53.", "abstract": ["We show that, in vitro, Ca2+-dependent protein kinase C (PKC) phosphorylates recombinant murine p53 protein on several residues contained within a conserved basic region of 25 amino acids, located in the C-terminal part of the protein.", "Accordingly, synthetic p53-(357-381)-peptide is phosphorylated by PKC at multiple Ser and Thr residues, including Ser360, Thr365, Ser370 and Thr377.", "We also establish that p53-(357-381)-peptide at micromolar concentrations has the ability to stimulate sequence-specific DNA binding by p53.", "That stimulation is lost upon phosphorylation by PKC.", "To further characterise the mechanisms that regulate PKC-dependent phosphorylation of p53-(357-381)-peptide, the phosphorylation of recombinant p53 and p53-(357-381)-peptide by PKC were compared.", "The results suggest that phosphorylation of full-length p53 on the C-terminal PKC sites is highly dependent on the accessibility of the phosphorylation sites and that a domain on p53 distinct from p53-(357-381)-peptide is involved in binding PKC.", "Accordingly, we have identified a conserved 27-amino-acid peptide, p53-(320-346)-peptide, within the C-terminal region of p53 and adjacent to residues 357-381 that interacts with PKC in vitro.", "The interaction between p53-(320-346)-peptide and PKC inhibits PKC autophosphorylation and the phosphorylation of substrates, including p53-(357-381)-peptide, neurogranin and histone H1.", "Conventional Ca2+-dependent PKC alpha, beta and gamma and the catalytic fragment of PKC (PKM) were nearly equally susceptible to inhibition by p53-(320-346)-peptide.", "The Ca2+-independent PKC delta was much less sensitive to inhibition.", "The significance of these findings for understanding the in vivo phosphorylation of p53 by PKC are discussed."], "structured": false}
{"doc_id": 36480032, "title": "Role of ocular pigment epithelial cells in immune privilege", "abstract": ["The ocular microenvironment is both immunosuppressive and anti-inflammatory in nature.", "Pigment epithelial (PE) cells isolated from the eye possess the ability to suppress the T cell receptor-dependent activation of T cells and the induction of regulatory T cells in vitro.", "This property is dependent on the cells\u2019 capacity to produce cell-surface and soluble inhibitory molecules, for example CD86 (B7-2), transforming growth factor (TGF)-\u03b2, thrombospondin-1, programmed cell death 1 ligand 1 (PD-L1/B7-H1), and cytotoxic T lymphocyte-associated antigen 2\u03b1.", "Cultured ocular PE cells from the iris, ciliary body, and retina can individually suppress T-cell activation via mechanisms that partially overlap.", "Moreover, PE-derived regulatory T cells acquire functions that play a role in establishing immune regulation in the eye.", "Multiple strategies are employed within the eye to control immune-mediated inflammation.", "This phenomenon is known as immune privilege and is instrumental in helping to prevent extensive damage to bystander cells that would otherwise lead to blindness.", "This review focuses on the immunosuppressive property and role of ocular PE cells in immune privileged sites."], "structured": false}
{"doc_id": 36497180, "title": "Drug-resistant Salmonella in the United States: an epidemiologic perspective.", "abstract": ["Salmonellosis poses a health problem of large proportions in the United States.", "Annually, it accounts for more than 40,000 reported cases, 500 deaths, and financial costs well in excess of $50 million.", "Antimicrobial resistance is increasing in Salmonella strains, a finding that has important public health implications.", "Although the chain of transmission of the bacteria is often complex, combined epidemiologic and laboratory studies with the use of new methods in molecular biology make it possible to trace antimicrobial-resistant salmonellae to their primary source--foods of animal origin.", "These studies suggest that the antimicrobial drugs to which food animals are exposed provide selective pressure that leads to the appearance and persistence of resistant strains."], "structured": false}
{"doc_id": 36540079, "title": "Glutamine-specific N-terminal amidase, a component of the N-end rule pathway.", "abstract": ["Deamidation of N-terminal Gln by Nt(Q)-amidase, an N-terminal amidohydrolase, is a part of the N-end rule pathway of protein degradation.", "We detected the activity of Nt(Q)-amidase, termed Ntaq1, in mouse tissues, purified Ntaq1 from bovine brains, identified its gene, and began analyzing this enzyme.", "Ntaq1 is highly conserved among animals, plants, and some fungi, but its sequence is dissimilar to sequences of other amidases.", "An earlier mutant in the Drosophila Cg8253 gene that we show here to encode Nt(Q)-amidase has defective long-term memory.", "Other studies identified protein ligands of the uncharacterized human C8orf32 protein that we show here to be the Ntaq1 Nt(Q)-amidase.", "Remarkably, \"high-throughput\" studies have recently solved the crystal structure of C8orf32 (Ntaq1).", "Our site-directed mutagenesis of Ntaq1 and its crystal structure indicate that the active site and catalytic mechanism of Nt(Q)-amidase are similar to those of transglutaminases."], "structured": false}
{"doc_id": 36547290, "title": "Brahma-related gene 1-dependent STAT3 recruitment at IL-6-inducible genes.", "abstract": ["IL-6 is an immunoregulatory cytokine with multiple functions in hemopoiesis, proliferation, and tumorigenesis.", "IL-6 triggers phosphorylation, dimerization, and nuclear translocation of STAT3, which binds to target promoters and activates transcription.", "Brahma-related gene 1 (BRG1), the enzymatic engine of the yeast-mating type-switching and sucrose-nonfermenting chromatin-remodeling complex, is essential for recruitment of STAT1 or STAT1/STAT2-containing complexes to IFN targets.", "We hypothesized that BRG1 might also be required for STAT3 recruitment.", "In this study, we show that induction of a subset of human IL-6-responsive genes is BRG1 dependent.", "BRG1 is constitutively present at these targets and is required for STAT3 recruitment, downstream histone modifications, and IL-6-induced chromatin remodeling.", "IL-6-induced recruitment of STAT3 to the IFN regulatory factor 1 promoter and subsequent mRNA synthesis is BRG1 dependent, even though IFN-gamma-mediated STAT1 recruitment to this locus is BRG1 independent.", "BRG1 also increased basal expression of IFN-induced transmembrane protein 3 and IFN-gamma-induced protein 16, and the basal chromatin accessibility at the promoter of IFN regulatory factor 1.", "The effect on basal expression was STAT3 independent, as revealed by small interfering RNA knockdown.", "Together with prior observations, these data reveal that BRG1 has a broad role in mediating STAT accessibility at multiple cytokine-responsive promoters and exposes promoter specific differences in both the effect of BRG1 on basal chromatin accessibility and on access of different STAT proteins to the same target."], "structured": false}
{"doc_id": 36558211, "title": "High and low fat consumers, their macronutrient intake and body mass index: further analysis of the National Diet and Nutrition Survey of British Adults.", "abstract": ["OBJECTIVES To explore the different characteristics of high and low fat consumers, in particular their macronutrient intake and body mass index.   \n", "DESIGN Reanalysis of data from the Dietary and Nutritional Survey of British Adults.", "Comparisons were made between groups defined as high and low fat consumers on the basis of 7-day weighed food records considered to be valid for energy intake.", "Individuals were classified in two ways according to the percentage energy from fat (FAT%) and the absolute amount of fat consumed (FATg).", "The criteria for classification of the high FAT% being > 45% (high fat) and < or = 35% (low fat).", "For the FATg group the threshold for the high fat group was > 138 g/day (men) and > 102 g/day (women), and for the low fat group < 85 g/day (men) and < 70 g/day (women).   \n", "SETTING Dietary data was collected from private households in Great Britain between 1986 and 1987.   ", "SUBJECTS From the total population of 2197, individuals who were slimming, ill or had an EI: BMR of < 1.2 were excluded in order to use data which was most likely to represent habitual energy intakes.", "From the remaining 1240 subjects, 10.8% of this sample (6.1% of the total population) were classified as low fat consumers (76 men and 58 women) and 15.4% high fat (8.7% of the total population, 93 men and 98 women).   \n", "MAIN OUTCOME MEASURES Macronutrient consumption and body mass index (BMI).   \n", "RESULTS 30% of the subjects changed fat group classification when the criteria of defining high and low fat groups altered from FAT% to FATg.", "Nutrient intakes differed according to definition of the groups.", "The high fat FATg group ate significantly more of all nutrients than the low fat FATg group.", "However, this was not seen for the FAT% analysis, with the high fat group eating more fat and less carbohydrate.", "The average BMI tended to be higher in the high fat than the low fat groups, particularly in the FATg analysis.", "However, the high fat group contained a wide range of BMIs.", "Further exploration of BMI in the high fat groups, showed that age (an 11-year difference) was the only variable to distinguish individuals in the top and bottom quartiles of BMI.   \n", "CONCLUSIONS High and low fat consumers differ according to a number of variables, and this is affected by how these groups are defined (FAT% or FATg).", "High fat consumers tend to have a higher BMI than low fat consumers, but not all high fat consumers are overweight or obese."], "structured": true}
{"doc_id": 36606083, "title": "Quantitative, genome-wide analysis of eukaryotic replication initiation and termination.", "abstract": ["Many fundamental aspects of DNA replication, such as the exact locations where DNA synthesis is initiated and terminated, how frequently origins are used, and how fork progression is influenced by transcription, are poorly understood.", "Via the deep sequencing of Okazaki fragments, we comprehensively document replication fork directionality throughout the S. cerevisiae genome, which permits the systematic analysis of initiation, origin efficiency, fork progression, and termination.", "We show that leading-strand initiation preferentially occurs within a nucleosome-free region at replication origins.", "Using a strain in which late origins can be induced to fire early, we show that replication termination is a largely passive phenomenon that does not rely on cis-acting sequences or replication fork pausing.", "The replication profile is predominantly determined by the kinetics of origin firing, allowing us to reconstruct chromosome-wide timing profiles from an asynchronous culture."], "structured": false}
{"doc_id": 36618603, "title": "The murine H19 gene is activated during embryonic stem cell differentiation in vitro and at the time of implantation in the developing embryo.", "abstract": ["The differentiation in vitro of murine embryonic stem cells to embryoid bodies mimics events that occur in vivo shortly before and after embryonic implantation.", "We have used this system, together with differential cDNA cloning, to identify genes the expression of which is regulated during early embryogenesis.", "Here we describe the isolation of several such cDNA clones, one of which corresponds to the gene H19.", "This gene is activated in extraembryonic cell types at the time of implantation, suggesting that it may play a role at this stage of development, and is subsequently expressed in all of the cells of the mid-gestation embryo with the striking exception of most of those of the developing central and peripheral nervous systems.", "After birth, expression of this gene ceases or is dramatically reduced in all tissues."], "structured": false}
{"doc_id": 36623997, "title": "Localization of Sir2p: the nucleolus as a compartment for silent information regulators.", "abstract": ["In wild-type budding yeast strains, the proteins encoded by SIR3, SIR4 and RAP1 co-localize with telomeric DNA in a limited number of foci in interphase nuclei.", "Immunostaining of Sir2p shows that in addition to a punctate staining that coincides with Rap1 foci, Sir2p localizes to a subdomain of the nucleolus.", "The presence of Sir2p at both the spacer of the rDNA repeat and at telomeres is confirmed by formaldehyde cross-linking and immunoprecipitation with anti-Sir2p antibodies.", "In strains lacking Sir4p, Sir3p becomes concentrated in the nucleolus, by a pathway requiring SIR2 and UTH4, a gene that regulates life span in yeast.", "The unexpected nucleolar localization of Sir2p and Sir3p correlates with observed effects of sir mutations on rDNA stability and yeast longevity, defining a new site of action for silent information regulatory factors."], "structured": false}
{"doc_id": 36637129, "title": "Optogenetics reveal delayed afferent synaptogenesis on grafted human-induced pluripotent stem cell-derived neural progenitors.", "abstract": ["Reprogramming of somatic cells into pluripotency stem cell state has opened new opportunities in cell replacement therapy and disease modeling in a number of neurological disorders.", "It still remains unknown, however, to what degree the grafted human-induced pluripotent stem cells (hiPSCs) differentiate into a functional neuronal phenotype and if they integrate into the host circuitry.", "Here, we present a detailed characterization of the functional properties and synaptic integration of hiPSC-derived neurons grafted in an in vitro model of hyperexcitable epileptic tissue, namely organotypic hippocampal slice cultures (OHSCs), and in adult rats in vivo.", "The hiPSCs were first differentiated into long-term self-renewing neuroepithelial stem (lt-NES) cells, which are known to form primarily GABAergic neurons.", "When differentiated in OHSCs for 6 weeks, lt-NES cell-derived neurons displayed neuronal properties such as tetrodotoxin-sensitive sodium currents and action potentials (APs), as well as both spontaneous and evoked postsynaptic currents, indicating functional afferent synaptic inputs.", "The grafted cells had a distinct electrophysiological profile compared to host cells in the OHSCs with higher input resistance, lower resting membrane potential, and APs with lower amplitude and longer duration.", "To investigate the origin of synaptic afferents to the grafted lt-NES cell-derived neurons, the host neurons were transduced with Channelrhodopsin-2 (ChR2) and optogenetically activated by blue light.", "Simultaneous recordings of synaptic currents in grafted lt-NES cell-derived neurons using whole-cell patch-clamp technique at 6 weeks after grafting revealed limited synaptic connections from host neurons.", "Longer differentiation times, up to 24 weeks after grafting in vivo, revealed more mature intrinsic properties and extensive synaptic afferents from host neurons to the lt-NES cell-derived neurons, suggesting that these cells require extended time for differentiation/maturation and synaptogenesis.", "However, even at this later time point, the grafted cells maintained a higher input resistance.", "These data indicate that grafted lt-NES cell-derived neurons receive ample afferent input from the host brain.", "Since the lt-NES cells used in this study show a strong propensity for GABAergic differentiation, the host-to-graft synaptic afferents may facilitate inhibitory neurotransmitter release, and normalize hyperexcitable neuronal networks in brain diseases, for example, such as epilepsy."], "structured": false}
{"doc_id": 36642096, "title": "Anti-CD3 monoclonal antibody in new-onset type 1 diabetes mellitus.", "abstract": ["BACKGROUND Type 1 diabetes mellitus is a chronic autoimmune disease caused by the pathogenic action of T lymphocytes on insulin-producing beta cells.", "Previous clinical studies have shown that continuous immune suppression temporarily slows the loss of insulin production.", "Preclinical studies suggested that a monoclonal antibody against CD3 could reverse hyperglycemia at presentation and induce tolerance to recurrent disease.   \n", "METHODS We studied the effects of a nonactivating humanized monoclonal antibody against CD3--hOKT3gamma1(Ala-Ala)--on the loss of insulin production in patients with type 1 diabetes mellitus.", "Within 6 weeks after diagnosis, 24 patients were randomly assigned to receive either a single 14-day course of treatment with the monoclonal antibody or no antibody and were studied during the first year of disease.   \n", "RESULTS Treatment with the monoclonal antibody maintained or improved insulin production after one year in 9 of the 12 patients in the treatment group, whereas only 2 of the 12 controls had a sustained response (P=0.01).", "The treatment effect on insulin responses lasted for at least 12 months after diagnosis.", "Glycosylated hemoglobin levels and insulin doses were also reduced in the monoclonal-antibody group.", "No severe side effects occurred, and the most common side effects were fever, rash, and anemia.", "Clinical responses were associated with a change in the ratio of CD4+ T cells to CD8+ T cells 30 and 90 days after treatment.   \n", "CONCLUSIONS Treatment with hOKT3gamma1(Ala-Ala) mitigates the deterioration in insulin production and improves metabolic control during the first year of type 1 diabetes mellitus in the majority of patients.", "The mechanism of action of the anti-CD3 monoclonal antibody may involve direct effects on pathogenic T cells, the induction of populations of regulatory cells, or both."], "structured": true}
{"doc_id": 36651210, "title": "Establishment and in vitro differentiation of a new embryonic stem cell line from human blastocyst.", "abstract": ["Embryonic stem cells have the ability to remain undifferentiated and proliferate indefinitely in vitro while maintaining the potential to differentiate into derivatives of all three embryonic germ layers.", "These cells have, therefore, potential for in vitro differentiation studies, gene function, and so on.", "The aim of this study was to produce a human embryonic stem cell line.", "An inner cell mass of a human blastocyst was separated and cultured on mouse embryonic fibroblasts in embryonic stem cell medium with related additives.", "The established line was evaluated by morphology; passaging; freezing and thawing; alkaline phosphatase; Oct-4 expression; anti-surface markers including Tra-1-60 and Tra-1-81; and karyotype and spontaneous differentiation.", "Differentiated cardiomyocytes and neurons were evaluated by transmission electron microscopy and immunocytochemistry.", "Here, we report the derivation of a new embryonic stem cell line (Royan H1) from a human blastocyst that remains undifferentiated in morphology during continuous passaging for more than 30 passages, maintains a normal XX karyotype, is viable after freezing and thawing, and expresses alkaline phosphatase, Oct-4, Tra-1-60, and Tra-1-81.", "These cells remain undifferentiated when grown on mouse embryonic fibroblast feeder layers in the presence or absence of recombinant human leukemia inhibitory factor.", "Royan H1 cells can differentiate in vitro in the absence of feeder cells and can produce embryoid bodies that can further differentiate into beating cardiomyocytes as well as neurons.", "These results define Royan H1 cells as a new human embryonic stem cell line."], "structured": false}
{"doc_id": 36653415, "title": "Lactate Metabolism in Human Lung Tumors", "abstract": ["Cancer cells consume glucose and secrete lactate in culture.", "It is unknown whether lactate contributes to energy metabolism in living tumors.", "We previously reported that human non-small-cell lung cancers (NSCLCs) oxidize glucose in the tricarboxylic acid (TCA) cycle.", "Here, we show that lactate is also a TCA cycle carbon source for NSCLC.", "In human NSCLC, evidence of lactate utilization was most apparent in tumors with high 18fluorodeoxyglucose uptake and aggressive oncological behavior.", "Infusing human NSCLC patients with 13C-lactate revealed extensive labeling of TCA cycle metabolites.", "In mice, deleting monocarboxylate transporter-1 (MCT1) from tumor cells eliminated lactate-dependent metabolite labeling, confirming tumor-cell-autonomous lactate uptake.", "Strikingly, directly comparing lactate and glucose metabolism in vivo indicated that lactate's contribution to the TCA cycle predominates.", "The data indicate that tumors, including bona fide human NSCLC, can use lactate as a fuel in vivo."], "structured": false}
{"doc_id": 36654066, "title": "Increased lipid peroxidation as a mechanism of methionine-induced atherosclerosis in rabbits.", "abstract": ["Methionine is converted by the transmethylation/transsulfuration pathway to homocysteine which may exert atherogenic effects by several mechanisms, including lipid peroxidation.", "Therefore, the excessive dietary methionine may induce the development of atherosclerosis.", "To test this hypothesis, plasma and aortic thiobarbituric acid reactive substances (TBARS), as well as activities of aortic and erythrocyte superoxide dismutase (SOD), catalase and selenium-dependent glutathione peroxidase (GPX) were measured in rabbits fed a diet enriched with 0.3% methionine for 6 or 9 months.", "Histological examinations of aortas also were performed.", "Feeding rabbits a methionine-enriched diet for 6 or 9 months resulted in significant increases in plasma and aortic TBARS levels and aortic antioxidant enzyme activities.", "However, a decrease in plasma antioxidant activity (AOA) was observed.", "In erythrocytes, SOD activity increased, catalase remained normal and GPX decreased in the treated animals.", "Histological examination of aortas showed typical atherosclerotic changes, such as intimal thickening, deposition of cholesterol, and calcification in methionine-fed rabbits.", "These results confirm that high-methionine diet may induce atherosclerosis in rabbits and indicate disturbances in lipid peroxidation and antioxidant processes as possible mechanisms of its atherogenic influence."], "structured": false}
{"doc_id": 36708463, "title": "Sex differences in sex chromosome gene expression in mouse brain.", "abstract": ["A major question is whether genes encoded on the sex chromosomes act directly in non-gonadal tissues to cause sex differences in development or function, or whether all sex differences in somatic tissues are induced by gonadal secretions.", "As part of this question we asked whether mouse X-Y homologous gene pairs are expressed in brain in a sex-specific fashion.", "Using RT-PCR and northern blot analysis, we assessed mRNA expression in brain of eight Y-linked genes as well as their X-linked homologues, at three ages: 13.5 days post coitum, the day of birth (P1) and adult.", "Transcripts of six Y genes were expressed at one or more ages: Usp9y, Ube1y, Smcy, Eif2s3y, Uty and Dby.", "Their expression also occurred in XY female brain, and therefore does not require testicular secretions.", "Six X-linked homologues (Usp9x, Ube1x, Smcx, Eif2s3x, Utx and Dbx) were also expressed in brain, and in adulthood all of these transcripts were expressed at significantly higher levels in brains of females than in brains of males, irrespective of their X-inactivation status.", "For five of these gene pairs, the expression of the Y-linked homologue in males was not sufficient to compensate for the female bias in X gene expression.", "Three X-Y gene pairs, Usp9x/y, Ube1x/y and Eif2s3x/y, appeared to be differentially regulated (expressed in brain in a different age- or tissue-dependent pattern), and hence may not be functionally equivalent.", "These sex differences in X-Y gene expression suggest several mechanisms by which these genes may participate in sex differences in brain development and function."], "structured": false}
{"doc_id": 36713289, "title": "Genome architecture, rearrangements and genomic disorders.", "abstract": ["An increasing number of human diseases are recognized to result from recurrent DNA rearrangements involving unstable genomic regions.", "These are termed genomic disorders, in which the clinical phenotype is a consequence of abnormal dosage of gene(s) located within the rearranged genomic fragments.", "Both inter- and intrachromosomal rearrangements are facilitated by the presence of region-specific low-copy repeats (LCRs) and result from nonallelic homologous recombination (NAHR) between paralogous genomic segments.", "LCRs usually span approximately 10-400 kb of genomic DNA, share >or= 97% sequence identity, and provide the substrates for homologous recombination, thus predisposing the region to rearrangements.", "Moreover, it has been suggested that higher order genomic architecture involving LCRs plays a significant role in karyotypic evolution accompanying primate speciation."], "structured": false}
{"doc_id": 36721932, "title": "painDETECT: a new screening questionnaire to identify neuropathic components in patients with back pain.", "abstract": ["OBJECTIVE Nociceptive and neuropathic components both contribute to pain.", "Since these components require different pain management strategies, correct pain diagnosis before and during treatment is highly desirable.", "As low back pain (LBP) patients constitute an important subgroup of chronic pain patients, we addressed the following issues: (i) to establish a simple, validated screening tool to detect neuropathic pain (NeP) components in chronic LBP patients, (ii) to determine the prevalence of neuropathic pain components in LBP in a large-scale survey, and (iii) to determine whether LBP patients with an NeP component suffer from worse, or different, co-morbidities.   \n", "METHODS In co-operation with the German Research Network on Neuropathic Pain we developed and validated the painDETECT questionnaire (PD-Q) in a prospective, multicentre study and subsequently applied it to approximately 8000 LBP patients.   \n", "RESULTS The PD-Q is a reliable screening tool with high sensitivity, specificity and positive predictive accuracy; these were 84% in a palm-top computerised version and 85%, 80% and 83%, respectively, in a corresponding pencil-and-paper questionnaire.", "In an unselected cohort of chronic LBP patients, 37% were found to have predominantly neuropathic pain.", "Patients with NeP showed higher ratings of pain intensity, with more (and more severe) co-morbidities such as depression, panic/anxiety and sleep disorders.", "This also affected functionality and use of health-care resources.", "On the basis of given prevalence of LBP in the general population, we calculated that 14.5% of all female and 11.4% of all male Germans suffer from LBP with a predominant neuropathic pain component.   \n", "CONCLUSION Simple, patient-based, easy-to-use screening questionnaires can determine the prevalence of neuropathic pain components both in individual LBP patients and in heterogeneous cohorts of such patients.", "Since NeP correlates with more intense pain, more severe co-morbidity and poorer quality of life, accurate diagnosis is a milestone in choosing appropriate therapy."], "structured": true}
{"doc_id": 36749390, "title": "Scoring of dual fluorescein and ICG inflammatory angiographic signs for the grading of posterior segment inflammation (dual fluorescein and ICG angiographic scoring system for uveitis)", "abstract": ["Purpose To propose a semiquantitative dual fluorescein angiography (FA) and indocyanine green angiography (ICGA) scoring system for uveitis that would assist in the follow-up of disease progression and monitoring response to treatment.", "Methods The scoring system was based on the FA scoring systems, the standardized ICGA protocol, and schematic interpretation of ICGA findings in posterior uveitis that have been previously published.", "We assigned scores to the fluorescein and ICG angiographic signs that represent ongoing inflammatory process in the posterior segment.", "We rated each angiographic sign according to the impact it has on our appreciation of active intraocular inflammation.", "In order to permit direct comparison between FA and ICGA, we multiplied the total ICGA score by a coefficient of 2 to adjust to the total score of FA.", "Results A total maximum score of 40 was assigned to the FA signs, including optic disc hyperfluorescence, macular edema, retinal vascular staining and/or leakage, capillary leakage, retinal capillary nonperfusion, neovascularization of the optic disc, neovascularization elsewhere, pinpoint leaks, and retinal staining and/or subretinal pooling.", "A total maximum score of 20 was assigned to the ICGA signs, including early stromal vessel hyperfluorescence, choroidal vasculitis, dark dots or areas (excluding atrophy), and optic disc hyperfluorescence.", "Conclusion The combined fluorescein and ICG angiographic scoring system proposed herein may help estimate the magnitude of retinal versus choroidal inflammation, monitor disease progression and response to treatment, and provide comparable data for clinical studies.", "The applicability of the proposed system needs to be tested in clinical settings, and intra- and interobserver variations need to be determined."], "structured": false}
{"doc_id": 36799998, "title": "Improving outcomes of acute kidney injury: report of an initiative", "abstract": ["Acute kidney injury (AKI) is a complex disorder comprising several etiological factors and occurring in multiple settings.", "The disorder has a variety of clinical manifestations that range from minimal elevation in serum creatinine level to anuric renal failure.", "We describe the formation of a multidisciplinary collaborative network focused on AKI.", "This Acute Kidney Injury Network has proposed uniform standards for diagnosing and classifying AKI.", "These proposed standards will need to be validated in future studies, a process that will be facilitated by the Acute Kidney Injury Network, which offers a forum that encourages acquisition of knowledge to improve patient outcomes."], "structured": false}
{"doc_id": 36816310, "title": "A Screen for Endocytic Motifs", "abstract": ["Sorting signals for cargo selection into coated vesicles are usually in the form of short linear motifs.", "Three motifs for clathrin-mediated endocytosis have been identified: YXXPhi, [D/E]XXXL[L/I] and FXNPXY.", "To search for new endocytic motifs, we made a library of CD8 chimeras with random sequences in their cytoplasmic tails, and used a novel fluorescence-activated cell sorting (FACS)-based assay to select for endocytosed constructs.", "Out of the five tails that were most efficiently internalized, only one was found to contain a conventional motif.", "Two contain dileucine-like sequences that appear to be variations on the [D/E]XXXL[L/I] motif.", "Another contains a novel internalization signal, YXXXPhiN, which is able to function in cells expressing a mutant mu2 that cannot bind YXXPhi, indicating that it is not a variation on the YXXPhi motif.", "Similar sequences are present in endogenous proteins, including a functional YXXXPhiN (in addition to a classical YXXPhi) in cytotoxic T-lymphocyte-associated protein 4 (CTLA-4).", "Thus, the repertoire of endocytic motifs is more extensive than the three well-characterized sorting signals."], "structured": false}
{"doc_id": 36830715, "title": "Microtubule stabilization reduces scarring and causes axon regeneration after spinal cord injury.", "abstract": ["Hypertrophic scarring and poor intrinsic axon growth capacity constitute major obstacles for spinal cord repair.", "These processes are tightly regulated by microtubule dynamics.", "Here, moderate microtubule stabilization decreased scar formation after spinal cord injury in rodents through various cellular mechanisms, including dampening of transforming growth factor-\u03b2 signaling.", "It prevented accumulation of chondroitin sulfate proteoglycans and rendered the lesion site permissive for axon regeneration of growth-competent sensory neurons.", "Microtubule stabilization also promoted growth of central nervous system axons of the Raphe-spinal tract and led to functional improvement.", "Thus, microtubule stabilization reduces fibrotic scarring and enhances the capacity of axons to grow."], "structured": false}
{"doc_id": 36831892, "title": "Histone tails: Directing the chromatin response to DNA damage.", "abstract": ["Considerable energetic investment is devoted to altering large stretches of chromatin adjacent to DNA double strand breaks (DSBs).", "Immediately ensuing DSB formation, a myriad of histone modifications are elicited to create a platform for inducible and modular assembly of DNA repair protein complexes in the vicinity of the DNA lesion.", "This complex signaling network is critical to repair DNA damage and communicate with cellular processes that occur in cis and in trans to the genomic lesion.", "Failure to properly execute DNA damage inducible chromatin changes is associated with developmental abnormalities, immunodeficiency, and malignancy in humans and in genetically engineered mouse models.", "This review will discuss current knowledge of DNA damage responsive histone changes that occur in mammalian cells, highlighting their involvement in the maintenance of genome integrity."], "structured": false}
{"doc_id": 36838958, "title": "Sestrin2 inhibits uncoupling protein 1 expression through suppressing reactive oxygen species.", "abstract": ["Uncoupling protein 1 (Ucp1), which is localized in the mitochondrial inner membrane of mammalian brown adipose tissue (BAT), generates heat by uncoupling oxidative phosphorylation.", "Upon cold exposure or nutritional abundance, sympathetic neurons stimulate BAT to express Ucp1 to induce energy dissipation and thermogenesis.", "Accordingly, increased Ucp1 expression reduces obesity in mice and is correlated with leanness in humans.", "Despite this significance, there is currently a limited understanding of how Ucp1 expression is physiologically regulated at the molecular level.", "Here, we describe the involvement of Sestrin2 and reactive oxygen species (ROS) in regulation of Ucp1 expression.", "Transgenic overexpression of Sestrin2 in adipose tissues inhibited both basal and cold-induced Ucp1 expression in interscapular BAT, culminating in decreased thermogenesis and increased fat accumulation.", "Endogenous Sestrin2 is also important for suppressing Ucp1 expression because BAT from Sestrin2(-/-) mice exhibited a highly elevated level of Ucp1 expression.", "The redox-inactive mutant of Sestrin2 was incapable of regulating Ucp1 expression, suggesting that Sestrin2 inhibits Ucp1 expression primarily through reducing ROS accumulation.", "Consistently, ROS-suppressing antioxidant chemicals, such as butylated hydroxyanisole and N-acetylcysteine, inhibited cold- or cAMP-induced Ucp1 expression as well.", "p38 MAPK, a signaling mediator required for cAMP-induced Ucp1 expression, was inhibited by either Sestrin2 overexpression or antioxidant treatments.", "Taken together, these results suggest that Sestrin2 and antioxidants inhibit Ucp1 expression through suppressing ROS-mediated p38 MAPK activation, implying a critical role of ROS in proper BAT metabolism."], "structured": false}
{"doc_id": 36855703, "title": "The non-catalytic function of XPG protein during dual incision in human nucleotide excision repair.", "abstract": ["XPG is a member of the FEN-1 structure-specific endonuclease family.", "It has 3'-junction cutting activity on bubble substrates and makes the 3'-incision in the human dual incision (excision nuclease) repair system.", "To investigate the precise role of XPG in nucleotide excision repair, we mutagenized two amino acid residues thought to be involved in DNA binding and catalysis, overproduced the mutant proteins using a baculovirus/insect cell system, and purified and characterized the mutant proteins.", "The mutation D77A had a modest effect on junction cutting and excision activity and gave rise to uncoupled 5'-incision by mammalian cell-free extracts.", "The D812A mutation completely abolished the junction cutting and 3'-incision activities of XPG, but the excision nuclease reconstituted with XPG (D812A) carried out normal 5'-incision at the 23rd-24th phosphodiester bonds 5' to a (6-4) photoproduct without producing any 3'-incision.", "It is concluded that Asp-812 is an active site residue of XPG and that in addition to making the 3'-incision, the physical presence of XPG in the protein-DNA complex is required non-catalytically for subsequent 5'-incision by XPF-ERCC1."], "structured": false}
{"doc_id": 36860856, "title": "A 40-Hz auditory potential recorded from the human scalp.", "abstract": ["Computer techniques readily extract from the brainwaves an orderly sequence of brain potentials locked in time to sound stimuli.", "The potentials that appear 8 to 80 msec after the stimulus resemble 3 or 4 cycles of a 40-Hz sine wave; we show here that these waves combined to form a single, stable, composite wave when the sounds are repeated at rates around 40 per sec. This phenomenon, the 40-Hz event-related potential (ERP), displays several properties of theoretical and practical interest.", "First, it reportedly disappears with surgical anesthesia, and it resembles similar phenomena in the visual and olfactory system, facts which suggest that adequate processing of sensory information may require cyclical brain events in the 30- to 50-Hz range.", "Second, latency and amplitude measurements on the 40-Hz ERP indicate it may contain useful information on the number and basilar membrane location of the auditory nerve fibers a given tone excites.", "Third, the response is present at sound intensities very close to normal adult thresholds for the audiometric frequencies, a fact that could have application in clinical hearing testing."], "structured": false}
{"doc_id": 36889513, "title": "Bile acids: natural ligands for an orphan nuclear receptor.", "abstract": ["Bile acids regulate the transcription of genes that control cholesterol homeostasis through molecular mechanisms that are poorly understood.", "Physiological concentrations of free and conjugated chenodeoxycholic acid, lithocholic acid, and deoxycholic acid activated the farnesoid X receptor (FXR; NR1H4), an orphan nuclear receptor.", "As ligands, these bile acids and their conjugates modulated interaction of FXR with a peptide derived from steroid receptor coactivator 1.", "These results provide evidence for a nuclear bile acid signaling pathway that may regulate cholesterol homeostasis."], "structured": false}
{"doc_id": 36904081, "title": "The yeast ribosomal protein L32 and its gene.", "abstract": ["The yeast ribosomal protein gene RPL32 of Saccharomyces cerevisiae is of particular interest for two reasons: 1) it is adjacent to another ribosomal protein gene, RP29, whose divergent transcription may be driven from the same control sequences, and 2) it appears that the splicing of its transcript is regulated by the product of the gene, ribosomal protein in L32.", "RPL32 has been analyzed in detail.", "It is essential for cell growth.", "Its sequence predicts L32 to be a protein of 105 amino acids, somewhat basic near the NH2 terminus, rather acidic near the COOH terminus, and homologous to ribosomal protein L30 of mammals.", "The reading frame has been confirmed by partial NH2-terminal analysis of L32.", "The nucleotide sequence also predicts an intron of 230 nucleotides, which begins with the unusual sequence GTCAGT and ends 40 nucleotides downstream of the consensus sequence TAC-TAAC.", "The intron has been confirmed by determination of the sequence of a cDNA clone.", "Transcription initiates 58 nucleotides upstream of the AUG initiation codon, and the polyadenylation site occurs 100 nucleotides downstream of the termination codon.", "Regulation of the transcription of ribosomal protein genes has been linked to two related consensus sequences.", "Analysis of the intergenic region between RP29 and RPL32 reveals three copies of these sequences.", "A deletion removing all three sequences reduces synthesis of a L32-LacZ fusion protein by more than 90%.", "Some residual activity, however, remains."], "structured": false}
{"doc_id": 36921186, "title": "Derivation conditions impact X-inactivation status in female human induced pluripotent stem cells.", "abstract": ["Female human induced pluripotent stem cell (hiPSC) lines exhibit variability in X-inactivation status.", "The majority of hiPSC lines maintain one transcriptionally active X (Xa) and one inactive X (Xi) chromosome from donor cells.", "However, at low frequency, hiPSC lines with two Xas are produced, suggesting that epigenetic alterations of the Xi occur sporadically during reprogramming.", "We show here that X-inactivation status in female hiPSC lines depends on derivation conditions.", "hiPSC lines generated by the Kyoto method (retroviral or episomal reprogramming), which uses leukemia inhibitory factor (LIF)-expressing SNL feeders, frequently had two Xas.", "Early passage Xa/Xi hiPSC lines generated on non-SNL feeders were converted into Xa/Xa hiPSC lines after several passages on SNL feeders, and supplementation with recombinant LIF caused reactivation of some of X-linked genes.", "Thus, feeders are a significant factor affecting X-inactivation status.", "The efficient production of Xa/Xa hiPSC lines provides unprecedented opportunities to understand human X-reactivation and -inactivation."], "structured": false}
{"doc_id": 36950726, "title": "Loss of 5-hydroxymethylcytosine and ten-eleven translocation 2 protein expression in malignant melanoma.", "abstract": ["Several research groups have recently reported on markedly reduced levels of 5-hydroxymethylcytosine (5hmC) in human breast, liver, lung, pancreatic, colon, prostate, brain, and myeloid cancers.", "We studied benign compound nevi (BCN, n=17), dysplastic compound nevi (DCN, n=15), superficial spreading melanomas [SSM, stratified in <1 mm (n=19) and >4 mm (n=18) Breslow tumor thickness], and cutaneous metastatic disease (CMD, n=24).", "Immunohistochemistry included specific antibodies against 5hmC, 5-methylcytosine (5mC), and ten-eleven translocation 2 protein (TET2).", "Immunohistological scoring showed significantly (P<0.0001) higher median 5hmC levels in BCN and DCN than in thin SSM, thick SSM, and CMD.", "5mC immunoreactivity did not differ significantly (P=0.15) between nevi and melanoma.", "The intensity of TET2 expression was predominantly weak but was found to be significantly (P<0.0001) more often in nevi than in thin SSM, thick SSM, and CMD.", "We have shown that 5hmC levels and TET2 expression are significantly reduced in advanced melanomas compared with nevi and thin melanomas.", "It is suggested that 5hmC and TET2 possibly play an important role in the epigenetic regulation of melanoma development and progression."], "structured": false}
{"doc_id": 36960449, "title": "Estimation of the dietary requirement for vitamin D in healthy adults.", "abstract": ["BACKGROUND Knowledge gaps have contributed to considerable variation among international dietary recommendations for vitamin D.   OBJECTIVE We aimed to establish the distribution of dietary vitamin D required to maintain serum 25-hydroxyvitamin D [25(OH)D] concentrations above several proposed cutoffs (ie, 25, 37.5, 50, and 80 nmol/L) during wintertime after adjustment for the effect of summer sunshine exposure and diet.   \n", "DESIGN A randomized, placebo-controlled, double-blind 22-wk intervention study was conducted in men and women aged 20-40 y (n = 238) by using different supplemental doses (0, 5, 10, and 15 microg/d) of vitamin D(3) throughout the winter.", "Serum 25(OH)D concentrations were measured by using enzyme-linked immunoassay at baseline (October 2006) and endpoint (March 2007).   \n", "RESULTS There were clear dose-related increments (P < 0.0001) in serum 25(OH)D with increasing supplemental vitamin D(3).", "The slope of the relation between vitamin D intake and serum 25(OH)D was 1.96 nmol x L(-1) x microg(-1) intake.", "The vitamin D intake that maintained serum 25(OH)D concentrations of >25 nmol/L in 97.5% of the sample was 8.7 microg/d.", "This intake ranged from 7.2 microg/d in those who enjoyed sunshine exposure, 8.8 microg/d in those who sometimes had sun exposure, and 12.3 microg/d in those who avoided sunshine.", "Vitamin D intakes required to maintain serum 25(OH)D concentrations of >37.5, >50, and >80 nmol/L in 97.5% of the sample were 19.9, 28.0, and 41.1 microg/d, respectively.   \n", "CONCLUSION The range of vitamin D intakes required to ensure maintenance of wintertime vitamin D status [as defined by incremental cutoffs of serum 25(OH)D] in the vast majority (>97.5%) of 20-40-y-old adults, considering a variety of sun exposure preferences, is between 7.2 and 41.1 microg/d."], "structured": true}
{"doc_id": 36962270, "title": "Rapid purification of homodimer and heterodimer HIV-1 reverse transcriptase by metal chelate affinity chromatography.", "abstract": ["We have modified an Escherichia coli vector expressing 66-kDa HIV-1 reverse transcriptase (p66) so that it simultaneously expresses this and the pol-coded protease.", "The twin expression cassette yields high quantities of both reverse transcriptase and protease; however, under these conditions, 50% of the over-expressed p66 reverse transcriptase is processed, resulting in accumulation of large quantities of p66/p51 enzyme.", "Furthermore, addition of a poly(histidine) affinity label at the amino terminus of the reverse-transcriptase-coding sequence (His-p66) permits a simple, rapid purification of milligram quantities of either p66 or p66/p51 enzyme from a crude lysate by metal chelate affinity chromatography.", "Purified His-p66 and His-p66/His-p51 reverse transcriptase exhibit both reverse transcriptase and RNase H activity.", "Purification by metal chelate chromatography of a p66/p51 enzyme wherein only the p66 component is labelled strengthens the argument for the existence of a heterodimer."], "structured": false}
{"doc_id": 36991551, "title": "Polyphenols of Cocoa: Inhibition of Mammalian 15-Lipoxygenase", "abstract": ["Abstract Some cocoas and chocolates are rich in ()epicatechin and its related oligomers, the procyanidins.", "Fractions of these compounds, isolated from the seeds of Theobroma cacao, caused dosedependent inhibition of isolated rabbit 15-lipoxygenase-1 with the larger oligomers being more active; the decamer fraction revealed an IC 50 of 0.8 M. Among the monomeric flavanols, epigallocatechin gallate (IC 50 = 4 M) and epicatechin gallate (5 M) were more potent than ()epicatechin (IC50 = 60 M).", "()Epicatechin and procyanidin nonamer also inhibited the formation of 15-hydroxyeicosatetraenoic acid from arachidonic acid in rabbit smooth muscle cells transfected with human 15-lipoxygenase-1.", "In contrast, inhibition of the lipoxygenase pathway in J774A.1 cells transfected with porcine leukocytetype 12- lipoxygenase (another representative of the 12/15- lipoxygenase family) was only observed upon sonication of the cells, suggesting a membrane barrier for flavanols in these cells.", "Moreover, epicatechin (IC50 approx.", "15 M) and the procyanidin decamer inhibited recombinant human platelet 12-lipoxygenase.", "These observations suggest general lipoxygenase inhibitory potency of flavanols and procyanidins that may contribute to their putative beneficial effects on the cardiovascular system in man.", "Thus, they may provide a plausible explanation for recent literature reports indicating that procyanidins decrease the leukotriene/prostacyclin ratio in humans and human aortic endothelial cells."], "structured": false}
{"doc_id": 37029185, "title": "Quality of life in patients with advanced heart failure.", "abstract": ["Although evaluation of the treatment of congestive heart failure is usually based on objective clinical outcomes, patient self-assessment is increasingly recognized as an important component of evaluation.", "A study was designed to measure the quality of life of 134 patients with symptoms of advanced heart failure who were being evaluated for possible heart transplantation.", "The patients' quality of life was assessed using a mix of subjective and objective measures, including functional status, physical symptoms, emotional state, and psychosocial adaptation.", "There was no significant relationship between patients' cardiac ejection fraction and any quality-of-life measures; however, the results of a 6-minute walking test, New York Heart Association classification, and self-reported functional status were all significantly correlated with psychosocial adjustment.", "Self-reported functional status, depression, and hostility accounted for 43% of the variance in total psychosocial adjustment to illness.", "These findings support the inclusion of quality of life as an outcome measure in any evaluation of treatment efficacy and suggest that interventions to improve the quality of life of patients with advanced heart failure need to be targeted at reducing depression and hostility and increasing daily activity levels."], "structured": false}
{"doc_id": 37037012, "title": "Regional vascular resistance during exercise: role of cardiac afferents and exercise training.", "abstract": ["This study was designed to determine whether cardiac vagal afferents exert an inhibitory influence on increases in regional vascular resistance during exercise and to determine whether endurance exercise training enhances the inhibitory influence of cardiac vagal afferents.", "We measured changes in regional vascular resistance in 12 rabbits at rest and during running at 12.6 m/min, 20% grade, before and after reversible denervation of cardiac afferents (intrapericardial procainamide HCl, 2%).", "In addition, these procedures were repeated in five of these rabbits following an 8-wk endurance exercise training program.", "Because intrapericardial injections of procainamide anesthetize both the efferent as well as the afferent innervation to the heart, it was necessary to determine the effects of blocking the efferent innervation on the regulation of regional vascular resistance during exercise.", "Rabbits were instrumented with Doppler ultrasonic flow probes around the renal (R), mesenteric (M), ascending, and terminal aortic (TA) arteries.", "Catheters were positioned in the central ear artery and vein and pericardial sac.", "Mean arterial pressure, heart rate, cardiac output, R, M, TA, and systemic (S) resistances were determined.", "Exercise changed R (+37 +/-", "4%), M (+88 +/-", "9%), TA (-62 +/-", "6%), and S (-34 +/-", "3) resistances.", "Subsequent cardiac efferent blockade alone had no significant effect on regional vascular resistance during exercise.", "Combined efferent and afferent blockade resulted in significant increases in R (+62 +/-", "6%) and M resistance (+134 +/-", "13%)", "but did not alter TA (-51 +/-", "4%) or S (-27 +/-", "2%) resistance during exercise.", "Exercise training significantly enhanced the inhibitory influence of cardiac afferents on R and M regional vascular resistance.(ABSTRACT TRUNCATED AT 250 WORDS)"], "structured": false}
{"doc_id": 37065914, "title": "Serum Soluble Corin is Decreased in Stroke.", "abstract": ["BACKGROUND AND PURPOSE Soluble corin was decreased in coronary heart disease.", "Given the connections between cardiac dysfunction and stroke, circulating corin might be a candidate marker of stroke risk.", "However, the association between circulating corin and stroke has not yet been studied in humans.", "Here, we aimed to examine the association in patients wtith stroke and community-based healthy controls.   \n", "METHODS Four hundred eighty-one patients with ischemic stroke, 116 patients with hemorrhagic stroke, and 2498 healthy controls were studied.", "Serum soluble corin and some conventional risk factors of stroke were examined.", "Because circulating corin was reported to be varied between men and women, the association between serum soluble corin and stroke was evaluated in men and women, respectively.   \n", "RESULTS Patients with ischemic and hemorrhagic stroke had a significantly lower level of serum soluble corin than healthy controls in men and women (all P values, <0.05).", "In multivariate analysis, men in the lowest quartile of serum soluble corin were more likely to have ischemic (odds ratio [OR], 4.90; 95% confidence interval, 2.99-8.03) and hemorrhagic (OR, 17.57; 95% confidence interval, 4.85-63.71) stroke than men in the highest quartile.", "Women in the lowest quartile of serum soluble corin were also more likely to have ischemic (OR, 3.10; 95% confidence interval, 1.76-5.44) and hemorrhagic (OR, 8.54; 95% confidence interval, 2.35-31.02) stroke than women in the highest quartile.", "ORs of ischemic and hemorrhagic stroke were significantly increased with the decreasing levels of serum soluble corin in men and women (all P values for trend, <0.001).   \n", "CONCLUSIONS Serum soluble corin was decreased in patients with stroke compared with healthy controls.", "Our findings raise the possibility that serum soluble corin may have a pathogenic role in stroke."], "structured": true}
{"doc_id": 37118634, "title": "Topical application of chlorhexidine to neonatal umbilical cords for prevention of omphalitis and neonatal mortality in a rural district of Pakistan: a community-based, cluster-randomised trial.", "abstract": ["BACKGROUND Umbilical cord infection (omphalitis) is a risk factor for neonatal sepsis and mortality in low-resource settings where home deliveries are common.", "We aimed to assess the effect of umbilical-cord cleansing with 4% chlorhexidine (CHX) solution, with or without handwashing with antiseptic soap, on the incidence of omphalitis and neonatal mortality.   \n", "METHODS We did a two-by-two factorial, cluster-randomised trial in Dadu, a rural area of Sindh province, Pakistan.", "Clusters were defined as the population covered by a functional traditional birth attendant (TBA), and were randomly allocated to one of four groups (groups A to D) with a computer-generated random number sequence.", "Implementation and data collection teams were masked to allocation.", "Liveborn infants delivered by participating TBAs who received birth kits were eligible for enrolment in the study.", "One intervention comprised birth kits containing 4% CHX solution for application to the cord at birth by TBAs and once daily by family members for up to 14 days along with soap and educational messages promoting handwashing.", "One intervention was CHX solution only and another was handwashing only.", "Standard dry cord care was promoted in the control group.", "The primary outcomes were incidence of neonatal omphalitis and neonatal mortality.", "The trial is registered with ClinicalTrials.gov, number NCT00682006.   \n", "FINDINGS 187 clusters were randomly allocated to one of the four study groups.", "Of 9741 newborn babies delivered by participating TBAs, factorial analysis indicated a reduction in risk of omphalitis with CHX application (risk ratio [RR]=0\u00b758, 95% CI 0\u00b741-0\u00b782; p=0\u00b7002) but no evidence of an effect of handwashing (RR=0\u00b783, 0\u00b761-1\u00b713; p=0\u00b724).", "We recorded strong evidence of a reduction in neonatal mortality in neonates who received CHX cleansing (RR=0\u00b762, 95 % CI 0\u00b745-0\u00b785; p=0\u00b7003) but no evidence of an effect of handwashing promotion on neonatal mortality (RR=1\u00b708, 0\u00b779-1\u00b748; p=0\u00b762).", "We recorded no serious adverse events.   \n", "INTERPRETATION Application of 4% CHX to the umbilical cord was effective in reducing the risk of omphalitis and neonatal mortality in rural Pakistan.", "Provision of CHX in birth kits might be a useful strategy for the prevention of neonatal mortality in high-mortality settings.   \n", "FUNDING", "The United States Agency for International Development."], "structured": true}
{"doc_id": 37138639, "title": "The IKK complex, a central regulator of NF-kappaB activation.", "abstract": ["The IKK kinase complex is the core element of the NF-kappaB cascade.", "It is essentially made of two kinases (IKKalpha and IKKbeta) and a regulatory subunit, NEMO/IKKgamma.", "Additional components may exist, transiently or permanently, but their characterization is still unsure.", "In addition, it has been shown that two separate NF-kappaB pathways exist, depending on the activating signal and the cell type, the canonical (depending on IKKbeta and NEMO) and the noncanonical pathway (depending solely on IKKalpha).", "The main question, which is still only partially answered, is to understand how an NF-kappaB activating signal leads to the activation of the kinase subunits, allowing them to phosphorylate their targets and eventually induce nuclear translocation of the NF-kappaB dimers.", "I will review here the genetic, biochemical, and structural data accumulated during the last 10 yr regarding the function of the three IKK subunits."], "structured": false}
{"doc_id": 37156349, "title": "Cognitive predictors of young children's readiness for powered mobility.", "abstract": ["Independent mobility in early childhood has been associated with the development of various cognitive and psychosocial skills.", "However, children with physical disabilities are not always able to move independently and may be at risk for delays in these areas.", "Early provision of powered mobility can offer young children an opportunity for independent mobility.", "Despite this, there is little information to help determine when a young child has the cognitive skills necessary to operate a powered wheelchair safely.", "This current research aims to identify these skills.", "A cognitive assessment battery and a wheelchair mobility training and assessment program were developed.", "Twenty-six children with physical disabilities between the ages of 20 and 36 months were evaluated on the cognitive assessment and participated in the wheelchair training and assessment program.", "A stepwise regression analysis was used to determine which of the cognitive skills predicted wheelchair mobility performance.", "The cognitive domains of spatial relations and problem solving were found to be significant and accounted for 57% of the variance in wheelchair skills.", "Developmental cut-off points on these scales as they relate to wheelchair skills are presented and clinical applications are discussed."], "structured": false}
{"doc_id": 37164306, "title": "Knockdown of the co-chaperone Hop promotes extranuclear accumulation of Stat3 in mouse embryonic stem cells.", "abstract": ["A key event in the mechanism of mouse embryonic stem cell (mESC) pluripotency is phosphorylation, dimerisation and translocation to the nucleus of the signal transducer and activator of transcription3, Stat3.", "We used RNAi to suppress the levels of the co-chaperone Hsp70/Hsp90 organising protein (Hop) in an mESC line.", "Hop knockdown caused 68% depletion in Stat3 mRNA levels, decreased soluble pYStat3 levels, and led to an extranuclear accumulation of Stat3.", "The major binding partner of Hop, Hsp90, co-localised with a small non-nuclear fraction of Stat3 in mESCs, and both Stat3 and Hop co-precipitated with Hsp90.", "Hop knockdown did not affect Nanog and Oct4 protein levels; however, Nanog mRNA levels were decreased.", "We found that in the absence of Hop, mESCs lost their pluripotent ability to form embryoid bodies with a basement membrane.", "These data suggest that Hop facilitates the phosphorylation and nuclear translocation of Stat3, implying a role for the Hsp70/Hsp90 chaperone heterocomplex machinery in pluripotency signalling."], "structured": false}
{"doc_id": 37182501, "title": "B-cell self-tolerance in humans.", "abstract": ["Two mechanisms account for generation of the human antibody repertoire; V(D)J recombination during the early stages of B-cell development in the bone marrow and somatic mutation of immunoglobulin genes in mature B cells responding to antigen in the periphery.", "V(D)J recombination produces diversity by random joining of gene segments and somatic mutation by introducing random point mutations.", "Both are required to attain the degree of antigen receptor diversification that is necessary for immune protection: defects in either mechanism are associated with increased susceptibility to infection.", "However, the downside of producing enormous random diversity in the antibody repertoire is the generation of autoantibodies.", "To prevent autoimmunity B cells expressing autoantibodies are regulated by strict mechanisms that either modify the specificity of autoantibodies or the fate of cells expressing such antibodies.", "Abnormalities in B-cell self-tolerance are associated with a large number of autoimmune diseases, but the precise nature of the defects is less well defined.", "Here we summarize recent data on the self-reactive B-cell repertoire in healthy humans and in patients with autoimmunity."], "structured": false}
{"doc_id": 37204802, "title": "JMJD6 Promotes Colon Carcinogenesis through Negative Regulation of p53 by Hydroxylation", "abstract": ["Jumonji domain-containing 6 (JMJD6) is a member of the Jumonji C domain-containing family of proteins.", "Compared to other members of the family, the cellular activity of JMJD6 is still not clearly defined and its biological function is still largely unexplored.", "Here we report that JMJD6 is physically associated with the tumor suppressor p53.", "We demonstrated that JMJD6 acts as an \u03b1-ketoglutarate- and Fe(II)-dependent lysyl hydroxylase to catalyze p53 hydroxylation.", "We found that p53 indeed exists as a hydroxylated protein in vivo and that the hydroxylation occurs mainly on lysine 382 of p53.", "We showed that JMJD6 antagonizes p53 acetylation, promotes the association of p53 with its negative regulator MDMX, and represses transcriptional activity of p53.", "Depletion of JMJD6 enhances p53 transcriptional activity, arrests cells in the G1 phase, promotes cell apoptosis, and sensitizes cells to DNA damaging agent-induced cell death.", "Importantly, knockdown of JMJD6 represses p53-dependent colon cell proliferation and tumorigenesis in vivo, and significantly, the expression of JMJD6 is markedly up-regulated in various types of human cancer especially in colon cancer, and high nuclear JMJD6 protein is strongly correlated with aggressive clinical behaviors of colon adenocarcinomas.", "Our results reveal a novel posttranslational modification for p53 and support the pursuit of JMJD6 as a potential biomarker for colon cancer aggressiveness and a potential target for colon cancer intervention."], "structured": false}
{"doc_id": 37205685, "title": "Spread of chloroquine resistance in Plasmodium falciparum.", "abstract": ["Malaria resistant to chloroquine has now been confirmed in more than 40 countries.", "The drug was introduced in 1934, but was not in large-scale use until the early 1950s.", "Anecdotal reports suggest that resistance emerged as early as 1957 both in Colombia and along the then Cambodia-Thailand border area.", "But by 1960, resistance in these areas was confirmed - and may represent two separate events.", "Resistance spread rapidly, with a new focus of resistance confirmed in East Africa by 1977.", "Chloroquine resistance represents a severe problem both for prophylaxis and treatment of malaria.", "In this aricle, David Payne traces the spread of resistance and discusses some of its implications."], "structured": false}
{"doc_id": 37205759, "title": "Obesity occurring in apolipoprotein E-knockout mice has mild effects on fertility.", "abstract": ["The Apolipoprotein (Apo) family is implicated in lipid metabolism.", "There are five types of Apo: Apoa, Apob, Apoc, Apod, and Apoe.", "Apoe has been demonstrated to play a central role in lipoprotein metabolism and to be essential for efficient receptor-mediated plasma clearance of chylomicron remnants and VLDL remnant particles by the liver.", "Apoe-deficient (Apoe(-/-)) mice develop atherosclerotic plaques spontaneously, followed by obesity.", "In this study, we investigated whether lipid deposition caused by Apoe knockout affects reproduction in female mice.", "The results demonstrated that Apoe(-/-) mice were severely hypercholesterolemic, with their cholesterol metabolism disordered, and lipid accumulating in the ovaries causing the ovaries to be heavier compared with the WT counterparts.", "In addition, estrogen and progesterone decreased significantly at D 100.", "Quantitative PCR analysis demonstrated that at D 100 the expression of cytochromeP450 aromatase (Cyp19a1), 3\u03b2-hydroxysteroid dehydrogenase (Hsd3b), mechanistic target of rapamycin (Mtor), and nuclear factor-\u03baB (Nfkb) decreased significantly, while that of BCL2-associated agonist of cell death (Bad) and tuberous sclerosis complex 2 (Tsc2) increased significantly in the Apoe(-/-) mice.", "However, there was no difference in the fertility rates of the Apoe(-/-) and WT mice; that is, obesity induced by Apoe knockout has no significant effect on reproduction.", "However, the deletion of Apoe increased the number of ovarian follicles and the ratio of ovarian follicle atresia and apoptosis.", "We believe that this work will augment our understanding of the role of Apoe in reproduction."], "structured": false}
{"doc_id": 37207226, "title": "Lipid metabolism and toxicity in the heart.", "abstract": ["The heart has both the greatest caloric needs and the most robust oxidation of fatty acids (FAs).", "Under pathological conditions such as obesity and type 2 diabetes, cardiac uptake and oxidation are not balanced and hearts accumulate lipid potentially leading to cardiac lipotoxicity.", "We will first review the pathways utilized by the heart to acquire FAs from the circulation and to store triglyceride intracellularly.", "Then we will describe mouse models in which excess lipid accumulation causes heart dysfunction and experiments performed to alleviate this toxicity.", "Finally, the known relationships between heart lipid metabolism and dysfunction in humans will be summarized."], "structured": false}
{"doc_id": 37248570, "title": "Malaria eradication back on the table.", "abstract": ["After a lapse of almost 40 years, malaria eradication is back on the global health agenda.", "Inspired by the Gates Malaria Forum in October 2007,1,2 key organizations are starting to debate the pros and cons of redefining eradication as an explicit goal of malaria control efforts.", "Attempts to eliminate malaria in southern Africa3 and Pacific Island states,4 and WHO\u2019s Global Malaria Programme agenda and field manual for malaria elimination,5,6 foreshadow this movement towards another global attempt at eradication.    ", "When marking 60 years of WHO\u2019s commitment to fighting malaria, we must ask what has been achieved, but also what can we learn from the past.", "We now know so much more about the biology of parasite-host responses, the determinants of endemicity and transmission dynamics, the social, economic and cultural implications of malaria at household, community and national levels, and the demands made upon health systems in endemic countries.", "We do not yet know how to synthesize and integrate this knowledge to achieve elimination in different settings.    ", "Regional malaria elimination campaigns were first conducted in the late 1940s, preparing the ground for the Global Malaria Eradication Program in 1955.", "This campaign succeeded in eliminating malaria from Europe, North America, the Caribbean and parts of Asia and South-Central America.7 But no major success occurred in sub-Saharan Africa, which accounts for 80% of today\u2019s burden of malaria.8 When the aspiration of global eradication was abandoned in 1969, the main reasons for failure were technical challenges of executing the strategy especially in Africa.    ", "The post-eradication era from 1969 to 1991 focused on technical issues, and research and development for new tools, leading to advances in drug and vaccine development, vector control and insecticide-treated nets.", "These decades also brought a better understanding of the social, economic and cultural dimensions of malaria.", "There was little global support provided specifically for malaria control in the newly independent states of Africa that were struggling to establish broad-based health systems and primary health care.", "By 1992, the combination of a worsening malaria situation and promising technical developments led to renewed global focus on malaria control.    ", "The Roll Back Malaria initiative, launched by WHO in 1998, led to the Abuja Declaration in 2000, which defined progressive intervention coverage targets for control designed to eliminate malaria as a public health problem, while emphasizing that this could only be achieved through vastly strengthened local health systems.9 Increased resources through the Global Fund to Fight AIDS, Tuberculosis and Malaria, the World Bank\u2019s Booster Program, the US President\u2019s Malaria Initiative and many others has meant that this page is finally beginning to turn as intervention coverage is rising.10    It is against this background that we hear this call for elimination/eradication.", "The challenges remain formidable.", "We all know that elimination in Africa is not possible with current tools.", "But efforts must focus beyond simply developing better tools, to include how existing and future tools can be strategically combined for maximum synergistic effectiveness when integrated into different health and social systems prevailing in endemic areas.", "Aiming at elimination and eradication further implies the need for effective surveillance strategies to monitor progress (again a challenge for health systems).", "This in turn requires a better understanding of malaria transmission heterogeneity in a globalized world with rapidly changing dynamics in environment, climate, migration and transnational cooperation.    ", "Maintaining long-term momentum in the face of success in regional elimination while waiting to achieve final eradication will be a major challenge.", "Shrinking the map by starting on the malaria margins with the \u201ceasy-to-eliminate\u201d settings will boost morale initially but may bring marginal benefits to such areas at the expense of those where the burden of malaria is highest.", "Any strategic plan \u2013 and here we learn again from the past \u2013 needs to be a synchronous global effort, locally adapted in all endemic areas.    ", "Although we lack sufficient knowledge, systems and tools to eradicate malaria today, we do have a window of political will and financial resources to refocus on the goal of effective control through universal coverage of appropriate interventions.", "The prerequisites for a successful start are: (i) a process of inclusive discourse to agree on global vision, goals and strategy; and (ii) a global plan for all endemic areas describing how, where and when we move from control towards elimination.", "What must distinguish the new era, especially in Africa, is a real rather than rhetorical emphasis on health systems.", "\u25a0"], "structured": false}
{"doc_id": 37248765, "title": "CI-994 (N-acetyl-dinaline) in combination with conventional anti-cancer agents is effective against acute myeloid leukemia in vitro and in vivo.", "abstract": ["N-acetyl-dinaline (CI-994) is an investigational anti-cancer drug which inhibits histone deacetylases.", "We evaluated the interaction between CI-994 and conventional chemotherapeutics used in acute myeloid leukemia (AML) in a rat model for AML and Brown Norway rat acute myelocytic leukemia (BNML).", "In vitro, CI-994 in combination with cytarabine (ara-C), daunorubicin and mitoxantrone, resulted in moderate synergism.", "In vivo, higher dosages of CI-994 induced complete remissions.", "CI-994/ara-C was very active against BNML.", "The combinations of CI-994/daunorubicin and CI-994/mitoxantrone were also active against BNML.", "This study demonstrates favorable in vitro and in vivo interactions between CI-994 and conventional anti-cancer agents used for the treatment of AML."], "structured": false}
{"doc_id": 37249641, "title": "CTCF and Cohesin in Genome Folding and Transcriptional Gene Regulation.", "abstract": ["Genome function, replication, integrity, and propagation rely on the dynamic structural organization of chromosomes during the cell cycle.", "Genome folding in interphase provides regulatory segmentation for appropriate transcriptional control, facilitates ordered genome replication, and contributes to genome integrity by limiting illegitimate recombination.", "Here, we review recent high-resolution chromosome conformation capture and functional studies that have informed models of the spatial and regulatory compartmentalization of mammalian genomes, and discuss mechanistic models for how CTCF and cohesin control the functional architecture of mammalian chromosomes."], "structured": false}
{"doc_id": 37256966, "title": "Melatonin synthesized by T lymphocytes as a ligand of the retinoic acid-related orphan receptor.", "abstract": ["Melatonin modulates a wide array of physiological events with pleiotropic effects on the immune system.", "While the relevance of specific melatonin membrane receptors has been well established for several biological functions, retinoic acid-related orphan receptor alpha (ROR\u03b1) has been suggested as a mediator of nuclear melatonin signalling by results obtained from pharmacological approaches.", "However, a melatonin-mediated downstream effect cannot be ruled out, and further evidence is needed to support a direct interaction between melatonin and ROR\u03b1.", "Here, we show that ROR\u03b1 is mainly located in human Jurkat T-cell nucleus, and it is co-immunoprecipitated with melatonin.", "Moreover, immunocytochemistry studies confirmed the co-localization of melatonin and ROR\u03b1.", "Melatonin promoted a time-dependent decrease in nuclear ROR\u03b1 levels, suggesting a role in the ROR\u03b1 transcriptional activity.", "Interestingly, ROR\u03b1 acts as a molecular switch implicated in the mutually exclusive generation of Th17 and Treg cells, both involved in the harm/protection balance of immune conditions such as autoimmunity or acute transplant rejection.", "Therefore, the identification of melatonin as a natural modulator of ROR\u03b1 gives it a tremendous therapeutic potential for a variety of clinical disorders."], "structured": false}
{"doc_id": 37269418, "title": "Age- and infection intensity-dependent cytokine and antibody production in human trichuriasis: the importance of IgE.", "abstract": ["The cytokine and antibody response to Trichuris trichiura infection was determined for 96 persons living in an area where the parasite is highly endemic and infection exhibits a convex age intensity profile.", "In response to stimulation with T. trichiura antigen, a small proportion of the study group produced interleukin (IL)-4 (7%), IL-9 (5%), and IL-13 (17%).", "A larger proportion produced IL-10 (97%), tumor necrosis factor (TNF)-alpha (93%), and interferon (IFN)-gamma (32%).", "The levels of TNF-alpha (P =.016) and IFN-gamma (P =.012) significantly increased with age, suggesting a switch to a more chronic infection phenotype.", "The predominant parasite-specific antibodies produced were IgG1, IgG4, IgA, and IgE. Unlike the IgG subclasses and IgA, parasite-specific IgE correlated negatively with infection intensity, as defined by egg output (P =.008), and positively with host age (P =.010).", "These findings suggest a mixed cytokine response in trichuriasis and an IgE-associated level of protection."], "structured": false}
{"doc_id": 37296667, "title": "The cryoprotective effect of trehalose supplementation on boar spermatozoa quality.", "abstract": ["In order to improve boar sperm quality during frozen-thawed process, the influence of the presence of trehalose on success of cryopreservation of boar sperm were investigated.", "We evaluated freeze-thawing tolerance of boar spermatozoa in a base cooling extender with the addition of different trehalose concentrations (0, 25, 50, 100 and 200mmol/l), and tried to determine the optimum concentration of trehalose.", "We chose sperm motility, acrosome integrity, membrane integrity and cryocapacitation as parameters to evaluate cryopreservation capacity of boar spermatozoa.", "We obtained the best results for 100mmol/l trehalose-supplemented extenders, with values of 49.89% for motility, 66.52% for acrosome integrity and 44.61% for membrane integrity, while freeze-thawing tolerance was diminished significantly for 200mmol/l of trehalose.", "Before and after capacitation, the CTC score for semen diluted by extender containing 100mmol/l trehalose was 3.68% and 43.82%, respectively.", "In conclusion, trehalose could confer a greater cryoprotective capacity to boar spermatozoa.", "Trehalose-supplementation with 100mmol/l concentration in basic extender could significantly improve sperm motility, membrane integrity and acrosome integrity parameters, and reduce boar spermatozoa cryocapacitation during the cryopreservation process."], "structured": false}
{"doc_id": 37297740, "title": "Roads to polyploidy: the megakaryocyte example.", "abstract": ["Polyploidy, recognized by multiple copies of the haploid chromosome number, has been described in plants, insects, and in mammalian cells such as, the platelet precursors, the megakaryocytes.", "Several of these cell types reach high ploidy via a different cell cycle.", "Megakaryocytes undergo an endomitotic cell cycle, which consists of an S phase interrupted by a gap, during which the cells enter mitosis but skip anaphase B and cytokinesis.", "Here, we review the mechanisms that lead to this cell cycle and to polyploidy in megakaryocytes, while also comparing them to those described for other systems in which high ploidy is achieved.", "Overall, polyploidy is associated with an orchestrated change in expression of several genes, of which, some may be a result of high ploidy and hence a determinant of a new cell physiology, while others are inducers of polyploidization.", "Future studies will aim to further explore these two groups of genes."], "structured": false}
{"doc_id": 37311371, "title": "Central memory and effector memory T cell subsets: function, generation, and maintenance.", "abstract": ["The memory T cell pool functions as a dynamic repository of antigen-experienced T lymphocytes that accumulate over the lifetime of the individual.", "Recent studies indicate that memory T lymphocytes contain distinct populations of central memory (TCM) and effector memory (TEM) cells characterized by distinct homing capacity and effector function.", "This review addresses the heterogeneity of TCM and TEM, their differentiation stages, and the current models for their generation and maintenance in humans and mice."], "structured": false}
{"doc_id": 37328025, "title": "The Werner and Bloom syndrome proteins help resolve replication blockage by converting (regressed) holliday junctions to functional replication forks.", "abstract": ["Cells cope with blockage of replication fork progression in a manner that allows DNA synthesis to be completed and genomic instability minimized.", "Models for resolution of blocked replication involve fork regression to form Holliday junction structures.", "The human RecQ helicases WRN and BLM (deficient in Werner and Bloom syndromes, respectively) are critical for maintaining genomic stability and thought to function in accurate resolution of replication blockage.", "Consistent with this notion, WRN and BLM localize to sites of blocked replication after certain DNA-damaging treatments and exhibit enhanced activity on replication and recombination intermediates.", "Here we examine the actions of WRN and BLM on a special Holliday junction substrate reflective of a regressed replication fork.", "Our results demonstrate that, in reactions requiring ATP hydrolysis, both WRN and BLM convert this Holliday junction substrate primarily to a four-stranded replication fork structure, suggesting they target the Holliday junction to initiate branch migration.", "In agreement, the Holliday junction binding protein RuvA inhibits the WRN- and BLM-mediated conversion reactions.", "Importantly, this conversion product is suitable for replication with its leading daughter strand readily extended by DNA polymerases.", "Furthermore, binding to and conversion of this Holliday junction are optimal at low MgCl(2) concentrations, suggesting that WRN and BLM preferentially act on the square planar (open) conformation of Holliday junctions.", "Our findings suggest that, subsequent to fork regression events, WRN and/or BLM could re-establish functional replication forks to help overcome fork blockage.", "Such a function is highly consistent with phenotypes associated with WRN- and BLM-deficient cells."], "structured": false}
{"doc_id": 37336085, "title": "Do Montelukast Sodium and N-Acetylcysteine Have a Nephroprotective Effect on Unilateral Ureteral Obstruction? A Placebo Controlled Trial in a Rat Model.", "abstract": ["PURPOSE We assessed the nephroprotective effects of montelukast sodium and N-acetylcysteine on secondary renal damage due to unilateral ureteral obstruction in a rat model.   ", "MATERIALS AND METHODS In this study 30 Wistar albino male rats were randomized into 3 groups, including placebo, N-acetylcysteine and montelukast sodium.", "Three rats served as the control group.", "The left ureter of the rats was sutured with 4-zero polyglactin sutures.", "Medications were given 3 days before obstruction and continued for 15 days.", "Dimercaptosuccinic acid renal scintigraphy was performed before obstruction and on day 15.", "Rats were sacrificed on day 15 and histopathological examinations were done.", "We biochemically assessed oxidative stress markers (myeloperoxidase and malondialdehyde), sulfhydryl and total nitrite for lipid peroxidation, oxidative protein damage and antioxidant levels, respectively.   \n", "RESULTS On pathological examination inflammation and tubular epithelial damage in the N-acetylcysteine and montelukast sodium groups were less than in the placebo group (p <0.05).", "No difference was seen in normal kidneys.", "Myeloperoxidase, malondialdehyde and total nitrite levels in the N-acetylcysteine group, and myeloperoxidase and malondialdehyde levels in the montelukast sodium group were lower than in the placebo group (p <0.05).", "No statistical difference was seen in sulfhydryl levels (p >0.05) or among the N-acetylcysteine, montelukast sodium and placebo groups on scintigraphy (p >0.05).", "No pathological, chemical and scintigraphic differences were seen among the N-acetylcysteine, montelukast sodium and sham treated groups (p >0.05).   \n", "CONCLUSIONS N-acetylcysteine and montelukast sodium have a protective effect against obstructive damage of the kidney.", "However, further investigations are needed."], "structured": true}
{"doc_id": 37362689, "title": "Oxidative phosphorylation: synthesis of mitochondrially encoded proteins and assembly of individual structural subunits into functional holoenzyme complexes.", "abstract": ["The bulk of ATP consumed by various cellular processes in higher eukaryotes is normally produced by five multimeric protein complexes (I-V) embedded within the inner mitochondrial membrane, in a process known as oxidative phosphorylation (OXPHOS).", "Maintenance of energy homeostasis under most physiological conditions is therefore contingent upon the ability of OXPHOS to meet cellular changes in bioenergetic demand, with a chronic failure to do so being a frequent cause of human disease.", "With the exception of Complex II, the structural subunits of OXPHOS complexes are encoded by both the nuclear and the mitochondrial genomes.", "The physical separation of the two genomes necessitates that the expression of the 13 mitochondrially encoded polypeptides be co-ordinated with that of relevant nuclear-encoded partners in order to assemble functional holoenzyme complexes.", "Complex biogenesis is a highly ordered process, and several nuclear-encoded factors that function at distinct stages in the assembly of individual OXPHOS complexes have been identified."], "structured": false}
{"doc_id": 37405449, "title": "Familial gastroesophageal reflux and development of Barrett's esophagus.", "abstract": ["The family of an elderly man with Barrett's esophagus was examined for gastroesophageal reflux and development of Barrett's esophagus.", "All five living children have gastroesophageal reflux or esophagitis, or both, and three have unequivocal Barrett's esophagus.", "Two third-generation descendents have gastroesophageal reflux.", "This pattern suggests autosomal dominant transmission of the gastroesophageal reflux trait.", "The family also has a high prevalence of cancer, which may represent the cancer family syndrome."], "structured": false}
{"doc_id": 37424881, "title": "The effect of folate fortification on folic acid-based homocysteine-lowering intervention and stroke risk: a meta-analysis.", "abstract": ["OBJECTIVE Folate and vitamin B12 are two vital regulators in the metabolic process of homocysteine, which is a risk factor of atherothrombotic events.", "Low folate intake or low plasma folate concentration is associated with increased stroke risk.", "Previous randomized controlled trials presented discordant findings in the effect of folic acid supplementation-based homocysteine lowering on stroke risk.", "The aim of the present review was to perform a meta-analysis of relevant randomized controlled trials to check the how different folate fortification status might affect the effects of folic acid supplementation in lowering homocysteine and reducing stroke risk.   \n", "DESIGN Relevant randomized controlled trials were identified through formal literature search.", "Homocysteine reduction was compared in subgroups stratified by folate fortification status.", "Relative risks with 95 % confidence intervals were used as a measure to assess the association between folic acid supplementation and stroke risk.   \n", "SETTING The meta-analysis included fourteen randomized controlled trials,   SUBJECTS A total of 39 420 patients.   \n", "RESULTS Homocysteine reductions were 26\u00b799 (sd 1\u00b791) %, 18\u00b738 (sd 3\u00b782) % and 21\u00b730 (sd 1\u00b798) %, respectively, in the subgroups without folate fortification, with folate fortification and with partial folate fortification.", "Significant difference was observed between the subgroups with folate fortification and without folate fortification (P=0\u00b705).", "The relative risk of stroke was 0\u00b788 (95 % CI 0\u00b777, 1\u00b700, P=0\u00b705) in the subgroup without folate fortification, 0\u00b794 (95 % CI 0\u00b758, 1\u00b754, P=0\u00b782) in the subgroup with folate fortification and 0\u00b791 (95 % CI 0\u00b782, 1\u00b701, P=0\u00b709) in the subgroup with partial folate fortification.   \n", "CONCLUSIONS Folic acid supplementation might have a modest benefit on stroke prevention in regions without folate fortification."], "structured": true}
{"doc_id": 37437064, "title": "On the origin and impact of mesenchymal stem cell heterogeneity: new insights and emerging tools for single cell analysis.", "abstract": ["Mesenchymal stem cells (MSCs) display substantial cell-to-cell variation.", "This heterogeneity manifests among donors, among tissue sources, and within cell populations.", "Such pervasive variability complicates the use of MSCs in regenerative applications and may limit their therapeutic efficacy.", "Most conventional assays measure MSC properties in bulk and, as a consequence, mask this cell-to-cell variation.", "Recent studies have identified extensive variability amongst and within clonal MSC populations, in dimensions including functional differentiation capacity, molecular state (e.g. epigenetic, transcriptomic, and proteomic status), and biophysical properties.", "While the origins of these variations remain to be elucidated, potential mechanisms include in vivo micro-anatomical heterogeneity, epigenetic bistability, and transcriptional fluctuations.", "Emerging tools for single cell analysis of MSC gene and protein expression may yield further insight into the mechanisms and implications of single cell variation amongst these cells, and ultimately improve the clinical utility of MSCs in tissue engineering and regenerative medicine applications.", "This review outlines the dimensions across which MSC heterogeneity is present, defines some of the known mechanisms that govern this heterogeneity, and highlights emerging technologies that may further refine our understanding and improve our clinical application of this unique cell type."], "structured": false}
{"doc_id": 37438296, "title": "Altered microRNA expression in bovine skeletal muscle with age.", "abstract": ["Age-dependent decline in skeletal muscle function leads to several inherited and acquired muscular disorders in elderly individuals.", "The levels of microRNAs (miRNAs) could be altered during muscle maintenance and repair.", "We therefore performed a comprehensive investigation for miRNAs from five different periods of bovine skeletal muscle development using next-generation small RNA sequencing.", "In total, 511 miRNAs, including one putatively novel miRNA, were identified.", "Thirty-six miRNAs were differentially expressed between prenatal and postnatal stages of muscle development including several myomiRs (miR-1, miR-206 and let-7 families).", "Compared with miRNA expression between different muscle tissues, 14 miRNAs were up-regulated and 22 miRNAs were down-regulated in the muscle of postnatal stage.", "In addition, a novel miRNA was predicted and submitted to the miRBase database as bta-mir-10020.", "A dual luciferase reporter assay was used to demonstrate that bta-mir-10020 directly targeted the 3'-UTR of the bovine ANGPT1 gene.", "The overexpression of bta-mir-10020 significantly decreased the DsRed fluorescence in the wild-type expression cassette compared to the mutant type.", "Using three computational approaches - miranda, pita and rnahybrid - these differentially expressed miRNAs were also predicted to target 3609 bovine genes.", "Disease and biological function analyses and the KEGG pathway analysis revealed that these targets were statistically enriched in functionality for muscle growth and disease.", "Our miRNA expression analysis findings from different states of muscle development and aging significantly expand the repertoire of bovine miRNAs now shown to be expressed in muscle and could contribute to further studies on growth and developmental disorders in this tissue type."], "structured": false}
{"doc_id": 37444589, "title": "Apoptosis occurs predominantly in bystander cells and not in productively infected cells of HIV- and SIV-infected lymph nodes", "abstract": ["Although 13 years have passed since identification of human immunodeficiency virus-1 (HIV-1) as the cause of AIDS, we do not yet know how HIV kills its primary target, the T cell that carries the CD4 antigen.", "We and others have shown an increase in the percentage of apoptotic cells among circulating CD4+ (and CD8+) T cells of HIV-seropositive individuals and an increase in frequency of apoptosis with disease progression.", "However, it is not known if this apoptosis occurs in infected or uninfected T cells.", "We show here, using in situ labelling of lymph nodes from HIV-infected children and SIV-infected macaques, that apoptosis occurs predominantly in bystander cells and not in the productively infected cells themselves.", "These data have implications for pathogenesis and therapy, namely, arguing that rational drug therapy may involve combination agents targeting viral replication in infected cells and apoptosis of uninfected cells."], "structured": false}
{"doc_id": 37450671, "title": "Neuronal origin of a cerebral amyloid: neurofibrillary tangles of Alzheimer's disease contain the same protein as the amyloid of plaque cores and blood vessels.", "abstract": ["The protein component of Alzheimer's disease amyloid [neurofibrillary tangles (NFT), amyloid plaque core and congophilic angiopathy] is an aggregated polypeptide with a subunit mass of 4 kd (the A4 monomer).", "Based on the degree of N-terminal heterogeneity, the amyloid is first deposited in the neuron, and later in the extracellular space.", "Using antisera raised against synthetic peptides, we show that the N terminus of A4 (residues 1-11) contains an epitope for neurofibrillary tangles, and the inner region of the molecule (residues 11-23) contains an epitope for plaque cores and vascular amyloid.", "The non-protein component of the amyloid (aluminum silicate) may form the basis for the deposition or amplification (possible self-replication) of the aggregated amyloid protein.", "The amyloid of Alzheimer's disease is similar in subunit size, composition but not sequence to the scrapie-associated fibril and its constituent polypeptides.", "The sequence and composition of NFT are not homologous to those of any of the known components of normal neurofilaments."], "structured": false}
{"doc_id": 37480103, "title": "Pregnancy characteristics and maternal risk of breast cancer.", "abstract": ["CONTEXT During pregnancy, serum levels of estrogen, progesterone, and other hormones are markedly higher than during other periods of life.", "Pregnancy hormones primarily are produced in the placenta, and signs of placental impairment may serve as indirect markers of hormone exposures during pregnancy.", "During pregnancy, these markers have been inconsistently associated with subsequent risk of breast cancer in the mother.   \n", "OBJECTIVE To examine associations between indirect markers of hormonal exposures, such as placental weight and other pregnancy characteristics, and maternal risk of developing breast cancer.   \n", "DESIGN AND SETTING Population-based cohort study using data from the Swedish Birth Register, the Swedish Cancer Register, the Swedish Cause of Death Register, and the Swedish Register of Population and Population Changes.   \n", "PARTICIPANTS Women included in the Sweden Birth Register who delivered singletons between 1982 and 1989, with complete information on date of birth and gestational age.", "Women were followed up until the occurrence of breast cancer, death, or end of follow-up (December 31, 2001).", "Cox proportional hazards models were used to estimate associations between hormone exposures and risks of breast cancer.   \n", "MAIN OUTCOME MEASURE Incidence of invasive breast cancer.   \n", "RESULTS Of 314,019 women in the cohort, 2216 (0.7%) developed breast cancer during the follow-up through 2001, of whom 2100 (95%) were diagnosed before age 50 years.", "Compared with women who had placentas weighing less than 500 g in 2 consecutive pregnancies, the risk of breast cancer was increased among women whose placentas weighed between 500 and 699 g in their first pregnancy and at least 700 g in their second pregnancy (or vice versa) (adjusted hazard ratio, 1.82; 95% confidence interval [CI], 1.07-3.08), and the corresponding risk was doubled among women whose placentas weighed at least 700 g in both pregnancies (adjusted hazard ratio, 2.05; 95% CI, 1.15-3.64).", "A high birth weight (> or =4000 g) in 2 successive births was associated with an increased risk of breast cancer before but not after adjusting for placental weight and other covariates (adjusted hazard ratio, 1.10; 95% CI, 0.76-1.59).   \n", "CONCLUSIONS Placental weight is positively associated with maternal risk of breast cancer.", "These results further support the hypothesis that pregnancy hormones are important modifiers of subsequent maternal breast cancer risk."], "structured": true}
{"doc_id": 37488367, "title": "Attention-deficit hyperactivity disorder: a category or a continuum? Genetic analysis of a large-scale twin study.", "abstract": ["OBJECTIVE To investigate heritability and continuum versus categorical approaches to attention-deficit hyperactivity disorder (ADHD), using a large-scale twin sample.   \n", "METHOD A cohort of 1,938 families with twins and siblings aged 4 to 12 years, recruited from the Australian National Health and Medical Research Council Twin Registry, was assessed for ADHD using a DSM-III-R-based maternal rating scale.", "Probandwise concordance rates and correlations in monozygotic and dizygotic twins and siblings were calculated, and heritability was examined using the De Fries and Fulker regression technique.   \n", "RESULTS There was a narrow (additive) heritability of 0.75 to 0.91 which was robust across familial relationships (twin, sibling, and twin-sibling) and across definitions of ADHD as part of a continuum or as a disorder with various symptom cutoffs.", "There was no evidence for nonadditive genetic variation or for shared family environmental effects.   \n", "CONCLUSIONS These findings suggest that ADHD is best viewed as the extreme of a behavior that varies genetically throughout the entire population rather than as a disorder with discrete determinants.", "This has implications for the classification of ADHD and for the identification of genes for this behavior, as well as implications for diagnosis and treatment."], "structured": true}
{"doc_id": 37549932, "title": "Antiapoptotic BCL-2 is required for maintenance of a model leukemia.", "abstract": ["Resistance to apoptosis, often achieved by the overexpression of antiapoptotic proteins, is common and perhaps required in the genesis of cancer.", "However, it remains uncertain whether apoptotic defects are essential for tumor maintenance.", "To test this, we generated mice expressing a conditional BCL-2 gene and constitutive c-myc that develop lymphoblastic leukemia.", "Eliminating BCL-2 yielded rapid loss of leukemic cells and significantly prolonged survival, formally validating BCL-2 as a rational target for cancer therapy.", "Loss of this single molecule resulted in cell death, despite or perhaps attributable to the presence of other oncogenic events.", "This suggests a generalizable model in which aberrations inherent to cancer generate tonic death signals that would otherwise kill the cell if not opposed by a requisite apoptotic defect(s)."], "structured": false}
{"doc_id": 37562370, "title": "Cellular and histopathological changes in the infrapatellar fat pad in the monoiodoacetate model of osteoarthritis pain.", "abstract": ["OBJECTIVE The infrapatellar fat pad (IPFP) has been identified as a source of anterior knee pain.", "Fibrosis and marked inflammatory infiltrate in the IPFP of patients with arthritis of the knee and reduction in pain post knee replacement in patients following resection of the IPFP have been observed.", "We have investigated changes in the IPFP of rats undergoing the monoiodoacetate (MIA) model of degenerative joint disease, a model that exhibits some histopathological similarities to osteoarthritis (OA).   \n", "METHODS Rats were injected intra-articularly with MIA and the development of weight bearing asymmetry was followed for 21 days as compared to vehicle-injected animals.", "In addition, IPFPs were removed from both ipsilateral and contralateral joints.", "Both inflammatory infiltrate and histopathological changes were analysed.   \n", "RESULTS MIA injection caused marked weight bearing asymmetry.", "Ipsilateral IPFP wet weights were significantly increased on days 1 and 3 in MIA-treated animals.", "MIA treatment also resulted in significant increases in IPFP total white blood cells and monocytes on days 1, 3, and 7 and neutrophils on days 1 and 3.", "This was supported by histopathological findings at early time points which progressed to adipocyte necrosis, IPFP fibrosis, patellar cartilage and subchondral bone necrosis with synovial hyperplasia at later timepoints.   \n", "CONCLUSIONS The current study clearly demonstrated that marked inflammatory changes in the IPFP occur during the early stage of the MIA model of OA which may contribute to the pain observed at this early stage.", "The role of the IPFP in later stages of the model needs to be further explored."], "structured": true}
{"doc_id": 37578311, "title": "Angiogenesis therapy: amidst the hype, the neglected potential for serious side effects.", "abstract": ["Although essentially unknown as a therapeutic concept as recently as a decade ago, it is difficult now to open a cardiology journal, attend a cardiology meeting, or scan a newspaper without being caught up in the excitement generated by the thought that angiogenesis therapy may soon have a major impact on the treatment of patients with atherosclerotic lesions obstructing arteries that supply the myocardium or legs.", "Potent therapeutic interventions, however, are rarely free of at least the potential for causing harmful effects.", "Angiogenesis therapy is no exception.", "Despite this and despite the fact that the only reasonably powered, randomized, double-blind clinical studies to date have failed to demonstrate primary end-point efficacy,1 thoughtful consideration of the serious side effects that might accompany any therapeutic benefit has been largely missing from scientific communications.  ", "For the lay media, a switch from this unbounded enthusiasm to profound skepticism occurred recently after a report of the tragic death of a young man caused by injection of large amounts of an adenoviral vector into the hepatic artery (unrelated to angiogenesis therapy).2 For the scientific community, however, there has been a general lack of in-depth discussion of the potential dangers inherent in angiogenesis interventions.", "Such a discussion is appropriate not only because of the event cited above but also because considerable mechanistic data are available that actually permit us to identify specific side effects that we might anticipate as potential complications of angiogenesis therapy.", "The following therefore is a discussion of potential complications based predominantly on our knowledge of the underlying biological activities of 2 of the most potent angiogenic cytokines, vascular endothelial growth factor (VEGF) and fibroblast growth factor (FGF).  ", "Angiogenic agents are thought to have the potential to induce neovascularization in many different tissues.", "This becomes important in that under clinical circumstances it \u2026"], "structured": false}
{"doc_id": 37583120, "title": "Body mass index and magnetic resonance markers of brain integrity in adults.", "abstract": ["OBJECTIVE Obesity and being overweight during adulthood have been consistently linked to increased risk for development of dementia later in life, especially Alzheimer's disease.", "They have also been associated with cognitive dysfunction and brain structural alterations in otherwise healthy adults.", "Although proton magnetic resonance spectroscopy may distinguish between neuronal and glial components of the brain and may point to neurobiological mechanisms underlying brain atrophy and cognitive changes, no spectroscopic studies have yet assessed the relationships between adiposity and brain metabolites.   \n", "METHODS We have utilized magnetic resonance imaging and proton magnetic resonance spectroscopic imaging data from 50 healthy middle-aged participants (mean age, 41.7 +/-", "8.5 years; 17 women), who were scanned as control subjects for another study.   \n", "RESULTS After adjustment for age and sex, greater body mass indices (BMIs) correlated with: (1) lower concentrations of N-acetylaspartate (spectroscopic marker of neuronal viability) in frontal (p = 0.001), parietal (p = 0.006), and temporal (p = 0.008) white matter; (2) lower N-acetylaspartate in frontal gray matter (p = 0.01); and (3) lower concentrations of choline-containing metabolites (associated with membrane metabolism) in frontal white matter (p = 0.05).   \n", "INTERPRETATION These results suggest that increased BMI at midlife is associated with neuronal and/or myelin abnormalities, primarily in the frontal lobe.", "Because white matter in the frontal lobes is more prone to the effects of aging than in other lobes, our results may reflect accelerated aging in individuals with high levels of adiposity.", "Thus, greater BMI may increase the odds of developing an age-related disease, such as Alzheimer's disease."], "structured": true}
{"doc_id": 37592824, "title": "Characteristics of medial temporal lobe epilepsy: II. Interictal and ictal scalp electroencephalography, neuropsychological testing, neuroimaging, surgical results, and pathology.", "abstract": ["Sixty-seven patients with temporal lobe epilepsy without circumscribed, potentially epileptogenic lesions, who were studied with intracranial electrodes and who became seizure free following temporal lobectomy were retrospectively evaluated with regard to preoperative scalp electroencephalographic (EEG) findings, neuropsychological test results, neuroimaging findings, results of surgery, and pathology of resected tissue.", "Interictal scalp EEG showed paroxysmal abnormalities during prolonged monitoring in 64 patients (96%).", "These were localized in the anterior temporal region in 60 (94%) of these 64 patients.", "Bilateral independent paroxysmal activity occurred in 42% of the patients and was preponderant over the side of seizure origin in half.", "Ictal EEG changes were rarely detected at the time of clinical seizure onset, but lateralized buildup of rhythmic seizure activity during the seizure occurred in 80% of patients.", "In 13%, the scalp EEG seizure buildup was, however, contralateral to the side of seizure origin as subsequently determined by depth EEG and curative surgery.", "Lateralized postictal slowing, when present, was a very reliable lateralizing finding.", "Neuropsychological testing provided lateralizing findings concordant with the side of seizure origin in 73% of patients.", "When neuropsychological testing produced discordant results or nonlateralizing findings, those patients were usually found to have right temporal seizure origin.", "Intracarotid amobarbital (Amytal) testing demonstrated absent or marginal memory functions on the side of seizure onset in 63% of patients, but 26 patients (37%) had bilaterally intact memory.", "In those patients who had magnetic resonance imaging, it was very sensitive in detecting subtle medial temporal abnormalities.", "These abnormalities were present in 23 of 28 magnetic resonance images, and corresponded with mesial temporal sclerosis on pathological examination in all but 2 patients.(ABSTRACT TRUNCATED AT 250 WORDS)"], "structured": false}
{"doc_id": 37608303, "title": "OPA1-dependent cristae modulation is essential for cellular adaptation to metabolic demand.", "abstract": ["Cristae, the organized invaginations of the mitochondrial inner membrane, respond structurally to the energetic demands of the cell.", "The mechanism by which these dynamic changes are regulated and the consequences thereof are largely unknown.", "Optic atrophy 1 (OPA1) is the mitochondrial GTPase responsible for inner membrane fusion and maintenance of cristae structure.", "Here, we report that OPA1 responds dynamically to changes in energetic conditions to regulate cristae structure.", "This cristae regulation is independent of OPA1's role in mitochondrial fusion, since an OPA1 mutant that can still oligomerize but has no fusion activity was able to maintain cristae structure.", "Importantly, OPA1 was required for resistance to starvation-induced cell death, for mitochondrial respiration, for growth in galactose media and for maintenance of ATP synthase assembly, independently of its fusion activity.", "We identified mitochondrial solute carriers (SLC25A) as OPA1 interactors and show that their pharmacological and genetic blockade inhibited OPA1 oligomerization and function.", "Thus, we propose a novel way in which OPA1 senses energy substrate availability, which modulates its function in the regulation of mitochondrial architecture in a SLC25A protein-dependent manner."], "structured": false}
{"doc_id": 37619697, "title": "Phenylpropanolamine and the risk of hemorrhagic stroke.", "abstract": ["BACKGROUND Phenylpropanolamine is commonly found in appetite suppressants and cough or cold remedies.", "Case reports have linked the use of products containing phenylpropanolamine to hemorrhagic stroke, often after the first use of these products.", "To study the association, we designed a case-control study.   \n", "METHODS Men and women 18 to 49 years of age were recruited from 43 U.S. hospitals.", "Eligibility criteria included the occurrence of a subarachnoid or intracerebral hemorrhage within 30 days before enrollment and the absence of a previously diagnosed brain lesion.", "Random-digit dialing identified two matched control subjects per patient.   \n", "RESULTS There were 702 patients and 1376 control subjects.", "For women, the adjusted odds ratio was 16.58 (95 percent confidence interval, 1.51 to 182.21; P=0.02) for the association between the use of appetite suppressants containing phenylpropanolamine and the risk of a hemorrhagic stroke and 3.13 (95 percent confidence interval, 0.86 to 11.46; P=0.08) for the association with the first use of a product containing phenylpropanolamine.", "All first uses of phenylpropanolamine involved cough or cold remedies.", "For men and women combined, the adjusted odds ratio was 1.49 (95 percent confidence interval, 0.84 to 2.64; P=0.17) for the association between the use of a product containing phenylpropanolamine and the risk of a hemorrhagic stroke, 1.23 (95 percent confidence interval, 0.68 to 2.24; P=0.49) for the association with the use of cough or cold remedies that contained phenylpropanolamine, and 15.92 (95 percent confidence interval, 1.38 to 184.13; P=0.03) for the association with the use of appetite suppressants that contained phenylpropanolamine.", "An analysis in men showed no increased risk of a hemorrhagic stroke in association with the use of cough or cold remedies containing phenylpropanolamine.", "No men reported the use of appetite suppressants.   \n", "CONCLUSIONS The results suggest that phenylpropanolamine in appetite suppressants, and possibly in cough and cold remedies, is an independent risk factor for hemorrhagic stroke in women."], "structured": true}
{"doc_id": 37628989, "title": "The safety of intravenous fluorescein for confocal laser endomicroscopy in the gastrointestinal tract.", "abstract": ["BACKGROUND Confocal laser endomicroscopy (CLE) is rapidly emerging as a valuable tool for gastrointestinal endoscopic imaging.", "Fluorescent contrast agents are used to optimize imaging with CLE, and intravenous fluorescein is the most widely used contrast agent.", "Fluorescein is FDA-cleared for diagnostic angiography of the retina.", "For these indications, the safety profile of fluorescein has been well-documented; however, to date, fluorescein is not cleared for use with CLE.   ", "AIMS To estimate the rate of serious and total adverse events attributable to intravenous fluorescein when used for gastrointestinal CLE.   \n", "METHODS We performed a cross sectional survey of 16 International Academic Medical Centres with active research protocols in CLE that involved intravenous fluorescein.", "Centres using i.v.", "fluorescein for CLE who were actively monitored for adverse events were included.   \n", "RESULTS Sixteen centres performed 2272 gastrointestinal CLE procedures.", "The most common dose of contrast agent was 2.5-5 mL of 10% sodium fluorescein.", "No serious adverse events were reported.", "Mild adverse events occurred in 1.4% of individuals, including nausea/vomiting, transient hypotension without shock, injection site erythema, diffuse rash and mild epigastric pain.", "The limitation is that only immediate post procedure events were actively monitored.   \n", "CONCLUSIONS Use of intravenous fluorescein for gastrointestinal CLE appears to be safe with few acute complications."], "structured": true}
{"doc_id": 37641175, "title": "Metabolic DNA as the origin of spontaneously released DNA?", "abstract": ["A DNA fraction is spontaneously released from living, but not dead or dying, human, other mammalian, avian, amphibian, plant, and prokaryote cells.", "The spontaneously released DNA fraction has been shown to be (a) present in both actively dividing and nondividing, differentiated cell populations; (b) labile; (c) associated with DNA-dependent RNA or DNA polymerase; (d) associated with an RNA fraction; and to have (e) a lower molecular weight than the typical genetic DNA fraction; and (f) Alu repeat sequences in increased proportions compared to a unique gene in plasma/serum.", "On the other hand, early autoradiographic and biochemical and quantitative cytochemical and cytophysical studies on DNA permitted the identification of a DNA fraction which was (1) present in both actively dividing and nondividing, differentiated cell populations; (2) labile; and (3) had a lower molecular weight than the typical genetic DNA fraction.", "This DNA fraction was termed metabolic DNA (m-DNA) and was proposed as possibly forming extra gene copies for the rapid production of m-RNA, to be destroyed subsequently.", "Therefore, we suggest that the metabolic DNA fraction might represent the precursor to the formation of the spontaneously released DNA fraction."], "structured": false}
{"doc_id": 37643601, "title": "The flavivirus precursor membrane-envelope protein complex: structure and maturation.", "abstract": ["Many viruses go through a maturation step in the final stages of assembly before being transmitted to another host.", "The maturation process of flaviviruses is directed by the proteolytic cleavage of the precursor membrane protein (prM), turning inert virus into infectious particles.", "We have determined the 2.2 angstrom resolution crystal structure of a recombinant protein in which the dengue virus prM is linked to the envelope glycoprotein E. The structure represents the prM-E heterodimer and fits well into the cryo-electron microscopy density of immature virus at neutral pH. The pr peptide beta-barrel structure covers the fusion loop in E, preventing fusion with host cell membranes.", "The structure provides a basis for identifying the stages of its pH-directed conformational metamorphosis during maturation, ending with release of pr when budding from the host."], "structured": false}
{"doc_id": 37673301, "title": "Peptide and non-peptide G-protein coupled receptors (GPCRs) in skeletal muscle.", "abstract": ["G-protein coupled receptors (GPCRs) represent a large class of cell surface receptors that mediate a multitude of functions.", "Over the years, a number of GPCRs and ancillary proteins have been shown to be expressed in skeletal muscle.", "Unlike the case with other muscle tissues like cardiac and vascular smooth muscle cells, there has been little attempt at systematically analyzing GPCRs in skeletal muscle.", "Here we have compiled all the GPCRs that are expressed in skeletal muscle.", "In addition, we review the known function of these receptors in both skeletal muscle tissue and in cultured skeletal muscle cells."], "structured": false}
{"doc_id": 37677954, "title": "Characterization of complete genome and small RNA profile of pagoda yellow mosaic associated virus, a novel badnavirus in China.", "abstract": ["A new badnavirus was discovered from pagoda trees showing yellow mosaic symptoms on the leaves by high throughput sequencing of small RNAs.", "The complete genome of this virus was determined to comprise 7424 nucleotides, and the virus shared 40.4-45.1% identity with that of other badnaviruses.", "The genome encodes five open reading frames (ORFs) on the plus strand, which includes three conserved badnaviral ORFs.", "These results suggest that this virus is a new member of the genus Badnavirus in the family Caulimoviridae.", "The virus is tentatively named pagoda yellow mosaic associated virus (PYMAV).", "Phylogenetic analysis suggested that this virus together with gooseberry vein banding virus (GVBV) and grapevine vein-clearing virus (GVCV) forms a separate group that is distinct two other well characterized badnaviral groups.", "Additionally, the viral derived small RNA (vsRNA) profile of PYMAV was analyzed and compared with that of viruses within the same family.", "Results showed that the most abundant PYMAV vsRNAs were 21-nt, whereas other viruses in the same family have a predominance of 22- or 24-nt vsRNA.", "The percentage of sense PYMAV vsRNA was almost equal to that of antisense vsRNA, whereas vsRNAs of other viruses in the family display preferences toward the sense strand of their genome.", "Furthermore, PYMAV vsRNAs were symmetrically distributed along the genome with no obvious vsRNA generating hotspots."], "structured": false}
{"doc_id": 37686718, "title": "Experimental approaches for the treatment of malignant gliomas.", "abstract": ["Malignant gliomas, which include glioblastomas and anaplastic astrocytomas, are the most common primary tumors of the brain.", "Over the past 30 years, the standard treatment for these tumors has evolved to include maximal safe surgical resection, radiation therapy and temozolomide chemotherapy.", "While the median survival of patients with glioblastomas has improved from 6 months to 14.6 months, these tumors continue to be lethal for the vast majority of patients.", "There has, however, been recent substantial progress in our mechanistic understanding of tumor development and growth.", "The translation of these genetic, epigenetic and biochemical findings into therapies that have been tested in clinical trials is the subject of this review."], "structured": false}
{"doc_id": 37699461, "title": "Reversal of hyperglycemia in mice by using human expandable insulin-producing cells differentiated from fetal liver progenitor cells.", "abstract": ["Beta-cell replacement is considered to be the most promising approach for treatment of type 1 diabetes.", "Its application on a large scale is hindered by a shortage of cells for transplantation.", "Activation of insulin expression, storage, and regulated secretion in stem/progenitor cells offers novel ways to overcome this shortage.", "We explored whether fetal human progenitor liver cells (FH) could be induced to differentiate into insulin-producing cells after expression of the pancreatic duodenal homeobox 1 (Pdx1) gene, which is a key regulator of pancreatic development and insulin expression in beta cells.", "FH cells possess a considerable replication capacity, and this was further extended by introduction of the gene for the catalytic subunit of human telomerase.", "Immortalized FH cells expressing Pdx1 activated multiple beta-cell genes, produced and stored considerable amounts of insulin, and released insulin in a regulated manner in response to glucose.", "When transplanted into hyperglycemic immunodeficient mice, the cells restored and maintained euglycemia for prolonged periods.", "Quantitation of human C-peptide in the mouse serum confirmed that the glycemia was normalized by the transplanted human cells.", "This approach offers the potential of a novel source of cells for transplantation into patients with type 1 diabetes."], "structured": false}
{"doc_id": 37722384, "title": "A review of the methods for human iPSC derivation.", "abstract": ["The ability to reprogram somatic cells to induced pluripotent stem cells (iPSCs) offers an opportunity to generate pluripotent patient-specific cell lines that can help model human diseases.", "These iPSC lines could also be powerful tools for drug discovery and the development of cellular transplantation therapies.", "Many methods exist for generating iPSC lines but those best suited for use in studying human diseases and developing therapies must be of adequate efficiency to produce iPSCs from samples that may be of limited abundance, capable of reprogramming cells from both skin fibroblasts and blood, and footprint-free.", "Several reprogramming techniques meet these criteria and can be utilized to derive iPSCs in projects with both basic scientific and therapeutic goals.", "Combining these reprogramming methods with small molecule modulators of signaling pathways can lead to successful generation of iPSCs from even the most recalcitrant patient-derived somatic cells."], "structured": false}
{"doc_id": 37727521, "title": "EB virus-encoded RNAs are recognized by RIG-I and activate signaling to induce type I IFN.", "abstract": ["Epstein-Barr virus (EBV)-encoded small RNAs (EBERs) are nonpolyadenylated, untranslated RNAs, exist most abundantly in latently EBV-infected cells, and are expected to show secondary structures with many short stem-loops.", "Retinoic acid-inducible gene I (RIG-I) is a cytosolic protein that detects viral double-stranded RNA (dsRNA) inside the cell and initiates signaling pathways leading to the induction of protective cellular genes, including type I interferons (IFNs).", "We investigated whether EBERs were recognized by RIG-I as dsRNA.", "Transfection of RIG-I plasmid induced IFNs and IFN-stimulated genes (ISGs) in EBV-positive Burkitt's lymphoma (BL) cells, but not in their EBV-negative counterparts or EBER-knockout EBV-infected BL cells.", "Transfection of EBER plasmid or in vitro-synthesized EBERs induced expression of type I IFNs and ISGs in RIG-I-expressing, EBV-negative BL cells, but not in RIG-I-minus counterparts.", "EBERs activated RIG-I's substrates, NF-kappaB and IFN regulatory factor 3, which were necessary for type I IFN activation.", "It was also shown that EBERs co-precipitated with RIG-I. These results indicate that EBERs are recognized by RIG-I and activate signaling to induce type I IFN in EBV-infected cells."], "structured": false}
{"doc_id": 37731372, "title": "Pregnancy in dialysis patients: a review of outcomes, complications, and management.", "abstract": ["Although uncommon, pregnancy occurs in women on chronic dialysis.", "In 1980 the incidence of pregnancy in women on dialysis was 0.9%.", "Studies from 1992 to 2003 indicate that pregnancy occurred in 1-7% of women on chronic dialysis.", "Half of the infants born to women on chronic dialysis survive.", "Of importance is that \"intensive dialysis\" of 16-24 hr/week is associated with improved infant survival.", "In this article, the incidence, duration, fetal and maternal complications, and outcomes of pregnancy in women on chronic dialysis are reviewed.", "The management of anemia, hypertension, electrolytes, bone minerals, and acid-base parameters in the pregnant dialysis patient is also summarized.", "Recommendations regarding the dialysis prescription for the pregnant woman on hemodialysis (HD) or peritoneal dialysis (PD) are also made.", "The complex and precarious condition of the pregnant woman on dialysis requires close collaboration between the patient, nephrologist, dialysis staff, obstetrician, and neonatologist to maximize the chance of a successful pregnancy."], "structured": false}
{"doc_id": 37762357, "title": "Potent immunosuppressive activities of cytomegalovirus-encoded interleukin-10.", "abstract": ["Cytomegalovirus (CMV) has highly evolved mechanisms for avoiding detection by the host immune system.", "Recently, in the genomes of human and primate CMV, a novel gene comprising segments of noncontiguous open reading frames was identified and found to have limited predicted homology to endogenous cellular interleukin-10 (IL-10).", "Here we investigate the biological activities of the CMV IL-10-like gene product and show it to possess potent immunosuppressive properties.", "Both purified bacterium-derived recombinant CMV IL-10 and CMV IL-10 expressed in supernatants of human cells were found to inhibit proliferation of mitogen-stimulated peripheral blood mononuclear cells (PBMCs), with specific activity comparable to that of recombinant human IL-10.", "In addition, CMV IL-10 expressed from human cells inhibited cytokine synthesis, as treatment of stimulated PBMCs and monocytes with CMV IL-10 led to a marked decrease in production of proinflammatory cytokines.", "Finally, CMV IL-10 was observed to decrease cell surface expression of both major histocompatibility complex (MHC) class I and class II molecules, while conversely increasing expression of the nonclassical MHC allele HLA-G. These results demonstrate for the first time that CMV has a biologically active IL-10 homolog that may contribute to immune evasion during virus infection."], "structured": false}
{"doc_id": 37768883, "title": "Evidence for the presence of urease apoprotein complexes containing UreD, UreF, and UreG in cells that are competent for in vivo enzyme activation.", "abstract": ["In vivo activation of Klebsiella aerogenes urease, a nickel-containing enzyme, requires the presence of functional UreD, UreF, and UreG accessory proteins and is further facilitated by UreE. These accessory proteins are proposed to be involved in metallocenter assembly (M. H. Lee, S. B. Mulrooney, M. J. Renner, Y. Markowicz, and R. P. Hausinger, J. Bacteriol.", "174:4324-4330, 1992).", "A series of three UreD-urease apoprotein complexes are present in cells that express ureD at high levels, and these complexes are thought to be essential for in vivo activation of the enzyme (I.-S. Park, M. B. Carr, and R. P. Hausinger, Proc.", "Natl.", "Acad.", "Sci.", "USA 91:3233-3237, 1994).", "In this study, we describe the effect of accessory gene deletions on urease complex formation.", "The ureE, ureF, and ureG gene products were found not to be required for formation of the UreD-urease complexes; however, the complexes from the ureF deletion mutant exhibited delayed elution during size exclusion chromatography.", "Because these last complexes were of typical UreD-urease sizes according to native gel electrophoretic analysis, we propose that UreF alters the conformation of the UreD-urease complexes.", "The same studies revealed the presence of an additional series of urease apoprotein complexes present only in cells containing ureD, ureF, and ureG, along with the urease subunit genes.", "These new complexes were shown to contain urease, UreD, UreF, and UreG. We propose that the UreD-UreF-UreG-urease apoprotein complexes represent the activation-competent form of urease apoprotein in the cell."], "structured": false}
{"doc_id": 37822406, "title": "Human somatic cell nuclear transfer using adult cells.", "abstract": ["Derivation of patient-specific human pluripotent stem cells via somatic cell nuclear transfer (SCNT) has the potential for applications in a range of therapeutic contexts.", "However, successful SCNT with human cells has proved challenging to achieve, and thus far has only been reported with fetal or infant somatic cells.", "In this study, we describe the application of a recently developed methodology for the generation of human ESCs via SCNT using dermal fibroblasts from 35- and 75-year-old males.", "Our study therefore demonstrates the applicability of SCNT for adult human cells and supports further investigation of SCNT as a strategy for regenerative medicine."], "structured": false}
{"doc_id": 37895688, "title": "\"Natural\" killer cells in the mouse. I. Cytotoxic cells with specificity for mouse Moloney leukemia cells. Specificity and distribution according to genotype.", "abstract": ["In the spleens of young, adult mice there exist naturally occurring killer lymphocytes with specificity for mouse Moloney leukemia cells.", "The lytic activity was directed against syngeneic or allogeneic Moloney leukemia cells to a similar extent, but was primarily expressed when tested against in vitro grown leukemia cells.", "Two leukemias of non-Moloney origin were resistant and so was the mastocytoma line P815.", "Although killer activity varied between different strains of mice, the specificity of lysis was the same as indicated by competition experiments using unlabeled Moloney or other tumor cells as inhibitors in the cytotoxic assays.", "Capacity to compete and sensitivy to lysis by the killer cells were found to be highly positively correlated.", "Analysis of the kinetics of the cytotoxic assay revealed a rapid induction of lysis within one to four hours, arguing against any conventional in vitro induction of immune response.", "No evidence was found of soluble factors playing any role in the cytolytic assay."], "structured": false}
{"doc_id": 37912677, "title": "Dose-response study on thyrotoxic patients undergoing positron emission tomography and radioiodine therapy", "abstract": ["With the acknowledged problems associated with assessment of functioning thyroid mass and hence radiation dose, our policy had been to give 75 MBq iodine-131 at 6-monthly intervals to patients with Graves' disease until they became euthyroid.", "Since positron emission tomography (PET) has been available at this hospital, the radiation dose to the thyroid has been calculated with an accuracy of \u223c20%, the thyroid mass being determined from an iodine-124 PET scan.", "A dose-response study has been carried out on 65 patients who have received single or cumulative radiation doses of <80 Gy.", "The results show that patients who receive a low radiation dose (<20 Gy) at their first treatment have a high probability of remaining toxic at 12 months.", "In contrast, patients who receive higher radiation doses (>40 Gy) at their first treatment have a high probability of control.", "The probability of becoming euthyroid increases more rapidly with increasing radiation dose than the probability of becoming hypothyroid.", "Following this dose-response study, a new treatment protocol has been introduced.", "A 124I PET tracer study prior to 131I therapy will be performed to enable a prescribed thyroid dose of 50 Gy to be delivered to patients with Graves' disease.", "Further 131I therapy will only be considered if patients are still toxic at 12 months."], "structured": false}
{"doc_id": 37916361, "title": "Increased serum soluble corin in mid pregnancy is associated with hypertensive disorders of pregnancy.", "abstract": ["OBJECTIVE The study of soluble corin in the circulation before hypertensive disorders of pregnancy (HDP) has been limited.", "Here we aimed to study serum soluble corin in mid pregnancy in patients with HDP and their age- and gestational weeks-matched controls.   \n", "METHODS Sixty-eight pairs of cases of HDP and controls were studied.", "Blood samples were obtained in mid pregnancy between 16 and 20 gestational weeks.", "Serum soluble corin was examined by enzyme-linked immunosorbent assay methods.", "The relationship between serum soluble corin and HDP was examined using conditional logistic regression models.   \n", "RESULTS Serum soluble corin in mid pregnancy was increased in cases with HDP compared with controls (median [interquartile range]: 1968 [1644-2332] pg/mL vs. 1700 [1446-2056] pg/mL, p=0.002).", "Participants were categorized into quartiles of serum soluble corin distributed in controls.", "Compared with the lowest quartile, participants in the highest quartile had a significantly increased risk for HDP (odds ratio [OR], 4.21; 95% confidence interval [95% CI], 1.31-13.53) after multivariate adjustment.", "Nevertheless, we did not find a significantly increased risk for participants in the second (OR, 1.75; 95% CI, 0.44-7.02) and third (OR, 2.80; 95% CI, 0.70-11.18) quartiles.", "Then the first three quartiles were merged as a reference group to calculate the OR of HDP for participants in the highest quartile and we found a significantly increased risk for HDP in individuals in the highest quartile (OR, 2.28, 95% CI, 1.02-5.06).   \n", "CONCLUSION Increased serum soluble corin in mid pregnancy was associated with an increased risk for HDP.", "Our findings suggest that increased serum soluble corin in mid pregnancy could be an indicator for HDP."], "structured": true}
{"doc_id": 37949139, "title": "The in vitro effect of dandelions antioxidants on microsomal lipid peroxidation.", "abstract": ["Dandelions have long been used in herbal medicine for their choleretic, diuretic, antiinflammatory, appetite-stimulating and laxative properties.", "An antioxidant property can be supposed as a basis of their-therapeutic effects.", "To understand the mechanism of the drug's action, the effects of natural extracts on a microsomal fraction of rat liver were examined.", "The extracts diminished the enzymatically induced-lipid peroxidation and reduced the cytochrome c with and without NADPH in a concentration dependent manner."], "structured": false}
{"doc_id": 37964706, "title": "Local Ca2+ influx through Ca2+ release-activated Ca2+ (CRAC) channels stimulates production of an intracellular messenger and an intercellular pro-inflammatory signal.", "abstract": ["Ca2+ entry through store-operated Ca2+ channels drives the production of the pro-inflammatory molecule leukotriene C4 (LTC4) from mast cells through a pathway involving Ca2+-dependent protein kinase C, mitogen-activated protein kinases ERK1/2, phospholipase A2, and 5-lipoxygenase.", "Here we examine whether local Ca2+ influx through store-operated Ca2+ release-activated Ca2+ (CRAC) channels in the plasma membrane stimulates this signaling pathway.", "Manipulating the amplitude and spatial extent of Ca2+ entry by altering chemical and electrical gradients for Ca2+ influx or changing the Ca2+ buffering of the cytoplasm all impacted on protein kinase C and ERK activation, generation of arachidonic acid and LTC4 secretion, with little change in the bulk cytoplasmic Ca2+ rise.", "Similar bulk cytoplasmic Ca2+ concentrations were achieved when CRAC channels were activated in 0.25 mm external Ca2+ versus 2 mm Ca2+ and 100 nm La3+, an inhibitor of CRAC channels.", "However, despite similar bulk cytoplasmic Ca2+, protein kinase C activation and LTC4 secretion were larger in 2 mm Ca2+ and La3+ than in 0.25 mm Ca2+, consistent with the central involvement of a subplasmalemmal Ca2+ rise.", "The nonreceptor tyrosine kinase Syk coupled CRAC channel opening to protein kinase C and ERK activation.", "Recombinant TRPC3 channels also activated protein kinase C, suggesting that subplasmalemmal Ca2+ rather than a microdomain exclusive to CRAC channels is the trigger.", "Hence a subplasmalemmal Ca2+ increase in mast cells is highly versatile in that it triggers cytoplasmic responses through generation of intracellular messengers as well as long distance changes through increased secretion of paracrine signals."], "structured": false}
{"doc_id": 37969403, "title": "Cytokine production patterns and lymphoproliferative responses in volunteers orally immunized with attenuated vaccine strains of Salmonella typhi.", "abstract": ["New recombinant strains of attenuated Salmonella typhi used as live oral vaccines elicit potent immune responses.", "This study examined the patterns of cytokine production and proliferation to specific S. typhi antigens in subjects orally immunized with attenuated S. typhi vaccines CVD 906, CVD 908, and CVD 908 expressing the circumsporozoite protein of Plasmodium falciparum.", "After immunization, sensitized lymphocytes were found in subjects' blood that exhibited significantly increased proliferative responses and interferon-gamma production to purified S. typhi flagella when compared with preimmunization levels.", "Significant negative correlations were observed between interleukin-4 production and both interferon-gamma production and proliferation to S. typhi flagella.", "These results demonstrate that oral immunization with attenuated S. typhi strains alone or with those carrying a foreign gene elicits strong systemic cell-mediated immunity to purified S. typhi antigens, including the production of cytokines compatible with T1-type responses."], "structured": false}
{"doc_id": 38009906, "title": "Molecular interplay of the noncoding RNA ANRIL and methylated histone H3 lysine 27 by polycomb CBX7 in transcriptional silencing of INK4a.", "abstract": ["Expression of the INK4b/ARF/INK4a tumor suppressor locus in normal and cancerous cell growth is controlled by methylation of histone H3 at lysine 27 (H3K27me) as directed by the Polycomb group proteins.", "The antisense noncoding RNA ANRIL of the INK4b/ARF/INK4a locus is also important for expression of the protein-coding genes in cis, but its mechanism has remained elusive.", "Here we report that chromobox 7 (CBX7) within the polycomb repressive complex 1 binds to ANRIL, and both CBX7 and ANRIL are found at elevated levels in prostate cancer tissues.", "In concert with H3K27me recognition, binding to RNA contributes to CBX7 function, and disruption of either interaction impacts the ability of CBX7 to repress the INK4b/ARF/INK4a locus and control senescence.", "Structure-guided analysis reveals the molecular interplay between noncoding RNA and H3K27me as mediated by the conserved chromodomain.", "Our study suggests a mechanism by which noncoding RNA participates directly in epigenetic transcriptional repression."], "structured": false}
{"doc_id": 38023457, "title": "Tumor necrosis factor alpha mediates apoptosis of brown adipocytes and defective brown adipocyte function in obesity.", "abstract": ["Severe quantitative and qualitative brown adipocyte defects are common in obesity.", "To investigate whether aberrant expression of tumor necrosis factor alpha (TNF-alpha) in obesity is involved in functional brown fat atrophy, we have studied genetically obese (ob/ob) mice with targeted null mutations in the genes encoding the two TNF receptors.", "The absence of both TNF receptors or p55 receptor alone resulted in a significant reduction in brown adipocyte apoptosis and an increase in beta(3)-adrenoreceptor and uncoupling protein-1 expression in obese mice.", "Increased numbers of multilocular functionally active brown adipocytes, and improved thermoregulation was also observed in obese animals lacking TNF-alpha function.", "These results indicate that TNF-alpha plays an important role in multiple aspects of brown adipose tissue biology and mediates the abnormalities that occur at this site in obesity."], "structured": false}
{"doc_id": 38025907, "title": "Engineered FGF19 eliminates bile acid toxicity and lipotoxicity leading to resolution of steatohepatitis and fibrosis in mice", "abstract": ["Nonalcoholic fatty liver disease (NAFLD) is an increasingly prevalent chronic liver disease for which no approved therapies are available.", "Despite intensive research, the cellular mechanisms that mediate NAFLD pathogenesis and progression are poorly understood.", "Although obesity, diabetes, insulin resistance, and related metabolic syndrome, all consequences of a Western diet lifestyle, are well-recognized risk factors for NAFLD development, dysregulated bile acid metabolism is emerging as a novel mechanism contributing to NAFLD pathogenesis.", "Notably, NAFLD patients exhibit a deficiency in fibroblast growth factor 19 (FGF19), an endocrine hormone in the gut-liver axis that controls de novo bile acid synthesis, lipogenesis, and energy homeostasis.", "Using a mouse model that reproduces the clinical progression of human NAFLD, including the development of simple steatosis, nonalcoholic steatohepatitis (NASH), and advanced \"burnt-out\" NASH with hepatocellular carcinoma, we demonstrate that FGF19 as well as an engineered nontumorigenic FGF19 analogue, M70, ameliorate bile acid toxicity and lipotoxicity to restore liver health.", "Mass spectrometry-based lipidomics analysis of livers from mice treated with FGF19 or M70 revealed significant reductions in the levels of toxic lipid species (i.e., diacylglycerols, ceramides and free cholesterol) and an increase in levels of unoxidized cardiolipins, an important component of the inner mitochondrial membrane.", "Furthermore, treatment with FGF19 or M70 rapidly and profoundly reduced levels of liver enzymes, resolved the histologic features of NASH, and enhanced insulin sensitivity, energy homeostasis, and lipid metabolism.", "Whereas FGF19 induced hepatocellular carcinoma formation following prolonged exposure in these mice, animals expressing M70 showed no evidence of liver tumorigenesis in this model.", "Conclusion: We have engineered an FGF19 hormone that is capable of regulating multiple pathways to deliver antisteatotic, anti-inflammatory, and antifibrotic activities and that represents a potentially promising therapeutic for patients with NASH.", "(Hepatology Communications 2017;1:1024-1042)."], "structured": false}
{"doc_id": 38028419, "title": "Leptin deficiency contributes to the pathogenesis of alcoholic fatty liver disease in mice.", "abstract": ["White adipose tissue (WAT) secretes adipokines, which critically regulate lipid metabolism.", "The present study investigated the effects of alcohol on adipokines and the mechanistic link between adipokine dysregulation and alcoholic fatty liver disease.", "Mice were fed alcohol for 2, 4, or 8 weeks to document changes in adipokines over time.", "Alcohol exposure reduced WAT mass and body weight in association with hepatic lipid accumulation.", "The plasma adiponectin concentration was increased at 2 weeks, but declined to normal at 4 and 8 weeks.", "Alcohol exposure suppressed leptin gene expression in WAT and reduced the plasma leptin concentration at all times measured.", "There is a highly positive correlation between plasma leptin concentration and WAT mass or body weight.", "To determine whether leptin deficiency mediates alcohol-induced hepatic lipid dyshomeostasis, mice were fed alcohol for 8 weeks with or without leptin administration for the last 2 weeks.", "Leptin administration normalized the plasma leptin concentration and reversed alcoholic fatty liver.", "Alcohol-perturbed genes involved in fatty acid \u03b2-oxidation, very low-density lipoprotein secretion, and transcriptional regulation were attenuated by leptin.", "Leptin also normalized alcohol-reduced phosphorylation levels of signal transducer Stat3 and adenosine monophosphate-activated protein kinase.", "These data demonstrated for the first time that leptin deficiency in association with WAT mass reduction contributes to the pathogenesis of alcoholic fatty liver disease."], "structured": false}
{"doc_id": 38037690, "title": "Three-dimensional chemical imaging of skin using stimulated Raman scattering microscopy", "abstract": ["Abstract.", "Stimulated Raman scattering (SRS) microscopy is used to generate structural and chemical three-dimensional images of native skin.", "We employed SRS microscopy to investigate the microanatomical features of skin and penetration of topically applied materials.", "Image depth stacks are collected at distinct wavelengths corresponding to vibrational modes of proteins, lipids, and water in the skin.", "We observed that corneocytes in stratum corneum are grouped together in clusters, 100 to 250 \u03bcm in diameter, separated by 10- to 25-\u03bcm-wide microanatomical skin-folds called canyons.", "These canyons occasionally extend down to depths comparable to that of the dermal\u2013epidermal junction below the flat surface regions in porcine and human skin.", "SRS imaging shows the distribution of chemical species within cell clusters and canyons.", "Water is predominately located within the cell clusters, and its concentration rapidly increases at the transition from stratum corneum to viable epidermis.", "Canyons do not contain detectable levels of water and are rich in lipid material.", "Oleic acid-d34 applied to the skin surface lines the canyons down to a depth of 50 \u03bcm below the surface of the skin.", "This observation could have implications on the evaluation of penetration profiles of bioactive materials measured using traditional methods, such as tape-stripping."], "structured": false}
{"doc_id": 38040186, "title": "Familial amyloidosis: a study of 52 North American-born patients examined during a 30-year period.", "abstract": ["Between 1961 and 1990, 52 patients with biopsy-proven familial amyloidosis born in North America were examined at the Mayo Clinic.", "At the time of diagnosis of familial amyloidosis, 83% of these patients had peripheral neuropathy, 33% had autonomic neuropathy, and 27% had cardiomyopathy.", "Renal disease was noted in fewer than 10%, and liver involvement was rare.", "The median age at diagnosis was 64 years.", "The sensitivity of various diagnostic biopsies was similar to that for primary amyloidosis: deposits of amyloid were found in 77 and 78% of the subcutaneous fat aspirates or rectal biopsy specimens, respectively, and in 41% of specimens of bone marrow.", "The median duration of survival of 5.8 years for patients with inherited amyloidosis was superior to that for patients with primary amyloidosis.", "When patients were stratified by organ involvement, the survival of patients with familial amyloidosis remained superior.", "The presence of cardiomyopathy and an interactive variable of age and the presence of autonomic neuropathy were powerful predictors of survival.", "Of the 52 patients, 22 died, 12 (55%) of cardiac failure or cardiac arrhythmia.", "Nine patients (41%) died of inanition in conjunction with progressive peripheral or autonomic neuropathy.", "Transthyretin was identified by immunohistochemical studies in 31 of the 34 tissue specimens tested.", "A transthyretin mutation was identified in 24 of the 31.", "A transthyretin mutation was found in five additional patients for whom tissue was unavailable for immunostaining."], "structured": false}
{"doc_id": 38043606, "title": "Mycobacterium tuberculosis and the environment within the phagosome.", "abstract": ["Once across the barrier of the epithelium, macrophages constitute the primary defense against microbial invasion.", "For most microbes, the acidic, hydrolytically competent environment of the phagolysosome is sufficient to kill them.", "Despite our understanding of the trafficking events that regulate phagosome maturation, our appreciation of the lumenal environment within the phagosome is only now becoming elucidated through real-time functional assays.", "The assays quantify pH change, phagosome/lysosome fusion, proteolysis, lipolysis, and beta-galactosidase activity.", "This information is particularly important for understanding pathogens that successfully parasitize the endosomal/lysosomal continuum.", "Mycobacterium tuberculosis infects macrophages through arresting the normal maturation process of the phagosome, retaining its vacuole at pH 6.4 with many of the characteristics of an early endosome.", "Current studies are focusing on the transcriptional response of the bacterium to the changing environment in the macrophage phagosome.", "Manipulation of these environmental cues, such as preventing the pH drop to pH 6.4 with concanamycin A, abrogates the majority of the transcriptional response in the bacterium, showing that pH is the dominant signal that the bacterium senses and responds to.", "These approaches represent our ongoing attempts to unravel the discourse that takes place between the pathogen and its host cell."], "structured": false}
{"doc_id": 38076716, "title": "High density DNA methylation array with single CpG site resolution.", "abstract": ["We have developed a new generation of genome-wide DNA methylation BeadChip which allows high-throughput methylation profiling of the human genome.", "The new high density BeadChip can assay over 480K CpG sites and analyze twelve samples in parallel.", "The innovative content includes coverage of 99% of RefSeq genes with multiple probes per gene, 96% of CpG islands from the UCSC database, CpG island shores and additional content selected from whole-genome bisulfite sequencing data and input from DNA methylation experts.", "The well-characterized Infinium\u00ae Assay is used for analysis of CpG methylation using bisulfite-converted genomic DNA.", "We applied this technology to analyze DNA methylation in normal and tumor DNA samples and compared results with whole-genome bisulfite sequencing (WGBS) data obtained for the same samples.", "Highly comparable DNA methylation profiles were generated by the array and sequencing methods (average R2 of 0.95).", "The ability to determine genome-wide methylation patterns will rapidly advance methylation research."], "structured": false}
{"doc_id": 38127792, "title": "Acentrosomal Microtubule Assembly in Mitosis: The Where, When, and How.", "abstract": ["In mitosis the cell assembles the bipolar spindle, a microtubule (MT)-based apparatus that segregates the duplicated chromosomes into two daughter cells.", "Most animal cells enter mitosis with duplicated centrosomes that provide an active source of dynamic MTs.", "However, it is now established that spindle assembly relies on the nucleation of acentrosomal MTs occurring around the chromosomes after nuclear envelope breakdown, and on pre-existing microtubules.", "Where chromosome-dependent MT nucleation occurs, when MT amplification takes place and how the two pathways function are still key questions that generate some controversies.", "We reconcile the data and present an integrated model accounting for acentrosomal microtubule assembly in the dividing cell."], "structured": false}
{"doc_id": 38131471, "title": "Molecular mechanisms of mammalian DNA repair and the DNA damage checkpoints.", "abstract": ["DNA damage is a relatively common event in the life of a cell and may lead to mutation, cancer, and cellular or organismic death.", "Damage to DNA induces several cellular responses that enable the cell either to eliminate or cope with the damage or to activate a programmed cell death process, presumably to eliminate cells with potentially catastrophic mutations.", "These DNA damage response reactions include: (a) removal of DNA damage and restoration of the continuity of the DNA duplex; (b) activation of a DNA damage checkpoint, which arrests cell cycle progression so as to allow for repair and prevention of the transmission of damaged or incompletely replicated chromosomes; (c) transcriptional response, which causes changes in the transcription profile that may be beneficial to the cell; and (d) apoptosis, which eliminates heavily damaged or seriously deregulated cells.", "DNA repair mechanisms include direct repair, base excision repair, nucleotide excision repair, double-strand break repair, and cross-link repair.", "The DNA damage checkpoints employ damage sensor proteins, such as ATM, ATR, the Rad17-RFC complex, and the 9-1-1 complex, to detect DNA damage and to initiate signal transduction cascades that employ Chk1 and Chk2 Ser/Thr kinases and Cdc25 phosphatases.", "The signal transducers activate p53 and inactivate cyclin-dependent kinases to inhibit cell cycle progression from G1 to S (the G1/S checkpoint), DNA replication (the intra-S checkpoint), or G2 to mitosis (the G2/M checkpoint).", "In this review the molecular mechanisms of DNA repair and the DNA damage checkpoints in mammalian cells are analyzed."], "structured": false}
{"doc_id": 38143689, "title": "Characterization of serotonin 5-HT2C receptor signaling to extracellular signal-regulated kinases 1 and 2.", "abstract": ["Serotonin 5-HT2C receptors (5-HT(2C)Rs) are almost exclusively expressed in the CNS, and implicated in disorders such as obesity, depression, and schizophrenia.", "The present study investigated the mechanisms governing the coupling of the 5-HT(2C)R to the extracellular signal-regulated kinases (ERKs) 1/2, using a Chinese hamster ovary (CHO) cell line stably expressing the receptor at levels comparable to those found in the brain.", "Using the non-RNA-edited isoform of the 5-HT(2C)R, constitutive ERK1/2 phosphorylation was observed and found to be modulated by full, partial and inverse agonists.", "Interestingly, agonist-directed trafficking of receptor stimulus was also observed when comparing effects on phosphoinositide accumulation and intracellular Ca2+ elevation to ERK1/2 phosphorylation, whereby the agonists, [+/-]-2,5-dimethoxy-4-iodoamphetamine (DOI) and quipazine, showed reversal of efficacy between the phosphoinositide/Ca2+ pathways, on the one hand, and the ERK1/2 pathway on the other.", "Subsequent molecular characterization found that 5-HT-stimulated ERK1/2 phosphorylation in this cellular background requires phospholipase D, protein kinase C, and activation of the Raf/MEK/ERK module, but is independent of both receptor- and non-receptor tyrosine kinases, phospholipase C, phosphoinositide 3-kinase, and endocytosis.", "Our findings underscore the potential for exploiting pathway-selective receptor states in the differential modulation of signaling pathways that play prominent roles in normal and abnormal neuronal signaling."], "structured": false}
{"doc_id": 38180456, "title": "Short-term medical service trips: a systematic review of the evidence.", "abstract": ["Short-term medical service trips (MSTs) aim to address unmet health care needs of low- and middle-income countries.", "The lack of critically reviewed empirical evidence of activities and outcomes is a concern.", "Developing evidence-based recommendations for health care delivery requires systematic research review.", "I focused on MST publications with empirical results.", "Searches in May 2013 identified 67 studies published since 1993, only 6% of the published articles on the topic in the past 20 years.", "Nearly 80% reported on surgical trips.", "Although the MST field is growing, its medical literature lags behind, with nearly all of the scholarly publications lacking significant data collection.", "By incorporating data collection into service trips, groups can validate practices and provide information about areas needing improvement."], "structured": false}
{"doc_id": 38211681, "title": "Comparison of Beck Depression Inventories -IA and -II in psychiatric outpatients.", "abstract": ["The amended (revised) Beck Depression Inventory (BDI-IA; Beck & Steer, 1993b) and the Beck Depression Inventory-II (BDI-II; Beck, Steer, & Brown, 1996) were self-administered to 140 psychiatric outpatients with various psychiatric disorders.", "The coefficient alphas of the BDI-IA and the BDI-II were, respectively, .89 and .91.", "The mean rating for Sadness on the BDI-IA was higher than it was on the BDI-II, but the mean ratings for Past Failure, Self-Dislike, Change in Sleeping Pattern, and Change in Appetite were higher on the BDI-II than they were on the BDI-IA.", "The mean BDI-II total score was approximately 2 points higher than it was for the BDI-IA, and the outpatients also endorsed approximately one more symptom on the BDI-II than they did on the BDI-IA.", "The correlations of BDI-IA and BDI-II total scores with sex, ethnicity, age, the diagnosis of a mood disorder, and the Beck Anxiety Inventory (Beck & Steer, 1993a) were within 1 point of each other for the same variables."], "structured": false}
{"doc_id": 38243984, "title": "Tumor engraftment in nude mice and enrichment in stroma- related gene pathways predict poor survival and resistance to gemcitabine in patients with pancreatic cancer.", "abstract": ["PURPOSE The goal of this study was to evaluate prospectively the engraftment rate, factors influencing engraftment, and predictability of clinical outcome of low-passage xenografts from patients with resectable pancreatic ductal adenocarcinoma (PDA) and to establish a bank of PDA xenografts.   ", "EXPERIMENTAL DESIGN Patients with resectable PDA scheduled for resection at the Johns Hopkins Hospital were eligible.", "Representative pieces of tumor were implanted in nude mice.", "The status of the SMAD4 gene and content of tumor-generating cells were determined by immunohistochemistry.", "Gene expression was carried out by using a U133 Plus 2.0 array.", "Patients were followed for progression and survival.   \n", "RESULTS A total of 94 patients with PDA were resected, 69 tumors implanted in nude mice, and 42 (61%) engrafted.", "Engrafted carcinomas were more often SMAD4 mutant, and had a metastatic gene expression signature and worse prognosis.", "Tumors from patients resistant to gemcitabine were enriched in stroma-related gene pathways.", "Tumors sensitive to gemcitabine were enriched in cell cycle and pyrimidine gene pathways.", "The time to progression for patients who received treatment with gemcitabine for metastatic disease (n = 7) was double in patients with xenografts sensitive to gemcitabine.   \n", "CONCLUSION A successful xenograft was generated in 61% of patients attempted, generating a pool of 42 PDA xenografts with significant biological information and annotated clinical data.", "Patients with PDA and SMAD4 inactivation have a better engraftment rate.", "Engraftment is a poor prognosis factor, and engrafted tumors have a metastatic gene expression signature.", "Tumors from gemcitabine-resistant patients were enriched in stromal pathways."], "structured": true}
{"doc_id": 38252314, "title": "The MCM8-MCM9 complex promotes RAD51 recruitment at DNA damage sites to facilitate homologous recombination.", "abstract": ["The minichromosome maintenance protein homologs MCM8 and MCM9 have previously been implicated in DNA replication elongation and prereplication complex (pre-RC) formation, respectively.", "We found that MCM8 and MCM9 physically associate with each other and that MCM8 is required for the stability of MCM9 protein in mammalian cells.", "Depletion of MCM8 or MCM9 in human cancer cells or the loss of function MCM9 mutation in mouse embryo fibroblasts sensitizes cells to the DNA interstrand cross-linking (ICL) agent cisplatin.", "Consistent with a role in the repair of ICLs by homologous recombination (HR), knockdown of MCM8 or MCM9 significantly reduces HR repair efficiency.", "Chromatin immunoprecipitation analysis using human DR-GFP cells or Xenopus egg extract demonstrated that MCM8 and MCM9 proteins are rapidly recruited to DNA damage sites and promote RAD51 recruitment.", "Thus, these two metazoan-specific MCM homologs are new components of HR and may represent novel targets for treating cancer in combination with DNA cross-linking agents."], "structured": false}
{"doc_id": 38296571, "title": "The 5TMM series: a useful in vivo mouse model of human multiple myeloma.", "abstract": ["The present invention provides a combination sink and dishwashing apparatus having a sink sharing a common side wall with a cabinet which defines a closed space.", "The cabinet has a wire basket for holding and washing a plurality of dishes within the cabinet.", "The common side wall is a part of the cabinet that defines the closed space and is positioned to form one side of the sink.", "The common side wall can be opened to allow the wire basket to slide from within the cabinet and into the sink, for loading and unloading the dishes.", "Within the cabinet, the invention contains a pump powered by a motor, the pump spraying water through a rotatably mounted spray arm onto the dishes to wash them, as with traditional dishwashing machines.", "The invention preferably includes a garbage disposal which is also powered by the motor.", "In an alternative embodiment, this invention can include two cabinets as described above, each located on opposing sides of the sink."], "structured": false}
{"doc_id": 38300781, "title": "Ionic protein-lipid interaction at the plasma membrane: what can the charge do?", "abstract": ["Phospholipids are the major components of cell membranes, but they have functional roles beyond forming lipid bilayers.", "In particular, acidic phospholipids form microdomains in the plasma membrane and can ionically interact with proteins via polybasic sequences, which can have functional consequences for the protein.", "The list of proteins regulated by ionic protein-lipid interaction has been quickly expanding, and now includes membrane proteins, cytoplasmic soluble proteins, and viral proteins.", "Here we review how acidic phospholipids in the plasma membrane regulate protein structure and function via ionic interactions, and how Ca(2+) regulates ionic protein-lipid interactions via direct and indirect mechanisms."], "structured": false}
{"doc_id": 38355793, "title": "A20 is overexpressed in glioma cells and may serve as a potential therapeutic target.", "abstract": ["OBJECTIVE A20 is a TNF-inducible primary response gene, which has been found to have antiapoptotic function in several cancer cells.", "This study investigates A20 expression in human glioma tissues and four glioma cell lines, and its effect on tumorigenesis of glioma cells and a mouse tumor model.   \n", "METHODS Human glioma tissue samples and cells were subject to reverse transcription-PCR (RT-PCR), western blotting and immunohistochemistry.", "Glioma cells was tested by flow cytometry.", "A xenograft tumor model in mice was utilized to examine the knock-down effect of specific A20 siRNAs on tumorigenesis.   \n", "RESULTS A20 was overexpressed in clinical glioma tissue samples (63.9%) and correlated with clinical staging.", "All four human glioma cell lines expressed A20, among which U87 displayed the strongest expression signals.", "Inhibiting A20 expression by siRNAs in vitro reduced the growth rates of glioma cells and resulted in G1/S arrest and increased apoptosis.", "In a mouse tumor model, local administration of siRNA significantly suppressed solid tumor growth.   \n", "CONCLUSIONS A20 was overexpressed both in human glioma tissues and cell lines, and inhibiting A20 expression greatly slowed tumor cell growth in culture and in mice.", "These findings indicated that A20 is involved in tumorigenesis of human glioma, and may serve as a future therapeutic target."], "structured": true}
{"doc_id": 38369817, "title": "Prevalence and size of directly detected patent foramen ovale in migraine with aura.", "abstract": ["BACKGROUND Transcranial contrast Doppler studies have shown an increased prevalence of right-to-left shunts in patients with migraine with aura compared with controls.", "The anatomy and size of these right-to-left shunts have never been directly assessed.   \n", "METHODS In a cross-sectional case-control study, the authors performed transesophageal contrast echocardiography in 93 consecutive patients with migraine with aura and 93 healthy controls.   \n", "RESULTS A patent foramen ovale was present in 44 (47% [95% CI 37 to 58%]) patients with migraine with aura and 16 (17% [95% CI 10 to 26%]) control subjects (OR 4.56 [95% CI 1.97 to 10.57]; p < 0.001).", "A small shunt was equally prevalent in migraineurs (10% [95% CI 5 to 18%]) and controls (10% [95% CI 5 to 18%]), but a moderate-sized or large shunt was found more often in the migraine group (38% [95% CI 28 to 48%] vs 8% [95% CI 2 to 13%] in controls; p < 0.001).", "The presence of more than a small shunt increased the odds of having migraine with aura 7.78-fold (95% CI 2.53 to 29.30; p < 0.001).", "Besides patent foramen ovale prevalence and shunt size, no other echocardiographic differences were found between the study groups.", "Headache and baseline characteristics did not differ in migraine patients with and without shunt.   \n", "CONCLUSIONS Nearly half of all patients with migraine with aura have a right-to-left shunt due to a patent foramen ovale.", "Shunt size is larger in migraineurs than controls.", "The clinical presentation of migraine is identical in patients with and without a patent foramen ovale."], "structured": true}
{"doc_id": 38376189, "title": "A Live Attenuated Chimeric West Nile Virus Vaccine, rWN/DEN4&Dgr;30, Is Well Tolerated and Immunogenic in Flavivirus-Naive Older Adult Volunteers", "abstract": ["West Nile virus (WNV) is a major cause of mosquito-borne illness in the United States.", "Human disease ranges from mild febrile illness to severe fatal neurologic infection.", "Adults aged >60 years are more susceptible to neuroinvasive disease accompanied by a high mortality rate or long-lasting neurologic sequelae.", "A chimeric live attenuated West Nile virus vaccine, rWN/DEN4&Dgr;30, was shown to be safe and immunogenic in healthy adults aged 18\u201350 years.", "This study evaluated rWN/DEN4&Dgr;30 in flavivirus-naive adults aged 50\u201365 years and found it to be safe and immunogenic.", "Outbreaks of WNV infection tend to be unpredictable, and a safe and effective vaccine will be an important public health tool."], "structured": false}
{"doc_id": 38380061, "title": "Localization and requirement for Myosin II at the dorsal-ventral compartment boundary of the Drosophila wing.", "abstract": ["As organisms develop, their tissues can become separated into distinct cell populations through the establishment of compartment boundaries.", "Compartment boundaries have been discovered in a wide variety of tissues, but in many cases the molecular mechanisms that separate cells remain poorly understood.", "In the Drosophila wing, a stripe of Notch activation maintains the dorsal-ventral compartment boundary, through a process that depends on the actin cytoskeleton.", "Here, we show that the dorsal-ventral boundary exhibits a distinct accumulation of Myosin II, and that this accumulation is regulated downstream of Notch signaling.", "Conversely, the dorsal-ventral boundary is depleted for the Par-3 homologue Bazooka.", "We further show that mutations in the Myosin heavy chain subunit encoded by zipper can impair dorsal-ventral compartmentalization without affecting anterior-posterior compartmentalization.", "These observations identify a distinct accumulation and requirement for Myosin activity in dorsal-ventral compartmentalization, and suggest a novel mechanism in which contractile tension along an F-actin cable at the compartment boundary contributes to compartmentalization."], "structured": false}
{"doc_id": 38401028, "title": "The cause of hepatic accumulation of fructose 1-phosphate on fructose loading.", "abstract": ["1.", "The changes in the metabolite content in freeze-clamped livers of fed rats occurring on perfusion with 10mm-d-fructose have been examined.", "2.", "The most striking effects of fructose were an accumulation of fructose 1-phosphate, as already known, up to 8.7mumol/g of liver within 10min, a loss of total adenine nucleotides (up to 35% after 40min) with a decrease in the ATP content to 23% within 10min, a sevenfold rise in the concentration of IMP to 1.1mumol/g and an eightfold rise of alpha-glycerophosphate to 1.1mumol/g.", "3.", "There was a transient decrease in P(i) from 4.2 to 1.7mumol/g.", "Within 40min the P(i) content recovered to the normal value, probably because of an uptake of P(i) from the perfusion medium.", "4.", "The degradation of the adenine nucleotides beyond the stage of AMP can be accounted for by the decrease of ATP and P(i).", "As ATP inhibits 5-nucleotidase, and as P(i) inhibits AMP deaminase any AMP arising in the tissue is liable to undergo dephosphorylation or deamination under the conditions occurring after fructose loading.", "5.", "The content of lactate increased to 4.3mumol/g at 80min; pyruvate also increased and the [lactate]/[pyruvate] ratio remained within physiological limits.", "6.", "The concentration of free fructose within the liver remained much below that in the perfusion medium, indicating that the rate of penetration of fructose into the tissue was lower than the rate of utilization.", "7.", "The fission of fructose 1-phosphate by liver aldolase is inhibited by several phosphorylated intermediates, especially by IMP.", "This inhibition is competitive with a K(i) of 0.1mm.", "8.", "The maximal rates of the enzymes synthesizing and splitting fructose 1-phosphate are about equal.", "The accumulation of fructose 1-phosphate on fructose loading is due to the inhibition of the fission of fructose 1-phosphate by the IMP arising from the degradation of the adenine nucleotides."], "structured": false}
{"doc_id": 38410121, "title": "Reported side effects to chloroquine, chloroquine plus proguanil, and mefloquine as chemoprophylaxis against malaria in Danish travelers.", "abstract": ["BACKGROUND The aim of the study was to provide data on the relative frequency of reported symptoms in travelers using chloroquine, chloroquine plus proguanil, and mefloquine.   \n", "METHOD The study was an open, nonrandomized study recording self-reported events in travelers recruited consecutively from two travel clinics in Copenhagen, Denmark.", "The main outcome measures were the relative proportion of travelers reporting particular symptoms in the three prophylaxis groups, compliance, hospitalization and premature termination of the travel.   \n", "RESULTS From May 1996 to April 1998 5, 446 travelers were included and 4,158 questionnaires (76.3%) returned.", "Compliance was significantly better in mefloquine users with 83.3% of short term travelers compared to 76.3% in chloroquine plus proguanil users.", "Also, 84.8%, 59.3% and 69.5% using chloroquine, chloroquine plus proguanil, and mefloquine respectively reported no symptoms and 0.6%, 1.1% and 2.8% reported \"unacceptable\" symptoms.", "Compared to chloroquine, mefloquine users had a significantly higher risk of reporting depression, RR 5.06 (95% CI 2.71 - 9.45), \"strange thoughts,\" RR 6.36 (95% CI 2.52 - 16.05) and altered spatial perception, RR 3.00 (95% CI 1.41 - 6.41).   \n", "CONCLUSION Overall mefloquine is tolerated at least as well as chloroquine plus proguanil and shows better compliance, however, symptoms related to the central nervous system are more prevalent in mefloquine users and when symptoms develop, they are perceived as more severe."], "structured": true}
{"doc_id": 38477436, "title": "Ubiquitinylation of the cytosolic domain of a type I membrane protein is not required to initiate its dislocation from the endoplasmic reticulum.", "abstract": ["Human cytomegalovirus US2 and US11 target newly synthesized class I major histocompatibility complex (MHC) heavy chains for rapid degradation by the proteasome through a process termed dislocation.", "The presence of US2 induces the formation of class I MHC heavy chain conjugates of increased molecular weight that are recognized by a conformation-specific monoclonal antibody, W6/32, suggesting that these class I MHC molecules retain their proper tertiary structure.", "These conjugates are properly folded glycosylated heavy chains modified by attachment of an estimated one, two, and three ubiquitin molecules.", "The folded ubiquitinated class I MHC heavy chains are not observed in control cells or in cells transfected with US11, suggesting that US2 targets class I MHC heavy chains for dislocation in a manner distinct from that used by US11.", "This is further supported by the fact that US2 and US11 show different requirements in terms of the conformation of the heavy chain molecule.", "Although ubiquitin conjugation may occur on the cytosolic tail of the class I MHC molecule, replacement of lysines in the cytosolic tail of heavy chains with arginine does not prevent their degradation by US2.", "In an in vitro system that recapitulates US2-mediated dislocation, heavy chains that lack these lysines still occur in an ubiquitin-modified form, but in the soluble (cytoplasmic) fraction.", "Such ubiquitin conjugation can only occur on the class I MHC lumenal domain and is likely to take place once class I MHC heavy chains have been discharged from the endoplasmic reticulum.", "We conclude that ubiquitinylation of class I MHC heavy chain is not required during the initial step of the US2-mediated dislocation reaction."], "structured": false}
{"doc_id": 38485364, "title": "The adaptor protein Tks5/Fish is required for podosome formation and function, and for the protease-driven invasion of cancer cells.", "abstract": ["Tks5/Fish is a scaffolding protein with five SH3 domains and one PX domain.", "In Src-transformed cells, Tks5/Fish localizes to podosomes, discrete protrusions of the ventral membrane.", "We generated Src-transformed cells with reduced Tks5/Fish levels.", "They no longer formed podosomes, did not degrade gelatin, and were poorly invasive.", "We detected Tks5/Fish expression in podosomes in invasive cancer cells, as well as in human breast cancer and melanoma samples.", "Tks5/Fish expression was also required for protease-driven matrigel invasion in human cancer cells.", "Finally, coexpression of Tks5/Fish and Src in epithelial cells resulted in the appearance of podosomes.", "Thus, Tks5/Fish appears to be required for podosome formation, for degradation of the extracellular matrix, and for invasion of some cancer cells."], "structured": false}
{"doc_id": 38493521, "title": "Corticosteroid injections for shoulder pain.", "abstract": ["BACKGROUND While many treatments, including corticosteroid injections in and around the shoulder, are advocated to be of benefit for shoulder pain, few are of proven efficacy.", "This review of corticosteroid injections for shoulder pain is one in a series of reviews of varying interventions for shoulder disorders.   \n", "OBJECTIVES To determine the efficacy and safety of corticosteroid injections in the treatment of adults with shoulder pain.   ", "SEARCH STRATEGY MEDLINE, EMBASE, CINAHL, Central and Science Citation Index were searched up to and including June 2002.   ", "SELECTION CRITERIA Randomised and pseudo-randomised trials in all languages of corticosteroid injections compared to placebo or another intervention, or of varying types and dosages of steroid injection in adults with shoulder pain.", "Specific exclusions were duration of shoulder pain less than three weeks, rheumatoid arthritis, polymyalgia rheumatica and fracture.   \n", "DATA COLLECTION AND ANALYSIS Trial inclusion and methodological quality was assessed by two independent reviewers according to predetermined criteria.", "Results are presented separately for rotator cuff disease, adhesive capsulitis, full thickness rotator cuff tear and mixed diagnoses, and, where possible, combined in meta-analysis.   \n", "MAIN RESULTS Twenty-six trials met inclusion criteria.", "The number, site and dosage of injections varied widely between studies.", "The number of participants per trial ranged from 20 to 114 (median 52 participants).", "Methodological quality was variable.", "For rotator cuff disease, subacromial steroid injection was demonstrated to have a small benefit over placebo in some trials however no benefit of subacromial steroid injection over NSAID was demonstrated based upon the pooled results of three trials.", "For adhesive capsulitis, two trials suggested a possible early benefit of intra-articular steroid injection over placebo but there was insufficient data for pooling of any of the trials.", "One trial suggested short-term benefit of intra-articular corticosteroid injection over physiotherapy in the short-term (success at seven weeks RR=1.66 (1.21, 2.28).   ", "REVIEWER'S CONCLUSIONS Despite many RCTs of corticosteroid injections for shoulder pain, their small sample sizes, variable methodological quality and heterogeneity means that there is little overall evidence to guide treatment.", "Subacromial corticosteroid injection for rotator cuff disease and intra-articular injection for adhesive capsulitis may be beneficial although their effect may be small and not well-maintained.", "There is a need for further trials investigating the efficacy of corticosteroid injections for shoulder pain.", "Other important issues that remain to be clarified include whether the accuracy of needle placement, anatomical site, frequency, dose and type of corticosteroid influences efficacy."], "structured": true}
{"doc_id": 38502066, "title": "IL-2 receptor signaling is essential for the development of Klrg1+ terminally differentiated T regulatory cells.", "abstract": ["Thymic-derived natural T regulatory cells (Tregs) are characterized by functional and phenotypic heterogeneity.", "Recently, a small fraction of peripheral Tregs has been shown to express Klrg1, but it remains unclear as to what extent Klrg1 defines a unique Treg subset.", "In this study, we show that Klrg1(+) Tregs represent a terminally differentiated Treg subset derived from Klrg1(-) Tregs.", "This subset is a recent Ag-responsive and highly activated short-lived Treg population that expresses enhanced levels of Treg suppressive molecules and that preferentially resides within mucosal tissues.", "The development of Klrg1(+) Tregs also requires extensive IL-2R signaling.", "This activity represents a distinct function for IL-2, independent from its contribution to Treg homeostasis and competitive fitness.", "These and other properties are analogous to terminally differentiated short-lived CD8(+) T effector cells.", "Our findings suggest that an important pathway driving Ag-activated conventional T lymphocytes also operates for Tregs."], "structured": false}
{"doc_id": 38528892, "title": "The aurora B kinase promotes inner and outer kinetochore interactions in budding yeast.", "abstract": ["The kinetochore is the macromolecular protein complex that mediates chromosome segregation.", "The Dsn1 component is crucial for kinetochore assembly and is phosphorylated by the Aurora B kinase.", "We found that Aurora B phosphorylation of Dsn1 promotes the interaction between outer and inner kinetochore proteins in budding yeast."], "structured": false}
{"doc_id": 38533515, "title": "AMP-activated/SNF1 protein kinases: conserved guardians of cellular energy", "abstract": ["The SNF1/AMP-activated protein kinase (AMPK) family maintains the balance between ATP production and consumption in all eukaryotic cells.", "The kinases are heterotrimers that comprise a catalytic subunit and regulatory subunits that sense cellular energy levels.", "When energy status is compromised, the system activates catabolic pathways and switches off protein, carbohydrate and lipid biosynthesis, as well as cell growth and proliferation.", "Surprisingly, recent results indicate that the AMPK system is also important in functions that go beyond the regulation of energy homeostasis, such as the maintenance of cell polarity in epithelial cells."], "structured": false}
{"doc_id": 38551172, "title": "Mammographic density, plasma vitamin D levels and risk of breast cancer in postmenopausal women.", "abstract": ["Mammographic density is a strong risk factor for breast cancer, but the underlying biology for this association is unknown.", "Studies suggest that vitamin D may reduce breast cancer risk and dietary vitamin D intake has been associated with reduced breast density.", "We conducted a case-control study nested within the Nurses' Health Study cohort consisting of 463 and 497 postmenopausal cases and controls, respectively.", "We examined the association between mammographic density and plasma levels of 25-hydroxyvitamin D [25(OH)D] and 1,25-dihydroxyvitamin D [1,25(OH)(2)D].", "We assessed whether plasma vitamin D metabolites modify the association between breast density and breast cancer.", "Percent mammographic density was measured from digitized film mammograms.", "Generalized linear models were used to determine mean percent breast density per quartile of vitamin D metabolite.", "Logistic regression models were used to calculate relative risks and confidence intervals.", "All models were adjusted for matching variables and potential confounders.", "We found no cross-sectional association between circulating levels of 25(OH)D or 1,25(OH)(2)D with mammographic density.", "Women in the highest tertile of mammographic density and lowest tertile of plasma 25(OH)D had 4 times greater risk of breast cancer than women with the lowest mammographic density and highest plasma 25(OH)D levels (RR = 3.8; 95% CI: 2.0-7.3).", "The overall interaction between mammographic density and plasma 25(OH)D was nonsignificant (p-het = 0.20).", "These results indicate that the association between mammographic density and breast cancer is independent of plasma vitamin D metabolites in postmenopausal women.", "Further research examining vitamin D, mammographic density and breast cancer risk is warranted."], "structured": false}
{"doc_id": 38587347, "title": "Finding the right niche: B-cell migration in the early phases of T-dependent antibody responses.", "abstract": ["Humoral immune responses depend on B cells encountering antigen, interacting with helper T cells, proliferating and differentiating into low-affinity plasma cells or, after organizing into a germinal center (GC), high-affinity plasma cells and memory B cells.", "Remarkably, each of these events occurs in association with distinct stromal cells in separate subcompartments of the lymphoid tissue.", "B cells must migrate from niche to niche in a rapid and highly regulated manner to successfully mount a response.", "The chemokine, CXCL13, plays a central role in guiding B cells to follicles whereas T-zone chemokines guide activated B cells to the T zone.", "Sphingosine-1-phosphate (S1P) promotes cell egress from the tissue, as well as marginal-zone B-cell positioning in the spleen.", "Recent studies have identified a role for the orphan receptor, EBV-induced molecule 2 (EBI2; GPR183), in guiding activated B cells to inter and outer follicular niche(s) and down-regulation of this receptor is essential for organizing cells into GCs.", "In this review, we discuss current understanding of the roles played by chemokines, S1P and EBI2 in the migration events that underlie humoral immune responses."], "structured": false}
{"doc_id": 38623601, "title": "Arginine Starvation Impairs Mitochondrial Respiratory Function in ASS1-Deficient Breast Cancer Cells", "abstract": ["Autophagy is the principal catabolic response to nutrient starvation and is necessary to clear dysfunctional or damaged organelles, but excessive autophagy can be cytotoxic or cytostatic and contributes to cell death.", "Depending on the abundance of enzymes involved in molecule biosynthesis, cells can be dependent on uptake of exogenous nutrients to provide these molecules.", "Argininosuccinate synthetase 1 (ASS1) is a key enzyme in arginine biosynthesis, and its abundance is reduced in many solid tumors, making them sensitive to external arginine depletion.", "We demonstrated that prolonged arginine starvation by exposure to ADI-PEG20 (pegylated arginine deiminase) induced autophagy-dependent death of ASS1-deficient breast cancer cells, because these cells are arginine auxotrophs (dependent on uptake of extracellular arginine).", "Indeed, these breast cancer cells died in culture when exposed to ADI-PEG20 or cultured in the absence of arginine.", "Arginine starvation induced mitochondrial oxidative stress, which impaired mitochondrial bioenergetics and integrity.", "Furthermore, arginine starvation killed breast cancer cells in vivo and in vitro only if they were autophagy-competent.", "Thus, a key mechanism underlying the lethality induced by prolonged arginine starvation was the cytotoxic autophagy that occurred in response to mitochondrial damage.", "Last, ASS1 was either low in abundance or absent in more than 60% of 149 random breast cancer biosamples, suggesting that patients with such tumors could be candidates for arginine starvation therapy."], "structured": false}
{"doc_id": 38630735, "title": "A prospective natural-history study of coronary atherosclerosis.", "abstract": ["BACKGROUND Atherosclerotic plaques that lead to acute coronary syndromes often occur at sites of angiographically mild coronary-artery stenosis.", "Lesion-related risk factors for such events are poorly understood.   \n", "METHODS In a prospective study, 697 patients with acute coronary syndromes underwent three-vessel coronary angiography and gray-scale and radiofrequency intravascular ultrasonographic imaging after percutaneous coronary intervention.", "Subsequent major adverse cardiovascular events (death from cardiac causes, cardiac arrest, myocardial infarction, or rehospitalization due to unstable or progressive angina) were adjudicated to be related to either originally treated (culprit) lesions or untreated (nonculprit) lesions.", "The median follow-up period was 3.4 years.   \n", "RESULTS The 3-year cumulative rate of major adverse cardiovascular events was 20.4%.", "Events were adjudicated to be related to culprit lesions in 12.9% of patients and to nonculprit lesions in 11.6%.", "Most nonculprit lesions responsible for follow-up events were angiographically mild at baseline (mean [\u00b1SD] diameter stenosis, 32.3\u00b120.6%).", "However, on multivariate analysis, nonculprit lesions associated with recurrent events were more likely than those not associated with recurrent events to be characterized by a plaque burden of 70% or greater (hazard ratio, 5.03; 95% confidence interval [CI], 2.51 to 10.11; P<0.001) or a minimal luminal area of 4.0 mm(2) or less (hazard ratio, 3.21; 95% CI, 1.61 to 6.42; P=0.001) or to be classified on the basis of radiofrequency intravascular ultrasonography as thin-cap fibroatheromas (hazard ratio, 3.35; 95% CI, 1.77 to 6.36; P<0.001).   \n", "CONCLUSIONS In patients who presented with an acute coronary syndrome and underwent percutaneous coronary intervention, major adverse cardiovascular events occurring during follow-up were equally attributable to recurrence at the site of culprit lesions and to nonculprit lesions.", "Although nonculprit lesions that were responsible for unanticipated events were frequently angiographically mild, most were thin-cap fibroatheromas or were characterized by a large plaque burden, a small luminal area, or some combination of these characteristics, as determined by gray-scale and radiofrequency intravascular ultrasonography.", "(Funded by Abbott Vascular and Volcano; ClinicalTrials.gov number, NCT00180466.)."], "structured": true}
{"doc_id": 38664102, "title": "What do medical schools teach about women's health and gender differences?", "abstract": ["PURPOSE To examine the curricula of U.S. medical schools to assess the inclusion of women's health and gender-specific information and identify institutional characteristics associated with this content.   \n", "METHOD Using data from the Association of American Medical Colleges' Curriculum Management and Information Tool (CurrMIT), in November 2003 to February 2004 the authors performed a curriculum search of schools that entered course/clerkships in CurrMIT to identify interdisciplinary women's health or gender-specific courses/clerkships.", "A subset of schools that entered comprehensive information in CurrMIT was searched for a specified list of women's health topics and or gender-specific content on any topic.", "Statistical analyses were performed to assess the relationship between frequency of topics and school characteristics.   \n", "RESULTS The authors identified 95 schools that entered related courses/clerkships.", "Ten courses/clerkships at nine schools met criteria for an interdisciplinary women's health course/clerkship.", "In the subset of 60 schools with comprehensive CurrMIT information, 18 specified women's health topics were identified, as well as 24 topics on gender-specific content, for a total of 42 topics.", "The number of topics taught ranged from zero to 26 (mean = 11).", "More than 50% of these schools taught 11 of the 18 specified topics, while fewer than 30% included gender-specific topics.", "There was no association in bivariate analysis between the mean number of topics taught and schools' characteristics; however, a women's health program (p= .01) and female dean (p= .06) were positively associated in a regression model.   \n", "CONCLUSIONS Few schools offer interdisciplinary women's health courses/clerkships or include gender-specific information in their curricula.", "A designated women's health program may increase this content in schools' curricula."], "structured": true}
{"doc_id": 38675228, "title": "A molecular framework for plant regeneration.", "abstract": ["Plants and some animals have a profound capacity to regenerate organs from adult tissues.", "Molecular mechanisms for regeneration have, however, been largely unexplored.", "Here we investigate a local regeneration response in Arabidopsis roots.", "Laser-induced wounding disrupts the flow of auxin-a cell-fate-instructive plant hormone-in root tips, and we demonstrate that resulting cell-fate changes require the PLETHORA, SHORTROOT, and SCARECROW transcription factors.", "These transcription factors regulate the expression and polar position of PIN auxin efflux-facilitating membrane proteins to reconstitute auxin transport in renewed root tips.", "Thus, a regeneration mechanism using embryonic root stem-cell patterning factors first responds to and subsequently stabilizes a new hormone distribution."], "structured": false}
{"doc_id": 38712515, "title": "Cocoa flavonols and procyanidins promote transforming growth factor-beta1 homeostasis in peripheral blood mononuclear cells.", "abstract": ["Evidence suggests that certain flavan-3-ols and procyanidins (FP) can have a positive influence on cardiovascular health.", "It has been previously reported that FP isolated from cocoa can potentially modulate the level and production of several signaling molecules associated with immune function and inflammation, including several cytokines and eicosanoids.", "In the present study, we examined whether FP fractions monomers through decamers modulate secretion of the cytokine transforming growth factor (TGF)-beta(1) from resting human peripheral blood mononuclear cells (PBMC).", "A total of 13 healthy subjects were studied and grouped according to their baseline production of TGF-beta(1).", "When cells from individuals with low baseline levels of TGF-beta(1) (n = 7) were stimulated by individual FP fractions (25 microg/ml), TGF-beta(1) release was enhanced in the range of 15%-66% over baseline (P < 0.05; monomer, dimer, and tetramer).", "The low-molecular-weight FP fractions (<or=pentamer) were more effective at augmenting TGF-beta(1) secretion than their larger counterparts (>or=hexamer), with the monomer and dimer inducing the greatest increases (66% and 68%, respectively).", "In contrast to the above, TGF-beta(1) secretion from high TGF-beta(1) baseline subjects (n = 6) was inhibited by individual FP fractions (P < 0.05; trimer through decamer).", "The inhibition was most pronounced with trimeric through decameric fractions (28%-42%), and monomers and dimers moderately inhibited TGF-beta(1) release (17% and 23%, respectively).", "Given the vascular actions associated with TGF-beta(1), we suggest that in healthy individuals, homeostatic modulation of its production by FP offers an additional mechanism by which FP-rich foods can potentially benefit cardiovascular health."], "structured": false}
{"doc_id": 38727075, "title": "BMP receptor IA is required in mammalian neural crest cells for development of the cardiac outflow tract and ventricular myocardium.", "abstract": ["The neural crest is a multipotent, migratory cell population arising from the border of the neural and surface ectoderm.", "In mouse, the initial migratory neural crest cells occur at the five-somite stage.", "Bone morphogenetic proteins (BMPs), particularly BMP2 and BMP4, have been implicated as regulators of neural crest cell induction, maintenance, migration, differentiation and survival.", "Mouse has three known BMP2/4 type I receptors, of which Bmpr1a is expressed in the neural tube sufficiently early to be involved in neural crest development from the outset; however, earlier roles in other domains obscure its requirement in the neural crest.", "We have ablated Bmpr1a specifically in the neural crest, beginning at the five-somite stage.", "We find that most aspects of neural crest development occur normally; suggesting that BMPRIA is unnecessary for many aspects of early neural crest biology.", "However, mutant embryos display a shortened cardiac outflow tract with defective septation, a process known to require neural crest cells and to be essential for perinatal viability.", "Surprisingly, these embryos die in mid-gestation from acute heart failure, with reduced proliferation of ventricular myocardium.", "The myocardial defect may involve reduced BMP signaling in a novel, minor population of neural crest derivatives in the epicardium, a known source of ventricular myocardial proliferation signals.", "These results demonstrate that BMP2/4 signaling in mammalian neural crest derivatives is essential for outflow tract development and may regulate a crucial proliferation signal for the ventricular myocardium."], "structured": false}
{"doc_id": 38735355, "title": "Early intermittent noninvasive ventilation for acute chest syndrome in adults with sickle cell disease: a pilot study", "abstract": ["Alveolar hypoxia and hypoxic vasoconstriction lead to trapping of sickle cells within the pulmonary vasculature.", "Improving alveolar ventilation and oxygenation may improve the outcome of acute chest syndrome (ACS).", "Prospective randomized single-center open study from November 1998 to February 2002 to test whether noninvasive ventilation (NIV) was more effective than oxygen alone in improving oxygenation on day 3 in adults with ACS and to evaluate the effects on pain, transfusion requirements, and length of stay.", "Seventy-one consecutive ACS episodes in 67 patients were randomly allocated to oxygen (n = 36) or NIV (n = 35) for 3 days in a medical step-down unit.", "Baseline respiratory rate and pain score were higher in the NIV group.", "NIV promptly lowered the respiratory rate, raised $$ {\\text{Pa}}_{{\\text{O}_{2}}} $$ , and decreased alveolar\u2013arterial oxygen gradient $$ (({\\text{A}} - {\\text{a}})_{{{\\text{O}}_{ 2} }} ) $$ , which remained unchanged with oxygen alone.", "$$ {\\text{Pa}}_{{{\\text{CO}}_{ 2} }} $$ significantly worsened only in the oxygen group.", "On day 3, the groups did not differ regarding the proportion of episodes with normal $$ {\\text{Pa}}_{{{\\text{O}}_{ 2} }} $$ (35% with NIV and 25% with oxygen; P = 0.5) or $$ (({\\text{A}} - {\\text{a}})_{{{\\text{O}}_{ 2} }} ) $$ .", "Patient satisfaction and compliance were lower with NIV.", "No differences were noted in pain relief, transfusions, or length of stay.", "In the subgroup of patients with severe hypoxemia $$ ( {\\text{Pa}}_{{{\\text{O}}_{ 2} }} \\le 6 5\\,{\\text{mmHg)}} $$ , physiological variables also improved faster with NIV, the differences being slightly more pronounced.", "Respiratory rate and gas exchange improved faster with NIV.", "However, NIV failed to significantly reduce the number of patients remaining hypoxemic at day 3, and was associated with greater patient discomfort."], "structured": false}
{"doc_id": 38745690, "title": "Serum Exosome MicroRNA as a Minimally-Invasive Early Biomarker of AML", "abstract": ["Relapse remains the major cause of mortality for patients with Acute Myeloid Leukemia (AML).", "Improved tracking of minimal residual disease (MRD) holds the promise of timely treatment adjustments to preempt relapse.", "Current surveillance techniques detect circulating blasts that coincide with advanced disease and poorly reflect MRD during early relapse.", "Here, we investigate exosomes as a minimally invasive platform for a microRNA (miRNA) biomarker.", "We identify a set of miRNA enriched in AML exosomes and track levels of circulating exosome miRNA that distinguish leukemic xenografts from both non-engrafted and human CD34+ controls.", "We develop biostatistical models that reveal circulating exosomal miRNA at low marrow tumor burden and before circulating blasts can be detected.", "Remarkably, both leukemic blasts and marrow stroma contribute to serum exosome miRNA.", "We propose development of serum exosome miRNA as a platform for a novel, sensitive compartment biomarker for prospective tracking and early detection of AML recurrence."], "structured": false}
{"doc_id": 38747567, "title": "Human cytomegalovirus encodes an MHC class I-like molecule (UL142) that functions to inhibit NK cell lysis.", "abstract": ["Clinical and low passage strains of human CMV (HCMV) encode an additional MHC class I-related molecule UL142, in addition to the previously described UL18.", "The UL142 open reading frame is encoded within the ULb' region which is missing from a number of common high passage laboratory strains.", "Cells expressing UL142 following transfection, and fibroblasts infected with a recombinant adenovirus-expressing UL142, were used to screen both polyclonal NK cells and NK cell clones, in a completely autologous system.", "Analysis of 100 NK cell clones derived from five donors, revealed 23 clones that were inhibited by fibroblasts expressing UL142 alone.", "Small-interfering RNA-mediated knockdown of UL142 mRNA expression in HCMV-infected cells resulted in increased sensitivity to lysis.", "From these data we conclude that UL142 is a novel HCMV-encoded MHC class I-related molecule which inhibits NK cell killing in a clonally dependent manner."], "structured": false}
{"doc_id": 38751591, "title": "Identification of the conserved serine/threonine residues important for gibberellin-sensitivity of Arabidopsis RGL2 protein.", "abstract": ["The DELLA proteins GAI, RGA, RGL1 and RGL2 in Arabidopsis are plant growth repressors, repressing diverse developmental processes.", "Studies have shown that gibberellin (GA) attenuates the repressive function of DELLA proteins by triggering their degradation via the proteasome pathway.", "However, it is not known if GA-induced protein degradation is the only pathway for regulating the bioactivity of DELLA proteins.", "We show here that tobacco BY2 cells represent a suitable system for studying GA signaling.", "RGL2 exists in a phosphorylated form in BY2 cells.", "RGL2 undergoes GA-induced degradation, and this process is blocked by proteasome inhibitors and serine/threonine phosphatase inhibitors; however, serine/threonine kinase inhibitors had no detectable effect, suggesting that dephosphorylation of serine/threonine is probably a prerequisite for degradation of RGL2 via the proteasome pathway.", "Site-directed substitution of all 17 conserved serine and threonine residues showed that six mutants (RGL2(S441D, RGL2(S542D), RGL2(T271E), RGL2(T319E), RGL2(T411E) and RGL2(T535E)) mimicking the status of constitutive phosphorylation are resistant to GA-induced degradation.", "This suggests that these sites are potential phosphorylation sites.", "A functional assay based on the expression of GA 20-oxidase revealed that RGL2(T271E) is probably a null mutant, RGL2(S441D), RGL2(S542D), RGL2(T319E) and RGL2(T411E) only retained about 4-17% of the activity of the wild type RGL2, whereas RGL2(T535E) retained about 66% of the activity of the wild type RGL2.", "However, expression of GA 20-oxidase in BY2 cells expressing these mutant proteins is still responsive to GA, suggesting that the stabilization of RGL2 protein is not the only pathway for regulating its bioactivity."], "structured": false}
{"doc_id": 38752049, "title": "A chart review of cyproheptadine for stimulant-induced weight loss.", "abstract": ["Youths with attention deficit hyperactivity disorder often experience weight loss on stimulants, which may limit optimal dosing and compliance.", "Cyproheptadine has been shown in medical samples to stimulate weight gain.", "We conducted a retrospective chart review of 28 consecutive pediatric psychiatry outpatients prescribed cyproheptadine for weight loss or insomnia while on stimulants.", "Of these, 4 patients never took cyproheptadine consistently, and 3 discontinued it within the first 7 days due to intolerable side effects.", "Data were analyzed for 21 other patients (age range 4-15 years) who continued with 4-8 mg of cyproheptadine nightly (mean final dose = 4.9 mg/day) for at least 14 days (mean duration = 104.7 days).", "Most had lost weight on stimulant alone (mean weight loss was 2.1 kg, mean weight velocity was -19.3 g/day).", "All 21 gained weight taking concomitant cyproheptadine, with a mean gain of 2.2 kg (paired t = 6.87, p < 0.0001) and a mean weight velocity of 32.3 g/day.", "Eleven of 17 patients who had reported initial insomnia on stimulant alone noted significant improvements in sleep with cyproheptadine added.", "We conclude that concomitant cyproheptadine may be useful in youths with attention deficit hyperactivity disorder for stimulant-induced weight loss, pending future randomized controlled trials."], "structured": false}
{"doc_id": 38784540, "title": "Life course breast cancer risk factors and adult breast density (United Kingdom)", "abstract": ["Objective To determine whether risk factors in childhood and early adulthood affect later mammographic breast density.", "Methods: Subjects were 628 women who attended a medical examination at the University of Glasgow Student Health Service (1948\u20131968), responded to a questionnaire (2001) and had a screening mammogram in Scotland (1989\u20132002).", "Mammograms (median age of 59years) were classified using a six category classification (SCC) of breast density percent.", "Logistic regression was used to determine associations between risk factors and having a high-risk mammogram (\u226525 dense).", "Results: In multi-variable analyses, high-risk mammograms were associated with parity (adjusted odds ratio (OR) per child: 0.77 (95 confidence interval (CI) 0.61\u20130.99)), age at first birth, OR per year: 1.05 (0.99\u20131.11), smoking at university, OR smokers versus non-smokers: 0.58 (0.36\u20130.92) and body mass index (BMI) while at university, OR per 1kg/m20.75 (0.69\u20130.82).", "No associations with SCC were found for age at menarche, birth weight, oral contraceptive (OC) use, height, leg length or exercise at age 20.", "Conclusions: We confirm previous findings that breast density is affected by reproductive events and some anthropometric measures, however most of the risk factors acting throughout the life course which we examined were not closely related to adult breast density."], "structured": false}
{"doc_id": 38793927, "title": "Osteoclast nuclei of myeloma patients show chromosome translocations specific for the myeloma cell clone: a new type of cancer-host partnership?", "abstract": ["A major clinical manifestation of bone cancers is bone destruction.", "It is widely accepted that this destruction is not caused by the malignant cells themselves, but by osteoclasts, multinucleated cells of monocytic origin that are considered to be the only cells able to degrade bone.", "The present study demonstrates that bone-resorbing osteoclasts from myeloma patients contain nuclei with translocated chromosomes of myeloma B-cell clone origin, in addition to nuclei without these translocations, by using combined FISH and immunohistochemistry on bone sections.", "These nuclei of malignant origin are transcriptionally active and appear fully integrated amongst the other nuclei.", "The contribution of malignant nuclei to the osteoclast population analysed in this study was greater than 30%.", "Osteoclast-myeloma clone hybrids contained more nuclei than normal osteoclasts and their occurrence correlated with the proximity of myeloma cells.", "Similar hybrid cells were generated in myeloma cell-osteoclast co-cultures, as revealed by tracing myeloma nuclei using translocations, bromo-deoxyuridine, or the Y chromosome of male myeloma cells in female osteoclasts.", "These observations indicate that hybrid cells can originate through fusion between myeloma cells and osteoclasts.", "In conclusion, malignant cells contribute significantly to the formation of bone-resorbing osteoclasts in multiple myeloma.", "Osteoclast-myeloma clone hybrids reflect a previously unrecognized mechanism of bone destruction in which malignant cells participate directly.", "The possibility that malignant cells corrupt host cells by the transfer of malignant DNA may have been underestimated to date in cancer research."], "structured": false}
{"doc_id": 38794814, "title": "Frequency modulation entrains slow neural oscillations and optimizes human listening behavior.", "abstract": ["The human ability to continuously track dynamic environmental stimuli, in particular speech, is proposed to profit from \"entrainment\" of endogenous neural oscillations, which involves phase reorganization such that \"optimal\" phase comes into line with temporally expected critical events, resulting in improved processing.", "The current experiment goes beyond previous work in this domain by addressing two thus far unanswered questions.", "First, how general is neural entrainment to environmental rhythms: Can neural oscillations be entrained by temporal dynamics of ongoing rhythmic stimuli without abrupt onsets?", "Second, does neural entrainment optimize performance of the perceptual system: Does human auditory perception benefit from neural phase reorganization?", "In a human electroencephalography study, listeners detected short gaps distributed uniformly with respect to the phase angle of a 3-Hz frequency-modulated stimulus.", "Listeners' ability to detect gaps in the frequency-modulated sound was not uniformly distributed in time, but clustered in certain preferred phases of the modulation.", "Moreover, the optimal stimulus phase was individually determined by the neural delta oscillation entrained by the stimulus.", "Finally, delta phase predicted behavior better than stimulus phase or the event-related potential after the gap.", "This study demonstrates behavioral benefits of phase realignment in response to frequency-modulated auditory stimuli, overall suggesting that frequency fluctuations in natural environmental input provide a pacing signal for endogenous neural oscillations, thereby influencing perceptual processing."], "structured": false}
{"doc_id": 38799797, "title": "Interventions by pharmacists in out-patient pharmaceutical care.", "abstract": ["Interventions by the pharmacists have always been considered as a valuable input by the health care community in the patient care process by reducing the medication errors, rationalizing the therapy and reducing the cost of therapy.", "The primary objective of this study was to determine the number and types of medication errors intervened by the dispensing pharmacists at OPD pharmacy in the Khoula Hospital during 2009 retrospectively.", "The interventions filed by the pharmacists and assistant pharmacists in OPD pharmacy were collected.", "Then they were categorized and analyzed after a detailed review.", "The results show that 72.3% of the interventions were minor of which 40.5% were about change medication order.", "Comparatively more numbers of prescriptions were intervened in female patients than male patients.", "98.2% of the interventions were accepted by the prescribers reflecting the awareness of the doctors about the importance of the pharmacy practice.", "In this study only 688 interventions were due to prescribing errors of which 40.5% interventions were done in changing the medication order of clarifying the medicine.", "14.9% of the interventions were related to administrative issues, 8.7% of the interventions were related to selection of medications as well as errors due to ignorance of history of patients.", "8.2% of the interventions were to address the overdose of medications.", "Moderately significant interventions were observed in 19.4% and 7.5% of them were having the impact on major medication errors.", "Pharmacists have intervened 20.8% of the prescriptions to prevent complications, 25.1% were to rationalize the treatment, 7.9% of them were to improve compliance.", "Based on the results we conclude that the role of pharmacist in improving the health care system is vital.", "We recommend more number of such research based studies to bring awareness among health care professionals, provide solution to the prescription and dispensing problems, as it can also improve the documentation system, emphasize the importance of it, reduce prescribing errors, and update the knowledge of pharmacists and other health care professionals."], "structured": false}
{"doc_id": 38805486, "title": "Biochemical studies on Mycobacterium tuberculosis UreG and comparative modeling reveal structural and functional conservation among the bacterial UreG family.", "abstract": ["Nickel is a fundamental micronutrient for cellular life, but it is toxic in soluble form at nonphysiological concentrations.", "Such potentially contradictory features required living organisms to develop efficient systems for nickel utilization and homeostasis.", "This is the case for incorporation of nickel into the active site of urease, a multistep, tightly regulated process, requiring the interplay of various accessory proteins.", "The understanding of this activation mechanism may find medical applications against ureolytic bacteria, among which Mycobacterium tuberculosis is a deadly pathogen for humans.", "The topic of this study is UreG, an essential chaperone in the in vivo activation of urease upon insertion of Ni2+ into the active site.", "The protein was examined using both experimental and computational approaches.", "In particular, the soluble M. tuberculosis UreG (MtUreG) was overexpressed in Escherichia coli and purified to homogeneity.", "The identity of the isolated protein was established by mass spectrometry.", "On-line size-exclusion chromatography and light scattering indicated that MtUreG exists as a dimeric form in solution.", "Determination of the free thiol concentration revealed that a disulfide bond is present in the dimer.", "The isolated MtUreG shows low GTPase activity under native conditions, with a kcat of 0.01 min-1.", "Circular dichroism spectroscopy demonstrated the presence of a well-defined secondary structure (8% alpha-helices, 29% beta-strands) in MtUreG, whereas NMR spectroscopy indicated that this protein does not behave as a rigid three-dimensional fold and thus can be assigned to the class of intrinsically unstructured polypeptides.", "The molecular model of MtUreG in the fully folded and functional form was built using fold recognition algorithms.", "An extensive similarity search was performed to determine conservation patterns in all known bacterial UreG sequences.", "The generation of a multiple-sequence alignment and the related phylogenetic tree allowed us to recognize key residues and motifs that are likely important for protein function.", "A structural database containing the homology-built models of the most representative UreG proteins was created, confirming the structural analogies among the UreG family.", "A flexible region, likely to be important for protein function, is identified.", "The structural conservation among this class of GTPases is discussed on the basis of their function in the urease assembly process."], "structured": false}
{"doc_id": 38808600, "title": "(99m)Tc-HisoDGR as a Potential SPECT Probe for Orthotopic Glioma Detection via Targeting of Integrin \u03b15\u03b21.", "abstract": ["Integrins, a large family of cell adhesion receptors, have been shown to play an important role for glioma proliferation and invasion.", "Several integrin receptors, including \u03b1v\u03b23, \u03b1v\u03b25, and \u03b15\u03b21, have generated clinical interest for glioma diagnosis and antitumor therapy.", "Integrin \u03b15\u03b21 has been highlighted as a prognostic and diagnostic marker in glioma, and its expression is correlated with a worse prognosis in high-grade glioma.", "However, unlike extensively studied integrins \u03b1v\u03b23 and \u03b1v\u03b25, very few integrin \u03b15\u03b21-specific radiotracers have been reported.", "Developing \u03b15\u03b21-specific radiotracers may provide alternative diagnosis and evaluation options in addition to well-studied \u03b1v\u03b23/\u03b1v\u03b25-specific tracers, and they may add new documents for profiling tumor progression.", "Here, a novel integrin \u03b15\u03b21-specific probe (99m)Tc-HisoDGR was fabricated for SPECT (single-photon emission computed tomography) imaging of glioma.", "To confirm its selective targeting of integrin \u03b15\u03b21 in vivo, the mouse models of \u03b15\u03b21-positive U87MG human glioma were subjected to SPECT/CT scans, and biodistribution experiments and blocking studies were performed.", "Small-animal SPECT/CT imaging experiments demonstrated that the tumors were clearly visualized in both subcutaneous and orthotopic glioma tumor models with clear background at 0.5, 1, and 2 h p.i.", "The tumor accumulation of (99m)Tc-HisoDGR showed significant reduction when excess cold isoDGR peptide was coinjected, suggesting that the tumor uptake was specifically mediated.", "Our work revealed that (99m)Tc-HisoDGR represented a powerful molecular probe for integrin \u03b15\u03b21-positive cancer imaging; moreover, it might be a promising tool for evaluating malignancy, predicting prognosis, selecting subpopulations of patients who might be sensitive to integrin \u03b15\u03b21-targeted drugs, and assessing and monitoring the response to integrin \u03b15\u03b21-targeted drugs in clinical trials."], "structured": false}
{"doc_id": 38811597, "title": "Effect of cyclic AMP-dependent protein phosphorylating conditions on the pH-dependent activity of tyrosine hydroxylase from beef and rat striata.", "abstract": ["Tyrosine hydroxylase (TH, EC 1.14.16.2) from beef brain striata was purified 23-fold from an extract of an acetone powder.", "If this enzyme preparation is treated with a cyclic AMP[-dependent protein phosphorylation system, there is a change in the pH dependence of the enzyme activity.", "The pH optimum at saturating tetrahydrobiopterin (BH4) concentration is shifted from below pH 6 to about pH 6.7.", "At pH 7, activation is expressed mainly as an increase in Vmax, whereas at pH 6, activation is expressed mainly as a decrease in Km for the pterin cofactor.", "Further, even with the control enzyme the Km for pterin cofactor declines precipitously as the pH is increased from 6 toward neutrality.", "Similar data were obtained with G-25 Sephadex-treated rat striatal TH.", "Experiments in which rat striatal synaptosomes were used demonstrated that the in situ activation of TH by phosphorylating conditions is expressed primarily as an increase in the maximum rate of dopamine synthesis.", "These results indicate that changes in TH activity caused by cyclic AMP-dependent protein phosphorylation will depend to a large extent on the pH of the TH environment."], "structured": false}
{"doc_id": 38830961, "title": "Interaction of TNF with TNF receptor type 2 promotes expansion and function of mouse CD4+CD25+ T regulatory cells.", "abstract": ["Although TNF is a major proinflammatory cytokine, increasing evidence indicates that TNF also has immunosuppressive feedback effects.", "We have demonstrated in this study that, in both resting and activated states, mouse peripheral CD4(+)CD25(+) T regulatory cells (Tregs) expressed remarkably higher surface levels of TNFR2 than CD4(+)CD25(-) T effector cells (Teffs).", "In cocultures of Tregs and Teffs, inhibition of proliferation of Teffs by Tregs was initially transiently abrogated by exposure to TNF, but longer exposure to TNF restored suppressive effects.", "Cytokine production by Teffs remained continually suppressed by Tregs.", "The profound anergy of Tregs in response to TCR stimulation was overcome by TNF, which expanded the Treg population.", "Furthermore, in synergy with IL-2, TNF expanded Tregs even more markedly up-regulated expression of CD25 and FoxP3 and phosphorylation of STAT5, and enhanced the suppressive activity of Tregs.", "Unlike TNF, IL-1beta and IL-6 did not up-regulate FoxP3-expressing Tregs.", "Furthermore, the number of Tregs increased in wild-type mice, but not in TNFR2(-/-) mice following sublethal cecal ligation and puncture.", "Depletion of Tregs significantly decreased mortality following cecal ligation and puncture.", "Thus, the stimulatory effect of TNF on Tregs resembles the reported costimulatory effects of TNF on Teffs, but is even more pronounced because of the higher expression of TNFR2 by Tregs.", "Moreover, our study suggests that the slower response of Tregs than Teffs to TNF results in delayed immunosuppressive feedback effects."], "structured": false}
{"doc_id": 38844612, "title": "The basics of epithelial-mesenchymal transition.", "abstract": ["The origins of the mesenchymal cells participating in tissue repair and pathological processes, notably tissue fibrosis, tumor invasiveness, and metastasis, are poorly understood.", "However, emerging evidence suggests that epithelial-mesenchymal transitions (EMTs) represent one important source of these cells.", "As we discuss here, processes similar to the EMTs associated with embryo implantation, embryogenesis, and organ development are appropriated and subverted by chronically inflamed tissues and neoplasias.", "The identification of the signaling pathways that lead to activation of EMT programs during these disease processes is providing new insights into the plasticity of cellular phenotypes and possible therapeutic interventions."], "structured": false}
{"doc_id": 38873881, "title": "Child maltreatment, other trauma exposure, and posttraumatic symptomatology among children with oppositional defiant and attention deficit hyperactivity disorders.", "abstract": ["Consecutive child psychiatric outpatient admissions with disruptive behavior or adjustment disorders were assessed by validated instruments for trauma exposure and posttraumatic stress disorder (PTSD) symptoms and other psychopathology.", "Four reliably diagnosed groups were defined in a retrospective case-control design: Attention Deficit Hyperactivity Disorder (ADHD), Oppositional Defiant Disorder (ODD), comorbid ADHD-ODD, and adjustment disorder controls.", "ODD and (although to a lesser extent) ADHD were associated with a history of physical or sexual maltreatment.", "PTSD symptoms were most severe if (a) ADHD and maltreatment co-occurred or (b) ODD and accident/illness trauma co-occurred.", "The association between ODD and PTSD Criterion D (hyperarousal/hypervigilance) symptoms remained after controlling for overlapping symptoms, but the association of ADHD with PTSD symptoms was largely due to an overlapping symptom.", "These findings suggest that screening for maltreatment, other trauma, and PTSD symptoms may enhance prevention, treatment, and research concerning childhood disruptive behavior disorders."], "structured": false}
{"doc_id": 38882175, "title": "Exercise-induced asthma screening of elite athletes: field versus laboratory exercise challenge.", "abstract": ["PURPOSE The purpose of this study was to compare a laboratory based exercise challenge (LBC) to a field based exercise challenge (FBC) for pulmonary function test (PFT) exercise-induced asthma (EIA) screening of elite athletes.   \n", "METHODS Twenty-three elite cold weather athletes (14 men, 9 women) PFT positive for EIA (FBC screened) served as subjects.", "Twenty-three gender and sport matched controls (nonasthmatics) were randomly selected to establish PFT reference values for normal elite athletes.", "Before FBC, athletes completed a medical history questionnaire for EIA symptoms.", "FBC evaluations consisted of baseline spirometry, actual or simulated competition, and 5, 10, and 15 min postexercise spirometry.", "PFT positive athletes were evaluated in the laboratory using an exercise challenge simulating race intensity (ambient conditions: 21 degrees C, 60% relative humidity).", "PFT procedures were identical to FBC.   \n", "RESULTS 91% of PFT positive and 48% of PFT normal athletes reported at least one symptom of EIA, with postrace cough most frequent.", "Baseline spirometry was the same for PFT positives and normal controls.", "Lower limit reference range (MN - 2 SD) of FEV1 for controls suggests that postexercise decrements of greater than approximately -7% indicate abnormal airway response in this population.", "Exercise time duration did not effect bronchial reactivity; 78% of FBC PFT positives were PFT normal post-LBC.   \n", "CONCLUSION Self-reported symptoms by elite athletes are not reliable in identifying EIA.", "Reference range criterion for FEV1 decrement in the elite athlete postexercise contrasts current recommended guidelines.", "Moreover, a large number of false negatives may occur in this population if EIA screening is performed with inadequate exercise and environmental stress."], "structured": true}
{"doc_id": 38886345, "title": "Use of a targeted oncolytic poxvirus, JX-594, in patients with refractory primary or metastatic liver cancer: a phase I trial.", "abstract": ["BACKGROUND JX-594 is a targeted oncolytic poxvirus designed to selectively replicate in and destroy cancer cells with cell-cycle abnormalities and epidermal growth factor receptor (EGFR)-ras pathway activation.", "Direct oncolysis plus granulocyte-macrophage colony-stimulating factor (GM-CSF) expression also stimulates shutdown of tumour vasculature and antitumoral immunity.", "We aimed to assess intratumoral injection of JX-594 in patients with refractory primary or metastatic liver cancer.   \n", "METHODS Between Jan 4, 2006, and July 4, 2007, 14 patients with histologically confirmed refractory primary or metastatic liver tumours (up to 10.9 cm total diameter) that were amenable to image-guided intratumoral injections were enrolled into this non-comparative, open-label, phase I dose-escalation trial (standard 3x3 design; two to six patients for each dose with 12-18 estimated total patients).", "Patients received one of four doses of intratumoral JX-594 (10(8) plaque-forming units [pfu], 3x10(8) pfu, 10(9) pfu, or 3x10(9) pfu) every 3 weeks at Dong-A University Hospital (Busan, South Korea).", "Patients were monitored after treatment for at least 48 h in hospital and for at least 4 weeks as out-patients.", "Adverse event-monitoring according to the National Cancer Institute Common Toxicity Criteria (version 3) and standard laboratory toxicity grading for haematology, liver and renal function, coagulation studies, serum chemistry, and urinalysis were done.", "The primary aims were to ascertain the maximum-tolerated dose (MTD) and safety of JX-594 treatment.", "Data were also collected on pharmacokinetics, pharmacodynamics, and efficacy.", "Analysis was per protocol.", "This study is registered with ClinicalTrials.gov, number NCT00629759.   \n", "FINDINGS Of 22 patients with liver tumours who were assessed for eligibility, eight patients did not meet inclusion criteria.", "Therefore, 14 patients, including those with hepatocellular, colorectal, melanoma, and lung cancer, were enrolled.", "Patients were heavily pretreated (5.6 previous treatments, SD 2.8, range 2.0-12.0) and had large tumours (7.0 cm diameter, SD 2.7, range 1.8-10.9).", "Patients received a mean of 3.4 (SD 2.2, range 1.0-8.0) cycles of JX-594.", "All patients were evaluable for toxicity.", "All patients experienced grade I-III flu-like symptoms, and four had transient grade I-III dose-related thrombocytopenia.", "Grade III hyperbilirubinaemia was dose-limiting in both patients at the highest dose; the MTD was therefore 1x10(9) pfu.", "JX-594 replication-dependent dissemination in blood was shown, with resultant infection of non-injected tumour sites.", "GM-CSF expression resulted in grade I-III increases in neutrophil counts in four of six patients at the MTD.", "Tumour responses were shown in injected and non-injected tumours.", "Ten patients were radiographically evaluable for objective responses; non-evaluable patients had contraindications to contrast medium (n=2) or no post-treatment scans (n=2).", "According to Response Evaluation Criteria in Solid Tumors (RECIST), three patients had partial response, six had stable disease, and one had progressive disease.   \n", "INTERPRETATION Intratumoral injection of JX-594 into primary or metastatic liver tumours was generally well-tolerated.", "Direct hyperbilirubinaemia was the dose-limiting toxicity.", "Safety was acceptable in the context of JX-594 replication, GM-CSF expression, systemic dissemination, and JX-594 had anti-tumoral effects against several refractory carcinomas.", "Phase II trials are now underway."], "structured": true}
{"doc_id": 38899659, "title": "PTH Signaling in Osteoprogenitors Is Essential for B-Lymphocyte Differentiation and Mobilization.", "abstract": ["Cells of the osteoblast lineage provide critical support for B lymphopoiesis in the bone marrow (BM).", "Parathyroid hormone (PTH) signaling in osteoblastic cells through its receptor (PPR) is an important regulator of hematopoietic stem cells; however, its role in regulation of B lymphopoiesis is not clear.", "Here we demonstrate that deletion of PPR in osteoprogenitors results in a significant loss of trabecular and cortical bone.", "PPR signaling in osteoprogenitors, but not in mature osteoblasts or osteocytes, is critical for B-cell precursor differentiation via IL-7 production.", "Interestingly, despite a severe reduction in B-cell progenitors in BM, mature B-lymphocytes were increased 3.5-fold in the BM of mice lacking PPR in osteoprogenitors.", "This retention of mature IgD(+) B cells in the BM was associated with increased expression of vascular cell adhesion molecule 1 (VCAM1) by PPR-deficient osteoprogenitors, and treatment with VCAM1 neutralizing antibody increased mobilization of B lymphocytes from mutant BM.", "Our results demonstrate that PPR signaling in early osteoblasts is necessary for B-cell differentiation via IL-7 secretion and for B-lymphocyte mobilization via VCAM1."], "structured": false}
{"doc_id": 38919140, "title": "Snail coordinately regulates downstream pathways to control multiple aspects of mammalian neural precursor development.", "abstract": ["The Snail transcription factor plays a key role in regulating diverse developmental processes but is not thought to play a role in mammalian neural precursors.", "Here, we have examined radial glial precursor cells of the embryonic murine cortex and demonstrate that Snail regulates their survival, self-renewal, and differentiation into intermediate progenitors and neurons via two distinct and separable target pathways.", "First, Snail promotes cell survival by antagonizing a p53-dependent death pathway because coincident p53 knockdown rescues survival deficits caused by Snail knockdown.", "Second, we show that the cell cycle phosphatase Cdc25b is regulated by Snail in radial precursors and that Cdc25b coexpression is sufficient to rescue the decreased radial precursor proliferation and differentiation observed upon Snail knockdown.", "Thus, Snail acts via p53 and Cdc25b to coordinately regulate multiple aspects of mammalian embryonic neural precursor biology."], "structured": false}
{"doc_id": 38944245, "title": "Endothelial KLF2 links local arterial shear stress levels to the expression of vascular tone-regulating genes.", "abstract": ["Lung Kr\u00fcppel-like factor (LKLF/KLF2) is an endothelial transcription factor that is crucially involved in murine vasculogenesis and is specifically regulated by flow in vitro.", "We now show a relation to local flow variations in the adult human vasculature: decreased LKLF expression was noted at the aorta bifurcations to the iliac and carotid arteries, coinciding with neointima formation.", "The direct involvement of shear stress in the in vivo expression of LKLF was determined independently by in situ hybridization and laser microbeam microdissection/reverse transcriptase-polymerase chain reaction in a murine carotid artery collar model, in which a 4- to 30-fold induction of LKLF occurred at the high-shear sites.", "Dissection of the biomechanics of LKLF regulation in vitro demonstrated that steady flow and pulsatile flow induced basal LKLF expression 15- and 36-fold at shear stresses greater than approximately 5 dyne/cm2, whereas cyclic stretch had no effect.", "Prolonged LKLF induction in the absence of flow changed the expression of angiotensin-converting enzyme, endothelin-1, adrenomedullin, and endothelial nitric oxide synthase to levels similar to those observed under prolonged flow.", "LKLF repression by siRNA suppressed the flow response of endothelin-1, adrenomedullin, and endothelial nitric oxide synthase (P < 0.05).", "Thus, we demonstrate that endothelial LKLF is regulated by flow in vivo and is a transcriptional regulator of several endothelial genes that control vascular tone in response to flow."], "structured": false}
{"doc_id": 39048693, "title": "Synapsin I Cre transgene expression in male mice produces germline recombination in progeny.", "abstract": ["The cre/LoxP system can produce conditional loss of gene function in specific cell types such as neurons.", "A transgenic mouse line, utilized by multiple studies, used the Synapsin I promoter to drive expression of cre (SynCre) to achieve neuronal-specific cre expression.", "Herein we describe that cre expression can also be observed in SynCre mice within the testes after being bred into a floxed transgenic mouse line.", "Cre transcript was expressed in testes resulting in recombination of the floxed substrate in testes.", "In the majority of cases, progeny of male SynCre mice inherited a germline recombined floxed allele, while this was never observed in progeny from female mice carrying the SynCre allele.", "This observation should alert investigators to a potential confound using these mice and enables male germ cell \"deletor\" strategies."], "structured": false}
{"doc_id": 39059143, "title": "Hospital mortality, length of stay, and preventable complications among critically ill patients before and after tele-ICU reengineering of critical care processes.", "abstract": ["CONTEXT The association of an adult tele-intensive care unit (ICU) intervention with hospital mortality, length of stay, best practice adherence, and preventable complications for an academic medical center has not been reported.   \n", "OBJECTIVE To quantify the association of a tele-ICU intervention with hospital mortality, length of stay, and complications that are preventable by adherence to best practices.   \n", "DESIGN, SETTING, AND PATIENTS Prospective stepped-wedge clinical practice study of 6290 adults admitted to any of 7 ICUs (3 medical, 3 surgical, and 1 mixed cardiovascular) on 2 campuses of an 834-bed academic medical center that was performed from April 26, 2005, through September 30, 2007.", "Electronically supported and monitored processes for best practice adherence, care plan creation, and clinician response times to alarms were evaluated.   \n", "MAIN OUTCOME MEASURES Case-mix and severity-adjusted hospital mortality.", "Other outcomes included hospital and ICU length of stay, best practice adherence, and complication rates.   \n", "RESULTS The hospital mortality rate was 13.6% (95% confidence interval [CI], 11.9%-15.4%) during the preintervention period compared with 11.8% (95% CI, 10.9%-12.8%) during the tele-ICU intervention period (adjusted odds ratio [OR], 0.40 [95% CI, 0.31-0.52]).", "The tele-ICU intervention period compared with the preintervention period was associated with higher rates of best clinical practice adherence for the prevention of deep vein thrombosis (99% vs 85%, respectively; OR, 15.4 [95% CI, 11.3-21.1]) and prevention of stress ulcers (96% vs 83%, respectively; OR, 4.57 [95% CI, 3.91-5.77], best practice adherence for cardiovascular protection (99% vs 80%, respectively; OR, 30.7 [95% CI, 19.3-49.2]), prevention of ventilator-associated pneumonia (52% vs 33%, respectively; OR, 2.20 [95% CI, 1.79-2.70]), lower rates of preventable complications (1.6% vs 13%, respectively, for ventilator-associated pneumonia [OR, 0.15; 95% CI, 0.09-0.23] and 0.6% vs 1.0%, respectively, for catheter-related bloodstream infection [OR, 0.50; 95% CI, 0.27-0.93]), and shorter hospital length of stay (9.8 vs 13.3 days, respectively; hazard ratio for discharge, 1.44 [95% CI, 1.33-1.56]).", "The results for medical, surgical, and cardiovascular ICUs were similar.   \n", "CONCLUSION In a single academic medical center study, implementation of a tele-ICU intervention was associated with reduced adjusted odds of mortality and reduced hospital length of stay, as well as with changes in best practice adherence and lower rates of preventable complications."], "structured": true}
{"doc_id": 39084565, "title": "CD11b+ monocytes abrogate Th17 CD4+ T cell-mediated experimental autoimmune myocarditis.", "abstract": ["Experimental autoimmune myocarditis (EAM) represents a Th17 T cell-mediated mouse model of postinflammatory heart disease.", "In BALB/c wild-type mice, EAM is a self-limiting disease, peaking 21 days after alpha-myosin H chain peptide (MyHC-alpha)/CFA immunization and largely resolving thereafter.", "In IFN-gammaR(-/-) mice, however, EAM is exacerbated and shows a chronic progressive disease course.", "We found that this progressive disease course paralleled persistently elevated IL-17 release from T cells infiltrating the hearts of IFN-gammaR(-/-) mice 30 days after immunization.", "In fact, IL-17 promoted the recruitment of CD11b(+) monocytes, the major heart-infiltrating cells in EAM.", "In turn, CD11b(+) monocytes suppressed MyHC-alpha-specific Th17 T cell responses IFN-gamma-dependently in vitro.", "In vivo, injection of IFN-gammaR(+/+)CD11b(+), but not IFN-gammaR(-/-)CD11b(+), monocytes, suppressed MyHC-alpha-specific T cells, and abrogated the progressive disease course in IFN-gammaR(-/-) mice.", "Finally, coinjection of MyHC-alpha-specific, but not OVA-transgenic, IFN-gamma-releasing CD4(+) Th1 T cell lines, together with MyHC-alpha-specific Th17 T cells protected RAG2(-/-) mice from EAM.", "In conclusion, CD11b(+) monocytes play a dual role in EAM: as a major cellular substrate of IL-17-induced inflammation and as mediators of an IFN-gamma-dependent negative feedback loop confining disease progression."], "structured": false}
{"doc_id": 39128592, "title": "The cytokine RANKL produced by positively selected thymocytes fosters medullary thymic epithelial cells that express autoimmune regulator.", "abstract": ["The thymic medulla provides a microenvironment where medullary thymic epithelial cells (mTECs) express autoimmune regulator and diverse tissue-restricted genes, contributing to launching self-tolerance.", "Positive selection is essential for thymic medulla formation via a previously unknown mechanism.", "Here we show that the cytokine RANK ligand (RANKL) was produced by positively selected thymocytes and regulated the cellularity of mTEC by interacting with RANK and osteoprotegerin.", "Forced expression of RANKL restored thymic medulla in mice lacking positive selection, whereas RANKL perturbation impaired medulla formation.", "These results indicate that RANKL produced by positively selected thymocytes is responsible for fostering thymic medulla formation, thereby establishing central tolerance."], "structured": false}
{"doc_id": 39164524, "title": "Fibrosis and adipogenesis originate from a common mesenchymal progenitor in skeletal muscle.", "abstract": ["Accumulation of adipocytes and collagen type-I-producing cells (fibrosis) is observed in muscular dystrophies.", "The origin of these cells had been largely unknown, but recently we identified mesenchymal progenitors positive for platelet-derived growth factor receptor alpha (PDGFR\u03b1) as the origin of adipocytes in skeletal muscle.", "However, the origin of muscle fibrosis remains largely unknown.", "In this study, clonal analyses show that PDGFR\u03b1(+) cells also differentiate into collagen type-I-producing cells.", "In fact, PDGFR\u03b1(+) cells accumulated in fibrotic areas of the diaphragm in the mdx mouse, a model of Duchenne muscular dystrophy.", "Furthermore, mRNA of fibrosis markers was expressed exclusively in the PDGFR\u03b1(+) cell fraction in the mdx diaphragm.", "Importantly, TGF-\u03b2 isoforms, known as potent profibrotic cytokines, induced expression of markers of fibrosis in PDGFR\u03b1(+) cells but not in myogenic cells.", "Transplantation studies revealed that fibrogenic PDGFR\u03b1(+) cells mainly derived from pre-existing PDGFR\u03b1(+) cells and that the contribution of PDGFR\u03b1(-) cells and circulating cells was limited.", "These results indicate that mesenchymal progenitors are the main origin of not only fat accumulation but also fibrosis in skeletal muscle."], "structured": false}
{"doc_id": 39174007, "title": "The pecking order of free radicals and antioxidants: lipid peroxidation, alpha-tocopherol, and ascorbate.", "abstract": ["Free radicals vary widely in their thermodynamic properties, ranging from very oxidizing to very reducing.", "These thermodynamic properties can be used to predict a pecking order, or hierarchy, for free radical reactions.", "Using one-electron reduction potentials, the predicted pecking order is in agreement with experimentally observed free radical electron (hydrogen atom) transfer reactions.", "These potentials are also in agreement with experimental data that suggest that vitamin E, the primary lipid soluble small molecule antioxidant, and vitamin C, the terminal water soluble small molecule antioxidant, cooperate to protect lipids and lipid structures against peroxidation.", "Although vitamin E is located in membranes and vitamin C is located in aqueous phases, vitamin C is able to recycle vitamin E; i.e., vitamin C repairs the tocopheroxyl (chromanoxyl) radical of vitamin E, thereby permitting vitamin E to function again as a free radical chain-breaking antioxidant.", "This review discusses: (i) the thermodynamics of free radical reactions that are of interest to the health sciences; (ii) the fundamental thermodynamic and kinetic properties that are associated with chain-breaking antioxidants; (iii) the unique interfacial nature of the apparent reaction of the tocopherol free radical (vitamin E radical) and vitamin C; and (iv) presents a hierarchy, or pecking order, for free radical electron (hydrogen atom) transfer reactions."], "structured": false}
{"doc_id": 39187170, "title": "Mitochondrial respiration in subcutaneous and visceral adipose tissue from patients with morbid obesity.", "abstract": ["Adipose tissue exerts important endocrine and metabolic functions in health and disease.", "Yet the bioenergetics of this tissue is not characterized in humans and possible regional differences are not elucidated.", "Using high resolution respirometry, mitochondrial respiration was quantified in human abdominal subcutaneous and intra-abdominal visceral (omentum majus) adipose tissue from biopsies obtained in 20 obese patients undergoing bariatric surgery.", "Mitochondrial DNA (mtDNA) and genomic DNA (gDNA) were determined by the PCR technique for estimation of mitochondrial density.", "Adipose tissue samples were permeabilized and respirometric measurements were performed in duplicate at 37 degrees C. Substrates (glutamate (G) + malate (M) + octanoyl carnitine (O) + succinate (S)) were added sequentially to provide electrons to complex I + II.", "ADP ((D)) for state 3 respiration was added after GM.", "Uncoupled respiration was measured after addition of FCCP.", "Visceral fat contained more mitochondria per milligram of tissue than subcutaneous fat, but the cells were smaller.", "Robust, stable oxygen fluxes were found in both tissues, and coupled state 3 (GMOS(D)) and uncoupled respiration were significantly (P < 0.05) higher in visceral (0.95 +/- 0.05 and 1.15 +/-", "0.06 pmol O(2) s(1) mg(1), respectively) compared with subcutaneous (0.76 +/- 0.04 and 0.98 +/- 0.05 pmol O(2) s(1) mg(1), respectively) adipose tissue.", "Expressed per mtDNA, visceral adipose tissue had significantly (P < 0.05) lower mitochondrial respiration.", "Substrate control ratios were higher and uncoupling control ratio lower (P < 0.05) in visceral compared with subcutaneous adipose tissue.", "We conclude that visceral fat is bioenergetically more active and more sensitive to mitochondrial substrate supply than subcutaneous fat.", "Oxidative phosphorylation has a higher relative activity in visceral compared with subcutaneous adipose tissue."], "structured": false}
{"doc_id": 39225849, "title": "Endogenous gamma-H2AX-ATM-Chk2 checkpoint activation in Bloom's syndrome helicase deficient cells is related to DNA replication arrested forks.", "abstract": ["The Bloom syndrome helicase (BLM) is critical for genomic stability.", "A defect in BLM activity results in the cancer-predisposing Bloom syndrome (BS).", "Here, we report that BLM-deficient cell lines and primary fibroblasts display an endogenously activated DNA double-strand break checkpoint response with prominent levels of phosphorylated histone H2AX (gamma-H2AX), Chk2 (p(T68)Chk2), and ATM (p(S1981)ATM) colocalizing in nuclear foci.", "Interestingly, the mitotic fraction of gamma-H2AX foci did not seem to be higher in BLM-deficient cells, indicating that these lesions form transiently during interphase.", "Pulse labeling with iododeoxyuridine and immunofluorescence microscopy showed the colocalization of gamma-H2AX, ATM, and Chk2 together with replication foci.", "Those foci costained for Rad51, indicating homologous recombination at these replication sites.", "We therefore analyzed replication in BS cells using a single molecule approach on combed DNA fibers.", "In addition to a higher frequency of replication fork barriers, BS cells displayed a reduced average fork velocity and global reduction of interorigin distances indicative of an elevated frequency of origin firing.", "Because BS is one of the most penetrant cancer-predisposing hereditary diseases, it is likely that the lack of BLM engages the cells in a situation similar to precancerous tissues with replication stress.", "To our knowledge, this is the first report of high ATM-Chk2 kinase activation and its linkage to replication defects in a BS model."], "structured": false}
{"doc_id": 39264456, "title": "Impact of TNF-alpha and IL-6 levels on development of cachexia in newly diagnosed NSCLC patients.", "abstract": ["OBJECTIVES We investigated the role of cytokines tumor necrosis factor-alpha (TNF-alpha) and interleukin-6 (IL-6) in cachexia development in newly diagnosed nonsmall cell lung cancer (NSCLC) patients.   \n", "METHODS : We evaluated 44 (M/F:41/3) NSCLC patients and 12 (M/F:10/2) age matched healthy smokers.", "NSCLC cases with a weight loss of > or =10% consisted the cachectic group (n:23, M/F:21/2) and the ones with <10% weight loss consisted the noncachectic group (n:21, M/F:19/2).   \n", "RESULTS Body mass index (BMI) of cachectics was significantly lower than that of noncachectics (21.0 +/- 2.9 versus 24.5 +/-", "3.6, P = 0.02) and controls (21.0 +/- 2.9 versus 25.5 +/- 2.6, P = 0.01).", "Serum TNF-alpha level did not differ between cachectic and noncachectics (37.3 +/-", "39.1 and 51.6 +/-", "84.2 pg/mL, respectively).", "However, it was significantly higher in NSCLC patients compared with controls (44.1 +/- 64.3 and 15.1 +/-", "14.3 pg/mL, P = 0.03).", "Serum IL-6 level was not different between 3 groups (6.4 +/- 4.1, 8.9 +/-", "16.3, and 4.1 +/-", "3.5 pg/mL, respectively)", "but it correlated significantly with TNF-alpha (r = 0.4, P = 0.006) and BMI (r = -0.3, P = 0.03).", "Erythrocyte sedimentation rate (ESR) correlated significantly with TNF-alpha (r = 0.4, P = 0.003) and BMI (r = -0.3, P = 0.03).", "Among 44 cases, survival of 12 and 17 patients was recorded in cachectics and noncachectics, with no statistical difference (12.2 +/- 3.7 and 11.2 +/-", "1.0 months, respectively).   \n", "CONCLUSIONS TNF-alpha and IL-6 levels did not differ significantly between cachectics and noncachectics.", "However, significant correlations between IL-6, BMI, and TNF-alpha suggested that these cytokines acted as cofactors in weight loss.", "Survival was neither influenced by BMI, nor the cytokine levels in the present study.", "The significant correlation of ESR with TNF-alpha suggested that ESR could provide valuable clue for considerable weight loss in the follow-up of NSCLC patients."], "structured": true}
{"doc_id": 39281140, "title": "Treatment of antidepressant-associated sexual dysfunction with sildenafil: a randomized controlled trial.", "abstract": ["CONTEXT Sexual dysfunction is a common adverse effect of antidepressants that frequently results in treatment noncompliance.   \n", "OBJECTIVE To assess the efficacy of sildenafil citrate in men with sexual dysfunction associated with the use of selective and nonselective serotonin reuptake inhibitor (SRI) antidepressants.   \n", "DESIGN, SETTING, AND PATIENTS Prospective, parallel-group, randomized, double-blind, placebo-controlled trial conducted between November 1, 2000, and January 1, 2001, at 3 US university medical centers among 90 male outpatients (mean [SD] age, 45 [8] years) with major depression in remission and sexual dysfunction associated with SRI antidepressant treatment.   \n", "INTERVENTION Patients were randomly assigned to take sildenafil (n = 45) or placebo (n = 45) at a flexible dose starting at 50 mg and adjustable to 100 mg before sexual activity for 6 weeks.   \n", "MAIN OUTCOME MEASURES The primary outcome measure was score on the Clinical Global Impression-Sexual Function (CGI-SF); secondary measures were scores on the International Index of Erectile Function, Arizona Sexual Experience Scale, Massachusetts General Hospital-Sexual Functioning Questionnaire, and Hamilton Rating Scale for Depression (HAM-D).   \n", "RESULTS Among the 90 randomized patients, 93% (83/89) of patients treated per protocol took at least 1 dose of study drug and 85% (76/89) completed week 6 end-point assessments with last observation carried forward analyses.", "At a CGI-SF score of 2 or lower, 54.5% (24/44) of sildenafil compared with 4.4% (2/45) of placebo patients were much or very much improved (P<.001).", "Erectile function, arousal, ejaculation, orgasm, and overall satisfaction domain measures improved significantly in sildenafil compared with placebo patients.", "Mean depression scores remained consistent with remission (HAM-D score < or =10) in both groups for the study duration.   \n", "CONCLUSION In our study, sildenafil effectively improved erectile function and other aspects of sexual function in men with sexual dysfunction associated with the use of SRI antidepressants.", "These improvements may allow patients to maintain adherence with effective antidepressant treatment."], "structured": true}
{"doc_id": 39281166, "title": "Noncoding transcription at enhancers: general principles and functional models.", "abstract": ["Mammalian genomes are extensively transcribed outside the borders of protein-coding genes.", "Genome-wide studies recently demonstrated that cis-regulatory genomic elements implicated in transcriptional control, such as enhancers and locus-control regions, represent major sites of extragenic noncoding transcription.", "Enhancer-templated transcripts provide a quantitatively small contribution to the total amount of cellular nonribosomal RNA; nevertheless, the possibility that enhancer transcription and the resulting enhancer RNAs may, in some cases, have functional roles, rather than represent mere transcriptional noise at accessible genomic regions, is supported by an increasing amount of experimental data.", "In this article we review the current knowledge on enhancer transcription and its functional implications."], "structured": false}
{"doc_id": 39285547, "title": "Microarray analysis of pneumococcal gene expression during invasive disease.", "abstract": ["Streptococcus pneumoniae is a leading cause of invasive bacterial disease.", "This is the first study to examine the expression of S. pneumoniae genes in vivo by using whole-genome microarrays available from The Institute for Genomic Research.", "Total RNA was collected from pneumococci isolated from infected blood, infected cerebrospinal fluid, and bacteria attached to a pharyngeal epithelial cell line in vitro.", "Microarray analysis of pneumococcal genes expressed in these models identified body site-specific patterns of expression for virulence factors, transporters, transcription factors, translation-associated proteins, metabolism, and genes with unknown function.", "Contributions to virulence predicted for several unknown genes with enhanced expression in vivo were confirmed by insertion duplication mutagenesis and challenge of mice with the mutants.", "Finally, we cross-referenced our results with previous studies that used signature-tagged mutagenesis and differential fluorescence induction to identify genes that are potentially required by a broad range of pneumococcal strains for invasive disease."], "structured": false}
{"doc_id": 39291138, "title": "Integration of Smad and MAPK pathways: a link and a linker revisited.", "abstract": ["Cells develop by reading mixed signals.", "Nowhere is this clearer than in the highly dynamic processes that propel embryogenesis, when critical cell-fate decisions are made swiftly in response to well-orchestrated growthfactor combinations.", "Learning how diverse signaling pathways are integrated is therefore essential for understanding physiology.", "This requires the identification, in tangible molecular terms, of key nodes for pathway integration that operate in vivo.", "A report in this issue, on the integration of Smad and Ras/MAPK pathways during neural induction (Pera et al. 2003), provides timely insights into the relevance of one such node.", "Pera et al. (2003) report that FGF8 and IGF2\u2014two growth factors that activate the Ras/MAPK pathway\u2014 favor neural differentiation and mesoderm dorsalization in Xenopus by inhibiting BMP (Bone Morphogenetic Protein) signaling.", "Mesoderm is formed from ectoderm in response to Nodal-related signals from the endoderm at the blastula stage and beyond (Fig. 1; for review, see De Robertis et al. 2000).", "BMP induces differentiation of ectoderm into epidermal cell fates at the expense of neural fates, and it ventralizes the mesoderm at the expense of dorsal fates (for review, see Weinstein and HemmatiBrivanlou 1999; De Robertis et al. 2000).", "Accordingly, neural differentiation and dorsal mesoderm formation are favored when BMP signaling is attenuated.", "Noggin, Chordin, Cerberus, and Follistatin, secreted by the Spemann organizer on the dorsal side at the gastrula stage, facilitate the formation of neural tissue by sequestering BMP (Weinstein and Hemmati-Brivanlou 1999; De Robertis et al. 2000).", "Experimentally blocking BMP signaling with a dominant-negative BMP receptor has a similar effect of promoting ectoderm neuralization (Weinstein and Hemmati-Brivanlou 1999).", "As it turns out, neural induction can also be achieved with FGF (fibroblast growth factor; Kengaku and Okamoto 1993; Lamb and Harland 1995; Hongo et al. 1999; Hardcastle et al. 2000; Streit et al. 2000; Wilson et al. 2000) and IGF (insulin-like growth factor; Pera et al. 2001; Richard-Parpaillon et al. 2002).", "Injection of transcripts encoding FGF8 or IFG2 into one animal-pole blastomere of a fourto eight-cell embryo results in an expanded neural plate at the injected side (Pera et al. 2003).", "Surprisingly, expression of a dominant-negative FGF receptor prevents neuralization of ectoderm explants by the BMP blocker Noggin (Launay et al. 1996).", "Likewise, the potent neuralizing effect of Chordin can be blocked by a dominant-negative FGF receptor or a morpholino oligonucleotide targeting the IGF receptor (Pera et al. 2003).", "Thus, the neuralizing effect of BMP inhibitors is somehow tied to FGF and IFG signaling.", "The question is, how?", "Because FGF8 and IFG2 activate MAPK, Pera et al. (2003) took heed from previous work showing that MAPK inhibits the BMP signal-transduction factor Smad1 (Kretzschmar et al. 1997a).", "Smad1 is directly phosphorylated by the BMP receptor, resulting in Smad1 activation (Kretzschmar et al. 1997b), and by MAPK in response to EGF, resulting in Smad1 inhibition (Kretzschmar et al. 1997a; Fig. 2).", "Smad transcription factors mediate gene responses to the entire TGF (Transforming Growth Factor) family, to which the BMPs belong (for review, see Massague 2000; Derynck and Zhang 2003).", "Smads 1, 5, and 8 act primarily downstream of BMP receptors and Smads 2 and 3 downstream of TGF , Activin and Nodal receptors.", "Smad proteins have two conserved globular domains\u2014the MH1 and MH2 domains (Fig. 2).", "The MH1 domain is involved in DNA binding and the MH2 domain in binding to cytoplasmic retention factors, activated receptors, nucleoporins in the nuclear pore, and DNA-binding cofactors, coactivators, and corepressors in the nucleus (for review, see Shi and Massague 2003).", "Receptor-mediated phosphorylation occurs at the carboxy-terminal sequence SXS.", "This enables the nuclear accumulation of Smads and their association with the shared partner Smad4 to form transcriptional complexes that are interpreted by the cell as a function of the context (Massague 2000).", "Between the MH1 and MH2 domains lies a linker region of variable sequence and length.", "Attention was drawn to this region when it was found that EGF (epidermal growth factor), a classical activator of the Ras/ MAPK pathway, causes phosphorylation of the Smad1 linker at four MAPK sites (PXSP sequences; Kretzschmar et al. 1997a).", "This prevents the nuclear localization of Smad1 and inhibits BMP signaling.", "Mutation of these E-MAIL j-massague@ski.mskcc.org; FAX (212) 717-3298.", "Article and publication are at http://www.genesdev.org/cgi/doi/10.1101/ gad.1167003."], "structured": false}
{"doc_id": 39300105, "title": "A brief analysis of clinical pharmacy interventions undertaken in an Australian teaching hospital.", "abstract": ["Selected clinical pharmacy interventions undertaken during a 30-day data capture period were analysed, seeking to gain a greater understanding of the nature of the drug-related problems involved.", "Pharmacists were asked to record only interventions that were of potentially major significance.", "A total of 67 interventions were submitted for analysis.", "In 28 cases (41.7% of the initial total) the intervention reports were excluded from further analysis after initial review.", "For the remaining 39 interventions, 20 patients (51%) were under the care of a medical unit, and cardiovascular/antithrombotic agents accounted for 17 reports (43.5%).", "The majority of interventions were implemented at the time of inpatient medication order review by the clinical pharmacist (n=25, 64%).", "The most common category of drug-related problem addressed in the interventions related to the prescription of inappropriately high doses of the correct drug for the patient (n=17, 43.6%).", "Deficiencies in technical knowledge accounted for less than 25% of all cases."], "structured": false}
{"doc_id": 39304380, "title": "Lethal complications of typhoid-cholera-vaccination. (Case report and review of the literature).", "abstract": ["Simultaneous parenteral vaccination against typhoid and cholera lead to death through either anaphylactic shock or endotoxic shock in a 36-year-old male.", "At autopsy the charactertic features of shock as well as chronic interstitial myocarditis were noted.", "Moreover, fresh histiocytic and lymphocytic nodules were found in the liver, heart and meninges.", "A review of the literature dealing with lethal complications following parenteral tyhoid vaccinations shows an increased risk in debilitated persons (emaciation, stress, cold).", "Most of the fatalities occurred in persons who had previous disturbances of the cardiovascular system, as in the case reviewed here.", "Cardiac failure, Landry's paralysis, renal failure and disturbances of skin, joints and intestines may also follow typhoid vaccinations.", "However, these latter complications are usually not lethal.", "The patients presented here had many of the conditions which are known to aggravate the situation and to lead to a lethal culmination.", "The review of this case and the disucussion following it shows that only healthy persons should receive the parenteral typhoid vaccination.", "Hopefully, the presentation of this material will help prevent fatalities of this type in the future."], "structured": false}
{"doc_id": 39326723, "title": "Functional genomics and proteomics approaches to study the ERBB network in cancer.", "abstract": ["Substantial progress in functional genomic and proteomic technologies has opened new perspectives in biomedical research.", "The sequence of the human genome has been mostly determined and opened new visions on its complexity and regulation.", "New technologies, like RNAi and protein arrays, allow gathering knowledge beyond single gene analysis.", "Increasingly, biological processes are studied with systems biological approaches, where qualitative and quantitative data of the components are utilized to model the respective processes, to predict effects of perturbations, and to then refine these models after experimental testing.", "Here, we describe the potential of applying functional genomics and proteomics, taking the ERBB family of growth-factor receptors as an example to study the signaling network and its impact on cancer."], "structured": false}
{"doc_id": 39334724, "title": "Evaluation of spatial filters to create smoothed maps of health data.", "abstract": ["Spatial filters have been used as an easy and intuitive way to create smoothed disease maps.", "Birth weight data from New York State for 1994 and 1995 are used to compare the traditional filter type of fixed geographical size with a filter size of constant or nearly constant population size.", "The latter are more appropriate for mapping disease in geographic areas with widely varying population density, such as New York State.", "Issues such as the choice of population size for the filter, the scale of smoothing, the ability to detect true spatial variation and the ability to smooth over random spatial noise are evaluated and discussed."], "structured": false}
{"doc_id": 39368721, "title": "Glucose tolerance and blood pressure: long term follow up in middle aged men.", "abstract": ["OBJECTIVE to investigate the role of glucose tolerance in the development of hypertension.   \n", "DESIGN Retrospective analysis of the results of a health check up in a group of clinically healthy middle aged men in the late 1960s (median year 1968).", "The subjects were invited to enter into a primary prevention trial for cardiovascular disease in 1974, when they underwent clinical examination for risk factors.", "The trial was completed in 1979, when the men were re-examined.", "Follow up was in 1986.   \n", "SETTING Institute of Occupational Health, Helsinki, Finland and second department of medicine, University of Helsinki.   ", "SUBJECTS In all, 3490 men born during 1919-34 participated in a health check up in the late 1960s.", "In 1974, 1815 of these men who were clinically healthy were entered into a primary prevention trial for cardiovascular disease.", "On clinical examination 1222 of the men were considered at high risk of cardiovascular disease.", "Of these, 612 received an intervention and were excluded from the study.", "A total of 593 men were without risk factors.", "The study comprised all of the men who did not have an intervention (n = 1203).", "In 1979, 1120 men were re-examined, and in 1986 945 men attended follow up.", "There were two groups for analysis: one comprising all subjects and the other comprising only men who were normotensive in 1968 and for whom complete information was available.   \n", "INTERVENTIONS By 1979, 103 men were taking antihypertensive drugs, and by 1986, 131 were taking antihypertensive drugs and 12 were taking drugs for hyperglycaemia.   \n", "MAIN OUTCOME MEASURES Blood glucose concentration one hour after a glucose load, blood pressure, and body weight were measured in 1968, 1974, and 1979.", "In 1986 blood pressure and body weight were recorded.   \n", "RESULTS Men who were hypertensive in 1986 had significantly higher blood pressures (p less than 0.0001) and (after adjustment for body mass index and alcohol intake) significantly higher blood glucose concentrations one hour after a glucose load at all examinations than those who were normotensive in 1986.", "Regression analysis showed that the higher the blood glucose concentration after a glucose load in 1968 the higher the blood pressure during the following years.", "Those men between the second and third tertiles of blood glucose concentration in 1968 had a significantly higher risk of developing hypertension (odds ratio 1.71, 95% confidence interval 1.05 to 2.77) compared with those below the first tertile.   \n", "CONCLUSION In this study men who developed hypertension tended to have shown an increased intolerance to glucose up to 18 years before the clinical manifestation of their disorder.", "Blood glucose concentration one hour after a glucose load was an independent predictor of future hypertension."], "structured": true}
{"doc_id": 39381118, "title": "At the gates of death.", "abstract": ["Apoptosis that proceeds via the mitochondrial pathway involves mitochondrial outer membrane permeabilization (MOMP), responsible for the release of cytochrome c and other proteins of the mitochondrial intermembrane space.", "This essential step is controlled and mediated by proteins of the Bcl-2 family.", "The proapoptotic proteins Bax and Bak are required for MOMP, while the antiapoptotic Bcl-2 proteins, including Bcl-2, Bcl-xL, Mcl-1, and others, prevent MOMP.", "Different proapoptotic BH3-only proteins act to interfere with the function of the antiapoptotic Bcl-2 members and/or activate Bax and Bak.", "Here, we discuss an emerging view, proposed by Certo et al. in this issue of Cancer Cell, on how these interactions result in MOMP and apoptosis."], "structured": false}
{"doc_id": 39389082, "title": "Structure of human RNase H1 complexed with an RNA/DNA hybrid: insight into HIV reverse transcription.", "abstract": ["We report here crystal structures of human RNase H1 complexed with an RNA/DNA substrate.", "Unlike B. halodurans RNase H1, human RNase H1 has a basic protrusion, which forms a DNA-binding channel and together with the conserved phosphate-binding pocket confers specificity for the B form and 2'-deoxy DNA.", "The RNA strand is recognized by four consecutive 2'-OH groups and cleaved by a two-metal ion mechanism.", "Although RNase H1 is overall positively charged, the substrate interface is neutral to acidic in character, which likely contributes to the catalytic specificity.", "Positions of the scissile phosphate and two catalytic metal ions are interdependent and highly coupled.", "Modeling of HIV reverse transcriptase (RT) with RNA/DNA in its RNase H active site suggests that the substrate cannot simultaneously occupy the polymerase active site and must undergo a conformational change to toggle between the two catalytic centers.", "The region that accommodates this conformational change offers a target to develop HIV-specific inhibitors."], "structured": false}
{"doc_id": 39390206, "title": "A diffusion tensor magnetic resonance imaging study of brain tissue from patients with migraine.", "abstract": ["OBJECTIVE To measure in vivo, using diffusion tensor magnetic resonance imaging (DT-MRI) the extent of pathological damage of normal appearing brain tissue (NABT) from patients with migraine.   \n", "METHODS Dual echo and DT-MRI scans of the brain were acquired from 34 patients with migraine and 17 sex and age matched healthy volunteers.", "Mean diffusivity (MD) and fractional anisotropy (FA) histograms of the NABT were obtained from all subjects and the histograms' peak heights and average NABT MD and FA measured.", "When present, average MD and FA values of T2 visible lesions were also measured.   \n", "RESULTS In comparison with healthy volunteers, patients with migraine had lower MD histogram peak height (p=0.02) of the NABT.", "No differences were found in FA histogram derived metrics between migraine patients and healthy subjects.", "No difference was found for any MD and FA histogram derived metrics between migraine patients with and without brain MRI lesions, and between patients with and without aura.   \n", "CONCLUSIONS This study shows that, although brain damage may extend beyond T2 weighted abnormalities in patients with migraine, the severity of these \"occult\" changes is mild compared with that found in other diseases associated with white matter abnormality."], "structured": true}
{"doc_id": 39391953, "title": "Determination of chloramphenicol residues in milk by enzyme-linked immunosorbent assay: improvement by biotin-streptavidin-amplified system.", "abstract": ["A sensitive biotin-streptavidin amplified enzyme-linked immunosorbent assay (BA-ELISA) method was developed for the determination of chloramphenicol residues in milk.", "The biotin-streptavidin system was applied to enhance the sensitivity.", "After optimization, the detection limit of the method was found to be 0.042 +/-", "0.006 ng mL(-1), which is 8-fold more sensitive than the traditional competitive ELISA using the same antibody and coating antigen.", "The amplification mechanism of the biotin-streptavidin system and the major factors affecting the sensitivity of detection are discussed.", "This method was successfully applied to determine the chloramphenicol residues in milk samples with a simple and rapid extraction procedure, and good recoveries (85.66-109.67%) were obtained.", "The result indicated that the biotin-streptavidin system may be a valuable tool to improve the specific detection of trace veterinary drug residues and could be widely used for routine monitoring of food samples."], "structured": false}
{"doc_id": 39424916, "title": "Wedelolactone exhibits anti-fibrotic effects on human hepatic stellate cell line LX-2.", "abstract": ["Wedelolactone is a major coumarin of Eclipta prostrata, which is used for preventing liver damage.", "However the effects of wedelolactone on hepatic fibrosis remained unexplored.", "The purpose of this study was to demonstrate the anti-fibrotic effects of wedelolactone on activated human hepatic stellate cell (HSC) line LX-2 and the possible underlying mechanisms by means of MTT assay, Hoechst staining, as well as real-time quantitative PCR and western blot.", "The results showed that wedelolactone reduced the cellular viability of LX-2 in a time and dose-dependent manner.", "After treatment of wedelolactone, the expressions of collagen I and \u03b1-smooth muscle actin, two biomarkers of LX-2 activation, were remarkably decreased.", "The apoptosis of LX-2 cells was induced by wedelolactone accompanied with the decreasing expression of anti-apoptotic Bcl-2 and increasing expression of pro-apoptotic Bax.", "In addition, phosphorylated status of extracellular signal-regulated kinase (ERK) and c-Jun N-terminal kinase (JNK) was up-regulated, but not in p38.", "Moreover, wedelolactone significantly repressed the level of phosphorylated inhibitor of nuclear factor \u03baB (I\u03baB) and p65 in nucleus in spite of tumor necrosis factor-\u03b1 stimulation.", "In conclusion, wedelolactone could significantly inhibit the activation of LX-2 cells, the underlying mechanisms of which included inducing Bcl-2 family involved apoptosis, up-regulating phosphorylated status of ERK and JNK expressions, and inhibiting nuclear factor-\u03baB (NF-\u03baB) mediated activity.", "Wedelolactone might present as a useful tool for the prevention and treatment of hepatic fibrosis."], "structured": false}
{"doc_id": 39426225, "title": "Adipose stem cells originate from perivascular cells.", "abstract": ["Recent research has shown that adipose tissues contain abundant MSCs (mesenchymal stem cells).", "The origin and location of the adipose stem cells, however, remain unknown, presenting an obstacle to the further purification and study of these cells.", "In the present study, we aimed at investigating the origins of adipose stem cells.", "\u03b1-SMA (\u03b1-smooth muscle actin) is one of the markers of pericytes.", "We harvested ASCs (adipose stromal cells) from \u03b1-SMA-GFP (green fluorescent protein) transgenic mice and sorted them into GFP-positive and GFP-negative cells by FACS.", "Multilineage differentiation tests were applied to examine the pluripotent ability of the \u03b1-SMA-GFP-positive and -negative cells.", "Immunofluorescent staining for \u03b1-SMA and PDGF-R\u03b2 (platelet-derived growth factor receptor \u03b2) were applied to identify the \u03b1-SMA-GFP-positive cells.", "Then \u03b1-SMA-GFP-positive cells were loaded on a collagen-fibronectin gel with endothelial cells to test their vascularization ability both in vitro and in vivo.", "Results show that, in adipose tissue, all of the \u03b1-SMA-GFP-positive cells congregate around the blood vessels.", "Only the \u03b1-SMA-GFP-positive cells have multilineage differentiation ability, while the \u03b1-SMA-GFP-negative cells can only differentiate in an adipogenic direction.", "The \u03b1-SMA-GFP-positive cells maintained expression of \u03b1-SMA during multilineage differentiation.", "The \u03b1-SMA-GFP-positive cells can promote the vascularization of endothelial cells in three-dimensional culture both in vitro and in vivo.", "We conclude that the adipose stem cells originate from perivascular cells and congregate around blood vessels."], "structured": false}
{"doc_id": 39443128, "title": "Interferon alpha and zidovudine therapy in adult T-cell leukaemia lymphoma: response and outcome in 15 patients.", "abstract": ["Adult T-cell leukaemia lymphoma (ATLL) is an aggressive disease caused by the human T-lymphotropic virus 1 (HTLV-I) with a short survival.", "Responses to interferon alpha (IFN-alpha) and zidovudine (AZT) have been documented but not with long-term follow-up.", "We treated 15 ATLL patients with IFN and AZT.", "Eleven patients had acute ATLL, two had lymphoma and two smouldering ATLL, with progression.", "The main features were: organomegaly (14), skin lesions (10), high white blood cell (WBC) count (11) and hypercalcaemia (9).", "Eleven patients had previously received chemotherapy and one had received an autograft.", "At the time of the study, seven patients had progressive disease and eight were in partial or complete clinical remission.", "Responses (PR) lasting 2+ to 44+ months were seen in 67%; 26% did not respond (NR) and one patient was not evaluable.", "Hypercalcaemia predicted a poor outcome but differences were not significant.", "Eight of the 15 patients have died 3-41 months from diagnosis.", "Median survival for the 15 patients was 18 months.", "Survival of the NR ranged from 4 to 20 months; six PR patients are alive 8-82 months from diagnosis.", "The differences in survival between NR (median: 6 months) and PR (55% of patients alive at 4 years) were statistically significant (P = 0.002).", "In conclusion, IFN and AZT improves the outcome of ATLL patients and helps maintain responses."], "structured": false}
{"doc_id": 39462488, "title": "Replisome stalling and stabilization at CGG repeats, which are responsible for chromosomal fragility", "abstract": ["Expanded CGG repeats cause chromosomal fragility and hereditary neurological disorders in humans.", "Replication forks stall at CGG repeats in a length-dependent manner in primate cells and in yeast.", "Saccharomyces cerevisiae proteins Tof1 and Mrc1 facilitate replication fork progression through CGG repeats.", "Remarkably, the fork-stabilizing role of Mrc1 does not involve its checkpoint function.", "Thus, chromosomal fragility might occur when forks stalled at expanded CGG repeats escape the S-phase checkpoint."], "structured": false}
{"doc_id": 39465575, "title": "Direct reprogramming of fibroblasts into neural stem cells by defined factors.", "abstract": ["Recent studies have shown that defined sets of transcription factors can directly reprogram differentiated somatic cells to a different differentiated cell type without passing through a pluripotent state, but the restricted proliferative and lineage potential of the resulting cells limits the scope of their potential applications.", "Here we show that a combination of transcription factors (Brn4/Pou3f4, Sox2, Klf4, c-Myc, plus E47/Tcf3) induces mouse fibroblasts to directly acquire a neural stem cell identity-which we term as induced neural stem cells (iNSCs).", "Direct reprogramming of fibroblasts into iNSCs is a gradual process in which the donor transcriptional program is silenced over time.", "iNSCs exhibit cell morphology, gene expression, epigenetic features, differentiation potential, and self-renewing capacity, as well as in vitro and in vivo functionality similar to those of wild-type NSCs.", "We conclude that differentiated cells can be reprogrammed directly into specific somatic stem cell types by defined sets of specific transcription factors."], "structured": false}
{"doc_id": 39481265, "title": "Epigenetics in lung fibrosis: from pathobiology to treatment perspective.", "abstract": ["PURPOSE OF REVIEW Idiopathic pulmonary fibrosis (IPF) is a fatal disease with limited treatment options and extensive gene expression changes identified in the lung parenchyma.", "Multiple lines of evidence suggest that epigenetic factors contribute to dysregulation of gene expression in IPF lung.", "Most importantly, risk factors that predispose to IPF - age, sex, cigarette smoke, and genetic variants - all influence epigenetic marks.", "This review summarizes recent findings of association of DNA methylation and histone modifications with the presence of disease and fibroproliferation.   ", "RECENT FINDINGS In addition to targeted studies focused on specific gene loci, genome-wide profiles of DNA methylation demonstrate widespread DNA methylation changes in IPF lung tissue and a substantial effect of these methylation changes on gene expression.", "Genetic loci that have been recently associated with IPF also contain differentially methylated regions, suggesting that genetic and epigenetic factors act in concert to dysregulate gene expression in IPF lung.   ", "SUMMARY Although we are in very early stages of understanding the role of epigenetics in IPF, the potential for the use of epigenetic marks as biomarkers and therapeutic targets is high and discoveries made in this field will likely bring us closer to better prognosticating and treating this fatal disease."], "structured": true}
{"doc_id": 39506601, "title": "Novel roles for KLF1 in erythropoiesis revealed by mRNA-seq.", "abstract": ["KLF1 (formerly known as EKLF) regulates the development of erythroid cells from bi-potent progenitor cells via the transcriptional activation of a diverse set of genes.", "Mice lacking Klf1 die in utero prior to E15 from severe anemia due to the inadequate expression of genes controlling hemoglobin production, cell membrane and cytoskeletal integrity, and the cell cycle.", "We have recently described the full repertoire of KLF1 binding sites in vivo by performing KLF1 ChIP-seq in primary erythroid tissue (E14.5 fetal liver).", "Here we describe the KLF1-dependent erythroid transcriptome by comparing mRNA-seq from Klf1(+/+) and Klf1(-/-) erythroid tissue.", "This has revealed novel target genes not previously obtainable by traditional microarray technology, and provided novel insights into the function of KLF1 as a transcriptional activator.", "We define a cis-regulatory module bound by KLF1, GATA1, TAL1, and EP300 that coordinates a core set of erythroid genes.", "We also describe a novel set of erythroid-specific promoters that drive high-level expression of otherwise ubiquitously expressed genes in erythroid cells.", "Our study has identified two novel lncRNAs that are dynamically expressed during erythroid differentiation, and discovered a role for KLF1 in directing apoptotic gene expression to drive the terminal stages of erythroid maturation."], "structured": false}
{"doc_id": 39532074, "title": "Self-assembling peptides optimize the post-traumatic milieu and synergistically enhance the effects of neural stem cell therapy after cervical spinal cord injury.", "abstract": ["INTRODUCTION The hostile environment after spinal cord injury (SCI) can compromise effects of regenerative therapies.", "We hypothesized that optimizing the post-traumatic environment with QL6 self-assembling peptides (SAPs) before neural precursor cell (NPC) transplantation would improve cell survival, differentiation and functional recovery.   \n", "METHODS A total of 90 Wistar rats received a clip-compression SCI at C7.", "Within each of two study arms, animals were randomized into 5 groups (NPC, SAP, NPC+SAP, vehicle, and sham).", "SAPs and NPCs were injected into the spinal cord 1day and 14days post-injury, respectively.", "Animals received growth factors over 7days and were immunosuppressed.", "Rats were sacrificed at 4weeks and sections of the cervical spinal cord prepared for immunohistochemistry (first study arm).", "Neurological function was assessed weekly for 8weeks using a battery of behavioral tests.", "Nine weeks post-SCI, the corticospinal tract was assessed using fiber-tracking (second arm).   \n", "RESULTS SAP-treated animals had significantly more surviving NPCs which showed increased differentiation to neurons and oligodendrocytes compared to controls.", "SAPs alone or in combination with NPCs resulted in smaller intramedullary cysts and larger volume of preserved tissue compared to other groups.", "The combined treatment group showed reduced astrogliosis and chondroitin sulfate proteoglycan deposition.", "Synaptic connectivity was increased in the NPC and combined treatment groups.", "Corticospinal tract preservation and behavioral outcomes improved with combinatorial treatment.   \n", "CONCLUSION Injecting SAPs after SCI enhances subsequent NPC survival, integration and differentiation and improves functional recovery.   ", "STATEMENT OF SIGNIFICANCE The hostile environment after spinal cord injury (SCI) can compromise effects of regenerative therapies.", "We hypothesized that improving this environment with self-assembling peptides (SAPs) before neural precursor cell (NPC) transplantation would support their beneficial effects.", "SAPs assemble once injected, providing a supportive scaffold for repair and regeneration.", "We investigated this in a rat model of spinal cord injury.", "More NPCs survived in SAP-treated animals and these showed increased differentiation compared to controls.", "SAPS alone or in combination with NPCs resulted in smaller cysts and larger volume of preserved tissue with the combined treatment also reducing scarring and improving behavioral outcomes.", "Overall, injection of SAPs was shown to improve the efficacy of NPC treatment, a promising finding for those with SCIs."], "structured": true}
{"doc_id": 39539647, "title": "A direct role for IFN-gamma in regulation of Th1 cell development.", "abstract": ["IL-12 has been identified as a major cytokine influencing the differentiation of CD4 cells to a Th1 phenotype, whereas a role for IFN-gamma is controversial.", "We investigated the interrelationship between IL-12 and IFN-gamma in promoting Th1 responses using naive CD4 cells reactive with pigeon cytochrome c from TCR transgenics and memory CD4 cells derived by in vivo priming with KLH.", "Without exogenous rIL-12 or rIFN-gamma, primary and memory effectors induced by Ag or anti-CD3 and anti-CD28 secreted variable levels of IL-2 and IFN-gamma.", "The level of IFN-gamma secreted by effectors correlated with endogenous IFN-gamma produced in primary cultures, and anti-IFN-gamma largely inhibited the development of effectors producing IFN-gamma.", "With optimal TCR stimulation and costimulation, endogenous IFN-gamma, without IL-12, was sufficient to elicit Th1 cells via an autocrine mechanism, whereas with suboptimal stimulation, exogenous rIFN-gamma or rIL-12 was required for Th1 development.", "However, rIL-12 was more effective than rIFN-gamma, partially because rIL-12 greatly enhanced autocrine production of IFN-gamma, and optimal development of the Th1 phenotype was mediated by the synergistic actions of both cytokines.", "Thus, both IFN-gamma and IL-12 can independently regulate Th1 development, but because of IFN-gamma-mediated feedback, their relative contributions are determined by the conditions of T cell stimulation.", "The extent of differentiation to a Th1 phenotype may, therefore, depend on the availability of both APC-derived IL-12 and autocrine IFN-gamma consequent to the overall strength of T cell stimulation."], "structured": false}
{"doc_id": 39545358, "title": "Neuregulin 1 promotes excitatory synapse development and function in GABAergic interneurons.", "abstract": ["Neuregulin 1 (NRG1) and its receptor ErbB4 are both susceptibility genes of schizophrenia.", "However, little is known about the underlying mechanisms of their malfunction.", "Although ErbB4 is enriched in GABAergic interneurons, the role of NRG1 in excitatory synapse formation in these neurons remains poorly understood.", "We showed that NRG1 increased both the number and size of PSD-95 puncta and the frequency and amplitude of miniature EPSCs (mEPSCs) in GABAergic interneurons, indicating that NRG1 stimulates the formation of new synapses and strengthens existing synapses.", "In contrast, NRG1 treatment had no effect on either the number or size of excitatory synapses in glutamatergic neurons, suggesting its synaptogenic effect is specific to GABAergic interneurons.", "Ecto-ErbB4 treatment diminished both the number and size of excitatory synapses, suggesting that endogenous NRG1 may be critical for basal synapse formation.", "NRG1 could stimulate the stability of PSD-95 in the manner that requires tyrosine kinase activity of ErbB4.", "Finally, deletion of ErbB4 in parvalbumin-positive interneurons led to reduced frequency and amplitude of mEPSCs, providing in vivo evidence that ErbB4 is important in excitatory synaptogenesis in interneurons.", "Together, our findings suggested a novel synaptogenic role of NRG1 in excitatory synapse development, possibly via stabilizing PSD-95, and this effect is specific to GABAergic interneurons.", "In light of the association of the genes of both NRG1 and ErbB4 with schizophrenia and dysfunction of GABAergic system in this disorder, these results provide insight into its potential pathological mechanism."], "structured": false}
{"doc_id": 39550665, "title": "Tolerance rather than immunity protects from Helicobacter pylori-induced gastric preneoplasia.", "abstract": ["BACKGROUND & AIMS Chronic infection with the bacterial pathogen Helicobacter pylori causes gastric disorders, ranging from chronic gastritis to gastric adenocarcinoma.", "Only a subset of infected persons will develop overt disease; most remains asymptomatic despite lifelong colonization.", "This study aims to elucidate the differential susceptibility to H pylori that is found both across and within populations.   \n", "METHODS We have established a C57BL/6 mouse model of H pylori infection with a strain that is capable of delivering the virulence factor cytotoxin-associated gene A (CagA) into host cells through the activity of a Cag-pathogenicity island-encoded type IV secretion system.   \n", "RESULTS Mice infected at 5-6 weeks of age with CagA(+)H pylori rapidly develop gastritis, gastric atrophy, epithelial hyperplasia, and metaplasia in a type IV secretion system-dependent manner.", "In contrast, mice infected during the neonatal period with the same strain are protected from preneoplastic lesions.", "Their protection results from the development of H pylori-specific peripheral immunologic tolerance, which requires transforming growth factor-\u03b2 signaling and is mediated by long-lived, inducible regulatory T cells, and which controls the local CD4(+) T-cell responses that trigger premalignant transformation.", "Tolerance to H pylori develops in the neonatal period because of a biased ratio of T-regulatory to T-effector cells and is favored by prolonged low-dose exposure to antigen.   \n", "CONCLUSIONS Using a novel CagA(+)H pylori infection model, we report here that the development of tolerance to H pylori protects from gastric cancer precursor lesions.", "The age at initial infection may thus account for the differential susceptibility of infected persons to H pylori-associated disease manifestations."], "structured": true}
{"doc_id": 39558597, "title": "Impaired mitochondrial fatty acid oxidation and insulin resistance in aging: novel protective role of glutathione.", "abstract": ["Aging is associated with impaired fasted oxidation of nonesterified fatty acids (NEFA) suggesting a mitochondrial defect.", "Aging is also associated with deficiency of glutathione (GSH), an important mitochondrial antioxidant, and with insulin resistance.", "This study tested whether GSH deficiency in aging contributes to impaired mitochondrial NEFA oxidation and insulin resistance, and whether GSH restoration reverses these defects.", "Three studies were conducted: (i) in 82-week-old C57BL/6 mice, the effect of naturally occurring GSH deficiency and its restoration on mitochondrial (13) C1 -palmitate oxidation and glucose metabolism was compared with 22-week-old C57BL/6 mice; (ii) in 20-week C57BL/6 mice, the effect of GSH depletion on mitochondrial oxidation of (13) C1 -palmitate and glucose metabolism was studied; (iii) the effect of GSH deficiency and its restoration on fasted NEFA oxidation and insulin resistance was studied in GSH-deficient elderly humans, and compared with GSH-replete young humans.", "Chronic GSH deficiency in old mice and elderly humans was associated with decreased fasted mitochondrial NEFA oxidation and insulin resistance, and these defects were reversed with GSH restoration.", "Acute depletion of GSH in young mice resulted in lower mitochondrial NEFA oxidation, but did not alter glucose metabolism.", "These data suggest that GSH is a novel regulator of mitochondrial NEFA oxidation and insulin resistance in aging.", "Chronic GSH deficiency promotes impaired NEFA oxidation and insulin resistance, and GSH restoration reverses these defects.", "Supplementing diets of elderly humans with cysteine and glycine to correct GSH deficiency could provide significant metabolic benefits."], "structured": false}
{"doc_id": 39559521, "title": "Control of central and peripheral tolerance by Aire.", "abstract": ["The negative selection of self-reactive thymocytes depends on the expression of tissue-specific antigens by medullary thymic epithelial cells.", "The autoimmune regulator (Aire) protein plays an important role in turning on these antigens, and the absence of even one Aire-induced tissue-specific antigen in the thymus can lead to autoimmunity in the antigen-expressing target organ.", "Recently, Aire protein has been detected in peripheral lymphoid organs, suggesting that peripheral Aire plays a complementary role here.", "In these peripheral sites, Aire was found to regulate the expression of a group of tissue-specific antigens that is distinct from those expressed in the thymus.", "Furthermore, transgenic antigen expression in extrathymic Aire-expressing cells (eTACs) can mediate deletional tolerance, but the immunological relevance of Aire-dependent, endogenous tissue-specific antigens remains to be determined."], "structured": false}
{"doc_id": 39571812, "title": "Congenital Hypogonadotropic Hypogonadism: A Trait Shared by Several Complex Neurodevelopmental Disorders.", "abstract": ["Reproductive function depends on the activity of the gonadotropic axis, which is controlled by a hypothalamic neural network whose main function is to regulate the secretion of gonadotropin-releasing hormone (GnRH).", "This endocrine network is not mature at birth, and several phases of activation-inactivation of the gonadotropic axis are necessary for its normal development.", "The postnatal maturation of the GnRH network lies under the control of a neurodevelopmental program that starts in fetal life and ends at puberty.", "There are many clinical situations in which this program is interrupted, leading to congenital hypogonadotropic hypogonadism (CHH) and an absence of puberty.", "For many years, attention has mainly been focused on the genetics of isolated CHH.", "More recently, the emergence of new genomics techniques has led to the description of genetic defects in very rare syndromes in which CHH is associated with complex neurological dysfunctions.", "Here, we review the clinical phenotype and genetic defects linked to such syndromic CHH.", "This analysis highlights the close link between the ubiquitin pathway, synaptic proteins and CHH, as well as unexpected mutations in genes encoding nucleolar proteins."], "structured": false}
{"doc_id": 39580129, "title": "Elevated expression of miR-24-3p is a potentially adverse prognostic factor in colorectal adenocarcinoma.", "abstract": ["OBJECTIVES Several miRNAs are aberrantly expressed in cancer.", "miR-24-3p is involved in cancer-related cellular processes, including cell cycle control, cell growth, proliferation, and apoptosis.", "In this study, we examined the potential diagnostic and prognostic significance of miR-24-3p expression in colorectal adenocarcinoma.   \n", "DESIGN AND METHODS Total RNA was isolated from 182 colorectal adenocarcinoma specimens and 86 paired non-cancerous colorectal mucosae.", "After polyadenylation of 2\u03bcg total RNA and reverse transcription into first-strand cDNA using an oligo-dT-adapter primer, miR-24-3p expression was quantified using an in-house-developed reverse-transcription real-time quantitative PCR method, based on the SYBR Green chemistry.", "SNORD43 (RNU43) was used as a reference gene.   \n", "RESULTS miR-24-3p levels do not significantly differ between colorectal adenocarcinoma and non-cancerous colorectal mucosae.", "Thus, miR-24-3p expression cannot be used for diagnostic purposes.", "However, high miR-24-3p expression predicts poor disease-free survival (DFS) and overall survival (OS) of colorectal adenocarcinoma patients.", "Multivariate Cox regression analysis confirmed that miR-24-3p overexpression is a significant predictor of relapse in colorectal adenocarcinoma and that its prognostic significance is independent of other established prognostic factors and treatment of patients.", "Of note, miR-24-3p overexpression retains its rather unfavorable prognostic value in the subgroup of patients with advanced yet locally restricted colorectal adenocarcinoma (T3) and in those without distant metastasis (M0).", "Moreover, miR-24-3p overexpression is a potentially unfavorable prognosticator for patients who were not treated with radiotherapy.   \n", "CONCLUSIONS Strong expression of miR-24-3p predicts poor DFS and OS of colorectal adenocarcinoma patients, independently of clinicopathological parameters that are currently used for prognosis in this human malignancy."], "structured": true}
{"doc_id": 39593548, "title": "Reforming the health sector in developing countries: the central role of policy analysis.", "abstract": ["Policy analysis is an established discipline in the industrialized world, yet its application to developing countries has been limited.", "The health sector in particular appears to have been neglected.", "This is surprising because there is a well recognized crisis in health systems, and prescriptions abound of what health policy reforms countries should introduce.", "However, little attention has been paid to how countries should carry out reforms, much less who is likely to favour or resist such policies.", "This paper argues that much health policy wrongly focuses attention on the content of reform, and neglects the actors involved in policy reform (at the international, national sub-national levels), the processes contingent on developing and implementing change and the context within which policy is developed.", "Focus on policy content diverts attention from understanding the processes which explain why desired policy outcomes fail to emerge.", "The paper is organized in 4 sections.", "The first sets the scene, demonstrating how the shift from consensus to conflict in health policy established the need for a greater emphasis on policy analysis.", "The second section explores what is meant by policy analysis.", "The third investigates what other disciplines have written that help to develop a framework of analysis.", "And the final section suggests how policy analysis can be used not only to analyze the policy process, but also to plan."], "structured": false}
{"doc_id": 39637840, "title": "The processing of Holliday junctions by BLM and WRN helicases is regulated by p53.", "abstract": ["BLM, WRN, and p53 are involved in the homologous DNA recombination pathway.", "The DNA structure-specific helicases, BLM and WRN, unwind Holliday junctions (HJ), an activity that could suppress inappropriate homologous recombination during DNA replication.", "Here, we show that purified, recombinant p53 binds to BLM and WRN helicases and attenuates their ability to unwind synthetic HJ in vitro.", "The p53 248W mutant reduces abilities of both to bind HJ and inhibit helicase activities, whereas the p53 273H mutant loses these abilities.", "Moreover, full-length p53 and a C-terminal polypeptide (residues 373-383) inhibit the BLM and WRN helicase activities, but phosphorylation at Ser(376) or Ser(378) completely abolishes this inhibition.", "Following blockage of DNA replication, Ser(15) phospho-p53, BLM, and RAD51 colocalize in nuclear foci at sites likely to contain DNA replication intermediates in cells.", "Our results are consistent with a novel mechanism for p53-mediated regulation of DNA recombinational repair that involves p53 post-translational modifications and functional protein-protein interactions with BLM and WRN DNA helicases."], "structured": false}
{"doc_id": 39652608, "title": "Trim and fill: A simple funnel-plot-based method of testing and adjusting for publication bias in meta-analysis.", "abstract": ["We study recently developed nonparametric methods for estimating the number of missing studies that might exist in a meta-analysis and the effect that these studies might have had on its outcome.", "These are simple rank-based data augmentation techniques, which formalize the use of funnel plots.", "We show that they provide effective and relatively powerful tests for evaluating the existence of such publication bias.", "After adjusting for missing studies, we find that the point estimate of the overall effect size is approximately correct and coverage of the effect size confidence intervals is substantially improved, in many cases recovering the nominal confidence levels entirely.", "We illustrate the trim and fill method on existing meta-analyses of studies in clinical trials and psychometrics."], "structured": false}
{"doc_id": 39661951, "title": "Familial Barrett's esophagus associated with adenocarcinoma.", "abstract": ["A family with six cases of Barrett's esophagus over three generations is described.", "The Barrett's esophagus affected only males, and there were three associated adenocarcinomas.", "The mechanism of inheritance is compatible with an autosomal dominant pattern with nearly complete penetrance.", "Other case reports in the literature are compared with this familial case of Barrett's esophagus with associated adenocarcinomas."], "structured": false}
{"doc_id": 39668245, "title": "Development of an insect model for the in vivo pathogenicity testing of yeasts.", "abstract": ["Conventional in vivo assays to determine the relative pathogenicity of yeast isolates rely upon the use of a range of mammalian species.", "The purpose of the work presented here was to investigate the possibility of using an insect (Galleria mellonella) as a model system for in vivo pathogenicity testing.", "The haemolymph of G. mellonella larvae was inoculated with PBS containing different concentrations of stationary phase yeasts of the genus Candida by injection at the last pro-leg.", "Larvae were incubated at 30 degrees C and monitored over 72 hours.", "Results indicate that G. mellonella can be killed by the pathogenic yeast Candida albicans and by a range of other Candida species but not to a significant extent by the yeast Saccharomyces cerevisiae.", "The kill kinetics for larvae inoculated with clinical and laboratory isolates of C. albicans indicate the former class of isolates to be more pathogenic.", "Differences in the relative pathogenicity of a range of Candida species may be distinguished using G. mellonella as a model.", "This work indicates that G. mellonella may be employed to give results consistent with data previously obtained using mammals in conventional in vivo pathogenicity testing.", "Larvae of G. mellonella are inexpensive to culture, easy to manipulate and their use may reduce the need to employ mammals for routine in vivo pathogenicity testing with a concomitant reduction in mammalian suffering."], "structured": false}
{"doc_id": 39728826, "title": "Use of TLS parameters to model anisotropic displacements in macromolecular refinement.", "abstract": ["An essential step in macromolecular refinement is the selection of model parameters which give as good a description of the experimental data as possible while retaining a realistic data-to-parameter ratio.", "This is particularly true of the choice of atomic displacement parameters, where the move from individual isotropic to individual anisotropic refinement involves a sixfold increase in the number of required displacement parameters.", "The number of refinement parameters can be reduced by using collective variables rather than independent atomic variables and one of the simplest examples of this is the TLS parameterization for describing the translation, libration and screw-rotation displacements of a pseudo-rigid body.", "This article describes the implementation of the TLS parameterization in the macromolecular refinement program REFMAC.", "Derivatives of the residual with respect to the TLS parameters are expanded in terms of the derivatives with respect to individual anisotropic U values, which in turn are calculated using a fast Fourier transform technique.", "TLS refinement is therefore fast and can be used routinely.", "Examples of TLS refinement are given for glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and a transcription activator GerE, for both of which there is data to only 2.0 A, so that individual anisotropic refinement is not feasible.", "GAPDH has been refined with between one and four TLS groups in the asymmetric unit and GerE with six TLS groups.", "In both cases, inclusion of TLS parameters gives improved refinement statistics and in particular an improvement in R and free R values of several percent.", "Furthermore, GAPDH and GerE have two and six molecules in the asymmetric unit, respectively, and in each case the displacement parameters differ significantly between molecules.", "These differences are well accounted for by the TLS parameterization, leaving residual local displacements which are very similar between molecules and to which NCS restraints can be applied."], "structured": false}
{"doc_id": 39729277, "title": "Sequence features surrounding the translation initiation sites assigned on the genome sequence of Synechocystis sp. strain PCC6803 by amino-terminal protein sequencing.", "abstract": ["To characterize the sequence features surrounding the translation initiation sites on the genome of Synechocystis sp. strain 6803, the total proteins extracted from the cell were resolved by two-dimensional electrophoresis, and the amino-terminal sequences of the relatively abundant protein spots were determined.", "By comparison of the determined amino-terminal sequences with the nucleotide sequence of the entire genome, the translation initiation sites of a total of 72 proteins were successfully assigned on the genome.", "The sequence features emerged from the nucleotide sequences at and surrounding the translation initiation sites were as follows: (1) In addition to the three initiation codons, ATG, GTG, and TTG, evidence was obtained that ATT was also used as a rare initiation codon; (2) the core sequences (GAGG, GGAG and AGGA) of the Shine-Dalgarno sequence were identified in the appropriate position preceding the 35 initiation sites (48.6%); and (3) the preferential sequence surrounding the initiation codons was formulated as 5'-YY[...]R-3' where Y and R denote pyrimidine and purine nucleotides, respectively, and three dots represent the initiation codons.", "The result obtained would provide valuable information for improvement of the gene-finding software, and the approach used in this study should be applicable for comprehensive analysis of the expression profiles of cellular proteins."], "structured": false}
{"doc_id": 39758684, "title": "Deregulated DNA polymerase beta induces chromosome instability and tumorigenesis.", "abstract": ["To reach the biological alterations that characterize cancer, the genome of tumor cells must acquire increased mutability resulting from a malfunction of a network of genome stability systems, e.g., cell cycle arrest, DNA repair, and high accuracy of DNA synthesis during DNA replication.", "Numeric chromosomal imbalance, referred to as aneuploidy, is the most prevalent genetic changes recorded among many types of solid tumors.", "We report here that ectopic expression in cells of DNA polymerase beta, an error-prone enzyme frequently over-regulated in human tumors, induces aneuploidy, an abnormal localization of the centrosome-associated gamma-tubulin protein during mitosis, a deficient mitotic checkpoint, and promotes tumorigenesis in nude immunodeficient mice.", "Thus, we find that alteration of polymerase beta expression appears to induce major genetic changes associated with a malignant phenotype."], "structured": false}
{"doc_id": 39763465, "title": "Combinatorial signaling by Sonic hedgehog and Wnt family members induces myogenic bHLH gene expression in the somite.", "abstract": ["We have demonstrated previously that a combination of signals from the neural tube and the floor plate/notochord complex synergistically induce the expression of myogenic bHLH genes and myogenic differentiation markers in unspecified somites.", "In this study we demonstrate that Sonic hedgehog (Shh), which is expressed in the floor plate/notochord, and a subset of Wnt family members (Wnt-1, Wnt-3, and Wnt-4), which are expressed in dorsal regions of the neural tube, mimic the muscle inducing activity of these tissues.", "In combination, Shh and either Wnt-1 or Wnt-3 are sufficient to induce myogenesis in somitic tissue in vitro.", "Therefore, we propose that myotome formation in vivo may be directed by the combinatorial activity of Shh secreted by ventral midline tissues (floor plate and notochord) and Wnt ligands secreted by the dorsal neural tube."], "structured": false}
{"doc_id": 39776978, "title": "Advances in osteoclast biology: old findings and new insights from mouse models", "abstract": ["The maintenance of adequate bone mass is dependent upon the controlled and timely removal of old, damaged bone.", "This complex process is performed by the highly specialized, multinucleated osteoclast.", "Over the past 15 years, a detailed picture has emerged describing the origins, differentiation pathways and activation stages that contribute to normal osteoclast function.", "This information has primarily been obtained by the development and skeletal analysis of genetically modified mouse models.", "Mice harboring mutations in specific genetic loci exhibit bone defects as a direct result of aberrations in normal osteoclast recruitment, formation or function.", "These findings include the identification of the RANK\u2013RANKL\u2013OPG system as a primary mediator of osteoclastogenesis, the characterization of ion transport and cellular attachment mechanisms and the recognition that matrix-degrading enzymes are essential components of resorptive activity.", "This Review focuses on the principal observations in osteoclast biology derived from genetic mouse models, and highlights emerging concepts that describe how the osteoclast is thought to contribute to the maintenance of adequate bone mass and integrity throughout life."], "structured": false}
{"doc_id": 39801095, "title": "DNA methylation in embryonic stem cells.", "abstract": ["Embryonic stem cells (ESCs) are pluripotent, self-renewing cells.", "These cells can be used in applications such as cell therapy, drug development, disease modeling, and the study of cellular differentiation.", "Investigating the interplay of epigenetics, genetics, and gene expression in control of pluripotence and differentiation could give important insights on how these cells function.", "One of the best known epigenetic factors is DNA methylation, which is a major mechanism for regulation of gene expression.", "This phenomenon is mostly seen in imprinted genes and X-chromosome inactivation where DNA methylation of promoter regions leads to repression of gene expression.", "Differential DNA methylation of pluripotence-associated genes such as Nanog and Oct4/Pou5f1 has been observed between pluripotent and differentiated cells.", "It is clear that tight regulation of DNA methylation is necessary for normal development.", "As more associations between aberrant DNA methylation and disease are reported, the demand for high-throughput approaches for DNA methylation analysis has increased.", "In this article, we highlight these methods and discuss recent DNA methylation studies on ESCs."], "structured": false}
{"doc_id": 39851630, "title": "Reserves, functional, immunoregulatory, and cytogenetic properties of bone marrow mesenchymal stem cells in patients with myelodysplastic syndromes.", "abstract": ["Defective hematopoiesis supporting capacity of bone marrow (BM) stroma has been implicated in the pathophysiology of myelodysplastic syndromes (MDS).", "The aim of this study is to explore whether the BM stroma progenitors, namely the mesenchymal stem cells (MSCs), are primarily affected in MDS by evaluating the reserves, the functional properties, as well as the cytogenetic characteristics, in comparison to BM hematopoietic cells, in patients with de novo MDS (n = 13).", "The number, differentiation potential toward adipocytes/chondrocytes/osteoblasts and immunosuppressive function in terms of inhibition of mitogen-induced T-cell proliferation did not differ significantly between patient and normal (n = 20) MSCs.", "Patient MSCs did not show any aberrations in the production of proinflammatory or growth-promoting cytokines and did not harbor the cytogenetic abnormalities present in hematopoietic cells.", "Occasional patient and normal MSC cultures, however, developed irrelevant chromosomal alterations (trisomies 5 and 7) with uncertain pathophysiologic significance.", "Compared to controls, patient MSCs displayed impaired proliferative and clonogenic potential through passages that might represent a nonspecific abnormality associated with the chronic inflammatory process present in patients' BM.", "These data suggest that BM MSCs from MDS patients do not belong to the abnormal clone and do not represent the main cellular source contributing to the inflammatory marrow microenvironment."], "structured": false}
{"doc_id": 39859981, "title": "Symmetric signalling within asymmetric dimers of the Staphylococcus aureus receptor histidine kinase AgrC.", "abstract": ["Virulence in Staphylococcus aureus is largely under control of the accessory gene regulator (agr) quorum-sensing system.", "The AgrC receptor histidine kinase detects its autoinducing peptide (AIP) ligand and generates an intracellular signal resulting in secretion of virulence factors.", "Although agr is a well-studied quorum-sensing system, little is known about the mechanism of AgrC activation.", "By co-immunoprecipitation analysis and intermolecular complementation of receptor mutants, we showed that AgrC forms ligand-independent dimers that undergo trans-autophosphorylation upon interaction with AIP.", "Remarkably, addition of specific AIPs to AgrC mutant dimers with only one functional sensor domain caused symmetric activation of either kinase domain despite the sensor asymmetry.", "Furthermore, mutant dimers involving one constitutive protomer demonstrated ligand-independent activity, irrespective of which protomer was kinase deficient.", "These results demonstrate that signalling through either individual AgrC protomer causes symmetric activation of both kinase domains.", "We suggest that such signalling across the dimer interface may be an important mechanism for dimeric quorum-sensing receptors to rapidly elicit a response upon signal detection."], "structured": false}
{"doc_id": 39863735, "title": "Attachment of the ubiquitin-related protein Urm1p to the antioxidant protein Ahp1p.", "abstract": ["Urm1p is a ubiquitin-related protein that serves as a posttranslational modification of other proteins.", "Urm1p conjugation has been implicated in the budding process and in nutrient sensing.", "Here, we have identified the first in vivo target for the urmylation pathway as the antioxidant protein Ahp1p.", "The attachment of Urm1p to Ahp1p requires the E1 for the urmylation pathway, Uba4p.", "Loss of the urmylation pathway components results in sensitivity to a thiol-specific oxidant, as does loss of Ahp1p, implying that urmylation has a role in an oxidative-stress response.", "Moreover, treatment of cells with thiol-specific oxidants affects the abundance of Ahp1p-Urm1p conjugates.", "These results suggest that the conjugation of Urm1p to Ahp1p could regulate the function of Ahp1p in antioxidant stress response in Saccharomyces cerevisiae."], "structured": false}
{"doc_id": 39892135, "title": "Sulfasalazine in the treatment of spondylarthropathy. A randomized, multicenter, double-blind, placebo-controlled study.", "abstract": ["OBJECTIVE To assess the efficacy and tolerability of sulfasalazine (SSZ) in the treatment of spondylarthropathy.   \n", "METHODS We conducted a 6-month randomized, placebo-controlled, double-blind, multicenter study of patients with spondylarthropathy whose disease had remained active despite treatment with nonsteroidal antiinflammatory drugs.", "Patients were treated with SSZ (3 gm/day) or placebo.", "The primary efficacy variables were the physician's and patient's overall assessments, pain, and morning stiffness.", "End points were analyzed in the intent-to-treat and completer patient populations; the time course of effect was analyzed in the completer patient population.   \n", "RESULTS Of the 351 patients enrolled, 263 (75%) completed the 6-month treatment period.", "The withdrawal rates were 35 (20%) and 53 (30%) in the placebo and SSZ groups, respectively.", "In the intent-to-treat analysis of end point efficacy, the between-treatment difference reached statistical significance only for 1 of the 4 primary outcome variables, the patient's overall assessment of disease activity, for which 60% of the patients taking SSZ improved by at least 1 point on a 5-point scale, in contrast to 44% of the patients taking placebo.", "Laboratory markers of inflammation also showed statistically significant change in favor of SSZ.", "In subgroup analysis, the most impressive effects were seen in patients with psoriatic arthritis, both for the 4 primary efficacy variables and for secondary efficacy variables such as the number of inflamed joints.", "Adverse events were more frequent in the SSZ group than the placebo group, but all were transient or reversible after cessation of treatment.   \n", "CONCLUSION The results of this study show that SSZ had greater efficacy than placebo in the treatment of active spondylarthropathy, notably in patients with psoriatic arthritis."], "structured": true}
{"doc_id": 39903312, "title": "A randomized trial of aspirin to prevent colorectal adenomas in patients with previous colorectal cancer.", "abstract": ["BACKGROUND Experimental studies in animals and observational studies in humans suggest that regular aspirin use may decrease the risk of colorectal adenomas, the precursors to most colorectal cancers.   \n", "METHODS We conducted a randomized, double-blind trial to determine the effect of aspirin on the incidence of colorectal adenomas.", "We randomly assigned 635 patients with previous colorectal cancer to receive either 325 mg of aspirin per day or placebo.", "We determined the proportion of patients with adenomas, the number of recurrent adenomas, and the time to the development of adenoma between randomization and subsequent colonoscopic examinations.", "Relative risks were adjusted for age, sex, cancer stage, the number of colonoscopic examinations, and the time to a first colonoscopy.", "The study was terminated early by an independent data and safety monitoring board when statistically significant results were reported during a planned interim analysis.   \n", "RESULTS A total of 517 randomized patients had at least one colonoscopic examination a median of 12.8 months after randomization.", "One or more adenomas were found in 17 percent of patients in the aspirin group and 27 percent of patients in the placebo group (P=0.004).", "The mean (+/-SD) number of adenomas was lower in the aspirin group than the placebo group (0.30+/-0.87 vs. 0.49+/-0.99, P=0.003 by the Wilcoxon test).", "The adjusted relative risk of any recurrent adenoma in the aspirin group, as compared with the placebo group, was 0.65 (95 percent confidence interval, 0.46 to 0.91).", "The time to the detection of a first adenoma was longer in the aspirin group than in the placebo group (hazard ratio for the detection of a new polyp, 0.64; 95 percent confidence interval, 0.43 to 0.94; P=0.022).   \n", "CONCLUSIONS Daily use of aspirin is associated with a significant reduction in the incidence of colorectal adenomas in patients with previous colorectal cancer."], "structured": true}
{"doc_id": 39929509, "title": "The Wilms tumour suppressor protein WT1 (+KTS isoform) binds alpha-actinin 1 mRNA via its zinc-finger domain.", "abstract": ["Mutations in WT1 are associated with developmental syndromes that affect the urogenital system and neoplasms, including Wilms tumour, acute myeloid leukemia, and breast and prostate cancers.", "The WT1 protein belongs to the early growth response family of zinc-finger transcription factors.", "Uniquely to WT1, an evolutionarily conserved alternative splice event inserts the tripeptide KTS, between zinc fingers 3 and 4.", "Whereas -KTS isoforms bind DNA and activate or repress transcription, +KTS isoforms bind DNA less efficiently and interact with splice factors and RNA in vitro and in vivo.", "Although candidate DNA targets have been found, physiological mRNA targets are yet to be defined.", "We examined the distribution of WT1 in ribonucleoprotein (RNP) complexes in nuclear extract prepared from M15 cells, a mouse mesonephric fetal kidney cell line.", "WT1 cofractionated with the splice factor PSF in large RNP particles >or=2 MDa.", "We also found that PSF co-immunoprecipitated with WT1, suggesting a functional interaction between these 2 multifunctional proteins.", "Using yeast three-hybrid library constructed from the co-immunoprecipitated RNA we found that WT1 (+KTS) binds close to or at the start codon of alpha-actinin 1 (ACTN1) mRNA.", "A band shift assay confirmed the ability of the WT1 zinc-finger domain (+KTS) to bind this sequence in vitro.", "ACTN1 is the first likely physiological mRNA target of WT1."], "structured": false}
{"doc_id": 39970500, "title": "How safe are psychiatric medications after a voluntary overdose?", "abstract": ["PURPOSE This study assessed psychiatric medications and their potential lethality in a representative sample of suicide attempts.   ", "MATERIALS AND METHODS During 1996-98, 563 suicide attempts were studied in a general hospital in Madrid (Spain).", "Medication overdose was used in 456 suicide attempts (81%).", "The ratio between dose taken and maximum prescription dose recommended was used to evaluate the medication toxicity.   \n", "RESULTS Benzodiazepines were the drugs most often used in self-poisoning (65% of overdoses), followed by new antidepressants (11%), tricyclic antidepressants (TCAs) (10%), and antipsychotics (8%).", "An overdose with any of the three latter psychiatric medications was significantly more frequent in patients prescribed those medications.", "The overdoses for TCA were potentially lethal in 47% of the cases.", "However, all patients who overdosed on psychiatric medications recovered well and were discharged without any sequelae.   ", "DISCUSSION This study suggests that psychiatric medications, particularly benzodiazepines, new antidepressants and antipsychotics, are relatively safe when they are used for self-poisoning.", "If patients with mental illnesses are under treated, there is a clear and documented higher risk for suicide.   \n", "CONCLUSION", "It is better to prescribe psychiatric medications, particularly the new ones, rather than withhold them due to an exaggerated fear of a lethal overdose"], "structured": true}
{"doc_id": 39984099, "title": "Health benefits, costs, and cost-effectiveness of earlier eligibility for adult antiretroviral therapy and expanded treatment coverage: a combined analysis of 12 mathematical models.", "abstract": ["BACKGROUND New WHO guidelines recommend ART initiation for HIV-positive persons with CD4 cell counts \u2264500 cells/\u00b5L, a higher threshold than was previously recommended.", "Country decision makers must consider whether to further expand ART eligibility accordingly.   \n", "METHODS We used multiple independent mathematical models in four settings-South Africa, Zambia, India, and Vietnam-to evaluate the potential health impact, costs, and cost-effectiveness of different adult ART eligibility criteria under scenarios of current and expanded treatment coverage, with results projected over 20 years.", "Analyses considered extending eligibility to include individuals with CD4 \u2264500 cells/\u00b5L or all HIV-positive adults, compared to the previous recommendation of initiation with CD4 \u2264350 cells/\u00b5L. We assessed costs from a health system perspective, and calculated the incremental cost per DALY averted ($/DALY) to compare competing strategies.", "Strategies were considered 'very cost-effective' if the $/DALY was less than the country's per capita gross domestic product (GDP; South Africa: $8040, Zambia: $1425, India: $1489, Vietnam: $1407) and 'cost-effective' if $/DALY was less than three times per capita GDP.   \n", "FINDINGS In South Africa, the cost per DALY averted of extending ART eligibility to CD4 \u2264500 cells/\u00b5L ranged from $237 to $1691/DALY compared to 2010 guidelines; in Zambia, expanded eligibility ranged from improving health outcomes while reducing costs (i.e. dominating current guidelines) to $749/DALY.", "Results were similar in scenarios with substantially expanded treatment access and for expanding eligibility to all HIV-positive adults.", "Expanding treatment coverage in the general population was therefore found to be cost-effective.", "In India, eligibility for all HIV-positive persons ranged from $131 to $241/DALY and in Vietnam eligibility for CD4 \u2264500 cells/\u00b5L cost $290/DALY.", "In concentrated epidemics, expanded access among key populations was also cost-effective.   \n", "INTERPRETATION Earlier ART eligibility is estimated to be very cost-effective in low- and middle-income settings, although these questions should be revisited as further information becomes available.", "Scaling-up ART should be considered among other high-priority health interventions competing for health budgets.   \n", "FUNDING The Bill and Melinda Gates Foundation and World Health Organization."], "structured": true}
{"doc_id": 39985001, "title": "Chronic daily headache: long-term prognosis following inpatient treatment with repetitive IV DHE.", "abstract": ["We retrospectively studied the long-term (2-year) outcome of 50 consecutive patients admitted to our inpatient headache program because of chronic daily headache (CDH) associated with the overuse of analgesics, ergotamine, or both.", "They had been detoxified, given repetitive intravenous dihydroergotamine (IV DHE) and prophylactic medications as part of the program, and had become headache-free on this regimen.", "At the time of admission, 37 of the 50 patients had transformed migraine (TM), 12 had new daily persistent headache (NDPH), and 1 had chronic tension-type headache; 29 of the patients with TM, 7 of those with NDPH, and the single patient with chronic tension-type headache had coexistent migraine.", "Substances abused, alone or in combination, included: caffeine in 39 patients (av.", "441 mg/d), acetaminophen in 32 (av.", "2187 mg/d), aspirin in 24 (av.", "1807 mg/d), ibuprofen in 9 (av.", "1156 mg/d), narcotics in 7 (av.", "10.1 mg morphine equivalents/d) and ergotamine in 11 (av.", "2.3 mg/d).", "Twenty patients were using preventive medication at the time of admission.", "Follow-up evaluations were performed at 3, 6, 12, and 24 months after discharge.", "Forty-three patients were analyzed at 3 months.", "Of these, 44% had an excellent or good result and 28% a fair result; 3 were overusing analgesics.", "At 24 months, 39 patients were analyzed: 59% had a good or excellent result and 28% a fair result; 5 were overusing analgesics, 4 of whom were doing poorly.(ABSTRACT TRUNCATED AT 250 WORDS)"], "structured": false}
{"doc_id": 40005757, "title": "Survival in a case of massive paraquat ingestion.", "abstract": ["Serious exposure to the herbicide paraquat usually results in death, either due to gastrointestinal caustic lesions, shock, and acute respiratory distress syndrome or related to the progressive development of pulmonary fibrosis associated with refractory hypoxemia.", "We report a case of suicidal paraquat ingestion in a 59-year-old man.", "Most of the indicators of poor prognosis were encountered in this patient.", "Treatment consisted of early digestive decontamination and hemodialysis, followed by antioxidant therapy, including the administration of deferoxamine (100 mg/kg in 24 h) and a continuous infusion of acetylcysteine (300 mg/kg/d during 3 weeks).", "The patient only developed a nonoliguric acute renal failure, a mild alteration of liver tests, and an impairment of CO transfer factor without any respiratory complaint.", "Renal and hepatic disturbances completely resolved within 1 month, whereas CO transfer factor remained altered 14 months later.", "This observation suggests that early administration of an antioxidant therapy, including deferoxamine and acetylcysteine could be usefully associated with measures that prevent digestive absorption or enhance elimination to limit systemic toxicity in potentially fatal paraquat poisoning."], "structured": false}
{"doc_id": 40044800, "title": "Cyclic GMP-AMP synthase is a cytosolic DNA sensor that activates the type I interferon pathway.", "abstract": ["The presence of DNA in the cytoplasm of mammalian cells is a danger signal that triggers host immune responses such as the production of type I interferons.", "Cytosolic DNA induces interferons through the production of cyclic guanosine monophosphate-adenosine monophosphate (cyclic GMP-AMP, or cGAMP), which binds to and activates the adaptor protein STING.", "Through biochemical fractionation and quantitative mass spectrometry, we identified a cGAMP synthase (cGAS), which belongs to the nucleotidyltransferase family.", "Overexpression of cGAS activated the transcription factor IRF3 and induced interferon-\u03b2 in a STING-dependent manner.", "Knockdown of cGAS inhibited IRF3 activation and interferon-\u03b2 induction by DNA transfection or DNA virus infection.", "cGAS bound to DNA in the cytoplasm and catalyzed cGAMP synthesis.", "These results indicate that cGAS is a cytosolic DNA sensor that induces interferons by producing the second messenger cGAMP."], "structured": false}
{"doc_id": 40078758, "title": "Eating pathology, emotion regulation, and emotional overeating in obese adults with Binge Eating Disorder.", "abstract": ["OBJECTIVE The purpose of the current study was to examine the relationship among emotional regulation, emotional overeating, and general eating pathology in a treatment seeking sample of adults with Binge Eating Disorder (BED).   \n", "METHOD The sample was composed of 326 adults (248 women, 78 men) who were obese and met DSM-IV-TR criteria for BED.", "Prior to treatment, participants completed the Difficulties in Emotion Regulation Scale (DERS), Emotional Overeating Questionnaire (EOQ), Beck Depression Inventory (BDI), and Eating Disorder Examination-Questionnaire (EDE-Q) as part of a larger assessment battery.   \n", "RESULTS A series of hierarchical regression analyses indicated that difficulties with emotion regulation accounted for unique variance in both emotional overeating and general eating pathology above and beyond sex and negative affect.   ", "DISCUSSION Emotion regulation may play a significant role in the maintenance of emotional overeating and eating pathology in obese adults with BED."], "structured": true}
{"doc_id": 40087494, "title": "Monoallelic expression and methylation of imprinted genes in human and mouse embryonic germ cell lineages.", "abstract": ["Imprinting is an epigenetic modification leading to monoallelic expression of some genes, and disrupted imprinting is believed to be a barrier to human stem cell transplantation, based on studies that suggest that epigenetic marks are unstable in mouse embryonic germ (EG) and embryonic stem (ES) cells.", "However, stem cell imprinting has not previously been examined directly in humans.", "We found that three imprinted genes, TSSC5, H19, and SNRPN, show monoallelic expression in in vitro differentiated human EG-derived cells, and a fourth gene, IGF2, shows partially relaxed imprinting at a ratio from 4:1 to 5:1, comparable to that found in normal somatic cells.", "In addition, we found normal methylation of an imprinting control region (ICR) that regulates H19 and IGF2 imprinting, suggesting that imprinting may not be a significant epigenetic barrier to human EG cell transplantation.", "Finally, we were able to construct an in vitro mouse model of genomic imprinting, by generating EG cells from 8.5-day embryos of an interspecific cross, in which undifferentiated cells show biallelic expression and acquire preferential parental allele expression after differentiation.", "This model should allow experimental manipulation of epigenetic modifications of cultured EG cells that may not be possible in human stem cell studies."], "structured": false}
{"doc_id": 40090058, "title": "Functional in vivo interactions between JNK1 and JNK2 isoforms in obesity and insulin resistance.", "abstract": ["The c-Jun N-terminal kinases (JNKs) are key regulators of inflammation and interfere with insulin action in cultured cells and whole animals.", "Obesity increases total JNK activity, and JNK1, but not JNK2, deficiency results in reduced adiposity and improved insulin sensitivity.", "Interestingly, a higher-than-normal level of JNK activation is observed in Jnk2(-/-) mice, particularly in the liver, indicating an interaction between the isoforms that might have masked the metabolic activity of JNK2 in isolated mutant mice.", "To address the role of the JNK2 isoform in metabolic homeostasis, we intercrossed Jnk1(-/-) and Jnk2(-/-) mice and examined body weight and glucose metabolism in the resulting mutant allele combinations.", "Among all of the viable genotypes examined, we observed only reduced body weight and increased insulin sensitivity in Jnk1(-/-) and Jnk1(+/-)Jnk2(-/-) mice.", "These two groups of mice also exhibited reduced total JNK activity and cytokine expression in liver tissue compared with all other genotypes examined.", "These data indicate that the JNK2 isoform is also involved in metabolic regulation, but its function is not obvious when JNK1 is fully expressed because of regulatory crosstalk between the two isoforms."], "structured": false}
{"doc_id": 40094786, "title": "The immunological synapse of CTL contains a secretory domain and membrane bridges.", "abstract": ["Cytotoxic T lymphocytes (CTL) rapidly destroy their targets.", "Here we show that although target cell death occurs within 5 min of CTL-target cell contact, an immunological synapse similar to that seen in CD4 cells rapidly forms in CTL, with a ring of adhesion proteins surrounding an inner signaling molecule domain.", "Lytic granule secretion occurs in a separate domain within the adhesion ring, maintaining signaling protein organization during exocytosis.", "Live and fixed cell studies show target cell plasma membrane markers are transferred to the CTL as the cells separate.", "Electron microscopy reveals continuities forming membrane bridges between the CTL and target cell membranes, suggesting a possible mechanism for this transfer."], "structured": false}
{"doc_id": 40096222, "title": "Compromised intestinal epithelial barrier induces adaptive immune compensation that protects from colitis.", "abstract": ["Mice lacking junctional adhesion molecule A (JAM-A, encoded by F11r) exhibit enhanced intestinal epithelial permeability, bacterial translocation, and elevated colonic lymphocyte numbers, yet do not develop colitis.", "To investigate the contribution of adaptive immune compensation in response to increased intestinal epithelial permeability, we examined the susceptibility of F11r(-/-)Rag1(-/-) mice to acute colitis.", "Although negligible contributions of adaptive immunity in F11r(+/+)Rag1(-/-) mice were observed, F11r(-/-)Rag1(-/-) mice exhibited increased microflora-dependent colitis.", "Elimination of T cell subsets and cytokine analyses revealed a protective role for TGF-\u03b2-producing CD4(+) T cells in F11r(-/-) mice.", "Additionally, loss of JAM-A resulted in elevated mucosal and serum IgA that was dependent upon CD4(+) T cells and TGF-\u03b2.", "Absence of IgA in F11r(+/+)Igha(-/-) mice did not affect disease, whereas F11r(-/-)Igha(-/-) mice displayed markedly increased susceptibility to acute injury-induced colitis.", "These data establish a role for adaptive immune-mediated protection from acute colitis under conditions of intestinal epithelial barrier compromise."], "structured": false}
{"doc_id": 40127292, "title": "Apoptosis and chemoresistance in transgenic cancer models", "abstract": ["Multidrug resistance remains an unresolved problem in clinical oncology.", "Over a decade ago genes encoding cellular efflux pumps were shown to confer resistance to a broad spectrum of biochemically unrelated anticancer drugs even before the compounds reached their intracellular targets.", "More recently it has become apparent that many drugs induce a common apoptotic program, such that mutations in this program can also produce multidrug resistance.", "However, a thorough evaluation of the contribution of apoptotic defects to this \"postdamage\" drug resistant phenotype is technically complicated, and this has led to uncertainty about the overall significance of apoptosis in therapy-induced cell death.", "For example, correlative analyses using patient specimens are limited by unknown background mutations in the biopsy material, and assays using cancer cell lines can be biased by unphysiological conditions.", "We sought to circumvent these restrictions by utilizing a tractable transgenic cancer model to examine the impact of apoptosis on treatment outcome.", "Here we discuss potential caveats of cell culture based assays, highlight features of genetically engineered mice as potential model systems, and describe a tractable transgenic mouse model to study drug responses in a series of primary lymphomas with genetically defined lesions treated at their natural site."], "structured": false}
{"doc_id": 40145839, "title": "NC-100717: a versatile RGD peptide scaffold for angiogenesis imaging.", "abstract": ["Targeting the molecular pathways associated with angiogenesis offers great potential in detecting disease pathology using in vivo imaging technologies.", "Initiation of angiogenesis requires activation and migration of endothelial cells in order for neovascularization to proceed.", "Endothelial cells associate with the extracellular matrix through specific interactions with a variety of cell adhesion receptors known as integrins.", "Peptides containing the tripeptide sequence RGD are known to bind with high affinity to the alphavbeta3 and alphavbeta5 integrins associated with angiogenesis.", "We present herein the synthesis and in vitro binding affinity of the RGD-containing peptide NC-100717 and a range of molecular probes derived from this intermediate."], "structured": false}
{"doc_id": 40156901, "title": "Dose-dependent effect of statins on the incidence of acute kidney injury after cardiac surgery.", "abstract": ["BACKGROUND Acute kidney injury (AKI) after cardiac surgery is associated with increased morbidity and mortality.   \n", "METHODS We assessed whether statin treatment is associated with a lower incidence of postoperative AKI in 2,104 consecutive patients who underwent coronary artery bypass graft or valve surgery at the Minneapolis Veterans Administration Medical Center.", "Acute kidney injury was defined as absolute increase greater than 0.3 mg/dL or relative increase greater than 50% in serum creatinine from baseline, within 48 hours after surgery or requiring postoperative hemodialysis per AKI network.", "Propensity scores were utilized to adjust for the differences between the statin and the no-statin treatment groups.", "All statins were converted to equivalent-dose simvastatin and divided at the median to construct high-dose (\u226540 mg) and low-dose (<40 mg) statin groups.   \n", "RESULTS Of the 2,104 patients, 1,435 (68%) were taking statins (638 high-dose) and 495 (24%) developed AKI (25% high-dose vs 40% low-dose vs 35% no-statin; p = 0.014).", "Estimated preoperative glomerular filtration rate (p = 0.003), diabetes mellitus (p=0.02), valve surgery with or without coronary artery bypass graft (p = 0.024), cardiopulmonary bypass time (p = 0.001), and intraaortic balloon pump (p = 0.055) were independent predictors of AKI.", "After propensity adjustment statin treatment was not associated with postoperative AKI (odds ratio 0.79; 95% confidence interval 0.59 to 1.06; p = 0.11 for high-dose v. no-statin).", "After full adjustment for all independent predictors of AKI, the results did not change.", "Statins also had no effect on the incidence of postoperative hemodialysis (0.8% high-dose vs 1.9% low-dose vs 1% no-statin; p = 0.15).   \n", "CONCLUSIONS Statin treatment is not associated with a lower incidence of AKI after cardiac surgery."], "structured": true}
{"doc_id": 40164383, "title": "Comparison of allogeneic vs autologous bone marrow\u2013derived mesenchymal stem cells delivered by transendocardial injection in patients with ischemic cardiomyopathy: the POSEIDON randomized trial.", "abstract": ["CONTEXT Mesenchymal stem cells (MSCs) are under evaluation as a therapy for ischemic cardiomyopathy (ICM).", "Both autologous and allogeneic MSC therapies are possible; however, their safety and efficacy have not been compared.   \n", "OBJECTIVE To test whether allogeneic MSCs are as safe and effective as autologous MSCs in patients with left ventricular (LV) dysfunction due to ICM.   \n", "DESIGN, SETTING, AND PATIENTS A phase 1/2 randomized comparison (POSEIDON study) in a US tertiary-care referral hospital of allogeneic and autologous MSCs in 30 patients with LV dysfunction due to ICM between April 2, 2010, and September 14, 2011, with 13-month follow-up.   \n", "INTERVENTION Twenty million, 100 million, or 200 million cells (5 patients in each cell type per dose level) were delivered by transendocardial stem cell injection into 10 LV sites.   \n", "MAIN OUTCOME MEASURES Thirty-day postcatheterization incidence of predefined treatment-emergent serious adverse events (SAEs).", "Efficacy assessments included 6-minute walk test, exercise peak VO2, Minnesota Living with Heart Failure Questionnaire (MLHFQ), New York Heart Association class, LV volumes, ejection fraction (EF), early enhancement defect (EED; infarct size), and sphericity index.   \n", "RESULTS Within 30 days, 1 patient in each group (treatment-emergent SAE rate, 6.7%) was hospitalized for heart failure, less than the prespecified stopping event rate of 25%.", "The 1-year incidence of SAEs was 33.3% (n = 5) in the allogeneic group and 53.3% (n = 8) in the autologous group (P = .46).", "At 1 year, there were no ventricular arrhythmia SAEs observed among allogeneic recipients compared with 4 patients (26.7%) in the autologous group (P = .10).", "Relative to baseline, autologous but not allogeneic MSC therapy was associated with an improvement in the 6-minute walk test and the MLHFQ score, but neither improved exercise VO2 max.", "Allogeneic and autologous MSCs reduced mean EED by \u221233.21% (95% CI, \u221243.61% to \u221222.81%; P < .001) and sphericity index but did not increase EF.", "Allogeneic MSCs reduced LV end-diastolic volumes.", "Low-dose concentration MSCs (20 million cells) produced greatest reductions in LV volumes and increased EF.", "Allogeneic MSCs did not stimulate significant donor-specific alloimmune reactions.   \n", "CONCLUSIONS In this early-stage study of patients with ICM, transendocardial injection of allogeneic and autologous MSCs without a placebo control were both associated with low rates of treatment-emergent SAEs, including immunologic reactions.", "In aggregate, MSC injection favorably affected patient functional capacity, quality of life, and ventricular remodeling.   \n", "TRIAL REGISTRATION clinicaltrials.gov Identifier: NCT01087996."], "structured": true}
{"doc_id": 40212412, "title": "Periosteal bone formation--a neglected determinant of bone strength.", "abstract": ["Life forms that have low body mass can hunt for food on the undersurface of branches or along shear cliff faces quite unperturbed by gravity.", "For larger animals, the hunt for dinner and the struggle to avoid becoming someone else's meal require rapid movement against gravity.", "This need is met by the lever function of long bones, three-dimensional masterpieces of biomechanical engineering that, by their material composition and structural design, achieve the contradictory properties of stiffness and flexibility, strength and lightness.1 Material stiffness results from the encrusting of the triple-helical structure of collagen type I with hydroxyapatite crystals, which confers . . ."], "structured": false}
{"doc_id": 40232172, "title": "Triglyceride depletion of brown adipose tissue enables analysis of mitochondrial respiratory function in permeabilized biopsies.", "abstract": ["The research on mitochondrial functions in adipocytes has increasingly evidenced that mitochondria plays an important role in the onset and/or progression of obesity and related pathologies.", "Mitochondrial function in brown adipose tissue (BAT) has been classically assessed by measuring either the levels/activity of mitochondrial enzymes, or the respiration in isolated mitochondria.", "Isolation of mitochondria is not advantageous because it demands significant time and amount of tissue and, as tissue homogenates, disrupts biochemical and physical connections of mitochondria within the cell.", "Here, we described a new and efficient protocol to analyze the mitochondrial respiratory states in BAT biopsies that relies on intracellular triglyceride depletion followed by tissue permeabilization.", "In addition to minimizing tissue requirements to \u223c17 mg wet weight, the proposed protocol enabled analysis of all mitochondrial respiratory states, including phosphorylation (OXPHOS), no-phosphorylation (LEAK), and uncoupled (ETS) states, as well as the use of substrates for complex I, complex II, and cytochrome c; together, these features demonstrated mitochondrial integrity and validated the preparation efficacy.", "Therefore, the protocol described here increases the possibilities of answering physiological questions related to small BAT regions of human and animal models, which shall help to unravel the mechanisms that regulate mitochondrial function in health and disease."], "structured": false}
{"doc_id": 40234452, "title": "HES-1 preserves purified hematopoietic stem cells ex vivo and accumulates side population cells in vivo.", "abstract": ["Mouse long-term hematopoietic reconstituting cells exist in the c-Kit+Sca-1+Lin- (KSL) cell population; among them, CD34(low/-) cells represent the most highly purified population of hematopoietic stem cells in the adult bone marrow.", "Here, we demonstrate that retrovirus-mediated transduction of CD34(low/-)c-Kit+Sca-1+Lin- (34-KSL) cells with the HES-1 gene, which encodes a basic helix-loop-helix transcription factor functioning downstream of the Notch receptor, and is a key molecule for the growth phase of neural stem cells in the embryo, preserves the long-term reconstituting activity of these cells in vitro.", "We also show that cells derived from the HES-1-transduced 34-KSL population produce progenies characterized by negative Hoechst dye staining, which defines the side population, and by CD34(low/-) profile in the bone marrow KSL population in each recipient mouse at ratios 3.5- and 7.8-fold those produced by nontransduced 34-KSL-derived competitor cells.", "We conclude that HES-1 preserves the long-term reconstituting hematopoietic activity of 34-KSL stem cells ex vivo.", "Up-regulation of HES-1 protein in the 34-KSL population before unnecessary cell division, that is, without retrovirus transduction, may represent a potent approach to absolute expansion of hematopoietic stem cells."], "structured": false}
{"doc_id": 40254495, "title": "Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development.", "abstract": ["Transcript regulation is essential for cell function, and misregulation can lead to disease.", "Despite technologies to survey the transcriptome, we lack a comprehensive understanding of transcript kinetics, which limits quantitative biology.", "This is an acute challenge in embryonic development, where rapid changes in gene expression dictate cell fate decisions.", "By ultra-high-frequency sampling of Xenopus embryos and absolute normalization of sequence reads, we present smooth gene expression trajectories in absolute transcript numbers.", "During a developmental period approximating the first 8 weeks of human gestation, transcript kinetics vary by eight orders of magnitude.", "Ordering genes by expression dynamics, we find that \"temporal synexpression\" predicts common gene function.", "Remarkably, a single parameter, the characteristic timescale, can classify transcript kinetics globally and distinguish genes regulating development from those involved in cellular metabolism.", "Overall, our analysis provides unprecedented insight into the reorganization of maternal and embryonic transcripts and redefines our ability to perform quantitative biology."], "structured": false}
{"doc_id": 40312663, "title": "Inflammasome activation by adenylate cyclase toxin directs Th17 responses and protection against Bordetella pertussis.", "abstract": ["Inflammasome-mediated IL-1beta production is central to the innate immune defects that give rise to certain autoinflammatory diseases and may also be associated with the generation of IL-17-producing CD4(+) T (Th17) cells that mediate autoimmunity.", "However, the role of the inflammasome in driving adaptive immunity to infection has not been addressed.", "In this article, we demonstrate that inflammasome-mediated IL-1beta plays a critical role in promoting Ag-specific Th17 cells and in generating protective immunity against Bordetella pertussis infection.", "Using a murine respiratory challenge model, we demonstrated that the course of B. pertussis infection was significantly exacerbated in IL-1R type I-defective (IL-1RI(-/-)) mice.", "We found that adenylate cyclase toxin (CyaA), a key virulence factor secreted by B. pertussis, induced robust IL-1beta production by dendritic cells through activation of caspase-1 and the NALP3-containing inflammasome complex.", "Using mutant toxins, we demonstrate that CyaA-mediated activation of caspase-1 was not dependent on adenylate cyclase enzyme activity but was dependent on the pore-forming capacity of CyaA. In addition, CyaA promoted the induction of Ag-specific Th17 cells in wild-type but not IL-1RI(-/-) mice.", "Furthermore, the bacterial load was enhanced in IL-17-defective mice.", "Our findings demonstrate that CyaA, a virulence factor from B. pertussis, promotes innate IL-1beta production via activation of the NALP3 inflammasome and, thereby, polarizes T cell responses toward the Th17 subtype.", "In addition to its known role in subverting host immunity, our findings suggest that CyaA can promote IL-1beta-mediated Th17 cells, which promote clearance of the bacteria from the respiratory tract."], "structured": false}
{"doc_id": 40323148, "title": "Infection and apoptosis as a combined inflammatory trigger.", "abstract": ["While inflammatory phagocytosis of microbial pathogens and non-inflammatory phagocytosis of apoptotic cells have each been studied extensively, the consequences of innate immune recognition of host cells undergoing apoptosis as a direct result of infection are unclear.", "In this situation, the innate immune system is confronted with mixed signals, those from apoptotic cells and those from the infecting pathogen.", "Nuclear receptor activation has been implicated downstream of apoptotic cell recognition while Toll-like receptors are the prototypical inflammatory receptors engaged during infection.", "When the two signals combine, a new set of events takes place beginning with transrepression of a subset of inflammatory-response genes and ending with the induction of a T helper-17 adaptive immune response.", "This response is best suited for clearing the infecting pathogen and repairing the damage that occurred to the host tissue during infection."], "structured": false}
{"doc_id": 40323454, "title": "Chronic lymphocytic leukemia with t(14;19)(q32;q13) is characterized by atypical morphologic and immunophenotypic features and distinctive genetic features.", "abstract": ["The t(14;19)(q32;q13) involving the IGH@ and BCL3 loci is an infrequent cytogenetic abnormality detected in B-cell malignancies.", "We describe the clinicopathologic, cytogenetic, and molecular genetic characteristics of 14 cases of chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL/SLL) with t(14;19)(q32;q13).", "All patients (10 men and 4 women) had lymphocytosis; 10 had lymphadenopathy.", "Blood and bone marrow lymphocytes were predominantly small, but cytologically and immunophenotypically atypical.", "In all cases, t(14;19) was found in the neoplastic stem line; it was the sole abnormality in 4.", "Ten cases showed additional cytogenetic abnormalities, including trisomy 12 in 9 and complex karyotypes in 7.", "Fluorescence in situ hybridization demonstrated IGH@/BCL3 fusion gene in all cases.", "In all cases, the IGHV genes were unmutated, but only 7 expressed ZAP70.", "Seven cases preferentially used IGHV4-39.", "Our results indicate that t(14;19)(q32;q13) identifies a subset of CLL/SLL with distinctive clinicopathologic and genetic features.", "Furthermore, t(14;19) may represent an early, possibly primary, genetic event."], "structured": false}
{"doc_id": 40343416, "title": "Risk factors for the development of gallstone recurrence following medical dissolution. The British-Italian Gallstone Study Group.", "abstract": ["OBJECTIVE To assess risk factors for gallstone recurrence following non-surgical treatment.   \n", "DESIGN A prospective follow-up of a multicentre cohort of post-dissolution gallstone patients.   \n", "SETTING Six gastroenterology units in the UK and Italy.   \n", "PARTICIPANTS One hundred and sixty-three patients with confirmed gallstone dissolution following non-surgical therapy (bile acids or lithotripsy plus bile acids), followed up by ultrasound scan and clinical assessment at 6-monthly intervals for up to 6 years (median, 25 months; range, 6-70 months).   \n", "OUTCOME MEASURES Subject-related variables (sex, age, height, weight, body mass index), gallstone-related variables (number, diameter, presence of symptoms, months to complete stone clearance), treatment modalities (bile acid therapy, extracorporeal shock wave lithotripsy) and follow-up related variables (weight change, use of non-steroidal anti-inflammatory agents, statins, pregnancies and/or use of oestrogens) were assessed by univariate and multivariate analysis as putative risk factors for gallstone recurrence.   \n", "RESULTS Forty-five gallstone recurrences were observed during the follow-up period.", "Multiple primary gallstones and length of time to achieve gallstone dissolution were the only variables associated with a significant increase in the recurrence rate.", "Appearance of biliary sludge during follow-up was also significantly related to development of gallstone recurrence.", "Use of statins or non-steroidal anti-inflammatory agents did not confer protection against recurrence.   \n", "CONCLUSIONS Patients with primary single stones are the best candidates for non-surgical treatment of gallstones, because of a low risk of gallstone recurrence.", "The positive association of recurrence with biliary sludge formation and time to dissolution of primary stones may provide indirect confirmation for the role of impaired gallbladder motility in the pathogenesis of this condition."], "structured": true}
{"doc_id": 40349336, "title": "Deletion of the developmentally essential gene ATR in adult mice leads to age-related phenotypes and stem cell loss.", "abstract": ["Developmental abnormalities, cancer, and premature aging each have been linked to defects in the DNA damage response (DDR).", "Mutations in the ATR checkpoint regulator cause developmental defects in mice (pregastrulation lethality) and humans (Seckel syndrome).", "Here we show that eliminating ATR in adult mice leads to defects in tissue homeostasis and the rapid appearance of age-related phenotypes, such as hair graying, alopecia, kyphosis, osteoporosis, thymic involution, fibrosis, and other abnormalities.", "Histological and genetic analyses indicate that ATR deletion causes acute cellular loss in tissues in which continuous cell proliferation is required for maintenance.", "Importantly, thymic involution, alopecia, and hair graying in ATR knockout mice were associated with dramatic reductions in tissue-specific stem and progenitor cells and exhaustion of tissue renewal and homeostatic capacity.", "In aggregate, these studies suggest that reduced regenerative capacity in adults via deletion of a developmentally essential DDR gene is sufficient to cause the premature appearance of age-related phenotypes."], "structured": false}
{"doc_id": 40365566, "title": "Conventional and monocyte-derived CD11b(+) dendritic cells initiate and maintain T helper 2 cell-mediated immunity to house dust mite allergen.", "abstract": ["Dendritic cells (DCs) are crucial for mounting allergic airway inflammation, but it is unclear which subset of DCs performs this task.", "By using CD64 and MAR-1 staining, we reliably separated CD11b(+) monocyte-derived DCs (moDCs) from conventional DCs (cDCs) and studied antigen uptake, migration, and presentation assays of lung and lymph node (LN) DCs in response to inhaled house dust mite (HDM).", "Mainly CD11b(+) cDCs but not CD103(+) cDCs induced T helper 2 (Th2) cell immunity in HDM-specific T cells in vitro and asthma in vivo.", "Studies in Flt3l(-/-) mice, lacking all cDCs, revealed that moDCs were also sufficient to induce Th2 cell-mediated immunity but only when high-dose HDM was given.", "The main function of moDCs was the production of proinflammatory chemokines and allergen presentation in the lung during challenge.", "Thus, we have identified migratory CD11b(+) cDCs as the principal subset inducing Th2 cell-mediated immunity in the LN, whereas moDCs orchestrate allergic inflammation in the lung."], "structured": false}
{"doc_id": 40367499, "title": "Interplay between the dividing cell and its neighbors regulates adherens junction formation during cytokinesis in epithelial tissue.", "abstract": ["How adherens junctions (AJs) are formed upon cell division is largely unexplored.", "Here, we found that AJ formation is coordinated with cytokinesis and relies on an interplay between the dividing cell and its neighbors.", "During contraction of the cytokinetic ring, the neighboring cells locally accumulate Myosin II and produce the cortical tension necessary to set the initial geometry of the daughter cell interface.", "However, the neighboring cell membranes impede AJ formation.", "Upon midbody formation and concomitantly to neighboring cell withdrawal, Arp2/3-dependent actin polymerization oriented by the midbody maintains AJ geometry and regulates AJ final length and the epithelial cell arrangement upon division.", "We propose that cytokinesis in epithelia is a multicellular process, whereby the cooperative actions of the dividing cell and its neighbors define a two-tiered mechanism that spatially and temporally controls AJ formation while maintaining tissue cohesiveness."], "structured": false}
{"doc_id": 40382183, "title": "Cancer stem cells in solid tumours: accumulating evidence and unresolved questions", "abstract": ["Solid tumours are an enormous cancer burden and a major therapeutic challenge.", "The cancer stem cell (CSC) hypothesis provides an attractive cellular mechanism to account for the therapeutic refractoriness and dormant behaviour exhibited by many of these tumours.", "There is increasing evidence that diverse solid tumours are hierarchically organized and sustained by a distinct subpopulation of CSCs.", "Direct evidence for the CSC hypothesis has recently emerged from mouse models of epithelial tumorigenesis, although alternative models of heterogeneity also seem to apply.", "The clinical relevance of CSCs remains a fundamental issue but preliminary findings indicate that specific targeting may be possible."], "structured": false}
{"doc_id": 40383969, "title": "The structure of the follistatin:activin complex reveals antagonism of both type I and type II receptor binding.", "abstract": ["TGF-beta ligands stimulate diverse cellular differentiation and growth responses by signaling through type I and II receptors.", "Ligand antagonists, such as follistatin, block signaling and are essential regulators of physiological responses.", "Here we report the structure of activin A, a TGF-beta ligand, bound to the high-affinity antagonist follistatin.", "Two follistatin molecules encircle activin, neutralizing the ligand by burying one-third of its residues and its receptor binding sites.", "Previous studies have suggested that type I receptor binding would not be blocked by follistatin, but the crystal structure reveals that the follistatin N-terminal domain has an unexpected fold that mimics a universal type I receptor motif and occupies this receptor binding site.", "The formation of follistatin:BMP:type I receptor complexes can be explained by the stoichiometric and geometric arrangement of the activin:follistatin complex.", "The mode of ligand binding by follistatin has important implications for its ability to neutralize homo- and heterodimeric ligands of this growth factor family."], "structured": false}
{"doc_id": 40412980, "title": "The activity of siRNA in mammalian cells is related to structural target accessibility: a comparison with antisense oligonucleotides.", "abstract": ["The biological activity of siRNA seems to be influenced by local characteristics of the target RNA, including local RNA folding.", "Here, we investigated quantitatively the relationship between local target accessibility and the extent of inhibition of the target gene by siRNA.", "Target accessibility was assessed by a computational approach that had been shown earlier to be consistent with experimental probing of target RNA.", "Two sites of ICAM-1 mRNA predicted to serve as accessible motifs and one site predicted to adopt an inaccessible structure were chosen to test siRNA constructs for suppression of ICAM-1 gene expression in ECV304 cells.", "The local target-dependent effectiveness of siRNA was compared with antisense oligonucleotides (asON).", "The concentration dependency of siRNA-mediated suppression indicates a >1000-fold difference between active siRNAs (IC50 approximately 0.2-0.5 nM) versus an inactive siRNA (IC50 > or = 1 microM) which is consistent with the activity pattern of asON when relating target suppression to predicted local target accessibility.", "The extremely high activity of the siRNA si2B (IC50 = 0.24 nM) indicates that not all siRNAs shown to be active at the usual concentrations of >10-100 nM belong to this highly active species.", "The observations described here suggest an option to assess target accessibility for siRNA and, thus, support the design of active siRNA constructs.", "This approach can be automated, work at high throughput and is open to include additional parameters relevant to the biological activity of siRNA."], "structured": false}
{"doc_id": 40429879, "title": "Rapid accumulation of mutations during seed-to-seed propagation of mismatch-repair-defective Arabidopsis.", "abstract": ["During the many cell divisions that precede formation of plant gametes, their apical-meristem and floral antecedents are continually exposed to endogenous and environmental mutagenic threats.", "Although some deleterious recessive mutations may be eliminated during growth of haploid gametophytes and functionally haploid early embryos (\"haplosufficiency quality-checking\"), the multiplicity of plant genome-maintenance systems suggests aggressive quality control during prior diploid growth.", "To test in Arabidopsis a hypothesis that prior mismatch repair (MMR) is paramount in defense of plant genetic fidelity, we propagated in parallel 36 MMR-defective (Atmsh2-1) and 36 wild-type lines.", "The Atmsh2-1 lines rapidly accumulated a wide variety of mutations: fifth-generation (G5) plants showed abnormalities in morphology and development, fertility, germination efficiency, seed/silique development, and seed set.", "Only two Atmsh2-1, but all 36 wild-type lines, appeared normal at G5.", "Analyses of insertion/deletion mutation at six repeat-sequence (microsatellite) loci showed each Atmsh2-1 line to have evolved its own \"fingerprint,\" the results of as many as 10 microsatellite mutations in a single line.", "Thus, MMR during diploid growth is essential for plant genomic integrity."], "structured": false}
{"doc_id": 40447899, "title": "Archaeal chromatin and transcription.", "abstract": ["Archaea contain a variety of sequence-independent DNA binding proteins consistent with the evolution of several different, sometimes overlapping and exchangeable solutions to the problem of genome compaction.", "Some of these proteins undergo residue-specific post-translational lysine acetylation or methylation, hinting at analogues of the histone modifications that regulate eukaryotic chromatin structure and transcription.", "Archaeal transcription initiation most closely resembles the eukaryotic RNA polymerase II (RNAPII) system, but Archaea do not appear to have homologues of the multisubunit complexes that remodel eukaryotic chromatin and activate RNAPII initiation.", "In contrast, they have sequence-specific regulators that repress and perhaps activate archaeal transcription by mechanisms superficially similar to the bacterial paradigm of regulating promoter binding by RNAP.", "Repressors compete with archaeal TATA-box binding protein (TBP) and TFB for the TATA-box and TFB-recognition elements (BRE) of the archaeal promoter, or with archaeal RNAP for the site of transcription initiation.", "Transcript-specific regulation by repressors binding to sites of transcript initiation is consistent with such sites having very little sequence conservation.", "However, most Archaea have only one TBP and/or TFB that presumably must therefore bind to similar TATA-box and BRE sequences upstream of most genes.", "Repressors that function by competing with TBP and/or TFB binding must therefore also make additional contacts with transcript-specific regulatory sites adjacent or remote from the TATA-box/BRE region.", "The fate of the archaeal TBP and TFB following transcription initiation remains to be determined.", "Based on functional homology with their eukaryotic RNAPII-system counterparts, archaeal TBP and possibly also TFB should remain bound to the TATA-box/BRE region after transcription initiation.", "However, this seems unlikely as it might limit repressor competition at this site to only the first round of transcription initiation."], "structured": false}
{"doc_id": 40473317, "title": "Temporal segregation of 4-1BB versus CD28-mediated costimulation: 4-1BB ligand influences T cell numbers late in the primary response and regulates the size of the T cell memory response following influenza infection.", "abstract": ["In this report, we demonstrate that CD28(-/-) mice are severely impaired in the initial expansion of D(b)/NP366-374-specific CD8 T cells in response to influenza virus infection, whereas 4-1BB ligand (4-1BBL)(-/-) mice show no defect in primary T cell expansion to influenza virus.", "In contrast, 4-1BBL(-/-) mice show a decrease in D(b)/NP366-374-specific T cells late in the primary response.", "Upon secondary challenge with influenza virus, 4-1BBL(-/-) mice show a decrease in the number of D(b)/NP366-374-specific T cells compared to wild-type mice such that the level of the CD8 T cell expansion during the in vivo secondary response is reduced to the level of a primary response, with concomitant reduction of CTL effector function.", "In contrast, Ab responses, as well as secondary CD4 T cell responses, to influenza are unaffected by 4-1BBL deficiency.", "Thus, CD28 is critical for initial T cell expansion, whereas 4-1BB/4-1BBL signaling affects T cell numbers much later in the response and is essential for the survival and/or responsiveness of the memory CD8 T cell pool."], "structured": false}
{"doc_id": 40476126, "title": "Functional role of high-affinity anandamide transport, as revealed by selective inhibition.", "abstract": ["Anandamide, an endogenous ligand for central cannabinoid receptors, is released from neurons on depolarization and rapidly inactivated.", "Anandamide inactivation is not completely understood, but it may occur by transport into cells or by enzymatic hydrolysis.", "The compound N-(4-hydroxyphenyl)arachidonylamide (AM404) was shown to inhibit high-affinity anandamide accumulation in rat neurons and astrocytes in vitro, an indication that this accumulation resulted from carrier-mediated transport.", "Although AM404 did not activate cannabinoid receptors or inhibit anandamide hydrolysis, it enhanced receptor-mediated anandamide responses in vitro and in vivo.", "The data indicate that carrier-mediated transport may be essential for termination of the biological effects of anandamide, and may represent a potential drug target."], "structured": false}
{"doc_id": 40500438, "title": "Silibinin inhibits the invasion of IL-6-stimulated colon cancer cells via selective JNK/AP-1/MMP-2 modulation in vitro.", "abstract": ["Silibinin is a flavonoid with antihepatotoxic properties and pleiotropic anticancer capabilities.", "This study investigated silibinin inhibition of cell invasion by down-regulating matrix metalloproteinase-2 (MMP-2) expression, via attenuation of activator protein-1 (AP-1) in IL-6-stimulated LoVo colon cancer cells.", "Western blot data showed that the expression of MMP-2 protein was reduced 1.6- or 1.7-fold over the control by treatment with silibinin or JNK inhibitor in the models.", "Similar results were revealed in zymography and confocal microscopy.", "Pretreatment with silibinin also abolished the binding activity of AP-1 and MMP-2 promoter activity via AP-1 binding, as observed by EMSA and luciferase assay.", "Finally, a [(3)H]-thymidine incorporation proliferation assay and cell migration assay demonstrated that silibinin inhibited IL-6-stimulated LoVo cell proliferation and invasion.", "Taken together, these data indicated that silibinin inhibits LoVo cell invasion with the reduction of MMP-2 presentation by attenuating AP-1 binding activity, suggesting a novel antimetastatic application for silibinin in colon cancer chemoprevention."], "structured": false}
{"doc_id": 40500723, "title": "Immigration cohorts and residential overcrowding in southern California", "abstract": ["To what degree do immigrants reduce their high rates of residential overcrowding with increasing length of residence in the United States?", "This question is addressed through the application of a \u201cdouble cohort\u201d method that nests birth cohorts within immigration cohorts.", "This method enables duration of immigration effects to be separated from aging effects as cohorts pass through life course phases, when family sizes may be growing or shrinking.", "The analysis finds that cohort trends differ sharply from the cross-sectional pattern observed at a single point in time.", "Cohorts\u2019 growth in income is found to contribute substantially to the decline in overcrowding over time.", "Cohort trends among Hispanic immigrants, however, diverge from those among others, indicating much less decrease in overcrowding and even increases over certain age spans."], "structured": false}
{"doc_id": 40558887, "title": "Expression of green fluorescent protein in the ureteric bud of transgenic mice: a new tool for the analysis of ureteric bud morphogenesis.", "abstract": ["The growth and branching of the ureteric bud is a complex process that is ultimately responsible for the organization of the collecting duct system as well as the number of nephrons in the metanephric kidney.", "While the genes involved in the regulation of this process have begun to be elucidated, our understanding of the cellular and molecular basis of ureteric bud morphogenesis remains rudimentary.", "Furthermore, the timing and sequence of branching and elongation that gives rise to the collecting system of the kidney can only be inferred from retrospective staining or microdissection of fixed preparations.", "To aid in the investigation of these issues, we developed strains of transgenic mice in which a green fluorescent protein (GFP) is expressed in the ureteric bud under the control of the Hoxb7 promoter.", "In these mice, GFP is expressed in every branch of the ureteric bud throughout renal development, and in its derivative epithelia in the adult kidney.", "As GFP fluorescence can be easily visualized in living tissue, this allows the dynamic pattern of ureteric bud growth and branching to be followed over several days when the kidneys are cultured in vitro.", "Using confocal microscopy, branching of the ureteric bud in all three dimensions can be analyzed.", "These mice represent an extremely powerful tool to characterize the normal patterns of ureteric bud morphogenesis and to investigate the response of the bud to growth factors, matrix elements, and other agents that regulate its growth and branching."], "structured": false}
{"doc_id": 40584205, "title": "Biological properties of herpes simplex virus 2 replication-defective mutant strains in a murine nasal infection model.", "abstract": ["We used a mouse nasal model of herpes simplex virus 2 (HSV-2) infection to examine the biological properties of HSV-2 wild-type (wt), TK-negative, and replication-defective strains in vivo.", "Nasal septa tissue is the major site of wt viral replication post intranasal (i.n.) inoculation.", "The HSV-2 strain 186 syn(+)-1 wt virus caused lethal encephalitis at doses of 10(4) PFU and above per nostril, and at lower doses no neurons in the trigeminal ganglia were positive for the latency-associated transcript, indicating a lack of latent infection.", "The 186DeltaKpn TK-negative mutant virus replicated in nasal septa tissue but showed low-level replication in trigeminal ganglia at only one timepoint.", "In situ hybridization of trigeminal ganglia showed that the number of LAT-positive neurons was proportional to the inoculum dose from 10(3) to 10(6) PFU per nare.", "The replication-defective mutant virus 5BlacZ showed no replication in nasal septa tissue and no persistence of viral DNA at the inoculation site or the trigeminal ganglia.", "Nevertheless, inoculation of 5BlacZ or the double-mutant dl5-29 at distal sites reduced acute replication and latent infection of 186DeltaKpn following intranasal challenge.", "This infection model provides a biological system to test the properties of HSV-2 strains and shows that replication-defective mutant strains do not persist at sites of inoculation or in sensory ganglia but can induce immune protection that reduces the latent viral load of a challenge virus."], "structured": false}
{"doc_id": 40590358, "title": "The sphingosine-1-phosphate receptor agonist FTY720 modulates dendritic cell trafficking in vivo.", "abstract": ["The pro-drug FTY720 is undergoing phase III clinical trials for prevention of allograft rejection.", "After phosphorylation, FTY720 targets the G protein-coupled-sphingosine-1-phosphate receptor 1 (S1PR1) on lymphocytes, thereby inhibiting their egress from lymphoid organs and their recirculation to inflammatory sites.", "Potential effects on dendritic cell (DC) trafficking have not been evaluated.", "Here, we demonstrate the expression of all five S1PR subtypes (S1PR1-5) by murine DCs.", "Administration of FTY720 to C57BL/10 mice markedly reduced circulating T and B lymphocytes within 24 h, but not blood-borne DCs, which were enhanced significantly for up to 96 h, while DCs in lymph nodes and spleen were reduced.", "Numbers of adoptively transferred, fluorochrome-labeled syngeneic or allogeneic DCs in blood were increased significantly in FTY720-treated animals, while donor-derived DCs and allostimulatory activity for host na\u00efve T cells within the spleen were reduced.", "Administration of the selective S1PR1 agonist SEW2871 significantly enhanced circulating DC numbers.", "Flow analysis revealed that CD11b, CD31/PECAM-1, CD54/ICAM-1 and CCR7 expression on blood-borne DCs was downregulated following FTY720 administration.", "Transendothelial migration of FTY720-P-treated immature DCs to the CCR7 ligand CCL19 was reduced.", "These novel data suggest that modulation of DC trafficking by FTY720 may contribute to its immunosuppressive effects."], "structured": false}
{"doc_id": 40608679, "title": "Sustained survivin expression from OX40 costimulatory signals drives T cell clonal expansion.", "abstract": ["Sustained signaling from the T cell receptor (TCR) and costimulatory molecules is thought necessary for generating high numbers of effector T cells.", "Here, we show that Survivin is controlled in peripheral T cells by OX40 cosignaling via sustained PI3k and PKB activation.", "Survivin is induced by OX40 independent of mitotic progression in late G1, and blocking Survivin suppresses S-phase transition and division of T cells and leads to apoptosis.", "Moreover, Survivin expression alone is sufficient to restore proliferation and to antagonize apoptosis in costimulation-deficient T cells and can rescue T cell expansion in vivo.", "Survivin allows effector T cells to accumulate in large numbers, but Bcl-2 family proteins are required for T cell survival after the phase of active division.", "Thus, sustained Survivin expression from costimulatory signaling maintains T cell division over time and regulates the extent of clonal expansion."], "structured": false}
{"doc_id": 40631095, "title": "The Combination of Exercise and Respiratory Training Improves Respiratory Muscle Function in Pulmonary Hypertension", "abstract": ["Increased dyspnea and reduced exercise capacity in pulmonary arterial hypertension (PAH) can be partly attributed to impaired respiratory muscle function.", "This prospective study was designed to assess the impact of exercise and respiratory training on respiratory muscle strength and 6-min walking distance (6MWD) in PAH patients.", "Patients with invasively confirmed PAH underwent 3 weeks of in-hospital exercise and respiratory training, which was continued at home for another 12 weeks.", "Medication remained constant during the study period.", "Blinded observers assessed efficacy parameters at baseline (I) and after 3 (II) and 15 weeks (III).", "Respiratory muscle function was assessed by twitch mouth pressure (TwPmo) during nonvolitional supramaximal magnetic phrenic nerve stimulation.", "Seven PAH patients (4 women; mean pulmonary artery pressure 45 \u00b1 11 mmHg, median WHO functional class 3.1 \u00b1 0.4, idiopathic/associated PAH n = 5/2) were included.", "The training program was feasible and well tolerated by all patients with excellent compliance.", "TwPmo was I: 0.86 \u00b1 0.37 kPa, II: 1.04 \u00b1 0.29 kPa, and III: 1.27 \u00b1 0.44 kPa, respectively.", "6MWD was I: 417 \u00b1 51 m, II: 509 \u00b1 39 m, and III: 498 \u00b1 39 m, respectively.", "Both TwPmo (+0.41 \u00b1 0.34 kPa, +56 \u00b1 39 %) and 6MWD (+81 \u00b1 30 m, +20 \u00b1 9 %) increased significantly in the period between baseline and the final assessment (pairwise comparison: p = 0.012/<0.001; RM-ANOVA considering I, II, III: p = 0.037/<0.001).", "Exercise and respiratory training as an adjunct to medical therapy may be effective in patients with PAH to improve respiratory muscle strength and exercise capacity.", "Future, randomized, controlled trials should be carried out to further investigate these findings."], "structured": false}
{"doc_id": 40632104, "title": "Dual role of the IL-12/IFN-gamma axis in the development of autoimmune myocarditis: induction by IL-12 and protection by IFN-gamma.", "abstract": ["IL-12 and IFN-gamma positively regulate each other and type 1 inflammatory responses, which are believed to cause tissue damage in autoimmune diseases.", "We investigated the role of the IL-12/IFN-gamma (Th1) axis in the development of autoimmune myocarditis.", "IL-12p40-deficient mice on a susceptible background resisted myocarditis.", "In the absence of IL-12, autospecific CD4(+) T cells proliferated poorly and showed increased Th2 cytokine responses.", "However, IFN-gamma-deficient mice developed fatal autoimmune disease, and blockade of IL-4R signaling did not confer susceptibility to myocarditis in IL-12p40-deficient mice, demonstrating that IL-12 triggers autoimmunity by a mechanism independent of the effector cytokines IFN-gamma and IL-4.", "In conclusion, our results suggest that the IL-12/IFN-gamma axis is a double-edged sword for the development of autoimmune myocarditis.", "Although IL-12 mediates disease by induction/expansion of Th1-type cells, IFN-gamma production from these cells limits disease progression."], "structured": false}
{"doc_id": 40655970, "title": "Somatic and Germline Diversification of a Putative Immunoreceptor within One Phylum: Dscam in Arthropods.", "abstract": ["Arthropod Dscam, the homologue of the human Down Syndrome cell adhesion molecule, is a receptor used by the nervous and immune systems.", "Unlike in vertebrates, evolutionary pressure has selected and maintained a vast Dscam diversity of isoforms, known to specifying neuronal identity during the nervous system differentiation.", "This chapter examines the different modes of Dscam diversification in the context of arthropods' evolution and that of their immune system, where its role is controversial.", "In the single Dscam gene of insects and crustaceans, mutually exclusive alternative splicing affects three clusters of duplicated exons encoding the variable parts of the receptor.", "The Dscam gene produces over 10,000 isoforms.", "In the more basal arthropods such as centipedes, Dscam diversity results from a combination of many germline genes (over 80) with, in about half of those, the possibility of alternative splicing affecting only one exon cluster.", "In the even more basal arthropods, such as chelicerates, no splicing possibility is detected, but there exist dozens of germline Dscam genes.", "Compared to controlling the expression of multiple germline genes, the somatic mutually alternative splicing within a single gene may offer a simplified way of expressing a large Dscam repertoire.", "Expressed by hemocytes, Dscam is considered a phagocytic receptor but is also encountered in solution.", "More information is necessary about its binding to pathogens, its role in phagocytosis, its possible role in specifying hemocyte identity, its kinetics of expression, and the regulation of its RNA splicing to understand how its diversity is linked to immunity."], "structured": false}
{"doc_id": 40666943, "title": "Epidemiology, health-related quality of life and economic burden of binge eating disorder: a systematic literature review", "abstract": ["PURPOSE To perform a systematic review on the epidemiology, the health-related quality of life (HRQoL) and economic burden of binge eating disorder (BED).   \n", "METHODS A systematic literature search of English-language articles was conducted using Medline, Embase, PsycINFO, PsycARTICLES, Academic Search Complete, CINAHL Plus, Business Source Premier and Cochrane Library.", "Literature search on epidemiology was limited to studies published between 2009 and 2013.", "Cost data were inflated and converted to 2012 US$ purchasing power parities.", "All of the included studies were assessed for quality.   \n", "RESULTS Forty-nine articles were included.", "Data on epidemiology were reported in 31, HRQoL burden in 16, and economic burden in 7 studies.", "Diagnosis of BED was made using 4th Edition of The Diagnostic and Statistical Manual of Mental Disorders (DSM-IV) criteria in 46 studies.", "Lifetime prevalence of BED was 1.1-1.9% in the general population (DSM-IV).", "BED was associated with significant impairment in aspects of HRQoL relating to both physical and mental health; the Short Form 36 Physical and Mental Component Summary mean scores varied between 31.1 to 47.3 and 32.0 to 49.8, respectively.", "Compared to individuals without eating disorder, BED was related to increased healthcare utilization and costs.", "Annual direct healthcare costs per BED patient ranged between $2,372 and $3,731.   \n", "CONCLUSIONS BED is a serious eating disorder that impairs HRQoL and is related to increased healthcare utilization and healthcare costs.", "The limited literature warrants further research, especially to better understand the long-term HRQoL and economic burden of BED."], "structured": true}
{"doc_id": 40667066, "title": "Subcellular steroid/nuclear receptor dynamics.", "abstract": ["Steroid hormones, thyroid hormones, retinoic acids, and vitamin D bind to their receptors, which are now called steroid/nuclear receptors, and liganded receptors translocate either intracellularly or intranuclearly and form large protein complexes with cofactors to induce or repress gene transcription.", "Therefore, steroid/nuclear receptors are ligand-dependent transcription factors.", "With the advent of green fluorescent protein (GFP) and its color variants, the subcellular distribution of many steroid/nuclear receptors has been found to be much more dynamic than previously thought, with some of the receptors shuttling between the cytoplasm and nucleus.", "Steroid/nuclear receptors can be divided into three categories based on their unliganded distribution: those that are primarily in the nucleus, those in the cytoplasm, and those with mixed cytoplasmic and nuclear distributions.", "However, in all cases, the addition of a ligand leads to almost complete nuclear translocation of the receptors.", "Hormonal stimulation induces intranuclear receptor distribution from a homogeneous pattern to a heterogeneous dot-like image.", "Ligand binding to steroid/nuclear receptors leads to the recruitment of many proteins including cofactors to provoke the redistribution of receptor complexes in the nucleus.", "This focal organization could involve more complex events than simple DNA binding sites for transcription.", "Protein activities and interactions of steroid/nuclear receptors can be imaged and localized in a single cell."], "structured": false}
{"doc_id": 40667577, "title": "EMT, the cytoskeleton, and cancer cell invasion", "abstract": ["The metastatic process, i.e. the dissemination of cancer cells throughout the body to seed secondary tumors at distant sites, requires cancer cells to leave the primary tumor and to acquire migratory and invasive capabilities.", "In a process of epithelial-mesenchymal transition (EMT), besides changing their adhesive repertoire, cancer cells employ developmental processes to gain migratory and invasive properties that involve a dramatic reorganization of the actin cytoskeleton and the concomitant formation of membrane protrusions required for invasive growth.", "The molecular processes underlying such cellular changes are still only poorly understood, and the various migratory organelles, including lamellipodia, filopodia, invadopodia and podosomes, still require a better functional and molecular characterization.", "Notably, direct experimental evidence linking the formation of migratory membrane protrusions and the process of EMT and tumor metastasis is still lacking.", "In this review, we have summarized recent novel insights into the molecular processes and players underlying EMT on one side and the formation of invasive membrane protrusions on the other side."], "structured": false}
{"doc_id": 40710501, "title": "Different response of human glioma tumor-initiating cells to epidermal growth factor receptor kinase inhibitors.", "abstract": ["Because a subpopulation of cancer stem cells (tumor-initiating cells, TICs) is believed to be responsible for the development, progression, and recurrence of many tumors, we evaluated the in vitro sensitivity of human glioma TICs to epidermal growth factor receptor (EGFR) kinase inhibitors (erlotinib and gefitinib) and possible molecular determinants for their effects.", "Cells isolated from seven glioblastomas (GBM 1-7) and grown using neural stem cell permissive conditions were characterized for in vivo tumorigenicity, expression of tumor stem cell markers (CD133, nestin), and multilineage differentiation properties, confirming that these cultures are enriched in TICs.", "TIC cultures were challenged with increasing concentrations of erlotinib and gefitinib, and their survival was evaluated after 1-4 days.", "In most cases, a time- and concentration-dependent cell death was observed, although GBM 2 was completely insensitive to both drugs, and GBM 7 was responsive only to the highest concentrations tested.", "Using a radioligand binding assay, we show that all GBM TICs express EGFR.", "Erlotinib and gefitinib inhibited EGFR and ERK1/2 phosphorylation/activation in all GBMs, irrespective of the antiproliferative response observed.", "However, under basal conditions GBM 2 showed a high Akt phosphorylation that was completely insensitive to both drugs, whereas GBM 7 was completely insensitive to gefitinib, and Akt inactivation occurred only for the highest erlotinib concentration tested, showing a precise relationship with the antiproliferative effects of the drug.", "Interestingly, in GBM 2, phosphatase and tensin homolog expression was significantly down-regulated, possibly accounting for the insensitivity to the drugs.", "In conclusion, glioma TICs are responsive to anti-EGFR drugs, but phosphatase and tensin homolog expression and Akt inhibition seem to be necessary for such effect."], "structured": false}
{"doc_id": 40721190, "title": "Structural features of the interaction of the 3'-untranslated region of mRNA containing exosomal RNA-specific motifs with YB-1, a potential mediator of mRNA sorting.", "abstract": ["We have previously shown that YB-1 is the only protein of the HEK293 cell cytoplasmic (S100) extract that specifically interacts with RNA hairpins each containing one of the motifs ACCAGCCU (1), CAGUGAGC (2) and UAAUCCCA (3), which had been identified as often found in exosomal RNA and proposed as potential cis-acting elements targeting RNAs into exosomes.", "Here we explored the interactions of YB-1 with a fragment of the 3'-untranslated region (UTR) of septin 14 mRNA (SEPT14 RNA), which contains all three motifs.", "We demonstrated the occurrence of YB-1 among proteins pulled down from the HEK293 S100 extract using biotinylated SEPT14 RNA.", "With recombinant YB-1, it was found that SEPT14 RNA can bind up to 5 moles of protein per mole of RNA in a cooperative manner, which was shown to be mainly facilitated by the presence of the above motifs.", "RNA hairpins with motifs 1 and 2 competed with SEPT14 RNA for binding to the protein, whereas that with motif 3 was less competitive, in accordance with the affinity of YB-1 for these RNA hairpins.", "With YB-1-bound RNA, nucleotides protected from attack by hydroxyl radicals were revealed in all three motifs, although hairpins with motif 2 and especially with motif 1 contained many protected nucleotides outside the motifs, suggesting that the specific environments of these motifs contribute significantly to the YB-1 binding.", "An analysis of the environments of motifs 1-3 in the HEK293 cell mRNA 3' UTRs gained from RNA-seq data led us to conclude that the primary binding sites of YB-1 in the 3' UTRs are hairpins containing some part of the motif along with its specific surroundings; the consensus sequences of these hairpins were derived.", "Thus, our findings provide a new understanding of the structural basis of the interactions between YB-1 and mRNAs carrying the aforementioned motifs."], "structured": false}
{"doc_id": 40735046, "title": "Periodic screening for breast cancer: the HIP Randomized Controlled Trial. Health Insurance Plan.", "abstract": ["This paper summarizes the findings of the first breast cancer screening trial, which was initiated in December 1963 to explore the efficacy of screening.", "Women aged 40-64 years were selected from enrollees in the Health Insurance Plan (HIP) of Greater New York and were randomly assigned to study and control groups.", "Study group women were invited for screening, an initial examination, and three annual reexaminations.", "Screening consisted of film mammography (cephalocaudal and lateral views of each breast) and clinical examination of breasts.", "Breast cancer and mortality from breast cancer were examined by treatment group (study vs. control) and by entry-age subgroup.", "By the end of 18 years from entry, the study group had about a 25% lower breast cancer mortality among women aged 40-49 and 50-59 at time of entry than did the control group.", "However, to a large extent the difference among the 40-49-year-olds occurred in the subgroup with breast cancer diagnosed after these women had passed their 50th birthday, and utility of screening women in their forties is questionable."], "structured": false}
{"doc_id": 40754510, "title": "Staphylococcus aureus infections.", "abstract": ["Micrococcus, which, when limited in its extent and activity, causes acute suppurative inflammation (phlegmon), produces, when more extensive and intense in its action on the human system, the most virulent forms of septicaemia and pyaemia.1 In an elegant series of clinical observations and laboratory studies published in 1880 and 1882, Ogston described staphylococcal disease and its role in sepsis and abscess formation.1,2 More than 100 years later, Staphylococcus aureus remains a versatile and dangerous pathogen in humans.", "The frequencies of both community-acquired and hospital-acquired staphylococcal infections have increased steadily, with little change in overall mortality.", "Treatment of these infections . . ."], "structured": false}
{"doc_id": 40760684, "title": "Structural overview of the nuclear receptor superfamily: insights into physiology and therapeutics.", "abstract": ["As ligand-regulated transcription factors, the nuclear hormone receptors are nearly ideal drug targets, with internal pockets that bind to hydrophobic, drug-like molecules and well-characterized ligand-induced conformational changes that recruit transcriptional coregulators to promoter elements.", "Yet, due to the multitude of genes under the control of a single receptor, the major challenge has been the identification of ligands with gene-selective actions, impacting disease outcomes through a narrow subset of target genes and not across their entire gene-regulatory repertoire.", "Here, we summarize the concepts and work to date underlying the development of steroidal and nonsteroidal receptor ligands, including the use of crystal structures, high-throughput screens, and rational design approaches for finding useful therapeutic molecules.", "Difficulties in finding selective receptor modulators require a more complete understanding of receptor interdomain communications, posttranslational modifications, and receptor-protein interactions that could be exploited for target gene selectivity."], "structured": false}
{"doc_id": 40769868, "title": "Differential assembly of inwardly rectifying K+ channel subunits, Kir4.1 and Kir5.1, in brain astrocytes.", "abstract": ["The inwardly rectifying K+ channel subunit Kir5.1 is expressed abundantly in the brain, but its precise distribution and function are still largely unknown.", "Because Kir5.1 is co-expressed with Kir4.1 in retinal glial Muller cells, we have compared the biochemical and immunological properties of Kir5.1 and Kir4.1 in the mouse brain.", "Immunoprecipitation experiments suggested that brain expressed at least two subsets of Kir channels, heteromeric Kir4.1/5.1 and homomeric Kir4.1.", "Immunolabeling using specific antibodies showed that channels comprising Kir4.1 and Kir5.1 subunits were assembled in a region-specific fashion.", "Heteromeric Kir4.1/5.1 was identified in the neocortex and in the glomeruli of the olfactory bulb.", "Homomeric Kir4.1 was confined to the hippocampus and the thalamus.", "Homomeric Kir5.1 was not identified.", "Kir4.1/5.1 and Kir4.1 expression appeared to occur only in astrocytes, specifically in the membrane domains facing the pia mater and blood vessels or in the processes surrounding synapses.", "Both Kir4.1/5.1 and Kir4.1 could be associated with PDZ domain-containing syntrophins, which might be involved in the subcellular targeting of these astrocyte Kir channels.", "Because heteromeric Kir4.1/5.1 and homomeric Kir4.1 have distinct ion channel properties (Tanemoto, M., Kittaka, N., Inanobe, A., and Kurachi, Y. (2000) J. Physiol.", "(Lond.) 525, 587-592 and Tucker, S. J., Imbrici, P., Salvatore, L., D'Adamo, M. C., and Pessia, M. (2000) J. Biol.", "Chem.", "275, 16404-16407), it is plausible that these channels play differential physiological roles in the K+ -buffering action of brain astrocytes in a region-specific manner."], "structured": false}
{"doc_id": 40781557, "title": "Low-grade serous ovarian cancer: a unique disease.", "abstract": ["Low-grade serous carcinomas represent approximately 10% of all serous ovarian carcinomas.", "A growing body of research has demonstrated several important differences between the clinical and molecular characteristics of these tumors and those of high-grade serous ovarian carcinomas.", "Patients with low-grade serous ovarian tumors are diagnosed at a younger age, have a longer overall survival, and have lower response rates to conventional chemotherapy.", "In addition, low-grade serous ovarian carcinomas have pathologic and molecular characteristics distinct from high-grade serous carcinomas, yet similar to serous tumors of low malignant potential.", "This suggests a common pathogenesis and a continuum of disease from serous tumors of low malignant potential to low-grade serous carcinomas.", "Further study, focusing specifically on low-grade serous carcinomas, is needed to determine the role of other chemotherapeutic agents, hormonal therapy, or targeted biologic agents in the treatment of this disease."], "structured": false}
{"doc_id": 40790033, "title": "Renal outcomes with different fixed-dose combination therapies in patients with hypertension at high risk for cardiovascular events (ACCOMPLISH): a prespecified secondary analysis of a randomised controlled trial.", "abstract": ["BACKGROUND The Avoiding Cardiovascular Events through Combination Therapy in Patients Living with Systolic Hypertension (ACCOMPLISH) trial showed that initial antihypertensive therapy with benazepril plus amlodipine was superior to benazepril plus hydrochlorothiazide in reducing cardiovascular morbidity and mortality.", "We assessed the effects of these drug combinations on progression of chronic kidney disease.   \n", "METHODS ACCOMPLISH was a double-blind, randomised trial undertaken in five countries (USA, Sweden, Norway, Denmark, and Finland).", "11 506 patients with hypertension who were at high risk for cardiovascular events were randomly assigned via a central, telephone-based interactive voice response system in a 1:1 ratio to receive benazepril (20 mg) plus amlodipine (5 mg; n=5744) or benazepril (20 mg) plus hydrochlorothiazide (12.5 mg; n=5762), orally once daily.", "Drug doses were force-titrated for patients to attain recommended blood pressure goals.", "Progression of chronic kidney disease, a prespecified endpoint, was defined as doubling of serum creatinine concentration or end-stage renal disease (estimated glomerular filtration rate <15 mL/min/1.73 m(2) or need for dialysis).", "Analysis was by intention to treat (ITT).", "This trial is registered with ClinicalTrials.gov, number NCT00170950.   \n", "FINDINGS The trial was terminated early (mean follow-up 2.9 years [SD 0.4]) because of superior efficacy of benazepril plus amlodipine compared with benazepril plus hydrochlorothiazide.", "At trial completion, vital status was not known for 143 (1%) patients who were lost to follow-up (benazepril plus amlodipine, n=70; benazepril plus hydrochlorothiazide, n=73).", "All randomised patients were included in the ITT analysis.", "There were 113 (2.0%) events of chronic kidney disease progression in the benazepril plus amlodipine group compared with 215 (3.7%) in the benazepril plus hydrochlorothiazide group (HR 0.52, 0.41-0.65, p<0.0001).", "The most frequent adverse event in patients with chronic kidney disease was peripheral oedema (benazepril plus amlodipine, 189 of 561, 33.7%; benazepril plus hydrochlorothiazide, 85 of 532, 16.0%).", "In patients with chronic kidney disease, angio-oedema was more frequent in the benazepril plus amlodipine group than in the benazepril plus hydrochlorothiazide group.", "In patients without chronic kidney disease, dizziness, hypokalaemia, and hypotension were more frequent in the benazepril plus hydrochlorothiazide group than in the benazepril plus amlodipine group.   \n", "INTERPRETATION Initial antihypertensive treatment with benazepril plus amlodipine should be considered in preference to benazepril plus hydrochlorothiazide since it slows progression of nephropathy to a greater extent.   \n", "FUNDING Novartis."], "structured": true}
{"doc_id": 40817021, "title": "Effects of exercise training on health status in patients with chronic heart failure: HF-ACTION randomized controlled trial.", "abstract": ["CONTEXT Findings from previous studies of the effects of exercise training on patient-reported health status have been inconsistent.   \n", "OBJECTIVE To test the effects of exercise training on health status among patients with heart failure.   \n", "DESIGN, SETTING, AND PATIENTS Multicenter, randomized controlled trial among 2331 medically stable outpatients with heart failure with left ventricular ejection fraction of 35% or less.", "Patients were randomized from April 2003 through February 2007.   \n", "INTERVENTIONS Usual care plus aerobic exercise training (n = 1172), consisting of 36 supervised sessions followed by home-based training, vs usual care alone (n = 1159).", "Randomization was stratified by heart failure etiology, which was a covariate in all models.   \n", "MAIN OUTCOME MEASURES Kansas City Cardiomyopathy Questionnaire (KCCQ) overall summary scale and key subscales at baseline, every 3 months for 12 months, and annually thereafter for up to 4 years.", "The KCCQ is scored from 0 to 100 with higher scores corresponding to better health status.", "Treatment group effects were estimated using linear mixed models according to the intention-to-treat principle.   \n", "RESULTS Median follow-up was 2.5 years.", "At 3 months, usual care plus exercise training led to greater improvement in the KCCQ overall summary score (mean, 5.21; 95% confidence interval, 4.42 to 6.00) compared with usual care alone (3.28; 95% confidence interval, 2.48 to 4.09).", "The additional 1.93-point increase (95% confidence interval, 0.84 to 3.01) in the exercise training group was statistically significant (P < .001).", "After 3 months, there were no further significant changes in KCCQ score for either group (P = .85 for the difference between slopes), resulting in a sustained, greater improvement overall for the exercise group (P < .001).", "Results were similar on the KCCQ subscales, and no subgroup interactions were detected.   \n", "CONCLUSIONS Exercise training conferred modest but statistically significant improvements in self-reported health status compared with usual care without training.", "Improvements occurred early and persisted over time.   \n", "TRIAL REGISTRATION clinicaltrials.gov Identifier: NCT00047437."], "structured": true}
{"doc_id": 40867854, "title": "Acute respiratory failure in patients with severe community-acquired pneumonia: a prospective randomized evaluation of noninvasive ventilation.", "abstract": ["In uncontrolled studies, noninvasive positive pressure ventilation (NPPV) was found useful in avoiding endotracheal intubation in patients with acute respiratory failure (ARF) caused by severe community-acquired pneumonia (CAP).", "We conducted a prospective, randomized study comparing standard treatment plus NPPV delivered through a face mask to standard treatment alone in patients with severe CAP and ARF.", "Patients fitting the American Thoracic Society criteria for severe CAP were included in presence of ARF (refractory hypoxemia and/or hypercapnia with acidosis).", "Exclusion criteria were: severe hemodynamic instability, requirement for emergent cardiopulmonary resuscitation, home mechanical ventilation or oxygen long-term supplementation, concomitant severe disease with a low expectation of life, inability to expectorate or contraindications to the use of the mask.", "Fifty-six consecutive patients (28 in each arm) were enrolled, and the two groups were similar at study entry.", "The use of NPPV was well tolerated, safe, and associated with a significant reduction in respiratory rate, need for endotracheal intubation (21% versus 50%; p = 0.03), and duration of intensive care unit (ICU) stay (1.8 \u00b1 0.7 d versus 6 \u00b1 1.8 d; p = 0.04).", "The two groups had a similar intensity of nursing care workload, time interval from study entry to endotracheal intubation, duration of hospitalization, and hospital mortality.", "Among patients with chronic obstructive pulmonary disease (COPD), those randomized to NPPV had a lower intensity of nursing care workload (p = 0.04) and improved 2-mo survival (88.9% versus 37.5%; p = 0.05).", "We conclude that in selected patients with ARF caused by severe CAP, NPPV was associated with a significant reduction in the rate of endotracheal intubation and duration of ICU stay.", "A 2-mo survival advantage was seen in patients with COPD."], "structured": false}
{"doc_id": 40900242, "title": "Smallest angiosperm genomes found in lentibulariaceae, with chromosomes of bacterial size.", "abstract": ["Nuclear holoploid genome sizes (C-values) have been estimated to vary about 800-fold in angiosperms, with the smallest established 1C-value of 157 Mbp recorded in Arabidopsis thaliana.", "In the highly specialized carnivorous family Lentibulariaceae now three taxa have been found that exhibit significantly lower values: Genlisea margaretae with 63 Mbp, G. aurea with 64 Mbp, and Utricularia gibba with 88 Mbp.", "The smallest mitotic anaphase chromatids in G. aurea have 2.1 Mbp and are thus of bacterial size (NB: E. coli has ca.", "4 Mbp).", "Several Utricularia species range somewhat lower than A. thaliana or are similar in genome size.", "The highest 1C-value known from species of Lentibulariaceae was found in Genlisea hispidula with 1510 Mbp, and results in about 24-fold variation for Genlisea and the Lentibulariaceae.", "Taking into account these new measurements, genome size variation in angiosperms is now almost 2000-fold.", "Genlisea and Utricularia are plants with terminal positions in the phylogeny of the eudicots, so that the findings are relevant for the understanding of genome miniaturization.", "Moreover, the Genlisea-Utricularia clade exhibits one of the highest mutational rates in several genomic regions in angiosperms, what may be linked to specialized patterns of genome evolution.", "Ultrasmall genomes have not been found in Pinguicula, which is the sister group of the Genlisea-Utricularia clade, and which does not show accelerated mutational rates.", "C-values in Pinguicula varied only 1.7-fold from 487 to 829 Mbp."], "structured": false}
{"doc_id": 40900567, "title": "Parasite multiplication potential and the severity of Falciparum malaria.", "abstract": ["The multiplication rates and invasiveness of Plasmodium falciparum parasites isolated from adult Thai patients hospitalized with uncomplicated malaria (n=34) were compared with those from persons with severe malaria (n=42).", "To simulate severe malaria and control for host effects, the in vitro cultures were adjusted to 1% parasitemia and used the same red blood cell donor.", "P. falciparum isolates from persons with severe malaria had initial cycle multiplication rates in vitro that were 3-fold higher than those from uncomplicated malaria (median [95% confidence interval], 8.3 [7. 1-10.5] vs. 2.8 [1.7-3.9]; P=.001).", "Parasites causing severe malaria exhibited unrestricted red blood cell invasion, whereas those from uncomplicated malaria were restricted to a geometric mean of 40 (31%-53%) of red blood cells.", "P. falciparum parasites causing severe malaria were less selective and multiplied more at high parasitemias than those causing uncomplicated malaria."], "structured": false}
{"doc_id": 40901687, "title": "PHD3-dependent hydroxylation of HCLK2 promotes the DNA damage response.", "abstract": ["The DNA damage response (DDR) is a complex regulatory network that is critical for maintaining genome integrity.", "Posttranslational modifications are widely used to ensure strict spatiotemporal control of signal flow, but how the DDR responds to environmental cues, such as changes in ambient oxygen tension, remains poorly understood.", "We found that an essential component of the ATR/CHK1 signaling pathway, the human homolog of the Caenorhabditis elegans biological clock protein CLK-2 (HCLK2), associated with and was hydroxylated by prolyl hydroxylase domain protein 3 (PHD3).", "HCLK2 hydroxylation was necessary for its interaction with ATR and the subsequent activation of ATR/CHK1/p53.", "Inhibiting PHD3, either with the pan-hydroxylase inhibitor dimethyloxaloylglycine (DMOG) or through hypoxia, prevented activation of the ATR/CHK1/p53 pathway and decreased apoptosis induced by DNA damage.", "Consistent with these observations, we found that mice lacking PHD3 were resistant to the effects of ionizing radiation and had decreased thymic apoptosis, a biomarker of genomic integrity.", "Our identification of HCLK2 as a substrate of PHD3 reveals the mechanism through which hypoxia inhibits the DDR, suggesting hydroxylation of HCLK2 is a potential therapeutic target for regulating the ATR/CHK1/p53 pathway."], "structured": false}
{"doc_id": 40905302, "title": "Economic implications of nighttime attending intensivist coverage in a medical intensive care unit.", "abstract": ["OBJECTIVE Our objective was to assess the cost implications of changing the intensive care unit staffing model from on-demand presence to mandatory 24-hr in-house critical care specialist presence.   \n", "DESIGN A pre-post comparison was undertaken among the prospectively assessed cohorts of patients admitted to our medical intensive care unit 1 yr before and 1 yr after the change.", "Our data were stratified by Acute Physiology and Chronic Health Evaluation III quartile and whether a patient was admitted during the day or at night.", "Costs were modeled using a generalized linear model with log-link and \u03b3-distributed errors.   \n", "SETTING A large academic center in the Midwest.   \n", "PATIENTS All patients admitted to the adult medical intensive care unit on or after January 1, 2005 and discharged on or before December 31, 2006.", "Patients receiving care under both staffing models were excluded.   \n", "INTERVENTION Changing the intensive care unit staffing model from on-demand presence to mandatory 24-hr in-house critical care specialist presence.   \n", "MEASUREMENTS AND MAIN RESULTS Total cost estimates of hospitalization were calculated for each patient starting from the day of intensive care unit admission to the day of hospital discharge.", "Adjusted mean total cost estimates were 61% lower in the post period relative to the pre period for patients admitted during night hours (7 pm to 7 am) who were in the highest Acute Physiology and Chronic Health Evaluation III quartile.", "No significant differences were seen at other severity levels.", "The unadjusted intensive care unit length of stay fell in the post period relative to the pre period (3.5 vs. 4.8) with no change in non-intensive care unit length of stay.   \n", "CONCLUSIONS We find that 24-hr intensive care unit intensivist staffing reduces lengths of stay and cost estimates for the sickest patients admitted at night.", "The costs of introducing such a staffing model need to be weighed against the potential total savings generated for such patients in smaller intensive care units, especially ones that predominantly care for lower-acuity patients."], "structured": true}
{"doc_id": 40913091, "title": "GENOTYPING OF THALASSEMIA IN MICROCYTIC HYPOCHROMIC ANEMIA PATIENTS FROM SOUTHWEST REGION OF IRAN", "abstract": ["Objective: To evaluate the frequency of \u03b1 -gene, s-gene, and hemoglobin variant numbers in subjects with Microcytic hypochromic anemia.", "Methodology: In total out of 850, 340 subjects with microcytic hypochromic anemia [MCV<80fl; MCH<27pg] from Southwest part of Iran, were studied in Research Center of Thalassemia and Hemoglobinopathies (RCTH) which is the only center working on hematology and oncology in Southwest (Khuzestan) region of Iran.", "These include 325 individuals: 171 with Beta-thalassemia trait, 88 with Alpha-thalassemia trait, 13 with thalassemia major, 11 with hemoglobin variants (HbS, HbC, and HbD Punjab ) and 42 with iron-deficiency anemia.", "The rest 15 patients diagnosed with no definite etiology.", "Results: Genotyping for -\u03b1 3.7 , -\u03b1 4.2 , \u2013 \u03b1 PA , - \u03b1 5NT and - - MED was done with gap-PCR.", "The overall frequency of - \u03b1 3.7 deletion in 325 individuals is 20%.", "Genotyping for 23 most known s-gene mutations was done with direct mutation analysis by Amplification Refractory Mutation System (ARMS).", "The most frequent mutations were CD 36/37, IVS II-I, and IVS I-110 with 9.7%, 11.7%, and 3.5% respected frequencies in 340 patients.", "There was statistically significant difference between Beta-thalassemia trait and Beta-thalassemia Major in case of MCV (p- value = 0.25) and MCH (P\u2013value =0.23) indices, and also MCH index between Beta-thalassemia trait and Hb Variants (P-value = 0.04).", "Conclusion: The \u03b1 -gene and s-gene mutation is quite common in the Southwest part of Iran.", "Molecular genotyping of \u03b1 -thalassemia and s-thalassemia help to diagnose unexplained microcytosis, and thus prevent unnecessary iron supplementation."], "structured": false}
{"doc_id": 40935722, "title": "Systemic biomarkers in exacerbations of COPD: the evolving clinical challenge.", "abstract": ["BACKGROUND Exacerbations of COPD (ECOPD) remain a major cause of mortality and morbidity.", "Despite advances in the understanding of their pathophysiology, their assessment relies primarily on clinical presentation, which can be variable and difficult to predict.", "A large number of biomarkers already have been assessed in this context, and some appear to be promising.   \n", "METHODS An online search for articles published until December 2010 was conducted using three terms for ECOPD, five terms for biomarkers, and five terms for the sampling method.", "Biomarkers were evaluated for their potential role in the establishment and confirmation of the diagnosis of ECOPD, the evaluation of etiology and severity, the prediction of prognosis, and the guidance of treatment decisions.   \n", "RESULTS Several systemic biomarkers have been measured in the context of ECOPD, and most have been found to increase at ECOPD onset and to subside during the course of exacerbations.", "Correlations have been reported among these biomarkers, but direct associations with clinical variables have been more difficult to establish.", "Although there are several limitations yet to be addressed, some of the biomarkers, most notably C-reactive protein for the identification of an ECOPD and procalcitonin for antibiotic guidance, may provide clinically relevant information.   \n", "CONCLUSIONS So far", ", no single biomarker has been able to gain wide acceptance, but some provide clinically useful information.", "The evaluation of such biomarkers in large decision-making studies is expected to become an area of intense investigation in the near future."], "structured": true}
{"doc_id": 40949706, "title": "Preoperative Predictors of Weight Loss Following Bariatric Surgery: Systematic Review", "abstract": ["Obesity affects 32% of adults in the USA.", "Surgery generates substantial weight loss, but 20\u201330% fails to achieve successful weight loss.", "Our objective was to identify preoperative psychosocial factors associated with weight loss following bariatric surgery.", "We performed a literature search of PubMed\u00ae and the Cochrane Database of Reviews of Effectiveness between 1988 and April 2010.", "Articles were screened for bariatric surgery and weight loss if they included a preoperative predictor of weight loss: body mass index (BMI), preoperative weight loss, eating disorders, or psychiatric disorder/substance abuse.", "One thousand seven titles were reviewed, 534 articles screened, and 115 included in the review.", "Factors that may be positively associated with weight loss after surgery include mandatory preoperative weight loss (7 of 14 studies with positive association).", "Factors that may be negatively associated with weight loss include preoperative BMI (37 out of 62 studies with negative association), super-obesity (24 out of 33 studies), and personality disorders (7 out of 14 studies).", "Meta-analysis revealed a decrease of 10.1% excess weight loss (EWL) for super-obese patients (95% confidence interval (CI) [3.7\u201316.5%]), though there was significant heterogeneity in the meta-analysis, and an increase of 5.9% EWL for patients with binge eating at 12 months after surgery (95% CI [1.9\u20139.8%]).", "Further studies are necessary to investigate whether preoperative factors can predict a clinically meaningful difference in weight loss after bariatric surgery.", "The identification of predictive factors may improve patient selection and help develop interventions targeting specific needs of patients."], "structured": false}
{"doc_id": 40963697, "title": "The tumor necrosis factor receptor stalk regions define responsiveness to soluble versus membrane-bound ligand.", "abstract": ["The family of tumor necrosis factor receptors (TNFRs) and their ligands form a regulatory signaling network that controls immune responses.", "Various members of this receptor family respond differently to the soluble and membrane-bound forms of their respective ligands.", "However, the determining factors and underlying molecular mechanisms of this diversity are not yet understood.", "Using an established system of chimeric TNFRs and novel ligand variants mimicking the bioactivity of membrane-bound TNF (mTNF), we demonstrate that the membrane-proximal extracellular stalk regions of TNFR1 and TNFR2 are crucial in controlling responsiveness to soluble TNF (sTNF).", "We show that the stalk region of TNFR2, in contrast to the corresponding part of TNFR1, efficiently inhibits both the receptor's enrichment/clustering in particular cell membrane regions and ligand-independent homotypic receptor preassembly, thereby preventing sTNF-induced, but not mTNF-induced, signaling.", "Thus, the stalk regions of the two TNFRs not only have implications for additional TNFR family members, but also provide potential targets for therapeutic intervention."], "structured": false}
{"doc_id": 40971746, "title": "A bird's-eye view of sex chromosome dosage compensation.", "abstract": ["Intensive study of a few genetically tractable species with XX/XY sex chromosomes has produced generalizations about the process of sex chromosome dosage compensation that do not fare well when applied to ZZ/ZW sex chromosome systems, such as those in birds.", "The inherent sexual imbalance in dose of sex chromosome genes has led to the evolution of sex-chromosome-wide mechanisms for balancing gene dosage between the sexes and relative to autosomal genes.", "Recent advances in our knowledge of avian genomes have led to a reexamination of sex-specific dosage compensation (SSDC) in birds, which is less effective than in known XX/XY systems.", "Insights about the mechanisms of SSDC in birds also suggest similarities to and differences from those in XX/XY species.", "Birds are thus offering new opportunities for studying dosage compensation in a ZZ/ZW system, which should shed light on the evolution of SSDC more broadly."], "structured": false}
{"doc_id": 40987633, "title": "The role of CHMP2BIntron5 in autophagy and frontotemporal dementia.", "abstract": ["Charged multivesicular body protein 2B (CHMP2B) - a component of the endosomal complex required for transport-III (ESCRT-III) - is responsible for the vital membrane deformation functions in autophagy and endolysosomal trafficking.", "A dominant mutation in CHMP2B (CHMP2BIntron5) is associated with a subset of heritable frontotemporal dementia - frontotemporal dementia linked to chromosome 3 (FTD-3).", "ESCRT-III recruits Vps4, an AAA-ATPase that abscises the membrane during various cellular processes including autophagy and intraluminal vesicle formation.", "CHMP2BIntron5 results in a C-terminus truncation removing an important Vps4 binding site as well as eliminating the normal autoinhibitory resting state of CHMP2B.", "CHMP2B is expressed in most cell types but seems to be especially vital for proper neuronal function.", "CHMP2BIntron5-mediated phenotypes include misregulation of transmembrane receptors, accumulation of multilamellar structures, abnormal lysosomal morphology, down regulation of a brain-specific micro RNA (miRNA-124), abnormal dendritic spine morphology, decrease in dendritic arborization, and cell death.", "Currently, transgenic-fly,-mouse, and -human cell lines are being used to better understand the diverse phenotypes and develop therapeutic approaches for the CHMP2BIntron5-induced FTD-3.", "This article is part of a Special Issue entitled SI:Autophagy."], "structured": false}
{"doc_id": 40996863, "title": "Restless legs syndrome and attention-deficit/hyperactivity disorder: a review of the literature.", "abstract": ["STUDY OBJECTIVE To review evidence on the association between restless legs syndrome (RLS) and attention-deficit/hyperactivity disorder (ADHD), to discuss the hypothetical mechanisms underlying this association, and to consider the potential interest for common pharmacologic treatments of RLS and ADHD when co-occurring.   \n", "METHOD A PubMed search.   \n", "RESULTS In clinical samples, up to 44% of subjects with ADHD have been found to have RLS or RLS symptoms, and up to 26% of subjects with RLS have been found to have ADHD or ADHD symptoms.", "Several mechanisms may explain this association.", "Sleep disruption associated with RLS might lead to inattentiveness, moodiness, and paradoxical overactivity.", "Diurnal manifestations of RLS, such as restlessness and inattention, might mimic ADHD symptoms.", "Alternatively, RLS might be comorbid with idiopathic ADHD.", "Subjects with RLS and a subset of subjects with ADHD might share a common dopamine dysfunction.", "Limited evidence suggests that some dopaminergic agents, such as levodopa/carbidopa, pergolide, and ropinirole, may be effective in children with RLS associated with ADHD symptoms.   \n", "CONCLUSIONS Although still limited, evidence from clinical studies demonstrates an association between RLS and ADHD or ADHD symptoms.", "Further clinical studies using standard criteria and procedures are needed to better estimate the degree of association.", "Epidemiologic studies are required to assess the relationship between ADHD and RLS symptoms in nonclinical samples.", "Further investigations should address the mechanisms underlying the relationship between RLS and ADHD.", "Several dopaminergic agents seem to be promising treatment for RLS associated with ADHD symptoms.", "To date, however, the absence of randomized and blinded controlled studies does not allow evidence-based recommendations."], "structured": true}
{"doc_id": 41022628, "title": "Impact of the KU80 pathway on NHEJ-induced genome rearrangements in mammalian cells.", "abstract": ["Using a substrate measuring deletion or inversion of an I-SceI-excised fragment and both accurate and inaccurate rejoining, we determined the impact of non-homologous end-joining (NHEJ) on mammalian chromosome rearrangements.", "Deletion is 2- to 8-fold more efficient than inversion, independent of the DNA ends structure.", "KU80 controls accurate rejoining, whereas in absence of KU mutagenic rejoining, particularly microhomology-mediated repair, occurs efficiently.", "In cells bearing both the NHEJ and a homologous recombination (HR) substrate containing a third I-SceI site, we show that NHEJ is at least 3.3-fold more efficient than HR, and translocation of the I-SceI fragment from the NHEJ substrate locus into the HR-I-SceI site can occur, but 50- to 100-fold less frequently than deletion.", "Deletions and translocations show both accurate and inaccurate rejoining, suggesting that they correspond to a mix of KU-dependent and KU-independent processes.", "Thus these processes should represent prominent pathways for DSB-induced genetic instability in mammalian cells."], "structured": false}
{"doc_id": 41024260, "title": "The multi-zinc finger protein ZNF217 contacts DNA through a two-finger domain.", "abstract": ["Classical C2H2 zinc finger proteins are among the most abundant transcription factors found in eukaryotes, and the mechanisms through which they recognize their target genes have been extensively investigated.", "In general, a tandem array of three fingers separated by characteristic TGERP links is required for sequence-specific DNA recognition.", "Nevertheless, a significant number of zinc finger proteins do not contain a hallmark three-finger array of this type, raising the question of whether and how they contact DNA.", "We have examined the multi-finger protein ZNF217, which contains eight classical zinc fingers.", "ZNF217 is implicated as an oncogene and in repressing the E-cadherin gene.", "We show that two of its zinc fingers, 6 and 7, can mediate contacts with DNA.", "We examine its putative recognition site in the E-cadherin promoter and demonstrate that this is a suboptimal site.", "NMR analysis and mutagenesis is used to define the DNA binding surface of ZNF217, and we examine the specificity of the DNA binding activity using fluorescence anisotropy titrations.", "Finally, sequence analysis reveals that a variety of multi-finger proteins also contain two-finger units, and our data support the idea that these may constitute a distinct subclass of DNA recognition motif."], "structured": false}
{"doc_id": 41074251, "title": "Knowledge, attitudes, risk perception, and cancer screening behaviors among cancer survivors.", "abstract": ["BACKGROUND Knowledge, attitudes, and risk perception in relation to second primary cancer (SPC) screening and their impact on screening practices in cancer survivors are largely unknown.   \n", "METHODS A total of 326 cancer survivors who had completed primary treatment for cancer >1 year previously were recruited from 6 oncology care outpatient clinics in the Republic of Korea.", "Survivors' knowledge, attitudes, perceived risk, and screening practices were assessed along with sociodemographic, behavioral, and clinical characteristics.", "Multivariate logistic regression was used to examine behavioral factors associated with the completion of all appropriate SPC screening according to national guidelines.   \n", "RESULTS Approximately 37.7% of survivors had undergone all appropriate SPC screening tests.", "Survivors were found to have a high perceived risk of SPC, high perceived benefits of screening, and positive attitudes toward cancer screening.", "However, they had limited knowledge regarding SPC screening tests and few had received a recommendation from a physician to undergo SPC screening.", "Although there was no association found between perceived risk and positive attitudes with screening behavior, higher knowledge was noted to be significantly associated with the completion of all appropriate SPC screening (adjusted odds ratio, 1.81; 95% confidence interval, 1.03-3.33).   \n", "CONCLUSIONS In the current study, cancer survivors were found to have limited knowledge regarding second cancer screening tests, which may have resulted in lower rates of completion of screening practices in this population."], "structured": true}
{"doc_id": 41087952, "title": "Ria1p (Ynl163c), a protein similar to elongation factors 2, is involved in the biogenesis of the 60S subunit of the ribosome in Saccharomyces cerevisiae", "abstract": ["RIA1 (YNL163c) is a quasi-essential gene that encodes a protein with strong similarities to elongation factors 2.", "Small C-terminal deletions in the protein lead to a severe growth defect.", "In the case of a 22-residue C-terminal deletion this can be suppressed by intragenic mutations in the RIA1 gene or dominant extragenic mutations in TIF6, which is thought to be involved in the biogenesis of the 60S subunit of the ribosome.", "The dominant TIF6 alleles can also suppress the phenotype associated with a complete deletion of the RIA1 gene.", "Depletion of Ria1p has a dramatic effect on the polysome profile: there is a severe reduction in the level of the 80S monosomes, an imbalance in the 40S/60S ratio, and halfmers appear.", "Dissociation of the monosomes and polysomes in the Ria1p depletion mutant revealed a specific reduction in the amount of 60S subunits.", "Localization experiments with HA-tagged derivatives of Ria1p did not detect any stable association of Ria1p with ribosome subunits, 80S monosomes or polysomes.", "Cell fractionation experiments show that Ria1p is found in both the cytoplasmic fraction and the nuclear fraction.", "Taken together, these data suggest that Ria1p is involved in the biogenesis of the 60S subunit of the ribosome."], "structured": false}
{"doc_id": 41120293, "title": "The Intestinal Immune System in Obesity and Insulin Resistance.", "abstract": ["Obesity and insulin resistance are associated with chronic inflammation in metabolic tissues such as adipose tissue and the liver.", "Recently, growing evidence has implicated the intestinal immune system as an important contributor to metabolic disease.", "Obesity predisposes to altered intestinal immunity and is associated with changes to the gut microbiota, intestinal barrier function, gut-residing innate and adaptive immune cells, and oral tolerance to luminal antigens.", "Accordingly, the gut immune system may represent a novel therapeutic target for systemic inflammation in insulin resistance.", "This review discusses the emerging field of intestinal immunity in obesity-related insulin resistance and how it affects metabolic disease."], "structured": false}
{"doc_id": 41131087, "title": "Human placental lactogen and unconjugated estriol concentrations in twin pregnancy: monitoring of fetal development in intrauterine growth retardation and single intrauterine fetal death.", "abstract": ["Human placental lactogen and unconjugated estriol concentrations in maternal serum were evaluated in 100 uneventful twin pregnancies, and these values were compared with those observed in 16 twin pregnancies associated with intrauterine growth retardation or single intrauterine fetal death.", "In pregnancies associated with intrauterine growth retardation (n = 8), human placental lactogen levels were at the lower limit of normal range for singleton pregnancies, whereas estriol levels were normal in most cases.", "When one of the fetuses had died before week 33 of pregnancy (n = 5), both human placental lactogen and estriol levels were low and they were almost at the levels in singleton pregnancy.", "When intrauterine fetal death occurred after week 36 of pregnancy (n = 3), both hormone levels remained normal until term.", "Thus human placental lactogen rather than estriol is a good indicator of intrauterine growth retardation in twin pregnancy.", "Both human placental lactogen and estriol are useful for the monitoring of the surviving fetus in the case of single intrauterine fetal death."], "structured": false}
{"doc_id": 41133176, "title": "Low antioxidant enzyme gene expression in pancreatic islets compared with various other mouse tissues.", "abstract": ["Using a sensitive Northern blot hybridization technique, gene expression of superoxide dismutase (SOD), catalase, and glutathione peroxidase was studied in pancreatic islets and for comparison in various other mouse tissues (liver, kidney, brain, lung, skeletal muscle, heart muscle, adrenal gland, and pituitary gland).", "Gene expression of the antioxidant enzymes was usually in the range of +/-", "50% of that in the liver.", "Only in pancreatic islets gene expression was substantially lower.", "The levels of the cytoplasmic Cu/Zn SOD and the mitochondrial Mn SOD gene expression were in the range of 30-40% of those in the liver.", "Glutathione peroxidase gene expression was 15%, and catalase gene expression was not at all detectable in pancreatic islets.", "These low levels of antioxidant enzyme gene expression may provide an explanation for the extraordinary sensitivity of pancreatic beta cells towards cytotoxic damage by diabetogenic compounds and during the development of human and animal diabetes."], "structured": false}
{"doc_id": 41159361, "title": "Cyclic nucleotide phosphodiesterase isozymes expressed in mouse skeletal muscle.", "abstract": ["To understand changes in cyclic nucleotide metabolism in muscle disease states, the expression of phosphodiesterase (PDE) isozymes in normal mouse leg muscle was examined.", "Four subcellular fractions were generated by differential centrifugation at 10,000 x g and 100,000 x g. cAMP PDE activity was found predominately in the soluble fractions, while cGMP PDE activity was more evenly distributed amongst soluble and particulate fractions.", "Pharmacological inhibitors demonstrate that PDE4 represents the major cAMP hydrolyzing activity and PDE2 represents the major cGMP hydrolyzing activity in mouse leg muscle.", "PDE1 is expressed at low levels, while PDE3 and PDE5 are intermediate.", "Between 20 and 40% of total PDE activity remained in the presence of inhibitors for PDE1-PDE5, indicating that other PDE families contribute to the total PDE pool.", "Reverse-transcription PCR with family-specific primers showed expression of mRNA for PDE7-PDE9, supporting this conclusion.", "Total PDE activity was found to be elevated in tissue extracts from a mouse model of Duchenne's muscular dystrophy."], "structured": false}
{"doc_id": 41161366, "title": "Exercise-induced asthma.", "abstract": ["The effect of exercise on ventilatory function was studied in 7 patients with asthma.", "Three showed appreciable decrease in forced expiratory volume in one second (FEV 1) after exercise.", "The degree of hyperventilation produced by exercise correlated with the postexercise decrease in FEV 1.", "Voluntary hyperventilation at rest produced a decrease in FEV 1 in all patients with asthma.", "Breathing 5.6 per cent carbon dioxide during voluntary hyperventilation instead of room air induced a larger ventilation and greater decrease in FEV1.", "Neither exercise nor voluntary hyperventilation had any significant effect on the FEV 1 in normal subjects and patients with chronic bronchitis.", "Both exercise\u00b7induced and hyperventilation-induced decrease in FEV 1 were inhibited by prior administration of isoproterenol but not by atropine.", "It is postulated that exercise-induced asthma is probably hyperventilation-induced asthma.", "Several underlying mechanisms by which airway obstruction is produced are possible."], "structured": false}
{"doc_id": 41165286, "title": "An antimicrobial protein of the gut symbiont Bacteroides fragilis with a MACPF domain of host immune proteins.", "abstract": ["Bacteroidales are the most abundant Gram-negative bacteria of the human intestinal microbiota comprising more than half of the bacteria in many individuals.", "Some of the factors that these bacteria use to establish and maintain themselves in this ecosystem are beginning to be identified.", "However, ecological competition, especially interference competition where one organism directly harms another, is largely unexplored.", "To begin to understand the relevance of this ecological principle as it applies to these abundant gut bacteria and factors that may promote such competition, we screened Bacteroides fragilis for the production of antimicrobial molecules.", "We found that the production of extracellularly secreted antimicrobial molecules is widespread in this species.", "The first identified molecule, described in this manuscript, contains a membrane attack complex/perforin (MACPF) domain present in host immune molecules that kill bacteria and virally infected cells by pore formation, and mutations affecting key residues of this domain abrogated its activity.", "This antimicrobial molecule, termed BSAP-1, is secreted from the cell in outer membrane vesicles and no additional proteins are required for its secretion, processing or immunity of the producing cell.", "This study provides the first insight into secreted molecules that promote competitive interference among Bacteroidales strains of the human gut."], "structured": false}
{"doc_id": 41182002, "title": "Directional perception of distributed sound sources.", "abstract": ["The perception of spatially distributed sound sources was investigated by conducting two listening experiments in anechoic conditions with 13 loudspeakers evenly distributed in the frontal horizontal plane emitting incoherent noise signals.", "In the first experiment, widely distributed sound sources with gaps in their distribution emitted pink noise.", "The results indicated that the exact loudspeaker distribution could not be perceived accurately and that the width of the distribution was perceived to be narrower than it was in reality.", "Up to three spatially distributed loudspeakers that were simultaneously emitting sound could be individually perceived.", "In addition, the number of loudspeakers that were indicated as emitting sound was smaller than the actual number.", "In the second experiment, a reference with 13 loudspeakers and test cases with fewer loudspeakers were presented and their perceived spatial difference was rated.", "The effect of the noise bandwidth was of particular interest.", "Noise with different bandwidths centered around 500 and 4000 Hz was used.", "The results indicated that when the number of loudspeakers was increased from four to seven, the perceived auditory event was very similar to that perceived with 13 loudspeakers at all bandwidths.", "The perceived differences were larger in wideband noise than in narrow-band noise."], "structured": false}
{"doc_id": 41226276, "title": "Adoptive T cell transfer for cancer immunotherapy in the era of synthetic biology.", "abstract": ["Adoptive T cell transfer for cancer and chronic infection is an emerging field that shows promise in recent trials.", "Synthetic-biology-based engineering of T lymphocytes to express high-affinity antigen receptors can overcome immune tolerance, which has been a major limitation of immunotherapy-based strategies.", "Advances in cell engineering and culture approaches to enable efficient gene transfer and ex vivo cell expansion have facilitated broader evaluation of this technology, moving adoptive transfer from a \"boutique\" application to the cusp of a mainstream technology.", "The major challenge currently facing the field is to increase the specificity of engineered T cells for tumors, because targeting shared antigens has the potential to lead to on-target off-tumor toxicities, as observed in recent trials.", "As the field of adoptive transfer technology matures, the major engineering challenge is the development of automated cell culture systems, so that the approach can extend beyond specialized academic centers and become widely available."], "structured": false}
{"doc_id": 41233511, "title": "Bruce treadmill test in children: normal values in a clinic population.", "abstract": ["The Bruce treadmill protocol is suitable for children as young as age 4 years.", "Maximal endurance time may be used as the sole criterion of exercise capacity, and normal values were established with 327 children having an innocent heart murmur.", "Mean endurance time in boys increased from 10.4 minutes at age 4 to 5 years, to 14.1 minutes at age 13 to 15 years.", "Mean endurance time in girls increased from 9.5 minutes at age 4 to 5 years to 12.3 minutes at age 10 to 12 years.", "Mean maximal heart rate ranged from 193 to 206 beats/min.", "Age differences in mean maximal and submaximal heart rates were small.", "There were negative correlations between endurance time and the ratio of weight to height.", "There were negative correlations between heart rates at treadmill stages 1 to 3 and the endurance times.", "The correlation coefficient of endurance time with maximal oxygen uptake was 0.88, but for clinical purposes endurance time alone is a satisfactory indicator of exercise performance."], "structured": false}
{"doc_id": 41239107, "title": "Immunoproteasome and LMP2 polymorphism in aged and Alzheimer's disease brains.", "abstract": ["In this study, we investigated the presence and role of immunoproteasome and its LMP2 subunit polymorphism at codon 60 in Alzheimer's disease (AD).", "Immunoproteasome was present in brain areas such as hippocampus and cerebellum and localized in neurons, astrocytes and endothelial cells.", "A higher expression of immunoproteasome was found in brain of AD patients than in brain of non-demented elderly, being its expression in young brain negligible or absent.", "Furthermore, AD affected regions showed a partial decrease in proteasome trypsin-like activity.", "The study of LMP2 polymorphism (R/H) showed that it does not influence LMP2 expression (neither the mRNA nor mature protein) in brain tissue.", "However, control brain areas of AD patients carrying the RR genotype showed an increased proteasome activity in comparison with RH carriers.", "To test whether this effect of the genotype might be related to AD onset we performed a genetic study, which allowed us to exclude an association of LMP2 codon 60 polymorphism with AD onset, despite its influence on the proteasome activity in human brain."], "structured": false}
{"doc_id": 41256402, "title": "The centrosome and its mode of inheritance: the reduction of the centrosome during gametogenesis and its restoration during fertilization.", "abstract": ["Neither the restoration of the centrosome during fertilization nor its reduction during gametogenesis is fully understood, but both are pivotal events in development.", "During each somatic cell cycle, the chromosomes, cytoplasm, and centrosomes duplicate in interphase, and all three split in two during each cell division.", "While it has long been recognized that both the sperm and the egg contribute equal haploid genomes during fertilization and that the vast majority of the cytoplasm is contributed by the egg, the relative contributions of the centrosome by each gamete are still in question.", "This article explores centrosome inheritance patterns and considers nine integral and secondarily derived activities of the centrosome.", "Boveri once hypothesized that \"The ripe egg possesses all of the elements necessary for development save an active division-center.", "The sperm, on the other hand, possesses such a center but lacks the protoplasmic substratum in which to operate.", "In this respect the egg and sperm are complementary structures; their union in syngamy thus restores to each the missing element necessary to further development.", "\"", "This article reviews the evidence gathered from 11 experimental strategies used to test this theory.", "While the majority of these approaches supports the hypothesis that the sperm introduces the centrosome at fertilization, the pattern did not reveal itself as universal, since parthenogenesis occurs in nature and can be induced artificially, since centrosome and centriole form de novo in extracts from unfertilized eggs and since the centrosome is derived from maternal sources during fertilization in some systems--notably, in mice.", "Models of the centrosome are proposed, along with speculative mechanisms which might lead to the cloaking of the reproducing element of the maternal centrosome during oogenesis and the retention of this structure by the paternal centrosome during spermatogenesis.", "Proteins essential for microtubule nucleation, like gamma-tubulin, are retained in the cytoplasm during oogenesis, but are largely lost during spermatogenesis.", "It is further postulated that the restoration of the zygotic centrosome at fertilization requires the attraction of maternal centrosomal components (in particular, gamma-tubulin and the 25S \"gamma-some\" particle) to the paternal reproducing element; this, along with post-translational modifications (including phosphorylation, disulfide reduction, and calcium ion binding), creates a functional zygote centrosome by blending both maternal and paternal constituents.(ABSTRACT TRUNCATED AT 400 WORDS)"], "structured": false}
{"doc_id": 41264017, "title": "Aggregation of vascular risk factors and risk of incident Alzheimer disease.", "abstract": ["BACKGROUND The prevalence of Alzheimer disease (AD) is increasing in the elderly, and vascular risk factors may increase its risk.   \n", "OBJECTIVE To explore the association of the aggregation of vascular risk factors with AD.   \n", "METHODS The authors followed 1,138 individuals without dementia at baseline (mean age 76.2) for a mean of 5.5 years.", "The presence of vascular risk factors was related to incident possible and probable AD.   \n", "RESULTS Four risk factors (diabetes, hypertension, heart disease, and current smoking) were associated with a higher risk of AD (p < 0.10) when analyzed individually.", "The risk of AD increased with the number of risk factors (diabetes + hypertension + heart disease + current smoking).", "The adjusted hazards ratio of probable AD for the presence of three or more risk factors was 3.4 (95% CI: 1.8, 6.3; p for trend < 0.0001) compared with no risk factors.", "Diabetes and current smoking were the strongest risk factors in isolation or in clusters, but hypertension and heart disease were also related to a higher risk of AD when clustered with diabetes, smoking, or each other.   \n", "CONCLUSIONS The risk of Alzheimer disease (AD) increased with the number of vascular risk factors.", "Diabetes and current smoking were the strongest risk factors, but clusters including hypertension and heart disease also increased the risk of AD.", "These associations are unlikely to be explained by misclassification of the outcome, given strong associations when only probable AD is considered."], "structured": true}
{"doc_id": 41293601, "title": "Hotspot mutations in H3F3A and IDH1 define distinct epigenetic and biological subgroups of glioblastoma.", "abstract": ["Glioblastoma (GBM) is a brain tumor that carries a dismal prognosis and displays considerable heterogeneity.", "We have recently identified recurrent H3F3A mutations affecting two critical amino acids (K27 and G34) of histone H3.3 in one-third of pediatric GBM.", "Here, we show that each H3F3A mutation defines an epigenetic subgroup of GBM with a distinct global methylation pattern, and that they are mutually exclusive with IDH1 mutations, which characterize a third mutation-defined subgroup.", "Three further epigenetic subgroups were enriched for hallmark genetic events of adult GBM and/or established transcriptomic signatures.", "We also demonstrate that the two H3F3A mutations give rise to GBMs in separate anatomic compartments, with differential regulation of transcription factors OLIG1, OLIG2, and FOXG1, possibly reflecting different cellular origins."], "structured": false}
{"doc_id": 41294031, "title": "Glucocorticoid with cyclophosphamide for paraquat-induced lung fibrosis.", "abstract": ["BACKGROUND Paraquat is an effective and widely used herbicide but is also a lethal poison.", "In many developing countries paraquat is widely available and inexpensive, making poisoning prevention difficult.", "However most of the people who become poisoned from paraquat have taken it as a means of suicide.", "Standard treatment for paraquat poisoning both prevents further absorption and reduces the load of paraquat in the blood through haemoperfusion or haemodialysis.", "The effectiveness of standard treatments is extremely limited.", "The immune system plays an important role in exacerbating paraquat-induced lung fibrosis.", "Immunosuppressive treatment using glucocorticoid and cyclophosphamide in combination is being developed and studied.   \n", "OBJECTIVES To assess the effects of glucocorticoid with cyclophosphamide on mortality in patients with paraquat-induced lung fibrosis.   ", "SEARCH METHODS To identify randomised controlled trials (RCTs) on this topic, we searched the Cochrane Injuries Group's Specialised Register (searched 1 February 2012), the Cochrane Central Register of Controlled Trials (CENTRAL) (The Cochrane Library 2012, Issue 1), MEDLINE (Ovid SP) (1946 January Week 3 2012), EMBASE (Ovid SP) (1947 to Week 4 2012), ISI Web of Science: Science Citation Index Expanded (SCI-EXPANDED) (1970 to January 2012), ISI Web of Science: Conference Proceedings Citation Index - Science (CPCI-S) (1990 to January 2012), Chinese Biomedical Literature and Retrieval System (CBM) (1978 to April 2012), Chinese Medical Current Contents (CMCC) (1995 to April 2012), and Chinese Medical Academic Conference (CMAC) (1994 to April 2012).", "Searches were completed on English language databases on 1 February 2012 and on Chinese language databases on 12 April 2012.   ", "SELECTION CRITERIA RCTs were included in this review.", "All patients were to receive standard care, plus the intervention or control.", "The intervention was glucocorticoid with cyclophosphamide in combination versus a control of a placebo, standard care alone or any other therapy in addition to standard care.   \n", "DATA COLLECTION AND ANALYSIS The mortality risk ratio (RR) and 95% confidence interval (CI) was calculated for each study on an intention-to-treat basis.", "Data for all-cause mortality at final follow-up were summarised in a meta-analysis using a fixed-effect model.   \n", "MAIN RESULTS This systematic review includes three trials with a combined total of 164 participants who had moderate to severe paraquat poisoning.", "Patients who received glucocorticoid with cyclophosphamide in addition to standard care had a lower risk of death at final follow-up than those receiving standard care only (RR 0.72; 95% CI 0.59 to 0.89).   ", "AUTHORS' CONCLUSIONS Based on the findings of three small RCTs of moderate to severely poisoned patients, glucocorticoid with cyclophosphamide in addition to standard care may be a beneficial treatment for patients with paraquat-induced lung fibrosis.", "To enable further study of the effects of glucocorticoid with cyclophosphamide for patients with moderate to severe paraquat poisoning, hospitals may provide this treatment as part of an RCT with allocation concealment."], "structured": true}
{"doc_id": 41298619, "title": "Hydroxyethyl starch (HES) versus other fluid therapies: effects on kidney function.", "abstract": ["BACKGROUND Hydroxyethyl starches (HES) are synthetic colloids commonly used for fluid resuscitation, yet controversy exists about their impact on kidney function.   \n", "OBJECTIVES To examine the effects of HES on kidney function compared to other fluid resuscitation therapies in different patient populations.   ", "SEARCH STRATEGY We searched the Cochrane Renal Group's specialised register, the Cochrane Central Register of Controlled Trials (CENTRAL, in The Cochrane Library), MEDLINE, EMBASE, MetaRegister and reference lists of articles.   ", "SELECTION CRITERIA Randomised controlled trials (RCTs) and quasi-RCTs in which HES was compared to an alternate fluid therapy for the prevention or treatment of effective intravascular volume depletion.", "Primary outcomes were renal replacement therapy (RRT), author-defined kidney failure and acute kidney injury (AKI) as defined by the RIFLE criteria.", "Secondary outcomes included serum creatinine and creatinine clearance.   \n", "DATA COLLECTION AND ANALYSIS Screening, selection, data extraction and quality assessments for each retrieved article were carried out by two authors using standardised forms.", "Authors were contacted when published data were incomplete.", "Preplanned sensitivity and subgroup analyses were performed after data were analysed with a random effects model.   \n", "MAIN RESULTS The review included 34 studies (2607 patients).", "Overall, the RR of author-defined kidney failure was 1.50 (95% CI 1.20 to 1.87; n = 1199) and 1.38 for requiring RRT (95% CI 0.89 to 2.16; n = 1236) in HES treated individuals compared with other fluid therapies.", "Subgroup analyses suggested increased risk in septic patients compared to non-septic (surgical/trauma) patients.", "Non-septic patient studies were smaller and had lower event rates, so subgroup differences may have been due to lack of statistical power in these studies.", "Only limited data was obtained for analysis of kidney outcomes by the RIFLE criteria.", "Overall, methodological quality of studies was good but subjective outcomes were potentially biased because most studies were unblinded.   ", "AUTHORS' CONCLUSIONS Potential for increased risk of AKI should be considered when weighing the risks and benefits of HES for volume resuscitation, particularly in septic patients.", "Large studies with adequate follow-up are required to evaluate the renal safety of HES products in non-septic patient populations.", "RIFLE criteria should be applied to evaluate kidney function in future studies of HES and, where data is available, to re-analyse those studies already published.", "There is inadequate clinical data to address the claim that safety differences exist between different HES products."], "structured": true}
{"doc_id": 41310252, "title": "Dietary fat and obesity: evidence from epidemiology.", "abstract": ["The epidemiological evidence that a high-fat diet promotes the development of obesity is considered suggestive but not definitive.", "The purpose of this paper is to provide a review of various epidemiological methods that have been used to address this issue as well as an updated summary of the existing evidence.", "Ecological studies describing dietary fat intake and obesity at the population level provide mixed results and are likely to be biased by both confounding and unknown data quality factors that differ systematically across the populations studied.", "Cross-sectional studies are generally in agreement that the concentration of fat in the diet is positively associated with relative weight.", "Prospective studies of diet in relation to subsequent weight change give inconsistent results.", "This may be due to behavioural factors such as dieting in response to weight gain; in addition, this type of study rarely takes into account the possible interaction between genetic predisposition and dietary fat in promoting weight gain.", "Finally, intervention studies in free-living subjects are considered, providing evidence of a consistent but short-lived period of active weight loss on low-fat diets.", "The experimental evidence on this relationship is more conclusive than the epidemiological evidence, although biological mechanisms remain controversial.", "Some areas for future epidemiological research involve: longitudinal studies of dietary fat intake as a predictor of growth in children; observational studies relating total dietary fat and specific types of fat to overall as well as regional adiposity; and randomized intervention studies of the effect of low-fat diets with particular emphasis on and familial predisposition to obesity and other possible modifying factors."], "structured": false}
{"doc_id": 41314611, "title": "Uncoupling of leading- and lagging-strand DNA replication during lesion bypass in vivo.", "abstract": ["Numerous agents attack DNA, forming lesions that impair normal replication.", "Specialized DNA polymerases transiently replace the replicative polymerase and copy past lesions, thus generating mutations, the major initiating cause of cancer.", "We monitored, in Escherichia coli, the kinetics of replication of both strands of DNA molecules containing a single replication block in either the leading or lagging strand.", "Despite a block in the leading strand, lagging-strand synthesis proceeded further, implying transient uncoupling of concurrent strand synthesis.", "Replication through the lesion requires specialized DNA polymerases and is achieved with similar kinetics and efficiencies in both strands."], "structured": false}
{"doc_id": 41325555, "title": "Phosphoinositide 3-kinase signalling--which way to target?", "abstract": ["Abstract Phosphoinositide 3-kinases (PI3Ks) are central to the control of cell growth, proliferation and survival, and drive the progression of tumours by activating phosphoinositide-dependent kinase, protein kinase B and the target of rapamycin.", "Other downstream effectors link PI3K to cell motility and the control of cardiovascular parameters.", "Current knowledge indicates that PI3Ks might qualify as drug targets for the treatment of cancer, chronic inflammation, allergy and cardiovascular failure.", "However, PI3Ks also modulate vital processes such as metabolic control and nutrient uptake.", "Here, mechanistic data and mouse phenotypic analyses are summarised, and the possible success of therapeutic inhibition of distinct PI3K isoforms is discussed."], "structured": false}
{"doc_id": 41329220, "title": "Determination of the time course of capacitation in mouse spermatozoa using a chlortetracycline fluorescence assay.", "abstract": ["The heads of mouse spermatozoa obtained 5 min after release from the excised caudae epididymides showed a characteristic fluorescence pattern in the presence of the fluorophore chlortetracycline (CTC).", "There was uniform fluorescence over the entire head with about half the sperm population showing a brighter line of fluorescence across the equatorial segment; this fluorescence pattern was designated \"F\".", "After 90-min incubation in culture medium (CM) containing 2% (w/v) bovine serum albumin, most of the sperm heads showed a dark band of nonfluorescence over the equatorial and postequatorial segment, while the anterior portion of the head showed bright fluorescence.", "This fluorescence pattern was designated \"B.\" The time course for the disappearance of pattern F matched the time course of the appearance of pattern B, with a half-time of 30 min.", "The transformation was complete in 90 min.", "At longer times of incubation in CM, the percentage of spermatozoa showing pattern B declined; fluorescence over the entire head was lost, characteristic of the pattern for acrosome-reacted sperm (P. M. Saling and B. T. Storey (1979).", "J. Cell Biol.", "83, 544-555).", "Mouse sperm showing pattern B were able to undergo the acrosome reaction, either spontaneously or by induction with acid-solubilized zonae pellucidae from mouse eggs (H.M. Florman and B. T. Storey (1982).", "Dev.", "Biol.", "91, 121-130).", "The latter reaction was blocked by its specific inhibitor 3-quinuclidinyl benzilate (QNB).", "Mouse sperm showing pattern F could not be induced to undergo the acrosome reaction by exposure to solubilized zonae.", "This implies that the change from fluorescence pattern F to fluorescence pattern B corresponds with changes in the sperm which make them susceptible to undergo the acrosome reaction.", "This change occurs during the time interval previously determined to be needed for capacitation of mouse sperm in vitro in CM (M. Inoue and D. P. Wolf (1975).", "Biol.", "Reprod.", "13, 340-346).", "These results imply that spermatozoa showing CTC fluorescence pattern B can be considered to be capacitated and that a functional definition for capacitation is the acquired ability to undergo the acrosome reaction rapidly when treated with acid-solubilized zonae pellucidae.", "The CTC fluorescence assay provides for the first time a means to monitor the time course of epididymal mouse sperm capacitation in vitro."], "structured": false}
{"doc_id": 41329906, "title": "[Detection of CRISPR and its relationship to drug resistance in Shigella].", "abstract": ["OBJECTIVE To detect clustered regularly interspaced short palindromic repeats (CRISPR) in Shigella, and to analyze its relationship to drug resistance.   \n", "METHODS Four pairs of primers were used for the detection of convincing CRISPR structures CRISPR-S2 and CRISPR-S4, questionable CRISPR structures CRISPR-S1 and CRISPR-S3 in 60 Shigella strains.", "All primers were designed using sequences in CRISPR database.", "CRISPR Finder was used to analyze CRISPR and susceptibilities of Shigella strains were tested by agar diffusion method.", "Furthermore, we analyzed the relationship between drug resistance and CRISPR-S4.   \n", "RESULTS The positive rate of convincing CRISPR structures was 95%.", "The four CRISPR loci formed 12 spectral patterns (A-L), all of which contained convincing CRISPR structures except type K. We found one new repeat and 12 new spacers.", "The multi-drug resistance rate was 53.", "33% .", "We found no significant difference between CRISPR-S4 and drug resistant.", "However, the repeat sequence of CRISPR-S4 in multi- or TE-resistance strains was mainly R4.1 with AC deletions in the 3' end, and the spacer sequences of CRISPR-S4 in multi-drug resistance strains were mainly Sp5.1, Sp6.1 and Sp7.   \n", "CONCLUSION CRISPR was common in Shigella.", "Variations df repeat sequences and diversities of spacer sequences might be related to drug resistance in Shigella."], "structured": true}
{"doc_id": 41337677, "title": "The helicase DDX41 senses intracellular DNA mediated by the adaptor STING in dendritic cells", "abstract": ["The recognition of pathogenic DNA is important to the initiation of antiviral responses.", "Here we report the identification of DDX41, a member of the DEXDc family of helicases, as an intracellular DNA sensor in myeloid dendritic cells (mDCs).", "Knockdown of DDX41 expression by short hairpin RNA blocked the ability of mDCs to mount type I interferon and cytokine responses to DNA and DNA viruses.", "Overexpression of both DDX41 and the membrane-associated adaptor STING together had a synergistic effect in promoting Ifnb promoter activity.", "DDX41 bound both DNA and STING and localized together with STING in the cytosol.", "Knockdown of DDX41 expression blocked activation of the mitogen-activated protein kinase TBK1 and the transcription factors NF-\u03baB and IRF3 by B-form DNA.", "Our results suggest that DDX41 is an additional DNA sensor that depends on STING to sense pathogenic DNA."], "structured": false}
{"doc_id": 41340212, "title": "Radiotherapy plus concomitant and adjuvant temozolomide for glioblastoma.", "abstract": ["BACKGROUND Glioblastoma, the most common primary brain tumor in adults, is usually rapidly fatal.", "The current standard of care for newly diagnosed glioblastoma is surgical resection to the extent feasible, followed by adjuvant radiotherapy.", "In this trial we compared radiotherapy alone with radiotherapy plus temozolomide, given concomitantly with and after radiotherapy, in terms of efficacy and safety.   \n", "METHODS Patients with newly diagnosed, histologically confirmed glioblastoma were randomly assigned to receive radiotherapy alone (fractionated focal irradiation in daily fractions of 2 Gy given 5 days per week for 6 weeks, for a total of 60 Gy) or radiotherapy plus continuous daily temozolomide (75 mg per square meter of body-surface area per day, 7 days per week from the first to the last day of radiotherapy), followed by six cycles of adjuvant temozolomide (150 to 200 mg per square meter for 5 days during each 28-day cycle).", "The primary end point was overall survival.   \n", "RESULTS A total of 573 patients from 85 centers underwent randomization.", "The median age was 56 years, and 84 percent of patients had undergone debulking surgery.", "At a median follow-up of 28 months, the median survival was 14.6 months with radiotherapy plus temozolomide and 12.1 months with radiotherapy alone.", "The unadjusted hazard ratio for death in the radiotherapy-plus-temozolomide group was 0.63 (95 percent confidence interval, 0.52 to 0.75; P<0.001 by the log-rank test).", "The two-year survival rate was 26.5 percent with radiotherapy plus temozolomide and 10.4 percent with radiotherapy alone.", "Concomitant treatment with radiotherapy plus temozolomide resulted in grade 3 or 4 hematologic toxic effects in 7 percent of patients.   \n", "CONCLUSIONS The addition of temozolomide to radiotherapy for newly diagnosed glioblastoma resulted in a clinically meaningful and statistically significant survival benefit with minimal additional toxicity."], "structured": true}
{"doc_id": 41354899, "title": "Drug interactions between oral contraceptives and antibiotics.", "abstract": ["OBJECTIVE To evaluate the evidence on possible drug interactions between antibiotics and oral contraceptives (OCs) that may lead to OC failure.   \n", "DATA SOURCES MEDLINE and Lexis/Nexis Medical Library searches for 1966-1999 using the key word \"oral contraceptives,\" cross-indexed with the terms \"antibiotics,\" \"adverse effects,\" and \"pregnancy,\" and MEDLINE search using the additional MeSH term \"drug interactions.", "\"", "No language restrictions were used.   \n", "METHODS OF STUDY SELECTION A total of 167 articles were retrieved for analysis.", "Another 32 articles were identified by review of the references cited in these publications.", "Articles were selected based on their ability to provide information on the relationship between antibiotic therapy and OC efficacy in otherwise compliant users (defined as women with unplanned pregnancies who reported compliance with their OC regimen).", "Additionally, studies that either directly measured the effects of antibiotics on the pharmacokinetics of OC components, or that analyzed the effects of antibiotics on measures of ovulation in OC users were accepted.   ", "TABULATION, INTEGRATION, AND RESULTS At least 30 cases have been reported of pregnancies occurring in women taking OCs and antibiotics, particularly rifampin.", "Approximately 20% of pregnant women reporting to family planning or abortion clinics reported concomitant OC and antibiotic use.", "Information from adverse event reporting databases generally mirrors the types of information gleaned from these case reports and clinical surveys and accounts for approximately one-third of reported cases.", "Retrospective surveys, primarily from dermatology-based practices, also have reported 24 pregnancies in OC users who concomitantly received therapy with antibiotics, most commonly tetracyclines and penicillins.", "Apparent OC failure rates in clinical surveys were within the usual range expected for patterns of typical use.", "In pooled results obtained from relatively small populations, oral antibiotics, with the exception of rifampin, have not significantly affected the pharmacokinetics of ethinyl estradiol, levonorgestrel, and norethindrone or reduced the serum concentrations of gonadotropins.", "However, individual patients have been identified who experienced significant decreases in the plasma concentration of these components of OCs and who appeared to ovulate.   \n", "CONCLUSION Rifampin impairs the effectiveness of OCs.", "Pharmacokinetic studies of other antibiotics have not shown any systematic interaction between antibiotics and OC steroids.", "However, individual patients do show large decreases in the plasma concentrations of ethinyl estradiol when they take certain other antibiotics, notably tetracycline and penicillin derivatives.", "Because it is not possible to identify these women in advance, a cautious approach is advised."], "structured": true}
{"doc_id": 41380943, "title": "Male Japanese quails with female brains do not show male sexual behaviors.", "abstract": ["During embryonic development, gonadal steroid hormones (androgens and estrogens) are thought to organize the sexual differentiation of the brain in the heterogametic sexes of higher vertebrates (males in mammals, females in birds).", "Brain differentiation of the homogametic sexes is thought to proceed by default, not requiring sex hormones for sex-specific organization.", "In gallinaceous birds such as the Japanese quail, female brain organization is thought to develop via estrogen-dependent demasculinization of a default male brain phenotype.", "We performed male donor-to-female host (MF), female-to-male (FM), male-to-male (MM), and female-to-female (FF) isotopic, isochronic transplantation of the forebrain primordium in Japanese quail embryos before gonadal differentiation had occurred; brain chimeras had a forebrain (including the hypothalamus) originating exclusively from donor cells.", "MM, FF, and MF chimeras all showed sexual behavior governed by the genetic sex of the host.", "In contrast, FM chimeras (genetically female forebrain, all other tissues genetically male) showed no mounting and only rudimentary crowing behavior.", "Although MM, FF, MF, and FM chimeras all showed host-typical production of steroid hormones during embryonic life, only FM chimeras were hypogonadal, had atypical low levels of circulating testosterone in adulthood, and showed reduction (crowing) or absence (mounting) of reproductive behaviors.", "Morphological features of the medial preoptic nucleus (a sexually dimorphic brain area) also were not male-like in FM males.", "These data demonstrate a brain-intrinsic, genetically determined component that organizes the sex-typical production of gonadal hormones in adulthood and call for a reevaluation of the mechanisms underlying brain sexual differentiation in other higher-vertebrate species."], "structured": false}
{"doc_id": 41403996, "title": "DNA joint dependence of pol X family polymerase action in nonhomologous end joining.", "abstract": ["DNA double strand breaks (DSBs) can be rejoined directly by the nonhomologous end-joining (NHEJ) pathway of repair.", "Nucleases and polymerases are required to promote accurate NHEJ when the terminal bases of the DSB are damaged.", "The same enzymes also participate in imprecise rejoining and joining of incompatible ends, important mutagenic events.", "Previous work has shown that the Pol X family polymerase Pol4 is required for some but not all NHEJ events that require gap filling in Saccharomyces cerevisiae.", "Here, we systematically analyzed DSB end configurations and found that gaps on both strands and overhang polarity are the principal factors that determine whether a joint requires Pol4.", "DSBs with 3'-overhangs and a gap on each strand strongly depended on Pol4 for repair, DSBs with 5'-overhangs of the same sequence did not.", "Pol4 was not required when 3'-overhangs contained a gap on only one strand, however.", "Pol4 was equally required at 3'-overhangs of all lengths within the NHEJ-dependent range but was dispensable outside of this range, indicating that Pol4 is specific to NHEJ.", "Loss of Pol4 did not affect the rejoining of DSBs that utilized a recessed microhomology or DSBs bearing 5'-hydroxyls but no gap.", "Finally, mammalian Pol X polymerases were able to differentially complement a pol4 mutation depending on the joint structure, demonstrating that these polymerases can participate in yeast NHEJ but with distinct properties."], "structured": false}
{"doc_id": 41493639, "title": "ABC of burns. Introduction.", "abstract": ["Burns are one of the most devastating conditions encountered in medicine.", "The injury represents an assault on all aspects of the patient, from the physical to the psychological.", "It affects all ages, from babies to elderly people, and is a problem in both the developed and developing world.", "All of us have experienced the severe pain that even a small burn can bring.", "However the pain and distress caused by a large burn are not limited to the immediate event.", "The visible physical and the invisible psychological scars are long lasting and often lead to chronic disability.", "Burn injuries represent a diverse and varied challenge to medical and paramedical staff.", "Correct management requires a skilled multidisciplinary approach that addresses all the problems facing a burn patient.    ", "This series provides an overview of the most important aspects of burn injuries for hospital and non-hospital healthcare workers.\u200bworkers.        ", "Figure 1    Top: Child with 70% full thickness burns, which required resuscitation, intensive care support, and extensive debridement and skin grafting.", "Left: The same child one year later at a burns camp, having made a good recovery.", "A reasonable outcome is possible ..."], "structured": false}
{"doc_id": 41496215, "title": "DNA methylation is a critical cell-intrinsic determinant of astrocyte differentiation in the fetal brain.", "abstract": ["Astrocyte differentiation, which occurs late in brain development, is largely dependent on the activation of a transcription factor, STAT3.", "We show that astrocytes, as judged by glial fibrillary acidic protein (GFAP) expression, never emerge from neuroepithelial cells on embryonic day (E) 11.5 even when STAT3 is activated, in contrast to E14.5 neuroepithelial cells.", "A CpG dinucleotide within a STAT3 binding element in the GFAP promoter is highly methylated in E11.5 neuroepithelial cells, but is demethylated in cells responsive to the STAT3 activation signal to express GFAP.", "This CpG methylation leads to inaccessibility of STAT3 to the binding element.", "We suggest that methylation of a cell type-specific gene promoter is a pivotal event in regulating lineage specification in the developing brain."], "structured": false}
{"doc_id": 41548287, "title": "DNMT1 Inhibition Reprograms Pancreatic Cancer Stem Cells via Upregulation of the miR-17-92 Cluster.", "abstract": ["Pancreatic ductal adenocarcinoma (PDAC) and other carcinomas are hierarchically organized, with cancer stem cells (CSC) residing at the top of the hierarchy, where they drive tumor progression, metastasis, and chemoresistance.", "As CSC and non-CSC share an identical genetic background, we hypothesize that differences in epigenetics account for the striking functional differences between these two cell populations.", "Epigenetic mechanisms, such as DNA methylation, play an important role in maintaining pluripotency and regulating the differentiation of stem cells, but the role of DNA methylation in pancreatic CSC is obscure.", "In this study, we investigated the genome-wide DNA methylation profile of PDAC CSC, and we determined the importance of DNA methyltransferases for CSC maintenance and tumorigenicity.", "Using high-throughput methylation analysis, we discovered that sorted CSCs have a higher level of DNA methylation, regardless of the heterogeneity or polyclonality of the CSC populations present in the tumors analyzed.", "Mechanistically, CSC expressed higher DNMT1 levels than non-CSC.", "Pharmacologic or genetic targeting of DNMT1 in CSCs reduced their self-renewal and in vivo tumorigenic potential, defining DNMT1 as a candidate CSC therapeutic target.", "The inhibitory effect we observed was mediated in part through epigenetic reactivation of previously silenced miRNAs, in particular the miR-17-92 cluster.", "Together, our findings indicate that DNA methylation plays an important role in CSC biology and also provide a rationale to develop epigenetic modulators to target CSC plasticity and improve the poor outcome of PDAC patients.", "Cancer Res; 76(15); 4546-58.", "\u00a92016 AACR."], "structured": false}
{"doc_id": 41599676, "title": "Mutation spectrum in the nephrin gene (NPHS1) in congenital nephrotic syndrome.", "abstract": ["Congenital nephrotic syndrome, Finnish type (CNF or NPHS1), is an autosomal recessive disease characterized by massive proteinuria and development of nephrotic syndrome shortly after birth.", "The disease is most common in Finland, but many patients have been identified in other populations.", "The disease is caused by mutations in the gene for nephrin which is a key component of the glomerual ultrafilter, the podocyte slit diaphragm.", "A total of 30 mutations have been reported in the nephrin gene in patients with congenital nephrotic syndrome worldwide.", "In the Finnish population, two main mutations have been found.", "These two nonsense mutations account for over 94% of all mutations in Finland.", "Most mutations found in non-Finnish patients are missense mutations, but they include also nonsense and splice site mutations, as well as deletions and insertions.", "This mutation update summarizes the nature of all previously reported nephrin mutations and, additionally, describes 20 novel mutations recently identified in our laboratory."], "structured": false}
{"doc_id": 41620295, "title": "The HSA domain binds nuclear actin-related proteins to regulate chromatin-remodeling ATPases", "abstract": ["We identify the helicase-SANT\u2013associated (HSA) domain as the primary binding platform for nuclear actin-related proteins (ARPs) and actin.", "Individual HSA domains from chromatin remodelers (RSC, yeast SWI-SNF, human SWI-SNF, SWR1 and INO80) or modifiers (NuA4) reconstitute their respective ARP\u2013ARP or ARP\u2013actin modules.", "In RSC, the HSA domain resides on the catalytic ATPase subunit Sth1.", "The Sth1 HSA is essential in vivo, and its omission causes the specific loss of ARPs and a moderate reduction in ATPase activity.", "Genetic selections for arp suppressors yielded specific gain-of-function mutations in two new domains in Sth1, the post-HSA domain and protrusion 1, which are essential for RSC function in vivo but not ARP association.", "Taken together, we define the role of the HSA domain and provide evidence for a regulatory relationship involving the ARP\u2013HSA module and two new functional domains conserved in remodeler ATPases that contain ARPs."], "structured": false}
{"doc_id": 41644178, "title": "Increased dendritic complexity and axonal length in cultured mouse cortical neurons overexpressing methyl-CpG-binding protein MeCP2", "abstract": ["Rett syndrome is caused by loss-of-function mutations in the gene encoding the methyl DNA-binding factor MeCP2.", "As brain mass and neuronal complexity tend to be diminished in Rett patients, we tested whether MeCP2 directly influences the morphological complexity of developing neurons.", "Our results show that cultured mouse neurons overexpressing MeCP2beta (MECP2A) develop more complex morphologies, having longer axonal and dendritic processes, and an increased number of axonal and dendritic terminal endings.", "We then tested whether overexpressing a mutant form of MeCP2beta lacking its carboxyl terminus would elicit the same effects.", "Interestingly, while neurons overexpressing this mutant failed to enhance axonal and dendritic process elongation, the complexity of their axonal and dendritic processes remained significantly elevated.", "Taken together, these data support the hypothesis that MeCP2 directly regulates neuronal maturation and/or synaptogenesis, and provides evidence that MeCP2 may influence neuritic elongation and process branching through different mechanisms."], "structured": false}
{"doc_id": 41646286, "title": "Folate affects apoptosis in human trophoblastic cells.", "abstract": ["Effects of folate deficiency on the rate of apoptosis in human cytotrophoblastic cells has been investigated.", "Apoptosis was determined in cytotrophoblastic cells after culture in 1.", "control medium, 2.", "folate-free medium and 3.", "folate-free medium plus 10% fetal calf serum.", "Apoptosis rates in cells cultured in mediums 2 and 3 were significantly higher than those cultured in the control medium (P<0.02 and P<0.03, respectively).", "In conclusion, human cytotrophoblastic cells show a significantly increased rate of apoptosis in vitro after culture in a folate-free medium.", "Possible explanations for the association between folate deficiency and pregnancy complications are suggested."], "structured": false}
{"doc_id": 41650417, "title": "Role of KRAS and EGFR as biomarkers of response to erlotinib in National Cancer Institute of Canada Clinical Trials Group Study BR.21.", "abstract": ["PURPOSE To evaluate the effect of KRAS and epidermal growth factor receptor (EGFR) genotype on the response to erlotinib treatment in the BR.21, placebo-controlled trial.   \n", "PATIENTS AND METHODS We analyzed 206 tumors for KRAS mutation, 204 tumors for EGFR mutation, and 159 tumors for EGFR gene copy by fluorescent in situ hybridization (FISH).", "We reanalyzed EGFR deletion/mutation using two highly sensitive techniques that detect abnormalities in samples with 5% to 10% tumor cellularity.", "KRAS mutation was analyzed by direct sequencing.   \n", "RESULTS Thirty patients (15%) had KRAS mutations, 34 (17%) had EGFR exon 19 deletion or exon 21 L858R mutations, and 61 (38%) had high EGFR gene copy (FISH positive).", "Response rates were 10% for wild-type and 5% for mutant KRAS (P = .69), 7% for wild-type and 27% for mutant EGFR (P = .03), and 5% for EGFR FISH-negative and 21% for FISH-positive patients (P = .02).", "Significant survival benefit from erlotinib therapy was observed for patients with wild-type KRAS (hazard ratio [HR] = 0.69, P = .03) and EGFR FISH positivity (HR = 0.43, P = .004) but not for patients with mutant KRAS (HR = 1.67, P = .31), wild-type EGFR (HR = 0.74, P = .09), mutant EGFR (HR = 0.55, P = .12), and EGFR FISH negativity (HR = 0.80, P = .35).", "In multivariate analysis, only EGFR FISH-positive status was prognostic for poorer survival (P = .025) and predictive of differential survival benefit from erlotinib (P = .005).   \n", "CONCLUSION EGFR mutations and high copy number are predictive of response to erlotinib.", "EGFR FISH is the strongest prognostic marker and a significant predictive marker of differential survival benefit from erlotinib."], "structured": true}
{"doc_id": 41707539, "title": "Immune dysregulation in major depression: a critical review of existing evidence.", "abstract": ["It is now well established that depression is associated with immune dysregulation.", "It is not, however, known whether this immune dysregulation plays a role in the pathophysiology of major depression or whether it increases the susceptibility of the depressed patient to immune-related disorders.", "This article presents a critical review of existing evidence for immune dysregulation in major depression, including changes in leucocyte trafficking, lymphocyte function, and markers of immune activation.", "Possible mediators of immune dysregulation in major depression are briefly discussed.", "Finally, the relationship between major depression and several medical conditions such as infection, allergy and autoimmune disorders, cardiovascular diseases, cancer and AIDS is critically reviewed."], "structured": false}
{"doc_id": 41710132, "title": "Regulation of E2Fs and senescence by PML nuclear bodies.", "abstract": ["The tumor suppressor PML (promyelocytic leukemia protein) regulates cellular senescence and terminal differentiation, two processes that implicate a permanent exit from the cell cycle.", "Here, we show that the mechanism by which PML induces a permanent cell cycle exit and activates p53 and senescence involves a recruitment of E2F transcription factors bound to their promoters and the retinoblastoma (Rb) proteins to PML nuclear bodies enriched in heterochromatin proteins and protein phosphatase 1\u03b1.", "Blocking the functions of the Rb protein family or adding back E2Fs to PML-expressing cells can rescue their defects in E2F-dependent gene expression and cell proliferation, inhibiting the senescent phenotype.", "In benign prostatic hyperplasia, a neoplastic disease that displays features of senescence, PML was found to be up-regulated and forming nuclear bodies.", "In contrast, PML bodies were rarely visualized in prostate cancers.", "The newly defined PML/Rb/E2F pathway may help to distinguish benign tumors from cancers, and suggest E2F target genes as potential targets to induce senescence in human tumors."], "structured": false}
{"doc_id": 41735503, "title": "The International Classification of Headache Disorders.", "abstract": ["A set of related medical disorders that lack a proper classification system and diagnostic criteria is like a society without laws.", "The result is incoherence at best, chaos at worst.", "For this reason, the International Classification of Headache Disorders (ICHD) is arguably the single most important breakthrough in headache medicine over the last 50 years.", "The ICHD identifies and categorizes more than a hundred different kinds of headache in a logical, hierarchal system.", "Even more important, it has provided explicit diagnostic criteria for all of the headache disorders listed.", "The ICHD quickly became universally accepted, and criticism of the classification has been minor relative to that directed at other disease classification systems.", "Over the 20 years following publication of the first edition of the ICHD, headache research has rapidly accelerated despite sparse allocation of resources to that effort.", "In summary, the ICHD has attained widespread acceptance at the international level and has substantially facilitated both clinical research and clinical care in the field of headache medicine."], "structured": false}
{"doc_id": 41774099, "title": "Call to Develop a Standard Acquisition Charge Model for Kidney Paired Donation", "abstract": ["We propose a Medicare Demonstration Project to develop a standard acquisition charge for kidney paired donation.", "A new payment strategy is required because Medicare and commercial insurance companies may not directly pay living donor costs intended to lead to transplantation of a beneficiary of a different insurance provider.", "Until the 1970s, when organ procurement organizations were empowered to serve as financial intermediaries to pay the upfront recovery expenses for deceased donor kidneys before knowing the identity of the recipient, there existed similar limitations in the recovery and placement of deceased donor organs.", "Analogous to the recovery of deceased donor kidneys, kidney paired donation requires the evaluation of living donors before identifying their recipient.", "Tissue typing, crossmatching and transportation of living donors or their kidneys represent additional financial barriers.", "Finally, the administrative expenses of the organizations that identify and coordinate kidney paired donation transplantation require reimbursement akin to that necessary for organ procurement organizations.", "To expand access to kidney paired donation for more patients, we propose a model to reimburse paired donation expenses analogous to the proven strategy used for over 30 years to pay for deceased donor solid organ transplantation in America."], "structured": false}
{"doc_id": 41781905, "title": "Oxidant stress promotes disease by activating CaMKII.", "abstract": ["CaMKII is activated by oxidation of methionine residues residing in the regulatory domain.", "Oxidized CaMKII (ox-CaMKII) is now thought to participate in cardiovascular and pulmonary diseases and cancer.", "This invited review summarizes current evidence for the role of ox-CaMKII in disease, considers critical knowledge gaps and suggests new areas for inquiry."], "structured": false}
{"doc_id": 41782935, "title": "Genetic diagnosis and prognosis of Alzheimer's disease: challenges and opportunities.", "abstract": ["Alzheimer's disease (AD), the most common form of dementia in western societies, is a pathologically and clinically heterogeneous disease with a strong genetic component.", "The recent advances in high-throughput genome technologies allowing for the rapid analysis of millions of polymorphisms in thousands of subjects has significantly advanced our understanding of the genomic underpinnings of AD susceptibility.", "During the last 5 years, genome-wide association and whole-exome- and whole-genome sequencing studies have mapped more than 20 disease-associated loci, providing insights into the molecular pathways involved in AD pathogenesis and hinting at potential novel therapeutic targets.", "This review article summarizes the challenges and opportunities of when using genomic information for the diagnosis and prognosis of AD."], "structured": false}
{"doc_id": 41790911, "title": "WNT5A regulates adipose tissue angiogenesis via antiangiogenic VEGF-A165b in obese humans.", "abstract": ["Experimental studies have suggested that Wingless-related integration site 5A (WNT5A) is a proinflammatory secreted protein that is associated with metabolic dysfunction in obesity.", "Impaired angiogenesis in fat depots has been implicated in the development of adipose tissue capillary rarefaction, hypoxia, inflammation, and metabolic dysfunction.", "We have recently demonstrated that impaired adipose tissue angiogenesis is associated with overexpression of antiangiogenic factor VEGF-A165b in human fat and the systemic circulation.", "In the present study, we postulated that upregulation of WNT5A is associated with angiogenic dysfunction and examined its role in regulating VEGF-A165b expression in human obesity.", "We biopsied subcutaneous and visceral adipose tissue from 38 obese individuals (body mass index: 44 \u00b1 7 kg/m2, age: 37 \u00b1 11 yr) during planned bariatric surgery and characterized depot-specific protein expression of VEGF-A165b and WNT5A using Western blot analysis.", "In both subcutaneous and visceral fat, VEGF-A165b expression correlated strongly with WNT5A protein (r = 0.9, P < 0.001).", "In subcutaneous adipose tissue where angiogenic capacity is greater than in the visceral depot, exogenous human recombinant WNT5A increased VEGF-A165b expression in both whole adipose tissue and isolated vascular endothelial cell fractions (P < 0.01 and P < 0.05, respectively).", "This was associated with markedly blunted angiogenic capillary sprout formation in human fat pad explants.", "Moreover, recombinant WNT5A increased secretion of soluble fms-like tyrosine kinase-1, a negative regulator of angiogenesis, in the sprout media (P < 0.01).", "Both VEGF-A165b-neutralizing antibody and secreted frizzled-related protein 5, which acts as a decoy receptor for WNT5A, significantly improved capillary sprout formation and reduced soluble fms-like tyrosine kinase-1 production (P < 0.05).", "We demonstrated a significant regulatory nexus between WNT5A and antiangiogenic VEGF-A165b in the adipose tissue of obese subjects that was linked to angiogenic dysfunction.", "Elevated WNT5A expression in obesity may function as a negative regulator of angiogenesis.", "NEW & NOTEWORTHY Wingless-related integration site 5a (WNT5A) negatively regulates adipose tissue angiogenesis via VEGF-A165b in human obesity."], "structured": false}
{"doc_id": 41811327, "title": "At least 1400 base pairs of 5'-flanking DNA is required for the correct expression of the HO gene in yeast.", "abstract": ["Homothallic yeast cells undergo a specific pattern of mating-type switching initiated by an endonuclease encoded by the HO gene.", "HO transcription is affected by cell type (a, alpha, and a/alpha), by cell age (mother or daughter), and by the cell cycle.", "This paper investigates the sequences involved in HO transcription by replacing genomic DNA with copies mutated in vitro.", "A region between -1000 and 1400 (called URS1) is necessary for transcription in addition to a \"TATA\"-like region at -90.", "The 900 bp of DNA separating URS1 from the \"TATA\" box is not necessary for transcription nor for a/alpha repression and some measure of mother/daughter control, but it is necessary for correct cell cycle control."], "structured": false}
{"doc_id": 41822527, "title": "Inflammation and its role in neuroprotection, axonal regeneration and functional recovery after spinal cord injury.", "abstract": ["Trauma to the central nervous system (CNS) triggers intraparenchymal inflammation and activation of systemic immunity with the capacity to exacerbate neuropathology and stimulate mechanisms of tissue repair.", "Despite our incomplete understanding of the mechanisms that control these divergent functions, immune-based therapies are becoming a therapeutic focus.", "This review will address the complexities and controversies of post-traumatic neuroinflammation, particularly in spinal cord.", "In addition, current therapies designed to target neuroinflammatory cascades will be discussed."], "structured": false}
{"doc_id": 41852733, "title": "Order of intron removal influences multiple splice outcomes, including a two-exon skip, in a COL5A1 acceptor-site mutation that results in abnormal pro-alpha1(V) N-propeptides and Ehlers-Danlos syndrome type I.", "abstract": ["Ehlers-Danlos syndrome (EDS) type I (the classical variety) is a dominantly inherited, genetically heterogeneous connective-tissue disorder.", "Mutations in the COL5A1 and COL5A2 genes, which encode type V collagen, have been identified in several individuals.", "Most mutations affect either the triple-helical domain of the protein or the expression of one COL5A1 allele.", "We identified a novel splice-acceptor mutation (IVS4-2A-->G) in the N-propeptide-encoding region of COL5A1, in one patient with EDS type I. The outcome of this mutation was complex: In the major product, both exons 5 and 6 were skipped; other products included a small amount in which only exon 5 was skipped and an even smaller amount in which cryptic acceptor sites within exon 5 were used.", "All products were in frame.", "Pro-alpha1(V) chains with abnormal N-propeptides were secreted and were incorporated into extracellular matrix, and the mutation resulted in dramatic alterations in collagen fibril structure.", "The two-exon skip occurred in transcripts in which intron 5 was removed rapidly relative to introns 4 and 6, leaving a large (270 nt) composite exon that can be skipped in its entirety.", "The transcripts in which only exon 5 was skipped were derived from those in which intron 6 was removed prior to intron 5.", "The use of cryptic acceptor sites in exon 5 occurred in transcripts in which intron 4 was removed subsequent to introns 5 and 6.", "These findings suggest that the order of intron removal plays an important role in the outcome of splice-site mutations and provide a model that explains why multiple products derive from a mutation at a single splice site."], "structured": false}
{"doc_id": 41877386, "title": "Kruppel-like factor KLF10 targets transforming growth factor-beta1 to regulate CD4(+)CD25(-) T cells and T regulatory cells.", "abstract": ["CD4(+)CD25(+) regulatory T cells (T regs) play a major role in the maintenance of self-tolerance and immune suppression, although the mechanisms controlling T reg development and suppressor function remain incompletely understood.", "Herein, we provide evidence that Kruppel-like factor 10 (KLF10/TIEG1) constitutes an important regulator of T regulatory cell suppressor function and CD4(+)CD25(-) T cell activation through distinct mechanisms involving transforming growth factor (TGF)-beta1 and Foxp3.", "KLF10 overexpressing CD4(+)CD25(-) T cells induced both TGF-beta1 and Foxp3 expression, an effect associated with reduced T-Bet (Th1 marker) and Gata3 (Th2 marker) mRNA expression.", "Consistently, KLF10(-/-) CD4(+)CD25(-) T cells have enhanced differentiation along both Th1 and Th2 pathways and elaborate higher levels of Th1 and Th2 cytokines.", "Furthermore, KLF10(-/-) CD4(+)CD25(-) T cell effectors cannot be appropriately suppressed by wild-type T regs.", "Surprisingly, KLF10(-/-) T reg cells have reduced suppressor function, independent of Foxp3 expression, with decreased expression and elaboration of TGF-beta1, an effect completely rescued by exogenous treatment with TGF-beta1.", "Mechanistic studies demonstrate that in response to TGF-beta1, KLF10 can transactivate both TGF-beta1 and Foxp3 promoters, implicating KLF10 in a positive feedback loop that may promote cell-intrinsic control of T cell activation.", "Finally, KLF10(-/-) CD4(+)CD25(-) T cells promoted atherosclerosis by approximately 2-fold in ApoE(-/-)/scid/scid mice with increased leukocyte accumulation and peripheral pro-inflammatory cytokines.", "Thus, KLF10 is a critical regulator in the transcriptional network controlling TGF-beta1 in both CD4(+)CD25(-) T cells and T regs and plays an important role in regulating atherosclerotic lesion formation in mice."], "structured": false}
{"doc_id": 41900731, "title": "Synchrotron radiation solution X-ray scattering study of the pH dependence of the quaternary structure of yeast pyruvate decarboxylase.", "abstract": ["The pH dependence of the quaternary structure of pyruvate decarboxylase from yeast was studied in the range 6.2 less than pH less than 8.4.", "There is an equilibrium with a midpoint around pH 7.5 between tetramers and dimers, and the catalytic activity of the enzyme depends on the volume fraction of tetramer.", "This equilibrium may provide an additional regulating mechanism besides substrate activation since accumulation of pyruvate would lead to a reduction in pH and hence an increase of the concentration of the catalytically active tetramer.", "Radiation damage during the X-ray scattering experiments results in a shift of this equilibrium and in the formation of octamers.", "These effects could be circumvented and analyzed using experimental and data processing methods which can be readily applied to other radiation-sensitive systems.", "The low-resolution shapes of the dimers and tetramers were determined from the scattering curves using spherical harmonics.", "The results indicate that a conformational change must occur in the dimers upon formation of the tetramers, in agreement with earlier circular dichroism measurements."], "structured": false}
{"doc_id": 41911192, "title": "Enhancement of anxiety-like responsiveness to the cannabinoid CB(1) receptor agonist HU-210 following chronic stress.", "abstract": ["The effect that chronic unpredictable stress had on the anxiety-like response elicited by the cannabinoid receptor agonist HU-210 [3-(1,1-dimethylheptyl)-(-)-11-hydroxy-delta 8-tetrahydrocannabinol] in the elevated plus maze was investigated here.", "Male Long-Evans rats were either unstressed or were subjected to a 21-day regimen of chronic unpredictable stress, and subsequently were subdivided into three testing groups (vehicle, 10 and 50 microg/kg of HU-210) and tested on the elevated plus maze.", "Results demonstrated that in unstressed animals, a low dose of HU-210 induced an anxiolytic response, whereas a high dose induced an anxiogenic response.", "Further, in stressed animals both the low and the high doses of HU-210 induced anxiogenic responses.", "These findings suggest that chronic stress enhances either cannabinoid receptor responsivity or one of the interacting systems implicated in emotional states."], "structured": false}
{"doc_id": 41913714, "title": "Cardiac glycosides inhibit TNF-\u03b1/NF-\u03baB signaling by blocking recruitment of TNF receptor-associated death domain to the TNF receptor", "abstract": ["Digitoxin and structurally related cardiac glycoside drugs potently block activation of the TNF-\u03b1/NF-\u03baB signaling pathway.", "We have hypothesized that the mechanism might be discovered by searching systematically for selective inhibitory action through the entire pathway.", "We report that the common action of these drugs is to block the TNF-\u03b1-dependent binding of TNF receptor 1 to TNF receptor-associated death domain.", "This drug action can be observed with native cells, such as HeLa, and reconstituted systems prepared in HEK293 cells.", "All other antiinflammatory effects of digitoxin on NF-\u03baB and c-Jun N-terminal kinase pathways appear to follow from the blockade of this initial upstream signaling event."], "structured": false}
{"doc_id": 41915616, "title": "Zinc supplementation during lactation: effects on maternal status and milk zinc concentrations.", "abstract": ["The effects of a zinc supplement on maternal zinc status and milk zinc concentrations through > or = 7 mo of lactation were examined.", "Seventy-one lactating women received either a daily 15-mg zinc supplement (ZS, n = 40) or placebo (NZS, n = 31) started by 2 wk postpartum in a double-blind, randomized design.", "Overall mean zinc intakes were 13.0 +/-", "3.4 mg/d for the NZS group and 25.7 +/-", "3.9 mg/d (including supplement) for the ZS group.", "Plasma zinc concentrations of the ZS group were significantly higher than those of the NZS group (P = 0.05).", "Milk zinc concentrations declined significantly over the course of the study for all subjects but were not affected by zinc supplementation.", "The mean dietary zinc intake observed in the nonsupplemented group was adequate to maintain normal maternal zinc status and milk zinc concentrations through > or = 7 mo lactation.", "Similar controlled intervention trials in less well-nourished populations will be required to assess the impact of lower zinc intakes on milk zinc concentrations."], "structured": false}
{"doc_id": 41925568, "title": "DMSO as a vehicle for central injections: tests with feeding elicited by norepinephrine injected into the paraventricular nucleus.", "abstract": ["Dimethyl sulfoxide (DMSO) is becoming increasingly popular as a vehicle in studies employing central injections.", "The aim of the present study was to determine whether the vehicle required for solubilization of substances for central injection [75% DMSO and 25% artificial CSF (aCSF)] would alter the well-characterized stimulatory response to norepinephrine (NE) injected into the paraventricular nucleus (PVN) on short-term food intake.", "To evaluate its suitability, we compared the effects of repeated unilateral injections of NE dissolved in two different vehicles (100% aCSF or 75% DMSO, 25% aCSF), in separate groups of animals every 48 h over a 30-day period.", "NE (40 nmol) stimulated food intake by approximately sevenfold compared to either vehicle alone, and the stimulatory effect was similar whether aCSF or 75% DMSO was used as a vehicle.", "Furthermore, the NE-induced feeding did not vary in magnitude across a series of 13 tests.", "These results suggest that 75% DMSO is a suitable vehicle for administering NE (and likely other water-insoluble substances)in small volumes of 0.3 microl into specific brain regions."], "structured": false}
{"doc_id": 41928290, "title": "Dodecameric structure and ATPase activity of the human TIP48/TIP49 complex.", "abstract": ["TIP48 and TIP49 are two related and highly conserved eukaryotic AAA(+) proteins with an essential biological function and a critical role in major pathways that are closely linked to cancer.", "They are found together as components of several highly conserved chromatin-modifying complexes.", "Both proteins show sequence homology to bacterial RuvB but the nature and mechanism of their biochemical role remain unknown.", "Recombinant human TIP48 and TIP49 were assembled into a stable high molecular mass equimolar complex and tested for activity in vitro.", "TIP48/TIP49 complex formation resulted in synergistic increase in ATPase activity but ATP hydrolysis was not stimulated in the presence of single-stranded, double-stranded or four-way junction DNA and no DNA helicase or branch migration activity could be detected.", "Complexes with catalytic defects in either TIP48 or TIP49 had no ATPase activity showing that both proteins within the TIP48/TIP49 complex are required for ATP hydrolysis.", "The structure of the TIP48/TIP49 complex was examined by negative stain electron microscopy.", "Three-dimensional reconstruction at 20 A resolution revealed that the TIP48/TIP49 complex consisted of two stacked hexameric rings with C6 symmetry.", "The top and bottom rings showed substantial structural differences.", "Interestingly, TIP48 formed oligomers in the presence of adenine nucleotides, whilst TIP49 did not.", "The results point to biochemical differences between TIP48 and TIP49, which may explain the structural differences between the two hexameric rings and could be significant for specialised functions that the proteins perform individually."], "structured": false}
{"doc_id": 41976370, "title": "Associations between work-related factors and specific disorders of the shoulder--a systematic review of the literature.", "abstract": ["OBJECTIVE Our aim was to provide a quantitative assessment of the exposure-response relationships between work-related physical and psychosocial factors and the occurrence of specific shoulder disorders in occupational populations.   \n", "METHODS A systematic review of the literature was conducted on the associations between type of work, physical load factors, and psychosocial aspects at work, on the one hand, and the occurrence of tendinitis of the biceps tendon, rotator cuff tears, subacromial impingement syndrome (SIS), and suprascapular nerve compression, on the other hand.", "Associations between work factors and shoulder disorders were expressed in quantitative measures as odds ratio (OR) or relative risk (RR).   \n", "RESULTS The occurrence of SIS was associated with force requirements >10% maximal voluntary contraction (MVC), lifting >20 kg >10 times/day, and high-level of hand force >1 hour/day (OR 2.8-4.2).", "Repetitive movements of the shoulder, repetitive motion of the hand/wrist >2 hours/day, hand-arm vibration, and working with hand above shoulder level showed an association with SIS (OR 1.04-4.7) as did upper-arm flexion > or =45 degrees > or =15% of time (OR 2.43) and duty cycle of forceful exertions > or =9% time or duty cycle of forceful pinch >0% of time (OR 2.66).", "High psychosocial job demand was also associated with SIS (OR 1.5-3.19).", "Jobs in the fish processing industry had the highest risk for both tendinitis of the biceps tendon as well as SIS (OR 2.28 and 3.38, respectively).", "Work in a slaughterhouse and as a betel pepper leaf culler were associated with the occurrence of SIS only (OR 5.27 and 4.68, respectively).", "None of the included articles described the association between job title/risk factors and the occurrence of rotator cuff tears or suprascapular nerve compression.   \n", "CONCLUSIONS Highly repetitive work, forceful exertion in work, awkward postures, and high psychosocial job demand are associated with the occurrence of SIS."], "structured": true}
{"doc_id": 41982985, "title": "Altered TCR signaling from geometrically repatterned immunological synapses.", "abstract": ["The immunological synapse is a specialized cell-cell junction that is defined by large-scale spatial patterns of receptors and signaling molecules yet remains largely enigmatic in terms of formation and function.", "We used supported bilayer membranes and nanometer-scale structures fabricated onto the underlying substrate to impose geometric constraints on immunological synapse formation.", "Analysis of the resulting alternatively patterned synapses revealed a causal relation between the radial position of T cell receptors (TCRs) and signaling activity, with prolonged signaling from TCR microclusters that had been mechanically trapped in the peripheral regions of the synapse.", "These results are consistent with a model of the synapse in which spatial translocation of TCRs represents a direct mechanism of signal regulation."], "structured": false}
{"doc_id": 42009630, "title": "Molecular regulation of histone H3 trimethylation by COMPASS and the regulation of gene expression.", "abstract": ["The Set1-containing complex COMPASS, which is the yeast homolog of the human MLL complex, is required for mono-, di-, and trimethylation of lysine 4 of histone H3.", "We have performed a comparative global proteomic screen to better define the role of COMPASS in histone trimethylation.", "We report that both Cps60 and Cps40 components of COMPASS are required for proper histone H3 trimethylation, but not for proper regulation of telomere-associated gene silencing.", "Purified COMPASS lacking Cps60 can mono- and dimethylate but is not capable of trimethylating H3(K4).", "Chromatin immunoprecipitation (ChIP) studies indicate that the loss subunits of COMPASS required for histone trimethylation do not affect the localization of Set1 to chromatin for the genes tested.", "Collectively, our results suggest a molecular requirement for several components of COMPASS for proper histone H3 trimethylation and regulation of telomere-associated gene expression, indicating multiple roles for different forms of histone methylation by COMPASS."], "structured": false}
{"doc_id": 42035464, "title": "Mitosis-specific anchoring of gamma tubulin complexes by pericentrin controls spindle organization and mitotic entry.", "abstract": ["Microtubule nucleation is the best known function of centrosomes.", "Centrosomal microtubule nucleation is mediated primarily by gamma tubulin ring complexes (gamma TuRCs).", "However, little is known about the molecules that anchor these complexes to centrosomes.", "In this study, we show that the centrosomal coiled-coil protein pericentrin anchors gamma TuRCs at spindle poles through an interaction with gamma tubulin complex proteins 2 and 3 (GCP2/3).", "Pericentrin silencing by small interfering RNAs in somatic cells disrupted gamma tubulin localization and spindle organization in mitosis but had no effect on gamma tubulin localization or microtubule organization in interphase cells.", "Similarly, overexpression of the GCP2/3 binding domain of pericentrin disrupted the endogenous pericentrin-gamma TuRC interaction and perturbed astral microtubules and spindle bipolarity.", "When added to Xenopus mitotic extracts, this domain uncoupled gamma TuRCs from centrosomes, inhibited microtubule aster assembly, and induced rapid disassembly of preassembled asters.", "All phenotypes were significantly reduced in a pericentrin mutant with diminished GCP2/3 binding and were specific for mitotic centrosomal asters as we observed little effect on interphase asters or on asters assembled by the Ran-mediated centrosome-independent pathway.", "Additionally, pericentrin silencing or overexpression induced G2/antephase arrest followed by apoptosis in many but not all cell types.", "We conclude that pericentrin anchoring of gamma tubulin complexes at centrosomes in mitotic cells is required for proper spindle organization and that loss of this anchoring mechanism elicits a checkpoint response that prevents mitotic entry and triggers apoptotic cell death."], "structured": false}
{"doc_id": 42065070, "title": "High levels of viral replication contrast with only transient changes in CD4(+) and CD8(+) cell numbers during the early phase of experimental infection with simian immunodeficiency virus SIVmnd-1 in Mandrillus sphinx.", "abstract": ["Early events during human immunodeficiency virus infections are considered to reflect the capacity of the host to control infection.", "We have studied early virus and host parameters during the early phase of simian immunodeficiency virus SIVmnd-1 nonpathogenic infection in its natural host, Mandrillus sphinx.", "Four mandrills were experimentally infected with a primary SIVmnd-1 strain derived from a naturally infected mandrill.", "Two noninfected control animals were monitored in parallel.", "Blood and lymph nodes were collected at three time points before infection, twice a week during the first month, and at days 60, 180, and 360 postinfection (p.i.).", "Anti-SIVmnd-1 antibodies were detected starting from days 28 to 32 p.i.", "Neither elevated temperature nor increased lymph node size were observed.", "The viral load in plasma peaked between days 7 to 10 p.i.", "(2 x 10(6) to 2 x 10(8) RNA equivalents/ml).", "Viremia then decreased 10- to 1,000-fold, reaching the viral set point between days 30 to 60 p.i.", "The levels during the chronic phase of infection were similar to that in the naturally infected donor mandrill (2 x 10(5) RNA equivalents/ml).", "The CD4(+) cell numbers and percentages in blood and lymph nodes decreased slightly (<10%) during primary infection, and CD8(+) cell numbers increased transiently.", "All values returned to preinfection infection levels by day 30 p.i.", "CD8(+) cell numbers or percentages, in peripheral blood and lymph nodes, did not increase during the 1 year of follow-up.", "In conclusion, SIVmnd-1 has the capacity for rapid and extensive replication in mandrills.", "Despite high levels of viremia, CD4(+) and CD8(+) cell numbers remained stable in the post-acute phase of infection, raising questions regarding the susceptibility of mandrill T cells to activation and/or cell death in response to SIVmnd-1 infection in vivo."], "structured": false}
{"doc_id": 42080024, "title": "Vascular endothelial growth factor stimulates bone repair by promoting angiogenesis and bone turnover.", "abstract": ["Several growth factors are expressed in distinct temporal and spatial patterns during fracture repair.", "Of these, vascular endothelial growth factor, VEGF, is of particular interest because of its ability to induce neovascularization (angiogenesis).", "To determine whether VEGF is required for bone repair, we inhibited VEGF activity during secondary bone healing via a cartilage intermediate (endochondral ossification) and during direct bone repair (intramembranous ossification) in a novel mouse model.", "Treatment of mice with a soluble, neutralizing VEGF receptor decreased angiogenesis, bone formation, and callus mineralization in femoral fractures.", "Inhibition of VEGF also dramatically inhibited healing of a tibial cortical bone defect, consistent with our discovery of a direct autocrine role for VEGF in osteoblast differentiation.", "In separate experiments, exogenous VEGF enhanced blood vessel formation, ossification, and new bone (callus) maturation in mouse femur fractures, and promoted bony bridging of a rabbit radius segmental gap defect.", "Our results at specific time points during the course of healing underscore the role of VEGF in endochondral vs. intramembranous ossification, as well as skeletal development vs. bone repair.", "The responses to exogenous VEGF observed in two distinct model systems and species indicate that a slow-release formulation of VEGF, applied locally at the site of bone damage, may prove to be an effective therapy to promote human bone repair."], "structured": false}
{"doc_id": 42095718, "title": "Psychiatric comorbidity in chronic daily headache.", "abstract": ["Clinical evidence suggests that chronic daily headache (CDH) occurs in association with psychopathologies: previous studies have focused particularly on migraine.", "To evaluate this association, we studied, using the DSM-IIIR criteria, a population of 88 patients (18M, 70F) affected by CDH (mean duration 7.4 +/-", "8.7 years).", "We documented the presence of a psychiatric disorder in 90% of this population.", "The most frequent diagnosis was a comorbidity of anxiety and mood disorders.", "The comorbidity of psychiatric disorders and headache has important implications as far as treatment is concerned."], "structured": false}
{"doc_id": 42106119, "title": "An Expanded Oct4 Interaction Network: Implications for Stem Cell Biology, Development, and Disease", "abstract": ["The transcription factor Oct4 is key in embryonic stem cell identity and reprogramming.", "Insight into its partners should illuminate how the pluripotent state is established and regulated.", "Here, we identify a considerably expanded set of Oct4-binding proteins in mouse embryonic stem cells.", "We find that Oct4 associates with a varied set of proteins including regulators of gene expression and modulators of Oct4 function.", "Half of its partners are transcriptionally regulated by Oct4 itself or other stem cell transcription factors, whereas one-third display a significant change in expression upon cell differentiation.", "The majority of Oct4-associated proteins studied to date show an early lethal phenotype when mutated.", "A fraction of the human orthologs is associated with inherited developmental disorders or causative of cancer.", "The Oct4 interactome provides a resource for dissecting mechanisms of Oct4 function, enlightening the basis of pluripotency and development, and identifying potential additional reprogramming factors."], "structured": false}
{"doc_id": 42150015, "title": "Reproductive and lifestyle determinants of anti-M\u00fcllerian hormone in a large population-based study.", "abstract": ["CONTEXT Anti-m\u00fcllerian hormone (AMH) is an ovarian reserve marker that is increasingly applied in clinical practice as a prognostic and diagnostic tool.", "Despite increased use of AMH in clinical practice, large-scale studies addressing the influence of possible determinants on AMH levels are scarce.   \n", "OBJECTIVE We aimed to address the role of reproductive and lifestyle determinants of AMH in a large population-based cohort of women.   \n", "DESIGN In this cross-sectional study, age-specific AMH percentiles were calculated using general linear modeling with CG-LMS (Cole and Green, Lambda, Mu, and Sigma model, an established method to calculate growth curves for children).   \n", "SETTING Women from the general community participating in the Doetinchem Cohort study were assessed.   \n", "PARTICIPANTS Two thousand three hundred twenty premenopausal women were included.   \n", "MAIN OUTCOME MEASURE The effect of female reproductive and lifestyle factors on shifts in age-specific AMH percentiles was studied.   \n", "RESULTS In comparison to women with a regular menstrual cycle, current oral contraceptive (OC) users, women with menstrual cycle irregularity, and pregnant women had significantly lower age-specific AMH percentiles (for OC use, 11 percentiles lower; for cycle irregularity, 11 percentiles lower; and for pregnancy, 17 percentiles lower [P value for all <.0001]).", "Age at menarche and age at first childbirth were not associated with the age-specific AMH percentile.", "Higher parity was associated with 2 percentiles higher age-specific AMH (P = .02).", "Of the lifestyle factors investigated, current smoking was associated with 4 percentiles lower age-specific AMH percentiles (P = .02), irrespective of the smoking dose.", "Body mass index, waist circumference, alcohol consumption, physical exercise, and socioeconomic status were not significantly associated with age-specific AMH percentiles.   \n", "CONCLUSIONS This study demonstrates that several reproductive and lifestyle factors are associated with age-specific AMH levels.", "The lower AMH levels associated with OC use and smoking seem reversible, as effects were confined to current use of OC or cigarettes.", "It is important to give careful consideration to the effect of such determinants when interpreting AMH in a clinical setting and basing patient management on AMH."], "structured": true}
{"doc_id": 42185082, "title": "Primary care and health insurance among women released from New York City jails.", "abstract": ["Factors associated with primary care utilization and health insurance coverage were examined among 511 women leaving jail in New York City from 1997-2001.", "One year after release, roughly half of the sample reported primary care utilization (47%) and health insurance coverage (56%).", "Neither outcome was more likely among those reporting diabetes, asthma, or depression.", "Primary care utilization was more likely among those reporting receipt of public benefits, health insurance coverage, moderate social support, avoidance of illegal activity, and HIV seropositivity.", "Health insurance coverage was associated with receipt of public benefits, hospitalization, primary care, and avoiding re-arrest.", "This study demonstrated that a majority of women leaving jail, including those with chronic diseases, lack primary care.", "These data highlight the need to plan for continuity of care from corrections to the community and suggest further that this can be facilitated with provision of health benefits and social support."], "structured": false}
{"doc_id": 42240424, "title": "The effects of prion protein proteolysis and disaggregation on the strain properties of hamster scrapie.", "abstract": ["Native mammalian prions exist in self-propagating strains that exhibit distinctive clinical, pathological and biochemical characteristics.", "Prion strain diversity is associated with variations in PrP(Sc) conformation, but it remains unknown precisely which physical properties of the PrP(Sc) molecules are required to encipher mammalian prion strain phenotypes.", "In this study, we subjected prion-infected brain homogenates derived from three different hamster scrapie strains to either (i) proteinase K digestion or (ii) sonication, and inoculated the modified samples into normal hamsters.", "The results show that the strain-specific clinical features and neuropathological profiles of inoculated animals were not affected by either treatment.", "Similarly, the strain-dependent biochemical characteristics of the PrP(Sc) molecules (including electrophoretic mobility, glycoform composition, conformational stability and susceptibility to protease digestion) in infected animals were unaffected by either proteolysis or sonication of the original inocula.", "These results indicate that the infectious strain properties of native prions do not appear to be altered by PrP(Sc) disaggregation, and that maintenance of such properties does not require the N-domain (approximately residues 23-90) of the protease-resistant PrP(Sc) molecules or protease-sensitive PrP(Sc) molecules."], "structured": false}
{"doc_id": 42267740, "title": "Methylation of histone H3 lysine-79 by Dot1p plays multiple roles in the response to UV damage in Saccharomyces cerevisiae.", "abstract": ["Various proteins have been found to play roles in both the repair of UV damaged DNA and heterochromatin-mediated silencing in the yeast Saccharomyces cerevisiae.", "In particular, factors that are involved in the methylation of lysine-79 of histone H3 by Dot1p have been implicated in both processes, suggesting a bipartite function for this modification.", "We find that a dot1 null mutation and a histone H3 point mutation at lysine-79 cause increased sensitivity to UV radiation, suggesting that lysine-79 methylation is important for efficient repair of UV damage.", "Epistasis analysis between dot1 and various UV repair genes indicates that lysine-79 methylation plays overlapping roles within the nucleotide excision, post-replication and recombination repair pathways, as well as RAD9-mediated checkpoint function.", "In contrast, epistasis analysis with the H3 lysine-79 point mutation indicates that the lysine-to-glutamic acid substitution exerts specific effects within the nucleotide excision repair and post-replication repair pathways, suggesting that this allele only disrupts a subset of the functions of lysine-79 methylation.", "The overall results indicate the existence of distinct and separable roles of histone H3 lysine-79 methylation in the response to UV damage, potentially serving to coordinate the various repair processes."], "structured": false}
{"doc_id": 42278130, "title": "Unmet need for personal assistance with activities of daily living among older adults.", "abstract": ["PURPOSE This study examined the prevalence, correlates, and negative consequences of unmet need for personal assistance with activities of daily living (ADLs) among older adults.   \n", "DESIGN AND METHODS The authors analyzed cross-sectional data from the 1994 National Health Interview Survey's Supplement on Aging.", "Data were weighted to be representative of the noninstitutionalized population aged 70 years and older.   \n", "RESULTS Overall, 20.7% of those needing help to perform 1 or more ADLs (an estimated 629,000 persons) reported receiving inadequate assistance; for individual ADLs, the prevalence of unmet need ranged from 10.2% (eating) to 20.1% (transferring).", "The likelihood of having 1 or more unmet needs was associated with lower household income, multiple ADL difficulties, and living alone.", "Nearly half of those with unmet needs reported experiencing a negative consequence (e.g., unable to eat when hungry) as a result of their unmet need.   ", "IMPLICATIONS Greater, targeted efforts are needed to reduce the prevalence and consequences of unmet need for ADL assistance in elderly persons."], "structured": true}
{"doc_id": 42279414, "title": "Multi-stage chemical carcinogenesis in mouse skin: Fundamentals and applications", "abstract": ["For more than 60 years, the chemical induction of tumors in mouse skin has been used to study mechanisms of epithelial carcinogenesis and evaluate modifying factors.", "In the traditional two-stage skin carcinogenesis model, the initiation phase is accomplished by the application of a sub-carcinogenic dose of a carcinogen.", "Subsequently, tumor development is elicited by repeated treatment with a tumor-promoting agent.", "The initiation protocol can be completed within 1\u20133 h depending on the number of mice used; whereas the promotion phase requires twice weekly treatments (1\u20132 h) and once weekly tumor palpation (1\u20132 h) for the duration of the study.", "Using the protocol described here, a highly reproducible papilloma burden is expected within 10\u201320 weeks with progression of a portion of the tumors to squamous cell carcinomas within 20\u201350 weeks.", "In contrast to complete skin carcinogenesis, the two-stage model allows for greater yield of premalignant lesions, as well as separation of the initiation and promotion phases."], "structured": false}
{"doc_id": 42291761, "title": "Preventing deaths by drowning in children in the United Kingdom: have we made progress in 10 years? Population based incidence study.", "abstract": ["Detailed information on drowning in children is not routinely collected by offices of national statistics.", "Few studies have been carried out in the United Kingdom, and none has been done on British children abroad.  ", "In 1988-9, two of the authors (AMK and JRS) combined information from national statistical offices, police forces (Royal Life Saving Society), and from a press cutting service (Royal Society for Prevention of Accidents) for a detailed analysis of deaths by drowning in children.1, 2, 3 This analysis found that 149 children had drowned in the United Kingdom during 1998-9.", "It also identified a safety agenda, which focused on young children in garden ponds and pools and on older children swimming without supervision.  ", "Over the past 10 years there have been initiatives on children's safety in water, particularly swimming.", "We obtained similar information for 1998-9 to identify changes that have \u2026"], "structured": false}
{"doc_id": 42298280, "title": "Hypoxic heterogeneity in human tumors: EF5 binding, vasculature, necrosis, and proliferation.", "abstract": ["We evaluated the levels and distribution of hypoxia in 31 human tumors using fluorescent immunohistochemical detection of binding by the 2-nitroimidazole, EF5.", "Hypoxia was found to be a heterogeneous property of human tumors.", "Necrosis was usually found adjacent to the highest level of binding in an individual patient's tumor.", "However, hypoxia often occurred without necrosis.", "In the group of tumors studied, the most common relationship between blood vessels (PECAM/CD31) and EF5 staining was consistent with diffusion-limited hypoxia; acute hypoxia occurred infrequently.", "Within a given patient's tumor, there was an inverse correlation between regions of proliferation (Ki-67) and regions of hypoxia.", "Again, however, when these parameters were examined in a group of patients, the absence of proliferation did not predict the presence of hypoxia.", "The relationships between hypoxia and other biologic endpoints are complex, but, within a given tumor's spatial relationships, they are in accord with known physiologic principles.", "Thus, our data emphasize that the relationships between hypoxia and other biologic parameters vary between patients.", "Necrosis, proliferation, and blood vessel distribution cannot predict the level or presence of hypoxia in an individual patient's tumor."], "structured": false}
{"doc_id": 42314147, "title": "The Sp1-like protein BTEB3 inhibits transcription via the basic transcription element box by interacting with mSin3A and HDAC-1 co-repressors and competing with Sp1.", "abstract": ["Sp1-like proteins are characterized by three conserved C-terminal zinc finger motifs that bind GC-rich sequences found in promoters of numerous genes essential for mammalian cell homeostasis.", "These proteins behave as transcriptional activators or repressors.", "Although significant information has been reported on the molecular mechanisms by which Sp1-like activators function, relatively little is known about mechanisms for repressor proteins.", "Here we report the functional characterization of BTEB3, a ubiquitously expressed Sp1-like transcriptional repressor.", "GAL4 assays show that the N terminus of BTEB3 contains regions that can act as direct repressor domains.", "Immunoprecipitation assays reveal that BTEB3 interacts with the co-repressor mSin3A and the histone deacetylase protein HDAC-1.", "Gel shift assays demonstrate that BTEB3 specifically binds the BTE site, a well characterized GC-rich DNA element, with an affinity similar to that of Sp1.", "Reporter and gel shift assays in Chinese hamster ovary cells show that BTEB3 can also mediate repression by competing with Sp1 for BTE binding.", "Thus, the characterization of this protein expands the repertoire of BTEB-like members of the Sp1 family involved in transcriptional repression.", "Furthermore, our results suggest a mechanism of repression for BTEB3 involving direct repression by the N terminus via interaction with mSin3A and HDAC-1 and competition with Sp1 via the DNA-binding domain."], "structured": false}
{"doc_id": 42330403, "title": "Perceptual limits in a simulated \"Cocktail party\".", "abstract": ["Numerosity judgments of simultaneous talkers were examined.", "Listeners were required to report the number of talkers heard when this number varied (1 to 13).", "Spatial location of talkers (1 or 6 locations), duration of talker voices (0.8 s, 5.0 s, and 15.0 s), and gender arrangement of talkers also were manipulated in four experiments.", "In all experiments, the proportion of correct numerosity judgments monotonically decreased as talker numbers increased.", "Perceptual limits, defined as talker numbers with proportion correct scores of 0.5, varied between 3 to 5 talkers, on average, depending on listening conditions, and were significantly higher for spatially separated talkers, for the longer voices, and for the mixed gender voices (Experiments 1, 2, and 3).", "In addition, Experiment 4 found that average numerosity response times increased monotonically over a range of one to four talkers.", "These results support the idea that, before counting talkers, listeners perceptually segregate talkers to render numerosity judgments.", "They also suggest that our functional auditory world for simultaneous voices may consist of, at most, three to five talkers depending on listening situations.", "In light of these results, possible causes for such perceptual limits are discussed."], "structured": false}
{"doc_id": 42373087, "title": "The MOS social support survey.", "abstract": ["This paper describes the development and evaluation of a brief, multidimensional, self-administered, social support survey that was developed for patients in the Medical Outcomes Study (MOS), a two-year study of patients with chronic conditions.", "This survey was designed to be comprehensive in terms of recent thinking about the various dimensions of social support.", "In addition, it was designed to be distinct from other related measures.", "We present a summary of the major conceptual issues considered when choosing items for the social support battery, describe the items, and present findings based on data from 2987 patients (ages 18 and older).", "Multitrait scaling analyses supported the dimensionality of four functional support scales (emotional/informational, tangible, affectionate, and positive social interaction) and the construction of an overall functional social support index.", "These support measures are distinct from structural measures of social support and from related health measures.", "They are reliable (all Alphas greater than 0.91), and are fairly stable over time.", "Selected construct validity hypotheses were supported."], "structured": false}
{"doc_id": 42373943, "title": "Can hematological parameters discriminate malaria from nonmalarious acute febrile illness in the tropics?", "abstract": ["BACKGROUND Malaria is considered as the main differential diagnosis of acute febrile illness in the tropics, and alteration of various hematological parameters has been observed in patients with malaria.   ", "AIM To ascertain if certain hematological parameters increase the probability of malaria in patients with acute febrile illnesses.   \n", "SETTINGS AND DESIGN Hospital based, prospective cohort study.   \n", "METHODS AND MATERIAL All consecutive in patients with fever of less than seven days in duration were included in the study.", "Patients where localizing cause for fever could be determined were excluded.", "Hematological parameters (Hemoglobin, Red cell distribution width (RDW), Leukocyte count, and platelet counts) were determined by using automated counter, and peripheral smear examination for malarial parasite was taken as gold standard for the diagnosis of malaria.   ", "STATISTICAL ANALYSIS USED Diagnostic accuracy was measured by computing sensitivity, specificity, predictive values and likelihood ratios.", "The precision of these estimates was evaluated using 95% confidence intervals.   \n", "RESULTS AND CONCLUSIONS A total of 184 patients were included in the study and 70 (38%) had a positive peripheral smear for malarial parasite.", "Thrombocytopenia alone (platelet countless than 150,000/mm3) was a predictor for malaria (Sn 60%, Sp 88%, LR+ 5.04) and in combination with anemia (Hb < 10 g/dl) it was next best parameter (Sn 69%, Sp 74%, LR+ 2.77).", "RDW and leukocyte count were not predictive.", "The conclusion of this study is that the presence of thrombocytopenia in a patient with acute febrile illness increases the probability of malarial infection."], "structured": true}
{"doc_id": 42377686, "title": "14q deletions are associated with trisomy 12, NOTCH1 mutations and unmutated IGHV genes in chronic lymphocytic leukemia and small lymphocytic lymphoma.", "abstract": ["Deletions of the long arm of chromosome 14 [del(14q)] are rare but recurrently observed in mature B-cell neoplasms, particularly in chronic lymphocytic leukemia (CLL).", "To further characterize this aberration, we studied 81 cases with del(14q): 54 of CLL and 27 of small lymphocytic lymphoma (SLL), the largest reported series to date.", "Using karyotype and fluorescence in situ hybridization (FISH), the most frequent additional abnormality was trisomy 12 (tri12), observed in 28/79 (35%) cases, followed by del13q14 (12/79, 15%), delTP53 (11/80, 14%) delATM (5/79, 6%), and del6q21 (3/76, 4%).", "IGHV genes were unmutated in 41/53 (77%) patients, with a high frequency of IGHV1-69 (21/52, 40%).", "NOTCH1 gene was mutated in 14/45 (31%) patients.", "There was no significant difference in cytogenetic and molecular abnormalities between CLL and SLL.", "Investigations using FISH and SNP-array demonstrated the heterogeneous size of the 14q deletions.", "However, a group with the same del(14)(q24.1q32.33) was identified in 48% of cases.", "In this group, tri12 (P = 0.004) and NOTCH1 mutations (P = 0.02) were significantly more frequent than in the other patients.", "In CLL patients with del(14q), median treatment-free survival (TFS) was 27 months.", "In conclusion, del(14q) is associated with tri12 and with pejorative prognostic factors: unmutated IGHV genes (with over-representation of the IGHV1-69 repertoire), NOTCH1 mutations, and a short TFS."], "structured": false}
{"doc_id": 42387637, "title": "Rapid DNA methylation changes after exposure to traffic particles.", "abstract": ["RATIONALE Exposure to particulate air pollution has been related to increased hospitalization and death, particularly from cardiovascular disease.", "Lower blood DNA methylation content is found in processes related to cardiovascular outcomes, such as oxidative stress, aging, and atherosclerosis.   \n", "OBJECTIVES We evaluated whether particulate pollution modifies DNA methylation in heavily methylated sequences with high representation throughout the human genome.   \n", "METHODS We measured DNA methylation of long interspersed nucleotide element (LINE)-1 and Alu repetitive elements by quantitative polymerase chain reaction-pyrosequencing of 1,097 blood samples from 718 elderly participants in the Boston area Normative Aging Study.", "We used covariate-adjusted mixed models to account for within-subject correlation in repeated measures.", "We estimated the effects on DNA methylation of ambient particulate pollutants (black carbon, particulate matter with aerodynamic diameter < or = 2.5 microm [PM2.5], or sulfate) in multiple time windows (4 h to 7 d) before the examination.", "We estimated standardized regression coefficients (beta) expressing the fraction of a standard deviation change in DNA methylation associated with a standard deviation increase in exposure.   \n", "MEASUREMENTS AND MAIN RESULTS Repetitive element DNA methylation varied in association with time-related variables, such as day of the week and season.", "LINE-1 methylation decreased after recent exposure to higher black carbon (beta = -0.11; 95% confidence interval [CI], -0.18 to -0.04; P = 0.002) and PM2.5 (beta = -0.13; 95% CI, -0.19 to -0.06; P < 0.001 for the 7-d moving average).", "In two-pollutant models, only black carbon, a tracer of traffic particles, was significantly associated with LINE-1 methylation (beta = -0.09; 95% CI, -0.17 to -0.01; P = 0.03).", "No association was found with Alu methylation (P > 0.12).   \n", "CONCLUSIONS We found decreased repeated-element methylation after exposure to traffic particles.", "Whether decreased methylation mediates exposure-related health effects remains to be determined."], "structured": true}
{"doc_id": 42404093, "title": "Incidence of adverse drug events and potential adverse drug events. Implications for prevention. ADE Prevention Study Group.", "abstract": ["OBJECTIVES To assess incidence and preventability of adverse drug events (ADEs) and potential ADEs.", "To analyze preventable events to develop prevention strategies.   \n", "DESIGN Prospective cohort study.   \n", "PARTICIPANTS All 4031 adult admissions to a stratified random sample of 11 medical and surgical units in two tertiary care hospitals over a 6-month period.", "Units included two medical and three surgical intensive care units and four medical and two surgical general care units.   \n", "MAIN OUTCOME MEASURES Adverse drug events and potential ADEs.   \n", "METHODS Incidents were detected by stimulated self-report by nurses and pharmacists and by daily review of all charts by nurse investigators.", "Incidents were subsequently classified by two independent reviewers as to whether they represented ADEs or potential ADEs and as to severity and preventability.   \n", "RESULTS Over 6 months, 247 ADEs and 194 potential ADEs were identified.", "Extrapolated event rates were 6.5 ADEs and 5.5 potential ADEs per 100 nonobstetrical admissions, for mean numbers per hospital per year of approximately 1900 ADEs and 1600 potential ADEs.", "Of all ADEs, 1% were fatal (none preventable), 12% life-threatening, 30% serious, and 57% significant.", "Twenty-eight percent were judged preventable.", "Of the life-threatening and serious ADEs, 42% were preventable, compared with 18% of significant ADEs.", "Errors resulting in preventable ADEs occurred most often at the stages of ordering (56%) and administration (34%); transcription (6%) and dispensing errors (4%) were less common.", "Errors were much more likely to be intercepted if the error occurred earlier in the process: 48% at the ordering stage vs 0% at the administration stage.   \n", "CONCLUSION Adverse drug events were common and often preventable; serious ADEs were more likely to be preventable.", "Most resulted from errors at the ordering stage, but many also occurred at the administration stage.", "Prevention strategies should target both stages of the drug delivery process."], "structured": true}
{"doc_id": 42421723, "title": "Induction of galactokinase in Saccharomyces cerevisiae: kinetics of induction and glucose effects.", "abstract": ["The induced synthesis of galactokinase and the repressing effects of glucose on this synthesis have been investigated in whole yeast cells rendered permeable by treatment with dimethyl sulfoxide.", "It was found that the induction response of uninduced cells to galactose is clearly dependent on the nature of the carbon source upon which the culture was grown prior to exposure to galactose.", "Glucose-grown cells exhibited a long lag before induction, whereas lactate-grown cells exhibited induced synthesis within 8 min.", "A concentration of 0.5% galactose was found to be optimal for induction.", "The addition of glucose to yeast cultures growing on galactose resulted in a severe transient repression of synthesis which was followed by a resumed rate of synthesis characteristic of a weaker permanent catabolite repression.", "Neither 2-deoxygalactose nor fucose acted as gratuitous inducers of the pathway, nor did they serve as a substrates for galactokinase."], "structured": false}
{"doc_id": 42441846, "title": "Gene--nutrition interactions in coronary artery disease: correlation between the MTHFR C677T polymorphism and folate and homocysteine status in a Korean population.", "abstract": ["INTRODUCTION Elevated plasma total homocysteine is a major risk for coronary artery disease (CAD).", "Methyltetrahydrofolate reductase (MTHFR) is a main regulatory enzyme in homocysteine metabolism; a common C677T mutation in the MTHFR gene results in decreased enzyme activity, and contributes to increased homocysteine levels and decreased folate levels.", "We investigated the frequency of MTHFR C677T alleles in a Korean population, determined the genotype-specific threshold levels of folate or vitamin B12, and investigated the relationship between the TT genotype and the risk of CAD.   ", "MATERIALS AND METHODS We enrolled a study population of 163 CAD patients and 50 control subjects, and screened the MTHFR C677T polymorphism using real-time PCR with melting point analysis.", "Levels of plasma homocysteine, folate and vitamin B12 were also determined.", "We then defined the genotype-specific threshold values of folate and vitamin B12 required to keep homocysteine levels in a normal range for individuals of each MTHFR C677T genotype.   \n", "RESULTS The frequency of the TT genotype was 18% in control subjects and 26% in patients group (P>0.05).", "Individuals homozygous for the TT genotype had significantly elevated homocysteine levels (P<0.05).", "The genotype-specific folate threshold level was significantly higher in TT individuals than in the CC or CT genotypes.", "The OR of individuals with low folate status and the TT genotype to estimate the relative risk of CAD was 2.2 and the OR of those with high folate status and the TT genotype was 1.5 (95% CI, 0.5-9.6 and 0.7-3.2, respectively).   \n", "CONCLUSION We were able to define a gene-nutrient interaction that shows a higher risk for CAD based on specific threshold folate levels required by different MTHFR C677T genotypes in a Korean population."], "structured": true}
{"doc_id": 42465769, "title": "Human bone marrow adipocytes block granulopoiesis through neuropilin-1-induced granulocyte colony-stimulating factor inhibition.", "abstract": ["Adipocytes are part of hematopoietic microenvironment, even though up to now in humans, their role in hematopoiesis is still questioned.", "We have previously shown that accumulation of fat cells in femoral bone marrow (BM) coincides with increased expression of neuropilin-1 (NP-1), while it is weakly expressed in hematopoietic iliac crest BM.", "Starting from this observation, we postulated that adipocytes might exert a negative effect on hematopoiesis mediated through NP-1.", "To test this hypothesis, we set up BM adipocytes differentiated into fibroblast-like fat cells (FLFC), which share the major characteristics of primitive unilocular fat cells, as an experimental model.", "As expected, FLFCs constitutively produced macrophage colony stimulating factor and induced CD34(+) differentiation into macrophages independently of cell-to-cell contact.", "By contrast, granulopoiesis was hampered by cell-to-cell contact but could be restored in transwell culture conditions, together with granulocyte colony stimulating factor production.", "Both functions were also recovered when FLFCs cultured in contact with CD34(+) cells were treated with an antibody neutralizing NP-1, which proved its critical implication in contact inhibition.", "An inflammatory cytokine such as interleukin-1 beta or dexamethasone modulates FLFC properties to restore granulopoiesis.", "Our data provide the first evidence that primary adipocytes exert regulatory functions during hematopoiesis that might be implicated in some pathological processes.", "Disclosure of potential conflicts of interest is found at the end of this article."], "structured": false}
{"doc_id": 42484543, "title": "The transcriptome profile of human embryonic stem cells as defined by SAGE.", "abstract": ["Human embryonic stem (ES) cell lines that have the ability to self-renew and differentiate into specific cell types have been established.", "The molecular mechanisms for self-renewal and differentiation, however, are poorly understood.", "We determined the transcriptome profiles for two proprietary human ES cell lines (HES3 and HES4, ES Cell International), and compared them with murine ES cells and other human tissues.", "Human and mouse ES cells appear to share a number of expressed gene products although there are numerous notable differences, including an inactive leukemia inhibitory factor pathway and the high preponderance of several important genes like POU5F1 and SOX2 in human ES cells.", "We have established a list of genes comprised of known ES-specific genes and new candidates that can serve as markers for human ES cells and may also contribute to the \"stemness\" phenotype.", "Of particular interest was the downregulation of DNMT3B and LIN28 mRNAs during ES cell differentiation.", "The overlapping similarities and differences in gene expression profiles of human and mouse ES cells provide a foundation for a detailed and concerted dissection of the molecular and cellular mechanisms governing their pluripotency, directed differentiation into specific cell types, and extended ability for self-renewal."], "structured": false}
{"doc_id": 42489926, "title": "Small-molecule antagonists of p53-MDM2 binding: research tools and potential therapeutics.", "abstract": ["p53 regulates a key pathway which protects normal tissues from tumor development that may result from diverse forms of stress.", "In the absence of stress, growth suppressive and proapoptotic activity of p53 is inhibited by MDM2 which binds p53 and negatively regulates its activity and stability.", "MDM2 antagonists could activate p53 and may offer a novel therapeutic approach to cancer.", "Recently, we identified the first potent and selective low molecular weight inhibitors of MDM2-p53 binding, the Nutlins.", "These molecules activate the p53 pathway and suppress tumor growth in vitro and in vivo.", "They represent valuable new tools for studying the p53 pathway and its defects in cancer.", "Nutlins induce p53-dependent apoptosis in human cancer cells but appear cytostatic to proliferating normal cells.", "Their potent activity against osteosarcoma xenografts suggests that MDM2 antagonists may have clinical utility in the treatment of tumors with wild-type p53."], "structured": false}
{"doc_id": 42520882, "title": "Slipped (CTG)\u2022(CAG) repeats can be correctly repaired, escape repair or undergo error-prone repair", "abstract": ["Expansion of (CTG)\u2022(CAG) repeats, the cause of 14 or more diseases, is presumed to arise through escaped repair of slipped DNAs.", "We report the fidelity of slipped-DNA repair using human cell extracts and DNAs with slip-outs of (CAG)20 or (CTG)20.", "Three outcomes occurred: correct repair, escaped repair and error-prone repair.", "The choice of repair path depended on nick location and slip-out composition (CAG or CTG).", "A new form of error-prone repair was detected whereby excess repeats were incompletely excised, constituting a previously unknown path to generate expansions but not deletions.", "Neuron-like cell extracts yielded each of the three repair outcomes, supporting a role for these processes in (CTG)\u2022(CAG) instability in patient post-mitotic brain cells.", "Mismatch repair (MMR) and nucleotide excision repair (NER) proteins hMSH2, hMSH3, hMLH1, XPF, XPG or polymerase \u03b2 were not required\u2014indicating that their role in instability may precede that of slip-out processing.", "Differential processing of slipped repeats may explain the differences in mutation patterns between various disease loci or tissues."], "structured": false}
{"doc_id": 42565477, "title": "High Dub3 expression in mouse ESCs couples the G1/S checkpoint to pluripotency.", "abstract": ["The molecular mechanism underlying G1/S checkpoint bypass in mouse embryonic stem cells (ESCs) remains unknown.", "DNA damage blocks S phase entry by inhibiting the CDK2 kinase through destruction of its activator, the Cdc25A phosphatase.", "We observed high Cdc25A levels in G1 that persist even after DNA damage in mouse ESCs.", "We also found higher expression of Dub3, a deubiquitylase that controls Cdc25A protein abundance.", "Moreover, we demonstrate that the Dub3 gene is a direct target of Esrrb, a key transcription factor of the self-renewal machinery.", "We show that Dub3 expression is strongly downregulated during neural conversion and precedes Cdc25A destabilization, while forced Dub3 expression in ESCs becomes lethal upon differentiation, concomitant to cell-cycle remodeling and lineage commitment.", "Finally, knockdown of either Dub3 or Cdc25A induced spontaneous differentiation of ESCs.", "Altogether, these findings couple the self-renewal machinery to cell-cycle control through a deubiquitylase in ESCs."], "structured": false}
{"doc_id": 42601237, "title": "Paracrine effects of direct intramyocardial implantation of bone marrow derived cells to enhance neovascularization in chronic ischaemic myocardium.", "abstract": ["OBJECTIVE To determine the optimal bone marrow (BM) cell types, and their potential mechanisms of action for neovascularization in chronic ischaemic myocardium.   \n", "METHODS AND RESULTS The functional effects, angiogenic potential and cytokine expression of direct intramyocardial implantation of autologous BM CD31-positive endothelial progenitor cells (EPC, n=9), BM mononuclear cells (MNCs, n=9), and saline (n=9) were compared in a swine model of chronic ischaemic myocardium.", "Autologous BM cells were harvested and catheter-based electromechanical mapping-guided direct intramyocardial injection was performed to target ischaemic myocardium.", "After 12 weeks, injection of BM-MNC resulted in significant improvements in left ventricular dP/dt (+21+/-8%, P=0.032), left ventricular pressure (+17+/-4%, P=0.048) and regional microsphere myocardial perfusion over ischaemic endocardium (+74+/-28%, P<0.05) and epicardium (+73+/-29%, P<0.05).", "No significant effects were observed following injection of BM-EPC or saline.", "Capillary density (1132+/-69 versus 903+/-44 per mm(2), P=0.047) and expression of mRNA of vascular endothelial growth factor (VEGF, 32.3+/-5.6 versus 13.1+/-3.7, P<0.05,) and angiopoietin-2 (23.9+/-3.6 versus 13.7+/-3.1, P<0.05) in ischaemic myocardium was significantly greater in the BM-MNC group than the saline group.", "The capillary density in ischaemic myocardium demonstrated a significant positive correlation with VEGF expression (r=0.61, P<0.001).   \n", "CONCLUSION Catheter-based direct intramyocardial injection of BM-MNC enhanced angiogenesis more effectively than BM-EPC or saline, possibly via a paracrine effect, with increased expression of VEGF that subsequently improved cardiac performance of ischaemic myocardium."], "structured": true}
{"doc_id": 42662816, "title": "Endogenous miRNA sponge lincRNA-RoR regulates Oct4, Nanog, and Sox2 in human embryonic stem cell self-renewal.", "abstract": ["The embryonic stem cell (ESC) transcriptional and epigenetic networks are controlled by a multilayer regulatory circuitry, including core transcription factors (TFs), posttranscriptional modifier microRNAs (miRNAs), and some other regulators.", "However, the role of large intergenic noncoding RNAs (lincRNAs) in this regulatory circuitry and their underlying mechanism remains undefined.", "Here, we demonstrate that a lincRNA, linc-RoR, may function as a key competing endogenous RNA to link the network of miRNAs and core TFs, e.g., Oct4, Sox2, and Nanog.", "We show that linc-RoR shares miRNA-response elements with these core TFs and that linc-RoR prevents these core TFs from miRNA-mediated suppression in self-renewing human ESC.", "We suggest that linc-RoR forms a feedback loop with core TFs and miRNAs to regulate ESC maintenance and differentiation.", "These results may provide insights into the functional interactions of the components of genetic networks during development and may lead to new therapies for many diseases."], "structured": false}
{"doc_id": 42693833, "title": "Foxp3(+) T cells regulate immunoglobulin a selection and facilitate diversification of bacterial species responsible for immune homeostasis.", "abstract": ["Foxp3(+) T cells play a critical role for the maintenance of immune tolerance.", "Here we show that in mice, Foxp3(+) T cells contributed to diversification of gut microbiota, particularly of species belonging to Firmicutes.", "The control of indigenous bacteria by Foxp3(+) T cells involved regulatory functions both outside and inside germinal centers (GCs), consisting of suppression of inflammation and regulation of immunoglobulin A (IgA) selection in Peyer's patches, respectively.", "Diversified and selected IgAs contributed to maintenance of diversified and balanced microbiota, which in turn facilitated the expansion of Foxp3(+) T cells, induction of GCs, and IgA responses in the gut through a symbiotic regulatory loop.", "Thus, the adaptive immune system, through cellular and molecular components that are required for immune tolerance and through the diversification as well as selection of antibody repertoire, mediates host-microbial symbiosis by controlling the richness and balance of bacterial communities required for homeostasis."], "structured": false}
{"doc_id": 42708716, "title": "The isolation and characterization of a cDNA encoding phospholipid-specific inositol polyphosphate 5-phosphatase.", "abstract": ["We report the cDNA cloning and characterization of a novel human inositol polyphosphate 5-phosphatase (5-phosphatase) that has substrate specificity unlike previously described members of this large gene family.", "All previously described members hydrolyze water soluble inositol phosphates.", "This enzyme hydrolyzes only lipid substrates, phosphatidylinositol 3,4,5-trisphosphate and phosphatidylinositol 4,5-bisphosphate.", "The cDNA isolated comprises 3110 base pairs and predicts a protein product of 644 amino acids and M(r) = 70,023.", "We designate this 5-phosphatase as type IV.", "It is a highly basic protein (pI = 8.8) and has the greatest affinity toward phosphatidylinositol 3,4,5-trisphosphate of known 5-phosphatases.", "The K(m) is 0.65 micrometer, 1/10 that of SHIP (5.95 micrometer), another 5-phosphatase that hydrolyzes phosphatidylinositol 3,4,5-trisphosphate.", "The activity of 5-phosphatase type IV is sensitive to the presence of detergents in the in vitro assay.", "Thus the enzyme hydrolyzes lipid substrates in the absence of detergents or in the presence of n-octyl beta-glucopyranoside or Triton X-100, but not in the presence of cetyltriethylammonium bromide, the detergent that has been used in other studies of the hydrolysis of phosphatidylinositol 4,5-bisphosphate.", "Remarkably SHIP, a 5-phosphatase previously characterized as hydrolyzing only substrates with d-3 phosphates, also readily hydrolyzed phosphatidylinositol 4,5-bisphosphate in the presence of n-octyl beta-glucopyranoside but not cetyltriethylammonium bromide.", "We used antibodies prepared against a peptide predicted by the cDNA to identify the 5-phosphatase type IV enzyme in human tissues and find that it is highly expressed in the brain as determined by Western blotting.", "We also performed Western blotting of mouse tissues and found high levels of expression in the brain, testes, and heart with lower levels of expression in other tissues.", "mRNA was detected in many tissues and cell lines as determined by Northern blotting."], "structured": false}
{"doc_id": 42731834, "title": "Lack of Absent in Melanoma 2 (AIM2) expression in tumor cells is closely associated with poor survival in colorectal cancer patients.", "abstract": ["Functional studies on colorectal cancer cells indicated a protective role of the interferon-inducible dsDNA sensor Absent in Melanoma 2 (AIM2) in cancer progression.", "Given that a high mutation rate and lack of AIM2 expression was previously detected in a subset of colorectal cancers, we here investigated the association of AIM2 expression in tumor cells and patient prognosis (5-year follow-up).", "A tissue microarray analysis of 476 matched tissue pairs (colorectal tumor and adjacent normal colon epithelium) was performed by two independent observers.", "Samples from 62 patients were excluded because of missing follow-up information or due to neo-adjuvant therapy before tissue sampling.", "Out of the remaining 414 tissue pairs, 279 (67.4%) displayed reduced AIM2 expression in cancer cells when compared to epithelial cells of their normal counterpart.", "Thirty-eight patients (9.18%) had completely lost AIM2 expression in tumor cells.", "After adjustment for sex, age, cancer stage, tumor site, tumor grade and chemotherapy, complete lack of AIM2 expression was associated with an up to 3-fold increase in overall mortality (HR=2.40; 95% CI=1.44-3.99) and disease specific mortality (HR=3.14; 95% CI=1.75-5.65) in comparison to AIM2-positive tumor samples.", "Our results demonstrate that lack of AIM2 expression is closely associated with poor outcome in colorectal cancer.", "The data thus strongly substantiate a protective role of AIM2 against progression of colorectal tumors.", "Further studies are required to assess whether lack of AIM2 expression may be used as a biomarker for the identification of colorectal cancer patients with poor prognosis."], "structured": false}
{"doc_id": 42782688, "title": "VSL#3 probiotic upregulates intestinal mucosal alkaline sphingomyelinase and reduces inflammation.", "abstract": ["BACKGROUND Alkaline sphingomyelinase, an enzyme found exclusively in bile and the intestinal brush border, hydrolyzes sphingomyelin into ceramide, sphingosine and sphingosine-1-phosphate, thereby inducing epithelial apoptosis.", "Reduced levels of alkaline sphingomyelinase have been found in premalignant and malignant intestinal epithelia and in ulcerative colitis tissue.", "Probiotic bacteria can be a source of sphingomyelinase.   \n", "OBJECTIVE To determine the effect of VSL#3 probiotic therapy on mucosal levels of alkaline sphingomyelinase, both in a mouse model of colitis and in patients with ulcerative colitis.   \n", "METHODS Interleukin-10 gene-deficient (IL10KO) and wild type control mice were treated with VSL#3 (10(9) colony-forming units per day) for three weeks, after which alkaline sphingomyelinase activity was measured in ileal and colonic tissue.", "As well, 15 patients with ulcerative colitis were treated with VSL#3 (900 billion bacteria two times per day for five weeks).", "Alkaline sphingomyelinase activity was measured through biopsies and comparison of ulcerative colitis disease activity index scores obtained before and after treatment.   \n", "RESULTS Lowered alkaline sphingomyelinase levels were seen in the colon (P=0.02) and ileum (P=0.04) of IL10KO mice, as compared with controls.", "Treatment of these mice with VSL#3 resulted in upregulation of mucosal alkaline sphingomyelinase activity in both the colon (P=0.04) and the ileum (P=0.01).", "VSL#3 treatment of human patients who had ulcerative colitis decreased mean (+/-", "SEM) ulcerative colitis disease activity index scores from 5.3+/-1.8946 to 0.70+/-0.34 (P=0.02) and increased mucosal alkaline sphingomyelinase activity.   \n", "CONCLUSION Mucosal alkaline sphingomyelinase activity is reduced in the intestine of IL10KO mice with colitis and in humans with ulcerative colitis.", "VSL#3 probiotic therapy upregulates mucosal alkaline sphingomyelinase activity."], "structured": true}
{"doc_id": 42787108, "title": "Nodal/Activin signaling predicts human pluripotent stem cell lines prone to differentiate toward the hematopoietic lineage.", "abstract": ["Lineage-specific differentiation potential varies among different human pluripotent stem cell (hPSC) lines, becoming therefore highly desirable to prospectively know which hPSC lines exhibit the highest differentiation potential for a certain lineage.", "We have compared the hematopoietic potential of 14 human embryonic stem cell (hESC)/induced pluripotent stem cell (iPSC) lines.", "The emergence of hemogenic progenitors, primitive and mature blood cells, and colony-forming unit (CFU) potential was analyzed at different time points.", "Significant differences in the propensity to differentiate toward blood were observed among hPSCs: some hPSCs exhibited good blood differentiation potential, whereas others barely displayed blood-differentiation capacity.", "Correlation studies revealed that the CFU potential robustly correlates with hemogenic progenitors and primitive but not mature blood cells.", "Developmental progression of mesoendodermal and hematopoietic transcription factors expression revealed no correlation with either hematopoietic initiation or maturation efficiency.", "Microarray studies showed distinct gene expression profile between hPSCs with good versus poor hematopoietic potential.", "Although neuroectoderm-associated genes were downregulated in hPSCs prone to hematopoietic differentiation many members of the Nodal/Activin signaling were upregulated, suggesting that this signaling predicts those hPSC lines with good blood-differentiation potential.", "The association between Nodal/Activin signaling and the hematopoietic differentiation potential was confirmed using loss- and gain-of-function functional assays.", "Our data reinforce the value of prospective comparative studies aimed at determining the lineage-specific differentiation potential among different hPSCs and indicate that Nodal/Activin signaling seems to predict those hPSC lines prone to hematopoietic specification."], "structured": false}
{"doc_id": 42800527, "title": "Addition of a Gastrointestinal Microbiome Modulator to Metformin Improves Metformin Tolerance and Fasting Glucose Levels.", "abstract": ["BACKGROUND Adverse effects of metformin are primarily related to gastrointestinal (GI) intolerance that could limit titration to an efficacious dose or cause discontinuation of the medication.", "Because some metformin side effects may be attributable to shifts in the GI microbiome, we tested whether a GI microbiome modulator (GIMM) used in combination with metformin would ameliorate the GI symptoms.   \n", "METHODS A 2-period crossover study design was used with 2 treatment sequences, either placebo in period 1 followed by GIMM in period 2 or vice versa.", "Study periods lasted for 2 weeks, with a 2-week washout period between.", "During the first week, type 2 diabetes patients (T2D) who experienced metformin GI intolerance took 500 mg metformin along with their assigned NM504 (GIMM) or placebo treatment with breakfast and with dinner.", "In the second week, the 10 subjects took 500 mg metformin (t.i.d.), with GIMM or placebo consumed with the first and third daily metformin doses.", "Subjects were permitted to discontinue metformin dosing if it became intolerable.   \n", "RESULTS The combination of metformin and GIMM treatment produced a significantly better tolerance score to metformin than the placebo combination (6.78 \u00b1 0.65 [mean \u00b1 SEM] versus 4.45 \u00b1 0.69, P = .0006).", "Mean fasting glucose levels were significantly (P < .02) lower with the metformin-GIMM combination (121.3 \u00b1 7.8 mg/dl) than with metformin-placebo (151.9 \u00b1 7.8 mg/dl).   \n", "CONCLUSION Combining a GI microbiome modulator with metformin might allow the greater use of metformin in T2D patients and improve treatment of the disease."], "structured": true}
{"doc_id": 42836872, "title": "Diverse tumorigenic pathways in ovarian serous carcinoma.", "abstract": ["This study was undertaken to analyze genetic alterations in 108 sporadic serous ovarian neoplasms to elucidate ovarian serous carcinogenesis.", "Our results demonstrate that K-ras mutations occur in approximately 50% of serous borderline tumors (SBTs), non-invasive micropapillary serous carcinomas (MPSCs), and invasive micropapillary serous carcinomas, which represent a morphological continuum of tumor progression.", "Moreover, progressive increase in the degree of allelic imbalance of chromosomes 1p, 5q, 8p, 18q, 22q, and Xp was observed comparing serous borderline tumors to noninvasive and invasive micropapillary serous carcinomas.", "In contrast, high-grade (conventional serous carcinoma) tumors contained wild-type K-ras in all 23 cases studied and a high frequency of allelic imbalance even in small (early) primary tumors similar to that found in advanced stage tumors.", "Based on these findings, we propose a dualistic model for ovarian serous carcinogenesis.", "One pathway involves a stepwise progression from SBT to noninvasive and then invasive MPSC.", "The other pathway is characterized by rapid progression from the ovarian surface epithelium or inclusion cysts to a conventional (high-grade) serous carcinoma."], "structured": false}
{"doc_id": 42855554, "title": "Tissue-inherent fate of GPI revealed by GPI-anchored GFP transgenesis.", "abstract": ["To clarify the fate of glycosylphosphatidylinositol (GPI) in mammals, we developed GPI-anchored enhanced green fluorescent protein (EGFP-GPI) and transgenic mice carrying this fusion construct.", "When it was introduced to culture cells, the EGFP-GPI protein was correctly sorted to plasma membranes and microsomes depending on GPI biosynthesis.", "Transgenic mice carrying EGFP-GPI were found to show a broad transgene expression.", "Histologically, a prominent polarized localization of EGFP-GPI protein was observed in various epithelia, the nervous system and liver and secreted from some exocrine glands, as well as non-polarized presence in non-epithelial tissues, demonstrating a tissue-inherent manner of GPI sorting."], "structured": false}
{"doc_id": 42865134, "title": "Essential role for the SANT domain in the functioning of multiple chromatin remodeling enzymes.", "abstract": ["The SANT domain is a novel motif found in a number of eukaryotic transcriptional regulatory proteins that was identified based on its homology to the DNA binding domain of c-myb.", "Here we show that the SANT domain is essential for the in vivo functions of yeast Swi3p, Ada2p, and Rsc8p, subunits of three distinct chromatin remodeling complexes.", "We also find that the Ada2p SANT domain is essential for histone acetyltransferase activity of native, Gcn5p-containing HAT complexes.", "Furthermore, kinetic analyses indicate that an intact SANT domain is required for an Ada2p-dependent enhancement of histone tail binding and enzymatic catalysis by Gcn5p.", "Our results are consistent with a general role for SANT domains in functional interactions with histone N-terminal tails."], "structured": false}
{"doc_id": 42873134, "title": "Mechanisms of pancreatic beta-cell death in type 1 and type 2 diabetes: many differences, few similarities.", "abstract": ["Type 1 and type 2 diabetes are characterized by progressive beta-cell failure.", "Apoptosis is probably the main form of beta-cell death in both forms of the disease.", "It has been suggested that the mechanisms leading to nutrient- and cytokine-induced beta-cell death in type 2 and type 1 diabetes, respectively, share the activation of a final common pathway involving interleukin (IL)-1beta, nuclear factor (NF)-kappaB, and Fas.", "We review herein the similarities and differences between the mechanisms of beta-cell death in type 1 and type 2 diabetes.", "In the insulitis lesion in type 1 diabetes, invading immune cells produce cytokines, such as IL-1beta, tumor necrosis factor (TNF)-alpha, and interferon (IFN)-gamma.", "IL-1beta and/or TNF-alpha plus IFN-gamma induce beta-cell apoptosis via the activation of beta-cell gene networks under the control of the transcription factors NF-kappaB and STAT-1.", "NF-kappaB activation leads to production of nitric oxide (NO) and chemokines and depletion of endoplasmic reticulum (ER) calcium.", "The execution of beta-cell death occurs through activation of mitogen-activated protein kinases, via triggering of ER stress and by the release of mitochondrial death signals.", "Chronic exposure to elevated levels of glucose and free fatty acids (FFAs) causes beta-cell dysfunction and may induce beta-cell apoptosis in type 2 diabetes.", "Exposure to high glucose has dual effects, triggering initially \"glucose hypersensitization\" and later apoptosis, via different mechanisms.", "High glucose, however, does not induce or activate IL-1beta, NF-kappaB, or inducible nitric oxide synthase in rat or human beta-cells in vitro or in vivo in Psammomys obesus.", "FFAs may cause beta-cell apoptosis via ER stress, which is NF-kappaB and NO independent.", "Thus, cytokines and nutrients trigger beta-cell death by fundamentally different mechanisms, namely an NF-kappaB-dependent mechanism that culminates in caspase-3 activation for cytokines and an NF-kappaB-independent mechanism for nutrients.", "This argues against a unifying hypothesis for the mechanisms of beta-cell death in type 1 and type 2 diabetes and suggests that different approaches will be required to prevent beta-cell death in type 1 and type 2 diabetes."], "structured": false}
{"doc_id": 42913391, "title": "Health-related quality of life among children with acute lymphoblastic leukemia.", "abstract": ["BACKGROUND The objective was to quantify the health-related quality of life (HRQL) of children treated for acute lymphoblastic leukemia (ALL) and identify specific disabilities for remediation.   ", "PROCEDURE Two types of subjects were included: ALL patients 5 plus years old in a multi-center clinical trial and general population control groups.", "Patients were assessed during all four major phases of active treatment and approximately 2 years after treatment.", "Health status and HRQL were measured using HEALTH UTILITIES INDEX\u00ae (HUI\u00ae) Mark 2 (HUI2) and Mark 3 (HUI3).", "HRQL scores were used to calculate quality-adjusted life years (QALYs).", "Excess disability rates identified attributes for remediation.   \n", "RESULTS HUI assessments (n = 749) were collected during the five phases.", "Mean HRQL increased from induction through the post-treatment phase (P < 0.001).", "There were no significant demographic or treatment effects on HRQL, except for type of asparaginase during continuation therapy (P = 0.005 for HUI2 and P = 0.007 for HUI3).", "Differences in mean HRQL scores between patients and controls were important (P < 0.001) during the active treatment phases but not during the post-treatment phase.", "Relative to controls, patients lost approximately 0.2 QALYs during active treatment.", "Disability was evident in mobility/ambulation, emotion, self-care and pain, and declined over time.   \n", "CONCLUSIONS Patients with ALL experienced important but declining deficits in HRQL during active treatment phases: Equivalent to losing approximately 2 months of life in perfect health.", "HRQL within the 2-years post-treatment phase was similar to controls.", "The policy challenge is to develop new treatment protocols producing fewer disabilities in mobility/ambulation, emotion, self-care, and pain without compromising survival."], "structured": true}
{"doc_id": 42944505, "title": "JUVENILE MORTALITY INCREASES WITH CLUTCH SIZE IN A NEOTROPICAL BIRD", "abstract": ["The change in avian clutch size with latitude is a celebrated example of geographic variation in a vertebrate life-history trait.", "Alternative hypotheses for this pattern invoke nest predation, limited food for nestlings, or post-fledging juvenile mortality as selection pressures leading to small clutch size of tropical birds.", "We manipulated the clutch size of Spotted Antbirds (Hylophylax naevioides) in central Panama to test these hypotheses.", "We observed that rates of nest predation were not influenced by parental activity at nests and parents could successfully feed nestlings in enlarged broods.", "Although larger broods produced the most fledged juveniles, these individuals were less likely to survive to dispersal than were juveniles that fledged from smaller broods.", "Consequently, nest productivity did not vary with clutch size.", "Post-fledging mortality was not related to nestling mass two to three days prior to fledging.", "Rather, differences in the allocation of parental investment per juvenile among differently sized broods appeared to influence juvenile survival probability.", "These results identify parental care during the post-fledging period as a potential key factor influencing the evolution of small clutch size in tropical birds."], "structured": false}
{"doc_id": 42950029, "title": "Diagnosis of rotator cuff tears.", "abstract": ["Rotator cuff tears account for almost 50% of major shoulder injuries but are sometimes difficult to diagnose.", "To aid diagnosis, we did a prospective study, comparing results of 23 clinical tests from 400 patients with and without rotator cuff tears.", "Three simple tests were predictive for rotator cuff tear: supraspinatus weakness, weakness in external rotation, and impingement.", "When all three were positive, or if two tests were positive and the patient was aged 60 or older, the individual had a 98% chance of having a rotator cuff tear; combined absence of these features excluded this diagnosis."], "structured": false}
{"doc_id": 43014661, "title": "Increased susceptibility to UV-induced skin carcinogenesis in polymerase eta-deficient mice.", "abstract": ["Xeroderma pigmentosum variant (XPV) patients with mutations in the DNA polymerase eta (pol eta) gene are hypersensitive to sunlight and have greatly increased susceptibility to sunlight-induced skin cancer.", "Consistent with the ability of Pol eta to efficiently bypass UV light-induced cyclobutane pyrimidine dimers, XPV cells lacking Pol eta have diminished capacity to replicate UV-damaged DNA and are sensitive to UV light-induced killing and mutagenesis.", "To better understand these and other Pol eta functions, we generated Pol eta-deficient mice.", "Mice homozygous for a null mutation in pol eta are viable, fertile, and do not show any obvious spontaneous defects during the first year of life.", "However, fibroblasts derived from these mutant mice are sensitive to killing by exposure to UV light, and all Pol eta-deficient mice develop skin tumors after UV irradiation, in contrast to the wild-type littermate controls that did not develop such tumors.", "These results and biochemical studies of translesion synthesis by mouse Pol eta indicate that Pol eta-dependent bypass of cyclobutane pyrimidine dimers suppresses UV light-induced skin cancer in mice.", "Moreover, 37.5% of pol eta heterozygous mice also developed skin cancer during 5 months after a 5-month exposure to UV light, suggesting that humans who are heterozygous for mutations in pol eta may also have an increased risk of skin cancer."], "structured": false}
{"doc_id": 43048059, "title": "Hydrogen sulfide interacts with nitric oxide in the heart: possible involvement of nitroxyl.", "abstract": ["AIMS The present study aims to investigate the interaction between nitric oxide (NO) and hydrogen sulfide (H(2)S), the two important gaseous mediators in rat hearts.   \n", "METHODS AND RESULTS Intracellular calcium in isolated cardiomyocytes was measured with a spectrofluorometric method using Fura-2.", "Myocyte contractility was measured with a video edge system.", "NaHS (50 \u00b5M, an H(2)S donor) had no significant effect on the resting calcium level, electrically induced (EI) calcium transients, and cell contractility in ventricular myocytes.", "Stimulating endogenous NO production with l-arginine or exogenous application of NO donors [sodium nitroprusside (SNP) and 2-(N,N-diethylamino)-diazenolate-2-oxide] decreased myocyte twitch amplitudes accompanied by slower velocities of both cell contraction and relaxation.", "Surprisingly, NaHS reversed the negative inotropic and lusitropic effects of the above three NO-increasing agents.", "In addition, the mixture of SNP + NaHS increased, whereas SNP alone decreased, the resting calcium level and the amplitudes of EI calcium transients.", "Angeli's salt, a nitroxyl anion (HNO) donor, mimicked the effect of SNP + NaHS on calcium handling and myocyte contractility.", "Three thiols, N-acetyl-cysteine, l-cysteine, and glutathione, abolished the effects of HNO and SNP + NaHS on myocyte contraction.", "Neither Rp-cAMP [a protein kinase A (PKA) inhibitor] nor Rp-cGMP [a protein kinase G (PKG) inhibitor] affected the effects of SNP + NaHS, suggesting a cAMP/PKA- or cGMP/PKG-independent mechanism.   \n", "CONCLUSION H(2)S may interact with NO to form a thiol sensitive molecule (probably HNO) which produces positive inotropic and lusitropic effects.", "Our findings may shed light on the interaction of NO and H(2)S and provide new clues to treat cardiovascular diseases."], "structured": true}
{"doc_id": 43054703, "title": "A novel mechanism of rapid nuclear neutrophil extracellular trap formation in response to Staphylococcus aureus.", "abstract": ["Neutrophil extracellular traps (NETs) are webs of DNA covered with antimicrobial molecules that constitute a newly described killing mechanism in innate immune defense.", "Previous publications reported that NETs take up to 3-4 h to form via an oxidant-dependent event that requires lytic death of neutrophils.", "In this study, we describe neutrophils responding uniquely to Staphylococcus aureus via a novel process of NET formation that did not require neutrophil lysis or even breach of the plasma membrane.", "The multilobular nucleus rapidly became rounded and condensed.", "During this process, we observed the separation of the inner and outer nuclear membranes and budding of vesicles, and the separated membranes and vesicles were filled with nuclear DNA.", "The vesicles were extruded intact into the extracellular space where they ruptured, and the chromatin was released.", "This entire process occurred via a unique, very rapid (5-60 min), oxidant-independent mechanism.", "Mitochondrial DNA constituted very little if any of these NETs.", "They did have a limited amount of proteolytic activity and were able to kill S. aureus.", "With time, the nuclear envelope ruptured, and DNA filled the cytoplasm presumably for later lytic NET production, but this was distinct from the vesicular release mechanism.", "Panton-Valentine leukocidin, autolysin, and a lipase were identified in supernatants with NET-inducing activity, but Panton-Valentine leukocidin was the dominant NET inducer.", "We describe a new mechanism of NET release that is very rapid and contributes to trapping and killing of S. aureus."], "structured": false}
{"doc_id": 43122426, "title": "131-I radioiodine therapy for hyperthyroidism in patients with Graves' disease, uninodular goitre and multinodular goitre.", "abstract": ["We studied 201 consecutive patients who received a relatively fixed dose of radioiodine for the treatment of hyperthyroidism between the years 1981-6.", "Patients with Graves' disease (170) were initially treated with a mean (SE) dose of 369 (10) MBq 131-I with a remission rate of 94% at 6 months and a cumulative relapse rate of 12% at one year and 21% at 5 years.", "The cumulative incidence of hypothyroidism was 26% at 3 months, 55% at 6 months, 61% at 1 year and 66% at 5 years.", "Patients with a uninodular goitre (10) were initially treated with a mean (SE) dose of 438 (85) MBq 131-I with a remission rate of 100% at 6 months, without relapse at 1 year but relapsing in 17% at 5 years.", "The cumulative incidence of hypothyroidism was 26% at 3 months, 30% at 6 months, 40% at 1 year and 40% at 5 years.", "Patients with a multinodular goitre (21) were initially treated with a mean (SE) dose of 613 (77) MBq 131-I with a remission rate of 79% at 6 months and a cumulative relapse rate of 26% at 1 year and 39% at 5 years.", "The cumulative incidence of hypothyroidism was 5% at 3 months, 14% at 6 months, 24% at 1 year and 24% at 5 years."], "structured": false}
{"doc_id": 43128141, "title": "Enteral nutrition in the critically ill patient.", "abstract": ["Timing and route of nutrition provided to critically ill patients can affect their outcome.", "Early enteral nutrition has been shown to decrease specifically infectious morbidity in the critically ill patient.", "There is a small group of patients who are malnourished on arrival to the intensive care unit and in these patients parenteral nutrition is beneficial."], "structured": false}
{"doc_id": 43156471, "title": "Genomewide analysis of nucleosome density histone acetylation and HDAC function in fission yeast.", "abstract": ["We have conducted a genomewide investigation into the enzymatic specificity, expression profiles, and binding locations of four histone deacetylases (HDACs), representing the three different phylogenetic classes in fission yeast (Schizosaccharomyces pombe).", "By directly comparing nucleosome density, histone acetylation patterns and HDAC binding in both intergenic and coding regions with gene expression profiles, we found that Sir2 (class III) and Hos2 (class I) have a role in preventing histone loss; Clr6 (class I) is the principal enzyme in promoter-localized repression.", "Hos2 has an unexpected role in promoting high expression of growth-related genes by deacetylating H4K16Ac in their open reading frames.", "Clr3 (class II) acts cooperatively with Sir2 throughout the genome, including the silent regions: rDNA, centromeres, mat2/3 and telomeres.", "The most significant acetylation sites are H3K14Ac for Clr3 and H3K9Ac for Sir2 at their genomic targets.", "Clr3 also affects subtelomeric regions which contain clustered stress- and meiosis-induced genes.", "Thus, this combined genomic approach has uncovered different roles for fission yeast HDACs at the silent regions in repression and activation of gene expression."], "structured": false}
{"doc_id": 43165768, "title": "In vitro antimicrobial activity of mangrove plant Sonneratia alba.", "abstract": ["OBJECTIVE To investigate the antimicrobial property of mangrove plant Sonneratia alba (S. alba).   \n", "METHODS The antimicrobial activity was evaluated using disc diffusion and microdilution methods against six microorganisms.", "Soxhlet apparatus was used for extraction with a series of solvents, n-hexane, ethyl acetate and methanol in sequence of increasing polarity.   \n", "RESULTS Methanol extract appeared to be the most effective extract while n-hexane extract showed no activity.", "The antimicrobial activities were observed against the gram positive bacteria Staphylococcus aureus (S. aureus) and Bacillus cereus (B. cereus), the gram negative Escherichia coli (E. coli) and the yeast Cryptococcus neoformans.", "Pseudomonas aeruginosa and Candida albicans appeared to be not sensitive to the concentrations tested since no inhibition zone was observed.", "E. coli (17.5 mm) appeared to be the most sensitive strain followed by S. aureus (12.5 mm) and B. cereus (12.5 mm).   \n", "CONCLUSIONS From this study, it can be concluded that S. alba exhibits antimicrobial activities against certain microorganisms."], "structured": true}
{"doc_id": 43192375, "title": "Obesity induces a phenotypic switch in adipose tissue macrophage polarization.", "abstract": ["Adipose tissue macrophages (ATMs) infiltrate adipose tissue during obesity and contribute to insulin resistance.", "We hypothesized that macrophages migrating to adipose tissue upon high-fat feeding may differ from those that reside there under normal diet conditions.", "To this end, we found a novel F4/80(+)CD11c(+) population of ATMs in adipose tissue of obese mice that was not seen in lean mice.", "ATMs from lean mice expressed many genes characteristic of M2 or \"alternatively activated\" macrophages, including Ym1, arginase 1, and Il10.", "Diet-induced obesity decreased expression of these genes in ATMs while increasing expression of genes such as those encoding TNF-alpha and iNOS that are characteristic of M1 or \"classically activated\" macrophages.", "Interestingly, ATMs from obese C-C motif chemokine receptor 2-KO (Ccr2-KO) mice express M2 markers at levels similar to those from lean mice.", "The antiinflammatory cytokine IL-10, which was overexpressed in ATMs from lean mice, protected adipocytes from TNF-alpha-induced insulin resistance.", "Thus, diet-induced obesity leads to a shift in the activation state of ATMs from an M2-polarized state in lean animals that may protect adipocytes from inflammation to an M1 proinflammatory state that contributes to insulin resistance."], "structured": false}
{"doc_id": 43220289, "title": "Psychological Outcome 4 Years after Restrictive Bariatric Surgery", "abstract": ["Extreme obesity is associated with severe psychiatric and somatic comorbidity and impairment of psychosocial functioning.", "Bariatric surgery is the most effective treatment not only with regard to weight loss but also with obesity-associated illnesses.", "Health-related psychological and psychosocial variables have been increasingly considered as important outcome variables of bariatric surgery.", "However, the long-term impact of bariatric surgery on psychological and psychosocial functioning is largely unclear.", "The aim of this study was to evaluate the relationship between the course of weight and psychological variables including depression, anxiety, health-related quality of life (HRQOL), and self-esteem up to 4 years after obesity surgery.", "By standardized questionnaires prior to (T1) and 1 year (T2), 2 years (T3), and 4 years (T4) after surgery, 148 patients (47 males (31.8 %), 101 females (68.2 %), mean age 38.8 \u00b1 10.2 years) were assessed.", "On average, participants lost 24.6 % of their initial weight 1 year after surgery, 25.1 % after 2 years, and 22.3 % after 4 years.", "Statistical analysis revealed significant improvements in depressive symptoms, physical dimension of quality of life, and self-esteem with peak improvements 1 year after surgery.", "These improvements were largely maintained.", "Significant correlations between weight loss and improvements in depression, physical aspects of HRQOL (T2, T3, and T4), and self-esteem (T3) were observed.", "Corresponding to the considerable weight loss after bariatric surgery, important aspects of mental health improved significantly during the 4-year follow-up period.", "However, parallel to weight regain, psychological improvements showed a slow but not significant decline over time."], "structured": false}
{"doc_id": 43224840, "title": "Dynamics of Microvillus Extension and Tether Formation in Rolling Leukocytes.", "abstract": ["P-selectin glycoprotein ligand-1 (PSGL-1) binding to P-selectin mediates leukocyte rolling under conditions of flow.", "In human neutrophils, a type of leukocyte belonging to the innate immune system, PSGL-1 molecules are located on the neutrophil's surface ruffles, called microvilli.", "Each newly formed P-selectin-PSGL-1 bond can become load bearing, imposing on its microvillus a pulling force that deforms the microvillus.", "Depending on the magnitude of the bond force, a microvillus can be extended, or a thin membrane cylinder (a tether) can be formed at the tip of the microvillus.", "Here we propose a Kelvin-Voigt viscoelastic material as an improved model for microvillus extension.", "Using a modified version of our Event-Tracking Model of Adhesion (ETMA), we demonstrate how P-selectin-PSGL-1 load-bearing bonds shape microvillus deformation during neutrophil rolling at low shear (wall shear rate of 50 s(-1), P-selectin site density of 150 molecules \u03bcm(-2)).", "We also discuss the impact of microvillus deformability on neutrophil rolling.", "We find that the average microvillus extension constitutes 65% of the total microvillus-tether complex extension, and that the rolling neutrophil may never fully rest.", "A quantitative comparison with the corresponding non-deformable microvilli case supports a concept that the ability of the microvillus to deform stabilizes cell rolling."], "structured": false}
{"doc_id": 43226130, "title": "Female Gender and Reproductive Factors Affecting Risk, Relapses and Progression in Multiple Sclerosis", "abstract": ["Multiple sclerosis (MS), a chronic inflammatory demyelina-ting and degenerative disease of the central nervous system, is a frequent cause of neurological disability in young adults.", "Female predominance has increased over the last decades.", "Although female gender carries a higher risk of developing relapsing remitting MS, being female and at child-bearing age also appears to provide some protection against cognitive decline and against progressive onset MS, an adverse predictive factor when considering long-term disability in MS.", "The risk of MS in women has been associated with an earlier age at menarche.", "In most studies, parity did not impact MS risk.", "However, the recently published association of higher parity and offspring number with a reduced risk of a first demyelinating event suggests a potential suppressive effect.", "Pregnancy in MS patients has been associated with a reduced relapse rate and a reduction of neurological symptoms, especially in the third trimester.", "Despite the increased relapse risk in the postpartum period, there is no indication of an adverse effect of childbirth on the long-term course of MS.", "Fertility treatment in MS has been associated with an increased relapse risk in the following 3-month period, especially when the procedure did not result in pregnancy and gonadotrophin-releasing hormone agonists were used.", "Altogether, there is substantial evidence to support a regulatory role of sex steroid hormones in MS.", "In the absence of correlations with single hormone blood levels, we can only speculate about the underlying mechanisms.", "In conclusion, the increased MS risk in women and the changes in relapse and progression risk in association with reproductive events suggest significant and complex interactions between immune, neuroendocrine and reproductive systems in MS."], "structured": false}
{"doc_id": 43283375, "title": "Spatial release from masking based on binaural processing for up to six maskers.", "abstract": ["Spatial Release from Masking (SRM) was measured for identification of a female target word spoken in the presence of male masker words.", "Target words from a single loudspeaker located at midline were presented when two, four, or six masker words were presented either from the same source as the target or from spatially separated masker sources.", "All masker words were presented from loudspeakers located symmetrically around the centered target source in the front azimuth hemifield.", "Three masking conditions were employed: speech-in-speech masking (involving both informational and energetic masking), speech-in-noise masking (involving energetic masking), and filtered speech-in-filtered speech masking (involving informational masking).", "Psychophysical results were summarized as three-point psychometric functions relating proportion of correct word identification to target-to-masker ratio (in decibels) for both the co-located and spatially separated target and masker sources cases.", "SRM was then calculated by comparing the slopes and intercepts of these functions.", "SRM decreased as the number of symmetrically placed masker sources increased from two to six.", "This decrease was independent of the type of masking, with almost no SRM measured for six masker sources.", "These results suggest that when SRM is dependent primarily on binaural processing, SRM is effectively limited to fewer than six sound sources."], "structured": false}
{"doc_id": 43311750, "title": "Nephrin mutations cause childhood- and adult-onset focal segmental glomerulosclerosis.", "abstract": ["Mutations in the NPHS1 gene cause congenital nephrotic syndrome of the Finnish type presenting before the first 3 months of life.", "Recently, NPHS1 mutations have also been identified in childhood-onset steroid-resistant nephrotic syndrome and milder courses of disease, but their role in adults with focal segmental glomerulosclerosis remains unknown.", "Here we developed an in silico scoring matrix to evaluate the pathogenicity of amino-acid substitutions using the biophysical and biochemical difference between wild-type and mutant amino acid, the evolutionary conservation of the amino-acid residue in orthologs, and defined domains, with the addition of contextual information.", "Mutation analysis was performed in 97 patients from 89 unrelated families, of which 52 presented with steroid-resistant nephrotic syndrome after 18 years of age.", "Compound heterozygous or homozygous NPHS1 mutations were identified in five familial and seven sporadic cases, including one patient 27 years old at onset of the disease.", "Substitutions were classified as 'severe' or 'mild' using this in silico approach.", "Our results suggest an earlier onset of the disease in patients with two 'severe' mutations compared to patients with at least one 'mild' mutation.", "The finding of mutations in a patient with adult-onset focal segmental glomerulosclerosis indicates that NPHS1 analysis could be considered in patients with later onset of the disease."], "structured": false}
{"doc_id": 43329366, "title": "Use of clomifene during early pregnancy and risk of hypospadias: population based case-control study.", "abstract": ["Clomifene is widely used for inducing ovulation.1 It is structurally related to diethylstilbestrol, which has been linked to vaginal and cervical clear cell adenocarcinoma in women exposed in utero.", "The adverse effect is less severe in sons, although links to testicular cancer and urogenital anomalies, such as epididymal cysts, have been reported.2 3 A recent study also found an increased risk of hypospadias in the sons of women exposed to diethylstilbestrol in utero.4 Clomifene has a half life of about five days, but its metabolites have been found in blood samples on day 22 of the menstrual cycle and in faeces up to six weeks after administration.5 The occurrence of hypospadias may be increasing.", "Little is known about the risk of hypospadias in boys born to women who have used clomifene to induce ovulation.  ", "### Methods and results  Our case-control study was done in the Danish counties of North Jutland, Aarhus, Viborg, and \u2026"], "structured": false}
{"doc_id": 43334921, "title": "Association of aspirin and NSAID use with risk of colorectal cancer according to genetic variants.", "abstract": ["IMPORTANCE Use of aspirin and other nonsteroidal anti-inflammatory drugs (NSAIDs) is associated with lower risk of colorectal cancer.   \n", "OBJECTIVE To identify common genetic markers that may confer differential benefit from aspirin or NSAID chemoprevention, we tested gene \u00d7 environment interactions between regular use of aspirin and/or NSAIDs and single-nucleotide polymorphisms (SNPs) in relation to risk of colorectal cancer.   \n", "DESIGN, SETTING, AND PARTICIPANTS Case-control study using data from 5 case-control and 5 cohort studies initiated between 1976 and 2003 across the United States, Canada, Australia, and Germany and including colorectal cancer cases (n=8634) and matched controls (n=8553) ascertained between 1976 and 2011.", "Participants were all of European descent.   ", "EXPOSURES Genome-wide SNP data and information on regular use of aspirin and/or NSAIDs and other risk factors.   \n", "MAIN OUTCOMES AND MEASURES Colorectal cancer.   \n", "RESULTS Regular use of aspirin and/or NSAIDs was associated with lower risk of colorectal cancer (prevalence, 28% vs 38%; odds ratio [OR], 0.69 [95% CI, 0.64-0.74]; P = 6.2 \u00d7 10(-28)) compared with nonregular use.", "In the conventional logistic regression analysis, the SNP rs2965667 at chromosome 12p12.3 near the MGST1 gene showed a genome-wide significant interaction with aspirin and/or NSAID use (P = 4.6 \u00d7 10(-9) for interaction).", "Aspirin and/or NSAID use was associated with a lower risk of colorectal cancer among individuals with rs2965667-TT genotype (prevalence, 28% vs 38%; OR, 0.66 [95% CI, 0.61-0.70]; P = 7.7 \u00d7 10(-33)) but with a higher risk among those with rare (4%) TA or AA genotypes (prevalence, 35% vs 29%; OR, 1.89 [95% CI, 1.27-2.81]; P = .002).", "In case-only interaction analysis, the SNP rs16973225 at chromosome 15q25.2 near the IL16 gene showed a genome-wide significant interaction with use of aspirin and/or NSAIDs (P = 8.2 \u00d7 10(-9) for interaction).", "Regular use was associated with a lower risk of colorectal cancer among individuals with rs16973225-AA genotype (prevalence, 28% vs 38%; OR, 0.66 [95% CI, 0.62-0.71]; P = 1.9 \u00d7 10(-30)) but was not associated with risk of colorectal cancer among those with less common (9%) AC or CC genotypes (prevalence, 36% vs 39%; OR, 0.97 [95% CI, 0.78-1.20]; P = .76).   \n", "CONCLUSIONS AND RELEVANCE In this genome-wide investigation of gene \u00d7 environment interactions, use of aspirin and/or NSAIDs was associated with lower risk of colorectal cancer, and this association differed according to genetic variation at 2 SNPs at chromosomes 12 and 15.", "Validation of these findings in additional populations may facilitate targeted colorectal cancer prevention strategies."], "structured": true}
{"doc_id": 43378932, "title": "Intravaginal ring eluting tenofovir disoproxil fumarate completely protects macaques from multiple vaginal simian-HIV challenges.", "abstract": ["Topical preexposure prophylaxis interrupts HIV transmission at the site of mucosal exposure.", "Intermittently dosed vaginal gels containing the HIV-1 reverse transcriptase inhibitor tenofovir protected pigtailed macaques depending on the timing of viral challenge relative to gel application.", "However, modest or no protection was observed in clinical trials.", "Intravaginal rings (IVRs) may improve efficacy by providing long-term sustained drug delivery leading to constant mucosal antiretroviral concentrations and enhancing adherence.", "Although a few IVRs have entered the clinical pipeline, 100% efficacy in a repeated macaque vaginal challenge model has not been achieved.", "Here we describe a reservoir IVR technology that delivers the tenofovir prodrug tenofovir disoproxil fumarate (TDF) continuously over 28 d. With four monthly ring changes in this repeated challenge model, TDF IVRs generated reproducible and protective drug levels.", "All TDF IVR-treated macaques (n = 6) remained seronegative and simian-HIV RNA negative after 16 weekly vaginal exposures to 50 tissue culture infectious dose SHIV162p3.", "In contrast, 11/12 control macaques became infected, with a median of four exposures assuming an eclipse of 7 d from infection to virus RNA detection.", "Protection was associated with tenofovir levels in vaginal fluid [mean 1.8 \u00d7 10(5) ng/mL (range 1.1 \u00d7 10(4) to 6.6 \u00d7 10(5) ng/mL)] and ex vivo antiviral activity of cervicovaginal lavage samples.", "These observations support further advancement of TDF IVRs as well as the concept that extended duration drug delivery devices delivering topical antiretrovirals could be effective tools in preventing the sexual transmission of HIV in humans."], "structured": false}
{"doc_id": 43385013, "title": "Epithelial and mesenchymal subpopulations within normal basal breast cell lines exhibit distinct stem cell/progenitor properties.", "abstract": ["It has been proposed that epithelial-mesenchymal transition (EMT) in mammary epithelial cells and breast cancer cells generates stem cell features, and that the presence of EMT characteristics in claudin-low breast tumors reveals their origin in basal stem cells.", "It remains to be determined, however, whether EMT is an inherent property of normal basal stem cells, and if the presence of a mesenchymal-like phenotype is required for the maintenance of all their stem cell properties.", "We used nontumorigenic basal cell lines as models of normal stem cells/progenitors and demonstrate that these cell lines contain an epithelial subpopulation (\"EpCAM+,\" epithelial cell adhesion molecule positive [EpCAM(pos)]/CD49f(high)) that spontaneously generates mesenchymal-like cells (\"Fibros,\" EpCAM(neg)/CD49f(med/low)) through EMT.", "Importantly, stem cell/progenitor properties such as regenerative potential, high aldehyde dehydrogenase 1 activity, and formation of three-dimensional acini-like structures predominantly reside within EpCAM+ cells, while Fibros exhibit invasive behavior and mammosphere-forming ability.", "A gene expression profiling meta-analysis established that EpCAM+ cells show a luminal progenitor-like expression pattern, while Fibros most closely resemble stromal fibroblasts but not stem cells.", "Moreover, Fibros exhibit partial myoepithelial traits and strong similarities with claudin-low breast cancer cells.", "Finally, we demonstrate that Slug and Zeb1 EMT-inducers control the progenitor and mesenchymal-like phenotype in EpCAM+ cells and Fibros, respectively, by inhibiting luminal differentiation.", "In conclusion, nontumorigenic basal cell lines have intrinsic capacity for EMT, but a mesenchymal-like phenotype does not correlate with the acquisition of global stem cell/progenitor features.", "Based on our findings, we propose that EMT in normal basal cells and claudin-low breast cancers reflects aberrant/incomplete myoepithelial differentiation."], "structured": false}
{"doc_id": 43390777, "title": "Involvement of members of the Rab family and related small GTPases in autophagosome formation and maturation", "abstract": ["Macroautophagy, the process by which cytosolic components and organelles are engulfed and degraded by a double-membrane structure, could be viewed as a specialized, multistep membrane transport process.", "As such, it intersects with the exocytic and endocytic membrane trafficking pathways.", "A number of Rab GTPases which regulate secretory and endocytic membrane traffic have been shown to play either critical or accessory roles in autophagy.", "The biogenesis of the pre-autophagosomal isolation membrane (or phagophore) is dependent on the functionality of Rab1.", "A non-canonical, Atg5/Atg7-independent mode of autophagosome generation from the trans-Golgi or endosome requires Rab9.", "Other Rabs, such as Rab5, Rab24, Rab33, and Rab7 have all been shown to be required, or involved at various stages of autophagosomal genesis and maturation.", "Another small GTPase, RalB, was very recently demonstrated to induce isolation membrane formation and maturation via its engagement of the exocyst complex, a known Rab effector.", "We summarize here what is now known about the involvement of Rabs in autophagy, and discuss plausible mechanisms with future perspectives."], "structured": false}
{"doc_id": 43417006, "title": "Comparative risk of new-onset diabetes mellitus for antihypertensive drugs: A network meta-analysis.", "abstract": ["New-onset diabetes mellitus (NOD) refers to forms of diabetes mellitus that develop during the therapeutic processes of other diseases such as hypertension.", "This study has been conducted in a network meta-analysis to compare antihypertensive drugs by identifying both the advantages and disadvantages on NOD by focusing on their respective effect rates.", "Odd ratios and corresponding 95% confidence intervals or credible intervals were calculated within pairwise and network meta-analysis.", "A total of 38 articles with 224 140 patients were included to evaluate the preventive effect of hypertension drugs on NOD.", "From the network meta-analysis it was evident that both angiotensin-converting enzyme inhibitor as well as angiotensin receptor blocker treatments are associated with a lower risk of developing NOD compared with placebo, with ranking probabilities of 79.81% and 72.77%, respectively, while \u03b2-blockers and calcium channel blockers may significantly increase the probability of developing NOD (\u03b2-blockers: odds ratio, 2.18 [95% credible intervals: 1.36-3.50]; calcium channel blockers: odds ratio, 1.16 [95% credible intervals, 1.05-1.29]).", "In conclusion, angiotensin receptor blockers have an advantage over the other treatments regarding the NOD."], "structured": false}
{"doc_id": 43419566, "title": "Transformation of mammalian cells by constitutively active MAP kinase kinase.", "abstract": ["Mitogen-activated protein (MAP) kinase kinase (MAPKK) activates MAP kinase in a signal transduction pathway that mediates cellular responses to growth and differentiation factors.", "Oncogenes such as ras, src, raf, and mos have been proposed to transform cells by prolonging the activated state of MAPKK and of components downstream in the signaling pathway.", "To test this hypothesis, constitutively active MAPKK mutants were designed that had basal activities up to 400 times greater than that of the unphosphorylated wild-type kinase.", "Expression of these mutants in mammalian cells activated AP-1-regulated transcription.", "The cells formed transformed foci, grew efficiently in soft agar, and were highly tumorigenic in nude mice.", "These findings indicate that constitutive activation of MAPKK is sufficient to promote cell transformation."], "structured": false}
{"doc_id": 43427621, "title": "Psychological treatment of malignant vasovagal syncope due to bloodphobia.", "abstract": ["A 17-year-old boy with frequent faints due to blood-injury phobia was studied.", "During cardiovascular reflex investigation in our syncope unit, 50 seconds of asystole were recorded.", "He was treated using systematic desensitization with muscular tension and cognitive techniques by the Pediatric Psychosocial Department and has not experienced syncopal events again."], "structured": false}
{"doc_id": 43483151, "title": "QT and QTc dispersion are accurate predictors of cardiac death in newly diagnosed non-insulin dependent diabetes: cohort study.", "abstract": ["Patients with non-insulin dependent diabetes mellitus have an excess risk of dying from cardiovascular disease.", "One small study suggested that a prolonged QT interval could predict cardiac death in patients with diabetic nephropathy who have received insulin treatment.", "The question now is whether the same is true in newly diagnosed diabetes in patients who have no apparent complications.", "In addition, QT dispersion, a new but related electrocardiographic variable, predicts cardiac death in patients who have chronic heart failure, peripheral vascular disease, or essential hypertension.1\u20133 We investigated whether it also predicted cardiac death in diabetic patients.  ", "The study group of 182 patients with non-insulin dependent diabetes mellitus (103 men; mean age 52.8 (SD 8.5) years) represented the Dundee cohort of the United Kingdom prospective diabetes study, which was recruited between 1982 and 1988.", "Patients were followed up for a mean of 10.3 (1.7) years.", "\u2026"], "structured": false}
{"doc_id": 43534665, "title": "Recombinant human IL-10 prevents the onset of diabetes in the nonobese diabetic mouse.", "abstract": ["The role of IL-10 in the pathogenesis of autoimmune diabetes mellitus was assessed in the nonobese diabetic (NOD) mouse.", "In these studies the effect of IL-10 was determined on three parameters of diabetes: The development of hyperglycemia, the development of insulitis, and the production of insulin by beta cells.", "Initial experiments investigated the effect of anticytokine antibodies on the development of disease.", "These results indicated that monoclonal anti-IFN-gamma antibody greatly reduced the incidence of hyperglycemia in female NOD mice, while anti-IL-4, IL-5, and IL-10 were ineffective.", "In subsequent studies, daily subcutaneous administration of IL-10, a known potent inhibitor of IFN-gamma production by TH1 T cells, to 9 and 10-week-old NODs was shown to delay the onset of disease and significantly reduce the incidence of diabetes.", "Histopathology performed on pancreatic tissue demonstrated that treatment with IL-10 reduced the severity of insulitis, prevented cellular infiltration of islet cells, and promoted normal insulin production by beta cells.", "Taken together these results indicate IL-10 suppresses the induction and progression of autoimmune pathogenesis associated with diabetes mellitus and suggest a potential therapeutic role for this cytokine in this autoimmune disease."], "structured": false}
{"doc_id": 43557480, "title": "Arterial hypertension and progression of chronic kidney disease in children during 10-year ambulatory observation.", "abstract": ["The aim of this study was the long-term retrospective analysis of chronic kidney disease (CKD) progression in children, especially with regard to the presence of hypertension (HTN).", "The average rate of progression of CKD was higher in patients with HTN than without HTN.", "Hypertension treatment requires multidrug schemes which need to be intensified with extended time of CKD duration."], "structured": false}
{"doc_id": 43566999, "title": "Exercise blood flow patterns within and among rat muscles after training.", "abstract": ["This study was designed to determine the influence of a long-term, moderate-intensity treadmill training program on the distribution of blood flow within and among muscles of rats during exercise.", "One group (T) of male Sprague-Dawley rats trained for 1 h/day for 13-17 wk at 30 m/min on a motor-driven treadmill.", "A second group (UT) of rats was conditioned for 10 min/day for 4 wk at the same speed.", "Muscle succinate dehydrogenase activities were higher in T than UT rats indicating a significant training effect.", "Blood flows (BFs) in 32 hindlimb muscles or muscle parts and other selected organs were measured in the two groups with radiolabeled microspheres during preexercise and while the rats ran for 30 s, 5 min, or 15 min at 30 m/min on the treadmill.", "The data indicate 1) there were no differences in total hindlimb muscle BF between UT and T rats at any time; however, 2) T rats had higher preexercise heart rates and higher muscle BFs in the deep red extensor muscles, suggesting a greater anticipatory response to the impending exercise; 3) T rats demonstrated more rapid elevations in BF in the red extensor muscles at the commencement of exercise; 4) T rats had higher BFs in red extensor muscles during exercise, whereas UT rats had higher BFs in white muscles; and 5) T rats maintained higher BFs in the visceral organs during exercise.", "These findings demonstrate that exercise training results in changes in the distribution of BF within and among muscles and among organs during exercise.", "Specifically, data indicate the high-oxidative motor units that are primarily recruited in the muscles during the initial stages of moderate treadmill exercise receive higher blood flows in the trained rats; this presumably contributes to increased resistance to fatigue."], "structured": false}
{"doc_id": 43587663, "title": "Serious infections after unrelated donor transplantation in 136 children: impact of stem cell source.", "abstract": ["How the infection risks compare after umbilical cord blood (UCB) and bone marrow (BM) transplantation is not known.", "Therefore, we compared serious infections in the 2 years after pediatric myeloablative unrelated donor transplantation with unmanipulated BM (n = 52), T cell-depleted (TCD) BM (n = 24), or UCB (n = 60) for the treatment of hematologic malignancy.", "Overall, the cumulative incidence of 1 or more serious infections was comparable between groups (BM, 81%; TCD, 83%; UCB, 90%; P = .12).", "Furthermore, by taking all serious infections into account and using multivariate techniques with unmanipulated BM as the reference, there were also no significant differences between groups (TCD relative risk [RR], 1.6; P = .10; UCB RR, 1.0; P = .84).", "Within the time periods days 0 to 42, days 43 to 100, and days 101 to 180, the only difference was a greater risk of viral infections from days 0 to 42 in TCD recipients (RR, 3.5; P = .02).", "Notably, after day 180, TCD recipients had a significantly increased infection risk (RR, 3.1; P = .03), whereas the risk in UCB recipients (RR, 0.5; P = .23) was comparable to that in BM recipients.", "Other factors associated with an increased infection risk in the 2 years after transplantation were age > or = 8 years, graft failure, and severe acute graft-versus-host disease.", "These data suggest that the risk of serious infection after pediatric UCB transplantation is comparable to that with unmanipulated BM."], "structured": false}
{"doc_id": 43602749, "title": "The NBS1\u2013Treacle complex controls ribosomal RNA transcription in response to DNA damage", "abstract": ["Chromosome breakage elicits transient silencing of ribosomal RNA synthesis, but the mechanisms involved remained elusive.", "Here we discover an in trans signalling mechanism that triggers pan-nuclear silencing of rRNA transcription in response to DNA damage.", "This is associated with transient recruitment of the Nijmegen breakage syndrome protein 1 (NBS1), a central regulator of DNA damage responses, into the nucleoli.", "We further identify TCOF1 (also known as Treacle), a nucleolar factor implicated in ribosome biogenesis and mutated in Treacher Collins syndrome, as an interaction partner of NBS1, and demonstrate that NBS1 translocation and accumulation in the nucleoli is Treacle dependent.", "Finally, we provide evidence that Treacle-mediated NBS1 recruitment into the nucleoli regulates rRNA silencing in trans in the presence of distant chromosome breaks."], "structured": false}
{"doc_id": 43619625, "title": "Inflammatory T cells rapidly induce differentiation of human bone marrow stromal cells into mature osteoblasts.", "abstract": ["Activated T cells secrete multiple osteoclastogenic cytokines which play a major role in the bone destruction associated with rheumatoid arthritis.", "While the role of T cells in osteoclastogenesis has received much attention recently, the effect of T cells on osteoblast formation and activity is poorly defined.", "In this study, we investigated the hypothesis that in chronic inflammation activated T cells contribute to enhanced bone turnover by promoting osteoblastic differentiation.", "We show that T cells produce soluble factors that induce alkaline phosphatase activity in bone marrow stromal cells and elevated expression of mRNA for Runx2 and osteocalcin.", "This data indicate that T cell derived factors have the capacity to stimulate the differentiation of bone marrow stromal cells into the osteoblast phenotype.", "RANKL mRNA was undetectable under any conditions in highly purified bone marrow stromal cells.", "In contrast, RANKL was constitutively expressed in primary osteoblasts and only moderately up-regulated by activated T cell conditioned medium.", "Interestingly, both bone marrow stromal cells and osteoblasts expressed mRNA for RANK, which was strongly up-regulated in both cell types by activated T cell conditioned medium.", "Although, mRNA for the RANKL decoy receptor, osteoprotegerin, was also up-regulated by activated T cell conditioned medium, it's inhibitory effects may be mitigated by a simultaneous rise in the osteoprotegerin competitor TNF-related apoptosis-inducing ligand.", "Based on our data we propose that during chronic inflammation, T cells regulate bone loss by a dual mechanism involving both direct stimulation of osteoclastogenesis, by production of osteoclastogenic cytokines, and indirectly by induction of osteoblast differentiation and up-regulation of bone turnover via coupling."], "structured": false}
{"doc_id": 43629704, "title": "Prevention of coronary heart disease with pravastatin in men with hypercholesterolemia. West of Scotland Coronary Prevention Study Group.", "abstract": ["BACKGROUND Lowering the blood cholesterol level may reduce the risk of coronary heart disease.", "This double-blind study was designed to determine whether the administration of pravastatin to men with hypercholesterolemia and no history of myocardial infarction reduced the combined incidence of nonfatal myocardial infarction and death from coronary heart disease.   \n", "METHODS We randomly assigned 6595 men, 45 to 64 years of age, with a mean (+/-", "SD) plasma cholesterol level of 272 +/-", "23 mg per deciliter (7.0 +/- 0.6 mmol per liter) to receive pravastatin (40 mg each evening) or placebo.", "The average follow-up period was 4.9 years.", "Medical records, electrocardiographic recordings, and the national death registry were used to determine the clinical end points.   \n", "RESULTS Pravastatin lowered plasma cholesterol levels by 20 percent and low-density-lipoprotein cholesterol levels by 26 percent, whereas there was no change with placebo.", "There were 248 definite coronary events (specified as nonfatal myocardial infarction or death from coronary heart disease) in the placebo group, and 174 in the pravastatin group (relative reduction in risk with pravastatin, 31 percent; 95 percent confidence interval, 17 to 43 percent; P < 0.001).", "There were similar reductions in the risk of definite nonfatal myocardial infarctions (31 percent reduction, P < 0.001), death from coronary heart disease (definite cases alone: 28 percent reduction, P = 0.13; definite plus suspected cases: 33 percent reduction, P = 0.042), and death from all cardiovascular causes (32 percent reduction, P = 0.033).", "There was no excess of deaths from noncardiovascular causes in the pravastatin group.", "We observed a 22 percent reduction in the risk of death from any cause in the pravastatin group (95 percent confidence interval, 0 to 40 percent; P = 0.051).   \n", "CONCLUSIONS Treatment with pravastatin significantly reduced the incidence of myocardial infarction and death from cardiovascular causes without adversely affecting the risk of death from noncardiovascular causes in men with moderate hypercholesterolemia and no history of myocardial infarction."], "structured": true}
{"doc_id": 43647194, "title": "Validation of a migraine-specific questionnaire for use in family studies.", "abstract": ["The availability of valid migraine-specific questionnaires is important when large numbers of migraine patients have to be analysed.", "The Finnish Migraine-Specific Questionnaire has been validated in two stages.", "In the first, a clinical diagnosis of migraine was reached, using International Headache Society criteria, in 100 consecutive patients.", "Migraine was then diagnosed independently on the basis of responses to the Finnish Migraine-Specific Questionnaire.", "In the second stage, responses to 100 questionnaires returned consecutively in a family study in progress were analysed, and respondents were contacted by telephone for interview and diagnosis of migraine.", "Contact proved impossible in six cases.", "The sensitivity of the questionnaire for migraine was 0.99 (167 out of 168; validation stages 1 and 2 combined) and specificity was 0.96 (25 out of 26 cases; validation stage 2).", "It also proved possible to differentiate between migraine with and without aura on the basis of responses to the Finnish Migraine-Specific Questionnaire: chance-corrected agreement (Cohen's kappa) was 0.804 in relation to diagnoses reached on the basis of responses to the Finnish Migraine-Specific Questionnaire and clinically was 0.858 in relation to diagnoses reached on the basis of responses to the Finnish Migraine-Specific Questionnaire combined with the results of the telephone interviews.", "A value for Cohen's kappa > 0.75 indicates good agreement.", "Therefore, use of the Finnish Migraine-Specific Questionnaire in research into migraine genetics is justified."], "structured": false}
{"doc_id": 43661837, "title": "Defining early lineage specification of human embryonic stem cells by the orchestrated balance of canonical Wnt/beta-catenin, Activin/Nodal and BMP signaling.", "abstract": ["The canonical Wnt/beta-catenin signaling has remarkably diverse roles in embryonic development, stem cell self-renewal and cancer progression.", "Here, we show that stabilized expression of beta-catenin perturbed human embryonic stem (hES)-cell self-renewal, such that up to 80% of the hES cells developed into the primitive streak (PS)/mesoderm progenitors, reminiscent of early mammalian embryogenesis.", "The formation of the PS/mesoderm progenitors essentially depended on the cooperative action of beta-catenin together with Activin/Nodal and BMP signaling pathways.", "Intriguingly, blockade of BMP signaling completely abolished mesoderm generation, and induced a cell fate change towards the anterior PS progenitors.", "The PI3-kinase/Akt, but not MAPK, signaling pathway had a crucial role in the anterior PS specification, at least in part, by enhancing beta-catenin stability.", "In addition, Activin/Nodal and Wnt/beta-catenin signaling synergistically induced the generation and specification of the anterior PS/endoderm.", "Taken together, our findings clearly demonstrate that the orchestrated balance of Activin/Nodal and BMP signaling defines the cell fate of the nascent PS induced by canonical Wnt/beta-catenin signaling in hES cells."], "structured": false}
{"doc_id": 43700577, "title": "Sphingosine can pre- and post-condition heart and utilizes a different mechanism from sphingosine 1-phosphate.", "abstract": ["Consistent with previous reports, sphingosine at a high concentration (5 microM) was cardiotoxic as evidenced by increased infarct size in response to ischemia/reperfusion in an ex vivo rat heart.", "Sphingosine 1-phosphate (S1P) at 5 microM was cardioprotective.", "However, at a physiologic concentration (0.4 microM) sphingosine as well as S1P was effective in protecting the heart from ischemia/reperfusion injury both when perfused prior to 40 min of ischemia (preconditioning) or when added to reperfusion media following ischemia (postconditioning).", "Protection by sphingosine and S1P was evidenced with both pre- and post-conditioning by a >75% recovery of left ventricular developed pressure during reperfusion and a decrease in infarct size from 45% of the risk area to less than 8%.", "When VPC23019, an S1P(1and3)G-protein coupled receptor antagonist, was added to the preconditioning or postconditioning medium along with S1P, it completely blocked S1P-induced protection.", "However, VPC 23019 did not affect the ability of 0.4 microM sphingosine to either precondition or postcondition hearts.", "Studies of preconditioning revealed that inhibition of protein kinase C with GF109203X blocked preconditioning by S1P.", "However, GF109203X did not affect preconditioning by 0.4 microM sphingosine.", "Likewise, cotreatment with the PI3 kinase inhibitor wortmanin blocked preconditioning by S1P but not by sphingosine.", "By contrast, inhibition of protein kinase G with KT5823 had no effect on S1P preconditioning but completely eliminated preconditioning by sphingosine.", "Also, the protein kinase A inhibitory peptide 14-22 amide blocked preconditioning by sphingosine but not S1P.", "These data reveal for the first time that sphingosine is not toxic at physiologic concentrations but rather is a potent cardioprotectant that utilizes a completely different mechanism than S1P; one that is independent of G-protein coupled receptors and utilizes cyclic nucleotide-dependent pathways."], "structured": false}
{"doc_id": 43711341, "title": "Coordination of p300-mediated chromatin remodeling and TRAP/mediator function through coactivator PGC-1alpha.", "abstract": ["Transcriptional coactivators showing physical and functional interactions with PPARgamma include the protein acetyl transferase p300, the TRAP/Mediator complex that interacts with the general transcription machinery, and the highly regulated PGC-1alpha.", "We show that PGC-1alpha directly interacts with TRAP/Mediator, through the PPARgamma-interacting subunit TRAP220, and stimulates TRAP/Mediator-dependent function on DNA templates.", "Further, while ineffective by itself, PGC-1alpha stimulates p300-dependent histone acetylation and transcription on chromatin templates in response to PPARgamma.", "These functions are mediated by largely independent PPARgamma, p300, and TRAP220 interaction domains in PGC-1alpha, whereas p300 and TRAP220 show ligand-dependent interactions with a common region of PPARgamma.", "Apart from showing PGC-1alpha functions both in chromatin remodeling and in preinitiation complex formation or function (transcription), these results suggest a key role for PGC-1alpha, through concerted but dynamic interactions, in coordinating these steps."], "structured": false}
{"doc_id": 43752562, "title": "Phospholipid synthesis and lipid composition of subcellular membranes in the unicellular eukaryote Saccharomyces cerevisiae.", "abstract": ["Subcellular membranes of Saccharomyces cerevisiae, including mitochondria, microsomes, plasma membranes, secretory vesicles, vacuoles, nuclear membranes, peroxisomes, and lipid particles, were isolated by improved procedures and analyzed for their lipid composition and their capacity to synthesize phospholipids and to catalyze sterol delta 24-methylation.", "The microsomal fraction is heterogeneous in terms of density and classical microsomal marker proteins and also with respect to the distribution of phospholipid-synthesizing enzymes.", "The specific activity of phosphatidylserine synthase was highest in a microsomal subfraction which was distinct from heavier microsomes harboring phosphatidylinositol synthase and the phospholipid N-methyltransferases.", "The exclusive location of phosphatidylserine decarboxylase in mitochondria was confirmed.", "CDO-diacylglycerol synthase activity was found both in mitochondria and in microsomal membranes.", "Highest specific activities of glycerol-3-phosphate acyltransferase and sterol delta 24-methyltransferase were observed in the lipid particle fraction.", "Nuclear and plasma membranes, vacuoles, and peroxisomes contain only marginal activities of the lipid-synthesizing enzymes analyzed.", "The plasma membrane and secretory vesicles are enriched in ergosterol and in phosphatidylserine.", "Lipid particles are characterized by their high content of ergosteryl esters.", "The rigidity of the plasma membrane and of secretory vesicles, determined by measuring fluorescence anisotropy by using trimethylammonium diphenylhexatriene as a probe, can be attributed to the high content of ergosterol."], "structured": false}
{"doc_id": 43855756, "title": "Use of health services by prison inmates: comparisons with the community.", "abstract": ["The future organisation of prison health care 1 recommends that the NHS and the Prison Service work together to plan and provide health care services for prisoners.", "Whereas previously the Prison Service had this responsibility alone.", "The NHS will therefore have to take stock of the current level at which prison health care is demanded and provided.", "A key part of the information base for joint planning therefore includes data on current service utilisation.", "This paper compares primary care and inpatient health service utilisation data for UK prisoners with health services utilisation data for equivalent community populations.  ", "In the community, primary care is provided principally by general practitioners and professions allied to medicine (mostly nurses).", "Residents in the community have access to the full range of NHS outpatient and inpatient facilities.", "Within prisons, primary care is provided by medical officers (some of whom are general practitioners), nursing grades and health care officers (who have received some training in health care).", "Some prisons have their own inpatient facilities (health care centre beds).", "These provide a low level of inpatient care and do not have a direct equivalent in the community.", "Prisoners also have access to NHS outpatient and inpatient facilities and to visiting specialists.  ", "The prison population has a high turnover and varies from day to day.", "Because of this, the prison population is expressed as an average daily population during a one year period.", "\u2026"], "structured": false}
{"doc_id": 43880096, "title": "Regulation of p53 in response to DNA damage", "abstract": ["Activation of p53 can occur in response to a number of cellular stresses, including DNA damage, hypoxia and nucleotide deprivation.", "Several forms of DNA damage have been shown to activate p53, including those generated by ionising radiation (IR), radio-mimetic drugs, ultraviolet light (UV) and chemicals such as methyl methane sulfonate (MMS).", "Under normal conditions, p53 levels are maintained at a low state by virtue of the extremely short-half life of the polypeptide.", "In addition to this, p53 normally exists in an largely inactive state that is relatively inefficient at binding to DNA and activating transcription.", "Activation of p53 in response to DNA damage is associated with a rapid increase in its levels and with an increased ability of p53 to bind DNA and mediate transcriptional activation.", "This then leads to the activation of a number of genes whose products trigger cell-cycle arrest, apoptosis, or DNA repair.", "Recent work has suggested that this regulation is brought about largely through DNA damage triggering a series of phosphorylation, de-phosphorylation and acetylation events on the p53 polypeptide.", "Here, we discuss the nature of these modifications, the enzymes that bring them about, and how changes in p53 modification lead to p53 activation."], "structured": false}
{"doc_id": 43890638, "title": "Hydrogen sulphide regulates intracellular pH in vascular smooth muscle cells.", "abstract": ["We investigated the role of hydrogen sulphide (H(2)S) in intracellular pH (pH(i)) regulation in vascular smooth muscle cells and its contribution on vasodilation.", "NaHS, a H(2)S donor, decreased pH(i) in a concentration-dependent manner ranging from 10 microM to 1mM. Neither inhibition of the Na(+)/H(+) exchanger with 5-(N-ethyl-N-isopropyl) amiloride, (EIPA, 10 microM), nor plasmalemmal Ca(2+)-ATPase with CdCl(2) (20nM) alters the effect of NaHS on pH(i).", "Blockade of the Cl(-)/HCO3- exchanger with 4,4'-diisothiocyanatostilbene-2,2'-disulfonic acid (DIDS) significantly attenuated the pH(i) lowering effect of NaHS.", "Moreover, NaHS significantly increased the activity of Cl(-)/HCO3- exchanger when measured with NH(4)Cl prepulse method.", "DIDS attenuated the vasorelaxation induced by NaHS whereas EIPA and CdCl(2) did not cause any change.", "In conclusion, H(2)S induced intracellular acidification via activation of Cl(-)/HCO3- exchanger, which is, at least partially, responsible for H(2)S-mediated vasorelaxation."], "structured": false}
{"doc_id": 43990286, "title": "Cell and biomolecule delivery for tissue repair and regeneration in the central nervous system.", "abstract": ["Tissue engineering frequently involves cells and scaffolds to replace damaged or diseased tissue.", "It originated, in part, as a means of effecting the delivery of biomolecules such as insulin or neurotrophic factors, given that cells are constitutive producers of such therapeutic agents.", "Thus cell delivery is intrinsic to tissue engineering.", "Controlled release of biomolecules is also an important tool for enabling cell delivery since the biomolecules can enable cell engraftment, modulate inflammatory response or otherwise benefit the behavior of the delivered cells.", "We describe advances in cell and biomolecule delivery for tissue regeneration, with emphasis on the central nervous system (CNS).", "In the first section, the focus is on encapsulated cell therapy.", "In the second section, the focus is on biomolecule delivery in polymeric nano/microspheres and hydrogels for the nerve regeneration and endogenous cell stimulation.", "In the third section, the focus is on combination strategies of neural stem/progenitor cell or mesenchymal stem cell and biomolecule delivery for tissue regeneration and repair.", "In each section, the challenges and potential solutions associated with delivery to the CNS are highlighted."], "structured": false}
{"doc_id": 44030361, "title": "The angiotensin II type 1 receptor blocker olmesartan preferentially improves nocturnal hypertension and proteinuria in chronic kidney disease", "abstract": ["Accumulated evidence suggests that an altered ambulatory blood pressure (BP) profile, particularly elevated nighttime BP, reflects target organ injury and is a better predictor of further cardiorenal risk than the clinic BP or daytime BP in hypertensive patients complicated by chronic kidney disease (CKD).", "In this study, we examined the beneficial effects of olmesartan, an angiotensin II type 1 receptor blocker (ARB), on ambulatory BP profiles and renal function in hypertensive CKD patients.", "Forty-six patients were randomly assigned to the olmesartan add-on group (n=23) or the non-ARB group (n=23).", "At baseline and after the 16-week treatment period, ambulatory BP monitoring was performed and renal function parameter measurements were collected.", "Although the baseline clinic BP levels and the after-treatment/baseline (A/B) ratios of clinic BP levels were similar in the olmesartan add-on and non-ARB groups, the A/B ratios of ambulatory 24-h and nighttime BP levels in the olmesartan add-on group were significantly lower.", "Furthermore, the A/B ratios of urinary protein, albumin and type IV collagen excretion in the olmesartan add-on group were significantly lower than those in the non-ARB group (urinary protein excretion, 0.72\u00b10.41 vs. 1.45\u00b11.48, P=0.030; urinary albumin excretion, 0.73\u00b10.37 vs. 1.50\u00b11.37, P=0.005; urinary type IV collagen excretion, 0.87\u00b10.42 vs. 1.48\u00b10.87, P=0.014) despite comparable A/B ratios for the estimated glomerular filtration rate in the two groups.", "These results indicate that in hypertensive patients with CKD, olmesartan add-on therapy improves the ambulatory BP profile via a preferential reduction in nighttime BP with concomitant renal injury inhibition."], "structured": false}
{"doc_id": 44048701, "title": "Surgical vs nonsurgical treatment of adults with displaced fractures of the proximal humerus: the PROFHER randomized clinical trial.", "abstract": ["IMPORTANCE The need for surgery for the majority of patients with displaced proximal humeral fractures is unclear, but its use is increasing.   \n", "OBJECTIVE To evaluate the clinical effectiveness of surgical vs nonsurgical treatment for adults with displaced fractures of the proximal humerus involving the surgical neck.   \n", "DESIGN, SETTING, AND PARTICIPANTS A pragmatic, multicenter, parallel-group, randomized clinical trial, the Proximal Fracture of the Humerus Evaluation by Randomization (PROFHER) trial, recruited 250 patients aged 16 years or older (mean age, 66 years [range, 24-92 years]; 192 [77%] were female; and 249 [99.6%] were white) who presented at the orthopedic departments of 32 acute UK National Health Service hospitals between September 2008 and April 2011 within 3 weeks after sustaining a displaced fracture of the proximal humerus involving the surgical neck.", "Patients were followed up for 2 years (up to April 2013) and 215 had complete follow-up data.", "The data for 231 patients (114 in surgical group and 117 in nonsurgical group) were included in the primary analysis.   \n", "INTERVENTIONS Fracture fixation or humeral head replacement were performed by surgeons experienced in these techniques.", "Nonsurgical treatment was sling immobilization.", "Standardized outpatient and community-based rehabilitation was provided to both groups.   \n", "MAIN OUTCOMES AND MEASURES Primary outcome was the Oxford Shoulder Score (range, 0-48; higher scores indicate better outcomes) assessed during a 2-year period, with assessment and data collection at 6, 12, and 24 months.", "Sample size was based on a minimal clinically important difference of 5 points for the Oxford Shoulder Score.", "Secondary outcomes were the Short-Form 12 (SF-12), complications, subsequent therapy, and mortality.   \n", "RESULTS There was no significant mean treatment group difference in the Oxford Shoulder Score averaged over 2 years (39.07 points for the surgical group vs 38.32 points for the nonsurgical group; difference of 0.75 points [95% CI, -1.33 to 2.84 points]; P = .48) or at individual time points.", "There were also no significant between-group differences over 2 years in the mean SF-12 physical component score (surgical group: 1.77 points higher [95% CI, -0.84 to 4.39 points];", "P = .18); the mean SF-12 mental component score (surgical group: 1.28 points lower [95% CI, -3.80 to 1.23 points]; P = .32); complications related to surgery or shoulder fracture (30 patients in surgical group vs 23 patients in nonsurgical group; P = .28), requiring secondary surgery to the shoulder (11 patients in both groups), and increased or new shoulder-related therapy (7 patients vs 4 patients, respectively; P = .58); and mortality (9 patients vs 5 patients; P = .27).", "Ten medical complications (2 cardiovascular events, 2 respiratory events, 2 gastrointestinal events, and 4 others) occurred in the surgical group during the postoperative hospital stay.   \n", "CONCLUSIONS AND RELEVANCE Among patients with displaced proximal humeral fractures involving the surgical neck, there was no significant difference between surgical treatment compared with nonsurgical treatment in patient-reported clinical outcomes over 2 years following fracture occurrence.", "These results do not support the trend of increased surgery for patients with displaced fractures of the proximal humerus.   \n", "TRIAL REGISTRATION isrctn.com Identifier: ISRCTN50850043."], "structured": true}
{"doc_id": 44172171, "title": "Kinetics and Fidelity of the Repair of Cas9-Induced Double-Strand DNA Breaks", "abstract": ["The RNA-guided DNA endonuclease Cas9 is a powerful tool for genome editing.", "Little is known about the kinetics and fidelity of the double-strand break (DSB) repair process that follows a Cas9 cutting event in living cells.", "Here, we developed a strategy to measure the kinetics of DSB repair for single loci in human cells.", "Quantitative modeling of repaired DNA in time series after Cas9 activation reveals variable and often slow repair rates, with half-life times up to \u223c10 hr.", "Furthermore, repair of the DSBs tends to be error prone.", "Both classical and microhomology-mediated end joining pathways contribute to the erroneous repair.", "Estimation of their individual rate constants indicates that the balance between these two pathways changes over time and can be altered by additional ionizing radiation.", "Our approach provides quantitative insights into DSB repair kinetics and fidelity in single loci and indicates that Cas9-induced DSBs are repaired in an unusual manner."], "structured": false}
{"doc_id": 44264297, "title": "Network meta-analysis for indirect treatment comparisons.", "abstract": ["I present methods for assessing the relative effectiveness of two treatments when they have not been compared directly in a randomized trial but have each been compared to other treatments.", "These network meta-analysis techniques allow estimation of both heterogeneity in the effect of any given treatment and inconsistency ('incoherence') in the evidence from different pairs of treatments.", "A simple estimation procedure using linear mixed models is given and used in a meta-analysis of treatments for acute myocardial infarction."], "structured": false}
{"doc_id": 44265107, "title": "Liver transplantation and opioid dependence.", "abstract": ["ContextChronic hepatitis C is the leading cause for liver transplantation in the United States.", "Intravenous drug use, the major risk factor, accounts for approximately 60% of hepatitis C virus transmission.", "Information from the United Network of Organ Sharing (UNOS) does not address substance use among liver transplantation patients.", "ObjectiveTo identify addiction-related criteria for admission to the UNOS liver transplantation waiting list and posttransplantation problems experienced by patients who are prescribed maintenance methadone.", "Design, Setting, and ParticipantsMail survey of all 97 adult US liver transplantation programs (belonging to UNOS) in March 2000 with telephone follow-up conducted in May and June 2000.Main Outcome MeasuresPrograms' acceptance and management of patients with past or present substance use disorder.", "ResultsOf the 97 programs surveyed, 87 (90%) responded.", "All accept applicants with a history of alcoholism or other addictions, including heroin dependence.", "Eighty-eight percent of the responding programs require at least 6 months of abstinence from alcohol; 83% from illicit drugs.", "Ninety-four percent have addiction treatment requirements.", "Consultations from substance abuse specialists are obtained by 86%.", "Patients receiving methadone maintenance are accepted by 56% of the responding programs.", "Approximately 180 patients receiving methadone maintenance are reported to have undergone liver transplantation.", "ConclusionsMost liver transplantation programs have established policies for patients with substance use disorders.", "Opiate-dependent patients receiving opiate replacement therapy seem underrepresented in transplantation programs.", "Little anecdotal evidence for negative impact of opiate replacement therapy on liver transplantation outcome was found.", "Policies requiring discontinuation of methadone in 32% of all programs contradict the evidence base for efficacy of long-term replacement therapies and potentially result in relapse of previously stable patients."], "structured": false}
{"doc_id": 44366096, "title": "RIG-I-mediated antiviral responses to single-stranded RNA bearing 5'-phosphates.", "abstract": ["Double-stranded RNA (dsRNA) produced during viral replication is believed to be the critical trigger for activation of antiviral immunity mediated by the RNA helicase enzymes retinoic acid-inducible gene I (RIG-I) and melanoma differentiation-associated gene 5 (MDA5).", "We showed that influenza A virus infection does not generate dsRNA and that RIG-I is activated by viral genomic single-stranded RNA (ssRNA) bearing 5'-phosphates.", "This is blocked by the influenza protein nonstructured protein 1 (NS1), which is found in a complex with RIG-I in infected cells.", "These results identify RIG-I as a ssRNA sensor and potential target of viral immune evasion and suggest that its ability to sense 5'-phosphorylated RNA evolved in the innate immune system as a means of discriminating between self and nonself."], "structured": false}
{"doc_id": 44384384, "title": "In-hospital switching between adenosine diphosphate receptor inhibitors in patients with acute myocardial infarction treated with percutaneous coronary intervention: Insights into contemporary practice from the TRANSLATE-ACS study.", "abstract": ["AIMS While randomized clinical trials have compared clopidogrel with higher potency adenosine diphosphate (ADP) receptor inhibitors among patients with acute myocardial infarction, little is known about the frequency, effectiveness and safety of switching between ADP receptor inhibitors in routine clinical practice.   \n", "METHODS AND RESULTS We studied 11,999 myocardial infarction patients treated with percutaneous coronary intervention at 230 hospitals from April 2010 to October 2012 in the TRANSLATE-ACS study.", "Multivariable Cox regression was used to compare six-month post-discharge risks of major adverse cardiovascular events (MACE: death, myocardial infarction, stroke, or unplanned revascularization) and Global Utilization of Streptokinase and t-PA for Occluded Coronary Arteries (GUSTO)-defined bleeding between in-hospital ADP receptor inhibitor switching versus continuation of the initially selected therapy.", "Among 8715 patients treated initially with clopidogrel, 994 (11.4%) were switched to prasugrel or ticagrelor; switching occurred primarily after percutaneous coronary intervention (60.9%) and at the time of hospital discharge (26.7%).", "Among 3284 patients treated initially with prasugrel or ticagrelor, 448 (13.6%) were switched to clopidogrel; 48.2% of switches occurred after percutaneous coronary intervention and 48.0% at hospital discharge.", "Switching to prasugrel or ticagrelor was not associated with increased bleeding when compared with continuation on clopidogrel (2.7% vs. 3.3%, adjusted hazard ratio 0.96, 95% confidence interval 0.64-1.42, p=0.82).", "Switching from prasugrel or ticagrelor to clopidogrel was not associated with increased MACE (8.9% vs. 7.7%, adjusted hazard ratio 1.06, 95% confidence interval 0.75-1.49, p=0.76) when compared with continuation on the higher potency agent.   \n", "CONCLUSIONS In-hospital ADP receptor inhibitor switching occurs in more than one in 10 myocardial infarction patients in contemporary practice.", "In this observational study, ADP receptor inhibitor switching does not appear to be significantly associated with increased hazard of MACE or bleeding."], "structured": true}
{"doc_id": 44387884, "title": "Platelet activation in type 2 diabetes mellitus.", "abstract": ["The abnormal metabolic state that accompanies diabetes renders arteries susceptible to atherosclerosis, being capable of altering the functional properties of multiple cell types, including endothelium and platelets.", "In particular, an altered platelet metabolism and changes in intraplatelet signaling pathways may contribute to the pathogenesis of atherothrombotic complications of diabetes.", "A variety of mechanisms may be responsible for enhanced platelet aggregation.", "Among them, hyperglycemia may represent a causal factor for in vivo platelet activation, and may be responsible for nonenzymatic glycation of platelet glycoproteins, causing changes in their structure and conformation, as well as alterations of membrane lipid dynamics.", "Furthermore, hyperglycemia-induced oxidative stress is responsible for enhanced peroxidation of arachidonic acid to form biologically active isoprostanes, which represents an important biochemical link between impaired glycemic control and persistent platelet activation.", "Finally, increased oxidative stress is responsible for activation of transcription factors and expression of redox-sensitive genes leading to a phenotypic switch of endothelium toward an adhesive, pro-thrombotic condition, initial platelet activation, adhesion and subsequent platelet aggregate formation.", "All this evidence is strengthened by the results of clinical trials documenting the beneficial effects of metabolic control on platelet function, and by the finding that aspirin treatment may even be more beneficial in diabetic than in high-risk non-diabetic patients.", "Attention to appropriate medical management of diabetic patients will have great impact on long-term outcome in this high-risk population."], "structured": false}
{"doc_id": 44408494, "title": "Nicotinic receptor-mediated neuroprotection in neurodegenerative disease models.", "abstract": ["Multiple lines of evidence, from molecular and cellular to epidemiological, have implicated nicotinic transmission in the pathology of Alzheimer's disease (AD) and Parkinson's disease (PD).", "This review article presents evidence for nicotinic acetylcholine receptor (nAChR)-mediated protection and the signal transduction involved in this mechanism.", "The data is based mainly on our studies using rat-cultured primary neurons.", "Nicotine-induced protection was blocked by an alpha7 nAChR antagonist, a phosphatidylinositol 3-kinase (PI3K) inhibitor, and an Src inhibitor.", "Levels of phosphorylated Akt, an effector of PI3K, Bcl-2 and Bcl-x were increased by nicotine administration.", "From these experimental data, our hypothesis for the mechanism of nAChR-mediated survival signal transduction is that the alpha7 nAChR stimulates the Src family, which activates PI3K to phosphorylate Akt, which subsequently transmits the signal to up-regulate Bcl-2 and Bcl-x.", "Up-regulation of Bcl-2 and Bcl-x could prevent cells from neuronal death induced by beta-amyloid (Abeta), glutamate and rotenone.", "These findings suggest that protective therapy with nAChR stimulation could delay the progress of neurodegenerative diseases such as AD and PD."], "structured": false}
{"doc_id": 44409062, "title": "High-throughput parallel proteogenomics: a bacterial case study.", "abstract": ["In recent years, a new paradigm for genome annotation has emerged, termed \"proteogenomics,\" that leverages peptide MS to annotate a genome.", "This is achieved by mapping peptides to a six-frame translation of a genome, including available splice databases, which may suggest refinements to gene models.", "Using this approach, it is possible to refine gene regions such as exon boundaries, novel genes, gene boundaries, frame shifts, reverse strands, translated UTRs, and novel splice junctions.", "One of the challenges of proteogenomics is how best to (1) tackle assigning confidence to any resulting annotation and (2) apply these gene model refinements, either through manual annotation or through an automated process via training gene prediction tools.", "This is not a straightforward process, as many gene prediction tools have their defined suitability for niche genomes (either eukaryotic or prokaryotic) trained on and refined with model organisms such as Arabidopsis thaliana and Escherichia coli, and varying degrees of features that can leverage the use of external evidence.", "In this study, we outline a suitable approach toward preprocessing mass spectra and optimizing the MS/MS search for a given dataset.", "We also discuss future challenges, which continue to pose a problem in the field of proteogenomics, and better strategies to successfully tackle them with, using existing tools.", "We use Bradyrhizobium diazoefficiens (Nitrogen-fixing bacteria), with a 9.1 Mb genome as a case study, utilizing the latest in second-generation proteogenomics tools with multiple gene models for cross-validation of proteogenomics annotations."], "structured": false}
{"doc_id": 44420873, "title": "Keratinocyte-specific transglutaminase of cultured human epidermal cells: relation to cross-linked envelope formation and terminal differentiation.", "abstract": ["The predominant form of the cross-linking enzyme, transglutaminase, in cultured normal human epidermal keratinocytes, is found in cell particulate material and can be solubilized by nonionic detergent.", "It elutes as a single peak upon either anion-exchange or gel-filtration chromatography.", "Monoclonal antibodies raised to the particulate enzyme cross-react with one of two transglutaminases in the cell cytosol.", "The second cytosolic transglutaminase, which has distinct kinetic and physical properties from the first, does not cross-react and is not essential for formation of the keratinocyte cross-linked envelope in vitro.", "The anti-transglutaminase antibodies stain the more differentiated layers of epidermis in a pattern similar to that given by anti-involucrin antiserum.", "These observations support the hypothesis that the transglutaminase so identified is involved in cross-linked envelope formation in vivo."], "structured": false}
{"doc_id": 44500794, "title": "The effects of genetic and pharmacological blockade of the CB1 cannabinoid receptor on anxiety.", "abstract": ["The aim of this study was to compare the effects of the genetic and pharmacological disruption of CB1 cannabinoid receptors on the elevated plus-maze test of anxiety.", "In the first experiment, the behaviour of CB1-knockout mice and wild-type mice was compared.", "In the second experiment, the cannabinoid antagonist SR141716A (0, 1, and 3 mg/kg) was administered to both CB1-knockout and wild type mice.", "Untreated CB1-knockout mice showed a reduced exploration of the open arms of the plus-maze apparatus, thus appearing more anxious than the wild-type animals, however no changes in locomotion were noticed.", "The vehicle-injected CB1-knockout mice from the second experiment also showed increased anxiety as compared with wild types.", "Surprisingly, the cannabinoid antagonist SR141716A reduced anxiety in both wild type and CB1 knockout mice.", "Locomotor behaviour was only marginally affected.", "Recent evidence suggests the existence of a novel cannabinoid receptor in the brain.", "It has also been shown that SR141716A binds to both the CB1 and the putative novel receptor.", "The data presented here supports these findings, as the cannabinoid receptor antagonist affected anxiety in both wild type and CB1-knockout mice.", "Tentatively, it may be suggested that the discrepancy between the effects of the genetic and pharmacological blockade of the CB1 receptor suggests that the novel receptor plays a role in anxiety."], "structured": false}
{"doc_id": 44562058, "title": "Immune activation and HIV persistence: implications for curative approaches to HIV infection.", "abstract": ["Despite complete or near-complete suppression of human immunodeficiency virus (HIV) replication with combination antiretroviral therapy, both HIV and chronic inflammation/immune dysfunction persist indefinitely.", "Untangling the association between the virus and the host immune environment during therapy might lead to novel interventions aimed at either curing the infection or preventing the development of inflammation-associated end-organ disease.", "Chronic inflammation and immune dysfunction might lead to HIV persistence by causing virus production, generating new target cells, enabling infecting of activated and resting target cells, altering the migration patterns of susceptible target cells, increasing the proliferation of infected cells, and preventing normal HIV-specific clearance mechanisms from function.", "Chronic HIV production or replication might contribute to persistent inflammation and immune dysfunction.", "The rapidly evolving data on these issues strongly suggest that a vicious cycle might exist in which HIV persistence causes inflammation that in turn contributes to HIV persistence."], "structured": false}
{"doc_id": 44562221, "title": "Tissue-specific alterations in the glucocorticoid sensitivity of immune cells following repeated social defeat in mice", "abstract": ["Endogenous glucocorticoids (GC) play an important role in the termination of the inflammatory response following infection and tissue injury.", "However, recent findings indicate that stress can impair the anti-inflammatory capacities of these hormones.", "Lipopolysaccharide (LPS)-stimulated splenocytes of mice that were repeatedly subjected to social disruption (SDR) stress were less sensitive to the immunosuppressive effects of corticosterone (CORT) as demonstrated by an increased production of pro-inflammatory cytokines and enhanced cell survival.", "Myeloid cells expressing the marker CD11b were shown to play a key role in this process.", "Here we investigated the role of the bone marrow as a potential source of the GC-insensitive cells.", "The study revealed that LPS-stimulated bone marrow cells, in the absence of experimental stress, were virtually GC-resistant and retained high levels of cell viability after treatment with CORT.", "Recurrent exposure to the acute stressor over a period of 2, 4 or 6 days led to an increase in the GC sensitivity of the bone marrow cells.", "This increase in GC sensitivity was associated with enhanced mRNA expression of granulocyte-macrophage colony-stimulating factor (GM-CSF), an increase in the number of myeloid progenitors, and a decrease in the proportion of mature CD11b+ cells.", "The changes in the cellular composition of the bone marrow were accompanied by an increase in splenic CD11b+ cell numbers.", "Simultaneous assessment of the GC sensitivity in bone marrow and spleen revealed a significant negative correlation between both tissues suggesting that social stress causes the redistribution of GC-insensitive myeloid cells from the bone marrow to the spleen."], "structured": false}
{"doc_id": 44562904, "title": "Delays in the diagnosis of lung cancer.", "abstract": ["BACKGROUND Many patients with lung cancer report delays in diagnosing their disease.", "This may contribute to advanced stage at diagnosis and poor long term survival.", "This study explores the delays experienced by patients referred to a regional cancer centre with lung cancer.   \n", "METHODS A prospective cohort of patients referred with newly diagnosed lung cancer were surveyed over a 3 month period to assess delays in diagnosis.", "Patients were asked when they first experienced symptoms, saw their doctor, what tests were done, when they saw a specialist and when they started treatment.", "Descriptive statistics were used to summarize the different time intervals.   \n", "RESULTS 56 of 73 patients consented (RR 77%).", "However only 52 patients (30M, 22F) were interviewed as 2 died before being interviewed and two could not be contacted.", "The mean age was 68yrs.", "Stage distribution was as follows (IB/IIA 10%, stage IIIA 20%, IIIB/IV 70%).", "Patients waited a median of 21 days (iqr 7-51d) before seeing a doctor and a further 22d (iqr 0-38d) to complete any investigations.", "The median time from presentation to specialist referral was 27d (iqr 12-49d) and a further 23.5d (iqr 10-56d) to complete investigations.", "The median wait to start treatment once patients were seen at the cancer centre was 10d (iqr 2-28d).", "The overall time from development of first symptoms to starting treatment was 138d (iqr 79-175d).   \n", "CONCLUSIONS Lung cancer patients experience substantial delays from development of symptoms to first initiating treatment.", "There is a need to promote awareness of lung cancer symptoms and develop and evaluate rapid assessment clinics for patients with suspected lung cancers."], "structured": true}
{"doc_id": 44572913, "title": "Calcium and peak bone mass.", "abstract": ["On the basis of previous epidemiological, clinical and experimental studies, it was demonstrated that adequate calcium intake during growth may influence peak bone mass/density, and may be instrumental in preventing subsequent postmenopausal and senile osteoporosis.", "Calcium intake during adolescence appears to affect skeletal calcium retention directly, and a calcium intake of up to 1600 mg d-1 may be required.", "Therefore, adolescent females at the time of puberty probably represent the optimal population for early prevention of osteoporosis with calcium.", "Young individuals must be in positive calcium balance to provide the calcium necessary for skeletal modelling and consolidation, but the degree of positive balance required to achieve peak bone mass and density is unknown.", "To assess calcium requirements in young individuals, and also to evaluate the determinants of calcium metabolism during the period of acquisition of peak bone mass, 487 calcium balances from previously published reports have been collected and analysed according to developmental phase and calcium intake.", "The results of this analysis showed that calcium intake and skeletal modelling/turnover are the most important determinants of calcium balance during growth.", "The highest requirements for calcium are during infancy and adolescence, and then during childhood and young adulthood.", "Infants (adequate vitamin D supply) and adolescents have higher calcium absorption than children and young adults to meet their high calcium requirements.", "Calcium absorption during the periods of rapid bone modelling/turnover is probably mediated by Nicolaysen's endogenous factor.", "Urinary calcium increases with age, and reaches a maximum by the end of puberty.", "The results also show that calcium intake has little effect on urinary calcium excretion during the period of most rapid skeletal formation: a weak correlation is present in children and young adults.", "On the basis of the above studies it was suggested that the RDA for calcium should be higher than currently established for children, adolescents, and young adults, in order to ensure a level of skeletal retention of calcium sufficient for maximal peak bone mass.", "In addition to nutrition, heredity (both parents) and endocrine factors (sexual development) appear to have profound effects on peak bone mass formation.", "Most of the skeletal mass will be accumulated by late adolescence, indicating early timing of peak bone mass."], "structured": false}
{"doc_id": 44586415, "title": "Most clinical tests cannot accurately diagnose rotator cuff pathology: a systematic review.", "abstract": ["QUESTION Do clinical tests accurately diagnose rotator cuff pathology?   \n", "DESIGN A systematic review of investigations into the diagnostic accuracy of clinical tests for rotator cuff pathology.   \n", "PARTICIPANTS People with shoulder pain who underwent clinical testing in order to diagnose rotator cuff pathology.   \n", "OUTCOME MEASURES The diagnostic accuracy of clinical tests was determined using likelihood ratios.   \n", "RESULTS Thirteen studies met the inclusion criteria.", "The 13 studies evaluated 14 clinical tests in 89 separate evaluations of diagnostic accuracy.", "Only one evaluation, palpation for supraspinatus ruptures, resulted in significant positive and negative likelihood ratios.", "Eight of the 89 evaluations resulted in either significant positive or negative likelihood ratios.", "However, none of these eight positive or negative likelihood ratios were found in other studies.", "Of the 89 evaluations of clinical tests 71 (80%) did not result in either significant positive or negative likelihood ratio evaluations across different studies.   \n", "CONCLUSION Overall, most tests for rotator cuff pathology were inaccurate and cannot be recommended for clinical use.", "At best, suspicion of a rotator cuff tear may be heightened by a positive palpation, combined Hawkins/painful arc/infraspinatus test, Napoleon test, lift-off test, belly-press test, or drop-arm test, and it may be reduced by a negative palpation, empty can test or Hawkins-Kennedy test."], "structured": true}
{"doc_id": 44614949, "title": "Skeletal muscle interleukin\u20106 regulates metabolic factors in iWAT during HFD and exercise training", "abstract": ["OBJECTIVE To investigate the role of skeletal muscle (SkM) interleukin (IL)-6 in the regulation of adipose tissue metabolism.   \n", "METHODS Muscle-specific IL-6 knockout (IL-6 MKO) and IL-6(loxP/loxP) (Floxed) mice were subjected to standard rodent diet (Chow), high-fat diet (HFD), or HFD in combination with exercise training (HFD ExTr) for 16 weeks.   \n", "RESULTS Total fat mass increased (P < 0.05) in both genotypes with HFD.", "However, HFD IL-6 MKO mice had lower (P < 0.05) inguinal adipose tissue (iWAT) mass than HFD Floxed mice.", "Accordingly, iWAT glucose transporter 4 (GLUT4) protein content, 5'AMP activated protein kinase (AMPK)(Thr172) phosphorylation, and fatty acid synthase (FAS) mRNA content were lower (P < 0.05) in IL-6 MKO than Floxed mice on Chow.", "In addition, iWAT AMPK(Thr172) and hormone-sensitive lipase (HSL)(Ser565) phosphorylation as well as perilipin protein content was higher (P < 0.05) in HFD IL-6 MKO than HFD Floxed mice, and pyruvate dehydrogenase E1\u03b1 (PDH-E1\u03b1) protein content was higher (P < 0.05) in HFD ExTr IL-6 MKO than HFD ExTr Floxed mice.   \n", "CONCLUSIONS These findings indicate that SkM IL-6 affects iWAT mass through regulation of glucose uptake capacity as well as lipogenic and lipolytic factors."], "structured": true}
{"doc_id": 44624045, "title": "Risk of hospitalization or death from ischemic heart disease among British vegetarians and nonvegetarians: results from the EPIC-Oxford cohort study.", "abstract": ["BACKGROUND Few previous prospective studies have examined differences in incident ischemic heart disease (IHD) risk between vegetarians and nonvegetarians.   \n", "OBJECTIVE The objective was to examine the association of a vegetarian diet with risk of incident (nonfatal and fatal) IHD.   \n", "DESIGN A total of 44,561 men and women living in England and Scotland who were enrolled in the European Prospective Investigation into Cancer and Nutrition (EPIC)-Oxford study, of whom 34% consumed a vegetarian diet at baseline, were part of the analysis.", "Incident cases of IHD were identified through linkage with hospital records and death certificates.", "Serum lipids and blood pressure measurements were available for 1519 non cases, who were matched to IHD cases by sex and age.", "IHD risk by vegetarian status was estimated by using multivariate Cox proportional hazards models.   \n", "RESULTS After an average follow-up of 11.6 y, there were 1235 IHD cases (1066 hospital admissions and 169 deaths).", "Compared with nonvegetarians, vegetarians had a lower mean BMI [in kg/m(2); -1.2 (95% CI: -1.3, -1.1)], non-HDL-cholesterol concentration [-0.45 (95% CI: -0.60, -0.30) mmol/L], and systolic blood pressure [-3.3 (95% CI: -5.9, -0.7) mm Hg].", "Vegetarians had a 32% lower risk (HR: 0.68; 95% CI: 0.58, 0.81) of IHD than did nonvegetarians, which was only slightly attenuated after adjustment for BMI and did not differ materially by sex, age, BMI, smoking, or the presence of IHD risk factors.   \n", "CONCLUSION Consuming a vegetarian diet was associated with lower IHD risk, a finding that is probably mediated by differences in non-HDL cholesterol, and systolic blood pressure."], "structured": true}
{"doc_id": 44629665, "title": "The Supporting Independent Immunization and Vaccine Advisory Committees (SIVAC) initiative: a country-driven, multi-partner program to support evidence-based decision making.", "abstract": ["Multiple health priorities, limited human resources and logistical capacities, as well as expensive vaccines with limited funds available increase the need for evidence-based decision making in immunization programs.", "The aim of the Supporting Independent Immunization and Vaccine Advisory Committees (SIVAC) Initiative is to support countries in the establishment or strengthening of National Immunization Technical Advisory Groups (NITAGs) that provide recommendations on immunization policies and programs (e.g., vaccination schedules, improvements of routine immunization coverage, new vaccine introduction, etc.).", "SIVAC, a program funded by the Bill & Melinda Gates Foundation, is based on a country-driven, step-by-step process that ensures its support is tailored to country needs and emphasizes NITAG sustainability.", "SIVAC supports countries by reinforcing the capacities of the NITAG scientific and technical secretariat and by providing specific support activities established in consultation with the country and other international partners.", "Additionally, SIVAC and partners have built an electronic platform, the NITAG Resource Center, that provides information, tools, and briefings to NITAGs and the immunization community."], "structured": false}
{"doc_id": 44640124, "title": "Redox-relevant aspects of the extracellular matrix and its cellular contacts via integrins.", "abstract": ["SIGNIFICANCE The extracellular matrix (ECM) fulfills essential functions in multicellular organisms.", "It provides the mechanical scaffold and environmental cues to cells.", "Upon cell attachment, the ECM signals into the cells.", "In this process, reactive oxygen species (ROS) are physiologically used as signalizing molecules.   ", "RECENT ADVANCES ECM attachment influences the ROS-production of cells.", "In turn, ROS affect the production, assembly and turnover of the ECM during wound healing and matrix remodeling.", "Pathological changes of ROS levels lead to excess ECM production and increased tissue contraction in fibrotic disorders and desmoplastic tumors.", "Integrins are cell adhesion molecules which mediate cell adhesion and force transmission between cells and the ECM.", "They have been identified as a target of redox-regulation by ROS.", "Cysteine-based redox-modifications, together with structural data, highlighted particular regions within integrin heterodimers that may be subject to redox-dependent conformational changes along with an alteration of integrin binding activity.   ", "CRITICAL ISSUES In a molecular model, a long-range disulfide-bridge within the integrin \u03b2-subunit and disulfide bridges within the genu and calf-2 domains of the integrin \u03b1-subunit may control the transition between the bent/inactive and upright/active conformation of the integrin ectodomain.", "These thiol-based intramolecular cross-linkages occur in the stalk domain of both integrin subunits, whereas the ligand-binding integrin headpiece is apparently unaffected by redox-regulation.   ", "FUTURE DIRECTIONS Redox-regulation of the integrin activation state may explain the effect of ROS in physiological processes.", "A deeper understanding of the underlying mechanism may open new prospects for the treatment of fibrotic disorders."], "structured": false}
{"doc_id": 44660616, "title": "Prevalence of hypertension and pre-hypertension among adolescents.", "abstract": ["OBJECTIVE To determine the prevalence of hypertension and pre-hypertension on the basis of the 2004 National High Blood Pressure Education Program Working Group guidelines in an adolescent school-screening population.   ", "STUDY DESIGN Cross-sectional assessment of blood pressure (BP) in 6790 adolescents (11-17 years) in Houston schools was conducted from 2003 to 2005.", "Initial measurements included height, weight, and 4 oscillometric BP readings.", "Repeat measurements were obtained on 2 subsequent occasions in students with persistently elevated BP.", "Final prevalence was adjusted for loss to follow-up and logistic regression used to assess risk factors.   \n", "RESULTS BP distribution at initial screen was 81.1% normal, 9.5% pre-hypertension, and 9.4% hypertension (8.4% Stage 1; 1% Stage 2).", "Prevalence after 3 screenings was 81.1% normal, 15.7% pre-hypertension, and 3.2% hypertension (2.6% Stage 1; 0.6% Stage 2).", "Hypertension and pre-hypertension increased with increasing body mass index.", "Sex, race, and classification as either at-risk for overweight or overweight were independently associated with pre-hypertension.", "Only classification as overweight was associated with hypertension.   \n", "CONCLUSIONS Application of new classification guidelines for adolescents with elevated BP reveals approximately 20% are at risk for hypertension.", "Further research determining the significance of each BP category and refining definitions to account for BP variability is warranted."], "structured": true}
{"doc_id": 44672703, "title": "Increased short- and long-term risk of inflammatory bowel disease after salmonella or campylobacter gastroenteritis.", "abstract": ["BACKGROUND & AIMS Various commensal enteric and potentially pathogenic bacteria may be involved in the pathogenesis of inflammatory bowel diseases (IBD).", "We compared the risk of IBD between a cohort of patients with documented Salmonella or Campylobacter gastroenteritis and an age- and gender-matched control group from the same population in Denmark.   \n", "METHODS We identified 13,324 patients with Salmonella/Campylobacter gastroenteritis from laboratory registries in North Jutland and Aarhus counties, Denmark, from 1991 through 2003, and 26,648 unexposed controls from the same counties.", "Of these, 176 exposed patients with IBD before the infection, their 352 unexposed controls, and 80 unexposed individuals with IBD before the Salmonella/Campylobacter infection were excluded.", "The final study cohort of 13,148 exposed and 26,216 unexposed individuals were followed for up to 15 years (mean, 7.5 years).   \n", "RESULTS A first-time diagnosis of IBD was reported in 107 exposed (1.2%) and 73 unexposed individuals (0.5%).", "By age, gender, and comorbidity adjusted Cox proportional hazards regression analysis, the hazard ratio (95% confidence interval) for IBD was 2.9 (2.2-3.9) for the whole period and 1.9 (1.4-2.6) if the first year after the Salmonella/Campylobacter infection was excluded.", "The increased risk in exposed subjects was observed throughout the 15-year observation period.", "The increased risk was similar for Salmonella (n = 6463) and Campylobacter (n = 6685) and for a first-time diagnosis of Crohn's disease (n = 47) and ulcerative colitis (n = 133).   \n", "CONCLUSIONS In our population-based cohort study with complete follow-up, an increased risk of IBD was demonstrated in individuals notified in laboratory registries with an episode of Salmonella/Campylobacter gastroenteritis."], "structured": true}
{"doc_id": 44674301, "title": "Establishment of a cell line (NPC/HK1) from a differentiated squamous carcinoma of the nasopharynx.", "abstract": ["A long-term cell culture epithelioid cell line was established from a recurrent squamous carcinoma of the nasopharynx of a Chinese male 17 1/2 years after radiation therapy.", "The cell line, designated NPC/HK1, has been passed 72 times over a period 1 year.", "The cells have been shown by light and electron microscopies to be of the squamous epithelial type.", "When they were transplanted subcutaneously into the back of athymic nude BALB/c (nu/nu) mice, tumors developed at the sites of inoculation, which on histological examination were shown to be well-differentiated squamous carcinomas, similar in morphology to the recurrent human tumor from which they were derived.", "Karyotypic analysis of cells from the cell line demonstrates an aneuploid human type with a modal chromosome number of 74 with both numerical and structural aberrations.", "Viral particles or Epstein-Barr viral nuclear antigen (EBNA) has not been demonstrated in the cells from the primary culture or several of the subcultures tested.", "The presence of EBNA in touch smears prepared from the biopsy tissue was inconclusive.", "Infection of the subcultured cells with EBV from P3HR1 and B95-8 cells was unsuccessful."], "structured": false}
{"doc_id": 44693226, "title": "Effect of lipid restriction on mitochondrial free radical production and oxidative DNA damage.", "abstract": ["Many studies have shown that caloric restriction (40%) decreases mitochondrial reactive oxygen species (ROS) generation in rodents.", "Moreover, we have recently found that 7 weeks of 40% protein restriction without strong caloric restriction also decreases ROS production in rat liver.", "This is interesting since it has been reported that protein restriction can also extend longevity in rodents.", "In the present study we have investigated the possible role of dietary lipids in the effects of caloric restriction on mitochondrial oxidative stress.", "Using semipurified diets, the ingestion of lipids in male Wistar rats was decreased by 40% below controls, while the other dietary components were ingested at exactly the same level as in animals fed ad libitum.", "After 7 weeks of treatment the liver mitochondria of lipid-restricted animals showed significant increases in oxygen consumption with complex I-linked substrates (pyruvate/malate and glutamate/malate).", "Neither mitochondrial H(2)O(2) production nor oxidative damage to mitochondrial or nuclear DNA was modified in lipid-restricted animals.", "Oxidative damage to mitochondrial DNA was one order of magnitude higher than that of nuclear DNA in both dietary groups.", "These results deny a role for lipids and reinforce the possible role of dietary proteins as being responsible for the decrease in mitochondrial ROS production and DNA damage in caloric restriction."], "structured": false}
{"doc_id": 44724517, "title": "Kruppel-like factor 2 is a transcriptional regulator of chronic and acute inflammation.", "abstract": ["Although myeloid cell activation is requisite for an optimal innate immune response, this process must be tightly controlled to prevent collateral host tissue damage.", "Kruppel-like factor 2 (KLF2) is a potent regulator of myeloid cell proinflammatory activation.", "As an approximately 30% to 50% reduction in KLF2 levels has been observed in human subjects with acute or chronic inflammatory disorders, we studied the biological response to inflammation in KLF2(+/-) mice.", "Herein, we show that partial deficiency of KLF2 modulates the in vivo response to acute (sepsis) and subacute (skin) inflammatory challenge.", "Mechanistically, we link the anti-inflammatory effects of KLF2 to the inhibition of NF-\u03baB transcriptional activity.", "Collectively, the observations provide biologically relevant insights into KLF2-mediated modulation of these inflammatory processes that could potentially be manipulated for therapeutic gain."], "structured": false}
{"doc_id": 44737533, "title": "Simian immunodeficiency viruses replication dynamics in African non-human primate hosts: common patterns and species-specific differences.", "abstract": ["METHODS To define potential common features of simian immunodeficiency virus (SIV) infections in different naturally infected host species, we compared the dynamics of viral replication in 31 African green monkeys (10 sabeus, 15 vervets and seven Caribbean AGMs), 14 mandrills and three sooty mangabeys (SMs) that were experimentally infected with their species-specific viruses.   \n", "RESULTS After infection, these SIVs replicated rapidly reaching viral loads (VLs) of 10(5)-10(9) copies/ml of plasma between days 9-14 post-infection (p.i).", "Set point viremia was established between days 42 and 60 p.i., with levels of approximately 10(5)-10(6) copies/ml in SM and mandrills, and lower levels (10(3)-10(5) copies/ml) in AGMs.", "VL during the chronic phase did not correlate with viral genome structure: SIVmnd-2 (a vpx-containing virus) and SIVmnd-1 (which does not contain vpu or vpx) replicated to similar levels in mandrills.", "VL was dependent on virus strain: vervets infected with three different viral strains showed different patterns of viral replication.", "The pattern of viral replication of SIVagm.sab, which uses both CCR5 and CXCR4 co-receptors was similar to those of the other viruses.   \n", "CONCLUSIONS Our results show a common pattern of SIV replication in naturally and experimentally infected hosts.", "This is similar overall to that observed in pathogenic SIV infection of macaques.", "This result indicates that differences in clinical outcome between pathogenic and non-pathogenic infections rely on host responses rather than the characteristics of the virus itself."], "structured": true}
{"doc_id": 44801733, "title": "The role of the transcription factor KLF2 in vascular development and disease.", "abstract": ["The zinc-finger transcription factor KLF2 transduces the physical forces exerted by blood flow into molecular signals responsible for a wide range of biological responses.", "Following its initial recognition as a flow-responsive endothelial transcription factor, KLF2 is now known to be expressed in a range of cell types and to participate in a number of processes during development and disease such as endothelial homeostasis, vasoregulation, vascular growth/remodeling, and inflammation.", "In this review, we summarize the current understanding about KLF2 with a focus on its effects on vascular biology."], "structured": false}
{"doc_id": 44827480, "title": "Implementation of contemporary oral antiplatelet treatment guidelines in patients with acute coronary syndrome undergoing percutaneous coronary intervention: a report from the GReek AntiPlatelet rEgistry (GRAPE).", "abstract": ["BACKGROUND Few data exist about the implementation of contemporary oral antiplatelet treatment guidelines in patients with acute coronary syndrome (ACS) undergoing percutaneous coronary intervention (PCI).   \n", "METHODS GReek AntiPlatelet rEgistry (GRAPE), initiated on January 2012, is a prospective, observational, multicenter cohort study focusing on contemporary use of P2Y12 inhibitors.", "In 1434 patients we evaluated appropriateness of P2Y12 selection initially and at discharge by applying an eligibility-assessing algorithm based on P2Y12 inhibitors' contraindications/specific warnings and precautions.   \n", "RESULTS Appropriate, less preferable and inappropriate P2Y12 inhibitor selections were made initially in 45.8%, 47.2% and 6.6% and at discharge in 64.1%, 29.2% and 6.6% of patients, respectively.", "The selection of clopidogrel was most commonly less preferable, both initially (69.7%) and at discharge (75.6%).", "Appropriate selection of newer agents was high initially (79.2%-82.8%), with further increase as selection at discharge (89.4%-89.8%).", "Inappropriate selection of the newer agents was 17.2%-20.8% initially, decreasing to 10.2%-10.6% at discharge.", "Conditions and co-medications related to increased bleeding risk, presentation with ST elevation myocardial infarction and the absence of reperfusion within the first 24h were the most powerful predictors of appropriate P2Y12 selection initially, whereas age \u226575 years, conditions and co-medications related to increased bleeding risk and regional trends mostly affected appropriate P2Y12 selection at discharge.   \n", "CONCLUSIONS In GRAPE, adherence with the recently released guidelines on oral antiplatelet therapy was satisfactory.", "Clopidogrel was most commonly used as a less preferable selection, while prasugrel or ticagrelor selection was mostly appropriate.", "Certain factors may predict initial and at discharge guideline implementation.", "Clinical Trial Registration-clinicaltrials.gov Identifier: NCT01774955 http://clinicaltrials.gov/."], "structured": true}
{"doc_id": 44830890, "title": "Comorbidity of depressive and anxiety disorders in chronic daily headache and its subtypes.", "abstract": ["OBJECTIVE To investigate the frequency of depressive and anxiety disorders in patients with chronic daily headache.   \n", "BACKGROUND There is a lack of data in the literature on the extent of psychiatric comorbidity in patients with different subtypes of chronic daily headache.   \n", "METHODS We recruited consecutive patients with chronic daily headache seen in a headache clinic from November 1998 to December 1999.", "The subtypes of chronic daily headache were classified according to the criteria proposed by Silberstein et al. A psychiatrist evaluated the patients according to the structured Mini-International Neuropsychiatric Interview to assess the comorbidity of depressive and anxiety disorders.   \n", "RESULTS Two hundred sixty-one patients with chronic daily headache were recruited.", "The mean age was 46 years, and 80% were women.", "Transformed migraine was diagnosed in 152 patients (58%) and chronic tension-type headache in 92 patients (35%).", "Seventy-eight percent of patients with transformed migraine had psychiatric comorbidity, including major depression (57%), dysthymia (11%), panic disorder (30%), and generalized anxiety disorder (8%).", "Sixty-four percent of patients with chronic tension-type headache had psychiatric diagnoses, including major depression (51%), dysthymia (8%), panic disorder (22%), and generalized anxiety disorder (1%).", "The frequency of anxiety disorders was significantly higher in patients with transformed migraine after controlling for age and sex (P =.02).", "Both depressive and anxiety disorders were significantly more frequent in women.   \n", "CONCLUSION Psychiatric comorbidity, especially major depression and panic disorders, was highly prevalent in patients with chronic daily headache seen in a headache clinic.", "These results demonstrate that women and patients with transformed migraine are at higher risk of psychiatric comorbidity."], "structured": true}
{"doc_id": 44935041, "title": "The precursor form of IL-1alpha is an intracrine proinflammatory activator of transcription.", "abstract": ["Although most cytokines are studied for biological effects after engagement of their specific cell surface membrane receptors, increasing evidence suggests that some function in the nucleus.", "In the present study, the precursor form of IL-1alpha was overexpressed in various cells and assessed for activity in the presence of saturating concentrations of IL-1 receptor antagonist to prevent receptor signaling.", "Initially diffusely present in the cytoplasm of resting cells, IL-1alpha translocated to the to nucleus after activation by endotoxin, a Toll-like receptor ligand.", "The IL-1alpha precursor, but not the C-terminal mature form, activated the transcriptional machinery in the GAL4 system by 90-fold; a 50-fold increase was observed using only the IL-1alpha propiece, suggesting that transcriptional activation was localized to the N terminus where the nuclear localization sequence resides.", "Under conditions of IL-1 receptor blockade, intracellular overexpression of the precursor and propiece forms of IL-1alpha were sufficient to activate NF-kappaB and AP-1.", "Stable transfectants overproducing precursor IL-1alpha released the cytokines IL-8 and IL-6 but also exhibited a significantly lower threshold of activation to subpicomolar concentrations of tumor necrosis factor alpha or IFN-gamma.", "Thus, intracellular functions of IL-1alpha might play an unforeseen role in the genesis of inflammation.", "During disease-driven events, the cytosolic precursor moves to the nucleus, where it augments transcription of proinflammatory genes.", "Because this mechanism of action is not affected by extracellular inhibitors, reducing intracellular functions of IL-1alpha might prove beneficial in some inflammatory conditions."], "structured": false}
{"doc_id": 44947611, "title": "Three-dimensional structure of the AAH26994.1 protein from Mus musculus, a putative eukaryotic Urm1.", "abstract": ["We have used NMR spectroscopy to determine the solution structure of protein AAH26994.1 from Mus musculus and propose that it represents the first three-dimensional structure of a ubiquitin-related modifier 1 (Urm1) protein.", "Amino acid sequence comparisons indicate that AAH26994.1 belongs to the Urm1 family of ubiquitin-like modifier proteins.", "The best characterized member of this family has been shown to be involved in nutrient sensing, invasive growth, and budding in yeast.", "Proteins in this family have only a weak sequence similarity to ubiquitin, and the structure of AAH26994.1 showed a much closer resemblance to MoaD subunits of molybdopterin synthases (known structures are of three bacterial MoaD proteins with 14%-26% sequence identity to AAH26994.1).", "The structures of AAH26994.1 and the MoaD proteins each contain the signature ubiquitin secondary structure fold, but all differ from ubiquitin largely in regions outside of this fold.", "This structural similarity bolsters the hypothesis that ubiquitin and ubiquitin-related proteins evolved from a protein-based sulfide donor system of the molybdopterin synthase type."], "structured": false}
{"doc_id": 45015767, "title": "Concurrent endometrial carcinoma in women with a biopsy diagnosis of atypical endometrial hyperplasia: a Gynecologic Oncology Group study.", "abstract": ["BACKGROUND Adenocarcinoma of the endometrium is the most common gynecologic malignancy in the United States, accounting for approximately 36,000 diagnoses of invasive carcinoma annually.", "The most common histologic type, endometrioid adenocarcinoma (EC), accounts for 75-80% of patients.", "The objective of this work was to estimate the prevalence of concurrent carcinoma in women with a biopsy diagnosis of the precursor lesion, atypical endometrial hyperplasia (AEH).   \n", "METHODS This prospective cohort study included women who had a community diagnosis of AEH.", "Diagnostic biopsy specimens were reviewed independently by three gynecologic pathologists who used International Society of Gynecologic Pathologists/World Health Organization criteria.", "Study participants underwent hysterectomy within 12 weeks of entry onto protocol without interval treatment.", "The hysterectomy slides also were reviewed by the study pathologists, and their findings were used in the subsequent analyses.   \n", "RESULTS Between November 1998 and June 2003, 306 women were enrolled on the study.", "Of these, 17 women were not included in the analysis: Two patients had unreadable slides because of poor processing or insufficient tissue, 2 patients had only slides that were not endometrial, the slides for 5 patients were not available for review, and 8 of the hysterectomy specimens were excluded because they showed evidence of interval intervention, either progestin effect or ablation.", "In total, 289 patients were included in the current analysis.", "The study panel review of the AEH biopsy specimens was interpreted as follows: 74 of 289 specimens (25.6%) were diagnosed as less than AEH, 115 of 289 specimens (39.8%) were diagnosed as AEH, and 84 of 289 specimens (29.1%) were diagnosed as endometrial carcinoma.", "In 5.5% (16 of 289 specimens), there was no consensus on the biopsy diagnosis.", "The rate of concurrent endometrial carcinoma for analyzed specimens was 42.6% (123 of 289 specimens).", "Of these, 30.9% (38 of 123 specimens) were myoinvasive, and 10.6% (13 of 123 specimens) involved the outer 50% of the myometrium.", "Among the women who had hysterectomy specimens with carcinoma, 14 of 74 women (18.9%) had a study panel biopsy consensus diagnosis of less than AEH, 45 of 115 women (39.1%) had a study panel biopsy consensus diagnosis of AEH, and 54 of 84 women (64.3%) had a study panel diagnosis of carcinoma.", "Among women who had no consensus in their biopsy diagnosis, 10 of 16 women (62.5%) had carcinoma in their hysterectomy specimens.   \n", "CONCLUSIONS The prevalence of endometrial carcinoma in patients who had a community hospital biopsy diagnosis of AEH was high (42.6%).", "When considering management strategies for women who have a biopsy diagnosis of AEH, clinicians and patients should take into account the considerable rate of concurrent carcinoma."], "structured": true}
{"doc_id": 45027320, "title": "The prevalence and clustering of four major lifestyle risk factors in an English adult population.", "abstract": ["BACKGROUND The aim of this study was to examine the clustering of four major lifestyle risk factors (smoking, heavy drinking, lack of fruit and vegetables consumption, and lack of physical activity), and to examine the variation across different socio-demographic groups in the English adult population.   \n", "METHODS The study population was derived from the 2003 Health Survey for England (n=11,492).", "Clustering was examined by comparing the observed and expected prevalence of the different possible combinations.", "A multinomial multilevel regression model was conducted to examine the socio-demographic variation in the clustering of the four risk factors.   \n", "RESULTS The study found that, when using British health recommendations, a majority of the English population have multiple lifestyle risk factors at the same time.", "Clustering was found at both ends of the lifestyle spectrum and was more pronounced for women than for men.", "Overall, multiple risk factors were more prevalent among men, lower social class households, singles, and people who are economically inactive, but less prevalent among home owners and older age groups.   \n", "CONCLUSIONS The clustering of multiple risk factors provides support for multiple-behavior interventions as opposed to single-behavior interventions."], "structured": true}
{"doc_id": 45096063, "title": "Cutting edge: interleukin 17 signals through a heteromeric receptor complex.", "abstract": ["IL-17 is an inflammatory cytokine produced primarily by a unique lineage of CD4 T cells that plays critical roles in the pathogenesis of multiple autoimmune diseases.", "IL-17RA is a ubiquitously expressed receptor that is essential for IL-17 biologic activity.", "Despite widespread receptor expression, the activity of IL-17 is most classically defined by its ability to induce the expression of inflammatory cytokines, chemokines, and other mediators by stromal cells.", "The lack of IL-17 responsiveness in mouse stromal cells genetically deficient in IL-17RA is poorly complemented by human IL-17RA, suggesting the presence of an obligate ancillary component whose activity is species specific.", "This component is IL-17RC, a distinct member of the IL-17R family.", "Thus, the biologic activity of IL-17 is dependent on a complex composed of IL-17RA and IL-17RC, suggesting a new paradigm for understanding the interactions between the expanded family of IL-17 ligands and their receptors."], "structured": false}
{"doc_id": 45143088, "title": "Long non-coding RNAs with low expression levels in cells are enriched in secreted exosomes.", "abstract": ["Long non-coding RNAs (lncRNAs) are involved in regulating chromatin modifications, gene transcription, mRNA translation, and protein function.", "We recently reported a high variation in the basal expression levels of a panel of lncRNAs in HeLa and MCF-7 cells and their differential response to DNA damage induction.", "Here, we hypothesized that lncRNA molecules with different cellular expression may have a differential abundance in secreted exosomes, and their exosome levels would reflect cellular response to DNA damage.", "MALAT1, HOTAIR, lincRNA-p21, GAS5, TUG1, CCND1-ncRNA in exosomes secreted from cultured cells were characterized.", "A different expression pattern of lncRNAs in exosomes was seen compared to cells.", "RNA molecules with relative low expression levels (lincRNA-p21, HOTAIR, ncRNA-CCND1) were highly enriched in exosomes.", "TUG1 and GAS5 levels were moderately elevated in exosomes, whereas MALAT1--which was the most abundant molecule in cells--was present at levels comparable to its cellular levels.", "lincRNA-p21 and ncRNA-CCND1 were the main molecules; exosome levels of them best reflect the change of their cellular levels upon exposure of the cells to bleomycin-induced DNA damage.", "In conclusion, we provide evidence that lncRNAs have a differential abundance in exosomes, indicating a selective loading."], "structured": false}
{"doc_id": 45153864, "title": "Olanzapine depot exposure in male rats: Dose-dependent lipogenic effects without concomitant weight gain.", "abstract": ["Treatment with second-generation antipsychotic agents such as olanzapine frequently results in metabolic adverse effects, e.g. hyperphagia, weight gain and dyslipidaemia in patients of both genders.", "The molecular mechanisms underlying metabolic adverse effects are still largely unknown, and studies in rodents represent an important approach in their exploration.", "However, the validity of the rodent model is hampered by the fact that antipsychotics induce weight gain in female, but not male, rats.", "When administered orally, the short half-life of olanzapine in rats prevents stable plasma concentrations of the drug.", "We recently showed that a single intramuscular injection of long-acting olanzapine formulation yields clinically relevant plasma concentrations accompanied by several dysmetabolic features in the female rat.", "In the current study, we show that depot injections of 100-250 mg/kg olanzapine yielded clinically relevant plasma olanzapine concentrations also in male rats.", "In spite of transient hyperphagia, however, olanzapine resulted in weight loss rather than weight gain.", "The resultant negative feed efficiency was accompanied by a slight elevation of thermogenesis markers in brown adipose tissue for the highest olanzapine dose, but the olanzapine-related reduction in weight gain remains to be explained.", "In spite of the absence of weight gain, an olanzapine dose of 200mg/kg or above induced significantly elevated plasma cholesterol levels and pronounced activation of lipogenic gene expression in the liver.", "These results confirm that olanzapine stimulates lipogenic effects, independent of weight gain, and raise the possibility that endocrine factors may influence gender specificity of metabolic effects of antipsychotics in the rat."], "structured": false}
{"doc_id": 45154987, "title": "Glutamate mediates the function of melanocortin receptor 4 on Sim1 neurons in body weight regulation.", "abstract": ["The melanocortin receptor 4 (MC4R) is a well-established mediator of body weight homeostasis.", "However, the neurotransmitter(s) that mediate MC4R function remain largely unknown; as a result, little is known about the second-order neurons of the MC4R neural pathway.", "Single-minded 1 (Sim1)-expressing brain regions, which include the paraventricular nucleus of hypothalamus (PVH), represent key brain sites that mediate melanocortin action.", "We conditionally restored MC4R expression in Sim1 neurons in the background of Mc4r-null mice.", "The restoration dramatically reduced obesity in Mc4r-null mice.", "The anti-obesity effect was completely reversed by selective disruption of glutamate release from those same Sim1 neurons.", "The reversal was caused by lower energy expenditure and hyperphagia.", "Corroboratively, selective disruption of glutamate release from adult PVH neurons led to rapid obesity development via reduced energy expenditure and hyperphagia.", "Thus, this study establishes glutamate as the primary neurotransmitter that mediates MC4Rs on Sim1 neurons in body weight regulation."], "structured": false}
{"doc_id": 45166582, "title": "Intracellular sterol dynamics.", "abstract": ["We review the cellular mechanisms implicated in cholesterol trafficking and distribution.", "Recent studies have provided new information about the distribution of sterols within cells, including analysis of its transbilayer distribution.", "The cholesterol interaction with other lipids and its engagement in various trafficking processes will determine its proper level in a specific membrane; making the cholesterol distribution uneven among the various intracellular organelles.", "The cholesterol content is important since cholesterol plays an essential role in membranes by controlling their physicochemical properties as well as key cellular events such as signal transduction and protein trafficking.", "Cholesterol movement between cellular organelles is highly dynamic, and can be achieved by vesicular and non-vesicular processes.", "Various studies have analyzed the proteins that play a significant role in these processes, giving us new information about the relative importance of these two trafficking pathways in cholesterol transport.", "Although still poorly characterized in many trafficking routes, several potential sterol transport proteins have been described in detail; as a result, molecular mechanisms for sterol transport among membranes start to be appreciated."], "structured": false}
{"doc_id": 45199834, "title": "A plasma membrane component able to bind and alter virions of poliovirus type 1: studies on cell-free alteration using a simplified assay.", "abstract": ["Abstract Intact HeLa cells can bind virions of poliovirus type 1 and can subsequently convert them to altered particles by incubation at 37\u00b0.", "Altered particles sediment more slowly than virions, have lost VP-4, and are disrupted by sodium dodecyl sulfate, but their RNA is intact and ribonuclease insensitive.", "These characteristics allow assay of altered particles and of particles that have released their RNA, using nuclease digestion with or without sodium dodecyl sulfate treatment.", "With this simple assay procedure, quantitative parameters of binding and alteration can be measured.", "The binding-altering activity can be localized in plasma membranes, and pure membranes can be shown to carry out alteration.", "The membrane-bound activity is abolished by proteases and by nonionic detergents.", "Only altered particles are formed by membranes; release of RNA is not caused by membranes but is caused by intact cells.", "Binding and alteration are processes that are closely associated; it is possible that alteration is a consequence of binding by multiple receptors in a fluid membrane."], "structured": false}
{"doc_id": 45200347, "title": "Resequencing studies of nonmodel organisms using closely related reference genomes: optimal experimental designs and bioinformatics approaches for population genomics.", "abstract": ["Decreasing costs of next-generation sequencing (NGS) experiments have made a wide range of genomic questions open for study with nonmodel organisms.", "However, experimental designs and analysis of NGS data from less well-known species are challenging because of the lack of genomic resources.", "In this work, we investigate the performance of alternative experimental designs and bioinformatics approaches in estimating variability and neutrality tests based on the site-frequency-spectrum (SFS) from individual resequencing data.", "We pay particular attention to challenges faced in the study of nonmodel organisms, in particular the absence of a species-specific reference genome, although phylogenetically close genomes are assumed to be available.", "We compare the performance of three alternative bioinformatics approaches \u2013 genotype calling, genotype\u2013haplotype calling and direct estimation without calling genotypes.", "We find that relying on genotype calls provides biased estimates of population genetic statistics at low to moderate read depth (2\u20138X).", "Genotype\u2013haplotype calling returns more accurate estimates irrespective of the divergence to the reference genome, but requires moderate depth (8\u201320X).", "Direct estimation without calling genotypes returns the most accurate estimates of variability and of most SFS tests investigated, including at low read depth (2\u20134X).", "Studies without species-specific reference genome should thus aim for low read depth and avoid genotype calling whenever individual genotypes are not essential.", "Otherwise, aiming for moderate to high depth at the expense of number of individuals, and using genotype\u2013haplotype calling, is recommended."], "structured": false}
{"doc_id": 45218443, "title": "Thalassemia and malaria: new insights into an old problem.", "abstract": ["The hemoglobinopathies are probably the world's most common genetic diseases: The World Health Organization has estimated that at least 5% of the population are carriers for one or other of the most serious forms, the alpha- and beta-thalassemias and the structural variant hemoglobins S, C, and E, which are found at polymorphic frequencies in many countries.", "All these hemoglobinopathies are believed to provide protection against malaria, and it is thought that, in malarial regions of the world, natural selection has been responsible for elevating and maintaining their gene frequencies, an idea first proposed 50 years ago by J.B.S. Haldane.", "Epidemiological studies undertaken in the 1950s on hemoglobin S in Africa provided support for the \"malaria hypothesis,\" but until recently it has proved extremely difficult to verify it for the thalassemias.", "The application of molecular methods has, however, provided new opportunities to address this old question.", "Population and molecular genetic analysis of thalassemia variants, and microepidemiological studies of the relationship between alpha-thalassemia and malaria in the southwest Pacific, have provided unequivocal evidence for protection.", "Surprisingly, some of this protection appears to derive from enhanced susceptibility in very young thalassemic children to both Plasmodium falciparum and, especially, P. vivax, and this early exposure appears to provide the basis for better protection in later life."], "structured": false}
{"doc_id": 45244537, "title": "Endocrine control of spermatogenesis: Role of FSH and LH/ testosterone.", "abstract": ["Evaluation of testicular functions (production of sperm and androgens) is an important aspect of preclinical safety assessment and testicular toxicity is comparatively far more common than ovarian toxicity.", "This chapter focuses (1) on the histological sequelae of disturbed reproductive endocrinology in rat, dog and nonhuman primates and (2) provides a review of our current understanding of the roles of gonadotropins and androgens.", "The response of the rodent testis to endocrine disturbances is clearly different from that of dog and primates with different germ cell types and spermatogenic stages being affected initially and also that the end-stage spermatogenic involution is more pronounced in dog and primates compared to rodents.", "Luteinizing hormone (LH)/testosterone and follicle-stimulating hormone (FSH) are the pivotal endocrine factors controlling testicular functions.", "The relative importance of either hormone is somewhat different between rodents and primates.", "Generally, however, both LH/testosterone and FSH are necessary for quantitatively normal spermatogenesis, at least in non-seasonal species."], "structured": false}
{"doc_id": 45276789, "title": "Extravasation injuries on regional neonatal units.", "abstract": ["This survey of regional neonatal intensive care units determined a prevalence of 38 per 1000 neonates who sustained an extravasation injury that caused skin necrosis.", "Most injuries occurred in infants of 26 weeks gestation or less, with parenteral nutrition infused through intravenous cannulae.", "Common treatments were exposing wounds to the air, infiltration with hyaluronidase and saline, and occlusive dressings."], "structured": false}
{"doc_id": 45287266, "title": "Nonstructural protein 3-4A: the Swiss army knife of hepatitis C virus.", "abstract": ["Hepatitis C virus (HCV) nonstructural protein 3-4A (NS3-4A) is a complex composed of NS3 and its cofactor NS4A.", "It harbours serine protease as well as NTPase/RNA helicase activities and is essential for viral polyprotein processing, RNA replication and virion formation.", "Specific inhibitors of the NS3-4A protease significantly improve sustained virological response rates in patients with chronic hepatitis C when combined with pegylated interferon-\u03b1 and ribavirin.", "The NS3-4A protease can also target selected cellular proteins, thereby blocking innate immune pathways and modulating growth factor signalling.", "Hence, NS3-4A is not only an essential component of the viral replication complex and prime target for antiviral intervention but also a key player in the persistence and pathogenesis of HCV.", "This review provides a concise update on the biochemical and structural aspects of NS3-4A, its role in the pathogenesis of chronic hepatitis C and the clinical development of NS3-4A protease inhibitors."], "structured": false}
{"doc_id": 45336190, "title": "Phase 2 safety trial targeting amyloid beta production with a gamma-secretase inhibitor in Alzheimer disease.", "abstract": ["OBJECTIVE To evaluate the safety, tolerability, and amyloid beta (Abeta) response to the gamma-secretase inhibitor LY450139 in Alzheimer disease.   \n", "DESIGN Multicenter, randomized, double-blind, dose-escalation, placebo-controlled trial.   \n", "SETTING Community-based clinical research centers.", "Patients Fifty-one individuals with mild to moderate Alzheimer disease were randomized to receive placebo (n=15) or LY450139 (100 mg [n=22] or 140 mg [n=14]), with 43 completing the treatment phase.", "Intervention The LY450139 groups received 60 mg/d for 2 weeks, then 100 mg/d for 6 weeks, and then either 100 or 140 mg/d for 6 additional weeks.   \n", "MAIN OUTCOME MEASURES Primary outcome measures were adverse events, plasma and cerebrospinal fluid Abeta levels, vital signs, electrocardiographic data, and laboratory safety test results.", "Secondary outcome measures included the Alzheimer's Disease Assessment Scale cognitive subscale and the Alzheimer's Disease Cooperative Study Activities of Daily Living Scale.   \n", "RESULTS Group differences were seen in skin and subcutaneous tissue concerns (P=.05), including 3 possible drug rashes and 3 reports of hair color change in the treatment groups.", "There were 3 adverse event-related discontinuations, including 1 transient bowel obstruction.", "The plasma Abeta(40) concentration was reduced by 58.2% for the 100-mg group and 64.6% for the 140-mg group (P<.001).", "No significant reduction was seen in cerebrospinal fluid Abeta levels.", "No group differences were seen in cognitive or functional measures.   \n", "CONCLUSIONS LY450139 was generally well tolerated at doses of up to 140 mg/d for 14 weeks, with several findings indicating the need for close clinical monitoring in future studies.", "Decreases in plasma Abeta concentrations were consistent with inhibition of gamma-secretase.", "Trial Registration clinicaltrials.gov Identifier: NCT00244322."], "structured": true}
{"doc_id": 45341480, "title": "Reduction in skin grafting after the introduction of hydrofiber dressings in partial thickness burns: a comparison between a hydrofiber and silver sulphadiazine.", "abstract": ["AIM/PURPOSE The aim of this study was to compare clinical outcome of children with scald burns treated with a hydrofiber dressing (Aquacel(\u00ae), Convatec Inc.) with the former standard of care with silver sulfadiazine (Flammazine(\u00ae); Solvay Pharmaceuticals), considering surgical intervention and length of stay (LOS).   \n", "METHODS A retrospective study of all consecutive children from zero to four years with primary scald burns up to 10% admitted to the Burn Centre of the Maasstad Hospital Rotterdam between January 1987 and January 2010 were reviewed.", "For data collection a prospective computerized database was used.", "For comparison the study period was divided into two periods representing the period before and after the introduction of the hydrofiber dressing (HFD), respectively 1987-1999 (period 1) and 1999-2010 (period 2).   \n", "RESULTS Over the whole study period 27.3% of 502 patients treated with silver sulfadiazine (Ag-SD) underwent surgery, while before the introduction of HFD 30.5% of 338 Ag-SD treated patients were operated upon.", "After the introduction of the HFD 20.7% of 164 patients treated with Ag-SD eventually underwent skin grafting, a significant difference with the 11.6% of 302 patients whose wounds were dressed with HFD (p<0.01).   \n", "CONCLUSIONS Compared to silver sulfadiazine treatment a reduced number of surgical interventions was observed in mixed partial thickness scald burns up to 10% TBSA burned in children aged 0-4 years after the introduction of hydrofiber dressings.", "The mode of treatment with this wound dressing also limited hospital length of stay."], "structured": true}
{"doc_id": 45364685, "title": "Induction of the heat-shock response by carbon dioxide in Chironomus thummi.", "abstract": ["The effects of a set of stress treatments on gene expression of Chironomus thummi salivary gland cells have been analyzed.", "Among the treatments assayed, only during recovery from carbon dioxide have we observed a response similar to that previously described after heat-shock treatment: induction of the heat-shock puffs and synthesis of the heat-shock polypeptides.", "In these conditions, puffing and transcription of telomeric regions were observed, which led to the appearance of the temperature-inducible telomeric Balbiani ring T-BR-III.", "Other treatments failed to induce the heat-shock response, despite promoting real stress conditions to C. thummi larvae or salivary gland cells."], "structured": false}
{"doc_id": 45401535, "title": "Candida albicans-Staphylococcus aureus polymicrobial peritonitis modulates host innate immunity.", "abstract": ["Despite advances in medical device fabrication and antimicrobial treatment therapies, fungal-bacterial polymicrobial peritonitis remains a serious complication for surgery patients, those on peritoneal dialysis, and the critically ill.", "Using a murine model of peritonitis, we have demonstrated that monomicrobial infection with Candida albicans or Staphylococcus aureus is nonlethal.", "However, coinfection with these same doses leads to a 40% mortality rate and increased microbial burden in the spleen and kidney by day 1 postinfection.", "Using a multiplex enzyme-linked immunosorbent assay, we have also identified a unique subset of innate proinflammatory cytokines (interleukin-6, granulocyte colony-stimulating factor, keratinocyte chemoattractant, monocyte chemoattractant protein-1, and macrophage inflammatory protein-1\u03b1) that are significantly increased during polymicrobial versus monomicrobial peritonitis, leading to increased inflammatory infiltrate into the peritoneum and target organs.", "Treatment of coinfected mice with the cyclooxygenase (COX) inhibitor indomethacin reduces the infectious burden, proinflammatory cytokine production, and inflammatory infiltrate while simultaneously preventing any mortality.", "Further experiments demonstrated that the immunomodulatory eicosanoid prostaglandin E2 (PGE2) is synergistically increased during coinfection compared to monomicrobial infection; indomethacin treatment also decreased elevated PGE2 levels.", "Furthermore, addition of exogenous PGE2 into the peritoneal cavity during infection overrode the protection provided by indomethacin and restored the increased mortality and microbial burden.", "Importantly, these studies highlight the ability of fungal-bacterial coinfection to modulate innate inflammatory events with devastating consequences to the host."], "structured": false}
{"doc_id": 45408403, "title": "Techniques and probes for the study of Xenopus tropicalis development.", "abstract": ["The frog Xenopus laevis has provided significant insights into developmental and cellular processes.", "However, X. laevis has an allotetraploid genome precluding its use in forward genetic analysis.", "Genetic analysis may be applicable to Xenopus (Silurana) tropicalis, which has a diploid genome and a shorter generation time.", "Here, we show that many tools for the study of X. laevis development can be applied to X. tropicalis.", "By using the developmental staging system of Nieuwkoop and Faber, we find that X. tropicalis embryos develop at similar rates to X. laevis, although they tolerate a narrower range of temperatures.", "We also show that many of the analytical reagents available for X. laevis can be effectively transferred to X. tropicalis.", "The X. laevis protocol for whole-mount in situ hybridization to mRNA transcripts can be successfully applied to X. tropicalis without alteration.", "Additionally, X. laevis probes often work in X. tropicalis--alleviating the immediate need to clone the X. tropicalis orthologs before initiating developmental studies.", "Antibodies that react against X. laevis proteins can effectively detect the X. tropicalis protein by using established immunohistochemistry procedures.", "Antisense morpholino oligonucleotides (MOs) offer a new alternative to study loss of gene activity during development.", "We show that MOs function in X. tropicalis.", "Finally, X. tropicalis offers the possibility for forward genetics and genomic analysis."], "structured": false}
{"doc_id": 45414636, "title": "Requirement of c-myb in T cell development and in mature T cell function.", "abstract": ["Previous reports have suggested that the protooncogene c-myb participates in T cell development in the thymus and mature T cell proliferation.", "We have generated two T cell-specific c-myb knockout mouse models, myb/LckCre and myb/CD4Cre.", "We have demonstrated that c-myb is required for the development of thymocytes at the DN3 stage, for survival and proliferation of double-positive thymocytes, for differentiation of single-positive CD4 and CD8 T cells, and for the proliferative responses of mature T cells.", "In addition, our data show that c-myb is directly involved in the formation of double-positive CD4+CD8+CD25+, CD4+CD25+, and CD8+CD25+ T cells, developmental processes that may imply a role for c-myb in autoimmune dysfunction."], "structured": false}
{"doc_id": 45447613, "title": "Effect of losartan on ambulatory short-term blood pressure variability and cardiovascular remodeling in hypertensive patients on hemodialysis.", "abstract": ["OBJECTIVE Previous studies have shown increases in ambulatory short-term blood pressure (BP) variability to be related to cardiovascular disease.", "In this study, we examined whether an angiotensin II type 1 receptor blocker losartan would improve ambulatory short-term BP variability in hypertensive patients on hemodialysis.   \n", "METHODS Forty hypertensive patients on hemodialysis therapy were randomly assigned to the losartan treatment group (n=20) or the control treatment group (n=20).", "At baseline and 6 and 12 months after the treatment, 24-h ambulatory BP monitoring was performed.", "Echocardiography and measurements of brachial-ankle pulse wave velocity (baPWV) and biochemical parameters were also performed before and after therapy.   \n", "RESULTS After 6- and 12-months of treatment, nighttime short-term BP variability, assessed on the basis of the coefficient of variation of ambulatory BP, was significantly decreased in the losartan group, but remained unchanged in the control group.", "Compared with the control group, losartan significantly decreased left ventricular mass index (LVMI), baPWV, and the plasma levels of brain natriuretic peptide and advanced glycation end products (AGE).", "Furthermore, multiple regression analysis showed significant correlations between changes in LVMI and changes in nighttime short-term BP variability, as well as between changes in LVMI and changes in the plasma levels of AGE.   \n", "CONCLUSION These results suggest that losartan is beneficial for the suppression of pathological cardiovascular remodeling though its inhibitory effect on ambulatory short-term BP variability during nighttime."], "structured": true}
{"doc_id": 45449835, "title": "Interleukin-17 mRNA expression in blood and CSF mononuclear cells is augmented in multiple sclerosis.", "abstract": ["Myelin-directed autoimmunity is considered to play a key role in the pathogenesis of multiple sclerosis (MS).", "Increased production of both pro- and anti-inflammatory cytokines is a common finding in MS.", "Interleukin-17 (IL-17) is a recently described cytokine produced in humans almost exclusively by activated memory T cells, which can induce the production of proinflammatory cytokines and chemokines from parenchymal cells and macrophages.", "In situ hybridisation with synthetic oligonucleotide probes was adopted to detect and enumerate IL-17 mRNA expressing mononuclear cells (MNC) in blood and cerebrospinal fluid (CSF) from patients with MS and control individuals.", "Numbers of IL-17 mRNA expressing blood MNC were higher in patients with MS and acute aseptic meningoencephalitis (AM) compared to healthy individuals.", "Higher numbers of IL-17 mRNA expressing blood MNC were detected in MS patients examined during clinical exacerbation compared to remission.", "Patients with MS had higher numbers of IL-17 mRNA expressing MNC in CSF compared to blood.", "This increase in numbers of IL-17 mRNA expressing MNC in CSF was not observed in patients with AM.", "Our results thus demonstrate increased numbers of IL-17 mRNA expressing MNC in MS with higher numbers in CSF than blood, and with the highest numbers in blood during clinical exacerbations."], "structured": false}
{"doc_id": 45457778, "title": "A European perspective on population studies of dementia.", "abstract": ["The change in the world's age demographics and the predicted rise in the incidence of age-related diseases, including dementia, is a source of major public health concern.", "Major research effort in both the United States and Europe has been targeted toward understanding the pathogenesis and epidemiology of dementia.", "This article presents a general overview of the history of dementia research in Europe and how it compares with that in the United States.", "The review highlights the common issues which both U.S. and European researchers have identified and attempted to tackle.", "To maximize information gained from studies across the world, better harmonization of methodology is needed, as informed from current research practice."], "structured": false}
{"doc_id": 45461275, "title": "The cost of providing comprehensive HIV treatment in PEPFAR-supported programs.", "abstract": ["BACKGROUND PEPFAR, national governments, and other stakeholders are investing unprecedented resources to provide HIV treatment in developing countries.", "This study reports empirical data on costs and cost trends in a large sample of HIV treatment sites.   \n", "DESIGN In 2006-2007, we conducted cost analyses at 43 PEPFAR-supported outpatient clinics providing free comprehensive HIV treatment in Botswana, Ethiopia, Nigeria, Uganda, and Vietnam.   \n", "METHODS We collected data on HIV treatment costs over consecutive 6-month periods starting from scale-up of dedicated HIV treatment services at each site.", "The study included all patients receiving HIV treatment and care at study sites [62,512 antiretroviral therapy (ART) and 44,394 pre-ART patients].", "Outcomes were costs per patient and total program costs, subdivided by major cost categories.   \n", "RESULTS Median annual economic costs were US$ 202 (2009 USD) for pre-ART patients and US$ 880 for ART patients.", "Excluding antiretrovirals, per patient ART costs were US$ 298.", "Care for newly initiated ART patients cost 15-20% more than for established patients.", "Per patient costs dropped rapidly as sites matured, with per patient ART costs dropping 46.8% between first and second 6-month periods after the beginning of scale-up, and an additional 29.5% the following year.", "PEPFAR provided 79.4% of funding for service delivery, and national governments provided 15.2%.   \n", "CONCLUSION Treatment costs vary widely between sites, and high early costs drop rapidly as sites mature.", "Treatment costs vary between countries and respond to changes in antiretroviral regimen costs and the package of services.", "Whereas cost reductions may allow near-term program growth, programs need to weigh the trade-off between improving services for current patients and expanding coverage to new patients."], "structured": true}
{"doc_id": 45487164, "title": "A sperm cytoskeletal protein that signals oocyte meiotic maturation and ovulation.", "abstract": ["Caenorhabditis elegans oocytes, like those of most animals, arrest during meiotic prophase.", "Sperm promote the resumption of meiosis (maturation) and contraction of smooth muscle-like gonadal sheath cells, which are required for ovulation.", "We show that the major sperm cytoskeletal protein (MSP) is a bipartite signal for oocyte maturation and sheath contraction.", "MSP also functions in sperm locomotion, playing a role analogous to actin.", "Thus, during evolution, MSP has acquired extracellular signaling and intracellular cytoskeletal functions for reproduction.", "Proteins with MSP-like domains are found in plants, fungi, and other animals, suggesting that related signaling functions may exist in other phyla."], "structured": false}
{"doc_id": 45548062, "title": "Unmet need for mental health care among U.S. children: variation by ethnicity and insurance status.", "abstract": ["OBJECTIVE Policy discussions regarding the mental health needs of children and adolescents emphasize a lack of use of mental health services among youth, but few national estimates are available.", "The authors use three national data sets and examine ethnic disparities in unmet need (defined as having a need for mental health evaluation but not using any services in a 1-year period) to provide such estimates.   \n", "METHOD The authors conducted secondary data analyses in three nationally representative household surveys fielded in 1996-1998: the National Health Interview Survey, the National Survey of American Families, and the Community Tracking Survey.", "They determined rates of mental health service use by children and adolescents 3-17 years of age and differences by ethnicity and insurance status.", "Among the children defined as in need of mental health services, defined by an estimator of mental health problems (selected items from the Child Behavior Checklist), they examined the association of unmet need with ethnicity and insurance status.   \n", "RESULTS In a 12-month period, 2%-3% of children 3-5 years old and 6%-9% of children and adolescents 6-17 years old used mental health services.", "Of children and adolescents 6-17 years old who were defined as needing mental health services, nearly 80% did not receive mental health care.", "Controlling for other factors, the authors determined that the rate of unmet need was greater among Latino than white children and among uninsured than publicly insured children.   \n", "CONCLUSIONS These findings reveal that most children who need a mental health evaluation do not receive services and that Latinos and the uninsured have especially high rates of unmet need relative to other children.", "Rates of use of mental health services are extremely low among preschool children.", "Research clarifying the reasons for high rates of unmet need in specific groups can help inform policy and clinical programs."], "structured": true}
{"doc_id": 45581752, "title": "Conditional economic incentives for reducing HIV risk behaviors: integration of psychology and behavioral economics.", "abstract": ["OBJECTIVE This article reviews psychology and behavioral economic approaches to HIV prevention, and examines the integration and application of these approaches in conditional economic incentive (CEI) programs for reducing HIV risk behavior.   \n", "METHODS We discuss the history of HIV prevention approaches, highlighting the important insights and limitations of psychological theories.", "We provide an overview of the theoretical tenets of behavioral economics that are relevant to HIV prevention, and utilize CEIs as an illustrative example of how traditional psychological theories and behavioral economics can be combined into new approaches for HIV prevention.   \n", "RESULTS Behavioral economic interventions can complement psychological frameworks for reducing HIV risk by introducing unique theoretical understandings about the conditions under which risky decisions are amenable to intervention.", "Findings from illustrative CEI programs show mixed but generally promising effects of economic interventions on HIV and sexually transmitted infection (STI) prevalence, HIV testing, HIV medication adherence, and drug use.   \n", "CONCLUSIONS CEI programs can complement psychological interventions for HIV prevention and behavioral risk reduction.", "To maximize program effectiveness, CEI programs must be designed according to contextual and population-specific factors that may determine intervention applicability and success."], "structured": true}
{"doc_id": 45638119, "title": "ALDH1 is a marker of normal and malignant human mammary stem cells and a predictor of poor clinical outcome.", "abstract": ["Application of stem cell biology to breast cancer research has been limited by the lack of simple methods for identification and isolation of normal and malignant stem cells.", "Utilizing in vitro and in vivo experimental systems, we show that normal and cancer human mammary epithelial cells with increased aldehyde dehydrogenase activity (ALDH) have stem/progenitor properties.", "These cells contain the subpopulation of normal breast epithelium with the broadest lineage differentiation potential and greatest growth capacity in a xenotransplant model.", "In breast carcinomas, high ALDH activity identifies the tumorigenic cell fraction, capable of self-renewal and of generating tumors that recapitulate the heterogeneity of the parental tumor.", "In a series of 577 breast carcinomas, expression of ALDH1 detected by immunostaining correlated with poor prognosis.", "These findings offer an important new tool for the study of normal and malignant breast stem cells and facilitate the clinical application of stem cell concepts."], "structured": false}
{"doc_id": 45651303, "title": "Interleukin-6 and interleukin-8 levels in serum and synovial fluid of patients with osteoarthritis.", "abstract": ["Concentrations of interleukin (IL)-6 and IL-8 in serum and synovial fluid obtained from patients with osteoarthritis (OA) of the knee were determined by the chemiluminescence-ELISA (CL-ELISA) method, the sensitivity of which is 100-1,000 times greater than that of the conventional ELISA method.", "The results were compared with those obtained from patients with rheumatoid arthritis (RA) and from healthy subjects.", "The mean IL-6 and IL-8 levels in synovial fluid indicated higher concentrations in RA than in OA.", "The IL-6 and IL-8 levels in serum were significantly higher in RA and OA relative to controls.", "Among OA patients in whom remarkable improvement was noted in hydrarthrosis, the synovial fluid IL-6 and IL-8 levels at the initial examination were relatively higher, and were markedly decreased after treatment with sodium hyaluronate (NaHA).", "Among those in whom no improvement was noted in hydrarthrosis, the synovial fluid IL-6 and IL-8 levels at the time of initial examination were relatively lower, and hydrarthrosis was not significantly improved even after treatment with NaHA.", "In addition, there was a tendency for the synovial fluid IL-6 and IL-8 levels to decrease as HA levels increased.", "Evaluation of X-ray findings revealed that the IL-6 levels in synovial fluid at the initial examination in low-grade cases tended to be significantly higher than in high-grade cases.", "In low-grade cases, as determined by X-ray findings, there was a significant decrease in IL-6 levels in synovial fluid after treatment with NaHA."], "structured": false}
{"doc_id": 45764440, "title": "Inhibition of SRC expression and activity inhibits tumor progression and metastasis of human pancreatic adenocarcinoma cells in an orthotopic nude mouse model.", "abstract": ["The nonreceptor protein tyrosine kinase Src is overexpressed in 70% of pancreatic adenocarcinomas.", "Here, we describe the effect of molecular and pharmacological down-regulation of Src on incidence, growth, and metastasis of pancreatic tumor cells in an orthotopic model.", "Src expression in L3.6pl human pancreatic tumor cells was reduced by stable expression of a plasmid encoding small interfering RNA (siRNA) to c-src.", "In stable siRNA clones, Src expression was reduced >80%, with no change in expression of the related kinases c-Yes and c-Lyn, and proliferation rates were similar in all clones.", "Phosphorylation of Akt and p44/42 Erk mitogen-activated protein kinase and production of VEGF and IL-8 in culture supernatants were also reduced (P < 0.005).", "On orthotopic implantation of varying cell numbers into nude mice, tumor incidence was unchanged; however, in the siRNA clones, large tumors failed to develop, and incidence of metastasis was significantly reduced, suggesting that c-Src activity is critical to tumor progression.", "To examine this possibility further, animals bearing established wild-type tumors were treated with the Src/Abl-selective inhibitor BMS-354825 (dasatinib).", "Tumor size was decreased, and incidence of metastases was significantly reduced in treated mice compared with controls.", "These results demonstrate that Src activation contributes to pancreatic tumor progression in this model, offering Src as a candidate for targeted therapy."], "structured": false}
{"doc_id": 45770026, "title": "Eicosapentaenoic acid is converted via \u03c9-3 epoxygenation to the anti-inflammatory metabolite 12-hydroxy-17,18-epoxyeicosatetraenoic acid.", "abstract": ["Eicosapentaenoic acid (EPA) has beneficial effects in many inflammatory disorders.", "In this study, dietary EPA was converted to 17,18-epoxyeicosatetraenoic acid (17,18-EpETE) by \u03c9-3 epoxygenation in the mouse peritoneal cavity.", "Mediator lipidomics revealed a series of novel oxygenated metabolites of 17,18-EpETE, and one of the major metabolites, 12-hydroxy-17,18-epoxyeicosatetraenoic acid (12-OH-17,18-EpETE), displayed a potent anti-inflammatory action by limiting neutrophil infiltration in murine zymosan-induced peritonitis.", "12-OH-17,18-EpETE inhibited leukotriene B4-induced neutrophil chemotaxis and polarization in vitro in a low nanomolar range (EC50 0.6 nM).", "The complete structures of two natural isomers were assigned as 12S-OH-17R,18S-EpETE and 12S-OH-17S,18R-EpETE, using chemically synthesized stereoisomers.", "These natural isomers displayed potent anti-inflammatory action, whereas the unnatural stereoisomers were essentially devoid of activity.", "These results demonstrate that 17,18-EpETE derived from dietary EPA is converted to a potent bioactive metabolite 12-OH-17,18-EpETE, which may generate an endogenous anti-inflammatory metabolic pathway."], "structured": false}
{"doc_id": 45820464, "title": "Scrapie in mice. Agent-strain differences in the distribution and intensity of grey matter vacuolation.", "abstract": ["Five strains of scrapie agent were used as intracerebral inocula for 2 inbred mouse strains, C57BL and VM, and their F1 cross.", "The degree of vacuolation in specified regions of the brain, and the relative distribution of this damage in 9 regions represented as a \u201clesion profile\u201d, was different for each agent.", "Any of the 5 scrapie agents could be distinguished from the others with a very high degree of reliability solely on the basis of these histological parameters, using either strain of mouse.", "The lesion profile was unaffected by the dose of the agent, using doses of ME7 agent ranging over 6 orders of magnitude in C57BL mice.    ", "The genotype of mouse had a marked effect on the overall degree of vacuolation and on the shape of the lesion profile: these effects were more profound with some agents than others.", "In certain areas of the brain, depending upon the strain of agent used, the (C57BL \u00d7 VM)F1 cross was found to have either significantly more or significantly less vacuolation than either parental genotype.", "The genetic control of the lesion profile was found to be too complex for more detailed analysis in these data."], "structured": false}
{"doc_id": 45875990, "title": "Cyclin A2 is an RNA binding protein that controls Mre11 mRNA translation", "abstract": ["Cyclin A2 activates the cyclin-dependent kinases Cdk1 and Cdk2 and is expressed at elevated levels from S phase until early mitosis.", "We found that mutant mice that cannot elevate cyclin A2 are chromosomally unstable and tumor-prone.", "Underlying the chromosomal instability is a failure to up-regulate the meiotic recombination 11 (Mre11) nuclease in S phase, which leads to impaired resolution of stalled replication forks, insufficient repair of double-stranded DNA breaks, and improper segregation of sister chromosomes.", "Unexpectedly, cyclin A2 controlled Mre11 abundance through a C-terminal RNA binding domain that selectively and directly binds Mre11 transcripts to mediate polysome loading and translation.", "These data reveal cyclin A2 as a mechanistically diverse regulator of DNA replication combining multifaceted kinase-dependent functions with a kinase-independent, RNA binding\u2013dependent role that ensures adequate repair of common replication errors."], "structured": false}
{"doc_id": 45908102, "title": "Cluster sampling to assess immunization coverage: a review of experience with a simplified sampling method.", "abstract": ["The Expanded Program on Immunization (EPI) is using a simplified cluster sampling method, based on the random selection of 210 children in 30 clusters of 7 children each, to estimate immunization coverage levels.", "This article analyzes the results of this method in actual and computer simulated surveys.", "Results from 60 actual surveys conducted in 25 countries were available for analysis, for a total of 446 sample estimations of immunization coverage.", "83% of the sample results had 95% confidence limits within + or - 10%, and none of the surveys had 95% confidence limits exceeding + or - 13%.", "In addition, 12 hypothetical population strata with immunization coverage rates ranging from 10%-99% were established for the purposes of computer simulation, and 10 hypothetical communities were established by allocating to them various proportions of each of the strata.", "These simulated surveys also supported the validity of the EPI method: over 95% of the results were less than + or - 10% from the actual population mean.", "The precision of this method, as estimated from the results of both actual and simulated surveys, is considered satisfactory for the requirements of the EPI.", "Among the actual surveys, the proportion of results whose confidence limits exceeded + or - 10% was greatest (50%) when immunization coverage in the sample was 45%-54%."], "structured": false}
{"doc_id": 45920278, "title": "Gender differences in the utilization of health care services.", "abstract": ["BACKGROUND Studies have shown that women use more health care services than men.", "We used important independent variables, such as patient sociodemographics and health status, to investigate gender differences in the use and costs of these services.   \n", "METHODS New adult patients (N = 509) were randomly assigned to primary care physicians at a university medical center.", "Their use of health care services and associated charges were monitored for 1 year of care.", "Self-reported health status was measured using the Medical Outcomes Study Short Form-36 (SF-36).", "We controlled for health status, sociodemographic information, and primary care physician specialty in the statistical analyses.   \n", "RESULTS Women had significantly lower self-reported health status and lower mean education and income than men.", "Women had a significantly higher mean number of visits to their primary care clinic and diagnostic services than men.", "Mean charges for primary care, specialty care, emergency treatment, diagnostic services, and annual total charges were all significantly higher for women than men; however, there were no differences for mean hospitalizations or hospital charges.", "After controlling for health status, sociodemographics, and clinic assignment, women still had higher medical charges for all categories of charges except hospitalizations.   \n", "CONCLUSIONS Women have higher medical care service utilization and higher associated charges than men.", "Although the appropriateness of these differences was not determined, these findings have implications for health care."], "structured": true}
{"doc_id": 46112052, "title": "Recombinant human tumor necrosis factor administered as a 24-hour intravenous infusion. A phase I and pharmacologic study.", "abstract": ["Recombinant human tumor necrosis factor (rH-TNF) is a cytokine with direct antitumor properties.", "In a phase I trial we continuously infused rH-TNF for 24 hours.", "We gave a total of 115 courses of therapy to 50 patients.", "Doses ranged from 4.5 to 645 micrograms of rH-TNF/m2.", "Systemic toxicity, including fever, chills, fatigue, and hypotension, increased with the dose of rH-TNF administered.", "Doses greater than 454 micrograms/m2 frequently caused severe lethargy and fatigue, which precluded hospital discharge of the patient at the completion of therapy.", "The dose-limiting toxicity was hypotension, and five patients treated at the two highest dose levels required dopamine treatment.", "Other organ-specific toxicity was modest and spontaneously resolved after 48 hours.", "The 24-hour infusions of rH-TNF were associated with significant decreases in serum cholesterol and high-density lipoprotein levels.", "Pharmacokinetic studies using an enzyme-linked immunosorbent assay demonstrated peak plasma rH-TNF levels of 90-900 pg/mL. Despite continuous infusion of rH-TNF, no steady-state level was achieved.", "The recommended phase II dose for rH-TNF as a 24-hour continuous infusion is 545 micrograms/m2."], "structured": false}
{"doc_id": 46127781, "title": "Detection and comparison of epidermal growth factor receptor mutations in cells and fluid of malignant pleural effusion in non-small cell lung cancer.", "abstract": ["Cells or cell-free fluid of malignant pleural effusion could be important clinical specimen for epidermal growth factor receptor (EGFR) mutation screening in advanced non-small cell lung cancer (NSCLC) patients.", "However, their usefulness in mutation detection has not been well compared.", "In this study we recruited 26 East Asian NSCLC patients with malignant pleural effusion, determined the mutation status of EGFR in both cells and matched cell-free fluid with the use of sequencing and mutant-enriched PCR.", "After comparing the mutation spectrums, we found both the cells and cell-free pleural fluid may be feasible clinical specimen for EGFR mutation detection in unresectable NSCLC given sensitive genotyping assays employed.", "Direct sequencing could miss a significant portion of mutations in these heterogeneous specimens.", "More sensitive methods, such as mutant-enriched PCR and gene scan, could provide more reliable mutational information."], "structured": false}
{"doc_id": 46135768, "title": "Materials and Methods Figs. S1 to S15 References Supporting Online Materials", "abstract": ["Endosomal Toll-like receptors (TLRs) 7 and 9 recognize viral pathogens and induce signals leading to the activation of nuclear factor \u03baB (NF-\u03baB)-dependent proinflammatory cytokines and interferon regulatory factor 7 (IRF7)-dependent type I interferons (IFNs).", "Recognition of viral nucleic acids by TLR9 requires its cleavage in the endolysosomal compartment.", "Here, we show that TLR9 signals leading to the activation of type I IFN, but not proinflammatory cytokine genes, require TLR9 trafficking from endosomes to a specialized lysosome-related organelle.", "Furthermore, we identify adapter protein-3 as the protein complex responsible for the trafficking of TLR9 to this subcellular compartment.", "Our results reveal an intracellular mechanism for bifurcation of TLR9 signals by selective receptor trafficking within the endosomal system."], "structured": false}
{"doc_id": 46153874, "title": "Sedimentation velocity method in the analytical ultracentrifuge for the study of protein-protein interactions.", "abstract": ["Sedimentation analysis in the analytical ultracentrifuge can be employed to detect macromolecular interactions.", "Whenever two molecules interact the mass of the resulting complex is increased and this is reflected in the sedimentation behavior.", "In this chapter we discuss how this phenomenon can be utilized to determine quantitative parameters of an interaction.", "An example, interaction of single-stranded DNA binding protein with a subunit of DNA polymerase III holoenzyme is given together with a thorough treatment of the relating theory and a description of evaluation algorithms."], "structured": false}
{"doc_id": 46182525, "title": "Structural trends in the aging femoral neck and proximal shaft: analysis of the Third National Health and Nutrition Examination Survey dual-energy X-ray absorptiometry data.", "abstract": ["Hip scans of U.S. adults aged 20-99 years acquired in the Third National Health and Nutrition Examination Survey (NHANES III) using dual-energy X-ray absorptiometry (DXA) were analyzed with a structural analysis program.", "The program analyzes narrow (3 mm wide) regions at specific locations across the proximal femur to measure bone mineral density (BMD) as well as cross-sectional areas (CSAs), cross-sectional moments of inertia (CSMI), section moduli, subperiosteal widths, and estimated mean cortical thickness.", "Measurements are reported here on a non-Hispanic white subgroup of 2,719 men and 2,904 women for a cortical region across the proximal shaft 2 cm distal to the lesser trochanter and a mixed cortical/trabecular region across the narrowest point of the femoral neck.", "Apparent age trends in BMD and section modulus were studied for both regions by sex after correction for body weight.", "The BMD decline with age in the narrow neck was similar to that seen in the Hologic neck region; BMD in the shaft also declined, although at a slower rate.", "A different pattern was seen for section modulus; furthermore, this pattern depended on sex.", "Specifically, the section modulus at both the narrow neck and the shaft regions remains nearly constant until the fifth decade in females and then declined at a slower rate than BMD.", "In males, the narrow neck section modulus declined modestly until the fifth decade and then remained nearly constant whereas the shaft section modulus was static until the fifth decade and then increased steadily.", "The apparent mechanism for the discord between BMD and section modulus is a linear expansion in subperiosteal diameter in both sexes and in both regions, which tends to mechanically offset net loss of medullary bone mass.", "These results suggest that aging loss of bone mass in the hip does not necessarily mean reduced mechanical strength.", "Femoral neck section moduli in the elderly are on the average within 14% of young values in females and within 6% in males."], "structured": false}
{"doc_id": 46193388, "title": "Turning blood into brain: cells bearing neuronal antigens generated in vivo from bone marrow.", "abstract": ["Bone marrow stem cells give rise to a variety of hematopoietic lineages and repopulate the blood throughout adult life.", "We show that, in a strain of mice incapable of developing cells of the myeloid and lymphoid lineages, transplanted adult bone marrow cells migrated into the brain and differentiated into cells that expressed neuron-specific antigens.", "These findings raise the possibility that bone marrow-derived cells may provide an alternative source of neurons in patients with neurodegenerative diseases or central nervous system injury."], "structured": false}
{"doc_id": 46193478, "title": "A negative staining method for high resolution electron microscopy of viruses.", "abstract": ["Abstract A simple technique has been developed for the study of the external form and structure of virus particles.", "High contrast with good preservation is obtained by mixing virus preparations with 1% phosphotungstic acid adjusted to pH 7.5 and spraying directly onto electron microscope supporting films made from evaporated carbon.", "The application of the technique to tobacco mosaic virus and turnip yellow mosaic virus is described.", "Structural details suggested by X-ray diffraction methods have been resolved."], "structured": false}
{"doc_id": 46202852, "title": "Nef induces multiple genes involved in cholesterol synthesis and uptake in human immunodeficiency virus type 1-infected T cells.", "abstract": ["Several recent reports indicate that cholesterol might play an important role in human immunodeficiency virus type 1 (HIV-1) replication.", "We investigated the effects of HIV-1 infection on cholesterol biosynthesis and uptake using microarrays.", "HIV-1 increased gene expression of cholesterol genes in both transformed T-cell lines and primary CD4(+) T cells.", "Consistent with our microarray data, (14)C-labeled mevalonate and acetate incorporation was increased in HIV-1-infected cells.", "Our data also demonstrate that changes in cholesterol biosynthesis and uptake are only observed in the presence of functional Nef, suggesting that increased cholesterol synthesis may contribute to Nef-mediated enhancement of virion infectivity and viral replication."], "structured": false}
{"doc_id": 46248894, "title": "Long noncoding RNA as modular scaffold of histone modification complexes", "abstract": ["Long intergenic noncoding RNAs (lincRNAs) regulate chromatin states and epigenetic inheritance.", "Here, we show that the lincRNA HOTAIR serves as a scaffold for at least two distinct histone modification complexes.", "A 5' domain of HOTAIR binds polycomb repressive complex 2 (PRC2), whereas a 3' domain of HOTAIR binds the LSD1/CoREST/REST complex.", "The ability to tether two distinct complexes enables RNA-mediated assembly of PRC2 and LSD1 and coordinates targeting of PRC2 and LSD1 to chromatin for coupled histone H3 lysine 27 methylation and lysine 4 demethylation.", "Our results suggest that lincRNAs may serve as scaffolds by providing binding surfaces to assemble select histone modification enzymes, thereby specifying the pattern of histone modifications on target genes."], "structured": false}
{"doc_id": 46266579, "title": "Therapeutic Clearance of Amyloid by Antibodies to Serum Amyloid P Component.", "abstract": ["BACKGROUND The amyloid fibril deposits that cause systemic amyloidosis always contain the nonfibrillar normal plasma protein, serum amyloid P component (SAP).", "The drug (R)-1-[6-[(R)-2-carboxy-pyrrolidin-1-yl]-6-oxo-hexanoyl]pyrrolidine-2-carboxylic acid (CPHPC) efficiently depletes SAP from the plasma but leaves some SAP in amyloid deposits that can be specifically targeted by therapeutic IgG anti-SAP antibodies.", "In murine amyloid A type amyloidosis, the binding of these antibodies to the residual SAP in amyloid deposits activates complement and triggers the rapid clearance of amyloid by macrophage-derived multinucleated giant cells.   \n", "METHODS We conducted an open-label, single-dose-escalation, phase 1 trial involving 15 patients with systemic amyloidosis.", "After first using CPHPC to deplete circulating SAP, we infused a fully humanized monoclonal IgG1 anti-SAP antibody.", "Patients with clinical evidence of cardiac involvement were not included for safety reasons.", "Organ function, inflammatory markers, and amyloid load were monitored.   \n", "RESULTS There were no serious adverse events.", "Infusion reactions occurred in some of the initial recipients of larger doses of antibody; reactions were reduced by slowing the infusion rate for later patients.", "At 6 weeks, patients who had received a sufficient dose of antibody in relation to their amyloid load had decreased liver stiffness, as measured with the use of transient elastography.", "These patients also had improvements in liver function in association with a substantial reduction in hepatic amyloid load, as shown by means of SAP scintigraphy and measurement of extracellular volume by magnetic resonance imaging.", "A reduction in kidney amyloid load and shrinkage of an amyloid-laden lymph node were also observed.   \n", "CONCLUSIONS Treatment with CPHPC followed by an anti-SAP antibody safely triggered clearance of amyloid deposits from the liver and some other tissues.", "(Funded by GlaxoSmithKline; ClinicalTrials.gov number, NCT01777243.)."], "structured": true}
{"doc_id": 46277811, "title": "LPA Gene, Ethnicity, and Cardiovascular Events", "abstract": ["Background: The relationship of LPA single nucleotide polymorphisms (SNPs), apolipoprotein(a) isoforms, and lipoprotein(a) [Lp(a)] levels with major adverse cardiovascular events (MACE) in different ethnic groups is not well known.", "Methods: LPA SNPs, apolipoprotein(a) isoforms, Lp(a), and oxidized phospholipids on apolipoprotein B-100 (OxPL-apoB) levels were measured in 1792 black, 1030 white, and 597 Hispanic subjects enrolled in the Dallas Heart Study.", "Their interdependent relationships and prospective association with MACE after median 9.5-year follow-up were determined.", "Results: LPA SNP rs3798220 was most prevalent in Hispanics (42.38%), rs10455872 in whites (14.27%), and rs9457951 in blacks (32.92%).", "The correlation of each of these SNPs with the major apolipoprotein(a) isoform size was highly variable and in different directions among ethnic groups.", "In the entire cohort, Cox regression analysis with multivariable adjustment revealed that quartiles 4 of Lp(a) and OxPL-apoB were associated with hazard ratios (95% confidence interval) for time to MACE of 2.35 (1.50\u20133.69, P<0.001) and 1.89 (1.26\u20132.84, P=0.003), respectively, versus quartile 1.", "Addition of the major apolipoprotein(a) isoform and the 3 LPA SNPs to these models attenuated the risk, but significance was maintained for both Lp(a) and OxPL-apoB. Evaluating time to MACE in specific ethnic groups, Lp(a) was a positive predictor and the size of the major apolipoprotein(a) isoform was an inverse predictor in blacks, the size of the major apolipoprotein(a) isoform was an inverse predictor in whites, and OxPL-apoB was a positive predictor in Hispanics.", "Conclusions: The prevalence and association of LPA SNPs with size of apolipoprotein(a) isoforms, Lp(a), and OxPL-apoB levels are highly variable and ethnicity-specific.", "The relationship to MACE is best explained by elevated plasma Lp(a) or OxPL-apoB levels, despite significant ethnic differences in LPA genetic markers."], "structured": false}
{"doc_id": 46305977, "title": "Protein kinase CK2 modulates developmental functions of the abscisic acid responsive protein Rab17 from maize.", "abstract": ["The maize abscisic acid responsive protein Rab17 is a highly phosphorylated late embryogenesis abundant protein involved in plant responses to stress.", "In this study, we provide evidence of the importance of Rab17 phosphorylation by protein kinase CK2 in growth-related processes under stress conditions.", "We show the specific interaction of Rab17 with the CK2 regulatory subunits CK2 beta-1 and CK2 beta-3, and that these interactions do not depend on the phosphorylation state of Rab17.", "Live-cell fluorescence imaging of both CK2 and Rab17 indicates that the intracellular dynamics of Rab17 are regulated by CK2 phosphorylation.", "We found both CK2 beta subunits and Rab17 distributed over the cytoplasm and nucleus.", "By contrast, catalytic CK2 alpha subunits and a Rab17 mutant protein (mRab17) that is not a substrate for CK2 phosphorylation remain accumulated in the nucleoli.", "A dual-color image shows that the CK2 holoenzyme accumulates mainly in the nucleus.", "The importance of Rab17 phosphorylation in vivo was assessed in transgenic plants.", "The overexpression of Rab17, but not mRab17, arrests the process of seed germination under osmotic stress conditions.", "Thus, the role of Rab17 in growth processes is mediated through its phosphorylation by protein kinase CK2."], "structured": false}
{"doc_id": 46328296, "title": "Reduced plasma concentrations of nitrogen oxide in individuals with essential hypertension.", "abstract": ["Patients with essential hypertension exhibit blunted endothelium-dependent vasodilator responses, which may be largely attributable to reduced bioactivity of nitric oxide (NO).", "Therefore, we measured the end product of NO, nitrate plus nitrite (nitrogen oxide), and examined the relationship between the degree of hypertension and plasma nitrate plus nitrite levels in patients with essential hypertension.", "The combined plasma concentration of nitrate plus nitrite, end products of NO metabolism, was reduced in individuals with essential hypertension relative to that in control subjects (15.7+/-1.1 versus 22.8+/-1.4 mmol x L(-1), P<.001); individuals with borderline hypertension showed values that were intermediate between those of the other two groups (18.2+/-1.2 mmol x L(-1), P<.001).", "The plasma nitrogen oxide concentration showed significant inverse correlations with both systolic and diastolic blood pressures.", "The basal concentration of nitrogen oxide in the plasma was reduced, at least in the peripheral circulation, in individuals with essential hypertension."], "structured": false}
{"doc_id": 46346525, "title": "Isolation of superoxide dismutase mutants in Escherichia coli: is superoxide dismutase necessary for aerobic life?", "abstract": ["Mu transposons carrying the chloramphenicol resistance marker have been inserted into the cloned Escherichia coli genes sodA and sodB coding for manganese superoxide dismutase (MnSOD) and iron superoxide dismutase (FeSOD) respectively, creating mutations and gene fusions.", "The mutated sodA or sodB genes were introduced into the bacterial chromosome by allelic exchange.", "The resulting mutants were shown to lack the corresponding SOD by activity measurements and immunoblot analysis.", "Aerobically, in rich medium, the absence of FeSOD or MnSOD had no major effect on growth or sensitivity to the superoxide generator, paraquat.", "In minimal medium aerobic growth was not affected, but the sensitivity to paraquat was increased, especially in the sodA mutant.", "A sodA sodB double mutant completely devoid of SOD was also obtained.", "It was able to grow aerobically in rich medium, its catalase level was unaffected and it was highly sensitive to paraquat and hydrogen peroxide; the double mutant was unable to grow aerobically on minimal glucose medium.", "Growth could be restored by removing oxygen, by providing an SOD-overproducing plasmid or by supplementing the medium with the 20 amino acids.", "It is concluded that the total absence of SOD in E. coli creates a conditional sensitivity to oxygen."], "structured": false}
{"doc_id": 46353045, "title": "Late presentation of HIV-infected individuals.", "abstract": ["Late presentation remains a major concern despite the dramatically improved prognosis realized by ART.", "We define a first presentation for HIV care during the course of HIV infection as 'late' if an AIDS-defining opportunistic disease is apparent, or if CD4+ T-cells are <200/microl.", "In the Western world, approximately 10 and 30% of HIV-infected individuals still present with CD4+ T-cells <50 and <200/microl, respectively; estimates are substantially higher for developing countries.", "Diagnosis and treatment of opportunistic diseases and intense supportive in-hospital care take precedence over ART.", "Benefits of starting ART without delay, that is, when opportunistic diseases are still active, include faster resolution of opportunistic diseases and a decreased risk of recurrence.", "The downside of starting ART without delay could include toxicity, drug interactions and immune reconstitution inflammatory syndrome (IRIS).", "Among asymptomatic or oligosymptomatic individuals presenting late, where ART and primary prophylaxis are initiated, approximately 10-20% will become symptomatic from drug toxicity or undiagnosed opportunistic complications, including IRIS, which require appropriate therapies.", "In this review we describe late presentation to HIV care, the scale of the problem, the evaluation of a late-presenting patient and challenges associated with initiation of potent antiretroviral therapy (ART) in the setting of acute opportunistic infections and other comorbidities."], "structured": false}
{"doc_id": 46355579, "title": "Rapid clearance of human papillomavirus and implications for clinical focus on persistent infections.", "abstract": ["Health professionals and the public need to understand the natural history of human papillomavirus (HPV) infections of the cervix to best use the information provided by new molecular screening tests.", "We investigated outcomes of 800 carcinogenic HPV infections detected in 599 women at enrollment into a population-based cohort (Guanacaste, Costa Rica).", "For individual infections, we calculated cumulative proportions of three outcomes (viral clearance, persistence without cervical intraepithelial neoplasia grade 2 or worse [CIN2+], or persistence with new diagnosis of CIN2+) at successive 6-month time points for the first 30 months of follow-up.", "Cervical specimens were tested for carcinogenic HPV genotypes using an L1 degenerate-primer polymerase chain reaction method.", "Infections typically cleared rapidly, with 67% (95% confidence interval [CI] = 63% to 70%) clearing by 12 months.", "However, among infections that persisted at least 12 months, the risk of CIN2+ diagnosis by 30 months was 21% (95% CI = 15% to 28%).", "The risk of CIN2+ diagnosis was highest among women younger than 30 years with HPV-16 infections that persisted for at least 12 months (53%; 95% CI = 29% to 76%).", "These findings suggest that the medical community should emphasize persistence of cervical HPV infection, not single-time detection of HPV, in management strategies and health messages."], "structured": false}
{"doc_id": 46437558, "title": "The role of alcohol in the Russian mortality crisis.", "abstract": ["AIMS Alcohol is believed to be an important factor behind the sharp rise in mortality during the period 1990-94 in Russia.", "However, the rise in the standard alcohol consumption proxy does not seem to be sufficient to explain all the increase in mortality.", "This study adopts a novel approach to exploring the role of the alcohol factor in the increased mortality by investigating whether the mismatch between trends in mortality and recorded alcohol consumption is due to an underestimation of the consumption increase.   \n", "DESIGN AND MEASUREMENTS First, the alcohol effect on the male accident rate was estimated using data for the period 1959-89.", "Next, the estimated alcohol effect and the observed accident mortality rate for the period 1990-98 were used to backcast alcohol consumption during that period.", "Thirdly, the backcasted alcohol series was used to predict trajectories in alcohol poisoning mortality, the homicide rate and all-cause mortality during the period 1990-98.   \n", "FINDINGS", "There was a markedly stronger increase in the backcasted consumption proxy than in the standard alcohol consumption proxy during the period 1990-98.", "There was a substantial gap between the observed mortality rates and the rates predicted from the standard alcohol consumption proxy, whereas the predictions from the backcasted alcohol proxy were much closer to the target.   \n", "CONCLUSIONS Much of the rise in Russian mortality in 1990-94 appears to have been due to the increase in population drinking, but this increase is grossly underestimated by the commonly used consumption proxy combining alcohol sales, estimation of illicit alcohol production and proportion of alcohol-positive violent deaths."], "structured": true}
{"doc_id": 46451940, "title": "The lateral hypothalamus: a primary site mediating excitatory amino acid-elicited eating.", "abstract": ["Lateral hypothalamic (LH) injections of the excitatory neurotransmitter glutamate, or its excitatory amino acid (EAA) agonists, kainic acid (KA), D,L-alpha-amino-3-hydroxy-5-methyl-isoxazole propionic acid (AMPA), or N-methyl-D-aspartic acid (NMDA), can rapidly elicit an intense feeding response in satiated rats.", "To determine whether the LH is the actual locus of this effect, we compared these compounds' ability to stimulate feeding when injected into the LH, versus when injected into sites bracketing this region.", "Food intake in groups of adult male rats was measured 1 h after injection of glutamate (30-900 nmol), KA (0.1-1.0 nmol), AMPA (0.33-3.3 nmol), NMDA (0.33-33.3 nmol) or vehicle, through chronically implanted guide cannulas, into one of seven brain sites.", "These sites were: the LH, the anterior and posterior tips of the LH, the thalamus immediately dorsal to the LH, the amygdala just lateral to the LH, or the paraventricular and perifornical areas medial to the LH.", "The results show that across doses and agonists the eating-stimulatory effects were largest with injections into the LH.", "In the LH, glutamate between 300 and 900 nmol elicited a dose-dependent eating response of up to 5 g within 1 h (P < 0.01).", "Each of the other agonists at doses of 3.3 nmol or less elicited eating responses of at least 10 g with injections into this site.", "Injections into the other brain sites produced either no eating, or occasionally smaller and less consistent eating responses.(ABSTRACT TRUNCATED AT 250 WORDS)"], "structured": false}
{"doc_id": 46478393, "title": "A Gateway\u00ae compatible vector for gene silencing in bloodstream form Trypanosoma brucei.", "abstract": ["RNA interference is the most rapid method for generation of conditional knockdown mutants in Trypanosoma brucei.", "The dual T7 promoter (pZJM) and the stem-loop vectors have been widely used to generate stable inducible RNAi cell lines with the latter providing tighter regulatory control.", "However, the steps for cloning stem-loop constructs are cumbersome requiring either multiple cloning steps or multi-fragment ligation reactions.", "We report the development of a vector (pTrypRNAiGate) derived from pLEW100 that utilizes the Gateway\u00ae recombination system to facilitate easy production of hairpin RNA constructs.", "This approach allows the final stem-loop RNAi construct to be generated from a single cloning step of the PCR-derived gene fragment followed by an in vitro recombination reaction.", "The new vector facilitates high-throughput applications for gene silencing and provides a tool for functional genomics in T. brucei."], "structured": false}
{"doc_id": 46485368, "title": "Prolonged effect of calcium supplementation on risk of colorectal adenomas in a randomized trial.", "abstract": ["BACKGROUND Calcium supplementation has been shown to decrease the risk of recurrence of colorectal adenomas in randomized trials.", "However, the duration of this protective effect after cessation of active supplementation is not known.   \n", "METHODS In the Calcium Polyp Prevention Study, 930 subjects with a previous colorectal adenoma were randomly assigned from November 1988 through April 1992 to receive placebo or 1200 mg of elemental calcium daily for 4 years.", "The Calcium Follow-up Study was an observational phase of the trial that tracked adenoma occurrence for an average of 7 years after the end of randomized treatment and gathered information regarding the use of medications, vitamins, and supplements during that time.", "We obtained follow-up information for 822 subjects, 597 of whom underwent at least one colonoscopy after the end of study treatment and are included in this analysis.", "Generalized linear models were used to compute relative risks (RRs) and 95% confidence intervals (CIs) for the effect of randomized calcium treatment on risk of adenoma recurrence during the first 5 years after study treatment ended and during the subsequent 5 years.", "Statistical tests were two-sided.   \n", "RESULTS During the first 5 years after randomized treatment ended, subjects in the calcium group still had a substantially and statistically significantly lower risk of any adenoma than those in the placebo group (31.5% versus 43.2%; adjusted RR = 0.63, 95% CI = 0.46 to 0.87, P = .005) and a smaller and not statistically significant reduction in risk of advanced adenomas (adjusted RR = 0.85, 95% CI = 0.43 to 1.69, P = .65).", "However, the randomized treatment was not associated with the risk of any type of polyp during the next 5 years.", "The findings were broadly similar when the analysis was restricted to subjects who did not report use of any calcium supplements after the treatment phase of the trial ended.   \n", "CONCLUSION The protective effect of calcium supplementation on risk of colorectal adenoma recurrence extends up to 5 years after cessation of active treatment, even in the absence of continued supplementation."], "structured": true}
{"doc_id": 46517055, "title": "Influence of DNA on the activities and inhibition of neutrophil serine proteases in cystic fibrosis sputum.", "abstract": ["Uncontrolled proteolysis by neutrophil serine proteases (NSPs) in lung secretions is a hallmark of cystic fibrosis (CF).", "We have shown that the active neutrophil elastase, protease 3, and cathepsin G in CF sputum resist inhibition in part by exogenous protease inhibitors.", "This resistance may be due to their binding to neutrophil extracellular traps (NETs) secreted by the activated neutrophils in CF sputum and to genomic DNA released from senescent and dead neutrophils.", "Treating CF sputum with DNase dramatically increases its elastase activity, which can then be stoichiometrically inhibited by exogenous elastase inhibitors.", "However, DNase treatment does not increase the activities of protease 3 and cathepsin G, indicating their different distribution and/or binding in CF sputum.", "Purified blood neutrophils secrete NETs when stimulated by the opportunistic CF bacteria Pseudomonas aeruginosa and Staphylococcus aureus.", "The activities of the three proteases were unchanged in these conditions, but subsequent DNase treatment produced a dramatic increase in all three proteolytic activities.", "Neutrophils activated with a calcium ionophore did not secrete NETs but released huge amounts of active proteases whose activities were not modified by DNase.", "We conclude that NETs are reservoirs of active proteases that protect them from inhibition and maintain them in a rapidly mobilizable status.", "Combining the effects of protease inhibitors with that of DNA-degrading agents could counter the deleterious proteolytic effects of NSPs in CF lung secretions."], "structured": false}
{"doc_id": 46565020, "title": "Clinical effects of Abeta immunization (AN1792) in patients with AD in an interrupted trial.", "abstract": ["BACKGROUND AN1792 (beta-amyloid [Abeta]1-42) immunization reduces Abeta plaque burden and preserves cognitive function in APP transgenic mice.", "The authors report the results of a phase IIa immunotherapy trial of AN1792(QS-21) in patients with mild to moderate Alzheimer disease (AD) that was interrupted because of meningoencephalitis in 6% of immunized patients.   \n", "METHODS This randomized, multicenter, placebo-controlled, double-blind trial of IM AN1792 225 microg plus the adjuvant QS-21 50 microg (300 patients) and saline (72 patients) included patients aged 50 to 85 years with probable AD, Mini-Mental State Examination (MMSE) 15 to 26.", "Injections were planned for months 0, 1, 3, 6, 9, and 12.", "Safety and tolerability were evaluated, and pilot efficacy (AD Assessment Scale-Cognitive Subscale [ADAS-Cog], MRI, neuropsychological test battery [NTB], CSF tau, and Abeta42) was assessed in anti-AN1792 antibody responder patients (immunoglobulin G titer > or = 1:2,200).   \n", "RESULTS Following reports of meningoencephalitis (overall 18/300 [6%]), immunization was stopped after one (2 patients), two (274 patients), or three (24 patients) injections.", "Of the 300 AN1792(QS-21)-treated patients, 59 (19.7%) developed the predetermined antibody response.", "Double-blind assessments were maintained for 12 months.", "No significant differences were found between antibody responder and placebo groups for ADAS-Cog, Disability Assessment for Dementia, Clinical Dementia Rating, MMSE, or Clinical Global Impression of Change, but analyses of the z-score composite across the NTB revealed differences favoring antibody responders (0.03 +/- 0.37 vs -0.20 +/- 0.45; p = 0.020).", "In the small subset of subjects who had CSF examinations, CSF tau was decreased in antibody responders (n = 11) vs placebo subjects (n = 10; p < 0.001).   \n", "CONCLUSION Although interrupted, this trial provides an indication that Abeta immunotherapy may be useful in Alzheimer disease."], "structured": true}
{"doc_id": 46565968, "title": "Quantitative characterization of metastatic disease in the spine. Part I. Semiautomated segmentation using atlas-based deformable registration and the level set method.", "abstract": ["Quantitative assessment of metastatic disease in bone is often considered immeasurable and, as such, patients with skeletal metastases are often excluded from clinical trials.", "In order to effectively quantify the impact of metastatic tumor involvement in the spine, accurate segmentation of the vertebra is required.", "Manual segmentation can be accurate but involves extensive and time-consuming user interaction.", "Potential solutions to automating segmentation of metastatically involved vertebrae are demons deformable image registration and level set methods.", "The purpose of this study was to develop a semiautomated method to accurately segment tumor-bearing vertebrae using the aforementioned techniques.", "By maintaining morphology of an atlas, the demons-level set composite algorithm was able to accurately differentiate between trans-cortical tumors and surrounding soft tissue of identical intensity.", "The algorithm successfully segmented both the vertebral body and trabecular centrum of tumor-involved and healthy vertebrae.", "This work validates our approach as equivalent in accuracy to an experienced user."], "structured": false}
{"doc_id": 46594244, "title": "Activation of lysosomal function during dendritic cell maturation.", "abstract": ["In response to a variety of stimuli, dendritic cells (DCs) transform from immature cells specialized for antigen capture into mature cells specialized for T cell stimulation.", "During maturation, the DCs acquire an enhanced capacity to form and accumulate peptide-MHC (major histocompatibility complex) class II complexes.", "Here we show that a key mechanism responsible for this alteration was the generalized activation of lysosomal function.", "In immature DCs, internalized antigens were slowly degraded and inefficiently used for peptide loading.", "Maturation induced activation of the vacuolar proton pump that enhanced lysosomal acidification and antigen proteolysis, facilitating efficient formation of peptide-MHC class II complexes.", "Lysosomal function in DCs thus appears to be specialized for the developmentally regulated processing of internalized antigens."], "structured": false}
{"doc_id": 46602807, "title": "Comparison of agar dilution, microdilution, and disk elution methods for measuring the synergy of cefotaxime and its metabolite against anaerobes.", "abstract": ["The activities of cefotaxime (CTX) and desacetyl cefotaxime (des-CTX) were tested both singly and in combination against 173 anaerobic clinical isolates.", "The MIC of CTX for 50% of 60 Bacteroides fragilis isolates was 22.4 micrograms/ml in broth, compared with 47.4 micrograms/ml in agar.", "This reduced efficacy in agar was seen with all species tested and is in apparent conflict with reported clinical efficacy of the drug.", "Synergy between CTX and des-CTX was observed with 70 to 100% of the isolates, including 60% of all Bacteroides spp.", "tested.", "The susceptibility results in a synergy system correlated well with those noted in a broth-disk elution method incorporating 32 micrograms of CTX and 8 micrograms of des-CTX per ml.", "The correlation was poorer when the broth-disk method contained 16 micrograms of CTX and 8 micrograms of des-CTX per ml."], "structured": false}
{"doc_id": 46617075, "title": "Retinoblastoma regulatory pathway in lung cancer.", "abstract": ["Lung cancer is the leading cause of cancer related deaths accounting for more deaths than breast, colon and prostate cancers combined.", "The Rb-p16 regulatory pathway plays an essential role in tumor suppression in the lung epithelium.", "This is evidenced by the nearly universal alterations in Rb-p16 pathway components in lung cancer, and the increased incidence of pulmonary carcinomas in persons with germline Rb mutations.", "Interestingly, p16 loss and Rb mutations preferentially occur in phenotypically distinct lung cancer subtypes.", "Analysis of human tumors has identified progressive preneoplastic lesions that accumulate molecular alterations in an orderly sequence.", "Epigenetic p16 gene modifications represent an early event in lung cancer progression.", "This review summarizes the human studies that demonstrate a critical role for the Rb-p16 tumor suppressor pathway in lung carcinogenesis, and discusses how these findings in combination with genetically engineered mouse models have significantly contributed to our understanding of lung cancer pathogenesis."], "structured": false}
{"doc_id": 46695481, "title": "Human papillomavirus and Papanicolaou tests to screen for cervical cancer.", "abstract": ["BACKGROUND Screening for cervical cancer based on testing for human papillomavirus (HPV) increases the sensitivity of detection of high-grade (grade 2 or 3) cervical intraepithelial neoplasia, but whether this gain represents overdiagnosis or protection against future high-grade cervical epithelial neoplasia or cervical cancer is unknown.   \n", "METHODS In a population-based screening program in Sweden, 12,527 women 32 to 38 years of age were randomly assigned at a 1:1 ratio to have an HPV test plus a Papanicolaou (Pap) test (intervention group) or a Pap test alone (control group).", "Women with a positive HPV test and a normal Pap test result were offered a second HPV test at least 1 year later, and those who were found to be persistently infected with the same high-risk type of HPV were then offered colposcopy with cervical biopsy.", "A similar number of double-blinded Pap smears and colposcopies with biopsy were performed in randomly selected women in the control group.", "Comprehensive registry data were used to follow the women for a mean of 4.1 years.", "The relative rates of grade 2 or 3 cervical intraepithelial neoplasia or cancer detected at enrollment and at subsequent screening examinations were calculated.   \n", "RESULTS At enrollment, the proportion of women in the intervention group who were found to have lesions of grade 2 or 3 cervical intraepithelial neoplasia or cancer was 51% greater (95% confidence interval [CI], 13 to 102) than the proportion of women in the control group who were found to have such lesions.", "At subsequent screening examinations, the proportion of women in the intervention group who were found to have grade 2 or 3 lesions or cancer was 42% less (95% CI, 4 to 64) and the proportion with grade 3 lesions or cancer was 47% less (95% CI, 2 to 71) than the proportions of control women who were found to have such lesions.", "Women with persistent HPV infection remained at high risk for grade 2 or 3 lesions or cancer after referral for colposcopy.   \n", "CONCLUSIONS The addition of an HPV test to the Pap test to screen women in their mid-30s for cervical cancer reduces the incidence of grade 2 or 3 cervical intraepithelial neoplasia or cancer detected by subsequent screening examinations.", "(ClinicalTrials.gov number, NCT00479375 [ClinicalTrials.gov].)."], "structured": true}
{"doc_id": 46743299, "title": "Chronic Exercise Increases Both Inducible and Endothelial Nitric Oxide Synthase Gene Expression in Endothelial Cells of Rat Aorta", "abstract": ["Chronic exercise upregulates endothelial nitric oxide synthase (eNOS) gene expression.", "Whether the expression of inducible nitric oxide synthase (iNOS) is affected by exercise is unknown.", "We therefore investigated the effects of chronic exercise on iNOS and eNOS expression in isolated rat aortic endothelial and smooth muscle cells separately.", "Five-week-old male Wistar rats were randomly divided into control and exercise groups.", "After 10 weeks of running training, animals were sacrificed under ether anesthesia.", "The standard curve quantitative competitive reverse transcriptase-polymerase chain reaction method was used to quantify NOS mRNA expression in isolated endothelial/smooth muscle cells.", "To evaluate the functional role of iNOS, we examined phenylephrine-induced vascular responses with or without pretreatment with aminoguanidine.", "We found that (1) expression of iNOS and eNOS mRNA in endothelial cells was increased by chronic exercise and (2) chronic exercise blunted phenylephrine-induced vascular responses, probably by increasing NO release via iNOS.", "Our results show that chronic exercise increases both iNOS and eNOS gene expression in endothelium.", "These alterations may be partially responsible for the change in vascular response after exercise."], "structured": false}
{"doc_id": 46764350, "title": "Frontal stroke syndromes.", "abstract": ["The frontal lobe is the largest lobe of the brain, and it is thus commonly involved in stroke.", "Moreover, almost one in five strokes is limited to the prerolandic areas.", "This high frequency of anatomical involvement is in sharp contrast with the apparent rarity of clinical frontal dysfunction in stroke.", "It is remarkable that frontal behavioral syndromes have been rather uncommonly reported in patients with stroke as compared to patients with other diseases, such as brain tumor.", "This fact is paradoxical, because an acute process (stroke) is expected to yield more clinical dysfunction than a more chronic disease (tumor).", "A volume effect may be the main factor leading to this phenomenon.", "Another interesting aspect of frontal strokes is the contribution of so-called 'silent' strokes, the recurrence of which may nevertheless lead to intellectual decline and compromise recovery from another stroke with more specific neurologic dysfunction.", "The contribution of stroke to understanding of frontal lobe dysfunction is important, because of the focal nature of this disease, and great opportunity for clinical-topographic classification correlations.", "One of the first modern attempts to develop a clinical-topographic classification of frontal lobe lesions came from the school of Luria, who tried to delineate three main types of frontal lobe syndromes (premotor syndrome, prefrontal syndrome, medial-frontal syndrome).", "Recent anatomic correlates using MRI make it possible to improve this classification.", "We suggest considering six main clinical-anatomic frontal stroke syndromes: (1) prefrontal; (2) premotor; (3) superior medial; (4) orbital-medial; (5) basal forebrain; (6) white matter.", "Finally, another fascinating topic relates to frontal lobe symptomatology due to stroke sparing the frontal cortex or white matter.", "This occurs mainly in three instances: lenticulo-capsular stroke, caudate stroke, and thalamic stroke.", "Studies using blood flow or metabolism measurements suggest that diaschisis (frontal lobe dysfunction from a remote lesion) may play a role.", "We believe that this is more likely to be related to dynamic interruption of complex circuitry than to static frontal lobe deactivation."], "structured": false}
{"doc_id": 46765242, "title": "Interaction of cytosine arabinoside and lovastatin in human leukemia cells.", "abstract": ["Cytosine arabinoside (ara-C) is widely used for the treatment of leukemias and displays significant toxicities.", "Lovastatin, an HMG-CoA reductase inhibitor, is extensively used to treat hypercholesterolemia.", "To determine whether lovastatin could augment ara-C's activity we have examined their effects in the human erythroleukemia K562 cell line and the ara-C resistant ARAC8D cell line.", "A synergistic interaction between the two drugs was found.", "We have demonstrated that the interaction does not occur at the level of RAS but may involve lovastatin's effect of downregulating MAPK activity and preventing ara-C-induced MAPK activation.", "These studies represent the first description of a potentially beneficial interaction between lovastatin and ara-C that could be applied to the treatment of human leukemia."], "structured": false}
{"doc_id": 46816158, "title": "The crystal structure of TAL effector PthXo1 bound to its DNA target.", "abstract": ["DNA recognition by TAL effectors is mediated by tandem repeats, each 33 to 35 residues in length, that specify nucleotides via unique repeat-variable diresidues (RVDs).", "The crystal structure of PthXo1 bound to its DNA target was determined by high-throughput computational structure prediction and validated by heavy-atom derivatization.", "Each repeat forms a left-handed, two-helix bundle that presents an RVD-containing loop to the DNA.", "The repeats self-associate to form a right-handed superhelix wrapped around the DNA major groove.", "The first RVD residue forms a stabilizing contact with the protein backbone, while the second makes a base-specific contact to the DNA sense strand.", "Two degenerate amino-terminal repeats also interact with the DNA.", "Containing several RVDs and noncanonical associations, the structure illustrates the basis of TAL effector-DNA recognition."], "structured": false}
{"doc_id": 46837626, "title": "Prediction of creatinine clearance from serum creatinine.", "abstract": ["A formula has been developed to predict creatinine clearance (Ccr) from serum creatinine (Scr) in adult males: (see article)(15% less in females).", "Derivation included the relationship found between age and 24-hour creatinine excretion/kg in 249 patients aged 18-92.", "Values for Ccr were predicted by this formula and four other methods and the results compared with the means of two 24-hour Ccr's measured in 236 patients.", "The above formula gave a correlation coefficient between predicted and mean measured Ccr's of 0.83; on average, the difference predicted and mean measured values was no greater than that between paired clearances.", "Factors for age and body weight must be included for reasonable prediction."], "structured": false}
{"doc_id": 46926352, "title": "Dendritic cells, T cells and lymphatics: dialogues in migration and beyond.", "abstract": ["Immune cells continuously recirculate through lymph vessels en route from peripheral tissues to the blood.", "Leuyte trafficking into and within lymph vessels is mediated by an interply with lymphatic endothelial cells (LECs).", "However, lymphatic vessels are much more than mere conduits for fluid and immune cell transport.", "Data accumulating during past several years indicate that LECs support T cell survival, induce tolerance to self-antigens, inhibit exaggerated T cell proliferation during immune response and maintain T cell memory.", "Reciprocally, leukocytes impact LEC biology: lymphatic vessel permeability depends on DCs while lymphocytes regulate LEC proliferation during inflammation.", "Altogether, these novel results provide important insights on intimate connections between LECs and leukocytes that contribute to the understanding of immune responses."], "structured": false}
{"doc_id": 47018050, "title": "CRISPR\u2013Cas9 genome editing induces a p53-mediated DNA damage response", "abstract": ["Here, we report that genome editing by CRISPR\u2013Cas9 induces a p53-mediated DNA damage response and cell cycle arrest in immortalized human retinal pigment epithelial cells, leading to a selection against cells with a functional p53 pathway.", "Inhibition of p53 prevents the damage response and increases the rate of homologous recombination from a donor template.", "These results suggest that p53 inhibition may improve the efficiency of genome editing of untransformed cells and that p53 function should be monitored when developing cell-based therapies utilizing CRISPR\u2013Cas9.", "CRISPR\u2013Cas9-induced DNA damage triggers p53 to limit the efficiency of gene editing in immortalized human retinal pigment epithelial cells."], "structured": false}
{"doc_id": 47240151, "title": "Comparative Structural Analysis of Lipid Binding START Domains", "abstract": ["BACKGROUND Steroidogenic acute regulatory (StAR) protein related lipid transfer (START) domains are small globular modules that form a cavity where lipids and lipid hormones bind.", "These domains can transport ligands to facilitate lipid exchange between biological membranes, and they have been postulated to modulate the activity of other domains of the protein in response to ligand binding.", "More than a dozen human genes encode START domains, and several of them are implicated in a disease.   ", "PRINCIPAL FINDINGS We report crystal structures of the human STARD1, STARD5, STARD13 and STARD14 lipid transfer domains.", "These represent four of the six functional classes of START domains.   ", "SIGNIFICANCE Sequence alignments based on these and previously reported crystal structures define the structural determinants of human START domains, both those related to structural framework and those involved in ligand specificity.   ", "ENHANCED VERSION This article can also be viewed as an enhanced version in which the text of the article is integrated with interactive 3D representations and animated transitions.", "Please note that a web plugin is required to access this enhanced functionality.", "Instructions for the installation and use of the web plugin are available in Text S1."], "structured": true}
{"doc_id": 49208216, "title": "Staphylococcus aureus infection dynamics", "abstract": ["Staphylococcus aureus is a human commensal that can also cause systemic infections.", "This transition requires evasion of the immune response and the ability to exploit different niches within the host.", "However, the disease mechanisms and the dominant immune mediators against infection are poorly understood.", "Previously it has been shown that the infecting S. aureus population goes through a population bottleneck, from which very few bacteria escape to establish the abscesses that are characteristic of many infections.", "Here we examine the host factors underlying the population bottleneck and subsequent clonal expansion in S. aureus infection models, to identify underpinning principles of infection.", "The bottleneck is a common feature between models and is independent of S. aureus strain.", "Interestingly, the high doses of S. aureus required for the widely used \"survival\" model results in a reduced population bottleneck, suggesting that host defences have been simply overloaded.", "This brings into question the applicability of the survival model.", "Depletion of immune mediators revealed key breakpoints and the dynamics of systemic infection.", "Loss of macrophages, including the liver Kupffer cells, led to increased sensitivity to infection as expected but also loss of the population bottleneck and the spread to other organs still occurred.", "Conversely, neutrophil depletion led to greater susceptibility to disease but with a concomitant maintenance of the bottleneck and lack of systemic spread.", "We also used a novel microscopy approach to examine abscess architecture and distribution within organs.", "From these observations we developed a conceptual model for S. aureus disease from initial infection to mature abscess.", "This work highlights the need to understand the complexities of the infectious process to be able to assign functions for host and bacterial components, and why S. aureus disease requires a seemingly high infectious dose and how interventions such as a vaccine may be more rationally developed."], "structured": false}
{"doc_id": 49429882, "title": "Strategies for optimizing maternal nutrition to promote infant development", "abstract": ["BACKGROUND The growing appreciation of the multi-faceted importance of optimal maternal nutrition to the health and development of the infant and young child is tempered by incompletely resolved strategies for combatting challenges.   \n", "OBJECTIVE To review the importance of maternal nutrition and strategies being employed to optimize outcomes.   \n", "METHODS Selected data from recent literature with special focus on rationale for and currently published results of maternal nutrition supplements, including lipid based nutrition supplements.   \n", "RESULTS 1) An impelling rationale for improving the maternal and in utero environment of low resource populations has emerged to achieve improved fetal and post-natal growth and development.", "2) Based partly on population increases in adult height over one-two generations, much can be achieved by reducing poverty.", "3) Maternal, newborn and infant characteristics associated with low resource environments include evidence of undernutrition, manifested by underweight and impaired linear growth.", "4) Apart from broad public health and educational initiatives, to date, most specific efforts to improve fetal growth and development have included maternal nutrition interventions during gestation.", "5) The relatively limited but real benefits of both iron/folic acid (IFA) and multiple micronutrient (MMN) maternal supplements during gestation have now been reasonably defined.", "6) Recent investigations of a maternal lipid-based primarily micronutrient supplement (LNS) have not demonstrated a consistent benefit beyond MMN alone.", "7) However, effects of both MMN and LNS appear to be enhanced by commencing early in gestation.   \n", "CONCLUSIONS Poor maternal nutritional status is one of a very few specific factors in the human that not only contributes to impaired fetal and early post-natal growth but for which maternal interventions have demonstrated improved in utero development, documented primarily by both improvements in low birth weights and by partial corrections of impaired birth length.", "A clearer definition of the benefits achievable by interventions specifically focused on correcting maternal nutrition deficits should not be limited to improvements in the quality of maternal nutrition supplements, but on the cumulative quantity and timing of interventions (also recognizing the heterogeneity between populations).", "Finally, in an ideal world these steps are only a prelude to improvements in the total environment in which optimal nutrition and other health determinants can be achieved."], "structured": true}
{"doc_id": 49432306, "title": "Key questions about the checkpoint blockade-are microRNAs an answer?", "abstract": ["The introduction of immune-checkpoint blockade in the cancer therapy led to a paradigm change of the management of late stage cancers.", "There are already multiple FDA approved checkpoint inhibitors and many other agents are undergoing phase 2 and early phase 3 clinical trials.", "The therapeutic indication of immune checkpoint inhibitors expanded in the last years, but still remains unclear who can benefit.", "MicroRNAs are small RNAs with no coding potential.", "By complementary pairing to the 3' untranslated region of messenger RNA, microRNAs exert posttranscriptional control of protein expression.", "A network of microRNAs directly and indirectly controls the expression of checkpoint receptors and several microRNAs can target multiple checkpoint molecules, mimicking the therapeutic effect of a combined immune checkpoint blockade.", "In this review, we will describe the microRNAs that control the expression of immune checkpoints and we will present four specific issues of the immune checkpoint therapy in cancer: (1) imprecise therapeutic indication, (2) difficult response evaluation, (3) numerous immunologic adverse-events, and (4) the absence of response to immune therapy.", "Finally, we propose microRNAs as possible solutions for these pitfalls.", "We consider that in the near future microRNAs could become important therapeutic partners of the immune checkpoint therapy."], "structured": false}
{"doc_id": 49556906, "title": "Metformin reverses established lung fibrosis in a bleomycin model", "abstract": ["Fibrosis is a pathological result of a dysfunctional repair response to tissue injury and occurs in a number of organs, including the lungs1.", "Cellular metabolism regulates tissue repair and remodelling responses to injury2-4.", "AMPK is a critical sensor of cellular bioenergetics and controls the switch from anabolic to catabolic metabolism5.", "However, the role of AMPK in fibrosis is not well understood.", "Here, we demonstrate that in humans with idiopathic pulmonary fibrosis (IPF) and in an experimental mouse model of lung fibrosis, AMPK activity is lower in fibrotic regions associated with metabolically active and apoptosis-resistant myofibroblasts.", "Pharmacological activation of AMPK in myofibroblasts from lungs of humans with IPF display lower fibrotic activity, along with enhanced mitochondrial biogenesis and normalization of sensitivity to apoptosis.", "In a bleomycin model of lung fibrosis in mice, metformin therapeutically accelerates the resolution of well-established fibrosis in an AMPK-dependent manner.", "These studies implicate deficient AMPK activation in non-resolving, pathologic fibrotic processes, and support a role for metformin (or other AMPK activators) to reverse established fibrosis by facilitating deactivation and apoptosis of myofibroblasts."], "structured": false}
{"doc_id": 50670403, "title": "Are expert athletes 'expert' in the cognitive laboratory? A meta-analytic review of cognition and sport expertise", "abstract": ["SUMMARY Recent literature has demonstrated the usefulness of fitness and computer-based cognitive training as a means to enhance cognition and brain function.", "However, it is unclear whether the combination of fitness and cognitive training that results from years of extensive sport training also results in superior performance on tests of cognitive processes.", "In this study we examine, in a quantitative meta-analysis (k \u00bc20), the relationship between expertise in sports and laboratory-based measures of cognition.", "We found that athletes performed better on measures of processing speed and a category of varied attentionalparadigms, andathletesfrominterceptive sporttypesandmalesshowedthelargesteffects.", "Based on our results, more research should be done with higher-level cognitive tasks, such as tasks of executive function and more varied sub-domains of visual attention.", "Furthermore, future studies should incorporate more female athletes and use a diverse range of sport types and levelsof expertise."], "structured": false}
{"doc_id": 51386222, "title": "Effects of Age, Sex, and Ethnicity on the Association Between Apolipoprotein E Genotype and Alzheimer Disease: A Meta-analysis", "abstract": ["Objective.", "\u2014To examine more closely the association between apolipoprotein E (APOE) genotype and Alzheimer disease (AD) by age and sex in populations of various ethnic and racial denominations.", "Data Sources.", "\u2014Forty research teams contributed data onAPOEgenotype, sex, age at disease onset, and ethnic background for 5930 patients who met criteria for probable or definite AD and 8607 controls without dementia who were recruited from clinical, community, and brain bank sources.", "Main Outcome Measures.", "\u2014Odds ratios (ORs) and 95% confidence intervals (Cls) for AD, adjusted for age and study and stratified by major ethnic group (Caucasian, African American, Hispanic, and Japanese) and source, were computed forAPOEgenotypes \u22082/\u22082,\u22082/\u22083,\u22082/\u22084,\u22083/\u22084 and \u22084/\u22084 relative to the \u22083/\u22083 group.", "The influence of age and sex on the OR for each genotype was assessed using logistic regression procedures.", "Results.", "\u2014Among Caucasian subjects from clinic- or autopsy-based studies, the risk of AD was significantly increased for people with genotypes \u22082/\u22084 (OR=2.6, 95% Cl=1.6-4.0), \u22083/\u22084 (OR=3.2, 95% Cl=2.8-3.8), and \u22084/\u22084 (OR=14.9, 95% CI=10.8-20.6); whereas, the ORs were decreased for people with genotypes \u22082/\u22082 (OR=0.6, 95% Cl=0.2-2.0) and \u22082/\u22083 (OR=0.6, 95% Cl=0.5-0.8).", "TheAPOE\u22084-AD association was weaker among African Americans and Hispanics, but there was significant heterogeneity in ORs among studies of African Americans (P Conclusions.", "\u2014TheAPOE\u22084 allele represents a major risk factor for AD in all ethnic groups studied, across all ages between 40 and 90 years, and in both men and women.", "The association betweenAPOE\u22084 and AD in African Americans requires clarification, and the attenuated effect ofAPOE\u22084 in Hispanics should be investigated further."], "structured": false}
{"doc_id": 51706771, "title": "Comparison of glioblastoma (GBM) molecular classification methods.", "abstract": ["Glioblastoma (GBM) is the most aggressive and common form of brain cancer in adults.", "GBM is characterized by poor survival and remarkably high tumors heterogeneity (both intertumoral and intratumoral), and lack of effective therapies.", "Recent high-throughput data revealed heterogeneous genetic/genomic/epigenetic features and led to multiple methods aiming to classify tumors according to the key molecular events that drive the most aggressive cellular components so that targeted therapies can be developed for individual subtypes.", "However, GBM molecular subtypes have not led to improvement of patients outcomes.", "Targeted or tailored therapies for specific mutations or subtypes largely failed due to the complexities arising from intratumoral molecular heterogeneity.", "Most tumors develop resistance to treatment and soon recur.", "GBM stem cells (GSCs) have been identified.", "Recent single cell sequencing studies of GBM suggest that intratumoral cellular heterogeneity can be partially explained by tumor cell hierarchy arising from GBM stem cells.", "Therefore, the molecular subtypes based on patient derived GSCs may potentially lead to more effective subtype-specific treatments.", "In this paper, we review the molecular alterations of GBM and molecular subtyping methods as well as subtype plasticity in primary and recurrent tumors emphasizing the clinical relevance of potential targets for further drug development."], "structured": false}
{"doc_id": 51728753, "title": "Mesenchymal Stromal Cells: From Discovery to Manufacturing and Commercialization", "abstract": ["Over the last decades, mesenchymal stromal cells (MSC) have been the focus of intense research by academia and industry due to their unique features.", "MSC can be easily isolated and expanded through in vitro culture by taking full advantage of their self-renewing capacity.", "In addition, MSC exert immunomodulatory effects and can be differentiated into various lineages, which makes them highly attractive for clinical applications in cell-based therapies.", "In this review, we attempt to provide a brief historical overview of MSC discovery, characterization, and the first clinical studies conducted.", "The current MSC manufacturing platforms are reviewed with special attention regarding the use of bioreactors for the production of GMP-compliant clinically relevant cell numbers.", "The first commercial MSC-based products are also addressed, as well as the remaining challenges to the widespread use of MSC-derived products."], "structured": false}
{"doc_id": 51817902, "title": "Delta\u2013Notch\u2014and then? Protein interactions and proposed modes of repression by Hes and Hey bHLH factors", "abstract": ["Hes and Hey genes are the mammalian counterparts of the Hairy and Enhancer-of-split type of genes in Drosophila and they represent the primary targets of the Delta-Notch signaling pathway.", "Hairy-related factors control multiple steps of embryonic development and misregulation is associated with various defects.", "Hes and Hey genes (also called Hesr, Chf, Hrt, Herp or gridlock) encode transcriptional regulators of the basic helix-loop-helix class that mainly act as repressors.", "The molecular details of how Hes and Hey proteins control transcription are still poorly understood, however.", "Proposed modes of action include direct binding to N- or E-box DNA sequences of target promoters as well as indirect binding through other sequence-specific transcription factors or sequestration of transcriptional activators.", "Repression may rely on recruitment of corepressors and induction of histone modifications, or even interference with the general transcriptional machinery.", "All of these models require extensive protein-protein interactions.", "Here we review data published on protein-protein and protein-DNA interactions of Hairy-related factors and discuss their implications for transcriptional regulation.", "In addition, we summarize recent progress on the identification of potential target genes and the analysis of mouse models."], "structured": false}
{"doc_id": 51865482, "title": "The Long Noncoding RNA CAREL Controls Cardiac Regeneration.", "abstract": ["BACKGROUND Adult mammalian heart loses regeneration ability following ischemic injury due to the loss of cardiomyocyte mitosis.", "However, the molecular mechanisms underlying the post-mitotic nature of cardiomyocytes remain largely unknown.   \n", "OBJECTIVES", "The purpose of this study was to define the essential role of long noncoding ribonucleic acids (lncRNAs) in heart regeneration during postnatal and adult injury.   \n", "METHODS Myh6-driving cardiomyocyte-specific lncRNA-CAREL transgenic mice and adenovirus-mediated in vivo silencing of endogenous CAREL were used in this study.", "The effect of CAREL on cardiomyocyte replication and heart regeneration after apical resection or myocardial infarction was assessed by detecting mitosis and cytokinesis.   \n", "RESULTS An lncRNA CAREL was found significantly up-regulated in cardiomyocytes from neonatal mice (P7) in parallel with loss of regenerative capacity.", "Cardiac-specific overexpression of CAREL in mice reduced cardiomyocyte division and proliferation and blunted neonatal heart regeneration after injury.", "Conversely, silencing of CAREL in vivo markedly promoted cardiac regeneration and improved heart functions after myocardial infarction in neonatal and adult mice.", "CAREL acted as a competing endogenous ribonucleic acid for miR-296 to derepress the expression of Trp53inp1 and Itm2a, the target genes of miR-296.", "Consistently, overexpression of miR-296 significantly increased cardiomyocyte replication and cardiac regeneration after injury.", "Decline of cardiac regenerative ability in CAREL transgenic mice was also rescued by miR-296.", "A short fragment containing the conserved sequence of CAREL reduced the proliferation of human induced pluripotent stem cell-derived cardiomyocytes as the full-length CAREL.   \n", "CONCLUSIONS LncRNA CAREL regulates cardiomyocyte proliferation and heart regeneration in postnatal and adult heart after injury by acting as a competing endogenous ribonucleic acid on miR-296 that targets Trp53inp1 and Itm2a."], "structured": true}
{"doc_id": 51952430, "title": "BCAP links IL-1R to the PI3K\u2013mTOR pathway and regulates pathogenic Th17 cell differentiation", "abstract": ["The toll-like receptor (TLR) and interleukin (IL)-1 family of receptors share several signaling components, including the most upstream adapter, MyD88.", "We previously reported the discovery of B cell adapter for phosphoinositide 3-kinase (BCAP) as a novel toll-IL-1 receptor homology domain-containing adapter that regulates inflammatory responses downstream of TLR signaling.", "Here we find that BCAP plays a critical role downstream of both IL-1 and IL-18 receptors to regulate T helper (Th) 17 and Th1 cell differentiation, respectively.", "Absence of T cell intrinsic BCAP did not alter development of naturally arising Th1 and Th17 lineages but led to defects in differentiation to pathogenic Th17 lineage cells.", "Consequently, mice that lack BCAP in T cells had reduced susceptibility to experimental autoimmune encephalomyelitis.", "More importantly, we found that BCAP is critical for IL-1R-induced phosphoinositide 3-kinase-Akt-mechanistic target of rapamycin (mTOR) activation, and minimal inhibition of mTOR completely abrogated IL-1\u03b2-induced differentiation of pathogenic Th17 cells, mimicking BCAP deficiency.", "This study establishes BCAP as a critical link between IL-1R and the metabolic status of activated T cells that ultimately regulates the differentiation of inflammatory Th17 cells."], "structured": false}
{"doc_id": 51972698, "title": "Adapting the WHO package of essential noncommunicable disease interventions, Samoa", "abstract": ["Problem Samoa has been struggling to address the burden of noncommunicable diseases at the health system, community and individual levels.   ", "Approach The World Health Organization (WHO) package of essential noncommunicable disease interventions for primary health care in low-resource settings was adopted in seven villages throughout Samoa in 2015.", "The National Steering Committee Members designed and implemented a screening process, and local facilitators and health-care workers collected health and lifestyle data.", "The WHO/International Society of Hypertension risk assessment was used on villagers older than 40 years to identify people at high risk of noncommunicable disease.   ", "Local setting Samoa is a small island developing state with increasing morbidity and mortality due to noncommunicable diseases.", "A national representative survey indicated that 50.1% (595/1188) of the Samoan adult population is at high risk of such diseases.", "High numbers of noncommunicable diseases are undiagnosed or untreated, because of shortage of health-care staff and lack of awareness of risk factors.   ", "Relevant changes The teams collected data from 2234 adults.", "For people older than 40 years, 6.7% (54/804) were identified as being at high-risk and were encouraged to seek treatment or manage risk factors.", "Community members developed an awareness programme to improve understanding of lifestyle risk factors.   ", "Lessons learnt Engaging community members was crucial in conducting a successful screening campaign.", "By identifying those villagers at high risk of developing noncommunicable diseases, early intervention was possible.", "Education improved awareness of the symptom-free nature of early-stage noncommunicable diseases."], "structured": false}
{"doc_id": 52072815, "title": "Alcohol use and burden for 195 countries and territories, 1990\u20132016: a systematic analysis for the Global Burden of Disease Study 2016", "abstract": ["Summary Background Alcohol use is a leading risk factor for death and disability, but its overall association with health remains complex given the possible protective effects of moderate alcohol consumption on some conditions.", "With our comprehensive approach to health accounting within the Global Burden of Diseases, Injuries, and Risk Factors Study 2016, we generated improved estimates of alcohol use and alcohol-attributable deaths and disability-adjusted life-years (DALYs) for 195 locations from 1990 to 2016, for both sexes and for 5-year age groups between the ages of 15 years and 95 years and older.", "Methods Using 694 data sources of individual and population-level alcohol consumption, along with 592 prospective and retrospective studies on the risk of alcohol use, we produced estimates of the prevalence of current drinking, abstention, the distribution of alcohol consumption among current drinkers in standard drinks daily (defined as 10 g of pure ethyl alcohol), and alcohol-attributable deaths and DALYs.", "We made several methodological improvements compared with previous estimates: first, we adjusted alcohol sales estimates to take into account tourist and unrecorded consumption; second, we did a new meta-analysis of relative risks for 23 health outcomes associated with alcohol use; and third, we developed a new method to quantify the level of alcohol consumption that minimises the overall risk to individual health.", "Findings Globally, alcohol use was the seventh leading risk factor for both deaths and DALYs in 2016, accounting for 2\u00b72% (95% uncertainty interval [UI] 1\u00b75\u20133\u00b70) of age-standardised female deaths and 6\u00b78% (5\u00b78\u20138\u00b70) of age-standardised male deaths.", "Among the population aged 15\u201349 years, alcohol use was the leading risk factor globally in 2016, with 3\u00b78% (95% UI 3\u00b72\u20134\u00b73) of female deaths and 12\u00b72% (10\u00b78\u201313\u00b76) of male deaths attributable to alcohol use.", "For the population aged 15\u201349 years, female attributable DALYs were 2\u00b73% (95% UI 2\u00b70\u20132\u00b76) and male attributable DALYs were 8\u00b79% (7\u00b78\u20139\u00b79).", "The three leading causes of attributable deaths in this age group were tuberculosis (1\u00b74% [95% UI 1\u00b70\u20131\u00b77] of total deaths), road injuries (1\u00b72% [0\u00b77\u20131\u00b79]), and self-harm (1\u00b71% [0\u00b76\u20131\u00b75]).", "For populations aged 50 years and older, cancers accounted for a large proportion of total alcohol-attributable deaths in 2016, constituting 27\u00b71% (95% UI 21\u00b72\u201333\u00b73) of total alcohol-attributable female deaths and 18\u00b79% (15\u00b73\u201322\u00b76) of male deaths.", "The level of alcohol consumption that minimised harm across health outcomes was zero (95% UI 0\u00b70\u20130\u00b78) standard drinks per week.", "Interpretation Alcohol use is a leading risk factor for global disease burden and causes substantial health loss.", "We found that the risk of all-cause mortality, and of cancers specifically, rises with increasing levels of consumption, and the level of consumption that minimises health loss is zero.", "These results suggest that alcohol control policies might need to be revised worldwide, refocusing on efforts to lower overall population-level consumption.", "Funding Bill & Melinda Gates Foundation."], "structured": false}
{"doc_id": 52095986, "title": "The Dual Immunoregulatory function of Nlrp12 in T Cell-Mediated Immune Response: Lessons from Experimental Autoimmune Encephalomyelitis", "abstract": ["Although the etiology of multiple sclerosis (MS) remains enigmatic, the role of T cells is unquestionably central in this pathology.", "Immune cells respond to pathogens and danger signals via pattern-recognition receptors (PRR).", "Several reports implicate Nlrp12, an intracellular PRR, in the development of a mouse MS-like disease, called Experimental Autoimmune Encephalomyelitis (EAE).", "In this study, we used induced and spontaneous models of EAE, as well as in vitro T cell assays, to test the hypothesis that Nlrp12 inhibits Th1 response and prevents T-cell mediated autoimmunity.", "We found that Nlrp12 plays a protective role in induced EAE by reducing IFN\u03b3/IL-4 ratio in lymph nodes, whereas it potentiates the development of spontaneous EAE (spEAE) in 2D2 T cell receptor (TCR) transgenic mice.", "Looking into the mechanism of Nlrp12 activity in T cell response, we found that it inhibits T cell proliferation and suppresses Th1 response by reducing IFN\u03b3 and IL-2 production.", "Following TCR activation, Nlrp12 inhibits Akt and NF-\u03baB phosphorylation, while it has no effect on S6 phosphorylation in the mTOR pathway.", "In conclusion, we propose a model that can explain the dual immunoregulatory function of Nlrp12 in EAE.", "We also propose a model explaining the molecular mechanism of Nlrp12-dependent regulation of T cell response."], "structured": false}
{"doc_id": 52175065, "title": "Acute and chronic exercise in patients with heart failure with reduced ejection fraction: evidence of structural and functional plasticity and intact angiogenic signalling in skeletal muscle", "abstract": ["KEY POINTS The vascular endothelial growth factor (VEGF) responses to acute submaximal exercise and training effects in patients with heart failure with reduced ejection fraction (HFrEF) were investigated.", "Six patients and six healthy matched controls performed knee-extensor exercise (KE) at 50% of maximum work rate before and after (only patients) KE training.", "Muscle biopsies were taken to assess skeletal muscle structure and the angiogenic response.", "Before training, during this submaximal KE exercise, patients with HFrEF exhibited higher leg vascular resistance and greater noradrenaline spillover.", "Skeletal muscle structure and VEGF response were generally not different between groups.", "Following training, resistance was no longer elevated and noradrenaline spillover was curtailed in the patients.", "Although, in the trained state, VEGF did not respond to acute exercise, capillarity was augmented.", "Muscle fibre cross-sectional area and percentage area of type I fibres increased and mitochondrial volume density exceeded that of controls.", "Structural/functional plasticity and appropriate angiogenic signalling were observed in skeletal muscle of patients with HFrEF.   ", "ABSTRACT This study examined the response to acute submaximal exercise and the effect of training in patients with heart failure with reduced ejection fraction (HFrEF).", "The acute angiogenic response to submaximal exercise in HFrEF after small muscle mass training is debated.", "The direct Fick method, with vascular pressures, was performed across the leg during knee-extensor exercise (KE) at 50% of maximum work rate (WRmax ) in patients (n = 6) and controls (n = 6) and then after KE training in patients.", "Muscle biopsies facilitated the assessment of skeletal muscle structure and vascular endothelial growth factor (VEGF) mRNA levels.", "Prior to training, HFrEF exhibited significantly higher leg vascular resistance (LVR) (\u224815%) and significantly greater noradrenaline spillover (\u2248385%).", "Apart from mitochondrial volume density, which was significantly lower (\u224822%) in HFrEF, initial skeletal muscle structure, including capillarity, was not different between groups.", "Resting VEGF mRNA levels, and the increase with exercise, was not different between patients and controls.", "Following training, LVR was no longer elevated and noradrenaline spillover was curtailed.", "Skeletal muscle capillarity increased with training, as assessed by capillary-to-fibre ratio (\u224813%) and number of capillaries around a fibre (NCAF ) (\u224819%).", "VEGF mRNA was now not significantly increased by acute exercise.", "Muscle fibre cross-sectional area and percentage area of type I fibres both increased significantly with training (\u224818% and \u224821%, respectively), while the percentage area of type II fibres fell significantly (\u224811%), and mitochondrial volume density now exceeded that of controls.", "These data reveal structural and functional plasticity and appropriate angiogenic signalling in skeletal muscle of HFrEF patients."], "structured": false}
{"doc_id": 52176296, "title": "2017 revisions of McDonald criteria shorten the time to diagnosis of multiple sclerosis in clinically isolated syndromes", "abstract": ["To investigate the impact of the 2017 revisions of McDonald criteria on the diagnosis of multiple sclerosis (MS) in a cohort of patients with clinically isolated syndrome (CIS) and dissemination in space (DIS) of demyelinating lesions.", "We retrospectively analyzed 137 patients with CIS + DIS from two Italian MS centers.", "Application of the 2017 revisions of McDonald criteria in our cohort led to a diagnosis of MS in 82.5% of the patients who could have not been diagnosed with MS according to the previous criteria at the time of the first demyelinating event.", "After a follow-up of 3.8 \u00b1 2.9 years, 85.8% of these patients eventually satisfied also the previous (2010) criteria.", "Application of the 2017 revisions of McDonald criteria results in an earlier diagnosis of MS in a large percentage of CIS patients destined to convert to MS."], "structured": false}
{"doc_id": 52180874, "title": "Efficacy of PD-1 or PD-L1 inhibitors and PD-L1 expression status in cancer: meta-analysis", "abstract": ["OBJECTIVE To evaluate the relative efficacy of programmed cell death 1 (PD-1) or programmed cell death ligand 1 (PD-L1) inhibitors versus conventional drugs in patients with cancer that were PD-L1 positive and PD-L1 negative.   \n", "DESIGN Meta-analysis of randomised controlled trials.   \n", "DATA SOURCES PubMed, Embase, Cochrane database, and conference abstracts presented at the American Society of Clinical Oncology and European Society of Medical Oncology up to March 2018.   ", "REVIEW METHODS Studies of PD-1 or PD-L1 inhibitors (avelumab, atezolizumab, durvalumab, nivolumab, and pembrolizumab) that had available hazard ratios for death based on PD-L1 positivity or negativity were included.", "The threshold for PD-L1 positivity or negativity was that PD-L1 stained cell accounted for 1% of tumour cells, or tumour and immune cells, assayed by immunohistochemistry staining methods.   \n", "RESULTS 4174 patients with advanced or metastatic cancers from eight randomised controlled trials were included in this study.", "Compared with conventional agents, PD-1 or PD-L1 inhibitors were associated with significantly prolonged overall survival in both patients that were PD-L1 positive (n=2254, hazard ratio 0.66, 95% confidence interval 0.59 to 0.74) and PD-L1 negative (1920, 0.80, 0.71 to 0.90).", "However, the efficacies of PD-1 or PD-L1 blockade treatment in patients that were PD-L1 positive and PD-L1 negative were significantly different (P=0.02 for interaction).", "Additionally, in both patients that were PD-L1 positive and PD-L1 negative, the long term clinical benefits from PD-1 or PD-L1 blockade were observed consistently across interventional agent, cancer histotype, method of randomisation stratification, type of immunohistochemical scoring system, drug target, type of control group, and median follow-up time.   \n", "CONCLUSIONS PD-1 or PD-L1 blockade therapy is a preferable treatment option over conventional therapy for both patients that are PD-L1 positive and PD-L1 negative.", "This finding suggests that PD-L1 expression status alone is insufficient in determining which patients should be offered PD-1 or PD-L1 blockade therapy."], "structured": true}
{"doc_id": 52188256, "title": "Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries.", "abstract": ["This article provides a status report on the global burden of cancer worldwide using the GLOBOCAN 2018 estimates of cancer incidence and mortality produced by the International Agency for Research on Cancer, with a focus on geographic variability across 20 world regions.", "There will be an estimated 18.1 million new cancer cases (17.0 million excluding nonmelanoma skin cancer) and 9.6 million cancer deaths (9.5 million excluding nonmelanoma skin cancer) in 2018.", "In both sexes combined, lung cancer is the most commonly diagnosed cancer (11.6% of the total cases) and the leading cause of cancer death (18.4% of the total cancer deaths), closely followed by female breast cancer (11.6%), prostate cancer (7.1%), and colorectal cancer (6.1%) for incidence and colorectal cancer (9.2%), stomach cancer (8.2%), and liver cancer (8.2%) for mortality.", "Lung cancer is the most frequent cancer and the leading cause of cancer death among males, followed by prostate and colorectal cancer (for incidence) and liver and stomach cancer (for mortality).", "Among females, breast cancer is the most commonly diagnosed cancer and the leading cause of cancer death, followed by colorectal and lung cancer (for incidence), and vice versa (for mortality); cervical cancer ranks fourth for both incidence and mortality.", "The most frequently diagnosed cancer and the leading cause of cancer death, however, substantially vary across countries and within each country depending on the degree of economic development and associated social and life style factors.", "It is noteworthy that high-quality cancer registry data, the basis for planning and implementing evidence-based cancer control programs, are not available in most low- and middle-income countries.", "The Global Initiative for Cancer Registry Development is an international partnership that supports better estimation, as well as the collection and use of local data, to prioritize and evaluate national cancer control efforts.", "CA: A Cancer Journal for Clinicians 2018;0:1-31.", "\u00a9 2018 American Cancer Society."], "structured": false}
{"doc_id": 52805891, "title": "Gut Microbiota Is a Key Modulator of Insulin Resistance in TLR 2 Knockout Mice", "abstract": ["Environmental factors and host genetics interact to control the gut microbiota, which may have a role in the development of obesity and insulin resistance.", "TLR2-deficient mice, under germ-free conditions, are protected from diet-induced insulin resistance.", "It is possible that the presence of gut microbiota could reverse the phenotype of an animal, inducing insulin resistance in an animal genetically determined to have increased insulin sensitivity, such as the TLR2 KO mice.", "In the present study, we investigated the influence of gut microbiota on metabolic parameters, glucose tolerance, insulin sensitivity, and signaling of TLR2-deficient mice.", "We investigated the gut microbiota (by metagenomics), the metabolic characteristics, and insulin signaling in TLR2 knockout (KO) mice in a non-germ free facility.", "Results showed that the loss of TLR2 in conventionalized mice results in a phenotype reminiscent of metabolic syndrome, characterized by differences in the gut microbiota, with a 3-fold increase in Firmicutes and a slight increase in Bacteroidetes compared with controls.", "These changes in gut microbiota were accompanied by an increase in LPS absorption, subclinical inflammation, insulin resistance, glucose intolerance, and later, obesity.", "In addition, this sequence of events was reproduced in WT mice by microbiota transplantation and was also reversed by antibiotics.", "At the molecular level the mechanism was unique, with activation of TLR4 associated with ER stress and JNK activation, but no activation of the IKK\u03b2-I\u03baB-NF\u03baB pathway.", "Our data also showed that in TLR2 KO mice there was a reduction in regulatory T cell in visceral fat, suggesting that this modulation may also contribute to the insulin resistance of these animals.", "Our results emphasize the role of microbiota in the complex network of molecular and cellular interactions that link genotype to phenotype and have potential implications for common human disorders involving obesity, diabetes, and even other immunological disorders."], "structured": false}
{"doc_id": 52824661, "title": "TGF\u2010\u03b2\u2010mediated exosomal lnc\u2010MMP2\u20102 regulates migration and invasion of lung cancer cells to the vasculature by promoting MMP2 expression", "abstract": ["Previous studies indicated that transforming growth factor (TGF)-\u03b2-mediated exosomal microRNAs (miRNAs) regulate the migration and invasion of lung cancer cells; however, whether and how TGF-\u03b2-mediated exosomal long noncoding (lnc) RNAs regulate migration and invasion of lung cancer cells remains unclear.", "Here, coculture experiments showed that TGF-\u03b2 pretreatment increased the migration and invasion potential of lung cancer cells and TGF-\u03b2 pretreated A549 cells increases vascular permeability.", "Furthermore, we found that TGF-\u03b2-mediated exosomes, as carriers of intercellular communication, regulated lung cancer invasion, and vascular permeability.", "Transcriptional analysis also revealed that lnc-MMP2-2 was highly enriched in TGF-\u03b2-mediated exosomes and might function by increasing the expression of matrix metalloproteinase (MMP)2 through its enhancer activity, with ectopic expression and silencing of lnc-MMP2-2 affecting lung cancer invasion and vascular permeability.", "Additionally, lnc-MMP2-2 and MMP2 expression was assessed semiquantitatively, and tissue-specific correlations between lnc-MMP2-2 and MMP2 expression were evaluated.", "These results suggested that exosomal lnc-MMP2-2 might regulate the migration and invasion of lung cancer cells into the vasculature by promoting MMP2 expression, suggesting this lncRNA as a novel therapeutic target and predictive marker of tumor metastasis in lung cancer."], "structured": false}
{"doc_id": 52827184, "title": "Surviving Sepsis Campaign: International Guidelines for Management of Sepsis and Septic Shock 2016", "abstract": ["Objective: To provide an update to \u201cSurviving Sepsis Campaign Guidelines for Management of Sepsis and Septic Shock: 2012.", "\u201d Design: A consensus committee of 55 international experts representing 25 international organizations was convened.", "Nominal groups were assembled at key international meetings (for those committee members attending the conference).", "A formal conflict-of-interest (COI) policy was developed at the onset of the process and enforced throughout.", "A stand-alone meeting was held for all panel members in December 2015.", "Teleconferences and electronic-based discussion among subgroups and among the entire committee served as an integral part of the development.", "Methods: The panel consisted of five sections: hemodynamics, infection, adjunctive therapies, metabolic, and ventilation.", "Population, intervention, comparison, and outcomes (PICO) questions were reviewed and updated as needed, and evidence profiles were generated.", "Each subgroup generated a list of questions, searched for best available evidence, and then followed the principles of the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) system to assess the quality of evidence from high to very low, and to formulate recommendations as strong or weak, or best practice statement when applicable.", "Results: The Surviving Sepsis Guideline panel provided 93 statements on early management and resuscitation of patients with sepsis or septic shock.", "Overall, 32 were strong recommendations, 39 were weak recommendations, and 18 were best-practice statements.", "No recommendation was provided for four questions.", "Conclusions: Substantial agreement exists among a large cohort of international experts regarding many strong recommendations for the best care of patients with sepsis.", "Although a significant number of aspects of care have relatively weak support, evidence-based recommendations regarding the acute management of sepsis and septic shock are the foundation of improved outcomes for these critically ill patients with high mortality."], "structured": false}
{"doc_id": 52850476, "title": "Mitochondrial genome variation and the origin of modern humans.", "abstract": ["The analysis of mitochondrial DNA (mtDNA) has been a potent tool in our understanding of human evolution, owing to characteristics such as high copy number, apparent lack of recombination, high substitution rate and maternal mode of inheritance.", "However, almost all studies of human evolution based on mtDNA sequencing have been confined to the control region, which constitutes less than 7% of the mitochondrial genome.", "These studies are complicated by the extreme variation in substitution rate between sites, and the consequence of parallel mutations causing difficulties in the estimation of genetic distance and making phylogenetic inferences questionable.", "Most comprehensive studies of the human mitochondrial molecule have been carried out through restriction-fragment length polymorphism analysis, providing data that are ill suited to estimations of mutation rate and therefore the timing of evolutionary events.", "Here, to improve the information obtained from the mitochondrial molecule for studies of human evolution, we describe the global mtDNA diversity in humans based on analyses of the complete mtDNA sequence of 53 humans of diverse origins.", "Our mtDNA data, in comparison with those of a parallel study of the Xq13.3 region in the same individuals, provide a concurrent view on human evolution with respect to the age of modern humans."], "structured": false}
{"doc_id": 52865789, "title": "Deficiency of Interleukin-15 Confers Resistance to Obesity by Diminishing Inflammation and Enhancing the Thermogenic Function of Adipose Tissues", "abstract": ["OBJECTIVE IL-15 is an inflammatory cytokine secreted by many cell types.", "IL-15 is also produced during physical exercise by skeletal muscle and has been reported to reduce weight gain in mice.", "Contrarily, our findings on IL-15 knockout (KO) mice indicate that IL-15 promotes obesity.", "The aim of this study is to investigate the mechanisms underlying the pro-obesity role of IL-15 in adipose tissues.   \n", "METHODS Control and IL-15 KO mice were maintained on high fat diet (HFD) or normal control diet.", "After 16 weeks, body weight, adipose tissue and skeletal mass, serum lipid levels and gene/protein expression in the adipose tissues were evaluated.", "The effect of IL-15 on thermogenesis and oxygen consumption was also studied in primary cultures of adipocytes differentiated from mouse preadipocyte and human stem cells.   \n", "RESULTS Our results show that IL-15 deficiency prevents diet-induced weight gain and accumulation of lipids in visceral and subcutaneous white and brown adipose tissues.", "Gene expression analysis also revealed elevated expression of genes associated with adaptive thermogenesis in the brown and subcutaneous adipose tissues of IL-15 KO mice.", "Accordingly, oxygen consumption was increased in the brown adipocytes from IL-15 KO mice.", "In addition, IL-15 KO mice showed decreased expression of pro-inflammatory mediators in their adipose tissues.   \n", "CONCLUSIONS Absence of IL-15 results in decreased accumulation of fat in the white adipose tissues and increased lipid utilization via adaptive thermogenesis.", "IL-15 also promotes inflammation in adipose tissues that could sustain chronic inflammation leading to obesity-associated metabolic syndrome."], "structured": true}
{"doc_id": 52868579, "title": "Chromatin signatures of pluripotent cell lines.", "abstract": ["Epigenetic genome modifications are thought to be important for specifying the lineage and developmental stage of cells within a multicellular organism.", "Here, we show that the epigenetic profile of pluripotent embryonic stem cells (ES) is distinct from that of embryonic carcinoma cells, haematopoietic stem cells (HSC) and their differentiated progeny.", "Silent, lineage-specific genes replicated earlier in pluripotent cells than in tissue-specific stem cells or differentiated cells and had unexpectedly high levels of acetylated H3K9 and methylated H3K4.", "Unusually, in ES cells these markers of open chromatin were also combined with H3K27 trimethylation at some non-expressed genes.", "Thus, pluripotency of ES cells is characterized by a specific epigenetic profile where lineage-specific genes may be accessible but, if so, carry repressive H3K27 trimethylation modifications.", "H3K27 methylation is functionally important for preventing expression of these genes in ES cells as premature expression occurs in embryonic ectoderm development (Eed)-deficient ES cells.", "Our data suggest that lineage-specific genes are primed for expression in ES cells but are held in check by opposing chromatin modifications."], "structured": false}
{"doc_id": 52873726, "title": "Regulation of Hippo pathway transcription factor TEAD by p38 MAPK-induced cytoplasmic translocation", "abstract": ["The Hippo pathway controls organ size and tissue homeostasis, with deregulation leading to cancer.", "The core Hippo components in mammals are composed of the upstream serine/threonine kinases Mst1/2, MAPK4Ks and Lats1/2.", "Inactivation of these upstream kinases leads to dephosphorylation, stabilization, nuclear translocation and thus activation of the major functional transducers of the Hippo pathway, YAP and its paralogue TAZ.", "YAP/TAZ are transcription co-activators that regulate gene expression primarily through interaction with the TEA domain DNA-binding family of transcription factors (TEAD).", "The current paradigm for regulation of this pathway centres on phosphorylation-dependent nucleocytoplasmic shuttling of YAP/TAZ through a complex network of upstream components.", "However, unlike other transcription factors, such as SMAD, NF-\u03baB, NFAT and STAT, the regulation of TEAD nucleocytoplasmic shuttling has been largely overlooked.", "In the present study, we show that environmental stress promotes TEAD cytoplasmic translocation via p38 MAPK in a Hippo-independent manner.", "Importantly, stress-induced TEAD inhibition predominates YAP-activating signals and selectively suppresses YAP-driven cancer cell growth.", "Our data reveal a mechanism governing TEAD nucleocytoplasmic shuttling and show that TEAD localization is a critical determinant of Hippo signalling output."], "structured": false}
{"doc_id": 52874170, "title": "How do I perform a lumbar puncture and analyze the results to diagnose bacterial meningitis?", "abstract": ["CONTEXT Diagnostic lumbar punctures (LPs), commonly used to rule out meningitis, are associated with adverse events.   \n", "OBJECTIVE To systematically review the evidence about diagnostic LP techniques that may decrease the risk of adverse events and the evidence about test accuracy of cerebrospinal fluid (CSF) analysis in adult patients with suspected bacterial meningitis.   \n", "DATA SOURCES We searched the Cochrane Library, MEDLINE (using Ovid and PubMed) from 1966 to January 2006 and EMBASE from 1980 to January 2006 without language restrictions to identify relevant studies and identified others from the bibliographies of retrieved articles.   ", "STUDY SELECTION We included randomized trials of patients aged 18 years or older undergoing interventions to facilitate a successful diagnostic LP or to potentially reduce adverse events.", "Studies assessing the accuracy of biochemical analysis of the CSF for possible bacterial meningitis were also identified.   \n", "DATA EXTRACTION Two investigators independently appraised study quality and extracted relevant data.", "For studies of the LP technique, data on the intervention and the outcome were extracted.", "For studies of the laboratory diagnosis of bacterial meningitis, data on the reference standard and test accuracy were extracted.   \n", "DATA SYNTHESIS We found 15 randomized trials.", "A random-effects model was used for quantitative synthesis.", "Five studies of 587 patients compared atraumatic needles with standard needles and found a nonsignificant decrease in the odds of headache with an atraumatic needle (absolute risk reduction [ARR], 12.3%; 95% confidence interval [CI], -1.72% to 26.2%).", "Reinsertion of the stylet before needle removal decreased the risk of headache (ARR, 11.3%; 95% CI, 6.50%-16.2%).", "The combined results from 4 studies of 717 patients showed a nonsignificant decrease in headache in patients who were mobilized after LP (ARR, 2.9%; 95% CI, -3.4 to 9.3%).", "Four studies on the accuracy of biochemical analysis of CSF in patients with suspected meningitis met inclusion criteria.", "A CSF-blood glucose ratio of 0.4 or less (likelihood ratio [LR], 18; 95% CI, 12-27]), CSF white blood cell count of 500/muL or higher (LR, 15; 95% CI, 10-22), and CSF lactate level of 31.53 mg/dL or more (> or =3.5 mmol/L; LR, 21; 95% CI, 14-32) accurately diagnosed bacterial meningitis.   \n", "CONCLUSIONS These data suggest that small-gauge, atraumatic needles may decrease the risk of headache after diagnostic LP.", "Reinsertion of the stylet before needle removal should occur and patients do not require bed rest after the procedure.", "Future research should focus on evaluating interventions to optimize the success of a diagnostic LP and to enhance training in procedural skills."], "structured": true}
{"doc_id": 52887689, "title": "Guidelines for the use and interpretation of assays for monitoring autophagy.", "abstract": ["In 2008 we published the first set of guidelines for standardizing research in autophagy.", "Since then, research on this topic has continued to accelerate, and many new scientists have entered the field.", "Our knowledge base and relevant new technologies have also been expanding.", "Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms.", "Various reviews have described the range of assays that have been used for this purpose.", "Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes.", "A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi).", "In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy.", "In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity.", "Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes.", "These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used.", "In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy.", "In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them.", "Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field."], "structured": false}
{"doc_id": 52893592, "title": "Subversion of Systemic Glucose Metabolism as a Mechanism to Support the Growth of Leukemia Cells.", "abstract": ["From an organismal perspective, cancer cell populations can be considered analogous to parasites that compete with the host for essential systemic resources such as glucose.", "Here, we employed leukemia models and human leukemia samples to document a form of adaptive homeostasis, where malignant cells alter systemic physiology through impairment of both host insulin sensitivity and insulin secretion to provide tumors with increased glucose.", "Mechanistically, tumor cells induce high-level production of IGFBP1 from adipose tissue to mediate insulin sensitivity.", "Further, leukemia-induced gut dysbiosis, serotonin loss, and incretin inactivation combine to suppress insulin secretion.", "Importantly, attenuated disease progression and prolonged survival are achieved through disruption of the leukemia-induced adaptive homeostasis.", "Our studies provide a paradigm for systemic management of leukemic disease."], "structured": false}
{"doc_id": 52925737, "title": "Tumor-derived exosomes induce N2 polarization of neutrophils to promote gastric cancer cell migration", "abstract": ["BACKGROUND Exosomes are extracellular vesicles that mediate cellular communication in health and diseases.", "Neutrophils could be polarized to a pro-tumor phenotype by tumor.", "The function of tumor-derived exosomes in neutrophil regulation remains unclear.   \n", "METHODS We investigated the effects of gastric cancer cell-derived exosomes (GC-Ex) on the pro-tumor activation of neutrophils and elucidated the underlying mechanisms.   \n", "RESULTS GC-Ex prolonged neutrophil survival and induced expression of inflammatory factors in neutrophils.", "GC-Ex-activated neutrophils, in turn, promoted gastric cancer cell migration.", "GC-Ex transported high mobility group box-1 (HMGB1) that activated NF-\u03baB pathway through interaction with TLR4, resulting in an increased autophagic response in neutrophils.", "Blocking HMGB1/TLR4 interaction, NF-\u03baB pathway, and autophagy reversed GC-Ex-induced neutrophil activation.", "Silencing HMGB1 in gastric cancer cells confirmed HMGB1 as a key factor for GC-Ex-mediated neutrophil activation.", "Furthermore, HMGB1 expression was upregulated in gastric cancer tissues.", "Increased HMGB1 expression was associated with poor prognosis in patients with gastric cancer.", "Finally, gastric cancer tissue-derived exosomes acted similarly as exosomes derived from gastric cancer cell lines in neutrophil activation.   \n", "CONCLUSION We demonstrate that gastric cancer cell-derived exosomes induce autophagy and pro-tumor activation of neutrophils via HMGB1/TLR4/NF-\u03baB signaling, which provides new insights into mechanisms for neutrophil regulation in cancer and sheds lights on the multifaceted role of exosomes in reshaping tumor microenvironment."], "structured": true}
{"doc_id": 52944377, "title": "ROS-induced R loops trigger a transcription-coupled but BRCA1/2-independent homologous recombination pathway through CSB", "abstract": ["Actively transcribed regions of the genome are protected by transcription-coupled DNA repair mechanisms, including transcription-coupled homologous recombination (TC-HR).", "Here we used reactive oxygen species (ROS) to induce and characterize TC-HR at a transcribed locus in human cells.", "As canonical HR, TC-HR requires RAD51.", "However, the localization of RAD51 to damage sites during TC-HR does not require BRCA1 and BRCA2, but relies on RAD52 and Cockayne Syndrome Protein B (CSB).", "During TC-HR, RAD52 is recruited by CSB through an acidic domain.", "CSB in turn is recruited by R loops, which are strongly induced by ROS in transcribed regions.", "Notably, CSB displays a strong affinity for DNA:RNA hybrids in vitro, suggesting that it is a sensor of ROS-induced R loops.", "Thus, TC-HR is triggered by R loops, initiated by CSB, and carried out by the CSB-RAD52-RAD51 axis, establishing a BRCA1/2-independent alternative HR pathway protecting the transcribed genome."], "structured": false}
{"doc_id": 53033275, "title": "Autophagy and its potent modulators from phytochemicals in cancer treatment", "abstract": ["Autophagy is a ubiquitous catabolic process by which damaged or harmful intracellular components are delivered to the lysosomes for self-digestion and recycling.", "It is critical in cancer treatment.", "Therapy-induced autophagy predominantly acts as a pro-survival mechanism, but progressive autophagy can lead to non-apoptotic cell death, also known as autophagic cell death.", "Plants or herbs contain various natural compounds that are widely used in the treatment of many types of malignancies.", "Emerging evidence indicates that phytochemicals targeting the autophagic pathway are promising agents for cancer treatment.", "However, these compounds play different roles in autophagy.", "In this review, we discussed the role of autophagy in cancer development and therapy, and focussed on elucidating the anti-cancer activities of autophagic modulators, especially phytochemicals.", "Notably, we described a novel premise that the dynamic role of phytochemicals should be evaluated in regulation of autophagy in cancer."], "structured": false}
{"doc_id": 53211308, "title": "Exosomal miR-99a-5p is elevated in sera of ovarian cancer patients and promotes cancer cell invasion by increasing fibronectin and vitronectin expression in neighboring peritoneal mesothelial cells", "abstract": ["BACKGROUND microRNAs (miRNAs) stably exist in circulating blood and are encapsulated in extracellular vesicles such as exosomes.", "The aims of this study were to identify which exosomal miRNAs are highly produced from epithelial ovarian cancer (EOC) cells, to analyze whether serum miRNA can be used to discriminate patients with EOC from healthy volunteers, and to investigate the functional role of exosomal miRNAs in ovarian cancer progression.   \n", "METHODS Exosomes were collected from the culture media of serous ovarian cancer cell lines, namely TYK-nu and HeyA8 cells.", "An exosomal miRNA microarray revealed that several miRNAs including miR-99a-5p were specifically elevated in EOC-derived exosomes.", "Expression levels of serum miR-99a-5p in 62 patients with EOC, 26 patients with benign ovarian tumors, and 20 healthy volunteers were determined by miRNA quantitative reverse transcription-polymerase chain reaction.", "To investigate the role of exosomal miR-99a-5p in peritoneal dissemination, neighboring human peritoneal mesothelial cells (HPMCs) were treated with EOC-derived exosomes and then expression levels of miR-99a-5p were examined.", "Furthermore, mimics of miR-99a-5p were transfected into HPMCs and the effect of miR-99a-5p on cancer invasion was analyzed using a 3D culture model.", "Proteomic analysis with the tandem mass tag method was performed on HPMCs transfected with miR-99a-5p and then potential target genes of miR-99a-5p were examined.   \n", "RESULTS The serum miR-99a-5p levels were significantly increased in patients with EOC, compared with those in benign tumor patients and healthy volunteers (1.7-fold and 2.8-fold, respectively).", "A receiver operating characteristic curve analysis showed with a cut-off of 1.41 showed sensitivity and specificity of 0.85 and 0.75, respectively, for detecting EOC (area under the curve = 0.88).", "Serum miR-99a-5p expression levels were significantly decreased after EOC surgeries (1.8 to 1.3, p = 0.002), indicating that miR-99a-5p reflects tumor burden.", "Treatment with EOC-derived exosomes significantly increased miR-99a-5p expression in HPMCs.", "HPMCs transfected with miR-99a-5p promoted ovarian cancer invasion and exhibited increased expression levels of fibronectin and vitronectin.   \n", "CONCLUSIONS Serum miR-99a-5p is significantly elevated in ovarian cancer patients.", "Exosomal miR-99a-5p from EOC cells promotes cell invasion by affecting HPMCs through fibronectin and vitronectin upregulation and may serve as a target for inhibiting ovarian cancer progression."], "structured": true}
{"doc_id": 53302393, "title": "The Pfam protein families database.", "abstract": ["Pfam is a widely used database of protein families, currently containing more than 13,000 manually curated protein families as of release 26.0.", "Pfam is available via servers in the UK (http://pfam.sanger.ac.uk/), the USA (http://pfam.janelia.org/) and Sweden (http://pfam.sbc.su.se/).", "Here, we report on changes that have occurred since our 2010 NAR paper (release 24.0).", "Over the last 2 years, we have generated 1840 new families and increased coverage of the UniProt Knowledgebase (UniProtKB) to nearly 80%.", "Notably, we have taken the step of opening up the annotation of our families to the Wikipedia community, by linking Pfam families to relevant Wikipedia pages and encouraging the Pfam and Wikipedia communities to improve and expand those pages.", "We continue to improve the Pfam website and add new visualizations, such as the 'sunburst' representation of taxonomic distribution of families.", "In this work we additionally address two topics that will be of particular interest to the Pfam community.", "First, we explain the definition and use of family-specific, manually curated gathering thresholds.", "Second, we discuss some of the features of domains of unknown function (also known as DUFs), which constitute a rapidly growing class of families within Pfam."], "structured": false}
{"doc_id": 53779698, "title": "Exercise as a therapeutic approach to improve blood pressure in patients with peripheral arterial disease: current literature and future directions.", "abstract": ["INTRODUCTION Patients with symptomatic peripheral artery disease (PAD) exhibit reduced functional capacity and increased mortality due to cardiovascular disease.", "Although exercise has been a cornerstone for clinical treatment to improve walking capacity in patients with symptomatic PAD, its effects on cardiovascular parameters have been poorly explored.", "Areas covered: This review examines the role of exercise in improving blood pressure in patients with symptomatic PAD and summarizes the current evidence on the acute (single bout of exercise) and chronic effects of walking and resistance exercise on blood pressure and its determinants.", "Expert commentary: In patients with symptomatic PAD, exercise promotes acute and chronic reductions in blood pressure.", "These effects were observed particularly after walking and resistance exercise.", "Future studies are necessary to investigate the effects of other exercise modalities, especially non-painful exercises, on cardiovascular function in patients with symptomatic PAD."], "structured": false}
{"doc_id": 54482327, "title": "Morin Exhibits Anti-Inflammatory Effects on IL-1\u03b2-Stimulated Human Osteoarthritis Chondrocytes by Activating the Nrf2 Signaling Pathway", "abstract": ["Background/Aims: Osteoarthritis (OA) is a multifactorial disease that is associated with inflammation in joints.", "The purpose of the present study was to investigate the anti-inflammatory activity and mechanism of morin on human osteoarthritis chondrocytes stimulated by IL-1\u03b2.", "Methods: The levels of NO and PGE2 were measured by the Griess method and ELISA.", "The levels of MMP1, MMP3, and MMP13 were also measured by ELISA.", "Results: The results revealed that IL-1\u03b2 significantly increased the production of NO, PGE2, MMP1, MMP3, and MMP13.", "Additionally, the increases were significantly attenuated by treatment with morin.", "Furthermore, IL-1\u03b2-induced NF-\u03baB activation was suppressed by morin.", "In addition, the expression of Nrf2 and HO-1 were increased by morin and knockdown of Nrf2 could prevent the anti-inflammatory effects of morin.", "Conclusion: In conclusion, this study suggested that morin attenuated IL-1\u03b2-induced inflammation by activating the Nrf2 signaling pathway."], "structured": false}
{"doc_id": 54490092, "title": "Impact of blood pressure variability on cardiovascular events in elderly patients with hypertension.", "abstract": ["Blood pressure variability is one of the characteristic features of hypertension in the elderly.", "However, its clinical significance remains to be determined.", "We therefore examined the impact of blood pressure variability on the development of cardiovascular events in elderly hypertensive patients.", "A total of 106 consecutive hypertensive patients aged more than 60 years old (mean age, 73.9 +/-", "8.1 years old; male, 54%), all of whom underwent 24-h ambulatory blood pressure monitoring, were followed up (median, 34 months; range, 3-60 months).", "During the follow-up period, 39 cardiovascular events were observed, including 14 cases of cerebral infarction and 7 cases of acute myocardial infarction.", "The coefficient of variation (CV) of 24-h systolic blood pressure (SBP) values was used as an index of blood pressure variability.", "The patients showed a mean CV value of 10.6%, and were divided into two groups according to this mean value as a cut-off point: a high CV group (n = 46) and a low CV group (n = 60).", "Although baseline clinical characteristics were similar in the two groups, Kaplan-Meier plots for event-free survival revealed that the rate of cardiovascular events was significantly higher in high CV group than in low CV group (p < 0.05).", "Cox's proportional hazards analysis showed that increased blood pressure variability (a high CV value of 24-h SBP) was an independent predictive variable for cardiovascular events.", "The CV value of daytime SBP and the SD value of both 24-h SBP and daytime SBP also had positive correlations with the onset of cardiovascular events.", "These results suggest that increased blood pressure variability may be an independent risk factor for cardiovascular events in elderly hypertensive patients."], "structured": false}
{"doc_id": 54561384, "title": "Reprogramming committed murine blood cells to induced hematopoietic stem cells with defined factors.", "abstract": ["Hematopoietic stem cells (HSCs) sustain blood formation throughout life and are the functional units of bone marrow transplantation.", "We show that transient expression of six transcription factors Run1t1, Hlf, Lmo2, Prdm5, Pbx1, and Zfp37 imparts multilineage transplantation potential onto otherwise committed lymphoid and myeloid progenitors and myeloid effector cells.", "Inclusion of Mycn and Meis1 and use of polycistronic viruses increase reprogramming efficacy.", "The reprogrammed cells, designated induced-HSCs (iHSCs), possess clonal multilineage differentiation potential, reconstitute stem/progenitor compartments, and are serially transplantable.", "Single-cell analysis revealed that iHSCs derived under optimal conditions exhibit a gene expression profile that is highly similar to endogenous HSCs.", "These findings demonstrate that expression of a set of defined factors is sufficient to activate the gene networks governing HSC functional identity in committed blood cells.", "Our results raise the prospect that blood cell reprogramming may be a strategy for derivation of transplantable stem cells for clinical application."], "structured": false}
{"doc_id": 54561709, "title": "Genetic variability in a frozen batch of MCF-7 cells invisible in routine authentication affecting cell function", "abstract": ["Common recommendations for cell line authentication, annotation and quality control fall short addressing genetic heterogeneity.", "Within the Human Toxome Project, we demonstrate that there can be marked cellular and phenotypic heterogeneity in a single batch of the human breast adenocarcinoma cell line MCF-7 obtained directly from a cell bank that are invisible with the usual cell authentication by short tandem repeat (STR) markers.", "STR profiling just fulfills the purpose of authentication testing, which is to detect significant cross-contamination and cell line misidentification.", "Heterogeneity needs to be examined using additional methods.", "This heterogeneity can have serious consequences for reproducibility of experiments as shown by morphology, estrogenic growth dose-response, whole genome gene expression and untargeted mass-spectroscopy metabolomics for MCF-7 cells.", "Using Comparative Genomic Hybridization (CGH), differences were traced back to genetic heterogeneity already in the cells from the original frozen vials from the same ATCC lot, however, STR markers did not differ from ATCC reference for any sample.", "These findings underscore the need for additional quality assurance in Good Cell Culture Practice and cell characterization, especially using other methods such as CGH to reveal possible genomic heterogeneity and genetic drifts within cell lines."], "structured": false}
{"doc_id": 54562433, "title": "The Mammalian-Specific Protein Armcx1 Regulates Mitochondrial Transport during Axon Regeneration", "abstract": ["Mitochondrial transport is crucial for neuronal and axonal physiology.", "However, whether and how it impacts neuronal injury responses, such as neuronal survival and axon regeneration, remain largely unknown.", "In an established mouse model with robust axon regeneration, we show that Armcx1, a mammalian-specific gene encoding a mitochondria-localized protein, is upregulated after axotomy in this high regeneration condition.", "Armcx1 overexpression enhances mitochondrial transport in adult retinal ganglion cells (RGCs).", "Importantly, Armcx1 also promotes both neuronal survival and axon regeneration after injury, and these effects depend on its mitochondrial localization.", "Furthermore, Armcx1 knockdown undermines both neuronal survival and axon regeneration in the high regenerative capacity model, further supporting a key role of Armcx1 in regulating neuronal injury responses in the adult central nervous system (CNS).", "Our findings suggest that Armcx1 controls mitochondrial transport during neuronal repair."], "structured": false}
{"doc_id": 55040297, "title": "A diversity of beta diversities: straightening up a concept gone awry. Part 1. Defining beta diversity as a function of alpha and gamma diversity", "abstract": ["The term beta diversity has been used to refer to a wide variety of phenomena.", "Although all of these encompass some kind of compositional heterogeneity between places, many are not related to each other in any predictable way.", "The present two-part review aims to put the different phenomena that have been called beta diversity into a common conceptual framework, and to explain what each of them measures.", "In this first part, the focus is on defining a beta component of diversity.", "This involves deciding what diversity is and how the observed total or gamma diversity (g) is partitioned into alpha (a) and beta (b) components.", "Several different definitions of \u2018\u2018beta diversity\u2019\u2019 that result from these decisions have been used in the ecological literature.", "True beta diversity is obtained when the total effective number of species in a dataset (true gamma diversity g) is multiplicatively partitioned into the effective number of species per compositionally distinct"], "structured": false}
{"doc_id": 55128127, "title": "A cross-cultural study of wine consumers with respect to health benefits of wine", "abstract": ["The objective of the present study was to examine consumer preference and consumption behaviour with respect to the health benefits of wine for two contextually and culturally diverse consumer groups, namely Koreans and Australians.", "Participants were required to be wine consumers over the age of 18.", "Responses were collected by means of an online questionnaire.", "The results indicated that perceived health benefits of red wine were higher in the Australian sample than the Korean sample.", "Similarly, Australian consumers had more health related wine knowledge than Korean consumers.", "Red wine was the preferred wine style for both Korean and Australian consumers; however, the proportion of preference for red wine was significantly higher in the Korean sample.", "With respect to the expenditure on wine products, AUD$11\u2013$19 was the preferred price range for both groups.", "The results also indicated that health-oriented wine is more attractive to Korean consumers than Australian consumers.", "In relation to gender, Korean women preferred red wine as much as men, but Australian women consumed significantly more white wine than men.", "Such findings inform winemakers and wine marketers on the appropriateness of weighting wine production and marketing to health aspects in order to maximize consumer"], "structured": false}
{"doc_id": 56391045, "title": "DIASPORA BONDS: TAPPING THE DIASPORA DURING DIFFICULT TIMES", "abstract": ["India and Israel have raised over US$35 billion by tapping into the wealth of their diaspora communities.", "These diaspora bonds represent a stable and cheap source of external finance, often when countries lost access to international capital markets.", "For diaspora investors, these bonds offer the opportunity to help their country of origin while also providing an investment opportunity.", "The potential for diaspora bonds is significant for many countries with large diasporas abroad.", "However, diaspora bond issuance from countries with weak governance and high sovereign risk may require support for institutional capacity building and credit enhancement from multilateral or bilateral agencies.", "Haiti, for instance, could raise several hundred million dollars by issuing diaspora bonds provided a guarantee structure is created to build trust in the country's public institutions."], "structured": false}
{"doc_id": 56486733, "title": "Peroxisome Proliferator Activated Receptor gamma (PPAR\u03b3) Agonist Rosiglitazone Ameliorate Airway Inflammation by Inhibiting Toll-Like Receptor 2 (TLR2)/Nod-Like Receptor with Pyrin Domain Containing 3 (NLRP3) Inflammatory Corpuscle Activation in Asthmatic Mice", "abstract": ["BACKGROUND The purpose of this study was to explore the function and mechanism of peroxisome proliferator activated receptor agonist (PPAR\u03b3) in the toll-like receptor 2 (TLR2)/nod-like receptor with pyrin domain containing 3 (NLRP3) inflammatory corpuscle pathway of asthmatic mice.", "MATERIAL AND METHODS Eighteen female mice (C57) were randomly divided into 4 groups: the control group, the asthma model group challenged by ovalbumin (OVA), the rosiglitazone group, and the PPAR\u03b3 agonist rosiglitazone treatment group.", "The infiltration of peribronchial inflammatory cells as well as the proliferation and mucus secretion of bronchial epithelial goblet cells were observed by hematoxylin and eosin and periodic acid-Schiff staining.", "Western blots were employed to detect the expression levels of TLR2, PPAR\u03b3, nuclear factor-kappa B (NF-kappaB), NLRP3, and ASC [apoptosis-associated speck-like protein containing C-terminal caspase recruitment domain [CARD]).\n", "RESULTS The number of inflammatory cells and eosinophils, and the levels of OVAs IgE, interleukin-4 (IL-4), and IL-13 were significantly higher in the C57 asthma group compared to the C57 control group and the treatment group (P<0.05).", "The infiltration of peribronchiolar inflammatory cells, wall thickening, goblet cell hyperplasia, and mucus secretion in the treatment group were all significantly decreased compared to those in the asthma group.", "PPARg expression in the treatment group was significantly higher compared to the asthma group and the control group (P<0.05).", "The protein expression levels of TLR2, NF-kappaB, NLRP3, and ASC were significantly lower compared to the asthma group but were higher compared to the control group (P<0.05).\n", "CONCLUSIONS PPAR\u03b3 rosiglitazone ameliorates airway inflammation by inhibiting NF-kappaB expression in asthmatic mice, and further inhibits the activation of TLR2/NLRP3 inflammatory corpuscles."], "structured": true}
{"doc_id": 56528795, "title": "Omi/HtrA2 Participates in Age-Related Autophagic Deficiency in Rat Liver", "abstract": ["Liver is a vital organ with many important functions, and the maintenance of normal hepatic function is necessary for health.", "As an essential mechanism for maintaining cellular homeostasis, autophagy plays an important role in ensuring normal organ function.", "Studies have indicated that the degeneration of hepatic function is associated with autophagic deficiency in aging liver.", "However, the underlying mechanisms still remain unclear.", "The serine protease Omi/HtrA2 belongs to the HtrA family and promotes apoptosis through either the caspase-dependent or caspase-independent pathway.", "Mice lacking Omi/HtrA2 exhibited progeria symptoms (premature aging), which were similar to the characteristics of autophagic insufficiency.", "In this study, we demonstrated that both the protein level of Omi/HtrA2 in liver and hepatic function were reduced as rats aged, and there was a positive correlation between them.", "Furthermore, several autophagy-related proteins (LC3II/I, Beclin-1 and LAMP2) in rat liver were decreased significantly with the increasing of age.", "Finally, inhibition of Omi/HtrA2 resulted in reduced autophagy and hepatic dysfunction.", "In conclusion, these results suggest that Omi/HtrA2 participates in age-related autophagic deficiency in rat liver.", "This study may offer a novel insight into the mechanism involved in liver aging."], "structured": false}
{"doc_id": 56893404, "title": "Macrosomia and Hyperinsulinaemic Hypoglycaemia in Patients with Heterozygous Mutations in the HNF4A Gene", "abstract": ["Background  Macrosomia is associated with considerable neonatal and maternal morbidity.", "Factors that predict macrosomia are poorly understood.", "The increased rate of macrosomia in the offspring of pregnant women with diabetes and in congenital hyperinsulinaemia is mediated by increased foetal insulin secretion.", "We assessed the in utero and neonatal role of two key regulators of pancreatic insulin secretion by studying birthweight and the incidence of neonatal hypoglycaemia in patients with heterozygous mutations in the maturity-onset diabetes of the young (MODY) genes HNF4A (encoding HNF-4\u03b1) and HNF1A/TCF1 (encoding HNF-1\u03b1), and the effect of pancreatic deletion of Hnf4a on foetal and neonatal insulin secretion in mice."], "structured": false}
{"doc_id": 57121667, "title": "ART adherence clubs: A long-term retention strategy for clinically stable patients receiving antiretroviral therapy", "abstract": ["The ART-adherence club model described here provides patient-friendly access to antiretroviral therapy (ART) for clinically stable patients.", "It reduces the burden that stable patients place on healthcare facilities, increasing clinical human resources for new patients, and those clinically unstable and at risk of failing treatment.", "In the model, 30 patients are allocated to an ART club.", "The group meets either at a facility or community venue for less than an hour every 2 months.", "Group meetings are facilitated by a lay club facilitator who provides a quick clinical assessment, referral where necessary, and dispenses pre-packed ART.", "From January 2011 to December 2012, after adoption for phased rollout by the Western Cape Government, more than 600 ART clubs were established in Cape Town, providing ART care to over 16 000 patients.", "This extensive, rapid rollout demonstrates active buy-in from patients and facility staff.", "South Africa should consider a similar model for national rollout."], "structured": false}
{"doc_id": 57574395, "title": "Exercise-linked FNDC5/irisin rescues synaptic plasticity and memory defects in Alzheimer\u2019s models", "abstract": ["Defective brain hormonal signaling has been associated with Alzheimer's disease (AD), a disorder characterized by synapse and memory failure.", "Irisin is an exercise-induced myokine released on cleavage of the membrane-bound precursor protein fibronectin type III domain-containing protein 5 (FNDC5), also expressed in the hippocampus.", "Here we show that FNDC5/irisin levels are reduced in AD hippocampi and cerebrospinal fluid, and in experimental AD models.", "Knockdown of brain FNDC5/irisin impairs long-term potentiation and novel object recognition memory in mice.", "Conversely, boosting brain levels of FNDC5/irisin rescues synaptic plasticity and memory in AD mouse models.", "Peripheral overexpression of FNDC5/irisin rescues memory impairment, whereas blockade of either peripheral or brain FNDC5/irisin attenuates the neuroprotective actions of physical exercise on synaptic plasticity and memory in AD mice.", "By showing that FNDC5/irisin is an important mediator of the beneficial effects of exercise in AD models, our findings place FNDC5/irisin as a novel agent capable of opposing synapse failure and memory impairment in AD."], "structured": false}
{"doc_id": 57762078, "title": "Influence of antidepressant therapy on sick leave in primary care: ADAS, a comparative observational study", "abstract": ["Background Compared to other European countries, Sweden's yearly sick leave expenditures are moderate.", "Common mental disorders (CMD) are important causes of sick leave, affecting 10-15% of the adult population.", "A Swedish register based study indicates that antidepressant therapy for patients on long-term sick leave for CMD leads to longer sick leave and higher frequency of non-time-limited sickness compensation as compared to psychotherapy, work oriented rehabilitation, and other therapies.   ", "Aim To verify if patients on antidepressant therapy and on long-term sick leave for depression, anxiety and stress-related mental disorders have a longer sick leave than patients treated with other therapies.   ", "Method Prospective, observational study at 28 primary health care centers in the Region V\u00e4stra G\u00f6taland, Sweden, including 192 patients on sick leave for CMD.", "Outcome measures were gross and net sick leave days.   ", "Interpretation There were no significant differences in sick leave days (gross or net) due to CMD when comparing the patients treated and not treated with antidepressants during the 12 month observation period.", "The groups differed at baseline only concerning frequency of exhaustion disorder, with a higher frequency of exhaustion disorder in the group without antidepressants.", "Analysis of other possible factors associated with shorter or longer sick leave only showed associations with the patient's own perception of possibility of returning to work in near and distant future.", "An important factor associated with longer sick leave was the patient's own perception of possibility of return to present workplace.", "As CMD are important causes of sick leave and sick leave costs, this factor should be highlighted in future research on the rehabilitation process."], "structured": false}
{"doc_id": 57783564, "title": "CDX2 inhibits the proliferation and tumor formation of colon cancer cells by suppressing Wnt/\u03b2-catenin signaling via transactivation of GSK-3\u03b2 and Axin2 expression", "abstract": ["Caudal-related homeobox transcription factor 2 (CDX2), an intestine-specific nuclear transcription factor, has been strongly implicated in the tumourigenesis of various human cancers.", "However, the functional role of CDX2 in the development and progression of colorectal cancer (CRC) is not well known.", "In this study, CDX2 knockdown in colon cancer cells promoted cell proliferation in vitro, accelerated tumor formation in vivo, and induced a cell cycle transition from G0/G1 to S phase, whereas CDX2 overexpression inhibited cell proliferation.", "TOP/FOP-Flash reporter assay showed that CDX2 knockdown or CDX2 overexpression significantly increased or decreased Wnt signaling activity.", "Western blot assay showed that downstream targets of Wnt signaling, including \u03b2-catenin, cyclin D1 and c-myc, were up-regulated or down-regulated in CDX2-knockdown or CDX2-overexpressing colon cancer cells.", "In addition, suppression of Wnt signaling by XAV-939 led to a marked suppression of the cell proliferation enhanced by CDX2 knockdown, whereas activation of this signaling by CHIR-99021 significantly enhanced the cell proliferation inhibited by CDX2 overexpression.", "Dual-luciferase reporter and quantitative chromatin immunoprecipitation (qChIP) assays further confirmed that CDX2 transcriptionally activates glycogen synthase kinase-3\u03b2 (GSK-3\u03b2) and axis inhibition protein 2 (Axin2) expression by directly binding to the promoter of GSK-3\u03b2 and the upstream enhancer of Axin2.", "In conclusion, these results indicated that CDX2 inhibits the proliferation and tumor formation of colon cancer cells by suppressing Wnt/\u03b2-catenin signaling."], "structured": false}
{"doc_id": 58006489, "title": "Prostaglandin E2 mediates sensory nerve regulation of bone homeostasis", "abstract": ["Whether sensory nerve can sense bone density or metabolic activity to control bone homeostasis is unknown.", "Here we found prostaglandin E2 (PGE2) secreted by osteoblastic cells activates PGE2 receptor 4 (EP4) in sensory nerves to regulate bone formation by inhibiting sympathetic activity through the central nervous system.", "PGE2 secreted by osteoblasts increases when bone density decreases as demonstrated in osteoporotic animal models.", "Ablation of sensory nerves erodes the skeletal integrity.", "Specifically, knockout of the EP4 gene in the sensory nerves or cyclooxygenase-2 (COX2) in the osteoblastic cells significantly reduces bone volume in adult mice.", "Sympathetic tone is increased in sensory denervation models, and propranolol, a \u03b22-adrenergic antagonist, rescues bone loss.", "Furthermore, injection of SW033291, a small molecule to increase PGE2 level locally, significantly boostes bone formation, whereas the effect is obstructed in EP4 knockout mice.", "Thus, we show that PGE2 mediates sensory nerve to control bone homeostasis and promote regeneration."], "structured": false}
{"doc_id": 58050905, "title": "The Bone and Joint Decade 2000-2010.", "abstract": ["The World Health Organisation has declared the period 2000 to 2010 the Bone and Joint Decade.", "This is indeed timely and appropriate.", "Hundreds of millions of people in the world today are beset with a host of disabilities caused by trauma, ageing and degeneration and other affections of the musculo-skeletal system.", "With the state of art of orthopaedic surgery and rheumatology, sufferers of bone and joint disabilities have benefited a great deal from advances in pharmacology, newer techniques of imaging, surgery and man-made materials to replace diseased or damaged bone and cartilage.", "However, man-made materials, being non-living, are subject to wear and tear and loosening in the host bone.", "As we advance into the Bone and Joint Decade, further improvement in the treatment of bone and joint diseases lies in more basic cartilage and bone research.", "The Human Genome Project has provided us with a better understanding of disease genes and the possibility of gene manipulation to prevent and treat specific diseases.", "Cartilage cells culture and transplant are already a reality.", "Tissue engineering, i.e. growing cells in three-dimensional substrates of collagen or synthetic biodegradable polymers, started in the 1980s, will in future be used to replace damaged bone and cartilage parts with living and bone and cartilaginous tissues, respectively.", "The first steps have been taken; more research needs to be done.", "And it is not unreasonable to expect a significant breakthrough in the treatment of bone and joint diseases at the end of this decade.", "Ann Acad Med Singapore 2002; 31:621-2"], "structured": false}
{"doc_id": 58564850, "title": "Prevalence of late-life depression and gap in mental health service use across European regions.", "abstract": ["Background We aimed to determine the prevalence and gap in use of mental health services for late-life depression in four European regions (Western Europe, Scandinavia, Southern Europe and Central and Eastern Europe) and explore socio-demographic, social and health-related factors associated with it.", "Methods We conducted a cross-sectional study based on data from the Survey on Health, Ageing and Retirement in Europe.", "Participants were a population-based sample of 28 796 persons (53% women, mean age 74 years old) residing in Europe.", "Mental health service use was estimated using information about the diagnosis or treatment for depression.", "Results The prevalence of late-life depression was 29% in the whole sample and was highest in Southern Europe (35%), followed by Central and Eastern Europe (32%), Western Europe (26%) and lowest in Scandinavia (17%).", "Factors that had the strongest association with depression were total number of chronic diseases, pain, limitations in instrumental activities of daily living, grip strength and cognitive impairment.", "The gap in mental health service use was 79%.", "Conclusions We suggest that interventions to decrease the burden of late-life depression should be targeted at individuals that are affected by chronic somatic comorbidities and are limited in mental and physical functioning.", "Promotion of help-seeking of older adults, de-stigmatization of mental illness and education of general practitioners could help decrease the gap in mental health service utilization."], "structured": false}
{"doc_id": 59453688, "title": "Impedance and Interface Properties of Al/Methyl-Red/p-InP Solar Cell", "abstract": ["An Al/methyl-red/p-InP solar cell was fabricated via solution-processing method and was characterized by using current-voltage (I-V) and capacitance-voltage-frequency (C-V-f) measurements at room temperature.", "From dark I-V characteristics, the values of ideality factor and barrier height of the device were calculated as 1.11 eV and 2.02, respectively.", "It has been seen that the device exhibited a good photovoltaic behavior with a maximum open circuit voltage of 0.38 V and short-circuit current of 2.8 nA under only 200 lx light intensity.", "The barrier height and acceptor carrier concentration values for the Al/methyl-red/p-InP devices were extracted as 1.27 eV and from linear region of its characteristics, respectively.", "The difference between (I-V) and (C-V) for Al/methyl-red/p-InP device was attributed the different nature of the I-V and C-V measurements.", "Also, the energy distribution curves of the interface states and their time constants were obtained from the experimental conductance properties of the Al/methyl-red/p-InP structure at room temperature.", "The interface state densities and their relaxation times of the device have ranged from and s at (1.11-) eV to and s at (0.79-) eV, respectively.", "It was seen that both the interface state density and the relaxation time of the interface states have decreased with bias voltage from experimental results."], "structured": false}
{"doc_id": 60206680, "title": "R: A Language for Data Analysis and Graphics", "abstract": ["Abstract In this article we discuss our experience designing and implementing a statistical computing language.", "In developing this new language, we sought to combine what we felt were useful features from two existing computer languages.", "We feel that the new language provides advantages in the areas of portability, computational efficiency, memory management, and scoping."], "structured": false}
{"doc_id": 60515890, "title": "The Mouse Brain in Stereotaxic Coordinates", "abstract": ["\"", "The Mouse Brain in Stereotaxic Coordinates\" is the most widely used and cited atlas of the mouse brain in print.", "It provides researchers and students with both accurate stereotaxic coordinates for laboratory use, and detailed delineations and indexing of structures for reference.", "The accompanying DVD provides drawings of brains structures that can be used as templates for making figures for publication.", "The 3rd edition is both a major revision and an expansion of previous editions.", "Delineations and photographs in the horizontal plane of section now complement the coronal and sagittal series, and all the tissue sections are now shown in high resolution digital color photography.", "The photographs of the sections and the intermediate sections are also provided on the accompanying DVD in high-resolution JP 2000 format.", "The delineations of structures have been revised, and naming conventions made consistent with Paxinos and Watson's \"Rat Brain in Stereotaxic Coordinates, 6th Edition\".", "The 3rd edition of this atlas is now in more practical 14\"x11\" format for convenient lab use.", "This edition is in full color throughout.", "It includes a CD of all plates and diagrams, as well as Adobe Illustrator files of the diagrams, and a variety of additional useful material.", "Coronal and sagittal diagrams are completely reworked and updated.", "Rhombomeric borders are included in sagittal figures, for the first time in mammals.", "Microscopic plates are scanned with a new method in much higher quality."], "structured": false}
{"doc_id": 61050894, "title": "ggplot2: Elegant Graphics for Data Analysis", "abstract": ["ggplot2: Elegant Graphics for Data Analysis is a new addition to the UseR!", "series by Springer, probably the fastest expanding source of resources for computational statistics at the current moment.", "The books in this series are all linked with R, either presenting a new package developed by the own authors of the book or describing how to applying statistical techniques with the different packages available in R. ggplot2 is an implementation in R of The Grammar of Graphics (Wilkinson 2005) a systematic approach to the specification of statistical graphics that was introduced in a book previously reviewed in the Journal of Statistical Software by Cox (2007).", "This implementation has been developed by Hadley Wickham, who is also the author of the book reviewed here."], "structured": false}
{"doc_id": 63858430, "title": "Multiple Imputation For Nonresponse In Surveys", "abstract": ["multiple imputation for nonresponse in surveys is available in our book collection an online access to it is set as public so you can download it instantly.", "Our book servers hosts in multiple locations, allowing you to get the most less latency time to download any of our books like this one.", "Merely said, the multiple imputation for nonresponse in surveys is universally compatible with any devices to read."], "structured": false}
{"doc_id": 67045088, "title": "Inhibition of the dipeptidyl peptidase DPP4 (CD26) reveals IL-33-dependent eosinophil-mediated control of tumor growth", "abstract": ["Post-translational modification of chemokines mediated by the dipeptidyl peptidase DPP4 (CD26) has been shown to negatively regulate lymphocyte trafficking, and its inhibition enhances T cell migration and tumor immunity by preserving functional chemokine CXCL10.", "By extending those initial findings to pre-clinical models of hepatocellular carcinoma and breast cancer, we discovered a distinct mechanism by which inhibition of DPP4 improves anti-tumor responses.", "Administration of the DPP4 inhibitor sitagliptin resulted in higher concentrations of the chemokine CCL11 and increased migration of eosinophils into solid tumors.", "Enhanced tumor control was preserved in mice lacking lymphocytes and was ablated after depletion of eosinophils or treatment with degranulation inhibitors.", "We further demonstrated that tumor-cell expression of the alarmin IL-33 was necessary and sufficient for eosinophil-mediated anti-tumor responses and that this mechanism contributed to the efficacy of checkpoint-inhibitor therapy.", "These findings provide insight into IL-33- and eosinophil-mediated tumor control, revealed when endogenous mechanisms of DPP4 immunoregulation are inhibited.", "Eosinophils have been described mainly in allergy settings but are increasingly appreciated as being involved in other aspects of immunity.", "Albert and colleagues use a clinically approved inhibitor of the dipeptidyl peptidase DPP4 to facilitate the recruitment of eosinophils to mouse tumors, where they are essential in tumor destruction."], "structured": false}
{"doc_id": 67787658, "title": "Cycling Quiescence in Temozolomide Resistant Glioblastoma Cells Is Partly Explained by microRNA-93 and -193-Mediated Decrease of Cyclin D", "abstract": ["Glioblastoma multiforme (GBM) is a fatal malignancy of the central nervous system, commonly associated with chemoresistance.", "The alkylating agent Temozolomide (TMZ) is the front-line chemotherapeutic agent and has undergone intense studies on resistance.", "These studies reported on mismatch repair gene upregulation, ABC-targeted drug efflux, and cell cycle alterations.", "The mechanism by which TMZ induces cell cycle arrest has not been well-established.", "TMZ-resistant GBM cells have been linked to microRNA (miRNA) and exosomes.", "A cell cycle miRNA array identified distinct miRNAs only in exosomes from TMZ-resistant GBM cell lines and primary spheres.", "We narrowed the miRs to miR-93 and -193 and showed in computational analyses that they could target Cyclin D1.", "Since Cyclin D1 is a major regulator of cell cycle progression, we performed cause-effect studies and showed a blunting effects of miR-93 and -193 in Cyclin D1 expression.", "These two miRs also decreased cell cycling quiescence and induced resistance to TMZ.", "Taken together, our data provide a mechanism by which GBM cells can exhibit TMZ-induced resistance through miRNA targeting of Cyclin D1.", "The data provide a number of therapeutic approaches to reverse chemoresistance at the miRNA, exosomal and cell cycle points."], "structured": false}
{"doc_id": 68317730, "title": "Longitudinal changes in maternal corin and mid-regional proatrial natriuretic peptide in women at risk of pre-eclampsia", "abstract": ["Objectives Corin, an atrial natriuretic peptide-converting enzyme, has been found to promote trophoblast invasion and spiral artery remodeling.", "Reduced maternal plasma atrial natriuretic peptide (ANP) levels and elevated corin levels have been reported in pregnancies complicated by PE.", "The aim of this study was to investigate longitudinal changes in maternal plasma levels of corin and midregional proatrial natriuretic peptide (MR-PANP) in pregnancies that develop preeclampsia (PE) and gestational hypertension (GH).", "Methods Nested case control study drawn from a larger prospective longitudinal study in singleton pregnancies identified by screening at 11 + 0 \u2212 13 + 6 weeks\u2019 gestation as being at high risk for PE.", "Blood samples were taken every four weeks until delivery.", "Values were compared in pregnancies that developed preterm-PE (requiring delivery before 37 weeks), term-PE, GH, and those that remained normotensive.", "The distribution of maternal plasma corin and PANP were made Gaussian after log 10 transformation.", "Analysis of repeated measures with multilevel mixed-effects linear model (fixed effects and random effects) was performed.", "The multilevel model was compared to one-level model by the likelihood radio (LR) test.", "Results A total of 471 samples were analyzed from 122 women, including 85 that remained normotensive, 12 that developed GH, 13 term-PE and 12 preterm-PE.", "In the normotensive group, log10corin levels were associated with gestational age ( p p  = 0.001).", "In the GH and term-PE groups, corin did not differ significantly from the normotensive group ( p  = 0.64 and p  = 0.16, respectively).", "Compared to the normotensive group, MR-PANP levels were significantly higher in the pregnancies that developed preterm-PE and GH ( p  = 0.046 and p  = 0.019, respectively), but not term-PE ( p  = 0.47).", "Conclusions Maternal plasma corin and MR-PANP could potentially be useful biomarkers for the prediction of preterm-PE.", "Disclosures A. Khalil: Research Support Recipient; Commercial Interests: USCOM, Roche, Alere, NICOM, Q-fFN;", "Speaker: Roche."], "structured": false}
{"doc_id": 69045262, "title": "Children's Exercise Physiology", "abstract": ["The reorganized and newly revised \"Children's Exercise Physiology, Second Edition, \" presents the most up-to-date research, methodology, and approaches related to children's physiologic responses to exercise.", "The book examines not only the current major issues that separate children from adults, but also the underlying mechanisms of these differences.", "Readers will learn what makes children different from adults physiologically--such as size, biochemical differences, neuromuscular differences, and lack of sexual and hormonal maturation--and the reasons for these differences.", "Those involved with young athletes, disease management, and health promotion will gain valuable insight into the physiologic determinants of exercise performance.", "Children's exercise physiology is a fast-moving field.", "In the eight years since the first edition of this book was published, much new information has surfaced.", "This streamlined new edition contains 13 instead of 15 chapters, an introduction, and updated features: -Chapter objectives, discussion questions and research directions, and a glossary of terms promote learning.-A reorganized table of contents improves the flow from chapter to chapter.-A new final chapter covers the role of the central nervous system.", "Also included is in-depth discussion of the determinants of aerobic fitness and VO2 kinetics and the significance of maximal aerobic power in children.", "With improved chapters on thermoregulation and metabolic and endocrinologic responses to exercise, you can be confident you're getting the latest information with \"Children's Exercise Physiology, Second Edition.", "\""], "structured": false}
{"doc_id": 70439309, "title": "Cost-effectiveness in health and medicine", "abstract": ["1.", "Cost-Effectiveness Analysis as a Guide to Resource Allocation in Health: Roles and Limitations 2.", "Theoretical Foundations of Cost-Effectiveness Analysis 3.", "Framing and Designing the Cost-Effectiveness Analysis 4.", "Identifying and Valuing Outcomes 5.", "Assessing the Effectiveness of Health Interventions 6.", "Estimating Costs in Cost-Effectiveness Analysis 7.", "Time Preference 8.", "Reflecting Uncertainty in Cost-Effectiveness Analysis 9.", "Reporting Cost-Effectiveness Studies and Results Appendix A: Summary of Recommendations for the Reference Case Appendix B: Cost-Effectiveness of Strategies to Prevent Neural Tube Defects Appendix C: The Cost-Effectiveness of Dietary and Pharmacologic Therapy for Cholesterol Reduction in Adults"], "structured": false}
{"doc_id": 70455704, "title": "Weight gain during pregnancy: reexamining the guidelines.", "abstract": ["As women of childbearing age have become heavier, the trade-off between maternal and child health created by variation in gestational weight gain has become more difficult to reconcile.", "Weight Gain During Pregnancy responds to the need for a reexamination of the 1990 Institute of Medicine guidelines for weight gain during pregnancy.", "It builds on the conceptual framework that underscored the 1990 weight gain guidelines and addresses the need to update them through a comprehensive review of the literature and independent analyses of existing databases.", "The book explores relationships between weight gain during pregnancy and a variety of factors (e.g., the mother's weight and height before pregnancy) and places this in the context of the health of the infant and the mother, presenting specific, updated target ranges for weight gain during pregnancy and guidelines for proper measurement.", "New features of this book include a specific range of recommended gain for obese women.", "Weight Gain During Pregnancy is intended to assist practitioners who care for women of childbearing age, policy makers, educators, researchers, and the pregnant women themselves to understand the role of gestational weight gain and to provide them with the tools needed to promote optimal pregnancy outcomes."], "structured": false}
{"doc_id": 70516463, "title": "To err is human. Building a safer health system", "abstract": ["Human beings, make errors Healthcare Services is a complex industry prone to accidents.", "The IOM Report [1] points out that some systems are more prone to accidents than others.", "When a system fails there are often multiple faults.", "In healthcare,human errors are the greatest contributors to accidents,however when human error is to blame it often depends upon failures within the system.", "These failures exists in the system before the error occurs, the same as with latent errors which are difficult to identify since they may be hidden in computers or within the various managerial layers.", "Most of the errors can be prevented by designing systems that make it hard for people to do the wrong thing and easy for people to do the right thing.", "In healthcare, this means designing processes that are able to ensure that patients are safe from accidental injury.", "As healthcare and the system that delivers it become more complex, the opportunities for errors abound.", "The IOM report \u201cTo Err is Human\u201d proposes an approach for reducing medical errors and improving patient safety.", "The environment within which this occurs has a critical influence on quality.", "This influence may contain two dimensions; the first consists of the domain of quality which includes the practice that is consistent with current medical knowledge.", "The second dimension consists of forces in the external environment that can drive quality improvement in the delivery system.", "Although the risk of dying as a result of a medical error, far surpasses the risk of dying in an airline accident, public attention has been more focused on improving safety in the airline industry than in healthcare systems.", "Because of the absence of standardized nomenclature, it is important to define what an error is and what is an adverse event, the IOM Report defines them in the following way: \u201cAn error is the failure of a planned action to be completed as intended or the use of a wrong plan to achieve an aim.", "\u201d An adverse event is an injury caused by medical management rather than the underlying condition of the patient.", "An adverse event attributable to error is a \u201cpreventable adverse event\u201d."], "structured": false}
{"doc_id": 70633421, "title": "Excess risk of lymphomas, leukemia and myeloma in patients with rheumatoid arthritis", "abstract": ["The incidence of malignant neoplasms among 11 483 male and 34 618 female individuals with rheumatoid arthritis was studied using two separate nationwide data registers covering the whole Finnish population: the Social Insurance Institution9s Population Data Register, which includes information on medication for certain chronic diseases, and the Finnish Cancer Registry, with data on all cancer patients diagnosed in Finland.", "The follow-up comprised a total of 213 911 person years.", "The total incidence of all malignant neoplasms was higher in males and on the level expected in females.", "The expected number of cases of leukemia, lymphomas, Hodgkin9s disease and myeloma in both sexes was 59\u00b76 as compared with the 130 cases observed.", "This difference is statistically highly significant (p"], "structured": false}
{"doc_id": 70704988, "title": "Advanced Human Nutrition", "abstract": ["Advanced Human Nutrition, Second Edition provides an in-depth overview of the human body and details why nutrients are important from a biochemical, physiological, and molecular perspective.", "Figures help illustrate the content and bring the meaning to life to enhance the reader's understanding.", "Complex pathways, for example, are presented in a student-friendly fashion, as are diagrams that illustrate metabolism and the molecular functions of nutrients.", "Multiple elements within the text, such as \"Here's Where You Have Been\" and \"Here's Where You Are Going,\" help drive home key points from the chapter and provide real-world examples to bring the content to life.", "Topics covered include: * cell aging, damage and repair systems * human nutrition, digestion, and absorption with relation to organs, exocrine and endocrine functions, histology, and absorptive activities * microflora and satiety/hunger mechanisms * macronutrients during exercise and the role of liquids and sports drinks * prevalent diseases in western cultures such as coronary heart disease, cancer, and osteoporosis An Instructor's Manual, PowerPoint Presentations, and a TestBank are available are free downloads."], "structured": false}
{"doc_id": 70895396, "title": "The Endothelium: Modulator of Cardiovascular Function", "abstract": ["Introduction.", "Methods To Study Endothelium-Dependent Responses.", "Endothelium-Derived Relaxing Factor.", "Physiological Actions.", "Other Relaxing Substances Released By the Endothelium.", "Production of Contracting Agents.", "Local Regulation of Endothelium-Dependent Responses.", "Neurohumoral Regulation.", "Heterogeneity and Chronic Modulation.", "Disease.", "Therapeutic Implications.", "References.", "Subject Index."], "structured": false}
{"doc_id": 71341302, "title": "Vegetarian vs. conventional diabetic diet \u2013 A 1-year follow-up", "abstract": ["Abstract Objective Our previous 6-month, randomized study demonstrated the beneficial effect of a vegetarian (V) compared to a conventional diet (C) with similar caloric restriction on cardiovascular risk factors for patients with type 2 diabetes (T2D), namely increased insulin sensitivity, reduced body weight, reduced volume of visceral and subcutaneous fat, decreased LDL-cholesterol and improved oxidative stress markers and chosen adipokines.", "We conducted post-trial monitoring to determine whether the improved outcomes persisted 1 year after the end of the study.", "Methods 62 subjects with T2D who completed the study were asked to come for a 1-year follow-up to measure weight, waist circumference, HbA1c and blood lipids.", "No attempts were made to maintain their previously assigned diets.", "Results 44 patients (71%) attended the post-trial monitoring.", "Hypoglycemic agents were increased by 14% in V and by 26% in C; insulin therapy was introduced in 5% in V and in 13% in C one year after the end of the intervention.", "Neither weight nor waist circumference changed significantly in either group.", "HbA1c increased ( p  \u2264 0.05) similarly in both groups (+0.49 \u00b1 1.04% in V vs. +0.42 \u00b1 0.8% in C).", "Blood lipids did not change in either group.", "Conclusion One year after the end of the intervention, the positive effects of a vegetarian diet on cardiovascular risk factors compared to a conventional diet were partially maintained."], "structured": false}
{"doc_id": 71625969, "title": "Alcohol, wine, and health", "abstract": ["Abstract Background: For the past 20 years numerous epidemiological studies have correlated the consumption of alcohol and a variety of disease states: overall mortality, arteriosclerotic vascular diseases, hypertension, cancers, peptic ulcer, respiratory infections, gall stones, kidney stones, age-related macular degeneration, bone density, and cognitive function.", "Methods: A review of these articles reveals that each of these studies has compared the outcome of individuals at various levels of alcohol consumption with that of abstainers.", "Results: Each analysis has identified a U-shaped or J-shaped curve of reduced relative risk for a given disease state compared with abstainers.", "A clear definition of consumption in moderation becomes evident: for men it should not exceed 2 to 4 drinks per day, and for women it should not exceed 1 to 2 drinks per day.", "Conclusions:", "Alcohol by itself has favorable effects on the level of high-density lipoprotein cholesterol, and inhibition of platelet aggregation.", "Wine, particularly red wine, has high levels of phenolic compounds that favorably influence multiple biochemical systems, such as increased high-density lipoprotein cholesterol, antioxidant activity, decreased platelet aggregation and endothelial adhesion, suppression of cancer cell growth, and promotion of nitric oxide production."], "structured": false}
{"doc_id": 71628189, "title": "Contraceptive practices of women requesting termination of pregnancy : A study from China", "abstract": ["Abstract In order to develop a program for prevention of unwanted pregnancies, we conducted a survey of contraceptive practices and reasons for contraceptive failures of 1520 women seeking abortion at eight large hospitals in Zheng Zhou City, Henan Province, P.R. China, during the period from March 1996 to May 1996.", "The most frequent cause of the unplanned pregnancy was contraceptive failure (71.9%); 61.7% (938) of these current pregnancies were potentially predictable by virtue of nonuse of contraception (427) or by recognition of contraceptive failures (511).", "Among the contraceptive failures, the proportion of condom mishaps was the highest (29.7%), next was IUD failures (23.5%), then rhythm miscalculation (15.9%).", "Most of abortion seekers (77.1%) used some contraceptive methods previously.", "But, only 19.7% of them used a contraceptive method at the first sexual intercourse.", "Among 1520 abortion seekers, 57.6% had used condoms previously; 50.9% of the condom users had at least one instance of condom mishap.", "The rhythm method had been used by 31.7% of abortion seekers previously; 59.1% of the rhythm users had at least one instance of rhythm failure.", "Of the 16.8% of abortion seekers who had used pills, 58.0% of them had pill failures.", "Among condom and pill failures, most of them (46.4% condom users and 56.0% pill users) belonged to the user failure category (poor complicance).", "Of those seeking abortion, 56.4% had experienced at least one instance of previous abortion; 5.3% had experienced previous abortions at least two times.", "Emergency contraception had been utilized by only 10 subjects prior to this current pregnancy."], "structured": false}
{"doc_id": 72180760, "title": "Oncologists' perceptions of the effects of cancer patients' companions on physician-patient interactions", "abstract": ["To determine physicians' perceptions of the effects that the companions of cancer patients have on physician-patient communication, semistructured interviews were conducted with 12 oncologists (6 medical, 4 surgical, and 2 radiation) from a total population of 21 oncologists.", "The physicians estimated that threefourths of their patients brought companions with them to consultations and said that these consultations were more complex for the physician.", "The behaviors of the companions varied from domination to passive note taking, and the companions who were young professional men or older women who accompanied their husbands were the most assertive and asked the most questions.", "All possible coalitions were observed during medical visits.", "The physicians perceived that companions and patients often had different agendas and noted differences in the companions' behaviors according to their gender and whether they lived in rural or urban areas."], "structured": false}
{"doc_id": 72372925, "title": "Wolff's Headache and Other Head Pain.", "abstract": ["There has never been a book on headache that came close to that of the late Harold Wolff.", "The second edition was published 10 years ago; it was and is a masterpiece of writing, an exhaustive yet engrossing delineation of Wolff's long study and understanding of headache.", "The new edition, revised by Dalessio, serves to bring certain aspects of headache up to date, most of them having to do with drug therapy.", "The emphasis on total therapy rather than simply drug therapy has been preserved, however.", "Dalessio has altered slightly the form of the book, although the \"new chapters\" on cluster headache and trigeminal neuralgia are merely transplants from other sections of the original.", "Migraine, the main part of the book, has been reshaped, with some anecdotal portions removed, but little has been added.", "It is of interest that nothing in the section on observations of methysergide (UML-491 in Wolff's"], "structured": false}
{"doc_id": 72580164, "title": "Ansichten von Haus\u00e4rzten zur Versorgung von unheilbar kranken Patienten am Lebensende - Ergebnisse einer Befragung in Niedersachsen", "abstract": ["Background: Family doctors play an important role in the health care for terminal ill and patients.", "The current level of palliative care in Germany is strongly criticised, however, empirical data is scare, particularly with respect to family doctors.", "Methods: Therefore, the attitudes of family doctors (sample: n= 257) in four representative regions in Lower Saxony were studied by using semi-structured telephone interviews.", "This was part of a health system researchers\u2019 expert report.", "Results: 71doctors could be interviewed (28%).", "On the average, they cared for four palliative patients with cancer diseases and eight palliative patients with other diseases than cancer at that time.", "Many of the doctors were available for their patients around the clock, particularly in the final phase.", "The main area for improvement was considered to be the psychosocial support \u2013 rather than pain therapy, which is usually focussed.", "Furthermore, a considerable openness for the establishment of new palliative care structures was shown.", "Conclusion: Family doctors are highly motivated for palliative care and open for improvements.", "In the process, the diversity of opinion among professions and disciplines about the current situation and the further development of palliative care should be respected and considered."], "structured": false}
{"doc_id": 72933407, "title": "Novel Risk Factors for Systemic Atherosclerosis: A Comparison of C-Reactive Protein, Fibrinogen, Homocysteine, Lipoprotein(a), and Standard Cholesterol Screening as Predictors of Peripheral Arterial Disease", "abstract": ["ContextSeveral novel risk factors for atherosclerosis have recently been proposed, but few comparative data exist to guide clinical use of these emerging biomarkers.", "ObjectiveTo compare the predictive value of 11 lipid and nonlipid biomarkers as risk factors for development of symptomatic peripheral arterial disease (PAD).Design, Setting, and ParticipantsNested case-control study using plasma samples collected at baseline from a prospective cohort of 14 916 initially healthy US male physicians aged 40 to 84 years, of whom 140 subsequently developed symptomatic PAD (cases); 140 age- and smoking status\u2013matched men who remained free of vascular disease during an average 9-year follow-up period were randomly selected as controls.", "Main Outcome MeasureIncident PAD, as determined by baseline total cholesterol, high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), total cholesterol\u2013HDL-C ratio, triglycerides, homocysteine, C-reactive protein (CRP), lipoprotein(a), fibrinogen, and apolipoproteins (apo) A-I and B-100.ResultsIn univariate analyses, plasma levels of total cholesterol (P<.001), LDL-C (P = .001), triglycerides (P = .001), apo B-100 (P = .001), fibrinogen (P = .02), CRP (P = .006), and the total cholesterol\u2013HDL-C ratio (P<.001) were all significantly higher at baseline among men who subsequently developed PAD compared with those who did not, while levels of HDL-C (P = .009) and apo A-I (P = .05) were lower.", "Nonsignificant baseline elevations of lipoprotein(a) (P = .40) and homocysteine (P = .90) were observed.", "In multivariable analyses, the total cholesterol\u2013HDL-C ratio was the strongest lipid predictor of risk (relative risk [RR] for those in the highest vs lowest quartile, 3.9; 95% confidence interval [CI], 1.7-8.6), while CRP was the strongest nonlipid predictor (RR for the highest vs lowest quartile, 2.8; 95% CI, 1.3-5.9).", "In assessing joint effects, addition of CRP to standard lipid screening significantly improved risk prediction models based on lipid screening alone (P<.001).ConclusionsOf 11 atherothrombotic biomarkers assessed at baseline, the total cholesterol\u2013HDL-C ratio and CRP were the strongest independent predictors of development of peripheral arterial disease.", "C-reactive protein provided additive prognostic information over standard lipid measures."], "structured": false}
{"doc_id": 73136607, "title": "Assessment of older people: Self-maintaining and instrumental activities of daily living.", "abstract": ["THE use of formal devices for assessing function is becoming standard in agencies serving the elderly.", "In the Gerontological Society's recent contract study on functional assessment (Howell, 1968), a large assortment of rating scales, checklists, and other techniques in use in applied settings was easily assembled.", "The present state of the trade seems to be one in which each investigator or practitioner feels an inner compusion to make his own scale and to cry that other existent scales cannot possibly fit his own setting.", "The authors join this company in presenting two scales first standardized on their own population (Lawton, 1969).", "They take some comfort, however, in the fact that one scale, the Physical Self-Maintenance Scale (PSMS), is largely a scale developed and used by other investigators (Lowenthal, 1964), which was adapted for use in our own institution.", "The second of the scales, the Instrumental Activities of Daily Living Scale (IADL), taps a level of functioning heretofore inadequately represented in attempts to assess everyday functional competence.", "Both of the scales have been tested further for their usefulness in a variety of types of institutions and other facilities serving community-resident older people.", "Before describing in detail the behavior measured by these two scales, we shall briefly describe the schema of competence into which these behaviors fit (Lawton, 1969).", "Human behavior is viewed as varying in the degree of complexity required for functioning in a variety of tasks.", "The lowest level is called life maintenance, followed by the successively more complex levels of func-"], "structured": false}
{"doc_id": 73323408, "title": "Diabetes in pregnancy: management of diabetes and its complications from preconception to the postnatal period (NG3)", "abstract": ["In February 2015 the National Institute for Health and Care Excellence (NICE) published new guidance (NG3) on the management of diabetes in pregnancy.", "Care teams need to be aware of this guidance and implement its recommendations.", "These include preconception care with target HbA1c 48 mmol/mol.", "Women at risk of gestational diabetes mellitus (GDM) should have a 75 g oral glucose tolerance test (OGTT).", "Diagnostic criteria for GDM have changed to fasting glucose of 5.6 mmol/L or above or 2 hour glucose of 7.8 mmol/L or above.", "Glycaemic targets in all diabetic pregnancies have changed to fasting glucose below 5.3 mmol/L (4\u20135.2 mmol/L if on insulin) and 1 hour postprandial glucose below 7.8 mmol/L if these can be achieved safely.", "Continuous glucose monitoring and insulin pump therapy should not be used routinely but can be used if glycaemic control is problematic.", "Capillary ketone testing should be routine for women with type 1 diabetes when hyperglycaemic and for all women with diabetes including, GDM when acutely unwell.", "More flexibility is offered around recommended delivery timing: 37+0 weeks to 38+6 weeks for women with types 1 and 2 diabetes; prior to 40+6 in GDM (and earlier if complications arise).", "Postnatal testing following GSM should be by fasting glucose (not OGTT) at 6\u201313 weeks post partum.", "Testing later than this can use HbA1c.", "Introducing these changes will have resource implications, including a likely increase in the number of women diagnosed with GDM."], "structured": false}
{"doc_id": 73473433, "title": "Mental health difficulties across childhood and mental health service use: findings from a longitudinal population-based study.", "abstract": ["BACKGROUND Over the past 20 years the prevalence of child and adolescent mental disorders in high-income countries has not changed despite increased investment in mental health services.", "Insufficient contact with mental health services may be a contributing factor; however, it is not known what proportion of children have sufficient contact with health professionals to allow delivery of treatment meeting minimal clinical practice guidelines, or how long children experience symptoms prior to receiving treatment.", "AimsTo investigate the level of mental healthcare received by Australian children from age 4 years to 14 years.   \n", "METHOD Trajectories of mental health symptoms were mapped using the Strengths and Difficulties Questionnaire.", "Health professional attendances and psychotropic medications dispensed were identified from linked national Medicare Benefits Schedule (MBS) and Pharmaceutical Benefits Scheme records.   \n", "RESULTS Four trajectories of mental health symptoms were identified (low, high-decreasing, moderate-increasing and high-increasing).", "Most children with mental health symptoms had few MBS mental health attendances, and only a minority received care meeting study criteria for minimally adequate treatment.", "Children in the high-increasing and moderate-increasing trajectories were more likely to access care, yet there was no evidence of improvement in symptoms.   \n", "CONCLUSIONS It is important that children and adolescents with mental health problems receive treatment that meets minimal practice guidelines.", "Further research is needed to identify the quality of care currently provided to children with mental health difficulties and how clinicians can be best funded and supported to provide care meeting minimal practice guidelines.", "Declaration of interestsNone."], "structured": true}
{"doc_id": 74137632, "title": "Rembrandt Scholz", "abstract": ["This paper examines the potential impact of changes in medical care on changing population health in Lithuania, Hungary and Romania, with west Germany included for comparison.", "We used the concept of deaths from certain causes that should not occur in the presence of timely and effective health care (amenable mortality) and calculated the contribution of changes in mortality from these conditions to changes in life expectancy between birth and age 75 [e (0-75)] for the periods 1980/81 to 1988 and 1992 to 1997.  ", "Temporary life expectancy improved consistently in west Germany (men: 2.7 years, women: 1.6 years).", "In contrast, gains were relatively small in the other countries, except among Hungarian women, who gained 1.3 years.", "Romanian men lost 1.3 years.", "In the 1980s, falling infant mortality made a substantial contribution to improvements in temporary life expectancy in all countries, of about a quarter to half a year.", "Of this, more than half can be attributed to amenable conditions.  ", "At older ages, falling amenable mortality contributed about 40% among those aged over 40 in Germany and, to a lesser extent, Hungary, while causing a loss of life expectancy in Romania.  ", "In the 1990s, improvements in infant mortality continued to make substantial contributions to life expectancy in Lithuania and Hungary but had little impact in either Germany or Romania.", "Among adults, improvements in amenable mortality continued to benefit Hungarians and west Germans.", "In Lithuania, up to two-thirds of the gain in temporary life expectancy were attributable to falling mortality from ischaemic heart disease whereas medical care otherwise seems to have had a negative impact.", "Romanian men and women experienced increases in amenable mortality that contributed up to a half of the overall loss of life expectancy.  ", "Our findings suggest that during the last 20 years changes in medical care had considerable impact, positively as well as negatively, on changing mortality in selected central and eastern European countries."], "structured": false}
{"doc_id": 74701974, "title": "The Women's Interagency HIV Study", "abstract": ["The Women's Interagency HIV Study comprises the largest U.S. cohort to date of human immunodeficiency virus (HIV)-seropositive women (N = 2,058) with a comparison cohort of seronegative women (N = 568).", "The methodology, training, and quality assurance activities employed are described.", "The study pop"], "structured": false}
{"doc_id": 75636923, "title": "Prevalence of the Metabolic Syndrome Among Us Adults: Findings From the Third National Health and Nutrition Examination Survey", "abstract": ["Metabolic syndrome is diagnosed when three or more of the following criteria are met: abdominal obesity (waist circumference more than 102 cm in men and 88 cm in women); hypertriglyceridemia of 150 mg/dl or above; a high-density lipoprotein (HDL) cholesterol level less than 40 mg/dl in men or 50 mg/dl in women; blood pressure of 130/85 mm Hg or higher; or fasting glucose of at least 110 mg/dl.", "Individuals with metabolic syndrome are likelier than others to develop diabetes and cardiovascular disease and have increased mortality from all causes (and from cardiovascular disease in particular).", "The investigators attempted to determine the prevalence of the syndrome in the United States by analyzing data on 8814 men and women 20 years of age or older who took part in the Third National Health and Nutrition Examination Survey in the years 1988 to 1994.", "This is a cross-sectional health survey of a sample of the noninstitutionalized civilian American population.", "The overall age-adjusted prevalence of metabolic syndrome was 23.7%.", "The prevalence rose from 6.7% in persons 20 to 29 years of age to 42% in those aged 70 years and more.", "There was virtually no gender-related difference in prevalence rates for the combined racial groups.", "Metabolic syndrome was most prevalent in Mexican Americans and least prevalent in whites, African Americans, and \"others.", "\"", "Among both African Americans and Mexican Americans, women had higher prevalence rates than men.", "Extrapolating from age-specific prevalence rates and US census counts from the year 2000, 47 million US residents have metabolic syndrome.", "Considering its prevalence, it seems important to estimate the direct medical costs of metabolic syndrome.", "In the great majority of cases the critical causes are improper nutrition and insufficient physical activity, emphasizing the importance of controlling obesity and encouraging physical activity in the United States."], "structured": false}
{"doc_id": 76415938, "title": "Baseline cytology, human papillomavirus testing, and risk for cervical neoplasia: A 10-year cohort analysis", "abstract": ["As more is learned about the development of cervical cancer, the value of annual Pap smear screening for all women is being questioned.", "This study was conducted to investigate whether women at higher risk for the development of cervical cancer could be identified by testing for the presence of human papillomavirus (HPV) in the cervical smear.", "These women could be followed annually, and the interval between screening Pap smears for women at lower risk could be increased.", "Study participants were women enrolled in the Kaiser Permanente healthcare plan in Portland, Oregon, who underwent annual Pap smear screening between April 1989, and November 1990.", "More than 20,000 women (20,810 of 23,702) had satisfactory cervical smears with sufficient samples for HPV testing, which was conducted using a polymerase chain reaction-based method with MYO9/11 primers.", "Most women (83.6%) had at least one follow-up smear during the study period; however, women with atypical squamous cells (ASC) or worse had more smears than women with normal results (mean, 4.4 vs. 3.3).", "Follow-up was conducted more or less annually for a total period of 122 months.", "HPV results were not used in deciding patient management.", "Ninety-six percent of the 20,810 baseline Pap smears were diagnosed as negative (N = 20,156).", "Thirteen percent of these patients tested positive for HPV.", "The baseline smears of 654 of the 20,810 women (3.1%) were classified as ASC or worse.", "Of these 654 smears, 417 (63.8%) were positive for HPV.", "One hundred seventy-eight women had a cytologic diagnosis of a low-grade squamous intraepithelial lesion or worse; of these, 143 (80.3%) tested positive for HPV.", "During the 10 years of follow-up, 171 patients developed cervical intraepithelial neoplasia (CIN) 3 or cervical cancer.", "The baseline smear was normal in 112 of these women and ASC or worse in 59 (34.5%).", "Only half (49.2%) of the 58 patients diagnosed within the first 45 months of follow-up had an abnormal baseline smear.", "During this first 45 months, 7.85% of the women whose initial Pap test was at least ASC were diagnosed with CIN 3 or cancer.", "The cumulative incidence at 10 years of follow-up was 10.2%.", "Sixty of the 171 women with CIN 3 or cervical cancer had a negative baseline HPV test.", "Of the 118 women who were diagnosed during the first 45 months of follow-up, 89 (79.4%) were HPV positive initially.", "The cumulative incidence of CIN 3 or cancer among the group with a positive baseline HPV test was 6.92% over 10 years but only 1.73% at 45 months.", "The risk of developing CIN 3 or cancer remained elevated throughout the study in those women with a positive baseline HPV test.", "The predictive ability of the baseline Pap smear diminished as the follow-up interval increased.", "Fifteen percent of the patients (N = 3216) had a positive Pap smear, a positive HPV test, or both at the initial examination.", "One hundred twenty-three (71.9%) were among the 171 women who developed CIN 3 or cancer.", "Eighty-six percent (102 of 123) of the patients who were diagnosed within the first 45 months were positive with at least one of the screening studies.", "The cumulative incidence over 45 months for women who had positive HPV testing and/or abnormal Pap smear results was 4.54%.", "Women with negative results in both screening tests had a cumulative risk of 0.16% for the same period.", "At 10 years the cumulative risk incidence for these two groups was 6.83% and 0.79%, respectively, yielding a negative predictive value of 99.1% for combined testing."], "structured": false}
{"doc_id": 76463821, "title": "Preconception Care and the Risk of Congenital Anomalies in the Offspring of Women With Diabetes Mellitus: A Meta-Analysis", "abstract": ["Preconception care (PCC) and strict periconceptional glycemic control are both used to minimize the risk of congenital birth defects in offspring of women with type 1 or type 2 diabetes mellitus (DM).", "These malformations are ascribed in large measure to poor periconceptional control.", "This study evaluated PCC by a meta-analysis of published studies of PCC in women with DM, published from 1970 to 2000.", "Two reviewers independently abstracted the data, and the rate and relative risk (RR) of major and minor malformations were pooled from eligible studies using a random effects model.", "Early first-trimester values of glycosylated hemoglobin were recorded.", "Eight retrospective and eight prospective cohort studies were included; they were carried out in Europe, the United Kingdom, the United States, and Israel.", "Most participants had type 1 DM, but three studies included women with type 2 DM.", "Women given PCC tended to be about 2 years older on average than the others.", "Methods of PCC were quite variable, although most centers provided some maternal education about the pregnancy risks associated with poor glycemic control.", "In seven studies reporting early gestational glycosylated hemoglobin values, mean levels were consistently lower in PCC patients.", "Among 2104 offspring, the pooled rate for major and minor anomalies was 2.4% in the PCC group and 7.7% in non-PCC recipients, for a pooled RR of 0.32.", "Among 2651 offspring, major malformations were less prevalent in the PCC group (2.1 vs. 6.5%; pooled RR = 0.36).", "Comparable results were obtained when only prospective studies were analyzed and in studies where the infant examiners were unaware of the mothers' PCC status.", "The lowest risk of major anomalies was in a study that administered folic acid periconceptionally to its PCC recipients; the RR was 0.11.", "This meta-analysis, which included both retrospective and prospective studies, demonstrates an association of PCC with a significantly lower risk of congenital anomalies in the offspring of women with established DM.", "The lowered risk was accompanied by significantly lower glycosylated hemoglobin values in the first trimester in recipients of PCC."], "structured": false}
{"doc_id": 76776022, "title": "Beh\u00e7et's disease associated with a lymphoproliferative disorder, mixed cryoglobulinemia, and an immune complex mediated vasculitis.", "abstract": ["Abstract A woman, now 59 has been followed for 13 years with several manifestations of Behcet's disease.", "These were aphthous stomatitis, genital ulcers, uveitis causing blindness, recurrent erythema nodosum, and synovitis.", "In 1970 a poorly differentiated diffuse lymphocytic lymphoma appeared and was treated with radiotherapy.", "In 1976 she developed a mixed cryoglobulinemia and an immune complex mediated vasculitis manifested by purpura and neuropathy which improved on prednisone and chlorambucil therapy.", "The subsequent course of her lymphoproliferative disorder suggest that it was in fact benign."], "structured": false}
{"doc_id": 77971703, "title": "Older People at the End of Life: Delivery of Care and Needs for Improvement from the Perspective of Bereaved Relatives", "abstract": ["BACKGROUND Due to demographic changes with an increasing number of older people with chronic illness and multimorbidity palliative care for geriatric patients has become increasingly important.", "The aim of this study was to explore the perspective of bereaved relatives with regard to their experiences and expectations concerning the delivery of care for older people in the last phase of life.\n", "METHODS Qualitative interviews with 12 relatives of deceased older patients (aged 60 years or older).", "The interviews were recorded, transcribed, coded and analysed using the approach of qualitative content analysis according to Mayring.\n", "RESULTS The bereaved relatives perceived that the care for geriatric patients in the last phase of life was inappropriate in various respects.", "They criticised overtreatment (e.g. skin cancer diagnostic) as well as unmet needs (e.g. treatment of pain, patient centred care, communication).", "Family doctors were seen as the primary contact persons in the professional health system.\n", "CONCLUSIONS From the perspective of bereaved relatives care for older people in the last phase of life has serious deficits.", "They criticise an inappropriate priority setting and the disregard of palliative care.", "There is a need for better communication and information exchange regarding the needs and expectations of patients and relatives, and regarding the targets of treatment.", "Therefore it may be helpful to use advance directives more intensively.", "Furthermore, it seems to be necessary to strengthen generalist palliative care particularly delivered by family doctors and community nurses."], "structured": true}
{"doc_id": 79231308, "title": "Role of Computerized Physician Order Entry Systems in Facilitating Medication Errors", "abstract": ["as compared with 103 (8.2 percent) in the control group; the Kaplan-Meier estimates of the likelihood of freedom from deep-vein thrombosis or pulmonary embolism at 90 days were 94.1 percent (95 percent confidence interval, 92.5 to 95.4 percent) and 90.6 percent (95 percent confidence interval, 88.7 to 92.2 percent), respectively (P 0.001).", "The computer alert reduced the risk of deep-vein thrombosis or pulmonary embolism at 90 days by 41 percent (hazard ratio, 0.59; 95 percent confidence interval, 0.43 to 0.81; P 0.001).\n", "CONCLUSIONS The institution of a computer-alert program increased physicians\u2019 use of prophylaxis and markedly reduced the rates of deep-vein thrombosis and pulmonary embolism among hospitalized patients at risk.", "Editorial Comment: Most hospitals have adopted electronic systems to alert physicians of drug interactions or possible substitutions, as well as other measures designed to improve the quality of care and decrease expenses.", "This approach was taken one step further by these authors, who evaluated whether notifying physicians that their patients were at increased risk for venous thromboembolism would decrease the incidence of deep vein thrombosis or pulmonary embolism.", "The premise was that simply notifying the physician would increase the use of appropriate prophylactic measures.", "Major surgery (defined as anything requiring general anesthesia), cancer and age greater than 75 years were included among the risk factors, each of which frequently applies to a urology population.", "In fact, more than 13% of the patients in the intervention group had a known diagnosis of a genitourinary cancer.", "The computer alert decreased the risk of deep vein thrombosis or pulmonary embolism by 41%.", "There are 2 lessons urologists can learn from this study.", "First, many urology patients are at increased risk for venous thromboembolism and appropriate prophylaxis should be used.", "In addition, although computer alert systems may seem intrusive at times, clinicians can expect to see more and more of them if there is further documentation that they improve the quality of care."], "structured": true}
{"doc_id": 79336156, "title": "Beta-band oscillations--signalling the status quo?", "abstract": ["In this review, we consider the potential functional role of beta-band oscillations, which at present is not yet well understood.", "We discuss evidence from recent studies on top-down mechanisms involved in cognitive processing, on the motor system and on the pathophysiology of movement disorders that suggest a unifying hypothesis: beta-band activity seems related to the maintenance of the current sensorimotor or cognitive state.", "We hypothesize that beta oscillations and/or coupling in the beta-band are expressed more strongly if the maintenance of the status quo is intended or predicted, than if a change is expected.", "Moreover, we suggest that pathological enhancement of beta-band activity is likely to result in an abnormal persistence of the status quo and a deterioration of flexible behavioural and cognitive control."], "structured": false}
{"doc_id": 79696454, "title": "Safety, pharmacokinetics and efficacy of IMCgp100, a first-in-class soluble TCR-antiCD3 bispecific t cell redirector with solid tumour activity: Results from the FIH study in melanoma.", "abstract": ["3016Background: T cell-based bispecific agents have shown activity in hematologic cancers, but solid tumor efficacy remains elusive.", "IMCgp100 is a bispecific biologic comprising an affinityenhanced TCR specific for gp100 and an anti-CD3 scFV.", "In vitro, IMCgp100 binds gp100+ melanoma cells causing redirection of cytotoxicity and induction of potent immune effects.", "Methods: The Phase I was conducted in HLA-A2+ pts with advanced melanoma, using a 3+3 design to define the MTD.", "Pts were treated with IMCgp100 (iv) weekly (QW, Arm 1) or daily (4QD3W, Arm 2) to evaluate safety, PK and efficacy.", "The recommended phase 2 regimen (RP2D-QW) was defined.", "Results: In the Ph I dose escalation,31 pts received doses from 5ng/kg to 900ng/kg.", "In arm 1 dose-limiting toxicity of gr 3 or 4 hypotension was seen and associated with rapid trafficking of peripheral lymphocytes to skin and tumor.", "The MTD was determined to be 600ng/kg QW.", "IMCgp100 has an approximately dose-proportional profile with a plasma T1/2 of 5-6 hrs at the RP2..."], "structured": false}
{"doc_id": 80109277, "title": "The Bitterest Pills: The Troubling Story of Antipsychotic Drugs", "abstract": ["\u00a9 Joanna Moncrieff 2013.", "All rights reserved.", "A challenging reappraisal of the history of antipsychotics, revealing how they were transformed from neurological poisons into magical cures, their benefits exaggerated and their toxic effects minimized or ignored."], "structured": false}
{"doc_id": 80522346, "title": "Variables Affecting Kinetics of Minimal Residual Disease Clearance in Children with Lymphoblastic Leukaemia; Results of the United Kingdom Medical Research Council (UK MRC) Protocols ALL97, ALL97/99 and ALL2003.", "abstract": ["We studied the influence of patient, leukaemia and treatment characteristics on the kinetics of Minimal Residual Disease (MRD) clearance in children with lymphoblastic leukaemia treated using an intensive risk stratified approach.", "UK MRC protocol ALL97 (1997\u20131999), and its amended version ALL 97/99 (1999\u20132002), compared the efficacy and toxicity of dexamethasone (DEX) with prednisolone (PRED), and 6-thioguanine (TG) with 6-Mercaptopurine (MP) in a randomised fashion.", "The trial produced a 5 year event-free survival (EFS) of 80%, with better systemic and Central Nervous System outcomes in DEX compared with PRED recipients but no difference between TG and MP recipients.", "Several changes to the risk stratification and treatment regimens during the period of the trial provided an opportunity to determine their impact on MRD clearance.", "We compared this with clearance in those treated on the successor trial ALL 2003 (more intensive induction containing DEX and Pegylated Asparaginase).", "The variables investigated for their potential influence on MRD status at the end of induction (EOI) were: NCI Risk; Asparaginase intensity (Erwinia Asparaginase [ERW] in ALL 97 and early part of ALL97/99 vs native or Pegylated E. Coli Asparaginase [E. Coli] in later part of ALL 97/99 and ALL2003); DEX vs PRED; and marrow response at day 8/15 of induction (Slow Early Response [SER] >25% blasts vs Rapid Early Response [RER] \u2a7d 25% blasts).", "MRD was assessed using either a semi-quantitative sequence-specific PCR (ALL97) or Real-Time Quantitative PCR (ALL99 and ALL 2003) of antigen receptor gene re-arrangements at EOI.", "MRD status was defined as NEG if no MRD was detected by two markers sensitive to 10 \u22124 ; POS if > 10 \u22124 , and Positive Outside Quantitative Range (POQR) if positive \u22124 .", "Results were available from retrospective testing in 66 ALL97 and 76 ALL97/99 patients, and 204 ALL2003 patients monitored prospectively.", "There was no significant difference in the proportions of patients MRD NEG, POS or POQR in steroid or NCI sub-groups.", "Significantly more ERW Asparaginase recipients were MRD POS compared with E.Coli (p \u22124 at EOI have the same low risk of relapse as those who have undetectable MRD."], "structured": false}
{"doc_id": 81498132, "title": "Chromosome numbers in certain Indian species ofUtricularia L. (Lentibulariaceae)", "abstract": ["Chromosome numbers from meiotic studies have been reported for the following species ofUtricularia: U. aurea Lour.", "(n=21);U. baoule\u00ebnsis A. Chev.", "(n=10);U. caerulea L. (n=20);U. inflexa var.stellaris (Linn.f.) P. Taylor (n=21);U. minutissima Vahl (n=8);U. scandens Benj.", "(n=6, 7); andU. stricticaulis Stapf (n=7).", "There are two cyto-races inU. scandens."], "structured": false}
{"doc_id": 82665667, "title": "Detection of [Ca2+]I Changes In Sub-Plasma Membrane Micro Domains in A Single Living Cell By an Optical Fiber-Based Nanobiosensor", "abstract": ["An optical fiber-based nanobiosensor, for advanced detection of [Ca 2+ ]i (i.e. intracellular Ca 2+ concentration) changes in sub-plasma membrane microdomains in a single living smooth muscle cell and a single living cardiomyocyte, was successfully prepared by coating silver and then immobilizing Calcium Green-1 Dextran, a calcium ion sensitive dye, on the distal end of the nanoprobe.", "The constructed nanobiosensor was capable of detecting ultra-low and local intracellular calcium ion concentration within the nanomolar range, which is around the physiological level of free cytosolic calcium ion in a single living cell.", "The response time was less than milliseconds enabling the detection of transient elementary calcium ion signaling events associated with calcium ion microdomains.", "The effects of stimulants such as high potassium buffer solution and norepinephrine solution were also investigated.", "The resulting system could thus greatly facilitate the development of an advanced nano-diagnostic platform for in vivo and real-time sensing/diagnosing of [Ca 2+ ]i at the single cell level."], "structured": false}
{"doc_id": 82971616, "title": "Construction of plant bacterial artificial chromosome (BAC) libraries: an illustrated guide.", "abstract": ["J. Agric.", "Genomics, 5 ABSTRACT Bacterial artificial chromosome (BAC) libraries have become invaluable tools in plant genetic research.", "However, it is difficult for new practitioners to create plant BAC libraries de novo because published protocols are not particularly detailed, and plant cells possess features that make isolation of clean, high molecular weight DNA troublesome.", "In this document we present an illustrated, step-by-step protocol for constructing plant BAC libraries.", "This protocol is sufficiently detailed to be of use to both new and experienced investigators.", "We hope that by reducing the obstacles to BAC cloning in plants, we will foster new and accelerated progress in plant genomics."], "structured": false}
{"doc_id": 83308790, "title": "Activation by IKK\u03b1 of a second, evolutionary conserved, NF-\u03baB signaling pathway", "abstract": ["In mammals, the canonical nuclear factor \u03baB (NF-\u03baB) signaling pathway activated in response to infections is based on degradation of I\u03baB inhibitors.", "This pathway depends on the I\u03baB kinase (IKK), which contains two catalytic subunits, IKK\u03b1 and IKK\u03b2.", "IKK\u03b2 is essential for inducible I\u03baB phosphorylation and degradation, whereas IKK\u03b1 is not.", "Here we show that IKK\u03b1 is required for B cell maturation, formation of secondary lymphoid organs, increased expression of certain NF-\u03baB target genes, and processing of the NF-\u03baB2 (p100) precursor.", "IKK\u03b1 preferentially phosphorylates NF-\u03baB2, and this activity requires its phosphorylation by upstream kinases, one of which may be NF-\u03baB\u2013inducing kinase (NIK).", "IKK\u03b1 is therefore a pivotal component of a second NF-\u03baB activation pathway based on regulated NF-\u03baB2 processing rather than I\u03baB degradation."], "structured": false}
{"doc_id": 83667891, "title": "Identification and transmission of Piper yellow mottle virus and Cucumber mosaic virus infecting black pepper (Piper nigrum) in Sri Lanka", "abstract": ["Sri Lankan black pepper with symptoms of yellow mottle disease contained a mixture of viruses:", "Piper yellow mottle virus (PYMV) particles (30 \u00d7 130 nm), Cucumber mosaic virus (CMV, 30 nm diameter isometric particles), and unidentified, isometric virus-like particles (30 nm diameter).", "An effective purification procedure is described for PYMV.", "Immunosorbent and conventional electron microscopy successfully detected badnavirus particles only when at least partially purified extracts were used.", "PYMV was confirmed as the cause of the disease, with the other two viruses apparently playing no part in producing symptoms.", "PYMV was transmitted by grafting, by the insect vectors citrus mealy bug (Planococcus citri) and black pepper lace bug (Diconocoris distanti), but not by mechanical inoculation or through seeds.", "The CMV isolate was transmitted to indicator plants by mechanical inoculation and by the vector Aphis gossypii, but not by Myzus persicae; but neither mechanical nor insect transmission of CMV to black pepper was successful.", "A sensitive polymerase chain reaction assay was developed to detect PYMV in black pepper."], "structured": false}
{"doc_id": 83707680, "title": "A forkhead-domain gene is mutated in a severe speech and language disorder", "abstract": ["Individuals affected with developmental disorders of speech and language have substantial difficulty acquiring expressive and/or receptive language in the absence of any profound sensory or neurological impairment and despite adequate intelligence and opportunity1.", "Although studies of twins consistently indicate that a significant genetic component is involved1,2,3, most families segregating speech and language deficits show complex patterns of inheritance, and a gene that predisposes individuals to such disorders has not been identified.", "We have studied a unique three-generation pedigree, KE, in which a severe speech and language disorder is transmitted as an autosomal-dominant monogenic trait4.", "Our previous work mapped the locus responsible, SPCH1, to a 5.6-cM interval of region 7q31 on chromosome 7 (ref.", "5).", "We also identified an unrelated individual, CS, in whom speech and language impairment is associated with a chromosomal translocation involving the SPCH1 interval6.", "Here we show that the gene FOXP2, which encodes a putative transcription factor containing a polyglutamine tract and a forkhead DNA-binding domain, is directly disrupted by the translocation breakpoint in CS.", "In addition, we identify a point mutation in affected members of the KE family that alters an invariant amino-acid residue in the forkhead domain.", "Our findings suggest that FOXP2 is involved in the developmental process that culminates in speech and language."], "structured": false}
{"doc_id": 84085333, "title": "The Growth and Sporulation of the Benign and Malignant Tertian Malarial Parasites in the Culture Tube and in the Human Host", "abstract": ["Researches on the cultivation of the parasites of malaria in Liverpool were commenced some time ago at my suggestion by Dr. Sinton, and then, with better success, by Drs.", "J. G. Thomson and McLellan, and by Dr. D. Thomson.", "We are greatly obliged to Sir Edwin Durning-Lawrence, Bart., for giving us the services of Dr. J. G. Thomson for this important enquiry.\u2014", "Ronald Ross, 21st May, 1913."], "structured": false}
{"doc_id": 84244109, "title": "Innate immunity to a facultative intracellular bacterial pathogen.", "abstract": ["The murine response to Listeria monocytogenes has long been considered a paradigm of T-cell-mediated immunity.", "There is, however, substantial evidence that T-cell-deficient mice are capable of surviving a L. monocytogenes challenge.", "Recently, advances have been made in our understanding of the cell biology and pathogenesis of infection."], "structured": false}
{"doc_id": 84379954, "title": "Diversity and Evenness: A Unifying Notation and Its Consequences", "abstract": ["Three commonly used measures of diversity, Simpson's index, Shannon's entropy, and the total number of species, are related to Renyi's definition of a generalized entropy.", "A unified concept of diversity is presented, according to which there is a continuum of possible diversity measures.", "In a sense which becomes apparent, these measures provide estimates of the effective number of species present, and differ only in their tendency to include or to ignore the relatively rarer species.", "The notion of the diversity of a community as opposed to that of a sample is examined, and is related to the asymptotic form of the species\u2014abundance curve.", "A new and plausible definition of evenness is derived."], "structured": false}
{"doc_id": 84580585, "title": "Guide to yeast genetics and molecular biology", "abstract": ["This volume and its companion, Volume 350, are specifically designed to meet the needs of graduate students and postdoctoral students as well as researchers, by providing all the up-to-date methods necessary to study genes in yeast.", "Procedures are included that enable newcomers to set up a yeast laboratory and to master basic manipulations.", "Relevant background and reference information given for procedures can be used as a guide to developing protocols in a number of disciplines.", "Specific topics addressed in this book include cytology, biochemistry, cell fractionation, and cell biology."], "structured": false}
{"doc_id": 84784389, "title": "Cutadapt removes adapter sequences from high-throughput sequencing reads", "abstract": ["When small RNA is sequenced on current sequencing machines, the resulting reads are usually longer than the RNA and therefore contain parts of the 3' adapter.", "That adapter must be found and removed error-tolerantly from each read before read mapping.", "Previous solutions are either hard to use or do not offer required features, in particular support for color space data.", "As an easy to use alternative, we developed the command-line tool cutadapt, which supports 454, Illumina and SOLiD (color space) data, offers two adapter trimming algorithms, and has other useful features.", "Cutadapt, including its MIT-licensed source code, is available for download at http://code.google.com/p/cutadapt/"], "structured": false}
{"doc_id": 84884645, "title": "Reproductive physiology of marsupials", "abstract": ["Preface 1.", "Historical introduction 2.", "Breeding biology of marsupials by family 3.", "Sexual differentiation and development 4.", "Male anatomy and spermatogenesis 5.", "The female urogenital tract and oogenesis 6.", "Ovarian function and control 7.", "Pregnancy and parturition 8.", "Lactation 9.", "Neuroendocrine control of seasonal breeding 10.", "Marsupials and the evolution of mammalian reproduction References Index."], "structured": false}
{"doc_id": 85326624, "title": "Stage-Specific and Differential Notch Dependency at the \u03b1\u03b2 and \u03b3\u03b4 T Lineage Bifurcation", "abstract": ["Summary Signals transduced by Notch receptors are indispensable for T cell specification and differentiation of \u03b1\u03b2 T lineage cells.", "However, the role of Notch signals during \u03b1\u03b2 versus \u03b3\u03b4 T lineage decision remains controversial.", "Here, we addressed this question by employing a clonal analysis of CD4 \u2212 CD8 \u2212 (DN) progenitor potential to position the divergence of \u03b1\u03b2 and \u03b3\u03b4 T cell lineages to the late DN2 to DN3 developmental stages.", "Accordingly, \u03b1\u03b2 and \u03b3\u03b4 precursor frequencies within these T cell progenitor subsets were determined, both in the presence and absence of Notch signaling through Delta-like 1.", "Notch signals were found to be critical for the DN to CD4 + CD8 + (DP) transition, irrespective of the identity (pT\u03b1\u03b2 or \u03b3\u03b4) of the inducing T cell receptor complex, whereas \u03b3\u03b4 T cells developed from \u03b3\u03b4TCR-expressing T cell progenitors in the absence of further Notch ligand interaction.", "Collectively, our findings demonstrate a differential, stage-specific requirement for Notch receptor-ligand interactions in the differentiation of \u03b1\u03b2 and \u03b3\u03b4 T cells from T cell progenitors."], "structured": false}
{"doc_id": 85394684, "title": "Investigating the Intron Recognition Mechanism in Eukaryotes", "abstract": ["Recent studies indicate that many introns, as well as the complex spliceosomal mechanism to remove them, were present early in eukaryotic evolution.", "This study examines intron and exon characteristics from annotations of whole genomes to investigate the intron recognition mechanism.", "Exon definition uses the exon as the unit of recognition, placing length constraints on the exon but not on the intron (allowing it a greater range of lengths).", "In contrast, intron definition uses the intron itself as the unit of recognition and thus removes constraints on internal exon length forced by the use of an exon definition mechanism.", "Thus, intron and exon lengths within a genome can reflect the constraints imposed by its splicing.", "This study shows that it is possible firstly to recover valid intron and exon information from genome annotation.", "We then compare internal intron and exon information from a range of eukaryotic genomes and investigate possible evolutionary length constraints on introns and exons and how they can impact on the intron recognition mechanism.", "Results indicate that exon definition-based mechanisms may predominate in vertebrates although the exact system in fish is expected to show some differences with the better characterized system from mammals.", "We also raise the possibility that the last common ancestor of plants and animals contained some type of exon definition and that this mechanism was replaced in some genes and lineages by intron definition, possibly as a result of intron loss and/or intron shortening."], "structured": false}
{"doc_id": 85665741, "title": "BRAF mutation predicts for MEK-dependence in non-small cell lung cancer (NSCLC).", "abstract": ["5247 Constitutive ERK signaling is common in human cancer and is often the result of activating mutations of BRAF, RAS and upstream receptor tyrosine kinases.", "Missense BRAF kinase domain mutations are frequently observed in melanoma, colon and thyroid cancers and less frequently in lung and other cancer types.", "The vast majority (>90%) involve a glutamic acid for valine substitution at codon 600 (V600E), which results in elevated BRAF kinase activity.", "BRAF kinase domain mutations with intermediate and impaired kinase activity have also been identified, most frequently in NSCLC.", "We have previously reported that tumors with V600E BRAF mutation are selectively sensitive to MEK inhibition.", "Using the potent and selective MEK1/2 inhibitor PD0325901 (Pfizer), we examined a panel of NSCLC cell lines with mutant EGFR, KRAS, and/or low, intermediate and high-activity BRAF kinase domain mutations for MEK dependence.", "In all but one case, EGFR, KRAS and BRAF mutations were mutually exclusive with the exception being a cell line with concurrent NRAS and intermediate activity BRAF mutations.", "Consistent with our prior results, NSCLC cells with V600E BRAF mutation were exquisitely sensitive to MEK inhibition (PD0325901 IC50 of 2nM).", "The proliferation of cells with non-V600E mutations, including those with high (G469A), intermediate (L597V) and impaired (G466V) kinase activities, was also MEK dependent with IC50\u2019s ranging between 2.7 and 80 nM. Inhibition of MEK in these cells resulted in downregulation of cyclin D1 and G1 growth arrest, with variable induction of apoptosis.", "Despite high basal ERK activity, NSCLC tumor cells with EGFR mutation were uniformly resistant to MEK inhibition (at doses of up to 500nM), despite effective and prolonged inhibition of ERK phosphorylation.", "Tumor cells with RAS mutation had a more variable response, with some cell lines demonstrating sensitivity, while others were completely resistant.", "There was no correlation between basal ERK activity and sensitivity to MEK inhibition.", "A strong inverse correlation between Akt activity and PD0325901 sensitivity was observed.", "These results suggest that MEK inhibition may be useful therapeutically in tumors with V600E and non-V600E BRAF kinase domain mutations.", "The results also suggest that inhibition of both MEK and Akt signaling may be required in NSCLC tumors with high basal AKT activity."], "structured": false}
{"doc_id": 85693958, "title": "THE REGULATION OF NUMBERS OF TROPICAL OCEANIC BIRDS", "abstract": ["SUMMARY    The ways in which the numbers of tropical sea-birds might be limited are considered; it is argued that food is the only factor likely to be generally effective in limiting numbers, but it seems improbable that food shortage could exert a density-dependent control of the mortality of the birds outside the breeding season.        ", "Wynne-Edwards' hypothesis that colonies of sea-birds are able to keep their own numbers below the level at which food shortage would become acute, primarily by exerting control on the output of young, is rejected as unproven and improbable.        ", "It is suggested that colonies of tropical oceanic birds deplete the food in the waters round them, and that as the populations increase competition for food becomes more intense, and relatively fewer adults succeed in raising chicks.", "This would provide a density-dependent control of the output of young and could regulate the numbers of the birds.        ", "The peculiarities of long-lived sea-birds (e.g. clutches of one, long fledging periods, deferred maturity) which Wynne-Edwards suggests are adaptations evolved in order to lower the reproductive rate until it balances the mortality, apparently could not be evolved as such; they are more probably adaptations enabling the birds sometimes to raise single chicks in spite of competition for food that makes it impossible to raise more than one.", "It is considered that variation in the age of first breeding provides an important supplement to variation in reproductive success in regulating the numbers of long-lived tropical sea-birds.        ", "The possible applications of this hypothesis to sea-birds breeding in higher latitudes are briefly considered, as are its implications in relation to conservation and exploitation of populations of sea-birds."], "structured": false}
{"doc_id": 86129154, "title": "Induced pluripotent stem cell lines derived from human somatic cells.", "abstract": ["Somatic cell nuclear transfer allows trans-acting factors present in the mammalian oocyte to reprogram somatic cell nuclei to an undifferentiated state.", "We show that four factors (OCT4, SOX2, NANOG, and LIN28) are sufficient to reprogram human somatic cells to pluripotent stem cells that exhibit the essential characteristics of embryonic stem (ES) cells.", "These induced pluripotent human stem cells have normal karyotypes, express telomerase activity, express cell surface markers and genes that characterize human ES cells, and maintain the developmental potential to differentiate into advanced derivatives of all three primary germ layers.", "Such induced pluripotent human cell lines should be useful in the production of new disease models and in drug development, as well as for applications in transplantation medicine, once technical limitations (for example, mutation through viral integration) are eliminated."], "structured": false}
{"doc_id": 86160128, "title": "Fenugreek (Trigonella foenum-graecum): A Review of Health Beneficial Physiological Effects", "abstract": ["Among the spices that are esoteric food adjuncts being used to enhance flavoring and color, fenugreek (Trigonella foenum-graecum) also modifies the texture of food.", "This seed spice is also employed for medicinal purpose in many traditional systems as antibacterial, gastric stimulant, against anorexia, antidiabetic agent and as a galactogogue.", "In recent decades, several health beneficial physiological attributes of fenugreek seeds have been seen in animal studies as well as human trials.", "These include antidiabetic effect, hypocholesterolemic influence, antioxidant potency, digestive stimulant action, and hepatoprotective effect.", "Among these beneficial physiological effects, the antidiabetic and hypocholesterolemic property of fenugreek, both of which are mainly attributable to the intrinsic dietary fiber constituent, have promising nutraceutical value.", "This article presents an overview of experimental evidence for the nutraceutical potential of fenugreek seeds."], "structured": false}
{"doc_id": 86211914, "title": "The Rat Brain in Stereotaxic Coordinates", "abstract": ["The preceding editions made \"The Rat Brain in Stereotaxic Coordinates\" the second most cited book in science.", "This Fifth Edition is the result of years of research providing the user with the drawings of the completely new set of coronal sections, now from one rat, and with significantly improved resolution by adding a third additional section level as compared to earlier editions.", "Numerous new nuclei and structures also have been identified.", "The drawings are presented in two color, providing a much better contrast for use, and the accompanying CD-ROM contains all of the drawings from the atlas as well as the corresponding color micrographs (which are not included in the book).", "Affordable, comprehensive, compact, and convenient, the Fifth Edition continues the legacy of this major neuroscience publication and is a guide to all students and scientists who study the rat brain.", "It contains 161 coronal diagrams based on a single brain and includes a CD-ROM featuring all of the drawings from the book, plus the accompanying color micrographs that are not in the printed atlas.", "The delineations are drawn entirely new from a new set of sections.", "The diagrams are spaced at constant 120 m intervals resulting in the high resolution and convenience of use.", "The drawings use blue color lines and black labels to facilitate extraction of information.", "The stereotaxic grid was derived using the same techniques that produced the widely praised stereotaxic grid of the previous editions.", "Over 1000 structures are identified, a number for the first time in this edition."], "structured": false}
{"doc_id": 86217760, "title": "The Self-Incompatibility Genes of Brassica: Expression and Use in Genetic Ablation of Floral Tissues", "abstract": ["INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .", "394 POLLINATION AND POLLEN TUBE GROWTH . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .", "395 Interaction s between the M ale G ameto phyte and Pistil . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .", "395 SelfIncom patibili ty Systems: Gameto phytic and S poro phyti c Determin ation of Pollen Phenoty pe . .", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".. .", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", "397 DEVELOPMENTAL S TUDIES OF REPRODUCTIVE STRUCTURES . .", ".", ".", ".", ".", ".", ".", ".. .", ". ... .", ".", ".", ".", "398 Tissues of the Pistil with Special Reference to Pollination Functions 398 The Male Gametophyte . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .", "399 MOLECULAR ANALYSIS OF SELF-INCOMPATIBILITY . .", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", "40 1 The S-M ultigene F amily o j Brassica. .", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".. .", ".", ".", ".", ".", ".", ".", ".", ".", "402 Allelism at the S-Lo cus and the SLG Gene\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\" 402 The S-Locus Related (SLR) Genes 405 Molecular Complexity oj the S-Locus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .", "407 EXPRESSION OF THE SLG GENE IN PIS TILS AND ANTHERS . .", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", "409 Expression in Cruc ifers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .", ".. .", ".", ".", ".", ".", ".", ".", ".", ".", "409 Express ion in Tr ansgen ic Tob acco and the Rel at ionship of G ameto phytic and S poro phyt ic Incompatibilities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .", "4 10 GENETIC INTERACTIONS IN SELF-INCOMPATIBILITY RESPONSES . .", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", "4 1 2 The Analysis o j Se lf-Com patible Lines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .", "4 1 2 The An alysis o j Transgenic Pl ants . .", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", "4 1 3 GENETIC ABLATION O F FLORAL TISSUES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .", "415 As a Tool Jor the Study o j Pl ant Develo pmen t . .", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".. .", ".", ".", ".", ".", ".", ".. .", ".", ".", ".", ".", ".", ".", ".", ".", "415 As a Tool Jar Cro p Im pro vement . .", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", "\"\"\" 416"], "structured": false}
{"doc_id": 86231298, "title": "The Ulp1 SUMO isopeptidase distinct domains required for viability, nuclear envelope localization, and substrate specificity", "abstract": ["Protein modification by the ubiquitin-like SUMO protein contributes to many cellular regulatory mechanisms.", "In Saccharomyces cerevisiae, both sumoylating and desumoylating activities are essential for viability.", "Of its two known desumoylating enzymes, Ubl-specific protease (Ulp)1 and Ulp2/Smt4, Ulp1 is specifically required for cell cycle progression.", "A \u223c200-residue segment, the Ulp domain (UD), is conserved among Ulps and includes a core cysteine protease domain that is even more widespread.", "Here we demonstrate that the Ulp1 UD by itself can support wild-type growth rates and in vitro can cleave SUMO from substrates.", "However, in cells expressing only the UD of Ulp1, many SUMO conjugates accumulate to high levels, indicating that the nonessential Ulp1 NH2-terminal domain is important for activity against a substantial fraction of sumoylated targets.", "The NH2-terminal domain also includes sequences necessary and sufficient to concentrate Ulp1 at nuclear envelope sites.", "Remarkably, NH2-terminally deleted Ulp1 variants are able, unlike full-length Ulp1, to suppress defects of cells lacking the divergent Ulp2 isopeptidase.", "Thus, the NH2-terminal regulatory domain of Ulp1 restricts Ulp1 activity toward certain sumoylated proteins while enabling the cleavage of others.", "These data define key functional elements of Ulp1 and strongly suggest that subcellular localization is a physiologically significant constraint on SUMO isopeptidase specificity."], "structured": false}
{"doc_id": 86326468, "title": "Gastropathies in the Lundehund", "abstract": ["The mucin profiles of the gastric mucosa in Lundehunds suffering from intestinal lymphangiectasia were examined and compared to the mucin profiles in control dogs from other breeds.", "A previous study performed on this material had shown that all examined Lundehunds had gastritis and about 30% had gastric carcinoma.", "Neutral and acid mucins were identified using the periodic acid-Schiff (PAS) and Alcian blue (pH 2.5) periodic acid-Schiff (AB-PAS) methods.", "The acid mucins were divided into sialomucins and sulfomucins based on their reaction with high-iron diamine Alcian blue, pH 2.5 (HID-AB).", "In Lundehunds with chronic atrophic gastritis in the fundic and body regions the surface and foveolar epithelium showed a predominantly normal mucin profile although some Lundehunds had a reduced mucin content.", "The mucous neck cells extended from below the gastric foveolae towards the muscularis mucosae.", "Morphometric examination showed that the abnormal presence of mucous neck cells occupied 41% of the height of the gastric mucosa in Lundehunds compared to only 19% in the control dogs (p<0.05).", "Of the four Lundehunds with gastric carcinoma, two possessed neoplastic cells that contained minimal or no mucins.", "The amount and type of mucin in the neoplastic cells of the remaining two Lundehunds varied both between individuals and within a neoplasm.", "This study shows that the abnormal presence of mucous neck cells and the associated pseudopyloric metaplasia comprised the predominant changes in the gastric mucin profiles of Lundehunds."], "structured": false}
{"doc_id": 86602746, "title": "MicroRNAs: small RNAs with a big role in gene regulation", "abstract": ["Key PointsMicroRNAs (miRNAs) are a family of \u223c21\u201325-nucleotide small RNAs that negatively regulate gene expression at the post-transcriptional level.", "The founding members of the miRNA family, lin-4 and let-7, were identified through genetic screens for defects in the temporal regulation of Caenorhabditis elegans larval development.", "Owing to genome-wide cloning efforts, hundreds of miRNAs have now been identified in almost all metazoans, including flies, plants and mammals.", "MiRNAs exhibit temporally and spatially regulated expression patterns during diverse developmental and physiological processes.", "Most of the miRNAs that have been characterized so far seem to regulate aspects of development, including larval developmental transitions and neuronal development in C. elegans, growth control and apoptosis in Drosophila melanogaster, haematopoietic differentiation in mammals, and leaf development, flower development and embryogenesis in Arabidopsis thaliana.", "The majority of the animal miRNAs that have been characterized so far affect protein synthesis from their target mRNAs.", "On the other hand, most of the plant miRNAs studied so far direct the cleavage of their targets.", "The degree of complementarity between a miRNA and its target, at least in part, determines the regulatory mechanism.", "In animals, primary transcripts of miRNAs are processed sequentially by two RNase-III enzymes, Drosha and Dicer, into a small, imperfect dsRNA duplex (miRNA:miRNA*) that contains both the mature miRNA strand and its complementary strand (miRNA*).", "Relative instability at the 5\u2032 end of the mature miRNA leads to the asymmetric assembly of the mature miRNA into the effector complex, the RNA-induced silencing complex (RISC).Ago proteins are a key component of the RISC.", "Multiple Ago homologues in various metazoan genomes indicate the existence of multiple RISCs that carry out related but specific biological functions.", "Bioinformatic prediction of miRNA targets has provided an important tool to explore the functions of miRNAs.", "However, the overall success rate of such predictions remains to be determined by experimental validation.", "AbstractMicroRNAs are a family of small, non-coding RNAs that regulate gene expression in a sequence-specific manner.", "The two founding members of the microRNA family were originally identified in Caenorhabditis elegans as genes that were required for the timed regulation of developmental events.", "Since then, hundreds of microRNAs have been identified in almost all metazoan genomes, including worms, flies, plants and mammals.", "MicroRNAs have diverse expression patterns and might regulate various developmental and physiological processes.", "Their discovery adds a new dimension to our understanding of complex gene regulatory networks."], "structured": false}
{"doc_id": 86694016, "title": "Molecular mechanisms of invadopodium formation: the role of the N-WASP\u2013Arp2/3 complex pathway and cofilin", "abstract": ["Invadopodia are actin-rich membrane protrusions with a matrix degradation activity formed by invasive cancer cells.", "We have studied the molecular mechanisms of invadopodium formation in metastatic carcinoma cells.", "Epidermal growth factor (EGF) receptor kinase inhibitors blocked invadopodium formation in the presence of serum, and EGF stimulation of serum-starved cells induced invadopodium formation.", "RNA interference and dominant-negative mutant expression analyses revealed that neural WASP (N-WASP), Arp2/3 complex, and their upstream regulators, Nck1, Cdc42, and WIP, are necessary for invadopodium formation.", "Time-lapse analysis revealed that invadopodia are formed de novo at the cell periphery and their lifetime varies from minutes to several hours.", "Invadopodia with short lifetimes are motile, whereas long-lived invadopodia tend to be stationary.", "Interestingly, suppression of cofilin expression by RNA interference inhibited the formation of long-lived invadopodia, resulting in formation of only short-lived invadopodia with less matrix degradation activity.", "These results indicate that EGF receptor signaling regulates invadopodium formation through the N-WASP\u2013Arp2/3 pathway and cofilin is necessary for the stabilization and maturation of invadopodia."], "structured": false}
{"doc_id": 86704258, "title": "Genome downsizing in polyploid plants", "abstract": ["All else being equal, polyploids are expected to have larger C-values (amount of DNA in the unreplicated gametic nucleus) than their diploid progenitors, increasing in direct proportion with ploidy.", "This expectation is observed in some polyploid series, especially those newly formed, but there are examples suggesting that C-values in particular polyploids are less than expected.", "The availability of the Angiosperm DNA C-values database (http:// www.rbgkew.org.uk/cvavhomepage.html) has allowed this question to be addressed across a broad range of angiosperms and has revealed striking results deviating from expectation: (i) mean 1C DNA amount did not increase in direct proportion with ploidy, and (ii) mean DNA amount per basic genome (calculated by dividing the 2C value by ploidy) tended to decrease with increasing ploidy.", "These results suggest that loss of DNA following polyploid formation, or genome downsizing, may be a widespread phenomenon of considerable biological significance.", "Recent advances in our understanding of the molecular events that take place following polyploid formation together with new data on how DNA amounts can both increase and decrease provide some insights into how genome downsizing may take place.", "The nature of the evolutionary forces that may be driving DNA loss are also discussed."], "structured": false}
{"doc_id": 87337034, "title": "Construction of an antisense CYP86MF gene plasmid vector and production of a male-sterile Chinese cabbage transformant by the pollen-tube method", "abstract": ["SummaryA plant expression vector pBIA9-AMF containing an antisense fragment of the CYP86MF gene and the tapetum-specific A9 promoter was constructed.", "Plasmid vectors were introduced by floral-dipping and pollen-tube transformation methods to Chinese cabbage pak-choi (Brassica campestris ssp.", "chinensis (L.) Makino var.", "communis Tsen et Lee, syn.", "B. rapa ssp.", "chinensis (L.) Makino var.", "communis Tsen et Lee) and flowering Chinese cabbage (B. campestris ssp.", "chinensis (L.) Makino var.", "parachinensis (Bailey) Tsen et Lee).", "Results showed that KanR seedlings could be obtained by the pollen-tube method through germination tests of T1 progeny seeds, but not by the floral-dipping method.", "One of the two KanR seedlings proved that the antisense fragment of the CYP86MF gene was integrated into the Chinese cabbage genome by PCR amplification and Southern blotting.", "Northern hybridization indicated that the CYP86MF gene, under the A9 promoter, was inhibited in the transformant, and self-infertility was found in the trans..."], "structured": false}
{"doc_id": 87430549, "title": "Stem Cells,Cancer and Cancer Stem Cells", "abstract": ["Stem cells are defined as cells able to both extensively self-renew and differentiate into progenitors.", "Research data show that more resistant stem cells than common cancer cells exist in cancer patients.", "To identify unrecognized differences between cancer stem cells and cancer cells might be able to develope effective classification,diagnose and treat ment for cancer."], "structured": false}
{"doc_id": 87610599, "title": "Characterization and culture of human embryonic stem cells", "abstract": ["Objective To explore the in vitro maintenance and characterization of human embryonic stem cells(hESCs).Methods hESCs were cultured on feeder layer with ES culture medium,which consists of 20% Knockout Serum Replacement,Knockout DMEM and 10 ng/mL bFGF.Undifferentiated status of hESCs was identified by cell morphology,and the expressions of cell surface marker SSEA-1,SSEA-3 and TRA-1-60.G banding technique was employed for cell karyotype analysis.", "Pluropotency of cells were analyzed via in vitro embyoid body(EB) formation and in vivo terotoma formation.", "Results Most of cells showed undifferentiated properties in cell morphology and normal karyotype throughout extended culture periods.", "They maintained undifferentiated status with positive immunoreactivity to SSEA-3,SSEA-4 and TRA-1-60.in vitro EB formation and in vivo teratoma formation demonstrated the pluripotency of human ES cells.", "Conclusion The fundamental requirement to hESCs for research and clinical application were their undifferentiated status and pluropotency in culture.", "Our result demonstrated their potential for these purposes."], "structured": false}
{"doc_id": 87986426, "title": "Detection of Sugarcane bacilliform virus isolate and its influence on yield and quality of cane in Yunnan", "abstract": ["Sugarcane bacilliform virus(SCBV) was detected by PCR from sugarcane showing chlorosis and mottle symptom from Kaiyuan,Yunnan Province.", "Part sequence of replicase gene of the isolate SCBV-Kaiyuan was determined.", "Sequence analysis indicated that the 589 bp of SCBV-Kaiyuan shared identities of 73.2%-74.0% and 83.1%-84.1% at nucleotide and amino acid levels with SCBV-Australia respectively,66.7%-68.4% and 65.6%-67.7% with SCBV-Morocco.", "The quality and yield of the sugarcane infected with SCBV-Kaiyuan was also investigated.", "The juice extraction,sucrose content,gravity purity and average stalk weight were decreased 1.55%,1.24%,2.22% and 0.26 kg in plants infected with SCBV-Kaiyuan,but reducing sugar was increased by 0.21% in infected plants."], "structured": false}
{"doc_id": 90064424, "title": "Mitotic chromosomes fold by condensin-dependent helical winding of chromatin loop arrays", "abstract": ["During mitosis, chromosomes fold into compacted rod shaped structures.", "We combined imaging and Hi-C of synchronous DT40 cell cultures with polymer simulations to determine how interphase chromosomes are converted into compressed arrays of loops characteristic of mitotic chromosomes.", "We found that the interphase organization is disassembled within minutes of prophase entry and by late prophase chromosomes are already folded as arrays of consecutive loops.", "During prometaphase, this array reorganizes to form a helical arrangement of nested loops.", "Polymer simulations reveal that Hi-C data are inconsistent with solenoidal coiling of the entire chromatid, but instead suggest a centrally located helically twisted axis from which consecutive loops emanate as in a spiral staircase.", "Chromosomes subsequently shorten through progressive helical winding, with the numbers of loops per turn increasing so that the size of a helical turn grows from around 3 Mb (~40 loops) to ~12 Mb (~150 loops) in fully condensed metaphase chromosomes.", "Condensin is essential to disassemble the interphase chromatin conformation.", "Analysis of mutants revealed differing roles for condensin I and II during these processes.", "Either condensin can mediate formation of loop arrays.", "However, condensin II was required for helical winding during prometaphase, whereas condensin I modulated the size and arrangement of loops inside the helical turns.", "These observations identify a mitotic chromosome morphogenesis pathway in which folding of linear loop arrays produces long thin chromosomes during prophase that then shorten by progressive growth of loops and helical winding during prometaphase."], "structured": false}
{"doc_id": 90756514, "title": "REVIEW ON CLINICALLY DEVELOPING ANTIBIOTICS", "abstract": ["The world is running out of antibiotics.", "Between 1940 and 1962, more than 20 new classes of antibiotics were marketed.", "Since then, only two new classes of antibiotics were marketed.", "Now, not enough analogues are reaching the market to stem the tide of antibiotic resistance, particularly among gram-negative bacteria which indicates the need of novel antibiotics for their effective action.", "This review describes those antibiotics in late-stage clinical development.", "Most of them belong to existing antibiotic classes and a few with a narrow spectrum of activity are novel compounds directed against novel targets.", "The reasons for some of the past failures to find new molecules and a path forward to help attract investments to fund the discovery of new antibiotics are described."], "structured": false}
{"doc_id": 94109411, "title": "Improved Au/Zn/Au ohmic contacts for p-type InP", "abstract": ["In this work, an innovated Si3N4 as an out-diffusion barrier layer to Au/Zn/Au contact system for p-type InP has been proposed.", "Before the contacts were annealed, Si3N4 layer was deposited on the Au(200\u00c5)/Zn(700\u00c5)/Au(200\u00c5), then the Si3N4 was removed by HF and a 2000A layer of pure gold was deposited to facilitate wire bonding.", "The specific contact resistance dropped to a minimum value of 6\u00d710-7 \u03a9 \u2022 cm2 (for an acceptor concentration of about 3\u00d71018 cm-3) and the contact became perfectly Ohmic.", "Besides, Si3N4 layer is an excellent passivation layer and antireflection coating in InP/InGaAs/InP (p-i-n) photodiodes."], "structured": false}
{"doc_id": 94365950, "title": "The reclamation of brine generated from desalination process by bipolar membrane electrodialysis", "abstract": ["Abstract Some techno-economical analyses and environmental impact evaluation have proved that bipolar membrane electrodialysis (BMED) is feasible for the reclamation of industrial saline water.", "However, to date, the technology cannot be put into practice due to some unsolved application-oriented problems, such as the requirements of BMED for feed solution, the availability of the produced acid and base, relatively high salt concentration of the effluent, and relatively low desalinating efficiency and capacity.", "In this work, a novel hybrid process, which coupled conventional electrodialysis installed with monovalent selective cation-exchange membranes with BMED running in a constant-voltage mode, was designed to reclaim brine generated from surface water desalination by the ion-exchange process.", "Subsequently, the response surface methodology was employed to establish the empirical models for understanding the influences of some initial operating conditions on BMED performance.", "Finally, the BMED-based reclamation scheme was confirmed again by a continuous BMED experiment on real solution.", "Specially, the effects of product concentration on current efficiency and energy consumption were investigated.", "In this case, an acceptable current efficiency and energy consumption were obtained on the basis of the conventional membranes and spacers when the product concentration was set as 0.9 M, which is adequate for the regeneration of ion-exchange resins."], "structured": false}
{"doc_id": 95102458, "title": "Process analysis and economic evaluation for Poly(3-hydroxybutyrate) production by fermentation", "abstract": ["Abstract Several processes for the production and recovery of poly(3-hydroxybutyrate) (PHB) by Alcaligenes eutrophus, Alcaligenes latus, Methylobacterium organophilum, and recombinant Escherichia coli were designed based on the previously reported data and analyzed by computer-aided bioprocess design.", "PHB productivity, content, and yield significantly affected the final price of PHB.", "For the annual production of 2,850 tonnes of purified PHB, the process employing A. eutrophus with the recovery method of surfactant-hypochlorite digestion resulted in lowest price of PHB, $ 5.58/kg.", "As the production scale increased to one million tonnes per year, the price of PHB dropped to $ 4.75/kg.", "The cost of carbon substrate significantly affected the overall economics in large production scale.", "Therefore, the production cost can be considerably lowered when agricultural wastes, such as whey and molasses, are used."], "structured": false}
{"doc_id": 95764370, "title": "Modification in the chemical bath deposition apparatus, growth and characterization of CdS semiconducting thin films for photovoltaic applications", "abstract": ["Abstract In this paper, growth and characterization of CdS thin films by Chemical Bath Deposition (CBD) technique using the reaction between CdCl 2 , (NH 2 ) 2 CS and NH 3 in an aqueous solution has been reported.", "The parameters actively involved in the process of deposition have been identified.", "A commonly available CBD system has been sucessfully modified to obtain the precious control over the pH of the solution at 90\u00b0C during the deposition and studies have been made to understand the fundamental parameters like concentrations of the solution, pH and temperature of the solution involved in the chemical bath deposition of CdS. It is confirmed that the pH of the solution plays a vital role in the quality of the CBD\u2013CdS films.", "Structural, optical and electrical properties have been analysed for the as-deposited and annealed films.", "XRD studies on the CBD\u2013CdS films reveal that the change in Cadmium ion concentration in the bath results in the change in crystallization from cubic phase with (1 1 1) predominant orientation to a hexagonal phase with (0 0 2) predominant orientation.", "The structural changes due to varying cadmium ion concentration in the bath affects the optical and electrical properties.", "Optimum electrical resistivity, band gap and refractive index value are observed for the annealed films deposited from 0.8 M cadmium ion concentration.", "The films are suitable for solar cell fabrication.", "Further on, annealing the samples at 350\u00b0C in H 2 for 30 min resulted in an increased diffraction intensity as well as shifts in the peak towards lower scattering angles due to enlarged CdS unit cell.", "This in turn brought about an increase in the lattice parameters and narrowing in the band-gap values.", "The results are compared with the analysis of previous work."], "structured": false}
{"doc_id": 96222213, "title": "Combined sampler robot and high-performance liquid chromatography: a fully automated system for biological small-angle X-ray scattering experiments at the Synchrotron SOLEIL SWING beamline", "abstract": ["Small-angle X-ray scattering for macromolecules in solution is now widely used in structural biology to complement high-resolution structure determination obtained by X-ray crystallography or NMR.", "In the context of third-generation synchrotron sources, this increasing interest leads to developments in sample environments and automation.", "The presence of an online purification system is justified by the need for sample monodispersity.", "A combined system including an auto-sampler robot and online high-performance liquid chromatography (HPLC) has been developed and optimized at the SWING beamline of Synchrotron SOLEIL (Gif-sur-Yvette, France).", "In the sample changer mode, a few microlitres of sample can be injected between two air bubbles and circulated at a controlled speed of typically 40 \u00b5l min\u22121.", "A maximum of 14 samples per hour could be measured in this mode by remote controlling the sample injections.", "In the HPLC mode, an initially polydisperse sample can be separated into each of its components before immediate data acquisition.", "The sample cell is thermostated, and offers a visualization control and online UV\u2013Vis absorption monitoring."], "structured": false}
{"doc_id": 97566194, "title": "Feasibility assessment of desalination application in Australian traditional agriculture", "abstract": ["Abstract Within some data limitations, the paper provides a first assessment of areas in Australia with potential for implementing desalination technologies to supply agricultural water.", "At the national scale, these areas were identified based on a set of selected criteria: distance from land currently used for irrigated agriculture and feedlots; distance from town sites; exclusion of areas of environmental protection; exclusion of areas with surface elevation greater than 600 m AHD; and exclusion of regions with limited groundwater resources.", "Industries involved in the production of high-value crops are most likely to benefit from desalinated water as they use more-efficient irrigation practices and have the highest gross value of irrigated agricultural production.", "Groundwater was identified as the most likely feedwater source for cost-effective desalination, which is also the case worldwide.", "Brine disposal is a major factor in overall cost effectiveness of desalination.", "When feedwater salinity is relatively low, mixing permeate with feedwater leads to an increase in water production and a reduction in water cost.", "It was estimated that Australian farmers are unlikely to pay more than AU$1.2/kL for agricultural water.", "Generally for agriculture, desalinated water is still more expensive than water from other sources; however, there are likely to be circumstances when the costs could be comparable."], "structured": false}
{"doc_id": 99829811, "title": "Development of a specific monoclonal antibody assay and a rapid testing strip for the detection of apramycin residues in food samples", "abstract": ["ABSTRACTA specific monoclonal antibody (MAb) against apramycin (AP) was produced and used to develop an indirect competitive enzyme-linked immunosorbent assay (idcELISA) and a rapid testing strip for the detection of AP residues in foods.", "MAb exhibited negligible cross-reactivity with other aminoglycosides.", "Under optimized conditions in 0.01 M PBS, the half maximum inhibitory concentration (IC50) of MAb was 0.41 ng/ml with a limit of detection (LOD) of 0.15 ng/ml.", "The ELISA results were obtained within 90 min.", "The mean recoveries from all the spiked food samples were within the range of 79.02\u2013105.49%, with coefficients of variation in the range of 2.21\u201311.4%.", "The strip test results obtained within 5 min had visual LODs in the range 2.5\u20135 \u00b5g/kg (ng/ml) for all food samples tested.", "Therefore, the developed strip test represents a fast and convenient detection method of AP residues in foods."], "structured": false}
{"doc_id": 104143831, "title": "Utilization of Desalination Brine for Sodium Hydroxide Production: Technologies, Engineering Principles, Recovery Limits, and Future Directions", "abstract": ["As global desalination capacity continues its rapid growth, the impetus for reducing the adverse environmental impacts of brine discharge grows concurrently.", "Although modern brine outfall designs have significantly limited such impacts, they are costly.", "Recovering valuable components and chemical derivatives from brine has potential to resolve both environmental and economic concerns.", "In this article, methods for producing sodium hydroxide (\u201ccaustic\u201d) from seawater reverse osmosis (SWRO) brine for internal reuse, which typically involve brine purification, brine concentration, and sodium chloride electrolysis, are reviewed.", "Because process energy consumption drives process cost and caustic purity determines product usability in drinking water systems, reviewed technologies are benchmarked against thermodynamic minimum energy consumption and maximum (stoichiometric) NaOH production rates.", "After individual reviews of brine purification, concentration, and electrolysis technologies, five existing facilities ..."], "structured": false}
{"doc_id": 108886332, "title": "Training toddlers seated on mobile robots to drive indoors amidst obstacles", "abstract": ["The goal of this research is to train children seated on mobile robots to purposefully and safely drive indoors.", "Our previous studies show that in about six weeks of training, infants can learn to drive directly to a goal using conventional joysticks.", "However, they are unable to acquire the advanced skill to avoid obstacles while driving.", "This limits mobility impaired children from exploring their home environment safely, which in turn impacts their cognitive and social developments in the important early years.", "In this paper, we describe results where toddlers are trained to drive a robot within an obstacle course.", "Using algorithms based on artificial potential fields to avoid obstacles, we create force field on the joystick that trains them to navigate while avoiding obstacles.", "In this \u2018assist-as-needed\u2019 approach, if the child steers the mobile robot outside a force tunnel centered around the desired direction, the driver experiences a bias force on the hand.", "The results suggest that force-feedback joystick results in faster learning than with a conventional joystick."], "structured": false}
{"doc_id": 109795294, "title": "Coming soon to a Wal-Mart near you", "abstract": ["According to the Web site of the Association for Automatic Identification and Data Capture Technologies [http://www.aimglobal.org/technologies/rfid], \"radio frequency identification (RFID) technology is an automatic way to collect product, place, and time or transaction data quickly and easily without human intervention or error.", "\"", "With the ability to track everything from crates of disposable razors to individual peanut-butter jars on the store shelves, RFID technology offers the potential of \"real-time supply chain visibility.", "\" Promoters of RFID technology feel [C. Humer, 2003] that \"RF tags are to this decade what the Internet was to the 1990's-a promise of radical change in the way business is done.", "\"", "However, before the full potential of RFID technology can be realized, several hurdles need to be overcome: reliability, cost, lack of standards, and security.", "As these hurdles gradually diminish, Wal-Mart publicly embraces the technology."], "structured": false}
{"doc_id": 109946221, "title": "Innovative beneficial reuse of reverse osmosis concentrate using bipolar membrane electrodialysis and electrochlorination processes", "abstract": ["Reverse osmosis (RO) is a widely used and rapidly growing desalination technology.", "A major disadvantage of this process is that the concentrate from the RO process, which could be as much as 25% of the feed stream, represents a polluting stream.", "This waste stream could pose a significant challenge to the implementation of this process, particularly for inland communities which do not have the option of ocean disposal.", "An excellent environmentally benign approach to disposal could be beneficial reuse of the waste stream.", "This study presents two innovative beneficial reuse strategies for RO concentrate produced by an integrated membrane system (IMS) from a wastewater reclamation facility.", "The technologies evaluated in this study included bipolar membrane electrodialysis (BMED) for conversion of RO concentrate into mixed acid and mixed base streams, and electrochlorination (EC) for onsite chlorine generation.", "Bench-scale studies conducted with BMED demonstrated that RO concentrate could be desalted while producing mixed acids and mixed bases with concentrations as high as 0.2N.", "Similarly, the EC process was capable of producing a 0.6% hypochlorite solution from RO concentrate.", "The acids and bases as well as the hypochlorite produced could be directly applied to the RO process as well as upstream pre-treatment processes.", "A preliminary economic evaluation of the viability of these two approaches was conducted by conducting rough order of magnitude cost estimates based on the bench-scale performance of these processes on RO concentrate.", "A comparison of the overall costs of an Integrated Membrane System utilizing these innovative reuse strategies with conventional disposal options and thermal zero liquid discharge treatment is presented.", "This comparison indicates that a reuse approach might be economically viable for inland wastewater reuse facilities that utilize RO membranes and have limited options for concentrate disposal."], "structured": false}
{"doc_id": 116075383, "title": "Amplification of siRNA in Caenorhabditis elegans generates a transgenerational sequence-targeted histone H3 lysine 9 methylation footprint", "abstract": ["Exogenous double-stranded RNA (dsRNA) has been shown to exert homology-dependent effects at the level of both target mRNA stability and chromatin structure.", "Using C. elegans undergoing RNAi as an animal model, we have investigated the generality, scope and longevity of dsRNA-targeted chromatin effects and their dependence on components of the RNAi machinery.", "Using high-resolution genome-wide chromatin profiling, we found that a diverse set of genes can be induced to acquire locus-specific enrichment of histone H3 lysine 9 trimethylation (H3K9me3), with modification footprints extending several kilobases from the site of dsRNA homology and with locus specificity sufficient to distinguish the targeted locus from the other 20,000 genes in the C. elegans genome.", "Genetic analysis of the response indicated that factors responsible for secondary siRNA production during RNAi were required for effective targeting of chromatin.", "Temporal analysis revealed that H3K9me3, once triggered by dsRNA, can be maintained in the absence of dsRNA for at least two generations before being lost.", "These results implicate dsRNA-triggered chromatin modification in C. elegans as a programmable and locus-specific response defining a metastable state that can persist through generational boundaries."], "structured": false}
{"doc_id": 116556376, "title": "Physicians' initial management of acute low back pain versus evidence-based guidelines. Influence of sciatica.", "abstract": ["BACKGROUND Little information is available on physician characteristics and patient presentations that may influence compliance with evidence-based guidelines for acute low back pain.   \n", "OBJECTIVE To assess whether physicians' management decisions are consistent with the Agency for Health Research Quality's guideline and whether responses varied with the presentation of sciatica or by physician characteristics.   \n", "DESIGN Cross-sectional study using a mailed survey.   \n", "PARTICIPANTS Participants were randomly selected from internal medicine, family practice, general practice, emergency medicine, and occupational medicine specialties.   \n", "MEASUREMENTS A questionnaire asked for recommendations for 2 case scenarios, representing patients without and with sciatica, respectively.   \n", "RESULTS Seven hundred and twenty surveys were completed (response rate=25%).", "In cases 1 (without sciatica) and 2 (with sciatica), 26.9% and 4.3% of physicians fully complied with the guideline, respectively.", "For each year in practice, the odds of guideline noncompliance increased 1.03 times (95% confidence interval [CI]=1.01 to 1.05) for case 1.", "With occupational medicine as the referent specialty, general practice had the greatest odds of noncompliance (3.60, 95% CI=1.75 to 7.40) in case 1, followed by internal medicine and emergency medicine.", "Results for case 2 reflected the influence of sciatica with internal medicine having substantially higher odds (vs case 1) and the greatest odds of noncompliance of any specialty (6.93, 95% CI=1.47 to 32.78), followed by family practice and emergency medicine.   \n", "CONCLUSIONS A majority of primary care physicians continue to be noncompliant with evidence-based back pain guidelines.", "Sciatica dramatically influenced clinical decision-making, increasing the extent of noncompliance, particularly for internal medicine and family practice.", "Physicians' misunderstanding of sciatica's natural history and belief that more intensive initial management is indicated may be factors underlying the observed influence of sciatica."], "structured": true}
{"doc_id": 117907685, "title": "Appropriate Critical Values When Testing for a Single Multivariate Outlier by Using the Mahalanobis Distance", "abstract": ["The Mahalanobis distance is a well-known criterion which may be used for detecting outliers in multivariate data.", "However, there are some discrepancies about which critical values are suitable for this purpose.", "Following a comparison with Wilks's method, this paper shows that the previously recommended {p(n-1)/(n-p)}F p,n\u2212p are unsuitable, and p(n-1) 2 F p,n\u2212p\u22121 /n(n\u2212p\u22121+pF p,n\u2212p\u22121 ) are the correct critical values when searching for a single outlier The importance of which critical values should be used is illustrated when searching for a single outlier in a clinical laboratory data set containing 10 patients and five variables.", "The jackknifed Mahalanobis distance is also discussed and the relevant critical values are given.", "Finally, upper bounds for the usual Mahalanobis distance and the jackknifed version are discussed."], "structured": false}
{"doc_id": 118215171, "title": "How to calculate sample size in animal studies", "abstract": ["Researcher must calculate the sample size before starting of any animal study.", "It should be adequate enough to detect a small significant difference between the groups.", "Small sample size is not only responsible for the insignificant result but also for the less power of the study.  ", "Calculation of sample size involves complex statistics but it can be simplified to help the researchers who are not from statistical background."], "structured": false}
{"doc_id": 120385993, "title": "On the Theory and Computation of Evolutionary Distances", "abstract": ["This paper gives a formal definition of the biological concept of evolutionary distance and an algorithm to compute it.", "For any set S of finite sequences of varying lengths this distance is a real-valued function on $S \\times S$, and it is shown to be a metric under conditions which are wide enough to include the biological application.", "The algorithm, introduced here, lends itself to computer programming and provides a method to compute evolutionary distance which is shorter than the other methods currently in use."], "structured": false}
{"doc_id": 121001457, "title": "Over 30% efficient InGaP/GaAs tandem solar cells", "abstract": ["A two-terminal monolithic InGaP/GaAs tandem solar cell with a new efficiency record of 30.28% is realized with a practical large area of 4 cm2 under one-sun air-mass 1.5 global illumination.", "We report improvements of the tandem cell performance by introducing a double-hetero (hereafter DH) structure InGaP tunnel junction, in which the InGaP layers are surrounded by high band gap AlInP barriers.", "The DH structure by AlInP barriers increase the peak current of InGaP tunnel junction.", "The AlInP barrier directly below the InGaP top cell, which takes the part of a back surface field (hereafter BSF) layer, is found to be considerably effective in reflecting minority carriers in the top cell.", "The AlInP BSF layer does not only form a high potential barrier but also prevents the diffusion of zinc from a high doped tunnel junction toward the top cell during epitaxial growth.", "Furthermore, an InGaP tunnel junction reduces the absorption loss, which exists in a GaAs tunnel junction, and increases the photogenerated curr..."], "structured": false}
{"doc_id": 121581019, "title": "Electrical, optical, and structural properties of indium-tin-oxide thin films for organic light-emitting devices", "abstract": ["High-quality indium\u2013tin\u2013oxide (ITO) thin films (200\u2013850 nm) have been grown by pulsed laser deposition (PLD) on glass substrates without a postdeposition annealing treatment.", "The structural, electrical, and optical properties of these films have been investigated as a function of target composition, substrate deposition temperature, background gas pressure, and film thickness.", "Films were deposited from various target compositions ranging from 0 to 15 wt % of SnO2 content.", "The optimum target composition for high conductivity was 5 wt % SnO2+95 wt % In2O3.", "Films were deposited at substrate temperatures ranging from room temperature to 300 \u00b0C in O2 partial pressures ranging from 1 to 100 mTorr.", "Films were deposited using a KrF excimer laser (248 nm, 30 ns full width at half maximum) at a fluence of 2 J/cm2.", "For a 150-nm-thick ITO film grown at room temperature in an oxygen pressure of 10 mTorr, the resistivity was 4\u00d710\u22124 \u03a9 cm and the average transmission in the visible range (400\u2013700 nm) was 85%.", "For a 170-n..."], "structured": false}
{"doc_id": 126549848, "title": "Disaster Management and Community Planning, and Public Participation: How to Achieve Sustainable Hazard Mitigation", "abstract": ["The paper offers first a brief historical overview of disaster management planning.", "Second, it reviews Australian and American research findings and show that they urge the field of disaster management to shift its focus from response and recovery to sustainable hazard mitigation.", "It is argued that in order for this shift to occur, it is necessary to integrate disaster management and community planning.", "Current practice seldom reflects such a synthesis, and this is one of the reasons why hazard awareness is absent from local decision-making processes.", "Third, it is asserted that if mitigative strategies are to be successfully implemented, then the disaster management process must incorporate public participation at the local decision-making level.", "The paper concludes with a case study of California's Portola Valley, which demonstrates that when public participation is integrated into disaster management planning and community planning, the result is sustainable hazard mitigation."], "structured": false}
{"doc_id": 129199129, "title": "A second generation of homogenized Canadian monthly surface air temperature for climate trend analysis", "abstract": ["[1] This study presents a second generation of homogenized monthly mean surface air temperature data set for Canadian climate trend analysis.", "Monthly means of daily maximum and of daily minimum temperatures were examined at 338 Canadian locations.", "Data from co-located observing sites were sometimes combined to create longer time series for use in trend analysis.", "Time series of observations were then adjusted to account for nation-wide change in observing time in July 1961, affecting daily minimum temperatures recorded at 120 synoptic stations; these were adjusted using hourly temperatures at the same sites.", "Next, homogeneity testing was performed to detect and adjust for other discontinuities.", "Two techniques were used to detect non-climatic shifts in de-seasonalized monthly mean temperatures: a multiple linear regression based test and a penalized maximal t test.", "These discontinuities were adjusted using a recently developed quantile-matching algorithm: the adjustments were estimated with the use of a reference series.", "Based on this new homogenized temperature data set, annual and seasonal temperature trends were estimated for Canada for 1950\u20132010 and Southern Canada for 1900\u20132010.", "Overall, temperature has increased at most locations.", "For 1950\u20132010, the annual mean temperature averaged over the country shows a positive trend of 1.5\u00b0C for the past 61 years.", "This warming is slightly more pronounced in the minimum temperature than in the maximum temperature; seasonally, the greatest warming occurs in winter and spring.", "The results are similar for Southern Canada although the warming is considerably greater in the minimum temperature compared to the maximum temperature over the period 1900\u20132010."], "structured": false}
{"doc_id": 140098548, "title": "Prevention of radiographic-contrast-agent-induced reductions in renal function by acetylcysteine.", "abstract": ["BACKGROUND Radiographic contrast agents can cause a reduction in renal function that may be due to reactive oxygen species.", "Whether the reduction can be prevented by the administration of antioxidants is unknown.   \n", "METHODS We prospectively studied 83 patients with chronic renal insufficiency (mean [+/-SD] serum creatinine concentration, 2.4+/-1.3 mg per deciliter [216+/-116 micromol per liter]) who were undergoing computed tomography with a nonionic, low-osmolality contrast agent.", "Patients were randomly assigned either to receive the antioxidant acetylcysteine (600 mg orally twice daily) and 0.45 percent saline intravenously, before and after administration of the contrast agent, or to receive placebo and saline.   \n", "RESULTS Ten of the 83 patients (12 percent) had an increase of at least 0.5 mg per deciliter (44 micromol per liter) in the serum creatinine concentration 48 hours after administration of the contrast agent: 1 of the 41 patients in the acetylcysteine group (2 percent) and 9 of the 42 patients in the control group (21 percent; P=0.01; relative risk, 0.1; 95 percent confidence interval, 0.02 to 0.9).", "In the acetylcysteine group, the mean serum creatinine concentration decreased significantly (P<0.001), from 2.5+/-1.3 to 2.1+/-1.3 mg per deciliter (220+/-118 to 186+/-112 micromol per liter) 48 hours after the administration of the contrast medium, whereas in the control group, the mean serum creatinine concentration increased nonsignificantly (P=0.18), from 2.4+/-1.3 to 2.6+/-1.5 mg per deciliter (212+/-114 to 226+/-133 micromol per liter) (P<0.001 for the comparison between groups).   \n", "CONCLUSIONS Prophylactic oral administration of the antioxidant acetylcysteine, along with hydration, prevents the reduction in renal function induced by contrast agents in patients with chronic renal insufficiency."], "structured": true}
{"doc_id": 140907540, "title": "Sample size calculation in epidemiological studies", "abstract": ["Summary Sample-size determination is often an important step in planning an epidemiological study.", "There are several approaches to determining sample size.", "It depends on the type of the study.", "Descriptive, observational and randomized controlled studies have different formulas to calculate sample size.", "In this article, we discuss the formulas that can help to estimate sample size in an epidemiological trial.", "We present a few examples from clinical practice, which may contribute to the understanding of this problem.", "Keywords: sample size determination Determining an appropriate sample size for a clinical trial is an essential step in the statistical design of the pro-ject.", "An adequate sample size helps ensure that the stu-dy will yield reliable information, regardless of whether the ultimate data suggest a clinically important difference between the treatments being studied, or the study is in-tended to measure the accuracy of a diagnostic test or the incidence of a disease.", "Unfortunately, many studies pub-lished in medical literature are conducted with inadequate sample sizes, making the interpretation of negative results dif\ufb01cult.", "Conductingastudywithaninadequatesamplesize is not only futile, it is also unethical.", "Exposing pa-tients to the risks inherent in a research is justi\ufb01ableon-ly if there is a realistic possibility that the results will be-ne\ufb01tthosesubjects,futuresubjects,orleadtosubstantialscienti\ufb01cprogress.", "How many individuals will I need to study?", "This ques-tion iscommonly asked by a clinical investigator and ex-poses oneof many issues that are best to be settled before actually carryingout a study.", "Consultation with a statisti-cian is worthwhilein addressing many issues of study de-sign, but a statisticianis not always readily available.", "Sample Size (n) is the number of individuals in a group under study.", "The larger the sample size, the grea-ter the precision and, thus, power for a given study de-sign to detect an effect of a given size.", "For statisticians, an n > 30 is usually suf\ufb01cientfortheCentralLimitTheo-rem to hold so that normal theory approximations can be used for measures such as the standard error of the mean.", "However, this sample size (n = 30) is unrelated to the cli-nicians\u2019 objective of detecting biologically signi\ufb01cantef-fects, which determines the speci\ufb01csamplesizeneededfor a speci\ufb01cstudy[1]."], "structured": false}
{"doc_id": 142559798, "title": "Tammarniit (Mistakes): Inuit Relocation in the Eastern Arctic, 1939-63", "abstract": ["Preface Introduction 1.", "Are Inuit Indians?:", "Relief, Jurisdiction, and Government Responsibility 2.", "Social Welfare and Social Crisis in the Eastern Arctic 3.", "Planning for Relocation in the Eastern Arctic 4.", "Recolonizing the Arctic Islands: The 1953 Relocations to Resolute Bay and Craig Harbour 5.", "The Ennadai Lake Relocations, 1950-60 6.", "The Garry Lake Famine 7.", "The Whale Cove Relocation 8.", "Relocation and Responsibility, 1955-63 Notes Bibliography Index"], "structured": false}
{"doc_id": 142562844, "title": "Levels of selection in evolution", "abstract": ["Ever since the groundbreaking work of George Williams, W. D. Hamilton, and Richard Dawkins, evolutionary biologists have recognized that natural selection generally does not operate for the good of the group, but rather for the good of lower-level units such as the individual, the cell, even the gene.", "One of the fundamental problems of biology is: what keeps competition between these various levels of natural selection from destroying the common interests to be gained from cooperation?", "In this volume twelve prominent scientists explore this question, presenting a comprehensive survey of the current theoretical and empirical research in evolutionary biology.", "Recent studies show that at many levels of biological organization, mechanisms have evolved to prevent potential conflict in natural selection.", "Editor Laurent Keller's aim in this book is to bring together leading researchers from all biological disciplines to outline these potential conflicts and discuss how they are resolved.", "A multi-level approach of this kind allows important insights into the evolution of life, as well as bridging the long-standing conceptual chasm between molecular and organismal biologists.", "The chapters here follow a rigorous theoretical framework, giving the book an overall synergy that is unique to multi-authored books.", "The contributors, in addition to the editor, are H. Charles J. Godfray, Edward Allen Herre, Dawn M. Kitchen, Egbert Giles Leigh, Jr., Catherine M. Lessells, Richard E. Michod, Leonard Nunney, Craig Packer, Andrew Pomiankowski, H. Kern Reeve, John Maynard Smith, and Eors Szathmary.", "\""], "structured": false}
{"doc_id": 143381103, "title": "A psychometric evaluation of the Beck Depression Inventory\u2013II.", "abstract": ["This article provides psychometric information on the second edition of the Beck Depression Inventory (BDI-II; A. T. Beck, R. A. Steer, & G. K. Brown, 1996), with respect to internal consistency, factorial validity, and gender differences.", "Both measures demonstrated high internal reliability in the full student sample.", "Significant differences between the mean BDI and BDI-II scores necessitated the development of new cutoffs for analogue research on the BDI-II.", "Results from exploratory and confirmatory factor analyses indicated that a 2-factor solution optimally summarized the data for both versions of the inventory and accounted for a cumulative 41% and 46% of the common variance in BDI and BDI-II responses, respectively.", "These factor solutions were reliably cross-validated, although the importance of each factor varied by gender.", "The authors conclude that the BDI-II is a stronger instrument than the BDI in terms of its factor structure."], "structured": false}
{"doc_id": 143796742, "title": "Why people feel crowded: An examination of objective and subjective crowding", "abstract": ["Prior studies have found only a modest relationship between objective and subjective crowding, defying logic and commonsensical notions of why people feel crowded.", "Using data from a representative sample of Bangkok, Thailand, where the level of household crowding is four times that in western societies, we explore several possibilities of why this is the case.", "Examining seven different indicators of objective crowding, our analyses suggest that the modest relationship is not an artifact of measurement.", "Contrary to the assumption of prior investigations, the findings indicate that the objective-subjective crowding relationship is nonlinear and that there is a ceiling effect muting the impact of increased objective crowding.", "The analyses further suggest that the strength of the relationship is mitigated somewhat, with part of the feeling of being crowded accounted for by household circumstances, such as the degree of control an individual has over the use of household space."], "structured": false}
{"doc_id": 143868995, "title": "Self-Report and Tests of Memory Aging", "abstract": ["Memory complaints have not correlated well with tests of memory.", "However, given self-report questions, which tap processes of everyday remembering.", "sixty volunteers aged 21-84 years adequately rated their memory competence.", "Categorized into four memory processes, self-report and six tests of verbal, faces, story and nonverbal auditory, visual, and tactual memory ,were canonically correlated (r = 0.67) and both sets of measures declined with age in parallel.", "Thc old were more accurate than the young in their ratings but by no means on all tests and expectation to perform poorly seemed to have influenced some performances."], "structured": false}
{"doc_id": 144555102, "title": "Code of the Street: Decency, Violence, and the Moral Life of the Inner City", "abstract": ["Inner-city black America is often defined by random, senseless street violence.", "In fact, although violence is a salient feature, its use is far from random; it is regulated through an informal but well-known code of the street.", "How you dress, how you talk, whether you make eye-contact, your understanding of the pecking order - such crucial details can have life-or-death consequences and young people are particularly at risk.", "In this anatomy of the inner-city psyche, the author shows how the code is a response to the lack of well-paid jobs; to the stigma of race; to rampant drug use; to alienation and to lack of hope.", "The police exercise no control, and the individual's safety and sense of worth are defined by how much respect he can command in public; this deference is based physical and psycholgical control and on an implied threat of violence.", "The most powerful force counteracting the code is the strong, loving decent family.", "Unfortunately, the culture of the street thrives and often defeats decency because it controls public space so that individuals with better aspirations are often entangled in the code."], "structured": false}
{"doc_id": 144801076, "title": "A generic measure of relationship satisfaction.", "abstract": ["The variety of interpersonal relationships in contemporary society necessitates the development of brief, reliable measures of satisfaction that are applicable to many types of close relationships.", "This article describes the development of such a measure.", "In Study I, the 7-item Relationship Assessment Scale (RAS) was administered to 125 subjects who reported themselves to be \"in love.", "\"", "Analyses revealed a unifactorial scale structure, substantial factor loadings, and moderate intercorrelations among the items.", "The scale correlated significantly with measures of love, sexual attitudes, self-disclosure, commitment, and investment in a relationship.", "In Study II, the scale was administered to 57 couples in ongoing relationships.", "Analyses supported a single factor, alpha reliability of .86, and correlations with relevant relationship measures.", "The scale correlated .80 with a longer criterion measure, the Dyadic Adjustment Scale (Spanier, 1976), and both scales were effective (with a subsample) in discriminating couples who stayed together from couples who broke up.", "The RAS is a brief, psychometrically sound, generic measure of relationship satisfaction."], "structured": false}
{"doc_id": 145335387, "title": "ECONOMIC RESTRUCTURING AND SUBURBANIZATION IN CHINA", "abstract": ["As in other countries, suburbanization in China occurred after the cities had experienced a period of sustained industrial and population growth.", "This study examines suburbanization in Beijing, Shanghai, Shenyang, and Dalian.", "As a result of economic restructuring, the urban core registered net population loss from 1982 to 1990 because of decentralization while the inner suburbs gained population.", "Among the forces driving suburbanization were marketization of urban land, the shift of industrial land to tertiary use, transportation improvement, the availability of foreign and domestic capital, housing rehabilitation in the city, and new housing construction in the suburbs.", "There were certain similarities but major differences between American and Chinese suburbanization.", "Unlike the current metropolitan landscape in the United States where suburban growth has given rise to a polycentric spatial structure, suburbanization in China is still at the incipient stage of development with suburbs dominated by centra..."], "structured": false}
{"doc_id": 145383432, "title": "The Assumption of Caregiving: Grandmothers Raising the Children of the Crack Cocaine Epidemic:", "abstract": ["In this article, selected findings are presented from a study of the experiences of 71 African American women who have become the sole caregivers for at least one grandchild or great-grandchild as a result of the involvement of the parent in use of crack cocaine.", "Despite the unique circumstances of each situation, three patterns of the assumption of caregiving emerged from analysis of the intensive interviews and participant observation: sudden assumption, negotiated assumption, and inevitable assumption of the permanent caregiver role.", "Each pattern is described along six dimensions: forewarning, initiation, the trigger event, the caregiver's goal, her assumed trajectory of the caregiving period, and her perceived influence on her own destiny.", "These accounts provide important information for those who work with women, children, and families, as well as unique insight into the consequences of the crack cocaine epidemic."], "structured": false}
{"doc_id": 145416918, "title": "The effect of information related to fat content and taste on consumer responses to a reduced-fat frankfurter and a reduced-fat chocolate bar", "abstract": ["The effects of product information on responses to frankfurter sausages and chocolate bars were studied by comparing sensory and hedonic ratings in two conditions: blind tasting and tasting with information present.", "Furthermore, the effect of information alone was investigated by having the subjects rate the expected sensory and hedonic intensities of the products on the basis of packages with different claims.", "Three groups of subjects were tested by giving them different information: The basic group (no added claims, n = 31), the reduced-fat group (products claimed to have reduced-fat, n=29) and the flavorful group (products claimed to have full meat/chocolate flavor, n = 31).", "Product information increased the rated pleasantness of the frankfurter in all three information groups compared to the blind ratings.", "The information did not affect the pleasantness of the chocolate bars.", "The expected attribute intensities of the frankfurters and chocolates were rated lower by the reduced-fat group than by the other groups.", "Overall, the effect of product information was more clearly seen in ratings of sensory attributes than in pleasantness ratings."], "structured": false}
{"doc_id": 145716849, "title": "Transnationalism and identity", "abstract": ["Transnationalism and identity are concepts that inherently call for juxtaposition.", "This is so because many peoples' transnational networks of exchange and participation are grounded upon some perception of common identity; conversely, the identities of numerous individuals and groups of people are negotiated within social worlds that span more than one place.", "In this introductory article, the transnational perspective on migration studies is first discussed, followed by some critiques and outstanding questions.", "The final section summarises points raised by the contributing authors of the main articles in this themed issue of JEMS, especially with regard to various ways transnational settings and dynamics affect the construction, negotiation and reproduction of identities."], "structured": false}
{"doc_id": 146653163, "title": "Social Isolation and Social Support: An Applied Perspective", "abstract": ["Considerable empirical evidence substantiates the importance of social networks and support to health and well-being among the elderly.", "But considerably more research is necessary before successful interventions can be more generally implemented to positively alter an elder's network.", "In this article, the authors discuss social supportand isolationfrom an appliedperspective.", "They have combined presentations originally made at a National Institute on Aging-sponsored symposium on applied gerontology held in August 1992.", "They make some general observations concerning the field of applied social relations in later life, describe the mental health aspects of these relations, list some fundamental principles and existing technology for this field, describe the use of a brief screening instrument for social isolation developed by one of the authors (Lubben), and explore varying domains of knowledge concerning elder soical relations.", "They conclude by outlining some areas that they see as requiring the attention o..."], "structured": false}
{"doc_id": 147107523, "title": "Wine and health: faraway concepts?", "abstract": ["Purpose \u2013 The purpose of this paper is to explore consumers\u2019 perceptions and beliefs in the health benefits of wine and the relationship with wine consumption patterns.", "Design/methodology/approach \u2013 In store face-to-face survey results from 402 wine consumers were elaborated with two-step cluster analysis.", "ANOVA confirmed differences among groups.", "Groups were profiled by a \u03c72 significance analysis when adequate.", "A multivariate binary logistic regression estimated wine consumption influence on healthiness perceptions.", "Findings \u2013 Consumers converge into four groups: two health-oriented \u2013 optimistic and medical; two non-health-oriented \u2013 unintentional drinker and unconvinced.", "Groups are not significantly differentiated in socio-economic terms.", "Wine consumption behaviour influences health orientation, specifically for monthly and wine drinkers, vs weekly and other alcohol drinkers.", "Health-oriented consumers favourably welcome and are willing to pay more for health-enhancing wine.", "Consumers believe that wine c..."], "structured": false}
{"doc_id": 153755807, "title": "The Changing Problem of Overcrowded Housing", "abstract": ["Abstract Overcrowding has increased in the U.S. after decades of decline\u2014dramatically so in some locales and for some ethnic groups.", "The nature of the problem and its very definition for policy purposes are also changing.", "We examine the special characteristics of the overcrowded, where they are located, why the incidence of crowding has resurged, and why it is confined to specific locales.", "Ethnicity, age, immigration, and poverty play important roles, but housing market conditions appear much less important.", "We also show that the planning standard used to judge overcrowding is a relative one that has varied over time, and that the social norms vary among ethnic groups.", "The issue of overcrowding may exemplify the current perplexities about imposing uniform standards in an evolving multiethnic society.", "Worst-case housing needs would be better targeted in highly impacted locales by allowing more \u201cplace diversity\u201d in the setting of standards."], "structured": false}
{"doc_id": 154050141, "title": "Best response dynamics and socially stable strategies", "abstract": ["Abstract An evolutionarily stable strategy (Maynard Smith and Price, Nature (London) 246 (1973), 15\u201318) is a strategy which is robust against a tiny invasion of mutants.", "Best response dynamics is a dynamic process in which the frequency of a strategy increases only if it is a best response to the present strategy distribution.", "Gilboa and Matsui ( Econometrica 59 (1991), 859\u2013867) proposed a stability concept directly derived from this dynamic process.", "Modifying the above two stability concepts, this paper shows the equivalence between the static concept and the dynamic one.", "Their set-valued versions always exist.", "Examples are given to see their usefulness in analyzing forward induction and preplay communication."], "structured": false}
{"doc_id": 154243324, "title": "From youth to adult homelessness", "abstract": ["Governments have shown an interest in early intervention strategies to reduce youth homelessness, but critics say that early intervention programs lack clear outcomes.", "This paper investigates what happens when early intervention programs are not in place and young people progress to adult homelessness.", "The paper assesses the 'social adaptation' hypothesis that the longer young people are homeless the more they adapt to homelessness as a way of life.", "The paper uses information on 1,677 individuals who first became homeless when they were 18 or younger.", "Three-quarters of the sample had progressed to adult homelessness (defined as 25 or older) and one-quarter were now young adults aged 19 to 24.", "The findings confirm that the longer people are homeless, the more difficult it becomes to get out of homelessness.", "However, the social adaptation account overstates the extent to which people accept homelessness as a 'way of life'.", "People can return to conventional accommodation if they are given long-term support.", "The paper concludes with three policy recommendations."], "structured": false}
{"doc_id": 154549459, "title": "Urban spatial development in the land policy reform era: evidence from Beijing", "abstract": ["This paper examines the characteristics of urban spatial development in Beijing and identifies the extent to which these characteristics can be attributed to the emerging land market in Beijing as well as the impact of land policy reform.", "Based on the observations of land use rights granted from 1993 to the first half of 2000 in the built-up area of Beijing, empirical analyses illustrate that both land prices and land development density decrease with distance to the city core.", "It further provides evidence that the slope of the land rent curve also depends on land use types.", "This leads to the conclusion that the land market influences land development decisions and urban form.", "Finally, it shows that the slope of the land rent curve and the elasticity of land-capital substitution change over time.", "The former declines, as expected.", "This is because Beijing's massive investments in transport have reduced transport costs, which in turn has shifted the land rent curve.", "The latter rises, implying the price effect on land development density.", "Both changes\u00e2\u20ac\u201din land rent function and the elasticity of land-capital substitution-point to the maturing of the Beijing land market.", "It should be mentioned that there are enormous land developments outside the land market (land development on administratively allocated land).", "These developments can significantly distort urban land use patterns portrayed through this study."], "structured": false}
{"doc_id": 154763124, "title": "The Mismatch Argument: The Construction of a Housing Orthodoxy in Australia", "abstract": ["Australia's housing policy discourse contains many orthodoxies.", "While orthodoxies are never totally accepted within a discourse, they are the dominant notions within them and as such carry significant symbolic authority.", "One orthodoxy that has particular authority in Australia is the notion that there is a 'mismatch' in the housing system between the available stock and the size of households to the extent that there is significant underutilisation and underoccupancy of housing.", "The mismatch argument's power as orthodoxy is such that the idea is assumed in much housing policy discussion.", "Criticism of the mismatch orthodoxy can take many approaches, such as empirical, conceptual and discursive.", "The discursive critique focuses not on the empirical relationship between households and dwellings, but on the statements about that relationship.", "The resulting analysis shows how the mismatch orthodoxy arose in Australia and its effects on housing discourse.", "This paper examines the construction of the mismatch orthodoxy, from its first uses in the early 1970s to its entrenchment in national and state housing policy research in the early 1990s.", "It shows how the structures of the discourse construct the orthodoxy, despite empirical and conceptual criticisms of it.", "Of particular importance is the effect the orthodoxy has on people deemed to be underutilising their dwellings, and on how the orthodoxy affects policy interpretations, such as occupancy standards."], "structured": false}
{"doc_id": 154796494, "title": "Citizen Participation and Citizen Evaluation in Disaster Recovery", "abstract": ["In April 1997, Grand Forks, North Dakota, and East Grand Forks, Minnesota, experienced a disastrous flood.", "Both cities have been textbook examples of success according to the Federal Emergency Management Agency.", "They have an updated infrastructure, paid for largely by the federal government.", "Their downtowns are on the road to recovery with new construction and businesses.", "The paths of the two cities have diverged in the social and political aftermath of the flood.", "East Grand Forks, following consultant suggestions, instituted extensive citizen participation initiatives.", "East Grand Forks has experienced political stability and citizen satisfaction.", "Grand Forks relied primarily on bureaucratic guidance to react to the disaster.", "Grand Forks has experienced changes in government structure, turnover of elected and appointed officials, and much less positive citizen evaluation.", "This study examines the effect of perceptions of citizen participation on the citizens\u2019 evaluation of the success of the recovery."], "structured": false}
{"doc_id": 155200372, "title": "Population growth, urban sprawl and landscape integrity of Beijing City", "abstract": ["The detailed landscape pattern of the urban area within the 6th ring road in Beijing City was identified using airborne remote sensing data acquired between 1997 and 2002.", "The landscape indices at landscape level were computed using Fragstats 3.3, and changes in land use/cover types in Beijing from 1997 to 2002 were examined.", "The results show that urban built area (UBA) and farmland changed greatly within the 6th ring road, and that farmland had been replaced by UBA.", "The number of patches increased by 106.6%, mean patch area decreased by 51.6%, the splitting index increased by 94.3%, and the landscape diversity index increased by 17.8%.", "The landscape pattern had become more fragmented and diversified in these 5 years.", "The main driving forces for landscape change were the increasing demand for land for construction due to the growing population, unreasonable urban growth, and improvements in housing standards.", "The landscape pattern change in Beijing led by rapid urbanisation has negatively influenced urban..."], "structured": false}
{"doc_id": 167469018, "title": "Drink Choice: Factors Influencing the Intention to Drink Wine", "abstract": ["This paper explores the reasons why consumers choose wine over other alcoholic beverages, with a focus upon the beliefs held by consumers towards the behaviour of wine drinking.", "The research findings show that attitudes are somewhat more predictive of the intention to drink wine than perceived social pressure.", "Nevertheless, both attitudinal and normative elements are required to adequately explain wine consumption.", "Despite the fact that the issue of health figured prominently amongst the salient beliefs identified in the qualitative phase of the research, the subsequent quantitative research found that drinking wine because of its purported health benefits was not a significant attitudinal or behavioural factor.", "Drinking wine because it provides \u2018a variety of tastes and flavours\u2019 and because it \u2018goes well with food\u2019 was found to be significantly more important.", "The results suggest that efforts to actively promote awareness of the health benefits of wine drinking may have limited value."], "structured": false}
{"doc_id": 167944455, "title": "Application of growth technologies in enhancing food security and sustainability", "abstract": ["Anabolic steroids have been widely used in the beef cattle industry for over 50 years as safe and effective growth-promoting agents, and today, more than 90% of all feedlot cattle in the US receive some type of steroidal implant during their lifetime (NAHMS, USDA 2000).", "A list of approval of growth promotants by the FDA is shown in Table 1.", "Generally, implants have been shown to increase growth rate 8 to 28%, improve feed efficiency 5 to 20%, and enhance lean tissue mass of the carcass 3 to 10% (Duckett and Owens, 1997).", "This improvement in production efficiency has multiple benefits: 1) it clearly and dramatically reduces production costs by reducing the amount of feed required per unit of gain (Avery and Avery, 2007); 2) it reduces the amount of land necessary to produce equivalent amounts of food for consumers; 3) it limits the production of greenhouse gases by reducing the number of animals required to produce equivalent amounts of beef (Avery and Avery, 2007); and 4) it extends cost savings to consumers by providing a year-round, affordable supply of beef at reduced prices (Lawrence and Ibarburu, 2006).", "Since animal products contribute significantly to the total caloric and nutrient intake in the human population, altering the composition of growth toward more lean tissue and less adipose tissue results in a healthier product with fewer calories that still is rich in beneficial nutrients.", "In addition to steroidal implants, a newer class of orally active growth promotants, known as b-adrenergic agonists (BAA; Ractopamine-HCl; 2003 and Zilpaterol-HCl; 2006), have been approved for use in finishing beef cattle in the last decade.", "These products provide similar production benefits as steroidal implants, but differ in application and mode of action.", "Beta-adrenergic agonists are fed during the last 20 to 42 days of the cattle finishing period, depending on the specific product.", "The purpose of this paper is to explain how anabolic implants and BAA work and their benefits to beef cattle production."], "structured": false}
{"doc_id": 168265642, "title": "Metabolic modifiers as performance-enhancing technologies for livestock production", "abstract": ["With the current and predicted increase in world population, growing global demand and consumption of food will result in increasing competition for land, water, and energy.", "In turn, this will severely affect our ability to produce food as will the urgent requirement to reduce the impact of food systems on the environment (Godfray et al., 2010).", "Globalization has boosted trade in livestock inputs and products and resulted in industry growth, and concurrently livestock production has undergone a complex process of technical and geographical change (Gerber et al., 2007).", "This has resulted in a challenge to livestock producers; growing demand for their produce with a dwindling supply of resources, with the only solution being a significant increase in efficiency.", "Also, as incomes increase in the burgeoning economies, so does the demand for high-quality animal proteins such as meat, milk, and eggs; thus the Food and Agriculture Organization of the United Nations suggests that food requirements will increase by 70% by 2050 (Anonymous, 2009).", "The recent success in developed and emerging technologies suggests that the animal industries are well placed to prosper through these new challenges.", "To ensure these technologies\u2014such as metabolic modifiers including somatotropin, immunization against gonadotropin-releasing factor, and orally active dietary additives like ractopamine, zilpaterol, cysteamine, chromium, betaine, and dietary neuroleptics\u2014can be effectively utilized throughout the animal industries, further emphasis is required on their acceptance and development.", "As a result of these technological advancements, producers have benefited because of improved production efficiencies while meat packers have improved processing efficiencies because of increased lean meat yield.", "Ostensibly, the consumer has also benefited because meat is leaner and less expensive to purchase.", "However, there have been some concerns that the focus on increasing production efficiency and lean meat yield has been to the detriment of meat quality (Dunshea et al., 2005).", "It is also interesting that at a time of apparently greater need for these technologies, there are external influences such as market differentiation and trade barriers as well as consumer resistance that challenge the use of technologies.", "A tenet of this article is that if we are to meet the increased global demand for animal protein, then we must continue to develop and adopt technologies to improve livestock efficiency, but we must be cognizant of the potential barriers affecting acceptance."], "structured": false}
{"doc_id": 195317463, "title": "Assessment of hemodynamic efficacy and safety of 6% hydroxyethylstarch 130/0.4 vs. 0.9% NaCl fluid replacement in patients with severe sepsis: The CRYSTMAS study", "abstract": ["Inadequate initial treatment and delayed hemodynamic stabilization (HDS) may be associated with increased risk of death in severe sepsis patients.", "In order to compare the hemodynamic efficacy and safety of 6% HES 130/0.4 and NaCl 0.9% for HDS in patients with severe sepsis, we designed a prospective, multicenter, active-controlled, double-blind, randomized study in intensive care units.", "174 out of 196 patients reached HDS (88 and 86 patients for HES and NaCl, respectively).", "Significantly less HES was used to reach HDS vs. NaCl (1,379 \u00b1886 ml in the HES group and 1,709 \u00b11,164 ml in the NaCl group (mean difference = -331\u00b1 1,033, 95% CI -640 to -21, P = 0.0185).", "Time to reach HDS was 11.8 10.1 hours vs. 14.3 \u00b111.1 hours for HES and NaCl, respectively.", "Total quantity of study drug infused over four consecutive days, ICU and hospital LOS, and area under the curve of SOFA score were comparable.", "Acute renal failure occurred in 24 (24.5%) and 19 (20%) patients for HES and NaCl, respectively (P = 0.454).", "There was no difference between AKIN and RIFLE criteria among groups and no difference in mortality, coagulation, or pruritus up to 90 days after treatment initiation.", "Significantly less volume was required to achieve HDS for HES vs. NaCl in the initial phase of fluid resuscitation in severe sepsis patients without any difference for adverse events in both groups.", "NCT00464204"], "structured": false}
{"doc_id": 195680777, "title": "Comparisons between different polychemotherapy regimens for early breast cancer: meta-analyses of long-term outcome among 100,000 women in 123 randomised trials.", "abstract": ["BACKGROUND Moderate differences in efficacy between adjuvant chemotherapy regimens for breast cancer are plausible, and could affect treatment choices.", "We sought any such differences.   \n", "METHODS We undertook individual-patient-data meta-analyses of the randomised trials comparing: any taxane-plus-anthracycline-based regimen versus the same, or more, non-taxane chemotherapy (n=44,000); one anthracycline-based regimen versus another (n=7000) or versus cyclophosphamide, methotrexate, and fluorouracil (CMF; n=18,000); and polychemotherapy versus no chemotherapy (n=32,000).", "The scheduled dosages of these three drugs and of the anthracyclines doxorubicin (A) and epirubicin (E) were used to define standard CMF, standard 4AC, and CAF and CEF.", "Log-rank breast cancer mortality rate ratios (RRs) are reported.   \n", "FINDINGS In trials adding four separate cycles of a taxane to a fixed anthracycline-based control regimen, extending treatment duration, breast cancer mortality was reduced (RR 0\u00b786, SE 0\u00b704, two-sided significance [2p]=0\u00b70005).", "In trials with four such extra cycles of a taxane counterbalanced in controls by extra cycles of other cytotoxic drugs, roughly doubling non-taxane dosage, there was no significant difference (RR 0\u00b794, SE 0\u00b706, 2p=0\u00b733).", "Trials with CMF-treated controls showed that standard 4AC and standard CMF were equivalent (RR 0\u00b798, SE 0\u00b705, 2p=0\u00b767), but that anthracycline-based regimens with substantially higher cumulative dosage than standard 4AC (eg, CAF or CEF) were superior to standard CMF (RR 0\u00b778, SE 0\u00b706, 2p=0\u00b70004).", "Trials versus no chemotherapy also suggested greater mortality reductions with CAF (RR 0\u00b764, SE 0\u00b709, 2p<0\u00b70001) than with standard 4AC (RR 0\u00b778, SE 0\u00b709, 2p=0\u00b701) or standard CMF (RR 0\u00b776, SE 0\u00b705, 2p<0\u00b70001).", "In all meta-analyses involving taxane-based or anthracycline-based regimens, proportional risk reductions were little affected by age, nodal status, tumour diameter or differentiation (moderate or poor; few were well differentiated), oestrogen receptor status, or tamoxifen use.", "Hence, largely independently of age (up to at least 70 years) or the tumour characteristics currently available to us for the patients selected to be in these trials, some taxane-plus-anthracycline-based or higher-cumulative-dosage anthracycline-based regimens (not requiring stem cells) reduced breast cancer mortality by, on average, about one-third.", "10-year overall mortality differences paralleled breast cancer mortality differences, despite taxane, anthracycline, and other toxicities.   \n", "INTERPRETATION 10-year gains from a one-third breast cancer mortality reduction depend on absolute risks without chemotherapy (which, for oestrogen-receptor-positive disease, are the risks remaining with appropriate endocrine therapy).", "Low absolute risk implies low absolute benefit, but information was lacking about tumour gene expression markers or quantitative immunohistochemistry that might help to predict risk, chemosensitivity, or both.   \n", "FUNDING Cancer Research UK; British Heart Foundation; UK Medical Research Council."], "structured": true}
{"doc_id": 195683603, "title": "Invariant NKT cells modulate the suppressive activity of IL-10-secreting neutrophils differentiated with serum amyloid A.", "abstract": ["Neutrophils are the main effector cells during inflammation, but they can also control excessive inflammatory responses by secreting anti-inflammatory cytokines.", "However, the mechanisms that modulate their plasticity remain unclear.", "We now show that systemic serum amyloid A 1 (SAA-1) controls the plasticity of neutrophil differentiation.", "SAA-1 not only induced anti-inflammatory interleukin 10 (IL-10)-secreting neutrophils but also promoted the interaction of invariant natural killer T cells (iNKT cells) with those neutrophils, a process that limited their suppressive activity by diminishing the production of IL-10 and enhancing the production of IL-12.", "Because SAA-1-producing melanomas promoted differentiation of IL-10-secreting neutrophils, harnessing iNKT cells could be useful therapeutically by decreasing the frequency of immunosuppressive neutrophils and restoring tumor-specific immune responses."], "structured": false}
{"doc_id": 195689316, "title": "Body-mass index and cause-specific mortality in 900 000 adults: collaborative analyses of 57 prospective studies.", "abstract": ["BACKGROUND The main associations of body-mass index (BMI) with overall and cause-specific mortality can best be assessed by long-term prospective follow-up of large numbers of people.", "The Prospective Studies Collaboration aimed to investigate these associations by sharing data from many studies.   \n", "METHODS Collaborative analyses were undertaken of baseline BMI versus mortality in 57 prospective studies with 894 576 participants, mostly in western Europe and North America (61% [n=541 452] male, mean recruitment age 46 [SD 11] years, median recruitment year 1979 [IQR 1975-85], mean BMI 25 [SD 4] kg/m(2)).", "The analyses were adjusted for age, sex, smoking status, and study.", "To limit reverse causality, the first 5 years of follow-up were excluded, leaving 66 552 deaths of known cause during a mean of 8 (SD 6) further years of follow-up (mean age at death 67 [SD 10] years): 30 416 vascular; 2070 diabetic, renal or hepatic; 22 592 neoplastic; 3770 respiratory; 7704 other.   \n", "FINDINGS In both sexes, mortality was lowest at about 22.5-25 kg/m(2).", "Above this range, positive associations were recorded for several specific causes and inverse associations for none, the absolute excess risks for higher BMI and smoking were roughly additive, and each 5 kg/m(2) higher BMI was on average associated with about 30% higher overall mortality (hazard ratio per 5 kg/m(2) [HR] 1.29 [95% CI 1.27-1.32]): 40% for vascular mortality (HR 1.41 [1.37-1.45]); 60-120% for diabetic, renal, and hepatic mortality (HRs 2.16 [1.89-2.46], 1.59 [1.27-1.99], and 1.82 [1.59-2.09], respectively); 10% for neoplastic mortality (HR 1.10 [1.06-1.15]); and 20% for respiratory and for all other mortality (HRs 1.20 [1.07-1.34] and 1.20 [1.16-1.25], respectively).", "Below the range 22.5-25 kg/m(2), BMI was associated inversely with overall mortality, mainly because of strong inverse associations with respiratory disease and lung cancer.", "These inverse associations were much stronger for smokers than for non-smokers, despite cigarette consumption per smoker varying little with BMI.   \n", "INTERPRETATION Although other anthropometric measures (eg, waist circumference, waist-to-hip ratio) could well add extra information to BMI, and BMI to them, BMI is in itself a strong predictor of overall mortality both above and below the apparent optimum of about 22.5-25 kg/m(2).", "The progressive excess mortality above this range is due mainly to vascular disease and is probably largely causal.", "At 30-35 kg/m(2), median survival is reduced by 2-4 years; at 40-45 kg/m(2), it is reduced by 8-10 years (which is comparable with the effects of smoking).", "The definite excess mortality below 22.5 kg/m(2) is due mainly to smoking-related diseases, and is not fully explained."], "structured": true}
{"doc_id": 195689757, "title": "Targeting metabolic remodeling in glioblastoma multiforme.", "abstract": ["A key aberrant biological difference between tumor cells and normal differentiated cells is altered metabolism, whereby cancer cells acquire a number of stable genetic and epigenetic alterations to retain proliferation, survive under unfavorable microenvironments and invade into surrounding tissues.", "A classic biochemical adaptation is the metabolic shift to aerobic glycolysis rather than mitochondrial oxidative phosphorylation, regardless of oxygen availability, a phenomenon termed the \"Warburg Effect\".", "Aerobic glycolysis, characterized by high glucose uptake, low oxygen consumption and elevated production of lactate, is associated with a survival advantage as well as the generation of substrates such as fatty acids, amino acids and nucleotides necessary in rapidly proliferating cells.", "This review discusses the role of key metabolic enzymes and their association with aerobic glycolysis in Glioblastoma Multiforme (GBM), an aggressive, highly glycolytic and deadly brain tumor.", "Targeting key metabolic enzymes involved in modulating the \"Warburg Effect\" may provide a novel therapeutic approach either singularly or in combination with existing therapies in GBMs."], "structured": false}
{"doc_id": 196664003, "title": "Signaling architectures that transmit unidirectional information despite retroactivity", "abstract": ["A signaling pathway transmits information from an upstream system to downstream systems, ideally in a unidirectional fashion.", "A key obstacle to unidirectional transmission is retroactivity, the additional reaction flux that affects a system once its species interact with those of downstream systems.", "This raises the fundamental question of whether signaling pathways have developed specialized architectures that overcome retroactivity and transmit unidirectional signals.", "Here, we propose a general procedure based on mathematical analysis that provides an answer to this question.", "Using this procedure, we analyze the ability of a variety of signaling architectures to transmit one-way (from upstream to downstream) signals, as key biological parameters are tuned.", "We find that single stage phosphorylation and phosphotransfer systems that transmit signals from a kinase show a stringent design trade-off that hampers their ability to overcome retroactivity.", "Interestingly, cascades of these architectures, which are highly represented in nature, can overcome this trade-off and thus enable unidirectional transmission.", "By contrast, phosphotransfer systems, and single and double phosphorylation cycles that transmit signals from a substrate are unable to mitigate retroactivity effects, even when cascaded, and hence are not well suited for unidirectional information transmission.", "Our results identify signaling architectures that, allowing unidirectional transmission of signals, embody modular processes that conserve their input/output behavior across multiple contexts.", "These findings can be used to decompose natural signal transduction networks into modules, and, at the same time, they establish a library of devices that can be used in synthetic biology to facilitate modular circuit design."], "structured": false}
{"doc_id": 198133135, "title": "Association between pre-diabetes, type 2 diabetes and trabecular bone score: The Vietnam Osteoporosis Study.", "abstract": ["AIMS Trabecular bone score (TBS) is a surrogate indicator of bone microarchitecture.", "The presenent study sought to examine the association between type 2 diabetes (T2D) and trabecular bone score (TBS) in adult Vietnamese men and women.   \n", "METHODS The study was part of the Vietnam Osteoporosis Study, in which 2702 women and 1398 men aged \u226530 yrs were recruited from the general community in Ho Chi Minh City.", "HbA1c levels were measured by the ADAMS\u2122 A1c HA-8160 (Arkray, Kyoto, Japan), and classified into 3 groups: normal if HbA1c <5.7%; pre-diabetes (5.7 to 6.4%); and diabetes (>6.4%).", "TBS was evaluated by iNsight Software, version 2.1 (Medimaps, Merignac, France) on lumbar spine BMD scan (Hologic Horizon).", "Differences in TBS between diabetic status were analyzed by the multivariable regression model with adjustment for age and body mass index.   \n", "RESULTS The prevalence of pre-diabetes and diabetes in men and women was 30.2% and 8.3%, respectively.", "In women, TBS was lower in pre-diabetes (-0.02; P<0.001) and diabetes (-0.02; P<0.001) compared with normal individuals.", "In men, there was no statistically significant difference in TBS between diabetic status.", "Moreover, TBS was significantly inversely correlated with HbA1c levels in women (P = 0.01), but not in men (P = 0.89).   \n", "CONCLUSION Women, but not men, with type 2 diabetes and pre-diabetes have lower TBS than individuals without diabetes.", "These data suggest that diabetes and prediabetes are associated with deterioration of bone microarchitecture."], "structured": true}
{"doc_id": 198309074, "title": "Adhesion molecules and chemokines: relation to anthropometric, body composition, biochemical and dietary variables", "abstract": ["Introduction: Among the inflammatory mediators involved in the pathogenesis of obesity, the cell adhesion molecules Pselectin, E-selectin, VCAM-1, ICAM-1 and the chemokine MCP-1 stand out.", "They play a crucial role in adherence of cells to endothelial surfaces, in the integrity of the vascular wall and can be modulated by body composition and dietary pattern.", "Objectives: To describe and discuss the relation of these cell adhesion molecules and chemokines to anthropometric, body composition, dietary and biochemical markers.", "Methods: Papers were located using scientific databases by topic searches with no restriction on year of publication.", "Results: All molecules were associated positively with anthropometric markers, but controversial results were found for ICAM-1 and VCAM-1.", "Not only obesity, but visceral fat is more strongly correlated with E-selectin and MCP-1 levels.", "Weight loss influences the reduction in the levels of these molecules, except VCAM-1.", "The distribution of macronutrients, excessive consumption of saturated and trans fat and a Western dietary pattern are associated with increased levels.", "The opposite could be observed with supplementation of w-3 fatty acid, healthy dietary pattern, high calcium diet and high dairy intake.", "Regarding the biochemical parameters, they have inverse relation to HDLC and positive relation to total cholesterol, triglycerides, blood glucose, fasting insulin and insulin resistance.", "Conclusion: Normal anthropometric indicators, body composition, biochemical parameters and eating pattern positively modulate the subclinical inflammation that results from obesity by reducing the cell adhesion molecules and chemokines."], "structured": false}