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_id stringlengths 4 9	title stringlengths 2 300	text stringlengths 174 10k
4983	Microstructural development of human newborn cerebral white matter assessed in vivo by diffusion tensor magnetic resonance imaging.	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,...
5836	Induction of myelodysplasia by myeloid-derived suppressor cells.	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 mark...
7912	BC1 RNA, the transcript from a master gene for ID element amplification, is able to prime its own reverse transcription.	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 p...
18670	The DNA Methylome of Human Peripheral Blood Mononuclear Cells	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 ...
19238	The human myelin basic protein gene is included within a 179-kilobase transcription unit: expression in the immune and central nervous systems.	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 transc...
33370	Targeting A20 Decreases Glioma Stem Cell Survival and Tumor Growth	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 N...
36474	Efficient targeting of expressed and silent genes in human ESCs and iPSCs using zinc-finger nucleases	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–specific lineage reporters, as well as reliable tools to disrupt, repair or overexpress genes by gene targeting, a...
54440	Empirical Bayesian models for analysing molecular serotyping microarrays	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...
70115	Bayesian measures of model complexity and fit	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 devian...
70490	Simplifying likelihood ratios	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 “probability” and “odds” of disease. This article describes a simpler method of interpreting likelihood ratios, one that avoids calculat...
72159	induction of early IFN-inducible genes in the absence of type	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-l...
79447	Arteriolar function in visceral adipose tissue is impaired in human obesity.	OBJECTIVE The purpose of this study was to characterize the relationship between adipose tissue phenotype and depot-specific microvascular function in fat. METHODS AND RESULTS In 30 obese subjects (age 42±11 years, body mass index 46±11 kg/m(2)) undergoing bariatric surgery, we intraoperatively collected visceral and s...
87758	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	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 A...
92308	Loss of immune escape mutations during persistent HCV infection in pregnancy enhances replication of vertically transmitted viruses	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...
92499	The journey of developing hematopoietic stem cells.	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 ...
97884	The sacroiliac joint in the spondyloarthropathies.	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...
102662	A rapid method for extraction of cotton (Gossypium spp.) genomic DNA suitable for RFLP or PCR analysis	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...
103007	Cross sectional stature and weight reference curves for the UK, 1990.	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 ...
104130	The suture provides a niche for mesenchymal stem cells of craniofacial bones	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 craniofa...
106301	Cardiac neural crest cells contribute to the dormant multipotent stem cell in the mammalian heart	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 neuro...
116792	The mammalian target of rapamycin signaling pathway mediates epileptogenesis in a model of temporal lobe epilepsy.	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 com...
118568	Acute administration of recombinant Angiopoietin-1 ameliorates multiple-organ dysfunction syndrome and improves survival in murine sepsis.	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 Ti...
120626	Mechanisms linking obesity to insulin resistance and type 2 diabetes	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. W...
123859	Tracking the fate of glomerular epithelial cells in vivo using serial multiphoton imaging in novel mouse models with fluorescent lineage tags	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...
140874	CTCF binding at the H19 imprinting control region mediates maternally inherited higher-order chromatin conformation to restrict enhancer access to Igf2.	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 chrom...
143251	De novo assembly of a PML nuclear subcompartment occurs through multiple pathways and induces telomere elongation.	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-associ...
152245	Effects of an opal termination codon preceding the nsP4 gene sequence in the O'Nyong-Nyong virus genome on Anopheles gambiae infectivity.	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 terminatio...
153744	Down-regulation of a host microRNA by a Herpesvirus saimiri noncoding RNA.	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 wit...
159469	HTRF: A Technology Tailored for Drug Discovery –A Review of Theoretical Aspects and Recent Applications	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) wi...
164189	Chk1 inhibits replication factory activation but allows dormant origin firing in existing factories	Replication origins are licensed by loading MCM2-7 hexamers before entry into S phase. However, only ∼10% 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 ap...
164985	Fra-1 protooncogene regulates IL-6 expression in macrophages and promotes the generation of M2d macrophages	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 J...
169264	Analysis of SiO2 nanoparticles binding proteins in rat blood and brain homogenate	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 wit...
175735	Inferring nucleosome positions with their histone mark annotation from ChIP data	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 immunoprecip...
188911	Generation of large numbers of dendritic cells from mouse bone marrow cultures supplemented with granulocyte/macrophage colony-stimulating factor	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 re...
195352	Insulin action and resistance in obesity and type 2 diabetes	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 ...
202259	Effect of lowering blood pressure on cardiovascular events and mortality in patients on dialysis: a systematic review and meta-analysis of randomised controlled trials	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 ...
207972	Interaction of an adenovirus E3 14.7-kilodalton protein with a novel tumor necrosis factor alpha-inducible cellular protein containing leucine zipper domains.	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-alph...
213017	PML induces compaction, TRF2 depletion and DNA damage signaling at telomeres and promotes their alternative lengthening.	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 ...
219475	Gr-1+CD11b+ myeloid cells tip the balance of immune protection to tumor promotion in the premetastatic lung.	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 ...
226488	Activin/Nodal signalling in stem cells.	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. W...
236204	Distinct RNA-dependent RNA polymerases are required for RNAi triggered by double-stranded RNA versus truncated transgenes in Paramecium tetraurelia	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...
238409	Mechanisms of Renal Cell Apoptosis Induced by Cyclosporine A: A Systematic Review of in vitro Studies	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 ...
243694	Blood stem cells emerge from aortic endothelium by a novel type of cell transition	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 speci...
253672	Probable person to person transmission of novel avian influenza A (H7N9) virus in Eastern China, 2013: epidemiological investigation	OBJECTIVE To determine whether the novel avian influenza H7N9 virus can transmit from person to person and its efficiency. DESIGN Epidemiological investigations conducted after a family cluster of two patients with avian H7N9 in March 2013. SETTING Wuxi, Eastern China. PARTICIPANTS Two patients, their close contacts, a...
263364	Genetic Variation in the Interleukin-28B Gene Is Associated with Spontaneous Clearance and Progression of Hepatitis C Virus in Moroccan Patients	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 ...
266641	CD127 expression inversely correlates with FoxP3 and suppressive function of human CD4+ T reg cells	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 (CD12...
275294	Environmental factors that influence the cutaneous production of vitamin D	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, precholecalc...
279052	Genomic imprinting in development, growth, behavior and stem cells.	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...
285794	Quantitative Detection of Hepatitis C Virus RNA by Light Cycler PCR and Comparison with Two Different PCR Assays	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...
293661	Targeting arginine metabolism pathway to treat arginine-dependent cancers.	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 ...
301838	Rank Signaling Links the Development of Invariant γδ T Cell Progenitors and Aire+ Medullary Epithelium	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 sh...
301866	Long-term immune deficiency after allogeneic stem cell transplantation: B-cell deficiency is associated with late infections.	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 c...
306006	The stimulatory potency of T cell antigens is influenced by the formation of the immunological synapse.	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 ce...
306311	Control of glutamate clearance and synaptic efficacy by glial coverage of neurons.	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, whethe...
308862	Duration of androgen suppression in the treatment of prostate cancer.	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 suppressi...
313394	A Functional Neuroimaging Study of Sound Localization: Visual Cortex Activity Predicts Performance in Early-Blind Individuals	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 c...
313403	High-Infiltration of Tumor-Associated Macrophages Predicts Unfavorable Clinical Outcome for Node-Negative Breast Cancer	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 corr...
317204	Murine Dishevelled 3 Functions in Redundant Pathways with Dishevelled 1 and 2 in Normal Cardiac Outflow Tract, Cochlea, and Neural Tube Development	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 th...
323030	Dynamics of adherens junctions in epithelial establishment, maintenance, and remodeling	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 eac...
323335	Long-term outcome of patients with asystole induced by head-up tilt test.	AIMS To analyse the long-term outcome of the largest reported cohort of patients presenting asystole during head-up tilt test. 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-s...
327319	ZINC 15 – Ligand Discovery for Everyone	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, ...
335029	Condensin-mediated remodeling of the mitotic chromatin landscape in fission yeast	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 an...
341324	Efficacy of the 6-month thrice-weekly regimen in the treatment of new sputum smear-positive pulmonary tuberculosis under clinical trial conditions.	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 ...
343052	Curcumin attenuates inflammatory response in IL-1beta-induced human synovial fibroblasts and collagen-induced arthritis in mouse model.	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...
344240	Loss of IGF-IEa or IGF-IEb impairs myogenic differentiation.	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 an...
350542	Antimicrobial peptide pleurocidin synergizes with antibiotics through hydroxyl radical formation and membrane damage, and exerts antibiofilm activity.	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. METHODS The interaction between pleuroci...
356218	Outcome of pregnancy in women with moderate or severe renal insufficiency.	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. METHODS We determined the frequency and types of maternal and obstetrical complicat...
364522	High-mobility group box-1 protein induces osteogenic phenotype changes in aortic valve interstitial cells.	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 inv...
365896	RiboSys, a high-resolution, quantitative approach to measure the in vivo kinetics of pre-mRNA splicing and 3'-end processing in Saccharomyces cerevisiae.	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 integra...
368506	Generation of mice with a conditional allele for the p75(NTR) neurotrophin receptor gene.	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 model...
371289	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 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...
374902	Universal voluntary HIV testing with immediate antiretroviral therapy as a strategy for elimination of HIV transmission: a mathematical model.	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....
380526	Common variants in DGKK are strongly associated with risk of hypospadias	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 addi...
381602	Neutrophils Suppress Intraluminal NK Cell-Mediated Tumor Cell Clearance and Enhance Extravasation of Disseminated Carcinoma Cells.	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 ...
393001	High Km soluble 5'-nucleotidase from human placenta. Properties and allosteric regulation by IMP and ATP.	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...
406733	Histones are incorporated in trans during reassembly of the yeast PHO5 promoter.	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 inacti...
409280	National study of physician awareness and adherence to cardiovascular disease prevention guidelines.	BACKGROUND Few data have evaluated physician adherence to cardiovascular disease (CVD) prevention guidelines according to physician specialty or patient characteristics, particularly gender. METHODS AND RESULTS An online study of 500 randomly selected physicians (300 primary care physicians, 100 obstetricians/gynecolog...
410286	TECHNICAL ADVANCE Floral dip: a simplified method for Agrobacterium-mediated	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 eliminat...
418246	Pathway connectivity and signaling coordination in the yeast stress-activated signaling network	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 interact...
427082	Premigratory and migratory neural crest cells are multipotent in vivo.	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...
427865	Implementing the ESHRE 'poor responder' criteria in research studies: methodological implications.	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 i...
432261	Generation of gene-edited rats by delivery of CRISPR/Cas9 protein and donor DNA into intact zygotes using electroporation	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 ssOD...
435529	Uridylation of miRNAs by HEN1 SUPPRESSOR1 in Arabidopsis	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...
437924	Pre-Exposure Prophylaxis to Prevent HIV Infection: Current Status, Future Opportunities and Challenges	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 dis...
439670	Prepregnancy BMI and the risk of gestational diabetes: a systematic review of the literature with meta-analysis.	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)...
456304	Multiple risk behaviour: increasing socio-economic gap over time?	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. METHODS Cross-sectional data from the Belgian Hea...
457630	Variations and Trends in Health Burden of Visual Impairment Due to Cataract: A Global Analysis.	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 catarac...
461550	Multiplex genome engineering using CRISPR/Cas systems.	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 differe...
463309	Transformation of intact yeast cells treated with alkali cations.	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 concent...
463533	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	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. METHODS A multi-stage stratified cluster sampling method ...
464511	Memory and Modularity in Cell-Fate Decision Making	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 generat...
469066	Lpd depletion reveals that SRF specifies radial versus tangential migration of pyramidal neurons	During corticogenesis, pyramidal neurons (∼80% 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 substr...
470625	Identification of p18 INK4c as a tumor suppressor gene in glioblastoma multiforme.	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 amplif...
471735	Two-stage control of an oxidative stress regulon: the Escherichia coli SoxR protein triggers redox-inducible expression of the soxS regulatory gene.	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 s...
471921	Air pollution and cardiovascular disease: a statement for healthcare professionals from the Expert Panel on Population and Prevention Science of the American Heart Association.	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 me...
474325	Non-invasive ventilation in chronic obstructive pulmonary disease patients: helmet versus facial mask	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 ...
485020	Case Management and Client Access to Health and Social Services in Outpatient Substance Abuse Treatment	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 k...
493346	Evidence that the Ipl1-Sli15 (Aurora Kinase-INCENP) Complex Promotes Chromosome Bi-orientation by Altering Kinetochore-Spindle Pole Connections	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 kinetoc...
496873	CRITICAL REVIEW Cutaneous Vasculitis Update: Diagnostic Criteria,	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 sta...
502591	E2F-dependent histone acetylation and recruitment of the Tip60 acetyltransferase complex to chromatin in late G1.	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 w...

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Dataset Card for BEIR Benchmark

scifact is one of the datasets from the Fact Checking task within BEIR, measuring scientific article retrieval for a given scientific claim.

Dataset Summary

BEIR is a heterogeneous benchmark built from 18 diverse datasets representing 9 information retrieval tasks.

Fact-checking: FEVER, Climate-FEVER, SciFact
Question-Answering: NQ, HotpotQA, FiQA-2018
Bio-Medical IR: TREC-COVID, BioASQ, NFCorpus
News Retrieval: TREC-NEWS, Robust04
Argument Retrieval: Touche-2020, ArguAna
Duplicate Question Retrieval: Quora, CqaDupstack
Citation-Prediction: SCIDOCS
Tweet Retrieval: Signal-1M
Entity Retrieval: DBPedia

Languages

All tasks are in English (en).

Dataset Structure

This dataset uses the standard BEIR retrieval layout and includes:

corpus: one row per document with _id, title, text
queries: one row per query with _id, title, text

Data Fields

_id (string): unique identifier
title (string): title (empty string when unavailable)
text (string): document/query text

Data Instances

A high level example of any BEIR dataset:

corpus = {
    "doc1" : {
        "title": "Albert Einstein",
        "text": "Albert Einstein was a German-born theoretical physicist. who developed the theory of relativity, \
                 one of the two pillars of modern physics (alongside quantum mechanics). His work is also known for \
                 its influence on the philosophy of science. He is best known to the general public for his massâ€“energy \
                 equivalence formula E = mc2, which has been dubbed 'the world's most famous equation'. He received the 1921 \
                 Nobel Prize in Physics 'for his services to theoretical physics, and especially for his discovery of the law \
                 of the photoelectric effect', a pivotal step in the development of quantum theory."
        },
    "doc2" : {
        "title": "", # Keep title an empty string if not present
        "text": "Wheat beer is a top-fermented beer which is brewed with a large proportion of wheat relative to the amount of \
                 malted barley. The two main varieties are German WeiÃŸbier and Belgian witbier; other types include Lambic (made\
                 with wild yeast), Berliner Weisse (a cloudy, sour beer), and Gose (a sour, salty beer)."
    },
}

queries = {
    "q1" : "Who developed the mass-energy equivalence formula?",
    "q2" : "Which beer is brewed with a large proportion of wheat?"
}

qrels = {
    "q1" : {"doc1": 1},
    "q2" : {"doc2": 1},
}

Scifact Data Splits

Subset	Split	Rows
corpus	corpus	5,183
queries	queries	1,109

BEIR Direct Download

You can also download BEIR datasets directly (without loading through Hugging Face datasets) using the links below.

Dataset	Website	BEIR-Name	Type	Queries	Corpus	Rel D/Q	Down-load	md5
MSMARCO	Homepage	`msmarco`	`train` `dev` `test`	6,980	8.84M	1.1	Link	`444067daf65d982533ea17ebd59501e4`
TREC-COVID	Homepage	`trec-covid`	`test`	50	171K	493.5	Link	`ce62140cb23feb9becf6270d0d1fe6d1`
NFCorpus	Homepage	`nfcorpus`	`train` `dev` `test`	323	3.6K	38.2	Link	`a89dba18a62ef92f7d323ec890a0d38d`
BioASQ	Homepage	`bioasq`	`train` `test`	500	14.91M	8.05	No	How to Reproduce?
NQ	Homepage	`nq`	`train` `test`	3,452	2.68M	1.2	Link	`d4d3d2e48787a744b6f6e691ff534307`
HotpotQA	Homepage	`hotpotqa`	`train` `dev` `test`	7,405	5.23M	2.0	Link	`f412724f78b0d91183a0e86805e16114`
FiQA-2018	Homepage	`fiqa`	`train` `dev` `test`	648	57K	2.6	Link	`17918ed23cd04fb15047f73e6c3bd9d9`
Signal-1M(RT)	Homepage	`signal1m`	`test`	97	2.86M	19.6	No	How to Reproduce?
TREC-NEWS	Homepage	`trec-news`	`test`	57	595K	19.6	No	How to Reproduce?
ArguAna	Homepage	`arguana`	`test`	1,406	8.67K	1.0	Link	`8ad3e3c2a5867cdced806d6503f29b99`
Touche-2020	Homepage	`webis-touche2020`	`test`	49	382K	19.0	Link	`46f650ba5a527fc69e0a6521c5a23563`
CQADupstack	Homepage	`cqadupstack`	`test`	13,145	457K	1.4	Link	`4e41456d7df8ee7760a7f866133bda78`
Quora	Homepage	`quora`	`dev` `test`	10,000	523K	1.6	Link	`18fb154900ba42a600f84b839c173167`
DBPedia	Homepage	`dbpedia-entity`	`dev` `test`	400	4.63M	38.2	Link	`c2a39eb420a3164af735795df012ac2c`
SCIDOCS	Homepage	`scidocs`	`test`	1,000	25K	4.9	Link	`38121350fc3a4d2f48850f6aff52e4a9`
FEVER	Homepage	`fever`	`train` `dev` `test`	6,666	5.42M	1.2	Link	`5a818580227bfb4b35bb6fa46d9b6c03`
Climate-FEVER	Homepage	`climate-fever`	`test`	1,535	5.42M	3.0	Link	`8b66f0a9126c521bae2bde127b4dc99d`
SciFact	Homepage	`scifact`	`train` `test`	300	5K	1.1	Link	`5f7d1de60b170fc8027bb7898e2efca1`
Robust04	Homepage	`robust04`	`test`	249	528K	69.9	No	How to Reproduce?

Citation Information

@inproceedings{
thakur2021beir,
title={{BEIR}: A Heterogeneous Benchmark for Zero-shot Evaluation of Information Retrieval Models},
author={Nandan Thakur and Nils Reimers and Andreas R{\"u}ckl{\'e} and Abhishek Srivastava and Iryna Gurevych},
booktitle={Thirty-fifth Conference on Neural Information Processing Systems Datasets and Benchmarks Track (Round 2)},
year={2021},
url={https://openreview.net/forum?id=wCu6T5xFjeJ}
}