Datasets:
Tasks:
Text Retrieval
Formats:
parquet
Sub-tasks:
document-retrieval
Languages:
English
Size:
1K - 10K
License:
_id stringlengths 4 9 | title stringlengths 7 300 | text stringlengths 353 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,... |
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 ... |
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... |
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... |
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... |
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... |
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 ... |
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... |
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 ... |
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... |
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... |
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... |
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... |
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... |
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... |
623486 | Centrifugal elutriation as a method for isolation of large numbers of functionally intact human peripheral blood monocytes. | 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... |
663464 | Age‐associated microRNA expression in human peripheral blood is associated with all‐cause mortality and age‐related traits | 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... |
712320 | Visualization of volatile substances in different organelles with an atmospheric-pressure mass microscope. | 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 sp... |
750781 | Coronary bypass graft patency in patients with diabetes in the Bypass Angioplasty Revascularization Investigation (BARI). | 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. METHODS AND RESULTS Among 1526 patients in BARI who underwent CABG as initial revascularization, 99 of... |
778436 | Negative effect of the transcriptional activator GAL4 | The yeast transcriptional activator GAL4 binds specific sites on DNA to activate transcription of adjacent genes1–5. 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... |
810480 | Localization of a gene for partial epilepsy to chromosome 10q | There is strong evidence for a genetic contribution to epilepsy, but it is commonly assumed that this genetic contribution is limited to ‘generalized’ epilepsies, and that most forms of ‘partial’ epilepsy are nongenetic. In a linkage analysis of a single family containing 11 affected individuals, we obtained strong evi... |
849771 | Impact of low alcohol verbal descriptors on perceived strength: An experimental study | 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 de... |
883747 | IL-1β, IL-4 and IL-12 control the fate of group 2 innate lymphoid cells in human airway inflammation in the lungs | 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 1β (IL-1β) directly activated human ILC2s and that IL-12 induced the conversion of these activated ILC2s into interferon-γ... |
885056 | Summary | 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 mo... |
947631 | Capsule endoscopy in acute upper gastrointestinal hemorrhage: a prospective cohort study. | 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. PATIENTS AND METHODS We evaluated adults with acute upper gastrointestinal hemorrhage presenting to the emergency departments of two academic cen... |
984825 | Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells | 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 p... |
1065627 | Microenvironment rigidity modulates responses to the HER2 receptor tyrosine kinase inhibitor lapatinib via YAP and TAZ transcription factors. | 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 t... |
1067605 | Effective population size and patterns of molecular evolution and variation | 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... |
1084062 | Activation of Serotonin 2C Receptors in Dopamine Neurons Inhibits Binge-like Eating in Mice | BACKGROUND Neural networks that regulate binge eating remain to be identified, and effective treatments for binge eating are limited. METHODS We combined neuroanatomic, pharmacologic, electrophysiological, Cre-lox, and chemogenetic approaches to investigate the functions of 5-hydroxytryptamine (5-HT) 2C receptor (5-HT2... |
1102268 | The Incidence and Repetition of Hospital-Treated Deliberate Self Harm: Findings from the World's First National Registry | 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 est... |
1145473 | Abnormalities in the myeloid progenitor compartment in Down syndrome fetal liver precede acquisition of GATA1 mutations. | 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... |
1220287 | FTY720 (fingolimod) is a neuroprotective and disease-modifying agent in cellular and mouse models of Huntington disease. | 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 eventu... |
1225513 | Specificity Residues Determine Binding Affinity for Two-Component Signal Transduction Systems | 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 reacti... |
1256116 | YEASTRACT: providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interface | 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 associatio... |
1281769 | Hyperactive Neuroendocrine Secretion Causes Size, Feeding, and Metabolic Defects of C. elegans Bardet-Biedl Syndrome Mutants | 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-... |
1287809 | Cost-effectiveness of 10-Year Risk Thresholds for Initiation of Statin Therapy for Primary Prevention of Cardiovascular Disease. | 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. OBJECTIVE To estimate the cost-effectiveness of various 10-year ASC... |
1320137 | The twin-arginine translocation (Tat) protein export pathway | 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 ma... |
1389264 | Combination inhibition of PI3K and mTORC1 yields durable remissions in orthotopic patient-derived xenografts of HER2-positive breast cancer brain metastases | 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 inhibit... |
1398021 | Familial hiatal hernia in a large five generation family confirming true autosomal dominant inheritance. | 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. METHODS All family members were interviewed and investigated by barium meal for ... |
1412089 | Diminished performance on neuropsychological testing in late life depression is correlated with microstructural white matter abnormalities. | 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 exami... |
1449692 | Gestational protein restriction affects trophoblast differentiation. | 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 t... |
1469751 | Aptamer-functionalized lipid nanoparticles targeting osteoblasts as a novel RNA interference–based bone anabolic strategy | 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, a... |
1495563 | [Clinical study on the therapeutic effect of acupuncture in the treatment of post-stroke depression]. | OBJECTIVE To observe the therapeutic effect of "Xingnao Kaiqiao Zhenfa" (Acupuncture Technique for Restoring Consciousness) in the treatment of post-stroke depression. 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 fema... |
1507222 | Increased gene expression of brown fat uncoupling protein (UCP)1 and skeletal muscle UCP2 and UCP3 in MAC16-induced cancer cachexia. | 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... |
1522336 | In vitro Anti-Tumor Effects of Statins on Head and Neck Squamous Cell Carcinoma: A Systematic Review | 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. METHODS Studies were gathered by sear... |
1605196 | Atg5-independent autophagy regulates mitochondrial clearance and is essential for iPSC reprogramming | 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 pro... |
1617327 | Bone progenitor dysfunction induces myelodysplasia and secondary leukemia | 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, b... |
1631583 | Getting started with yeast. | 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 g... |
1641873 | Meiosis in Drosophila: seeing is believing. | 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 ... |
1759213 | 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 | OBJECTIVE To examine the safety of using aliskiren combined with agents used to block the renin-angiotensin system. DESIGN Systematic review and meta-analysis of randomised controlled trials. DATA SOURCES Medline, Embase, the Cochrane Library, and two trial registries, published up to 7 May 2011. STUDY SELECTION Publis... |
1781626 | Socioeconomic factors, material inequalities, and perceived control in self-rated health: cross-sectional data from seven post-communist countries. | 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, ... |
1782201 | Integrin αvβ3/c-src “Oncogenic Unit” Promotes Anchorage-independence and Tumor Progression | 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 o... |
1791637 | Genomewide Analysis of PRC1 and PRC2 Occupancy Identifies Two Classes of Bivalent Domains | 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 m... |
1871230 | Getting to the site of inflammation: the leukocyte adhesion cascade updated | 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 par... |
1887056 | Increased stress-induced inflammatory responses in male patients with major depression and increased early life stress. | OBJECTIVE The authors sought to determine innate immune system activation following psychosocial stress in patients with major depression and increased early life stress. METHOD Plasma interleukin (IL)-6, lymphocyte subsets, and DNA binding of nuclear factor (NF)-kB in peripheral blood mononuclear cells were compared i... |
1910120 | Lpcat3-dependent production of arachidonoyl phospholipids is a key determinant of triglyceride secretion | 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) secr... |
1933281 | CD169+ MACROPHAGES PRESENT LIPID ANTIGENS TO MEDIATE EARLY ACTIVATION OF INVARIANT NKT CELLS IN LYMPH NODES | 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 activa... |
1958440 | Human chorionic gonadotropin levels in maternal blood in late pregnancy: relation to birthweight, sex and condition of the infant at birth. | 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 fe... |
2015929 | Astrocytes from Familial and Sporadic ALS Patients are Toxic to Motor Neurons | 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 sup... |
2060137 | Cardiac myocyte remodeling mediated by N-cadherin-dependent mechanosensing. | 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... |
2130391 | Cancer-associated adipocytes exhibit an activated phenotype and contribute to breast cancer invasion. | 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 ... |
2140497 | Independent Association of Lobular Involution and Mammographic Breast Density With Breast Cancer Risk | 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. METHODS To evaluate whether lobular involution and MBD are independently associated with breast cancer risk in... |
2159648 | Bone loss and vascular calcification: A bi-directional interplay? | 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 initiatio... |
2192419 | Local proliferation dominates lesional macrophage accumulation in atherosclerosis | 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, howe... |
2236768 | Infection-induced NETosis is a dynamic process involving neutrophil multitasking in vivo | 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 v... |
2242416 | Swim training suppresses tumor growth in mice. | 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... |
2344892 | Human milk proresolving mediators stimulate resolution of acute inflammation | 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 reduce... |
2356950 | Epigenetic regulation of miR-184 by MBD1 governs neural stem cell proliferation and differentiation. | 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 reg... |
2359152 | Landscape of genetic lesions in 944 patients with myelodysplastic syndromes | 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/... |
2405259 | Tet2 is required to resolve inflammation by recruiting Hdac2 to specifically repress IL-6 | 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... |
2437807 | In vitro differentiation of transplantable neural precursors from human embryonic stem cells | 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 a... |
2492146 | Comparative Safety of Targeted Therapies for Metastatic Colorectal Cancer between Elderly and Younger Patients: a Study Using the International Pharmacovigilance Database | 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 Vigi... |
2566674 | Ribose 2′-O-methylation provides a molecular signature for the distinction of self and non-self mRNA dependent on the RNA sensor Mda5 | The 5′ cap structures of higher eukaryote mRNAs have ribose 2′-O-methylation. Likewise, many viruses that replicate in the cytoplasm of eukaryotes have evolved 2′-O-methyltransferases to autonomously modify their mRNAs. However, a defined biological role for 2′-O-methylation of mRNA remains elusive. Here we show that 2... |
2576811 | Junctional actin assembly is mediated by Formin-like 2 downstream of Rac1 | 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 ... |
2587396 | Association of Blood Monocyte and Platelet Markers with Carotid Artery Characteristics: The Atherosclerosis Risk in Communities Carotid MRI Study | 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 participan... |
2601135 | 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 | 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 stud... |
2613411 | Cell cycle, CDKs and cancer: a changing paradigm | 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... |
2679511 | The BLM helicase contributes to telomere maintenance through processing of late-replicating intermediate structures | 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 replicatio... |
2727303 | Microtubule-associated histone deacetylase 6 supports the calcium store sensor STIM1 in mediating malignant cell behaviors. | 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-operat... |
2754534 | DNA methylation status predicts cell type-specific enhancer activity. | 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 n... |
2762601 | Reflecting on 25 years with MYC | 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,... |
2831620 | Protein Lysine Acetylated/Deacetylated Enzymes and the Metabolism-Related Diseases | 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/lysi... |
2842550 | Pharmacodynamics and pharmacokinetics of eptifibatide in patients with acute coronary syndromes: prospective analysis from PURSUIT. | 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 ... |
2904102 | Characterization of biochemical properties of Bacillus subtilis RecQ helicase. | 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... |
2988714 | Coupled local translation and degradation regulate growth cone collapse | 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 protei... |
3034412 | Calcium absorption varies within the reference range for serum 25-hydroxyvitamin D. | 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. OBJECTIVE To quantify calcium absorption at two levels of vitamin D repletion, using pharmacokinetic methods and commercially ... |
3113630 | Nuclear accumulation of HDAC4 in ATM deficiency promotes neurodegeneration in ataxia-telangiectasia | 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 enha... |
3140772 | Neuronal circuitry mechanism regulating adult quiescent neural stem cell fate decision | 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 loc... |
3152612 | Identification and characterization of a novel monocyte/macrophage differentiation-dependent gene that is responsive to lipopolysaccharide, ceramide, and lysophosphatidylcholine. | 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 downregul... |
3155731 | Tissue-resident memory T cells: local specialists in immune defence | 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... |
3173489 | Defective replication stress response inhibits lymphomagenesis and impairs lymphocyte reconstitution | 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 b... |
3230361 | Generation and characterization of methyl-lysine histone antibodies. | 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 thei... |
3285059 | Lack of Skeletal Muscle IL-6 Affects Pyruvate Dehydrogenase Activity at Rest and during Prolonged Exercise | 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 mus... |
3315558 | Genetic analysis of human obesity in an Italian sample. | 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 fa... |
3329824 | Incidence and risk of central nervous system metastases as site of first recurrence in patients with HER2-positive breast cancer treated with adjuvant trastuzumab. | 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 tra... |
3353748 | Metaplasia and transdifferentiation: from pure biology to the clinic | 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 manipu... |
3360428 | Multipoint Kras oncogene mutations potentially indicate mucinous carcinoma on the entire spectrum of mucinous ovarian neoplasms | 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... |
3413083 | Patterns of chlamydia testing in different settings and implications for wider STI diagnosis and care: a probability sample survey of the British population | 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 o... |
End of preview. Expand in Data Studio
scifact (Decontaminated)
A decontaminated version of the scifact dataset from the BEIR benchmark, with samples found in the mgte-en pre-training dataset removed.
Decontamination methodology
Contamination was detected using a two-pass approach against the full mgte-en dataset (484 GB, 1,235 parquet files):
Pass 1: Exact hash matching
All texts (queries and corpus documents) were normalized (lowercased, unicode NFKD, whitespace collapsed) and hashed with xxHash-64. The same normalization + hashing was applied to every query and document field in mgte-en. Any sample whose hash appeared in mgte-en was flagged as contaminated.
Pass 2: 13-gram containment (GPT-3 style)
Following the methodology introduced in the GPT-3 paper (Brown et al., 2020), word-level 13-grams were extracted from all remaining samples. For each sample, containment was computed as:
containment = |ngrams_in_sample ∩ ngrams_in_mgte| / |ngrams_in_sample|
Samples with containment >= 0.5 were flagged as near-duplicates.
Qrels filtering
Relevance judgments (qrels) referencing any removed query or corpus document were also removed.
Decontamination results
| Component | Original | Clean | Removed |
|---|---|---|---|
| Corpus | 5,183 | 858 | 4,325 |
| Queries | 1,109 | 391 | 718 |
Qrels per split
| Split | Original | Clean | Removed |
|---|---|---|---|
| test | 339 | 43 | 296 |
| train | 919 | 20 | 899 |
Usage
from datasets import load_dataset
corpus = load_dataset("lightonai/scifact-decontaminated", "corpus", split="corpus")
queries = load_dataset("lightonai/scifact-decontaminated", "queries", split="queries")
Citation
Please cite the original BEIR benchmark:
@inproceedings{thakur2021beir,
title={BEIR: A Heterogeneous Benchmark for Zero-shot Evaluation of Information Retrieval Models},
author={Thakur, Nandan and Reimers, Nils and Rücklé, Andreas and Srivastava, Abhishek and Gurevych, Irena},
booktitle={NeurIPS Datasets and Benchmarks},
year={2021}
}
License
MIT (same as original BEIR)
- Downloads last month
- 10