Datasets:

BeIR
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trec-covid

_id stringlengths 8 8	title stringlengths 0 1.19k	text stringlengths 0 122k
ug7v899j	Clinical features of culture-proven Mycoplasma pneumoniae infections at King Abdulaziz University Hospital, Jeddah, Saudi Arabia	OBJECTIVE: This retrospective chart review describes the epidemiology and clinical features of 40 patients with culture-proven Mycoplasma pneumoniae infections at King Abdulaziz University Hospital, Jeddah, Saudi Arabia. METHODS: Patients with positive M. pneumoniae cultures from respiratory specimens from January 1997...
02tnwd4m	Nitric oxide: a pro-inflammatory mediator in lung disease?	Inflammatory diseases of the respiratory tract are commonly associated with elevated production of nitric oxide (NO•) and increased indices of NO• -dependent oxidative stress. Although NO• is known to have anti-microbial, anti-inflammatory and anti-oxidant properties, various lines of evidence support the contribution ...
ejv2xln0	Surfactant protein-D and pulmonary host defense	Surfactant protein-D (SP-D) participates in the innate response to inhaled microorganisms and organic antigens, and contributes to immune and inflammatory regulation within the lung. SP-D is synthesized and secreted by alveolar and bronchiolar epithelial cells, but is also expressed by epithelial cells lining various e...
2b73a28n	Role of endothelin-1 in lung disease	Endothelin-1 (ET-1) is a 21 amino acid peptide with diverse biological activity that has been implicated in numerous diseases. ET-1 is a potent mitogen regulator of smooth muscle tone, and inflammatory mediator that may play a key role in diseases of the airways, pulmonary circulation, and inflammatory lung diseases, b...
9785vg6d	Gene expression in epithelial cells in response to pneumovirus infection	Respiratory syncytial virus (RSV) and pneumonia virus of mice (PVM) are viruses of the family Paramyxoviridae, subfamily pneumovirus, which cause clinically important respiratory infections in humans and rodents, respectively. The respiratory epithelial target cells respond to viral infection with specific alterations ...
zjufx4fo	Sequence requirements for RNA strand transfer during nidovirus discontinuous subgenomic RNA synthesis	Nidovirus subgenomic mRNAs contain a leader sequence derived from the 5′ end of the genome fused to different sequences (‘bodies’) derived from the 3′ end. Their generation involves a unique mechanism of discontinuous subgenomic RNA synthesis that resembles copy-choice RNA recombination. During this process, the nascen...
5yhe786e	Debate: Transfusing to normal haemoglobin levels will not improve outcome	Recent evidence suggests that critically ill patients are able to tolerate lower levels of haemoglobin than was previously believed. It is our goal to show that transfusing to a level of 100 g/l does not improve mortality and other clinically important outcomes in a critical care setting. Although many questions remain...
8zchiykl	The 21st International Symposium on Intensive Care and Emergency Medicine, Brussels, Belgium, 20-23 March 2001	The 21st International Symposium on Intensive Care and Emergency Medicine was dominated by the results of recent clinical trials in sepsis and acute respiratory distress syndrome (ARDS). The promise of extracorporeal liver replacement therapy and noninvasive ventilation were other areas of interest. Ethical issues also...
8qnrcgnk	Heme oxygenase-1 and carbon monoxide in pulmonary medicine	Heme oxygenase-1 (HO-1), an inducible stress protein, confers cytoprotection against oxidative stress in vitro and in vivo. In addition to its physiological role in heme degradation, HO-1 may influence a number of cellular processes, including growth, inflammation, and apoptosis. By virtue of anti-inflammatory effects,...
jg13scgo	Technical Description of RODS: A Real-time Public Health Surveillance System	This report describes the design and implementation of the Real-time Outbreak and Disease Surveillance (RODS) system, a computer-based public health surveillance system for early detection of disease outbreaks. Hospitals send RODS data from clinical encounters over virtual private networks and leased lines using the He...
5tkvsudh	Conservation of polyamine regulation by translational frameshifting from yeast to mammals	Regulation of ornithine decarboxylase in vertebrates involves a negative feedback mechanism requiring the protein antizyme. Here we show that a similar mechanism exists in the fission yeast Schizosaccharomyces pombe. The expression of mammalian antizyme genes requires a specific +1 translational frameshift. The efficie...
6lvn10f4	Heterogeneous nuclear ribonucleoprotein A1 regulates RNA synthesis of a cytoplasmic virus	Heterogeneous nuclear ribonucleoprotein (hnRNP A1) is involved in pre-mRNA splicing in the nucleus and translational regulation in the cytoplasm. In the present study, we demonstrate that hnRNP A1 also participates in the transcription and replication of a cytoplasmic RNA virus, mouse hepatitis virus (MHV). Overexpress...
tvxpckxo	A Method to Identify p62's UBA Domain Interacting Proteins	The UBA domain is a conserved sequence motif among polyubiquitin binding proteins. For the first time, we demonstrate a systematic, high throughput approach to identification of UBA domain-interacting proteins from a proteome-wide perspective. Using the rabbit reticulocyte lysate in vitro expression cloning system, we ...
mcuixluu	Vaccinia virus infection disrupts microtubule organization and centrosome function	We examined the role of the microtubule cytoskeleton during vaccinia virus infection. We found that newly assembled virus particles accumulate in the vicinity of the microtubule-organizing centre in a microtubule- and dynein–dynactin complex-dependent fashion. Microtubules are required for efficient intracellular matur...
6iu1dtyl	The site of origin of the 1918 influenza pandemic and its public health implications
t35n7bk9	Multi-faceted, multi-versatile microarray: simultaneous detection of many viruses and their expression profiles	There are hundreds of viruses that infect different human organs and cause diseases. Some fatal emerging viral infections have become serious public health issues worldwide. Early diagnosis and subsequent treatment are therefore essential for fighting viral infections. Current diagnostic techniques frequently employ po...
eiqypt0m	Herpes simplex virus type 1 and normal protein permeability in the lungs of critically ill patients: a case for low pathogenicity?	INTRODUCTION: The pathogenicity of late respiratory infections with herpes simplex virus type 1 (HSV-1) in the critically ill is unclear. METHODS: In four critically ill patients with persistent pulmonary infiltrates of unknown origin and isolation of HSV-1 from tracheal aspirate or bronchoalveolar lavage fluid, at 7 (...
sgmk96vr	Logistics of community smallpox control through contact tracing and ring vaccination: a stochastic network model	BACKGROUND: Previous smallpox ring vaccination models based on contact tracing over a network suggest that ring vaccination would be effective, but have not explicitly included response logistics and limited numbers of vaccinators. METHODS: We developed a continuous-time stochastic simulation of smallpox transmission, ...
di0fcy0j	Protection of pulmonary epithelial cells from oxidative stress by hMYH adenine glycosylase	BACKGROUND: Oxygen toxicity is a major cause of lung injury. The base excision repair pathway is one of the most important cellular protection mechanisms that responds to oxidative DNA damage. Lesion-specific DNA repair enzymes include hOgg1, hMYH, hNTH and hMTH. METHODS: The above lesion-specific DNA repair enzymes we...
4k8f7ou1	Bioinformatic mapping of AlkB homology domains in viruses	BACKGROUND: AlkB-like proteins are members of the 2-oxoglutarate- and Fe(II)-dependent oxygenase superfamily. In Escherichia coli the protein protects RNA and DNA against damage from methylating agents. 1-methyladenine and 3-methylcytosine are repaired by oxidative demethylation and direct reversal of the methylated ba...
wnnsmx60	Managing emerging infectious diseases: Is a federal system an impediment to effective laws?	In the 1980's and 1990's HIV/AIDS was the emerging infectious disease. In 2003–2004 we saw the emergence of SARS, Avian influenza and Anthrax in a man made form used for bioterrorism. Emergency powers legislation in Australia is a patchwork of Commonwealth quarantine laws and State and Territory based emergency powers ...
gdsfkw1b	Protein secretion in Lactococcus lactis : an efficient way to increase the overall heterologous protein production	Lactococcus lactis, the model lactic acid bacterium (LAB), is a food grade and well-characterized Gram positive bacterium. It is a good candidate for heterologous protein delivery in foodstuff or in the digestive tract. L. lactis can also be used as a protein producer in fermentor. Many heterologous proteins have alrea...
yba7mdtb	Detection and characterization of horizontal transfers in prokaryotes using genomic signature	Horizontal DNA transfer is an important factor of evolution and participates in biological diversity. Unfortunately, the location and length of horizontal transfers (HTs) are known for very few species. The usage of short oligonucleotides in a sequence (the so-called genomic signature) has been shown to be species-spec...
bbvxu8op	Comparisons of substitution, insertion and deletion probes for resequencing and mutational analysis using oligonucleotide microarrays	Although oligonucleotide probes complementary to single nucleotide substitutions are commonly used in microarray-based screens for genetic variation, little is known about the hybridization properties of probes complementary to small insertions and deletions. It is necessary to define the hybridization properties of th...
e62cfqt7	A Gene Encoding Sialic-Acid-Specific 9-O-Acetylesterase Found in Human Adult Testis	Using differential display RT-PCR, we identified a gene of 2750 bp from human adult testis, named H-Lse, which encoded a putative protein of 523 amino acids and molecular weight of 58 kd with structural characteristics similar to that of mouse lysosome sialic-acid-specific 9-O-acetylesterase. Northern blot analysis sho...
4cvy9u28	The role of mast cells in the pathogenesis of pain in chronic pancreatitis	BACKGROUND: The biological basis of pain in chronic pancreatitis is poorly understood. Mast cells have been implicated in the pathogenesis of pain in other conditions. We hypothesized that mast cells play a role in the pain of chronic pancreatitis. We examined the association of pain with mast cells in autopsy specimen...
zowp10ts	Recombination Every Day: Abundant Recombination in a Virus during a Single Multi-Cellular Host Infection	Viral recombination can dramatically impact evolution and epidemiology. In viruses, the recombination rate depends on the frequency of genetic exchange between different viral genomes within an infected host cell and on the frequency at which such co-infections occur. While the recombination rate has been recently eval...
5dk231qs	Torsional restraint: a new twist on frameshifting pseudoknots	mRNA pseudoknots have a stimulatory function in programmed −1 ribosomal frameshifting (−1 PRF). Though we previously presented a model for how mRNA pseudoknots might activate the mechanism for −1 PRF, it did not address the question of the role that they may play in positioning the mRNA relative to the ribosome in this...
snqdma0s	Correcting errors in synthetic DNA through consensus shuffling	Although efficient methods exist to assemble synthetic oligonucleotides into genes and genomes, these suffer from the presence of 1–3 random errors/kb of DNA. Here, we introduce a new method termed consensus shuffling and demonstrate its use to significantly reduce random errors in synthetic DNA. In this method, errors...
1pq6dkl5	Towards standardization of RNA quality assessment using user-independent classifiers of microcapillary electrophoresis traces	While it is universally accepted that intact RNA constitutes the best representation of the steady-state of transcription, there is no gold standard to define RNA quality prior to gene expression analysis. In this report, we evaluated the reliability of conventional methods for RNA quality assessment including UV spect...
754nln40	Factors affecting translation at the programmed −1 ribosomal frameshifting site of Cocksfoot mottle virus RNA in vivo	The ratio between proteins P27 and replicase of Cocksfoot mottle virus (CfMV) is regulated via a −1 programmed ribosomal frameshift (−1 PRF). A minimal frameshift signal with a slippery U UUA AAC heptamer and a downstream stem–loop structure was inserted into a dual reporter vector and directed −1 PRF with an efficienc...
p34ezktf	Australian public health policy in 2003 – 2004	In Australia, compared with other developed countries the many and varied programs which comprise public health have continued to be funded poorly and unsystematically, particularly given the amount of publicly voiced political support. In 2003, the major public health policy developments in communicable disease contro...
l3z27806	GIDEON: a comprehensive Web-based resource for geographic medicine	GIDEON (Global Infectious Diseases and Epidemiology Network) is a web-based computer program designed for decision support and informatics in the field of Geographic Medicine. The first of four interactive modules generates a ranked differential diagnosis based on patient signs, symptoms, exposure history and country o...
yz2wbpuu	Globalization and Health	This debut editorial of Globalization and Health introduces the journal, briefly delineating its goals and objectives and outlines its scope of subject matter. 'Open Access' publishing is expected to become an increasingly important format for peer reviewed academic journals and that Globalization and Health is 'Open A...
kvhoa2se	The 'polysemous' codon--a codon with multiple amino acid assignment caused by dual specificity of tRNA identity.	In some Candida species, the universal CUG leucine codon is translated as serine. However, in most cases, the serine tRNAs responsible for this non-universal decoding (tRNA(Ser)CAG) accept in vitro not only serine, but also, to some extent, leucine. Nucleotide replacement experiments indicated that m1G37 is critical fo...
cgl34ykt	A universal BMV-based RNA recombination system—how to search for general rules in RNA recombination	At present, there is no doubt that RNA recombination is one of the major factors responsible for the generation of new RNA viruses and retroviruses. Numerous experimental systems have been created to investigate this complex phenomenon. Consequently, specific RNA structural motifs mediating recombination have been iden...
ajlctjeb	Neutrophil elastase, an acid-independent serine protease, facilitates reovirus uncoating and infection in U937 promonocyte cells	BACKGROUND: Mammalian reoviruses naturally infect their hosts through the enteric and respiratory tracts. During enteric infections, proteolysis of the reovirus outer capsid protein σ3 is mediated by pancreatic serine proteases. In contrast, the proteases critical for reovirus replication in the lung are unknown. Neutr...
cl9gpt9w	The influence of locked nucleic acid residues on the thermodynamic properties of 2′-O-methyl RNA/RNA heteroduplexes	The influence of locked nucleic acid (LNA) residues on the thermodynamic properties of 2′-O-methyl RNA/RNA heteroduplexes is reported. Optical melting studies indicate that LNA incorporated into an otherwise 2′-O-methyl RNA oligonucleotide usually, but not always, enhances the stabilities of complementary duplexes form...
t40ybhgb	Draft versus finished sequence data for DNA and protein diagnostic signature development	Sequencing pathogen genomes is costly, demanding careful allocation of limited sequencing resources. We built a computational Sequencing Analysis Pipeline (SAP) to guide decisions regarding the amount of genomic sequencing necessary to develop high-quality diagnostic DNA and protein signatures. SAP uses simulations to ...
zwbc7nnn	An ontology for immune epitopes: application to the design of a broad scope database of immune reactivities	BACKGROUND: Epitopes can be defined as the molecular structures bound by specific receptors, which are recognized during immune responses. The Immune Epitope Database and Analysis Resource (IEDB) project will catalog and organize information regarding antibody and T cell epitopes from infectious pathogens, experimental...
1r65yam5	Evaluation of potential reference genes in real-time RT-PCR studies of Atlantic salmon	BACKGROUND: Salmonid fishes are among the most widely studied model fish species but reports on systematic evaluation of reference genes in qRT-PCR studies is lacking. RESULTS: The stability of six potential reference genes was examined in eight tissues of Atlantic salmon (Salmo salar), to determine the most suitable g...
oa4lzkru	Fierce creatures	Zoonoses, diseases that jump from animals to humans, are a growing health problem around the world. Understanding their causes and their effects on humans have therefore become an important topic for global public health
qva0jt86	Relevance of human metapneumovirus in exacerbations of COPD	BACKGROUND AND METHODS: Human metapneumovirus (hMPV) is a recently discovered respiratory virus associated with bronchiolitis, pneumonia, croup and exacerbations of asthma. Since respiratory viruses are frequently detected in patients with acute exacerbations of COPD (AE-COPD) it was our aim to investigate the frequenc...
vw8xjo9t	Bioethical Implications of Globalization: An International Consortium Project of the European Commission	The BIG project looks at some of the ethical concerns surrounding globalization and health.
bnnl700a	Public awareness of risk factors for cancer among the Japanese general population: A population-based survey	BACKGROUND: The present study aimed to provide information on awareness of the attributable fraction of cancer causes among the Japanese general population. METHODS: A nationwide representative sample of 2,000 Japanese aged 20 or older was asked about their perception and level of concern about various environmental an...
m71xkuo9	Sequence specific visual detection of LAMP reactions by addition of cationic polymers	BACKGROUND: Development of a practical gene point-of-care testing device (g-POCT device) requires innovative detection methods for demonstrating the results of the gene amplification reaction without the use of expensive equipment. We have studied a new method for the sequence-specific visual detection of minute amount...
s64v656n	Injection drug use and HIV/AIDS in China: Review of current situation, prevention and policy implications	Illicit drug abuse and HIV/AIDS have increased rapidly in the past 10 to 20 years in China. This paper reviews drug abuse in China, the HIV/AIDS epidemic and its association with injection drug use (IDU), and Chinese policies on illicit drug abuse and prevention of HIV/AIDS based on published literature and unpublished...
oluq7v0h	Development of a humanized monoclonal antibody with therapeutic potential against West Nile virus	Neutralization of West Nile virus (WNV) in vivo correlates with the development of an antibody response against the viral envelope (E) protein. Using random mutagenesis and yeast surface display, we defined individual contact residues of 14 newly generated monoclonal antibodies against domain III of the WNV E protein. ...
tw6wusxe	Local public health workers' perceptions toward responding to an influenza pandemic	BACKGROUND: Current national preparedness plans require local health departments to play an integral role in responding to an influenza pandemic, a major public health threat that the World Health Organization has described as "inevitable and possibly imminent". To understand local public health workers' perceptions to...
58czem0j	On pandemics and the duty to care: whose duty? who cares?	BACKGROUND: As a number of commentators have noted, SARS exposed the vulnerabilities of our health care systems and governance structures. Health care professionals (HCPs) and hospital systems that bore the brunt of the SARS outbreak continue to struggle with the aftermath of the crisis. Indeed, HCPs – both in clinical...
x7wg7e9s	Epicatechins Purified from Green Tea (Camellia sinensis) Differentially Suppress Growth of Gender-Dependent Human Cancer Cell Lines	The anticancer potential of catechins derived from green tea is not well understood, in part because catechin-related growth suppression and/or apoptosis appears to vary with the type and stage of malignancy as well as with the type of catechin. This in vitro study examined the biological effects of epicatechin (EC), e...
utglk4af	Markers of exacerbation severity in chronic obstructive pulmonary disease	BACKGROUND: Patients with chronic obstructive pulmonary disease (COPD) can experience 'exacerbations' of their conditions. An exacerbation is an event defined in terms of subjective descriptors or symptoms, namely dyspnoea, cough and sputum that worsen sufficiently to warrant a change in medical management. There is a ...
i5fcedbo	Scientific Abstracts
bjjft7ut	Society of General Internal Medicine: 28th Annual Meeting New Orleans, LA May 11–14, 2005: Out of Chaos: The Critical Role of Generalists, ABSTRACTS OF SUBMISSIONS ACCEPTED FOR PRESENTATIOIN
urk7fe34	CLINICAL VIGNETTES
u09rn09u	ABSTRACTS
kvztcwu2	Clinical Vignettes
9r62ffew	Differentially profiling the low-expression transcriptomes of human hepatoma using a novel SSH/microarray approach	BACKGROUND: The main limitation in performing genome-wide gene-expression profiling is the assay of low-expression genes. Approaches with high throughput and high sensitivity for assaying low-expression transcripts are urgently needed for functional genomic studies. Combination of the suppressive subtractive hybridizat...
d3cko4j2	From Functional Genomics to Functional Immunomics: New Challenges, Old Problems, Big Rewards	The development of DNA microarray technology a decade ago led to the establishment of functional genomics as one of the most active and successful scientific disciplines today. With the ongoing development of immunomic microarray technology—a spatially addressable, large-scale technology for measurement of specific imm...
hwlvk68z	Transmission patterns of smallpox: systematic review of natural outbreaks in Europe and North America since World War II	BACKGROUND: Because smallpox (variola major) may be used as a biological weapon, we reviewed outbreaks in post-World War II Europe and North America in order to understand smallpox transmission patterns. METHODS: A systematic review was used to identify papers from the National Library of Medicine, Embase, Biosis, Coch...
w5fxen70	Reliability of case definitions for public health surveillance assessed by Round-Robin test methodology	BACKGROUND: Case definitions have been recognized to be important elements of public health surveillance systems. They are to assure comparability and consistency of surveillance data and have crucial impact on the sensitivity and the positive predictive value of a surveillance system. The reliability of case definitio...
mq6bterc	Ventilator associated pneumonia and infection control	Ventilator associated pneumonia (VAP) is the leading cause of morbidity and mortality in intensive care units. The incidence of VAP varies from 7% to 70% in different studies and the mortality rates are 20–75% according to the study population. Aspiration of colonized pathogenic microorganisms on the oropharynx and gas...
yxhk1qm3	Sentinel surveillance for human enterovirus 71 in Sarawak, Malaysia: lessons from the first 7 years	BACKGROUND: A major outbreak of human enterovirus 71-associated hand, foot and mouth disease in Sarawak in 1997 marked the beginning of a series of outbreaks in the Asia Pacific region. Some of these outbreaks had unusually high numbers of fatalities and this generated much fear and anxiety in the region. METHODS: We e...
bpnfupzv	26th International Symposium on Intensive Care and Emergency Medicine, 21–24 March 2006, Brussels, Belgium
j3p1u80n	Model-Based Design of Growth-Attenuated Viruses	Live-virus vaccines activate both humoral and cell-mediated immunity, require only a single boosting, and generally provide longer immune protection than killed or subunit vaccines. However, growth of live-virus vaccines must be attenuated to minimize their potential pathogenic effects, and mechanisms of attenuation by...
5eqdrd52	Delivery Systems for the Direct Application of siRNAs to Induce RNA Interference (RNAi) In Vivo	RNA interference (RNAi) is a powerful method for specific gene silencing which may also lead to promising novel therapeutic strategies. It is mediated through small interfering RNAs (siRNAs) which sequence-specifically trigger the cleavage and subsequent degradation of their target mRNA. One critical factor is the abil...
p5jtwb3l	Electrochemical Molecular Analysis Without Nucleic Acid Amplification	Electrochemical biosensors have revolutionized glucose monitoring but have not yet fulfilled their promise of a low cost, direct detection replacement for genetic amplification tests such as PCR [K. Kerman, M. Kobayashi, E. Tamiya, Recent trends in electro-chemical DNA biosensor technology, Meas. Sci. Technol. 15 (2004...
c5hrdrtu	Identification of new participants in the rainbow trout (Oncorhynchus mykiss) oocyte maturation and ovulation processes using cDNA microarrays	BACKGROUND: The hormonal control of oocyte maturation and ovulation as well as the molecular mechanisms of nuclear maturation have been thoroughly studied in fish. In contrast, the other molecular events occurring in the ovary during post-vitellogenesis have received far less attention. METHODS: Nylon microarrays displ...
pk7pnmlo	An object simulation model for modeling hypothetical disease epidemics – EpiFlex	BACKGROUND: EpiFlex is a flexible, easy to use computer model for a single computer, intended to be operated by one user who need not be an expert. Its purpose is to study in-silico the epidemic behavior of a wide variety of diseases, both known and theoretical, by simulating their spread at the level of individuals co...
nhb4o6ty	Multiplexed Genetic Analysis Using an Expanded Genetic Alphabet	BACKGROUND: All states require some kind of testing for newborns, but the policies are far from standardized. In some states, newborn screening may include genetic tests for a wide range of targets, but the costs and complexities of the newer genetic tests inhibit expansion of newborn screening. We describe the develop...
xgwbl8em	Antisense-induced ribosomal frameshifting	Programmed ribosomal frameshifting provides a mechanism to decode information located in two overlapping reading frames by diverting a proportion of translating ribosomes into a second open reading frame (ORF). The result is the production of two proteins: the product of standard translation from ORF1 and an ORF1–ORF2 ...
69gftii4	The gene of an archaeal α-l-fucosidase is expressed by translational frameshifting	The standard rules of genetic translational decoding are altered in specific genes by different events that are globally termed recoding. In Archaea recoding has been unequivocally determined so far only for termination codon readthrough events. We study here the mechanism of expression of a gene encoding for a α-l-fuc...
vefs1h6o	Role of RNA helicases in HIV-1 replication	Viruses are replication competent genomes which are relatively gene-poor. Even the largest viruses (i.e. Herpesviruses) encode only slightly >200 open reading frames (ORFs). However, because viruses replicate obligatorily inside cells, and considering that evolution may be driven by a principle of economy of scale, it ...
1ypgij14	MIMOX: a web tool for phage display based epitope mapping	BACKGROUND: Phage display is widely used in basic research such as the exploration of protein-protein interaction sites and networks, and applied research such as the development of new drugs, vaccines, and diagnostics. It has also become a promising method for epitope mapping. Research on new algorithms that assist an...
1axxmq84	Endogenous Cell Repair of Chronic Demyelination	In multiple sclerosis lesions, remyelination typically fails with repeated or chronic demyelinating episodes and results in neurologic disability. Acute demyelination models in rodents typically exhibit robust spontaneous remyelination that prevents appropriate evaluation of strategies for improving conditions of insuf...
cxzlmfst	Automated identification of multiple micro-organisms from resequencing DNA microarrays	There is an increasing recognition that detailed nucleic acid sequence information will be useful and even required in the diagnosis, treatment and surveillance of many significant pathogens. Because generating detailed information about pathogens leads to significantly larger amounts of data, it is necessary to develo...
br2p09pg	Molecular dynamics simulations of human [Formula: see text]: the role of modified bases in mRNA recognition	Accuracy in translation of the genetic code into proteins depends upon correct tRNA–mRNA recognition in the context of the ribosome. In human [Formula: see text] three modified bases are present in the anticodon stem–loop—2-methylthio-N6-threonylcarbamoyladenosine at position 37 (ms(2)t(6)A37), 5-methoxycarbonylmethyl-...
kt9pmfdr	A novel endonuclease IV post-PCR genotyping system	Here we describe a novel endonuclease IV (Endo IV) based assay utilizing a substrate that mimics the abasic lesions that normally occur in double-stranded DNA. The three component substrate is characterized by single-stranded DNA target, an oligonucleotide probe, separated from a helper oligonucleotide by a one base ga...
5fl0rk90	Pandemic influenza preparedness: an ethical framework to guide decision-making	BACKGROUND: Planning for the next pandemic influenza outbreak is underway in hospitals across the world. The global SARS experience has taught us that ethical frameworks to guide decision-making may help to reduce collateral damage and increase trust and solidarity within and between health care organisations. Good pan...
kuf3ssdb	Open lung biopsy in early-stage acute respiratory distress syndrome	INTRODUCTION: Acute respiratory distress syndrome (ARDS) has heterogeneous etiologies, rapid progressive change and a high mortality rate. To improve the outcome of ARDS, accurate diagnosis is essential to the application of effective early treatment. The present study investigated the clinical effects and safety of op...
rr2wwvue	Association and Host Selectivity in Multi-Host Pathogens	The distribution of multi-host pathogens over their host range conditions their population dynamics and structure. Also, host co-infection by different pathogens may have important consequences for the evolution of hosts and pathogens, and host-pathogen co-evolution. Hence it is of interest to know if the distribution ...
1n0rg5vd	The Effectiveness of Contact Tracing in Emerging Epidemics	BACKGROUND: Contact tracing plays an important role in the control of emerging infectious diseases, but little is known yet about its effectiveness. Here we deduce from a generic mathematical model how effectiveness of tracing relates to various aspects of time, such as the course of individual infectivity, the (variab...
nzh87aux	The Waiting Time for Inter-Country Spread of Pandemic Influenza	BACKGROUND: The time delay between the start of an influenza pandemic and its subsequent initiation in other countries is highly relevant to preparedness planning. We quantify the distribution of this random time in terms of the separate components of this delay, and assess how the delay may be extended by non-pharmace...
1y5nej0m	Neutralizing Antibody Fails to Impact the Course of Ebola Virus Infection in Monkeys	Prophylaxis with high doses of neutralizing antibody typically offers protection against challenge with viruses producing acute infections. In this study, we have investigated the ability of the neutralizing human monoclonal antibody, KZ52, to protect against Ebola virus in rhesus macaques. This antibody was previously...
fvfjz7al	Public health preparedness in Alberta: a systems-level study	BACKGROUND: Recent international and national events have brought critical attention to the Canadian public health system and how prepared the system is to respond to various types of contemporary public health threats. This article describes the study design and methods being used to conduct a systems-level analysis o...
lntn11a9	The immunoregulatory and allergy-associated cytokines in the aetiology of the otitis media with effusion.	Inflammation in the middle ear mucosa, which can be provoked by different primary factors such as bacterial and viral infection, local allergic reactions and reflux, is the crucial event in the pathogenesis of otitis media with effusion (OME). Unresolved acute inflammatory responses or defective immunoregulation of mid...
nzk8m912	Bench-to-bedside review: Critical illness-associated cognitive dysfunction – mechanisms, markers, and emerging therapeutics	Cognitive dysfunction is common in critically ill patients, not only during the acute illness but also long after its resolution. A large number of pathophysiologic mechanisms are thought to underlie critical illness-associated cognitive dysfunction, including neuro-transmitter abnormalities and occult diffuse brain in...
ps3mnpzq	ProCAT: a data analysis approach for protein microarrays	Protein microarrays provide a versatile method for the analysis of many protein biochemical activities. Existing DNA microarray analytical methods do not translate to protein microarrays due to differences between the technologies. Here we report a new approach, ProCAT, which corrects for background bias and spatial ar...
m56agj4z	Positional clustering improves computational binding site detection and identifies novel cis-regulatory sites in mammalian GABA(A) receptor subunit genes	Understanding transcription factor (TF) mediated control of gene expression remains a major challenge at the interface of computational and experimental biology. Computational techniques predicting TF-binding site specificity are frequently unreliable. On the other hand, comprehensive experimental validation is difficu...
x2zq0lnt	The Transmissibility of Highly Pathogenic Avian Influenza in Commercial Poultry in Industrialised Countries	BACKGROUND: With the increased occurrence of outbreaks of H5N1 worldwide there is concern that the virus could enter commercial poultry farms with severe economic consequences. METHODOLOGY/PRINCIPAL FINDINGS: We analyse data from four recent outbreaks of highly pathogenic avian influenza (HPAI) in commercial poultry to...
hf3nytb2	The influenza pandemic preparedness planning tool InfluSim	BACKGROUND: Planning public health responses against pandemic influenza relies on predictive models by which the impact of different intervention strategies can be evaluated. Research has to date rather focused on producing predictions for certain localities or under specific conditions, than on designing a publicly av...
byp2eqhd	Immune pathways and defence mechanisms in honey bees Apis mellifera	Social insects are able to mount both group-level and individual defences against pathogens. Here we focus on individual defences, by presenting a genome-wide analysis of immunity in a social insect, the honey bee Apis mellifera. We present honey bee models for each of four signalling pathways associated with immunity,...
s4y6uxsb	ElaD, a Deubiquitinating Protease Expressed by E. coli	BACKGROUND: Ubiquitin and ubiquitin-like proteins (Ubl) are designed to modify polypeptides in eukaryotes. Covalent binding of ubiquitin or Ubls to substrate proteins can be reversed by specific hydrolases. One particular set of cysteine proteases, the CE clan, which targets ubiquitin and Ubls, has homologs in eukaryot...
9zmyojbu	Mutational analysis of human CEACAM1: the potential of receptor polymorphism in increasing host susceptibility to bacterial infection	A common overlapping site on the N-terminal IgV-like domain of human carcinoembryonic antigen (CEA)-related cell adhesion molecules (CEACAMs) is targeted by several important human respiratory pathogens. These include Neisseria meningitidis (Nm) and Haemophilus influenzae (Hi) that can cause disseminated or persistent ...
4y8ghcpq	Immune reconstitution inflammatory syndrome (IRIS): review of common infectious manifestations and treatment options	The immune reconstitution inflammatory syndrome (IRIS) in HIV-infected patients initiating antiretroviral therapy (ART) results from restored immunity to specific infectious or non-infectious antigens. A paradoxical clinical worsening of a known condition or the appearance of a new condition after initiating therapy ch...
63bos83o	Global Surveillance of Emerging Influenza Virus Genotypes by Mass Spectrometry	BACKGROUND: Effective influenza surveillance requires new methods capable of rapid and inexpensive genomic analysis of evolving viral species for pandemic preparedness, to understand the evolution of circulating viral species, and for vaccine strain selection. We have developed one such approach based on previously des...
hqc7u9w3	Transmission Parameters of the 2001 Foot and Mouth Epidemic in Great Britain	Despite intensive ongoing research, key aspects of the spatial-temporal evolution of the 2001 foot and mouth disease (FMD) epidemic in Great Britain (GB) remain unexplained. Here we develop a Markov Chain Monte Carlo (MCMC) method for estimating epidemiological parameters of the 2001 outbreak for a range of simple tran...
87zt7lew	Efficient replication of pneumonia virus of mice (PVM) in a mouse macrophage cell line	Pneumonia virus of mice (PVM; family Paramyxoviridae, subfamily Pneumovirinae) is a natural respiratory pathogen of rodent species and an important new model for the study of severe viral bronchiolitis and pneumonia. However, despite high virus titers typically detected in infected mouse lung tissue in vivo, cell lines...
wgxt36jv	Designing and conducting tabletop exercises to assess public health preparedness for manmade and naturally occurring biological threats	BACKGROUND: Since 2001, state and local health departments in the United States (US) have accelerated efforts to prepare for high-impact public health emergencies. One component of these activities has been the development and conduct of exercise programs to assess capabilities, train staff and build relationships. Thi...
qbldmef1	Transcript-level annotation of Affymetrix probesets improves the interpretation of gene expression data	BACKGROUND: The wide use of Affymetrix microarray in broadened fields of biological research has made the probeset annotation an important issue. Standard Affymetrix probeset annotation is at gene level, i.e. a probeset is precisely linked to a gene, and probeset intensity is interpreted as gene expression. The increas...

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Dataset Card for BEIR Benchmark

trec-covid is one of the datasets from the Bio-Medical Retrieval task within BEIR, measuring scientific article retrieval for a given query on COVID-19.

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},
}

TREC-COVID Data Splits

Subset	Split	Rows
corpus	corpus	171,332
queries	queries	50

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}
}