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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 ... |
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... |
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... |
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 (... |
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... |
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... |
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... |
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... |
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... |
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 |
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. |
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 | |
kvztcwu2 | Clinical Vignettes | |
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... |
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... |
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... |
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... |
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... |
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... |
i9arl3oi | Selective redox regulation of cytokine receptor signaling by extracellular thioredoxin-1 | The thiol-disulfide oxidoreductase thioredoxin-1 (Trx1) is known to be secreted by leukocytes and to exhibit cytokine-like properties. Extracellular effects of Trx1 require a functional active site, suggesting a redox-based mechanism of action. However, specific cell surface proteins and pathways coupling extracellular... |
lz37rh82 | s-RT-MELT for rapid mutation scanning using enzymatic selection and real time DNA-melting: new potential for multiplex genetic analysis | The rapidly growing understanding of human genetic pathways, including those that mediate cancer biology and drug response, leads to an increasing need for extensive and reliable mutation screening on a population or on a single patient basis. Here we describe s-RT-MELT, a novel technology that enables highly expanded ... |
gyzbzx53 | Electrospray ionisation-cleavable tandem nucleic acid mass tag–peptide nucleic acid conjugates: synthesis and applications to quantitative genomic analysis using electrospray ionisation-MS/MS | The synthesis and characterization of isotopomer tandem nucleic acid mass tag–peptide nucleic acid (TNT–PNA) conjugates is described along with their use as electrospray ionisation-cleavable (ESI-Cleavable) hybridization probes for the detection and quantification of target DNA sequences by electrospray ionisation tand... |
z2u5frvq | Antibody-Based HIV-1 Vaccines: Recent Developments and Future Directions: A summary report from a Global HIV Vaccine Enterprise Working Group | The authors discuss humoral immune responses to HIV and approaches to designing vaccines that induce viral neutralizing and other potentially protective antibodies. |
gaemgm0t | Transmissibility of the Influenza Virus in the 1918 Pandemic | BACKGROUND: With a heightened increase in concern for an influenza pandemic we sought to better understand the 1918 Influenza pandemic, the most devastating epidemic of the previous century. METHODOLOGY/PRINCIPAL FINDINGS: We use data from several communities in Maryland, USA as well as two ships that experienced well-... |
in6w5d2y | Simian virus 40 vectors for pulmonary gene therapy | BACKGROUND: Sepsis remains the leading cause of death in critically ill patients. One of the primary organs affected by sepsis is the lung, presenting as the Acute Respiratory Distress Syndrome (ARDS). Organ damage in sepsis involves an alteration in gene expression, making gene transfer a potential therapeutic modalit... |
navrmhqm | The intrinsically disordered C‐terminal domain of the measles virus nucleoprotein interacts with the C‐terminal domain of the phosphoprotein via two distinct sites and remains predominantly unfolded | Measles virus is a negative‐sense, single‐stranded RNA virus within theMononegavirales order,which includes several human pathogens, including rabies, Ebola, Nipah, and Hendra viruses. Themeasles virus nucleoprotein consists of a structured N‐terminal domain, and of an intrinsically disordered C‐terminal domain, N(TAIL... |
fj9l8che | The evolution of human influenza A viruses from 1999 to 2006: A complete genome study | BACKGROUND: Knowledge about the complete genome constellation of seasonal influenza A viruses from different countries is valuable for monitoring and understanding of the evolution and migration of strains. Few complete genome sequences of influenza A viruses from Europe are publicly available at the present time and t... |
7jszm1nd | Functional Analysis of the 5′ Genomic Sequence of a Bovine Norovirus | BACKGROUND: Jena Virus (JV), a bovine Norovirus, causes enteric disease in cattle and represents a potential model for the study of enteric norovirus infection and pathogenesis. The positive sense RNA genome of JV is organised into ORF1 (non-structural proteins), ORF2 (major capsid protein) and ORF3 (minor capsid prote... |
8rrkf78o | Expression of Foot-and-Mouth Disease Virus Capsid Proteins in Silkworm-Baculovirus Expression System and Its Utilization as a Subunit Vaccine | BACKGROUND: Foot-and-mouth disease (FMD) is a highly contagious disease of livestock that causes severe economic loss in susceptible cloven-hoofed animals. Although the traditional inactivated vaccine has been proved effective, it may lead to a new outbreak of FMD because of either incomplete inactivation of FMDV or th... |
7vvj0vfs | The Moraxella adhesin UspA1 binds to its human CEACAM1 receptor by a deformable trimeric coiled-coil | Moraxella catarrhalis is a ubiquitous human-specific bacterium commonly associated with upper and lower respiratory tract infections, including otitis media, sinusitis and chronic obstructive pulmonary disease. The bacterium uses an autotransporter protein UspA1 to target an important human cellular receptor carcinoemb... |
gy2b7of9 | Deletion of human metapneumovirus M2-2 increases mutation frequency and attenuates growth in hamsters | BACKGROUND: Human metapneumovirus (hMPV) infection can cause acute lower respiratory tract illness in infants, the immunocompromised, and the elderly. Currently there are no licensed preventative measures for hMPV infections. Using a variant of hMPV/NL/1/00 that does not require trypsin supplementation for growth in ti... |
4z38v9rg | Seasonality of Influenza A(H3N2) Virus: A Hong Kong Perspective (1997–2006) | BACKGROUND: The underlying basis for the seasonality of influenza A viruses is still uncertain. Phylogenetic studies investigated this phenomenon but have lacked sequences from more subtropical and tropical regions, particularly from Southeast Asia. METHODOLOGY/PRINCIPAL FINDINGS: 281 complete hemagglutinin (HA) and ne... |
3dgjv0x1 | HIV-Specific T-Cells Accumulate in the Liver in HCV/HIV Co-Infection | BACKGROUND AND AIMS: Hepatitis C Virus (HCV)-related liver disease progresses more rapidly in individuals co-infected with Human Immunodeficiency Virus-1 (HIV), although the underlying immunologic mechanisms are unknown. We examined whether HIV-specific T-cells are identified in the liver of HCV/HIV co-infected individ... |
seass3p0 | An analysis of hospital preparedness capacity for public health emergency in four regions of China: Beijing, Shandong, Guangxi, and Hainan | BACKGROUND: Hospital preparedness is critical for the early detection and management of public health emergency (PHE). Understanding the current status of PHE preparedness is the first step in planning to enhance hospitals' capacities for emergency response. The objective of this study is to understand the current stat... |
pr9i9swk | Nasal Delivery of an Adenovirus-Based Vaccine Bypasses Pre-Existing Immunity to the Vaccine Carrier and Improves the Immune Response in Mice | Pre-existing immunity to human adenovirus serotype 5 (Ad5) is common in the general population. Bypassing pre-existing immunity could maximize Ad5 vaccine efficacy. Vaccination by the intramuscular (I.M.), nasal (I.N.) or oral (P.O.) route with Ad5 expressing Ebola Zaire glycoprotein (Ad5-ZGP) fully protected naïve mic... |
sswimukk | Resource Allocation during an Influenza Pandemic | Resource Allocation during an Influenza Pandemic |
g370ygbu | Biodefense versus bioterrorism | Genomics was essential for identifying the source of the deadly anthrax strain released after the September 11 terrorist attacks in the US. The same research that is needed to combat low-probability bioterror attacks is needed to combat high-probability natural infectious agents. |
sasijnks | Self-Interest versus Group-Interest in Antiviral Control | Antiviral agents have been hailed to hold considerable promise for the treatment and prevention of emerging viral diseases like H5N1 avian influenza and SARS. However, antiviral drugs are not completely harmless, and the conditions under which individuals are willing to participate in a large-scale antiviral drug treat... |
osioowtp | IL-1β, IL-6, and RANTES as Biomarkers of Chikungunya Severity | BACKGROUND: Little is known about the immunopathogenesis of Chikungunya virus. Circulating levels of immune mediators and growth factors were analyzed from patients infected during the first Singaporean Chikungunya fever outbreak in early 2008 to establish biomarkers associated with infection and/or disease severity. M... |
k2glr4pd | Antimicrobial and antioxidant activities of Cortex Magnoliae Officinalis and some other medicinal plants commonly used in South-East Asia | BACKGROUND: Eight medicinal plants were tested for their antimicrobial and antioxidant activities. Different extraction methods were also tested for their effects on the bioactivities of the medicinal plants. METHODS: Eight plants, namely Herba Polygonis Hydropiperis (Laliaocao), Folium Murraya Koenigii (Jialiye), Rhiz... |
akvhi38e | Chinese journals: a guide for epidemiologists | Chinese journals in epidemiology, preventive medicine and public health contain much that is of potential international interest. However, few non-Chinese speakers are acquainted with this literature. This article therefore provides an overview of the contemporary scene in Chinese biomedical journal publication, Chines... |
3tt99oax | Polyomaviruses KI and WU in Immunocompromised Patients with Respiratory Disease | Polyomaviruses KI (KIPyV) and WU (WUPyV) were recently identified, mainly in respiratory specimens from children. Among 200 patients with respiratory disorders admitted to Saint Louis Hospital, Paris, France, KIPyV was detected in 8% and WUPyV in 1%. KIPyV was significantly more frequent among human stem cell transplan... |
vg57cnqw | Proteolytic processing of a precursor protein for a growth-promoting peptide by a subtilisin serine protease in Arabidopsis | Phytosulfokines (PSKs) are secreted, sulfated peptide hormones derived from larger prepropeptide precursors. Proteolytic processing of one of the precursors, AtPSK4, was demonstrated by cleavage of a preproAtPSK4–myc transgene product to AtPSK4–myc. Cleavage of proAtPSK4 was induced by placing root explants in tissue c... |
50wqhp04 | International Course on Emerging Viruses in the Amazon Region | |
i55gwn3s | Avian Influenza Virus Glycoproteins Restrict Virus Replication and Spread through Human Airway Epithelium at Temperatures of the Proximal Airways | Transmission of avian influenza viruses from bird to human is a rare event even though avian influenza viruses infect the ciliated epithelium of human airways in vitro and ex vivo. Using an in vitro model of human ciliated airway epithelium (HAE), we demonstrate that while human and avian influenza viruses efficiently ... |
tex6bgab | Small Interfering RNA Targeting M2 Gene Induces Effective and Long Term Inhibition of Influenza A Virus Replication | RNA interference (RNAi) provides a powerful new means to inhibit viral infection specifically. However, the selection of siRNA-resistant viruses is a major concern in the use of RNAi as antiviral therapeutics. In this study, we conducted a lentiviral vector with a H1-short hairpin RNA (shRNA) expression cassette to del... |
6c3zb3g4 | Health workers' views on quality of prevention of mother-to-child transmission and postnatal care for HIV-infected women and their children | BACKGROUND: Prevention of mother-to-child transmission has been considered as not a simple intervention but a comprehensive set of interventions requiring capable health workers. Viet Nam's extensive health care system reaches the village level, but still HIV-infected mothers and children have received inadequate healt... |
wk9oxl4n | Inhibition of Lassa Virus Glycoprotein Cleavage and Multicycle Replication by Site 1 Protease-Adapted α(1)-Antitrypsin Variants | BACKGROUND: Proteolytic processing of the Lassa virus envelope glycoprotein precursor GP-C by the host proprotein convertase site 1 protease (S1P) is a prerequisite for the incorporation of the subunits GP-1 and GP-2 into viral particles and, hence, essential for infectivity and virus spread. Therefore, we tested in th... |
g4puurhk | Role of nitric oxide in management of acute respiratory distress syndrome | The current mortality rate of patients suffering from acute respiratory distress syndrome (ARDS) is between 45% and 92%, with most dying within the first two weeks of the illness. In an effort to combat such an alarmingly high mortality rate, various treatment therapies such as low tidal volume ventilation strategies, ... |
3p81yr4n | Poster Exhibition | |
bnkbwh3w | Heliox reduces respiratory system resistance in respiratory syncytial virus induced respiratory failure | INTRODUCTION: Respiratory syncytial virus (RSV) lower respiratory tract disease is characterised by narrowing of the airways resulting in increased airway resistance, air-trapping and respiratory acidosis. These problems might be overcome using helium-oxygen gas mixture. However, the effect of mechanical ventilation wi... |
ucn7t3sg | Regulation of the apoptosis-inducing kinase DRAK2 by cyclooxygenase-2 in colorectal cancer | BACKGROUND: Cyclooxygenase-2 (COX-2) is over-expressed in colorectal cancer (CRC), rendering tumour cells resistant to apoptosis. Selective COX-2 inhibition is effective in CRC prevention, although having adverse cardiovascular effects, thus focus has shifted to downstream pathways. METHODS: Microarray experiments iden... |
xjspi65a | Evolutionarily Conserved Herpesviral Protein Interaction Networks | Herpesviruses constitute a family of large DNA viruses widely spread in vertebrates and causing a variety of different diseases. They possess dsDNA genomes ranging from 120 to 240 kbp encoding between 70 to 170 open reading frames. We previously reported the protein interaction networks of two herpesviruses, varicella-... |
0p8lk12m | Gene Expression Profiling in Cells with Enhanced γ-Secretase Activity | BACKGROUND: Processing by γ-secretase of many type-I membrane protein substrates triggers signaling cascades by releasing intracellular domains (ICDs) that, following nuclear translocation, modulate the transcription of different genes regulating a diverse array of cellular and biological processes. Because the list of... |
nn09hh29 | Using Dynamic Stochastic Modelling to Estimate Population Risk Factors in Infectious Disease: The Example of FIV in 15 Cat Populations | BACKGROUND: In natural cat populations, Feline Immunodeficiency Virus (FIV) is transmitted through bites between individuals. Factors such as the density of cats within the population or the sex-ratio can have potentially strong effects on the frequency of fight between individuals and hence appear as important populat... |
dqqcajjd | The OptAIDS project: towards global halting of HIV/AIDS | |
ugbwvy6j | Early Assessment of Anxiety and Behavioral Response to Novel Swine-Origin Influenza A(H1N1) | BACKGROUND: Since late April, 2009, a novel influenza virus A (H1N1), generally referred to as the “swine flu,” has spread around the globe and infected hundreds of thousands of people. During the first few days after the initial outbreak in Mexico, extensive media coverage together with a high degree of uncertainty ab... |
oi9j5o0n | European Hedgehogs as Hosts for Borrelia spp., Germany | |
c8snsa4z | Relapsing macrophage activating syndrome in a 15-year-old girl with Still's disease: a case report | INTRODUCTION: Macrophage activating syndrome is a severe, potentially life-threatening condition that may accompany Still's disease. It is characterized by fever, hepatosplenomegaly, lymphadenopathy, severe cytopenia, serious liver dysfunction, coagulopathy and neurologic involvement. The principal treatment for patien... |
zwgnkegf | Fluorescence Competition Assay Measurements of Free Energy Changes for RNA Pseudoknots | [Image: see text] RNA pseudoknots have important functions, and thermodynamic stability is a key to predicting pseudoknots in RNA sequences and to understanding their functions. Traditional methods, such as UV melting and differential scanning calorimetry, for measuring RNA thermodynamics are restricted to temperature ... |
d08buwtu | Analysis of Memory B Cell Responses and Isolation of Novel Monoclonal Antibodies with Neutralizing Breadth from HIV-1-Infected Individuals | BACKGROUND: The isolation of human monoclonal antibodies (mAbs) that neutralize a broad spectrum of primary HIV-1 isolates and the characterization of the human neutralizing antibody B cell response to HIV-1 infection are important goals that are central to the design of an effective antibody-based vaccine. METHODS AND... |
hwjkbpqp | Abstracts from the 11th International Congress of Behavioral Medicine | |
u3yvpcnr | HIV-related restrictions on entry, residence and stay in the WHO European Region: a survey | BACKGROUND: Back in 1987, the World Health Organization (WHO) concluded that the screening of international travellers was an ineffective way to prevent the spread of HIV. However, some countries still restrict the entrance and/or residency of foreigners with an HIV infection. HIV-related travel restrictions have serio... |
54f3q2o5 | Successful treatment of HIV-associated multicentric Castleman's disease and multiple organ failure with rituximab and supportive care: a case report | INTRODUCTION: Multicentric Castleman's Disease (MCD), a lymphoproliferative disorder associated with Human Herpes Virus-8 (HHV-8) infection, is increasing in incidence amongst HIV patients. This condition is associated with lymphadenopathy, polyclonal gammopathy, hepato-splenomegaly and systemic symptoms. A number of s... |
25v5mr3c | Mitigation Approaches to Combat the Flu Pandemic | Management of flu pandemic is a perpetual challenge for the medical fraternity since time immemorial. Animal to human transmission has been observed thrice in the last century within an average range of 11-39 years of antigenic recycling. The recent outbreak of influenza A (H1N1, also termed as swine flu), first report... |
sw4wtxdk | NSs Encoded by Groundnut Bud Necrosis Virus Is a Bifunctional Enzyme | Groundnut bud necrosis virus (GBNV), a member of genus Tospovirus in the family Bunyaviridae, infects a large number of leguminosae and solanaceae plants in India. With a view to elucidate the function of nonstructural protein, NSs encoded by the small RNA genome (S RNA), the NSs protein of GBNV- tomato (Karnataka) [1]... |
d2mb2b3d | TLR agonist–Stat3 siRNA conjugates: cell-specific gene silencing and enhanced antitumor immune responses | Efficient delivery of siRNA to specific cell populations in vivo remains a formidable challenge to its successful therapeutic application. We describe a novel siRNA-based approach – synthetically linking siRNA to an oligonucleotide TLR9 agonist – that targets and silences genes in TLR9(+) myeloid cells and B cells, bot... |
o4k7auph | Rapid Accumulation of Virulent Rift Valley Fever Virus in Mice from an Attenuated Virus Carrying a Single Nucleotide Substitution in the M RNA | BACKGROUND: Rift Valley fever virus (RVFV), a member of the genus Phlebovirus within the family Bunyaviridae, is a negative-stranded RNA virus with a tripartite genome. RVFV is transmitted by mosquitoes and causes fever and severe hemorrhagic illness among humans, while in livestock it causes fever and high abortion ra... |
ge5iri3v | Global Public Health Security | National public health institutes will play a key role in implementation of the revised International Health Regulations. |
zizfgz7d | Generation of Human CEACAM1 Transgenic Mice and Binding of Neisseria Opa Protein to Their Neutrophils | BACKGROUND: Human CEACAM1 is a cell-cell adhesion molecule with multiple functions including insulin clearance in the liver, vasculogenesis in endothelial cells, lumen formation in the mammary gland, and binding of certain human pathogens. PRINCIPAL FINDINGS: Three genomic BAC clones containing the human CEACAM1 gene w... |
cge5uve3 | TUBERCULOUS SARCOIDOSIS: DOES IT EXIST? | |
q26f8pv4 | DotKnot: pseudoknot prediction using the probability dot plot under a refined energy model | RNA pseudoknots are functional structure elements with key roles in viral and cellular processes. Prediction of a pseudoknotted minimum free energy structure is an NP-complete problem. Practical algorithms for RNA structure prediction including restricted classes of pseudoknots suffer from high runtime and poor accurac... |
gzxu7nkh | China's Engagement with Global Health Diplomacy: Was SARS a Watershed? | As part of the PLoS Medicine series on Global Health Diplomacy, Lai-Han Chan and colleagues provide a case study of China's growing engagement in global health diplomacy following the SARS epidemic. |
se4unhi8 | Synthesis and Pharmacological Evaluation of Schiff Bases of 4-(2-Aminophenyl)-Morpholines | In the present study, a novel series of 4-(2-aminophenyl)morpholines were synthesized and characterized by IR, (1)H-NMR, (13)C NMR and mass spectral analysis. The synthesized compounds were screened for analgesic (100 and 200 mg/kg), antiinflammatory (200 and 400 mg/kg), antibacterial (Bacillus subtilis, Bacillus cereu... |
34sy55hi | Acute Encephalopathy Associated with Influenza A Infection in Adults | We report acute encephalopathy associated with influenza A infection in 3 adults. We detected high cerebrospinal fluid (CSF) and plasma concentrations of CXCL8/IL-8 and CCL2/MCP-1 (CSF/plasma ratios >3), and interleukin-6, CXCL10/IP-10, but no evidence of viral neuroinvasion. Patients recovered without sequelae. Hypera... |
yvgzkt8a | Journals, Academics, and Pandemics | In the wake of the SARS epidemic and the H1N1 pandemic, the PLoS Medicine editors ask whether journal publishing is an efficient enough mechanism for information sharing. |
wcyv6w47 | Age groups and spread of influenza: implications for vaccination strategy | BACKGROUND: The unpredictable nature of the potentially devastating impact of 2009 pH1N1 influenza pandemic highlights the need for pandemic preparedness planning, where modeling studies could be most useful for simulations of possible future scenarios. METHODS: A compartmental model with pre-symptomatic and asymptomat... |
chd9ezba | Role of CD14 in lung inflammation and infection | This article is one of ten reviews selected from the Yearbook of Intensive Care and Emergency Medicine 2010 (Springer Verlag) and co-published as a series in Critical Care. Other articles in the series can be found online at http://ccforum.com/series/yearbook. Further information about the Yearbook of Intensive Care an... |
k2vbgqk7 | Human Pregnancy Specific Beta-1-Glycoprotein 1 (PSG1) Has a Potential Role in Placental Vascular Morphogenesis | Previous studies suggest that human pregnancy specific beta-1-glycoproteins (PSGs) play immunomodulatory roles during pregnancy; however, other possible functions of PSGs have yet to be explored. We have observed that PSGs induce transforming growth factor beta 1 (TGFB1), which among its other diverse functions inhibit... |
782iew86 | Human bocaviruses are highly diverse, dispersed, recombination prone, and prevalent enteric infections | A new species of parvovirus tentatively named human bocavirus 4 (HBoV4) was genetically characterized. Among 641 feces samples from children and adults the most commonly detected bocaviruses species were HBoV2>HBoV3>HBoV4>HBoV1 with HBoV2 prevalence of 21% and 26% in Nigerian and Tunisian children. HBoV3 and HBoV4 spec... |
om92cx5q | On the possible role of robustness in the evolution of infectious diseases | Robustness describes the capacity for a biological system to remain canalized despite perturbation. Genetic robustness affords maintenance of phenotype despite mutational input, necessarily involving the role of epistasis. Environmental robustness is phenotypic constancy in the face of environmental variation, where ep... |
3n05cb49 | Insights into the Evolution and Emergence of a Novel Infectious Disease | Many zoonotic, novel infectious diseases in humans appear as sporadic infections with spatially and temporally restricted outbreaks, as seen with influenza A(H5N1). Adaptation is often a key factor for successfully establishing sustained human-to-human transmission. Here we use simple mathematical models to describe di... |
480d3yfv | Diagnostic value of triggering receptor expressed on myeloid cells-1 and C-reactive protein for patients with lung infiltrates: an observational study | BACKGROUND: Differential diagnosis of patients with lung infiltrates remains a challenge. Triggering receptor expressed on myeloid cells (TREM)-1 is a neutrophil and monocyte receptor up-regulated during infection. The aim of this study was to evaluate the diagnostic accuracy of TREM-1 and of C-reactive protein (CRP) f... |
v4jochbe | Nodeomics: Pathogen Detection in Vertebrate Lymph Nodes Using Meta-Transcriptomics | The ongoing emergence of human infections originating from wildlife highlights the need for better knowledge of the microbial community in wildlife species where traditional diagnostic approaches are limited. Here we evaluate the microbial biota in healthy mule deer (Odocoileus hemionus) by analyses of lymph node meta-... |
19sejitq | Efficacy of Oseltamivir-Zanamivir Combination Compared to Each Monotherapy for Seasonal Influenza: A Randomized Placebo-Controlled Trial | BACKGROUND: Neuraminidase inhibitors are thought to be efficacious in reducing the time to alleviation of symptoms in outpatients with seasonal influenza. The objective of this study was to compare the short-term virological efficacy of oseltamivir-zanamivir combination versus each monotherapy plus placebo. METHODS AND... |
3njrml7x | Eosinophilic infiltrate in a patient with severe Legionella pneumonia as a levofloxacin-related complication: a case report | INTRODUCTION: Legionella pneumonia can appear with different levels of severity and it can often present with complications such as acute respiratory distress syndrome. CASE PRESENTATION: We report the case of a 44-year-old Caucasian man with Legionella pneumonia with successive development of severe acute respiratory ... |
c8yzoen7 | Hybridization properties of long nucleic acid probes for detection of variable target sequences, and development of a hybridization prediction algorithm | One of the main problems in nucleic acid-based techniques for detection of infectious agents, such as influenza viruses, is that of nucleic acid sequence variation. DNA probes, 70-nt long, some including the nucleotide analog deoxyribose-Inosine (dInosine), were analyzed for hybridization tolerance to different amounts... |
2aku9prp | Liposome-Coupled Antigens Are Internalized by Antigen-Presenting Cells via Pinocytosis and Cross-Presented to CD8(+) T Cells | We have previously demonstrated that antigens chemically coupled to the surface of liposomes consisting of unsaturated fatty acids were cross-presented by antigen-presenting cells (APCs) to CD8(+) T cells, and that this process resulted in the induction of antigen-specific cytotoxic T lymphocytes. In the present study,... |
k2a0q9y8 | Human immunome, bioinformatic analyses using HLA supermotifs and the parasite genome, binding assays, studies of human T cell responses, and immunization of HLA-A*1101 transgenic mice including novel adjuvants provide a foundation for HLA-A03 restricted CD8(+)T cell epitope based, adjuvanted vaccine protective against ... | BACKGROUND: Toxoplasmosis causes loss of life, cognitive and motor function, and sight. A vaccine is greatly needed to prevent this disease. The purpose of this study was to use an immmunosense approach to develop a foundation for development of vaccines to protect humans with the HLA-A03 supertype. Three peptides had ... |
b66bb2ri | PhEVER: a database for the global exploration of virus–host evolutionary relationships | Fast viral adaptation and the implication of this rapid evolution in the emergence of several new infectious diseases have turned this issue into a major challenge for various research domains. Indeed, viruses are involved in the development of a wide range of pathologies and understanding how viruses and host cells in... |
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trec-covid (Decontaminated)
A decontaminated version of the trec-covid 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 | 171,332 | 99,522 | 71,810 |
| Queries | 50 | 50 | 0 |
Qrels per split
| Split | Original | Clean | Removed |
|---|---|---|---|
| test | 66,336 | 40,657 | 25,679 |
Usage
from datasets import load_dataset
corpus = load_dataset("lightonai/trec-covid-decontaminated", "corpus", split="corpus")
queries = load_dataset("lightonai/trec-covid-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)
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