niryuu/sni-each-converted huggingface dataset:
Paragraph: Crystal structures of complexes of an antiviral lectin griffithsin (GRFT) with glucose and N-acetylglucosamine were solved and refined at high resolution. In both complexes, all six monosaccharide-binding sites of GRFT were occupied and the mode of binding was similar to that of mannose. In our previous attempts to obtain a complex with N-acetylglucosamine by soaking, only a single site was occupied; thus, cocrystallization was clearly superior despite lower concentration of the ligand. Isothermal titration calorimetric experiments with N-acetylglucosamine, glucose, and mannose provided enthalpic evidence of distinct binding differences between the three monosaccharides. A comparison of the mode of binding of different monosaccharides is discussed in the context of the antiviral activity of GRFT, based on specific binding to high-mannose-containing complex carbohydrates found on viral envelopes. 
 Title: Crystallographic studies of the complexes of antiviral protein griffithsin with glucose and N-acetylglucosamine
Output: True
Paragraph: Background: The first cases of influenza A/H1N1 (swine flu) were confirmed in the UK on 27th April 2009, after a novel virus first identified in Mexico rapidly evolved into a pandemic. The swine flu outbreak was the first pandemic in more than 40 years and for many, their first encounter with a major influenza outbreak. This study examines public understandings of the pandemic, exploring how people deciphered the threat and perceived they could control the risks. Methods: Purposive sampling was used to recruit seventy three people (61 women and 12 men) to take part in 14 focus group discussions around the time of the second wave in swine flu cases. Results: These discussions showed that there was little evidence of the public over-reacting, that people believed the threat of contracting swine flu was inevitable, and that they assessed their own self-efficacy for protecting against it to be low. Respondents assessed a greater risk to their health from the vaccine than from the disease. Such findings could have led to apathy about following the UK Governments recommended health protective behaviours, and a sub-optimal level of vaccine uptake. More generally, people were confused about the difference between seasonal influenza and swine flu and their vaccines. Conclusions: This research suggests a gap in public understandings which could hinder attempts to communicate about novel flu viruses in the future. There was general support for the government's handling of the pandemic, although its public awareness campaign was deemed ineffectual as few people changed their current hand hygiene practices. There was less support for the media who were deemed to have over-reported the swine flu pandemic. 
 Title: Public views of the uk media and government reaction to the 2009 swine flu pandemic
Output: True
Paragraph: The human severe acute respiratory syndrome coronavirus (SARS-CoV) and the NL63 coronaviruses are human respiratory pathogens for which no effective antiviral treatment exists. The papain-like cysteine proteases encoded by the coronavirus (SARS-CoV: PLpro; NL63: PLP1 and PLP2) represent potential targets for antiviral drug development. Three recent inhibitor-bound PLpro structures highlight the role of an extremely flexible six-residue loop in inhibitor binding. The high binding site plasticity is a major challenge in computational drug discovery/design efforts. From conventional molecular dynamics and accelerated molecular dynamics (aMD) simulations, we find that with conventional molecular dynamics simulation, PLpro translationally samples the open and closed conformation of BL2 loop on a picosecond-nanosecond timescale but does not reproduce the peptide bond inversion between loop residues Tyr269 and Gln270 that is observed on inhibitor GRL0617 binding. Only aMD simulation, starting from the closed loop conformation, reproduced the 180°ϕ-ψ dihedral rotation back to the open loop state. The Tyr-Gln peptide bond inversion appears to involve a progressive conformational change of the full loop, starting at one side, and progressing to the other. We used the SARS-CoV apo X-ray structure to develop a model of the NL63-PLP2 catalytic site. Superimposition of the PLP2 model on the PLpro X-ray structure identifies binding site residues in PLP2 that contribute to the distinct substrate cleavage site specificities between the two proteases. The topological and electrostatic differences between the two protease binding sites also help explain the selectivity of non-covalent PLpro inhibitors. 
 Title: Comparison of SARS and NL63 Papain-Like Protease Binding Sites and Binding Site Dynamics: Inhibitor Design Implications
Output: True
Paragraph: Avian infectious bronchitis virus (IBV) encodes 15 nonstructural proteins (nsps) which play crucial roles in RNA transcription and genome replication. One of them, nsp3, contains an ADRP (adenosine diphosphate-ribose-1 0 -phosphatase) domain which was revealed in recent studies to have ADP-ribose-1 0 -monophosphatase (Appr-1 0 -pase) activity. Appr-1 0 -pase catalyzes the conversion of ADPribose-1 0 -monophosphate (Appr-1 0 -p) to ADP-ribose in the tRNA-splicing pathway. The gene segment encoding the IBV nsp3 ADRP domain has been cloned and expressed in Escherichia coli. The protein has been crystallized and the crystals diffracted to 1.8 Å resolution. They belonged to space group P1, with unit-cell parameters a = 41.1, b = 43.2, c = 48.9 Å , = 78.0, = 80.0, = 73.6 . Each asymmetric unit contains two molecules. 
 Title: Structural Biology and Crystallization Communications Purification, crystallization and preliminary crystallographic analysis of avian infectious bronchitis virus nsp3 ADRP domain
Output: False
Paragraph: Our coalition of public health experts, doctors, and scientists worldwide want to draw attention to the need for high-quality evaluation protocols of the potential beneficial effect of hydroxychloroquine (HCQ) as a post-exposure drug for exposed people, meaning people with close contact with positive tested patients, including home and medical caregivers. We have reviewed the mechanisms of antiviral effect of HCQ, the risk-benefit ratio taking into consideration the PK/PD of HCQ and the thresholds of efficacy. We have studied its use as an antimalarial, an antiviral, and an immunomodulating drug and concluded that the use of HCQ at does matching that of the standard treatment of Systemic Lupus erythematous, which has proven safety and efficacy in terms of HCQ blood and tissue concentration adapted to bodyweight (2,3), at 6mg/kg/day 1 (loading dose) followed by 5 mg/kg/day, with a maximum limit of 600 mg/day in all cases should swiftly be clinically evaluated as a post-exposure drug for exposed people. J o u r n a l P r e -p r o o f Journal Pre-proof epidemic. However, its administration should be done under medical control to avo id potential side effects and to prevent an uncontrolled use leading to supply shortages. J o u r n a l P r e -p r o o f Journal Pre-proof J o u r n a l P r e -p r o o f Journal Pre-proof J o u r n a l P r e -p r o o f Journal Pre-proof J o u r n a l P r e -p r o o f Journal Pre-proof J o u r n a l P r e -p r o o f Journal Pre-proof 
 Title: To appear in: One Health
Output: True
Paragraph: Over the past few decades, global metapopulation epidemic simulations built with worldwide air-transportation data have been the main tool for studying how epidemics spread from the origin to other parts of the world (e.g., for pandemic influenza, SARS, and Ebola). However, it remains unclear how disease epidemiology and the air-transportation network structure determine epidemic arrivals for different populations around the globe. Here, we fill this knowledge gap by developing and validating an analytical framework that requires only basic analytics from stochastic processes. We apply this framework retrospectively to the 2009 influenza pandemic and 2014 Ebola epidemic to show that key epidemic parameters could be robustly estimated in real-time from public data on local and global spread at very low computational cost. Our framework not only elucidates the dynamics underlying global spread of epidemics but also advances our capability in nowcasting and forecasting epidemics. 
 Title: Characterizing the dynamics underlying global spread of epidemics
Output: True
Paragraph: Background: Early administration of appropriate antimicrobials has been correlated with a better prognosis in bacteremic patients, but a research highlighting a comparison of the adverse impact of inappropriate empirical antibiotic therapy between patient with Gram-positive and Gram-negative bacteremia is insufficient. Methods: In a retrospective cohort study, adults with communityonset monomicrobial bacteremia during the 6-year period were enrolled. Clinical information was retrieved from medical records, using a predetermined case record form. Antimicrobial susceptibility was determined by the disk diffusion method, based on performance standards of the Clinical Laboratory Standard Institute in 2016. A propensity-score-matched analysis was performed to control for the baseline characteristics at bacteremia onset between the Gram-positive and Gram-negative groups. The propensity score was calculated by the independent predictors of 28-day crude mortality recognized by a multivariable logistic regression model. Results: The total 2,053 adults (Gram-positive, 566 patients and Gram-negative, 1,487) presenting with community-onset monomicrobial bacteremia between the six-year period were recruited. Bacteremia severity (a Pitt bacteremia score) at onset and initial manifestation was different between two groups. On the basis of seven independent predictors of 28-day mortality recognized by the multivariate regression.566 of the 1,487 patients in the Gramnegative group were matched to 566 patients in the Gram-positive group with the closest propensity scores. After appropriate propensity-score matching, no significant differences were observed in baseline characteristics and patient outcomes between the two groups, in terms of age, bacteremia severity, major comorbidities, comorbidity severity, and 28-day mortality. 
 Title: P1-BT01 Comparing the effects of inappropriate empirical antibiotic therapy on mortality in adults with community-onset gram- positive and gram-negative bacteremia
Output: False
Paragraph: Background: For real time surveillance, detection of abnormal disease patterns is based on a difference between patterns observed, and those predicted by models of historical data. The usefulness of outbreak detection strategies depends on their specificity; the false alarm rate affects the interpretation of alarms. We evaluate the specificity of five traditional models: autoregressive, Serfling, trimmed seasonal, wavelet-based, and generalized linear. We apply each to 12 years of emergency department visits for respiratory infection syndromes at a pediatric hospital, finding that the specificity of the five models was almost always a non-constant function of the day of the week, month, and year of the study (p < 0.05). We develop an outbreak detection method, called the expectation-variance model, based on generalized additive modeling to achieve a constant specificity by accounting for not only the expected number of visits, but also the variance of the number of visits. The expectation-variance model achieves constant specificity on all three time scales, as well as earlier detection and improved sensitivity compared to traditional methods in most circumstances. Modeling the variance of visit patterns enables real-time detection with known, constant specificity at all times. With constant specificity, public health practitioners can better interpret the alarms and better evaluate the cost-effectiveness of surveillance systems. 
 Title: BMC Medical Informatics and Decision Making Automated real time constant-specificity surveillance for disease outbreaks
Output: False
Paragraph: The aetiology of community acquired pneumonia varies according to the region in which it is acquired. This review discusses those causes of CAP that occur in the tropics and might not be readily recognizable when transplanted to other sites. Various forms of pneumonia including the viral causes such as influenza (seasonal and avian varieties), the coronaviruses and the Hantavirus as well as bacterial causes, specifically the pneumonic form of Yersinia pestis and melioidosis are discussed. 
 Title: Pneumonia in the tropics: Report from the Task Force on tropical diseases by the World Federation of Societies of Intensive and Critical Care Medicine
Output: False
Paragraph: Methods-We identified ABS episodes in a prospective, longitudinal cohort study of 294 children (6 to 35 months of age at enrollment), who were followed-up for one year to capture all URI episodes and complications. At the initial URI visit seen by the study personnel (median day=4 from symptoms onset), nasopharyngeal samples were obtained for bacterial cultures and viral studies. Results-Of 1295 documented URI episodes, 103 (8%) episodes (in 73 children) were complicated by ABS, 32 of which were concurrent with acute otitis media. The majority (72%) of ABS episodes were diagnosed based on persistent symptoms or a biphasic course. Average age at ABS diagnosis was 18.8±7.2 months; white children were more likely to have ABS episodes than blacks (p=0.01). Hispanic/Latino ethnicity (p<0.0001) was negatively associated, and adequate PCV-7 immunization status (p=0.001) appeared to increase the risk of ABS. Girls had more ABS episodes than boys (0.5±0.8 vs 0.3±0.6 episodes/year, respectively, p=0.03). Viruses were detected in 63% during the initial URI visit; rhinovirus detection was positively correlated with ABS risk (p=0.01). Bacterial cultures were positive in 82/83 (99%) available samples obtained at the initial URI visit; polymicrobial (56%), Moraxella catarrhalis (20%) and Streptococcus pneumoniae (10%) were the most common cultures. Presence of pathogenic bacteria overall and presence of M. catarrhalis during URI were positively correlated with the risk for ABS (p=0.04 for both). Conclusion-ABS complicates 8% of URI in young children. Girls have more frequent ABS episodes than boys. Presence of rhinovirus and M. catarrhalis during URI are positively correlated with the risk for ABS complication. 
 Title: Acute Bacterial Sinusitis Complicating Viral Upper Respiratory Tract Infection in Young Children
Output: False
Paragraph: inoculation of adult Balb/c Byj mice, the MHV-4 strain of mouse hepatitis virus (MHV) had an LD,, of ~0.1 PFU, whereas its monoclonal antibody resistant variant V5A13.1 had an LD,, of lo*.' PFU. To determine the basis for this difference in neurovirulence we have studied the acute central nervous system (CNS) infection of these two viruses by in situ hybridization. Both viruses infected the same, specific neuroanatomical areas, predominantly neurons, and spread via the cerebrospinal fluid, along neuronal pathways and between adjacent cells. The neuronal nuclei infected and the spread of virus within the brain are described. The main difference between the parental and variant viruses was the rate at which the infection spread. MHV-4 spread rapidly, destroying large numbers of neurons and the animals died within 4 days of infection. The variant virus spread to the same areas of the brain but at a slower rate. This difference in the rate of virus spread was also apparent from the brain virus titers. The slower rate of spread of the variant virus appears to allow intervention by the immune response. Consistent with this, the variant virus spread slowly in athymic nu/nu mice, but in the absence of an intact immune response, infection and destruction of neurons eventually reached the same extent as that of the parental virus and the mice died within 6 days of infection. We conclude that the V5A13.1 variant of MHV4 is neuroattenuated by its slower rate of spread in the CNS. 0 1992 Academic Press, Inc. 
 Title: The V5A13.1 Envelope Glycoprotein Deletion Mutant of Mouse Hepatitis Virus Type-4 Is Neuroattenuated by Its Reduced Rate of Spread in the Central Nervous System
Output: True
Paragraph: Few comprehensive data exist regarding the epidemiology of severe acute respiratory infections (SARI) in low income countries. This study aimed at identifying etiologies and describing clinical features of SARI-associated hospitalization in Madagascar. It is a prospective surveillance of SARI in 2 hospitals for 3 years. Nasopharyngeal swabs, sputum, and blood were collected from SARI patients enrolled and tested for viruses and bacteria. Epidemiological and clinical information were obtained from case report forms. Overall, 876 patients were enrolled in the study, of which 83.1% (728/876) were tested positive for at least one pathogen. Viral and bacterial infections occurred in 76.1% (667/876) and 35.8% (314/876) of tested samples, respectively. Among all detected viruses, respiratory syncytial virus (RSV) was the most common (37.7%; 348/924) followed by influenza virus A (FLUA, 18.4%; 170/924), rhinovirus (RV, 13.5%; 125/924), and adenovirus (ADV, 8.3%; 77/ 924). Among bacteria, Streptococcus pneumoniae (S. pneumoniae, 50.3%, 189/370) was the most detected followed by Haemophilus influenzae type b (Hib, 21.4%; 79/370), and Klebsiella (4.6%; 17/370). Other Streptococcus species were found in 8.1% (30/370) of 
 Title: Epidemiology of severe acute respiratory infections from hospital-based surveillance in Madagascar
Output: False
Paragraph: RATIONALE: In infancy, rhinovirus illnesses and severe RSV bronchiolitis indicate increased risk for recurrent wheezing and asthma, but there is less information about other viruses. We evaluated the frequency and severity of metapneumovirus (HMPV) and coronavirus (HCV) infections in a high-risk group of infants. METHODS: Nasal lavage samples were obtained in the first year of life during scheduled study visits and symptomatic respiratory illnesses as part of the Childhood Origins of Asthma Project (COAST). Samples (n 5 567) were analyzed by Respiratory Multicode Assay (RMA) for HMPV, HCV-229E, HCV-OC43, HCV-NL63 and HCV-SARS. RESULTS: HMPV was isolated in 10.7% of samples during illnesses (n 5 291), and also occurred with other respiratory viruses (4.8%). 47.8% of HMPV illnesses included wheezing. HCV were isolated in 19.2% of the samples during illnesses and included HCV-OC43 (10.0%) and HCV-NL63 (9.6%). In addition, HCV was commonly detected together with other respiratory viruses (6.5%). Of all HCV illnesses (n 5 42), 33.3% included wheezing; however, HCV-NL63 had a significantly higher wheezing rate compared to HCV-OC43 (37.5% vs. 4.5%, p 5 0.028). Children who had at least one HCV-NL63 illness during infancy were significantly more likely to have asthma at age 6 compared to those without HCV-NL63 illnesses (52.2% vs. 25.0%, p 5 0.007). Having either HCV-OC43 or HMPV was not a risk factor for asthma at age 6. CONCLUSIONS: Improvements in viral diagnostics has allowed for identification of viruses that are difficult to culture. In infancy, HCV-NL63, HCV-OC43 and HMPV were significant causes of wheezing illnesses, however, only HCV-NL63 was significantly associated with asthma development at age six. 
 Title: 574 Coronavirus NL63 Illnesses in Infancy are a Risk Factor for Asthma at Age Six 575 Seasonal Distribution Of Respiratory Viruses In Pediatric
Output: True
Paragraph: The worldwide impact of COVID 19 continues to be felt as hospitals in all countries reduce elective and nonurgent cases to allow staffing and resources to be deployed elsewhere. Urgent gynaecological and cancer procedures are continuing, and it is imperative all theatre staff are protected and risks of SARS-CoV-2 viral transmission reduced when operating on asymptomatic, suspected or confirmed COVID 19 patients. In particular, there are concerns relating to the transmission of COVID 19 during gynaecological laparoscopic surgery, arising from the potential generation of SARS-CoV-2 contaminated aerosols from CO2 leakage and the creation of smoke from the use of energy devices. The aim of this paper is to review all the up to date evidence, including experiences from China and Italy, to guide the safe management of such patients when undergoing gynaecological procedures. 
 Title: Covid 19 pandemic and gynaecological laparoscopic surgery: knowns and unknowns
Output: True
Paragraph: Staphylococcus aureus is a common cause of infections in humans. The emergence of virulent, antibiotic-resistant strains of S. aureus is a significant public health concern. Most virulence and resistance factors in S. aureus are encoded by mobile genetic elements, and transduction by bacteriophages represents the main mechanism for horizontal gene transfer. The baseplate is a specialized structure at the tip of bacteriophage tails that plays key roles in host recognition, cell wall penetration, and DNA ejection. We have used high-resolution cryo-electron microscopy to determine the structure of the S. aureus bacteriophage 80α baseplate at 3.75 Å resolution, allowing atomic models to be built for most of the major tail and baseplate proteins, including two tail fibers, the receptor binding protein, and part of the tape measure protein. Our structure provides a structural basis for understanding host recognition, cell wall penetration and DNA ejection in viruses infecting Gram-positive bacteria. Comparison to other phages demonstrates the modular design of baseplate proteins, and the adaptations to the host that take place during the evolution of staphylococci and other pathogens. The emergence of virulent strains of Staphylococcus aureus that are resistant to most antibiotics has become a major public health concern. Virulence and resistance determinants in S. aureus are usually carried on mobile genetic elements (MGEs). Transduction by bacteriophages provides the main means by which MGEs are disseminated horizontally through the bacterial population, and is therefore essential to the evolution of pathogenicity of S. aureus and other pathogens. The baseplate is a complex structure at the tip of bacteriophage tails that serves multiple roles, including host recognition and binding, cell wall penetration, and ejection of the phage DNA. We have determined the structure of the baseplate from bacteriophage 80α, a representative of phages involved in host pathogenicity and in the mobilization of MGEs in S. aureus. Our structure provides a basis for understanding host recognition and infection by phages infecting Gram-positive hosts, and the PLOS Pathogens | https://doi. 
 Title: Structure of the host cell recognition and penetration machinery of a Staphylococcus aureus bacteriophage
Output: False
Paragraph: Genome Detective is a web-based, user-friendly software application to quickly and accurately assemble all known virus genomes from next generation sequencing datasets. This application allows the identification of phylogenetic clusters and genotypes from assembled genomes in FASTA format. Since its release in 2019, we have produced a number of typing tools for emergent viruses that have caused large outbreaks, such as Zika and Yellow Fever Virus in Brazil. Here, we present The Genome Detective Coronavirus Typing Tool that can accurately identify novel coronavirus (2019-nCoV) sequences isolated in China and around the world. The tool can accept up to 2,000 sequences per submission and the analysis of a new whole genome sequence will take approximately one minute. The tool has been tested and validated with hundreds of whole genomes from ten coronavirus species, and correctly classified all of the SARS-related coronavirus (SARSr-CoV) and all of the available public data for 2019-nCoV. The tool also allows tracking of new viral mutations as the outbreak expands globally, which may help to accelerate the development of novel diagnostics, drugs and vaccines. 
 Title: Title: Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes Short title: Automated tool for phylogenetic and mutational analysis of coronaviruses genomes
Output: True
Paragraph: For many infectious disease processes such as emerging zoonoses and vaccine-preventable diseases, 0vR 0 v1 and infections occur as self-limited stuttering transmission chains. A mechanistic understanding of transmission is essential for characterizing the risk of emerging diseases and monitoring spatio-temporal dynamics. Thus methods for inferring R 0 and the degree of heterogeneity in transmission from stuttering chain data have important applications in disease surveillance and management. Previous researchers have used chain size distributions to infer R 0 , but estimation of the degree of individual-level variation in infectiousness (as quantified by the dispersion parameter, k) has typically required contact tracing data. Utilizing branching process theory along with a negative binomial offspring distribution, we demonstrate how maximum likelihood estimation can be applied to chain size data to infer both R 0 and the dispersion parameter that characterizes heterogeneity. While the maximum likelihood value for R 0 is a simple function of the average chain size, the associated confidence intervals are dependent on the inferred degree of transmission heterogeneity. As demonstrated for monkeypox data from the Democratic Republic of Congo, this impacts when a statistically significant change in R 0 is detectable. In addition, by allowing for superspreading events, inference of k shifts the threshold above which a transmission chain should be considered anomalously large for a given value of R 0 (thus reducing the probability of false alarms about pathogen adaptation). Our analysis of monkeypox also clarifies the various ways that imperfect observation can impact inference of transmission parameters, and highlights the need to quantitatively evaluate whether observation is likely to significantly bias results. 
 Title: Inference of R 0 and Transmission Heterogeneity from the Size Distribution of Stuttering Chains
Output: True
Paragraph: A 70-year-old woman was admitted to our hospital for dyspnea and a fever of 2 weeks duration. Chest imaging showed bilateral infiltration, and a rapid diagnostic test for influenza virus, Mycoplasma pneumoniae, Streptococcus pneumoniae, and Legionella spp. was negative. She was intubated and mechanically ventilated and underwent bronchoalveolar lavage. Bronchoalveolar lavage fluid yielded no significant pathogens, and the multiplex polymerase chain reaction test was positive only for human bocavirus. Specific antibodies against significant pathogens were not increased in paired sera, so we diagnosed her with primary human bocavirus pneumonia. 
 Title: Fatal Primary Human Bocavirus Pneumonia in an Immunocompetent Adult
Output: True
Paragraph: M36 is the first member of a novel class of potent HIV-1 entry inhibitors based on human engineered antibody domains (eAds). It exhibits broad inhibitory activity suggesting that its CD4-induced epitope is highly conserved. Here, we describe fine mapping of its epitope by using several approaches. First, a panel of mimotopes was affinity-selected from a random peptide library and potential m36-binding residues were computationally predicted. Second, homology modeling of m36 and molecular docking of m36 onto gp120 revealed potentially important residues in gp120-m36 interactions. Third, the predicted contact residues were verified by site-directed mutagenesis. Taken together, m36 epitope comprising three discontinuous sites including six key gp120 residues (Site C1: Thr123 and Pro124; Site C3: Glu370 and Ile371; Site C4: Met426 and Trp427) were identified. In the 3D structure of gp120, the sites C1 and C4 are located in the bridging sheet and the site C3 is within the b15-a3 excursion, which play essential roles for the receptor-and coreceptor-binding and are major targets of neutralizing antibodies. Based on these results we propose a precise localization of the m36 epitope and suggest a mechanism of its broad inhibitory activity which could help in the development of novel HIV-1 therapeutics based on eAds. 
 Title: Epitope Mapping of M36, a Human Antibody Domain with Potent and Broad HIV-1 Inhibitory Activity
Output: True
Paragraph: Four types of porcine epidemic diarrhea virus (PEDV) variants with a large deletion in the spike protein were detected, together with the original US PEDV, from pig fecal and oral fluid samples collected during 2016-2017 in the US. Two of the variants are similar to those identified in Japan: one contains a 194-aa deletion, the same as PEDV variant TTR-2/ JPN/2014, while the other contains a 204-aa deletion, the same as PEDV variant JKa-292/CS1de204. Two new S1 NTDdel PEDV variants were found: one contains a 201-aa deletion located at residues 30-230 and the other contains a 202-aa deletion located at residues 24-225 of the S protein. This is the first report on coinfection of S1 NTD-del PEDV variants and the original US PEDV strain in US pigs, indicating that PEDV continues to evolve in pigs and might be responsible for disease pattern changes. 
 Title: New variants of porcine epidemic diarrhea virus with large deletions in the spike protein, identified in the United States, 2016-2017
Output: False
Paragraph: In order to evaluate the efficacy of convalescent plasma therapy in the treatment of patients with severe acute respiratory syndrome (SARS), 80 SARS patients were given convalescent plasma at Prince of Wales Hospital, Hong Kong, between 20 March and 26 May 2003. Good outcome was defined as discharge by day 22 following the onset of SARS symptoms. Poor outcome was defined as death or hospitalization beyond 22 days. A higher day-22 discharge rate was observed among patients who were given convalescent plasma before day 14 of illness (58.3% vs 15.6%; P<0.001) and among those who were PCR positive and seronegative for coronavirus at the time of plasma infusion (66.7% vs 20%; P=0.001). 
 Title: Use of convalescent plasma therapy in SARS patients in Hong Kong
Output: False
Paragraph: Toll-like receptors (TLRs) are sentinel receptors of the host innate immune system that recognize conserved 'pathogen-associated molecular patterns' of invading microbes, including viruses. The activation of TLRs establishes antiviral innate immune responses and coordinates the development of long-lasting adaptive immunity in order to control viral pathogenesis. However, microbe-induced damage to host tissues may release 'danger-associated molecular patterns' that also activate TLRs, leading to an overexuberant inflammatory response and, ultimately, to tissue damage. Thus, TLRs have proven to be promising targets as therapeutics for the treatment of viral infections that result in inflammatory damage or as adjuvants in order to enhance the efficacy of vaccines. Here, we explore recent advances in TLR biology with a focus on novel drugs that target TLRs (agonists and antagonists) for antiviral therapy. 
 Title: Novel drugs targeting Toll-like receptors for antiviral therapy
Output: False
Paragraph: Background: The homogeneous mixing assumption is widely adopted in epidemic modelling for its parsimony and represents the building block of more complex approaches, including very detailed agent-based models. The latter assume homogeneous mixing within schools, workplaces and households, mostly for the lack of detailed information on human contact behaviour within these settings. The recent data availability on high-resolution face-to-face interactions makes it now possible to assess the goodness of this simplified scheme in reproducing relevant aspects of the infection dynamics. Methods: We consider empirical contact networks gathered in different contexts, as well as synthetic data obtained through realistic models of contacts in structured populations. We perform stochastic spreading simulations on these contact networks and in populations of the same size under a homogeneous mixing hypothesis. We adjust the epidemiological parameters of the latter in order to fit the prevalence curve of the contact epidemic model. We quantify the agreement by comparing epidemic peak times, peak values, and epidemic sizes. Results: Good approximations of the peak times and peak values are obtained with the homogeneous mixing approach, with a median relative difference smaller than 20 % in all cases investigated. Accuracy in reproducing the peak time depends on the setting under study, while for the peak value it is independent of the setting. Recalibration is found to be linear in the epidemic parameters used in the contact data simulations, showing changes across empirical settings but robustness across groups and population sizes. Conclusions: An adequate rescaling of the epidemiological parameters can yield a good agreement between the epidemic curves obtained with a real contact network and a homogeneous mixing approach in a population of the same size. The use of such recalibrated homogeneous mixing approximations would enhance the accuracy and realism of agent-based simulations and limit the intrinsic biases of the homogeneous mixing. Mathematical models provide a theoretical framework that can be applied to improve our understanding of the spread of infectious diseases in a host population [1] [2] [3] [4] . A vast range of approaches has recently been developed for the analysis and interpretation of epidemic data, 
 Title: Recalibrating disease parameters for increasing realism in modeling epidemics in closed settings
Output: False
Paragraph: The outpost position of the olfactory bulb (OB) between the direct inputs from sensory neurons of the nasal epithelium and other parts of the brain suggests its highest vulnerability among all brain structures to penetration of exogenous agents. A number of neurotropic viruses have been found to invade the brain through the OB. There is growing evidence that microscopic particles of toxic dusts can propagate from the nasal epithelium to the OB and further into the brain. These harmful agents impair cellular elements of the brain. Apparently, cells in the OB are the most affected, as they are the first to encounter viral infections and toxic particles. It is well known that neuronal and glial progenitors are continuously generated from neuronal stem cells in the subventricular zone of the adult brain and then migrate predominantly into the OB. Therefore, it is feasible to suggest that substitution of injured or dead cells in the OB by new-born neurons, differentiating from progenitors, plays a role in protecting the OB neuronal microcircuits from destruction. Furthermore, some cytokines and chemokines released in response to infection and/or intoxication can modulate different stages of neurogenesis (proliferation, migration, and differentiation). We hypothesize that continuous neurogenesis in the olfactory system throughout adulthood evolved as a protective mechanism to prevent impairment of the most ancient but vitally important sensory system. In addition, differentiation of a substantial portion of progenitors to glial cells, including macrophages and microglia, may create an additional barrier to exogenous agents on their way deep to the brain. 
 Title: Neurogliogenesis in the mature olfactory system: A possible protective role against infection and toxic dust
Output: True
Paragraph: Background: The Middle Eastern Respiratory Syndrome Coronavirus is a serious and emerging issue in Saudi Arabia and the world. A response was required to reduce possible disease transmission between the hospital and university. College of Nursing academic staff developed a programme in response to the educational and emotional needs of participants. Methods: A MERS-CoV Task Force responded to the rapidly unfolding epidemic. The aim was to find out what nursing staff and nursing students in the college knew about MERS-CoV. While most gaps in knowledge were addressed after an intense information seminar, other learning needs were identified and responded to. The Task Force developed mandatory information sessions for all nursing faculty, students and staff. All staff were informed by email, letters and posters. There are 28 faculty staff, 84 support staff and 480 students in the College of Nursing. The information settings all took place within the College of Nursing, Princess Nourah University, Kingdom of Saudi Arabia. Questionnaires were given to faculty, students and staff to understand their baseline knowledge. After the sessions, faculty, students and staff were asked about what was learned through the sessions, and what educational needs still needed to be addressed. Approval was sought and received by the Ethics Committee for the College of Nursing. Participants completed informed consent forms and the voluntary nature of the study was explained. Results: The total number of people attending the education sessions was133, including 65 students. 18 faculty members attended and 57 support staff. Data was gathered on gaps in participant knowledge and a plan was developed to address the gaps. Policies were established around student participation in clinical and return to work practices for staff with any symptoms. Conclusion: In hospitals there is above average risk for exposure to infectious diseases. Student nurses travel between hospital and university, with the capacity to act as a conduit of pathogens to large, susceptible populations. Nursing colleges must respond thoroughly to protect students and staff and prevent spread of disease into the university community in the midst of an epidemic. 
 Title: An educational programme for nursing college staff and students during a MERS-coronavirus outbreak in Saudi Arabia
Output: False
Paragraph: Background: Whether information sources influence health protective behaviours during influenza pandemics or other emerging infectious disease epidemics is uncertain. Methodology: Data from cross-sectional telephone interviews of 1,001 Hong Kong adults in June, 2009 were tested against theory and data-derived hypothesized associations between trust in (formal/informal) information, understanding, selfefficacy, perceived susceptibility and worry, and hand hygiene and social distancing using Structural Equation Modelling with multigroup comparisons. Principal Findings: Trust in formal (government/media) information about influenza was associated with greater reported understanding of A/H1N1 cause (b = 0.36) and A/H1N1 prevention self-efficacy (b = 0.25), which in turn were associated with more hand hygiene (b = 0.19 and b = 0.23, respectively). Trust in informal (interpersonal) information was negatively associated with perceived personal A/H1N1 susceptibility (b = 20.21), which was negatively associated with perceived selfefficacy (b = 20.42) but positively associated with influenza worry (b = 0.44). Trust in informal information was positively associated with influenza worry (b = 0.16) which was in turn associated with greater social distancing (b = 0.36). Multigroup comparisons showed gender differences regarding paths from trust in formal information to understanding of A/H1N1 cause, trust in informal information to understanding of A/H1N1 cause, and understanding of A/H1N1 cause to perceived self-efficacy. Conclusions/Significance: Trust in government/media information was more strongly associated with greater self-efficacy and handwashing, whereas trust in informal information was strongly associated with perceived health threat and avoidance behaviour. Risk communication should consider the effect of gender differences. 
 Title: Situational Awareness and Health Protective Responses to Pandemic Influenza A (H1N1) in Hong Kong: A Cross- Sectional Study
Output: True
Paragraph: Nanomaterial, due to its unique physical, chemical and biological properties compared to its bulk counterparts, has the potential to provide a product superior to its bulk predecessor. In this study, a novel alumina nanofiber filter was assessed for its removal and retention capability for MS2 aerosol. Its physical removal efficiency in the 10-400 nm range was 94.35%, while its viable removal efficiency was 98.87%, which was slightly lower than three conventional HEPA filters tested. However, its pressure drop was much lower than HEPA filters, yielding a higher filter quality than HEPA filters. The average extracted fraction from the nanofiber filter was 8.64×10 −2 ± 7.00×10 −2 , which is three orders lower than other HEPA filters, demonstrating that the viruses were effectively retained in the nanofiber filter. Furthermore, the performance of the nanofiber filter showed no dependence on relative humidity. In conclusion, this novel alumina nanofiber filter presents advantageous potential for removal and retention of viral aerosol agents. 
 Title: Removal and retention of viral aerosols by a novel alumina nanofiber filter
Output: False
Paragraph: In response to the severe acute respiratory syndrome (SARS) pandemic of 2003 and the influenza pandemic of 2009, many countries instituted border measures as a means of stopping or slowing the spread of disease. The measures, usually consisting of a combination of border entry/exit screening, quarantine, isolation, and communications, were resource intensive, and modeling and observational studies indicate that border screening is not effective at detecting infectious persons. Moreover, border screening has high opportunity costs, financially and in terms of the use of scarce public health staff resources during a time of high need. We discuss the border-screening experiences with SARS and influenza and propose an approach to decision-making for future pandemics. We conclude that outbreak-associated communications for travelers at border entry points, together with effective communication with clinicians and more effective disease control measures in the community, may be a more effective approach to the international control of communicable diseases. 
 Title: Entry Screening for Infectious Diseases in Humans PERSPECTIVE Find emerging infectious disease information on
Output: False
Paragraph: Currently, a wide range of analytical methods is available for virus detection in environmental water samples. Molecular methods such as polymerase chain reaction (PCR) and quantitative real time PCR (qPCR) have the highest sensitivity and specificity to investigate virus contamination in water, so they are the most commonly used in environmental virology. Despite great sensitivity of PCR, the main limitation is the lack of the correlation between the detected viral genome and viral infectivity, which limits conclusions regarding the significance for public health. To provide information about the infectivity of the detected viruses, cultivation on animal cell culture is the gold standard. However, cell culture infectivity assays are laborious, time consuming and costly. Also, not all viruses are able to produce cytopathic effect and viruses such as human noroviruses have no available cell line for propagation. In this brief review, we present a summary and critical evaluation of different approaches that have been recently proposed to overcome limitations of the traditional cell culture assay and PCR assay such as integrated cell culture-PCR, detection of genome integrity, detection of capsid integrity, and measurement of oxidative damages on viral capsid protein. Techniques for rapid detection of infectious viruses such as fluorescence microscopy and automated flow cytometry have also been suggested to assess virus infectivity in water samples. 
 Title: Methods to detect infectious human enteric viruses in environmental water samples
Output: False
Paragraph: Despite intense efforts to develop novel and better tools to identify known viruses and to discover new viruses, establishing etiological roles for viruses in human disease is challenging. In large part, this may be attributed to the high variability of viral species and the difficulties in developing broad-spectrum, yet specific, diagnostic assays. To overcome this problem, a novel method for the detection of viruses is described in the current manuscript. The technique relies on the addition of synthetic oligonucleotides to both termini of RNA fragments in a sequence-dependent manner during first-and second-strand DNA synthesis; these oligonucleotides are used subsequently for amplification of the viral nucleic acids of interest. The recognition of the target sequence by the oligonucleotides is mediated by short (6-8 nt) conserved regions, which facilitates development of broad-spectrum assays. The method has been tested for coronaviruses, although it may be also adopted for other RNA viruses. 
 Title: HexaPrime: A novel method for detection of coronaviruses
Output: False
Paragraph: The lengthy duration of multidrug therapy needed to cure tuberculosis (TB) poses significant challenges for global control of the disease. Moreover, chronic inflammation associated with TB leads to pulmonary damage that can remain even after successful cure. Thus, there is a great need for the development of effective shorter drug regimens to improve clinical outcome and strengthen TB control. Host-directed therapy (HDT) is emerging as a novel adjunctive strategy to enhance the efficacy and shorten the duration of TB treatment. Previously, we showed that the administration of CC-3052, a phosphodiesterase-4 inhibitor (PDE4i), reduced the host inflammatory response during Mycobacterium tuberculosis (Mtb) infection and improved the antimicrobial efficacy of isoniazid (INH) in both the mouse and rabbit models. In the present study, we evaluated the pharmacokinetics and explored the mechanism underlying the efficacy of a more potent PDE4i, CC-11050, as adjunct to INH treatment in a mouse model of pulmonary Mtb infection. Genome-wide lung transcriptome analysis confirmed the dampening of inflammation and associated network genes that we previously reported with CC-3052. Consistent with the reduction in inflammation, a significant improvement in Mtb control and pathology was observed in the lungs of mice treated with CC-11050 plus INH, compared to INH alone. This important confirmatory study will be used to help design upcoming human clinical trials with CC-11050 as an HDT for TB treatment. 
 Title: Pharmacologic inhibition of host Phosphodiesterase-4 improves isoniazid-Mediated clearance of Mycobacterium tuberculosis
Output: False
Paragraph: In the past decade, clinical microbiology laboratories have undergone important changes with the introduction of molecular biology techniques and laboratory automation. In the future, there will be a need for more rapid diagnoses, increased standardization of testing and greater adaptability to cope with new threats from infectious microorganisms, such as agents of bioterrorism and emerging pathogens. The combination of the new tools that are now being developed in research laboratories, the general reorganization of clinical laboratories and improved communication between physicians and clinical microbiologists should lead to profound changes in the way that clinical microbiologists work. The following terms in this article are linked online to: Entrez: http://www.ncbi.nlm.nih.gov/entrez mecA Infectious Disease Information: http://www.cdc.gov/ncidod/diseases/index.htm: Bacillus anthracis | cytomegalovirus | group A streptococcus | group B streptococci | hepatitis C | HIV | influenza | Lyme disease | Plasmodium spp. | pneumonia | Q fever | rotavirus | rubella | SARS | Staphylococcus aureus | Toxoplasma gondii FURTHER INFORMATION GenBank: http://www.ncbi.nih.gov/Genbank/ Access to this interactive links box is free online. 
 Title: WHAT DOES THE FUTURE HOLD FOR CLINICAL MICROBIOLOGY?
Output: False