niryuu/sni-each-converted huggingface dataset:
Paragraph: WHAT'S KNOWN ON THIS SUBJECT: Rhinoviruses are commonly detected in both acutely ill and asymptomatic infants and children. The finding may represent new infection or prolonged presence of rhinovirus RNA in the respiratory tract. WHAT THIS STUDY ADDS: In young, otherwise healthy infants, shedding of RNA from the same rhinovirus strain rarely persisted longer than 30 days. abstract BACKGROUND: Current molecular diagnostic methods have detected rhinovirus RNA in a high proportion of asymptomatic infants and children, raising the question of the clinical significance of these findings. This study investigates the prevalence of prolonged rhinovirus RNA presence in the upper respiratory tract of infants during the first year of life. In a longitudinal study, infants were followed from birth up to 12 months. Nasopharyngeal specimens were collected monthly (months 1-6 and month 9) and during an upper respiratory infection. Rhinoviruses were detected by quantitative reverse-transcription polymerase chain reaction. Presence of repeated rhinovirus RNA was evaluated by nucleotide sequence analysis. A total of 2153 specimens from 362 infants were studied; 341 distinct rhinovirus infections in 216 infants were identified. Follow-up specimens were available within 30 days for 179 infections, creating the sample set to assess prolonged rhinovirus presence. Of the 179 infections, 46 involved the detection of the same rhinovirus strain in repeated specimens, including 8 events of prolonged presence of the same strain (detected in specimens collected .30 days apart), representing 4.5% of the evaluable rhinovirus infections. There were 26 events in which a rhinovirus strain was replaced by a different strain within a 30-day interval, representing 14.5% of the 179 infections. CONCLUSIONS: Although rhinovirus infections are common in healthy infants, prolonged presence of rhinovirus RNA in the respiratory tract after an upper respiratory infection was uncommon (,5%). Detection of rhinovirus RNA in an infant most likely represents an infection within a 30-day period. KEY WORDS rhinovirus, RNA, PCR, upper respiratory tract infection, persistence ABBREVIATIONS AOM-acute otitis media cDNA-complementary DNA PCR-polymerase chain reaction qPCR-quantitative polymerase chain reaction qRT-PCR-quantitative, real-time, reverse-transcription polymerase chain reaction URI-upper respiratory infection UTMB-University of Texas Medical Branch 
 Title: Duration of Rhinovirus Shedding in the Upper Respiratory Tract in the First Year of Life
Output: False
Paragraph: A SEIR simulation model for the COVID-19 pandemic was developed (http://covidsim.eu) and applied to a hypothetical European country of 10 million population. Our results show which interventions potentially push the epidemic peak into the subsequent year (when vaccinations may be available) or which fail. Different levels of control (via contact reduction) resulted in 22% to 63% of the population sick, 0.2% to 0.6% hospitalised, and 0.07% to 0.28% dead (n=6,450 to 28,228). 
 Title: Modelling the Potential Health Impact of the COVID-19 Pandemic on a Hypothetical European Country
Output: True
Paragraph: Background. Hematopoietic cell transplant (HCT) recipients are frequently infected with respiratory viruses (RVs) in the upper respiratory tract (URT), but the concordance between URT and lower respiratory tract (LRT) RV detection is not well characterized. Methods. Hematopoietic cell transplant candidates and recipients with respiratory symptoms and LRT and URT RV testing via multiplex PCR from 2009 to 2016 were included. Logistic regression models were used to analyze risk factors for LRT RV detection. Results. Two-hundred thirty-five HCT candidates or recipients had URT and LRT RV testing within 3 days. Among 115 subjects (49%) positive for a RV, 37% (42 of 115) had discordant sample pairs. Forty percent (17 of 42) of discordant pairs were positive in the LRT but negative in the URT. Discordance was common for adenovirus (100%), metapneumovirus (44%), rhinovirus (34%), and parainfluenza virus type 3 (28%); respiratory syncytial virus was highly concordant (92%). Likelihood of LRT detection was increased with URT detection (oods ratio [OR] = 73.7; 95% confidence interval [CI], and in cytomegalovirus-positive recipients (OR = 3.70; 95% CI, 1.30-10.0). Conclusions. High rates of discordance were observed for certain RVs. Bronchoalveolar lavage sampling may provide useful diagnostic information to guide management in symptomatic HCT candidates and recipients. 
 Title: The Journal of Infectious Diseases Predictive Value of Respiratory Viral Detection in the Upper Respiratory Tract for Infection of the Lower Respiratory Tract With Hematopoietic Stem Cell Transplantation
Output: False
Paragraph: The current outbreak of coronavirus disease 2019 (COVID-19) has become a global crisis due to its quick and wide spread over the world. A good understanding of the dynamic of the disease would greatly enhance the control and prevention of COVID-19. However, to the best of our knowledge, the unique features of the outbreak have limited the applications of all existing models. In this paper, a novel stochastic model is proposed which aims to account for the unique transmission dynamics of COVID-19 and capture the effects of intervention measures implemented in Mainland China. We find that, (1) instead of aberration, there is a remarkable amount of asymptomatic individuals, (2) an individual with symptoms is approximately twice more likely to pass the disease to others than that of an asymptomatic patient, (3) the transmission rate has reduced significantly since the implementation of control 1 . CC-BY-NC-ND 4.0 International license It is made available under a author/funder, who has granted medRxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) The copyright holder for this preprint . 
 Title: Prediction of the COVID-19 outbreak based on a realistic stochastic model
Output: True
Paragraph: Sprague-Dawley rats were injected intraperitoneally with a suspension of Trypanosoma brucei brucei. An early induction of major histocompatibility complex (MHC) class I antigens as well as an infiltration of macrophage-like cells and cytotoxic T-cells was detected with immunohistochemical techniques in circumventricular organs, such as the median eminence, neurohypophysis, subfornical organ, pineal gland and area postrema. These areas, which lack a blood-brain barrier, correspond to those showing early invasion of trypanosomes. In addition, there was a marked induction of MHC class I in neurons in two hypothalamic nuclei, the paraventricular and supraoptic nuclei. Neurons in these two nuclei are located behind the blood-brain barrier, but project to the neurohypophysis and to the median eminence, thereby exposing their axon terminals to factors circulating in the blood or released locally from invading trypanosomes or from macrophages or cytotoxic T-cells. It is suggested that the alteration in the nerve cell bodies in the hypothalamic nuclei is caused by retrograde axonal signals from these target areas. 
 Title: Early major histocompatibility complex (MHC) class I antigen induction in hypothalamic supraoptic and paraventricular nuclei in trypanosome-infected rats
Output: True
Paragraph: Introduction: A novel H1N1 vaccine was manufactured in response to the pandemic in 2009. This study describes the willingness to be vaccinated for H1N1 among healthcare workers (HCWs) in primary healthcare clinics with and without chronic medical conditions, their reasons for refusing vaccination and whether they sought additional information to make an informed decision for the vaccination. Materials and methods: An anonymous survey was conducted in November 2009 among all medical, nursing, allied health and operations HCWs in nine primary care clinics in Singapore. Participants were asked if they had any chronic medical conditions associated with influenza-related complications (example: asthma, stroke, heart disease, cancer, diabetes mellitus, renal disease), their perception towards vaccination for H1N1 and against seasonal influenza within the preceding 2 years. Results: The initial response rate was 80%, of which 711 (54.7%) of the completed surveys were analysed. Among the 711 respondents, 16.6% reported having at least 1 chronic disease. Asthma (10.8%), hypertension (10.4%) and dyslipidaemia (9.8%) were the main chronic conditions. Only 39.4% of respondents were willing to be vaccinated against H1N1. Males were 2.07 (95% CI 1.19-3.62) times more likely than females to receive the H1N1 vaccination; the 45-54 and 55+ years old were 2.12 (95% CI 1.06-4.24) and 2.44 (95% CI 1.13-5.27) times more willing than those below 25 years old; and those who considered accepting the seasonal influenza vaccine were 7.0 times more likely than those who did not (95%CI 4.48-10.92).The 2 principal barriers were "fear of side effects" and "unsure of vaccine's effectiveness". Although 78% attended some H1N1-related talks, only 7% of all HCWs felt that they had sufficient information. Most wanted more information about the vaccine's safety profile and contraindications. Conclusion: Fewer than 40% of HCWs expressed willingness to receive the H1N1 vaccination, lower than past rates of influenza vaccine. HCWs in primary care clinics who had a chronic condition did not perceive themselves to be at higher risk of developing H1N1-related complications and were not more willing than the rest of the HCWs to accept H1N1 vaccination. Vaccine's side effects and effectiveness were the main concerns. Uptake of H1N1 vaccine may improve with targeted health information covering the vaccine's safety profile. 
 Title: Healthcare workers and H1N1 vaccination: Does having a chronic disease make a difference?
Output: False
Paragraph: National evidence-based guidelines for preventing healthcare-associated infections (HCAI) in National Health Service (NHS) hospitals in England were commissioned by the Department of Health (DH) and developed during 1998-2000 by a nurse-led multi-professional team of researchers and specialist clinicians. Following extensive consultation, they were published in January 2001. 1 These guidelines describe the precautions healthcare workers should take in three areas: standard principles for preventing HCAI, which include hospital environmental hygiene, hand hygiene, the use of personal protective equipment, and the safe use and disposal of sharps; preventing infections associated with the use of short-term indwelling urethral catheters; and preventing infections associated with central venous catheters. The evidence for these guidelines was identified by multiple systematic reviews of experimental and nonexperimental research and expert opinion as reflected in systematically identified professional, national and international guidelines, which were formally assessed by a validated appraisal process. In 2003, we developed complementary national guidelines for preventing HCAI in primary and community care on behalf of the National Collaborating Centre for Nursing and Supportive Care (National Institute for Health and Clinical Excellence). 2 A cardinal feature of evidence-based guidelines is that they are subject to timely review in order that new research evidence and technological advances can be identified, appraised and, if shown to be effective in preventing HCAI, incorporated into amended guidelines. Periodically updating the evidence base and guideline recommendations is essential in order to maintain their validity and authority. Consequently, the DH commissioned a review of new evidence published following the last systematic reviews. We have now updated the evidence base for making infection prevention and control recommendations. A critical assessment of the updated evidence indicated that the original epic guidelines published in 2001 remain robust, relevant and appropriate but that adjustments need to be 
 Title: epic2: National Evidence-Based Guidelines for Preventing Healthcare-Associated Infections in NHS Hospitals in England 1 Introductory section 1.1 Guideline Development Team
Output: False
Paragraph: Using sequence data to infer population dynamics is playing an increasing role in the analysis of outbreaks. The most common methods in use, based on coalescent inference, have been widely used but not extensively tested against simulated epidemics. Here, we use simulated data to test the ability of both parametric and non-parametric methods for inference of effective population size (coded in the popular BEAST package) to reconstruct epidemic dynamics. We consider a range of simulations centred on scenarios considered plausible for pandemic influenza, but our conclusions are generic for any exponentially growing epidemic. We highlight systematic biases in non-parametric effective population size estimation. The most prominent such bias leads to the false inference of slowing of epidemic spread in the recent past even when the real epidemic is growing exponentially. We suggest some sampling strategies that could reduce (but not eliminate) some of the biases. Parametric methods can correct for these biases if the infected population size is large. We also explore how some poor sampling strategies (e.g. that over-represent epidemiologically linked clusters of cases) could dramatically exacerbate bias in an uncontrolled manner. Finally, we present a simple diagnostic indicator, based on coalescent density and which can easily be applied to reconstructed phylogenies, that identifies time-periods for which effective population size estimates are less likely to be biased. We illustrate this with an application to the 2009 H1N1 pandemic. Pandemic growth rates from sequences E. de Silva et al. 1799 Pandemic growth rates from sequences E. de Silva et al. 1807  
 Title: Inferring pandemic growth rates from sequence data
Output: True
Paragraph: The unmet need for effective antivirals against potential agents of bioterrorism and emerging infections is obvious; however, the challenges to develop such drugs are daunting. Even with the passage of Project BioShield and more recently the BARDA legislation, there is still not a clear market for these types of drugs and limited federal funding available to support expensive drug development studies. SIGA Technologies, Inc. is a small biotech company committed to developing novel products for the prevention and treatment of severe infectious diseases, with an emphasis on products for diseases that could result from bioterrorism. Through trials and error SIGA has developed an approach to this problem in order to establish the infrastructure necessary to successfully advance new antiviral drugs from the discovery stage on through to licensure. The approach that we have taken to drug development is biology driven and dependent on a dispersive development model utilizing essential collaborations with academic, federal, and private sector partners. This consortium approach requires success in acquiring grants and contracts as well as iterative communication with the government and regulatory agencies. However, it can work as evidenced by the rapid progress of our lead antiviral against smallpox, ST-246, and should serve as the template for development of new antivirals against important biological pathogens. 
 Title: Discovery and development of antiviral drugs for biodefense: Experience of a small biotechnology company
Output: True
Paragraph: We investigate the properties of a simple discrete time stochastic epidemic model. The model is Markovian of the SIR type in which the total population is constant and individuals meet a random number of other individuals at each time step. Individuals remain infectious for R time units, after which they become removed or immune. Individual transition probabilities from susceptible to diseased states are given in terms of the binomial distribution. An expression is given for the probability that any individuals beyond those initially infected become diseased. In the model with a finite recovery time R, simulations reveal large variability in both the total number of infected individuals and in the total duration of the epidemic, even when the variability in number of contacts per day is small. In the case of no recovery, R = 1, a formal diffusion approximation is obtained for the number infected. The mean for the diffusion process can be approximated by a logistic which is more accurate for larger contact rates or faster developing epidemics. For finite R we then proceed mainly by simulation and investigate in the mean the effects of varying the parameters p (the probability of transmission), R, and the number of contacts per day per individual. A scale invariant property is noted for the size of an outbreak in relation to the total population size. Most notable are the existence of maxima in the duration of an epidemic as a function of R and the extremely large differences in the sizes of outbreaks which can occur for small changes in R. These findings have practical applications in controlling the size and duration of epidemics and hence reducing their human and economic costs. 
 Title: Some properties of a simple stochastic epidemic model of SIR type
Output: True
Paragraph: Viral epitranscriptomics is a newly emerging field that has identified unique roles for RNA modifications in modulating life cycles of RNA viruses. Despite the observation of a handful of modified viral RNAs five decades ago, very little was known about how these modifications regulate viral life cycles, until recently. Here we review the pro-and anti-viral effects of methyl-6-adenosine in distinct viral life cycles, the role of 2 0 O-methyl modifications in RNA stability and innate immune sensing, and functions of adenosine to inosine modifications in retroviral life cycles. With roles for over 100 modifications in RNA still unknown, this is a rapidly emerging field that is destined to suggest novel antiviral therapies. Cell Host & Microbe 21, June 14, 2017 ª 2017 Elsevier Inc. 661 Figure 1. Adenosine Modifications and the Respective Enzymes that Facilitate These Chemical Modifications N 6 -methyladenosine and N 6 ,2-O-dimethyladenosine are reversible RNA modifications, while inosine and 2 0 -O-methyladenosine seem to be irreversible. Of the modifications listed, only 2 0 -O-methyltransferases are encoded by viral genes (WNV, West Nile virus; DV, dengue virus; H-CoV, human coronavirus), further supporting the important role for this modification in modulating viral sensing by innate immune pathways. 
 Title: Making the Mark: The Role of Adenosine Modifications in the Life Cycle of RNA Viruses
Output: False
Paragraph: This paper discusses the issue of selecting the design solution that best accords with an articulated preference of multiple criteria with an acceptable performance band. The application of a newly developed multi-criteria decision-making tool called RR-PARETO2 is presented. An example of HVAC design is used to illustrate how solutions could be selected within a multi-criteria optimization framework. In this example, five criteria have been selected, namely, power consumption, thermal comfort, risk of airborne infection of influenza and tuberculosis and effective differential temperature ( t eq ) of body parts. The goal is to select the optimal air exchange rate that makes reasonable trade-offs among all the objectives. Two scenarios have been studied. In the first scenario, there is an influenza outbreak and the important objective is to prevent the spread of infection. In the second scenario, energy prices are high and the primary objective is to reduce energy. In both scenarios, RR-PARETO2 algorithm selects solutions that make reasonable trade-offs among conflicting objectives. The example illustrates how objectives such as reduction of airborne disease transmission and maximizing thermal comfort can be incorporated in the design of a practical, full-scale HVAC system. 
 Title: A preference driven multi-criteria optimization tool for HVAC design and operation
Output: True
Paragraph: The RNA-dependent RNA polymerases (RdRPs) encoded by the RNA viruses are a unique class of nucleic acid polymerases. Each viral RdRP contains a 500-600 residue catalytic module with palm, fingers, and thumb domains forming an encircled human right hand architecture. Seven polymerase catalytic motifs are located in the RdRP palm and fingers domains, comprising the most conserved parts of the RdRP and are responsible for the RNA-only specificity in catalysis. Functional regions are often found fused to the RdRP catalytic module, resulting in a high level of diversity in RdRP global structure and regulatory mechanism. In this review, we surveyed all 46 RdRP-sequence available virus families of the positive-strand RNA viruses listed in the 2018b collection of the International Committee on Virus Taxonomy (ICTV) and chose a total of 49 RdRPs as representatives. By locating hallmark residues in RdRP catalytic motifs and by referencing structural and functional information in the literature, we were able to estimate the N-and C-terminal boundaries of the catalytic module in these RdRPs, which in turn serve as reference points to predict additional functional regions beyond the catalytic module. Interestingly, a large number of virus families may have additional regions fused to the RdRP N-terminus, while only a few of them have such regions on the C-terminal side of the RdRP. The current knowledge on these additional regions, either in three-dimensional (3D) structure or in function, is quite limited. In the five RdRP-structure available virus families in the positive-strand RNA viruses, only the Flaviviridae family has the 3D structural information resolved for such regions. Hence, future efforts to solve full-length RdRP structures containing these regions and to dissect the functional contribution of them are necessary to improve the overall understanding of the RdRP proteins as an evolutionarily integrated group, and our analyses here may serve as a guideline for selecting representative RdRP systems in these studies. 
 Title: A Structure-Function Diversity Survey of the RNA-Dependent RNA Polymerases From the Positive-Strand RNA Viruses
Output: True
Paragraph: The presence of immunoglobulin oligoclonal bands in the cerebrospinal fluid of Multiple Sclerosis (MS) patients supports the hypothesis of an infectious etiology, although the antigenic targets remain elusive. Neurotropic mouse hepatitis virus (MHV) infection in mice provides a useful tool for studying mechanisms of demyelination in a virus-induced experimental model of MS. This study uses Affymetrix microarray analysis to compare differential spinal cord mRNA levels between mice infected with demyelinating and non-demyelinating strains of MHV to identify host immune genes expressed in this demyelinating disease model. The study reveals that during the acute stage of infection, both strains induce inflammatory innate immune response genes, whereas upregulation of several immunoglobulin genes during chronic stage infection is unique to infection with the demyelinating strain. Results suggest that the demyelinating strain induced an innate-immune response during acute infection that may promote switching of Ig isotype genes during chronic infection, potentially playing a role in antibody-mediated progressive demyelination even after viral clearance. 
 Title: Demyelinating strain of mouse hepatitis virus infection bridging innate and adaptive immune response in the induction of demyelination
Output: True
Paragraph: Interferons (IFNs) were discovered as antiviral agents 50 years ago, and enormous progress has been made since then. Nowadays, IFNs (specifically type I IFNs), have been ascribed as the cytokines that bridge the innate and adaptive immunity soon after the recognition of pathogen-associated molecular patterns (PAMPs) by the infected host. Notably, a unifying mechanism for type I IFN production has been established upon innate immune detection. Thus, TLR 3, 4, 7 and 9 associate endosomal recognition of PAMPs to type I IFN responses, a mechanism that has been shown in plasmacytoid dendritic cells to be dependent on the PI3K/mTOR/S6K pathway. It is worth noting that pathogen recognition triggers a fine-tuned controlled program that not only includes the production of antiviral (IFN) and pro-inflammatory cytokines to initiate the antiviral response but also signals the cessation of the response through the induction of suppressors of cytokine signaling (SOCS). SOCS in turn is under tight regulation of the TAM receptors (protein tyrosine kinase receptors TYRO3, AXL and MER), and activation of which thereby protects the host from the threats of autoimmune diseases. 
 Title: Current review Interferons: Signaling, antiviral and viral evasion
Output: False
Paragraph: Theiler's murine encephalomyelitis virus (TMEV) establishes a persistent infection in the central nervous system (CNS). To examine the role of type I interferon (IFN-I)-mediated signals in TMEV infection, mice lacking a subunit of the type I IFN receptor (IFN-IR KO mice) were utilized. In contrast to wildtype mice, IFN-IR KO mice developed rapid fatal encephalitis accompanied with greater viral load and infiltration of immune cells to the CNS. The proportion of virus-specific CD4 + and CD8 + T cell responses in the CNS was significantly lower in IFN-IR KO mice during the early stage of infection. Levels of IFN-γ and IL-17 produced by isolated primed CD4 + T cells in response to DCs from TMEV-infected IFN-IRKO mice were also lower than those stimulated by DCs from TMEV-infected wildtype control mice. The less efficient stimulation of virus-specific T cells by virus-infected antigen presenting cells is attributable in part to the low level expression of activation markers on TMEV-infected cells from IFN-IR KO mice. However, due to high levels of cellular infiltration and viral loads in the CNS, the overall numbers of virus-specific T cells are higher in IFN-IR KO mice during the later stage of viral infection. These results suggest that IFN-I-mediated signals play important roles in controlling cellular infiltration to the CNS and shaping local T cell immune responses. 
 Title: TYPE I INTERFERON SIGNALS CONTROL THEILER'S VIRUS INFECTION SITE, CELLULAR INFILTRATION AND T CELL STIMULATION IN THE CNS
Output: True
Paragraph: The two dimensional molecular tagging velocimetry (2D-MTV) has been used to measure velocity fields of the flow in a micro mixer. Instead of commonly used micro particles an optical tagging of the flow has been performed by using a caged dye. The pattern generation is done by imaging a mask for the first time. This allows to generate nearly any imaginable pattern. The flow induces a deformation of the optically written pattern that can be tracked by laser induced fluorescence. The series of raw images acquired in this way were analyzed quantitatively with a novel optical flow based technique. The reference measurements have been carried out allowing to draw conclusions about the accuracy of this procedure. A comparison to the standard technique of lPIV has also been conducted. Apart from measuring flow velocities in microfluidic mixing processes, the spatial distribution of concentration fields for different species has also been measured. To this end, a new technique has been developed that allows spatial measurements from Planar Spontaneous Raman Scattering (PSRS). The Raman stray light of the relevant species has been spectrally selected by a narrow bandpass filter and thus detected unaffectedly by the Raman stray light of other species. The successful operation of this measurement procedure in micro flows will be demonstrated exemplary for a mixing process of water and ethanol. 
 Title: Micro-flow analysis by molecular tagging velocimetry and planar Raman-scattering
Output: True
Paragraph: Severe acute respiratory syndrome (SARS) is an emerging infectious disease associated with a novel coronavirus and causing worldwide outbreaks. SARS coronavirus (SARS-CoV) is an enveloped RNA virus, which contains several structural proteins. Among these proteins, spike (S) protein is responsible for binding to specific cellular receptors and is a major antigenic determinant, which induces neutralizing antibody. In order to analyze the antigenicity and receptor-binding ability of SARS-CoV S protein, we expressed the S protein in Escherichia coli using a pET expression vector. After the isopropyl-b-D D -thiogalactoside induction, S protein was expressed in the soluble form and purified by nickel-affinity chromatography to homogeneity. The amount of S protein recovered was 0.2-0.3 mg/100 ml bacterial culture. The S protein was recognized by sera from SARS patients by ELISA and Western blot, which indicated that recombinant S protein retained its antigenicity. By biotinylated ELISA and Western blot using biotinlabeled S protein as the probe, we identified 130-kDa and 140-kDa proteins in Vero cells that might be the cellular receptors responsible for SARS-CoV infection. Taken together, these results suggested that recombinant S protein exhibited the antigenicity and receptor-binding ability, and it could be a good candidate for further developing SARS vaccine and anti-SARS therapy. 
 Title: Antigenicity and receptor-binding ability of recombinant SARS coronavirus spike protein
Output: False
Paragraph: Shiga toxin-producing Escherichia coli are pathogenic bacteria found in the gastrointestinal tract of humans. Severe infections could lead to life-threatening complications, especially in young children and the elderly. Understanding the distribution of the incubation period, which is currently inconsistent and ambiguous, can help in controlling the burden of disease. We conducted a systematic review of outbreak investigation reports, extracted individual incubation data and summary estimates, tested for heterogeneity, classified studies into subgroups with limited heterogeneity, and undertook a meta-analysis to identify factors that may contribute to the distribution of the pathogen's incubation period. Twenty-eight studies were identified for inclusion in the review (1 of which included information on 2 outbreaks), and the resulting I 2 value was 77%, indicating high heterogeneity. Studies were classified into 5 subgroups, with the mean incubation period ranging from 3.5 to 8.1 days. The length of the incubation period increased with patient age and decreased by 7.2 hours with every 10% increase in attack rate. 
 Title: Review Incubation Period of Shiga Toxin-Producing Escherichia coli
Output: False
Paragraph: Specific cleavage of proteins by proteases is essential for several cellular, physiological, and viral processes. Chymotrypsin-related proteases that form the PA clan in the MEROPS classification of proteases is one of the largest and most diverse group of proteases. The PA clan comprises serine proteases from bacteria, eukaryotes, archaea, and viruses and chymotrypsin-related cysteine proteases from positive-strand RNA viruses. Despite low amino acid sequence identity, all PA clan proteases share a conserved double β-barrel structure. Using an automated structure-based hierarchical clustering method, we identified a common structural core of 72 amino acid residues for 143 PA clan proteases that represent 12 protein families and 11 subfamilies. The identified core is located around the catalytic site between the two β-barrels and resembles the structures of the smallest PA clan proteases. We constructed a structure-based distance tree derived from the properties of the identified common core. Our structure-based analyses support the current classification of these proteases at the subfamily level and largely at the family level. Structural alignment and structure-based distance trees could thus be used for directing objective classification of PA clan proteases and to strengthen their higher order classification. Our results also indicate that the PA clan proteases of positive-strand RNA viruses are related to cellular heatshock proteases, which suggests that the exchange of protease genes between viruses and cells might have occurred more than once. OPEN ACCESS Citation: Mönttinen HAM, Ravantti JJ, Poranen MM (2019) Structural comparison strengthens the higher-order classification of proteases related to chymotrypsin. PLoS ONE 14(5): e0216659. https:// 
 Title: Structural comparison strengthens the higher-order classification of proteases related to chymotrypsin
Output: True
Paragraph: Plant molecular pharming is a promising system to produce important recombinant proteins such as therapeutic antibodies, pharmaceuticals, enzymes, growth factors, and vaccines. The system provides an interesting alternative method to the direct extraction of proteins from inappropriate source material while offering the possibility to overcome problems related to product safety and source availability. Multiple factors including plant hosts, genes of interest, expression vector cassettes, and extraction and purification techniques play important roles in the plant molecular pharming. Plant species, as a biosynthesis platform, are a crucial factor in achieving high yields of recombinant protein in plant. The choice of recombinant gene and its expression strategy is also of great importance in ensuring a high amount of the recombinant proteins. Many studies have been conducted to improve expression, accumulation, and purification of the recombinant protein from molecular pharming systems. Re-engineered vectors and expression cassettes are also pivotal tools in enhancing gene expression at the transcription and translation level, and increasing protein accumulation, stability, retention and targeting of specific organelles. In this review, we report recent advances and strategies of plant molecular pharming while focusing on the choice of plant hosts and the role of some molecular pharming elements and approaches: promoters, codon optimization, signal sequences, and peptides used for upstream design, purification and downstream processing. A. Makhzoum 
 Title: Recent advances on host plants and expression cassettes' structure and function in plant molecular pharming
Output: False
Paragraph: Middle East Respiratory Syndrome Coronavirus (MERS-CoV) is an emerging zoonotic virus considered as one of the major public threat with a total number of 2 298 laboratory-confirmed cases and 811 associated deaths reported by World Health Organization as of January 2019. The transmission of the virus was expected to be from the camels found in Middle Eastern countries via the animal and human interaction. The genome structure provided information about the pathogenicity and associated virulent factors present in the virus. Recent studies suggested that there were limited insight available on the development of novel therapeutic strategies to induce immunity against the virus. The severities of MERS-CoV infection highlight the necessity of effective approaches for the development of various therapeutic remedies. Thus, the present review comprehensively and critically illustrates the recent aspects on the epidemiology of the virus, the structural and functional features of the viral genome, viral entry and transmission, major mechanisms of pathogenesis and associated virulent factors, current animal models, detection methods and novel strategies for the development of vaccines against MERS-CoV. The review further illustrates the molecular and computational virtual screening platforms which provide insights for the identification of putative drug targets and novel lead molecules toward the development of therapeutic remedies. 
 Title: Recent Aspects on the Pathogenesis Mechanism, Animal Models and Novel Therapeutic Interventions for Middle East Respiratory Syndrome Coronavirus Infections
Output: False
Paragraph: In a field trial on a farm in Turkey, we tested whether specific egg-yolk antibodies had a prophylactic effect on neonatal diarrhea. Owing to its antibody spectrum, this egg powder was very suitable for this farm since mainly rotavirus was identified. Regardless of the dosage (2 g, 4 g, or 8 g egg powder), the calves (n = 164) which received specific egg-yolk antibodies via the whole egg during the first 14 days of life showed significant improvements in risk and duration of diarrhea and in body weight gain compared with calves of the control group (n = 80) which had not received any egg powder. These significant differences in body weight still persisted after 3 months of life. The mortality risk in the control group amounted to 8.8%, while in all egg powder groups (n = 164) only one calf died as a result of diarrhea. Breed-dependent differences in the parameters were not observed. 
 Title: PREVENTIVE VETERINARY MEDICINE Dose-dependent effects of specific egg-yolk antibodies on diarrhea of newborn calves
Output: False
Paragraph: A novel strain of H1N1 influenza A virus (pH1N1) emerged in 2009, causing a worldwide pandemic. Several studies suggest that this virus is antigenically more closely related to human influenza viruses that circulated prior to 1957 than viruses of more recent seasonal influenza varieties. The extent to which individuals who are naïve to the 2009 pH1N1 virus carry crossreactive CD8+ T cells is not known, but a certain degree of reactivity would be expected since there is substantial conservation among the internal proteins of the virus. In the present study, we examined production of multiple cytokines in response to virus from CD8+ T cells in healthy adult subjects, between 18 and 50 years of age (born post 1957), who had no evidence of exposure to the 2009 pH1N1 virus, and had blood collected prior to the emergence of the pandemic in April of 2009. Human peripheral blood mononuclear cells (PBMC) were stimulated in vitro with a panel of live viruses, and assayed by intracellular cytokine staining and flow cytometry. Although results were variable, most subjects exhibited cytokine positive CD8+ T cells in response to pH1N1. Cytokine producing cells were predominantly single positive (IL2, IFNγ, or TNFα); triplecytokine producing cells were relatively rare. This result suggests that although many adults carry cross-reactive T cells against the emergent pandemic virus, these cells are in a functionally limited state, possibly because these subjects have not had recent exposure to either seasonal or pandemic influenza strains. 
 Title: CD8+ T Cell Immunity to 2009 Pandemic and Seasonal H1N1 Influenza Viruses NIH Public Access Author Manuscript
Output: False
Paragraph: Frameshifting results from two main mechanisms: genomic insertions or deletions (indels) or programmed ribosomal frameshifting. Whereas indels can disrupt normal protein function, programmed ribosomal frameshifting can result in dual-coding genes, each of which can produce multiple functional products. Here, I summarize technical advances that have made it possible to identify programmed ribosomal frameshifting events in a systematic way. The results of these studies suggest that such frameshifting occurs in all genomes, and I will discuss methods that could help characterize the resulting alternative proteomes. 
 Title: On programmed ribosomal frameshifting: the alternative proteomes
Output: True
Paragraph: Host responses can contribute to the severity of viral infection, through the failure of innate antiviral mechanisms to recognize and restrict the pathogen, the development of intense systemic inflammation leading to circulatory failure or through tissue injury resulting from overly exuberant cell-mediated immune responses. High-throughput genomics methods are now being used to identify the biochemical pathways underlying ineffective or damaging host responses in a number of acute and chronic viral infections. This article reviews recent gene-expression studies of 1918 H1N1 influenza and Ebola hemorrhagic fever in cell culture and animal models, focusing on how genomics experiments can be used to increase our understanding of the mechanisms that permit those viruses to cause rapidly overwhelming infection. Particular attention is paid to how evasion of type I IFN responses in infected cells might contribute to over-activation of inflammatory responses. Reviewing recent research and describing how future studies might be tailored to understand the relationship between the infected cell and its environment, this article discusses how the rapidly growing field of high-throughput genomics can contribute to a more complete understanding of severe, acute viral infections and identify novel targets for therapeutic intervention. 
 Title: Applications of high-throughput genomics to antiviral research: evasion of antiviral responses and activation of inflammation during fulminant RNA virus infection
Output: False
Paragraph: The carbohydrate contents of coronavirus glycoproteins El and E2 have been analyzed. E2 has complex and mannose-rich-type oligosaccharide side-chains, which are attached by N-glycosidic linkages to the polypeptide. Glycosylation of E2 is initiated at the co-translational level, and it is inhibited by tunicamycin, 2deoxy-glucose, and 2-deoxy-2-fluoro-glucose. Thus, E2 belongs to a glycoprotein type found in many other enveloped viruses. El, in contrast, represents a different class of glycoprotein. The following observations indicate that its carbohydrate side-chains have O-glycosidir linkage. (1) The constituent sugars of El are ,Vacrtylglucosamine, N-acet,ylgalactosamine, galactose, and neuraminic acid : mannose and fucose are absent. (2) The side-chains can be removed by ,!elimination. (3) Glycosylation of El is not sensitive to the compounds interfering with ,Vglycosylation. El is the first viral glycoprotein analyzed that contains only O-glycosidic linkages. Coronaviruses are therefore a suitable model system to study biosynthesis and processing of this type of glycoprotein. cw,22-2~:~6/~1/~~0~93-18 ~02.00/0 Q 1981 Academic Press Inc. (London) Ltd. 
 Title: Coronavirus Glycoprotein El, a New Type of Viral Glycoprotein
Output: True
Paragraph:  Adults who did not work in the outbreak were worse in mental and physical health, distress and life satisfaction.  The identification of whose health and wellbeing is more affected by the disruption enables more targeted assistance.  The early evidence from China can help countries that consider implementing confinement policies to contain COVID-19. We assess the health and wellbeing of normal adults living and working after one month of confinement to contain the COVID-19 outbreak in China. On Feb 20-21, 2020, we surveyed 369 adults in 64 cities in China that varied in their rates of confirmed coronavirus cases on their health conditions, distress and life satisfaction. 27% of the participants worked at the office, 38% resorted to working from home, and 25% stopped working due to the outbreak. Those who stopped working reported worse mental and physical health conditions as well as distress. The severity of in an individual's home city predicts their life satisfaction, and this relationship is contingent upon individuals' existing chronic health issues and their hours of exercise. Our evidence supports the need to pay attention to the health of people who were not affected by the virus epidemiologically, especially for people who stopped working during the outbreak. Our results highlight that physically active people might be more susceptible to wellbeing issues during the lockdown. Policymakers who are considering introducing restrictive measures to contain COVID-19 may benefit from understanding such health and wellbeing implications. 
 Title: E-mail Address for Each Author
Output: True
Paragraph: Emerging and reemerging viral diseases of livestock and human beings are in sharp rise in recent years. Importantly, many of these viruses, including influenza, Hendra, Nipah and corona are of zoonotic importance. Several viral diseases of livestock such as bluetongue, peste des petits ruminants, camel pox, equine infectious anaemia, chicken anaemia and sheep-associated malignant catarrhal fever are crossing their traditional boundaries. Emergence of new serotypes and variant forms of viruses as in the case of blue tongue virus, avian infectious bronchitis virus, Newcastle disease virus adds additional level of complexity. The increased incidence of emerging and reemerging viral diseases could be attributed to several factors including deforestation and surge in direct contact of livestock and humans with wild animals and birds. This special issue of ''Indian Journal of Virology'' is focused on diverse aspects of above diseases: isolation and characterization of viruses, epidemiology, pathogenesis, diagnosis, prevention measures and vaccine development. 
 Title: Emerging viral diseases of livestock in the developing world
Output: False
Paragraph: Acute respiratory tract infections (ARTI), including the common cold, pharyngitis, sinusitis, otitis media, bronchiolitis and pneumonia are the most common diagnoses among patients seeking medical care in western countries, and account for most antibiotic prescriptions. While a confirmed and fast ARTI diagnosis is key for antibiotic prescribing, empiric antimicrobial treatment remains common, because viral symptoms are often clinically similar and difficult to distinguish from those caused by bacteria. As a result, inappropriate antibiotic prescriptions are high and in certain settings likely higher than the commonly estimated 30%. The QIAstat Respiratory Panel ® assay (QIAstat RP) is a multiplexed in vitro diagnostics test for the rapid simultaneous detection of 21 pathogens directly from respiratory samples, including human mastadenovirus A-G, primate bocaparvovirus 1+2, human coronavirus (HKU1, NL63, OC43, 229E), human metapneumovirus A/B, rhinovirus/enterovirus, influenza A virus (no subtype, subtype H1, H1N1/2009, H3), influenza B virus, human respirovirus 1+3, human orthorubulavirus 2+4, human orthopneumovirus, Bordetella pertussis, Chlamydia pneumoniae, Mycoplasma pneumoniae and Legionella pneumophila. We describe the first multicenter study of 445 respiratory samples, collected through the 2016-2017 and 2018 respiratory seasons, with performance compared against BioFire FilmArray RP v1.7 and discrepancy testing by Seegene Allplex RP. The QIAstat RP demonstrated a positive percentage of agreement of 98.0% (95% CI: 96.0-99.1%) and a negative percentage agreement of 99.8% (95% CI: 99.6-99.9%). With use of this comprehensive and rapid test, improved patient outcomes and antimicrobial stewardship may potentially be achieved. 
 Title: Multicenter evaluation of the QIAstat Respiratory Panel-A new rapid highly multiplexed PCR based assay for diagnosis of acute respiratory tract infections
Output: False
Paragraph: The acute respiratory distress syndrome (ARDS) is a lethal inflammatory disorder of the lung. Its incidence is estimated at 75 cases per 100,000 population and appears to be increasing [1] . Even with optimal treatment, mortality is about 30% [1-3]. As such, ARDS represents a major public health problem. The effects of two recent crises created by unusual viral infections of the respiratory tract -the severe acute respiratory syndrome (SARS) epidemic caused by the novel SARS coronavirus [4, 5] and the bird flu [6] highlight the importance of research into ARDS. Both viruses cause an ARDS-like picture. Because lung repair and regeneration contribute substantially to the pathophysiology of ARDS, understanding these processes is essential [7] . This chapter focuses on specific cell populations and markers involved in cell division and regeneration. In addition, a brief review of two pathways intimately associated with cell division is provided because of their potential for pharmacologic manipulation. 
 Title: Cell Regeneration in Lung Injury
Output: True