niryuu/sni-each-converted huggingface dataset:
Paragraph: Newly available data sets present an exciting opportunity to investigate how human population movement contributes to the spread of infectious diseases across large geographical distances. It is now possible to construct realistic models of infectious disease dynamics for the purposes of understanding global-scale epidemics. Nevertheless, a remaining unanswered question is how best to leverage the new data to parameterize models of movement, and whether one's choice of movement model impacts modeled disease outcomes. We adapt three well-studied models of infectious disease dynamics, the SIR model; the SIS model; and the Ross-Macdonald model, to incorporate either of two candidate movement models. We describe the effect that the choice of movement model has on each disease model's results, finding that in all cases there are parameter regimes where choosing one movement model instead of another has a profound impact on epidemiological outcomes. We further demonstrate the importance of choosing an appropriate movement model using the applied case of malaria transmission and importation on Bioko Island, Equatorial Guinea, finding that one model produces intelligible predictions of R 0 while the other produces nonsensical results. Mathematical modeling | Infectious disease dynamics | Human population movement | Malaria DT Citron developed the project and carried out the analysis. DL Smith provided guidance and context for the project. CA Guerra provided the data for building the Bioko Island model. SL Wu, JM Henry, HM Sánchez C, and D Dolgert discussed and reviewed the analysis. 
 Title: Comparing Metapopulation Dynamics of Infectious Diseases under Di erent Models of Human Movement
Output: False
Paragraph: Human respiratory syncytial virus (HRSV) is a major cause of pediatric infection and also causes disease in the elderly and those with underlying respiratory problems. There is no vaccine for HRSV and anti-viral therapeutics are not broadly applicable. To investigate the effect of HRSV biology in children, nasopharyngeal aspirates were taken from children with different viral loads and a combined high throughput RNAseq and label free quantitative proteomics approach was used to characterize the nucleic acid and proteins in these samples. HRSV proteins were identified in the nasopharyngeal aspirates from infected children, and their abundance correlated with viral load (Ct value), confirming HRSV infection. Analysis of the HRSV genome indicated that the children were infected with sub-group A virus and that minor variants in nucleotide frequency occurred in discrete clusters along the HRSV genome, and within a patient clustered distinctly within the glycoprotein gene. Data from the samples were binned into four groups; no-HRSV infection (control), high viral load (Ct < 20), medium viral load (Ct = 20-25), and low viral load (Ct > 25). Cellular proteins associated with the anti-viral response (e.g., ISG15) were identified in the nasopharyngeal aspirates and their abundance was correlated with viral load. These combined approaches have not been used before to study HRSV biology in vivo and can be readily applied to the study the variation of virus host interactions. Table S1 : ANOVA Comparison of abundance. Author Contributions: Conceptualization, W.A. and J.A.H.; methodology, W.A., D.A.M., N.Y.R., and S.A.; software, W.A. and D.A.M.; formal analysis, W.A., G.P., N.Y.R., and S.A.; resources, E.C.-G.; data curation, S.A.; writing-original draft preparation, W.A. and J.A.H.; writing-review and editing, all authors.; supervision, J.A.H. and O.T.; project administration, W.A. and J.A.H.; funding acquisition, W.A. and J.A.H. 
 Title: High Resolution Analysis of Respiratory Syncytial Virus Infection In Vivo
Output: True
Paragraph: Emerging outbreaks of zoonotic diseases are affecting humans at an alarming rate. Until the ecological factors associated with zoonoses are better understood, disease emergence will continue. For Lyme disease, disease suppression has been demonstrated by a dilution effect, whereby increasing species diversity decreases disease prevalence in host populations. To test the dilution effect in another disease, we examined 17 ecological variables associated with prevalence of the directly transmitted Sin Nombre virus (genus Hantavirus, etiologic agent of hantavirus pulmonary syndrome) in its wildlife host, the deer mouse (Peromyscus maniculatus). Only species diversity was statistically linked to infection prevalence: as species diversity decreased, infection prevalence increased. The increase was moderate, but prevalence increased exponentially at low levels of diversity, a phenomenon described as zoonotic release. The results suggest that species diversity affects disease emergence. Conference summaries/reports are published online only. Manuscripts submitted for online publication may include illustrations and relevant links. For more information on online only requirements, please refer to author guidelines at 
 Title: Increased Host Species Diversity and Decreased Prevalence of Sin Nombre Virus Notice to Readers and Contributing Authors
Output: True
Paragraph: Mice aged 1, 4 or 8 weeks were inoculated with haemagglutinating encephalomyelitis virus (HEV), strain 67N, by the intracerebral (i.c.), intranasal (i.n.), intraperitoneal (i.p.), subcutaneous (s.c.), intravenous (i.v.) or oral route, with different doses. In 1-week-old mice, mortality and mean time to death were mostly the same regardless of the inoculation route, except for the oral route, which appeared to be the least effective. The virus killed 4-week-old mice readily by all routes of inoculation except the oral, and 8-weekold mice by i.c., i.n. or s.c. inoculation. In descending order of efficacy, the routes of HEV infection were: i.c., i.n., s.c., i.p., i.v. and oral. To follow the spread of HEV from peripheral nerves to the central nervous system (CNS), the virus was inoculated subcutaneously into the right hind leg of 4-week-old mice. The virus was first detected in the spinal cord on day 2, and in the brain on day 3. The brain titres became higher than those of the spinal cord, reaching a maximum of 10 7 PFU/0.2 g when the animals were showing CNS signs. Viral antigen was first detected immunohistochemically in the lumbar spinal cord and the dorsal root ganglion ipsilateral to the inoculated leg; it was detected later in the pyramidal cells of the hippocampus and cerebral cortex, and in the Purkinje cells of the cerebellum but not in the ependymal cells, choroid plexus cells or other glial cells. The infected neurons showed no cytopathological changes. q 
 Title: Neurotropism of Swine Haemagglutinating Encephalomyelitis Virus (Coronavirus) in Mice Depending upon Host Age and Route of Infection
Output: True
Paragraph: Eukaryotes and bacteria can be infected with a wide variety of RNA viruses. On average, these pathogens share little sequence similarity and use different replication and transcription strategies. Nevertheless, the members of nearly all RNA virus families depend on the activity of a virally encoded RNA-dependent polymerase for the condensation of nucleotide triphosphates. This review provides an overview of our current understanding of the viral RNAdependent polymerase structure and the biochemistry and biophysics that is involved in replicating and transcribing the genetic material of RNA viruses. 
 Title: Common and unique features of viral RNA-dependent polymerases
Output: True
Paragraph: Albumin and IgG were quantitated in paired cerebrospinal fluid (CSF) and serum samples from dogs with demyelinating canine distemper virus (CDV) infection by means of rocket immunoelectrophoresis. The IgG index as indicator for intrathecal immunoglobulin synthesis was normal in animals with non-inflammatory demyelinating lesions and elevated in dogs with inflammatory myelin lesions. Specific antibodies against CDV and myelin were quantitated in CSF and serum from 8 dogs with an elevated IgG index. Eight of these dogs had significant amounts of antimyelin antibody and 4 dogs had neutralizing anti-CDV antibody in the CSF. Whereas the pathogenetic significance of antimyelin antibodies remains uncertain, the intrathecal antiviral immune response provides a plausible explanation for immunopathologic destruction of myelin in distemper. 
 Title: Studies on the Intrathecal Humoral Immune Response in Canine Distemper Encephalitis
Output: False
Paragraph: In the endoplasmic reticulum (ER), the sugar chain is initially introduced onto newly synthesized proteins as a triantennary tetradecasaccharide (Glc3Man9GlcNAc2). The attached oligosaccharide chain is subjected to stepwise trimming by the actions of specific glucosidases and mannosidases. In these processes, the transiently expressed N-glycans, as processing intermediates, function as signals for the determination of glycoprotein fates, i.e., folding, transport, or degradation through interactions of a series of intracellular lectins. The monoglucosylated glycoforms are hallmarks of incompletely folded states of glycoproteins in this system, whereas the outer mannose trimming leads to ER-associated glycoprotein degradation. This review outlines the recently emerging evidence regarding the molecular and structural basis of this glycoprotein quality control system, which is regulated through dynamic interplay among intracellular lectins, glycosidases, and glycosyltransferase. Structural snapshots of carbohydrate-lectin interactions have been provided at the atomic level using X-ray crystallographic analyses. Conformational ensembles of uncomplexed triantennary high-mannose-type oligosaccharides have been Molecules 2015, 20 2476 characterized in a quantitative manner using molecular dynamics simulation in conjunction with nuclear magnetic resonance spectroscopy. These complementary views provide new insights into glycoprotein recognition in quality control coupled with N-glycan processing. 
 Title: molecules Emerging Structural Insights into Glycoprotein Quality Control Coupled with N-Glycan Processing in the Endoplasmic Reticulum
Output: True
Paragraph: By focusing on the Masters of Public Health course, this study took a pragmatic approach to exploring the interface between public health education and public health practice. The commonly utilized 'three domains of practice' framework could provide a robust and explicit link between educational provision and practice for public health. This model provides the workforce, the university, the students and the potential funders of the course with an easily comprehensible framework for understanding how the modules of an MSc can support the development of competency within the context of practice. 
 Title: The three domains of public health: An internationally relevant basis for public health education?
Output: True
Paragraph: A new disease, the severe acute respiratory distress syndrome (SARS), caused by the SARS coronavirus (SARS-CoV), emerged at the beginning of 2003 and rapidly spread throughout the world. Although the disease had disappeared in June 2003 its re-emergence cannot be excluded. The development of vaccines against SARS-CoV may take years. Therefore, the availability of effective antiviral drugs against SARS-CoV may be crucial for the control of future SARS outbreaks. In this review, experimental and clinical data about potential anti-SARS drugs is summarised and discussed. Animal model studies will be needed to help to determine which interventions warrant controlled clinical testing. 
 Title: Development of antiviral therapy for severe acute respiratory syndrome
Output: False
Paragraph: Background: As the gatekeepers of rural residents' health, teams of village doctors play a vital role in improving rural residents' health. However, the high turnover of village doctors, both individually and collectively, threaten the stability of village medical teams. This research evaluated the influence of job satisfaction, resilience, and work engagement on the village doctors' turnover intention, and explored the mediating role of work engagement and resilience between job satisfaction and the turnover intention of village doctors in China. Methods: A quantitative study using a self-administered questionnaire containing mostly structured items was conducted among village doctors with a sample size of 2693 from 1345 rural clinics in Shandong province, China, during May and June 2019. All variables including demographic characteristics, job satisfaction, resilience, work engagement and turnover intention were based on available literature, and measured on a 5-or 6-point Likert scale. Such statistical methods as one-way ANOVA, bivariate correlation, exploratory factor analysis (EFA), and Structural Equation Modelling (SEM) were used. Results: Up to 46.9% of the subjects had a higher turnover intention and more than 26.3% of them had a medium turnover intention. The job satisfaction of village doctors could not only have a direct negative effect on turnover intention (β = − 0.37, p < 0.001), but also have an indirect effect through work engagement (β = − 0.04,=< 0.001). Meanwhile, work engagement also had a direct negative impact on turnover intention (β = − 0.13, p < 0.001), and resilience had an indirect negative impact on turnover intention through work engagement (β = − 0.09, p < 0.001). The above results of this study strongly confirmed that job satisfaction, resilience, and work engagement were early, powerful predicators of village doctors' turnover intention. (Continued on next page) Conclusion: According to the results, the following should be taken seriously to improve job satisfaction: reasonable and fair income, effective promotion mechanism, fair social old-age security, reasonable workload, and strong psychological coping mechanisms for work stress. The turnover intention of village doctors could be reduced through improving job satisfaction, resilience and work engagement. 
 Title: The influence of job satisfaction, resilience and work engagement on turnover intention among village doctors in China: a cross-sectional study
Output: False
Paragraph: Drugs that inhibit the production of angiotensin II (AngII) or its access to the type 1 angiotensin receptor (AT 1 R) are prescribed to alleviate high blood pressure and its cardiovascular complications. Accordingly, much research has focused on the molecular pharmacology of AT 1 R activation and signaling. An emerging theme is that the AT 1 R generates G protein dependent as well as independent signals and that these transduction systems separately contribute to AT 1 R biology in health and disease. Regulatory molecules termed arrestins are central to this process as is the capacity of AT 1 R to crosstalk with other receptor systems, such as the widely studied transactivation of growth factor receptors. AT 1 R function can also be modulated by polymorphisms in the AGTR gene, which may significantly alter receptor expression and function; a capacity of the receptor to dimerize/oligomerize with altered pharmacology; and by the cellular environment in which the receptor resides. Together, these aspects of the AT 1 R "flavour" the response to angiotensin; they may also contribute to disease, determine the efficacy of current drugs and offer a unique opportunity to develop new therapeutics that antagonize only selective facets of AT 1 R function. 
 Title: Type 1 angiotensin receptor pharmacology: Signaling beyond G proteins
Output: False
Paragraph: By using a nested case-control design, the authors studied the effectiveness of the influenza vaccine in reducing severe and fatal complications in 4,241 and 5,966 primary care, working-age patients aged 18-64 years who had asthma or chronic obstructive pulmonary disease during the 1998-1999 and 1999-2000 influenza epidemics in the Netherlands. Patients developing fatal or nonfatal exacerbations of lung disease, pneumonia, congestive heart failure, or myocardial infarction during either epidemic were considered cases. For each case, four age-and sex-matched controls were randomly sampled, and patient records were reviewed. Conditional logistic regression and propensity scores were used to assess vaccine effectiveness after adjustment for confounding factors. In seasons one and two, respectively, 87% (47/54) and 85% (171/202) of the cases and 74% (155/210) and 75% (575/766) of the controls had been vaccinated. After adjustments, vaccination was not associated with reductions in complications (season one: odds ratio = 0.95, 95% confidence interval (CI): 0.26, 3.48; season two: odds ratio = 1.07, 95% CI: 0.59, 1.96; pooled odds ratio = 1.07, 95% CI: 0.63, 1.80). Because influenza vaccination appeared not to be associated with a clinically relevant reduction in severe morbidity, other measures need to be explored. case-control studies; immunization; influenza; lung diseases; middle age; vaccines Abbreviations: CI, confidence interval; COPD, chronic obstructive pulmonary disease. 
 Title: Conventional Influenza Vaccination Is Not Associated with Complications in Working-Age Patients with Asthma or Chronic Obstructive Pulmonary Disease
Output: False
Paragraph: In the present studies, we report the cloning and structural characterization of the HFGL2 gene and its functional role in human fulminant hepatitis. The HFGL2 gene is approximately 7 kb in length with 2 exons. The putative promoter contains cis element consensus sequences that strongly suggest the inducibility of its expression. From the nucleotide sequence of the human gene, a 439-amino acid long protein is predicted. The overall identity between the murine fgl2 and hfgl2 coded proteins is over 70%. About 225 amino acids at the carboxyl end of these molecules are almost 90% identical, and correspond to a well-conserved fibrinogen-related domain. Both HFGL2 and FGL2 encode a type II transmembrane protein with a predicted catalytic domain toward the amino terminus of the protein. Transient transfection of Chinese hamster ovary (CHO) cells with a fulllength cDNA of HFGL2 coding region resulted in high levels of prothrombinase activity. Livers from 8 patients transplanted for fulminant viral hepatitis were examined for extent of necrosis, inflammation, fibrin deposition, and HFGL2 induction. In situ hybridization showed positive staining of macrophages in areas of active hepatocellular necrosis. Fibrin stained positively in these areas and was confirmed by electron microscopy. These studies define a unique prothrombinase gene (HFGL2) and implicate its importance in the pathogenesis of fulminant viral hepatitis. 
 Title: Molecular and Functional Analysis of the Human Prothrombinase Gene (HFGL2) and Its Role in Viral Hepatitis
Output: True
Paragraph: Background: Sublingual (s.l.) administration of soluble protein antigens, inactivated viruses, or virus-like particles has been shown to induce broad immune responses in mucosal and extra-mucosal tissues. Recombinant replication-defective adenovirus vectors (rADVs) infect mucosa surface and therefore can serve as a mucosal antigen delivery vehicle. In this study we examined whether s.l. immunization with rADV encoding spike protein (S) (rADV-S) of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) induces protective immunity against SARS-CoV and could serve as a safe mucosal route for delivery of rADV. Results: Here, we show that s.l. administration of rADV-S induced serum SARS-CoV neutralizing and airway IgA antibodies in mice. These antibody responses are comparable to those induced by intranasal (i.n.) administration. In addition, s.l. immunization induced antigen-specific CD8 + T cell responses in the lungs that are superior to those induced by intramuscular immunization. Importantly, unlike i.n. administration, s.l. immunization with rADV did not redirect the rADV vector to the olfactory bulb. Conclusion: Our study indicates that s.l. immunization with rADV-S is safe and effective in induction of a broad spectrum of immune responses and presumably protection against infection with SARS-CoV. 
 Title: Sublingual immunization with recombinant adenovirus encoding SARS-CoV spike protein induces systemic and mucosal immunity without redirection of the virus to the brain
Output: False
Paragraph: The tertiary structures of the S1 and S2 domains of the spike protein of the coronavirus which is responsible of the severe acute respiratory syndrome (SARS) have been recently predicted. Here a molecular assembly of SARS coronavirus peplomer which accounts for the available functional data is suggested. The interaction between S1 and S2 appears to be stabilised by a large hydrophobic network of aromatic side chains present in both domains. This feature results to be common to all coronaviruses, suggesting potential targeting for drugs preventing coronavirus-related infections. 
 Title: Prediction of quaternary assembly of SARS coronavirus peplomer
Output: False
Paragraph: In a patient with acute respiratory illness (cough, sputum production, chest pain, and/or dyspnea), the need for chest imaging depends on the severity of illness, age of the patient, clinical history, physical and laboratory findings, and other risk factors. Chest radiographs seem warranted when one or more of the following are present: age Ն 40; dementia; a positive physical examination; hemoptysis; associated abnormalities (leukocytosis, hypoxemia); or other risk factors, including coronary artery disease, congestive heart failure, or druginduced acute respiratory failure. Chest CT may be warranted in complicated cases of severe pneumonia and in febrile neutropenic patients with normal or nonspecific chest radiographic findings. Literature on the indications and usefulness of radiologic studies for acute respiratory illness in different clinical settings is reviewed. Acute respiratory illness (ARI) is defined as Ն1 of the following: cough, sputum production, chest pain, or dyspnea (with or without fever). The workup of a patient with ARI, including the need for chest radiography and 
 Title: ACR Appropriateness Criteria ® on Acute Respiratory Illness
Output: False
Paragraph: Using fusions between the Escherichia coli genes argI and lacZ, it has been demonstrated that ribosomal frameshifting occurs at a frequency of between 3% and 16% within the argI mRNA, soon after the initiation codon. The frameshift involves a phenylalanyl-tRNA shifting into the + 1 frame at the sequence UUU-U/C. The shift does not occur if the in-frame phenylalanine codon UUU is replaced by UUC. The level of frameshifting is higher in dense cultures and is not dependent on phenylalanine starvation. In the wild-type argI gene this frameshifting event would be an error, leading to a truncated, non-functional protein. Therefore, it is unlike the numerous examples of required frameshifting events that have been described in other genes. 
 Title: A ribosomal frameshifting error during translation of the argl mRNA of Escherichia coil
Output: False
Paragraph: Background. Administration of convalescent plasma, serum, or hyperimmune immunoglobulin may be of clinical benefit for treatment of severe acute respiratory infections (SARIs) of viral etiology. We conducted a systematic review and exploratory meta-analysis to assess the overall evidence. Methods. Healthcare databases and sources of grey literature were searched in July 2013. All records were screened against the protocol eligibility criteria, using a 3-stage process. Data extraction and risk of bias assessments were undertaken. Results. We identified 32 studies of SARS coronavirus infection and severe influenza. Narrative analyses revealed consistent evidence for a reduction in mortality, especially when convalescent plasma is administered early after symptom onset. Exploratory post hoc meta-analysis showed a statistically significant reduction in the pooled odds of mortality following treatment, compared with placebo or no therapy (odds ratio, 0.25; 95% confidence interval, .14-.45; I 2 = 0%). Studies were commonly of low or very low quality, lacked control groups, and at moderate or high risk of bias. Sources of clinical and methodological heterogeneity were identified. Conclusions. Convalescent plasma may reduce mortality and appears safe. This therapy should be studied within the context of a well-designed clinical trial or other formal evaluation, including for treatment of Middle East respiratory syndrome coronavirus CoV infection. 
 Title: The Effectiveness of Convalescent Plasma and Hyperimmune Immunoglobulin for the Treatment of Severe Acute Respiratory Infections of Viral Etiology: A Systematic Review and Exploratory Meta-analysis
Output: True
Paragraph: Bio-aerosols originate from different sources and their potentially pathogenic nature may form a hazard to healthcare workers and patients. So far no extensive review on existing evidence regarding bio-aerosols is available. This study aimed to review evidence on bio-aerosols in healthcare and the dental setting. The objectives were 1) What are the sources that generate bio-aerosols?; 2) What is the microbial load and composition of bio-aerosols and how were they measured?; and 3) What is the hazard posed by pathogenic micro-organisms transported via the aerosol route of transmission? Systematic scoping review design. Searched in PubMed and EMBASE from inception to 09-03-2016. References were screened and selected based on abstract and full text according to eligibility criteria. Full text articles were assessed for inclusion and summarized. The results are presented in three separate objectives and summarized for an overview of evidence. The search yielded 5,823 studies, of which 62 were included. Dental hand pieces were found to generate aerosols in the dental settings. Another 30 sources from human activities, interventions and daily cleaning performances in the hospital also generate aerosols. Fiftyfive bacterial species, 45 fungi genera and ten viruses were identified in a hospital setting and 16 bacterial and 23 fungal species in the dental environment. Patients with certain risk factors had a higher chance to acquire Legionella in hospitals. Such infections can lead to irreversible septic shock and death. Only a few studies found that bio-aerosol generating procedures resulted in transmission of infectious diseases or allergic reactions. 
 Title: A scoping review on bio-aerosols in healthcare and the dental environment
Output: False
Paragraph: We show that a model antigen, ovalbumin (OVA), can be chemically conjugated to the exterior of a small heat shock protein (sHsp) cage that has structural similarities to virus-like particles (VLPs). OVA-sHsp conjugation efficiency was dependent upon the stoichiometry and the length of the small molecule linker utilized, and the attachment position on the sHsp cage. When conjugated OVA-sHsp was delivered intranasally to naïve mice, the resulting immune response to OVA was accelerated and intensified, and OVA-specific IgG1 responses were apparent within 5 days after a single immunizing dose, illustrating its utility for vaccine development. If animals were pretreated with a disparate VLP, P22 (a non-replicative bacteriophage capsid), before OVA-sHsp conjugate immunization, OVA-specific IgG1 responses were apparent already by 4 days after a single immunizing dose of conjugate in OVA-naïve mice. Additionally, the mice pretreated with P22 produced high titer mucosal IgA, and isotype-switched OVA-specific serum IgG. Similarly, sHsp pretreatment enhanced the accumulation of lung germinal center B cells, T follicular helper cells, and increased polymeric Ig receptor expression, priming the lungs for subsequent IgG and IgA responses to influenza virus challenge. Thus, sHsp nanoparticles elicited quick and intense antibody responses and these accelerated responses could similarly be induced to antigen chemically conjugated to the sHsp. Pretreatment of mice with P22 further accelerated the onset of the antibody response to OVA-sHsp, demonstrating the utility of conjugating antigens to VLPs for pre-, or possibly post-exposure prophylaxis of lung, all without the need for adjuvant. 
 Title: A virus-like particle vaccine platform elicits heightened and hastened local lung mucosal antibody production after a single dose NIH Public Access Author Manuscript
Output: False
Paragraph: The 3% end of the turkey coronavirus (TCV) genome (1740 bases) including the nucleocapsid (N) gene and 3% untranslated region (UTR) were sequenced and compared with published sequences of other avian and mammalian coronaviruses. The deduced sequence of the TCV N protein was determined to be 409 amino acids with a molecular mass of approximately 45 kDa. The TCV N protein was identical in size and had greater than 90% amino acid identity with published N protein sequences of infectious bronchitis virus (IBV); less than 21% identity was observed with N proteins of bovine coronavirus and transmissible gastroenteritis virus. The 3% UTR showed some variation among the three TCV strains examined, with two TCV strains, Minnesota and Indiana, containing 153 base segments which are not present in the NC95 strain. Nucleotide sequence identity between the 3% UTRs of TCV and IBV was greater than 78%. Similarities in both size and sequence of TCV and IBV N proteins and 3% UTRs provide additional evidence that these avian coronaviruses are closely related. 
 Title: Sequence analysis of the turkey coronavirus nucleocapsid protein gene and 3% untranslated region identifies the virus as a close relative of infectious bronchitis virus
Output: False
Paragraph: xMAP technology is applicable for high-throughput, multiplex and simultaneous detection of different analytes within a single complex sample. xMAP multiplex assays are currently available in various nucleic acid and immunoassay formats, enabling simultaneous detection and typing of pathogenic viruses, bacteria, parasites and fungi and also antigen or antibody interception. As an open architecture platform, the xMAP technology is beneficial to end users and therefore it is used in various pharmaceutical, clinical and research laboratories. The main aim of this review is to summarize the latest findings and applications in the field of pathogen detection using microsphere-based multiplex assays. 
 Title: xMAP Technology: Applications in Detection of Pathogens
Output: True
Paragraph: The intestine of pigs harbors a mass of microorganisms which are essential for intestinal homeostasis and host health. Intestinal microbial disorders induce enteric inflammation and metabolic dysfunction, thereby causing adverse effects on the growth and health of pigs. In the human medicine, fecal microbiota transplantation (FMT), which engrafts the fecal microbiota from a healthy donor into a patient recipient, has shown efficacy in intestinal microbiota restoration. In addition, it has been used widely in therapy for human gastrointestinal diseases, including Clostridium difficile infection, inflammatory bowel diseases, and irritable bowel syndrome. Given that pigs share many similarities with humans, in terms of anatomy, nutritional physiology, and intestinal microbial compositions, FMT may also be used to restore the normal intestinal microbiota of pigs. However, feasible procedures for performing FMT in pigs remains unclear. Here, we summarize a standardized preparation for FMT in pigs by combining the standard methodology for human FMT with pig production. The key issues include the donor selection, fecal material preparation, fecal material transfer, stool bank establishment, and the safety for porcine FMT. Optimal donors should be selected to ensure the efficacy of porcine FMT and reduce the risks of transmitting infectious diseases to recipients during FMT. Preparing for fresh fecal material is highly recommended. Alternatively, frozen fecal suspension can also be prepared as an optimal choice because it is convenient and has similar efficacy. Oral administration of fecal suspension could be an optimal method for porcine fecal material transfer. Furthermore, the dilution ratio of fecal materials and the frequency of fecal material transfer could be adjusted according to practical situations in the pig industry. To meet the potential large-scale requirement in the pig industry, it is important to establish a stool bank to make porcine FMT readily available. Future studies should also focus on providing more robust safety data on FMT to improve the safety and tolerability of the recipient pigs. This standardized preparation for porcine FMT can facilitate the development of microbial targeted therapies and improve the intestinal health of pigs. Frontiers in Microbiology | www.frontiersin.org Frontiers in Microbiology | www.frontiersin.org 
 Title: Standardized Preparation for Fecal Microbiota Transplantation in Pigs
Output: False
Paragraph: Background: COVID-19 diagnosis is a critical problem, mainly due to the lack or delay in the test results. We aimed to obtain a model to predict SARS-CoV-2 infection in suspected patients reported to the Brazilian surveillance system. Methods: We analyzed suspected patients reported to the National Surveillance System that corresponded to the following case definition: patients with respiratory symptoms and fever, who traveled to regions with local or community transmission or who had close contact with a suspected or confirmed case. Based on variables routinely collected, we obtained a multiple model using logistic regression. The area under the receiver operating characteristic curve (AUC) and accuracy indicators were used for validation. Results: We described 1468 COVID-19 cases (confirmed by RT-PCR) and 4271 patients with other illnesses. With a data subset, including 80% of patients from Sao Paulo (SP) and Rio Janeiro (RJ), we obtained a function which reached an AUC of 95.54% (95% CI: 94.41% -96.67%) for the diagnosis of COVID-19 and accuracy of 90.1% (sensitivity 87.62% and specificity 92.02%). In a validation dataset including the other 20% of patients from SP and RJ, this model exhibited an AUC of 95.01% (92.51% -97.5%) and accuracy of 89.47% (sensitivity 87.32% and specificity 91.36%). Conclusion: We obtained a model suitable for the clinical diagnosis of COVID-19 based on routinely collected surveillance data. Applications of this tool include early identification for specific treatment and isolation, rational use of laboratory tests, and input for modeling epidemiological trends. 
 Title: A model to predict SARS-CoV-2 infection based on the first three- month surveillance data in Brazil
Output: True
Paragraph: The SARS-CoV-2 pandemic demonstrates the need for accurate and convenient approaches to 2 diagnose and therapeutically monitor respiratory viral infections. We demonstrated that self-3 sampling with foam swabs is well-tolerated and provides quantitative viral output concordant 4 with flocked swabs. Using longitudinal home-based self-sampling, we demonstrate nasal 5 cytokine levels correlate and cluster according to immune cell of origin. Periods of stable viral 6 loads are followed by rapid elimination, which could be coupled with cytokine expansion and 7 contraction using mathematical models. Nasal foam swab self-sampling at home provides a 8 precise, mechanistic readout of respiratory virus shedding and local immune responses. 9 . CC-BY-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: Reliability of self-sampling for accurate assessment of respiratory virus viral and immunologic kinetics
Output: False
Paragraph: publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active. 4 W underink RG, Cammarata SK, Oliphant TH, Kollef MH; Linezolid Nosocomial Pneumonia Study Group : Continuation of a randomized, double-blind, multicenter study linezolid versus vancomycin in the treatment of patients with nosocomial pneumonia. Clin Ther 2003 ; 25 : 980-92. 5 Fung HB, Kirschenbaum HL, Ojofeitimi BO : Linezolid: an oxazolidinone antimicrobiol agent. Clin Ther 2001 ; 23 : 356-91. 6 P erry CM, Jarvis B : Linezolid: a review of its use in the management of serious gram positive infections. 
 Title: ********** Le taux de mortalité du SRAS a été estimé à 13,2 % chez les moins de 60 ans et à 43,3 % chez les plus de 60 ans Epidemiological determinants of spread of causal agent of severe acute respiratory syndrome in
Output: True
Paragraph: Field epidemiology involves the implementation of quick and targeted public health interventions with the aid of epidemiological methods. In this article, we share our practical experiences in outbreak management and in safeguarding the population against novel diseases. Given that cities represent the financial nexuses of the global economy, global health security necessitates the safeguard of cities against epidemic diseases. Singapore's public health landscape has undergone a systemic and irreversible shift with global connectivity, rapid urbanization, ecological change, increased affluence, as well as shifting demographic patterns over the past two decades. Concomitantly, the threat of epidemics, ranging from severe acute respiratory syndrome and influenza A (H1N1) to the resurgence of vector-borne diseases as well as the rise of modern lifestyle-related outbreaks, have worsened difficulties in safeguarding public health amidst much elusiveness and unpredictability. One critical factor that has helped the country overcome these innate and man-made public health vulnerabilities is the development of a resilient field epidemiology service, which includes our enhancement of surveillance and response capacities for outbreak management, and investment in public health leadership. We offer herein the Singapore story as a case study in meeting the challenges of disease control in our modern built environment. 
 Title: The Singapore Field Epidemiology Service: Insights Into Outbreak Management
Output: False
Paragraph: The dynamics of coronavirus disease 2019 (COVID-19) transmissibility after symptom onset remains unknown. We conducted a prospective case-ascertained study on laboratory-confirmed COVID-19 cases and their contacts. Secondary clinical attack rate (considering symptomatic cases only) was analyzed for different exposure windows after symptom onset of index cases and for different exposure settings. Thirty-two confirmed patients were enrolled and 12 paired data (index-secondary cases) were identified among the 1,043 contacts. The secondary clinical attack rate was 0.9% (95% CI 0.5-1.7%). The attack rate was higher among those whose exposure to index cases started within five days of symptom onset (2.4%, 95% CI 1.1-4.5%) than those who were exposed later (zero case from 605 close contacts, 95% CI 0-0.61%). The attack rate was also higher among household contacts (13.6%, 95% CI 4.7-29.5%) and nonhousehold family contacts (8.5%, 95% CI 2.4-20.3%) than that in healthcare or other settings. The higher secondary clinical attack rate for contacts near symptom onset remained when the analysis was restricted to household and family contacts. There was a trend of increasing attack rate with the age of contacts (p for trend < 0.001). High transmissibility of COVID-19 near symptom onset suggests that finding and isolating symptomatic patients alone may not suffice to contain the epidemic, and more generalized social distancing measures are required. Rapid reduction of transmissibility over time implies that prolonged hospitalization of mild cases might not be necessary in large epidemics. 
 Title: High transmissibility of COVID-19 near symptom onset
Output: True
Paragraph: Phylogenetic analyses have provided strong evidence that amino acid changes in spike (S) protein of animal and human SARS coronaviruses (SARS-CoVs) during and between two zoonotic transfers (2002/03 and 2003/04) are the result of positive selection. While several studies support that some amino acid changes between animal and human viruses are the result of inter-species adaptation, the role of neutralizing antibodies (nAbs) in driving SARS-CoV evolution, particularly during intraspecies transmission, is unknown. A detailed examination of SARS-CoV infected animal and human convalescent sera could provide evidence of nAb pressure which, if found, may lead to strategies to effectively block virus evolution pathways by broadening the activity of nAbs. Here we show, by focusing on a dominant neutralization epitope, that contemporaneousand cross-strain nAb responses against SARS-CoV spike protein exist during natural infection. In vitro immune pressure on this epitope using 2002/03 strain-specific nAb 80R recapitulated a dominant escape mutation that was present in all 2003/ 04 animal and human viruses. Strategies to block this nAb escape/naturally occurring evolution pathway by generating broad nAbs (BnAbs) with activity against 80R escape mutants and both 2002/03 and 2003/04 strains were explored. Structure-based amino acid changes in an activation-induced cytidine deaminase (AID) ''hot spot'' in a light chain CDR (complementarity determining region) alone, introduced through shuffling of naturally occurring non-immune human VL chain repertoire or by targeted mutagenesis, were successful in generating these BnAbs. These results demonstrate that nAb-mediated immune pressure is likely a driving force for positive selection during intra-species transmission of SARS-CoV. Somatic hypermutation (SHM) of a single VL CDR can markedly broaden the activity of a strain-specific nAb. The strategies investigated in this study, in particular the use of structural information in combination of chain-shuffling as well as hot-spot CDR mutagenesis, can be exploited to broaden neutralization activity, to improve anti-viral nAb therapies, and directly manipulate virus evolution. Citation: Sui J, Aird DR, Tamin A, Murakami A, Yan M, et al. (2008) Broadening of Neutralization Activity to Directly Block a Dominant Antibody-Driven SARS-Coronavirus Evolution Pathway. PLoS Pathog 4(11): e1000197. This is an open-access article distributed under the terms of the Creative Commons Public Domain declaration which stipulates that, once placed in the public domain, this work may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. 
 Title: Broadening of Neutralization Activity to Directly Block a Dominant Antibody-Driven SARS-Coronavirus Evolution Pathway
Output: True
Paragraph: This chapter defi nes and describes early warning systems (EWS) by examining structures and functions of EWS. The focus of this book is on climate change, but other hazards help to better illustrate and understand EWS in the context of climate change. These include hazards which manifest rapidly, such as tsunamis, as well as creeping hazards which manifest slowly, such as drought. The fundamental tenet is that each EWS needs to be viewed as a social process which often involves technical components embedded in their social context. That leads to a preference for a 'First Mile' approach for designing EWS, which involves communities from the beginning of developing an EWS, rather than a 'Last Mile' approach, which adds people and communities towards the end of the design process. By keeping people and communities at the centre of an EWS from the beginning, the EWS can contribute to daily life and livelihoods, thereby supporting wider disaster risk reduction and sustainable development endeavours, rather than being a separate system waiting to be triggered only when a hazard appears. Yet any EWS has limitations. Those limitations need to be recognised and overcome through other approaches, with possibilities being to consider 'medium warning' and 'late warning' systems rather than just early warning. 
 Title: Early Warning Systems Defi ned
Output: False
Paragraph: The epidemic caused by the novel coronavirus in Wuhan at the end of 2019 has become an urgent public event of worldwide concern. However, due to the changing data of the epidemic, there is no scientific estimate of the cure rate and case fatality rate of the epidemic. This study proposes a method to estimate the cure rate and case fatality rate of COVID-19. The ratio of cumulative discharges on a given day to the sum of cumulative discharges on a given day and cumulative deaths before j days is used to estimate the cure rate. Moreover, the case fatality ratio can also be estimated. After simulation calculations, j is statistically appropriate when it is 8-10, and it is also clinically appropriate. When j is 9, based on the available data, it is inferred that the cure rate of this epidemic is about 93% and the case fatality rate is about 7%. This method of estimating the cure rate can be used to evaluate the effectiveness of treatment in different medical schemes and different regions, and has great value and significance for decision-making in the epidemic. improvement of medical conditions, and rich experience in treatment, patients with COVID-19 will be treated more effectively. Consequently, the CR will increase, and the CFR will decrease. The authors declare no conflict of interest. 
 Title: Estimating the cure rate and case fatality rate of the ongoing epidemic COVID-19
Output: False
Paragraph: A decline in protective immune responses following vaccination is one of the main features of immunosenescence. Improved vaccine candidates for elderly adults are thus urgently needed. For scientific and regulatory requirements, such new vaccines must first be evaluated at the preclinical level, and there is a continuing quest for the ideal animal model with which to perform such studies. The main advantages and limitations of murine models, those most commonly used for human vaccine research, and of large animal models are reviewed and discussed. 
 Title: Vaccines for the Elderly: The Quest for the Ideal Animal Model
Output: False
Paragraph: Porcine epidemic diarrhoea virus (PEDV) is a single-stranded, positive-sense RNA virus that belongs to the Coronaviridae. PEDV causes severe diarrhoea and dehydration in nursing piglets, which leads to significant economic losses to the swine industry worldwide. Stress granules (SGs) are sites of mRNA storage that are formed under various stress conditions including viral infections. Increasing evidence suggests that SGs function in antiviral innate immunity of host cells to limit virus replication. Ras-GTPase-activating protein (SH3 domain) binding protein 1 (G3BP1) is a key stress granule-resident protein that nucleates stress granule assembly. Depletion of G3BP1 inhibits SGs formation and overexpression of G3BP1 nucleates SGs assembly. We observed that knockdown of G3BP1 by silencing RNA significantly increased PEDV replication. Overexpression of exogenous G3BP1, on the other hand, lowered virus replication by 100-fold compared to vector control. An increase in the levels of mRNAs of pro-inflammatory cytokines such as interleukin-1β (IL-1β) and tumor necrosis factor-α (TNF-α) was also observed in PEDV-infected G3BP1 depleted cells compared to PEDV-infected control cells. Taken together, our results suggest that G3BP1 plays an antiviral role and impairs PEDV replication. 
 Title: GTPase-activating protein-binding protein 1 (G3BP1) plays an antiviral role against porcine epidemic diarrhea virus
Output: True