niryuu/sni-each-converted huggingface dataset:
Paragraph: A number of features were included in the final models, including article counts, indicator counts and slopes. In Table 2 -1, the ten features with highest Gini importance are listed for Model 0 → 1 and Model 1 → 0, predicting Y 1 i jt and training on all available weeks. There is substantial overlap between the lists for the two models. For both models, the article count and the mortality, outbreak worsening and novelty indicators were among the most important features. The mortality indicator describes whether or not fatalities were reported during the week, the outbreak worsening indicator captures mentions of increasing cases or worsening conditions, and the novelty indicator measures whether the disease is described as new or unfamiliar. The finding that the novelty indicator was among the most important features is consistent with previous research that has shown that outbreaks of novel diseases are more likely to have associated social response (Fast et al, 2015; McGrath, 1991) . Table 2-1: The ten features with highest Gini importance for Model 0 → 1 and Model 1 → 0 Model 0 → 1 Model 1 → 0 Social Response Indicator EWMA as a Percentage of UCL In this section, we present results for the 30 countries used for model specification and tuning and compare with the overall results in order to access the extent to which tuning and model specification may have affected results for these countries. We experimented with different model specifications and combinations of features on a subset of data consisting of 30 countries, prior to applying our models to the entire collection of countries. Table 2 -2 presents the model performance metrics for both the entire collection of 72 countries and for the subset of 30 countries used for model specification and tuning. Model performance was slightly diminished on the entire collection of countries compared with the 30 countries used for model specification and tuning. In part, the poorer performance can be explained by the fact that the average number of articles per week in the entire collection of countries was lower than in the 30 countries used for model specification -0.14 articles per week versus 3.50 articles per week. We have shown that in general our models perform best on country-disease pairs that receive substantial news coverage. 
 Title: Predicting Social Response to Infectious Disease Outbreaks from Internet-based News Streams Online Resource 2: Supplemental Model Results Article Count without Duplicates 3 Week Slope of EWMA Article Count with Duplicates Disease Name Mortality Indicator Article Count without Duplicates 3 Week Slope of Mortality Indicator Article Count with Duplicates Outbreak Worsening Indicator Mortality Indicator 3 Week Slope of Outbreak Worsening Indicator Outbreak Worsening Indicator Population Fear Indicator Novelty Indicator Novelty Indicator Officials Fear Indicator 2 Results for the 30 Countries Used for Model Specification and Tuning
Output: False
Paragraph: Since then, large-scale sporadic outbreaks of PED caused by PEDV variants have occasionally occurred in China. However, the molecular diversity and epidemiology of PEDV in different provinces has not been completely understood. To determine the molecular diversity of PEDV in the Hubei Province of China, we collected 172 PED samples from 34 farms across the province in 2016 and performed reverse transcription polymerase chain reaction (RT-PCR) by targeting the nucleocapsid (N) gene. Seventy-four samples were found to be PEDVpositive. We further characterized the complete spike (S) glycoprotein genes from the positive samples and found 21 different S genes with amino acid mutations. The PEDV isolates here presented most of the genotypes which were found previously in field isolates in East and South-East Asia, North America, and Europe. Besides the typical Genotypes I and II, the INDEX groups were also found. Importantly, 58 new amino acids mutant sites in the S genes, including 44 sites in S1 and 14 sites in S2, were first described. Our results revealed that the S genes of PEDV showed variation and that diverse genotypes of PEDV coexisted and were responsible for the PED outbreaks in Hubei in 2016. This work highlighted the complexity of the epidemiology of PEDV and emphasized the need for reassessing the efficacy of classic PEDV vaccines against emerging variant strains and developing new vaccines to facilitate the prevention and control of PEDV in fields. 
 Title: Coexistence of multiple genotypes of porcine epidemic diarrhea virus with novel mutant S genes in the Hubei Province of China in 2016
Output: True
Paragraph: The etiological agent of severe acute respiratory syndrome (SARS) has been identified as a novel coronavirus SARS-CoV. Similar to other coronaviruses, spike (S)-glycoprotein of the virus interacts with a cellular receptor and mediates membrane fusion to allow viral entry into susceptible target cells. Accordingly, S-protein plays an important role in virus infection cycle and is the primary target of neutralizing antibodies. To begin to understand its biochemical and immunological properties, we expressed both full-length and ectodomain of the protein in various primate cells. Our results show that the protein has an electrophoretic mobility of about 160 -170 kDa. The protein is glycosylated with high mannose and/or hybrid oligosaccharides, which account for approximately 30 kDa of the apparent protein mass. The detection of S-protein by immunoassays was difficult using human convalescent sera, suggesting that the protein may not elicit strong humoral immune response in virus-infected patients. We were able to pseudotype murine leukemia virus particles with S-protein and produce SARS pseudoviruses. Pseudoviruses infected Vero E6 cells in a pH-independent manner and the infection could be specifically inhibited by convalescent sera. Consistent with low levels of antibodies against S-protein, neutralizing activity was weak with 50% neutralization titers ranging between 1:15 to 1:25. To facilitate quantifying pseudovirus-infected cells, which are stained blue with X-Gal, we devised an automated procedure using an ELISPOT analyzer. The high-throughput capacity of this procedure and the safety of using SARS pseudoviruses should make possible large-scale analyses of neutralizing antibody responses against SARS-CoV. D 
 Title: Development of a safe neutralization assay for SARS-CoV and characterization of S-glycoprotein
Output: False
Paragraph: To assess the viability of isolation and contact tracing to control onwards transmission from imported cases of 2019-nCoV. We developed a stochastic transmission model, parameterised to the 2019-nCoV outbreak. We used the model to quantify the potential effectiveness of contact tracing and isolation of cases at controlling a 2019 nCoV-like pathogen. We considered scenarios that varied in: the number of initial cases; the basic reproduction number R0; the delay from symptom onset to isolation; the probability contacts were traced; the proportion of transmission that occurred before symptom onset, and the proportion of subclinical infections. We assumed isolation prevented all further transmission in the model. Outbreaks were deemed controlled if transmission ended within 12 weeks or before 5000 cases in total. We measured the success of controlling outbreaks using isolation and contact tracing, and quantified the weekly maximum number of cases traced to measure feasibility of public health effort. Findings: While simulated outbreaks starting with only 5 initial cases, R0 of 1.5 and little transmission before symptom onset could be controlled even with low contact tracing probability, the prospects of controlling an outbreak dramatically dropped with the number of initial cases, with higher R0, and with more transmission before symptom onset. Across different initial numbers of cases, the majority of scenarios with an R0 of 1.5 were controllable with under 50% of contacts successfully traced. For R0 of 2.5 and 3.5, more than 70% and 90% of contacts respectively had to be traced to control the majority of outbreaks. The delay between symptom onset and isolation played the largest role in determining whether an outbreak was controllable for lower values of R0. For higher values of R0 and a large initial number of cases, contact tracing and isolation was only potentially feasible when less than 1% of transmission occurred before symptom onset. Interpretation: We found that in most scenarios contact tracing and case isolation alone is unlikely to control a new outbreak of 2019-nCov within three months. The probability of control decreases with longer delays from symptom onset to isolation, fewer cases ascertained by contact tracing, and increasing transmission before symptoms. This model can be modified to reflect updated transmission characteristics and more specific definitions of outbreak control to assess the potential success of local response efforts. 
 Title: Title: Feasibility of controlling 2019-nCoV outbreaks by isolation of cases and contacts
Output: True
Paragraph: Macroscopic descriptions of populations commonly assume that encounters between individuals are well mixed; i.e. each individual has an equal chance of coming into contact with any other individual. Relaxing this assumption can be challenging though, due to the difficulty of acquiring detailed knowledge about the non-random nature of encounters. Here, we fitted a mathematical model of dengue virus transmission to spatial time-series data from Pakistan and compared maximum-likelihood estimates of 'mixing parameters' when disaggregating data across an urban-rural gradient. We show that dynamics across this gradient are subject not only to differing transmission intensities but also to differing strengths of nonlinearity due to differences in mixing. Accounting for differences in mobility by incorporating two fine-scale, density-dependent covariate layers eliminates differences in mixing but results in a doubling of the estimated transmission potential of the large urban district of Lahore. We furthermore show that neglecting spatial variation in mixing can lead to substantial underestimates of the level of effort needed to control a pathogen with vaccines or other interventions. We complement this analysis with estimates of the relationships between dengue transmission intensity and other putative environmental drivers thereof. License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited. 
 Title: Big city, small world: density, contact rates, and transmission of dengue across Pakistan
Output: False
Paragraph: Recent results have provided increasing evidence for the existence of an intermediate membrane compartment between the rough endoplasmic reticulum and the Golgi complex which seems to function in protein sorting and the regulation of membrane traffic in the early part of the exocytic pathway . Localization of resident marker proteins has shown that this compartment consists of both peripheral and central elements . The aim of the present review is to combine the data on the pre-Golgi compartment with previous ideas of membrane traffic at the ER-Golgi interface . We propose a model which describes how mobile, endosome-like elements of the pre-Golgi compartment function in the generation of the compositional andfunctional boundary between the widely distributed ER and the more central4 located Golgi stacks . 
 Title: Pathways of protein sorting and membrane traffic between the rough endoplasmic reticulum and the Golgi complex jaakko Saraste *t and Esa Kuismanent
Output: True
Paragraph: Supplementary Figure 1. Phylogenetic tree for complete genomes of 91 representative IOL CHIKV strains constructed using the maximum likelihood method. Bootstrap values and sl1-4-specific substitutions are indicated. The SL07 strain used as a genetic background for all in vivo experiments is highlighted with an asterisk. The purple arrow highlights strain LK(EH)CH18608 with the E2-K233E substitution. The blue diamond highlights the Thailand-2009_CK11/53 strain of sl1 used in competition experiment (see Supplementary Fig. 2) . The bar indicates 0.2% nucleotide sequence divergence. (a) Schematic representation of the experimental design. Table shows genetic differences between the competing viruses. A 1:1 ratio (based on pfu) of wt (SL07-226V_Apa) and mut (contains one of the sl2-specific mutations) viruses was presented to Thai colony A. 
 Title: Supplementary information
Output: False
Paragraph: Background: Fevers of unknown origin constitute a substantial disease burden in Southeast Asia. In majority of the cases, the cause of acute febrile illness is not identified. Methods: We used MassTag PCR, a multiplex assay platform, to test for the presence of 15 viral respiratory agents from 85 patients with unexplained respiratory illness representing six disease clusters that occurred in Cambodia between 2009 and 2012. Results: We detected a virus in 37 (44%) of the cases. Human rhinovirus, the virus detected most frequently, was found in both children and adults. The viruses most frequently detected in children and adults, respectively, were respiratory syncytial virus and enterovirus 68. Sequence analysis indicated that two distinct clades of enterovirus 68 were circulating during this time period. Conclusions: This is the first report of enterovirus 68 in Cambodia and contributes to the appreciation of this virus as an important respiratory pathogen. 
 Title: Multiplex PCR analysis of clusters of unexplained viral respiratory tract infection in Cambodia
Output: False
Paragraph: Viruses may be regarded as dynamic nucleoprotein assemblies capable of assisted multiplication within cells, and of propagation between cells and organisms. Infectious virus particles (virions) assembled in a host cell are dynamic, generally metastable particles: They are robust enough to protect the viral genome outside the cell, but are also poised to undergo structural changes and execute mechanochemical actions required for infection of other cells. This chapter provides an introduction to the structural and physical biology of viruses by including: (i) an elementary overview on virions and the structural basis of virus function; (ii) a concise summary on basic techniques used in structural or physical virology; (iii) brief structure-based general descriptions of the different stages in the virus cycle, especially those in which virions and/or their components are involved. These contents may facilitate a better understanding of the specialized subjects treated in the rest of the book. This chapter is also intended as a "road map" to help interconnect and integrate in a single picture the different topics described in depth in the 21 monographic chapters in this book. 
 Title: Introduction: The Structural Basis of Virus Function
Output: False
Paragraph: Meliacine (MA), an antiviral principle present in partially purified leaf extracts of Melia azedarach L., prevents the development of herpetic stromal keratitis (HSK) in mice by diminishing the viral load in the eye and the severity of lesions caused by a virus-induced immunopathological reaction. The tetranortriterpenoid 1-cinnamoyl-3,11-dihydroxymeliacarpin (CDM), obtained from MA purification, displays anti-herpetic activity and impedes nuclear factor B (NF-B) activation in HSV-1 infected conjunctival cells. To extend our understanding about CDM biological properties, we investigated its anti-HSV-1 activity as well as the effect on NF-B activation and cytokine secretion induced by viral (HSV-1) and no-viral (LPS) stimuli, in corneal cells and macrophages. CDM exerted a potent anti-HSV-1 effect on corneal cells and inhibited NF-B translocation to the nucleus, leading to a decrease in IL-6 production. Besides, CDM seemed to modulate IL-6 and TNF-␣ responses in macrophages, whether they were infected with HSV-1 or stimulated with LPS. However, CDM did not affect NF-B activation in these cells, suggesting that an alternative NF-B cell signaling pathway would be involved in the modulation of cytokine production. We conclude that, in addition to its antiviral effect, CDM would be acting as an immunomodulating compound which would be responsible for the improvement of murine HSK already reported. 
 Title: A natural tetranortriterpenoid with immunomodulating properties as a potential anti-HSV agent
Output: False
Paragraph: Zika virus (ZIKV) has been associated with serious health conditions, and an intense search to discover different ways to prevent and treat ZIKV infection is underway. Berberine and emodin possess several pharmacological properties and have been shown to be particularly effective against the entry and replication of several viruses. We show that emodin and berberine trigger a virucidal effect on ZIKV. When the virus was exposed to 160 µM of berberine, a reduction of 77.6% in the infectivity was observed; when emodin was used (40 µM), this reduction was approximately 83.3%. Dynamic light scattering data showed that both compounds significantly reduce the hydrodynamic radius of virus particle in solution. We report here that berberine and emodin, two natural compounds, have strong virucidal effect in Zika virus. 
 Title: Natural Products Isolated from Oriental Medicinal Herbs Inactivate Zika Virus
Output: False
Paragraph: Previous studies have shown that mice can be protected from a lethal infection with the neurotropic JHM strain of mouse hepatitis virus (JHMV) by the adoptive transfer of delayed-type hypersensitivity (DTH)-inducer T cell clones specific for the virus. Protection does not involve the suppression of virus replication in the central nervous system (CNS) or via augmentation of the antiviral antibody response. In the present report we have compared the CNS lesions induced by JHMV in lethally infected and T cell clone protected mice. The presence of virus-specific T cell clones induced a transient increase in mononuclear cell infiltration into the parenchyma of the brains of protected mice, consistent with previous data suggesting that a DTH response was responsible for protection. Immunohistochemical studies suggested further that virus was not replicating in the ependyma or cellular infiltrate, but that the presence of the T cell clone prevented neuronal infection. While the mechanism of effectively altering the in vivo cellular tropism is unknown, survival is accompanied by increased specific destruction of target tissues with fulminant CNS demyelination and an increased incidence of persistent infection. 
 Title: Studies on the mechanism of protection from acute viral encephalomyelitis by delayed-type hypersensitivity inducer T cell clones
Output: True
Paragraph: We have developed a reverse genetics system for the avian coronavirus infectious bronchitis virus (IBV) in which a full-length cDNA corresponding to the IBV genome is inserted into the vaccinia virus genome under the control of a T7 promoter sequence. Vaccinia virus as a vector for the full-length IBV cDNA has the advantage that modifications can be introduced into the IBV cDNA using homologous recombination, a method frequently used to insert and delete sequences from the vaccinia virus genome. Here we describe the use of transient dominant selection as a method for introducing modifications into the IBV cDNA. We have used it successfully for the substitution of specific nucleotides, deletion of genomic regions, and the exchange of complete genes. Infectious recombinant IBVs are generated in situ following the transfection of vaccinia virus DNA containing the modified IBV cDNA into cells infected with a recombinant fowlpox virus expressing T7 DNA-dependent RNA polymerase. 
 Title: Transient Dominant Selection for the Modification and Generation of Recombinant Infectious Bronchitis Coronaviruses
Output: True
Paragraph: The envelope of hepatitis B virus (HBV), containing the L, M, and S proteins, is essential for virus entry and maturation. For direct visualization of HBV, we determined whether envelope assembly could accommodate the green fluorescent protein (GFP). While the Cterminal addition of GFP to S trans-dominant negatively inhibited empty envelope particle secretion, the N-terminal GFP fusion to S (GFP.S) was co-integrated into the envelope, giving rise to fluorescent particles. Microscopy and topogenesis analyses demonstrated that the proper intracellular distribution and folding of GFP.S, required for particle export were rescued by interprotein interactions with wild-type S. Thereby, a dual location of GFP, inside and outside the envelope, was observed. GFP.S was also efficiently packaged into the viral envelope, and these GFP-tagged virions retained the capacity for attachment to HBV receptor-positive cells in vitro. Together, GFP-tagged virions should be suitable to monitor HBV uptake and egress in live hepatocytes. D 2004 Elsevier Inc. All rights reserved. 
 Title: Functional incorporation of green fluorescent protein into hepatitis B virus envelope particles
Output: True
Paragraph: Viral late domains are used by many viruses to recruit the cellular endosomal sorting complex required for transport (ESCRT) to mediate membrane scission during viral budding. Unlike the P(S/T)AP and YPX (1-3) L late domains, which interact directly with the ESCRT proteins Tsg101 and ALIX, the molecular linkage connecting the PPXY late domain to ESCRT proteins is unclear. The mammarenavirus lymphocytic choriomeningitis virus (LCMV) matrix protein, Z, contains only one late domain, PPXY. We previously found that this domain in LCMV Z, as well as the ESCRT pathway, are required for the release of defective interfering (DI) particles but not infectious virus. To better understand the molecular mechanism of ESCRT recruitment by the PPXY late domain, affinity purification-mass spectrometry was used to identify host proteins that interact with the Z proteins of the Old World mammarenaviruses LCMV and Lassa virus. Several Nedd4 family E3 ubiquitin ligases interact with these matrix proteins and in the case of LCMV Z, the interaction was PPXY-dependent. We demonstrated that these ligases directly ubiquitinate LCMV Z and mapped the specific lysine residues modified. A recombinant LCMV containing a Z that cannot be ubiquitinated maintained its ability to produce both infectious virus and DI particles, suggesting that direct ubiquitination of LCMV Z alone is insufficient for recruiting ESCRT proteins to mediate virus release. However, Nedd4 ligases appear to be important for DI PLOS Pathogens | https://doi.org/10. 
 Title: NEDD4 family ubiquitin ligases associate with LCMV Z's PPXY domain and are required for virus budding, but not via direct ubiquitination of Z
Output: True
Paragraph: Background: The pteropine orthoreovirus (PRV) was isolated from monkey (Macaca fascicularis) faecal samples collected from human-inhabited areas in Lopburi Province, Thailand. These samples were initially obtained to survey for the presence of hepatitis E virus (HEV). Results: Two virus isolates were retrieved by virus culture of 55 monkey faecal samples. Liquid chromatographytandem mass spectrometry (LC-MS/MS) was successfully used to identify the viruses as the segmented dsRNA orthoreovirus. Phylogenetic analysis of the Lopburi orthoreovirus whole-genomes revealed relationships with the well-characterised PRVs Pulau (segment L1), Cangyuan (segments L2, M3 and S3), Melaka (segments L3 and M2), Kampar (segments M1 and S2) and Sikamat (segments S1 and S4) of Southeast Asia and China with nucleotide sequence identities of 93.5-98.9%. RT-PCR showed that PRV was detected in 10.9% (6/55) and HEV was detected in 25.5% (14/55) of the monkey faecal samples. Conclusions: PRV was isolated from monkey faeces for the first time in Thailand via viral culture and LC-MS/MS. The genetic diversity of the virus genome segments suggested a re-assortment within the PRV species group. The overall findings emphasise that monkey faeces can be sources of zoonotic viruses, including PRV and HEV, and suggest the need for active virus surveillance in areas of human and monkey co-habitation to prevent and control emerging zoonotic diseases in the future. 
 Title: Mass spectrometry-based identification and whole-genome characterisation of the first pteropine orthoreovirus isolated from monkey faeces in Thailand
Output: False
Paragraph: In this paper, we analyze a delayed SEIR epidemic model in which the latent and infected states are infective. The model has a globally asymptotically stable disease-free equilibrium whenever a certain epidemiological threshold, known as the basic reproduction number R 0 , is less than or equal to unity. We investigate the effect of the time delay on the stability of endemic equilibrium when R 0 > 1. We give criteria that ensure that endemic equilibrium is asymptotically stable for all time delays and a Hopf bifurcation occurs as time delay exceeds the critical value. We give formulae for the direction of Hopf bifurcations and the stability of bifurcated periodic solutions by applying the normal form theory and the center manifold reduction for functional differential equations. Numerical simulations are presented to illustrate the analytical results. 
 Title: Hopf bifurcation analysis of a delayed SEIR epidemic model with infectious force in latent and infected period
Output: False
Paragraph: The cellular serine protease TMPRSS2, a member of the type II transmembrane serine protease (TTSP) family, cleaves and activates the hemagglutinin of influenza A viruses (FLUAV) in cell culture and is essential for spread of diverse FLUAV in mice. Non-human primates (NHP), in particular rhesus and cynomolgus macaques, serve as animal models for influenza and experimental FLUAV infection of common marmosets has recently also been reported. However, it is currently unknown whether the NHP orthologues of human TMPRSS2 cleave and activate FLUAV hemagglutinin and contribute to viral spread in respiratory tissue. Here, we cloned and functionally analyzed the macaque and marmoset orthologues of human TMPRSS2. In addition, we analyzed the macaque orthologues of human TMPRSS4 and HAT, which also belong to the TTSP family. We found that all NHP orthologues of human TMPRSS2, TMPRSS4 and HAT cleave and activate HA upon directed expression and provide evidence that endogenous TMPRSS2 is expressed in the respiratory epithelium of rhesus macaques. Finally, we demonstrate that a serine protease inhibitor active against TMPRSS2 suppresses FLUAV spread in precision-cut lung slices of human, macaque and marmoset origin. These results indicate that FLUAV depends on serine protease activity for spread in diverse NHP and in humans. Moreover, our findings suggest that macaques and marmosets may serve as models to study FLUAV activation by TMPRSS2 in human patients. Conceptualization: PZ SP. Formal analysis: PZ SP. Funding acquisition: SP. Investigation: PZ PMB SB KWG IN AH ASM SK SD KS CB CC JG KMR FD. Methodology: AB. Project administration: SP. Resources: SK AB. Supervision: PZ SB SK AB. Validation: PZ SP. Visualization: PZ SP. 
 Title: Non-human primate orthologues of TMPRSS2 cleave and activate the influenza virus hemagglutinin
Output: False
Paragraph: Attenuated viral vaccines can be generated by targeting essential pathogenicity factors. We report here the rational design of an attenuated recombinant coronavirus vaccine based on a deletion in the coding sequence of the nonstructural protein 1 (nsp1). In cell culture, nsp1 of mouse hepatitis virus (MHV), like its SARS-coronavirus homolog, strongly reduced cellular gene expression. The effect of nsp1 on MHV replication in vitro and in vivo was analyzed using a recombinant MHV encoding a deletion in the nsp1-coding sequence. The recombinant MHV nsp1 mutant grew normally in tissue culture, but was severely attenuated in vivo. Replication and spread of the nsp1 mutant virus was restored almost to wild-type levels in type I interferon (IFN) receptor-deficient mice, indicating that nsp1 interferes efficiently with the type I IFN system. Importantly, replication of nsp1 mutant virus in professional antigen-presenting cells such as conventional dendritic cells and macrophages, and induction of type I IFN in plasmacytoid dendritic cells, was not impaired. Furthermore, even low doses of nsp1 mutant MHV elicited potent cytotoxic T cell responses and protected mice against homologous and heterologous virus challenge. Taken together, the presented attenuation strategy provides a paradigm for the development of highly efficient coronavirus vaccines. 
 Title: Coronavirus Non-Structural Protein 1 Is a Major Pathogenicity Factor: Implications for the Rational Design of Coronavirus Vaccines
Output: False
Paragraph: This paper describes the molecular detection of respiratory viruses from nasopharyngeal flocked swabs (flocked swabs) and nasopharyngeal washes (washes) in a clinical setting. Washes and flocked swabs collected from children < 3 years old hospitalized with a lower respiratory tract infection were tested for parainfluenza virus 1-3, respiratory syncytial virus, influenza A and B and metapneumovirus (Group 1) and adenovirus, rhinovirus and coronavirus (Group 2) using realtime reverse transcriptase PCR (rRT-PCR). A consensuses standard was used to determine sensitivity and compare cycle thresholds (C T ) of washes and flocked swabs for each virus and group of viruses. Sensitivities ranged from 79 to 89% and 69 to 94% for flocked swabs and washes, respectively, excluding AdV which had a sensitivity of 35% for flocked swabs. When the flocked swabs and washes of Group 1 viruses were collected on the day of admission, the sensitivity of both sample types was 100%. Wash specimens had a lower C T value and higher sensitivity than flocked swabs; however there was no statistical difference in the sensitivity of a flocked swab (89%) versus wash (93%) for the detection of Group 1 viruses, particularly when samples were collected on the same day. Flocked swabs may be a useful alternative to washes for detection of respiratory viruses in clinical settings. 
 Title: Comparison of nasopharyngeal flocked swabs and nasopharyngeal wash collection methods for respiratory virus detection in hospitalized children using real-time polymerase chain reaction HHS Public Access
Output: False
Paragraph: Three tests were compared to diagnose herpes virus infection: electron microscopy (EM), viral culture (VC) and cytodiagnosis (Tzanck smear). The study comprised 67 patients with skin or mucous membrane lesions suggestive of herpes simplex virus (HSV) infection. The sensitivity of EM increased 25% after virus concentration by ultracentrifugation. Herpes virus infection was confirmed in 55 of the 67 cases by EM or VC or both. EM detected 53 herpes virus-positive lesion samples of which 14 were not detected by VC; only two lesion samples that were herpes virus-positive in VC were not detected by EM. The sensitivities of EM, VC, and Tzanck smear for the group of 55 herpes virus-positive cases were 96%, 75% and 76%, respectively. The specificity of the Tzanck smear was 83% (prevalence 82%). Colloidal gold immuno-EM was used to rapidly type HSV-1, HSV-2 and varicella zoster virus (VZV) present in skin and mucous membrane lesions in less than 4 h. Immuno-EM was able to detect antiviral antibodies on viral envelopes and viral cores in lesion samples with negative VC. Antiviral antibodies do not interfere with typing of herpes viruses by immuno-EM. It is suggested that formation of viral immune complexes and inactivation of virus particles by antibodies may have caused a Correspondence to: E. Folkers, 
 Title: Improved detection of HSV by electron microscopy in clinical specimens using ultracentrifugation and cdlloidal gold immunoelectron microscopy: comparison with viral culture atld, cytodiagnosis
Output: True
Paragraph: Background: Upper respiratory tract infections (URTIs), including rhinitis, nasopharyngitis, tonsillitis and otitis media (OM), comprise of 88% of total respiratory infections, especially in children. Therefore effective prevention and treatment of RTIs remain a high priority worldwide. Preclinical and clinical data highlight the rationale for the use and effectiveness of immunity-targeted approaches, including targeted immunisations and nonspecific immunomodulation in the prevention and management of recurrent upper RTIs. The idea of this review was to summarise the current evidence and address key questions concerning the use of conservative and immunity-targeted approaches to recurrent and chronic URTIs, with a focus on the paediatric population. Health Source: Nursing/Academic Edition; MEDLINE; clinicaltrials.gov; and Cochrane databases. In total, 84 articles were retrieved and reviewed. Two independent researchers focused on primary and secondary endpoints in systematic reviews, metaanalyses and randomised, controlled trials, using immunity-directed strategies as the control group or within a subpopulation of larger studies. Existing guidelines and interventional/observational studies on novel applications were also included. Results: Children are particularly susceptible to RTIs due to the relative immaturity of their immune systems, as well as other potential predisposing factors such as day care attendance and/or toxic environmental factors (eg increased pathogenic microbial exposure and air pollutants). Recurrent URTIs can affect otherwise healthy children, leading to clinical sequelae and complications, including the development of chronic conditions or the need for surgery. Available pre-clinical and clinical data highlight the rationale for the use and effectiveness of immunity-targeted approaches, including targeted immunisations (flu and pneumococcal vaccines) and non-specific immunomodulation (bacterial lysates), in the prevention and management of recurrent croup, tonsillitis, otitis media, recurrent acute rhinosinusitis and chronic rhinosinusitis. In this review, we summarise the current evidence and provide data demonstrating that some immunity-targeted strategies, including vaccination and immunomodulation, have proved effective in the treatment and prevention of recurrent and chronic URTIs in children. FELESZKO Et aL. 
 Title: Immunity-targeted approaches to the management of chronic and recurrent upper respiratory tract disorders in children
Output: True
Paragraph: Background: Nosocomial, or healthcare-associated infections (HAI), exact a high medical and financial toll on patients, healthcare workers, caretakers, and the health system. Interpersonal contact patterns play a large role in infectious disease spread, but little is known about the relationship between health care workers' (HCW) movements and contact patterns within a heath care facility and HAI. Quantitatively capturing these patterns will aid in understanding the dynamics of HAI and may lead to more targeted and effective control strategies in the hospital setting. Methods: Staff at 3 urban university-based tertiary care hospitals in Canada completed a detailed questionnaire on demographics, interpersonal contacts, in-hospital movement, and infection prevention and control practices. Staff were divided into categories of administrative/support, nurses, physicians, and "Other HCWs" -a fourth distinct category, which excludes physicians and nurses. Using quantitative network modeling tools, we constructed the resulting HCW "co-location network" to illustrate contacts among different occupations and with locations in hospital settings. Results: Among 3048 respondents (response rate 38%) an average of 3.79, 3.69 and 3.88 floors were visited by each HCW each week in the 3 hospitals, with a standard deviation of 2.63, 1.74 and 2.08, respectively. Physicians reported the highest rate of direct patient contacts (> 20 patients/day) but the lowest rate of contacts with other HCWs; nurses had the most extended (> 20 min) periods of direct patient contact. "Other HCWs" had the most direct daily contact with all other HCWs. Physicians also reported significantly more locations visited per week than nurses, other HCW, or administrators; nurses visited the fewest. Public spaces such as the cafeteria had the most staff visits per week, but the least mean hours spent per visit. Inpatient settings had significantly more HCW interactions per week than outpatient settings. Conclusions: HCW contact patterns and spatial movement demonstrate significant heterogeneity by occupation. Control strategies that address this diversity among health care workers may be more effective than "one-strategy-fitsall" HAI prevention and control programs. 
 Title: Contact among healthcare workers in the hospital setting: developing the evidence base for innovative approaches to infection control
Output: False
Paragraph: A total of 116 hospitalized patients with confirmed COVID-19 pneumonia and SARS-CoV-2-specific immunoglobulins tested in Tongji hospital were retrospectively investigated. Clinical, laboratory, radiological characteristics and outcomes data were compared between mild-moderate group and died group. Further, a paired case-control study was conducted where each deceased case was matched to three mild-moderate patients of similar age. Among 116 subjects included, 101 mild-moderate patients survived and 15 cases died. SARS-CoV-2-specific IgM levels peaked in forth week after onset of COVID-19 pneumonia, while serum IgG levels increased over 8 weeks. Serum IgM levels were higher in deceased patients than mild-moderate patients (P = 0.024), but not IgG. Serum IgM levels were negatively correlated with clinical outcome, eosinophil count and albumin levels (r = -0.269, P = 0.003; r = -0.188, P = 0.043; and r = -0.198, P = 0.033, resp.). The area under the ROC curve (AUC) for IgM antibody was 0.681 (95% CI: 0.517-0.845, P = 0.024). In case-control study paired by age, serum IgM was higher in deceased patients than mild-moderate patients (P = 0.019), positively correlated with leucocyte count (r = 0.260, P = 0.045), while negatively correlated with clinical outcome and albumin levels (r = -0.337, P = 0.008; r = -0.265, P = 0.041). AUC for IgM levels was 0.704 (95% CI: 0.534-0.873, P = 0.019). These results indicate that dynamics of SARS-CoV-2 specific IgM and IgG antibodies was similar with that of SARS-CoV, while elevated serum IgM levels indicate poor outcome in patients with COVID-19 pneumonia. All rights reserved. No reuse allowed without permission. author/funder, who has granted medRxiv a license to display the preprint in perpetuity. 
 Title: Elevated serum IgM levels indicate poor outcome in patients with coronavirus disease 2019 pneumonia: A retrospective case-control study
Output: True
Paragraph: This chapter explores the role of science journalism in contributing towards public education about science in Singapore, an aspect which is underexplored in the literature. Though the key platforms for promoting public understanding of science are spearheaded mainly by institutions that promote informal science learning as well as by learned societies, the contribution from newspapers is also important. Content analysis of one continuous week of a national newspaper was undertaken, and the results show that coverage of science and technology was modest and predominantly news driven. For news stories set locally, there was a pronounced emphasis on the use of institutional actors in the text as well as quotations. Articles on health/medicine and earth science elicited the most coverage in the press. Some suggestions for using newspaper science to introduce inquiry in the science classroom are discussed. 
 Title: Public Education About Science in Singapore: The Role of Science Journalism via Newspapers
Output: True
Paragraph: The study aim was to investigate the prevalence and clinical relevance of viral findings by multiplex PCR from the nasopharynx of clinically septic patients during a winter season. During 11 weeks of the influenza epidemic period in January-March 2012, consecutive adult patients suspected to be septic (n = 432) were analyzed with cultures from blood and nasopharynx plus multiplex PCR for respiratory viruses on the nasopharyngeal specimen. The results were compared with those from microbiology analyses ordered as part of standard care. During the winter season, viral respiratory pathogens, mainly influenza A virus, human metapneumovirus, coronavirus, and respiratory syncytial virus were clinically underdiagnosed in 70% of patients positive by the multiplex PCR assay. During the first four weeks of the influenza epidemic, few tests for influenza were ordered by clinicians, indicating low awareness that the epidemic had started. Nasopharyngeal findings of Streptococcus pneumoniae and Haemophilus influenzae by culture correlated to pneumonia diagnosis, and in those patients laboratory signs of viral coinfections were common but rarely suspected by clinicians. The role of respiratory viral infections in patients presenting with a clinical picture of sepsis is underestimated. Specific antiviral treatment might be beneficial in some cases and may reduce spread in a hospital setting. Diagnosing viral infections may promote reduction of unnecessary antibiotic use. It can also be a tool for decisions concerning patient logistics, in order to minimize exposure of susceptible patients and personnel. 
 Title: Respiratory viral infections are underdiagnosed in patients with suspected sepsis
Output: True
Paragraph: Detailed information on the source, spread and evolution of respiratory syncytial virus (RSV) during seasonal community outbreaks remains sparse. Molecular analyses of attachment (G) gene sequences from hospitalized cases suggest that multiple genotypes and variants co-circulate during epidemics and that RSV persistence over successive seasons is characterized by replacement and multiple new introductions of variants. No studies have defined the patterns of introduction, spread and evolution of RSV at the local community and household level. We present a whole genome sequence analysis of 131 RSV group A viruses collected during 6-month household-based RSV infection surveillance in Coastal Kenya, 2010 within an area of 12 km 2 . RSV infections were identified by regular symptom-independent screening of all household members twice weekly. Phylogenetic analysis revealed that the RSV A viruses in nine households were closely related to genotype GA2 and fell within a single branch of the global phylogeny. Genomic analysis allowed the detection of householdspecific variation in seven households. For comparison, using only G gene analysis, household-specific variation was found only in one of the nine households. Nucleotide changes were observed both intra-host (viruses identified from same individual in follow-up sampling) and inter-host (viruses identified from different household members) and these coupled with sampling dates enabled a partial reconstruction of the within household transmission chains. The genomic evolutionary rate for the household dataset was estimated as 2.307 Â 10 À 3 (95% highest posterior density: 0.935-4.165Â 10 À 3 ) substitutions/site/year. We conclude that (i) at the household level, most RSV infections arise from the introduction of a single virus variant followed by accumulation of household specific variation and (ii) analysis of complete virus genomes is crucial to better understand viral transmission in the community. A key question arising is whether prevention of RSV introduction or spread within the household by vaccinating key transmitting household members would lead to a reduced onward community-wide transmission. 
 Title: Transmission patterns and evolution of respiratory syncytial virus in a community outbreak identified by genomic analysis
Output: True
Paragraph: A cross-sectional study was carried out over a period of 12 months to investigate the occurrence of human bocavirus (HBoV) infection in infants hospitalized for respiratory infections in a teaching hospital in Salvador, Brazil, and to describe the clinical manifestations of this infection. Nasopharyngeal aspirates were collected from the children and immunofluorescence and polymerase chain reaction were performed to investigate the presence of respiratory viruses. HBoV was detected in 4 out of 66 patients. Two of the HBoV-positive infants were co-infected with other viruses. The principal clinical findings in HBoV-positive children were: nasal obstruction, catarrh, cough, fever and dyspnea. This study revealed HBoV infection in children aged <2 months, suggesting that the infection may occur at a very early age. 
 Title: Research Letters Human Bocavirus in Very Young Infants Hospitalized with Acute Respiratory Infection in Northeast Brazil
Output: False
Paragraph: Background: Lower respiratory tract infections (LRTI) are responsible for a considerable number of deaths among children, particularly in developing countries. In Egypt and the Middle East region, there is a lack of data regarding the viral causes of LRTI. In this study, we aimed to identify the relative prevalence of various respiratory viruses that contribute to LRTIs in young children. Although, nucleic acid-based methods have gained importance as a sensitive tool to determine the viral infections, their use is limited because of their prohibitive cost in low-income countries. Therefore, we applied three different laboratory methods, and presented the different virus prevalence patterns detected by each method. Methods: We collected nasopharyngeal aspirate samples, demographic data and, clinical data from 450 children under five years of age who presented with LRTI at Abou El Reesh hospital in Cairo during a one-year period. To identify the viral causes of the LRTI we used direct fluorescence assay, real-time reverse-transcriptase polymerase chain reaction (rt-RT-PCR), and shell vial culture. We tested for eight major respiratory viruses. Results: Two hundred sixty-nine patients (59.9%) had a viral infection, among which 10.8% had a co-infection with two or more viruses. By all three methods, respiratory syncytial virus (RSV) was the most predominant, and parainfluenza virus type 2 (HPIV-2), influenza B virus (FLUBV) were the least predominant. Other viral prevalence patterns differed according to the detection method used. The distribution of various viruses among different age groups and seasonal distribution of the viruses were also determined. Conclusions: RSV and human adenovirus were the most common respiratory viruses detected by rt-RT-PCR. Co-infections were found to be frequent among children and the vast majority of co-infections were detected by nucleic acid-based detection assays. 
 Title: Viral etiologies of lower respiratory tract infections among Egyptian children under five years of age
Output: False
Paragraph: Traditional Chinese medicine (TCM) is currently the best-preserved and most influential traditional medical system with the largest number of users worldwide. In recent years, the trend of TCM adoption has increased greatly, but the process of TCM internationalization has suffered from a series of setbacks for both internal and external reasons. Thus, the process of TCM internationalization faces formidable challenges, although it also has favourable opportunities. Using SWOT analysis, this paper investigates the strengths, weaknesses, opportunities and threats for TCM. These findings can serve as references for TCM enterprises with global ambitions. 
 Title: SWOT analysis and revelation in traditional Chinese medicine internationalization
Output: True
Paragraph: We analyzed temporal stability and geographic trends in cumulative case-fatality rates and average doubling times of severe acute respiratory syndrome (SARS). In part, we account for correlations between case-fatality rates and doubling times through differences in control measures. Factors that may alter future estimates of casefatality rates, reasons for heterogeneity in doubling times among countries, and implications for the control of SARS are discussed. 
 Title: Severe Acute Respiratory Syndrome: Temporal Stability and Geographic Variation in Case-Fatality Rates and Doubling Times
Output: False