niryuu/sni-each-converted huggingface dataset:
Paragraph: Rhinosinusitis (RS) is a heterogeneous group of diseases. It is a significant and increasing health problem that affects about 15% of the population in Western countries. It has a substantial impact on patients' healthrelated quality of life and daily functioning and represents a huge financial burden to society and the health care system as a result of the direct and indirect costs. In addition, RS is not well-understood, and little is known about the etiology and pathophysiology. In the past decade, many papers have been published that have changed our understanding of RS. RS is commonly classified into acute and chronic RS based on symptom duration. In acute RS, an inflammatory reaction initiated by a viral infection characterizes most uncomplicated, mild to moderate cases. Therefore, the first line of treatment for these cases are intranasal steroids and not antibiotics. In severe and complicated cases, antibiotics combined with topical steroids remain the treatment of choice. On the other hand, chronic RS is actually subdivided into two distinct entities (chronic rhinosinusitis with and without polyps), as growing evidence indicates that these entities have specific inflammatory pathways and cytokine profiles. The authors review recent data regarding the clinical presentations, cytokine profiles, tissue remodeling, and modalities of treatment for each form of RS. 
 Title: Actual Concepts in Rhinosinusitis: A Review of Clinical Presentations, Inflammatory Pathways, Cytokine Profiles, Remodeling, and Management
Output: False
Paragraph: To evaluate the aetiological agents and epidemiologic features of severe fever with thrombocytopenia syndrome (SFTS) in Hubei province, China, sera from patients were collected from January to December 2011. All cases occurred from April to December, and the epidemic peaked from May to August. The ages of patients ranged from 10 to 86 years (median = 55 years), and the incidence of SFTS increased with age. The female:male ratio of cases was 1.008:1, and 54.6% (77/141) and 1.4% (2/141) of the cases were confirmed by qPCR to be SFTSV and Hantavirus (HV) infection, respectively. No case of simultaneous infection with two or more pathogens was found. The research in this paper showed that some suspected SFTS cases are confused with HV infection due to similar symptoms. The analysis showed that the distribution of SFTSV has a marked regional aggregation in Hubei province. 
 Title: Pathogens and epidemiologic feature of severe fever with thrombocytopenia syndrome in Hubei province, China
Output: False
Paragraph: The outbreaks of emerging infectious diseases caused by pathogens such as SARS coronavirus, H5N1, H1N1, and recently H7N9 influenza viruses, have been associated with significant mortality and morbidity in humans. Neutralizing antibodies from individuals who have recovered from an infection confer therapeutic protection to others infected with the same pathogen. However, survivors may not always be available for providing plasma or for the cloning of monoclonal antibodies (mAbs). The genome and the immunoglobulin genes in rhesus macaques and humans are highly homologous; therefore, we investigated whether neutralizing mAbs that are highly homologous to those of humans (human-like) could be generated. Using the H5N1 influenza virus as a model, we first immunized rhesus macaques with recombinant adenoviruses carrying a synthetic gene encoding hemagglutinin (HA). Following screening an antibody phage display library derived from the B cells of immunized monkeys, we cloned selected macaque immunoglobulin heavy chain and light chain variable regions into the human IgG constant region, which generated human-macaque chimeric mAbs exhibiting over 97% homology to human antibodies. Selected mAbs demonstrated potent neutralizing activities against three clades (0, 1, 2) of the H5N1 influenza viruses. The in vivo protection experiments demonstrated that the mAbs effectively protected the mice even when administered up to 3 days after infection with H5N1 influenza virus. In particular, mAb 4E6 demonstrated sub-picomolar binding affinity to HA and superior in vivo protection efficacy without the loss of body weight and obvious lung damage. The analysis of the 4E6 escape mutants demonstrated that the 4E6 antibody bound to a conserved epitope region containing two amino acids on the globular head of HA. Our study demonstrated the generation of neutralizing mAbs for potential application in humans in urgent preparedness against outbreaks of new influenza infections or other virulent infectious diseases. 
 Title: Rapid Generation of Human-Like Neutralizing Monoclonal Antibodies in Urgent Preparedness for Influenza Pandemics and Virulent Infectious Diseases
Output: True
Paragraph: Objectives: To explore the epidemiological and clinical factors predictive of the case fatality rate (CFR) of Middle East respiratory syndrome-coronavirus (MERS-CoV) infection in an outbreak in Daejeon, the Republic of Korea. Methods: We reviewed the outbreak investigation reports and medical records of 1 index case and 25 additional MERS cases in hospitals A (14 cases) and B (11 cases), and conducted an in-depth interview with the index case. Results: The CFR in hospital B was higher than that in hospital A (63.6% vs. 28.6%, respectively). Higher MERS-CoV exposure conditions were also found in hospital B, including aggravated pneumonia in the index case and nebulizer use in a six-bed admission room. The host factors associated with high CFR were pre-existing pneumonia, smoking history, an incubation period of less than 5 days, leukocytosis, abnormal renal function at diagnosis, and respiratory symptoms such as sputum and dyspnea. Conclusions: The conditions surrounding MERS-CoV exposure and the underlying poor pulmonary function due to a smoking history or pre-existing pneumonia may explain the high CFR in hospital B. The clinical features described above may enable prediction of the prognosis of MERS cases. 
 Title: High fatality rates and associated factors in two hospital outbreaks of MERS in Daejeon, the Republic of Korea
Output: True
Paragraph: This chapter provides an overview of the global use of herpetofauna in traditional folk medicine and the implications for conservation. The results indicate that 331 species (284 reptiles and 47 amphibians) are used in traditional folk medicine around the world. Among the species recorded, 182 reptiles and 42 amphibians are listed in the IUCN Red List. Additionally, 93 reptiles are in some of the appendices of CITES. These numbers demonstrate the importance of understanding such medicinal uses in the context of reptile conservation as well as the need for considering sociocultural factors when establishing management plans directed toward the sustainable use of these reptiles. 
 Title: Herpetofauna Used in Traditional Folk Medicine: Conservation Implications
Output: True
Paragraph: word count: 91 Manuscript word count: 713 J o u r n a l P r e -p r o o f 2 Abstract The well-being of the health care workforce is the cornerstone of every well-functioning health system. As a result of the pandemic, medical healthcare providers are under an enormous amount of workload pressure along with increased total health expenditures. The overwhelming burden of COVID-19 illness could lead to caregiver burnout. Direct-to-consumer telemedicine can enable patients to connect with their healthcare provider at a distance. This virtual platform could be used by smartphones or webcam-enabled computers and allows physicians to effectively screen patients with early signs of COVID-19 before they reach to hospital. 
 Title: Journal Pre-proof COVID-19 and Telemedicine: Immediate action required for maintaining healthcare providers well-being COVID-19 and Telemedicine: Immediate action required for maintaining healthcare providers well-being
Output: True
Paragraph: Objective: To describe the clinical presentation and laboratory diagnosis of pregnant women with respiratory syncytial virus (RSV) infection. Methods: Pregnant women in their second and third trimester were enrolled during the course of routine prenatal care visits when they were asymptomatic within the preceding two weeks (healthy controls) or when they reported symptoms of acute respiratory illness (ARI) of 7 days of duration (cases). Clinical outcomes were assessed at enrollment and two weeks after. Re-enrollment was allowed. Nasalpharyngeal secretions were evaluated for respiratory pathogens by real-time reverse transcription polymerase chain reaction (PCR). Sera were tested for RSV-specific antibody responses by Western Blot, microneutralization assay, and palivizumab competitive antibody assay. Results: During the 2015-2016 respiratory virus season, 7 of 65 (11%) pregnant women with ARI at their initial enrollment and 8 of 77 (10%) pregnant women with ARI during the study period (initial or reenrollment) had PCR-confirmed RSV infection. Four (50%) PCR-confirmed RSV ARI cases reported symptoms of a lower respiratory tract illness (LRTI), one was hospitalized. Combining PCR and serology data, the RSV attack rate at initial enrollment was 12% (8 of 65), and 13% (10 of 77) based on ARI episodes. Among healthy controls, 28 of 88 (32%) had a Western Blot profile suggestive of a recent RSV infection either in the prior and/or current season. Conclusion: RSV had an attack rate of 10-13% among ambulatory pregnant women receiving routine prenatal care during the respiratory virus season. The serology results of healthy controls suggest a potentially higher attack rate. Future studies should be aware of the combined diagnostic strength of PCR and serology to identify RSV infection. As maternal RSV vaccine candidates are evaluated to protect young infants, additional priority should be placed on outcomes of pregnant women. 
 Title: Clinical characteristics and outcomes of respiratory syncytial virus infection in pregnant women
Output: False
Paragraph: Any discussion of quantitative abnormalities of lymphocytes and immunoglobulins is necessarily linked because the B-cell compartment is responsible for immunoglobulin production, and the T-cell compartment helps provide the stimulus. Nevertheless, clinicians are often consulted when a quantitative disorder of one or the other is recognized. Thus, although overlapping, the defects are presented separately. 
 Title: LYMPHOCYTOSIS, LYMPHOCYTOPENIA, HYPERGAMMAGLOBULINEMIA, AND HYPOGAMMAGLOBULINEMIA
Output: False
Paragraph: a summary of the evolution of infectiousness over time. When who-infects-whom is observed, the Nelson-Aalen estimator produces an unbiased estimate of the cumulative hazard function of the contact interval distribution. When who-infects-whom is not observed, we use an EM algorithm to average the Nelson-Aalen estimates from all possible combinations of who-infected-whom consistent with the observed data. This converges to a nonparametric maximum likelihood estimate of the cumulative hazard function that we call the marginal Nelson-Aalen estimate. We study the behavior of these methods in simulations and use them to analyze household surveillance data from the 2009 influenza A(H1N1) pandemic. 
 Title: Nonparametric survival analysis of infectious disease data Summary
Output: True
Paragraph: The spatial and spatio-temporal scan statistics proposed by Kulldorff have been applied to a number of geographical disease cluster detection problems. As the shape of the scanning window used in these methods is circular or elliptic, they cannot find irregularly shaped clusters, say clusters occurring along river valleys or in cases where disease transmission is linked to the road network. In this study, we propose a more flexible geometric structure to be used as a spatial or spatio-temporal scanning window. A particle swarm optimization (PSO) is used to optimize the scanning window to determine disease clusters. We evaluated the proposed method over a number of spatial and spatio-temporal datasets (Breast cancer mortality in Northeastern US 1988-1992 and different types of cancer in New Mexico 1982 -2007 . Experimental results demonstrate that the introduced approach surpasses the results produced by the circular and elliptic scan statistics in terms of efficiency, especially when dealing with irregularly shaped clusters. 
 Title: Regular paper A new PSO-optimized geometry of spatial and spatio-temporal scan statistics for disease outbreak detection
Output: True
Paragraph: Purpose: The field of HIV-1 vaccinology has evolved during the last 30 years from the first viral vector HIV gene insert constructs to vaccination regimens using a myriad of strategies. These strategies now include germline-targeting, lineagebased, and structure-guided immunogen design. This narrative review outlines the historical context of HIV vaccinology and subsequently highlights the scientific discoveries during the last 6 years that promise to propel the field forward. Methods: We conducted a search of 2 electronic databases, PubMed and EMBASE, for experimental studies that involved new HIV immunogen designs between 2013 and 2019. During the title and abstract reviews, publications were excluded if they were written in language other than English and/or were a letter to the editor, a commentary, or a conference-only presentation. We then used ClinicalTrials.gov to identify completed and ongoing clinical trials using these strategies. Findings: The HIV vaccinology field has undergone periods of significant growth during the last 3 decades. Findings elucidated in preclinical studies have revealed the importance of the interaction between the cellular and humoral immune system. As a result, several new rationally designed vaccine strategies have been developed and explored in the last 6 years, including native-like envelope trimers, nanoparticle, and mRNA vaccine design strategies among others. Several of these strategies have shown enough promise in animal models to progress toward first-inhuman Phase I clinical trials. Implications: Rapid developments in preclinical and early-phase clinical studies suggest that a tolerable and effective HIV vaccine may be on the horizon. (Clin Ther. xxxx;xxx:xxx)  
 Title: Innovations in HIV-1 Vaccine Design
Output: False
Paragraph: Expression of genes in plant chloroplasts provides an opportunity for enhanced production of target proteins. We report the introduction and expression of a fusion DPT protein containing immunoprotective exotoxin epitopes of Corynebacterium diphtheriae, Bordetella pertussis, and Clostridium tetani in tobacco chloroplasts. Using biolistic-mediated transformation, a plant-optimized synthetic DPT gene was successfully transferred to tobacco plastomes. Putative transplastomic T0 plants were identi-Wed by PCR, and Southern blot analysis conWrmed homoplasmy in T1 progeny. ELISA assays demonstrated that the DPT protein retained antigenicity of the three components of the fusion protein. The highest level of expression in these transplastomic plants reached 0.8% of total soluble protein. To assess whether the functional recombinant protein expressed in tobacco plants would induce speciWc antibodies in test animals, a mice feeding experiment was conducted. For mice orally immunized with freeze-dried transplastomic leaves, production of IgG and IgA antibodies speciWc to each toxin were detected in serum and mucosal tissues. 
 Title: Expression of a multi-epitope DPT fusion protein in transplastomic tobacco plants retains both antigenicity and immunogenicity of all three components of the functional oligomer
Output: True
Paragraph: Objectives: The rapid emergence of drug-resistant Shigella sonnei is a serious public health problem. This study aimed to characterise the antimicrobial resistance patterns, molecular subtypes, and integron types and resistance gene cassettes in S. sonnei from Jiangsu Province, China. Methods: In total, 340 S. sonnei were collected in 2002-2011 throughout Jiangsu Province. Antimicrobial susceptibility testing, pulsed-field gel electrophoresis (PFGE), PCR amplification of integrons, restriction fragment length polymorphism (RFLP) and DNA sequencing of cassette regions were performed. Results: Resistance rates to ampicillin (67.7%), nalidixic acid (75.2%), tetracycline (73.7%) and trimethoprim/sulfamethoxazole (68.7%) remained high. Strains from Centre and South Jiangsu showed higher resistance and multiresistance rates compared with the North. PFGE analysis indicated that largescale clonal transmission among different cities occurred several times during 10 years. Among all strains, 55.9% (190/340) harboured class 1 integrons, 80.3% (273/340) harboured class 2 integrons and 49.4% (168/340) harboured an atypical class 1 integron. Resistance rates to nine antimicrobials in the class 1 integron-positive group were significantly higher than in the negative group (P < 0.05). Seven different gene cassettes were detected in class 1 integrons. The most prevalent type was aacA4-cmlA1 (114/286). Class 2 integrons carried the gene cassette array dfrA1-sat1-aadA1, and the atypical class 1 integron carried bla OXA-30 -aadA1. Conclusions: The increasing antimicrobial resistance and significant clonal transmission of S. sonnei circulating in Jiangsu were closely related to the high prevalence of integrons and gene cassettes. Longterm cross-regional monitoring of antimicrobial resistance is urgently required for S. sonnei. 
 Title: A 10-year surveillance of antimicrobial susceptibility patterns in Shigella sonnei isolates circulating in Jiangsu Province, China
Output: False
Paragraph: Background: Although several therapeutic options have become available for patients with Cutaneous T-cell Lymphoma (CTCL), no therapy has been curative. Recent studies have demonstrated that CTCL cells overexpress the CC chemokine receptor 4 (CCR4). Methodology/Principal Findings: In this study, a xenograft model of CTCL was established and a recombinant adenoassociated viral serotype 8 (AAV8) vector expressing a humanized single-chain variable fragment (scFv)-Fc fusion (scFvFc or ''minibody'') of anti-CCR4 monoclonal antibody (mAb) h1567 was evaluated for curative treatment. Human CCR4 + tumorbearing mice treated once with intravenous infusion of AAV8 virions encoding the h1567 (AAV8-h1567) minibody showed anti-tumor activity in vivo and increased survival. The AAV8-h1567 minibody notably increased the number of tumorinfiltrating Ly-6G + FccRIIIa(CD16A) + murine neutrophils in the tumor xenografts over that of AAV8-control minibody treated mice. Furthermore, in CCR4 + tumor-bearing mice co-treated with AAV8-h1567 minibody and infused with human peripheral blood mononuclear cells (PBMCs), marked tumor infiltration of human CD16A + CD56 + NK cells was observed. The h1567 minibody also induced in vitro ADCC activity through both mouse neutrophils and human NK cells. Conclusions/Significance: Overall, our data demonstrate that the in vivo anti-tumor activity of h1567 minibody is mediated, at least in part, through CD16A + immune effector cell ADCC mechanisms. These data further demonstrate the utility of the AAV-minibody gene transfer system in the rapid evaluation of candidate anti-tumor mAbs and the potency of h1567 as a potential novel therapy for CTCL. 
 Title: Human Anti-CCR4 Minibody Gene Transfer for the Treatment of Cutaneous T-Cell Lymphoma
Output: True
Paragraph: Frog virus 3 (FV3) is the best characterized member of the family Iridoviridae. FV3 study has provided insights into the replication of other family members, and has served as a model of viral transcription, genome replication, and virus-mediated host-shutoff. Although the broad outlines of FV3 replication have been elucidated, the precise roles of most viral proteins remain unknown. Current studies using knock down (KD) mediated by antisense morpholino oligonucleotides (asMO) and small, interfering RNAs (siRNA), knock out (KO) following replacement of the targeted gene with a selectable marker by homologous recombination, ectopic viral gene expression, and recombinant viral proteins have enabled researchers to systematically ascertain replicativeand virulence-related gene functions. In addition, the application of molecular tools to ecological studies is providing novel ways for field biologists to identify potential pathogens, quantify infections, and trace the evolution of ecologically important viral species. In this review, we summarize current studies using not only FV3, but also other iridoviruses infecting ectotherms. As described below, general principles ascertained using FV3 served as a model for the family, and studies utilizing other ranaviruses and megalocytiviruses have confirmed and extended our understanding of iridovirus replication. Collectively, these and future efforts will elucidate molecular events in viral OPEN ACCESS Viruses 2011, 3 1960 replication, intrinsic and extrinsic factors that contribute to disease outbreaks, and the role of the host immune system in protection from disease. 
 Title: The Molecular Biology of Frog Virus 3 and other Iridoviruses Infecting Cold-Blooded Vertebrates
Output: True
Paragraph: During the replication cycle of Sindbis virus minus-strand synthesis stops normally at the time that plus-strand synthesis reaches a maximum rate. We have isolated and characterized revertants of ts24, a member of the A complementation group of Sindbis HR mutants, that we had demonstrated previously to have a temperature-sensitive defect in the regulation of minus-strand synthesis. These revertants of t&4 replicated efficiently at 40' but nevertheless retained the temperature sensitive defect in the regulation of minus-strand synthesis: they continued to synthesize minus strands late in the replication cycle at 40" but not at 30" and in the presence or absence of protein synthesis. Although failure to regulate the synthesis of minus strands resulted in continuous minus-strand synthesis and in the accumulation of minus strands, the rate of plus-strand synthesis was not increased concertedly. Minus strands synthesized after the rate of plus-strand synthesis had become constant were demonstrated to be utilized as templates for 26 S mRNA synthesis. Thus, the change from an increasing to a constant rate of plus-strand synthesis during the alphavirus replication cycle cannot be governed solely by the number of minus strands that accumulate in infected cells. We present a model for the preferential utilization of minus strands as a mechanism for the cessation of minus-strand synthesis that occurs normally during alphavirus replication. 
 Title: The Effect of Loss of Regulation of Minus-Strand RNA Synthesis on Sindbis Virus Replication
Output: True
Paragraph: Interleukin-11 (IL-11), a well-known anti-inflammatory factor, provides protection from intestinal epithelium damage caused by physical or chemical factors. However, little is known of the role of IL-11 during viral infections. In this study, IL-11 expression at mRNA and protein levels were found to be high in Vero cells and the jejunum of piglets during porcine epidemic diarrhea virus (PEDV) infection, while IL-11 expression was found to be positively correlated with the level of viral infection. Pretreatment with recombinant porcine IL-11 (pIL-11) was found to suppress PEDV replication in Vero E6 cells, while IL-11 knockdown promoted viral infection. Furthermore, pIL-11 was found to inhibit viral infection by preventing PEDV-mediated apoptosis of cells by activating the IL-11/STAT3 signaling pathway. Conversely, application of a STAT3 phosphorylation inhibitor significantly antagonized the anti-apoptosis function of pIL-11 and counteracted its inhibition of PEDV. Our data suggest that IL-11 is a newfound PEDV-inducible cytokine, and its production enhances the anti-apoptosis ability of epithelial cells against PEDV infection. The potential of IL-11 to be used as a novel therapeutic against devastating viral diarrhea in piglets deserves more attention and study. 
 Title: Antiviral activity of interleukin-11 as a response to porcine epidemic diarrhea virus infection
Output: True
Paragraph: In Infectious salmon anaemia virus (ISAV), deletions in the highly polymorphic region (HPR) in the near membrane domain of the haemagglutinin-esterase (HE) stalk, influence viral fusion. It is suspected that selected mutations in the associated Fusion (F) protein may also be important in regulating fusion activity. To better understand the underlying mechanisms involved in ISAV fusion, several mutated F proteins were generated from the Scottish Nevis and Norwegian SK779/06 HPR0. Co-transfection with constructs encoding HE and F were performed, fusion activity assessed by content mixing assay and the degree of proteolytic cleavage by western blot. Substitutions in Nevis F demonstrated that K276 was the most likely cleavage site in the protein. Furthermore, amino acid substitutions at three sites and two insertions, all slightly upstream of K276, increased fusion activity. Co-expression with HE harbouring a full-length HPR produced high fusion activities when trypsin and low pH were applied. In comparison, under normal culture conditions, groups containing a mutated HE with an HPR deletion were able to generate moderate fusion levels, while those with a full length HPR HE could not induce fusion. This suggested that HPR length may influence how the HE primes the F protein and promotes fusion activation by an ubiquitous host protease and/or facilitate subsequent post-cleavage refolding steps. Variations in fusion activity through accumulated mutations on surface glycoproteins have also been reported in other orthomyxoviruses and paramyxoviruses. This may in part contribute to the different virulence and tissue tropism reported for HPR0 and HPR deleted ISAV genotypes. 
 Title: Dual Mutation Events in the Haemagglutinin- Esterase and Fusion Protein from an Infectious Salmon Anaemia Virus HPR0 Genotype Promote Viral Fusion and Activation by an Ubiquitous Host Protease
Output: False
Paragraph: Long-read sequencing technologies are invaluable for determining complex RNA transcript architectures but are error-prone. Numerous "hybrid correction" algorithms have been developed for genomic data that correct long reads by exploiting the accuracy and depth of short reads sequenced from the same sample. These algorithms are not suited for correcting more complex transcriptome sequencing data. We have created a novel algorithm called TALC (Transcription Aware Long Read Correction) which models changes in RNA expression and isoform representation in a weighted De-Bruijn graph to correct long reads from transcriptome studies. We show that transcription aware correction by TALC improves the accuracy of the whole spectrum of downstream RNA-seq applications and is thus necessary for transcriptome analyses that use long read technology. 
 Title: TALC: Transcription Aware Long Read Correction
Output: False
Paragraph: Data used for modelling the household transmission of infectious diseases, such as influenza, have inherent multilevel structures and correlated property, which make the widely used conventional infectious disease transmission models (including the Greenwood model and the Reed-Frost model) not directly applicable within the context of a household (due to the crowded domestic condition or socioeconomic status of the household). Thus, at the household level, the effects resulting from individual-level factors, such as vaccination, may be confounded or modified in some way. We proposed the Bayesian hierarchical randomeffects (random intercepts and random slopes) model under the context of generalised linear model to capture heterogeneity and variation on the individual, generation, and household levels. It was applied to empirical surveillance data on the influenza epidemic in Taiwan. The parameters of interest were estimated by using the Markov chain Monte Carlo method in conjunction with the Bayesian directed acyclic graphical models. Comparisons between models were made using the deviance information criterion. Based on the result of the random-slope Bayesian hierarchical method under the context of the Reed-Frost transmission model, the regression coefficient regarding the protective effect of vaccination varied statistically significantly from household to household. The result of such a heterogeneity was robust to the use of different prior distributions (including non-informative, sceptical, and enthusiastic ones). By integrating out the uncertainty of the parameters of the posterior distribution, the predictive distribution was computed to forecast the number of influenza cases allowing for random-household effect. 
 Title: Analysis of household data on influenza epidemic with Bayesian hierarchical model
Output: True
Paragraph: Surveillance European bat lyssavirus Rabies Zoonoses Conservation A B S T R A C T Worldwide, there are more than 1100 species of the Order Chiroptera, 45 of which are present in Europe, and 16 in the UK. Bats are reservoirs of, or can be infected by, several viral diseases, including rabies virus strains (in the Lyssavirus genus). Within this genus are bat variants that have been recorded in Europe; European bat lyssavirus 1 (EBLV-1), European bat lyssavirus 2 (EBLV-2) and, four currently unclassified isolates. Since 1977, 783 cases of EBLVs (by isolation of viral RNA) have been recorded in Europe. EBLV-1 or EBLV-2 has been identified in 12 bat species, with over 95% of EBLV-1 infections identified in Eptesicus serotinus. EBLV-2 is associated with Myotis species (Myotis daubentonii and Myotis dasycneme). A programme of passive surveillance in the United Kingdom between 1987 and 2004 tested 4871 bats for lyssaviruses. Of these, four M. daubentonii (3.57% of submitted M. daubentonii) were positive for EBLV-2. Potential bias in the passive surveillance includes possible overrepresentation of synanthropic species and regional biases caused by varying bat submission numbers from different parts of the UK. In 2003, active surveillance in the UK began, and has detected an antibody prevalence level of 1-5% of EBLV-2 in M. daubentonii (n = 350), and one bat with antibodies to EBLV-1 in E. serotinus (n = 52). No cases of live lyssavirus infection or lyssavirus viral RNA have been detected through active surveillance. Further research and monitoring regarding prevalence, transmission, pathogenesis and immunity is required to ensure that integrated bat conservation continues throughout Europe, whilst enabling informed policy decision regarding both human and wildlife health issues. 
 Title: European bat lyssaviruses: Distribution, prevalence and implications for conservation
Output: True
Paragraph: medRxiv preprint [Abstract]Objective Coronavirus disease 2019 (COVID-19) has become pandemic in the world. The need for IgG-IgM combined antibody test is booming, but data on diagnostic indexes evaluation was inadequate. The aim of this study was to evaluate diagnostic indexes of a rapid IgG-IgM combined antibody test for SARS-CoV-2. Methods A total of 179 patients were enrolled. Serum were collected for IgG-IgM combined antibody test and corresponding nasal and pharyngeal swab specimens were collected for SARS-CoV-2 RT-PCR. According to SARS-CoV-2 RT-PCR results, patients under study were categorized as PCR positive group in 90 patients and PCR negative group in 89 patients. Results 1. Of the 90 PCR positive samples, 77 were tested positive by SARS-CoV-2 IgG-IgM test kit, yielding a sensitivity of 85.6%. Meanwhile, of the 89 PCR negative sample, 8 samples were detected positive, resulting in a specificity of 91%. Positive predictive value, negative predictive value and accuracy of this test kit was 95.1%, 82.7%, and 88.3%, respectively. Kappa efficiency between IgG/IgM test kit and RT-PCR were 0.75. 2. Accuracy in mild/common and severe/critical subgroup were 73.9% and 97.7%, respectively. Accuracy in clinical confirmed, suspected cases and other disease subgroups were 70%, 60%, and 100%, respectively. 3. Patients were further divided into '0 -7', '8 -15' and '>= 16' groups according to the time from illness onset to sample collection. Sensitivity, specificity and accuracy in these three groups were 18.8%, 77.8% and 40%; 100%, 50% and 87.5%; 100%, 64.3%, and 93.9, respectively. Conclusion The sensitivity and specificity of this ease-of-use IgG/IgM combined test kit were adequate, plus short turnaround time, no specific requirements for additional equipment or skilled technicians, all of these collectively contributed to its competence for mass testing. At the current stage, it cannot take the place of SARA-CoV-2 nucleic acid RT-PCR, but can be served as a complementary option for RT-PCR. The combination of RT-PCR and IgG-IgM combined test kit could provide further insight into SARS-CoV-2 infection diagnosis. 
 Title: Diagnostic Indexes of a Rapid IgG/IgM Combined Antibody Test for SARS-CoV-2
Output: True
Paragraph: Clinical and public health laboratories have experienced unprecedented challenges in the form of demands to comply with revised regulations and economic pressures to be more efficient while preparing to respond to everything from pandemic influenza to bioterrorism. These forces have been an impetus for laboratorians to communicate, cooperate, and collaborate as never before and to seek the common ground where knowledge and resources can be shared to weather the profound economic and political forces at work today. The appearance of newly emerging and reemergent infections caused by agents of foodborne illness, anthrax, smallpox, plague, influenza, and other diseases has fostered cooperative network enterprises between clinical and public health laboratories, allowing the early detection of outbreaks of common and unusual pathogens and the measurement of the effectiveness of public health measures. 
 Title: Public Health and Clinical Laboratories: Partners in the Age of Emerging Infections
Output: True
Paragraph: Humans are colonized after birth by microbial organisms that form a heterogeneous community, collectively termed microbiota. The genomic pool of this macro-community is named microbiome. The gut microbiota is essential for the complete development of the immune system, representing a binary network in which the microbiota interact with the host providing important immune and physiologic function and conversely the bacteria protect themselves from host immune defense. Alterations in the balance of the gut microbiome due to a combination of environmental and genetic factors can now be associated with detrimental or protective effects in experimental autoimmune diseases. These gut microbiome alterations can unbalance the gastrointestinal immune responses and influence distal effector sites leading to CNS disease including both demyelination and affective disorders. The current range of risk factors for MS includes genetic makeup and environmental elements. Of interest to this review is the consistency between this range of MS risk factors and the gut microbiome. We postulate that the gut microbiome serves as the niche where different MS risk factors merge, thereby influencing the disease process. (J. Ochoa-Repáraz). FEBS Letters 588 (2014) 4214-4222 j o u r n a l h o m e p a g e : w w w . F E B S L e t t e r s . o r g 2. Environmental, genetics and microbial risk factors associated with CNS demyelinating disease Environmental, genetic, immunological and infectious diseases have been associated with MS [2]. The genetic background is thought to be a critical epidemiologic risk factor. As reviewed by Compton and colleagues, the familial recurrence rate in MS is 20% [7] . Monozygotic twins, sharing the 100% of the genetic information, have an MS lifetime risk of approximately 25-30%, siblings with two affected parents approximately a 20%, whereas dizygotic twins have a 5% lifetime risk, frequencies that suggest that the genetic background could interact with other risk factors. Alterations in immuno-regulatory or structural genes might increase the susceptibility to MS. Differences in the human leukocyte antigen (HLA) system-genes in the chromosome 6 that serve as the major histocompatibility complex (MHC) in humans-haplotypes DRBl*1501 and DQ6 have been suggested as genetic risk factors [8] . Recent genome-wide association studies (GWAS) reveal an evident effect of these genetic risk factors, with particular importance of HLA class II region, but also class I [9,10]. Interestingly, the genetic factors associated with MS are involved in immunological processes [11] , providing strong theoretical support to the autoimmune nature of MS, and moreover, provides the potential framework that environmental factors may be intimately involved in the modulation and/or perhaps even the trigger for disease susceptibility. 
 Title: Gut microbiome and the risk factors in central nervous system autoimmunity
Output: False
Paragraph: Pneumonia is a leading killer of children younger than 5 years despite high vaccination coverage, improved nutrition, and widespread implementation of the Integrated Management of Childhood Illnesses algorithm. Assessing the effect of interventions on childhood pneumonia is challenging because the choice of case definition and surveillance approach can affect the identification of pneumonia substantially. In anticipation of an intervention trial aimed to reduce childhood pneumonia by lowering household air pollution, we created a working group to provide recommendations regarding study design and implementation. We suggest to, first, select a standard case definition that combines acute (≤14 days) respiratory symptoms and signs and general danger signs with ancillary tests (such as chest imaging and pulse oximetry) to improve pneumonia identification; second, to prioritise active hospital-based pneumonia surveillance over passive case finding or home-based surveillance to reduce the risk of non-differential misclassification of pneumonia and, as a result, a reduced effect size in a randomised trial; and, lastly, to consider longitudinal follow-up of children younger than 1 year, as this age group has the highest incidence of severe pneumonia. 
 Title: Review Challenges in the diagnosis of paediatric pneumonia in intervention field trials: recommendations from a pneumonia field trial working group
Output: False
Paragraph: In three successive experiments, the immune functions of pigs persistently infected with the Ž . porcine reproductive and respiratory syndrome virus PRRSV have been evaluated. Non-specific Ž . immune responses were analyzed over a period of 12 weeks post-infection PI . In addition, the capacity of PRRSV-infected pigs to develop an efficient immune response against pseudorabies Ž . virus PRV glycoproteins and to resist to a subsequent virulent challenge was investigated. Our results demonstrate that PRRSV produced minor effects on the immune system of pigs. The skin Ž . delayed type hypersensitivity DTH in response to phytohemagglutinine injection was slightly diminished one week after challenge, but was restored thereafter. However, three weeks after the infection, the total white blood cell count, and the number of CD2 q , CD8 q and IgM q cells were enhanced. The increase in numbers of CD8 q cells persisted for three consecutive weeks. Serum immunoglobulins in infected pigs also increased by week 3 PI and up to 8 weeks PI. These results show that PRRSV may have stimulating effects on the pig immune system during the phase of 0165-2427r98r$19.00 q 1998 Elsevier Science B.V. All rights reserved. Ž . PII S 0 1 6 5 -2 4 2 7 9 7 0 0 1 3 4 -7 ( ) E. Albina et al.r Veterinary Immunology and Immunopathology 61 1998 49-66 50 long-lasting infection. After immunization with PRV glycoproteins, the production of anti-PRV antibodies and skin DTH response against PRV glycoproteins were not affected. On the contrary, following a virulent PRV challenge, PRRSV-infected pigs developed a better secondary antibody response and their resistance to the infection was as effective as in control pigs. Taken together, our data do not support a systemic immunosuppressive effect of PRRSV, during the persistent phase of infection. Other mechanisms may therefore apply to explain the emergence of secondary infections in endemically infected herds. q 1998 Elsevier Science B.V. 
 Title: Immune responses in pigs infected with porcine reproductive and respiratory syndrome virus ž / PRRSV
Output: False
Paragraph: Infectious bronchitis is considered to be one of the most devastating diseases in poultry. Control of its spread is typically attempted through biosecurity measures and extensive vaccination. However, the remarkable genetic and antigenic variability of the virus, which originate from both mutations and recombination events, represents an unsolved challenge for this disease. The present study reports on the emergence and spread of recombinant clusters detected in Italy and Spain between 2012 and 2014. A total of 36 Spanish and Italian infectious bronchitis virus (IBV) field strains were investigated and genetically characterized using phylogenetic, molecular, recombination and selection pressure analyses of the complete S1 gene. Based on the partial S1 sequencing, 27 IBV strains originating from Spain and nine from Italy were initially classified as being closely related to the Guandong/Xindadi (XDN) genotype. Phylogenetic analysis of the complete S1 gene revealed that the XDN strains formed a homogeneous clade with the Spanish IBV isolates within the QX genotype, whereas there was higher variability within the Italian strains. Recombination analysis determined that these strains belonged to four groups, which originated from independent recombination events between the QX and 793B IBV genotypes. Our data support the hypothesis of two different scenarios: firstly, in Spain, the large and homogeneous clade probably originated from a single offspring of the recombinant founder, which became dominant and spread throughout the country. Secondly, the nine Italian recombinants, which are characterized by three different recombination patterns, probably represent less fitted strains, because they were less viable with respect to their recombinant parents. ARTICLE HISTORY 
 Title: A novel variant of the infectious bronchitis virus resulting from recombination events in Italy and Spain
Output: True
Paragraph: Fowl adenovirus serotype 4 (FAdV-4) is the causative agent of hydropericardium syndrome. To clarify the effects of FAdV-4 on immune organs in birds, we conducted a detailed examination of dynamic morphology and damage mechanisms in chickens randomly divided into 4 groups (FAdV-4, vaccination, FAdV-4 plus vaccination, and control). FAdV-4 caused the depletion of lymphocytes and subsequent growth impairment in the thymus and bursa. Chickens infected with FAdV-4 and subjected to vaccination experienced greater inhibition of antibody responses to inactivated vaccines against Newcastle disease and avian influenza virus subtype H9 than uninfected and vaccinated chickens. The mechanisms underlying adenovirus-mediated lymphoid organ damage were further investigated via transferase-mediated dUTP nickend labeling and apoptotic genes transcription analyses. Notably, lymphocytes apoptosis in lymphoid organs and expression of specific gene transcripts was significantly upregulated after infection (P < 0.05). Furthermore, increased expression of interleukin (IL)-6, IL-8, and tumor necrosis factor (TNF)-α mRNA was observed (P < 0.05), compared to the control group. Our collective findings suggested that FAdV-4 caused structural and functional damage of immune organs via apoptosis along with induction of a severe inflammatory response. 
 Title: Immunosuppressive potential of fowl adenovirus serotype 4
Output: False
Paragraph: Infectious diseases that are caused by pathogenic microorganisms can spread fast and far, from one person to another, directly or indirectly. Prompt quarantining of the infected from the rest, coupled with contact tracing, has been an effective measure to encounter outbreaks. However, urban life and international travel make containment difficult. Furthermore, the length of incubation periods of some contagious diseases like SARS enable infected passengers to elude health screenings before first symptoms appear and thus to carry the disease further. Detecting and visualizing contact-tracing networks, and immediately identifying the routes of infection, are thus important. We apply information visualization and hidden cluster detection for finding cliques of potentially infected people during incubation. Preemptive control and early quarantine are hence possible by our method. Our prototype Infectious Disease Detection and Quarantine Management System (IDDQMS), which can identify and trace clusters of infection by mining patients' history, is introduced in this paper. 
 Title: Hidden Cluster Detection for Infectious Disease Control and Quarantine Management
Output: False
Paragraph: A Resequencing Pathogen Microarray (RPM) is a single, highly multiplexed assay for detecting and differentiating similarly related pathogens by using closely overlapping probe sets to determine a target organism's nucleotide sequence. In this study, a new RPM (RPM-IVDC1) that consisted of 224-bp detector tiles corresponding to 9 influenza A subtypes, 11 rhinoviruses, 28 enteroviruses and 38 other respiratory viruses was developed and optimized to provide individual and simultaneous detection sensitivities ranging from 15 to 750 genomic copies for 16 common respiratory pathogens. A total of 110 consecutive patients with community-acquired pneumonia (CAP) admitted to 5 district general hospitals in Beijing during a 1-year period were assessed using the new assay. Among the children (under age 5) and adult patients (above age 18), respiratory syncytial virus (RSV) and rhinovirus (RV) were the most common etiological agents, respectively, which is consistent with reference assays. Atypical pathogens that may cause CAP-like illness, including rubella virus, measles virus, influenza type C virus, human herpesvirus (HHV) were also detected. The results show the capability of RPM-IVDC1 for the accurate detection and identification of multiple virus types, which may be of significant use in epidemic surveillance and outbreak investigations of atypical pathogens. Citation: 
 Title: Acquired Pneumonia
Output: True
Paragraph: Viruses hijack host cell functions and optimize them for viral replication causing a severe threat to human health. However, viruses are also tools to understand cell biology and they may be effective reagents in nano-medicine. Studies from the molecular to cellular levels are aimed at understanding the details of viral life cycles and the underlying virus-host interactions. Recent developments in electron microscopy tomography allow viral and cellular events to be observed in fine structural detail in three-dimension. By combining high-resolution structures of individual proteins and macro-complexes obtained by crystallography and electron cryo-microscopy and image reconstruction with reconstructions performed on sub-tomographic volumes, electron tomography has advanced the structural and mechanistic understanding of virus infections both in vitro and in host cells. 
 Title: Viral Life Cycles Captured in Three-Dimensions with Electron Microscopy Tomography
Output: False
Paragraph: Cytokine storm during viral infection is a prospective predictor of morbidity and mortality, yet the cellular sources remain undefined. Here, using genetic and chemical tools to probe functions of the S1P 1 receptor, we elucidate cellular and signaling mechanisms that are important in initiating cytokine storm. Whereas S1P 1 receptor is expressed on endothelial cells and lymphocytes within lung tissue, S1P 1 agonism suppresses cytokines and innate immune cell recruitment in wild-type and lymphocyte-deficient mice, identifying endothelial cells as central regulators of cytokine storm. Furthermore, our data reveal immune cell infiltration and cytokine production as distinct events that are both orchestrated by endothelial cells. Moreover, we demonstrate that suppression of early innate immune responses through S1P 1 signaling results in reduced mortality during infection with a human pathogenic strain of influenza virus. Modulation of endothelium with a specific agonist suggests that diseases in which amplification of cytokine storm is a significant pathological component could be chemically tractable. 
 Title: Endothelial Cells Are Central Orchestrators of Cytokine Amplification during Influenza Virus Infection
Output: True