niryuu/sni-each-converted huggingface dataset:
Paragraph: The seasonal outbreaks of influenza infection cause globally respiratory illness, or even death in all age groups. Given early-warning signals preceding the influenza outbreak, timely intervention such as vaccination and isolation management effectively decrease the morbidity. However, it is usually a difficult task to achieve the real-time prediction of influenza outbreak due to its complexity intertwining both biological systems and social systems. By exploring rich dynamical and high-dimensional information, our dynamic network marker/biomarker (DNM/DNB) method opens a new way to identify the tipping point prior to the catastrophic transition into an influenza pandemics. In order to detect the early-warning signals before the influenza outbreak by applying DNM method, the historical information of clinic hospitalization caused by influenza infection between years 2009 and 2016 were extracted and assembled from public records of Tokyo and Hokkaido, Japan. The early-warning signal, with an average of 4week window lead prior to each seasonal outbreak of influenza, was provided by DNM-based on the hospitalization records, providing an opportunity to apply proactive strategies to prevent or delay the onset of influenza outbreak. Moreover, the study on the dynamical changes of hospitalization in local district networks unveils the influenza transmission dynamics or landscape in network level. city network, critical transition, dynamic network biomarker (DNB), dynamic network marker (DNM), early-warning signal, influenza outbreak 
 Title: Detecting early-warning signals of influenza outbreak based on dynamic network marker
Output: True
Paragraph: Introduction: The aim of the study was to demonstrate interleukin-18 (IL-18) expression in keratinocytes from psoriatic lesions in comparison to keratinocytes from uninvolved skin and to study the change of expression after therapeutic interventions. Material and methods: This study included 16 patients of different clinical subtypes of psoriasis. Interleukin-18 gene expression analysis was performed using real time quantitative PCR. Three biopsies were obtained from each patient. Two were taken from the lesional psoriatic skin and from uninvolved skin before starting treatment. A third lesional skin biopsy was taken at the end of 2 months of treatment. The treatment was in the form of topical steroids or oral systemic methotrexate. Results: Of all 16 studied patients, significantly increased IL-18 expression was noted in keratinocytes from psoriatic lesions before and after treatment when compared to keratinocytes from uninvolved skin (p = 0.001 and p = 0.002 respectively). The IL-18 expression in the skin lesions after treatment was significantly lower than lesional skin before treatment (p = 0.023). In psoriatic skin lesions of all studied patients IL-18 expression was significantly correlated with disease duration (r = 0.40 and p = 0.01) and clinical severity of psoriasis (r = 0.72 and p = 0.001). Conclusions: Increased IL-18 expression in keratinocytes from psoriatic lesions of our patients and its correlation with disease duration and severity supported the concept of psoriasis as a T cell mediated autoimmune disease. This could establish therapeutic and preventive approaches for psoriasis that ultimately lead to improved outcomes for patients. 
 Title: Interleukin-18 expression and the response to treatment in patients with psoriasis
Output: False
Paragraph: The genetic determinism of viral traits can generally be dissected using either forward or reverse genetics because the clonal reproduction of viruses does not require the use of approaches based on laboratory crosses. Nevertheless, we hypothesized that recombinant viruses could be analyzed as sexually reproducing organisms, using either a quantitative trait loci (QTL) approach or a locus-by-locus fixation index (F ST ). Locus-by-locus F ST analysis, and four different regressions and interval mapping algorithms of QTL analysis were applied to a phenotypic and genotypic dataset previously obtained from 47 artificial recombinant genomes generated between two begomovirus species. Both approaches assigned the determinant of within-host accumulation-previously identified using standard virology approaches-to a region including the 5' end of the replication-associated protein (Rep) gene and the upstream intergenic region. This study provides a proof of principle that QTL and population genetics tools can be extended to characterize the genetic determinants of viral traits. 
 Title: Mapping genetic determinants of viral traits with F ST and quantitative trait locus (QTL) approaches
Output: False
Paragraph: This article discusses several conditions that are distinct entities but share the common thread of abnormal lung parenchyma that regularly leads to patient referral for surgical consideration. The article summarizes key aspects of the 3 conditions and provides advice and recommendations for evaluation and treatment based on published reports in the medical literature. A pneumothorax is defined as air in the pleural space, between the parietal and visceral pleura. This condition may be caused by trauma or underlying lung disease, but sometimes happens spontaneously without obvious cause. When a pneumothorax develops, there is loss of the negative intrapleural pressure that is needed for lung inflation, and the lung on the affected side collapses and cannot expand properly. This collapse leads to a ventilation-perfusion mismatch because there is continued perfusion of a poorly ventilated lung. Arterial hypoxemia can occur with 50% collapse of the lung. If there is a continued air leak with increasing positive intrapleural pressure, this can lead to a tension pneumothorax and can lead to compromise of venous return to the heart, decreasing cardiac output, and causing hemodynamic collapse. Pneumothorax can be spontaneous, traumatic, or iatrogenic. Primary spontaneous pneumothorax typically occurs in young, healthy, tall, thin, male smokers and is 
 Title: Pneumothorax, Bullous Disease, and Emphysema
Output: True
Paragraph: A nucleotide variability in the sequence of the gene encoding for the transmembrane protein M of canine coronavirus (CCV) is described. A total of 177 faecal samples from pups with enteritis were analysed by a PCR and n-PCR specific for CCV. Four samples, collected from a dog presenting a long-duration shedding of CCV, and a sample from another diarrhoeic dog, were found positive by PCR but negative by n-PCR. Sequence analysis of the samples revealed silent nucleotide substitutions in the binding site of the internal primer used for the n-PCR. Moreover, the nucleotide substitutions occurring over the whole fragment of the five samples analysed were similar. 
 Title: Variation of the sequence in the gene encoding for transmembrane protein M of canine coronavirus (CCV)
Output: True
Paragraph: One Health approaches have tended to focus on closer collaboration among veterinarians and medical professionals, but remain unclear about how ecological approaches could be applied or how they might benefit public health and disease control. In this chapter, we review ecological concepts, and discuss their relevance to health, with an emphasis on emerging infectious diseases (EIDs). Despite the fact that most EIDs originate in wildlife, few studies account for the population, community, or ecosystem ecology of the host, reservoir, or vector. The dimensions of ecological approaches to public health that we propose in this chapter are, in essence, networks of population dynamics, community structure, and ecosystem matrices incorporating concepts of complexity, resilience, and biogeochemical processes. 
 Title: The Human Environment Interface: Applying Ecosystem Concepts to Health
Output: False
Paragraph: Coronavirus disease 2019 (COVID-2019) has been recognized as a global threat, and several studies are being conducted using various mathematical models to predict the probable evolution of this epidemic. These mathematical models based on various factors and analyses are subject to potential bias. Here, we propose a simple econometric model that could be useful to predict the spread of COVID-2019. We performed Auto Regressive Integrated Moving Average (ARIMA) model prediction on the Johns Hopkins epidemiological data to predict the epidemiological trend of the prevalence and incidence of COVID-2019. For further comparison or for future perspective, case definition and data collection have to be maintained in real time. 
 Title: Application of the ARIMA model on the COVID- 2019 epidemic dataset
Output: True
Paragraph: Two species of membrane-associated glycoproteins have been identified in the coronavirus virion. They are readily distinguished on the basis of size, radiolabeling characteristics, and location in relation to the lipid bilayer. The larger glycoprotein is highly labeled by both radiolabeled fucose and glucosamine. This species is found in two forms, GP180 and GP90, with apparent molecular weights of 180,000 and 90,000. GP180 can be converted to GP90 in vitro by treatment of virions with trypsin. Analysis of tryptic digests of GP90 and GPl80 give identical peptide patterns. Based on pronase and bromelain sensitiyities, GP180/90 is the only protein which is located entirely external to the viral envelope. It appears to comprise the characteristic long, petal-shaped peplomers of the virion. The smaller glycoprotein, GP23, has an apparent molecular weight of 23,000 and is labeled by radiolabeled glucosamine but not by fucose. The level of glucosamine-labeling of GP23 is about l/10 that of GP180/90. GP23 appears to possess two distinct domains: a smaller, carbohydrate containing region which is found outside the viral envelope, and a larger portion, highly labeled by methionine, which is integrally associated with the viral membrane. A new nomenclature is proposed for the three major coronavirus structural proteins. The two envelope glycoproteins, GP23 and GP180/90 are designated El and E2, respectively; the inner core protein, ~~50, is designated N. 
 Title: Characterization of a Coronavirus' II. Glycoproteins of the Viral Envelope: Tryptic Peptide Analysis
Output: True
Paragraph: Paneth cells are secretory epithelial cells of the innate immune system of the intestine of several mammals, including alpacas. Little is known about the latter; thus, in the present study we described the morphology and histochemical characteristics of Paneth cells in healthy fetuses, and young and adult alpacas. For this purpose, samples of duodenum, jejunum and ileum were taken from 6 fetuses at different days of pregnancy (between days 221-330), 66 offsprings (between 0 and 45-days-old) and 5 adult alpacas (>2-years-old). Samples were fixed in 10% buffered formalin and processed for histological and morphometrical analysis using HE and Masson Trichomicís technique. Immunohistochemistry was used to identify Paneth cells using anti-lysozyme antibody. In addition, the lectinhistochemichal bindingpattern of Paneth cellís granules was evaluated. Lyzozyme was immunohistochemically detected in the granules of Paneth cells from day 283 of pregnancy in all the small intestinal sections of the studied fetuses. In newborn alpacas Paneth cells were initially found in the duodenum, but the following days (days 18-21 after birth) they were also found in the ileum. Their size gradually increased after birth, but then no significant differences were found. In adult alpacas the number was lower than offsprings. We suggest that Paneth cells early differentiate in the small intestine of alpacas, and the increase in their number during the first two weeks of life strongly support their possible involvement in the intestinal defensive functions against the enteric diseases that occur during the lactancy stage. 
 Title: Characterization of paneth cells in alpacas (Vicugna pacos, Mammalia, Camelidae)
Output: True
Paragraph: 16S rRNA gene is one of the preferred targets for resolving species phylogenesis issues in microbiological-related contexts. However, the identification of single-nucleotide variations capable of distinguishing a sequence among a set of homologous ones can be problematic. Here we present ORMA (Oligonucleotide Retrieving for Molecular Applications), a set of scripts for discriminating positions search and for performing the selection of high-quality oligonucleotide probes to be used in molecular applications. Two assays based on Ligase Detection Reaction (LDR) are presented. First, a new set of probe pairs on cyanobacteria 16S rRNA sequences of 18 different species was compared to that of a previous study. Then, a set of LDR probe pairs for the discrimination of 13 pathogens contaminating bovine milk was evaluated. The software determined more than 100 candidate probe pairs per dataset, from more than 300 16S rRNA sequences, in less than 5 min. Results demonstrated how ORMA improved the performance of the LDR assay on cyanobacteria, correctly identifying 12 out of 14 samples, and allowed the perfect discrimination among the 13 milk pathogenic-related species. ORMA represents a significant improvement from other contexts where enzyme-based techniques have been employed on already known mutations of a single base or on entire subsequences. 
 Title: ORMA: a tool for identification of species-specific variations in 16S rRNA gene and oligonucleotides design
Output: False
Paragraph: SARS coronavirus (SARS-CoV) develops an antagonistic mechanism by which to evade the antiviral activities of interferon (IFN). Previous studies suggested that SARS-CoV papain-like protease (PLpro) inhibits activation of the IRF3 pathway, which would normally elicit a robust IFN response, but the mechanism(s) used by SARS PLpro to inhibit activation of the IRF3 pathway is not fully known. In this study, we uncovered a novel mechanism that may explain how SARS PLpro efficiently inhibits activation of the IRF3 pathway. We found that expression of the membrane-anchored PLpro domain (PLpro-TM) from SARS-CoV inhibits STING/ TBK1/IKKε-mediated activation of type I IFNs and disrupts the phosphorylation and dimerization of IRF3, which are activated by STING and TBK1. Meanwhile, we showed that PLpro-TM physically interacts with TRAF3, TBK1, IKKε, STING, and IRF3, the key components that assemble the STING-TRAF3-TBK1 complex for activation of IFN expression. However, the interaction between the components in STING-TRAF3-TBK1 complex is disrupted by PLpro-TM. Furthermore, SARS PLpro-TM reduces the levels of ubiquitinated forms of RIG-I, STING, TRAF3, TBK1, and IRF3 in the STING-TRAF3-TBK1 complex. These results collectively point to a new mechanism used by SARS-CoV through which PLpro negatively regulates IRF3 activation by interaction with STING-TRAF3-TBK1 complex, yielding a SARS-CoV countermeasure against host innate immunity. 
 Title: SARS coronavirus papain-like protease inhibits the type I interferon signaling pathway through interaction with the STING-TRAF3- TBK1 complex
Output: False
Paragraph: Background: Rapid and accurate laboratory diagnoses of viral infections are crucial for the management and treatment of patients with viral infections. Conventional methods for virus detection are labourious, time consuming, and only a single virus can be analysed in one assay. Objectives: The objective of this study was to develop a novel real-time PCR method for multiple virus detection by melting curve analysis using Taqman probes in a single reaction. Study design: As a model, six respiratory viruses were detected in one tube using three fluorophores. The specificity was assessed by cross-reaction tests with other common respiratory pathogens. The analytical sensitivity was assessed by testing the limit of detection of the assay using artificial plasmids as the positive template. The clinical evaluation of the established assay was evaluated for the detection of respiratory viruses in clinical samples, and the results were compared with direct fluorescent antibody testing (DFA). Results: The six respiratory viruses were clearly distinguished by their respective melting temperature values in the corresponding fluorescence detection channels. No cross reactions were observed by cross reaction tests. The detection limits of this assay were 2 to 2 × 10 3 copies per reaction for each virus. The clinical evaluation of this assay was demonstrated by analysing 352 clinical samples, and 67(19.0%) samples were positive for at least one virus. The accordance rate between the established PCR and DFA testing was high, and ranged from 94.57% to 100%. Conclusions: Taqman probe-based melting curve analysis is well suited for detection of multiple viruses in clinical and research laboratories because of its high throughput, reliability, and cost savings. 
 Title: A novel multiplex PCR for virus detection by melting curve analysis
Output: False
Paragraph: In this study, infrared thermography (IRT) was assessed as a means of detecting foot-and-mouth disease virus (FMDV)-infected cattle before and after the development of clinical signs. Preliminary IRT imaging demonstrated that foot temperatures increased in FMDVinfected animals. The maximum foot temperatures of healthy (n = 53), directly inoculated (DI) (n = 12), contact (CT) (n = 6), and vaccine trial (VT) (n = 21) cattle were measured over the course of FMD infection. A cut-off value was established at 34.4°C (sensitivity = 61.1%, specificity = 87.7%) with the aim of detecting FMDV-infected animals both before and after clinical signs were observed. Seven of 12 (58%) DI and 3/6 (50%) CT animals showed maximum foot temperatures exceeding the 34.4°C cut-off before the development of foot vesicles. In contrast, only 5/21 (24%) VT animals displayed pre-clinical foot temperatures above this cut-off possibly indicating partial vaccine protection of this group. These results show IRT as a promising screening technology to quickly identify potentially infected animals for confirmatory diagnostic testing during FMD outbreaks. Further evaluation of this technology is needed to determine the value of IRT in detecting animals with mild clinical signs or sub-clinical infections. Published by Elsevier Ltd. 
 Title: Detection of foot-and-mouth disease virus infected cattle using infrared thermography
Output: True
Paragraph: Human coronavirus NL63 (HCoV-NL63) is a global respiratory tract pathogen; however, the epidemiology of this virus in subtropical area is not well known. To evaluate the epidemics and disease spectrum of HCoV-NL63 infection in children in Taiwan, we prospectively screened children admitted to the hospital with respiratory tract infection from May 2004 to April 2005. Every enrolled child had a nasopharyngeal aspirate (NPA) sample taken. Quantitative RT-PCR was used to detect 1b gene of HCoV-NL63. A total of 539 NPAs were collected. Seven (1.3%) were positive for HCoV-NL63. All cases were boys younger than 3 years of age and most cases occurred in autumn. Co-infection with other pathogens was observed in three cases. The most common symptoms/signs of HCoV-NL63 infection were cough, fever, and inspiratory stridor. HCoV-NL63 was the most common pathogen (14.7%) in children with croup and was the cause of three cases of croup in October. The odds ratio of croup in children infected with HCoV-NL63 was 43.4 (95% CI 8.1∼233.1). In conclusion, HCoV-NL63 is an important respiratory tract pathogen as the main cause in children admitted to the hospital in Taiwan. Keywords Coronavirus infections . Respiratory tract infections . Croup . Taiwan seasons in temperate countries, and peaks in summer in Hong Kong [3] . This study is aimed to understand the seasonal distribution and clinical manifestations of HCoV-NL63 infection in children in Taiwan. 
 Title: Clinical manifestations of human coronavirus NL63 infection in children in Taiwan
Output: True
Paragraph: Background: China has made substantial progress in tackling its HIV and AIDS epidemic. But the changing patterns of HIV and AIDS incidence based on the longitudinal observation data were rarely studied. Methods: The reporting incidence (RI) and mortality data on HIV and AIDS in China covering 31 provinces from 2004 to 2014 were collected from the Chinese Public Health Science Data Center. To decompose the time-series data, Empirical Mode Decomposition (EMD) was applied to properly describe the trends of HIV and AIDS incidence. A mathematical model was used to estimate the relative change of incidence among provinces and age groups. Results: A total of 483,010 newly HIV infections and 214,205 AIDS cases were reported between 2004 and 2014 nationwide. HIV infection increased from 13,258 in 2004 (RI 1.02 per 100,000 person years) to 74,048 in 2014 (RI 5.46 per 100,000). The number of AIDS cases increased from 3054 in 2004 (RI 0.23 per 100,000) to 45,145 in 2014 (RI 3.33 per 100,000). The overall relative changes for HIV infection and AIDS incidence were 1.11 (95% confidence interval [CI] 1.10-1.13) and 1.28 (95% CI 1.23-1.33), respectively. The relative increase for HIV and AIDS RI was higher in northwest provinces while lower in Henan, Xinjiang, Guangxi and Yunnan. The overall relative changes for HIV infection were 1.12 (95% CI 1.11-1.14) in males and 1.10 (95% CI 1.06-1.13) in females. For AIDS RI, the relative increases were 1.31 (95% CI 1.26-1.36) in males and 1.22 (95% CI 1.17-1.28) in females. The lowest relative increase was detected among young adults, while the largest relative increase (odds ratio [OR] > 1.30) was detected in people aged 55 years or above. Conclusions: HIV and AIDS showed an increasing trend in China from 2004 to 2014, respectively, but the epidemic tended to be under control among provinces and young people that used to have a high HIV and AIDS incidence. Northwest China and older people could be new "hop-spots" for HIV and AIDS risk. 
 Title: Changing epidemiological patterns of HIV and AIDS in China in the post-SARS era identified by the nationwide surveillance system
Output: True
Paragraph: Background: The cynomolgus monkey (Macaca fascicularis) has been increasingly used as a non-human primate model in biomedical research. As establishing baseline thoracic radiography for the cynomolgus monkey is essential, we tested the hypothesis that age and sex may affect the thoracic radiography parameters of this species. Methods: Here, 697 healthy cynomolgus monkeys were segregated by sex and age (three age groups: 25-36 months, 37-48 months, 49-60 months). The lung length (LL), maximal interior thoracic depth (TD), maximal interior thoracic breadth (TBr), cardiac silhouette breadth (CBr), cardiothoracic ratio (CR), right and left costophrenic angles (RCA and LCA), and right hilar height ratio (R-HHR) were assessed by chest film. Statistical analysis was applied to examine the effect of age, sex, and age 6 sex interactions. Results: Significant effects by age were shown for LL, TD, TBr, CBr, and CR. Significant effects by sex were found for TD, TBr, CBr, CR, and R-HHR. Significant effects by age 6sex were observed for TD, TBr, CBr, and CR. Both TD and TBr increased with age in both sexes, and both were significantly higher in males than in females in the group aged 49-60 months. CBr increased with age and was significantly higher in males than in females across all age groups. CR declined with age and was significantly higher in males than females across all age groups, and CR was similar or slightly higher relative to those previously found in other non-human primate species. As to the other parameters with no significant sex nor age-related differences, the R-HHR was greater than 1.00, and the angulation of bilateral costophrenic angles were sharp. The thoracic radiographic parameters for the healthy cynomolgus monkey presented here should prove useful in veterinary practice, research involving non-human primate models of respiratory or cardiovascular disorders, and morphological studies on cynomolgus monkeys. 
 Title: Normal Thoracic Radiographic Appearance of the Cynomolgus Monkey (Macaca fascicularis)
Output: True
Paragraph: Background: Measles caused by a paramyxovirus, characterized by fever, malaise, cough, coryza conjunctivitis, a maculopapular rash is known to result in pneumonia, encephalitis and death. Fatal cases of measles in Sri Lanka are rare after implementation of the National Immunization Programme in 1984. Thereafter 0.1% case fatality rate was observed during October 1999-June 2000 which is a very low figure compared to other regional countries. Immunization guidelines were further revised in 2001, 2011 and in 2012 when additional immunization was recommended to age group 4-21 years; who are likely to have inadequate immunization, in order to achieve elimination of Measles by 2020. However, in 2013-2014, 4690 cases were reported and the majority were children less than 1 year of age. The occurrence in adults is hard to retrieve in published epidemiological reports, however had been 38% (out of 1008 patients) in the 3rd quarter of 2013. During this outbreak 73/101 (72%) reported from the North Central Province of Sri Lanka had been more than 12 years of age with 50% being more than 29 years. 14 Sri lankan adult patients [median age 32 years (range 25-48)] who presented sporadically from June 2014 to March 2016, with confirmed measles infection were enrolled retrospectively after informed consent. Details with regards to their clinical presentation, immunization and other relevant areas were collected using an interviewer administered questionnaire or using patient management records. The patients presented with high fever, headache, severe body aches, sore throat, dry cough, intense tearing, red eyes and posterior cervical lymphadenopathy over 3-5 days duration. Later they developed discrete maculopapular rash helping the diagnosis. They had a variable degree of leucopenia, lymphocytosis, thrombocytopenia and derangements in the liver functions mimicking any other acute febrile illnesses such as dengue, chikungunya, leptospirosis or Zika virus infection. At least a 3-5 day delay in the diagnosis was observed (even after the appearance of the rash in some patients), due to non-awareness of its occurrence, unfamiliarity of measles in adults, non-specific nature of the illness and non-availability of rapid diagnostics, risking transmission to the immune-compromised or non-immune staff or patients. Identification of the source of infection in these sporadic adult cases and their virologic surveillance and molecular epidemiology will be important to interrupt the transmission and to achieve the targeted elimination of measles from Sri Lanka by 2020. 
 Title: Sporadic cases of adult measles: a research article
Output: False
Paragraph: Avipoxviruses are divided into three clades: canarypox-like viruses, fowlpox-like viruses, and psittacinepox-like viruses. Several molecular clock and demographic models available in the BEAST package were compared on three avipoxvirus genes (P4b, cnpv186 and DNA polymerase genes), which enabled to determine that avipoxviruses evolved at a rate of 2-8 Â 10 À5 substitution/site/year, in the range of poxviruses previously reported evolution rates. In addition, the date of mean time of divergence of avipoxviruses from a common ancestor was extrapolated to be about 10,000-30,000 years ago, at the same period as modern poxvirus species. Our findings will facilitate epidemiological investigations on avipoxviruses' spread, origin and circulation. 
 Title: Time scale evolution of avipoxviruses-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/)
Output: True
Paragraph: There is an increasing recognition that detailed nucleic acid sequence information will be useful and even required in the diagnosis, treatment and surveillance of many significant pathogens. Because generating detailed information about pathogens leads to significantly larger amounts of data, it is necessary to develop automated analysis methods to reduce analysis time and to standardize identification criteria. This is especially important for multiple pathogen assays designed to reduce assay time and costs. In this paper, we present a successful algorithm for detecting pathogens and reporting the maximum level of detail possible using multipathogen resequencing microarrays. The algorithm filters the sequence of base calls from the microarray and finds entries in genetic databases that most closely match. Taxonomic databases are then used to relate these entries to each other so that the microorganism can be identified. Although developed using a resequencing microarray, the approach is applicable to any assay method that produces base call sequence information. The success and continued development of this approach means that a non-expert can now perform unassisted analysis of the results obtained from partial sequence data. 
 Title: Automated identification of multiple micro-organisms from resequencing DNA microarrays
Output: False
Paragraph: Multiprotein complexes catalyze vital biological functions in the cell. A paramount objective of the SPINE2 project was to address the structural molecular biology of these multiprotein complexes, by enlisting and developing enabling technologies for their study. An emerging key prerequisite for studying complex biological specimens is their recombinant overproduction. Novel reagents and streamlined protocols for rapidly assembling co-expression constructs for this purpose have been designed and validated. The high-throughput pipeline implemented at IGBMC Strasbourg and the ACEMBL platform at the EMBL Grenoble utilize recombinant overexpression systems for heterologous expression of proteins and their complexes. Extension of the ACEMBL platform technology to include eukaryotic hosts such as insect and mammalian cells has been achieved. Efficient production of large multicomponent protein complexes for structural studies using the baculovirus/insect cell system can be hampered by a stoichiometric imbalance of the subunits produced. A polyprotein strategy has been developed to overcome this bottleneck and has been successfully implemented in our MultiBac baculovirus expression system for producing multiprotein complexes. Abbreviations: BEVS, baculovirus expression vector system; CFP, cyan florescent protein; CMV, cytomegalovirus; dpa, day of proliferation arrest; dsRed, red fluorescent protein; E. coli, Escherichia coli; EGFP, enhanced green fluorescent protein; EM, electron microscopy; FRET, fluorescence resonance energy transfer; HT, high throughput; kb, kilo base; kDa, kilo dalton; MOI, multiplicity of infection; NMR, nuclear magnetic resonance (spectroscopy); ORF, open reading frame; Ori, origin of replication; p10, p10 baculoviral late promoter; polh, polyhedrin baculoviral very late promoter; R6Kc, bacteriophage R6Kc; SDS-PAGE, sodium dodecylsulfate-polyacryamide gel electrophoresis; Sf9, Sf21, Spodoptera frugiperda cell lines 9 or 21, respectively; SLIC, sequence and ligation independent cloning; tcs, TEV protease cleavage site; TEV, tobacco etch virus, resp. a protease (N1A) from this virus; YFP, yellow fluorescent protein. 
 Title: Robots, pipelines, polyproteins: Enabling multiprotein expression in prokaryotic and eukaryotic cells
Output: False
Paragraph: Several polypeptide products of MHV-A59 ORF 1 a were characterized in MHV-A59 infected DBT cells, using antisera directed against fusion proteins encoded in the first 6.5 kb of ORFla. These included the previously identified N-terminal ORF 1 a product, ~28, as well as 290-, 240-, and 50-kDa polypeptides. P28 was always detected as a discrete band without larger precursors, suggesting rapid cleavage of p28 immediately after its synthesis. Once p28 was cleaved there was little degradation of the protein over a 2-hr period. The intracellular cleavage of p28 was not inhibited by the protease inhibitor leupeptin, in contrast to results obtained during in vitro translation of genome RNA (Denison and Perlman, 1986). These data suggest that different protease activities may be responsible for the cleavage of p28 in vitro and in Go. The 290-kDa protein was an intermediate cleavage product derived from a precursor of greater than 400 kDa. The 290-kDa product was subsequently cleaved into secondary products of 50 and 240 kDa. The intracellular cleavage of the 290-kDa polypeptide was inhibited by leupeptin at concentrations which did not inhibit the early cleavage of p28 or the cleavage of the 290-kDa product from its larger polyprotein precursor. In the presence of zinc chloride, a product of >320 kDa was detected, which appears to incorporate p28 at its amino terminus. This suggests that at least two protease activities may be necessary for processing of ORFl a proteins, one of which cleaves p28 and is sensitive to zinc chloride but resistant to leupeptin, and the other which cleaves the 290-kDa precursor and is sensitive to both inhibitors. Both the 290-and 240-kDa proteins should contain sequences predicted to encode two papain-like prOtesS? activities. 0 1992 Academic PVE.S. Inc. 
 Title: Intracellular Processing of the N-Terminal ORF la Proteins of the Coronavirus MHV-A59 Requires Multiple Proteolytic Events
Output: True
Paragraph: In the present study, a multiplex reverse transcriptase polymerase chain reaction combined with a chip hybridization assay (ProDect BCS RV CHIP) was evaluated as an alternative to the combination of immunofluorescent antibody test and shell vial cell culture considered as gold standard for the detection of respiratory viruses. Among 100 specimens, 40 were positive using the combination of immunofluorescent antibody test and shell vial cell culture assay in which 9 of them were infected by two different viruses (27 parainfluenza virus type 3, 10 adenovirus, 9 respiratory syncytial virus, 2 influenza type B, and 1 influenza type A). ProDect BCS RV CHIP detected only 10 positive specimens in which one of them was infected by two different viruses (5 respiratory syncytial virus, 3 parainfluenza virus type 3, 2 adenovirus, and 1 influenza virus type B). The sensitivity, specificity, PPV, NPV, and diagnostic accuracy of ProDect BCS RV CHIP were 25.0%, 100%, 100%, 66.6%, and 70.0%, respectively, compared to the combination of shell vial cell culture and immunofluorescent antibody test. As a result, the specificity of ProDect BCS RV CHIP is high, however, the sensitivity (25%) of the assay is not sufficient for routine laboratory use. 
 Title: Comparison of the "ProDect BCS RV CHIP" assay with the combination of shell vial cell culture and immunofluorescence antibody test for the detection of respiratory viruses
Output: False
Paragraph: The isolation of neutralizing monoclonal antibodies (nmAbs) against the Zika virus (ZIKV) might lead to novel preventative strategies for infections in at-risk individuals, primarily pregnant women. Here we describe the characterization of human mAbs from the plasmablasts of an acutely infected patient. One of the 18 mAbs had the unusual feature of binding to and neutralizing ZIKV despite not appearing to have been diversified by affinity maturation. This mAb neutralized ZIKV (Neut 50~2 μg/ml) but did not react with any of the four dengue virus serotypes. Except for the expected junctional diversity created by the joining of the V-(D)-J genes, there was no deviation from immunoglobulin germline genes. This is a rare example of a human mAb with neutralizing activity in the absence of detectable somatic hypermutation. Importantly, binding of this mAb to ZIKV was specifically inhibited by human plasma from ZIKV-exposed individuals, suggesting that it may be of value in a diagnostic setting. 
 Title: A human inferred germline antibody binds to an immunodominant epitope and neutralizes Zika virus
Output: False
Paragraph: A convenient and practical method for the synthesis of 2-alkylthio-4-amino-5-cyano-6-aryl(alkyl)pyrimidines has been developed via a three-component, one-pot reaction from aldehydes, malononitrile and S-alkylisothiouronium salts in water at room temperature. A series of polysubstituted pyrimidines were prepared by this method in moderate to excellent yields. In addition, two kinds of pyrimidine-fused heterocyclic derivatives with potential pharmacological activity were constructed from our 2-alkylthio-4-amino-5-cyano-6-arylpyrimidines. 
 Title: An efficient three-component, one-pot synthesis of 2-alkylthio-4-amino-5-cyano-6-aryl(alkyl)pyrimidines in water
Output: True
Paragraph: In response to SARS-CoV infection, neutralizing antibodies are generated against the Spike (S) protein. Determination of the active regions that allow viral escape from neutralization would enable the use of these antibodies for future passive immunotherapy. We immunized mice with UV-inactivated SARS-CoV to generate three anti-S monoclonal antibodies, and established several neutralization escape mutants with S protein. We identified several amino acid substitutions, including Y442F and V601G in the S1 domain and D757N and A834V in the S2 region. In the presence of each neutralizing antibody, double mutants with substitutions in both domains exhibited a greater growth advantage than those with only one substitution. Importantly, combining two monoclonal antibodies that target different epitopes effected almost complete suppression of wild type virus replication. Thus, for effective passive immunotherapy, it is important to use neutralizing antibodies that recognize both the S1 and S2 regions. 
 Title: A single amino acid substitution in the S1 and S2 Spike protein domains determines the neutralization escape phenotype of SARS-CoV
Output: True
Paragraph: Single cell suspensions obtained from day 7 human embryoid bodies (d7EBs) injected i.v. 1 hour after cecal ligation and puncture significantly reduced lung inflammation and edema as well as production of tumor necrosis factor-␣ and interferon-␥ in lungs compared with controls, whereas interleukin-10 production remained elevated. d7EB cell transplantation also reduced mortality to 50% from 90% in the control group. The protection was ascribed to d7EB cell interaction with lung resident CD11b؉ cells, and was correlated with the ability of d7EB cells to reduce it also reduced production of proinflammatory cytokines by CD11؉ cells, and to endothelial NO synthase-derived NO by d7EB cells, leading to inhibition of inducible macrophage-type NO synthase activation in CD11b؉ cells. The protective progenitor cells were positive for the endothelial and hematopoietic lineage marker angiotensin converting enzyme (ACE). Only the ACE؉ fraction modulated the proinflammatory profile of CD11b؉ cells and reduced mortality in septic mice. In contrast to the nonprotective ACE-cell fraction, the ACE؉ cell fraction also produced NO. These findings suggest that an ACE؉ subset of human embryonic stem cell-derived progenitor cells has a highly specialized anti-inflammatory function that ameliorates sepsis-induced lung inflammation and reduces mortality. 
 Title: Interaction of a Specific Population of Human Embryonic Stem Cell-Derived Progenitor Cells with CD11bϩ Cells Ameliorates Sepsis-Induced Lung Inflammatory Injury
Output: False
Paragraph: The interferon (IFN) system is one of the most important defensive responses of mammals against viruses, and is rapidly evoked when the pathogen-associated molecular patterns (PAMPs) of viruses are sensed. Non-self, virus-derived RNA species have been identified as the PAMPs of RNA viruses. In the present study, we compared different types of IFN-β-inducing and -non-inducing viruses in the context of Sendai virus infection. We found that some types of unusual viral RNA species were produced by infections with IFN-β-inducing viruses and accumulated into distinct cytoplasmic structures in an RNA-type-dependent manner. One of these structures was similar to the so-called antiviral stress granules (avSGs) formed by an infection with IFN-inducing viruses whose C proteins were knocked-out or mutated. Non-encapsidated, unusual viral RNA harboring the 5 -terminal region of the viral genome as well as RIG-I and typical SG markers accumulated in these granules. Another was a non-SG-like inclusion formed by an infection with the Cantell strain; a copyback-type DI genome, but not an authentic viral genome, specifically accumulated in the inclusion, whereas RIG-I and SG markers did not. The induction of IFN-β was closely associated with the production of these unusual RNAs as well as the formation of the cytoplasmic structures. 
 Title: a section of the journal Frontiers in Microbiology IFN-β-inducing, unusual viral RNA species produced by paramyxovirus infection accumulated into distinct cytoplasmic structures in an RNA-type-dependent manner
Output: True
Paragraph: Influenza has been well documented to significantly contribute to winter increase of mortality in the temperate countries, but its severity in the subtropics and tropics was not recognized until recently and geographical variations of disease burden in these regions remain poorly understood. In this study, we applied a standardized modeling strategy to the mortality and virology data from three Asian cities: subtropical Guangzhou and Hong Kong, and tropical Singapore, to estimate the disease burden of influenza in these cities. We found that influenza was associated with 10.6, 13.4 and 8.3 deaths per 100,000 population in Guangzhou, Hong Kong and Singapore, respectively. The annual rates of excess deaths in the elders were estimated highest in Guangzhou and lowest in Singapore. The excess death rate attributable to A/H1N1 subtype was found slightly higher than the rates attributable to A/H3N2 during the study period of 2004-2006 based on the data from Hong Kong and Guangzhou. Our study revealed a geographical variation in the disease burden of influenza in these subtropical and tropical cities. These results highlight a need to explore the determinants for severity of seasonal influenza. 
 Title: Influenza associated mortality in the subtropics and tropics: Results from three Asian cities
Output: False
Paragraph: Faeces samples from 218, 1 to 30-day-old, diarrheic dairy calves in 65 dairy herds were screened for the presence of Cryptosporidium and concurrent infections with rotavirus, coronavirus, F5 Escherichia coli and Salmonella spp. Calves were grouped according to their age as follows: 1±7, 8±14, 15±21 and 22±30 days. Cryptosporidium infection was detected in 43.8%, 71.9%, 63.2% and 6.9% of the calves in the respective age groups. Significant differences in the detection rate of Cryptosporidium were found between the age group 22±30 days and all other age groups, and between the age group 1±7 days and the age groups 8±14 days and 15±21 days. Cryptosporidium was the only enteropathogen detected in 60 of the 114 (52.6%) diarrheic calves. Concurrent infections with other enteropathogen(s) were detected in 64.3%, 46.3%, 39.5% and 0% of the Cryptosporidium-infected calves in the age groups 1±7, 8±14, 15±21 and 22±30 days, respectively. A significant age-associated decrease in the detection rate of mixed infections (p < 0.05) was found. The detection rates of the other enteropathogens considered in calves with Cryptosporidium infection were 87% for rotavirus, 11.1% for coronavirus, 27.8% for F5 E. coli and 1.8% for Salmonella. # 
 Title: Cryptosporidium and concurrent infections with other major enterophatogens in 1 to 30-day-old diarrheic dairy calves in central Spain
Output: False
Paragraph: Influenza infection is a major cause of morbidity and mortality worldwide, especially during pandemics outbreaks. Emerging data indicate that phase II antioxidant enzyme pathways could play a role in virusassociated inflammation and immune clearance. While Nrf2-dependent gene expression is known to modify inflammation, a mechanistic role in viral susceptibility and clearance has yet to be elucidated. Therefore, we utilized differentiated human nasal epithelial cells (NEC) and an enzymatic virus-like particle entry assay, to examine the role Nrf2-dependent gene expression has on viral entry and replication. Herein, lentiviral vectors that express Nrf2-specific short hairpin (sh)-RNA effectively decreased both Nrf2 mRNA and Nrf2 protein expression in transduced human NEC from healthy volunteers. Nrf2 knockdown correlated with a significant increase in influenza virus entry and replication. Conversely, supplementation with the potent Nrf2 activators sulforaphane (SFN) and epigallocatechin gallate (EGCG) significantly decreased viral entry and replication. The suppressive effects of EGCG on viral replication were abolished in cells with knocked-down Nrf2 expression, suggesting a causal relationship between the EGCG-induced activation of Nrf2 and the ability to protect against viral infection. Interestingly, the induction of Nrf2 via nutritional supplements SFN and EGCG increased antiviral mediators/responses: RIG-I, IFN-β, and MxA at baseline in the absence of infection. Our data indicate that there is an inverse relationship between the levels of Nrf2 expression and the viral entry/ replication. We also demonstrate that supplementation with Nrf2-activating antioxidants inhibits viral replication in human NEC, which may prove to be an attractive therapeutic intervention. Taken together, these data indicate potential mechanisms by which Nrf2-dependent gene expression regulates susceptibility to influenza in human epithelial cells. 
 Title: Nrf2 expression modifies influenza A entry and replication in nasal epithelial cells ☆
Output: False
Paragraph: In 1981, a new virus (virus 132) was described for the first time with morphological and biochemical similarities to rotaviruses (RVs), but without antigenic similarity to any of the previously known rotavirus groups. Subsequently, it was re-designated as D/132, and formed a new serogroup among rotaviruses, the group D rotavirus (RVD). Since their identification, RVs are the leading cause of enteritis and diarrhea in humans and various animal species, and are also associated with abridged growth, particularly in avian species. Recently, RVD has been suggested to play a role in the pathogenesis of runting and stunting syndrome (RSS), alongside other viruses such as reovirus, astrovirus, coronavirus, and others, all of which cause colossal economic losses to the poultry industry. RVD has been reported from several countries worldwide, and to date, only one complete genome sequence for RVD is available. Neither an immunodiagnostic nor a vaccine is available for the detection and prevention of RVD infection. Despite our growing understanding about this particular group, questions remain regarding its exact prevalence and pathogenecity, and the disease-associated annual losses for the poultry industry. Here, we describe the current knowledge about the identification, epidemiology, diagnosis, and prevention of RVD in poultry. 
 Title: Avian Group D Rotaviruses: Structure, Epidemiology, Diagnosis, and Perspectives on Future Research Challenges
Output: False
Paragraph: MinimM-disease (MD) cats raised in a barrier-maintained feline breeding colony routinely become coronavirus (CV) antibody-positive at 5-8 weeks of age and remain seropositive indefinitely. In addition, they shed coronavirus-like particles (CVLPs) in their feces which are morphologically distinct from "typical" coronaviruses. 0ronasal, intraperitoneal, intraduodenal, and intravenous inoculations of CVLPs were uniformly unsuccessful in the seroconversion of eats to CV, whereas subsequent prolonged close contact with colony eats did result in seroconversion. Such evidence indicates that MD eats in this barrier colony are infected with at least two non-crossreactive agents: (1) feline enteric CVLPs, which are shed in feces and are morphologically and antigenicMly distinct from established coronaviruses (CVs), and (2) a virus which is antigenically cross-reactive with CVs, but which is apparently shed by some route other than the lower gastrointestinal tract. 
 Title: Archives of Virology Experimental Studies of a Corona irus and Coronavirus-Like Agent in a Barrier-Maintained Feline Breedinfl Colony
Output: True