niryuu/sni-each-converted huggingface dataset:
Paragraph: Low Clostridium leptum levels are a risk factor for the development of asthma. C. leptum deficiency exacerbates asthma; however, the impact of early-life C. leptum exposure on cesarean-delivered mice remains unclear. This study is to determine the effects of early-life C. leptum exposure on asthma development in infant mice. We exposed infant mice to C. leptum (fed-CL) and then induced asthma using the allergen ovalbumin (OVA). Fed-CL increased regulatory T (Treg) cells in cesarean-delivered mice compared with vaginally delivered mice. Compared with OVA-exposed mice, mice exposed to C. leptum + OVA did not develop the typical asthma phenotype, which includes airway hyper-responsiveness, cell infiltration, and T helper cell subset (Th1, Th2, Th9, Th17) inflammation. Early-life C. leptum exposure induced an immunosuppressive environment in the lung concurrent with increased Treg cells, resulting in the inhibition of Th1, Th2, Th9, and Th17 cell responses. These findings demonstrate a mechanism whereby C. leptum exposure modulates adaptive immunity and leads to failure to develop asthma upon OVA sensitization later in life. Fig 2. Schematic of a mouse model of early-life C. leptum ± OVA asthma. All analyses were carried out 48 h after the final protocol day. HE, hematoxylin-eosin; AL(OH) 3 , aluminum hydroxide. 
 Title: Early-Life Exposure to Clostridium leptum Causes Pulmonary Immunosuppression
Output: True
Paragraph: A conserved 11-nucleotide sequence, UGAAUGAAGUU, at the 3 end of the genomic RNA of coronavirus mouse hepatitis virus was required for host protein binding and viral RNA synthesis. An RNA probe containing this 11-nucleotide sequence bound four cellular proteins with a highly labeled protein of 120 kDa and three minor species with sizes of 103, 81, and 55 kDa. Mutation of the 11-nucleotide motif abolished cellular protein binding. The RNA-protein complexes observed with cytoplasmic extracts from MHV-JHM-infected cells in both RNase protection/gel mobility shift and UV cross-linking assays were indistinguishable from those observed with extracts from uninfected cells. Both negative-strand synthesis and positivestrand replication of viral defective interfering RNAs in the presence of helper virus were affected by mutations that disrupt RNA-protein complex formation, even though the 11 mutated nucleotides were converted to the wild-type sequence, presumably by recombination with helper virus. Kinetic analysis indicated that recombination between DI RNA and helper virus occurred relatively early in the MHV replicative cycle at 5.5 to 7.5 hr postinfection, a time when viral RNA synthesis and replication of positive-strand DI RNA were at barely detectable levels. A DI RNA with a mutation upstream of the protein binding element replicated as efficiently as wild type without undergoing recombination. Thus, the 11-nucleotide conserved host protein binding motif appears to play an important role in viral RNA replication. ᭧ 
 Title: A Conserved Motif at the 3 End of Mouse Hepatitis Virus Genomic RNA Required for Host Protein Binding and Viral RNA Replication
Output: True
Paragraph: The exported cases of 2019 novel coronavirus infection that were confirmed outside China provide an opportunity to estimate the cumulative incidence and confirmed case fatality risk (cCFR) in mainland China. Knowledge of the cCFR is critical to characterize the severity and understand the pandemic potential of COVID-19 in the early stage of the epidemic. Using the exponential growth rate of the incidence, the present study statistically estimated the cCFR and the basic reproduction number-the average number of secondary cases generated by a single primary case in a naïve population. We modeled epidemic growth either from a single index case with illness onset on 8 December 2019 (Scenario 1), or using the growth rate fitted along with the other parameters (Scenario 2) based on data from 20 exported cases reported by 24 January 2020. The cumulative incidence in China by 24 January was estimated at 6924 cases (95% confidence interval [CI]: 4885, 9211) and 19,289 cases (95% CI: 10,901, 30,158), respectively. The latest estimated values of the cCFR were 5.3% (95% CI: 3.5%, 7.5%) for Scenario 1 and 8.4% (95% CI: 5.3%, 12.3%) for Scenario 2. The basic reproduction number was estimated to be 2.1 (95% CI: 2.0, 2.2) and 3.2 (95% CI: 2.7, 3.7) for Scenarios 1 and 2, respectively. Based on these results, we argued that the current COVID-19 epidemic has a substantial potential for causing a pandemic. The proposed approach provides insights in early risk assessment using publicly available data. 
 Title: Clinical Medicine Real-Time Estimation of the Risk of Death from Novel Coronavirus (COVID-19) Infection: Inference Using Exported Cases
Output: False
Paragraph: Viral disease caused by the Yellow head virus (YHV) had great impact on economic loss in the aquaculture industry. Prevention or curing YHV disease is still not possible due to the lack of understanding of the basic mechanisms of YHV infection. In this report, the endocytosis inhibitors (chlorpromazine (CPZ), amiloride and methyl-β-cyclodextrin (MβCD)) were used to identify the cellular entry pathway of YHV. Pretreating shrimp with CPZ but not amiloride or MβCD followed by YHV challenge resulted in a significant reduction of YHV levels, suggesting that YHV entered the shrimp cells via clathrin-mediated endocytosis. Next, the major component of the clathrin-coated vesicle, Penaeus monodon clathrin heavy chain (PmCHC) was cloned and characterized. The complete coding sequence of PmCHC is 5055 bp encoding a putative protein of 1684 amino acids. Specific silencing of PmCHC mRNA by dsRNA-PmCHC showed an inhibition of YHV replication for 48 h post YHV injection as well as exhibiting a delay in shrimp mortality. These results indicated that PmCHC was an essential component for YHV infection of shrimp cells. 
 Title: Successful yellow head virus infection of Penaeus monodon requires clathrin heavy chain
Output: False
Paragraph: Background: Respiratory viral infections are a major cause of hospitalisation in infants <1 year and might cause severe symptoms in preterm infants. Our aim was to analyse admissions due to respiratory infections in moderate, late and term infants, and to identify risk factors for hospitalisation in preterm versus term. Methods: Prospective study in a cohort of moderate and late preterm, and term infants born between October/2011 and December/2012. Admissions due to respiratory infections during the first year of life were analysed and compared among moderate (32---33), late (34---36) and term infants. Sixteen respiratory viruses were detected by RT-PCR. Clinical data were collected. Results: 30 (20.9%) out of 143 preterm infants required admission for respiratory infection, versus 129 (6.9%) of 1858 term infants born in the same period (p < 0.0001, OR: 3.6 CI 2.0 to 5.0). Hospitalised children had a higher prevalence of hyaline membrane disease (HMD) at birth (p < 0.001, OR: 7.7 CI: 2.121 to 27.954) and needed more mechanical ventilation (p < 0.001, OR: 5.7 CI: 1.813 to 18.396). Virus was identified in 25/30 (83%) preterm babies, and in 110/129 (85%) term infants. The most frequent viruses in preterm infants were RSV (76%) rhinovirus (20%). Clinical and epidemiological characteristics among term and preterm infants were similar. Conclusions: The risk of respiratory admissions during the first year of life is up to 3.6 times higher in moderate and late preterm. Once admitted, clinical features of respiratory episodes requiring hospitalisation are similar among term and preterm infants. Hyaline membrane disease and mechanical ventilation were also risk factors for respiratory admissions. 
 Title: Allergologia et immunopathologia Hospital admission due to respiratory viral infections in moderate preterm, late preterm and term infants during their first year of life
Output: False
Paragraph: Enterobacterial pathogens that have acquired antibiotic resistance genes are a leading cause of community and hospital acquired infections. In such a situation vaccination is considered as a better option to prevent such infections. In the current study reverse vaccinology approach has been used to select peptides from already known immunogenic proteins to design a chimeric construct. We selected Yersiniabactin receptor of Escherichia coli UMN026 and Flagellin of Stenotrophomonas maltophila. B-cell linear epitopes were predicted using Bepipred prediction tool. Peptide binding with reference sets of 27 alleles of MHC class I and class II was also analyzed. The predicted peptides-MHC complexes were further validated using simulation dynamics. The insilico construction of chimera was done by restriction mapping and codon optimization. Chimera was evaluated using the immunoinformatic approach as done for the selected proteins. From the 673 amino acids of FyuA protein, a region from 1 to 492 was selected for containing more linear epitopes and the processing scores obtained were significant for MHC class I and class II binding. Similarly, from Flagellin, a region between 60 and 328 amino acids was selected and the peptides present in the selected region showed lower percentile ranks for binding with MHC molecules. The simulation studies validated the predictions of peptide-MHC complexes. The selected gene fragments accommodating maximum part of these peptides were used to design a chimaeric construct of 2454 bp. From the immunoinformatic analysis, the chimera was found to be more immunogenic in terms of increased number of B-cell and T-cell epitopes along with increased coverage of global populations with allelic variability. Abbreviations: MHC, Major histocompatibility complex; RV, reverse vaccinology; HLA, human leukocyte antigen; HCV, hepatitis c virus; MERS-CoV, middle east respirator syndrome coronavirus; OMPs, outer membrane proteins; IEDB, immune epitope database and analysis resource; NCBI, national center for biotechnology information; NEB, new england biolabs; DNA, deoxyribonucleic acid; PDB, protein data bank; USA, United States of America; BLASTp, basic local alignment tool for proteins ⁎ 
 Title: A multiepitopic theoretical fusion construct based on in-silico epitope screening of known vaccine candidates for protection against wide range of enterobacterial pathogens
Output: False
Paragraph: Multiple sclerosis (MS) is a chronic inflammatory disease that is characterized by leukocyte infiltration and subsequent axonal damage, demyelinating inflammation, and formation of sclerosing plaques in brain tissue. The results of various studies in patients indicate that autoimmunity and inflammation make an important impact on the pathogenesis of MS. Chemokines are key mediators of inflammation development and cell migration, mediating various immune cell responses, including chemotaxis and immune activation, and are important in immunity and inflammation, therefore we focus on chemokines and their receptors in multiple sclerosis. In this article, we summarize the study of the role of prominent chemokines and their receptors in MS patients and MS animal modelsand discuss their potential significance in inflammatory injury and repair of MS. We have also summarized the progress in the treatment of multiple sclerosis antagonists in recent years with chemokine receptors as targets. 
 Title: The role of chemokines and chemokine receptors in multiple sclerosis
Output: True
Paragraph: containing 36 ppm germanium. The present study was conducted to better understand the effects of GB on immune responses in a mouse model, and to demonstrate the clearance effects of this mineral against Porcine reproductive and respiratory syndrome virus (PRRSV) in experimentally infected pigs as an initial step towards the development of a feed supplement that would promote immune activity and help prevent diseases. In the mouse model, dietary supplementation with GB enhanced concanavalin A (ConA)-induced lymphocyte proliferation and increased the percentage of CD3+CD8+ T lymphocytes. In pigs experimentally infected with PRRSV, viral titers in lungs and lymphoid tissues from the GB-fed group were significantly decreased compared to those of the control group 12 days post-infection. Corresponding histopathological analyses demonstrated that GB-fed pigs displayed less severe pathological changes associated with PRRSV infection compared to the control group, indicating that GB promotes PRRSV clearance. These antiviral effects in pigs may be related to the ability of GB to increase CD3+CD8+ T lymphocyte production observed in the mice. Hence, this mineral may be an effective feed supplement for increasing immune activity and preventing disease. Keywords: germanium biotite, immune enhancement, porcine reproductive and respiratory syndrome virus 136 Bock-Gie Jung et al. 
 Title: Veterinary Science pISSN 1229-845X, eISSN 1976-555X
Output: True
Paragraph: The WHO has declared SARS-CoV-2 outbreak a public health emergency of international concern. However, to date, there was hardly any study in characterizing the immune responses, especially adaptive immune responses to SARS-CoV-2 infection. In this study, we collected blood from COVID-19 patients who have recently become virus-free and therefore were discharged, and analyzed their SARS-CoV-2-specific antibody and T cell responses. We observed SARS-CoV-2-specific humoral and cellular immunity in the patients. Both were detected in newly discharged patients, suggesting both participate in immune-mediated protection to viral infection. However, follow-up patients (2 weeks post discharge) exhibited high titers of IgG antibodies, but with low levels of virus-specific T cells, suggesting that they may enter a quiescent state. Our work has thus provided a basis for further analysis of protective immunity to SARS-CoV-2, and understanding the pathogenesis of COVID-19, especially in the severe cases. It has also implications in designing an effective vaccine to protect and treat SARS-CoV-2 infection. : medRxiv preprint PBMCs were washed with PBS plus 2% FBS (Gibco, Grand Island, NY), and then Fc blocking reagent (Meltenyi Biotec, Inc., Auburn, CA) was added followed by a wash with PBS plus 2% FBS. Cells were then incubated for 30 min on ice with anti-CD45 (H130) (BioLegend), anti-CD3 (OKT3) (BioLegend), anti-CD8 (SK1) (BD), anti-CD56 (HCD56) (BioLegend), anti-All rights reserved. No reuse allowed without permission. the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. : medRxiv preprint 9 CD38 (HIT2) (BioLegend) and live/dead fixable aqua dye (eF660, eBioscience), washed twice with PBS plus 2% FBS and then stored at 4 °C until acquired by FACS Verse (BD Biosciences, San Jose, CA). Data were analyzed using FlowJo software (Version 10.0.8, Tree Star Inc., Ashland, Or). Prism 7 software is used for statistical analysis. Student's t test was performed for twogroup analysis. Pearson's correlation coefficients were calculated. P values less than 0.05 were considered to be statistically significant. 
 Title: Characterization of anti-viral immunity in recovered individuals infected by SARS-CoV-2
Output: False
Paragraph: Background: Osteonecrosis is an incapacitating disorder with high morbidity. Though extracorporeal shockwave therapy (ESWT) provides a noninvasive treatment option, controversial subjects still exist about its effectiveness, indications, and mechanism of action. Methods: An electronic databases search was performed using PubMed, Embase, and the Cochrane library to collect clinical trials, case reports, and cases series on this topic and then useful data were extracted and appraised by experienced clinicians. We evaluated the quality of included evidences by using the Oxford Centre for evidence-based medicine (EBM) Levels of Evidence. Results: A total of 17 articles including 2 case reports, 9 open label trials, 2 cohorts, and 6 randomized controlled trials were considered to be eligible for this systematic review. Visual analog scale (VAS), Harris hip scores, and the imaging results were the frequently-used outcome estimates of included studies. Conclusion: By systematically analyzing these evidences, we could conclude that ESWT could act as a safe and effective method to improve the motor function and relieve the pain of patients with osteonecrosis of femoral hip, especially those at early stage. Imaging revealed that bone marrow edema was significantly relieved, but the necrotic bone could not be reversed after ESWT. This technique could slow or even block the progression of ONFH and therefore reduce the demand for surgery. Collaboration with other conservative modalities would not improve the curative benefits of ESWT. Meanwhile, ONFH with various risk factors showed similar reaction to this noninvasive treatment method. However, these conclusions should be interpreted carefully for the low-quality of included publications and further studies are requisite to validate the effect of ESWT in ONFH. Abbreviations: allo-HSCT = allogeneic hematopoietic stem cell transplantation, ARCO = association research circulation osseous, BMP = bone morphogenic protein, CD = core decompression, EBM = evidence-based medicine, ESWT = extracorporeal shockwave therapy, ESWT = extracorporeal shockwave therapy, HBO = hyperbaric oxygen therapy, ONFH = osteonecrosis of femoral head, RUNX2 = Runt-related transcription factor 2, SARS = severe acute respiratory syndrome, SF-12 = 12-item Short Form, SLE = systemic lupus erythematosus, SR = systematic review, THA = total hip arthroplasty, VAS = visual analog scale, VEGF = vessel endothelial growth factor, WOMAC = Western Ontario and McMaster Universities Arthritis Index. 
 Title: Extracorporeal shockwave therapy in osteonecrosis of femoral head A systematic review of now available clinical evidences
Output: False
Paragraph: Background: Calf disease may result in great economic losses. To implement prevention strategies it is important to gain information on management and to point out risk factors. The objective of this internet based survey was to describe calf management practices on registered dairy breeding farms in Austria and to estimate differences in calf disease incidences depending on farm structure and management practices. Results: A total of 1287 questionnaires were finally analysed (response rate 12.2 %). Herd characteristics and regional distribution of farms indicated that this survey gives a good overview on calf management practices on registered dairy farms in Austria. The median number of cows per farm was 20 (interquartile range 13-30). Significant differences regarding farm characteristics and calf management between small and large farms (≤20 vs >20 cows) were present. Only 2.8 % of farmers tested first colostrum quality by use of a hydrometer. Storing frozen colostrum was more prevalent on large farms (80.8 vs 64.2 %). On 85.1 % of the farms, whole milk, including waste milk, was fed to the calves. Milk replacer and waste milk were more often used on large farms. In accordance with similar studies from other countries, calf diarrhoea was indicated as the most prevalent disease. Multivariable logistic regression analysis revealed that herd size was associated with calf diarrhoea and calf respiratory tract disease, with higher risk of disease on large farms. Furthermore, feeding waste milk to the calves was associated with increasing calf diarrhoea incidence on farm. In the final model with calf respiratory tract disease as outcome, respondents from organic farms reported less often a respiratory tract disease incidence of over 10 % compared with conventional farms [odds ratio (OR) 0.40, 95 % confidence interval (CI) 0.21-0.75] and farmers that housed calves individually or in groups after birth significantly reported more often to have an incidence of respiratory tract disease >10 % compared with farms where all calves were housed individually (OR 2.28, 95 % CI 1.16-4.48). The results obtained in this study provide an overview on calf management on dairy breeding farms in Austria and may help to further point out areas to be improved on farm. Abbreviations OR: odds ratio; 95 % CI: 95 % confidence interval; p.n.: post natum. Additional file 1. The original online questionnaire in German, distributed to the farmers. 
 Title: Results of an online questionnaire to survey calf management practices on dairy cattle breeding farms in Austria and to estimate differences in disease incidences depending on farm structure and management practices Open Access
Output: False
Paragraph: Rift Valley fever virus (RVFV) (genus Phlebovirus, family Bunyaviridae) is a negative-stranded RNA virus with a tripartite genome. RVFV is transmitted by mosquitoes and causes fever and severe hemorrhagic illness among humans, and fever and high rates of abortions in livestock. A nonstructural RVFV NSs protein inhibits the transcription of host mRNAs, including interferon-b mRNA, and is a major virulence factor. The present study explored a novel function of the RVFV NSs protein by testing the replication of RVFV lacking the NSs gene in the presence of actinomycin D (ActD) or a-amanitin, both of which served as a surrogate of the host mRNA synthesis suppression function of the NSs. In the presence of the hosttranscriptional inhibitors, the replication of RVFV lacking the NSs protein, but not that carrying NSs, induced doublestranded RNA-dependent protein kinase (PKR)-mediated eukaryotic initiation factor (eIF)2a phosphorylation, leading to the suppression of host and viral protein translation. RVFV NSs promoted post-transcriptional downregulation of PKR early in the course of the infection and suppressed the phosphorylated eIF2a accumulation. These data suggested that a combination of RVFV replication and NSs-induced host transcriptional suppression induces PKR-mediated eIF2a phosphorylation, while the NSs facilitates efficient viral translation by downregulating PKR and inhibiting PKR-mediated eIF2a phosphorylation. Thus, the two distinct functions of the NSs, i.e., the suppression of host transcription, including that of type I interferon mRNAs, and the downregulation of PKR, work together to prevent host innate antiviral functions, allowing efficient replication and survival of RVFV in infected mammalian hosts. 
 Title: Rift Valley Fever Virus NSs Protein Promotes Post-Transcriptional Downregulation of Protein Kinase PKR and Inhibits eIF2a Phosphorylation
Output: False
Paragraph: SARS-CoV, as the pathogeny of severe acute respiratory syndrome (SARS), is a mystery that the origin of the virus is still unknown even a few isolates ofthe virus were completely sequenced. To explore the genesis of SARS-ON, the FDOD method previously developed by us was applied to comparing complete genomes from 12 SARS-CoV isolates to those from 12 previously identified coronaviruses and an unrooted phylogenetic tree was constructed. Our results show that all SARS-CoV isolates were clustered into a clique and previously identified coronaviruses formed the other clique. Meanwhile, the three groups of coronaviruses depart from each other clearly in our tree that is consistent with the results of prevenient papers. Differently, from the topology of the phylogenetic tree we found that SARS-CoV is more close to group 1 within genus coronavirus. The topology map also shows that the 12 SARS-CoV isolates may be divided into two groups determined by the association with the SARS-CoV from the Hotel M in Hong Kong that may give some information about the infectious relationship of the SARS. 
 Title: Phylogeny of SARS-CoV as inferred from complete genome comparison
Output: True
Paragraph: In this study, a high-resolution frontal area density (FAD) map that depicts the surface roughness of urban Hong Kong is produced using a mapping method that takes into account the dense urban morphology and the site wind availability of the territory. Using the MM5/CALMET model simulated wind data of Hong Kong, the FAD map of three urban zones are calculated: podium (0-15 m), building (15-60 m), and urban canopy (0-60 m). The wind tunnel test data is used to correlate the FAD understanding of the three zones. The grid sensitivity test indicates that 200 m × 200 m is the reasonable resolution for the FAD map; the test also establishes that the lower urban podium zone yields the best correlation with the experimental data. The study further establishes that the simpler two-dimensional ground coverage ratio (GCR), which is readily available in the planning circle, can be used to predict the area's average pedestrian level urban ventilation performance of the city. Working with their inhouse GIS team using available data, it allows the planners a way to understand the urban ventilation of the city for decisions related to air paths, urban permeability and site porosity. 
 Title: Improving the wind environment in high-density cities by understanding urban morphology and surface roughness: A study in Hong Kong
Output: False
Paragraph: Since mid-December of 2019, coronavirus disease 2019 (COVID-19) has been spreading from Wuhan, China. The confirmed COVID-19 patients in South Korea are those who came from or visited China. As secondary transmissions have occurred and the speed of transmission is accelerating, there are rising concerns about community infections. The 54-year old male is the third patient diagnosed with COVID-19 in Korea. He is a worker for a clothing business and had mild respiratory symptoms and intermittent fever in the beginning of hospitalization, and pneumonia symptoms on chest computerized tomography scan on day 6 of admission. This patient caused one case of secondary transmission and three cases of tertiary transmission. Hereby, we report the clinical findings of the index patient who was the first to cause tertiary transmission outside China. Interestingly, after lopinavir/ritonavir (Kaletra, AbbVie) was administered, β-coronavirus viral loads significantly decreased and no or little coronavirus titers were observed. 
 Title: Brief Communication
Output: True
Paragraph: The major structural protein VP2 of porcine parvovirus (PPV) was used as the model parvovirus antigen, which has been expressed in Lactobacillus casei fusing with Escherichia coli heat-labile enterotoxin B subunit (LTB) as mucosal adjuvant. The VP2-LTB DNA fragment was cloned into vector pPG611 or pPG612 to generated inducible surface-displayed and secretion expression systems based on xylose promoter, designated as rLc:pPG611-VP2-LTB (recombinant L. casei) and rLc:pPG612-VP2-LTB, respectively. Expression of the fusion protein was verified by SDS-PAGE, Western blot immunofluorescence and electron microscopy. It was observed that the level of IgG or sIgA from mice orally immunized with VP2-LTB was higher than that from mice received VP2 and negative control, which demonstrated significantly statistically different. Especially, the titer of IgG or sIgA in mice immunized with rLc:pPG612-VP2-LTB is the highest in this study. In summary, LTB as mucosal adjuvant was able to effectively facilitate induction of mucosal and systemic immunity by L. casei-expressing VP2 fusion protein. 
 Title: Comparison of the immune responses induced by oral immunization of mice with Lactobacillus casei-expressing porcine parvovirus VP2 and VP2 fused to Escherichia coli heat-labile enterotoxin B subunit protein
Output: False
Paragraph: Background: Most virus detection methods are geared towards the detection of specific single viruses or just a few known targets, and lack the capability to uncover the novel viruses that cause emerging viral infections. To address this issue, we developed a computational method that identifies the conserved viral sequences at the genus level for all viral genomes available in GenBank, and established a virus probe library. The virus probes are used not only to identify known viruses but also for discerning the genera of emerging or uncharacterized ones. Results: Using the microarray approach, the identity of the virus in a test sample is determined by the signals of both genus and species-specific probes. The genera of emerging and uncharacterized viruses are determined based on hybridization of the viral sequences to the conserved probes for the existing viral genera. A detection and classification procedure to determine the identity of a virus directly from detection signals results in the rapid identification of the virus. We have demonstrated the validity and feasibility of the above strategy with a small number of viral samples. The probe design algorithm can be applied to any publicly available viral sequence database. The strategy of using separate genus and species probe sets enables the use of a straightforward virus identity calculation directly based on the hybridization signals. Our virus identification strategy has great potential in the diagnosis of viral infections. The virus genus and specific probe database and the associated summary tables are available at 
 Title: Design of microarray probes for virus identification and detection of emerging viruses at the genus level
Output: True
Paragraph: The genetic predisposition to severe A(H1N1)2009 (A[H1N1]pdm09) influenza was evaluated in 409 patients, including 162 cases with severe infection and 247 controls with mild infection. We prioritized candidate variants based on the result of a pilot genome-wide association study and a lung expression quantitative trait locus data set. The GG genotype of rs2070788, a higher-expression variant of TMPRSS2, was a risk variant (odds ratio, 2.11; 95% confidence interval, 1.18-3.77; P = .01) to severe A(H1N1)pdm09 influenza. A potentially functional single-nucleotide polymorphism, rs383510, accommodated in a putative regulatory region was identified to tag rs2070788. Luciferase assay results showed the putative regulatory region was a functional element, in which rs383510 regulated TMPRSS2 expression in a genotype-specific manner. Notably, rs2070788 and rs383510 were significantly associated with the susceptibility to A(H7N9) influenza in 102 patients with A(H7N9) influenza and 106 healthy controls. Therefore, we demonstrate that genetic variants with higher TMPRSS2 expression confer higher risk to severe A(H1N1)pdm09 influenza. The same variants also increase susceptibility to human A(H7N9) influenza. 
 Title: Identification of TMPRSS2 as a Susceptibility Gene for Severe 2009 Pandemic A(H1N1) Influenza and A(H7N9) Influenza
Output: False
Paragraph: Plants are able to perform post-translational maturations of therapeutic proteins required for their functional biological activity and suitable in vivo pharmacokinetics. Plants can be a low-cost, large-scale production platform of recombinant biopharmaceutical proteins such as vaccines and antibodies. Plants, however, lack mechanisms of processing authentic human N-glycosylation, which imposes a major limitation in their use as an expression system for therapeutic glycoproducts. Efforts have been made to circumvent plant-specific Nglycosylation, as well as to supplement the plant's endogenous system with human glycosyltransferases for nonimmunogenic and humanized N-glycan production. Herein we review studies on the potential of plants to serve as production systems for therapeutic and prophylactic biopharmaceuticals. We have especially focused on recombinant vaccines and antibodies and new expression strategies to overcome the existing problems associated with their production in plants. 
 Title: Expression of Recombinant Vaccines and Antibodies in Plants
Output: False
Paragraph: The enveloped baculoviras\insect cell system has been used extensively for expression of recombinant proteins, including viral fusion proteins. We tested wiid-tyl~ baculovirus for endogenous fusion protein activity. Syncytia formation, dye transfer, and capacitance chanses were observed after incubating infected Spodopterafrugiperda cells in acidic media, consistent with fusion protein activity. Only a short acidic pulse of 10 s is needed to trisect syncytia formation. Identical results were obtained with recombinant baculovirus. This new ~ys:e,r~ !,_ convenient for studying pH activated ccll~dl fusion. However, using this enveloped virus to study ~he mechanism of recomlHzant fusion proteins rexluires caution. Membrane fusion; Viral fusion; Enveloped virus; Cell-cell fusion; Baculovirus exprer~ion system Published by Elsevier Science Publishers B. It. 92] Volume 304, number 2,3 FEBS LETTERS 
 Title: Acidic pH induces fusion of cells infected with baculovirus to form syncytia
Output: False
Paragraph: Phylogenetic tree of coronaviruses (CoVs) including the human SARS-associated virus is reconstructed from complete genomes by using our newly developed Kstring composition approach. The relation of the human SARS-CoV to other coronaviruses, i.e. the rooting of the tree is suggested by choosing an appropriate outgroup. SARS-CoV makes a separate group closer but still distant from G2 (CoVs in mammalian host). The relation between different isolates of the human SARS virus is inferred by first constructing an ultrametric distance matrix from counting sequence variations in the genomes. The resulting tree is consistent with clinic relations between the SARS-CoV isolates. In addition to a larger variety of coronavirus genomes these results provide phylogenetic knowledge based on independent novel methodology as compared to recent phylogenetic studies on SARS-CoV. DOl: lO.1360/03wc0254 I) In the revised paper the 4 partial genomes were replaced by the updated complete ones. 2) The error rate in sequencing BJOI is estimated to be 0.94 in 10 kb, Private communication from authors of [3] . 
 Title: Molecular phylogeny of coronaviruses including human SARS-CoV
Output: True
Paragraph: Diagnosis of the etiologic agent of respiratory viral infection relies traditionally on culture or antigen detection. This pilot was conducted evaluation comparing performance characteristics of the RT-PCR and Electrospray Ionization Mass Spectrometry (RT-PCR/ESI-MS) platform to conventional virological methods for identifying multiple clinically relevant respiratory viruses in nasopharyngeal aspirates. The RT-PCR/ESI-MS respiratory virus surveillance kit was designed to detect respiratory syncytial virus, influenza A and B, parainfluenza types 1-4, adenoviridae types A-F, coronaviridae, human bocavirus, and human metapneumovirus. Patients (N=192) attending an emergency department during the 2007-8 respiratory season consented, and "excess" frozen archived nasopharyngeal aspirates were analysed; 46 were positive by conventional virology and 69 by RT-PCR/ESI-MS, among which there were six samples with multiple viral pathogens detected. The sensitivity and specificity of the assay were 89.1% and 80.3%, respectively. Additional viruses that were not identified by conventional virology assays were detected (4 human bocaviruses and 7 coronaviruses). Samples in which the RT-PCR/ESI-MS results disagreed with conventional virology were sent for analysis by a third method using a commercial RT-PCR-based assay, which can identify viruses not detectable by conventional virologic procedures. Time to first result of RT-PCR/ESI-MS was 8 hours. RT-PCR/ESI-MS demonstrated capacity to detect respiratory viruses identifiable and unidentifiable by conventional methods rapidly. 
 Title: Author manuscript; available in PMC
Output: True
Paragraph: 1 This children's game also goes by whisper down the lane or telephone, depending on the country where it is played. While the pioneering studies discussed below were well done and careful to state that their evidence did not confirm the sole or ultimate reservoir, this message of restraint has been lost in some recent reviews and popular media. Our goal here is to reiterate the original message and highlight future directions. 
 Title: Assessing the Evidence Supporting Fruit Bats as the Primary Reservoirs for Ebola Viruses
Output: True
Paragraph: New strategies to prevent and treat influenza virus infections are urgently needed. A recently discovered class of monoclonal antibodies (mAbs) neutralizing an unprecedented spectrum of influenza virus subtypes may have the potential for future use in humans. Here, we assess the efficacies of CR6261, which is representative of this novel class of mAbs, and oseltamivir in mice. We show that a single injection with 15 mg/kg CR6261 outperforms a 5-day course of treatment with oseltamivir (10 mg/kg/day) with respect to both prophylaxis and treatment of lethal H5N1 and H1N1 infections. These results justify further preclinical evaluation of broadly neutralizing mAbs against influenza virus for the prevention and treatment of influenza virus infections. 
 Title: Pre-and Postexposure Use of Human Monoclonal Antibody against H5N1 and H1N1 Influenza Virus in Mice: Viable Alternative to Oseltamivir
Output: False
Paragraph: Carbocyclic nucleosides (À)-5 0 -homocarbovir and (þ)-epi-4 0 -homocarbovir were prepared from an acylnitroso-derived hetero DielseAlder cycloadduct. A kinetic enzymatic resolution generated an enantiopure aminocyclopentenol and Pd(0)-mediated decarboxylative allylations of allyl 2,2,2-trifluoroethyl malonates were used to install the 4 0 -hydroxyethyl groups. Late stage derivatization gave access to the cyclopropylamine analogs, (À)-5 0 -homoabacavir, and (þ)-epi-4 0 -homoabacavir. All carbonucleoside target molecules were evaluated for antiviral activity. 
 Title: Enantioselective syntheses of carbocyclic nucleosides 5 0 -homocarbovir, epi-4 0 -homocarbovir, and their cyclopropylamine analogs using facially selective Pd-mediated allylations
Output: False
Paragraph: Exotic wildlife can act as reservoirs of diseases that are endemic in the area or can be the source of new emerging diseases through interspecies transmission. The recent emergence of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) highlights the importance of virus surveillance in wild animals. Here, we report the identification of a novel bat coronavirus through surveillance of coronaviruses in wildlife. In particular, 63% (12 of 19) of fecal samples from Miniopterus pusillus were positive for the virus. These findings suggest that this virus might be commonly circulating in M. pusillus in Hong Kong. 
 Title: Identification of a Novel Coronavirus in Bats
Output: True
Paragraph: RLadyBug is an S4 package for the simulation, visualization and estimation of stochastic epidemic models in R. Maximum likelihood and Bayesian inference can be performed to estimate the parameters in a susceptible-exposed-infectious-recovered (SEIR) model, which is a stochastic model for describing a single outbreak of an infectious disease. The package is thus one step towards statistical software supporting parameter estimation, calculation of confidence intervals and hypothesis testing for transmission models. 
 Title: RLadyBug-An R package for stochastic epidemic models
Output: False
Paragraph: Although several reports suggest that the entry of infectious bronchitis virus (IBV) depends on lipid rafts and low pH, the endocytic route and intracellular trafficking are unclear. In this study, we aimed to shed greater light on early steps in IBV infection. By using chemical inhibitors, RNA interference, and dominant negative mutants, we observed that lipid rafts and low pH was indeed required for virus entry; IBV mainly utilized the clathrin mediated endocytosis (CME) for entry; GTPase dynamin 1 was involved in virus containing vesicle scission; and the penetration of IBV into cells led to active cytoskeleton rearrangement. By using R18 labeled virus, we found that virus particles moved along with the classical endosome/lysosome track. Functional inactivation of Rab5 and Rab7 significantly inhibited IBV infection. Finally, by using dual R18/DiOC labeled IBV, we observed that membrane fusion was induced after 1 h.p.i. in late endosome/lysosome. 
 Title: Infectious bronchitis virus entry mainly depends on clathrin mediated endocytosis and requires classical endosomal/lysosomal system
Output: True
Paragraph: Research has shown that obesity appears to spread through social ties. However, the association between other characteristics of social networks and obesity is unclear. This study aimed to identify the association between social network characteristics and body mass index (BMI, kg/m 2 ) in an elderly Korean population. : This cross-sectional study analyzed data from 657 Koreans (273 men, 384 women) aged 60 years or older who participated in the Korean Social Life, Health, and Aging Project. Network size is a count of the number of friends. Density of communication network is the number of connections in the social network reported as a fraction of the total links possible in the personal (ego-centric) network. Average frequency of communication (or meeting) measures how often network members communicate (or meet) each other. The association of each social network measure with BMI was investigated by multiple linear regression analysis. Results: After adjusting for potential confounders, the men with lower density (<0.71) and higher network size (4-6) had the higher BMI (β=1.089, p=0.037) compared to the men with higher density (>0.83) and lower size (1-2), but not in the women (p=0.393). The lowest tertile of communication frequency was associated with higher BMI in the women (β=0.885, p=0.049), but not in the men (p=0.140). Our study suggests that social network structure (network size and density) and activation (communication frequency and meeting frequency) are associated with obesity among the elderly. There may also be gender differences in this association. 
 Title: Social Network Characteristics and Body Mass Index in an Elderly Korean Population
Output: True
Paragraph: Human cytomegalovirus (HCMV) is a ubiquitous betaherpesvirus that frequently causes morbidity and mortality in individuals with insufficient immunity, such as transplant recipients, AIDS patients, and congenitally infected newborns. Several antiviral drugs are approved to treat HCMV infections. However, resistant HCMV mutants can arise in patients receiving long-term therapy. Additionally, side effects and the risk to cause birth defects limit the use of currently approved antivirals against HCMV. Therefore, the identification of new drug targets is of clinical relevance. Recent work identified DNA-damage binding protein 1 (DDB1) and the family of the cellular cullin (Cul) RING ubiquitin (Ub) ligases (CRLs) as host-derived factors that are relevant for the replication of human and mouse cytomegaloviruses. The first-in-class CRL inhibitory compound Pevonedistat (also called MLN4924) is currently under investigation as an anti-tumor drug in several clinical trials. Cytomegaloviruses exploit CRLs to regulate the abundance of viral proteins, and to induce the proteasomal degradation of host restriction factors involved in innate and intrinsic immunity. Accordingly, pharmacological blockade of CRL activity diminishes viral replication in cell culture. In this review, we summarize the current knowledge concerning the relevance of DDB1 and CRLs during cytomegalovirus replication and discuss chances and drawbacks of CRL inhibitory drugs as potential antiviral treatment against HCMV. 
 Title: Molecular Sciences Cellular Cullin RING Ubiquitin Ligases: Druggable Host Dependency Factors of Cytomegaloviruses
Output: True
Paragraph: Porcine reproductive and respiratory syndrome virus (PRRSV) represents a significantly economical challenge to the swine industry worldwide. In this study, we investigated the importance of cellular and viral lipid rafts in PRRSV infection. First, we demonstrated that PRRSV glycoproteins, Gp3 and Gp4, were associated with lipid rafts during viral entry, and disruption of cellular lipid rafts inhibited PRRSV entry. We also showed the raft-location of CD163, which might contribute to the glycoproteins-raft association. Subsequently, raft disruption caused a significant reduction of viral RNA production. Moreover, Nsp9 was shown to be distributed in rafts, suggesting that rafts probably serve as a platform for PRRSV replication. Finally, we confirmed that disassembly of rafts on the virus envelope may affect the integrity of PRRSV particles and cause the leakage of viral proteins, which impaired PRRSV infectivity. These findings might provide insights on our understanding of the mechanism of PRRSV infection. 
 Title: Lipid rafts both in cellular membrane and viral envelope are critical for PRRSV efficient infection
Output: False
Paragraph: Co-infections by multiple pathogens have important implications in many aspects of health, epidemiology and evolution. However, how to disentangle the non-linear dynamics of the immune response when two infections take place at the same time is largely unexplored. Using data sets of the immune response during influenza-pneumococcal coinfection in mice, we employ here topological data analysis to simplify and visualise high dimensional data sets. We identified persistent shapes of the simplicial complexes of the data in the three infection scenarios: single viral infection, single bacterial infection, and co-infection. The immune response was found to be distinct for each of the infection scenarios and we uncovered that the immune response during the co-infection has three phases and two transition points. During the first phase, its dynamics is inherited from its response to the primary (viral) infection. The immune response has an early shift (few hours post coinfection) and then modulates its response to react against the secondary (bacterial) infection. Between 18 and 26 h post co-infection the nature of the immune response changes again and does no longer resembles either of the single infection scenarios. 
 Title: Topological data analysis to model the shape of immune responses during co-infections
Output: True
Paragraph: Hepatitis E virus (HEV) has recently emerged to cause chronic infection in some immunosuppressed individuals, including extrahepatic manifestations in acute and chronic patients. Mammalian MAPK-JNK1/2 is expressed in hepatocytes, which is known to be involved in anti-apoptotic signaling pathway for the establishment of persistent infection. Though in vitro modulation of cellular MAPK-ERK cascade by HEV-ORF3 protein is suggested to have a role in host pathobiology, activation of the JNK module has not been studied so far. In this report, we have shown for the first time, evidence of MAPK-JNK1/2 activation by HEV-ORF3, using viral replicon as well as expression vector in human hepatoma cells. Phospho-ELISA based relative quantitaion has demonstrated *54% and *66% phosphorylation of JNK1/2 in replicon-RNA and ORF3-vector DNA transfected cells, respectively. Our finding however, suggests further molecular studies to validate a role of JNK1/2 in HEV pathogenesis. 
 Title: Evidence of MAPK-JNK1/2 activation by hepatitis E virus ORF3 protein in cultured hepatoma cells
Output: True
Paragraph: Coronavirus envelope (E) protein is a small integral membrane protein with multi-functions in virion assembly, morphogenesis and virus-host interaction. Different coronavirus E proteins share striking similarities in biochemical properties and biological functions, but seem to adopt distinct membrane topology. In this report, we study the membrane topology of the SARS-CoV E protein by immunofluorescent staining of cells differentially permeabilized with detergents and proteinase K protection assay. It was revealed that both the N-and C-termini of the SARS-CoV E protein are exposed to the cytoplasmic side of the membranes (N cyto C cyto ). In contrast, parallel experiments showed that the E protein from infectious bronchitis virus (IBV) spanned the membranes once, with the N-terminus exposed luminally and the C-terminus exposed cytoplasmically (N exo(lum) -C cyto ). Intriguingly, a minor proportion of the SARS-CoV E protein was found to be modified by N-linked glycosylation on Asn 66 and inserted into the membranes once with the C-terminus exposed to the luminal side. The presence of two distinct membrane topologies of the SARS-CoV E protein may provide a useful clue to the pathogenesis of SARS-CoV. 
 Title: Biochemical evidence for the presence of mixed membrane topologies of the severe acute respiratory syndrome coronavirus envelope protein expressed in mammalian cells
Output: True