niryuu/sni-each-converted huggingface dataset:
Paragraph: Middle East respiratory syndrome coronavirus is a contagious respiratory pathogen that is contracted via close contact with an infected subject. Transmission of the pathogen has occurred through animal-to-human contact at first followed by human-to-human contact within families and health care facilities. This study is based on a retrospective analysis of the Middle East respiratory syndrome coronavirus outbreak in the Kingdom of Saudi Arabia between June 2012 and July 2015. A Geoadditive variable model for binary outcomes was applied to account for both individual level risk factors as well spatial variation via a fully Bayesian approach. Out of 959 confirmed cases, 642 (67%) were males and 317 (33%) had died. Three hundred and sixty four (38%) cases occurred in Ar Riyad province, while 325 (34%) cases occurred in Makkah. Individuals with some comorbidity had a significantly higher likelihood of dying from MERS-CoV compared with those who did not suffer comorbidity [Odds ratio (OR) = 2.071; 95% confidence interval (CI): 1.307, 3.263]. Health-care workers were significantly less likely to die from the disease compared with non-health workers [OR = 0.372, 95% CI: 0.151, 0.827]. Patients who had fatal clinical experience and those with clinical and subclinical experiences were equally less likely to die from the disease compared with patients who did not have fatal clinical experience and those without clinical and subclinical experiences respectively. The odds of dying from the disease was found to increase as age increased beyond 25 years and was much higher for individuals with any underlying comorbidities. 
 Title: Spatial modelling of contribution of individual level risk factors for mortality from Middle East respiratory syndrome coronavirus in the Arabian Peninsula
Output: False
Paragraph: Background-While screening programs have reduced the risk of infectious disease transmission by donors in human and veterinary blood banking, bacterial contamination of blood products has emerged as a major complication in human medicine. Objectives-To describe a Pseudomonas fluorescens (Pf)-contaminated feline packed RBC (pRBC) unit and experimentally investigate Pf-contaminated canine pRBCs. Methods-Canine pRBCs were inoculated with Pf-rich pRBCs from the sentinel feline unit and stored at 4°C or 20°C for 72 hours. Aliquots from the pRBCs were serially evaluated by microscopy, culture, and a eubacterial 16S rRNA real-time PCR assay. Pf-contaminated feline unit turned black after 22 days of storage and was removed from the blood bank; a source was not found, and no other contaminated units were identified. Canine pRBCs spiked with 5 or 25 μL of the sentinel unit became culture-and/or 16S PCRpositive at ≥8 hours at 20°C and 48 hours at 4°C and developed a color change at ≥24 hours. Sensitivity studies indicated that without incubation, inoculation of ≥100 μL Pf-rich pRBCs was necessary for a positive 16S PCR test result. Conclusions-P. fluorescens grows in stored pRBCs slowly at 4°C and rapidly at 20°C. Screening of blood products for color change, estimating bacterial concentration with microscopy, and 16S PCR testing are simple and fast ways to detect bacteria in stored blood. Aseptic collection, temperature-controlled storage, and regular visual monitoring of stored units is recommended. Discolored units should not be transfused, but examined for bacterial contamination or other blood product quality problems. 
 Title: Pseudomonas fluorescens contamination of a feline packed red blood cell unit and studies of canine units
Output: False
Paragraph: This paper articulates the disproportionate policy perspective and uses it to mount four challenges for the new policy design orientation. First, in contrast to the new policy design thinking, disproportionate policy options may be systematically designed, and at times, successfully implemented. Second, in contrast to the new policy design thinking, there are certain conditions under which policymakers may tend to develop effective response, with cost considerations becoming only secondary in importance if at all (read, policy overreaction), or cost-conscious response, with effectiveness considerations becoming only secondary in importance if at all (read, policy underreaction). Third, in contrast to the new policy design thinking, disproportionate policy options may be designed for purposes other than implementation (e.g., to be used as signaling devices or as context-setters). Fourth, in contrast to new policy design thinking, there are certain conditions under which the emotional arena of policy may be equally, if not more, important than the substantive one. The paper concludes that so far the literature on new policy design has not responded to the emergence of the disproportionate policy perspective, but a robust research agenda awaits those answering this paper's call for action. 
 Title: The implications of the emerging disproportionate policy perspective for the new policy design studies
Output: False
Paragraph: Neonatal enteritis caused by the porcine epidemic diarrhea virus (PEDV) is an important cause of high mortality and economic losses to the swine industry. Virus neutralization (V/N) assays are commonly requested in diagnostic laboratories for the assessment of protective antibodies. However, the visual assessment of viral cytopathic effects by operators to determine antibody titers or for viral quantification is a tedious, subjective and time-consuming process, especially when high volume testing is involved. To improve the ease of testing, a colorimetric virus neutralization and TCID 50 assays were developed and validated in this study using (3-(4,5dimethylthiazol-2-yl) Tr-2,5-diphenyltetrazolium-bromide) (MTT), a colorimetric agent which measures cell viability. The respective conventional assays were used as the gold standards. An OD cut off value of ≤0.53, selected by receiver operating characteristics analysis, could distinguish between wells with and without CPE accurately. Performance and reproducibility parameters of the colorimetric assays were comparable to the conventional assays. The described methods can reduce testing time in diagnostic laboratories, while significantly improving current protocols. 
 Title: A convenient colorimetric assay for the quantification of porcine epidemic diarrhea virus and neutralizing antibodies
Output: True
Paragraph: In the USA, infectious diseases continue to exact a substantial toll on health and health-care resources. Endemic diseases such as chronic hepatitis, HIV, and other sexually transmitted infections aff ect millions of individuals and widen health disparities. Additional concerns include health-care-associated and foodborne infections-both of which have been targets of broad prevention eff orts, with success in some areas, yet major challenges remain. Although substantial progress in reduction of the burden of vaccine-preventable diseases has been made, continued cases and outbreaks of these diseases persist, driven by various contributing factors. Worldwide, emerging and reemerging infections continue to challenge prevention and control strategies while the growing problem of antimicrobial resistance needs urgent action. An important priority for control of infectious disease is to ensure that scientifi c and technological advances in molecular diagnostics and bioinformatics are well integrated into public health. Broad and diverse partnerships across governments, health care, academia, and industry, and with the public, are essential to eff ectively reduce the burden of infectious diseases. 
 Title: The Health of Americans 2 Challenges of infectious diseases in the USA
Output: False
Paragraph: The protein sequence-structure gap results from the contrast between rapid, low-cost deep sequencing, and slow, expensive experimental structure determination techniques. Comparative homology modelling may have the potential to close this gap by predicting protein structure in target sequences using existing experimentally solved structures as templates. This paper presents the first use of force-directed graphs for the visualization of sequence space in two dimensions, and applies them to the choice of suitable RNA-dependent RNA polymerase (RdRP) target-template pairs within human-infective RNA virus genera. Measures of centrality in protein sequence space for each genus were also derived and used to identify centroid nearest-neighbour sequences (CNNs) potentially useful for production of homology models most representative of their genera. Homology modelling was then carried out for targettemplate pairs in different species, different genera and different families, and model quality assessed using several metrics. Reconstructed ancestral RdRP sequences for individual genera were also used as templates for the production of ancestral RdRP homology models. High quality ancestral RdRP models were consistently produced, as were good quality models for target-template pairs in the same genus. Homology modelling between genera in the same family produced mixed results and inter-family modelling was unreliable. We present a protocol for the production of optimal RdRP homology models for use in further experiments, e.g. docking to discover novel anti-viral compounds. (219 words) 
 Title: Visualization of protein sequence space with force-directed graphs, and their application to the choice of target-template pairs for homology modelling
Output: True
Paragraph: The collapse of iconic, keystone populations of sockeye (Oncorhynchus nerka) and Chinook (Oncorhynchus tshawytscha) salmon in the Northeast Pacific is of great concern. It is thought that infectious disease may contribute to declines, but little is known about viruses endemic to Pacific salmon. Metatranscriptomic sequencing and surveillance of dead and moribund cultured Chinook salmon revealed a novel arenavirus, reovirus and nidovirus. Sequencing revealed two different arenavirus variants which each infect wild Chinook and sockeye salmon. In situ hybridisation localised arenavirus mostly to blood cells. Population surveys of >6000 wild juvenile Chinook and sockeye salmon showed divergent distributions of viruses, implying different epidemiological processes. The discovery in dead and dying farmed salmon of previously unrecognised viruses that are also widely distributed in wild salmon, emphasizes the potential role that viral disease may play in the population dynamics of wild fish stocks, and the threat that these viruses may pose to aquaculture. 
 Title: Endangered wild salmon infected by newly discovered viruses
Output: True
Paragraph: Background: Members of the Baculoviridae encode two types of proteins that mediate virus:cell membrane fusion and penetration into the host cell. Alignments of primary amino acid sequences indicate that baculovirus fusion proteins of group I nucleopolyhedroviruses (NPV) form the GP64 superfamily. The structure of these viral penetrenes has not been determined. The GP64 superfamily includes the glycoprotein (GP) encoded by members of the Thogotovirus genus of the Orthomyxoviridae. The entry proteins of other baculoviruses, group II NPV and granuloviruses, are class I penetrenes. Results: Class III penetrenes encoded by members of the Rhabdoviridae and Herpesviridae have an internal fusion domain comprised of beta sheets, other beta sheet domains, an extended alpha helical domain, a membrane proximal stem domain and a carboxyl terminal anchor. Similar sequences and structural/functional motifs that characterize class III penetrenes are located collinearly in GP64 of group I baculoviruses and related glycoproteins encoded by thogotoviruses. Structural models based on a prototypic class III penetrene, vesicular stomatitis virus glycoprotein (VSV G), were established for Thogoto virus (THOV) GP and Autographa california multiple NPV (AcMNPV) GP64 demonstrating feasible cysteine linkages. Glycosylation sites in THOV GP and AcMNPV GP64 appear in similar model locations to the two glycosylation sites of VSV G. These results suggest that proteins in the GP64 superfamily are class III penetrenes. 
 Title: Virology Journal Proteomics computational analyses suggest that baculovirus GP64 superfamily proteins are class III penetrenes
Output: False
Paragraph: Like most viruses that replicate in the cytoplasm, mammalian reoviruses assemble membranous neo-organelles called inclusions that serve as sites of viral genome replication and particle morphogenesis. Viral inclusion formation is essential for viral infection, but how these organelles form is not well understood. We investigated the biogenesis of reovirus inclusions. Correlative light and electron microscopy showed that endoplasmic reticulum (ER) membranes are in contact with nascent inclusions, which form by collections of membranous tubules and vesicles as revealed by electron tomography. ER markers and newly synthesized viral RNA are detected in inclusion internal membranes. Live-cell imaging showed that early in infection, the ER is transformed into thin cisternae that fragment into small tubules and vesicles. We discovered that ER tubulation and vesiculation are mediated by the reovirus NS and NS proteins, respectively. Our results enhance an understanding of how viruses remodel cellular compartments to build functional replication organelles. IMPORTANCE Viruses modify cellular structures to build replication organelles. These organelles serve as sites of viral genome replication and particle morphogenesis and are essential for viral infection. However, how these organelles are constructed is not well understood. We found that the replication organelles of mammalian reoviruses are formed by collections of membranous tubules and vesicles derived from extensive remodeling of the peripheral endoplasmic reticulum (ER). We also observed that ER tubulation and vesiculation are triggered by the reovirus NS and NS proteins, respectively. Our results enhance an understanding of how viruses remodel cellular compartments to build functional replication organelles and provide functions for two enigmatic reovirus replication proteins. Most importantly, this research uncovers a new mechanism by which viruses form factories for particle assembly. 
 Title: Reovirus NS and NS Proteins Remodel the Endoplasmic Reticulum to Build Replication Neo-Organelles
Output: True
Paragraph: Upon recognition of viral components by pattern recognition receptors, such as the toll-like receptors (TLRs) and retinoic acid-inducible gene I (RIG-I)-like helicases, cells are activated to produce type I interferon (IFN) and proinflammatory cytokines. These pathways are tightly regulated by the host to prevent an inappropriate cellular response, but viruses can modulate these pathways to proliferate and spread. In this study, we revealed a novel mechanism in which hepatitis C virus (HCV) evades the immune surveillance system to proliferate by activating microRNA-21 (miR-21). We demonstrated that HCV infection upregulates miR-21, which in turn suppresses HCV-triggered type I IFN production, thus promoting HCV replication. Furthermore, we demonstrated that miR-21 targets two important factors in the TLR signaling pathway, myeloid differentiation factor 88 (MyD88) and interleukin-1 receptor-associated kinase 1 (IRAK1), which are involved in HCV-induced type I IFN production. HCV-mediated activation of miR-21 expression requires viral proteins and several signaling components. Moreover, we identified a transcription factor, activating protein-1 (AP-1), which is partly responsible for miR-21 induction in response to HCV infection through PKCe/JNK/c-Jun and PKCa/ERK/c-Fos cascades. Taken together, our results indicate that miR-21 is upregulated during HCV infection and negatively regulates IFN-a signaling through MyD88 and IRAK1 and may be a potential therapeutic target for antiviral intervention. 
 Title: HCV-Induced miR-21 Contributes to Evasion of Host Immune System by Targeting MyD88 and IRAK1
Output: False
Paragraph: publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active. The Microbiology of Respiratory System Infections. http://dx. The variant 1 of the human bocavirus (HBoV-1) that causes respiratory infections in primates and humans belongs to the family of Parvoviridae, subfamily Parvovirinae, genus Bocaparvovirus, was discovered originally in 2005 by Tobias Allander 1 and his team and represents together with the strains HBoV-3 and the gorilla bocavirus the species Primate bocaparvovirus 1. 2 The discovery of HBoV-1 was one among a series of virus discoveries in the first decade of our millennium that was based on novel virus discovery systems developed in order to reduce the considerable number of cases in which a clinical diagnosis of a respiratory infection could not be confirmed by detection of a pathogen. Following the initial description of the virus, a huge number of clinical studies and case reports have been published which were supplemented by some basic research reports. Unfortunately, HBoV research still relies on clinical studies and case reports with accompanying cell culture studies as the major source of information on HBoV biology, as so far no animal model has been identified. 
 Title: RESPIRATORY INFECTIONS OF THE HUMAN BOCAVIRUS
Output: True
Paragraph: Background: Taiwan has been considered free from canine parvovirus type 2c (CPV-2c) based on the last report of canine parvovirus type 2 (CPV-2) surveillance. However, since January 2015, the first report of CPV-2c in a puppy has occurred in Taiwan. There is currently limited information about the CPV-2c variant in Taiwan. In the present study, we characterized the previously unidentified CPV-2c variant and investigated the distribution of CPV-2 variants in Taiwan. Methods: During January 2014 to April 2016, fecal or rectal swab samples from 99 dogs with suspected CPV-2 infection in Taiwan were collected. Eighty-eight were identified as being either CPV-2a, −2b or -2c variants positive by real-time PCR and sequence analysis. Results: Sequence analysis of the 88 isolates confirmed CPV-2c as the dominant variant (54.6 %), followed by CPV-2b (26.1 %) and . Phylogenetic analysis demonstrated that the recent CPV-2c variants are similar to the Chinese CPV-2c strain but can be considered as novel Asian CPV-2c isolates. Conclusion: The present study provides evidence for the existence of a novel CPV-2c variant in Taiwan. 
 Title: Identification of a novel canine parvovirus type 2c in Taiwan
Output: True
Paragraph: Objective The aim of this study was to explore the prevalent characteristics of HBoV1 and its co-infection. Methods PCR was used to detect HBoV1-DNA (HBoV1) and other viruses. A multivariate logistic regression model was used to explore possibility of co-detected for related viruses. The positivity rates in Nanjing and Lanzhou were 9.38% (74/789) and 11.62% (161/1386), respectively (P>0.05). The HBoV1 positive group was younger than negative group (P<0.05). Seasonal differences were noted, with a higher frequency of infection in December and July. HBoV1-positive children [72.34% (169/235)] were co-infected with other respiratory viruses. Multifactorial analysis showed no correlations between HBoV1 and the clinical classification, region, gender, age, or treatment as an outpatient or in a hospital. Correlations were identified between HBoV1 infections with ADV (OR=1.53, 95% CI 1.03-2.28), RSV (OR=0.71, 95% CI 0.52-0.98), and IFVA (OR=1.77, 95% CI 1.00-3.13). Conclusions Presence of HBoV1 in nasopharyngeal aspirates did not correlate with region or gender, although the prevalence of HBoV1 was higher in younger children. There were no correlations between HBoV1 and other variables, except for the season and ADV, RSV, or IFVA infections. 
 Title: Original Article Detection of Human Bocavirus in Children with Acute Respiratory Tract Infections in Lanzhou and Nanjing, China *
Output: False
Paragraph: The serological response profile of severe acute respiratory syndrome (SARS) coronavirus (CoV) infection was defined by neutralization tests and subclass-specific immunofluorescent (IF) tests using serial sera from 20 patients. SARS CoV total immunoglobulin (Ig) (IgG, IgA, and IgM [IgGAM]) was the first antibody to be detectable. There was no difference in time to seroconversion between the patients who survived (n ‫؍‬ 14) and those who died (n ‫؍‬ 6). Although SARS CoV IgM was still detectable by IF tests with 8 of 11 patients at 7 months postinfection, the geometric mean titers dropped from 282 at 1 month postinfection to 19 at 7 months (P ‫؍‬ 0.001). In contrast, neutralizing antibody and SARS CoV IgGAM and IgG antibody titers remained stable over this period. The SARS CoV antibody response was sometimes associated with an increase in preexisting IF IgG antibody titers for human coronaviruses OC43, 229E, and NL63. There was no change in IF IgG titer for virus capsid antigen from the herpesvirus that was used as an unrelated control, Epstein-Barr virus. In contrast, patients who had OC43 infections, and probably also 229E infections, without prior exposure to SARS CoV had increases of antibodies specific for the infecting virus but not for SARS CoV. There is a need for awareness of cross-reactive antibody responses between coronaviruses when interpreting IF serology. 
 Title: Serological Responses in Patients with Severe Acute Respiratory Syndrome Coronavirus Infection and Cross-Reactivity with Human Coronaviruses 229E, OC43, and NL63
Output: True
Paragraph: Monoclonal antibodies (MAbs) directed against herpes simplex virus (HSV)-coded glycoproteins gB, gC, gD and gE were employed in an in vitro model of neuroinvasiveness using sensory neurons from rat dorsal root ganglion (DRG) cells . The neurons were cultured in a two-chamber system allowing infection via the neuritic extensions exclusively . The effects of 30 MAbs on viral replication of the encephalitis-derived HSV-1 strain 2762 and its less neuroinvasive variant 2762p11 were assayed in this model . One MAb reactive with gD gave a nine-fold reduction of the virus yields of both strains . One MAb directed against gB gave an enhanced virus yield of strain 2762, but not of the 2762p11 variant . Another gB-reactive MAb decreased the virus yield of strain 2762pll, but not of 2762 after neuritic infection . The findings indicate that an alteration of gB has occurred during the passage of the strain 2762 . Mutants of the same strain were derived by infecting hybridomas producing MAb reactive with gB, gC, gD and gE, respectively . The gB hybridoma mutant showed a significantly lower neuroinvasiveness in the DRG model, and was non-virulent after snout infection of mice . We suggest that the structure of gB of the strain 2762 is of importance for the neuroinvasiveness of this strain . 
 Title: Mapping neuroinvasiveness of the herpes simplex virus type 1 encephalitis-inducing strain 2762 by the use of monoclonal antibodies
Output: True
Paragraph: Object Meteorological parameters are the important factors influencing the infectious diseases like severe acute respiratory syndrome (SARS). in Wuhan, China. Then, the generalized additive model was applied to explore the impact of temperature, humidity and diurnal temperature range on daily mortality of COVID-19. There were in total 2299 COVID-19 mortality counts in Wuhan. A positive association with COVID-19 mortality was observed for diurnal temperature range (r = 0.44), but negative association for relative humidity (r = −0.32). In addition, each 1 unit increase in diurnal temperature range was only associated with a 2.92% (95% CI: 0.61%, 5.28%) increase in COVID-19 mortality at lag 3. However, both per 1 unit increase of temperature and absolute humidity were related to the decreased COVID-19 mortality at lag 3 and lag 5, respectively. In summary, this study suggests the temperature variation and humidity may be important factors affecting the COVID-19 mortality. 
 Title: Effects of temperature variation and humidity on the mortality of COVID-19 in Wuhan
Output: False
Paragraph: Human memory B cells and plasma cells represent a rich source of antibodies that have been selected in response to human pathogens. In the last decade, different methods have been developed to interrogate the human memory repertoire and isolate monoclonal antibodies. I will discuss how a target-agnostic approach based on highthroughput screening of antibodies produced by cultured B cells and plasma cells has not only provided potent and broadly neutralizing antibodies against a range of pathogens, but has also advanced our understanding of basic aspects of the immune response, from host-pathogen interaction to the role of somatic mutations in affinity maturation and in the diversification of the antibody response. Most surprisingly, this approach has also revealed a new mechanism of diversification based on templated insertion of non-Ig DNA into antibody genes that we discovered in the context of the immune response to malaria infection. 
 Title: Louis-Jeantet Prize Winner: Commentary Dissecting human antibody responses: useful, basic and surprising findings
Output: False
Paragraph: In this review we discuss studies that applied atmospheric dispersion models (ADM) to bioaerosols that are pathogenic to humans and livestock in the context of risk assessment studies. Traditionally, ADMs have been developed to describe the atmospheric transport of chemical pollutants, radioactive matter, dust, and particulate matter. However, they have also enabled researchers to simulate bioaerosol dispersion. To inform risk assessment, the aims of this review were fourfold, namely (1) to describe the most important physical processes related to ADMs and pathogen transport, (2) to discuss studies that focused on the application of ADMs to pathogenic bioaerosols, (3) to discuss emission and inactivation rate parameterisations, and (4) to discuss methods for conversion of concentrations to infection probabilities (concerning quantitative microbial risk assessment). The studies included human, livestock, and industrial sources. Important factors for dispersion included wind speed, atmospheric stability, topographic effects, and deposition. Inactivation was mainly governed by humidity, temperature, and ultraviolet radiation. A majority of the reviewed studies, however, lacked quantitative analyses and application of full quantitative microbial risk assessments (QMRA). Qualitative conclusions based on geographical dispersion maps and threshold doses were encountered frequently. Thus, to improve risk assessment for future outbreaks and releases, we recommended determining well-quantified emission and inactivation rates and applying dosimetry and dose-response models to estimate infection probabilities in the population at risk. 
 Title: Atmospheric dispersion modelling of bioaerosols that are pathogenic to humans and livestock -A review to inform risk assessment studies
Output: True
Paragraph: J o u r n a l P r e -p r o o f Highlights • As of 10 March 2020, Italy has reported 9,172 COVID-19 cases with 463 deaths. • We reported real-time reproductive numbers (R(t))and case fatality rate in in selected European countries (Italy, France, Germany, and Spain) by 9 March 2020. • The R(t) was greater than 2 in the selected European countries, indicating the outbreak will continue. Objectives: As a global pandemic is inevitable, real-time monitoring of transmission is vital for containing the spread of COVID-19. The main objective was to report real-time effective reproduction numbers (R(t)) case fatality rate (CFR). Methods: Data were mainly obtained from WHO website, up to 9 March 2020. R(t) was estimated by exponential growth rate (EG) and time dependent (TD) methods. "R0" package in R was employed to estimate R(t) by fitting the existing epidemic curve. Both naïve CFR (nCFR) and adjust CFR (aCFR) were estimated. : In EG method, R(t) was 3.27 [3.17-3.38] for Italy, 6.32 [5.72-6.99] for France, 6.07 [5.51-6.69] for Germany, 5.08 [4.51-5.74] for Spain. With TD method, the R value for March 9 was 3.10 J o u r n a l P r e -p r o o f [2.21-4.11] for Italy, 6.56 [2.04-12.26] for France, 4.43 [1.83-7.92] for Germany, and 3.95 [0-10.19] for Spain. Conclusions: This study provides important findings on an early outbreak of COVID-19 in Europe. Due to the recent rapid increase in new cases of COVID-19, real-time monitoring of the transmissibility and mortality in Spain and France is a priority J o u r n a l P r e -p r o o f disease 2019 in China. N Engl J Med. 2020; 9. Kucharski AJ, Edmunds WJ. Case fatality rate for Ebola virus disease in west Africa. Lancet. 2014;384(9950):1260. J o u r n a l P r e -p r o o f 
 Title: Journal Pre-proof Monitoring Transmissibility and Mortality of COVID-19 in Europe TITLE PAGE Monitoring Transmissibility and Mortality of COVID-19 in Europe
Output: True
Paragraph: Background. Immunotherapy with monoclonal antibodies (MAbs) offers safe interventions for the prevention of infection in patients after organ transplantation and for the treatment of cancers and autoimmune diseases. MAb 201 is a severe acute respiratory syndrome-associated coronavirus (SARS-CoV)-specific MAb that prevents establishment of viral replication in vitro and prevents viral replication in vivo when administered prophylactically. The efficacy of MAb 201 in the treatment of SARS was evaluated in golden Syrian hamsters, an animal model that supports SARS-CoV replication to high levels and displays severe pathological changes associated with infection, including pneumonitis and pulmonary consolidation. Methods. Golden Syrian hamsters that were intranasally inoculated with SARS-CoV were treated with various doses of MAb 201 or an irrelevant MAb 24 h after inoculation. Two to 7 days after infection, the hamsters were killed, and their lungs were collected for evaluation of viral titers and pathological findings. Results. Postexposure treatment with MAb 201 can alleviate the viral burden and associated pathological findings in a golden Syrian hamster model of SARS-CoV infection. After a hamster is treated with MAb 201, its viral burden is reduced by -50% tissue-culture infectious doses per gram of tissue, and the severity of 2.4 3.9 10 10 associated pathological findings, including interstitial pneumonitis and consolidation, is also remarkably reduced. Conclusions. The demonstration of successful postexposure MAb 201 therapy in an animal model that demonstrates viral replication and associated pulmonary pathological findings suggests that MAb 201 may be useful in the arsenal of tools to combat SARS. In late 2002, severe acute respiratory syndrome-associated coronavirus (SARS-CoV) was identified as the 
 Title: Therapy with a Severe Acute Respiratory Syndrome- Associated Coronavirus-Neutralizing Human Monoclonal Antibody Reduces Disease Severity and Viral Burden in Golden Syrian Hamsters
Output: True
Paragraph: study, we present the results of comprehensive bioinformatics analyses of the abundance and roles of intrinsic disorder in 3,411 ribosomal proteins from 32 species. We show that many ribosomal proteins are intrinsically disordered or hybrid proteins that contain ordered and disordered domains. Predicted globular domains of many ribosomal proteins contain noticeable regions of intrinsic disorder. We also show that disorder in ribosomal proteins has different characteristics compared to other proteins that interact with RNa and DNa including overall abundance, evolutionary conservation, and involvement in protein-protein interactions. Furthermore, intrinsic disorder is not only abundant in the ribosomal proteins, but we demonstrate that it is absolutely necessary for their various functions. Abstract Intrinsic disorder (i.e., lack of a unique 3-D structure) is a common phenomenon, and many biologically active proteins are disordered as a whole, or contain long disordered regions. these intrinsically disordered proteins/regions constitute a significant part of all proteomes, and their functional repertoire is complementary to functions of ordered proteins. In fact, intrinsic disorder represents an important driving force for many specific functions. an illustrative example of such disordercentric functional class is RNa-binding proteins. In this Z. Peng and C. J. Oldfield contributed equally to this study. Electronic supplementary material the online version of this article ( 
 Title: A creature with a hundred waggly tails: intrinsically disordered proteins in the ribosome
Output: False
Paragraph: Background: Health officials face particular challenges in communicating with the public about emerging infectious diseases of unknown severity such as the 2009 H1N1(swine 'flu) pandemic (pH1N1). Statements intended to create awareness and convey the seriousness of infectious disease threats can draw accusations of scaremongering, while officials can be accused of complacency if such statements are not made. In these communication contexts, news journalists, often reliant on official sources to understand issues are pivotal in selecting and emphasising aspects of official discourse deemed sufficiently newsworthy to present to the public. This paper presents a case-study of news communication regarding the emergence of pH1N1. Methods: We conducted a content analysis of all television news items about pH1N1. We examined news and current affairs items broadcast on 5 free-to-air Sydney television channels between April 25 2009 (the first report) and October 9 (prior to the vaccine release) for statements about [1] the seriousness of the disease [2] how the public could minimise contagion [3] government responses to emerging information. Results: pH1N1 was the leading health story for eight of 24 weeks and was in the top 5 for 20 weeks. 353 news items were identified, yielding 3086 statements for analysis, with 63.4% related to the seriousness of the situation, 12.9% providing advice for viewers and 23.6% involving assurances from government. Coverage focused on infection/mortality rates, the spread of the virus, the need for public calm, the vulnerability of particular groups, direct and indirect advice for viewers, and government reassurances about effective management. Conclusions: Overall, the reporting of 2009 pH1N1 in Sydney, Australia was generally non-alarmist, while conveying that pH1N1 was potentially serious. Daily infection rate tallies and commentary on changes in the pandemic alert level were seldom contextualised to assist viewers in understanding personal relevance. Suggestions are made about how future reporting of emerging infectious diseases could be enhanced. 
 Title: Communicating uncertainty -how Australian television reported H1N1 risk in 2009: a content analysis
Output: True
Paragraph: The use of N95 respirators prevents spread of respiratory infectious agents, but leakage hampers its protection. Manufacturers recommend a user seal check to identify on-site gross leakage. However, no empirical evidence is provided. Therefore, this study aims to examine validity of a user seal check on gross leakage detection in commonly used types of N95 respirators. Methods: A convenience sample of 638 nursing students was recruited. On the wearing of 3 different designs of N95 respirators, namely 3M-1860s, 3M-1862, and Kimberly-Clark 46827, the standardized user seal check procedure was carried out to identify gross leakage. Repeated testing of leakage was followed by the use of a quantitative fit testing (QNFT) device in performing normal breathing and deep breathing exercises. Sensitivity, specificity, predictive values, and likelihood ratios were calculated accordingly. Results: As indicated by QNFT, prevalence of actual gross leakage was 31.0%-39.2% with the 3M respirators and 65.4%-65.8% with the Kimberly-Clark respirator. Sensitivity and specificity of the user seal check for identifying actual gross leakage were approximately 27.7% and 75.5% for 3M-1860s, 22.1% and 80.5% for 3M-1862, and 26.9% and 80.2% for Kimberly-Clark 46827, respectively. Likelihood ratios were close to 1 (range, 0.89-1.51) for all types of respirators. The results did not support user seal checks in detecting any actual gross leakage in the donning of N95 respirators. However, such a check might alert health care workers that donning a tightfitting respirator should be performed carefully. 
 Title: Evaluation of the user seal check on gross leakage detection of 3 different designs of N95 filtering facepiece respirators
Output: False
Paragraph: Reproductive success in the eight founder strains of the Collaborative Cross (CC) was measured using a diallel-mating scheme. Over a 48-month period we generated 4,448 litters, and provided 24,782 weaned pups for use in 16 different published experiments. We identified factors that affect the average litter size in a cross by estimating the overall contribution of parent-of-origin, heterosis, inbred, and epistatic effects using a Bayesian zero-truncated overdispersed Poisson mixed model. The phenotypic variance of litter size has a substantial contribution (82%) from unexplained and environmental sources, but no detectable effect of seasonality. Most of the explained variance was due to additive effects (9.2%) and parental sex (maternal vs. paternal strain; 5.8%), with epistasis accounting for 3.4%. Within the parental effects, the effect of the dam's strain explained more than the sire's strain (13.2% vs. 1.8%), and the dam's strain effects account for 74.2% of total variation explained. Dams from strains C57BL/6J and NOD/ShiLtJ increased the expected litter size by a mean of 1.66 and 1.79 pups, whereas dams from strains WSB/EiJ, PWK/PhJ, and CAST/EiJ reduced expected litter size by a mean of 1.51, 0.81, and 0.90 pups. Finally, there was no strong evidence for strain-specific effects on sex ratio distortion. Overall, these results demonstrate that strains vary substantially in their reproductive ability depending on their genetic background, and that litter size is largely determined by dam's strain rather than sire's strain effects, as expected. This analysis adds to our understanding of factors that influence litter size in mammals, and also helps to explain breeding successes and failures in the extinct lines and surviving CC strains. KEYWORDS 
 Title: A Diallel of the Mouse Collaborative Cross Founders Reveals Strong Strain-Specific Maternal Effects on Litter Size
Output: False
Paragraph: The recently reported Middle East respiratory syndrome coronavirus (MERS-CoV) is phylogenetically closely related to the bat coronaviruses (BatCoVs) HKU4 and HKU5. However, the evolutionary pathway of MERS-CoV is still unclear. A receptor binding domain (RBD) in the MERS-CoV envelope-embedded spike protein specifically engages human CD26 (hCD26) to initiate viral entry. The high sequence identity in the viral spike protein prompted us to investigate if HKU4 and HKU5 can recognize hCD26 for cell entry. We found that HKU4-RBD, but not HKU5-RBD, binds to hCD26, and pseudotyped viruses embedding HKU4 spike can infect cells via hCD26 recognition. The structure of the HKU4-RBD/hCD26 complex revealed a hCD26-binding mode similar overall to that observed for MERS-RBD. HKU4-RBD, however, is less adapted to hCD26 than MERS-RBD, explaining its lower affinity for receptor binding. Our findings support a bat origin for MERS-CoV and indicate the need for surveillance of HKU4-related viruses in bats. 
 Title: Article Bat Origins of MERS-CoV Supported by Bat Coronavirus HKU4 Usage of Human Receptor CD26
Output: False
Paragraph: The response to the novel coronavirus outbreak in China suggests that many of the lessons from the 2003 SARS epidemic have been implemented and the response improved as a consequence. Nevertheless some questions remain and not all lessons have been successful. The national and international response demonstrates the complex link between public health, science and politics when an outbreak threatens to impact on global economies and reputations. The unprecedented measures implemented in China are a bold attempt to control the outbreakwe need to understand their effectiveness to balance costs and benefits for similar events in the future. 
 Title: Epidemiology and Infection SARS to novel coronavirus -old lessons and new lessons
Output: False
Paragraph: We review the basic concepts of intervention analysis in the context of structural time series models and we apply this methodology to investigate the possible reduction in monthly crime rates reported from January 1984 up to and including December 2010 after Virginia abolished parole and reformed sentencing in January 1995. We find that the change in legislation has significantly reduced the burglary rates and to a lesser extent the murder rates in Virginia. The robustness of our results is investigated with an automatic detection of breaks procedure as well as with analyses of quarterly rather than monthly data. 
 Title: Intervention time series analysis of crime rates: The case of sentence reform in Virginia
Output: True
Paragraph: Rhinovirus (RV) role in pathogenesis of severe childhood disease remains controversial. We aimed to explore the association between RV molecular subtyping, nasopharyngeal viral loads and viremia with childhood pneumonia. Nasopharyngeal and blood samples from cases and controls were tested for RV and the 5′ non-coding region sequenced. The cases compared to controls had a similar prevalence of RV detection in the nasopharynx (23 % vs. 22 %, P = 0.66), similar RV species distribution (A, B, C = 44 %, 8%, 44 % vs. 48 %, 7%, 38 %; respectively; P = 0.66) and similar viral load (4.0 and 3.7 log10 copies/mL, P = 0.062). However, RV-viremia was 4.01-fold (aOR 95 % CI: 1.26-12.78) more prevalent among cases (7%) than controls (2%), P = 0.019. Furthermore, among cases and controls RV-C was more commonly associated with viremia (14 % and 4%, P = 0.023), than RV-A (2% and 1%; P = 0.529). Thus RV-viremia could be used as a measure for attributing causality to RV in children hospitalized for pneumonia. 
 Title: A prospective case-control study on the association of Rhinovirus nasopharyngeal viral load and viremia in South African children hospitalized with severe pneumonia
Output: False
Paragraph: To develop CpG oligodeoxynucleotides (CpG ODNs) based therapy for prevention and treatment of severe acute respiratory syndrome (SARS), we selected a novel CpG ODN (BW001), which displays B-type CpG ODN structure feature at the 5V and A-type CpG ODN structure feature at the 3V, and tested for its anti-SARS-CoV activity. We found that the supernatants of human PBMCs stimulated by BW001 significantly protected Vero cells from SARS-CoV infection. BW001 could stimulate human PBMCs and pDCs to secrete high level of IFN-a and promote human PBMCs and B cells to proliferate. Furthermore, we demonstrated that BW001 could activate CD19 + B cells and CD56 + NK cells in human PBMCs. In addition, BW001 could enhance NK cytotoxicity and IFN-g secretion in human PBMCs. Together, BW001 represents a novel type of CpG ODN and may have potential for the development of treatment and prevention for SARS as well as other viral associated diseases. D 
 Title: Anti-SARS-CoV immunity induced by a novel CpG oligodeoxynucleotide
Output: False
Paragraph: Maternally-derived antibody to enterotropic mouse hepatitis virus (MHV) strain Y was transferred to pups by both intrauterine (IgG) and lactogenic (IgA and IgG) routes. Antibody present in the gastric whey of pups suckling immune dams dropped to undetectable levels by weaning age (21 days post partum). MHV-specific IgG was found in the serum of passively immune pups up to 10 weeks of age. Immune dams transferred equal levels of antibody to 3 consecutive litters of pups, without evidence of decline. Immunoblots showed that IgA and IgG in whey and serum were directed against nucleoprotein N and glycoprotein S. MHV-specific IgM was not detected in any sample. 
 Title: Maternally-derived passive immunity to enterotropic mouse hepatitis virus
Output: False
Paragraph: Innate immunity and adaptive immunity play critical roles in maintaining normal physiological functions and the development of diseases. In innate immune responses, heterogeneous autophagy can directly remove intracellular pathogens while activating PRRs, including TLRs and NLRs, to trigger their signal transduction pathways and promote NKT cell activation, cytokine secretion, and phagocytosis. In adaptive immune responses, the autophagy reaction has an important effect on the homeostasis, function, and differentiation of T lymphocytes, the survival, and development of B lymphocytes and the survival of plasma cells. This review highlights the key role that autophagy plays in the innate immune system and the acquired immune system. Further clarifying the mechanism by which autophagy regulates the immune system is essential for elucidating the precise mechanisms of various diseases and for developing new treatment methods. 
 Title: Autophagy and the Immune Response
Output: True
Paragraph: This paper discusses actions aimed at sustainable management of healthcare wastes (HCW) in China, taking into account the current national situation in this field, as well as the requirements deriving from the Stockholm Convention on Persistent Organic Pollutants and the WHO recommendations. By the end of 2005, there were 149 low-standard HCW disposal facilities in operation in China, distributed throughout different areas. According to the National Hazardous Waste and Healthcare Waste Disposal Facility Construction Plan, 331 modern, high-standard, centralized facilities will be built up in China in municipal level cities. Although incineration is still the main technical option for HCW disposal in China, it is expected that, especially for medium and small size facilities, non-incineration technologies will develop quickly and will soon become the main technical option. The basic management needs -both from the point of view of pollution control and final disposal -have been defined, and a system of technical and environmental standards has been formulated and implemented; however, there are still some shortages. This is particularly true when considering the best available techniques and best environmental practices developed under the Stockholm Convention, with which the present technological and managing situations are not completely compliant. In this framework, the lifecycle (from generation to final disposal of wastes) of HCW and holistic approaches (technology verification, facilities operation, environmental supervision, environmental monitoring, training system, financial mechanism, etc.) towards HCW management are the most important criteria for the sustainable and reliable management of HCW in China. 
 Title: Sustainable management measures for healthcare waste in China
Output: True