niryuu/sni-each-converted huggingface dataset:
Paragraph: Rhinovirus (RV) is a frequent pathogen in young children, eliciting symptoms ranging from common colds to wheezing illnesses and lower respiratory tract infections. The recently identified RV-C seems to be associated with asthma exacerbations and more severe disease, but results vary. We studied the prevalence and severity of infection with RV in an unselected birth cohort. Children with respiratory symptoms entered the symptomatic arm of the cohort and were compared with asymptomatic children. Severity of wheezing and other respiratory symptoms was registered. Respiratory viruses were evaluated using throat and nasopharyngeal swabs on first presentation and after recovery (wheezing children). RV genotyping was performed on RV-PCR positive samples. RV was the most prevalent respiratory virus and was found in 58/140 symptomatic children (41%), 24/96 (25%) control children and 19/74 (26%) wheezing symptomatic children after recovery (p <0.05) and did not differ between wheezing and non-wheezing symptomatic childrendrespectively, 42% (38/90) and 40% (20/50). RV-A was the most commonly detected species (40/68, 59%), followed by RV-C (22/68, 32%) and RV-B (6/68, 9%). RV-B was more frequently detected in asymptomatic children (5/6, p <0.05). There was no significant difference in the frequency of RV species between wheezing and non-wheezing symptomatic children. Children with RV mono-infection had more severe symptoms, but no association between RV species and severity of disease was seen. In an unselected birth cohort from the Netherlands with mild respiratory disease RV was the most prevalent respiratory virus. RV(-C) infection was not associated with more severe disease or wheezing. J.G. Wildenbeest, CMI 2016;22:736.e9e736.e15  
 Title: Prevalence of rhinoviruses in young children of an unselected birth cohort from the Netherlands
Output: True
Paragraph: This study was conducted to determine the perceptions of zoonotic disease risk among Australian veterinarians, the infection control practices they use to protect themselves from zoonotic diseases, and the factors influencing their use of these protective practices. A questionnaire was designed and piloted prior to its administration to veterinarians at the annual Australian Veterinary Association Conference in May 2011. The questionnaire comprised 21 closed, semi-closed and open questions. Data from the questionnaire were analyzed using ordinal logistic regression analyses to determine significant factors for veterinarians' use of personal protective equipment (PPE). A total of 344 veterinarians completed the questionnaire of which 63.7% were women, 63.2% worked in small/companion animal practice, and 79.9% worked in private veterinary practice. Of the respondents, 44.9% reported contracting a zoonosis during their careers with 19.7% reporting a suspected case and 25.2% reporting a confirmed incidence. Around 40-60% of veterinarians perceived exposure to zoonosis likely or very likely in a variety of situations. With reference to current national industry guidelines, the reported use of PPE was less than "adequate" for most scenarios except for performing postmortems, surgery or dental procedures. No PPE was used by 60-70% of veterinarians for treating respiratory and neurological cases and by 40-50% when treating gastrointestinal and dermatological cases. Workplace conditions need improvement as 34.8% of workplaces did not have isolation units for infected animals, 21.1% did not have separate eating areas for staff, and 57.1% did not have complete PPE kits for use. Veterinarians were more likely to use PPE if they had undertaken postgraduate education, perceived that zoonosis exposure from animals and procedures was likely, consciously considered PPE use for every case they dealt with and believed that liability issues and risks encouraged use of PPE. In contrast, those working in private practices, those who tended to 'just hope for the best' when trying to avoid zoonotic diseases, and those who were not aware of industry guidelines were less likely to use PPE. The results suggest that veterinarians' perceptions and workplace policies and culture substantially influence their use of PPE. Efforts should be made to encourage veterinarians and their workplaces to use infection control practices to protect themselves and their staff from zoonotic diseases. 
 Title: Zoonotic disease risk perceptions and infection control practices of Australian veterinarians: Call for change in work culture
Output: True
Paragraph: Background: Influenza-like illness (ILI) may be caused by a variety of pathogens. Clinical observations are of little help to recognise myxovirus infection and implement appropriate prevention measures. The limited use of molecular tools underestimates the role of other common pathogens. Objectives: During the early weeks of the 2009-2010 flu pandemic, a clinical and virological survey was conducted in adult and paediatric patients with ILI referred to two French University hospitals in Paris and Tours. Aims were to investigate the different pathogens involved in ILI and describe the associated symptoms. Methods: H1N1v pandemic influenza diagnosis was performed with real time RT-PCR assay. Other viral aetiologies were investigated by the molecular multiplex assay RespiFinder19H. Clinical data were collected prospectively by physicians using a standard questionnaire. Results: From week 35 to 44, endonasal swabs were collected in 413 patients. Overall, 68 samples (16.5%) were positive for H1N1v. In 13 of them, other respiratory pathogens were also detected. Among H1N1v negative samples, 213 (61.9%) were positive for various respiratory agents, 190 in single infections and 23 in mixed infections. The most prevalent viruses in H1N1v negative single infections were rhinovirus (62.6%), followed by parainfluenza viruses (24.2%) and adenovirus (5.3%). 70.6% of H1N1v cases were identified in patients under 40 years and none after 65 years. There was no difference between clinical symptoms observed in patients infected with H1N1v or with other pathogens. Our results highlight the high frequency of non-influenza viruses involved in ILI during the pre-epidemic period of a flu alert and the lack of specific clinical signs associated with influenza infections. Rapid diagnostic screening of a large panel of respiratory pathogens may be critical to define and survey the epidemic situation and to provide critical information for patient management. 
 Title: High Burden of Non-Influenza Viruses in Influenza-Like Illness in the Early Weeks of H1N1v Epidemic in France
Output: True
Paragraph: Although the initial outbreaks of the deadly coronavirus that causes severe acute respiratory syndrome (SARS-CoV) were controlled by public health measures, the development of vaccines and antiviral agents for SARS-CoV is essential for improving control and treatment of future outbreaks. One potential target for SARS-CoV antiviral drug development is the 3C-like protease (3CLpro). This enzyme is an attractive target since it is essential for viral replication, and since there are now a number of high resolution x-ray structures of SARS-CoV 3CLpro available making structure-based drug-design possible. As a result, SARS-CoV 3CLpro has become the focus of numerous drug discovery efforts worldwide, but as a consequence, a variety of different 3CLpro expression constructs and kinetic assays have been independently developed making evaluation and comparison between potential inhibitors problematic. Here, we review the literature focusing on different SARS-CoV 3CLpro expression constructs and assays used to measure enzymatic activity. Moreover, we provide experimental evidence showing that the activity of 3CLpro enzymatic is significantly reduced when non-native sequences or affinity-tags are added to the N-or C-termini of the enzyme, or when the enzyme used in assays is at concentrations below the equilibrium dissociation constant of the 3CLpro dimer. We demonstrate for the first time the utility of a highly sensitive and novel Alexa488-QSY7 FRET-based peptide substrate designed for routine analysis and high-throughput screening, and show that kinetic constants determined from FRET-based assays that are uncorrected for inner-filter effects can lead to artifacts. Finally, we evaluated the effects of common assay components including DTT, NaCl, EDTA and DMSO on enzymatic activity, and we recommend standardized assay conditions and constructs for routine SARS-CoV 3CLpro assays to facilitate direct comparisons between SARS-CoV 3CLpro inhibitors under development worldwide. 
 Title: Evaluating the 3C-like protease activity of SARS-Coronavirus: Recommendations for Standardized Assays for Drug Discovery NIH Public Access
Output: True
Paragraph: Asthma is a highly prevalent chronic respiratory disease affecting 300 million people worldwide. A significant fraction of the cost and morbidity of asthma derives from acute care for asthma exacerbations. In the United States alone, there are approximately 15.0 million outpatient visits, 2 million emergency room visits, and 500,000 hospitalizations each year for management of acute asthma. Common respiratory viruses, especially rhinoviruses, cause the majority of exacerbations in children and adults. Infection of airway epithelial cells with rhinovirus causes the release of proinflammatory cytokines and chemokines, as well as recruitment of inflammatory cells, particularly neutrophils, lymphocytes, and eosinophils. The host response to viral infection is likely to influence susceptibility to asthma exacerbation. Having had at least one exacerbation is an important risk factor for recurrent exacerbations suggesting an "exacerbation-prone" subset of asthmatics. Factors underlying for the "exacerbation-prone" phenotype are incompletely understood but include extrinsic factors: cigarette smoking, medication noncompliance, psychosocial factors, and co-morbidities such as gastroesophageal reflux disease, rhinosinusitis, obesity, and intolerance to non-steroidal antiinflammatory medications; as well as intrinsic factors such as deficient epithelial cell production of the anti-viral type I interferons (IFN-α and IFN-β). A better understanding of the biologic mechanisms of host susceptibility to recurrent exacerbations will be important for developing more effective preventions and treatments aimed at reducing the significant cost and morbidity associated with this important global health problem. Corresponding author and reprint requests: John V. Fahy, M.D., M.Sc., Box 0130, 
 Title: Acute Exacerbations of Asthma: Epidemiology, Biology and the Exacerbation-Prone Phenotype
Output: False
Paragraph: Apoptosis is an important mechanism to maintain homeostasis in mammals, and disruption of the apoptosis regulation mechanism triggers a range of diseases, such as cancer, autoimmune diseases, and developmental disorders. The severity of influenza A virus (IAV) infection is also closely related to dysfunction of apoptosis regulation. In the virus infected cells, the functions of various host cellular molecules involved in regulation of induction of apoptosis are modulated by IAV proteins to enable effective virus replication. The modulation of the intracellular signaling pathway inducing apoptosis by the IAV infection also affects extracellular mechanisms controlling apoptosis, and triggers abnormal host responses related to the disease severity of IAV infections. This review focuses on apoptosis related molecules involved in IAV replication and pathogenicity, the strategy of the virus propagation through the regulation of apoptosis is also discussed. 
 Title: Relevance of signaling molecules for apoptosis induction on influenza A virus replication
Output: True
Paragraph: Porcine epidemic diarrhea virus (PEDV) invades porcine intestinal epithelial cells (IECs) and causes diarrhea and dehydration in pigs. In the present study, we showed a suppression of PEDV infection in porcine jejunum intestinal epithelial cells (IPEC-J2) by an increase in autophagy. Autophagy was activated by rapamycin at a dose that does not affect cell viability and tight junction permeability. The induction of autophagy was examined by LC3I/LC3II conversion. To confirm the autophagic-flux (entire autophagy pathway), autophagolysosomes were examined by an immunofluorescence assay. Pretreatment with rapamycin significantly restricted not only a 1 h infection but also a longer infection (24 h) with PEDV, while this effect disappeared when autophagy was blocked. Co-localization of PEDV and autophagosomes suggests that PEDV could be a target of autophagy. Moreover, alleviation of PEDVinduced cell death in IPEC-J2 cells pretreated with rapamycin demonstrates a protective effect of rapamycin against PEDV-induced epithelial cell death. Collectively, the present study suggests an early prevention against PEDV infection in IPEC-J2 cells via autophagy that might be an effective strategy for the restriction of PEDV, and opens up the possibility of the use of rapamycin in vivo as an effective prophylactic and prevention treatment. 
 Title: Rapamycin-induced autophagy restricts porcine epidemic diarrhea virus infectivity in porcine intestinal epithelial cells
Output: False
Paragraph: Variation in temperature and R 0 amongst Canadian sites 2 Table S1 . Basic characteristics of sites used in this study 4 Figure S1 . The locations of sites used in the study 5 Figure S2 . Model-estimated R 0 and DD > 0°C using observed daily temperature 5 Figure S3 . Climate classification tree for the sites 6 Figure S4. Daily normal of ANUSPLIN daily maximum temperatures for each cluster 6 Model sensitivity analysis 7 Table S2. The parameters used in sensitivity analysis 9 Fig S5. Local sensitivity analysis 10 Fig S6. Results of global sensitivity analysis 11 Validation of climate model output 11 Table S3 . Basic information about RCM simulations 13 Figure S7 . Mean DD > 0°C for each cluster using observed and model temperature 14 Figure S8. Mean R 0 for each cluster using observed and climate model temperature 14 Mapping R 0 15 Figure S9. Plots of model-estimated R 0 values plotted against DD > 0°C 16 References 17 
 Title: Supplemental Material Estimated Effects of Projected Climate Change on the B asic Reproductive Number of the Lyme Disease Vector Ixodes scapularis
Output: False
Paragraph: Known human coronaviruses are believed to have originated in animals and made use of intermediate hosts for transmission to humans. The intermediate hosts of most of the human coronaviruses are known, but not for HCoV-NL63. This study aims to assess the possible role of some major domestic livestock species as intermediate hosts of HCoV-NL63. We developed a testing algorithm for high throughput screening of livestock sera with ELISA and confirmation with recombinant immunofluorescence assay testing for antibodies against HCoV-NL63 in livestock. Optimization of the ELISA showed a capability of the assay to significantly distinguish HCoV-NL63 from HCoV-229E (U = 27.50, p < 0.001) and HCoV-OC43 (U = 55.50, p < 0.001) in coronavirus-characterized sera. Evaluation of the assay with collected human samples showed no significant difference in mean optical density values of immunofluorescence-classified HCoV-NL63-positive and HCoV-NL63-negative samples (F (1, 215) = 0.437, p = 0.509). All the top 5% (n = 8) most reactive human samples tested by ELISA were HCoV-NL63 positive by immunofluorescence testing. In comparison, only a proportion (84%, n = 42) of the top 25% were positive by immunofluorescence testing, indicating an increased probability of the highly ELISA reactive samples testing positive by the immunofluorescence assay. None of the top 5% most ELISA reactive livestock samples were positive for HCoV-NL63-related viruses by immunofluorescence confirmation. Ghanaian domestic livestock are not likely intermediate hosts of HCoV-NL63-related coronaviruses. 
 Title: Development of a Whole-Virus ELISA for Serological Evaluation of Domestic Livestock as Possible Hosts of Human Coronavirus NL63
Output: True
Paragraph: Microbial cultures and/or microbial associated diseases often have a characteristic smell. Volatile organic compounds (VOCs) are produced by all microorganisms as part of their normal metabolism. The types and classes of VOC produced is wide, including fatty acids and their derivatives (e.g. hydrocarbons, aliphatic alcohols and ketones), aromatic compounds, nitrogen containing compounds, and volatile sulfur compounds. A diversity of ecological niches exist in the human body which can support a polymicrobial community, with the exact VOC profile of a given anatomical site being dependent on that produced by both the host component and the microbial species present. The detection of VOCs is of interest to various disciplines, hence numerous analytical approaches have been developed to accurately characterize and measure VOCs in the laboratory, often from patient derived samples. Using these technological advancements it is evident that VOCs are indicative of both health and disease states. Many of these techniques are still largely confined to the research laboratory, but it is envisaged that in future bedside 'VOC profiling' will enable rapid characterization of microbial associated disease, providing vital information to healthcare practitioners. 
 Title: TOPICAL REVIEW Microbial volatile compounds in health and disease conditions
Output: True
Paragraph: Rapid detection of infectious disease outbreaks is often crucial for their effective control. One example is highly pathogenic avian influenza (HPAI ) such as H5N1 in commercial poultry flocks. There are no quantitative data, however, on how quickly the effects of HPAI infection in poultry flocks can be detected. Here, we study, using an individual-based mathematical model, time to detection in chicken flocks. Detection is triggered when mortality, food or water intake or egg production in layers pass recommended thresholds suggested from the experience of past HPAI outbreaks. We suggest a new threshold for caged flocks-the cage mortality detection threshold-as a more sensitive threshold than current ones. Time to detection is shown to depend nonlinearly on R 0 and is particularly sensitive for R 0 !10. It also depends logarithmically on flock size and number of birds per cage. We also examine how many false alarms occur in uninfected flocks when we vary detection thresholds owing to background mortality. The false alarm rate is shown to be sensitive to detection thresholds, dependent on flock size and background mortality and independent of the length of the production cycle. We suggest that current detection thresholds appear sufficient to rapidly detect the effects of a high R 0 HPAI strain such as H7N7 over a wide range of flock sizes. Time to detection of the effects of a low R 0 HPAI strain such as H5N1 can be significantly improved, particularly for large flocks, by lowering detection thresholds, and this can be accomplished without causing excessive false alarms in uninfected flocks. The results are discussed in terms of optimizing the design of disease surveillance programmes in general. 
 Title: Detection of mortality clusters associated with highly pathogenic avian influenza in poultry: a theoretical analysis
Output: False
Paragraph: Virus infections elicit an immediate innate response involving antiviral factors. The activities of some of these factors are, in turn, blocked by viral countermeasures. The ensuing battle between the host and the viruses is crucial for determining whether the virus establishes a foothold and/or induces adaptive immune responses. A comprehensive systems-level understanding of the repertoire of anti-viral effectors in the context of these immediate virus-host responses would provide significant advantages in devising novel strategies to interfere with the initial establishment of infections. Recent efforts to identify cellular factors in a comprehensive and unbiased manner, using genome-wide siRNA screens and other systems biology -omics‖ methodologies, have revealed several potential anti-viral effectors for viruses like Human immunodeficiency virus type 1 (HIV-1), Hepatitis C virus (HCV), West Nile virus (WNV), and influenza virus. This review describes the discovery of novel viral restriction factors and discusses how the integration of different methods in systems biology can be used to more comprehensively identify the intimate interactions of viruses and the cellular innate resistance. 
 Title: Systems-Biology Approaches to Discover Anti-Viral Effectors of the Human Innate Immune Response
Output: False
Paragraph: The novel coronavirus disease was first reported in Wuhan, China in December 2019 and is now pandemic all over the world. Previous study has reported several COVID-19 cases with conjunctivitis. However, the complete profiling of COVID-19 related ocular symptoms and diseases are still missing. We aim to investigate the ocular manifestations and clinical characteristics of COVID-19 patients. Methods: A total of five hundred and thirty-four patients were recruited at Mobile Cabin Hospital and Tongji Hospital. We collected information on demographic characteristics, exposure history, ocular symptoms, systemic concomitant symptoms, eye drop medication, eye protections, radiologic findings, and SARS-CoV-2 detection in nasopharyngeal swabs by RT-PCR from questionnaires and electronic medical records. 
 Title: Ocular manifestations and clinical characteristics of 534 cases of COVID-19 in China: A cross-sectional study
Output: False
Paragraph: There exists significant interest in developing statistical and computational tools for inferring 'who infected whom' in an infectious disease outbreak from densely sampled case data, with most recent studies focusing on the analysis of whole genome sequence data. However, genomic data can be poorly informative of transmission events if mutations accumulate too slowly to resolve individual transmission pairs or if there exist multiple pathogens lineages within-host, and there has been little focus on incorporating other types of outbreak data. We present here a methodology that uses contact data for the inference of transmission trees in a statistically rigorous manner, alongside genomic data and temporal data. Contact data is frequently collected in outbreaks of pathogens spread by close contact, including Ebola virus (EBOV), severe acute respiratory syndrome coronavirus (SARS-CoV) and Mycobacterium tuberculosis (TB), and routinely used to reconstruct transmission chains. As an improvement over previous, ad-hoc approaches, we developed a probabilistic model that relates a set of contact data to an underlying transmission tree and integrated this in the outbreaker2 inference framework. By analyzing simulated outbreaks under various contact tracing scenarios, we demonstrate that contact data significantly improves our ability to reconstruct transmission trees, even under realistic limitations on the coverage of the contact tracing effort and the amount of non-infectious mixing between cases. Indeed, contact data is equally or more informative than fully sampled whole genome sequence data in certain scenarios. We then use our method to analyze the early stages of the 2003 SARS outbreak in Singapore and describe the range of transmission scenarios consistent with contact data and genetic sequence in a probabilistic manner for the first time. This simple yet flexible model can easily be incorporated into existing tools for outbreak reconstruction and should permit a better integration of genomic and epidemiological data for inferring transmission chains. PLOS Computational Biology | https://doi. 
 Title: Bayesian inference of transmission chains using timing of symptoms, pathogen genomes and contact data
Output: True
Paragraph: To examine the effect of provision of information about the infection control in the specific infection disease treatment unit in a city hospital on the outpatient's intention of outpatient service use, respondents who underwent outpatient medical care at the hospital (N = 821) were asked whether or not they intended to continue the outpatient visit at the hospital if a severe acute respiratory syndrome (SARS) patient was admitted to the unit. Although 56% of respondents replied that they could continue to visit the department if a SARS patient was admitted to the unit in the hospital before they read the information, the proportion of those who intended to continue outpatient care significantly increased by 15% after they read it. The logistic regression analyses revealed that respondents who had frequently visited the outpatient department (P < 0.001), those who felt relieved by reading the information about the unit (P < 0.001), and those who did not worry about nosocomial SARS infection inside the hospital (P < 0.001) were significantly more likely to reply that they would continue outpatient visits. We estimated that admission of a SARS patient to the unit would result in a 20% decrease in the cumulative total number of outpatients in the hospital during a 180-day interval after admission of a SARS patient to the unit, and the cumulative total number of outpatients increased by 7% after they read the information. This study suggests that providing outpatients with appropriate information about SARS infection control in the hospital had a statistically significant and substantial impact on the outpatients' intention to continue outpatient visits at the hospital. 
 Title: Estimation of the impact of providing outpatients with information about SARS infection control on their intention of outpatient visit
Output: True
Paragraph: Background: Immunosuppressive therapy for renal allograft recipients has changed substantially since the introduction of the anti-CD25 monoclonal antibody, basiliximab. We hypothesized that recent improvements in immunosuppressive treatment may reduce the incidence of osteonecrosis of the femoral head (ONFH). This study aimed to investigate transitional changes in the incidence of OFNH among renal transplant recipients by MRI. Methods: Participants comprised 110 patients who had undergone renal transplantation from 2003 to 2012, during which time basiliximab was in regular use at our institute (Recent group), and 232 patients who had undergone RT between 1986 and 2003 (Past group). We compared ONFH incidence between the two groups and evaluated risk factors for ONFH, including immunosuppressants (calcineurin inhibitors, basiliximab, and/or steroids) and postoperative renal function. Results: Incidence of ONFH was lower in the Recent group (0%) than in the Past group (3.4%; p ¼ 0.043). In the Recent group, age was greater, ABO/human leukocyte antigen incompatibility was worse, while steroid dose was decreased and post-transplant renal function was improved. Cumulative methylprednisolone dose at postoperative week 2 and delayed graft function were identified as risk factors for ONFH. Conclusion: Risk of ONFH after renal transplantation has fallen with the advent of regular use of basiliximab, although this agent does not appear to be a factor directly associated with the incidence of ONFH. Study design: Clinical prognostic study (Level III case control study). 
 Title: Original Article
Output: True
Paragraph: A B S T R A C T The innate immune system possesses a multitude of pathways to sense and respond to microbial pathogens. One such family are the interferons (IFNs), a family of cytokines that are involved in several cellular functions. Type I IFNs are appreciated to be important in several viral and bacterial diseases, while the recently identified type III IFNs (IFNL1, IFNL2, IFNL3, IFNL4) have been studied primarily in the context of viral infection. Viral and bacterial infections however are not mutually exclusive, and often the presence of a viral pathogen increases the pathogenesis of bacterial infection. The role of type III IFN in bacterial and viral-bacterial co-infections has just begun to be explored. In this mini review we discuss type III IFN signaling and its role in microbial pathogenesis with an emphasis on the work that has been conducted with bacterial pathogens. 
 Title: Mini review Microbial pathogenesis and type III interferons
Output: True
Paragraph: Background Ministers of health, donor agencies, philanthropists, and international agencies will meet at Bamako, Mali, in November, 2008, to review global priorities for health research. These individuals and organisations previously set health priorities for WHO, either through its regular budget or extra-budgetary funds. We asked what insights can be gained as to their priorities from previous decisions within the context of WHO. Methods We compared the WHO biennial budgetary allocations with the burden of disease from 1994-95 to 2008-09. Pacifi c and Africa-that are at diff ering stages of epidemiological transition. We further assessed whether the allocations diff ered on the basis of the source of funds (assessed and voluntary contributions) and the mechanism for deciding how funds were spent. Interpretation Decision makers at Bamako should consider the implications of the present misalignment of global health priorities and disease burden for health research worldwide. Funds allocated by external donors substantially diff er from those allocated by WHO member states. The meeting at Bamako provides an opportunity to consider how this disparity might be addressed. Funding None. 
 Title: WHO's budgetary allocations and burden of disease: a comparative analysis
Output: False
Paragraph: Background: Mice lacking the type I interferon receptor (IFNAR 2/2 mice) reproduce relevant aspects of Crimean-Congo hemorrhagic fever (CCHF) in humans, including liver damage. We aimed at characterizing the liver pathology in CCHF virusinfected IFNAR 2/2 mice by immunohistochemistry and employed the model to evaluate the antiviral efficacy of ribavirin, arbidol, and T-705 against CCHF virus. Methodology/Principal Findings: CCHF virus-infected IFNAR 2/2 mice died 2-6 days post infection with elevated aminotransferase levels and high virus titers in blood and organs. Main pathological alteration was acute hepatitis with extensive bridging necrosis, reactive hepatocyte proliferation, and mild to moderate inflammatory response with monocyte/macrophage activation. Virus-infected and apoptotic hepatocytes clustered in the necrotic areas. Ribavirin, arbidol, and T-705 suppressed virus replication in vitro by $3 log units (IC 50 0.6-2.8 mg/ml; IC 90 1.2-4.7 mg/ml). Ribavirin [100 mg/(kg6d)] did not increase the survival rate of IFNAR 2/2 mice, but prolonged the time to death (p,0.001) and reduced the aminotransferase levels and the virus titers. Arbidol [150 mg/(kg6d)] had no efficacy in vivo. Animals treated with T-705 at 1 h [15, 30, and 300 mg/(kg6d)] or up to 2 days [300 mg/(kg6d)] post infection survived, showed no signs of disease, and had no virus in blood and organs. Co-administration of ribavirin and T-705 yielded beneficial rather than adverse effects. Conclusions/Significance: Activated hepatic macrophages and monocyte-derived cells may play a role in the proinflammatory cytokine response in CCHF. Clustering of infected hepatocytes in necrotic areas without marked inflammation suggests viral cytopathic effects. T-705 is highly potent against CCHF virus in vitro and in vivo. Its in vivo efficacy exceeds that of the current standard drug for treatment of CCHF, ribavirin. 
 Title: Evaluation of Antiviral Efficacy of Ribavirin, Arbidol, and T-705 (Favipiravir) in a Mouse Model for Crimean-Congo Hemorrhagic Fever
Output: False
Paragraph: The development of intestinal lesions after inoculation with Brachyspira hyodysenteriae was followed by repeated endoscopy and biopsy sampling through a caecal cannula. Seven eight-week-old pigs were cannulated and inoculated, two were cannulated but not inoculated, and two pigs were inoculated but not cannulated. Endoscopy, biopsy, and blood sampling to determine SAA (serum amyloid A), haptoglobin, cortisol, and WBC counts were performed at scheduled time-points. At the third day of disease, endoscopy showed a hyperaemic, perturbed mucosa and excessive amount of mucus. Histologically, crypt hyperplasia, depletion of goblet cell mucus, and erosions were noted. Simultaneously, elevated acute phase proteins and circulating monocytes, and decreased number of intraepithelial CD3 + cells were observed. After five days the pigs recovered. Intestinal lesions were demarcated and interspersed among apparently normal mucosa and blood parameters returned to initial values. Endoscopy through an intestinal cannula made it possible to follow the development of intestinal alterations in vivo and describe the sequential events during the course of swine dysentery. The number of animals used in a study could thus be minimised and the precision of the experiment increased. 
 Title: Consecutive pathological and immunological alterations during experimentally induced swine dysentery - A study performed by repeated endoscopy and biopsy samplings through an intestinal cannula
Output: True
Paragraph: Improved vaccines and adjuvants are being developed to reduce the threat posed by a terrorist attack involving aerosolized anthrax spores. Nevertheless, uncertainty persists concerning the relative benefits of inducing mucosal vs systemic immunity to host survival following inhalational exposure to anthrax spores. This work examines the effect of delivering the licensed human vaccine (Anthrax Vaccine Adsorbed, AVA) combined with a CpG oligodeoxynucleotide (ODN) adjuvant intraperitoneally or intranasally to A/J mice. Results indicate that protection from inhalational anthrax correlates with the induction of a strong systemic rather than mucosal immune response, and demonstrate that protection is significantly improved and accelerated by the addition of CpG ODN. 
 Title: Systemic but not mucosal immunity induced by AVA prevents inhalational anthrax
Output: True
Paragraph: Regulation of proteolysis plays a critical role in a myriad of important cellular processes. The key to better understanding the mechanisms that control this process is to identify the specific substrates that each protease targets. To address this, we have developed iProt-Sub, a powerful bioinformatics tool for the accurate prediction of protease-specific substrates and their cleavage sites. Importantly, iProt-Sub represents a significantly advanced version of its successful predecessor, PROSPER. It provides optimized cleavage site prediction models with better prediction performance and coverage for more species-specific proteases (4 major protease families and 38 different proteases). iProt-Sub integrates heterogeneous Jiangning Song received his BEng and DEng degrees from Jiangnan University, China. He is affiliated with the Advisory Professor of several Universities. His research interests are in computational biology and biomedicine, protein structure prediction, low-frequency internal motion of protein/DNA molecules and its biological functions, diffusion-controlled reactions of enzymes, as well as graphic rules in enzyme kinetics and other biological systems. sequence and structural features and uses a two-step feature selection procedure to further remove redundant and irrelevant features in an effort to improve the cleavage site prediction accuracy. Features used by iProt-Sub are encoded by 11 different sequence encoding schemes, including local amino acid sequence profile, secondary structure, solvent accessibility and native disorder, which will allow a more accurate representation of the protease specificity of approximately 38 proteases and training of the prediction models. Benchmarking experiments using cross-validation and independent tests showed that iProt-Sub is able to achieve a better performance than several existing generic tools. We anticipate that iProt-Sub will be a powerful tool for proteome-wide prediction of protease-specific substrates and their cleavage sites, and will facilitate hypothesis-driven functional interrogation of protease-specific substrate cleavage and proteolytic events. 
 Title: Author(s)
Output: True
Paragraph: Coronaviruses (CoVs) have caused outbreaks of deadly pneumonia in humans since the beginning of the 21st century. The severe acute respiratory syndrome coronavirus (SARS-CoV) emerged in 2002 and was responsible for an epidemic that spread to five continents with a fatality rate of 10% before being contained in 2003 (with additional cases reported in 2004). The Middle-East respiratory syndrome coronavirus (MERS-CoV) emerged in the Arabian Peninsula in 2012 and has caused recurrent outbreaks in humans with a fatality rate of 35%. SARS-CoV and MERS-CoV are zoonotic viruses that crossed the species barrier using bats/palm civets and dromedary camels, respectively. No specific treatments or vaccines have been approved against any of the six human coronaviruses, highlighting the need to investigate the principles governing viral entry and cross-species transmission as well as to prepare for zoonotic outbreaks which are likely to occur due to the large reservoir of CoVs found in mammals and birds. Here, we review our understanding of the infection mechanism used by coronaviruses derived from recent structural and biochemical studies. 
 Title: Structural insights into coronavirus entry
Output: True
Paragraph: Hospital-acquired infections (HAIs) are serious problems for healthcare systems, especially in developing countries where public health infrastructure and technology for infection preventions remain undeveloped. Here, we characterized how strategy and technology could be mobilized to improve the effectiveness of infection prevention and control in hospitals during the outbreaks of Ebola, Middle East respiratory syndrome (MERS), and severe acute respiratory syndrome (SARS) in Asia and West Africa. Published literature on the hospital-borne outbreaks of SARS, Ebola, and MERS in Asia and West Africa was comprehensively reviewed. The results showed that healthcare systems and hospital management in affected healthcare facilities had poor strategies and inadequate technologies and human resources for the prevention and control of HAIs, which led to increased morbidity, mortality, and unnecessary costs. We recommend that governments worldwide enforce disaster risk management, even when no outbreaks are imminent. Quarantine and ventilation functions should be taken into consideration in architectural design of hospitals and healthcare facilities. We also recommend that health authorities invest in training healthcare workers for disease outbreak response, as their preparedness is essential to reducing disaster risk. 
 Title: Strategy and technology to prevent hospital-acquired infections: Lessons from SARS, Ebola, and MERS in Asia and West Africa
Output: True
Paragraph: Angiotensin-converting enzyme 2 (ACE2) is highly expressed in the kidney proximal tubule, where it cleaves angiotensin (Ang) II to Ang-(1-7). Urinary ACE2 levels increase in diabetes, suggesting that ACE2 may be shed from tubular cells. The aim of this study was to determine if ACE2 is shed from proximal tubular cells, to characterize ACE2 fragments, and to study pathways for shedding. Studies involved primary cultures of mouse proximal tubular cells, with ACE2 activity measured using a synthetic substrate, and analysis of ACE2 fragments by immunoblots and mass spectrometry. The culture media from mouse proximal tubular cells demonstrated a time-dependent increase in ACE2 activity, suggesting constitutive ACE2 shedding. ACE2 was detected in media as two bands at ,90 kDa and ,70 kDa on immunoblots. By contrast, full-length ACE2 appeared at ,100 kDa in cell lysates or mouse kidney cortex. Mass spectrometry of the two deglycosylated fragments identified peptides matching mouse ACE2 at positions 18-706 and 18-577, respectively. The C-terminus of the 18-706 peptide fragment contained a non-tryptic site, suggesting that Met 706 is a candidate ACE2 cleavage site. Incubation of cells in high D-glucose (25 mM) (and to a lesser extent Ang II) for 48-72 h increased ACE2 activity in the media (p,0.001), an effect blocked by inhibition of a disintegrin and metalloproteinase (ADAM)17. High D-glucose increased ADAM17 activity in cell lysates (p,0.05). These data indicate that two glycosylated ACE2 fragments are constitutively shed from mouse proximal tubular cells. ACE2 shedding is stimulated by high D-glucose, at least partly via an ADAM17-mediated pathway. The results suggest that proximal tubular shedding of ACE2 may increase in diabetes, which could enhance degradation of Ang II in the tubular lumen, and increase levels of Ang-(1-7). 
 Title: Characterization of Angiotensin-Converting Enzyme 2 Ectodomain Shedding from Mouse Proximal Tubular Cells
Output: False
Paragraph: Emerging viruses pose a major threat to humans and livestock with global public health and economic burdens. Vaccination remains an effective tool to reduce this threat, and yet, the conventional cell culture often fails to produce sufficient vaccine dose. As an alternative to cell-culture based vaccine, virus-like particles (VLPs) are considered as a highpriority vaccine strategy against emerging viruses. VLPs represent highly ordered repetitive structures via macromolecular assemblies of viral proteins. The particulate nature allows efficient uptake into antigen presenting cells stimulating both innate and adaptive immune responses towards enhanced vaccine efficacy. Increasing research activity and translation opportunity necessitate the advances in the design of VLPs and new bioprocessing modalities for efficient and cost-effective production. Herein, we describe major achievements and challenges in this endeavor, with respect to designing strategies to harnessing the immunogenic potential, production platforms, downstream processes, and some exemplary cases in developing VLP-based vaccines. 
 Title: Exploiting virus-like particles as innovative vaccines against emerging viral infections
Output: True
Paragraph: A potent immunosuppressive drug cyclosporin A (CsA) is known to inhibit human cell infection by the pathogenic protozoan parasite Leishmania major both in vitro and in vivo. The proposed mechanism of action involves CsA binding to Leishmania major-expressed cyclophilin and subsequent down-regulation of signaling events necessary for establishing productive infection. Recently, we identified a ubiquitously expressed membrane protein, CD147, as a signaling receptor for extracellular cyclophilins in mammalian cells. Here we demonstrate that, while being enzymatically active, the Leishmania cyclophilin, unlike its human homologue, does not interact with CD147 on the cell surface of target cells. CD147 facilitates neither Leishmania binding nor infection. Primary structure and biochemical analyses revealed that the parasite's cyclophilin is defective in heparan binding, an event required for signaling interaction between CD147 and human cyclophilin. When the heparan-binding motif was reconstituted in Leishmania cyclophilin, it regained the CD147-dependent signaling activity. These results underscore a critical role of cyclophilinheparan interactions in CD147-mediated signaling events and argue against the role of Leishmania cyclophilin in parasite binding to target cells. 
 Title: Functional analysis of Leishmania major cyclophilin
Output: True
Paragraph: This article examines the history of dog mess in Paris, from its 'discovery' in the late 1920s to the management regime of the early twenty-first century. Mayor Jacques Chirac's anti-excrement campaigns in the 1980s are a particular focus. Situating the meaning and management of dog mess within histories of public hygiene and disgust, and mobilising insights from work on public hygiene, biopolitics and governmentality, this article shows how Chirac's attempt to produce self-regulating and responsible dog owners through education failed to persuade them to overcome their disgust at their pets' excrement. Fining alongside education proved a more effective management strategy. The history of dog mess in Paris highlights the biopolitical problems raised by animal excrement decades after the apogee of the public hygiene movement, and shows how human-animal partnerships expose the limits of governmentality approaches to public hygiene and neo-liberal urban governance. 
 Title: Combating Canine 'Visiting Cards': Public Hygiene and the Management of Dog Mess in Paris since the 1920s
Output: True
Paragraph: The major pigment in eggshells of brownegg laying hens is protoporphyrin IX, but traces of biliverdin and its zinc chelates are also present. The pigment appears to be synthesized in the shell gland. The protoporphyrin IX synthetic pathway is well defined, but precisely where and how it is synthesized in the shell gland of the brown-egg laying hen is still ambiguous. The pigment is deposited onto all shell layers including the shell membranes, but most of it is concentrated in the outermost layer of the calcareous shell and in the cuticle. Recently, the genes that are involved in pigment synthesis have been identified, but the genetic control of synthesis and deposition of brown pigment in the commercial laying hen is not fully understood. The brown coloration of the shell is an important shell quality parameter and has a positive influence on consumer preference. The extent of pigment deposition is influenced by the housing system, hen age, hen strain, diet, stressors, and certain diseases such as infectious bronchitis. In this article, the physiological and biochemical characteristics of the brown pigment in commercial brown-egg layers are reviewed in relation to its various functions in the poultry industry. 
 Title: Review Eggshell color in brown-egg laying hens -a review
Output: True
Paragraph: Objective: To focus on the potential beneficial effects of the pleiotropic effects of dipeptidyl peptidase-4 inhibitors (DPP4is) on attenuating progression of diabetic kidney disease in reducing the long-term effect of the acute kidney injury (AKI) to chronic kidney disease (CKD) transition. , were analyzed, and patients with diabetes weaning from dialysis-requiring AKI were identified. Cox proportional hazards models and inverse-weighted estimates of the probability of treatment were used to adjust for treatment selection bias. The outcomes were incident end-stage renal disease (ESRD) and mortality, major adverse cardiovascular events, and hospitalized heart failure. Results: Of a total of 6165 patients with diabetes weaning from dialysis-requiring AKI identified, 5635 (91.4%) patients were DPP4i nonusers and 530 (8.6%) patients were DPP4i users. Compared with DPP4i nonusers, DPP4i users had a lower risk of ESRD (hazard ratio, 0.81; 95% CI, 0.70-0.94; P¼.04) and allcause mortality (hazard ratio, 0.28; 95% CI, 0.23-0.34; P<.001) after adjustments for CKD, advanced CKD, and angiotensin-converting enzyme inhibitor or angiotensin II receptor blocker use. In contrast, the risk of major adverse cardiovascular events and hospitalized heart failure did not differ significantly between groups. Conclusion: Dipeptidyl peptidase-4 inhibitor users had a lower risk of ESRD and mortality than did nonusers among patients with diabetes after weaning from dialysis-requiring AKI. Therefore, a prospective study of AKI to CKD transitions after episodes of AKI is needed to optimally target DPP4i interventions. 
 Title: Patients and Methods: Data from the National Health Insurance Research Database from
Output: False