niryuu/sni-each-converted huggingface dataset:
Paragraph: Six volunteers experienced severe inflammatory response during the Phase I clinical trial of a monoclonal antibody that was designed to stimulate a regulatory T cell response. Soon after the trial began, each volunteer experienced a ''cytokine storm'', a dramatic increase in cytokine concentrations. The monoclonal antibody, TGN1412, raised serum concentrations of both pro-and anti-inflammatory cytokines to very hich values during the first day, while lymphocyte and monocyte concentrations plummeted. Because the subjects were healthy and had no prior indications of immune deficiency, this event provided an unusual opportunity to study the dynamic interactions of cytokines and other measured parameters. Here, the response histories of nine cytokines have been modeled by a set of linear ordinary differential equations. A general search procedure identifies parameters of the model, whose response fits the data well during the five-day measurement period. The eighteenth-order model reveals plausible cause-and-effect relationships among the cytokines, showing how each cytokine induces or inhibits other cytokines. It suggests that perturbations in IL2, IL8, and IL10 have the most significant inductive effect, while IFN-c and IL12 have the greatest inhibiting effect on other cytokine concentrations. Although TNF-a is a major pro-inflammatory factor, IFN-c and three other cytokines have faster initial and median response to TGN1412 infusion. Principal-component analysis of the data reveals three clusters of similar cytokine responses: [TNF-a, IL1, IL10], IL2, IL4, IL8, and IL12], and [IL6]. IL1, IL6, IL10, and TNF-a have the highest degree of variability in response to uncertain initial conditions, exogenous effects, and parameter estimates. This study illuminates details of a cytokine storm event, and it demonstrates the value of linear modeling for interpreting complex, coupled biological system dynamics from empirical data. Citation: Yiu HH, Graham AL, Stengel RF (2012) Dynamics of a Cytokine Storm. PLoS ONE 7(10): e45027. 
 Title: Dynamics of a Cytokine Storm
Output: False
Paragraph: Intracellular trafficking and localization studies of spike protein from SARS and OC43 showed that SARS spike protein is localized in the ER or ERGIC compartment and OC43 spike protein is predominantly localized in the lysosome. Differential localization can be explained by signal sequence. The sequence alignment using Clustal W shows that the signal sequence present at the cytoplasmic tail plays an important role in spike protein localization. A unique GYQEL motif is identified at the cytoplasmic terminal of OC43 spike protein which helps in localization in the lysosome, and a novel KLHYT motif is identified in the cytoplasmic tail of SARS spike protein which helps in ER or ERGIC localization. This study sheds some light on the role of cytoplasmic tail of spike protein in cell-to-cell fusion, coronavirus host cell fusion and subsequent pathogenicity. [Sadasivan J, Singh M and Sarma JD 2017 Cytoplasmic tail of coronavirus spike protein has intracellular targeting signals. J. Biosci. 42 231-244] 
 Title: Cytoplasmic tail of coronavirus spike protein has intracellular targeting signals
Output: False
Paragraph: Brazzein protein comes from an edible fruit, which has a long history of being a staple in the local human diet in Africa. The attractive features of brazzein as a potential commercial sweetener include its small size (53 amino acid residues), its stability over wide ranges of temperature and pH, and the similarity of its sweetness to sucrose. Heterologous production of brazzein is complicated by the fact that the protein contains four disulfide bridges and requires a specific N-terminal sequence. Our previous protocol for producing the protein from Escherichia coli involved several steps with low overall yield: expression as a fusion protein, denaturation and renaturation, oxidation of the cysteines, and cleavage by cyanogen bromide at an engineered methionine adjacent to the desired N-terminus. The new protocol described here, which is much faster and leads to a higher yield of native protein, involves the production of brazzein in E. coli as a fusion with SUMO. The isolated protein product contains the brazzein domain folded with correct disulfide bonds formed and is then cleaved with a specific SUMO protease to liberate native brazzein. This protocol represents an important advancement that will enable more efficient research into the interaction between brazzein and the receptor as well as investigations to test the potential of brazzein as a commercially viable natural low calorie sweetener. 
 Title: Efficient and rapid protein expression and purification of small high disulfide containing sweet protein brazzein in E. coli
Output: True
Paragraph: During the lifecycle of many enveloped viruses, a nucleocapsid core buds through the cell membrane to acquire an outer envelope of lipid membrane and viral glycoproteins. However, the presence of a nucleocapsid core is not required for assembly of infectious particles. To determine the role of the nucleocapsid core, we develop a coarse-grained computational model with which we investigate budding dynamics as a function of glycoprotein and nucleocapsid interactions, as well as budding in the absence of a nucleocapsid. We find that there is a transition between glycoprotein-directed budding and nucleocapsid-directed budding that occurs above a threshold strength of nucleocapsid interactions. The simulations predict that glycoprotein-directed budding leads to significantly increased size polydispersity and particle polymorphism. This polydispersity can be explained by a theoretical model accounting for the competition between bending energy of the membrane and the glycoprotein shell. The simulations also show that the geometry of a budding particle leads to a barrier to subunit diffusion, which can result in a stalled, partially budded state. We present a phase diagram for this and other morphologies of budded particles. Comparison of these structures against experiments could establish bounds on whether budding is directed by glycoprotein or nucleocapsid interactions. Although our model is motivated by alphaviruses, we discuss implications of our results for other enveloped viruses. 
 Title: Why Enveloped Viruses Need Cores-The Contribution of a Nucleocapsid Core to Viral Budding
Output: False
Paragraph: Telephone: +61 7 405 974 555 Facsimile: +61 7 3636 5578 Word count Abstract 249 words Main text 2394 words Key words respiratory viruses gastrointestinal infection children real-time polymerase chain reaction cohort studies Page 2 of 33 For peer review only -http://bmjopen.bmj.com/site/about/guidelines.xhtml BMJ Open ARTICLE SUMMARY Article focus Infectious diseases are a common cause of morbidity in early childhood, even in developed economies. A diagnostic gap exists for common respiratory and gastrointestinal syndromes, with the likelihood that as yet undiscovered pathogens are involved. Existing knowledge about these common illnesses relies on research conducted before the rapid developments in molecular diagnostics of recent decades or focusses on disease at the severe end of the spectrum -hospitalisations -affecting a limited number of children and discounting the burden of more common, but less severe, community-managed illness. This protocol outlines a dynamic birth cohort study that will allow for a detailed description of the epidemiology of respiratory and gastrointestinal viruses during the first two years of life. The large biobank of specimens to be collated will act as a rich source of material to answer targeted research questions, including the role of virus acquisition and shedding on clinical illness and the discovery of new infectious agents. As study procedures, including specimen collection and return, are conducted by parents, findings will be free from Hawthorne effects from frequent interactions with study staff. Systematic weekly sampling will provide a control set of specimens for the individual and the cohort, allowing quantification of virus-specific attributable risk to illness. Non-random recruitment and enrolment requires awareness and assessment of potential bias and confounding prior to broad-based generalisation. Similar studies in the past have oversampled from higher socioeconomic households, and we attempt to avoid this by using a recruitment strategy that targets pregnant women in both public and private hospital settings. . van der Zalm MM, Uiterwaal CS, de Jong BM, et al. Viral specimen collection by parents increases response rate in population-based virus studies. J Allergy Clin Immunol 2006;117:955-6; author reply 56-7. 
 Title: Title page Observational Research in Childhood Infectious Diseases (ORChID): a dynamic birth cohort study Author affiliations
Output: False
Paragraph: Background: The current Ebola outbreak in West Africa and the large scale wild Polio virus outbreak in several countries are the top most issues among international public health and scientific communities' debates and concerns. These two outbreaks were judged to be declared as Public Health Emergency of International Concern (PHEIC) during 2014. This is the first time ever to have such circumstance of two PHEICs at the same time. Discussion: PHEIC, which has to be declared by WHO Director General after a recommendation of IHR Emergency Committee; is observed to start in countries with fragile health system and conflict areas. Then it rapidly spread to threaten the global public health. The year 2014 has uniquely witnessed declaration of two events as PHEIC according to IHR (2005); Polio and Ebola Virus Disease (EVD). Both outbreaks are caused by viruses such as H1N1 which was previously declared as PHEIC in 2009. Summary: Public Health Emergencies of International Concern in 2014 occurred in countries with weak health systems and conflicts and threatening the whole globe. International collaborative work is required to contain the event and to mobilize resources/capacities between countries. Moreover, public health surveillance systems as core capacity for IHR (2005) should be strengthened in all countries with focus on those with limited capacity and ongoing conflicts. The ultimate aim is timely detection of potential PHEIC events in the future along with early preparedness and response plans. 
 Title: Public Health Emergency of International Concern (PHEIC) has Declared Twice in 2014; Polio and Ebola at the Top
Output: False
Paragraph: Because of its essential role in gas exchange and oxygen delivery, the lung has evolved a variety of strategies to control inflammation and maintain homeostasis. Invasion of the lung by pathogens (and in some instances exposure to certain noninfectious particulates) disrupts this equilibrium and triggers a cascade of events aimed at preventing or limiting colonization (and more importantly infection) by pathogenic microorganisms. In this review we focus on viral infection of the lung and summarize recent advances in our understanding of the triggering of innate and adaptive immune responses to viral respiratory tract infection, mechanisms of viral clearance, and the wellrecognized consequences of acute viral infection complicating underlying lung diseases, such as asthma. 
 Title: Viral infection of the lung: Host response and sequelae
Output: False
Paragraph: Respiratory syncytial virus Nasopharyngeal aspirate Bronchiolitis Respiratory PCR Background: Bronchiolitis is the most common reason for hospitalization in young children. In addition to respiratory syncytial virus (RSV), other viruses have been increasingly implicated. Guidance on testing has also changed. Aims: To compare clinicopathological outcomes in young children admitted with bronchiolitis due to RSV in comparison with rhinovirus (RV), and identify associated risk/ epidemiological factors. Methods: Children aged less than two years admitted to hospital with a clinical diagnosis of bronchiolitis with positive results for either RSV or RV were included in this study. Polymerase-chain-reaction-negative cases using an extended respiratory virus panel served as a control group. Retrospective data were collected on sex, risk factors, respiratory support, intravenous fluids and antibiotics. Outcomes such as length of stay (LOS) and need for transfer to the high-dependency unit/paediatric intensive care unit were included. Findings: Two hundred and twenty-seven out of 437 nasopharyngeal aspirate samples were positive for either RSV (N ¼ 162) or RV (N ¼ 65). The median age of cases was three months and 75% had at least one risk factor. Risk factors were higher in the RV group (P ¼ 0.004). RV accounted for the majority of cases outside the RSV season (P < 0.01). RVassociated bronchiolitis had a longer LOS (more than seven days) (P < 0.05) and increased need for chest X-rays and/or antibiotics (P < 0.05). Use of intravenous fluids and respiratory support were higher in the RV group, but the difference was not significant. Conclusions: RV is the second most common pathogen associated with bronchiolitis and is isolated all year round. This may be important in those with risk factors resulting in prolonged LOS. Further research is necessary to establish the exact role of RV in this common condition, particularly outside the traditional RSV season. Crown 
 Title: Respiratory-syncytial-virus-and rhinovirus-related bronchiolitis in children aged <2 years in an English district general hospital
Output: False
Paragraph: We describe here the design, synthesis, molecular modeling, and biological evaluation of a series of small molecule, nonpeptide inhibitors of SARS-CoV PLpro. Our initial lead compound was identified via high-throughput screening of a diverse chemical library. We subsequently carried out structure-activity relationship studies, and optimized the lead structure to potent inhibitors that have shown antiviral activity against SARS-CoV infected Vero E6 cells. Based upon the X-ray crystal structure of one of the potent inhibitors 24-bound to SARS-CoV PLpro, a drug-design template was created. Our structure-based modification led to the design of a more potent inhibitor, 2 (enzyme IC 50 = 0.46 μM; antiviral EC 50 = 12.5 μM). Interestingly, its methylamine derivative 49 displayed good enzyme inhibitory potency (IC 50 = 1.3 μM) and most potent SARS antiviral activity (EC 50 = 2.5 μM) in the series. We have carried out computational docking studies and generated a predictive 3D-QSAR model for SARS-CoV PLpro inhibitors. 
 Title: Structure-Based Design, Synthesis, and Biological Evaluation of a Series of Novel and Reversible Inhibitors for the Severe Acute Respiratory Syndrome-Coronavirus Papain-Like Protease
Output: True
Paragraph: The diagnostics of respiratory viral infections has improved markedly during the last 15 years with the development of PCR techniques. Since 1997, several new respiratory viruses and their subgroups have been discovered: influenza A viruses H5N1 and H1N1, human metapneumovirus, coronaviruses SARS, NL63 and HKU1, human bocavirus, human rhinoviruses C and D and potential respiratory pathogens, the KI and WU polyomaviruses and the torque teno virus. The detection of previously known viruses has also improved. Currently, a viral cause of respiratory illness is almost exclusively identifiable in children, but in the elderly, the detection rates of a viral etiology are below 40%, and this holds also true for exacerbations of chronic respiratory illnesses. The new viruses cause respiratory symptoms like the common cold, cough, bronchitis, bronchiolitis, exacerbations of asthma and chronic obstructive pulmonary disease and pneumonia. Acute respiratory failure may occur. These viruses are distributed throughout the globe and affect people of all ages. Data regarding these viruses and the elderly are scarce. This review introduces these new viruses and reviews their clinical significance, especially with regard to the elderly population. 
 Title: New Respiratory Viruses and the Elderly
Output: False
Paragraph: Groundnut bud necrosis virus belongs to the genus Tospovirus, infects a wide range of crop plants and causes severe losses. To understand the role of the nucleocapsid protein in the viral life cycle, the protein was overexpressed in E. coli and purified by Ni-NTA chromatography. The purified N protein was well folded and was predominantly alpha-helical. Deletion analysis revealed that the C-terminal unfolded region of the N protein was involved in RNA binding. Furthermore, the N protein could be phosphorylated in vitro by Nicotiana benthamiana plant sap and by purified recombinant kinases such as protein kinase CK2 and calcium-dependent protein kinase. This is the first report of phoshphorylation of a nucleocapsid protein in the family Bunyaviridae. The possible implications of the present findings for the viral life cycle are discussed. Abbreviations Groundnut bud necrosis virus TSWV Tomato spotted wilt virus RNP Ribonucleoprotein N protein Nucleocapsid protein CK2 Protein kinase CK2 CDPK Calcium-dependent protein kinase Electronic supplementary material The online version of this article ( 
 Title: Investigations on the RNA binding and phosphorylation of groundnut bud necrosis virus nucleocapsid protein
Output: True
Paragraph: Objective. In treating highly infectious COVID-19 pneumonia, ICU nurses face a high 34 risk of developing somatic symptom disorder (SSD). The present study aims to investigate 35 the symptoms and causes of SSD of ICU nurses treating COVID-19 pneumonia. The research 36 results are expected to provide evidence for the establishment of a better management 37 strategy. Methods. This study enrolled a total of 140 ICU nurses who were selected by Jiangsu 39 Province Hospital to work in Wuhan (the epicenter of the COVID-19 epidemic in China) on 40 3 rd February 2020. A questionnaire "Somatic Symptom Disorders for ICU Nurses in Wuhan 41 No.1 Hospital" was designed based on the "International Classification of Functioning, 42 Disability and Health" (ICF). Exploratory factor analysis was performed to cluster the 43 symptoms, and logistic regression analysis to find the risk factors of the symptoms. 44 Results. Five major symptoms were chest-discomfort-and-palpitation (31.4%), dyspnea 45 (30.7%), nausea (21.4%), headache (19.3%), and dizziness (17.9%). In exploratory factor 46 analysis, the symptoms were classified into three clusters: Cluster A of breathing and sleep 47 disturbances (dizziness, sleepiness, dyspnea); Cluster B of gastrointestinal complaints and 48 pain (nausea, headache), and Cluster C of general symptoms (xerostomia, fatigue, 49 chest-discomfort-and-palpitation). In Cluster A, urine/feces splash, sex, and sputum splash 50 were independent predictive factors. In Cluster B, fall of protective glasses and urine/feces 51 splash were independent predictive factors. In Cluster C, urine/feces splash and urine/feces 52 clearance were independent predictive factors. 53 Conclusion. The ICU nurses in Wuhan showed varying and overlapping SSDs. These 54 SSDs could be classified into three symptom clusters. Based on the characteristics of their 55 SSDs, specific interventions could be implemented to safeguard the health of ICU nurses. 56 57 
 Title: Journal Pre-proof Symptom Cluster of ICU nurses treating COVID-19 pneumonia patients in Wuhan, China Running Title: SSDs of ICU nurses treating COVID-19 pneumonia patients Symptom Cluster of ICU nurses treating COVID-19 pneumonia patients in Wuhan, China Somatic Symptom Disorders of ICU Nurses treating COVID-19 pneumonia patients in
Output: False
Paragraph: BACKGROUND: The goal of this study was to determine if IV magnesium, useful for severe pediatric asthma, reduces time to medical readiness for discharge in patients with bronchiolitis when added to supportive care. We compared a single dose of 100 mg/kg of IV magnesium sulfate vs placebo for acute bronchiolitis. Patients received bronchodilator therapy, nebulized hypertonic saline, and 5 days of dexamethasone if there was eczema and/or a family history of asthma. Time to medical readiness for discharge was the primary efficacy outcome. Bronchiolitis severity scores and need for infirmary or hospital admission and for clinic revisits within 2 weeks were secondary outcomes. Cardiorespiratory instability onset was the safety outcome. RESULTS: A total of 162 previously healthy infants diagnosed with bronchiolitis aged 22 days to 17.6 months (median, 3.7 months) were enrolled. Approximately one-half of patients had eczema and/or a family history of asthma; 86.4% had positive findings on nasopharyngeal virus swabs. Geometric mean time until medical readiness for discharge was 24.1 h (95% CI, 20.0-29.1) for the 78 magnesium-treated patients and 25.3 h (95% CI, 20.3-31.5) for the 82 patients receiving placebo (ratio, 0.95 [95% CI, 0.52-1.80]; P ¼ .91). Mean bronchiolitis severity scores over time were similar for the two groups. The frequency of clinic visits in the subsequent 2 weeks (33.8% and 27.2%, respectively) was also similar. Fifteen magnesium recipients (19.5%) vs five placebo recipients (6.2%) were readmitted to the infirmary or hospital within 2 weeks (P ¼ .016). No acute cardiorespiratory side effects were reported. CONCLUSIONS: IV magnesium did not provide benefit for patients with acute bronchiolitis and may be harmful. 
 Title: IV Magnesium Sulfate for Bronchiolitis A Randomized Trial
Output: True
Paragraph: The direct chemoselective differential functionalization of the ring-C hydroxyl groups present in the Amaryllidaceae alkaloid lycorine is described allowing for selective manipulation of the 1,2-hydroxyl groups. A mini-library comprised of synthetic and natural lycorane alkaloids was prepared and their apoptosis-inducing activity investigated in human leukemia (Jurkat) cells. Further insights into the nature of this interesting apoptosis-inducing pharmacophore are described, including the requirement of both free hydroxyl groups in ring-C. 
 Title: Structure-activity studies on the lycorine pharmacophore: A potent inducer of apoptosis in human leukemia cells
Output: False
Paragraph: This chapter looks at the use of microlithographically fabricated biochip platforms for DNA diagnostics and prognostics, although protein and RNA biochips are also briefly considered. Biodetection methods such as ion-selective electrodes (ISEs), microelectromechanical systems (MEMS) devices such as microcantilevers, optical, piezoelectric-based acoustic wave, and mass spectrometry are briefly discussed. Emphasis is given to label-free electrochemical (impedimetric, voltammetric, and amperometric) detection. The production of DNA biochips is highlighted as are the operation and design of the experiments to reveal gene expression and SNP data. Applications discussed include the monitoring of microbes, cancer classification studies, and patient stratification in drug development. Finally, challenges and issues facing the development of diagnostic and prognostic biochips are discussed in detail. 
 Title: Biochip Platforms for DNA Diagnostics
Output: True
Paragraph: Background. Pneumonia, the leading infectious cause of child mortality globally, mainly afflicts developing countries. This prospective observational study aimed to assess the microorganisms associated with pneumonia in children aged <5 years in developing and emerging countries. Methods. A multicenter, case-control study by the GABRIEL (Global Approach to Biological Research, Infectious diseases and Epidemics in Low-income countries) network was conducted between 2010 and 2014 in Cambodia, China, Haiti, India (2 sites), Madagascar, Mali, Mongolia, and Paraguay. Cases were hospitalized children with radiologically confirmed pneumonia; controls were children from the same setting without any features suggestive of pneumonia. Nasopharyngeal swabs were collected from all subjects; 19 viruses and 5 bacteria were identified by reverse-transcription polymerase chain reaction. Associations between microorganisms and pneumonia were quantified by calculating the adjusted population attributable fraction (aPAF) after multivariate logistic regression analysis adjusted for sex, age, time period, other pathogens, and site. Results. Overall, 888 cases and 870 controls were analyzed; ≥1 microorganism was detected in respiratory samples in 93.0% of cases and 74.4% of controls (P < .001). Streptococcus pneumoniae, Mycoplasma pneumoniae, human metapneumovirus, rhinovirus, respiratory syncytial virus (RSV), parainfluenza virus 1, 3, and 4, and influenza virus A and B were independently associated with pneumonia; aPAF was 42.2% (95% confidence interval [CI], 35.5%-48.2%) for S. pneumoniae, 18.2% (95% CI, 17.4%-19.0%) for RSV, and 11.2% (95% CI, 7.5%-14.7%) for rhinovirus. Conclusions. Streptococcus pneumoniae, RSV, and rhinovirus may be the major microorganisms associated with pneumonia infections in children <5 years of age from developing and emerging countries. Increasing S. pneumoniae vaccination coverage may substantially reduce the burden of pneumonia among children in developing countries. 
 Title: Clinical Infectious Diseases Clinical Infectious Diseases ® 2017;65(4):604-12 Microorganisms Associated With Pneumonia in Children <5 Years of Age in Developing and Emerging Countries: The GABRIEL Pneumonia Multicenter, Prospective, Case-Control Study
Output: True
Paragraph: The outcome of Mycobacterium tuberculosis infection and the immunological response to the bacillus Calmette-Guerin (BCG) vaccine are highly variable in humans. Deciphering the relative importance of host genetics, environment, and vaccine preparation for the efficacy of BCG has proven difficult in natural populations. We developed a model system that captures the breadth of immunological responses observed in outbred individual mice, which can be used to understand the contribution of host genetics to vaccine efficacy. This system employs a panel of highly diverse inbred mouse strains, consisting of the founders and recombinant progeny of the "Collaborative Cross" project. Unlike natural populations, the structure of this panel allows the serial evaluation of genetically identical individuals and the quantification of genotype-specific effects of interventions such as vaccination. When analyzed in the aggregate, our panel resembled natural populations in several important respects: the animals displayed a broad range of susceptibility to M. tuberculosis, differed in their immunological responses to infection, and were not durably protected by BCG vaccination. However, when analyzed at the genotype level, we found that these phenotypic differences were heritable. M. tuberculosis susceptibility varied between lines, from extreme sensitivity to progressive M. tuberculosis clearance. Similarly, only a minority of the genotypes was protected by vaccination. The efficacy of BCG was genetically separable from susceptibility to M. tuberculosis, and the lack of efficacy in the aggregate analysis was driven by nonresponsive lines that mounted a qualitatively distinct response to infection. These observations support an important role for host genetic diversity in determining BCG efficacy and provide a new resource to rationally develop more broadly efficacious vaccines. IMPORTANCE Tuberculosis (TB) remains an urgent global health crisis, and the efficacy of the currently used TB vaccine, M. bovis BCG, is highly variable. The design of more broadly efficacious vaccines depends on understanding the factors that limit the protection imparted by BCG. While these complex factors are difficult to disentangle in natural populations, we used a model population of mice to understand the role of host genetic composition in BCG efficacy. We found that the ability of BCG to protect mice with different genotypes was remarkably variable. The efficacy of BCG did not depend on the intrinsic susceptibility of the animal but, instead, correlated with qualitative differences in the immune responses to the pathogen. These studies suggest that host genetic polymorphism is a critical determinant of vaccine efficacy and provide a model system to develop interventions that will be useful in genetically diverse populations. 
 Title: Tuberculosis Susceptibility and Vaccine Protection Are Independently Controlled by Host Genotype
Output: True
Paragraph: Background: The prevalence and risk factors for infection with enteropathogens in dogs frequenting dog parks have been poorly documented, and infected dogs can pose a potential zoonotic risk for owners. Hypothesis/Objectives: To determine the prevalence and risk factors of infection with enteropathogens and zoonotic Giardia strains in dogs attending dog parks in Northern California and to compare results of fecal flotation procedures performed at a commercial and university parasitology laboratory. Animals: Three-hundred dogs attending 3 regional dog parks in Northern California. Methods: Prospective study. Fresh fecal specimens were collected from all dogs, scored for consistency, and owners completed a questionnaire. Specimens were analyzed by fecal centrifugation flotation, DFA, and PCR for detection of 11 enteropathogens. Giardia genotyping was performed for assemblage determination. Results: Enteropathogens were detected in 114/300 dogs (38%), of which 62 (54%) did not have diarrhea. Frequency of dog park attendance correlated significantly with fecal consistency (P = .0039), but did not correlate with enteropathogen detection. Twenty-seven dogs (9%) were infected with Giardia, and genotyping revealed nonzoonotic assemblages C and D. The frequency of Giardia detection on fecal flotation was significantly lower at the commercial laboratory versus the university laboratory (P = .013), and PCR for Giardia was negative in 11/27 dogs (41%) that were positive on fecal flotation or DFA. Conclusions and Clinical Importance: Enteropathogens were commonly detected in dogs frequenting dog parks, and infection with Giardia correlated with fecal consistency. PCR detection of Giardia had limited diagnostic utility, and detection of Giardia cysts by microscopic technique can vary among laboratories. 
 Title: Prevalence of Enteropathogens in Dogs Attending 3 Regional Dog Parks in Northern California
Output: False
Paragraph: is one of the most common causes of acute viral hepatitis in the world with an estimated 20 million infections per year. Although the mortality rate is less than 1% among the general population, pregnant women can have a fatality rate of up to 30%. Additionally, chronic hepatitis E has increasingly become a significant clinical problem in immunocompromised individuals. Effective antivirals against HEV are needed. Areas covered-This review article addresses the current state of knowledge of HEV infections with regard to animal and cell culture model systems that are important for antiviral discovery and testing, our current understanding of the molecular mechanisms of virus replication, our understanding of how each viral protein functions, and areas that can potentially be exploited as therapeutic targets. Expert opinion-Lack of an efficient cell culture system for HEV propagation, the limited knowledge of HEV lifecycle, and the inherent self-limiting infection within the normal populace make the development of new therapeutic agents against HEV challenging. There are many promising therapeutic targets, and the tools for identifying and testing potential antivirals are rapidly evolving. The development of effective therapeutics against HEV in immunocompromised and pregnant patient populations is warranted. 
 Title: Therapeutic Targets for the Treatment of Hepatitis E Virus Infection HHS Public Access
Output: False
Paragraph: The presence of canine parvovirus type 2 (CPV-2), 2a and 2b has been described in Brazil, however, the type 2c had not been reported until now. In the current study, seven out of nine samples from dogs with diarrhea were characterized as CPV-2c, indicating that this virus is already circulating in the Brazilian canine population. Key words: canine parvovirus type 2c, sequence analysis, Brazil. The canine parvovirus type 2 (CPV-2) emerged as a novel pathogen in the late 70`s (1) and rapidly spread worldwide. Within few years, the virus underwent a rapid evolution and, new antigenic types, termed CPV-2a and 17) , completely replaced the original type 2 (21, 
 Title: FIRST DETECTION OF CANINE PARVOVIRUS TYPE 2C IN BRAZIL
Output: True
Paragraph: Background: As designated points of entry (PoEs) play a critical role in preventing the transmission of international public health risks, huge efforts have been invested in Taiwan to improve the core capacities specified in the International Health Regulations 2005 (IHR 2005). This article reviews how Taiwan strengthened the core capacities at the Taoyuan International Airport (TIA) and the Port of Kaohsiung (PoK) by applying a new, practicable model. Design: An IHR PoE program was initiated for implementing the IHR core capacities at designated PoEs. The main methods of this program were 1) identifying the designated PoEs according to the pre-determined criteria, 2) identifying the competent authority for each health measure, 3) building a close collaborative relationship between stakeholders from the central and PoE level, 4) designing three stages of systematic assessment using the assessment tool published by the World Health Organization (WHO), and 5) undertaking action plans targeting the gaps identified by the assessments. Results: Results of the self-assessment, preliminary external assessment, and follow-up external assessment revealed a continuous progressive trend at the TIA (86, 91, and 100%, respectively), and at the PoK (77, 97, and 99.9%, respectively). The results of the follow-up external assessment indicated that both these designated PoEs already conformed to the IHR requirements. These achievements were highly associated with strong collaboration, continuous empowerment, efficient resource integration, and sustained commitments. Conclusions: Considering that many countries had requested for an extension on the deadline to fulfill the IHR 2005 core capacity requirements, Taiwan's experiences can be a source of learning for countries striving to fully implement these requirements. Further, in order to broaden the scope of public health protection into promoting global security, Taiwan will keep its commitments on multisectoral cooperation, human resource capacity building, and maintaining routine and emergency capacities. 
 Title: Building core capacities at the designated points of entry according to the International Health Regulations 2005: a review of the progress and prospects in Taiwan
Output: False
Paragraph: In this article we review important established, newly emergent and potential viral diseases of cats, dogs and rabbits. Topics covered include virus epidemiology, disease pathogenesis, existing and prospective immunoprophylaxis against the viruses. For some feline viruses, notably the immunodeficiency virus, leukaemia virus and peritonitis virus, available vaccines are poorly efficacious but there are good prospects for this. A further challenge for the industry is likely to be due to viruses jumping species and the emergence of more virulent variants of established viruses resulting from mutations as has been the case for the canine parvovirus, coronaviruses and feline calicivirus. 
 Title: Review of companion animal viral diseases and immunoprophylaxis
Output: True
Paragraph: The unfolded protein response (UPR) adjusts the cell's protein folding capacity in the endoplasmic reticulum (ER) according to need. IRE1 is the most conserved UPR sensor in eukaryotic cells. It has remained controversial, however, whether mammalian and yeast IRE1 use a common mechanism for ER stress sensing. Here, we show that similar to yeast, human IRE1a's ER-lumenal domain (hIRE1a LD) binds peptides with a characteristic amino acid bias. Peptides and unfolded proteins bind to hIRE1a LD's MHC-like groove and induce allosteric changes that lead to its oligomerization. Mutation of a hydrophobic patch at the oligomerization interface decoupled peptide binding to hIRE1a LD from its oligomerization, yet retained peptide-induced allosteric coupling within the domain. Importantly, impairing oligomerization of hIRE1a LD abolished IRE1's activity in living cells. Our results provide evidence for a unifying mechanism of IRE1 activation that relies on unfolded protein binding-induced oligomerization. 
 Title: An unfolded protein-induced conformational switch activates mammalian IRE1
Output: True
Paragraph: PA-X, a fusion protein belonging to influenza A viruses (IAVs), integrating the N-terminal 191 amino acids of PA gene and the ribosomal frame-shifting product that lengthens out to 41 or 61 amino acids. Since its discovery in 2012, multiple functions have been attributed to this small protein, including a process, where wide-spread protein synthesis in infected host cells is shut down (called host shutoff), and viral replication, polymerase activity, viral-induced cell apoptosis, PA nuclear localization, and virulence are modulated. However, many of its proposed functions may be specific to strain, subtype, host, or cell line. In this review, we start by describing the well-defined global host-shutoff ability of PA-X and the potential mechanisms underlying it. We move on to the role played by PA-X in modulating innate and acquired immune responses in the host. We then systematically discuss the role played by PA-X in modulating the virulence of influenza viruses of different subtypes and host origins, and finish with a general overview of the research advances made in identifying the host cell partners that interact with PA-X. To uncover possible clues about the differential effects of PA-X in modulating viral virulence, we focus on systemically evaluating polymorphisms in PA-X from various viral subtypes and hosts, including avian and human H5N1, H5N6, H9N2, and H7N9 viruses. Finally, we conclude with a proposition regarding the possible future research directions for this important protein. 
 Title: PA-X: a key regulator of influenza A virus pathogenicity and host immune responses
Output: True
Paragraph: The surveillance and prevention of pathogenic microbiological contamination are the most important tasks of biosafety management in the lab. There is an urgent need to establish an effective and unbiased method to evaluate and monitor such contamination. This study aims to investigate the utility of next generation sequencing (NGS) method to detect possible contamination in the microbiology laboratory. Environmental samples were taken at multiple sites at the lab including the inner site of centrifuge rotor, the bench used for molecular biological tests, the benches of biosafety cabinets used for viral culture, clinical sample pre-treatment and nucleic acids extraction, by scrubbing the sites using sterile flocked swabs. The extracted total nucleic acids were used to construct the libraries for deep sequencing according to the protocol of Ion Torrent platform. At least 1G raw data was obtained for each sample. The reads of viruses and bacteria accounted for 0.01 ± 0.02%, and 77.76 ± 12.53% of total reads respectively. The viral sequences were likely to be derived from gene amplification products, the nucleic acids contaminated in fetal bovine serum. Reads from environmental microorganisms were also identified. Our results suggested that NGS method was capable of monitoring the nucleic acids contaminations from different sources in the lab, demonstrating its promising utility in monitoring and assessing the risk of potential laboratory contamination. The risk of contamination from reagents, remnant DNA and environment should be considered in data analysis and results interpretation. 
 Title: Application of next generation sequencing technology on contamination monitoring in microbiology laboratory
Output: True
Paragraph: Acute respiratory infections (ARI) are a major cause of morbidity worldwide. 1 Some of the earliest studies to describe the epidemiology of these infections were household cohort studies. [2] [3] [4] [5] [6] [7] The largest of these were conducted in Seattle, Washington and Tecumseh, Michigan in the 1960s and 1970s 6,7 and they provided information on the relative frequency, seasonality and symptomatic characteristics of ARI shortly after many respiratory viruses were first identified. 7 Given that the role of household structure in seasonal incidence and transmission of respiratory viruses was the primary objective, an individual's longitudinal history of infection was not a major focus. Indeed, during the first phase of the Tecumseh Study of Respiratory Illness, households were maintained on report for only 1 year, and then gradually replaced so that the entire community could be represented over time. 8 These historical studies relied on cell culture for virus identification, a method that requires specimens to be processed quickly and is considerably less sensitive than current molecular methods. 9 For this reason, the Tecumseh study and others relied extensively on serodiagnosis of influenza infection using twice yearly blood specimens. 10 It was not possible to time infections in those who only were serologically positive, limiting the ability to do robust analyses of transmission patterns. 11 With current molecular techniques, it has become much easier to identify a broad range of agents of respiratory infection. This allows documentation of infection, co-infection and subsequent re-infection. Collecting specimens within a short time from the onset of symptoms still maximizes the likelihood of accurate and timely identification of viruses associated with a respiratory illness for studies of transmission and vaccine effectiveness. Collection of regular blood specimens continues to be valuable as well, for both virus identification and for analysis of serologic correlates of protection. The Household Influenza Vaccine Evaluation (HIVE) Study is an ongoing prospective household cohort study that began in 2010. The HIVE Study was based on the original Tecumseh Study of Respiratory Illness 6 with several key modifications to illness surveillance and to laboratory methods for identification of respiratory viruses. While respiratory virus infections in general could be studied, the primary objective was to estimate the effectiveness of influenza vaccines using a cohort design for comparison with studies using the testnegative design (TND). Under the TND, specimens are collected from participants who meet a respiratory illness case V C The Author(s) 
 Title: Data Resource Profile Data resource profile: Household Influenza Vaccine Evaluation (HIVE) Study Data resource basics
Output: True
Paragraph: Mouse models are important tools both for studying the pathogenesis of infectious diseases and for the preclinical evaluation of vaccines and therapies against a wide variety of human pathogens. The use of genetically defined inbred mouse strains, humanized mice, and gene knockout mice has allowed the research community to explore how pathogens cause disease, define the role of specific host genes in either controlling or promoting disease, and identify potential targets for the prevention or treatment of a wide range of infectious agents. This review discusses several of the most commonly used mouse model systems, as well as new resources such as the Collaborative Cross as models for studying infectious diseases. (Clin Ther. 2019;41:1912e1922)  
 Title: Mouse Models as Resources for Studying Infectious Diseases
Output: False
Paragraph: Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) is the most important endemic pathogen in the U.S. swine industry. Despite control efforts involving improved biosecurity and different vaccination protocols, the virus continues to circulate and evolve. One of the foremost challenges in its control is high levels of genetic and antigenic diversity. Here, we quantify the co-circulation, emergence and sequential turnover of multiple PRRSV lineages in a single swine-producing region in the United States over a span of 9 years (2009)(2010)(2011)(2012)(2013)(2014)(2015)(2016)(2017). By classifying over 4,000 PRRSV sequences (open-reading frame 5) into phylogenetic lineages and sub-lineages, we document the ongoing diversification and temporal dynamics of the PRRSV population, including the rapid emergence of a novel sub-lineage that appeared to be absent globally pre-2008. In addition, lineage 9 was the most prevalent lineage from 2009 to 2010, but its occurrence fell to 0.5% of all sequences identified per year after 2014, coinciding with the emergence or re-emergence of lineage 1 as the dominant lineage. The sequential dominance of different lineages, as well as three different sublineages within lineage 1, is consistent with the immune-mediated selection hypothesis for the sequential turnover in the dominant lineage. As host populations build immunity through natural infection or vaccination toward the most common variant, this dominant (sub-) lineage may be replaced by an emerging variant to which the population is more susceptible. An analysis of patterns of non-synonymous and synonymous mutations revealed evidence of positive selection on immunologically important regions of the genome, further supporting the potential that immune-mediated selection shapes the evolutionary and epidemiological dynamics for this virus. This has important implications for patterns of emergence and re-emergence of genetic variants of PRRSV that have negative impacts on the swine industry. Constant surveillance on PRRSV occurrence is crucial to a better understanding of the epidemiological and evolutionary dynamics of co-circulating viral lineages. Further studies utilizing whole genome sequencing and exploring the extent of cross-immunity between heterologous PRRS viruses could shed further light on PRRSV immunological response and aid in developing strategies that might be able to diminish disease impact. 
 Title: Temporal Dynamics of Co-circulating Lineages of Porcine Reproductive and Respiratory Syndrome Virus
Output: False
Paragraph: When the central nervous system (CNS) is under viral attack, defensive antiviral responses must necessarily arise from the CNS itself to rapidly and efficiently curb infections with minimal collateral damage to the sensitive, specialized and non-regenerating neural tissue. This presents a unique challenge because an intact blood-brain barrier (BBB) and lack of proper lymphatic drainage keeps the CNS virtually outside the radar of circulating immune cells that are at constant vigilance for antigens in peripheral tissues. Limited antigen presentation skills of CNS cells in comparison to peripheral tissues is because of a total lack of dendritic cells and feeble expression of major histocompatibility complex (MHC) proteins in neurons and glia. However, research over the past two decades has identified immune effector mechanisms intrinsic to the CNS for immediate tackling, attenuating and clearing of viral infections, with assistance pouring in from peripheral circulation in the form of neutralizing antibodies and cytotoxic T cells at a later stage. Specialized CNS cells, microglia and astrocytes, were regarded as sole sentinels of the brain for containing a viral onslaught but neurons held little recognition as a potential candidate for protecting itself from the proliferation and pathogenesis of neurotropic viruses. Accumulating evidence however indicates that extracellular insult causes neurons to express immune factors characteristic of lymphoid tissues. This article aims to comprehensively analyze current research on this conditional alteration in the protein expression repertoire of neurons and the role it plays in CNS innate immune response to counter viral infections. ß 
 Title: Neurons under viral attack: Victims or warriors?
Output: False