niryuu/sni-each-converted huggingface dataset:
Paragraph: Viroporins are small, hydrophobic trans-membrane viral proteins that oligomerize to form hydrophilic pores in the host cell membranes. These proteins are crucial for the pathogenicity and replication of viruses as they aid in various stages of the viral life cycle, from genome uncoating to viral release. In addition, the ion channel activity of viroporin causes disruption in the cellular ion homeostasis, in particular the calcium ion. Fluctuation in the calcium level triggers the activation of the host defensive programmed cell death pathways as well as the inflammasome, which in turn are being subverted for the viruses' replication benefits. This review article summarizes recent developments in the functional investigation of viroporins from various viruses and their contributions to viral replication and virulence. Recent categorization places viroporins into two major classes based on the number of TMD that are then further classified into A or B subclasses based on their membrane topology [2] . Single TMD viroporins in subclass A have their N terminus facing the ER lumen while those in subclass B have their C-terminal tails in the ER lumen. For Class IIA and IIB viroporins, both N-and C-terminus are inside the ER lumen or the cytoplasmic matrix, respectively (Figure 1 ). An additional third class of viroporins may be necessary as viroporins with three-pass TMD have been proposed, such as the non-structural protein 4 (NSP4) of rotavirus [49] and 3a of severe acute respiratory syndrome SARS-CoV [31]. Due to their high structural variability under different conditions, solving the architecture of viroporins under physiological environment has been difficult. However, recent advancement in technology such as the ability to characterize protein structure at the atomic resolution using nuclear magnetic resonance (NMR) 
 Title: Viral Membrane Channels: Role and Function in the Virus Life Cycle
Output: True
Paragraph: Background. The diagnosis of severe acute respiratory syndrome (SARS) is difficult early in the illness, because its presentation resembles that of other nonspecific viral fevers, such as dengue. Dengue fever is endemic in many of the countries in which the large SARS outbreaks occurred in early 2003. Misdiagnosis may have serious public health consequences. We aimed to determine simple laboratory features to differentiate SARS from dengue. Methods. We compared the laboratory features of 55 adult patients with SARS at presentation (who were all admitted before radiological changes had occurred) and 147 patients with dengue. Features independently predictive of dengue were modeled by multivariate logistic regression to create a diagnostic tool with 100% specificity for dengue. Results. Multivariate analysis identified 3 laboratory features that together are highly predictive of a diagnosis of dengue and able to rule out the possibility of SARS: platelet count of ! platelets/L, white blood cell 
 Title: Use of Simple Laboratory Features to Distinguish the Early Stage of Severe Acute Respiratory Syndrome from Dengue Fever
Output: False
Paragraph: Many viruses that replicate in the cytoplasm compartmentalize their genome replication and transcription in organelle-like structures that enhance replication efficiency and protection from host defenses. In particular, recent studies with diverse positive-strand RNA viruses have further elucidated the ultrastructure of membrane-bound RNA replication complexes and how these complexes function in close coordination with virion assembly and budding. The structure, function, and assembly of some positive-strand RNA virus replication complexes have parallels and potential evolutionary links with the replicative cores of doublestrand RNA virus and retrovirus virions and more general similarities with the replication factories of cytoplasmic DNA viruses. . In vivo self-interaction of nodavirus RNA replicase protein a revealed by fluorescence resonance energy transfer. J. Virol. 79, 8909-8919. Egger, D., and Bienz, K. (2002) . Recombination of poliovirus RNA proceeds in mixed replication complexes originating from distinct replication start sites. J. Virol. 76, 10960-10971. Egger, D., Teterina, N., Ehrenfeld, E., and Bienz, K. (2000). Formation of the poliovirus replication complex requires coupled viral translation, vesicle production, and viral RNA synthesis. J. Virol. 74, 6570-6580. Froshauer, S., Kartenbeck, J., and Helenius, A. (1988). Alphavirus RNA replicase is located on the cytoplasmic surface of endosomes and lysosomes. 
 Title: Cell Host & Microbe Review Cytoplasmic Viral Replication Complexes
Output: False
Paragraph: Objective: This study investigated the sources of stress, corresponding symptoms, and stress relief among nurses of the first Chinese anti-Ebola medical team during the Sierra Leone aid mission. Method: A purposive sampling method was used and 10 nurses were selected from the first Chinese anti-Ebola medical team that was dispatched to Sierra Leone. Data were collected via phone and semistructured interviews, then analyzed using Colaizzi's seven-step method. Results: The data showed three major themes: (1) The causes of stress during the Sierra Leone aid mission mainly related to unsafety, responsibility, and unfamiliarity; (2) Physical, cognitive, emotional, and behavioral symptoms were documented; (3) Nurses experienced relief from stress after the mission. Conclusion: Targeted measures, proper responses and good community support can effectively lower stress among nurses on anti-Ebola missions. 
 Title: Sources and symptoms of stress among nurses in the first Chinese anti-Ebola medical team during the Sierra Leone aid mission: A qualitative study-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/)
Output: True
Paragraph: Ebolaviruses constitute a public health threat, particularly in Central and Western Africa. Host cell factors required for spread of ebolaviruses may serve as targets for antiviral intervention. Lectins, TAM receptor tyrosine kinases (Tyro3, Axl, Mer), T cell immunoglobulin and mucin domain (TIM) proteins, integrins, and Niemann-Pick C1 (NPC1) have been reported to promote entry of ebolaviruses into certain cellular systems. However, the factors used by ebolaviruses to invade macrophages, major viral targets, are poorly defined. Here, we show that mannose-specific lectins, TIM-1 and Axl augment entry into certain cell lines but do not contribute to Ebola virus (EBOV)-glycoprotein (GP)-driven transduction of macrophages. In contrast, expression of Mer, integrin αV, and NPC1 was required for efficient GP-mediated transduction and EBOV infection of macrophages. These results define cellular factors hijacked by EBOV for entry into macrophages and, considering that Mer and integrin αV promote phagocytosis of apoptotic cells, support the concept that EBOV relies on apoptotic mimicry to invade target cells. 
 Title: Analysis of Ebola Virus Entry Into Macrophages
Output: False
Paragraph: HTS with microtiter plates has been the major tool used in the pharmaceutical industry to explore chemical diversity space and to identify active compounds and pharmacophores for specific biological targets. However, HTS faces a daunting challenge regarding the fast-growing numbers of drug targets arising from genomic and proteomic research, and large chemical libraries generated from highthroughput synthesis. There is an urgent need to find new ways to profile the activity of large numbers of chemicals against hundreds of biological targets in a fast, low-cost fashion. Chemical microarray can rise to this challenge because it has the capability of identifying and evaluating small molecules as potential therapeutic reagents. During the past few years, chemical microarray technology, with different surface chemistries and activation strategies, has generated many successes in the evaluation of chemicalprotein interactions, enzyme activity inhibition, target identification, signal pathway elucidation and cell-based functional analysis. The success of chemical microarray technology will provide unprecedented possibilities and capabilities for parallel functional analysis of tremendous amounts of chemical compounds. 
 Title: Chemical microarray: a new tool for drug screening and discovery
Output: True
Paragraph: Background: The 2003 outbreak of severe acute respiratory syndrome (SARS) infected over 8000 people and killed 774. Transmission of SARS occurred through direct and indirect contact and large droplet nuclei. The World Health Organization recommended the use of household disinfectants, which have not been previously tested against SARS coronavirus (SARS-CoV), to disinfect potentially contaminated environmental surfaces. There is a need for a surrogate test system given the limited availability of the SARS-CoV for testing and biosafety requirements necessary to safely handle it. In this study, the antiviral activity of standard household products was assayed against murine hepatitis virus (MHV), as a potential surrogate for SARS-CoV. Methods: A surface test method, which involves drying an amount of virus on a surface and then applying the product for a specific contact time, was used to determine the virucidal activity. The virus titers and log reductions were determined by the Reed and Muench tissue culture infective dose (TCID) 50 end point method. Results: When tested as directed, common household disinfectants or antiseptics, containing either 0.050% of triclosan, 0.12% of PCMX, 0.21% of sodium hypochlorite, 0.23% of pine oil, or 0.10% of a quaternary compound with 79% of ethanol, demonstrated a 3-log reduction or better against MHV without any virus recovered in a 30-second contact time. Conclusion: Common household disinfectants and antiseptics were effective at inactivating MHV, a possible surrogate for SARS-CoV, from surfaces when used as directed. In an outbreak caused by novel agents, it is important to know the effectiveness of disinfectants and antiseptics to prevent or reduce the possibility of human-to-human transmission via surfaces. NOTE. Calculations were performed using the Reed and Muench TCID 50 end point expressed as log 10 TCID 50 /mL. 8,9 CPE, cytopathogenic effect; MHV, murine hepatitis virus; Rep, replicate; PCMX, parachlorometaxylenol. *Test procedure performed not using sephadex columns but still met the 3-log reduction success criteria. 
 Title: The antiviral action of common household disinfectants and antiseptics against murine hepatitis virus, a potential surrogate for SARS coronavirus
Output: False
Paragraph: Most recent emerging infectious diseases have been zoonotic in origin. It is our contention that one of the factors responsible for such emergence is the trade in wildlife and bushmeat in particular. This article considers the effect of increasing diversity in the species hunted on the probability of global epidemics such as SARS. In particular, we develop a mathematical model of the probability of such an outbreak in terms of the number of species hunted, the number of susceptibles, and the rate of contact. Hence, we postulate that local biodiversity loss and increasing rates of animal trafficking, and trade and transportation of animals to large cities-where there is a greater potential for person-to-person transmission-may increase the probability of such outbreaks dramatically. 
 Title: Wildlife Trade and the Emergence of Infectious Diseases
Output: True
Paragraph: Background: China's one-child-per-couple policy, introduced in 1979, led to profound demographic changes for nearly a quarter of the world's population. Several decades later, the consequences include decreased fertility rates, population aging, decreased household sizes, changes in family structure, and imbalanced sex ratios. The epidemiology of communicable diseases may have been affected by these changes since the transmission dynamics of infectious diseases depend on demographic characteristics of the population. Of particular interest is influenza because China and Southeast Asia lie at the center of a global transmission network of influenza. Moreover, changes in household structure may affect influenza transmission. Is it possible that the pronounced demographic changes that have occurred in China have affected influenza transmission? Methods and Findings: To address this question, we developed a continuous-time, stochastic, individual-based simulation model for influenza transmission. With this model, we simulated 30 years of influenza transmission and compared influenza transmission rates in populations with and without the one-child policy control. We found that the average annual attack rate is reduced by 6.08% (SD 2.21%) in the presence of the one-child policy compared to a population in which no demographic changes occurred. There was no discernible difference in the secondary attack rate, 20.15% (SD 1.85%), between the populations with and without a one-child policy. We also forecasted influenza transmission over a ten-year time period in a population with a two-child policy under a hypothesis that a two-child-per-couple policy will be carried out in 2015, and found a negligible difference in the average annual attack rate compared to the population with the one-child policy. Conclusions: This study found that the average annual attack rate is slightly lowered in a population with a one-child policy, which may have resulted from a decrease in household size and the proportion of children in the population. 
 Title: Effect of the One-Child Policy on Influenza Transmission in China: A Stochastic Transmission Model
Output: False
Paragraph: Objectives: Cow and calf performance in a semi-confined cow-calf production system was compared with total confinement using summer-born calves. Material and Methods: The experiment was conducted over 3 yr in eastern Nebraska (ENREC) and 2 yr in western Nebraska (PREC) in a randomized complete block design. Lactating, crossbred beef cows (n = 127 at ENREC; n = 56 at PREC) with summer-born calves were used from November to April. Treatments were (1) drylot feeding or (2) cornstalk grazing with supplementation. Dry-lot pairs were limit fed a crop residue and distillersbased diet to meet energy requirements of a lactating cow. A dried distillers grain-based pellet was supplemented to pairs on cornstalks at a rate of 2.4 kg of DM/pair daily. Dry-lot cow-calf pairs were limit fed 12.1 kg of DM/d throughout the trial. Results and Discussion: At ENREC, cows wintered on cornstalks lost BW and had a 0.46-unit decrease in BCS (P < 0.01), whereas cows in the dry-lot gained BW and had a 0.24-unit increase in BCS. At PREC, BCS increased by 0.03 units for cows wintered in the dry-lot and decreased by 0.26 units for cows wintered on cornstalks (P < 0.04). At both locations, calves fed in a dry-lot had greater ADG and BW per day of age compared with calves offered cornstalk grazing with supplementation (P ≤ 0.03). Implications and Applications: A partial budget suggests that lower winter production inputs compensate for reduced performance of calves when cow-calf pairs are wintered on cornstalks, making residue grazing a viable option in partial confinement systems. 
 Title: Performance of cows and summer-born calves and economics in semi-confined and confined beef systems
Output: False
Paragraph: A one-tube reverse transcription-polymerase chain reaction (RT-PCR) for absolute feline coronavirus (FCoV) quantitation was developed. The assay is based on the 5% nuclease activity of the Thermus fla6us (Tfl) polymerase and a fluorogenic probe which generates fluorescence when it is cleaved. The fluorogenic probe, also called TaqMan™ probe (Perkin Elmer, Foster City, USA), is an oligonucleotide designed to bind between the two PCR primers to the target cDNA and is labeled with a reporter and a quencher dye. In the intact probe, the quencher dye suppresses the fluorescence of the reporter dye by Fö rster-type energy transfer. During the polymerase extension steps the Tfl exonuclease activity cleaves the hybridised probe resulting in the generation of fluorescent emission of the reporter dye. The threshold cycle (C T value) indicates the increase of reporter fluorescence and is directly related to the initial amount of target cDNA or RNA, respectively. Fluorescence is monitored in real time after each cycle by a Perkin-Elmer ABI Prism ® 7700 Sequence Detector. After completion of amplification, the C T values of the samples are calculated back to a standard curve, generated by amplification of diluted standard molecules. The one-tube RT-PCR described below allows precise quantitation, is highly sensitive, rapid (no separate reverse transcription step and no post-amplification steps), easy to handle, allows for a high sample throughput, shows a very good reproducibility, and can be executed with a low risk of contamination. The design of the primers-probe combination enables the detection of all known FCoV strains and is also useful for the detection of canine coronavirus, transmissible gastroenteritis virus and porcine respiratory coronavirus. 
 Title: One-tube fluorogenic reverse transcription-polymerase chain reaction for the quantitation of feline coronaviruses
Output: False
Paragraph: Background: SARS coronavirus (SARS-CoV) was identified as the etiological agent of SARS, and extensive investigations indicated that it originated from an animal source (probably bats) and was recently introduced into the human population via wildlife animals from wet markets in southern China. Previous studies revealed that the spike (S) protein of SARS had experienced adaptive evolution, but whether other functional proteins of SARS have undergone adaptive evolution is not known. We employed several methods to investigate selective pressure among different SARS-CoV groups representing different epidemic periods and hosts. Our results suggest that most functional proteins of SARS-CoV have experienced a stepwise adaptive evolutionary pathway. Similar to previous studies, the spike protein underwent strong positive selection in the early and middle phases, and became stabilized in the late phase. In addition, the replicase experienced positive selection only in human patients, whereas assembly proteins experienced positive selection mainly in the middle and late phases. No positive selection was found in any proteins of bat SARS-like-CoV. Furthermore, specific amino acid sites that may be the targets of positive selection in each group are identified. This extensive evolutionary analysis revealed the stepwise evolution of different functional proteins of SARS-CoVs at different epidemic stages and different hosts. These results support the hypothesis that SARS-CoV originated from bats and that the spill over into civets and humans were more recent events. 
 Title: Differential stepwise evolution of SARS coronavirus functional proteins in different host species
Output: True
Paragraph: Mathematical models of infectious disease spread are important tools for assessing the threat of a novel pathogen and offer the best information for mitigating an outbreak. Here we present a metapopulation model of disease spread in Great Britain defined at the level of electoral wards. Using data from the United Kingdom 2001 census and the National Travel Survey to define the amount of travel performed by individuals between wards, we examine the effect of assumptions on the regularity of travel. Routine, daily commuter-type movements, characteristic of the working population are shown to lead to a slower epidemic spread compared to movements with random destinations. We demonstrate that routine movements slow down the epidemic spread compared to a standard metapopulation setting by up to 25%. We also show that spurious long distance movements present in the census data do not have a significant impact on the development of a potential epidemic in Great Britain. 
 Title: The role of routine versus random movements on the spread of disease in Great Britain
Output: True
Paragraph: Rationale: Pneumocystis jirovecii causes severe pneumonia in immunocompromised hosts. Human immunodeficiency virus infection, malignancy, solid organ or hematopoietic cell transplantation, and primary immune deficiency compose the risk factors for Pneumocystis pneumonia (PCP) in children, and PCP can be an initial clinical manifestation of primary immune deficiency. Patient concerns: A 5-month-old infant presented with cyanosis and tachypnea. He had no previous medical or birth history suggesting primary immune deficiency. He was diagnosed with interstitial pneumonia on admission. Diagnoses: He was diagnosed with PCP, and further evaluations revealed underlying X-linked hyper-IgM syndrome. Interventions: He was treated with trimethoprim/sulfamethoxazole for PCP, and eventually received allogeneic hematopoietic cell transplantation for hyper-IgM syndrome. Outcomes: Twenty months have passed after transplantation without severe complications. Lessons: PCP should be considered in infants presenting with severe interstitial pneumonia even in the absence of evidence of immune deficiency. Primary immune deficiency should also be suspected in infants diagnosed with PCP. Abbreviations: HD = hospital day, HIGM = hyper-IgM, HIV = human immunodeficiency virus, PCP = Pneumocystis pneumonia, PCR = polymerase chain reaction, PID = primary immune deficiency, TMP/SMX = trimethoprim/sulfamethoxazole. 
 Title: Pneumocystis jirovecii pneumonia as an initial manifestation of hyper-IgM syndrome in an infant A case report
Output: False
Paragraph: Clara cells are non-ciliated, secretory bronchiolar epithelial cells that serve to detoxify harmful inhaled substances. Clara cells also function as stem/progenitor cells for repair in the bronchioles. Clara cell secretory protein (CCSP) is specifically expressed in pulmonary Clara cells and is widely used as a Clara cell marker. In addition CCSP promoter is commonly used to direct gene expression into the lung in transgenic models. The discovery of CCSP immunoreactivity in plasma membranes of airway lining cells prompted us to explore the possibility of enriching Clara cells by flow cytometry. We established a novel and simple method for the isolation of CCSP-expressing cell Clara cells using a combination of mechanical and enzymatic dissociation followed by flow cytometry sorting technology. We showed that ,25% of dissociated cells from whole lung expressed CCSP. In the resulting preparation, up to 98% of cells expressed CCSP. Notably, we found that several common stem cell markers including CD44, CD133, Sca-1 and Sox2 were expressed in CCSP + cells. Moreover, CCSP + cells were able to form spheroid colonies in vitro with 0.97% efficiency. Parallel studies in vivo confirmed that a small population of CCSP 2 expressing cells in mouse airways also demonstrates stem cell-like properties such as label retention and harboring rare bronchioalveolar stem cells (BASCs) in terminal bronchioles (TBs). We conclude that CCSP + cells exhibit a number of stem cell-like features including stem cell marker expression, bronchosphere colony formation and self-renewal ability. Clara cell isolation by flow cytometry sorting is a useful method for investigating the function of primary Clara cells in stem cell research and mouse models. 
 Title: Novel Method for Isolation of Murine Clara Cell Secretory Protein-Expressing Cells with Traces of Stemness
Output: True
Paragraph: The central importance of cell polarity control is emphasized by the frequency with which it is targeted by many diverse viruses. It is clear that in targeting key polarity control proteins, viruses affect not only host cell polarity, but also influence many cellular processes, including transcription, replication, and innate and acquired immunity. Examination of the interactions of different virus proteins with the cell and its polarity controls during the virus life cycles, and in virally-induced cell transformation shows ever more clearly how intimately all cellular processes are linked to the control of cell polarity. 
 Title: Upsetting the Balance: When Viruses Manipulate Cell Polarity Control
Output: True
Paragraph: Rotavirus is a non-enveloped virus that depends on cellular lipids for cell entry and associates with lipid rafts during assembly. However, the effects of cellular lipids on rotavirus assembly are still not fully understood. The present study analyzes the effects of lovastatin, an inhibitor of cholesterol biosynthesis, during rotavirus infection in MA104 cells with regard to viral growth and particle assembly. Following viral infection, a 2-log relative reduction of viral titers was observed in drug-treated cells, while viral mRNA levels in infected cells remained unaltered in both groups. Furthermore, the levels of some viral proteins in drug-treated cells were elevated. The observed discordance between the viral RNA and protein levels and the decrease in infectivity titers of viral progeny in the drug-treated cells suggested that the drug affects viral assembly, the viral proteins not being properly incorporated into virions. Transmission electron microscopic (TEM) analysis revealed that in drug-treated cells there was an increase in ''empty-looking'' rotavirus particles devoid of an electron-dense core as compared to the normal, electron-dense particles seen in untreated infected cells. The present study thus provides visual evidence of defective rotavirus particle assembly as a result of cholesterol depletion. 
 Title: Defective rotavirus particle assembly in lovastatin-treated MA104 cells
Output: True
Paragraph: This report explains the employing of a combination test of traditional cell culture with a quantitative real-time PCR for assessment of the antiviral effect of zinc sulfate (ZnSO 4 ) on herpes simplex virus (HSV)-infected Vero cells. Our evidence showed that the treatment with 0.3 mM ZnSO 4 strongly inhibited the replication of virus progeny (MOI 0.001) at least 68-fold less. On the other hand, the IC50 demonstrated that the highest activity of ZnSO 4 was at the 0.23 mM concentration. 
 Title: Zinc Sulfate in Narrow Range as an In Vitro Anti-HSV-1 Assay
Output: True
Paragraph: Respiratory pathogens are thought to be involved in the pathogenesis and exacerbations of asthma at all ages; however, little is known about the airway microbiome in the elderly. Aim of the study: To identify respiratory pathogens in the induced sputum (IS) of elderly asthmatics, and to determine the association between pathogens and the markers of asthma activity. Material and methods: Twenty-nine subjects with stable asthma, 15 above 65 years of age and 14 aged 30-49 years, underwent clinical evaluation, fractional exhaled nitric oxide measurement, and sputum induction. Pathogens were detected by multiplex reverse transcription polymerase chain reaction. The periostin concentration of IS supernatants was measured by enzyme-linked immunosorbent assay. Serum eosinophil cationic protein and total IgE levels were measured by ImmunoCAP. Conclusions: Despite the existence of differences in some clinical and inflammatory characteristics of asthma between elderly and non-elderly asthmatics, the pathogen detection rates in the IS from the two groups are similar. 
 Title: The profile of respiratory pathogens in induced sputum of elderly and non-elderly asthmatics
Output: True
Paragraph: Hospitals develop nurse schedules that cover a period of 4-6 weeks and are posted several weeks in advance. Once posted, changes to the schedule require voluntary participation by the nurses, making it difficult for hospitals to respond to changes in nursing needs and availability of nurses. At the same time, nursing needs' forecasts developed several weeks in advance are often wrong. In each hospital setting, there may exist several promising strategies to enhance scheduling flexibility and reduce the mismatch between the nursing needs and the availability of nurses. However, methodologies to evaluate such strategies, before testing them in expensive pilot implementation, do not exist. We demonstrate how such evaluations can be carried out using historical data. Furthermore, we demonstrate the use of our approach by evaluating the benefits of a strategy where nurses are divided into two cohorts and schedules are phase shifted for the two cohorts. Staggering schedules allows nursing unit managers to benefit from more frequent updating of needs' assessments without having to change work rules. Upon applying our approach to data from a large urban hospital, we discovered that in this example staggering did not improve the performance of nurse schedules. We discuss possible reasons for this result, its implications for hospital managers, and other potential uses of our approach. 
 Title: On evaluating the impact of flexibility enhancing strategies on the performance of nurse schedules
Output: False
Paragraph: Background: Treatments for autoimmune diseases aim to dampen autoreactivity while preserving normal immune function. In CD4 + T cells, the transcription factor Oct1/Pou2f1 is a dispensable transcription factor for T cell development and response to primary infection, but promotes expression of target genes, including Il2 and Ifng, under conditions of antigen reencounter. As a result, they are more strongly expressed upon secondary stimulation. Such repeated antigen encounters occur in memory recall responses, in autoimmunity where self-antigen can be recognized multiple times, and in chronic infection where foreign antigen is persistent. Based on these previous findings, we hypothesized that Oct1 loss would protect animals from autoimmunity but maintain normal responses to pathogens in the CNS. Objective: We used a conditional mouse Oct1 (Pou2f1) allele and a CD4-Cre driver to determine the effect of T cellspecific Oct1 loss on autoimmune-and viral-induced neuroinflammation using an autoantigen-driven EAE model of autoimmunity and a JHMV model of viral infection. Results: Oct1 conditional deletion mitigated clinical scores and reduced infiltrating T cells and cytokine production in the EAE model. Consistently, Oct1-deficient CD4 + T cells stimulated in vitro showed increased expression of markers associated with T cell anergy, particularly in the absence of co-stimulatory signals. In contrast, anti-viral T cell effector functions are intact in the absence of Oct1, with no changes in neuroinflammation, infiltrating T cells or cytokine production. Conclusion: Our findings uncover a significant difference between the effect of Oct1 loss on autoimmune and antipathogen responses, which potentially could be exploited for therapeutic benefit. 
 Title: T cell-selective deletion of Oct1 protects animals from autoimmune neuroinflammation while maintaining neurotropic pathogen response
Output: False
Paragraph: A 1.5-month-old Kangal breed puppy from a dairy cattle farm died after showing severe diarrhoea and incoordination. Necropsy examination revealed multifocal pulmonary consolidation and necrosis and fibrinohaemorrhagic enteritis. Microscopically, there was necrotic and purulent bronchopneumonia, myocarditis and non-purulent encephalitis. In the jejunum and ileum there was villous atrophy and crypt hyperplasia with oocyst-like and schizont-like structures in the epithelia. Immunohistochemically, Neospora caninum antigen was detected in association with the intestinal protozoal structures, degenerative neurons and areas of necrosis in the lungs and heart. Polymerase chain reaction confirmed that the organism was N. caninum and not Toxoplasma gondii. The seroprevalence for N. caninum was 74.2% (49/66 animals) for the cattle and 57.1% (4/7 animals) for dogs on this farm. This report documents fatal systemic neosporosis and enteroepithelial stages of N. caninum in a naturally infected puppy. To the authors' knowledge, this is the first definition of intestinal neosporosis in a naturally infected dog as well as the first evidence of fatal canine neosporosis in Turkey. 
 Title: Neospora caninum: the First Demonstration of the Enteroepithelial Stages in the Intestines of a Naturally Infected Dog ScienceDirect Neosporosis in Dog
Output: False
Paragraph: As a key factor in endemic and epidemic dynamics, the geographical distribution of viruses has been frequently interpreted in the light of their genetic histories. Unfortunately, inference of historical dispersal or migration patterns of viruses has mainly been restricted to model-free heuristic approaches that provide little insight into the temporal setting of the spatial dynamics. The introduction of probabilistic models of evolution, however, offers unique opportunities to engage in this statistical endeavor. Here we introduce a Bayesian framework for inference, visualization and hypothesis testing of phylogeographic history. By implementing character mapping in a Bayesian software that samples time-scaled phylogenies, we enable the reconstruction of timed viral dispersal patterns while accommodating phylogenetic uncertainty. Standard Markov model inference is extended with a stochastic search variable selection procedure that identifies the parsimonious descriptions of the diffusion process. In addition, we propose priors that can incorporate geographical sampling distributions or characterize alternative hypotheses about the spatial dynamics. To visualize the spatial and temporal information, we summarize inferences using virtual globe software. We describe how Bayesian phylogeography compares with previous parsimony analysis in the investigation of the influenza A H5N1 origin and H5N1 epidemiological linkage among sampling localities. Analysis of rabies in West African dog populations reveals how virus diffusion may enable endemic maintenance through continuous epidemic cycles. From these analyses, we conclude that our phylogeographic framework will make an important asset in molecular epidemiology that can be easily generalized to infer biogeogeography from genetic data for many organisms. 
 Title: Bayesian Phylogeography Finds Its Roots
Output: True
Paragraph: The objective of this longitudinal study was to identify growth curves and related predictors of depressive symptoms among Chinese adolescent earthquake survivors. A total of 1573 adolescent survivors of the 8-magnitude Wenchuan earthquake were assessed through the Depression Self-Rating Scale for Children (cutoff for probable clinical depression: 15), Social Support Rate Scale, Adolescent Self-Rating Life Events Checklist, and a self-designed questionnaire covering earthquake exposure and demographic information at 6-, 12-, 18-, 24-and 30-months after the earthquake. Data were analyzed using growth mixture modeling (GMM) and multinomial logistic regression. The prevalence rates of depressive symptoms were 27.6%, 40.6%, 30.9%, 37.5% and 29.8% at 6-, 12-, 18-, 24-and 30-months, respectively. GMM analysis showed four patterns of growth curves for depressive symptoms: chronic depression (25.6% of the sample), recovery (1.7%), delayed depression (4.3%), and resilience (68.4%). Female gender was related with decreased probability of resilience. Direct witness of tragic scenes during the earthquake was related with higher risk for chronic depression. More negative life events and fewer social support were also common predictors of not developing the resilience pattern. The need of providing appropriate individualized interventions for high-risk adolescent earthquake survivors is indicated. 
 Title: Latent growth curves and predictors of depressive symptoms among Chinese adolescent earthquake survivors ☆
Output: True
Paragraph: The world is waiting with apprehension for the predicted pandemic of H5N1 (avian) influenza as an increasing number of countries in Asia, Europe and Africa report cases of influenza in migrating birds. All is not 'despondency', however. Targeted and controlled administration of antiviral drugs, alone or in combination, to contacts and cases, together with well tried public health measures, should slow down the spread of the infection and allow time for vaccines to be developed, thus preventing a worldwide pandemic of the type that occurred in 1918. 
 Title: Influenza is now a preventable disease
Output: False
Paragraph: Several small animal models have been developed for the study of severe acute respiratory syndrome coronavirus (SARS-CoV) replication and pathogenesis. Syrian golden hamsters are among the best small animal models, though little clinical illness and no mortality are observed after virus infection. Cyclophosphamide was used to immunosuppress hamsters leading to a prolonged disease course and higher mortality after SARS-CoV infection. In addition, there was a significant weight loss, expanded tissue tropism, and increased viral pathology in the lung, heart, kidney, and nasal turbinate tissues. Infection with recombinant SARS-CoV viruses bearing disruptions in the gene 7 coding region showed no significant change in replication kinetics, tissue tropism, morbidity, or mortality suggesting that the ORF7a (7a) and ORF7b (7b) proteins are not required for virus replication in immunosuppressed hamsters. This modified hamster model may provide a useful tool for SARS-CoV pathogenesis studies, evaluation of antiviral therapy, and analysis of additional SARS-CoV mutants. 
 Title: An immunosuppressed Syrian golden hamster model for SARS-CoV infection
Output: True
Paragraph: Coronavirus Autophagy ER stress Unfolded protein response Mitogen-activated protein kinase A B S T R A C T Coronavirus infection induces the generation of autophagosomes, and certain host proteins regulating cellular autophagy are hijacked by some coronaviruses to facilitate the formation of double membrane vesicles. However, mechanisms underlying coronavirus-induced autophagy remain largely unknown. In this study, we demonstrate that autophagosome formation and apparent autophagic flux are induced in cells infected with infectious bronchitis virus (IBV)a gammacoronavirus. Notably, IBV-induced autophagy was dependent on autophagy related 5 (ATG5) but not beclin1 (BECN1), although both are essential proteins in the canonical autophagy pathway. Moreover, the ER stress sensor inositol requiring enzyme 1 (IRE1), but not its substrate Xbox protein 1 (XBP1), was also essential for the induction of autophagy during IBV infection. Finally, the antiapoptotic extracellular signal-regulated kinase 1/2 (ERK1/2) also contributed to IBV-induced autophagy. Our findings add new knowledge to the regulatory mechanisms governing coronavirus-induced autophagy, highlighting an extensive cross-talk among cellular signaling pathways during coronavirus infection. 
 Title: The ER stress sensor IRE1 and MAP kinase ERK modulate autophagy induction in cells infected with coronavirus infectious bronchitis virus
Output: True
Paragraph: In northeastern Thai (Isaan) culture traditional raw fish dishes and raw fish-eating habits are common. Eating and sharing meals together among the community's members, especially relatives and neighbours, are a common practice in both daily life and social gathering events. Fish are a significant protein source and are associated with variety of traditional recipes. Cyprinid fish are one of the most preferred fish by Isaan villagers for daily consumption because they are accessible and affordable. Consumption of these fish probably causes the persistence of high endemicity of human liver fluke infection, particularly with Opisthorchis viverrini, in northeast Thailand. Because the consumption of raw cyprinid fish is a well-documented risk factor for liver fluke infection, sharing of risky raw fish dishes may influence disease transmission through a community. Social network analysis was used to investigate fish and fish-based meal sharing among household members in Isaan villages in liver fluke endemic areas. The findings from three studies confirmed the persistence of traditional Isaan raw fish consumption and food-sharing practice. Social connections via food sharing among villagers played an important role in liver fluke infection and transmission dynamics as a risk factor. Thus these sociocultural factors should be taken into account in designing strategies for control of opisthorchiasis and other food-borne illnesses at the community level. 
 Title: Social Influence in Liver Fluke Transmission: Application of Social Network Analysis of Food Sharing in Thai Isaan Culture
Output: False
Paragraph: Objective: The purpose of our study was to review the initial high-resolution CT (HRCT) findings in pneumonia patients with presumed/laboratory-confirmed novel swine-origin influenza A (H1N1) virus (S-OIV) infection and detect pneumonia earlier. Materials and methods: High-resolution CT (HRCT) findings of 106 patients with presumed/laboratoryconfirmed novel S-OIV (H1N1) infection were reviewed. The 106 patients were divided into two groups according to the serious condition of the diseases. The pattern (consolidation, ground-glass, nodules, and reticulation), distribution, and extent of abnormality on the HRCT were evaluated in both groups. The dates of the onset of symptoms of the patients were recorded. Results: The predominant CT findings in the patients at presentation were unilateral or bilateral multifocal asymmetric ground-glass opacities alone (n = 29, 27.4%), with unilateral or bilateral consolidation (n = 50, 47.2%). The consolidation had peribronchovascular and subpleural predominance. The areas of consolidation were found mainly in the posterior, middle and lower regions of the lungs. Reticular opacities were found in 6 cases of the initial MDCT scan. The extent of disease was greater in group 1 patients requiring advanced mechanical ventilation, with diffuse involvement in 19 patients (63.3%) of group 1 patients, and only 15/76 (19.7%) of group 2 patients (p < 0.01, 2 test). 20 cases (19%) of the 106 patients had small bilateral or unilateral pleural effusions. None had evidence of hilar or mediastinal lymph node enlargement on CT performed at admission or later. Conclusions: The most common radiographic and CT findings in patients with S-OIV infection are unilateral or bilateral ground-glass opacities with or without associated focal or multifocal areas of consolidation. On HRCT, the ground-glass opacities had a predominant peribronchovascular and subpleural distribution. CT plays an important role in the early recognition of severe S-OIV (H1N1). 
 Title: Pneumonia in novel swine-origin influenza A (H1N1) virus infection: High-resolution CT findings
Output: True
Paragraph: Early warning systems for outbreaks of infectious diseases are an important application of the ecological theory of epidemics. A key variable predicted by early warning systems is the final outbreak size. However, for directly transmitted diseases, the stochastic contact process by which outbreaks develop entails fundamental limits to the precision with which the final size can be predicted. I studied how the expected final outbreak size and the coefficient of variation in the final size of outbreaks scale with control effectiveness and the rate of infectious contacts in the simple stochastic epidemic. As examples, I parameterized this model with data on observed ranges for the basic reproductive ratio (R 0 ) of nine directly transmitted diseases. I also present results from a new model, the simple stochastic epidemic with delayed-onset intervention, in which an initially supercritical outbreak (R 0 . 1) is brought under control after a delay. The coefficient of variation of final outbreak size in the subcritical case (R 0 , 1) will be greater than one for any outbreak in which the removal rate is less than approximately 2.41 times the rate of infectious contacts, implying that for many transmissible diseases precise forecasts of the final outbreak size will be unattainable. In the delayed-onset model, the coefficient of variation (CV) was generally large (CV . 1) and increased with the delay between the start of the epidemic and intervention, and with the average outbreak size. These results suggest that early warning systems for infectious diseases should not focus exclusively on predicting outbreak size but should consider other characteristics of outbreaks such as the timing of disease emergence. 
 Title: Limits to Forecasting Precision for Outbreaks of Directly Transmitted Diseases
Output: True
Paragraph: Rosa SGV and Santos WC. Clinical trials on drug repositioning for COVID-19 treatment. Rev Panam Salud Publica. 2020;44:e40. ABSTRACT The World Health Organization (WHO) was informed on December 2019 about a coronavirus pneumonia outbreak in Wuhan, Hubei province (China). Subsequently, on March 12, 2020, 125,048 cases and 4,614 deaths were reported. Coronavirus is an enveloped RNA virus, from the genus Betacoronavirus, that is distributed in birds, humans, and other mammals. WHO has named the novel coronavirus disease as COVID-19. More than 80 clinical trials have been launched to test coronavirus treatment, including some drug repurposing or repositioning for COVID-19. Hence, we performed a search in March 2020 of the clinicaltrials.gov database. The eligibility criteria for the retrieved studies were: contain a clinicaltrials.gov base identifier number; describe the number of participants and the period for the study; describe the participants' clinical conditions; and utilize interventions with medicines already studied or approved for any other disease in patients infected with the novel coronavirus SARS-CoV-2 (2019-nCoV). It is essential to emphasize that this article only captured trials listed in the clinicaltrials.gov database. We identified 24 clinical trials, involving more than 20 medicines, such as human immunoglobulin, interferons, chloroquine, hydroxychloroquine, arbidol, remdesivir, favipiravir, lopinavir, ritonavir, oseltamivir, methylprednisolone, bevacizumab, and traditional Chinese medicines (TCM). Although drug repurposing has some limitations, repositioning clinical trials may represent an attractive strategy because they facilitate the discovery of new classes of medicines; they have lower costs and take less time to reach the market; and there are existing pharmaceutical supply chains for formulation and distribution. 
 Title: Clinical trials on drug repositioning for COVID-19 treatment
Output: False
Paragraph: Feline infectious peritonitis (FIP) is a highly fatal disease caused by a virulent feline coronavirus in domestic and wild cats. We have previously reported the synthesis of potent coronavirus 3C-like protease (3CLpro) inhibitors and the efficacy of a protease inhibitor, GC376, in client-owned cats with FIP. In this study, we studied the effect of the amino acid changes in 3CLpro of feline coronavirus from a feline patient who received antiviral treatment for prolonged duration. We generated recombinant 3CLpro containing the identified amino acid changes (N25S, A252S or K260 N) and determined their susceptibility to protease inhibitors in the fluorescence resonance energy transfer assay. The assay showed that N25S in 3CLpro confers a small change (up to 1.68-fold increase in the 50% inhibitory concentration) in susceptibility to GC376, but other amino acid changes do not affect susceptibility. Modelling of 3CLpro carrying the amino acid changes was conducted to probe the structural basis for these findings. The results of this study may explain the observed absence of clinical resistance to the long-term antiviral treatment in the patients. 
 Title: Characterization of amino acid substitutions in feline coronavirus 3C-like protease from a cat with feline infectious peritonitis treated with a protease inhibitor
Output: False