niryuu/sni-each-converted huggingface dataset:
Paragraph: Cell fusion is a ubiquitous process fundamental to physiological and pathophysiological events common to multiple cell types and species. Performed ex vivo , cell fusion is a versatile research and therapeutic tool for gene mapping, antibody production, discovering new mechanisms in biological processes, inventing alternative therapies for cell reprogramming, restoring organ function, and creating cellular therapeutics for cancer treatment. Cell fusion can be successfully applied by creating cellular therapeutic of donor -recipient chimeric cell (DRCC) in the fi eld of solid organ and vascularized composite allotransplantation (VCA). Immunomodulatory DRCC therapy has the potential to reduce or even eliminate the need for toxic, life-long immunosuppression and to prevent both acute and chronic rejection. This innovative VCA treatment is a combination of ex vivo created chimeric cell therapy with a short-term selective protocol of monoclonal antibody and Cyclosporine A. The utilization of short-term immunosuppressive protocol will provide the opportunity for chimeric cell engraftment, proliferation, and re-education of recipient's immune system resulting in prolongation of allograft survival. The use of chimeric cells, as a supportive treatment for VCA, would improve the conditions of severely disfi gured patients by offering safe alternative approach and providing better functional and aesthetic results compared to standard reconstructive procedures. 
 Title: 72 Cellular Therapy Models: Ex Vivo Chimera Model by Cell Fusion
Output: False
Paragraph: Emerging and re-emerging pathogens represent a substantial threat to public health, as demonstrated with numerous outbreaks over the past years, including the 2013-2016 outbreak of Ebola virus in western Africa. Coronaviruses are also a threat for humans, as evidenced in 2002/2003 with infection by the severe acute respiratory syndrome coronavirus (SARS-CoV), which caused more than 8000 human infections with 10% fatality rate in 37 countries. Ten years later, a novel human coronavirus (Middle East respiratory syndrome coronavirus, MERS-CoV), associated with severe pneumonia, arose in the Kingdom of Saudi Arabia. Until December 2016, MERS has accounted for more than 1800 cases and 35% fatality rate. Finding an animal model of disease is key to develop vaccines or antivirals against such emerging pathogens and to understand its pathogenesis. Knowledge of the potential role of domestic livestock and other animal species in the transmission of pathogens is of importance to understand the epidemiology of the disease. Little is known about MERS-CoV animal host range. In this paper, experimental data on potential hosts for MERS-CoV is reviewed. Advantages and limitations of different animal models are evaluated in relation to viral pathogenesis and transmission studies. Finally, the relevance of potential new target species is discussed. 
 Title: Searching for animal models and potential target species for emerging pathogens: Experience gained from Middle East respiratory syndrome (MERS) coronavirus
Output: False
Paragraph: Chickens from two inbred lines selected for high (L10H) or low (L10L) mannose-binding lectin (MBL) serum concentrations were infected with infectious bronchitis virus (IBV), and innate as well as adaptive immunological parameters were measured throughout the experimental period. Chickens with high MBL serum concentrations were found to have less viral load in the trachea than chickens with low MBL serum concentrations indicating that these chickens were less severely affected by the infection. This study is the first to show that MBL expression is present in the lungs of healthy chickens and that the expression is upregulated at days 3 postinfection (p.i.) in L10H chickens. Furthermore, in the liver of infected chickens, the MBL expression was upregulated at day 7 p.i., despite the fact that the MBL serum concentrations were decreased below baseline at that time point. The number of TCRcd + CD8a + cells in the blood of noninfected chickens increased from week 0 to 3 p.i. However, the number of cells was higher in L10H chickens than in L10L chickens throughout the experiment. No increase was observed in the number of TCRcd + CD8a + cells in the blood of the infected L10H and L10L chickens. The numbers of B cells at week 3 p.i. were higher for noninfected L10L chickens than for the other chickens. No differences were observed between the infected and noninfected L10H chickens or between the infected L10H and L10L chickens. Furthermore, at week 3 p.i., the number of monocytes was higher in infected and noninfected L10H chickens than in the infected and noninfected L10L chickens. Thus, these results indicate that MBL is produced locally and may be involved in the regulation of the cellular immune response after an IBV infection. However, MBL did not appear to influence the humoral immune response after IBV infection in this study. 
 Title: Characterization of Cellular and Humoral Immune Responses After IBV Infection in Chicken Lines Differing in MBL Serum Concentration
Output: False
Paragraph: The World Health Organisation has declared a pandemic caused by the newly discovered SARS-CoV-2. Due to growing demand for reagents used for SARS-CoV-2 RNA extraction for subsequent molecular diagnostics, there is a worldwide risk of kit-and/or reagent-shortages for extraction. With a detection sensitivity of 97.4% (95% CI=86.2-99.9%), we describe a simple, fast, alternative workflow for molecular detection of SARS-CoV-2, where samples are simply heat-processed for 5 minutes at 98˚C prior to the RT-qPCR reaction. 
 Title: Title: An alternative workflow for molecular detection of SARS-CoV-2 -escape from the NA
Output: False
Paragraph: Dengue virus (DV) infection depends on a step of membrane fusion, which occurs in the acidic environment of the endosome. This process is mediated by virus surface envelope glycoprotein, in which the loop between residues D98-G112 is considered to be crucial, acting as a fusion peptide. Here, we have characterized functionally and structurally the interaction between the DV fusion peptide and different model membranes by fluorescence and NMR. Its interaction was strongest in dodecylphosphocholine (DPC) micelles and anionic phosphatidylcholine/phosphatidylglycerol vesicles, the only vesicle that was fused by DV fusion peptide. The three-dimensional structure of DV fusion peptide bound to DPC micelles was solved by solution homonuclear NMR with an r.m.s.d. of 0.98 Å. The most striking result obtained from the solution structure was the hydrophobic triad formed by residues W101, L107, and F108, pointing toward the same direction, keeping the segment between G102 and G106 in a loop conformation. The interaction of DV fusion peptide with phosphatidylcholine/phosphatidylglycerol vesicles was also mapped by transfer-nuclear Overhauser enhancement (NOE) experiments, in which the majority of the NOE cross-peaks were from the hydrophobic triad, corroborating the DPCbound structure. Substitution of the residue W101 by an alanine residue completely abolished membrane binding and, thus, fusion by the peptide and its NOE cross-peaks. In conclusion, the 15-residue DV fusion peptide has intrinsic ability to promote membrane fusion, most likely due to the hydrophobic interaction among the residues W101, L107, and F108, which maintains its loop in the correct spatial conformation. 
 Title: Interaction of the Dengue Virus Fusion Peptide with Membranes Assessed by NMR: The Essential Role of the Envelope Protein Trp101 for Membrane Fusion
Output: True
Paragraph: Purpose: COVID-19 has become global threaten. CT acts as an important method of 60 diagnosis. However, human-based interpretation of CT imaging is time consuming. 61 More than that, substantial inter-observer-variation cannot be ignored. We aim at 62 developing a diagnostic tool for artificial intelligence (AI)-based classification of CT 63 images for recognizing COVID-19 and other common infectious diseases of the lung. 64 Experimental Design: In this study, images were retrospectively collected and 65 prospectively analyzed using machine learning. CT scan images of the lung that show 66 or do not show COVID-19 were used to train and validate a classification framework 67 based on convolutional neural network. Five conditions including COVID-19 68 pneumonia, non-COVID-19 viral pneumonia, bacterial pneumonia, pulmonary 69 tuberculosis, and normal lung were evaluated. Training and validation set of images 70 were collected from Wuhan Jin Yin-Tan Hospital whereas test set of images were 71 collected from Zhongshan Hospital Xiamen University and the fifth Hospital of 72 Wuhan. 73 Results: Accuracy, sensitivity, and specificity of the AI framework were reported. For 74 test dataset, accuracies for recognizing normal lung, COVID-19 pneumonia, 75 non-COVID-19 viral pneumonia, bacterial pneumonia, and pulmonary tuberculosis 76 were 99.4%, 98.8%, 98.5%, 98.3%, and 98.6%, respectively. For the test dataset, 77 accuracy, sensitivity, specificity, PPV, and NPV of recognizing COVID-19 were 78 98.8%, 98.2%, 98.9%, 94.5%, and 99.7%, respectively. 79 All rights reserved. No reuse allowed without permission. the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. 
 Title: Deep Learning-Based Recognizing COVID-19 Deep Learning-Based Recognizing COVID-19 and other Common Infectious Diseases of the Lung by Chest CT 2 Scan Images
Output: False
Paragraph: first two authors contribute equally. Zika virus can be passed from a pregnant woman to her fetus, thus leading to birth defects including more than microcephaly. It has been recently estimated that one-third of the world population will be infected by Zika, but unfortunately no vaccine or medicine is available so far. Zika NS2B-NS3pro is essential for its replication and thus represents an attractive target for drug discovery/design. Here we characterized conformation, Zika NS2B-NS3pro complexes by both experiments and MD simulations. The results unveil the unique properties of Zika NS2B-NS3pro which are very different from Dengue one. Particularly, CD and NMR studies indicate that unlike Dengue, the C-terminal region of Zika NS2B with a significant sequence variation is highly disordered in the open conformation. Indeed, MD simulations reveal that up to 100 ns, the Dengue NS2B C-terminus constantly has close contacts with its NS3pro domain. By a sharp contrast, the Zika NS2B C-terminus loses the contacts with its NS3pro domain after 10 ns, further forming a short β-sheet characteristic of the closed conformation at 30 ns. Furthermore, we found that a small molecule, previously identified as an active site inhibitor for other flaviviral NS2B-NS3pro, inhibited Zika NS2B-NS3pro potently in an allosteric manner. Our study provides the first insight into the dynamics of Zika NS2B-NS3pro and further deciphers that it is susceptible to allosteric inhibition, which thus bears critical implications for the future development of therapeutic allosteric inhibitors. author/funder. All rights reserved. No reuse allowed without permission. 
 Title: Catalysis, inhibition and dynamics of Zika NS2B-NS3pro Unique properties of Zika NS2B-NS3pro complexes as decoded by experiments and MD simulations Catalysis, inhibition and dynamics of Zika NS2B-NS3pro
Output: False
Paragraph: Avian infectious bronchitis virus (IBV) is a member of the family Coronaviridae. A binding domain that mediates the attachment of the virus to its receptor has been identified in the S1 protein of prototype IBV strain M41. In this study, we identified this binding domain in a different strain, as well as the cellular proteins that interact with it. First, we expressed the S1 N proteins (residues 19-270) of M41 and another isolate, SCZJ3, and compared the binding capacities of recombinant S1 N -M41 and S1 N -SCZJ3 to host tissues. Protein histochemistry showed that both S1 N -M41 and S1 N -SCZJ3 could bind to lung and kidney, and that recombinant S1 N -SCZJ3 displayed a distinctive staining pattern in the proventriculus. Recombinant S1 N -SCZJ3 was then employed to purify binding-associated proteins in lung, kidney, and proventriculus. Using an affinity chromatography assay, two common bands of about 60 kDa and 70 kDa were obtained from the total tissue proteins. These protein bands were identified by liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) as protein disulfide isomerase (PDI) and heat shock protein 70 (HSP70). Finally, infection of chicken embryo kidney (CEK) cells by SCZJ3 was found to be inhibited by anti-HSP70 but not anti-PDI polyclonal antibody. These data indicate that HSP70 is part of the receptor complex of IBV and might help to understand the mechanism of S-mediated cell entry of IBV. 
 Title: Heat shock protein 70 in lung and kidney of specific-pathogen-free chickens is a receptor-associated protein that interacts with the binding domain of the spike protein of infectious bronchitis virus
Output: False
Paragraph: Transmissible gastroenteritis (TGE) is a contagious and infectious disease that is characterized by severe vomiting and diarrhea of swine , especially piglet, and caused by transmissible gastroenteritis coronavirus (TGEV) . TGEV infection provokes mitochondrial damage of porcine intestinal epthelial cell (IPEC), which is responsible for inflammation and cell death. In our previous study, we have demonstrated that circular RNA circEZH2 was down-regulated during TGEV infection and promoted the activation of nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) via targeting miR-22 in porcine intestinal epithelial cell line (IPEC-J2). Activation of NF-κB is an important factor for mitochondrial damage. Mitochondrial permeability transition pore (mPTP) opening is a key reason for mitochondrial damage. So, we speculate that circEZH2 may regulate TGEV-induced mPTP opening via NF-kB pathway. In the present study, we found that mPTP opening of IPEC-J2 was occured during TGEV infection and suppressed by circEZH2 via attaching miR-22. Hexokinase 2 (HK2) and interleukin 6 (IL-6) were identified as the targets of miR-22. Silencing HK2 enhanced TGEV-induced mPTP opening, while no effect on NF-κB pathway. Silencing IL-6 promoted TGEV-induced mPTP opening and inhibited NF-κB pathway. Inhibitor of NF-κB increased TGEV-induced mPTP opening. The data revealed that TGEV-induced mPTP opening was regulated via two pathways: circEZH2/miR-22/HK2 axis and circEZH2/miR-22/IL-6/NF-κB axis. 
 Title: Circular RNA CircEZH2 Suppresses Transmissible Gastroenteritis Coronavirus-induced Opening of Mitochondrial Permeability Transition Pore via Targeting MiR-22 in IPEC-J2
Output: True
Paragraph: Molecular infectious disease diagnostic tests have undergone major advances in the past decade and will continue to rapidly evolve. Assays have become extraordinarily simple to perform, eliminating the need for pre-analytic sample preparation and post-amplification analysis. This allows these tests to be performed in settings without sophisticated expertise in molecular biology, including locations with limited resources. Additionally, the sensitivity and specificity of these assays is superb and many offer extremely fast turn-around times. These tests have major impacts on patient care, but also have some limitations. ARTICLE HISTORY 
 Title: Sample-to-result molecular infectious disease assays: clinical implications, limitations and potential
Output: False
Paragraph: Severe acute respiratory syndrome (SARS) is a highly infectious, rapidly progressive, emerging disease. Early diagnosis and preventive measures are key for treatment and minimization of secondary spread. In the context of the armed forces, aggressive containment measures are essential to prevent an outbreak. In this study, we present the first reported case, to our knowledge, of SARS in a naval diver. The special physical requirements for divers and the potential complications associated with deep sea diving necessitate extensive investigation before certification of fitness for diving after SARS. In the early recovery period, potential problems during diving are caused by inadequate lung ventilation in relation to exercise level and increased breathing resistance attributable to weak respiratory muscles, with corresponding risk of hypoxia and hypercapnia, as well as decreased ability to respond to nonrespiratory problems during diving. Problems in the late recovery period include increased risk of diving complications (such as pulmonary barotrauma) resulting from fibrosis and scarring within the lung parenchyma, which are known complications of SARS. From our experience, we suggest that computed tomographic scans of the thorax, lung function tests, and careful follow-up monitoring should play a vital role in the assessment of patients during the convalescent period, before certification of fitness to dive. 
 Title: Severe Acute Respiratory Syndrome in a Naval Diver
Output: True
Paragraph: We developed a novel concept that allows to considerably improve the performance of conventionally used ÿltering-facepiece respirators against ÿne and ultraÿne aerosols including airborne viral and bacterial agents. The concept is based on the continuous emission of unipolar ions. The e ect was evaluated through the real-time monitoring of the concentration and size distribution of ÿne and ultraÿne aerosol particles. The measurements were conducted inside and outside of a respiratory mask that was face sealed on a breathing manikin. A commonly used Type N95 respirator and surgical mask were utilized for the tests. The manikin was placed in a 24.3-m 3 indoor test chamber and exposed to polydisperse surrogate aerosols simulating viral and bacterial particles with respect to the aerodynamic size. The particle penetration through the mask was found to decrease by one-to-two orders of magnitude as a result of continuous unipolar ion emission in the chamber. The ux of air ions migrated to the breathing zone and imparted electrical charges of the same polarity to the aerosol particles and the respirator ÿlter surface. This created an electrostatic shield along the external surface of the ÿlter, thus enhancing the protection characteristics provided by the respirator. The above performance enhancement e ect is crucial for minimizing the infectious risk in the cases when the conventional ÿltering-facepiece respirators are not able to provide an adequate protection against airborne viruses and bacteria. ? 
 Title: Unipolar ion emission enhances respiratory protection against ÿne and ultraÿne particles
Output: True
Paragraph: A 7-methylguanosine linked to the 5′ end of an mRNA, via a 5′-5′ triphosphate linkage, to mark the extreme 5′ terminus of a eukaryotic mRNA. In addition to having regulatory roles in pre-mRNA processing and mRNA stability, the cap structure controls ribosome recruitment to the mRNA 5′ end. Abstract | Viruses are fully reliant on the translation machinery of their host cells to produce the polypeptides that are essential for viral replication. Consequently, viruses recruit host ribosomes to translate viral mRNAs, typically using virally encoded functions to seize control of cellular translation factors and the host signalling pathways that regulate their activity. This not only ensures that viral proteins will be produced, but also stifles innate host defences that are aimed at inhibiting the capacity of infected cells for protein synthesis. Remarkably, nearly every step of the translation process can be targeted by virally encoded functions. This Review discusses the diverse strategies that viruses use to subvert host protein synthesis functions and regulate mRNA translation in infected cells. 
 Title: 7-methylguanosine cap Viral subversion of the host protein synthesis machinery
Output: True
Paragraph: As the prevalence of cancer and transmittable disease persists, the development of new and more advanced therapies remains a priority in medical research. An emerging platform for the treatment of these illnesses is the use of materials formed via peptide assembly where the bulk material itself acts as the therapeutic. Higher ordered peptide structures with defined chemistry are capable of cellular targeting, recognition, and internalization. Recent design efforts are being made to exploit the nanoscale definition of the materials formed by assembling peptides to target cancer and microbial cells and to function as vaccines. This review focuses on assembled peptide materials that actively participate in the biological processes important to cancer and transmittable diseases to exert an anticipated functional outcome. 
 Title: Materials from peptide assembly: towards the treatment of cancer and transmittable disease
Output: True
Paragraph: To assess the role of spatial proximity, defined as patients sharing bays, in the spread of norovirus during outbreaks in hospitals. Enhanced surveillance of norovirus outbreaks between November 2009 and November 2011. Data were gathered during 149 outbreaks of norovirus in hospital wards from five hospitals in two major cities in England serving a population of 2 million. We used the time between the first two cases of each outbreak to estimate the serial interval for norovirus in this setting. This distribution and dates of illness onset were used to calculate epidemic trees for each outbreak. We then used a permutation test to assess whether proximity, for all outbreaks, was more extreme than would be expected by chance under the null hypothesis that proximity was not associated with transmission risk. Sixty-five outbreaks contained complete data on both onset dates and ward position. We estimated the serial interval to be 1.86 days (95% confidence intervals 1.6-2.2 days), and with this value found strong evidence to reject the null hypothesis that proximity was unimportant (p < 0.001). Sensitivity analysis using different values of the serial interval showed that there was evidence to reject the null hypothesis provided the assumed serial interval was less than 2.5 days. Our results provide evidence that patients occupying the same bay as patients with symptomatic norovirus infection are at an increased risk of becoming infected by these patients compared with patients elsewhere in the same ward. 
 Title: Does spatial proximity drive norovirus transmission during outbreaks in hospitals? Title Does spatial proximity drive norovirus transmission during outbreaks in hospitals?
Output: True
Paragraph: Healthcare settings have played a major role in propagation of Ebola virus (EBOV) outbreaks. Healthcare workers (HCWs) have elevated risk of contact with EBOV-infected patients, particularly if safety precautions are not rigorously practiced. We conducted a serosurvey to determine seroprevalence against multiple EBOV antigens among HCWs of Boende Health Zone, Democratic Republic of the Congo, the site of a 2014 EBOV outbreak. Interviews and specimens were collected from 565 consenting HCWs. Overall, 234 (41.4%) of enrolled HCWs were reactive to at least 1 EBOV protein: 159 (28.1%) were seroreactive for anti-glycoprotein immunoglobulin G (IgG), 89 (15.8%) were seroreactive for anti-nucleoprotein IgG, and 54 (9.5%) were VP40 positive. Additionally, sera from 16 (2.8%) HCWs demonstrated neutralization capacity. These data demonstrate that a significant proportion of HCWs have the ability to neutralize virus, despite never having developed Ebola virus disease symptoms, highlighting an important and poorly documented aspect of EBOV infection and progression. 
 Title: The Journal of Infectious Diseases Serologic Markers for Ebolavirus Among Healthcare Workers in the Democratic Republic of the Congo
Output: True
Paragraph: Feline coronaviruses (FCoV) comprise two biotypes: feline enteric coronaviruses (FECV) and feline infectious peritonitis viruses (FIPV). FECV is associated with asymptomatic persistent enteric infections, while FIPV causes feline infectious peritonitis (FIP), a usually fatal systemic disease in domestic cats and some wild Felidae. FIPV arises from FECV by mutation. FCoV also occur in two serotypes, I and II, of which the serotype I viruses are by far the most prevalent in the field. Yet, most of our knowledge about FCoV infections relates to serotype II viruses, particularly about the FIPV, mainly because type I viruses grow poorly in cell culture. Hence, the aim of the present work was the detailed study of the epidemiologically most relevant viruses, the avirulent serotype I viruses. Kittens were inoculated oronasally with different doses of two independent FECV field strains, UCD and RM. Persistent infection could be reproducibly established. The patterns of clinical symptoms, faecal virus shedding and seroconversion were monitored for up to 10 weeks revealing subtle but reproducible differences between the two viruses. Faecal virus, i.e. genomic RNA, was detected during persistent FECV infection only in the large intestine, downstream of the appendix, and could occasionally be observed also in the blood. The implications of our results, particularly our insights into the persistently infected state, are discussed. coronavirus / experimental infection / FECV / persistence / cat 
 Title: Pathogenic characteristics of persistent feline enteric coronavirus infection in cats
Output: False
Paragraph: a b s t r a c t Feasibility of degradation of Triton X-100 as a widely used and resistive surfactant in aqueous media was studied via some homogeneous and heterogeneous AOPs of UV/TiO 2 , UV/H 2 O 2 and UV/S 2 O 8 2− . For treatment of solutions containing 20 mg/L of Triton, the optimum obtained conditions are: 5.0 mg/L of nano TiO 2 , 270.3 mg/L of KPS, and 34.0 mg/L of H 2 O 2 (1 mM of the oxidants), initial natural pH of 5.4 and temperature of 45 • C. Under these conditions, the degradation efficiency for the UV/TiO 2 , UV/H 2 O 2 and UV/S 2 O 8 2− processes exceeds 71.9% (in 60 min), 80.9% (in 60 min) and 98.5% (in only 30 min) respectively. It was found that simultaneous application of these heterogeneous and homogeneous AOPs (UV/TiO 2 /H 2 O 2 or S 2 O 8 2− ) is not desirable due to some physico-chemical retarding effects. The influence of temperature on the reactions was examined in the range of 15-45 • C and a kinetic power law model jointed with the Arrhenius equation was introduced. A pseudo first order reaction rate is appropriate for UV/S 2 O 8 2− and UV/TiO 2 processes under optimum conditions, while this order for UV/H 2 O 2 process is 2.27. Meanwhile, the initial rates of degradation in UV/TiO 2 process can be described well by the Langmuir-Hinshelwood kinetic model. Analysis of energy consumptions (thermal and electrical) revealed that increasing in temperature is an effective factor for lowering the energy cost of the preferred process of UV/S 2 O 8 2− . 
 Title: Homogeneous and heterogeneous AOPs for rapid degradation of Triton X-100 in aqueous media via UV light, nano titania hydrogen peroxide and potassium persulfate
Output: False
Paragraph: Background: Salmonellosis in water buffalo (Bubalus bubalis) calves is a widespread disease characterized by severe gastrointestinal lesions, profuse diarrhea and severe dehydration, occasionally exhibiting a systemic course. Several Salmonella serovars seem to be able to infect water buffalo, but Salmonella isolates collected from this animal species have been poorly characterized. In the present study, the prevalence of Salmonella spp. in water buffalo calves affected by lethal gastroenteritis was assessed, and a polyphasic characterization of isolated strains of S. Typhimurium was performed. Results: The microbiological analysis of the intestinal contents obtained from 248 water buffalo calves affected by lethal gastroenteritis exhibited a significant prevalence of Salmonella spp. (25%), characterized by different serovars, most frequently Typhimurium (21%), Muenster (11%), and Give (11%). The 13 S. Typhimurium isolates were all associated with enterocolitis characterized by severe damage of the intestine, and only sporadically isolated with another possible causative agent responsible for gastroenteritis, such as Cryptosporidium spp., Rotavirus or Clostridium perfringens. Other Salmonella isolates were mostly isolated from minor intestinal lesions, and often (78% of cases) isolated with other microorganisms, mainly toxinogenic Escherichia coli (35%), Cryptosporidium spp. (20%) and Rotavirus (10%). The S. Typhimurium strains were characterized by phage typing and further genotyped by polymerase chain reaction (PCR) detection of 24 virulence genes. The isolates exhibited nine different phage types and 10 different genetic profiles. Three monophasic S. Typhimurium (B:4,12:i:-) isolates were also found and characterized, displaying three different phage types and three different virulotypes. The molecular characterization was extended to the 7 S. Muenster and 7 S. Give isolates collected, indicating the existence of different virulotypes also within these serovars. Three representative strains of S. Typhimurium were tested in vivo in a mouse model of mixed infection. The most pathogenic strain was characterized by a high number of virulence factors and the presence of the locus agfA, coding for a thin aggregative fimbria. Conclusions: These results provide evidence that Salmonella is frequently associated with gastroenteritis in water buffalo calves, particularly S. Typhimurium. Moreover, the variety in the number and distribution of different virulence markers among the collected S. Typhimurium strains suggests that within this serovar there are different pathotypes potentially responsible for different clinical syndromes. 
 Title: Diversity of Salmonella spp. serovars isolated from the intestines of water buffalo calves with gastroenteritis
Output: False
Paragraph: Annotation The process of adding descriptive information to a data set and the individual data elements that comprise that data set. May include both computational analyses and manual curation. Curation The process of manually adding descriptive information or explanatory material to a data set usually based on a review of the existing literature. Database A collection of information, usually stored electronically on a computer. Database, hierarchical (XML) Extensible markup language. A formally defined hierarchical organization of data. A database software package designed to operate on a particular computer platform and operating system. Database schema A map of the database structure, including all of the fields, tables, and relationships that comprise the framework for storage of information within that database. Database, relational A database structure that provides the ability to define formal relationships between all data elements stored within the database. Ontology A controlled vocabulary used to formally describe (for our purposes) a biological process or entity. SQL Structured Query Language. A computer language used to query relational databases for information. 
 Title: Virus Databases
Output: False
Paragraph: Health care providers' (HCPs') duty to care during communicable disease outbreaks has resurfaced as an important and contentious topic. This renewed interest follows the re-emergence of communicable diseases, largely thought to have disappeared and therefore irrelevant to modern day practitioners. The 2003 SARS outbreak particularly presented propitious circumstances for reconsidering this issue. This study seeks to characterize the views of individuals on the nature and limits of this duty. The authors employed qualitative methods to gather lay and expert perspectives. Individual interviews were conducted with 67 participants consisting of HCPs, spiritual leaders, regulators, and members of the public from the greater Toronto area. Participants' views were analyzed and organized according to three main themes, constituting a framework that combines micro-, meso-, and macro-level structures and processes: the scope of obligations of HCPs, the roles of health care institutions, and the broader social context, respectively. Our data suggest that the duty to care must be placed in a wider context to include considerations that transcend individual provider obligations. It thus follows, based on our data, that the duty to care cannot be left to personal choice or an appeal to morality based on an ethic derived entirely from individual obligations. The micro-meso-macro analytical framework that we have developed can guide the articulation of accepted norms of duty to care during epidemics and the development of policy for public health crises. It can also enhance the focus of our current expectations of HCPs' duty during epidemics. This can be achieved by informing regulatory bodies, collaborating with policy makers and engaging the public. r 
 Title: A qualitative study of the duty to care in communicable disease outbreaks
Output: True
Paragraph: The worldwide outbreak of the swine-origin 2009 H1N1 influenza A virus (IAV) and an increasing number of influenza cases caused by a highly pathogenic avian influenza (HPAI) H5N1 have accelerated the need to develop vaccines and antiviral agents against IAVs. Among various antivirals, neutralizing monoclonal antibodies (mAbs) are considered important passive therapeutics having an immediate effect against viral pathogens. Here we report a pseudovirus neutralization assay for rapid screening of neutralizing mAbs targeting hemagglutinin (HA) of H5N1 and H1N1 IAV. In this study, we generated six pseudoviruses with an HIV-1 backbone, respectively, expressing HA of four clades of H5N1 IAV and the 2009 epidemic H1N1 IAV. The resulting pseudoviruses were able to infect a variety of human and non-human cells, with 293T cells from human kidney as the most susceptible target cells. Using the established pseudovirus neutralization assay, we showed that three of ten selected mAbs specific to HA could potently neutralize infection of a pseudovirus bearing HA from the homologous IAV A/VietNam/1194/ 2004(H5N1) strain. This was highly consistent with the result of a microneutralization assay testing the same strain of a live IAV. Since the pseudovirus neutralization assay does not involve an infectious virus and can be performed without the requirement of a biosafety-3 laboratory, it may be applied for safe and rapid screening of neutralizing mAbs and antiviral agents targeting HA of IAVs. 
 Title: Development of a safe and convenient neutralization assay for rapid screening of influenza HA-specific neutralizing monoclonal antibodies
Output: True
Paragraph: Background: Household studies provide opportunities to understand influenza-like-illness (ILI) transmission, but data from (sub)tropical developing countries are scarce. Objective: To determine the viral etiology and epidemiology of ILI in households. Study design: ILI was detected by active case finding amongst a cohort of 263 northern Vietnam households between 2008 and 2013. Health workers collected nose and throat swabs for virus detection by multiplex real-time RT-PCR. Results: ILI was detected at least once in 219 (23.7%) of 945 household members. 271 (62.3%) of 435 nose/throat swabs were positive for at least one of the 15 viruses tested. Six viruses predominated amongst positive swabs: Rhinovirus (28%), Influenza virus (17%), Coronavirus (8%), Enterovirus (5%), Respiratory syncytial virus (3%), Metapneumovirus virus (2.5%) and Parainfluenza virus 3 (1.8%). There was no clear seasonality, but 78% of episodes occurred in Winter/Spring for Influenza compared to 32% for Rhinovirus. Participants, on average, suffered 0.49 ILI, and 0.29 virus-positive ILI episodes, with no significant effects of gender, age, or household size. In contrast to US and Australian community studies, the frequency of ILI decreased as the number of household members aged below 5 years increased (p = 0.006). Conclusion: The findings indicate the need for tailored ILI control strategies, and for better understanding of how local childcare practices and seasonality may influence transmission and the role of children. 
 Title: Epidemiology and etiology of influenza-like-illness in households in Vietnam; it's not all about the kids!
Output: True
Paragraph: The innate immune response provides the first line of defense against viruses and other pathogens by responding to specific microbial molecules. Influenza A virus (IAV) produces double-stranded RNA as an intermediate during the replication life cycle, which activates the intracellular pathogen recognition receptor RIG-I and induces the production of proinflammatory cytokines and antiviral interferon. Understanding the mechanisms that regulate innate immune responses to IAV and other viruses is of key importance to develop novel therapeutic strategies. Here we used myeloid cell specific A20 knockout mice to examine the role of the ubiquitin-editing protein A20 in the response of myeloid cells to IAV infection. A20 deficient macrophages were hyperresponsive to double stranded RNA and IAV infection, as illustrated by enhanced NF-kB and IRF3 activation, concomitant with increased production of proinflammatory cytokines, chemokines and type I interferon. In vivo this was associated with an increased number of alveolar macrophages and neutrophils in the lungs of IAV infected mice. Surprisingly, myeloid cell specific A20 knockout mice are protected against lethal IAV infection. These results challenge the general belief that an excessive host proinflammatory response is associated with IAV-induced lethality, and suggest that under certain conditions inhibition of A20 might be of interest in the management of IAV infections. 
 Title: A20 (Tnfaip3) Deficiency in Myeloid Cells Protects against Influenza A Virus Infection
Output: True
Paragraph: LETTERS that the quantitative assessment of the effectiveness of public health intervention measures for SARS is a difficult task for modelers. To make models useful for assessing the effects of specific intervention measures and for predicting the future dynamics during an ongoing epidemic, we need improved knowledge on the transmission mechanisms, pathogenesis, and the epidemiologic determinants of the spread of the virus. Any retrospective analysis of the 2003 SARS epidemic that improves our knowledge of SARS epidemiology is welcome. 
 Title: SARS epi-demiology and cumulative case curve
Output: False
Paragraph: Background-Tobacco related lung diseases including chronic obstructive pulmonary disease (COPD), are major causes of lung-related disability and death worldwide. Acute exacerbation of COPD (AE-COPD) is commonly associated with upper and lower respiratory viral infections and may result in respiratory failure in those with advanced lung disease. Objective-We sought to determine the mechanism underlying COPD exacerbation, and host response to pathogen-derived factors. Methods-Over a 24 months period, we assessed the viral causes for upper and lower respiratory infections in COPD (n=155) and control (n=103) subjects. We collected nasal and bronchoalveolar lavage (BAL) fluid and peripheral blood under baseline and exacerbated condition. We determined the effect of human rhinovirus (HRV) proteinases on T cell activation in humans, and in mice. Results-HRVs are isolated from nasal and lung fluid from subjects with AE-COPD. BAL fluid, and CD4 T cells from COPD patients exhibited a type 1 T helper (Th1), and Th2 cell cytokine phenotype during acute infection. HRV-encoded proteinase 2A activated monocyte-derived dendritic cells in vitro, and induced strong Th1, and Th2 immune responses from CD4 T cells. Intranasal 
 Title: Human Rhinovirus Proteinase 2A Induces Th1 and Th2 Immunity in COPD
Output: False
Paragraph: Selection of the translational initiation site in most eukaryotic mRNAs appears to occur via a scanning mechanism which predicts that proximity to the 5 0 end plays a dominant role in identifying the start codon. This 'position effect' is seen in cases where a mutation creates an AUG codon upstream from the normal start site and translation shifts to the upstream site. The position effect is evident also in cases where a silent internal AUG codon is activated upon being relocated closer to the 5 0 end. Two mechanisms for escaping the first-AUG rulereinitiation and context-dependent leaky scanning -enable downstream AUG codons to be accessed in some mRNAs. Although these mechanisms are not new, many new examples of their use have emerged. Via these escape pathways, the scanning mechanism operates even in extreme cases, such as a plant virus mRNA in which translation initiates from three start sites over a distance of 900 nt. This depends on careful structural arrangements, however, which are rarely present in cellular mRNAs. Understanding the rules for initiation of translation enables understanding of human diseases in which the expression of a critical gene is reduced by mutations that add upstream AUG codons or change the context around the AUG START codon. The opposite problem occurs in the case of hereditary thrombocythemia: translational efficiency is increased by mutations that remove or restructure a small upstream open reading frame in thrombopoietin mRNA, and the resulting overproduction of the cytokine causes the disease. This and other examples support the idea that 5 0 leader sequences are sometimes structured deliberately in a way that constrains scanning in order to prevent harmful overproduction of potent regulatory proteins. The accumulated evidence reveals how the scanning mechanism dictates the pattern of transcription -forcing production of monocistronic mRNAs -and the pattern of translation of eukaryotic cellular and viral genes. q 
 Title: Pushing the limits of the scanning mechanism for initiation of translation
Output: False
Paragraph: Zika is a viral disease transmitted mainly by mosquitoes of the genus Aedes. In recent years, it has expanded geographically, changing from an endemic mosquito-borne disease across equatorial Asia and Africa, to an epidemic disease causing large outbreaks in several areas of the world. With the recent Zika virus (ZIKV) outbreaks in the Americas, the disease has become a focus of attention of public health agencies and of the international research community, especially due to an association with neurological disorders in adults and to the severe neurological and ophthalmological abnormalities found in fetuses and newborns of mothers exposed to ZIKV during pregnancy. A large number of studies have been published in the last 3 years, revealing the structure of the virus, how it is transmitted and how it affects human cells. Many different animal models have been developed, which recapitulate several features of ZIKV disease and its neurological consequences. Moreover, several vaccine candidates are now in active preclinical development, and three of them have already entered phase I clinical trials. Likewise, many different compounds targeting viral and cellular components are being tested in in vitro and in experimental animal models. This review aims to discuss the current state of this rapidly growing literature from a multidisciplinary perspective, as well as to present an overview of the public health response to Zika and of the perspectives for the prevention and treatment of this disease. 
 Title: Zika Virus: What Have We Learnt Since the Start of the Recent Epidemic?
Output: False
Paragraph: Although the genetic basis of Duchenne muscular dystrophy has been known for almost thirty years, the cellular and molecular mechanisms characterizing the disease are not completely understood and an efficacious treatment remains to be developed. In this study we analyzed proteomics data obtained with the SomaLogic technology from blood serum of a cohort of patients and matched healthy subjects. We developed a workflow based on biomarker identification and network-based pathway analysis that allowed us to describe different deregulated pathways. In addition to muscle-related functions, we identified other biological processes such as apoptosis, signaling in the immune system and neurotrophin signaling as significantly modulated in patients compared with controls. Moreover, our network-based analysis identified the involvement of FoxO transcription factors as putative regulators of different pathways. On the whole, this study provided a global view of the molecular processes involved in Duchenne muscular dystrophy that are decipherable from serum proteome. 
 Title: Combined use of protein biomarkers and network analysis unveils deregulated regulatory circuits in Duchenne muscular dystrophy
Output: False
Paragraph: Multiple sclerosis (MS) is a debilitating disease of the central nervous system (CNS) that has been extensively studied using the animal model experimental autoimmune encephalomyelitis (EAE). It is believed that CD4 + T lymphocytes play an important role in the pathogenesis of this disease by mediating the demyelination of neuronal axons via secretion of proinflammatory cytokines resulting in the clinical manifestations. Although a great deal of information has been gained in the last several decades about the cells involved in the inflammatory and disease mediating process, important questions have remained unanswered. It has long been held that initial neuroantigen presentation and T cell activation events occur in the immune periphery and then translocate to the CNS. However, an increasing body of evidence suggests that antigen (Ag) presentation might initiate within the CNS itself. Importantly, it has remained unresolved which antigen presenting cells (APCs) in the CNS are the first to acquire and present neuroantigens during EAE/MS to T cells, and what the conditions are under which this takes place, ie, whether this occurs in the healthy CNS or only during inflammatory conditions and what the related cytokine microenvironment is comprised of. In particular, the central role of interferon-g as a primary mediator of CNS pathology during EAE has been challenged by the emergence of Th17 cells producing interleukin-17. This review describes our current understanding of potential APCs in the CNS and the contribution of these and other CNS-resident cells to disease pathology. Additionally, we discuss the question of where Ag presentation is initiated and under what conditions neuroantigens are made available to APCs with special emphasis on which cytokines may be important in this process. 
 Title: The Critical Role of Antigen-Presentation-Induced Cytokine Crosstalk in the Central Nervous System in Multiple Sclerosis and Experimental Autoimmune Encephalomyelitis
Output: True