niryuu/sni-each-converted huggingface dataset:
Paragraph: The etiology of Porcine respiratory disease complex is complicated by infections with multiple pathogens, and multiple infections increase the difficulty in identifying the causal pathogen. In this present study, we developed a detection system of microbes from porcine respiratory by using TaqMan real-time PCR (referred to as Dempo-PCR) to screen a broad range of pathogens associated with porcine respiratory diseases in a single run. We selected 17 porcine respiratory pathogens (Actinobacillus pleuropneumoniae, Boldetella bronchiseptica, Haemophilus parasuis, Pasteurella multocida, Pasteurella multocida toxin, Streptococcus suis, Mycoplasma hyopneumoniae, Mycoplasma hyorhinis, Mycoplasma hyosynovie, porcine circovirus 2, pseudorabies virus, porcine cytomegalovirus, swine influenza A virus, porcine reproductive and respiratory virus US strain, EU strain, porcine respiratory coronavirus and porcine hemagglutinating encephalomyelitis virus) as detection targets and designed novel specific primer-probe sets for seven of them. In sensitivity test by using standard curves from synthesized DNA, all primer-probe sets showed high sensitivity. However, porcine reproductive and respiratory virus is known to have a high frequency of genetic mutations, and the primer and probe sequences will need to be checked at a considerable frequency when performing Dempo-PCR from field samples. A total of 30 lung samples from swine showing respiratory symptoms on six farms were tested by the Dempo-PCR to validate the assay's clinical performance. As the results, 12 pathogens (5 virus and 7 bacteria) were detected and porcine reproductive and respiratory virus US strain, Mycoplasma hyorhinis, Haemophilus parasuis, and porcine cytomegalovirus were detected at high frequency. These results suggest that Dempo-PCR assay can be applied as a screening system with wide detection targets. 
 Title: FULL PAPER Virology Development of a one-run real-time PCR detection system for pathogens associated with porcine respiratory diseases
Output: True
Paragraph: Objective To describe the epidemiology and clinical impact of respiratory viruses in a neonatal intensive care unit (NICU). Study design We conducted a retrospective observational study of infants with respiratory viruses detected by multiplex reverse-transcriptase PCR from May 2012 to May 2017. The proportion of symptomatic vs. asymptomatic infants and associated morbidity were assessed. The association of infection prevention and control (IP&C) strategies and transmission was ascertained. Results Respiratory viruses were detected in 83 infants representing 86 unique episodes during which infants remained asymptomatic in 15 (17%). Of the 71 symptomatic episodes, only 45% were associated with increased respiratory and/or nutritional support. Rhinovirus/enteroviruses were most common (69%) and involved nine of 12 transmission events. IP&C strategies including restricting visitors <12 years of age and screening exposed infants were associated with decreased transmission rates. Conclusions NICU patients can be asymptomatic carriers of respiratory viruses. Identification of such infants is important to prevent transmission in the NICU. * Lisa Saiman 
 Title: Impact of respiratory viruses in the neonatal intensive care unit
Output: True
Paragraph: Several arenaviruses can cause viral hemorrhagic fever, a severe disease with case-fatality rates in hospitalized individuals ranging from 15-30%. Because of limited prophylaxis and treatment options, new medical countermeasures are needed for these viruses classified by the National Institutes of Allergy and Infectious Diseases (NIAID) as top priority biodefense Category A pathogens. Recombinant consensus interferon alpha (cIFN-a) is a licensed protein with broad clinical appeal. However, while cIFN-a has great therapeutic value, its utility for biodefense applications is hindered by its short in vivo half-life, mode and frequency of administration, and costly production. To address these limitations, we describe the use of DEF201, a replicationdeficient adenovirus vector that drives the expression of cIFN-a, for pre-and post-exposure prophylaxis of acute arenaviral infection modeled in hamsters. Intranasal administration of DEF201 24 h prior to challenge with Pichindé virus (PICV) was highly effective at protecting animals from mortality and preventing viral replication and liver-associated disease. A significant protective effect was still observed with a single dosing of DEF201 given two weeks prior to PICV challenge. DEF201 was also efficacious when administered as a treatment 24 to 48 h post-virus exposure. The protective effect of DEF201 was largely attributed to the expression of cIFN-a, as dosing with a control empty vector adenovirus did not protect hamsters from lethal PICV challenge. Effective countermeasures that are highly stable, easily administered, and elicit long lasting protective immunity are much needed for arena and other viral infections. The DEF201 technology has the potential to address all of these issues and may serve as a broad-spectrum antiviral to enhance host defense against a number of viral pathogens. Citation: Gowen BB, Ennis J, Russell A, Sefing EJ, Wong M-H, et al. (2011) Use of Recombinant Adenovirus Vectored Consensus IFN-a to Avert Severe Arenavirus Infection. PLoS ONE 6(10): e26072. 
 Title: Use of Recombinant Adenovirus Vectored Consensus IFN-a to Avert Severe Arenavirus Infection
Output: True
Paragraph: Nerve growth factor (NGF) is overexpressed in patients with inflammatory lung diseases, including virus infections. Airway surface liquid (ASL), which is regulated by epithelial cell ion transport, is essential for normal lung function. No information is available regarding the effect of NGF on ion transport of airway epithelium. To investigate whether NGF can affect ion transport, human primary air-interface cultured epithelial cells were placed in Ussing chambers to obtain transepithelial voltage (À7.1 AE 3.4 mV), short-circuit current (I sc , 5.9 AE 1.0 lA), and transepithelial resistance (750 OÁcm 2 ), and to measure responses to ion transport inhibitors. Amiloride (apical, 3.5 9 10 À5 mol/L) decreased I sc by 55.3%. Apically applied NGF (1 ng/mL) reduced I sc by 5.3% in 5 min; basolaterally applied NGF had no effect. The response to amiloride was reduced (41.6%) in the presence of NGF. K-252a (10 nmol/ L, apical) did not itself affect Na + transport, but it attenuated the NGFinduced reduction in Na + transport, indicating the participation of the trkA receptor in the NGF-induced reduction in Na + transport. PD-98059 (30 lmol/L, apical and basolateral) did not itself affect Na + transport, but attenuated the NGF-induced reduction in Na + transport, indicating that trkA activated the Erk 1/2 signaling cascade. NGF stimulated phosphorylation of Erk 1/2 and the b-subunit of ENaC. K-252a and PD-98059 inhibited these responses. NGF had no effect on I sc in the presence of apical nystatin (50 lmol/L). These results indicate that NGF inhibits Na + transport through a trkA-Erk 1/2-activated signaling pathway linked to ENaC phosphorylation. 
 Title: Nerve growth factor reduces amiloride-sensitive Na + transport in human airway epithelial cells
Output: True
Paragraph: Vaccines have been the single most significant advancement in public health, preventing morbidity and mortality in millions of people annually. Vaccine development has traditionally focused on whole organism vaccines, either live attenuated or inactivated vaccines. While successful for many different infectious diseases whole organisms are expensive to produce, require culture of the infectious agent, and have the potential to cause vaccine associated disease in hosts. With advancing technology and a desire to develop safe, cost effective vaccine candidates, the field began to focus on the development of recombinantly expressed antigens known as subunit vaccines. While more tolerable, subunit vaccines tend to be less immunogenic. Attempts have been made to increase immunogenicity with the addition adjuvants, either immunostimulatory molecules or an antigen delivery system that increases immune responses to vaccines. An area of extreme interest has been the application of nanotechnology to vaccine development, which allows for antigens to be expressed on a particulate delivery system. One of the most exciting examples of nanovaccines are rationally designed protein nanoparticles. These nanoparticles use some of the basic tenants of structural biology, biophysical chemistry, and vaccinology to develop protective, safe, and easily manufactured vaccines. Rationally developed nanoparticle vaccines are one of the most promising candidates for the future of vaccine development. 
 Title: Vaccine Technologies: From Whole Organisms to Rationally Designed Protein Assemblies HHS Public Access Author manuscript
Output: True
Paragraph: Fecal microbial transplantation (FMT), a treatment for certain gastrointestinal conditions associated with dysbiosis in people, is also empirically employed in horses with colitis. This study used microbiota high-throughput sequencing to compare the fecal microbial profile of healthy horses to that of geriatric microbial transplant recipients experiencing diarrhea and tested whether FMT restores microbiota diversity. To evaluate the effect of environment and donor characteristics on the intestinal microbiota, fecal samples were collected per rectum from 15 healthy young-adult (2-12 years) and 15 geriatric (�20 years) horses. Additionally, FMT was performed for 3 consecutive days in 5 geriatric horses with diarrhea using feces from the same healthy donor. Fecal samples were collected from both donor and recipient prior to each FMT and from recipients 24 hours following the last FMT. The profile of the fecal bacterial microbiota was compared using 16S amplicon sequencing. 
 Title: The fecal microbiota of healthy donor horses and geriatric recipients undergoing fecal microbial transplantation for the treatment of diarrhea
Output: True
Paragraph: In this work, we use a within-host viral dynamic model to describe the SARS-CoV-2 kinetics in host. Chest radiograph score data are used to estimate the parameters of that model. Our result shows that the basic reproductive number of SARS-CoV-2 in host growth is around 3.79. Using the same method we also estimate the basic reproductive number of MERS virus is 8.16 which is higher than SARS-CoV-2. The PRCC method is used to analyze the sensitivities of model parameters and the drug effects on virus growth are also implemented to analyze the model. 
 Title: The within-host viral kinetics of SARS-CoV-2
Output: False
Paragraph: Most murine hepatitis virus (MHV) strains, as their name suggests, infect the liver. However, several murine strains are tropic for the central nervous system (CNS) and cause encephalitis with subsequent CNS demyelination. The CNS demyelination shares pathological similarities with human CNS demyelinating diseases such as multiple sclerosis (MS). These viruses are, therefore, used to study the role of the immune system in viral clearance from the CNS, in CNS demyelination, and in remyelination. Nevertheless, it is still unclear exactly how MHV induces demyelination and to what extent the immune system plays a role in this pathology. Here we review this eld in the context of the immune response to MHV in the liver and the CNS focusing on studies that have been published in the past 5 years. Journal of NeuroVirology (2002) 8, 76-85. 
 Title: Murine hepatitis virus-A model for virus-induced CNS demyelination
Output: False
Paragraph: Used since ancient times especially for the local treatment of pulmonary diseases, lungs and airways are a versatile target route for the administration of both local and systemic drugs. Despite the existence of different platforms and devices for the pulmonary administration of drugs, only a few formulations are marketed, partly due to physiological and technological limitations. Respiratory infections represent a significant burden to health systems worldwide mainly due to intrahospital infections that more easily affect immune-compromised patients. Moreover, tuberculosis (TB) is an endemic infectious disease in many developing nations and it has resurged in the developed world associated with the human immunodeficiency virus/acquired immunodeficiency syndrome (HIV/AIDS) epidemic. Currently, medicine faces the specter of antibiotic resistance. Besides the development of new anti-infectious drugs, the development of innovative and more efficient delivery systems for drugs that went off patent appears as a promising strategy pursued by the pharmaceutical industry to improve the therapeutic outcomes and to prolong the utilities of their intellectual property portfolio. In this context, nanotechnology-based drug delivery systems (nano-DDS) emerged as a promising approach to circumvent the limitations of conventional formulations and to treat drug resistance, opening the hypothesis for new developments in this area. 
 Title: Nanotechnology and pulmonary delivery to overcome resistance in infectious diseases ☆
Output: False
Paragraph: PRRSV live vaccines are widely used in pig farming practice and are usually not adjuvanted. For safety issues, it would be useful to reduce the antigenic load of such vaccines while preserving their efficacy. In this study we show that the addition of polymer or oil adjuvants in a PRRS live vaccine enhanced the protection to challenge of vaccinated animals compared to a non-adjuvanted commercial reference. Moreover, for both types of adjuvants, despite lower antibody titers, the protection to challenge given by the adjuvanted vaccine containing only 50% of the antigen load was equivalent to the protection given by the non-adjuvanted vaccine. These results demonstrate that the addition of relevant adjuvants can enhance the efficacy of the protection conferred to animals by live vaccines. 
 Title: of the 5th vaccine conference organizing committee. of the 5th vaccine conference organizing committee
Output: False
Paragraph: The genome of bacteriophage q~6 is composed of three unique segments of double-stranded RNA packaged within a procapsid. One segment can recombine with another in regions that share little sequence similarity. Although the recombination is therefore heterologous, the crossover points usually consist of two to six identical nucleotides. The frequency of recombinants is enhanced by conditions that prevent or hinder the minus strand synthesis of a single plus strand segment. Recombination serves as a repair system as well as a means of changing the genetic structure of the virus. The reaction can be studied in an in-vitro packaging and replication system involving purified procapsids and ssRNA. Although there are striking differences in the mechanisms of recombination in RNA viruses, there are also strong similarities. All seem to use a copy-choice template switching action for recombination. The q~ 6 system is a useful model for the recombination of other segmented double-stranded RNA viruses such as the Reoviridae. 
 Title: Heterologous recombination in the segmented dsRNA genome of bacteriophage (I)6 General background of viral RNA recombination
Output: True
Paragraph: Aim To identify the risk factors in children under five years of age for severe acute lower respiratory infections (ALRI), which are the leading cause of child mortality. We performed a systematic review of published literature available in the public domain. We conducted a quality assessment of all eligible studies according to GRADE criteria and performed a meta-analysis to report the odds ratios for all risk factors identified in these studies. We identified 36 studies that investigated 19 risk factors for severe ALRI. Of these, 7 risk factors were significantly associated with severe ALRI in a consistent manner across studies, with the following meta-analysis estimates of odds ratios (with 95% confidence intervals): low birth weight 3.18 (1.02-9.90), lack of exclusive breastfeeding 2.34 (1.42-3.88), crowding -more than 7 persons per household 1.96 (1.53-2.52), exposure to indoor air pollution 1.57 (1.06-2.31), incomplete immunization 1.83 (1.32-2.52), undernutrition -weight-for-age less than 2 standard deviations 4.47 (2.10-9.49), and HIV infection 4.15 (2.57-9.74). This study highlights the role of the above seven risk factors in the development of severe pneumonia in under-five children. In addition, it emphasizes the need for further studies investigating other potential risk factors. Since these risk factors are potentially preventable, health policies targeted at reducing their prevalence provide a basis for decreasing the burden of childhood pneumonia. 
 Title: Risk factors for severe acute lower respiratory infections in children -a systematic review and meta-analysis
Output: True
Paragraph: Uniform polymeric nanoparticles with various morphologies of projection coronas like the viruses in the coronavirus group have been formed by the self-organization of macromolecular chains polymerizing in a dispersion system of styrene (St), acrylonitrile (AN) and poly(ethylene glycol) monomethoxymonomethacrylate (PEGm) in a polar solvent (water/ethanol). An increase in the water composition reduced the crystallization degree of AN units, resulting in a variety of the nanoparticle morphology such as the increased particle size, the reduced projection size, the increased projection number, and the decreased inter-projection distance. The difference in the projection morphology strongly affected a dispersibility in water. q 
 Title: One-step nanomorphology control of self-organized projection coronas in uniform polymeric nanoparticles *
Output: False
Paragraph: Data management and integration are complicated and ongoing problems that will require commitment of resources and expertise from the various biological science communities. Primary components of successful cross-scale integration are smooth information management and migration from one context to another. We call for a broadening of the definition of bioinformatics and bioinformatics training to span biological disciplines and biological scales. Training programs are needed that educate a new kind of informatics professional, Biological Information Specialists, to work in collaboration with various discipline-specific research personnel. Biological Information Specialists are an extension of the informationist movement that began within library and information science (LIS) over 30 years ago as a professional position to fill a gap in clinical medicine. These professionals will help advance science by improving access to scientific information and by freeing scientists who are not interested in data management to concentrate on their science. 
 Title: Journal of Biomedical Discovery and Collaboration Biological information specialists for biological informatics
Output: True
Paragraph: To investigate the efficacy of intracerebral (IC) immunization in preventing viral spread in the brain, we immunized mice with inactivated rabies virus via the subcutaneous (SC) or IC route, followed by administration of a lethal dose of rabies virus (challenge virus standard strain), directly into the brains of immunized mice. Progressive paralytic neurological signs were observed in control and 75% of SC immunized mice, whereas only 20% of IC immunized mice exhibited symptoms. Neutralizing antibody titers in blood plasma were significantly elevated in SC and IC immunized mice, with the highest levels seen in IC immunized mice. Analysis of whole brain lysates revealed a strong induction of immunoglobulin in the brains of IC immunized mice that had virus neutralizing activity. Histopathological examination of brain tissue revealed mild encephalitis and disseminated viral antigen in control and SC immunized mice, but rare in IC immunized mice. These results suggest that IC immunization induces a preventive humoral immune response against intracerebrally inoculated rabies virus. Induction of neutralizing antibody in cerebrospinal fluid represents a putative therapeutic measure for the treatment of rabid animals and humans. 
 Title: Intracerebral vaccination suppresses the spread of rabies virus in the mouse brain
Output: True
Paragraph: In August 2014, children's hospitals in Kansas City, Missouri and Chicago, Illinois notified the Centers for Disease Control and Prevention (CDC) about increased numbers of pediatric patients hospitalized with severe respiratory illness (SRI). In response to CDC reports, Public Health Ontario Laboratories (PHOL) launched an investigation of patients being tested for enterovirus D-68 (EV-D68) in Ontario, Canada. The purpose of this investigation was to enhance our understanding of EV-D68 epidemiology and clinical features. Data for this study included specimens submitted for EV-D68 testing at PHOL from September 1, 2014 to October 31, 2014. Comparisons were made between patients who tested positive for the virus (cases) and those testing negative (controls). EV-D68 was identified in 153/907 (16.8%) of patients tested. In the logistic regression model adjusting for age, sex, setting and time to specimen collection, individuals younger than 20 years of age were more likely to be diagnosed with EV-D68 compared to those 20 and over, with peak positivity at ages 5-9 years. Cases were not more likely to be hospitalized than controls. Cases were more likely to be identified in September than October (OR 8.07; 95% CI 5.15 to 12.64). Routine viral culture and multiplex PCR were inadequate methods to identify EV-D68 due to poor sensitivity and inability to differentiate EV-D68 from other enterovirus serotypes or rhinovirus. Testing for EV-D68 in Ontario from July to December, 2014 detected the presence of EV-D68 virus among young children during September-October, 2014, with most cases detected in September. There was no difference in hospitalization status between cases and controls. In order to better understand the epidemiology of this virus, surveillance for EV-D68 should include testing of symptomatic individuals from all treatment settings and patient age groups, with collection and analysis of comprehensive clinical and epidemiological data. 
 Title: Epidemiology of Enterovirus D68 in Ontario
Output: True
Paragraph: Correspondence: Mingyue Zhu (mingyuezhu2002@163.com) or Mengsen Li (mengsenli@163.com) α-fetoprotein (AFP) is an early serum growth factor in foetal embryonic development and hepatic oncogenesis. A growing number of investigations of AFP as a tumour-specific biomarker have concluded that AFP is an important target for cancer treatment. AFP also plays an immunomodulatory role in the treatment of several autoimmune diseases, such as rheumatoid arthritis, multiple sclerosis, myasthenia gravis and thyroiditis. In an effort to support biochemical screening and drug design and discovery, we attempted to express and purify human AFP in a Bac-to-Bac system. Two key factors affecting the expression of recombinant human AFP (R-AFP), namely the infectious baculovirus inoculum volume and the culturing time post-infection, were optimized to maximize the yield. We achieved a high yield of approximately 1.5 mg/l of harvested medium with a 72-96 h incubation period after infection and an inoculum volume ratio of 1:100. We also assessed the role of R-AFP in the proliferation of the human liver cancer cell line Bel 7402, and the results indicated that R-AFP promoted the growth of hepatoma cells. We concluded that this method can produce high yields of R-AFP, which can be used for studies related to AFP. 
 Title: Expression and bioactivity of human α-fetoprotein in a Bac-to-Bac system
Output: True
Paragraph: This study was designed to determine the therapeutic efficacy and safety of the Shi-cha capsule, a Chinese herbal formula, in the treatment of patients with wind-cold type common cold. In our multi-center, prospective, double-blind, randomized, placebocontrolled, dose-escalation trial, patients with wind-cold type common cold received 0.6 g of Shi-cha capsule plus 0.6 g placebo (group A), 1.2 g of Shi-cha capsule (group B), or 1.2 g placebo (group C), three times daily for 3 days and followed up to 10 days. The primary end point was all symptom duration. The secondary end points were main symptom duration, minor symptom duration, the changes in cumulative symptom score, main symptom score, and minor symptom score 4 days after the treatment, as well as adverse events. A total of 377 patients were recruited and 360 met the inclusive criteria; 120 patients constituted each treatment group. Compared with patients in group C, patients in groups A and B had significant improvement in the all symptom duration, main symptom duration, minor symptom duration, as well as change from baseline of cumulative symptom score, main symptom score, and minor symptom score at day 4. The symptom durations and scores showed slight superiority of group B over group A, although these differences were not statistically significant. There were no differences in adverse events. The Shi-cha capsule is efficacious and safe for the treatment of patients with wind-cold type common cold. Larger trials are required to fully assess the benefits and safety of this treatment for common cold. 
 Title: Treatment of Common Cold Patients with the Shi-Cha Capsule: A Multicenter, Double-Blind, Randomized, Placebo-Controlled, Dose-Escalation Trial
Output: True
Paragraph: The present study aimed to investigate the effects of levodopa (LEV) on cellular apoptosis in a rabbit model of steroid-associated necrosis of the femoral head (SANFH). A total of 44 healthy adult Chinese rabbits were randomly divided into three groups: Group A (n=15), administered a combination of lipopolysaccharide and hormone to establish the SANFH animal model; group B (n=15), SANFH animal model as in group A orally administered LEV (0.4 g/kg/day) on the day of injection; and group C (n=14), the control group. On the 6th and 8th week of modeling, seven rabbits from each group were sacrificed to harvest bilateral femoral head specimens for hematoxylin and eosin staining and apoptosis detection by terminal deoxynucleotidyl transferase dUTP nick-end labeling assay analysis, as well as for observing pathological changes and analyzing cellular apoptosis. Eight weeks after modeling, the serum insulin-like growth factor (IGF)-1 levels of the three groups were measured. The empty lacunae rate and apoptosis index of bone cells in the treatment group were significantly lower than that of the model group (P<0.01). Eight weeks after treatment, the serum levels of IGF-1 were significantly higher than that of the model group (P<0.01). These findings suggested that LEV was able to reduce steroid-induced bone cellular apoptosis, reduce the occurrence of necrosis of the femoral head and, through in vivo metabolism, it may promote the synthesis and release of IGF-1, which could be one of its biological pathways to prevent and treat SANFH. Levodopa attenuates cellular apoptosis in steroid-associated necrosis of the femoral head 
 Title: EXPERIMENTAL AND THERAPEUTIC MEDICINE
Output: False
Paragraph: Waltner-Toews, D., Martin, S.W., Meek, A.H. and McMillan, I., 1986. Dairy calf management, morbidity and mortality in Ontario Holstein herds. I. The Data. Prey. Vet. Med., Heifer calf management practices and clinical outcomes were studied on 104 randomly selected Holstein dairy farms in southwestern Ontario between October 1980 and July 1983. Data were collected at both the farm level (all farms) and the individual calf level (1968 calves, 35 farms). Farm-level management data were collected by means of questionnaires and farm visits. Calf-level management data were recorded by farmers on forms provided. Treatments for disease and mortality data were recorded by the farmers on the calves up to the age of weaning, the age at which calves were no longer fed milk or milk substitutes on a regular basis. Farm size ranged from 23 to 154 calvings per year. Farm-level'mortality rates per sixmonth season (winter/summer) were skewed, with a mean of about 6%, a median of zero, and a range of 67%. Morbidity rates were similarly skewed. Four percent of liveborn heifer calves died, 20% were treated for scours, and 15% were treated for pneumonia before the age of weaning. Stated farm policies on calf rearing were implemented to varying degrees on different farms, as estimated from individual calf data. This posed particular problems for interpreting farm-level data, since the danger of committing an ecologic fallacy was high. The data set described in this paper formed the basis for an observational study of the interrelationships of heifer calf management and clinical outcomes. 
 Title: DAIRY CALF MANAGEMENT, MORBIDITY AND MORTALITY IN ONTARIO HOLSTEIN HERDS. I. THE DATA
Output: False
Paragraph: Despite a plethora of studies demonstrating significant morbidity and mortality due to community-acquired respiratory viral (CRV) infections in intensively treated hematology patients, and despite the availability of evidence-based guidelines for the diagnosis and management of respiratory viral infections in this setting, there is no uniform inclusion of respiratory viral infection management in the clinical hematology routine. Nevertheless, timely diagnosis and systematic management of CRV infections in intensively treated hematology patients has a demonstrated potential to significantly improve outcome. We have briefly summarized the recently published data on CRV infection epidemiology, as well as guidelines on the diagnosis and management of CRV infections in patients intensively treated for hematological malignancies. We have also assessed available treatment options, as well as mentioned novel agents currently in development. 
 Title: microorganisms Are Community Acquired Respiratory Viral Infections an Underestimated Burden in Hematology Patients?
Output: True
Paragraph: T cell epitopes can be used for the accurate monitoring of avian influenza virus (AIV) immune responses and the rational design of vaccines. No T cell epitopes have been previously identified in the H5N1 AIV virus nucleoprotein (NP) in chickens. For the first time, this study used homology modelling techniques to construct three-dimensional structures of the peptidebinding domains of chicken MHC class I molecules for four commonly encountered unique haplotypes, i.e., B4, B12, B15, and B19. H5N1 AIV NP was computationally parsed into octapeptides or nonapeptides according to the peptide-binding motifs of MHC class I molecules of the B4, B12, B15 and B19 haplotypes. Seventy-five peptide sequences were modelled and their MHC class I molecule-binding abilities were analysed by molecular docking. Twenty-five peptides (Ten for B4, six for B12, two for B15, and seven for B19) were predicted to be potential T cell epitopes in chicken. Nine of these peptides and one unrelated peptide were manually synthesized and their T cell responses were tested in vitro. Spleen lymphocytes were collected from SPF chickens that had been immunised with a NP-expression plasmid, pCAGGS-NP, and they were stimulated using the synthesized peptides. The secretion of chicken IFN-c and the proliferation of CD8 + T cells were tested using an ELISA kit and flow cytometry, respectively. The significant secretion of chicken IFN-c and proliferation of CD8 + T lymphocytes increased by 13.7% and 11.9% were monitored in cells stimulated with peptides NP [89][90][91][92][93][94][95][96][97] , respectively. The results indicate that peptides NP 89-97 (PKKTGGPIY) and NP 198-206 (KRGINDRNF) are NP T cell epitopes in chicken of certain haplotypes. The method used in this investigation is applicable to predicting T cell epitopes for other antigens in chicken, while this study also extends our understanding of the mechanisms of the immune response to AIV in chicken. 
 Title: Prediction and Identification of T Cell Epitopes in the H5N1 Influenza Virus Nucleoprotein in Chicken
Output: True
Paragraph: Background: Hirschsprung's disease (HSCR) is a type of megacolon induced by defi ciency or dysfunction of ganglion cells in the distal intestine and is associated with developmental disorders of the enteric nervous system. To explore the mechanisms of HSCR, we analyzed the RNAsequencing data of the expansion and the narrow segments of colon tissues separated from children with HSCR. Methods: RNA-sequencing of the expansion segments and the narrow segments of colon tissues isolated from children with HSCR was performed. After differentially expressed genes (DEGs) were identified using the edgeR package in R, functional and pathway enrichment analyses of DEGs were carried out using DAVID software. To further screen the key genes, protein-protein interaction (PPI) network and module analyses were conducted separately using Cytoscape software. Results: A total of 117 DEGs were identified in the expansion segment samples, including 47 up-regulated and 70 down-regulated genes. Functional enrichment analysis suggested that FOS and DUSP1 were implicated in response to endogenous stimulus. In the PPI network analysis, FOS (degree=20), EGR1 (degree=16), ATF3 (degree=9), NOS1 (degree=8), CCL5 (degree=8), DUSP1 (degree=7), CXCL3 (degree=6), VIP (degree=6), FOSB (degree=5), and NOS2 (degree=4) had higher degrees, which could interact with other genes. In addition, two significant modules (module 1 and module 2) were identifi ed from the PPI network. Conclusion: Several genes (including FOS, EGR1, ATF3, NOS1, CCL5, DUSP1, CXCL3, VIP, FOSB, and NOS2) might be involved in the development of HSCR through their effect on the nervous system. World J Pediatr 2017;13(3):267-273 
 Title: Genes involved in HSCR Identifying key genes associated with Hirschsprung's disease based on bioinformatics analysis of RNA-sequencing data
Output: False
Paragraph: Tuberculosis (TB) is the leading global infectious cause of death. Understanding TB transmission is critical to creating policies and monitoring the disease with the end goal of TB elimination. To our knowledge, there has been no systematic review of key transmission parameters for TB. We carried out a systematic review of the published literature to identify studies estimating either of the two key TB transmission parameters: the serial interval (SI) and the reproductive number. We identified five publications that estimated the SI and 56 publications that estimated the reproductive number. The SI estimates from four studies were: 0.57, 1.42, 1.44 and 1.65 years; the fifth paper presented age-specific estimates ranging from 20 to 30 years (for infants <1 year old) to <5 years (for adults). The reproductive number estimates ranged from 0.24 in the Netherlands (during 1933-2007) to 4.3 in China in 2012. We found a limited number of publications and many high TB burden settings were not represented. Certain features of TB dynamics, such as slow transmission, complicated parameter estimation, require novel methods. Additional efforts to estimate these parameters for TB are needed so that we can monitor and evaluate interventions designed to achieve TB elimination. https://www.cambridge.org/core/terms. https://doi. 
 Title: Epidemiology and Infection Quantifying TB transmission: a systematic review of reproduction number and serial interval estimates for tuberculosis
Output: False
Paragraph: Genomic RNA fingerprints of infectious bronchitis virus (IBV) strains M41 and Conn46 were prepared to identify Tl RNase-resistant oligonucleotides 'unique' to each of the two IBV strains. Such oligonucleotides were subsequently eluted from the gels and their nucleotide sequences determined. When oligonucleotide probes of those sequences were synthesized and used in a dot-blot hybridization assay, the probes lacked IBV strain-speciticity and reacted with the RNAs of homologous as well as heterologous IBV strains. Based on these results, the methods used in this study need to be applied to a large number of oligonucleotide probes, to find one or a few that might be suitable as IBV strain-or serotype-specific oligonucleotide probes. IBV strain M41; IBV strain Conn46; Monoclonal antibody; Nucleic acid probe; 
 Title: Oligonucleotide probes in infectious bronchitis virus diagnosis and strain identification
Output: False
Paragraph: Background: Influenza surveillance systems do not allow the identification of the true burden of illness caused by influenza in the community because they are restricted to consulting cases. A study was conducted to estimate the incidence and the burden of self-defined influenza, and to describe healthcare seeking behavior for self-defined influenza during the A(H1N1)2009 pandemic in the French population. Methods: We conducted a random-based retrospective cross-sectional telephone survey between May 2009 and April 2010 among a random sample of the French population. 
 Title: Burden of influenza, healthcare seeking behaviour and hygiene measures during the A (H1N1)2009 pandemic in France: a population based study
Output: False
Paragraph: Oral corticosteroids are the cornerstone of acute asthma management in the emergency department. Recent evidence has raised doubt about the efficacy of this treatment in preschool-aged children with viral-induced wheezing and in smoking adults. The aims of the study are to: (1) document the magnitude of response to oral corticosteroids in children presenting to the emergency department with moderate or severe asthma; (2) quantify potential determinants of response to corticosteroids, and (3) explore the role of gene polymorphisms associated with the responsiveness to corticosteroids The design is a prospective cohort study of 1008 children aged 1-17 years meeting a strict definition of asthma and presenting with a clinical score of ≥4 on the validated Pediatric Respiratory Assessment Measure (PRAM). All children will receive standardized severity-specific treatment with prednisone/prednisolone and co-interventions (salbutamol with/without ipratropium bromide). Determinants, namely viral aetiology, environmental tobacco smoke, and single nucleotide polymorphism will be objectively documented. The primary efficacy endpoint is hospital admission within 72 hours. Secondary endpoints include other measures of asthma severity and time to recovery within 7 days of the index visit. The study has 80% power for detecting a risk difference of 7.5% associated with each determinant from a baseline risk of 21%, at an α of 0.05. Ethical approval has been obtained from all participating institutions. An impaired response to systemic steroids in certain subgroups will challenge the current standard of practice and call for the immediate search for better approaches. A potential host-environment interaction will broaden our understanding 
 Title: Determinants Of Oral corticosteroid Responsiveness in Wheezing Asthmatic Youth (DOORWAY): protocol for a prospective multicentre cohort study of children with acute moderate-to-severe asthma exacerbations Determinants Of Oral corticosteroid Responsiveness in Wheezing Asthmatic Youth (DOORWAY): protocol for a prospective multicentre cohort study of children with acute moderate-to-severe asthma exacerbations
Output: False
Paragraph: Background: Fibrotic remodeling of airway and lung parenchymal compartments is attributed to pulmonary dysfunction with an involvement of reactive oxygen species (ROS) in chronic lung diseases such as idiopathic pulmonary fibrosis and asthma. Methods: The in vitro study elucidated inhibitory effects of astragalin, kaempferol-3-O-glucoside from leaves of persimmon and green tea seeds, on oxidative stress-induced airway fibrosis. The in vivo study explored the demoting effects of astragalin on epithelial to mesenchymal transition in BALB/c mice sensitized with ovalbumin (OVA). Results: The exposure of 20 μM H 2 O 2 for 72 h accelerated E-cadherin loss and vimentin induction in airway epithelial BEAS-2B cells, which was reversed by non-toxic astragalin at 1-20 μM. Astragalin allayed the airway tissue levels of ROS and vimentin enhanced by OVA challenge. Collagen type 1 production increased in H 2 O 2 -exposed epithelial cells and collagen fiber deposition was observed in OVA-challenged mouse airways. This study further investigated that the oxidative stress-triggered autophagic regulation was responsible for inducing airway fibrosis. H 2 O 2 highly enhanced the expression induction of the autophagy-related beclin-1 and light chains 3A/B (LC3A/B) within 4 h and astragalin blocked such induction by H 2 O 2 . This compound deterred the ROS-promoted autophagosome formation in BEAS-2B cells. Consistently, in OVA-sensitized mice the expression of beclin-1 and LC3A/B was highly induced, and oral administration of astragalin suppressed the autophagosome formation with inhibiting the induction of these proteins in OVA-challenged airway subepithelium. Induction of autophagy by spermidine influenced the epithelial induction of E-cadherin and vimentin that was blocked by treating astragalin. Conclusion: These results demonstrate that astragalin can be effective in allaying ROS-promoted bronchial fibrosis through inhibiting autophagosome formation in airways. 
 Title: Astragalin inhibits autophagy-associated airway epithelial fibrosis
Output: False
Paragraph: Macrophage colony-stimulating factor (CSF1) is an essential growth and differentiation factor for cells of the macrophage lineage. To explore the role of CSF1 in steady-state control of monocyte production and differentiation and tissue repair, we previously developed a bioactive protein with a longer half-life in circulation by fusing pig CSF1 with the Fc region of pig IgG1a. CSF1-Fc administration to pigs expanded progenitor pools in the marrow and selectively increased monocyte numbers and their expression of the maturation marker CD163. There was a rapid increase in the size of the liver, and extensive proliferation of hepatocytes associated with increased macrophage infiltration. Despite the large influx of macrophages, there was no evidence of liver injury and no increase in circulating liver enzymes. Microarray expression profiling of livers identified increased expression of macrophage markers, i.e., cytokines such as TNF, IL1, and IL6 known to influence hepatocyte proliferation, alongside cell cycle genes. The analysis also revealed selective enrichment of genes associated with portal, as opposed to centrilobular regions, as seen in hepatic regeneration. Combined with earlier data from the mouse, this study supports the existence of a CSF1-dependent feedback loop, linking macrophages of the liver with bone marrow and blood monocytes, to mediate homeostatic control of the size of the liver. The results also provide evidence of safety and efficacy for possible clinical applications of CSF1-Fc. hepatosplenomegaly; CD163; macrophages; hepatostat; M-CSF This study is based on extensive studies in the mouse of the role of CSF1 in monocyte-macrophage production and differentiation and the function of macrophages in the control of hepatocyte proliferation. We use a novel form of CSF1, an Fc fusion protein, to demonstrate that the findings in mice can be extended to large animals. We discuss the possible role for CSF1 in homeostatic control of the size of the liver. MACROPHAGE COLONY-STIMULATING FACTOR (CSF1) is an essential growth and differentiation factor for cells of the macrophage lineage (23). Subsequent to the original isolation of human CSF1 cDNA in the 1980s and demonstration that injection of the recombinant CSF1 protein can expand macrophage popu-* K. A. Sauter and L. A. Waddell contributed equally to this work. 
 Title: Macrophage colony-stimulating factor (CSF1) controls monocyte production and maturation and the steady-state size of the liver in pigs Licensed under Creative Commons Attribution CC-BY 3.0
Output: False
Paragraph: XendoU is the first endoribonuclease described in higher eukaryotes as being involved in the endonucleolytic processing of intron-encoded small nucleolar RNAs. It is conserved among eukaryotes and its viral homologue is essential in SARS replication and transcription. The large-scale purification and crystallization of recombinant XendoU are reported. The tendency of the recombinant enzyme to aggregate could be reversed upon the addition of chelating agents (EDTA, imidazole): aggregation is a potential drawback when purifying and crystallizing His-tagged proteins, which are widely used, especially in highthroughput structural studies. Purified monodisperse XendoU crystallized in two different space groups: trigonal P3 1 21, diffracting to low resolution, and monoclinic C2, diffracting to higher resolution. 
 Title: Structural Biology and Crystallization Communications Large-scale purification and crystallization of the endoribonuclease XendoU: troubleshooting with His-tagged proteins
Output: False
Paragraph: Heightened surveillance of acute febrile illness in China since 2004 led to the identification of a severe fever with thrombocytopenia syndrome (SFTS) with unknown etiology. Sporadic patients hospitalized with SFTS in 2009 and 2010 were identified and serum samples were collected. Sequence from a novel species of phlebovirus was identified by sequence independent single primer amplification (SISPA) from the serum of a patient with SFTS. The virus was isolated in Vero cell culture and its complete genome sequence was determined, only distantly related to other known phleboviruses. Electron microscopic analysis revealed a virion morphologically characteristic of phleboviruses. The virus was named as SFTS virus. The viral RNA and/or specific antibodies were detected from the blood of patients with SFTS. Serological assays demonstrated a virus-specific immune response in pairs of sera collected from patients at acute and convalescent phases. The pathogenic mechanisms of thrombocytopenia in human SFTS disease was resembled in a mouse model. The results had been collected to demonstrate that SFTS virus was etiologically associated with an acute and novel infectious disease, SFTS in humans. 
 Title: The Discovery Process of SFTS in China
Output: False
Paragraph: private residential drinking water wells, one dewatering well at a lignite mine, eight surface water sites, and lignite from an active coal mine were sampled in five Parishes of northwestern Louisiana, USA. Using a geographic information system (GIS), wells were selected that were likely to draw water that had been in contact with lignite; control wells were located in areas devoid of lignite deposits. Well water samples were analyzed for pH, conductivity, organic compounds, and nutrient and anion concentrations. All samples were further tested for presence of fungi (cultures maintained for up to 28 days and colonies counted and identified microscopically) and for metal and trace element concentration by inductively-coupled plasma mass spectrometry and atomic emission spectrometry. Surface water samples were tested for dissolved oxygen and presence of pathogenic leptospiral bacteria. The Spearman correlation method was used to assess the association between the endpoints for these field/laboratory analyses and incidence of cancer of the renal pelvis (RPC) based on data obtained from the Louisiana Tumor Registry for the five Parishes included in the study. Significant associations were revealed between the cancer rate and the presence in drinking water of organic compounds, the fungi Zygomycetes, the nutrients PO 4 and NH 3 , and 13 chemical elements. Presence of human pathogenic leptospires was detected in four out of eight (50%) of the surface water sites sampled. The present study of a stable rural Ó Springer Science+Business Media B.V. 2006 population examined possible linkages between aquifers containing chemically reactive lignite deposits, hydrologic conditions favorable to the leaching and transport of toxic organic compounds from the lignite into the groundwater, possible microbial contamination, and RPC risk. 
 Title: Possible linkages between lignite aquifers, pathogenic microbes, and renal pelvic cancer in northwestern Louisiana, USA
Output: True