niryuu/sni-each-converted huggingface dataset:
Paragraph: Globally, there are a number of emerging pathogens. For most, there are no licensed vaccines available for human use, although there is ongoing research and development. However, given the extensive and increasing list of emerging pathogens and the investment required to bring vaccines into clinical use, the task is huge. Overlaid on this task is the risk of anti-microbial resistance (AMR) acquisition by micro-organisms which can endow a relatively harmless organism with pathogenic potential. Furthermore, climate change also introduces a challenge by causing some of the insect vectors and environmental conditions prevalent in tropical regions to begin to spread out from these traditional areas, thus increasing the risk of migration of zoonotic disease. Vaccination provides a defence against these emerging pathogens. However, vaccines for pathogens which cause severe, but occasional, disease outbreaks in endemic pockets have suffered from a lack of commercial incentive for development to a clinical standard, encompassing Phase III clinical trials for efficacy. An alternative is to develop such vaccines to request US Emergency Use Authorization (EUA), or equivalent status in the United States, Canada and the European Union, making use of a considerable number of regulatory mechanisms that are available prior to licensing. This review covers the status of vaccine development for some of the emerging pathogens, the hurdles that need to be overcome to achieve EUA or an equivalent regional or national status and how these considerations may impact vaccine development for the future, such that a more comprehensive stockpile of promising vaccines can be achieved. 
 Title: Vaccines for emerging pathogens: prospects for licensure
Output: True
Paragraph: Proteins are essential macromolecules of life that carry out most cellular processes. Since proteins aggregate to perform function, and since protein-protein interaction (PPI) networks model these aggregations, one would expect to uncover new biology from PPI network topology. Hence, using PPI networks to predict protein function and role of protein pathways in disease has received attention. A debate remains open about whether network properties of ''biologically central (BC)'' genes (i.e., their protein products), such as those involved in aging, cancer, infectious diseases, or signaling and drugtargeted pathways, exhibit some topological centrality compared to the rest of the proteins in the human PPI network. To help resolve this debate, we design new network-based approaches and apply them to get new insight into biological function and disease. We hypothesize that BC genes have a topologically central (TC) role in the human PPI network. We propose two different concepts of topological centrality. We design a new centrality measure to capture complex wirings of proteins in the network that identifies as TC those proteins that reside in dense extended network neighborhoods. Also, we use the notion of domination and find dominating sets (DSs) in the PPI network, i.e., sets of proteins such that every protein is either in the DS or is a neighbor of the DS. Clearly, a DS has a TC role, as it enables efficient communication between different network parts. We find statistically significant enrichment in BC genes of TC nodes and outperform the existing methods indicating that genes involved in key biological processes occupy topologically complex and dense regions of the network and correspond to its ''spine'' that connects all other network parts and can thus pass cellular signals efficiently throughout the network. To our knowledge, this is the first study that explores domination in the context of PPI networks. 
 Title: Dominating Biological Networks
Output: False
Paragraph: MERS-coronavirus infection is currently responsible for considerable morbidity and mortality in Saudi Arabia. Understanding its burden, as an emerging infectious disease, is vital for devising appropriate control strategies. In this study, the burden of MERS-CoV was estimated over 31 months period from June 6, 2012 to January 5, 2015. The total number of patients was 835; 528 (63.2%) patients were male, 771 (92.3%) patients were ≥25 years of age, and 210 (25.1%) patients were healthcare workers. A total of 751 (89.9%) patients required hospitalization. The median duration between onset of illness and hospitalization was 2 days (interquartile range, 0-5). The median length of hospital stay was 14 days (IQR, 6-27). The overall case fatality rate was 43.1%. Basic reproductive number was 0.9. Being Saudi, non-healthcare workers, and age ≥65 years were significantly associated with higher mortality. In conclusion, MERS-CoV infection caused a substantial health burden in Saudi Arabia. 
 Title: JIPH-1222; No. of Pages 5
Output: True
Paragraph: The process of toilet-flushing can generate flushing-associated water droplets which can potentially expose humans to pathogen-laden aerosols. Very little is known about such aerosol dissemination or the means for minimizing exposure to these aerosols. This study has evaluated the efficacy of ultraviolet waveband C (UV-C) for disinfection of flushing-generated pathogen-laden aerosols through tests with localized disinfection systems for airborne and surface contaminations. Three types of bacteria were chosen for investigation: Staphylococcus epidermidis, Escherichia coli, and Salmonella typhimurium. Tests were conducted with UV-C tubes of 5 W and 10 W. High levels of disinfection efficacies were observed, ranging from 76% to 97% for bacteria-laden aerosols at sources of emission, and efficiencies of 53% to 79% for surface samples in localized systems. The results from the localized systems were further compared with those obtained with an upper-room ultraviolet germicidal irradiation (UVGI) system. As it is important to note, the UV-C doses and ozone emissions for the localized systems were found well below the limits recommended in current guidelines. This research has shown that the disinfection of flushing-generated pathogen-laden aerosols in proximity to the source of emission was more effective than at the more distant sites where aerosols may be dispersed to the environment. 
 Title: A pilot study on the disinfection efficacy of localized UV on the flushing- generated spread of pathogens
Output: True
Paragraph: A polyclonal antibody-based antigen-capture ELISA (AC-ELISA) has been developed for detection of Canine parvovirus (CPV) antigens in faecal samples of dogs. The assay uses rabbit anti-CPV polyclonal antibody as the capture antibody, guinea pig anti-CPV polyclonal antibody as tracing antibody and anti-guinea pig HRPO conjugate as the detection system. The optimum dilution of the capture antibody and the tracing antibody capable of detecting the CPV-2 antigens was found to be 1:1 600 and 1:400, respectively, in the check-board titration. In this study, a total of 152 samples (129 faecal samples and 23 cell culture supernatant) were tested both by AC-ELISA and by polymerase chain reaction (PCR). Of the samples tested, 69 and 78 samples were found positive by AC-ELISA and PCR, respectively. The AC-ELISA had relative sensitivity, relative specificity and accuracy of 88.4%, 100.0% and 91.4% respectively. The analytical sensitivity of AC-ELISA was estimated to be 10 2.8 TCID 50 /mL whereas PCR sensitivity was 10 0.8 TCID 50 /mL. The AC-ELISA is a simple, quick and reliable method for screening large numbers of faecal samples of dogs suspected of CPV infection. 
 Title: Development of a Polyclonal Antibody-based AC-ELISA and Its Comparison with PCR for Diagnosis of Canine Parvovirus Infection
Output: False
Paragraph: Monocytes are a heterogeneous population of bone marrow-derived cells that are recruited to sites of infection and inflammation in many models of human diseases, including those of the central nervous system (CNS). Ly6C hi / CCR2 hi inflammatory monocytes have been identified as the circulating precursors of brain macrophages, dendritic cells and arguably microglia in experimental autoimmune encephalomyelitis; Alzheimer's disease; stroke; and more recently in CNS infection caused by Herpes simplex virus, murine hepatitis virus, Theiler's murine encephalomyelitis virus, Japanese encephalitis virus and West Nile virus. The precise differentiation pathways and functions of inflammatory monocyte-derived populations in the inflamed CNS remains a contentious issue, especially in regard to the existence of monocyte-derived microglia. Furthermore, the contributions of monocyte-derived subsets to viral clearance and immunopathology are not well-defined. Thus, understanding the pathways through which inflammatory monocytes migrate to the brain and their functional capacity within the CNS is critical to inform future therapeutic strategies. This review discusses some of the key aspects of inflammatory monocyte trafficking to the brain and addresses the role of these cells in viral encephalitis. 
 Title: Inflammatory monocytes and the pathogenesis of viral encephalitis
Output: True
Paragraph: In this study, we report the complete genome sequence of two contemporary human coronavirus OC43 (HCoV-OC43) strains detected in 2003 and 2004, respectively. Comparative genetic analyses of the circulating strains and the prototype HCoV-OC43 strain (ATCC VR759) were performed. Remarkably, a lower than expected similarity is found between the complete genomes and more in particular between the spike genes of the BE03 and BE04 strains. This finding suggests the existence of two genetically distinct HCoV-OC43 strains, circulating in Belgium in 2003 and 2004. Spike gene sequencing of three additional 2003 and two additional 2004 HCoV-OC43 strains, and subsequent phylogenetic analysis confirm this assumption. Compared to the ATCC prototype HCoV-OC43 strain, an important amino acid substitution is present in the potential cleavage site sequence of the spike protein of all contemporary strains, restoring the N-RRXRR-C motif, associated with increased spike protein cleavability in bovine coronaviruses. We here describe specific characteristics associated with circulating HCoV-OC43 strains, and we provide substantial evidence for the genetic variability of HCoV-OC43. D 
 Title: Circulation of genetically distinct contemporary human coronavirus OC43 strains
Output: True
Paragraph: 1. Laundering with a detergent at a minimum temperature of 71°C (160° F) or at a lower temperature (22-50°C) with water containing detergent and 50-150 ppm of chlorine bleach. 2. Dry cleaning at elevated temperatures/dry cleaning at cold temperatures followed by steam pressing. It is not considered acceptable practice for detainees to share bedding. 
 Title: Infectious Diseases 235 From: Clinical Forensic Medicine: A Physician's Guide, 2nd Edition Infectious Diseases The Role of the Forensic Physician
Output: False
Paragraph: Purpose-Mathematical and simulation models are increasingly used to plan for and evaluate health sector responses to disasters, yet no clear consensus exists regarding best practices for the design, conduct, and reporting of such models. We examined a large selection of published health sector disaster response models to generate a set of best practice guidelines for such models. Methods-We reviewed a spectrum of published disaster response models addressing public health or healthcare delivery, focusing in particular on the type of disaster and response decisions considered, decision makers targeted, choice of outcomes evaluated, modeling methodology, and reporting format. We developed initial recommendations for best practices for creating and reporting such models and refined these guidelines after soliciting feedback from response modeling experts and from members of the Society for Medical Decision Making. Results-We propose six recommendations for model construction and reporting, inspired by the most exemplary models: Health sector disaster response models should address real-world problems; be designed for maximum usability by response planners; strike the appropriate balance between simplicity and complexity; include appropriate outcomes, which extend beyond those considered in traditional cost-effectiveness analyses; and be designed to evaluate the many uncertainties inherent in disaster response. Finally, good model reporting is particularly critical for disaster response models. Conclusions-Quantitative models are critical tools for planning effective health sector responses to disasters. The recommendations we propose can increase the applicability and interpretability of future models, thereby improving strategic, tactical, and operational aspects of preparedness planning and response. Modeling Methodology Disaster Evaluated † Decision Makers Considered * Geographic Setting Decisions Modeled § Outcomes ¶ (Reference) Purpose of Model/Study Modeling Methodology Disaster Evaluated † Decision Makers Considered * Geographic Setting Decisions Modeled § Outcomes ¶ (Reference) Purpose of Model/Study Modeling Methodology Disaster Evaluated † Decision Makers Considered * Geographic Setting 
 Title: Risk Analysis
Output: False
Paragraph: Biological weapons achieve their intended target effects through the infectivity of disease-causing infectious agents. The ability to use biological agents in warfare is prohibited by the Biological and Toxin Weapon Convention. Bioterrorism is defined as the deliberate release of viruses, bacteria or other agents used to cause illness or death in people, but also in animals or plants. It is aimed at creating casualties, terror, societal disruption, or economic loss, inspired by ideological, religious or political beliefs. The success of bioterroristic attempts is defined by the measure of societal disruption and panic, and not necessarily by the sheer number of casualties. Thus, making only a few individuals ill by the use of crude methods may be sufficient, as long as it creates the impact that is aimed for. The assessment of bioterrorism threats and motives have been described before. Biocrime implies the use of a biological agent to kill or make ill a single individual or small group of individuals, motivated by revenge or the desire for monetary gain by extortion, rather than by political, ideological, religious or other beliefs. The likelihood of a successful bioterrorist attack is not very large, given the technical difficulties and constraints. However, even if the number of casualties is likely to be limited, the impact of a bioterrorist attack can still be high. Measures aimed at enhancing diagnostic and therapeutic capabilities and capacities alongside training and education will improve the ability of society to combat 'regular' infectious diseases outbreaks, as well as mitigating the effects of bioterrorist attacks. 
 Title: Biological warfare, bioterrorism, and biocrime
Output: False
Paragraph: Initial in vitro investigations demonstrated type I interferons (IFNs: IFN-a, IFN-b) to inhibit replication of SARS coronavirus (SARS-CoV), but found the nucleoside analogue ribavirin ineffective in Vero cells. In this report, ribavirin was shown to inhibit SARS-CoV replication in five different cell types of animal or human origin at therapeutically achievable concentrations. Since clinical anti-SARS-CoV activity of type I interferons or ribavirin is limited, we investigated the combination of IFN-b and ribavirin. Determination of the virus yield indicated highly synergistic anti-SARS-CoV action of the combination suggesting the consideration of ribavirin plus IFN-b for the treatment of SARS. 
 Title: Ribavirin and interferon-b synergistically inhibit SARS-associated coronavirus replication in animal and human cell lines
Output: True
Paragraph: For the purpose of this article, Asia refers to WHO's combined South-East Asia and Western Pacifi c regions and thus includes Australia and New Zealand. Asia has the highest number of tobacco users and is the prime target of transnational tobacco companies. The future of global tobacco control rests in this region and the challenges are clear. China, India, and Indonesia are key markets and Asia is a frontrunner in tobacco control measures, such as plain packaging of cigarettes. Some countries in Asia have a long history of tobacco control activities beginning in the 1970s, and WHO's Western Pacifi c Region is still the only region where all countries have ratifi ed WHO's Framework Convention on Tobacco Control. We reviewed the history, research, epidemiology, tobacco control action, obstacles, and potential responses and solutions to the tobacco epidemic in this region. Levels of development, systems of government, and population size are very diff erent between countries, with population size ranging from 1500 to 1·3 billion, but similarities exist in aspects of the tobacco epidemic, harms caused, obstacles faced, and tobacco control actions needed. 
 Title: Tobacco Control 2 Tobacco control in Asia
Output: False
Paragraph: Background: Coronavirus causes respiratory infections in humans. To determine the prevalence of human coronavirus (HCoV) infection among patients with influenza-like illness, 5833 clinical samples from nasopharyngeal swabs and aspirates collected between January 2012 and December 2013 were examined. Results: HCoV was found in 46 (0.79 %) samples. There were 19 (0.32 %) HCoV-HKU1, 19 (0.32 %) HCoV-NL63, 5 (0.09 %) HCoV-229E, and 3 (0.05 %) HCoV-OC43. None of the sample tested positive for MERS-CoV. The majority (54 %) of the HCoV-positive patients were between the ages of 0 and 5 years. HCoV was detected throughout the 2-year period and generally peaked from May to October, which coincided with the rainy season. Phylogenetic trees based on the alignment of the spike (S) gene sequences suggest an emergence of a new clade for HCoV-229E. The data in this study provide an insight into the prevalence of the recent circulating HCoVs in the region. 
 Title: Molecular epidemiology and characterization of human coronavirus
Output: False
Paragraph: Estimating the case-fatality risk (CFR)-the probability that a person dies from an infection given that they are a case-is a high priority in epidemiologic investigation of newly emerging infectious diseases and sometimes in new outbreaks of known infectious diseases. The data available to estimate the overall CFR are often gathered for other purposes (e.g., surveillance) in challenging circumstances. We describe two forms of bias that may affect the estimation of the overall CFR-preferential ascertainment of severe cases and bias from reporting delays-and review solutions that have been proposed and implemented in past epidemics. Also of interest is the estimation of the causal impact of specific interventions (e.g., hospitalization, or hospitalization at a particular hospital) on survival, which can be estimated as a relative CFR for two or more groups. When observational data are used for this purpose, three more sources of bias may arise: confounding, survivorship bias, and selection due to preferential inclusion in surveillance datasets of those who are hospitalized and/or die. We illustrate these biases and caution against causal interpretation of differential CFR among those receiving different interventions in observational datasets. Again, we discuss ways to reduce these biases, particularly by estimating outcomes in smaller but more systematically defined cohorts ascertained before the onset of symptoms, such as those identified by forward contact tracing. Finally, we discuss the circumstances in which these biases may affect non-causal interpretation of risk factors for death among cases. PLOS Neglected Tropical Diseases | 
 Title: Potential Biases in Estimating Absolute and Relative Case-Fatality Risks during Outbreaks
Output: False
Paragraph: With the high pervasiveness of viral diseases, the battle against viruses has never ceased. Here we discuss five cellular processes, namely "autophagy", "programmed cell death", "immune response", "cell cycle alteration", and "lipid metabolic reprogramming", that considerably guide viral replication after host infection in an orchestrated manner. On viral infection, "autophagy" and "programmed cell death" are two dynamically synchronized cell survival programs; "immune response" is a cell defense program typically suppressed by viruses; "cell cycle alteration" and "lipid metabolic reprogramming" are two altered cell housekeeping programs tunable in both directions. We emphasize on their functionalities in modulating viral replication, strategies viruses have evolved to tune these processes for their benefit, and how these processes orchestrate and govern cell fate upon viral infection. Understanding how viruses hijack host networks has both academic and industrial values in providing insights toward therapeutic strategy design for viral disease control, offering useful information in applications that aim to use viral vectors to improve human health such as gene therapy, and providing guidelines to maximize viral particle yield for improved vaccine production at a reduced cost. ARTICLE HISTORY 
 Title: Orchestrated efforts on host network hijacking: Processes governing virus replication
Output: True
Paragraph: The aim of the present survey was to evaluate the prevalence of Canine rotavirus (CRV) infection in companion dogs in Ahvaz district, Iran. The studied dogs were selected between referred cases to Shahid Chamran University of Ahvaz. Fecal samples were collected from 98 diarrheic dogs between December 2011 and August 2013. The dogs were classified according to age, sex, breed, clinical signs, and season. They were divided into three age groups (<3 months, 3-6 months, and >6 months), five different breeds, and another two groups on the basis of clinical symptoms (hemorrhagic and non-hemorrhagic diarrhea) using Chi-square analysis, Fischer's exact test, and Z test. The prevalence of rotavirus infection was 16.33 % (16 out of 98) (95 % CI for proportion 9.1-23.6 %) by means of immunochromatography assay (ICA) (Catalog No. RG18-03). The infection had significantly more prevalence in dogs less than 3 months (48.15 %; 13 out of 27) compared with dogs between 3 and 6 months (6.06 %; 2 out of 33) and above 6 months (2.63 %; 1 out of 38) (p<0.05). Prevalence was higher in males (17.54 %; 10 out of 57) than females (14.63 %; 6 out of 41), in winter season (21.74 %; 5 out of 23), and breed of German shepherd (19.05 %; 4 of 21), but the difference was not significant between the prevalence of infection relative to gender, season, and breed (p>0.05). Nevertheless, infection was significantly higher in none-hemorrhagic diarrheic dogs (23.08 %; 15 of 65) (p<0.05). The obtained results provide useful information on the epidemiology of Canine rotavirus in this area. 
 Title: Antigenic detection of Canine rotavirus group A in diarrheic dogs in Ahvaz district, Southwestern Iran
Output: False
Paragraph: KEYWORDS Cox proportional hazard model; dentist; mortality; standardized mortality ratios (SMRs) Background/Purpose: Controversy exists in the literature regarding whether dentists with multiple occupational exposures suffer from premature mortality. A cohort mortality study was conducted to evaluate the survival outcome and determine if potential exposure to harmful agents leads to premature mortality among dentists. Methods: Using the Life Table Analysis System, we calculated standardized mortality ratios (SMRs) for a cohort of 11,700 dentists affiliated with the Taiwan Dental Association. These dentists were followed from 1985e2009. Reference rates were derived from cause-, gender-, and age-specific mortality rates of the general population of Taiwan and 18,664 Taiwanese internists, who were considered to be more socioeconomically proximal to dentists. A Cox proportional hazard model was also constructed to determine multiple risk factors associated with mortality. Results: Compared with the general population, dentists in Taiwan consistently demonstrated reduced from all-cause mortality. However, compared with internists, significant and excess mortality were observed in dentists for overall mortality (SMR Z 1.13; 95% confidence interval [CI] Z 1.00 e1.26), drowning (SMR Z 6.62; 95% CI Z 2.15 e15.45), and heart diseases (SMR Z 1.66; 95% CI Z 1.22e2.21). After adjusting for other risk factors, the Cox model showed an increased hazard ratio of 1.17 (95% CI Z 1.01e1.37) for dentists. Conclusion: Taiwanese dentists demonstrated significant elevated SMRs for overall causes, drowning, and heart diseases. Careful precaution should be taken to reduce these trends. Future studies are also needed for in-depth exploration of the mechanisms regarding how professional stress and exposure contribute to the increased risk of mortality in Taiwanese dentists. 
 Title: Mortality among dentists in Taiwan, 1985e2009
Output: True
Paragraph: Antisense oligonucleotides and short interfering RNAs (siR-NAs) are nucleic acids-targeting reagents for gene expression modulation that are being developed as drugs for many applications. A number of useful synthetic nucleic acids analogues have been introduced recently to greatly improve their properties for use as therapeutics. However, their full effectiveness in cells and in vivo has often only been realized through development of suitable nonviral delivery systems. Among these, a range of natural and synthetic peptides have been found useful for enhancing cellular uptake and/or cell targeting of oligonucleotide analogues and siRNA. Such peptides are synthetically conjugated, used as noncovalent complexes, or used in combination with polymer, liposomal or exosome formulation techniques. This review begins by describing the modes of action of antisense reagents and siRNA and goes on to focus on recent advances in their peptide-mediated cell and in vivo delivery and how peptide use has influenced drug development. The review discusses the challenges associated with understanding the physiological and toxicological aspects of peptide-mediated delivery. Developments towards clinical use are also highlighted, with particular emphasis on peptide conjugates of oligonucleotide analogues used for treatment of neuromuscular diseases. 
 Title: Citation: Molecular Therapy-Nucleic Acids (2011) 1, e27; Molecular Therapy-Nucleic Acids (2012) 1, e27
Output: True
Paragraph: Purpose of Review This review summarizes the current understanding of virus attenuation by large-scale recoding of viral genomes and discusses what would ultimately be necessary for construction of better and safer live modified virus vaccines. Recent Findings It has been shown that codon and codon pair deoptimization are rapid and robust methods that can be used for the development of attenuated vaccine candidates. The viruses attenuated by large-scale recoding have the added value that they are extremely genetically stable. However, the exact mechanisms that lead to viral attenuation by recoding are yet to be determined. Summary While the advantages of large-scale recoding (speed, simplicity, potency, and universal applicability) have been known for more than a decade, this approach has been only inadequately explored and the attention was focused on a limited number of RNA viruses. Attenuation of viruses by large-scale recoding should be explored to combat known and future viral threats. 
 Title: Attenuation of Viruses by Large-Scale Recoding of their Genomes: the Selection Is Always Biased
Output: False
Paragraph: Background. Human bocavirus (HBoV) is a newly described parvovirus. HBoV1 has been associated with respiratory infections, including acute otitis media (AOM), but the knowledge on the significance of HBoV1 in upper respiratory tract infections (URI) and AOM in relation to other respiratory viruses is limited. The objective of this study was to compare the rate of detection of HBoV1 to that of other respiratory viruses in specimens from children with URI, with and without AOM complication. Methods. Nasopharyngeal secretions (NPS) were collected during URI from healthy children (6-35 months) followed prospectively for 1 year; specimens have been previously analyzed for broad spectrum of respiratory viruses. Archived NPS were analyzed for HBoV1 using a high-throughput, quantitative polymerase chain reaction method. Results. Seven hundred and seven NPS samples collected during URI episodes from 201 children were studied for HBoV1. A total of 94 (47%) children tested positive for HBoV1 DNA during 172 (24%) URI episodes; HBoV1 was present as the only virus in 44 (6%) URI episodes. Overall, 37% of URI episodes were complicated by AOM. Of URI associated with single virus (n = 303), the rate of AOM complicating URI associated with HBoV1 only was 52% (23 of 44); this was a higher AOM rate, compared to that of other respiratory viruses. Conclusions. Among URI associated with single respiratory virus, HBoV1-URI was commonly associated with AOM complication. The important role of HBoV1 on AOM pathogenesis needs to be studied further. 
 Title: Role of Human Bocavirus in Upper Respiratory Tract Infections and Acute Otitis Media
Output: False
Paragraph: Bronchiectasis is an increasingly recognised respiratory condition with limited therapeutic options and a complex spectrum of clinical manifestations that invariably includes chronic cough. As the primary presentation of bronchiectasis in most cases, chronic cough and its mechanistic underpinnings are of central importance but remain poorly understood in this setting. Bronchiectasis is also increasingly identified as an underlying cause of chronic cough highlighting the interrelationship between the two conditions that share overlapping clinical features. Several therapeutic approaches have illustrated positive effects on bronchiectasis-associated cough, however, more focused treatment of heterogeneous cough subtypes may yield better outcomes for patients. A current challenge is the identification of bronchiectasis and cough endophenotypes that may allow improved patient stratification and more targeted therapeutic matching of the right treatment to the right patient. Here we discuss the complex disease phenotypes of bronchiectasis and their interrelationship with cough while considering current and emerging treatment options. We discuss some key cough promoters in bronchiectasis including infection, allergy and immune dysfunction. 
 Title: Bronchiectasis and cough: An old relationship in need of renewed attention Chronic cough Bronchiectasis
Output: False
Paragraph: Herpes simplex virus (HSV) isolates derived from the central nervous system of ten patients with HSV-l-induced encephalitis, one patient with multiple sclerosis, and 14 patients with HSV-2-induced meningitis were investigated for neurovirnlence by assaying the LDs0 after nose and intracerebrai (i.c.) inoculation of mice. HSV-1 encephalitis strains were significantly more virulent after nose inoculation (i.e. neuroinvasive) when compared with HSV-1 isolates from patients with oral lesions only, whereas HSV-2 meningitis strains were significantly more virulent after i.c. inoculation when compared with HSV-2 isolates from patients with genital lesions only. No correlation between high neurovirulence (defined as low LDs0 for both routes of infection) and replication in cell cultures of neuronal and non-neuronal cell lines was found, but the weakly neuruvirulent HSV-1 strain isolated from a patient with multiple sclerosis gave low replication yields. After nose inoculation, a highly neuroinvasive HSV-1 laboratory reference strain replicated to high titers in nose tissue, the trigeminal ganglia and brainslem, while a strain with low neuroinvasiveness but high i.c. virulence replicated less well in the brains|era. Neuroinvasiveness of the virus strain might be one factor of relevance in the pathugenesis of HSV-1 encephalitis in man. 
 Title: Neurovirulence of Herpes Simplex Virus Types 1 and 2 Isolates in Diseases of the Central Nervous System
Output: False
Paragraph: Epidemiologic and cross-sectional studies suggest that early life farming and animal exposures are associated with major health benefits, influencing immune development and modifying the subsequent risk of allergic diseases, including asthma. The Wisconsin Infant Study Cohort (WISC) study was established in central Wisconsin to test the hypothesis that early life animal farm exposures are associated with distinct innate immune cell maturation trajectories, decreased allergen sensitization and reduced respiratory viral illness burden during the first 2 years of life. Beginning in 2013, a total of 240 families have been enrolled, 16,522 biospecimens have been collected, and 4098 questionnaires have been administered and entered into a secure database. Study endpoints include nasal respiratory virus identification and respiratory illness burden score, allergic sensitization, expression of allergic disease, and antiviral immune response maturation and profiles. The WISC study prospective design, broad biospecimen collections, and unique US rural community will provide insights into the role of environmental exposures on early life immune maturation profiles associated with protection from allergic sensitization and significant respiratory viral disease burden. The WISC study findings will ultimately inform development of new strategies to promote resistance to severe respiratory viral illnesses and design primary prevention approaches for allergic diseases for all infants. 
 Title: Respiratory health, allergies, and the farm environment: design, methods and enrollment in the observational Wisconsin Infant Study Cohort (WISC): a research proposal
Output: False
Paragraph: Twenty-seven field samples that showed positive in PEDV detection were collected from different farms of Fujian province from 2010 to 2012. Their heterogeneity was investigated by analysis of the ORF3 gene because of its potential function as a representation of virulence. According to the results, six Fujian strains in Group 1 showed a different genotype with unique point mutations, which might be used in differentiation between PEDV groups and brought potential antigenic variation. P55 and five reference strains in Group 2 had a long length deletion, showing another genotype and might be involved in the variation of virulence. Phylogenetic analysis revealed that the collected Fujian strains were very distant from the vaccine development strain CV777, which might be the reason why the vaccine was inefficient to control the disease. The results can help to reconsider the strategy of PEDV vaccine management and prevent outbreaks of PEDV-induced diarrhea more efficiently. 
 Title: Sequence Heterogeneity of the ORF3 Gene of Porcine Epidemic Diarrhea Viruses Field Samples in Fujian
Output: True
Paragraph: Epidermal growth factor (EGF) promotes gastrointestinal mucosal recovery by stimulating the mitogenic activity of intestinal crypt epithelial cells. The aim of this study was to determine the effects of EGF on atrophic enteritis induced in piglets by experimental infection with porcine epidemic diarrhoea virus (PEDV) strain Dr13. Two groups of 12 conventional, colostrum-deprived, 1-day-old, large White-Duroc cross breed piglets were inoculated orally with PEDV (3 · 10 5 50% tissue culture infective doses), with or without EGF (10 lg/kg/day, intraperitoneally once daily for 4 days after infection) and compared to 12 uninfected, untreated control piglets. PEDV + EGF piglets had less severe clinical signs than PEDV only piglets at 48 and 60 h post-infection (hpi). Histologically, the ratio of villous height:crypt depth of PEDV + EGF piglets was significantly higher than PEDV only piglets at 36 and 48 hpi. Immunohistochemistry for Ki67 demonstrated increased proliferation in intestinal crypt epithelial cells of PEDV + EGF piglets compared to PEDV only piglets at 36, 48 and 60 hpi. EGF stimulates proliferation of intestinal crypt epithelial cells and promotes recovery from atrophic enteritis in PEDV-infected piglets. 
 Title: Effects of epidermal growth factor on atrophic enteritis in piglets induced by experimental porcine epidemic diarrhoea virus
Output: False
Paragraph: Background: The continuing spread of the newly emerged H7N9 virus among poultry in China, as well as the possibility of human-to-human transmission, has attracted numerous efforts to develop an effective vaccine against H7N9. The use of nanoparticles in vaccinology is inspired by the fact that most pathogens have a dimension within the nano-size range and therefore can be processed efficiently by the immune system, which leads to a potent immune response. Herein, we report a facile approach to increase antigen size to achieve not only fast but also effective responses against the recombinant HA/H7N9 protein via a simple conjugation of the protein onto the surface of nanodiamond particles. In this study, trimeric Haemagglutinin (H7) that is transiently expressed in N. benthamiana was purified using affinity chromatography, and its trimeric state was revealed successfully by the cross-linking reaction. The trimeric H7 solution was subsequently mixed with a nanodiamond suspension in different ratios. The successful conjugation of the trimeric H7 onto the surface of nanodiamond particles was demonstrated by the changes in size and Zetapotential of the particles before and after protein coating, Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), and Western-blot analysis. Next, biofunction of the protein-nanodiamond conjugates was screened using a haemagglutination assay. A mixture containing 5 µg of trimeric H7 and 60 µg of nanodiamond corresponds to a ratio of 1:12 (w/w) of agglutinated chicken red blood cells at HA titer of 1024, which is 512-fold higher than the HA titer of free trimeric H7. After the 2nd and 3rd immunization in mice, ELISA and Western blot analyses demonstrated that the physical mixture of trimeric H7 protein and nanodiamond (1:12, w/w) elicited statistically significant stronger H7-specific-IgG response demonstrated by higher amounts of H7N9-specific IgG (over 15.4-fold with P < 0.05 after the second immunization). These results indicated a potential effect inherent to nanodiamond towards modulating immune systems, which should be further evaluated and broadly applied in nanovaccine development. 
 Title: Nanodiamond enhances immune responses in mice against recombinant HA/ H7N9 protein
Output: True
Paragraph: Ebola viruses and Marburg viruses, members of the filovirus family, are zoonotic pathogens that cause severe disease in people. The Ebola virus epidemic in West Africa, which was first recognized in early 2014, highlights the threat posed by these deadly viruses. Filovirus disease is characterized by uncontrolled virus replication and the activation of damaging host pathways. Underlying these phenomena is the potent suppression of host innate antiviral responses, particularly the type I interferon (IFN) response, which allows high levels of replication. Here we review the mechanisms deployed by filoviruses to block host innate immunity and discuss aspects of virus replication that promote disease. 
 Title: Filovirus pathogenesis and immune evasion: insights from Ebola virus and Marburg virus
Output: False
Paragraph: Cylindrical protein scaffolds are thought to stabilize membrane tubules, preventing membrane fission. In contrast, Snead et al. find that when scaffold proteins assemble, bulky disordered domains within them become acutely concentrated, generating steric pressure that destabilizes tubules, driving fission. Cellular membranes are continuously remodeled. The crescent-shaped bin-amphiphysinrvs (BAR) domains remodel membranes in multiple cellular pathways. Based on studies of BAR domains in isolation, the current paradigm is that they polymerize into cylindrical scaffolds that stabilize lipid tubules, preventing membrane fission. But in nature BAR domains are often part of multi-domain proteins that contain large intrinsically-disordered regions. Using in vitro and live cell assays, here we show that full-length BAR domaincontaining proteins, rather than stabilizing membrane tubules, are instead surprisingly potent drivers of membrane fission. Specifically, when BAR scaffolds assemble at membrane surfaces, their bulky disordered domains become crowded, generating steric pressure that destabilizes lipid tubules. More broadly, we observe this behavior with BAR domains that have a range of curvatures. These data challenge the idea that cellular membranes adopt the curvature of BAR scaffolds, suggesting instead that the ability to concentrate disordered domains is the key requirement for membrane remodeling and fission by BAR domain-containing proteins. All rights reserved. No reuse allowed without permission. 
 Title: BAR scaffolds drive membrane fission by crowding disordered domains
Output: False
Paragraph: Wedzicha JA: Respiratory syncytial virus, airway inflammation, and FEV1 decline in patients with chronic obstructive pulmonary disease. Am J Respir Crit Care Med 2006, 173:871-876. This paper demonstrated that persistent respiratory syncytial virus infection could contribute to the progression of COPD severity. Models of infection and exacerbations in COPD Papi et al. 263 www.sciencedirect.com 
 Title: Models of infection and exacerbations in COPD This review comes from a themed issue on Respiratory pharmacology Edited by Brendan Canning and Stephen Farmer
Output: True
Paragraph: Background: Current estimates suggest that even in the most resourced settings, the aetiology of encephalitis is identified in less than half of clinical cases. It is acknowledged that filling this gap needs a combination of rigorous sampling and improved diagnostic technologies. Next generation sequencing (NGS) methods are powerful tools with the potential for comprehensive and unbiased detection of pathogens in clinical samples. We reviewed the use of this new technology for the diagnosis of suspected infectious encephalitis, and discuss the feasibility for introduction of NGS methods as a frontline diagnostic test. Methods: A systematic literature review was performed, using MESH and text word searches for variants of "sequencing" and "encephalitis" in Medline and EMbase, and searching bibliographies and citations using the Web of Science database. Two authors independently reviewed, extracted and summarised data. The review identified 25 articles reporting 44 case reports of patients with suspected encephalitis for whom NGS was used as a diagnostic tool. We present the data and highlight themes arising from these cases. There are no randomly controlled trials to assess the utility of NGS as a diagnostic tool. Interpretation: There is increasing evidence of a role for NGS in the work-up of undiagnosed encephalitis. Lower costs and increasing accessibility of these technologies will facilitate larger studies of these patients. We recommend NGS should be considered as a front-line diagnostic * Corresponding author. Microbiology and Virology, Level 4 Camelia Botnar Labs, article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). test in chronic and recurring presentations and, given current sample-to-result turn-around times, as second-line in acute cases of encephalitis. 
 Title: Encephalitis diagnosis using metagenomics: application of next generation sequencing for undiagnosed cases
Output: False
Paragraph: within the receptor binding domain (RBD) of the MERS-CoV S protein. We used a complex consisting of the epitope peptide of the MERS-CoV S protein and CpG-DNA encapsulated in liposome complex to immunize mice, and produced the monoclonal antibodies 506-2G10G5 and 492-1G10E4E2. The western blotting data showed that both monoclonal antibodies detected the S protein and immunoprecipitated the native form of the S protein. Indirect immunofluorescence and confocal analysis suggested strong reactivity of the antibodies towards the S protein of MERS-CoV virus infected Vero cells. Furthermore, the 506-2G10G5 monoclonal antibody significantly reduced plaque formation in MERS-CoV infected Vero cells compared to normal mouse IgG and 492-1G10E4E2. Thus, we successfully produced a monoclonal antibody directed against the RBD domain of the S protein which could be used in the development of diagnostics and therapeutic applications in the future. [BMB Reports 2019; 52(6): 397-402] BMB Rep. 2019; 52(6): 397-402 www.bmbreports.org 
 Title: Generation and characterization of a monoclonal antibody against MERS-CoV targeting the spike protein using a synthetic peptide epitope-CpG-DNA-liposome complex
Output: True
Paragraph: Recently, Zika virus (ZIKV) has attracted much attention in consideration of its association with severe neurological complications including fetal microcephaly. However, there are currently no prophylactic vaccines or therapeutic drugs approved for clinical treatments of ZIKV infection. To determine the potential anti-ZIKV inhibitors, we screened a library of clinical drugs with good safety profiles. Erythromycin estolate (Ery-Est), one of the macrolide antibiotics, was found to effectively inhibit ZIKV infection in different cell types and significantly protect A129 mice from ZIKV-associated neurological signs and mortality. Through further investigation, Ery-Est was verified to inhibit ZIKV entry by disrupting the integrity of the viral membrane which resulted in the loss of ZIKV infectivity. Furthermore, Ery-Est also showed inhibitory activity against dengue virus (DENV) and yellow fever virus (YFV). Thus, Ery-Est may be a promising drug for patients with ZIKV infection, particularly pregnant women. 
 Title: Erythromycin Estolate Inhibits Zika Virus Infection by Blocking Viral Entry as a Viral Inactivator
Output: False
Paragraph: Pneumonia is one of the most common causes of death from infectious diseases worldwide, and the most common fatal infection acquired in hospitals. Despite advances in prevention strategies, such as antibiotic therapies and intensive care, significant improvement in the mortality rate is still lacking. This high mortality is largely due to the limitations in current clinical practices and laboratory tests, which delay the timing of adequate antibiotic therapy. In recent years, many indicators (biomarkers) are present in scenarios where infectious pathogens invade into the body. These biomarkers, as reflected in specific biological responses to infections, have been reported to demonstrate the ability to facilitate the diagnosis, risk stratification, and management of pneumonia. This review provides a schematic overview of these new potential biomarkers based on the categories of (1) microorganisms and their derivatives, (2) inflammation mediators, (3) inflammation response proteins, and (4) stress-sensing proteins. In addition, approaches to identifying new biomarkers are also briefly introduced. Although no current biomarker can solely achieve a definitive diagnosis, many of them can be complemented, rather than replaced outright, in routine clinical practices to improve decision-making processes regarding pneumonia. 
 Title: New markers in pneumonia
Output: True