niryuu/sni-each-converted huggingface dataset:
Paragraph: Purpose: Interest in a variety of neoplastic, functional, neurological, and age-related laryngeal disorders has contributed to the development of laryngology as an established subspecialty. Funding support plays a critical role in facilitating scholarship within the field. Our objectives were to evaluate who is receiving funding from the NIH for topics relevant to voice disorders, and further describe temporal trends in grants awarded. Methods: The NIH RePORTER database was searched for grants relevant to voice disorders. Data were further organized by PI specialty, academic department, and funding totals. Furthermore, PI scholarly impact, as measured by the h-index, was calculated. Results: A total of 830 funded fiscal years (for 232 unique projects) totaling $203 million have supported projects examining voice disorders. A plurality of projects (32.8%) was awarded to PIs in otolaryngology departments, followed by 17.2% to speech pathology/communication sciences departments. Although year-to-year variation was noted, otolaryngology departments received approximately 15% of funding annually. Funded otolaryngologists had similar scholarly impact values to individuals in other specialties. Conclusions: The study of voice disorders involves an interdisciplinary approach, as PIs in numerous specialties receive NIH funding support. As they receive a considerable proportion of this funding and had similar h-indices compared to other specialties involved, otolaryngologists 
 Title: Voicing an impact: who does the National Institutes of Health support for voice disorder research? ☆
Output: True
Paragraph: Viruses are dependent on the cellular translation machinery for protein synthesis. Part of the innate immune response to infection is activation of the stress kinase PKR which phosphorylates the alpha subunit of the initiation factor eIF2. This results in inhibition of translation and is intended to block virus replication. A downstream effect of translational shutoff involves the formation of cytoplasmic granules, termed stress granules (SGs), that contain mRNAs, initiation factors, ribosomal subunits, and other mRNA regulatory proteins. SGs hold mRNAs in a translationally inactive state until cells recover from stress. Recent studies have begun to elucidate the impact of SGs on virus replication. Not surprisingly, viruses from diverse families have been found to modulate SG formation in infected cells by associating with important SG effecter proteins. This review describes the current knowledge on SGs and their interaction with and impact on virus replication. The most highly regulated stage of protein synthesis occurs at the initiation step. The translation initation factor eIF2 plays a crucial role in this process. In non-stressed cells, eIF2 complexed with GDP associates with eIF2B, a nucleotide exchange factor, which exchanges GDP for GTP. This exchange allows the eIF2:GTP complex to associate with initiator methionine tRNA to form ternary complex (eIF2:GTP:tRNA Met ). Ternary complex brings the initiating methionine to the 43S ribosome pre-initiation complex. The 43S complex contains the 40S ribosome and a variety of additional initiation factors that play important roles in translation. The 43S complex then forms the 48S ribosomal complex by binding mRNA, which has itself been activated for translation via association with additional initiation factors. The 60S ribosomal subunit is then recruited, at which point GTP is hydrolyzed to GDP and eIF2:GDP is released from the ribosomal complex to again associate with eIF2B and be recharged with GTP to start the process anew [reviewed in [1, 2] ]. Following cellular stress, the alpha subunit of eIF2 is phosphorylated by one of four stress activated kinases; GCN, which is activated during nutrient starvation, PERK, which is activated following ER stress, HRI, which is activated following oxidative stress and heme deficiency, and PKR, which is activated following virus infection [reviewed in [3] ]. 
 Title: Stress Granules and Virus Replication HHS Public Access
Output: False
Paragraph: Among the most relevant elements contributing to define the One World One Health programme we find epidemics. The reason is that in recent decades, infectious diseases such as HIV/SIDA, SARS and Influenza have shown that we need new approaches and concepts in order to understand how biological emergencies and health alerts deploy new scales of action. Especially relevant has been the case of A(H1N1) influenza. This reached the status of global threat virtually from its onset, triggering an international response with a diffusion, visibility and rapidity unparalleled in previous health alerts. This article maintains that this global condition cannot be explained solely by the epidemiologic characteristics of the disease, such as mortality rate, severe cases, propagation capacity, etc. Resorting to the approach proposed by the Actor-Network Theory (ANT), this paper suggests that the action of certain sociotechnical operators was what built a heterogeneous network of ideas, concepts and materials that turned the A (H1N1) influenza into a global-scale phenomenon with unprecedented speed. Among these operators, the most important ones were: the speaking position, a discourse about threat, the protocols and guidelines that were used and, lastly, the maps that allowed a real-time monitoring of the influenza. The paper ends with the notion of panorama, as defined by Bruno Latour: a suggestion to describe the common denominator of the aforementioned operators, and a means to foresee the development of global scales for certain health alerts. The paper will conclude by proposing that this type of analysis would allow the One World One Health to understand with greater precision the dynamic of epidemics and thus make its principles of action much more specific as well as its definition of what global health should be. 
 Title: The global condition of epidemics: Panoramas in A (H1N1) influenza and their consequences for One World One Health programme
Output: True
Paragraph: Bronchopulmonary C-fi bers and a subset of mechanically sensitive, acid-sensitive myelinated sensory nerves play essential roles in regulating cough. These vagal sensory nerves terminate primarily in the larynx, trachea, carina, and large intrapulmonary bronchi. Other bronchopulmonary sensory nerves, sensory nerves innervating other viscera, as well as somatosensory nerves innervating the chest wall, diaphragm, and abdominal musculature regulate cough patterning and cough sensitivity. The responsiveness and morphology of the airway vagal sensory nerve subtypes and the extrapulmonary sensory nerves that regulate coughing are described. The brainstem and higher brain control systems that process this sensory information are complex, but our current understanding of them is considerable and increasing. The relevance of these neural systems to clinical phenomena, such as urge to cough and psychologic methods for treatment of dystussia, is high, and modern imaging methods have revealed potential neural substrates for some features of cough in the human. CHEST 2014; 146 ( 6 ): 1633 -1648 ABBREVIATIONS : ATP 5 adenosine triphosphate ; GERD 5 gastroesophageal reflux disease ; GIT 5 gastrointestinal tract ; nTS 5 nucleus tractus solitarius ; RAR 5 rapidly adapting receptor ; SAR 5 slowly adapting receptor ; TRPA1 5 transient receptor potential A1 ; TRPM8 5 transient receptor potential M8 ; TRPV1 5 transient receptor potential vanilloid 1 [ Evidence-Based Medicine ] 
 Title: Anatomy and Neurophysiology of Cough CHEST Guideline and Expert Panel Report
Output: False
Paragraph: We previously reported widespread differential expression of long non-protein-coding RNAs (ncRNAs) in response to virus infection. Here, we expanded the study through small RNA transcriptome sequencing analysis of the host response to both severe acute respiratory syndrome coronavirus (SARS-CoV) and influenza virus infections across four founder mouse strains of the Collaborative Cross, a recombinant inbred mouse resource for mapping complex traits. We observed differential expression of over 200 small The small RNAs identified also included many non-miRNA small RNAs, such as small nucleolar RNAs (snoRNAs), in addition to nonannotated small RNAs. An integrative sequencing analysis of both small RNAs and long transcripts from the same samples showed that the results revealing differential expression of miRNAs during infection were largely due to transcriptional regulation and that the predicted miRNA-mRNA IMPORTANCE Most studies examining the host transcriptional response to infection focus only on protein-coding genes. However, mammalian genomes transcribe many short and long non-protein-coding RNAs (ncRNAs). With the advent of deepsequencing technologies, systematic transcriptome analysis of the host response, including analysis of ncRNAs of different sizes, is now possible. Using this approach, we recently discovered widespread differential expression of host long (>200 nucleotide [nt]) ncRNAs in response to virus infection. Here, the samples described in the previous report were again used, but we sequenced another fraction of the transcriptome to study very short (about 20 to 30 nt) ncRNAs. We demonstrated that virus infection also altered expression of many short ncRNAs of diverse classes. Putting the results of the two studies together, we show that small RNAs may also play an important role in regulating the host response to virus infection. Citation Peng X, et al. 2011. Integrative deep sequencing of the mouse lung transcriptome reveals differential expression of diverse classes of small RNAs in response to respiratory virus infection. mBio 2(6):e00198-11. 
 Title: Integrative Deep Sequencing of the Mouse Lung Transcriptome Reveals Differential Expression of Diverse Classes of Small RNAs in Response to Respiratory Virus Infection
Output: True
Paragraph: The heptad repeats (HR1 and HR2) of the spike protein of SARS-CoV are highly conserved regions forming a critical 6-helix bundle during the fusion step of virus entry and are attractive targets of entry inhibitors. In this study, we report that a minimal HR2 peptide, P6 of 23-mer, can block the fusion of SARS-CoV with an IC 50 of 1.04 ± 0.22 M. This finding supports the structural prediction of the deep groove of HR1 trimer as a target for fusion inhibitors, and suggests P6 as a potential lead peptide for future drug development. Moreover, combination of an HR-1 peptide, N46, and its mutated version, N46eg, shows synergistic inhibition with an IC 50 of 1.39 ± 0.05 M and combination index of 0.75 ± 0.15, suggesting a common strategy to achieve promising inhibition by HR1 peptide for other class I envelope viruses. 
 Title: Identification of a minimal peptide derived from heptad repeat (HR) 2 of spike protein of SARS-CoV and combination of HR1-derived peptides as fusion inhibitors
Output: True
Paragraph: Microarray hybridization based identification of viral genotypes is increasingly assuming importance due to outbreaks of multiple pathogenic viruses affecting humans causing wide-spread morbidity and mortality. Surprisingly, microarray based identification of food-borne viruses, one of the largest groups of pathogenic viruses, causing more than 1.5 billion infections world-wide every year, has lagged behind. Cell-culture techniques are either unavailable or time consuming for routine application. Consequently, current detection methods for these pathogens largely depend on polymerase chain reaction (PCR) based techniques, generally requiring an investigator to preselect the target virus of interest. Here we describe the first attempt to use the microarray as an identification tool for these viruses. We have developed methodology to synthesize targets for virus identification without using PCR, making the process genuinely sequence independent. We show here that a tiling microarray can simultaneously detect and identify the genotype and strain of common food-borne viruses in a single experiment. 
 Title: Detection and Identification of Common Food-Borne Viruses with a Tiling Microarray
Output: True
Paragraph: In order to study the inactivation effects of electrostatic field of electret films on Bacillus subtilis, a plane-plane electrode system was used to simulate the electric field of the electret films and the viability of B. subtilis affected by electrostatic field for different applying durations was investigated. It was found that the survival ratio of B. subtilis can be considerably affected by the field and duration. It was also found that the viability of bacillus decreases with the increase of the duration. In addition, the comparative survival ratio (CSR) of B. subtilis decreases to 35% even during a short duration as the applied field reaches an enough high value of more than 15 kV/cm. These indicated that the uniform field inactivated the viability of B. subtilis availability. Based on the inactivation effect of the applied field on the B. subtilis, the effectiveness of charged polypropylene films on the inactivation of B. subtilis was measured and discussed. r 
 Title: Inactivation effects of electrostatic field on Bacillus subtilis
Output: True
Paragraph: Background: Entry of Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) and its envelope fusion with host cell membrane are controlled by a series of complex molecular mechanisms, largely dependent on the viral envelope glycoprotein Spike (S). There are still many unknowns on the implication of cellular factors that regulate the entry process. Methodology/Principal Findings: We performed a yeast two-hybrid screen using as bait the carboxy-terminal endodomain of S, which faces the cytosol during and after opening of the fusion pore at early stages of the virus life cycle. Here we show that the ezrin membrane-actin linker interacts with S endodomain through the F1 lobe of its FERM domain and that both the eight carboxy-terminal amino-acids and a membrane-proximal cysteine cluster of S endodomain are important for this interaction in vitro. Interestingly, we found that ezrin is present at the site of entry of S-pseudotyped lentiviral particles in Vero E6 cells. Targeting ezrin function by small interfering RNA increased S-mediated entry of pseudotyped particles in epithelial cells. Furthermore, deletion of the eight carboxy-terminal amino acids of S enhanced S-pseudotyped particles infection. Expression of the ezrin dominant negative FERM domain enhanced cell susceptibility to infection by SARS-CoV and S-pseudotyped particles and potentiated S-dependent membrane fusion. Conclusions/Significance: Ezrin interacts with SARS-CoV S endodomain and limits virus entry and fusion. Our data present a novel mechanism involving a cellular factor in the regulation of S-dependent early events of infection. 
 Title: Ezrin Interacts with the SARS Coronavirus Spike Protein and Restrains Infection at the Entry Stage
Output: True
Paragraph: Background: Local malaria transmission has decreased rapidly since the National Malaria Elimination Action Plan was launched in China in 2010. However, imported malaria cases from Africa and Southeast Asia still occur in China due to overseas laborers. Diagnosis by microscopy is the gold standard for malaria and is used in most hospitals in China. However, the current capacity of microscopists to manage malaria cases in hospitals and public health facilities to meet the surveillance needs to eliminate and prevent the reintroduction of malaria is unknown. Methods: Malaria diagnoses were assessed by comparing the percentage of first visit and confirmed malaria diagnoses at Centers for Disease Control and Prevention (CDCs) and hospitals. The basic personnel information for public health departments and hospitals at different levels was investigated. The skills of microscopists for blood smear preparation and slide interpretation were also examined at the county and township levels. Results: Inaccurate rate with 13.49% and 7.32%, respectively, in 2013 and 2014, from 341 and 355 reported cases from sub-provincial levels in Jiangsu province. Most of the 523 malaria cases reported in Nantong Prefecture from 2000 to 2014 involved patients who first visited county CDCs seeking treatment, however, none of these cases received confirmed diagnosis of malaria in townships or villages.The staff at county CDCs and hospitals with a higher education background performed better at making and interpreting blood smears than staff from townships. Conclusions: The network for malaria elimination in an entire province has been well established. However, an insufficient capacity for malaria diagnosis was observed, especially the preparing and reading the blood smears at the township and village levels, which is a challenge to achieving and maintaining malaria elimination. 
 Title: The challenge of maintaining microscopist capacity at basic levels for malaria elimination in Jiangsu Province, China
Output: False
Paragraph: Simultaneous extraction and separation of liquiritin, glycyrrhizic acid, and glabridin from licorice were developed by liquidliquid extraction with liquid chromatography separation. By utilizing different extraction solvents, procedures, and times, the optimum extraction conditions were established. The extracts of licorice were separated and determined using a C 18 column with a mobile phase consisting of acetonitrile-water (containing 1.0% acetic acid) with a gradient elution of 0~10 min from 20:80 to 60:40 (v/v). Preparative columns with different packing sizes were investigated to isolate the three compounds from the extracts of licorice. The 12 μm chromatographic column showed better separation for the three compounds from licorice. 0.29 mg/g for liquiritin, 1.43 mg/g for glycyrrhizic acid, and 0.07 mg/g for glabridin were obtained and the recoveries were 80.8, 89.7, and 72.5%, respectively. © KSBB 
 Title: Simultaneous Extraction and Separation of Liquiritin, Glycyrrhizic Acid, and Glabridin from Licorice Root with Analytical and Preparative Chromatography
Output: True
Paragraph: Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease characterized by a progressive upper and lower motor neuron degeneration. One of the peculiar clinical characteristics of ALS is the wide distribution in age of onset, which is probably caused by different combinations of intrinsic and exogenous factors. We investigated whether these modifying factors are converging into common pathogenic pathways leading either to an early or a late disease onset. This would imply the identification of phenotypic biomarkers, that can distinguish the two populations of ALS patients, and of relevant pathways to consider in a therapeutic intervention. Toward this aim a differential proteomic analysis was performed in peripheral blood mononuclear cells (PBMC) from a group of 16 ALS patients with an age of onset ≤55 years and a group of 16 ALS patients with an age of onset ≥75 years, and matched healthy controls. We identified 43 differentially expressed proteins in the two groups of patients. Gene ontology analysis revealed that there was a significant enrichment in annotations associated with protein folding and response to stress. We next validated a selected number of proteins belonging to this functional group in 85 patients and 83 age-and sex-matched healthy controls using immunoassays. The results of the validation study confirmed that there was a decreased level of peptidyl-prolyl cis-trans isomerase A (also known as cyclophilin A), heat shock protein HSP 90-alpha, 78 kDa glucose-regulated protein (also known as BiP) and protein deglycase DJ-1 in PBMC of ALS patients with an early onset. Similar results were obtained in PBMC and spinal cord from two SOD1 G93A mouse models with an early and late disease onset. This study suggests that a different ability to upregulate proteins involved in proteostasis, such as foldase and chaperone proteins, may be at the basis of a different susceptibility to ALS, putting forward the development of therapeutic approaches aiming at boosting the protein quality control system. 
 Title: Decreased Levels of Foldase and Chaperone Proteins Are Associated with an Early-Onset Amyotrophic Lateral Sclerosis
Output: False
Paragraph: The aim of this study was to determine the susceptibility of murine embryonic stem (mESCs) to mouse hepatitis virus (MHV-A59) and mouse minute virus (MMVp) and the effect of these viruses on germline transmission (GLT) and the serological status of recipients and pups. When recipients received 10 blastocysts, each injected with 10 0 TCID 50 MHV-A59, three out of five recipients and four out of 14 pups from three litters became seropositive. When blastocysts were injected with 10 -5 TCID 50 MMVp, all four recipients and 14 pups from four litters remained seronegative. The mESCs replicated MHV-A59 but not MMVp, MHV-A59 being cytolytic for mESCs. Exposure of mESCs to the viruses over four to five passages but not for 6 h affected GLT. Recipients were seropositive for MHV-A59 but not for MMVp when mESCs were cultured with the virus over four or five passages. The data show that GLT is affected by viruscontaminated mESCs. 
 Title: Impairment of germline transmission after blastocyst injection with murine embryonic stem cells cultured with mouse hepatitis virus and mouse minute virus
Output: True
Paragraph: Context: Coptidis rhizome (CR), also known as Huanglian in Chinese, is the rhizome of Coptis chinensis Franch., C. deltoidea C.Y. Cheng et Hsiao, or C. teeta Wall (Ranunculaceae). It has been widely used to treat bacillary dysentery, diabetes, pertussis, sore throat, aphtha, and eczema in China. Objectives: The present paper reviews the latest advances of CR, focusing on the botany, phytochemistry, traditional usages, pharmacokinetics, pharmacology and toxicology of CR and its future perspectives. Methods: Studies from 1985 to 2018 were reviewed from books; PhD. and MSc. dissertations; the state and local drug standards; PubMed; CNKI; Scopus; the Web of Science; and Google Scholar using the keywords Coptis, Coptidis Rhizoma, Huanglian, and goldthread. Results: Currently, 128 chemical constituents have been isolated and identified from CR. Alkaloids are the characteristic components, together with organic acids, coumarins, phenylpropanoids and quinones. The extracts/compounds isolated from CR cover a wide pharmacological spectrum, including antibacterial, antivirus, antifungal, antidiabetic, anticancer and cardioprotective effects. Berberine is the most important active constituent and the primary toxic component of CR. Conclusions: As an important herbal medicine in Chinese medicine, CR has the potential to treat various diseases. However, further research should be undertaken to investigate the clinical effects, toxic constituents, target organs and pharmacokinetics, and to establish criteria for quality control, for CR and its related medications. In addition, the active constituents, other than alkaloids, in both raw and processed products of CR should be investigated. ARTICLE HISTORY 
 Title: Coptidis Rhizoma: a comprehensive review of its traditional uses, botany, phytochemistry, pharmacology and toxicology
Output: False
Paragraph: Viruses assemble large macromolecular repeat structures that become part of the infectious particles or virions. Ribonucleocapsids (RNCs) of negative strand RNA viruses are a prime example where repetition of nucleoprotein (NP) along the genome creates a core polymeric helical scaffold that accommodates other nucleocapsid proteins including viral polymerase. The RNCs are transported through the cytosol for packaging into virions through association with viral matrix proteins at cell membranes. We hypothesized that RNC would be ideal targets for crosslinkers engineered to promote aberrant protein-protein interactions, thereby blocking their orderly transport and packaging. Previously, we had generated single-domain antibodies (sdAbs) against Filoviruses that have all targeted highly conserved C-terminal regions of NP known to be repetitively exposed along the length of the RNCs of Marburgvirus (MARV) and Ebolavirus (EBOV). Our crosslinker design consisted of dimeric sdAb expressed intracellularly, which we call Xintrabodies (X-for crosslinking). Electron microscopy of purified NP polymers incubated with purified sdAb constructs showed NP aggregation occurred in a genus-specific manner with dimeric and not monomeric sdAb. A virus-like particle (VLP) assay was used for initial evaluation where we found that dimeric sdAb inhibited NP incorporation into VP40-based VLPs whereas monomeric sdAb did not. Inhibition of NP packaging was genus specific. Confocal microscopy revealed dimeric sdAb was diffuse when expressed alone but focused on pools of NP when the two were coexpressed, while monomeric sdAb showed ambivalent partition. Infection of stable Vero cell lines expressing dimeric sdAb specific for either MARV or EBOV NP resulted in smaller plaques and reduced progeny of cognate virus relative to wild-type Vero cells. Though the impact was marginal at later time-points, the collective data suggest that viral replication can be reduced by crosslinking intracellular NP using relatively small amounts of dimeric sdAb to restrict NP packaging. The stoichiometry and ease of application of the approach would likely benefit from transitioning away from intracellular expression of crosslinking sdAb to exogenous delivery of antibody. By retuning sdAb specificity, the approach of crosslinking highly conserved regions of assembly critical proteins may well be applicable to inhibiting replication processes of a broad spectrum of viruses. 
 Title: Article 1197 1 Original research Citation: Darling TL, Sherwood LJ and Hayhurst A (2017) Intracellular Crosslinking of Filoviral Nucleoproteins with Xintrabodies Restricts Viral Packaging
Output: False
Paragraph: Background: While it is known that acute respiratory illness (ARI) is caused by an array of viruses, less is known about co-detections and the resultant comparative symptoms and illness burden. This study examined the co-detections, the distribution of viruses, symptoms, and illness burden associated with ARI between December 2012 and March 2013. Methods: Outpatients with ARI were assayed for presence of 18 viruses using multiplex reverse transcriptase polymerase chain reaction (MRT-PCR) to simultaneously detect multiple viruses. Results: Among 935 patients, 60% tested positive for a single virus, 9% tested positive for ≥1 virus and 287 (31%) tested negative. Among children (<18 years), the respective distributions were 63%, 14%, and 23%; whereas for younger adults (18-49 years), the distributions were 58%, 8%, and 34% and for older adults (≥50 years) the distributions were 61%, 5%, and 32% (P < 0.001). Co-detections were more common in children than older adults (P = 0.01), and less frequent in households without children (P = 0.003). Most frequently co-detected viruses were coronavirus, respiratory syncytial virus, and influenza A virus. Compared with single viral infections, those with co-detections less frequently reported sore throat (P = 0.01), missed fewer days of school (1.1 vs. 2 days; P = 0.04), or work (2 vs. 3 days; P = 0.03); other measures of illness severity did not vary. Conclusions: Among outpatients with ARI, 69% of visits were associated with a viral etiology. Co-detections of specific clusters of viruses were observed in 9% of ARI cases particularly in children, were less frequent in households without children, and were less symptomatic (e.g., lower fever) than single infections. 
 Title: influenza season
Output: True
Paragraph: Bagaza virus is a mosquito-borne flavivirus, first isolated in 1966 in Central African Republic. It has currently been identified in mosquito pools collected in the field in West and Central Africa. Emergence in wild birds in Europe and serological evidence in encephalitis patients in India raise questions on its genetic evolution and the diversity of isolates circulating in Africa. To better understand genetic diversity and evolution of Bagaza virus, we describe the full-genome characterization of 11 West African isolates, sampled from 1988 to 2014. Parameters such as genetic distances, N-glycosylation patterns, recombination events, selective pressures, and its codon adaptation to human genes are assessed. Our study is noteworthy for the observation of N-glycosylation and recombination in Bagaza virus and provides insight into its Indian origin from the 13th century. Interestingly, evidence of Bagaza virus codon adaptation to human house-keeping genes is also observed to be higher than those of other flaviviruses well known in human infections. Genetic variations on genome of West African Bagaza virus could play an important role in generating diversity and may promote Bagaza virus adaptation to other vertebrates and become an important threat in human health. 2 of 26 meningoencephalitis virus (ITV), a pathogen affecting poultry (turkeys) and close to West Nile virus (WNV) in several genomic regions [3, 11] . Although diverse studies have contributed greatly to our understanding of the transmission modes of BAGV [8, 12] and the pathogenesis of BAGV infection [13] , only one study has addressed BAGV genetic diversity, reporting a high homology >90% between Central African Republic, Indian and Spanish BAGV isolates [9] . In West Africa, there is a lack of data on BAGV genetic diversity. To fill this gap and gain better insights into BAGV molecular evolution, we characterized the full-genome of 11 BAGV isolates, sampled from 1988 to 2014 in Senegal and Côte d'Ivoire. Firstly, we assessed genetic distances, phylogenetically informative sites found in more than one sequence contributing to branch ordering, N-glycosylation patterns, recombination events, selective pressures on West African BAGV sequences and their evolutionary phylogenetic relationships with previously available BAGV genomes. Secondly, to assess evidence of future BAGV codon adaptation to human house-keeping genes, a bio-informatics approach was used for analysis of codon adaptation biases. 
 Title: Full-Genome Characterization and Genetic Evolution of West African Isolates of Bagaza Virus
Output: True
Paragraph: Background-Studies in adult long-term care facilities (LTCFs) have shown a correlation between hand hygiene (HH) and viral outbreak reduction, but no such studies have been conducted in pediatric LTCFs where the epidemiology of viral pathogens is different. Methods-We compared electronically monitored facility-wide HH frequency in the weeks immediately prior to outbreaks of acute respiratory or gastrointestinal infections versus control weeks in a 137-bed pediatric LTCF from October 2012-August 2015. Control weeks were the 8-14 day (control 1) and 15-21 day (control 2) periods prior to the onset of each outbreak. Results-There was no difference in HH frequency in the weeks leading up to the outbreaks versus control weeks (odds ratio [OR], 1.0; 95% confidence interval CI, 1.00-1.001 using control 1 and OR, 1.0; 95% CI, 1.00-1.001 using control 2). Conclusions-Our findings differed from those in adult LTFCs, possibly because of the greater contact between residents and staff in the pediatric setting, increased susceptibility to viral pathogens because of immunologic immaturity, or differences in the types of pathogens prevalent in each setting. Although HH may be important for limiting the number of residents infected during outbreaks, we found no association between HH frequency and subsequent outbreak onset. Long-term care; Pediatrics; Outbreaks; Acute respiratory infection Hand hygiene is the primary recommendation for preventing infections in health care settings. 1 A recent review identified several studies conducted in acute care which have 
 Title: Is hand hygiene frequency associated with the onset of outbreaks in pediatric long-term care?
Output: False
Paragraph: Empiric quantification of human mobility patterns is paramount for better urban planning, understanding social network structure and responding to infectious disease threats, especially in light of rapid growth in urbanization and globalization. This need is of particular relevance for developing countries, since they host the majority of the global urban population and are disproportionally affected by the burden of disease. We used Global Positioning System (GPS) data-loggers to track the fine-scale (within city) mobility patterns of 582 residents from two neighborhoods from the city of Iquitos, Peru. We used ,2.3 million GPS data-points to quantify age-specific mobility parameters and dynamic co-location networks among all tracked individuals. Geographic space significantly affected human mobility, giving rise to highly local mobility kernels. Most (,80%) movements occurred within 1 km of an individual's home. Potential hourly contacts among individuals were highly irregular and temporally unstructured. Only up to 38% of the tracked participants showed a regular and predictable mobility routine, a sharp contrast to the situation in the developed world. As a case study, we quantified the impact of spatially and temporally unstructured routines on the dynamics of transmission of an influenza-like pathogen within an Iquitos neighborhood. Temporally unstructured daily routines (e.g., not dominated by a single location, such as a workplace, where an individual repeatedly spent significant amount of time) increased an epidemic's final size and effective reproduction number by 20% in comparison to scenarios modeling temporally structured contacts. Our findings provide a mechanistic description of the basic rules that shape human mobility within a resource-poor urban center, and contribute to the understanding of the role of fine-scale patterns of individual movement and co-location in infectious disease dynamics. More generally, this study emphasizes the need for careful consideration of human social interactions when designing infectious disease mitigation strategies, particularly within resource-poor urban environments. Citation: Vazquez-Prokopec GM, Bisanzio D, Stoddard ST, Paz-Soldan V, Morrison AC, et al. (2013) Using GPS Technology to Quantify Human Mobility, Dynamic Contacts and Infectious Disease Dynamics in a Resource-Poor Urban Environment. PLoS ONE 8(4): e58802. 
 Title: Using GPS Technology to Quantify Human Mobility, Dynamic Contacts and Infectious Disease Dynamics in a Resource-Poor Urban Environment
Output: False
Paragraph: Background: Pairing up primers to amplify desired targets and avoid undesired cross reactions can be a combinatorial challenge. Effective prediction of specificity and inclusivity from multiplexed primers and TaqMan®/ Luminex® probes is a critical step in PCR design. Results: Code is described to identify all primer and probe combinations from a list of unpaired, unordered candidates that should produce a product. It predicts and extracts all amplicon sequences in a large sequence database from a list of primers and probes, allowing degenerate bases and user-specified levels of primer-target mismatch tolerance. Amplicons hit by TaqMan®/Luminex® probes are indicated, and products may be annotated with gene information from NCBI. Fragment length distributions are calculated to predict electrophoretic gel banding patterns. Simulate_PCR is the only freely available software that can be run from the command line for high throughput applications which can calculate all products from large lists of primers and probes compared to a large sequence database such as nt. It requires no prior knowledge of how primers should be paired. Degenerate bases are allowed and entire amplicon sequences are extracted and annotated with gene information. Examples are provided for sets of TaqMan®/Luminex® PCR signatures predicted to amplify all HIV-1 genomes, all Coronaviridae genomes, and a group of antibiotic resistance genes. The software is a command line perl script freely available as open source. 
 Title: Simulate_PCR for amplicon prediction and annotation from multiplex, degenerate primers and probes
Output: True
Paragraph: was performed with RdRpSeq-Fwd (similar to the first round) and RdRpSeq-Rnest primer by using MyFi ™ Mix Kit (Bioline, USA) according to the following parameters: 95 °C for 1 min, followed by 35 cycles at 95 °C for 15 seconds, 56 °C for 15 seconds, 72 °C for 20 seconds, and 2 min at 72 °C for terminal elongation[5]. The resulted amplicons were separated by gel electrophoresis, and the DNA fragments were excised, purified and subjected to sequencing in both directions. The obtained sequences were verified by basic local alignment search tool. As for the amplification of complete N gene region, cDNA was synthesized by using SuperScript III First Strand Synthesis System for RT-PCR (Invitrogen, USA) with NR2 primer (Table 1). Two microliters of the generated cDNA was subjected to one round of PCR cycle by using MyFi ™ Mix Kit (Bioline, USA) with NF1 and NR2 (Table 1) primers following the parameters: 95 °C for 1 min followed by 25 cycles at 95 °C for 15 seconds, 52 °C for 15 seconds and 72 °C for 30 seconds and terminal elongation at 72 °C for 5 min. Then, 0.5 μL of the resulted PCR amplicon was further subjected to the second round PCR following the abovementioned parameters. The resulted PCR product was separated by gel electrophoresis while the DNA fragment was excised, purified and subjected to sequencing by using NF1, NR1, NF2, NR2 and N350R primers. The obtained sequences were analyzed by using ChromasPro version 1.7.4 (Technelysium Pty Ltd, Australia). Multiple sequence alignment was performed by using Clustal X (version 2.0.11) with 44 human-derived (including the Malaysian case; MyH010414; GenBank accession No: KP769415) and 3 camel-derived MERS-CoV sequences[6]. Maximum likelihood analysis was conducted by using Molecular Evolutionary Genetics Analysis 6.06[7]. The evolutionary history was computed by using Tamura-Nei model with 1 000 replicates of bootstrap analysis. Extracted RNA from combination of throat and nasal swabs from the case was detected positive both in rRT-PCR and conventional RT-PCR for partial RdRp and N gene. The cycle threshold values for upE, ORF1a and ORF1b were 28.19, 29.16 and 33.36, respectively. Amplification of partial RdRp and N gene regions resulted in DNA fragment of ~240 bp and ~310 bp, respectively (data not shown). Initial sequencing result of these fragments showed highly identical nucleotide sequence (99%) to MERS-CoV strain Jeddah_1_2013 (KJ556336.1), further confirming the MERS-CoV infection. JX869059/Human/Jeddah/HCoV EMC/2012 KC776174/Human/Jordan/Jordan N3/2012 Clade A 0.0005 67 63 63 63 66 50 62 Clade B Figure 1. Phylogenetic analysis of N gene region of Malaysia MERS-CoV case together with 3 camel-derived and 43 human-derived MERS-CoV sequences from 2012-2014. Red diamond: Malaysian case; Blank diamond: sequences from the camel-derived MERS-CoV. 
 Title: Nucleocapsid gene analysis from an imported case of Middle East respiratory syndrome coronavirus, Malaysia Asian Pacific Journal of Tropical Disease
Output: True
Paragraph: Rapid diagnosis of respiratory virus infections contributes to patient care. This systematic review evaluates the diagnostic accuracy of rapid tests for the detection of respiratory viruses. We searched Medline and EMBASE for studies evaluating these tests against polymerase chain reaction as the reference standard. Of 179 studies included, 134 evaluated rapid tests for influenza viruses, 32 for respiratory syncytial virus (RSV), and 13 for other respiratory viruses. We used the bivariate random effects model for quantitative meta-analysis of the results. Most tests detected only influenza viruses or RSV. Summary sensitivity and specificity estimates of tests for influenza were 61.1% and 98.9%. For RSV, summary sensitivity was 75.3%, and specificity, 98.7%. We assessed the quality of studies using the Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2) checklist. Because of incomplete reporting, the risk of bias was often unclear. Despite their intended use at the point of care, 26.3% of tests were evaluated in a laboratory setting. Although newly developed tests seem more sensitive, high-quality evaluations of these tests are lacking. 
 Title: Clinical Infectious Diseases Rapid Tests for Influenza, Respiratory Syncytial Virus, and Other Respiratory Viruses: A Systematic Review and Meta-analysis
Output: True
Paragraph: Background: The interferon-gamma release assay (IGRA) is more specific than the tuberculin skin test to discriminate between tuberculosis (TB) and nontuberculous mycobacterial (NTM) diseases. Here we performed a retrospective study to evaluate the performance of the T-SPOT.TB in patients with NTM diseases. Methods: Between March, 2013 and Nov, 2015, a total of 58 patients with NTM diseases had a T-SPOT.TB performed were enrolled, 30 patients had definite NTM diseases, 28 had probable diseases. Their clinicopathological characteristics were reviewed and analyzed. Cultures for mycobacteria were performed. The indirect proportion method with Löwenstein-Jensen (L-J) medium was used for first-line drug susceptibility test. T-SPOT.TB assay was performed according to the manufacturer's instructions. Data were expressed as mean ± standard deviation (continuous variables) and as numbers and percentages (categorical variables). The χ 2 test was used for comparisons between proportions. Results: The average age was 51.8 ± 16.1 years (range 10 to 77 years), 58.6% (34/58) were male. 16.4% (9/55) were TB-PCR positive. 34 (58.6%) isolates were Mycobacterium intracellulare, ten (17.2%) were Mycobacterium chelonae and seven (12.1%) were Mycobacterium fortuitum. Fifty-two (89.7%) patients were NTM lung disease, five (8.6%) were pleural disease, and one (1.7%) lymphadenitis. The total positivity of T-SPOT.TB was 53.4% (31/58) among the whole group (probable and definite). For probable cases, the T-SPOT.TB assay was positive in 53.5% (15/28); for definite cases, 16 (53.3%) of 30 definite cases were positive. There was no statistical difference in the positivity rate between them (P < 0.01). Conclusions: In the study, we showed that a significant portion of NTM diseases were T-SPOT.TB positive in China. Although T-SPOT.TB is useful diagnostic method for differentiating TB from NTM diseases, in China, the IGRA assay show limited value in the discrimination. In addition, further research is needed to investigate the association between TB infection and treatment for NTM patients. 
 Title: The performance of interferon-gamma release assay in nontuberculous mycobacterial diseases: a retrospective study in China
Output: False
Paragraph: Recombinant severe acute respiratory syndrome (SARS) nucleocapsid and spike protein-based immunoglobulin G immunoassays were developed and evaluated. Our assays demonstrated high sensitivity and specificity to the SARS coronavirus in sera collected from patients as late as 2 years postonset of symptoms. These assays will be useful not only for routine SARS coronavirus diagnostics but also for epidemiological and antibody kinetic studies. 
 Title: Recombinant Protein-Based Assays for Detection of Antibodies to Severe Acute Respiratory Syndrome Coronavirus Spike and Nucleocapsid Proteins ᰔ Downloaded from
Output: False
Paragraph: The increased number of outbreaks of H5 and H7 LPAI and HPAI viruses in poultry has major public and animal health implications. The continuous rapid evolution of these subtypes and the emergence of new variants influence the ability to undertake effective surveillance. Retroviral pseudotypes bearing influenza haemagglutinin (HA) and neuraminidase (NA) envelope glycoproteins represent a flexible platform for sensitive, readily standardized influenza serological assays. We describe a multiplex assay for the study of neutralizing antibodies that are directed against both influenza H5 and H7 HA. This assay permits the measurement of neutralizing antibody responses against two antigenically distinct HAs in the same serum/plasma sample thus increasing the amount and quality of serological data that can be acquired from valuable sera. Sera obtained from chickens vaccinated with a monovalent H5N2 vaccine, chickens vaccinated with a bivalent H7N1/H5N9 vaccine, or turkeys naturally infected with an H7N3 virus were evaluated in this assay and the results correlated strongly with data obtained by HI assay. We show that pseudotypes are highly stable under basic cold-chain storage conditions and following multiple rounds of freeze-thaw. We propose that this robust assay may have practical utility for in-field serosurveillance and vaccine studies in resource-limited regions worldwide. 
 Title: Multiplex Evaluation of Influenza Neutralizing Antibodies with Potential Applicability to In-Field Serological Studies
Output: True
Paragraph: Viral infections are an important and often unrecognized component of disease in immunocompromised patients. The diagnosis and management of viral infections have expanded largely because of new quantitative molecular diagnostic assays. Well-recognized pathogens such as herpes simplex virus (HSV), cytomegalovirus (CMV), and respiratory viruses have been joined by newly recognized pathogens such as BK virus, human herpesvirus-6 (HHV-6), and human metapneumovirus in this highly susceptible patient population. The role of Epstein-Barr virus (EBV) and Human herpesvirus-8 (HHV-8) in lymphoproliferative diseases also continue to be clarified. As a result, the management of viral infections in patients with hematologic malignancies continues to be a growing challenge for the clinician. 
 Title: Pathogens Chapter 2 Viruses
Output: True
Paragraph: Y.-J. Jeong). † These two authors contributed equally to this work. The outbreak of severe acute respiratory syndrome (SARS) in 2002 affected thousands of people and an efficient diagnostic system is needed for accurate detection of SARS coronavirus (SARS CoV) to prevent or limit future outbreaks. Of the several SARS CoV structural proteins, the nucleocapsid protein has been shown to be a good diagnostic marker. In this study, an ssDNA aptamer that specifically binds to SARS CoV nucleocapsid protein was isolated from a DNA library containing 45-nuceotide random sequences in the middle of an 88mer single-stranded DNA. After twelve cycles of systematic evolution of ligands by exponential enrichment (SELEX) procedure, 15 ssDNA aptamers were identified. Enzyme-linked immunosorbent assay (ELISA) analysis was then used to identify the aptamer with the highest binding affinity to the SARS CoV nucleocapsid protein. Using this approach, an ssDNA aptamer that binds to the nucleocapsid protein with a K d of 4.93 ± 0.30 nM was identified. Western blot analysis further demonstrated that this ssDNA aptamer could be used to efficiently detect the SARS CoV nucleocapsid protein when compared with a nucleocapsid antibody. Therefore, we believe that the selected ssDNA aptamer may be a good alternative detection probe for the rapid and sensitive detection of SARS. 
 Title: Novel system for detecting SARS coronavirus nucleocapsid protein using an ssDNA aptamer
Output: True
Paragraph: publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active. Propensity-score matched analysis comparing clinical benefits of antimicrobial de-escalation and non-switch in adults with community-onset monomicrobial Escherichia coli, Klebsiella species, and Proteus mirabilis bacteremia 
 Title: Antimicrobial prescribing in Australian hospitals; antimicrobial choice and indications for inappropriate prescribing
Output: False