niryuu/sni-each-converted huggingface dataset:
Paragraph: Human influenza viruses cause regular epidemics and occasional pandemics with a substantial public health burden. Household transmission studies have provided valuable information on the dynamics of influenza transmission. We reviewed published studies and found that once one household member is infected with influenza, the risk of infection in a household contact can be up to 38%, and the delay between onset in index and secondary cases is around 3 days. Younger age was associated with higher susceptibility. In the future, household transmission studies will provide information on transmission dynamics including the correlation of virus shedding and symptoms with transmission, and the correlation of new measures of immunity with protection against infection. 
 Title: Household transmission of influenza virus
Output: True
Paragraph: Severe acute respiratory syndrome -associated coronavirus (SARS-CoV) was introduced to the United States through air travel. Although the risk of SARS-CoV transmission within aircraft cabins has been addressed by several studies, the magnitude of the risk remains unclear. Methods. We attempted to contact all persons with working US telephone numbers aboard seven US-bound fl ights carrying SARS patients. Consenting participants responded to a questionnaire, and a serum sample was collected at least 38 days after the fl ight and tested for SARS-CoV-associated antibodies. Participants reporting an illness compatible with SARS, with onset during the 2-to 10-day incubation period, were considered suspect cases; positive serology was required for confi rmed cases. Results. Among 1,766 passengers and crew, 339 (19%) persons were contacted. Of these, 312 (92%) completed questionnaires, and blood was collected from 127 (37%). Serology was negative for all 127 participants, including three of four who met the clinical case criteria for SARS, and the fourth had a mild illness that lasted only 5 days. Conclusions. Transmission of SARS-associated CoV was not observed, suggesting that the risk of transmission is not amplifi ed aboard aircraft. 
 Title: Risk of Severe Acute Respiratory Syndrome -Associated Coronavirus Transmission Aboard Commercial Aircraft
Output: False
Paragraph: Ontario nurses were employed as the front-line workers when SARS descended upon Toronto in March 2003. Once the crisis had subsided, many nurses remarked that SARS had forever altered their chosen profession; employment, which they once viewed as relatively safe, had been transformed into potentially life-threatening. This discussion provides descriptions of these expressions through nurses who experienced the crisis and chose to go on the public record. Secondly, it compares the subjective perceptions of those nurses to those held by nurses who worked through historical epidemics of unknown or contested epidemiology. The historical literature on nursing in yellow fever, cholera and influenza epidemics has been employed to offer insight. The goal is to determine whether the SARS outbreak was a unique experience for nurses or whether similar experiences were shared by nurses in the past? In summary, the reactions of nurses when confronted with the possibility of contracting a deadly disease remain altogether human, not dissimilar in past or present. Nurses' responses to SARS can be usefully studied within a larger historical vision of crisis nursing, and information or impressions from earlier crises are potentially of interest to the nursing profession. 
 Title: Godzilla in the corridor: The Ontario SARS crisis in historical perspective
Output: True
Paragraph: This study is the first attempt to investigate the drivers of Chinese industrial SO 2 and NO x emissions from both periodic and structural perspectives through a decomposition analysis using the logarithmic mean Divisia index (LMDI). The two pollutants' emissions were decomposed into output effects, structural effects, clean production effects, and pollution abatement effects. The results showed that China's industrial SO 2 discharge increased by 1.14 Mt during 2003-2014, and the contributions from the four effects were 23.17, − 1.88, − 3.80, and − 16.36 Mt, respectively. Likewise, NO x discharge changed by − 3.44 Mt over 2011-2014, and the corresponding contributions from the four effects were 2.97, − 0.62, − 1.84, and − 3.95 Mt. Thus, the output effect was mainly responsible for the growth of the two discharges. The average annual contribution rates of SO 2 and NO x from output were 14.33 and 5.97%, respectively, but pollution abatement technology presented the most obvious mitigating effects (− 10.11 and − 7.92%), followed by the mitigating effects of clean production technology (− 2.35 and − 3.7%), and the mitigation from the structural effect was the weakest (− 1.16 and − 1.25%, respectively), which meant pollutant reduction policies related to industrial structure adjustment should be a long-term measure for the two discharges. In addition, the sub-sectors of I20 (manufacture of raw chemical materials and chemical products), I24 (manufacture of non-metallic mineral products), and I26 (smelting and pressing of non-ferrous metals) were the major contributors to both discharges. Thus, these sub-sectors should be given priority consideration when designing mitigation-related measures. Last, some particular policy implications were recommended for reducing the two discharges, including that the government should seek a technological discharge reduction route. 
 Title: Multi-perspective comparisons and mitigation implications of SO 2 and NO x discharges from the industrial sector of China: a decomposition analysis
Output: False
Paragraph: The molecular events and evolutionary forces underlying lethal mutagenesis of virus (or virus extinction through an excess of mutations) are not well understood. Here we apply for the first time phylogenetic methods and Partition Analysis of Quasispecies (PAQ) to monitor genetic distances and intra-population structures of mutant spectra of foot-and-mouth disease virus (FMDV) quasispecies subjected to mutagenesis by base and nucleoside analogues. Results: Phylogenetic and PAQ analyses have revealed a highly dynamic variation of intrapopulation diversity of FMDV quasispecies. The population diversity first suffers striking expansions in the presence of mutagens and then compressions either when the presence of the mutagenic analogue was discontinued or when a mutation that decreased sensitivity to a mutagen was selected. The pattern of mutations found in the populations was in agreement with the behavior of the corresponding nucleotide analogues with FMDV in vitro. Mutations accumulated at preferred genomic sites, and dn/ds ratios indicate the operation of negative (or purifying) selection in populations subjected to mutagenesis. No evidence of unusually elevated genetic distances has been obtained for FMDV populations approaching extinction. Phylogenetic and PAQ analysis provide adequate procedures to describe the evolution of viral sequences subjected to lethal mutagenesis. These methods define the changes of intra-population structure more precisely than mutation frequencies and Shannon entropies. PAQ is very sensitive to variations of intrapopulation genetic distances. Strong negative (or purifying) selection operates in FMDV populations subjected to enhanced mutagenesis. The quantifications provide evidence that extinction does not imply unusual increases of intrapopulation complexity, in support of the lethal defection model of virus extinction. 
 Title: Topology of evolving, mutagenized viral populations: quasispecies expansion, compression, and operation of negative selection
Output: True
Paragraph: Background: Infection with Porcine Epidemic Diarrhea Virus (PEDV) causes vomiting, diarrhea, and dehydration in young pigs. The virus made its first appearance in the U.S. in 2013, where it caused substantial neonatal mortality and economic losses in the U.S. pork industry. Based on outbreak investigations, it is hypothesized that the virus could be transmitted through contaminated feed or contaminated feed surfaces. This potential risk created a demand for research on the inactivation kinetics of PEDV in different environments. Therefore, the objective of this study was to evaluate the survival of PEDV in 9 different feed ingredients when exposed to 60, 70, 80, and 90°C, as well as the survival on four different surfaces (galvanized steel, stainless steel, aluminum, and plastic). Results: Overall, there were no differences (P > 0.05) in virus survival among the different feed matrices studied when thermally processed at 60 to 90°C for 5, 10, 15, or 30 min. However, the time necessary to achieve a one log reduction in virus concentration was less (P < 0.05) when ingredients were exposed to temperatures from 70°C (3. 7 min), 80°C (2.4 min), and 90°C (2.3 min) compared with 60°C (4.4 min). The maximum inactivation level (3.9 log) was achieved when heating all ingredients at 90°C for 30 min. There were no differences in the amount of time necessary to cause a one log reduction in PEDV concentration among the different surfaces. Conclusions: The results of this study showed that PEDV survival among the 9 feed ingredients evaluated was not different when exposed to thermal treatments for up to 30 min. However, different combinations of temperature and time resulted in achieving a 3 to 4 log reduction of PEDV in all feed ingredients evaluated. Finally, PEDV survival was similar on galvanized steel, stainless steel, aluminum and plastic. 
 Title: Survival of porcine epidemic diarrhea virus (PEDV) in thermally treated feed ingredients and on surfaces
Output: False
Paragraph: Background: DNA vaccine immunogenicity has been limited by inefficient delivery. Needle-free delivery of DNA using a CO 2 -powered BiojectorH device was compared to delivery by needle and syringe and evaluated for safety and immunogenicity. Methods: Forty adults, 18-50 years, were randomly assigned to intramuscular (IM) vaccinations with DNA vaccine, VRC-HIVDNA016-00-VP, (weeks 0, 4, 8) by BiojectorH 2000 TM or needle and syringe (N/S) and boosted IM at week 24 with VRC-HIVADV014-00-VP (rAd5) with N/S at 10 10 or 10 11 particle units (PU). Equal numbers per assigned schedule had low (#500) or high (.500) reciprocal titers of preexisting Ad5 neutralizing antibody. Results: 120 DNA and 39 rAd5 injections were given; 36 subjects completed follow-up research sample collections. IFN-c ELISpot response rates were 17/19 (89%) for BiojectorH and 13/17 (76%) for N/S delivery at Week 28 (4 weeks post rAd5 boost). The magnitude of ELISpot response was about 3-fold higher in BiojectorH compared to N/S groups. Similar effects on response rates and magnitude were observed for CD8+, but not CD4+ T-cell responses by ICS. Env-specific antibody responses were about 10-fold higher in Biojector-primed subjects. Conclusions: DNA vaccination by BiojectorH was well-tolerated and compared to needle injection, primed for greater IFN-c ELISpot, CD8+ T-cell, and antibody responses after rAd5 boosting. 
 Title: DNA Vaccine Delivered by a Needle-Free Injection Device Improves Potency of Priming for Antibody and CD8+ T- Cell Responses after rAd5 Boost in a Randomized Clinical Trial
Output: True
Paragraph: Viral pathogens often generate strong CD4 + T cell responses that are best known for their ability to help B cell and CD8 + T cell responses. However, recent studies reveal additional roles for CD4 + T cells, some of which are independent of other lymphocytes, and indicate that memory cells are more effective in most functions than naïve CD4 T cells. Here, we review the full spectrum of antiviral functions of CD4 + T cells, including their helper activities, innate immune induction, and direct anti-viral roles, and suggest how these functions are integrated to provide highly protective responses against viral pathogens. 
 Title: Expanding roles for CD4 + T cells in immunity to viruses NIH Public Access
Output: False
Paragraph: Hendra and Nipah viruses are related emergent paramyxoviruses that infect and cause disease in animals and humans. Disease manifests as a generalized vasculitis affecting multiple organs, but is the most severe in the respiratory and central nervous systems. The high case fatality and person-to-person transmission associated with the most recent NiV outbreaks, and the recent re-emergence of HeV, emphasize the importance and necessity of effective therapeutics for these novel agents. In recent years henipavirus research has revealed a more complete understanding of pathogenesis and, as a consequence, viable approaches towards vaccines and therapeutics have emerged. All strategies target early steps in viral replication including receptor binding and membrane fusion. Animal models have been developed, some of which may prove more valuable than others for evaluating the efficacy of therapeutic agents and regimes. Assessments of protective host immunity and drug pharmacokinetics will be crucial to the further advancement of therapeutic compounds. 
 Title: Targeted Strategies for Henipavirus Therapeutics
Output: False
Paragraph: Background: Nurses leaving their jobs and the profession are an issue of international concern, with supplydemand gaps for nurses reported to be widening. There is a large body of existing literature, much of which is already in review form. In order to advance the usefulness of the literature for nurse and human resource managers, we undertook an overview (review of systematic reviews). The aim of the overview was to identify high quality evidence of the determinants and consequences of turnover in adult nursing. Methods: Reviews were identified which were published between 1990 and January 2015 in English using electronic databases (the Cochrane Database of Systematic Reviews, MEDLINE, EMBASE, Applied Social Sciences Index and Abstracts, CINAHL plus and SCOPUS) and forward searching. All stages of the review were conducted in parallel by two reviewers. Reviews were quality appraised using the Assessment of Multiple Systematic Reviews and their findings narratively synthesised. Results: Nine reviews were included. We found that the current evidence is incomplete and has a number of important limitations. However, a body of moderate quality review evidence does exist giving a picture of multiple determinants of turnover in adult nursing, with -at the individual level -nurse stress and dissatisfaction being important factors and -at the organisational level -managerial style and supervisory support factors holding most weight. The consequences of turnover are only described in economic terms, but are considered significant. In making a quality assessment of the review as well as considering the quality of the included primary studies and specificity in the outcomes they measure, the overview found that the evidence is not as definitive as previously presented from individual reviews. Further research is required, of rigorous research design, whether quantitative or qualitative, particularly against the outcome of actual turnover as opposed to intention to leave. 
 Title: The determinants and consequences of adult nursing staff turnover: a systematic review of systematic reviews
Output: False
Paragraph: The aim of this study was to quantify and compare interferon-c (IFN-c) concentrations in the serum of clinically normal cats infected with feline coronavirus (FCoV) with its concentration in the sera and effusions of cats with feline infectious peritonitis (FIP), a disease associated with infection with a mutated form of FCoV. Clinically normal FCoV-infected cats living in catteries with a high prevalence of FIP had the highest serum IFN-c concentrations. The serum concentration of IFN-c was not significantly different in cats with FIP compared with clinically normal FCoV-infected animals living in catteries with a low prevalence of the disease. Moreover, the concentration of IFN-c was significantly higher in the effusions than in the serum of cats with FIP, probably due to IFN-c production within lesions. These findings support the hypothesis that there is a strong, 'systemic' cell mediated immune response in clinically normal, FCoV-infected cats and that a similar process, albeit at a tissue level, is involved in the pathogenesis of FIP. 
 Title: Interferon-c in the serum and effusions of cats with feline coronavirus infection The Veterinary Journal
Output: True
Paragraph: Glycyrrhiza glabra L. has become an endangered medicinal plant due to the unabated extraction of glycyrrhizin. Glycyrrhizin is a triterpenoid saponin that is a root centric secondary metabolite having numerous pharmacological properties, such as anti-inflammatory, immunomodulatory, antiallergic, antiulcer, and is found to be effective even against HIV. Harvesting of the roots for high value glycyrrhizin destroys the whole plant causing existential threat to the plant itself and consequent damage to biodiversity. The present study establishes that hairy root cultures of G. glabra, using an optimized elicitor, can dramatically enhance focused production of glycyrrhizin at a much faster pace year-round without causing destruction of the plant. Hairy root cultures of G. glabra were developed using the Agrobacterium rhizogenes A4 strain. The glycyrrhizin content was enhanced using different biotic and abiotic elicitors, for example, PEG (polyethylene glycol), CdCl 2 , cellulase, and mannan at different concentrations and durations. PEG at 1% concentration enhanced the yield of glycyrrhizin up to 5.4fold after 24 h of exposure, whereas 200 µg mL −1 cellulase enhanced glycyrrhizin yield to 8.6-fold after 7 days of treatment. Mannan at 10 mg L −1 concentration enhanced the production of glycyrrhizin up to 7.8-fold after 10 days of stress. Among different antioxidant enzymes, SOD activity was significantly enhanced under drought, cellulase and mannan stress. This identification of elicitors can result in abundant supply of valuable glycyrrhizin to meet broad spectrum demand through commercial production without endangering G. glabra L. 
 Title: Elicitation Enhanced the Yield of Glycyrrhizin and Antioxidant Activities in Hairy Root Cultures of Glycyrrhiza glabra L
Output: True
Paragraph: Human metapneumovirus (hMPV) is a respiratory virus detected in ≥9% of allogeneic hematopoietic stem cell transplant (HSCT) recipients, in whom it can cause significant morbidity and mortality. Given the lack of effective antivirals, we investigated the potential for immunotherapeutic intervention, using adoptively transferred T cells. Thus, we characterized the cellular immune response to the virus and identified F, N, M2-1, M, and P as immunodominant target antigens. Reactive T cells were polyclonal (ie, they expressed CD4 and CD8), T-helper type 1 polarized, and polyfunctional (ie, they produced interferon γ, tumor necrosis factor α, granulocyte-macrophage colony-stimulating factor, and granzyme B), and they were able to kill autologous antigen-loaded targets. The detection of hMPV-specific T cells in HSCT recipients who endogenously controlled active infections support the clinical importance of T-cell immunity in mediating protective antiviral effects. Our results demonstrate the feasibility of developing an immunotherapy for immunocompromised patients with uncontrolled infections. 
 Title: Immunologic Profiling of Human Metapneumovirus for the Development of Targeted Immunotherapy
Output: True
Paragraph: In this review, we report a new reverse approach (from finding bioactive molecules to separating target compounds in the related plant) by using virtual screening, immobilized enzyme and polyclonal antibody, molecularly imprinted polymers for finding, and separating the active compounds from TCM. This approach is faster and more efficient than the traditional time-consuming approach (from selecting the plant to separating compounds following the bioassay guidance). 
 Title: New concepts and approaches for drug discovery based on traditional Chinese medicine
Output: True
Paragraph: The Shortest Common Supersequence Problem asks to obtain a shortest string that is a supersequence of every member of a given set of strings. It has applications, among others, in data compression and oligonucleotide microarray production. The problem is NP-hard, and the existing exact solutions are impractical for large instances. In this paper, a new beam search algorithm is proposed for the problem, which employs a probabilistic heuristic and uses the dominance property to further prune the search space. The proposed algorithm is compared with three recent algorithms proposed for the problem on both random and biological sequences, outperforming them all by quickly providing solutions of higher average quality in all the experimental cases. The Java source and binary files of the proposed IBS_SCS algorithm and our implementation of the DR algorithm and all the random and real datasets used in this paper are freely available upon request. 
 Title: Bahri), f.tabataba@ec.iut.ac.ir (F.S. Tabataba)
Output: True
Paragraph: The use of small animal models for the study of infectious disease is critical for understanding disease progression and for developing prophylactic and therapeutic treatment options. For many diseases, Syrian golden hamsters have emerged as an ideal animal model due to their low cost, small size, ease of handling, and ability to accurately reflect disease progression in humans. Despite the increasing use and popularity of hamsters, there remains a lack of available reagents for studying hamster immune responses. Without suitable reagents for assessing immune responses, researchers are left to examine clinical signs and disease pathology. This becomes an issue for the development of vaccine and treatment options where characterizing the type of immune response generated is critical for understanding protection from disease. Despite the relative lack of reagents for use in hamsters, significant advances have been made recently with several hamster specific immunologic methods being developed. Here we discuss the progress of this development, with focus on classical methods used as well as more recent molecular methods. We outline what methods are currently available for use in hamsters and what is readily used as well as what limitations still exist and future perspectives of reagent and assay development for hamsters. This will provide valuable information to researchers who are deciding whether to use hamsters as an animal model. Syrian hamster • Golden hamster • Syrian golden hamster • Immunological tools • Molecular methods • Mesocricetus auratus • Animal models 
 Title: Syrian Hamsters as a Small Animal Model for Emerging Infectious Diseases: Advances in Immunologic Methods
Output: True
Paragraph: isolates of bovine viral diarrhea virus (cpBVDV) have been analyzed. For both viruses two regions of their genomic RNAs were found to be duplicated and rearranged. The viral genomes contain a small duplicated element (SD) derived from the genomic 5' end far downstream of its original context. This sequence is followed by a larger duplication which encompasses the region coding for the protein p80(LD), a molecular marker for cpBVDV. The SD element codes for the viral protease ~20. In the case of the viruses analyzed here the aminoterminus of p80 is generated by autoproteolytic removal of the preceding SD-encoded protease. For one of the cpBVDV isolates a specific fusion protein (~28) could be identified which is composed of p20 and part of ~10, another viral protein. of the respective noncytopathogenic counterpart revealed that duplication and rearrangement of sequences as well as the expression of p28 and p80 are specific for the cytopathogenic virus. 
 Title: Rearrangement of Viral Sequences in Cytopathogenic Pestiviruses
Output: True
Paragraph: The initial cluster of severe pneumonia cases that triggered the COVID-19 epidemic was identified in Wuhan, China in December 2019. While early cases of the disease were linked to a wet market, human-to-human transmission has driven the rapid spread of the virus throughout China. The Chinese government has implemented containment strategies of city-wide lockdowns, screening at airports and train stations, and isolation of suspected patients; however, the cumulative case count keeps growing every day. The ongoing outbreak presents a challenge for modelers, as limited data are available on the early growth trajectory, and the epidemiological characteristics of the novel coronavirus are yet to be fully elucidated. We use phenomenological models that have been validated during previous outbreaks to generate and assess short-term forecasts of the cumulative number of confirmed reported cases in Hubei province, the epicenter of the epidemic, and for the overall trajectory in China, excluding the province of Hubei. We collect daily reported cumulative confirmed cases for the 2019-nCoV outbreak for each Chinese province from the National Health Commission of China. Here, we provide 5, 10, and 15 day forecasts for five consecutive days, February 5th through February 9th, with quantified uncertainty based on a generalized logistic growth model, the Richards growth model, and a sub-epidemic wave model. Our most recent forecasts reported here, based on data up until February 9, 2020, largely agree across the three models presented and suggest an average range of 7409e7496 additional confirmed cases in Hubei and 1128e1929 additional cases in other provinces within the next five days. Models also predict an average total cumulative case count between 37,415 and 38,028 in Hubei and 11,588e13,499 in other provinces by February 24, 2020. Mean estimates and uncertainty bounds for both Hubei and other provinces have remained relatively stable in the last three reporting dates (February 7th e 9th). We also observe that each of the models predicts that the epidemic has reached saturation in both Hubei and other provinces. Our findings suggest that the containment strategies implemented in China are successfully reducing transmission and that the epidemic growth has slowed in recent days. 
 Title: -NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/)
Output: True
Paragraph: Immunological checkpoints, such as the inhibitory CD200 receptor (CD200R), play a dual role in balancing the immune system during microbial infection. On the one hand these inhibitory signals prevent excessive immune mediated pathology but on the other hand they may impair clearance of the pathogen. We studied the influence of the inhibitory CD200-CD200R axis on clearance and pathology in two different virus infection models. We find that lack of CD200R signaling strongly enhances type I interferon (IFN) production and viral clearance and improves the outcome of mouse hepatitis corona virus (MHV) infection, particularly in female mice. MHV clearance is known to be dependent on Toll like receptor 7 (TLR7)-mediated type I IFN production and sex differences in TLR7 responses previously have been reported for humans. We therefore hypothesize that CD200R ligation suppresses TLR7 responses and that release of this inhibition enlarges sex differences in TLR7 signaling. This hypothesis is supported by our findings that in vivo administration of synthetic TLR7 ligand leads to enhanced type I IFN production, particularly in female Cd200 2/2 mice and that CD200R ligation inhibits TLR7 signaling in vitro. In influenza A virus infection we show that viral clearance is determined by sex but not by CD200R signaling. However, absence of CD200R in influenza A virus infection results in enhanced lung neutrophil influx and pathology in females. Thus, CD200-CD200R and sex are host factors that together determine the outcome of viral infection. Our data predict a sex bias in both beneficial and pathological immune responses to virus infection upon therapeutic targeting of CD200-CD200R. 
 Title: CD200 Receptor Controls Sex-Specific TLR7 Responses to Viral Infection
Output: False
Paragraph: China ratified the International Covenant on Economic, Social and Cultural Rights in 2001. It thus bears obligations under Article 12 of the covenant to take appropriate measures at the domestic level to realize the right to health in China. Accountability is an important component of the right to health. This article examines whether the Western concept of accountability, recently imported into China, has the potential to improve the protection of the right to health within China's existing political, legal, and cultural framework. In so doing, it reviews current Chinese institutional mechanisms and considers the use of less formal mechanisms by which duty-bearers might be held accountable in China. More specifically, this article provides an overview of a range of health-related accountability mechanisms, including judicial, political, administrative, professional, and social accountability arrangements. It concludes that although there is the basis of an accountability framework for the right to health in China, the effective operation of accountability mechanisms is hindered by longstanding cultural and political barriers. 
 Title: Mechanisms of Accountability for the Realization of the Right to Health in China
Output: False
Paragraph: Polyomaviruses are naked viruses with an icosahedral capsid that surrounds a circular double-stranded DNA molecule of about 5000 base-pairs. Their genome encodes at least five proteins: large and small tumor antigens and the capsid proteins VP1, VP2 and VP3. The tumor antigens are expressed during early stages of the viral life cycle and are implicated in the regulation of viral transcription and DNA replication, while the capsid proteins are produced later during infection. Members of the Polyomaviridae family have been isolated in birds (Avipolyomavirus) and mammals (Orthopolyomavirus and Wukipolyomavirus). Some mammalian polyomaviruses encode an additional protein, referred to as agnoprotein, which is a relatively small polypeptide that exerts multiple functions. This review discusses the structure, post-translational modifications, and functions of agnoprotein, and speculates why not all polyomaviruses express this protein. 
 Title: Agnoprotein of mammalian polyomaviruses
Output: False
Paragraph: Primary Ciliary Dyskinesia is a heterogeneous genetic disease that is characterized by cilia dysfunction of the epithelial cells lining the respiratory tracts, resulting in recurrent respiratory tract infections. Despite lifelong physiological therapy and antibiotics, the lungs of affected patients are progressively destroyed, leading to respiratory insufficiency. Recessive mutations in Dynein Axonemal Intermediate chain type 1 (DNAI1) gene have been described in 10% of cases of Primary Ciliary Dyskinesia. Our goal was to restore normal ciliary beating in DNAI1-deficient human airway epithelial cells. A lentiviral vector based on Simian Immunodeficiency Virus pseudotyped with Vesicular Stomatitis Virus Glycoprotein was used to transduce cultured human airway epithelial cells with a cDNA of DNAI1 driven by the Elongation Factor 1 promoter. Transcription and translation of the transduced gene were tested by RT-PCR and western blot, respectively. Human airway epithelial cells that were DNAI1-deficient due to compound heterozygous mutations, and consequently had immotile cilia and no outer dynein arm, were transduced by the lentivirus. Cilia beating was recorded and electron microscopy of the cilia was performed. Transcription and translation of the transduced DNAI1 gene were detected in human cells treated with the lentivirus. In addition, immotile cilia recovered a normal beat and outer dynein arms reappeared. We demonstrated that it is possible to obtain a normalization of ciliary beat frequency of deficient human airway epithelial cells by using a lentivirus to transduce cells with the therapeutic gene. This preliminary step constitutes a conceptual proof that is indispensable in the perspective of Primary Ciliary Dyskinesia's in vivo gene therapy. This is the first time that recovery of cilia beating is demonstrated in this disease. 
 Title: Ciliary Beating Recovery in Deficient Human Airway Epithelial Cells after Lentivirus Ex Vivo Gene Therapy
Output: True
Paragraph: The cross-species transmission of viruses from one host species to another is responsible for the majority of emerging infections. However, it is unclear whether some virus families have a greater propensity to jump host species than others. If related viruses have an evolutionary history of co-divergence with their hosts there should be evidence of topological similarities between the virus and host phylogenetic trees, whereas host jumping generates incongruent tree topologies. By analyzing co-phylogenetic processes in 19 virus families and their eukaryotic hosts we provide a quantitative and comparative estimate of the relative frequency of virus-host co-divergence versus cross-species transmission among virus families. Notably, our analysis reveals that cross-species transmission is a near universal feature of the viruses analyzed here, with virus-host co-divergence occurring less frequently and always on a subset of viruses. Despite the overall high topological incongruence among virus and host phylogenies, the Hepadnaviridae, Polyomaviridae, Poxviridae, Papillomaviridae and Adenoviridae, all of which possess double-stranded DNA genomes, exhibited more frequent co-divergence than the other virus families studied here. At the other extreme, the virus and host trees for all the RNA viruses studied here, particularly the Rhabdoviridae and the Picornaviridae, displayed high levels of topological incongruence, indicative of frequent host switching. Overall, we show that cross-species transmission plays a major role in virus evolution, with all the virus families studied here having the potential to jump host species, and that increased sampling will likely reveal more instances of host jumping. 
 Title: Comparative analysis estimates the relative frequencies of co-divergence and cross- species transmission within viral families
Output: False
Paragraph: Background: Despite advances in surveillance and prevention, pneumonia and influenza (P&I) remain among the leading causes of mortality in the United States. Elderly adults experience the most severe morbidity from influenza-associated diseases, and have the highest rates of seasonal migration within the U.S. compared to other subpopulations. The objective of this study is to assess spatiotemporal patterns in influenza-associated hospitalizations in the elderly, by time, geography, and intensity of P&I. Given the high seasonal migration of individuals to Florida, this state was examined more closely using harmonic regression to assess spatial and temporal patterns of P&I hospitalizations by state of residence. Methods: Data containing all Medicare-eligible hospitalizations in the United States for 1991-2006 with P&I (ICD-9-CM codes 480-487) were abstracted for the 65+ population. Hospitalizations were classified by state of residence, provider state, and date of admissions, specifically comparing those admitted between October and March to those admitted between April and September. We then compared the hospitalization profile data of Florida residents with that of out-of-state residents by state of primary residence and time of year (in-season or out-ofseason). 
 Title: Snowbirds and infection-new phenomena in pneumonia and influenza hospitalizations from winter migration of older adults: A spatiotemporal analysis
Output: False
Paragraph: The vascular endothelium can be considered as an organ/tissue which comprises a monolayer of endothelial cells which serve as a semipermeable cellular barrier separating the inner space of blood vessels from its surrounding tissue and to control the exchange of fluids and cells between the two compartments. Since the pulmonary circulation receives the entire cardiac output, the large surface area of the lung microvasculature is well suited for sensing mechanical, chemical, and cellular injury by inhaled or circulating substances. This endothelial barrier is dynamically regulated through exposure to these various stimuli of physiological and pathological origin and serves to regulate multiple key biological processes (including lung fluid balance and solute transport between vascular compartments). For example, an increase in vascular permeability is a necessary feature of the body's defense mechanism to provide injured tissues with access to leucocytes, resulting in tissue edema due to fluid extravasation. However, during conditions of intense lung inflammation such as observed in acute lung injury or its severer form of acute respiratory distress syndrome, the large surface area becomes a liability and provides the opportunity for profound vascular permeability resulting in massive fluid accumulation in the alveolar space and progressively leading to pulmonary failure. Alterations in vascular permeability occur not only in acute inflammatory lung disorders primarily caused by sepsis, pneumonia, and trauma which result in high rates of patient morbidity and mortality, but are an attractive target for therapeutic intervention in subacute lung inflammatory disorders such as ischemia-reperfusion injury, radiation lung injury, and asthma. Thus, understanding the mechanisms of endothelial barrier dysfunction is vital for the management and treatment of key and enigmatic pulmonary disorders. 
 Title: Acute Lung Injury: The Injured Lung Endothelium, Therapeutic Strategies for Barrier Protection, and Vascular Biomarkers
Output: False
Paragraph: Human parainfluenza viruses (HPIVs) are common causes of severe pediatric respiratory viral disease. We characterized wild-type HPIV2 infection in an in vitro model of human airway epithelium (HAE) and found that the virus replicates to high titer, sheds apically, targets ciliated cells, and induces minimal cytopathology. Replication of an experimental, live attenuated HPIV2 vaccine strain, containing both temperature sensitive (ts) and non-ts attenuating mutations, was restricted >30-fold compared to rHPIV2-WT in HAE at 32°C and exhibited little productive replication at 37°C. This restriction paralleled attenuation in the upper and lower respiratory tract of African green monkeys, supporting the HAE model as an appropriate and convenient system for characterizing HPIV2 vaccine candidates. 
 Title: Growth restriction of an experimental live attenuated human parainfluenza virus type 2 vaccine in human ciliated airway epithelium in vitro parallels attenuation in African green monkeys
Output: False
Paragraph: Most pandemics-eg, HIV/AIDS, severe acute respiratory syndrome, pandemic influenzaoriginate in animals, are caused by viruses, and are driven to emerge by ecological, behavioural, or socioeconomic changes. Despite their substantial effects on global public health and growing understanding of the process by which they emerge, no pandemic has been predicted before infecting human beings. We review what is known about the pathogens that emerge, the hosts that they originate in, and the factors that drive their emergence. We discuss challenges to their control and new efforts to predict pandemics, target surveillance to the most crucial interfaces, and identify prevention strategies. New mathematical modelling, diagnostic, communications, and informatics technologies can identify and report hitherto unknown microbes in other species, and thus new risk assessment approaches are needed to identify microbes most likely to cause human disease. We lay out a series of research and surveillance opportunities and goals that could help to overcome these challenges and move the global pandemic strategy from response to pre-emption. 
 Title: Prediction and prevention of the next pandemic zoonosis
Output: False
Paragraph: Many viruses cause disease within an infected host after spread from an initial portal of entry to secondary sites of replication. Viruses can disseminate via the bloodstream or through nerves. Mammalian orthoreoviruses (reoviruses) are neurotropic viruses that use both bloodborne and neural pathways to spread systemically within their hosts to cause disease. Using a robust mouse model and a dynamic reverse genetics system, we have identified a viral receptor and a viral nonstructural protein that are essential for hematogenous reovirus dissemination. Junctional adhesion molecule-A (JAM-A) is a member of the immunoglobulin superfamily expressed in tight junctions and on hematopoietic cells that serves as a receptor for all reovirus serotypes. Expression of JAM-A is required for infection of endothelial cells and development of viremia in mice, suggesting that release of virus into the bloodstream from infected endothelial cells requires JAM-A. Nonstructural protein σ1s is implicated in cell cycle arrest and apoptosis in reovirus-infected cells but is completely dispensable for reovirus replication in cultured cells. Surprisingly, a recombinant σ1s-null reovirus strain fails to spread hematogenously in infected mice, suggesting that σ1s facilitates apoptosis of reovirus-infected intestinal epithelial cells. It is possible that apoptotic bodies formed as a consequence of σ1s expression lead to reovirus uptake by dendritic cells for subsequent delivery to the mesenteric lymph node and the blood. Thus, both host and viral factors are required for efficient hematogenous dissemination of reovirus. Understanding mechanisms of reovirus bloodborne spread may shed light on how microbial pathogens invade the bloodstream to disseminate and cause disease in infected hosts. 
 Title: Mechanisms of Reovirus Bloodstream Dissemination
Output: True
Paragraph: We conducted an epidemiologic investigation among survivors of an outbreak of Middle East respiratory syndrome coronavirus (MERS-CoV) infection in Jordan. A second-trimester stillbirth occurred during the course of an acute respiratory illness that was attributed to MERS-CoV on the basis of exposure history and positive results of MERS-CoV serologic testing. This is the first occurrence of stillbirth during an infection with MERS-CoV and may have bearing upon the surveillance and management of pregnant women in settings of unexplained respiratory illness potentially due to MERS-CoV. Future prospective investigations of MERS-CoV should ascertain pregnancy status and obtain further pregnancy-related data, including biological specimens for confirmatory testing. 
 Title: Stillbirth During Infection With Middle East Respiratory Syndrome Coronavirus
Output: True
Paragraph: Dicer Dicer is an endoribonuclease member of RNase III family encoded by dicer gene, which has the function of cleaving long double-stranded RNA or pre-miRNA into siRNA or miRNA that are in 20-25 base pairs length with 2 nt overhangs at 3 0 ends. MicroRNA (miRNA) miRNA is a kind of 22 nt small non-coding RNA fragments discovered in viruses, plants, animals and human, which have the functions of post-transcriptional regulation in gene expression. p19 protein Plant tombusvirus 19 kDa protein (p19) is an RNA silencing suppressor protein. p19 selectively binds to exactly matched, double-stranded antiviral siRNAs of 21 nt, but not to imperfectly paired miRNAs, ssRNAs or other dsRNAs. Prokaryotic siRNA (pro-siRNA) Pro-siRNA are bacterial RNase III products that have chemical and functional properties similar to eukaryotic siRNAs. Ribonucleic acid (RNA) RNA is a linear molecule composed of four types of smaller molecules called ribonucleotide bases: adenine (A), cytosine (C), guanine (G), and uracil (U). Comprehensive Biotechnology, 3rd edition, Volume 5 
 Title: The Discovery of RNAi 561 5.42.2 Mechanism of RNA Interference 562 5.42.3 RNAi Screening 567 5.42.5 Technical Considerations for Using RNAi Technology 568 5
Output: True
Paragraph: Overlapping genes represent a fascinating evolutionary puzzle, since they encode two functionally unrelated proteins from the same DNA sequence. They originate by a mechanism of overprinting, in which point mutations in an existing frame allow the expression (the "birth") of a completely new protein from a second frame. In viruses, in which overlapping genes are abundant, these new proteins often play a critical role in infection, yet they are frequently overlooked during genome annotation. This results in erroneous interpretation of mutational studies and in a significant waste of resources. Therefore, overlapping genes need to be correctly detected, especially since they are now thought to be abundant also in eukaryotes. Developing better detection methods and conducting systematic evolutionary studies require a large, reliable benchmark dataset of known cases. We thus assembled a highquality dataset of 80 viral overlapping genes whose expression is experimentally proven. Many of them were not present in databases. We found that overall, overlapping genes differ significantly from non-overlapping genes in their nucleotide and amino acid composition. In particular, the proteins they encode are enriched in high-degeneracy amino acids and depleted in low-degeneracy ones, which may alleviate the evolutionary constraints acting on overlapping genes. Principal component analysis revealed that the vast majority of overlapping genes follow a similar composition bias, despite their heterogeneity in length and function. Six proven mammalian overlapping genes also followed this bias. We propose that this apparently near-universal composition bias may either favour the birth of overlapping genes, or/and result from selection pressure acting on them. 
 Title: Overlapping genes and the proteins they encode differ significantly in their sequence composition from non-overlapping genes
Output: False
Paragraph: Several hitherto unknown (E)-but-2-enyl nucleoside phosphonoamidate analogs (ANPs) were prepared directed with nitrogen reagents by cross-metathesis in water-under ultrasound irradiation. Two diastereoisomers were formally identified by X-ray diffraction. These compounds were evaluated against a large spectrum of DNA and RNA viruses. Among them, the phosphonoamidate thymine analogue 19 emerged as the best prodrug against varicella-zoster virus (VZV) with EC 50 values of 0.33 and 0.39 mM for wild-type and thymidine kinase deficient strains, respectively, and a selectivity index !200 mM. This breakthrough approach paves the way for new purine and pyrimidine (E)-but-2-enyl phosphonoamidate analogs. Abbreviations: VZV, varicella zoster virus; VV, vaccinia virus; HSV, herpes simplex virus; VSV, vesicular stomatitis virus; DNA, deoxyribonucleic acid; RNA, ribonucleic acid; CC50, compound concentration affording 50% inhibition of cell growth; EC50, compound concentration affording 50% inhibition of the viral cytopathicity; MCC, minimum cytotoxic concentration required to afford a microscopically detectable alteration of cell morphology; ACN, acetonitrile; DCM, dichloromethane. 
 Title: Highly convergent synthesis and antiviral activity of (E)-but-2-enyl nucleoside phosphonoamidates
Output: True