niryuu/sni-each-converted huggingface dataset:
Paragraph: Objective: The aim of this study was to analyze the etiology and clinical consequences of viral respiratory infections in 18 elderly care centers (ECC) in Lisbon, which housed a total of 1022 residents. Methods: Nasopharyngeal swabs were collected whenever an elderly had symptoms of acute respiratory infections (ARI). PCR and RT-PCR were performed for influenza A/B, human parainfluenza virus 1-4, adenovirus, human metapneumovirus (HMPV), respiratory syncytial virus (RSV), rhinovirus, enterovirus, human coronavirus and human Bocavirus (HBoV). Array cards for atypical bacteria were also used in severe cases. Results: In total, 188 episodes of ARI were reported, being rhinovirus the most frequently detected (n = 53), followed by influenza A(H3) (n = 19) and HBoV (n = 14). Severe infections were reported in 19 patients, 11 of which were fatal, Legionela pneumophila, rhinovirus, HMPV and RSV associated with these fatalities. Nine influenza strains were analyzed, all antigenically dissimilar from vaccine strain 2013/14. "Age", "HMPV" and "Respiratory disease" showed an association with severe infection. Conclusions: In this study an etiologic agent could be found in 60% of the acute respiratory episodes. These data provides information about the circulating viruses in ECC and highlights the importance of searching both viruses and atypical bacteria in severe ARI. 
 Title: Respiratory infections in elderly people: Viral role in a resident population of elderly care centers in Lisbon
Output: True
Paragraph: Influenza viruses replicate within the nucleus of the host cell. This uncommon RNA virus trait provides influenza with the advantage of access to the nuclear machinery during replication. However, it also increases the complexity of the intracellular trafficking that is required for the viral components to establish a productive infection. The segmentation of the influenza genome makes these additional trafficking requirements especially challenging, as each viral RNA (vRNA) gene segment must navigate the network of cellular membrane barriers during the processes of entry and assembly. To accomplish this goal, influenza A viruses (IAVs) utilize a combination of viral and cellular mechanisms to coordinate the transport of their proteins and the eight vRNA gene segments in and out of the cell. The aim of this review is to present the current mechanistic understanding for how IAVs facilitate cell entry, replication, virion assembly, and intercellular movement, in an effort to highlight some of the unanswered questions regarding the coordination of the IAV infection process. 
 Title: influenza A virus Cell entry, Replication, virion Assembly and Movement
Output: True
Paragraph: Japanese encephalitis virus (JEV), one of the causes for epidemic encephalitis, belongs to the family of Flaviviridae. In this study, we demonstrated that cellular DEAD-box RNA helicase DDX5 plays an important role in JEV replication. The knockdown of DDX5 was able to decrease JEV replication, and overexpression of DDX5 mutants lacking the helicase activity also reduced JEV replication, suggesting the helicase activity is essential for JEV replication. DDX5 knockdown did not affect virus assembly and release. GST-pulldown and co-immunoprecipitation experiments demonstrated that DDX5 could interact with JEV core protein, non-structural protein 3 (NS3) and 5 (NS5-MTase and NS5-RdRp domains). Meanwhile, we also confirmed that DDX5 interacts with these viral proteins during JEV infection. Confocal microscopy analysis showed that endogenous DDX5 is recruited to the cytoplasm and colocalizes with these viral proteins and viral RNA. RNA-pulldown experiment showed that DDX5 only binds to the JEV 3 0 untranslated region (UTR). Finally, we confirmed the role of DDX5 in JEV RNA replication using JEV-replicon system. In conclusion, we identified DDX5 as a positive regulator for JEV replication. 
 Title: The DEAD-box RNA helicase DDX5 acts as a positive regulator of Japanese encephalitis virus replication by binding to viral 3 0 UTR
Output: False
Paragraph: Co-inhibitory pathways have a fundamental function in regulating T cell responses and control the balance between promoting efficient effector functions and restricting immune pathology. The TIGIT pathway has been implicated in promoting T cell dysfunction in chronic viral infection. Importantly, TIGIT signaling is functionally linked to IL-10 expression, which has an effect on both virus control and maintenance of tissue homeostasis. However, whether TIGIT has a function in viral persistence or limiting tissue pathology is unclear. Here we report that TIGIT modulation effectively alters the phenotype and cytokine profile of T cells during influenza and chronic LCMV infection, but does not affect virus control in vivo. Instead, TIGIT has an important effect in limiting immune pathology in peripheral organs by inducing IL-10. Our data therefore identify a function of TIGIT in limiting immune pathology that is independent of viral clearance. 
 Title: TIGIT limits immune pathology during viral infections
Output: True
Paragraph: Drinking waters are treated for enteric virus via a number of disinfection techniques including chemical oxidants, irradiation, and heat, however the inactivation mechanisms during disinfection remain elusive. Owing to the fact that a number of significant waterborne virus strains are not readily culturable in vitro at this time (e.g. norovirus, hepatitis A), the susceptibility of these viruses to disinfection is largely unknown. An in-depth understanding of the mechanisms involved in virus inactivation would aid in predicting the susceptibility of non-culturable virus strains to disinfection and would foster the development of improved disinfection methods. Recent technological advances in virology research have provided a wealth of information on enteric virus compositions, structures, and biological functions. This knowledge will allow for physical/chemical descriptions of virus inactivation and thus further our understanding of virus disinfection to the most basic mechanistic level. 
 Title: Virus disinfection mechanisms: the role of virus composition, structure, and function
Output: False
Paragraph: A key process in the regulation of protein activities and thus cellular signaling pathways is the modification of proteins by post-translational mechanisms. Knowledge about the enzymes (writers and erasers) that attach and remove post-translational modifications, the targets that are modified and the functional consequences elicited by specific modifications, is crucial for understanding cell biological processes. Moreover detailed knowledge about these mechanisms and pathways helps to elucidate the molecular causes of various diseases and in defining potential targets for therapeutic approaches. Intracellular adenosine diphosphate (ADP)-ribosylation refers to the nicotinamide adenine dinucleotide (NAD + )-dependent modification of proteins with ADP-ribose and is catalyzed by enzymes of the ARTD (ADP-ribosyltransferase diphtheria toxin like, also known as PARP) family as well as some members of the Sirtuin family. Poly-ADP-ribosylation is relatively well understood with inhibitors being used as anti-cancer agents. However, the majority of ARTD enzymes and the ADP-ribosylating Sirtuins are restricted to catalyzing mono-ADP-ribosylation. Although writers, readers and erasers of intracellular mono-ADPribosylation have been identified only recently, it is becoming more and more evident that this reversible post-translational modification is capable of modulating key intracellular processes and signaling pathways. These include signal transduction mechanisms, stress pathways associated with the endoplasmic reticulum and stress granules, and chromatin-associated processes such as transcription and DNA repair. We hypothesize that mono-ADP-ribosylation controls, through these different pathways, the development of cancer and infectious diseases. OPEN ACCESS Cells 2015, 4 570 
 Title: Intracellular Mono-ADP-Ribosylation in Signaling and Disease
Output: True
Paragraph: The known genetic diversity of the hepaciviruses and pegiviruses has increased greatly in recent years through the discovery of viruses related to hepatitis C virus and human pegivirus in bats, bovines, equines, primates, and rodents. Analysis of these new species is important for research into animal models of hepatitis C virus infection and into the zoonotic origins of human viruses. Here, we provide the first systematic phylogenetic and evolutionary analysis of these two genera at the wholegenome level. Phylogenies confirmed that hepatitis C virus is most closely related to viruses from horses whereas human pegiviruses clustered with viruses from African primates. Within each genus, several well-supported lineages were identified and viral diversity was structured by both host species and location of sampling. Recombination analyses provided evidence of interspecific recombination in hepaciviruses, but none in the pegiviruses. Putative mosaic genome structures were identified in NS5B gene region and were supported by multiple tests. The identification of interspecific recombination in the hepaciviruses represents an important evolutionary event that could be clarified by future sampling of novel viruses. We also identified parallel amino acid changes shared by distantly related lineages that infect similar types of host. Notable parallel changes were clustered in the NS3 and NS4B genes and provide a useful starting point for experimental studies of the evolution of Hepacivirus host-virus interactions. 
 Title: Evolutionary and Phylogenetic Analysis of the Hepaciviruses and Pegiviruses
Output: False
Paragraph: We conducted a cross-sectional study of risk factors for herd-level kid positivity for Cryptosporidium parvum oocysts in dairy-goat farms (Deux-Sèvres, western France). From January to March 2003, faeces from a convenient sample of 879 5-to 30-day-old goat kids from 60 herds were examined microscopically after staining with carbol fuschin. Oocyst shedding was scored semi-quantitatively (0 to 4+) allowing us to obtain a cumulative score per herd. Standardized questionnaires with information about management practices were collected in each farm. We found positive kids in 32 of 60 herds (53.3%) and in 142 animals out of 879 (16.2%). We used logistic regression for two risk-factor model: (1) simple positive (case: herd score !1+, at least one positive kid in the herd, versus control: herd score = 0), (2) strongly positive (case: overall herd score !3+ versus control: herd score <3+). Risk factors associated with simple positive herds were period of sampling compared to the peak of births (After versus Before, OR = 4.2, 95% CI 1.2, 15.3) and practice of kid grouping by age or weight (Yes versus No, OR = 4.4, 95% CI 1.0, 19.1). Risk factors associated with strongly positive herds were period of investigation (February/March versus January, OR = 12.7, 95% CI 2.1, 76.6), exposure to graminaceous plants in forage (OR = 11.6, 95% CI 1.7, 81.0) and type of ventilation in the goat premises (Vertical versus Wind effect, OR = 14.7, 95% CI 2.1, 106.1). No important association was found between www.elsevier.com/locate/prevetmed Preventive Veterinary Medicine 77 (2006) 109-121 kid-management practices and herd positivity. These results suggest a major role of the environment of kids during their first hours of life in the adult-goat premises regarding the transmission of C. parvum infection. 
 Title: Herd-level risk factors for Cryptosporidium infection in dairy-goat kids in western France
Output: True
Paragraph: induced host immune response , but the relative contribution of each remains largely unknown. For example , C57BL/6 (B6) mice infected with mouse hepatitis virus (JHM strain , JHMV) develop severe encephalitis , with death occurring within 7 days. Here, we show that the host response to a single JHMVspecific immunodominant CD4 T-cell epitope is critical for severe disease. We engineered a recombinant JHMV with mutations in the immunodominant CD4 T-cell epitope (rJ.M Y135Q ). Infection of naïve B6 mice with this virus resulted in mild disease with no mortality. However , introduction of a CD4 T-cell epitope from Listeria monocytogenes into rJ.M Y135Q generated a highly virulent virus. The decrease in disease severity was not due to a switch from Th1 to Th2 predominance in rJ.M Y135Q -infected mice , an effect on CD8 T-cell function , or differential expression of tumor necrosis factor-␣ by JHMV-specific CD4 T cells. These results show that the response to a single virus-specific CD4 T-cell epitope may contribute to a pathogenic host response in the setting of acute viral disease and that abrogation of this response ameliorates clinical disease without diminishing virus clearance. 
 Title: Pathogenic Role for Virus-Specific CD4 T Cells in Mice with Coronavirus-Induced Acute Encephalitis
Output: True
Paragraph: The dynamics of infectious diseases spread via direct person-to-person transmission (such as influenza, smallpox, HIV/AIDS, etc.) depends on the underlying host contact network. Human contact networks exhibit strong community structure. Understanding how such community structure affects epidemics may provide insights for preventing the spread of disease between communities by changing the structure of the contact network through pharmaceutical or non-pharmaceutical interventions. We use empirical and simulated networks to investigate the spread of disease in networks with community structure. We find that community structure has a major impact on disease dynamics, and we show that in networks with strong community structure, immunization interventions targeted at individuals bridging communities are more effective than those simply targeting highly connected individuals. Because the structure of relevant contact networks is generally not known, and vaccine supply is often limited, there is great need for efficient vaccination algorithms that do not require full knowledge of the network. We developed an algorithm that acts only on locally available network information and is able to quickly identify targets for successful immunization intervention. The algorithm generally outperforms existing algorithms when vaccine supply is limited, particularly in networks with strong community structure. Understanding the spread of infectious diseases and designing optimal control strategies is a major goal of public health. Social networks show marked patterns of community structure, and our results, based on empirical and simulated data, demonstrate that community structure strongly affects disease dynamics. These results have implications for the design of control strategies. Citation: Salathé M, Jones JH (2010) Dynamics and Control of Diseases in Networks with Community Structure. PLoS Comput Biol 6(4): e1000736. 
 Title: Dynamics and Control of Diseases in Networks with Community Structure
Output: False
Paragraph: Proteolytic processing of the mouse hepatitis virus strain A59 (MHV-A59) replicase gene product, pp1a, results in polypeptides p28, p65, p50, and p240 in infected cells. Based on previously identi ed p28 and p65 cleavage sites, a p50 cleavage site was proposed to occur between Ala-1262 and Ala-1263. Results of mutagenesis and in vitro cleavage assays show that PLP-1 was able to cleave in trans when the proposed p50 cleavage sequence replaced the p28 cleavage sequence. Mutagenesis was also used to investigate cleavage between Gly-904 and Val-905, a cleavage site predicted to produce a precursor of p65, p72, that was detected in cells infected with MHV strain JHM, but not with MHV-A59. No cleavage could be detected using substrate that carried both the p65 site and the predicted p72 cleavage sequence. Thus, it appeared that PLP-1 could recognize the proposed p50 sequence but not the predicted p72 site under the in vitro conditions used. 
 Title: Further in vitro characterization of mouse hepatitis virus papain-like proteinase 1: Cleavage sequence requirements within PP1a
Output: True
Paragraph: Attenuated, live viral vaccines have been extraordinarily successful in protecting against many diseases. The main drawbacks in their development and use have been reliance on an unpredictable method of attenuation and the potential for evolutionary reversion to high virulence. Methods of genetic engineering now provide many safer alternatives to live vaccines, so if live vaccines are to compete with these alternatives in the future, they must either have superior immunogenicity or they must be able to overcome these former disadvantages. Several live vaccine designs that were historically inaccessible are now feasible because of advances in genome synthesis. Some of those methods are addressed here, with an emphasis on whether they enable predictable levels of attenuation and whether they are stable against evolutionary reversion. These new designs overcome many of the former drawbacks and position live vaccines to be competitive with alternatives. Not only do new methods appear to retard evolutionary reversion enough to prevent vaccine-derived epidemics, but it may even be possible to permanently attenuate live vaccines that are transmissible but cannot evolve to higher virulence under prolonged adaptation. 
 Title: Evolutionary reversion of live viral vaccines: Can genetic engineering subdue it?
Output: False
Paragraph: The fourth outbreak of the Coronaviruses, known as the 2019-nCoV, has occurred in Wuhan city of Hubei province in China in December 2019. We propose a timevarying sparse vector autoregressive (VAR) model to retrospectively analyze and visualize the dyamic transmission routes of this outbreak in mainland China over January 31 -February 19, 2020. Our results demonstrate that the influential interprovince routes from Hubei have become unidentifiable since February 4, whereas the self-transmission in each province was accelerating over February 4-15. From February 16, all routes became less detectable, and no influential transmissions could be identified on February 18 and 19. Such evidence supports the effectiveness of government interventions, including the travel restrictions in Hubei. Implications of our results suggest that in addition to the origin of the outbreak, virus preventions are of crucial importance in provinces with the largest migrant workers percentages (e.g., Jiangxi, Henan and Anhui) to controlling the spread of 2019-nCoV. 
 Title: How does the outbreak of 2019-nCoV spread in mainland China? A retrospective analysis of the dynamic transmission routes *
Output: False
Paragraph: There is a large, global unmet need for the development of countermeasures to combat intracellular pathogens. The development of novel antimicrobials is expensive and slow and typically focuses on selective inhibition of proteins encoded by a single pathogen, thereby providing a narrow spectrum of coverage. The repurposing of approved drugs targeting host functions required for microbial infections represents a promising alternative. This review summarizes progress and challenges in the repurposing of approved drugs as host-targeted broad-spectrum agents for the treatment of intracellular pathogens. These strategies include targeting both cellular factors required for infection by various viruses, intracellular bacteria, and/or protozoa as well as factors that modulate the host immune response to these microbial infections. The repurposed approach offers complementary means to develop therapeutics against existing and emerging intracellular microbial threats. 
 Title: Combating Intracellular Pathogens with Repurposed Host-Targeted Drugs
Output: True
Paragraph: NICEATM and ICCVAM convened an international workshop to review the state of the science of human and veterinary vaccine potency and safety testing methods and to identify opportunities to advance new and improved methods that can further reduce, refine, and replace animal use. Six topics were addressed in detail by speakers and workshop participants and are reported in a series of six reports. This workshop report, the second in the series, provides recommendations for current and future use of nonanimal methods and strategies for veterinary vaccine potency testing. Workshop participants recommended that future efforts to replace animal use give priority to vaccines (1) that use large numbers of animals per test and for which many serials are produced annually, (2) that involve significant animal pain and distress during procedures, (3) for which the functional protective antigen has been identified, (4) that involve foreign animal/zoonotic organisms that are dangerous to humans, and (5) that involve pathogens that can be easily spread to wildlife populations. Vaccines identified as the highest priorities were those for rabies, Leptospira spp., Clostridium spp., Erysipelas, foreign animal diseases (FAD), poultry diseases, and fish diseases. Further research on the identification, purification, and characterization of vaccine protective antigens in veterinary vaccines was also identified as a priority. critical knowledge and data gaps, including opportunities to apply new science and technology. Recommendations included (1) investigations into the relative impact of various adjuvants on antigen quantification assays, (2) investigations into extraction methods that could be used for vaccines containing adjuvants that can interfere with antigen assays, and (3) review of the current status of rabies and tetanus human vaccine in vitro potency methods for their potential application to the corresponding veterinary vaccines. Workshop participants recommended enhanced international harmonization and cooperation and closer collaborations between human and veterinary researchers to expedite progress. Implementation of the workshop recommendations is expected to advance alternative in vitro methods for veterinary vaccine potency testing that will benefit animal welfare and replace animal use while ensuring continued protection of human and animal health. 
 Title: NICEATM-ICCVAM # International Workshop on Alternative Methods to Reduce, Refine, and Replace the Use of Animals in Vaccine Potency and Safety Testing: Non-animal replacement methods for veterinary vaccine potency testing: state of the science and future directions peer-review under responsibility of the National Toxicology Program Interagency Center for the Evaluation of Alternative Toxicological Methods (NICEATM). peer-review under responsibility of the National Toxicology Program Interagency Center for the Evaluation of Alternative Toxicological Methods (NICEATM)
Output: True
Paragraph: To replicate and disseminate, viruses need to manipulate and modify the cellular machinery for their own benefit. We are interested in translation, which is one of the key steps of gene expression and viruses that have developed several strategies to hijack the ribosomal complex. The type 1 human immunodeficiency virus is a good paradigm to understand the great diversity of translational control. Indeed, scanning, leaky scanning, internal ribosome entry sites, and adenosine methylation are used by ribosomes to translate spliced and unspliced HIV-1 mRNAs, and some require specific cellular factors, such as the DDX3 helicase, that mediate mRNA export and translation. In addition, some viral and cellular proteins, including the HIV-1 Tat protein, also regulate protein synthesis through targeting the protein kinase PKR, which once activated, is able to phosphorylate the eukaryotic translation initiation factor eIF2α, which results in the inhibition of cellular mRNAs translation. Finally, the infection alters the integrity of several cellular proteins, including initiation factors, that directly or indirectly regulates translation events. In this review, we will provide a global overview of the current situation of how the HIV-1 mRNAs interact with the host cellular environment to produce viral proteins. 
 Title: Molecular Sciences Review Focus on Translation Initiation of the HIV-1 mRNAs
Output: False
Paragraph: To control the latent social risk of disease, the government usually spreads accurate information and attempts to improve the public's attitude toward adopting prevention. However, these methods with the Knowledge, Attitudes, and Practices (KAP) model do not always work. Therefore, we used the theory of planned behavior (TPB) to understand dog owners' behavior and distinguished the knowledge effect as objective knowledge (OK) and subjective knowledge (SK). A total of 310 dog owners completed a questionnaire based on our model. We employed structural equation modeling to verify the structural relationships and found three main results. First, our model was fit, and each path was significant. People with better attitudes, stronger subjective norms, and more perceptive behavioral control have stronger behavioral intention. Second, perceived behavioral control, not attitude, was the best predictive index in this model. Finally, on perceived behavioral control, subjective knowledge showed more influence than objective knowledge. We successfully extended TPB to explain the behavioral intention of dog owners and presented more workable recommendations. To reduce the latent social risk of disease, the government should not only address dog owners' attitudes, but also their OPEN ACCESS Int. J. Environ. Res. Public Health 2014, 11 5935 subjective norms and perceptive behavioral control. Indeed, perceptive behavioral control and SK showed the most influence in this model. It is implied that the self-efficacy of dog owners is the most important factor in such a behavior. Therefore, the government should focus on enhancing dog owners' self-efficacy first while devoted to prevention activities. 
 Title: How to Reduce the Latent Social Risk of Disease: The Determinants of Vaccination against Rabies in Taiwan
Output: True
Paragraph: Leaf and root extracts Anti-leukemia and pseudorabies virus In vitro a b s t r a c t Aim of the study: Isatis indigotica (I. indigotica), Cruciferae, has been used in Chinese medicine for antileukemia and anti-severe acute respiratory syndrome (SARS). The aim of this study was to evaluate the cytotoxicity of Isatis indigotica extracts on human leukemia cell line (HL-60) and the antiviral activity on swine pseudorabies virus (PrV) in in vitro assays. Materials and methods: Extracts and derived fractions of Isatis indigotica were prepared from root (R) and leaf (L) using methanol (M), ethyl acetate (E) and distilled water (D). The cytotoxic effect of extracts on swine peripheral blood mononuclear cells (PBMCs) and HL-60 was assessed by MTT method. The cytopathic effect (CPE) reduction, plaque reduction and inhibition assays on viral replication, and virucidal activity were further conducted to investigate the anti-PrV activity. Results: Indirubin, one of the biological active compounds of Isatis indigotica, had the most significant cytotoxicity on HL-60 cells and inhibitory effect on PrV replication. Extracts from roots and leaves of Isatis indigotica also presented CPE inhibition either before or after infection of PrV on porcine kidney (PK-15) cells. Leaf extracts had better virucidal activity than roots, and ethyl acetate extracts exhibited the highest efficacy among extracts tested. Conclusion: Isatis indigotica posses a valuable virucidal effect in disease control of pseudorabies virus infection in swine. 
 Title: The cytotoxicity to leukemia cells and antiviral effects of Isatis indigotica extracts on pseudorabies virus
Output: True
Paragraph: Bronchoalveolar lavage (BAL) is a major diagnostic tool in lung diseases, including viral respiratory infections. We aimed to better define the situations where viral tests should be performed on BAL fluid (BALF). We retrospectively studied all cases where viral tests [immunofluorescence, immunocytochemistry, viral culture, and/or polymerase chain reaction (PCR)] were performed on BALF during a period of 1 year (2008) in our institution. We compared the characteristics of patients with virus-positive versus virusnegative BALF. Of the 636 BALF samples sent to the microbiology laboratory, 232 underwent viral tests. Of these, 70 (30 %) were positive and identified 85 viruses: herpes simplex virus (HSV)-1 (n027), cytomegalovirus (CMV, n023), Epstein-Barr virus (EBV, n018), human herpesvirus (HHV)-6 (n012), respiratory syncytial virus (RSV, n03), rhinovirus (n01), and adenovirus (n01). The variables associated with positive viral tests on univariate analysis were immunosuppression [human immunodeficiency virus (HIV), corticosteroids >10 mg/day for ≥3 weeks, or other immunosuppressive therapy], ground-glass attenuations on computed tomography (CT) scanning, late-onset ventilator-associated pneumonia (VAP), and durations of (i) hospital stay, (ii) intensive care unit (ICU) stay, and (iii) mechanical ventilation before BAL (p<0.01 for each comparison). On multivariate analysis, only immunosuppression [odds ratio (OR) 6.4, 95 % confidence interval (CI) [2.8-14.3], p<0.0001] and groundglass attenuations (OR 3.7,], p00.0004) remained associated with virus-positive BAL. None of the viral tests performed on BALF for the initial assessment of diffuse infiltrative lung disease (n015) was positive. PCR improved the diagnostic yield of viral tests on BALF by 50 %. Testing for viruses on BALF should be mostly restricted to immunocompromised patients with acute respiratory diseases and/or patients with unexplained ground-glass attenuations on CT scanning. 
 Title: Which patients should be tested for viruses on bronchoalveolar lavage fluid?
Output: False
Paragraph: The UBA domain is a conserved sequence motif among polyubiquitin binding proteins. For the first time, we demonstrate a systematic, high throughput approach to identification of UBA domain-interacting proteins from a proteome-wide perspective. Using the rabbit reticulocyte lysate in vitro expression cloning system, we have successfully identified eleven proteins that interact with p62's UBA domain, and the majority of the eleven proteins are associated with neurodegenerative disorders, such as Alzheimer's disease. Therefore, p62 may play a novel regulatory role through its UBA domain. Our approach provides an easy route to the characterization of UBA domain interacting proteins and its application will unfold the important roles that the UBA domain plays. 
 Title: A Method to Identify p62's UBA Domain Interacting Proteins
Output: True
Paragraph: The immunogenicity of SARS-CoV nucleocapsid DNA vaccine and the immunoregulatory activity of interleukin-2 (IL-2) were investigated. DNA vaccine plasmids, pcDNA-N and pcDNA-IL2, were constructed and inoculated into BALB/c mice with or without pcDNA-IL2 by intramuscular injection. Cellular and humoral immune responses were assessed by indirect ELISA, lymphocyte proliferation assays, ELISPOT and FACS. The nucleocapsid DNA vaccine had good immunogenicity and can induce specific humoral and cellular immunity in BALB/c mice, while IL-2 plays an immunoadjuvant role and enhances specific immune responses. This study provides a frame of reference for the design of DNA vaccines against SARS-CoV. 
 Title: Enhancing immune responses against SARS-CoV nucleocapsid DNA vaccine by co-inoculating interleukin-2 expressing vector in mice
Output: True
Paragraph: This article presents a systematic framework of 12 essentials, or basic elements, of science-based policy. The 12 essentials are grouped into three categories, or areas, as follows: 1) knowledge generation, which includes credible design, accurate data, sound analysis, and comprehensive synthesis; 2) knowledge exchange, which includes relevant content, appropriate translation, timely dissemination, and modulated release; and 3) knowledge uptake, which includes accessible information, readable message, motivated user, and rewarding outcome. 
 Title: Twelve Essentials of Science-based Policy • Centers for Disease Control and Prevention 7
Output: True
Paragraph: An RNA-based, non-cytopathic replicon vector system, based on the flavivirus Kunjin, has shown considerable promise as a new vaccine delivery system. Here we describe the testing in mice of four different SIVmac239 gag vaccines delivered by Kunjin replicon virus-like-particles. The four vaccines encoded the wild type gag gene, an RNA-optimised gag gene, a codon-optimised gag gene and a modified gag-pol gene construct. The vaccines behaved quite differently for induction of effector memory and central memory responses, for mediation of protection, and with respect to insert stability, with the SIV gag-pol vaccine providing the optimal performance. These results illustrate that for an RNA-based vector the RNA sequence of the antigen can have profound and unforeseen consequences on vaccine behaviour. 
 Title: Kunjin replicon-based simian immunodeficiency virus gag vaccines
Output: True
Paragraph: We provide the first empirical evidence for the role of airline travel in long-range dissemination of influenza. Our results suggest an important influence of international air travel on the timing of influenza introduction, as well as an influence of domestic air travel on the rate of inter-regional influenza spread in the US. Pandemic preparedness strategies should account for a possible benefit of airline travel restrictions on influenza spread. 
 Title: Empirical Evidence for the Effect of Airline Travel on Inter-Regional Influenza Spread in the United States
Output: True
Paragraph: The recent Zika outbreak in the Americas, Ebola epidemic in West Africa and the increased frequency and impact of emerging and re-emerging infections of animal origin have increased the calls for greater preparedness in early detection and responses to public health events. One-Health approaches that emphasize collaborations between human health, animal health and environmental health sectors for the prevention, early detection and response to disease outbreaks have been hailed as a key strategy. Here we highlight three main efforts that have progressed the implementation of One Health in Kenya. 
 Title: Disease Surveillance, Vector and Zoological Services, Ministry of Agriculture, Livestock and Fisheries
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. 852 • Head and/or body tremor. • Twitching. • Tremor is an involuntary, rhythmic, oscillatory movement of all or part of the body. It results from the alternate or synchronous contraction of reciprocally innervated, antagonistic muscles. • Disease of the nervous system (central and peripheral) and muscle may result in tremor, shaking or twitching. • Usually tremors with increased amplitudes and slower frequencies (coarse tremor) are associated with cerebellar disorders. Those tremors with decreased amplitudes and faster frequencies (fine tremor) are associated with diffuse central nervous system disease or muscle weakness. • Tremor can have differing amplitudes (the distance traveled during the movement) and frequencies (how fast the tremor is). 
 Title: 39. The cat with tremor or twitching Diseases causing tremor or twitching COARSE TREMOR AND TWITCHING (INTENTIONAL)
Output: False
Paragraph: Motivation: Abstract shape analysis, first proposed in 2004, allows one to extract several relevant structures from the folding space of an RNA sequence, preferable to focusing in a single structure of minimal free energy. We report recent extensions to this approach. Results: We have rebuilt the original RNASHAPES as a repository of components that allows us to integrate several established tools for RNA structure analysis: RNASHAPES, RNAALISHAPES and PKNOTSRG, including its recent extension PKISS. As a spin-off, we obtain heretofore unavailable functionality: e. g. with PKISS, we can now perform abstract shape analysis for structures holding pseudoknots up to the complexity of kissing hairpin motifs. The new tool PALIKISS can predict kissing hairpin motifs from aligned sequences. Along with the integration, the functionality of the tools was also extended in manifold ways. Availability and implementation: As before, the tool is available on the Bielefeld Bioinformatics server at 
 Title: Sequence analysis The RNA shapes studio
Output: True
Paragraph: Background: The 2010 cholera outbreak in northern Nigeria affected over 40,000 people, with a case fatality rate (CFR) of ≥3.75%. We assessed the emergency response of health care workers (HCWs) involved in case management. Method: This was a cross-sectional study with data collected through a selfadministered questionnaire. Data entry and analysis were performed using Epi info software. Results: A total of 56 HCWs were interviewed. The mean age was 31 years (SD ± 8.16 years). The majority of the HCWs (80%; n = 45) were aged 18-39 years. Most were community health extension workers (60%), and 3.6% (n = 2) were medical doctors. Many of the HCWs had less than 2 years of work experience (42%). Additionally, 82% of the respondents had <1 week of cholera emergency response training, and 50% of the HCWs managed >20 suspected cases of cholera per day. Although 78% of HCWs reported the practice of universal safety precautions, 32% (n = 18) knew HCWs who developed symptoms of cholera during the epidemic, most of which was believed to be hospital acquired (78%). We also found that 77% (n = 43) of HCWs had no access to the required emergency response supplies. Conclusion: Inadequate training, a lack of qualified HCWs and a limited supply of emergency response kits were reported. Therefore, the government and stakeholders should address the gaps noted to adequately control and prevent future epidemics. 
 Title: An assessment of the emergency response among health workers involved in the 2010 cholera outbreak in northern Nigeria Cholera outbreak emergency response in Nigeria
Output: True
Paragraph: Autophagy, a vital catabolic process that degrades cytoplasmic components within the lysosome, serves as an essential cytoprotective response to pathologic stresses that occur during diseases such as cancer, ischemia, and infection. In addition to its role as a stress response pathway, autophagy plays an essential quality control function in the cell by promoting basal turnover of long-lived proteins and organelles as well as selectively degrading damaged cellular components. This homeostatic function protects against a wide variety of diseases including neurodegeneration, myopathy, liver disease, and diabetes. This review discusses our current understanding of these two principal functions for autophagy as a physiologic stress response and quality control mechanism within mammalian cells and details how alterations in autophagy promote human disease. 
 Title: Autophagy As A Stress Response And Quality Control Mechanism-Implications for Cell Injury and Human Disease
Output: True
Paragraph: The immune system is an awe-inspiring control structure that maintains a delicate and constantly changing balance between pro-immune functions that fight infection and cancer, regulatory or suppressive functions involved in immune tolerance, and homeostatic resting states. These activities are determined by integrating signals in space and time; thus, improving control over the densities, combinations, and durations with which immune signals are delivered is a central goal to better combat infectious disease, cancer, and autoimmunity. Self-assembly presents a unique opportunity to synthesize materials with well-defined compositions and controlled physical arrangement of molecular building blocks. This review highlights strategies exploiting these capabilities to improve the understanding of how precisely-displayed cues interact with immune cells and tissues. We present work centered on fundamental properties that regulate the nature and magnitude of immune response, highlight pre-clinical and clinical applications of self-assembled technologies in vaccines, cancer, and autoimmunity, and describe some of the key manufacturing and regulatory hurdles facing these areas. 
 Title: Engineering self-assembled materials to study and direct immune function ☆-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/)
Output: True
Paragraph: Background: ISG15 is an Ubiquitin-like protein, highly induced by Type I Interferons. Upon the cooperative activity of specific Ubiquitinating enzymes, ISG15 can be conjugated to its substrates. Increasing evidence points to a role for protein ISGylation in anti-viral and anti-tumoral defense. Principal Findings: We identified ISG15 from Old World Monkeys (OWm) as a hyper-efficient protein modifier. Western blot analysis visualized more efficient conjugation of OWmISG15 relative to HuISG15 in human (Hu), monkey and mouse (Mo) cell-lines. Moreover, the substrates of OWmISG15 identified upon Tandem Affinity Purification followed by LC-MS/MS identification largely outnumbered these of HuISG15 itself. Several Ubiquitin-Conjugating enzymes were identified as novel ISGylated substrates. Introduction of a N89D mutation in HuISG15 improved its ISGylation capacity, and additional Q31K/ T33A/D133N mutations yielded a HuISG15 variant with an ISGylation efficiency comparable to OWmISG15. Homology modeling and structural superposition situate N89 in the interaction interface with the Activating enzyme. Analysis of the UbE1L residues in this interface revealed a striking homology between OWmUbE1L and HuUbE1, the Activating enzyme of Ubiquitin. In line with this observation, we found efficient activation of AgmISG15, but not HuISG15 or MoISG15, by HuUbE1, thus providing a likely explanation for OWm hyperISGylation. Conclusions: This study discloses the poor conjugation competence of HuISG15 compared to OWmISG15 and maps the critical determinants for efficient conjugation. HyperISGylation may greatly assist ISGylation studies and may enhance its function as positive regulator of Interferon-related immune responses or as anti-tumoral modulator. 
 Title: HyperISGylation of Old World Monkey ISG15 in Human Cells
Output: True
Paragraph: To cause infections, microbial pathogens elaborate a multitude of factors that interact with host components. Using these host-pathogen interactions to their advantage, pathogens attach, invade, disseminate, and evade host defense mechanisms to promote their survival in the hostile host environment. Many viruses, bacteria, and parasites express adhesins that bind to cell surface heparan sulfate proteoglycans (HSPGs) to facilitate their initial attachment and subsequent cellular entry. Some pathogens also secrete virulence factors that modify HSPG expression. HSPGs are ubiquitously expressed on the cell surface of adherent cells and in the extracellular matrix. HSPGs are composed of one or several heparan sulfate (HS) glycosaminoglycan chains attached covalently to specific core proteins. For most intracellular pathogens, cell surface HSPGs serve as a scaffold that facilitates the interaction of microbes with secondary receptors that mediate host cell entry. Consistent with this mechanism, addition of HS or its pharmaceutical functional mimic, heparin, inhibits microbial attachment and entry into cultured host cells, and HS-binding pathogens can no longer attach or enter cultured host cells whose HS expression has been reduced by enzymatic treatment or chemical mutagenesis. In pathogens where the specific HS adhesin has been identified, mutant strains lacking HS adhesins are viable and show normal growth rates, suggesting that the capacity to interact with HSPGs is strictly a virulence activity. The goal of this chapter is to provide a mechanistic overview of our current understanding of how certain microbial pathogens subvert HSPGs to promote their infection, using specific HSPGpathogen interactions as representative examples. 
 Title: Heparan Sulfate Proteoglycans in Infection
Output: True
Paragraph: Plants have emerged as a modern production system to produce recombinant proteins-antigens that can be used as subunit vaccines. The ideal plant candidate for this purpose should be capable to sustain high levels of expression of foreign proteins without adverse effects on its growth and development. It is also essential that it has large biomass, is edible and suitable for long-term storage and delivery. This work is a part of an effort to develop Cruciferae-based production system using transgenic vegetable plants collard and cauliflower. Several parameters were tested and optimized to achieve an efficient stable transformation of these recalcitrant species with constructs containing expression cassettes for the known viral antigens. Using the original procedure we obtained transgenic collard cv Morris Heading that express high levels of smallpox vaccine candidate (B5) in leaves and retain its normal phenotype. Transgenic cauliflower plants cv Early Snowball were obtained in similar procedure and have shown detectable amounts of SARS coronavirus spike-protein (SARS-CoV S1) in floret tissue of mature curd. To our knowledge, this is the first report on generation of transgenic collard plants ever and the first successful attempt to use these vegetables for production of pharmaceutical proteins. # 
 Title: Collard and cauliflower as a base for production of recombinant antigens
Output: False
Paragraph: Choice of interaction function is one of the most important parts for modelling a food chain. Many models have been proposed as a diseased-prey predator model with Holling type-I or type-II or type-III interactions, but there is no model with general Holling type interactions. In this paper, we study a diseased prey-predator model with general Holling type interactions. Local stability conditions of equilibrium points are derived. We obtain the permanence and impermanence conditions of the system. The conditions for global stability of the system are also derived. The system exhibits limit cycle, period-2, higher periodic oscillations and chaotic behaviour for different values of Holling parameters. One parameter bifurcation analysis is done with respect to general Holling parameters and infection rate. We utilize the MATCONT package to analyse the detailed bifurcation scenario as the two important interaction parameters are varied. It is interesting to note that a diseased system becomes a disease free system for proper choice of interaction functions. Our results give an idea for constructing a realistic food chain model through proper choice of general Holling parameters. 
 Title: Diseased prey predator model with general Holling type interactions
Output: True
Paragraph: Aim of this study was to de termine and furthe r characte rize the se rum aminope ptidase -M in childre n with live r dise ase s. Based on our ne w assay, we have shown two fractions of the e nzyme . Activity of the ® rst fraction is e xpre sse d in undilute d se rum at pH adjuste d from 8.5 (pH of storage d se rum) to 7.4. Activity of the se cond fraction (cryptic activity) appe ars in the serum (pH 7.4) as a result of dilution and/or addition of aniline naphthale ne sulfonic acid. In childre n with Alagille syndrome , e xtrahe patic biliary duct atre sia, Byle r's dise ase , and acute hepatitis due to he patitis B virus infection, activitie s of both fractions are highly elevate d as compare d to healthy childre n or those with chronic viral he patitis. More over, se rum aminopeptidase -M se ems to re¯e ct othe r aspe cts of the pathological proce ss than those re¯ected by the alanine aminotransfe rase and g -glutamyltranspe ptidase . Due to incre ase d activity and broad substrate speci® city, the e nzyme se e ms to be also a cofactor of chole stasis and he patitis. 
 Title: Further Studies on Aminopeptidase-M in Blood in Children with Cholestatic Liver Diseases and Viral Hepatitis
Output: False