niryuu/sni-each-converted huggingface dataset:
Paragraph: Background: COVID-19 is an emerging disease caused by the SARS-CoV-2 virus; no specific medication has been identified to date. We aimed to investigate the administered medications and intervention times for patients who completely recovered from COVID-19. Methods: This single-center, retrospective, and observational study included 55 patients with COVID-19 who were transferred to Shenyang Sixth People's Hospital between January 20 and March 15, 2020. Demographic information, symptoms, laboratory indicators, treatment processes, and clinical outcomes were collected. Administered drugs and intervention times were compared in 47 and eight patients with mild and severe symptoms, respectively. Findings: All 55 patients recovered. Fifty-three patients (96·36%) received antiviral therapy, including 45 in the mild group (median treatment: 14 days; 17 received umifenovir) and all eight severe-group patients (median treatment: 17·5 days; four received lopinavir/ritonavir). Twenty-nine patients (52·72%) were administered antibiotics, including 21 in the mild group (median treatment: 13·5 days; 15 received moxifloxacin) and all eight in the severe group (median treatment: 9 days; two received linezolid). Moreover, seven patients (12·72%) were treated with glucocorticoids and nine (16·36%) with immunomodulators. 
 Title: Article Medical treatment of 55 patients with COVID-19 from seven cities in northeast China who fully recovered: a single-center, retrospective, observational study
Output: True
Paragraph: This paper concerns study of the genome of the Wuhan Seafood Market isolate believed to represent the causative agent of the disease COVID-19. This is to find a short section or sections of viral protein sequence suitable for preliminary design proposal for a peptide synthetic vaccine and a peptidomimetic therapeutic, and to explore some design possibilities. The project was originally directed towards a use case for the Q-UEL language and its implementation in a knowledge management and automated inference system for medicine called the BioIngine, but focus here remains mostly on the virus itself. However, using Q-UEL systems to access relevant and emerging literature, and to interact with standard publically available bioinformatics tools on the Internet, did help quickly identify sequences of amino acids that are well conserved across many coronaviruses including 2019-nCoV. KRSFIEDLLFNKV was found to be particularly well conserved in this study and corresponds to the region around one of the known cleavage sites of the SARS virus that are believed to be required for virus activation for cell entry. This sequence motif and surrounding variations formed the basis for proposing a specific synthetic vaccine epitope and peptidomimetic agent. The work can, nonetheless, be described in traditional bioinformatics terms, and readily reproduced by others, albeit with the caveat that new data and research into 2019-nCoV is emerging and evolving at an explosive pace. Preliminary studies using molecular modeling and docking, and in that context the potential value of certain known herbal extracts, are also described. 
 Title: Computers and viral diseases. Preliminary bioinformatics studies on the design of a synthetic vaccine and a preventative peptidomimetic antagonist against the SARS-CoV-2 (2019-nCoV, COVID-19) coronavirus
Output: False
Paragraph: Carefully calibrated transmission models have the potential to guide public health officials on the nature and scale of the interventions required to control epidemics. In the context of the ongoing Ebola virus disease (EVD) epidemic in Liberia, Drake and colleagues, in this issue of PLOS Biology, employed an elegant modeling approach to capture the distributions of the number of secondary cases that arise in the community and health care settings in the context of changing population behaviors and increasing hospital capacity. Their findings underscore the role of increasing the rate of safe burials and the fractions of infectious individuals who seek hospitalization together with hospital capacity to achieve epidemic control. However, further modeling efforts of EVD transmission and control in West Africa should utilize the spatial-temporal patterns of spread in the region by incorporating spatial heterogeneity in the transmission process. Detailed datasets are urgently needed to characterize temporal changes in population behaviors, contact networks at different spatial scales, population mobility patterns, adherence to infection control measures in hospital settings, and hospitalization and reporting rates. 
 Title: Characterizing the Transmission Dynamics and Control of Ebola Virus Disease
Output: True
Paragraph: A new coronavirus (severe acute respiratory syndrome coronavirus [SARS-CoV]) has been identified to be the etiological agent of severe acute respiratory syndrome. Given the highly contagious and acute nature of the disease, there is an urgent need for the development of diagnostic assays that can detect SARS-CoV infection. A total of 81 sera, including 67 from convalescent patients and seven pairs from two time points of infection, were analyzed, and all showed immunoreactivity towards the nucleocapsid protein (N). Sera from some of the patients also showed immunoreactivity to U274 (59 of 81 [73%]), a protein that is unique to SARS-CoV. In addition, all of the convalescent-phase sera showed immunoreactivity to the spike (S) protein when analyzed by an immunofluorescence method utilizing mammalian cells stably expressing S. However, samples from the acute phase (2 to 9 days after the onset of illness) did not react with S, suggesting that antibodies to N may appear earlier than antibodies to S. Alternatively, this could be due to the difference in the sensitivities of the two methods. The immunoreactivities to these recombinant viral proteins are highly specific, as sera from 100 healthy donors did not react with any of them. These results suggest that recombinant N, S, and U274 proteins may be used as antigens for the development of serological assays for SARS-CoV. 
 Title: Profiles of Antibody Responses against Severe Acute Respiratory Syndrome Coronavirus Recombinant Proteins and Their Potential Use as Diagnostic Markers
Output: False
Paragraph: We summarize herein the results of various virologic studies of acute otitis media (AOM) conducted at our site over a ten -year period. Among 566 children with AOM, respiratory syncytial virus (RSV) was the most common virus identified in either middle ear fluid or nasal wash; it was found in 16% of all children and 38% of virus-positive children. Seventy-one percent of the children with RSV were one year of age or older, which was significantly older than all other viruses combined (P = 0.045). RSV infection was associated with the common bacterial pathogens causing AOM. Past efforts to develop vaccines for RSV have emphasized prevention of lower respiratory tract infection in infants, which is a more serious problem but less common than AOM. Our results suggest that RSV vaccines that work only against infection in older children may have value in preventing AOM, the most common pediatric disease. 
 Title: ROLE OF RESPIRATORY SYNCYTIAL VIRUS IN ACUTE OTITIS MEDIA: IMPLICATIONS FOR VACCINE DEVELOPMENT
Output: False
Paragraph: Background: Molecular assays for diagnosis of Flu A, Flu B, and RSV with short turn-around-time (TAT) are of considerable clinical importance. In addition, rapid and accurate diagnosis of a large panel of viral and atypical pathogens can be crucial in immunocompromised patients. Objectives: First, to evaluate the performance of the Simplexa™ Direct assay system in comparison with direct fluorescent antibody (DFA) and customized Taqman® Array Card (TAC) testing for RSV, Flu A, and Flu B in immunocompromised patients. Second, to evaluate different algorithms for the detection of respiratory pathogens in terms of cost, turn-around-time (TAT) and diagnostic yield. Study design: We collected 125 nasopharyngeal swabs (NTS) and 25 BAL samples from symptomatic immunocompromised patients. Samples for which Simplexa™ and TAC results were discordant underwent verification testing. The TAC assay is based on singleplex RT-PCR, targeting 24 viruses, 8 bacteria and 2 fungi simultaneously. Results: The overall sensitivity was significantly lower for DFA testing than for the two molecular methods (p < 0.05). Performance characteristics of Simplexa™ testing were not significantly different compared to TAC testing (p > 0.1). For BAL samples only, the sensitivity and specificity of the Simplexa™ assay was 100%. In total, 6.7, 16 and 18% of samples were positive for Flu A, Flu B or RSV by DFA, Simplexa™ and TAC testing, respectively. When considering not only these pathogens but also all results for TAC, the method identified 93 samples with one or more respiratory pathogens (62%). A co-infection rate of 15.3% was found by TAC. The estimated costs and TAT were 8.2€ and 2 h for DFA, 31.8€ and 1.5 h for Simplexa™ and 55€ and 3 h for TAC testing. Conclusions: Performing the Simplexa™ test 24 h a day/7 days a week instead of DFA would considerably improve the overall sensitivity and time-to-result, albeit at a higher cost generated in the laboratory. Performing the TAC would increase the diagnostic yield and detection of co-infections significantly. 
 Title: Performance evaluation of direct fluorescent antibody, Focus Diagnostics Simplexa™ Flu A/B & RSV and multi-parameter customized respiratory Taqman® array card in immunocompromised patients
Output: False
Paragraph: Muscle wasting is one of the main features of cancer cachexia, a multifactorial syndrome frequently occurring in oncologic patients. The onset of cachexia is associated with reduced tolerance and response to antineoplastic treatments, eventually leading to clinical conditions that are not compatible with survival. Among the mechanisms underlying cachexia, protein and energy dysmetabolism play a major role. In this regard, several potential treatments have been proposed, mainly on the basis of promising results obtained in preclinical models. However, at present, no treatment yet reached validation to be used in the clinical practice, although several drugs are currently tested in clinical trials for their ability to improve muscle metabolism in cancer patients. Along this line, the results obtained in both experimental and clinical studies clearly show that cachexia can be effectively approached by a multidirectional strategy targeting nutrition, inflammation, catabolism, and inactivity at the same time. In the present study, approaches aimed to modulate muscle metabolism in cachexia will be reviewed. 
 Title: Modulating Metabolism to Improve Cancer-Induced Muscle Wasting
Output: False
Paragraph: The ability of emerging pathogens to infect new species is likely related to the diversity of pathogen variants present in existing reservoirs and their degree of genomic plasticity, which determines their ability to adapt to new environments. Certain simian immunodeficiency viruses (SIVcpz, SIVsm) have demonstrated tremendous success in infecting new species, including humans, resulting in the HIV-1 and HIV-2 epidemics. Although SIV diversification has been studied on a population level, the essential substrates for cross-species transmission, namely SIV sequence diversity and the types and extent of viral diversification present in individual reservoir animals have not been elucidated. To characterize this intra-host SIV diversity, we performed sequence analyses of clonal viral envelope (env) V1V2 and gag p27 variants present in individual SIVsm-infected sooty mangabeys over time. Results: SIVsm demonstrated extensive intra-animal V1V2 length variation and amino acid diversity (le38%), and continual variation in V1V2 N-linked glycosylation consensus sequence frequency and location. Positive selection was the predominant evolutionary force. Temporal sequence shifts suggested continual selection, likely due to evolving antibody responses. In contrast, gag p27 was predominantly under purifying selection. SIVsm V1V2 sequence diversification is at least as great as that in HIV-1 infected humans, indicating that extensive viral diversification in and of itself does not inevitably lead to AIDS. Positive diversifying selection in this natural reservoir host is the engine that has driven the evolution of the uniquely adaptable SIV/HIV envelope protein. These studies emphasize the importance of retroviral diversification within individual host reservoir animals as a critical substrate in facilitating cross-species transmission. 
 Title: Evolution of the uniquely adaptable lentiviral envelope in a natural reservoir host
Output: False
Paragraph: Highlights d N 1 -2 0 O-methylation is crucial to block RIG-I activation by viral and self RNA d Self-RNA exclusion is singularly governed by the conserved H830 in RIG-I d H830A alteration leads to indiscriminate recognition of endogenous RNA by RIG-I d Cellular N 1 -2 0 O-methyltransferase knockdown renders endogenous RNA stimulatory SUMMARY The cytosolic helicase retinoic acid-inducible gene-I (RIG-I) initiates immune responses to most RNA viruses by detecting viral 5 0 -triphosphorylated RNA (pppRNA). Although endogenous mRNA is also 5 0 -triphosphorylated, backbone modifications and the 5 0 -ppp-linked methylguanosine ( m7 G) cap prevent immunorecognition. Here we show that the methylation status of endogenous capped mRNA at the 5 0 -terminal nucleotide (N 1 ) was crucial to prevent RIG-I activation. Moreover, we identified a single conserved amino acid (H830) in the RIG-I RNA binding pocket as the mediator of steric exclusion of N 1 -2 0 O-methylated RNA. H830A alteration (RIG-I(H830A)) restored binding of N 1 -2 0 O-methylated pppRNA. Consequently, endogenous mRNA activated the RIG-I(H830A) mutant but not wild-type RIG-I. Similarly, knockdown of the endogenous N 1 -2 0 O-methyltransferase led to considerable RIG-I stimulation in the absence of exogenous stimuli. Studies involving yellow-fever-virus-encoded 2 0 O-methyltransferase and RIG-I(H830A) revealed that viruses exploit this mechanism to escape RIG-I. Our data reveal a new role for cap N 1 -2 0 O-methylation in RIG-I tolerance of self-RNA. 
 Title: A Conserved Histidine in the RNA Sensor RIG-I Controls Immune Tolerance to N 1 -2 0 O-Methylated Self RNA Article A Conserved Histidine in the RNA Sensor RIG-I Controls Immune Tolerance to N 1 -2 0 O-Methylated Self RNA
Output: False
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. Abbreviations: IL-1, interleukin 1; IFN-7, interferon 7; NOS-2, nitric oxide synthase; TNF-c(, tumor necrosis factor ~. TRENDS IN MICR()BI()I_()GY 
 Title: M i " if ti ur ne coronavlrus n ec on: a paradigm for virus-induced demyelinating disease
Output: True
Paragraph: Several studies have shown a reduced efficacy of influenza vaccines in the elderly compared to young adults. In this study, we evaluated the immunogenicity and protective efficacy of a commercially available inactivated influenza vaccine (Fluzone 1 ) in young adult and aged mice. C57/BL6 mice were administered a single or double immunization of Fluzone 1 with or without CpG and challenged intranasally with H1N1 A/California/09 virus. A double immunization of Fluzone 1 adjuvanted with CpG elicited the highest level of protection in young adult mice which was associated with increases in influenza specific IgG, elevated HAI titres, reduced viral titres and lung inflammation. In contrast, the vaccine schedule which provided fully protective immunity in young adult mice conferred limited protection in aged mice. Antigen presenting cells from aged mice were found to be less responsive to in vitro stimulation by Fluzone and CpG which may partially explain this result. Our data are supportive of studies that have shown limited effectiveness of influenza vaccines in the elderly and provide important information relevant to the design of more immunogenic vaccines in this age group. 
 Title: CpG Improves Influenza Vaccine Efficacy in Young Adult but Not Aged Mice
Output: False
Paragraph: Chitin is a linear polysaccharide of N-acetylglucosamine, which is highly abundant in nature and mainly produced by marine crustaceans. Chitosan is obtained by hydrolytic deacetylation. Both polysaccharides are renewable resources, simply and cost-effectively extracted from waste material of fish industry, mainly crab and shrimp shells. Research over the past five decades has revealed that chitosan, in particular, possesses unique and useful characteristics such as chemical versatility, polyelectrolyte properties, gel-and film-forming ability, high adsorption capacity, antimicrobial and antioxidative properties, low toxicity, and biocompatibility and biodegradability features. A plethora of chemical chitosan derivatives have been synthesized yielding improved materials with suggested or effective applications in water treatment, biosensor engineering, agriculture, food processing and storage, textile additives, cosmetics fabrication, and in veterinary and human medicine. The number of studies in this research field has exploded particularly during the last two decades. Here, we review recent advances in utilizing chitosan and chitosan derivatives in different technical, agricultural, and biomedical fields. A large number of chitosan-based composites were investigated for removal of metal ions from aqueous solutions. They include chitosan-polymer macromolecular complexes (as cellulose, cellulosic matrix like cotton fibers, alginate, polyvinyl alcohol, polyvinyl chloride), chitosan ceramics, as well as clay and silicate composites (bentonite, montmorillonite, perlite, and zeolite) (Wan Ngah et al. 2011) . Due to the vast number of scientific publications on chitosan-based adsorption that have been published, only a representative sample is depicted for Cr(VI) and Cu(II). Cognate composites were devised as adsorbents of other metal ions (Cd, As, Fe, Pb, Co, Pb, Hg, Ni, Zn, U) that can be found in the detailed reviews of Reddy and Lee ( 
 Title: Chitin/Chitosan: Versatile Ecological, Industrial, and Biomedical Applications
Output: False
Paragraph: In today's global economy and affordable vacation travel, it is increasingly important that visitors to another country and their physician be familiar with emerging infections, infections unique to a specific geographic region, and risks related to the process of travel. This is never more important than for patients with primary immunodeficiency disorders (PIDD). A recent review addressing common causes of fever in travelers provides important information for the general population 
 Title: Emerging Infections and Pertinent Infections Related to Travel for Patients with Primary Immunodeficiencies
Output: False
Paragraph: Activating mutations in the phosphoinositide 3-kinase (PI3K) signaling pathway are frequently identified in cancer. To identify pathways that support PI3K oncogenesis, we performed a genome-wide RNAi screen in isogenic cell lines harboring wild-type or mutant PIK3CA to search for PI3K synthetic-lethal (SL) genes. A combined analysis of these results with a meta-analysis of two other large-scale RNAi screening data sets in PI3K mutant cancer cell lines converged on ribosomal protein translation and proteasomal protein degradation as critical nononcogene dependencies for PI3K-driven tumors. Genetic or pharmacologic inhibition of either pathway alone, but not together, selectively killed PI3K mutant tumor cells in an mTOR-dependent manner. The expression of ribosomal and proteasomal components was significantly up-regulated in primary human colorectal tumors harboring PI3K pathway activation. Importantly, a PI3K SL gene signature containing the top hits of the SL genes identified in our metaanalysis robustly predicted overall patient survival in colorectal cancer, especially among patients with tumors with an activated PI3K pathway. These results suggest that disruption of protein turnover homeostasis via ribosome or proteasome inhibition may be a novel treatment strategy for PI3K mutant human tumors. 
 Title: Functional genomics reveals that tumors with activating phosphoinositide 3-kinase mutations are dependent on accelerated protein turnover
Output: False
Paragraph: Newton's Principia introduces four rules of reasoning for natural philosophy. Although useful, there is a concern about whether Newton's rules guarantee truth. After redirecting the discussion from truth to validity, I show that these rules are valid insofar as they fulfill Goodman's criteria for inductive rules and Newton's own methodological program of experimental philosophy; provided that cross-checks are used prior to applications of rule 4 and immediately after applications of rule 2 the following activities are pursued: (1) research addressing observations that systematically deviate from theoretical idealizations and (2) applications of theory that safeguard ongoing research from proceeding down a garden path. # 
 Title: Do Newton's rules of reasoning guarantee truth . . . must they?
Output: False
Paragraph: Background: Due to the emergence of drug resistance in herpes simplex virus type 1 (HsV-1), researchers are trying to find other methods for treating herpes simplex virus type 1 infections. Probiotic bacteria are effective in macrophage activation and may have antiviral activities. Objective: this study aimed at verifying the direct effect of Lactobacillus rhamnosus, a probiotic bacterium, in comparison with Escherichia coli, a non-probiotic one, on HsV-1 infection, and determining its effect on macrophage activation for in vitro elimination of HsV-1 infection. Methods: the above bacteria were introduced into HsV-1 infected Vero cells, and their effects were examined using both Mtt and plaque assay. to determine macrophage activation against in vitro HsV-1 infection, J774 cells were exposed to these bacteria; then, macrophage viability was examined with the Mtt method, and tumor necrosis factor alpha (tnf-α), interferon-gamma (ifn-γ), and nitric oxide (no) assessments were performed using the ELisA method. Results: A significant increased viability of macrophages was observed (p < 0.05) in the presence of Lactobacillus rhamnosus before and after HsV-1 infection when compared with Escherichia coli as a non-probiotic bacterium. However, tumor necrosis factor α concentration produced by Escherichia coli-treated J774 cells was significantly higher than Lactobacillus rhamnosus-treated J774 cells (p < 0.05). interferon-gamma and no production were not different in the groups treated with Escherichia coli or with Lactobacillus rhamnosus. Conclusion: the results of this study indicate that Lactobacillus rhamnosus enhances macrophage viability for HsV-1 elimination and activation against HsV-1 more effectively, when compared with non-probiotic Escherichia coli. it also seems that receptor occupation of macrophage sites decreases HsV-1 infectivity by both of the studied bacteria. In vitro study of the effect of a probiotic bacterium Lactobacillus rhamnosus against herpes simplex virus type 1 
 Title: The Brazilian Journal of INFECTIOUS DISEASES
Output: True
Paragraph: Some single-stranded positive-sense RNA [ssRNA(+)] viruses, including Flavivirus, generate specific organelle-like structures in the host endoplasmic reticulum (ER). These structures are called virus replication organelles and consist of two distinct subdomains, the vesicle packets (VPs) and the convoluted membranes (CMs). The VPs are clusters of small vesicle compartments and are considered to be the site of viral genome replication. The CMs are electron-dense amorphous structures observed in proximity to the VPs, but the exact roles of CMs are mostly unknown. Several recent studies have revealed that flaviviruses recruit several host factors that are usually used for the biogenesis of other conventional organelles and usurp their function to generate virus replication organelles. In the current review, we summarize recent studies focusing on the role of host factors in the formation of virus replication organelles and discuss how these intricate membrane structures are organized. 
 Title: Molecular Sciences Review Flavivirus Replication Organelle Biogenesis in the Endoplasmic Reticulum: Comparison with Other Single-Stranded Positive-Sense RNA Viruses
Output: False
Paragraph: Despite being simple eukaryotic organisms, the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe have been widely used as a model to study human pathologies and the replication of human, animal, and plant viruses, as well as the function of individual viral proteins. The complete genome of S. cerevisiae was the first of eukaryotic origin to be sequenced and contains about 6,000 genes. More than 75% of the genes have an assigned function, while more than 40% share conserved sequences with known or predicted human genes. This strong homology has allowed the function of human orthologs to be unveiled starting from the data obtained in yeast. RNA plant viruses were the first to be studied in yeast. In this paper, we focus on the use of the yeast model to study the function of the proteins of human immunodeficiency virus type 1 (HIV-1) and the search for its cellular partners. This human retrovirus is the cause of AIDS. The WHO estimates that there are 33.4 million people worldwide living with HIV/AIDS, with 2.7 million new HIV infections per year and 2.0 million annual deaths due to AIDS. Current therapy is able to control the disease but there is no permanent cure or a vaccine. By using yeast, it is possible to dissect the function of some HIV-1 proteins and discover new cellular factors common to this simple cell and humans that may become potential therapeutic targets, leading to a long-lasting treatment for AIDS. 
 Title: Yeast and the AIDS Virus: The Odd Couple
Output: False
Paragraph: Enhancing citizens' and communities' resilience is critical to adapt successfully to ongoing challenges faced by communities, as well as acute shocks resulting from disasters. While significant progress has been made in this area, several research and practice gaps remain. A crucial next step to advance resilience is the development of a resilience-oriented workforce. This narrative review examines existing literature to determine key components of a resilience-oriented workforce, with a focus on organizational structures, training and education, and leadership models. Reviewed articles spanned a variety of study types, including needs assessments of existing workforce, program evaluations, and reviews/commentaries. A resilience-oriented workforce spans many disciplines and training programs will need to reflect that. It requires a collaborative organizational model that promotes information sharing structures. Leadership models should foster a balance between workforce autonomy and operation as a collective entity. Optimal strategies to develop a resilience-oriented workforce have yet to be realized and future research will need to collect and synthesize data to promote and evaluate the growth of this field. 
 Title: Beyond Disaster Preparedness: Building a Resilience-Oriented Workforce for the Future
Output: False
Paragraph: Pentraxin 3 (PTX3) is a soluble pattern recognition receptor which is classified as a long-pentraxin in the pentraxin family. It is known to play an important role in innate immunity, inflammatory regulation, and female fertility. PTX3 is synthesized by specific cells, primarily in response to inflammatory signals. Among these various cells, neutrophils have a unique PTX3 production system. Neutrophils store PTX3 in neutrophil-specific granules and then the stored PTX3 is released and localizes in neutrophil extracellular traps (NETs). Although certain NET components have been identified, such as histones and anti-microbial proteins, the detailed mechanisms by which NETs localize, as well as capture and kill microbes, have not been fully elucidated. PTX3 is a candidate diagnostic marker of infection and vascular damage. In severe infectious diseases such as sepsis, the circulating PTX3 concentration increases greatly (up to 100 ng/mL, i.e., up to 100-fold of the normal level). Even though it is clearly implied that PTX3 plays a protective role in sepsis and certain other disorders, the detailed mechanisms by which it does so remain unclear. A proteomic study of PTX3 ligands in septic patients revealed that PTX3 forms a complex with certain NET component proteins. This suggests a role for PTX3 in which it facilitates the efficiency of anti-microbial protein pathogen clearance by interacting with both pathogens and anti-microbial proteins. We discuss the possible relationships between PTX3 and NET component proteins in the host protection afforded by the innate immune response. The PTX3 complex has the potential to be a highly useful diagnostic marker of sepsis and other inflammatory diseases. 
 Title: Host-protective effect of circulating pentraxin 3 (PTX3) and complex formation with neutrophil extracellular traps
Output: True
Paragraph: The reliable and rapid detection of viral pathogens that cause respiratory infections provide physicians several advantages in treating patients and managing outbreaks. The Luminex respiratory virus panel (RVP) assay has been shown to be comparable to or superior to culture/direct fluorescent-antibody assays (DFAs) and nucleic acid tests that are used to diagnose respiratory viral infections. We developed a multiplex asymmetric reverse transcription (RT)-PCR assay that can simultaneously differentiate all influenza A virus epidemic subtypes. The amplified products were hybridized with an electrochemical DNA sensor, and the results were automatically acquired. The limits of detection (LoDs) of both the Luminex RVP assay and the multiplex RT-PCRelectrochemical DNA sensor were 10 1 TCID 50 for H1N1 virus and 10 2 TCID 50 for H3N2 virus. The specificity assessment of the multiplex RT-PCR-electrochemical DNA sensor showed no cross-reactivity among different influenza A subtypes or with other noninfluenza respiratory viruses. In total, 3098 respiratory tract specimens collected from padiatric patients diagnosed with pneumonia were tested. More than half (43, 53.75%) of the specimens positive for influenza A viruses could not be further subtyped using the Luminex RVP assay. Among the remaining 15 specimens that were not subtyped, not degraded, and in sufficient amounts for the multiplex RT-PCR-electrochemical DNA sensor test, all (100%) were H3N2 positive. Therefore, the sensitivity of the Luminex RVP assay for influenza A virus was 46.25%, whereas the sensitivity of the multiplex RT-PCR-electrochemical DNA sensor for the clinical H1N1 and H3N2 specimens was 100%. The sensitivities of the multiplex RT-PCR-electrochemical DNA sensor for the avian H5N1, H5N6, H9N2, and H10N8 viruses were 100%, whereas that for H7N9 virus was 85.19%. We conclude that the multiplex RT-PCR-electrochemical DNA sensor is a reliable method for the rapid and accurate detection of highly variable influenza A viruses in respiratory infections with greater detection sensitivity than that of the Frontiers in Microbiology | www.frontiersin.org 1 June 2018 | Volume 9 | Article 1405 Xu et al. Influenza A Viruses Detection Luminex xTAG assay. The high mutation rate of influenza A viruses, particularly H3N2 during the 2014 to 2016 epidemic seasons, has a strong impact on diagnosis. A study involving more positive specimens from all influenza A virus epidemic subtypes is required to fully assess the performance of the assay. 
 Title: ) A Multiplex Asymmetric Reverse Transcription-PCR Assay Combined With an Electrochemical DNA Sensor for Simultaneously Detecting and Subtyping Influenza A Multiplex Asymmetric Reverse Transcription-PCR Assay Combined With an Electrochemical DNA Sensor for Simultaneously Detecting and Subtyping Influenza A Viruses
Output: True
Paragraph: lung transplantation and thought to represent chronic rejection. Increased expression of Pentraxin 3 (PTX3), an acute phase protein, was associated with worse outcome in lung transplant patients. To determine the role of recipient PTX3 in development of chronic rejection, we used a minor alloantigen-mismatched murine orthotopic single lung transplant model. Male C57BL/10 mice were used as donors. Male PTX3 knockout (KO) mice and their wild type (WT) littermates on 129/SvEv/C57BL6/J background were used as recipients. In KO recipients, 7/13 grafted lungs were consolidated without volume recovery on CT scan, while only 2/9 WT mice showed similar graft consolidation. For grafts where lung volume could be reliably analyzed by CT scan, the lung volume recovery was significantly reduced in KO mice compared to WT. Interstitial inflammation, parenchymal fibrosis and bronchiolitis obliterans scores were significantly higher in KO mice. Presence of myofibroblasts and lymphoid aggregation was significantly enhanced in the grafts of PTX3 KO recipients. Recipient PTX3 deficiency enhanced chronic rejection-like lesions by promoting a fibrotic process in the airways and lung parenchyma. The underlying mechanisms and potential protective role of exogenous PTX3 as a therapy should be further explored. 
 Title: Pentraxin 3 deficiency enhances features of chronic rejection in a mouse orthotopic lung transplantation model
Output: True
Paragraph: Human erythrocytes infected with the malarialparasite Plasmodium falciparum contain flattened membrane lamellae. It has been suggested that the lamellae may be involved in the sorting of malarial proteins to the cytoplasm and the cell membrane of the host erythrocyte. We have previously shown that the lamellae accumulate sphingolipids by virtue of their lipid composition in a manner similar to the trans-Golgi and the trans-Golgi network in mammalian cells. In this paper, we show by immunofluorescence microscopy that a monoclonal antibody to the lamellae labeled a perinuclear organetle that colocalized with WGA and the mannose-6-phosphate receptor in cultured mammalian cells. Immunoelectron microscopy experiments revealed that LWLI labels cisternae of the trans-face and the trans-Golgi network. Western blot analysis of subcellular fractions using LWLI detected a 170 kD protein which is associated with the luminal side of Golgi membranes of rat liver and is conserved in all cell lines studied. Our results indicate that (i) the 170 kD protein is a novel marker of the mammalian trans-Golgi and the trans-Golgi network and (ii) in addition to similarities in their morphological and lipid characteristics, the lamellae induced by P. falciparum in erythrocytes share proteinaceous determinants with the Golgi apparatus of mammalian cells. 
 Title: Recognition of a 170 kD protein in mammalian Golgi complexes by an antibody against malarial intraerythrocytic lamellae
Output: False
Paragraph: The objective of this study was to obtain insight into the adverse health effects of airborne particulate matter (PM) collected from live bird markets and to determine whether biological material in PM accounts for immune-related inflammatory response. Mice were exposed to a single or repeated dose of PM, after which the expression of toll-like receptors (TLRs), cytokines, and chemokines in the lungs of infected mice were examined by enzyme-linked immunosorbent assay and histopathological analysis. Results after single and repeated PM stimulation with PM + + 2.5 , PM − 2.5 , PM 10 , and PM − 10 indicated that TLR2 and TLR4 played a dominant role in the inflammatory responses of the lung. Further analysis demonstrated that the expression levels of IL-1β, TNF-α, IFN-γ, IL-8, IP-10, and MCP-1 increased significantly, which could eventually contribute to lung injury. Moreover, biological components in PM were critical in mediating immune-related inflammatory responses and should therefore not be overlooked. 
 Title: Immunity-Related Protein Expression and Pathological Lung Damage in Mice Poststimulation with Ambient Particulate Matter from Live Bird Markets
Output: True
Paragraph: Feline infectious peritonitis (FIP) is the most frequent lethal infectious disease in cats. However, understanding of FIP pathogenesis is still incomplete. Mutations in the ORF 3c/ORF 7b genes are proposed to play a role in the occurrence of the fatal FIPV biotype. Here, we investigated 282 tissue specimens from 28 cats that succumbed to FIP. Within one cat, viral sequences from different organs were similar or identical, whereas greater discrepancies were found comparing sequences from various cats. Eleven of the cats exhibited deletions in the 3c gene, resulting in truncated amino acid sequences. The 7b gene was affected by deletions only in one cat. In three of the FIP cats, coronavirus isolates with both intact 3c genes as well as 7b genes of full length could also be detected. Thus, deletions or stop codons in the 3c sequence seem to be a frequent but not compelling feature of FIPVs. 
 Title: Mutations in the 3c and 7b genes of feline coronavirus in spontaneously affected FIP cats
Output: False
Paragraph: Objectives. Over time, quarantine has become a classic public health intervention and has been used repeatedly when newly emerging infectious diseases have threatened to spread throughout a population. Here, we weigh the economic costs and benefits associated with implementing widespread quarantine in Toronto during the SARS outbreaks of 2003. Methods. We compared the costs of two outbreak scenarios: in Scenario A, SARS is able to transmit itself throughout a population without any significant public health interventions. In Scenario B, quarantine is implemented early on in an attempt to contain the virus. By evaluating these situations, we can investigate whether or not the use of quarantine is justified by being either cost-saving, life saving, or both. Results. Our results indicate that quarantine is effective in containing newly emerging infectious diseases, and also cost saving when compared to not implementing a widespread containment mechanism. Conclusions. This paper illustrates that it is not only in our humanitarian interest for public health and healthcare officials to remain aggressive in their response to newly emerging infections, but also in our collective economic interest. Despite somewhat daunting initial costs, quarantine saves both lives and money. 
 Title: c Ann Arbor Veterans Affairs Hospital
Output: True
Paragraph: Infection with coronavirus results in the accumulation of genomic-sized mRNA and six to eight subgenomic mRNAs that make up a 3Ј coterminal nested-set structure. Genome-length negative-strand RNA and subgenomic-length negative-strand RNAs, each of which corresponds to each of the subgenomic mRNAs, also accumulate in infected cells. The present study examined whether the genome-length negative-strand RNA serves as a template for subgenomic mRNA synthesis. Genomelength replicative intermediate (RI) RNA was purified by two-dimensional gel electrophoresis of intracellular RNAs from cells infected with mouse hepatitis virus. RNase A treatment of the purified genome-length RI resulted in the production of the genome-length replicative form RNA, indicating that the genome-length RI included genome-length template RNA. RNase protection assays using the purified genome-length RI and two probes, which corresponded to the 5Ј 300-nt region of mRNA 6 and to the same region of mRNA 7, showed the presence of nascent leader sequence-containing subgenomic mRNAs in the genome-length RI. These data demonstrated that the genome-length negative-strand RNA serves as a template for subgenomic mRNA synthesis. 
 Title: RAPID COMMUNICATION Nascent Synthesis of Leader Sequence-Containing Subgenomic mRNAs in Coronavirus Genome-Length Replicative Intermediate RNA
Output: True
Paragraph: h i g h l i g h t s • A modified community network model with heterogeneity among communities is proposed. • A mathematical epidemic model for each community is presented based on this network. • Study the effect of the location of initial infection node on epidemic spreading. • Study the impact of the heterogeneity among communities on epidemic spreading. a b s t r a c t A large number of real world networks exhibit community structure, and different communities may often possess heterogeneity. In this paper, considering the heterogeneity among communities, we construct a new community network model in which the communities show significant differences in average degree. Based on this heterogeneous community network, we propose a novel mathematical epidemic model for each community and study the epidemic dynamics in this network model. We find that the location of the initial infection node only affects the spreading velocity and barely influences the epidemic prevalence. And the epidemic threshold of entire network decreases with the increase of heterogeneity among communities. Moreover, the epidemic prevalence increases with the increase of heterogeneity around the epidemic threshold, while the converse situation holds when the infection rate is much greater than the epidemic threshold. (B. Song). example, the severe acute respiratory syndrome (SARS) in 2003, the H1N1 influenza A virus in 2009, the H7N9 avian influenza virus in 2013, the Ebola virus in 2014 and the Middle East respiratory syndrome coronavirus (MERS-CoV) in 2015. The problem of epidemic spreading has gained great attention over the years and people want to predict the epidemic spread trend and take effective public health measures with limited vaccine supply. As the topology properties of networks have a profound impact on the dynamics of epidemic spreading, it is necessary to consider the effect of community structure on epidemic spreading. So far, a lot of results on epidemic dynamics in community networks have been obtained [12, 14, 16, 29, 30] . To simulate the real network, many different kinds of community network models were constructed based on classical networks, and some individual behavior characteristics in real networks (such as random walk, long-range jump and awareness) were also taken into account. Liu and Hu studied the SIS (susceptible-infected-susceptible) dynamics on a random community network model with probability p (q) of intra-(inter-) 
 Title: Modeling and analysis of epidemic spreading on community networks with heterogeneity
Output: True
Paragraph: Aims: We undertook this study to define the incidence of toxigenic Clostridium difficile in our hospital and to characterise the isolates. Methods: All unformed stool was tested for the presence of Toxin A (TcdA) and Toxin B (TcdB), and cultured for C. difficile. Culture filtrates were also tested for TcdA and TcdB. Detection of tcdA and tcdB genes was carried out for A 2 B + strains by polymerase chain reaction (PCR).The minimum inhibitory concentrations (MICs) of metronidazole, vancomycin and clindamycin for all isolates were tested using the Etest. PCR ribotyping was carried out on all isolates. Results: The incidence of Clostridium difficile associated disease (CDAD) was 3.2 cases per 1000 admissions or discharges and 53.8 cases per 100 000 patient days. Most cases occurred in renal and haematology patients. CDAD was more common in patients aged over 50 years and of male gender. The Indian population was under-represented. Fourteen (11.8%) isolates were A 2 B + . All strains were susceptible to metronidazole but one strain showed intermediate resistance to vancomycin. Only 12.8% of the isolates were susceptible to clindamycin. Thirty-five isolates had PCR ribotype A, of which 29 (83%) had a clindamycin MIC .256 mg/L. Thirty-three had PCR ribotype B, of which only one (3%) had a clindamycin MIC .256 mg/L. The 14 A 2 B + strains were all PCR ribotype C, and had a range of MICs for clindamycin from 2 to .256 mg/L. Conclusions: The incidence of CDAD in our hospital is relatively low. Isolates remain susceptible to metronidazole and vancomycin. 
 Title: Epidemiology of Clostridium difficile infection in a large teaching hospital in Singapore
Output: False
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. between virus names and species names would be to change the current names of virus species into nonlatinized binomial names. Such a system, which has been advocated by plant virologists for many years, consists in replacing the word 'virus' appearing at the end of the existing species name by the genus name which also ends in '-virus'. Measles virus then becomes Measles morbillivirus, Hepatitis A virus becomes Hepatitis A hepatovirus, and Tobacco mosaic virus becomes Tobacco mosaic tobamovirus. The advantage of such a system, which could be implemented without problems for about 98% of all virus species names, is that inclusion of the genus name in the species name provides additional information about the properties of the virus. A changeover to binomial species names would not affect the common names of viruses in English or other languages since names such as measles virus or 'virus de la rougeole' would remain the same. The ICTV is currently debating the possibility of introducing binomial species names and some decision is likely to be made in the near future. Given that the common names of viruses are used repeatedly in scientific texts there is a need for abbreviating them and the ICTV has published several lists of recommended acronyms for virus names. Since the names of virus species are used only very seldom in publications, there is no need to abbreviate them. If binomial names of virus species were introduced in the future, the abbreviations of common names of viruses will of course not be affected. 
 Title: Viruses and Bioterrorism
Output: True
Paragraph: The relative motion of moving objects is an essential research topic in geographical information science (GIScience), which supports the innovation of geodatabases, spatial indexing, and geospatial services. This analysis is very popular in the domains of urban governance, transportation engineering, logistics and geospatial information services for individuals or industrials. Importantly, data models of moving objects are one of the most crucial approaches to support the analysis for dynamic relative motion between moving objects, even in the age of big data and cloud computing. Traditional geographic information systems (GIS) usually organize moving objects as point objects in absolute coordinated space. The derivation of relative motions among moving objects is not efficient because of the additional geo-computation of transformation between absolute space and relative space. Therefore, current GISs require an innovative approach to directly store, analyze and interpret the relative relationships of moving objects to support their efficient analysis. This paper proposes a relative space-based GIS data model of moving objects (RSMO) to construct, operate and analyze moving objects' relationships and introduces two algorithms (relationship querying and relative relationship dynamic pattern matching) to derive and analyze the dynamic relationships of moving objects. Three scenarios (epidemic spreading, tracker finding, and motion-trend derivation of nearby crowds) are implemented to demonstrate the feasibility of the proposed model. The experimental results indicates the execution times of the proposed model are approximately 5-50% those of the absolute GIS method for the same function of these three scenarios. It's better computational performance of the proposed model when analyzing the relative relationships of moving objects than the absolute methods in a famous commercial GIS software based on this experimental results. The proposed approach fills the gap of traditional GIS and shows promise for relative space-based geo-computation, analysis and service. 
 Title: ISPRS Journal of Photogrammetry and Remote Sensing Relative space-based GIS data model to analyze the group dynamics of moving objects
Output: True