niryuu/sni-each-converted huggingface dataset:
Paragraph: In terms of its highly pathogenic nature, there remains a significant need to further define the immune pathology of SARScoronavirus (SARS-CoV) infection, as well as identify correlates of immunity to help develop vaccines for severe coronaviral infections. Here we use a SARS-CoV infection-reinfection ferret model and a functional genomics approach to gain insight into SARS immunopathogenesis and to identify correlates of immune protection during SARS-CoV-challenge in ferrets previously infected with SARS-CoV or immunized with a SARS virus vaccine. We identified gene expression signatures in the lungs of ferrets associated with primary immune responses to SARS-CoV infection and in ferrets that received an identical second inoculum. Acute SARS-CoV infection prompted coordinated innate immune responses that were dominated by antiviral IFN response gene (IRG) expression. Reinfected ferrets, however, lacked the integrated expression of IRGs that was prevalent during acute infection. The expression of specific IRGs was also absent upon challenge in ferrets immunized with an inactivated, Al(OH) 3 -adjuvanted whole virus SARS vaccine candidate that protected them against SARS-CoV infection in the lungs. Lack of IFN-mediated immune enhancement in infected ferrets that were previously inoculated with, or vaccinated against, SARS-CoV revealed 9 IRG correlates of protective immunity. This data provides insight into the molecular pathogenesis of SARS-CoV and SARS-like-CoV infections and is an important resource for the development of CoV antiviral therapeutics and vaccines. Citation: Cameron MJ, Kelvin AA, Leon AJ, Cameron CM, Ran L, et al. (2012) Lack of Innate Interferon Responses during SARS Coronavirus Infection in a Vaccination and Reinfection Ferret Model. PLoS ONE 7(9): e45842. 
 Title: Lack of Innate Interferon Responses during SARS Coronavirus Infection in a Vaccination and Reinfection Ferret Model
Output: False
Paragraph: Emerging and re-emerging infectious diseases are an expanding global threat to public health, security, and economies. Increasing populations, urbanization, deforestation, climate change, anti-vaccination movements, war, and international travel are some of the contributing factors to this trend. The recent Ebola, MERS-CoV, and Zika outbreaks demonstrated we are insufficiently prepared to respond with proven safe and effective countermeasures (i.e., vaccines and therapeutics). The State University of New York Upstate Medical University and the Trudeau Institute convened a summit of key opinion and thought leaders in the life sciences and biomedical research and development enterprises to explore global biopreparedness challenges, take an inventory of existing capabilities and capacities related to preparation and response, assess current ''gaps," and prospect what could be done to improve our position. Herein we describe the summit proceedings, ''Translational Immunology Supporting Biomedical Countermeasure Development for Emerging Vector-borne Viral Diseases," held October 2-3, 2018, at the Trudeau Institute in Saranac Lake, NY. 
 Title: Summit proceedings: Biomedical countermeasure development for emerging vector-borne viral diseases
Output: False
Paragraph: Common marmoset (Callithrix jacchus) is emerging as a clinically relevant nonhuman primate model for various diseases, but is hindered by the availability of marmoset cell lines, which are critical for understanding the disease pathogenesis and drug/toxicological screening prior to animal testing. Here we describe the generation of immortalized marmoset hepatic progenitor cells (MHPCs) by lentivirus-mediated transfer of the simian virus 40 large T antigen gene in fetal liver polygonal cells. MHPCs proliferate indefinitely in vitro without chromosomal alteration and telomere shortening. These cells possess hepatic progenitor cell-specific gene expression profiles with potential to differentiate into both hepatocytic and cholangiocytic lineages in vitro and in vivo and also can be genetically modified. Importantly, injected MHPCs repopulated the injured liver of fumarylacetoacetate hydrolase (Fah)-deficient mice with hepatocyte-like cells. MHPCs also engraft as cholangiocytes into bile ducts of 3,5-diethoxycarbonyl-1,4dihydrocollidine (DDC)-induced bile ductular injured mice. MHPCs provide a tool to enable efficient derivation and genetic modification of both hepatocytes and cholangiocytes for use in disease modeling, tissue engineering, and drug screening. 
 Title: Immortalized common marmoset (Callithrix jacchus) hepatic progenitor cells possess bipotentiality in vitro and in vivo
Output: True
Paragraph: Among the various respiratory viruses infecting human beings, coronaviruses are important pathogens, which usually infect the upper respiratory tract, where they are mainly associated with common colds. However, in more vulnerable populations, such as newborns, infants, the elderly and immunecompromised individuals, these opportunistic pathogens can also affect the lower respiratory tract, leading to pneumonia, exacerbations of asthma, and various types of respiratory distress syndrome. The respiratory involvement of human coronaviruses has been clearly established since the 1960s. Nevertheless, for almost three decades now, data reported in the scientific literature has also demonstrated that, like it was described for other human viruses, coronaviruses have neuroinvasive capacities since they can spread from the respiratory tract to the central nervous system (CNS). Once there, infection of CNS cells (neurotropism) could lead to human health problems, such as encephalitis and long-term neurological diseases. Neuroinvasive coronaviruses could damage the CNS as a result of misdirected host immune responses that could be associated with autoimmunity in susceptible individuals (virusinduced neuroimmunopathology) and/or viral replication, which directly induces damage to CNS cells (virus-induced neuropathology). Given all these properties, it has been suggested that these opportunistic human respiratory pathogens could be associated with the triggering or the exacerbation of neurologic diseases for which the etiology remains poorly understood. Herein, we present host and viral factors that participate in the regulation of the possible pathogenic processes associated with CNS infection by human coronaviruses and we try to decipher the intricate interplay between virus and host target cells in order to characterize their role in the virus life cycle as well as in the capacity of the cell to respond to viral invasion. 
 Title: Human coronaviruses: Viral and cellular factors involved in neuroinvasiveness and neuropathogenesis
Output: True
Paragraph: 【摘要】 背景与目的 自身抗体作为新的肿瘤标志物在肺癌的早期诊断和预后评价中可能发挥重要作用，本 研究利用多肽芯片检测非小细胞肺癌患者血清中表皮生长因子受体(epidermal growth factor receptor, EGFR)的自身抗 体，并筛选自身抗体识别的抗原表位。方法 使用Intavis公司ASPSL多肽芯片合成仪合成EGFR多肽芯片，利用多肽芯 片检测非小细胞肺癌患者血清中EGFR自身抗体，并筛选自身抗体识别的抗原表位。结果 使用EGFR多肽芯片检测 了20例非小细胞肺癌患者，结果有6例阳性，阳性率为30%，在该6例阳性患者中发现了9个高频位点，并且有8个高 频位点集中在EGFR胞外段的第III和第IV结构域。结论 本研究为我们进一步研究EGFR和EGFR自身抗体的功能提供 了新的线索。 【关键词】 肺肿瘤；EGFR；多肽芯片；自身抗体 【中图分类号】 R734.2 【Abstract】 Background and objective Autoantibodies as new tumor markers may play an important role in the early diagnosis and evaluating the prognosis of lung cancer. In this study, we detect epidermal growth factor receptor (EGFR) autoantibodies using peptide array and screen the epitopes which are recognized by EGFR autoantibodies. Methods Peptide array covering the extracellular domain of EGFR protein was synthesized by a synthesizer (ASPSL) made by Intavis company. EGFR autoantibodies in the serums of non-small cell lung cancer patients was detected using peptide array. Results Six of 20 patients were found to have EGFR autoantibodis. The positive rate is 30%. Nine high frequency spots were found in the 6 positive patients and 8 high frequency spots clustered in the III and IV domains. Conclusion These findings will offer new clues for the futher studies of EGFR and EGFR autoantibodies. 
 Title: 应用多肽芯片研究非小细胞肺癌患者血清中 的EGFR自身抗体 李元 岳文涛 王玥 张丽娜 顾勐 许绍发 Detecting EGFR Autoantibodies in Serums of NSCLC Patients with Peptide Array
Output: True
Paragraph: Background: The elevated risk of occupational infection such as tuberculosis among health workers in many countries raises the question of whether the quality of occupational health and safety (OHS) and infection prevention and control (IPC) can be improved by auditing. The objectives of this study were to measure (1) audited compliance of primary health-care facilities in South Africa with national standards for OHS and IPC, (2) change in compliance at reaudit three years after baseline, and (3) the inter-rater reliability of the audit. Methods: The study analyzed audits of 60 primary health-care facilities in the Western Cape Province of South Africa. Baseline external audits in the time period 2011e2012 were compared with follow-up internal audits in 2014e2015. Audits at 25 facilities that had both internal and external audits conducted in 2014/2015 were used to measure reliability. Results: At baseline, 25% of 60 facilities were "noncompliant" (audit score<50%), 48% "conditionally compliant" (score >50 < 80%), and only 27% "compliant" (score >80%). Overall, there was no significant improvement in compliance three years after baseline. Percentage agreement on specific items between internal and external audits ranged from 28% to 92% and kappa from -0.8 to 0.41 (poor to moderate). Conclusion: Low baseline compliance with OHSeIPC measures and lack of improvement over three years reflect the difficulties of quality improvement in these domains. Low inter-rater reliability of the audit instrument undermines the audit process. Evidence-based investment of effort is required if repeat auditing is to contribute to occupational risk reduction for health workers. 
 Title: Repeat Auditing of Primary Health-care Facilities Against Standards for Occupational Health and Infection Control: A Study of Compliance and Reliability-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/)
Output: False
Paragraph: 2 Provide a structured summary including, as applicable: background; objectives; data sources; study eligibility criteria, participants, and interventions; study appraisal and synthesis methods; results; limitations; conclusions and implications of key findings; systematic review registration number. Abstract P1 Rationale 3 Describe the rationale for the review in the context of what is already known. 
 Title: PRISMA 2009 Checklist Section/topic # Checklist item Reported on page # TITLE Title 1 Identify the report as a systematic review, meta-analysis, or both. N/A
Output: False
Paragraph: Neurocysticercosis (NC) is a serious public health problem in Taenia solium endemic areas and in some immigrants and international travelers. A key intervention in preventing NC is elimination of taeniasis by chemotherapy. Currently, two safe and effective taenicides, namely niclosamide and praziquantel, are available. Both are on WHO Essential Drug list, but are often inaccessible in T. solium endemic areas. Natural remedies, still widely used in some endemic areas, are frequently carcinogenic or highly toxic and as such should be discontinued. Chemotherapeutic intervention to control T. solium taeniasis/cysticercosis, whilst theoretically feasible, has several practical obstacles. These include poor public awareness, problems with diagnosing Taenia carriers, poor availability of taenicides where needed and low priority afforded to the control of NC. These can be overcome, respectively, by effective health education, wider use of newly developed coproantigen tests, strengthening of health services infrastructure and essential drugs distribution, and increasing the priority given to prevention of NC, as a leading cause of epilepsy in T. solium endemic areas. Information is accumulating on rational approaches to population-based short-term chemotherapeutic control measures. These are: widely available modern diagnostic tools and taenicides, treatment of any case of taeniasis, confirmed or probable, focus-oriented chemotherapy, irrespective of Taenia species implicated, improved sanitation, cooperation of veterinary and medical services, linkage with programs against epilepsy and cooperation of better educated communities. Now, it remains to take an advantage of existing tools and experience. D 
 Title: Role of chemotherapy of taeniasis in prevention of neurocysticercosis
Output: True
Paragraph: Containment of the SARS coronavirus (SCV) outbreak was accompanied by the rapid characterization of this new pathogen's genome sequence in 2003, encouraging the development of anti-SCV therapeutics using short interfering RNA (siRNA) inhibitors. A pair of siRNA duplexes identified as potent SCV inhibitors in vitro was evaluated for in vivo efficacy and safety in a rhesus macaque SARS model using intranasal administration with clinical viable delivery carrier in three dosing regimens. Observations of SCV-induced SARS-like symptoms, measurements of SCV RNA presence in the respiratory tract, microscopic inspections of lung histopathology, and immunohistochemistry sections from 21 tested macaques consistently demonstrated siRNA-mediated anti-SCV activity. The prophylactic and therapeutic efficacies resulted in relief of animals from SCV infectioninduced fever, diminished SCV in upper airway and lung alveoli, and milder acute diffuse alveoli damage (DAD). The dosages of siRNA used, 10 to 40 mg/kg, did not show any sign of siRNA-induced toxicity. These results support that a clinical investigation of this anti-SARS siRNA therapeutic agent is warranted. The study also illustrates the capability of siRNA to enable a massive reduction in development time for novel targeted therapeutic agents. We detail a representative example of large-mammal siRNA use. 
 Title: Application of siRNA Against SARS in the Rhesus Macaque Model
Output: False
Paragraph: Each problem that I solved became a rule, which served afterwards to solve other problems." -Rene Descartes the management of large-scale chemical, biological, radiological, nuclear, and explosives (CBRNE) events with mass casualties. These projects are funded by Defence Research and Development Canada, an agency within the Federal Department of National Defence, within its CBRNE Research and Technology Initiative (CRTI) preparing Canada's CBRNE response capabilities. Each project involves numerous public and private civilian partners as well as university partners, which is the category to which our team belongs. We are subcontracted by an industry client in charge of developing the software. When an adverse event escalates into a criminal investigation, it becomes very difficult to control and combine information into a manageable format. Numerous professionals representing different responder agencies, public health authorities, and others are involved, or become involved as the magnitude of an adverse event with mass casualties unfolds. In such events, chaos and uncertainty prevail; things happen very quickly, well before the first responders arrive on the scene, and last until a clearer picture of the nature and scope of the event can be formed, a command post has been set up, and a responsible action plan can be formulated and executed. The combined role of the first-responder teams is to preserve life, property, and equipment, while preventing the damage from spreading, providing triage to casualties on Usability in Government Systems. 
 Title: Emergency Response in Simulated Terrorist Attacks: Usability Lessons Learned 7
Output: False
Paragraph: The location of autocrine interactions between the v-sis protein and PDGF receptors remains uncertain and controversial. To examine whether receptor-ligand interactions can occur intracellularly, we have constructed fusion proteins that anchor v-sis to specific intracellular membranes. Fusion of a cis-Golgi retention signal from a coronavirus E1 glycoprotein to v-sis protein completely abolished its transforming ability when transfected into NIH3T3 cells. Fusion proteins incorporating mutations in this retention signal were not retained within the Golgi complex but instead were transported to the cell surface, resulting in efficient transformation. All chimeric proteins were shown to dimerize properly. Derivatives of some of these constructs were also constructed bearing the cytoplasmic tail from the glycoprotein of vesicular stomatitis virus (VSV-G). These constructs allowed examination of subcellular localization by double-label immunofluorescence, using antibodies that distinguish between the extraceUular PDGF-related domain and the VSV-G cytoplasmic tail. Colocalization of sis-E1-G with Golgi markers confirmed its targeting to the early Golgi complex. The sis-E1 constructs, targeted to the early Golgi complex, exhibited no proteo-lyric processing whereas the mutant forms of sis-E1 exhibited normal proteolytic processing. Treatment with suramin, a polyanionic compound that disrupts ligand/receptor interactions at the cell surface, was able to revert the transformed phenotype induced by the mutant sis-E1 constructs described here. Our results demonstrate that autocrine interactions between the v-sis oncoprotein and PDGF receptors within the early Golgi complex do not result in functional signal transduction. Another v-sis fusion protein was constructed by attaching the transmembrane domain and COOHterminus of TGN38, a protein that localizes to the trans-Golgi network (TGN). This construct was primarily retained intracellularly, although some of the fusion protein reached the surface. Deletion of the COOH-terminal region of the TGN38 retention signal abrogated the TGN-localization, as evidenced by very prominent cell surface localization, and resulted in increased transforming activity. The behavior of the sis-TGN38 derivatives is discussed within the context of the properties of TGN38 itself, which is known to recycle from the cell surface to the TGN. 
 Title: The v-sis Oncoprotein Loses Transforming Activity When Targeted to the Early Golgi Complex
Output: False
Paragraph: Zika virus (ZIKV) infection can be the cause of congenital malformations, including microcephaly in infants and can cause other disorders such as Guillain-Barré syndrome, meningoencephalitis, and myelitis, which can also occur in some infected adults. However, at this time, there is no drug approved to treat ZIKV infection. Drug repurposing is the promptest way to obtain an effective drug during a global public health emergency such as the spread of Zika virus. In this study, we report a US Food and Drug Admistration-approved drug that is safe for pediatric use. Nitazoxanide and its bioactive metabolite, tizoxanide, have anti-ZIKV potential in vitro, and we identified that they exerts antiviral effect possibly by targeting the viral postattachment step. 
 Title: Pediatric Drug Nitazoxanide: A Potential Choice for Control of Zika
Output: False
Paragraph: There is a dire need for personal protective equipment (PPE) within healthcare settings during the 33 COVID-19 pandemic. In particular, single use disposable N95 face masks have been limited in 34 supply. We have developed an Injection Molded Autoclavable, Scalable, Conformable (iMASC) 35 system for aerosol-based protection. The iMASC system was designed as a reusable liquid 36 silicone rubber mask with disposable N95 filter cartridges that can fit most face sizes and shapes. 37 This system reduced the amount of N95 filter while preserving breathability and fit. Using finite 38 element analysis, we demonstrated mask deformation and reaction forces from facial scans of 39 twenty different wearers. In addition, we validated these findings by successful fit testing in 40 twenty participants in a prospective clinical trial. The iMASC system has the potential to protect 41 our healthcare workers with a reusable N95-comparable face mask that is rapidly scalable. 42 All rights reserved. No reuse allowed without permission. author/funder, who has granted medRxiv a license to display the preprint in perpetuity. 
 Title: Injection Molded Autoclavable, Scalable, Conformable (iMASC) system for 2 aerosol-based protection 3 4
Output: False
Paragraph: The non-structural proteins (nsp or replicase proteins) of coronaviruses are relatively conserved and can be effective targets for drugs. Few studies have been conducted into the function of the severe acute respiratory syndrome coronavirus (SARS-CoV) nsp5. In this study, bioinformatics methods were employed to predict the secondary structure and construct 3-D models of the SARS-CoV GD strain nsp5. Sequencing and sequential comparison was performed to analyze the mutation trend of the polymerase nsp5 gene during the epidemic process using a nucleotide-nucleotide basic local alignment search tool (BLASTN) and a protein-protein basic local alignment search tool (BLASTP). The results indicated that the nsp5 gene was steady during the epidemic process and the protein was homologous with other coronavirus nsp5 proteins. The protein encoded by the nsp5 gene was expressed in COS-7 cells and analyzed by sodium dodecylsulfate-polyacrylamide gel electrophoresis (SDS-PAGE). This study provided the foundation for further exploration of the protein's biological function, and contributed to the search for anti-SARS-CoV drugs. 
 Title: Sequence Analysis and Structural Prediction of the Severe Acute Respiratory Syndrome Coronavirus nsp5
Output: True
Paragraph: Background: Coronaviruses (CoVs) can be classified into alphacoronavirus (group 1), betacoronavirus (group 2), and gammacoronavirus (group 3) based on diversity of the protein sequences. Their 3C-like protease (3CL pro ), which catalyzes the proteolytic processing of the polyproteins for viral replication, is a potential target for anti-coronaviral infection. Methodology/Principal Findings: Here, we profiled the substrate specificities of 3CL pro from human CoV NL63 (group 1), human CoV OC43 (group 2a), severe acute respiratory syndrome coronavirus (SARS-CoV) (group 2b) and infectious bronchitis virus (IBV) (group 3), by measuring their activity against a substrate library of 1968 of variants with single substitutions at P5 to P3' positions. The results were correlated with structural properties like side chain volume, hydrophobicity, and secondary structure propensities of substituting residues. All 3CL pro prefer Gln at P1 position, Leu at P2 position, basic residues at P3 position, small hydrophobic residues at P4 position, and small residues at P1' and P2' positions. Despite 3CL pro from different groups of CoVs share many similarities in substrate specificities, differences in substrate specificities were observed at P4 positions, with IBV 3CL pro prefers P4-Pro and SARS-CoV 3CL pro prefers P4-Val. By combining the most favorable residues at P3 to P5 positions, we identified super-active substrate sequences 'VARLQQSGF' that can be cleaved efficiently by all 3CL pro with relative activity of 1.7 to 3.2, and 'VPRLQQSGF' that can be cleaved specifically by IBV 3CL pro with relative activity of 4.3. Conclusions/Significance: The comprehensive substrate specificities of 3CL pro from each of the group 1, 2a, 2b, and 3 CoVs have been profiled in this study, which may provide insights into a rational design of broad-spectrum peptidomimetic inhibitors targeting the proteases. 
 Title: Profiling of Substrate Specificities of 3C-Like Proteases from Group 1, 2a, 2b, and 3 Coronaviruses
Output: True
Paragraph: IL-35 is the newest member of IL-12 family. A dimeric protein consisting of two separate subunits has manifested suppressive actions on immune system, which is counterproductive in the context of cancers. Various reports have confirmed its inhibitory role on immune system which is carried out via formation of IL-35-producing regulatory T cells (iTr35), increased Treg development and suppressive Th17 cells growth. Although last decade has seen a great deal of scientific interest on this subject, the exact role, precise signal transduction and elaborative functions of IL-35 in tumor microenvironment (TME) remained elusive. Search for anti-IL-35 therapies have exhibited limited success in animal models. Contrarily, few studies have denied the idea that IL-35 plays a role in cancer. The purpose of this review is to analyze the reported scientific data on continuous symphony of IL-35 in cancers since the inception of former. 
 Title: Interleukin-35 as an Emerging Player in Tumor Microenvironment
Output: True
Paragraph: Despite flaviviruses remaining the leading cause of systemic human infections worldwide, ocular manifestations of these mosquito-transmitted viruses are considered relatively uncommon in part due to under-reporting. However, recent outbreaks of Zika virus (ZIKV) implicated in causing multiple ocular abnormalities, such as conjunctivitis, retinal hemorrhages, chorioretinal atrophy, posterior uveitis, optic neuritis, and maculopathies, has rejuvenated a significant interest in understanding the pathogenesis of flaviviruses, including ZIKV, in the eye. In this review, first, we summarize the current knowledge of the major flaviviruses (Dengue, West Nile, Yellow Fever, and Japanese Encephalitis) reported to cause ocular manifestations in humans with emphasis on recent ZIKV outbreaks. Second, being an immune privilege organ, the eye is protected from systemic infections by the presence of blood-retinal barriers (BRB). Hence, we discuss how flaviviruses modulate retinal innate response and breach the protective BRB to cause ocular or retinal pathology. Finally, we describe recently identified infection signatures of ZIKV and discuss whether these system biology-predicted genes or signaling pathways (e.g., cellular metabolism) could contribute to the pathogenesis of ocular manifestations and assist in the development of ocular antiviral therapies against ZIKV and other flaviviruses. 
 Title: Ocular Manifestations of Emerging Flaviviruses and the Blood-Retinal Barrier
Output: False
Paragraph: Nipah Virus (NiV) came into limelight recently due to an outbreak in Kerala, India. NiV causes severe disease and death in people with over 75% case fatality rate. It is a public health concern and has the potential to become a global pandemic. Lack of treatment has forced the containment methods to be restricted to isolation and surveillance. WHO's 'R&D Blueprint list of priority diseases' (2018) indicates that there is an urgent need for accelerated research & development for addressing NiV. In the quest for druglike NiV inhibitors (NVIs) a thorough literature search followed by systematic data curation was conducted. Rigorous data analysis was done with curated NVIs for prioritizing druglike compounds. For the same, more than 1800 descriptors of NVIs were computed and comparative analysis was performed with the FDA approved small molecules and antivirals. These compounds were further evaluated through PAINS filter to study their toxicity profile. Simultaneously, compounds were also prioritized based on the robustness of the assays through which they were identified. Our efforts lead to the creation of a well-curated structured knowledgebase of 182 NVIs with 98 small molecule inhibitors. The reported IC50/EC50 values for some of these inhibitors are in the nanomolar range -as low as 0.47 nM. In order to prioritize these inhibitors, we performed several tests and applied filters to identify drug-like non-toxic compounds. Of 98, a few compounds passed DruLito & PAINS filters exhibiting drug-like properties and were also prioritized in an independent screen based only the assay robustness. The NVIs have diverse structural features and offer a wide spectrum of ways in which they can be developed further as druglike molecules. We report a knowledgebase for furthering the development of NVIs. The platform has a diverse set of 98 NVIs of which a few have been prioritized based on a combined evidence strategy. The platform has the provision to submit new inhibitors as and when reported by the community for further enhancement of NiV inhibitor landscape. 
 Title: A Combined Evidence Approach to Prioritize Nipah Virus Inhibitors
Output: False
Paragraph: Ehrlichia chaffeensis is an obligatory intracellular bacterium that causes a potentially fatal emerging zoonosis, human monocytic ehrlichiosis. E. chaffeensis has a limited capacity for biosynthesis and metabolism and thus depends mostly on host-synthesized nutrients for growth. Although the host cell cytoplasm is rich with these nutrients, as E. chaffeensis is confined within the early endosome-like membrane-bound compartment, only host nutrients that enter the compartment can be used by this bacterium. How this occurs is unknown. We found that ehrlichial replication depended on autophagy induction involving class III phosphatidylinositol 3-kinase (PtdIns3K) activity, BECN1 (Beclin 1), and ATG5 (autophagy-related 5). Ehrlichia acquired host cell preincorporated amino acids in a class III PtdIns3Kdependent manner and ehrlichial growth was enhanced by treatment with rapamycin, an autophagy inducer. Moreover, ATG5 and RAB5A/B/C were routed to ehrlichial inclusions. RAB5A/B/C siRNA knockdown, or overexpression of a RAB5-specific GTPase-activating protein or dominant-negative RAB5A inhibited ehrlichial infection, indicating the critical role of GTP-bound RAB5 during infection. Both native and ectopically expressed ehrlichial type IV secretion effector protein, Etf-1, bound RAB5 and the autophagy-initiating class III PtdIns3K complex, PIK3C3/VPS34, and BECN1, and homed to ehrlichial inclusions. Ectopically expressed Etf-1 activated class III PtdIns3K as in E. chaffeensis infection and induced autophagosome formation, cleared an aggregation-prone mutant huntingtin protein in a class III PtdIns3K-dependent manner, and enhanced ehrlichial proliferation. These data support the notion that E. chaffeensis secretes Etf-1 to induce autophagy to repurpose the host cytoplasm and capture nutrients for its growth through RAB5 and class III PtdIns3K, while avoiding autolysosomal killing. 
 Title: Ehrlichia secretes Etf-1 to induce autophagy and capture nutrients for its growth through RAB5 and class III phosphatidylinositol 3-kinase
Output: False
Paragraph: We isolated a replication-competent, neurotropic retrovirus (FrC6 virus) and its molecular clone A8 from the NB-tropic Friend murine leukemia virus (FLV) complex. For detection and characterization of the FrC6 and A8 viruses, monoclonal antibodies (MAbs) against the FLV complex were established. Thirty MAbs, each of which reacted with the FLV-producing cell line, were tested for potential neutralizing activities; only two MAbs inhibited the proliferation of the A8 virus. These two MAbs were ineffective or had very weak neutralizing activities toward the non-neurotropic FLV strain clone 57 virus. Further characterization of MAbs by immunoprecipitation revealed that 4 MAbs recognized the envelope protein of the A8 virus. Two of these 4 MAbs recognized the surface glycoprotein gp70, requiring the conformational epitope of the virus for this recognition, while the other two MAbs, which were reactive with the transmembrane protein pl5E, were conformationindependent. Both of the MAbs against gp70 distinguished neuropathogenic and non-neuropathogenic viruses to some extent, through neutralizing activity or binding activity detected by immunoprecipitation, whereas the two MAbs against pl5E reacted with the viruses in a similar manner. Furthermore, one of the MAbs distinguished the viral antigen in the wall of the vacuolation that composes the spongiotic lesion induced by FrC6 viral infection of the brain. The Friend virus complex, composed of the replication-competent Friend murine leukemia virus (FLV) and the replication-defective spleen focus-forming virus * Corresponding author. Fax: +81 (426) 91 9315. 0168-1702/95/$09.50 
 Title: Characterization of monoclonal antibodies recognizing neurotropic Friend murine leukemia virus
Output: False
Paragraph: We report the dynamic change process of target genes by RT-PCR testing of SARS-Cov-2 during the course of a COVID-19 patient: from successive negative results to successive single positive nucleocapsid gene, to two positive target genes (orf1ab and nucleocapsid) by RT-PCR testing of SARS-Cov-2, and describe the diagnosis, clinical course, and management of the case. In this case, negative results of RT-PCR testing was not excluded to diagnose a suspected COVID-19 patient, clinical signs and symptoms, other laboratory findings, and chest CT images should be taken into account for the absence of enough positive evidence. This case highlights the importance of successive sampling and testing SARS-Cov-2 by RT-PCR as well as the increased value of single positive target gene from pending to positive in two specimens to diagnose laboratory-confirmed COVID-19. 
 Title: Dynamic change process of target genes by RT-PCR testing of SARS-Cov-2 during the course of a Coronavirus Disease 2019 patient
Output: False
Paragraph: Anibamine, a novel pyridine quaternary alkaloid recently isolated from Aniba sp., has been found to effectively bind to the chemokine receptor CCR5 with an IC 50 at 1 μM in competition with 125 I-gp120, an HIV viral envelope protein binding to CCR5 with high affinity. Since CCR5, a G-proteincoupled receptor, is an essential co-receptor for the human immunodeficiency virus type I (HIV-1) entry to host cells, a CCR5 antagonist that inhibits the cellular entry of HIV-1 provides a new therapy choice for the treatment of HIV. Anibamine provides a novel structural skeleton that is remarkably different from all lead compounds previously identified as CCR5 antagonists. Here, we report comparative docking studies of anibamine with several other known CCR5 antagonists in two CCR5 homology models built based on the crystal structures of bovine rhodopsin and human β 2 -adrenergic receptor. The binding pocket of anibamine has some common features shared with other high affinity CCR5 antagonists, suggesting that they may bind in similar binding sites and/or modes. At the same time, several unique binding features of anibamine were identified and it will likely prove beneficial in future molecular design of novel CCR5 antagonists based on the anibamine scaffold. 
 Title: A Comparative Docking Study of Anibamine as the First Natural Product CCR5 Antagonist in CCR5 Homology Models
Output: False
Paragraph: Case summary This work describes the diagnosis and successful treatment of a 2-year-old domestic cat infected with Leishmania species and presenting fever, and ulcerative and nodular skin lesions after being treated for pyodermatitis for 1 year without clinical improvement. After anamnesis the cat was submitted to a complete clinical examination. Blood was collected for determination of haematological and biochemical parameters, detection of feline leukaemia virus (FeLV), feline immunodeficiency virus (FIV), feline coronavirus (FCoV) and Leishmania amastigotes. Fine-needle aspiration puncture from the skin nodules was also performed. After definitive diagnosis the animal was treated and followed up over a 2 year period. The animal tested negative for FIV-specific antibodies, FeLV antigen and feline coronavirus RNA. Leishmania amastigotes in the skin nodules were confirmed by cytology and molecular diagnosis. Treatment was initiated with allopurinol, resulting in a slight clinical improvement. Thus, N-methyl-glucamine antimoniate was added and administered for 30 days, with complete closure of the ulcerative lesions in the hindlimbs requiring a surgical approach. Close monitoring of the patient in the following 24 months indicated that combined therapy was safe and clinical cure was achieved without further relapses or side effects. Relevance and novel information Considering the increasing number of feline leishmaniosis cases and the inconsistent results of most therapeutic protocols described in the literature, the use of new approaches, especially in refractory cases, is essential. Although the use of allopurinol and N-methyl-glucamine antimoniate is off-label in cats, in this case the combination treatment was followed by an extensive analytical monitoring, supporting their safety and effectiveness. 
 Title: Successful treatment of feline leishmaniosis using a combination of allopurinol and N-methyl- glucamine antimoniate
Output: True
Paragraph: Since late 2013, after an absence of seven years, outbreaks of porcine epidemic diarrhea virus (PEDV) infection have reemerged and swept rapidly across Japan, resulting in significant economic losses. In this study, we report the emergence, mixed infection, and genetic characterization of 15 novel field PEDV variants with large genomic deletions. The sizes of deletion varied between 582 nt (194 aa) and 648 nt (216 aa) at positions 28-714 (10-238) on the S gene (protein). Among 17 PEDV samples isolated from individual pigs, all of them contained at least two distinct genotypes with large genomic deletions, and 94.1% of them were found to consist of strains with an intact S gene. These variants were found in eight primary and nine recurrent outbreaks, and they might be associated with persistent PEDV infection in the farms. Full-length S and ORF3 genes of eight variants derived from 2 samples were characterized. This is the first report of mixed infections caused by various genotypes of PEDV and would be important for the studies of viral isolation, pathogenesis, and molecular epidemiology of the disease. 
 Title: Novel Porcine Epidemic Diarrhea Virus (PEDV) Variants with Large Deletions in the Spike (S) Gene Coexist with PEDV Strains Possessing an Intact S Gene in Domestic Pigs in Japan: A New Disease Situation
Output: False
Paragraph: Plant-made or "biofarmed" viral vaccines are some of the earliest products of the technology of plant molecular farming, and remain some of the brightest prospects for the success of this field. Proofs of principle and of efficacy exist for many candidate viral veterinary vaccines; the use of plant-made viral antigens and of monoclonal antibodies for therapy of animal and even human viral disease is also well established. This review explores some of the more prominent recent advances in the biofarming of viral vaccines and therapies, including the recent use of ZMapp for Ebolavirus infection, and explores some possible future applications of the technology. Recent candidate viral vaccines produced in plants Hepatitis B virus (HBV) vaccines are one of the blockbuster vaccine success stories of modern times: since identification of the virus in the 1960s, it took less than 
 Title: Plant-based vaccines against viruses
Output: False
Paragraph: Porcine reproductive and respiratory syndrome (PRRS) has been one of the most economically important diseases affecting swine industry worldwide and causes great economic losses each year. PRRS virus (PRRSV) replicates mainly in porcine alveolar macrophages (PAMs) and dendritic cells (DCs) and develops persistent infections, antibody-dependent enhancement (ADE), interstitial pneumonia and immunosuppression. But the molecular mechanisms of PRRSV infection still are poorly understood. Here we report on the first genome-wide host transcriptional responses to classical North American type PRRSV (N-PRRSV) strain CH 1a infection using Solexa/Illumina's digital gene expression (DGE) system, a tagbased high-throughput transcriptome sequencing method, and analyse systematically the relationship between pulmonary gene expression profiles after N-PRRSV infection and infection pathology. Our results suggest that N-PRRSV appeared to utilize multiple strategies for its replication and spread in infected pigs, including subverting host innate immune response, inducing an anti-apoptotic and anti-inflammatory state as well as developing ADE. Upregulation expression of virus-induced pro-inflammatory cytokines, chemokines, adhesion molecules and inflammatory enzymes and inflammatory cells, antibodies, complement activation were likely to result in the development of inflammatory responses during N-PRRSV infection processes. N-PRRSV-induced immunosuppression might be mediated by apoptosis of infected cells, which caused depletion of immune cells and induced an anti-inflammatory cytokine response in which they were unable to eradicate the primary infection. Our systems analysis will benefit for better understanding the molecular pathogenesis of N-PRRSV infection, developing novel antiviral therapies and identifying genetic components for swine resistance/susceptibility to PRRS. 
 Title: Understanding PRRSV Infection in Porcine Lung Based on Genome-Wide Transcriptome Response Identified by Deep Sequencing
Output: False
Paragraph: A total of 1002 patients were recruited and 892 were enrolled (110 were excluded based on pre-determined exclusion criteria). Based on the reference standard process described in the 'Methods' section, patients were assigned to four different diagnosis groups: (i) bacterial; (ii) viral; (iii) no apparent infectious disease or healthy (controls); and (iv) indeterminate. Patients diagnosed by the panel as having mixed infections (bacteria plus virus) were labeled as bacterial because they are managed similarly (e.g. treated with antibiotics) (see 'Methods', Fig. 1A ). In total, 89% of all enrolled patients were assigned a diagnosis, a rate which approaches the literature-documented limit [1-3]. The following sections provide a detailed description of patient characteristics, which includes all the patients with a final diagnosis (n=794): 765 patients included in the study cohort and 29 patients for which the serum samples were depleted during the screening phase (Fig. 1).  Patients of all ages were recruited to the study. The patients with agreed diagnosis (diagnosed patients; n=794) included more pediatric (≤18 years) than adult (>18 years) patients (445 patients [56%] vs 349 [44%]). The age distribution was relatively uniform for patients aged 20-80 years and peaked at <4 years of age for pediatric patients (Fig.  S2) . The observed age distribution for pediatric patients is consistent with that expected and represents the background distribution in the inpatient setting [4] (e.g., the emergency department [ED], pediatrics departments, and internal departments). Patients of both genders were recruited to the study. The patient population was balanced in respect to gender distribution (47% females, 53% males). 
 Title: 3. Supporting Information S3 -Cohort characteristics 3.1. Summary of the patient cohorts used in this study
Output: False
Paragraph: The formation of antibodies to interferon-beta (IFN-b), a protein-based disease-modifying agent for multiple sclerosis (MS), is a problem in clinical practice. These antibodies may neutralize the biological effects of the protein drug, potentially decreasing its therapeutic effects. By high-resolution HLA class I and II typing we identified two HLA class II alleles associated with the development of antibodies to IFN-b. In two independent continuous and binary-trait association studies, HLA-DRB1*0401 and HLA-DRB1*0408 (odds ratio: 5.15)-but not other HLA alleles-were strongly associated with the development of binding and neutralizing antibodies to IFN-b. The associated HLA-DRB1*04 alleles differ from nonassociated HLA-DRB1*04 alleles by a glycine-to-valine substitution in position 86 of the epitope-binding alpha-helix of the HLA class II molecule. The peptide-binding motif of HLA-DRB1*0401 and *0408 might promote binding and presentation of an immunogenic peptide, which may eventually break Tcell tolerance and facilitate antibody development to IFN-b. In summary, we identified genetic factors determining the immunogenicity of IFN-b, a protein-based disease-modifying agent for the treatment of MS. 
 Title: ARTICLE HLA-DRB1*0401 and HLA-DRB1*0408 Are Strongly Associated with the Development of Antibodies against Interferon-b Therapy in Multiple Sclerosis
Output: True
Paragraph: Many viruses encode antagonists to prevent interferon (IFN) induction. Infection of fibroblasts with the murine hepatitis coronavirus (MHV) and SARS-coronavirus (SARS-CoV) did not result in nuclear translocation of interferon-regulatory factor 3 (IRF3), a key transcription factor involved in IFN induction, and induction of IFN mRNA transcription. Furthermore, MHV and SARS-CoV infection could not prevent IFN induction by poly (I:C) or Sendai virus, suggesting that these CoVs do not inactivate IRF3-mediated transcription regulation, but apparently prevent detection of replicative RNA by cellular sensory molecules. Our data indicate that shielding of viral RNA to host cell sensors might be the main general mechanism for coronaviruses to prevent IFN induction. 
 Title: Group 2 coronaviruses prevent immediate early interferon induction by protection of viral RNA from host cell recognition
Output: True
Paragraph: Background. Acute bacterial sinusitis is a frequent complication of viral upper respiratory infection (URI). We describe the clinical and virologic features of URIs that remain uncomplicated and those that precede an episode of sinusitis. We hypothesize that certain viruses are more likely to lead to acute sinusitis, and we compare viruses identified at the time of diagnosis of sinusitis with those identified early in the URI. Methods. Children aged 48-96 months were followed longitudinally for 1 year. Nasal samples were obtained at surveillance visits, on Day 3-4 of the URI, and on Day 10, when sinusitis was diagnosed. Molecular diagnostic testing was performed on nasal washes for common respiratory viruses and pathogenic bacteria. A standardized score was used to quantify symptom severity. Results. We evaluated 519 URIs, and 37 illnesses in 31 patients met the criteria for sinusitis. Respiratory syncytial virus was detected more frequently in URI visits that led to sinusitis, compared to in uncomplicated URIs (10.8% vs 3.4%; P = .05). New viruses were detected in 29% of sinusitis episodes, and their pattern was different than those patterns observed at surveillance. The median number of URIs per subject per year was 1 (range 0-9) in uncomplicated URI subjects and 3 (range 1-9) in sinusitis subjects (P < .001). Conclusions. Children who developed sinusitis experienced more frequent URIs, compared to children whose URIs remained uncomplicated. When nasal samples were obtained on the day of diagnosis of acute sinusitis, nearly 30% of children had a new virus identified, suggesting that some children deemed to have sinusitis were experiencing sequential viral infections. 
 Title: Clinical Infectious Diseases Clinical and Virological Characteristics of Acute Sinusitis in Children
Output: True
Paragraph: Background: Influenza A(H1N1)pdm09 virus infection in Norwegian pigs was largely subclinical. This study tested the hypothesis that the infection causes negligible impact on pigs' growth performance in terms of feed conversion efficiency, daily feed intake, daily growth, age on reaching 100 kg bodyweight and overall feed intake. A sample of 1955 pigs originating from 43 breeding herds was classified into five infection status groups; seronegative pigs (n = 887); seropositive pigs (n = 874); pigs positive for virus at bodyweight between 33 kg and 60 kg (n = 123); pigs positive for virus at bodyweight between 61 kg and 80 kg (n = 34) and pigs positive for virus at bodyweight between 81 kg and 100 kg (n = 37). Each pig had daily recordings of feed intake and bodyweight from 33 kg to 100 kg. Marginal effects of the virus infection on the outcomes were estimated by multi-level linear regression, which accounted for known fixed effects (breed, birthdate, average daily feed intake and growth phase) and random effects (cluster effects of pig and herd). Results: The seropositive and virus positive pigs had decreased (P value<0.05) growth performance compared to seronegative pigs even though feed intake was not decreased. Reduced feed conversion efficiency led to lower average daily growth, additional feed requirement and longer time needed to reach the 100 kg bodyweight. The effects were more marked (P value<0.03) in pigs infected at a younger age and lasted a longer period. Despite increased feed intake observed, their growth rates were lower and they took more time to reach 100 kg bodyweight compared to the seronegative pigs. Conclusion: Our study rejected the null hypothesis that the virus infection had negligible adverse effects on growth performance of Norwegian pigs. 
 Title: Adverse effects of Influenza A(H1N1)pdm09 virus infection on growth performance of Norwegian pigs -a longitudinal study at a boar testing station
Output: False