niryuu/sni-each-converted huggingface dataset:
Paragraph: Background We investigated the temporal progression of the clinical, radiological, and virological changes in a community outbreak of severe acute respiratory syndrome (SARS). We followed up 75 patients for 3 weeks managed with a standard treatment protocol of ribavirin and corticosteroids, and assessed the pattern of clinical disease, viral load, risk factors for poor clinical outcome, and the usefulness of virological diagnostic methods. Findings Fever and pneumonia initially improved but 64 (85%) patients developed recurrent fever after a mean of 8·9 (SD 3·1) days, 55 (73%) had watery diarrhoea after 7·5 (2·3) days, 60 (80%) had radiological worsening after 7·4 (2·2) days, and respiratory symptoms worsened in 34 (45%) after 8·6 (3·0) days. In 34 (45%) patients, improvement of initial pulmonary lesions was associated with appearance of new radiological lesions at other sites. Nine (12%) patients developed spontaneous pneumomediastinum and 15 (20%) developed acute respiratory distress syndrome (ARDS) in week 3. Quantitative reverse-transcriptase (RT) PCR of nasopharyngeal aspirates in 14 patients (four with ARDS) showed peak viral load at day 10, and at day 15 a load lower than at admission. Age and chronic hepatitis B virus infection treated with lamivudine were independent significant risk factors for progression to ARDS (p=0·001). SARS-associated coronavirus in faeces was seen on RT-PCR in 65 (97%) of 67 patients at day 14. The mean time to seroconversion was 20 days. Interpretation The consistent clinical progression, shifting radiological infiltrates, and an inverted V viral-load profile suggest that worsening in week 2 is unrelated to uncontrolled viral replication but may be related to immunopathological damage. 
 Title: Clinical progression and viral load in a community outbreak of coronavirus-associated SARS pneumonia: a prospective study
Output: True
Paragraph: A novel coronavirus, termed the severe acute respiratory syndrome coronavirus (SARS-CoV), infected humans in Guangdong, China, in November 2002 and the subsequent efficient human-to-human transmissions of this virus caused profound disturbances in over 30 countries worldwide in 2003. Eventually, this epidemic was controlled by isolation and there has been no human infection reported since January 2004. However, research on different aspects of the SARS-CoV is not waning, as it is not known if this virus will re-emerge, especially since its origins and potential reservoir(s) are unresolved. The SARS-CoV genome is nearly 30 kb in length and contains 14 potential open reading frames (ORFs). Some of these ORFs encode for genes that are homologous to proteins found in all known coronaviruses, namely the replicase genes (ORFs 1a and 1b) and the four structural proteins: nucleocapsid, spike, membrane and envelope, and these proteins are expected to be essential for the replication of the virus. The remaining eight ORFs encodes for accessory proteins, varying in length from 39 to 274 amino acids, which are unique to SARS-CoV. This review will summarize the expeditious research on these accessory viral proteins in three major areas: (i) the detection of antibodies against accessory proteins in the serum of infected patients, (ii) the expression, processing and cellular localization of the accessory proteins, and (iii) the effects of the accessory proteins on cellular functions. These in-depth molecular and biochemical characterizations of the SARS-CoV accessory proteins, which have no homologues in other coronaviruses, may offer clues as to why the SARS-CoV causes such a severe and rapid attack in humans, while other coronaviruses that infect humans seem to be more forgiving. 
 Title: Understanding the accessory viral proteins unique to the severe acute respiratory syndrome (SARS) coronavirus
Output: True
Paragraph: Porcine deltacoronavirus (PDCoV) is an emerging swine coronavirus causing diarrhea and intestinal damage in nursing piglets. Previous work showed that PDCoV infection inhibits type I interferon (IFN) production. To further identify and characterize the PDCoV-encoded IFN antagonists will broaden our understanding of its pathogenesis. Nonstructural protein 15 (nsp15) encodes an endoribonuclease that is highly conserved among vertebrate nidoviruses (coronaviruses and arteriviruses) and plays a critical role in viral replication and transcription. Here, we found that PDCoV nsp15 significantly inhibits Sendai virus (SEV)-induced IFN-β production. PDCoV nsp15 disrupts the phosphorylation and nuclear translocation of NF-κB p65 subunit, but not antagonizes the activation of transcription factor IRF3. Interestingly, site-directed mutagenesis found that PDCoV nsp15 mutants (H129A, H234A, K269A) lacking endoribonuclease activity also suppress SEV-induced IFN-β production and NF-κB activation, suggesting that the endoribonuclease activity is not required for its ability to antagonize IFN-β production. Taken together, our results demonstrate that PDCoV nsp15 is an IFN antagonist and it inhibits interferon-β production via an endoribonuclease activity-independent mechanism. 
 Title: Porcine deltacoronavirus nsp15 antagonizes interferon-β production independently of its endoribonuclease activity
Output: False
Paragraph: Background: Human rhinoviruses (HRVs) are the most frequently detected pathogens in acute respiratory tract infections (ARTIs) and yet little is known about the prevalence, recurrence, structure and clinical impact of individual members. During 2007, the complete coding sequences of six previously unknown and highly divergent HRV strains were reported. To catalogue the molecular and clinical features distinguishing the divergent HRV strains, we undertook, for the first time, in silico analyses of all available polyprotein sequences and performed retrospective reviews of the medical records of cases in which variants of the prototype strain, HRV-QPM, had been detected. Methodology/Principle Findings: Genomic analyses revealed that the six divergent strains, residing within a clade we previously called HRV A2, had the shortest polyprotein of all picornaviruses investigated. Structure-based amino acid alignments identified conserved motifs shared among members of the genus Rhinovirus as well as substantive deletions and insertions unique to the divergent strains. Deletions mostly affected regions encoding proteins traditionally involved in antigenicity and serving as HRV and HEV receptor footprints. Because the HRV A2 strains cannot yet be cultured, we created homology models of predicted HRV-QPM structural proteins. In silico comparisons confirmed that HRV-QPM was most closely related to the major group HRVs. HRV-QPM was most frequently detected in infants with expiratory wheezing or persistent cough who had been admitted to hospital and required supplemental oxygen. It was the only virus detected in 65% of positive individuals. These observations contributed to an objective clinical impact ranging from mild to severe. The divergent strains did not meet classification requirements for any existing species of the genus Rhinovirus or Enterovirus. HRV A2 strains should be partitioned into at least one new species, putatively called Human rhinovirus C, populated by members detected with high frequency, from individuals with respiratory symptoms requiring hospital admission. 
 Title: Distinguishing Molecular Features and Clinical Characteristics of a Putative New Rhinovirus Species, Human Rhinovirus C (HRV C)
Output: False
Paragraph: Understanding how disease affects commercial production is imperative for pig producers to quantify its full impact on pig performance, carcass quality, and net returns. The objective of this experiment was to assess the productivity and economic importance of naturally occurring health challenges (HC) under commercial conditions. Three 1,000 pig grow-finish facilities received 936 pigs each. The experimental period started approximately 34 d post placement at an average start BW of 13.1 ± 0.2 kg. 
 Title: Impact of health challenges on pig growth performance, carcass characteristics, and net returns under commercial conditions
Output: False
Paragraph: Severe acute respiratory syndrome-associated coronavirus (SARS-CoV) Annexin A2 Autoantigen Anti-spike domain 2 (S2) Interleukin-6 (IL-6) Interferon-␥ (IFN-␥) a b s t r a c t Severe acute respiratory syndrome-associated coronavirus (SARS-CoV) infection causes lung failure characterized by atypical pneumonia. We previously showed that antibodies against SARS-CoV spike domain 2 (S2) in the patient sera can cross-react with human lung epithelial cells; however, the autoantigen is not yet identified. In this study, we performed proteomic studies and identified several candidate autoantigens recognized by SARS patient sera in human lung type II epithelial cell A549. Among the candidate proteins, annexin A2, which was identified by mass spectrometry analysis and had the highest score by Mascot data search, was further characterized and investigated for its role as an autoantigen. By confocal microscopic observation, SARS patient sera and anti-S2 antibodies were co-localized on A549 cells and both of them were co-localized with anti-annexin A2 antibodies. Anti-annexin A2 antibodies bound to purified S2 proteins, and anti-S2 bound to immunoprecipitated annexin A2 from A549 cell lysate in a dose-dependent manner. Furthermore, an increased surface expression and raft-structure distribution of annexin A2 was present in A549 cells after stimulation with SARS-induced cytokines interleukin-6 and interferon-␥. Cytokine stimulation increased the binding capability of anti-S2 antibodies to human lung epithelial cells. Together, the upregulated expression of annexin A2 by SARS-associated cytokines and the cross-reactivity of anti-SARS-CoV S2 antibodies to annexin A2 may have implications in SARS disease pathogenesis. 
 Title: Annexin A2 on lung epithelial cell surface is recognized by severe acute respiratory syndrome-associated coronavirus spike domain 2 antibodies
Output: False
Paragraph: Objective: In order to investigate the clinical and epidemiological rules of severe acute respiratory syndrome (sArs), rates and levels sArs coronavirus (sArs-coV) IgG antibodies of the patients and community populations from several areas were detected. Methods: Indirect immunofluorescent assay (IFA) and double-antigen sandwich enzyme-linked immunosorbent assay (ELIsA) were used to detect the sArs coronavirus-specific IgG antibodies in sera of 1700, including 1453 general populations from Hongkong, Marco, Guangzhou and Peking and 257 SARS patients from Guangzhou and Peking. The dynamics of the serum antibodies of SARS patients were observed from 3 to 360 days after onset of symptoms. Results: 90% of 257 patient serum specimens after 20 days of disease onset showed positive SARS-CoV IgG either using ELISA or IFA . 257 SARS patients, antibodies titers increased steadily in early 4 to 6 months after onset of SARS. The titers of most cases came to the peak in the 6th month. Then antibodies titers declined rapidly in some cases. However, all specimens still were positive for SARS-CoV IgG in the 48th month. Conclusions: this study suggest that few inapparent infectious patients exist during sArs epidemic. serum IgG antibodies has diagnostic value for SARS in the late course of disease and the antibodies present more than 48 months. (Int J Biomed Sci 2005; 1: 72-75)  
 Title: Seroepidemiological Study on SARS-CoV IgG Antibodies of Different Populations from Several Areas
Output: False
Paragraph: The Sec7 domain ADP-ribosylation factor (Arf) guanine nucleotide exchange factors (GEFs) are found in all eukaryotes, and are involved in membrane remodeling processes throughout the cell. This review is focused on members of the GBF/Gea and BIG/Sec7 subfamilies of Arf GEFs, all of which use the class I Arf proteins (Arf1-3) as substrates, and play a fundamental role in traYcking in the endoplasmic reticulum (ER)-Golgi and endosomal membrane systems. Members of the GBF/Gea and BIG/Sec7 subfamilies are large proteins on the order of 200 kDa, and they possess multiple homology domains. Phylogenetic analyses indicate that both of these subfamilies of Arf GEFs have members in at least Wve out of the six eukaryotic supergroups, and hence were likely present very early in eukaryotic evolution. The homology domains of the large Arf1 GEFs play important functional roles, and are involved in interactions with numerous protein partners. The large Arf1 GEFs have been implicated in several human diseases. They are crucial host factors for the replication of several viral pathogens, including poliovirus, coxsackievirus, mouse hepatitis coronavirus, and hepatitis C virus. Mutations in the BIG2 Arf1 GEF have been linked to autosomal recessive periventricular heterotopia, a disorder of neuronal migration that leads to severe malformation of the cerebral cortex. Understanding the roles of the Arf1 GEFs in membrane dynamics is crucial to a full understanding of traYcking in the secretory and endosomal pathways, which in turn will provide essential insights into human diseases that arise from misregulation of these pathways. 
 Title: Large Arf1 guanine nucleotide exchange factors: evolution, domain structure, and roles in membrane traYcking and human disease
Output: False
Paragraph: Background: Should an emerging infectious disease outbreak or an environmental disaster occur, the collection of epidemiological data must start as soon as possible after the event's onset. Questionnaires are usually built de novo for each event, resulting in substantially delayed epidemiological responses that are detrimental to the understanding and control of the event considered. Moreover, the public health and/or academic institution databases constructed with responses to different questionnaires are usually difficult to merge, impairing necessary collaborations. We aimed to show that e-commerce concepts and software tools can be readily adapted to enable rapid collection of data after an infectious disease outbreak or environmental disaster. Here, the 'customers' are the epidemiologists, who fill their shopping 'baskets' with standardised questions. Methods: For each epidemiological field, a catalogue of questions is constituted by identifying the relevant variables based on a review of the published literature on similar circumstances. Each question is tagged with information on its source papers. Epidemiologists can then tailor their own questionnaires by choosing appropriate questions from this catalogue. The software immediately provides them with ready-to-use forms and online questionnaires. All databases constituted by the different EpiBasket users are interoperable, because the corresponding questionnaires are derived from the same corpus of questions. Results: A proof-of-concept prototype was developed for Knowledge, Attitudes and Practice (KAP) surveys, which is one of the fields of the epidemiological investigation frequently explored during, or after, an outbreak or environmental disaster. The catalogue of questions was initiated from a review of the KAP studies conducted during or after the 2003 severe acute respiratory syndrome epidemic. Conclusion: Rapid collection of standardised data after an outbreak or environmental disaster can be facilitated by transposing the e-commerce paradigm to epidemiology, taking advantage of the powerful software tools already available. 
 Title: EpiBasket: how e-commerce tools can improve epidemiological preparedness
Output: False
Paragraph: The nucleolus is the largest nuclear organelle and is the primary site of ribosome subunit biogenesis in eukaryotic cells. It is assembled around arrays of ribosomal DNA genes, forming specific chromosomal features known as nucleolar organizing regions (NORs) which are the sites of ribosomal DNA transcription. While the nucleolus main activity involve different steps of ribosome biogenesis, the presence of proteins with no obvious relationship with ribosome subunit production suggests additional functions for the nucleolus, such as regulation of mitosis, cell cycle progression, stress response and biogenesis of multiple ribonucleoprotein complexes. The many novel factors and separate classes of proteins identified within the nucleolus support this view that the nucleolus may perform additional functions beyond its known role in ribosome subunit biogenesis. Here we review our knowledge of the nucleolar functions and will provide a detailed picture of how the nucleolus is involved in many cellular pathways. 
 Title: The Nucleolus: Structure and Function
Output: False
Paragraph: Mouse hepatitis (MH) virus was grown in SR-CDF1-DBT, a mouse cell line, and purified by ammonium sulfate precipitation and by density gradient centrifugation. Extraction of RNA from purified virions with 1 % SDS and sedimentation analysis of the RNA revealed a major 50S component and two minor components. Treatment of virions with phenol/chloroform also produced the 50S component, although its yield was lower. MH virion RNA can bind to a poly(U)-fiberglass filter, indicating that MH virion RNA contains poly(A). A poly(A>like fragment was isolated by digestion with ribonuclease A [EC 3.1.4.22] and Tl [EC 3.1.4.8] and by DEAE-Sephadex column chromatography. Analysis of the fragment for base composition showed it to be an adenine-rich material. Its chain length was about 90 nucleotides, as determined by ion-exchange chromatography and gel electrophoresis. 
 Title: Polyadenylate in the Virion RNA of Mouse Hepatitis Virus
Output: False
Paragraph: In this study, we aimed to detect viruses in hard ticks using the small RNA sequencing based method. 24 A 235-bp DNA segment was detected in Dermacentor nuttalli (hard ticks) and D. silvarum (hard ticks) from 25 sheep and bovine, respectively. The detected 235-bp segment had an identity of 99% to a 235-bp DNA 26 segment of African Swine Fever Virus (ASFV) and contained three single nucleotide mutations (C38T, 27 C76T and A108C). C38T, resulting in an single amino acid mutation G66D, suggests the existence of a new 28 ASFV strain, which is different from all reported ASFV strains in NCBI GenBank database. These results 29 also suggest that ASFV could have a wide range of hosts or vectors, beyond the well known Suidae family 30 and soft ticks. Our findings pave the way toward further studies of ASFV transmission and development of 31 prevention and control measures. 
 Title: DNA segment of African Swine Fever Virus 1 first detected in hard ticks from sheep and bovine
Output: True
Paragraph: Purpose: Bovine Rotavirus and Bovine Coronavirus are the most important causes of diarrhea in newborn calves and in some other species such as pigs and sheep. Rotavirus VP8 subunit is the major determinant of the viral infectivity and neutralization. Spike glycoprotein of coronavirus is responsible for induction of neutralizing antibody response. Methods: In the present study, several prediction programs were used to predict B and Tcells epitopes, secondary and tertiary structures, antigenicity ability and enzymatic degradation sites. Finally, a chimeric antigen was designed using computational techniques. The chimeric VP8-S2 antigen was constructed. It was cloned and sub-cloned into pGH and pET32a(+) expression vector. The recombinant pET32a(+)-VP8-S2 vector was transferred into E.oli BL21CodonPlus (DE3) as expression host. The recombinant VP8-S2 protein was purified by Ni-NTA chromatography column. The results of colony PCR, enzyme digestion and sequencing showed that the VP8-S2 chimeric antigen has been successfully cloned and sub-cloned into pGH and pET32a(+).The results showed that E.coli was able to express VP8-S2 protein appropriately. This protein was expressed by induction of IPTG at concentration of 1mM and it was confirmed by Ni-NTA column, dot-blotting analysis and SDS-PAGE electrophoresis. The results of this study showed that E.coli can be used as an appropriate host to produce the recombinant VP8-S2 protein. This recombinant protein may be suitable to investigate to produce immunoglobulin, recombinant vaccine and diagnostic kit in future studies after it passes biological activity tests in vivo in animal model and or other suitable procedure. 
 Title: Design and Construction of Chimeric VP8-S2 Antigen for Bovine Rotavirus and Bovine Coronavirus
Output: False
Paragraph: To trace the possible route of introduction of porcine epidemic diarrhea virus (PEDV), the phylogenetic relationships of PEDV strains in the regions of epidemicity in the Philippines to PEDV strains that are endemic in other countries were investigated. Partial nucleotide sequences of the S1 spike gene was determined from the PEDV-positive samples and compared with S1 sequences from other countries. Phylogenetic analysis indicated that PEDV strains in the Philippines segregate into two groups. 
 Title: Phylogenetic tracking of current porcine epidemic diarrhea virus (PEDV) strains in the Philippines
Output: True
Paragraph: Shigellosis, a bacillary dysentery, is closely associated with diarrhoea in human and causes infection of 165 million people worldwide per year. Casein-degrading serine protease autotransporter of enterobacteriaceae (SPATE) subfamily protein SigA, an outer membrane protein, exerts both cytopathic and enterotoxic effects especially cytopathic to human epithelial cell type-2 (HEp-2) and is shown to be highly immunogenic. In the present study, we have tried to impose the vaccinomics approach for designing a common peptide vaccine candidate against the immunogenic SigA of Shigella spp. At first, 44 SigA proteins from different variants of S. flexneri, S. dysenteriae, S. boydii, and S. sonnei were assessed to find the most antigenic protein. We retrieved 12 peptides based on the highest score for human leukocyte antigen (HLA) supertypes analysed by NetCTL. Initially, these peptides were assessed for the affinity with MHC class I and class II alleles, and four potential core epitopes VTARAGLGY, FHTVTVNTL, HTTWTLTGY, and IELAGTLTL were selected. From these, FHTVTVNTL and IELAGTLTL peptides were shown to have 100% conservancy. Finally, IELAGTLTL was shown to have the highest population coverage (83.86%) among the whole world population. In vivo study of the proposed epitope might contribute to the development of functional and unique widespread vaccine, which might be an operative alleyway to thwart dysentery from the world. 
 Title: Vaccinomics Approach for Designing Potential Peptide Vaccine by Targeting Shigella spp. Serine Protease Autotransporter Subfamily Protein SigA
Output: True
Paragraph: Introduction: Fever of unknown origin (FUO) is a common initial presentation leading to a diagnostic challenge. Patient concerns: A 3-month history of moderate-to-high fever was reported in an otherwise healthy 54-year-old man. Enhanced computed tomography (CT) scans of his chest showed a remarkable progressive enlargement of bilateral cervical, supraclavicular, hilar, and mediastinal lymph nodes within 2 weeks. Bronchofibroscopy manifested obvious luminal stenosis with swelling, thick pale mucosa, and disappearing of structures of trachea cricoid cartilage, followed by a 18F-fluorodeoxyglucose positron-emission tomography-computed tomography (18F-FDG PET/CT) with intense symmetric FDG uptake in larynx, tracheobronchial tree, and hilar, mediastinal, and axillary lymph nodes being demonstrated. Diagnosis: A diagnosis of relapsing polychondritis (RP) was finally reached. Interventions: The patient received methylprednisolone 40 mg daily with a gradual tapering in a 4-month follow-up. Outcomes: The patient experienced no relapse of fever and lymph nodes enlargement in the 4-month follow-up. Lessons: Even though long-term fever with multiple lymphadenectasis usually lead to a diagnosis of lymphoma, the bronchoscopic features and evidence from 18F-FDG PET/CT in this case were much more approximate to RP, indicating an importance of a sensible differential diagnosis of RP in patients who present with nonspecific features such as FUO and lymph nodes enlargement. Keeping a high index of clinical suspicion in these patients can help recognize uncommon of RP and promote diagnosis and treatment. Our case highlights the significance of 18F-FDG PET/CT in helping reaching the diagnosis of RP in this condition. This report provides new data regarding the diagnostic difficulties of this rare type of autoimmune disease, and further investigations are needed as cases accumulate. Abbreviations: 18F-FDG PET/CT = 18F-fluorodeoxyglucose positron-emission tomography-computed tomography, FUO = fever of unknown origin, RP = relapsing pholychondritis. 
 Title: An unusual cause of fever of unknown origin with enlarged lymph nodes-relapsing polychondritis A case report
Output: False
Paragraph: Background: Some island nations have explicit components of their influenza pandemic plans for providing travel warnings and restricting incoming travellers. But the potential value of such restrictions has not been quantified. We developed a probabilistic model and used parameters from a published model (i.e., InfluSim) and travel data from Pacific Island Countries and Territories (PICTs). 
 Title: BMC Infectious Diseases Small islands and pandemic influenza: Potential benefits and limitations of travel volume reduction as a border control measure
Output: True
Paragraph: Diagnosis of MERS-Cov still a major concern in most of daignostic laboratories. To date the Real-time Polymerase Chain reaction (RT-PCR) is the mainstay for diagnosis of MERS-CoV. RT-PCR has limitations, including a long turnaround time and lack of common measurements and correlations with Viral Load (VL). It is recommended to screen for MERS-CoV using RT-PCR of the upstream of envelope gene (upE) followed by confirmation of the presence of one of the following genes; open reading frame 1A, 1B genes or nucleocapsid (N) gene. Scientists are looking to implement viral sequencing on all negative samples by RT-PCR and they beleive that can be exposed to another level of testing using sequencing of the RNA-dependent RNA polymerase (RdRp) gene or N gene and in this case a positive result is diagnostic. It is also very important to maintain a contineous and random sequencing for MERS-Cov samples to be able to pick early viral mutations. Serological assays still not widely or routinely performed, and a lot of studies looking to implement such method in routine patient's testings. 
 Title: MERS-CoV diagnosis: An update
Output: True
Paragraph: Among approximately 1000 adenoviruses from chimpanzees and bonobos studied recently, the Pan Adenovirus type 3 (PanAd3, isolated from a bonobo, Pan paniscus) has one of the best profiles for a vaccine vector, combining potent transgene immunogenicity with minimal pre-existing immunity in the human population. In this study, we inserted into a replication defective PanAd3 a transgene expressing a fusion protein of conserved influenza antigens nucleoprotein (NP) and matrix 1 (M1). We then studied antibody and T cell responses as well as protection from challenge infection in a mouse model. A single intranasal administration of PanAd3-NPM1 vaccine induced strong antibody and T cell responses, and protected against high dose lethal influenza virus challenge. Thus PanAd3 is a promising candidate vector for vaccines, including universal influenza vaccines. 
 Title: Vaccination to Conserved Influenza Antigens in Mice Using a Novel Simian Adenovirus Vector, PanAd3, Derived from the Bonobo Pan paniscus
Output: True
Paragraph: Infectious bronchitis virus (IBV) infections in poultry cause great economic losses to the poultry industry worldwide. The emergence of viral variants complicates disease control. The IBV strains in Taiwan were clustered into two groups, Taiwan group I and Taiwan group II, based on the S1 gene. A variant was previously identified and showed a distinct S1 gene homology with other local strains. This study investigated the 3 7.3 kb genome of eight Taiwan strains isolated from 1992 to 2007. The genes of interest were directly sequenced. Sequence analyses were performed to detect any recombination event among IBVs. The results demonstrated that all of the examined viruses maintained the typical IBV genome organization as 5 -S-3a-3b-E-M-5a-5b-N-UTR-3 . In the phylogenetic analyses, various genes from one strain were clustered into separate groups. Moreover, frequent recombination events were identified in the Simplot analyses among the Taiwan and China CK/CH/LDL/97I-type strains. Putative crossover sites were located in the S1, S2, 3b, M genes and the intergenic region between the M and 5a genes. All of the recombinants showed chimeric IBV genome arrangements originated from Taiwan and China-like parental strains. Field IBVs in Taiwan undergo genetic recombination and evolution. 
 Title: Identification of Taiwan and China-like recombinant avian infectious bronchitis viruses in Taiwan
Output: True
Paragraph: ABSTRCT 29 Given the scale and rapid spread of severe acute respiratory syndrome coronavirus 2 30 (SARS-CoV-2, known as 2019-nCov) infection , the ongoing global 31 SARS-CoV-2 outbreak has become a huge public health issue. Rapid and precise 32 diagnostic methods are thus immediately needed for diagnosing COVID-19, 33 providing timely treatment and facilitating infection control. A one-step reverse 34 transcription loop-mediated isothermal amplification (RT-LAMP) coupled with 35 nanoparticles-based biosensor (NBS) assay (RT-LAMP-NBS) was successfully 36 established for rapidly and accurately diagnosing COVID-19. A simple equipment 37 (such as heating block) was required for maintaining a constant temperature (63°C) 38 for only 40 min. Using two designed LAMP primer sets, F1ab (opening reading frame 39 1a/b) and np (nucleoprotein) genes of SARS-CoV-2 were simultaneously amplified 40 and detected in a 'one-step' and 'single-tube' reaction, and the detection results were 41 easily interpreted by NBS. The sensitivity of SARS-CoV-2 RT-LAMP-NBS was 12 42 copies (each of detection target) per reaction, and no cross-reactivity was generated 43 from non-SARS-CoV-2 templates. Among clinically diagnosed COVID-19 patients, 44 the analytical sensitivity of SARS-CoV-2 was 100% (33/33) in the oropharynx swab 45 samples, and the assay's specificity was also 100% (96/96) when analyzed the clinical 46 samples collected from non-COVID-19 patients. The total diagnosis test from sample 47 collection to result interpretation only takes approximately 1 h. In sum, the 48 RT-LAMP-NBS is a promising tool for diagnosing the current SARS-CoV-2 49 infection in first line field, public health and clinical laboratories, especially for 50 resource-challenged regions. 51 
 Title: Title Page: 1 Reverse transcription loop-mediated isothermal amplification combined with 2 nanoparticles-based biosensor for diagnosis of COVID-19 3 4 Laboratory of Pediatric Respiratory Infection Disease, National Clinical Research
Output: True
Paragraph: The transportation of embryos obtained from animal models, endangered species and nondomestic farmed animals (e.g., deer) can reduce/eliminate the need for shipping postnatal animals and thus has gamed the interest of the biomedical and conservation fields. Efficient movement of germ plasm worldwide requires established ctyobanks. Embryo cryopreservation has become a routinely successful technology for many species and efforts to develop usable cryobanks for many target species am ongoing. Recommended regulations for the movement of embryos from nontraditional (i.e. other than domestic livestock) species are nonexistent. Efforts are underway to establish domestic and international handling guidelines and to recommend suitable quarantine conditions to facilitate embryo importation. Further basic research on specific zona pellucida-pathogen interactions is encouraged to support embryo movement efforts. 
 Title: EMBRYO IMPORTATION AND CRYOBANKING STRATEGIES FOR LABORATORY ANIMALS ANDWlLDLIFEsPECIES
Output: True
Paragraph: Introduction. Cytosolic pattern recognition receptors (PRR) have been shown to detect nucleic acids from RNA and DNA viruses in order to launch a type I interferon mediated antiviral state [1]. Here we show that RNA of the facultative intracellular bacterium Salmonella typhimurium is a ligand for RIG-I, triggers production of type-I interferons and contributes to pathogenicity in vivo. Methods. We use RIG-IÀ/À MEFs [2] or human epithelial cells depleted of RIG-I by lentiviral shRNA transduction for transfection and infection experiments. IFNbeta production was measured by 293T IFNbeta-reporter cells or qPCR. Intracellular bacterial titers were determined by gentamycin protection assay. In vivo infection experiments were performed as described [3] using SL1344 or SL1344 aroA deficient Salmonella strains in RIG-I+/+ and RIG-IÀ/À mice [4]. Results. Infection of fibroblasts and epithelial cells with S. typhimurium, but not with non-invasive E. coli, triggers IFNbeta transcription, suggesting that intracellular replication is required. RIG-I dependent recognition of bacterial RNA is dominant in non-phagocytic cells, as shown in RIG-I knockout and knockdown model cells. Despite presence of other pathogen-associated patterns (PAMP), like LPS or flagellin, no IFNbeta was produced in fibroblasts and epithelial cells lacking RIG-I upon S. typhimurium infection. In contrast, in macrophages TLR dependent recognition of bacterial PAMPs through TRIF/Myd88 overcomes RIG-I deficiency and leads to robust induction of type I interferon. We observed higher bacterial titers at early time points after infection in the cecum of S. typhimurium infected RIG-IÀ/À mice, when compared to wild type animals. However, at later stages of infection, S. typhimurium overcomes the innate response leading to similar weight loss and mortality in wildtype and RIG-IÀ/À mice. Conclusion. In summary, our data implicate a role of RIG-I mediated innate immune recognition of bacterial RNA in early control of bacterial replication, most likely mediated by non-phagocytic intestinal epithelial cells targeted by S. typhimurium. Disclosure of interest: None declared. Combined action of type I and type III IFN restricts initial replication of SARScoronavirus in the lung but fails to inhibit systemic virus spread 
 Title: P133 RIG-I mediates recognition of Salmonella RNA in non-phagocytic cells and con- tributes to early bacterial replication in vivo P135 Defining the intracellular innate immune synapse
Output: False
Paragraph: 2H phosphoesterases catalyze reactions on nucleotide substrates and contain two conserved histidine residues in the active site. Very limited information is currently available on the details of the active site and substrate/product binding during the catalytic cycle of these enzymes. We performed a comprehensive X-ray crystallographic study of mouse 2′,3′-cyclic nucleotide 3′-phosphodiesterase (CNPase), a membraneassociated enzyme present at high levels in the tetrapod myelin sheath. We determined crystal structures of the CNPase phosphodiesterase domain complexed with substrate, product, and phosphorothioate analogues. The data provide detailed information on the CNPase reaction mechanism, including substrate binding mode and coordination of the nucleophilic water molecule. Linked to the reaction, an open/close motion of the β5-α7 loop is observed. The role of the N terminus of helix α7-unique for CNPase in the 2H family-during the reaction indicates that 2H phosphoesterases differ in their respective reaction mechanisms despite the conserved catalytic residues. Furthermore, based on small-angle X-ray scattering, we present a model for the full-length enzyme, indicating that the two domains of CNPase form an elongated molecule. Finally, based on our structural data and a comprehensive bioinformatics study, we discuss the conservation of CNPase in various organisms. 
 Title: Crystallographic Analysis of the Reaction Cycle of 2′,3′-Cyclic Nucleotide 3′-Phosphodiesterase, a Unique Member of the 2H Phosphoesterase Family
Output: True
Paragraph: The development of the complex network graphs permits us to describe any real system such as social, neural, computer or genetic networks by transforming real properties in topological indices (TIs). This work uses Randic's star networks in order to convert the protein primary structure data in specific topological indices that are used to construct a natural/random protein classification model. The set of natural proteins contains 1046 protein chains selected from the pre-compiled CulledPDB list from PISCES Dunbrack's Web Lab. This set is characterized by a protein homology of 20%, a structure resolution of 1.6 Å and R-factor lower than 25%. The set of random amino acid chains contains 1046 sequences which were generated by Python script according to the same type of residues and average chain length found in the natural set. A new Sequence to Star Networks (S2SNet) wxPython GUI application (with a Graphviz graphics back-end) was designed by our group in order to transform any character sequence in the following star network topological indices: Shannon entropy of Markov matrices, trace of connectivity matrices, Harary number, Wiener index, Gutman index, Schultz index, Moreau-Broto indices, Balaban distance connectivity index, Kier-Hall connectivity indices and Randic connectivity index. The model was constructed with the General Discriminant Analysis methods from STATISTICA package and gave training/predicting set accuracies of 90.77% for the forward stepwise model type. In conclusion, this study extends for the first time the classical TIs to protein star network TIs by proposing a model that can predict if a protein/fragment of protein is natural or random using only the amino acid sequence data. This classification can be used in the studies of the protein functions by changing some fragments with random amino acid sequences or to detect the fake amino acid sequences or the errors in proteins. These results promote the use of the S2SNet application not only for protein structure analysis but also for mass spectroscopy, clinical proteomics and imaging, or DNA/RNA structure analysis. 
 Title: Natural/random protein classification models based on star network topological indices
Output: False
Paragraph: Porcine hemagglutinating encephalomyelitis (PHE) is caused by the coronavirus hemagglutinating encephalomyelitis virus (PHE-CoV), and the recent, rapid spread of PHE-CoV in piglets from many countries emphasizes the urgent need for a PHE-CoV vaccine. Here we use a murine model for evaluation of the induction of humoral and cellular immune responses by inactivated and PHE-CoV DNA vaccines in order to define the immune correlates for protection against PHE-CoV. The inactivated vaccine was composed of purified PHE-CoV and aluminum hydroxide gel (alum), which was chosen as an adjuvant because of its long history of safety for human use. The PHE-CoV DNA vaccine was constructed by subcloning the S1 gene of PHE-CoV into the pVAX1 vector to create the recombinant plasmid pV-S1. Our results showed that the inactivated PHE-CoV vaccine (IPV) elicited a high level of humoral immunity, resulting in good protection efficacy against PHE-CoV challenge. The IPV induced the IgG1 subclass of serum antibodies and expression of the cytokine interleukin-4 (IL-4), suggesting that the IPV generated a predominantly Th2-type immune response. The DNA vaccine was found to mediate primarily a cellular immune response with high levels of IgG2a and the cytokines IL-2 and gamma interferon (IFN-␥). However, mice that were vaccinated twice with the DNA vaccine and boosted with the IPV could mount a sufficient neutralizing antibody response against live PHE-CoV, with little variation in IgG1 and IgG2a levels, and showed high levels of IL-2 and IL-4. This response may activate both B and T cells to mount a specific humoral and cellular immune response that could, in turn, elicit a phagocyte-mediated defense against PHE-CoV infections to achieve viral clearance. 
 Title: Comparative Evaluation of Two Hemagglutinating Encephalomyelitis Coronavirus Vaccine Candidates in Mice
Output: True
Paragraph: The highly pathogenic avian influenza (HPAI) H5N1 viruses, especially the laboratory-generated H5N1 mutants, have demonstrated the potential to cross the species barrier and infect mammals and humans. Consequently, the design of an effective and safe anti-H5N1 vaccine is essential. We previously demonstrated that the full-length hemagglutinin 1 (HA1) could induce significant neutralizing antibody response and protection. Here, we intended to identify the critical neutralizing domain (CND) in an optimal conformation that can elicit strong cross-neutralizing antibodies and protection against divergent H5N1 strains. We thus constructed six recombinant proteins covering different regions of HA1 of A/Anhui/ 1/2005(H5N1), each of which was fused with foldon (Fd) and Fc of human IgG. We found that the critical fragment fused with Fd/Fc (HA-13-263-Fdc, H5 numbering) that could elicit the strongest neutralizing antibody response is located in the N-terminal region of HA1 (residues 13-263), which covers the receptor-binding domain (RBD, residues 112-263). We then constructed three additional recombinants fused with Fd plus His tag (HA-13-263-Fd-His), Fc only (HA-13-263-Fc), and His tag only (HA-13-263-His), respectively. We found that the HA-13-263-Fdc, which formed an oligomeric conformation, induced the strongest neutralizing antibody response and cross-protection against challenges of two tested H5N1 virus strains covering clade 1: A/VietNam/1194/2004 (VN/1194) or clade 2.3.4: A/Shenzhen/406H/06 (SZ/406H), while HA-13-263-Fc dimer and HA-13-263-Fd-His trimer elicited higher neutralizing antibody response and protection than HA-13-263-His monomer. These results suggest that the oligomeric form of the CND containing the RBD can be further developed as an effective and safe vaccine for cross-protection against divergent strains of H5N1 viruses. 
 Title: A Critical HA1 Neutralizing Domain of H5N1 Influenza in an Optimal Conformation Induces Strong Cross-Protection
Output: False
Paragraph: To investigate the factors associated with death and describe the gestational outcomes in pregnant women with influenza A(H1N1)pdm09, we conducted a case-control study (deaths and recovered) in hospitalized pregnant women with laboratory-confirmed influenza A (H1N1)pdm09 with severe acute respiratory illness (SARI) in the state of São Paulo from June 9 to December 1, 2009. All cases were evaluated, and four controls that were matched by the epidemiological week of hospitalization of the case were randomly selected for each case. Cases and controls were selected from the National Disease Notification System-SINAN Influenza-web. The hospital records from 126 hospitals were evaluated, and home interviews were conducted using standardized forms. A total of 48 cases and 185 controls were investigated. Having had a previous health visit to a healthcare provider for an influenza episode before hospital admission was a risk factor for death (adjusted OR (OR adj ) of 7.93, 95% CI 2.19-28.69). Although not significant in the multiple analysis (OR adj of 2.13, 95% CI 0.91-5.00), the 3 rd trimester deserves attention, with an OR = 2.22, 95% CI 1.13-4.37 in the univariate analysis. Antiviral treatment was a protective factor when administered within 48 hours of symptom onset (OR adj = 0.16, 95% CI 0.05-0.50) and from 48 to 72 hours (OR adj = 0.09, 95% CI 0.01-0.87). There was a higher proportion of fetal deaths and preterm births among cases (p = 0.001) and live births with low weight (p = 0.019), compared to control subjects who gave birth during hospitalization. After discharge, control subjects had a favorable neonatal outcome. Early antiviral treatment during the presence of a flu-like illness is an important factor in reducing mortality from influenza in pregnant women and unfavorable neonatal outcomes. It is important to monitor pregnant women, particularly in the 3 rd trimester of gestation, with influenza illness for diagnosis and early treatment. 
 Title: Author Contributions
Output: True
Paragraph: Introduction-HIV-1 uses a programmed -1 ribosomal frameshift to generate Gag-Pol, the precursor of its enzymes, when its full-length mRNA is translated by the ribosomes of the infected cells. This change in the reading frame occurs at a so-called slippery sequence that is followed by a specific secondary structure, the frameshift stimulatory signal. This signal controls the frameshift efficiency. The synthesis of HIV-1 enzymes is critical for the virus replication and therefore, the -1 ribosomal frameshift could be the target of novel antiviral drugs. Areas covered-This review examines various approaches used to select drugs interfering with the -1 frameshift of HIV-1. These include the selection and modification of chemical compounds that specifically bind to the frameshift stimulatory signal, the use of antisense oligonucleotides targeting this signal and the selection of compounds that modulate HIV-1 frameshift, by using bicistronic reporters where the expression of the second cistron depends upon HIV-1 frameshift. Expert opinion-The most promising approach is the selection and modification of compounds specifically targeting HIV-1 frameshift stimulatory signal. The use of antisense oligonucleotides binding to the frameshift stimulatory signal is still questionable. The use of bicistronic reporters preferentially selects compounds that modulate the frameshift by targeting the ribosomes, which is less promising. 
 Title: Targeting frameshifting in the human immunodeficiency virus
Output: True
Paragraph: Chikungunya virus (CHIKV) is a mosquito-borne arthrogenic alphavirus that causes acute febrile illness in humans accompanied by joint pains and in many cases, persistent arthralgia lasting weeks to years. The re-emergence of CHIKV has resulted in numerous outbreaks in the eastern hemisphere, and threatens to expand in the foreseeable future. Unfortunately, no effective treatment is currently available. The present study reports the use of resazurin in a cell-based high-throughput assay, and an image-based high-content assay to identify and characterize inhibitors of CHIKV-infection in vitro. CHIKV is a highly cytopathic virus that rapidly kills infected cells. Thus, cell viability of HuH-7 cells infected with CHIKV in the presence of compounds was determined by measuring metabolic reduction of resazurin to identify inhibitors of CHIKV-associated cell death. A kinase inhibitor library of 4,000 compounds was screened against CHIKV infection of HuH-7 cells using the resazurin reduction assay, and the cell toxicity was also measured in non-infected cells. Seventy-two compounds showing $50% inhibition property against CHIKV at 10 mM were selected as primary hits. Four compounds having a benzofuran core scaffold (CND0335, CND0364, CND0366 and CND0415), one pyrrolopyridine (CND0545) and one thiazol-carboxamide (CND3514) inhibited CHIKV-associated cell death in a dose-dependent manner, with EC 50 values between 2.2 mM and 7.1 mM. Based on image analysis, these 6 hit compounds did not inhibit CHIKV replication in the host cell. However, CHIKV-infected cells manifested less prominent apoptotic blebs typical of CHIKV cytopathic effect compared with the control infection. Moreover, treatment with these compounds reduced viral titers in the medium of CHIKV-infected cells by up to 100-fold. In conclusion, this cell-based high-throughput screening assay using resazurin, combined with the image-based high content assay approach identified compounds against CHIKV having a novel antiviral activity -inhibition of virus-induced CPE -likely by targeting kinases involved in apoptosis. 
 Title: Identification of Novel Compounds Inhibiting Chikungunya Virus-Induced Cell Death by High Throughput Screening of a Kinase Inhibitor Library
Output: True