niryuu/sni-each-converted huggingface dataset:
Paragraph: Dendritic cells (DCs) are recognized as highly potent antigen-presenting cells that are able to stimulate cytotoxic T lymphocyte (CTL) responses with antitumor activity. Consequently, DCs have been explored as cellular vaccines in cancer immunotherapy. To that end, DCs are modified with tumor antigens to enable presentation of antigen-derived peptides to CTLs. In this review we discuss the use of viral vectors for in situ modification of DCs, focusing on their clinical applications as anticancer vaccines. Among the viral vectors discussed are those derived from viruses belonging to the families of the Poxviridae, Adenoviridae, Retroviridae, Togaviridae, Paramyxoviridae, and Rhabdoviridae. We will further shed light on how the combination of viral vector-based vaccination with T-cell supporting strategies will bring this strategy to the next level. Since their discovery in 1973, it was clear that dendritic cells (DCs) stood out above the immune cell pack (1, 2). They are morphologically distinct from all other immune cell types and are gifted with an unparalleled capacity to take up, process and present self and foreign antigens to both CD4 + and CD8 + T cells. DCs are critical intermediaries between the innate and adaptive immune systems, as they stimulate, regulate, and shape both immunity and tolerance in all its disguises. Ralph Steinmann, who discovered these cells, was awarded the Nobel Prize for Medicine in 2011, because the discovery of DCs changed medicine (3). Dendritic cells in both humans and mice represent a population of at least four different subtypes with distinct phenotypical and functional characteristics (4-7). These subsets are: plasmacytoid DCs (pDCs), two subsets of conventional DCs (cDC1 and cDC2), and inflammatory DCs. The latter represent a monocyte-derived subset that appears during inflammatory responses (Table 1) . Recently, additional types of human blood DCs, monocytes, and progenitors were revealed using single cell RNA-sequencing. The group of Prof. Nir Hacohen identified pDCs next to cDC progenitor-derived cDC1 (Clec9A + ) and two types of CD1c + cDC2, of which one can also be derived from CD14 + DCs. Furthermore they found a CD141 − CD1c − CD11c + DC subset derived from CD16 + monocytes and an AXL + Siglec6 + subset (8). Future research will have to unravel a possible murine representative for the human cDC2 and AXL + Siglec6 + DC subset. Also, Langerhans cells have been considered an important DC subset for vaccination as they are localized in the epidermis (HLA-DR + CD11c + CD1a + CD207 + ). However, recent evidence suggests that they are related to macrophages, another antigen-presenting cell (APC) type with potential antitumor activity (9). 
 Title: The Journey of in vivo Virus Engineered Dendritic Cells From Bench to Bedside: A Bumpy Road
Output: True
Paragraph: We describe the unusual structure of a vaccinia virus late mRNA. In these molecules, the protein-coding sequences of a major late structural polypeptide are preceded by long leader RNAa, which In some cases are thousands of nucleotides long. These sequences map to different regions of the viral genome and in one instance are separated from the late gene by more than 100 kb of DNA. Moreover, the leader sequences map either upstream or downstream of the late gene, are transcribed from either DNA strand, and are fused to the late gene coding sequence via a poly(A) stretch. This demonstrates that vaccinia virus produces late mRNAs by tagging the protein-coding sequences onto the 3' end of other RNAa. 
 Title: Vaccinia Virus Produces Late mRNAs by Discontinuous Synthesis
Output: False
Paragraph: and Golgi apparatus of the unicellular green alga, Micrasterias americana, is facilitated by 50-70 nm vesicles that form from part-rough, part-smooth transitional regions of the endoplasmic reticulum. In growing cells, the vesicles are present at the normal growth temperature of 23 ~ However, at 16 ~ vesicle accumulations occur. Golgi apparatus of non-growing cells exhibited both larger numbers of vesicles and larger dictyosomes at all temperatures. In non-growing cells, vesicle numbers also were increased at 16~ The 16 ~ block was reconstituted in a cell-free system using Golgi apparatusand endoplasmic reticulum-enriched fractions prepared from suspension cultures. When incubated in the presence of ATP and cytosol, transitional endoplasmic reticulum fragments of Micrasterias responded by formation of membrane blebs and vesicles resembling those seen in situ. When prepared from cells metabolically labeled with [3H]leucine, the isolated transition elements supported the transfer of radioactivity to Golgi apparatus preparations immobilized on nitrocellulose strips. The transfer was time-and temperaturedependent and stimulated by ATP. The ATP-dependent component of transfer expressed at 23 ~ was reduced or absent at temperatures of 16 ~ or below. This suggested that membrane transfer mediated by transition vesicles was the same rate-limiting step in endoplasmic reticulum to Golgi apparatus membrane trafficking both in situ and in the cell-free system. Growth, as evidenced by a progressively altered Micrasterias morphology, was slowed at low temperatures but showed no abrupt temperature transition as seen with_ the vesicular traffic between the endoplasmic reticulum and the Golgi apparatus. 
 Title: Pl ffDPI.ASMA Vesicular membrane transfer between endoplasmic reticulum and Golgi apparatus of a green alga, Micrasterias americana A 16 ~ block and reconstitution in a cell-free system
Output: False
Paragraph: Oncolytic virus therapy is based on the ability of viruses to effectively infect and kill tumor cells without destroying the normal tissues. While some viruses seem to have a natural preference for tumor cells, most viruses require the modification of their tropism to specifically enter and replicate in such cells. This review aims to describe the transductional targeting strategies currently employed to specifically redirect viruses towards surface receptors on tumor cells. Three major strategies can be distinguished; they involve (i) the incorporation of new targeting specificity into a viral surface protein, (ii) the incorporation of a scaffold into a viral surface protein to allow the attachment of targeting moieties, and (iii) the use of bispecific adapters to mediate targeting of a virus to a specified moiety on a tumor cell. Of each strategy key features, advantages and limitations are discussed and examples are given. Because of their potential to cause sustained, multiround infection-a desirable characteristic for eradicating tumorsparticular attention is given to viruses engineered to become self-targeted by the genomic expression of a bispecific adapter protein. 
 Title: Retargeting of Viruses to Generate Oncolytic Agents
Output: True
Paragraph: Screening for thousands of viruses and other pathogenic microorganisms, including bacteria, fungi, and parasites, in human tumor tissues will provide a better understanding of the contributory role of the microbiome in the predisposition for, causes of, and therapeutic responses to the associated cancer. Metagenomic assays designed to perform these tasks will have to include rapid and economical processing of large numbers of samples, supported by straightforward data analysis pipeline and flexible sample preparation options for multiple input tissue types from individual patients, mammals, or environmental samples. To meet these requirements, the PathoChip platform was developed by targeting viral, prokaryotic, and eukaryotic genomes with multiple DNA probes in a microarray format that can be combined with a variety of upstream sample preparation protocols and downstream data analysis. PathoChip screening of DNA plus RNA from formalin-fixed, paraffin-embedded tumor tissues demonstrated the utility of this platform, and the detection of oncogenic viruses was validated using independent PCR and deep sequencing methods. These studies demonstrate the use of the PathoChip technology combined with PCR and deep sequencing as a valuable strategy for detecting the presence of pathogens in human cancers and other diseases. Citation Baldwin DA, Feldman M, Alwine JC, Robertson ES. 2014. Metagenomic assay for identification of microbial pathogens in tumor tissues. mBio 5(5):e01714-14. 
 Title: Metagenomic Assay for Identification of Microbial Pathogens in Tumor Tissues
Output: True
Paragraph: Severe acute respiratory syndrome coronavirus (SARS-CoV) 7a is an accessory protein with no known homologues. In this study, we report the interaction of a SARS-CoV 7a and small glutamine-rich tetratricopeptide repeat-containing protein (SGT). SARS-CoV 7a and human SGT interaction was identified using a two-hybrid system screen and confirmed with interaction screens in cell culture and cellular co-localization studies. The SGT domain of interaction was mapped by deletion mutant analysis and results indicated that tetratricopeptide repeat 2 (aa 125-158) was essential for interaction. We also showed that 7a interacted with SARS-CoV structural proteins M (membrane) and E (envelope), which have been shown to be essential for virus-like particle formation. Taken together, our results coupled with data from studies of the interaction between SGT and HIV-1 vpu indicated that SGT could be involved in the life-cycle, possibly assembly of SARS-CoV. 
 Title: Severe acute respiratory syndrome coronavirus protein 7a interacts with hSGT q
Output: True
Paragraph: We investigated the antiviral activity of Arbidol, an antiviral chemical compound, against Coxsackie virus B5 (CVB 5 ) in vitro and in vivo. Arbidol not only prevented the cytopathic effect (CPE) of CVB 5 , as demonstrated in an MTT colorimetric assay, when added during or after viral infection, with a 50% inhibitory concentration (IC 50 ) from 2.66 to 6.62 lg/ml, but it also decreased the CVB 5 -RNA level in infected host cells, as shown in semi-quantitative RT-PCR. BALB/c mice were used as an animal model to test the Arbidol activity in vivo. Orally administered Arbidol at 50 mg/kg body weight/day (once a day) significantly reduced mean virus yields in the lungs and heart as well as mortality after infection for 6 days. Our results demonstrate that in vitro and in vivo infection with CVB 5 can be effectively treated by Arbidol. 
 Title: Antiviral activity of Arbidol against Coxsackie virus B5 in vitro and in vivo
Output: False
Paragraph: Type 1 interferons (IFN-I) exert pleiotropic biological effects during viral infections, all which contribute to balancing virus control and immune pathology. Despite extensive antiviral functions that subdue virus replication, recent studies demonstrate pathogenic and pro-viral roles for IFN-I signaling during acute and persistent virus infection. IFN-I signaling can promote morbidity and mortality through induction of aberrant inflammatory responses during acute viral infection. In contrast, IFN-I signaling during persistent viral infection supports immune suppression, lymphoid tissue disorganization and CD4 T cell dysfunction. Systematic characterization of the cellular populations and intricacies of IFN-I signaling that promote pathology or immune suppression during acute and persistent viral infections, respectively, should inform the development of treatments and modalities to control viral associated pathologies. 
 Title: Type I interferons in viral control and immune regulation
Output: False
Paragraph: Background: Severe pneumonia is responsible for great mortality and morbidity worldwide, and early-applied effective antiinfective therapy can improve the prognosis of patients. However, identification of infectious agents in severe pneumonia remains a major challenge so far. In this study, the potential utility of transmission electron microscopy (TEM) in detecting nonbacterial pathogens in patients with severe pneumonia was retrospectively evaluated. Materials and Methods: A total of 106 patients diagnosed with severe pneumonia at our hospital from September 2015 to December 2017 were included, and their baseline clinical characteristics were collected. Nonbacterial infectious agents detected by TEM in bronchoalveolar lavage fluid (BALF) and serological tests were summarized. The detection rates were further compared between TEM and serological tests. Results: BALF examination under the transmission electron microscope revealed 24 viruses, 16 mycoplasmas, 18 chlamydia, 2 fungi and 74 bacteria in 99 samples, among which 61 samples were mixed infections. The combined use of serological tests and TEM significantly improved the detection rate of nonbacterial infectious agents in patients with severe pneumonia. Conclusions: Our data support that implementation of TEM could improve the sensitivity for detecting viruses, atypical pathogens and mixed infections in BALF from patient of severe pneumonia. Therefore, TEM may be used as an auxiliary diagnostic method of other microbiological tests in severe pneumonia. 
 Title: Transmission Electron Microscopy Improves the Diagnostic Sensitivity in Nonbacterial Etiology of Severe Pneumonia: A Retrospective Study
Output: True
Paragraph: Provision of an adequate mass of IgG from maternal colostrum is essential to health and survival of neonatal calves. Colostrum supplements (CS) have been developed to provide supplemental immunoglobulin when maternal colostrum is of poor quality. However, colostrum replacers (CR) that provide ≥100 g of IgG have not been formulated. Our objective was to determine the absorption of IgG in newborn calves fed CS derived from bovine serum or CR derived from bovine immunoglobulin concentrate. The CS were prepared by collecting, processing, and spray drying bovine serum and blending with other ingredients to provide 45 to 50 g of IgG per dose. The CR were prepared by further processing bovine serum to increase IgG concentration to >50% IgG and blending with other ingredients to provide 100 to 122 g of IgG per dose. Holstein calves (n = 160) were fed 90 to 244 g of IgG from CS or CR in 1 or 2 feedings in two experiments. Blood was collected from each calf by jugular venipuncture at 0 and 24 h of age and plasma IgG was determined by turbidimetric immunoassay. Apparent efficiency of IgG absorption was calculated. Plasma IgG concentrations at 24 h of age were indicative of IgG intake and averaged 5.5 to 14.1 g/L in calves fed CS and CR. Mean apparent efficiency of IgG absorption in calves fed CS was 25 and 28% in experiments 1 and 2, respectively. Mean apparent efficiency of IgG absorption in calves fed CR ranged from 19 to 32% and were affected by method of processing and number of times fed. Treatment of plasma with polyethylene glycol reduced the efficiency of IgG absorption in experiment 1. The addition of animal fat to CR had no effect on IgG absorption. A second feeding of CR increased plasma IgG, but efficiency of absorption was reduced. Mean body weights at 60 d of 2059 age were not affected by treatment and ranged from 64.3 to 78.2 kg. Plasma IgG concentration in calves fed ≥122 g of IgG from Ig concentrate approached (9.9 g/L) or exceeded 10 g/L, indicating successful transfer of passive immunity. Provision of IgG to prevent failure of passive transfer is possible with CR containing >20% IgG when fed at 454 g per dose. ( Abbreviation key: AEA = apparent efficiency of IgG absorption; CR = colostrum replacer; CS = colostrum supplement; MC = maternal colostrum. 
 Title: Formulation of Colostrum Supplements, Colostrum Replacers and Acquisition of Passive Immunity in Neonatal Calves 1
Output: True
Paragraph: evaluated the association between changes in the incidence of AKI and COVID-19 disease and clinical outcomes by using logistic regression models. Results: A total of 287 patients, 55 with AKI and 232 without AKI, were included in the analysis. Compared to patients without AKI, AKI patients were older, predominantly male, and were more likely to present with hypoxia and have pre-existing hypertension and cerebrovascular disease. Moreover, AKI patients had higher levels of white blood cells, D-dimer, aspartate aminotransferase, total bilirubin, creatine kinase, lactate dehydrogenase, procalcitonin, C-reactive protein, a higher prevalence of hyperkalemia, lower lymphocyte counts, and higher chest computed tomographic scores. The incidence of stage 1 AKI was 14.3%, and the incidence of stage 2 or 3 AKI was 4.9%. Patients with AKI had substantially higher mortality. Conclusions: AKI is an important complication of COVID-19. Older age, male, multiple pre-existing comorbidities, lymphopenia, increased infection indicators, elevated D-dimer, and impaired heart and liver functions were the risk factors of AKI. AKI patients who progressed to stages 2 or 3 AKI had a higher mortality rate. 
 Title: Acute kidney injury in patients hospitalized with COVID-19 in Wuhan, China: A single-center retrospective observational study MDRD Modification of Diet in Renal Disease CT Computed tomography PCR Polymerase chain reaction ACE2 Angiotensin converting enzyme II SARS-CoV Serve acute respiratory syndrome coronavirus WHO World Healthy Organization
Output: True
Paragraph: Evidence demonstrating that human rhinovirus (HRV) disease is not exclusively limited to the upper airways and may cause lower respiratory complications, together with the frequency of HRV infections and the increasing number of immunocompromised patients underline the need for rapid and accurate diagnosis of HRV infections. In this study, we developed the first quantitative real-time nucleic acid sequence-based amplification assay with an internal control using molecular beacon probes for selective and sensitive detection of human rhinovirus serotypes. We described a simple method to accurately quantify RNA target by computing the time to positivity (TTP) values for HRV RNA. Quantification capacity was assessed by plotting these TTP values against the starting number of target molecules. By using this simple method, we have significantly increased the diagnostic accuracy, precision, and trueness of real-time NASBA assay. Specificity of the method was verified in both in silico and experimental studies. Moreover, for assessment of clinical reactivity of the assay, NASBA has been validated on bronchoalveolar lavage (BAL) specimens. Our quantitative NASBA assay was found to be very specific, accurate, and precise with high repeatability and reproducibility. 
 Title: Development of a Quantitative Real-Time Nucleic Acid Sequence-Based Amplification Assay with an Internal Control Using Molecular Beacon Probes for Selective and Sensitive Detection of Human Rhinovirus Serotypes
Output: False
Paragraph: The human metapneumovirus (hMPV) is a newly described member of the Paramyxoviridae family belonging to the Metapneumovirus genus. Since its initial description in 2001, hMPV has been reported in most parts of the world and isolated from the respiratory tract of subjects from all age groups. Despite the fact that prospective and case-control studies have been limited, the epidemiology and clinical manifestations associated with hMPV have been found to be reminiscent of those of the human respiratory syncytial virus, with most severe respiratory tract infections occurring in infants, elderly subjects, and immunocompromised hosts. Additional research is needed to define the pathogenesis of this viral infection and the host's specific immune response. Acute respiratory tract infections (ARTIs) are a major cause of morbidity and mortality worldwide. A variety of viruses, including the influenza viruses, human respiratory syncytial virus (hRSV), parainfluenza viruses, adenoviruses, rhinoviruses, and coronaviruses, have been associated with clinical syndromes ranging from mild illnesses, such as the common cold, to more severe devastating conditions, such as pneumonia. However, ∼50% of the cases of community-acquired pneumonia in adults and 15%-35% of cases of bronchiolitis and pneumonia in pediatric patients are still without a known etiology [1-3]. Along with inadequate diagnostic methods, this observation also suggests that other respiratory tract infectious agents may exist and remain to be identified. A new respiratory virus, the human metapneumovirus (hMPV) was first isolated in 2001 from nasopharyngeal aspirates (NPAs) obtained from young children in The Netherlands [4] . On the basis of morphological, biochemical, and genetic features, hMPV was tentatively classified with avian metapneumovirus (APV), the causative agent of an upper respiratory tract disease in turkeys and other birds [5], in the Metapneumovirus genus. The latter, together with the Pneumovirus genus (containing hRSV as the type species), is Note added in proof. Human metapneumovirus was recently isolated from previously virus-negative nasal wash specimens from 49 (20%) of 248 young children consulting at the Vanderbilt Clinic (Nashville, TN) for lower respiratory tract illnesses [44] . Extrapolation of these results to the entire cohort of patients observed at this institution over a 25-year period (1976-2001) suggests that the prevalence of human metapneumovirus infection was ∼12% in all outpatient children with lower respiratory tract diseases. 
 Title: Human Metapneumovirus: A New Player among Respiratory Viruses
Output: True
Paragraph: Over 10 percent of recovered and discharged patients retested positive for SARS-CoV-2, raising a public health concern whether they could be potential origins of infection. In this study, we found that detectable viral genome in discharged patients might only mean the presence of viral fragments, and could hardly form an infection origin for its extremely low concentration. All rights reserved. No reuse allowed without permission. the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. 
 Title: Title: Failed detection of the full-length genome of SARS-CoV-2 by ultra-deep sequencing from the recovered and discharged patients retested viral PCR positive Authors
Output: False
Paragraph: In eukaryotes, the degradation of cellular mRNAs is accomplished by Xrn1p and 24 the cytoplasmic exosome. Because viral RNAs often lack canonical caps or poly-A tails, 25 they can also be vulnerable to degradation by these host exonucleases. Yeast lack 26 sophisticated mechanisms of innate and adaptive immunity, but do use RNA 27 degradation as an antiviral defense mechanism. One model is that the RNA of yeast 28 viruses is subject to degradation simply as a side effect of the intrinsic exonuclease 29 activity of proteins involved in RNA metabolism. Contrary to this model, we find a highly 30 refined, species-specific relationship between Xrn1p and the "L-A" totiviruses of different 31 Saccharomyces yeast species. We show that the gene XRN1 has evolved rapidly under 32 positive natural selection in Saccharomyces yeast, resulting in high levels of Xrn1p 33 protein sequence divergence from one yeast species to the next. We also show that 34 these sequence differences translate to differential interactions with the L-A virus, where 35 Xrn1p from S. cerevisiae is most efficient at controlling the L-A virus that chronically 36 infects S. cerevisiae, and Xrn1p from S. kudriavzevii is most efficient at controlling the L-37 A-like virus that we have discovered within S. kudriavzevii. All Xrn1p orthologs are 38 equivalent in their interaction with another virus-like parasite, the Ty1 retrotransposon. 
 Title: Restriction Factor in Yeasts 2 3
Output: True
Paragraph: Live attenuated recombinant measles vaccine virus (MV) Edmonston-Zagreb (EZ) strain was evaluated as a viral vector to express the ectodomains of fusion protein of respiratory syncytial virus (RSV F) or glycoprotein 350 of Epstein-Barr virus (EBV gp350) as candidate vaccines for prophylaxis of RSV and EBV. The glycoprotein gene was inserted at the 1 st or the 3 rd position of the measles virus genome and the recombinant viruses were generated. Insertion of the foreign gene at the 3 rd position had a minimal impact on viral replication in vitro. RSV F or EBV gp350 protein was secreted from infected cells. In cotton rats, EZ-RSV F and EZ-EBV gp350 induced MV-and insert-specific antibody responses. In addition, both vaccines also induced insert specific interferon gamma (IFN-) secreting T cell response. EZ-RSV F protected cotton rats from pulmonary replication of RSV A2 challenge infection. In rhesus macaques, although both EZ-RSV F and EZ-EBV gp350 induced MV specific neutralizing antibody responses, only RSV F specific antibody response was detected. Thus, the immunogenicity of the foreign antigens delivered by measles vaccine virus is dependent on the nature of the insert and the animal models used for vaccine evaluation. 
 Title: Evaluation of Measles Vaccine Virus as a Vector to Deliver Respiratory Syncytial Virus Fusion Protein or Epstein-Barr Virus Glycoprotein gp350
Output: True
Paragraph: Porcine reproductive and respiratory syndrome virus (PRRSV) is not only a poor inducer of type I interferon but also inhibits the efficient induction of type I interferon by porcine transmissible gastroenteritis virus (TGEV) and synthetic dsRNA molecules, Poly I:C. However, the mechanistic basis by which PRRSV interferes with the induction of type I interferon in its natural host cells remains less well defined. The purposes of this review are to summarize the key findings in supporting the post-transcriptional control of type I interferon in its natural host cells and to propose the possible role of translational control in the regulation of type I interferon induction by PRRSV. 
 Title: Post-Transcriptional Control of Type I Interferon Induction by Porcine Reproductive and Respiratory Syndrome Virus in Its Natural Host Cells
Output: False
Paragraph: Metabolomics aims to measure and characterise the complex composition of metabolites in a biological system. Metabolomics studies involve sophisticated analytical techniques such as mass spectrometry and nuclear magnetic resonance spectroscopy, and generate large amounts of 2 of 55 high-dimensional and complex experimental data. Open source processing and analysis tools are of major interest in light of innovative, open and reproducible science. The scientific community has developed a wide range of open source software, providing freely available advanced processing and analysis approaches. The programming and statistics environment R has emerged as one of the most popular environments to process and analyse Metabolomics datasets. A major benefit of such an environment is the possibility of connecting different tools into more complex workflows. Combining reusable data processing R scripts with the experimental data thus allows for open, reproducible research. This review provides an extensive overview of existing packages in R for different steps in a typical computational metabolomics workflow, including data processing, biostatistics, metabolite annotation and identification, and biochemical network and pathway analysis. Multifunctional workflows, possible user interfaces and integration into workflow management systems are also reviewed. In total, this review summarises more than two hundred metabolomics specific packages primarily available on CRAN, Bioconductor and GitHub. 
 Title: metabolites H OH OH The metaRbolomics Toolbox in Bioconductor and beyond
Output: True
Paragraph: Background: Feline Infectious Peritonitis (FIP) is a lethal systemic disease, caused by the FIP Virus (FIPV); a virulent mutant of Feline Enteric Coronavirus (FECV). Currently, the viruses virulence determinants and host gene expressions during FIPV infection are not fully understood. Methods: RNA sequencing of Crandell Rees Feline Kidney (CRFK) cells, infected with FIPV strain 79-1146 at 3 hours post infection (h.p.i), were sequenced using the Illumina next generation sequencing approach. Bioinformatic's analysis, based on Felis catus 2X annotated shotgun reference genome, using CLC bio Genome Workbench mapped both control and infected cell reads to 18899 genes out of 19046 annotated genes. Kal's Z test statistical analysis was used to analyse the differentially expressed genes from the infected CRFK cells. Real time RT-qPCR was developed for further transcriptional profiling of three genes (PD-1, PD-L1 and A3H) in infected CRFK cells and Peripheral Blood Mononuclear Cells (PBMCs) from healthy and FIP-diseased cats. Results: Based on Kal's Z-test, with False Discovery Rate (FDR) <0.05 and >1.99 fold change on gene expressions, a total of 61 genes were differentially expressed by both samples, where 44 genes were up-regulated and the remainder were down-regulated. Most genes were closely clustered together, suggesting a homogeneous expression. The majority of the genes that were significantly regulated, were those associated with monocytes-macrophage and Th1 cell functions, and the regulation of apoptosis. Real time RT-qPCR developed focusing on 2 up-regulated genes (PD-L1 and A3H) together with an apoptosis associated gene PD-1 expressions in FIPV infected CRFK cells and in PBMCs from healthy and FIP diagnosed cats produced concordant results with transcriptome data. Conclusion: The possible roles of these genes, and their importance in feline coronaviruses infection, are discussed. 
 Title: Transcriptional profiling of feline infectious peritonitis virus infection in CRFK cells and in PBMCs from FIP diagnosed cats
Output: True
Paragraph: Background: Flavivirus infected cells produce infectious virions and subviral particles, both of which are formed by the assembly of prM and E envelope proteins and are believed to undergo the same maturation process. Dengue recombinant subviral particles have been produced in cell cultures with either modified or chimeric proteins but not using the native forms of prM and E. Methodology/Principal Findings: We have used a codon optimization strategy to obtain an efficient expression of native viral proteins and production of recombinant subviral particles (RSPs) for all four dengue virus (DV) serotypes. A stable HeLa cell line expressing DV1 prME was established (HeLa-prME) and RSPs were analyzed by immunofluorescence and transmission electron microscopy. We found that E protein is mainly present in the endoplasmic reticulum (ER) where assembly of RSPs could be observed. Biochemical characterization of DV1 RSPs secretion revealed both prM protein cleavage and homodimerization of E proteins before their release into the supernatant, indicating that RSPs undergo a similar maturation process as dengue virus. Pulse chase experiment showed that 8 hours are required for the secretion of DV1 RSPs. We have used HeLa-prME to develop a semi-quantitative assay and screened a human siRNA library targeting genes involved in membrane trafficking. Knockdown of 23 genes resulted in a significant reduction in DV RSP secretion, whereas for 22 others we observed an increase of RSP levels in cell supernatant. Conclusions/Significance: Our data describe the efficient production of RSPs containing native prM and E envelope proteins for all dengue serotypes. Dengue RSPs and corresponding producing cell lines are safe and novel tools that can be used in the study of viral egress as well as in the development of vaccine and drugs against dengue virus. 
 Title: Efficient Assembly and Secretion of Recombinant Subviral Particles of the Four Dengue Serotypes Using Native prM and E Proteins
Output: False
Paragraph: Epidemiological and laboratory studies have shown that green tea and green tea catechins exert beneficial effects on a variety of diseases, including cancer, metabolic syndrome, infectious diseases, and neurodegenerative diseases. In most cases, (−)-epigallocatechin gallate (EGCG) has been shown to play a central role in these effects by green tea. Catechins from other plant sources have also shown health benefits. Many studies have revealed that the binding of EGCG and other catechins to proteins is involved in its action mechanism. Computational docking analysis (CMDA) and X-ray crystallographic analysis (XCA) have provided detailed information on catechin-protein interactions. Several of these studies have revealed that the galloyl moiety anchors it to the cleft of proteins through interactions with its hydroxyl groups, explaining the higher activity of galloylated catechins such as EGCG and epicatechin gallate than non-galloylated catechins. In this paper, we review the results of CMDA and XCA of EGCG and other plant catechins to understand catechin-protein interactions with the expectation of developing new drugs with health-promoting properties. 
 Title: molecules Computational Molecular Docking and X-ray Crystallographic Studies of Catechins in New Drug Design Strategies
Output: True
Paragraph: Timely detection of an inhalational anthrax outbreak is critical for clinical and public health management. Syndromic surveillance has received considerable investment, but little is known about how it will perform relative to routine clinical case finding for detection of an inhalational anthrax outbreak. We conducted a simulation study to compare clinical case finding with syndromic surveillance for detection of an outbreak of inhalational anthrax. After simulated release of 1 kg of anthrax spores, the proportion of outbreaks detected first by syndromic surveillance was 0.59 at a specificity of 0.9 and 0.28 at a specificity of 0.975. The mean detection benefit of syndromic surveillance was 1.0 day at a specificity of 0.9 and 0.32 days at a specificity of 0.975. When syndromic surveillance was sufficiently sensitive to detect a substantial proportion of outbreaks before clinical case finding, it generated frequent false alarms. 
 Title: Evaluating Detection of an Inhalational Anthrax Outbreak Detecting an Inhalational Anthrax Outbreak Emerging Infectious Diseases • www Detecting an Inhalational Anthrax Outbreak Emerging Infectious Diseases • www
Output: True
Paragraph: Background: Mesenchymal stem cells (MSCs) might act as fine-tuners of inflammation during acute lung injury. We assessed the effects of adoptive transfer of MSCs in acid aspiration acute lung injury and explored the role of long pentraxin PTX3. Methods: We conducted a prospective experimental interventional study on wildtype (WT) and PTX3-deficient (PTX3 −/− ) mice. Acute lung injury was induced in WT and PTX3 −/− mice by instillation of hydrochloric acid into the right bronchus. One hour later, animals received intraperitoneal sterile phosphate-buffered saline (PBS), WT-MSCs (1 × 10 6 ) or PTX3 −/− -MSCs (1 × 10 6 ). Twenty-four hours after injury, we measured the effects of treatments on arterial blood gases, wet/dry lung weight (W/ D), CT scan analysis of lung collapse, neutrophils, TNFα and CXCL1 in bronchoalveolar lavage, and plasma PTX3. D-dimer was assayed in 1 week and OHproline in 2 weeks to track the fibrotic evolution. Results: In 24 h, in comparison to PBS, WT-MSCs improved oxygenation and reduced W/D and alveolar collapse. These effects were associated with decreased concentrations of alveolar neutrophils and cytokines. WT-MSCs increased D-dimer concentration and decreased OH-proline levels, too. Treatment with PTX3 −/− -MSCs ameliorated oxygenation, W/D, and alveolar TNFα, though to a lesser extent than WT-MSCs. PTX3 −/− -MSCs did not improve lung collapse, neutrophil count, CXCL1, D-dimer, and OH-proline concentrations. The protective effects of WT-MSCs were dampened by lack of endogenous PTX3, too. Conclusions: In acid aspiration acute lung injury, MSCs improve pulmonary function and limit fibrosis by fine-tuning inflammation. The role of PTX3 in determining MSCs' effects might merit further scrutiny. 
 Title: Intraperitoneal adoptive transfer of mesenchymal stem cells enhances recovery from acid aspiration acute lung injury in mice
Output: False
Paragraph: Introduction Since acute respiratory tract infections inflict a high burden of disease in children worldwide, a multiplex reverse transcription polymerase chain reaction combined with a microwell hybridization assay (m-RT-PCR-ELISA) to detect 19 different respiratory pathogens was developed and validated. Methods A total of 430 respiratory specimens were retrospectively tested in parallel by both the advanced 19-valent m-RT-PCR-ELISA as well as by culture or individual RT-PCR assays used in clinical routine. The mean (median) sensitivity of the m-RT-PCR-ELISA in the retrospective test was 93.3% (95.1%; range 83.3-100 %), and the mean (median) specificity was 99.8 and 100 % (range 98.6-100 %), respectively. The mean positive predictive value was 99.3 % (range 93.4-100 %) and the mean negative predictive value was 95.3 % (range 98.4-100 %). Feasibility and clinical value of the 19-valent method was prospectively shown on 16,231 incoming clinical specimens from patients between 0 and 16 years of age with acute respiratory tract infections admitted to pediatric hospitals or private practices from October 2003 to June 2010 in three regions in Germany (Kiel, Mainz, Freiburg; Freiburg to June 2007 only). At least one microorganism was detected in 10,765 of 16,231 (66.3 %) clinical specimens: 5,044 RV, 1,999 RSV, 1,286 AV, 944 EV, 737 seasonal IVA, 173 pandemic IVA H1N1 -2009, 899 MPV, 518 CV, 383 PIV3, 268 PIV1, 259 Mpn, 205 IVB, 164 PIV2, 144 PIV4, 103 Bp, 29 Cpn and 29 Bpp, while reovirus and Lpn were not present in these specimens from a pediatric population. More than one organism could be detected in 13.4 % of the specimens. Conclusions The m-RT-PCR-ELISA evaluated here improves the spectrum for diagnosing respiratory infections and is a feasible instrument for individual diagnostic and epidemiological studies. Keywords m-RT-PCR-ELISA Á Respiratory tract infections Á Validation Á Sensitivity Á Diagnosis Á Enterovirus (EV) Á Influenza virus type A (IVA) Á Influenza virus type B (IVB) Á Respiratory syncytial virus (RSV) Á Parainfluenza virus type 1 (PIV1) Á Parainfluenza virus type 2 (PIV2) Á Parainfluenza virus type 3 (PIV3) Á Parainfluenza virus type 4 (PIV4) Á Adenovirus (AV) Á Rhinovirus (RV) Á Human metapneumovirus (MPV) Á Coronavirus (CV) Á Reovirus (ReoV) Á Mycoplasma pneumoniae (Mpn) Á 
 Title: Validation of a multiplex reverse transcriptase PCR ELISA for the detection of 19 respiratory tract pathogens
Output: False
Paragraph: Segmental and focal pathological changes were found in the glomeruli and tubules of postoperative renal-biopsy specimens from seven cases of clinically confirmed endemic (Balkan) nephropathy. In the glomeruli, there was mesangial reaction and segmental thickening of the basement membrane with subendothelial and membranous depositions. In the tubules there was spongiform degeneration and fusion of cells. In all the cells of the nephron numerous cytoplasmic vesicles containing free and budding particles (80-200 nm) were found. These particles had the characteristics of a coronavirus. Balkan 
 Title: Presse m&eacute;d. 1975, 4, 1211. 11. Smith
Output: True
Paragraph: Until now, the risk of HEV infection in schizophrenia was unknown. The present results showed that the seroprevalence of anti-HEV IgG and anti-HEV IgM in schizophrenia were significantly higher than that in healthy controls. Anti-HEV IgG positivity increased with age and with the duration of disease in schizophrenia patients. Moreover, schizophrenia patients with increased CD4 ? /CD8 ? T-cell ratios ([2.03) had higher anti-HEV IgG detection rates than those with normal ratios (1.05-2.03). Compared with the schizophrenia patients who tested anti-HEV IgG negative, the levels of interleukin-4 and interleukin-10 (Th2 cytokines) were significantly higher, while the interleukin-12 (Th1 cytokine) level was significantly lower, in those with anti-HEV IgG positivity. Of five schizophrenia patients who were anti-HEV IgM positive, four had elevated CD4 ? /CD8 ? T-cell ratios. HEV RNA was isolated from one of these four patients and classified as genotype 4. Anti-HEV IgM positivity was not detected among healthy controls. Therefore, schizophrenia patients exhibited a higher risk of HEV infection than controls. 
 Title: Increased risk of hepatitis E virus infection in schizophrenia
Output: False
Paragraph: This study contributes to the fields of hospitality and tourism by examining interactions between business conditions and financial performance of tourism firms in both China and Taiwan. We investigate whether the improvement of business conditions enhances financial performance of tourism firms and whether financial success of tourism firms matters to business development. In general, cointegration test results support a long-run equilibrium relationship between the two variables, business conditions and financial performance of tourism firms, and Granger causality test results show that these two factors reinforce each other in both China and Taiwan. This study therefore documents significant contributions of financial success of tourism firms to business development and strengthening of financial performance of tourism firms by business conditions. Some managerial implications are also discussed. r 
 Title: Interactions between business conditions and financial performance of tourism firms: Evidence from China and Taiwan
Output: False
Paragraph: The severe acute respiratory syndrome-coronavirus (SARS-CoV) caused an outbreak of atypical pneumonia in 2003. The SARS-CoV viral genome encodes several proteins which have no homology to proteins in any other coronaviruses, and a number of these proteins have been implicated in viral cytopathies. One such protein is 3a, which is also known as X1, ORF3 and U274. 3a expression is detected in both SARS-CoV infected cultured cells and patients. Among the different functions identified, 3a is a capable of inducing apoptosis. We previously showed that caspase pathways are involved in 3a-induced apoptosis. In this study, we attempted to find out protein domains on 3a that are essential for its pro-apoptotic function. Protein sequence analysis reveals that 3a possesses three major protein signatures, the cysteine-rich, Yxx and diacidic domains. We showed that 3a proteins carrying respective mutations in these protein domains exhibit reduced pro-apoptotic activities, indicating the importance of these domains on 3a's pro-apoptotic function. It was previously reported that 3a possesses potassium ion channel activity. We further demonstrated that the blockade of 3a's potassium channel activity abolished caspase-dependent apoptosis. This report provides the first evidence that ion channel activity of 3a is required for its proapoptotic function. As ion channel activity has been reported to regulate apoptosis in different pathologic conditions, finding ways to modulate the ion channel activity may offer a new direction toward the inhibition of apoptosis triggered by SARS-CoV. 
 Title: The ion channel activity of the SARS-coronavirus 3a protein is linked to its pro-apoptotic function
Output: True
Paragraph: Purpose: To examine the feasibility of using a computer tool for stratifying the severity of Coronavirus Disease 2019 (COVID-19) based on computed tomography (CT) images. Materials and methods: We retrospectively examined 44 confirmed COVID-19 cases. All cases were evaluated separately by radiologists (visually) and through an in-house computer software. The degree of lesions was visually scored by the radiologist, as follows, for each of the 5 lung lobes: 0, no lesion present; 1, <1/3 involvement; 2, >1/3 and < 2/3 involvement; and 3, >2/3 involvement. Lesion density was assessed based on the proportion of ground-glass opacity (GGO), consolidation and fibrosis of the lesions. The parameters obtained using the computer tool included lung volume (mL), lesion volume (mL), lesion percentage (%), and mean lesion density (HU) of the whole lung, right lung, left lung, and each lobe. The scores obtained by the radiologists and quantitative results generated by the computer software were tested for correlation. A Chi-square test was used to test the consistency of radiologist-and computerderived lesion percentage in the right/left lung, upper/lower lobe, and each of the 5 lobes. The results showed a strong to moderate correlation between lesion percentage scores obtained by radiologists and the computer software (r ranged from 0.7679 to 0.8373, P < 0.05), and a moderate correlation between the proportion of GGO and mean lesion density (r ¼ À0.5894, P < 0.05), and proportion of consolidation and mean lesion density (r ¼ 0.6282, P < 0.05). Computer-aided quantification showed a statistical significant higher lesion percentage for lower lobes than that assessed by the radiologists (c 2 ¼ 8.160, P ¼ 0.004). Conclusions: Our experiments demonstrated that the computer tool could reliably and accurately assess the severity and distribution of pneumonia on CT scans. 
 Title: Quantitative computed tomography analysis for stratifying the severity of Coronavirus Disease 2019-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/)
Output: False
Paragraph: The major physiological function of milk is the transport of amino acids, carbohydrates, lipids and minerals to mammalian offspring. Caseins, the major milk proteins, are secreted in the form of a micelle consisting of protein and calciumphosphate. We have analysed the role of the milk protein a-casein by inactivating the corresponding gene in mice. Absence of a-casein protein significantly curtails secretion of other milk proteins and calcium-phosphate, suggesting a role for a-casein in the establishment of casein micelles. In contrast, secretion of albumin, which is not synthesized in the mammary epithelium, into milk is not reduced. The absence of a-casein also significantly inhibits transcription of the other casein genes. a-Casein deficiency severely delays pup growth during lactation and results in a life-long body size reduction compared to control animals, but has only transient effects on physical and behavioural development of the pups. The data support a critical role for a-casein in casein micelle assembly. The results also confirm lactation as a critical window of metabolic programming and suggest milk protein concentration as a decisive factor in determining adult body weight. 
 Title: Milk Lacking a-Casein Leads to Permanent Reduction in Body Size in Mice
Output: True
Paragraph: This study applied a financial portfolio theory to estimate optimal market mixes to minimize the instability of inbound tourist market demand. An empirical analysis was applied to inbound tourists to Taiwan. The results shed light on diversification in tourism market and offer tourism authorities and policy-makers explicit guidelines for risk management in the destination planning process. Specifically, using optimal mixes with various return/risk options can facilitate a more stable pattern of arrivals from foreign countries. To achieve the Doubling Tourist Arrivals Plan, introduced by the Taiwanese government in 2002, the tourism authorities should take the high-return/ high-risk option and shift available resources to Japan. More policy implications are provided to guide tourism authorities and policy makers. r 
 Title: Financial portfolio approach to optimal tourist market mixes
Output: False
Paragraph: This research reports the design, analysis, integration, and test of a prototype of a real-time convective polymerase chain reaction (RT-cPCR) machine that uses a color charged coupled device (CCD) for detecting the emission of fluorescence intensity from an RT-cPCR mix in a microliter volume glass capillary. Because of its simple mechanism, DNA amplification involves employing the cPCR technique with no need for thermocycling control. The flow pattern and temperature distribution can greatly affect the cPCR process in the capillary tube, a computational fluid dynamics (CFD) simulation was conducted in this study for the first time to estimate the required period of an RT-cPCR cycle. This study also tested the PCR mix containing hepatitis B virus (HBV) plasmid samples by using SYBR Green I fluorescence labeling dye to assess the prototype performance. The measured results from the image-processing scheme indicate that the RT-cPCR prototype with a CCD-based fluorometer can achieve similar DNA quantification reproducibility compared to commercial machines, even when the initial DNA concentration in the test PCR mix is reduced to 10 copies/L 
 Title: A real-time convective PCR machine in a capillary tube instrumented with a CCD-based fluorometer
Output: False