niryuu/sni-each-converted huggingface dataset:
Paragraph: To reduce the use of antibiotics in animal agriculture, a number of effective or commercially viable alternatives have been implemented by food animal producers or are under development. Perhaps the most well-established strategies are flock and herd management practices to mitigate disease introduction and spread, and, subsequently, reduce the need for antibiotic use. While vaccines in food animal production have been used to prevent both bacterial and viral diseases, but historically, most vaccines have targeted viral diseases. Though vaccines against viral diseases can help reduce the need for antibiotic use by controlling the spread of secondary bacterial infections, more recent vaccines under development specifically target bacteria. New developments in selecting and potentially tailoring bacteriophages provide a promising avenue for controlling pathogenic bacteria without the need for traditional small-molecule antibiotics. In this article we discuss these established and emerging strategies, which are anticipated to reduce the reliance on antibiotics in food animal production and should reduce the prevalence and transmission to humans of antimicrobial resistant bacteria from these systems. 
 Title: ANNALS OF THE NEW YORK ACADEMY OF SCIENCES From farm management to bacteriophage therapy: strategies to reduce antibiotic use in animal agriculture
Output: False
Paragraph: In this paper, we extend the model of Liu and Zhang (Math Comput Model 54:836-845, 2011) by incorporating three control terms and apply optimal control theory to the resulting model. Optimal control strategies are proposed to minimize both the disease burden and the intervention cost. We prove the existence and uniqueness of optimal control paths and obtain these optimal paths analytically using Pontryagin's Maximum Principle. We analyse our results numerically to compare various strategies of proposed controls. It is observed that implementation of three controls is most effective and less expensive among all the strategies. Thus, we conclude that in order to reduce tuberculosis threat all the three controls must be taken into consideration concurrently. 
 Title: Optimal control analysis of a tuberculosis model R , RR
Output: True
Paragraph: To assess the economic impact of bovine coronavirus (BCV) and bovine respiratory syncytial virus (BRSV) infections, accurate estimates of their associated effects on animal performance are needed. This study aimed to quantify the variation in individual test-day milk yield and somatic cell count, risk of reproductive failure after first service of dairy cows, and risk of death of calves and heifers according to the BCV and BRSV status of the herd. Three types of status were defined for BCV and BRSV infections, based on 1) the dynamics over a 7-mo period of BCV-and BRSV-specific antibody levels in pooled milk of primiparous cows; 2) the possible occurrence of presumably BCV-and BRSV-related clinical outbreaks; and 3) the combination of both pieces of information. A total of 36,184 test days, 2,716 cows with a first service, and 4,104 calves and heifers in 65 Swedish herds were included in the analyses. Animal performance associated with BCV and BRSV infections was quantified using hierarchical mixed generalized and survival models, after adjustment for covariates known to influence the performance under study. A significant reduction in milk yield was observed for cows in presumably BRSV recently infected herds, as well as in herds having a presumably BRSV-related clinical outbreak (of 0.57 and 0.91 kg/d, respectively), compared with cows in presumably infection-free herds. There was also a significant increase in somatic cell count (of 12,000 cells/mL) for cows located in herds with a BRSV outbreak. The risk of failure after first service, as well as the risk of death in calf and heifer, was numerically higher in BRSV-infected herds, although this was not statistically significant. In contrast, BCV infection herd status, as defined in the present study, was not significantly associated with any production losses in animals from infected herds compared with those in infection-free herds. 
 Title: Associations between bovine coronavirus and bovine respiratory syncytial virus infections and animal performance in Swedish dairy herds
Output: False
Paragraph: Although hepatitis C virus (HCV) affects approximately 130-170 million people worldwide, no vaccines are available. HCV is an important cause of chronic hepatitis, cirrhosis and hepatocellular carcinoma, leading to the need for liver transplantation. In this study, curcumin, a constituent used in traditional Chinese medicine, has been evaluated for its anti-HCV activity and mechanism, using a human hepatoma cell line containing the HCV genotype 1b subgenomic replicon. Below the concentration of 20% cytotoxicity, curcumin dose-dependently inhibited HCV replication by luciferase reporter gene assay, HCV RNA detection and HCV protein analysis. Under the same conditions, curcumin also dose-dependently induced heme oxygenase-1 with the highest induction at 24 h. Hemin, a heme oxygenase-1 inducer, also inhibited HCV protein expression in a dose-dependent manner. The knockdown of heme oxygenase-1 partially reversed the curcumin-inhibited HCV protein expression. In addition to the heme oxygenase-1 induction, signaling molecule activities of AKT, extracellular signal-regulated kinases (ERK) and nuclear factor-κB (NF-κB) were inhibited by curcumin. Using specific inhibitors of PI3K-AKT, MEK-ERK and NF-κB, the results suggested that only PI3K-AKT inhibition is positively involved in curcumin-inhibited HCV replication. Inhibition of ERK and NF-κB was likely to promote HCV protein expression. In summary, curcumin inhibited HCV replication by heme oxygenase-1 induction and AKT pathway inhibition. Although curcumin also inhibits ERK and NF-κB activities, it slightly increased the HCV protein expression. This result may provide information when curcumin is used as an adjuvant in anti-HCV therapy. 
 Title: Curcumin inhibits HCV replication by induction of heme oxygenase-1 and suppression of AKT
Output: True
Paragraph: Apolipoprotein D (ApoD) gene expression is increased in several neurological disorders such as Alzheimer's disease (AD) and multiple sclerosis. We previously showed that transgenic mice that overexpress human ApoD show a better resistance against paraquat or OC43 coronavirusinduced neurodegeneration. Here, we identified several nuclear factors from the cortex of control and OC43-infected mice which bind a fragment of the proximal ApoD promoter in vitro. Of interest, we detected apolipoprotein E (ApoE). Human ApoE consists of three isoforms (E2, E3, and E4) with the E4 and E2 alleles representing a greater and a lower risk for developping AD, respectively. Our results show that ApoE is located in the nucleus and on the ApoD promoter in human hepatic and glioblastoma cells lines. Furthermore, overexpression of ApoE3 and ApoE4 isoforms but not ApoE2 significantly inhibited the ApoD promoter activity in U87 cells (E3/E3 genotype) cultured under normal or different stress conditions while ApoE knock-down by siRNA had a converse effect. Consistent with these results, we also demonstrated by ChIP assay that E3 and E4 isoforms, but not E2, bind the ApoD promoter. Moreover, using the Allen Brain Atlas in situ hybridization database, we observed an inverse correlation between ApoD and ApoE mRNA expression during development and in several regions of the mouse brain, notably in the cortex, hippocampus, plexus choroid, and cerebellum. This negative correlation was also observed for cortex layers IV-VI based on a new Transcriptomic Atlas of the Mouse Neocortical Layers. These findings reveal a new function for ApoE by regulating ApoD gene expression. 
 Title: Binding and Repressive Activities of Apolipoprotein E3 and E4 Isoforms on the Human ApoD Promoter
Output: True
Paragraph: The abdominal region is the large part of the body extending from the diaphragm to the pelvis. It includes the abdominal and pelvic cavities, bound by bone and muscle. The peritoneum is the largest and most complexly arranged serous membrane in the body. It forms the lining of the peritoneal cavity, which extends in abdominal cavity and contains the gastrointestinal tract; major abdominal organs, such as the liver, spleen, pancreas, urinary bladder, ovaries, and uterus; and many nerves, vessels, and lymph nodes. The peritoneum extends caudally in the pelvic cavity in males and females (as vaginal tunic and vaginal process, respectively). It is a serous membrane, divided into the parietal peritoneum, which covers the inner surface of the abdominal wall (the abdominal fascia) and the pelvic and scrotal cavities; the visceral peritoneum, which covers the abdominal, pelvic, and scrotal organs; and the connecting peritoneum, which extends between organs or between an organ and the parietal peritoneum, forming peritoneal folders that are divided into mesenteries, omenta, and ligaments. The purpose of the peritoneum is to provide a frictionless surface over which the viscera can move. It also serves as a site of fluid transport. A capillary film of serous fluid separates the parietal and visceral layers of the peritoneum from one another and lubricates the peritoneal surfaces. The retroperitoneal region extends dorsal to the peritoneal and pelvic cavities from the diaphragm to the pelvic inlet. It is bordered dorsally by the vertebrae and paraspinal muscles and laterally by the muscular abdominal and pelvic walls. The kidneys, ureters, and adrenal glands are considered to be retroperitoneal organs. The descending aorta, caudal vena cava, lumbar lymph nodes, cisterna chili, lymphatics, fat, and much of the abdominal wall musculature are also are also located in the 
 Title: The Peritoneal Cavity, Retroperitoneum, and Abdominal Wall
Output: True
Paragraph: The viral RNA-dependent RNA polymerase (RdRp) is essential for multiplication of all RNA viruses. The sequence diversity of an RNA virus population contributes to its ability to infect the host. This diversity emanates from errors made by the RdRp during RNA synthesis. The physical basis for RdRp fidelity is unclear but is linked to conformational changes occurring during the nucleotide-addition cycle. To understand RdRp dynamics that might influence RdRp function, we have analyzed all-atom molecular dynamics simulations on the nanosecond timescale of four RdRps from the picornavirus family that exhibit 30-74% sequence identity. Principal component analysis showed that the major motions observed during the simulations derived from conserved structural motifs and regions of known function. The dynamics of residues participating in the same biochemical property, for example, RNA binding, nucleotide binding or catalysis, were correlated even when spatially distant on the RdRp structure. The conserved and correlated dynamics of functional structural elements suggest coevolution of dynamics with structure and function of the RdRp. Crystal structures of all picornavirus RdRps exhibit a template-nascent RNA duplex channel too small to fully accommodate duplex RNA. Simulations revealed opening and closing motions of the RNA and nucleoside triphosphate channels, which might be relevant to nucleoside triphosphate entry, inorganic pyrophosphate exit and translocation. A role for nanosecond timescale dynamics in RdRp fidelity is supported by the altered dynamics of the high-fidelity G64S derivative of PV RdRp relative to wild-type enzyme. 
 Title: Molecular Dynamics Simulations of Viral RNA Polymerases Link Conserved and Correlated Motions of Functional Elements to Fidelity
Output: True
Paragraph: Background: Given that YKL-40 is a known marker of inflammation, we sought to determine its association with urinary tract infection (UTI) in febrile children. Methods: In total, 44 children aged 0 to 24 months with febrile UTI and 35 age-and sexmatched controls with fever from other causes were enrolled in the study. ELISA was performed to determine the level of YKL-40 in urine collected from each child. The ratio of urinary YKL-40 to creatinine (Cr) was higher in the children with a UTI than in the controls (P < 0.001). The area under the ROC curve for detecting UTI was 0.88 for the urinary YKL-40/Cr ratio, 0.86 for pyuria, and 0.71 for positive nitrite on urinalysis. We applied a cut-off value of 125.23 pg/mg to urinary YKL-40/Cr for detecting UTI. Eight of nine children in the control group with pyuria had urinary YKL-40/Cr levels lower than 125.23 pg/mg, and the one child in the UTI group without pyuria or positive nitrite had a urinary YKL-40/Cr level greater than 125.23 pg/mg. Determining the levels of urinary YKL-40/Cr may help identify true cases of UTI in febrile young children, especially when they have pyuria but not nitrite, or have neither pyuria nor nitrite in the urine. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. 
 Title: Urinary YKL-40 as a Candidate Biomarker for Febrile Urinary Tract Infection in Young Children
Output: False
Paragraph: Chronic hepatitis B virus (HBV) infection, affecting approximately 240 million people worldwide, is a major public health problem that elevates the risk of developing liver cirrhosis and hepatocellular carcinoma. Given that current anti-HBV drugs are limited to interferon-based regimens and nucleos(t)ide analogs, the development of new anti-HBV agents is urgently needed. The viral entry process is generally an attractive target implicated in antiviral strategies. Using primary cells from humans and Tupaia belangeri, as well as HepaRG cells, important determinants of viral entry have been achieved. Recently, sodium taurocholate cotransporting polypeptide (NTCP) was identified as an HBV entry receptor and enabled the establishment of a susceptible cell line that can efficiently support HBV infection. This finding will allow a deeper understanding of the requirements for efficient HBV infection, including the elucidation of the molecular entry mechanism. In addition, pharmacological studies suggest that NTCP is able to serve as a therapeutic target. This article summarizes our current knowledge on the mechanisms of HBV entry and the role of NTCP in this process. Int. J. Mol. Sci. 2014, 15 2893  
 Title: NTCP and Beyond: Opening the Door to Unveil Hepatitis B Virus Entry
Output: False
Paragraph: Background: Bronchiolitis is a common lower respiratory tract infection in infancy. The aim of this review is to present the clinical profi le of viral bronchiolitis, the different culprit viruses and the disease severity in relation to the viral etiology. Data sources: Databases including PubMed and Google Scholar were searched for articles about the clinical features of bronchiolitis and its viral etiology. The most relevant articles to the scope of this review were analyzed. Results: Currently there are two main definitions for bronchiolitis which are not identical, the European definition and the American one. The most common viral pathogen that causes bronchiolitis is respiratory syncytial virus which was identified in 1955; now many other viruses have been implicated in the etiology of bronchiolitis such as rhinovirus, adenovirus, metapneumovirus, and bocavirus. Several studies have attempted to investigate the correlation of bronchiolitis severity with the type of detected virus or viruses. However, the results were not consitent. Conclusions: For the time being, the diagnosis of bronchiolitis remains clinical. The isolation of the responsible respiratory pathogens does not seem to confer to the prognosis of the disease severity. World J Pediatr 2017;13(4):293-299 
 Title: Viral bronchiolitis in infancy Etiology and clinical features of viral bronchiolitis in infancy
Output: False
Paragraph: Severe acute respiratory syndrome coronavirus (SARS-CoV) encodes eight accessory proteins, the functions of which are not yet fully understood. SARS-CoV protein 6 (P6) is one of the previously studied accessory proteins that have been documented to enhance viral replication and suppress host interferon (IFN) signaling pathways. Through yeast two-hybrid screening, we identified eight potential cellular P6-interacting proteins from a human spleen cDNA library. KEYWORDS severe acute respiratory syndrome coronavirus (SARS-CoV); P6; N-Myc (and STAT) interactor (Nmi); interferon (IFN) signaling pathway; ubiquitination; proteosomal degradation 
 Title: Severe acute respiratory syndrome coronavirus protein 6 mediates ubiquitin-dependent proteosomal degradation of N-Myc (and STAT) interactor
Output: False
Paragraph: Acute lung injury (ALI), and its more severe form, acute respiratory distress syndrome (ARDS), are syndromes of acute hypoxemic respiratory failure resulting from a variety of direct and indirect injuries to the gas exchange parenchyma of the lungs. The clinical syndrome is characterized by critical hypoxemia (partial pressure of oxygen in arterial blood/fraction of inspired oxygen <300 for ALI and <200 for ARDS), bilateral pulmonary infiltrates suggesting edema, no clinical or measured evidence of cardiac failure, and no other explanation for these findings. Pulmonary or nonpulmonary infections with sepsis are the most common causes of ALI and ARDS, although gastric aspiration, massive transfusions, trauma, and other factors contribute. 1 The diversity of causes and the stereotyped physiologic and pathologic responses have made modeling human ALI and ARDS difficult, but new themes are evolving from experimental studies, some of which are reviewed in this article. Most of what is known about the pathology of ALI and ARDS comes from the studies of patients who have died, although a limited number of patients have undergone open lung biopsy (Fig. 1) . The pathologic changes include an early phase of diffuse alveolar damage, with an increase in endothelial permeability, evidence of intravascular thrombi, severe epithelial injury with denudation of alveolar wall basement membranes, accumulation of protein and fibrin-rich alveolar infiltrates in the airspaces, and abundant alveolar neutrophilic infiltrates. If patients survive, these changes progress for days to a repair phase, characterized by hyaline membrane formation, transition from neutrophilic to mononuclear infiltrates, and the appearance of intra-alveolar and 
 Title: Experimental Models and Emerging Hypotheses for Acute Lung Injury Lung injury Animal model Respiratory distress
Output: True
Paragraph: Immunization of pigs with a modified live porcine reproductive and respiratory syndrome virus (PRRSV) vaccine initially elicits a weak interferon (IFN)-g response. To improve the immune response, an adjuvant consisting of plasmid encoding either porcine interleukin (IL)-12 or IFN-a was co-administered during vaccination. In the presence of either adjuvant, at least a threefold increase in the primary virus-specific IFN-g response was observed. While this enhancement was only transient (1 week) when the IL-12 expressing plasmid was used, the effect was not only still apparent at 6 weeks after vaccination in the presence of the IFN-a expressing plasmid but even after challenge with a virulent genetically divergent PRRSV. In contrast, no effect of either adjuvant on the production of anti-virus antibodies was noticed throughout the study. Despite the apparent augmentation of a T helper (Th) 1 type response by the inclusion of IFN-a or IL-12 during vaccination, this modulation did not necessarily correlate with a reduction in viremia. Since a similar increase in the degree of the IFN-g response to the PRRSV vaccine could be achieved by substituting polyinosinic-polycytidylic acid in lieu of either cytokine, exposure to PRRSV in the presence of a variety of Th 1 polarizing molecules can positively influence the development of the cell-mediated immune response of swine to this pathogen. Conceivably, such intervention could be applied to improve the formulation of anti-PRRSV vaccines. # 
 Title: Cytokines and synthetic double-stranded RNA augment the T helper 1 immune response of swine to porcine reproductive and respiratory syndrome virus
Output: True
Paragraph: Host infection by microbial pathogens cues global changes in microbial and host cell biology that facilitate microbial replication and disease. The complete maps of thousands of bacterial and viral genomes have recently been defined; however, the rate at which physiological or biochemical functions have been assigned to genes has greatly lagged. The National Institute of Allergy and Infectious Diseases (NIAID) addressed this gap by creating functional genomics centers dedicated to developing high-throughput approaches to assign gene function. These centers require broad-based and collaborative research programs to generate and integrate diverse data to achieve a comprehensive understanding of microbial pathogenesis. High-throughput functional genomics can lead to new therapeutics and better understanding of the next generation of emerging pathogens by rapidly defining new general mechanisms by which organisms cause disease and replicate in host tissues and by facilitating the rate at which functional data reach the scientific community. 
 Title: Next-Generation High-Throughput Functional Annotation of Microbial Genomes
Output: False
Paragraph: Virus population disease dynamics in various species of ecosystem keep the research interests alive for many centuries. In this research article, an attempt has been made to understand the qualitative behavior of a virus infection model with Lytic and Non-Lytic Immune Responses by perturbing with randomness (white noise) via Lyapunov technique. The conditions for the extinction and permanence of the viral infection in the interacting populations has been found, analyzed and supported with numerical simulations. An application to HIV infection model has also been presented for drawing a comparative study of the model under various modeling methods. The research findings of this paper reveal that a study that includes random fluctuations of the environment prove to be the ideal way to bring out the qualitative analysis of a mathematical model that will depict the real world scenario. 
 Title: Effects of randomness on viral infection model with application
Output: True
Paragraph: Background: Conflicts between professional duties and fear of influenza transmission to family members may arise among health care professionals (HCP). We surveyed employees at our university hospital regarding ethical issues arising during the management of an influenza pandemic. Of 644 respondents, 182 (28%) agreed that it would be professionally acceptable for HCP to abandon their workplace during a pandemic in order to protect themselves and their families, 337 (52%) disagreed with this statement and 125 (19%) had no opinion, with a higher rate of disagreement among physicians (65%) and nurses (54%) compared with administrators (32%). Of all respondents, 375 (58%) did not believe that the decision to report to work during a pandemic should be left to the individual HCP and 496 (77%) disagreed with the statement that HCP should be permanently dismissed for not reporting to work during a pandemic. Only 136 (21%) respondents agreed that HCW without children should primarily care for the influenza patients. Our results suggest that a modest majority of HCP, but only a minority of hospital administrators, recognises the obligation to treat patients despite the potential risks. Professional ethical guidelines allowing for balancing the needs of society with personal risks are needed to help HCP fulfil their duties in the case of a pandemic influenza. 
 Title: BMC Public Health Influenza pandemic and professional duty: family or patients first? A survey of hospital employees
Output: True
Paragraph: A dataset of 103 SARS-CoV isolates (101 human patients and 2 palm civets) was investigated on different aspects of genome polymorphism and isolate classification. The number and the distribution of single nucleotide variations (SNVs) and insertions and deletions, with respect to a "profile", were determined and discussed ("profile" being a sequence containing the most represented letter per position). Distribution of substitution categories per codon positions, as well as synonymous and non-synonymous substitutions in coding regions of annotated isolates, was determined, along with amino acid (a.a.) property changes. Similar analysis was performed for the spike (S) protein in all the isolates (55 of them being predicted for the first time). The ratio Ka/Ks confirmed that the S gene was subjected to the Darwinian selection during virus transmission from animals to humans. Isolates from the dataset were classified according to genome polymorphism and genotypes. Genome polymorphism yields to two groups, one with a small number of SNVs and another with a large number of SNVs, with up to four subgroups with respect to insertions and deletions. We identified three basic nine-locus genotypes: TTTT/TTCGG, CGCC/TTCAT, and TGCC/TTCGT, with four subgenotypes. Both classifications proposed are in accordance with the new insights into possible epidemiological spread, both in space and time. 
 Title: SARS-CoV Genome Polymorphism: A Bioinformatics Study
Output: True
Paragraph: Ubiquitin (UB) is a protein modifier that regulates many essential cellular processes. To initiate protein modification by UB, the E1 enzyme activates the C-terminal carboxylate of UB to launch its transfer through the E1-E2-E3 cascade onto target proteins. In this study, we used phage display to profile the specificity of the two human E1 enzymes, Ube1 and Uba6, towards the Cterminal sequence of UB ending with 71 LRLRGG 76 . Phage selection revealed that while Arg72 of UB is absolutely required for E1 recognition, UB residues at positions 71, 73 and 74 can be replaced with bulky aromatic side chains, and Gly75 of UB can be changed to Ser, Asp and Asn for efficient E1 activation. We have thus found that the E1 enzymes have substantial promiscuity regarding the UB C-terminal sequence. The UB variants from phage selection can also be transferred from E1 to E2 enzymes, however, they are blocked from further transfer to the E3 enzymes. This suggests that the C-terminal sequence of UB is important for its discharge from E2 and subsequent transfer to E3. In addition, we observed that the Leu73Phe and Leu73Tyr single mutants of UB are resistant to cleavage by deubiquitinating enzymes (DUBs), although they can be assembled by the E1-E2-E3 cascade into poly-UB chains, thus indicating differences in UB Cterminal specificities between the E1 and DUBs. Consequently these UB mutants may provide stability to UB polymers attached to cellular proteins and facilitate the elucidation of the biological signals encoded in the UB chains. Ubiquitin (UB) is a 76-residue protein that is attached to cellular proteins through an isopeptide bond between the C-terminal carboxylate of UB and the ε-amino group of a Lys residue on the modified protein. 1 Protein modifications by UB are associated with a myriad of cellular functions, including regulation of protein degradation, designation of protein 
 Title: Specificity of the E1-E2-E3 Enzymatic Cascade for Ubiquitin C- terminal Sequences Identified by Phage Display HHS Public Access Author manuscript Supplementary Material Refer to Web version on PubMed Central for supplementary material
Output: False
Paragraph: Notably, DC roles in regulating innate CD11b + Ly-6C hi monocyte functions during neuroinflammation have not yet been addressed. Using selective ablation of CD11c hi PDCA-1 int/lo DCs without alteration in CD11c int PDCA-1 hi plasmacytoid DC number, we found that CD11c hi DCs are essential to control neuroinflammation caused by infection with neurotropic Japanese encephalitis virus, through early and increased infiltration of CD11b + Ly-6C hi monocytes and higher expression of CC chemokines. More interestingly, selective CD11c hi DC ablation provided altered differentiation and function of infiltrated CD11b + Ly-6C hi monocytes in the CNS through Flt3-L and GM-CSF, which was closely associated with severely enhanced neuroinflammation. Furthermore, CD11b + Ly-6C hi monocytes generated in CD11c hi DC-ablated environment had a deleterious rather than protective role during neuroinflammation, and were more quickly recruited into inflamed CNS, depending on CCR2, thereby exacerbating neuroinflammation via enhanced supply of virus from the periphery. Therefore, our data demonstrate that CD11c hi DCs provide a critical and unexpected role to preserve the immune-privileged CNS in lethal neuroinflammation via regulating the differentiation, function, and trafficking of CD11b + Ly-6C hi monocytes. 
 Title: CD11c hi Dendritic Cells Regulate Ly-6C hi Monocyte Differentiation to Preserve Immune-privileged CNS in Lethal Neuroinflammation OPEN
Output: False
Paragraph: Licorice, the oldest Chinese traditional medicine, is widely used in the treatment of human diseases. Due to the deficiency of wild resource, selecting and breeding becomes a key issue to expanding the supply of licorice. Spaceflight technology will become a new method for medicinal plants. The aim of this study was to investigate the effect of spaceflight on the components and anti-inflammatory activity in licorice. After flowing on a recoverable satellite for 18 days, licorice seeds were germinated and grown to maturity and the parallel groundbased seeds were also planted under the same conditions. The main components in licorice root were analyzed through HPLC. The contents of two components in spaceflight groups were higher than that of the ground control ones. Three acute inflammatory models including xyleneinduced auricular edema, carrageenan-induced paw edema and acetic acid-induced vascular permeability were utilized to compare the anti-inflammatory activity of licorice pre and post spaceflight. The licorice extract showed the significant anti-inflammation activity. After the spaceflight, the pharmacological activity of licorice got higher than that of the ground control one. All of the models gained the tendency that the spaceflight group of species Hangjinqi had the strongest activity than other groups. The research provided the scientific data for a new breeding of medicinal plant through the spaceflight and indicated that the technology of space flight may be a new effective method for the breeding and cultivation of licorice. 
 Title: Effects of Space Flight on the Chemical Constituents and Anti-Inflammatory Activity of Licorice (Glycyrrhiza uralensis Fisch)
Output: True
Paragraph: This paper presents the results of investigations whose aim was to describe the influence of the pressure difference level on the ability of contaminants migration between neighbouring rooms in dynamic conditions associated with door swing. The analysis was based on airflow visualization made with cold smoke, which simulated the heavy contaminants. The test room was pressurized to a specific level and then the door was opened to observe the trail of the smoke plume in the plane of the door. The door was opened in both directions: to the positively and negatively pressurized room. This study focuses on the visualization of smoke plume discharge and an uncertainty analysis is not applicable. Unlike other studies which focus on the analysis of pressure difference, the present study looks at the contaminants which are heavier than air and on "pumping out" the contaminants by means of door swing. Setting the proper level of pressure difference between the contaminated room and the neighbouring rooms can prove instrumental in ensuring protection against toxic contaminants migration. This study helped to establish the threshold of pressure difference necessary to reduce migration of heavy contaminants to neighbouring rooms. 
 Title: Influence of the Pressure Difference and Door Swing on Heavy Contaminants Migration between Rooms
Output: True
Paragraph: Human immunodeficiency virus (HIV) is a global health concern affecting millions of individuals with a wide variety of currently circulating subtypes affecting various regions of the globe. HIV relies on multiple regulatory proteins to modify the host cell to promote replication in infected T cells, and these regulatory proteins can have subtle phenotypic differences between subtypes. One of these proteins, HIV-1 Trans-Activator of Transcription (Tat), is capable of RNA interference (RNAi) Silencing Suppressor (RSS) activity and induction of cell death in T cells. However, the subtype-specific RSS activity and induction of cell death have not been explored. We investigated the ability of Tat subtypes and variants to induce RSS activity and cell death. TatB, from HIV-1 subtype B, was found to be a potent RSS activator by 40% whereas TatC, from HIV-1 subtype C, showed 15% RSS activity while subtype TatC variants exhibited varying levels. A high level of cell death (50-53%) was induced by subtype TatB when compared to subtype TatC (25-28%) and varying levels were observed with subtype TatC variants. These differential activities could be due to variations in the functional domains of Tat. These observations further our understanding of subtype-specific augmentation of Tat in HIV-1 replication and pathogenesis. 
 Title: In-Vitro Subtype-Specific Modulation of HIV-1 Trans-Activator of Transcription (Tat) on RNAi Silencing Suppressor Activity and Cell Death
Output: False
Paragraph: The ability to rapidly and reliably develop hypotheses on the function of newly discovered protein sequences requires systematic and comprehensive analysis. Such an analysis, embodied within the DS GeneAtlas1 1 pipeline, has been used to critically evaluate the severe acute respiratory syndrome (SARS) genome with the goal of identifying new potential targets for viral therapeutic intervention. This paper discusses several new functional hypotheses on the roles played by the constituent gene products of SARS, and will serve as an example of how such assignments can be developed or extended on other systems of interest. 
 Title: Assessment of putative protein targets derived from the SARS genome 1
Output: True
Paragraph: Molecular techniques have enabled major advances in the speed and sensitivity of the laboratory diagnosis of respiratory infections. Although the polymerase chain reaction is the most commonly used, there are several other methods available, which have applicability across the range of microbial pathogens. This review does not intend to be a comprehensive treatise on the rapid diagnosis of respiratory infections. There are several excellent textbooks that cover the field in detail 1,2 . It will, instead, focus on recent and future trends. Laboratory diagnosis is essential in the overwhelming majority of clinical conditions that require specific therapy. It is a misconception, for example, that streptococcal pharyngitis can be reliably differentiated on clinical grounds from viral pharyngitis in an individual patient. Probability estimates can be made (for instance common cold symptoms have an 80% negative predictive value for the diagnosis of bacterial pharyngitis), but confirmation is only after laboratory examination. Most diagnostic advances in the last decade have focused on detection technologies. It should not be forgotten, however, that sampling inadequacies are the prime reason for failure to identify aetiology. It is well recognised that, for most respiratory viruses, the delay in transport of the specimen to the laboratory is usually the major factor in both slowness of the process and a failure to make a diagnosis. There has been some success in applying near-patient testing. This has, in general, made the diagnosis of respiratory tract virus infection more reliable and speedier. It has had particular use in differentiating respiratory syncytial virus cases who might need admission from other causes of viral respiratory tract infection. Another important consideration is the type of specimen used. For lower respiratory tract bacterial infections, sputum is the gold standard specimen, but the quality of the specimen is key because oral and gastrointestinal secretions may contaminate it. Ideally, there should be fewer than 10 squamous cells and greater than 25 leukocytes in a low power (x100 
 Title: Recent advances in the rapid diagnosis of respiratory tract infection
Output: False
Paragraph: Plasmacytoid dendritic cells (pDC) have been shown to efficiently sense HCV-or HIV-infected cells, using a virion-free pathway. Here, we demonstrate for classical swine fever virus, a member of the Flaviviridae, that this process is much more efficient in terms of interferon-alpha induction when compared to direct stimulation by virus particles. By employment of virus replicon particles or infectious RNA which can replicate but not form de novo virions, we exclude a transfer of virus from the donor cell to the pDC. pDC activation by infected cells was mediated by a contact-dependent RNA transfer to pDC, which was sensitive to a TLR7 inhibitor. This was inhibited by drugs affecting the cytoskeleton and membrane cholesterol. We further demonstrate that a unique viral protein with ribonuclease activity, the viral E rns protein of pestiviruses, efficiently prevented this process. This required intact ribonuclease function in intracellular compartments. We propose that this pathway of activation could be of particular importance for viruses which tend to be mostly cell-associated, cause persistent infection, and are non-cytopathogenic. 
 Title: Efficient Sensing of Infected Cells in Absence of Virus Particles by Blasmacytoid Dendritic Cells Is Blocked by the Viral Ribonuclease E rns
Output: False
Paragraph: Background: The dendritic cell-specific intercellular adhesion molecule 3 grabbing non-integrin (DC-SIGN) is an important pathogen recognition receptor of the innate immune system. DC-SIGN promoter variants play important role in the susceptibility to various infectious diseases. Nasopharyngeal carcinoma (NPC) is a malignancy that is common in southern China and whether DC-SIGN promoter variants have effects on susceptibility to NPC is still unknown. The aim of this study is to ascertain the potential involvement of DC-SIGN promoter single nucleotide polymorphisms (SNPs) in NPC susceptibility. Methods: We conducted a case control study based on Cantonese population including 444 NPC patients and 464 controls matched on age and sex. The 1041 bp of DC-SIGN promoter region was directly sequenced for all samples. Sequence alignment and SNP search were inspected using DNAStar analysis programs and haplotype frequencies were estimated in Haploview V 4.0. The associations between the SNPs and the risk of NPC were analyzed using chi-square test and non-conditional logistic regression analysis with SPSS 13.0 software. Results: A total of six variants were observed in the DC-SIGN promoter region and DC-SIGN -139 GG and -939 AA were significantly associated with NPC risk with adjusted Odds Ratios (ORs) of 2.10 (95% confidence interval [CI] = 1.23-3.59; P = 0.006) and 2.52 (1.29-4.93; P = 0.007) respectively and subjects carrying the risk allele DC-SIGN -871 G had 1.47-fold (95% CI = 1.14-1.90) increased risks of developing NPC (P = 0.003). Haplotype analysis revealed that h1 'AAAG' was significantly associated with protection against NPC (OR = 0.69; P = 0.0002) and the association was still significant when using 1000 permutation test runs (P = 0.001). Conclusions: Our study indicated that DC-SIGN promoter variants appear to be involved in the susceptibility to NPC and the detailed mechanism of this effect need further studies. * Odds ratios and Pvalues were calculated using the chi-square test. # Odds ratios and P-Values were calculated by adjusting for age, sex, educational level. Xu et al. 
 Title: Sequencing of DC-SIGN promoter indicates an association between promoter variation and risk of nasopharyngeal carcinoma in cantonese
Output: False
Paragraph: Journal Pre-proof 1 such as ventilators in limited supply, preparations should be made ahead of time on how to allocate these finite resources. More information about COVID-19 can be found in [2], [3], and [7] . The best course of action to "flatten the curve" is to follow WHO guidelines. The best way to keep hospitals under capacity is social distancing: limiting or cancelling large gatherings, only travelling when necessary, and keeping a distance from others all help to prevent the spread. The presented heuristic is based on the exponential growth of the data collected Journal Pre-proof J o u r n a l P r e -p r o o f 4 WWK, MAM, WP, AW-D, PFZ, DS, TA, AHZ, MD, AND JM by WHO situation reports for days 31 to 57. As pointed out in [4] the predictability could be improved by pairwise comparisons based on abductive reasoning [5]. Abduction is frequently used in diagnostic expert systems. The abductive reasoning (or inference) process was used for this study. It is a type of logical inference which starts with a set of observations and then searches for Journal Pre-proof J o u r n a l P r e -p r o o f 1,000,000 COVID-19 CASES X Journal Pre-proof J o u r n a l P r e -p r o o f 
 Title: Journal Pre-proof 1000,000 cases of COVID-19 outside of China: The date predicted by a simple heuristic 1,000,000 CASES OF COVID-19 OUTSIDE OF CHINA: THE DATE PREDICTED BY A SIMPLE HEURISTIC
Output: True
Paragraph: Background: The 3C-like protease (3CL pro ) of severe acute respiratory syndrome-coronavirus is required for autoprocessing of the polyprotein, and is a potential target for treating coronaviral infection. Methodology/Principal Findings: To obtain a thorough understanding of substrate specificity of the protease, a substrate library of 19|8 variants was created by performing saturation mutagenesis on the autocleavage sequence at P5 to P3' positions. The substrate sequences were inserted between cyan and yellow fluorescent proteins so that the cleavage rates were monitored by in vitro fluorescence resonance energy transfer. The relative cleavage rate for different substrate sequences was correlated with various structural properties. P5 and P3 positions prefer residues with high b-sheet propensity; P4 prefers small hydrophobic residues; P2 prefers hydrophobic residues without b-branch. Gln is the best residue at P1 position, but observable cleavage can be detected with His and Met substitutions. P1' position prefers small residues, while P2' and P3' positions have no strong preference on residue substitutions. Noteworthy, solvent exposed sites such as P5, P3 and P3' positions favour positively charged residues over negatively charged one, suggesting that electrostatic interactions may play a role in catalysis. A super-active substrate, which combined the preferred residues at P5 to P1 positions, was found to have 2.8 fold higher activity than the wild-type sequence. Conclusions/Significance: Our results demonstrated a strong structure-activity relationship between the 3CL pro and its substrate. The substrate specificity profiled in this study may provide insights into a rational design of peptidomimetic inhibitors. 
 Title: Profiling of Substrate Specificity of SARS-CoV 3CL pro
Output: False
Paragraph: Purpose: Respiratory infection is the most common cause for acute exacerbation of chronic obstructive pulmonary disease (AE-COPD). The aim of this work was to study the etiology of the respiratory infection in order to assess the usefulness of the clinical and analytical parameters used for COPD identification. Patients and methods: We included 132 patients over a period of 2 years. The etiology of the respiratory infection was studied by conventional sputum, paired serology tests for atypical bacteria, and viral diagnostic techniques (immunochromatography, immunofluorescence, cell culture, and molecular biology techniques). We grouped the patients into four groups based on the pathogens isolated (bacterial versus. viral, known etiology versus unknown etiology) and compared the groups. Results: A pathogen was identified in 48 patients. The pathogen was identified through sputum culture in 34 patients, seroconversion in three patients, and a positive result from viral techniques in 14 patients. No significant differences in identifying etiology were observed in the clinical and analytical parameters within the different groups. The most cost-effective tests were the sputum test and the polymerase chain reaction. Conclusion: Based on our experience, clinical and analytical parameters are not useful for the etiological identification of COPD exacerbations. Diagnosing COPD exacerbation is difficult, with the conventional sputum test for bacterial etiology and molecular biology techniques for viral etiology providing the most profitability. Further studies are necessary to identify respiratory syndromes or analytical parameters that can be used to identify the etiology of new AE-COPD cases without the laborious diagnostic techniques. 
 Title: Microbiological study of patients hospitalized for acute exacerbation of chronic obstructive pulmonary disease (AE-COPD) and the usefulness of analytical and clinical parameters in its identification (VIRAE study)
Output: False
Paragraph: Purpose: To assess lung lesions in patients with pneumonia complicating novel influenza A (H1N1) by serial high-resolution computed tomography (HRCT) during the early, progressive and convalescent stages. Samples and methods: Serial HRCT scans in 39 patients with pneumonia complicating novel influenza A (H1N1) were reviewed for predominant patterns of lung abnormalities as well as distribution and extent of involvement. Longitudinal changes were assessed at different time points. Results: In the early stage, the most common HRCT finding was patchy ground-glass opacity (GGO) (n ¼ 4, 54.7%). In the progressive stage, bilaterally distributed GGO mixed with consolidation was the most commonly observed feature (n ¼ 28, 71.8%). The diffuse pattern deteriorated to a peak (n ¼ 17, 43.6%) at this stage. In the convalescent stage, the most common finding was fibrosis (n ¼ 25, 64.1%). Averagely, fibrosis was observed at d 18.5 ± 6.4 after the onset of symptoms. Three patterns of longitudinal changes of the lesions were observed, including: type 1, improvement after deterioration; type 2, concurrent improvement and deterioration followed by improvement; and type 3, gradual improvement. Type 1 was the more common pattern (n ¼ 27, 69.2%). Complete serial HRCT scans from initial and final scan were obtained in 24 patients, and the mean CT score peaked at d 8e14 of the illness. Conclusion: HRCT may play a role in detecting and characterizing pulmonary lesions for the cases of pneumonia complicating influenza A. In addition, it may contribute to monitoring longitudinal changes of pneumonia and assessing therapeutic response. 
 Title: Longitudinal changes of pneumonia complicating novel influenza A (H1N1) by high-resolution computed tomography-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/)
Output: False
Paragraph: Human coronaviruses are one of the main causes of upper respiratory tract infections in humans. While more often responsible for mild illness, they have been associated with illnesses that require hospitalization. In this study, an assay for one of the human coronaviruses, OC43, was developed using a truncated recombinant nucleocapsid (N) protein antigen in an enzyme immunosorbent assay (ELISA) and evaluated using serum collected from HCoV-OC43-infected patients, healthy adults, and patients with other respiratory virus infections. Results showed that the diagnostic sensitivity and specificity of the assay were 90.9% (10/11) and 82.9% (39/47), respectively. To evaluate the clinical utility of the ELISA, serum samples collected from patients during an outbreak of HCoV-OC43 infection and previously identified as positive by HCoV-OC43 whole N ELISA were screened resulting in 100% diagnosis agreement between the testing methods. These results suggest that this assay offers a reliable method to detect HCoV-OC43 infection and may be a useful tool in coronavirus seroepidemiological studies. Published by Elsevier B.V. 0166-0934/$ -see front matter Published by Elsevier B.V. 
 Title: Development of a recombinant truncated nucleocapsid protein based immunoassay for detection of antibodies against human coronavirus OC43 ଝ
Output: True