niryuu/sni-each-converted huggingface dataset:
Paragraph: Objectives: This study was conducted to investigate the correlation between antibiotic consumption and the incidence of health-care-associated infections (HCAIs) caused by methicillin-resistant Staphylococcus aureus (MRSA) (HCAI-MRSA) and vancomycin-resistant enterococci (VREs) (HCAI-VREs) at a university hospital in Taiwan during the period from 2000 to 2010. Methods: Data on annual patient-days and annual consumption (defined daily dose/1000 patient-days) of glycopeptides (vancomycin and teicoplanin), linezolid, fusidic acid, tigecycline, and daptomycin were analyzed. Yearly aggregated data on the number of nonduplicate clinical MRSA and VRE isolates causing HCAI were collected. Journal of Microbiology, Immunology and Infection (2015) 48, 431e436 aureus; Results: Overall, the consumption of teicoplanin and linezolid significantly increased during the study period. A significant decrease in the incidence of HCAI-MRSA and a significant increase in the incidence of HCAI-VRE were found during the study period. A significant correlation was found between the increased use of teicoplanin and linezolid and the decreased incidence of HCAI-MRSA. By contrast, positive correlations were found between the consumption of teicoplanin and tigecycline and the incidence of HCAI-VRE. Conclusion: This study identified various correlations between the consumption of antibiotics and the incidence of HCAI-MRSA and HCAI-VRE. Strict implementation of infection-control guidelines and reinforcement of administering appropriate antibiotic agents would be helpful in decreasing the incidence of MRSA and VRE in hospitals. 
 Title: Correlation between antimicrobial consumption and incidence of health-care- associated infections due to methicillin- resistant Staphylococcus aureus and vancomycin-resistant enterococci at a university hospital in Taiwan from 2000 to 2010
Output: False
Paragraph: Objective: To survey fertility patients' agreement with ASRM recommendations during the pandemic and the emotional impact on them. Design: An online survey was sent to current fertility patients Setting: New York City academic fertility practice at the epicenter of the COVID-19 pandemic Patient(s): Fertility patients seen within the last year Intervention(s): None Main Outcome Measures(s): Patient agreement with the ASRM recommendations during the COVID-19 pandemic and the emotional impact rated on a Likert scale. Result(s): A total of 518 patients completed the survey for a response rate of 17%. Fifty percent of respondents had a cycle canceled due to the COVID-19 pandemic. Of those who had a cycle cancelled, 85% of respondents found it to be moderately to extremely upsetting with 22% rating it to be equivalent to the loss of a child. There was no difference on the emotional impact based on the type of cycle cancelled. Fifty-five percent of patients agreed that diagnostic procedures such as hysterosalpingograms should be cancelled while 36% of patients agreed all fertility cycles should be cancelled. Patients were slightly more likely to agree with the ASRM guidelines if they have an upcoming cycle cancelled (p = 0.041). Of all respondents 82% would have preferred to have the option to start a treatment cycle in consultation with their doctor. 
 Title: THE EMOTIONAL IMPACT OF THE ASRM GUIDELINES ON FERTILITY PATIENTS DURING THE COVID-19 PANDEMIC
Output: True
Paragraph: Given the high mortality rate (>50%) and potential danger of intrapersonal transmission, highly pathogenic avian influenza (HPAI) H5N1 epidemics still pose a significant threat to humans. γδ T cells, which participate on the front line of the host immune defense, demonstrate both innate, and adaptive characteristics in their immune response and have potent antiviral activity against various viruses. However, the roles of γδ T cells in HPAI H5N1 viral infection remain unclear. In this study, we found that γδ T cells provided a crucial protective function in the defense against HPAI H5N1 viral infection. HPAI H5N1 viruses could directly activate γδ T cells, leading to enhanced CD69 expression and IFN-γ secretion. Importantly, we found that the trimer but not the monomer of HPAI H5N1 virus hemagglutinin (HA) proteins could directly activate γδ T cells. HA-induced γδ T cell activation was dependent on both sialic acid receptors and HA glycosylation, and this activation could be inhibited by the phosphatase calcineurin inhibitor cyclosporin A but not by the phosphatidylinositol 3-kinase (PI3-K) inhibitors wortmannin and LY294002. Our findings provide a further understanding the mechanism underlying γδ T cell-mediated innate and adoptive immune responses against HPAI H5N1 viral infection, which helps to develop novel therapeutic strategies for the treatment of H5N1 infection in the future. 
 Title: γδ T Cells Provide Protective Function in Highly Pathogenic Avian H5N1 Influenza A Virus Infection
Output: True
Paragraph: Chemokines have been demonstrated to serve an important role in a variety of diseases, particularly in tumor progression. There have been numerous studies that have reported that T cells serve major roles in tumor progression. However, the function of CXC motif chemokine ligand 9 (CXCL9) in prostate cancer remains unknown. The present study aimed to investigate the role of CXCL9 in prostate cancer. A prostate cancer mouse model was generated by treating C57/BL-6 and B6.Cg-Selplgtm1Fur/J mice with 3,2'-dimethyl 4-aminobiphenyl (DMAB). Hematoxylin and eosin staining detected the histopathological alterations of mouse prostate tissues. Immunohistochemistry (IHC) staining determined cell proliferation of the mice. Flow cytometry was used to detect the alterations of T cells in C57+DMAB or CXCL9+DMAB mice. Immunofluorescence revealed that there was positive expression of interleukin-6 (IL-6) and transforming growth factor (TGF)-β in the mouse tissues. The survival rates of C57+DMAB and CXCL9+DMAB mice was analyzed. The association of CXCL9 expression and clinical stages was also evaluated. Results revealed that prostate cancer pathology and cell proliferation in CXCL9+DMAB mice were significantly greater compared with the C57+DMAB mice. Compared with C57+DMAB mice, the number of T cells in peripheral blood and spleen of CXCL9+DMAB mice was significantly reduced. IHC demonstrated that the expression of IL-6 and TGF-β was significantly downregulated in the CXCL9+DMAB mice. The survival rate of CXCL9+DMAB mice was significantly decreased compared with the C57+DMAB mice. In addition, reverse transcription-quantitative polymerase chain reaction analysis demonstrated that CXCL9 mRNA expression in clinical samples was positively associated with clinical pathological stages of prostate cancer. In conclusion, CXCL9 may promote prostate cancer progression via inhibition of cytokines from T cells. ST and YG conceived and designed the experiments; ST, FS, YL and YG performed the experiments; ST, KW and YG analyzed the data; ST, KW, FS and YG contributed reagents/materials/analysis tools and ST and YG wrote the manuscript. Animal experiments were approved by the Medical Ethics Committee of Linyi People's Hospital. These tissue samples were collected with the consent of the patients and the study was approved by the Medical Ethics Committee of the Linyi People's Hospital. 
 Title: CXCL9 promotes prostate cancer progression through inhibition of cytokines from T cells
Output: True
Paragraph: on behalf of the members of the MERS-CoV outbreak investigation team of The Netherlands Abstract Background: In May 2014, Middle East respiratory syndrome coronavirus (MERS-CoV) infection, with closely related viral genomes, was diagnosed in two Dutch residents, returning from a pilgrimage to Medina and Mecca, Kingdom of Saudi Arabia (KSA). These patients travelled with a group of 29 other Dutch travellers. We conducted an epidemiological assessment of the travel group to identify likely source(s) of infection and presence of potential risk factors. Methods: All travellers, including the two cases, completed a questionnaire focussing on potential human, animal and food exposures to MERS-CoV. The questionnaire was modified from the WHO MERS-CoV questionnaire, taking into account the specific route and activities of the travel group. Results: Twelve non-cases drank unpasteurized camel milk and had contact with camels. Most travellers, including one of the two patients (Case 1), visited local markets, where six of them consumed fruits. Two travellers, including Case 1, were exposed to coughing patients when visiting a hospital in Medina. Four travellers, including Case 1, visited two hospitals in Mecca. All travellers had been in contact with Case 1 while he was sick, with initially non-respiratory complaints. The cases were found to be older than the other travellers and both had co-morbidities. Conclusions: This epidemiological study revealed the complexity of MERS-CoV outbreak investigations with multiple potential exposures to MERS-CoV reported such as healthcare visits, camel exposure, and exposure to untreated food products. Exposure to MERS-CoV during a hospital visit is considered a likely source of infection for Case 1 but not for Case 2. For Case 2, the most likely source could not be determined. Exposure to MERS-CoV via direct contact with animals or dairy products seems unlikely for the two Dutch cases. Furthermore, exposure to a common but still unidentified source cannot be ruled out. More comprehensive research into sources of infection in the Arabian Peninsula is needed to strengthen and specify the prevention of MERS-CoV infections. 
 Title: Travel-related MERS-CoV cases: an assessment of exposures and risk factors in a group of Dutch travellers returning from the Kingdom of Saudi Arabia, May 2014
Output: True
Paragraph: We present the sequence of an open reading frame (ORF) at the 3' end of human astrovirus serotype 1. Primer extension experiments showed that the RNA expressing this gene is shorter than the complete ORF, and could form a protein of M r 85 540. The protein was expressed by recombinant baculovirus and was recognized by anti-virion serum, indicating a structural role. Sequence comparison indicates that astrovirus serotypes 1 and 2 differ markedly in the C-terminal half of the protein but are well conserved towards the N-terminus. 
 Title: Identification and sequence determination of the capsid protein gene of human astrovirus serotype 1
Output: True
Paragraph: Background. Data on causes of death due to respiratory illness in Africa are limited. Methods. From January to April 2013, 28 African countries were invited to participate in a review of severe acute respiratory illness (SARI)-associated deaths identified from influenza surveillance during 2009-2012. Results. Twenty-three countries (82%) responded, 11 (48%) collect mortality data, and 8 provided data. Data were collected from 37 714 SARI cases, and 3091 (8.2%; range by country, 5.1%-25.9%) tested positive for influenza virus. There were 1073 deaths (2.8%; range by country, 0.1%-5.3%) reported, among which influenza virus was detected in 57 (5.3%). Case-fatality proportion (CFP) was higher among countries with systematic death reporting than among those with sporadic reporting. The influenza-associated CFP was 1.8% (57 of 3091), compared with 2.9% (1016 of 34 623) for influenza virus-negative cases (P < .001). Among 834 deaths (77.7%) tested for other respiratory pathogens, rhinovirus (107 [12.8%]), adenovirus (64 [6.0%]), respiratory syncytial virus (60 [5.6%]), and Streptococcus pneumoniae (57 [5.3%]) were most commonly identified. Among 1073 deaths, 402 (37.5%) involved people aged 0-4 years, 462 (43.1%) involved people aged 5-49 years, and 209 (19.5%) involved people aged ≥50 years. Conclusions. Few African countries systematically collect data on outcomes of people hospitalized with respiratory illness. Stronger surveillance for deaths due to respiratory illness may identify risk groups for targeted vaccine use and other prevention strategies. 
 Title: 17 Ministry of Health and Social Welfare-Tanzania
Output: False
Paragraph: One of the main tasks in biological sequence analysis is biological sequence comparison. Numerous efficient methods have been developed for sequence comparison. Traditional sequence comparison is based on sequence alignment. In this report, we propose a novel alignment-free method based on the relative Lempel-Ziv complexity to compare biological sequences. The vertebrate transferring genomes and the spike protein sequences are prepared and tested to evaluate the validity of the method. We use this method to build phylogenetic tree of two groups of the sequences. The result demonstrates that our method is powerful and efficient. 
 Title: A relative Lempel-Ziv complexity: Application to comparing biological sequences
Output: True
Paragraph: Objectives: Many patients with influenza have more than one viral agent with co-infection frequencies reported as high as 20%. The impact of respiratory virus copathogens on influenza disease is unclear. We sought to determine if respiratory virus co-infection with pandemic H1N1 altered clinical disease. Methods: Respiratory samples from 229 and 267 patients identified with and without H1N1 influenza respectively were screened for the presence of 13 seasonal respiratory viruses by multiplex RT-PCR. Disease severity between coinfected and monoinfected H1N1 patients were quantified using a standardized clinical severity scale. Influenza viral load was calculated by quantitative RT-PCR. Results: Thirty (13.1%) influenza samples screened positive for the presence of 31 viral copathogens. The most prominent copathogens included rhinovirus (61.3%), and coronaviruses (16.1%). Median clinical severity of both monoinfected and coinfected groups were 1. Patients coinfected with rhinovirus tended to have lower clinical severity (median 0), whereas non-rhinovirus co-infections had substantially higher clinical severity (median 2). No difference in H1N1 viral load was observed between coinfected and monoinfected groups. Conclusions: Respiratory viruses co-infect patients with influenza disease. Patients coinfected with rhinovirus had less severe disease while non-rhinovirus co-infections were associated with substantially higher severity without changes in influenza viral titer. 
 Title: Rate and influence of respiratory virus co-infection on pandemic (H1N1) influenza disease *
Output: False
Paragraph: In response to viral infection, the expression of numerous host genes, including predominantly a number of proinflammatory cytokines and chemokines, is usually up-regulated at both transcriptional and translational levels. It was noted that in cells infected with coronavirus, transcription and translation of some of these genes were differentially induced. Drastic induction of their expression at the transcriptional level was observed in cells infected with coronavirus. However, induction of the same genes at the translational level was usually found to be minimal to moderate. To investigate the underlying mechanisms, yeast two-hybrid screen was carried out using SARS-CoV proteins as baits, revealing that a subunit of the eukaryotic initiation factor 3 (eIF3), eIF3f, may interact with the N-terminal region of the SARS-CoV spike (S) protein. This interaction was subsequently confirmed by co-immunoprecipitation and immunofluorescent staining. Meanwhile, parallel experiments confirmed that eIF3f could also interact with the S protein of another coronavirus, the avian coronavirus infectious bronchitis virus (IBV). These interactions led to the inhibition of translation of a reporter gene in both in vitro expression system and intact cells. Interestingly, IBV-infected cells stably expressing a Flag-tagged eIF3f showed much higher translation of IL-6 and IL-8, suggesting that the interaction between coronavirus S protein and eIF3f plays a functional role in controlling the expression of host genes, especially genes that are induced during coronavirus infection cycles. This study reveals a novel mechanism exploited by coronavirus to regulate viral pathogenesis. 
 Title: Coronavirus Spike Protein Inhibits Host Cell Translation by Interaction with eIF3f
Output: True
Paragraph: Intestinal parasitic infections (IPIs) remain a widespread public health concern causing severe implications in both developed and developing countries. Globally, numerous studies have been carried out ranging from various communities to schoolchildren as well as indigenous communities. The infections are commonly caused by helminths (e.g. Ascaris lumbricoides, Trichuris trichiura and hookworm) and protozoa (e.g. Blastocystis hominis, Cryptosporidium sp., Entamoeba histolytica and Giardia duodenalis). Poor sanitation and poverty are some of the factors associated with IPIs. With the ever-increasing impact of IPIs, newer detection approaches have been developed and studied. The efficacy of diagnostic method is crucial to give an accurate identification of these parasites. Recent developments of diagnostic tools such as serology-and molecular-based assays are assisting the conventional method of microscopy in detecting and further confirming current or past infections and the specific species of parasites. Ongoing investigations in parasitic infections using these advanced tools will provide useful information that will enable the evaluation of the effectiveness of the current control program and thus, assist future planning for improved strategies in eradicating these parasitic infections. 
 Title: Advancements in Parasite Diagnosis and Challenges in the Management of Parasitic Infections: A Mini Review
Output: False
Paragraph: Bats and rodents are being increasingly recognized as reservoirs of emerging zoonotic viruses. Various studies have investigated bat viruses in tropical regions, but to date there are no data regarding viruses with zoonotic potential that circulate in bat and rat populations in Viet Nam. To address this paucity of data, we sampled three bat farms and three wet markets trading in rat meat in the Mekong Delta region of southern Viet Nam. Faecal and urine samples were screened for the presence of RNA from paramyxoviruses, coronaviruses and filoviruses. Paramyxovirus RNA was detected in 4 of 248 (1%) and 11 of 222 (4.9%) bat faecal and urine samples, respectively. Coronavirus RNA was detected in 55 of 248 (22%) of bat faecal samples; filovirus RNA was not detected in any of the bat samples. Further, coronavirus RNA was detected in 12 of 270 (4.4%) of rat faecal samples; all samples tested negative for paramyxovirus. Phylogenetic analysis revealed that the bat paramyxoviruses and bat and rat coronaviruses were related to viruses circulating in bat and rodent populations globally, but showed no cross-species mixing of viruses between bat and rat populations within Viet Nam. Our study shows that potentially novel variants of paramyxoviruses and coronaviruses commonly circulate in bat and rat populations in Viet Nam. Further characterization of the viruses and additional human and animal surveillance is required to evaluate the likelihood of viral spillover and to assess whether these viruses pose a risk to human health. bats, coronavirus, paramyxovirus, rats, Viet Nam, zoonotic viruses *VIZIONS consortium group members are present in Appendix 1. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. 
 Title: Detection of potentially novel paramyxovirus and coronavirus viral RNA in bats and rats in the Mekong Delta region of southern Viet Nam
Output: True
Paragraph: We investigated the incidences and characteristics of pediatric traumatic injuries requiring emergency department visits, through a complementary approach using both nationwidesample and single-institutional data. Data for children (aged <15 years) identified with traumatic injuries during a 10-year period from the Korean National Health Insurance Sharing Service (n = 35,064 among 10,114,909 randomly sampled cases from the claim records of the National Health Insurance) and the authors' institute (n = 39,228) were retrospectively reviewed. The incidences and characteristics of the injuries were investigated using both datasets; additionally, detailed information regarding the injury environments was investigated using the single-institutional data. The findings were similar across both datasets. The incidence of injuries increased during the study period; the head was most commonly injured, whereas the trunk or proximal extremities were rarely injured; low-energy head injuries accounted for >50% of the cases in children aged <5 years, although the incidences of lowerextremity injuries and fractures increased in older children. Single-institutional data demonstrated that the proportion of indoor playground and trampoline-related injuries increased rapidly during the study period, and outdoor injuries and seasonal variation (with peak incidences in May and June) were more prominent in older children. Based on similarities between both datasets, the detailed results regarding pediatric traumatic injuries obtained from the singleinstitutional data could be generalized nationally with adequate external validity. To prevent traumatic injuries, it may be more effective to wear protective equipment covering the head and distal extremities rather than the trunk or proximal extremities; simple clothing, such as caps, could prevent many injuries in preschoolers. Among older children, safety guidelines for outdoor sports/leisure activities are needed. The increase in pediatric traumatic injuries may be partially explained by the increased availability of indoor playgrounds and installation of trampolines. Stricter adherence to the preventive guidelines is needed. Low-energy injuries (that is, superficial injuries such as abrasions or open wounds such as lacerations) were the most common injury type for children aged <5 years. Although fracture is a rare injury type in young children, it was relatively common in children aged >5 years and became the most common injury type in children aged >11 years (bold font). Data are presented as n (%). 
 Title: Characteristics and trends of traumatic injuries in children visiting emergency departments in South Korea: A retrospective serial cross-sectional study using both nationwide-sample and single-institutional data
Output: False
Paragraph: Interferon-induced transmembrane protein 3 (IFITM3) is a restriction factor that can be induced by viral infection and interferons (IFNs). It inhibits the entry and replication of many viruses, which are independent of receptor usage but dependent on processes that occur in endosomes. In this study, we demonstrate that IFITM3 plays important roles in regulating the RNA-virus-triggered production of IFN-β in a negative-feedback manner. Overexpression of IFITM3 inhibited Sendai virus-triggered induction of IFN-β, whereas knockdown of IFITM3 had the opposite effect. We also showed that IFITM3 was constitutively associated with IRF3 and regulated the homeostasis of IRF3 by mediating the autophagic degradation of IRF3. These findings suggest a novel inhibitory function of IFITM3 on the RNA-virus-triggered production of type I IFNs and cellular antiviral responses. 
 Title: IFITM3 inhibits virus-triggered induction of type I interferon by mediating autophagosome-dependent degradation of IRF3
Output: True
Paragraph: The cellular receptor for human coronavirus NL63 (HCoV-NL63), a group I coronavirus, is angiotensin-converting enzyme2 (ACE2). ACE2 is also the receptor for the SARS coronavirus (SARS-CoV), a group II coronavirus. Here we describe the ability of HCoV-NL63 to utilize a number of ACE2 variants previously characterized as SARS-CoV receptors. Several ACE2 variants that reduced SARS-CoV S-protein association similarly reduced that of HCoV-NL63, whereas alteration of a number of solvent-exposed ACE2 residues did not interfere with binding by either S protein. One notable exception is ACE2 residue 354, at the boundary of the SARS-CoV binding site, whose alteration markedly inhibited utilization by the HCoV-NL63 but not SARS-CoV S proteins. In addition, the SARS-CoV S-protein receptor-binding domain inhibited entry mediated by the HCoV-NL63 S protein. These studies indicate that HCoV-NL63, like SARS-CoV, associates region of human ACE2 that includes a key loop formed by β-strands 4 and 5. 
 Title: The S proteins of human coronavirus NL63 and severe acute respiratory syndrome coronavirus bind overlapping regions of ACE2
Output: True
Paragraph: Bats are natural reservoirs of coronaviruses and other viruses with zoonotic potential. Florida has indigenous non-migratory populations of Brazilian free-tailed bats (Tadarida brasiliensis) that mostly roost in colonies in artificial structures. Unlike their counterparts in Brazil and Mexico, the viruses harbored by the Florida bats have been underexplored. We report the detection of an alphacoronavirus RNA-dependent RNA polymerase (RdRp) gene sequence in the feces of two of 19 different T. brasiliensis that were capture/release bats that had been evaluated for overall health. The RdRp sequence is similar but not identical to previously detected sequences in the feces of two different species of bats (T. brasiliensis and Molossus molossus) in Brazil. In common with the experience of others doing similar work, attempts to isolate the virus in cell cultures were unsuccessful. We surmise that this and highly related alphacoronavirus are carried by Brazilian free-tailed bats living in a wide eco-spatial region. As various coronaviruses (CoVs) that affect humans emerged from bats, our study raises the question whether CoVs such as the one detected in our work are yet-to-be-detected pathogens of humans and animals other than bats. 
 Title: Detection of Alphacoronavirus vRNA in the Feces of Brazilian Free-Tailed Bats (Tadarida brasiliensis) from a Colony in Florida, USA
Output: False
Paragraph: Background: Disseminated or fatal Zika virus (ZIKV) infections were reported in immunosuppressed patients. Existing interferon-signaling/receptor-deficient mouse models may not be suitable for evaluating treatment effects of recombinant interferons. Methods: We developed a novel mouse model for ZIKV infection by immunosuppressing BALB/c mice with dexamethasone. Results: Dexamethasone-immunosuppressed male mice (6-8 weeks) developed disseminated infection as evidenced by the detection of ZIKV-NS1 protein expression and high viral loads in multiple organs. They had ≥10% weight loss and high clinical scores soon after dexamethasone withdrawal (10 dpi), which warranted euthanasia at 12 dpi. Viral loads in blood and most tissues at 5 dpi were significantly higher than those at 12 dpi (P b 0.05). Histological examination revealed prominent inflammatory infiltrates in multiple organs, and CD45+ and CD8+ inflammatory cells were seen in the testis. These findings suggested that clinical deterioration occurred during viral clearance by host immune response. Type I interferon treatments improved clinical outcome of mice (100% vs 0% survival). Conclusions: Besides virus dissemination, inflammation of various tissues, especially orchitis, may be potential complications of ZIKV infection with significant implications on disease transmission and male fertility. Interferon treatment should be considered in patients at high risks for ZIKV-associated complications when the potential benefits outweigh the side effects of treatment. 
 Title: Zika Virus Infection in Dexamethasone-immunosuppressed Mice Demonstrating Disseminated Infection with Multi-organ Involvement Including Orchitis Effectively Treated by Recombinant Type I Interferons
Output: False
Paragraph: TBX2 and TBX3 are members of the T-box family of transcription factors, which are implicated in embryonic development. Unlike most members of the T-box family, TBX2 and TBX3 are the only mammalian T-box factors which function as transcriptional repressors, mediated by the repression domain in the C-terminal. In addition to a role in development, recent evidence suggests that TBX2 and TBX3 are overexpressed in a number of cancers, including melanoma, breast, liver, lung, pancreas, ovarian, and cervical cancers. However, there is little information about the mechanisms for how these T-box genes contribute to tumorigenesis. Upregulation of TBX2 and TBX3 suppresses the expression of p14 ARF and p21 CIP1 and promotes bypass of senescence through inactivation of p53 pathway. TBX2 functionally interacts with pRb, and pRb modulates TBX2 functional specificity. In addition, TBX2 is a player of Wnt signaling while TBX3 is a downstream target of the Wnt/beta-catenin pathway, and overexpression of TBX2 and TBX3 represses the expression of Ecadherin, which is demonstrated to be a prerequisite for epithelial tumor cell invasion. Moreover, TBX2 is shown to interact with EGR1 to block multiple downstream tumor suppressors. Here, we review the current knowledge on TBX2 and TBX3 in tumorigenesis and prospect their special value for development of targetbased anticancer drugs. 
 Title: TBX2 and TBX3: The special value for anticancer drug targets
Output: True
Paragraph: The sensitivities and specificities of an immunofluorescence assay and an enzyme immunoassay for detection of antibodies specific for severe acute respiratory syndrome coronavirus (SARS-CoV) were compared for 148 laboratory-confirmed SARS cases. The appearance and persistence of SARS-CoV-specific antibodies were assessed, with immunoglobulin G detected in 59% of samples collected within 14 days and persisting for 60 to 95 days after the onset of illness. 
 Title: Kinetics of Severe Acute Respiratory Syndrome (SARS) Coronavirus-Specific Antibodies in 271 Laboratory-Confirmed Cases of SARS
Output: True
Paragraph: Background: We present here the recent update of AMS algorithm for identification of post-translational modification (PTM) sites in proteins based only on sequence information, using artificial neural network (ANN) method. The query protein sequence is dissected into overlapping short sequence segments. Ten different physicochemical features describe each amino acid; therefore nine residues long segment is represented as a point in a 90 dimensional space. The database of sequence segments with confirmed by experiments post-translational modification sites are used for training a set of ANNs. The efficiency of the classification for each type of modification and the prediction power of the method is estimated here using recall (sensitivity), precision values, the area under receiver operating characteristic (ROC) curves and leave-one-out tests (LOOCV). The significant differences in the performance for differently optimized neural networks are observed, yet the AMS 3.0 tool integrates those heterogeneous classification schemes into the single consensus scheme, and it is able to boost the precision and recall values independent of a PTM type in comparison with the currently available state-of-the art methods. The standalone version of AMS 3.0 presents an efficient way to indentify post-translational modifications for whole proteomes. The training datasets, precompiled binaries for AMS 3.0 tool and the source code are available at Additional file 1 Supplementary materials for the publication. Supplementary.xls contains detailed results of training and testing of AMS 3.0 tool in MS Excel file format. Additional file 2 PTM predictor software with training data. PTM_Archive.tar.gz includes the predictor software binaries together with all trained ANNs in tar.gz compressed form. 
 Title: AMS 3.0: prediction of post-translational modifications
Output: True
Paragraph: Necessary screenings must be performed to control the spread of the Corona Virus in daily life and to make a preliminary diagnosis of suspicious cases. The long duration of pathological laboratory tests and the wrong test results led the researchers to focus on different fields. Fast and accurate diagnoses are essential for effective interventions with COVID-19. The information obtained by using X-ray and Computed Tomography (CT) images is vital in making clinical diagnoses. Therefore it was aimed to develop a machine learning method for the detection of viral epidemics by analyzing X-ray images. In this study, images belonging to 6 situations, including coronavirus images, are classified. Since the number of images in the dataset is deficient and unbalanced, it is more convenient to analyze these images with hand-crafted feature extraction methods. For this purpose, firstly, all the images in the dataset are extracted with the help of four feature extraction algorithms. These extracted features are combined in raw form. The unbalanced data problem is eliminated by producing feature vectors with the SMOTE algorithm. Finally, the feature vector is reduced in size by using a stacked auto-encoder and principal component analysis to remove interconnected features in the feature vector. According to the obtained results, it is seen that the proposed method has leveraging performance, especially in order to make the diagnosis of COVID-19 in a short time and effectively. 
 Title: Classification of Coronavirus Images using Shrunken Features
Output: False
Paragraph: The prevalence of antibodies to bovine coronavirus (BCV) and bovine respiratory syncytial virus (BRSV) infections was studied in 20 conventional and 20 organic dairy herds. The organic farms had produced 'certified' milk for at least 2 years. On two occasions, with a 1-year interval, 699 serum samples from 624 peri-parturient cows were tested by ELISA for antibodies to BCV and BRSV. Accompanying data relating to the sampled animals were collected in order to identify potential factors associated with increased antibody prevalence. The antibody prevalence was high at both sampling times with approximately 85% and 80% of animals positive for antibodies to BCV and to BRSV, respectively. Conventional herds had a significantly higher mean antibody prevalence to BCV and BRSV than the organically managed herds (P < 0.01). Animal age was significantly associated with increased antibody prevalence (P < 0.001). The findings of this study suggest that organic farm management may be effective in reducing the seroprevalence of these viruses relative to conventional farming methods. 
 Title: Reduced likelihood of bovine coronavirus and bovine respiratory syncytial virus infection on organic compared to conventional dairy farms
Output: True
Paragraph: Cyclophilin A has attracted attention recently as a new target of anti-human immunodeficiency virus type 1 (HIV-1) drugs. However, so far no drug against HIV-1 infection exhibiting this mechanism of action has been approved. To identify new potent candidates for inhibitors, we performed in silico screening of a commercial database of more than 1,300 drug-like compounds by using receptorbased docking studies. The candidates selected from docking studies were subsequently tested using biological assays to assess anti-HIV activities. As a result, two compounds were identified as the most active. Specifically, both exhibited anti-HIV activity against viral replication at a low concentration and relatively low cytotoxicity at the effective concentration inhibiting viral growth by 50 %. 
 Title: Discovery of novel low-molecular-weight HIV-1 inhibitors interacting with cyclophilin A using in silico screening and biological evaluations
Output: True
Paragraph: Acute otitis media (AOM) is an inflammatory response to microbes in the middle ear, sometimes associated with rupture of the tympanic membrane. Human leukocytes produce different patterns of inflammatory mediators in vitro when stimulated with Gram-positive and Gram-negative bacteria, respectively. Here, we investigated the cytokine and prostaglandin E 2 (PGE 2 ) responses in middle ear fluids (MEFs) from children with spontaneously perforated AOM, and related the mediator levels to the presence of pathogens detected by culture (live) or PCR (live or dead). Furthermore, the in vivo cytokine pattern was compared with that induced in leukocytes stimulated by dead bacteria in vitro. MEFs with culturable pathogenic bacteria contained more interleukin (IL)-1b (median: 110 lg/L vs. <7.5 lg/L), tumour necrosis factor (TNF) (6.3 lg/L vs. <2.5 lg/L), IL-8 (410 lg/L vs. 38 lg/L) and IL-10 (0.48 lg/L vs. <0.30 lg/L) than culture-negative fluids, irrespective of PCR findings. IL-6 and PGE 2 were equally abundant (69-110 lg/L) in effusions with live, dead or undetectable bacteria. Cytokine levels were unrelated to bacterial species and to the presence or absence of virus. Similar levels of TNF and IL-6 as found in the MEFs were obtained by in vitro stimulation of leukocytes, whereas 11 times more IL-1b and 3.5 times more IL-8 were produced in vivo, and 22 times more IL-10 was produced in vitro. Vigorous production of proinflammatory cytokines accompanies AOM with membrane rupture, regardless of the causative agent, but the production seems to cease rapidly once the bacteria are killed and fragmented. IL-6 and PGE 2 , however, remain after bacterial disintegration, and may play a role in the resolution phase. 
 Title: High cytokine levels in perforated acute otitis media exudates containing live bacteria
Output: False
Paragraph: Novel surveillance strategies are needed to detect the rapid and continuous emergence of infectious disease agents. Ideally, new sampling strategies should be simple to implement, technologically uncomplicated, and applicable to areas where emergence events are known to occur. To this end, xenosurveillance is a technique that makes use of blood collected by hematophagous arthropods to monitor and identify vertebrate pathogens. Mosquitoes are largely ubiquitous animals that often exist in sizable populations. As well, many domestic or peridomestic species of mosquitoes will preferentially take blood-meals from humans, making them a unique and largely untapped reservoir to collect human blood. OPEN ACCESS Citation: Fauver JR, Weger-Lucarelli J, Fakoli LS, III, Bolay K, Bolay FK, Diclaro JW, II, et al. (2018) Xenosurveillance reflects traditional sampling techniques for the identification of human pathogens: A comparative study in West Africa. PLoS Negl Trop Dis 12(3): e0006348. https://doi. 
 Title: Xenosurveillance reflects traditional sampling techniques for the identification of human pathogens: A comparative study in West Africa
Output: False
Paragraph: Cytokine expression patterns of T cells can be regulated by pre-commitment to stable effector phenotypes, further modification of moderately stable phenotypes, and quantitative changes in cytokine production in response to acute signals. We showed previously that the epidermal growth factor family member Amphiregulin is expressed by T cell receptor-activated mouse CD4 T cells, particularly Th2 cells, and helps eliminate helminth infection. Here we report a detailed analysis of the regulation of Amphiregulin expression by human T cell subsets. Signaling through the T cell receptor induced Amphiregulin expression by most or all T cell subsets in human peripheral blood, including naive and memory CD4 and CD8 T cells, Th1 and Th2 in vitro T cell lines, and subsets of memory CD4 T cells expressing several different chemokine receptors and cytokines. In these different T cell types, Amphiregulin synthesis was inhibited by an antagonist of protein kinase A, a downstream component of the cAMP signaling pathway, and enhanced by ligands that increased cAMP or directly activated protein kinase A. Prostaglandin E2 and adenosine, natural ligands that stimulate adenylyl cyclase activity, also enhanced Amphiregulin synthesis while reducing synthesis of most other cytokines. Thus, in contrast to mouse T cells, Amphiregulin synthesis by human T cells is regulated more by acute signals than precommitment of T cells to a particular cytokine pattern. This may be appropriate for a cytokine more involved in repair than attack functions during most inflammatory responses. 
 Title: The Acute Environment, Rather than T Cell Subset Pre- Commitment, Regulates Expression of the Human T Cell Cytokine Amphiregulin
Output: False
Paragraph: Mesenchymal stem cells (MSCs) spontaneously fuse with somatic cells in vivo, albeit rarely, and the fusion products are capable of tissue-specific function (mature trait) or proliferation (immature trait), depending on the microenvironment. That stem cells can be programmed, or somatic cells reprogrammed, in this fashion suggests that stem cell fusion holds promise as a therapeutic approach for the repair of damaged tissues, especially tissues not readily capable of functional regeneration, such as the myocardium. In an attempt to increase the frequency of stem cell fusion and, in so doing, increase the potential for cardiac tissue repair, we expressed the fusogen of the vesicular stomatitis virus (VSV-G) in human MSCs. We found VSV-G expressing MSCs (vMSCs) fused with cardiomyocytes (CMs) and these fusion products adopted a CM-like phenotype and morphology in vitro. In vivo, vMSCs delivered to damaged mouse myocardium via a collagen patch were able to home to the myocardium and fuse to cells within the infarct and peri-infarct region of the myocardium. This study provides a basis for the investigation of the biological impact of fusion of stem cells with CMs in vivo and illustrates how viral fusion proteins might better enable such studies. 
 Title: Directed Fusion of Mesenchymal Stem Cells with Cardiomyocytes via VSV-G Facilitates Stem Cell Programming
Output: False
Paragraph: In trial 1, phase 1, 48 male Holstein calves initially 2 to 4 d of age were transported 3.5 h to the research facility. Calves were randomly selected to either receive a s.c. injection of Zuprevo (Merck Animal Health, Summit, NJ; 4 mg of tildipirosin/kg of BW; TIL) the day after arrival (d 0) and again at weaning (d 42) or receive no injections (CON). Calves were fed 0.66 kg of milk replacer DM daily for 39 d and then 0.33 kg daily for 3 d. A starter was fed free choice for the 56 d of phase 1. In trial 1, phase 2, the same calves from phase 1 grouped by CON and TIL were moved to group pens (4 pens per treatment, 4 calves per pen) for the next 56 d. The starter was blended with 5% chopped grass hay and fed free choice. Trial 2 was similar to trial 1, phase 2 and used 48 two-month-old male Holstein calves. Calves were randomly selected to receive either a s.c. injection of Zuprevo (4 mg of tildipirosin/kg of BW; TIL) on d 0 or no injections (CON). In trial 1, phase 1, preweaning ADG and BCS change; postweaning starter intake and hip width change; overall starter intake, ADG, and hip width change; final hip width; and final BCS were greater for TIL than CON. During phase 2 of trial 1 and trial 2, calf ADG and hip width change were greater for TIL than CON. Overall, in transported Holstein calves, TIL improved ADG and structural growth by approximately 13%. 
 Title: Case Study: Control of respiratory disease in male Holstein calves with tildipirosin and effect on health and growth from 0 to 4 months of age
Output: False
Paragraph: , produce more severe disease in the elderly, yet the molecular mechanisms governing age-related susceptibility remain poorly studied. Advanced age was significantly associated with increased SARS-related deaths, primarily due to the onset of early-and late-stage acute respiratory distress syndrome (ARDS) and pulmonary fibrosis. Infection of aged, but not young, mice with recombinant viruses bearing spike glycoproteins derived from early human or palm civet isolates resulted in death accompanied by pathological changes associated with ARDS. In aged mice, a greater number of differentially expressed genes were observed than in young mice, whose responses were significantly delayed. Differences between lethal and nonlethal virus phenotypes in aged mice could be attributed to differences in host response kinetics rather than virus kinetics. SARS-CoV infection induced a range of interferon, cytokine, and pulmonary wound-healing genes, as well as several genes associated with the onset of ARDS. Mice that died also showed unique transcriptional profiles of immune response, apoptosis, cell cycle control, and stress. Cytokines associated with ARDS were significantly upregulated in animals experiencing lung pathology and lethal disease, while the same animals experienced downregulation of the ACE2 receptor. These data suggest that the magnitude and kinetics of a disproportionately strong host innate immune response contributed to severe respiratory stress and lethality. Although the molecular mechanisms governing ARDS pathophysiology remain unknown in aged animals, these studies reveal a strategy for dissecting the genetic pathways by which SARS-CoV infection induces changes in the host response, leading to death. 
 Title: Early Upregulation of Acute Respiratory Distress Syndrome-Associated Cytokines Promotes Lethal Disease in an Aged-Mouse Model of Severe Acute Respiratory Syndrome Coronavirus Infection ᰔ
Output: True
Paragraph: An enzyme-linked immunosorbent assay (ELISA) and a rapid immunochromatographic test for detection of immunoglobulin G (IgG) antibodies in severe acute respiratory syndrome (SARS) patients were developed by utilizing the well-characterized recombinant proteins Gst-N and Gst-U274. The ELISA detected IgG antibodies to SARS-CoV in all 74 convalescent-phase samples from SARS patients while weakly cross-reacting to only 1 of the 210 control sera from healthy donors. This finding thus led to a kit sensitivity, specificity, and accuracy of 100, 99.5, and 99.6%, respectively. The test thus provided a positive predictive value (PPV) of 98.7% and a negative predictive value (NPV) of 100%. In addition, the ELISA gave a positive delta of 5.4 and a negative delta of 3.6, indicating an excellent differentiation between positives and negatives. The same recombinant proteins were also applied to a newly developed platform for the development of a 15-min rapid test. The resulting rapid test has an excellent agreement of 99.6%, with a kappa value of 1.00, with the ELISA. Again, this rapid test was able to detect 100% of the samples tested (n ‫؍‬ 42) while maintaining a specificity of 99.0% (n ‫؍‬ 210). The PPV and NPV for the rapid test thus reached 95.3 and 100%, respectively. 
 Title: Recombinant Protein-Based Enzyme-Linked Immunosorbent Assay and Immunochromatographic Tests for Detection of Immunoglobulin G Antibodies to Severe Acute Respiratory Syndrome (SARS) Coronavirus in SARS Patients
Output: False
Paragraph: Endoplasmic reticulum (ER) stress can be activated by various pathological and physiological conditions including the unfolded protein response (UPR) to restore homeostasis. The UPR signaling pathways initiated by double-stranded RNA-activated protein kinase (PKR) like ER kinase (PERK), inositol requiring enzyme 1 α (IRE1α), and activating transcription factor 6 (ATF6) are vital for tumor growth, aggressiveness, microenvironment remodeling, and resistance to cancer therapeutics. This review focuses on the role of ER stress and activity of UPR signaling pathways involved in tumor formation and uncontrolled cell proliferation during various cancers and viral malignancies. 
 Title: Virus and tumor microenvironment induced ER stress and unfolded protein response: from complexity to therapeutics
Output: False