niryuu/sni-each-converted huggingface dataset:
Paragraph: Caliciviruses are important human and animal pathogens. Novel caliciviruses have been identified recently in dogs, raising questions about their pathogenic role and concerns regarding their zoonotic potential. By screening stool samples of young or juvenile dogs using RT-PCR assays, sapoviruses (SaVs) were found in 7/320 (2.2%) samples of animals with acute gastroenteritis while they were not detected in healthy animals (0/119). The sequence of a nearly 3 kb portion at the 3′ end of the genome, encompassing the RNA-dependent RNA polymerase (RdRp), the capsid region (ORF1) and the ORF2 were determined for three strains. A distinctive genetic feature in canine SaVs was a 4-nucleotide (nt) interval between the ORF1 and ORF2. Two strains (Bari/4076/ 07/ITA and Bari/253/07/ITA) were very closely related in the RdRp and capsid regions to the strain AN210D/ 09/USA (90.4-93.9% nt), while strain Bari/5020/07/ITA displayed only 71.0-72.0% nt identity to this group of canine SaVs and 76.0% to strain AN196/09/USA. Overall, these findings indicate that the canine SaVs detected in Italy may represent distinct capsid types, although all currently known SaVs segregate into the novel proposed genogroup, tentatively named as GXIII. 
 Title: Detection and molecular characterization of sapoviruses in dogs
Output: True
Paragraph: Viral zoonoses have represented a significant public health problem throughout history, affecting all continents. Furthermore, many viral zoonoses have emerged or reemerged in recent years, highlighting the importance of such diseases. Emerging viral zoonoses encompass a vast number of different viruses and many different transmission modes. There are many factors influencing the epidemiology of the various zoonoses, such as ecological changes, changes in agriculture and food production, the movement of pathogens, including via travel and trade, human behavior and demographical factors, and microbial changes and adaptation. Costeffective prevention and control of emerging viral zoonoses necessitates an interdisciplinary and holistic approach and international cooperation. Surveillance, laboratory capability, research, training and education, and last but not least, information and communication are key elements. 
 Title: Zoonoses in the Emergence of Human Viral Diseases
Output: True
Paragraph: Introduction: Determining the cause of community-acquired pneumonia (CAP) remains problematic. In this observational study, we systematically applied currently approved diagnostic techniques in patients hospitalized for CAP in order to determine the proportion in which an etiological agent could be identified. Methods: All patients admitted with findings consistent with CAP were included. Sputum and blood cultures, urine tests for pneumococcal and Legionella antigens, nasopharyngeal swab for viral PCR, and serum procalcitonin were obtained in nearly every case. Admissionrelated electronic medical records were reviewed in entirety. Results: By final clinical diagnosis, 44 patients (17.0%) were uninfected. A causative bacterium was identified in only 60 (23.2%) cases. PCR identified a respiratory virus in 42 (16.2%), 12 with documented bacterial coinfection. In 119 (45.9%), no cause for CAP was found; 69 (26.6%) of these had a syndrome indistinguishable from bacterial pneumonia. Procalcitonin was elevated in patients with bacterial infection and low in uninfected patients or those with viral infection, but with substantial overlap. Conclusions: Only 23.2% of 259 patients admitted with a CAP syndrome had documented bacterial infection; another 26.6% had no identified bacterial etiology, but findings closely resembled those of bacterial infection. Nevertheless, all 259 received antibacterial therapy. Journal of Infection (2013) 67, 11e18 Careful attention to the clinical picture may identify uninfected patients or those with viral infection, perhaps with reassurance by a non-elevated procalcitonin. Determining an etiologic diagnosis remains elusive. Better discriminators of bacterial infection are sorely needed. Published by Elsevier Ltd on behalf of The British Infection Association. 
 Title: Can an etiologic agent be identified in adults who are hospitalized for community-acquired pneumonia: Results of a one-year study
Output: True
Paragraph: Similarity in time series is an important feature of dynamical systems such as financial systems, with potential use for clustering of series in system. Here, we mainly introduce a novel method: the reconstructed phase space information clustering method to analyze the financial markets. The method is used to examine the similarity of different sequences by calculating the distances between them, which the main difference from previous method is the way to map the original time series to symbolic sequences. Here we make use of the state space reconstruction to construct the symbolic sequences and quantify the similarity of different stock markets and exchange rate markets considering the chaotic behavior between the complex time series. And we compare the results of similarity of artificial and real data using the modified method, information categorization method and system clustering method. We conclude that the reconstructed phase space information clustering method is effective to research the close relationship in time series and for short time series especially. Besides, we report the results of similarity of different exchange rate time series in different periods and find the effect of the exchange rate regime in 2008 on the time series. Also we acquire some characteristics of exchange rate time 
 Title: The similarity analysis of financial stocks based on information clustering
Output: False
Paragraph: Our objective here is to review the novel delivery platform based on Bacteriophage MS2 virus-like particles (VLPs), including introduction to their structure, their potential as a delivery platform, and their expected use in medicine and other fields. Bacteriophage MS2 VLPs are nanoparticles devoid of viral genetic material and can self-assemble from the coat protein into an icosahedral capsid. As a novel delivery platform, they possess numerous features that make them suitable and attractive for targeted delivery of RNAs or DNAs, epitope peptides, and drugs within the protein capsid. In short, as a novel delivery platform, MS2 VLPs are suitable for delivery of targeted agents and hold promise for use in diagnostics, vaccines, and therapeutic modalities. 
 Title: A novel delivery platform based on Bacteriophage MS2 virus-like particles
Output: False
Paragraph: A major entry route for the gammaretrovirus amphotropic murine leukemia virus (A-MLV) into NIH 3T3 fibroblasts is via caveola-dependent endocytosis. However, during the infection time, few viral particles can be observed intracellularly. Analyzing the dynamics of the A-MLV infection process by using total internal reflection fluorescence microscopy, we show that the majority of viruses are extracellular and bound to the fibronectin matrix. Moreover, the amounts of bound virus and of fibronectin correlated. Using confocal microscopy, nanoparticles targeted to fibronectin by a III1C-fibronectin fragment or anti-fibronectin antibody were detected intracellularly in NIH 3T3 cells; unconjugated nanoparticles neither bound to cells nor were detectable intracellularly. Furthermore, A-MLV colocalized intracellularly with the fibronectin-targeted nanoparticles, suggesting that they were taken up by the same cellular pathway. Both A-MLV entry and fibronectin turnover depend on caveolar endocytosis, and we found that inhibiting viral binding to the extracellular NIH 3T3 fibronectin-matrix dramatically reduced A-MLV infection, indeed, showing an active role of fibronectin in infection. We suggest that binding to the cellular fibronectin matrix provides a new mechanism by which viruses can enter cells. 
 Title: Matrix Fibronectin Binds Gammaretrovirus and Assists in Entry: New Light on Viral Infections ᰔ † Downloaded from
Output: True
Paragraph: In an investigation of blood-sucking insects and arboviruses, a virus (YN12243) was isolated from Culicoides samples collected in the Sino-Burmese border region of Yunnan Province, China. The virus caused cytopathic effect (CPE) in C6/36 cells and passaged stably. Polyacrylamide gel analysis showed that the genome of YN12243 was composed of 12 segments of double-stranded RNA (dsRNA), with a distribution pattern of 6-6. The nucleotide and amino acid sequences of the coding region (1-12 segments) were 17,803 bp and 5,925 amino acids in length, respectively. The phylogenetic analysis of VP1 protein (RdRp) revealed that YN12243 belonged to genus Seadornavirus of family Reoviridae, and further analysis indicated that YN12243 belongs to the Banna virus (BAV) genotype A2. Additionally, YN12243 was located in the same evolutionary cluster as BAV strains isolated from different mosquito species, suggesting that the BAV isolated from Culicoides does not have species barriers. These results indicate that Culicoides can also be a vector for BAV. In view of the hematophagous habits of Culicoides on cattle, horses, deer, and other large animals, as well as the possibility of spreading and causing a variety of animal arboviral diseases, it is important to improve infection detection and monitor the BAV in large livestock. 
 Title: SCIENCE CHINA Genome sequencing and phylogenetic analysis of Banna virus (genus Seadornavirus, family Reoviridae) isolated from Culicoides
Output: True
Paragraph: A total of 29 faecal samples collected from dogs with diarrhoea following canine parvovirus (CPV) vaccination were tested by minor groove binder (MGB) probe assays for discrimination between CPV vaccine and field strains and by diagnostic tests for detection of other canine pathogens. Fifteen samples tested positive only for CPV field strains; however, both vaccine and field strains were detected in three samples. Eleven samples were found to contain only the vaccine strain, although eight of them tested positive for other pathogens of dogs. Only three samples were found to contain the vaccine strain without evidence of canine pathogens. The present study confirms that most cases of parvovirus-like disease occurring shortly after vaccination are related to infection with field strains of canine parvovirus type 2 (CPV-2) rather than to reversion to virulence of the modified live virus contained in the vaccine. 
 Title: Occurrence of severe gastroenteritis in pups after canine parvovirus vaccine administration: A clinical and laboratory diagnostic dilemma
Output: True
Paragraph: Mucosal vaccination offers great advantage for inducing protective immune response to prevent viral transmission and dissemination. Here, we report our findings of a head-to-head comparison of two viral vectors modified vaccinia Ankara (MVA) and a novel replication-competent modified vaccinia Tian Tan (MVTT) for inducing neutralizing antibodies (Nabs) via intramuscular and mucosal vaccinations in mice. MVTT is an attenuated variant of the wild-type VTT, which was historically used as a smallpox vaccine for millions of Chinese people. The spike glycoprotein (S) of SARS-CoV was used as the test antigen after the S gene was constructed in the identical genomic location of two vectors to generate vaccine candidates MVTT-S and MVA-S. Using identical doses, MVTT-S induced lower levels (,2-3-fold) of anti-SARS-CoV neutralizing antibodies (Nabs) than MVA-S through intramuscular inoculation. MVTT-S, however, was capable of inducing consistently 20-to-100-fold higher levels of Nabs than MVA-S when inoculated via either intranasal or intraoral routes. These levels of MVTT-S-induced Nab responses were substantially (,10-fold) higher than that induced via the intramuscular route in the same experiments. Moreover, pre-exposure to the wild-type VTT via intranasal or intraoral route impaired the Nab response via the same routes of MVTT-S vaccination probably due to the pre-existing anti-VTT Nab response. The efficacy of intranasal or intraoral vaccination, however, was still 20-to-50-fold better than intramuscular inoculation despite the subcutaneous pre-exposure to wild-type VTT. Our data have implications for people who maintain low levels of anti-VTT Nabs after historical smallpox vaccination. MVTT is therefore an attractive live viral vector for mucosal vaccination. 
 Title: A Novel Replication-Competent Vaccinia Vector MVTT Is Superior to MVA for Inducing High Levels of Neutralizing Antibody via Mucosal Vaccination
Output: True
Paragraph: Background: Production of native antigens for serodiagnosis of helminthic infections is laborious and hampered by batchto-batch variation. For serodiagnosis of echinococcosis, especially cystic disease, most screening tests rely on crude or purified Echinococcus granulosus hydatid cyst fluid. To resolve limitations associated with native antigens in serological tests, the use of standardized and highly pure antigens produced by chemical synthesis offers considerable advantages, provided appropriate diagnostic sensitivity and specificity is achieved. Methodology/Principal Findings: Making use of the growing collection of genomic and proteomic data, we applied a set of bioinformatic selection criteria to a collection of protein sequences including conceptually translated nucleotide sequence data of two related tapeworms, Echinococcus multilocularis and Echinococcus granulosus. Our approach targeted alphahelical coiled-coils and intrinsically unstructured regions of parasite proteins potentially exposed to the host immune system. From 6 proteins of E. multilocularis and 5 proteins of E. granulosus, 45 peptides between 24 and 30 amino acids in length were designed. These peptides were chemically synthesized, spotted on microarrays and screened for reactivity with sera from infected humans. Peptides reacting above the cut-off were validated in enzyme-linked immunosorbent assays (ELISA). Peptides identified failed to differentiate between E. multilocularis and E. granulosus infection. The peptide performing best reached 57% sensitivity and 94% specificity. This candidate derived from Echinococcus multilocularis antigen B8/1 and showed strong reactivity to sera from patients infected either with E. multilocularis or E. granulosus. Conclusions/Significance: This study provides proof of principle for the discovery of diagnostically relevant peptides by bioinformatic selection complemented with screening on a high-throughput microarray platform. Our data showed that a single peptide cannot provide sufficient diagnostic sensitivity whereas pooling several peptide antigens improved sensitivity; thus combinations of several peptides may lead the way to new diagnostic tests that replace, or at least complement conventional immunodiagnosis of echinococcosis. Our strategy could prove useful for diagnostic developments in other pathogens. 
 Title: Serodiagnosis of Echinococcus spp. Infection: Explorative Selection of Diagnostic Antigens by Peptide Microarray
Output: False
Paragraph: AlGaN/GaN high electron mobility transistors (HEMTs) were used to sense the binding between double stranded DNA (dsDNA) and the severe acute respiratory syndrome coronavirus (SARS-CoV) nucleocapsid protein (N protein). The sensing signals were the drain current change of the HEMTs induced by the protein-dsDNA binding. Binding-site models using surface coverage ratios were utilized to analyze the signals from the HEMT-based sensors to extract the dissociation constants and predict the number of binding sites. Two dissociation constants, K D1 = 0.0955 nM, K D2 = 51.23 nM, were obtained by fitting the experimental results into the two-binding-site model. The result shows that this technique is more competitive than isotope-labeling electrophoretic mobility shift assay (EMSA). We demonstrated that AlGaN/GaN HEMTs were highly potential in constructing a semiconductor-based-sensor binding assay to extract the dissociation constants of nucleotide-protein interaction. 
 Title: Investigation of C-terminal domain of SARS nucleocapsid protein-Duplex DNA interaction using transistors and binding-site models Biographies
Output: True
Paragraph: Implementing national to community-based "One Health" strategy for human, animal and environmental challenges and migrating-led consequences offer great opportunities, and its value of sustained development and wellbeing is an imperative. "One Health" strategy in policy commitment, partnership and financial investment are much needed in advocacy, contextual health human-animal and environmental development. Therefore, appropriate and evidence-based handling and management strategies in moving forward universal health coverage and sustainable development goals (SDGs) are essential components to the China-Africa health development initiatives. It is necessary to understand how to strengthen robust and sustainable "One Health" approach implementation in national and regional public health and disaster risk reduction programs. Understanding the foundation of "One Health" strategy in China-Africa public health cooperation is crucial in fostering health systems preparedness and smart response against emerging and re-emerging threats and epidemics. Building the value of China-Africa "One Health" strategy partnerships, frameworks and capacity development and implementation through leveraging on current and innovative China-Africa health initiatives, but also, mobilizing efforts on climatic changes and disasters mitigation and lifestyle adaptations strategies against emerging and current infectious diseases threats are essential to establish epidemic surveillance-response system under the concept of global collaborative coordination and lasting financing mechanisms. Further strengthen local infrastructure and workforce 
 Title: The value of China-Africa health development initiatives in strengthening "One Health" strategy R EVIEWS
Output: False
Paragraph: It is an exciting time in the field of microbiology because of the expansion of rapid diagnostic tests. Pathogen testing previously was performed by traditional laboratory methods such as bacterial, fungal, and viral culture or ova and parasite (O&P) examination. Testing could have a slow time to results; some testing lacked sensitivity, and most testing was centralized in the laboratory. Newer advances in pathogen detection assays are now providing rapid results and have greater sensitivity and specificity, and many assays are moving out of the centralized laboratory and to the patient as pointof-care tests. In this review, the authors chose to highlight the currently available US Food and Drug Administration (FDA)-cleared molecular assays for various infectious syndromes relevant to the pediatric population. Although outcome studies in this area are sparse, rapid results may result in decreased time to optimal antimicrobial treatment and improved patient outcomes. Disclosure Statement: E. McElvania is a consultant for Luminex Corporation. M.D. Gonzalez has no disclosures. KEYWORDS Rapid diagnostic assays Group A streptococcus Influenza RSV Syndromic multiplex panels Gastrointestinal panel Respiratory panel Meningitis encephalitis panel Compared with traditional rapid antigen testing, new diagnostics assays for Group A Streptococcus, influenza, and respiratory syncytial virus combine rapid turnaround time with high sensitivity and specificity. There has been a surge in the availability of multiplex syndromic panels that test for a broad range of pathogens associated with a single clinical presentation. Molecular infectious disease testing that was previously performed in microbiology laboratories is now being developed in easy-to-use platforms, which are available at point of care. 
 Title: New Developments in Rapid Diagnostic Testing for Children
Output: False
Paragraph: Background: Proenkephalin (PENK) has been suggested as a novel biomarker for kidney function. We investigated the diagnostic and prognostic utility of plasma PENK in comparison with neutrophil gelatinase-associated lipocalin (NGAL) and estimated glomerular filtration rates (eGFR) in septic patients. Methods: A total of 167 septic patients were enrolled: 99 with sepsis, 37 with septic shock, and 31 with suspected sepsis. PENK and NGAL concentrations were measured and GFR was estimated by using the isotope dilution mass spectrometry traceable-Modification of Diet in Renal Disease (MDRD) Study and three Chronic Kidney Disease Epidemiology Collaboration (CKD-EPI) equations: CKD-EPICr, CDK-EPICysC, and CKD-EPICr-CysC. The PENK, NGAL, and eGFR results were compared according to sepsis severity, presence or absence of acute kidney injury (AKI), and clinical outcomes. Results: The PENK, NGAL, and eGFR results were significantly associated with sepsis severity and differed significantly between patients with and without AKI only in the sepsis group (all P < 0.05). PENK was superior to NGAL in predicting AKI (P = 0.022) and renal replacement therapy (RRT) (P = 0.0085). Regardless of the variable GFR category by the different eGFR equations, PENK showed constant and significant associations with all eGFR equations. Unlike NGAL, PENK was not influenced by inflammation and predicted the 30day mortality. Conclusions: PENK is a highly sensitive and objective biomarker of AKI and RRT and is useful for prognosis prediction in septic patients. With its diagnostic robustness and predictive power for survival, PENK constitutes a promising biomarker in critical care settings including sepsis. 
 Title: Original Article Clinical Chemistry Proenkephalin, Neutrophil Gelatinase-Associated Lipocalin, and Estimated Glomerular Filtration Rates in Patients With Sepsis
Output: True
Paragraph: The chemokine CXCL10 is produced during infection and inflammation to activate the chemokine receptor CXCR3, an important regulator of lymphocyte trafficking and activation. The goal of this study was to assess the contributions of CXCL10 to the pathogenesis of experimental septic shock in mice. Methods: Septic shock was induced by cecal ligation and puncture (CLP) in mice resuscitated with lactated Ringer's solution and, in some cases, the broad spectrum antibiotic Primaxin. Studies were performed in CXCL10 knockout mice and mice treated with anti-CXCL10 immunoglobulin G (IgG). Endpoints included leukocyte trafficking and activation, core body temperature, plasma cytokine concentrations, bacterial clearance and survival. Results: CXCL10 was present at high concentrations in plasma and peritoneal cavity during CLP-induced septic shock. Survival was significantly improved in CXCL10 knockout (CXCL10KO) mice and mice treated with anti-CXCL10 IgG compared to controls. CXCL10KO mice and mice treated with anti-CXCL10 IgG showed attenuated hypothermia, lower concentrations of interleukin-6 (IL-6) and macrophage inhibitory protein-2 (MIP-2) in plasma and lessened natural killer (NK) cell activation compared to control mice. Compared to control mice, bacterial burden in blood and lungs was lower in CXCL10-deficient mice but not in mice treated with anti-CXCL10 IgG. Treatment of mice with anti-CXCL10 IgG plus fluids and Primaxin at 2 or 6 hours after CLP significantly improved survival compared to mice treated with non-specific IgG under the same conditions. Conclusions: CXCL10 plays a role in the pathogenesis of CLP-induced septic shock and could serve as a therapeutic target during the acute phase of septic shock. 
 Title: The role of CXCL10 in the pathogenesis of experimental septic shock
Output: False
Paragraph: In this paper, we demonstrate the uses of some simple mathematical models for the study of disease dynamics in a pandemic situation with a focus on influenza. These models are employed to evaluate the effectiveness of various control programs via vaccination and antiviral treatment. We use susceptible-, infectious-, recovered-type epidemic models consisting of ordinary differential equations. These models allow us to derive threshold conditions that can be used to assess the effectiveness of vaccine and drug use and to determine disease outcomes. Simulations are helpful for examining the potential consequences of control options under different scenarios. Particularly, results from models with constant parameters and models with time-dependent parameter functions are compared, demonstrating the significant differences in model outcomes. Results suggest that the effectiveness of vaccination and drug treatment can be very sensitive to factors including the time of introduction of the pathogen into the population, the beginning time of control programs, and the levels of control measures. More importantly, in some cases, the benefits of vaccination and antiviral use might be significantly compromised if these control programs are not designed appropriately. Mathematical models can be very useful for understanding the effects of various factors on the spread and control of infectious diseases. Particularly, the models can help identify potential adverse effects of vaccination and drug treatment in the case of pandemic influenza. 
 Title: Theme: Emerging Concepts for Vaccine Development and Vaccination Modeling the Effects of Vaccination and Treatment on Pandemic Influenza
Output: True
Paragraph: The dominant viral etiologies responsible for acute respiratory infections (ARIs) are poorly understood, particularly among hospitalized patients. Improved etiological insight is needed to improve clinical management and prevention of ARIs. Methods: Clinical and demographic information and throat swabs were collected from 607 patients from 2011 to 2013 in Shandong Province, China. Multiplex RT-PCR (SeeplexTM RV detection, Seegene) was performed to detected 12 respiratory viral pathogens. Results: A total of 607 hospitalized patients were enrolled from 2011 to 2013. Viruses were identified in 35.75 % (217/607) of cases, including 78 influenza virus A and B (IVA and IVB), 47 para-influenza viruses (PIVs), 41 respiratory syncytial virus (RSV) and 38 adenovirus (ADV). For the children under 15 year old, the common detected viruses were influenza viruses, RSV, PIVS and ADV, while the principal respiratory viruses were human coronaviruses (HCoV), PIVs, influenza viruses for the old adults. Co-infections with multiple viruses were detected in 15.67 % of patients. Children under 5 years were more likely to have one or more detectable virus associated with their ARI. The peak of ARI caused by the respiratory viruses occurred in winter. Conclusion: This study demonstrated respiratory viruses were the major cause of hospitalized ARI patients in Shandong Province, influenza virus was the most common detected, RSV was the highest incidence among the young children (≤5 years). These findings also gave a better understand of virus distribution among different age and seasons, which help to consider potential therapeutic approaches and develop effective prevention strategies for respiratory virus infection. 
 Title: Viral Etiology of acute respiratory tract infections in hospitalized children and adults in Shandong Province, China
Output: False
Paragraph: The safety and the efficacy of a modified-live (ML) canine coronavirus (CCoV) vaccine strain 257/98-3c was evaluated in 14 dogs seronegative and virus negative for CCoV. For the safety test, four dogs were inoculated, two by intramuscular and two by oronasal route, with 10 times the vaccinal dose. During the observation period (28 days) all dogs did not display any local or systemic reaction. For the efficacy test, eight dogs were vaccinated by intramuscular (four dogs-group A) or by oronasal route (four dogs-group B). Two dogs were maintained as non-vaccinated controls. In the dogs of group A, vaccinal virus was not detected in faecal samples by virus isolation (VI) and by PCR assay, while in the dogs of group B, the virus was revealed for six median days only by PCR. Twenty-eight days later, the vaccinated and control dogs were challenged with a field CCoV strain. After the challenge, the vaccinated dogs did not display clinical signs and the dogs of group A shed virus for 5.5 median days, evaluated by VI, and for 10 median days evaluated by PCR. Virus shedding was not observed, both by VI and PCR assay, in the dogs of group B. The two control dogs displayed moderate clinical signs and the virus was detected by VI for 14.5 median days starting from day 3 post-challenge (dpc 3) and by PCR assay for 23 median days starting from dpc 1. 
 Title: Safety and efficacy of a modified-live canine coronavirus vaccine in dogs
Output: True
Paragraph: Respiratory syncytial virus (RSV) is the leading cause of bronchiolitis and viral pneumonia in infants and young children worldwide. In the Middle East and Arab countries, the burden of RSV-associated hospitalizations is not well characterized. We sought to determine the burden and clinical/epidemiological characteristics of RSV hospitalization in young children in Amman, Jordan. We investigated risk factors for severity including vitamin D levels. Methods: We conducted viral surveillance with clinical and demographic data in children <2 years admitted with respiratory symptoms and/or fever at the Al-Bashir Government Hospital from March16, 2010 to March 31, 2013. Nasal/throat swabs were obtained and placed into lysis buffer, and frozen at −80 • C until testing by real-time RT-PCR for 11 respiratory viruses. Heel stick blood or sera samples for 25hydroxyvitamin D [25(OH)D] levels were obtained and sent to a central laboratory for mass spectrometry. Results: Of the 3168 children, >80% testing positive for one virus, with RSV the most common virus detected (44%). The RSV-associated hospitalization rate was highest in children <6 months with an annual range of 21.1-25.9 per 1000, compared to 6.0-8.0 in 6-11-month-olds and 1.6-2.5 in 12-23-month-olds. RSV-positive children compared with RSV-negative were more likely to be previously healthy without underlying medical conditions, less likely to be born prematurely, had a higher frequency of supplemental oxygen use, and had lower median vitamin D levels. Risk factors for oxygen use in RSV-positive children included underlying medical conditions, lack of breastfeeding, younger age, and higher viral load. Conclusion: RSV is a major cause of illness in hospitalized Jordanian children and is associated with increased severity compared to other respiratory viruses. Children with RSV in the Middle East would benefit from future RSV vaccines and antiviral therapy. 
 Title: Natural history and epidemiology of respiratory syncytial virus infection in the Middle East: Hospital surveillance for children under age two in Jordan
Output: True
Paragraph: The present study was undertaken to evaluate chikungunya virus (CHIKV) proteins for RNAi suppressor activity. We systematically analyzed all nine CHIKV proteins for RNAi suppressor activity using Sf21 RNAi sensor cell line based assay. Two non-structural proteins, namely, nsP2 and nsP3 were found to exhibit RNAi suppressor activity. We further validated the findings in natural hosts, namely in Aedes and in mammalian cell lines and further through EMSA and Agrobacterium infiltration in GFP silenced transgenic tobacco plants. Domains responsible for maximum RNAi suppressor activity were also identified within these proteins. RNA binding motifs in these domains were identified and their participation in RNAi suppression evaluated using site directed mutagenesis. Sequence alignment of these motifs across all species of known alphaviruses revealed conservation of these motifs emphasizing on a similar role of action in other species of alphaviruses as well. Further validation of RNAi suppressor activity of these proteins awaits establishment of specific virus infection models. RNA interference (RNAi) is a conserved evolutionary mechanism designed to impart an antiviral defence system across organisms ranging from plants, fungi, arthropods and nematodes 1-4 . The phenomenon, triggered by the production of double stranded RNA (dsRNA) by the pathogen upon infection, leads to the activation of the RNA interference silencing complex (RISC) by loading of dsRNA/siRNA into the complex ultimately leading to cleavage of the viral RNA 5,6,7 . Several components of RISC participate in the cleavage, most important being ribonuclease III Dicer (DCR) and Argonaute protein (AGO). Dicer acts on dsRNA to generate small RNA (sRNA) that are loaded into the AGO, resulting in cleavage 8,9 ; however, some RNAi pathways are independent of Dicer and other components like RNA-dependent RNA polymerase (RdRP) produce short RNA transcripts that directly bind to AGO 10 . Similarly, much is now known about the Piwi pathway that is specifically active in the germline 11 . In response to RNAi in plants and insects, viruses infecting these systems utilise some of their own proteins/sequence elements that counteract the antiviral RNAi pathway 12 . These viral suppressors of RNAi (VSRs) act through different mechanisms, either by binding to long dsRNA and protecting them from Dicer 7,13 or short RNAs 14 or through multi-mode mechanisms 15,16 . Recently it has been shown that some viruses encode host-specific VSRs due to co-evolution of the virus and the host, emphasising on the importance of analysing suppressor activity in relevant host 17 . Amongst medically important pathogenic viruses, arboviruses form an important subset of viruses due to the complexity of their host preferences 18 . These viruses, mainly constituted by genera flavivirus and alphavirus, 
 Title: Analysis of chikungunya virus proteins reveals that non-structural proteins nsP2 and nsP3 exhibit RNA interference (RNAi) suppressor activity OPEN
Output: False
Paragraph: ARTICLES We synthesized three overlapping 19-amino-acid peptides spanning the F binding domain of RhoA (amino acids 67-110) and used these to study the effect of peptides on virus-induced syncytium formation. Pretreatment of virus inoculum with the RhoA 77-95 peptide completely blocked plaque formation, whereas pretreatment with RhoA 87-105 did not have any effect on the plaque formation relative to media-treated controls (Fig. 1) . The RhoA 67-85 peptide did not block RSV-induced syncytium forma- by reduction of peak titer by 2 log 10 in RSV-infected mice. These findings indicate that the interaction between these two paramyxovirus fusion proteins and RhoA is an important target for new antiviral strategies. 
 Title: A RhoA-derived peptide inhibits syncytium formation induced by respiratory syncytial virus and parainfluenza virus type 3
Output: False
Paragraph: In the current COVID-19 pandemic, a significant proportion of cases shed SARS-Coronavirus-2 (SARS-CoV-2) with their faeces. To determine if SARS-CoV-2 is present in sewage during the emergence of COVID-19 in the Netherlands, sewage samples of 7 cities and the airport were tested using RT-PCR against three fragments of the nucleocapsid protein gene (N1-3) and one fragment of the envelope protein gene (E). No SARS-CoV-2 was detected in samples of February 6, three weeks before the first case was reported in the Netherlands on February 27. On March 5, the N1 fragment was detected in sewage of five sites. On March 15/16, the N1 fragment was detected in sewage of six sites, and the N3 and E fragment were detected at 5 and 4 sites respectively. This is the first report of detection of SARS-CoV-2 in sewage. The detection of the virus in sewage, even when the COVID-19 prevalence is low, indicates that sewage surveillance could be a sensitive tool to monitor the circulation of the virus in the population. All rights reserved. No reuse allowed without permission. the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. 
 Title: Title page Title Presence of SARS-Coronavirus-2 in sewage. Authors and their affiliations
Output: False
Paragraph: A.K. and M.M.S. contributed equally to this work. We generated the near-full genome sequence of Middle East respiratory syndrome coronavirus (MERS-CoV) from a collected nasal sample of dromedary camel in Egypt. The newly characterized Egyptian strain has high similarity to the previously characterized Egyptian virus and both of viruses fell into a cluster distinct from other MERS-CoVs. 
 Title: Complete Genome Sequence of Middle East Respiratory Syndrome Coronavirus Isolated from a Dromedary Camel in Egypt
Output: True
Paragraph: We describe a Multiplex Primer Prediction (MPP) algorithm to build multiplex compatible primer sets to amplify all members of large, diverse and unalignable sets of target sequences. The MPP algorithm is scalable to larger target sets than other available software, and it does not require a multiple sequence alignment. We applied it to questions in viral detection, and demonstrated that there are no universally conserved priming sequences among viruses and that it could require an unfeasibly large number of primers ($3700 18-mers or $2000 10-mers) to generate amplicons from all sequenced viruses. We then designed primer sets separately for each viral family, and for several diverse species such as foot-and-mouth disease virus (FMDV), hemagglutinin (HA) and neuraminidase (NA) segments of influenza A virus, Norwalk virus, and HIV-1. We empirically demonstrated the application of the software with a multiplex set of 16 short (10 nt) primers designed to amplify the Poxviridae family to produce a specific amplicon from vaccinia virus. 
 Title: Multiplex primer prediction software for divergent targets
Output: True
Paragraph: OBJECTIVE-To estimate risk of infant respiratory morbidity associated with cesarean delivery before labor and ruptured membranes among HIV-1-infected women. METHODS-In a prospective cohort study of HIV-1-infected women and their infants, mode of delivery was determined by clinicians at the participating sites. For this analysis, "elective cesarean delivery" was defined as any cesarean delivery, regardless of gestational age, without labor and with duration of ruptured membranes of less than 5 minutes. Nonelective cesarean deliveries were those performed after the onset of labor, rupture of membranes, or both. Vaginal delivery included normal spontaneous and instrument deliveries. Associations between mode of delivery and infant respiratory morbidity were assessed using χ 2 or Fisher's exact test. Adjusted odds of respiratory distress syndrome by delivery mode were assessed using multivariable logistic regression. RESULTS-Among 1,194 mother-infant pairs, there were significant differences according to mode of delivery in median gestational age (weeks) at delivery (vaginal, n=566, median=38.8; nonelective cesarean, n=216, median=38.0; and elective cesarean, n=412, median 38.1; P<.001) and incidence of respiratory distress syndrome (vaginal, n=9, 1.6%, reference; nonelective cesarean, n=16, 7.4%; elective cesarean, n=18; 4.4%; (P<.001). In analyses adjusted for gestational age and birth weight, mode of delivery was not statistically significantly associated 
 Title: Mode of Delivery and Infant Respiratory Morbidity Among Infants Born to HIV-1-Infected Women NIH Public Access Author Manuscript
Output: True
Paragraph: Introduction: Infectious acute respiratory disease (ARD) is a significant cause of worldwide morbidity, disproportionately affecting individuals living in crowded conditions, such as found at military training centers, school dormitories, and correctional facilities. Vaccines have been used to protect against ARD; however, these are not always available or effective. The medical literature on preventive nonvaccine ARD interventions (NOVARDIs) for infectious diseases, which addressed personal measures, administrative controls, and engineering controls, was studied during 2000 to 2004. Population-based studies in community settings (non-health care) were reviewed in detail to evaluate the effectiveness of NOVARDIs. Budgetary and logistic factors as well as acceptance were considered in formulating recommendations for implementation of NOVARDIs in military training centers. Thirty-eight population-based studies contained in 35 publications were examined. Three studies contained information on multiple NOVARDIs. Nine studies supported the use of personal measures relating to hand hygiene. Ten studies supported administrative controls such as cohorting military training units to reduce contact between units (4 studies), providing adequate personal space to reduce crowding (5), and cloth barriers between beds (1); and 14 studies supported the use of engineering controls such as increased indoor air dilution and ventilation (2), dust suppression (4), and air sterilization (8). Conclusions: Promoting hand hygiene and reducing crowding through the provision of adequate living space and cohorting of training units may offer benefits in respiratory disease control. These interventions, along with UV lights and air dilution/ventilation, deserve further evaluation in controlled studies to assess their efficacy. NOVARDIs could benefit military and other populations living in close contact. (Am J Prev Med 2005;28(3):305-316) 
 Title: Selected Nonvaccine Interventions to Prevent Infectious Acute Respiratory Disease
Output: False
Paragraph: Background: False negative results of SARS-CoV-2 nucleic acid detection pose threats to COVID-19 patients and medical workers alike. Objective: To develop multivariate models to determine clinical characteristics that contribute to false negative results of SARS-CoV-2 nucleic acid detection, and use them to predict false negative results as well as time windows for testing positive. Design: Retrospective Cohort Study (Ethics number of Tongji Hospital Measurements: Clinical information on CT imaging reports, blood routine tests, and clinic symptoms were collected. A multivariate logistic regression was used to explain and predict false negative testing results of SARS-CoV-2 detection. A multivariate accelerated failure model was used to analyze and predict delayed time windows for testing positive. Results: Of the 1,324 outpatients who diagnosed of COVID-19, 633 patients tested positive in their first SARS-CoV-2 nucleic acid test (47.8%), with a mean age of 51 years (SD=14.9); the rest, which had a mean age of 47 years (SD=15.4), tested negative in the first test. "Ground glass opacity" in a CT imaging report was associated with a lower chance of false negatives (aOR, 0.56), and reduced the length of time window for testing positive by 26%. "Consolidation" was associated with a higher chance of false negatives (aOR, 1.57), and extended the length of time window for testing positive by 44%. In blood routine tests, basophils (aOR, 1.28) and eosinophils (aOR, 1.29) were associated with a higher chance of false negatives, and were found to extend the time window for testing positive by 23% and 41%, respectively. Age and gender also affected the significantly. Limitation: Data were generated in a large single-center study. Testing outcome and positive window of SARS-CoV-2 detection for COVID-19 patients were associated with CT imaging results, blood routine tests, and clinical symptoms. Taking into account relevant information in CT imaging reports, blood routine tests, and clinical symptoms helped reduce a false negative testing outcome. The predictive AFT model, what we believe to be one of the first statistical models for predicting time window of SARS-CoV-2 detection, could help clinicians improve the accuracy and efficiency of the diagnosis, and hence, optimizes the timing of nucleic acid detection and alleviates the shortage of nucleic acid detection kits around the world. All rights reserved. No reuse allowed without permission. author/funder, who has granted medRxiv a license to display the preprint in perpetuity. 
 Title: Analysis and Prediction of COVID-19 Patients' False Negative Results for SARS-CoV-2 Detection with Pharyngeal Swab Specimen: A Retrospective Study Running Title: Prediction of False Negative Results for SARS-CoV-2 Detection
Output: False
Paragraph: Background: Acute ischemic stroke (AIS) in pediatric populations accounts for more than half of pediatric strokes and is associated with significant morbidity and mortality. Pediatric AIS can present with nonspecific symptoms or symptoms that mimic alternate pathology. Case Report: A 4-month-old female presented to the emergency department for fever, decreased oral intake, and ''limp'' appearance after antibiotic administration. She was febrile, tachypneic, and hypoxic. Her skin was mottled with 3-s capillary refill, her anterior fontanelle was tense, and she had mute Babinski reflex bilaterally but was moving all extremities. The patient was hyponatremic, thrombocytopenic, and tested positive for influenza A. A computed tomography scan of the brain revealed an acute infarction involving the right frontal, parietal, temporal, and occipital lobes in addition to hyperdensities concerning for thrombosed cortical veins. The patient was transferred for specialty evaluation and was discharged 2 weeks later on levetiracetam. Why Should an Emergency Physician be Aware of This?: Pediatric AIS can present with nonspecific symptoms that mimic alternate pathology. A high level of suspicion is needed so as not to miss the diagnosis of pediatric AIS in the emergency department. A thorough neurologic assessment is warranted, and subtle abnormalities should be investigated further. Ó 
 Title: Clinical Communications: Pediatrics CEREBROVASCULAR ACCIDENT IN A PEDIATRIC PATIENT PRESENTING WITH INFLUENZA
Output: False
Paragraph: Pneumonia is an acute inflammation of the lower respiratory tract. Lower respiratory tract infection is a major cause of mortality worldwide. Pneumonia is most common at the extremes of life. Predisposing factors in children include an underdeveloped immune system together with other factors, such as malnutrition and overcrowding. In adults, tobacco smoking is the single most important preventable risk factor. The commonest infecting organisms in children are respiratory viruses and Streptoccocus pneumoniae. In adults, pneumonia can be broadly classified, on the basis of chest radiographic appearance, into lobar pneumonia, bronchopneumonia and pneumonia producing an interstitial pattern. Lobar pneumonia is most commonly associated with community acquired pneumonia, bronchopneumonia with hospital acquired infection and an interstitial pattern with the so called atypical pneumonias, which can be caused by viruses or organisms such as Mycoplasma pneumoniae. Most cases of pneumonia can be managed with chest radiographs as the only form of imaging, but CT can detect pneumonia not visible on the chest radiograph and may be of value, particularly in the hospital setting. Complications of pneumonia include pleural effusion, empyema and lung abscess. The chest radiograph may initially indicate an effusion but ultrasound is more sensitive, allows characterisation in some cases and can guide catheter placement for drainage. CT can also be used to characterise and estimate the extent of pleural disease. Most lung abscesses respond to medical therapy, with surgery and image guided catheter drainage serving as options for those cases who do not respond. 
 Title: Pneumonia in the immunocompetent patient
Output: False