niryuu/sni-each-converted huggingface dataset:
Paragraph: Background: The four types of human parainfluenza viruses (PIV) are important causes of community-acquired pneumonia, particularly in children; however, limited information exists about the incidence of PIV in critically ill patients. The aim of this study is to describe the spectrum, incidence and clinical features of PIV-associated infections diagnosed during the hospital stay of patients admitted to pediatric intensive care unit (PICU) and intensive care unit (ICU) of 5 medical centers across Kuwait. Methods: This was a population-based, retrospective study from 2013 to 2015. Specimens were analyzed by molecular methods. This analysis was performed using the database of Virology Unit, Mubarak Al-Kabeer Hospital. Data from 1510 admitted patients with suspected respiratory viral infections was extracted. Results: The database contained a total of 39 (2.6%) patients infected with PIV (53.8% male and 46.2% females) and 20 (51.3%) were under 1 year of age. The most frequently isolated type was type 3 (28, 71.8%) followed by type 1 (9, 23.1%). At admission the most common clinical diagnosis was pneumonia in 12 patients (30.8%, p < 0.05) followed by bronchiolitis in 10 patients (25.6%). Conclusion: PIV plays an important yet unrecognized role in the outcomes of PIUC and ICU patients. Our results contribute to the limited epidemiologic data of PIV in PIUC and ICU in this region. 
 Title: The potential influence of human parainfluenza viruses detected during hospitalization among critically ill patients in Kuwait, 2013-2015
Output: True
Paragraph: Fast and slow axonal transport of protein have been studied in the optic nerves of mice infected with Semliki Forest Virus (SFV) that causes patchy demyelination throughout the CNS. Intravitreal injections of [3H]proline were given at regular intervals after virus inoculation, the labelled protein in the superior colliculi was then measured after survival periods of 18 h or 10 days, for fast and slow axonal transport studies, respectively. Fast transport studies showed an enhanced amount of protein arriving at the optic nerve terminals (superior colliculus) of the SFV-infected mice prior to the onset of demyelination. In contrast, the slow transport studies showed an enhanced amount of protein at the superior colliculus of the SFV-infected mice during the demyelination period. There was no concomitant increase in labelled protein in the retina at any time after the SFV infection. It is proposed that alteration in the transport of the protein constituents other than major myelin specific components may cause disruption of myelin maintenance in SFV infection. 
 Title: The Relationship between Axonal Transport of Protein and Demyelination in the Optic Nerves of Mice Infected with Semliki Forest Virus
Output: True
Paragraph: Cellular C-type lectins have been reported to facilitate filovirus infection by binding to glycans on filovirus glycoprotein (GP). However, it is not clearly known whether interaction between C-type lectins and GP mediates all the steps of virus entry (i.e., attachment, internalization, and membrane fusion). In this study, we generated vesicular stomatitis viruses pseudotyped with mutant GPs that have impaired structures of the putative receptor binding regions and thus reduced ability to infect the monkey kidney cells that are routinely used for virus propagation. We found that infectivities of viruses with the mutant GPs dropped in C-type lectin-expressing cells, parallel with those in the monkey kidney cells, whereas binding activities of these GPs to the Ctype lectins were not correlated with the reduced infectivities. These results suggest that C-type lectin-mediated entry of filoviruses requires other cellular molecule(s) that may be involved in virion internalization or membrane fusion. 
 Title: C-type lectins do not act as functional receptors for filovirus entry into cells
Output: False
Paragraph: Q.-W. Jiang). 95% confidence interval (CI): 0.42, 0.66), DARH (OR ¼ 0.73, 95% CI: 0.53, 1.00), and daily average wind velocity (DAWV; OR ¼ 0.81, 95% CI: 0.68, 0.96). Adjustment for the onset time of a primary case led to little change in the results. In addition, in Hebei Province, a major affected area in China, only DAWV (OR ¼ 0.38, 95% CI: 0.20, 0.72) was a significant predictor of secondary attack rate with adjustment for the onset time of primary case. In Inner Mongolia, another major affected area in China, DAWV (OR ¼ 0.50, 95% CI: 0.26, 0.94) and DHS (OR ¼ 0.27, 95% CI: 0.09, 0.81) were significant predictors of secondary attack rate with adjustment for the onset time of primary case. Conclusions: Our results suggest that the SARS outbreak was significantly associated with DAWV, and that DAAP, DARH and DHS may also have influenced the SARS outbreak to some extent. However, because of ecological fallacy and uncontrolled confounding effects that may have biased the results, the association between the SARS outbreak and these meteorological factors and air pollution deserve further investigation. 
 Title: Influence of meteorological factors and air pollution on the outbreak of severe acute respiratory syndrome
Output: True
Paragraph: Recently bats have been associated with the emergence of diseases, both as reservoirs for several new viral diseases in humans and other animals and, in the northern Americas, as hosts for a devastating fungal disease that threatens to drive several bat species to regional extinction. However, despite these catastrophic events little Information is available on bat defences or how they interact with their pathogens. Even less is known about the response of bats to infection during torpor or long-term hibernation. Using tissue samples collected at the termination of an experiment to explore the pathogenesis of White Nose Syndrome in Little Brown Bats, we determined if hibernating bats infected with the fungus Pseudogymnoascus destructans could respond to infection by activating genes responsible for innate immune and stress responses. Lesions due to fungal infection and, in some cases, secondary bacterial infections, were restricted to the skin. However, we were unable to obtain sufficient amounts of RNA from these sites. We therefore examined lungs for response at an epithelial surface not linked to the primary site of infection. We found that bats responded to infection with a significant increase in lungs of transcripts for Cathelicidin (an anti-microbial peptide) as well as the immune modulators tumor necrosis factor alpha and interleukins 10 and 23. In conclusion, hibernating bats can respond to experimental P. destructans infection by activating expression of innate immune response genes. 
 Title: Activation of Innate Immune-Response Genes in Little Brown Bats (Myotis lucifugus) Infected with the Fungus Pseudogymnoascus destructans
Output: True
Paragraph: 2 The abbreviations used are: S, spike; SARS-CoV, severe acute respiratory syndrome coronavirus; MLV, murine leukemia virus; DC-SIGN, dendritic cell-specific intercellular adhesion molecule-3-gubbing non-integrin, ACE2, argiotensin I conserting enzyme 2. FIGURE 4. Introduction of alanine residues in the S2 region modulates elastase-induced virus entry mediated by SARS-CoV S. A and B, pseudotyped virion infections were performed as described for Fig. 2. Infection was induced by treatment with elastase (A) or trypsin (B). Results are presented as relative light units (RLU). Error bars represent the S.E. of three independent experiments. C, cleavage of SARS-CoV by elastase. HEK293T cells expressing the wild type (WT) or mutant SARS-CoV spike protein were treated with 50 g/ml elastase. Cell surface proteins were biotinylated and precipitated, and cleavage products of the SARS-CoV spike protein were analyzed in Western blot with an antibody recognizing the C9 tag at the C terminus of the protein. 
 Title: Elastase-mediated Activation of the Severe Acute Respiratory Syndrome Coronavirus Spike Protein at Discrete Sites within the S2 Domain * □ S
Output: False
Paragraph: There are a number of antivirals as well as antiviral strategies that could be envisaged to prevent or treat severe acute respiratory syndrome (SARS) (or similar) coronavirus (CoV) infections. Targets for the prophylactic or therapeutic interventions include interaction of the spike (S) glycoprotein (S1 domain) with the host cell receptor, fusion of the S2 domain with the host cell membrane, processing of the replicase polyproteins by the virus-encoded proteases (3C-like cysteine protease [3CLpro] and papain-like cysteine protease) and other virus-encoded enzymes such as the NTPase/helicase and RNA-dependent RNA polymerase. Human monoclonal antibody blocking S1 may play an important role in the immunoprophylaxis of SARS. Fusion inhibitors reminiscent of enfuvirtide in the case of HIV may also be developed for SARS-CoV. Various peptidomimetic and nonpeptidic inhibitors of 3CLpro have been described, the best ones inhibiting SARS-CoV replication with a selectivity index greater than 1000. Human interferons, in particular αand β-interferon, as well as short interfering RNAs could further be pursued for the control of SARS. Various other compounds, often with an ill-defined mode of action but selectivity indexes up to 100, have been reported to exhibit in vitro activity against SARS-CoV: valinomycin, glycopeptide antibiotics, plant lectins, hesperetin, glycyrrhizin, aurintricarboxylic acid, chloroquine, niclosamide, nelfinavir and calpain inhibitors. 
 Title: Potential antivirals and antiviral strategies against SARS coronavirus infections
Output: True
Paragraph: Background: Detection of respiratory viruses by time-resolved fluoroimmunoassay based on monoclonal antibodies were developed in our laboratories in the late 1980s and they have been successfully used in daily diagnosis for more than seven years. Later, similar Biotin-EIAs were developed but the sensitivities were unsatisfactory. Objectives: Further optimization of monoclonal Biotin-EIAs and comparison of the optimized assays with TR-FIAs. Study design: Variations in test format, diluents, incubation times and temperatures, and different monoclonal antibodies were tested, and the final comparisons were made with TR-FIA using stored nasopharyngeal aspirates. Results: The improvements in Biotin-EIA featured four changes which increased sensitivity in the assay: (a) test diluent contained diethylenetriamino-pentaacetic acid; (b) antigen and biotinylated detector antibody were added simultaneously; (c) reaction time was extended from 1 h at 37°C to overnight at 4°C; (d) from the thirteen monoclonal antibodies used in TR-FIA, ten were optimal also in Biotin-EIA, but in the parainfluenza 1 and 2 assays other monoclonals proved more sensitive. Out of 257 originally positive specimens tested in the comparison studies, 192 (74.7%) were again positive and 54 (21.0%) were negative in both assays; nine were negative in TR-FIA but positive in Biotin-EIA, while two specimens were negative in Biotin-EIA but positive in TR-FIA. The overall agreement between the two assays was 95.7%. 
 Title: Clinical and Diagnostic Virology Comparison of monoclonal biotin-avidin enzyme immunoassay and monoclonal time-resolved fluoroimmunoassay in detection of respiratory virus antigens
Output: False
Paragraph: The first known cases of Middle East respiratory syndrome (MERS), associated with infection by a novel coronavirus (CoV), occurred in 2012 in Jordan but were reported retrospectively. The case first to be publicly reported was from Jeddah, in the Kingdom of Saudi Arabia (KSA). Since then, MERS-CoV sequences have been found in a bat and in many dromedary camels (DC). MERS-CoV is enzootic in DC across the Arabian Peninsula and in parts of Africa, causing mild upper respiratory tract illness in its camel reservoir and sporadic, but relatively rare human infections. Precisely how virus transmits to humans remains unknown but close and lengthy exposure appears to be a requirement. The KSA is the focal point of MERS, with the majority of human cases. In humans, MERS is mostly known as a lower respiratory tract (LRT) disease involving fever, cough, breathing difficulties and pneumonia that may progress to acute respiratory distress syndrome, multiorgan failure and death in 20 % to 40 % of those infected. However, MERS-CoV has also been detected in mild and influenza-like illnesses and in those with no signs or symptoms. Older males most obviously suffer severe disease and MERS patients often have comorbidities. Compared to severe acute respiratory syndrome (SARS), another sometimes-fatal zoonotic coronavirus disease that has since disappeared, MERS progresses more rapidly to respiratory failure and acute kidney injury (it also has an affinity for growth in kidney cells under laboratory conditions), is more frequently reported in patients with underlying disease and is more often fatal. Most human cases of MERS have been linked to lapses in infection prevention and control (IPC) in healthcare settings, with approximately 20 % of all virus detections reported among healthcare workers (HCWs) and higher exposures in those with occupations that bring them into close contact with camels. Sero-surveys have found widespread evidence of past infection in adult camels and limited past exposure among humans. Sensitive, validated reverse transcriptase real-time polymerase chain reaction (RT-rtPCR)-based diagnostics have been available almost from the start of the emergence of MERS. While the basic virology of MERS-CoV has advanced over the past three years, understanding of the interplay between camel, environment, and human remains limited. 
 Title: MERS coronavirus: diagnostics, epidemiology and transmission
Output: False
Paragraph: In 2012, a novel human coronavirus emerged and was tentatively named ''Middle East respiratory syndrome coronavirus'' (MERS-CoV). The high mortality rate of MERS-CoV focused attention on the ecology of the virus. It has been found that MERS-CoV belongs to the group C lineage of the genus Betacoronavirus. Coronavirus surveillance studies in different populations of bats have suggested that they are probable reservoirs for this novel virus, and phylogenetic analysis of both the spike (S1) and RNA-dependent RNA polymerase proteins of MERS-CoV have revealed that it is related to bat viruses. Recently, the MERS-CoV and its neutralizing antibodies were detected in dromedary camels. Despite the limited number of reported cases of person-to-person transmission, the rapid evolution of the virus poses a continuous threat to humans worldwide. This paper reviews the current state of knowledge regarding the virology, clinical spectrum, evolution, diagnosis and treatment of MERS-CoV infections. 
 Title: Middle East respiratory syndrome coronavirus (MERS-CoV): evidence and speculations
Output: False
Paragraph: We have solved the three-dimensional crystal structure of the stem-loop II motif (s2m) RNA element of the SARS virus genome to 2.7-Å resolution. SARS and related coronaviruses and astroviruses all possess a motif at the 39 end of their RNA genomes, called the s2m, whose pathogenic importance is inferred from its rigorous sequence conservation in an otherwise rapidly mutable RNA genome. We find that this extreme conservation is clearly explained by the requirement to form a highly structured RNA whose unique tertiary structure includes a sharp 908 kink of the helix axis and several novel longer-range tertiary interactions. The tertiary base interactions create a tunnel that runs perpendicular to the main helical axis whose interior is negatively charged and binds two magnesium ions. These unusual features likely form interaction surfaces with conserved host cell components or other reactive sites required for virus function. Based on its conservation in viral pathogen genomes and its absence in the human genome, we suggest that these unusual structural features in the s2m RNA element are attractive targets for the design of anti-viral therapeutic agents. Structural genomics has sought to deduce protein function based on three-dimensional homology. Here we have extended this approach to RNA by proposing potential functions for a rigorously conserved set of RNA tertiary structural interactions that occur within the SARS RNA genome itself. Based on tertiary structural comparisons, we propose the s2m RNA binds one or more proteins possessing an oligomer-binding-like fold, and we suggest a possible mechanism for SARS viral RNA hijacking of host protein synthesis, both based upon observed s2m RNA macromolecular mimicry of a relevant ribosomal RNA fold. Citation: Robertson MP, Igel H, Baertsch R, Haussler D, Ares M, et al. (2004) The structure of a rigorously conserved RNA element within the SARS virus genome. PLoS Biol 3(1): e5. PLoS Biology | www.plosbiology.org January 2005 | Volume 3 | Issue 1 | e5 0086 Open access, freely available online PL o S BIOLOGY PLoS Biology | www.plosbiology.org January 2005 | Volume 3 | Issue 1 | e5 0087 Crystal Structure of SARS s2m RNA PLoS Biology | www.plosbiology.org 
 Title: The Structure of a Rigorously Conserved RNA Element within the SARS Virus Genome
Output: True
Paragraph: Cynomolgus macaques are common across South East Asian countries including Thailand. The National Primate Research Center of Thailand, Chulalongkorn University (NPRCT-CU) captures wild-borne cynomolgus macaque for research use. Limited information is available on the enteric viruses and possible zoonotic infections into or from cynomolgus macaques. We characterized and compare the fecal virome of two populations; healthy wild-originated captive cynomolgus macaques (n = 43) reared in NPRCT-CU and healthy wild cynomolgus macaques (n = 35). Over 90% of recognized viral sequence reads amplified from feces were from bacterial viruses. Viruses from seven families of mammalian viruses were also detected (Parvoviridae, Anelloviridae, Picornaviridae, Adenoviridae, Papillomaviridae, Herpesviridae, and Caliciviridae). The genomes of a member of a new picornavirus genus we named Mafapivirus, a primate chapparvovirus, and a circular Rep-encoding single-strand (CRESS) DNA virus were also characterized. Higher abundance of CRESS DNA viruses of unknown tropism and invertebrate-tropic ambidensovirus were detected in wild versus captive macaques likely reflecting dietary differences. Short term rearing in captivity did not have a pronounced effect on the diversity of mammalian viruses of wild cynomolgus macaques. This study is the first report of the fecal virome of cynomolgus macaques, non-human primates frequently used in biomedical research and vaccination studies. 
 Title: High Diversity and Novel Enteric Viruses in Fecal Viromes of Healthy Wild and Captive Thai Cynomolgus Macaques (Macaca fascicularis)
Output: True
Paragraph: Background 35 The reasons for the large differences between countries in the sizes of their SARS 36 CoV-2 epidemics is unknown. Individual level studies have found that the use of face 37 masks was protective for the acquisition and transmission of a range of respiratory 38 viruses including SARS CoV-1. We hypothesized that population level usage of face 39 masks may be negatively associated SARS CoV-2 spread. 40 41 At a country level, linear regression was used to assess the association between 43 
 Title: Widespread use of face masks in public may slow the spread of SARS CoV-2: 1 an ecological study 2 3 4
Output: True
Paragraph: Human metapneumovirus (hMPV) and respiratory syncytial virus (RSV) are important respiratory pathogens with similar symptomatology. The aim of this prospective birth cohort study was to identify risk factors for an hMPV or RSV infection during the first year of life in unselected healthy children. We followed 217 children from birth to 1 year of age. Nasal swabs and symptom diaries were collected monthly. Anti-hMPV and anti-RSV IgG antibodies by age 1 year were detected by ELISA, and nasal swabs were analysed for hMPV and RSV by RT-PCR. Logistic regression was used for risk factor analysis. Anti-hMPV IgG was found in 38 children (17.5%), and anti-RSV IgG in 172 children (79%). Risk factors for being anti-hMPV IgG-positive were: (1) being born in the spring (OR =2.36; 95% CI:1.06-5.27), and (2) having older siblings (OR=3.82; 95% CI:1.75-8.34). Risk factors for being anti-RSV IgG-positive were: (1) gestational age <38 weeks (OR=3.39; 95% CI:1.42-8.05), (2) increasing paternal age (OR=1.85 per 5 yrs; 95% CI:1.28-2.68), and (3) wall-to-wall carpeting (OR=3.15; 95% CI:1.29-7.68). Being born in the spring was associated with decreased odds of being anti-RSV IgG-positive (OR=0.27, 95% CI:0.09-0.85). Risk factors for RSV hospitalisation (n= 11) were: (1) older siblings (OR=4.49; 95% CI: 1.08-18.73) and (2) smoking in the household (OR=5.06; 95% CI: 1.36-18.76). Exclusive breastfeeding for the first 14 days of life protected against hospitalisation (OR= 0.21; 95% CI:0.06-0.79). In conclusion, this study identifies risk factors for mild and asymptomatic hMPV infections in infancy. Abbreviations hMPV human metapneumovirus RSV respiratory syncytial virus OR odds ratio PBS phosphate-buffered saline NPA nasopharyngeal aspirate RT-PCR reverse transcription-polymerase chain reaction ELISA enzyme-linked immunosorbent assay RT room temperature M-PBS PBS with 2% skim-milk powder HRP horseradish peroxidase TMB tetramethyl benzidine OD optical density SD standard deviation PDV Phocine Distemper Virus Eur 
 Title: A community study of clinical traits and risk factors for human metapneumovirus and respiratory syncytial virus infection during the first year of life
Output: False
Paragraph: Acyclic 2 0 -azanucleosides with a phosphonomethoxy function in the side chain were obtained by coupling of diethyl {2-[N-(pivaloyloxymethyl)-N-(p-toluenesulfonyl)amino]ethoxymethyl}phosphonate with the pyrimidine nucleobases via the Vorbrüggen-type protocol. The compounds were evaluated in vitro for activity against a broad variety of RNA and DNA viruses. 
 Title: Synthesis and antiviral activity evaluation of acyclic 2 0 -azanucleosides bearing a phosphonomethoxy function in the side chain
Output: False
Paragraph: Background: Human metapneumovirus (hMPV) is a Paramyxovirus known to cause acute respiratory tract infections in children and young adults. To date, there is no study from the Aseer region of Saudi Arabia determining the proportion and severity of hMPV infection among pediatric hospitalized patients with respiratory infections. Objectives: The objective of this study is to determine the presence of hMPV antigens in the nasopharyngeal secretions of pediatric patients hospitalized with respiratory tract infections in the Aseer region of Saudi Arabia. Materials and Methods: This prospective, serological hospital-based study included all pediatric patients who were admitted to Aseer Central Hospital, Abha, Saudi Arabia, from July 2016 to November 2017 with upper and/or lower respiratory tract infections. Basic demographics of patients and their clinical data on and after admission were recorded. Direct fluorescent antibody assay was used to detect the presence of hMPV antigens in the obtained nasopharyngeal secretion specimens. Results: During the study, 91 pediatric patients were hospitalized due to upper and/or lower respiratory tract infections, of which 9.9% were positive for hMPV. These patients were aged 9 months to 16 years, were from Abha city or its surrounding localities and were mostly (77.8%) hospitalized during autumn or winter. The most common diagnosis on admission was bronchopneumonia (55.5%) and aspiration pneumonia (22.2%), and some patients also had underlying chronic conditions such as chronic heart disease (22.2%) and bronchial asthma (11.1%). The results obtained indicated that hMPV is a potential etiologic factor for the commonly occurring acute respiratory infections in hospitalized children from the Aseer region of Saudi Arabia. hMPV infection was also found to be associated with complicated respiratory conditions such as bronchopneumonia, chronic heart disease and bronchial asthma. 
 Title: Human metapneumovirus in Pediatric Patients with Acute Respiratory Tract Infections in the Aseer Region of Saudi Arabia
Output: False
Paragraph: Strategies that can improve health and maximize growth in the preweaning period should improve the subsequent production and longevity of replacement animals. Few data are available that quantify feed and water consumption, as well as growth, in healthy versus non-healthy calves-the objective of this study. A database of Holstein calves (<1 wk of age; n = 313) was developed to compare calves that developed diarrhea in the first 21 d after arrival from commercial farms to the research facility versus calves that remained healthy. Individual calf data from 4 experiments included daily intake of milk replacer, free water, electrolyte solution, and starter grain, as well as weekly body weight (BW) and frame measures for 21 d after arrival. Calves with a fecal score of >2 for ≥3 consecutive days over the first 21 d of each experiment were retrospectively classified as diarrheic (DIA; n = 96); the remainder were classified as healthy (HEA; n = 217). Other health issues were minimal. The likelihood of elevated fecal score occurrence and the cumulative number of days with an elevated score were greater for DIA calves than for HEA calves. The initial total protein concentration in blood did not differ between classifications. Cumulative milk replacer dry matter intake (DMI) and water consumed from milk replacer were significantly less for DIA calves than for HEA calves, because DIA calves were more likely to refuse milk replacer. Cumulative starter DMI was decreased for DIA versus HEA calves. As a result, cumulative total DMI was significantly less for DIA calves than for HEA calves. Cumulative free water intake did not differ between classifications. The DIA calves were more likely to receive electrolyte solution and have more days given electrolyte solution than HEA calves. As a result, total cumulative intake of electrolyte solution was greater in DIA calves than in HEA calves. Cumulative total water intake did not differ between classifications. Initial BW did not differ between classifications; however, a classification × time interaction for BW indicated that HEA calves were heavier than DIA calves and had greater ADG. Significant classification × time interactions for hip height and heart girth revealed that HEA calves had a larger frame size. Gain-feed ratios for both milk replacer intake and total DMI differed between classifications: DIA calves were less feed-efficient than HEA calves. In conclusion, diarrhea in young calves decreases DMI, BW gain, and feed efficiency relative to HEA calves within 21 d of arrival. 
 Title: Intake and growth in transported Holstein calves classified as diarrheic or healthy within the first 21 days after arrival in a retrospective observational study
Output: True
Paragraph: Previously described polyclonal or monoclonal antibodies (mAb) to rabbit CD5, raised against expressed recombinant protein or peptides, recognize CD5 on most rabbit B cells. The mAb KEN-5 was originally reported to recognize rabbit CD5. However, KEN-5 binds almost exclusively to T cells and only to a minor population of B cells. We show here that by Enzyme-linked Immunosorbent Assay (ELISA), KEN-5 binds to recombinant rabbit CD5. This interaction is partially inhibited by polyclonal goat anti-CD5 antibody. In addition, immunoprecipitations from lysates of surface biotinylated rabbit lymphocytes with KEN-5 or our anti-CD5 mAb isolate molecules that migrate identically on gels with the same approximate relative molecular mass of 67,000 M r . By flow cytometric analyses of individual cells from spleen, thymus and appendix, KEN-5 recognizes CD5like molecules mainly on T cells and on 3-6% of IgM + B cells. Immunohistochemical staining of splenic and appendix tissues and confocal immunofluorescent imaging confirm and extend results from flow cytometric analyses. Quantitation of fluorescent colocalization indicates that staining by KEN-5 colocalizes with staining by anti-CD5 on small percentages lymphocytes in splenic tissue sections. As CD5 has both N-and O-linked glycosylation, we hypothesised that differential binding of KEN-5 to T cells and B-cells may be explained by different glycan structures on the CD5 present on T compared to B cells. This hypothesis is supported by ELISA data that show that deglycosylation diminishes the binding of KEN-5 to recombinant rabbit CD5. Screening KEN-5 on an array with 406 glycans was inconclusive. Although we did not identify a strongly binding glycan structure, the data are suggestive that the epitope recognized by KEN-5 may be influenced by glycan structures. The epitope this mAb recognizes may either be the glycan itself, or more likely, is influenced by neighboring glycan structure. Our findings suggest that development, selection and function of different B-and T-cell subsets or their preferential survival may be directly or indirectly dependent on different glycan structures associated with CD5 or CD5-like molecules expressed on T cells compared to B cells. 
 Title: Characterization of Rabbit CD5 Isoforms NIH Public Access Author Manuscript
Output: True
Paragraph: A 28-nucleotide mRNA pseudoknot that overlaps the P1 and P2 genes of sugarcane yellow leaf virus (ScYLV) stimulates −1 ribosomal frameshifting. The in vitro frameshifting efficiency is decreased ≈8 fold upon substitution of the 3′ most loop 2 nucleotide (C27) to adenosine, which accepts a hydrogen bond from the 2′-OH of C14 in stem S1. The solution structures of the wild-type (WT) and the C27A ScYLV RNA pseudoknots show that while the RNAs adopt virtually identical overall structures, there are significant structural differences at the helical junctions of the two RNAs. Specifically, C8 + in loop L1 in the C8 + ·(G12-C28) L1-S2 major groove base triple is displaced by ≈2.3 Å relative to the accepting stem 2 base pair (G12-C28) in the C27A RNA. Here, we employ a double mutant cycle approach to analyze the pairwise coupling of the C8 + ·(G12-C28) and C27·(C14-G7) or A27·(C14-G7) hydrogen bonds in the WT and C27A ScYLV RNAs, respectively, and compare these findings with previous results from the beet western yellows virus (BWYV) RNA. We find that the pairwise coupling free energy (δ AB i ) is favorable for the WT RNA (-0.7 ±0.1 kcal·mol −1 ), thus revealing that formation of these two hydrogen bonds is positively cooperative. In contrast, δ AB i is +0.9 ±0.4 kcal·mol −1 for the poorly functional C27A ScYLV RNA, indicative of non-additive hydrogen bond formation. These results reveal that cooperative hydrogen bond formation across the helical stem junction in H-type pseudoknots correlates with enhanced frameshift stimulation by luteoviral mRNA pseudoknots. pseudoknot; frameshifting; protonated cytidine; hydrogen bond coupling Intricately folded motifs in both the noncoding and coding regions of mRNAs are known to regulate all steps of the translation cycle. RNA functions in cap-independent translational initiation by providing a binding site for 40S ribosomal subunits in internal ribosomal entry sites (IRES) (1). Riboswitches are naturally occurring aptamers that bind metabolites including adenine, guanine, S-adenosylmethionine, and thiamine pyrophosphatase that directly regulate the expression of enzymes linked to their production or degradation (2). Folded RNA motifs found in coding regions of mRNAs regulate ribosomal recoding by stimulating stop codon suppression, stop codon redefinition, or change the translational reading frame, an example of which is −1 programmed ribosomal frameshifting (−1 PRF) (3,4). −1 PRF occurs during translational elongation where the mRNA slips back by one nucleotide into the "−1" reading frame relative to the reference "0" frame. In RNA viruses, −1 PRF is used to produce several † 
 Title: Pairwise coupling analysis of helical junction hydrogen bonding interactions in luteoviral RNA pseudoknots † NIH Public Access Author Manuscript
Output: True
Paragraph: Sixteen longSAGE libraries from four different clinical stages of cervical intraepithelial neoplasia have enabled us to identify novel cell-surface biomarkers indicative of CIN stage. By comparing gene expression profi les of cervical tissue at early and advanced stages of CIN, several genes are identifi ed to be novel genetic markers. We present fi fty-six cell-surface gene products differentially expressed during progression of CIN. These cell surface proteins are being examined to establish their capacity for optical contrast agent binding. Contrast agent visualization will allow real-time assessment of the physiological state of the disease process bringing vast benefi t to cancer care. The data discussed in this publication have been submitted to NCBIs Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) and are accessible through GEO Series accession number GSE6252. 
 Title: Using LongSAGE to Detect Biomarkers of Cervical Cancer Potentially Amenable to Optical Contrast Agent Labelling
Output: False
Paragraph: Worldwide community-acquired pneumonia (CAP) is one of the most frequent infectious diseases and a leading cause of death. Several studies have shown that a pathogen could be identified only in 50 to 60% of all patients, although in children < 6 month infectious agents can be detected in about 90%. Viral infections are most frequent in children < 2 years (80%), whereas bacterial infections increase with age. RSV, influenzaviruses, rhinoviruses, parainfluenzaviruses and adenoviruses are the most common viruses associated with CAP in children. Among adenoviruses a predominance of adenovirus 7 has been reported in several countries with emergence of highly pathogenic variants with significant lethality in young children. Many childhood respiratory infections are caused by more than one pathogen and up to 30% mixed viral / bacterial infections can be observed. CAP in immunocompetent adults is rare, whereas persons with underlaying diseases have an increased incidence of CAP. In the elderly, RSV, influenzaviruses, parainfluenzaviruses and less frequent adenoviruses are predominant viruses causing pneumonia. Less frequently associated with CAP are the newly discovered human metapneumovirus and the coronaviruses NL63 and HKU1. Hantaviruses, involved in the hantavirus pulmonary syndrome, belong to the emerging pathogens to date in North, Middle and South America. For optimum diagnosis the whole spectrum of potential respiratory viral agents should be included and multiple diagnostic techniques have to be used. In view of the high relevance of influenzavirus for CAP influenza vaccination is highly advisable for prevention of CAP, especially in high-risk groups. 
 Title: Community-Acquired Pneumonia Viral pathogens and epidemiology, detection, therapy and resistance
Output: True
Paragraph: A novel human coronavirus (HCoV-EMC) was recently identified in the Middle East as the causative agent of a severe acute respiratory syndrome (SARS) resembling the illness caused by SARS coronavirus (SARS-CoV). Although derived from the CoV family, the two viruses are genetically distinct and do not use the same receptor. Here, we investigated whether HCoV-EMC and SARS-CoV induce similar or distinct host responses after infection of a human lung epithelial cell line. HCoV-EMC was able to replicate as efficiently as SARS-CoV in Calu-3 cells and similarly induced minimal transcriptomic changes before 12 h postinfection. Later in infection, HCoV-EMC induced a massive dysregulation of the host transcriptome, to a much greater extent than SARS-CoV. Both viruses induced a similar activation of pattern recognition receptors and the interleukin 17 (IL-17) pathway, but HCoV-EMC specifically down-regulated the expression of several genes within the antigen presentation pathway, including both type I and II major histocompatibility complex (MHC) genes. This could have an important impact on the ability of the host to mount an adaptive host response. A unique set of 207 genes was dysregulated early and permanently throughout infection with HCoV-EMC, and was used in a computational screen to predict potential antiviral compounds, including kinase inhibitors and glucocorticoids. Overall, HCoV-EMC and SARS-CoV elicit distinct host gene expression responses, which might impact in vivo pathogenesis and could orient therapeutic strategies against that emergent virus. HCoV-EMC and SARS-CoV. We used this information to predict potential effective drugs against HCoV-EMC, a method that could be more generally used to identify candidate therapeutics in future disease outbreaks. These data will help to generate hypotheses and make rapid advancements in characterizing this new virus. RS, Katze MG. 2013 . Cell host response to infection with novel human coronavirus EMC predicts potential antivirals and important differences with SARS coronavirus. mBio 4(3):e00165-13. 
 Title: Cell Host Response to Infection with Novel Human Coronavirus EMC Predicts Potential Antivirals and Important Differences with SARS Coronavirus
Output: True
Paragraph: Human infections with a novel coronavirus (SARS-CoV-2) were first identified via syndromic surveillance in December of 2019 in Wuhan China. Since identification, infections (coronavirus disease-2019; COVID-19) caused by this novel pathogen have spread globally, with more than 250,000 confirmed cases as of March 21, 2020. An open-label clinical trial has just concluded, suggesting improved resolution of viremia with use of two existing therapies: hydroxychloroquine (HCQ) as monotherapy, and in combination with azithromycin (HCQ-AZ). [1, 2]. The results of this important trial have major implications for global policy in the rapid scale-up and response to this pandemic. The authors present results with p-values for differences in proportions between the study arms, but their analysis is not able to provide effect size estimates. To address this gap, more modern analytical methods including survival models, have been applied to these data, and show modest to no impact of HCQ treatment, with more significant effects from the HCQ-AZ combination, potentially suggesting a role for co-infections in COVID-19 pathogenesis. The trial of Gautret and colleagues, with consideration of the effect sizes, and p-values from multiple models, does not provide sufficient evidence to support wide-scale rollout of HCQ monotherapy for the treatment of COVID-19; larger randomzied studies should be considered. However, these data do suggest further study of HCQ-AZ combination therapy should be prioritized as rapidly as possible. 
 Title: QUANTIFYING TREATMENT EFFECTS OF HYDROXYCHLOROQUINE AND AZITHROMYCIN FOR COVID-19: A SECONDARY ANALYSIS OF AN OPEN LABEL NON-RANDOMIZED CLINICAL TRIAL A PREPRINT
Output: False
Paragraph: To the memory of Rossiter H. Crozier , an evolutionary biologist, who with his generosity and inquisitiveness inspired many students and scientists, in Australia and abroad. doi: bioRxiv preprint 2 Molecular phylogenetics plays a key role in comparative genomics and has an increasinglysignificant impacts on science, industry, government, public health, and society. We posit that the current phylogenetic protocol is missing two critical steps, and that their absence allows model misspecification and confirmation bias to unduly influence our phylogenetic estimates. Based on the potential offered by well-established but under-used procedures (e.g., assessment of phylogenetic assumptions and tests of goodness-of-fit), we introduce a new phylogenetic protocol that will reduce confirmation bias and increase the accuracy of phylogenetic estimates. doi: bioRxiv preprint CONFIRMATION BIAS IN PHYLOGENETICS Bayesian methods (77-82)), or using non-parametric phylogenetic methods (i.e., parsimony methods (66,68,70,71,(83)(84)(85)). In reality, many researchers analyze their data using a range of model-based phylogenetic methods, and reports that only use parsimony methods are increasingly rare. Depending on the chosen phylogenetic method, researchers may have to select a suitable model of sequence evolution (i.e., a model that combines the substitution model and the rates-across-sites model) to apply to the sub-MSA. This choice is often made by using model-selection methods (6,86-97). Having chosen a phylogenetic method and, in relevant cases, a suitable model of sequence evolution, the next step involves obtaining accurate estimates of the tree and evolutionary processes that led to the data. Phylogenetic methods are implemented in many programs (66-85) and, depending on the methods chosen, users often also obtain the nonparametric bootstrap probability (98) or clade credibility (99) to measure support for divergence events in the phylogeny. 
 Title: A new phylogenetic protocol: Dealing with model misspecification and confirmation bias in molecular phylogenetics
Output: False
Paragraph: Although the influenza vaccine is relatively safe and effective, serious complications can develop in rare cases. We encountered two cases of interstitial pneumonia that developed after vaccination during the 2014-2015 influenza season. Overall, nine cases, including the two presented here, have been recorded in PubMed and the Cochrane library; eight patients were treated with corticosteroids, and all nine survived, suggesting a good prognosis. Interstitial pneumonia is rare; however, we found an increase in its incidence after 2009. Therefore, clinicians must be aware of the possibility of this complication and duly educate all patients in advance. 
 Title: CASE REPORT Interstitial Pneumonia Associated with the Influenza Vaccine: A Report of Two Cases
Output: True
Paragraph: Small interfering RNAs (siRNAs) have become the most powerful and widely used gene silencing reagents for reverse functional genomics and molecular therapeutics. The key challenge for achieving effective gene silencing in particular for the purpose of the therapeutics is primarily dependent on the effectiveness and specificity of the RNAi targeting sequence. However, only a limited number of siRNAs is capable of inducing highly effective and sequence-specific gene silencing by RNA interference (RNAi) mechanism. In addition, the efficacy of siRNA-induced gene silencing can only be experimentally measured based on inhibition of the target gene expression. Therefore, it is important to establish a fully robust and comparative validating system for determining the efficacy of designed siRNAs. In this study, we have developed a reliable and quantitative reporter-based siRNA validation system that consists of a short synthetic DNA fragment containing an RNAi targeting sequence of interest and two expression vectors for targeting reporter and triggering siR-NA expression. The efficacy of the siRNAs is measured by their abilities to inhibit expression of the targeting reporter gene with easily quantified readouts including enhanced green fluorescence protein (EGFP) and firefly luciferase. Using fully analyzed siRNAs against human hepatitis B virus (HBV) surface antigen (HBsAg) and tumor suppressor protein p53, we have demonstrated that this system could effectively and faithfully report the efficacy of the corresponding siRNAs. In addition, we have further applied this system for screening and identification of the highly effective siRNAs that could specifically inhibit expression of mouse matrix metalloproteinase-7 (MMP-7), Epstein-Barr virus (EBV) latent membrane protein 1 (LMP1), and human serine/threonine kinase AKT1. Since only a readily available short synthetic DNA fragment is needed for constructing this novel reporter-based siRNA validation system, this system not only provides a powerful strategy for screening highly effective siRNAs but also implicates in the use of RNAi for studying novel gene function in mammals. 
 Title: A novel siRNA validation system for functional screening and identification of effective RNAi probes in mammalian cells
Output: True
Paragraph: Copy Number Variations (CNVs) of regions of the human genome have been associated with multiple diseases. We present an algorithm which is mathematically sound and computationally efficient to accurately analyze CNV in a DNA sample utilizing a nanofluidic device, known as the digital array. This numerical algorithm is utilized to compute copy number variation and the associated statistical confidence interval and is based on results from probability theory and statistics. We also provide formulas which can be used as close approximations. 
 Title: Mathematical Analysis of Copy Number Variation in a DNA Sample Using Digital PCR on a Nanofluidic Device
Output: False
Paragraph: MBP-tagged TRIM25 protein was expressed in E.coli Rosetta 2 (DE3) TM cells (Millipore). Transformed cells were grown in LB broth containing 0.2% glucose at 37 °C. Then, 0.2 mM IPTG was added and the cells were incubated under shaking conditions for 18 h at 25 °C, after which the cells were harvested by centrifugation. The pellet was resuspended in T1 buffer (20 mM Tris/Cl(pH 7.4), 1 mM EDTA, 1 mM sodium azide, and 1 mM DTT) and sonicated. After centrifugation, the supernatant was loaded onto a DEAE ion-exchange column (GE healthcare) and the flow throw was collected. Next, the pooled sample was applied to amylose resin (NEB). The column was washed with T2 buffer (T1 buffer + 200 mM NaCl) and eluted with T3 buffer (T2 buffer + 10 mM maltose). The purity of the proteins was analyzed by 10% SDS-PAGE. The final yield of MBP-TRIM25 was determined by the Bradford assay with BSA as the standard and the samples were stored at �80 °C. His-tagged RIG-I was expressed in E. coli BL21(DE3) cells. The transformed cells were grown in LB broth at 37 °C and then further incubated at 4 °C for 3 h. Subsequently, 0.25 mM IPTG was added and the cells were incubated under shaking conditions for 18 h at 25 °C, after which the cells were harvested by centrifugation. The pellet was resuspended in R1 buffer (50 mM HEPES; pH 7.4, 10% glycerol, 500 mM NaCl, 0.2% NP-40, 10 mM imidazole, 1 mM PMSF, 0.5 mg/ml lysozyme, and protease inhibitor cocktail) and sonicated. After centrifugation, the supernatant was applied to a Ni-NTA chelating agarose (Incospham). The column was washed with R2 buffer (50 mM HEPES; pH 7.4, 10% glycerol, 500 mM NaCl, 0.2% NP-40, and 50 mM imidazole) and the His-tagged RIG-I was eluted by increasing the imidazole concentration. The purest fractions were applied to a heparin-Sepharose column (GE healthcare), and the resin was washed with R3 buffer (50 mM Tris/Cl(pH 7.4), 10% glycerol, 0.2% NP-40, and 20 mM NaCl) and eluted with increasing concentrations of NaCl (up to 500 mM). The final yield of His-RIG-I was determined by the Bradford assay (Bio-Rad) with BSA as the standard. RNA Aptamers Specific to NS1 Protein of Influenza Virus Hye-Min Woo et al. 
 Title: Molecules and Cells Supplementary Materials
Output: False
Paragraph: Interferon-stimulated gene 15 (ISG15) is a member of the ubiquitin-like modifiers (ULM) family, which adopts a βgrasp fold domain(s) similar to ubiquitin (Ub) with only minor sequence homology. ISG15 consists of two Ub-like domains and aids the immune system in neutralizing infections by numerous pathogens and plays an important role in defending cells against many viruses including influenza A. Recently, Ub was found to be a substrate for ISG15, which can be ISGylated on Lys29 and Lys48, while the former is more dominant. The discovery of such hybrid ISG15-Ub chains brought forward various fundamental questions regarding the nature and effect of this conjugation. To further investigate the role of hybrid ISG15-Ub chains, the pure homogeneous material of these chains is needed in workable quantities. By applying advanced chemical strategies for protein synthesis, we report the total chemical synthesis of a 231-residue ISG15-Lys29-Ub hybrid chain. During the synthesis we encountered insoluble peptide fragments, and therefore we developed a new reversible Acm based solubilizing tag to efficiently tackle this hurdle. This new Acm tag was compared with the known Arg based Acm solubilizing tag and was found to be more reliable in terms of incorporation and efficiency as demonstrated in the synthesis of the native ISG15-Ub hybrid chain. 
 Title: Total Chemical Synthesis of ISGylated-Ubiquitin Hybrid Chain Assisted by Acetamidomethyl Derivatives with Dual Functions
Output: True