niryuu/sni-each-converted huggingface dataset:
Paragraph: Background: The role of disulfide bond remodeling in HIV-1 infection is well described, but the process still remains incompletely characterized. At present, the data have been predominantly obtained using established cell lines and/or CXCR4-tropic laboratory-adapted virus strains. There is also ambiguity about which disulfide isomerases/ reductases play a major role in HIV-1 entry, as protein disulfide isomerase (PDI) and/or thioredoxin (Trx) have emerged as the two enzymes most often implicated in this process. We have extended our previous findings and those of others by focusing on CCR5-using HIV-1 strains and their natural targets -primary human macrophages and CD4 + T lymphocytes. We found that the nonspecific thiol/ disulfide exchange inhibitor, 5,5'-dithiobis(2-nitrobenzoic acid) (DTNB), significantly reduced HIV-1 entry and infection in cell lines, human monocyte-derived macrophages (MDM), and also phytohemagglutinin (PHA)stimulated peripheral blood mononuclear cells (PBMC). Subsequent studies were performed using specific anti-PDI or Trx monoclonal antibodies (mAb) in HIV-1 envelope pseudotyped and wild type (wt) virus infection systems. Although human donor-to-donor variability was observed as expected, Trx appeared to play a greater role than PDI in HIV-1 infection of MDM. In contrast, PDI, but not Trx, was predominantly involved in HIV-1 entry and infection of the CD4 + /CCR5 + T cell line, PM-1, and PHA-stimulated primary human T lymphocytes. Intriguingly, both PDI and Trx were present on the surface of MDM, PM-1 and PHA-stimulated CD4 + T cells. However, considerably lower levels of Trx were detected on freshly isolated CD4 + lymphocytes, compared to PHA-stimulated cells. Conclusions: Our findings clearly demonstrate the role of thiol/disulfide exchange in HIV-1 entry in primary T lymphocytes and MDM. They also establish a cell-type specificity regarding the involvement of particular disulfide isomerases/reductases in this process and may provide an explanation for differences among previously published studies. More importantly, from an in vivo perspective, the preferential utilization of PDI may be relevant to the HIV-1 entry and establishment of virus reservoirs in resting CD4 + cells, while the elevated levels of Trx reported in the chronic stages of HIV-1 infection may facilitate the virus entry in macrophages and help to sustain high viremia during the decline of T lymphocytes. 
 Title: Cell-type specific requirements for thiol/disulfide exchange during HIV-1 entry and infection
Output: True
Paragraph: Context: Over the past decade, a number of high-impact natural hazard events, together with the increased recognition of pandemic risks, have intensified interest in health systems' ability to prepare for, and cope with, "surges" (sudden large-scale escalations) in treatment needs. In this article, we identify key concepts and components associated with this emerging research theme. We consider the requirements for a standardized conceptual framework for future research capable of informing policy to reduce the morbidity and mortality impacts of such incidents. Here our objective is to appraise the consistency and utility of existing conceptualizations of health systems' surge capacity and their components, with a view to standardizing concepts and measurements to enable future research to generate a cumulative knowledge base for policy and practice. A systematic review of the literature on concepts of health systems' surge capacity, with a narrative summary of key concepts relevant to public health. The academic literature on surge capacity demonstrates considerable variation in its conceptualization, terms, definitions, and applications. This, together with an absence of detailed and comparable data, has hampered efforts to develop standardized conceptual models, measurements, and metrics. Some degree of consensus is evident for the components of surge capacity, but more work is needed to integrate them. The overwhelming concentration in the United States complicates the generalizability of existing approaches and findings. The concept of surge capacity is a useful addition to the study of health systems' disaster and/or pandemic planning, mitigation, and response, 
 Title: Health Systems' "Surge Capacity": State of the Art and Priorities for Future Research
Output: True
Paragraph: Viruses are a significant cause of morbidity and mortality around the world. Determining the minimum dose of virus particles that can initiate infection, termed the minimum infective dose (MID), is important for the development of risk assessment models in the fields of food and water treatment and the implementation of appropriate infection control strategies in healthcare settings. Both respiratory and enteric viruses can be shed at high titers from infected individuals even when the infection is asymptomatic. Presence of pre-existing antibodies has been shown to affect the infectious dose and to be protective against reinfection for many, but not all viruses. Most respiratory viruses appear to be as infective in humans as in tissue culture. Doses of \1 TCID 50 of influenza virus, rhinovirus, and adenovirus were reported to infect 50% of the tested population. Similarly, low doses of the enteric viruses, norovirus, rotavirus, echovirus, poliovirus, and hepatitis A virus, caused infection in at least some of the volunteers tested. A number of factors may influence viruses' infectivity in experimentally infected human volunteers. These include host and pathogen factors as well as the experimental methodology. As a result, the reported infective doses of human viruses have to be interpreted with caution. 
 Title: Minimum Infective Dose of the Major Human Respiratory and Enteric Viruses Transmitted Through Food and the Environment
Output: True
Paragraph: The cellular responses to infection are many, and include programmed cell death to inhibit microbial dissemination and the production and secretion of interferons (IFNs), which confer resistance to uninfected cells. In addition to the antimicrobial effects of IFNs, these cytokines have been used clinically for the treatment of various neoplasias to inhibit proliferation and stimulate apoptosis. However, the precise mechanisms of action of IFNs remain to be completely understood. One of the primary response genes induced after an infection or treatment with type I or III IFN is known as IFN-stimulated gene 54 (ISG54) or IFN-induced gene with tetratricopeptide repeats 2 (IFIT2). ISG54/IFIT2 is a member of a family of IFN-induced genes related in the sequence and structure. Expression of this protein has been found to promote cellular apoptosis by a mitochondrial pathway dependent on the action of Bcl2 proteins. ISG54/IFIT2 does not function as a monomer, and it forms complexes with itself and with the related ISG56/IFIT1 and ISG60/IFIT3 proteins to elicit complex cellular responses. The apoptotic response to ISG54/IFIT2 may contribute to other functions that have been reported, including translational regulation, inhibition of tumor colonization, and protection against a lethal viral infection. 
 Title: A Death-Promoting Role for ISG54/IFIT2
Output: True
Paragraph: 29 Background: Our understanding of the corona virus disease 2019 (COVID-19) continues to 30 evolve. However, there are many unknowns about its epidemiology. 31 Purpose: To synthesize the number of deaths from confirmed COVID-19 cases, incubation 32 period, as well as time from onset of COVID-19 symptoms to first medical visit, ICU admission, 33 recovery and death of COVID-19. Data Synthesis: Out of 1675 non-duplicate studies identified, 57 were included. Pooled mean 41 incubation period was 5.84 (99% CI: 4.83, 6.85) days. Pooled mean number of days from the 42 onset of COVID-19 symptoms to first clinical visit was 4.82 (95% CI: 3.48, 6.15), ICU admission 43 was 10.48 (95% CI: 9.80, 11.16), recovery was 17.76 (95% CI: 12.64, 22.87), and until death 44 was 15.93 (95% CI: 13.07, 18.79). Pooled probability of COVID-19-related death was 0.02 (95% 45 CI: 0.02, 0.03). 46 Limitations: Studies are observational and findings are mainly based on studies that recruited 47 patient from clinics and hospitals and so may be biased toward more severe cases. 48 We found that the incubation period and lag between the onset of symptoms and diagnosis 50 of COVID-19 is longer than other respiratory viral infections including MERS and SARS; 51 . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not peer-reviewed) The copyright holder for this preprint . 
 Title: Epidemiological Characteristics of COVID-19; a Systemic Review and Meta-Analysis 1
Output: True
Paragraph: Background: Outbreaks of avian influenza (AI) caused by infection with low pathogenic H9N2 viruses have occurred in poultry, resulting in serious economic losses in Asia and the Middle East. It has been difficult to eradicate the H9N2 virus because of its low pathogenicity, frequently causing in apparent infection. It is important for the control of AI to assess whether the H9N2 virus acquires pathogenicity as H5 and H7 viruses. In the present study, we investigated whether a non-pathogenic H9N2 virus, A/chicken/Yokohama/aq-55/2001 (Y55) (H9N2), acquires pathogenicity in chickens when a pair of di-basic amino acid residues is introduced at the cleavage site of its HA molecule. 
 Title: H9N2 influenza virus acquires intravenous pathogenicity on the introduction of a pair of di-basic amino acid residues at the cleavage site of the hemagglutinin and consecutive passages in chickens
Output: False
Paragraph: Frenz et al. have developed a new method for refinement of glycoprotein structures against low-resolution cryoEM and X-ray crystallography data. This new method is able to make significantly larger changes to the glycan geometry compared with previous methods, including the ability to changing the glycan's anomer. 
 Title: Automatically Fixing Errors in Glycoprotein Structures with Rosetta Graphical Abstract Highlights d New method for refinement of carbohydrates with low- resolution electron density d Improved physical geometry of glycans in protein structures d Compatible with cryoEM and X-ray crystallography data Automatically Fixing Errors in Glycoprotein Structures with Rosetta
Output: False
Paragraph: Background: Influenza A H5N1 has killed millions of birds and raises serious public health concern because of its potential to spread to humans and cause a global pandemic. While the early focus was in Asia, recent evidence suggests that Egypt is a new epicenter for the disease. This includes characterization of a variant clade 2.2.1.1, which has been found almost exclusively in Egypt. We analyzed 226 HA and 92 NA sequences with an emphasis on the H5N1 2.2.1.1 strains in Egypt using a Bayesian discrete phylogeography approach. This allowed modeling of virus dispersion between Egyptian governorates including the most likely origin. Results: Phylogeography models of hemagglutinin (HA) and neuraminidase (NA) suggest Ash Sharqiyah as the origin of virus spread, however the support is weak based on Kullback-Leibler values of 0.09 for HA and 0.01 for NA. Association Index (AI) values and Parsimony Scores (PS) were significant (p-value < 0.05), indicating that dispersion of H5N1 in Egypt was geographically structured. In addition, the Ash Sharqiyah to Al Gharbiyah and Al Fayyum to Al Qalyubiyah routes had the strongest statistical support. Conclusion: We found that the majority of routes with strong statistical support were in the heavily populated Delta region. In particular, the Al Qalyubiyah governorate appears to represent a popular location for virus transition as it represented a large portion of branches in both trees. However, there remains uncertainty about virus dispersion to and from this location and thus more research needs to be conducted in order to examine this. Phylogeography can highlight the drivers of H5N1 emergence and spread. This knowledge can be used to target public health efforts to reduce morbidity and mortality. For Egypt, future work should focus on using data about vaccination and live bird markets in phylogeography models to study their impact on H5N1 diffusion within the country. 
 Title: Phylogeography of influenza A H5N1 clade 2.2.1.1 in Egypt
Output: True
Paragraph: Background: The importance of aerosols in the spread of viruses like influenza is still a subject of debate. Indeed, most viruses can also be transmitted through direct contact and droplets. Therefore, the importance of the airborne route in a clinical context is difficult to determine. The aim of this study was to design a chamber system to study the airborne transmission of viruses between ferrets. Methods: A system composed of three chambers connected in series, each one housing one ferret and preventing direct contact, was designed. The chambers were designed to house the ferrets for several days and to study the transmission of viruses from an infected (index) ferret to two naïve ferrets via aerosols and droplets or aerosols only. A particle separator was designed that can be used to modulate the size of the particles traveling between the chambers. The chamber system was validated using standard dust as well as with ferrets infected with influenza A virus. Conclusions: The 50% efficiency cut-off of the separator could be modulated between a 5-µm and an 8-µm aerodynamic diameter. In the described setup, influenza A virus was transmitted through the aerosol route in two out of three experiments, and through aerosols and droplets in all three experiments. 
 Title: Design and Validation with Influenza A Virus of an Aerosol Transmission Chamber for Ferrets
Output: True
Paragraph: The development and use of topical microbicides potentially offers an additional strategy to reduce the spread of the Human Immunodeficiency Virus (HIV). Carbohydrate-binding agents (CBAs) that show specificity for high mannose carbohydrates on the surface of the heavily glycosylated envelope of HIV are endowed with potent anti-HIV activity. In fact, a number of algal lectins such as cyanovirin-N, microvirin, microcystis viridis lectin, scytovirin, Oscillatoria agardhii agglutinin and griffithsin are considered as potential microbicide candidates to prevent the sexual transmission of HIV through topical applications. They not only inhibit infection of cells by cell-free virus but they can also efficiently prevent virus transmission from virus-infected cells to uninfected CD4 + target T-lymphocytes and DC-SIGN-directed capture of HIV-1 and transmission to CD4 + T lymphocytes. This review focuses on the structural properties and carbohydrate specificity of these algal lectins, their antiviral activity against HIV and several other enveloped viruses, their safety profile and viral resistance patterns. 
 Title: Algal Lectins as Potential HIV Microbicide Candidates
Output: False
Paragraph: There is increasing evidence that viral infection, expression of viral protein or the presence of viral DNA causes the host cell cycle to arrest during G2/M. The mechanisms used by viruses to cause arrest vary widely; some involve the activation of the cellular pathways that induce arrest in response to DNA damage, while others use completely novel means. The analysis of virus-mediated arrest has not been proven easy, and in most cases the consequences of arrest for the virus life cycle are not well defined. However, a number of effects of arrest are being investigated and it will be interesting to see to what extent perturbation of the G2/M transition is involved in viral infections. Crown 
 Title: G2/M cell cycle arrest in the life cycle of viruses
Output: True
Paragraph: RNA degradation by RNase L during 2-5A-mediated decay (2-5AMD) is a conserved mammalian stress response to viral and endogenous double-stranded RNA (dsRNA). 2-5AMD onsets rapidly and facilitates a switch of protein synthesis from homeostasis to production of interferons (IFNs). To understand the mechanism of this protein synthesis reprogramming, we examined 2-5AMD in human cells. 2-5AMD triggers polysome collapse characteristic of a translation initiation defect, but translation initiation complexes and ribosomes purified from the translation-arrested cells remain functional. Using spike-in RNA-seq we found that basal messenger RNAs (mRNAs) rapidly decay, while mRNAs encoding IFNs and IFN-stimulated genes evade 2-5AMD and accumulate. The IFN evasion results from the combined effect of better mRNA stability and positive feedback amplification in the IFN response. Therefore, 2-5AMD and transcription act in concert to revamp the cellular mRNA composition. The resulting preferential accumulation of innate immune mRNAs establishes "prioritized" synthesis of defense proteins. 
 Title: Concerted 2-5A-Mediated mRNA Decay and Transcription Reprogram Protein Synthesis in dsRNA Response
Output: True
Paragraph: China is facing the serious situation of 2019-novel coronavirus (2019-nCoV) infection. The health care institutions have actively participated in the prevention, diagnosis, and treatment of the disease. Proper regulation of inhospital policy may help control virus spreading. We developed seven key clinical questions about the prevention and control of 2019-novel coronavirus infection in a hospital, and provided recommendations based on the best available evidence and expert experience. We interpret the recommendations for better feasibility in Chinese hospital. We hope to provide evidence and reference for the domestic medical institutions to reasonably adjust the hospital workflow during 2019-nCoV infection period. 
 Title: Precison Clinical Medicine Supplementary Material Disease control of 2019-novel coronavirus infection in hospital: West China urgent recommendation
Output: False
Paragraph: SARS-CoV-2 emerged by the end of 2019 to rapidly spread in 2020. At present, it is of utmost 31 importance to understand the virus biology and to rapidly assess the potential of existing drugs 32 and develop new active compounds. While some animal models for such studies are under 33 development, most of the research is carried out in the Vero E6 cells. Here, we propose fully 34 differentiated human airway epithelium cultures as a model for studies on the SARS-CoV-2. 35 Further, we also provide basic characteristics of the system. 36 37 
 Title: Replication of SARS-CoV-2 in human respiratory Aleksandra Milewska a
Output: True
Paragraph: Background: Emerging and understudied pathogens often lack information that most commonly used analytical tools require, such as negative controls or baseline data; thus, new analytical strategies are needed to analyze transmission patterns and drivers of disease emergence. Zoonotic infections with Vaccinia virus (VACV) were first reported in Brazil in 1999, VACV is an emerging zoonotic Orthopoxvirus, which primarily infects dairy cattle and farmers in close contact with infected cows. Prospective studies of emerging pathogens could provide critical data that would inform public health planning and response to outbreaks. By using the location of 87-recorded outbreaks and publicly available bioclimatic data, we demonstrate one such approach. Using an ecological niche model (ENM) algorithm, we identify the environmental conditions under which VACV outbreaks have occurred, and determine additional locations in two affected countries that may be susceptible to transmission. Further, we show how suitability for the virus responds to different levels of various environmental factors and highlight the most important factors in determining its transmission. Methods: A literature review was performed and the geospatial coordinates of 87 molecularly confirmed VACV outbreaks in Brazil were identified. An ENM was generated using MaxENT software by combining principal component analysis results of 19 bioclim spatial layers, and 25 randomly selected subsets of the original list of 87 outbreaks. The final ENM predicted all areas where Brazilian outbreaks occurred, one out of five of the Colombian outbreak regions and identified new regions within Brazil that are suitable for transmission based on bioclimatic factors. Further, the most important factors in determining transmission suitability are precipitation of the wettest quarter, annual precipitation, mean temperature of the coldest quarter and mean diurnal range. The analyses here provide a means by which to study patterns of an emerging infectious disease and identify regions that are potentially suitable for its transmission, in spite of the paucity of high-quality critical data. Policy and methods for the control of infectious diseases often use a reactionary model, addressing diseases only after significant impact on human health has ensued. The methodology used in the present work allows the identification of areas where disease is likely to appear, which could be used for directed intervention. 
 Title: Ecological niche modeling to determine potential niche of Vaccinia virus: a case only study
Output: False
Paragraph: Objectives: We compared the expelled air dispersion distances during coughing from a human patient simulator (HPS) lying at 45u with and without wearing a surgical mask or N95 mask in a negative pressure isolation room. Methods: Airflow was marked with intrapulmonary smoke. Coughing bouts were generated by short bursts of oxygen flow at 650, 320, and 220L/min to simulate normal, mild and poor coughing efforts, respectively. The coughing jet was revealed by laser light-sheet and images were captured by high definition video. Smoke concentration in the plume was estimated from the light scattered by smoke particles. Significant exposure was arbitrarily defined where there was $ 20% of normalized smoke concentration. Results: During normal cough, expelled air dispersion distances were 68, 30 and 15 cm along the median sagittal plane when the HPS wore no mask, a surgical mask and a N95 mask, respectively. In moderate lung injury, the corresponding air dispersion distances for mild coughing efforts were reduced to 55, 27 and 14 cm, respectively, p , 0.001. The distances were reduced to 30, 24 and 12 cm, respectively during poor coughing effort as in severe lung injury. Lateral dispersion distances during normal cough were 0, 28 and 15 cm when the HPS wore no mask, a surgical mask and a N95 mask, respectively. Conclusions: Normal cough produced a turbulent jet about 0.7 m towards the end of the bed from the recumbent subject. N95 mask was more effective than surgical mask in preventing expelled air leakage during coughing but there was still significant sideway leakage. 
 Title: Exhaled Air Dispersion during Coughing with and without Wearing a Surgical or N95 Mask
Output: True
Paragraph: Middle East respiratory syndrome coronavirus (MERS-CoV) has caused fatal infections, some through hospital-acquired transmission, in affected regions since its emergence in 2012. Although the virus is not pandemic among humans, it poses a great threat to public health due to its zoonotic origin. Thus, both preventative and therapeutic countermeasures are urgently needed. In this study, we discovered a panel of neutralizing monoclonal antibodies (mAbs) against MERS-CoV, which mapped to a wide range of regions on the spike (S) protein of the virus. In addition to mAbs with neutralizing epitopes located on the receptor-binding domain, one mAb, 5F9, which binds to the N-terminal domain (NTD) of the MERS-CoV S1 subunit, showed efficient neutralizing activity against the wild-type MERS-CoV strain EMC/2012, with a half maximal inhibitory concentration of 0.2 μg/mL. We concluded that a novel neutralizing epitope for MERS-CoV also resides on the NTD of the S protein, indicating that the NTD might be important during the viral infection process. Our findings have significant implications for further vaccine design and for the development of prophylactic and therapeutic monoclonal immunotherapies against MERS-CoV infection. 
 Title: Emerging Microbes & Infections (2017) 6, e37
Output: False
Paragraph: Chronic obstructive pulmonary disease (COPD) exacerbations are an important cause of the considerable morbidity and mortality found in COPD. COPD exacerbations increase with increasing severity of COPD, and some patients are prone to frequent exacerbations leading to hospital admission and readmission. These frequent exacerbations may have considerable impact on quality of life and activities of daily living. Factors that increase the risk for COPD exacerbations are associated with increased airway inflammation caused by common pollutants and bacterial and/or viral infections. These inflammatory responses cause mucus hypersecretion and, thereby, airway obstruction and associated exacerbations. While chronic mucus hypersecretion is a significant risk factor for frequent and severe exacerbations, patients with chronic mucus hypersecretion have a lower rate of relapse after initial treatment for acute exacerbation. The benefit of antibiotics for treatment of COPD exacerbations is small but significant. While the mechanisms of actions are not clear, mucolytic agents reduce the number of days of disability in subjects with exacerbations. Reducing mucous cell numbers in small airways could be a useful way to reduce chronic mucus hypersecretion. Our studies suggest that programmed cell death is crucial in the resolution of metaplastic mucous cells, and understanding these mechanisms may provide novel therapies to reduce the risk of COPD exacerbations. 
 Title: Exacerbations of chronic obstructive pulmonary disease and chronic mucus hypersecretion
Output: False
Paragraph: Typically not assisted by proofreading, the RNAdependent RNA polymerases (RdRPs) encoded by the RNA viruses may need to independently control its fidelity to fulfill virus viability and fitness. However, the precise mechanism by which the RdRP maintains its optimal fidelity level remains largely elusive. By solving 2.1-2.5Å resolution crystal structures of the classical swine fever virus (CSFV) NS5B, an RdRP with a unique naturally fused N-terminal domain (NTD), we identified high-resolution intramolecular interactions between the NTD and the RdRP palm domain. In order to dissect possible regulatory functions of NTD, we designed mutations at residues Y471 and E472 to perturb key interactions at the NTD-RdRP interface. When crystallized, some of these NS5B interface mutants maintained the interface, while the others adopted an 'open' conformation that no longer retained the intra-molecular interactions. Data from multiple in vitro RdRP assays indicated that the perturbation of the NTD-RdRP interactions clearly reduced the fidelity level of the RNA synthesis, while the processivity of the NS5B elongation complex was not affected. Collectively, our work demonstrates an explicit and unique mode of polymerase fidelity modulation and provides a vivid example of co-evolution in multi-domain enzymes. 
 Title: A unique intra-molecular fidelity-modulating mechanism identified in a viral RNA-dependent RNA polymerase
Output: True
Paragraph: Van Zaane, D., IJzerman, 3. and De Leeuw, P.W., 1986. Intestinal antibody response after vaccination and infection with rotavirus of calves fed colostrum with or without rotavirus antibody. Vet. Immunol. Immunopathol., 11:45-63. The intestinal and systemic antibody response of cah'es vaccinated and/or challenged with rotavirus was studied employing isotype-specific ELISAs for the detection of IgG1, IgG2, IgM and IgA antibodies to rotavirus. Monoclonal antibodies to bovine immunoglobulin isotypes of proven specificity were used as conjugated or catching antibody. Five days after oral inoculation (dpi) of a 5-day-old gnotobiotic calf with rotavirus, IgM rotavirus antibodies were excreted in faeces, followed 5 days later by IgA rotavirus antibodies. The increase in IgM rotavirus antibody titre coincided with the inability to detect further rotavirus excretion. Faeces IgM and IgA rotavirus antibody titres fell to low levels within 3 weeks post infection. IgG 1 and IgG 2 rotavirus antibodies were not detected in faecal samples. In serum, antibodies to rotavirus of all four isotypes were detected, starting with IgM at 5 dpi. Two SPF-calves, which were fed colostrum free of rotavirus antibodies, were vaccinated with a modified live rotavirus vaccine and challenged with virulent rotavirus 6 days later. Upon vaccination, the cah'es showed an antibody response similar to the response of the infected gnotobiotic calf. Intestinal IgM rotavirus antibodies were excreted before or on the day of challenge and appeared to be associated with protection against challenge infection with virulent virus and rotavirus-induced diarrhoea. In 3 control calves, which were challenged only, the antibody patterns also resembled that of the gnotobiotic calf and again the appearance of IgM rotavirus antibodies coincided with the end of the rotavirus detection period. Two other groups of :3 SPF-calves were treated similarly, but the calves were fed co]ostrum with rotavirus antibodies during the first 48 h of life. These calves excreted passively acquired IgG 1 and IgG 2 rotavirus antibodies in their faeces from 2 to 6 days after birth. After vaccination, no IgM or IgA antibody activity in serum or faeces was detectable. Upon challenge, all calves developed diarrhoea and excreted rotavirus. Seven to 10 days after challenge low levels of IgM rotavirus antibody were detected for a short period. These data indicate that the intestinal antibody response of young calves to an enteric viral infection is associated with the excretion of IgM antibodies, immediately followed by IgA antibodies. This response is absent or diminished in ealves with passively acquired specific antibodies which may explain the failure to induce a protective intestinal immune response by oral vaccination with modified live rotavirus of calves fed co]ostrum containing rotavirus antibodies. 
 Title: INTESTINAL ANTIBODY RESPONSE AFTER VACCINATION AND INFECTION WITH ROTAVIRUS OF CALVES FED COLOSTRUM WITH OR WITHOUT ROTAVIRUS ANTIBODY
Output: False
Paragraph: It is reported that bacterial colonization of the airway in neonates affects the likelihood and severity of subsequent wheezing in childhood. This study aimed to explore the impact of bacterial colonization on the severity of virus-induced wheezing, and accompanying airway inflammation. Nasopharyngeal aspirates (NPAs) from 68 hospitalized children with bronchiolitis and 85 children with recurrent wheezing were obtained. Eleven common respiratory viruses were sought by PCR and/or direct fluorescence assay. Bacteria were isolated from NPAs by routine culture methods. Cell numbers and concentrations of cytokines/chemokines in the NPAs were measured, and nucleated cells were characterized. The frequency of bacterial colonization in children with recurrent wheezing was significantly higher than in children with an initial attack of bronchiolitis. Bacterial colonization accompanying virus infection had no effect on clinical manifestations, duration of hospitalization, concentrations of cytokines/chemokines (except interleukin-10 (IL-10)) or cellularity in the children with bronchiolitis; however, among the children with recurrent wheezing, those who had coexistent non-invasive bacterial colonization and virus infection presented more frequent cyanosis, longer duration of hospitalization, a higher concentration of IL-10 and a higher percentage of neutrophils in NPAs than those with virus infection but without bacterial colonization. Bacterial colonization was common in children with virus-induced wheezing, particularly in the situation of recurrent wheezing. To some extent, bacterial colonization accompanying virus infection may contribute to the severity of the wheezing because of its impact on airway inflammation. 
 Title: Impact of bacterial colonization on the severity, and accompanying airway inflammation, of virus-induced wheezing in children
Output: True
Paragraph: We review behavioural change models (BCMs) for infectious disease transmission in humans. Following the Cochrane collaboration guidelines and the PRISMA statement, our systematic search and selection yielded 178 papers covering the period 2010-2015. We observe an increasing trend in published BCMs, frequently coupled to (re)emergence events, and propose a categorization by distinguishing how information translates into preventive actions. Behaviour is usually captured by introducing information as a dynamic parameter (76/178) or by introducing an economic objective function, either with (26/178) or without (37/178) imitation. Approaches using information thresholds (29/178) and exogenous behaviour formation (16/178) are also popular. We further classify according to disease, prevention measure, transmission model (with 81/178 population, 6/178 metapopulation and 91/178 individuallevel models) and the way prevention impacts transmission. We highlight the minority (15%) of studies that use any real-life data for parametrization or validation and note that BCMs increasingly use social media data and generally incorporate multiple sources of information (16/178), multiple types of information (17/178) or both (9/178). We conclude that individual-level models are increasingly used and useful to model behaviour changes. Despite recent advancements, we remain concerned that most models are purely theoretical and lack representative data and a validation process. 
 Title: Behavioural change models for infectious disease transmission: a systematic review (2010-2015)
Output: False
Paragraph: This paper describes the isolation of porcine epidemic diarrhea (PED) virus in Vero and porcine cell cultures, and the in¯uence of age on disease in experimental infection. PED virus was isolated from the small intestine of piglets inoculated with PED samples and cultured in Vero, porcine bladder and kidney cells propagated in collagen-coated tissue culture plates in maintenance medium (MM) containing trypsin. In porcine bladder and kidney cell cultures inoculated with isolated PED virus, cytopathic effects (CPE) including cell fusion were detected. Speci®c brilliant¯uorescence was observed in the cytoplasm of these cells. Two-and 7-day old, and 2-, 4-, 8-and 12-week old speci®c pathogen-free (SPF) pigs were orally inoculated with PED virus isolated from an outbreak. All 2-and 7-day old pigs inoculated developed severe watery diarrhea from post-inoculation day (PID) 1 and died between PID 3 and 4. Although three of ®ve 2-week old pigs developed diarrhea on PID 1±4, they eventually recovered. In the 4-week old group, three of ®ve pigs had mild diarrhea for 1±2 days. None of the 8-and 12-week old pigs showed any clinical signs. Antibodies against PED virus were detected in all surviving pigs by virus neutralization (VN) test and immuno¯uorescence assay (IFA). Therefore, there is an age-dependent resistance to pathogenic PED virus infection in pigs. # 
 Title: Isolation of porcine epidemic diarrhea virus in porcine cell cultures and experimental infection of pigs of different ages
Output: False
Paragraph: Pneumoviruses have been identified as causative agents in several respiratory disease outbreaks in habituated wild great apes. Based on phylogenetic evidence, transmission from humans is likely. However, the pathogens have never been detected in the local human population prior to or at the same time as an outbreak. Here, we report the first simultaneous detection of a human respiratory syncytial virus (HRSV) infection in western lowland gorillas (Gorilla gorilla gorilla) and in the local human population at a field program in the Central African Republic. A total of 15 gorilla and 15 human fecal samples and 80 human throat swabs were tested for HRSV, human metapneumovirus, and other respiratory viruses. We were able to obtain identical sequences for HRSV A from four gorillas and four humans. In contrast, we did not detect HRSV or any other classic human respiratory virus in gorilla fecal samples in two other outbreaks in the same field program. Enterovirus sequences were detected but the implication of these viruses in the etiology of these outbreaks remains speculative. Our findings of HRSV in wild but human-habituated gorillas underline, once again, the risk of interspecies transmission from humans to endangered great apes. 
 Title: Codetection of Respiratory Syncytial Virus in Habituated Wild Western Lowland Gorillas and Humans During a Respiratory Disease Outbreak
Output: True
Paragraph: Background: SARS-CoV entry into target cells is a unique and complex process. Results: Cell entry mediated by SARS-CoV S was strongly inhibited after knockdown of PI4KB. Conclusion: PI4KB is required for SARS-CoV S-mediated entry, and this function is dependent on its kinase activity. Significance: Our results indicate a new function for PI4KB and suggest a new drug target for preventing SARS-CoV infection. Further research suggested that PI4P plays an essential role in SARS-CoV spike-mediated entry, which is regulated by the PI4P lipid microenvironment. We further demonstrate that PI4KB does not affect virus entry at the SARS-CoV S-ACE2 binding interface or at the stage of virus internalization but rather at or before virus fusion. Taken together, these results indicate a new function for PI4KB and suggest a new drug target for preventing SARS-CoV infection. 
 Title: Phosphatidylinositol 4-Kinase III␤ Is Required for Severe Acute Respiratory Syndrome Coronavirus Spike-mediated Cell Entry *
Output: False
Paragraph: FIGURE 26.8 Impaction in an ostrich. The proventriculus and ventriculus are markedly distended and filled with coarse roughage-unopened (A) and opened (B). (Photos Courtesy of M. Brash, Animal Health Laboratory [AHL], University of Guelph) FIGURE 26.9 Shell abnormalities in ostrich eggs. Malformed, wrinkled egg shells. The causes of this nonspecific change are poorly understood but are postulated to include viral infection, particularly with adenovirus and Newcastle disease virus, bacterial salpingitis, nutritional deficiencies or imbalances, and other abnormalities of the oviduct. 
 Title: Palaeognathae: Apterygiformes, Casuariiformes, Rheiformes, Struthioniformes; Tinamiformes
Output: True
Paragraph: ELISAs provide a valuable tool in the detection and diagnosis of virus infection. The ability to produce recombinant viral proteins will ensure that future ELISAs are safe, specific and rapid. This latter point being the most crucial advantage in that even if a virus cannot be cultured, provided gene sequence is available, it is possible to rapidly respond to emerging viruses and new viral strains of existing pathogens. Indeed, ELISAs based on peptides (corresponding to epitopes) also hold great promise, as in this case no cloning or expression of a recombinant protein is required. Both recombinant protein and peptide based systems lend themselves to large scale production and purification. These approaches can also be used to distinguish recombinant vaccines from parental or wild type viruses. 
 Title: Recombinant viral proteins for use in diagnostic ELISAs to detect virus infection
Output: True
Paragraph: Infl uenza viruses cause respiratory tract infections that in patients with underlying lung diseases such as chronic obstructive pulmonary disease (COPD) are associated with exacerbations and excess morbidity and mortality. Typically, infl uenza B is associated with relatively mild, local outbreaks, whereas infl uenza A is the cause of world-wide pandemics. Upon infection, two antigens present on the viral surface, hemagglutinin and neuraminidase result in human immunity, but since many subtypes of these antigens exist that vary over time, immunity in the population is blunted. Vaccination is advocated in high-risk groups including patients with underlying (lung) diseases and in the elderly, and needs to be repeated annually with vaccines expected to cover the expected change in viral antigenicity. When started early, antiviral drugs, especially neuraminidase-inhibitors can be prescribed in adjunct to nonspecifi c interventions in an attempt to shorten disease duration and to prevent complications in case of an infl uenza infection. Currently, the effectiveness of antiviral drugs specifi cally in patients with COPD has not been proven. 
 Title: Occasional review: Infl uenza in COPD: pathogenesis, prevention, and treatment
Output: True
Paragraph: Identifying recombinant sequences in an era of large genomic databases is challenging as it requires an efficient algorithm to identify candidate recombinants and parents, as well as appropriate statistical methods to correct for the large number of comparisons performed. In 2007, a computation was introduced for an exact nonparametric mosaicism statistic that gave high-precision P values for putative recombinants. This exact computation meant that multiplecomparisons corrected P values also had high precision, which is crucial when performing millions or billions of tests in large databases. Here, we introduce an improvement to the algorithmic complexity of this computation from O(mn 3 ) to O(mn 2 ), where m and n are the numbers of recombination-informative sites in the candidate recombinant. This new computation allows for recombination analysis to be performed in alignments with thousands of polymorphic sites. Benchmark runs are presented on viral genome sequence alignments, new features are introduced, and applications outside recombination analysis are discussed. 
 Title: Improved Algorithmic Complexity for the 3SEQ Recombination Detection Algorithm
Output: False
Paragraph: Background: This scoping review maps population-based surveys and mental health literacy (MHL) interventions undertaken in China during 1997-2018 in order to identify research gaps. Method: Following Arksey and O'Malley's framework for a scoping review, five English databases (Medline, PsycINFO, Cochrane library, Web of Science and CINAHL) and two Chinese ones (CNKI and WanFang) were systematically searched, identifying both reports of surveys and evaluation of interventions from Jan 1997 to Oct 2018. Results: MHL research has developed rapidly in China in terms of numbers of studies and geographic coverage over the past two decades. There were 350 peer-reviewed publications included in this review, covering diverse settings and participants. Of these publications, 313 (89.4%) were published in Chinese-language journals and 37 in English-language journals; 303 (86.6%) reported on survey findings and 47 reported on the evaluation of MHL interventions. MHL research in China has mainly focused on the assessment of mental health-related knowledge and beliefs. Much less attention has been given to developing and evaluating relevant interventions. MHL related to general mental health and suicide were most commonly studied, with less focus on specific disorders, although some studies covered depression, psychosis and anxiety disorders. The majority of MHL tools utilized in the studies reported in this review were developed in China (n = 97, 80.2% ) and almost half of these studies (57.8%) did not provide enough details concerning psychometrics. Conclusions: More interventions targeting the general public and aiming to improve MHL and promote behaviour change, are needed in China. These should be evaluated with high-quality study designs, such as randomised controlled trials. Proper validation of tools used for measuring MHL should also be addressed in future studies. 
 Title: Population-based surveys and interventions for mental health literacy in China during 1997-2018: a scoping review
Output: False
Paragraph: Immunosenescence influences many components of the immune system. Most importantly, profound changes in T cell function are evident in older individuals. The impact of aging on specific T cell subsets has been difficult to examine, but recent advances in murine model systems and new insights into T cell function have allowed for the more precise examination of how T cell responses change with aging. Importantly, recent studies have shown that age-related enhancement of both Th17 generation and regulatory T cell function may contribute to significant changes in immune function. In this review, we summarize the current views on how aging influences the factors that impact T cell function and how this can affect the immune response to infections, vaccinations, and tumors. 
 Title: Effects of aging on T cell function
Output: True
Paragraph: Recombinant vesicular stomatitis virus (VSV) is widely used as a vaccine platform. However, the capacity of VSV-based vaccines to induce mucosal immunity has not been fully investigated. In the present study, a recombinant VSV expressing coxsackievirus B3 (CVB3) major immunogen VP1 has been generated and the immune protection elicited by VSV-VP1 was evaluated. We demonstrated that intranasal delivery of VSV-VP1 can induce a potent antigen-specific mucosal immune response as well as a systemic immune response, particularly the induction of polyfunctional T cells. Importantly, mice immunized with VSV-VP1 were better protected against CVB3-induced viral myocarditis than those receiving a chitosan-formulated DNA vaccine. Increased dendritic cell (DC) maturation in the mesenteric lymph node (MLN) was observed in the mice vaccinated with VSV-VP1, which could be a potential mechanism for the protective immune response. These findings support VSV as a viral delivery vector that can induce robust mucosal immunity that should be considered for further vaccine development. 
 Title: A vesicular stomatitis virus-based mucosal vaccine promotes dendritic cell maturation and elicits preferable immune response against coxsackievirus B3 induced viral myocarditis
Output: False
Paragraph: Background: During the early phases of the 2009 pandemic, subjects with influenza-like illness only had laboratory testing specific for the new A(H1N1)pdm09 virus. Findings: Between 25 th May and 7 th June 2009, during the pandemic CONTAIN phase, A(H1N1)pdm09 virus was detected using nucleic acid tests in only 56 of 1466 (3.8%) samples meeting the clinical case definition required for A(H1N1)pdm09 testing. Two hundred and fifty-five randomly selected A(H1N1)pdm09 virus-negative samples were tested for other respiratory viruses using a real-time multiplex PCR assay. Of the 255 samples tested, 113 (44.3%) had other respiratory viruses detected: rhinoviruses 63.7%, seasonal influenza A 17.6%, respiratory syncytial virus 7.9%, human metapneumovirus 5.3%, parainfluenzaviruses 4.4%, influenza B virus 4.4%, and enteroviruses 0.8%. Viral co-infections were present in 4.3% of samples. Conclusions: In the very early stages of a new pandemic, limiting testing to only the novel virus will miss other clinically important co-circulating respiratory pathogens. 
 Title: Pandemic clinical case definitions are non- specific: multiple respiratory viruses circulating in the early phases of the 2009 influenza pandemic in New South Wales, Australia
Output: True
Paragraph: Elevated low-density lipoprotein cholesterol (LDL-C) is one of the major contributors to cardiovascular heart disease (CHD), the leading cause of death worldwide. Due to severe side effects of statins, alternative treatment strategies are required for statin-intolerant patients. Monoclonal antibodies (mAbs) targeting proprotein convertase subtilisin/kexin type 9 (PCSK9) have shown great efficacy in LDL-C reduction. Limitations for this approach include the need for multiple injections as well as increased costs associated with patient management. Here, we engineered a DNA-encoded mAb (DMAb) targeting PCSK9 (daPCSK9), as an alternative approach to protein-based lipid-lowering therapeutics, and we characterized its expression and activity. A single intramuscular administration of mouse daPCSK9 generated expression in vivo for over 42 days that corresponded with a substantial decrease of 28.6% in non-high-density lipoprotein cholesterol (non-HDL-C) and 10.3% in total cholesterol by day 7 in wild-type mice. Repeated administrations of the DMAb plasmid led to increasing expression, with DMAb levels of 7.5 mg/mL at day 62. daPCSK9 therapeutics may provide a novel, simple, less frequent, cost-effective approach to reducing LDL-C, either as a stand-alone therapy or in combination with other LDL-lowering therapeutics for synergistic effect. 
 Title: Development of Novel DNA-Encoded PCSK9 Monoclonal Antibodies as Lipid-Lowering Therapeutics
Output: True