niryuu/sni-each-converted huggingface dataset:
Paragraph: Background: Cotton blue disease (CBD), an important global cotton crop pathology responsible for major economic losses, is prevalent in the major cotton-producing states of Brazil. Typical CBD symptoms include stunting due to internodal shortening, leaf rolling, intense green foliage, and yellowing veins. Atypical CBD symptoms, including reddish and withered leaves, were also observed in Brazilian cotton fields in 2007. Recently, a Polerovirus named Cotton leafroll dwarf virus (CLRDV) was shown to be associated with CBD. Results: To understand the distribution and genetic diversity of CLRDV in Brazil, we analyzed 23 CBD-symptomatic plants from susceptible cotton varieties originating from five of the six most important cotton-growing states, from 2004-2007. Here, we report on CLRDV diversity in plants with typical or atypical CBD symptoms by comparing viral coat protein, RNA polymerase (RdRp), and intergenic region genomic sequences. The virus had a widespread distribution with a low genetic diversity; however, three divergent isolates were associated with atypical CBD symptoms. These divergent isolates had a CLRDV-related coat protein but a distinct RdRp sequence, and probably arose from recombination events. Based on the taxonomic rules for the family Luteoviridae, we propose that these three isolates represent isolates of a new species in the genus Polerovirus. 
 Title: Virology Journal Widespread distribution and a new recombinant species of Brazilian virus associated with cotton blue disease
Output: True
Paragraph: In the last 20 years, surface plasmon resonance (SPR) and its advancement with imaging (SPRi) emerged as a suitable and reliable platform in clinical analysis for labelfree, sensitive, and real-time monitoring of biomolecular interactions. Thus, we report in this review the state of the art of clinical target detection with SPR-based biosensors in complex matrices (e.g., serum, saliva, blood, and urine) as well as in standard solution when innovative approaches or advanced instrumentations were employed for improved detection. The principles of SPR-based biosensors are summarized first, focusing on the physical properties of the transducer, on the assays design, on the immobilization chemistry, and on new trends for implementing system analytical performances (e.g., coupling with nanoparticles (NPs). Then we critically review the detection of analytes of interest in molecular diagnostics, such as hormones (relevant also for anti-doping control) and biomarkers of interest in inflammatory, cancer, and heart failure diseases. Antibody detection is reported in relation to immune disorder diagnostics. Subsequently, nucleic acid targets are considered for revealing genetic diseases (e.g., point mutation and single nucleotides polymorphism, SNPs) as well as new emerging clinical markers (microRNA) and for pathogen detection. Finally, examples of pathogen detection by immunosensing were also analyzed. A parallel comparison with the reference methods was duly made, indicating the progress brought about by SPR technologies in clinical routine analysis. 
 Title: Surface plasmon resonance applications in clinical analysis
Output: True
Paragraph: Currently available diagnostic assays for leptospirosis cannot differentiate vaccine from infection serum antibody. Several leptospiral proteins that are upregulated during infection have been described, but their utility as a diagnostic marker is still unclear. In this study, we undertook a lipidomics approach to determine if there are any differences in the serum lipid profiles of horses naturally infected with pathogenic Leptospira spp. and horses vaccinated against a commercially available bacterin. Utilizing a high-resolution mass spectrometry serum lipidomics analytical platform, we demonstrate that cyclic phosphatidic acids, diacylglycerols, and hydroperoxide oxidation products of choline plasmalogens are elevated in the serum of naturally infected as well as vaccinated horses. Other lipids of interest were triacylglycerols that were only elevated in the serum of infected horses and sphingomyelins that were increased only in the serum of vaccinated horses. This is the first report looking at the equine serum lipidome during leptospiral infection and vaccination. 
 Title: Lipidomic analysis of immune activation in equine leptospirosis and Leptospira- vaccinated horses
Output: False
Paragraph: Background: The recent emergence of zoonotic diseases such as Highly Pathogenic Avian Influenza (HPAI) and Severe Acute Respiratory Syndrome (SARS) have contributed to dominant Global Health narratives around health securitisation and pandemic preparedness, calling for greater co-operation between the health, veterinary and environmental sectors in the ever-evolving One Health movement. A decade later, One Health advocates face increasing pressure to translate the approach from theory into action. Methodology/Principal Findings: A qualitative case study methodology was used to examine the emerging relationships between international One Health dialogue and its practical implementation in the African health policy context. A series of Key Informant Interviews (n = 32) with policy makers, government officials and academics in Nigeria, Tanzania and Uganda are presented as three separate case studies. Each case examines a significant aspect of One Health operationalisation, framed around the control of both emerging and Neglected Zoonotic Diseases including HPAI, Human African Trypanosomiasis and rabies. The research found that while there is general enthusiasm and a strong affirmative argument for adoption of One Health approaches in Africa, identifying alternative contexts away from a narrow focus on pandemics will help broaden its appeal, particularly for national or regionally significant endemic and neglected diseases not usually addressed under a ''global'' remit. Conclusions/Significance: There is no 'one size fits all' approach to achieving the intersectoral collaboration, significant resource mobilisation and political co-operation required to realise a One Health approach. Individual country requirements cannot be underestimated, dismissed or prescribed in a top down manner. This article contributes to the growing discussion regarding not whether One Health should be operationalised, but how this may be achieved. 
 Title: One Health: Past Successes and Future Challenges in Three African Contexts
Output: False
Paragraph: S2 Contents S1. General information …S3 Plasmid construction …S3 Preparation of mRNA and 70S initiation complex for rapid kinetics …S6 Supplementary References. …S7 S3 Escherichia coli strain DH5α was used to amplify plasmid DNA. Oligonucleotides were purchased from Invitrogen. The compounds NCTn (n = 5, 6, 7, and 8) used in this study were synthesized as previously reported (1). Chemicals were from Roche, Sigma, or Merck. Radioactive compounds were from Hartmann Analytic. Ribosomes from E. coli MRE 600, fMet-tRNA fMet , Leu-tRNA Leu , EF-Tu, EF-G, and initiation factors were prepared as described (2-5). tRNA Gly , tRNA Lys , tRNA Val were prepared from total E. coli tRNA by consecutive column chromatographies on Sepharose 4B (GE Healthcare), Phenyl Sepharose (GE Healthcare), and DEAE Toyopearl (Tosoh Bioscience). Aminoacylated tRNAs were purified by reversed-phase HPLC on an RP-18 HPLC column (250 mm × 10.5 mm, Merck) equilibrated with buffer (20 mM ammonium acetate, pH 5.0, 10 mM magnesium acetate, 400 mM NaCl) using a gradient of 0%-15%) ethanol. Aa-tRNAs were precipitated with ethanol and dissolved in water; concentrations were determined photometrically by absorbance at 260 nm. 
 Title: Small synthetic molecule as an activator for −1 ribosomal frameshifting S2
Output: True
Paragraph: Background The aim of this study was to assess multiplex PCR analysis in detecting causative viruses in children with febrile seizures. Methods The study was a retrospective analysis comparing data from a pre-multiplex era (2009) with a period after the introduction of routine respiratory multiplex analysis (2010-2013) in children with febrile seizures. Results We included 200 children with febrile seizures (mean age: 29.5 ± 1.4.months; 104 male) in the study. In 2009, in 10 out of 49 (20 %) children, microbiology testing (bacterial/fungal) was positive compared with a rate of 74 out of 151 (49 %) children during 2010-2013 (p < 0.01). The rate of positive virological studies increased from 10 (20 %) in 2009 to 73 (48.3 %) in the period 2010-2013 (p < 0.01). Multiplex PCR analysis confirmed viral infections in 52 of 73 cases (71.2 %). Conclusion Routine multiplex PCR analysis fosters the detection of respiratory viruses in children with febrile seizure. The precise role of multiplex analysis in the J. 
 Title: Role of multiplex PCR analysis in children with febrile seizures management of these children awaits further clarifi- cation
Output: True
Paragraph: Before the SARS outbreak only two human coronaviruses (HCoV) were known: HCoV-OC43 and HCoV-229E. With the discovery of SARS-CoV in 2003, a third family member was identified. Soon thereafter, we described the fourth human coronavirus (HCoV-NL63), a virus that has spread worldwide and is associated with croup in children. We report here the complete genome sequence of two HCoV-NL63 clinical isolates, designated Amsterdam 57 and Amsterdam 496. The genomes are 27,538 and 27,550 nucleotides long, respectively, and share the same genome organization. We identified two variable regions, one within the 1a and one within the S gene, whereas the 1b and N genes were most conserved. Phylogenetic analysis revealed that HCoV-NL63 genomes have a mosaic structure with multiple recombination sites. Additionally, employing three different algorithms, we assessed the evolutionary rate for the S gene of group Ib coronaviruses to be ∼ 3 × 10 − 4 substitutions per site per year. Using this evolutionary rate we determined that HCoV-NL63 diverged in the 11th century from its closest relative HCoV-229E. 
 Title: Mosaic Structure of Human Coronavirus NL63, One Thousand Years of Evolution
Output: True
Paragraph: First identified in 2012, Middle East respiratory syndrome coronavirus (MERS-CoV) is a novel virus that can cause acute respiratory distress syndrome (ARDS), multiorgan failure, and death, with a case fatality rate of~35%. An animal model that supports MERS-CoV infection and causes severe lung disease is useful to study pathogenesis and evaluate therapies and vaccines. The murine dipeptidyl peptidase 4 (Dpp4) protein is not a functional receptor for MERS-CoV; thus, mice are resistant to MERS-CoV infection. We generated human DPP4 knock-in (hDPP4 KI) mice by replacing exons 10-12 at the mouse Dpp4 locus with exons 10-12 from the human DPP4 gene. The resultant human DPP4 KI mice are permissive to MERS-CoV (HCoV-EMC/2012 strain) infection but develop no disease. To generate a mouse model with associated morbidity and mortality from respiratory disease, we serially passaged HCoV-EMC/2012 strain in the lungs of young hDPP4 KI mice. After 30 in vivo passages, an adapted virus clone was isolated and designated MERS MA 6.1.2. This virus clone produced significantly higher titers than the parental clone in the lungs of hDPP4 KI mice and caused diffuse lung injury and a fatal respiratory infection. In this chapter, we will describe in detail the procedures used to mouse adapt MERS-CoV by serial passage of the virus in lungs. We also describe the methods used to isolate virus clones and characterize virus infection. 
 Title: Chapter 13 Development of a Mouse-Adapted MERS Coronavirus
Output: True
Paragraph: Edwardsiella tarda is a major pathogen in aquatic environments that can cause heavy economic losses. An improved method for quick and accurate detection of E . tarda by loop-mediated isothermal amplifi cation (LAMP) with two additional loop primers was developed by targeting the EsrB gene ( EsrB -LAMP). In this method, the Mg 2+ concentration, reaction temperature, and reaction time were optimized to 8 mmol/L, 61°C, and 40 min, respectively. The detection limit with the EsrB gene was as low as 10 copies, which is 100 times more sensitive than that of conventional polymerase chain reaction (PCR). The EsrB -LAMP assay was shown more sensitive and rapid than previously reported LAMP assays targeting the hemolysin gene ( hemolysin -LAMP) for detection of E . tarda . The EsrB -LAMP was also highly specifi c to E . tarda and had no cross-reaction with 13 other strains of bacteria. The assay can be carried out in a simple heating device and the EsrB -LAMP products can be visually detected by adding fl uorescent dye to the reaction mixture. Taken together, the improved EsrB -LAMP diagnostic protocol has the potential for detection of E . tarda from indoor and outdoor samples. 
 Title: An improved method for detection of Edwardsiella tarda by loop-mediated isothermal amplifi cation by targeting the EsrB gene*
Output: False
Paragraph: We evaluated the usefulness of a serum Aspergillus PCR assay for the diagnosis and prognosis of invasive aspergillosis in a study involving 941 patients for a total of 5146 serum samples. Fifty-one patients had proven/probable aspergillosis. We compared galactomannan (GM), PCR and mycologic analysis of pulmonary samples in both neutropenic and nonneutropenic patients. PCR performed in serum yielded 66.7% sensitivity, 98.7% specificity, 75.6% positive predictive value and 98.0% negative predictive value, while the GM index yielded 78.4% sensitivity, 87.5% specificity, 27% positive predictive value and 98.6% negative predictive value. The inclusion of PCR in the European Organization for Research and Treatment of Cancer (EORTC) and the Mycosis Study Group (MSG) mycologic criteria permitted the reclassification of nine other cases from possible to probable aspergillosis and increased the sensitivity to 71.7%. Combining the GM index with serum PCR increased the detection rate of invasive aspergillosis with 88.2% sensitivity. PCR was systematically negative in 16 patients with noninvasive forms of aspergillosis (namely aspergilloma and chronic aspergillosis). Remaining PCR positive after a period of 14 to 20 days of treatment was related to poor outcome at 30 and 90 days. Our results also indicate that, unlike the determination of the GM index, the initial fungus load as determined by PCR was highly predictive of 90-day mortality, with the rate of the latter being 15.8% for patients with <150 copies/mL vs. 73.2% for patients at or above that cutoff (p <0.0001). Therefore, PCR appears to be a powerful and interesting tool for the identification of patients with invasive aspergillosis who might benefit from more intense care. 
 Title: Aspergillus PCR in serum for the diagnosis, follow-up and prognosis of invasive aspergillosis in neutropenic and nonneutropenic patients
Output: True
Paragraph: Gold nanoparticles (GNPs) have been widely utilized to develop various biosensors for molecular diagnosis, as they can be easily functionalized and exhibit unique optical properties explained by plasmonic effects. These unique optical properties of GNPs allow the expression of an intense color under light that can be tuned by altering their size, shape, composition, and coupling with other plasmonic nanoparticles. Additionally, they can also enhance other optical signals, such as fluorescence and Raman scattering, making them suitable for biosensor development. In this review, we provide a detailed discussion of the currently developed biosensors based on the aforementioned unique optical features of GNPs. Mainly, we focus on four different plasmonic biosensing methods, including localized surface plasmon resonance (LSPR), surface-enhanced Raman spectroscopy (SERS), fluorescence enhancement, and quenching caused by plasmon and colorimetry changes based on the coupling of GNPs. We believe that the topics discussed here are useful and able to provide a guideline in the development of novel GNP-based biosensors in the future. 
 Title: Molecular Sciences Application of Gold Nanoparticle to Plasmonic Biosensors
Output: True
Paragraph: Different viruses belonging to the genus Vesivirus infect a broad range of animals, and cause gastroenteritis, vesicular skin lesions, hemorrhagic disease, respiratory diseases and other conditions. A recent report on Vesivirus viremia, as detected by PCR, in samples from patients with hepatitis of unknown etiology in the USA suggested a zoonotic potential for vesiviruses. These results have not been confirmed by another laboratory. In order to do so, a generic PCR assay on the RNA polymerase region was developed, and validated with RNA from 69 different Vesivirus species. Except SMSV serotype-8, all species tested were detected, including the ones that were suggested to be involved in zoonotic transmission in the USA (SMSV serotype-5). The generic Vesivirus assay was used on RNA extracted from serum samples from patients with hepatitis, stool samples from patients with gastroenteritis, throat-swab specimens of patients with rash illnesses, throat-swab and nose-swabs of patients with acute respiratory diseases, and cell cultures with cytopathologic effect from enterovirus surveillance in which no pathogen was found. None were found positive. In this study a generic Vesivirus assay was developed and it was concluded that vesiviruses are an unlikely cause of common illnesses in humans in the Netherlands. 
 Title: A new generic real-time reverse transcription polymerase chain reaction assay for vesiviruses; vesiviruses were not detected in human samples
Output: False
Paragraph: Background: This study was initiated to evaluate, for the first time, the performance and quality of the influenzalike illness (ILI) surveillance system in Tunisia. The evaluation covered the period of 2012-2015 and used different data sources to measure indicators related to data quality and completeness, representativeness, timeliness, simplicity, acceptability, flexibility, stability and utility. Results: During the evaluation period, 485.221 ILI cases were reported among 6.386.621 outpatients at 268 ILI sentinel sites. To conserve resources, cases were only enrolled and tested for influenza during times when the number of patients meeting the ILI case definition exceeded 7% (10% after 2014) of the total number of outpatients for the week. When this benchmark was met, five to 10 patients were enrolled and sampled by nasopharyngeal swabs the following week. In total, The National Influenza Center (NIC) received 2476 samples, of which 683 (27.6%) were positive for influenza. The greatest strength of the system was its representativeness and flexibility. The timeliness of the data and the acceptability of the surveillance system performed moderately well; however, the utility of the data and the stability and simplicity of the surveillance system need improvement. Overall, the performance of the Tunisian influenza surveillance system was evaluated as performing moderately well for situational awareness in the country and for collecting representative influenza virologic samples. Conclusions: The influenza surveillance system in Tunisia provided pertinent evidence for public health interventions related to influenza situational awareness. To better monitor influenza, we propose that ILI surveillance should be limited to sites that are currently performing well and the quality of data collected should be closely monitored and improved. 
 Title: Evaluation of the influenza-like illness surveillance system in Tunisia, 2012-2015
Output: True
Paragraph: The aim of this study was to evaluate some immunological patterns involved in natural and acquired resistance against MHV3 using the original model of genetically modified lines of mice selected for high (H III ) and low (L III ) antibody responsiveness. As previously shown, a lower pre-existing anti-MHV antibody level was found in susceptible H III mice as compared to resistant L III mice. Mortality rates of the F 1 (H Â L) hybrids and F 2 and backcross segregants reflected co-dominance of both characters and the survivors had higher preexisting anti-MHV antibody titers. The present data show that both lines had the potential to synthesize antibodies and that the resistance acquired by the susceptible H III mice paralleled the antibody synthesis. Nevertheless, higher antibody titers were necessary to confer resistance in H III mice than in L III ones. When compared to uvMHV3, a single immunization with a related infectious MHV strain induced a higher antibody synthesis and led the H III mice to resist the MHV3 challenge. A direct correlation between the antibody level and resistance to infection was always observed in H III mice. Although mounting a Th2 response as indicated by IgG1 responses, they were also able to readily synthesize large amounts of IgG2a antibodies after immunization or during infection, reflecting a Th1 response. The transfer of anti-MHV antibodies to susceptible H III mice was capable of conferring resistance to MHV3, providing the antibodies were present before virus infection and in large amounts. The resistance and the survival time of these animals increased with the level of antibody administered. If these direct and clear data suggest that H III mice can acquire resistance through antibodies, the basis of the resistance of the resistant L III mice may rely on mechanisms less dependent on antibodies. 
 Title: Antibody responsiveness during immunization and challenge of genetically modified antibody responder mice with murine hepatitis virus 3
Output: True
Paragraph: Polysaccharide Production Extraction Structural elucidation Bioactivity A B S T R A C T Cordyceps (Ophiocordyceps sinensis) sinensis, the Chinese caterpillar fungus, is a unique and precious medicinal fungus in traditional Chinese medicine which has been used as a prestigious tonic and therapeutic herb in China for centuries. Polysaccharides are bioactive constituents of C. sinensis, exhibiting several activities such as immunomodulation, antitumour, antioxidant and hypoglycaemic. As natural C. sinensis fruiting body-caterpillar complexes are very rare and expensive, the polysaccharides documented over the last 15-20 years from this fungal species were mostly extracted from cultivated fungal mycelia (intracellular polysaccharides) or from mycelial fermentation broth (exopolysaccharides). Extraction and purification of the polysaccharides is a tedious process involving numerous steps of liquid and solid phase separations. Nevertheless, a large number of polysaccharide structures have been purified and elucidated. However, relationships between the structures and activities of these polysaccharides are not well established. This review provides a comprehensive summary of the most recent developments in various aspects (i.e., production, extraction, structure, and bioactivity) of the intracellular and exopolysaccharides from mycelial fermentation of C. sinensis fungi. The contents and data will serve as useful references for further investigation, production and application of these polysaccharides in functional foods and therapeutic agents. 
 Title: Recent advances in Cordyceps sinensis polysaccharides: Mycelial fermentation, isolation, structure, and bioactivities: A review
Output: True
Paragraph: Background. The common cold or upper respiratory infection (URI) is highly prevalent among young children and often results in otitis media (OM). The incidence and characteristics of OM complicating URI due to specific viruses have not been well studied. Methods. We performed a prospective, longitudinal cohort study of 294 healthy children (age range, 6 months to 3 years). Each child was observed for 1 year to assess the occurrence of URI, acute OM (AOM), and OM with effusion (OME) complicating URI due to specific viruses. Results. We documented 1295 URI episodes (5.06 episodes per child-year) and 440 AOM episodes (1.72 episodes per child-year). Virus studies were performed for 864 URI episodes; 63% were virus positive. Rhinovirus and adenovirus were most frequently detected during URI. The overall incidence of OM that complicated URI was 61%, including a 37% incidence of AOM and a 24% incidence of OME. Young age was the most important predictor of AOM that complicated URI. AOM occurred in approximately one-half of children with URI due to adenovirus, respiratory syncytial virus, or coronavirus and in approximately one-third of those with URI due to influenza virus, parainfluenza virus, enterovirus, or rhinovirus. Conclusions. More than 60% of episodes of symptomatic URI among young children were complicated by AOM and/or OME. Young age and specific virus types were predictors of URI complicated by AOM. For young children, the strategy to prevent OM should involve prevention of viral URI. The strategy may be more effective if the priority is given to development of means to prevent URI associated with adenovirus and respiratory syncytial virus. The common cold or upper respiratory infection (URI), a disease caused by a variety of viruses, is a universal illness. Particularly susceptible to URI are young children, especially those who attend day care centers [1] [2] [3] . URI in young children is often complicated by otitis media (OM) [4, 5] . The high prevalence of URI has made OM one of the most common diseases seen in pediatric practice and the emergency department [6, 7] . OM leads to widespread use of antibiotics and per- 
 Title: Viral Upper Respiratory Tract Infection and Otitis Media Complication in Young Children
Output: False
Paragraph: Background. Chronic lung allograft dysfunction (CLAD) is a major cause of allograft loss post-lung transplantation. Prior studies have examined the association between respiratory virus infection (RVI) and CLAD were limited by older diagnostic techniques, study design, and case numbers. We examined the association between symptomatic RVI and CLAD using modern diagnostic techniques in a large contemporary cohort of lung transplant recipients (LTRs). Methods. We retrospectively assessed clinical variables including acute rejection, cytomegalovirus pneumonia, upper and lower RVI, and the primary endpoint of CLAD (determined by 2 independent reviewers) in 250 LTRs in a single university transplantation program. Univariate and multivariate Cox models were used to analyze the relationship between RVI and CLAD in a time-dependent manner, incorporating different periods of risk following RVI diagnosis. Results. Fifty patients (20%) were diagnosed with CLAD at a median of 95 weeks post-transplantation, and 79 (32%) had 114 episodes of RVI. In multivariate analysis, rejection and RVI were independently associated with CLAD (adjusted hazard ratio [95% confidence interval]) 2.2 (1.2-3.9), P = .01 and 1.9 (1.1-3.5), P = .03, respectively. The association of RVI with CLAD was stronger the more proximate the RVI episode: 4.8 (1.9-11.6), P < .01; 3.4 (1.5-7.5), P < .01; and 2.4 (1.2-5.0), P = .02 in multivariate analysis for 3, 6, and 12 months following RVI, respectively. Conclusions. Symptomatic RVI is independently associated with development of CLAD, with increased risk at shorter time periods following RVI. Prospective studies to characterize the virologic determinants of CLAD and define the underlying mechanisms are warranted. 
 Title: Clinical Infectious Diseases Symptomatic Respiratory Virus Infection and Chronic Lung Allograft Dysfunction
Output: False
Paragraph: In this proof-of-concept study, we model the spread of SARS-CoV-2 in various environments with a stochastic susceptible-infectious-recovered (SIR) compartmental model. We fit this model to the latest epidemic data with an approximate Bayesian computation (ABC) technique. Within this SIR-ABC framework, we extrapolate long-term infection curves for several regions and evaluate their steepness. We propose several applications and extensions of the SIR-ABC technique. 
 Title: Stochastic Compartmental Modelling of SARS-CoV-2 with Approximate Bayesian Computation
Output: False
Paragraph: The size and diversity of ribosome display libraries depends upon stability of the complex formed between the ribosome, mRNA and translated protein. To investigate if mRNA secondary structure improves stability of the complex, we tested a pseudoknot, originating from the genomic RNA of infectious bronchitis virus (IBV), a member of the positive-stranded coronavirus group. We used the previously-isolated anti-DNA scFv, 3D8, as a target protein. During in vitro translation in rabbit reticulocyte lysate, we observed that incorporation of the pseudoknot into the mRNA resulted in production of a translational intermediate that corresponded to the expected size for ribosomal arrest at the pseudoknot. Complexes containing the mRNA pseudoknot exhibited a higher efficiency of affinity selection than that those without, indicating that the pseudoknot improves stability of the mRNA-ribosome-antibody complex in a eukaryotic translation system. Thus, in order to improve the efficiency of selection, this relatively short pseudoknot sequence could be incorporated into ribosome display. 
 Title: A pseudoknot improves selection efficiency in ribosome display
Output: True
Paragraph: Xenotropic murine leukemia virus-related virus (XMRV) is a gammaretrovirus that was originally identified from human prostate cancer patients and subsequently linked to chronic fatigue syndrome. Recent studies showed that XMRV is a recombinant mouse retrovirus; hence, its association with human diseases has become questionable. Here, we demonstrated that XMRV envelope (Env)-mediated pseudoviral infection is not blocked by lysosomotropic agents and cellular protease inhibitors, suggesting that XMRV entry is not pH-dependent. The full length XMRV Env was unable to induce syncytia formation and cell-cell fusion, even in cells overexpressing the viral receptor, XPR1. However, truncation of the C-terminal 21 or 33 amino acid residues in the cytoplasmic tail (CT) of XMRV Env induced substantial membrane fusion, not only in the permissive 293 cells but also in the nonpermissive CHO cells that lack a functional XPR1 receptor. The increased fusion activities of these truncations correlated with their enhanced SU shedding into culture media, suggesting conformational changes in the ectodomain of XMRV Env. Noticeably, further truncation of the CT of XMRV Env proximal to the membrane-spanning domain severely impaired the Env fusogenicity, as well as dramatically decreased the Env incorporations into MoMLV oncoretroviral and HIV-1 lentiviral vectors resulting in greatly reduced viral transductions. Collectively, our studies reveal that XMRV entry does not require a low pH or low pH-dependent host proteases, and that the cytoplasmic tail of XMRV Env critically modulates membrane fusion and cell entry. Our data also imply that additional cellular factors besides XPR1 are likely to be involved in XMRV entry. Citation: Cô té M, Zheng Y-M, Liu S-L (2012) Membrane Fusion and Cell Entry of XMRV Are pH-Independent and Modulated by the Envelope Glycoprotein's Cytoplasmic Tail. PLoS ONE 7(3): e33734. 
 Title: Membrane Fusion and Cell Entry of XMRV Are pH- Independent and Modulated by the Envelope Glycoprotein's Cytoplasmic Tail
Output: True
Paragraph: Background: Respiratory protection effi ciency of facemasks is critically important in the battle against communicable respiratory infections such as infl uenza and severe acute respiratory syndrome (SARS). We studied the spatial distributions of simulated virus-laden respiratory droplets when human subjects wore facemasks and were exposed to regulatory viral droplets by conducting in vivo experiments in facemask use. Methods: Transmission pathway of aerosols of Fluorescein-KCl solution through facemasks and protective effi ciency of facemasks were examined by using normal surgical facemasks and two facemasks with exhaust valves (Facemask A) and exhaust holes (Facemask B) covered with the same surgical fi lters situated at the back of the facemasks. Fluorescein-KCl solution was sprayed onto the faces of participants wearing the facemasks and performing intermittent exercises on a treadmill in a climatic chamber. Results: Experimental results showed that when droplets spread onto a person face-to-face over short distances, 92.3% to 99.5% of droplets were blocked by the front surface of the facemask, whereas only 0.5% to 7.7% of droplets reached the back of the facemask. Both facemasks A and B had near or over 99% protection effi ciency, compared with that of 95.5% to 97% of surgical facemasks. Using the same fi lters as normal surgical masks, facemasks A and B provided more effective respiratory protection against communicable respiratory infections such as infl uenza and SARS by the location of the breathing pathway to the back of the facemasks. Conclusions: Separating the breathing pathway from the virus-contaminated area in facemasks can provide more effective protection against communicable respiratory infections such as infl uenza and SARS. 
 Title: Transmission of communicable respiratory infections and facemasks
Output: True
Paragraph: A hallmark of disease is that most pathogens are able to infect more than one host species. However, for most pathogens, we still have a limited understanding of how this affects epidemiology, persistence and virulence of infections-including several zoonotic pathogens that reside in wild animal reservoirs and spillover into humans. In this chapter, we review the current knowledge of mallard (Anas platyrhynchos) as host for pathogens. This species is widely distributed, often occupying habitats close to humans and livestock, and is an important game bird species and the ancestor to domestic ducks-thereby being an excellent model species to highlight aspects of the wildlife, domestic animal interface and the relevance for human health. We discuss mallard as host for a range of pathogens but focus more in depth of it as a reservoir host for influenza A virus (IAV). Over the last decades, IAV research has surged, prompted in part to the genesis and spread of highly pathogenic virus variants that have been devastating to domestic poultry and caused a number of human spillover infections. The aim of this chapter is to synthesise and review the intricate interactions of virus, host and environmental factors governing IAV epidemiology and evolution. 
 Title: Of Ducks and Men: Ecology and Evolution of a Zoonotic Pathogen in a Wild Reservoir Host
Output: False
Paragraph: Zika virus (ZIKV) belongs to the Flavivirus genus of the Flaviviridae family. It is an arbovirus that can cause congenital abnormalities and is sexually transmissible. A series of outbreaks accompanied by unexpected severe clinical complications have captured medical attention to further characterize the clinical features of congenital ZIKV syndrome and its underlying pathophysiological mechanisms. Endoplasmic reticulum (ER) and ER-related proteins are essential in ZIKV genome replication. This review highlights the subcellular localization of ZIKV to the ER and ZIKV modulation on the architecture of the ER. This review also discusses ZIKV interaction with ER proteins such as signal peptidase complex subunit 1 (SPCS1), ER membrane complex (EMC) subunits, and ER translocon for viral replication. Furthermore, the review covers several important resulting effects of ZIKV infection to the ER and cellular processes including ER stress, reticulophagy, and paraptosis-like death. Pharmacological targeting of ZIKVaffected ER-resident proteins and ER-associated components demonstrate promising signs of combating ZIKV infection and rescuing host organisms from severe neurologic sequelae. 
 Title: Endoplasmic reticulum: a focal point of Zika virus infection
Output: False
Paragraph: The present study describes the development of SYBR Green based real-time polymerase chain reaction (real-time PCR) for detection and quantitation of canine parvovirus type 2 (CPV 2) in faecal samples of dogs. In this assay, the primers were designed and custom-synthesized based on nucleotide sequence of VP2 gene of CPV 2. A standard curve was plotted using 10-fold serial dilution of standard plasmid DNA and Ct value. The standard curve was found to be linear over a 10 −7 dilution. The real-time PCR results were expressed as the number of DNA copies of CPV 2 per mg of faecal samples and showed range of 1.0 × 10 3 to 7.0 × 10 9 copies of viral DNA per mg of stool samples. The analytical sensitivity of the SYBR Green based real-time PCR was shown to be equivalent to 10 copies. Faecal samples (47) from dogs suspected of CPV 2 infection were analyzed by real-time PCR, haemagglutination (HA) assay and by a conventional PCR and 24, 20 and 22 samples were found positive for CPV 2, respectively. Comparison between the results of three different assays revealed that real-time PCR is more sensitive than HA and conventional PCR and allow the detection of low titers of CPV 2 in infected dogs. 
 Title: Development of a SYBR Green based real-time PCR assay for detection and quantitation of canine parvovirus in faecal samples
Output: True
Paragraph: Bovine respiratory disease (BRD) often occurs when active respiratory virus infections (BHV-1, etc.) impair resistance to Mannheimia haemolytica infection in the lower respiratory tract. The interactions that occur when the respiratory epithelium encounters these viral and bacterial pathogens are poorly understood. We used Agilent bovine gene microarray chips containing 44,000 transcripts to elucidate bovine bronchial epithelial cell (BBEC) responses following in vitro exposure to BHV-1 alone, M. haemolytica alone, or both BHV-1 and M. haemolytica. Microarray analysis revealed differential regulation (>2-fold) of 978 transcripts by BHV-1 alone, 2040 transcripts by M. haemolytica alone, and 2189 genes by BHV-1 and M. haemolytica in combination. M. haemolytica treatment produced significantly greater inductions (>10-fold) of several inflammation associated genes, such as CXCL2, IL-6, IL-1␣, e-selectin, and IL-8, than to BHV-1 alone. Functional analysis of the microarray data revealed a significant upregulation of genes involved in important biological processes such as inflammation (TNF-␣, IL-8, Tlr-2, IL-1, CXCL2, CSF2), vascular functions (VEGF, EDN2) and leukocyte migration (ICAM1, IL-16) during a co-infection with BHV-1 and M. haemolytica compared to either pathogen alone. This study provides evidence to support that lung epithelial cells are a source of mediators that may promote inflammatory changes observed during bovine respiratory disease. 
 Title: Gene expression profiling of bovine bronchial epithelial cells exposed in vitro to bovine herpesvirus 1 and Mannheimia haemolytica
Output: False
Paragraph: Since accurate forecasting of tourist arrivals is very important for planning for potential tourism demand and improving the tourism infrastructure, various tourist arrivals forecasting methods have been developed. The purpose of this study is to apply the adaptive network-based fuzzy inference system (ANFIS) model to forecast the tourist arrivals to Taiwan and demonstrate the forecasting performance of this model. Based on the mean absolute percentage errors and statistical results, we can see that the ANFIS model has better forecasting performance than the fuzzy time series model, grey forecasting model and Markov residual modified model. Thus, the ANFIS model is a promising alternative for forecasting the tourist arrivals. We also use the ANFIS model to forecast the monthly tourist arrivals to Taiwan from Japan, Hong Kong and Macao, and the United States. 
 Title: Forecasting tourist arrivals by using the adaptive network-based fuzzy inference system
Output: False
Paragraph: An antigenic variant of avian infectious bronchitis virus (IBV), a coronavirus, was isolated and characterized. This strain, CUT2, possesses a number of unusual features, which have not been previously observed in IBV. The S1 glycoprotein of CU-T2 carries virus-neutralizing and serotype-specific epitopes of two IBV serotypes, Arkansas (Ark) and Massachusetts (Mass). Sequence analysis revealed that the virus, originally an Ark serotype, has acquired the Mass-specific epitope by mutation(s). This provides evidence that point mutations may lead to generation of IBV antigenic variants in the field. It was further observed that two independent recombination events involving three different IBV strains had occurred in the $2 glycoprotein gene and N protein gene of CU-T2, indicating that genomic RNA recombination in IBV may occur in multiple genes in nature. It was especially significant that a sequence of Holland 52 (a vaccine strain) had replaced half of the N gene of CU-T2. This proves that recombination among vaccine strains is contributing to the generation of IBV variants in the field. Based on these observations it is predicted that every IBV field isolate could have unique genetic nature. Therefore, several recently reported diagnostic and serotyping methods of IBV which are based on dot-blot hybridization, restriction fragment length polymorphism (RFLP), and polymerase chain reaction (PCR), may not reveal the true antigenic and/or genetic nature of IBV isolates, and may in fact yield misleading information. 
 Title: A novel variant of avian infectious bronchitis virus resulting from recombination among three different strains
Output: True
Paragraph: We have investigated the role of two polymorphic sites (R190W and N192K) on the binding and activation of the formyl peptide receptor (FPR) by viral and formyl peptides. WEDWVGWI, a peptide with antiviral activity derived from the membrane proximal region of feline immunodeficiency virus, binds with high affinity to FPR. The three tryptophans in the peptide are all essential for FPR binding, just as they were essential for antiviral activity (Giannecchini, S. et al., J. Virol. 77 (2003) 3724). Formyl-NleWEDWVGWI behaved as a weak partial agonist with FPR W190/N192 but a stronger partial agonist with FPR R190/K192 and FPR R190/N192. Formyl-NleNleWEDWVGWI behaved as a full agonist toward all three FPRs but exhibited a much higher EC 50 with W190/N192 FPR (300±45 nM) than for R190/K192 FPR (40±3 nM) or R190/N192 (60 ±8 nM). Formyl-MYKWPWYVWL preferentially activated R190/K192 and R190/N192 FPRs by >5 fold compared to W190/N192 FPR. Formyl-MFEDAVAWF, a peptide derived from a protein in Mycobacterium avium subsp. paratuberculosis and formyl-MFTFEPFPTN, a peptide derived from the N-terminus of chemotaxis inhibitory protein of Staphylococcus aureus with an added N-terminal methionine exhibited the greatest selectivity for R190/K192 and R190/N192 FPRs with ~10 fold lower EC 50S than that observed with FPR W190/N192. Thus, individuals with the W190 polymorphism may display a reduced ability to detect certain formyl peptides. 
 Title: Differential activation of polymorphisms of the formyl peptide receptor by formyl peptides
Output: True
Paragraph: A novel series of diethyl {4-[(5-substituted-1,3-dioxo-1H-benzo[de]isoquinolin-2(3H)-yl)methyl]-1H-1,2,3-triazol-1-yl}alkylphosphonates designed as analogues of amonafide was synthesized. All phosphonates were assessed for antiviral activity against a broad range of DNA and RNA viruses and several of them showed potency against varicella-zoster virus (VZV) [EC 50 (50% effective concentration) = 27.6-91.5 µM]. Compound 16b exhibited the highest activity against a thymidine kinase-deficient (TK − ) VZV strain (EC 50 = 27.59 µM), while 16d was the most potent towards TK + VZV (EC 50 = 29.91 µM). Cytostatic properties of the compounds 14a-i-17a-i were studied on L1210, CEM, HeLa and HMEC-1 cell lines and most of them were slightly cytostatic for HeLa [IC 50 (50% inhibitory concentration) = 29-130 µM] and L1210 cells [IC 50 (50% inhibitory concentration) = 14-142 µM]. 
 Title: Synthesis and the Biological Activity of Phosphonylated 1,2,3-Triazolenaphthalimide Conjugates
Output: True
Paragraph: Dendritic cells are potent antigen-capture and -presenting cells that play a key role in the initiation and regulation of the adaptive immune response. This process of immune homeostasis, as maintained by dendritic cells, is susceptible to dysregulation by certain pathogens during chronic infections. Such dysregulation may lead to disease perpetuation with potentially severe systemic consequences. Here we discuss in detail how intracellular pathogens exploit dendritic cells and evade degradation by altering or evading autophagy. This novel mechanism explains in part the chronic, persistent nature observed in several immuno-inflammatory diseases, including periodontal disease. Also, here we propose a hypothetical model on the plausible role of autophagy in the context of periodontal disease. Promotion of autophagy may open new therapeutic strategies in the search for a "cure" for periodontal disease in humans. 
 Title: Dendritic cells: microbial clearance via autophagy and potential immunobiological consequences for periodontal disease
Output: True
Paragraph: Various viruses can be considered as one of the most frequent causes of human diseases, from mild illnesses to really serious sicknesses that end fatally. Numerous viruses are also pathogenic to animals and plants, and many of them, mutating, become pathogenic also to humans. Several cases of affecting humans by originally animal viruses have been confirmed. Viral infections cause significant morbidity and mortality in humans, the increase of which is caused by general immunosuppression of the world population, changes in climate, and overall globalization. In spite of the fact that the pharmaceutical industry pays great attention to human viral infections, many of clinically used antivirals demonstrate also increased toxicity against human cells, limited bioavailability, and thus, not entirely suitable therapeutic profile. In addition, due to resistance, a combination of antivirals is needed for life-threatening infections. Thus, the development of new antiviral agents is of great importance for the control of virus spread. On the other hand, the discovery and development of structurally new antivirals represent risks. Therefore, another strategy is being developed, namely the reformulation of existing antivirals into nanoformulations and investigation of various metal and metalloid nanoparticles with respect to their diagnostic, prophylactic, and therapeutic antiviral applications. This chapter is focused on nanoscale materials/formulations with the potential to be used for the treatment or inhibition of the spread of viral diseases caused by human immunodeficiency virus, influenza A viruses (subtypes H3N2 and H1N1), avian influenza and swine influenza viruses, respiratory syncytial virus, herpes simplex virus, hepatitis B and C viruses, Ebola and Marburg viruses, Newcastle disease virus, dengue and Zika viruses, and pseudorabies virus. Effective antiviral long-lasting and target-selective nanoformulations developed for oral, intravenous, intramuscular, intranasal, intrarectal, intravaginal, and intradermal applications are discussed. Benefits of nanoparticle-based vaccination formulations with the potential to secure cross protection against divergent viruses are outlined as well. 
 Title: Nanoformulations: A Valuable Tool in the Therapy of Viral Diseases Attacking Humans and Animals
Output: False
Paragraph: Immunodeficiency Virus (HIV). In the present study, we screened plasma of 88 HIV-1 infected ART naïve individuals for their neutralization potential using a standard panel of 18 pseudoviruses belonging to different subtypes and different levels of neutralization. We identified 12 samples with good breadth of neutralization (neutralized >90% of the viruses). Four of these samples neutralized even the difficult-to-neutralize tier-3 pseudoviruses with great potency (GMT > 600). Analysis of neutralization specificities indicated that four samples had antibodies with multiple epitope binding specificities, viz. CD4-binding site (CD4BS), glycans in the V1/V2 and V3 regions and membrane proximal external region (MPER). Our findings indicate the strong possibility of identifying highly potent bNAbs with known or novel specificities from HIV-1 subtype C infected individuals from India that can be exploited as therapeutic tools or lead molecules for the identification of potential epitopes for design of a protective HIV-1 vaccine. 
 Title: Broad and potent cross clade neutralizing antibodies with multiple specificities in the plasma of HIV-1 subtype C infected individuals
Output: True