niryuu/sni-each-converted huggingface dataset:
Paragraph: Background: Hepatitis C virus (HCV) is a blood-borne flavivirus that infects many millions of people worldwide. Relatively little is known, however, concerning the stability of HCV and reliable procedures for inactivating this virus. Methods: In the current study, the thermostability of cell culture-derived HCV (HCVcc, JFH-1 strain) under different environmental temperatures (37°C, room temperature, and 4°C) and the ability of heat, UVC light irradiation, and aldehyde and detergent treatments to inactivate HCVcc were evaluated. The infectious titers of treated viral samples were determined by focus-forming unit (FFU) assay using an indirect immunofluorescence assay for HCV NS3 in hepatoma Huh7-25-CD81 cells highly permissive for HCVcc infection. MTT cytotoxicity assay was performed to determine the concentrations of aldehydes or detergents at which they were no longer cytotoxic. Results: HCVcc in culture medium was found to survive 37°C and room temperature (RT, 25 ± 2°C) for 2 and 16 days, respectively, while the virus was relatively stable at 4°C without drastic loss of infectivity for at least 6 weeks. HCVcc in culture medium was sensitive to heat and could be inactivated in 8 and 4 min when incubated at 60°C and 65°C, respectively. However, at 56°C, 40 min were required to eliminate HCVcc infectivity. Addition of normal human serum to HCVcc did not significantly alter viral stability at RT or its susceptibility to heat. UVC light irradiation (wavelength = 253.7 nm) with an intensity of 450 μW/cm 2 efficiently inactivated HCVcc within 2 min. Exposures to formaldehyde, glutaraldehyde, ionic or nonionic detergents all destroyed HCVcc infectivity effectively, regardless of whether the treatments were conducted in the presence of cell culture medium or human serum. Conclusions: The results provide quantitative evidence for the potential use of a variety of approaches for inactivating HCV. The ability of HCVcc to survive ambient temperatures warrants precautions in handling and disposing of objects and materials that may have been contaminated with HCV. 
 Title: Thermal stability and inactivation of hepatitis C virus grown in cell culture
Output: True
Paragraph: Human intestinal maltase (HMA) is an αglucosidase responsible for the hydrolysis of α-1,4-linkages from the non-reducing end of malto-oligosaccharides. HMA has become an important target in the treatment of type-2 diabetes. In this study, epigallocatechin gallate (EGCG) and EGCG glucoside (EGCG-G1) were identified as inhibitors of HMA by an in vitro assay with IC 50 of 20 ± 1.0 and 31.5 ± 1.0 µM, respectively. A Lineweaver-Burk plot confirmed that EGCG and EGCG-G1 were competitive inhibitors of maltose substrate against HMA and inhibition kinetic constants (K i ) calculated from a Dixon plot were 5.93 ± 0.26 and 7.88 ± 0.57 µM, respectively. Both EGCG and EGCG-G1 bound to the active site of HMA with numerous hydrophobic and hydrogen bond interactions. 
 Title: Inhibitory Effects of Epigallocatechin Gallate and Its Glucoside on the Human Intestinal Maltase Inhibition
Output: True
Paragraph: Background: Nonadditivity in fitness effects from two or more mutations, termed epistasis, can result in compensation of deleterious mutations or negation of beneficial mutations. Recent evidence shows the importance of epistasis in individual evolutionary pathways. However, an unresolved question in molecular evolution is how often and how significantly fitness effects change in alternative genetic backgrounds. Results: To answer this question, we quantified the effects of all single mutations and double mutations between all positions in the IgG-binding domain of protein G (GB1). By observing the first two steps of all possible evolutionary pathways using this fitness profile, we were able to characterize the extent and magnitude of pairwise epistasis throughout an entire protein molecule. Furthermore, we developed a novel approach to quantitatively determine the effects of single mutations on structural stability (DDG U ). This enabled determination of the importance of stability effects in functional epistasis. Conclusions: Our results illustrate common biophysical mechanisms for occurrences of positive and negative epistasis. Our results show pervasive positive epistasis within a conformationally dynamic network of residues. The stability analysis shows that significant negative epistasis, which is more common than positive epistasis, mostly occurs between combinations of destabilizing mutations. Furthermore, we show that although significant positive epistasis is rare, many deleterious mutations are beneficial in at least one alternative mutational background. The distribution of conditionally beneficial mutations throughout the domain demonstrates that the functional portion of sequence space can be significantly expanded by epistasis. 
 Title: Article A Comprehensive Biophysical Description of Pairwise Epistasis throughout an Entire Protein Domain
Output: True
Paragraph: Background: Micro-organisms transmitted from vertebrate animalsincluding livestockto humans account for an estimated 60% of human pathogens. Micro-organisms can be transmitted through inhalation, ingestion, via conjunctiva or physical contact. Close contact with animals is crucial for transmission. The role of intensity and type of contact patterns between livestock and humans for disease transmission is poorly understood. In this systematic review we aimed to summarise current knowledge regarding patterns of human-livestock contacts and their role in micro-organism transmission. Methods: We included peer-reviewed publications published between 1996 and 2014 in our systematic review if they reported on human-livestock contacts, human cases of livestock-related zoonotic diseases or serological epidemiology of zoonotic diseases in human samples. We extracted any information pertaining the type and intensity of human-livestock contacts and associated zoonoses. Results: 1522 papers were identified, 75 were included: 7 reported on incidental zoonoses after brief animalhuman contacts (e.g. farm visits), 10 on environmental exposures and 15 on zoonoses in developing countries where backyard livestock keeping is still customary. 43 studies reported zoonotic risks in different occupations. Occupations at risk included veterinarians, culling personnel, slaughterhouse workers and farmers. For culling personnel, more hours exposed to livestock resulted in more frequent occurrence of transmission. Slaughterhouse workers in contact with live animals were more often positive for zoonotic micro-organisms compared to co-workers only exposed to carcasses. Overall, little information was available about the actual mode of micro-organism transmission. Conclusions: Little is known about the intensity and type of contact patterns between livestock and humans that result in micro-organism transmission. Studies performed in occupational settings provide some, but limited evidence of exposure response-like relationships for livestock-human contact and micro-organism transmission. Better understanding of contact patterns driving micro-organism transmission from animals to humans is needed to provide options for prevention and thus deserves more attention. 
 Title: Human-livestock contacts and their relationship to transmission of zoonotic pathogens, a systematic review of literature-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/)
Output: True
Paragraph: The mammalian eye is protected against pathogens and infl ammation in a relatively immune-privileged environment. Stringent mechanisms are activated that regulate external injury, infection, and autoimmunity. The eye contains a variety of cells expressing vasoactive neuropeptides (VNs), and their receptors, located in the sclera, cornea, iris, ciliary body, ciliary process, and the retina. VNs are important activators of adenylate cyclase, deriving cyclic adenosine monophosphate (cAMP) from adenosine triphosphate (ATP). Impairment of VN function would arguably impede cAMP production and impede utilization of ATP. Thus VN autoimmunity may be an etiological factor in retinopathy involving perturbations of purinergic signaling. A sound blood supply is necessary for the existence and functional properties of the retina. This paper postulates that impairments in the endothelial barriers and the blood-retinal barrier, as well as certain infl ammatory responses, may arise from disruption to VN function. Phosphodiesterase inhibitors and purinergic modulators may have a role in the treatment of postulated VN autoimmune retinopathy. 
 Title: Vasoactive neuropeptides in clinical ophthalmology: An association with autoimmune retinopathy?
Output: True
Paragraph: This study used the Technology Acceptance Model (TAM) to examine taxpayers' acceptance of the Internet tax-filing system. Based on data collected from 141 experienced taxpayers in Taiwan, the acceptance and the impact of quality antecedents on taxpayers' perceived usefulness (PU) and perceived ease of use (PEOU) of the system were assessed and evaluated. The results indicated that the model of Internet tax-filing system was accepted with a reasonable goodness-of-fit. Three important findings include the following items. First, TAM proves to be a valid model to explain the taxpayers' acceptance of the Internet tax-filers' system. Meanwhile, PU has created more impact than PEOU on taxpayers' intention to use the system. Second, PU is positively influenced by such factors as information system quality (ISQ), information quality (IQ), as well as perceived credibility (PC). Third, IQ has a positive impact on PEOU. Based on the research findings, implications and limitations are then discussed for future possible research. D 2005 Elsevier Inc. All rights reserved. Keywords: Technology acceptance model (TAM); DeLone and McLean model (D&M model); Internet tax-filing acceptance 0740-624X/$ -see front matter D 
 Title: An empirical study on the impact of quality antecedents on tax payers' acceptance of Internet tax-filing systems
Output: True
Paragraph: A rapid review was performed to determine (1) the number and causes of reported laboratory-acquired infections (LAI) in the Asia-Pacific region; (2) their significance and threat to the community; (3) the primary risk factors associated with LAIs; (4) the consequences in the event of a LAI or pathogen escape; and (5) to make general recommendations regarding biosafety practices for diagnosis and research in the Asia-Pacific region. A search for LAI and zoonoses in the Asia-Pacific region using online search engines revealed a relatively low number of reports. Only 27 LAI reports were published between 1982 and 2016. The most common pathogens associated with LAIs were dengue virus, Arthroderma spp., Brucella spp., Mycobacterium spp., Rickettsia spp., and Shigella spp. Seventy-eight percent (21 out of 27 LAI reports) occurred in high-income countries (i.e., Australia, Japan, South Korea, Singapore, and Taiwan) where laboratories were likely to comply with international biosafety standards. Two upper-middle income countries (China (2), and Malaysia (2)) and one lower-middle income country (India (2)) reported LAI incidents. The majority of the reports (fifty-two percent (14/27)) of LAIs occurred in research laboratories. Five LAI reports were from clinical or diagnostic laboratories that are considered at the frontier for zoonotic disease detection. Governments and laboratories in the Asia-Pacific region should be encouraged to report LAI cases as it provides a useful tool to monitor unintended release of zoonotic pathogens and to further improve laboratory biosafety. Non-reporting of LAI events could pose a risk of disease transmission from infected laboratory staff to communities and the environment. The international community has an important and continuing role to play in supporting laboratories in the Asia-Pacific region to ensure that they maintain the safe working environment for the staff and their families, and the wider community. 
 Title: Tropical Medicine and Infectious Disease A Review of Laboratory-Acquired Infections in the Asia-Pacific: Understanding Risk and the Need for Improved Biosafety for Veterinary and Zoonotic Diseases
Output: False
Paragraph: Hepatitis C virus (HCV) induces cytopathic effects in the form of hepatocytes apoptosis thought to be resulted from the interaction between viral proteins and host factors. Using pathway specific PCR array, we identified 9 apoptosis-related genes that are dysregulated during HCV infection, of which the BH3only pro-apoptotic Bcl-2 family protein, BIK, was consistently up-regulated at the mRNA and protein levels. Depletion of BIK protected host cells from HCV-induced caspase-3/7 activation but not the inhibitory effect of HCV on cell viability. Furthermore, viral RNA replication and release were significantly suppressed in BIK-depleted cells and over-expression of the RNA-dependent RNA polymerase, NS5B, was able to induce BIK expression. Immunofluorescence and co-immunoprecipitation assays showed co-localization and interaction of BIK and NS5B, suggesting that BIK may be interacting with the HCV replication complex through NS5B. These results imply that BIK is essential for HCV replication and that NS5B is able to induce BIK expression. 
 Title: NS5B induces up-regulation of the BH3-only protein, BIK, essential for the hepatitis C virus RNA replication and viral release
Output: True
Paragraph: Bacterial and viral co-infections of the respiratory tract are life-threatening and present a global burden to the global community. Staphylococcus aureus, Streptococcus pneumoniae, and Streptococcus pyogenes are frequent colonizers of the upper respiratory tract. Imbalances through acquisition of seasonal viruses, e.g., Influenza A virus, can lead to bacterial dissemination to the lower respiratory tract, which in turn can result in severe pneumonia. In this review, we summarize the current knowledge about bacterial and viral co-infections of the respiratory tract and focus on potential experimental models suitable for mimicking this disease. Transmission of IAV and pneumonia is mainly modeled by mouse infection. Few studies utilizing ferrets, rats, guinea pigs, rabbits, and non-human primates are also available. The knowledge gained from these studies led to important discoveries and advances in understanding these infectious diseases. Nevertheless, mouse and other infection models have limitations, especially in translation of the discoveries to humans. Here, we suggest the use of human engineered lung tissue, human ex vivo lung tissue, and porcine models to study respiratory co-infections, which might contribute to a greater translation of the results to humans and improve both, animal and human health. 
 Title: Port d'Entrée for Respiratory Infections -Does the Influenza A Virus Pave the Way for Bacteria?
Output: False
Paragraph: Separation of DNA replication and transcription, which occur in the nucleus, from protein syn thesis, which occurs in the cytoplasm, allows a more precise regulation of these processes. Selective exchange of macromolecules between the two compartments is mediated by proteins of the nuclear pore complex (NPC). Receptor proteins of the karyopherin family interact with NPC components and transfer their cargos between the nucleus and cytoplasm. Nucleocytoplasmic transport pathways are regulated at multiple levels by modulating the expression or function of individual cargoes, transport receptors, or the transport channel. The regulatory levels have increasingly broad effects on the transport pathways and affect a wide range of pro cesses from gene expression to development and differentiation. 
 Title: Original Russian Text ©
Output: True
Paragraph: Zika virus (ZIKV) infection can cause severe congenital diseases, such as microcephaly, ocular defects and arthrogryposis in fetuses, and Guillain-Barré syndrome in adults. Efficacious therapeutic treatments for infected patients, as well as prophylactic treatments to prevent new infections are needed for combating ZIKV infection. Here, we report that ZIKV-specific human polyclonal antibodies (SAB-155), elicited in transchromosomal bovine (TcB), provide significant protection from infection by ZIKV in STAT2 knockout (KO) golden Syrian hamsters both prophylactically and therapeutically. These antibodies also prevent testicular lesions in this hamster model. Our data indicate that antibody-mediated immunotherapy is effective in treating ZIKV infection. Because suitable quantities of highly potent human polyclonal antibodies can be quickly produced from the TcB system against ZIKV and have demonstrated therapeutic efficacy in a small animal model, they have the potential as an effective countermeasure against ZIKV infection. 
 Title: Human Polyclonal Antibodies Produced from Transchromosomal Bovine Provides Prophylactic and Therapeutic Protections Against Zika Virus Infection in STAT2 KO Syrian Hamsters
Output: True
Paragraph: Coronavirus particles serve three fundamentally important functions in infection. The virion provides the means to deliver the viral genome across the plasma membrane of a host cell. The virion is also a means of escape for newly synthesized genomes. Lastly, the virion is a durable vessel that protects the genome on its journey between cells. This review summarizes the available X-ray crystallography, NMR, and cryoelectron microscopy structural data for coronavirus structural proteins, and looks at the role of each of the major structural proteins in virus entry and assembly. The potential wider conservation of the nucleoprotein fold identified in the Arteriviridae and Coronaviridae families and a speculative model for the evolution of corona-like virus architecture are discussed. 
 Title: Supramolecular Architecture of the Coronavirus Particle
Output: True
Paragraph: Databases and computational tools for mimotopes have been an important part of phage display study. Five special databases and eighteen algorithms, programs and web servers and their applications are reviewed in this paper. Although these bioinformatics resources have been widely used to exclude target-unrelated peptides, characterize small molecules-protein interactions and map protein-protein interactions, a lot of problems are still waiting to be solved. With the improvement of these tools, they are expected to serve the phage display community better. 
 Title: molecules Bioinformatics Resources and Tools for Phage Display
Output: True
Paragraph: Mice expressing the Cre recombinase from within the lysozyme M locus (LysMcre mice) were purchased from the Jackson Laboratory (Strain # 004781). Atg5 flox/flox and Atg5 flox/flox +LysMcre mice with two different backgrounds ( Figures 1C and 1D from mixed 129-C57BL/6 mice and all the others from C57BL/6 mice) were used for this study and consistent phenotypes between different backgrounds were observed. To generate bone marrow derived macrophages (BMDM), mouse bone marrows were isolated and cultured on non-tissue-culture treated plate for 7 days in BMDM media (Dulbeco's Modified Eagle Medium, 10% fetal bovine serum, 5% horse serum, 10% CMG14-12 (Takeshita et al., 2000) , 1x MEM nonessential amino acids, 1mM sodium pyruvate, 2 mM L-glutamine). At day 7, adherent BMDMs were dissociated from the plate and set up for experiment. At day 10, media were changed to fresh media and IFNγ were treated if necessary. At day 11, cells were used for MNV infection or autophagy analysis. Depending on the deletion status of floxed gene (e.g. Atg7 flox/flox +LysMcre), BMDMs were cultured up to 21 days and used for infection study. For EMCV and MHV, BMDMs were prepared as previously described (Zhao et al., 2007) . 
 Title: Cell Host & Microbe Supplemental Information Nondegradative Role of Atg5-Atg12/ Atg16L1 Autophagy Protein Complex in Antiviral Activity of Interferon Gamma
Output: False
Paragraph: In order to determine the minimum RNase A concentration to degrade siRNA completely, siRNA (300 ng) was incubated with different amounts of RNase A in TE 1X pH 8 buffer (0.02, 0.07, 0.162, 0.348, 0.7, and 3.3 g RNase A per 1 g siRNA) for 45 min at 37C, in presence or absence of RiboLock ® RNase Inhibitor (RI, 1L = 40U). The concentration of 0.35 g RNase A per 1 g siRNA has been reported in literature to be enough to degrade a large fraction of siRNA in polyplexes, 1, 2 and based on that, the amount of RNase A was varied in this experiment. Next, samples were frozen at -20C overnight, and loaded in the slots of casted agarose gel (1.5 % w/v in TAE 1X pH 8.2 buffer) stained with ethidium bromide (0.5 g  mL -1 ). The electrophoresis was performed at 60V (E0160-VWR Mini Gel Electrophoresis) for 40 min, and the siRNA-dye migration was visualized under UV irradiation (FOTO/Analyst ® Investigator/Eclipse with UV Transilluminator Fotodyne Inc.) and the images were recorded using the FOTO/Analyst ® PC Image software (v.5). The result is shown in Figure S1 , and clearly indicates that free siRNA (not protected by RNase inhibitor) was completely degraded by RNAse A starting at concentration 0.162 g RNase A per 1 g siRNA, since no siRNA band was observed in lane 6 compared to lane 7 and lane 1. 
 Title: Poly(amidoamine) Dendrimer Nanocarriers and their Aerosol Formulations for siRNA Delivery to the Lung Epithelium
Output: True
Paragraph: Multilateral agencies define and operationalized health and development in a variety of ways. The World Health Organization (WHO) and the World Bank are two dominant actors in health and development. Each espouses a different ideal of health as it relates to the process of development. The WHO defines health as a human right, and focuses on health outcomes as inputs to and the result of development. The World Bank's approach to development focuses largely on macro-economic growth as input to human capabilities. The World Bank became a leading actor in international health policy in the 1990s when it operationalized health as an outcome of financial and health care systems. This chapter looks at programming efforts by the WHO and the World Bank to foster development via investment in health or through macro-economic adjustment. Results are mixed. Efforts to improve primary care were successful in improving health outcomes of children under five, but made little impact on maternal mortality. Structural adjustment programs achieved moderate success with medium-to long-term economic growth but increased health inequities. These mixed achievements resulted in an effort by the United Nations to foster a multi-sectoral approach to development espoused in the Millennium Development Goals and Sustainable Development Goals. 
 Title: International Organizations and Their Approaches to Fostering Development
Output: True
Paragraph: Background: Although allergic asthma is a complex area with many interacting factors involved, the 'hygiene hypothesis' proposes that a lack of exposure to infection during childhood may polarise the immune system towards allergen-reactive Th2-type responses in genetically susceptible individuals. Toll-like receptors (TLRs) play a key role within the innate immune system and TLR7 agonists have previously been shown to up-regulate Th1 responses and down-regulate Th2 responses to allergens in murine models of allergic or chronic asthma. This study aimed to examine the efficacy and safety of the novel TRL7 agonist AZD8848, which has been developed as an antedrug. Methods: In this double-blind, randomised, parallel-group study, AZD8848 60 μg or placebo was administered intranasally once-weekly for 8 weeks in patients with mild-to-moderate allergic asthma (NCT00999466). Efficacy assessments were performed at 1 and 4 weeks after the last dose. The primary outcome was the late asthmatic response (LAR) fall in forced expiratory volume in 1 s (FEV 1 ) after allergen challenge at 1-week post-treatment. Results: AZD8848 significantly reduced average LAR fall in FEV 1 by 27% vs. placebo at 1 week after treatment (p = 0.035). This effect was sustained at 4 weeks post-treatment; however, it did not reach clinical significance. AZD8848 reduced post-allergen challenge methacholine-induced airway hyper-responsiveness (AHR) vs. placebo at 1 week post-dosing (treatment ratio: 2.20, p = 0.024), with no effect at 4 weeks. There was no significant difference between the two groups in plasma cytokine, sputum Th2 cytokine or eosinophil responses post-allergen challenge at 1 week after treatment. The incidence of adverse events was similar in the two groups. AZD8848 was generally well tolerated. Conclusions and clinical relevance: In patients with allergic asthma, TLR7 agonists could potentially reduce allergen responsiveness by stimulating Type 1 interferon responses to down-regulate the dominant Th2 responses. Trial registration: clinicaltrials.gov identifier NCT00999466. 
 Title: Effects of the Toll-like receptor 7 (TLR7) agonist, AZD8848, on allergen-induced responses in patients with mild asthma: a double-blind, randomised, parallel-group study
Output: False
Paragraph: Aims: This paper aims to summarise the growing literature concerning an imminent future influenza pandemic, from the primary care perspective. Methods: Sources of literature were scanned and relevant material short-listed for further study from: (1) WHO and CDC websites; (2) PUBMED; and (3) papers mentioned in references of full-text papers. Results: Outbreaks of avian influenza in Asia and elsewhere indicate that the world may be moving towards a pandemic influenza outbreak. The WHO Global Influenza Preparedness Plan 2005 unifies the world with the vision of tackling the next pandemic influenza outbreak as a global effort that includes healthcare provider and patient alike. Conclusions: We need to update ourselves and keep our staff and patients informed to make infection control measures part of our daily activities. In areas where there are contacts with animal reservoirs of influenza A, patients need to be reminded that they need to protect themselves from being infected. 
 Title: The pandemic influenza threat: a review from the primary care perspective
Output: False
Paragraph: The cleavage mechanism of severe acute respiratory syndrome (SARS) coronavirus main proteinase (M pro or 3CL pro ) for the octapeptide AVLQSGFR is studied using molecular mechanics (MM) and quantum mechanics (QM). The catalytic dyad His-41 and Cys-145 in the active pocket between domain I and II seem to polarize the -electron density of the peptide bond between Gln and Ser in the octapeptide, leading to an increase of positive charge on C(CO) of Gln and negative charge on N(NH) of Ser. The possibility of enhancing the chemical bond between Gln and Ser based on the "distorted key" theory [Anal. Biochem. 233 (1996) 1] is examined. The scissile peptide bond between Gln and Ser is found to be solidified through "hybrid peptide bond" by changing the carbonyl group CO of Gln to CH 2 or CF 2 . This leads to a break of the -bond system for the peptide bond, making the octapeptide (AVLQSGFR) a "distorted key" and a potential starting system for the design of anti SARS drugs. 
 Title: Polyprotein cleavage mechanism of SARS CoV M pro and chemical modification of the octapeptide
Output: True
Paragraph: Background: Severe acute respiratory syndrome (SARS) is a recently recognized condition of viral origin associated with substantial morbidity and mortality rates in adults. Little information is available on its radiologic manifestations in children. Objective: The goal of this study was to characterize the radiographic presentation of children with SARS. Materials and methods: We abstracted data (n=62) on the radiologic appearance and course of SARS in pediat-ric patients with suspect (n=25) or probable (n=37) SARS, diagnosed in five hospital sites located in three cities: Toronto, Singapore, and Hong Kong. Available chest radiographs and thoracic CTs were reviewed for the presence of the following radiographic findings: airspace disease, air bronchograms, airways inflammation and peribronchial thickening, interstitial disease, pleural effusion, and hilar adenopathy. Results: A total of 62 patients (suspect=25, probable=37) were evaluated for SARS. Patient ages ranged from 5.5 months to 17 years and 11.5 months (average, 6 years and 10 months) with a female-tomale ratio of 32:30. Forty-one patients (66.1%) were in close contact with other probable, suspect, or quarantined cases; 10 patients (16.1%) had recently traveled to WHO-designated affected areas within 10 days; and 7 patients (11.2%) were transferred from other hospitals that had SARS patients. Three patients, who did not have close/hospital contact or travel history to affected areas, were classified 
 Title: Severe acute respiratory syndrome (SARS): chest radiographic features in children
Output: True
Paragraph: Data are limited regarding 2 new human polyomaviruses, KI polyomavirus (KIPyV) and WU polyomavirus (WUPyV), in immunocompromised patients. We used realtime PCR to test for these and 12 respiratory viruses in 2,732 nasal wash samples collected during the fi rst year after allogeneic hematopoietic cell transplantation from 222 patients. Specimens were collected weekly until day 100; then at least every 3 months. One year after hematopoietic cell transplantation, the cumulative incidence estimate was 26% for KIPyV and 8% for WUPyV. Age <20 years predicted detection of KIPyV (hazard ratio [HR] 4.6) and WUPyV (HR 4.4), and detection of a respiratory virus in the previous 2 weeks predicted KIPyV detection (HR 3.4). Sputum production and wheezing were associated with detection of KIPyV in the past week and WUPyV in the past month. There were no associations with polyomavirus detection and acute graft versus host disease, cytomegalovirus reactivation, neutropenia, lymphopenia, hospitalization, or death. 
 Title: WU and KI Polyomaviruses in Respiratory Samples from Allogeneic Hematopoietic Cell Transplant Recipients
Output: False
Paragraph: This paper characterises a virulent strain (CB/05) of canine coronavirus (CCoV) isolated from the internal organs of pups that had died of a systemic disease without evidence of other common canine pathogens. High viral RNA titres were detected in the internal organs by a real-time RT-PCR assay specific for CCoV type II. Sequence analysis of the 3 end (8.7 kb) of the genomic RNA of strain CB/05 revealed conserved structural as well as non-structural proteins, with the exception of a truncated form of non-structural protein 3b. The exceptional form was due to a 38-nucleotide deletion and a frame shift in ORF3b that introduced an early stop codon. By phylogenetic analysis of the structural proteins, the spike (S) protein was found to cluster with feline coronavirus type II strain 79-1683, whereas, the envelope (E), membrane (M) and nucleocapsid (N) proteins segregated together with the reference strain Purdue of transmissible gastroenteritis virus of swine. 
 Title: Molecular characterisation of the virulent canine coronavirus CB/05 strain ଝ
Output: False
Paragraph: Prohibitins (PHBs) are scaffold proteins that modulate many signaling pathways controlling cell survival, metabolism, and inflammation. Several drugs that target PHBs have been identified and evaluated for various clinical applications. Preclinical and clinical studies indicate that these PHB ligands may be useful in oncology, cardiology, and neurology, as well as against obesity. This review covers the physiological role of PHBs in health and diseases and current developments concerning PHB ligands. 
 Title: Chemistry & Biology Review Prohibitin Ligands in Cell Death and Survival: Mode of Action and Therapeutic Potential
Output: False
Paragraph: Infectious diseases represent a continuous and increasing threat to human health and welfare. Due to emerging diseases, increasing resistances, international travelling, and the risk of bioterroristic attacks, infectious diseases concern the whole world and can only be combated by internationally coordinated and interdisciplinary approaches. When assessing the worldwide publication activities on infectious diseases in the years 1994-2004 accessible via the ISI Science Citation Index Expanded s , an overall increase by 24% can be monitored. Furthermore, it becomes evident that highest research priorities are given to HIV/AIDS, hepatitis C, tuberculosis, respiratory infections, and sepsis. Ten countries -including the USA, the UK, France, Germany, and Japan -contributed to more than 80% of these publications; nation-specific research priorities focusing on the current problems in the respective country can be estimated. Countries with the highest disease burdens are still not given the opportunity to contribute adequately to the scientific field. Based on our data, relatively increasing publication activities include those on respiratory infections, tuberculosis, malaria, hepatitis, and sepsis, whereas decreasing activities were determined for AIDS, diarrhoea, meningitis, schistosomiasis, and other diseases. Accordingly, the prevalence of many infectious diseases occurring in tropical countries is not clearly reflected in the worldwide publication activities. 
 Title: Infectious diseases -A global challenge
Output: True
Paragraph: In leporids, IL17A had been implicated in the host defense against extracellular pathogens, such as Francisella tularensis that infects hares and rabbits and causes the zoonotic disease tularemia. Here, we studied IL17A from five lagomorphs, European rabbit, pygmy rabbit, brush rabbit, European brown hare, and American pika. We observed that this protein is highly conserved between these species, with a similarity of 97-99% in leporids and ∼88% between leporids and American pika. The exon/intron structure, Nglycosylation sites, and cysteine residues are conserved between lagomorphs. However, at codon 88, one of the interaction sites between IL17A and its receptor IL17RA, there is an Arg>Pro mutation that only occurs in European rabbit and European brown hare. This could induce critical alterations in the IL17A structure and conformation and consequently modify its function. The differences observed between leporids and humans or rodents might also represent important alterations in protein structure and function. In addition, as for other interleukins, IL17A sequences of human and European rabbit are more closely related than the sequences of human and mouse or European rabbit and mouse. This study gives further support to the hypothesis that European rabbit might be a more suitable animal model for studies on human IL17. 
 Title: Evolutionary Insights into IL17A in Lagomorphs
Output: True
Paragraph: Several serological interrelationships between various members of the coronavirus group have been revealed in neutralization, complement fixation, and geldiffusion tests, using human and hyperimmune animal sera. Several members of this group of human and animal pathogens are shown to cross-react in one or more type of test, but one member, avian infectious bronchitis virus, was shown to be unrelated. Mouse hepatitis virus (MHVs) was found to be antigenieally related to a number of human types of coronavirus. Difficulties were encountered in the investigation of paired human sera in demonstrating the specificity of antibody rises, placing doubt on the values of some serological studies. The significance of these interrelationships is discussed in the light of other investigations. BRADBURNE : Antigenic Relationships amongst Coronaviruses 353 organ cultures of human embryo nasal and tracheal epithelium. These isolates comprise at least three, and probably more, distinct serological types as judged by neutralization tests using convalescent human sera (B~A]) BUR~ and T~R~IiL, 1969; McI~Tos~ et al., 1969). This work describes the detection of several serological relationships between the viruses isolated from man, and those of mouse hepatitis and avian infectious bronchitis. The majority of these results were obtained before similar studies were reported by MCINTos~ et al. (1969); furthermore, different reagents were used and several extra cross-reactions were detected. 2.1. Tissue Cultures These were all propagated in this laboratory. Roller tube neutralization tests were performed in monolayer cultures of human embryo diploid lung cells (HDCS). These were either a strain derived at the Unit, or the WI-38 cell strain. Plaque neutralization tests were made using monolayers of L 132 cells in 50 mm plastic Pctri dishes (Sterilin). The L 132 cell line is a continuous epitheloid cell line which was derived from human embryo lung (DAvis, 1960) and has been shown to be sensitive to several respiratory viruses, including 4 strains of coronaviruses (BRAD-]~Vl~N]~, 1969). All cultures were maintained at 33~ after inoculation. 
 Title: Antigenic Relationships amongst Coronaviruses
Output: True
Paragraph: New variants of infectious bronchitis virus (IBV) have emerged in Australia despite its geographical isolation and intensive vaccination programs. In the present study, the 3 0 terminal 7.2 kb of the genome of a recently isolated variant of IBV (N1/03) was sequenced and compared with the sequences of classical and novel strains of IBV, the two main groups of these viruses in Australia. The comparison revealed that recombination between classical and novel IBVs was responsible for the emergence of the new variant. It was concluded that novel IBVs, which have not been detected since 1993, and which are phylogenically more distant from classical IBVs than turkey coronaviruses, might still be circulating and contributing to the evolution of IBV in Australia. 
 Title: Naturally occurring recombination between distant strains of infectious bronchitis virus
Output: True
Paragraph: Zika flavivirus infection during pregnancy appears to produce higher risk of microcephaly, and also causes multiple neurological problems such as Guillain-Barré syndrome. The Zika virus is now widespread in Central and South America, and is anticipated to become an increasing risk in the southern United States. With continuing global travel and the spread of the mosquito vector, the exposure is expected to accelerate, but there are no currently approved treatments against the Zika virus. The Zika NS2B/NS3 protease is an attractive drug target due to its essential role in viral replication. Our studies have identified several compounds with inhibitory activity (IC 50 ) and binding affinity (K D ) of ∼5-10 μM against the Zika NS2B-NS3 protease from testing 71 HCV NS3/NS4A inhibitors that were initially discovered by high-throughput screening of 40,967 compounds. Competition surface plasmon resonance studies and mechanism of inhibition analyses by enzyme kinetics subsequently determined the best compound to be a competitive inhibitor with a K i value of 9.5 μM. We also determined the X-ray structure of the Zika NS2B-NS3 protease in a "pre-open conformation", a conformation never observed before for any flavivirus proteases. This provides the foundation for new structure-based inhibitor design. Zika flavivirus; NS2B/NS3 serine protease; Small molecule inhibitor; apo ZIKV NS2B-NS3 pro structure Lee et al. 
 Title: Identification of novel small molecule inhibitors against NS2B/NS3 serine protease from Zika virus Graphical abstract HHS Public Access
Output: True
Paragraph: The study of this chapter will enable you to: 1. Discuss the importance of the Department of Health and Human Services (HHS) Category C agents. List the most important pathogens currently found on the HHS Category C list. 3. Discuss the recent history of Nipah virus, hantavirus, West Nile fever virus, and the coronaviruses that are the causes of severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS). West Nile fever, SARS, and MERS. Understand the challenges that public health officials and emergency management practitioners might face when an intentional release of a Category C agent occurs in their community. 
 Title: Category C Diseases and Agents Where the telescope ends, the microscope begins. Which of the two has the grander view?
Output: True
Paragraph: This study proposes an optimization model for optimal treatment of bacterial infections. Using an influence diagram as the knowledge and decision model, we can conduct two kinds of reasoning simultaneously: diagnostic reasoning and treatment planning. The input information of the reasoning system are conditional probability distributions of the network model, the costs of the candidate antibiotic treatments, the expected effects of the treatments, and extra constraints regarding belief propagation. Since the prevalence of the pathogens and infections are determined by many site-by-site factors, which are not compliant with conventional approaches for approximate reasoning, we introduce fuzzy information. The output results of the reasoning model are the likelihood of a bacterial infection, the most likely pathogen(s), the suggestion of optimal treatment, the gain of life expectancy for the patient related to the optimal treatment, the probability of coverage associated with the antibiotic treatment, and the cost-effect analysis of the treatment prescribed. 
 Title: A diagnostic reasoning and optimal treatment model for bacterial infections with fuzzy information
Output: False
Paragraph: In this paper, we propose to advance and transform today's healthcare system using a model of networked health care called Cybercare. Cybercare means "health care in cyberspace"for example, doctors consulting with patients via videoconferencing across a distributed network; or patients receiving care locallyin neighborhoods, "minute clinics," and homesusing information technologies such as telemedicine, smartphones, and wearable sensors to link to tertiary medical specialists. This model contrasts with traditional health care, in which patients travel (often a great distance) to receive care from providers in a central hospital. The Cybercare model shifts health care provision from hospital to home; from specialist to generalist; and from treatment to prevention. Cybercare employs advanced technology to deliver services efficiently across the distributed networkfor example, using telemedicine, wearable sensors and cell phones to link patients to specialists and upload their medical data in near-real time; using information technology (IT) to rapidly detect, track, and contain the spread of a global pandemic; or using cell phones to manage medical care in a disaster situation. Cybercare uses seven "pillars" of technology to provide medical care: genomics; telemedicine; robotics; simulation, including virtual and augmented reality; artificial intelligence (AI), including intelligent agents; the electronic medical record (EMR); and smartphones. All these technologies are evolving and 
 Title: Cybercare 2.0: meeting the challenge of the global burden of disease in 2030
Output: True
Paragraph: Infection is an important cause of stillbirth world-wide; in low and middle income countries (LMICs), 50% or more are likely caused by infection. In contrast, in high income countries, only10-25% of stillbirths are caused by infection. Syphilis, where prevalent, causes the majority of infectious stillbirths and is the infection most amenable to screening and treatment. Ascending bacterial infection is a common cause of stillbirth, but prevention has proven elusive. Many viral infections are causal for stillbirth but aside from vaccination for common childhood diseases, it is unclear how most viral-caused stillbirths may be prevented. Malaria, because of its high prevalence and extensive placental damage accounts for large numbers of stillbirths. Intermittent malarial prophylaxis and insecticide impregnated bed nets should decrease stillbirths. Many animal and vector-borne infections cause stillbirth. Because this relationship is especially important in LMICs, research that more clearly defines this relationship is crucial to reduce the unacceptably high stillbirth rates in those areas. 
 Title: INFECTION -RELATED STILLBIRTHS
Output: False
Paragraph: Autophagy is a cellular process that catabolizes cytoplasmic components and maintains energy homeostasis. As a stress response, the autophagy machinery interconnects a wide range of cellular pathways, enhancing the spread of certain pathogens while limiting others, and has become a highly active research area over the past several years. Independent laboratories have recently reported that autophagy vesicles accumulate in hepatitis C virus (HCV) infected cells and that autophagy proteins can function as proviral factors required for HCV replication. In this review, we summarize what is currently known about the interplay between autophagy and HCV and the possible mechanisms whereby autophagy proteins might favor HCV propagation. 
 Title: Impact of the Autophagy Machinery on Hepatitis C Virus Infection
Output: True
Paragraph: The cheetah population in Namibia is the largest free-ranging population in the world and a key population for research regarding the health status of this species. We used serological methods and quantitative real-time PCR to test free-ranging and captive Namibian cheetahs for the presence of feline leukemia virus (FeLV), a gammaretrovirus that can be highly aggressive in populations with low genetic diversity, such as cheetahs. We also assessed the presence of antibodies to other gammaretroviruses and the responses to a FeLV vaccine developed for domestic cats. Up to 19% of the free-ranging cheetahs, 27% of the captive nonvaccinated cheetahs, and 86% of the captive vaccinated cheetahs tested positive for FeLV antibodies. FeLV-antibody-positive freeranging cheetahs also tested positive for Rauscher murine leukemia virus antibodies. Nevertheless, FeLV was not detectable by quantitative real-time PCR and no reverse transcriptase activity was detectable by product-enhanced reverse transcriptase assay in the plasma of cheetahs or the supernatants from cultures of peripheral blood mononuclear cells. The presence of antibodies to gammaretroviruses in clinically healthy specimens may be caused either by infection with a low-pathogenic retrovirus or by the expression of endogenous retroviral sequences. The strong humoral immune responses to FeLV vaccination demonstrate that cheetahs can respond to the vaccine and that vaccination against FeLV infection may be beneficial should FeLV infection ever become a threat, as was seen in Iberian lynx and Florida panthers. 
 Title: Gammaretrovirus-Specific Antibodies in Free-Ranging and Captive Namibian Cheetahs
Output: False
Paragraph: In this contribution, the classification of protein binding sites using the physicochemical properties exposed to their pockets is presented. We recently introduced Cavbase, a method for describing and comparing protein binding pockets on the basis of the geometrical and physicochemical properties of their active sites. Here, we present algorithmic and methodological enhancements in the Cavbase property description and in the cavity comparison step. We give examples of the Cavbase similarity analysis detecting pronounced similarities in the binding sites of proteins unrelated in sequence. A similarity search using SARS M pro protease subpockets as queries retrieved ligands and ligand fragments accommodated in a physicochemical environment similar to that of the query. This allowed the characterization of the protease recognition pockets and the identification of molecular building blocks that can be incorporated into novel antiviral compounds. A cluster analysis procedure for the functional classification of binding pockets was implemented and calibrated using a diverse set of enzyme binding sites. Two relevant protein families, the a-carbonic anhydrases and the protein kinases, are used to demonstrate the scope of our cluster approach. We propose a relevant classification of both protein families, on the basis of the binding motifs in their active sites. The classification provides a new perspective on functional properties across a protein family and is able to highlight features important for potency and selectivity. Furthermore, this information can be used to identify possible cross-reactivities among proteins due to similarities in their binding sites. 
 Title: From the Similarity Analysis of Protein Cavities to the Functional Classification of Protein Families Using Cavbase Keywords: protein binding pockets; classification of protein binding pockets; cluster analysis of protein binding pockets; protein kinases; SARS protease
Output: True