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                  <text>Coronavirus</text>
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                  <text>Dominio científico: Coronavirus</text>
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                <text>IL-12 RB1 genetic variants contribute to human susceptibility to severe acute respiratory syndrome infection among Chinese.</text>
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                <text>Fang Tang, Wei Liu, Fang Zhang, Zhong-Tao Xin, Mao-Ti Wei, Pan-He Zhang, Hong Yang, Hinh Ly, Wu-Chun Cao</text>
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                <text>BACKGROUND: Cytokines play important roles in antiviral action. We examined whether polymorphisms of interleukin (IL)-12 receptor B1 (IL-12RB1) affect the susceptibility to and outcome of severe acute respiratory syndrome (SARS). METHODS: A case-control study was carried out in Chinese SARS patients and healthy controls. The genotypes of 4SNPs on IL-12 RB1 gene, +705A/G,+1158T/C, +1196G/C and +1664 C/T, were determined by PCR-RFLP. Haplotypes were estimated from the genotype data using the expectation-maximisation algorithm. RESULTS: Comparison between patients and close contacts showed that individuals with the +1664 C/T (CT and TT) genotype had a 2.09-fold (95% confidence interval [CI], 1.90-7.16) and 2.34-fold (95% CI, 1.79-13.37) increased risk of developing SARS, respectively. For any of the other three polymorphisms, however, no significant difference can be detected in allele or genotype frequencies between patients and controls. Additionally, estimation of the frequencies of multiple-locus haplotypes revealed potential risk haplotypes (GCCT) for SARS infection. CONCLUSIONS: Our data indicate that genetic variants of IL12RB1confer genetic susceptibility to SARS infection, but not necessary associated with the progression of the disease in Chinese population.</text>
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                <text>DOI: 10.1371/journal.pone.0002183</text>
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                <text>PLoS ONE</text>
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                  <text>Dominio científico: Coronavirus</text>
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                <text>A k-mer-based method for the identification of phenotype-associated genomic biomarkers and predicting phenotypes of sequenced bacteria.</text>
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                <text>Erki Aun, Age Brauer, Veljo Kisand, Tanel Tenson, Maido Remm</text>
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                <text>We have developed an easy-to-use and memory-efficient method called PhenotypeSeeker that (a) identifies phenotype-specific k-mers, (b) generates a k-mer-based statistical model for predicting a given phenotype and (c) predicts the phenotype from the sequencing data of a given bacterial isolate. The method was validated on 167 Klebsiella pneumoniae isolates (virulence), 200 Pseudomonas aeruginosa isolates (ciprofloxacin resistance) and 459 Clostridium difficile isolates (azithromycin resistance). The phenotype prediction models trained from these datasets obtained the F1-measure of 0.88 on the K. pneumoniae test set, 0.88 on the P. aeruginosa test set and 0.97 on the C. difficile test set. The F1-measures were the same for assembled sequences and raw sequencing data; however, building the model from assembled genomes is significantly faster. On these datasets, the model building on a mid-range Linux server takes approximately 3 to 5 hours per phenotype if assembled genomes are used and 10 hours per phenotype if raw sequencing data are used. The phenotype prediction from assembled genomes takes less than one second per isolate. Thus, PhenotypeSeeker should be well-suited for predicting phenotypes from large sequencing datasets. PhenotypeSeeker is implemented in Python programming language, is open-source software and is available at GitHub (https://github.com/bioinfo-ut/PhenotypeSeeker/).</text>
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                <text>2018</text>
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                <text>DOI: 10.1371/journal.pcbi.1006434</text>
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                <text>PLoS Computational Biology</text>
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                <text>Public Library of Science (PLoS)</text>
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                <text>Biology (General)</text>
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                  <text>Coronavirus</text>
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                  <text>Dominio científico: Coronavirus</text>
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                <text>Feature selection methods for identifying genetic determinants of host species in RNA viruses.</text>
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                <text>Ricardo Águas, Neil M. Ferguson</text>
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          <element elementId="41">
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            <description>An account of the resource</description>
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                <text>Despite environmental, social and ecological dependencies, emergence of zoonotic viruses in human populations is clearly also affected by genetic factors which determine cross-species transmission potential. RNA viruses pose an interesting case study given their mutation rates are orders of magnitude higher than any other pathogen--as reflected by the recent emergence of SARS and Influenza for example. Here, we show how feature selection techniques can be used to reliably classify viral sequences by host species, and to identify the crucial minority of host-specific sites in pathogen genomic data. The variability in alleles at those sites can be translated into prediction probabilities that a particular pathogen isolate is adapted to a given host. We illustrate the power of these methods by: 1) identifying the sites explaining SARS coronavirus differences between human, bat and palm civet samples; 2) showing how cross species jumps of rabies virus among bat populations can be readily identified; and 3) de novo identification of likely functional influenza host discriminant markers.</text>
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                <text>DOI: 10.1371/journal.pcbi.1003254</text>
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                <text>PLoS Computational Biology</text>
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                <text>Biology (General)</text>
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              <description>An account of the resource</description>
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                  <text>Dominio científico: Coronavirus</text>
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                <text>Using routine surveillance data to estimate the epidemic potential of emerging zoonoses: application to the emergence of US swine origin influenza A H3N2v virus.</text>
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                <text>Simon Cauchemez, Scott Epperson, Matthew Biggerstaff, David Swerdlow, Lyn Finelli, Neil M. Ferguson</text>
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                <text>BACKGROUND:Prior to emergence in human populations, zoonoses such as SARS cause occasional infections in human populations exposed to reservoir species. The risk of widespread epidemics in humans can be assessed by monitoring the reproduction number R (average number of persons infected by a human case). However, until now, estimating R required detailed outbreak investigations of human clusters, for which resources and expertise are not always available. Additionally, existing methods do not correct for important selection and under-ascertainment biases. Here, we present simple estimation methods that overcome many of these limitations. METHODS AND FINDINGS:Our approach is based on a parsimonious mathematical model of disease transmission and only requires data collected through routine surveillance and standard case investigations. We apply it to assess the transmissibility of swine-origin influenza A H3N2v-M virus in the US, Nipah virus in Malaysia and Bangladesh, and also present a non-zoonotic example (cholera in the Dominican Republic). Estimation is based on two simple summary statistics, the proportion infected by the natural reservoir among detected cases (G) and among the subset of the first detected cases in each cluster (F). If detection of a case does not affect detection of other cases from the same cluster, we find that R can be estimated by 1-G; otherwise R can be estimated by 1-F when the case detection rate is low. In more general cases, bounds on R can still be derived. CONCLUSIONS:We have developed a simple approach with limited data requirements that enables robust assessment of the risks posed by emerging zoonoses. We illustrate this by deriving transmissibility estimates for the H3N2v-M virus, an important step in evaluating the possible pandemic threat posed by this virus. Please see later in the article for the Editors' Summary.</text>
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                <text>2013</text>
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                <text>DOI: 10.1371/journal.pmed.1001399</text>
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                <text>PLoS Medicine</text>
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                <text>Public Library of Science (PLoS)</text>
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                <text>Medicine</text>
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                  <text>Dominio científico: Coronavirus</text>
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                <text>Predicting peptide structures in native proteins from physical simulations of fragments.</text>
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                <text>Vincent A. Voelz, M Scott Shell, Ken A. Dill</text>
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                <text>It has long been proposed that much of the information encoding how a protein folds is contained locally in the peptide chain. Here we present a large-scale simulation study designed to examine the extent to which conformations of peptide fragments in water predict native conformations in proteins. We perform replica exchange molecular dynamics (REMD) simulations of 872 8-mer, 12-mer, and 16-mer peptide fragments from 13 proteins using the AMBER 96 force field and the OBC implicit solvent model. To analyze the simulations, we compute various contact-based metrics, such as contact probability, and then apply Bayesian classifier methods to infer which metastable contacts are likely to be native vs. non-native. We find that a simple measure, the observed contact probability, is largely more predictive of a peptide's native structure in the protein than combinations of metrics or multi-body components. Our best classification model is a logistic regression model that can achieve up to 63% correct classifications for 8-mers, 71% for 12-mers, and 76% for 16-mers. We validate these results on fragments of a protein outside our training set. We conclude that local structure provides information to solve some but not all of the conformational search problem. These results help improve our understanding of folding mechanisms, and have implications for improving physics-based conformational sampling and structure prediction using all-atom molecular simulations.</text>
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                <text>DOI: 10.1371/journal.pcbi.1000281</text>
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                <text>PLoS Computational Biology</text>
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                  <text>Dominio científico: Coronavirus</text>
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                <text>Differential sensitivity of bat cells to infection by enveloped RNA viruses: coronaviruses, paramyxoviruses, filoviruses, and influenza viruses.</text>
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                <text>Markus Hoffmann, Marcel Alexander Müller, Jan Felix Drexler, Jörg Glende, Meike Erdt, Tim Gützkow, Christoph Losemann, Tabea Binger, Hongkui Deng, Christel Schwegmann-Weßels, Karl-Heinz Esser, Christian Drosten, Georg Herrler</text>
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                <text>Bats (Chiroptera) host major human pathogenic viruses including corona-, paramyxo, rhabdo- and filoviruses. We analyzed six different cell lines from either Yinpterochiroptera (including African flying foxes and a rhinolophid bat) or Yangochiroptera (genera Carollia and Tadarida) for susceptibility to infection by different enveloped RNA viruses. None of the cells were sensitive to infection by transmissible gastroenteritis virus (TGEV), a porcine coronavirus, or to infection mediated by the Spike (S) protein of SARS-coronavirus (SARS-CoV) incorporated into pseudotypes based on vesicular stomatitis virus (VSV). The resistance to infection was overcome if cells were transfected to express the respective cellular receptor, porcine aminopeptidase N for TGEV or angiotensin-converting enzyme 2 for SARS-CoV. VSV pseudotypes containing the S proteins of two bat SARS-related CoV (Bg08 and Rp3) were unable to infect any of the six tested bat cell lines. By contrast, viral pseudotypes containing the surface protein GP of Marburg virus from the family Filoviridae infected all six cell lines though at different efficiency. Notably, all cells were sensitive to infection by two paramyxoviruses (Sendai virus and bovine respiratory syncytial virus) and three influenza viruses from different subtypes. These results indicate that bat cells are more resistant to infection by coronaviruses than to infection by paramyxoviruses, filoviruses and influenza viruses. Furthermore, these results show a receptor-dependent restriction of the infection of bat cells by CoV. The implications for the isolation of coronaviruses from bats are discussed.</text>
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                <text>DOI: 10.1371/journal.pone.0072942</text>
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                <text>PLoS ONE</text>
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                  <text>Dominio científico: Coronavirus</text>
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                <text>Evaluation of phage display discovered peptides as ligands for prostate-specific membrane antigen (PSMA).</text>
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                <text>Duanwen Shen, Fei Xie, W Barry Edwards</text>
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                <text>The aim of this study was to identify potential ligands of PSMA suitable for further development as novel PSMA-targeted peptides using phage display technology. The human PSMA protein was immobilized as a target followed by incubation with a 15-mer phage display random peptide library. After one round of prescreening and two rounds of screening, high-stringency screening at the third round of panning was performed to identify the highest affinity binders. Phages which had a specific binding activity to PSMA in human prostate cancer cells were isolated and the DNA corresponding to the 15-mers were sequenced to provide three consensus sequences: GDHSPFT, SHFSVGS and EVPRLSLLAVFL as well as other sequences that did not display consensus. Two of the peptide sequences deduced from DNA sequencing of binding phages, SHSFSVGSGDHSPFT and GRFLTGGTGRLLRIS were labeled with 5-carboxyfluorescein and shown to bind and co-internalize with PSMA on human prostate cancer cells by fluorescence microscopy. The high stringency requirements yielded peptides with affinities KD~1 µM or greater which are suitable starting points for affinity maturation. While these values were less than anticipated, the high stringency did yield peptide sequences that apparently bound to different surfaces on PSMA. These peptide sequences could be the basis for further development of peptides for prostate cancer tumor imaging and therapy.</text>
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                <text>DOI: 10.1371/journal.pone.0068339</text>
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                <text>PLoS ONE</text>
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                  <text>Dominio científico: Coronavirus</text>
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                <text>Genetic characterization of the hemagglutinin genes of wild-type measles virus circulating in china, 1993-2009.</text>
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                <text>Song-Tao Xu, Yan Zhang, Zhen Zhu, Chunyu Liu, Naiying Mao, Yixin Ji, Hui-Ling Wang, Xiao Hong Jiang, Chongshan Li, Wei Tang, Daxing Feng, Changyin Wang, Lei Zheng, Yu eLei, Hua Ling, Chunfang Zhao, Yan MA, Jilan He, Yan Wang, Ping Li, Ronghui Guan, Shujie Zhou, Jian-Hui Zhou, Shuang Wang, Hong Zhang, Huanying Zheng, Leng Liu, Hemuti Ma, Jing Guan, Peishan Lu, Yan Feng, Yanjun Zhang, Shunde Zhou, Ying Xiong, Zhuoma Ba, Hui Chen, Xiuhui Yang, Fang Bo, Yujie Ma, Yong Liang, Yake Lei, Suyi Gu, Wei Liu, Meng Chen, David Featherstone, Youngmee Jee, William J. Bellini, Paul A. Rota, Wenbo Xu</text>
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                <text>BACKGROUND: China experienced several large measles outbreaks in the past two decades, and a series of enhanced control measures were implemented to achieve the goal of measles elimination. Molecular epidemiologic surveillance of wild-type measles viruses (MeV) provides valuable information about the viral transmission patterns. Since 1993, virologic surveillnace has confirmed that a single endemic genotype H1 viruses have been predominantly circulating in China. A component of molecular surveillance is to monitor the genetic characteristics of the hemagglutinin (H) gene of MeV, the major target for virus neutralizing antibodies. PRINCIPAL FINDINGS: Analysis of the sequences of the complete H gene from 56 representative wild-type MeV strains circulating in China during 1993-2009 showed that the H gene sequences were clustered into 2 groups, cluster 1 and cluster 2. Cluster1 strains were the most frequently detected cluster and had a widespread distribution in China after 2000. The predicted amino acid sequences of the H protein were relatively conserved at most of the functionally significant amino acid positions. However, most of the genotype H1 cluster1 viruses had an amino acid substitution (Ser240Asn), which removed a predicted N-linked glycosylation site. In addition, the substitution of Pro397Leu in the hemagglutinin noose epitope (HNE) was identified in 23 of 56 strains. The evolutionary rate of the H gene of the genotype H1 viruses was estimated to be approximately 0.76×10(-3) substitutions per site per year, and the ratio of dN to dS (dN/dS) was</text>
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                <text>2013</text>
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              <elementText elementTextId="912">
                <text>DOI: 10.1371/journal.pone.0073374</text>
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              <elementText elementTextId="913">
                <text>PLoS ONE</text>
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              <elementText elementTextId="914">
                <text>Public Library of Science (PLoS)</text>
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                  <text>Dominio científico: Coronavirus</text>
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                <text>Cyclomorphosis in Daphnia lumholtzi Sars (Crustacea: Cladocera)  -An Intermittent Species from a Subtropical Water body</text>
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              <elementText elementTextId="900">
                <text>M P Sharma and A K Dasgupta</text>
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            <description>An account of the resource</description>
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                <text>Cyclomorphosis in Daphnia lumholtzi Sars (Crustacea: Cladocera)  -An Intermittent Species from a Subtropical Water body</text>
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                <text>2015</text>
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                <text>DOI: </text>
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              <elementText elementTextId="904">
                <text>Proceedings of Indian National Science Academy</text>
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