Descriptor: "MESH: Classification" - Searchworks@Jio Institute Digital Library Search Results

Your search keyword '"MESH: Classification"' showing total 21 results

Start Over Descriptor "MESH: Classification"

21 results on '"MESH: Classification"'

1. SHAMAN: a user-friendly website for metataxonomic analysis from raw reads to statistical analysis

Author: Pierre Lechat, Laurence Motreff, Amine Ghozlane, Stevenn Volant, Christophe Malabat, Perrine Woringer, Pascal Campagne, Sean Kennedy, Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Pôle Biomics (C2RT), Centre de Ressources et de Recherche Technologique - Center for Technological Resources and Research (C2RT), Institut Pasteur [Paris] (IP)-Institut Pasteur [Paris] (IP), Institut Pasteur, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), and Institut Pasteur [Paris]-Institut Pasteur [Paris]
Subjects: Source code, Computer science, Statistics as Topic, Biochemistry, Workflow, MESH: Body Fluids, Feces, User-Computer Interface, 0302 clinical medicine, Structural Biology, RNA, Ribosomal, 16S, lcsh:QH301-705.5, media_common, Visualization, 0303 health sciences, Applied Mathematics, Microbiota, MESH: Feces, Classification, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Computer Science Applications, Body Fluids, MESH: RNA, Ribosomal, 16S, MESH: Classification, MESH: Internet, 030220 oncology & carcinogenesis, Child, Preschool, Web application, lcsh:R858-859.7, DNA microarray, MESH: Metagenomics, media_common.quotation_subject, education, Differential analysis, lcsh:Computer applications to medicine. Medical informatics, Set (abstract data type), MESH: Workflow, 03 medical and health sciences, MESH: Software, Humans, MESH: Microbiota, Microbiome, Molecular Biology, MESH: Statistics as Topic, 030304 developmental biology, MESH: User-Computer Interface, User Friendly, Internet, Information retrieval, MESH: Humans, MESH: Child, Preschool, MESH: Metagenome, 16S ribosomal RNA, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, lcsh:Biology (General), Metagenomics, Container (abstract data type), Metagenome, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Software
Abstract: Background Comparing the composition of microbial communities among groups of interest (e.g., patients vs healthy individuals) is a central aspect in microbiome research. It typically involves sequencing, data processing, statistical analysis and graphical display. Such an analysis is normally obtained by using a set of different applications that require specific expertise for installation, data processing and in some cases, programming skills. Results Here, we present SHAMAN, an interactive web application we developed in order to facilitate the use of (i) a bioinformatic workflow for metataxonomic analysis, (ii) a reliable statistical modelling and (iii) to provide the largest panel of interactive visualizations among the applications that are currently available. SHAMAN is specifically designed for non-expert users. A strong benefit is to use an integrated version of the different analytic steps underlying a proper metagenomic analysis. The application is freely accessible at http://shaman.pasteur.fr/, and may also work as a standalone application with a Docker container (aghozlane/shaman), conda and R. The source code is written in R and is available at https://github.com/aghozlane/shaman. Using two different datasets (a mock community sequencing and a published 16S rRNA metagenomic data), we illustrate the strengths of SHAMAN in quickly performing a complete metataxonomic analysis. Conclusions With SHAMAN, we aim at providing the scientific community with a platform that simplifies reproducible quantitative analysis of metagenomic data.
Published: 2020
Full Text: View/download PDF

2. Classification structurelle du kératocône par tomographie en cohérence optique en pratique clinique : une étude rétrospective transversale

Author: Gatto, Victor, Thèses d'exercice et mémoires - UFR de Médecine Montpellier-Nîmes, Université de Montpellier (UM), and Vincent Daien
Subjects: MESH: Classification, OCT, MESH: Cornée, MESH: Cornea, Structure, MESH: Keratoconus, MESH: Kératocône, Sévérité, Severity, MESH: Tomography, optical coherence (OCT), [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract: There are many clinical and topographic classifications of keratoconus but only one, proposed by Sandali et al., used optical coherence tomography (OCT) to evaluate the corneal structure. The purpose of this study was to evaluate the classification in clinical practice.Methode: we performed a retrospective analysis of all patients with keratoconus who consulted at Montpellier University Hospital between July 2018 and July 2020. The diagnosis of keratoconus was based on a range of clinical and topographic features. Exclusion criteria were a history of ocular surgery. Patients with keratoconus were classified according to 5 stages of increasing severity based on the appearance of corneal OCT. We analyzed the functional, clinical and topographic characteristics according to the stages. We also analyzed the error of corneal thickness measurement by topography and described the proposed treatments by stage.Results: we included 143 eyes in 143 patients with keratoconus and 35 eyes in 35 healthy patients. Of the keratoconus patients, 116, 8, 9, 6, and 4 were at stage 1, 2, 3, 4, and 5 of the classification, respectively. The severity of structural damage on OCT was associated with greater severity of functional, anatomic and topographic damage. The difference in corneal thickness measurement between OCT and topography was higher with more severe stage. The proposed treatments for the more severe stages were more invasive.Conclusion: the structural classification examined seems able to classify keratoconus severity. We found similar results to the study of Sandali et al. The classification is not well known by practitioners but could find increasing interest for keratoconus with improvement and wider use of anterior segment OCT.; Il existe de nombreuses classifications cliniques et topographiques du kératocône mais une seule, proposée par Sandali et al. utilise la tomographie en cohérence optique (OCT) pour évaluer la structure cornéenne. L’objectif de cette étude est d’évaluer cette classification en pratique clinique.Matériel et méthode : nous avons effectué une analyse rétrospective de tous les patients atteints de kératocône ayant consulté au CHU de Montpellier entre juillet 2018 et juillet 2020. Le diagnostic de kératocône était posé sur un faisceau d’arguments cliniques et topographiques. Les critères d’exclusion étaient les antécédents de chirurgie oculaire. Les patients atteints de kératocône ont été classé d’après la classification utilisée en 5 stades de sévérité croissante en fonction de l’aspect de leur OCT cornéen. Nous avons analysé les caractéristiques fonctionnelles, clinique et topographique en fonction des stades. Nous avons analysé l’erreur de mesure d’épaisseur cornéenne par la topographie et décrit les traitements proposés en fonction du stade.Résultats : nous avons inclus 143 yeux de 143 patients atteints de kératocône et 35 yeux de 35 patients sains. Parmi les patients atteints de kératocône, 116, 8, 9, 6, 4 ont été classés respectivement en stade 1, 2, 3, 4, 5 de la classification. La sévérité de l’atteinte structurelle en OCT était associée à une plus grande sévérité de l’atteinte fonctionnelle, anatomique et topographique. La différence de mesure d’épaisseur cornéenne entre l’OCT et la topographie était plus élevée pour les stades plus sévères. Les traitements proposés étaient plus invasifs pour les stades plus sévères.Conclusion : cette classification structurelle semble bien être un marqueur de sévérité du kératocône. Nous avons retrouvé des résultats similaires à l’étude de Sandali et al. Elle est peu connue des praticiens et semble peu adaptée aux kératocônes modérés. Elle pourrait trouver un intérêt croissant avec le perfectionnement et l’usage plus large de l’OCT de segment antérieur dans le kératocône.
Published: 2021

3. Changes to virus taxonomy and to the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2021)

Author: Walker, Peter J, Siddell, Stuart G, Lefkowitz, Elliot J, Mushegian, Arcady R, Adriaenssens, Evelien M, Alfenas-Zerbini, Poliane, Davison, Andrew J, Dempsey, Donald M, Dutilh, Bas E, García, María Laura, Harrach, Balázs, Harrison, Robert L, Hendrickson, R Curtis, Junglen, Sandra, Knowles, Nick J, Krupovic, Mart, Kuhn, Jens H, Lambert, Amy J, Łobocka, Małgorzata, Nibert, Max L, Oksanen, Hanna M, Orton, Richard J, Robertson, David L, Rubino, Luisa, Sabanadzovic, Sead, Simmonds, Peter, Smith, Donald B, Suzuki, Nobuhiro, Van Dooerslaer, Koenraad, Vandamme, Anne-Mieke, Varsani, Arvind, Zerbini, Francisco Murilo, Sub Bioinformatics, Theoretical Biology and Bioinformatics, Instituto de Higiene e Medicina Tropical (IHMT), Global Health and Tropical Medicine (GHTM), TB, HIV and opportunistic diseases and pathogens (THOP), University of Queensland [Brisbane], University of Bristol [Bristol], University of Alabama at Birmingham [ Birmingham] (UAB), National Science Foundation [Arlington] (NSF), Quadram Institute Biosciences, Universidade Federal de Vicosa (UFV), MRC - University of Glasgow Centre for Virus Research, Utrecht University [Utrecht], Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET), Institute for Veterinary Medical Research [Budapest] (AOTI), Centre for Agricultural Research [Budapest] (ATK), Hungarian Academy of Sciences (MTA)-Hungarian Academy of Sciences (MTA), Invasive Insect Biocontrol and Behavior Laboratory [Beltsville, USA], USDA Agricultural Research Service [Beltsville, Maryland], USDA-ARS : Agricultural Research Service-USDA-ARS : Agricultural Research Service, Charité - UniversitätsMedizin = Charité - University Hospital [Berlin], Institute for Animal Health, the Pirbright Institute, Virologie des archées - Archaeal Virology, Institut Pasteur [Paris], Integrated Research Facility at Fort Detrick (IRF-Frederick), National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH)-National Institutes of Health [Bethesda] (NIH), Centers for Disease Control and Prevention, Polish Academy of Sciences (PAN), Harvard Medical School [Boston] (HMS), University of Helsinki, Istituto per la Protezione Sostenibile delle Piante (CNR-IPSP), UOS Torino, Mississippi State University [Mississippi], University of Oxford [Oxford], Okayama University, University of Arizona, Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA), Arizona State University [Tempe] (ASU), E.M.A. gratefully acknowledges funding by the U.K. Biotechnology and Biological Sciences Research Council (BBSRC), this research was funded by the BBSRC Institute Strategic Programme Gut Microbes and Health BB/R012490/1 and its constituent projects BBS/E/F/000PR10353 and BBS/E/F/000PR10356. A.J.D. is supported by the U.K. Medical Research Council (MC_UU_12014/3). B.E.D. is supported by Netherlands Organization for Scientific Research (NWO) Vidi grant 864.14.004. B.H. is supported by the National Research, Development and Innovation Office—NKFIH (NN128309). N.J.K. is partially supported by core funding provided by the Biotechnology and Biological Sciences Research Council, UK. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture. USDA is an Equal Opportunity Provider and Employer. This work was supported in part through Laulima Government Solutions, LLC prime contract with the US National Institute of Allergy and Infectious Diseases (NIAID) under Contract No. HHSN272201800013C. J.H.K. performed this work as an employee of Tunnell Government Services (TGS), a subcontractor of Laulima Government Solutions, LLC under Contract No. HHSN272201800013C. A.R.M. is a Program Director at the U.S. National Science Foundation (NSF), the statements and opinions expressed herein are made in a personal capacity and do not constitute endorsement by NSF or the government of the United States. H.M.O was supported by the University of Helsinki and Academy of Finland by funding for FINStruct and Instruct Centre FI, part of Biocenter Finland and Instruct-ERIC. D.L.R. is supported by the U.K. Medical Research Council (MC_UU_1201412). R.J.O. and D.B.S. are supported by the Wellcome Trust (WT108418AIA). S.S. acknowledges partial support from the Special Research Initiative (MAFES), Mississippi State University, and from the National Institute of Food and Agriculture, US Department of Agriculture, Hatch Project 1021494. Except for Donald M. Dempsey, R. Curtis Hendrickson, Richard J. Orton and Donald B. Smith, the authors were members of the ICTV Executive Committee during the relevant period. The views and conclusions contained in this document are those of the authors and should not be interpreted as necessarily representing the official policies, either expressed or implied, of the US Department of Health and Human Services, or of the institutions and companies affiliated with the authors., Sub Bioinformatics, Theoretical Biology and Bioinformatics, Quadram Institute Bioscience [Norwich, U.K.] (QIB), Biotechnology and Biological Sciences Research Council (BBSRC), Universidade Federal de Viçosa = Federal University of Viçosa (UFV), The Pirbright Institute, Université Paris Cité (UPCité)-Microbiologie Intégrative et Moléculaire (UMR6047), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Helsingin yliopisto = Helsingfors universitet = University of Helsinki, CNR Istituto per la Protezione Sostenibile delle Piante [Torino, Italia] (IPSP), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), University of Oxford, and Molecular and Integrative Biosciences Research Programme
Subjects: International Cooperation, education, virus, Viroids/classification, Viruses, Unclassified/classification, MESH: Viruses, ICTV, 03 medical and health sciences, SDG 17 - Partnerships for the Goals, SDG 3 - Good Health and Well-being, Virology, Taverne, SDG 14 - Life Below Water, MESH: Phylogeny, Phylogeny, Taxonomy, 030304 developmental biology, SDG 15 - Life on Land, 11832 Microbiology and virology, 0303 health sciences, Unclassified/classification, Code, 030306 microbiology, Viruses/classification, General Medicine, Classification, Viroids, 3. Good health, MESH: Viroids, MESH: Classification, MESH: International Cooperation, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Viruses, MESH: Viruses, Unclassified, Viruses, Unclassified, Classification/methods
Abstract: Funding Information: E.M.A. gratefully acknowledges funding by the U.K. Biotechnology and Biological Sciences Research Council (BBSRC); this research was funded by the BBSRC Institute Strategic Programme Gut Microbes and Health BB/R012490/1 and its constituent projects BBS/E/F/000PR10353 and BBS/E/F/000PR10356. A.J.D. is supported by the U.K. Medical Research Council (MC_UU_12014/3). B.E.D. is supported by Netherlands Organization for Scientific Research (NWO) Vidi grant 864.14.004. B.H. is supported by the National Research, Development and Innovation Office—NKFIH (NN128309). N.J.K. is partially supported by core funding provided by the Biotechnology and Biological Sciences Research Council, UK. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture. USDA is an Equal Opportunity Provider and Employer. This work was supported in part through Laulima Government Solutions, LLC prime contract with the US National Institute of Allergy and Infectious Diseases (NIAID) under Contract No. HHSN272201800013C. J.H.K. performed this work as an employee of Tunnell Government Services (TGS), a subcontractor of Laulima Government Solutions, LLC under Contract No. HHSN272201800013C. A.R.M. is a Program Director at the U.S. National Science Foundation (NSF); the statements and opinions expressed herein are made in a personal capacity and do not constitute endorsement by NSF or the government of the United States. H.M.O was supported by the University of Helsinki and Academy of Finland by funding for FINStruct and Instruct Centre FI, part of Biocenter Finland and Instruct-ERIC. D.L.R. is supported by the U.K. Medical Research Council (MC_UU_1201412). R.J.O. and D.B.S. are supported by the Wellcome Trust (WT108418AIA). S.S. acknowledges partial support from the Special Research Initiative (MAFES), Mississippi State University, and from the National Institute of Food and Agriculture, US Department of Agriculture, Hatch Project 1021494. Except for Donald M. Dempsey, R. Curtis Hendrickson, Richard J. Orton and Donald B. Smith, the authors were members of the ICTV Executive Committee during the relevant period. The views and conclusions contained in this document are those of the authors and should not be interpreted as necessarily representing the official policies, either expressed or implied, of the US Department of Health and Human Services, or of the institutions and companies affiliated with the authors. Publisher Copyright: © 2021, This is a U.S. government work and not under copyright protection in the U.S.; foreign copyright protection may apply. This article reports the changes to virus taxonomy approved and ratified by the International Committee on Taxonomy of Viruses (ICTV) in March 2021. The entire ICTV was invited to vote on 290 taxonomic proposals approved by the ICTV Executive Committee at its meeting in October 2020, as well as on the proposed revision of the International Code of Virus Classification and Nomenclature (ICVCN). All proposals and the revision were ratified by an absolute majority of the ICTV members. Of note, ICTV mandated a uniform rule for virus species naming, which will follow the binomial 'genus-species' format with or without Latinized species epithets. The Study Groups are requested to convert all previously established species names to the new format. ICTV has also abolished the notion of a type species, i.e., a species chosen to serve as a name-bearing type of a virus genus. The remit of ICTV has been clarified through an official definition of ‘virus’ and several other types of mobile genetic elements. The ICVCN and ICTV Statutes have been amended to reflect these changes. publishersversion inpress
Published: 2021
Full Text: View/download PDF

4. Changes to virus taxonomy and the Statutes ratified by the International Committee on Taxonomy of Viruses (2020)

Author: Walker, Peter J, Siddell, Stuart G, Lefkowitz, Elliot J, Mushegian, Arcady R, Adriaenssens, Evelien M, Dempsey, Donald M, Dutilh, Bas E, Harrach, Balázs, Harrison, Robert L, Hendrickson, R Curtis, Junglen, Sandra, Knowles, Nick J, Kropinski, Andrew M, Krupovic, Mart, Kuhn, Jens H, Nibert, Max, Orton, Richard J, Rubino, Luisa, Sabanadzovic, Sead, Simmonds, Peter, Smith, Donald B, Varsani, Arvind, Zerbini, Francisco Murilo, Davison, Andrew J, Sub Bioinformatics, Theoretical Biology and Bioinformatics, University of Queensland [Brisbane], University of Bristol [Bristol], University of Alabama at Birmingham [ Birmingham] (UAB), Division of Molecular and Cellular Biosciences [Alexandria, USA] (MCB), National Science Foundation [Arlington] (NSF), Quadram Institute, Biotechnology and Biological Sciences Research Council (BBSRC), Utrecht University [Utrecht], Hungarian Academy of Sciences (MTA), United States Department of Agriculture (USDA), Humboldt University Of Berlin, The Pirbright Institute, Virologie des archées - Archaeal Virology, Institut Pasteur [Paris] (IP), National Institutes of Health [Bethesda] (NIH), Harvard Medical School [Boston] (HMS), MRC - University of Glasgow Centre for Virus Research, National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Mississippi State University [Mississippi], University of Oxford, Arizona State University [Tempe] (ASU), Universidade Federal de Viçosa = Federal University of Viçosa (UFV), The authors declare no conflicts of interest. A.R.M. is a Program Director at the U.S. National Science Foundation (NSF), the statements and opinions expressed herein are made in a personal capacity and do not constitute endorsement by NSF or the government of the United States. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture. USDA is an Equal Opportunity Provider and Employer. The content of this publication does not necessarily reflect the views or policies of the US Department of Health and Human Services or of the institutions and companies affiliated with the authors. This work was supported in part through Laulima Government Solutions, LLC’s prime contract with the US National Institute of Allergy and Infectious Diseases (NIAID) under Contract No. HHSN272201800013C. J.H.K. performed this work as an employee of Tunnell Government Services (TGS), a subcontractor of Laulima Government Solutions, LLC under Contract No. HHSN272201800013C. N.J.K. is partially supported by core funding provided by the Biotechnology and Biological Sciences Research Council, UK. B.E.D. is supported by Netherlands Organization for Scientific Research (NWO) Vidi grant 864.14.004 and European Research Council (ERC) Consolidator grant 865694: DiversiPHI. B.H. is partially supported by National Research, Development and Innovation Office – NKFIH, NN128309. S.S. acknowledges partial support from Mississippi Agricultural and Forestry Experiment Station (MAFES), Mississippi State University and the National Institute of Food and Agriculture, US Department of Agriculture, Hatch Project 1021494. E.M.A. was funded by the Biotechnology and Biological Sciences Research Council (BBSRC), this research was funded by the BBSRC Institute Strategic Programme Gut Microbes and Health BB/R012490/1 and its constituent projects BBS/E/F/000PR10353 and BBS/E/F/000PR10356. S.J. is supported by the Federal Ministry of Education and Research (BMBF) under project number 01KI1716 as part of the Research Network Zoonotic Infectious Diseases. FMZ is partially supported by CAPES (Finance Code 001). None of the work reported involved research on human participants or animals. All authors have contributed to this work and agreed to its publication. Except for Donald M. Dempsey, R. Curtis Hendrickson, Richard J. Orton and Donald B. Smith, the authors were members of the ICTV Executive Committee during the relevant period., European Project: 865694,H2020-EU.1.1. - EXCELLENT SCIENCE - European Research Council (ERC),DiversiPHI(2020), Sub Bioinformatics, Theoretical Biology and Bioinformatics, Humboldt University of Berlin, Institute for Animal Health, the Pirbright Institute, Institut Pasteur [Paris], Consiglio Nazionale delle Ricerche (CNR), University of Oxford [Oxford], and Universidade Federal de Vicosa (UFV)
Subjects: 0303 health sciences, MESH: Terminology as Topic, 030306 microbiology, education, General Medicine, Biology, no key words, Virology, Executive committee, Statute, MESH: Viruses, 03 medical and health sciences, MESH: Classification, Law, Taverne, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Classification methods, Taxonomy (biology), Virus classification, health care economics and organizations, MESH: Virology, 030304 developmental biology
Abstract: International audience; This article reports the changes to virus classification and taxonomy approved and ratified by the International Committee on Taxonomy of Viruses (ICTV) in March 2020. The entire ICTV was invited to vote on 206 taxonomic proposals approved by the ICTV Executive Committee at its meeting in July 2019, as well as on the proposed revision of the ICTV Statutes. All proposals and the revision of the Statutes were approved by an absolute majority of the ICTV voting membership. Of note, ICTV has approved a proposal that extends the previously established realm Riboviria to encompass nearly all RNA viruses and reverse-transcribing viruses, and approved three separate proposals to establish three realms for viruses with DNA genomes.
Published: 2020
Full Text: View/download PDF

5. Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks

Author: Simon Roux, J. Rodney Brister, Ho Bin Jang, Olivier Zablocki, Mart Krupovic, Jens H. Kuhn, Evelien M. Adriaenssens, Matthew B. Sullivan, Andrew M. Kropinski, Rob Lavigne, Dann Turner, Benjamin Bolduc, Ohio State University [Columbus] (OSU), Integrated Research Facility at Fort Detrick (IRF-Frederick), National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH)-National Institutes of Health [Bethesda] (NIH), DOE Joint Genome Institute [Walnut Creek], U.S. Department of Energy [Washington] (DOE), Institute of Integrative Biology [Liverpool, UK], University of Liverpool, Quadram Institute, National Center for Biotechnology Information (NCBI), National Institutes of Health [Bethesda] (NIH), Ontario Veterinary College [Univ. Guelph, Canada], University of Guelph, Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris], Faculty of BioScience Engineering [KU Leuven, Belgium], Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), University of the West of England [Bristol] (UWE Bristol), High-performance computational support was provided as an award from the Ohio Supercomputer Center to M.B.S. Funding was provided in part by the Department of Energy’s Genome Sciences Program Soil Microbiome Scientific Focus Area award (no. SCW1632) to Lawrence Livermore National Laboratory, NSF Biological Oceanography awards (OCE no. 1536989 and OCE no. 1756314), and a Gordon and Betty Moore Foundation Investigator Award (no. 3790) to M.B.S. Funding was provided to J.R.B. by the Intramural Research Program of the National Institutes of Health (NIH) National Library of Medicine. The work conducted by the US Department of Energy Joint Genome Institute is supported by the Office of Science of the US Department of Energy under Contract DE-AC02-05CH11231 to S.R. This work was funded in part through Battelle Memorial Institute’s prime contract with the US National Institute of Allergy and Infectious Diseases (NIAID) under Contract no. HHSN272200700016I to J.H.K. The content of this publication does not necessarily reflect the views or policies of the US Department of Health and Human Services or of the institutions and companies affiliated with the authors., We thank L. Bollinger, G. Trubl and I. Tolstoy for their comments on improving the manuscript, as well as Z.-Q. You for helping push the network analytics., Biotechnology and Biological Sciences Research Council (BBSRC), and Institut Pasteur [Paris] (IP)
Subjects: MESH: Genome, Viral/genetics, Classification and taxonomy, MESH: Viruses/classification, MESH: Gene Regulatory Networks/genetics, Applied Microbiology and Biotechnology, Genome, 0302 clinical medicine, RefSeq, TOOL, Bacteriophages, Gene Regulatory Networks, Viral, MESH: Phylogeny, Phylogeny, 0303 health sciences, MESH: Metagenomics, Classification, MESH: Classification, Viruses, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Molecular Medicine, ICTV BACTERIAL, POPULATIONS, Taxonomy (biology), MESH: Prokaryotic Cells/virology, MESH: Viruses/genetics, Centre for Research in Biosciences, MESH: Bacteriophages/genetics, Life Sciences & Biomedicine, Biotechnology, Biomedical Engineering, Bioengineering, PHAGE, Computational biology, Genome, Viral, Biology, CLASSIFICATION, 03 medical and health sciences, MD Multidisciplinary, Human virome, Virus classification, 030304 developmental biology, virus classification, archaeal and bacterial virus taxonomy, scalable framework, gene-sharing networks, Science & Technology, ARCHAEAL VIRUSES, Hierarchical clustering, Computational biology and bioinformatics, Prokaryotic Cells, MESH: Metagenome/genetics, Biotechnology & Applied Microbiology, Metagenomics, EVOLUTIONARY, Metagenome, UPDATE, ECOGENOMICS, Bacterial virus, 030217 neurology & neurosurgery, Software, GENERATION
Abstract: Microbiomes from every environment contain a myriad of uncultivated archaeal and bacterial viruses, but studying these viruses is hampered by the lack of a universal, scalable taxonomic framework. We present vConTACT v.2.0, a network-based application utilizing whole genome gene-sharing profiles for virus taxonomy that integrates distance-based hierarchical clustering and confidence scores for all taxonomic predictions. We report near-identical (96%) replication of existing genus-level viral taxonomy assignments from the International Committee on Taxonomy of Viruses for National Center for Biotechnology Information virus RefSeq. Application of vConTACT v.2.0 to 1,364 previously unclassified viruses deposited in virus RefSeq as reference genomes produced automatic, high-confidence genus assignments for 820 of the 1,364. We applied vConTACT v.2.0 to analyze 15,280 Global Ocean Virome genome fragments and were able to provide taxonomic assignments for 31% of these data, which shows that our algorithm is scalable to very large metagenomic datasets. Our taxonomy tool can be automated and applied to metagenomes from any environment for virus classification. ispartof: NATURE BIOTECHNOLOGY vol:37 issue:6 pages:632-+ ispartof: location:United States status: published
Published: 2019
Full Text: View/download PDF

6. 8e édition de la classification TNM des cancers de l'oropharynx HPV induits : évaluation de la performance et étude de l'impact pronostique du tabagisme

Author: Chekkoury Idrissi, Younes, Université Paris Descartes - Faculté de Médecine (UPD5 Médecine), Université Paris Descartes - Paris 5 (UPD5), and Haitham Mirghani
Subjects: MESH: Genes, p16, HPV, [SDV]Life Sciences [q-bio], Oropharynx, P16, Classification, MESH: Prognosis, MESH: Classification, MESH: Papillomaviridae, Tabac, Pronostic, MESH: Neoplasms, MESH: Tobacco, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology, Cancer, MESH: Oropharynx
Abstract: Les carcinomes de l'oropharynx induits par les papillomavirus oncogènes (COP HPV+) représentent une entité distincte au sein des cancers des VADS. La 7ème classification TNM de l'American Joint Committee on Cancer / Union for International Cancer Control (AJCC/UICC) est devenue insuffisante pour rendre compte de leur pronostic, bien plus favorable que celui des COP HPV- . Plusieurs classifications spécifiques aux COP HPV+ ont été publiées mais certaines n'ont jamais été validées de façon indépendante. Celle qui a été retenue en tant que 8ème édition de la TNM a été mise au point par un consortium international (ICON-S). Les stades T et N y sont refondés et regroupés en 3 stades (I/II/III), rendant mieux compte du pronostic des patients. Cette nouvelle édition doit entrer en vigueur en 2018, bien que peu d’équipes aient évalué ses performances. De plus, elle est basée uniquement sur des critères anatomiques ; le tabagisme n'y figure pas bien que son impact sur la survie soit désormais établi. Dans notre étude, la 8ème TNM a permis de mieux stratifier les COP HPV + que la 7ème TNM mais n'a pas surpassé certaines classifications « concurrentes ». De plus, le pronostic des stades I et II était comparable, seul le stade III avait une survie significativement moins favorable. Le tabagisme au-delà de 20 paquets-années a significativement majoré le risque de décès, en particulier pour les stades "avancés" T4/N2c/N3. Nos résultats suggèrent que la 8ème TNM pourrait être améliorée pour pouvoir s'appliquer à l'ensemble les COP HPV+. L'intégration de critères non-anatomiques, permettant de mieux rendre compte de l’individualité de chaque patient, peut constituer l’une des pistes pour la mise au point de classifications ultérieures.
Published: 2017

7. Special Issue: Mathematical and Computational Evolutionary Biology-2015

Author: David Bryant, Olivier Gascuel, University of Otago [Dunedin, Nouvelle-Zélande], Bioinformatique évolutive - Evolutionary Bioinformatics, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Computationnelle (IBC), Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), and Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris]
Subjects: 0106 biological sciences, 0301 basic medicine, MEDLINE, Library science, MESH: Biological Evolution, Biological evolution, Biology, 010603 evolutionary biology, 01 natural sciences, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], 03 medical and health sciences, MESH: Classification, Editorial, 030104 developmental biology, Genetics, Ecology, Evolution, Behavior and Systematics, MESH: Congresses as Topic, Introductory Journal Article, MESH: Computational Biology
Abstract: International audience; This special issue of Systematic Biology contains review articles contributed by keynote speakers at the “Mathematical and Computational EvolutionaryBiology” conference (MCEB; see web sites below), held in 2015. This is the seventh conference in this series, the first being held in Paris in 2003 with keynote addresses from such notables as Joe Felsenstein, Ziheng Yang, and Walter Fitch. Oxford University Press published two books based on the 2003 and 2005 Paris meetings (Gascuel 2005; Gascuel and Steel 2007).
Published: 2017
Full Text: View/download PDF

8. Ratification vote on taxonomic proposals to the International Committee on Taxonomy of Viruses (2016)

Author: Michael J. Adams, Elliot J. Lefkowitz, Andrew M. Q. King, Balázs Harrach, Robert L. Harrison, Nick J. Knowles, Andrew M. Kropinski, Mart Krupovic, Jens H. Kuhn, Arcady R. Mushegian, Max Nibert, Sead Sabanadzovic, Hélène Sanfaçon, Stuart G. Siddell, Peter Simmonds, Arvind Varsani, Francisco Murilo Zerbini, Alexander E. Gorbalenya, Andrew J. Davison, GlaxoSmithKline [Stevenage, UK] (GSK), GlaxoSmithKline [Headquarters, London, UK] (GSK), University of Alabama at Birmingham [ Birmingham] (UAB), Hungarian Academy of Sciences (MTA), United States Department of Agriculture (USDA), The Pirbright Institute, Biotechnology and Biological Sciences Research Council (BBSRC), University of Guelph, Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris] (IP), National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH), National Science Foundation [Arlington] (NSF), Harvard Medical School [Boston] (HMS), Agriculture and Agri-Food (AAFC), University of Bristol [Bristol], University of Oxford, University of Canterbury [Christchurch], Universidade Federal de Viçosa = Federal University of Viçosa (UFV), Leiden University Medical Center (LUMC), Universiteit Leiden, University of Glasgow, This work was supported in part through Battelle Memorial Institute’s prime contract with the US National Institute of Allergy and Infectious Diseases (NIAID) under Contract No. HHSN272200700016I. A subcontractor to Battelle Memorial Institute who performed this work is: J.H.K., an employee of Tunnell Government Services, Inc., Institute for Animal Health, the Pirbright Institute, Institut Pasteur [Paris], Agriculture and Agri-Food [Ottawa] (AAFC), University of Oxford [Oxford], and Universidade Federal de Vicosa (UFV)
Subjects: 0301 basic medicine, viruses, [SDV]Life Sciences [q-bio], education, 030106 microbiology, MESH: Viruses, 03 medical and health sciences, Virology Division News, Virology, skin and connective tissue diseases, health care economics and organizations, Type Species, General Medicine, Classification, Melon Necrotic Spot Virus, Enterobacterium Phage, 3. Good health, Human Polyomavirus, Cherry Necrotic Rusty Mottle Virus, MESH: Classification, 030104 developmental biology, Viruses, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, sense organs, Type species, MESH: Virology
Abstract: International audience; This article lists the changes to virus taxonomy approved and ratified by the International Committee on Taxonomy of Viruses (ICTV) in April 2016.Changes to virus taxonomy (the Universal Scheme of Virus Classification of the International Committee on Taxonomy of Viruses [ICTV]) now take place annually and are the result of a multi-stage process. In accordance with the ICTV Statutes ( http://www.ictvonline.org/statutes.asp ), proposals submitted to the ICTV Executive Committee (EC) undergo a review process that involves input from the ICTV Study Groups (SGs) and Subcommittees (SCs), other interested virologists, and the EC. After final approval by the EC, proposals are then presented for ratification to the full ICTV membership by publication on an ICTV web site ( http://www.ictvonline.org/ ) followed by an electronic vote. The latest set of proposals approved by the EC was made available on the ICTV website by January 2016 ( https://talk.ictvonline.org/files/proposals/ ). A list of these proposals was then emailed on 28 March 2016 to the 148 members of ICTV, namely the EC Members, Life Members, ICTV Subcommittee Members (including the SG chairs) and ICTV National Representatives. Members were then requested to vote on whether to ratify the taxonomic proposals (voting closed on 29 April 2016).
Published: 2016
Full Text: View/download PDF

9. A classification system for virophages and satellite viruses

Author: Jens H. Kuhn, Matthias G. Fischer, Mart Krupovic, Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris], National Institutes of Health [Bethesda] (NIH), Max Planck Institute for Medical Research [Heidelberg], Max-Planck-Gesellschaft, and Institut Pasteur [Paris] (IP)
Subjects: 0301 basic medicine, Virophages, viruses, [SDV]Life Sciences [q-bio], Molecular Sequence Data, Genome, Viral, Biology, MESH: Base Sequence, Genome, Virus, Animal Diseases, 03 medical and health sciences, MESH: Plant Diseases, Virology, Hepatitis Delta, Virus Giant, Animals, MESH: Animals, MESH: Phylogeny, Gene, Necrosis Virus, Phylogeny, Plant Diseases, Genetics, MESH: Molecular Sequence Data, Base Sequence, Virophage, RNA, General Medicine, Classification, Virus Helper, Capsid Protein, MESH: Satellite Viruses, MESH: Animal Diseases, Satellite virus, MESH: Classification, 030104 developmental biology, Satellite Viruses, Viral evolution, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, RNA, Satellite, Virus Tobacco, MESH: Genome, Viral, MESH: RNA, Satellite
Abstract: International audience; Satellite viruses encode structural proteins required for the formation of infectious particles but depend on helper viruses for completing their replication cycles. Because of this unique property, satellite viruses that infect plants, arthropods, or mammals, as well as the more recently discovered satellite-like viruses that infect protists (virophages), have been grouped with other, so-called "sub-viral agents." For the most part, satellite viruses are therefore not classified. We argue that possession of a coat-protein-encoding gene and the ability to form virions are the defining features of a bona fide virus. Accordingly, all satellite viruses and virophages should be consistently classified within appropriate taxa. We propose to create four new genera - Albetovirus, Aumaivirus, Papanivirus, and Virtovirus - for positive-sense single-stranded (+) RNA satellite viruses that infect plants and the family Sarthroviridae, including the genus Macronovirus, for (+)RNA satellite viruses that infect arthopods. For double-stranded DNA virophages, we propose to establish the family Lavidaviridae, including two genera, Sputnikvirus and Mavirus.
Published: 2016
Full Text: View/download PDF

10. DVV: A Taxonomy for Mixed Reality Visualization in Image Guided Surgery

Author: Pierre Jannin, Marta Kersten-Oertel, D. L. Collins, McConnell Brain Imaging Centre (MNI), Montreal Neurological Institute and Hospital, McGill University = Université McGill [Montréal, Canada]-McGill University = Université McGill [Montréal, Canada], Vision, Action et Gestion d'informations en Santé (VisAGeS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-SIGNAUX ET IMAGES NUMÉRIQUES, ROBOTIQUE (IRISA-D5), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS), Laboratoire Traitement du Signal et de l'Image (LTSI), Université de Rennes (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: MESH: Terminology as Topic, Computer science, Virtual reality, computer.software_genre, 030218 nuclear medicine & medical imaging, User-Computer Interface, 03 medical and health sciences, 0302 clinical medicine, Data visualization, Human–computer interaction, Terminology as Topic, Taxonomy (general), Computer Graphics, Image Processing, Computer-Assisted, Humans, MESH: Models, Theoretical, MESH: User-Computer Interface, MESH: Humans, Multimedia, End user, business.industry, Reproducibility of Results, Models, Theoretical, Classification, MESH: Image Processing, Computer-Assisted, Computer Graphics and Computer-Aided Design, Mixed reality, Visualization, MESH: Reproducibility of Results, MESH: Classification, Surgery, Computer-Assisted, Signal Processing, MESH: Programming Languages, Programming Languages, MESH: Surgery, Computer-Assisted, [SDV.IB]Life Sciences [q-bio]/Bioengineering, Augmented reality, Computer Vision and Pattern Recognition, Augmented virtuality, MESH: Computer Graphics, business, computer, 030217 neurology & neurosurgery, Software
Abstract: International audience; Mixed reality visualizations are increasingly studied for use in image guided surgery (IGS) systems, yet few mixed reality systems have been introduced for daily use into the operating room (OR). This may be the result of several factors: the systems are developed from a technical perspective, are rarely evaluated in the field, and/or lack consideration of the end user and the constraints of the OR. We introduce the Data, Visualization processing, View (DVV) taxonomy which defines each of the major components required to implement a mixed reality IGS system. We propose that these components be considered and used as validation criteria for introducing a mixed reality IGS system into the OR. A taxonomy of IGS visualization systems is a step toward developing a common language that will help developers and end users discuss and understand the constituents of a mixed reality visualization system, facilitating a greater presence of future systems in the OR. We evaluate the DVV taxonomy based on its goodness of fit and completeness. We demonstrate the utility of the DVV taxonomy by classifying 17 state-of-the-art research papers in the domain of mixed reality visualization IGS systems. Our classification shows that few IGS visualization systems' components have been validated and even fewer are evaluated.
Published: 2012
Full Text: View/download PDF

11. The origin of eukaryotes and their relationship with the Archaea: are we at a phylogenomic impasse?

Author: Simonetta Gribaldo, Vincent Daubin, Anthony M. Poole, Patrick Forterre, Céline Brochier-Armanet, Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris], Stockholm University, University of Canterbury [Christchurch], Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Institut de génétique et microbiologie [Orsay] (IGM), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), A.M.P. is a Royal Swedish Academy of Sciences Research Fellow supported by a grant from the Knut and Alice Wallenberg Foundation. V.D. is supported by the grants 'Phylariane', 'Ecogenome' and 'Living Deep' from the French ANR (National Agency for Research). C.B.A. is supported by an Action Thématique et Incitative sur Programme (ATIP) of the French Centre National de la Recherche Scientifique (CNRS)., ANR-08-BLAN-0090,EcoGenome,From a genomic species definition toward an Ecological Species Concept for bacteria(2008), ANR-10-BLAN-1725,Living Deep,Bases génomiques et moléculaires de la piézophilie chez Pyrococcus yayanosii CH1, un piézophile obligatoire(2010), and Institut Pasteur [Paris] (IP)
Subjects: 0303 health sciences, General Immunology and Microbiology, 030306 microbiology, Ecology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Lineage (evolution), Tree of life (biology), MESH: Biological Evolution, Context (language use), Biology, biology.organism_classification, Microbiology, MESH: Bacteria, MESH: Classification, MESH: Eukaryota, 03 medical and health sciences, Infectious Diseases, Evolutionary biology, MESH: Archaea, MESH: Genome, 030304 developmental biology, Ancestor, Archaea
Abstract: The origin of eukaryotes and their evolutionary relationship with the Archaea is a major biological question and the subject of intense debate. In the context of the classical view of the universal tree of life, the Archaea and the Eukarya have a common ancestor, the nature of which remains undetermined. Alternative views propose instead that the Eukarya evolved directly from a bona fide archaeal lineage. Several recent large-scale phylogenomic studies using an array of approaches are divided in supporting either one or the other scenario, despite analysing largely overlapping data sets of universal genes. We examine the reasons for such a lack of consensus and consider how alternative approaches may enable progress in answering this fascinating and as-yet-unresolved question.
Published: 2010
Full Text: View/download PDF

12. Four years of DNA barcoding: Current advances and prospects

Author: Lise Frézal, Raphaël Leblois, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biologie Intégrative des Populations, École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Origine, structure et évolution de la biodiversité (OSEB), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), and École Pratique des Hautes Études (EPHE)
Subjects: 0106 biological sciences, MESH: Sequence Analysis, DNA, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Barcode, 01 natural sciences, DNA barcoding, law.invention, law, MESH: DNA Fingerprinting, Species identification, MESH: Animals, DNA taxonomy, 0303 health sciences, Animal life, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Classification, DNA Barcoding, MESH: Classification, Infectious Diseases, Cytochrome c oxidase, Microbiology (medical), Cytochrome C Oxidase Subunit 1, Zoology, Biology, DNA, Mitochondrial, International species databank, 010603 evolutionary biology, Microbiology, COI, 03 medical and health sciences, Species Specificity, DNA barcode, Genetics, Animals, MESH: Species Specificity, Dna taxonomy, Animal species, Molecular Biology, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Electronic Data Processing, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], MESH: DNA, Mitochondrial, Sequence Analysis, DNA, DNA Fingerprinting, Evolutionary biology, Classification methods, MESH: Automatic Data Processing, BOLD
Abstract: International audience; Research using cytochrome c oxidase barcoding techniques on zoological specimens was initiated by Hebert et al. [Hebert, P.D.N., Ratnasingham, S., deWaard, J.R., 2003. Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proc. R. Soc. Lond. B 270, S96-S99]. By March 2004, the Consortium for the Barcode of Life started to promote the use of a standardized DNA barcoding approach, consisting of identifying a specimen as belonging to a certain animal species based on a single universal marker: the DNA barcode sequence. Over the last 4 years, this approach has become increasingly popular and advances as well as limitations have clearly emerged as increasing amounts of organisms have been studied. Our purpose is to briefly expose DNA Barcode of Life principles, pros and cons, relevance and universality. The initially proposed Barcode of life framework has greatly evolved, giving rise to a flexible description of DNA barcoding and a larger range of applications.
Published: 2008
Full Text: View/download PDF

13. Missing data estimation in morphometrics: how much is too much?

Author: Gilles Escarguel, Julien Clavel, Gildas Merceron, Laboratoire de Géologie de Lyon - Terre, Planètes, Environnement (LGL-TPE), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut national des sciences de l'Univers (INSU - CNRS)-Université Jean Monnet - Saint-Étienne (UJM)-Centre National de la Recherche Scientifique (CNRS), Institut International de Paléoprimatologie, Paléontologie Humaine : Evolution et Paléoenvironnement (IPHEP), Université de Poitiers-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Géologie de Lyon - Terre, Planètes, Environnement [Lyon] (LGL-TPE), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École normale supérieure - Lyon (ENS Lyon), and Centre National de la Recherche Scientifique (CNRS)-Université de Poitiers
Subjects: MESH: Principal Component Analysis, Principal Component Analysis, Multivariate statistics, Threshold limit value, Coverage probability, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Biology, Classification, Missing data, computer.software_genre, MESH: Classification, MESH: Computer Simulation, Statistics, Principal component analysis, Genetics, Superimposition, Computer Simulation, Data mining, Imputation (statistics), Evolutionary dynamics, MESH: Phylogeny, [SDU.STU.PG]Sciences of the Universe [physics]/Earth Sciences/Paleontology, computer, Phylogeny, Ecology, Evolution, Behavior and Systematics
Abstract: International audience; Fossil-based estimates of diversity and evolutionary dynamics mainly rely on the study of morphological variation. Unfortunately, organism remains are often altered by post-mortem taphonomic processes such as weathering or distortion. Such a loss of information often prevents quantitative multivariate description and statistically-controlled comparisons of extinct species based on morphometric data. A common way to deal with missing data involves imputation methods that directly fill the missing cases with model estimates. Over the last years, several empirically-determined thresholds for the maximum acceptable proportion of missing values have been proposed in the literature, whereas other studies showed that this limit actually depends on various properties of the study data set and of the selected imputation method, and is by no way generalizable. We evaluate the relative performances of seven multiple imputation (MI) techniques through a simulation-based analysis under three distinct patterns of missing data distribution. Overall, Fully Conditional Specification and Expectation-Maximization algorithms provide the best compromises between imputation accuracy and coverage probability. MI techniques appear remarkably robust to the violation of basic assumptions such as the occurrence of taxonomically or anatomically biased patterns of missing data distribution, making differences in simulation results between the three patterns of missing data distribution much smaller than differences between the individual MI techniques. Based on these results, rather than proposing a new (set of) threshold value(s), we develop an approach combining the use of MIs with procrustean superimposition of principal component analysis results, in order to directly visualize the effect of individual missing data imputation on an ordinated space. We provide an R function for users to implement the proposed procedure.
Published: 2014
Full Text: View/download PDF

14. Virus nomenclature below the species level: a standardized nomenclature for natural variants of viruses assigned to the family Filoviridae

Author: John M. Dye, Sergey V. Netesov, Janusz T. Paweska, Mark S. Lever, Travis K. Warren, Peter B. Jahrling, Jean L. Patterson, Stephan Becker, Alexander Bukreyev, Jens H. Kuhn, Lisa E. Hensley, Kartik Chandran, Eric M. Leroy, Sophie J. Smither, J. Rodney Brister, Erica Ollmann Saphire, Victoria Wahl-Jensen, Yiming Bao, Steven B. Bradfute, Manfred Weidmann, Robert Swanepoel, Karl M. Johnson, Jonathan S. Towner, Gene G. Olinger, Viktor E. Volchkov, Olga Dolnik, Anna N. Honko, Louise Pitt, Sina Bavari, Gary P. Kobinger, Guido van der Groen, Sheli R. Radoshitzky, Gustavo Palacios, Robert A. Davey, Sven Enterlein, Elke Mühlberger, Stuart T. Nichol, Institut für Virologie, Philipps University, Centre International de Recherches Médicales de Franceville (CIRMF), National Institute for Communicable Diseases [Johannesburg] (NICD), University of Göttingen - Georg-August-Universität Göttingen, Centers for Disease Control and Prevention [Atlanta] (CDC), and Centers for Disease Control and Prevention
Subjects: MESH: Terminology as Topic, [SDV]Life Sciences [q-bio], Filoviridae, Computational biology, medicine.disease_cause, Article, 03 medical and health sciences, Virology, MESH: Filoviridae Infections, medicine, MESH: Animals, Nomenclature, Virus classification, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Genetics, 0303 health sciences, Ebola virus, MESH: Humans, biology, 030306 microbiology, General Medicine, Genome project, biology.organism_classification, 3. Good health, Gene nomenclature, MESH: Classification, MESH: Filoviridae, Homo sapiens, Taxonomy (biology)
Abstract: The task of international expert groups is to recommend the classification and naming of viruses. The International Committee on Taxonomy of Viruses Filoviridae Study Group and other experts have recently established an almost consistent classification and nomenclature for filoviruses. Here, further guidelines are suggested to include their natural genetic variants. First, this term is defined. Second, a template for full-length virus names (such as “Ebola virus H.sapiens-tc/COD/1995/Kikwit-9510621”) is proposed. These names contain information on the identity of the virus (e.g., Ebola virus), isolation host (e.g., members of the species Homo sapiens), sampling location (e.g., Democratic Republic of the Congo (COD)), sampling year, genetic variant (e.g., Kikwit), and isolate (e.g., 9510621). Suffixes are proposed for individual names that clarify whether a given genetic variant has been characterized based on passage zero material (-wt), has been passaged in tissue/cell culture (-tc), is known from consensus sequence fragments only (-frag), or does (most likely) not exist anymore (-hist). We suggest that these comprehensive names are to be used specifically in the methods section of publications. Suitable abbreviations, also proposed here, could then be used throughout the text, while the full names could be used again in phylograms, tables, or figures if the contained information aids the interpretation of presented data. The proposed system is very similar to the well-known influenzavirus nomenclature and the nomenclature recently proposed for rotaviruses. If applied consistently, it would considerably simplify retrieval of sequence data from electronic databases and be a first important step toward a viral genome annotation standard as sought by the National Center for Biotechnology Information (NCBI). Furthermore, adoption of this nomenclature would increase the general understanding of filovirus-related publications and presentations and improve figures such as phylograms, alignments, and diagrams. Most importantly, it would counter the increasing confusion in genetic variant naming due to the identification of ever more sequences through technological breakthroughs in high-throughput sequencing and environmental sampling.
Published: 2013
Full Text: View/download PDF

15. Massively parallel tag sequencing reveals the complexity of anaerobic marine protistan communities

Author: Virginia P. Edgcomb, William D. Orsi, Anke Behnke, Thorsten Stoeck, Maria J. Rodriguez-Mora, Andrei Y. Chistoserdov, Richard Christen, Linda A. Amaral-Zettler, Dept of Ecology, University of Kaiserslautern, Dpt of Ecology, Institut de signalisation, biologie du développement et cancer (ISBDC), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA), Josephine Bay Paul Center, Marine Biological Laboratory, University of Louisiana, Northeastern University [Boston], and Woods Hole Oceanographic Institution (WHOI)
Subjects: MESH: Sequence Analysis, DNA, Library, Physiology, Plant Science, Genome, Structural Biology, MESH: Animals, Taxonomic rank, [SDV.BDD]Life Sciences [q-bio]/Development Biology, lcsh:QH301-705.5, MESH: Bacteria, Anaerobic, Sequence Tagged Sites, Sanger sequencing, 0303 health sciences, Agricultural and Biological Sciences(all), Ecology, Eukaryota, Biodiversity, Classification, MESH: Classification, MESH: Eukaryota, symbols, General Agricultural and Biological Sciences, Biotechnology, Research Article, DNA, Bacterial, Rare biosphere, Biology, MESH: Biodiversity, General Biochemistry, Genetics and Molecular Biology, Sequence-tagged site, 03 medical and health sciences, symbols.namesake, Bacteria, Anaerobic, MESH: Sequence Tagged Sites, MESH: Ciliophora, Animals, Seawater, 14. Life underwater, Ciliophora, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Biochemistry, Genetics and Molecular Biology(all), 030306 microbiology, MESH: Seawater, Cell Biology, Sequence Analysis, DNA, MESH: DNA, Bacterial, lcsh:Biology (General), Evolutionary biology, Pyrosequencing, Species richness, Developmental Biology
Abstract: Background Recent advances in sequencing strategies make possible unprecedented depth and scale of sampling for molecular detection of microbial diversity. Two major paradigm-shifting discoveries include the detection of bacterial diversity that is one to two orders of magnitude greater than previous estimates, and the discovery of an exciting 'rare biosphere' of molecular signatures ('species') of poorly understood ecological significance. We applied a high-throughput parallel tag sequencing (454 sequencing) protocol adopted for eukaryotes to investigate protistan community complexity in two contrasting anoxic marine ecosystems (Framvaren Fjord, Norway; Cariaco deep-sea basin, Venezuela). Both sampling sites have previously been scrutinized for protistan diversity by traditional clone library construction and Sanger sequencing. By comparing these clone library data with 454 amplicon library data, we assess the efficiency of high-throughput tag sequencing strategies. We here present a novel, highly conservative bioinformatic analysis pipeline for the processing of large tag sequence data sets. Results The analyses of ca. 250,000 sequence reads revealed that the number of detected Operational Taxonomic Units (OTUs) far exceeded previous richness estimates from the same sites based on clone libraries and Sanger sequencing. More than 90% of this diversity was represented by OTUs with less than 10 sequence tags. We detected a substantial number of taxonomic groups like Apusozoa, Chrysomerophytes, Centroheliozoa, Eustigmatophytes, hyphochytriomycetes, Ichthyosporea, Oikomonads, Phaeothamniophytes, and rhodophytes which remained undetected by previous clone library-based diversity surveys of the sampling sites. The most important innovations in our newly developed bioinformatics pipeline employ (i) BLASTN with query parameters adjusted for highly variable domains and a complete database of public ribosomal RNA (rRNA) gene sequences for taxonomic assignments of tags; (ii) a clustering of tags at k differences (Levenshtein distance) with a newly developed algorithm enabling very fast OTU clustering for large tag sequence data sets; and (iii) a novel parsing procedure to combine the data from individual analyses. Conclusion Our data highlight the magnitude of the under-sampled 'protistan gap' in the eukaryotic tree of life. This study illustrates that our current understanding of the ecological complexity of protist communities, and of the global species richness and genome diversity of protists, is severely limited. Even though 454 pyrosequencing is not a panacea, it allows for more comprehensive insights into the diversity of protistan communities, and combined with appropriate statistical tools, enables improved ecological interpretations of the data and projections of global diversity.
Published: 2009
Full Text: View/download PDF

16. AutoClass@IJM: a powerful tool for Bayesian classification of heterogeneous data in biology

Author: Fiona Achcar, Denis Mestivier, Jean-Michel Camadro, Institut Jacques Monod (IJM (UMR_7592)), and Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS)
Subjects: MESH: Bayes Theorem, MESH: Algorithms, Biology, Machine learning, computer.software_genre, Computational resource, Bioinformatics, 03 medical and health sciences, Upload, Naive Bayes classifier, User-Computer Interface, MESH: Gene Expression Profiling, MESH: Software, 0302 clinical medicine, Computer cluster, Genetics, Cluster Analysis, Relevance (information retrieval), Cluster analysis, 030304 developmental biology, Oligonucleotide Array Sequence Analysis, MESH: User-Computer Interface, 0303 health sciences, Internet, business.industry, Gene Expression Profiling, Bayes Theorem, Articles, Missing data, Classification, MESH: Cluster Analysis, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], MESH: Classification, MESH: Internet, MESH: Oligonucleotide Array Sequence Analysis, Artificial intelligence, User interface, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], business, computer, 030217 neurology & neurosurgery, Algorithms, Software
Abstract: International audience; Recently, several theoretical and applied studies have shown that unsupervised Bayesian classification systems are of particular relevance for biological studies. However, these systems have not yet fully reached the biological community mainly because there are few freely available dedicated computer programs, and Bayesian clustering algorithms are known to be time consuming, which limits their usefulness when using personal computers. To overcome these limitations, we developed AutoClass@IJM, a computational resource with a web interface to AutoClass, a powerful unsupervised Bayesian classification system developed by the Ames Research Center at N.A.S.A. AutoClass has many powerful features with broad applications in biological sciences: (i) it determines the number of classes automatically, (ii) it allows the user to mix discrete and real valued data, (iii) it handles missing values. End users upload their data sets through our web interface; computations are then queued in our cluster server. When the clustering is completed, an URL to the results is sent back to the user by e-mail. AutoClass@IJM is freely available at: http://ytat2.ijm.univ-paris-diderot.fr/AutoclassAtIJM.html.
Published: 2009
Full Text: View/download PDF

17. Diversity of Wolbachia isolated from the Cubitermes sp. affinis subarquatus complex of species (Termitidae), revealed by multigene phylogenies

Author: Virginie Roy, Myriam Harry, Biodiversité et fonctionnement du sol (BIOSOL), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)
Subjects: MESH: Sequence Analysis, DNA, MESH: Cytoskeletal Proteins, MESH: Isoptera, Genus, RNA, Ribosomal, 16S, MESH: Animals, MESH: Phylogeny, MESH: Bacterial Proteins, Phylogeny, reproductive and urinary physiology, Recombination, Genetic, 0303 health sciences, biology, Classification, Eusociality, Bacterial Typing Techniques, MESH: RNA, Ribosomal, 16S, Termitidae, MESH: Classification, MESH: Wolbachia, Wolbachia, MESH: Recombination, Genetic, MESH: Genes, Bacterial, Bacterial Outer Membrane Proteins, Zoology, Isoptera, Microbiology, MESH: Bacterial Typing Techniques, 03 medical and health sciences, Bacterial Proteins, Phylogenetics, Botany, parasitic diseases, Genetics, Animals, Molecular Biology, 030304 developmental biology, 030306 microbiology, Host (biology), MESH: Bacterial Outer Membrane Proteins, Sequence Analysis, DNA, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, 16S ribosomal RNA, Cytoskeletal Proteins, Genes, Bacterial, bacteria, Arthropod, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: International audience; Wolbachia are endosymbiotic bacteria that may alter the reproductive mechanisms of arthropod hosts. Eusocial termites provide considerable scope for Wolbachia studies owing to their ancient origin, their great diversity and their considerable ecological, biological and behavioral plasticity. This article describes the phylogenetic distribution of Wolbachia infecting termites of the Cubitermes genus, which are particularly abundant soil-feeders in equatorial Africa. Fourteen colonies of the Cubitermes sp. affinis subarquatus complex of species were screened using five bacterial genes (wsp, ftsZ, coxA, fbpA and 16S rRNA genes) and a striking diversity of Wolbachia strains was identified within these closely related species. In the host complex, three Wolbachia variants were found that were not in the super groups usually reported for termites (F and H), each infecting one or two Cubitermes species.
Published: 2007
Full Text: View/download PDF

18. Taxonomic position and geographical distribution of the common sheep G1 and camel G6 strains of Echinococcus granulosus in three African countries

Author: Jean-Mathieu Bart, P. Koskei, Renaud Piarroux, S. Maillard, Jenny Knapp, M. C. Benchikh-Elfegoun, Bruno Gottstein, Institut de l'Ouest : Droit et Europe (IODE), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Chrono-environnement (UMR 6249) (LCE), Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Institute of Parasitology, University of Bern, Infections Parasitaires : Transmission, Physiopathologie et Thérapeutiques (IP-TPT), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)-Service de Santé des Armées, Institut de l'Ouest : Droit et Europe ( IODE ), Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire Chrono-environnement ( LCE ), Université Bourgogne Franche-Comté ( UBFC ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Franche-Comté ( UFC ), Infections Parasitaires : Transmission, Physiopathologie et Thérapeutiques ( IP-TPT ), Institut de Recherche pour le Développement ( IRD ) -Aix Marseille Université ( AMU ) -Assistance Publique - Hôpitaux de Marseille ( APHM ) -Service de Santé des Armées-Université de Montpellier ( UM ), Millon, Laurence, Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Chrono-environnement - CNRS - UBFC (UMR 6249) (LCE), Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Centre National de la Recherche Scientifique (CNRS), and Service de Santé des Armées-Assistance Publique - Hôpitaux de Marseille (APHM)-Aix Marseille Université (AMU)-Institut de Recherche pour le Développement (IRD)
Subjects: MESH : Algeria, MESH : Classification, MESH : Echinococcosis, MESH: Echinococcus granulosus, Animal Diseases, 030308 mycology & parasitology, 0302 clinical medicine, MESH: Demography, MESH : Mauritania, MESH: Animals, Echinococcus granulosus, MESH: Phylogeny, Phylogeny, 0303 health sciences, 630 Agriculture, Phylogenetic tree, biology, MESH : Animal Diseases, Mauritania, MESH: Camels, General Medicine, Classification, MESH: Classification, Infectious Diseases, Taxonomy (biology), MESH: Algeria, MESH : Ethiopia, MESH: Mauritania, MESH : Demography, Camelus, 030231 tropical medicine, Cestoda, Zoology, MESH: Sheep, MESH: Ethiopia, Bovidae, MESH : Sheep, [ SDV.EE.SANT ] Life Sciences [q-bio]/Ecology, environment/Health, 03 medical and health sciences, MESH: Echinococcosis, Echinococcosis, Phylogenetics, parasitic diseases, Animals, Humans, Helminths, [SDV.EE.SANT] Life Sciences [q-bio]/Ecology, environment/Health, Demography, [SDV.EE.SANT]Life Sciences [q-bio]/Ecology, environment/Health, Sheep, MESH: Humans, General Veterinary, MESH : Camels, MESH : Echinococcus granulosus, MESH : Humans, MESH : Phylogeny, biology.organism_classification, MESH: Animal Diseases, Echinococcus, Algeria, Insect Science, Parasitology, Ethiopia, MESH : Animals
Abstract: International audience; The taxonomic and phylogenetic status of Echinococcus granulosus strains are still controversial and under discussion. In the present study, we investigated the genetic polymorphism of E. granulosus isolates originating from three countries of Africa, including a region of Algeria, where the common G1 sheep and the camel G6 strains coexist sympatrically. Seventy-one hydatid cysts were collected from sheep, cattle, camels, and humans. Two mitochondrial markers (cox1 and nad1) were used for strain identification. Two nuclear markers (actII and hbx2) were used to study the possible occurrence of cross-fertilization. Despite the heterogeneity observed among the G1 isolates, they were all localized within one robust cluster. A second strong cluster was also observed containing all of the G6 isolates. Both strains appeared as two distinct groups, and no cases of interbreeding were found. Thus, the attribution of a species rank can be suggested. We also found the Tasmanian sheep G2 strain for the first time in Africa. Because of the slight variations observed between the common sheep and the Tasmanian sheep strains, further studies should be carried out to elucidate the epidemiological relevance of this genetic discrimination.
Published: 2007
Full Text: View/download PDF

19. Learning of auditory equivalence classes for vowels by rats

Author: Jan Eriksson, Alessandro E. P. Villa, Neuroheuristic Research Group, ISI Foundation, Neurosciences précliniques, Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire de Neurobiophysique, Université Joseph Fourier - Grenoble 1 (UJF), and Issartel, Jean-Paul
Subjects: Male, Sound Spectrography, Audiology, 01 natural sciences, Generalization, Psychological, MESH: Association Learning, Discrimination Learning, Behavioral Neuroscience, MESH: Animals, 10. No inequality, 010301 acoustics, media_common, Artificial neural network, 05 social sciences, General Medicine, Classification, MESH: Classification, Formant, Categorization, Speech Perception, MESH: Sound Spectrography, Psychology, psychological phenomena and processes, Auditory perception, medicine.medical_specialty, MESH: Rats, media_common.quotation_subject, MESH: Phonetics, Models, Neurological, MESH: Generalization (Psychology), behavioral disciplines and activities, 050105 experimental psychology, MESH: Computer Simulation, Phonetics, MESH: Rats, Long-Evans, MESH: Models, Neurological, Vowel, Perception, 0103 physical sciences, medicine, Reaction Time, Animals, 0501 psychology and cognitive sciences, Computer Simulation, Rats, Long-Evans, Communication, business.industry, Association Learning, Fundamental frequency, MESH: Speech Perception, MESH: Discrimination Learning, MESH: Male, Associative learning, Rats, MESH: Reaction Time, Animal Science and Zoology, business
Abstract: International audience; Four male Long-Evans rats were trained to discriminate between synthetic vowel sounds using a GO/NOGO response choice task. The vowels were characterized by an increase in fundamental frequency correlated with an upward shift in formant frequencies. In an initial phase we trained the subjects to discriminate between two vowel categories using two exemplars from each category. In a subsequent phase the ability of the rats to generalize the discrimination between the two categories was tested. To test whether rats might exploit the fact that attributes of training stimuli covaried, we used non-standard stimuli with a reversed relation between fundamental frequency and formants. The overall results demonstrate that rats are able to generalize the discrimination to new instances of the same vowels. We present evidence that the performance of the subjects depended on the relation between fundamental and formant frequencies that they had previously been exposed to. Simple simulation results with artificial neural networks could reproduce most of the behavioral results and support the hypothesis that equivalence classes for vowels are associated with an experience-driven process based on general properties of peripheral auditory coding mixed with elementary learning mechanisms. These results suggest that rats use spectral and temporal cues similarly to humans despite differences in basic auditory capabilities.
Published: 2006
Full Text: View/download PDF

20. Species concepts versus species criteria

Author: Richard Paul, Biochimie et Biologie Moléculaire des Insectes, and Institut Pasteur [Paris] (IP)
Subjects: [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, business.industry, MESH: Biological Evolution, Biology, computer.software_genre, MESH: Classification, Infectious Diseases, Text mining, MESH: Animals, Parasitology, Artificial intelligence, MESH: Phylogeny, business, MESH: Parasites, computer, ComputingMilieux_MISCELLANEOUS, Natural language processing
Abstract: International audience
Published: 2002
Full Text: View/download PDF

21. Possibility and Challenges of Conversion of Current Virus Species Names to Linnaean Binomials

Author: Sbina Bavari, Susan Payne, Alexander Bukreyev, Arvind Varsani, Víctor Romanowski, Kartik Chandran, Ralf G. Dietzgen, Mark D. Stenglein, Anna N. Clawson, Sead Sabanadzovic, Gael Kurath, Andrea Maisner, Peter J. Walker, Ralf Dürrwald, Juan Carlos de la Torre, Eric M. Leroy, Mária Benko, Keizo Tomonaga, Gary P. Kobinger, Robert A. Lamb, Hideki Kondo, F. Murilo Zerbini, Martin Schwemmle, Robert B. Tesh, Gaya K. Amarasinghe, Andrew J. Easton, Michael J. Buchmeier, Jean-Paul Gonzalez, Anna E. Whitfield, Nikos Vasilakis, Jonathan S. Towner, Pierre Formenty, Jens H. Kuhn, Norbert Nowotny, Roger Hewson, Ayato Takada, Mart Krupovic, Igor S. Lukashevich, David M. Stone, Clarence J. Peters, Sheli R. Radoshitzky, Bertus K. Rima, Janusz T. Paweska, Masayuki Horie, Christopher S. Clegg, Victoria Wahl-Jensen, Christopher F. Basler, Sébastian Emonet, Charles H. Calisher, Lin-Fa Wang, Rémi N. Charrel, Jean L. Patterson, Elodie Ghedin, Dennis Rubbenstroth, Dàohóng Jiāng, Sergey V. Netesov, Hélène Sanfaçon, Thomas S. Postler, Ron A. M. Fouchier, Peter L. Collins, Noël Tordo, Maria S. Salvato, John M. Dye, Arcady Mushegian, Sophie J. Smither, Joseph L. DeRisi, Olga Dolnik, Kim R. Blasdell, Balázs Harrach, Viktor E. Volchkov, Thomas Briese, Andrew M. Kropinski, Columbia University College of Physicians and Surgeons, Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Washington University School of Medicine (WUSM), University of Washington [Seattle], Georgia State University, University System of Georgia (USG), Army Medical Research Institute of Infectious Diseases [USA] (USAMRIID), Institute for Soil Sciences and Agricultural Chemistry (ATK TAKI), Centre for Agricultural Research [Budapest] (ATK), Hungarian Academy of Sciences (MTA)-Hungarian Academy of Sciences (MTA), Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Columbia Mailman School of Public Health, University of California [Irvine] (UCI), University of California, The University of Texas Medical Branch (UTMB), College of Veterinary Medicine and Biomedical Sciences, Colorado State University [Fort Collins] (CSU), Albert Einstein College of Medicine [New York], Emergence des Pathologies Virales (EPV), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Les Mandinaux, National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH), Department of Immunology and Microbial Science, Scripps Research Institute, Department of Medicine [San Francisco], University of California [San Francisco] (UCSF), University of California-University of California, Queensland Alliance for Agriculture and Food Innovation (QAAFI), University of Queensland [Brisbane], Philipps University of Marburg, IDT Biologika, School of Life Sciences, Warwick University, Unité de Virologie, Institut de Recherche Biomédicale des Armées (IRBA), Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), Department of Viroscience [Rotterdam, The Netherlands], Erasmus University Medical Center [Rotterdam] (Erasmus MC), Center for Genomics and Systems Biology, Department of Biology [New York], New York University [New York] (NYU), NYU System (NYU)-NYU System (NYU)-New York University [New York] (NYU), NYU System (NYU)-NYU System (NYU), Health for Development, Public Health England [Salisbury] (PHE), Kagoshima University, State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Research Centre in Infectious Diseases, CHUL Research Centre and Department of Microbiology and Immunology, Université Laval [Québec] (ULaval)-Faculty of Medicine, Institute of Plant Science and Resources, Okayama University, University of Guelph, Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris], US Geological Survey [Seattle], United States Geological Survey [Reston] (USGS), Northwestern University [Evanston], Centre International de Recherches Médicales de Franceville (CIRMF), Department of Pharmacology and Toxicology, University of Louisville, Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Infectious Disease, University of Texas at Austin [Austin], Novosibirsk State University (NSU), University of Veterinary Medicine [Vienna] (Vetmeduni), Mohammed Bin Rashid University of Medicine and Health Sciences (MBRU), Texas Biomedical Research Institute [San Antonio, TX], Texas A&M University System, National Institute for Communicable Diseases [Johannesburg] (NICD), Queen's University [Belfast] (QUB), Instituto de Biotecnología y Biología Molecular [La Plata] (IBBM), Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET)-Facultad de Ciencias Exactas [La Plata], Universidad Nacional de la Plata [Argentine] (UNLP)-Universidad Nacional de la Plata [Argentine] (UNLP), University of Freiburg [Freiburg], Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology [Mstate, USA] (BCH-EPP), Mississippi State University [Mississippi], Summerland Research and Development Centre, Agriculture and Agri-Food [Ottawa] (AAFC), University of Maryland School of Medicine, University of Maryland System, Defence Science and Technology Laboratory (Dstl), Ministry of Defence (UK) (MOD), Department of Microbiology, Immunology and Pathology, Centre for Environment, Fisheries and Aquaculture Science [Weymouth] (CEFAS), Hokkaido University [Sapporo, Japan], Institute for Virus Research, Kyoto University [Kyoto], Stratégies antivirales, Institut Pasteur de Guinée, Réseau International des Instituts Pasteur (RIIP), Viral Special Pathogens Branch, Centers for Disease Control and Prevention-WHO Collaborative Centre for Viral Hemorrhagic Fevers, Bases moléculaires de la pathogénicité virale – Molecular Basis of Viral Pathogenicity (BMPV), Centre International de Recherche en Infectiologie - UMR (CIRI), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), National Biodefense Analysis and Countermeasures Center [Frederick], U.S. Social Security Administration, CSIRO Health & Biosecurity, Department of Agriculture, Fisheries and Forestry, Ecoscience Precinct, GPO Box 267, Brisbane, Duke-NUS Medical School [Singapore], Center for Fundamental and Applied Microbiomics, Arizona State University [Tempe] (ASU)-Biodesign Institute, Kansas State University, Departamento de Fitopatologia [Viçosa, Brazil] (BIOAGRO), Universidade Federal de Vicosa (UFV), This work was supported in part through Battelle Memorial Institute’s prime contract with the US National Institute of Allergy and Infectious Diseases (NIAID) under Contract No. HHSN272200700016I. A subcontractor to Battelle Memorial Institute who performed this work is J.H.K., an employee of Tunnell Government Services, Inc. This work was also funded in part under National Institutes of Health (NIH) contract HHSN272201000040I/HHSN27200004/D04 and R24AI120942 (N.V., R.B.T.), and the National Science Foundation (NSF) Individual Research and Development (IR/D) program (A.R.M.)., We thank Laura Bollinger (NIH/NIAID Integrated Research Facility at Fort Detrick, Frederick, MD, USA) for critically editing the manuscript, Andrew J. Davison (MRC – University of Glasgow Centre for Virus Research, Glasgow, UK) and Michael J. Adams (Department of Plant Pathology and Microbiology, Rothamsted Research, Harpenden, Herts, UK) of the ICTV Executive Committee for suggestions on manuscript improvement, and Arya Ariël Kuhn for sustained vocal support and (dia)critical remarks, Albert Einstein College of Medicine, Institut Hospitalier Universitaire Méditerranée Infection (IHU AMU), Queensland Alliance for Agriculture and Food Innovation, University of Queensland (UQ), Public Health England [Porton Down, Salisbury], Faculty of Medicine-Laval University [Québec], Okayama University [Okayama], Centre International de Recherches Médicales de Franceville, Texas Biomedical Research Institute [San Antonio, Texas], A&M University, National Institute for Communicable Diseases (NICD), Centre for Experimental Medicine [Queen’s University of Belfast], Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Hokkaido University, Bases moléculaires de la pathogénicité virale – Molecular Basis of Viral Pathogenicity, Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Duke NUS Medical School, Departamento de Fitopatologia/BIOAGRO, Virology, U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID), Columbia University [New York], University of California [Irvine] (UC Irvine), University of California (UC), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)-Institut National de la Santé et de la Recherche Médicale (INSERM), The Scripps Research Institute [La Jolla, San Diego], University of California [San Francisco] (UC San Francisco), University of California (UC)-University of California (UC), Philipps Universität Marburg = Philipps University of Marburg, University of Warwick [Coventry], Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Huazhong Agricultural University [Wuhan] (HZAU), Institut Pasteur [Paris] (IP), Agriculture and Agri-Food (AAFC), Kyoto University, Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and Universidade Federal de Viçosa = Federal University of Viçosa (UFV)
Subjects: 0301 basic medicine, MESH: Terminology as Topic, media_common.quotation_subject, Biología, 030106 microbiology, Binomials, Zoology, Biology, Points of View, 03 medical and health sciences, Genus, Terminology as Topic, Genetics, MESH: Classification, Epithet, Arenaviridae, Ecology, Evolution, Behavior and Systematics, Virus classification, media_common, Order Mononegavirales, Evolutionary Biology, Virus taxonomy, Classification, MESH: Viruses, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Virus nomenclature, Genealogy, Ictv, International committee on taxonomy of viruses, 030104 developmental biology, Homo sapiens, Viruses, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.IMM]Life Sciences [q-bio]/Immunology, Mononegavirales
Abstract: Botanical, mycological, zoological, and prokaryotic species names follow the Linnaean format, consisting of an italicized Latinized binomen with a capitalized genus name and a lower case species epithet (e.g., Homo sapiens). Virus species names, however, do not follow a uniform format, and, even when binomial, are not Linnaean in style. In this thought exercise, we attempted toconvert all currently official names ofspecies included in the viru sfamily Arenaviridae and the virus order Mononegavirales to Linnaean binomials, and to identify and address associated challenges and concerns. Surprisingly, this endeavor was not as complicated or time-consuming as even the authors of this article expected when conceiving the experiment., La lista completa de autores que integran el documento puede consultarse en el archivo, Instituto de Biotecnologia y Biologia Molecular
Full Text: View/download PDF

Catalog

Books, media, physical & digital resources

See catalog results

Searchworks

Select search scope, currently: Articles

Catalog

books, media & more in Jio Institute collections

Articles

journal articles & other e-resources

Refine your results

21 results on '"MESH: Classification"'

1. SHAMAN: a user-friendly website for metataxonomic analysis from raw reads to statistical analysis

2. Classification structurelle du kératocône par tomographie en cohérence optique en pratique clinique : une étude rétrospective transversale

3. Changes to virus taxonomy and to the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2021)

4. Changes to virus taxonomy and the Statutes ratified by the International Committee on Taxonomy of Viruses (2020)

5. Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks

6. 8e édition de la classification TNM des cancers de l'oropharynx HPV induits : évaluation de la performance et étude de l'impact pronostique du tabagisme

7. Special Issue: Mathematical and Computational Evolutionary Biology-2015

8. Ratification vote on taxonomic proposals to the International Committee on Taxonomy of Viruses (2016)

9. A classification system for virophages and satellite viruses

10. DVV: A Taxonomy for Mixed Reality Visualization in Image Guided Surgery

11. The origin of eukaryotes and their relationship with the Archaea: are we at a phylogenomic impasse?

12. Four years of DNA barcoding: Current advances and prospects

13. Missing data estimation in morphometrics: how much is too much?

14. Virus nomenclature below the species level: a standardized nomenclature for natural variants of viruses assigned to the family Filoviridae

15. Massively parallel tag sequencing reveals the complexity of anaerobic marine protistan communities

16. AutoClass@IJM: a powerful tool for Bayesian classification of heterogeneous data in biology

17. Diversity of Wolbachia isolated from the Cubitermes sp. affinis subarquatus complex of species (Termitidae), revealed by multigene phylogenies

18. Taxonomic position and geographical distribution of the common sheep G1 and camel G6 strains of Echinococcus granulosus in three African countries

19. Learning of auditory equivalence classes for vowels by rats

20. Species concepts versus species criteria

21. Possibility and Challenges of Conversion of Current Virus Species Names to Linnaean Binomials

Catalog

Searchworks

Select search scope, currently: Articles Catalog books, media & more in Jio Institute collections Articles journal articles & other e-resources

Search

Search Constraints

Refine your results

Search Limiters

Topic

Publication Year Range

Language

Journal

Database

Publisher

21 results on '"MESH: Classification"'

Search Results

Catalog

Select search scope, currently: Articles

Catalog

books, media & more in Jio Institute collections

Articles

journal articles & other e-resources